Amino_Acid_Change Amino_Acid_length Codon_Change Effect_Impact Exon_Rank Functional_Class Gene_Coding Gene_Name Genotype_Number Transcript_BioType Transcript_ID Type FILENAME SAMPLE CHROM POS REF ALT ID QUAL FILTER aaf_1kg_afr_float aaf_1kg_all_float aaf_1kg_amr_float aaf_1kg_eas_float aaf_1kg_eur_float aaf_1kg_sas_float aaf_esp_aa aaf_esp_all aaf_esp_ea AC ac_exac_afr ac_exac_all ac_exac_amr ac_exac_eas ac_exac_fin ac_exac_nfe ac_exac_oth ac_exac_sas AN an_exac_afr an_exac_all an_exac_amr an_exac_eas an_exac_fin an_exac_nfe an_exac_oth an_exac_sas BQB clinvar_pathogenic clinvar_sig common_pathogenic cosmic_ids DP DP4 EFF EXOME_CHIP HOB ICB IDV IMF in_1kg INDEL in_esp in_exac LOF MQ MQ0F MQB MQSB NMD RPB rs_ids SGB VDB D025211_combined_R1_DP S60 305 tcA/tcG LOW 1 SILENT CODING OR4F5 G protein_coding NM_001005484.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 69270 A G 0 121 0 . 0 . 0 . 0 . 0 . 2 166 1019 48 114 11 467 12 201 2 568 1584 76 116 14 560 18 232 0 . 0 . 0 20 0,0,20,0 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S60|305|OR4F5|protein_coding|CODING|NM_001005484.1|1|G) 0 . 0 . 0 . 0 . 1 0 29 0 0 . 0 . rs201219564 -0.692067 0.085506 20 T141A 305 Aca/Gca MODERATE 1 MISSENSE CODING OR4F5 G protein_coding NM_001005484.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 69511 A G 0 228 0 . 0 . 0 . 0 0.544101 0.759766 0.887429 2 4392 72743 6155 8379 3289 37731 572 12225 2 7392 77432 6474 8384 3320 38832 596 12434 0 . 0 . 0 216 0,0,125,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5|protein_coding|CODING|NM_001005484.1|1|G) 1 0 . 0 . 0 . 1 1 0 35 0 0 0.939806 0 . rs75062661 -0.693147 0.0326458 216 S269 305 tcT/tcC LOW 1 SILENT CODING OR4F5 C protein_coding NM_001005484.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 69897 T C 0 175 0 0.407 0.6881 0.6254 0.876 0.7942 0.8098 0 . 0 1 90 530 28 62 0 292 5 53 2 214 694 36 64 0 320 6 54 0.998851 0 . 0 . 28 10,0,4,14 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S269|305|OR4F5|protein_coding|CODING|NM_001005484.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 32 0 0.406103 0.489886 0 0.144832 rs200676709 -0.691153 0.743763 28 H78Y 681 Cac/Tac MODERATE 3 MISSENSE CODING SAMD11 T protein_coding NM_152486.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 865694 C T 0 222 0 0.0227 0.0525 0.0965 0.1389 0.002 0.0245 0.0184594 0.00731783 0.00162904 1 206 2572 1002 880 4 85 17 378 2 5990 67500 6256 5484 1960 36384 484 10942 0.776069 0 . 0 . 249 27,59,45,103 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|681|SAMD11|protein_coding|CODING|NM_152486.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96305 rs9988179 -0.693147 0.517938 249 P123 681 ccC/ccG LOW 5 SILENT CODING SAMD11 G protein_coding NM_152486.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 871215 C G 0 222 0 0.0197 0.0535 0.0937 0.1438 0.004 0.0286 0.0261008 0.0103798 0.00232558 1 304 3247 1208 982 39 205 26 483 2 10330 120626 11554 8630 6614 66094 898 16506 0.949643 0 . 0 . 233 41,72,35,60 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P123|681|SAMD11|protein_coding|CODING|NM_152486.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.205677 rs28419423 -0.693147 0.0873193 233 681 LOW 9 CODING SAMD11 G protein_coding NM_152486.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 877782 C G 0 144 0 0.0257 0.0549 0.0937 0.1399 0.002 0.0337 0 . 0 1 6 262 21 20 0 8 1 206 2 144 5590 98 152 2 1306 64 3824 1 0 . 0 . 8 1,0,3,4 SPLICE_SITE_REGION+INTRON(LOW||||681|SAMD11|protein_coding|CODING|NM_152486.2|9|G),DOWNSTREAM(MODIFIER||1801||749|NOC2L|protein_coding|CODING|NM_015658.3||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0.992367 0 1 rs79037098 -0.636426 0.119488 8 W343R 681 Tgg/Cgg MODERATE 10 MISSENSE CODING SAMD11 C protein_coding NM_152486.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 877831 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 596 15915 1036 842 102 5476 140 7723 2 596 15916 1036 842 102 5476 140 7724 0 . 0 . 0 12 0,0,7,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W343R|681|SAMD11|protein_coding|CODING|NM_152486.2|10|C),DOWNSTREAM(MODIFIER||1752||749|NOC2L|protein_coding|CODING|NM_015658.3||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6672356 -0.662043 0.166412 12 681 154 MODIFIER 14 CODING SAMD11 C protein_coding NM_152486.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 879687 T C 0 9.7 0 0.9062 0.9211 0.9193 0.9137 0.9523 0.9182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||154||681|SAMD11|protein_coding|CODING|NM_152486.2|14|C),UTR_3_PRIME(MODIFIER||387||749|NOC2L|protein_coding|CODING|NM_015658.3|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2839 -0.379885 0 1 749 387 MODIFIER 19 CODING NOC2L C protein_coding NM_015658.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 879687 T C 0 9.7 0 0.9062 0.9211 0.9193 0.9137 0.9523 0.9182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||154||681|SAMD11|protein_coding|CODING|NM_152486.2|14|C),UTR_3_PRIME(MODIFIER||387||749|NOC2L|protein_coding|CODING|NM_015658.3|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2839 -0.379885 0 1 L615 749 Ctg/Ttg LOW 16 SILENT CODING NOC2L A protein_coding NM_015658.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 881627 G A 0 222 0 0.0643 0.4419 0.438 0.624 0.6332 0.5706 0.156222 0.474777 0.637907 1 1436 68060 5557 5642 4075 41521 514 9315 2 10282 120386 11482 8600 6550 66084 896 16492 0.953471 0 . 0 COSM1344685 140 35,26,37,27 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L615|749|NOC2L|protein_coding|CODING|NM_015658.3|16|A),DOWNSTREAM(MODIFIER||1666||681|SAMD11|protein_coding|CODING|NM_152486.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.44961 rs2272757 -0.693147 0.656246 140 T394 749 acT/acC LOW 10 SILENT CODING NOC2L G protein_coding NM_015658.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 887801 A G 0 228 0 0.9062 0.9223 0.9193 0.9206 0.9523 0.9172 0.906037 0.927418 0.938372 2 9378 112748 11041 7873 6320 62122 855 15159 2 10312 120524 11552 8626 6584 66046 898 16506 0 . 0 . COSM426785 113 0,0,72,25 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T394|749|NOC2L|protein_coding|CODING|NM_015658.3|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3828047 -0.693147 0.650046 113 E306 749 gaA/gaG LOW 9 SILENT CODING NOC2L C protein_coding NM_015658.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 888639 T C 0 228 0 0.907 0.9227 0.9193 0.9206 0.9533 0.9172 0.90581 0.927264 0.938256 2 9403 112762 11040 7876 6323 62105 856 15159 2 10338 120530 11550 8632 6586 66018 900 16506 0 . 0 . 0 121 0,0,45,62 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E306|749|NOC2L|protein_coding|CODING|NM_015658.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748596 -0.693147 0.0380126 121 I300V 749 Atc/Gtc MODERATE 9 MISSENSE CODING NOC2L C protein_coding NM_015658.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 888659 T C 0 228 0 0.907 0.9227 0.9193 0.9206 0.9533 0.9172 0.905768 0.92733 0.938372 2 9351 112291 11006 7854 6259 61823 852 15146 2 10280 120032 11516 8606 6520 65720 896 16494 0 . 0 . 0 106 0,0,35,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I300V|749|NOC2L|protein_coding|CODING|NM_015658.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748597 -0.693147 0.17376 106 749 LOW 8 CODING NOC2L C protein_coding NM_015658.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 889158 G C 0 228 0 0.829 0.9044 0.9135 0.9365 0.9523 0.9172 0.823797 0.896231 0.933341 2 8299 109596 10843 7836 5849 60839 816 15114 2 9990 118114 11416 8514 6110 64754 860 16470 0 . 0 . 0 96 0,0,53,35 SPLICE_SITE_REGION+INTRON(LOW||||749|NOC2L|protein_coding|CODING|NM_015658.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs13303056 -0.693147 0.0850569 96 749 LOW 8 CODING NOC2L C protein_coding NM_015658.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 889159 A C 0 228 0 0.829 0.9044 0.9135 0.9365 0.9523 0.9172 0.823342 0.895385 0.932294 2 8310 109696 10847 7836 5865 60900 820 15118 2 10002 118218 11420 8516 6126 64816 864 16474 0 . 0 . 0 96 0,0,53,35 SPLICE_SITE_REGION+INTRON(LOW||||749|NOC2L|protein_coding|CODING|NM_015658.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs13302945 -0.693147 0.0850569 96 A203 642 gcG/gcC LOW 4 SILENT CODING KLHL17 C protein_coding NM_198317.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 897325 G C 0 228 0 0.6959 0.8592 0.8847 0.9157 0.9433 0.9172 0.72752 0.85889 0.926163 2 7421 109211 10871 7837 6181 60950 828 15123 2 10292 120318 11564 8632 6614 65816 892 16508 0 . 0 . 0 128 0,0,59,50 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A203|642|KLHL17|protein_coding|CODING|NM_198317.2|4|C),UPSTREAM(MODIFIER||2646||749|NOC2L|protein_coding|CODING|NM_015658.3||C),UPSTREAM(MODIFIER||4552||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4970441 -0.693147 0.414178 128 642 159 MODIFIER 12 CODING KLHL17 A protein_coding NM_198317.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 900730 G A 0 24.3 0 0.2005 0.6474 0.7061 0.7083 0.9095 0.8773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.00083264 0 . 0 . 21 1,12,0,8 UTR_3_PRIME(MODIFIER||159||642|KLHL17|protein_coding|CODING|NM_198317.2|12|A),UPSTREAM(MODIFIER||1147||611|PLEKHN1|protein_coding|CODING|NM_032129.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.909914 rs3935066 -0.651104 0.281388 21 642 401 MODIFIER 12 CODING KLHL17 G protein_coding NM_198317.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 900972 T G 0 95 0 0.9334 0.9301 0.9179 0.9216 0.9553 0.9172 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||401||642|KLHL17|protein_coding|CODING|NM_198317.2|12|G),UPSTREAM(MODIFIER||905||611|PLEKHN1|protein_coding|CODING|NM_032129.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9697711 -0.556411 0.560696 4 642 452 MODIFIER 12 CODING KLHL17 C protein_coding NM_198317.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 901023 T C 0 54 0 0.7867 0.8866 0.8934 0.9196 0.9503 0.9172 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||452||642|KLHL17|protein_coding|CODING|NM_198317.2|12|C),UPSTREAM(MODIFIER||854||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13303351 -0.511536 0.833544 3 A43V 611 gCt/gTt MODERATE 2 MISSENSE CODING PLEKHN1 T protein_coding NM_032129.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 902128 C T 0 163 0 0.0295 0.0561 0.0922 0.1409 0.003 0.0337 0.0248792 0.00965752 0.00195551 1 131 1550 568 411 1 44 8 387 2 1590 25092 2168 1650 242 10562 206 8674 0.77073 0 . 0 . 19 6,2,6,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|611|PLEKHN1|protein_coding|CODING|NM_032129.2|2|T),DOWNSTREAM(MODIFIER||1029||642|KLHL17|protein_coding|CODING|NM_198317.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890706 rs28499371 -0.662043 0.167636 19 A166 611 gcA/gcC LOW 6 SILENT CODING PLEKHN1 C protein_coding NM_032129.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 906272 A C 0 74 0 0.2065 0.1801 0.1787 0.3304 0.0755 0.0982 0.144434 0.0987875 0.0754872 1 1559 13920 2014 2576 702 5238 106 1725 2 8044 109928 11036 8180 5802 59852 784 16230 0.895781 0 . 0 . 10 1,5,2,2 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A166|611|PLEKHN1|protein_coding|CODING|NM_032129.2|6|C),DOWNSTREAM(MODIFIER||4307||790|PERM1|protein_coding|CODING|NM_001291366.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.00775 0.916482 0 0.783809 rs28507236 -0.556411 0.160409 10 R487P 611 cGt/cCt MODERATE 14 MISSENSE CODING PLEKHN1 C protein_coding NM_032129.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 909238 G C 0 228 0 0.8169 0.7766 0.6931 0.8869 0.6183 0.8303 0.780837 0.650131 0.583256 2 7934 79409 7930 7528 3644 38381 617 13375 2 10056 118778 11472 8576 6434 64882 886 16472 0 . 0 . 0 22 0,0,12,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R487P|611|PLEKHN1|protein_coding|CODING|NM_032129.2|14|C),DOWNSTREAM(MODIFIER||1341||790|PERM1|protein_coding|CODING|NM_001291366.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3829740 -0.692562 0.00397224 22 G488 611 ggA/ggG LOW 14 SILENT CODING PLEKHN1 G protein_coding NM_032129.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 909242 A G 0 179 0 0.2723 0.1318 0.1225 0.1637 0.0189 0.0317 0.214838 0.0837313 0.0166511 1 2325 7033 1454 1305 250 1142 49 508 2 10024 118530 11490 8556 6368 64758 874 16460 0.82746 0 . 0 . 23 7,5,6,5 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G488|611|PLEKHN1|protein_coding|CODING|NM_032129.2|14|G),DOWNSTREAM(MODIFIER||1337||790|PERM1|protein_coding|CODING|NM_001291366.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.486669 rs3829739 -0.676189 0.0192408 23 S511P 611 Tcc/Ccc MODERATE 14 MISSENSE CODING PLEKHN1 C protein_coding NM_032129.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 909309 T C 0 198 0 0.239 0.2542 0.2248 0.2758 0.1839 0.3456 0.24261 0.194885 0.170433 1 2539 26446 2589 2185 1420 12024 213 5476 2 9858 116452 11332 8440 6048 63644 858 16272 0.945235 0 . 0 . 35 13,5,4,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S511P|611|PLEKHN1|protein_coding|CODING|NM_032129.2|14|C),DOWNSTREAM(MODIFIER||1270||790|PERM1|protein_coding|CODING|NM_001291366.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999713 rs3829738 -0.670168 0.0225549 35 R529 611 Aga/Cga LOW 14 SILENT CODING PLEKHN1 C protein_coding NM_032129.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 909363 A C 0 136 0 0.118 0.0645 0.0519 0.1081 0.005 0.0174 0.0894737 0.0342244 0.00606485 1 965 3058 452 699 90 575 21 256 2 6916 87772 8292 6560 3992 47442 650 13920 0.647373 0 . 0 . 23 6,8,2,5 SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R529|611|PLEKHN1|protein_coding|CODING|NM_032129.2|14|C),DOWNSTREAM(MODIFIER||1216||790|PERM1|protein_coding|CODING|NM_001291366.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.872525 rs62639990 -0.636426 0.427859 23 611 439 MODIFIER 16 CODING PLEKHN1 T protein_coding NM_032129.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 910394 C T 0 67 0 0.5855 0.4555 0.4193 0.4593 0.3211 0.4397 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,2,0 UTR_3_PRIME(MODIFIER||439||611|PLEKHN1|protein_coding|CODING|NM_032129.2|16|T),DOWNSTREAM(MODIFIER||185||790|PERM1|protein_coding|CODING|NM_001291366.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs28477686 -0.453602 0.32 5 611 483 MODIFIER 16 CODING PLEKHN1 G protein_coding NM_032129.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 910438 A G 0 64 0 0.789 0.9305 0.9481 0.999 0.9682 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||483||611|PLEKHN1|protein_coding|CODING|NM_032129.2|16|G),DOWNSTREAM(MODIFIER||141||790|PERM1|protein_coding|CODING|NM_001291366.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6685581 -0.511536 0.0295886 3 790 649 MODIFIER 4 CODING PERM1 C protein_coding NM_001291366.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 910903 T C 0 9.7 0 0.7496 0.9147 0.9409 0.999 0.9592 0.9867 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||649||790|PERM1|protein_coding|CODING|NM_001291366.1|4|C),DOWNSTREAM(MODIFIER||419||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4970429 -0.379885 0 1 V777A 790 gTg/gCg MODERATE 4 MISSENSE CODING PERM1 G protein_coding NM_001291366.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 911595 A G 0 228 0 0.4092 0.7103 0.8012 0.9246 0.7873 0.7526 0 . 0 2 361 9934 165 366 19 3434 100 5489 2 724 12882 216 400 22 4410 142 6968 0 . 0 . 0 18 0,0,8,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V777A|790|PERM1|protein_coding|CODING|NM_001291366.1|4|G),DOWNSTREAM(MODIFIER||1111||611|PLEKHN1|protein_coding|CODING|NM_032129.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7417106 -0.686358 0.0275695 18 E693Q 790 Gag/Cag MODERATE 2 MISSENSE CODING PERM1 G protein_coding NM_001291366.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 914333 C G 0 228 0 0.2436 0.5563 0.6542 0.8056 0.6034 0.6043 0 . 0 2 145 4502 82 234 9 1530 43 2459 2 342 6804 112 292 12 2412 70 3564 0 . 0 . 0 30 0,0,21,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E693Q|790|PERM1|protein_coding|CODING|NM_001291366.1|2|G),DOWNSTREAM(MODIFIER||3849||611|PLEKHN1|protein_coding|CODING|NM_032129.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs13302979 -0.693054 0.975639 30 Q520E 790 Cag/Gag MODERATE 2 MISSENSE CODING PERM1 C protein_coding NM_001291366.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 914852 G C 0 182 0 0.1793 0.5126 0.6138 0.7123 0.5994 0.5961 0 . 0 2 178 8079 132 316 73 2592 75 4713 2 662 13578 230 448 116 4460 148 7514 0 . 0 . 0 11 0,0,1,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q520E|790|PERM1|protein_coding|CODING|NM_001291366.1|2|C),DOWNSTREAM(MODIFIER||4368||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs13303368 -0.676189 0.0186843 11 S512G 790 Agc/Ggc MODERATE 2 MISSENSE CODING PERM1 C protein_coding NM_001291366.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 914876 T C 0 228 0 0.9418 0.9669 0.9539 0.999 0.9592 0.9847 0 . 0 2 668 13574 214 453 339 4278 143 7479 2 698 14046 224 454 348 4558 150 7614 0 . 0 . 0 14 0,0,3,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S512G|790|PERM1|protein_coding|CODING|NM_001291366.1|2|C),DOWNSTREAM(MODIFIER||4392||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs13302983 -0.686358 0.858666 14 A490 790 gcA/gcG LOW 2 SILENT CODING PERM1 C protein_coding NM_001291366.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 914940 T C 0 228 0 0.177 0.5096 0.6095 0.7123 0.5895 0.5971 0 . 0 2 184 8347 146 315 230 2642 79 4751 2 682 14210 250 450 394 4652 158 7624 0 . 0 . 0 24 0,0,14,9 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A490|790|PERM1|protein_coding|CODING|NM_001291366.1|2|C),DOWNSTREAM(MODIFIER||4456||611|PLEKHN1|protein_coding|CODING|NM_032129.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs13303033 -0.692717 0.106181 24 L395 790 Ttg/Ctg LOW 2 SILENT CODING PERM1 G protein_coding NM_001291366.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 915227 A G 0 228 0 0.764 0.9181 0.9409 0.999 0.9592 0.9847 0 . 0 2 729 15588 278 492 1377 5007 181 7524 2 930 16302 294 492 1410 5318 192 7666 0 . 0 . 0 144 0,0,71,64 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L395|790|PERM1|protein_coding|CODING|NM_001291366.1|2|G),DOWNSTREAM(MODIFIER||4743||611|PLEKHN1|protein_coding|CODING|NM_032129.2||G) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.990107 0 . rs13303355 -0.693147 0.0359104 144 R44S 247 agG/agT MODERATE 1 MISSENSE CODING HES4 A protein_coding NM_001142467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 935222 C A 0 167 0 0.0356 0.4938 0.6268 0.7718 0.5895 0.6339 0.138635 0.436702 0.569509 2 657 51683 6516 5014 2370 26919 388 9819 2 3258 78176 8566 6180 3618 41512 598 14444 0 . 0 . 0 25 0,0,0,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R44S|247|HES4|protein_coding|CODING|NM_001142467.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs2298214 -0.692831 0.276897 25 247 106 MODIFIER 1 CODING HES4 G protein_coding NM_001142467.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 935459 A G 0 9.7 0 0.323 0.6771 0.7896 0.8482 0.7893 0.7843 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||106||247|HES4|protein_coding|CODING|NM_001142467.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3128113 -0.379885 0 1 247 139 MODIFIER 1 CODING HES4 T protein_coding NM_001142467.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 935492 G T 0 39.3 0 0.323 0.6771 0.7896 0.8482 0.7893 0.7843 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||139||247|HES4|protein_coding|CODING|NM_001142467.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3121571 -0.453602 0.58 2 165 84 MODIFIER 1 CODING ISG15 G protein_coding NM_005101.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 948870 C G 0 228 0 0.7194 0.903 0.9308 0.999 0.9573 0.9765 0.739447 0.889845 0.955323 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 72 0,0,60,12 UTR_5_PRIME(MODIFIER||84||165|ISG15|protein_coding|CODING|NM_005101.3|1|G) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs4615788 -0.693147 0.0241291 72 165 33 MODIFIER 1 CODING ISG15 C protein_coding NM_005101.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 948921 T C 0 228 0 0.7201 0.9032 0.9308 0.999 0.9573 0.9765 0.747956 0.885787 0.956385 2 7633 113562 11138 8638 6397 63034 845 15877 2 10334 120606 11564 8640 6608 66052 898 16510 0 . 0 . 0 103 0,0,75,23 UTR_5_PRIME(MODIFIER||33||165|ISG15|protein_coding|CODING|NM_005101.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs15842 -0.693147 0.166913 103 V98 165 gtA/gtG LOW 2 SILENT CODING ISG15 G protein_coding NM_005101.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 949654 A G 0 228 0 0.5083 0.8257 0.9179 0.9266 0.9453 0.9622 0.573309 0.820363 0.946964 2 5821 110144 11026 7979 6263 62537 830 15688 2 10328 120752 11572 8622 6612 66204 902 16512 0 . 0 . 0 365 0,0,228,92 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V98|165|ISG15|protein_coding|CODING|NM_005101.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8997 -0.693147 0.092268 365 2067 LOW 6 CODING AGRN C protein_coding NM_001305275.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 977330 T C 0 228 0 0.6899 0.8852 0.9207 0.999 0.9245 0.9663 0.719446 0.852593 0.920777 2 7033 107758 10926 8480 6060 58729 802 15728 2 9802 117568 11452 8482 6384 64108 860 16480 0 2 benign 0 . 268 0,0,188,57 SPLICE_SITE_REGION+INTRON(LOW||||2067|AGRN|protein_coding|CODING|NM_001305275.1|6|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.922706 0 . rs2799066 -0.693147 0.00901406 268 S1022 2067 tcA/tcG LOW 18 SILENT CODING AGRN G protein_coding NM_001305275.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 981931 A G 0 228 0 0.4554 0.7977 0.8905 0.9633 0.9125 0.9059 0.526843 0.780216 0.909821 2 4889 101717 10519 8086 5617 57283 751 14572 2 9530 116016 11296 8380 6062 63520 836 16392 0 2 benign 0 COSM1126908 64 0,0,30,27 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1022|2067|AGRN|protein_coding|CODING|NM_001305275.1|18|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2465128 -0.693147 0.00141765 64 F1186 2067 ttT/ttC LOW 21 SILENT CODING AGRN C protein_coding NM_001305275.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 982994 T C 0 228 0 0.5151 0.8359 0.9035 0.999 0.9205 0.9663 0.542215 0.791173 0.918721 2 5457 108492 10891 8628 6277 60651 833 15755 2 10192 120690 11562 8632 6614 66280 900 16510 0 2 benign 0 . 90 0,0,46,32 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1186|2067|AGRN|protein_coding|CODING|NM_001305275.1|21|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10267 -0.693147 0.352627 90 T1387 2067 acT/acC LOW 24 SILENT CODING AGRN C protein_coding NM_001305275.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 984302 T C 0 228 0 0.2405 0.5457 0.6614 0.8294 0.5636 0.5654 0.279378 0.458626 0.549389 2 894 20978 2026 2107 354 10490 146 4961 2 2320 33326 2676 2498 532 16422 254 8624 0 2 benign 0 . 30 0,0,12,15 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1387|2067|AGRN|protein_coding|CODING|NM_001305275.1|24|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9442391 -0.693021 0.0481634 30 2067 LOW 33 CODING AGRN T protein_coding NM_001305275.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 987200 C T 0 228 0 0.4017 0.7887 0.8876 0.9931 0.9145 0.9018 0.457974 0.756923 0.909979 2 4626 105202 10799 8610 6187 59582 810 14588 2 10234 120136 11530 8638 6552 65798 890 16494 0 2 benign 0 . 220 0,0,90,104 SPLICE_SITE_REGION+INTRON(LOW||||2067|AGRN|protein_coding|CODING|NM_001305275.1|33|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9803031 -0.693147 0.275604 220 D2041 2067 gaC/gaT LOW 38 SILENT CODING AGRN T protein_coding NM_001305275.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 990280 C T 0 228 0 0.2617 0.5853 0.7262 0.8214 0.6779 0.5838 0.332168 0.579155 0.705385 2 812 13680 632 698 90 6406 110 4932 2 2308 21454 816 854 124 9154 184 8014 0 2 benign 0 . 96 0,0,54,31 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D2041|2067|AGRN|protein_coding|CODING|NM_001305275.1|38|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4275402 -0.693147 0.316863 96 2067 156 MODIFIER 38 CODING AGRN T protein_coding NM_001305275.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 990517 C T 0 228 0 0.8419 0.9179 0.928 0.999 0.8877 0.9611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 39 0,0,12,26 UTR_3_PRIME(MODIFIER||156||2067|AGRN|protein_coding|CODING|NM_001305275.1|38|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2710872 -0.693143 0.178092 39 2067 412 MODIFIER 38 CODING AGRN T protein_coding NM_001305275.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 990773 C T 0 228 0 0.6233 0.846 0.9107 0.9931 0.8787 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,58,26 UTR_3_PRIME(MODIFIER||412||2067|AGRN|protein_coding|CODING|NM_001305275.1|38|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2799072 -0.693147 0.42018 95 2067 445 MODIFIER 38 CODING AGRN A protein_coding NM_001305275.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 990806 G A 0 228 0 0.6241 0.8462 0.9107 0.9931 0.8787 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 0,0,54,33 UTR_3_PRIME(MODIFIER||445||2067|AGRN|protein_coding|CODING|NM_001305275.1|38|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2799073 -0.693147 0.150145 99 2067 623 MODIFIER 38 CODING AGRN A protein_coding NM_001305275.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 990984 G A 0 210 0 0.8555 0.9223 0.9323 0.999 0.8887 0.9611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,1,36 UTR_3_PRIME(MODIFIER||623||2067|AGRN|protein_coding|CODING|NM_001305275.1|38|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8014 -0.693141 0.21758 37 249 1532 MODIFIER 1 CODING RNF223 C protein_coding NM_001205252.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1009478 G C 0 9.7 0 0.8313 0.8133 0.8012 0.9177 0.7336 0.772 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1532||249|RNF223|protein_coding|CODING|NM_001205252.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9442367 -0.379885 0 1 198 932 MODIFIER 10 CODING C1orf159 T protein_coding NM_017891.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1017341 G T 0 112 0 0.8245 0.8091 0.7997 0.9177 0.7256 0.7689 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_3_PRIME(MODIFIER||932||198|C1orf159|protein_coding|CODING|NM_017891.4|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1133647 -0.590765 0.884235 6 198 129 MODIFIER 10 CODING C1orf159 C protein_coding NM_017891.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1018144 T C 0 228 0 0.2617 0.5377 0.6571 0.7907 0.5586 0.544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 113 0,0,77,33 UTR_3_PRIME(MODIFIER||129||198|C1orf159|protein_coding|CODING|NM_017891.4|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9442395 -0.693147 0.0228029 113 I119 198 atT/atC LOW 7 SILENT CODING C1orf159 G protein_coding NM_017891.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1021346 A G 0 222 0 0.239 0.1789 0.1311 0.122 0.1809 0.1881 0.243305 0.187144 0.158372 1 2542 20408 1013 827 1579 11316 184 2947 2 10244 119996 11472 8582 6590 65730 890 16488 0.965965 0 . 0 . 127 21,37,22,39 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I119|198|C1orf159|protein_coding|CODING|NM_017891.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.860769 rs10907177,rs386515862 -0.693147 0.285553 127 G25S 673 Ggc/Agc MODERATE 4 MISSENSE CODING TTLL10 A protein_coding NM_001130045.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1114668 G A 0 222 0 0.1778 0.107 0.0461 0.125 0.0547 0.09 0.138728 0.086728 0.0641106 1 329 1582 21 86 19 511 13 603 2 2098 19062 394 586 124 7968 182 7710 0.994528 0 . 0 . 109 40,18,29,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G25S|673|TTLL10|protein_coding|CODING|NM_001130045.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0996678 rs6668667 -0.693146 0.843309 109 S448N 673 aGt/aAt MODERATE 13 MISSENSE CODING TTLL10 A protein_coding NM_001130045.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1120431 G A 0 222 0 0.3608 0.1853 0.0562 0.1478 0.0517 0.2157 0.32138 0.143626 0.0525581 1 3406 12774 665 1020 440 3456 87 3700 2 10214 118134 11290 8548 5952 65020 852 16258 0.0794354 0 . 0 . 186 58,34,46,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S448N|673|TTLL10|protein_coding|CODING|NM_001130045.1|13|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.989513 0.985982 0 0.812743 rs1320571 -0.693147 0.139499 186 P624 673 ccA/ccG LOW 16 SILENT CODING TTLL10 G protein_coding NM_001130045.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1133077 A G 0 14.7 0 0.5983 0.5465 0.5202 0.88 0.2495 0.4571 0 . 0 1 103 3899 37 109 1 715 36 2898 2 194 10216 88 132 4 2526 112 7160 0.8 0 . 0 . 7 4,1,2,0 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P624|673|TTLL10|protein_coding|CODING|NM_001130045.1|16|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.4 rs2274789 -0.453602 0.18 7 673 46 MODIFIER 16 CODING TTLL10 C protein_coding NM_001130045.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1133273 T C 0 115 0 0.5363 0.5292 0.513 0.88 0.2495 0.4571 0 . 0 1 28 134 0 16 0 63 3 24 2 60 342 2 20 0 190 4 66 0.972604 0 . 0 . 17 1,8,1,5 UTR_3_PRIME(MODIFIER||46||673|TTLL10|protein_coding|CODING|NM_001130045.1|16|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.99308 rs12031928 -0.616816 0.789228 17 255 58 MODIFIER 4 CODING TNFRSF18 C protein_coding NM_148901.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1138913 T C 0 164 0 0.4917 0.1985 0.0893 0.1518 0.0557 0.0746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997099 0 . 0 . 58 33,3,15,2 UTR_3_PRIME(MODIFIER||58||255|TNFRSF18|protein_coding|CODING|NM_148901.1|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.830347 rs3819001 -0.690438 0.872981 58 P179 255 ccA/ccG LOW 4 SILENT CODING TNFRSF18 C protein_coding NM_148901.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1139202 T C 0 218 0 0.5174 0.2055 0.0893 0.1518 0.0557 0.0757 0.354739 0.152427 0.051606 1 2247 6931 512 642 149 2465 54 862 2 4458 45892 3848 3506 1000 22610 338 10132 0.0743026 0 . 0 COSM423482 32 0,16,4,12 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P179|255|TNFRSF18|protein_coding|CODING|NM_148901.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.398338 rs2298213 -0.689466 0.0514699 32 277 150 MODIFIER 7 CODING TNFRSF4 C protein_coding NM_003327.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1146785 G C 0 150 0 0.0106 0.0367 0.0173 0.13 0.0149 0.0123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960561 0 . 0 . 29 14,0,14,1 UTR_3_PRIME(MODIFIER||150||277|TNFRSF4|protein_coding|CODING|NM_003327.3|7|C),UPSTREAM(MODIFIER||4696||255|TNFRSF18|protein_coding|CODING|NM_148901.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.991465 rs2298209 -0.688148 0.390867 29 277 82 MODIFIER 7 CODING TNFRSF4 A protein_coding NM_003327.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1146853 G A 0 209 0 0.0129 0.0371 0.0159 0.13 0.0149 0.0123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.775439 0 . 0 . 52 18,4,25,4 UTR_3_PRIME(MODIFIER||82||277|TNFRSF4|protein_coding|CODING|NM_003327.3|7|A),UPSTREAM(MODIFIER||4764||255|TNFRSF18|protein_coding|CODING|NM_148901.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.342227 rs2298210 -0.693079 0.261941 52 E178 277 gaG/gaA LOW 5 SILENT CODING TNFRSF4 T protein_coding NM_003327.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1147422 C T 0 222 0 0.4297 0.4984 0.5043 0.7837 0.2117 0.5879 0.379452 0.264224 0.205236 1 3721 41557 7234 6215 1410 13506 263 9208 2 8952 110800 11054 8410 5500 60084 786 16014 0.991977 0 . 0 . 124 46,12,42,11 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E178|277|TNFRSF4|protein_coding|CODING|NM_003327.3|5|T),DOWNSTREAM(MODIFIER||4866||362|SDF4|protein_coding|CODING|NM_016176.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.290044 rs17568 -0.693147 0.0796062 124 D190 362 gaT/gaC LOW 4 SILENT CODING SDF4 G protein_coding NM_016176.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1158631 A G 0 228 0 0.9985 0.9533 0.9294 1 0.8608 0.956 0.978892 0.91996 0.889767 2 10200 111067 11066 8648 5666 58978 825 15684 2 10382 121168 11566 8650 6612 66540 906 16512 0 . 0 . 0 153 0,0,57,85 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|362|SDF4|protein_coding|CODING|NM_016176.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6603781 -0.693147 0.00015604 153 S156 802 tcG/tcA LOW 6 SILENT CODING SCNN1D A protein_coding NM_001130413.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1220954 G A 0 222 0 0.7073 0.4427 0.3386 0.6498 0.0368 0.363 0.613439 0.210746 0.0352645 1 1305 4246 116 368 4 352 31 2070 2 2030 13448 356 570 42 5566 124 4760 0.288041 0 . 0 . 193 70,37,53,10 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S156|802|SCNN1D|protein_coding|CODING|NM_001130413.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.335596 rs12751100 -0.693147 0.00329647 193 R344P 802 cGc/cCc MODERATE 8 MISSENSE CODING SCNN1D C protein_coding NM_001130413.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1222267 G C 0 222 0 0.2587 0.3033 0.281 0.63 0.0189 0.3354 0.227335 0.0887159 0.0178239 1 2445 18283 4121 5042 149 1316 77 5133 2 10082 119120 11494 8588 6564 65020 880 16492 0.591019 0 . 0 . 142 44,41,17,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R344P|802|SCNN1D|protein_coding|CODING|NM_001130413.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91982 rs11260579 -0.693147 0.193711 142 E544Q 802 Gag/Cag MODERATE 12 MISSENSE CODING SCNN1D C protein_coding NM_001130413.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1223385 G C 0 96 0 0.354 0.3277 0.2925 0.6111 0.0229 0.3384 0.271809 0.101653 0.0170343 1 581 3409 107 334 2 165 20 2200 2 1614 14020 314 540 28 4614 136 6774 0.513192 0 . 0 . 19 1,9,0,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E544Q|802|SCNN1D|protein_coding|CODING|NM_001130413.3|12|C),DOWNSTREAM(MODIFIER||4379||834|ACAP3|protein_coding|CODING|NM_030649.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999014 rs2228579 -0.651104 0.0474063 19 T645 802 acG/acA LOW 16 SILENT CODING SCNN1D A protein_coding NM_001130413.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1226292 G A 0 222 0 0.0189 0.1731 0.1153 0.5387 0.005 0.2188 0.0182028 0.0105475 0.00666355 1 194 9475 1687 4005 30 510 42 3007 2 8176 98790 9670 8014 3690 53876 664 14700 0.124786 0 . 0 . 180 53,38,45,27 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T645|802|SCNN1D|protein_coding|CODING|NM_001130413.3|16|A),DOWNSTREAM(MODIFIER||1472||834|ACAP3|protein_coding|CODING|NM_030649.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.113697 rs2273276 -0.693147 0.382104 180 802 259 MODIFIER 18 CODING SCNN1D C protein_coding NM_001130413.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1227249 T C 0 222 0 0.1528 0.1148 0.0893 0.1567 0.0437 0.1115 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998826 0 . 0 . 164 66,5,66,14 UTR_3_PRIME(MODIFIER||259||802|SCNN1D|protein_coding|CODING|NM_001130413.3|18|C),DOWNSTREAM(MODIFIER||515||834|ACAP3|protein_coding|CODING|NM_030649.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.619483 rs621668 -0.693147 0.000585976 164 834 LOW 11 CODING ACAP3 C protein_coding NM_030649.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1233941 T C 0 228 0 0.8169 0.4968 0.2608 0.7659 0.0825 0.3804 0.712369 0.290191 0.0740396 2 7436 29986 4065 6471 936 5250 187 5641 2 10158 118658 11462 8546 6546 64618 876 16452 0 . 0 . 0 68 0,0,65,0 SPLICE_SITE_REGION+INTRON(LOW||||834|ACAP3|protein_coding|CODING|NM_030649.2|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs1739855,rs386543582 -0.693147 9.92695e-21 68 G94 606 ggG/ggC LOW 6 SILENT CODING CPSF3L G protein_coding NM_001256456.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1254841 C G 0 222 0 0.3018 0.7137 0.8545 0.8353 0.9205 0.8323 0.398094 0.751269 0.932209 1 3962 101929 9144 7123 5828 61220 743 13909 2 10296 120256 11558 8626 6612 65864 892 16408 0.81088 0 . 0 . 123 25,48,9,27 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G94|606|CPSF3L|protein_coding|CODING|NM_001256456.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.798922 rs10907179 -0.693139 0.678522 123 R156 214 cgC/cgT LOW 3 SILENT CODING CPTP T protein_coding NM_001029885.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1262966 C T 0 222 0 0.4834 0.7626 0.8732 0.8323 0.9155 0.8323 0.581161 0.81306 0.931251 1 4957 93005 8095 6285 5020 54613 681 13354 2 8168 106710 10032 7540 5708 58720 800 15742 0.989664 0 . 0 . 73 27,6,31,5 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R156|214|CPTP|protein_coding|CODING|NM_001029885.1|3|T),UPSTREAM(MODIFIER||2899||606|CPSF3L|protein_coding|CODING|NM_001256456.1||T),UPSTREAM(MODIFIER||3760||852|TAS1R3|protein_coding|CODING|NM_152228.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.705744 rs307349 -0.693139 0.521156 73 214 1 MODIFIER 3 CODING CPTP A protein_coding NM_001029885.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1263144 G A 0 222 0 0.7935 0.8498 0.8991 0.8313 0.9235 0.8344 0.852814 0.908324 0.935775 1 7885 105608 9335 7058 5819 60753 766 13992 2 9464 118700 11512 8552 6608 65176 886 16502 0.199956 0 . 0 . 140 47,24,27,27 UTR_3_PRIME(MODIFIER||1||214|CPTP|protein_coding|CODING|NM_001029885.1|3|A),UPSTREAM(MODIFIER||3077||606|CPSF3L|protein_coding|CODING|NM_001256456.1||A),UPSTREAM(MODIFIER||3582||852|TAS1R3|protein_coding|CODING|NM_152228.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916093 rs307350 -0.693147 0.0125138 140 214 219 MODIFIER 3 CODING CPTP A protein_coding NM_001029885.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1263362 G A 0 222 0 0.3048 0.7147 0.8573 0.8323 0.9205 0.8344 0.401734 0.770377 0.930818 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969223 0 . 0 . 53 1,29,5,17 UTR_3_PRIME(MODIFIER||219||214|CPTP|protein_coding|CODING|NM_001029885.1|3|A),UPSTREAM(MODIFIER||3295||606|CPSF3L|protein_coding|CODING|NM_001256456.1||A),UPSTREAM(MODIFIER||3364||852|TAS1R3|protein_coding|CODING|NM_152228.2||A) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.989082 rs4970433 -0.692562 0.977356 53 214 314 MODIFIER 3 CODING CPTP C protein_coding NM_001029885.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1263457 T C 0 228 0 0.9803 0.9515 0.9813 0.9117 0.9662 0.9172 0.992775 0.975909 0.968573 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,8,7 UTR_3_PRIME(MODIFIER||314||214|CPTP|protein_coding|CODING|NM_001029885.1|3|C),UPSTREAM(MODIFIER||3390||606|CPSF3L|protein_coding|CODING|NM_001256456.1||C),UPSTREAM(MODIFIER||3269||852|TAS1R3|protein_coding|CODING|NM_152228.2||C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs307351 -0.688148 0.900601 17 P416 852 ccC/ccT LOW 3 SILENT CODING TAS1R3 T protein_coding NM_152228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1268159 C T 0 222 0 0.3185 0.1406 0.1052 0.0794 0.0487 0.0828 0.267061 0.116705 0.0397952 1 2716 10239 2102 728 351 3011 80 1251 2 9446 113932 11296 8434 5898 62502 802 15554 0.765803 0 . 0 . 123 24,28,33,30 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P416|852|TAS1R3|protein_coding|CODING|NM_152228.2|3|T),DOWNSTREAM(MODIFIER||3883||214|CPTP|protein_coding|CODING|NM_001029885.1||T),DOWNSTREAM(MODIFIER||2499||670|DVL1|protein_coding|CODING|NM_004421.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.879951 rs3813210 -0.693147 0.0205334 123 C757R 852 Tgc/Cgc MODERATE 6 MISSENSE CODING TAS1R3 C protein_coding NM_152228.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1269554 T C 0 228 0 0.9803 0.9519 0.9813 0.9137 0.9662 0.9172 0.989945 0.977374 0.970959 2 7101 80454 7410 5371 3134 44523 535 12380 2 7192 83696 7500 5884 3346 45800 574 13400 0 . 0 . 0 123 0,0,49,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C757R|852|TAS1R3|protein_coding|CODING|NM_152228.2|6|C),DOWNSTREAM(MODIFIER||1104||670|DVL1|protein_coding|CODING|NM_004421.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs307377 -0.693147 0.0277502 123 852 142 MODIFIER 6 CODING TAS1R3 A protein_coding NM_152228.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1269986 G A 0 214 0 0.2837 0.1276 0.085 0.0794 0.0437 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999803 0 . 0 . 32 0,11,3,18 UTR_3_PRIME(MODIFIER||142||852|TAS1R3|protein_coding|CODING|NM_152228.2|6|A),DOWNSTREAM(MODIFIER||672||670|DVL1|protein_coding|CODING|NM_004421.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.302049 rs35424002 -0.692352 0.0438123 32 852 485 MODIFIER 6 CODING TAS1R3 G protein_coding NM_152228.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1270329 A G 0 9.7 0 0.9803 0.9517 0.9813 0.9127 0.9662 0.9172 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||485||852|TAS1R3|protein_coding|CODING|NM_152228.2|6|G),DOWNSTREAM(MODIFIER||329||670|DVL1|protein_coding|CODING|NM_004421.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs188647 -0.379885 0 1 852 515 MODIFIER 6 CODING TAS1R3 C protein_coding NM_152228.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1270359 T C 0 9.7 0 0.9803 0.9517 0.9813 0.9127 0.9662 0.9172 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||515||852|TAS1R3|protein_coding|CODING|NM_152228.2|6|C),DOWNSTREAM(MODIFIER||299||670|DVL1|protein_coding|CODING|NM_004421.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs307374 -0.379885 0 1 P122 670 ccA/ccG LOW 4 SILENT CODING DVL1 C protein_coding NM_004421.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1277533 T C 0 228 0 1 0.998 0.9986 0.999 0.994 0.998 0.999771 0.999072 0.998715 2 4747 46411 2581 3444 766 25153 315 9405 2 4748 46524 2582 3452 798 25208 316 9420 0 . 0 . 0 42 0,0,12,28 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P122|670|DVL1|protein_coding|CODING|NM_004421.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs307362 -0.693145 0.729937 42 670 45 MODIFIER 1 CODING DVL1 A protein_coding NM_004421.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1284490 G A 0 96 0 0.4902 0.763 0.8746 0.8234 0.9155 0.8333 0.7144 0.873124 0.953104 1 927 21065 558 1279 762 10448 149 6942 2 1294 23476 662 1472 850 11012 174 8012 1 0 . 0 . 8 0,1,0,7 UTR_5_PRIME(MODIFIER||45||670|DVL1|protein_coding|CODING|NM_004421.2|1|A),DOWNSTREAM(MODIFIER||3579||450|MXRA8|protein_coding|CODING|NM_001282585.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 1 rs150789461 -0.636426 0.00794617 8 450 336 MODIFIER 10 CODING MXRA8 G protein_coding NM_001282585.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1288345 A G 0 31.3 0 0.9803 0.9517 0.9813 0.9127 0.9662 0.9172 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||336||450|MXRA8|protein_coding|CODING|NM_001282585.1|10|G),UPSTREAM(MODIFIER||3853||670|DVL1|protein_coding|CODING|NM_004421.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13249 -0.453602 0.38 2 450 210 MODIFIER 10 CODING MXRA8 T protein_coding NM_001282585.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1288471 C T 0 125 0 0.4894 0.7664 0.8761 0.8333 0.9215 0.8344 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950149 0 . 0 . 23 12,0,9,0 UTR_3_PRIME(MODIFIER||210||450|MXRA8|protein_coding|CODING|NM_001282585.1|10|T),UPSTREAM(MODIFIER||3979||670|DVL1|protein_coding|CODING|NM_004421.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.695144 rs3766183 -0.662043 0.180184 23 450 98 MODIFIER 10 CODING MXRA8 G protein_coding NM_001282585.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1288583 C G 0 222 0 0.7322 0.8436 0.951 0.8423 0.9254 0.8354 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.940826 0 . 0 . 72 23,10,18,13 UTR_3_PRIME(MODIFIER||98||450|MXRA8|protein_coding|CODING|NM_001282585.1|10|G),UPSTREAM(MODIFIER||4091||670|DVL1|protein_coding|CODING|NM_004421.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.833001 rs3845295 -0.69311 0.355514 72 149 129 MODIFIER 4 CODING MRPL20 T protein_coding NM_017971.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1337334 G T 0 169 0 0.1195 0.3708 0.3646 0.869 0.0924 0.4877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,21,0 UTR_3_PRIME(MODIFIER||129||149|MRPL20|protein_coding|CODING|NM_017971.3|4|T),UPSTREAM(MODIFIER||2616||520|CCNL2|protein_coding|CODING|NM_030937.4||T),INTRAGENIC(MODIFIER|||||LOC148413||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1171 -0.692352 0.309176 21 149 15 MODIFIER 1 CODING MRPL20 C protein_coding NM_017971.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1342612 G C 0 228 0 0.2383 0.4303 0.415 0.871 0.17 0.5143 0.237059 0.190218 0.166316 2 1367 19850 2045 3835 315 6130 125 6033 2 4614 56286 4204 4402 1712 28652 414 12288 1 0 . 0 COSN503927 69 0,1,17,45 UTR_5_PRIME(MODIFIER||15||149|MRPL20|protein_coding|CODING|NM_017971.3|1|C) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.93855 0 1 rs2275915 -0.693147 0.0121421 69 S42 163 tcG/tcA LOW 1 SILENT CODING TMEM88B A protein_coding NM_001146685.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1361633 G A 0 228 0 0.1989 0.4 0.3631 0.875 0.1193 0.4969 0 . 0 2 133 3431 43 301 4 512 26 2412 2 552 7638 116 332 12 2246 58 4322 0 . 0 . 0 25 0,0,14,10 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S42|163|TMEM88B|protein_coding|CODING|NM_001146685.1|1|A),UPSTREAM(MODIFIER||4809||399|ANKRD65|protein_coding|CODING|NM_001145210.2||A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12022947 -0.692831 0.778732 25 P45L 163 cCg/cTg MODERATE 1 MISSENSE CODING TMEM88B T protein_coding NM_001146685.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1361641 C T 0 228 0 0.8631 0.6813 0.5418 0.9891 0.2167 0.6953 0 . 0 2 479 5330 60 296 4 746 42 3703 2 600 8496 114 298 8 2208 74 5194 0 . 0 . 0 24 0,0,13,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P45L|163|TMEM88B|protein_coding|CODING|NM_001146685.1|1|T),UPSTREAM(MODIFIER||4817||399|ANKRD65|protein_coding|CODING|NM_001145210.2||T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12030806 -0.692562 0.867997 24 P150T 163 Ccg/Acg MODERATE 2 MISSENSE CODING TMEM88B A protein_coding NM_001146685.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1363123 C A 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 21 0 10 0 0 1 10 2 74 3936 34 76 0 690 38 3024 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccg/Acg|P150T|163|TMEM88B|protein_coding|CODING|NM_001146685.1|2|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 0 . 0 . rs185086231 -0.379885 0 1 P335 445 ccA/ccG LOW 3 SILENT CODING VWA1 G protein_coding NM_022834.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1374834 A G 0 32.6 0 0.8283 0.6697 0.5447 0.9911 0.2087 0.6871 0 . 0 2 84 3456 25 106 0 277 35 2929 2 128 6522 52 106 0 1348 78 4810 0 . 0 . 0 2 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P335|445|VWA1|protein_coding|CODING|NM_022834.4|3|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs1892289 -0.379885 0 2 445 643 MODIFIER 3 CODING VWA1 G protein_coding NM_022834.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1375810 C G 0 228 0 0.6112 0.5821 0.4669 0.9732 0.1889 0.6258 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,18,54 UTR_3_PRIME(MODIFIER||643||445|VWA1|protein_coding|CODING|NM_022834.4|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4590 -0.693147 0.00377644 75 445 1047 MODIFIER 3 CODING VWA1 G protein_coding NM_022834.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1376214 C G 0 228 0 0.8888 0.6869 0.5548 0.9911 0.2078 0.6871 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,2,17 UTR_3_PRIME(MODIFIER||1047||445|VWA1|protein_coding|CODING|NM_022834.4|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1240698 -0.69168 0.684188 20 445 1400 MODIFIER 3 CODING VWA1 G protein_coding NM_022834.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1376567 A G 0 46.3 0 0.7859 0.62 0.5317 0.8938 0.1849 0.6237 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1400||445|VWA1|protein_coding|CODING|NM_022834.4|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1240697 -0.453602 0.92 2 445 3006 MODIFIER 3 CODING VWA1 A protein_coding NM_022834.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1378173 G A 0 9.7 0 0.2776 0.4305 0.3674 0.8671 0.1312 0.5399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3006||445|VWA1|protein_coding|CODING|NM_022834.4|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs711180 -0.379885 0 1 411 491 MODIFIER 1 CODING ATAD3C T protein_coding NM_001039211.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1385573 C T 0 6.3 0 0.3986 0.3191 0.2089 0.6071 0.0467 0.273 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||491||411|ATAD3C|protein_coding|CODING|NM_001039211.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1240588 -0.379885 0 1 411 LOW 6 CODING ATAD3C C protein_coding NM_001039211.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1391597 T C 0 198 0 . 0 . 0 . 0 . 0 . 2 70 188 10 68 2 11 2 25 2 3280 85230 5352 120 5606 61310 706 8856 0 . 0 . 0 15 0,0,4,11 SPLICE_SITE_REGION+INTRON(LOW||||411|ATAD3C|protein_coding|CODING|NM_001039211.2|6|C) 0 . 0 . 0 . 0 . 1 0 33 0 0 0.0851732 0 . rs71628970 -0.688148 0.111591 15 A307 411 gcG/gcT LOW 10 SILENT CODING ATAD3C T protein_coding NM_001039211.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1396238 G T 0 228 0 0.3691 0.2582 0.1354 0.4861 0.006 0.2198 0.29841 0.0948314 0.00628535 2 3123 12734 1508 4256 128 439 56 3224 2 10200 119072 11434 8592 6554 65136 888 16268 0.623711 0 . 0 . 231 0,2,107,87 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A307|411|ATAD3C|protein_coding|CODING|NM_001039211.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.93299 rs72896283 -0.693147 0.108601 231 411 106 MODIFIER 12 CODING ATAD3C A protein_coding NM_001039211.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1404016 G A 0 228 0 0.4523 0.2825 0.1441 0.4871 0.007 0.2239 0.361156 0.117617 0.00699387 2 3298 12628 1492 4142 234 464 60 2938 2 7706 94994 9752 8122 5350 51380 682 12002 0.485563 0 . 0 . 120 1,2,57,50 UTR_3_PRIME(MODIFIER||106||411|ATAD3C|protein_coding|CODING|NM_001039211.2|12|A),UPSTREAM(MODIFIER||3119||648|ATAD3B|protein_coding|CODING|NM_031921.5||A) 1 0 . 0 . 1 0 1 1 0 58 0 0.976043 0.92599 0 0.981606 rs12089719 -0.693147 0.195232 120 411 326 MODIFIER 12 CODING ATAD3C T protein_coding NM_001039211.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1404236 C T 0 212 0 0.6014 0.4067 0.3055 0.622 0.0795 0.3303 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,1,25 UTR_3_PRIME(MODIFIER||326||411|ATAD3C|protein_coding|CODING|NM_001039211.2|12|T),UPSTREAM(MODIFIER||2899||648|ATAD3B|protein_coding|CODING|NM_031921.5||T) 0 . 0 . 0 1 0 . 0 . 57 0 0 1 0 . rs1240730 -0.692976 0.116954 27 411 558 MODIFIER 12 CODING ATAD3C C protein_coding NM_001039211.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1404468 T C 0 6.3 0 0.8328 0.4704 0.3228 0.621 0.0815 0.3303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||558||411|ATAD3C|protein_coding|CODING|NM_001039211.2|12|C),UPSTREAM(MODIFIER||2667||648|ATAD3B|protein_coding|CODING|NM_031921.5||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1240731 -0.379885 0 1 411 1504 MODIFIER 12 CODING ATAD3C C protein_coding NM_001039211.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1405414 T C 0 46.3 0 0.8321 0.4696 0.3228 0.621 0.0785 0.3303 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1504||411|ATAD3C|protein_coding|CODING|NM_001039211.2|12|C),UPSTREAM(MODIFIER||1721||648|ATAD3B|protein_coding|CODING|NM_031921.5||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs113538972,rs113944058,rs1240733 -0.453602 0.78 2 G36 648 ggT/ggC LOW 1 SILENT CODING ATAD3B C protein_coding NM_031921.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1407372 T C 0 9.7 0 0.9546 0.6877 0.4424 0.9891 0.2177 0.6738 0 . 0 1 15 61 3 0 0 12 2 29 2 20 222 14 0 2 138 4 44 0 . 0 . 0 1 0,0,0,1 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G36|648|ATAD3B|protein_coding|CODING|NM_031921.5|1|C),DOWNSTREAM(MODIFIER||1834||411|ATAD3C|protein_coding|CODING|NM_001039211.2||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs188574574 -0.379885 0 1 T335 648 acC/acA LOW 10 SILENT CODING ATAD3B A protein_coding NM_031921.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1421531 C A 0 228 0 0.8502 0.4826 0.3228 0.622 0.0924 0.3569 0.729687 0.294679 0.0717609 2 7806 29860 4559 5450 1289 5100 201 5455 2 10376 120592 11544 8620 6604 66058 900 16490 0 . 0 . 0 158 0,0,92,48 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T335|648|ATAD3B|protein_coding|CODING|NM_031921.5|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs56587801,rs819976 -0.693147 0.305215 158 R386Q 648 cGg/cAg MODERATE 11 MISSENSE CODING ATAD3B A protein_coding NM_031921.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1421991 G A 0 228 0 0.5817 0.3862 0.2824 0.5764 0.0795 0.3149 0 . 0 2 4687 22966 3457 4733 945 4555 150 4439 2 8488 106848 10372 8108 5892 57658 800 15530 0 . 0 . 0 95 0,0,19,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R386Q|648|ATAD3B|protein_coding|CODING|NM_031921.5|11|A) 0 . 0 . 0 1 0 . 1 0 46 0 0 2.33137e-07 0 . rs860213 -0.693147 0.0698488 95 A413 648 gcA/gcG LOW 12 SILENT CODING ATAD3B G protein_coding NM_031921.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1423267 A G 0 228 0 0.848 0.4868 0.3386 0.626 0.0994 0.3589 0.728098 0.301676 0.0831589 2 7803 30722 4614 5507 1334 5736 210 5518 2 10388 120986 11566 8628 6610 66398 902 16494 0 . 0 . 0 143 0,0,61,67 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A413|648|ATAD3B|protein_coding|CODING|NM_031921.5|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs819977 -0.693147 0.0576667 143 I467 648 atT/atC LOW 14 SILENT CODING ATAD3B C protein_coding NM_031921.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1425700 T C 0 228 0 0.8487 0.4858 0.3357 0.623 0.0994 0.3579 0.732062 0.302876 0.0830426 2 7797 30643 4610 5465 1332 5710 204 5525 2 10336 120364 11544 8632 6608 65862 892 16490 1 0 . 0 COSM423664 199 1,0,136,43 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I467|648|ATAD3B|protein_coding|CODING|NM_031921.5|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs819980 -0.693147 0.595569 199 T522 648 acG/acA LOW 15 SILENT CODING ATAD3B A protein_coding NM_031921.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1426003 G A 0 228 0 0.0038 0.0623 0.1023 0.2282 0.002 0.0041 0.00251486 0.00186567 0.00153121 2 28 2839 950 1553 95 113 18 82 2 7450 85996 6616 6472 3620 48204 602 13032 0 . 0 . 0 76 0,0,19,56 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T522|648|ATAD3B|protein_coding|CODING|NM_031921.5|15|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.993326 0 . rs143153541 -0.693147 0.269693 76 648 88 MODIFIER 16 CODING ATAD3B G protein_coding NM_031921.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1431285 T G 0 180 0 0.003 0.0387 0.0965 0.1181 0.001 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.019062 0 . 0 . 19 0,4,2,12 UTR_3_PRIME(MODIFIER||88||648|ATAD3B|protein_coding|CODING|NM_031921.5|16|G) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.892087 0.53125 0 0.0652634 rs3842878 -0.686358 0.888366 19 G15D 634 gGc/gAc MODERATE 1 MISSENSE CODING ATAD3A A protein_coding NM_018188.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1447692 G A 0 135 0 0.2194 0.1797 0.1282 0.3343 0.005 0.183 0.102612 0.0329584 0.00289855 2 235 1185 200 394 13 50 10 283 2 710 9286 770 884 142 5688 62 1030 0 . 0 . 0 8 0,0,2,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G15D|634|ATAD3A|protein_coding|CODING|NM_018188.3|1|A) 1 0 . 0 . 1 0 1 1 0 50 0 0 0 0 . rs2274435 -0.651104 0.195133 8 G36 634 ggG/ggC LOW 1 SILENT CODING ATAD3A C protein_coding NM_018188.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1447756 G C 0 55 0 0.8298 0.4623 0.3573 0.505 0.1203 0.3476 0 . 0 2 24 55 3 0 0 5 0 23 2 30 232 14 6 2 132 4 44 0 . 0 . 0 4 0,0,0,4 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G36|634|ATAD3A|protein_coding|CODING|NM_018188.3|1|C) 0 . 0 . 0 1 0 . 1 0 34 0 0 . 0 . rs1240736,rs28627708 -0.556411 0.472095 4 R96Q 634 cGg/cAg MODERATE 3 MISSENSE CODING ATAD3A A protein_coding NM_018188.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1452551 G A 0 74 0 0.2156 0.1779 0.1282 0.3323 0.004 0.182 0 . 0 1 151 458 23 111 0 18 5 150 2 1826 17084 374 512 34 7286 168 6884 0.643095 0 . 0 . 12 3,1,4,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R96Q|634|ATAD3A|protein_coding|CODING|NM_018188.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.361741 0.361741 0 0.0803868 rs1619925 -0.636426 0.00115826 12 S101N 634 aGc/aAc MODERATE 3 MISSENSE CODING ATAD3A A protein_coding NM_018188.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1452566 G A 0 74 0 0.2057 0.1727 0.1282 0.3214 0.004 0.18 0 . 0 1 80 170 9 52 0 9 2 18 2 2142 18686 382 510 34 7798 182 7638 0.562708 0 . 0 . 12 3,1,4,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S101N|634|ATAD3A|protein_coding|CODING|NM_018188.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.361741 0.361741 0 0.0803868 rs1619896 -0.636426 0.00115826 12 A117 634 gcC/gcT LOW 3 SILENT CODING ATAD3A T protein_coding NM_018188.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1452615 C T 0 87 0 0.1649 0.1232 0.0793 0.2153 0.002 0.1278 0.0154076 0.00503492 0 1 61 76 5 3 0 2 1 4 2 2488 19894 396 544 40 8542 188 7696 0.564628 0 . 0 . 11 3,2,0,6 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A117|634|ATAD3A|protein_coding|CODING|NM_018188.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.8618 0.716531 0 0.356607 rs2478791 -0.616816 0.0110037 11 L342 634 ctT/ctG LOW 8 SILENT CODING ATAD3A G protein_coding NM_018188.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1458255 T G 0 228 0 0.3737 0.2386 0.1527 0.3879 0.007 0.2014 0 . 0 2 1477 6217 752 1604 80 202 44 2058 2 6506 104002 9726 6206 4980 61180 758 14646 0.928823 0 . 0 . 109 7,3,14,79 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L342|634|ATAD3A|protein_coding|CODING|NM_018188.3|8|G) 0 . 0 . 0 1 0 . 1 0 55 0 0.312132 0.0823356 0 0.711982 rs28675990 -0.693147 0.205807 109 634 LOW 8 CODING ATAD3A G protein_coding NM_018188.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1458285 A G 0 181 0 0.6543 0.3345 0.2133 0.3492 0.0557 0.2597 0 . 0 2 1697 7060 873 365 241 1880 63 1941 2 4662 92666 8080 4594 4188 57770 676 12696 0.818427 0 . 0 . 83 1,5,4,73 SPLICE_SITE_REGION+INTRON(LOW||||634|ATAD3A|protein_coding|CODING|NM_018188.3|8|G) 0 . 0 . 0 1 0 . 1 0 52 0 0.541379 0.0313455 0 0.187827 rs6675874 -0.693147 0.483379 83 634 LOW 9 CODING ATAD3A T protein_coding NM_018188.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1458954 C T 0 228 0 0.3124 0.2143 0.1427 0.3581 0.006 0.1984 0.276668 0.0959557 0.00337209 2 2887 10842 1406 3096 221 320 57 2855 2 9958 117028 11278 8518 5904 64230 854 16286 0.997177 0 . 0 . 165 2,4,59,88 SPLICE_SITE_REGION+INTRON(LOW||||634|ATAD3A|protein_coding|CODING|NM_018188.3|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.885367 rs3737714 -0.693147 0.28432 165 634 94 MODIFIER 16 CODING ATAD3A A protein_coding NM_018188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1469546 G A 0 228 0 0.7209 0.8385 0.8372 0.9931 0.7336 0.9468 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,6,23 UTR_3_PRIME(MODIFIER||94||634|ATAD3A|protein_coding|CODING|NM_018188.3|16|A),DOWNSTREAM(MODIFIER||612||173|TMEM240|protein_coding|CODING|NM_001114748.1||A) 0 . 0 . 0 1 0 . 0 . 56 0 0 0.178173 0 . rs3128344 -0.693079 6.15259e-06 31 634 146 MODIFIER 16 CODING ATAD3A G protein_coding NM_018188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1469598 C G 0 125 0 0.857 0.7206 0.5634 0.9405 0.4314 0.7188 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||146||634|ATAD3A|protein_coding|CODING|NM_018188.3|16|G),DOWNSTREAM(MODIFIER||560||173|TMEM240|protein_coding|CODING|NM_001114748.1||G) 0 . 0 . 0 1 0 . 0 . 54 0 0 . 0 . rs9439464 -0.651104 0.0238078 8 634 147 MODIFIER 16 CODING ATAD3A C protein_coding NM_018188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1469599 G C 0 125 0 0.8623 0.722 0.5634 0.9405 0.4314 0.7188 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||147||634|ATAD3A|protein_coding|CODING|NM_018188.3|16|C),DOWNSTREAM(MODIFIER||559||173|TMEM240|protein_coding|CODING|NM_001114748.1||C) 0 . 0 . 0 1 0 . 0 . 54 0 0 . 0 . rs3128343 -0.651104 0.0238078 8 634 154 MODIFIER 16 CODING ATAD3A T protein_coding NM_018188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1469606 C T 0 134 0 0.6271 0.5829 0.3573 0.9266 0.2674 0.6534 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||154||634|ATAD3A|protein_coding|CODING|NM_018188.3|16|T),DOWNSTREAM(MODIFIER||552||173|TMEM240|protein_coding|CODING|NM_001114748.1||T) 0 . 0 . 0 1 0 . 0 . 51 0 0 . 0 . rs35611435 -0.676189 0.0981849 11 194 338 MODIFIER 5 CODING SSU72 A protein_coding NM_014188.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1477108 G A 0 107 0 0.0809 0.1306 0.1268 0.2778 0.005 0.1779 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,0 UTR_3_PRIME(MODIFIER||338||194|SSU72|protein_coding|CODING|NM_014188.2|5|A),UPSTREAM(MODIFIER||1368||173|TMEM240|protein_coding|CODING|NM_001114748.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1046878 -0.511536 0.740702 5 194 202 MODIFIER 5 CODING SSU72 C protein_coding NM_014188.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1477244 T C 0 114 0 0.9266 0.6979 0.5663 0.8671 0.3062 0.7106 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_3_PRIME(MODIFIER||202||194|SSU72|protein_coding|CODING|NM_014188.2|5|C),UPSTREAM(MODIFIER||1504||173|TMEM240|protein_coding|CODING|NM_001114748.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs386447251,rs7290 -0.616816 0.773942 6 P133 194 ccT/ccC LOW 4 SILENT CODING SSU72 G protein_coding NM_014188.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1479333 A G 0 228 0 0.91 0.6937 0.5634 0.8671 0.3062 0.7137 0.816841 0.471782 0.295 2 8608 55629 6802 7633 2175 18840 402 11169 2 10366 120908 11552 8638 6612 66330 904 16506 0.947917 0 . 0 . 105 2,0,40,56 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P133|194|SSU72|protein_coding|CODING|NM_014188.2|4|G),UPSTREAM(MODIFIER||3593||173|TMEM240|protein_coding|CODING|NM_001114748.1||G) 1 0 . 0 . 1 0 1 1 0 58 0 0.958333 0.833753 0 0.640625 rs7533 -0.693147 0.630018 105 226 5 MODIFIER 1 CODING C1orf233 C protein_coding NM_001242659.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1534710 G C 0 228 0 0.003 0.0485 0.0187 0.1895 0.0258 0.0092 0 . 0 2 1 185 2 35 51 24 3 69 2 76 4256 32 102 748 790 46 2462 0 . 0 . 0 20 0,0,13,7 UTR_3_PRIME(MODIFIER||5||226|C1orf233|protein_coding|CODING|NM_001242659.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs79079518 -0.692067 0.457877 20 405 2723 MODIFIER 9 CODING SLC35E2B T protein_coding NM_001110781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1594498 C T 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2723||405|SLC35E2B|protein_coding|CODING|NM_001110781.2|9|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs7416520 -0.379885 0 1 405 2023 MODIFIER 9 CODING SLC35E2B G protein_coding NM_001110781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1595198 A G 0 10.7 0 0.9198 0.8626 0.9236 0.6657 0.9553 0.8497 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2023||405|SLC35E2B|protein_coding|CODING|NM_001110781.2|9|G),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4307513 -0.453602 0.64 2 405 1683 MODIFIER 9 CODING SLC35E2B C protein_coding NM_001110781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1595538 T C 0 32.6 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1683||405|SLC35E2B|protein_coding|CODING|NM_001110781.2|9|C),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|C) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs6700227 -0.379885 0 2 405 247 MODIFIER 9 CODING SLC35E2B T protein_coding NM_001110781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1596974 C T 0 119 0 0.9183 0.8742 0.9337 0.6984 0.9642 0.8609 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||247||405|SLC35E2B|protein_coding|CODING|NM_001110781.2|9|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4074020 -0.636426 0.125342 7 V312I 405 Gtc/Atc MODERATE 8 MISSENSE CODING SLC35E2B T protein_coding NM_001110781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1599812 C T 0 221 0 . 0 . 0 . 0 . 0 . 1 3240 45743 4369 2785 2713 25485 358 6793 2 6674 96420 8824 6710 5580 53666 730 14236 0.0654039 0 . 0 . 151 35,8,71,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V312I|405|SLC35E2B|protein_coding|CODING|NM_001110781.2|8|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 0 0.5 1 0 . 0 . 0 1 0 42 0 2.35683e-06 1.43956e-05 0 0.186282 rs12729295,rs76114385 -0.693147 0.966625 151 S286 405 agT/agC LOW 8 SILENT CODING SLC35E2B G protein_coding NM_001110781.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1599888 A G 0 221 0 . 0 . 0 . 0 . 0 . 1 6663 59476 5428 3737 3251 31942 438 8017 2 9064 116508 11086 8016 6498 65078 884 15882 0.361367 0 . 0 . 258 28,36,142,16 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S286|405|SLC35E2B|protein_coding|CODING|NM_001110781.2|8|G),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|G) 0 0.5 1 0 . 0 . 0 1 0 48 0 9.60969e-18 1.73484e-14 0 7.74633e-11 rs2072923,rs74500811 -0.693147 0.306758 258 S654 783 agT/agC LOW 18 SILENT CODING CDK11A G protein_coding NM_001313896.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1635022 A G 0 17.2 0 . 0 . 0 . 0 0.37812 0.122961 0.0157317 1 963 2122 150 115 31 582 10 271 2 2660 80458 6992 4698 4594 49876 632 11006 0.939786 0 . 0 . 75 25,33,9,2 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S654|783|CDK11A|protein_coding|CODING|NM_001313896.1|18|G),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|G) 1 0.5 1 0 . 0 . 1 1 0 56 0 0.00394083 0.807394 0 0.000871439 rs1136978 -0.676189 0.00860055 75 A572 783 gcG/gcA LOW 16 SILENT CODING CDK11A T protein_coding NM_001313896.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1635565 C T 0 222 0 0.5 0.246 0.1167 0.2183 0.0646 0.2096 0.42481 0.174422 0.0546269 1 4297 15879 1373 1942 682 3904 84 3597 2 9452 114504 11120 8352 6316 63570 822 14872 0.80278 0 . 0 COSM146371,COSM146372 132 24,39,22,34 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A572|783|CDK11A|protein_coding|CODING|NM_001313896.1|16|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.986036 0.980358 0 0.572111 rs11488591 -0.693147 0.0372654 132 Y506 783 taC/taT LOW 14 SILENT CODING CDK11A A protein_coding NM_001313896.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1636044 G A 0 124 0 0.9433 0.648 0.562 0.4643 0.5924 0.5562 0.879693 0.663348 0.564434 1 5942 56722 4510 2852 3187 31768 406 8057 2 6738 100496 9268 7144 5568 56640 750 14388 0.914442 0 . 0 COSM146375 129 44,44,21,8 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y506|783|CDK11A|protein_coding|CODING|NM_001313896.1|14|A),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 53 0 3.18756e-06 0.0224019 0 0.915659 rs1059822,rs61745144 -0.693079 0.277138 129 I485 783 atT/atC LOW 13 SILENT CODING CDK11A G protein_coding NM_001313896.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1636355 A G 0 10.8 0 . 0 . 0 . 0 . 0 . 1 1425 3228 172 294 40 775 10 512 2 8566 116362 11272 8216 6500 65724 874 15210 0.600493 0 . 0 . 144 75,25,0,31 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I485|783|CDK11A|protein_coding|CODING|NM_001313896.1|13|G),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|G) 0 0.5 1 0 . 0 . 0 1 0 54 0 2.26623e-06 0.0192889 0 0.00278226 rs2377226 -0.69311 0.0570886 144 D393N 783 Gac/Aac MODERATE 11 MISSENSE CODING CDK11A T protein_coding NM_001313896.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1638925 C T 0 222 0 0.4455 0.2278 0.1138 0.2083 0.0636 0.2035 0.380159 0.160299 0.0535024 1 3835 15223 1326 1873 687 3875 88 3539 2 9234 114744 11030 8330 6322 63126 836 15866 0.694795 0 . 0 COSM1335882,COSM1335881 153 63,17,36,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D393N|783|CDK11A|protein_coding|CODING|NM_001313896.1|11|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 43 0 0.144301 1.03749e-08 0 0.979965 rs200982240 -0.693147 0.0962145 153 G370R 783 Ggg/Agg MODERATE 11 MISSENSE CODING CDK11A T protein_coding NM_001313896.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1638994 C T 0 67 0 0.8797 0.3437 0.1398 0.1796 0.0716 0.2127 0.725719 0.259796 0.0478776 1 5688 15131 1192 1232 623 3265 84 3047 2 7418 92226 8710 7032 5046 49362 682 13976 0.0914639 0 . 0 . 191 66,49,0,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G370R|783|CDK11A|protein_coding|CODING|NM_001313896.1|11|T),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 41 0 0.996059 0.000416505 0 0.0140305 rs139262276 -0.693147 0.000543886 191 783 LOW 9 CODING CDK11A A protein_coding NM_001313896.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1639687 G A 0 96 0 . 0 . 0 . 0 0.315593 0.122991 0.0390115 1 1134 3689 159 441 150 941 23 841 2 3014 25750 1380 2310 1306 13330 216 4194 0.446113 0 . 0 . 28 6,12,2,8 SPLICE_SITE_REGION+INTRON(LOW||||783|CDK11A|protein_coding|CODING|NM_001313896.1|9|A),INTRON(MODIFIER||||793|CDK11B|protein_coding|CODING|NM_001787.2|6|A) 1 0.5 1 0 . 0 . 1 1 0 36 0 0.745088 0.00951227 0 0.986018 rs200014331 -0.670168 0.635404 28 R105 793 agA/agG LOW 4 SILENT CODING CDK11B C protein_coding NM_001787.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1650807 T C 0 222 0 0.4992 0.7474 0.879 0.7788 0.9215 0.7781 0 . 0 1 3815 57739 5645 4007 3279 32980 436 7577 2 9800 120700 11574 8620 6614 66718 900 16474 0.627418 0 . 0 . 110 22,24,23,36 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R105|793|CDK11B|protein_coding|CODING|NM_001787.2|4|C),SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R105|783|CDK11A|protein_coding|CODING|NM_001313896.1|4|C) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.982014 0.989443 0 0.98653 rs1137005 -0.693147 0.990183 110 R105 783 agA/agG LOW 4 SILENT CODING CDK11A C protein_coding NM_001313896.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1650807 T C 0 222 0 0.4992 0.7474 0.879 0.7788 0.9215 0.7781 0 . 0 1 3815 57739 5645 4007 3279 32980 436 7577 2 9800 120700 11574 8620 6614 66718 900 16474 0.627418 0 . 0 . 110 22,24,23,36 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R105|793|CDK11B|protein_coding|CODING|NM_001787.2|4|C),SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R105|783|CDK11A|protein_coding|CODING|NM_001313896.1|4|C) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.982014 0.989443 0 0.98653 rs1137005 -0.693147 0.990183 110 R93W 793 Cgg/Tgg MODERATE 4 MISSENSE CODING CDK11B A protein_coding NM_001787.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1650845 G A 0 222 0 0.4992 0.7474 0.879 0.7788 0.9215 0.7781 0.366227 0.449592 0.487974 1 3814 57709 5644 4010 3279 32976 436 7550 2 9796 120640 11572 8626 6614 66714 900 16418 0.841075 0 . 0 . 97 22,22,23,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R93W|793|CDK11B|protein_coding|CODING|NM_001787.2|4|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R93W|783|CDK11A|protein_coding|CODING|NM_001313896.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.987508 0.853218 0 0.62337 rs1059831 -0.693146 0.0661371 97 R93W 783 Cgg/Tgg MODERATE 4 MISSENSE CODING CDK11A A protein_coding NM_001313896.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1650845 G A 0 222 0 0.4992 0.7474 0.879 0.7788 0.9215 0.7781 0.366227 0.449592 0.487974 1 3814 57709 5644 4010 3279 32976 436 7550 2 9796 120640 11572 8626 6614 66714 900 16418 0.841075 0 . 0 . 97 22,22,23,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R93W|793|CDK11B|protein_coding|CODING|NM_001787.2|4|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R93W|783|CDK11A|protein_coding|CODING|NM_001313896.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.987508 0.853218 0 0.62337 rs1059831 -0.693146 0.0661371 97 793 LOW 3 CODING CDK11B T protein_coding NM_001787.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1653028 C T 0 222 0 0.4985 0.7474 0.879 0.7788 0.9225 0.7781 0.561422 0.81277 0.929788 1 5315 101589 9948 6526 5862 60912 785 12241 2 9704 118826 11358 8474 6566 65640 880 16204 0.490059 0 . 0 . 114 28,25,28,22 SPLICE_SITE_REGION+INTRON(LOW||||793|CDK11B|protein_coding|CODING|NM_001787.2|3|T),SPLICE_SITE_REGION+INTRON(LOW||||783|CDK11A|protein_coding|CODING|NM_001313896.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.289858 0.580571 0 0.999913 rs16825265 -0.693147 0.23953 114 783 LOW 3 CODING CDK11A T protein_coding NM_001313896.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1653028 C T 0 222 0 0.4985 0.7474 0.879 0.7788 0.9225 0.7781 0.561422 0.81277 0.929788 1 5315 101589 9948 6526 5862 60912 785 12241 2 9704 118826 11358 8474 6566 65640 880 16204 0.490059 0 . 0 . 114 28,25,28,22 SPLICE_SITE_REGION+INTRON(LOW||||793|CDK11B|protein_coding|CODING|NM_001787.2|3|T),SPLICE_SITE_REGION+INTRON(LOW||||783|CDK11A|protein_coding|CODING|NM_001313896.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.289858 0.580571 0 0.999913 rs16825265 -0.693147 0.23953 114 266 3259 MODIFIER 6 CODING SLC35E2 G protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1660635 T G 0 26.3 0 0.4864 0.7226 0.8444 0.7768 0.9135 0.7035 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||3259||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|G),UPSTREAM(MODIFIER||4776||793|CDK11B|protein_coding|CODING|NM_001787.2||G),UPSTREAM(MODIFIER||4631||783|CDK11A|protein_coding|CODING|NM_001313896.1||G) 0 . 0 . 0 1 0 . 0 . 40 0 0 . 0 . rs2377220 -0.453602 0.36 2 266 3168 MODIFIER 6 CODING SLC35E2 C protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1660726 T C 0 39.3 0 0.3865 0.4718 0.5908 0.4474 0.493 0.5061 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3168||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|C),UPSTREAM(MODIFIER||4867||793|CDK11B|protein_coding|CODING|NM_001787.2||C),UPSTREAM(MODIFIER||4722||783|CDK11A|protein_coding|CODING|NM_001313896.1||C) 0 . 0 . 0 1 0 . 0 . 55 0 0 . 0 . rs1061884 -0.453602 0.84 2 266 3159 MODIFIER 6 CODING SLC35E2 C protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1660735 T C 0 39.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3159||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|C),UPSTREAM(MODIFIER||4876||793|CDK11B|protein_coding|CODING|NM_001787.2||C),UPSTREAM(MODIFIER||4731||783|CDK11A|protein_coding|CODING|NM_001313896.1||C) 0 . 0 . 0 . 0 . 0 . 55 0 0 . 0 . rs1061883 -0.453602 0.84 2 266 1466 MODIFIER 6 CODING SLC35E2 G protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1662428 A G 0 9.7 0 0.4349 0.6997 0.8386 0.7649 0.9076 0.6779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1466||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2281171 -0.379885 0 1 266 43 MODIFIER 6 CODING SLC35E2 C protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1663851 G C 0 222 0 0.0492 0.3011 0.5115 0.3403 0.4235 0.3262 0.0986752 0.305044 0.410739 1 529 23898 2781 1577 1020 14240 191 3560 2 5078 59102 4700 3992 2190 32082 444 10616 0.995078 0 . 0 . 132 54,14,36,15 UTR_3_PRIME(MODIFIER||43||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.933661 rs2294486 -0.693147 0.00138704 132 266 33 MODIFIER 6 CODING SLC35E2 A protein_coding NM_182838.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1663861 G A 0 222 0 0.0492 0.3011 0.513 0.3403 0.4235 0.3252 0.100137 0.306011 0.411449 1 648 30286 4012 1998 1352 18064 231 3981 2 5454 70216 6518 4824 2764 38738 516 11402 0.900658 0 . 0 . 135 54,11,39,17 UTR_3_PRIME(MODIFIER||33||266|SLC35E2|protein_coding|CODING|NM_182838.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978082 rs2294487 -0.693147 0.0636308 135 R229H 266 cGt/cAt MODERATE 5 MISSENSE CODING SLC35E2 T protein_coding NM_182838.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1666175 C T 0 39.8 0 . 0 . 0 . 0 . 0 . 1 1805 29518 3083 1661 1669 16658 251 4391 2 7372 72914 6748 5096 4042 37778 580 11298 0.171098 0 . 0 . 278 136,64,44,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R229H|266|SLC35E2|protein_coding|CODING|NM_182838.2|5|T) 0 0.5 1 0 . 0 . 0 1 0 40 0 0.000387574 3.06428e-08 0 0.00447112 rs61777509 -0.693147 0.769624 278 R204W 266 Cgg/Tgg MODERATE 5 MISSENSE CODING SLC35E2 A protein_coding NM_182838.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1666251 G A 0 65 0 . 0 . 0 . 0 . 0 . 1 370 33088 3755 1794 2281 20791 262 3835 2 9978 107380 10200 7596 5894 58124 802 14786 0.00516306 0 . 0 . 407 138,118,73,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R204W|266|SLC35E2|protein_coding|CODING|NM_182838.2|5|A) 0 0.5 1 0 . 0 . 0 1 0 45 0 0.00918106 6.69577e-14 0 2.80942e-05 rs77655487 -0.693147 0.871135 407 L13 266 ctG/ctC LOW 2 SILENT CODING SLC35E2 G protein_coding NM_182838.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1670958 C G 0 102 0 . 0 . 0 . 0 . 0 . 2 39 201 6 6 0 117 0 33 2 74 280 8 8 0 144 0 46 0 . 0 . 0 8 0,0,8,0 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L13|266|SLC35E2|protein_coding|CODING|NM_182838.2|2|G) 0 . 0 . 0 . 0 . 1 0 30 0 0 . 0 . rs146637450 -0.651104 0.169891 8 591 923 MODIFIER 14 CODING NADK T protein_coding NM_001198994.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1683420 A T 0 99 0 0.0439 0.3037 0.5259 0.3423 0.4125 0.3456 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 56 26,15,14,1 UTR_3_PRIME(MODIFIER||923||591|NADK|protein_coding|CODING|NM_001198994.1|14|T) 0 0.5 1 0 . 1 0 . 0 . 50 0 0.165589 2.26581e-07 0 0.209922 rs8841 -0.688148 0.0948853 56 591 443 MODIFIER 14 CODING NADK A protein_coding NM_001198994.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1683900 G A 0 105 0 0.0469 0.3257 0.5591 0.3423 0.4861 0.3548 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.683497 0 . 0 . 12 2,3,1,5 UTR_3_PRIME(MODIFIER||443||591|NADK|protein_coding|CODING|NM_001198994.1|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.564628 rs1062090 -0.616816 0.0901918 12 591 174 MODIFIER 14 CODING NADK G protein_coding NM_001198994.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1684169 C G 0 222 0 0.0469 0.3263 0.5591 0.3452 0.4861 0.3548 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.421822 0 . 0 . 92 35,11,30,4 UTR_3_PRIME(MODIFIER||174||591|NADK|protein_coding|CODING|NM_001198994.1|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.954092 rs7796 -0.693132 0.0288803 92 P549 591 ccG/ccA LOW 14 SILENT CODING NADK T protein_coding NM_001198994.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1684472 C T 0 222 0 0.0552 0.3397 0.5634 0.3452 0.505 0.3896 0.124829 0.381194 0.512328 1 1085 49138 5953 2795 2583 30580 376 5766 2 8274 105676 9766 7548 4780 59920 774 14614 0.99369 0 . 0 . 115 33,22,25,21 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P549|591|NADK|protein_coding|CODING|NM_001198994.1|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953006 rs386609880,rs7407 -0.693147 0.307721 115 R394W 591 Cgg/Tgg MODERATE 10 MISSENSE CODING NADK A protein_coding NM_001198994.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1686081 G A 0 222 0 0.0015 0.0224 0.036 0.002 0.0288 0.0552 0.00363141 0.0220667 0.0315116 1 40 3082 175 24 64 1934 34 811 2 10402 121260 11576 8654 6614 66658 906 16450 0.772604 0 . 0 . 88 20,23,13,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R394W|591|NADK|protein_coding|CODING|NM_001198994.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.409561 rs75816936 -0.693136 0.224352 88 591 LOW 2 CODING NADK G protein_coding NM_001198994.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1696659 A G 0 228 0 0.4955 0.7412 0.8703 0.8304 0.9314 0.6943 0.596232 0.827157 0.945465 2 5890 104160 10296 6957 6040 62573 805 11599 2 10220 120810 11566 8638 6614 66418 904 16450 0 . 0 . 0 172 0,0,107,49 SPLICE_SITE_REGION+INTRON(LOW||||591|NADK|protein_coding|CODING|NM_001198994.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5021859 -0.693147 0.000881744 172 181 138 MODIFIER 1 CODING CALML6 G protein_coding NM_138705.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1846582 A G 0 228 0 0.9516 0.8439 0.8401 0.8145 0.7903 0.7863 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,33,3 UTR_5_PRIME(MODIFIER||138||181|CALML6|protein_coding|CODING|NM_138705.2|1|G),DOWNSTREAM(MODIFIER||2447||209|TMEM52|protein_coding|CODING|NM_178545.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2748987,rs386573252 -0.693139 0.51996 37 M141T 209 aTg/aCg MODERATE 5 MISSENSE CODING TMEM52 G protein_coding NM_178545.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1849529 A G 0 222 0 0.053 0.352 0.5072 0.4623 0.4901 0.3906 0.120744 0.370598 0.498605 1 1099 53478 6502 3966 3128 32223 414 6146 2 10340 120622 11548 8622 6600 66112 894 16506 0.957987 0 . 0 COSM146377 108 35,15,35,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M141T|209|TMEM52|protein_coding|CODING|NM_178545.3|5|G),DOWNSTREAM(MODIFIER||796||181|CALML6|protein_coding|CODING|NM_138705.2||G),DOWNSTREAM(MODIFIER||3861||1639|CFAP74|protein_coding|CODING|NM_001304360.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997129 rs28640257 -0.693147 0.53353 108 S1579 1639 tcT/tcC LOW 38 SILENT CODING CFAP74 G protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1854109 A G 0 222 0 0.562 0.5988 0.6196 0.6359 0.5368 0.6595 0.520881 0.531908 0.537558 1 5368 68142 7693 5560 3626 34834 497 10564 2 10264 120038 11538 8612 6602 65630 892 16500 0.813241 0 . 0 COSM146378 119 43,17,34,14 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1579|1639|CFAP74|protein_coding|CODING|NM_001304360.1|38|G),UPSTREAM(MODIFIER||3369||209|TMEM52|protein_coding|CODING|NM_178545.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.798512 rs2803348 -0.693147 0.924618 119 V1148I 1639 Gtt/Att MODERATE 28 MISSENSE CODING CFAP74 T protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1859131 C T 0 222 0 0.1891 0.1845 0.1931 0.1746 0.2366 0.1288 0 . 0 1 217 3339 57 76 345 1362 39 1243 2 904 15752 290 486 1026 5204 178 7664 0.80109 0 . 0 . 278 66,46,80,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1148I|1639|CFAP74|protein_coding|CODING|NM_001304360.1|28|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0586728 rs4648734 -0.693147 0.00149315 278 G1069R 1639 Ggg/Agg MODERATE 26 MISSENSE CODING CFAP74 T protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1861582 C T 0 222 0 0.0575 0.3558 0.5029 0.4752 0.4911 0.3926 0 . 0 1 79 4671 79 102 5 1556 63 2787 2 568 12368 188 204 8 3648 132 7620 0.879734 0 . 0 . 239 80,31,76,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G1069R|1639|CFAP74|protein_coding|CODING|NM_001304360.1|26|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.714677 rs2803295 -0.693147 0.710845 239 Y856 1639 taT/taC LOW 22 SILENT CODING CFAP74 G protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1873514 A G 0 222 0 0.5477 0.5925 0.611 0.6379 0.5308 0.6564 0 . 0 1 285 6951 107 142 6 1703 76 4632 2 576 12110 188 198 10 3572 130 7436 0.976587 0 . 0 . 205 41,68,28,48 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y856|1639|CFAP74|protein_coding|CODING|NM_001304360.1|22|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.992319 rs2803326 -0.693147 0.0645225 205 K853E 1639 Aag/Gag MODERATE 22 MISSENSE CODING CFAP74 C protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1873525 T C 0 222 0 0.5477 0.5925 0.611 0.6379 0.5308 0.6564 0 . 0 1 283 6943 107 142 3 1701 76 4631 2 576 12110 188 198 6 3572 130 7440 0.969801 0 . 0 . 180 31,65,26,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K853E|1639|CFAP74|protein_coding|CODING|NM_001304360.1|22|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.999779 rs2803327 -0.693147 0.00360807 180 V800L 1639 Gtg/Ctg MODERATE 21 MISSENSE CODING CFAP74 G protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1875858 C G 0 222 0 0.1445 0.385 0.5144 0.4792 0.495 0.408 0 . 0 1 119 4801 77 99 1 1565 63 2877 2 578 12330 184 200 2 3620 128 7618 0.36729 0 . 0 . 94 7,35,16,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V800L|1639|CFAP74|protein_coding|CODING|NM_001304360.1|21|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.981338 0.994357 0 0.819567 rs2803336 -0.693147 0.206665 94 D799 1639 gaT/gaC LOW 21 SILENT CODING CFAP74 G protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1875859 A G 0 222 0 0.1899 0.3978 0.5187 0.4792 0.496 0.408 0 . 0 1 141 4819 78 99 1 1560 63 2877 2 580 12326 184 200 2 3614 128 7618 0.878602 0 . 0 . 95 7,36,16,32 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D799|1639|CFAP74|protein_coding|CODING|NM_001304360.1|21|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.981964 0.9945 0 0.911979 rs2803337 -0.693147 0.206665 95 A687 1639 gcC/gcT LOW 18 SILENT CODING CFAP74 A protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1887245 G A 0 222 0 0.1044 0.1813 0.219 0.2292 0.2316 0.1575 0.125546 0.206831 0.246613 1 1329 27296 2666 1794 1483 16838 196 2990 2 9774 120400 11522 8592 6570 66552 898 16492 0.956046 0 . 0 COSM1626697 91 33,16,8,21 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A687|1639|CFAP74|protein_coding|CODING|NM_001304360.1|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.46913 rs28575980 -0.693079 0.0160999 91 G628C 1639 Ggc/Tgc MODERATE 17 MISSENSE CODING CFAP74 A protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1888193 C A 0 222 0 0.1067 0.1869 0.232 0.2282 0.2455 0.1605 0.130958 0.21876 0.263331 1 1315 27394 2643 1736 1461 17052 202 2985 2 8986 112714 10782 8132 5912 62518 838 15546 0.70295 0 . 0 . 65 10,23,18,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G628C|1639|CFAP74|protein_coding|CODING|NM_001304360.1|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.166309 rs3820011,rs386587188 -0.69311 0.428789 65 L488 1639 Ctg/Ttg LOW 13 SILENT CODING CFAP74 A protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1896440 G A 0 222 0 0.2489 0.2167 0.2032 0.2718 0.2276 0.1145 0.231803 0.240619 0.244927 1 2485 27795 2556 2213 1619 16457 185 2280 2 9584 118106 11266 8502 6176 65320 852 16406 0.654036 0 . 0 . 77 20,16,16,16 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L488|1639|CFAP74|protein_coding|CODING|NM_001304360.1|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.185062 rs16824585 -0.69312 0.28563 77 I363V 1639 Atc/Gtc MODERATE 11 MISSENSE CODING CFAP74 C protein_coding NM_001304360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1900232 T C 0 222 0 0.4312 0.3878 0.438 0.3125 0.4314 0.3262 0.410433 0.435143 0.447173 1 4223 51014 5258 2751 2573 29926 373 5910 2 9798 120718 11568 8610 6608 66726 898 16510 0.0583115 0 . 0 . 109 8,52,7,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I363V|1639|CFAP74|protein_coding|CODING|NM_001304360.1|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622884 rs16824588,rs386540761 -0.693146 0.0174794 109 L145 1639 ctG/ctA LOW 6 SILENT CODING CFAP74 T protein_coding NM_001304360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1916890 C T 0 228 0 0.6573 0.4385 0.2795 0.4335 0.3082 0.3947 0.57928 0.410408 0.327524 2 6109 45007 3253 3781 2593 22472 310 6489 2 9792 120556 11558 8602 6612 66586 896 16510 0 . 0 . 0 79 0,0,59,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L145|1639|CFAP74|protein_coding|CODING|NM_001304360.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3795280 -0.693147 0.282613 79 S272 452 agC/agT LOW 7 SILENT CODING GABRD T protein_coding NM_000815.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1960674 C T 0 228 0 0.0121 0.1983 0.2089 0.4415 0.1143 0.2781 0.0321918 0.0977572 0.131345 2 190 10191 875 1643 292 4499 81 2611 2 3308 35468 1912 2818 742 17322 296 9070 0.781022 0 . 0 . 152 0,2,28,109 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S272|452|GABRD|protein_coding|CODING|NM_000815.4|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.131387 rs28408173 -0.693147 0.022256 152 A368 452 gcC/gcT LOW 9 SILENT CODING GABRD T protein_coding NM_000815.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1961466 C T 0 222 0 0.0008 0.0391 0.0187 0.119 0.0249 0.0378 0.00614195 0.0203515 0.0276353 1 67 4636 291 1060 447 2149 49 573 2 10076 118634 11520 8590 6614 64712 882 16240 0.958275 0 . 0 . 116 23,22,28,31 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A368|452|GABRD|protein_coding|CODING|NM_000815.4|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.606204 rs28398772 -0.693147 0.00576556 116 D88 592 gaT/gaC LOW 3 SILENT CODING PRKCZ C protein_coding NM_002744.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1987993 T C 0 228 0 0.8873 0.6699 0.402 0.9454 0.3429 0.6186 0.81911 0.50469 0.343605 2 8620 55844 5222 8223 2179 22068 372 9160 2 10378 120804 11536 8644 6512 66344 906 16484 0 . 0 . 0 79 0,0,15,59 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D88|592|PRKCZ|protein_coding|CODING|NM_002744.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12184 -0.693147 0.260041 79 P106 592 ccA/ccG LOW 4 SILENT CODING PRKCZ G protein_coding NM_002744.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 1991014 A G 0 228 0 0.0719 0.2376 0.2032 0.4752 0.1928 0.2873 0.0916931 0.153083 0.184535 2 921 25145 2401 4109 1297 12151 174 4092 2 10372 120924 11550 8610 6580 66406 900 16506 0.920863 0 . 0 COSM146379,COSM146380 148 2,0,73,66 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P106|592|PRKCZ|protein_coding|CODING|NM_002744.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.5 rs1878745 -0.693147 0.0237848 148 A358 592 gcC/gcG LOW 12 SILENT CODING PRKCZ G protein_coding NM_002744.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2103506 C G 0 222 0 0 0.016174 0.0014 0.0744 0 0.0051 0.00136178 0.000691988 0.000348837 1 11 895 6 737 23 44 8 66 2 10112 113820 11456 8572 6432 64040 812 12396 0.365852 0 . 0 . 107 29,24,25,16 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A358|592|PRKCZ|protein_coding|CODING|NM_002744.4|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.781918 rs2280272 -0.693145 0.00821729 107 283 30 MODIFIER 8 CODING FAAP20 T protein_coding NM_001282670.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2121118 C T 0 185 0 0.5787 0.7021 0.6455 0.8641 0.6083 0.8384 0.580645 0.598107 0.607051 1 5862 77591 7577 7248 3871 38997 563 13473 2 9746 115314 11104 8442 5964 62868 846 16344 0.448872 0 . 0 . 61 23,3,28,3 UTR_3_PRIME(MODIFIER||30||283|FAAP20|protein_coding|CODING|NM_001282670.1|8|T),DOWNSTREAM(MODIFIER||4284||592|PRKCZ|protein_coding|CODING|NM_002744.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.887457 rs2503701 -0.69311 0.00466774 61 G56R 283 Ggt/Cgt MODERATE 4 MISSENSE CODING FAAP20 G protein_coding NM_001282670.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2130262 C G 0 222 0 0 0.016773 0.0014 0.0754 0 0.0072 0 . 0 1 1 57 0 22 0 3 5 26 2 568 12252 186 198 12 3590 132 7566 0.991282 0 . 0 . 99 16,31,23,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Cgt|G56R|283|FAAP20|protein_coding|CODING|NM_001282670.1|4|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.115071 rs144802031 -0.693147 0.481603 99 283 13680 MODIFIER 1 CODING FAAP20 G protein_coding NM_001282670.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2144107 A G 0 9.7 0 0.9531 0.9267 0.928 0.9772 0.8231 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||13680||283|FAAP20|protein_coding|CODING|NM_001282670.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2503715 -0.379885 0 1 728 2302 MODIFIER 7 CODING SKI T protein_coding NM_003036.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2240506 C T 0 32.6 0 0 0.017971 0 0.0883 0 0.001 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2302||728|SKI|protein_coding|CODING|NM_003036.3|7|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs117433242 -0.379885 0 2 497 63 MODIFIER 14 CODING MORN1 G protein_coding NM_024848.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2252759 A G 0 103 0 0.6604 0.4836 0.3415 0.4246 0.3151 0.5798 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.904729 0 . 0 . 12 4,1,4,1 UTR_3_PRIME(MODIFIER||63||497|MORN1|protein_coding|CODING|NM_024848.2|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.857112 rs35513983 -0.590765 0.391905 12 L448P 497 cTg/cCg MODERATE 14 MISSENSE CODING MORN1 G protein_coding NM_024848.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2252973 A G 0 204 0 0 0.0027955 0 0.0139 0 0 0 . 0 1 0 25 0 20 0 1 1 3 2 2560 15600 446 1152 106 7658 140 3538 0.79189 0 . 0 . 19 4,3,6,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L448P|497|MORN1|protein_coding|CODING|NM_024848.2|14|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.989343 rs201836187 -0.670168 0.366223 19 196 1113 MODIFIER 7 CODING RER1 G protein_coding NM_007033.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2335676 A G 0 32.6 0 0.6059 0.7764 0.8156 0.8304 0.8926 0.8037 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1113||196|RER1|protein_coding|CODING|NM_007033.4|7|G),DOWNSTREAM(MODIFIER||565||346|PEX10|protein_coding|CODING|NM_153818.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1129333 -0.379885 0 2 196 1647 MODIFIER 7 CODING RER1 T protein_coding NM_007033.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2336210 C T 0 156 0 0.093 0.243 0.2392 0.4087 0.2823 0.2372 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.983048 0 . 0 . 50 20,3,26,1 UTR_3_PRIME(MODIFIER||1647||196|RER1|protein_coding|CODING|NM_007033.4|7|T),DOWNSTREAM(MODIFIER||31||346|PEX10|protein_coding|CODING|NM_153818.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.663894 rs1129332 -0.693021 0.820762 50 346 173 MODIFIER 6 CODING PEX10 T protein_coding NM_153818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2337032 C T 0 148 0 0.1815 0.3065 0.268 0.4544 0.3062 0.3507 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.731096 0 . 0 . 33 16,0,16,0 UTR_3_PRIME(MODIFIER||173||346|PEX10|protein_coding|CODING|NM_153818.1|6|T),DOWNSTREAM(MODIFIER||147||196|RER1|protein_coding|CODING|NM_007033.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.268955 rs1129171 -0.689466 0.5843 33 T97 346 acA/acG LOW 3 SILENT CODING PEX10 C protein_coding NM_153818.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2340200 T C 0 228 0 0.5688 0.6989 0.7666 0.7282 0.7913 0.7014 0.600999 0.743811 0.816977 2 6186 93011 8868 6245 5289 53763 682 11978 2 10296 120572 11518 8596 6514 66246 898 16504 1 3 likely-benign 0 . 110 1,0,79,22 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T97|346|PEX10|protein_coding|CODING|NM_153818.1|3|C),DOWNSTREAM(MODIFIER||3315||196|RER1|protein_coding|CODING|NM_007033.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2494598 -0.693147 0.000239046 110 I843 1416 atC/atT LOW 19 SILENT CODING PLCH2 T protein_coding NM_014638.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2430617 C T 0 222 0 0.1725 0.3666 0.4481 0.4812 0.4821 0.3344 0.215207 0.386639 0.473678 1 2067 51403 5319 4451 2616 30641 398 5911 2 9362 118104 11334 8526 6438 65342 876 16226 0.68614 0 . 0 . 131 49,15,49,7 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I843|1416|PLCH2|protein_coding|CODING|NM_014638.3|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.805589 rs2296442 -0.693147 0.0228378 131 Q692R 781 cAg/cGg MODERATE 18 MISSENSE CODING PANK4 C protein_coding NM_018216.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2441358 T C 0 222 0 0.7148 0.4619 0.3444 0.4702 0.2127 0.4509 0.656961 0.36988 0.222998 1 6548 36640 4121 3604 1384 14415 238 6330 2 9776 111242 10500 8098 5104 61368 796 15600 0.401834 0 . 0 COSM330287 133 42,28,29,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q692R|781|PANK4|protein_coding|CODING|NM_018216.2|18|C),DOWNSTREAM(MODIFIER||4389||1416|PLCH2|protein_coding|CODING|NM_014638.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.522766 rs2494620,rs386495647 -0.693147 0.439917 133 A555V 781 gCg/gTg MODERATE 13 MISSENSE CODING PANK4 A protein_coding NM_018216.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2444414 G A 0 222 0 0.0136 0.2256 0.2983 0.3046 0.3867 0.2137 0.0717204 0.272112 0.374826 1 677 37636 2600 3157 2326 24537 307 4032 2 10208 119832 11522 8548 6604 65646 888 16416 0.850665 0 . 0 . 218 27,81,26,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A555V|781|PANK4|protein_coding|CODING|NM_018216.2|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.683383 rs7535528 -0.693147 0.430261 218 K139 781 aaA/aaG LOW 3 SILENT CODING PANK4 C protein_coding NM_018216.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2452569 T C 0 228 0 0.91 0.846 0.8084 0.9563 0.7316 0.7904 0.898774 0.795248 0.742209 2 9357 94546 9897 8326 4526 49109 692 12639 2 10374 121126 11568 8650 6612 66508 904 16510 0 . 0 . 0 86 0,0,45,32 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K139|781|PANK4|protein_coding|CODING|NM_018216.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2985862 -0.693147 0.0699037 86 A117T 283 Gcc/Acc MODERATE 4 MISSENSE CODING TNFRSF14 A protein_coding NM_003820.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2491306 G A 0 222 0 0.0356 0.0212 0.0072 0.0337 0.004 0.0164 0.0339253 0.0157238 0.00640876 1 302 1146 32 284 6 310 6 206 2 6360 72132 6154 5556 1996 39930 528 11608 0.264639 1 not-provided 0 . 235 68,44,59,34 PROTEIN_INTERACTION_LOCUS(HIGH||||283|TNFRSF14|protein_coding|CODING||4|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A117T|283|TNFRSF14|protein_coding|CODING|NM_003820.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979999 rs2234163 -0.693147 0.192724 235 283 73 MODIFIER 8 CODING TNFRSF14 A protein_coding NM_003820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2494785 G A 0 222 0 0.7776 0.632 0.5591 0.5734 0.493 0.6902 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.873786 0 . 0 . 61 7,13,16,18 UTR_3_PRIME(MODIFIER||73||283|TNFRSF14|protein_coding|CODING|NM_003820.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.674969 rs8725 -0.693132 0.00808972 61 283 1502 MODIFIER 8 CODING TNFRSF14 T protein_coding NM_003820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2496214 C T 0 105 0 0.6536 0.5976 0.5476 0.5734 0.493 0.6902 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.832887 0 . 0 . 20 8,2,10,0 UTR_3_PRIME(MODIFIER||1502||283|TNFRSF14|protein_coding|CODING|NM_003820.3|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.617018 rs10910090,rs111221470 -0.670168 0.560195 20 283 1870 MODIFIER 8 CODING TNFRSF14 C protein_coding NM_003820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2496582 G C 0 228 0 0.9985 0.9938 0.9899 1 0.9821 0.9959 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,10,23 UTR_3_PRIME(MODIFIER||1870||283|TNFRSF14|protein_coding|CODING|NM_003820.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111221467,rs2843396 -0.693127 0.170068 35 283 1937 MODIFIER 8 CODING TNFRSF14 G protein_coding NM_003820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2496649 C G 0 184 0 0.6868 0.5968 0.5259 0.5685 0.4692 0.6861 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.780412 0 . 0 . 21 3,7,4,7 UTR_3_PRIME(MODIFIER||1937||283|TNFRSF14|protein_coding|CODING|NM_003820.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.636444 rs111221468,rs7544646 -0.676189 0.0508437 21 283 1941 MODIFIER 8 CODING TNFRSF14 G protein_coding NM_003820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2496653 A G 0 190 0 0.9024 0.6667 0.572 0.5734 0.492 0.6912 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.990132 0 . 0 . 21 3,7,4,7 UTR_3_PRIME(MODIFIER||1941||283|TNFRSF14|protein_coding|CODING|NM_003820.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.636444 rs111221935,rs7515633 -0.676189 0.0508437 21 246 1526 MODIFIER 7 CODING FAM213B A protein_coding NM_001195736.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2522392 G A 0 214 0 0.0144 0.1963 0.2277 0.2927 0.325 0.1881 0.0626434 0.240744 0.331501 1 289 12595 550 1367 429 8816 81 1063 2 3528 34242 1660 3166 996 21006 234 3652 0.996895 0 . 0 . 72 31,4,33,4 UTR_3_PRIME(MODIFIER||1526||246|FAM213B|protein_coding|CODING|NM_001195736.1|7|A),UTR_3_PRIME(MODIFIER||37||779|MMEL1|protein_coding|CODING|NM_033467.3|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.295978 rs2296443 -0.693141 0.461182 72 779 37 MODIFIER 24 CODING MMEL1 A protein_coding NM_033467.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2522392 G A 0 214 0 0.0144 0.1963 0.2277 0.2927 0.325 0.1881 0.0626434 0.240744 0.331501 1 289 12595 550 1367 429 8816 81 1063 2 3528 34242 1660 3166 996 21006 234 3652 0.996895 0 . 0 . 72 31,4,33,4 UTR_3_PRIME(MODIFIER||1526||246|FAM213B|protein_coding|CODING|NM_001195736.1|7|A),UTR_3_PRIME(MODIFIER||37||779|MMEL1|protein_coding|CODING|NM_033467.3|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.295978 rs2296443 -0.693141 0.461182 72 M518T 779 aTg/aCg MODERATE 16 MISSENSE CODING MMEL1 G protein_coding NM_033467.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2526746 A G 0 222 0 0.7284 0.5413 0.487 0.5407 0.332 0.5429 0.681344 0.453175 0.336279 1 7057 49969 5233 4295 2472 22136 375 8401 2 10354 120636 11538 8600 6566 66180 894 16504 0.606499 0 . 0 . 77 18,15,21,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M518T|779|MMEL1|protein_coding|CODING|NM_033467.3|16|G),DOWNSTREAM(MODIFIER||3838||246|FAM213B|protein_coding|CODING|NM_001195736.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998893 rs3748816 -0.693141 0.123968 77 779 LOW 13 CODING MMEL1 C protein_coding NM_033467.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2528133 T C 0 222 0 0.3835 0.5016 0.5519 0.4722 0.6889 0.4632 0.425783 0.59388 0.68 1 4283 72692 6591 4357 4208 44612 523 8118 2 9944 118738 11424 8484 6556 65056 878 16396 0.992337 0 . 0 . 37 7,6,4,17 SPLICE_SITE_REGION+INTRON(LOW||||779|MMEL1|protein_coding|CODING|NM_033467.3|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990003 rs2843401 -0.692352 0.330638 37 V308 779 gtG/gtT LOW 10 SILENT CODING MMEL1 A protein_coding NM_033467.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2535613 C A 0 222 0 0.6112 0.496 0.4481 0.5288 0.3121 0.5297 0.571493 0.403645 0.317632 1 5747 46110 4872 4173 2359 20438 359 8162 2 10014 118000 11486 8522 6568 64202 880 16328 0.885667 0 . 0 . 49 16,3,17,6 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtT|V308|779|MMEL1|protein_coding|CODING|NM_033467.3|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992049 rs4648562 -0.692717 0.165404 49 A98 779 gcT/gcC LOW 5 SILENT CODING MMEL1 G protein_coding NM_033467.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2541269 A G 0 222 0 0.7027 0.5315 0.4885 0.5357 0.33 0.5337 0.655243 0.441258 0.331628 1 6797 48187 5197 4269 2473 21688 366 7397 2 10330 117126 11524 8602 6594 65132 874 14070 0.639801 0 . 0 . 91 7,45,5,29 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A98|779|MMEL1|protein_coding|CODING|NM_033467.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890598 rs10797440 -0.693132 0.0594903 91 A14 779 gcC/gcT LOW 2 SILENT CODING MMEL1 A protein_coding NM_033467.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2560882 G A 0 145 0 0.2693 0.4615 0.5101 0.4633 0.672 0.4683 0.368813 0.590494 0.706135 1 639 10000 169 235 242 4521 92 4102 2 1784 17134 286 470 316 6492 172 7614 0.962269 0 . 0 . 26 8,7,4,6 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A14|779|MMEL1|protein_coding|CODING|NM_033467.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.624282 rs4648658 -0.670168 0.324775 26 P7 779 ccA/ccC LOW 2 SILENT CODING MMEL1 G protein_coding NM_033467.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2560903 T G 0 184 0 0.4334 0.5158 0.5519 0.4683 0.6909 0.4703 0.49757 0.640413 0.715461 1 880 9623 176 228 168 4253 77 3841 2 1736 15804 290 456 216 6014 144 6948 0.896649 0 . 0 . 27 8,7,5,6 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P7|779|MMEL1|protein_coding|CODING|NM_033467.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.583494 rs4648659 -0.676189 0.355721 27 L437 566 Ttg/Ctg LOW 7 SILENT CODING TTC34 G protein_coding NM_001242672.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2573199 A G 0 228 0 0.9818 0.9347 0.8847 0.9931 0.8628 0.9202 0 . 0 2 419 10922 144 174 214 2943 118 6910 2 432 12058 154 174 254 3358 136 7550 0 . 0 . 0 32 0,0,7,23 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L437|566|TTC34|protein_coding|CODING|NM_001242672.1|7|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4648662 -0.693097 0.0951295 32 G244E 566 gGg/gAg MODERATE 5 MISSENSE CODING TTC34 T protein_coding NM_001242672.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2576959 C T 0 221 0 0.034 0.0282 0.0072 0.0754 0 0.0153 0 . 0 1 15 170 3 19 0 15 3 115 2 442 10030 150 182 34 2822 112 6288 0.999914 0 . 0 . 45 4,14,2,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G244E|566|TTC34|protein_coding|CODING|NM_001242672.1|5|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.999655 rs28547181 -0.692717 0.0045458 45 H5 377 caC/caT LOW 1 SILENT CODING ACTRT2 T protein_coding NM_080431.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2938265 C T 0 222 0 0.1324 0.2017 0.2406 0.3978 0.161 0.1074 0.141625 0.166154 0.178721 1 1508 23079 3703 3638 904 11545 159 1622 2 9990 118886 11558 8616 6612 65852 890 15368 0.741265 0 . 0 . 59 13,16,13,10 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H5|377|ACTRT2|protein_coding|CODING|NM_080431.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.68734 rs4576609 -0.692717 0.276277 59 S149 377 tcT/tcG LOW 1 SILENT CODING ACTRT2 G protein_coding NM_080431.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2938697 T G 0 222 0 0.1657 0.2091 0.2435 0.3958 0.163 0.0982 0.167045 0.17515 0.179302 1 1840 23194 3707 3583 901 11507 160 1496 2 10350 120620 11554 8592 6604 66114 896 16510 0.945188 0 . 0 . 78 30,12,21,15 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S149|377|ACTRT2|protein_coding|CODING|NM_080431.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99594 rs3795262 -0.693139 0.250808 78 377 25 MODIFIER 1 CODING ACTRT2 T protein_coding NM_080431.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 2939409 G T 0 222 0 0.0862 0.0781 0.0159 0.2034 0.001 0.0613 0.0548165 0.0222807 0.00572029 1 657 3468 67 1651 15 315 22 741 2 9734 114074 11528 8590 6614 64738 834 12036 0.324571 0 . 0 . 173 37,51,21,43 UTR_3_PRIME(MODIFIER||25||377|ACTRT2|protein_coding|CODING|NM_080431.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.666245 rs12564513 -0.693147 0.034315 173 S148 1276 tcC/tcT LOW 4 SILENT CODING PRDM16 T protein_coding NM_022114.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3301721 C T 0 222 0 0.0386 0.3405 0.3285 0.622 0.2684 0.5409 0.0816659 0.204889 0.266846 1 782 39547 4788 5131 2047 17892 283 8624 2 9748 120022 11552 8600 6614 66110 896 16502 0.784623 0 . 0 . 93 30,5,39,11 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S148|1276|PRDM16|protein_coding|CODING|NM_022114.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.692522 rs2282198 -0.693147 0.482234 93 S533P 1276 Tcg/Ccg MODERATE 9 MISSENSE CODING PRDM16 C protein_coding NM_022114.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3328358 T C 0 228 0 0.9924 0.9451 0.9006 0.998 0.8419 0.9642 0.967319 0.877738 0.835593 2 9377 106618 10644 8502 6000 55694 795 15606 2 9646 119838 11516 8504 6594 66268 896 16414 0 . 0 . 0 173 0,0,104,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcg/Ccg|S533P|1276|PRDM16|protein_coding|CODING|NM_022114.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs870124 -0.693147 0.0565631 173 1276 50 MODIFIER 17 CODING PRDM16 G protein_coding NM_022114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3350425 A G 0 222 0 0.2663 0.1454 0.1398 0.1964 0.008 0.0746 0.213993 0.077114 0.0118524 1 2107 7097 1485 1584 26 756 28 1111 2 8726 112606 11110 7914 6428 61740 850 15838 0.996206 0 . 0 . 80 3,31,6,37 UTR_3_PRIME(MODIFIER||50||1276|PRDM16|protein_coding|CODING|NM_022114.3|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945942 rs2493270 -0.693146 0.130621 80 1276 1972 MODIFIER 17 CODING PRDM16 C protein_coding NM_022114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3352347 T C 0 46.3 0 0.9947 0.8824 0.7133 0.8075 0.9423 0.8661 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 1,1,2,0 UTR_3_PRIME(MODIFIER||1972||1276|PRDM16|protein_coding|CODING|NM_022114.3|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1537405 -0.453602 0.06 5 1276 2166 MODIFIER 17 CODING PRDM16 C protein_coding NM_022114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3352541 T C 0 18.2 0 0.6687 0.744 0.6153 0.7659 0.8419 0.8139 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||2166||1276|PRDM16|protein_coding|CODING|NM_022114.3|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1065247 -0.453602 0.28 3 1276 2409 MODIFIER 17 CODING PRDM16 G protein_coding NM_022114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3352784 A G 0 32.6 0 0.9955 0.8854 0.719 0.8046 0.9453 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2409||1276|PRDM16|protein_coding|CODING|NM_022114.3|17|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2493267 -0.379885 0 2 P267 709 ccA/ccG LOW 4 SILENT CODING ARHGEF16 G protein_coding NM_014448.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3383898 A G 0 222 0 0.8563 0.86 0.8343 0.8026 0.9125 0.8885 0.87211 0.897413 0.908433 1 1797 17270 323 439 126 7360 166 7059 2 2062 19134 376 544 140 7976 182 7854 0.20885 0 . 0 . 497 139,112,102,79 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P267|709|ARHGEF16|protein_coding|CODING|NM_014448.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.288069 rs6424078 -0.693147 0.029608 497 H370Y 709 Cac/Tac MODERATE 7 MISSENSE CODING ARHGEF16 T protein_coding NM_014448.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3389727 C T 0 222 0 0.385 0.6845 0.755 0.6746 0.8638 0.865 0.468225 0.735353 0.872209 1 4706 97113 7819 5703 5971 57701 763 14450 2 10348 120638 11552 8632 6614 66086 898 16508 0.597665 0 . 0 . 238 63,58,55,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H370Y|709|ARHGEF16|protein_coding|CODING|NM_014448.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910789 rs2185639 -0.693147 0.472146 238 S497 709 tcT/tcC LOW 11 SILENT CODING ARHGEF16 C protein_coding NM_014448.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3394456 T C 0 228 0 0.8971 0.9706 0.9928 1 0.998 0.9959 0.908341 0.968445 0.999066 2 9231 118739 11484 8634 6612 65414 883 16481 2 10216 119908 11550 8634 6612 65504 888 16504 0 . 0 . 0 663 0,0,319,298 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S497|709|ARHGEF16|protein_coding|CODING|NM_014448.3|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4638054 -0.693147 0.0121428 663 V559 709 gtG/gtA LOW 12 SILENT CODING ARHGEF16 A protein_coding NM_014448.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3395039 G A 0 222 0 0.3873 0.6861 0.7637 0.6766 0.8628 0.863 0.471351 0.734238 0.869053 1 4700 96159 7782 5680 5965 56929 758 14345 2 10200 119646 11548 8604 6614 65382 890 16408 0.56488 0 . 0 . 604 181,127,137,98 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V559|709|ARHGEF16|protein_coding|CODING|NM_014448.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.659934 rs10797395 -0.693147 0.0264033 604 S604 709 tcC/tcA LOW 12 SILENT CODING ARHGEF16 A protein_coding NM_014448.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3395174 C A 0 222 0 0.0061 0.0913 0.1427 0.1935 0.0577 0.0992 0.0194597 0.0519882 0.0685908 1 165 10883 2906 1814 370 4278 60 1290 2 9454 111990 11338 8410 6294 62018 798 13678 0.460933 0 . 0 . 311 30,112,43,105 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|tcC/tcA|S604|709|ARHGEF16|protein_coding|CODING|NM_014448.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96574 rs61734742 -0.693147 0.00604348 311 709 37 MODIFIER 15 CODING ARHGEF16 C protein_coding NM_014448.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3397188 T C 0 228 0 0.9697 0.9918 0.9986 1 1 1 0.978709 0.992714 0.999883 2 8954 112446 11215 8298 5977 61655 817 15530 2 9182 112692 11226 8298 5980 61656 818 15532 0 . 0 . 0 431 0,0,102,295 UTR_3_PRIME(MODIFIER||37||709|ARHGEF16|protein_coding|CODING|NM_014448.3|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2487677 -0.693147 8.68165e-05 431 709 304 MODIFIER 15 CODING ARHGEF16 A protein_coding NM_014448.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3397455 G A 0 113 0 0.3979 0.6933 0.7608 0.6796 0.8658 0.8814 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.707404 0 . 0 . 12 0,3,0,9 UTR_3_PRIME(MODIFIER||304||709|ARHGEF16|protein_coding|CODING|NM_014448.3|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.995736 rs1051515 -0.662043 0.513454 12 709 519 MODIFIER 15 CODING ARHGEF16 G protein_coding NM_014448.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3397670 C G 0 25.9 0 0 0.0208 0.0014 0.0982 0 0.0041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_3_PRIME(MODIFIER||519||709|ARHGEF16|protein_coding|CODING|NM_014448.3|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs139034353 -0.453602 0.66 3 1541 2382 MODIFIER 37 CODING MEGF6 G protein_coding NM_001409.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3404710 A G 0 65 0 0.3222 0.2083 0.2032 0.256 0.0954 0.1247 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 7 1,1,0,4 UTR_3_PRIME(MODIFIER||2382||1541|MEGF6|protein_coding|CODING|NM_001409.3|37|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs4648389 -0.556411 0.0127498 7 1541 1796 MODIFIER 37 CODING MEGF6 C protein_coding NM_001409.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3405296 T C 0 9.7 0 0.7201 0.346 0.2911 0.2837 0.161 0.1339 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1796||1541|MEGF6|protein_coding|CODING|NM_001409.3|37|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4648505 -0.379885 0 1 R916L 1541 cGg/cTg MODERATE 22 MISSENSE CODING MEGF6 A protein_coding NM_001409.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3416449 C A 0 228 0 0.3177 0.5683 0.6556 0.4355 0.7515 0.7935 0.40966 0.63742 0.748115 2 881 21464 1239 761 303 11308 197 6775 2 1872 29694 2000 1488 408 15026 258 8642 0 . 0 . 0 36 0,0,5,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R916L|1541|MEGF6|protein_coding|CODING|NM_001409.3|22|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7553399 -0.693132 0.888221 36 C410 1541 tgT/tgC LOW 10 SILENT CODING MEGF6 G protein_coding NM_001409.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3427351 A G 0 222 0 0.0061 0.0781 0.1398 0.131 0.0875 0.0675 0.0224374 0.0637325 0.0844387 1 183 10758 2495 1062 512 5300 54 1152 2 8506 110632 11168 8356 5742 61028 782 15050 0.776141 0 . 0 COSM1342037 212 54,60,40,46 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C410|1541|MEGF6|protein_coding|CODING|NM_001409.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.245165 rs2821000 -0.693147 0.384425 212 T356 1541 acA/acC LOW 9 SILENT CODING MEGF6 G protein_coding NM_001409.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3428160 T G 0 222 0 0.7511 0.5 0.4049 0.6409 0.2863 0.3027 0.674458 0.421195 0.296071 1 6748 44175 5386 5696 1689 19571 279 4806 2 9648 118982 11508 8562 6484 65494 872 16414 0.223896 0 . 0 . 268 84,28,91,41 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T356|1541|MEGF6|protein_coding|CODING|NM_001409.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.32297 rs2820999 -0.693147 8.77769e-06 268 S131G 1541 Agc/Ggc MODERATE 4 MISSENSE CODING MEGF6 C protein_coding NM_001409.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3496479 T C 0 228 0 0.8691 0.8528 0.8919 0.7054 0.9155 0.8906 0.879124 0.90418 0.915998 2 6315 82916 7616 4678 3487 48144 610 12066 2 7314 93888 8742 6804 3834 52838 668 13688 0.811765 0 . 0 COSM1162425 94 0,2,39,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S131G|1541|MEGF6|protein_coding|CODING|NM_001409.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.735294 rs2794340 -0.693147 0.0580605 94 1541 112 MODIFIER 1 CODING MEGF6 G protein_coding NM_001409.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3527944 C G 0 91 0 0.8389 0.9367 0.9813 0.9851 0.9692 0.954 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_5_PRIME(MODIFIER||112||1541|MEGF6|protein_coding|CODING|NM_001409.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10797402 -0.590765 0.661214 5 272 83 MODIFIER 5 CODING TPRG1L G protein_coding NM_182752.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3545250 T G 0 222 0 0.0045 0.0791 0.0634 0.1925 0.0388 0.1155 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.982127 0 . 0 . 97 5,33,3,54 UTR_3_PRIME(MODIFIER||83||272|TPRG1L|protein_coding|CODING|NM_182752.3|5|G),DOWNSTREAM(MODIFIER||2081||460|WRAP73|protein_coding|CODING|NM_017818.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.777044 rs3795257 -0.693147 0.0972204 97 272 445 MODIFIER 5 CODING TPRG1L G protein_coding NM_182752.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3545612 A G 0 57 0 0.0303 0.2051 0.1571 0.3313 0.2525 0.2965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||445||272|TPRG1L|protein_coding|CODING|NM_182752.3|5|G),DOWNSTREAM(MODIFIER||1719||460|WRAP73|protein_coding|CODING|NM_017818.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1128474 -0.453602 0.52 3 A378 460 gcA/gcG LOW 11 SILENT CODING WRAP73 C protein_coding NM_017818.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3548136 T C 0 228 0 0.8926 0.9061 0.8458 0.995 0.836 0.9479 0.876193 0.850485 0.837326 2 8706 103286 9898 8453 5758 54462 750 15259 2 9926 118354 11386 8478 6476 64822 864 16402 0 . 0 . 0 91 0,0,41,41 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A378|460|WRAP73|protein_coding|CODING|NM_017818.3|11|C),DOWNSTREAM(MODIFIER||1442||272|TPRG1L|protein_coding|CODING|NM_182752.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2760321 -0.693147 0.145629 91 L224 460 Ctg/Ttg LOW 7 SILENT CODING WRAP73 A protein_coding NM_017818.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3551792 G A 0 168 0 0.0045 0.0787 0.0634 0.1915 0.0388 0.1145 0.00930549 0.0312164 0.0424419 1 88 8903 1305 1944 331 3284 74 1877 2 10336 121012 11540 8614 6612 66510 906 16494 0.999527 0 . 0 . 104 2,36,1,64 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L224|460|WRAP73|protein_coding|CODING|NM_017818.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.449598 rs2296034 -0.693147 0.201168 104 T173 636 acC/acT LOW 5 SILENT CODING TP73 T protein_coding NM_005427.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3638674 C T 0 228 0 0.7738 0.736 0.7219 0.5268 0.9135 0.728 0.772603 0.849462 0.888811 2 7914 97248 7153 4458 5602 58878 739 12504 2 10284 120050 11530 8606 6610 65626 890 16504 1 0 . 0 . 218 0,1,75,126 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|636|TP73|protein_coding|CODING|NM_005427.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1801174 -0.693147 0.00133605 218 636 1455 MODIFIER 14 CODING TP73 T protein_coding NM_005427.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3651098 C T 0 39.3 0 0.115 0.3996 0.5807 0.2728 0.7545 0.4213 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1455||636|TP73|protein_coding|CODING|NM_005427.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1181869 -0.453602 0.86 2 636 1483 MODIFIER 14 CODING TP73 T protein_coding NM_005427.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3651126 G T 0 9.7 0 0.115 0.4004 0.5807 0.2728 0.7535 0.4264 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1483||636|TP73|protein_coding|CODING|NM_005427.3|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1181868 -0.379885 0 1 925 1531 MODIFIER 22 CODING CEP104 C protein_coding NM_014704.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3730435 T C 0 42.3 0 0.8986 0.6524 0.4611 0.5724 0.5427 0.6503 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1531||925|CEP104|protein_coding|CODING|NM_014704.3|22|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6695834 -0.453602 0.1 2 925 311 MODIFIER 22 CODING CEP104 CT protein_coding NM_014704.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3731654 C CT 0 228 0 0.9402 0.6981 0.5144 0.6617 0.5716 0.6687 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 1,0,54,10 UTR_3_PRIME(MODIFIER||311||925|CEP104|protein_coding|CODING|NM_014704.3|22|CT) 0 . 0 68 0.957747 1 1 0 . 0 60 0 0 1 0 . rs3838969,rs72502778 -0.693147 0.474089 71 A686V 925 gCg/gTg MODERATE 15 MISSENSE CODING CEP104 A protein_coding NM_014704.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3745924 G A 0 228 0 0.0802 0.2105 0.1311 0.5208 0.0557 0.2822 0.0882887 0.0604336 0.0461628 2 955 17144 3087 4437 621 3364 115 4565 2 10088 120098 11520 8564 6596 65972 904 16454 0 . 0 . 0 84 0,0,37,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A686V|925|CEP104|protein_coding|CODING|NM_014704.3|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275831,rs386563283 -0.693147 0.263869 84 R220K 362 aGg/aAg MODERATE 5 MISSENSE CODING DFFB A protein_coding NM_001282669.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3786245 G A 0 222 0 0.093 0.1328 0.1052 0.2054 0.1153 0.1493 0.0946437 0.0947255 0.0947674 1 975 13646 1524 1978 903 6282 97 1887 2 10160 119552 11490 8570 6524 65472 882 16454 0.999785 0 . 0 COSM426206 129 40,23,36,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R220K|362|DFFB|protein_coding|CODING|NM_001282669.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.10817 rs12738235 -0.693147 0.757558 129 P342 362 ccA/ccG LOW 7 SILENT CODING DFFB G protein_coding NM_001282669.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3800242 A G 0 222 0 0.3124 0.3558 0.3256 0.3482 0.4105 0.3875 0.338402 0.412886 0.451047 1 3510 48137 2984 2882 2458 29383 373 6547 2 10350 121212 11564 8642 6614 66640 908 16494 0.881474 0 . 0 . 74 16,17,18,12 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P342|362|DFFB|protein_coding|CODING|NM_001282669.1|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989614 rs3205087 -0.693097 0.119673 74 243 450 MODIFIER 4 CODING C1orf174 A protein_coding NM_207356.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3806074 G A 0 9.7 0 0.7655 0.6777 0.6268 0.6141 0.7197 0.6176 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||450||243|C1orf174|protein_coding|CODING|NM_207356.2|4|A),DOWNSTREAM(MODIFIER||4081||362|DFFB|protein_coding|CODING|NM_001282669.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4075974 -0.379885 0 1 243 166 MODIFIER 4 CODING C1orf174 C protein_coding NM_207356.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3806358 T C 0 196 0 0.0991 0.1452 0.1124 0.2331 0.1262 0.1595 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.449232 0 . 0 . 35 14,1,15,0 UTR_3_PRIME(MODIFIER||166||243|C1orf174|protein_coding|CODING|NM_207356.2|4|C),DOWNSTREAM(MODIFIER||4365||362|DFFB|protein_coding|CODING|NM_001282669.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.425901 rs10909819 -0.688148 0.206325 35 243 LOW 3 CODING C1orf174 A protein_coding NM_207356.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3806643 T A 0 222 0 0.5696 0.4215 0.3602 0.4335 0.3241 0.3528 0.51271 0.37944 0.311163 1 5597 42847 4018 3572 2541 21089 317 5713 2 10380 120832 11504 8606 6594 66360 902 16486 0.968286 0 . 0 . 154 29,44,30,32 SPLICE_SITE_REGION+INTRON(LOW||||243|C1orf174|protein_coding|CODING|NM_207356.2|3|A),DOWNSTREAM(MODIFIER||4650||362|DFFB|protein_coding|CODING|NM_001282669.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.637257 rs4520357 -0.693147 0.013122 154 T53R 243 aCg/aGg MODERATE 3 MISSENSE CODING C1orf174 C protein_coding NM_207356.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 3807593 G C 0 228 0 0.9992 0.9978 0.9986 0.999 0.993 0.999 0.997728 0.994075 0.992204 2 9884 120033 11555 8653 6575 66003 904 16459 2 9896 120748 11578 8654 6614 66588 906 16512 0 . 0 . 0 105 0,0,54,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aGg|T53R|243|C1orf174|protein_coding|CODING|NM_207356.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4274008 -0.693147 0.0324749 105 G202D 411 gGc/gAc MODERATE 2 MISSENSE CODING AJAP1 A protein_coding NM_001042478.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 4772535 G A 0 222 0 0 0.011781 0.0331 0.0357 0 0 0.000453926 0.000230698 0.000116306 1 6 699 422 237 0 10 4 20 2 8090 97684 9400 7060 4192 53764 724 14454 0.238587 0 . 0 . 187 48,38,42,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G202D|411|AJAP1|protein_coding|CODING|NM_001042478.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.797907 rs76065876 -0.693147 0.0709413 187 E1190 1426 gaA/gaG LOW 26 SILENT CODING NPHP4 C protein_coding NM_015102.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 5926507 T C 0 228 0 0.1619 0.3197 0.379 0.2837 0.4135 0.4315 0.19845 0.349018 0.419699 2 1542 36977 3240 1720 2076 22406 273 5720 2 5752 80310 7034 5170 4160 45454 598 12142 0 2 benign 0 COSM1126976 57 0,0,22,32 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1190|1426|NPHP4|protein_coding|CODING|NM_015102.4|26|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs555164 -0.693147 0.818847 57 1426 HIGH 20 CODING NPHP4 T protein_coding NM_015102.4 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 5935162 A T 0 228 0 0.91 0.8433 0.8401 0.7907 0.8111 0.8425 0.893793 0.843133 0.817231 2 7281 85665 7450 5737 5162 47221 640 12174 2 8136 102440 9378 7014 5614 56864 776 14658 0 2 benign 0 . 92 0,0,38,46 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||1426|NPHP4|protein_coding|CODING|NM_015102.4|20|T) 1 0 . 0 . 1 0 1 1 (NPHP4|NPHP4|1|1.00) 60 0 0 1 0 . rs1287637 -0.693147 0.665571 92 S392 415 tcA/tcG LOW 16 SILENT CODING KCNAB2 G protein_coding NM_001199862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6158562 A G 0 228 0 0.6415 0.5439 0.6095 0.4018 0.6093 0.4448 0.639419 0.61458 0.60186 2 6570 69195 7827 3491 3658 39883 483 7283 2 10290 120348 11482 8610 6596 65986 904 16480 0.546219 0 . 0 . 144 2,0,82,37 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S392|415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|G),DOWNSTREAM(MODIFIER||3285||1954|CHD5|protein_coding|CODING|NM_015557.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.735294 rs2229002 -0.693147 0.678775 144 415 398 MODIFIER 16 CODING KCNAB2 G protein_coding NM_001199862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6159032 A G 0 86 0 0.6747 0.6833 0.6974 0.753 0.7167 0.5787 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||398||415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|G),DOWNSTREAM(MODIFIER||2815||1954|CHD5|protein_coding|CODING|NM_015557.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4908772 -0.556411 0.23997 4 415 1929 MODIFIER 16 CODING KCNAB2 G protein_coding NM_001199862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6160563 A G 0 9.7 0 0.7655 0.8061 0.7205 0.994 0.7614 0.774 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1929||415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|G),DOWNSTREAM(MODIFIER||1284||1954|CHD5|protein_coding|CODING|NM_015557.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9434641 -0.379885 0 1 415 2236 MODIFIER 16 CODING KCNAB2 A protein_coding NM_001199862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6160870 G A 0 6.3 0 0.1051 0.1432 0.1499 0.1825 0.1093 0.184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2236||415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|A),DOWNSTREAM(MODIFIER||977||1954|CHD5|protein_coding|CODING|NM_015557.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3789527 -0.379885 0 1 415 2242 MODIFIER 16 CODING KCNAB2 G protein_coding NM_001199862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6160876 A G 0 42.3 0 0.7398 0.7915 0.7147 0.9931 0.7614 0.7393 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2242||415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|G),DOWNSTREAM(MODIFIER||971||1954|CHD5|protein_coding|CODING|NM_015557.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1056860 -0.453602 0.92 2 415 2324 MODIFIER 16 CODING KCNAB2 G protein_coding NM_001199862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6160958 A G 0 36.3 0 0.7368 0.7909 0.7147 0.9931 0.7614 0.7403 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2324||415|KCNAB2|protein_coding|CODING|NM_001199862.1|16|G),DOWNSTREAM(MODIFIER||889||1954|CHD5|protein_coding|CODING|NM_015557.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs538 -0.453602 0.6 2 1954 4286 MODIFIER 42 CODING CHD5 C protein_coding NM_015557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6162054 T C 0 228 0 0.6785 0.7045 0.6801 0.8641 0.7306 0.5654 0 . 0 2 289 6958 90 246 9 2243 77 4004 2 404 11258 144 294 12 3534 122 6748 0 . 0 . 0 19 0,0,12,7 UTR_3_PRIME(MODIFIER||4286||1954|CHD5|protein_coding|CODING|NM_015557.2|42|C),DOWNSTREAM(MODIFIER||801||415|KCNAB2|protein_coding|CODING|NM_001199862.1||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6696489 -0.69168 0.311825 19 1954 3933 MODIFIER 42 CODING CHD5 G protein_coding NM_015557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6162407 A G 0 222 0 0.2103 0.4018 0.2695 0.7847 0.2664 0.499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.942979 0 . 0 . 299 67,59,85,51 UTR_3_PRIME(MODIFIER||3933||1954|CHD5|protein_coding|CODING|NM_015557.2|42|G),DOWNSTREAM(MODIFIER||1154||415|KCNAB2|protein_coding|CODING|NM_001199862.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.915194 rs3827728 -0.693147 6.68515e-10 299 1954 3757 MODIFIER 42 CODING CHD5 A protein_coding NM_015557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6162583 G A 0 228 0 0.7761 0.6785 0.6441 0.6429 0.6531 0.6339 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,3,41 UTR_3_PRIME(MODIFIER||3757||1954|CHD5|protein_coding|CODING|NM_015557.2|42|A),DOWNSTREAM(MODIFIER||1330||415|KCNAB2|protein_coding|CODING|NM_001199862.1||A) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.997564 0 . rs3810993 -0.693146 0.124807 44 1954 2415 MODIFIER 42 CODING CHD5 T protein_coding NM_015557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6163925 C T 0 39.3 0 0.7451 0.7015 0.6873 0.751 0.7117 0.591 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2415||1954|CHD5|protein_coding|CODING|NM_015557.2|42|T),DOWNSTREAM(MODIFIER||2672||415|KCNAB2|protein_coding|CODING|NM_001199862.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3810989 -0.453602 0.5 2 1954 1932 MODIFIER 42 CODING CHD5 A protein_coding NM_015557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6164408 G A 0 9.7 0 0.1112 0.1567 0.1556 0.1905 0.1113 0.2311 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1932||1954|CHD5|protein_coding|CODING|NM_015557.2|42|A),DOWNSTREAM(MODIFIER||3155||415|KCNAB2|protein_coding|CODING|NM_001199862.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2092507 -0.379885 0 1 S1539P 1954 Tcg/Ccg MODERATE 31 MISSENSE CODING CHD5 G protein_coding NM_015557.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6184092 A G 0 228 0 0.612 0.7276 0.5994 0.994 0.5994 0.8323 0.600999 0.587959 0.581279 2 6200 78179 6793 8589 4635 38625 594 12743 2 10208 118992 11246 8616 6472 65258 878 16314 0 . 0 . 0 146 0,0,76,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcg/Ccg|S1539P|1954|CHD5|protein_coding|CODING|NM_015557.2|31|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2843493 -0.693147 0.105007 146 I831 1954 atT/atC LOW 16 SILENT CODING CHD5 G protein_coding NM_015557.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6196869 A G 0 228 0 0.3366 0.5178 0.4697 0.7996 0.3946 0.6329 0.342488 0.389974 0.414302 2 3592 58481 5858 6880 3574 28169 466 9942 2 10388 120952 11530 8638 6588 66416 904 16488 0 . 0 . 0 50 0,0,25,21 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I831|1954|CHD5|protein_coding|CODING|NM_015557.2|16|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2250358,rs386562551 -0.693147 0.181537 50 N793 1954 aaC/aaT LOW 15 SILENT CODING CHD5 A protein_coding NM_015557.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6202245 G A 0 222 0 0.0371 0.1328 0.0605 0.3323 0.1113 0.1299 0.0567408 0.0948024 0.114302 1 541 14335 489 2990 743 7248 101 2223 2 10406 121382 11578 8636 6614 66730 908 16510 0.928323 0 . 0 COSM426530 155 46,33,39,25 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N793|1954|CHD5|protein_coding|CODING|NM_015557.2|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.736842 rs2273032 -0.693147 0.00115008 155 1954 LOW 11 CODING CHD5 G protein_coding NM_015557.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6204222 C G 0 222 0 0.1967 0.1669 0.1326 0.1359 0.0944 0.2577 0.210168 0.138705 0.102093 1 2109 16687 2149 1141 694 6847 95 3652 2 10402 121284 11566 8648 6614 66662 906 16486 0.9998 0 . 0 . 85 12,25,11,30 SPLICE_SITE_REGION+INTRON(LOW||||1954|CHD5|protein_coding|CODING|NM_015557.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.28204 rs17489787 -0.693145 0.0179228 85 V368 1954 gtA/gtG LOW 8 SILENT CODING CHD5 C protein_coding NM_015557.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6209363 T C 0 222 0 0.7216 0.5238 0.2147 0.6538 0.3082 0.5634 0.650477 0.409965 0.286744 1 6779 47022 2750 5706 2745 19975 346 8721 2 10202 117210 10938 8528 6300 64170 872 16200 0.470442 0 . 0 . 75 25,5,31,10 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V368|1954|CHD5|protein_coding|CODING|NM_015557.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841322 rs12565328 -0.693145 0.274894 75 P96T 186 Ccc/Acc MODERATE 4 MISSENSE CODING HES3 A protein_coding NM_001024598.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6305292 C A 0 228 0 0.3079 0.5579 0.755 0.5615 0.6849 0.6217 0.485075 0.66121 0.739386 2 109 6829 140 113 6 2050 77 4334 2 264 10470 176 190 6 2910 112 6812 1 0 . 0 . 20 1,0,7,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P96T|186|HES3|protein_coding|CODING|NM_001024598.3|4|A),DOWNSTREAM(MODIFIER||2114||609|GPR153|protein_coding|CODING|NM_207370.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs61760836 -0.69168 0.249713 20 A99 186 gcC/gcA LOW 4 SILENT CODING HES3 A protein_coding NM_001024598.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6305303 C A 0 228 0 0.3079 0.5575 0.7536 0.5615 0.6839 0.6217 0.51204 0.683312 0.758556 2 100 6425 110 94 9 1875 71 4166 2 240 9806 134 164 10 2644 104 6510 0 . 0 . 0 21 0,0,9,12 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A99|186|HES3|protein_coding|CODING|NM_001024598.3|4|A),DOWNSTREAM(MODIFIER||2103||609|GPR153|protein_coding|CODING|NM_207370.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs61760837 -0.692352 0.621695 21 609 703 MODIFIER 6 CODING GPR153 G protein_coding NM_207370.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6308695 A G 0 76 0 0.4244 0.6126 0.7781 0.5933 0.7256 0.6534 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||703||609|GPR153|protein_coding|CODING|NM_207370.2|6|G),DOWNSTREAM(MODIFIER||3057||186|HES3|protein_coding|CODING|NM_001024598.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12744452 -0.511536 0.309755 3 609 79 MODIFIER 6 CODING GPR153 G protein_coding NM_207370.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6309319 C G 0 9.7 0 0.2708 0.5715 0.7594 0.5903 0.7117 0.681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||79||609|GPR153|protein_coding|CODING|NM_207370.2|6|G),DOWNSTREAM(MODIFIER||3681||186|HES3|protein_coding|CODING|NM_001024598.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1883608 -0.379885 0 1 R209H 609 cGc/cAc MODERATE 3 MISSENSE CODING GPR153 T protein_coding NM_207370.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6313938 C T 0 228 0 0.702 0.6991 0.7939 0.6131 0.7117 0.7035 0 . 0 2 6777 77787 8738 4553 3973 42112 573 11061 2 9380 109950 10634 7664 5676 59856 792 15948 0 . 0 . 0 99 0,0,57,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R209H|609|GPR153|protein_coding|CODING|NM_207370.2|3|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12735670 -0.693147 0.429924 99 T48 609 acA/acG LOW 2 SILENT CODING GPR153 C protein_coding NM_207370.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6314822 T C 0 228 0 0.8086 0.7314 0.8012 0.6181 0.7127 0.7137 0.790967 0.731816 0.701512 2 8234 85904 9488 5117 4561 46307 649 11548 2 10388 121122 11564 8634 6610 66524 902 16500 0 . 0 . 0 144 0,0,49,81 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T48|609|GPR153|protein_coding|CODING|NM_207370.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11590458 -0.693147 0.00977146 144 702 4037 MODIFIER 12 CODING NOL9 A protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6581877 G A 0 6.3 0 0.4274 0.7236 0.8516 0.7897 0.8579 0.8272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4037||702|NOL9|protein_coding|CODING|NM_024654.4|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7540913 -0.379885 0 1 702 3109 MODIFIER 12 CODING NOL9 A protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6582805 G A 0 9.7 0 0.3003 0.6801 0.8415 0.7758 0.8509 0.8047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3109||702|NOL9|protein_coding|CODING|NM_024654.4|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11122049 -0.379885 0 1 702 2213 MODIFIER 12 CODING NOL9 C protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6583701 T C 0 9.7 0 0.652 0.7999 0.8761 0.8383 0.8867 0.817 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2213||702|NOL9|protein_coding|CODING|NM_024654.4|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10158949 -0.379885 0 1 702 1890 MODIFIER 12 CODING NOL9 G protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6584024 A G 0 46.3 0 0.9266 0.9794 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1890||702|NOL9|protein_coding|CODING|NM_024654.4|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4908557 -0.453602 0.64 2 702 1813 MODIFIER 12 CODING NOL9 G protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6584101 A G 0 9.7 0 0.438 0.7286 0.8487 0.8234 0.8579 0.8057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1813||702|NOL9|protein_coding|CODING|NM_024654.4|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4908558 -0.379885 0 1 702 1687 MODIFIER 12 CODING NOL9 C protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6584227 G C 0 63 0 0.0008 0.0619 0.0115 0.2867 0.004 0.0082 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1687||702|NOL9|protein_coding|CODING|NM_024654.4|12|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17029590 -0.453602 0.94 3 702 893 MODIFIER 12 CODING NOL9 G protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6585021 A G 0 70 0 0.9266 0.9794 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||893||702|NOL9|protein_coding|CODING|NM_024654.4|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6696498 -0.453602 0.76 3 702 375 MODIFIER 12 CODING NOL9 T protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6585539 C T 0 116 0 0.475 0.7328 0.8545 0.7917 0.8579 0.8057 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,1 UTR_3_PRIME(MODIFIER||375||702|NOL9|protein_coding|CODING|NM_024654.4|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1064835 -0.590765 0.768087 5 702 110 MODIFIER 12 CODING NOL9 T protein_coding NM_024654.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6585804 C T 0 228 0 0.5038 0.7416 0.8602 0.7917 0.8598 0.8057 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 0,0,65,4 UTR_3_PRIME(MODIFIER||110||702|NOL9|protein_coding|CODING|NM_024654.4|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13513 -0.693147 0.023023 71 702 LOW 11 CODING NOL9 T protein_coding NM_024654.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6586070 C T 0 228 0 0.9266 0.9794 0.9914 1 1 1 0.928053 0.975473 0.999767 2 9646 120614 11551 8654 6614 66732 906 16511 2 10406 121408 11578 8654 6614 66738 906 16512 0 . 0 . 0 209 0,0,77,105 SPLICE_SITE_REGION+INTRON(LOW||||702|NOL9|protein_coding|CODING|NM_024654.4|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7548042 -0.693147 0.0223617 209 S58A 702 Tcc/Gcc MODERATE 1 MISSENSE CODING NOL9 C protein_coding NM_024654.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6614391 A C 0 135 0 0.8722 0.9563 0.9841 0.9692 0.995 0.9969 0.894137 0.961256 0.994898 2 619 8932 194 515 152 3353 70 4029 2 748 9128 196 544 152 3368 70 4050 0 . 0 . 0 12 0,0,0,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S58A|702|NOL9|protein_coding|CODING|NM_024654.4|1|C),UPSTREAM(MODIFIER||947||841|TAS1R1|protein_coding|CODING|NM_138697.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs6693391 -0.680642 0.0859232 12 W50R 702 Tgg/Cgg MODERATE 1 MISSENSE CODING NOL9 G protein_coding NM_024654.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6614415 A G 0 175 0 0.9281 0.9798 0.9914 1 1 1 0.916009 0.972997 0.998972 2 1275 16289 570 1350 560 7638 106 4790 2 1416 16434 574 1350 560 7638 106 4790 0 . 0 . 0 10 0,0,1,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W50R|702|NOL9|protein_coding|CODING|NM_024654.4|1|G),UPSTREAM(MODIFIER||923||841|TAS1R1|protein_coding|CODING|NM_138697.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6693400 -0.670168 0.727693 10 R10W 702 Cgg/Tgg MODERATE 1 MISSENSE CODING NOL9 A protein_coding NM_024654.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6614535 G A 0 9.7 0 0.4266 0.7222 0.8473 0.7927 0.8608 0.818 0.569606 0.786797 0.886691 1 3191 83101 9518 5919 4653 47049 561 12210 2 6064 98394 10284 7472 5104 53982 686 14802 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R10W|702|NOL9|protein_coding|CODING|NM_024654.4|1|A),UPSTREAM(MODIFIER||803||841|TAS1R1|protein_coding|CODING|NM_138697.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0 . 0 . rs4908923 -0.379885 0 1 K347E 841 Aag/Gag MODERATE 3 MISSENSE CODING TAS1R1 G protein_coding NM_138697.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6635231 A G 0 228 0 0.7216 0.9233 0.9841 1 0.999 0.9959 0.764412 0.919729 0.999302 2 7781 115832 11389 8526 6592 65632 862 15050 2 10306 118574 11520 8526 6592 65690 874 15066 0 . 0 . 0 40 0,0,22,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K347E|841|TAS1R1|protein_coding|CODING|NM_138697.3|3|G),UPSTREAM(MODIFIER||4820||688|ZBTB48|protein_coding|CODING|NM_001278647.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10864628,rs386475499 -0.693143 0.162673 40 A372T 841 Gca/Aca MODERATE 3 MISSENSE CODING TAS1R1 A protein_coding NM_138697.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6635306 G A 0 222 0 0.0582 0.1354 0.0648 0.3204 0.1223 0.1125 0.0689968 0.106412 0.125581 1 679 16060 528 2716 1448 8851 109 1729 2 9964 119010 11520 8566 6600 65104 892 16364 0.988725 0 . 0 COSM1343925 50 14,13,6,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A372T|841|TAS1R1|protein_coding|CODING|NM_138697.3|3|A),UPSTREAM(MODIFIER||4745||688|ZBTB48|protein_coding|CODING|NM_001278647.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999396 rs34160967 -0.691153 0.249373 50 597 2332 MODIFIER 4 CODING KLHL21 A protein_coding NM_014851.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6651093 G A 0 32.6 0 0.0106 0.147 0.072 0.4137 0.1352 0.1217 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2332||597|KLHL21|protein_coding|CODING|NM_014851.3|4|A),DOWNSTREAM(MODIFIER||1753||688|ZBTB48|protein_coding|CODING|NM_001278647.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs201171 -0.379885 0 2 597 707 MODIFIER 4 CODING KLHL21 A protein_coding NM_014851.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6652718 G A 0 64 0 0.2005 0.2694 0.2622 0.1984 0.3738 0.3333 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||707||597|KLHL21|protein_coding|CODING|NM_014851.3|4|A),DOWNSTREAM(MODIFIER||3378||688|ZBTB48|protein_coding|CODING|NM_001278647.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2235567 -0.511536 0.0681597 3 597 680 MODIFIER 4 CODING KLHL21 A protein_coding NM_014851.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6652745 G A 0 48.5 0 0.2655 0.2879 0.268 0.2004 0.3748 0.3333 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||680||597|KLHL21|protein_coding|CODING|NM_014851.3|4|A),DOWNSTREAM(MODIFIER||3405||688|ZBTB48|protein_coding|CODING|NM_001278647.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7513688 -0.511536 0.074936 3 300 347 MODIFIER 1 CODING PHF13 G protein_coding NM_153812.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6673780 C G 0 31.9 0 0.171 0.2396 0.2478 0.1548 0.3539 0.2965 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_5_PRIME(MODIFIER||347||300|PHF13|protein_coding|CODING|NM_153812.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12402498,rs386430318 -0.453602 0.7 3 300 47 MODIFIER 4 CODING PHF13 T protein_coding NM_153812.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6681744 C T 0 142 0 0.736 0.6947 0.6167 0.5784 0.7018 0.8067 0.715842 0.713033 0.711592 1 6544 76989 4873 4898 3900 43810 592 12372 2 8920 112254 10600 7972 6264 61460 850 16188 0.86274 0 . 0 . 20 2,9,2,5 UTR_3_PRIME(MODIFIER||47||300|PHF13|protein_coding|CODING|NM_153812.2|4|T),UPSTREAM(MODIFIER||3181||239|THAP3|protein_coding|CODING|NM_001195753.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.936488 rs3747994 -0.636426 0.217488 20 559 808 MODIFIER 16 CODING DNAJC11 T protein_coding NM_018198.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6694927 C T 0 222 0 0.3525 0.3007 0.2709 0.1895 0.3638 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.391988 0 . 0 . 56 17,17,10,11 UTR_3_PRIME(MODIFIER||808||559|DNAJC11|protein_coding|CODING|NM_018198.3|16|T),DOWNSTREAM(MODIFIER||1285||239|THAP3|protein_coding|CODING|NM_001195753.1||T),INTRAGENIC(MODIFIER|||||THAP3||CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.614132 rs2294532 -0.692352 0.22046 56 559 755 MODIFIER 16 CODING DNAJC11 A protein_coding NM_018198.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6694980 G A 0 222 0 0.7012 0.6805 0.6138 0.5764 0.6948 0.7924 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.79526 0 . 0 . 60 22,8,13,15 UTR_3_PRIME(MODIFIER||755||559|DNAJC11|protein_coding|CODING|NM_018198.3|16|A),DOWNSTREAM(MODIFIER||1338||239|THAP3|protein_coding|CODING|NM_001195753.1||A),INTRAGENIC(MODIFIER|||||THAP3||CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.604313 rs1043683 -0.693054 0.231508 60 559 612 MODIFIER 16 CODING DNAJC11 T protein_coding NM_018198.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6695123 C T 0 222 0 0.7322 0.6893 0.6167 0.5764 0.6958 0.7924 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957183 0 . 0 . 152 47,27,30,33 UTR_3_PRIME(MODIFIER||612||559|DNAJC11|protein_coding|CODING|NM_018198.3|16|T),DOWNSTREAM(MODIFIER||1481||239|THAP3|protein_coding|CODING|NM_001195753.1||T),INTRAGENIC(MODIFIER|||||THAP3||CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.228255 rs1043681 -0.693147 0.0504983 152 559 491 MODIFIER 16 CODING DNAJC11 G protein_coding NM_018198.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6695244 A G 0 222 0 0.7103 0.6953 0.6138 0.6339 0.6958 0.7955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.989687 0 . 0 . 87 18,35,9,19 UTR_3_PRIME(MODIFIER||491||559|DNAJC11|protein_coding|CODING|NM_018198.3|16|G),DOWNSTREAM(MODIFIER||1602||239|THAP3|protein_coding|CODING|NM_001195753.1||G),INTRAGENIC(MODIFIER|||||THAP3||CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.601718 rs10523 -0.693054 0.360777 87 G360 559 ggT/ggC LOW 10 SILENT CODING DNAJC11 G protein_coding NM_018198.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 6704635 A G 0 222 0 0.8676 0.8331 0.9625 0.5704 0.9245 0.8712 0.876986 0.899969 0.911744 1 9130 107240 11179 5163 5781 60671 782 14534 2 10398 121372 11578 8638 6614 66726 908 16510 0.650823 0 . 0 . 139 42,31,31,19 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G360|559|DNAJC11|protein_coding|CODING|NM_018198.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986932 rs200458 -0.693147 0.124395 139 N327 1673 aaC/aaT LOW 9 SILENT CODING CAMTA1 T protein_coding NM_015215.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7723588 C T 0 222 0 0.0061 0.0595 0.0735 0.0198 0.1431 0.0767 0.03064 0.10449 0.142326 1 233 12764 480 133 1176 9451 74 1217 2 10360 118370 11544 8636 6606 65748 880 14596 0.608365 3 likely-benign 0 . 287 45,99,39,91 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N327|1673|CAMTA1|protein_coding|CODING|NM_015215.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.791011 rs3737906,rs386430303 -0.693147 0.182422 287 S450 1673 tcG/tcA LOW 9 SILENT CODING CAMTA1 A protein_coding NM_015215.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7723957 G A 0 222 0 0.3873 0.4002 0.4539 0.3313 0.4304 0.4192 0.374035 0.429955 0.458605 1 3940 53953 5810 2997 3308 31013 346 6539 2 10390 121254 11566 8614 6600 66670 906 16508 0.917009 3 likely-benign 0 . 190 66,34,46,37 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S450|1673|CAMTA1|protein_coding|CODING|NM_015215.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992762 rs12128526 -0.693147 0.110543 190 1673 LOW 11 CODING CAMTA1 G protein_coding NM_015215.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7737799 A G 0 222 0 0.5855 0.5917 0.5375 0.6587 0.5686 0.593 0.585338 0.556282 0.541395 1 6155 66268 5625 5567 3195 35320 540 9866 2 10388 120536 11520 8616 6580 66392 904 16136 0.990926 0 . 0 . 147 50,23,39,20 SPLICE_SITE_REGION+INTRON(LOW||||1673|CAMTA1|protein_coding|CODING|NM_015215.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.877903 rs3011926 -0.693147 0.415054 147 1673 1866 MODIFIER 23 CODING CAMTA1 A protein_coding NM_015215.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7828417 C A 0 203 0 0.0045 0.0923 0.1988 0.2679 0.0119 0.0368 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.951361 0 . 0 . 66 25,13,12,6 UTR_3_PRIME(MODIFIER||1866||1673|CAMTA1|protein_coding|CODING|NM_015215.3|23|A),UPSTREAM(MODIFIER||2912||100|VAMP3|protein_coding|CODING|NM_004781.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.814627 rs3813809 -0.691153 0.638458 66 1673 2675 MODIFIER 23 CODING CAMTA1 G protein_coding NM_015215.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7829226 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 162 0,0,75,69 UTR_3_PRIME(MODIFIER||2675||1673|CAMTA1|protein_coding|CODING|NM_015215.3|23|G),UPSTREAM(MODIFIER||2103||100|VAMP3|protein_coding|CODING|NM_004781.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs707456 -0.693147 0.00118984 162 1673 2735 MODIFIER 23 CODING CAMTA1 G protein_coding NM_015215.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7829286 A G 0 222 0 0.0711 0.0571 0.0605 0.0119 0.0915 0.047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98972 0 . 0 . 127 20,41,19,36 UTR_3_PRIME(MODIFIER||2735||1673|CAMTA1|protein_coding|CODING|NM_015215.3|23|G),UPSTREAM(MODIFIER||2043||100|VAMP3|protein_coding|CODING|NM_004781.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.98972 rs41454244 -0.693147 0.140191 127 100 92 MODIFIER 1 CODING VAMP3 A protein_coding NM_004781.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7831352 C A 0 222 0 0.0068 0.0933 0.1988 0.2698 0.0119 0.0368 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.981287 0 . 0 . 48 21,1,15,6 UTR_5_PRIME(MODIFIER||92||100|VAMP3|protein_coding|CODING|NM_004781.3|1|A),DOWNSTREAM(MODIFIER||1586||1673|CAMTA1|protein_coding|CODING|NM_015215.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.49943 rs72853889 -0.692352 0.0237366 48 100 1221 MODIFIER 5 CODING VAMP3 C protein_coding NM_004781.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7840926 G C 0 41.4 0 0.795 0.8373 0.8415 0.9653 0.7634 0.8354 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 2,1,3,0 UTR_3_PRIME(MODIFIER||1221||100|VAMP3|protein_coding|CODING|NM_004781.3|5|C),UPSTREAM(MODIFIER||3563||1210|PER3|protein_coding|CODING|NM_001289862.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.574341 rs697679 -0.511536 0.0983484 6 S446 1210 agT/agC LOW 12 SILENT CODING PER3 C protein_coding NM_001289862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7870048 T C 0 222 0 0.972 0.879 0.7608 0.7232 0.9324 0.9427 0.960281 0.937414 0.925698 1 10021 108181 7332 6240 6300 61999 836 15453 2 10402 121336 11570 8636 6614 66698 908 16508 0.597234 0 . 0 . 176 35,38,32,52 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S446|1210|PER3|protein_coding|CODING|NM_001289862.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.5887 rs228669 -0.693147 0.0066917 176 P753 1210 ccG/ccA LOW 18 SILENT CODING PER3 A protein_coding NM_001289862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7887248 G A 0 222 0 0.5333 0.5168 0.4597 0.8026 0.3718 0.3896 0.506193 0.406483 0.355553 1 4847 50515 6848 6876 2207 23335 344 6058 2 9212 116304 11424 8548 6544 63540 868 16168 0.462745 0 . 0 . 63 17,13,13,6 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P753|1210|PER3|protein_coding|CODING|NM_001289862.1|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.772677 rs2859387 -0.69168 0.00978298 63 L835P 1210 cTg/cCg MODERATE 18 MISSENSE CODING PER3 C protein_coding NM_001289862.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7887493 T C 0 228 0 0.9758 0.9752 0.9654 1 0.9513 0.9806 0.973218 0.961018 0.954767 2 10119 117630 11453 8645 6379 64013 887 16134 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 78 0,0,54,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L835P|1210|PER3|protein_coding|CODING|NM_001289862.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs228696 -0.693147 0.325218 78 S872 1210 tcG/tcA LOW 18 SILENT CODING PER3 A protein_coding NM_001289862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7887605 G A 0 222 0 0.0076 0.0964 0.2046 0.2728 0.0189 0.0378 0.0142987 0.0242196 0.0293023 1 119 9407 4125 2374 79 1982 51 677 2 10406 121396 11578 8638 6614 66740 908 16512 0.278057 0 . 0 . 177 51,32,54,24 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S872|1210|PER3|protein_coding|CODING|NM_001289862.1|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999369 rs17031614 -0.693147 0.0584094 177 T1019 1210 acA/acG LOW 19 SILENT CODING PER3 G protein_coding NM_001289862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7890064 A G 0 222 0 0.2421 0.2448 0.2118 0.1478 0.2863 0.3292 0 . 0 1 1116 10813 584 476 616 6453 94 1474 2 7644 80250 9452 7090 4090 41800 594 9580 0.998933 0 . 0 . 120 19,17,44,33 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1019|1210|PER3|protein_coding|CODING|NM_001289862.1|19|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.776243 0.976162 0 2.74817e-07 rs12023156 -0.693147 0.619441 120 1210 1122 MODIFIER 22 CODING PER3 G protein_coding NM_001289862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7903937 C G 0 222 0 0 0.0015974 0 0.0079 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.503023 0 . 0 . 92 27,20,20,14 UTR_3_PRIME(MODIFIER||1122||1210|PER3|protein_coding|CODING|NM_001289862.1|22|G),DOWNSTREAM(MODIFIER||3735||139|UTS2|protein_coding|CODING|NM_021995.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.11926 rs141260595 -0.693132 0.351638 92 1210 1432 MODIFIER 22 CODING PER3 T protein_coding NM_001289862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7904247 C T 0 228 0 0.9796 0.9762 0.9654 1 0.9513 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,21,31 UTR_3_PRIME(MODIFIER||1432||1210|PER3|protein_coding|CODING|NM_001289862.1|22|T),DOWNSTREAM(MODIFIER||3425||139|UTS2|protein_coding|CODING|NM_021995.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs228677 -0.693147 0.000769334 56 1210 1660 MODIFIER 22 CODING PER3 A protein_coding NM_001289862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7904475 G A 0 228 0 0.9796 0.9762 0.9654 1 0.9513 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,5,6 UTR_3_PRIME(MODIFIER||1660||1210|PER3|protein_coding|CODING|NM_001289862.1|22|A),DOWNSTREAM(MODIFIER||3197||139|UTS2|protein_coding|CODING|NM_021995.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.950952 0 . rs228678 -0.676189 0.760674 11 S89N 139 aGt/aAt MODERATE 4 MISSENSE CODING UTS2 T protein_coding NM_021995.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7909737 C T 0 222 0 0.0552 0.1128 0.2075 0.2808 0.0179 0.0481 0.051317 0.0367636 0.0293091 1 514 10032 4092 2426 78 1998 53 871 2 10304 120798 11496 8616 6602 66416 902 16462 0.965746 0 . 0 . 117 25,25,20,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S89N|139|UTS2|protein_coding|CODING|NM_021995.2|4|T),DOWNSTREAM(MODIFIER||4497||1210|PER3|protein_coding|CODING|NM_001289862.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.707193 rs2890565,rs386576415 -0.693147 0.625602 117 T21M 139 aCg/aTg MODERATE 1 MISSENSE CODING UTS2 A protein_coding NM_021995.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7913430 G A 0 222 0 0.4259 0.4784 0.4092 0.3522 0.5706 0.6339 0.474126 0.536983 0.569186 1 4877 63477 3452 3046 2983 38240 513 10366 2 10404 121386 11578 8638 6612 66734 908 16512 0.724905 0 . 0 . 122 35,30,23,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T21M|139|UTS2|protein_coding|CODING|NM_021995.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.820753 rs228648 -0.693147 0.594927 122 R16Q 139 cGg/cAg MODERATE 1 MISSENSE CODING UTS2 T protein_coding NM_021995.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 7913445 C T 0 222 0 0.0719 0.0851 0.0994 0.0357 0.1829 0.0429 0.0830685 0.145394 0.177326 1 816 16430 728 330 1864 11835 118 739 2 10406 121400 11578 8654 6610 66734 908 16510 0.945015 0 . 0 . 122 28,21,27,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R16Q|139|UTS2|protein_coding|CODING|NM_021995.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996275 rs13306061 -0.693147 0.0570155 122 P348 782 ccA/ccG LOW 5 SILENT CODING SLC45A1 G protein_coding NM_001080397.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8390495 A G 0 228 0 0.7368 0.7764 0.7824 0.8482 0.7366 0.7924 0.746812 0.743639 0.742014 2 7051 88310 8782 7128 5465 46469 656 12759 2 9292 114794 11224 8362 6384 62316 856 16360 0 . 0 . 0 66 0,0,42,21 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P348|782|SLC45A1|protein_coding|CODING|NM_001080397.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058619 -0.693147 0.00992796 66 782 96 MODIFIER 9 CODING SLC45A1 A protein_coding NM_001080397.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8404169 T A 0 218 0 0.9871 0.9966 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,3,6 UTR_3_PRIME(MODIFIER||96||782|SLC45A1|protein_coding|CODING|NM_001080397.2|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.924584 0 . rs6685844 -0.662043 0.067912 10 1566 2212 MODIFIER 23 CODING RERE T protein_coding NM_001042681.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8412935 C T 0 228 0 0.298 0.5 0.5634 0.8413 0.4712 0.4059 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 98 0,0,61,26 UTR_3_PRIME(MODIFIER||2212||1566|RERE|protein_coding|CODING|NM_001042681.1|23|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386617835,rs8627 -0.693147 0.0191066 98 1566 2158 MODIFIER 23 CODING RERE G protein_coding NM_001042681.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8412989 A G 0 228 0 0.9463 0.8488 0.7911 0.9286 0.7068 0.8221 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,34,49 UTR_3_PRIME(MODIFIER||2158||1566|RERE|protein_coding|CODING|NM_001042681.1|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1064826 -0.693147 0.415539 95 R1317 1566 cgG/cgT LOW 20 SILENT CODING RERE A protein_coding NM_001042681.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8418644 C A 0 228 0 0.8638 0.7975 0.7795 0.8978 0.669 0.7495 0.835698 0.730781 0.677382 2 7845 81288 8803 7478 3227 42521 570 10844 2 9332 112568 11092 8414 5618 62648 790 14674 0 . 0 . COSM681943 84 0,0,53,26 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgT|R1317|1566|RERE|protein_coding|CODING|NM_001042681.1|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11121172 -0.693147 0.84437 84 R1315 1566 cgA/cgG LOW 20 SILENT CODING RERE C protein_coding NM_001042681.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8418650 T C 0 228 0 0.8691 0.8001 0.7795 0.8998 0.671 0.7515 0.841648 0.733863 0.678979 2 7919 81503 8820 7495 3280 42710 577 10702 2 9384 112814 11114 8432 5720 62858 802 14504 0 . 0 . 0 85 0,0,53,28 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R1315|1566|RERE|protein_coding|CODING|NM_001042681.1|20|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058766 -0.693147 0.811171 85 P825 1566 ccG/ccA LOW 18 SILENT CODING RERE T protein_coding NM_001042681.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8421092 C T 0 28.5 0 0.1899 0.4579 0.5115 0.8353 0.4553 0.3957 0.201535 0.327534 0.389826 1 81 1130 60 151 5 739 9 85 2 316 2128 94 174 10 1316 18 200 1 0 . 0 COSM426746 3 0,1,2,0 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P825|1566|RERE|protein_coding|CODING|NM_001042681.1|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2784735 -0.453602 0.38 3 P788 1566 ccA/ccG LOW 18 SILENT CODING RERE C protein_coding NM_001042681.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 8421203 T C 0 152 0 0.8411 0.7999 0.7925 0.9206 0.6819 0.7464 0.818445 0.729167 0.684037 2 1384 7998 298 659 141 4723 62 731 2 1656 10642 364 716 208 6648 80 970 0 . 0 . COSM426747 8 0,0,7,1 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P788|1566|RERE|protein_coding|CODING|NM_001042681.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs13596 -0.651104 0.878874 8 M68L 313 Atg/Ctg MODERATE 2 MISSENSE CODING CA6 C protein_coding NM_001270500.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9009444 A C 0 228 0 0.5598 0.5014 0.4712 0.4127 0.5358 0.5 0.545393 0.531139 0.523837 2 5577 59270 4301 3675 3592 34183 442 7500 2 10344 120770 11478 8578 6548 66434 898 16490 1 0 . 0 COSM1599877,COSM1599878 44 1,0,23,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ctg|M68L|313|CA6|protein_coding|CODING|NM_001270500.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274328 -0.693145 0.800043 44 G70A 313 gGc/gCc MODERATE 2 MISSENSE CODING CA6 C protein_coding NM_001270500.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9009451 G C 0 228 0 0.0053 0.0946 0.0461 0.1647 0.1054 0.1667 0.0208806 0.0701215 0.0953488 2 191 11169 411 1530 506 5782 92 2657 2 10352 120846 11532 8602 6542 66432 896 16490 1 0 . 0 . 45 1,0,23,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G70A|313|CA6|protein_coding|CODING|NM_001270500.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274329 -0.693145 0.872244 45 G76 313 ggG/ggC LOW 2 SILENT CODING CA6 C protein_coding NM_001270500.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9009470 G C 0 228 0 0.5946 0.2622 0.1037 0.1647 0.1213 0.1708 0.492056 0.239351 0.109884 2 5180 17533 699 1535 542 6668 111 2798 2 10286 120564 11532 8594 6532 66236 894 16490 1 0 . 0 . 43 1,0,18,19 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G76|313|CA6|protein_coding|CODING|NM_001270500.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274330 -0.693141 0.0263275 43 S90G 313 Agc/Ggc MODERATE 3 MISSENSE CODING CA6 G protein_coding NM_001270500.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9017204 A G 0 222 0 0.1135 0.3438 0.3919 0.5575 0.2913 0.455 0.159101 0.249808 0.296279 1 1602 39041 5121 4812 1674 19046 298 6488 2 10234 117682 11440 8584 6482 65410 860 14672 0.931063 0 . 0 . 58 23,10,15,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S90G|313|CA6|protein_coding|CODING|NM_001270500.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93699 rs2274333 -0.692562 0.364723 58 N256 313 aaC/aaT LOW 7 SILENT CODING CA6 T protein_coding NM_001270500.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9030964 C T 0 222 0 0.1165 0.2885 0.2983 0.5357 0.2097 0.3405 0.162279 0.190835 0.205465 1 1628 30231 3843 4732 1013 13561 222 5232 2 10406 121390 11576 8634 6614 66740 908 16512 0.993982 0 . 0 . 173 53,39,42,25 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N256|313|CA6|protein_coding|CODING|NM_001270500.1|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.726849 rs3737665 -0.693147 0.688372 173 G287E 313 gGg/gAg MODERATE 8 MISSENSE CODING CA6 A protein_coding NM_001270500.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9034421 G A 0 222 0 0.3222 0.4601 0.4265 0.6815 0.3887 0.5153 0.330849 0.348405 0.356133 1 803 13404 798 1026 504 6199 105 3969 2 1742 25088 1430 1520 1250 12218 200 6728 0.458159 0 . 0 . 96 27,11,26,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G287E|313|CA6|protein_coding|CODING|NM_001270500.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.784097 rs3765964 -0.693147 0.409389 96 501 404 MODIFIER 12 CODING SLC2A5 T protein_coding NM_003039.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9097241 C T 0 95 0 0.5893 0.49 0.3804 0.6657 0.3549 0.3916 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||404||501|SLC2A5|protein_coding|CODING|NM_003039.2|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5840 -0.556411 0.27062 4 501 394 MODIFIER 12 CODING SLC2A5 G protein_coding NM_003039.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9097251 A G 0 99 0 0.5893 0.491 0.3818 0.6696 0.3549 0.3916 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||394||501|SLC2A5|protein_coding|CODING|NM_003039.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1063137 -0.556411 0.27062 4 R218C 335 Cgc/Tgc MODERATE 3 MISSENSE CODING GPR157 A protein_coding NM_024980.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9165685 G A 0 222 0 0.0113 0.147 0.2651 0.1905 0.2147 0.1319 0.0499319 0.162156 0.219651 1 435 24341 3695 1729 1480 14134 167 2701 2 9394 109372 10246 7822 5292 61766 764 14088 0.985884 0 . 0 . 138 25,33,25,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R218C|335|GPR157|protein_coding|CODING|NM_024980.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.594702 rs72637739 -0.693147 0.250961 138 A223 802 gcG/gcA LOW 3 SILENT CODING H6PD A protein_coding NM_001282587.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9307033 G A 0 222 0 0.1074 0.2226 0.2622 0.4038 0.2445 0.1411 0.15842 0.211595 0.238837 1 1532 27113 2675 3636 1064 15486 204 2516 2 10396 121312 11566 8620 6614 66700 906 16510 0.985111 0 . 0 . 86 28,10,28,11 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A223|802|H6PD|protein_coding|CODING|NM_001282587.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972916 rs7524046 -0.693144 0.640443 86 A258 802 gcT/gcC LOW 3 SILENT CODING H6PD C protein_coding NM_001282587.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9307138 T C 0 222 0 0.2867 0.2758 0.281 0.4196 0.2445 0.1411 0.302996 0.261033 0.239535 1 3120 28978 2748 3805 1060 15512 207 2526 2 10390 121256 11564 8622 6594 66672 902 16512 0.763353 0 . 0 . 76 17,23,7,19 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A258|802|H6PD|protein_coding|CODING|NM_001282587.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939157 rs11121350 -0.692976 0.115579 76 R464Q 802 cGg/cAg MODERATE 5 MISSENSE CODING H6PD A protein_coding NM_001282587.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9323910 G A 0 221 0 0.4932 0.3896 0.3732 0.4812 0.2485 0.3119 0.457785 0.306628 0.229186 1 4767 34468 3880 4005 1514 15472 237 4593 2 10318 120890 11548 8622 6610 66390 904 16498 0.476761 0 uncertain 0 . 28 3,3,11,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R464Q|802|H6PD|protein_coding|CODING|NM_001282587.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.901075 rs6688832 -0.692067 0.0795877 28 L132 273 ctC/ctT LOW 2 SILENT CODING SPSB1 T protein_coding NM_025106.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9416346 C T 0 222 0 0.0651 0.1971 0.1758 0.2798 0.3161 0.183 0.0966863 0.230432 0.298953 1 948 30549 1409 2576 2147 19961 246 3262 2 10288 120506 11546 8618 6610 66178 896 16370 0.673719 0 . 0 . 190 50,40,44,39 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L132|273|SPSB1|protein_coding|CODING|NM_025106.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998505 rs3795309 -0.693147 0.156945 190 273 208 MODIFIER 3 CODING SPSB1 G protein_coding NM_025106.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9427842 A G 0 89 0 0.121 0.3534 0.4582 0.3601 0.4493 0.4877 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.732319 0 . 0 . 19 0,13,1,5 UTR_3_PRIME(MODIFIER||208||273|SPSB1|protein_coding|CODING|NM_025106.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.214711 rs2275458 -0.616816 0.105076 19 273 235 MODIFIER 3 CODING SPSB1 A protein_coding NM_025106.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9427869 G A 0 16.4 0 0.3722 0.6488 0.7406 0.6766 0.8211 0.7515 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.91051 0 . 0 . 15 0,12,1,2 UTR_3_PRIME(MODIFIER||235||273|SPSB1|protein_coding|CODING|NM_025106.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.846482 rs2275457,rs386563261 -0.511536 0.672523 15 273 714 MODIFIER 3 CODING SPSB1 T protein_coding NM_025106.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9428348 C T 0 222 0 0 0.022 0.0014 0.1032 0.001 0.0041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.797558 0 . 0 . 52 10,15,5,16 UTR_3_PRIME(MODIFIER||714||273|SPSB1|protein_coding|CODING|NM_025106.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.911684 rs76773239 -0.692352 0.23676 52 273 1135 MODIFIER 3 CODING SPSB1 A protein_coding NM_025106.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9428769 G A 0 140 0 0.8411 0.9537 0.9755 1 0.995 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||1135||273|SPSB1|protein_coding|CODING|NM_025106.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9728893 -0.662043 0.331571 9 P579L 666 cCg/cTg MODERATE 9 MISSENSE CODING TMEM201 T protein_coding NM_001130924.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9670834 C T 0 228 0 0.5008 0.6711 0.7651 0.6468 0.8022 0.7249 0.558526 0.730837 0.805783 2 1086 13992 309 360 40 6275 137 5785 2 1954 18556 384 574 54 7752 176 7662 1 0 . 0 . 86 1,0,24,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P579L|666|TMEM201|protein_coding|CODING|NM_001130924.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4926472 -0.693147 0.00738427 86 666 638 MODIFIER 11 CODING TMEM201 A protein_coding NM_001130924.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9673779 C A 0 9.7 0 0.8828 0.7987 0.902 0.6716 0.8062 0.7352 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||638||666|TMEM201|protein_coding|CODING|NM_001130924.2|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4450053 -0.379885 0 1 666 1031 MODIFIER 11 CODING TMEM201 G protein_coding NM_001130924.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9674172 C G 0 32.6 0 0.2186 0.2161 0.1254 0.5476 0.0109 0.1462 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1031||666|TMEM201|protein_coding|CODING|NM_001130924.2|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11121452 -0.379885 0 2 1044 404 MODIFIER 24 CODING PIK3CD C protein_coding NM_005026.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9787508 T C 0 228 0 0.9864 0.9171 0.8213 0.9633 0.9046 0.8569 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 78 0,0,41,34 UTR_3_PRIME(MODIFIER||404||1044|PIK3CD|protein_coding|CODING|NM_005026.3|24|C),DOWNSTREAM(MODIFIER||1571||981|CLSTN1|protein_coding|CODING|NM_001009566.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1135426 -0.693147 0.605649 78 1044 736 MODIFIER 24 CODING PIK3CD T protein_coding NM_005026.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9787840 G T 0 40.3 0 0.1384 0.3636 0.4366 0.5208 0.5636 0.2485 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,0,3 UTR_3_PRIME(MODIFIER||736||1044|PIK3CD|protein_coding|CODING|NM_005026.3|24|T),DOWNSTREAM(MODIFIER||1239||981|CLSTN1|protein_coding|CODING|NM_001009566.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1135427 -0.511536 0.470313 4 981 87 MODIFIER 1 CODING CLSTN1 C protein_coding NM_001009566.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9883878 T C 0 23.7 0 0.9992 0.9998 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 START_GAINED(LOW||||981|CLSTN1|protein_coding|CODING|NM_001009566.2|1|C),UTR_5_PRIME(MODIFIER||87||981|CLSTN1|protein_coding|CODING|NM_001009566.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6686034 -0.379885 0 2 211 3747 MODIFIER 8 CODING LZIC A protein_coding NM_001316974.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 9986710 G A 0 9.7 0 0.8147 0.9495 0.9885 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3747||211|LZIC|protein_coding|CODING|NM_001316974.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2788606 -0.379885 0 1 1302 272 MODIFIER 1 CODING UBE4B T protein_coding NM_001105562.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10093457 C T 0 148 0 0.8722 0.4475 0.2017 0.372 0.1769 0.4039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,0 UTR_5_PRIME(MODIFIER||272||1302|UBE4B|protein_coding|CODING|NM_001105562.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7528979 -0.636426 0.965379 8 S984 1302 agT/agC LOW 22 SILENT CODING UBE4B C protein_coding NM_001105562.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10218439 T C 0 228 0 0.8033 0.3658 0.1873 0.2956 0.1392 0.2065 0.667726 0.313471 0.131977 2 7223 24636 1398 2572 1055 9023 149 3216 2 10404 121384 11576 8646 6614 66732 906 16506 1 0 . 0 COSM146388 161 1,0,86,58 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S984|1302|UBE4B|protein_coding|CODING|NM_001105562.2|22|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2273299 -0.693147 0.480235 161 A95 1770 gcC/gcG LOW 4 SILENT CODING KIF1B G protein_coding NM_015074.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10318652 C G 0 222 0 0.056 0.23 0.3199 0.2887 0.3052 0.2638 0.0914662 0.22728 0.29686 1 892 32637 4076 2568 1947 19164 235 3755 2 10404 121378 11572 8636 6614 66734 908 16510 0.833248 255 other 0 COSM146389,COSM146390 117 20,25,25,27 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A95|1770|KIF1B|protein_coding|CODING|NM_015074.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.963875 rs12402052 -0.693147 0.189297 117 T1721 1770 acC/acA LOW 46 SILENT CODING KIF1B A protein_coding NM_015074.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10435324 C A 0 222 0 0.0575 0.2316 0.3199 0.2827 0.3091 0.272 0.0937358 0.230509 0.300581 1 901 32974 4092 2501 1958 19404 236 3882 2 10404 121378 11574 8636 6612 66732 908 16512 0.400897 255 other 0 COSM146393 71 16,14,24,10 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T1721|1770|KIF1B|protein_coding|CODING|NM_015074.3|46|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997266 rs11121552 -0.693132 0.362682 71 1770 2042 MODIFIER 47 CODING KIF1B T protein_coding NM_015074.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10438687 C T 0 86 0 0.7973 0.5465 0.5216 0.3591 0.4851 0.4816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.163881 0 . 0 . 18 0,11,0,7 UTR_3_PRIME(MODIFIER||2042||1770|KIF1B|protein_coding|CODING|NM_015074.3|47|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.0503002 rs1536262,rs386536222 -0.636426 0.669559 18 1770 2247 MODIFIER 47 CODING KIF1B A protein_coding NM_015074.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10438892 G A 0 46.3 0 0.3351 0.3337 0.3732 0.3462 0.338 0.2863 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2247||1770|KIF1B|protein_coding|CODING|NM_015074.3|47|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1002076 -0.453602 0.22 2 1770 3911 MODIFIER 47 CODING KIF1B G protein_coding NM_015074.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10440556 A G 0 102 0 0.3661 0.3488 0.3833 0.3462 0.3628 0.2894 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||3911||1770|KIF1B|protein_coding|CODING|NM_015074.3|47|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1138791 -0.556411 0.879194 4 D40 483 gaT/gaC LOW 3 SILENT CODING PGD C protein_coding NM_002631.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10460485 T C 0 222 0 0.0658 0.2338 0.3199 0.2817 0.3111 0.271 0.0975942 0.2332 0.302674 1 949 33219 4120 2535 1963 19546 237 3869 2 10400 121314 11572 8636 6612 66692 904 16498 0.999845 0 . 0 COSM146394 92 22,29,20,15 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D40|483|PGD|protein_coding|CODING|NM_002631.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.934116 rs1049887 -0.693136 0.22664 92 D244 483 gaC/gaT LOW 8 SILENT CODING PGD T protein_coding NM_002631.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10473196 C T 0 222 0 0.3457 0.3351 0.3732 0.3403 0.338 0.2853 0.329778 0.32831 0.327558 1 3431 39157 4503 3225 2263 21189 279 4267 2 10406 121352 11568 8634 6608 66720 904 16512 0.947501 0 . 0 COSM146395 142 39,32,35,22 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D244|483|PGD|protein_coding|CODING|NM_002631.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987934 rs2229687 -0.693147 0.264073 142 138 248 MODIFIER 5 CODING APITD1 G protein_coding NM_199294.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10502710 A G 0 117 0 0.7095 0.8207 0.8069 0.8631 0.9314 0.8231 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,0,7 UTR_3_PRIME(MODIFIER||248||138|APITD1|protein_coding|CODING|NM_199294.2|5|G),INTRON(MODIFIER||||164|APITD1-CORT|protein_coding|CODING|NM_198544.3|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2847337,rs386575227 -0.636426 0.399755 7 A129 164 gcC/gcT LOW 5 SILENT CODING APITD1-CORT T protein_coding NM_198544.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10511544 C T 0 222 0 0.0212 0.2875 0.3112 0.4871 0.3907 0.319 0.0797365 0.28966 0.397161 1 704 44020 3755 4226 2585 27016 380 5354 2 9736 119646 11438 8614 6552 65936 896 16474 0.918902 0 . 0 COSM1332194,COSM1332195 74 20,14,23,13 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A129|164|APITD1-CORT|protein_coding|CODING|NM_198544.3|5|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A70|105|CORT|protein_coding|CODING|NM_001302.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.760312 rs628462 -0.693139 0.628972 74 A70 105 gcC/gcT LOW 2 SILENT CODING CORT T protein_coding NM_001302.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10511544 C T 0 222 0 0.0212 0.2875 0.3112 0.4871 0.3907 0.319 0.0797365 0.28966 0.397161 1 704 44020 3755 4226 2585 27016 380 5354 2 9736 119646 11438 8614 6552 65936 896 16474 0.918902 0 . 0 COSM1332194,COSM1332195 74 20,14,23,13 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A129|164|APITD1-CORT|protein_coding|CODING|NM_198544.3|5|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A70|105|CORT|protein_coding|CODING|NM_001302.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.760312 rs628462 -0.693139 0.628972 74 S144 164 tcT/tcC LOW 5 SILENT CODING APITD1-CORT C protein_coding NM_198544.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10511589 T C 0 228 0 0.8759 0.8676 0.8213 0.8591 0.9344 0.8292 0.906136 0.926912 0.937544 2 8865 107483 8841 7104 5653 62106 816 14098 2 9884 119896 11422 8624 6550 66040 898 16478 0 . 0 . COSM146398,COSM146397 70 0,0,39,26 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S144|164|APITD1-CORT|protein_coding|CODING|NM_198544.3|5|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S85|105|CORT|protein_coding|CODING|NM_001302.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs666103 -0.693147 0.109758 70 S85 105 tcT/tcC LOW 2 SILENT CODING CORT C protein_coding NM_001302.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10511589 T C 0 228 0 0.8759 0.8676 0.8213 0.8591 0.9344 0.8292 0.906136 0.926912 0.937544 2 8865 107483 8841 7104 5653 62106 816 14098 2 9884 119896 11422 8624 6550 66040 898 16478 0 . 0 . COSM146398,COSM146397 70 0,0,39,26 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S144|164|APITD1-CORT|protein_coding|CODING|NM_198544.3|5|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S85|105|CORT|protein_coding|CODING|NM_001302.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs666103 -0.693147 0.109758 70 D338 377 gaC/gaT LOW 9 SILENT CODING PEX14 T protein_coding NM_004565.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10689924 C T 0 222 0 0.059 0.0843 0.036 0.13 0.0368 0.1544 0.0586097 0.0438394 0.0362791 1 621 7065 369 967 272 2534 48 2254 2 9590 111854 10468 8114 5076 61760 818 16028 0.695969 2 benign 0 . 85 17,17,18,24 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D338|377|PEX14|protein_coding|CODING|NM_004565.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931723 rs2128414 -0.693146 0.0119826 85 1759 1157 MODIFIER 21 CODING CASZ1 A protein_coding NM_001079843.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10697842 G A 0 222 0 0 0.0053914 0 0.0248 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.844218 0 . 0 . 80 20,19,19,18 UTR_3_PRIME(MODIFIER||1157||1759|CASZ1|protein_coding|CODING|NM_001079843.2|21|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.68935 rs142845529 -0.693141 0.0488106 80 F1071 1759 ttT/ttC LOW 16 SILENT CODING CASZ1 G protein_coding NM_001079843.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10708142 A G 0 222 0 0.5431 0.3293 0.1945 0.2421 0.2068 0.3517 0.435321 0.267235 0.18152 1 2825 16094 964 1019 570 7098 112 3506 2 5464 47832 3094 3434 1516 25480 350 8494 0.817545 0 . 0 . 131 45,16,26,15 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1071|1759|CASZ1|protein_coding|CODING|NM_001079843.2|16|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999994 rs386613133,rs778228 -0.693145 0.0448475 131 A978 1759 gcG/gcA LOW 14 SILENT CODING CASZ1 T protein_coding NM_001079843.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10709441 C T 0 222 0 0.5416 0.3129 0.1427 0.2321 0.1839 0.3405 0.445608 0.267662 0.176744 1 4115 23375 1066 1601 923 10754 169 4747 2 8236 93578 8334 6858 3772 51708 672 13998 0.978736 0 . 0 COSM423354 87 21,24,12,21 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A978|1759|CASZ1|protein_coding|CODING|NM_001079843.2|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962061 rs284299 -0.693127 0.165586 87 S783 1759 tcA/tcG LOW 11 SILENT CODING CASZ1 C protein_coding NM_001079843.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10713765 T C 0 94 0 0.7194 0.5451 0.4539 0.3095 0.5646 0.5971 0.662844 0.586903 0.548285 1 6148 61505 4879 2531 4130 35449 476 7892 2 9146 112898 11300 8370 6446 63526 816 13294 0.275467 0 . 0 COSM1332224 19 4,8,2,5 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S783|1759|CASZ1|protein_coding|CODING|NM_001079843.2|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.649117 rs284294 -0.636426 0.687651 19 D49 1759 gaC/gaT LOW 5 SILENT CODING CASZ1 A protein_coding NM_001079843.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 10725498 G A 0 222 0 0.2216 0.1795 0.1412 0.1498 0.169 0.1912 0.162791 0.156044 0.15262 1 1779 20295 2036 1336 1680 10385 187 2892 2 9276 117076 11372 8374 6350 64490 852 16362 0.894194 0 . 0 . 124 45,18,41,13 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D49|1759|CASZ1|protein_coding|CODING|NM_001079843.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959641 rs284322,rs386575076 -0.693147 0.0945162 124 C617 823 tgC/tgT LOW 12 SILENT CODING C1orf127 A protein_coding NM_001170754.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11008341 G A 0 222 0 0.3699 0.1777 0.1254 0.2093 0.0557 0.0481 0.332047 0.140474 0.0423256 1 3465 10898 931 1809 547 3118 96 932 2 10348 120918 11570 8636 6614 66340 898 16512 0.894213 0 . 0 . 105 19,29,16,28 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C617|823|C1orf127|protein_coding|CODING|NM_001170754.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99871 rs10864483 -0.693146 0.0878389 105 G565 823 ggC/ggG LOW 12 SILENT CODING C1orf127 C protein_coding NM_001170754.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11008497 G C 0 222 0 0.4009 0.3249 0.2867 0.2371 0.1849 0.4836 0.337494 0.231124 0.176628 1 3672 31951 4166 2198 1711 12459 251 7494 2 10164 120062 11496 8588 6594 65854 902 16464 0.976723 0 . 0 . 97 31,14,30,13 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G565|823|C1orf127|protein_coding|CODING|NM_001170754.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.69595 rs1281017 -0.693146 0.110051 97 P499 823 ccA/ccG LOW 12 SILENT CODING C1orf127 C protein_coding NM_001170754.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11008695 T C 0 222 0 0.0522 0.2119 0.2565 0.2321 0.1421 0.4468 0.061734 0.110411 0.135349 1 611 24615 3870 2139 1363 9826 203 6603 2 10320 120602 11556 8620 6598 66304 894 16310 0.525124 0 . 0 . 200 49,37,45,45 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P499|823|C1orf127|protein_coding|CODING|NM_001170754.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.59286 rs17036032 -0.693147 0.0140331 200 A353T 823 Gcc/Acc MODERATE 10 MISSENSE CODING C1orf127 T protein_coding NM_001170754.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11014118 C T 0 222 0 0.0666 0.2194 0.2752 0.2331 0.164 0.4294 0.0758057 0.125711 0.151279 1 764 25680 4009 2143 1440 10668 219 6437 2 10404 121352 11576 8644 6614 66708 906 16500 0.711945 0 . 0 . 101 19,38,17,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A353T|823|C1orf127|protein_coding|CODING|NM_001170754.1|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974448 rs386497238,rs45537241 -0.693144 0.911933 101 I286T 823 aTt/aCt MODERATE 9 MISSENSE CODING C1orf127 G protein_coding NM_001170754.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11015165 A G 0 222 0 0.0991 0.2282 0.2752 0.2341 0.164 0.4294 0.100091 0.134246 0.151744 1 1021 25940 4021 2142 1418 10676 220 6442 2 10402 121354 11568 8636 6614 66718 906 16510 0.999741 0 . 0 . 94 23,19,21,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I286T|823|C1orf127|protein_coding|CODING|NM_001170754.1|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977353 rs75130475 -0.693145 0.00325857 94 R144 823 Cgg/Agg LOW 5 SILENT CODING C1orf127 T protein_coding NM_001170754.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11024271 G T 0 222 0 0.0469 0.0897 0.0836 0.2302 0.0527 0.045 0.0408534 0.0415962 0.0419767 1 461 7507 832 2001 481 2702 74 956 2 10256 120544 11436 8606 6552 66402 904 16388 0.363597 0 . 0 . 131 33,28,30,20 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R144|823|C1orf127|protein_coding|CODING|NM_001170754.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894929 rs11121662 -0.693147 0.000615088 131 686 225 MODIFIER 11 CODING MASP2 G protein_coding NM_006610.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11086717 A G 0 101 0 0.3759 0.7097 0.8026 0.8651 0.84 0.8006 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 0 . 0 . 7 2,0,3,1 UTR_3_PRIME(MODIFIER||225||686|MASP2|protein_coding|CODING|NM_006610.3|11|G),DOWNSTREAM(MODIFIER||1168||414|TARDBP|protein_coding|CODING|NM_007375.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.75 rs1033638,rs386512253 -0.556411 0.354838 7 S493 686 tcC/tcT LOW 11 SILENT CODING MASP2 A protein_coding NM_006610.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11087524 G A 0 222 0 0.2973 0.6875 0.7983 0.8651 0.84 0.7965 0.361098 0.673151 0.833023 1 3631 95363 9614 7506 5469 55317 734 13092 2 10404 121404 11576 8652 6614 66738 908 16512 0.796672 0 . 0 . 215 63,29,51,44 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S493|686|MASP2|protein_coding|CODING|NM_006610.3|11|A),DOWNSTREAM(MODIFIER||1975||414|TARDBP|protein_coding|CODING|NM_007375.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.839345 rs1782455 -0.693147 0.121315 215 V377A 686 gTg/gCg MODERATE 9 MISSENSE CODING MASP2 G protein_coding NM_006610.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11090897 A G 0 222 0 0.171 0.1184 0.0461 0.1984 0.0199 0.1176 0.128007 0.0553591 0.0181395 1 1358 6408 227 1831 62 1323 43 1564 2 10402 121238 11566 8626 6612 66662 904 16466 0.912916 0 . 0 . 98 19,32,10,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V377A|686|MASP2|protein_coding|CODING|NM_006610.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.877422 rs2273346,rs386439513 -0.693141 0.150219 98 A297 302 gcC/gcA LOW 8 SILENT CODING SRM T protein_coding NM_003132.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11114940 G T 0 222 0 0.2481 0.1677 0.1167 0.1806 0.0249 0.229 0.207217 0.0851915 0.0226744 1 2157 10275 1666 1480 322 1806 75 2769 2 10026 116416 11388 8492 6146 64382 840 15142 0.26426 0 . 0 COSM423425 57 3,18,9,20 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A297|302|SRM|protein_coding|CODING|NM_003132.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974775 rs13616 -0.693079 0.0234195 57 D282 302 gaC/gaT LOW 7 SILENT CODING SRM A protein_coding NM_003132.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11115061 G A 0 118 0 0.0038 0.0335 0.0476 0.0417 0.001 0.089 0.00181571 0.000691988 0.000116279 1 28 2197 755 336 0 20 12 1046 2 9592 117384 11410 8486 6570 64112 866 16348 0.895781 0 . 0 . 10 1,3,4,2 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D282|302|SRM|protein_coding|CODING|NM_003132.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.00775 0.952347 0 0.503877 rs11540046 -0.616816 0.496552 10 S34 302 tcA/tcG LOW 1 SILENT CODING SRM C protein_coding NM_003132.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11119899 T C 0 190 0 1 1 1 1 1 1 0 . 0 2 6714 102068 10572 7766 5264 55554 698 15500 2 6714 102068 10572 7766 5264 55554 698 15500 0 . 0 . 0 10 0,0,1,8 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S34|302|SRM|protein_coding|CODING|NM_003132.2|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7545802 -0.662043 0.560036 10 R723 885 cgC/cgT LOW 20 SILENT CODING EXOSC10 A protein_coding NM_001001998.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11132217 G A 0 228 0 0.2035 0.6062 0.755 0.7837 0.7416 0.7229 0.288924 0.585883 0.738023 2 2804 85236 9332 6878 4780 48882 643 11917 2 10402 121388 11578 8652 6614 66728 908 16506 0 . 0 . 0 67 0,0,24,33 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R723|885|EXOSC10|protein_coding|CODING|NM_001001998.2|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1130683 -0.693147 0.364135 67 R702H 885 cGt/cAt MODERATE 19 MISSENSE CODING EXOSC10 T protein_coding NM_001001998.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11134043 C T 0 222 0 0.0023 0.0333 0.0476 0.0417 0 0.091 0.00181571 0.000691988 0.000116279 1 26 2228 757 340 0 22 11 1072 2 10400 121334 11546 8654 6614 66706 906 16508 0.954281 0 . 0 . 165 61,8,52,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R702H|885|EXOSC10|protein_coding|CODING|NM_001001998.2|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.967233 rs117771172 -0.693147 0.203581 165 P463 885 ccG/ccC LOW 11 SILENT CODING EXOSC10 G protein_coding NM_001001998.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11141187 C G 0 228 0 0.5378 0.7724 0.8415 0.9405 0.7694 0.8701 0.55833 0.692603 0.761395 2 5692 94504 10293 8143 5114 50781 715 13766 2 10394 121310 11570 8652 6610 66668 906 16510 0 . 0 . 0 48 0,0,25,16 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P463|885|EXOSC10|protein_coding|CODING|NM_001001998.2|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2258621 -0.693145 0.473643 48 E74K 885 Gaa/Aaa MODERATE 2 MISSENSE CODING EXOSC10 T protein_coding NM_001001998.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11158105 C T 0 222 0 0.0061 0.0345 0.049 0.0417 0 0.091 0.00522015 0.0018453 0.000116279 1 52 2257 759 339 0 25 11 1071 2 9738 118366 11302 8574 6546 65304 884 16018 0.99922 0 . 0 . 126 54,11,30,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E74K|885|EXOSC10|protein_coding|CODING|NM_001001998.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.377816 rs62623443 -0.693147 0.0144753 126 A1823 2549 gcC/gcT LOW 39 SILENT CODING MTOR A protein_coding NM_004958.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11190730 G A 0 222 0 0.0832 0.0543 0.0504 0.0417 0 0.0869 0.0672116 0.0229929 0.000348837 1 673 2794 735 328 0 29 12 1017 2 8468 94126 7866 6756 4442 51980 666 13948 0.996129 0 . 0 . 78 10,20,12,32 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1823|2549|MTOR|protein_coding|CODING|NM_004958.3|39|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.665301 rs17848553 -0.693146 0.179187 78 A1577 2549 gcG/gcA LOW 33 SILENT CODING MTOR T protein_coding NM_004958.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11205058 C T 0 222 0 0.0635 0.5475 0.7017 0.8165 0.7356 0.6217 0.176804 0.545902 0.735 1 1652 82297 8516 7097 4792 48853 636 10751 2 10402 121396 11576 8652 6614 66734 908 16510 0.361635 0 . 0 . 96 22,18,21,22 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1577|2549|MTOR|protein_coding|CODING|NM_004958.3|33|T),INTRAGENIC(MODIFIER|||||MTOR-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.964505 rs1057079,rs386514433 -0.693146 0.733711 96 E51D 346 gaG/gaC MODERATE 1 MISSENSE CODING ANGPTL7 C protein_coding NM_021146.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11249789 G C 0 222 0 0.0885 0.0551 0.049 0.0407 0 0.0859 0.0744439 0.0254498 0.000348837 1 765 2967 784 337 0 32 12 1037 2 10382 121042 11500 8588 6596 66580 902 16494 0.957364 0 . 0 . 113 36,21,29,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E51D|346|ANGPTL7|protein_coding|CODING|NM_021146.3|1|C),INTRON(MODIFIER||||2549|MTOR|protein_coding|CODING|NM_004958.3|28|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.743732 rs28990992 -0.693147 0.146507 113 R1154 2549 cgG/cgC LOW 23 SILENT CODING MTOR G protein_coding NM_004958.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11272468 C G 0 222 0 0.0023 0.0321 0.0461 0.0417 0 0.0859 0.00181571 0.000691988 0.000116279 1 26 2187 754 341 0 20 11 1035 2 10404 121344 11572 8640 6612 66698 908 16510 0.71464 0 . 0 . 90 22,16,28,12 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R1154|2549|MTOR|protein_coding|CODING|NM_004958.3|23|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.415934 rs17036536 -0.693145 0.905823 90 N999 2549 aaC/aaT LOW 19 SILENT CODING MTOR A protein_coding NM_004958.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11288758 G A 0 228 0 0.3351 0.7005 0.8141 0.9187 0.7237 0.865 0.40059 0.617561 0.728721 2 3995 90124 10081 7955 4920 48792 702 13679 2 10398 121316 11556 8654 6600 66688 908 16512 0 . 0 . 0 191 0,0,87,85 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N999|2549|MTOR|protein_coding|CODING|NM_004958.3|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1064261 -0.693147 0.21492 191 D479 2549 gaT/gaC LOW 10 SILENT CODING MTOR G protein_coding NM_004958.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11301714 A G 0 222 0 0.2239 0.6396 0.7622 0.878 0.7237 0.7822 0.305946 0.585345 0.728488 1 3021 87002 9294 7623 4930 48782 688 12664 2 10400 121346 11576 8652 6614 66708 908 16488 0.963883 0 . 0 . 81 25,8,25,14 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D479|2549|MTOR|protein_coding|CODING|NM_004958.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.968186 rs1135172 -0.693144 0.0208653 81 2549 3099 MODIFIER 1 CODING MTOR G protein_coding NM_004958.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11322565 C G 0 37.3 0 0.093 0.5381 0.6816 0.7817 0.6899 0.6309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.574341 0 . 0 . 7 1,2,0,3 UTR_5_PRIME(MODIFIER||3099||2549|MTOR|protein_coding|CODING|NM_004958.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.861511 rs2295079 -0.511536 0.921489 7 338 904 MODIFIER 2 CODING UBIAD1 C protein_coding NM_013319.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11347092 T C 0 9.7 0 0.4539 0.2234 0.1066 0.2381 0.0437 0.1646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||904||338|UBIAD1|protein_coding|CODING|NM_013319.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3765906 -0.379885 0 1 G182S 1392 Ggc/Agc MODERATE 2 MISSENSE CODING PTCHD2 A protein_coding NM_020780.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11561593 G A 0 222 0 0.143 0.3718 0.6311 0.2718 0.659 0.3047 0.251836 0.513046 0.634152 1 1796 59718 7287 2250 3845 38946 471 5123 2 7810 107396 10840 7970 5940 60372 784 13680 0.769684 0 . 0 . 50 5,19,6,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G182S|1392|PTCHD2|protein_coding|CODING|NM_020780.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.407067 rs2817580 -0.692717 0.254826 50 A650T 1392 Gct/Act MODERATE 8 MISSENSE CODING PTCHD2 A protein_coding NM_020780.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11579470 G A 0 222 0 0.0545 0.3598 0.6556 0.2698 0.6471 0.3599 0.140238 0.460762 0.615689 1 1247 65648 8566 2267 4268 42129 536 6635 2 9782 120642 11568 8574 6614 66700 894 16510 0.535411 0 . 0 . 75 23,12,18,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A650T|1392|PTCHD2|protein_coding|CODING|NM_020780.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962566 rs2072994 -0.69311 0.300894 75 G661A 1392 gGc/gCc MODERATE 8 MISSENSE CODING PTCHD2 C protein_coding NM_020780.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11579504 G C 0 222 0 0.0908 0.1899 0.0951 0.4444 0.1054 0.2157 0.104847 0.13146 0.144307 1 1122 19614 1072 4027 795 9130 132 3336 2 9792 120616 11570 8600 6614 66632 896 16512 0.745865 0 . 0 . 74 21,17,17,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G661A|1392|PTCHD2|protein_coding|CODING|NM_020780.1|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972839 rs2072993 -0.693097 0.137674 74 P999 1392 ccG/ccA LOW 15 SILENT CODING PTCHD2 A protein_coding NM_020780.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11589911 G A 0 228 0 0.0726 0.1823 0.0994 0.4385 0.1064 0.2035 0.0897306 0.124284 0.140685 2 901 18686 976 3893 824 8816 136 3140 2 9760 120248 11552 8594 6610 66334 892 16506 0 . 0 . 0 117 0,0,75,27 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P999|1392|PTCHD2|protein_coding|CODING|NM_020780.1|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2076468 -0.693147 8.91336e-05 117 1392 19 MODIFIER 21 CODING PTCHD2 T protein_coding NM_020780.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11596762 C T 0 228 0 0.8865 0.4804 0.2003 0.499 0.17 0.4305 0.684912 0.342837 0.190314 2 1152 5886 202 442 111 1864 49 2066 2 1474 14610 794 880 316 6724 140 4282 1 0 . 0 . 49 1,0,34,12 UTR_3_PRIME(MODIFIER||19||1392|PTCHD2|protein_coding|CODING|NM_020780.1|21|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2235666 -0.693147 0.208642 49 296 15 MODIFIER 6 CODING FBXO2 C protein_coding NM_012168.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11708736 T C 0 228 0 0.348 0.505 0.6196 0.4077 0.7783 0.455 0.39555 0.628404 0.747731 2 3870 76705 6651 3493 5227 48786 586 8092 2 9810 118358 11382 8524 6496 64834 874 16438 1 0 . 0 . 147 0,1,87,48 UTR_3_PRIME(MODIFIER||15||296|FBXO2|protein_coding|CODING|NM_012168.5|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1055547 -0.693147 0.0102404 147 296 LOW 1 CODING FBXO2 G protein_coding NM_012168.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11714368 T G 0 7.9 0 0.8207 0.7991 0.8732 0.7659 0.7972 0.7536 0.820205 0.813945 0.81055 1 360 8567 86 116 0 2481 99 5425 2 456 11356 112 156 0 3232 126 7274 0.666667 0 . 0 . 8 1,5,0,2 SPLICE_SITE_REGION+INTRON(LOW||||296|FBXO2|protein_coding|CODING|NM_012168.5|1|G),UPSTREAM(MODIFIER||546||255|FBXO44|protein_coding|CODING|NM_001014765.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.5 rs2272983 -0.453602 0.26 8 255 524 MODIFIER 7 CODING FBXO44 T protein_coding NM_001014765.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11721854 C T 0 9.7 0 0.7118 0.5415 0.5389 0.4504 0.4304 0.5215 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||524||255|FBXO44|protein_coding|CODING|NM_001014765.1|7|T),UPSTREAM(MODIFIER||2296||293|FBXO6|protein_coding|CODING|NM_018438.5||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2294641 -0.379885 0 1 159 425 MODIFIER 5 CODING AGTRAP A protein_coding NM_020350.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11810674 G A 0 38.3 0 0.0477 0.2302 0.2896 0.3343 0.3111 0.2444 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||425||159|AGTRAP|protein_coding|CODING|NM_020350.4|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1128059 -0.453602 0.82 2 159 442 MODIFIER 5 CODING AGTRAP T protein_coding NM_020350.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11810691 C T 0 9.7 0 0.0477 0.2294 0.2896 0.3323 0.3091 0.2444 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||442||159|AGTRAP|protein_coding|CODING|NM_020350.4|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1128065 -0.379885 0 1 159 516 MODIFIER 5 CODING AGTRAP A protein_coding NM_020350.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11810765 T A 0 9.7 0 0.8941 0.9712 0.9942 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||516||159|AGTRAP|protein_coding|CODING|NM_020350.4|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6540993 -0.379885 0 1 P263S 1449 Ccc/Tcc MODERATE 3 MISSENSE CODING C1orf167 T protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11826630 C T 0 222 0 0.5431 0.6296 0.7752 0.7302 0.6958 0.4714 0 . 0 1 216 2887 86 109 1 1159 32 1284 2 436 4550 122 154 2 1686 44 2106 0.926598 0 . 0 . 80 17,17,28,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P263S|1449|C1orf167|protein_coding|CODING|NM_001010881.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.721455 rs6668699 -0.693145 0.561115 80 P442 1449 ccA/ccG LOW 4 SILENT CODING C1orf167 G protein_coding NM_001010881.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11827304 A G 0 228 0 0.8858 0.9681 0.987 1 1 1 0 . 0 2 563 13982 187 218 1096 4128 172 7618 2 622 14044 188 218 1096 4130 172 7618 0 . 0 . 0 61 0,0,33,21 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P442|1449|C1orf167|protein_coding|CODING|NM_001010881.1|4|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6540996 -0.693147 6.24434e-05 61 R578W 1449 Cgg/Tgg MODERATE 7 MISSENSE CODING C1orf167 T protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11831615 C T 0 222 0 0.5159 0.6963 0.8141 0.88 0.7237 0.6391 0 . 0 1 302 8817 129 184 885 2593 108 4616 2 564 13728 188 206 1140 3850 160 7620 0.895427 0 . 0 . 59 13,11,21,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R578W|1449|C1orf167|protein_coding|CODING|NM_001010881.1|7|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.906175 rs6667720 -0.693097 0.745967 59 P654H 1449 cCc/cAc MODERATE 8 MISSENSE CODING C1orf167 A protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11832289 C A 0 222 0 0.0113 0.122 0.0793 0.1052 0.1799 0.2597 0 . 0 1 32 3432 37 43 259 1066 36 1959 2 894 15972 288 482 1210 5268 184 7646 0.679751 0 . 0 . 30 2,8,7,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P654H|1449|C1orf167|protein_coding|CODING|NM_001010881.1|8|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.634421 rs61773952 -0.690438 0.0990373 30 L661 1449 ctG/ctC LOW 8 SILENT CODING C1orf167 C protein_coding NM_001010881.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11832311 G C 0 73 0 0.379 0.5685 0.7594 0.7649 0.6272 0.4264 0 . 0 1 362 8622 201 361 886 3246 117 3449 2 882 15818 278 474 1320 5194 188 7482 0.882497 0 . 0 . 28 5,13,0,8 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L661|1449|C1orf167|protein_coding|CODING|NM_001010881.1|8|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.986207 rs10779764 -0.651104 0.50952 28 W758R 1449 Tgg/Cgg MODERATE 10 MISSENSE CODING C1orf167 C protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11836628 T C 0 222 0 0.5174 0.7001 0.817 0.8839 0.7286 0.6452 0 . 0 1 462 6695 205 432 22 2700 72 2802 2 858 9704 254 478 32 3790 100 4192 0.729703 0 . 0 . 85 7,32,13,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W758R|1449|C1orf167|protein_coding|CODING|NM_001010881.1|10|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.99789 rs6699881 -0.693146 0.689301 85 R776C 1449 Cgc/Tgc MODERATE 10 MISSENSE CODING C1orf167 T protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11836682 C T 0 222 0 0.3812 0.5705 0.7594 0.7698 0.6252 0.4305 0 . 0 1 281 2495 163 290 18 1525 30 188 2 730 4192 212 384 30 2444 44 348 0.856925 0 . 0 . 75 11,20,13,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R776C|1449|C1orf167|protein_coding|CODING|NM_001010881.1|10|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.425932 rs7538516 -0.693144 0.130639 75 S824I 1449 aGc/aTc MODERATE 11 MISSENSE CODING C1orf167 T protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11838848 G T 0 222 0 0.3828 0.5707 0.7594 0.7698 0.6252 0.4294 0 . 0 1 372 8606 204 368 803 3280 120 3459 2 914 15982 292 486 1188 5288 190 7624 0.689183 0 . 0 . 94 17,23,18,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S824I|1449|C1orf167|protein_coding|CODING|NM_001010881.1|11|T),INTRAGENIC(MODIFIER|||||LOC102724659||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.728002 rs6697244 -0.693147 0.00125838 94 R920H 1449 cGt/cAt MODERATE 13 MISSENSE CODING C1orf167 A protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11839966 G A 0 222 0 0.3828 0.5699 0.7594 0.7649 0.6243 0.4315 0 . 0 1 363 7538 191 352 18 3062 89 3463 2 866 14394 274 462 28 4982 152 7630 0.984928 0 . 0 . 44 8,9,14,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R920H|1449|C1orf167|protein_coding|CODING|NM_001010881.1|13|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.721475 rs4846043 -0.69168 0.385327 44 R922Q 1449 cGg/cAg MODERATE 13 MISSENSE CODING C1orf167 A protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11839972 G A 0 222 0 0.059 0.1352 0.0821 0.1032 0.1809 0.2618 0 . 0 1 59 3145 35 39 6 973 34 1999 2 816 14198 264 440 22 4896 152 7608 0.989791 0 . 0 . 44 14,6,8,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R922Q|1449|C1orf167|protein_coding|CODING|NM_001010881.1|13|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.737728 rs41275462 -0.689466 0.478325 44 W931R 1449 Tgg/Cgg MODERATE 13 MISSENSE CODING C1orf167 C protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11839998 T C 0 228 0 0.6029 0.8798 0.9539 0.994 0.9791 0.9816 0 . 0 2 515 13301 246 417 19 4608 145 7351 2 810 14032 256 418 20 4808 152 7568 0 . 0 . 0 33 0,0,11,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W931R|1449|C1orf167|protein_coding|CODING|NM_001010881.1|13|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4846044 -0.693097 0.347452 33 A1035 1449 gcC/gcT LOW 15 SILENT CODING C1orf167 T protein_coding NM_001010881.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11844330 C T 0 222 0 0.1415 0.498 0.7334 0.7649 0.6173 0.4151 0 . 0 1 191 7905 191 370 747 3089 110 3207 2 864 14696 274 486 1086 5016 176 6794 0.815493 0 . 0 . 95 23,16,29,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1035|1449|C1orf167|protein_coding|CODING|NM_001010881.1|15|T),DOWNSTREAM(MODIFIER||1457||656|MTHFR|protein_coding|CODING|NM_005957.4||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.838731 rs10864543 -0.693146 0.0643544 95 656 2978 MODIFIER 12 CODING MTHFR T protein_coding NM_005957.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11847759 C T 0 169 0 0.354 0.5585 0.7421 0.7738 0.6252 0.4141 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.44315 0 . 0 . 25 11,4,5,5 UTR_3_PRIME(MODIFIER||2978||656|MTHFR|protein_coding|CODING|NM_005957.4|12|T),INTRON(MODIFIER||||1449|C1orf167|protein_coding|CODING|NM_001010881.1|17|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.946121 rs3737966,rs386491612 -0.670168 0.321667 25 656 2598 MODIFIER 12 CODING MTHFR A protein_coding NM_005957.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11848139 G A 0 222 0 0.0234 0.1268 0.0865 0.1022 0.1859 0.2597 0 . 0 1 46 2839 33 41 220 915 35 1549 2 866 11990 268 474 1080 4146 148 5008 0.999714 0 . 0 . 93 27,24,15,16 UTR_3_PRIME(MODIFIER||2598||656|MTHFR|protein_coding|CODING|NM_005957.4|12|A),INTRON(MODIFIER||||1449|C1orf167|protein_coding|CODING|NM_001010881.1|18|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.986873 rs11559040 -0.69311 0.217212 93 656 1858 MODIFIER 12 CODING MTHFR G protein_coding NM_005957.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11848879 A G 0 209 0 0.7504 0.9305 0.9741 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,1,26 UTR_3_PRIME(MODIFIER||1858||656|MTHFR|protein_coding|CODING|NM_005957.4|12|G),INTRON(MODIFIER||||1449|C1orf167|protein_coding|CODING|NM_001010881.1|20|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2077360 -0.693021 0.252223 27 R1432G 1449 Aga/Gga MODERATE 21 MISSENSE CODING C1orf167 G protein_coding NM_001010881.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11849447 A G 0 228 0 0.7595 0.9329 0.9741 1 1 1 0 . 0 2 727 14795 286 486 344 5136 156 7660 2 906 14988 290 486 344 5142 158 7662 0 . 0 . 0 97 0,0,27,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R1432G|1449|C1orf167|protein_coding|CODING|NM_001010881.1|21|G),UTR_3_PRIME(MODIFIER||1290||656|MTHFR|protein_coding|CODING|NM_005957.4|12|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs868014 -0.693147 0.48367 97 656 1290 MODIFIER 12 CODING MTHFR G protein_coding NM_005957.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11849447 A G 0 228 0 0.7595 0.9329 0.9741 1 1 1 0 . 0 2 727 14795 286 486 344 5136 156 7660 2 906 14988 290 486 344 5142 158 7662 0 . 0 . 0 97 0,0,27,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R1432G|1449|C1orf167|protein_coding|CODING|NM_001010881.1|21|G),UTR_3_PRIME(MODIFIER||1290||656|MTHFR|protein_coding|CODING|NM_005957.4|12|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs868014 -0.693147 0.48367 97 656 372 MODIFIER 12 CODING MTHFR G protein_coding NM_005957.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11850365 T G 0 158 0 0.475 0.6284 0.8127 0.7738 0.6769 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.412317 0 . 0 . 39 22,0,15,2 UTR_3_PRIME(MODIFIER||372||656|MTHFR|protein_coding|CODING|NM_005957.4|12|G),DOWNSTREAM(MODIFIER||723||1449|C1orf167|protein_coding|CODING|NM_001010881.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.913711 rs4846049 -0.690438 0.0202086 39 F435 656 ttC/ttT LOW 8 SILENT CODING MTHFR A protein_coding NM_005957.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11854457 G A 0 228 0 0.6558 0.903 0.9683 0.996 0.997 0.998 0.682705 0.890512 0.996977 2 7110 117722 11399 8645 6614 66563 892 16499 2 10404 121406 11578 8654 6614 66738 906 16512 0 2 benign 0 . 48 0,0,25,17 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F435|656|MTHFR|protein_coding|CODING|NM_005957.4|8|A),DOWNSTREAM(MODIFIER||4815||1449|C1orf167|protein_coding|CODING|NM_001010881.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4846051 -0.693146 0.694774 48 E429A 656 gAa/gCa MODERATE 8 MISSENSE CODING MTHFR G protein_coding NM_005957.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11854476 T G 0 222 0 0.1513 0.2494 0.1513 0.2192 0.3131 0.4172 0.155016 0.259573 0.31314 1 1651 35805 1800 1857 2069 21297 276 6855 2 10394 121372 11574 8644 6614 66732 908 16506 0.969338 2|255|0|1 benign|other|uncertain|not-provided 0 . 48 15,8,12,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E429A|656|MTHFR|protein_coding|CODING|NM_005957.4|8|G),DOWNSTREAM(MODIFIER||4834||1449|C1orf167|protein_coding|CODING|NM_001010881.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.407581 rs1801131 -0.691153 0.766257 48 E198G 869 gAg/gGg MODERATE 8 MISSENSE CODING CLCN6 G protein_coding NM_001286.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11884555 A G 0 228 0 1 0.9998 1 1 0.999 1 0.999546 0.999154 0.998953 2 10399 121317 11573 8654 6614 66670 907 16500 2 10402 121394 11578 8654 6614 66738 908 16500 0 . 0 . 0 121 0,0,53,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E198G|869|CLCN6|protein_coding|CODING|NM_001286.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs198400 -0.693147 0.269123 121 869 558 MODIFIER 23 CODING CLCN6 G protein_coding NM_001286.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11900838 A G 0 9.7 0 0.0106 0.1132 0.0735 0.0942 0.1849 0.226 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||558||869|CLCN6|protein_coding|CODING|NM_001286.3|23|G),DOWNSTREAM(MODIFIER||4929||151|NPPA|protein_coding|CODING|NM_006172.3||G),INTRAGENIC(MODIFIER|||||NPPA-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17350396 -0.379885 0 1 634 463 MODIFIER 3 CODING KIAA2013 C protein_coding NM_138346.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11979909 T C 0 36.3 0 0.8321 0.6759 0.5303 0.6806 0.5517 0.6912 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||463||634|KIAA2013|protein_coding|CODING|NM_138346.2|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3209284 -0.453602 0.14 2 F458 634 ttT/ttC LOW 2 SILENT CODING KIAA2013 G protein_coding NM_138346.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 11983206 A G 0 228 0 0.8321 0.6753 0.5317 0.6796 0.5537 0.6861 0.746795 0.593349 0.515067 2 7167 67771 5269 5575 3983 34758 497 10522 2 9140 114304 11090 8374 6130 63024 846 15700 1 0 . 0 . 106 0,1,46,51 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F458|634|KIAA2013|protein_coding|CODING|NM_138346.2|2|G) 1 0 . 0 . 1 0 1 1 0 49 0 1 0.0354856 0 1 rs3795408 -0.693147 0.248273 106 F145 774 ttC/ttT LOW 4 SILENT CODING PLOD1 T protein_coding NM_001316320.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12009955 C T 0 228 0 0.0159 0.2678 0.3357 0.3631 0.3052 0.4233 0.068089 0.229279 0.31186 2 656 39790 4236 3218 3038 21311 318 7013 2 10374 121262 11572 8628 6614 66666 902 16506 0 . 0 . 0 34 0,0,13,18 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F145|774|PLOD1|protein_coding|CODING|NM_001316320.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7529452 -0.69311 0.00686312 34 N449 774 aaC/aaT LOW 13 SILENT CODING PLOD1 T protein_coding NM_001316320.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12024235 C T 0 228 0 0.2693 0.3484 0.3545 0.3839 0.3151 0.4489 0.29074 0.31078 0.321047 2 3023 44046 4338 3394 3435 22173 362 7321 2 10396 121320 11574 8630 6614 66686 908 16512 0 . 0 . 0 120 0,0,31,80 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N449|774|PLOD1|protein_coding|CODING|NM_001316320.1|13|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1130529 -0.693147 0.295012 120 757 8902 MODIFIER 1 CODING MFN2 G protein_coding NM_001127660.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12040324 A G 0 9.7 0 0.6369 0.5729 0.4438 0.6399 0.4433 0.6421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||8902||757|MFN2|protein_coding|CODING|NM_001127660.1|1|G),DOWNSTREAM(MODIFIER||4725||774|PLOD1|protein_coding|CODING|NM_001316320.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2236054 -0.379885 0 1 757 8747 MODIFIER 1 CODING MFN2 C protein_coding NM_001127660.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12040479 T C 0 39.3 0 0.7247 0.61 0.4582 0.6875 0.4433 0.6544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||8747||757|MFN2|protein_coding|CODING|NM_001127660.1|1|C),DOWNSTREAM(MODIFIER||4880||774|PLOD1|protein_coding|CODING|NM_001316320.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2180183 -0.453602 0.52 2 757 58 MODIFIER 18 CODING MFN2 G protein_coding NM_001127660.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12071680 A G 0 228 0 0.8903 0.7324 0.5879 0.6994 0.6769 0.7127 0.83237 0.709155 0.655563 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996781 0 . 0 . 155 2,1,31,104 UTR_3_PRIME(MODIFIER||58||757|MFN2|protein_coding|CODING|NM_001127660.1|18|G) 1 0 . 0 . 1 0 1 0 . 60 0 1 1 0 0.116588 rs1042842 -0.693147 0.0286751 155 757 896 MODIFIER 18 CODING MFN2 C protein_coding NM_001127660.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12072518 G C 0 102 0 0.4304 0.5441 0.5072 0.5853 0.6093 0.6145 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||896||757|MFN2|protein_coding|CODING|NM_001127660.1|18|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3088064 -0.556411 0.160409 4 K167E 388 Aag/Gag MODERATE 4 MISSENSE CODING MIIP G protein_coding NM_021933.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12082926 A G 0 228 0 0.795 0.6693 0.598 0.5516 0.7276 0.6115 0.785066 0.738275 0.714302 2 7660 77217 5936 4462 4749 44330 586 9494 2 9608 109398 10000 7768 5696 60754 826 14746 1 0 . 0 . 90 1,0,39,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K167E|388|MIIP|protein_coding|CODING|NM_021933.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2295283 -0.693147 0.429394 90 S200 388 tcC/tcG LOW 5 SILENT CODING MIIP G protein_coding NM_021933.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12089142 C G 0 222 0 0.0053 0.01258 0 0.0486 0 0.0072 0.0024966 0.000845763 0 1 36 443 3 351 0 2 2 49 2 10368 120920 11556 8640 6606 66342 902 16506 0.897323 0 . 0 . 106 25,23,28,22 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S200|388|MIIP|protein_coding|CODING|NM_021933.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.212912 rs79856956 -0.693147 0.0660703 106 E207 388 gaA/gaG LOW 5 SILENT CODING MIIP G protein_coding NM_021933.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12089163 A G 0 222 0 0.0053 0.01258 0 0.0486 0 0.0072 0.0024966 0.000845763 0 1 36 446 3 352 0 2 2 51 2 10372 120904 11558 8636 6606 66324 900 16508 0.220803 0 . 0 . 106 25,24,30,23 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E207|388|MIIP|protein_coding|CODING|NM_021933.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.626029 rs2295284 -0.693147 0.945656 106 R247W 388 Cgg/Tgg MODERATE 7 MISSENSE CODING MIIP T protein_coding NM_021933.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12089845 C T 0 222 0 0 0.010383 0 0.0446 0 0.0072 0 7.6899e-05 0.000116306 1 1 353 2 296 0 3 2 49 2 10020 117256 11320 8548 5818 64636 848 16066 0.672638 0 . 0 . 212 64,34,64,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R247W|388|MIIP|protein_coding|CODING|NM_021933.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999598 rs2295289 -0.693147 0.0189581 212 L249 388 Ctg/Ttg LOW 7 SILENT CODING MIIP T protein_coding NM_021933.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12089851 C T 0 222 0 0 0.011182 0 0.0486 0 0.0072 0 . 0 1 2 405 3 347 0 2 2 49 2 9988 117152 11302 8542 5798 64560 854 16108 0.273779 0 . 0 . 214 64,36,59,37 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L249|388|MIIP|protein_coding|CODING|NM_021933.3|7|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.975458 rs2295290 -0.693147 0.000996259 214 H280Q 388 caC/caG MODERATE 7 MISSENSE CODING MIIP G protein_coding NM_021933.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12089946 C G 0 222 0 0.0053 0.01258 0 0.0486 0 0.0072 0.00204267 0.000692095 0 1 28 432 3 349 0 2 2 48 2 9724 115884 11174 8458 5732 63782 836 16178 0.910152 0 . 0 . 164 29,52,24,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H280Q|388|MIIP|protein_coding|CODING|NM_021933.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.598213 rs117146839 -0.693147 0.780841 164 D305 388 gaC/gaT LOW 8 SILENT CODING MIIP T protein_coding NM_021933.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12090154 C T 0 222 0 0 0.011182 0 0.0486 0 0.0072 0 7.6888e-05 0.000116279 1 2 412 5 346 0 7 2 50 2 10172 119796 11496 8606 6520 65608 894 16500 0.199652 0 . 0 . 102 21,24,16,32 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D305|388|MIIP|protein_coding|CODING|NM_021933.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977098 rs74797667 -0.693147 0.319883 102 388 97 MODIFIER 10 CODING MIIP T protein_coding NM_021933.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12091962 C T 0 219 0 0 0.011182 0 0.0486 0 0.0072 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998709 0 . 0 . 43 2,22,4,14 UTR_3_PRIME(MODIFIER||97||388|MIIP|protein_coding|CODING|NM_021933.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.102379 rs2295292 -0.691153 0.533516 43 388 104 MODIFIER 10 CODING MIIP G protein_coding NM_021933.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12091969 A G 0 193 0 0 0.011182 0 0.0486 0 0.0072 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.521967 0 . 0 . 43 2,23,2,15 UTR_3_PRIME(MODIFIER||104||388|MIIP|protein_coding|CODING|NM_021933.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976558 rs2295293 -0.690438 0.922702 43 R297C 595 Cgt/Tgt MODERATE 8 MISSENSE CODING TNFRSF8 T protein_coding NM_001243.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12175729 C T 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121408 11578 8654 6614 66736 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 134 0,0,61,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R297C|595|TNFRSF8|protein_coding|CODING|NM_001243.4|8|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1763642 -0.693147 0.0164726 134 S449 595 agT/agC LOW 14 SILENT CODING TNFRSF8 C protein_coding NM_001243.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12198297 T C 0 222 0 0.5053 0.2915 0.1801 0.3988 0.1292 0.138 0.441887 0.239251 0.135739 1 4494 22682 2197 3471 1272 8822 171 2255 2 9754 117578 11478 8524 6540 64040 870 16372 0.533041 0 . 0 . 45 21,2,15,2 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S449|595|TNFRSF8|protein_coding|CODING|NM_001243.4|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.533041 rs476488 -0.690438 0.743141 45 461 922 MODIFIER 10 CODING TNFRSF1B T protein_coding NM_001066.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12267999 C T 0 9.7 0 0.4599 0.3592 0.2464 0.2966 0.4364 0.2883 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||922||461|TNFRSF1B|protein_coding|CODING|NM_001066.2|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1061628 -0.379885 0 1 P2886 4388 ccA/ccC LOW 41 SILENT CODING VPS13D C protein_coding NM_015378.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12401868 A C 0 228 0 0.7398 0.7967 0.7579 0.8978 0.7913 0.8027 0.759192 0.788559 0.803605 2 7854 96022 8084 7810 4950 53403 725 13196 2 10404 121388 11578 8652 6612 66722 908 16512 0 . 0 . 0 77 0,0,58,12 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P2886|4388|VPS13D|protein_coding|CODING|NM_015378.3|41|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs28551666 -0.693147 0.0801349 77 302 181 MODIFIER 6 CODING DHRS3 C protein_coding NM_004753.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12628188 T C 0 167 0 0.2716 0.3043 0.2017 0.3631 0.339 0.3252 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,18,0 UTR_3_PRIME(MODIFIER||181||302|DHRS3|protein_coding|CODING|NM_004753.6|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs386593853,rs4580 -0.691153 0.00104791 18 302 LOW 5 CODING DHRS3 A protein_coding NM_004753.6 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12628459 G A 0 228 0 0.2322 0.1268 0.0519 0.1736 0.0398 0.0787 0.20926 0.0945717 0.035814 2 2156 7745 357 1569 172 2269 57 1165 2 10406 121402 11578 8646 6614 66738 908 16512 1 0 . 0 . 87 1,0,16,57 SPLICE_SITE_REGION+INTRON(LOW||||302|DHRS3|protein_coding|CODING|NM_004753.6|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11121940 -0.693147 0.0771827 87 P160 302 ccA/ccG LOW 4 SILENT CODING DHRS3 C protein_coding NM_004753.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12638964 T C 0 228 0 0.8011 0.8047 0.7291 0.7282 0.8469 0.8988 0.827508 0.846609 0.856395 2 8446 99325 7363 6209 5190 56682 725 14710 2 10252 119460 11350 8560 6258 65754 872 16414 0.744186 0 . 0 . 46 1,1,14,29 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P160|302|DHRS3|protein_coding|CODING|NM_004753.6|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.976744 rs2275875 -0.693146 0.569345 46 407 46 MODIFIER 1 CODING AADACL3 A protein_coding NM_001103170.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12776134 C A 0 218 0 0.5756 0.7085 0.8718 0.619 0.8211 0.7485 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 47 0,0,45,0 UTR_5_PRIME(MODIFIER||46||407|AADACL3|protein_coding|CODING|NM_001103170.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3010874 -0.693147 0.057479 47 *13C 407 tgA/tgC HIGH 1 MISSENSE CODING AADACL3 C protein_coding NM_001103170.2 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12776218 A C 0 228 0 0.8812 0.8564 0.8948 0.7321 0.8638 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 0,0,63,28 STOP_LOST(HIGH|MISSENSE|tgA/tgC|*13C|407|AADACL3|protein_coding|CODING|NM_001103170.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3000860 -0.693147 0.500561 99 T55 407 acA/acT LOW 1 SILENT CODING AADACL3 T protein_coding NM_001103170.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12776344 A T 0 228 0 0.4009 0.6565 0.8473 0.619 0.8151 0.7423 0.510054 0.726267 0.831308 2 4659 93933 9853 5535 5323 55322 716 12525 2 9802 120754 11576 8616 6612 66736 900 16512 1 0 . 0 . 118 1,0,44,60 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T55|407|AADACL3|protein_coding|CODING|NM_001103170.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3000859,rs386496734 -0.693147 0.149525 118 D84 407 gaT/gaC LOW 2 SILENT CODING AADACL3 C protein_coding NM_001103170.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12779560 T C 0 228 0 0.9228 0.8494 0.8818 0.7817 0.83 0.817 0.914921 0.856757 0.829362 2 8947 100574 10299 6696 5123 55125 750 13634 2 9806 120762 11576 8618 6614 66736 900 16512 0 . 0 . 0 114 0,0,69,38 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D84|407|AADACL3|protein_coding|CODING|NM_001103170.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3010876 -0.693147 0.391692 114 S104P 407 Tcc/Ccc MODERATE 2 MISSENSE CODING AADACL3 C protein_coding NM_001103170.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12779618 T C 0 228 0 0.9228 0.848 0.879 0.7817 0.826 0.816 0.915832 0.857479 0.829535 2 8925 100437 10290 6696 5126 55022 750 13628 2 9808 120766 11576 8620 6612 66738 900 16512 1 0 . 0 . 120 1,0,63,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S104P|407|AADACL3|protein_coding|CODING|NM_001103170.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3010877 -0.693147 0.00100322 120 C252F 407 tGt/tTt MODERATE 4 MISSENSE CODING AADACL3 T protein_coding NM_001103170.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12785494 G T 0 228 0 0.4849 0.6823 0.7752 0.7798 0.7296 0.7342 0.523732 0.667115 0.732047 2 5113 86597 9546 6708 4612 48039 642 11937 2 9782 120580 11568 8600 6614 66628 900 16488 1 0 . 0 . 61 1,0,37,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tTt|C252F|407|AADACL3|protein_coding|CODING|NM_001103170.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs111199207,rs7513079 -0.693147 0.0200127 61 407 107 MODIFIER 4 CODING AADACL3 G protein_coding NM_001103170.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12786070 A G 0 189 0 0.7814 0.7636 0.7983 0.7798 0.7316 0.7311 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,1,15 UTR_3_PRIME(MODIFIER||107||407|AADACL3|protein_coding|CODING|NM_001103170.2|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3000930 -0.689466 0.138479 16 F191L 194 Ttc/Ctc MODERATE 4 MISSENSE CODING C1orf158 C protein_coding NM_152290.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12820870 T C 0 228 0 0.9153 0.8235 0.8545 0.7808 0.7873 0.7587 0.893327 0.824619 0.789419 2 9364 96158 10017 6731 5021 51859 715 12451 2 10398 120918 11578 8638 6610 66580 904 16210 0 . 0 . 0 40 0,0,14,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F191L|194|C1orf158|protein_coding|CODING|NM_152290.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1132185 -0.693139 0.0172256 40 M157T 483 aTg/aCg MODERATE 2 MISSENSE CODING PRAMEF12 C protein_coding NM_001080830.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12835868 T C 0 228 0 0.5696 0.7165 0.8213 0.7183 0.7982 0.7546 0.606673 0.736814 0.803488 2 6273 93901 9803 6318 5152 53091 705 12559 2 10336 121328 11576 8644 6614 66738 908 16512 1 0 . 0 . 307 1,0,191,96 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M157T|483|PRAMEF12|protein_coding|CODING|NM_001080830.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1812242,rs386545851 -0.693147 0.121032 307 I448 483 atT/atA LOW 3 SILENT CODING PRAMEF12 A protein_coding NM_001080830.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12837634 T A 0 228 0 0.3729 0.6633 0.8055 0.7192 0.8012 0.7556 0.429414 0.682224 0.811744 2 4401 92626 9756 6322 5183 53689 703 12572 2 10398 121312 11572 8624 6610 66704 906 16498 1 0 . 0 . 204 1,0,60,121 SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I448|483|PRAMEF12|protein_coding|CODING|NM_001080830.4|3|A) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.995876 0 1 rs848578 -0.693147 0.493119 204 483 98 MODIFIER 3 CODING PRAMEF12 C protein_coding NM_001080830.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12837840 G C 0 184 0 0.3737 0.6625 0.8055 0.7183 0.7972 0.7556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,1,11 UTR_3_PRIME(MODIFIER||98||483|PRAMEF12|protein_coding|CODING|NM_001080830.4|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs848577 -0.680642 0.645013 13 474 1802 MODIFIER 1 CODING PRAMEF1 C protein_coding NM_023013.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12851575 G C 0 39.3 0 0.0386 0.2999 0.2983 0.504 0.3469 0.3957 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||1802||474|PRAMEF1|protein_coding|CODING|NM_023013.4|1|C) 0 . 0 . 0 1 0 . 0 . 50 0 0 . 0 . rs2744049 -0.453602 0.52 2 L9 474 ctA/ctC LOW 2 SILENT CODING PRAMEF1 C protein_coding NM_023013.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12853403 A C 0 222 0 0.2466 0.3894 0.3458 0.5595 0.3767 0.4509 0 . 0 1 2507 43107 4806 4279 2218 23038 304 5955 2 9802 119070 11422 8472 6554 65796 892 16132 0.897008 0 . 0 . 125 33,32,22,30 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctC|L9|474|PRAMEF1|protein_coding|CODING|NM_023013.4|2|C) 0 0.5 1 0 . 1 0 . 1 0 53 0 0.000467 0.0150484 0 0.502109 rs1737157 -0.693147 0.152374 125 L105* 474 tTg/tAg HIGH 3 NONSENSE CODING PRAMEF1 A protein_coding NM_023013.4 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854090 T A 0 35.5 0 . 0 . 0 . 0 . 0 . 1 3448 56763 5559 3974 3281 32410 437 7654 2 9570 119524 11484 8376 6604 66276 898 16316 0.376968 0 . 0 COSM1626359,COSM1626358 640 305,140,88,45 STOP_GAINED(HIGH|NONSENSE|tTg/tAg|L105*|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|A) 0 0.5 1 0 . 0 . 0 1 (PRAMEF1|PRAMEF1|1|1.00) 45 0 8.88875e-24 0.012154 (PRAMEF1|PRAMEF1|1|1.00) 0.38056 rs79698223 -0.693147 0.118065 640 D107 474 gaT/gaC LOW 3 SILENT CODING PRAMEF1 C protein_coding NM_023013.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854097 T C 0 4.4 0 0.1619 0.3275 0.379 0.3631 0.4205 0.3824 0 . 0 1 3444 56767 5554 4069 3281 32370 434 7615 2 9568 119136 11448 8392 6596 66064 898 16170 0.12913 0 . 0 COSM1626361,COSM1626360 690 342,138,100,44 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D107|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|C) 0 0.5 1 0 . 1 0 . 1 0 45 0 5.60622e-30 0.516476 0 0.602492 rs76193255 -0.693147 0.500666 690 R213H 474 cGc/cAc MODERATE 3 MISSENSE CODING PRAMEF1 A protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854414 G A 0 91 0 . 0 . 0 . 0 . 0 . 1 4751 39201 3355 3596 1465 19295 268 6471 2 10152 118348 11186 8502 6492 65016 896 16104 0.851593 0 . 0 . 517 132,225,14,117 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R213H|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|A) 0 0.5 1 0 . 0 . 0 1 0 50 0 0 1.50512e-07 0 0.16765 rs1063769 -0.693147 0.00199356 517 P218S 474 Cca/Tca MODERATE 3 MISSENSE CODING PRAMEF1 T protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854428 C T 0 222 0 . 0 . 0 . 0 0.217658 0.282485 0.315698 1 2275 36925 3983 3283 2009 20214 262 4899 2 10372 121274 11562 8646 6614 66682 908 16490 0.638321 0 . 0 . 488 98,221,42,97 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P218S|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|T) 1 0.5 1 0 . 0 . 1 1 0 49 0 0.000170588 4.11927e-11 0 0.337688 rs1769774 -0.693147 0.0298866 488 Q252E 474 Caa/Gaa MODERATE 3 MISSENSE CODING PRAMEF1 G protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854530 C G 0 228 0 0.9259 0.8672 0.8919 0.7986 0.8638 0.8446 0.905583 0.872808 0.856013 2 9452 103459 10322 6845 5587 56850 783 13620 2 10358 120964 11544 8568 6596 66584 906 16408 0 . 0 . 0 264 0,0,101,141 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q252E|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|G) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.951407 0 . rs1063776 -0.693147 0.0230219 264 V256 474 gtT/gtC LOW 3 SILENT CODING PRAMEF1 C protein_coding NM_023013.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12854544 T C 0 222 0 0.2254 0.359 0.3127 0.5159 0.3509 0.4192 0.253064 0.323823 0.360084 1 2617 43873 4877 4374 2217 23403 305 6080 2 10280 120874 11526 8574 6604 66598 906 16386 0.515527 0 . 0 . 263 47,87,57,50 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V256|474|PRAMEF1|protein_coding|CODING|NM_023013.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 57 0 2.97445e-07 0.998913 0 0.786169 rs1063778 -0.693147 0.339618 263 A372G 474 gCc/gGc MODERATE 4 MISSENSE CODING PRAMEF1 G protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12855835 C G 0 228 0 1 1 1 1 1 1 0 . 0 2 9984 119413 11484 8600 6610 66221 890 15624 2 9984 119416 11484 8600 6610 66224 890 15624 0 . 0 . 0 261 0,0,131,118 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A372G|474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|G) 0 . 0 . 0 1 0 . 1 0 45 0 0 0.899272 0 . rs1063795 -0.693147 7.46867e-05 261 R375 474 cgG/cgC LOW 4 SILENT CODING PRAMEF1 C protein_coding NM_023013.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12855845 G C 0 228 0 1 1 1 1 1 1 0 . 0 2 10072 119350 11446 8568 6598 66176 892 15598 2 10072 119356 11446 8568 6598 66182 892 15598 0 . 0 . 0 243 0,0,119,115 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R375|474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|C) 0 . 0 . 0 1 0 . 1 0 44 0 0 0.17346 0 . rs1063797 -0.693147 0.000564469 243 R386S 474 agA/agC MODERATE 4 MISSENSE CODING PRAMEF1 C protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12855878 A C 0 84 0 . 0 . 0 . 0 . 0 . 1 2275 37290 3930 3598 2030 20147 268 5042 2 9922 114776 10708 8134 6356 63354 860 15442 0.995962 0 . 0 . 235 93,59,3,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R386S|474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|C) 0 0.5 1 0 . 0 . 0 1 0 47 0 0.165082 1.61161e-11 0 0.696092 rs1052908 -0.693147 0.786524 235 F430L 474 ttC/ttG MODERATE 4 MISSENSE CODING PRAMEF1 G protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12856010 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 2772 54888 5639 4253 3255 30992 429 7548 2 9632 118078 11488 8618 6578 64558 894 16310 0.354768 0 . 0 . 858 321,147,170,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttC/ttG|F430L|474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|G) 0 0.5 1 0 . 0 . 0 1 0 36 0 0.690208 0.988215 0 0.901011 rs61775053 -0.693147 0.00500432 858 P464L 474 cCg/cTg MODERATE 4 MISSENSE CODING PRAMEF1 T protein_coding NM_023013.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12856111 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 4040 57233 5698 4249 3259 31915 436 7636 2 8470 115336 11424 8552 6534 64088 878 15390 0.0770612 0 . 0 . 535 75,174,46,175 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P464L|474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|T) 0 0.5 1 0 . 0 . 0 1 0 35 0 0.0464731 0.80065 0 0.998817 rs61775054 -0.693147 0.01915 535 474 8 MODIFIER 4 CODING PRAMEF1 A protein_coding NM_023013.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12856153 G A 0 96 0 . 0 . 0 . 0 . 0 . 1 3118 47082 4651 3511 2857 26640 350 5955 2 6886 97270 9470 7280 5838 54872 730 12194 0.981443 0 . 0 . 315 26,138,0,135 UTR_3_PRIME(MODIFIER||8||474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|A) 0 0.5 1 0 . 0 . 0 1 0 31 0 0.00360446 0.54518 0 0.852698 rs61775055 -0.693147 2.49724e-11 315 474 128 MODIFIER 4 CODING PRAMEF1 C protein_coding NM_023013.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12856273 A C 0 67 0 0.2201 0.3425 0.3084 0.4851 0.341 0.3865 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.971121 0 . 0 . 25 1,17,1,6 UTR_3_PRIME(MODIFIER||128||474|PRAMEF1|protein_coding|CODING|NM_023013.4|4|C) 0 0.5 1 0 . 1 0 . 0 . 44 0 0.992701 0.521739 0 0.172032 rs2493877 -0.636426 0.361296 25 L315 477 ctC/ctA LOW 4 SILENT CODING PRAMEF11 T protein_coding NM_001146344.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12885289 G T 0 150 0 0.1899 0.391 0.3501 0.6895 0.4553 0.318 0 . 0 2 1014 12165 561 706 599 6569 106 2610 2 6538 67952 6052 3060 3374 38994 480 9454 1 0 . 0 COSM462789 15 0,1,0,14 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L315|477|PRAMEF11|protein_coding|CODING|NM_001146344.2|4|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 49 0 1 0 . 1 rs200907281 -0.686358 0.260041 15 E144G 477 gAa/gGa MODERATE 3 MISSENSE CODING PRAMEF11 C protein_coding NM_001146344.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12887549 T C 0 228 0 0.5885 0.7845 0.7262 0.998 0.7714 0.8845 0 . 0 2 5707 91241 8800 8547 4728 48857 685 13917 2 9368 117706 11494 8558 6594 64394 888 16410 0 . 0 . 0 644 0,0,280,305 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E144G|477|PRAMEF11|protein_coding|CODING|NM_001146344.2|3|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 48 0 0 0.27261 0 . rs2994114 -0.693147 0.0783402 644 L87W 477 tTg/tGg MODERATE 2 MISSENSE CODING PRAMEF11 C protein_coding NM_001146344.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12888389 A C 0 228 0 0.5144 0.6526 0.6138 0.8254 0.6431 0.6984 0 . 0 2 3081 45547 4074 3715 2666 23907 374 7730 2 6330 83948 6910 5746 4956 45514 684 13808 0.816667 0 . 0 . 62 2,0,41,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L87W|477|PRAMEF11|protein_coding|CODING|NM_001146344.2|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 44 0 0.283333 0.171427 0 0.833333 rs1830486 -0.693147 0.0510775 62 A86 293 gcA/gcG LOW 1 SILENT CODING HNRNPCL4 C protein_coding NM_001302551.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12907885 T C 0 228 0 0.9614 0.9139 0.9121 0.8125 0.9433 0.9254 0 . 0 2 5175 60196 5578 4315 3295 33172 452 8209 2 10400 121392 11574 8654 6614 66730 908 16512 0 . 0 . 0 142 0,0,48,80 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL4|protein_coding|CODING|NM_001302551.1|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL3|protein_coding|CODING|NM_001146181.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL1|protein_coding|CODING|NM_001013631.2|2|C) 0 . 0 . 0 1 0 . 1 0 52 0 0 2.66131e-08 0 . rs848418 -0.693147 0.000328158 142 A86 293 gcA/gcG LOW 1 SILENT CODING HNRNPCL3 C protein_coding NM_001146181.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12907885 T C 0 228 0 0.9614 0.9139 0.9121 0.8125 0.9433 0.9254 0 . 0 2 5175 60196 5578 4315 3295 33172 452 8209 2 10400 121392 11574 8654 6614 66730 908 16512 0 . 0 . 0 142 0,0,48,80 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL4|protein_coding|CODING|NM_001302551.1|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL3|protein_coding|CODING|NM_001146181.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL1|protein_coding|CODING|NM_001013631.2|2|C) 0 . 0 . 0 1 0 . 1 0 52 0 0 2.66131e-08 0 . rs848418 -0.693147 0.000328158 142 A86 293 gcA/gcG LOW 2 SILENT CODING HNRNPCL1 C protein_coding NM_001013631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12907885 T C 0 228 0 0.9614 0.9139 0.9121 0.8125 0.9433 0.9254 0 . 0 2 5175 60196 5578 4315 3295 33172 452 8209 2 10400 121392 11574 8654 6614 66730 908 16512 0 . 0 . 0 142 0,0,48,80 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL4|protein_coding|CODING|NM_001302551.1|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL3|protein_coding|CODING|NM_001146181.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A86|293|HNRNPCL1|protein_coding|CODING|NM_001013631.2|2|C) 0 . 0 . 0 1 0 . 1 0 52 0 0 2.66131e-08 0 . rs848418 -0.693147 0.000328158 142 293 136 MODIFIER 2 CODING HNRNPCL1 A protein_coding NM_001013631.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12908278 C A 0 149 0 0.5393 0.5002 0.536 0.4077 0.5268 0.4898 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.989082 0 . 0 . 64 4,28,1,27 UTR_5_PRIME(MODIFIER||136||293|HNRNPCL1|protein_coding|CODING|NM_001013631.2|2|A),UPSTREAM(MODIFIER||121||293|HNRNPCL4|protein_coding|CODING|NM_001302551.1||A),UPSTREAM(MODIFIER||43||293|HNRNPCL3|protein_coding|CODING|NM_001146181.2||A) 0 0.5 1 0 . 1 0 . 0 . 50 0 5.29019e-05 0.195997 0 0.333613 rs3860363 -0.693054 0.385025 64 474 8 MODIFIER 4 CODING PRAMEF2 A protein_coding NM_023014.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12921642 G A 0 150 0 . 0 . 0 . 0 . 0 . 1 2323 28538 2494 2184 1578 16955 205 2799 2 5678 68286 6126 5518 3818 39648 514 6984 0.00229729 0 . 0 . 503 87,200,102,32 UTR_3_PRIME(MODIFIER||8||474|PRAMEF2|protein_coding|CODING|NM_023014.1|4|A) 0 0.5 1 0 . 0 . 0 1 0 36 0 0.0519346 0.177769 0 0.367947 rs2994093 -0.693147 0.0235619 503 474 82 MODIFIER 4 CODING PRAMEF2 G protein_coding NM_023014.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12921716 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.134647 0 . 0 . 254 9,130,6,101 UTR_3_PRIME(MODIFIER||82||474|PRAMEF2|protein_coding|CODING|NM_023014.1|4|G) 0 0.5 1 0 . 0 . 0 . 0 38 0 0.000322795 0.000104438 0 0.632052 rs2994094 -0.693147 6.31907e-05 254 R144K 478 aGa/aAa MODERATE 3 MISSENSE CODING PRAMEF4 T protein_coding NM_001009611.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12942119 C T 0 222 0 0.0303 0.2208 0.3285 0.2183 0.3201 0.3027 0.0858444 0.241231 0.324906 1 572 31010 3105 1995 1438 19080 256 4564 2 7580 108036 10316 8184 6178 59580 820 15378 0.999531 0 . 0 . 627 137,145,150,140 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R144K|478|PRAMEF4|protein_coding|CODING|NM_001009611.4|3|T) 1 0.5 1 0 . 1 0 1 1 0 43 0 0.360841 1.1021e-20 0 0.963085 rs61781964,rs75355616 -0.693147 0.682853 627 S307 474 tcG/tcA LOW 4 SILENT CODING PRAMEF8 A protein_coding NM_001012276.3.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12979729 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 130 3331 269 249 111 2304 36 232 2 7376 58828 4980 4982 2492 29790 472 8736 0.889158 0 . 0 . 240 73,40,63,36 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S307|474|PRAMEF8|protein_coding|CODING|NM_001012276.3.2|4|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S307|474|PRAMEF7|protein_coding|CODING|NM_001012277.4.3|4|A) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.534198 0.902037 0 0.992135 rs146836223 -0.693147 0.681461 240 S307 474 tcG/tcA LOW 4 SILENT CODING PRAMEF7 A protein_coding NM_001012277.4.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12979729 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 130 3331 269 249 111 2304 36 232 2 7376 58828 4980 4982 2492 29790 472 8736 0.889158 0 . 0 . 240 73,40,63,36 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S307|474|PRAMEF8|protein_coding|CODING|NM_001012276.3.2|4|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S307|474|PRAMEF7|protein_coding|CODING|NM_001012277.4.3|4|A) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.534198 0.902037 0 0.992135 rs146836223 -0.693147 0.681461 240 V346A 474 gTt/gCt MODERATE 4 MISSENSE CODING PRAMEF8 C protein_coding NM_001012276.3.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12979845 T C 0 222 0 . 0 . 0 . 0 0.0861364 0.181082 0.229818 1 1059 30482 3344 1798 1853 18632 219 3577 2 9514 118388 11484 8566 6572 64948 892 16412 0.36172 0 . 0 . 207 42,56,40,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V346A|474|PRAMEF8|protein_coding|CODING|NM_001012276.3.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V346A|474|PRAMEF7|protein_coding|CODING|NM_001012277.4.3|4|C) 1 0.5 1 0 . 0 . 1 1 0 32 0 0.912487 0.000280811 0 0.885116 rs142026718,rs1890765 -0.693147 1.93355e-05 207 V346A 474 gTt/gCt MODERATE 4 MISSENSE CODING PRAMEF7 C protein_coding NM_001012277.4.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 12979845 T C 0 222 0 . 0 . 0 . 0 0.0861364 0.181082 0.229818 1 1059 30482 3344 1798 1853 18632 219 3577 2 9514 118388 11484 8566 6572 64948 892 16412 0.36172 0 . 0 . 207 42,56,40,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V346A|474|PRAMEF8|protein_coding|CODING|NM_001012276.3.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V346A|474|PRAMEF7|protein_coding|CODING|NM_001012277.4.3|4|C) 1 0.5 1 0 . 0 . 1 1 0 32 0 0.912487 0.000280811 0 0.885116 rs142026718,rs1890765 -0.693147 1.93355e-05 207 L105M 479 Ttg/Atg MODERATE 2 MISSENSE CODING PRAMEF18 A protein_coding NM_001099850.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036247 T A 0 162 0 . 0 . 0 . 0 . 0 . 2 165 2309 159 124 81 1366 28 386 2 988 41788 6252 3606 2396 25804 286 2456 1 0 . 0 . 103 1,0,100,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L105M|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L107M|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|A) 0 . 0 . 0 . 0 . 1 0 23 0 1 1 0 1 rs201369259 -0.693147 5.1111e-11 103 L107M 481 Ttg/Atg MODERATE 2 MISSENSE CODING PRAMEF22 A protein_coding NM_001100631.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036247 T A 0 162 0 . 0 . 0 . 0 . 0 . 2 165 2309 159 124 81 1366 28 386 2 988 41788 6252 3606 2396 25804 286 2456 1 0 . 0 . 103 1,0,100,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L105M|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L107M|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|A) 0 . 0 . 0 . 0 . 1 0 23 0 1 1 0 1 rs201369259 -0.693147 5.1111e-11 103 P121L 479 cCc/cTc MODERATE 2 MISSENSE CODING PRAMEF18 T protein_coding NM_001099850.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036296 C T 0 42 0 0.0809 0.0831 0.0447 0.1062 0.0686 0.1043 0 . 0 1 3 92 6 9 2 67 2 3 2 42 828 70 50 12 632 12 10 0.952843 0 . 0 . 58 38,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P121L|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P123L|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 0.5 1 0 . 1 0 . 1 0 24 0 0.844819 0 . 0.67693 rs201492352 -0.692067 0.416223 58 P123L 481 cCc/cTc MODERATE 2 MISSENSE CODING PRAMEF22 T protein_coding NM_001100631.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036296 C T 0 42 0 0.0809 0.0831 0.0447 0.1062 0.0686 0.1043 0 . 0 1 3 92 6 9 2 67 2 3 2 42 828 70 50 12 632 12 10 0.952843 0 . 0 . 58 38,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P121L|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P123L|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 0.5 1 0 . 1 0 . 1 0 24 0 0.844819 0 . 0.67693 rs201492352 -0.692067 0.416223 58 R132 479 agG/agA LOW 2 SILENT CODING PRAMEF18 A protein_coding NM_001099850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036330 G A 0 175 0 . 0 . 0 . 0 . 0 . 2 0 2 0 0 0 2 0 0 2 0 2 0 0 0 2 0 0 0 . 0 . 0 34 0,0,29,5 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R132|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|A),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R134|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|A) 0 . 0 . 0 . 0 . 1 0 23 0 0 0.00237196 0 . rs200053605,rs61780077 -0.693132 0.00372529 34 R134 481 agG/agA LOW 2 SILENT CODING PRAMEF22 A protein_coding NM_001100631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036330 G A 0 175 0 . 0 . 0 . 0 . 0 . 2 0 2 0 0 0 2 0 0 2 0 2 0 0 0 2 0 0 0 . 0 . 0 34 0,0,29,5 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R132|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|A),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R134|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|A) 0 . 0 . 0 . 0 . 1 0 23 0 0 0.00237196 0 . rs200053605,rs61780077 -0.693132 0.00372529 34 V171 479 gtC/gtG LOW 2 SILENT CODING PRAMEF18 G protein_coding NM_001099850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036447 C G 0 228 0 . 0 . 0 . 0 . 0 . 2 4 19 0 0 0 15 0 0 2 4 20 0 0 0 16 0 0 0 . 0 . 0 179 0,0,127,52 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V171|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|G),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V173|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|G) 0 . 0 . 0 . 0 . 1 0 25 0 0 1.5559e-05 0 . rs1320957,rs199683676 -0.693147 0.201878 179 V173 481 gtC/gtG LOW 2 SILENT CODING PRAMEF22 G protein_coding NM_001100631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036447 C G 0 228 0 . 0 . 0 . 0 . 0 . 2 4 19 0 0 0 15 0 0 2 4 20 0 0 0 16 0 0 0 . 0 . 0 179 0,0,127,52 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V171|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|G),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V173|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|G) 0 . 0 . 0 . 0 . 1 0 25 0 0 1.5559e-05 0 . rs1320957,rs199683676 -0.693147 0.201878 179 P218L 479 cCg/cTg MODERATE 2 MISSENSE CODING PRAMEF18 T protein_coding NM_001099850.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036587 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 7404 82039 7132 6173 4018 44798 611 11903 2 10380 121358 11578 8654 6614 66714 908 16510 0.671499 0 . 0 . 507 4,0,200,240 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P218L|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P220L|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 . 0 . 0 . 0 . 1 0 30 0 0.879436 1.92358e-07 0 0.891401 rs61780078,rs77788641 -0.693147 4.28247e-09 507 P220L 481 cCg/cTg MODERATE 2 MISSENSE CODING PRAMEF22 T protein_coding NM_001100631.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036587 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 7404 82039 7132 6173 4018 44798 611 11903 2 10380 121358 11578 8654 6614 66714 908 16510 0.671499 0 . 0 . 507 4,0,200,240 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P218L|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P220L|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 . 0 . 0 . 0 . 1 0 30 0 0.879436 1.92358e-07 0 0.891401 rs61780078,rs77788641 -0.693147 4.28247e-09 507 S240 479 tcC/tcT LOW 2 SILENT CODING PRAMEF18 T protein_coding NM_001099850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036654 C T 0 162 0 . 0 . 0 . 0 . 0 . 1 1299 18804 1021 1410 666 10876 135 3397 2 9496 119082 11568 8636 6608 65484 900 16390 0.210051 0 . 0 . 326 30,174,14,87 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S240|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S242|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.833821 0.0853741 0 0.980055 rs201636235 -0.693147 5.77737e-21 326 S242 481 tcC/tcT LOW 2 SILENT CODING PRAMEF22 T protein_coding NM_001100631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13036654 C T 0 162 0 . 0 . 0 . 0 . 0 . 1 1299 18804 1021 1410 666 10876 135 3397 2 9496 119082 11568 8636 6608 65484 900 16390 0.210051 0 . 0 . 326 30,174,14,87 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S240|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|2|T),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S242|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|2|T) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.833821 0.0853741 0 0.980055 rs201636235 -0.693147 5.77737e-21 326 T462 479 acG/acT LOW 3 SILENT CODING PRAMEF18 T protein_coding NM_001099850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13038327 G T 0 92 0 . 0 . 0 . 0 . 0 . 1 49 284 17 12 1 189 6 10 2 96 562 34 24 2 376 10 20 0.958048 0 . 0 . 13 5,0,8,0 SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T462|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|3|T),SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T464|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|3|T) 0 0.5 1 0 . 0 . 0 1 0 48 0 0.679965 0 . 0.989343 rs199598633 -0.651104 0.5 13 T464 481 acG/acT LOW 3 SILENT CODING PRAMEF22 T protein_coding NM_001100631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13038327 G T 0 92 0 . 0 . 0 . 0 . 0 . 1 49 284 17 12 1 189 6 10 2 96 562 34 24 2 376 10 20 0.958048 0 . 0 . 13 5,0,8,0 SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T462|479|PRAMEF18|protein_coding|CODING|NM_001099850.2|3|T),SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T464|481|PRAMEF22|protein_coding|CODING|NM_001100631.1|3|T) 0 0.5 1 0 . 0 . 0 1 0 48 0 0.679965 0 . 0.989343 rs199598633 -0.651104 0.5 13 479 104 MODIFIER 3 CODING PRAMEF18 C protein_coding NM_001099850.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13038485 T C 0 39.4 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,3,0 UTR_3_PRIME(MODIFIER||104||479|PRAMEF18|protein_coding|CODING|NM_001099850.2|3|C),DOWNSTREAM(MODIFIER||104||481|PRAMEF22|protein_coding|CODING|NM_001100631.1||C) 0 0.5 1 0 . 0 . 0 . 0 46 0 1 0 . 1 rs201016201 -0.511536 0.37344 4 479 180 MODIFIER 3 CODING PRAMEF18 C protein_coding NM_001099850.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13038561 A C 0 123 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.611111 0 . 0 . 11 0,2,1,8 UTR_3_PRIME(MODIFIER||180||479|PRAMEF18|protein_coding|CODING|NM_001099850.2|3|C),DOWNSTREAM(MODIFIER||180||481|PRAMEF22|protein_coding|CODING|NM_001100631.1||C) 0 0.5 1 0 . 0 . 0 . 0 44 0 0.777778 1 0 0.611111 rs141794630,rs61780086 -0.662043 0.0188473 11 479 244 MODIFIER 3 CODING PRAMEF18 T protein_coding NM_001099850.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13038625 C T 0 3.3 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992153 0 . 0 . 34 1,27,0,5 UTR_3_PRIME(MODIFIER||244||479|PRAMEF18|protein_coding|CODING|NM_001099850.2|3|T),DOWNSTREAM(MODIFIER||244||481|PRAMEF22|protein_coding|CODING|NM_001100631.1||T) 0 0.5 1 0 . 0 . 0 . 0 50 0 0.286294 1 0 0.0220813 rs201588803 -0.590765 0.0588947 34 478 187 MODIFIER 4 CODING PRAMEF25 A protein_coding NM_001310134.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052539 G A 0 94 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996597 0 . 0 . 56 35,1,18,0 UTR_3_PRIME(MODIFIER||187||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|A|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||187||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|A|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.00512184 1 0 0.639859 rs201172464 -0.691153 0.0891879 56 478 187 MODIFIER 4 CODING PRAMEF26 A protein_coding NM_001306072.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052539 G A 0 94 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996597 0 . 0 . 56 35,1,18,0 UTR_3_PRIME(MODIFIER||187||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|A|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||187||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|A|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.00512184 1 0 0.639859 rs201172464 -0.691153 0.0891879 56 478 137 MODIFIER 4 CODING PRAMEF25 T protein_coding NM_001310134.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052589 A T 0 136 0 0.4841 0.5407 0.5432 0.6637 0.5249 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.724544 0 . 0 . 128 68,6,51,1 UTR_3_PRIME(MODIFIER||137||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||137||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 50 0 0.346032 0.792703 0 0.884462 rs71225489 -0.693147 6.85803e-05 128 478 137 MODIFIER 4 CODING PRAMEF26 T protein_coding NM_001306072.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052589 A T 0 136 0 0.4841 0.5407 0.5432 0.6637 0.5249 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.724544 0 . 0 . 128 68,6,51,1 UTR_3_PRIME(MODIFIER||137||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||137||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 50 0 0.346032 0.792703 0 0.884462 rs71225489 -0.693147 6.85803e-05 128 478 67 MODIFIER 4 CODING PRAMEF25 T protein_coding NM_001310134.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052659 A T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0735779 0 . 0 . 294 181,3,82,15 UTR_3_PRIME(MODIFIER||67||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||67||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.972302 0.354278 0 9.3015e-05 rs374409005 -0.693147 0.783683 294 478 67 MODIFIER 4 CODING PRAMEF26 T protein_coding NM_001306072.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052659 A T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0735779 0 . 0 . 294 181,3,82,15 UTR_3_PRIME(MODIFIER||67||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON),UTR_3_PRIME(MODIFIER||67||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|4|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.972302 0.354278 0 9.3015e-05 rs374409005 -0.693147 0.783683 294 478 HIGH 3 CODING PRAMEF25 A protein_coding NM_001310134.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052789 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 2146 53972 5217 4113 3245 32065 453 6733 2 10320 120932 11578 8646 6614 66354 908 16512 0.309298 0 . 0 COSM1316938,COSM1316937 701 190,164,125,144 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|3|A|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|3|A|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 1 (PRAMEF25|PRAMEF25|1|1.00),(PRAMEF26|PRAMEF26|1|1.00) 59 0 0.654605 0.216552 0 0.800258 rs61780142 -0.693147 0.0517627 701 478 HIGH 3 CODING PRAMEF26 A protein_coding NM_001306072.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13052789 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 2146 53972 5217 4113 3245 32065 453 6733 2 10320 120932 11578 8646 6614 66354 908 16512 0.309298 0 . 0 COSM1316938,COSM1316937 701 190,164,125,144 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||478|PRAMEF25|protein_coding|CODING|NM_001310134.1|3|A|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||478|PRAMEF26|protein_coding|CODING|NM_001306072.1|3|A|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 1 (PRAMEF25|PRAMEF25|1|1.00),(PRAMEF26|PRAMEF26|1|1.00) 59 0 0.654605 0.216552 0 0.800258 rs61780142 -0.693147 0.0517627 701 N151D 293 Aac/Gac MODERATE 2 MISSENSE CODING HNRNPCL2 C protein_coding NM_001136561.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13183422 T C 0 222 0 0.2239 0.1564 0.0706 0.0546 0.0915 0.2975 0.115607 0.0816908 0.066939 1 1868 13533 586 343 508 6693 74 3461 2 10174 121126 11566 8638 6612 66722 906 16508 0.97661 0 . 0 . 105 45,16,30,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N151D|293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.993562 0.990959 0 0.421138 rs28564063 -0.693146 0.201 105 H145R 293 cAc/cGc MODERATE 2 MISSENSE CODING HNRNPCL2 C protein_coding NM_001136561.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13183439 T C 0 228 0 0.5764 0.6797 0.6556 0.7163 0.664 0.8149 0 . 0 2 7421 91501 8371 6738 5125 49636 666 13544 2 10330 121324 11576 8650 6614 66734 908 16512 0.586451 0 . 0 . 123 3,2,88,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H145R|293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|C) 0 . 0 . 0 1 0 . 1 0 56 0 0.563019 0.930588 0 0.794668 rs28713604 -0.693147 0.336846 123 L26P 293 cTt/cCt MODERATE 2 MISSENSE CODING HNRNPCL2 G protein_coding NM_001136561.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13183796 A G 0 222 0 0.0333 0.0429 0.0216 0.0407 0.0159 0.1012 0.0332851 0.0219106 0.0169705 1 304 3480 259 315 53 1194 14 1341 2 10110 120622 11538 8486 6608 66526 908 16446 0.477367 0 . 0 . 233 67,49,52,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L26P|293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 52 0 0.139353 0.987151 0 0.170949 rs141765631 -0.693147 0.0528534 233 293 101 MODIFIER 2 CODING HNRNPCL2 A protein_coding NM_001136561.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13183973 G A 0 228 0 0.385 0.5683 0.6037 0.5228 0.6481 0.7556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.86151 0 . 0 . 46 1,2,13,29 UTR_5_PRIME(MODIFIER||101||293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|A) 0 . 0 . 0 1 0 . 0 . 42 0 0.034619 0.0722658 0 0.0516641 rs3929664 -0.693146 0.251535 46 293 173 MODIFIER 2 CODING HNRNPCL2 G protein_coding NM_001136561.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13184045 A G 0 155 0 0.2602 0.1703 0.085 0.0546 0.1034 0.2975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.865648 0 . 0 . 33 3,10,1,18 START_GAINED(LOW||||293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|G),UTR_5_PRIME(MODIFIER||173||293|HNRNPCL2|protein_coding|CODING|NM_001136561.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 56 0 0.437755 0.850154 0 0.20359 rs61780796 -0.69168 0.926634 33 479 180 MODIFIER 3 CODING PRAMEF18 G protein_coding NM_001099850.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13328653 T G 0 24.4 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||180||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|3|G),DOWNSTREAM(MODIFIER||180||481|PRAMEF22|protein_coding|CODING|NM_001100631.1.2||G) 0 . 0 . 0 . 0 . 0 . 30 0 0 . 0 . rs28460165 -0.453602 0.02 2 H122R 476 cAt/cGt MODERATE 3 MISSENSE CODING PRAMEF5 G protein_coding NM_001013407.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13365921 A G 0 58 0 . 0 . 0 . 0 . 0 . 2 0 0 0 0 0 0 0 0 2 8 26 0 2 0 16 0 0 0.911488 0 . 0 . 22 0,3,0,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF5|protein_coding|CODING|NM_001013407.2.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF6|protein_coding|CODING|NM_001010889.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H123R|477|PRAMEF27|protein_coding|CODING|NM_001300891.1.3|2|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 23 0 0.603761 0 . 0.0313953 rs199562274 -0.69168 0.000981104 22 H122R 476 cAt/cGt MODERATE 3 MISSENSE CODING PRAMEF6 G protein_coding NM_001010889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13365921 A G 0 58 0 . 0 . 0 . 0 . 0 . 2 0 0 0 0 0 0 0 0 2 8 26 0 2 0 16 0 0 0.911488 0 . 0 . 22 0,3,0,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF5|protein_coding|CODING|NM_001013407.2.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF6|protein_coding|CODING|NM_001010889.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H123R|477|PRAMEF27|protein_coding|CODING|NM_001300891.1.3|2|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 23 0 0.603761 0 . 0.0313953 rs199562274 -0.69168 0.000981104 22 H123R 477 cAt/cGt MODERATE 2 MISSENSE CODING PRAMEF27 G protein_coding NM_001300891.1.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13365921 A G 0 58 0 . 0 . 0 . 0 . 0 . 2 0 0 0 0 0 0 0 0 2 8 26 0 2 0 16 0 0 0.911488 0 . 0 . 22 0,3,0,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF5|protein_coding|CODING|NM_001013407.2.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H122R|476|PRAMEF6|protein_coding|CODING|NM_001010889.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H123R|477|PRAMEF27|protein_coding|CODING|NM_001300891.1.3|2|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 23 0 0.603761 0 . 0.0313953 rs199562274 -0.69168 0.000981104 22 476 83 MODIFIER 4 CODING PRAMEF5 A protein_coding NM_001013407.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13368816 T A 0 90 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||83||476|PRAMEF5|protein_coding|CODING|NM_001013407.2.2|4|A),UTR_3_PRIME(MODIFIER||83||476|PRAMEF6|protein_coding|CODING|NM_001010889.2|4|A),DOWNSTREAM(MODIFIER||83||477|PRAMEF27|protein_coding|CODING|NM_001300891.1.3||A|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 0 . 24 0 0 . 0 . rs2359052 -0.676189 3.59515e-05 11 476 83 MODIFIER 4 CODING PRAMEF6 A protein_coding NM_001010889.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13368816 T A 0 90 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||83||476|PRAMEF5|protein_coding|CODING|NM_001013407.2.2|4|A),UTR_3_PRIME(MODIFIER||83||476|PRAMEF6|protein_coding|CODING|NM_001010889.2|4|A),DOWNSTREAM(MODIFIER||83||477|PRAMEF27|protein_coding|CODING|NM_001300891.1.3||A|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 0 . 24 0 0 . 0 . rs2359052 -0.676189 3.59515e-05 11 474 16 MODIFIER 4 CODING PRAMEF14 A protein_coding NM_001024661.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448034 G A 0 38.5 0 . 0 . 0 . 0 . 0 . 2 3 7 0 0 0 3 1 0 2 18 28 2 0 0 6 2 0 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||16||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),UTR_3_PRIME(MODIFIER||16||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs201058086 -0.511536 0.0714862 3 474 16 MODIFIER 4 CODING PRAMEF13 A protein_coding NM_001291380.1.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448034 G A 0 38.5 0 . 0 . 0 . 0 . 0 . 2 3 7 0 0 0 3 1 0 2 18 28 2 0 0 6 2 0 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||16||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),UTR_3_PRIME(MODIFIER||16||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs201058086 -0.511536 0.0714862 3 474 13 MODIFIER 4 CODING PRAMEF14 G protein_coding NM_001024661.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448037 A G 0 38.5 0 . 0 . 0 . 0 . 0 . 2 3 7 0 0 0 3 1 0 2 18 28 2 0 0 6 2 0 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||13||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),UTR_3_PRIME(MODIFIER||13||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs199521323 -0.511536 0.0714862 3 474 13 MODIFIER 4 CODING PRAMEF13 G protein_coding NM_001291380.1.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448037 A G 0 38.5 0 . 0 . 0 . 0 . 0 . 2 3 7 0 0 0 3 1 0 2 18 28 2 0 0 6 2 0 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||13||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),UTR_3_PRIME(MODIFIER||13||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs199521323 -0.511536 0.0714862 3 474 8 MODIFIER 4 CODING PRAMEF14 T protein_coding NM_001024661.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448042 C T 0 67 0 . 0 . 0 . 0 . 0 . 2 3 13 0 0 0 7 1 2 2 20 34 2 0 0 8 2 2 0 . 0 . 0 5 0,0,5,0 UTR_3_PRIME(MODIFIER||8||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|T),UTR_3_PRIME(MODIFIER||8||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|T),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|T) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs370590461 -0.590765 0.110342 5 474 8 MODIFIER 4 CODING PRAMEF13 T protein_coding NM_001291380.1.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448042 C T 0 67 0 . 0 . 0 . 0 . 0 . 2 3 13 0 0 0 7 1 2 2 20 34 2 0 0 8 2 2 0 . 0 . 0 5 0,0,5,0 UTR_3_PRIME(MODIFIER||8||474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|T),UTR_3_PRIME(MODIFIER||8||474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|T),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|T) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs370590461 -0.590765 0.110342 5 P464L 474 cCg/cTg MODERATE 4 MISSENSE CODING PRAMEF14 A protein_coding NM_001024661.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448084 G A 0 120 0 . 0 . 0 . 0 . 0 . 2 177 468 14 22 8 205 2 40 2 296 618 16 32 8 218 4 44 0 . 0 . 0 38 0,0,38,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P464L|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P464L|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 25 0 0 . 0 . rs138924513 -0.693143 0.000402724 38 P464L 474 cCg/cTg MODERATE 4 MISSENSE CODING PRAMEF13 A protein_coding NM_001291380.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448084 G A 0 120 0 . 0 . 0 . 0 . 0 . 2 177 468 14 22 8 205 2 40 2 296 618 16 32 8 218 4 44 0 . 0 . 0 38 0,0,38,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P464L|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P464L|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 25 0 0 . 0 . rs138924513 -0.693143 0.000402724 38 G453 474 ggT/ggC LOW 4 SILENT CODING PRAMEF14 G protein_coding NM_001024661.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448116 A G 0 46.8 0 . 0 . 0 . 0 . 0 . 1 28 203 4 0 8 118 2 43 2 298 742 18 28 16 294 4 84 0.707041 0 . 0 . 59 39,0,20,0 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G453|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G453|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 0.5 1 0 . 0 . 0 1 0 25 0 0.318255 0 . 0.009081 rs148992058,rs55945833 -0.692067 5.09597e-05 59 G453 474 ggT/ggC LOW 4 SILENT CODING PRAMEF13 G protein_coding NM_001291380.1.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448116 A G 0 46.8 0 . 0 . 0 . 0 . 0 . 1 28 203 4 0 8 118 2 43 2 298 742 18 28 16 294 4 84 0.707041 0 . 0 . 59 39,0,20,0 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G453|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G453|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 0.5 1 0 . 0 . 0 1 0 25 0 0.318255 0 . 0.009081 rs148992058,rs55945833 -0.692067 5.09597e-05 59 L432P 474 cTa/cCa MODERATE 4 MISSENSE CODING PRAMEF14 G protein_coding NM_001024661.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448180 A G 0 92 0 . 0 . 0 . 0 . 0 . 2 26 63 1 1 2 31 0 2 2 338 486 12 38 6 72 2 18 0.95 0 . 0 . 22 2,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L432P|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L432P|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 25 0 0.225 0 . 0.425 rs199555791 -0.692067 2.29318e-05 22 L432P 474 cTa/cCa MODERATE 4 MISSENSE CODING PRAMEF13 G protein_coding NM_001291380.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448180 A G 0 92 0 . 0 . 0 . 0 . 0 . 2 26 63 1 1 2 31 0 2 2 338 486 12 38 6 72 2 18 0.95 0 . 0 . 22 2,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L432P|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L432P|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 25 0 0.225 0 . 0.425 rs199555791 -0.692067 2.29318e-05 22 D426N 474 Gat/Aat MODERATE 4 MISSENSE CODING PRAMEF14 T protein_coding NM_001024661.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448199 C T 0 146 0 . 0 . 0 . 0 . 0 . 2 36 183 3 2 7 125 2 8 2 514 844 28 74 10 182 6 30 0.993834 0 . 0 . 47 3,0,43,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D426N|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D426N|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|T),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|T) 0 . 0 . 0 . 0 . 1 0 31 0 0.213517 0 . 0.189468 rs143762964 -0.693146 0.988405 47 D426N 474 Gat/Aat MODERATE 4 MISSENSE CODING PRAMEF13 T protein_coding NM_001291380.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448199 C T 0 146 0 . 0 . 0 . 0 . 0 . 2 36 183 3 2 7 125 2 8 2 514 844 28 74 10 182 6 30 0.993834 0 . 0 . 47 3,0,43,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D426N|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D426N|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|T),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|T) 0 . 0 . 0 . 0 . 1 0 31 0 0.213517 0 . 0.189468 rs143762964 -0.693146 0.988405 47 L398 474 Ttg/Ctg LOW 4 SILENT CODING PRAMEF14 G protein_coding NM_001024661.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448283 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 9023 119469 11490 8440 6603 66594 901 16418 2 10380 121372 11578 8648 6614 66732 908 16512 1 0 . 0 . 396 1,0,259,83 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L398|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L398|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 33 0 1 0.00012607 0 1 rs80327699 -0.693147 0.00111092 396 L398 474 Ttg/Ctg LOW 4 SILENT CODING PRAMEF13 G protein_coding NM_001291380.1.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448283 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 9023 119469 11490 8440 6603 66594 901 16418 2 10380 121372 11578 8648 6614 66732 908 16512 1 0 . 0 . 396 1,0,259,83 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L398|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|G),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L398|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 . 0 . 1 0 33 0 1 0.00012607 0 1 rs80327699 -0.693147 0.00111092 396 H375R 474 cAc/cGc MODERATE 4 MISSENSE CODING PRAMEF14 C protein_coding NM_001024661.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448351 T C 0 228 0 . 0 . 0 . 0 . 0 . 2 5582 85778 8454 6857 4162 48050 662 12011 2 6832 93918 8746 7098 4520 52204 706 13812 0 . 0 . COSM1600232 199 0,0,58,125 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H375R|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H375R|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 . 0 . 1 0 33 0 0 0.425281 0 . rs71183793 -0.693147 0.00140227 199 H375R 474 cAc/cGc MODERATE 4 MISSENSE CODING PRAMEF13 C protein_coding NM_001291380.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448351 T C 0 228 0 . 0 . 0 . 0 . 0 . 2 5582 85778 8454 6857 4162 48050 662 12011 2 6832 93918 8746 7098 4520 52204 706 13812 0 . 0 . COSM1600232 199 0,0,58,125 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H375R|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H375R|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 . 0 . 1 0 33 0 0 0.425281 0 . rs71183793 -0.693147 0.00140227 199 M310V 474 Atg/Gtg MODERATE 4 MISSENSE CODING PRAMEF14 C protein_coding NM_001024661.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448547 T C 0 125 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 104 770 56 35 4 474 5 92 2 174 962 64 44 4 564 8 104 0 . 0 . 0 21 0,0,0,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M310V|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M310V|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs200801174 -0.692352 0.0913517 21 M310V 474 Atg/Gtg MODERATE 4 MISSENSE CODING PRAMEF13 C protein_coding NM_001291380.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448547 T C 0 125 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 104 770 56 35 4 474 5 92 2 174 962 64 44 4 564 8 104 0 . 0 . 0 21 0,0,0,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M310V|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M310V|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs200801174 -0.692352 0.0913517 21 D309 474 gaC/gaT LOW 4 SILENT CODING PRAMEF14 A protein_coding NM_001024661.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448548 G A 0 123 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 105 746 54 35 6 458 5 83 2 174 934 62 44 6 546 8 94 0 . 0 . 0 21 0,0,0,21 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D309|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D309|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs201453721 -0.692352 0.0913517 21 D309 474 gaC/gaT LOW 4 SILENT CODING PRAMEF13 A protein_coding NM_001291380.1.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448548 G A 0 123 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 105 746 54 35 6 458 5 83 2 174 934 62 44 6 546 8 94 0 . 0 . 0 21 0,0,0,21 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D309|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|A),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D309|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs201453721 -0.692352 0.0913517 21 E308 474 gaA/gaG LOW 4 SILENT CODING PRAMEF14 C protein_coding NM_001024661.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448551 T C 0 125 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 103 714 47 30 2 451 5 76 2 174 898 54 38 2 538 8 84 0 . 0 . 0 21 0,0,0,21 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E308|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E308|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs199771678,rs61778595 -0.692352 0.0913517 21 E308 474 gaA/gaG LOW 4 SILENT CODING PRAMEF13 C protein_coding NM_001291380.1.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13448551 T C 0 125 0 0.6861 0.8405 0.9135 0.8968 0.8887 0.8896 0 . 0 2 103 714 47 30 2 451 5 76 2 174 898 54 38 2 538 8 84 0 . 0 . 0 21 0,0,0,21 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E308|474|PRAMEF14|protein_coding|CODING|NM_001024661.2.2|4|C),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E308|474|PRAMEF13|protein_coding|CODING|NM_001291380.1.2|4|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 29 0 0 . 0 . rs199771678,rs61778595 -0.692352 0.0913517 21 Y290C 474 tAc/tGc MODERATE 4 MISSENSE CODING PRAMEF10 G protein_coding NM_001039361.4.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13634723 A G 0 64 0 0.146 0.1334 0.1095 0.0794 0.1054 0.2178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.839448 0 . 0 . 97 65,7,18,2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tAc/tGc|Y290C|474|PRAMEF10|protein_coding|CODING|NM_001039361.4.2|4|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tAc/tGc|Y290C|474|PRAMEF33P|protein_coding|CODING|NM_001291381.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 31 0 0.367381 0.168893 0 0.217599 rs202107783 -0.692067 0.000633667 97 Y290C 474 tAc/tGc MODERATE 4 MISSENSE CODING PRAMEF33P G protein_coding NM_001291381.1.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13634723 A G 0 64 0 0.146 0.1334 0.1095 0.0794 0.1054 0.2178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.839448 0 . 0 . 97 65,7,18,2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tAc/tGc|Y290C|474|PRAMEF10|protein_coding|CODING|NM_001039361.4.2|4|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tAc/tGc|Y290C|474|PRAMEF33P|protein_coding|CODING|NM_001291381.1.2|4|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 31 0 0.367381 0.168893 0 0.217599 rs202107783 -0.692067 0.000633667 97 S427L 479 tCg/tTg MODERATE 3 MISSENSE CODING PRAMEF19 A protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13695685 G A 0 146 0 . 0 . 0 . 0 . 0 . 2 3728 45603 2592 3453 2502 26661 380 6287 2 3746 46446 2598 3456 2602 27290 386 6368 0 . 0 . 0 92 0,0,92,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S427L|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 29 0 0 . 0 . rs201167498 -0.693147 2.78123e-07 92 G393A 479 gGt/gCt MODERATE 3 MISSENSE CODING PRAMEF19 G protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13695787 C G 0 228 0 0.9864 0.9912 0.9971 0.999 0.9821 0.9949 0 . 0 2 5896 80310 7637 6738 4459 47266 574 7740 2 6002 81674 7662 6742 4590 48214 582 7882 0 . 0 . 0 232 0,0,224,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G393A|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 1 0 . 1 0 28 0 0 0.150568 0 . rs202245256 -0.693147 0.00973539 232 C383 479 tgC/tgT LOW 3 SILENT CODING PRAMEF19 A protein_coding NM_001099790.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13695816 G A 0 228 0 . 0 . 0 . 0 . 0 . 2 9006 116864 11492 8632 6466 64125 893 16250 2 9038 118130 11510 8636 6588 65052 900 16406 0 . 0 . 0 389 0,0,276,78 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C383|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 . 0 . 1 0 33 0 0 0.000251666 0 . rs148990958 -0.693147 0.537043 389 T331A 479 Aca/Gca MODERATE 3 MISSENSE CODING PRAMEF19 C protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13695974 T C 0 172 0 0.9947 0.9938 0.9957 0.998 0.9831 0.998 0 . 0 2 169 1328 55 154 61 846 13 30 2 336 3364 86 166 250 2302 22 202 0 . 0 . 0 161 0,0,0,161 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T331A|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 25 0 0 . 0 . rs142734546 -0.693147 7.95849e-06 161 W315R 479 Tgg/Cgg MODERATE 3 MISSENSE CODING PRAMEF19 G protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13696022 A G 0 125 0 0.9992 0.9952 0.9971 0.999 0.9831 0.9969 0 . 0 2 88 1878 36 36 132 1495 14 77 2 116 2828 48 38 218 2232 22 154 0 . 0 . 0 77 0,0,0,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W315R|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 1 0 . 1 0 24 0 0 . 0 . rs201136502 -0.693147 0.532438 77 C312 479 tgT/tgC LOW 3 SILENT CODING PRAMEF19 G protein_coding NM_001099790.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13696029 A G 0 123 0 0.9992 0.9924 0.9914 0.999 0.9771 0.9928 0 . 0 2 147 2577 53 79 169 1977 18 134 2 176 3370 62 82 244 2584 24 198 0 . 0 . 0 73 0,0,0,73 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C312|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|G),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|G) 0 . 0 . 0 1 0 . 1 0 24 0 0 . 0 . rs200753201,rs2359295 -0.693147 0.257956 73 D306E 479 gaT/gaA MODERATE 3 MISSENSE CODING PRAMEF19 T protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13696047 A T 0 122 0 0.9992 0.993 0.9971 0.999 0.9722 0.9969 0 . 0 2 203 2730 73 131 132 1923 19 249 2 232 3894 88 140 230 2858 26 320 0 . 0 . 0 65 0,0,0,65 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D306E|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|T),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|T) 0 . 0 . 0 1 0 . 1 0 24 0 0 . 0 . rs199733857,rs2101624 -0.693147 0.133985 65 S304F 479 tCc/tTc MODERATE 3 MISSENSE CODING PRAMEF19 A protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13696054 G A 0 121 0 0.9992 0.9938 0.9971 0.999 0.9761 0.9969 0 . 0 2 120 1789 46 62 82 1343 13 123 2 144 2776 50 66 168 2158 20 170 0 . 0 . 0 62 0,0,0,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S304F|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|A),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|A) 0 . 0 . 0 1 0 . 1 0 24 0 0 . 0 . rs200378484 -0.693147 0.0560983 62 K292R 479 aAg/aGg MODERATE 3 MISSENSE CODING PRAMEF19 C protein_coding NM_001099790.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13696090 T C 0 107 0 0.9992 0.9952 0.9971 0.999 0.9831 0.9969 0 . 0 2 202 2366 84 127 75 1634 18 226 2 212 2644 86 128 102 1846 20 250 1 0 . 0 . 49 0,1,0,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K292R|479|PRAMEF19|protein_coding|CODING|NM_001099790.2|3|C),INTRON(MODIFIER||||479|PRAMEF18|protein_coding|CODING|NM_001099850.2.2|1|C) 0 . 0 . 0 1 0 . 1 0 26 0 1 0 . 1 rs201393220,rs731980 -0.693147 0.280698 49 A342V 474 gCt/gTt MODERATE 3 MISSENSE CODING PRAMEF17 T protein_coding NM_001099851.3.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13718562 C T 0 48.1 0 . 0 . 0 . 0 . 0 . 1 3 10 0 4 0 2 0 1 2 1408 64248 7772 5196 4918 36488 518 7948 0.841258 0 . 0 . 41 4,21,0,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A342V|474|PRAMEF17|protein_coding|CODING|NM_001099851.3.2|3|T) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.0554176 0.0484595 0 0.0536599 rs200166042 -0.689466 1.39646e-07 41 V135L 475 Gtg/Ctg MODERATE 3 MISSENSE CODING PRAMEF20 C protein_coding NM_001099852.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13744712 G C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 4 0 0 0 4 0 0 2 0 4 0 0 0 4 0 0 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V135L|475|PRAMEF20|protein_coding|CODING|NM_001099852.2|3|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 0 . 0 . rs199886862 -0.379885 0 1 P39 238 ccC/ccT LOW 1 SILENT CODING PDPN T protein_coding NM_006474.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13910417 C T 0 222 0 0.6293 0.5631 0.4798 0.6577 0.329 0.6759 0.557299 0.405668 0.328016 1 5505 52436 6268 6041 2527 21476 376 10243 2 9592 117228 11470 8596 6572 64038 874 16086 0.999875 0 . 0 COSM423659 81 20,12,23,21 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P39|238|PDPN|protein_coding|CODING|NM_006474.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.364724 rs355025 -0.693146 0.421326 81 A223G 238 gCa/gGa MODERATE 5 MISSENSE CODING PDPN G protein_coding NM_006474.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13940864 C G 0 228 0 0.9985 0.9814 0.9885 1 0.9304 0.9867 0.990468 0.966861 0.954767 2 10332 115972 11452 8653 5734 62641 861 16299 2 10406 121406 11578 8654 6614 66736 908 16510 0 . 0 . 0 203 0,0,92,75 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A223G|238|PDPN|protein_coding|CODING|NM_006474.4|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2486188 -0.693147 0.147768 203 238 1491 MODIFIER 6 CODING PDPN G protein_coding NM_006474.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 13943897 T G 0 77 0 0.3767 0.3998 0.3372 0.4157 0.3419 0.5184 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||1491||238|PDPN|protein_coding|CODING|NM_006474.4|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12408407 -0.511536 0.431015 3 D283E 1718 gaT/gaA MODERATE 8 MISSENSE CODING PRDM2 A protein_coding NM_012231.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14105139 T A 0 222 0 0.208 0.3712 0.5375 0.3988 0.327 0.4908 0.250567 0.320621 0.356512 1 2460 41135 5709 2871 2210 21118 289 6478 2 10098 115442 10410 8114 6454 63836 870 15660 0.589294 0 . 0 . 136 40,27,34,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D283E|1718|PRDM2|protein_coding|CODING|NM_012231.4|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.323057 rs2076324 -0.693147 0.464508 136 E336 1718 gaG/gaA LOW 8 SILENT CODING PRDM2 A protein_coding NM_012231.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14105298 G A 0 222 0 0.2012 0.3163 0.5389 0.373 0.3101 0.2618 0.243532 0.310395 0.344651 1 2564 43163 7228 3169 2344 22881 310 4667 2 10376 121232 11568 8628 6610 66662 904 16484 0.881803 0 . 0 . 95 17,36,16,20 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E336|1718|PRDM2|protein_coding|CODING|NM_012231.4|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985424 rs1203678,rs386522591 -0.693139 0.870457 95 S1608 1718 tcA/tcG LOW 8 SILENT CODING PRDM2 G protein_coding NM_012231.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14109114 A G 0 222 0 0.2322 0.365 0.5418 0.3988 0.328 0.4223 0.263958 0.330847 0.365116 1 2791 46960 7284 3302 2410 24152 333 6688 2 10320 121008 11558 8622 6608 66520 904 16476 0.0955335 0 . 0 . 74 7,28,13,22 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1608|1718|PRDM2|protein_coding|CODING|NM_012231.4|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874979 rs1203651,rs386522587 -0.693136 0.203639 74 P1706 1718 ccA/ccG LOW 9 SILENT CODING PRDM2 G protein_coding NM_012231.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14143003 A G 0 222 0 0.9319 0.8213 0.8573 0.7073 0.8569 0.727 0.934635 0.874443 0.843605 1 9682 100203 9272 6195 5396 56398 761 12499 2 10406 121374 11562 8650 6608 66732 908 16508 0.679232 0 . 0 . 68 20,17,11,15 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1706|1718|PRDM2|protein_coding|CODING|NM_012231.4|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.304243 rs1046331,rs386513114 -0.692976 0.117746 68 1718 6802 MODIFIER 10 CODING PRDM2 A protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14149844 T A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.436225 0 . 0 . 68 20,13,14,14 UTR_3_PRIME(MODIFIER||6802||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.876349 rs1046333 -0.693054 0.228092 68 1718 6990 MODIFIER 10 CODING PRDM2 T protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150032 C T 0 222 0 0.7262 0.6593 0.7493 0.5764 0.7356 0.5123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.971061 0 . 0 . 60 10,16,13,19 UTR_3_PRIME(MODIFIER||6990||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.814266 rs2697967 -0.69312 0.203548 60 1718 7074 MODIFIER 10 CODING PRDM2 T protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150116 C T 0 155 0 0.7284 0.7147 0.7723 0.622 0.7893 0.6738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.854897 0 . 0 . 30 0,15,1,14 UTR_3_PRIME(MODIFIER||7074||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.892469 rs2697966 -0.688148 0.253349 30 1718 7463 MODIFIER 10 CODING PRDM2 C protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150505 T C 0 98 0 0.73 0.7157 0.7752 0.623 0.7893 0.6738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991701 0 . 0 . 14 8,0,5,1 UTR_3_PRIME(MODIFIER||7463||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875173 rs2697965 -0.616816 0.394382 14 1718 7667 MODIFIER 10 CODING PRDM2 T protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150709 C T 0 222 0 0.8601 0.8193 0.8573 0.8075 0.8479 0.7198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.882761 0 . 0 . 94 25,22,15,23 UTR_3_PRIME(MODIFIER||7667||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.913929 rs2697964 -0.693143 0.864683 94 1718 7672 MODIFIER 10 CODING PRDM2 A protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150714 G A 0 222 0 0.8601 0.8193 0.8573 0.8075 0.8479 0.7198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960472 0 . 0 . 93 25,21,13,24 UTR_3_PRIME(MODIFIER||7672||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.866214 rs2744680 -0.693141 0.858993 93 1718 7698 MODIFIER 10 CODING PRDM2 T protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150740 G T 0 222 0 0.8601 0.8191 0.8559 0.8075 0.8479 0.7198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.739134 0 . 0 . 86 20,21,7,26 UTR_3_PRIME(MODIFIER||7698||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.990804 rs2697963 -0.693127 0.207849 86 1718 7950 MODIFIER 10 CODING PRDM2 C protein_coding NM_012231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 14150992 T C 0 15.2 0 0.8563 0.8179 0.8559 0.8075 0.8469 0.7198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,2,1,0 UTR_3_PRIME(MODIFIER||7950||1718|PRDM2|protein_coding|CODING|NM_012231.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2697962,rs386572141 -0.379885 0 5 A706T 775 Gca/Aca MODERATE 14 MISSENSE CODING KAZN A protein_coding NM_201628.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15438990 G A 0 222 0 0.264 0.4421 0.4438 0.6558 0.3966 0.5082 0.281888 0.362923 0.404468 1 2488 47653 5848 5409 2435 23838 344 7291 2 7846 99306 9400 7740 5064 54872 720 13664 0.999379 0 . 0 . 78 16,18,21,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A706T|775|KAZN|protein_coding|CODING|NM_201628.2|14|A),INTRAGENIC(MODIFIER|||||TMEM51-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970011 rs10803354 -0.693139 0.422064 78 R763C 775 Cgt/Tgt MODERATE 15 MISSENSE CODING KAZN T protein_coding NM_201628.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15441090 C T 0 222 0 0 0.0513 0 0.1746 0.001 0.0818 0.00158874 0.00253729 0.00302326 1 14 1991 20 948 6 165 15 823 2 5788 60934 3946 4378 3482 32498 500 10342 0.99769 0 . 0 . 122 30,28,27,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R763C|775|KAZN|protein_coding|CODING|NM_201628.2|15|T),INTRAGENIC(MODIFIER|||||TMEM51-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850233 rs12048768 -0.693147 0.0270564 122 775 144 MODIFIER 15 CODING KAZN T protein_coding NM_201628.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15441275 C T 0 69 0 0.4274 0.6028 0.6066 0.7044 0.6372 0.6973 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.475187 0 . 0 . 17 1,9,0,7 UTR_3_PRIME(MODIFIER||144||775|KAZN|protein_coding|CODING|NM_201628.2|15|T),INTRAGENIC(MODIFIER|||||TMEM51-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995249 rs1055412 -0.636426 0.705301 17 775 2237 MODIFIER 15 CODING KAZN G protein_coding NM_201628.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15443368 A G 0 9.7 0 0.9826 0.9764 0.964 0.9921 0.9473 0.9908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2237||775|KAZN|protein_coding|CODING|NM_201628.2|15|G),INTRAGENIC(MODIFIER|||||TMEM51-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1476356,rs386533605 -0.379885 0 1 775 2639 MODIFIER 15 CODING KAZN G protein_coding NM_201628.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15443770 A G 0 9.7 0 0.9826 0.9764 0.964 0.9921 0.9473 0.9908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2639||775|KAZN|protein_coding|CODING|NM_201628.2|15|G),INTRAGENIC(MODIFIER|||||TMEM51-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10754880 -0.379885 0 1 253 LOW 1 CODING TMEM51 A protein_coding NM_001136216.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15479283 G A 0 9.7 0 0.6188 0.7734 0.8501 0.9405 0.7525 0.7771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 SPLICE_SITE_REGION+INTRON(LOW||||253|TMEM51|protein_coding|CODING|NM_001136216.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1076726 -0.379885 0 1 Y88H 126 Tat/Cat MODERATE 3 MISSENSE CODING C1orf195 G protein_coding NM_001278501.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15495110 A G 0 222 0 0.3623 0.2853 0.2565 0.3452 0.1779 0.2505 0 . 0 1 357 3770 73 162 334 1016 45 1783 2 1046 17154 300 486 1658 5786 212 7666 0.962315 0 . 0 . 158 31,45,29,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y88H|126|C1orf195|protein_coding|CODING|NM_001278501.1|3|G),INTRON(MODIFIER||||253|TMEM51|protein_coding|CODING|NM_001136216.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.464351 rs78615461 -0.693147 0.852875 158 R16 126 cgA/cgG LOW 2 SILENT CODING C1orf195 C protein_coding NM_001278501.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15497727 T C 0 228 0 0.9085 0.9563 0.9582 0.994 0.9523 0.9847 0 . 0 2 828 15525 285 485 1136 5065 173 7553 2 914 16066 292 486 1226 5300 182 7666 0 . 0 . 0 107 0,0,72,22 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R16|126|C1orf195|protein_coding|CODING|NM_001278501.1|2|C),INTRON(MODIFIER||||253|TMEM51|protein_coding|CODING|NM_001136216.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6429722 -0.693147 0.606012 107 253 186 MODIFIER 3 CODING TMEM51 T protein_coding NM_001136216.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541398 C T 0 63 0 0.0408 0.1498 0.1527 0.3304 0.162 0.0961 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 8 3,0,4,0 UTR_5_PRIME(MODIFIER||186||253|TMEM51|protein_coding|CODING|NM_001136216.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 1.01283 rs3753318 -0.556411 0.646346 8 253 185 MODIFIER 3 CODING TMEM51 G protein_coding NM_001136216.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541399 A G 0 63 0 0.0658 0.1569 0.1556 0.3304 0.163 0.0961 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 8 3,0,4,0 UTR_5_PRIME(MODIFIER||185||253|TMEM51|protein_coding|CODING|NM_001136216.1|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 1.01283 rs3753317 -0.556411 0.646346 8 253 177 MODIFIER 3 CODING TMEM51 T protein_coding NM_001136216.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541407 C T 0 64 0 0.348 0.4123 0.5072 0.5437 0.3489 0.362 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 8 4,0,3,0 UTR_5_PRIME(MODIFIER||177||253|TMEM51|protein_coding|CODING|NM_001136216.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.810265 rs3753316 -0.511536 0.748679 8 253 172 MODIFIER 3 CODING TMEM51 A protein_coding NM_001136216.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541412 G A 0 19.1 0 0.0658 0.1566 0.1556 0.3294 0.162 0.0961 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.28717 0 . 0 . 7 3,0,3,0 UTR_5_PRIME(MODIFIER||172||253|TMEM51|protein_coding|CODING|NM_001136216.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 0 . 0.861511 rs3753315 -0.511536 0.0941127 7 253 47 MODIFIER 3 CODING TMEM51 T protein_coding NM_001136216.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541537 C T 0 228 0 0.6914 0.8572 0.9035 0.9762 0.8857 0.8967 0.702549 0.813271 0.86996 2 6383 96647 10587 8112 5807 53989 712 11057 2 9026 110410 11364 8350 6554 62242 804 12070 0 . 0 . 0 37 0,0,30,5 UTR_5_PRIME(MODIFIER||47||253|TMEM51|protein_coding|CODING|NM_001136216.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3753314 -0.693136 0.338018 37 N8 253 aaT/aaC LOW 3 SILENT CODING TMEM51 C protein_coding NM_001136216.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15541607 T C 0 222 0 0.0764 0.1591 0.1556 0.3294 0.162 0.0951 0.0819337 0.13932 0.168721 1 839 18906 1492 2521 653 11337 130 1934 2 10146 119870 11540 8568 6608 65942 892 16174 0.909045 0 . 0 . 120 40,7,44,6 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N8|253|TMEM51|protein_coding|CODING|NM_001136216.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.69789 rs3820065 -0.693147 0.00117153 120 1412 4506 MODIFIER 1 CODING FHAD1 G protein_coding NM_052929.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15573775 A G 0 39.3 0 0.6989 0.5483 0.4107 0.4315 0.4463 0.6677 0 . 0 2 1 32 1 0 0 2 0 28 2 2 44 2 0 0 4 0 36 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||4506||1412|FHAD1|protein_coding|CODING|NM_052929.1|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs1780598 -0.453602 0.1 2 P100 1412 ccG/ccA LOW 3 SILENT CODING FHAD1 A protein_coding NM_052929.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15599025 G A 0 169 0 0.0234 0.1276 0.1571 0.1409 0.164 0.1963 0.0368497 0.123522 0.161219 1 81 3318 78 93 237 1321 39 1469 2 1964 19528 372 582 906 7986 206 7512 0.67248 0 . 0 . 46 2,23,2,18 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P100|1412|FHAD1|protein_coding|CODING|NM_052929.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953569 rs75432354 -0.692067 0.816543 46 L1391 1412 ctG/ctA LOW 31 SILENT CODING FHAD1 A protein_coding NM_052929.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15723843 G A 0 222 0 0.0983 0.3107 0.2925 0.4504 0.4533 0.32 0.140896 0.364652 0.461974 1 352 8669 136 290 756 4553 121 2461 2 2358 23034 434 626 1724 9722 256 7914 0.834371 0 . 0 . 123 28,26,28,29 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L1391|1412|FHAD1|protein_coding|CODING|NM_052929.1|31|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.819332 rs2294490 -0.693147 0.0467919 123 1412 124 MODIFIER 31 CODING FHAD1 G protein_coding NM_052929.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15724033 A G 0 123 0 0.9062 0.745 0.5807 0.7063 0.7356 0.6933 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.468314 0 . 0 . 25 0,11,0,14 UTR_3_PRIME(MODIFIER||124||1412|FHAD1|protein_coding|CODING|NM_052929.1|31|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.955682 rs2253372 -0.686358 0.0227798 25 240 28 MODIFIER 4 CODING EFHD2 T protein_coding NM_024329.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15755248 C T 0 222 0 0.0424 0.1701 0.1671 0.246 0.1501 0.2873 0.0426123 0.100844 0.130517 1 170 5731 302 394 102 2501 45 2217 2 3128 28030 1128 1304 356 13306 246 8562 0.996695 0 . 0 . 55 9,20,6,14 UTR_3_PRIME(MODIFIER||28||240|EFHD2|protein_coding|CODING|NM_024329.5|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996695 rs3765372 -0.692067 0.352708 55 A99 269 gcA/gcC LOW 4 SILENT CODING CELA2A C protein_coding NM_033440.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15789297 A C 0 222 0 0.6762 0.3988 0.3213 0.2321 0.3161 0.3354 0.608488 0.425342 0.331512 1 6373 41248 3143 2066 1633 21856 314 5863 2 10404 121346 11568 8634 6606 66720 908 16506 0.981136 0 . 0 COSM301916 86 19,10,40,11 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A99|269|CELA2A|protein_coding|CODING|NM_033440.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948474 rs3815787,rs55772743 -0.693147 0.0906561 86 A35 269 gcG/gcA LOW 2 SILENT CODING CELA2B A protein_coding NM_015849.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15803016 G A 0 222 0 0 0.0065895 0.0014 0.0288 0.002 0.001 0.000453926 0.00107643 0.00139535 1 2 321 22 156 1 121 3 16 2 10406 121408 11578 8654 6612 66738 908 16512 0.540074 0 . 0 . 136 38,26,32,28 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A35|269|CELA2B|protein_coding|CODING|NM_015849.2|2|A),DOWNSTREAM(MODIFIER||4430||269|CELA2A|protein_coding|CODING|NM_033440.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.430954 rs145776598 -0.693147 0.0778343 136 G79R 269 Ggg/Agg MODERATE 4 MISSENSE CODING CELA2B A protein_coding NM_015849.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15808767 G A 0 222 0 0.2776 0.3265 0.3473 0.5685 0.2416 0.2157 0.260781 0.250807 0.245698 1 2751 33573 4268 4804 1806 16545 242 3157 2 10394 121212 11568 8630 6610 66624 906 16480 0.885935 0 . 0 . 59 15,16,16,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G79R|269|CELA2B|protein_coding|CODING|NM_015849.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999964 rs3820071 -0.692831 0.342848 59 D114N 269 Gac/Aac MODERATE 4 MISSENSE CODING CELA2B A protein_coding NM_015849.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15808872 G A 0 222 0 0.2769 0.3151 0.2896 0.5575 0.2376 0.2147 0.261235 0.250807 0.245465 1 2743 32906 3812 4685 1771 16516 241 3138 2 10406 121378 11572 8638 6612 66732 908 16510 0.965179 0 . 0 . 77 19,19,16,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D114N|269|CELA2B|protein_coding|CODING|NM_015849.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.599425 rs3766160 -0.693021 0.563311 77 T158 269 acG/acA LOW 5 SILENT CODING CELA2B A protein_coding NM_015849.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15809876 G A 0 222 0 0.348 0.3462 0.3545 0.5694 0.2416 0.2157 0.322061 0.271538 0.245636 1 3434 34272 4289 4799 1808 16548 243 3151 2 10376 121044 11554 8620 6612 66544 902 16436 0.985649 0 . 0 . 112 21,34,11,39 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T158|269|CELA2B|protein_coding|CODING|NM_015849.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.998334 0.999509 0 0.846433 rs10927792 -0.693147 0.521711 112 Q177R 269 cAg/cGg MODERATE 6 MISSENSE CODING CELA2B G protein_coding NM_015849.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15812432 A G 0 228 0 0.9773 0.9932 0.9942 1 1 1 0.979346 0.992849 0.999767 2 10220 121192 11562 8650 6614 66731 907 16508 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 106 0,0,60,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q177R|269|CELA2B|protein_coding|CODING|NM_015849.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6429745 -0.693147 0.000143295 106 Q221R 416 cAg/cGg MODERATE 5 MISSENSE CODING CASP9 C protein_coding NM_001229.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15832543 T C 0 222 0 0.7398 0.5849 0.4986 0.6538 0.5149 0.4376 0.703813 0.587652 0.52814 1 7280 65095 4531 5608 4189 35855 528 7104 2 10392 121234 11560 8614 6612 66642 906 16508 0.78946 0 . 0 . 79 6,25,12,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q221R|416|CASP9|protein_coding|CODING|NM_001229.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.42797 rs1052576 -0.693143 0.11391 79 F136 416 ttT/ttC LOW 2 SILENT CODING CASP9 G protein_coding NM_001229.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15844615 A G 0 222 0 0.739 0.5849 0.4986 0.6538 0.5149 0.4387 0.703359 0.587498 0.52814 1 7278 65106 4534 5616 4191 35854 529 7104 2 10406 121350 11566 8626 6614 66726 908 16504 0.86848 0 . 0 COSM146414 248 86,34,76,30 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F136|416|CASP9|protein_coding|CODING|NM_001229.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.560903 rs1132312 -0.693147 0.0314238 248 A28V 416 gCc/gTc MODERATE 1 MISSENSE CODING CASP9 A protein_coding NM_001229.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15850613 G A 0 38.1 0 0.739 0.5847 0.4986 0.6538 0.5149 0.4376 0 . 0 1 1482 10414 190 818 72 4284 83 3485 2 2168 20722 404 1360 118 8340 158 8174 0.900802 0 . 0 . 8 3,2,3,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A28V|416|CASP9|protein_coding|CODING|NM_001229.4|1|A),UPSTREAM(MODIFIER||2695||782|DNAJC16|protein_coding|CODING|NM_015291.3||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.900802 1 0 0.450401 rs1052571 -0.511536 0.645206 8 782 287 MODIFIER 15 CODING DNAJC16 C protein_coding NM_015291.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15894959 T C 0 9.7 0 0.3124 0.3544 0.3112 0.6052 0.2962 0.2434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||287||782|DNAJC16|protein_coding|CODING|NM_015291.3|15|C),DOWNSTREAM(MODIFIER||3235||352|AGMAT|protein_coding|CODING|NM_024758.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1467513 -0.379885 0 1 782 2086 MODIFIER 15 CODING DNAJC16 G protein_coding NM_015291.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15896758 A G 0 25.1 0 0.0015 0.0367 0.0663 0.0407 0.0199 0.0767 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 7 0,4,0,3 UTR_3_PRIME(MODIFIER||2086||782|DNAJC16|protein_coding|CODING|NM_015291.3|15|G),DOWNSTREAM(MODIFIER||1436||352|AGMAT|protein_coding|CODING|NM_024758.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 1.01283 rs141112816 -0.511536 0.807564 7 G105R 352 Ggg/Cgg MODERATE 2 MISSENSE CODING AGMAT G protein_coding NM_024758.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15909850 C G 0 222 0 0.9017 0.6332 0.5274 0.6359 0.5288 0.4499 0.850885 0.653852 0.552907 1 8871 68387 4623 5436 4307 37412 539 7199 2 10370 120640 11454 8598 6554 66370 900 16394 0.935163 0 . 0 . 56 9,11,11,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Cgg|G105R|352|AGMAT|protein_coding|CODING|NM_024758.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965639 rs6429757 -0.693079 0.0461435 56 352 LOW 1 CODING AGMAT G protein_coding NM_024758.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 15909895 A G 0 222 0 0.8298 0.6128 0.5202 0.6359 0.5278 0.4489 0.790513 0.632093 0.55093 1 7495 62562 4184 5037 3825 34720 497 6804 2 9464 109172 9786 7872 5786 60464 824 14976 0.545445 0 . 0 . 44 6,12,4,18 SPLICE_SITE_REGION+INTRON(LOW||||352|AGMAT|protein_coding|CODING|NM_024758.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82243 rs6429758 -0.692562 0.487357 44 304 1741 MODIFIER 5 CODING SLC25A34 A protein_coding NM_207348.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16067642 G A 0 51 0 0 0.0087859 0 0.0427 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.761677 0 . 0 . 40 27,2,7,1 UTR_3_PRIME(MODIFIER||1741||304|SLC25A34|protein_coding|CODING|NM_207348.2|5|A),UPSTREAM(MODIFIER||1345||343|TMEM82|protein_coding|CODING|NM_001013641.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.79221 rs191174782 -0.651104 0.00952064 40 304 1742 MODIFIER 5 CODING SLC25A34 T protein_coding NM_207348.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16067643 C T 0 44.3 0 0 0.0087859 0 0.0427 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.537025 0 . 0 . 41 26,2,8,1 UTR_3_PRIME(MODIFIER||1742||304|SLC25A34|protein_coding|CODING|NM_207348.2|5|T),UPSTREAM(MODIFIER||1344||343|TMEM82|protein_coding|CODING|NM_001013641.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.920477 rs184051975 -0.662043 0.0128834 41 S191F 374 tCc/tTc MODERATE 5 MISSENSE CODING FBLIM1 T protein_coding NM_001024215.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16096934 C T 0 228 0 0.3843 0.6424 0.6931 0.8284 0.6501 0.7556 0.430776 0.616638 0.71186 2 4358 82621 8739 6936 4111 45929 587 11961 2 10388 121224 11568 8634 6610 66614 904 16506 0 . 0 . 0 137 0,0,63,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S191F|374|FBLIM1|protein_coding|CODING|NM_001024215.1|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10927851 -0.693147 0.211387 137 L1091P 3664 cTa/cCa MODERATE 11 MISSENSE CODING SPEN C protein_coding NM_015001.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16256007 T C 0 222 0 0.9758 0.649 0.7118 0.3214 0.5577 0.5941 0.905356 0.68776 0.576279 1 9458 74247 8849 2824 3993 38252 544 10327 2 10286 120656 11518 8590 6608 66300 904 16450 0.800087 0 . 0 . 65 23,6,16,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1091P|3664|SPEN|protein_coding|CODING|NM_015001.2|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.686482 rs848209 -0.692914 0.325209 65 N2360D 3664 Aac/Gac MODERATE 11 MISSENSE CODING SPEN G protein_coding NM_015001.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16259813 A G 0 222 0 0.9758 0.649 0.7118 0.3214 0.5577 0.5941 0.91103 0.689605 0.576163 1 9476 74272 8847 2821 3994 38262 543 10329 2 10308 120844 11528 8606 6602 66424 902 16474 0.937663 0 . 0 . 60 12,21,11,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N2360D|3664|SPEN|protein_coding|CODING|NM_015001.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981954 rs848210 -0.692976 0.362847 60 F334 810 ttC/ttT LOW 8 SILENT CODING ZBTB17 A protein_coding NM_001287603.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16271260 G A 0 196 0 0.0779 0.2083 0.3098 0.0169 0.3052 0.41 0.108488 0.236814 0.302558 1 1052 33526 3915 142 1360 19846 245 6966 2 9280 112726 10712 7862 5410 62650 816 15996 0.980625 0 . 0 . 22 5,5,5,7 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F334|810|ZBTB17|protein_coding|CODING|NM_001287603.1|8|A),DOWNSTREAM(MODIFIER||4310||3664|SPEN|protein_coding|CODING|NM_015001.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.912244 rs9661939 -0.680642 0.00618332 22 A207 810 gcT/gcC LOW 6 SILENT CODING ZBTB17 G protein_coding NM_001287603.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16272250 A G 0 222 0 0.472 0.483 0.6311 0.3175 0.502 0.544 0.457708 0.477192 0.487179 1 4645 61807 8244 2811 3345 32788 445 9529 2 9826 118134 11480 8542 6420 64604 864 16398 0.811586 0 . 0 . 46 14,9,12,9 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A207|810|ZBTB17|protein_coding|CODING|NM_001287603.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.557592 rs848217 -0.692352 0.00536168 46 D6 169 gaC/gaT LOW 1 SILENT CODING C1orf64 T protein_coding NM_178840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16330816 C T 0 222 0 0.1369 0.1951 0.2089 0.2917 0.1581 0.2025 0.15066 0.147557 0.145969 1 1308 17386 2464 2156 770 8082 116 2490 2 6912 79118 6778 6060 2708 44050 524 12086 0.981207 0 . 0 . 310 76,67,81,54 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D6|169|C1orf64|protein_coding|CODING|NM_178840.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.533952 rs1763617 -0.693147 0.0358809 310 T80 169 acC/acT LOW 2 SILENT CODING C1orf64 T protein_coding NM_178840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16332571 C T 0 222 0 0.0514 0.0841 0.0576 0.0823 0.0736 0.1595 0.0594644 0.0591266 0.0589535 1 657 8952 981 641 204 4102 54 2313 2 10404 121054 11570 8650 6614 66598 904 16314 0.361449 0 . 0 . 174 44,36,40,34 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T80|169|C1orf64|protein_coding|CODING|NM_178840.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973573 rs1763612 -0.693147 0.0746442 174 170 1493 MODIFIER 3 CODING HSPB7 T protein_coding NM_014424.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16340582 C T 0 26.3 0 0.0008 0.0067891 0 0.0327 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 3,0,1,1 UTR_3_PRIME(MODIFIER||1493||170|HSPB7|protein_coding|CODING|NM_014424.4|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs142764481 -0.453602 0.02 5 170 1051 MODIFIER 3 CODING HSPB7 A protein_coding NM_014424.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16341024 G A 0 63 0 0.0008 0.0009984 0 0.004 0 0 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1051||170|HSPB7|protein_coding|CODING|NM_014424.4|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs139255885 -0.453602 0.8 3 170 426 MODIFIER 3 CODING HSPB7 T protein_coding NM_014424.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16341649 C T 0 100 0 0.7194 0.6338 0.4207 0.7639 0.5358 0.636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||426||170|HSPB7|protein_coding|CODING|NM_014424.4|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1048238 -0.511536 0.672523 4 170 342 MODIFIER 3 CODING HSPB7 C protein_coding NM_014424.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16341733 T C 0 47.5 0 0.7216 0.6528 0.4582 0.7639 0.5944 0.6431 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||342||170|HSPB7|protein_coding|CODING|NM_014424.4|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1048237 -0.511536 0.857144 3 T117 170 acT/acC LOW 3 SILENT CODING HSPB7 G protein_coding NM_014424.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16342237 A G 0 228 0 0.7216 0.6526 0.4582 0.7639 0.5944 0.6421 0.697004 0.623039 0.585136 2 7213 69370 4304 6341 3762 38488 512 8750 2 10240 116816 11448 8542 6540 64900 850 14296 0.039582 0 . 0 . 135 1,4,30,92 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T117|170|HSPB7|protein_coding|CODING|NM_014424.4|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.999309 rs1739840 -0.693147 0.164946 135 A33 170 gcT/gcC LOW 1 SILENT CODING HSPB7 G protein_coding NM_014424.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344360 A G 0 228 0 0.7103 0.649 0.4553 0.7639 0.5934 0.6421 0.682561 0.618136 0.585136 2 7011 70071 4266 6341 3656 38560 519 9718 2 10154 118898 11322 8568 6264 65322 868 16400 0.693798 0 . 0 . 139 1,1,70,59 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A33|170|HSPB7|protein_coding|CODING|NM_014424.4|1|G),UPSTREAM(MODIFIER||4126||687|CLCNKA|protein_coding|CODING|NM_004070.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.689922 rs732286 -0.693147 0.246 139 S19 170 tcC/tcT LOW 1 SILENT CODING HSPB7 A protein_coding NM_014424.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344402 G A 0 228 0 0.7103 0.649 0.4553 0.7639 0.5934 0.6421 0.681117 0.617407 0.584767 2 7107 70705 4310 6381 3738 38895 532 9742 2 10306 120148 11468 8600 6468 65926 890 16490 0.634615 0 . 0 . 118 0,2,57,47 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S19|170|HSPB7|protein_coding|CODING|NM_014424.4|1|A),UPSTREAM(MODIFIER||4084||687|CLCNKA|protein_coding|CODING|NM_004070.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.730769 rs945416 -0.693147 0.0209117 118 170 36 MODIFIER 1 CODING HSPB7 A protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344494 G A 0 228 0 0.7088 0.6484 0.4553 0.7639 0.5924 0.6421 0.680073 0.617015 0.584756 2 6297 67378 4232 6245 3588 36808 498 9710 2 9048 112800 10900 8376 6080 61362 824 16210 0.804348 0 . 0 . 103 2,0,45,47 UTR_5_PRIME(MODIFIER||36||170|HSPB7|protein_coding|CODING|NM_014424.4|1|A),UPSTREAM(MODIFIER||3992||687|CLCNKA|protein_coding|CODING|NM_004070.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.902174 rs1572381 -0.693147 0.317998 103 170 167 MODIFIER 1 CODING HSPB7 G protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344625 C G 0 228 0 0.7405 0.6482 0.451 0.7619 0.5686 0.6278 0 . 0 2 771 9509 166 462 241 3417 103 4349 2 1046 16532 364 606 396 6086 170 7864 0 . 0 . 0 66 0,0,22,34 UTR_5_PRIME(MODIFIER||167||170|HSPB7|protein_coding|CODING|NM_014424.4|1|G),UPSTREAM(MODIFIER||3861||687|CLCNKA|protein_coding|CODING|NM_004070.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs945417 -0.693147 5.08283e-05 66 170 206 MODIFIER 1 CODING HSPB7 A protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344664 G A 0 121 0 0.3502 0.4361 0.3084 0.6736 0.4185 0.4162 0 . 0 1 316 5607 89 318 66 1998 70 2750 2 860 14516 276 490 136 4946 158 7650 0.308109 0 . 0 . 38 4,14,0,18 UTR_5_PRIME(MODIFIER||206||170|HSPB7|protein_coding|CODING|NM_014424.4|1|A),UPSTREAM(MODIFIER||3822||687|CLCNKA|protein_coding|CODING|NM_004070.3||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.995506 rs872222 -0.691153 0.277406 38 170 225 MODIFIER 1 CODING HSPB7 T protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344683 C T 0 204 0 0.0446 0.0817 0.0548 0.0833 0.0716 0.1595 0 . 0 1 57 1501 17 49 9 282 9 1078 2 788 14084 260 482 82 4706 148 7618 0.764748 0 . 0 . 31 0,17,3,10 UTR_5_PRIME(MODIFIER||225||170|HSPB7|protein_coding|CODING|NM_014424.4|1|T),UPSTREAM(MODIFIER||3803||687|CLCNKA|protein_coding|CODING|NM_004070.3||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.641872 rs872221 -0.683931 0.506326 31 170 272 MODIFIER 1 CODING HSPB7 C protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344730 T C 0 228 0 0.7557 0.7488 0.6009 0.9762 0.6779 0.683 0 . 0 2 535 8822 132 422 41 2927 92 4673 2 710 13676 232 440 52 4510 142 7590 0 . 0 . 0 15 0,0,2,13 UTR_5_PRIME(MODIFIER||272||170|HSPB7|protein_coding|CODING|NM_014424.4|1|C),UPSTREAM(MODIFIER||3756||687|CLCNKA|protein_coding|CODING|NM_004070.3||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs945418 -0.688148 0.239048 15 170 400 MODIFIER 1 CODING HSPB7 T protein_coding NM_014424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16344858 C T 0 135 0 0.7065 0.6386 0.4452 0.7619 0.5686 0.6288 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,5 UTR_5_PRIME(MODIFIER||400||170|HSPB7|protein_coding|CODING|NM_014424.4|1|T),UPSTREAM(MODIFIER||3628||687|CLCNKA|protein_coding|CODING|NM_004070.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs945419 -0.616816 0.810983 6 R83G 687 Agg/Ggg MODERATE 4 MISSENSE CODING CLCNKA G protein_coding NM_004070.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16351275 A G 0 228 0 0.7201 0.643 0.4467 0.7688 0.5636 0.6299 0.696096 0.600877 0.552093 2 7305 68233 4214 6438 3506 37099 510 9161 2 10374 121058 11564 8632 6594 66480 904 16510 1 0 . 0 . 111 1,0,68,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R83G|687|CLCNKA|protein_coding|CODING|NM_004070.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10927887 -0.693147 0.00643067 111 H357Q 687 caT/caA MODERATE 12 MISSENSE CODING CLCNKA A protein_coding NM_004070.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16355638 T A 0 128 0 0.0439 0.0859 0.0562 0.0992 0.0746 0.1616 0.0460735 0.055795 0.0607825 1 511 9053 1000 782 204 4176 55 2325 2 9960 118048 11388 8572 6340 64480 864 16444 0.624282 0 . 0 . 65 39,1,23,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H357Q|687|CLCNKA|protein_coding|CODING|NM_004070.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 50 0 0.540433 0.629032 0 0.557106 rs79751787 -0.692831 0.0349143 65 A447T 687 Gcc/Acc MODERATE 14 MISSENSE CODING CLCNKA A protein_coding NM_004070.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16356501 G A 0 228 0 0.7496 0.6486 0.4467 0.7669 0.5577 0.6268 0.712665 0.601338 0.544302 2 7478 67808 4192 6431 3476 36663 503 9065 2 10356 120822 11550 8624 6578 66310 898 16506 0 . 0 . 0 79 0,0,38,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A447T|687|CLCNKA|protein_coding|CODING|NM_004070.3|14|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1805152 -0.693147 0.49623 79 687 LOW 17 CODING CLCNKA C protein_coding NM_004070.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16358932 T C 0 228 0 0.7693 0.749 0.5951 0.9742 0.669 0.681 0.756922 0.695218 0.663605 2 7945 83268 6730 8396 4793 44499 634 10271 2 10380 120990 11568 8648 6606 66378 902 16508 0 . 0 . 0 137 0,0,105,21 SPLICE_SITE_REGION+INTRON(LOW||||687|CLCNKA|protein_coding|CODING|NM_004070.3|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10803407 -0.693147 0.0114628 137 687 163 MODIFIER 20 CODING CLCNKA T protein_coding NM_004070.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16360316 A T 0 228 0 0.6619 0.5893 0.4006 0.752 0.4781 0.5716 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.577243 0 . 0 . 67 4,4,16,41 UTR_3_PRIME(MODIFIER||163||687|CLCNKA|protein_coding|CODING|NM_004070.3|20|T) 0 . 0 . 0 1 0 . 0 . 43 0 0.0119618 0.720232 0 0.00439349 rs57537563 -0.693147 0.00336262 67 687 194 MODIFIER 20 CODING CLCNKA G protein_coding NM_004070.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16360347 A G 0 19.5 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999667 0 . 0 . 77 19,36,6,5 UTR_3_PRIME(MODIFIER||194||687|CLCNKA|protein_coding|CODING|NM_004070.3|20|G) 0 0.5 1 0 . 0 . 0 . 0 41 0 0.0153334 0.0448522 0 0.0561061 rs61772373 -0.676189 0.000125511 77 687 271 MODIFIER 20 CODING CLCNKA C protein_coding NM_004070.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16360424 G C 0 156 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.151732 0 . 0 . 38 1,19,3,13 UTR_3_PRIME(MODIFIER||271||687|CLCNKA|protein_coding|CODING|NM_004070.3|20|C) 0 0.5 1 0 . 0 . 0 . 0 35 0 0.981922 0.833241 0 0.624121 rs58783141 -0.689466 0.00235182 38 687 291 MODIFIER 20 CODING CLCNKA T protein_coding NM_004070.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16360444 C T 0 121 0 0.6475 0.5731 0.379 0.7401 0.4563 0.5583 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,0,19 UTR_3_PRIME(MODIFIER||291||687|CLCNKA|protein_coding|CODING|NM_004070.3|20|T) 0 . 0 . 0 1 0 . 0 . 27 0 0 . 0 . rs112701437 -0.69168 2.41513e-07 19 R27L 687 cGc/cTc MODERATE 2 MISSENSE CODING CLCNKB T protein_coding NM_000085.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16371067 G T 0 222 0 0.2549 0.5555 0.6916 0.6498 0.6561 0.6646 0.300045 0.526296 0.642209 1 2508 59164 6139 4411 2222 34542 396 8946 2 7608 92256 8094 6686 3788 52616 620 12844 0.735347 0 . 0 . 126 35,20,29,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R27L|687|CLCNKB|protein_coding|CODING|NM_000085.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.8603 rs2015352 -0.693147 0.0985063 126 S108 687 tcA/tcG LOW 4 SILENT CODING CLCNKB G protein_coding NM_000085.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16373124 A G 0 228 0 0.3147 0.7404 0.8487 0.9881 0.832 0.8896 0.399682 0.672151 0.811744 2 4033 97342 10500 8566 5038 54045 725 14435 2 10398 121340 11572 8654 6606 66692 906 16512 0 . 0 . 0 199 0,0,95,80 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S108|687|CLCNKB|protein_coding|CODING|NM_000085.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5257 -0.693147 0.0929872 199 G164 687 ggG/ggC LOW 5 SILENT CODING CLCNKB C protein_coding NM_000085.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16374533 G C 0 228 0 0.7231 0.894 0.9337 0.999 0.9394 0.9417 0.76532 0.878441 0.936395 2 7926 112626 11099 8645 6118 62730 840 15268 2 10384 121124 11556 8648 6608 66566 904 16458 0 . 0 . 0 243 0,0,100,119 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G164|687|CLCNKB|protein_coding|CODING|NM_000085.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2014562 -0.693147 0.054273 243 687 LOW 6 CODING CLCNKB T protein_coding NM_000085.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16374994 C T 0 228 0 0.3094 0.7386 0.8487 0.9881 0.832 0.8875 0 . 0 2 3981 96982 10484 8553 5039 53776 724 14425 2 10346 121106 11564 8642 6606 66534 904 16510 0 . 0 . 0 149 0,0,82,65 SPLICE_SITE_REGION+INTRON(LOW||||687|CLCNKB|protein_coding|CODING|NM_000085.4|6|T) 0 . 0 . 0 1 0 . 1 0 58 0 0 0.966923 0 . rs1889788 -0.693147 0.532874 149 A214G 687 gCa/gGa MODERATE 7 MISSENSE CODING CLCNKB G protein_coding NM_000085.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16375063 C G 0 228 0 0.4992 0.8273 0.9006 0.998 0.9264 0.9407 0 . 0 2 5804 108817 10859 8630 6079 61357 822 15266 2 10304 120824 11542 8636 6598 66336 904 16504 0 . 0 . 0 175 0,0,89,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A214G|687|CLCNKB|protein_coding|CODING|NM_000085.4|7|G) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.797195 0 . rs1889789 -0.693147 0.00803487 175 A214 687 gcA/gcC LOW 7 SILENT CODING CLCNKB C protein_coding NM_000085.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16375064 A C 0 228 0 0.4992 0.8273 0.9006 0.998 0.9264 0.9407 0 . 0 2 5803 108804 10857 8628 6075 61357 820 15264 2 10304 120816 11538 8634 6594 66342 902 16502 0 . 0 . 0 175 0,0,89,62 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A214|687|CLCNKB|protein_coding|CODING|NM_000085.4|7|C) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.797195 0 . rs1889790 -0.693147 0.00803487 175 A287V 687 gCg/gTg MODERATE 9 MISSENSE CODING CLCNKB T protein_coding NM_000085.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16376191 C T 0 228 0 0.4939 0.8299 0.9107 0.998 0.9384 0.9417 0 . 0 2 5606 106816 10656 8047 6036 60431 814 15226 2 10028 117428 11188 8058 6522 64290 886 16456 0 . 0 . 0 134 0,0,112,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A287V|687|CLCNKB|protein_coding|CODING|NM_000085.4|9|T) 0 . 0 . 0 1 0 . 1 0 56 0 0 0.00410273 0 . rs7367494 -0.693147 0.0359201 134 C292 687 tgT/tgC LOW 10 SILENT CODING CLCNKB C protein_coding NM_000085.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16376319 T C 0 228 0 0.4939 0.8301 0.9107 0.999 0.9384 0.9417 0.580345 0.815085 0.935349 2 5865 110642 11036 8652 6126 62825 837 15301 2 10402 121404 11578 8654 6614 66736 908 16512 0 . 0 . 0 153 0,0,31,107 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C292|687|CLCNKB|protein_coding|CODING|NM_000085.4|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7368151 -0.693147 0.0011558 153 M562T 687 aTg/aCg MODERATE 16 MISSENSE CODING CLCNKB C protein_coding NM_000085.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16380196 T C 0 228 0 0.646 0.8383 0.9179 0.8353 0.9692 0.91 0.700635 0.888248 0.984411 2 7155 112699 11029 6982 6186 65150 839 15358 2 10358 121050 11562 8640 6612 66466 902 16510 0 . 0 . 0 162 0,0,90,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M562T|687|CLCNKB|protein_coding|CODING|NM_000085.4|16|C),DOWNSTREAM(MODIFIER||4068||280|FAM131C|protein_coding|CODING|NM_182623.2||C) 1 0 . 0 . 1 0 1 1 0 52 0 0 0.000325367 0 . rs5253 -0.693147 0.0139978 162 K578E 687 Aag/Gag MODERATE 16 MISSENSE CODING CLCNKB G protein_coding NM_000085.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16380243 A G 0 228 0 0.82 0.7017 0.5519 0.8056 0.6262 0.6186 0.799365 0.70083 0.650349 2 8227 79304 5820 6831 4860 43386 592 9588 2 10336 120418 11504 8592 6542 66046 902 16496 0 . 0 . 0 156 0,0,65,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K578E|687|CLCNKB|protein_coding|CODING|NM_000085.4|16|G),DOWNSTREAM(MODIFIER||4021||280|FAM131C|protein_coding|CODING|NM_182623.2||G) 1 0 . 0 . 1 0 1 1 0 50 0 0 5.74119e-09 0 . rs2275166 -0.693147 0.0182313 156 L581 687 Ctg/Ttg LOW 16 SILENT CODING CLCNKB T protein_coding NM_000085.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16380252 C T 0 228 0 0.5734 0.6136 0.5 0.8016 0.6123 0.5562 0.57921 0.611333 0.627791 2 5990 74783 5537 6785 4756 42470 557 8688 2 10324 120418 11494 8590 6540 66082 900 16488 0 . 0 . 0 150 0,0,58,80 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L581|687|CLCNKB|protein_coding|CODING|NM_000085.4|16|T),DOWNSTREAM(MODIFIER||4012||280|FAM131C|protein_coding|CODING|NM_182623.2||T) 1 0 . 0 . 1 0 1 1 0 50 0 0 2.97918e-06 0 . rs2275167 -0.693147 0.00987342 150 687 37 MODIFIER 20 CODING CLCNKB C protein_coding NM_000085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16383448 A C 0 228 0 0.9032 0.901 0.9265 0.8244 0.9632 0.8947 0 . 0 2 8864 107101 10483 6471 5604 60660 784 14235 2 9674 113924 10946 8104 6152 62630 846 15572 0.999875 0 . 0 . 158 4,1,53,91 UTR_3_PRIME(MODIFIER||37||687|CLCNKB|protein_coding|CODING|NM_000085.4|20|C),DOWNSTREAM(MODIFIER||816||280|FAM131C|protein_coding|CODING|NM_182623.2||C) 0 . 0 . 0 1 0 . 1 0 50 0 0.865455 0.000517312 0 0.501235 rs10803415 -0.693147 0.0130661 158 687 170 MODIFIER 20 CODING CLCNKB T protein_coding NM_000085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16383581 G T 0 221 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.700189 0 . 0 . 137 32,0,60,40 UTR_3_PRIME(MODIFIER||170||687|CLCNKB|protein_coding|CODING|NM_000085.4|20|T),DOWNSTREAM(MODIFIER||683||280|FAM131C|protein_coding|CODING|NM_182623.2||T) 0 0.5 1 0 . 0 . 0 . 0 48 0 0.991228 0.997426 0 0.0375515 rs1057844 -0.693147 0.0316756 137 687 194 MODIFIER 20 CODING CLCNKB G protein_coding NM_000085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16383605 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.835155 0 . 0 . 142 42,0,72,26 UTR_3_PRIME(MODIFIER||194||687|CLCNKB|protein_coding|CODING|NM_000085.4|20|G),DOWNSTREAM(MODIFIER||659||280|FAM131C|protein_coding|CODING|NM_182623.2||G) 0 0.5 1 0 . 0 . 0 . 0 47 0 0.796135 0.866263 0 0.00108626 rs1057845,rs76515451 -0.693147 0.202736 142 687 257 MODIFIER 20 CODING CLCNKB G protein_coding NM_000085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16383668 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 1039 15309 316 526 530 5218 176 7504 2 1040 15310 316 526 530 5218 176 7504 0 . 0 . 0 252 0,0,188,45 UTR_3_PRIME(MODIFIER||257||687|CLCNKB|protein_coding|CODING|NM_000085.4|20|G),DOWNSTREAM(MODIFIER||596||280|FAM131C|protein_coding|CODING|NM_182623.2||G) 0 . 0 . 0 1 0 . 1 0 50 0 0 0.0066808 0 . rs6660218 -0.693147 0.000924942 252 687 331 MODIFIER 20 CODING CLCNKB G protein_coding NM_000085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16383742 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 652 10604 213 266 830 3753 124 4766 2 1108 17084 316 538 1356 5864 202 7700 0.0319405 0 . 0 . 459 106,74,142,92 UTR_3_PRIME(MODIFIER||331||687|CLCNKB|protein_coding|CODING|NM_000085.4|20|G),DOWNSTREAM(MODIFIER||522||280|FAM131C|protein_coding|CODING|NM_182623.2||G) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.337243 0.00250309 0 0.941518 rs1057857 -0.693147 0.0205696 459 280 579 MODIFIER 7 CODING FAM131C C protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384353 T C 0 171 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.1875 0 . 0 . 12 1,1,3,5 UTR_3_PRIME(MODIFIER||579||280|FAM131C|protein_coding|CODING|NM_182623.2|7|C),DOWNSTREAM(MODIFIER||532||687|CLCNKB|protein_coding|CODING|NM_000085.4||C) 0 0.5 1 0 . 0 . 0 . 0 56 0 0.875 0.783809 0 0.625 rs2863442 -0.651104 0.933643 12 280 374 MODIFIER 7 CODING FAM131C T protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384558 C T 0 114 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.62023 0 . 0 . 11 4,0,2,2 UTR_3_PRIME(MODIFIER||374||280|FAM131C|protein_coding|CODING|NM_182623.2|7|T),DOWNSTREAM(MODIFIER||737||687|CLCNKB|protein_coding|CODING|NM_000085.4||T) 0 0.5 1 0 . 0 . 0 . 0 56 0 0.868321 0.833333 0 0.248092 rs7418808 -0.556411 0.634447 11 280 354 MODIFIER 7 CODING FAM131C A protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384578 G A 0 74 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 10 4,0,1,2 UTR_3_PRIME(MODIFIER||354||280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||757||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 0 . 0 . 0 55 0 0.810265 0.8 0 0.810265 rs3978472 -0.511536 0.539554 10 280 276 MODIFIER 7 CODING FAM131C T protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384656 G T 0 111 0 0.9531 0.9205 0.9352 0.8353 0.9672 0.9059 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,2 UTR_3_PRIME(MODIFIER||276||280|FAM131C|protein_coding|CODING|NM_182623.2|7|T),DOWNSTREAM(MODIFIER||835||687|CLCNKB|protein_coding|CODING|NM_000085.4||T) 0 . 0 . 0 1 0 . 0 . 42 0 0 0.2 0 . rs2863443 -0.636426 0.118055 7 280 148 MODIFIER 7 CODING FAM131C G protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384784 A G 0 228 0 0.646 0.7774 0.8228 0.8571 0.7823 0.8354 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 89 1,0,85,3 UTR_3_PRIME(MODIFIER||148||280|FAM131C|protein_coding|CODING|NM_182623.2|7|G),DOWNSTREAM(MODIFIER||963||687|CLCNKB|protein_coding|CODING|NM_000085.4||G) 0 . 0 . 0 1 0 . 0 . 56 0 1 0.233753 0 1 rs2019490 -0.693147 0.00269676 89 280 131 MODIFIER 7 CODING FAM131C T protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384801 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 116 1,0,110,5 UTR_3_PRIME(MODIFIER||131||280|FAM131C|protein_coding|CODING|NM_182623.2|7|T),DOWNSTREAM(MODIFIER||980||687|CLCNKB|protein_coding|CODING|NM_000085.4||T) 0 . 0 . 0 . 0 . 0 . 58 0 1 0.393268 0 1 rs6656097 -0.693147 0.00303298 116 280 64 MODIFIER 7 CODING FAM131C A protein_coding NM_182623.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384868 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.865885 0 . 0 . 237 88,21,73,15 UTR_3_PRIME(MODIFIER||64||280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||1047||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 0 . 0 . 0 56 0 0.919015 0.951514 0 0.794291 rs12756288 -0.693147 0.27631 237 L263 280 ctC/ctA LOW 7 SILENT CODING FAM131C T protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384986 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 345 1992 65 149 5 876 19 533 2 794 4708 182 308 12 2234 42 1136 0.88832 0 . 0 COSM1335875 223 41,74,21,68 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L263|280|FAM131C|protein_coding|CODING|NM_182623.2|7|T),DOWNSTREAM(MODIFIER||1165||687|CLCNKB|protein_coding|CODING|NM_000085.4||T) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.996602 0.961966 0 0.522419 rs28496958 -0.693147 0.276778 223 P259 280 ccC/ccG LOW 7 SILENT CODING FAM131C C protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384998 G C 0 222 0 0.4032 0.3768 0.2795 0.4315 0.336 0.3957 0 . 0 1 370 2561 71 164 5 1017 29 905 2 840 5950 196 338 12 2544 66 1954 0.998058 0 . 0 COSM1601158 182 34,63,15,59 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P259|280|FAM131C|protein_coding|CODING|NM_182623.2|7|C),DOWNSTREAM(MODIFIER||1177||687|CLCNKB|protein_coding|CODING|NM_000085.4||C) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.918809 0.999627 0 0.492056 rs1807285 -0.693147 0.00801211 182 P259L 280 cCc/cTc MODERATE 7 MISSENSE CODING FAM131C A protein_coding NM_182623.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16384999 G A 0 222 0 0.4032 0.3768 0.2795 0.4315 0.336 0.3957 0 . 0 1 346 2560 69 165 4 1025 31 920 2 848 6008 192 340 10 2562 70 1986 0.852876 0 . 0 COSM1601159 181 34,62,15,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P259L|280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||1178||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.913917 0.999821 0 0.554556 rs1807284 -0.693147 0.00801211 181 R245W 280 Cgg/Tgg MODERATE 7 MISSENSE CODING FAM131C A protein_coding NM_182623.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16385042 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 447 3347 94 221 8 1281 35 1261 2 1022 8202 262 470 18 3402 82 2946 0.876519 0 . 0 COSM1733522 113 17,39,25,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R245W|280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||1221||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.239417 0.028157 0 0.125267 rs77667563 -0.693147 0.786578 113 S200 280 agC/agT LOW 7 SILENT CODING FAM131C A protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16385175 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 4102 47931 3412 4393 1726 27201 316 6781 2 7768 86378 6466 6576 3540 49444 570 12014 0.688306 0 . 0 . 176 35,16,54,47 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S200|280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||1354||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 0 . 0 1 0 47 0 0.880139 0.584705 0 0.995624 rs17853748 -0.693147 5.19729e-05 176 S197 280 agC/agT LOW 7 SILENT CODING FAM131C A protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16385184 G A 0 160 0 . 0 . 0 . 0 . 0 . 1 1673 23326 997 2574 878 14134 159 2911 2 6960 76644 4642 6138 3114 44232 500 11058 0.824102 0 . 0 COSM530219 184 68,53,22,15 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S197|280|FAM131C|protein_coding|CODING|NM_182623.2|7|A),DOWNSTREAM(MODIFIER||1363||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 0 0.5 1 0 . 0 . 0 1 0 46 0 0.84066 0.667581 0 0.958972 rs75273615 -0.693141 0.159417 184 Q181 280 caA/caG LOW 6 SILENT CODING FAM131C C protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16386008 T C 0 228 0 0.5061 0.7216 0.7709 0.8343 0.7654 0.817 0 . 0 2 4836 85851 9638 6745 3998 47148 626 12860 2 9222 114500 11082 8284 6108 63012 844 15948 0 . 0 . 0 102 0,0,54,37 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q181|280|FAM131C|protein_coding|CODING|NM_182623.2|6|C),DOWNSTREAM(MODIFIER||2187||687|CLCNKB|protein_coding|CODING|NM_000085.4||C) 0 . 0 . 0 1 0 . 1 0 54 0 0 0.683363 0 . rs2863452 -0.693147 3.09454e-05 102 D133 280 gaC/gaT LOW 5 SILENT CODING FAM131C A protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16386416 G A 0 228 0 0.4871 0.7105 0.768 0.8155 0.7584 0.8139 0.542118 0.685214 0.75683 2 4829 88058 9933 6854 4046 48506 635 13255 2 9416 117594 11414 8508 6252 64724 862 16418 0.67094 0 . 0 COSM424446 128 2,0,89,28 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D133|280|FAM131C|protein_coding|CODING|NM_182623.2|5|A),DOWNSTREAM(MODIFIER||2595||687|CLCNKB|protein_coding|CODING|NM_000085.4||A) 1 0 . 0 . 1 0 1 1 0 58 0 0.931624 0.948322 0 0.991453 rs9442230 -0.693147 9.23288e-10 128 P123R 280 cCg/cGg MODERATE 5 MISSENSE CODING FAM131C C protein_coding NM_182623.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16386447 G C 0 228 0 0.9531 0.9159 0.9337 0.8185 0.9662 0.9018 0 . 0 2 8124 105839 10616 6388 5374 59969 744 14624 2 8610 111412 11052 8036 5802 61338 800 15774 0.341298 0 . 0 . 99 3,0,56,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cGg|P123R|280|FAM131C|protein_coding|CODING|NM_182623.2|5|C),DOWNSTREAM(MODIFIER||2626||687|CLCNKB|protein_coding|CODING|NM_000085.4||C) 0 . 0 . 0 1 0 . 1 0 57 0 0.75473 0.73456 0 0.947121 rs11576236 -0.693147 1.23043e-05 99 R107Q 280 cGa/cAa MODERATE 5 MISSENSE CODING FAM131C T protein_coding NM_182623.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16386495 C T 0 127 0 0.056 0.397 0.3458 0.7966 0.4374 0.4407 0 . 0 2 795 38467 3409 4674 2048 22094 257 5190 2 6146 83812 7892 6292 4272 46794 588 11828 0.816551 0 . 0 . 67 1,2,0,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R107Q|280|FAM131C|protein_coding|CODING|NM_182623.2|5|T),DOWNSTREAM(MODIFIER||2674||687|CLCNKB|protein_coding|CODING|NM_000085.4||T) 0 . 0 . 0 1 0 . 1 0 57 0 0.750343 1 0 0.935966 rs71510977 -0.693147 0.0368424 67 R72 280 agA/agG LOW 4 SILENT CODING FAM131C C protein_coding NM_182623.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16388646 T C 0 228 0 0.7163 0.8167 0.8588 0.8304 0.8738 0.8497 0.720947 0.821773 0.871172 2 7038 101887 10517 7158 5038 57332 728 14076 2 9728 119644 11524 8602 6322 66170 890 16408 0 . 0 . 0 106 0,0,42,51 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R72|280|FAM131C|protein_coding|CODING|NM_182623.2|4|C),DOWNSTREAM(MODIFIER||4825||687|CLCNKB|protein_coding|CODING|NM_000085.4||C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.930952 0 . rs2863456 -0.693147 0.0513653 106 976 297 MODIFIER 17 CODING EPHA2 T protein_coding NM_004431.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16451413 C T 0 228 0 0.8843 0.9058 0.938 0.869 0.9672 0.8865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 111 0,1,51,54 UTR_3_PRIME(MODIFIER||297||976|EPHA2|protein_coding|CODING|NM_004431.3|17|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1803527 -0.693147 0.995196 111 P329 976 ccC/ccT LOW 5 SILENT CODING EPHA2 A protein_coding NM_004431.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16464673 G A 0 222 0 0.3396 0.3494 0.4294 0.1458 0.4215 0.4417 0.360581 0.388786 0.403233 1 3487 43869 3897 1013 2106 25507 330 7529 2 9630 115838 11104 8318 6164 63422 856 16344 0.965969 0 . 0 . 121 39,21,36,19 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P329|976|EPHA2|protein_coding|CODING|NM_004431.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.765725 rs2230597 -0.693147 0.0173662 121 258 398 MODIFIER 1 CODING RSG1 G protein_coding NM_030907.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16563635 A G 0 66 0 0.8366 0.7111 0.5648 0.8472 0.7018 0.5143 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||398||258|RSG1|protein_coding|CODING|NM_030907.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs717863 -0.453602 0.82 3 717 2849 MODIFIER 10 CODING FBXO42 C protein_coding NM_018994.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16574316 T C 0 9.7 0 0.5008 0.6356 0.5576 0.8532 0.7584 0.5225 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2849||717|FBXO42|protein_coding|CODING|NM_018994.2|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3738632 -0.379885 0 1 717 2783 MODIFIER 10 CODING FBXO42 C protein_coding NM_018994.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16574382 A C 0 61 0 0.4304 0.2706 0.2133 0.1746 0.334 0.1288 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2783||717|FBXO42|protein_coding|CODING|NM_018994.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6693451 -0.453602 0.84 3 717 2135 MODIFIER 10 CODING FBXO42 C protein_coding NM_018994.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16575030 T C 0 9.7 0 0.1074 0.1819 0.1888 0.1746 0.334 0.1288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2135||717|FBXO42|protein_coding|CODING|NM_018994.2|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17369676 -0.379885 0 1 717 329 MODIFIER 10 CODING FBXO42 G protein_coding NM_018994.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16576836 A G 0 119 0 0.4304 0.2706 0.2133 0.1746 0.334 0.1288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.995519 0 . 0 . 46 22,3,19,0 UTR_3_PRIME(MODIFIER||329||717|FBXO42|protein_coding|CODING|NM_018994.2|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.844939 rs7536390 -0.69168 0.275893 46 P471A 717 Cct/Gct MODERATE 10 MISSENSE CODING FBXO42 C protein_coding NM_018994.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16577908 G C 0 222 0 0.4312 0.2708 0.2133 0.1746 0.334 0.1288 0.423059 0.38044 0.358605 1 4451 36736 1923 1632 2227 23709 265 2529 2 10206 121052 11562 8638 6594 66636 908 16508 0.18446 0 . 0 . 157 52,18,50,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P471A|717|FBXO42|protein_coding|CODING|NM_018994.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.692434 rs12069239 -0.693147 0.121784 157 S5 717 tcG/tcA LOW 2 SILENT CODING FBXO42 T protein_coding NM_018994.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16641899 C T 0 182 0 0.0469 0.3574 0.3372 0.6786 0.4235 0.3926 0.120064 0.303398 0.397326 1 1148 48083 4164 5885 3369 26636 399 6482 2 10382 121126 11548 8630 6600 66592 906 16468 0.910594 0 . 0 . 40 2,18,2,18 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S5|717|FBXO42|protein_coding|CODING|NM_018994.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.81706 rs2273311,rs386563155 -0.692067 0.569158 40 152 1449 MODIFIER 4 CODING SZRD1 A protein_coding NM_001114600.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16723084 G A 0 46.3 0 0.0575 0.3562 0.3228 0.6825 0.4175 0.3845 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1449||152|SZRD1|protein_coding|CODING|NM_001114600.2|4|A),DOWNSTREAM(MODIFIER||2054||469|SPATA21|protein_coding|CODING|NM_198546.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3738605 -0.453602 0.56 2 Q184R 469 cAg/cGg MODERATE 6 MISSENSE CODING SPATA21 C protein_coding NM_198546.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16736132 T C 0 222 0 0.0159 0.1528 0.1686 0.1726 0.3161 0.138 0.0640036 0.238659 0.32814 1 577 29269 1538 1619 1837 20667 226 2805 2 9338 115932 11118 8442 5530 64660 846 15998 0.798671 0 . 0 . 77 21,9,22,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q184R|469|SPATA21|protein_coding|CODING|NM_198546.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.629996 rs4661746 -0.693145 0.0344641 77 469 LOW 5 CODING SPATA21 T protein_coding NM_198546.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16736546 C T 0 228 0 0.5953 0.6206 0.5346 0.9097 0.6421 0.3957 0.633049 0.647012 0.654067 2 5376 67741 5628 7813 4725 39536 479 4184 2 8668 105696 11304 8454 6472 60684 762 9352 0 . 0 . 0 38 0,0,9,26 SPLICE_SITE_REGION+INTRON(LOW||||469|SPATA21|protein_coding|CODING|NM_198546.1|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10907226 -0.693136 0.52326 38 169 319 MODIFIER 1 CODING FAM231B C protein_coding NM_001310155.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16865242 T C 0 11.3 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.833333 0 . 0 . 9 3,3,2,0 START_GAINED(LOW||||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|C),UTR_5_PRIME(MODIFIER||319||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|C) 0 0.5 1 0 . 0 . 0 . 0 56 0 0 0.600535 0 0.333333 rs368134926 -0.453602 0.1 9 169 293 MODIFIER 1 CODING FAM231B G protein_coding NM_001310155.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16865268 A G 0 98 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.899815 0 . 0 . 14 4,2,6,1 UTR_5_PRIME(MODIFIER||293||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|G) 0 0.5 1 0 . 0 . 0 . 0 53 0 0.245404 0.944459 0 0.245404 rs200174302 -0.636426 0.157598 14 169 138 MODIFIER 1 CODING FAM231B T protein_coding NM_001310155.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16865423 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.708999 0 . 0 . 106 59,3,34,6 START_GAINED(LOW||||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|T),UTR_5_PRIME(MODIFIER||138||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|T) 0 0.5 1 0 . 0 . 0 . 0 42 0 0.0138053 0.148634 0 0.00516288 rs61769549 -0.693145 0.257501 106 169 109 MODIFIER 1 CODING FAM231B G protein_coding NM_001310155.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16865452 A G 0 104 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.888647 0 . 0 . 128 89,6,22,10 UTR_5_PRIME(MODIFIER||109||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|G) 0 0.5 1 0 . 0 . 0 . 0 38 0 0.0343894 0.0280344 0 3.18215e-05 rs4661369 -0.69312 2.94717e-05 128 S38T 169 aGc/aCc MODERATE 1 MISSENSE CODING FAM231B C protein_coding NM_001310155.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16865673 G C 0 223 0 . 0 . 0 . 0 . 0 . 2 6 99 5 22 1 38 1 26 2 344 5292 110 60 142 1724 50 2862 0.948854 0 . 0 . 39 4,0,6,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S38T|169|FAM231B|protein_coding|CODING|NM_001310155.1|1|C) 0 . 0 . 0 . 0 . 1 0 33 0 0.539484 0.868647 0 0.180092 rs201269061 -0.693136 0.36725 39 P158L 169 cCc/cTc MODERATE 1 MISSENSE CODING FAM231B T protein_coding NM_001310155.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16866033 C T 0 228 0 0.4508 0.5853 0.4467 0.9038 0.5378 0.5859 0 . 0 2 210 3596 56 126 692 1062 62 1388 2 416 6478 124 140 1154 1996 96 2552 0 . 0 . 0 101 0,0,33,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P158L|169|FAM231B|protein_coding|CODING|NM_001310155.1|1|T) 0 . 0 . 0 1 0 . 1 0 45 0 0 4.7147e-08 0 . rs147443431 -0.693147 0.510438 101 169 227 MODIFIER 1 CODING FAM231B A protein_coding NM_001310155.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16866297 T A 0 47.5 0 0.6074 0.6637 0.5014 0.9812 0.5895 0.6043 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||227||169|FAM231B|protein_coding|CODING|NM_001310155.1|1|A) 0 . 0 . 0 1 0 . 0 . 30 0 0 . 0 . rs200136456 -0.511536 0.756524 3 1140 1300 MODIFIER 29 CODING NBPF1 C protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16889138 T C 0 25.9 0 0.8116 0.78 0.8084 0.6815 0.8042 0.7935 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||1300||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 0 . 1 rs156890 -0.453602 0.88 3 1140 1015 MODIFIER 29 CODING NBPF1 C protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16889423 G C 0 23 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||1015||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 0 . 1 rs156892 -0.453602 0.18 3 1140 572 MODIFIER 29 CODING NBPF1 A protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16889866 G A 0 72 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.988166 0 . 0 . 22 8,4,8,0 UTR_3_PRIME(MODIFIER||572||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|A) 0 0.5 1 0 . 0 . 0 . 0 38 0 0.764448 0.751477 0 0.558035 rs3981525 -0.651104 0.702288 22 1140 308 MODIFIER 29 CODING NBPF1 C protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890130 A C 0 184 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.928877 0 . 0 . 98 44,17,23,9 UTR_3_PRIME(MODIFIER||308||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 0 . 0 . 0 52 0 2.26233e-06 0.809254 0 0.254741 rs1043523 -0.69312 0.0565055 98 1140 262 MODIFIER 29 CODING NBPF1 C protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890176 A C 0 222 0 0.4977 0.5335 0.5418 0.505 0.5666 0.5716 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992438 0 . 0 . 171 66,27,62,10 UTR_3_PRIME(MODIFIER||262||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 1 0 . 0 . 50 0 1.30148e-10 0.19475 0 0.112267 rs3868814 -0.693147 0.0284165 171 1140 155 MODIFIER 29 CODING NBPF1 T protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890283 G T 0 228 0 0.9818 0.9846 0.9769 1 0.9712 0.9918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 555 0,1,460,62 UTR_3_PRIME(MODIFIER||155||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|T) 0 . 0 . 0 1 0 . 0 . 53 0 1 0.000684401 0 1 rs156893 -0.693147 0.19337 555 1140 118 MODIFIER 29 CODING NBPF1 C protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890320 T C 0 30.6 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.828177 0 . 0 . 755 474,89,118,33 UTR_3_PRIME(MODIFIER||118||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 0 . 0 . 0 54 0 0.998203 8.85011e-21 0 0.845374 rs3900707 -0.693147 0.416966 755 1140 10 MODIFIER 29 CODING NBPF1 A protein_coding NM_017940.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890428 T A 0 155 0 . 0 . 0 . 0 0.0560599 0.11364 0.14314 1 2008 42195 4021 3916 2520 23060 308 6362 2 9932 118672 11246 8454 6504 65238 896 16402 0.240664 0 . 0 . 2267 1191,402,304,131 UTR_3_PRIME(MODIFIER||10||1140|NBPF1|protein_coding|CODING|NM_017940.4|29|A) 1 0.5 1 0 . 0 . 1 1 0 59 0 0.97786 0.126941 0 0.188129 rs3900708 -0.693147 0.00117531 2267 Y1088F 1140 tAc/tTc MODERATE 29 MISSENSE CODING NBPF1 A protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890598 T A 0 181 0 . 0 . 0 . 0 . 0 . 1 5267 63014 6030 4343 3462 34867 471 8574 2 10386 121138 11552 8630 6604 66564 908 16494 0.891735 0 . 0 . 2125 512,927,167,286 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y1088F|1140|NBPF1|protein_coding|CODING|NM_017940.4|29|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.952475 4.92503e-05 0 0.068215 rs2990550 -0.693147 0.191297 2125 L1074 1140 ttG/ttA LOW 29 SILENT CODING NBPF1 T protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890639 C T 0 34 0 . 0 . 0 . 0 . 0 . 1 3362 54037 5060 3941 3132 30301 413 7828 2 9816 117900 11028 8346 6498 64946 890 16376 0.702292 0 . 0 . 1442 361,710,77,179 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1074|1140|NBPF1|protein_coding|CODING|NM_017940.4|29|T) 0 0.5 1 0 . 0 . 0 1 0 57 0 3.02005e-06 0.945942 0 0.76783 rs1043750 -0.693147 0.0413171 1442 V1073I 1140 Gtc/Atc MODERATE 29 MISSENSE CODING NBPF1 T protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890644 C T 0 177 0 . 0 . 0 . 0 . 0 . 1 5017 59664 5754 4189 3287 32828 441 8148 2 10316 120912 11556 8578 6602 66488 900 16472 0.914493 0 . 0 . 1385 307,653,106,215 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1073I|1140|NBPF1|protein_coding|CODING|NM_017940.4|29|T) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.99598 0.936153 0 0.671051 rs2992339 -0.693147 0.00492736 1385 M1064V 1140 Atg/Gtg MODERATE 29 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890671 T C 0 222 0 0.5091 0.5461 0.5591 0.5169 0.5885 0.5736 0 . 0 1 5322 67037 6384 4406 3707 37403 493 9322 2 10388 121384 11576 8654 6614 66734 908 16510 0.887242 0 . 0 . 1099 181,422,139,281 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M1064V|1140|NBPF1|protein_coding|CODING|NM_017940.4|29|C) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.00172614 0.997064 0 0.00239687 rs2419526 -0.693147 0.011939 1099 G1063 1140 ggC/ggT LOW 29 SILENT CODING NBPF1 A protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16890672 G A 0 222 0 0.5091 0.5461 0.5591 0.5169 0.5885 0.5736 0 . 0 1 5321 67035 6386 4406 3707 37401 493 9321 2 10390 121394 11578 8654 6614 66738 908 16512 0.236212 0 . 0 . 1101 182,422,139,281 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1063|1140|NBPF1|protein_coding|CODING|NM_017940.4|29|A) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.00171867 0.997389 0 0.0583811 rs2419525 -0.693147 0.0118735 1101 T1039M 1140 aCg/aTg MODERATE 28 MISSENSE CODING NBPF1 A protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16891365 G A 0 221 0 . 0 . 0 . 0 . 0 . 1 1245 20274 2052 3460 1284 9855 163 2215 2 7288 91122 8640 7672 5074 48602 706 13140 0.787634 0 . 0 . 1276 160,671,76,285 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1039M|1140|NBPF1|protein_coding|CODING|NM_017940.4|28|A) 0 0.5 1 0 . 0 . 0 1 0 55 0 0 0.499099 0 0.849868 rs201912185,rs2289552 -0.693147 0.0102064 1276 1140 LOW 26 CODING NBPF1 G protein_coding NM_017940.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16892310 T G 0 97 0 . 0 . 0 . 0 . 0 . 1 2702 28082 2488 1684 1831 16338 214 2825 2 6442 73778 5682 3722 4706 39616 618 12992 0.46504 0 . 0 . 62 33,0,2,26 SPLICE_SITE_REGION+INTRON(LOW||||1140|NBPF1|protein_coding|CODING|NM_017940.4|26|G) 0 0.5 1 0 . 0 . 0 1 0 38 0 6.95174e-09 1.82227e-09 0 2.87609e-10 rs201123634,rs61771015 -0.693054 1.85731e-07 62 K850Q 1140 Aag/Cag MODERATE 23 MISSENSE CODING NBPF1 G protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16895634 T G 0 228 0 . 0 . 0 . 0 . 0 . 2 6750 74830 6966 6850 4077 39689 570 9928 2 9794 119672 11560 8650 6522 65858 902 16386 0.00110428 0 . 0 . 1929 65,1,492,1207 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K850Q|1140|NBPF1|protein_coding|CODING|NM_017940.4|23|G) 0 . 0 . 0 . 0 . 1 0 34 0 5.73788e-30 0 0 4.44819e-39 rs61771025,rs75027498 -0.693147 2.9573e-05 1929 E732D 1140 gaG/gaC MODERATE 21 MISSENSE CODING NBPF1 G protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16901184 C G 0 62 0 . 0 . 0 . 0 . 0 . 1 1 19 0 15 0 2 0 1 2 8832 116996 11534 8610 6562 64144 884 16430 0.274505 0 . 0 COSN161250 1084 122,690,26,179 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E732D|1140|NBPF1|protein_coding|CODING|NM_017940.4|21|G) 0 0.5 1 0 . 0 . 0 1 0 35 0 0.236903 1.08326e-07 0 0.353405 rs374894160 -0.693147 0.049661 1084 K726E 1140 Aaa/Gaa MODERATE 20 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16901668 T C 0 228 0 . 0 . 0 . 0 0.303679 0.296751 0.292857 2 3596 44643 4205 5029 2731 23231 336 5515 2 10150 119978 11506 8608 6584 65888 894 16348 0.974507 0 . 0 . 845 17,6,336,372 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K726E|1140|NBPF1|protein_coding|CODING|NM_017940.4|20|C) 1 0 . 0 . 0 . 1 1 0 45 0 7.39233e-08 0 0 0.219374 rs3901679 -0.693147 4.12946e-07 845 N710 1140 aaC/aaT LOW 20 SILENT CODING NBPF1 A protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16901714 G A 0 228 0 . 0 . 0 . 0 . 0 . 2 6009 68047 6700 5610 3995 35739 511 9483 2 9878 118420 11414 8478 6572 64934 892 16252 0.434016 0 . 0 . 557 13,16,70,434 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N710|1140|NBPF1|protein_coding|CODING|NM_017940.4|20|A) 0 . 0 . 0 . 0 . 1 0 43 0 4.64853e-08 3.72231e-30 0 0.995092 rs138796798,rs61772335 -0.693147 0.00361696 557 N666S 1140 aAt/aGt MODERATE 19 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16902884 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 2578 28570 2670 3632 1405 13906 227 4152 2 8216 97296 9224 7896 5182 52144 764 13870 0.00891897 0 . 0 . 519 60,153,67,237 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N666S|1140|NBPF1|protein_coding|CODING|NM_017940.4|19|C) 0 0.5 1 0 . 0 . 0 1 0 30 0 0.862737 0.00258184 0 0.00070416 rs74630591 -0.693147 0.519585 519 C663R 1140 Tgc/Cgc MODERATE 19 MISSENSE CODING NBPF1 G protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16902894 A G 0 228 0 0.73 0.6815 0.6455 0.7996 0.6183 0.5849 0 . 0 2 4839 50479 4271 5848 3001 24974 403 7143 2 8382 111526 10828 8134 6288 61320 874 15700 0 . 0 . 0 430 0,0,132,298 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C663R|1140|NBPF1|protein_coding|CODING|NM_017940.4|19|G) 0 . 0 . 0 1 0 . 1 0 28 0 0 1.45264e-06 0 . rs28453011,rs61772339 -0.693147 0.0201308 430 N602Y 1140 Aat/Tat MODERATE 18 MISSENSE CODING NBPF1 A protein_coding NM_017940.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16903912 T A 0 209 0 . 0 . 0 . 0 . 0 . 2 7719 82271 7975 7202 4682 42499 632 11562 2 8948 117362 11522 8448 6604 64452 892 16496 0 . 0 . 0 85 0,0,3,82 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Aat/Tat|N602Y|1140|NBPF1|protein_coding|CODING|NM_017940.4|18|A) 0 . 0 . 0 . 0 . 1 0 26 0 0 0.336154 0 . rs61772344 -0.693147 0.000652043 85 C591G 1140 Tgc/Ggc MODERATE 17 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16905718 A C 0 121 0 . 0 . 0 . 0 . 0 . 1 2454 36655 3131 3245 2556 19896 284 5089 2 5732 78152 6802 6534 5374 42244 616 10850 0.976551 0 . 0 . 98 12,32,0,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C591G|1140|NBPF1|protein_coding|CODING|NM_017940.4|17|C) 0 0.5 1 0 . 0 . 0 1 0 37 0 0.0212814 0.847925 0 0.174773 rs3738661 -0.693147 4.96856e-09 98 P549 1140 ccT/ccC LOW 17 SILENT CODING NBPF1 G protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16905842 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 1398 14162 1129 1187 986 7094 126 2242 2 3818 52272 4154 2800 3424 28958 450 8668 0 . 0 . 0 86 0,0,75,11 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P549|1140|NBPF1|protein_coding|CODING|NM_017940.4|17|G) 0 . 0 . 0 . 0 . 1 0 35 0 0 0.00895757 0 . rs200194071 -0.693147 0.357287 86 Q431 1140 caG/caA LOW 14 SILENT CODING NBPF1 T protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16909052 C T 0 126 0 0.8729 0.8253 0.8141 0.8393 0.7763 0.8047 0 . 0 2 9001 106701 10904 8200 6181 57087 789 14539 2 9142 112426 11158 8228 6370 60980 834 15714 0.0769882 0 . 0 . 90 6,0,0,84 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q431|1140|NBPF1|protein_coding|CODING|NM_017940.4|14|T) 0 . 0 . 0 1 0 . 1 0 36 0 0.992668 0.992668 0 0.100587 rs140548913 -0.693147 0.00159728 90 L415 1140 ctC/ctG LOW 14 SILENT CODING NBPF1 C protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16909100 G C 0 77 0 . 0 . 0 . 0 . 0 . 1 3602 50250 4956 3719 2894 27567 388 7124 2 7992 108656 10684 7776 6238 59508 826 15632 0.395028 0 . 0 . 48 10,20,0,18 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L415|1140|NBPF1|protein_coding|CODING|NM_017940.4|14|C) 0 0.5 1 0 . 0 . 0 1 0 34 0 0.0210315 0.994858 0 0.0258003 rs143269469 -0.691153 0.133212 48 K406E 1140 Aag/Gag MODERATE 14 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16909129 T C 0 41.6 0 . 0 . 0 . 0 . 0 . 1 4473 56613 5563 4012 3263 30702 438 8162 2 8476 111224 10944 7972 6480 60346 858 16148 0.453994 0 . 0 . 48 13,20,0,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K406E|1140|NBPF1|protein_coding|CODING|NM_017940.4|14|C) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.000430783 0.999933 0 0.982286 rs199798572 -0.688148 0.969763 48 P404L 1140 cCg/cTg MODERATE 14 MISSENSE CODING NBPF1 A protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16909134 G A 0 13.9 0 . 0 . 0 . 0 . 0 . 1 1276 9003 831 1373 476 3934 65 1048 2 7104 89818 8132 5722 5422 48536 696 14206 0.998675 0 . 0 . 46 13,22,0,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P404L|1140|NBPF1|protein_coding|CODING|NM_017940.4|14|A) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.0306937 0.996361 0 0.291178 rs201581469 -0.676189 0.868938 46 Q379H 1140 caG/caC MODERATE 14 MISSENSE CODING NBPF1 G protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16909208 C G 0 83 0 . 0 . 0 . 0 . 0 . 1 133 1690 122 305 126 876 12 116 2 4816 54552 3548 2714 3168 28978 460 10868 0.2163 0 . 0 . 70 2,17,51,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q379H|1140|NBPF1|protein_coding|CODING|NM_017940.4|14|G) 0 0.5 1 0 . 0 . 0 1 0 30 0 0.768118 0.62325 0 0.128109 rs200714079,rs61773582 -0.693147 0.0111541 70 C320G 1140 Tgc/Ggc MODERATE 12 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16912014 A C 0 222 0 0.3729 0.404 0.4063 0.4484 0.3897 0.4131 0 . 0 1 2299 25537 1555 2127 1722 13322 225 4287 2 4716 51942 3150 4286 3510 27096 458 8726 0.684647 0 . 0 . 200 37,37,44,82 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C320G|1140|NBPF1|protein_coding|CODING|NM_017940.4|12|C) 0 0.5 1 0 . 1 0 . 1 0 43 0 0.331829 0.917256 0 0.49376 rs143097321 -0.693147 0.0106335 200 A319 1140 gcC/gcT LOW 12 SILENT CODING NBPF1 A protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16912015 G A 0 29.5 0 0.0197 0.1324 0.1758 0.1577 0.1362 0.2239 0 . 0 1 377 12487 786 1219 890 6419 123 2673 2 5012 47608 2906 3398 3102 24502 434 8254 0.208576 0 . 0 . 202 69,96,12,25 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A319|1140|NBPF1|protein_coding|CODING|NM_017940.4|12|A) 0 0.5 1 0 . 1 0 . 1 0 43 0 0.596842 0.985123 0 0.998344 rs58689366 -0.693141 0.0626824 202 S247A 1140 Tct/Gct MODERATE 11 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16913584 A C 0 228 0 . 0 . 0 . 0 0.109033 0.155295 0.178955 2 1675 27275 2669 3166 1811 14486 210 3258 2 9432 118852 11458 8364 6486 65772 888 16452 0.940271 0 . 0 . 406 3,3,126,209 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S247A|1140|NBPF1|protein_coding|CODING|NM_017940.4|11|C) 1 0 . 0 . 0 . 1 1 0 41 0 0.051738 1.43869e-26 0 0.962693 rs629538 -0.693147 0.147346 406 N237 1140 aaC/aaT LOW 11 SILENT CODING NBPF1 A protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16913612 G A 0 228 0 . 0 . 0 . 0 0.0568699 0.135012 0.175012 2 1077 28751 3257 3628 1823 15363 222 3381 2 9662 119250 11448 8360 6496 65952 882 16450 0.943544 0 . 0 . 367 3,0,87,219 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N237|1140|NBPF1|protein_coding|CODING|NM_017940.4|11|A) 1 0 . 0 . 0 . 1 1 0 41 0 0.403417 1.35479e-14 0 0.878163 rs629889 -0.693147 1.16036e-08 367 S216G 1140 Agc/Ggc MODERATE 11 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16913677 T C 0 188 0 0.1755 0.2458 0.2378 0.5099 0.1849 0.137 0 . 0 2 380 6488 588 2049 277 2693 56 445 2 9068 112514 10830 7118 6270 63078 844 15306 1 0 . 0 . 84 0,1,1,82 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S216G|1140|NBPF1|protein_coding|CODING|NM_017940.4|11|C) 0 . 0 . 0 1 0 . 1 0 38 0 1 1 0 1 rs200743207,rs71263230 -0.693147 3.33864e-07 84 K135E 1140 Aag/Gag MODERATE 9 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16915434 T C 0 33.5 0 . 0 . 0 . 0 . 0 . 1 15 173 3 1 1 139 2 12 2 2250 25392 1280 1780 1958 12156 260 5708 0.941608 0 . 0 . 35 6,19,6,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K135E|1140|NBPF1|protein_coding|CODING|NM_017940.4|9|C) 0 0.5 1 0 . 0 . 0 1 0 39 0 0.000148242 0.000447986 0 0.0107001 rs202129231 -0.670168 0.240287 35 N124S 1140 aAt/aGt MODERATE 9 MISSENSE CODING NBPF1 C protein_coding NM_017940.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16915466 T C 0 47.4 0 . 0 . 0 . 0 . 0 . 1 1 40 0 1 0 38 0 0 2 1274 12408 482 762 768 5738 138 3246 0.112099 0 . 0 . 59 29,13,15,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N124S|1140|NBPF1|protein_coding|CODING|NM_017940.4|9|C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.338039 0.000721864 0 0.445319 rs200264463 -0.690438 0.000481009 59 A5 1140 gcT/gcC LOW 7 SILENT CODING NBPF1 G protein_coding NM_017940.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16918502 A G 0 222 0 0.2579 0.493 0.536 0.6101 0.6024 0.547 0 . 0 1 5062 60575 5789 4319 3307 33377 455 8266 2 9852 120830 11578 8642 6614 66728 904 16512 0.930739 0 . 0 . 922 150,182,215,300 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A5|1140|NBPF1|protein_coding|CODING|NM_017940.4|7|G) 0 0.5 1 0 . 1 0 . 1 0 50 0 2.88232e-35 3.34943e-07 0 0.360406 rs3925698 -0.693147 0.00666371 922 1140 177 MODIFIER 6 CODING NBPF1 T protein_coding NM_017940.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16918693 A T 0 172 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99239 0 . 0 . 351 84,156,27,50 UTR_5_PRIME(MODIFIER||177||1140|NBPF1|protein_coding|CODING|NM_017940.4|6|T) 0 0.5 1 0 . 0 . 0 . 0 46 0 0.834109 8.85381e-06 0 0.159013 rs12134336 -0.693147 0.0254722 351 1140 16614 MODIFIER 2 CODING NBPF1 T protein_coding NM_017940.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16935130 C T 0 108 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.392817 0 . 0 . 236 107,67,34,9 UTR_5_PRIME(MODIFIER||16614||1140|NBPF1|protein_coding|CODING|NM_017940.4|2|T) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.852869 rs1762921 -0.693146 0.799531 236 1140 21482 MODIFIER 1 CODING NBPF1 A protein_coding NM_017940.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16939997 AC A 0 71 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 2,2,4,1 UTR_5_PRIME(MODIFIER||21482||1140|NBPF1|protein_coding|CODING|NM_017940.4|1|A) 0 0.5 1 6 0.6 0 1 0 . 0 60 0 0 0.924584 0 . rs79338600 -0.590765 0.778467 10 1140 21495 MODIFIER 1 CODING NBPF1 T protein_coding NM_017940.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16940011 C T 0 121 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.406082 0 . 0 . 12 2,2,5,0 UTR_5_PRIME(MODIFIER||21495||1140|NBPF1|protein_coding|CODING|NM_017940.4|1|T) 0 0.5 1 0 . 0 . 0 . 0 60 0 0.974597 1 0 0.243649 rs61394154 -0.590765 0.764622 12 1140 21563 MODIFIER 1 CODING NBPF1 C protein_coding NM_017940.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 16940079 A C 0 24.2 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979382 0 . 0 . 11 4,4,2,1 UTR_5_PRIME(MODIFIER||21563||1140|NBPF1|protein_coding|CODING|NM_017940.4|1|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 0.950952 0 0.594025 rs1759197 -0.511536 0.345596 11 689 2264 MODIFIER 15 CODING MST1L A protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17081463 G A 0 9.7 0 0.8593 0.9251 0.9395 0.9802 0.9215 0.9509 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2264||689|MST1L|protein_coding|CODING|NM_001271733.1|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs56154546 -0.379885 0 1 689 1872 MODIFIER 15 CODING MST1L G protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17081855 C G 0 25.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1872||689|MST1L|protein_coding|CODING|NM_001271733.1|15|G) 0 . 0 . 0 . 0 . 0 . 29 0 0 . 0 . rs2610593 -0.453602 0.06 2 689 1463 MODIFIER 15 CODING MST1L T protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17082263 TG T 0 10.6 0 0.5182 0.4986 0.4971 0.4891 0.4722 0.5102 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1463||689|MST1L|protein_coding|CODING|NM_001271733.1|15|T) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs56384488 -0.379885 0 1 689 745 MODIFIER 15 CODING MST1L A protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17082982 G A 0 29.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||745||689|MST1L|protein_coding|CODING|NM_001271733.1|15|A) 0 . 0 . 0 . 0 . 0 . 28 0 0 1 0 . rs1033404 -0.453602 0.76 2 689 267 MODIFIER 15 CODING MST1L C protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083460 T C 0 224 0 0.4455 0.4313 0.402 0.5288 0.3777 0.3875 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,9,4 UTR_3_PRIME(MODIFIER||267||689|MST1L|protein_coding|CODING|NM_001271733.1|15|C) 0 . 0 . 0 1 0 . 0 . 48 0 0 0.269146 0 . rs9659870 -0.683931 0.220473 14 689 159 MODIFIER 15 CODING MST1L A protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083568 G A 0 6.6 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.797457 0 . 0 . 47 30,9,7,0 UTR_3_PRIME(MODIFIER||159||689|MST1L|protein_coding|CODING|NM_001271733.1|15|A) 0 0.5 1 0 . 0 . 0 . 0 58 0 0.780852 0.608452 0 0.755264 rs10159208 -0.636426 0.200896 47 689 56 MODIFIER 15 CODING MST1L G protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083671 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.723701 0 . 0 . 171 87,2,71,5 UTR_3_PRIME(MODIFIER||56||689|MST1L|protein_coding|CODING|NM_001271733.1|15|G) 0 0.5 1 0 . 0 . 0 . 0 48 0 0.142351 0.0483089 0 0.998717 rs1057420 -0.693147 0.000448481 171 689 42 MODIFIER 15 CODING MST1L A protein_coding NM_001271733.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083685 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 2300 48002 5221 4144 3036 27108 362 5831 2 8220 108802 11060 8508 6382 60780 810 13042 0.816166 0 . 0 . 182 87,7,65,9 UTR_3_PRIME(MODIFIER||42||689|MST1L|protein_coding|CODING|NM_001271733.1|15|A) 0 0.5 1 0 . 0 . 0 1 0 47 0 0.295832 0.0150855 0 0.757988 rs3197973 -0.693147 1.31999e-05 182 T664A 689 Aca/Gca MODERATE 15 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083807 T C 0 228 0 0.5545 0.6897 0.7435 0.8819 0.6789 0.6472 0 . 0 2 3449 46485 4993 4663 3198 24537 351 5294 2 7042 79834 7416 5696 4866 43828 602 10384 0 . 0 . COSM1499802 157 0,0,91,66 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T664A|689|MST1L|protein_coding|CODING|NM_001271733.1|15|C) 0 . 0 . 0 1 0 . 1 0 32 0 0 8.66274e-09 0 . rs1057346,rs9286084 -0.693147 0.962947 157 G637S 689 Ggt/Agt MODERATE 15 MISSENSE CODING MST1L T protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17083888 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 1239 15870 1107 1405 1334 8495 133 2157 2 2754 37100 2514 2846 2910 20288 332 5456 0.489409 0 . 0 . 284 66,71,51,56 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Ggt/Agt|G637S|689|MST1L|protein_coding|CODING|NM_001271733.1|15|T) 0 0.5 1 0 . 0 . 0 1 0 38 0 0.822972 0.671564 0 0.844559 rs75141545 -0.693147 0.0666524 284 689 LOW 14 CODING MST1L T protein_coding NM_001271733.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17084006 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 4074 51987 5167 4176 2998 27898 412 7262 2 8144 105288 10486 8228 6016 56674 828 14912 0.967547 0 . 0 . 170 45,16,82,21 SPLICE_SITE_REGION+INTRON(LOW||||689|MST1L|protein_coding|CODING|NM_001271733.1|14|T) 0 0.5 1 0 . 0 . 0 1 0 35 0 0.202249 0.00101169 0 0.670103 rs2446544 -0.693147 0.0118488 170 L530 689 Cta/Tta LOW 12 SILENT CODING MST1L A protein_coding NM_001271733.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17084510 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 2316 20292 1820 3185 1245 9362 183 2181 2 8770 105710 10082 7888 5778 57852 782 14558 0.996785 0 . 0 COSM463396,COSM463395 339 105,91,34,73 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L530|689|MST1L|protein_coding|CODING|NM_001271733.1|12|A) 0 0.5 1 0 . 0 . 0 1 0 45 0 0.00150772 2.38455e-19 0 0.997459 rs11260921,rs61769731 -0.693147 0.00332393 339 R503G 689 Cgg/Ggg MODERATE 11 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17084968 G C 0 33 0 . 0 . 0 . 0 . 0 . 1 4743 55911 5483 3912 3069 30300 425 7979 2 9818 117566 11352 8268 6442 64476 882 16328 0.964953 0 . 0 COSM1127275 452 228,117,44,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Ggg|R503G|689|MST1L|protein_coding|CODING|NM_001271733.1|11|C) 0 0.5 1 0 . 0 . 0 1 0 46 0 0.861418 0.000133187 0 0.995169 rs2761533 -0.693147 0.0757256 452 G490E 689 gGg/gAg MODERATE 11 MISSENSE CODING MST1L T protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085006 C T 0 96 0 . 0 . 0 . 0 . 0 . 1 1846 12251 681 1777 626 5913 91 1317 2 9498 111798 10506 7520 6112 61908 816 15438 0.886976 0 . 0 . 494 223,136,62,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G490E|689|MST1L|protein_coding|CODING|NM_001271733.1|11|T) 0 0.5 1 0 . 0 . 0 1 0 46 0 0.23066 0.418507 0 0.929422 rs201784242 -0.693147 0.0639395 494 A427T 689 Gca/Aca MODERATE 10 MISSENSE CODING MST1L T protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085412 C T 0 188 0 0.4811 0.4599 0.4654 0.4554 0.4175 0.4755 0 . 0 1 4756 55881 5587 4140 3102 30091 416 7789 2 9802 117822 11430 8518 6482 64438 892 16260 0.229512 0 . 0 . 364 158,80,63,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A427T|689|MST1L|protein_coding|CODING|NM_001271733.1|10|T) 0 0.5 1 0 . 1 0 . 1 0 52 0 5.10792e-10 0.0048881 0 0.672781 rs872964 -0.693147 0.0831154 364 I422V 689 Att/Gtt MODERATE 10 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085427 T C 0 221 0 . 0 . 0 . 0 . 0 . 1 5222 59255 5936 4215 3269 32046 438 8129 2 10194 119504 11498 8558 6526 65484 896 16348 0.99506 0 . 0 . 400 147,100,73,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I422V|689|MST1L|protein_coding|CODING|NM_001271733.1|10|C) 0 0.5 1 0 . 0 . 0 1 0 52 0 7.23212e-18 0.000426508 0 0.00508119 rs2002186 -0.693147 6.08325e-06 400 M397V 689 Atg/Gtg MODERATE 10 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085502 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 3768 56442 5573 4269 3179 31083 440 8130 2 8448 115202 11316 8586 6444 63178 880 16350 0.904829 0 . 0 . 428 98,59,95,125 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M397V|689|MST1L|protein_coding|CODING|NM_001271733.1|10|C) 0 0.5 1 0 . 0 . 0 1 0 47 0 3.97865e-14 2.12787e-06 0 0.710162 rs2329006 -0.693147 0.208746 428 L386P 689 cTg/cCg MODERATE 9 MISSENSE CODING MST1L G protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085564 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 2182 17021 1161 827 1063 8352 144 3292 2 7784 100930 9650 6984 5494 55516 788 14714 0.127283 0 . 0 . 280 54,111,33,66 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L386P|689|MST1L|protein_coding|CODING|NM_001271733.1|9|G) 0 0.5 1 0 . 0 . 0 1 0 46 0 3.23227e-22 0.957192 0 0.257401 rs3851921 -0.693147 0.292297 280 689 LOW 8 CODING MST1L G protein_coding NM_001271733.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085671 C G 0 214 0 . 0 . 0 . 0 . 0 . 1 3953 51606 5375 4058 2874 27345 377 7624 2 8054 108368 11028 8254 6032 58282 794 15924 0.546633 0 . 0 . 157 30,72,13,32 SPLICE_SITE_REGION+INTRON(LOW||||689|MST1L|protein_coding|CODING|NM_001271733.1|8|G) 0 0.5 1 0 . 0 . 0 1 0 46 0 0.000103062 0.299862 0 0.661006 rs3863806 -0.693147 0.126017 157 T329 689 acC/acA LOW 8 SILENT CODING MST1L T protein_coding NM_001271733.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17085834 G T 0 228 0 . 0 . 0 . 0 . 0 . 2 7185 91183 8999 6675 5043 49919 681 12681 2 8470 115426 11238 8466 6288 63916 864 16184 0 . 0 . 0 104 0,0,54,42 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T329|689|MST1L|protein_coding|CODING|NM_001271733.1|8|T) 0 . 0 . 0 . 0 . 1 0 51 0 0 0.00547075 0 . rs2005622 -0.693147 0.00106023 104 H282R 689 cAc/cGc MODERATE 7 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17086052 T C 0 67 0 0.9992 0.9948 0.9928 0.999 0.9871 0.9939 0 . 0 2 5229 63284 5623 4757 2454 33962 471 10788 2 5242 63928 5646 4760 2496 34508 474 10802 0 . 0 . 0 7 0,0,5,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H282R|689|MST1L|protein_coding|CODING|NM_001271733.1|7|C) 0 . 0 . 0 1 0 . 1 0 22 0 0 0.6 0 . rs1057286,rs77745384 -0.636426 0.000692271 7 S152G 689 Agc/Ggc MODERATE 4 MISSENSE CODING MST1L C protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17086870 T C 0 228 0 0.3472 0.5004 0.4553 0.7867 0.503 0.4417 0 . 0 2 777 11539 873 950 594 5963 120 2262 2 5792 71848 6768 2848 3410 40570 548 11912 0 . 0 . COSM899454,COSM899453 66 0,0,36,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S152G|689|MST1L|protein_coding|CODING|NM_001271733.1|4|C) 0 . 0 . 0 1 0 . 1 0 33 0 0 0.0406938 0 . rs201604637,rs2261727 -0.693147 0.76735 66 A73 689 gcG/gcC LOW 3 SILENT CODING MST1L G protein_coding NM_001271733.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17087365 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 5510 66328 6866 4623 3624 35990 504 9211 2 10298 120226 11378 8550 6580 66134 906 16380 0.943837 0 . 0 . 429 87,58,138,94 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A73|689|MST1L|protein_coding|CODING|NM_001271733.1|3|G) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.0149104 0.00847647 0 0.365754 rs2446556 -0.693147 0.275143 429 P67L 689 cCc/cTc MODERATE 2 MISSENSE CODING MST1L A protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17087465 G A 0 221 0 . 0 . 0 . 0 . 0 . 1 4984 55533 5482 4205 3068 29711 408 7675 2 10310 118924 11392 8544 6472 65012 896 16298 0.997022 0 . 0 . 354 88,140,35,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P67L|689|MST1L|protein_coding|CODING|NM_001271733.1|2|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.0805098 0.97851 0 0.9743 rs11260924 -0.693147 0.0577715 354 S28L 689 tCg/tTg MODERATE 2 MISSENSE CODING MST1L A protein_coding NM_001271733.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17087582 G A 0 221 0 . 0 . 0 . 0 . 0 . 1 5083 56832 5615 4056 3146 30803 420 7709 2 10202 118490 11448 8410 6490 64840 894 16206 0.465928 0 . 0 COSM1499789 183 44,77,18,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S28L|689|MST1L|protein_coding|CODING|NM_001271733.1|2|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.0100191 0.733852 0 0.988477 rs10907280 -0.693147 0.0141322 183 2017 14 MODIFIER 1 CODING CROCC G protein_coding NM_014675.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17248500 A G 0 222 0 . 0 . 0 . 0 0.339792 0.431953 0.479344 1 874 9799 225 381 55 4162 99 4003 2 2296 19470 418 738 108 8020 188 7702 0.997831 0 . 0 . 226 87,22,69,25 UTR_5_PRIME(MODIFIER||14||2017|CROCC|protein_coding|CODING|NM_014675.4|1|G) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.692896 rs6683035 -0.693147 0.566224 226 R7G 2017 Agg/Ggg MODERATE 1 MISSENSE CODING CROCC G protein_coding NM_014675.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17248532 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 2784 22359 614 1092 180 9799 206 7684 2 2784 22364 614 1092 180 9802 206 7686 0 . 0 . 0 237 0,0,114,90 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R7G|2017|CROCC|protein_coding|CODING|NM_014675.4|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6586566 -0.693147 0.0798088 237 T71 2017 acA/acG LOW 3 SILENT CODING CROCC G protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17250836 A G 0 222 0 . 0 . 0 . 0 0.378348 0.34128 0.322284 1 3865 39506 3478 3729 2143 21565 306 4420 2 9982 117318 11290 8560 6168 64354 878 16086 0.852542 0 . 0 COSM424603 94 24,9,44,12 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T71|2017|CROCC|protein_coding|CODING|NM_014675.4|3|G) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.980275 rs57174186 -0.693147 0.116279 94 A439V 2017 gCg/gTg MODERATE 11 MISSENSE CODING CROCC T protein_coding NM_014675.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17264920 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 1934 17233 1143 1830 411 9174 135 2606 2 4656 43050 2534 3810 898 22026 328 8798 0.501098 0 . 0 COSM1127264 391 109,50,113,75 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A439V|2017|CROCC|protein_coding|CODING|NM_014675.4|11|T) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.985524 0.998509 0 0.264945 rs4463721 -0.693147 0.0588832 391 D445 2017 gaT/gaC LOW 11 SILENT CODING CROCC C protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17264939 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 2099 19627 1398 2104 540 10539 153 2794 2 4986 48104 3086 4372 1166 24906 368 9220 0.687127 0 . 0 COSM1127263 387 103,66,96,84 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D445|2017|CROCC|protein_coding|CODING|NM_014675.4|11|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.984034 0.977514 0 0.994874 rs4558023 -0.693147 0.0120983 387 P511S 2017 Ccc/Tcc MODERATE 12 MISSENSE CODING CROCC T protein_coding NM_014675.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17265560 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 2558 31925 3033 3313 1478 17241 242 4060 2 6010 81904 8154 7158 3538 44754 574 11716 0.693855 0 . 0 COSM424610 76 18,11,25,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P511S|2017|CROCC|protein_coding|CODING|NM_014675.4|12|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.610852 rs9435793 -0.693132 0.114463 76 D586H 2017 Gac/Cac MODERATE 13 MISSENSE CODING CROCC C protein_coding NM_014675.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17266536 G C 0 222 0 . 0 . 0 . 0 . 0 . 1 1482 27327 2197 3304 1413 14669 245 4017 2 8622 106504 10184 7972 5714 57816 810 15386 0.593013 0 . 0 . 290 66,60,72,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Cac|D586H|2017|CROCC|protein_coding|CODING|NM_014675.4|13|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.634029 rs9435714 -0.693147 0.0164313 290 A655 2017 gcG/gcA LOW 14 SILENT CODING CROCC A protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17270751 G A 0 222 0 0.0182 0.2376 0.3242 0.4643 0.2495 0.227 0 . 0 1 87 3857 127 341 52 1612 40 1598 2 1570 15718 364 704 122 5832 150 6976 0.974435 0 . 0 . 189 44,53,38,36 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A655|2017|CROCC|protein_coding|CODING|NM_014675.4|14|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.99606 rs12025984 -0.693147 0.0601707 189 L808 2017 ctA/ctG LOW 17 SILENT CODING CROCC G protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17273396 A G 0 222 0 . 0 . 0 . 0 0.05 0.120956 0.157113 1 190 7581 329 988 186 3693 73 2122 2 2652 27718 962 2134 528 12732 246 8464 0.993006 0 . 0 COSM424614 91 14,29,16,24 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L808|2017|CROCC|protein_coding|CODING|NM_014675.4|17|G) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.751197 rs7537468 -0.693145 0.256345 91 T824 2017 acG/acA LOW 17 SILENT CODING CROCC A protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17273444 G A 0 222 0 . 0 . 0 . 0 0.0429779 0.110578 0.145435 1 158 5629 185 636 76 2556 59 1959 2 2270 22920 654 1392 238 10016 212 8138 0.92777 0 . 0 COSM424615 56 4,23,4,24 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T824|2017|CROCC|protein_coding|CODING|NM_014675.4|17|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.988586 rs7545185 -0.693054 0.464262 56 2017 LOW 17 CODING CROCC C protein_coding NM_014675.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17273493 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 920 8252 182 331 81 3366 85 3287 2 1732 18004 394 680 168 7254 190 7586 0.980457 0 . 0 . 35 2,14,4,15 SPLICE_SITE_REGION+INTRON(LOW||||2017|CROCC|protein_coding|CODING|NM_014675.4|17|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.980457 rs7537563 -0.69168 0.665105 35 A1715 2017 gcT/gcC LOW 32 SILENT CODING CROCC C protein_coding NM_014675.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17295679 T C 0 228 0 0.9947 0.9447 0.9496 0.9663 0.8907 0.907 0.984311 0.926362 0.89672 2 9063 102185 10314 7964 4725 55282 726 14111 2 9228 111616 10730 8250 5166 61704 780 15758 0 . 0 . 0 121 0,0,61,49 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1715|2017|CROCC|protein_coding|CODING|NM_014675.4|32|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4920574 -0.693147 0.0901033 121 2017 73 MODIFIER 37 CODING CROCC C protein_coding NM_014675.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17299014 A C 0 164 0 0.5499 0.5511 0.5245 0.5556 0.5626 0.5552 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,16 UTR_3_PRIME(MODIFIER||73||2017|CROCC|protein_coding|CODING|NM_014675.4|37|C),DOWNSTREAM(MODIFIER||1985||183|MFAP2|protein_coding|CODING|NM_002403.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6661019 -0.689466 0.0297528 18 A173 183 gcG/gcA LOW 9 SILENT CODING MFAP2 T protein_coding NM_002403.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17301448 C T 0 190 0 0.2057 0.3411 0.389 0.6151 0.2833 0.2669 0 . 0 2 296 3967 117 367 11 1602 50 1524 2 1146 11170 300 568 26 4660 116 4354 0 . 0 . 0 72 0,0,72,0 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A173|183|MFAP2|protein_coding|CODING|NM_002403.3|9|T),DOWNSTREAM(MODIFIER||1974||2017|CROCC|protein_coding|CODING|NM_014675.4||T) 0 . 0 . 0 1 0 . 1 0 57 0 0 . 0 . rs2235933 -0.693147 0.00196575 72 1180 LOW 26 CODING ATP13A2 A protein_coding NM_022089.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17313454 G A 0 228 0 0.1467 0.3065 0.3646 0.5774 0.2525 0.2577 0.168634 0.215285 0.239186 2 1782 33030 4228 4755 2148 16037 261 3819 2 10328 120580 11534 8622 6544 66148 896 16508 0.121212 2 benign 0 . 185 0,2,53,112 SPLICE_SITE_REGION+INTRON(LOW||||1180|ATP13A2|protein_coding|CODING|NM_022089.3|26|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.160606 rs7531163 -0.693147 0.00101027 185 S930 1180 tcG/tcA LOW 25 SILENT CODING ATP13A2 T protein_coding NM_022089.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17314702 C T 0 228 0 0.1369 0.2909 0.3429 0.5774 0.2058 0.2546 0.149569 0.178072 0.192674 2 1585 29291 3965 4769 2041 13023 232 3676 2 10398 121320 11560 8632 6608 66704 908 16510 0 2 benign 0 . 122 0,0,78,30 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S930|1180|ATP13A2|protein_coding|CODING|NM_022089.3|25|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3738815 -0.693147 0.0548877 122 A6 280 gcC/gcA LOW 1 SILENT CODING SDHB T protein_coding NM_003000.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17380497 G T 0 228 0 0.8797 0.9571 0.9769 0.996 0.9722 0.9918 0.909401 0.951469 0.973017 2 8379 109622 11013 8398 4796 60373 789 15874 2 9208 112768 11152 8410 4888 62234 806 16070 1 2|2 benign|benign 0 . 178 1,0,123,32 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A6|280|SDHB|protein_coding|CODING|NM_003000.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2746462 -0.693147 0.78006 178 665 1650 MODIFIER 16 CODING PADI2 G protein_coding NM_007365.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17393889 A G 0 9.7 0 0.3971 0.4257 0.3876 0.5873 0.3002 0.454 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1650||665|PADI2|protein_coding|CODING|NM_007365.2|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7516087 -0.379885 0 1 665 926 MODIFIER 16 CODING PADI2 C protein_coding NM_007365.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17394613 T C 0 228 0 0.7035 0.8694 0.9222 0.9812 0.8907 0.9192 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 104 0,0,45,47 UTR_3_PRIME(MODIFIER||926||665|PADI2|protein_coding|CODING|NM_007365.2|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10157828 -0.693147 0.00855096 104 665 916 MODIFIER 16 CODING PADI2 T protein_coding NM_007365.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17394623 C T 0 228 0 0.7035 0.8692 0.9222 0.9812 0.8907 0.9182 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 109 0,0,47,49 UTR_3_PRIME(MODIFIER||916||665|PADI2|protein_coding|CODING|NM_007365.2|16|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10157387 -0.693147 0.0283279 109 665 764 MODIFIER 16 CODING PADI2 A protein_coding NM_007365.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17394775 G A 0 228 0 0.4054 0.4277 0.3862 0.5873 0.3002 0.454 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 41 1,0,7,31 UTR_3_PRIME(MODIFIER||764||665|PADI2|protein_coding|CODING|NM_007365.2|16|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2235927,rs386562067 -0.693143 0.152427 41 665 258 MODIFIER 16 CODING PADI2 C protein_coding NM_007365.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17395281 T C 0 124 0 0.3449 0.4113 0.3847 0.5873 0.2992 0.454 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||258||665|PADI2|protein_coding|CODING|NM_007365.2|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2235926 -0.616816 0.670308 6 G243 665 ggT/ggG LOW 7 SILENT CODING PADI2 C protein_coding NM_007365.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17413121 A C 0 228 0 0.267 0.3636 0.2939 0.5585 0.2584 0.4509 0.248979 0.251346 0.252558 2 2637 35975 3099 4924 2367 15990 278 6680 2 10380 121188 11568 8634 6608 66584 904 16510 0 . 0 . 0 150 0,0,94,41 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G243|665|PADI2|protein_coding|CODING|NM_007365.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2076615 -0.693147 0.0874174 150 L178 665 ctC/ctT LOW 6 SILENT CODING PADI2 A protein_coding NM_007365.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17419024 G A 0 228 0 0.0877 0.2813 0.3631 0.5099 0.1869 0.3466 0.114843 0.167922 0.195116 2 1152 29588 4402 4296 1998 12570 226 4944 2 10358 119364 11526 8622 6590 66038 882 15348 0 . 0 . 0 59 0,0,9,47 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L178|665|PADI2|protein_coding|CODING|NM_007365.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11203297 -0.693147 0.014869 59 P623 664 ccG/ccT LOW 16 SILENT CODING PADI3 T protein_coding NM_016233.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17609448 G T 0 222 0 0.1725 0.405 0.415 0.623 0.4374 0.454 0.231276 0.370983 0.442558 1 2348 53171 5019 5531 2999 28909 427 7938 2 10352 120868 11484 8608 6572 66458 900 16494 0.243469 0 . 0 . 71 26,14,14,13 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P623|664|PADI3|protein_coding|CODING|NM_016233.2|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940085 rs2293920 -0.693021 0.477036 71 G55S 663 Ggc/Agc MODERATE 2 MISSENSE CODING PADI4 A protein_coding NM_012387.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17657534 G A 0 228 0 0.4508 0.5246 0.5432 0.5635 0.5755 0.5184 0.484567 0.545364 0.576512 2 4942 68081 5800 5039 3948 39194 512 8646 2 10402 121310 11564 8634 6608 66688 908 16506 1 0 . 0 . 111 0,1,67,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G55S|663|PADI4|protein_coding|CODING|NM_012387.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11203366 -0.693147 0.00219703 111 V82A 663 gTg/gCg MODERATE 2 MISSENSE CODING PADI4 C protein_coding NM_012387.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17657616 T C 0 228 0 0.4796 0.5333 0.5476 0.5635 0.5726 0.5245 0.508852 0.553514 0.576395 2 5186 68379 5813 5035 3944 39177 511 8713 2 10380 121220 11556 8626 6600 66648 904 16506 1 0 . 0 . 124 1,0,47,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V82A|663|PADI4|protein_coding|CODING|NM_012387.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11203367 -0.693147 0.0369704 124 G112A 663 gGg/gCg MODERATE 3 MISSENSE CODING PADI4 C protein_coding NM_012387.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17660499 G C 0 228 0 0.4607 0.522 0.5403 0.5585 0.5537 0.5215 0.486382 0.529064 0.55093 2 4977 66235 5742 5012 3732 37625 496 8651 2 10398 121264 11556 8624 6608 66666 908 16504 0 . 0 . 0 176 0,0,70,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G112A|663|PADI4|protein_coding|CODING|NM_012387.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs874881 -0.693147 0.0140722 176 L117 663 Ttg/Ctg LOW 4 SILENT CODING PADI4 C protein_coding NM_012387.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17662662 T C 0 228 0 0.5401 0.5919 0.585 0.6151 0.661 0.5716 0.581253 0.636245 0.664419 2 5932 76836 6027 5433 4509 44932 561 9442 2 10338 120560 11420 8580 6570 66292 906 16454 0 . 0 . 0 123 0,0,53,48 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L117|663|PADI4|protein_coding|CODING|NM_012387.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1748033 -0.693147 0.109245 123 R383 663 cgC/cgA LOW 10 SILENT CODING PADI4 A protein_coding NM_012387.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17674537 C A 0 228 0 0.3517 0.4213 0.4121 0.5635 0.3469 0.4519 0.371085 0.358373 0.35186 2 3853 47031 4771 5050 2276 23536 343 7202 2 10352 120734 11500 8608 6574 66386 904 16410 1 0 . 0 . 80 0,1,22,46 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R383|663|PADI4|protein_coding|CODING|NM_012387.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2240335 -0.693147 0.251651 80 694 16 MODIFIER 1 CODING PADI6 T protein_coding NM_207421.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17698725 C T 0 228 0 0.3752 0.2614 0.1571 0.3085 0.1948 0.2014 0.331584 0.255521 0.21662 2 3399 26865 1809 2530 1109 14361 190 3467 2 9832 120554 11568 8572 6612 66628 898 16444 1 0 . 0 . 79 1,0,56,17 UTR_5_PRIME(MODIFIER||16||694|PADI6|protein_coding|CODING|NM_207421.4|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1204873 -0.693147 0.301311 79 P165 694 ccT/ccC LOW 5 SILENT CODING PADI6 C protein_coding NM_207421.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17707601 T C 0 222 0 0.1029 0.1621 0.1196 0.2788 0.1292 0.1861 0.0929933 0.140697 0.163046 1 928 17901 1512 2162 683 9758 147 2711 2 7128 88062 7184 6810 4744 49248 692 12256 0.971367 0 . 0 . 132 39,30,25,23 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P165|694|PADI6|protein_coding|CODING|NM_207421.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990451 rs6669650 -0.693147 0.555859 132 694 138 MODIFIER 17 CODING PADI6 A protein_coding NM_207421.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17728072 G A 0 129 0 0.1104 0.2242 0.2507 0.3264 0.2038 0.2751 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.938795 0 . 0 . 18 1,9,2,6 UTR_3_PRIME(MODIFIER||138||694|PADI6|protein_coding|CODING|NM_207421.4|17|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.102932 rs34167614 -0.651104 0.0428737 18 694 185 MODIFIER 17 CODING PADI6 G protein_coding NM_207421.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17728119 A G 0 178 0 0.6921 0.6342 0.6542 0.5427 0.6103 0.6605 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,1,8 UTR_3_PRIME(MODIFIER||185||694|PADI6|protein_coding|CODING|NM_207421.4|17|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2526830 -0.662043 0.106182 9 522 2022 MODIFIER 12 CODING RCC2 G protein_coding NM_001136204.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17733564 T G 0 32.6 0 0.6914 0.635 0.6542 0.5456 0.6143 0.6585 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2022||522|RCC2|protein_coding|CODING|NM_001136204.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs56185243,rs7191 -0.379885 0 2 522 1590 MODIFIER 12 CODING RCC2 A protein_coding NM_001136204.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17733996 G A 0 123 0 0.0083 0.1206 0.0836 0.2897 0.0964 0.1493 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.986883 0 . 0 . 40 19,2,19,0 UTR_3_PRIME(MODIFIER||1590||522|RCC2|protein_coding|CODING|NM_001136204.2|12|A) 0 0.5 1 0 . 1 0 . 0 . 58 0 0.96037 0.921053 0 0.605253 rs3193024 -0.69168 0.298879 40 W991R 1279 Tgg/Cgg MODERATE 26 MISSENSE CODING ARHGEF10L C protein_coding NM_018125.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 17991052 T C 0 228 0 0.9992 0.9998 1 1 1 1 0.999319 0.999769 1 2 10217 118943 11460 8624 6172 65804 864 15802 2 10222 118948 11460 8624 6172 65804 864 15802 0 . 0 . 0 125 0,0,54,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W991R|1279|ARHGEF10L|protein_coding|CODING|NM_018125.3|26|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6695710 -0.693147 0.12309 125 N1110 1279 aaC/aaT LOW 29 SILENT CODING ARHGEF10L T protein_coding NM_018125.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18023365 C T 0 228 0 0.5855 0.7847 0.8674 0.8363 0.8171 0.909 0.634589 0.764801 0.831512 2 6406 94227 10316 7016 5131 52776 718 11864 2 10220 115346 11502 8598 6570 64346 848 13262 0 . 0 . 0 106 0,0,81,15 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1110|1279|ARHGEF10L|protein_coding|CODING|NM_018125.3|29|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2270978 -0.693147 0.138498 106 D1158 1279 gaT/gaC LOW 29 SILENT CODING ARHGEF10L C protein_coding NM_018125.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18023509 T C 0 228 0 0.7186 0.8347 0.8775 0.8988 0.8171 0.9131 0.755703 0.806203 0.832012 2 6871 91998 9616 7273 4225 49441 660 13912 2 9230 110166 10680 8144 5406 60336 774 15596 0 . 0 . 0 119 0,0,33,78 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1158|1279|ARHGEF10L|protein_coding|CODING|NM_018125.3|29|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2270977 -0.693147 0.00417593 119 I1219V 1279 Atc/Gtc MODERATE 29 MISSENSE CODING ARHGEF10L G protein_coding NM_018125.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18023690 A G 0 228 0 0.6694 0.8227 0.8746 0.8988 0.8211 0.9162 0.71409 0.795131 0.836685 2 6328 95367 10216 7476 4968 51035 714 14630 2 9032 114150 11326 8350 6302 61954 834 16352 0 . 0 . 0 65 0,0,31,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I1219V|1279|ARHGEF10L|protein_coding|CODING|NM_018125.3|29|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2270976 -0.693147 0.408871 65 1279 2 MODIFIER 29 CODING ARHGEF10L A protein_coding NM_018125.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18023877 G A 0 222 0 0.1082 0.0954 0.049 0.0615 0.1153 0.1258 0.103687 0.0956998 0.0915976 1 1004 10333 385 579 932 6312 82 1039 2 8770 105188 11212 8366 6260 59380 744 10456 0.189982 0 . 0 . 62 8,24,6,22 UTR_3_PRIME(MODIFIER||2||1279|ARHGEF10L|protein_coding|CODING|NM_018125.3|29|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948255 rs11589634 -0.693054 0.398329 62 A3S 366 Gca/Tca MODERATE 2 MISSENSE CODING ACTL8 T protein_coding NM_030812.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18149510 G T 0 222 0 0.143 0.3057 0.3228 0.4315 0.4374 0.2485 0.202451 0.347609 0.421977 1 2060 46357 3616 3559 3390 29030 357 4345 2 10152 118234 11328 8500 6416 65532 878 15428 0.989844 0 . 0 . 153 73,6,57,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A3S|366|ACTL8|protein_coding|CODING|NM_030812.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95883 rs694214 -0.693147 0.6417 153 G21 366 ggC/ggA LOW 2 SILENT CODING ACTL8 A protein_coding NM_030812.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18149566 C A 0 222 0 0.3215 0.4828 0.5807 0.6865 0.4732 0.4315 0.343395 0.421959 0.462209 1 3627 60255 7934 5687 3833 31935 445 6794 2 10398 121268 11558 8650 6600 66648 906 16508 0.853615 0 . 0 . 192 66,21,58,17 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G21|366|ACTL8|protein_coding|CODING|NM_030812.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2296035 -0.693147 0.0724672 192 467 42 MODIFIER 10 CODING IGSF21 G protein_coding NM_032880.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18704862 A G 0 228 0 0.7655 0.6042 0.5634 0.6052 0.4433 0.5798 0.709487 0.518145 0.420116 2 6910 54352 6341 4950 2678 24558 385 8530 2 9636 107566 10188 7716 5548 58460 816 15202 1 0 . 0 . 62 0,1,13,44 UTR_3_PRIME(MODIFIER||42||467|IGSF21|protein_coding|CODING|NM_032880.4|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1043459,rs386512951 -0.693147 0.0793207 62 P141R 777 cCc/cGc MODERATE 1 MISSENSE CODING KLHDC7A G protein_coding NM_152375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18807897 C G 0 228 0 0.5688 0.647 0.7147 0.8958 0.6113 0.4847 0.595671 0.621324 0.633771 2 5603 77660 9379 7730 4174 41877 577 8320 2 9684 119608 11542 8596 6578 66194 886 16128 0 . 0 . 0 111 0,0,59,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P141R|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2992755 -0.693147 0.040111 111 P155T 777 Cct/Act MODERATE 1 MISSENSE CODING KLHDC7A A protein_coding NM_152375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18807938 C A 0 228 0 0.174 0.2668 0.2464 0.623 0.1252 0.1851 0.191679 0.15938 0.143434 2 1759 24175 3206 5371 1151 9560 153 2975 2 9690 120030 11560 8594 6606 66264 890 16426 1 0 . 0 . 111 0,1,50,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P155T|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2992754 -0.693147 0.127467 111 H273N 777 Cat/Aat MODERATE 1 MISSENSE CODING KLHDC7A A protein_coding NM_152375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18808292 C A 0 228 0 0.6604 0.6729 0.7277 0.8958 0.6113 0.4847 0.665002 0.641012 0.628721 2 6914 79285 9432 7783 4190 42043 595 8328 2 10396 121242 11574 8652 6604 66632 904 16480 0 . 0 . 0 169 0,0,108,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Aat|H273N|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2992753 -0.693147 0.0210568 169 A330 777 gcT/gcA LOW 1 SILENT CODING KLHDC7A A protein_coding NM_152375.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18808465 T A 0 228 0 0.6611 0.6727 0.7277 0.8948 0.6113 0.4836 0.663326 0.640333 0.628558 2 6135 75850 9322 7642 4052 39820 569 8310 2 9156 115670 11410 8502 6334 62970 870 16428 0 . 0 . 0 86 0,0,27,55 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A330|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3007718 -0.693147 0.0635166 86 T351P 777 Aca/Cca MODERATE 1 MISSENSE CODING KLHDC7A C protein_coding NM_152375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18808526 A C 0 228 0 0.6611 0.6727 0.7277 0.8948 0.6113 0.4836 0.663662 0.641001 0.629638 2 5824 74931 9255 7569 3948 39491 545 8299 2 8706 114364 11330 8426 6178 62504 836 16384 0 . 0 . COSM424852 55 0,0,18,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Cca|T351P|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2992752 -0.693147 0.915326 55 G412 777 ggG/ggC LOW 1 SILENT CODING KLHDC7A C protein_coding NM_152375.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18808711 G C 0 228 0 0.1725 0.2638 0.2349 0.625 0.1173 0.1861 0.191784 0.145779 0.122209 2 1742 22465 3101 5278 1045 8222 144 2933 2 9520 117858 11436 8432 6566 64584 880 16440 1 0 . 0 . 85 1,0,52,22 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G412|777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2992751 -0.693147 0.42727 85 777 87 MODIFIER 1 CODING KLHDC7A T protein_coding NM_152375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18809896 A T 0 228 0 0.6248 0.6428 0.7061 0.8958 0.5815 0.4243 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 58 0,0,26,26 UTR_3_PRIME(MODIFIER||87||777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2992745 -0.693147 0.454061 58 777 535 MODIFIER 1 CODING KLHDC7A T protein_coding NM_152375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18810344 G T 0 228 0 0.5635 0.6212 0.6844 0.8958 0.5686 0.4254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 33 0,0,22,8 UTR_3_PRIME(MODIFIER||535||777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2992740 -0.693097 0.331298 33 777 675 MODIFIER 1 CODING KLHDC7A A protein_coding NM_152375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18810484 G A 0 228 0 0.1785 0.261 0.2334 0.6032 0.1163 0.1881 0 . 0 2 166 2405 64 297 1 536 24 1317 2 908 14598 288 484 30 5070 152 7666 0 . 0 . 0 49 0,0,30,19 UTR_3_PRIME(MODIFIER||675||777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1889861 -0.693147 0.00373787 49 777 677 MODIFIER 1 CODING KLHDC7A C protein_coding NM_152375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18810486 A C 0 228 0 0.2421 0.3161 0.2983 0.7083 0.1193 0.227 0 . 0 2 229 2788 76 343 1 548 26 1565 2 904 14586 288 480 30 5070 152 7662 0 . 0 . 0 49 0,0,30,19 UTR_3_PRIME(MODIFIER||677||777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1889862 -0.693147 0.00384856 49 777 1859 MODIFIER 1 CODING KLHDC7A C protein_coding NM_152375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 18811668 T C 0 228 0 0.705 0.7151 0.7536 0.8958 0.659 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 124 1,0,64,46 UTR_3_PRIME(MODIFIER||1859||777|KLHDC7A|protein_coding|CODING|NM_152375.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3007719 -0.693147 0.396285 124 E248 520 gaG/gaA LOW 5 SILENT CODING PAX7 A protein_coding NM_002584.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19018405 G A 0 222 0 0.0061 0.101 0.0865 0.251 0.0557 0.1319 0.0168029 0.0404553 0.0525704 1 150 9965 1463 1958 495 3955 81 1863 2 9810 115664 11190 8450 5764 63702 836 15912 0.988514 0 . 0 . 101 23,33,12,24 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E248|520|PAX7|protein_coding|CODING|NM_002584.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.776089 rs2076020 -0.693139 0.869441 101 T257 520 acA/acC LOW 5 SILENT CODING PAX7 C protein_coding NM_002584.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19018432 A C 0 222 0 0.0499 0.1248 0.0908 0.2569 0.0557 0.1851 0.0572467 0.0547777 0.0535133 1 554 10796 1464 1954 470 3916 86 2352 2 9412 109044 10432 7950 5284 59980 808 15178 0.919949 0 . 0 . 83 15,33,6,27 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T257|520|PAX7|protein_coding|CODING|NM_002584.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.334363 rs2076019 -0.693127 0.146785 83 P293 520 ccA/ccG LOW 6 SILENT CODING PAX7 G protein_coding NM_002584.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19027239 A G 0 228 0 0.643 0.4886 0.3876 0.6042 0.2575 0.4703 0.588516 0.372059 0.261163 2 6114 44109 5539 5150 2033 18348 345 6580 2 10216 117720 11338 8516 6280 64382 862 16126 0 . 0 . COSM424864,COSM1473185 61 0,0,39,15 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P293|520|PAX7|protein_coding|CODING|NM_002584.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2743201 -0.693147 0.724698 61 I790 839 atC/atT LOW 6 SILENT CODING TAS1R2 A protein_coding NM_152232.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19166243 G A 0 228 0 0.0363 0.0845 0.0231 0.1141 0.0557 0.1922 0.0444848 0.0455943 0.0461628 2 411 8037 206 811 571 3304 52 2682 2 10382 121050 11534 8624 6538 66588 904 16480 1 0 . 0 . 131 1,0,58,65 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I790|839|TAS1R2|protein_coding|CODING|NM_152232.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12075191 -0.693147 0.0575412 131 A574T 839 Gcc/Acc MODERATE 6 MISSENSE CODING TAS1R2 T protein_coding NM_152232.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19166893 C T 0 228 0 0.0575 0.0911 0.0274 0.1141 0.0557 0.1943 0.0662733 0.0530524 0.0462791 2 635 8283 216 810 570 3307 53 2692 2 10312 120902 11562 8624 6602 66390 902 16510 0 . 0 . 0 85 0,0,59,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A574T|839|TAS1R2|protein_coding|CODING|NM_152232.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6662276 -0.693147 0.0165351 85 S9C 839 tCc/tGc MODERATE 1 MISSENSE CODING TAS1R2 C protein_coding NM_152232.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19186129 G C 0 228 0 0.8207 0.7979 0.8415 0.7748 0.7833 0.7751 0.830231 0.792557 0.773256 2 8513 94716 9644 6501 4630 51737 681 13010 2 10406 121364 11574 8648 6606 66712 908 16510 0 . 0 . 0 102 0,0,45,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tGc|S9C|839|TAS1R2|protein_coding|CODING|NM_152232.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9701796 -0.693147 0.151568 102 563 118 MODIFIER 15 CODING ALDH4A1 T protein_coding NM_003748.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19199221 C T 0 166 0 0.1982 0.4714 0.5519 0.6567 0.4513 0.6135 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999755 0 . 0 . 29 14,3,9,3 UTR_3_PRIME(MODIFIER||118||563|ALDH4A1|protein_coding|CODING|NM_003748.3|15|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.868336 rs11740,rs386521004 -0.680642 0.43896 29 D460 563 gaT/gaC LOW 13 SILENT CODING ALDH4A1 G protein_coding NM_003748.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19201956 A G 0 222 0 0.705 0.7372 0.8112 0.7063 0.7386 0.7587 0.679301 0.702214 0.713953 1 7173 88581 9562 6190 4619 47876 653 12508 2 10404 121374 11576 8642 6612 66722 906 16512 0.98637 0 . 0 . 137 20,46,23,36 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D460|563|ALDH4A1|protein_coding|CODING|NM_003748.3|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.581664 rs2230708,rs386561790 -0.693147 0.124919 137 A417 563 gcC/gcT LOW 12 SILENT CODING ALDH4A1 A protein_coding NM_003748.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19202896 G A 0 222 0 0.4569 0.516 0.6513 0.6002 0.4453 0.4857 0.435089 0.454713 0.464767 1 4537 60280 8097 5246 2836 30925 450 8189 2 10154 118910 11390 8446 6402 65274 890 16354 0.655859 0 . 0 . 180 49,36,36,31 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A417|563|ALDH4A1|protein_coding|CODING|NM_003748.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.145587 rs2230707 -0.693147 0.005731 180 S410 563 tcA/tcG LOW 12 SILENT CODING ALDH4A1 C protein_coding NM_003748.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19202917 T C 0 222 0 0.4728 0.6609 0.768 0.7063 0.7137 0.7382 0.484793 0.62302 0.693837 1 4828 80044 8872 5910 4019 43763 597 12055 2 9560 113950 10966 8124 5920 62422 856 16102 0.861031 0 . 0 COSM1337325,COSM1337326 179 43,47,28,38 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S410|563|ALDH4A1|protein_coding|CODING|NM_003748.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.793709 rs7550938 -0.693147 0.345833 179 A407 563 gcA/gcG LOW 12 SILENT CODING ALDH4A1 C protein_coding NM_003748.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19202926 T C 0 222 0 0.4728 0.6601 0.768 0.7044 0.7117 0.7382 0.483651 0.621347 0.69186 1 4626 77118 8607 5677 3679 42078 565 11886 2 9080 109220 10596 7766 5394 59746 810 15828 0.438741 0 . 0 COSM1337328,COSM1337327 174 40,45,28,42 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A407|563|ALDH4A1|protein_coding|CODING|NM_003748.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.395141 rs2230706 -0.693147 0.56482 174 H4959 5183 caT/caC LOW 102 SILENT CODING UBR4 G protein_coding NM_020765.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19411129 A G 0 228 0 0.8366 0.7189 0.7349 0.8105 0.6074 0.5685 0.806627 0.671459 0.602209 2 8370 78202 9405 7017 3465 40268 523 9154 2 10396 121292 11570 8640 6598 66708 906 16474 0 . 0 . 0 113 0,0,67,35 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H4959|5183|UBR4|protein_coding|CODING|NM_020765.2|102|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1043905,rs386512973 -0.693147 0.0204816 113 M4867L 5183 Atg/Ttg MODERATE 100 MISSENSE CODING UBR4 A protein_coding NM_020765.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19413261 T A 0 228 0 0.5408 0.6014 0.6844 0.7589 0.5785 0.4857 0.548343 0.559895 0.565814 2 5690 70702 8948 6579 3336 37829 485 7835 2 10402 121272 11564 8636 6596 66668 904 16502 0 . 0 . 0 151 0,0,68,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M4867L|5183|UBR4|protein_coding|CODING|NM_020765.2|100|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12584 -0.693147 0.00768045 151 K4793 5183 aaG/aaA LOW 98 SILENT CODING UBR4 T protein_coding NM_020765.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19415304 C T 0 228 0 0.5091 0.5919 0.6787 0.7589 0.5775 0.4847 0.527009 0.552591 0.565698 2 5455 70465 8944 6574 3341 37836 485 7830 2 10392 121342 11572 8642 6604 66718 908 16506 1 0 . 0 . 32 1,0,22,6 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K4793|5183|UBR4|protein_coding|CODING|NM_020765.2|98|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1043899 -0.693054 0.322035 32 V4039 5183 gtT/gtC LOW 82 SILENT CODING UBR4 G protein_coding NM_020765.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19433449 A G 0 228 0 0.8366 0.7192 0.7334 0.8105 0.6083 0.5706 0.806854 0.671767 0.602558 2 8296 77552 9308 6930 3393 39964 512 9149 2 10296 120036 11438 8548 6376 66076 888 16414 0 . 0 . 0 48 0,0,20,25 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4039|5183|UBR4|protein_coding|CODING|NM_020765.2|82|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6426677 -0.693147 0.181445 48 L3327 5183 ctG/ctC LOW 68 SILENT CODING UBR4 G protein_coding NM_020765.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19447843 C G 0 228 0 0.5424 0.6004 0.6844 0.7589 0.5775 0.4796 0.549024 0.560126 0.565814 2 5705 70688 8947 6567 3340 37862 484 7783 2 10388 121226 11566 8628 6606 66630 902 16506 1 0 . 0 COSM1337405 94 1,0,51,40 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L3327|5183|UBR4|protein_coding|CODING|NM_020765.2|68|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1044010 -0.693147 0.0189939 94 5183 LOW 16 CODING UBR4 G protein_coding NM_020765.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19510394 A G 0 228 0 0.8374 0.7169 0.7305 0.8105 0.6064 0.5613 0.807535 0.67169 0.602093 2 8375 78104 9393 7020 3467 40222 521 9106 2 10402 121200 11558 8636 6602 66598 906 16498 1 0 . 0 . 98 1,0,39,53 SPLICE_SITE_REGION+INTRON(LOW||||5183|UBR4|protein_coding|CODING|NM_020765.2|16|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3762396 -0.693147 0.216673 98 S345T 993 aGt/aCt MODERATE 10 MISSENSE CODING EMC1 G protein_coding NM_015047.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19565344 C G 0 228 0 0.7315 0.5723 0.5101 0.7401 0.3469 0.4601 0.683613 0.469553 0.359884 2 7072 53625 6552 6237 1701 24111 323 7629 2 10402 121366 11576 8634 6614 66722 908 16510 0 . 0 . 0 132 0,0,55,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S345T|993|EMC1|protein_coding|CODING|NM_015047.2|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs709683 -0.693147 0.11115 132 993 LOW 4 CODING EMC1 G protein_coding NM_015047.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19568972 A G 0 228 0 0.7625 0.5819 0.5115 0.7401 0.3509 0.4622 0.712438 0.482239 0.364302 2 7378 54335 6588 6226 1701 24430 323 7689 2 10396 121192 11550 8620 6610 66622 906 16488 0 . 0 . 0 104 0,0,31,66 SPLICE_SITE_REGION+INTRON(LOW||||993|EMC1|protein_coding|CODING|NM_015047.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs710865 -0.693147 0.300426 104 239 138 MODIFIER 1 CODING MRTO4 A protein_coding NM_016183.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19578192 G A 0 228 0 0.4198 0.6454 0.6988 0.8264 0.6282 0.7434 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,9,5 UTR_5_PRIME(MODIFIER||138||239|MRTO4|protein_coding|CODING|NM_016183.3|1|A),UPSTREAM(MODIFIER||139||993|EMC1|protein_coding|CODING|NM_015047.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2294942 -0.686358 0.686276 14 239 221 MODIFIER 8 CODING MRTO4 A protein_coding NM_016183.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19585545 G A 0 39.3 0 0.9849 0.9159 0.8833 0.9266 0.8549 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||221||239|MRTO4|protein_coding|CODING|NM_016183.3|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs761305 -0.453602 0.7 2 T323A 331 Act/Gct MODERATE 7 MISSENSE CODING AKR7A3 C protein_coding NM_012067.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19609254 T C 0 222 0 0.7451 0.8315 0.8674 0.8413 0.8499 0.8937 0.746703 0.797322 0.823215 1 7755 100344 9699 7057 5675 55002 744 14412 2 10372 121326 11574 8650 6614 66704 908 16504 0.989355 0 . 0 . 118 31,20,33,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T323A|331|AKR7A3|protein_coding|CODING|NM_012067.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.509877 0.645649 0 0.960786 rs1738025 -0.693147 0.150139 118 N215D 331 Aat/Gat MODERATE 5 MISSENSE CODING AKR7A3 C protein_coding NM_012067.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19611241 T C 0 222 0 0.6415 0.8077 0.8646 0.8502 0.8579 0.8967 0.661664 0.773658 0.83093 1 6858 100102 9722 7090 5713 55526 744 14449 2 10400 121386 11576 8644 6614 66734 908 16510 0.599749 0 . 0 . 74 19,24,10,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N215D|331|AKR7A3|protein_coding|CODING|NM_012067.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932026 rs1738023 -0.692914 0.226721 74 V138M 331 Gtg/Atg MODERATE 3 MISSENSE CODING AKR7A3 T protein_coding NM_012067.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19612477 C T 0 222 0 0.3646 0.4633 0.5432 0.6905 0.3817 0.3896 0.366985 0.363441 0.361628 1 3759 51185 7544 5867 2826 24429 354 6406 2 10254 120762 11518 8610 6572 66422 902 16484 0.915599 0 . 0 . 71 17,21,9,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V138M|331|AKR7A3|protein_coding|CODING|NM_012067.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.993841 0.806283 0 0.770249 rs2231198 -0.693097 0.0544506 71 291 4863 MODIFIER 1 CODING PQLC2 A protein_coding NM_001040125.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19639309 G A 0 222 0 0 0.0393 0.0159 0.1319 0.008 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.684257 0 . 0 . 123 40,18,26,26 UTR_5_PRIME(MODIFIER||4863||291|PQLC2|protein_coding|CODING|NM_001040125.1|1|A),UPSTREAM(MODIFIER||669||359|AKR7A2|protein_coding|CODING|NM_003689.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.919343 rs2231192 -0.693147 0.71343 123 301 567 MODIFIER 9 CODING CAPZB C protein_coding NM_001282162.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19665456 CA C 0 99 0 0.0242 0.0986 0.0908 0.1706 0.1213 0.1074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 27,35,5,16 UTR_3_PRIME(MODIFIER||567||301|CAPZB|protein_coding|CODING|NM_001282162.1|9|C) 0 0.5 1 19 0.191919 1 1 0 . 0 60 0 0 1 0 . rs148424975 -0.692352 0.251882 99 301 527 MODIFIER 9 CODING CAPZB C protein_coding NM_001282162.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19665497 A C 0 209 0 0.1732 0.246 0.2651 0.3254 0.2256 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89074 0 . 0 . 86 22,32,14,8 UTR_3_PRIME(MODIFIER||527||301|CAPZB|protein_coding|CODING|NM_001282162.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.843157 rs6889 -0.692562 0.854026 86 G156 301 ggC/ggG LOW 5 SILENT CODING CAPZB C protein_coding NM_001282162.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19684006 G C 0 222 0 0 0.0357 0.0144 0.129 0.002 0.0378 0.00204604 0.00278597 0.0031348 1 21 2545 459 1147 22 296 13 587 2 9656 120250 11528 8596 6612 66490 894 16474 0.994437 0 . 0 . 61 24,8,14,8 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G156|301|CAPZB|protein_coding|CODING|NM_001282162.1|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.389548 rs3748755 -0.692562 0.27062 61 140 1032 MODIFIER 5 CODING MINOS1 T protein_coding NM_001204083.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19953118 G T 0 228 0 0.9985 0.99 0.9827 1 0.9682 0.9959 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,20,35 UTR_3_PRIME(MODIFIER||1032||140|MINOS1|protein_coding|CODING|NM_001204083.1|5|T),INTRON(MODIFIER||||195|MINOS1-NBL1|protein_coding|CODING|NM_001204088.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1534985 -0.693147 0.045872 59 140 2867 MODIFIER 5 CODING MINOS1 A protein_coding NM_001204083.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 19954953 G A 0 36.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2867||140|MINOS1|protein_coding|CODING|NM_001204083.1|5|A),INTRON(MODIFIER||||195|MINOS1-NBL1|protein_coding|CODING|NM_001204088.1|2|A) 0 . 0 . 0 . 0 . 0 . 60 0 0 1 0 . rs58995319 -0.453602 0.02 2 R478 634 cgT/cgC LOW 15 SILENT CODING TMCO4 G protein_coding NM_181719.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20020993 A G 0 222 0 0.525 0.6601 0.6787 0.5823 0.8042 0.7618 0.567181 0.72751 0.809651 1 5931 92302 7216 5170 5563 54652 722 13048 2 10380 121206 11562 8616 6612 66628 904 16504 0.558829 0 . 0 . 167 44,43,23,41 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R478|634|TMCO4|protein_coding|CODING|NM_181719.4|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.32256 rs4370779 -0.693147 1.64205e-05 167 R478H 634 cGt/cAt MODERATE 15 MISSENSE CODING TMCO4 T protein_coding NM_181719.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20020994 C T 0 222 0 0.1853 0.4301 0.5389 0.2837 0.669 0.589 0.263958 0.512686 0.640116 1 2651 69501 5698 2318 4670 43444 569 10151 2 10374 121212 11570 8628 6608 66624 902 16506 0.976471 0 . 0 . 169 44,45,23,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R478H|634|TMCO4|protein_coding|CODING|NM_181719.4|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.602869 rs4515815 -0.693147 1.64205e-05 169 144 267 MODIFIER 6 CODING PLA2G2A T protein_coding NM_000300.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20301927 A T 0 109 0 0.2708 0.1815 0.2435 0.1091 0.159 0.1145 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.00775 0 . 0 . 11 4,0,5,1 UTR_3_PRIME(MODIFIER||267||144|PLA2G2A|protein_coding|CODING|NM_000300.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.727822 rs876018 -0.616816 0.241952 11 T32 144 acG/acC LOW 4 SILENT CODING PLA2G2A G protein_coding NM_000300.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20304962 C G 0 222 0 0.0053 0.097 0.1009 0.2282 0.0775 0.1033 0.018384 0.0672766 0.0923256 1 183 12775 1889 1981 639 6059 91 1933 2 10400 121268 11552 8628 6592 66686 908 16502 0.523996 0 . 0 . 81 27,19,19,10 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T32|144|PLA2G2A|protein_coding|CODING|NM_000300.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997503 rs2236771 -0.693079 0.412279 81 G3 138 ggC/ggT LOW 2 SILENT CODING PLA2G5 T protein_coding NM_000929.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20411332 C T 0 222 0 0.0953 0.2514 0.2608 0.3065 0.338 0.3098 0.126645 0.274258 0.349884 1 1301 40031 2722 2647 2746 24668 335 5612 2 10406 121396 11578 8644 6614 66736 908 16510 0.968548 0 . 0 COSM146435 124 41,20,43,10 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G3|138|PLA2G5|protein_coding|CODING|NM_000929.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.712269 rs2020887 -0.693147 0.98925 124 S80G 145 Agc/Ggc MODERATE 3 MISSENSE CODING PLA2G2D C protein_coding NM_012400.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20442054 T C 0 222 0 0.966 0.7694 0.6974 0.7569 0.5934 0.7485 0.903087 0.690912 0.582209 1 9531 80191 7897 6680 3911 39067 590 12515 2 10404 121372 11566 8650 6606 66726 908 16512 0.816435 0 . 0 . 97 19,24,16,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S80G|145|PLA2G2D|protein_coding|CODING|NM_012400.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974616 rs584367 -0.693141 0.358382 97 211 1497 MODIFIER 5 CODING PLA2G2F T protein_coding NM_022819.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20476391 C T 0 20.3 0 0.4652 0.4137 0.3674 0.619 0.2704 0.3129 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,3,0,2 UTR_3_PRIME(MODIFIER||1497||211|PLA2G2F|protein_coding|CODING|NM_022819.3|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs818571 -0.453602 0.72 5 Q137R 150 cAg/cGg MODERATE 4 MISSENSE CODING PLA2G2C C protein_coding NM_001316722.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20490518 T C 0 222 0 0.7466 0.6599 0.4942 0.7272 0.5835 0.6697 0.724164 0.636356 0.594199 1 6933 70999 4445 6193 3433 38222 504 11269 2 9490 116794 10826 8430 6420 64688 864 16076 0.999423 0 . 0 . 71 24,17,15,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q137R|150|PLA2G2C|protein_coding|CODING|NM_001316722.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.752333 rs6426616 -0.692831 0.966795 71 280 LOW 1 CODING UBXN10 C protein_coding NM_152376.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20512652 A C 0 9.7 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 SPLICE_SITE_REGION+INTRON(LOW||||280|UBXN10|protein_coding|CODING|NM_152376.4|1|C),INTRAGENIC(MODIFIER|||||UBXN10-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7530964 -0.379885 0 1 280 1911 MODIFIER 2 CODING UBXN10 A protein_coding NM_152376.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20519808 G A 0 222 0 0.4334 0.3506 0.2824 0.4087 0.1869 0.3957 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.759238 0 . 0 . 149 50,19,36,20 UTR_3_PRIME(MODIFIER||1911||280|UBXN10|protein_coding|CODING|NM_152376.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.82102 rs1061588 -0.693147 0.0587192 149 280 2835 MODIFIER 2 CODING UBXN10 C protein_coding NM_152376.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20520732 T C 0 222 0 0.6051 0.4263 0.3329 0.4127 0.2237 0.4734 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99909 0 . 0 . 89 27,17,21,16 UTR_3_PRIME(MODIFIER||2835||280|UBXN10|protein_coding|CODING|NM_152376.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.381126 rs7542020 -0.693141 0.663847 89 1215 19676 MODIFIER 1 CODING VWA5B1 C protein_coding NM_001039500.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20617419 T C 0 9.7 0 0.0946 0.2324 0.2925 0.3651 0.2256 0.2464 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||19676||1215|VWA5B1|protein_coding|CODING|NM_001039500.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12738826 -0.379885 0 1 N469S 1215 aAc/aGc MODERATE 10 MISSENSE CODING VWA5B1 G protein_coding NM_001039500.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20656824 A G 0 222 0 0.0113 0.1799 0.1859 0.3601 0.167 0.2311 0.0382948 0.135129 0.177247 1 72 4070 85 222 103 1593 47 1948 2 2206 20376 412 624 364 8660 196 7914 0.999093 0 . 0 COSM425144 128 25,38,19,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N469S|1215|VWA5B1|protein_coding|CODING|NM_001039500.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.312454 rs2072752 -0.693147 0.0163402 128 K634R 1215 aAa/aGa MODERATE 13 MISSENSE CODING VWA5B1 G protein_coding NM_001039500.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20662938 A G 0 222 0 0.1641 0.224 0.2046 0.3601 0.172 0.2321 0.171243 0.183968 0.189503 1 375 4134 89 217 191 1548 42 1672 2 2038 16544 374 596 644 7470 162 5260 0.992956 0 . 0 . 99 19,34,18,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K634R|1215|VWA5B1|protein_coding|CODING|NM_001039500.2|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931326 rs10916769 -0.693141 0.040382 99 R880H 1215 cGc/cAc MODERATE 17 MISSENSE CODING VWA5B1 A protein_coding NM_001039500.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20671961 G A 0 222 0 0.2443 0.3017 0.3458 0.3532 0.3181 0.2781 0.24711 0.306176 0.331867 1 556 6591 145 205 518 2671 82 2414 2 2080 21280 404 602 1602 8448 232 7912 0.144094 0 . 0 COSM1338396 167 50,25,38,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R880H|1215|VWA5B1|protein_coding|CODING|NM_001039500.2|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.477384 rs11582960 -0.693147 0.704984 167 E1204K 1215 Gag/Aag MODERATE 22 MISSENSE CODING VWA5B1 A protein_coding NM_001039500.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20680718 G A 0 222 0 0.208 0.2294 0.1801 0.2887 0.2237 0.2382 0 . 0 1 344 4208 81 162 12 1617 43 1949 2 1500 16724 358 558 52 6526 168 7562 0.973897 0 . 0 . 142 31,33,28,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1204K|1215|VWA5B1|protein_coding|CODING|NM_001039500.2|22|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.907738 rs2072751 -0.693147 0.000131639 142 1215 4 MODIFIER 22 CODING VWA5B1 G protein_coding NM_001039500.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20680760 A G 0 228 0 0.5681 0.5879 0.549 0.9087 0.4284 0.4755 0 . 0 2 617 6099 176 457 54 2006 63 2726 2 1068 11556 306 514 88 4458 126 4996 0 . 0 . 0 99 0,0,25,62 UTR_3_PRIME(MODIFIER||4||1215|VWA5B1|protein_coding|CODING|NM_001039500.2|22|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs230180 -0.693147 0.913727 99 1215 336 MODIFIER 22 CODING VWA5B1 G protein_coding NM_001039500.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20681092 C G 0 150 0 0.3124 0.4802 0.4352 0.9008 0.3439 0.4458 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,2 UTR_3_PRIME(MODIFIER||336||1215|VWA5B1|protein_coding|CODING|NM_001039500.2|22|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs926267 -0.556411 0.560696 6 352 193 MODIFIER 4 CODING MUL1 G protein_coding NM_024544.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20826990 C G 0 111 0 0 0.0033946 0 0.0169 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.809011 0 . 0 . 9 3,0,5,1 UTR_3_PRIME(MODIFIER||193||352|MUL1|protein_coding|CODING|NM_024544.2|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 1 0 0.577865 rs180860887 -0.616816 0.469001 9 T145 146 acC/acT LOW 4 SILENT CODING CDA T protein_coding NM_001785.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20945055 C T 0 222 0 0.379 0.3111 0.317 0.244 0.3231 0.272 0.395824 0.342304 0.314884 1 4032 37399 3436 2066 2152 21072 251 4390 2 10384 121114 11556 8632 6580 66554 904 16504 0.730051 0 . 0 COSM146436 82 15,25,11,21 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T145|146|CDA|protein_coding|CODING|NM_001785.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.238077 rs1048977 -0.69312 0.710277 82 581 LOW 1 CODING PINK1 G protein_coding NM_032409.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20964328 A G 0 217 0 0.7405 0.8219 0.8026 0.8165 0.8976 0.8732 0.771675 0.84338 0.880116 1 7936 104598 9422 7007 6117 58770 802 14544 2 10356 121304 11576 8648 6612 66696 908 16508 0.174265 0 . 0 . 42 20,2,16,3 SPLICE_SITE_REGION+INTRON(LOW||||581|PINK1|protein_coding|CODING|NM_032409.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989715 rs2298298 -0.69168 0.522735 42 581 LOW 4 CODING PINK1 A protein_coding NM_032409.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20972048 G A 0 222 0 0.7352 0.8207 0.8026 0.8145 0.8956 0.8783 0.775079 0.844226 0.879651 1 7965 104559 9409 6978 6081 58715 804 14607 2 10382 121192 11566 8624 6574 66634 906 16506 0.988856 0 . 0 . 264 84,56,71,23 SPLICE_SITE_REGION+INTRON(LOW||||581|PINK1|protein_coding|CODING|NM_032409.2|4|A),INTRAGENIC(MODIFIER|||||PINK1-AS||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.690973 rs3131713 -0.693147 1.39357e-07 264 581 37 MODIFIER 8 CODING PINK1 T protein_coding NM_032409.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20977221 A T 0 222 0 0.7844 0.8345 0.8112 0.8165 0.8917 0.8783 0.802769 0.853353 0.879274 1 7809 98589 8585 6446 5663 55163 771 14152 2 9766 114122 10550 7964 6194 62796 864 15988 0.487324 0 . 0 . 57 9,20,9,12 UTR_3_PRIME(MODIFIER||37||581|PINK1|protein_coding|CODING|NM_032409.2|8|T),DOWNSTREAM(MODIFIER||1039||456|DDOST|protein_coding|CODING|NM_005216.4||T),INTRAGENIC(MODIFIER|||||PINK1-AS||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.682122 rs686658 -0.692352 0.329521 57 581 181 MODIFIER 8 CODING PINK1 G protein_coding NM_032409.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20977365 C G 0 80 0 0.7844 0.8367 0.8127 0.8204 0.8976 0.8783 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 6 0,2,1,2 UTR_3_PRIME(MODIFIER||181||581|PINK1|protein_coding|CODING|NM_032409.2|8|G),DOWNSTREAM(MODIFIER||895||456|DDOST|protein_coding|CODING|NM_005216.4||G),INTRAGENIC(MODIFIER|||||PINK1-AS||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs513414 -0.511536 0.160333 6 581 265 MODIFIER 8 CODING PINK1 T protein_coding NM_032409.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20977449 G T 0 29.4 0 0.4962 0.5218 0.6095 0.4603 0.5994 0.4775 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,1,1,1 UTR_3_PRIME(MODIFIER||265||581|PINK1|protein_coding|CODING|NM_032409.2|8|T),DOWNSTREAM(MODIFIER||811||456|DDOST|protein_coding|CODING|NM_005216.4||T),INTRAGENIC(MODIFIER|||||PINK1-AS||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs512550 -0.453602 0.14 4 581 415 MODIFIER 8 CODING PINK1 G protein_coding NM_032409.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20977599 C G 0 20.4 0 0.0061 0.115 0.1527 0.127 0.1938 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 4 1,1,0,2 UTR_3_PRIME(MODIFIER||415||581|PINK1|protein_coding|CODING|NM_032409.2|8|G),DOWNSTREAM(MODIFIER||661||456|DDOST|protein_coding|CODING|NM_005216.4||G),INTRAGENIC(MODIFIER|||||PINK1-AS||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs8064 -0.453602 0.76 4 456 40 MODIFIER 11 CODING DDOST C protein_coding NM_005216.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20978832 T C 0 222 0 0.7421 0.8249 0.804 0.8274 0.8936 0.8783 0.771344 0.844024 0.881251 1 5322 64491 4648 4106 3272 38331 506 8306 2 6806 74166 5636 4942 3596 43312 568 9306 0.889031 0 . 0 . 66 27,9,21,5 UTR_3_PRIME(MODIFIER||40||456|DDOST|protein_coding|CODING|NM_005216.4|11|C),DOWNSTREAM(MODIFIER||828||581|PINK1|protein_coding|CODING|NM_032409.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986634 rs6893 -0.692976 0.745806 66 R8G 456 Cgt/Ggt MODERATE 1 MISSENSE CODING DDOST C protein_coding NM_005216.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20987873 G C 0 228 0 0.9017 0.973 0.9942 1 0.999 1 0.925697 0.974613 0.999649 2 8428 112219 11049 8232 6066 61491 833 16120 2 9186 113062 11104 8232 6066 61516 838 16120 0 . 0 . 0 127 0,0,50,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Ggt|R8G|456|DDOST|protein_coding|CODING|NM_005216.4|1|C),DOWNSTREAM(MODIFIER||2634||1029|KIF17|protein_coding|CODING|NM_020816.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs537816 -0.693147 0.042631 127 D933E 1029 gaC/gaG MODERATE 14 MISSENSE CODING KIF17 C protein_coding NM_020816.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 20992819 G C 0 222 0 0.7572 0.7045 0.7464 0.5536 0.8241 0.636 0.760781 0.790251 0.805349 1 7918 91307 8144 4725 5293 53611 708 10908 2 10406 121378 11574 8632 6612 66736 908 16510 0.678317 0 . 0 . 57 7,21,7,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D933E|1029|KIF17|protein_coding|CODING|NM_020816.3|14|C),UPSTREAM(MODIFIER||4782||456|DDOST|protein_coding|CODING|NM_005216.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836993 rs631357 -0.692831 0.00359971 57 T729 1029 acT/acC LOW 10 SILENT CODING KIF17 G protein_coding NM_020816.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21011346 A G 0 222 0 0.3116 0.2254 0.1455 0.3353 0.0855 0.1963 0.271507 0.150123 0.0879748 1 1759 9686 701 1705 100 3451 64 1906 2 5520 52086 3726 4466 1180 26604 386 10204 0.967305 0 . 0 . 173 31,47,31,56 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T729|1029|KIF17|protein_coding|CODING|NM_020816.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986508 rs12028811 -0.693147 0.237847 173 A665 1029 gcG/gcA LOW 9 SILENT CODING KIF17 T protein_coding NM_020816.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21012563 C T 0 222 0 0.0136 0.0323 0.0159 0.1032 0.0169 0.0123 0.0163821 0.0179851 0.0188014 1 48 694 23 211 0 279 5 128 2 2876 22248 524 1090 84 9486 214 7974 0.957372 0 . 0 . 206 40,59,30,69 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A665|1029|KIF17|protein_coding|CODING|NM_020816.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.758156 rs72650870 -0.693147 0.405187 206 V402M 1029 Gtg/Atg MODERATE 6 MISSENSE CODING KIF17 T protein_coding NM_020816.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21024901 C T 0 228 0 0.4455 0.5968 0.719 0.6498 0.6869 0.5675 0.498411 0.591419 0.63907 2 5090 74941 7625 5418 4418 42441 548 9401 2 10350 120680 11544 8602 6592 66204 896 16492 0.950276 0 . 0 COSM1338584 207 1,1,97,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V402M|1029|KIF17|protein_coding|CODING|NM_020816.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.88674 rs522496 -0.693147 0.334052 207 I341V 1029 Atc/Gtc MODERATE 5 MISSENSE CODING KIF17 C protein_coding NM_020816.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21031042 T C 0 222 0 0.1021 0.1637 0.062 0.2927 0.0915 0.2607 0.0971403 0.088267 0.0837209 1 1012 14579 1036 2735 276 5260 109 4151 2 10398 121290 11570 8620 6596 66686 908 16512 0.949821 0 . 0 . 370 152,54,101,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I341V|1029|KIF17|protein_coding|CODING|NM_020816.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.429937 rs2296225 -0.693147 9.76078e-05 370 P339 1029 ccG/ccA LOW 5 SILENT CODING KIF17 T protein_coding NM_020816.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21031046 C T 0 222 0 0.23 0.1857 0.1354 0.3998 0.0507 0.0798 0.201089 0.100031 0.0482558 1 2205 12422 2184 3459 272 3176 65 1061 2 10400 121286 11572 8600 6600 66694 908 16512 0.510261 0 . 0 COSM182847 382 115,42,145,53 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P339|1029|KIF17|protein_coding|CODING|NM_020816.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983346 rs2296226 -0.693147 0.0429396 382 Y90 1029 taC/taT LOW 2 SILENT CODING KIF17 A protein_coding NM_020816.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21042094 G A 0 228 0 0.0741 0.2804 0.1614 0.7232 0.1451 0.3262 0.0837494 0.113409 0.128605 2 863 24356 3073 6478 545 8188 162 5047 2 10364 120964 11558 8632 6602 66402 900 16506 0.614634 0 . 0 . 238 1,1,106,99 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y90|1029|KIF17|protein_coding|CODING|NM_020816.3|2|A),DOWNSTREAM(MODIFIER||4131||423|SH2D5|protein_coding|CODING|NM_001103161.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.94878 rs12046928 -0.693147 0.179729 238 R13 1029 cgT/cgC LOW 1 SILENT CODING KIF17 G protein_coding NM_020816.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21044161 A G 0 228 0 0.6006 0.7121 0.621 0.8879 0.7167 0.7413 0.629144 0.669573 0.690235 2 4977 75760 7245 7255 3869 40119 499 11796 2 7896 106234 10562 8018 5372 57688 742 15956 0 . 0 . 0 124 0,0,12,107 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R13|1029|KIF17|protein_coding|CODING|NM_020816.3|1|G),DOWNSTREAM(MODIFIER||2064||423|SH2D5|protein_coding|CODING|NM_001103161.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs601329 -0.693147 5.33516e-09 124 1029 20 MODIFIER 1 CODING KIF17 C protein_coding NM_020816.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21044219 A C 0 228 0 0.9887 0.9247 0.804 0.994 0.839 0.9407 0.969729 0.88199 0.838352 2 1841 28053 1604 1573 570 12890 236 9339 2 1922 32902 2132 1574 762 16080 274 10158 0 . 0 . 0 33 0,0,3,28 UTR_5_PRIME(MODIFIER||20||1029|KIF17|protein_coding|CODING|NM_020816.3|1|C),DOWNSTREAM(MODIFIER||2006||423|SH2D5|protein_coding|CODING|NM_001103161.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs601392 -0.69311 0.321483 33 423 1716 MODIFIER 10 CODING SH2D5 A protein_coding NM_001103161.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21046569 G A 0 46.3 0 0.062 0.2736 0.1542 0.7123 0.1451 0.3241 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1716||423|SH2D5|protein_coding|CODING|NM_001103161.1|10|A),UPSTREAM(MODIFIER||2059||1029|KIF17|protein_coding|CODING|NM_020816.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12022873 -0.453602 0.58 2 423 1193 MODIFIER 10 CODING SH2D5 T protein_coding NM_001103161.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21047092 A T 0 54 0 0.7882 0.7584 0.6412 0.8879 0.6849 0.7434 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,0 UTR_3_PRIME(MODIFIER||1193||423|SH2D5|protein_coding|CODING|NM_001103161.1|10|T),UPSTREAM(MODIFIER||2582||1029|KIF17|protein_coding|CODING|NM_020816.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs671905 -0.453602 0.82 4 423 881 MODIFIER 10 CODING SH2D5 G protein_coding NM_001103161.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21047404 A G 0 29.3 0 0.351 0.1653 0.1095 0.0992 0.0686 0.1217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 1,1,1,1 UTR_3_PRIME(MODIFIER||881||423|SH2D5|protein_coding|CODING|NM_001103161.1|10|G),UPSTREAM(MODIFIER||2894||1029|KIF17|protein_coding|CODING|NM_020816.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.5 rs3738144 -0.453602 0.42 5 423 560 MODIFIER 10 CODING SH2D5 G protein_coding NM_001103161.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21047725 A G 0 150 0 0.7027 0.7348 0.6311 0.8879 0.6849 0.7454 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,2 UTR_3_PRIME(MODIFIER||560||423|SH2D5|protein_coding|CODING|NM_001103161.1|10|G),UPSTREAM(MODIFIER||3215||1029|KIF17|protein_coding|CODING|NM_020816.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs659046 -0.556411 0.152777 6 Q187 423 caG/caA LOW 6 SILENT CODING SH2D5 T protein_coding NM_001103161.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21050958 C T 0 228 0 0.9849 0.8796 0.7622 0.9802 0.7714 0.8282 0.957025 0.82026 0.756042 2 9143 95584 8839 8508 4904 49766 676 13748 2 9520 118686 11490 8566 6482 65252 876 16500 0 . 0 . 0 163 0,0,104,44 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q187|423|SH2D5|protein_coding|CODING|NM_001103161.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs592060 -0.693147 0.553575 163 1621 597 MODIFIER 35 CODING EIF4G3 C protein_coding NM_001198801.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21133215 T C 0 206 0 0.0015 0.0369 0.0447 0.0883 0.0109 0.0532 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992626 0 . 0 . 32 1,18,5,7 UTR_3_PRIME(MODIFIER||597||1621|EIF4G3|protein_coding|CODING|NM_001198801.1|35|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.268262 rs74522845 -0.680642 0.18368 32 L1316 1621 Tta/Cta LOW 28 SILENT CODING EIF4G3 G protein_coding NM_001198801.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21167404 A G 0 228 0 0.7769 0.9377 0.9755 1 1 1 0.814798 0.936875 0.999419 2 8480 119363 11479 8654 6614 66723 903 16510 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 131 0,0,62,57 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L1316|1621|EIF4G3|protein_coding|CODING|NM_001198801.1|28|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2230573 -0.693147 0.127513 131 770 146 MODIFIER 19 CODING ECE1 C protein_coding NM_001397.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21546302 T C 0 84 0 0 0.0013978 0 0.0069 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.896474 0 . 0 . 13 7,0,4,1 UTR_3_PRIME(MODIFIER||146||770|ECE1|protein_coding|CODING|NM_001397.2|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 1 0 0.896474 rs372073084 -0.590765 0.503385 13 Y114C 633 tAc/tGc MODERATE 3 MISSENSE CODING NBPF3 G protein_coding NM_032264.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21795388 A G 0 222 0 0.1445 0.4239 0.4755 0.5804 0.5417 0.4826 0.220154 0.440258 0.553023 1 2136 62751 6346 4851 3540 37305 509 8064 2 10358 121102 11550 8634 6604 66584 908 16464 0.999089 0 . 0 COSM425331 235 31,66,36,79 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tAc/tGc|Y114C|633|NBPF3|protein_coding|CODING|NM_032264.4|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945123 rs1827293 -0.693147 0.703699 235 E262 633 gaG/gaA LOW 7 SILENT CODING NBPF3 A protein_coding NM_032264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21799924 G A 0 222 0 0.0076 0.0513 0.0893 0.0813 0.0249 0.0798 0.0133908 0.015762 0.0169767 1 134 4626 1186 900 212 1137 18 1039 2 10406 121404 11576 8648 6614 66740 908 16512 0.996198 0 . 0 . 462 161,75,140,47 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E262|633|NBPF3|protein_coding|CODING|NM_032264.4|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.785163 rs80145424 -0.693147 0.162658 462 S501 633 tcG/tcA LOW 13 SILENT CODING NBPF3 A protein_coding NM_032264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21808159 G A 0 198 0 0.3192 0.4671 0.4827 0.4871 0.495 0.6063 0 . 0 1 3301 58000 5808 4347 3168 31442 442 9492 2 9564 118052 11494 8588 6562 64848 880 16116 0.522726 0 . 0 . 152 51,27,25,14 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S501|633|NBPF3|protein_coding|CODING|NM_032264.4|13|A) 0 0.5 1 0 . 1 0 . 1 0 32 0 0.91589 0.692699 0 0.688261 rs71512991 -0.693144 0.000371135 152 G517 633 ggA/ggC LOW 13 SILENT CODING NBPF3 C protein_coding NM_032264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21808207 A C 0 70 0 . 0 . 0 . 0 . 0 . 1 2392 43386 4321 3378 2616 24607 339 5733 2 8130 96634 9230 7180 5774 54668 720 10932 0.966223 0 . 0 . 90 0,56,0,34 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G517|633|NBPF3|protein_coding|CODING|NM_032264.4|13|C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.94345 0 . 0.442222 rs146564096 -0.693132 0.0107276 90 L523 633 Ttg/Ctg LOW 13 SILENT CODING NBPF3 C protein_coding NM_032264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21808223 T C 0 70 0 . 0 . 0 . 0 . 0 . 1 2388 38217 3614 2948 2462 22037 292 4476 2 7806 89882 8290 6794 5562 51580 664 9186 0.906839 0 . 0 . 80 0,50,0,30 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L523|633|NBPF3|protein_coding|CODING|NM_032264.4|13|C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.938005 0 . 0.269268 rs145079058 -0.693097 0.000154094 80 K548N 633 aaG/aaC MODERATE 14 MISSENSE CODING NBPF3 C protein_coding NM_032264.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21809014 G C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 25 314 14 23 2 240 6 4 2 50 468 24 36 2 344 6 6 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K548N|633|NBPF3|protein_coding|CODING|NM_032264.4|14|C) 0 0.5 1 0 . 0 . 0 1 0 49 0 0 . 0 . rs200063908 -0.379885 0 1 Y591 633 taT/taC LOW 15 SILENT CODING NBPF3 C protein_coding NM_032264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21809750 T C 0 90 0 . 0 . 0 . 0 . 0 . 2 3729 75895 7735 5614 4154 39896 603 14164 2 8824 106706 10072 7606 5928 57658 824 15794 1 0 . 0 . 40 0,1,0,39 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y591|633|NBPF3|protein_coding|CODING|NM_032264.4|15|C) 0 . 0 . 0 . 0 . 1 0 27 0 1 0 . 1 rs202069483 -0.693144 0.22877 40 F625L 633 Ttc/Ctc MODERATE 15 MISSENSE CODING NBPF3 C protein_coding NM_032264.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21809850 T C 0 108 0 0.0166 0.0569 0.1023 0.0804 0.0288 0.0838 0 . 0 1 64 1012 158 120 72 423 8 167 2 5558 37134 2502 2386 2632 21404 306 2346 0.983252 0 . 0 . 28 0,14,0,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F625L|633|NBPF3|protein_coding|CODING|NM_032264.4|15|C) 0 0.5 1 0 . 1 0 . 1 0 49 0 0.350844 0 . 0.476498 rs199951062 -0.686358 0.208536 28 633 45 MODIFIER 15 CODING NBPF3 C protein_coding NM_032264.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21809924 G C 0 147 0 0.9758 0.9922 0.9957 0.999 0.998 0.999 0 . 0 2 2510 15164 841 936 1224 8734 122 797 2 2610 15284 844 936 1224 8750 122 798 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||45||633|NBPF3|protein_coding|CODING|NM_032264.4|15|C) 0 . 0 . 0 1 0 . 1 0 48 0 0 . 0 . rs200210375 -0.676189 0.677213 11 633 323 MODIFIER 15 CODING NBPF3 G protein_coding NM_032264.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21810202 T G 0 19.4 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||323||633|NBPF3|protein_coding|CODING|NM_032264.4|15|G) 0 . 0 . 0 . 0 . 0 . 26 0 0 . 0 . rs200265424 -0.453602 0.1 2 633 696 MODIFIER 15 CODING NBPF3 C protein_coding NM_032264.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21810575 T C 0 48.5 0 0.3139 0.6088 0.6671 0.6984 0.6332 0.8487 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||696||633|NBPF3|protein_coding|CODING|NM_032264.4|15|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 . 0 . rs3010179 -0.511536 0.460446 3 S110 524 agT/agC LOW 5 SILENT CODING ALPL C protein_coding NM_000478.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21889635 T C 0 228 0 0.8495 0.9295 0.9539 0.9821 0.9374 0.9581 0.867907 0.921728 0.949302 2 8953 114254 11269 8527 6159 62733 859 15754 2 10334 120906 11576 8632 6610 66340 904 16510 0 2 benign 0 . 259 0,0,144,90 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S110|524|ALPL|protein_coding|CODING|NM_000478.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1780316 -0.693147 0.000100866 259 Y263H 524 Tac/Cac MODERATE 7 MISSENSE CODING ALPL C protein_coding NM_000478.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21894735 T C 0 222 0 0.2655 0.267 0.268 0.4534 0.1203 0.227 0.251702 0.158773 0.111163 1 2643 21651 2976 3897 1258 7149 142 3586 2 10362 120886 11518 8612 6554 66440 902 16498 0.744552 2 benign 0 . 149 36,50,22,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y263H|524|ALPL|protein_coding|CODING|NM_000478.4|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823416 rs3200254 -0.693147 0.819884 149 524 LOW 8 CODING ALPL C protein_coding NM_000478.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21900151 T C 0 221 0 0.236 0.258 0.2666 0.4484 0.1203 0.227 0.191103 0.130478 0.0994186 1 2286 20231 2702 3574 1179 6870 138 3482 2 9990 117550 11138 8330 6302 64896 884 16010 0.946513 0 . 0 . 138 54,33,15,19 SPLICE_SITE_REGION+INTRON(LOW||||524|ALPL|protein_coding|CODING|NM_000478.4|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.68963 rs74063111 -0.693132 0.544173 138 P292 524 ccA/ccG LOW 9 SILENT CODING ALPL G protein_coding NM_000478.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21900171 A G 0 222 0 0.2821 0.2716 0.2709 0.4474 0.1252 0.227 0.25783 0.16231 0.113372 1 2707 21457 2840 3695 1246 7294 140 3535 2 10146 119030 11270 8426 6410 65666 894 16218 0.96699 0 . 0 . 144 47,44,20,19 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P292|524|ALPL|protein_coding|CODING|NM_000478.4|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91197 rs3200255 -0.693144 0.513927 144 524 65 MODIFIER 12 CODING ALPL T protein_coding NM_000478.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21904206 C T 0 197 0 0.2405 0.3367 0.3833 0.3135 0.3738 0.4192 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.831377 0 . 0 . 37 3,15,3,16 UTR_3_PRIME(MODIFIER||65||524|ALPL|protein_coding|CODING|NM_000478.4|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.211592 rs1697405 -0.69168 0.680753 37 524 126 MODIFIER 12 CODING ALPL G protein_coding NM_000478.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21904267 A G 0 228 0 0.8555 0.8682 0.9078 0.8006 0.8638 0.9315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,3,17 UTR_3_PRIME(MODIFIER||126||524|ALPL|protein_coding|CODING|NM_000478.4|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1697406 -0.692067 0.333832 20 524 433 MODIFIER 12 CODING ALPL G protein_coding NM_000478.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21904574 A G 0 228 0 0.0068 0.222 0.33 0.5427 0.0964 0.2352 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 46 0,1,18,23 UTR_3_PRIME(MODIFIER||433||524|ALPL|protein_coding|CODING|NM_000478.4|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2242421 -0.693145 0.00507204 46 T518 727 acC/acT LOW 18 SILENT CODING RAP1GAP A protein_coding NM_001145658.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21932625 G A 0 222 0 0.0295 0.1406 0.2867 0.2401 0.0765 0.1503 0.0493182 0.0855294 0.104104 1 300 9149 1672 1222 128 3734 65 2028 2 4646 45942 3574 3912 738 23028 318 9726 0.872689 0 . 0 . 210 62,21,62,23 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T518|727|RAP1GAP|protein_coding|CODING|NM_001145658.1|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0659683 rs2275365 -0.693147 0.031225 210 727 LOW 15 CODING RAP1GAP T protein_coding NM_001145658.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21935433 G T 0 222 0 0.2209 0.4547 0.5101 0.6518 0.4533 0.5297 0.263504 0.41527 0.493023 1 2659 59402 6777 5611 2920 32344 422 8669 2 10406 121376 11574 8634 6614 66732 908 16508 0.947516 0 . 0 . 137 24,34,27,33 SPLICE_SITE_REGION+INTRON(LOW||||727|RAP1GAP|protein_coding|CODING|NM_001145658.1|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.477106 rs861212 -0.693147 0.185515 137 Y154 727 taC/taT LOW 7 SILENT CODING RAP1GAP A protein_coding NM_001145658.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 21943820 G A 0 228 0 0.1884 0.3261 0.5072 0.5298 0.2495 0.2526 0.189177 0.235403 0.259087 2 1288 20466 2804 2858 468 9870 150 3028 2 4924 51106 4252 4686 1180 25760 376 9928 0.965718 0 . 0 . 150 4,1,91,38 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y154|727|RAP1GAP|protein_coding|CODING|NM_001145658.1|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.498591 rs2275360 -0.693147 0.0315722 150 H27 1035 caC/caT LOW 1 SILENT CODING USP48 A protein_coding NM_032236.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22109370 G A 0 228 0 0.028 0.2817 0.5274 0.5893 0.2197 0.1973 0.0635397 0.166277 0.218588 2 203 9128 1192 1200 98 4134 82 2219 2 1898 25090 1662 1720 236 11134 206 8234 0 . 0 . 0 18 0,0,3,15 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H27|1035|USP48|protein_coding|CODING|NM_032236.5|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10917042,rs386515910 -0.691153 0.175109 18 N134T 272 aAc/aCc MODERATE 2 MISSENSE CODING LDLRAD2 C protein_coding NM_001013693.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22141206 A C 0 48.5 0 0.4697 0.6128 0.7695 0.6319 0.6988 0.5869 0.520865 0.635016 0.693025 2 1054 21719 1486 899 689 10880 196 6515 2 1902 31430 1740 1302 960 15294 268 9964 0 . 0 . COSM425366 3 0,0,0,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N134T|272|LDLRAD2|protein_coding|CODING|NM_001013693.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs10917051 -0.511536 0.732596 3 S4351 4392 tcA/tcG LOW 97 SILENT CODING HSPG2 C protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22149935 T C 0 228 0 0.677 0.7804 0.7493 0.8155 0.833 0.8517 0.722323 0.792328 0.828096 2 5092 72811 6379 5380 2986 40710 514 11750 2 6978 88750 8296 6556 3606 48528 636 14150 0 . 0 . 0 30 0,0,27,3 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S4351|4392|HSPG2|protein_coding|CODING|NM_001291860.1|97|C),UTR_3_PRIME(MODIFIER||1227||272|LDLRAD2|protein_coding|CODING|NM_001013693.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs897467 -0.693097 0.00878647 30 272 1227 MODIFIER 5 CODING LDLRAD2 C protein_coding NM_001013693.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22149935 T C 0 228 0 0.677 0.7804 0.7493 0.8155 0.833 0.8517 0.722323 0.792328 0.828096 2 5092 72811 6379 5380 2986 40710 514 11750 2 6978 88750 8296 6556 3606 48528 636 14150 0 . 0 . 0 30 0,0,27,3 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S4351|4392|HSPG2|protein_coding|CODING|NM_001291860.1|97|C),UTR_3_PRIME(MODIFIER||1227||272|LDLRAD2|protein_coding|CODING|NM_001013693.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs897467 -0.693097 0.00878647 30 272 1549 MODIFIER 5 CODING LDLRAD2 T protein_coding NM_001013693.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22150257 C T 0 228 0 0.0726 0.3752 0.4611 0.6488 0.4801 0.3333 0.141008 0.3745 0.49407 2 1411 52986 6036 5351 2994 31224 426 5544 2 9782 115354 11102 8216 6208 62912 864 16270 0 . 0 . 0 67 0,0,15,46 UTR_3_PRIME(MODIFIER||1549||272|LDLRAD2|protein_coding|CODING|NM_001013693.2|5|T),INTRON(MODIFIER||||4392|HSPG2|protein_coding|CODING|NM_001291860.1|95|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3736357 -0.693147 0.0389221 67 4392 LOW 70 CODING HSPG2 A protein_coding NM_001291860.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22167785 G A 0 222 0 0.0129 0.0573 0.0216 0.1994 0.006 0.0491 0.0127099 0.00815008 0.00581395 1 153 3984 606 1756 4 595 44 826 2 10168 119636 11544 8572 6440 65598 888 16426 0.819077 0 . 0 . 130 25,29,28,30 SPLICE_SITE_REGION+INTRON(LOW||||4392|HSPG2|protein_coding|CODING|NM_001291860.1|70|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.147497 rs2270695 -0.693147 0.0195719 130 4392 LOW 70 CODING HSPG2 A protein_coding NM_001291860.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22167786 G A 0 222 0 0.0129 0.0573 0.0216 0.1994 0.006 0.0491 0.012483 0.00815008 0.00593023 1 153 3983 606 1756 4 595 44 825 2 10168 119640 11538 8576 6442 65608 888 16420 0.849746 0 . 0 . 129 24,30,28,30 SPLICE_SITE_REGION+INTRON(LOW||||4392|HSPG2|protein_coding|CODING|NM_001291860.1|70|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.267228 rs2270696 -0.693147 0.0195719 129 4392 LOW 45 CODING HSPG2 T protein_coding NM_001291860.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22182173 C T 0 228 0 0.0061 0.0525 0.0202 0.1915 0.001 0.0481 0.00409277 0.00292893 0.00233209 2 26 1714 195 805 3 134 18 533 2 3852 40314 2146 3220 836 20108 308 9844 0.986842 2 benign 0 . 90 0,2,49,27 SPLICE_SITE_REGION+INTRON(LOW||||4392|HSPG2|protein_coding|CODING|NM_001291860.1|45|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.171053 rs2290498 -0.693147 0.00113619 90 A1504V 4392 gCg/gTg MODERATE 36 MISSENSE CODING HSPG2 A protein_coding NM_001291860.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22191454 G A 0 207 0 0.5893 0.6915 0.781 0.8889 0.7256 0.5276 0.619808 0.699136 0.739632 2 4514 68707 7703 6405 2960 38535 490 8100 2 6918 92062 9316 7084 3838 50828 630 13448 0 . 0 . 0 9 0,0,6,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A1504V|4392|HSPG2|protein_coding|CODING|NM_001291860.1|36|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.924584 0 . rs897471 -0.662043 0.0157188 9 V1300 4392 gtG/gtA LOW 32 SILENT CODING HSPG2 T protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22199245 C T 0 228 0 0.2088 0.4249 0.4078 0.4058 0.6471 0.5204 0.294051 0.524692 0.642857 2 2603 60394 3862 3477 3398 38895 451 7708 2 7696 99554 7600 6916 4782 57602 710 14248 0 . 0 . COSM425375 93 0,0,28,56 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1300|4392|HSPG2|protein_coding|CODING|NM_001291860.1|32|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2229482,rs386561726 -0.693147 0.144054 93 N766S 4392 aAt/aGt MODERATE 17 MISSENSE CODING HSPG2 C protein_coding NM_001291860.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22206649 T C 0 228 0 0.7466 0.9299 0.9784 1 1 0.999 0.810486 0.935184 0.99907 2 8228 119030 11485 8648 6614 66654 894 16507 2 10394 121326 11574 8648 6614 66678 906 16512 0 . 0 . 0 89 0,0,40,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N766S|4392|HSPG2|protein_coding|CODING|NM_001291860.1|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs989994 -0.693147 0.746004 89 A704 4392 gcC/gcT LOW 16 SILENT CODING HSPG2 A protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22206942 G A 0 228 0 0.7466 0.9299 0.9784 1 1 0.999 0.810486 0.935184 0.99907 2 8198 118729 11477 8644 6518 66504 888 16500 2 10346 121006 11566 8644 6518 66528 900 16504 0 . 0 . 0 73 0,0,41,31 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A704|4392|HSPG2|protein_coding|CODING|NM_001291860.1|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1874793 -0.693147 0.383695 73 M639V 4392 Atg/Gtg MODERATE 15 MISSENSE CODING HSPG2 C protein_coding NM_001291860.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22207235 T C 0 228 0 0.9039 0.9736 0.9928 1 1 1 0.929157 0.975659 0.999418 2 7275 96055 8944 7330 3664 54357 677 13808 2 7894 96720 8970 7330 3664 54376 678 13808 0 . 0 . 0 216 0,0,89,103 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M639V|4392|HSPG2|protein_coding|CODING|NM_001291860.1|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1874792 -0.693147 0.0334516 216 L248 4392 ctT/ctC LOW 8 SILENT CODING HSPG2 G protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22214127 A G 0 159 0 0.7065 0.5363 0.5793 0.6498 0.3191 0.3824 0.629596 0.427341 0.323721 1 6588 50426 6899 5396 2317 22253 361 6612 2 10284 120772 11542 8614 6604 66354 900 16474 0.995381 0 . 0 . 17 3,5,3,6 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L248|4392|HSPG2|protein_coding|CODING|NM_001291860.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995381 rs2229478 -0.662043 0.915915 17 G158 4392 ggG/ggT LOW 6 SILENT CODING HSPG2 A protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22216574 C A 0 222 0 0.2163 0.4445 0.4164 0.3522 0.6839 0.6217 0.302996 0.550285 0.676977 1 3056 70024 4595 3229 4292 44405 540 9907 2 10406 121372 11564 8642 6614 66728 906 16512 0.989938 0 . 0 . 100 25,28,11,28 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G158|4392|HSPG2|protein_coding|CODING|NM_001291860.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.616436 rs2254358 -0.693144 0.60313 100 L148 4392 ctG/ctC LOW 6 SILENT CODING HSPG2 G protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22216604 C G 0 222 0 0.2163 0.4445 0.4164 0.3522 0.6839 0.6217 0.302996 0.550361 0.677093 1 3056 70029 4599 3224 4288 44415 540 9907 2 10406 121364 11568 8638 6610 66724 906 16512 0.713392 0 . 0 . 81 16,25,7,29 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L148|4392|HSPG2|protein_coding|CODING|NM_001291860.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.168021 rs2254357 -0.693139 0.476883 81 F108 4392 ttC/ttT LOW 4 SILENT CODING HSPG2 A protein_coding NM_001291860.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22217108 G A 0 228 0 0.8139 0.9481 0.9798 1 1 1 0.865411 0.953791 0.99907 2 8819 119722 11513 8654 6614 66716 897 16509 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 84 0,0,48,33 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F108|4392|HSPG2|protein_coding|CODING|NM_001291860.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2501260 -0.693147 0.469636 84 S51 270 agC/agT LOW 3 SILENT CODING CELA3B T protein_coding NM_007352.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22307340 C T 0 222 0 0.711 0.8492 0.9352 0.755 0.9722 0.9458 0 . 0 1 5678 100629 9906 5623 5515 57673 753 15481 2 8396 109108 10774 7956 5590 59464 806 16122 0.932185 0 . 0 . 130 46,30,34,13 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S51|270|CELA3B|protein_coding|CODING|NM_007352.2|3|T) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.00116863 0.0733203 0 0.0379157 rs7528228 -0.693147 0.0810202 130 T57 270 acC/acG LOW 3 SILENT CODING CELA3B G protein_coding NM_007352.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22307358 C G 0 222 0 0.7042 0.8476 0.9366 0.754 0.9722 0.9468 0 . 0 1 6034 103476 10095 5847 5347 59747 742 15664 2 8666 111732 10938 8134 5418 61470 794 16312 0.270672 0 . 0 . 128 37,33,35,16 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T57|270|CELA3B|protein_coding|CODING|NM_007352.2|3|G) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.0101892 0.0484533 0 0.310188 rs7528300 -0.693147 0.0023445 128 R79W 270 Cgg/Tgg MODERATE 4 MISSENSE CODING CELA3B T protein_coding NM_007352.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22307538 C T 0 222 0 0.8442 0.8934 0.9625 0.755 0.992 0.9519 0.857013 0.946332 0.992093 1 8929 115995 10924 6474 6608 66213 877 15970 2 10402 121392 11576 8644 6614 66736 908 16512 0.190804 0 . 0 . 105 27,28,15,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R79W|270|CELA3B|protein_coding|CODING|NM_007352.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.911867 rs7528405 -0.693146 0.0978157 105 P146 270 ccG/ccC LOW 5 SILENT CODING CELA3B C protein_coding NM_007352.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22310262 G C 0 222 0 0.7958 0.8794 0.9539 0.755 0.992 0.9519 0.808216 0.928692 0.990458 1 8462 115359 10881 6466 6608 66116 872 15954 2 10390 121350 11576 8652 6614 66698 908 16512 0.501217 0 . 0 . 159 34,52,21,39 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P146|270|CELA3B|protein_coding|CODING|NM_007352.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.000107163 0.38418 0 0.720668 rs10733033,rs41401347 -0.693147 0.176979 159 270 LOW 5 CODING CELA3B T protein_coding NM_007352.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22310674 C T 0 222 0 0.7095 0.8492 0.9366 0.755 0.9722 0.9468 0.758965 0.901661 0.974767 1 7759 112670 10773 6472 6541 64785 850 15490 2 10386 120722 11572 8646 6614 66472 902 16130 0.999686 0 . 0 . 92 31,15,34,8 SPLICE_SITE_REGION+INTRON(LOW||||270|CELA3B|protein_coding|CODING|NM_007352.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.751418 rs7538207 -0.693146 0.770133 92 P181 270 ccG/ccC LOW 6 SILENT CODING CELA3B C protein_coding NM_007352.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22310725 G C 0 222 0 . 0 . 0 . 0 0.755788 0.87944 0.942791 1 7732 110508 10666 6470 6158 62969 823 15690 2 10406 121376 11570 8642 6614 66726 906 16512 0.683476 0 . 0 . 126 29,16,41,22 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P181|270|CELA3B|protein_coding|CODING|NM_007352.2|6|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.963926 rs3820287 -0.693147 0.347446 126 N214 270 aaT/aaC LOW 6 SILENT CODING CELA3B C protein_coding NM_007352.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22310824 T C 0 222 0 0.8434 0.8932 0.9625 0.755 0.992 0.9519 0.85724 0.946316 0.991973 1 8929 115777 10924 6475 6608 66110 875 15856 2 10404 121186 11576 8648 6614 66636 906 16402 0.794168 0 . 0 . 92 7,27,8,42 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N214|270|CELA3B|protein_coding|CODING|NM_007352.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.897628 0.772631 0 0.999491 rs1803531 -0.693147 0.209319 92 I260 270 atT/atC LOW 7 SILENT CODING CELA3B C protein_coding NM_007352.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22313161 T C 0 222 0 0.792 0.8808 0.9496 0.7629 0.992 0.9591 0.806854 0.928418 0.990698 1 8379 115319 10849 6483 6606 66106 867 16029 2 10372 121260 11550 8638 6612 66674 906 16508 0.0672462 0 . 0 . 133 44,26,27,23 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I260|270|CELA3B|protein_coding|CODING|NM_007352.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 54 0 0.103641 0.0512905 0 0.0228333 rs1803530 -0.693147 0.00710114 133 A241G 270 gCc/gGc MODERATE 7 MISSENSE CODING CELA3A G protein_coding NM_005747.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22336277 C G 0 222 0 0.9047 0.8958 0.902 0.7431 0.9771 0.953 0.921029 0.957211 0.975698 1 9583 114514 9958 6478 6462 65229 864 15940 2 10358 121192 11558 8588 6608 66666 908 16506 0.736662 0 . 0 . 119 40,21,28,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A241G|270|CELA3A|protein_coding|CODING|NM_005747.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.600466 rs3820285 -0.693146 0.568206 119 P250 270 ccC/ccT LOW 7 SILENT CODING CELA3A T protein_coding NM_005747.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22336305 C T 0 222 0 0.2315 0.2865 0.4107 0.4018 0.2207 0.2219 0.260554 0.238967 0.227907 1 2401 29085 4359 2807 1439 14058 207 3814 2 10274 120048 11218 8434 6564 66240 888 16430 0.971981 0 . 0 . 134 49,18,35,17 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P250|270|CELA3A|protein_coding|CODING|NM_005747.4|7|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.944631 0.774755 0 0.734907 rs9187 -0.693147 0.00986302 134 T251 270 acG/acA LOW 7 SILENT CODING CELA3A A protein_coding NM_005747.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22336308 G A 0 222 0 0.2307 0.2855 0.4078 0.3998 0.2207 0.2219 0.258738 0.236737 0.225465 1 2406 29109 4378 2816 1437 14052 207 3813 2 10278 120060 11238 8436 6562 66228 888 16430 0.688463 0 . 0 . 134 48,19,36,17 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T251|270|CELA3A|protein_coding|CODING|NM_005747.4|7|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.985802 0.711753 0 0.868453 rs12908 -0.693147 0.0178212 134 351 2053 MODIFIER 5 CODING WNT4 C protein_coding NM_030761.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22444490 A C 0 46.3 0 0.9985 0.9641 0.9683 0.999 0.9245 0.9192 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2053||351|WNT4|protein_coding|CODING|NM_030761.4|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4655023 -0.453602 0.56 2 351 1568 MODIFIER 5 CODING WNT4 T protein_coding NM_030761.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22444975 C T 0 9.7 0 0.1702 0.3349 0.3833 0.6687 0.1938 0.3241 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1568||351|WNT4|protein_coding|CODING|NM_030761.4|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10737462 -0.379885 0 1 351 925 MODIFIER 5 CODING WNT4 C protein_coding NM_030761.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22445616 CAG C 0 27.2 0 0.7126 0.7756 0.7262 0.869 0.7316 0.8446 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||925||351|WNT4|protein_coding|CODING|NM_030761.4|5|C) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs55866536 -0.379885 0 1 Y595C 1239 tAc/tGc MODERATE 10 MISSENSE CODING ZBTB40 G protein_coding NM_001083621.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22835677 A G 0 228 0 0.9395 0.8225 0.8429 0.8929 0.7167 0.6861 0.903995 0.781793 0.719186 2 9472 92844 10370 7771 4673 48110 663 11785 2 10406 121404 11574 8652 6614 66738 908 16512 0 . 0 . 0 138 0,0,76,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y595C|1239|ZBTB40|protein_coding|CODING|NM_001083621.1|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs209729 -0.693147 0.00475593 138 V997M 1239 Gtg/Atg MODERATE 15 MISSENSE CODING ZBTB40 A protein_coding NM_001083621.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22846709 G A 0 228 0 1 0.9984 0.9971 1 0.994 1 0.998865 0.996079 0.994651 2 10396 120996 11552 8646 6598 66400 905 16499 2 10404 121358 11576 8646 6614 66698 908 16512 0 . 0 . 0 81 0,0,38,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V997M|1239|ZBTB40|protein_coding|CODING|NM_001083621.1|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs209720,rs386557128 -0.693147 0.687207 81 P1182 1239 ccG/ccC LOW 19 SILENT CODING ZBTB40 C protein_coding NM_001083621.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22852715 G C 0 228 0 0.1225 0.3181 0.2205 0.4692 0.3936 0.4182 0.159782 0.298016 0.368837 2 1651 41520 1834 3925 2272 24531 320 6987 2 10400 121330 11568 8632 6606 66708 906 16510 0.935065 0 . 0 . 86 2,0,45,32 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P1182|1239|ZBTB40|protein_coding|CODING|NM_001083621.1|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.181818 rs881646 -0.693147 0.0462952 86 1239 3712 MODIFIER 19 CODING ZBTB40 C protein_coding NM_001083621.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22856601 T C 0 9.7 0 0.1626 0.3295 0.2205 0.4702 0.3976 0.4172 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3712||1239|ZBTB40|protein_coding|CODING|NM_001083621.1|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1062663 -0.379885 0 1 G92 245 ggA/ggG LOW 3 SILENT CODING C1QA G protein_coding NM_015991.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22965438 A G 0 222 0 0.7905 0.6164 0.5965 0.6111 0.3956 0.6278 0.710046 0.487965 0.374621 1 5373 44159 5062 3613 1800 19711 321 8279 2 7190 81976 7482 5856 3570 43634 598 13646 0.696638 0 . 0 . 94 37,9,24,12 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G92|245|C1QA|protein_coding|CODING|NM_015991.2|3|G),UPSTREAM(MODIFIER||4680||245|C1QC|protein_coding|CODING|NM_001114101.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987464 rs172378 -0.693139 0.504406 94 245 21 MODIFIER 3 CODING C1QC A protein_coding NM_001114101.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22974297 C A 0 222 0 0.8896 0.5877 0.4957 0.622 0.3827 0.4202 0.797095 0.512917 0.367326 1 8091 52479 5812 4876 2438 24044 376 6842 2 10024 118252 11376 8318 6438 64790 874 16432 0.390986 0 . 0 . 57 2,27,3,22 UTR_3_PRIME(MODIFIER||21||245|C1QC|protein_coding|CODING|NM_001114101.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.260869 rs9434 -0.692914 0.0703696 57 253 79 MODIFIER 3 CODING C1QB G protein_coding NM_000491.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 22987958 A G 0 102 0 0.9985 0.9914 0.987 1 0.9751 0.9928 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_3_PRIME(MODIFIER||79||253|C1QB|protein_coding|CODING|NM_000491.3|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10580 -0.590765 0.534935 5 P459 1055 ccG/ccA LOW 6 SILENT CODING EPHB2 A protein_coding NM_001309193.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23208925 G A 0 222 0 0.1989 0.2145 0.1585 0.4901 0.0755 0.1339 0.165229 0.118022 0.0938372 1 1821 16622 1473 4480 608 6055 122 2063 2 10406 121368 11574 8632 6610 66728 906 16512 0.991234 0 . 0 COSM1178395 76 16,15,18,20 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P459|1055|EPHB2|protein_coding|CODING|NM_001309193.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.745726 rs2229872 -0.693143 0.162673 76 G515 1055 ggT/ggC LOW 7 SILENT CODING EPHB2 C protein_coding NM_001309193.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23219493 T C 0 228 0 0.9992 0.9982 0.9957 1 0.995 1 0.99773 0.994157 0.992326 2 10385 120932 11555 8654 6596 66338 906 16498 2 10400 121376 11574 8654 6614 66716 908 16510 0 . 0 . 0 128 0,0,73,47 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G515|1055|EPHB2|protein_coding|CODING|NM_001309193.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs309472 -0.693147 0.377313 128 N281K 576 aaC/aaA MODERATE 6 MISSENSE CODING LACTBL1 T protein_coding NM_001289974.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23280424 G T 0 222 0 0.2322 0.3944 0.4798 0.5605 0.3648 0.4121 0 . 0 1 249 5345 131 277 10 1745 51 2882 2 890 14438 288 478 32 4968 154 7628 0.927252 0 . 0 . 90 39,4,37,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N281K|576|LACTBL1|protein_coding|CODING|NM_001289974.1|6|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.550535 rs12048993 -0.693146 0.10895 90 1076 3757 MODIFIER 4 CODING LUZP1 T protein_coding NM_001142546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23411631 C T 0 181 0 0 0.009385 0 0.0437 0 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99914 0 . 0 . 30 3,12,2,13 UTR_3_PRIME(MODIFIER||3757||1076|LUZP1|protein_coding|CODING|NM_001142546.1|4|T),DOWNSTREAM(MODIFIER||1447||876|KDM1A|protein_coding|CODING|NM_001009999.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.986331 rs117560651 -0.688148 0.891553 30 1076 2361 MODIFIER 4 CODING LUZP1 C protein_coding NM_001142546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23413027 T C 0 206 0 0.8427 0.7472 0.6225 0.8065 0.828 0.5624 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.908075 0 . 0 . 28 5,7,5,10 UTR_3_PRIME(MODIFIER||2361||1076|LUZP1|protein_coding|CODING|NM_001142546.1|4|C),DOWNSTREAM(MODIFIER||2843||876|KDM1A|protein_coding|CODING|NM_001009999.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.908075 rs605775 -0.688148 0.37356 28 1076 1930 MODIFIER 4 CODING LUZP1 G protein_coding NM_001142546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23413458 T G 0 64 0 0.8124 0.7384 0.6182 0.8065 0.827 0.5624 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1930||1076|LUZP1|protein_coding|CODING|NM_001142546.1|4|G),DOWNSTREAM(MODIFIER||3274||876|KDM1A|protein_coding|CODING|NM_001009999.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs580878 -0.511536 0.707536 3 1076 286 MODIFIER 4 CODING LUZP1 C protein_coding NM_001142546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23415102 T C 0 222 0 0.8139 0.7388 0.6182 0.8065 0.827 0.5624 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972978 0 . 0 . 99 25,28,15,21 UTR_3_PRIME(MODIFIER||286||1076|LUZP1|protein_coding|CODING|NM_001142546.1|4|C),DOWNSTREAM(MODIFIER||4918||876|KDM1A|protein_coding|CODING|NM_001009999.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.964853 rs386605436,rs683893 -0.693139 0.914441 99 D868N 1076 Gac/Aac MODERATE 3 MISSENSE CODING LUZP1 T protein_coding NM_001142546.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23418153 C T 0 208 0 0.8404 0.7462 0.6225 0.8065 0.827 0.5613 0.818656 0.825696 0.829302 1 8603 93291 5725 7020 5826 55877 733 9507 2 10402 121380 11576 8642 6614 66734 908 16504 0.987504 0 . 0 . 46 12,16,6,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D868N|1076|LUZP1|protein_coding|CODING|NM_001142546.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991037 rs10799790 -0.689466 0.442372 46 S498 1076 agC/agT LOW 3 SILENT CODING LUZP1 A protein_coding NM_001142546.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23419261 G A 0 222 0 0.643 0.6905 0.5937 0.8065 0.828 0.5624 0.656378 0.769799 0.827907 1 6824 91362 5660 7019 5826 55801 726 9506 2 10404 121344 11576 8640 6612 66712 908 16492 0.907407 0 . 0 . 71 15,15,15,20 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S498|1076|LUZP1|protein_coding|CODING|NM_001142546.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.634393 rs477717 -0.693136 0.0377583 71 Q461K 1076 Cag/Aag MODERATE 3 MISSENSE CODING LUZP1 T protein_coding NM_001142546.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23419374 G T 0 220 0 0.5923 0.6769 0.5922 0.8065 0.828 0.5624 0.615524 0.755728 0.827558 1 6325 90798 5637 7018 5824 55783 726 9485 2 10338 121230 11572 8644 6610 66692 908 16466 0.950089 0 . 0 . 39 10,10,5,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q461K|1076|LUZP1|protein_coding|CODING|NM_001142546.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.116791 rs3765407 -0.690438 0.19831 39 G458S 1076 Ggc/Agc MODERATE 3 MISSENSE CODING LUZP1 T protein_coding NM_001142546.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23419383 C T 0 222 0 0.6422 0.6903 0.5937 0.8065 0.828 0.5624 0.656605 0.769875 0.827907 1 6792 91286 5654 7018 5824 55780 726 9492 2 10354 121224 11572 8638 6612 66680 908 16460 0.89637 0 . 0 . 40 9,11,6,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G458S|1076|LUZP1|protein_coding|CODING|NM_001142546.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.723841 rs477830 -0.691153 0.396938 40 T300 1076 acA/acG LOW 3 SILENT CODING LUZP1 C protein_coding NM_001142546.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23419855 T C 0 222 0 0.8434 0.7474 0.6225 0.8065 0.828 0.5624 0.821834 0.826926 0.829535 1 8633 93367 5742 7019 5826 55895 733 9519 2 10402 121390 11574 8652 6614 66732 908 16508 0.69546 0 . 0 . 224 67,29,61,33 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T300|1076|LUZP1|protein_coding|CODING|NM_001142546.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.532455 rs1983965 -0.693147 0.411081 224 N360 377 aaT/aaC LOW 1 SILENT CODING HTR1D G protein_coding NM_000864.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23519633 A G 0 222 0 0.1581 0.2063 0.2709 0.1845 0.0934 0.364 0.178393 0.129863 0.105 1 1773 19495 3795 1542 479 6515 118 5273 2 10206 120532 11566 8630 6612 66120 904 16494 0.44389 0 . 0 . 90 26,16,18,16 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N360|377|HTR1D|protein_coding|CODING|NM_000864.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992809 rs6300 -0.693132 0.209692 90 636 4321 MODIFIER 11 CODING HNRNPR C protein_coding NM_001102398.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23632626 G C 0 9.7 0 0.9047 0.8654 0.9424 0.8194 0.9125 0.7566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4321||636|HNRNPR|protein_coding|CODING|NM_001102398.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs670257 -0.379885 0 1 470 2494 MODIFIER 4 CODING ZNF436 C protein_coding NM_001077195.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23685968 T C 0 39.3 0 0.0151 0.1216 0.1066 0.1796 0.0656 0.274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2494||470|ZNF436|protein_coding|CODING|NM_001077195.1|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs41300120 -0.453602 0.28 2 470 2216 MODIFIER 4 CODING ZNF436 T protein_coding NM_001077195.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23686246 C T 0 228 0 0.5719 0.7987 0.8905 0.9077 0.9145 0.8088 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 135 0,0,89,29 UTR_3_PRIME(MODIFIER||2216||470|ZNF436|protein_coding|CODING|NM_001077195.1|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13523 -0.693147 0.154313 135 470 635 MODIFIER 4 CODING ZNF436 C protein_coding NM_001077195.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23687827 T C 0 222 0 0.329 0.2742 0.2392 0.2738 0.1909 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999983 0 . 0 . 166 44,36,32,34 UTR_3_PRIME(MODIFIER||635||470|ZNF436|protein_coding|CODING|NM_001077195.1|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998592 rs644749 -0.693147 0.325413 166 N314 470 aaT/aaC LOW 4 SILENT CODING ZNF436 G protein_coding NM_001077195.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23688933 A G 0 222 0 0.1861 0.51 0.6499 0.6349 0.7256 0.498 0.278484 0.577964 0.731395 1 2681 78728 7218 5523 4826 48962 598 8920 2 10404 121354 11566 8622 6612 66730 908 16512 0.86219 0 . 0 . 90 23,15,27,14 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N314|470|ZNF436|protein_coding|CODING|NM_001077195.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.72062 rs2849028,rs386575250 -0.693145 0.456953 90 H264 470 caC/caT LOW 4 SILENT CODING ZNF436 A protein_coding NM_001077195.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23689083 G A 0 222 0 0.0151 0.1212 0.1066 0.1776 0.0656 0.274 0.0265547 0.0578195 0.0738372 1 257 13383 2213 1575 436 4682 93 4127 2 10404 121404 11576 8652 6614 66738 908 16512 0.999483 0 . 0 COSM146441 69 6,20,18,23 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H264|470|ZNF436|protein_coding|CODING|NM_001077195.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.719986 rs3795308 -0.693145 0.879023 69 470 1654 MODIFIER 1 CODING ZNF436 A protein_coding NM_001077195.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23696152 G A 0 228 0 0.5106 0.7817 0.889 0.9067 0.9145 0.8067 0.592147 0.808165 0.918837 2 6024 105021 10820 7915 6222 60771 783 12486 2 10198 118614 11502 8612 6598 65870 886 14948 0 . 0 . 0 99 0,0,64,27 START_GAINED(LOW||||470|ZNF436|protein_coding|CODING|NM_001077195.1|1|A),UTR_5_PRIME(MODIFIER||1654||470|ZNF436|protein_coding|CODING|NM_001077195.1|1|A),INTRAGENIC(MODIFIER|||||ZNF436-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386604183,rs665977 -0.693147 0.293781 99 348 443 MODIFIER 11 CODING TCEA3 G protein_coding NM_003196.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23707516 C G 0 9.7 0 0.5333 0.7903 0.8919 0.9077 0.9195 0.8119 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||443||348|TCEA3|protein_coding|CODING|NM_003196.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs651036 -0.379885 0 1 348 267 MODIFIER 11 CODING TCEA3 G protein_coding NM_003196.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23707692 A G 0 182 0 0.4682 0.7726 0.8876 0.9077 0.9195 0.8119 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,13,0 UTR_3_PRIME(MODIFIER||267||348|TCEA3|protein_coding|CODING|NM_003196.2|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs650102 -0.683931 0.115966 14 348 14 MODIFIER 1 CODING TCEA3 T protein_coding NM_003196.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23751140 G T 0 222 0 0.0855 0.4457 0.611 0.5506 0.672 0.4744 0.229454 0.531873 0.674321 1 1691 72977 7536 4906 4846 44700 543 8755 2 9434 118376 11458 8430 6586 65222 876 16370 0.965264 0 . 0 . 40 5,9,8,10 UTR_5_PRIME(MODIFIER||14||348|TCEA3|protein_coding|CODING|NM_003196.2|1|T),DOWNSTREAM(MODIFIER||3916||903|ASAP3|protein_coding|CODING|NM_017707.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982124 rs71514235 -0.691153 0.0382226 40 903 836 MODIFIER 25 CODING ASAP3 C protein_coding NM_017707.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23755513 T C 0 228 0 0.8381 0.8706 0.8818 0.881 0.8907 0.8753 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 119 0,0,44,63 UTR_3_PRIME(MODIFIER||836||903|ASAP3|protein_coding|CODING|NM_017707.3|25|C),UPSTREAM(MODIFIER||4241||348|TCEA3|protein_coding|CODING|NM_003196.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111195681,rs1198430 -0.693147 6.15738e-05 119 903 633 MODIFIER 25 CODING ASAP3 C protein_coding NM_017707.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23755716 T C 0 119 0 0.8381 0.871 0.8818 0.881 0.8907 0.8773 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,0,7 UTR_3_PRIME(MODIFIER||633||903|ASAP3|protein_coding|CODING|NM_017707.3|25|C),UPSTREAM(MODIFIER||4444||348|TCEA3|protein_coding|CODING|NM_003196.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1198431 -0.636426 0.252943 7 903 194 MODIFIER 25 CODING ASAP3 C protein_coding NM_017707.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23756155 T C 0 158 0 0.8381 0.871 0.8818 0.881 0.8907 0.8773 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,16,0 UTR_3_PRIME(MODIFIER||194||903|ASAP3|protein_coding|CODING|NM_017707.3|25|C),UPSTREAM(MODIFIER||4883||348|TCEA3|protein_coding|CODING|NM_003196.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1198432 -0.689466 0.242712 16 437 578 MODIFIER 7 CODING E2F2 G protein_coding NM_004091.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23835794 A G 0 9.7 0 0.41 0.4499 0.4539 0.5605 0.5268 0.3078 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||578||437|E2F2|protein_coding|CODING|NM_004091.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3218211 -0.379885 0 1 437 8 MODIFIER 7 CODING E2F2 G protein_coding NM_004091.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23836364 A G 0 228 0 0.0499 0.3488 0.4193 0.5605 0.5219 0.3067 0.13527 0.380114 0.505583 2 1092 46693 3768 4790 3017 30848 335 2843 2 8654 98772 10014 8000 5136 58670 666 7632 0 . 0 . 0 84 0,0,51,21 UTR_3_PRIME(MODIFIER||8||437|E2F2|protein_coding|CODING|NM_004091.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2075993 -0.693147 0.288565 84 Q226H 437 caG/caT MODERATE 4 MISSENSE CODING E2F2 A protein_coding NM_004091.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23847464 C A 0 222 0 0.062 0.3552 0.4092 0.5992 0.5089 0.3037 0.128007 0.375827 0.502791 1 1179 54680 4177 5346 3818 34062 414 5684 2 10398 121138 11528 8624 6604 66628 906 16450 0.810076 0 . 0 . 59 9,20,8,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q226H|437|E2F2|protein_coding|CODING|NM_004091.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972533 rs2075995 -0.692976 0.764112 59 119 790 MODIFIER 3 CODING ID3 A protein_coding NM_002167.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23884661 G A 0 228 0 0.7186 0.7356 0.6427 0.9058 0.6312 0.7566 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 128 0,0,30,85 UTR_3_PRIME(MODIFIER||790||119|ID3|protein_coding|CODING|NM_002167.4|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1050096 -0.693147 0.358327 128 T105A 119 Act/Gct MODERATE 2 MISSENSE CODING ID3 C protein_coding NM_002167.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23885498 T C 0 228 0 0.9894 0.8904 0.7392 0.9692 0.7575 0.9192 0.939855 0.821928 0.761512 2 9885 97391 8077 8439 4476 50758 736 15020 2 10396 121178 11524 8652 6586 66612 904 16504 0 . 0 . 0 117 0,0,70,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T105A|119|ID3|protein_coding|CODING|NM_002167.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11574 -0.693147 0.0747213 117 119 156 MODIFIER 1 CODING ID3 C protein_coding NM_002167.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 23886073 T C 0 158 0 0.3805 0.4351 0.3963 0.5972 0.4801 0.3231 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,0,17 UTR_5_PRIME(MODIFIER||156||119|ID3|protein_coding|CODING|NM_002167.4|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2742946 -0.690438 0.515604 17 178 37 MODIFIER 1 CODING RPL11 G protein_coding NM_000975.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24018277 C G 0 228 0 0.9213 0.9768 0.9957 0.996 0.999 0.9959 0.953019 0.983854 0.999651 2 9875 120748 11538 8638 6612 66716 907 16462 2 10406 121400 11578 8652 6614 66730 908 16512 1 2 benign 0 . 122 1,0,78,31 START_GAINED(LOW||||178|RPL11|protein_coding|CODING|NM_000975.3|1|G),UTR_5_PRIME(MODIFIER||37||178|RPL11|protein_coding|CODING|NM_000975.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10917413 -0.693147 0.113863 122 S738 798 agC/agT LOW 10 SILENT CODING TCEB3 T protein_coding NM_003198.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24083494 C T 0 228 0 0.0885 0.2005 0.2421 0.2698 0.3101 0.138 0.131866 0.248808 0.308721 2 1363 32299 2119 2167 2481 21438 231 2500 2 10362 119118 11564 8640 6610 66166 882 14894 0 . 0 . 0 67 0,0,24,42 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S738|798|TCEB3|protein_coding|CODING|NM_003198.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2076345,rs386556583 -0.693147 0.679016 67 231 379 MODIFIER 10 CODING LYPLA2 T protein_coding NM_007260.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24121601 C T 0 228 0 0.9939 0.9044 0.8905 0.8264 0.9235 0.8538 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 85 0,0,63,9 UTR_3_PRIME(MODIFIER||379||231|LYPLA2|protein_coding|CODING|NM_007260.2|10|T),DOWNSTREAM(MODIFIER||488||348|GALE|protein_coding|CODING|NM_000403.3||T) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.929242 0 . rs1063433 -0.693147 0.922654 85 325 486 MODIFIER 9 CODING HMGCL T protein_coding NM_000191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24128467 C T 0 6.3 0 0.9251 0.8834 0.879 0.8234 0.9235 0.8507 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||486||325|HMGCL|protein_coding|CODING|NM_000191.2|9|T),UPSTREAM(MODIFIER||1433||348|GALE|protein_coding|CODING|NM_000403.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11714 -0.379885 0 1 L218 325 ctA/ctG LOW 7 SILENT CODING HMGCL C protein_coding NM_000191.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24134721 T C 0 228 0 0.9728 0.8874 0.8876 0.7817 0.9254 0.8415 0.960962 0.926265 0.908488 2 10061 109755 10428 6846 6370 60815 827 14408 2 10406 121384 11578 8644 6614 66724 908 16510 1 2 benign 0 . 137 2,0,71,54 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L218|325|HMGCL|protein_coding|CODING|NM_000191.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.784 rs719400 -0.693147 0.630955 137 Q286R 466 cAg/cGg MODERATE 5 MISSENSE CODING FUCA1 C protein_coding NM_000147.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24180962 T C 0 228 0 0.1021 0.2113 0.2464 0.2808 0.332 0.138 0.145937 0.268184 0.330814 2 1509 33884 2174 2215 2647 22596 242 2501 2 10406 121394 11576 8642 6614 66736 908 16512 1 2 benign 0 . 85 1,0,49,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q286R|466|FUCA1|protein_coding|CODING|NM_000147.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs13551 -0.693147 0.312881 85 139 65 MODIFIER 3 CODING PNRC2 T protein_coding NM_017761.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24288432 C T 0 52 0 0.0106 0.011781 0.0043 0.0327 0.007 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.458241 0 . 0 . 10 1,2,3,4 UTR_3_PRIME(MODIFIER||65||139|PNRC2|protein_coding|CODING|NM_017761.3|3|T),DOWNSTREAM(MODIFIER||2405||262|SRSF10|protein_coding|CODING|NM_054016.3.2||T) 0 0.5 1 0 . 1 0 . 0 . 21 0 0.733186 0.895781 0 0.366593 rs115735413 -0.636426 0.427859 10 262 3383 MODIFIER 6 CODING SRSF10 T protein_coding NM_054016.3.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24294249 C T 0 23 0 0.9463 0.9838 0.9885 1 0.998 1 0 . 0 2 148 627 25 30 0 334 8 82 2 592 1218 68 30 0 434 10 84 0 . 0 . 0 8 0,0,8,0 UTR_3_PRIME(MODIFIER||3383||262|SRSF10|protein_coding|CODING|NM_054016.3.2|6|T),DOWNSTREAM(MODIFIER||4300||139|PNRC2|protein_coding|CODING|NM_017761.3||T) 0 . 0 . 0 1 0 . 1 0 13 0 0 . 0 . rs146630384,rs4276860 -0.651104 0.471462 8 262 3005 MODIFIER 6 CODING SRSF10 T protein_coding NM_054016.3.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24294627 C T 0 14.8 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||3005||262|SRSF10|protein_coding|CODING|NM_054016.3.2|6|T),DOWNSTREAM(MODIFIER||4678||139|PNRC2|protein_coding|CODING|NM_017761.3||T) 0 . 0 . 0 . 0 . 0 . 14 0 0 . 0 . rs115208097,rs35973750 -0.556411 0.211317 4 1437 35 MODIFIER 37 CODING MYOM3 C protein_coding NM_152372.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24383819 T C 0 228 0 0.5303 0.6925 0.5663 0.9514 0.7276 0.6984 0.596495 0.677563 0.717587 2 5491 81420 6603 8178 4681 46594 580 9293 2 9572 115388 11246 8566 6450 65278 840 13436 1 0 . 0 . 51 0,1,40,7 UTR_3_PRIME(MODIFIER||35||1437|MYOM3|protein_coding|CODING|NM_152372.3|37|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7540491 -0.693147 0.0400769 51 R1124Q 1437 cGg/cAg MODERATE 28 MISSENSE CODING MYOM3 T protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24393563 C T 0 222 0 0.4871 0.2804 0.1599 0.1964 0.1421 0.3149 0.356824 0.209926 0.138789 1 1986 11707 772 850 204 4643 85 3167 2 4212 38064 2508 2602 590 18158 312 9682 0.40047 0 . 0 . 137 33,23,42,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1124Q|1437|MYOM3|protein_coding|CODING|NM_152372.3|28|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.361087 rs16829071 -0.693147 0.0241471 137 I1066T 1437 aTc/aCc MODERATE 26 MISSENSE CODING MYOM3 G protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24394811 A G 0 222 0 0.2262 0.1961 0.1427 0.1964 0.1372 0.2536 0.178482 0.148662 0.13431 1 1974 19753 1477 1671 789 9640 147 4055 2 9806 120748 11576 8610 6614 66730 900 16512 0.976231 0 . 0 . 76 15,12,26,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I1066T|1437|MYOM3|protein_coding|CODING|NM_152372.3|26|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.791902 rs12145360 -0.693145 0.301154 76 A815 1437 gcC/gcT LOW 20 SILENT CODING MYOM3 A protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24406647 G A 0 222 0 0.3238 0.3542 0.3444 0.4276 0.4423 0.2362 0.311656 0.38806 0.42473 1 3160 47284 3977 3816 3249 28811 333 3938 2 9766 120226 11562 8584 6586 66492 892 16344 0.256521 0 . 0 . 46 7,13,8,14 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A815|1437|MYOM3|protein_coding|CODING|NM_152372.3|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.662991 rs4649175 -0.692562 0.107882 46 E670 1437 gaG/gaA LOW 17 SILENT CODING MYOM3 T protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24409165 C T 0 222 0 0.1929 0.1845 0.1398 0.1925 0.1332 0.2495 0.154181 0.137442 0.129216 1 1741 19139 1450 1649 779 9338 145 4037 2 9778 120170 11568 8604 6612 66504 896 16208 0.57682 0 . 0 . 150 42,27,26,41 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E670|1437|MYOM3|protein_coding|CODING|NM_152372.3|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.141292 rs4320728 -0.693147 0.224714 150 G662R 1437 Ggg/Agg MODERATE 17 MISSENSE CODING MYOM3 T protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24409191 C T 0 222 0 0.0159 0.2568 0.3213 0.4266 0.4364 0.1769 0.0828798 0.310037 0.419447 1 715 43599 3798 3801 3251 28654 306 3074 2 9686 118374 11550 8578 6612 66154 876 14918 0.796349 0 . 0 . 147 31,42,29,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G662R|1437|MYOM3|protein_coding|CODING|NM_152372.3|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.562061 rs4320729 -0.693147 0.771547 147 E591 1437 gaA/gaG LOW 15 SILENT CODING MYOM3 C protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24413159 T C 0 222 0 0.3646 0.3748 0.353 0.4623 0.4463 0.2403 0.35018 0.402905 0.427709 1 3571 48284 4000 4125 3250 28989 339 4010 2 9776 120346 11536 8592 6578 66526 892 16446 0.999452 0 . 0 . 80 27,10,20,16 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E591|1437|MYOM3|protein_coding|CODING|NM_152372.3|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999757 rs6424152 -0.693139 0.587728 80 D528G 1437 gAc/gGc MODERATE 14 MISSENSE CODING MYOM3 C protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24416059 T C 0 228 0 0.9289 0.9788 0.9841 1 0.999 1 0.935142 0.979036 0.999636 2 6922 93668 8661 6838 3954 53428 662 13203 2 7438 94232 8690 6838 3954 53446 662 13204 0 . 0 . 0 65 0,0,35,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D528G|1437|MYOM3|protein_coding|CODING|NM_152372.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4393101 -0.693147 0.418248 65 P524 1437 ccC/ccG LOW 14 SILENT CODING MYOM3 C protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24416070 G C 0 222 0 0.4561 0.5006 0.4078 0.7321 0.5 0.3885 0.427692 0.472597 0.49382 1 3120 41621 3185 4494 1954 23943 267 4658 2 6724 82142 6672 6150 3380 46700 558 11958 0.180071 0 . 0 . 70 19,11,20,8 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P524|1437|MYOM3|protein_coding|CODING|NM_152372.3|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.106541 rs7533060 -0.693054 0.20425 70 P503 1437 ccG/ccA LOW 14 SILENT CODING MYOM3 T protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24416133 C T 0 222 0 0.1876 0.1739 0.1254 0.1845 0.1143 0.2403 0.152238 0.122144 0.10751 1 1091 10548 625 1012 295 4844 77 2604 2 5146 52572 3088 4114 1418 28622 378 9806 0.73957 0 . 0 COSM1340817 76 18,14,13,18 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P503|1437|MYOM3|protein_coding|CODING|NM_152372.3|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.342354 rs4276859 -0.69311 0.194407 76 P376 1437 ccA/ccG LOW 11 SILENT CODING MYOM3 C protein_coding NM_152372.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24418768 T C 0 222 0 0.472 0.3762 0.3199 0.3522 0.4662 0.2188 0.448568 0.446172 0.445068 1 4469 44762 2792 3116 3623 28217 343 2202 2 9536 109862 11476 8486 6602 63748 778 9236 0.977415 0 . 0 . 64 12,21,6,20 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P376|1437|MYOM3|protein_coding|CODING|NM_152372.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.935071 rs7556176 -0.692976 0.018036 64 M344T 1437 aTg/aCg MODERATE 10 MISSENSE CODING MYOM3 G protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24419496 A G 0 222 0 0.4486 0.379 0.3242 0.3512 0.496 0.2321 0.439716 0.46369 0.475121 1 4321 48894 2776 3040 3611 30726 390 4030 2 9290 112978 10228 8070 6042 63316 842 15190 0.891544 0 . 0 . 68 23,11,15,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M344T|1437|MYOM3|protein_coding|CODING|NM_152372.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.865613 rs4233050 -0.693021 0.595344 68 R318H 1437 cGt/cAt MODERATE 10 MISSENSE CODING MYOM3 T protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24419574 C T 0 222 0 0 0.0067891 0 0.0337 0 0 0 . 0 1 0 203 2 196 0 2 2 1 2 9600 118602 11470 8514 6478 65330 882 16328 0.991034 0 . 0 . 66 10,12,11,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R318H|1437|MYOM3|protein_coding|CODING|NM_152372.3|10|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.789338 rs189467208 -0.693132 0.000706262 66 T266M 1437 aCg/aTg MODERATE 9 MISSENSE CODING MYOM3 A protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24421474 G A 0 222 0 0.2746 0.3199 0.2911 0.3383 0.4771 0.2209 0.271711 0.396623 0.454954 1 2773 46639 2702 2943 3733 30266 374 3848 2 9636 118304 11390 8518 6552 65972 878 15358 0.988723 0 . 0 . 91 16,15,24,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T266M|1437|MYOM3|protein_coding|CODING|NM_152372.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989483 rs6678540 -0.693147 0.505402 91 D258H 1437 Gat/Cat MODERATE 8 MISSENSE CODING MYOM3 G protein_coding NM_152372.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24421950 C G 0 222 0 0.5416 0.4105 0.3386 0.377 0.497 0.2301 0.498407 0.482 0.474496 1 5093 51240 3001 3277 3840 31613 402 4014 2 9800 120596 11574 8618 6614 66686 898 16406 0.958747 0 . 0 . 113 38,28,16,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D258H|1437|MYOM3|protein_coding|CODING|NM_152372.3|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.826335 rs4319261 -0.693143 0.00451645 113 574 179 MODIFIER 7 CODING IL22RA1 T protein_coding NM_021258.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24447116 C T 0 77 0 0.2814 0.4868 0.5504 0.7262 0.4095 0.5521 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.366897 0 . 0 . 17 11,0,3,2 UTR_3_PRIME(MODIFIER||179||574|IL22RA1|protein_coding|CODING|NM_021258.3|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.628992 rs3795302 -0.590765 0.969621 17 574 81 MODIFIER 7 CODING IL22RA1 A protein_coding NM_021258.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24447214 G A 0 222 0 0.795 0.7171 0.5706 0.7282 0.6233 0.8006 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.357835 0 . 0 . 46 15,5,16,4 UTR_3_PRIME(MODIFIER||81||574|IL22RA1|protein_coding|CODING|NM_021258.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.532543 rs3795300 -0.692067 0.389733 46 R518G 574 Cgt/Ggt MODERATE 7 MISSENSE CODING IL22RA1 C protein_coding NM_021258.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24447468 G C 0 222 0 0.2874 0.4663 0.4035 0.7252 0.3996 0.5542 0.303904 0.372597 0.407791 1 3211 50617 4889 6029 2103 25446 355 8584 2 10400 121270 11554 8628 6600 66680 906 16502 0.970912 0 . 0 . 70 27,7,17,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Ggt|R518G|574|IL22RA1|protein_coding|CODING|NM_021258.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.418465 rs3795299 -0.69311 0.802583 70 P312 574 ccC/ccT LOW 7 SILENT CODING IL22RA1 A protein_coding NM_021258.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24448084 G A 0 222 0 0.0787 0.2053 0.2219 0.2649 0.3141 0.1912 0.110758 0.236814 0.301395 1 1158 34832 2588 2511 3079 21937 273 3286 2 10238 119498 11424 8574 6394 65970 878 16020 0.722912 0 . 0 COSM146449 79 22,13,20,17 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P312|574|IL22RA1|protein_coding|CODING|NM_021258.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.503347 rs17852648 -0.693141 0.22246 79 P145 574 ccA/ccC LOW 4 SILENT CODING IL22RA1 G protein_coding NM_021258.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24460797 T G 0 222 0 0.6989 0.5236 0.4625 0.2956 0.6123 0.4734 0.693373 0.633246 0.602442 1 7208 68932 4472 2761 4193 41273 537 8488 2 10396 120610 11544 8608 6600 66510 904 16048 0.985365 0 . 0 . 163 24,58,26,41 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P145|574|IL22RA1|protein_coding|CODING|NM_021258.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903593 rs17852649 -0.693147 0.133938 163 P45 574 ccG/ccA LOW 2 SILENT CODING IL22RA1 T protein_coding NM_021258.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24465113 C T 0 222 0 0.261 0.4706 0.5231 0.7619 0.3628 0.5276 0.272356 0.344303 0.381163 1 2831 51131 7038 6312 2337 24448 352 7813 2 10396 121228 11548 8628 6568 66678 904 16506 0.747606 0 . 0 . 130 42,25,26,21 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P45|574|IL22RA1|protein_coding|CODING|NM_021258.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943957 rs10903022 -0.693147 0.79762 130 520 2398 MODIFIER 7 CODING IFNLR1 A protein_coding NM_170743.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24481222 G A 0 9.7 0 0.5234 0.4812 0.5778 0.2877 0.5706 0.4632 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2398||520|IFNLR1|protein_coding|CODING|NM_170743.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7516266 -0.379885 0 1 520 872 MODIFIER 7 CODING IFNLR1 G protein_coding NM_170743.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24482748 T G 0 76 0 0.9334 0.98 0.9914 1 0.994 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||872||520|IFNLR1|protein_coding|CODING|NM_170743.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2153334,rs386558920 -0.511536 0.045681 3 520 628 MODIFIER 7 CODING IFNLR1 G protein_coding NM_170743.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24482992 C G 0 39.3 0 0.7201 0.6933 0.7089 0.4921 0.7972 0.7464 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||628||520|IFNLR1|protein_coding|CODING|NM_170743.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7531447 -0.453602 0.7 2 520 165 MODIFIER 7 CODING IFNLR1 A protein_coding NM_170743.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24483455 G A 0 149 0 0.9894 0.996 0.9986 1 0.995 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,11,0 UTR_3_PRIME(MODIFIER||165||520|IFNLR1|protein_coding|CODING|NM_170743.3|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7522997 -0.676189 0.195169 11 520 129 MODIFIER 7 CODING IFNLR1 G protein_coding NM_170743.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24483491 A G 0 166 0 0.9894 0.996 0.9986 1 0.995 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,22,0 UTR_3_PRIME(MODIFIER||129||520|IFNLR1|protein_coding|CODING|NM_170743.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7536412 -0.692562 0.30161 22 626 33 MODIFIER 16 CODING GRHL3 T protein_coding NM_198174.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24690894 C T 0 222 0 0.1732 0.0855 0.0677 0.0298 0.0189 0.1053 0 . 0 1 136 530 17 13 29 70 4 261 2 782 7606 218 398 1564 3134 108 1402 0.830424 0 . 0 . 110 16,31,15,37 UTR_3_PRIME(MODIFIER||33||626|GRHL3|protein_coding|CODING|NM_198174.2|16|T),INTRON(MODIFIER||||334|STPG1|protein_coding|CODING|NM_001199012.1|7|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.601056 rs74060321 -0.693147 0.00818793 110 N112 334 aaT/aaC LOW 5 SILENT CODING STPG1 G protein_coding NM_001199012.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24706269 A G 0 228 0 0.4894 0.4191 0.5101 0.4444 0.3618 0.2924 0.495234 0.393511 0.341395 2 5172 44966 4931 3780 2622 23205 325 4931 2 10402 121338 11566 8630 6608 66716 906 16510 1 0 . 0 COSM1340988,COSM1340987 109 1,0,63,36 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N112|334|STPG1|protein_coding|CODING|NM_001199012.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1064842 -0.693147 0.446082 109 I105V 334 Att/Gtt MODERATE 5 MISSENSE CODING STPG1 C protein_coding NM_001199012.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24706292 T C 0 228 0 0.3086 0.3656 0.4841 0.4444 0.3549 0.2883 0.33409 0.333231 0.332791 2 3472 42366 4770 3774 2604 22569 315 4862 2 10404 121292 11548 8632 6608 66690 904 16506 1 0 . 0 . 126 1,0,67,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I105V|334|STPG1|protein_coding|CODING|NM_001199012.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1142057 -0.693147 0.0906152 126 Q55 334 caA/caG LOW 3 SILENT CODING STPG1 C protein_coding NM_001199012.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24718075 T C 0 228 0 0.0961 0.2817 0.379 0.4593 0.2753 0.2873 0 . 0 2 117 4459 109 206 475 1453 62 2037 2 950 16848 296 486 1628 5618 204 7666 1 0 . 0 . 142 0,1,59,68 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q55|334|STPG1|protein_coding|CODING|NM_001199012.1|3|C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs2294520 -0.693147 0.123092 142 406 LOW 5 CODING NIPAL3 A protein_coding NM_020448.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24775967 G A 0 222 0 0.0325 0.1721 0.1614 0.3065 0.2256 0.1748 0.0812528 0.173382 0.220581 1 771 25350 2004 2515 1251 15533 195 3081 2 10402 121280 11574 8610 6614 66680 908 16492 0.160842 0 . 0 . 127 28,25,42,19 SPLICE_SITE_REGION+INTRON(LOW||||406|NIPAL3|protein_coding|CODING|NM_020448.4|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.627265 rs4648989 -0.693147 0.000218338 127 A263 406 gcC/gcT LOW 9 SILENT CODING NIPAL3 T protein_coding NM_020448.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24785393 C T 0 222 0 0.1589 0.3063 0.4409 0.4534 0.2773 0.2883 0.159782 0.227357 0.261977 1 1745 35896 5581 3937 1681 17958 262 4732 2 10406 121302 11546 8626 6612 66698 908 16506 0.684545 0 . 0 . 136 43,17,29,26 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A263|406|NIPAL3|protein_coding|CODING|NM_020448.4|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.413081 rs2272935 -0.693147 0.51372 136 P138 241 ccG/ccA LOW 4 SILENT CODING RCAN3 A protein_coding NM_001251977.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24859617 G A 0 222 0 0.2458 0.3836 0.3314 0.6786 0.3221 0.3661 0.266682 0.301553 0.319419 1 2684 41848 3904 5607 2132 21946 293 5282 2 10272 116328 11450 8626 6500 65070 848 13562 0.771622 0 . 0 . 101 28,24,19,18 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P138|241|RCAN3|protein_coding|CODING|NM_001251977.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.924799 rs196429 -0.693141 0.649851 101 P154 241 ccG/ccA LOW 4 SILENT CODING RCAN3 A protein_coding NM_001251977.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24859665 G A 0 222 0 0.2458 0.3836 0.3314 0.6776 0.3221 0.3671 0.266909 0.301784 0.319651 1 2705 42778 3940 5609 2137 22192 309 5886 2 10390 120432 11532 8628 6586 66316 894 16086 0.996335 0 . 0 . 80 18,25,15,17 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P154|241|RCAN3|protein_coding|CODING|NM_001251977.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932129 rs196430 -0.69312 0.116463 80 T221 241 acG/acA LOW 5 SILENT CODING RCAN3 A protein_coding NM_001251977.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24861704 G A 0 228 0 0.4667 0.5092 0.4006 0.7272 0.4573 0.4724 0.46414 0.462171 0.461163 2 4791 58310 4470 6127 3345 31436 410 7731 2 10384 120928 11564 8644 6610 66518 906 16302 0 . 0 . COSM1341222 79 0,0,40,30 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T221|241|RCAN3|protein_coding|CODING|NM_001251977.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs196432 -0.693147 0.277534 79 241 1518 MODIFIER 5 CODING RCAN3 T protein_coding NM_001251977.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 24863285 C T 0 9.7 0 0.1929 0.1188 0.0692 0.0526 0.1352 0.1053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1518||241|RCAN3|protein_coding|CODING|NM_001251977.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs111176620,rs11231 -0.379885 0 1 253 2447 MODIFIER 6 CODING CLIC4 A protein_coding NM_013943.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25169875 C A 0 100 0 0.798 0.9431 0.9755 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||2447||253|CLIC4|protein_coding|CODING|NM_013943.2|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4649025 -0.511536 0.868052 4 L360P 493 cTc/cCc MODERATE 8 MISSENSE CODING RHD C protein_coding NM_001282871.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25634143 T C 0 221 0 0.003 0.1356 0.049 0.2619 0.1491 0.2321 0 . 0 2 15 2894 18 40 260 457 37 2067 2 542 12516 174 202 1050 3328 158 7062 0.855476 0 . 0 . 45 2,1,34,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L360P|493|RHD|protein_coding|CODING|NM_001282871.1|8|C) 0 . 0 . 0 1 0 . 1 0 47 0 0.494169 0.467959 0 0.427473 rs2427766 -0.693145 0.418145 45 157 705 MODIFIER 7 CODING TMEM50A C protein_coding NM_014313.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25687901 T C 0 9.7 0 0.0991 0.4683 0.487 0.7569 0.4433 0.682 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||705||157|TMEM50A|protein_coding|CODING|NM_014313.3|7|C),DOWNSTREAM(MODIFIER||839||417|RHCE|protein_coding|CODING|NM_020485.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1053438 -0.379885 0 1 664 824 MODIFIER 11 CODING TMEM57 A protein_coding NM_018202.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25825781 G A 0 9.7 0 0.2421 0.5142 0.5173 0.7728 0.4513 0.6779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||824||664|TMEM57|protein_coding|CODING|NM_018202.5|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs61775206 -0.379885 0 1 664 1545 MODIFIER 11 CODING TMEM57 G protein_coding NM_018202.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25826502 A G 0 9.7 0 0.2005 0.5028 0.5144 0.7728 0.4513 0.6779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1545||664|TMEM57|protein_coding|CODING|NM_018202.5|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs34491689 -0.379885 0 1 308 986 MODIFIER 9 CODING LDLRAP1 CTG protein_coding NM_015627.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25894468 C CTG 0 228 0 0.7927 0.9034 0.9222 0.9395 0.9414 0.9632 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,29,7 UTR_3_PRIME(MODIFIER||986||308|LDLRAP1|protein_coding|CODING|NM_015627.2|9|CTG) 0 . 0 37 0.925 1 1 0 . 0 60 0 0 1 0 . rs10635955 -0.693139 0.0686693 40 308 1370 MODIFIER 9 CODING LDLRAP1 T protein_coding NM_015627.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25894853 G T 0 140 0 0.7148 0.5711 0.4755 0.5526 0.4732 0.5644 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,0,10 UTR_3_PRIME(MODIFIER||1370||308|LDLRAP1|protein_coding|CODING|NM_015627.2|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11563 -0.670168 0.61407 10 R151 630 cgT/cgC LOW 1 SILENT CODING MAN1C1 C protein_coding NM_020379.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 25944741 T C 0 222 0 0.5719 0.24 0.2061 0.2133 0.0089 0.0808 0.391257 0.132463 0.00664187 1 2869 7031 1490 1368 112 411 40 741 2 5564 59458 4938 5098 1898 30936 410 10614 0.302026 0 . 0 . 94 38,13,29,5 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R151|630|MAN1C1|protein_coding|CODING|NM_020379.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.834757 rs11247857 -0.693132 0.00280688 94 C142Y 590 tGc/tAc MODERATE 4 MISSENSE CODING SEPN1 A protein_coding NM_020451.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26131654 G A 0 228 0 0.7451 0.8419 0.8919 0.9395 0.7803 0.8998 0 . 0 2 7640 98290 10592 8122 4816 51851 731 14538 2 9790 120686 11576 8626 6614 66672 896 16512 0.902913 2 benign 0 . 108 2,0,45,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C142Y|590|SEPN1|protein_coding|CODING|NM_020451.2|4|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.92233 rs386500767,rs7349185 -0.693147 0.0461944 108 P391 590 ccT/ccC LOW 9 SILENT CODING SEPN1 C protein_coding NM_020451.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26138262 T C 0 228 0 0.5575 0.7919 0.8516 0.9683 0.7753 0.9018 0.633671 0.737172 0.788101 2 4293 66039 5260 5694 2366 36393 465 11568 2 6742 81204 5834 5906 3066 45970 578 13108 1 2 benign 0 COSM1127046 44 0,1,11,31 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P391|590|SEPN1|protein_coding|CODING|NM_020451.2|9|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs760597 -0.693146 0.767634 44 N502K 590 aaC/aaA MODERATE 12 MISSENSE CODING SEPN1 A protein_coding NM_020451.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26140573 C A 0 228 0 0.2118 0.6975 0.8285 0.9683 0.7753 0.9018 0.324148 0.63195 0.787229 2 2875 93473 10292 8314 4947 51799 712 14534 2 9784 120652 11562 8622 6608 66674 894 16508 1 2 benign 0 . 111 1,0,56,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N502K|590|SEPN1|protein_coding|CODING|NM_020451.2|12|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2294228 -0.693147 0.0402433 111 590 1612 MODIFIER 13 CODING SEPN1 C protein_coding NM_020451.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26143821 T C 0 9.7 0 0.4508 0.763 0.8458 0.9683 0.7753 0.9018 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1612||590|SEPN1|protein_coding|CODING|NM_020451.2|13|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),UPSTREAM(MODIFIER||2576||292|MTFR1L|protein_coding|CODING|NM_001099625.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3203750 -0.379885 0 1 292 3082 MODIFIER 1 CODING MTFR1L C protein_coding NM_001099625.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26146514 G C 0 9.7 0 0.0522 0.4808 0.6138 0.6587 0.506 0.7566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||3082||292|MTFR1L|protein_coding|CODING|NM_001099625.1|1|C),DOWNSTREAM(MODIFIER||1801||590|SEPN1|protein_coding|CODING|NM_020451.2||C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),INTRAGENIC(MODIFIER|||||LOC646471||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1127818 -0.379885 0 1 292 445 MODIFIER 7 CODING MTFR1L G protein_coding NM_001099625.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26158962 A G 0 228 0 0.7133 0.8365 0.8646 0.9782 0.7744 0.9008 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 77 0,0,47,25 UTR_3_PRIME(MODIFIER||445||292|MTFR1L|protein_coding|CODING|NM_001099625.1|7|G),INTRON(MODIFIER||||371|AUNIP|protein_coding|CODING|NM_001287490.1|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs15045 -0.693147 0.250526 77 346 665 MODIFIER 2 CODING PAQR7 T protein_coding NM_178422.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26188625 G T 0 9.7 0 0.7958 0.6887 0.6816 0.6687 0.506 0.7577 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||665||346|PAQR7|protein_coding|CODING|NM_178422.5|2|T),UPSTREAM(MODIFIER||2676||371|AUNIP|protein_coding|CODING|NM_001287490.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs213637 -0.379885 0 1 174 441 MODIFIER 5 CODING STMN1 T protein_coding NM_001145454.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26211773 C T 0 228 0 0.1725 0.5268 0.6527 0.6746 0.5318 0.7587 0.231214 0.444809 0.537712 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,12,30 UTR_3_PRIME(MODIFIER||441||174|STMN1|protein_coding|CODING|NM_001145454.2|5|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs159528,rs386539440 -0.693146 0.482168 45 392 7213 MODIFIER 1 CODING PAFAH2 C protein_coding NM_000437.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26324520 T C 0 116 0 0.0915 0.528 0.6844 0.7113 0.6551 0.6871 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,1 UTR_5_PRIME(MODIFIER||7213||392|PAFAH2|protein_coding|CODING|NM_000437.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11247841 -0.556411 0.303109 5 392 7275 MODIFIER 1 CODING PAFAH2 G protein_coding NM_000437.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26324582 T G 0 32.6 0 0.9939 0.9982 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 START_GAINED(LOW||||392|PAFAH2|protein_coding|CODING|NM_000437.3|1|G),UTR_5_PRIME(MODIFIER||7275||392|PAFAH2|protein_coding|CODING|NM_000437.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3008239 -0.379885 0 2 676 664 MODIFIER 1 CODING EXTL1 G protein_coding NM_004455.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26348474 A G 0 39.3 0 0.8896 0.8858 0.9207 0.9375 0.8618 0.8272 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||664||676|EXTL1|protein_coding|CODING|NM_004455.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3008245 -0.453602 0.96 2 H379N 676 Cac/Aac MODERATE 5 MISSENSE CODING EXTL1 A protein_coding NM_004455.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26357656 C A 0 228 0 0.2027 0.5942 0.732 0.75 0.6978 0.7587 0.289605 0.546594 0.678256 2 2851 81836 8888 6317 5395 45740 653 11992 2 10398 121380 11578 8636 6614 66736 908 16510 0 . 0 . 0 59 0,0,19,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H379N|676|EXTL1|protein_coding|CODING|NM_004455.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2736831 -0.693147 0.419371 59 676 356 MODIFIER 11 CODING EXTL1 C protein_coding NM_004455.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26362194 T C 0 76 0 0.5038 0.7115 0.8112 0.874 0.7018 0.7638 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||356||676|EXTL1|protein_coding|CODING|NM_004455.2|11|C),DOWNSTREAM(MODIFIER||2319||372|SLC30A2|protein_coding|CODING|NM_001004434.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2802315 -0.511536 0.251321 3 372 277 MODIFIER 8 CODING SLC30A2 G protein_coding NM_001004434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26365374 T G 0 46.3 0 0.1982 0.5913 0.7334 0.75 0.6918 0.7546 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||277||372|SLC30A2|protein_coding|CODING|NM_001004434.2|8|G),DOWNSTREAM(MODIFIER||2420||676|EXTL1|protein_coding|CODING|NM_004455.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4659404 -0.453602 0.1 2 372 102 MODIFIER 8 CODING SLC30A2 T protein_coding NM_001004434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26365549 C T 0 228 0 0.4713 0.7005 0.8055 0.874 0.6968 0.7607 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,18,5 UTR_3_PRIME(MODIFIER||102||372|SLC30A2|protein_coding|CODING|NM_001004434.2|8|T),DOWNSTREAM(MODIFIER||2595||676|EXTL1|protein_coding|CODING|NM_004455.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2997452 -0.692717 0.594397 23 353 484 MODIFIER 9 CODING TRIM63 A protein_coding NM_032588.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26377880 G A 0 228 0 0.4168 0.6583 0.8098 0.7669 0.6789 0.7444 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 87 0,0,77,6 UTR_3_PRIME(MODIFIER||484||353|TRIM63|protein_coding|CODING|NM_032588.3|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1135253 -0.693147 0.30187 87 353 362 MODIFIER 9 CODING TRIM63 T protein_coding NM_032588.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26378002 C T 0 228 0 0.1914 0.5919 0.7695 0.7669 0.672 0.7444 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 129 0,1,50,75 UTR_3_PRIME(MODIFIER||362||353|TRIM63|protein_coding|CODING|NM_032588.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1135251 -0.693147 0.0360124 129 341 268 MODIFIER 3 CODING PDIK1L C protein_coding NM_001243532.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26449335 CAA C 0 228 0 0.0106 0.1665 0.2176 0.3185 0.2624 0.0859 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 147 0,1,77,56 UTR_3_PRIME(MODIFIER||268||341|PDIK1L|protein_coding|CODING|NM_001243532.1|3|C) 0 . 0 139 0.945578 1 1 0 . 0 60 0 0 1 0 . rs3833547 -0.693147 6.76984e-06 147 H53R 271 cAc/cGc MODERATE 2 MISSENSE CODING FAM110D G protein_coding NM_024869.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26487940 A G 0 222 0 0.0401 0.1877 0.2305 0.2718 0.325 0.1288 0.069171 0.224212 0.297195 1 272 12182 795 778 415 8127 85 1710 2 2504 36800 2184 2128 856 19852 266 9010 0.972962 0 . 0 . 84 18,23,11,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H53R|271|FAM110D|protein_coding|CODING|NM_024869.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976481 rs3748856 -0.693132 0.524117 84 134 20 MODIFIER 1 CODING ZNF593 T protein_coding NM_015871.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26496455 C T 0 103 0 0.0401 0.1825 0.2147 0.2659 0.3191 0.1258 0.0617519 0.184044 0.245173 1 55 2481 28 189 20 1135 23 1031 2 366 7338 84 404 34 2614 66 3770 0.921243 0 . 0 . 15 7,0,8,0 START_GAINED(LOW||||134|ZNF593|protein_coding|CODING|NM_015871.4|1|T),UTR_5_PRIME(MODIFIER||20||134|ZNF593|protein_coding|CODING|NM_015871.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.412466 rs2232648 -0.651104 0.333755 15 134 133 MODIFIER 3 CODING ZNF593 C protein_coding NM_015871.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26497340 A C 0 81 0 0.7549 0.8409 0.8559 0.9712 0.7684 0.8865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_3_PRIME(MODIFIER||133||134|ZNF593|protein_coding|CODING|NM_015871.4|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs8768 -0.590765 0.489846 5 H694N 720 Cac/Aac MODERATE 21 MISSENSE CODING CNKSR1 A protein_coding NM_001297647.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26515956 C A 0 222 0 0.0779 0.118 0.0821 0.0962 0.1223 0.2157 0.0871539 0.118868 0.135116 1 848 16138 649 744 782 9473 124 3518 2 10400 121332 11574 8634 6610 66702 904 16508 0.990764 0 . 0 . 73 19,19,15,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H694N|720|CNKSR1|protein_coding|CODING|NM_001297647.1|21|A),UPSTREAM(MODIFIER||1163||472|CATSPER4|protein_coding|CODING|NM_198137.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.230731 rs1045105 -0.693054 0.0389913 73 R406 472 cgC/cgT LOW 9 SILENT CODING CATSPER4 T protein_coding NM_198137.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26527863 C T 0 222 0 0.0121 0.0899 0.0764 0.0972 0.1193 0.1667 0.0254199 0.0981854 0.135465 1 238 14711 612 773 737 9346 119 2886 2 10300 120886 11538 8618 6606 66450 898 16476 0.801394 0 . 0 . 80 21,20,20,17 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R406|472|CATSPER4|protein_coding|CODING|NM_198137.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.548648 rs17163674 -0.693141 0.542414 80 S213N 762 aGc/aAc MODERATE 4 MISSENSE CODING CEP85 A protein_coding NM_022778.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26582091 G A 0 222 0 0.0575 0.1863 0.2363 0.2599 0.3022 0.1299 0.0948706 0.235507 0.307558 1 902 30753 2939 2141 1980 20043 247 2501 2 10406 121394 11576 8642 6614 66736 908 16512 0.905946 0 . 0 . 176 47,30,38,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S213N|762|CEP85|protein_coding|CODING|NM_022778.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959576 rs3795686 -0.693147 0.0398315 176 762 209 MODIFIER 14 CODING CEP85 C protein_coding NM_022778.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26603993 A C 0 228 0 0.8812 0.7262 0.6945 0.4583 0.9304 0.6053 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 87 0,0,33,44 UTR_3_PRIME(MODIFIER||209||762|CEP85|protein_coding|CODING|NM_022778.3|14|C),UPSTREAM(MODIFIER||2220||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||C),DOWNSTREAM(MODIFIER||4780||520|UBXN11|protein_coding|CODING|NM_183008.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3820519 -0.693147 0.0983184 87 520 8 MODIFIER 16 CODING UBXN11 T protein_coding NM_183008.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26608782 C T 0 9.7 0 0.0582 0.1863 0.2349 0.2599 0.3022 0.1299 0.0909962 0.226454 0.283616 1 593 22841 2169 1443 1632 15705 172 1127 2 5018 71756 5620 3742 4738 46186 542 5910 0.6 0 . 0 . 8 4,1,1,1 UTR_3_PRIME(MODIFIER||8||520|UBXN11|protein_coding|CODING|NM_183008.2|16|T),DOWNSTREAM(MODIFIER||3253||762|CEP85|protein_coding|CODING|NM_022778.3||T),DOWNSTREAM(MODIFIER||769||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs34209692 -0.453602 0.6 8 P513 520 ccT/ccC LOW 16 SILENT CODING UBXN11 G protein_coding NM_183008.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26608814 A G 0 91 0 0.8865 0.75 0.7219 0.5169 0.9324 0.638 0 . 0 2 4039 48156 4358 2559 3156 29190 370 4484 2 6892 89850 8426 5390 5734 54302 678 8428 0 . 0 . 0 4 0,0,3,1 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P513|520|UBXN11|protein_coding|CODING|NM_183008.2|16|G),DOWNSTREAM(MODIFIER||3285||762|CEP85|protein_coding|CODING|NM_022778.3||G),DOWNSTREAM(MODIFIER||801||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6672357 -0.556411 0.211317 4 G504C 520 Ggt/Tgt MODERATE 16 MISSENSE CODING UBXN11 A protein_coding NM_183008.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26608843 C A 0 48.3 0 . 0 . 0 . 0 . 0 . 1 43 63 3 3 0 13 1 0 2 790 9956 2592 2582 172 1454 58 2308 1 0 . 0 COSM1602121 5 1,1,2,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G504C|520|UBXN11|protein_coding|CODING|NM_183008.2|16|A),DOWNSTREAM(MODIFIER||3314||762|CEP85|protein_coding|CODING|NM_022778.3||A),DOWNSTREAM(MODIFIER||830||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0 rs6667693 -0.511536 0.0249187 5 P501S 520 Ccc/Tcc MODERATE 16 MISSENSE CODING UBXN11 A protein_coding NM_183008.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26608852 G A 0 32.7 0 . 0 . 0 . 0 . 0 . 1 0 11 2 0 0 7 0 2 2 874 11130 2732 3180 174 1386 52 2732 0.916482 0 . 0 . 10 4,3,3,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P501S|520|UBXN11|protein_coding|CODING|NM_183008.2|16|A),DOWNSTREAM(MODIFIER||3323||762|CEP85|protein_coding|CODING|NM_022778.3||A),DOWNSTREAM(MODIFIER||839||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||A) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.733186 0.733186 0 0.733186 rs61775089 -0.511536 0.0822145 10 T391 520 acG/acA LOW 15 SILENT CODING UBXN11 T protein_coding NM_183008.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26609259 C T 0 222 0 0.3245 0.3846 0.3948 0.3095 0.6282 0.2853 0.421053 0.580952 0.661203 1 3739 63636 4436 2494 3935 42974 493 5565 2 9798 120672 11564 8600 6606 66694 900 16510 0.969603 0 . 0 . 42 14,10,8,8 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T391|520|UBXN11|protein_coding|CODING|NM_183008.2|15|T),DOWNSTREAM(MODIFIER||3730||762|CEP85|protein_coding|CODING|NM_022778.3||T),DOWNSTREAM(MODIFIER||1246||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.16726 rs7522905 -0.689466 0.750148 42 L312R 520 cTg/cGg MODERATE 12 MISSENSE CODING UBXN11 C protein_coding NM_183008.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26610891 A C 0 228 0 0.8828 0.727 0.6945 0.4603 0.9304 0.6053 0.882745 0.919189 0.937337 2 8641 99703 7229 3842 5937 62256 767 11031 2 9802 120476 11526 8580 6574 66644 890 16460 0 . 0 . 0 51 0,0,16,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L312R|520|UBXN11|protein_coding|CODING|NM_183008.2|12|C),DOWNSTREAM(MODIFIER||2878||93|SH3BGRL3|protein_coding|CODING|NM_031286.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4332350 -0.693146 0.0252634 51 S46 520 tcA/tcG LOW 5 SILENT CODING UBXN11 C protein_coding NM_183008.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26627478 T C 0 228 0 0.5885 0.5673 0.5735 0.4385 0.7356 0.4939 0.648219 0.727583 0.766635 2 6139 80735 6393 3703 4616 50351 630 8903 2 9808 120740 11574 8612 6602 66734 900 16510 1 0 . 0 . 105 0,1,42,53 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S46|520|UBXN11|protein_coding|CODING|NM_183008.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2276712 -0.693147 0.0071977 105 N40S 61 aAc/aGc MODERATE 2 MISSENSE CODING CD52 G protein_coding NM_001803.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26646726 A G 0 222 0 0.6301 0.5807 0.5807 0.4415 0.7356 0.498 0.666818 0.732047 0.765465 1 6820 81368 6367 3698 4615 50283 636 8949 2 10394 121250 11550 8616 6600 66678 908 16504 0.895431 0 . 0 COSM1180632 58 16,8,13,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N40S|61|CD52|protein_coding|CODING|NM_001803.2|2|G),DOWNSTREAM(MODIFIER||1624||1661|AIM1L|protein_coding|CODING|NM_001039775.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.594402 rs1071849 -0.692914 0.212586 58 I41M 61 atA/atG MODERATE 2 MISSENSE CODING CD52 G protein_coding NM_001803.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26646730 A G 0 222 0 0.6301 0.5807 0.5807 0.4415 0.7356 0.498 0.666818 0.732047 0.765465 1 6822 81368 6366 3698 4615 50280 636 8951 2 10396 121246 11546 8614 6600 66676 908 16506 0.884563 0 . 0 COSM1180633 56 14,9,13,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I41M|61|CD52|protein_coding|CODING|NM_001803.2|2|G),DOWNSTREAM(MODIFIER||1620||1661|AIM1L|protein_coding|CODING|NM_001039775.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.906252 rs17645 -0.692914 0.212586 56 1661 LOW 19 CODING AIM1L C protein_coding NM_001039775.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26648551 G C 0 228 0 0.5537 0.5597 0.5749 0.4405 0.7346 0.5 0.597367 0.707904 0.764535 2 6090 80486 6344 3736 4625 50211 628 8852 2 10392 120632 11530 8600 6608 66524 902 16076 0 . 0 . 0 65 0,0,29,31 SPLICE_SITE_REGION+INTRON(LOW||||1661|AIM1L|protein_coding|CODING|NM_001039775.3|19|C),DOWNSTREAM(MODIFIER||1537||61|CD52|protein_coding|CODING|NM_001803.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11247913 -0.693147 0.0763381 65 S1294N 1661 aGc/aAc MODERATE 11 MISSENSE CODING AIM1L T protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26663362 C T 0 222 0 0.6634 0.4559 0.3833 0.1825 0.5308 0.4315 0.631471 0.560932 0.524785 1 5639 50873 3163 1336 2386 31190 378 6781 2 8262 90772 7224 4842 3878 52320 678 13568 0.99919 0 . 0 . 76 28,8,29,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S1294N|1661|AIM1L|protein_coding|CODING|NM_001039775.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0579813 rs10751735 -0.693136 0.228364 76 S902Y 1661 tCc/tAc MODERATE 2 MISSENSE CODING AIM1L T protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26670444 G T 0 222 0 0.115 0.2065 0.2478 0.2669 0.2962 0.1462 0 . 0 1 123 2884 54 104 23 1220 39 1321 2 682 12336 218 310 52 3984 136 6954 0.640816 0 . 0 . 59 16,18,6,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S902Y|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.120406 rs36024412 -0.692717 0.217694 59 R847H 1661 cGc/cAc MODERATE 2 MISSENSE CODING AIM1L T protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26670609 C T 0 222 0 0.1142 0.2049 0.2478 0.2659 0.2913 0.1452 0 . 0 1 93 2673 41 67 21 1098 39 1314 2 572 12496 192 212 44 3756 134 7586 0.993031 0 . 0 . 54 8,10,18,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R847H|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.423576 rs34370465 -0.693127 0.536557 54 T799 1661 acG/acA LOW 2 SILENT CODING AIM1L T protein_coding NM_001039775.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26670752 C T 0 222 0 0.2413 0.2049 0.2003 0.1438 0.1928 0.2342 0 . 0 1 140 2730 43 33 4 745 27 1738 2 590 10606 188 216 12 3286 126 6188 0.755467 0 . 0 . 124 39,15,38,14 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T799|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.561512 rs11247923 -0.693147 0.281718 124 P689T 1661 Ccc/Acc MODERATE 2 MISSENSE CODING AIM1L T protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26671084 G T 0 222 0 0.1543 0.1809 0.1931 0.1458 0.1918 0.2331 0 . 0 1 109 3120 38 34 207 849 37 1846 2 564 13324 184 224 754 3880 160 7558 0.615544 0 . 0 . 42 15,3,18,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P689T|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.955391 rs12562454 -0.692717 0.14463 42 V634A 1661 gTc/gCc MODERATE 2 MISSENSE CODING AIM1L G protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26671248 A G 0 222 0 0.1543 0.1811 0.1931 0.1458 0.1918 0.2342 0 . 0 1 130 2929 48 35 5 790 27 1894 2 684 12788 230 226 16 3816 132 7684 0.896844 0 . 0 . 103 27,23,23,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V634A|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.945427 rs57268417 -0.693145 0.347182 103 F525S 1661 tTc/tCc MODERATE 2 MISSENSE CODING AIM1L G protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26671575 A G 0 95 0 0.5961 0.5058 0.4712 0.3274 0.7227 0.3691 0 . 0 1 0 46 0 0 0 0 0 46 2 202 4534 172 494 48 714 30 2874 0.536403 0 . 0 . 79 26,27,11,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F525S|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|G) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.0938424 0.990472 0 0.000465752 rs11579834 -0.689466 0.0051748 79 L524S 1661 tTg/tCg MODERATE 2 MISSENSE CODING AIM1L G protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26671578 A G 0 42.6 0 0.6006 0.505 0.4712 0.3214 0.7207 0.3671 0 . 0 1 5 57 0 0 0 0 0 52 2 216 4656 178 538 46 736 32 2910 0.928525 0 . 0 . 80 29,28,9,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L524S|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|G) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.0559576 0.994387 0 0.000435466 rs11579835 -0.683931 0.000125639 80 S487P 1661 Tct/Cct MODERATE 2 MISSENSE CODING AIM1L G protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26671690 A G 0 31.4 0 . 0 . 0 . 0 . 0 . 1 3 57 4 2 1 46 0 1 2 5084 64912 7732 6552 3304 32664 432 9144 0.977379 0 . 0 . 129 53,32,9,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S487P|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|G) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.495036 0.95501 0 0.328178 rs112674559 -0.689466 0.0444735 129 R25W 1661 Cgg/Tgg MODERATE 2 MISSENSE CODING AIM1L A protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26673076 G A 0 222 0 0.1505 0.1795 0.1931 0.1458 0.1918 0.2311 0.13804 0.176338 0.194072 1 928 15462 1313 983 609 8477 117 3035 2 4442 59162 4740 4060 2120 32198 450 11152 0.553158 0 . 0 . 105 18,27,22,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R25W|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.550916 rs11247924 -0.693147 0.112246 105 R14Q 1661 cGa/cAa MODERATE 2 MISSENSE CODING AIM1L T protein_coding NM_001039775.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26673108 C T 0 222 0 0.1505 0.1793 0.1931 0.1438 0.1918 0.2321 0.140042 0.174283 0.190203 1 600 9606 564 498 296 5151 79 2418 2 2930 35308 1974 2090 936 18466 296 8616 0.93795 0 . 0 . 78 15,19,17,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R14Q|1661|AIM1L|protein_coding|CODING|NM_001039775.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.11565 rs11247925 -0.693145 0.0940047 78 R288L 524 cGt/cTt MODERATE 4 MISSENSE CODING ZNF683 A protein_coding NM_001307925.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26691174 C A 0 222 0 0.1233 0.2634 0.4193 0.2778 0.341 0.2474 0.163414 0.292865 0.359186 1 1688 39424 4674 2231 2523 23747 306 4255 2 10348 121270 11564 8638 6614 66690 906 16510 0.337829 0 . 0 . 134 43,29,29,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cTt|R288L|524|ZNF683|protein_coding|CODING|NM_001307925.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959121 rs11247933 -0.693147 0.249351 134 H53R 524 cAt/cGt MODERATE 3 MISSENSE CODING ZNF683 C protein_coding NM_001307925.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26694245 T C 0 222 0 0.5862 0.493 0.3228 0.623 0.2863 0.5665 0.519065 0.363154 0.283221 1 4950 41187 3573 5044 1837 17649 285 7849 2 8960 104696 9660 7966 5356 57232 758 14764 0.42356 0 . 0 . 130 13,47,7,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H53R|524|ZNF683|protein_coding|CODING|NM_001307925.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992365 rs10794531 -0.693147 0.000376097 130 D48G 524 gAc/gGc MODERATE 3 MISSENSE CODING ZNF683 C protein_coding NM_001307925.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26694260 T C 0 208 0 0.2428 0.3446 0.2536 0.5794 0.1879 0.4663 0.217885 0.198477 0.188532 1 2057 29099 2942 4526 1307 12032 200 6035 2 7896 96008 8808 7626 4900 52648 696 13434 0.976721 0 . 0 . 104 8,43,3,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D48G|524|ZNF683|protein_coding|CODING|NM_001307925.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999608 rs10794532 -0.693147 0.000782112 104 524 LOW 1 CODING ZNF683 C protein_coding NM_001307925.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26699157 T C 0 88 0 0.6611 0.5156 0.3256 0.626 0.2922 0.5695 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974685 0 . 0 . 25 2,14,0,9 SPLICE_SITE_REGION+INTRON(LOW||||524|ZNF683|protein_coding|CODING|NM_001307925.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998399 rs11247937 -0.662043 0.618905 25 209 43 MODIFIER 4 CODING LIN28A C protein_coding NM_024674.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26752992 T C 0 222 0 0.8495 0.8433 0.8718 0.8631 0.7843 0.8548 0.851683 0.818273 0.801187 1 7459 89141 9159 6521 4887 47079 695 13341 2 8764 107548 9942 7366 6036 58974 828 15638 0.462856 0 . 0 . 73 6,31,6,27 UTR_3_PRIME(MODIFIER||43||209|LIN28A|protein_coding|CODING|NM_024674.5|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.202087 rs4659441 -0.693127 0.305654 73 209 2970 MODIFIER 4 CODING LIN28A G protein_coding NM_024674.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26755919 A G 0 228 0 0.9425 0.9279 0.9179 0.997 0.8469 0.9274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 123 0,0,38,76 UTR_3_PRIME(MODIFIER||2970||209|LIN28A|protein_coding|CODING|NM_024674.5|4|G),UPSTREAM(MODIFIER||2854||334|DHDDS|protein_coding|CODING|NM_024887.3||G) 0 . 0 . 0 1 0 . 0 . 57 0 0 0.996209 0 . rs41523453,rs9438623 -0.693147 0.00393226 123 334 664 MODIFIER 1 CODING DHDDS A protein_coding NM_024887.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26758773 G A 0 27.3 0 0.4818 0.4563 0.3098 0.7103 0.2346 0.4918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||664||334|DHDDS|protein_coding|CODING|NM_024887.3|1|A),DOWNSTREAM(MODIFIER||2554||209|LIN28A|protein_coding|CODING|NM_024674.5||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6656196 -0.453602 0.96 2 V253M 334 Gtg/Atg MODERATE 8 MISSENSE CODING DHDDS A protein_coding NM_024887.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26786627 G A 0 222 0 0.4811 0.4553 0.3069 0.7093 0.2346 0.4908 0.444394 0.287483 0.207093 1 4719 38025 3186 6245 1649 15039 284 6903 2 10400 121368 11572 8638 6614 66726 908 16510 0.716597 0 . 0 COSM146454 130 25,44,18,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V253M|334|DHDDS|protein_coding|CODING|NM_024887.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.238679 rs3816539 -0.693147 0.193274 130 334 1886 MODIFIER 9 CODING DHDDS T protein_coding NM_024887.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26797508 C T 0 91 0 0.4803 0.4551 0.3084 0.7093 0.2336 0.4908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.450401 0 . 0 . 8 0,3,1,4 UTR_3_PRIME(MODIFIER||1886||334|DHDDS|protein_coding|CODING|NM_024887.3|9|T),UPSTREAM(MODIFIER||1394||90|HMGN2|protein_coding|CODING|NM_005517.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.600535 rs2290588 -0.590765 0.396258 8 90 365 MODIFIER 6 CODING HMGN2 T protein_coding NM_005517.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26802004 G T 0 224 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,6,8 UTR_3_PRIME(MODIFIER||365||90|HMGN2|protein_coding|CODING|NM_005517.3|6|T),DOWNSTREAM(MODIFIER||4209||334|DHDDS|protein_coding|CODING|NM_024887.3||T) 0 . 0 . 0 . 0 . 0 . 33 0 0 0.991701 0 . rs139955356 -0.686358 0.0187114 14 744 46 MODIFIER 1 CODING RPS6KA1 T protein_coding NM_001006665.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26872346 C T 0 3.5 0 0.0265 0.0673 0.0288 0.13 0.0636 0.089 0.0287469 0.0388165 0.0438988 1 32 1144 23 77 6 367 15 624 2 938 14098 386 508 82 5100 146 6938 0.846482 0 . 0 . 15 8,4,3,0 START_GAINED(LOW||||744|RPS6KA1|protein_coding|CODING|NM_001006665.1|1|T),UTR_5_PRIME(MODIFIER||46||744|RPS6KA1|protein_coding|CODING|NM_001006665.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91051 rs71640330 -0.511536 0.771809 15 A178 744 gcT/gcC LOW 6 SILENT CODING RPS6KA1 C protein_coding NM_001006665.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26879920 T C 0 228 0 0.9675 0.9912 0.9986 1 1 1 0.976396 0.991927 0.999884 2 10151 121142 11572 8654 6611 66737 907 16510 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 72 0,0,27,42 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A178|744|RPS6KA1|protein_coding|CODING|NM_001006665.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4970490 -0.693147 0.06172 72 Y475 744 taT/taC LOW 15 SILENT CODING RPS6KA1 C protein_coding NM_001006665.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26887592 T C 0 228 0 0.5068 0.5104 0.3646 0.756 0.2903 0.592 0.462324 0.330617 0.26314 2 5025 46017 4957 6535 1953 18848 338 8361 2 10402 121330 11576 8646 6612 66674 908 16512 1 0 . 0 . 58 1,0,27,24 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y475|744|RPS6KA1|protein_coding|CODING|NM_001006665.1|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1064196 -0.693147 0.0591674 58 S556 744 tcC/tcT LOW 17 SILENT CODING RPS6KA1 T protein_coding NM_001006665.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26897990 C T 0 222 0 0 0.01218 0 0.0605 0 0 0.000907853 0.00030755 0 1 4 601 2 580 0 7 3 5 2 10380 121150 11546 8646 6560 66630 904 16484 0.953124 0 . 0 . 100 28,15,19,25 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S556|744|RPS6KA1|protein_coding|CODING|NM_001006665.1|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961516 rs11546000 -0.693146 0.0269971 100 744 43 MODIFIER 21 CODING RPS6KA1 G protein_coding NM_001006665.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26900735 C G 0 228 0 0.7557 0.7859 0.6974 0.8492 0.7783 0.8323 0.751475 0.757189 0.760116 2 7922 94342 8039 7302 5167 51827 707 13378 2 10388 121106 11532 8616 6596 66580 902 16492 0 . 0 . 0 81 0,0,41,38 UTR_3_PRIME(MODIFIER||43||744|RPS6KA1|protein_coding|CODING|NM_001006665.1|21|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs282179 -0.693147 0.362613 81 744 398 MODIFIER 21 CODING RPS6KA1 T protein_coding NM_001006665.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26901090 C T 0 33.5 0 0.6778 0.6518 0.5778 0.7133 0.5805 0.6789 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.916482 0 . 0 . 10 1,6,1,2 UTR_3_PRIME(MODIFIER||398||744|RPS6KA1|protein_coding|CODING|NM_001006665.1|21|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.916482 1 0 0.916482 rs11113 -0.511536 0.617121 10 744 627 MODIFIER 21 CODING RPS6KA1 A protein_coding NM_001006665.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 26901319 G A 0 191 0 0.3079 0.4487 0.3689 0.7063 0.2584 0.6258 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.400891 0 . 0 . 52 28,2,19,3 UTR_3_PRIME(MODIFIER||627||744|RPS6KA1|protein_coding|CODING|NM_001006665.1|21|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.962142 rs7726 -0.692562 0.950808 52 R264G 310 Aga/Gga MODERATE 4 MISSENSE CODING GPN2 C protein_coding NM_018066.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27210721 T C 0 228 0 0.9781 0.8732 0.8256 0.997 0.6292 0.8885 0.916931 0.724896 0.626512 2 9656 88740 9928 8639 4114 41712 656 14035 2 10400 121232 11558 8652 6594 66616 906 16506 0 . 0 . 0 55 0,0,21,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R264G|310|GPN2|protein_coding|CODING|NM_018066.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3170660 -0.693147 0.246559 55 R21Q 398 cGg/cAg MODERATE 2 MISSENSE CODING KDF1 T protein_coding NM_152365.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27278810 C T 0 222 0 0 0.015974 0 0.0784 0 0.001 0.000230627 7.8174e-05 0 1 3 793 3 752 0 11 5 19 2 8912 105036 11380 8374 6580 60144 748 8898 0.743698 0 . 0 . 68 17,17,16,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R21Q|398|KDF1|protein_coding|CODING|NM_152365.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984934 rs79374331 -0.693021 0.13986 68 W27R 227 Tgg/Cgg MODERATE 1 MISSENSE CODING TRNP1 C protein_coding NM_001013642.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27320356 T C 0 228 0 0.9334 0.982 0.9971 1 1 1 0.96 0.987873 0.998978 2 171 1687 20 44 0 486 8 958 2 178 1696 20 44 0 488 8 958 0 . 0 . 0 13 0,0,7,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W27R|227|TRNP1|protein_coding|CODING|NM_001013642.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.964642 0 . rs6689941 -0.676189 0.702665 13 T20K 425 aCg/aAg MODERATE 1 MISSENSE CODING FAM46B T protein_coding NM_052943.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27339103 G T 0 198 0 0.0416 0.3359 0.3833 0.7232 0.17 0.4714 0 . 0 2 47 3677 65 186 4 541 36 2798 2 582 12038 182 252 16 3300 126 7580 0 . 0 . 0 17 0,0,1,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T20K|425|FAM46B|protein_coding|CODING|NM_052943.3|1|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4970471 -0.690438 0.757161 17 815 2 MODIFIER 12 CODING SLC9A1 C protein_coding NM_003047.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27426796 T C 0 228 0 0.9939 0.9874 0.9784 1 0.9632 0.9969 0.990014 0.969928 0.959632 2 9773 105569 11217 8488 6086 60336 742 8927 2 9870 109002 11436 8488 6430 63006 768 9004 0 . 0 . 0 86 0,0,45,33 UTR_3_PRIME(MODIFIER||2||815|SLC9A1|protein_coding|CODING|NM_003047.4|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4266911 -0.693147 0.307445 86 E735 815 gaA/gaG LOW 12 SILENT CODING SLC9A1 C protein_coding NM_003047.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27427041 T C 0 228 0 1 0.9892 0.9798 1 0.9632 0.9969 0.993645 0.971321 0.959884 2 10365 117700 11363 8654 6260 63854 874 16330 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 61 0,0,17,37 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E735|815|SLC9A1|protein_coding|CODING|NM_003047.4|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4418629 -0.693147 0.00937074 61 T455I 1288 aCc/aTc MODERATE 9 MISSENSE CODING MAP3K6 A protein_coding NM_004672.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27688633 G A 0 222 0 0.0983 0.3105 0.2147 0.5397 0.3777 0.3599 0.147299 0.281793 0.350698 1 1478 39414 1830 4448 2591 22760 299 6008 2 10094 119702 11478 8592 6516 65710 888 16424 0.891938 0 . 0 . 121 38,23,23,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T455I|1288|MAP3K6|protein_coding|CODING|NM_004672.4|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.798865 rs1138294,rs386518127 -0.693147 0.749153 121 173 622 MODIFIER 5 CODING CD164L2 T protein_coding NM_207397.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27705915 C T 0 222 0 0.2012 0.1801 0.0144 0.3829 0.003 0.2423 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.000320597 0 . 0 . 80 20,17,20,14 UTR_3_PRIME(MODIFIER||622||173|CD164L2|protein_coding|CODING|NM_207397.3|5|T),UPSTREAM(MODIFIER||4600||299|FCN3|protein_coding|CODING|NM_003665.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.908778 rs2273269 -0.693132 0.0832632 80 M76V 173 Atg/Gtg MODERATE 2 MISSENSE CODING CD164L2 C protein_coding NM_207397.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27709020 T C 0 222 0 0.6082 0.3367 0.0764 0.3998 0.1362 0.2955 0.526782 0.242888 0.0974419 1 5564 21504 716 3174 956 6807 123 4164 2 10350 119578 11526 8606 6544 66020 884 15648 0.951097 0 . 0 . 37 10,5,17,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M76V|173|CD164L2|protein_coding|CODING|NM_207397.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.175131 rs2504779 -0.692067 0.202191 37 P349 498 ccA/ccG LOW 8 SILENT CODING WASF2 C protein_coding NM_006990.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27736478 T C 0 222 0 0.0628 0.1464 0.0058 0.3879 0.003 0.2577 0.0590104 0.0206828 0.00104651 1 626 7294 64 3075 0 95 41 3393 2 10398 120884 11576 8626 6584 66562 896 16242 0.00124993 0 . 0 . 165 48,24,45,33 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P349|498|WASF2|protein_coding|CODING|NM_006990.4|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.297398 rs2273270 -0.693147 0.386997 165 A935T 1603 Gct/Act MODERATE 6 MISSENSE CODING AHDC1 T protein_coding NM_001029882.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27875824 C T 0 228 0 1 0.998 1 1 0.9911 0.999 0.997957 0.994925 0.993372 2 10321 120069 11545 8640 6601 65960 899 16103 2 10334 120598 11572 8640 6604 66372 902 16174 0 . 0 . 0 62 0,0,12,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A935T|1603|AHDC1|protein_coding|CODING|NM_001029882.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4908364 -0.693147 0.011841 62 P715 1603 ccG/ccT LOW 6 SILENT CODING AHDC1 A protein_coding NM_001029882.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27876482 C A 0 228 0 0.9818 0.7929 0.7406 0.8204 0.6193 0.7249 0.919582 0.71689 0.61314 2 9364 80244 9218 6824 3611 39338 549 11340 2 10060 117778 11458 8592 6154 64614 860 16040 0 . 0 . COSM426019 72 0,0,34,35 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P715|1603|AHDC1|protein_coding|CODING|NM_001029882.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2076457 -0.693147 0.186572 72 529 LOW 6 CODING FGR C protein_coding NM_001042729.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 27943525 G C 0 222 0 0 0.01278 0.0432 0.0308 0 0.0031 0.000907853 0.000538213 0.000348837 1 9 1212 874 256 0 38 5 30 2 10406 121346 11566 8642 6614 66700 908 16510 0.86831 0 . 0 . 67 18,15,13,19 SPLICE_SITE_REGION+INTRON(LOW||||529|FGR|protein_coding|CODING|NM_001042729.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998624 rs2231876 -0.69312 0.0565055 67 A112 341 gcA/gcG LOW 5 SILENT CODING FAM76A G protein_coding NM_001143912.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28060574 A G 0 222 0 0.6241 0.253 0.0865 0.2669 0.0149 0.1002 0.51271 0.184146 0.015814 1 5538 11263 610 2290 23 1116 53 1633 2 10372 121240 11554 8638 6610 66662 904 16500 0.28537 0 . 0 . 85 23,19,29,7 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A112|341|FAM76A|protein_coding|CODING|NM_001143912.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.886384 rs6670793 -0.693139 0.00618761 85 276 1084 MODIFIER 9 CODING STX12 T protein_coding NM_177424.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28149924 A T 0 222 0 0.115 0.1124 0.036 0.2679 0.0189 0.0992 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99999 0 . 0 . 104 21,11,40,14 UTR_3_PRIME(MODIFIER||1084||276|STX12|protein_coding|CODING|NM_177424.2|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.969195 rs41305767 -0.693147 0.584199 104 V234 455 gtC/gtT LOW 6 SILENT CODING SMPDL3B T protein_coding NM_014474.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28282206 C T 0 222 0 0.1641 0.2402 0.3112 0.253 0.2704 0.2485 0.202224 0.254344 0.281047 1 1952 32434 3842 2149 1396 18595 227 4273 2 10248 120394 11576 8638 6614 66278 896 16144 0.715022 0 . 0 . 97 29,16,32,13 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V234|455|SMPDL3B|protein_coding|CODING|NM_014474.3|6|T),UPSTREAM(MODIFIER||3767||395|XKR8|protein_coding|CODING|NM_018053.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.620822 rs3813804 -0.693147 0.029495 97 V263A 455 gTc/gCc MODERATE 6 MISSENSE CODING SMPDL3B C protein_coding NM_014474.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28282292 T C 0 222 0 0.0703 0.1863 0.255 0.2123 0.2684 0.183 0.105311 0.231662 0.296395 1 1056 30413 2802 2285 2230 18675 246 3119 2 10404 121310 11562 8628 6604 66694 908 16510 0.745624 0 . 0 . 118 34,28,21,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V263A|455|SMPDL3B|protein_coding|CODING|NM_014474.3|6|C),UPSTREAM(MODIFIER||3681||395|XKR8|protein_coding|CODING|NM_018053.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.676073 rs3813803 -0.693146 0.00135902 118 455 185 MODIFIER 8 CODING SMPDL3B C protein_coding NM_014474.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28285534 T C 0 129 0 0.7761 0.9317 0.9683 0.998 0.9781 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,5 UTR_3_PRIME(MODIFIER||185||455|SMPDL3B|protein_coding|CODING|NM_014474.3|8|C),UPSTREAM(MODIFIER||439||395|XKR8|protein_coding|CODING|NM_018053.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12402958 -0.616816 0.108254 6 455 283 MODIFIER 8 CODING SMPDL3B T protein_coding NM_014474.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28285632 A T 0 64 0 0.7761 0.9321 0.9683 1 0.9781 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||283||455|SMPDL3B|protein_coding|CODING|NM_014474.3|8|T),UPSTREAM(MODIFIER||341||395|XKR8|protein_coding|CODING|NM_018053.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12402686 -0.511536 0.845642 3 395 340 MODIFIER 3 CODING XKR8 C protein_coding NM_018053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28294051 T C 0 32.6 0 0.7927 0.8492 0.9193 0.7272 0.9662 0.8814 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||340||395|XKR8|protein_coding|CODING|NM_018053.3|3|C),DOWNSTREAM(MODIFIER||2804||573|EYA3|protein_coding|CODING|NM_001990.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4243821 -0.379885 0 2 161 20721 MODIFIER 1 CODING TAF12 G protein_coding NM_001135218.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 28969314 A G 0 154 0 0.8381 0.9543 0.9798 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,8,1 UTR_5_PRIME(MODIFIER||20721||161|TAF12|protein_coding|CODING|NM_001135218.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4252958 -0.662043 0.507605 9 579 397 MODIFIER 1 CODING YTHDF2 A protein_coding NM_001173128.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29063236 G A 0 9.7 0 0.2247 0.4966 0.5504 0.7887 0.3936 0.6309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||397||579|YTHDF2|protein_coding|CODING|NM_001173128.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3738067 -0.379885 0 1 579 LOW 2 CODING YTHDF2 C protein_coding NM_001173128.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29063559 A C 0 174 0 0.8623 0.9613 0.9856 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,1 SPLICE_SITE_REGION(LOW||||579|YTHDF2|protein_coding|CODING|NM_001173128.1|2|C),UTR_5_PRIME(MODIFIER||74||579|YTHDF2|protein_coding|CODING|NM_001173128.1|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6697540 -0.636426 0.230436 8 579 74 MODIFIER 2 CODING YTHDF2 C protein_coding NM_001173128.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29063559 A C 0 174 0 0.8623 0.9613 0.9856 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,1 SPLICE_SITE_REGION(LOW||||579|YTHDF2|protein_coding|CODING|NM_001173128.1|2|C),UTR_5_PRIME(MODIFIER||74||579|YTHDF2|protein_coding|CODING|NM_001173128.1|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6697540 -0.636426 0.230436 8 C27F 372 tGc/tTc MODERATE 1 MISSENSE CODING OPRD1 T protein_coding NM_000911.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29138975 G T 0 190 0 0.9796 0.9445 0.9193 1 0.8678 0.9366 0.969769 0.91579 0.888801 2 1363 23407 1283 1252 487 10635 191 8196 2 1416 25448 1346 1252 536 11988 212 8698 0 . 0 . 0 15 0,0,14,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tTc|C27F|372|OPRD1|protein_coding|CODING|NM_000911.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1042114 -0.688148 0.0169633 15 G307 372 ggC/ggT LOW 3 SILENT CODING OPRD1 T protein_coding NM_000911.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29189597 C T 0 228 0 0.3056 0.5813 0.7032 0.754 0.5726 0.6984 0.342189 0.471009 0.536977 2 3210 65088 7872 6139 3182 33362 445 10878 2 8886 109978 10670 8062 5364 60678 788 15530 1 0 . 0 COSM1560682 131 1,0,62,54 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G307|372|OPRD1|protein_coding|CODING|NM_000911.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2234918 -0.693147 0.250661 131 864 1366 MODIFIER 21 CODING EPB41 C protein_coding NM_001166005.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29443675 T C 0 66 0 0.357 0.5797 0.6614 0.5089 0.7883 0.681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,4,0 UTR_3_PRIME(MODIFIER||1366||864|EPB41|protein_coding|CODING|NM_001166005.1|21|C),DOWNSTREAM(MODIFIER||2262||307|TMEM200B|protein_coding|CODING|NM_001003682.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs502393 -0.556411 0.118267 5 864 1414 MODIFIER 21 CODING EPB41 G protein_coding NM_001166005.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29443723 A G 0 83 0 0.7428 0.7153 0.7536 0.5119 0.8728 0.6984 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 5,0,6,0 UTR_3_PRIME(MODIFIER||1414||864|EPB41|protein_coding|CODING|NM_001166005.1|21|G),DOWNSTREAM(MODIFIER||2214||307|TMEM200B|protein_coding|CODING|NM_001003682.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.742931 rs2249138 -0.616816 0.945073 11 864 3205 MODIFIER 21 CODING EPB41 A protein_coding NM_001166005.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29445514 C A 0 43.4 0 0.3737 0.5485 0.6138 0.498 0.6829 0.6524 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 1,2,2,0 UTR_3_PRIME(MODIFIER||3205||864|EPB41|protein_coding|CODING|NM_001166005.1|21|A),DOWNSTREAM(MODIFIER||423||307|TMEM200B|protein_coding|CODING|NM_001003682.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs553253 -0.453602 0.96 6 307 606 MODIFIER 2 CODING TMEM200B G protein_coding NM_001003682.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29446811 A G 0 222 0 0.6838 0.7033 0.7334 0.5635 0.8559 0.6953 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.762744 0 . 0 . 81 37,11,22,4 UTR_3_PRIME(MODIFIER||606||307|TMEM200B|protein_coding|CODING|NM_001003682.3|2|G),DOWNSTREAM(MODIFIER||253||864|EPB41|protein_coding|CODING|NM_001166005.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.890666 rs2452788 -0.692976 0.651814 81 E253D 494 gaA/gaC MODERATE 6 MISSENSE CODING SRSF4 G protein_coding NM_005626.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29475648 T G 0 121 0 0.7231 0.7202 0.745 0.5635 0.8817 0.6943 0.766682 0.8493 0.891628 1 7758 99116 8549 4889 5961 59013 748 12198 2 10360 121188 11574 8630 6612 66594 908 16510 0.513192 0 . 0 . 20 6,4,3,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E253D|494|SRSF4|protein_coding|CODING|NM_005626.4|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.751866 rs2230679 -0.651104 0.461975 20 373 756 MODIFIER 10 CODING MECR G protein_coding NM_016011.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29519778 T G 0 39.3 0 0.7231 0.7181 0.7334 0.5625 0.8797 0.6943 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||756||373|MECR|protein_coding|CODING|NM_016011.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2640464 -0.453602 0.5 2 A199 373 gcA/gcG LOW 5 SILENT CODING MECR C protein_coding NM_016011.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29529699 T C 0 222 0 0.8238 0.7468 0.7493 0.5615 0.8807 0.6943 0.848547 0.876327 0.890556 1 5867 61121 5626 3656 2704 33726 445 9097 2 7072 75558 7690 6276 3050 38550 560 12360 0.448904 0 . 0 . 99 18,24,24,23 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A199|373|MECR|protein_coding|CODING|NM_016011.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.845475 rs1062924 -0.693147 0.358816 99 F96L 373 Ttc/Ctc MODERATE 3 MISSENSE CODING MECR G protein_coding NM_016011.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29542637 A G 0 222 0 0.7231 0.7181 0.7334 0.5625 0.8797 0.6943 0.765774 0.848839 0.891395 1 7769 99144 8535 4893 5947 59056 745 12199 2 10406 121380 11574 8630 6614 66736 908 16512 0.982612 0 . 0 . 112 32,26,18,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F96L|373|MECR|protein_coding|CODING|NM_016011.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.13322 rs1128400 -0.693143 0.195737 112 Y865 1446 taC/taT LOW 17 SILENT CODING PTPRU T protein_coding NM_005704.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 29630455 C T 0 228 0 0.3533 0.3752 0.3329 0.6419 0.1581 0.3834 0.318202 0.201907 0.142326 2 3331 31729 4941 5591 1247 10255 240 6124 2 10262 120590 11552 8612 6604 66148 906 16506 0 . 0 . 0 64 0,0,35,26 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y865|1446|PTPRU|protein_coding|CODING|NM_005704.4|17|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2295061,rs386564068 -0.693147 0.239096 64 496 1680 MODIFIER 8 CODING MATN1 G protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31184749 C G 0 80 0 0.4728 0.2652 0.2363 0.3353 0.1034 0.0992 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 2,0,3,1 UTR_3_PRIME(MODIFIER||1680||496|MATN1|protein_coding|CODING|NM_002379.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.75 rs1188398 -0.556411 0.735663 6 496 1666 MODIFIER 8 CODING MATN1 A protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31184763 G A 0 96 0 0.7133 0.5487 0.6484 0.5169 0.4702 0.3691 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 7 1,0,4,1 UTR_3_PRIME(MODIFIER||1666||496|MATN1|protein_coding|CODING|NM_002379.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1188399,rs386521806 -0.590765 0.665344 7 496 1650 MODIFIER 8 CODING MATN1 C protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31184779 T C 0 108 0 0.7458 0.5579 0.6513 0.5169 0.4702 0.3701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 8 1,0,4,0 UTR_3_PRIME(MODIFIER||1650||496|MATN1|protein_coding|CODING|NM_002379.3|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1188400 -0.556411 0.160409 8 496 1572 MODIFIER 8 CODING MATN1 G protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31184857 T G 0 64 0 0.7496 0.5585 0.6527 0.5169 0.4682 0.3691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1572||496|MATN1|protein_coding|CODING|NM_002379.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1188401 -0.511536 0.490096 3 496 1551 MODIFIER 8 CODING MATN1 G protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31184878 A G 0 39.3 0 0.7443 0.5571 0.6513 0.5179 0.4682 0.3691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1551||496|MATN1|protein_coding|CODING|NM_002379.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1188402 -0.453602 0.32 2 496 898 MODIFIER 8 CODING MATN1 T protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31185531 G T 0 39.3 0 0.1762 0.1522 0.1527 0.3353 0.0258 0.0603 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||898||496|MATN1|protein_coding|CODING|NM_002379.3|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs79516330 -0.453602 0.42 2 496 175 MODIFIER 8 CODING MATN1 G protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31186254 A G 0 222 0 0.8056 0.5933 0.6758 0.5992 0.4682 0.3701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.553671 0 . 0 . 146 24,44,27,48 UTR_3_PRIME(MODIFIER||175||496|MATN1|protein_coding|CODING|NM_002379.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.738786 rs1188405 -0.693147 0.357798 146 496 42 MODIFIER 8 CODING MATN1 T protein_coding NM_002379.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31186387 C T 0 222 0 0.4629 0.2626 0.2363 0.3353 0.1034 0.0992 0.369667 0.195618 0.105987 1 1166 3156 87 221 7 1010 34 631 2 2888 21250 428 688 48 9092 200 7906 0.561425 0 . 0 . 175 39,25,55,41 UTR_3_PRIME(MODIFIER||42||496|MATN1|protein_coding|CODING|NM_002379.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.813447 rs1746059 -0.693147 0.840837 175 T354 496 acT/acC LOW 5 SILENT CODING MATN1 G protein_coding NM_002379.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31188901 A G 0 222 0 0.8411 0.6042 0.6787 0.6052 0.4682 0.3701 0.772583 0.56151 0.453372 1 8135 62038 8357 5162 3576 30238 428 6142 2 10404 121376 11570 8634 6614 66734 908 16512 0.443555 0 . 0 . 140 44,34,25,29 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T354|496|MATN1|protein_coding|CODING|NM_002379.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.749709 rs20566,rs386497706 -0.693147 0.27224 140 262 879 MODIFIER 8 CODING LAPTM5 C protein_coding NM_006762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31205796 T C 0 9.7 0 0.9599 0.6366 0.6873 0.6012 0.4682 0.3732 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||879||262|LAPTM5|protein_coding|CODING|NM_006762.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8048 -0.379885 0 1 S40 262 tcA/tcG LOW 2 SILENT CODING LAPTM5 C protein_coding NM_006762.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31215364 T C 0 222 0 0.6188 0.6046 0.6873 0.6716 0.5258 0.5389 0.592374 0.523143 0.487674 1 6177 65815 8492 5922 3667 32125 481 8951 2 10206 119236 11382 8520 6300 65734 880 16214 0.812478 0 . 0 COSM426058 130 21,33,29,32 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S40|262|LAPTM5|protein_coding|CODING|NM_006762.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456404 rs1050663,rs386513930 -0.693147 0.0508134 130 262 76 MODIFIER 1 CODING LAPTM5 T protein_coding NM_006762.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31230668 C T 0 223 0 0.3411 0.2592 0.4164 0.2569 0.173 0.1278 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,1,34 UTR_5_PRIME(MODIFIER||76||262|LAPTM5|protein_coding|CODING|NM_006762.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2273979 -0.693136 0.0759956 36 442 1 MODIFIER 5 CODING SDC3 G protein_coding NM_014654.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31346057 A G 0 222 0 0.0174 0.1641 0.1729 0.5278 0.0149 0.135 0.0290513 0.0126865 0.00430233 1 327 10661 2512 4767 640 673 74 1668 2 10406 120642 11564 8632 6614 66488 900 16038 0.999875 0 . 0 . 86 30,14,25,7 UTR_3_PRIME(MODIFIER||1||442|SDC3|protein_coding|CODING|NM_014654.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.8962 rs3766284 -0.69312 0.478071 86 T329I 442 aCa/aTa MODERATE 4 MISSENSE CODING SDC3 A protein_coding NM_014654.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31347320 G A 0 222 0 0.0129 0.1611 0.1729 0.5218 0.0149 0.1319 0.018384 0.00907274 0.00430233 1 210 10416 2501 4676 640 672 74 1643 2 10406 121358 11574 8616 6614 66728 908 16512 0.995413 255 other 0 . 64 10,20,12,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T329I|442|SDC3|protein_coding|CODING|NM_014654.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89816 rs2282440 -0.693021 0.0476067 64 1188 415 MODIFIER 22 CODING PUM1 A protein_coding NM_001020658.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31405643 G A 0 222 0 0.0242 0.1208 0.1297 0.2688 0.0785 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870106 0 . 0 . 75 14,12,25,16 UTR_3_PRIME(MODIFIER||415||1188|PUM1|protein_coding|CODING|NM_001020658.1|22|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.918734 rs1803848 -0.693145 0.0943915 75 N779 1188 aaT/aaC LOW 15 SILENT CODING PUM1 G protein_coding NM_001020658.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31426815 A G 0 222 0 0.2859 0.3574 0.4726 0.3462 0.3767 0.364 0.307762 0.368522 0.399651 1 3171 50169 5911 2933 3389 27618 363 6784 2 10376 121302 11578 8634 6608 66702 908 16496 0.595349 0 . 0 . 68 16,12,15,19 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N779|1188|PUM1|protein_coding|CODING|NM_001020658.1|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991012 rs2275741 -0.693132 0.10281 68 207 562 MODIFIER 7 CODING NKAIN1 G protein_coding NM_024522.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31653988 A G 0 9.7 0 0.118 0.4179 0.5303 0.3452 0.7147 0.5133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||562||207|NKAIN1|protein_coding|CODING|NM_024522.2|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4949356 -0.379885 0 1 E271 357 gaG/gaA LOW 7 SILENT CODING SNRNP40 T protein_coding NM_004814.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31742050 C T 0 222 0 0 0.0011981 0 0.006 0 0 0 . 0 1 0 41 0 40 0 0 0 1 2 10398 120566 11576 8654 6614 66482 904 15938 0.558097 0 . 0 . 121 30,21,48,9 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E271|357|SNRNP40|protein_coding|CODING|NM_004814.2|7|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.742123 rs191830691 -0.693147 0.0733771 121 464 56 MODIFIER 11 CODING SERINC2 G protein_coding NM_001199038.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31907102 A G 0 228 0 0.3555 0.6556 0.8487 0.5734 0.9662 0.6892 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 96 0,0,19,70 UTR_3_PRIME(MODIFIER||56||464|SERINC2|protein_coding|CODING|NM_001199038.1|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7417775 -0.693147 0.0440138 96 464 411 MODIFIER 11 CODING SERINC2 G protein_coding NM_001199038.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 31907457 A G 0 228 0 0.7511 0.47 0.3761 0.5139 0.2495 0.3384 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 182 0,0,71,89 UTR_3_PRIME(MODIFIER||411||464|SERINC2|protein_coding|CODING|NM_001199038.1|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4233 -0.693147 0.500265 182 D1221 1604 gaC/gaT LOW 58 SILENT CODING COL16A1 A protein_coding NM_001856.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32127953 G A 0 228 0 0.5174 0.4718 0.4741 0.6369 0.4016 0.3108 0.479081 0.424505 0.398885 2 4626 48835 5318 5436 2293 25952 345 4865 2 9006 111282 10852 8426 5222 62060 782 14934 0.495743 0 . 0 . 261 3,4,115,117 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1221|1604|COL16A1|protein_coding|CODING|NM_001856.3|58|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.438233 rs2271928 -0.693147 0.000684894 261 P834 1604 ccT/ccC LOW 37 SILENT CODING COL16A1 G protein_coding NM_001856.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32148571 A G 0 228 0 0.9985 0.9994 0.9986 1 1 1 0.99769 0.99926 1 2 9758 120655 11571 8622 6614 66688 892 16510 2 9786 120684 11572 8622 6614 66688 892 16510 0 . 0 . 0 48 0,0,12,32 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P834|1604|COL16A1|protein_coding|CODING|NM_001856.3|37|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10737358 -0.693146 0.0203964 48 1216 118 MODIFIER 16 CODING SPOCD1 C protein_coding NM_144569.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32256086 T C 0 151 0 0.8676 0.7147 0.7406 0.4296 0.7356 0.7618 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.84246 0 . 0 . 25 10,0,13,1 UTR_3_PRIME(MODIFIER||118||1216|SPOCD1|protein_coding|CODING|NM_144569.5|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.436174 rs13426,rs386528642 -0.686358 0.88262 25 R436W 1216 Cgg/Tgg MODERATE 2 MISSENSE CODING SPOCD1 A protein_coding NM_144569.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32279629 G A 0 222 0 0.1876 0.3462 0.4957 0.4226 0.4374 0.2822 0.224694 0.3656 0.437791 1 2247 49046 5739 3806 3108 29734 340 4072 2 10352 120562 11550 8636 6608 66452 896 16068 0.482824 0 . 0 COSM146457 34 3,14,8,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R436W|1216|SPOCD1|protein_coding|CODING|NM_144569.5|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.525313 rs6669563 -0.689466 0.884131 34 T109A 1216 Act/Gct MODERATE 2 MISSENSE CODING SPOCD1 C protein_coding NM_144569.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32280610 T C 0 222 0 0.6399 0.6875 0.6671 0.7212 0.673 0.7464 0.637086 0.671767 0.689535 1 6587 82526 7308 6055 4399 45831 593 11753 2 10336 120974 11566 8630 6610 66418 902 16512 0.934851 0 . 0 . 29 7,3,11,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T109A|1216|SPOCD1|protein_coding|CODING|NM_144569.5|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.900088 rs6664445 -0.69168 0.159863 29 C297Y 546 tGt/tAt MODERATE 5 MISSENSE CODING IQCC A protein_coding NM_001160042.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32672932 G A 0 222 0 0.0023 0.103 0.1009 0.2946 0.0537 0.0941 0.0127099 0.039674 0.0534884 1 112 10691 1966 2564 521 3823 68 1637 2 10356 121174 11568 8630 6614 66606 906 16494 0.7617 0 . 0 . 101 18,23,22,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C297Y|546|IQCC|protein_coding|CODING|NM_001160042.1|5|A),UPSTREAM(MODIFIER||1763||349|DCDC2B|protein_coding|CODING|NM_001099434.1||A),DOWNSTREAM(MODIFIER||1941||241|CCDC28B|protein_coding|CODING|NM_001301011.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.754951 rs12032332 -0.693147 0.000705024 101 L77 268 ctG/ctA LOW 2 SILENT CODING TSSK3 A protein_coding NM_052841.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32829281 G A 0 120 0 0 0.0349 0.0043 0.1667 0 0.0041 0.00136178 0.000615101 0.000232558 1 16 1791 215 1455 0 18 6 81 2 10386 121362 11578 8640 6614 66726 908 16510 0.912009 0 . 0 . 42 19,2,16,0 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L77|268|TSSK3|protein_coding|CODING|NM_052841.3|2|A),UPSTREAM(MODIFIER||1437||127|FAM229A|protein_coding|CODING|NM_001167676.1||A),DOWNSTREAM(MODIFIER||953||474|BSDC1|protein_coding|CODING|NM_001300958.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958476 rs2270537 -0.689466 0.219284 42 474 2391 MODIFIER 10 CODING BSDC1 T protein_coding NM_001300958.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 32831543 C T 0 228 0 0.9811 0.9471 0.9193 1 0.8598 0.956 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,0,9,45 UTR_3_PRIME(MODIFIER||2391||474|BSDC1|protein_coding|CODING|NM_001300958.1|10|T),UPSTREAM(MODIFIER||3699||127|FAM229A|protein_coding|CODING|NM_001167676.1||T),DOWNSTREAM(MODIFIER||1619||268|TSSK3|protein_coding|CODING|NM_052841.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs476153 -0.693147 0.0135934 57 G418A 441 gGt/gCt MODERATE 5 MISSENSE CODING ZBTB8A C protein_coding NM_001040441.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33065947 G C 0 228 0 1 0.9998 1 1 0.999 1 1 0.999923 0.999884 2 10405 121409 11578 8654 6614 66738 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 307 0,0,138,152 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G418A|441|ZBTB8A|protein_coding|CODING|NM_001040441.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs704886 -0.693147 0.000122974 307 V151 425 gtT/gtC LOW 4 SILENT CODING RBBP4 C protein_coding NM_005610.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33133968 T C 0 228 0 0.8873 0.9679 0.9841 1 1 0.999 0.912165 0.96986 0.999419 2 9428 120355 11530 8654 6614 66718 901 16510 2 10402 121406 11578 8654 6614 66740 908 16510 0 . 0 . 0 131 0,0,56,61 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V151|425|RBBP4|protein_coding|CODING|NM_005610.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2762904,rs56084034 -0.693147 0.0187187 131 425 436 MODIFIER 12 CODING RBBP4 G protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33145742 A G 0 228 0 0.1891 0.5935 0.6369 0.7679 0.7515 0.7669 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,8,3 UTR_3_PRIME(MODIFIER||436||425|RBBP4|protein_coding|CODING|NM_005610.2|12|G),UTR_3_PRIME(MODIFIER||1709||482|SYNC|protein_coding|CODING|NM_030786.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9851 -0.676189 0.622324 12 482 1709 MODIFIER 5 CODING SYNC G protein_coding NM_030786.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33145742 A G 0 228 0 0.1891 0.5935 0.6369 0.7679 0.7515 0.7669 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,8,3 UTR_3_PRIME(MODIFIER||436||425|RBBP4|protein_coding|CODING|NM_005610.2|12|G),UTR_3_PRIME(MODIFIER||1709||482|SYNC|protein_coding|CODING|NM_030786.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9851 -0.676189 0.622324 12 425 1195 MODIFIER 12 CODING RBBP4 G protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33146501 A G 0 228 0 0.59 0.8215 0.7767 0.8938 0.9682 0.9407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 0,0,55,21 UTR_3_PRIME(MODIFIER||1195||425|RBBP4|protein_coding|CODING|NM_005610.2|12|G),UTR_3_PRIME(MODIFIER||950||482|SYNC|protein_coding|CODING|NM_030786.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs360511 -0.693147 0.522872 90 482 950 MODIFIER 5 CODING SYNC G protein_coding NM_030786.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33146501 A G 0 228 0 0.59 0.8215 0.7767 0.8938 0.9682 0.9407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 0,0,55,21 UTR_3_PRIME(MODIFIER||1195||425|RBBP4|protein_coding|CODING|NM_005610.2|12|G),UTR_3_PRIME(MODIFIER||950||482|SYNC|protein_coding|CODING|NM_030786.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs360511 -0.693147 0.522872 90 425 1837 MODIFIER 12 CODING RBBP4 T protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33147143 C T 0 166 0 0.8873 0.9681 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,17,0 UTR_3_PRIME(MODIFIER||1837||425|RBBP4|protein_coding|CODING|NM_005610.2|12|T),UTR_3_PRIME(MODIFIER||308||482|SYNC|protein_coding|CODING|NM_030786.2|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs360510 -0.690438 0.358623 17 482 308 MODIFIER 5 CODING SYNC T protein_coding NM_030786.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33147143 C T 0 166 0 0.8873 0.9681 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,17,0 UTR_3_PRIME(MODIFIER||1837||425|RBBP4|protein_coding|CODING|NM_005610.2|12|T),UTR_3_PRIME(MODIFIER||308||482|SYNC|protein_coding|CODING|NM_030786.2|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs360510 -0.690438 0.358623 17 425 5291 MODIFIER 12 CODING RBBP4 T protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33150597 C T 0 9.7 0 0.8873 0.9681 0.9841 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5291||425|RBBP4|protein_coding|CODING|NM_005610.2|12|T),INTRON(MODIFIER||||482|SYNC|protein_coding|CODING|NM_030786.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs634787 -0.379885 0 1 425 5292 MODIFIER 12 CODING RBBP4 C protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33150598 T C 0 9.7 0 0.4902 0.781 0.745 0.8681 0.9632 0.9223 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5292||425|RBBP4|protein_coding|CODING|NM_005610.2|12|C),INTRON(MODIFIER||||482|SYNC|protein_coding|CODING|NM_030786.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs398500 -0.379885 0 1 425 5412 MODIFIER 12 CODING RBBP4 C protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33150718 T C 0 9.7 0 0.8873 0.9681 0.9841 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5412||425|RBBP4|protein_coding|CODING|NM_005610.2|12|C),INTRON(MODIFIER||||482|SYNC|protein_coding|CODING|NM_030786.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs602580 -0.379885 0 1 425 5645 MODIFIER 12 CODING RBBP4 C protein_coding NM_005610.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33150951 T C 0 9.7 0 0.5915 0.8219 0.7767 0.8938 0.9682 0.9407 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5645||425|RBBP4|protein_coding|CODING|NM_005610.2|12|C),INTRON(MODIFIER||||482|SYNC|protein_coding|CODING|NM_030786.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs601637 -0.379885 0 1 R274Q 482 cGg/cAg MODERATE 2 MISSENSE CODING SYNC T protein_coding NM_030786.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33160878 C T 0 228 0 0.7829 0.8626 0.7738 0.8681 0.9652 0.9223 0.808526 0.911958 0.956945 2 1866 21310 378 580 1656 9271 225 7334 2 2306 23012 458 684 1692 9652 250 7970 0 . 0 . 0 50 0,0,30,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R274Q|482|SYNC|protein_coding|CODING|NM_030786.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs360042 -0.693147 0.41059 50 M163V 482 Atg/Gtg MODERATE 2 MISSENSE CODING SYNC C protein_coding NM_030786.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33161212 T C 0 228 0 0.7829 0.8626 0.7738 0.8681 0.9652 0.9223 0.807081 0.91152 0.956945 2 1839 20875 335 534 1659 9004 226 7278 2 2296 22566 416 624 1694 9370 252 7914 0 . 0 . 0 24 0,0,7,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M163V|482|SYNC|protein_coding|CODING|NM_030786.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs360041 -0.692352 0.0731757 24 1094 1697 MODIFIER 7 CODING KIAA1522 C protein_coding NM_020888.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33240185 G C 0 126 0 0.0113 0.141 0.1023 0.2262 0.1839 0.2117 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980844 0 . 0 . 39 18,2,19,0 UTR_3_PRIME(MODIFIER||1697||1094|KIAA1522|protein_coding|CODING|NM_020888.2|7|C),DOWNSTREAM(MODIFIER||655||528|YARS|protein_coding|CODING|NM_003680.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.930586 rs8717 -0.69168 0.626288 39 528 738 MODIFIER 1 CODING YARS C protein_coding NM_003680.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33283583 G C 0 9.7 0 0.0113 0.1414 0.1023 0.2272 0.1839 0.2127 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||738||528|YARS|protein_coding|CODING|NM_003680.3|1|C),INTRON(MODIFIER||||408|S100PBP|protein_coding|CODING|NM_001256121.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3737251 -0.379885 0 1 408 2449 MODIFIER 7 CODING S100PBP G protein_coding NM_001256121.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33324088 C G 0 181 0 0.0113 0.1414 0.1023 0.2282 0.1839 0.2117 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.958156 0 . 0 . 62 4,31,2,23 UTR_3_PRIME(MODIFIER||2449||408|S100PBP|protein_coding|CODING|NM_001256121.1|7|G),DOWNSTREAM(MODIFIER||3781||212|FNDC5|protein_coding|CODING|NM_153756.2||G|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998624 rs1284365 -0.692914 0.877136 62 408 2497 MODIFIER 7 CODING S100PBP C protein_coding NM_001256121.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33324136 T C 0 144 0 0.559 0.6747 0.6744 0.7708 0.6938 0.7127 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.791944 0 . 0 . 41 0,18,1,22 UTR_3_PRIME(MODIFIER||2497||408|S100PBP|protein_coding|CODING|NM_001256121.1|7|C),DOWNSTREAM(MODIFIER||3733||212|FNDC5|protein_coding|CODING|NM_153756.2||C|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.748114 rs9500 -0.692717 0.0087126 41 212 1730 MODIFIER 6 CODING FNDC5 A protein_coding NM_153756.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33328165 G A 0 222 0 0.4599 0.5835 0.6081 0.7341 0.5885 0.5726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957079 0 . 0 . 120 24,35,16,33 UTR_3_PRIME(MODIFIER||1730||212|FNDC5|protein_coding|CODING|NM_153756.2|6|A|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||3685||408|S100PBP|protein_coding|CODING|NM_001256121.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.930516 rs3480 -0.693147 0.0141769 120 732 235 MODIFIER 9 CODING RNF19B T protein_coding NM_153341.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33402172 C T 0 228 0 0.0265 0.1889 0.2378 0.2748 0.2525 0.2198 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.912147 0 . 0 . 63 0,3,16,38 UTR_3_PRIME(MODIFIER||235||732|RNF19B|protein_coding|CODING|NM_153341.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.437103 rs8040 -0.693147 0.0327726 63 G444 732 ggC/ggT LOW 6 SILENT CODING RNF19B A protein_coding NM_153341.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33409693 G A 0 228 0 0.0265 0.1885 0.2378 0.2748 0.2505 0.2198 0.0662733 0.169153 0.22186 2 588 27715 3747 2183 1593 15367 219 4018 2 10342 120446 11452 8556 6596 66142 902 16456 1 0 . 0 . 129 1,0,60,55 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G444|732|RNF19B|protein_coding|CODING|NM_153341.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs194645 -0.693147 0.797986 129 475 270 MODIFIER 5 CODING TRIM62 A protein_coding NM_018207.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33612508 G A 0 80 0 0.028 0.1799 0.1787 0.2014 0.2505 0.2914 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||270||475|TRIM62|protein_coding|CODING|NM_018207.2|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3766813 -0.556411 0.459448 4 475 LOW 2 CODING TRIM62 A protein_coding NM_018207.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33631069 C A 0 228 0 0.0537 0.1877 0.183 0.2014 0.2505 0.2935 0.0942325 0.187711 0.235581 2 732 21427 1652 1514 1134 12047 160 4188 2 5158 64196 5522 4572 2714 34354 476 11400 1 0 . 0 . 75 1,0,58,9 SPLICE_SITE_REGION+INTRON(LOW||||475|TRIM62|protein_coding|CODING|NM_018207.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2306257 -0.693147 0.125457 75 420 LOW 7 CODING ZNF362 C protein_coding NM_152493.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33760743 T C 0 222 0 0.9713 0.8173 0.8357 0.7589 0.7584 0.7168 0.936677 0.816854 0.755465 1 9830 95455 9598 6676 5446 51218 736 11951 2 10400 121344 11572 8640 6612 66706 908 16506 0.487127 0 . 0 . 86 43,1,30,2 SPLICE_SITE_REGION+INTRON(LOW||||420|ZNF362|protein_coding|CODING|NM_152493.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0323454 rs4641276 -0.69312 0.000728851 86 420 625 MODIFIER 9 CODING ZNF362 G protein_coding NM_152493.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33765272 A G 0 222 0 0.7383 0.4782 0.2911 0.375 0.3966 0.4499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.83857 0 . 0 . 70 23,10,20,8 UTR_3_PRIME(MODIFIER||625||420|ZNF362|protein_coding|CODING|NM_152493.2|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.901295 rs1132790 -0.693054 0.156018 70 858 1084 MODIFIER 14 CODING PHC2 T protein_coding NM_198040.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33789382 C T 0 222 0 0.6899 0.3862 0.2104 0.251 0.2803 0.3487 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.816936 0 . 0 . 151 17,60,17,37 UTR_3_PRIME(MODIFIER||1084||858|PHC2|protein_coding|CODING|NM_198040.2|14|T),UPSTREAM(MODIFIER||2683||340|A3GALT2|protein_coding|CODING|NM_001080438.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.614654 rs7264 -0.693147 0.21072 151 858 946 MODIFIER 14 CODING PHC2 A protein_coding NM_198040.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33789520 C A 0 228 0 0.8873 0.7228 0.4885 0.751 0.6312 0.7321 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,2,14 UTR_3_PRIME(MODIFIER||946||858|PHC2|protein_coding|CODING|NM_198040.2|14|A),UPSTREAM(MODIFIER||2821||340|A3GALT2|protein_coding|CODING|NM_001080438.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5861 -0.689466 0.155125 16 858 878 MODIFIER 14 CODING PHC2 C protein_coding NM_198040.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33789588 T C 0 216 0 0.8873 0.7226 0.4885 0.751 0.6312 0.7311 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,5,3 UTR_3_PRIME(MODIFIER||878||858|PHC2|protein_coding|CODING|NM_198040.2|14|C),UPSTREAM(MODIFIER||2889||340|A3GALT2|protein_coding|CODING|NM_001080438.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.900802 0 . rs1130804 -0.651104 0.617267 9 858 796 MODIFIER 14 CODING PHC2 A protein_coding NM_198040.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33789670 G A 0 179 0 0.0182 0.1749 0.17 0.2292 0.2346 0.273 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.446318 0 . 0 . 25 7,0,16,1 UTR_3_PRIME(MODIFIER||796||858|PHC2|protein_coding|CODING|NM_198040.2|14|A),UPSTREAM(MODIFIER||2971||340|A3GALT2|protein_coding|CODING|NM_001080438.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.918319 rs11061 -0.690438 0.294356 25 858 498 MODIFIER 14 CODING PHC2 T protein_coding NM_198040.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33789968 G T 0 222 0 0.0174 0.1585 0.1441 0.2113 0.1948 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.985066 0 . 0 . 56 14,15,16,9 UTR_3_PRIME(MODIFIER||498||858|PHC2|protein_coding|CODING|NM_198040.2|14|T),UPSTREAM(MODIFIER||3269||340|A3GALT2|protein_coding|CODING|NM_001080438.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.503798 rs1130800 -0.692914 0.0757941 56 Y849 858 taC/taT LOW 14 SILENT CODING PHC2 A protein_coding NM_198040.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33790496 G A 0 222 0 0.0182 0.1729 0.1715 0.2113 0.2416 0.273 0.0515207 0.180917 0.247209 1 462 25814 2037 1797 1203 15645 174 4496 2 10380 121030 11570 8618 6588 66516 902 16456 0.976747 0 . 0 . 119 52,8,38,7 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y849|858|PHC2|protein_coding|CODING|NM_198040.2|14|A),UPSTREAM(MODIFIER||3797||340|A3GALT2|protein_coding|CODING|NM_001080438.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.834168 rs11554674 -0.693147 0.140931 119 858 LOW 8 CODING PHC2 A protein_coding NM_198040.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33799900 G A 0 172 0 0.0182 0.1711 0.17 0.2113 0.2346 0.272 0.0508398 0.177072 0.241744 1 452 25357 2022 1800 1168 15260 172 4483 2 10270 120756 11524 8616 6546 66422 902 16476 0.679313 0 . 0 . 51 4,21,1,19 SPLICE_SITE_REGION+INTRON(LOW||||858|PHC2|protein_coding|CODING|NM_198040.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.126647 rs12734630 -0.692067 0.632157 51 V475M 858 Gtg/Atg MODERATE 8 MISSENSE CODING PHC2 T protein_coding NM_198040.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33820134 C T 0 222 0 0.0182 0.1715 0.17 0.2113 0.2346 0.274 0.0508398 0.177072 0.241744 1 453 25236 2006 1784 1136 15205 170 4482 2 10240 119230 11416 8558 6186 65842 878 16110 0.738735 0 . 0 . 151 21,35,34,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V475M|858|PHC2|protein_coding|CODING|NM_198040.2|8|T),INTRAGENIC(MODIFIER|||||LOC101929464||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.87072 rs12026290 -0.693147 0.0314008 151 P276 858 ccT/ccC LOW 6 SILENT CODING PHC2 G protein_coding NM_198040.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33832865 A G 0 228 0 0.8843 0.7282 0.4856 0.7708 0.6322 0.7444 0.852247 0.729817 0.667093 2 9046 83116 5599 6724 4403 44462 604 12278 2 10394 121336 11570 8642 6608 66704 908 16510 1 0 . 0 . 74 1,0,36,33 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P276|858|PHC2|protein_coding|CODING|NM_198040.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6425816 -0.693147 0.417267 74 A424 1043 gcC/gcA LOW 6 SILENT CODING ZSCAN20 A protein_coding NM_145238.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33957130 C A 0 222 0 0.0204 0.1945 0.2104 0.3651 0.162 0.2761 0.0452899 0.131744 0.172197 1 414 23515 2296 3321 1136 11666 168 4514 2 9794 120546 11564 8606 6614 66618 894 16456 0.766952 0 . 0 COSM146460 66 5,29,6,22 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A424|1043|ZSCAN20|protein_coding|CODING|NM_145238.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786474 rs3795419 -0.693054 0.201561 66 Y432D 1043 Tat/Gat MODERATE 6 MISSENSE CODING ZSCAN20 G protein_coding NM_145238.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33957152 T G 0 228 0 1 0.9992 1 1 0.996 1 0.999232 0.997704 0.996984 2 9791 120060 11569 8626 6457 66212 893 16512 2 9796 120736 11574 8626 6614 66714 900 16512 0 . 0 . 0 48 0,0,5,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y432D|1043|ZSCAN20|protein_coding|CODING|NM_145238.3|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4403594 -0.693147 0.0963527 48 A706 1043 gcA/gcG LOW 8 SILENT CODING ZSCAN20 G protein_coding NM_145238.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33960062 A G 0 228 0 0.8495 0.7526 0.6239 0.7381 0.7376 0.7434 0.840241 0.805376 0.788353 2 8121 89912 6107 6432 4595 51975 656 12026 2 9844 120800 11576 8640 6614 66720 904 16502 1 0 . 0 . 129 1,0,76,48 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A706|1043|ZSCAN20|protein_coding|CODING|NM_145238.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs9943259 -0.693147 0.595986 129 1043 71 MODIFIER 8 CODING ZSCAN20 G protein_coding NM_145238.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33961147 T G 0 220 0 0.8502 0.7528 0.6254 0.7381 0.7366 0.7434 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,1,23 UTR_3_PRIME(MODIFIER||71||1043|ZSCAN20|protein_coding|CODING|NM_145238.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3795420 -0.692831 0.602106 25 3631 5034 MODIFIER 71 CODING CSMD2 T protein_coding NM_001281956.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33980084 C T 0 222 0 0.0197 0.1955 0.219 0.3859 0.161 0.2556 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.734639 0 . 0 . 82 7,26,13,22 UTR_3_PRIME(MODIFIER||5034||3631|CSMD2|protein_coding|CODING|NM_001281956.1|71|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.988305 rs3816922 -0.693136 0.470105 82 3631 3888 MODIFIER 71 CODING CSMD2 T protein_coding NM_001281956.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 33981230 C T 0 9.7 0 0.8442 0.746 0.6124 0.7361 0.7346 0.7301 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3888||3631|CSMD2|protein_coding|CODING|NM_001281956.1|71|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2794600 -0.379885 0 1 Q1824 3631 caA/caG LOW 34 SILENT CODING CSMD2 C protein_coding NM_001281956.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34090679 T C 0 222 0 0.0749 0.0948 0.0418 0.1538 0.0845 0.1094 0.0655924 0.071813 0.075 1 692 9358 548 944 546 4862 68 1698 2 10342 120800 11560 8614 6540 66338 896 16510 0.78628 0 . 0 . 184 43,53,40,33 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1824|3631|CSMD2|protein_coding|CODING|NM_001281956.1|34|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.824905 rs16835683 -0.693147 0.00745359 184 E1800D 3631 gaA/gaT MODERATE 34 MISSENSE CODING CSMD2 A protein_coding NM_001281956.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34090751 T A 0 222 0 0.031 0.0405 0.0159 0.127 0.003 0.0204 0.0197458 0.0100723 0.00511628 1 225 2113 94 1116 11 405 13 249 2 10272 120372 11508 8606 6454 66202 888 16442 0.375546 0 . 0 . 145 24,42,25,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E1800D|3631|CSMD2|protein_coding|CODING|NM_001281956.1|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823464 rs35761029 -0.693147 0.826883 145 L1573 3631 ctC/ctT LOW 29 SILENT CODING CSMD2 A protein_coding NM_001281956.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34112303 G A 0 222 0 0.2716 0.1068 0.0504 0.1181 0.004 0.0184 0.208125 0.0745041 0.00604651 1 2279 4455 210 1145 17 538 25 241 2 10404 121372 11570 8644 6614 66726 908 16506 0.904945 0 . 0 . 60 18,10,21,8 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1573|3631|CSMD2|protein_coding|CODING|NM_001281956.1|29|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.8593 rs10798976,rs386515338 -0.693079 0.300571 60 3631 LOW 18 CODING CSMD2 T protein_coding NM_001281956.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34189917 C T 0 228 0 0.7602 0.7897 0.8156 0.994 0.6372 0.7577 0.746709 0.682531 0.649651 2 7620 85410 9408 8464 4459 43238 603 11618 2 10310 119614 11424 8484 6528 65662 902 16304 0 . 0 . 0 175 0,0,75,91 SPLICE_SITE_REGION+INTRON(LOW||||3631|CSMD2|protein_coding|CODING|NM_001281956.1|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs519370 -0.693147 0.220875 175 H578R 3631 cAc/cGc MODERATE 13 MISSENSE CODING CSMD2 C protein_coding NM_001281956.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34238283 T C 0 222 0 0.5333 0.3796 0.317 0.2659 0.2406 0.4765 0.486382 0.34092 0.266395 1 5171 36639 2914 2374 1476 17026 265 7413 2 10406 121334 11576 8610 6610 66712 908 16512 0.883589 0 . 0 . 84 26,17,21,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H578R|3631|CSMD2|protein_coding|CODING|NM_001281956.1|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.85286 rs474474 -0.693132 0.572053 84 A432 3631 gcC/gcT LOW 9 SILENT CODING CSMD2 A protein_coding NM_001281956.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34285342 G A 0 228 0 0.584 0.6016 0.6441 0.6627 0.5278 0.6084 0.568997 0.534446 0.516744 2 5948 66612 6721 5674 3652 34672 457 9488 2 10342 120586 11476 8564 6516 66340 898 16450 1 0 . 0 . 128 0,1,74,43 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A432|3631|CSMD2|protein_coding|CODING|NM_001281956.1|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs17342512 -0.693147 0.914878 128 K419 3631 aaG/aaA LOW 9 SILENT CODING CSMD2 T protein_coding NM_001281956.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34285381 C T 0 228 0 0.584 0.6014 0.6455 0.6627 0.5278 0.6063 0.569451 0.534753 0.516977 2 5985 67023 6780 5725 3699 34864 463 9507 2 10390 121234 11548 8628 6594 66662 908 16504 1 0 . 0 . 143 0,1,67,58 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K419|3631|CSMD2|protein_coding|CODING|NM_001281956.1|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11578857 -0.693147 0.0179299 143 186 3384 MODIFIER 1 CODING HMGB4 C protein_coding NM_145205.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34326409 T C 0 9.7 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||3384||186|HMGB4|protein_coding|CODING|NM_145205.5|1|C),INTRON(MODIFIER||||3631|CSMD2|protein_coding|CODING|NM_001281956.1|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1321626 -0.379885 0 1 186 1241 MODIFIER 2 CODING HMGB4 A protein_coding NM_145205.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34328552 G A 0 9.7 0 0.2368 0.4724 0.6254 0.5873 0.5417 0.4928 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||1241||186|HMGB4|protein_coding|CODING|NM_145205.5|2|A),INTRON(MODIFIER||||3631|CSMD2|protein_coding|CODING|NM_001281956.1|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2295606 -0.379885 0 1 Y35 186 taT/taC LOW 2 SILENT CODING HMGB4 C protein_coding NM_145205.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34329897 T C 0 228 0 0.9985 0.9882 0.987 1 0.9553 0.9969 0.990921 0.966861 0.954535 2 10250 117839 11366 8644 6399 63887 875 16418 2 10340 121316 11574 8644 6614 66728 904 16512 0 . 0 . 0 120 0,0,58,57 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y35|186|HMGB4|protein_coding|CODING|NM_145205.5|2|C),INTRON(MODIFIER||||3631|CSMD2|protein_coding|CODING|NM_001281956.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs911218 -0.693147 0.363231 120 E92A 186 gAa/gCa MODERATE 2 MISSENSE CODING HMGB4 C protein_coding NM_145205.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34330067 A C 0 228 0 0.9917 0.9012 0.9063 0.9008 0.7475 0.9335 0.946664 0.823159 0.759884 2 9926 99999 10473 7656 5169 51169 729 14877 2 10370 121042 11572 8638 6612 66432 906 16512 0 . 0 . 0 200 0,0,122,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E92A|186|HMGB4|protein_coding|CODING|NM_145205.5|2|C),INTRON(MODIFIER||||3631|CSMD2|protein_coding|CODING|NM_001281956.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10379 -0.693147 0.0834785 200 598 101 MODIFIER 7 CODING C1orf94 A protein_coding NM_001134734.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34684463 G A 0 228 0 0.7481 0.7716 0.7896 0.7917 0.7525 0.7894 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,7,30 UTR_3_PRIME(MODIFIER||101||598|C1orf94|protein_coding|CODING|NM_001134734.1|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386606988,rs705207 -0.693141 0.159417 41 598 210 MODIFIER 7 CODING C1orf94 C protein_coding NM_001134734.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34684571 CACACAT C 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,9 UTR_3_PRIME(MODIFIER||210||598|C1orf94|protein_coding|CODING|NM_001134734.1|7|C) 0 . 0 9 1 0 1 0 . 0 60 0 0 . 0 . rs3831264 -0.662043 0.285163 9 598 259 MODIFIER 7 CODING C1orf94 G protein_coding NM_001134734.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 34684621 A G 0 116 0 0.857 0.8339 0.8012 0.8274 0.7644 0.9039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,0,6 UTR_3_PRIME(MODIFIER||259||598|C1orf94|protein_coding|CODING|NM_001134734.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1061074 -0.616816 0.0190313 6 273 2202 MODIFIER 1 CODING GJB5 G protein_coding NM_005268.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35220730 A G 0 46.3 0 0.823 0.5415 0.4135 0.5248 0.3877 0.4274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||2202||273|GJB5|protein_coding|CODING|NM_005268.3|1|G),UPSTREAM(MODIFIER||4612||266|GJB4|protein_coding|CODING|NM_153212.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2275229 -0.453602 0.52 2 273 160 MODIFIER 2 CODING GJB5 C protein_coding NM_005268.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35223913 A C 0 222 0 0.0151 0.0829 0.0447 0.248 0.0467 0.0685 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.500025 0 . 0 . 59 19,16,10,9 UTR_3_PRIME(MODIFIER||160||273|GJB5|protein_coding|CODING|NM_005268.3|2|C),UPSTREAM(MODIFIER||1429||266|GJB4|protein_coding|CODING|NM_153212.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.983729 rs28695349 -0.69168 0.234169 59 266 948 MODIFIER 2 CODING GJB4 T protein_coding NM_153212.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35228604 C T 0 222 0 0.3828 0.2708 0.1556 0.1528 0.2386 0.3558 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997866 0 . 0 . 42 11,8,16,6 UTR_3_PRIME(MODIFIER||948||266|GJB4|protein_coding|CODING|NM_153212.2|2|T),DOWNSTREAM(MODIFIER||4491||273|GJB5|protein_coding|CODING|NM_005268.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.948 rs1985283 -0.692562 0.484002 42 266 1603 MODIFIER 2 CODING GJB4 G protein_coding NM_153212.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35229259 C G 0 222 0 0.0499 0.0693 0.0274 0.0913 0.0398 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.944144 0 . 0 . 76 6,33,7,26 UTR_3_PRIME(MODIFIER||1603||266|GJB4|protein_coding|CODING|NM_153212.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.993634 rs7549597 -0.693127 0.214875 76 N119 270 aaC/aaT LOW 2 SILENT CODING GJB3 T protein_coding NM_001005752.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35250720 C T 0 218 0 0.1051 0.0976 0.0331 0.122 0.0457 0.1616 0.0996369 0.0669691 0.0502326 1 1046 9086 794 952 427 3559 90 2218 2 10354 121272 11566 8642 6606 66686 908 16510 0.461957 2 benign 0 . 42 16,9,8,9 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N119|270|GJB3|protein_coding|CODING|NM_001005752.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622451 rs41310442 -0.690438 0.420886 42 270 369 MODIFIER 2 CODING GJB3 C protein_coding NM_001005752.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35251545 G C 0 228 0 0.3313 0.2582 0.1441 0.3175 0.1829 0.2566 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 60 0,1,22,35 UTR_3_PRIME(MODIFIER||369||270|GJB3|protein_coding|CODING|NM_001005752.1|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2236214 -0.693147 0.671467 60 270 559 MODIFIER 2 CODING GJB3 C protein_coding NM_001005752.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35251735 G C 0 228 0 0.1694 0.2129 0.1239 0.3194 0.1819 0.2566 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 88 0,0,62,17 UTR_3_PRIME(MODIFIER||559||270|GJB3|protein_coding|CODING|NM_001005752.1|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9118 -0.693147 0.0290801 88 Q49 333 caA/caG LOW 2 SILENT CODING GJA4 G protein_coding NM_002060.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35259961 A G 0 228 0 0.8533 0.6214 0.513 0.4841 0.6481 0.499 0.821607 0.706136 0.646977 2 8591 74941 5261 4124 4718 43328 581 8338 2 10406 121356 11572 8622 6612 66726 908 16510 0.972973 0 . 0 . 85 0,2,49,25 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q49|333|GJA4|protein_coding|CODING|NM_002060.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.459459 rs1764390 -0.693147 0.0753278 85 333 113 MODIFIER 2 CODING GJA4 A protein_coding NM_002060.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35260929 G A 0 228 0 0.9856 0.6556 0.5303 0.4831 0.6491 0.4826 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 90 1,0,58,22 UTR_3_PRIME(MODIFIER||113||333|GJA4|protein_coding|CODING|NM_002060.2|2|A) 0 . 0 . 0 1 0 . 0 . 59 0 1 1 0 1 rs3543 -0.693147 0.103508 90 333 416 MODIFIER 2 CODING GJA4 G protein_coding NM_002060.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35261232 C G 0 228 0 0.2685 0.2843 0.2406 0.3105 0.3161 0.2771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.660714 0 . 0 . 88 0,2,37,47 UTR_3_PRIME(MODIFIER||416||333|GJA4|protein_coding|CODING|NM_002060.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.517857 rs705193 -0.693147 0.0850058 88 92 2932 MODIFIER 3 CODING SMIM12 G protein_coding NM_001164824.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35318368 A G 0 165 0 0.9697 0.9732 0.9611 0.999 0.9404 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,4,2 UTR_3_PRIME(MODIFIER||2932||92|SMIM12|protein_coding|CODING|NM_001164824.1|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7529736 -0.616816 0.381141 7 92 2861 MODIFIER 3 CODING SMIM12 G protein_coding NM_001164824.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35318439 A G 0 73 0 0.9932 0.9798 0.964 1 0.9394 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2861||92|SMIM12|protein_coding|CODING|NM_001164824.1|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7529768 -0.511536 0.972043 3 92 58 MODIFIER 3 CODING SMIM12 C protein_coding NM_001164824.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35321242 A C 0 222 0 0.093 0.0986 0.0692 0.1518 0.0696 0.1022 0.0826146 0.0790526 0.0772273 1 844 9545 521 992 366 4868 79 1875 2 10000 120940 11570 8644 6610 66710 904 16502 0.997533 0 . 0 . 88 29,19,20,11 UTR_3_PRIME(MODIFIER||58||92|SMIM12|protein_coding|CODING|NM_001164824.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.957085 rs14103 -0.69311 0.0290764 88 P283L 979 cCt/cTt MODERATE 3 MISSENSE CODING DLGAP3 A protein_coding NM_001080418.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35370137 G A 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 8 0 5 0 0 0 3 2 10348 121152 11572 8640 6614 66558 908 16512 0.899885 0 . 0 . 91 22,15,27,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P283L|979|DLGAP3|protein_coding|CODING|NM_001080418.2|3|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.834778 rs371713295 -0.693147 0.361001 91 1325 LOW 12 CODING ZMYM6 T protein_coding NM_007167.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35470877 A T 0 187 0 0.0923 0.1314 0.0591 0.381 0.0258 0.0869 0.0828416 0.047209 0.0289535 1 853 9056 1131 3392 185 2102 76 1317 2 9848 113130 10876 8342 6304 61250 868 15642 0.964062 0 . 0 . 57 3,26,2,25 SPLICE_SITE_REGION+INTRON(LOW||||1325|ZMYM6|protein_coding|CODING|NM_007167.3|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.779914 rs10158284 -0.693021 0.0952528 57 V73M 1142 Gtg/Atg MODERATE 5 MISSENSE CODING ZMYM1 A protein_coding NM_001289088.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35562965 G A 0 185 0 0.8018 0.8291 0.7392 0.7411 0.9215 0.9254 0.831903 0.894716 0.925622 1 8070 106357 8323 6601 5762 61757 785 15059 2 9860 120806 11574 8640 6614 66712 902 16504 0.995012 0 . 0 . 79 38,5,26,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V73M|1142|ZMYM1|protein_coding|CODING|NM_001289088.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.929501 rs2971408 -0.693054 0.0976673 79 P259 707 ccC/ccG LOW 1 SILENT CODING SFPQ C protein_coding NM_005066.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35657874 G C 0 46.3 0 0.6324 0.4018 0.3991 0.6865 0.0437 0.1667 0 . 0 2 82 1168 12 84 0 81 11 898 2 190 9722 80 128 0 2294 110 6920 0 . 0 . 0 2 0,0,1,1 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P259|707|SFPQ|protein_coding|CODING|NM_005066.2|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs118141562 -0.453602 0.86 2 D1010 1049 gaT/gaC LOW 21 SILENT CODING KIAA0319L G protein_coding NM_024874.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35900615 A G 0 228 0 0.7239 0.4537 0.3674 0.7679 0.0497 0.2413 0.597821 0.224435 0.0331395 2 6429 24800 4817 6800 652 2546 154 3402 2 10396 121340 11554 8646 6614 66710 908 16512 0 . 0 . 0 60 0,0,26,27 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1010|1049|KIAA0319L|protein_coding|CODING|NM_024874.4|21|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3814302 -0.693147 0.486593 60 T588 1049 acT/acC LOW 11 SILENT CODING KIAA0319L G protein_coding NM_024874.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 35919979 A G 0 228 0 0.0348 0.0771 0.1052 0.2371 0.003 0.0256 0.0333636 0.0132247 0.00290698 2 366 4412 1072 2163 157 304 26 324 2 10404 121364 11574 8650 6612 66716 908 16500 0.757672 0 . 0 . 69 1,3,26,32 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T588|1049|KIAA0319L|protein_coding|CODING|NM_024874.4|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.724815 rs10796920 -0.693147 0.346296 69 1049 2767 MODIFIER 1 CODING KIAA0319L T protein_coding NM_024874.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36022859 C T 0 133 0 0.1059 0.0962 0.1138 0.2341 0.003 0.0245 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,5 UTR_5_PRIME(MODIFIER||2767||1049|KIAA0319L|protein_coding|CODING|NM_024874.4|1|T),UPSTREAM(MODIFIER||534||729|NCDN|protein_coding|CODING|NM_001014839.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs28366021 -0.616816 0.893344 6 729 78 MODIFIER 8 CODING NCDN A protein_coding NM_001014839.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36031342 T A 0 228 0 0.6543 0.4345 0.3646 0.7649 0.0497 0.2423 0 . 0 2 176 469 30 82 0 29 5 147 2 302 1634 66 98 4 624 14 526 0 . 0 . 0 21 0,0,16,4 UTR_3_PRIME(MODIFIER||78||729|NCDN|protein_coding|CODING|NM_001014839.1|8|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs58718331 -0.692067 0.401719 21 729 596 MODIFIER 8 CODING NCDN T protein_coding NM_001014839.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36031860 G T 0 227 0 0.1331 0.1048 0.1153 0.2401 0.003 0.0245 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,15,1 UTR_3_PRIME(MODIFIER||596||729|NCDN|protein_coding|CODING|NM_001014839.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12046738 -0.689466 0.810245 18 729 678 MODIFIER 8 CODING NCDN T protein_coding NM_001014839.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36031942 C T 0 228 0 0.289 0.1494 0.134 0.2421 0.006 0.0235 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,45,0 UTR_3_PRIME(MODIFIER||678||729|NCDN|protein_coding|CODING|NM_001014839.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs79080032 -0.693147 0.553212 51 442 180 MODIFIER 1 CODING TFAP2E T protein_coding NM_178548.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36038999 C T 0 161 0 0.0961 0.0937 0.1124 0.2361 0.003 0.0235 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,10,1 START_GAINED(LOW||||442|TFAP2E|protein_coding|CODING|NM_178548.3|1|T),UTR_5_PRIME(MODIFIER||180||442|TFAP2E|protein_coding|CODING|NM_178548.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11264176 -0.676189 0.39524 11 201 2108 MODIFIER 6 CODING PSMB2 T protein_coding NM_002794.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36066760 C T 0 6.3 0 0.1853 0.2554 0.3084 0.6587 0.0268 0.1319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2108||201|PSMB2|protein_coding|CODING|NM_002794.4|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11264180 -0.379885 0 1 201 1010 MODIFIER 6 CODING PSMB2 A protein_coding NM_002794.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36067858 G A 0 9.7 0 0.8328 0.519 0.4337 0.7738 0.1143 0.3088 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1010||201|PSMB2|protein_coding|CODING|NM_002794.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12082263 -0.379885 0 1 201 217 MODIFIER 1 CODING PSMB2 C protein_coding NM_002794.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36107250 G C 0 228 0 0.9811 0.9948 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 47 0,0,2,45 UTR_5_PRIME(MODIFIER||217||201|PSMB2|protein_coding|CODING|NM_002794.4|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs567476 -0.693147 0.0329189 47 229 261 MODIFIER 2 CODING C1orf216 T protein_coding NM_152374.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36180972 C T 0 116 0 0.1021 0.2276 0.3055 0.6726 0.0229 0.0941 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,1 UTR_3_PRIME(MODIFIER||261||229|C1orf216|protein_coding|CODING|NM_152374.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3795501 -0.590765 0.842333 6 229 2775 MODIFIER 1 CODING C1orf216 A protein_coding NM_152374.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36184697 G A 0 155 0 0.2156 0.2881 0.3602 0.6736 0.0905 0.1411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,2 UTR_5_PRIME(MODIFIER||2775||229|C1orf216|protein_coding|CODING|NM_152374.1|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs72659661 -0.590765 0.37035 6 229 2776 MODIFIER 1 CODING C1orf216 T protein_coding NM_152374.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36184698 A T 0 155 0 0.2156 0.2865 0.3573 0.6706 0.0875 0.1411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,2 UTR_5_PRIME(MODIFIER||2776||229|C1orf216|protein_coding|CODING|NM_152374.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs72659663 -0.590765 0.37035 6 1339 2789 MODIFIER 25 CODING CLSPN A protein_coding NM_022111.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36199308 G A 0 9.7 0 0.0968 0.2262 0.3069 0.6716 0.0229 0.0941 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2789||1339|CLSPN|protein_coding|CODING|NM_022111.3|25|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11264195 -0.379885 0 1 1339 1707 MODIFIER 25 CODING CLSPN A protein_coding NM_022111.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36200390 G A 0 9.7 0 0.9123 0.9758 0.9928 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1707||1339|CLSPN|protein_coding|CODING|NM_022111.3|25|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs609070 -0.379885 0 1 1339 1319 MODIFIER 25 CODING CLSPN C protein_coding NM_022111.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36200778 T C 0 9.7 0 0.2912 0.3093 0.3674 0.6726 0.0915 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1319||1339|CLSPN|protein_coding|CODING|NM_022111.3|25|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7530222 -0.379885 0 1 N525S 1339 aAc/aGc MODERATE 8 MISSENSE CODING CLSPN C protein_coding NM_022111.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36225948 T C 0 228 0 0.674 0.4537 0.4323 0.7401 0.1352 0.2035 0.591693 0.288713 0.133488 2 6375 32309 5402 6870 1022 9045 221 3374 2 10394 118868 11520 8648 6572 66038 888 14808 0 . 0 . 0 75 0,0,49,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N525S|1339|CLSPN|protein_coding|CODING|NM_022111.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7537203 -0.693147 0.0363358 75 P227 891 ccA/ccG LOW 6 SILENT CODING AGO1 G protein_coding NM_001317122.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36359669 A G 0 76 0 0.3994 0.3067 0.3314 0.6558 0.0129 0.1063 0.350431 0.124481 0.00872093 1 3637 16955 4615 6210 462 959 94 978 2 10224 111644 11492 8592 6614 64092 804 9826 0.941623 0 . 0 . 27 17,2,6,1 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P227|891|AGO1|protein_coding|CODING|NM_001317122.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.941623 rs2296470 -0.636426 0.0703243 27 T393 430 acA/acG LOW 10 SILENT CODING TEKT2 G protein_coding NM_014466.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36553673 A G 0 228 0 0.9123 0.9387 0.9395 0.999 0.9115 0.9397 0.92416 0.920332 0.918372 2 9385 110931 11062 8589 5928 60065 829 15073 2 10196 119902 11488 8596 6564 65720 900 16438 0 . 0 . 0 101 0,0,36,54 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T393|430|TEKT2|protein_coding|CODING|NM_014466.2|10|G),UPSTREAM(MODIFIER||780||363|ADPRHL2|protein_coding|CODING|NM_017825.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386590114,rs399393 -0.693147 0.0211259 101 703 12 MODIFIER 4 CODING COL8A2 A protein_coding NM_005202.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36563158 C A 0 228 0 0.4365 0.6564 0.611 0.5218 0.8976 0.8763 0.54108 0.783869 0.908256 2 5166 94760 7013 3986 5598 58677 720 13600 2 9890 118394 11524 8548 6610 65344 878 15600 0 . 0 . 0 65 0,0,41,17 UTR_3_PRIME(MODIFIER||12||703|COL8A2|protein_coding|CODING|NM_005202.3|4|A),DOWNSTREAM(MODIFIER||3625||363|ADPRHL2|protein_coding|CODING|NM_017825.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3738360 -0.693147 0.0178557 65 R104W 841 Cgg/Tgg MODERATE 2 MISSENSE CODING MAP7D1 T protein_coding NM_018067.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36636835 C T 0 222 0 0 0.014377 0 0.0437 0 0.0286 0.00113533 0.000461467 0.000116306 1 11 761 7 347 0 15 7 374 2 9870 117390 11512 8616 6526 64754 860 15252 0.948854 0 . 0 . 167 35,47,36,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R104W|841|MAP7D1|protein_coding|CODING|NM_018067.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.757937 rs2296266 -0.693147 0.0164763 167 S452 841 tcT/tcC LOW 8 SILENT CODING MAP7D1 C protein_coding NM_018067.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36642420 T C 0 228 0 0.8896 0.7504 0.781 0.9137 0.5755 0.5521 0.824905 0.662089 0.579727 2 6006 54776 6988 6368 1543 25637 334 7900 2 7116 81972 8388 6844 2542 43240 522 13320 0 . 0 . 0 33 0,0,2,31 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S452|841|MAP7D1|protein_coding|CODING|NM_018067.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs475591 -0.693127 0.0310211 33 Y107 955 taC/taT LOW 4 SILENT CODING THRAP3 T protein_coding NM_005119.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36752152 C T 0 228 0 0.1036 0.2476 0.2219 0.0754 0.4205 0.4601 0.139582 0.301015 0.383721 2 1356 39977 2168 511 2507 26509 339 6587 2 10400 121392 11576 8650 6614 66732 908 16512 1 0 . 0 COSM146465 95 1,0,35,50 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y107|955|THRAP3|protein_coding|CODING|NM_005119.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2242428 -0.693147 0.0620874 95 A201V 955 gCc/gTc MODERATE 4 MISSENSE CODING THRAP3 T protein_coding NM_005119.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36752433 C T 0 228 0 0.5197 0.7955 0.8602 0.9484 0.8837 0.8742 0.592828 0.781255 0.877791 2 5991 104652 10705 8140 6067 58629 780 14340 2 10358 121330 11576 8654 6614 66712 908 16508 0 . 0 . 0 102 0,0,35,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A201V|955|THRAP3|protein_coding|CODING|NM_005119.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6425977 -0.693147 0.0107655 102 165 8 MODIFIER 3 CODING EVA1B A protein_coding NM_001304762.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36787888 G A 0 228 0 0.0605 0.2346 0.2176 0.0784 0.4205 0.4519 0.105516 0.269665 0.352756 2 244 10529 478 149 412 7220 69 1957 2 1016 20844 1220 970 740 13218 132 3548 0 . 0 . 0 15 0,0,9,5 UTR_3_PRIME(MODIFIER||8||165|EVA1B|protein_coding|CODING|NM_001304762.1|3|A),DOWNSTREAM(MODIFIER||940||756|SH3D21|protein_coding|CODING|NM_001162530.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs58971913 -0.686358 0.162982 15 440 815 MODIFIER 11 CODING STK40 T protein_coding NM_001282546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36806541 C T 0 40.4 0 0 0.0019968 0 0.0099 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,0,3 UTR_3_PRIME(MODIFIER||815||440|STK40|protein_coding|CODING|NM_001282546.1|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs145305032 -0.511536 0.892765 4 123 3793 MODIFIER 1 CODING LSM10 G protein_coding NM_032881.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36863523 A G 0 63 0 0.9266 0.9647 0.9798 1 0.9473 0.9867 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_5_PRIME(MODIFIER||3793||123|LSM10|protein_coding|CODING|NM_032881.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6425986 -0.453602 0.5 3 G307R 379 Gga/Aga MODERATE 8 MISSENSE CODING OSCP1 T protein_coding NM_145047.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36886117 C T 0 222 0 0.32 0.253 0.1542 0.2599 0.2068 0.273 0.312755 0.248116 0.215 1 3315 26643 1287 2148 1176 14277 176 4264 2 10374 121254 11566 8640 6614 66662 908 16490 0.120941 0 . 0 COSM146468 100 41,9,27,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G307R|379|OSCP1|protein_coding|CODING|NM_145047.4|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940721 rs2275477,rs386563263 -0.693143 0.335047 100 T131A 379 Acc/Gcc MODERATE 3 MISSENSE CODING OSCP1 C protein_coding NM_145047.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36898067 T C 0 222 0 0.1604 0.2081 0.1369 0.2599 0.2048 0.273 0.180209 0.202214 0.213488 1 1837 24902 1183 2145 1175 14142 169 4251 2 10406 121366 11570 8624 6614 66738 906 16508 0.986258 0 . 0 COSM1342321,COSM83893 163 56,28,33,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T131A|379|OSCP1|protein_coding|CODING|NM_145047.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.269861 rs34409118 -0.693147 0.0752995 163 P69 257 ccC/ccT LOW 3 SILENT CODING MRPS15 A protein_coding NM_031280.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36927733 G A 0 228 0 0.9932 0.9786 0.9784 1 0.9334 0.9836 0.983432 0.947409 0.928953 2 10277 115073 11341 8652 5999 61864 859 16081 2 10406 121404 11578 8654 6610 66736 908 16512 0 . 0 . 0 109 0,0,66,34 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P69|257|MRPS15|protein_coding|CODING|NM_031280.3|3|A),DOWNSTREAM(MODIFIER||3911||863|CSF3R|protein_coding|CODING|NM_156039.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7065 -0.693147 0.0951715 109 T420 863 acT/acC LOW 10 SILENT CODING CSF3R G protein_coding NM_156039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36937059 A G 0 228 0 0.736 0.5925 0.4006 0.4484 0.5666 0.7096 0.716069 0.608565 0.553488 2 7495 68510 4459 3498 3963 37167 513 11415 2 10392 121298 11572 8642 6612 66668 906 16506 0.957168 0 . 0 . 76 3,0,40,29 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T420|863|CSF3R|protein_coding|CODING|NM_156039.3|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.60629 rs3917981 -0.693147 0.619498 76 R418 863 cgT/cgC LOW 10 SILENT CODING CSF3R G protein_coding NM_156039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 36937065 A G 0 222 0 0.1717 0.2464 0.2003 0.13 0.338 0.4059 0.20404 0.299708 0.348721 1 2036 38288 2886 886 2209 23192 288 6791 2 10394 121316 11570 8646 6612 66678 908 16508 0.615408 0 . 0 . 79 25,19,18,12 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R418|863|CSF3R|protein_coding|CODING|NM_156039.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.442411 rs3917980 -0.693097 0.822506 79 599 923 MODIFIER 1 CODING ZC3H12A G protein_coding NM_025079.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 37940175 A G 0 9.7 0 0.9902 0.9972 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||599|ZC3H12A|protein_coding|CODING|NM_025079.2|1|G),UTR_5_PRIME(MODIFIER||923||599|ZC3H12A|protein_coding|CODING|NM_025079.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2660565 -0.379885 0 1 201 250 MODIFIER 8 CODING MEAF6 C protein_coding NM_022756.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 37959450 T C 0 228 0 0.4864 0.7304 0.8357 0.9038 0.835 0.6994 0 . 0 2 1226 21367 693 860 2214 9636 256 6482 2 2130 27094 822 976 2486 11554 320 8806 0 . 0 . 0 132 0,0,63,55 UTR_3_PRIME(MODIFIER||250||201|MEAF6|protein_coding|CODING|NM_022756.5|8|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs215210 -0.693147 0.150892 132 201 230 MODIFIER 8 CODING MEAF6 G protein_coding NM_022756.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 37959470 C G 0 228 0 0.5492 0.7482 0.8415 0.9038 0.837 0.6994 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 131 0,0,52,68 UTR_3_PRIME(MODIFIER||230||201|MEAF6|protein_coding|CODING|NM_022756.5|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs215211 -0.693147 0.0988931 131 201 201 MODIFIER 8 CODING MEAF6 C protein_coding NM_022756.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 37959499 G C 0 222 0 0.0461 0.1863 0.1801 0.3482 0.2386 0.1595 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.658243 0 . 0 . 131 35,39,24,24 UTR_3_PRIME(MODIFIER||201||201|MEAF6|protein_coding|CODING|NM_022756.5|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.894725 rs215212 -0.693147 0.744807 131 396 3164 MODIFIER 4 CODING SNIP1 A protein_coding NM_024700.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38000185 G A 0 39.3 0 0.7262 0.8085 0.8703 0.9702 0.8419 0.6748 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||3164||396|SNIP1|protein_coding|CODING|NM_024700.3|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7515306 -0.453602 0.56 2 396 1281 MODIFIER 4 CODING SNIP1 T protein_coding NM_024700.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38002068 C T 0 222 0 0.0439 0.1935 0.1888 0.3492 0.2435 0.1871 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.770381 0 . 0 . 53 14,9,14,11 UTR_3_PRIME(MODIFIER||1281||396|SNIP1|protein_coding|CODING|NM_024700.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.362809 rs41267303 -0.692914 0.0934338 53 396 LOW 2 CODING SNIP1 G protein_coding NM_024700.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38006359 A G 0 228 0 0.4183 0.722 0.8386 0.9702 0.834 0.6789 0.485701 0.72382 0.845814 2 4851 96767 10212 8293 5889 55833 712 10977 2 10252 119050 11542 8604 6608 66056 892 15096 0 . 0 . 0 69 0,0,21,42 SPLICE_SITE_REGION+INTRON(LOW||||396|SNIP1|protein_coding|CODING|NM_024700.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2174769 -0.693147 0.826958 69 A87V 280 gCa/gTa MODERATE 2 MISSENSE CODING DNALI1 T protein_coding NM_003462.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38023316 C T 0 79 0 0.0681 0.2043 0.2046 0.3502 0.2535 0.1871 0.0969133 0.202829 0.257093 1 977 28614 2644 3182 1251 16672 242 3646 2 10350 121238 11570 8640 6612 66658 908 16500 0.409484 0 . 0 . 24 3,13,2,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A87V|280|DNALI1|protein_coding|CODING|NM_003462.3|2|T),UPSTREAM(MODIFIER||3371||396|SNIP1|protein_coding|CODING|NM_024700.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.373673 rs11749 -0.636426 0.166446 24 280 34 MODIFIER 6 CODING DNALI1 C protein_coding NM_003462.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38030696 T C 0 222 0 0.2247 0.4109 0.562 0.5694 0.4692 0.3323 0.250113 0.375519 0.439767 1 2518 53987 7084 4856 3626 30186 378 5339 2 10392 121270 11558 8630 6596 66678 908 16508 0.609661 0 . 0 COSN163046 164 34,43,37,33 UTR_3_PRIME(MODIFIER||34||280|DNALI1|protein_coding|CODING|NM_003462.3|6|C),DOWNSTREAM(MODIFIER||1717||731|GNL2|protein_coding|CODING|NM_013285.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.964322 rs6619 -0.693147 0.0456346 164 731 149 MODIFIER 1 CODING GNL2 T protein_coding NM_013285.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38061572 G T 0 228 0 0.5393 0.7558 0.853 0.9702 0.833 0.6789 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,5,22 UTR_5_PRIME(MODIFIER||149||731|GNL2|protein_coding|CODING|NM_013285.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386495699,rs6697632 -0.693021 0.00957285 29 263 1360 MODIFIER 9 CODING RSPO1 G protein_coding NM_001038633.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38077067 A G 0 39.3 0 0.7103 0.8017 0.8689 0.9702 0.828 0.6769 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1360||263|RSPO1|protein_coding|CODING|NM_001038633.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1134025 -0.453602 0.78 2 263 127 MODIFIER 8 CODING RSPO1 G protein_coding NM_001038633.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38078300 A G 0 228 0 0.2148 0.4687 0.5937 0.6766 0.5308 0.4448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 335 0,0,177,108 UTR_3_PRIME(MODIFIER||127||263|RSPO1|protein_coding|CODING|NM_001038633.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4652964 -0.693147 0.00221622 335 266 30 MODIFIER 5 CODING C1orf109 G protein_coding NM_001303031.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38148765 A G 0 228 0 0.8343 0.8285 0.7954 0.9514 0.7654 0.7822 0.816387 0.769183 0.745 2 8567 95213 9409 8383 5043 50270 670 12871 2 10402 121350 11576 8652 6610 66702 906 16502 0 . 0 . 0 84 0,0,46,28 UTR_3_PRIME(MODIFIER||30||266|C1orf109|protein_coding|CODING|NM_001303031.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs684260 -0.693147 0.0263423 84 279 679 MODIFIER 5 CODING YRDC C protein_coding NM_024640.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38268918 T C 0 9.7 0 0.2579 0.4395 0.5086 0.4772 0.5596 0.4734 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||679||279|YRDC|protein_coding|CODING|NM_024640.3|5|C),UPSTREAM(MODIFIER||4555||110|C1orf122|protein_coding|CODING|NM_198446.2||C),DOWNSTREAM(MODIFIER||1640||457|MANEAL|protein_coding|CODING|NM_001113482.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7686 -0.379885 0 1 753 5006 MODIFIER 11 CODING MTF1 C protein_coding NM_005955.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38275802 T C 0 228 0 0.6831 0.6825 0.6225 0.748 0.7087 0.6299 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,27,8 UTR_3_PRIME(MODIFIER||5006||753|MTF1|protein_coding|CODING|NM_005955.2|11|C),UPSTREAM(MODIFIER||1937||279|YRDC|protein_coding|CODING|NM_024640.3||C),DOWNSTREAM(MODIFIER||676||110|C1orf122|protein_coding|CODING|NM_198446.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs473279 -0.693136 0.463796 36 753 4427 MODIFIER 11 CODING MTF1 T protein_coding NM_005955.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38276381 C T 0 46.3 0 0.9501 0.9858 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||4427||753|MTF1|protein_coding|CODING|NM_005955.2|11|T),UPSTREAM(MODIFIER||2516||279|YRDC|protein_coding|CODING|NM_024640.3||T),DOWNSTREAM(MODIFIER||1255||110|C1orf122|protein_coding|CODING|NM_198446.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs473186 -0.453602 0.48 2 753 3811 MODIFIER 11 CODING MTF1 A protein_coding NM_005955.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38276997 G A 0 228 0 0.062 0.2095 0.2075 0.2619 0.2793 0.2843 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 69 0,0,37,28 UTR_3_PRIME(MODIFIER||3811||753|MTF1|protein_coding|CODING|NM_005955.2|11|A),UPSTREAM(MODIFIER||3132||279|YRDC|protein_coding|CODING|NM_024640.3||A),DOWNSTREAM(MODIFIER||1871||110|C1orf122|protein_coding|CODING|NM_198446.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs28411034 -0.693147 0.00433153 69 753 821 MODIFIER 11 CODING MTF1 C protein_coding NM_005955.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38279987 T C 0 36.3 0 0.0605 0.1927 0.1513 0.2649 0.2356 0.2822 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||821||753|MTF1|protein_coding|CODING|NM_005955.2|11|C),DOWNSTREAM(MODIFIER||4861||110|C1orf122|protein_coding|CODING|NM_198446.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3748682 -0.453602 0.66 2 T390 753 acA/acG LOW 8 SILENT CODING MTF1 C protein_coding NM_005955.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38289383 T C 0 228 0 0.0628 0.2115 0.2104 0.2639 0.2843 0.2843 0.10463 0.227049 0.289767 2 1058 31820 2314 2378 2514 19101 257 4198 2 10250 119846 11376 8580 6494 66046 894 16206 1 0 . 0 . 118 1,0,86,17 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T390|753|MTF1|protein_coding|CODING|NM_005955.2|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12751325 -0.693147 0.0589381 118 913 1333 MODIFIER 24 CODING INPP5B G protein_coding NM_005540.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38326654 A G 0 42.3 0 0.3003 0.5252 0.6009 0.4792 0.7266 0.6155 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1333||913|INPP5B|protein_coding|CODING|NM_005540.2|24|G),UPSTREAM(MODIFIER||1362||753|MTF1|protein_coding|CODING|NM_005955.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1136990 -0.453602 0.5 2 913 401 MODIFIER 24 CODING INPP5B T protein_coding NM_005540.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38327586 C T 0 125 0 0.8374 0.9555 0.9885 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||401||913|INPP5B|protein_coding|CODING|NM_005540.2|24|T),UPSTREAM(MODIFIER||2294||753|MTF1|protein_coding|CODING|NM_005955.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9660231 -0.636426 0.610244 7 913 5 MODIFIER 24 CODING INPP5B T protein_coding NM_005540.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38327982 G T 0 228 0 0.3011 0.5256 0.6009 0.4802 0.7266 0.6155 0.384368 0.603702 0.703609 2 3553 77243 6414 4311 5208 47427 561 9769 2 9776 120594 11536 8610 6612 66660 898 16502 0 . 0 . 0 73 0,0,46,24 UTR_3_PRIME(MODIFIER||5||913|INPP5B|protein_coding|CODING|NM_005540.2|24|T),UPSTREAM(MODIFIER||2690||753|MTF1|protein_coding|CODING|NM_005955.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3843 -0.693147 0.314817 73 M665T 913 aTg/aCg MODERATE 19 MISSENSE CODING INPP5B G protein_coding NM_005540.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38338795 A G 0 228 0 0.298 0.5236 0.5994 0.4752 0.7266 0.6155 0.378459 0.602778 0.703686 2 3536 77292 6432 4305 5209 47475 561 9774 2 9802 120754 11574 8620 6610 66738 900 16510 0 . 0 . 0 78 0,0,25,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M665T|913|INPP5B|protein_coding|CODING|NM_005540.2|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11488569 -0.693147 0.00556839 78 H45 913 caC/caT LOW 3 SILENT CODING INPP5B A protein_coding NM_005540.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38411445 G A 0 222 0 0.0431 0.2019 0.2262 0.2401 0.3181 0.2403 0.0844562 0.234417 0.308701 1 830 34282 2588 1997 2904 21978 247 3738 2 9696 119946 11558 8562 6600 66246 890 16394 0.441275 0 . 0 . 123 19,31,23,41 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H45|913|INPP5B|protein_coding|CODING|NM_005540.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.138042 rs871524 -0.693147 0.0272046 123 501 270 MODIFIER 17 CODING SF3A3 A protein_coding NM_006802.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38423588 G A 0 39.3 0 0.9766 0.9229 0.9121 1 0.8469 0.8569 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||270||501|SF3A3|protein_coding|CODING|NM_006802.2|17|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1050257 -0.453602 0.74 2 501 5 MODIFIER 17 CODING SF3A3 C protein_coding NM_006802.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38423853 G C 0 228 0 0.9766 0.9221 0.9121 1 0.8479 0.8517 0.963913 0.896817 0.862442 2 10063 107920 10902 8643 6170 57252 803 14087 2 10402 121382 11576 8654 6614 66722 908 16506 0 . 0 . 0 99 0,0,64,24 UTR_3_PRIME(MODIFIER||5||501|SF3A3|protein_coding|CODING|NM_006802.2|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9293 -0.693147 0.0811162 99 280 179 MODIFIER 6 CODING FHL3 A protein_coding NM_004468.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38462898 T A 0 228 0 0.8411 0.9361 0.9683 0.998 0.9533 0.9601 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 49 0,0,40,4 UTR_3_PRIME(MODIFIER||179||280|FHL3|protein_coding|CODING|NM_004468.4|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4274021 -0.693146 0.462086 49 280 172 MODIFIER 6 CODING FHL3 G protein_coding NM_004468.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38462905 C G 0 228 0 0.8411 0.9371 0.9683 0.998 0.9533 0.9652 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,42,5 UTR_3_PRIME(MODIFIER||172||280|FHL3|protein_coding|CODING|NM_004468.4|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12724533 -0.693147 0.575938 51 280 LOW 3 CODING FHL3 G protein_coding NM_004468.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38464639 C G 0 228 0 0.9924 0.998 1 1 1 1 0.99478 0.998232 1 2 10319 121195 11569 8650 6612 66633 906 16506 2 10382 121260 11570 8650 6612 66634 906 16506 0 . 0 . 0 43 0,0,29,12 SPLICE_SITE_REGION+INTRON(LOW||||280|FHL3|protein_coding|CODING|NM_004468.4|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4570384 -0.693145 0.00906277 43 451 906 MODIFIER 1 CODING POU3F1 G protein_coding NM_002699.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 38510154 A G 0 222 0 0.2602 0.3045 0.3386 0.7202 0.0417 0.182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.914842 0 . 0 . 134 36,28,31,21 UTR_3_PRIME(MODIFIER||906||451|POU3F1|protein_coding|CODING|NM_002699.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.868892 rs34860389 -0.693147 0.115998 134 103 642 MODIFIER 5 CODING MYCBP T protein_coding NM_012333.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39329700 G T 0 228 0 0.3298 0.2426 0.1902 0.3115 0.1272 0.2096 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 78 1,0,54,12 UTR_3_PRIME(MODIFIER||642||103|MYCBP|protein_coding|CODING|NM_012333.4|5|T),UPSTREAM(MODIFIER||4205||399|RRAGC|protein_coding|CODING|NM_022157.3||T),INTRAGENIC(MODIFIER|||||GJA9-MYCBP||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs11538784 -0.693147 0.0259039 78 383 517 MODIFIER 8 CODING RHBDL2 A protein_coding NM_001304746.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39351659 G A 0 167 0 0.9939 0.8744 0.9179 0.6984 0.9662 0.7689 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,18 UTR_3_PRIME(MODIFIER||517||383|RHBDL2|protein_coding|CODING|NM_001304746.1|8|A),UPSTREAM(MODIFIER||4361||515|GJA9|protein_coding|CODING|NM_030772.4||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9439088 -0.691153 0.166034 18 192 47 MODIFIER 1 CODING AKIRIN1 T protein_coding NM_024595.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39457006 C T 0 92 0 0.6248 0.6252 0.5865 0.7589 0.4414 0.7045 0 . 0 2 3 376 1 14 0 33 5 320 2 4 484 2 16 0 58 8 396 0 . 0 . 0 4 0,0,1,2 UTR_5_PRIME(MODIFIER||47||192|AKIRIN1|protein_coding|CODING|NM_024595.2|1|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12043492 -0.511536 0.862672 4 Q257 5430 caG/caA LOW 7 SILENT CODING MACF1 A protein_coding NM_012090.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39748921 G A 0 222 0 0.2685 0.594 0.6657 0.6498 0.7167 0.7996 0.354063 0.57781 0.692442 1 3518 82720 8161 5493 4931 46934 634 13049 2 10398 121324 11544 8642 6614 66714 906 16506 0.60223 0 . 0 . 108 20,24,36,18 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q257|5430|MACF1|protein_coding|CODING|NM_012090.5|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0471855 rs2275188 -0.693147 0.271422 108 1427 819 MODIFIER 1 CODING KIAA0754 C protein_coding NM_015038.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39881040 G C 0 63 0 0.7315 0.4044 0.3329 0.3462 0.2813 0.1994 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.934707 0 . 0 . 23 0,16,0,7 UTR_3_PRIME(MODIFIER||819||1427|KIAA0754|protein_coding|CODING|NM_015038.1|1|C),INTRON(MODIFIER||||5430|MACF1|protein_coding|CODING|NM_012090.5|52|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.799943 rs1180375 -0.636426 0.157598 23 A4350T 5430 Gcc/Acc MODERATE 73 MISSENSE CODING MACF1 A protein_coding NM_012090.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39908506 G A 0 222 0 0.5106 0.344 0.3156 0.3462 0.2823 0.2004 0.469587 0.361833 0.306628 1 4865 36160 3233 3088 1681 19581 266 3446 2 10324 120220 11422 8556 6572 66066 902 16378 0.993164 0 . 0 . 55 11,19,8,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4350T|5430|MACF1|protein_coding|CODING|NM_012090.5|73|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.131994 rs587404 -0.691153 0.252792 55 M84V 402 Atg/Gtg MODERATE 1 MISSENSE CODING BMP8A G protein_coding NM_181809.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39957913 A G 0 61 0 0.2897 0.6723 0.8069 0.6825 0.8887 0.8609 0.523977 0.790334 0.918019 1 2330 82553 8578 4973 4249 48373 581 13469 2 5176 96686 10158 7342 4808 53332 674 15196 1 0 . 0 . 4 1,0,2,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M84V|402|BMP8A|protein_coding|CODING|NM_181809.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 49 0 1 1 0 1 rs4660269 -0.511536 0.764235 4 M106V 402 Atg/Gtg MODERATE 1 MISSENSE CODING BMP8A G protein_coding NM_181809.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39957979 A G 0 15.2 0 0.1815 0.0607 0.0259 0.0179 0.0199 0.0082 0.0905536 0.0367676 0.0101311 1 931 1852 139 44 10 611 13 104 2 6478 100184 10688 7846 5152 54598 694 14728 1 0 . 0 . 5 2,1,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M106V|402|BMP8A|protein_coding|CODING|NM_181809.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 1 rs76039610 -0.379885 0 5 D224 402 gaC/gaT LOW 3 SILENT CODING BMP8A T protein_coding NM_181809.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39977575 C T 0 76 0 . 0 . 0 . 0 . 0 . 1 425 2841 150 205 48 1574 30 409 2 802 4226 210 320 70 2244 46 534 0.917201 0 . 0 . 20 0,10,0,10 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D224|402|BMP8A|protein_coding|CODING|NM_181809.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.931063 0 . 0.772706 rs200415763 -0.670168 0.134903 20 R293H 402 cGc/cAc MODERATE 5 MISSENSE CODING BMP8A A protein_coding NM_181809.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39988084 G A 0 48.6 0 . 0 . 0 . 0 . 0 . 1 2367 52839 5175 3379 2672 28248 394 10604 2 9670 111850 10624 8012 5948 61198 836 15562 0.103097 0 . 0 COSM1599867 84 42,15,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R293H|402|BMP8A|protein_coding|CODING|NM_181809.3|5|A),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.0162988 0.627971 0 0.234994 rs6525 -0.692067 0.00142389 84 402 4 MODIFIER 7 CODING BMP8A C protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39991474 A C 0 222 0 0.0756 0.0919 0.072 0.0218 0.2117 0.0767 0.00544712 0.0193757 0.0265116 1 863 16632 763 107 1369 11907 137 1486 2 10388 121252 11568 8644 6606 66634 906 16506 0.724767 0 . 0 . 65 12,23,11,13 UTR_3_PRIME(MODIFIER||4||402|BMP8A|protein_coding|CODING|NM_181809.3|7|C),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.964198 0.984155 0 0.999524 rs11583829 -0.692831 0.0261716 65 402 5 MODIFIER 7 CODING BMP8A A protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39991475 G A 0 222 0 0.0749 0.0917 0.072 0.0218 0.2117 0.0767 0 . 0 1 861 16614 763 107 1370 11892 137 1484 2 10388 121250 11568 8644 6606 66632 906 16506 0.912712 0 . 0 . 66 12,24,11,12 UTR_3_PRIME(MODIFIER||5||402|BMP8A|protein_coding|CODING|NM_181809.3|7|A),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.961625 0.984155 0 0.997557 rs2230006 -0.692717 0.0398281 66 402 118 MODIFIER 7 CODING BMP8A T protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39991588 G T 0 114 0 0.3601 0.3387 0.3617 0.4405 0.3678 0.1585 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.7613 0 . 0 COSN163050 23 1,11,0,11 UTR_3_PRIME(MODIFIER||118||402|BMP8A|protein_coding|CODING|NM_181809.3|7|T),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.923099 rs3738676 -0.676189 0.652386 23 402 1408 MODIFIER 7 CODING BMP8A G protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39992878 T G 0 36.3 0 0.329 0.5673 0.5879 0.5704 0.6402 0.7965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1408||402|BMP8A|protein_coding|CODING|NM_181809.3|7|G),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1180342 -0.453602 0.98 2 402 3020 MODIFIER 7 CODING BMP8A C protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39994490 T C 0 70 0 0.7912 0.9369 0.964 1 0.9881 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||3020||402|BMP8A|protein_coding|CODING|NM_181809.3|7|C),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs941281 -0.453602 0.44 3 402 3075 MODIFIER 7 CODING BMP8A T protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39994545 A T 0 32.6 0 0.2693 0.5172 0.549 0.5526 0.5328 0.7771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3075||402|BMP8A|protein_coding|CODING|NM_181809.3|7|T),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs755247 -0.379885 0 2 402 3076 MODIFIER 7 CODING BMP8A T protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39994546 A T 0 32.6 0 0.7912 0.9369 0.964 1 0.9881 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3076||402|BMP8A|protein_coding|CODING|NM_181809.3|7|T),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1727104 -0.379885 0 2 402 3640 MODIFIER 7 CODING BMP8A T protein_coding NM_181809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 39995110 C T 0 63 0 0.357 0.7752 0.8761 0.999 0.9046 0.9049 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||3640||402|BMP8A|protein_coding|CODING|NM_181809.3|7|T),INTRAGENIC(MODIFIER|||||PPIEL||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs755248 -0.453602 0.22 3 Q400 660 caG/caA LOW 8 SILENT CODING PABPC4 T protein_coding NM_001135653.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40030823 C T 0 222 0 0.0061 0.0373 0.0418 0.0179 0.1083 0.0235 0.018611 0.0652776 0.089186 1 158 7580 373 57 607 5938 53 394 2 10390 121308 11568 8650 6608 66676 908 16508 0.994198 0 . 0 . 113 35,30,20,17 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q400|660|PABPC4|protein_coding|CODING|NM_001135653.1|8|T),INTRAGENIC(MODIFIER|||||LOC101929516||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.647317 rs12127094 -0.693141 0.0451869 113 328 90 MODIFIER 5 CODING HEYL C protein_coding NM_014571.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40092089 T C 0 167 0 0.8888 0.9539 0.9712 0.999 0.9791 0.9571 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,20,0 UTR_3_PRIME(MODIFIER||90||328|HEYL|protein_coding|CODING|NM_014571.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2695320 -0.692067 0.0222219 20 H47R 328 cAc/cGc MODERATE 2 MISSENSE CODING HEYL C protein_coding NM_014571.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40098328 T C 0 228 0 1 0.9892 0.9942 0.999 0.9891 0.9611 0.998184 0.992542 0.989651 2 10386 120017 11542 8653 6600 66015 900 15921 2 10406 121390 11578 8654 6614 66724 908 16506 0 . 0 . 0 62 0,0,23,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H47R|328|HEYL|protein_coding|CODING|NM_014571.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs784625 -0.693147 0.028176 62 S158 368 agC/agT LOW 4 SILENT CODING NT5C1A A protein_coding NM_032526.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40129066 G A 0 222 0 0.003 0.0409 0.0216 0.1101 0.0437 0.0317 0.0106673 0.0310626 0.0415116 1 89 5173 386 987 362 2807 30 512 2 10384 120980 11528 8628 6510 66538 904 16488 0.931499 0 . 0 . 70 4,16,20,26 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S158|368|NT5C1A|protein_coding|CODING|NM_032526.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.828243 rs4660340 -0.693147 0.60616 70 191 3722 MODIFIER 5 CODING HPCAL4 C protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40144486 A C 0 9.7 0 0.438 0.5004 0.585 0.5466 0.4732 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3722||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1062103 -0.379885 0 1 191 3390 MODIFIER 5 CODING HPCAL4 T protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40144818 A T 0 9.7 0 0.466 0.3518 0.2392 0.2708 0.3529 0.3599 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3390||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10839 -0.379885 0 1 191 2592 MODIFIER 5 CODING HPCAL4 C protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40145616 A C 0 112 0 0.0061 0.2192 0.2983 0.4732 0.0915 0.3211 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.97757 0 . 0 . 45 23,4,11,1 UTR_3_PRIME(MODIFIER||2592||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.25281 rs12039225 -0.680642 0.213703 45 191 2358 MODIFIER 5 CODING HPCAL4 C protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40145850 G C 0 208 0 0.0053 0.0585 0.0461 0.1042 0.0924 0.0573 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.894613 0 . 0 . 29 2,9,3,15 UTR_3_PRIME(MODIFIER||2358||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.168332 rs17560858,rs386543958 -0.691153 0.56961 29 191 1955 MODIFIER 5 CODING HPCAL4 C protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40146253 T C 0 57 0 0.9191 0.8566 0.8271 0.8175 0.825 0.8661 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||1955||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs784629 -0.511536 0.868052 3 191 1791 MODIFIER 5 CODING HPCAL4 T protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40146417 G T 0 41.3 0 0.4365 0.5028 0.585 0.5466 0.4742 0.5184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.574341 0 . 0 . 6 3,0,3,0 UTR_3_PRIME(MODIFIER||1791||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 0 . 0.574341 rs736009 -0.511536 0.431015 6 191 391 MODIFIER 5 CODING HPCAL4 A protein_coding NM_001282396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40147817 C A 0 222 0 0.0053 0.0583 0.0461 0.1032 0.0924 0.0573 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.775072 0 . 0 . 54 4,18,5,21 UTR_3_PRIME(MODIFIER||391||191|HPCAL4|protein_coding|CODING|NM_001282396.1|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.988031 rs41312032 -0.692976 0.00441863 54 R115 191 cgC/cgA LOW 4 SILENT CODING HPCAL4 T protein_coding NM_001282396.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40149642 G T 0 228 0 0.9191 0.8562 0.8256 0.8165 0.825 0.8661 0.875795 0.829975 0.806512 2 9135 99895 9664 6833 5444 53588 773 14458 2 10346 120742 11538 8612 6604 66232 906 16504 0 . 0 . COSM426246 95 0,0,68,18 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R115|191|HPCAL4|protein_coding|CODING|NM_001282396.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs784634 -0.693147 0.195933 95 S40 191 agC/agT LOW 3 SILENT CODING HPCAL4 A protein_coding NM_001282396.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40150156 G A 0 222 0 0.4811 0.3558 0.2406 0.2698 0.3519 0.3609 0.458012 0.374673 0.331977 1 4748 40103 2428 2421 2270 21598 304 6334 2 10254 118208 11294 8514 6238 65252 876 15780 0.640568 0 . 0 COSM146475 89 28,8,26,13 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S40|191|HPCAL4|protein_coding|CODING|NM_001282396.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.944046 rs9662128 -0.693144 0.234069 89 S276T 402 aGc/aCc MODERATE 4 MISSENSE CODING BMP8B G protein_coding NM_001720.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40230336 C G 0 174 0 . 0 . 0 . 0 . 0 . 1 3870 41052 3762 3007 1873 20802 289 7449 2 10218 120168 11492 8570 6492 66022 898 16476 0.911365 0 . 0 . 155 68,34,26,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S276T|402|BMP8B|protein_coding|CODING|NM_001720.3|4|G),DOWNSTREAM(MODIFIER||750||314|PPIE|protein_coding|CODING|NM_001195007.1||G),DOWNSTREAM(MODIFIER||4861||517|OXCT2|protein_coding|CODING|NM_022120.1||G) 0 0.5 1 0 . 0 . 0 1 0 38 0 0.973093 4.90296e-05 0 0.337486 rs179472,rs76376226 -0.693145 0.00600252 155 517 43 MODIFIER 1 CODING OXCT2 T protein_coding NM_022120.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40235331 C T 0 43.2 0 . 0 . 0 . 0 . 0 . 1 96 549 47 50 9 314 5 28 2 2568 20906 1664 1436 832 12442 160 1804 0.695007 0 . 0 . 35 17,4,11,0 UTR_3_PRIME(MODIFIER||43||517|OXCT2|protein_coding|CODING|NM_022120.1|1|T),INTRON(MODIFIER||||402|BMP8B|protein_coding|CODING|NM_001720.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 46 0 5.15335e-05 0.98031 0 0.435454 rs144237350 -0.676189 0.00331261 35 D494N 517 Gac/Aac MODERATE 1 MISSENSE CODING OXCT2 T protein_coding NM_022120.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40235448 C T 0 104 0 . 0 . 0 . 0 . 0 . 1 875 5293 420 903 227 2502 38 328 2 7888 98178 9292 6640 5130 54430 712 14086 0.995683 0 . 0 . 128 61,18,24,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D494N|517|OXCT2|protein_coding|CODING|NM_022120.1|1|T),INTRON(MODIFIER||||402|BMP8B|protein_coding|CODING|NM_001720.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 46 0 3.18437e-09 0.97349 0 3.75049e-05 rs150795467 -0.69311 0.00282122 128 E480G 517 gAg/gGg MODERATE 1 MISSENSE CODING OXCT2 C protein_coding NM_022120.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40235489 T C 0 26.6 0 . 0 . 0 . 0 . 0 . 1 288 2344 71 431 163 1078 16 297 2 9090 106504 10118 7282 5510 59126 804 14574 0.00936457 0 . 0 . 137 61,29,5,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E480G|517|OXCT2|protein_coding|CODING|NM_022120.1|1|C),INTRON(MODIFIER||||402|BMP8B|protein_coding|CODING|NM_001720.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 49 0 5.01783e-18 0.000338334 0 0.48975 rs77857664 -0.693144 0.514333 137 F108 402 ttC/ttT LOW 1 SILENT CODING BMP8B A protein_coding NM_001720.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40253834 G A 0 22.2 0 0.0053 0.0439 0.0115 0.1171 0.0378 0.0501 0 . 0 1 57 3899 145 1035 185 1737 27 713 2 6590 101068 10702 7884 5344 55148 692 14708 0.833333 0 . 0 . 5 1,2,1,1 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F108|402|BMP8B|protein_coding|CODING|NM_001720.3|1|A) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.5 0.5 0 0 rs140337041 -0.453602 0.26 5 R97Q 402 cGg/cAg MODERATE 1 MISSENSE CODING BMP8B T protein_coding NM_001720.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40253868 C T 0 3.4 0 0.0053 0.0439 0.0115 0.1171 0.0378 0.0501 0.000968992 0.00573614 0.00807218 1 42 3015 113 773 125 1352 19 591 2 6272 96674 10294 7256 4920 52628 658 14646 0.5 0 . 0 . 5 0,3,0,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R97Q|402|BMP8B|protein_coding|CODING|NM_001720.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.5 0 . 0.333333 rs191429577 -0.453602 0.96 5 467 518 MODIFIER 11 CODING TRIT1 C protein_coding NM_017646.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40306898 T C 0 138 0 0.6157 0.5086 0.4107 0.5933 0.3946 0.4632 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||518||467|TRIT1|protein_coding|CODING|NM_017646.5|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7315 -0.616816 0.612255 6 I366 467 atC/atT LOW 9 SILENT CODING TRIT1 A protein_coding NM_017646.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40310221 G A 0 222 0 0.0023 0.0302 0.0072 0.1071 0.0268 0.0082 0.00590104 0.0156851 0.0206977 1 46 2966 89 952 209 1492 23 155 2 10212 120434 11470 8624 6594 66238 896 16400 0.804057 0 . 0 COSM1342577 88 18,19,21,20 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I366|467|TRIT1|protein_coding|CODING|NM_017646.5|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.2434 rs16826617 -0.693145 0.2199 88 F202L 467 ttT/ttA MODERATE 5 MISSENSE CODING TRIT1 T protein_coding NM_017646.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40315888 A T 0 222 0 0.2118 0.1711 0.1643 0.2946 0.0616 0.1063 0.170449 0.0898816 0.0486047 1 1780 12621 2376 2504 665 3732 95 1469 2 10402 121296 11550 8626 6614 66690 906 16508 0.829972 0 . 0 COSM146476 114 35,24,27,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F202L|467|TRIT1|protein_coding|CODING|NM_017646.5|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.48376 rs3738671 -0.693147 0.284001 114 P11 467 ccC/ccT LOW 1 SILENT CODING TRIT1 A protein_coding NM_017646.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40349131 G A 0 228 0 0.6157 0.5086 0.4107 0.5933 0.3946 0.4632 0.566954 0.451938 0.392998 2 5626 52036 5520 5059 2548 25590 359 7334 2 9768 116872 11282 8500 6090 64078 848 16306 1 0 . 0 COSM426251 209 0,1,57,133 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P11|467|TRIT1|protein_coding|CODING|NM_017646.5|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3845570,rs386498482 -0.693147 0.0982806 209 T392S 394 aCt/aGt MODERATE 3 MISSENSE CODING MYCL C protein_coding NM_001033082.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40363054 G C 0 228 0 0.9962 0.9357 0.9035 1 0.8917 0.8558 0.974807 0.90366 0.867209 2 10155 106116 10009 8647 5892 57782 781 12850 2 10388 119708 11566 8652 6608 66276 892 15326 0 . 0 . 0 33 0,0,16,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T392S|394|MYCL|protein_coding|CODING|NM_001033082.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3134614 -0.69311 0.334937 33 C229G 475 Tgt/Ggt MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533266 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9796 120594 11564 8618 6610 66652 896 16458 2 9796 120594 11564 8618 6610 66652 896 16458 0 . 0 . 0 56 0,0,23,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C229G|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs11207440 -0.693147 0.161227 56 C236G 475 Tgc/Ggc MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533287 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9778 120444 11526 8620 6586 66586 894 16454 2 9778 120444 11526 8620 6586 66586 894 16454 0 . 0 . 0 45 0,0,20,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C236G|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6665926 -0.693146 0.195596 45 I245S 475 aTt/aGt MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533315 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9744 120358 11510 8614 6580 66540 894 16476 2 9744 120358 11510 8614 6580 66540 894 16476 0 . 0 . 0 44 0,0,21,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I245S|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6665933 -0.693145 0.674054 44 C247G 475 Tgc/Ggc MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533320 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9748 120364 11512 8612 6574 66550 894 16474 2 9748 120364 11512 8612 6574 66550 894 16474 0 . 0 . 0 42 0,0,20,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C247G|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6665936 -0.693144 0.546059 42 Y249D 475 Tat/Gat MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533326 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9748 120402 11516 8612 6578 66576 894 16478 2 9748 120402 11516 8612 6578 66576 894 16478 0 . 0 . 0 45 0,0,23,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y249D|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6665937 -0.693146 0.515213 45 S256A 475 Tca/Gca MODERATE 8 MISSENSE CODING CAP1 G protein_coding NM_001105530.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40533347 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 9774 120540 11544 8616 6588 66644 896 16478 2 9774 120540 11544 8616 6588 66644 896 16478 0 . 0 . 0 54 0,0,32,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S256A|475|CAP1|protein_coding|CODING|NM_001105530.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6665944 -0.693147 0.533673 54 306 505 MODIFIER 9 CODING PPT1 C protein_coding NM_000310.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40539228 G C 0 39.3 0 0.5741 0.6607 0.6729 0.6329 0.7714 0.684 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||505||306|PPT1|protein_coding|CODING|NM_000310.3|9|C),DOWNSTREAM(MODIFIER||907||475|CAP1|protein_coding|CODING|NM_001105530.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1126972 -0.453602 0.44 2 306 83 MODIFIER 1 CODING PPT1 C protein_coding NM_000310.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40562993 T C 0 7.3 0 0.7269 0.8327 0.7824 0.881 0.8897 0.9029 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 11 0,9,1,1 UTR_5_PRIME(MODIFIER||83||306|PPT1|protein_coding|CODING|NM_000310.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.888889 rs6600313 -0.453602 0.1 11 S1022 1914 tcC/tcT LOW 8 SILENT CODING RLF T protein_coding NM_012421.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40703440 C T 0 222 0 0.0015 0.0288 0.0014 0.1329 0.001 0.0061 0.00113482 0.00115331 0.00116279 1 10 1472 3 1314 0 74 7 64 2 10154 120722 11518 8598 6610 66484 898 16460 0.996136 0 . 0 COSM146479 65 14,22,7,18 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1022|1914|RLF|protein_coding|CODING|NM_012421.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987074 rs2235986 -0.692914 0.375051 65 E1784D 1914 gaA/gaT MODERATE 8 MISSENSE CODING RLF T protein_coding NM_012421.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40705726 A T 0 155 0 0.2542 0.1484 0.1671 0.0625 0.1819 0.046 0.22719 0.209057 0.199767 1 2466 21278 1938 414 1652 13471 147 1190 2 10028 120264 11528 8626 6606 66128 900 16448 0.630255 0 . 0 COSM426263 45 19,7,14,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E1784D|1914|RLF|protein_coding|CODING|NM_012421.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.197924 rs10889205 -0.688148 0.797064 45 Q326R 689 cAg/cGg MODERATE 19 MISSENSE CODING COL9A2 C protein_coding NM_001852.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40773149 T C 0 228 0 0.4183 0.3974 0.4121 0.6171 0.2157 0.319 0.403314 0.278102 0.213953 2 4243 36242 5704 5121 1542 14550 220 4862 2 10236 119474 11360 8566 6280 65840 876 16316 0 . 0 . 0 159 0,0,64,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q326R|689|COL9A2|protein_coding|CODING|NM_001852.3|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2228564 -0.693147 0.000586534 159 S223 429 tcC/tcG LOW 7 SILENT CODING SMAP2 G protein_coding NM_022733.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40881041 C G 0 228 0 0.9924 0.9481 0.9222 0.9772 0.8847 0.9417 0.975261 0.915347 0.884651 2 10190 109001 10637 8372 5196 58593 827 15186 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 81 0,0,27,49 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S223|429|SMAP2|protein_coding|CODING|NM_022733.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs209606 -0.693147 0.167973 81 C115Y 534 tGt/tAt MODERATE 4 MISSENSE CODING ZFP69B A protein_coding NM_023070.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40923019 G A 0 222 0 0.0212 0.2216 0.3516 0.2986 0.2366 0.3057 0.0630958 0.165385 0.217791 1 587 30575 4280 2546 1863 15632 257 5410 2 10348 120940 11466 8630 6600 66576 904 16416 0.909656 0 . 0 . 78 33,8,22,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C115Y|534|ZFP69B|protein_coding|CODING|NM_023070.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994878 rs2272994 -0.693079 0.636446 78 526 7 MODIFIER 6 CODING ZFP69 G protein_coding NM_198494.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40961738 A G 0 222 0 0.0008 0.01877 0.0058 0.0774 0.001 0.0102 0.00023663 0.000549451 0.000704722 1 4 894 8 673 9 83 11 106 2 9378 110826 11456 8518 6604 63314 804 10752 0.950235 0 . 0 . 116 36,31,25,19 UTR_3_PRIME(MODIFIER||7||526|ZFP69|protein_coding|CODING|NM_198494.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.49753 rs75198900 -0.693146 0.581379 116 G172V 373 gGg/gTg MODERATE 3 MISSENSE CODING EXO5 T protein_coding NM_022774.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40980731 G T 0 222 0 0.6997 0.5421 0.536 0.5 0.3757 0.5481 0.637994 0.461864 0.371628 1 6782 53905 6830 4275 2266 24648 425 8679 2 10390 121288 11570 8634 6612 66666 908 16508 0.679255 0 . 0 . 76 24,18,22,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G172V|373|EXO5|protein_coding|CODING|NM_022774.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.655264 rs11208299 -0.693097 0.70937 76 373 704 MODIFIER 3 CODING EXO5 A protein_coding NM_022774.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 40982042 G A 0 120 0 0.1989 0.2742 0.3429 0.4504 0.1123 0.3119 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.763202 0 . 0 . 28 0,14,0,14 UTR_3_PRIME(MODIFIER||704||373|EXO5|protein_coding|CODING|NM_022774.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.962712 rs7522878 -0.686358 0.487266 28 T253 378 acT/acC LOW 5 SILENT CODING ZNF684 C protein_coding NM_152373.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41012754 T C 0 222 0 0.0008 0.015775 0.0058 0.0635 0 0.0102 0.000453926 0.000538213 0.000581395 1 5 814 10 603 5 59 5 127 2 10384 121272 11564 8618 6612 66686 906 16502 0.871596 0 . 0 . 151 38,29,46,20 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T253|378|ZNF684|protein_coding|CODING|NM_152373.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82115 rs80222621 -0.693147 0.331398 151 S340 378 tcC/tcT LOW 5 SILENT CODING ZNF684 T protein_coding NM_152373.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41013015 C T 0 222 0 0.1082 0.2492 0.3372 0.4514 0.1103 0.3119 0.112347 0.105336 0.101744 1 1157 22347 4691 3812 894 7328 140 4325 2 10292 121018 11544 8644 6612 66544 904 16478 0.405773 0 . 0 . 56 10,17,10,13 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S340|378|ZNF684|protein_coding|CODING|NM_152373.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.975257 0.980583 0 0.984772 rs2297755 -0.692717 0.575388 56 308 4946 MODIFIER 8 CODING RIMS3 A protein_coding NM_014747.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41087243 T A 0 6.3 0 0 0.0095847 0 0.0397 0 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4946||308|RIMS3|protein_coding|CODING|NM_014747.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs77231024 -0.379885 0 1 308 3984 MODIFIER 8 CODING RIMS3 A protein_coding NM_014747.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41088205 G A 0 74 0 0.1067 0.0938 0.0735 0.0367 0.1352 0.1074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.695312 0 . 0 . 14 7,0,6,0 UTR_3_PRIME(MODIFIER||3984||308|RIMS3|protein_coding|CODING|NM_014747.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.143152 rs61779210 -0.616816 0.387746 14 308 3612 MODIFIER 8 CODING RIMS3 T protein_coding NM_014747.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41088577 C T 0 222 0 0.1059 0.0937 0.0735 0.0367 0.1352 0.1074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.984811 0 . 0 . 219 72,53,33,36 UTR_3_PRIME(MODIFIER||3612||308|RIMS3|protein_coding|CODING|NM_014747.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.874359 rs17412556 -0.693147 0.719084 219 308 1939 MODIFIER 8 CODING RIMS3 G protein_coding NM_014747.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41090250 A G 0 72 0 0.7065 0.4357 0.3963 0.1825 0.4493 0.3446 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.356607 0 . 0 . 11 5,1,5,0 UTR_3_PRIME(MODIFIER||1939||308|RIMS3|protein_coding|CODING|NM_014747.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.8618 rs7520333 -0.590765 0.413797 11 308 1062 MODIFIER 8 CODING RIMS3 C protein_coding NM_014747.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41091127 T C 0 222 0 0.8979 0.7013 0.6772 0.5397 0.7903 0.5276 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.938442 0 . 0 . 87 9,36,3,35 UTR_3_PRIME(MODIFIER||1062||308|RIMS3|protein_coding|CODING|NM_014747.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.942951 rs570671 -0.693143 0.137935 87 695 1022 MODIFIER 14 CODING KCNQ4 T protein_coding NM_004700.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41305217 A T 0 64 0 0.8971 0.854 0.8372 0.9256 0.8479 0.7403 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1022||695|KCNQ4|protein_coding|CODING|NM_004700.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4660470 -0.511536 0.490096 3 184 359 MODIFIER 1 CODING CITED4 G protein_coding NM_133467.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41326886 C G 0 222 0 0.1354 0.2256 0.3703 0.4901 0.0716 0.1309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.93448 0 . 0 . 70 22,12,18,7 UTR_3_PRIME(MODIFIER||359||184|CITED4|protein_coding|CODING|NM_133467.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.256774 rs12044255 -0.692914 0.767846 70 Q58R 184 cAa/cGa MODERATE 1 MISSENSE CODING CITED4 C protein_coding NM_133467.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41327627 T C 0 24.4 0 0.1354 0.2258 0.3703 0.4901 0.0716 0.1319 0 . 0 2 1 117 1 5 0 5 1 104 2 8 716 6 10 0 46 8 638 0 . 0 . 0 2 0,0,0,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q58R|184|CITED4|protein_coding|CODING|NM_133467.2|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs116868841 -0.453602 0.26 2 R57P 184 cGc/cCc MODERATE 1 MISSENSE CODING CITED4 G protein_coding NM_133467.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41327630 C G 0 9.7 0 0.1354 0.2258 0.3703 0.4901 0.0716 0.1319 0 . 0 1 1 115 1 5 0 4 1 103 2 8 664 6 10 0 32 6 602 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R57P|184|CITED4|protein_coding|CODING|NM_133467.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs118006907 -0.379885 0 1 184 72 MODIFIER 1 CODING CITED4 A protein_coding NM_133467.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41327871 C A 0 32.3 0 0.1354 0.2258 0.3703 0.4901 0.0716 0.1319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.824834 0 . 0 . 13 7,0,3,0 UTR_5_PRIME(MODIFIER||72||184|CITED4|protein_coding|CODING|NM_133467.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.916482 0 . 0.916482 rs117112421 -0.511536 0.724364 13 184 74 MODIFIER 1 CODING CITED4 C protein_coding NM_133467.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41327873 G C 0 201 0 0.8457 0.6939 0.7061 0.7847 0.4573 0.6299 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,9,0 UTR_5_PRIME(MODIFIER||74||184|CITED4|protein_coding|CODING|NM_133467.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12081504 -0.662043 0.687358 12 591 3840 MODIFIER 1 CODING CTPS1 A protein_coding NM_001905.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41445123 G A 0 25.9 0 0.2814 0.2073 0.1729 0.1151 0.2873 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,0,2 UTR_5_PRIME(MODIFIER||3840||591|CTPS1|protein_coding|CODING|NM_001905.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12729920 -0.453602 0.58 3 G71 492 ggC/ggT LOW 1 SILENT CODING FOXO6 T protein_coding NM_001291281.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41827815 C T 0 211 0 0 0.0023962 0 0.0119 0 0 0 . 0 1 0 4 0 3 0 0 0 1 2 400 11184 122 202 4 3234 134 7088 0.873014 0 . 0 . 44 25,0,14,2 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G71|492|FOXO6|protein_coding|CODING|NM_001291281.2|1|T|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.637571 rs373620122 -0.689466 0.155665 44 A475T 492 Gcc/Acc MODERATE 2 MISSENSE CODING FOXO6 A protein_coding NM_001291281.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41848296 G A 0 87 0 0.2171 0.3868 0.6037 0.3482 0.5089 0.3763 0 . 0 1 119 5686 93 121 227 2004 67 3055 2 440 12816 166 314 372 3880 144 7500 0.953497 0 . 0 . 21 7,5,7,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A475T|492|FOXO6|protein_coding|CODING|NM_001291281.2|2|A|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.304076 rs4359027 -0.651104 0.0450942 21 178 40 MODIFIER 1 CODING EDN2 C protein_coding NM_001956.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41950312 T C 0 228 0 0.8578 0.897 0.9481 0.9494 0.9493 0.8057 0.884814 0.922758 0.942197 2 2437 18722 441 653 66 8500 166 6459 2 2818 21188 482 682 68 9108 200 7830 1 0 . 0 . 167 0,1,35,118 UTR_5_PRIME(MODIFIER||40||178|EDN2|protein_coding|CODING|NM_001956.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2984691 -0.693147 0.0458406 167 2406 3924 MODIFIER 9 CODING HIVEP3 T protein_coding NM_024503.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41972198 A T 0 6.3 0 0.087 0.4659 0.6542 0.499 0.5835 0.6892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3924||2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2492082 -0.379885 0 1 2406 3027 MODIFIER 9 CODING HIVEP3 G protein_coding NM_024503.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41973095 A G 0 152 0 0.1165 0.527 0.7608 0.4861 0.7435 0.7352 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,2 UTR_3_PRIME(MODIFIER||3027||2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2810587 -0.590765 0.173131 6 2406 2214 MODIFIER 9 CODING HIVEP3 T protein_coding NM_024503.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41973908 C T 0 76 0 0.0817 0.4593 0.6527 0.4772 0.5805 0.6892 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||2214||2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1969749 -0.511536 0.748679 3 2406 973 MODIFIER 9 CODING HIVEP3 C protein_coding NM_024503.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41975149 G C 0 9.7 0 0.9584 0.9886 0.9971 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||973||2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2759258 -0.379885 0 1 2406 105 MODIFIER 9 CODING HIVEP3 T protein_coding NM_024503.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41976017 C T 0 228 0 0.3336 0.6274 0.6398 0.996 0.5358 0.7301 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 103 1,0,67,23 UTR_3_PRIME(MODIFIER||105||2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs678110 -0.693147 0.12708 103 T2339A 2406 Acc/Gcc MODERATE 9 MISSENSE CODING HIVEP3 C protein_coding NM_024503.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41976328 T C 0 159 0 0.8669 0.9631 0.9899 1 0.998 1 0.914598 0.969067 0.997181 2 1279 16696 603 560 119 6924 176 7035 2 1450 16882 606 560 120 6934 176 7036 0 . 0 . 0 16 0,0,0,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T2339A|2406|HIVEP3|protein_coding|CODING|NM_024503.4|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs9439043 -0.689466 0.501807 16 D2109A 2406 gAc/gCc MODERATE 8 MISSENSE CODING HIVEP3 G protein_coding NM_024503.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41978566 T G 0 228 0 . 0 . 0 . 0 0.986431 0.995403 1 2 5240 60463 4477 3314 2254 33254 452 11472 2 5314 60544 4484 3314 2254 33254 452 11472 0 . 0 . 0 182 0,0,87,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D2109A|2406|HIVEP3|protein_coding|CODING|NM_024503.4|8|G) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs2991344 -0.693147 0.871734 182 A2023P 2406 Gct/Cct MODERATE 8 MISSENSE CODING HIVEP3 G protein_coding NM_024503.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41978825 C G 0 228 0 0.9781 0.9942 1 1 1 1 0.984567 0.994772 1 2 9981 120513 11562 8650 6614 66292 902 16512 2 10140 120682 11572 8650 6614 66292 902 16512 0 . 0 . 0 60 0,0,20,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A2023P|2406|HIVEP3|protein_coding|CODING|NM_024503.4|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2483689 -0.693147 0.598534 60 A1912 2406 gcT/gcC LOW 8 SILENT CODING HIVEP3 G protein_coding NM_024503.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 41979156 A G 0 228 0 0.6604 0.7344 0.719 0.9931 0.5835 0.7342 0.654304 0.62167 0.604986 2 6069 77048 8231 8480 4073 38355 542 11298 2 9214 115216 11252 8524 6114 63100 842 16170 0 . 0 . COSM426277 52 0,0,24,26 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1912|2406|HIVEP3|protein_coding|CODING|NM_024503.4|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs615177 -0.693147 0.968228 52 Q1219 2406 caG/caA LOW 4 SILENT CODING HIVEP3 T protein_coding NM_024503.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42046812 C T 0 228 0 0.9175 0.9772 0.9942 1 0.999 1 0.938039 0.978933 0.999884 2 9547 110546 11459 8574 6614 64236 794 9322 2 10234 111276 11490 8574 6614 64244 798 9322 0 . 0 . 0 71 0,0,40,23 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1219|2406|HIVEP3|protein_coding|CODING|NM_024503.4|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2810565 -0.693147 0.469697 71 H575R 2406 cAc/cGc MODERATE 4 MISSENSE CODING HIVEP3 C protein_coding NM_024503.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42048745 T C 0 228 0 0.9569 0.988 0.9957 1 1 1 0.96709 0.988851 1 2 10053 121019 11558 8652 6614 66727 905 16510 2 10400 121398 11578 8654 6614 66732 908 16512 0 . 0 . 0 72 0,0,24,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H575R|2406|HIVEP3|protein_coding|CODING|NM_024503.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2810566 -0.693147 0.390362 72 S479 2406 agC/agT LOW 4 SILENT CODING HIVEP3 A protein_coding NM_024503.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42049032 G A 0 228 0 0.8139 0.9493 0.9899 1 0.999 1 0.867907 0.954944 0.999535 2 8904 119394 11511 8654 6614 66599 893 16219 2 10404 120990 11578 8654 6614 66618 902 16220 0 . 0 . 0 48 0,0,19,26 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S479|2406|HIVEP3|protein_coding|CODING|NM_024503.4|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2984694 -0.693147 0.167199 48 L443 2406 ctG/ctC LOW 4 SILENT CODING HIVEP3 G protein_coding NM_024503.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42049140 C G 0 228 0 0.8139 0.9493 0.9899 1 0.999 1 0.868134 0.955021 0.999535 2 8902 119764 11511 8654 6612 66693 897 16495 2 10402 121360 11578 8654 6612 66712 906 16496 0 . 0 . 0 66 0,0,41,20 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L443|2406|HIVEP3|protein_coding|CODING|NM_024503.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2475842 -0.693147 0.0118647 66 2406 44030 MODIFIER 3 CODING HIVEP3 G protein_coding NM_024503.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42094498 A G 0 222 0 0.8336 0.5954 0.4625 0.4286 0.5557 0.5808 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.966062 0 . 0 . 84 13,33,8,26 UTR_5_PRIME(MODIFIER||44030||2406|HIVEP3|protein_coding|CODING|NM_024503.4|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.271144 rs2038976 -0.693132 0.0764723 84 P11T 112 Cca/Aca MODERATE 1 MISSENSE CODING GUCA2B A protein_coding NM_007102.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42619152 C A 0 222 0 0.1445 0.1791 0.0937 0.1597 0.1869 0.2986 0.16591 0.18107 0.188837 1 1597 21495 845 1390 1036 12088 174 4365 2 10130 118860 11380 8534 5956 65616 856 16388 0.795682 0 . 0 . 114 29,23,24,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P11T|112|GUCA2B|protein_coding|CODING|NM_007102.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0269862 rs2297567 -0.693147 0.0587339 114 S7F 115 tCc/tTc MODERATE 1 MISSENSE CODING GUCA2A A protein_coding NM_033553.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42630364 G A 0 222 0 0.0772 0.385 0.572 0.4028 0.6113 0.4172 0.164169 0.45 0.596519 1 444 11455 324 359 65 6223 119 3921 2 2832 22214 530 834 100 9746 208 7964 0.999222 0 . 0 . 160 38,38,35,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S7F|115|GUCA2A|protein_coding|CODING|NM_033553.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.633538 rs2071499 -0.693147 0.00267508 160 622 611 MODIFIER 13 CODING FOXJ3 T protein_coding NM_001198850.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42644770 C T 0 228 0 0.7723 0.8013 0.7205 0.7768 0.8827 0.8395 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,19,21 UTR_3_PRIME(MODIFIER||611||622|FOXJ3|protein_coding|CODING|NM_001198850.1|13|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs686247 -0.693145 0.779047 41 V162A 622 gTg/gCg MODERATE 5 MISSENSE CODING FOXJ3 G protein_coding NM_001198850.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42693597 A G 0 222 0 0.7632 0.7953 0.8862 0.8482 0.7913 0.7239 0.766682 0.782331 0.790349 1 7977 97513 10644 7149 5401 53436 717 12189 2 10406 121380 11576 8650 6612 66720 908 16508 0.938345 0 . 0 . 181 44,38,38,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V162A|622|FOXJ3|protein_coding|CODING|NM_001198850.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.803935 rs343376 -0.693147 0.0162538 181 S349 391 agT/agC LOW 5 SILENT CODING RIMKLA C protein_coding NM_173642.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42880516 T C 0 222 0 0.5197 0.4894 0.5173 0.3433 0.6441 0.4202 0.536541 0.602645 0.636512 1 5550 70380 6450 3125 4377 42552 563 7763 2 10402 121336 11564 8622 6612 66720 908 16508 0.816128 0 . 0 COSM146486 189 49,52,35,37 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S349|391|RIMKLA|protein_coding|CODING|NM_173642.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.156878 rs1055055,rs386514373 -0.693147 0.0164911 189 391 221 MODIFIER 5 CODING RIMKLA A protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42880866 G A 0 152 0 0.9682 0.9914 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,4 UTR_3_PRIME(MODIFIER||221||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2484436 -0.616816 0.0143884 6 391 4878 MODIFIER 5 CODING RIMKLA T protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42885523 C T 0 9.7 0 0.0477 0.1216 0.1124 0.2083 0.1501 0.1094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4878||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs16829473 -0.379885 0 1 391 5514 MODIFIER 5 CODING RIMKLA A protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42886159 T A 0 102 0 0.6006 0.6488 0.5951 0.6518 0.663 0.7342 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||5514||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10493110 -0.556411 0.497461 4 391 5540 MODIFIER 5 CODING RIMKLA G protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42886185 A G 0 102 0 0.5998 0.649 0.5937 0.6538 0.663 0.7352 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||5540||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10493109 -0.556411 0.497461 4 391 7399 MODIFIER 5 CODING RIMKLA A protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42888044 T A 0 9.7 0 0.0484 0.122 0.1138 0.2083 0.1491 0.1104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||7399||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3180736 -0.379885 0 1 391 7911 MODIFIER 5 CODING RIMKLA T protein_coding NM_173642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42888556 C T 0 46.3 0 0.382 0.5885 0.5836 0.6498 0.66 0.7342 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||7911||391|RIMKLA|protein_coding|CODING|NM_173642.3|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11210642 -0.453602 0.36 2 F316L 365 Ttt/Ctt MODERATE 7 MISSENSE CODING ZMYND12 G protein_coding NM_032257.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42898843 A G 0 228 0 0.6021 0.6494 0.5965 0.6508 0.662 0.7362 0.593736 0.645933 0.672674 2 6155 80553 6941 5745 4438 44479 594 12201 2 10396 121386 11576 8644 6614 66736 908 16512 0 . 0 . 0 113 0,0,34,70 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F316L|365|ZMYND12|protein_coding|CODING|NM_032257.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1034268 -0.693147 0.00779378 113 G38 365 ggG/ggC LOW 2 SILENT CODING ZMYND12 G protein_coding NM_032257.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42915727 C G 0 222 0 0.1778 0.2831 0.1571 0.4355 0.1879 0.456 0.187699 0.194141 0.197442 1 1892 28609 1479 3502 1127 13164 217 7228 2 10402 121320 11576 8638 6610 66682 908 16504 0.872112 0 . 0 . 124 27,32,20,26 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G38|365|ZMYND12|protein_coding|CODING|NM_032257.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.718124 rs12047095 -0.693147 0.0395789 124 311 91 MODIFIER 3 CODING PPCS G protein_coding NM_024664.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 42925688 T G 0 228 0 0.4735 0.4687 0.3026 0.5992 0.3519 0.5654 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 39 0,0,2,37 UTR_3_PRIME(MODIFIER||91||311|PPCS|protein_coding|CODING|NM_024664.3|3|G),UPSTREAM(MODIFIER||3750||365|ZMYND12|protein_coding|CODING|NM_032257.4||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9787162 -0.693144 0.216724 39 L290 783 Cta/Tta LOW 7 SILENT CODING CCDC30 T protein_coding NM_001080850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43042703 C T 0 222 0 0.177 0.2855 0.1571 0.4563 0.1879 0.4479 0.183386 0.193372 0.198488 1 1870 28146 1448 3559 914 13032 214 7109 2 10182 118630 11416 8458 6534 64876 890 16274 0.560011 0 . 0 . 102 31,19,29,12 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L290|783|CCDC30|protein_coding|CODING|NM_001080850.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.68287 rs12049046 -0.693145 0.789609 102 E364 783 gaA/gaG LOW 8 SILENT CODING CCDC30 G protein_coding NM_001080850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43047057 A G 0 222 0 0.1702 0.279 0.1499 0.4395 0.1879 0.4458 0.179755 0.192219 0.198605 1 1830 28085 1411 3455 919 13118 213 7139 2 10298 121144 11570 8646 6612 66646 906 16466 0.974347 0 . 0 . 119 39,26,27,18 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E364|783|CCDC30|protein_coding|CODING|NM_001080850.2|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.51318 rs12037518 -0.693147 0.421575 119 L561 783 ctG/ctA LOW 12 SILENT CODING CCDC30 A protein_coding NM_001080850.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43108188 G A 0 222 0 0.0234 0.1448 0.085 0.3105 0.1133 0.2127 0.0424421 0.0845763 0.106163 1 388 14620 896 2479 349 6969 95 3444 2 10404 120950 11574 8650 6614 66588 906 16214 0.222094 0 . 0 . 138 44,23,35,27 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L561|783|CCDC30|protein_coding|CODING|NM_001080850.2|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961429 rs12036818 -0.693147 0.0693271 138 783 156 MODIFIER 16 CODING CCDC30 C protein_coding NM_001080850.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43119855 A C 0 24.1 0 0.0121 0.1424 0.0865 0.3095 0.1133 0.2157 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.748798 0 . 0 . 13 0,10,0,3 UTR_3_PRIME(MODIFIER||156||783|CCDC30|protein_coding|CODING|NM_001080850.2|16|C),UPSTREAM(MODIFIER||4193||177|PPIH|protein_coding|CODING|NM_006347.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.879351 rs16829832 -0.511536 0.928514 13 A113 177 gcG/gcA LOW 7 SILENT CODING PPIH A protein_coding NM_006347.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43131653 G A 0 222 0 0.0363 0.1504 0.0908 0.3185 0.1233 0.2014 0.0517476 0.0944948 0.116395 1 502 15352 935 2416 360 7631 99 3409 2 10406 121386 11574 8640 6614 66732 908 16512 0.36839 0 . 0 . 150 42,23,42,24 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A113|177|PPIH|protein_coding|CODING|NM_006347.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982347 rs12244 -0.693147 0.239254 150 324 2321 MODIFIER 8 CODING YBX1 G protein_coding NM_004559.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43169007 A G 0 23.7 0 0.3336 0.3672 0.4135 0.3214 0.4314 0.3609 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2321||324|YBX1|protein_coding|CODING|NM_004559.4|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11210698 -0.379885 0 2 224 1733 MODIFIER 5 CODING CLDN19 T protein_coding NM_148960.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43199024 C T 0 9.7 0 0.1505 0.1254 0.0922 0.1815 0.1213 0.0613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1733||224|CLDN19|protein_coding|CODING|NM_148960.2|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs112310775 -0.379885 0 1 224 231 MODIFIER 5 CODING CLDN19 C protein_coding NM_148960.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43200526 T C 0 168 0 0.5212 0.6068 0.6239 0.6677 0.6024 0.6524 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,22,0 UTR_3_PRIME(MODIFIER||231||224|CLDN19|protein_coding|CODING|NM_148960.2|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs912075 -0.692562 0.141777 22 804 472 MODIFIER 14 CODING P3H1 T protein_coding NM_001243246.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43212111 C T 0 228 0 0.5227 0.6625 0.6599 0.7073 0.6849 0.7843 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,4,40 UTR_3_PRIME(MODIFIER||472||804|P3H1|protein_coding|CODING|NM_001243246.1|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6882 -0.693146 0.560642 44 804 152 MODIFIER 14 CODING P3H1 G protein_coding NM_001243246.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43212431 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 2822 29685 862 1126 1902 14085 292 8596 2 2822 29686 862 1126 1902 14086 292 8596 0 3 likely-benign 0 . 26 0,0,18,6 UTR_3_PRIME(MODIFIER||152||804|P3H1|protein_coding|CODING|NM_001243246.1|14|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4660662 -0.692831 0.304344 26 F710Y 804 tTt/tAt MODERATE 14 MISSENSE CODING P3H1 T protein_coding NM_001243246.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43212869 A T 0 222 0 0.0726 0.121 0.1585 0.2163 0.1213 0.0613 0.0714934 0.105259 0.122558 1 791 14964 2487 2140 596 7649 113 1188 2 10384 121290 11564 8642 6612 66670 906 16512 0.998557 0 . 0 . 65 21,10,17,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F710Y|804|P3H1|protein_coding|CODING|NM_001243246.1|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97426 rs3738496 -0.693127 0.579667 65 475 2 MODIFIER 3 CODING ERMAP A protein_coding NM_001017922.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43296118 G A 0 222 0 0.4546 0.3351 0.1744 0.4435 0.1859 0.3292 0.420563 0.269875 0.192674 1 4404 29334 1486 3431 855 12783 220 6155 2 10404 121352 11570 8638 6606 66716 908 16510 0.38036 0 . 0 . 141 41,21,37,19 UTR_5_PRIME(MODIFIER||2||475|ERMAP|protein_coding|CODING|NM_001017922.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.9547 rs12124733 -0.693147 0.0710175 141 475 645 MODIFIER 12 CODING ERMAP A protein_coding NM_001017922.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43309548 G A 0 9.7 0 0.9486 0.9393 0.9582 0.7976 0.998 0.999 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||645||475|ERMAP|protein_coding|CODING|NM_001017922.1|12|A),UPSTREAM(MODIFIER||2696||315|ZNF691|protein_coding|CODING|NM_001242739.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1484324 -0.379885 0 1 492 462 MODIFIER 10 CODING SLC2A1 G protein_coding NM_006516.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43392250 C G 0 228 0 0.6732 0.3834 0.3948 0.3085 0.1998 0.2495 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 53 1,0,47,4 UTR_3_PRIME(MODIFIER||462||492|SLC2A1|protein_coding|CODING|NM_006516.2|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs4658 -0.693147 0.0119068 53 A15 492 gcC/gcT LOW 2 SILENT CODING SLC2A1 A protein_coding NM_006516.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43408966 G A 0 228 0 0.1543 0.2404 0.3199 0.3185 0.2187 0.2423 0.175216 0.20183 0.215465 2 1799 28547 3452 2444 1590 14729 208 4325 2 9926 116692 11180 8456 5994 64266 848 16022 0.659801 2 benign 0 . 118 1,2,46,54 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A15|492|SLC2A1|protein_coding|CODING|NM_006516.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.706554 rs1385129 -0.693147 0.954754 118 492 197 MODIFIER 1 CODING SLC2A1 G protein_coding NM_006516.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43424519 T G 0 23.7 0 0.2595 0.232 0.2738 0.2401 0.2117 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968368 0 . 0 . 15 2,8,0,3 UTR_5_PRIME(MODIFIER||197||492|SLC2A1|protein_coding|CODING|NM_006516.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.914584 rs11537640 -0.511536 0.318564 15 S603 1283 tcG/tcA LOW 11 SILENT CODING CFAP57 A protein_coding NM_001195831.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43675467 G A 0 228 0 0.5408 0.6949 0.6772 0.6786 0.8877 0.7342 0.57399 0.773566 0.875814 2 5904 96040 6827 6248 5407 58548 717 12389 2 10404 121362 11568 8642 6608 66726 908 16506 0 . 0 . 0 107 0,0,74,22 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S603|1283|CFAP57|protein_coding|CODING|NM_001195831.2|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2453412,rs386478404 -0.693147 0.0579096 107 A778 1138 gcT/gcC LOW 14 SILENT CODING TIE1 C protein_coding NM_005424.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43779564 T C 0 228 0 0.8911 0.8031 0.6427 0.879 0.6272 0.9008 0.849977 0.692603 0.611977 2 8954 84856 8164 7660 4359 41250 607 13862 2 10400 121324 11564 8646 6604 66690 908 16512 0 . 0 . 0 194 0,0,62,118 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A778|1138|TIE1|protein_coding|CODING|NM_005424.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3120276 -0.693147 0.0017467 194 R321Q 635 cGg/cAg MODERATE 6 MISSENSE CODING MPL A protein_coding NM_005373.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43806166 G A 0 222 0 0 0.0069888 0 0.0347 0 0 0.000226963 7.6888e-05 0 1 3 244 1 240 0 0 0 0 2 10406 121412 11578 8654 6614 66740 908 16512 0.661106 1 not-provided 0 COSM1581265 114 12,33,18,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R321Q|635|MPL|protein_coding|CODING|NM_005373.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.262735 rs149265851 -0.693147 0.343218 114 R479Q 499 cGg/cAg MODERATE 11 MISSENSE CODING CDC20 A protein_coding NM_001255.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43828736 G A 0 222 0 0 0.0017971 0 0.0089 0 0 0.000226963 0.000153775 0.000116279 1 1 66 0 57 0 0 0 8 2 10392 121270 11574 8648 6614 66624 906 16512 0.860043 0 . 0 . 64 13,9,14,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R479Q|499|CDC20|protein_coding|CODING|NM_001255.2|11|A),DOWNSTREAM(MODIFIER||332||279|ELOVL1|protein_coding|CODING|NM_001256399.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975812 rs45461499 -0.693136 0.0281882 64 3375 62 MODIFIER 1 CODING SZT2 C protein_coding NM_015284.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43855578 G C 0 222 0 0.6974 0.5966 0.6484 0.5089 0.6382 0.4714 0.689306 0.660534 0.64802 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.372448 0 . 0 . 121 15,42,19,38 UTR_5_PRIME(MODIFIER||62||3375|SZT2|protein_coding|CODING|NM_015284.3|1|C),UPSTREAM(MODIFIER||95||301|MED8|protein_coding|CODING|NM_052877.4||C) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.771818 rs839753 -0.693147 0.00367092 121 3375 491 MODIFIER 71 CODING SZT2 C protein_coding NM_015284.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43916642 T C 0 222 0 0.7118 0.5849 0.6282 0.5069 0.5845 0.4632 0.670662 0.637251 0.622552 1 5614 66192 6378 4373 4089 37387 506 7845 2 8178 112822 11342 8186 6576 61476 842 16222 0.880709 0 . 0 . 109 21,40,14,22 UTR_3_PRIME(MODIFIER||491||3375|SZT2|protein_coding|CODING|NM_015284.3|71|C),DOWNSTREAM(MODIFIER||32||277|HYI|protein_coding|CODING|NM_001190880.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.141158 rs6954 -0.693139 0.146571 109 S18P 277 Tcc/Ccc MODERATE 1 MISSENSE CODING HYI G protein_coding NM_001190880.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43919413 A G 0 21.4 0 0.6967 0.5958 0.647 0.5089 0.6362 0.4714 0 . 0 1 617 9674 761 715 279 6394 59 849 2 832 13470 1112 1106 362 8582 84 1392 1 0 . 0 . 4 1,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S18P|277|HYI|protein_coding|CODING|NM_001190880.2|1|G),UTR_3_PRIME(MODIFIER||3262||3375|SZT2|protein_coding|CODING|NM_015284.3|71|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 1 rs6692611 -0.379885 0 4 3375 3262 MODIFIER 71 CODING SZT2 G protein_coding NM_015284.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 43919413 A G 0 21.4 0 0.6967 0.5958 0.647 0.5089 0.6362 0.4714 0 . 0 1 617 9674 761 715 279 6394 59 849 2 832 13470 1112 1106 362 8582 84 1392 1 0 . 0 . 4 1,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S18P|277|HYI|protein_coding|CODING|NM_001190880.2|1|G),UTR_3_PRIME(MODIFIER||3262||3375|SZT2|protein_coding|CODING|NM_015284.3|71|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 1 rs6692611 -0.379885 0 4 A602 1907 gcC/gcA LOW 11 SILENT CODING PTPRF A protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44058265 C A 0 228 0 0.4561 0.4465 0.317 0.5585 0.3966 0.4611 0.456877 0.421728 0.403721 2 4769 49121 3690 4937 2794 26413 346 6172 2 10274 116996 11450 8592 6562 65312 854 13952 0 . 0 . 0 65 0,0,9,51 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A602|1907|PTPRF|protein_coding|CODING|NM_002840.3|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3828151 -0.693147 0.0679921 65 V1137 1907 gtG/gtA LOW 19 SILENT CODING PTPRF A protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44071221 G A 0 228 0 0.4297 0.6024 0.5418 0.7579 0.7376 0.5798 0.472991 0.668999 0.769419 2 4857 84141 5785 6736 5117 51381 634 9631 2 10360 121076 11536 8644 6502 66626 902 16506 0 . 0 . 0 109 0,0,44,53 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1137|1907|PTPRF|protein_coding|CODING|NM_002840.3|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs631248 -0.693147 0.139514 109 T1197 1907 acC/acT LOW 20 SILENT CODING PTPRF T protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44072018 C T 0 228 0 0.0371 0.2782 0.268 0.4702 0.3569 0.3323 0.0948706 0.262802 0.348837 2 850 39265 3327 4167 2594 23288 281 4758 2 10404 121364 11572 8630 6610 66728 908 16512 0 . 0 . 0 152 0,0,82,56 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1197|1907|PTPRF|protein_coding|CODING|NM_002840.3|20|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1065772 -0.693147 2.78709e-05 152 P1213 1907 ccC/ccT LOW 20 SILENT CODING PTPRF T protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44072066 C T 0 228 0 0.0303 0.2812 0.2752 0.4702 0.3648 0.3436 0.0937358 0.270952 0.361744 2 813 40054 3419 4165 2536 23934 283 4904 2 10402 121358 11572 8634 6610 66724 908 16508 0 . 0 . 0 105 0,0,36,56 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1213|1907|PTPRF|protein_coding|CODING|NM_002840.3|20|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10890266 -0.693147 0.277151 105 1907 LOW 23 CODING PTPRF T protein_coding NM_002840.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44083110 C T 0 228 0 0.9455 0.7374 0.5764 0.7649 0.7167 0.5634 0.916931 0.805167 0.747907 2 9617 87245 5944 6805 4905 49997 644 9333 2 10402 121328 11562 8646 6608 66702 904 16504 0 . 0 . 0 84 0,0,53,25 SPLICE_SITE_REGION+INTRON(LOW||||1907|PTPRF|protein_coding|CODING|NM_002840.3|23|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs571862 -0.693147 0.267148 84 G1432 1907 ggT/ggC LOW 25 SILENT CODING PTPRF C protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44083507 T C 0 228 0 0.9455 0.7372 0.5764 0.7649 0.7157 0.5634 0.916931 0.805167 0.747907 2 9597 87079 5921 6786 4886 49913 645 9331 2 10382 121148 11538 8636 6574 66614 904 16500 0 . 0 . 0 41 0,0,9,31 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1432|1907|PTPRF|protein_coding|CODING|NM_002840.3|25|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs641365 -0.693145 0.341799 41 R1436 1907 agG/agA LOW 25 SILENT CODING PTPRF A protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44083519 G A 0 228 0 0.9455 0.7372 0.5764 0.7649 0.7157 0.5634 0.916931 0.80509 0.747791 2 9592 87013 5914 6779 4882 49878 642 9326 2 10376 121098 11540 8632 6572 66584 902 16492 0 . 0 . 0 36 0,0,5,31 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R1436|1907|PTPRF|protein_coding|CODING|NM_002840.3|25|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs641351 -0.693139 0.65673 36 R1504 1907 cgC/cgT LOW 27 SILENT CODING PTPRF T protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44084739 C T 0 228 0 0.9455 0.7374 0.5764 0.7649 0.7167 0.5634 0.916931 0.80509 0.747791 2 9617 87233 5940 6801 4903 49994 648 9330 2 10402 121294 11568 8646 6608 66684 908 16478 0 . 0 . 0 77 0,0,48,25 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R1504|1907|PTPRF|protein_coding|CODING|NM_002840.3|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1143701 -0.693147 0.177813 77 Y1861 1907 taC/taT LOW 33 SILENT CODING PTPRF T protein_coding NM_002840.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44086831 C T 0 228 0 0.5507 0.5705 0.5014 0.6855 0.6441 0.4519 0.581253 0.637244 0.66593 2 5932 74004 5348 6092 4317 44416 545 7354 2 10356 120690 11452 8596 6522 66402 898 16464 0 . 0 . 0 71 0,0,34,30 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1861|1907|PTPRF|protein_coding|CODING|NM_002840.3|33|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1143702 -0.693147 0.257034 71 A482E 1064 gCa/gAa MODERATE 11 MISSENSE CODING KDM4A A protein_coding NM_014663.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44137257 C A 0 228 0 0.9478 0.7402 0.5591 0.7946 0.7028 0.5706 0.922152 0.794326 0.728837 2 9636 85912 5833 7022 4856 48675 626 9264 2 10404 120824 11570 8652 6612 66594 902 16090 0 . 0 . 0 97 0,0,43,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gAa|A482E|1064|KDM4A|protein_coding|CODING|NM_014663.2|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs586339 -0.693147 0.135937 97 T128A 444 Aca/Gca MODERATE 5 MISSENSE CODING ST3GAL3 G protein_coding NM_174963.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44290530 A G 0 222 0 0.3139 0.2364 0.2378 0.1429 0.3459 0.1145 0.309318 0.335288 0.348633 1 2512 24257 1285 805 1918 15526 226 1985 2 6778 69776 4380 4154 4258 37532 610 12064 0.949333 3 likely-benign 0 . 55 7,15,8,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T128A|444|ST3GAL3|protein_coding|CODING|NM_174963.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.865513 rs37458 -0.693054 0.422905 55 444 303 MODIFIER 13 CODING ST3GAL3 G protein_coding NM_174963.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44396196 A G 0 222 0 0.0113 0.0507 0.0288 0.1349 0.0398 0.044 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.403931 0 . 0 . 65 13,19,7,20 UTR_3_PRIME(MODIFIER||303||444|ST3GAL3|protein_coding|CODING|NM_174963.3|13|G),UPSTREAM(MODIFIER||2796||228|ARTN|protein_coding|CODING|NM_001136215.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.916192 rs12561948 -0.693021 0.00099315 65 444 413 MODIFIER 13 CODING ST3GAL3 A protein_coding NM_174963.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44396306 G A 0 222 0 0 0.0033946 0 0.0149 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0900941 0 . 0 . 60 24,4,21,9 UTR_3_PRIME(MODIFIER||413||444|ST3GAL3|protein_coding|CODING|NM_174963.3|13|A),UPSTREAM(MODIFIER||2686||228|ARTN|protein_coding|CODING|NM_001136215.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.967577 rs191309321 -0.693097 0.198177 60 444 753 MODIFIER 13 CODING ST3GAL3 G protein_coding NM_174963.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44396646 C G 0 222 0 0.143 0.5188 0.6311 0.6071 0.7594 0.6084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.562438 0 . 0 . 110 26,25,20,36 UTR_3_PRIME(MODIFIER||753||444|ST3GAL3|protein_coding|CODING|NM_174963.3|13|G),UPSTREAM(MODIFIER||2346||228|ARTN|protein_coding|CODING|NM_001136215.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.771439 rs6801 -0.693147 0.775445 110 228 2153 MODIFIER 1 CODING ARTN T protein_coding NM_001136215.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44399176 A T 0 58 0 0.8457 0.9565 0.9813 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||2153||228|ARTN|protein_coding|CODING|NM_001136215.1|1|T),DOWNSTREAM(MODIFIER||2339||444|ST3GAL3|protein_coding|CODING|NM_174963.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2428958 -0.511536 0.698947 3 Q19R 228 cAg/cGg MODERATE 2 MISSENSE CODING ARTN G protein_coding NM_001136215.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44401384 A G 0 228 0 0.7368 0.8369 0.8732 0.8254 0.9115 0.8814 0.769632 0.872136 0.924651 2 7650 103293 9350 6977 5416 59184 748 13968 2 9982 116746 11108 8348 6178 64278 856 15996 0 . 0 . 0 147 0,0,63,70 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q19R|228|ARTN|protein_coding|CODING|NM_001136215.1|2|G),DOWNSTREAM(MODIFIER||4547||444|ST3GAL3|protein_coding|CODING|NM_174963.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2242637 -0.693147 0.225929 147 228 LOW 3 CODING ARTN T protein_coding NM_001136215.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44401966 C T 0 77 0 0.0431 0.0575 0.0317 0.125 0.0398 0.044 0 . 0 1 0 11 0 3 0 3 0 5 2 4 90 4 6 0 14 0 62 0.810265 0 . 0 . 8 2,1,2,2 SPLICE_SITE_REGION+INTRON(LOW||||228|ARTN|protein_coding|CODING|NM_001136215.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1.01283 1.01283 0 0.607698 rs115571163 -0.556411 0.47843 8 228 128 MODIFIER 4 CODING ARTN A protein_coding NM_001136215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44402565 G A 0 56 0 0.1021 0.501 0.6239 0.6012 0.7416 0.6022 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 6 0,2,0,4 UTR_3_PRIME(MODIFIER||128||228|ARTN|protein_coding|CODING|NM_001136215.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs12127737 -0.556411 0.0320192 6 D137 963 gaC/gaT LOW 2 SILENT CODING IPO13 T protein_coding NM_014652.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44415415 C T 0 222 0 0.0877 0.5052 0.6167 0.6161 0.7634 0.6104 0.204494 0.588421 0.785116 1 1914 81315 6236 5496 5189 51768 631 10081 2 10378 121184 11522 8618 6596 66658 908 16504 0.81508 0 . 0 . 114 32,13,29,25 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D137|963|IPO13|protein_coding|CODING|NM_014652.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.895082 rs2240447 -0.693147 0.704395 114 P140 963 ccA/ccG LOW 2 SILENT CODING IPO13 G protein_coding NM_014652.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44415424 A G 0 222 0 0 0.0517 0.036 0.1181 0.0348 0.0818 0.0118021 0.0268338 0.0345349 1 89 5472 727 980 146 2336 31 1163 2 10366 120982 11508 8632 6562 66554 906 16454 0.935371 0 . 0 . 109 29,27,27,18 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P140|963|IPO13|protein_coding|CODING|NM_014652.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.832913 rs41270385 -0.693147 0.296059 109 489 185 MODIFIER 6 CODING DPH2 C protein_coding NM_001384.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44438396 A C 0 115 0 0.2057 0.2173 0.2248 0.2123 0.1531 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.817757 0 . 0 . 28 1,14,0,12 UTR_3_PRIME(MODIFIER||185||489|DPH2|protein_coding|CODING|NM_001384.4|6|C),UPSTREAM(MODIFIER||1924||261|ATP6V0B|protein_coding|CODING|NM_001294333.1||C),DOWNSTREAM(MODIFIER||4702||963|IPO13|protein_coding|CODING|NM_014652.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.84246 rs783308 -0.680642 0.160505 28 489 763 MODIFIER 6 CODING DPH2 T protein_coding NM_001384.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44438974 C T 0 23 0 0.0567 0.4878 0.6037 0.6131 0.7445 0.5951 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,0,2 UTR_3_PRIME(MODIFIER||763||489|DPH2|protein_coding|CODING|NM_001384.4|6|T),UPSTREAM(MODIFIER||1346||261|ATP6V0B|protein_coding|CODING|NM_001294333.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7161 -0.453602 0.84 3 A19 261 gcG/gcC LOW 1 SILENT CODING ATP6V0B C protein_coding NM_001294333.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44440769 G C 0 49 0 0.0371 0.0803 0.0461 0.1786 0.0537 0.089 0.0450225 0.0441777 0.0437419 1 83 418 18 50 1 224 7 35 2 844 3848 144 188 16 2334 30 292 0.915545 0 . 0 . 25 4,13,0,6 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A19|261|ATP6V0B|protein_coding|CODING|NM_001294333.1|1|C),UPSTREAM(MODIFIER||4839||401|B4GALT2|protein_coding|CODING|NM_030587.2||C),DOWNSTREAM(MODIFIER||1726||489|DPH2|protein_coding|CODING|NM_001384.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997552 rs2286241 -0.616816 0.733113 25 401 17 MODIFIER 1 CODING B4GALT2 C protein_coding NM_030587.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44445667 T C 0 9.7 0 0.1914 0.1224 0.0576 0.1786 0.0527 0.089 0 . 0 1 66 855 6 28 0 177 10 568 2 310 10352 92 186 6 2834 124 6800 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||17||401|B4GALT2|protein_coding|CODING|NM_030587.2|1|C),DOWNSTREAM(MODIFIER||1695||261|ATP6V0B|protein_coding|CODING|NM_001294333.1||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs3762423 -0.379885 0 1 Q151H 401 caG/caC MODERATE 3 MISSENSE CODING B4GALT2 C protein_coding NM_030587.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44447413 G C 0 222 0 0.0356 0.0797 0.0461 0.1786 0.0527 0.089 0.0535633 0.054744 0.0553488 1 504 7802 861 1455 208 3430 56 1288 2 10210 119916 11546 8602 6612 65634 898 16414 0.969472 0 . 0 . 78 16,23,18,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q151H|401|B4GALT2|protein_coding|CODING|NM_030587.2|3|C),DOWNSTREAM(MODIFIER||3441||261|ATP6V0B|protein_coding|CODING|NM_001294333.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.783625 rs1859728 -0.693136 0.653527 78 I332 401 atC/atT LOW 6 SILENT CODING B4GALT2 T protein_coding NM_030587.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44451234 C T 0 222 0 0.0477 0.0935 0.0778 0.1528 0.1004 0.0982 0.0630958 0.0890358 0.102326 1 625 11249 1088 1088 446 6245 65 1692 2 10140 120306 11508 8604 6612 66110 896 16436 0.850769 0 . 0 COSM146491 65 28,3,21,3 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I332|401|B4GALT2|protein_coding|CODING|NM_030587.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.775667 rs1061781 -0.692831 0.430583 65 A305V 307 gCc/gTc MODERATE 9 MISSENSE CODING CCDC24 T protein_coding NM_152499.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44461822 C T 0 222 0 0.0113 0.0567 0.0418 0.1141 0.0417 0.0849 0.0225718 0.0334309 0.0389716 1 159 5085 678 842 123 2211 27 1045 2 6566 75790 7190 5720 3694 42196 548 9876 0.911099 0 . 0 . 63 12,15,19,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A305V|307|CCDC24|protein_coding|CODING|NM_152499.2|9|T),DOWNSTREAM(MODIFIER||4979||401|B4GALT2|protein_coding|CODING|NM_030587.2||T),DOWNSTREAM(MODIFIER||333||706|SLC6A9|protein_coding|CODING|NM_201649.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.914217 rs2301983 -0.693097 0.188762 63 706 13 MODIFIER 14 CODING SLC6A9 T protein_coding NM_201649.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44463204 C T 0 108 0 0.0121 0.0591 0.0461 0.1131 0.0427 0.093 0.0215615 0.0325234 0.0381395 1 171 5804 763 975 144 2378 33 1340 2 9188 117164 11444 8510 6586 64152 880 16404 0.180092 0 . 0 . 17 5,3,5,2 UTR_3_PRIME(MODIFIER||13||706|SLC6A9|protein_coding|CODING|NM_201649.3|14|T),DOWNSTREAM(MODIFIER||1006||307|CCDC24|protein_coding|CODING|NM_152499.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97357 rs2286245 -0.636426 0.0753159 17 S57T 389 aGc/aCc MODERATE 2 MISSENSE CODING KLF17 C protein_coding NM_173484.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44595113 G C 0 222 0 0.2231 0.4964 0.5159 0.628 0.6928 0.5143 0.297549 0.539828 0.663953 1 2867 71651 5885 5750 4250 44219 507 8173 2 10332 117696 11536 8608 6612 65812 870 13926 0.820132 0 . 0 . 103 28,9,37,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S57T|389|KLF17|protein_coding|CODING|NM_173484.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.423871 rs2429051 -0.693147 0.399437 103 N156S 389 aAt/aGt MODERATE 2 MISSENSE CODING KLF17 G protein_coding NM_173484.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44595410 A G 0 222 0 0.0915 0.2756 0.2594 0.4236 0.3966 0.2587 0.144349 0.295248 0.372558 1 1375 39949 3252 4047 2145 24240 301 4589 2 10326 120864 11502 8574 6600 66462 906 16494 0.994159 0 . 0 . 95 18,16,18,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N156S|389|KLF17|protein_coding|CODING|NM_173484.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.865962 rs2485652 -0.693147 0.136674 95 S161 389 tcG/tcA LOW 2 SILENT CODING KLF17 A protein_coding NM_173484.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44595426 G A 0 222 0 0.0915 0.2752 0.2579 0.4236 0.3966 0.2577 0.144803 0.295294 0.372412 1 1373 39932 3228 4049 2148 24246 301 4587 2 10340 120936 11518 8584 6596 66498 906 16494 0.643253 0 . 0 . 89 17,16,18,28 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S161|389|KLF17|protein_coding|CODING|NM_173484.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989666 rs2429050 -0.693147 0.2995 89 467 32 MODIFIER 11 CODING DMAP1 C protein_coding NM_001034023.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 44686322 T C 0 222 0 0.1876 0.2742 0.3357 0.2371 0.2584 0.4018 0.204267 0.266877 0.298953 1 2043 35680 3900 1922 1823 19409 286 6297 2 10114 118074 11196 8258 6424 64844 884 16354 0.483916 0 . 0 . 100 21,22,21,22 UTR_3_PRIME(MODIFIER||32||467|DMAP1|protein_coding|CODING|NM_001034023.1|11|C),DOWNSTREAM(MODIFIER||420||337|ERI3|protein_coding|CODING|NM_024066.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95281 rs12419 -0.693146 0.16743 100 V171 221 gtA/gtG LOW 2 SILENT CODING TCTEX1D4 C protein_coding NM_001013632.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45271828 T C 0 183 0 0.0764 0.1362 0.1427 0.1647 0.1759 0.1421 0.0972808 0.133344 0.151839 1 502 10917 799 936 426 6182 94 1978 2 3196 49554 3480 3632 1760 26424 382 10680 0.946541 0 . 0 . 139 4,65,1,67 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V171|221|TCTEX1D4|protein_coding|CODING|NM_001013632.3|2|C),UPSTREAM(MODIFIER||2326||291|BTBD19|protein_coding|CODING|NM_001136537.1||C),DOWNSTREAM(MODIFIER||161||646|PLK3|protein_coding|CODING|NM_004073.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945183 rs17885815 -0.693147 0.902608 139 291 272 MODIFIER 8 CODING BTBD19 C protein_coding NM_001136537.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45279716 G C 0 85 0 0.6029 0.4465 0.4424 0.4911 0.3191 0.3231 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 0,2,2,2 UTR_3_PRIME(MODIFIER||272||291|BTBD19|protein_coding|CODING|NM_001136537.1|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs11584031 -0.556411 0.337235 6 D829 1203 gaC/gaT LOW 16 SILENT CODING PTCH2 A protein_coding NM_003738.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45292866 G A 0 222 0 0.0847 0.1478 0.1671 0.1964 0.171 0.1452 0.0857921 0.139474 0.166977 1 883 19492 1998 1914 968 11002 146 2581 2 10384 121224 11572 8622 6606 66628 904 16508 0.710705 0 . 0 . 168 55,28,57,20 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D829|1203|PTCH2|protein_coding|CODING|NM_003738.4|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738504 rs2295996 -0.693147 0.119789 168 A685 1203 gcT/gcC LOW 14 SILENT CODING PTCH2 G protein_coding NM_003738.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45293518 A G 0 222 0 0.6021 0.4455 0.4409 0.4911 0.3191 0.32 0.584657 0.424419 0.342326 1 6058 46351 4848 4157 2281 22948 295 5764 2 10320 120530 11446 8582 6466 66340 896 16480 0.841816 0 . 0 . 121 30,18,43,13 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A685|1203|PTCH2|protein_coding|CODING|NM_003738.4|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517625 rs7525308 -0.693147 0.0439763 121 861 558 MODIFIER 21 CODING HECTD3 G protein_coding NM_024602.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45468606 A G 0 228 0 0.5439 0.6715 0.5692 0.7133 0.7863 0.7556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,10,2 UTR_3_PRIME(MODIFIER||558||861|HECTD3|protein_coding|CODING|NM_024602.5|21|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8681 -0.680642 0.564756 13 861 533 MODIFIER 21 CODING HECTD3 T protein_coding NM_024602.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45468631 A T 0 228 0 0.9728 0.9924 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,23,3 UTR_3_PRIME(MODIFIER||533||861|HECTD3|protein_coding|CODING|NM_024602.5|21|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4660829 -0.692976 0.00777181 27 T594 1185 acC/acG LOW 8 SILENT CODING ZSWIM5 C protein_coding NM_020883.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45504720 G C 0 222 0 0.3805 0.5104 0.4337 0.4544 0.6183 0.6871 0.400372 0.53463 0.596107 1 3800 68589 4871 4371 3975 40052 564 10956 2 9766 120592 11552 8594 6614 66668 898 16500 0.712538 0 . 0 . 99 21,23,23,23 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T594|1185|ZSWIM5|protein_coding|CODING|NM_020883.1|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.341936 rs7551698 -0.693147 0.935803 99 Q338H 549 caG/caC MODERATE 12 MISSENSE CODING MUTYH G protein_coding NM_001128425.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45797505 C G 0 162 0 0.2579 0.3135 0.4841 0.3909 0.2445 0.2587 0.263744 0.254115 0.249186 1 2317 28865 4841 2955 1188 13848 212 3504 2 8142 97294 9114 6868 4890 53264 704 14312 0.786325 2|2|2|2 benign|benign|benign|benign 0 . 25 4,11,6,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q338H|549|MUTYH|protein_coding|CODING|NM_001128425.1|12|G),DOWNSTREAM(MODIFIER||3159||371|HPDL|protein_coding|CODING|NM_032756.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894801 rs3219489 -0.670168 0.422799 25 510 359 MODIFIER 1 CODING TOE1 C protein_coding NM_025077.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45805566 G C 0 228 0 0.9992 0.9944 0.9856 1 0.9841 0.999 0 . 0 2 2032 37092 2536 2198 1581 19668 298 8779 2 2038 37546 2564 2198 1600 20024 300 8822 0 . 0 . 0 112 0,0,53,39 UTR_5_PRIME(MODIFIER||359||510|TOE1|protein_coding|CODING|NM_025077.3|1|C),DOWNSTREAM(MODIFIER||3989||571|TESK2|protein_coding|CODING|NM_007170.2||C),INTRON(MODIFIER||||549|MUTYH|protein_coding|CODING|NM_001128425.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs3219468 -0.693147 0.0712599 112 571 421 MODIFIER 11 CODING TESK2 G protein_coding NM_007170.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45810091 A G 0 222 0 0.6112 0.4093 0.5058 0.3859 0.2455 0.2607 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997397 0 . 0 . 76 10,27,7,25 UTR_3_PRIME(MODIFIER||421||571|TESK2|protein_coding|CODING|NM_007170.2|11|G),UPSTREAM(MODIFIER||3949||549|MUTYH|protein_coding|CODING|NM_001128425.1||G),DOWNSTREAM(MODIFIER||441||510|TOE1|protein_coding|CODING|NM_025077.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.151345 rs9429072 -0.69312 0.0201242 76 P435 571 ccC/ccT LOW 11 SILENT CODING TESK2 A protein_coding NM_007170.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45810923 G A 0 222 0 0.2852 0.1741 0.1095 0.1935 0.1044 0.1217 0.24776 0.149133 0.103511 1 2489 14061 1212 1793 447 6187 105 1828 2 9670 120200 11566 8600 6614 66340 898 16512 0.854356 0 . 0 . 41 9,8,11,7 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P435|571|TESK2|protein_coding|CODING|NM_007170.2|11|A),UPSTREAM(MODIFIER||4781||549|MUTYH|protein_coding|CODING|NM_001128425.1||A),DOWNSTREAM(MODIFIER||1273||510|TOE1|protein_coding|CODING|NM_025077.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.812932 rs3893383 -0.691153 0.0932977 41 571 33243 MODIFIER 1 CODING TESK2 A protein_coding NM_007170.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45956700 C A 0 36.3 0 0.8616 0.8237 0.8372 0.9365 0.6978 0.7761 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||33243||571|TESK2|protein_coding|CODING|NM_007170.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6429567 -0.453602 0.18 2 V107 282 gtG/gtA LOW 3 SILENT CODING MMACHC A protein_coding NM_015506.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45973928 G A 0 222 0 0.3654 0.4752 0.4957 0.5952 0.4771 0.4836 0.372335 0.416191 0.436974 1 3690 56273 6382 4931 3154 29560 437 8119 2 9794 120666 11572 8590 6606 66704 900 16500 0.998481 2 benign 0 . 50 15,10,17,4 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V107|282|MMACHC|protein_coding|CODING|NM_015506.2|3|A),DOWNSTREAM(MODIFIER||2779||199|PRDX1|protein_coding|CODING|NM_001202431.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993939 rs2275276 -0.692352 0.295748 50 282 1260 MODIFIER 4 CODING MMACHC A protein_coding NM_015506.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45976147 G A 0 6.3 0 0.59 0.7438 0.8199 0.9137 0.6948 0.773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1260||282|MMACHC|protein_coding|CODING|NM_015506.2|4|A),DOWNSTREAM(MODIFIER||560||199|PRDX1|protein_coding|CODING|NM_001202431.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386619229,rs882803 -0.379885 0 1 282 1377 MODIFIER 4 CODING MMACHC CT protein_coding NM_015506.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45976263 C CT 0 4.9 0 0.59 0.7438 0.8199 0.9137 0.6948 0.773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1377||282|MMACHC|protein_coding|CODING|NM_015506.2|4|CT),DOWNSTREAM(MODIFIER||443||199|PRDX1|protein_coding|CODING|NM_001202431.1||CT) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs5773883 -0.379885 0 1 199 137 MODIFIER 6 CODING PRDX1 A protein_coding NM_001202431.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 45976864 G A 0 74 0 0 0.0069888 0 0.0337 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997221 0 . 0 . 21 13,1,7,0 UTR_3_PRIME(MODIFIER||137||199|PRDX1|protein_coding|CODING|NM_001202431.1|6|A),DOWNSTREAM(MODIFIER||125||282|MMACHC|protein_coding|CODING|NM_015506.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.975265 rs3737192 -0.636426 0.347872 21 325 10780 MODIFIER 2 CODING AKR1A1 C protein_coding NM_001202413.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46016687 T C 0 18.4 0 0.5575 0.5341 0.4986 0.6379 0.4592 0.498 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,1,1,0 UTR_5_PRIME(MODIFIER||10780||325|AKR1A1|protein_coding|CODING|NM_001202413.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs9147 -0.379885 0 4 P302 788 ccG/ccA LOW 6 SILENT CODING NASP A protein_coding NM_002482.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46073489 G A 0 222 0 0.6831 0.5735 0.5346 0.6329 0.4861 0.4816 0.665683 0.540597 0.476512 1 6949 62651 6571 5245 3209 31887 466 8324 2 10346 120918 11480 8586 6600 66510 904 16492 0.937583 0 . 0 COSM1343061 129 37,26,24,27 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P302|788|NASP|protein_coding|CODING|NM_002482.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.264945 rs2230657 -0.693147 0.223229 129 S480 788 tcA/tcG LOW 7 SILENT CODING NASP G protein_coding NM_002482.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46078854 A G 0 221 0 0.733 0.6791 0.6527 0.6577 0.7177 0.6074 0.75034 0.720283 0.704884 1 7807 84295 7587 5457 5094 46956 641 10753 2 10354 120542 11512 8602 6582 66254 900 16338 0.999758 0 . 0 . 72 29,18,8,10 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S480|788|NASP|protein_coding|CODING|NM_002482.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999893 rs2230658 -0.691153 0.765708 72 T490 788 acC/acT LOW 7 SILENT CODING NASP T protein_coding NM_002482.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46078884 C T 0 222 0 0.7315 0.6783 0.6499 0.6577 0.7177 0.6074 0.747163 0.719207 0.704884 1 7797 84583 7584 5466 5106 47151 648 10831 2 10374 120894 11522 8610 6594 66454 904 16436 0.998952 0 . 0 . 91 37,16,18,9 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T490|788|NASP|protein_coding|CODING|NM_002482.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.244321 rs2230659 -0.693021 0.450037 91 A542 788 gcC/gcT LOW 9 SILENT CODING NASP T protein_coding NM_002482.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46079998 C T 0 222 0 0 0.0023962 0 0.0099 0 0.002 0 . 0 1 0 163 0 159 0 1 1 2 2 10384 121368 11576 8654 6612 66726 906 16510 0.861276 0 . 0 . 137 26,26,27,51 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A542|788|NASP|protein_coding|CODING|NM_002482.3|9|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.913516 rs144542036 -0.693147 0.680532 137 622 95 MODIFIER 13 CODING CCDC17 T protein_coding NM_001114938.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46085852 C T 0 219 0 0.7307 0.6781 0.6527 0.6577 0.7157 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.926834 0 . 0 . 38 12,1,20,1 UTR_3_PRIME(MODIFIER||95||622|CCDC17|protein_coding|CODING|NM_001114938.2|13|T),DOWNSTREAM(MODIFIER||1274||788|NASP|protein_coding|CODING|NM_002482.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.926834 rs2275085 -0.692352 0.0706438 38 622 68 MODIFIER 13 CODING CCDC17 G protein_coding NM_001114938.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46085879 C G 0 222 0 0.7337 0.6853 0.6527 0.6835 0.7187 0.6104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996709 0 . 0 . 49 14,1,23,3 UTR_3_PRIME(MODIFIER||68||622|CCDC17|protein_coding|CODING|NM_001114938.2|13|G),DOWNSTREAM(MODIFIER||1301||788|NASP|protein_coding|CODING|NM_002482.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999176 rs2275086 -0.692976 0.236569 49 S580N 622 aGc/aAc MODERATE 13 MISSENSE CODING CCDC17 T protein_coding NM_001114938.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46086077 C T 0 222 0 0.7292 0.6865 0.6542 0.6925 0.7207 0.6104 0.744096 0.719779 0.707326 1 6534 71913 5732 4840 4423 40573 560 9251 2 8712 101372 8596 7148 5650 56678 772 13816 0.88879 0 . 0 . 38 10,9,5,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S580N|622|CCDC17|protein_coding|CODING|NM_001114938.2|13|T),DOWNSTREAM(MODIFIER||1499||788|NASP|protein_coding|CODING|NM_002482.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.287865 rs3014246 -0.688148 0.0157932 38 P353L 622 cCg/cTg MODERATE 8 MISSENSE CODING CCDC17 A protein_coding NM_001114938.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46087577 G A 0 222 0 0.7292 0.6771 0.6542 0.6518 0.7177 0.6074 0.746482 0.71936 0.705465 1 7271 80804 7223 5305 4943 45283 605 10174 2 9532 113912 10710 8264 6310 63284 838 14974 0.954881 0 . 0 . 42 8,10,11,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P353L|622|CCDC17|protein_coding|CODING|NM_001114938.2|8|A),DOWNSTREAM(MODIFIER||2999||788|NASP|protein_coding|CODING|NM_002482.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930403 rs3014242 -0.69168 0.255357 42 622 LOW 2 CODING CCDC17 G protein_coding NM_001114938.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46089225 C G 0 222 0 0.733 0.6855 0.6556 0.6835 0.7207 0.6084 0 . 0 1 829 10379 206 305 85 3653 108 5193 2 1070 15004 306 442 102 5132 156 7796 0.937707 0 . 0 . 90 19,35,22,11 SPLICE_SITE_REGION+INTRON(LOW||||622|CCDC17|protein_coding|CODING|NM_001114938.2|2|G),DOWNSTREAM(MODIFIER||4647||788|NASP|protein_coding|CODING|NM_002482.3||G),DOWNSTREAM(MODIFIER||3751||474|GPBP1L1|protein_coding|CODING|NM_021639.4||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.373207 rs3014240 -0.693127 0.737153 90 474 236 MODIFIER 13 CODING GPBP1L1 A protein_coding NM_021639.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46093692 G A 0 222 0 0.267 0.3125 0.3444 0.3075 0.2793 0.3906 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.903789 0 . 0 . 59 24,3,22,5 UTR_3_PRIME(MODIFIER||236||474|GPBP1L1|protein_coding|CODING|NM_021639.4|13|A),UPSTREAM(MODIFIER||3961||622|CCDC17|protein_coding|CODING|NM_001114938.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.814759 rs1135850 -0.693021 0.112354 59 S442 474 agT/agC LOW 13 SILENT CODING GPBP1L1 G protein_coding NM_021639.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46094027 A G 0 222 0 0.2648 0.3225 0.3458 0.3472 0.2823 0.3998 0.253745 0.28087 0.294767 1 2566 36508 3923 3179 1488 19328 258 5766 2 10394 121326 11568 8632 6614 66704 908 16506 0.596837 0 . 0 COSM146499 66 8,20,6,22 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S442|474|GPBP1L1|protein_coding|CODING|NM_021639.4|13|G),UPSTREAM(MODIFIER||4296||622|CCDC17|protein_coding|CODING|NM_001114938.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.49375 rs1250,rs386524597 -0.693054 0.339927 66 K416 474 aaA/aaG LOW 12 SILENT CODING GPBP1L1 C protein_coding NM_021639.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46095272 T C 0 222 0 0.267 0.3191 0.3473 0.3165 0.2833 0.409 0.253064 0.281639 0.296279 1 2571 37003 3918 2991 1733 19606 267 5917 2 10406 121354 11572 8634 6608 66716 908 16510 0.976423 0 . 0 . 128 42,5,54,12 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K416|474|GPBP1L1|protein_coding|CODING|NM_021639.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.843943 rs1135812 -0.693147 0.277579 128 K264R 584 aAa/aGa MODERATE 4 MISSENSE CODING IPP C protein_coding NM_005897.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46195375 T C 0 222 0 0.2504 0.3149 0.3473 0.3135 0.2833 0.4131 0.246936 0.279409 0.296047 1 2502 36896 3913 2968 1729 19567 268 5949 2 10400 121350 11576 8646 6608 66704 906 16510 0.403362 0 . 0 COSM146501 115 24,19,21,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K264R|584|IPP|protein_coding|CODING|NM_005897.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.635035 rs28375469 -0.693147 0.247035 115 1798 216 MODIFIER 1 CODING MAST2 G protein_coding NM_015112.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46269352 T G 0 100 0 0.9924 0.998 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,0 UTR_5_PRIME(MODIFIER||216||1798|MAST2|protein_coding|CODING|NM_015112.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12081398 -0.556411 0.160409 5 D388E 1798 gaT/gaG MODERATE 10 MISSENSE CODING MAST2 G protein_coding NM_015112.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46476587 T G 0 228 0 0.9221 0.8744 0.8674 0.9841 0.7177 0.863 0.890583 0.786384 0.738908 2 8709 95631 10373 8469 4537 49187 681 13675 2 9800 120678 11570 8622 6610 66668 900 16508 0 . 0 . COSM1343092 61 0,0,17,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D388E|1798|MAST2|protein_coding|CODING|NM_015112.2|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11211247 -0.693147 0.01106 61 I659M 1798 atT/atG MODERATE 17 MISSENSE CODING MAST2 G protein_coding NM_015112.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46493460 T G 0 222 0 0.4259 0.4852 0.4827 0.6607 0.4463 0.4264 0.415925 0.429693 0.436037 1 4138 55687 6225 5526 2773 29388 400 7237 2 9802 120748 11572 8612 6612 66738 900 16512 0.999401 0 . 0 . 98 35,17,18,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I659M|1798|MAST2|protein_coding|CODING|NM_015112.2|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.951316 rs1707336 -0.693136 0.199886 98 S913 1798 tcA/tcG LOW 23 SILENT CODING MAST2 G protein_coding NM_015112.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46496709 A G 0 222 0 0.5794 0.644 0.6297 0.6984 0.7396 0.5869 0.630626 0.689819 0.718743 1 5864 82655 7567 5824 4899 47379 627 10495 2 9708 119656 11468 8518 6554 66184 884 16340 0.454483 0 . 0 . 57 9,22,10,14 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S913|1798|MAST2|protein_coding|CODING|NM_015112.2|23|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90034 rs925524 -0.692831 0.410311 57 V1174 1798 gtA/gtG LOW 26 SILENT CODING MAST2 G protein_coding NM_015112.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46498375 A G 0 222 0 0.7534 0.6877 0.6441 0.7073 0.7346 0.5613 0.75 0.723547 0.71 1 7693 84215 7597 5929 4926 47331 638 10101 2 10176 120810 11564 8614 6606 66630 906 16314 0.691194 0 . 0 . 78 14,23,10,27 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1174|1798|MAST2|protein_coding|CODING|NM_015112.2|26|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.845979 rs1622208 -0.693141 0.40162 78 G1468A 1798 gGg/gCg MODERATE 29 MISSENSE CODING MAST2 C protein_coding NM_015112.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46500744 G C 0 222 0 0.0008 0.0789 0.0476 0.1389 0.0298 0.1953 0.00916295 0.0216828 0.0277578 1 56 6274 682 1360 134 1604 42 2396 2 9086 117706 11476 8506 6536 64736 886 16480 0.970324 0 . 0 . 35 6,9,12,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G1468A|1798|MAST2|protein_coding|CODING|NM_015112.2|29|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931181 rs3737737,rs386488747 -0.690438 0.139981 35 G1703 1798 ggG/ggA LOW 29 SILENT CODING MAST2 A protein_coding NM_015112.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46501450 G A 0 222 0 0 0.0021965 0 0.0099 0 0.001 0 . 0 1 0 168 0 165 0 1 1 1 2 9760 120496 11554 8616 6610 66554 896 16506 0.437593 0 . 0 . 43 8,7,16,10 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1703|1798|MAST2|protein_coding|CODING|NM_015112.2|29|A),DOWNSTREAM(MODIFIER||4362||507|PIK3R3|protein_coding|CODING|NM_001303427.1||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.863708 rs201472561 -0.692976 0.538638 43 507 1677 MODIFIER 10 CODING PIK3R3 C protein_coding NM_001303427.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46507668 T C 0 36.3 0 0 0.0445 0.1254 0.128 0 0.0072 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1677||507|PIK3R3|protein_coding|CODING|NM_001303427.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11548677 -0.453602 0.84 2 507 576 MODIFIER 10 CODING PIK3R3 G protein_coding NM_001303427.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46508769 A G 0 222 0 0.5893 0.6382 0.6254 0.6885 0.7336 0.5634 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870697 0 . 0 . 42 12,8,13,5 UTR_3_PRIME(MODIFIER||576||507|PIK3R3|protein_coding|CODING|NM_001303427.1|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997333 rs1707337 -0.691153 0.480731 42 S343 507 agC/agT LOW 7 SILENT CODING PIK3R3 A protein_coding NM_001303427.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46521517 G A 0 222 0 0.5893 0.638 0.6254 0.6885 0.7336 0.5624 0.600999 0.671536 0.707674 1 6258 82425 7510 5814 4928 47262 632 10021 2 10382 121028 11570 8640 6610 66642 906 16278 0.954942 0 . 0 . 66 15,15,13,14 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S343|507|PIK3R3|protein_coding|CODING|NM_001303427.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.851333 rs785468 -0.693021 0.0342155 66 N329K 507 aaT/aaA MODERATE 7 MISSENSE CODING PIK3R3 T protein_coding NM_001303427.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46521559 A T 0 222 0 0.7474 0.6821 0.6412 0.6885 0.7346 0.5624 0.738084 0.718284 0.70814 1 7767 84204 7589 5814 4928 47343 640 10123 2 10386 121330 11576 8648 6612 66706 908 16494 0.835242 0 . 0 . 52 10,12,11,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N329K|507|PIK3R3|protein_coding|CODING|NM_001303427.1|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.808631 rs785467 -0.692976 0.856568 52 M623V 748 Atg/Gtg MODERATE 21 MISSENSE CODING POMGNT1 C protein_coding NM_001243766.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46655158 T C 0 228 0 0.789 0.9425 0.987 1 1 1 0.827735 0.941258 0.999419 2 8439 118490 11371 8638 6526 66301 892 16323 2 10268 120436 11456 8638 6526 66322 900 16326 0 2 benign 0 . 56 0,0,19,34 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Atg/Gtg|M623V|748|POMGNT1|protein_coding|CODING|NM_001243766.1|21|C),DOWNSTREAM(MODIFIER||3524||241|TSPAN1|protein_coding|CODING|NM_005727.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6659553 -0.693147 0.200257 56 A730 747 gcC/gcT LOW 19 SILENT CODING RAD54L T protein_coding NM_001142548.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46743900 C T 0 218 0 0.0257 0.1857 0.1167 0.2768 0.1382 0.4059 0.043123 0.0949562 0.121512 1 430 18628 1144 2590 547 7671 164 6082 2 9878 116768 11098 8500 5996 64418 834 16044 0.982926 0 . 0 . 43 16,7,7,9 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A730|747|RAD54L|protein_coding|CODING|NM_001142548.1|19|T),DOWNSTREAM(MODIFIER||172||812|LRRC41|protein_coding|CODING|NM_006369.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999898 rs1048771 -0.689466 0.705858 43 V609I 812 Gtt/Att MODERATE 6 MISSENSE CODING LRRC41 T protein_coding NM_006369.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46746164 C T 0 222 0 0.0265 0.1859 0.1167 0.2758 0.1392 0.4059 0.04335 0.0954175 0.122093 1 440 18949 1164 2646 569 7798 171 6161 2 10348 121280 11578 8642 6614 66678 908 16512 0.762693 0 . 0 . 73 12,24,8,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V609I|812|LRRC41|protein_coding|CODING|NM_006369.4|6|T),DOWNSTREAM(MODIFIER||2019||747|RAD54L|protein_coding|CODING|NM_001142548.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999405 rs11542623,rs386518841 -0.693136 0.426175 73 384 257 MODIFIER 1 CODING NSUN4 T protein_coding NM_199044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46806242 G T 0 45.8 0 0.1384 0.1338 0.147 0.0188 0.2783 0.0879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,0,3,0 START_GAINED(LOW||||384|NSUN4|protein_coding|CODING|NM_199044.3|1|T),UTR_5_PRIME(MODIFIER||257||384|NSUN4|protein_coding|CODING|NM_199044.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.333333 rs67545510 -0.511536 0.529687 5 384 106 MODIFIER 1 CODING NSUN4 C protein_coding NM_199044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46806393 T C 0 121 0 0.1392 0.1338 0.147 0.0188 0.2773 0.0879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.733615 0 . 0 . 48 26,2,13,1 UTR_5_PRIME(MODIFIER||106||384|NSUN4|protein_coding|CODING|NM_199044.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.932611 rs41293273 -0.686358 0.0274129 48 384 70 MODIFIER 1 CODING NSUN4 T protein_coding NM_199044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46806429 A T 0 213 0 0.115 0.1276 0.147 0.0188 0.2783 0.0879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.984977 0 . 0 . 79 34,7,29,4 UTR_5_PRIME(MODIFIER||70||384|NSUN4|protein_coding|CODING|NM_199044.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.84697 rs41293275 -0.693127 0.291531 79 384 19 MODIFIER 1 CODING NSUN4 T protein_coding NM_199044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46806480 C T 0 222 0 0.115 0.1274 0.147 0.0188 0.2773 0.0879 0.137665 0.237348 0.288372 1 1106 21279 1052 157 1307 16040 151 1466 2 6380 79542 5996 4232 3466 47542 594 11332 0.999948 0 . 0 . 113 51,10,35,6 UTR_5_PRIME(MODIFIER||19||384|NSUN4|protein_coding|CODING|NM_199044.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7959 rs17361749 -0.693145 0.781599 113 L18F 384 Ctc/Ttc MODERATE 1 MISSENSE CODING NSUN4 T protein_coding NM_199044.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46806550 C T 0 222 0 0.115 0.1272 0.147 0.0179 0.2773 0.0879 0.137148 0.239502 0.291928 1 1340 25506 1295 181 1863 18944 185 1698 2 9114 112352 10668 8100 5372 62788 804 15506 0.992555 0 . 0 . 143 39,35,31,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L18F|384|NSUN4|protein_coding|CODING|NM_199044.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.599797 rs41293277 -0.693147 0.74876 143 D97 384 gaT/gaC LOW 2 SILENT CODING NSUN4 C protein_coding NM_199044.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46810670 T C 0 222 0 0.1331 0.1318 0.147 0.0179 0.2724 0.092 0.152746 0.243426 0.289884 1 1539 26442 1343 182 2052 19372 200 1754 2 10406 121392 11578 8650 6610 66730 908 16510 0.848083 0 . 0 . 99 14,29,12,38 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D97|384|NSUN4|protein_coding|CODING|NM_199044.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.591463 rs17361763 -0.693147 0.01132 99 I365V 384 Ata/Gta MODERATE 6 MISSENSE CODING NSUN4 G protein_coding NM_199044.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46827456 A G 0 222 0 0.0552 0.2037 0.1254 0.2798 0.1501 0.4366 0.0637767 0.110795 0.134884 1 666 20823 1294 2721 601 8850 177 6514 2 10404 121346 11566 8612 6614 66732 908 16510 0.0502482 0 . 0 . 99 13,33,16,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I365V|384|NSUN4|protein_coding|CODING|NM_199044.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.447997 rs9865 -0.693146 0.604418 99 P374 384 ccC/ccT LOW 6 SILENT CODING NSUN4 T protein_coding NM_199044.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46827485 C T 0 222 0 . 0 . 0 . 0 0.152519 0.243349 0.289884 1 1538 26413 1339 182 2048 19351 200 1755 2 10370 120806 11498 8544 6590 66470 904 16430 0.685969 0 . 0 . 79 14,31,9,23 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P374|384|NSUN4|protein_coding|CODING|NM_199044.3|6|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.766819 rs1053624 -0.69312 0.0518324 79 384 210 MODIFIER 6 CODING NSUN4 C protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46827728 A C 0 222 0 0.1339 0.132 0.147 0.0179 0.2724 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.270994 0 . 0 . 78 25,14,19,11 UTR_3_PRIME(MODIFIER||210||384|NSUN4|protein_coding|CODING|NM_199044.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.680401 rs1053627 -0.693097 0.205073 78 384 251 MODIFIER 6 CODING NSUN4 T protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46827769 C T 0 222 0 0.1331 0.132 0.147 0.0179 0.2724 0.093 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.558871 0 . 0 . 83 25,13,22,10 UTR_3_PRIME(MODIFIER||251||384|NSUN4|protein_coding|CODING|NM_199044.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996601 rs1053628 -0.69312 0.526223 83 384 353 MODIFIER 6 CODING NSUN4 A protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46827871 G A 0 222 0 0.1331 0.1318 0.147 0.0179 0.2724 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999985 0 . 0 . 83 23,20,14,17 UTR_3_PRIME(MODIFIER||353||384|NSUN4|protein_coding|CODING|NM_199044.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.791019 rs6429599 -0.69311 0.00638266 83 384 591 MODIFIER 6 CODING NSUN4 G protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46828109 A G 0 17.5 0 0.1331 0.1318 0.147 0.0179 0.2724 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 1,2,0,2 UTR_3_PRIME(MODIFIER||591||384|NSUN4|protein_coding|CODING|NM_199044.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs17361819 -0.453602 0.28 5 384 842 MODIFIER 6 CODING NSUN4 T protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46828360 C T 0 32.6 0 0.0552 0.2037 0.1254 0.2798 0.1501 0.4366 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||842||384|NSUN4|protein_coding|CODING|NM_199044.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs41294484 -0.379885 0 2 384 1495 MODIFIER 6 CODING NSUN4 G protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46829013 A G 0 9.7 0 0.1331 0.1318 0.147 0.0179 0.2724 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1495||384|NSUN4|protein_coding|CODING|NM_199044.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17357711 -0.379885 0 1 384 2912 MODIFIER 6 CODING NSUN4 A protein_coding NM_199044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46830430 G A 0 9.7 0 0.5053 0.4185 0.2839 0.2976 0.4125 0.5276 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2912||384|NSUN4|protein_coding|CODING|NM_199044.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10252 -0.379885 0 1 C299 579 tgT/tgC LOW 7 SILENT CODING FAAH C protein_coding NM_001441.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46871986 T C 0 228 0 0.8585 0.8844 0.9265 0.995 0.8519 0.8088 0.851112 0.841765 0.836977 2 8897 104275 10779 8634 6117 56074 778 12996 2 10404 121354 11570 8652 6612 66700 904 16512 0 . 0 . 0 99 0,0,29,58 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C299|579|FAAH|protein_coding|CODING|NM_001441.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs324419 -0.693147 0.0148688 99 382 331 MODIFIER 4 CODING DMBX1 T protein_coding NM_147192.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46978497 C T 0 228 0 0.1672 0.2075 0.121 0.244 0.2187 0.274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,2,39 UTR_3_PRIME(MODIFIER||331||382|DMBX1|protein_coding|CODING|NM_147192.2|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2209172 -0.693145 0.00164837 42 382 780 MODIFIER 4 CODING DMBX1 T protein_coding NM_147192.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 46978946 C T 0 32.6 0 0.1664 0.2073 0.1225 0.244 0.2187 0.273 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||780||382|DMBX1|protein_coding|CODING|NM_147192.2|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs386487136,rs56393814 -0.379885 0 2 101 1715 MODIFIER 3 CODING KNCN G protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47011687 C G 0 134 0 0.618 0.5657 0.5029 0.6677 0.4801 0.5225 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,3 UTR_3_PRIME(MODIFIER||1715||101|KNCN|protein_coding|CODING|NM_001097611.1|3|G),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1258036 -0.590765 0.636041 5 101 1640 MODIFIER 3 CODING KNCN G protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47011762 A G 0 175 0 0.6407 0.5727 0.5086 0.6657 0.4821 0.5235 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,3,2 UTR_3_PRIME(MODIFIER||1640||101|KNCN|protein_coding|CODING|NM_001097611.1|3|G),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs885125 -0.590765 0.409395 7 101 1530 MODIFIER 3 CODING KNCN T protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47011872 C T 0 46.3 0 0.6112 0.5547 0.4971 0.6627 0.4463 0.5194 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1530||101|KNCN|protein_coding|CODING|NM_001097611.1|3|T),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs885126 -0.453602 0.48 2 101 954 MODIFIER 3 CODING KNCN C protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47012448 T C 0 9.7 0 0.1256 0.232 0.1383 0.3323 0.2286 0.3425 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||954||101|KNCN|protein_coding|CODING|NM_001097611.1|3|C),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4442318 -0.379885 0 1 101 700 MODIFIER 3 CODING KNCN G protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47012702 A G 0 125 0 0.9871 0.9103 0.9957 0.6915 0.9911 0.8885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,1 UTR_3_PRIME(MODIFIER||700||101|KNCN|protein_coding|CODING|NM_001097611.1|3|G),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs942079 -0.556411 0.491115 5 101 38 MODIFIER 3 CODING KNCN C protein_coding NM_001097611.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47013364 T C 0 228 0 0.9871 0.9093 0.9957 0.6905 0.9911 0.8845 0.983657 0.992201 0.996592 2 2597 17650 455 513 298 8289 161 5337 2 2642 18426 458 706 306 8340 174 5800 0 . 0 . 0 100 0,0,53,40 UTR_3_PRIME(MODIFIER||38||101|KNCN|protein_coding|CODING|NM_001097611.1|3|C),INTRAGENIC(MODIFIER|||||MKNK1-AS1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1258041 -0.693147 0.0768851 100 465 116 MODIFIER 2 CODING MKNK1 C protein_coding NM_003684.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47059934 T C 0 207 0 0.9902 0.9966 0.9986 1 0.998 0.999 0 . 0 2 8478 101324 9007 6734 6004 54882 770 15449 2 8546 101504 9016 6734 6038 54940 772 15458 0 . 0 . 0 27 0,0,1,26 UTR_5_PRIME(MODIFIER||116||465|MKNK1|protein_coding|CODING|NM_003684.5|2|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1258021 -0.693021 0.0269661 27 268 1848 MODIFIER 4 CODING MOB3C C protein_coding NM_145279.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47073478 CT C 0 9.7 0 0.121 0.3383 0.1787 0.6875 0.2296 0.4969 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1848||268|MOB3C|protein_coding|CODING|NM_145279.4|4|C),UPSTREAM(MODIFIER||3513||465|MKNK1|protein_coding|CODING|NM_003684.5||C) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs11333814 -0.379885 0 1 268 865 MODIFIER 4 CODING MOB3C G protein_coding NM_145279.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47074462 A G 0 228 0 0.0144 0.136 0.0793 0.128 0.174 0.3098 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 0,0,16,49 UTR_3_PRIME(MODIFIER||865||268|MOB3C|protein_coding|CODING|NM_145279.4|4|G),UPSTREAM(MODIFIER||4496||465|MKNK1|protein_coding|CODING|NM_003684.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2181413,rs386559968 -0.693147 0.60166 71 268 706 MODIFIER 4 CODING MOB3C C protein_coding NM_145279.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47074621 G C 0 228 0 0.8979 0.9714 0.9914 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,4,10 UTR_3_PRIME(MODIFIER||706||268|MOB3C|protein_coding|CODING|NM_145279.4|4|C),UPSTREAM(MODIFIER||4655||465|MKNK1|protein_coding|CODING|NM_003684.5||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1313388 -0.686358 0.167284 14 268 553 MODIFIER 4 CODING MOB3C A protein_coding NM_145279.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47074774 T A 0 228 0 0.472 0.6404 0.5533 0.9573 0.498 0.7495 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 67 0,0,52,7 UTR_3_PRIME(MODIFIER||553||268|MOB3C|protein_coding|CODING|NM_145279.4|4|A),UPSTREAM(MODIFIER||4808||465|MKNK1|protein_coding|CODING|NM_003684.5||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4275405 -0.693147 0.00545577 67 A171 268 gcA/gcG LOW 2 SILENT CODING MOB3C C protein_coding NM_145279.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47078637 T C 0 228 0 0.5779 0.6731 0.5677 0.9583 0.5 0.7607 0.572694 0.511386 0.479991 2 5798 69277 6764 8151 3640 32775 509 11640 2 10106 118358 11526 8620 6608 65576 884 15038 0 . 0 . 0 104 0,0,51,49 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A171|268|MOB3C|protein_coding|CODING|NM_145279.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4660947 -0.693147 0.46248 104 R24* 268 Cga/Tga HIGH 1 NONSENSE CODING MOB3C A protein_coding NM_145279.4 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47080679 G A 0 228 0 0.5643 0.6422 0.5202 0.9256 0.4751 0.7137 0.557876 0.49877 0.468488 2 5776 67615 6072 7930 3318 32048 502 11969 2 10392 121342 11566 8650 6610 66704 908 16512 0 . 0 . 0 82 0,0,41,30 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R24*|268|MOB3C|protein_coding|CODING|NM_145279.4|1|A) 1 0 . 0 . 1 0 1 1 (MOB3C|MOB3C|1|1.00) 60 0 0 1 (MOB3C|MOB3C|1|1.00) 0 rs386429394,rs6671527 -0.693147 0.609433 82 351 433 MODIFIER 9 CODING ATPAF1 A protein_coding NM_022745.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47101015 C A 0 165 0 0.5356 0.7408 0.9323 0.5288 0.9831 0.8517 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 17 1,0,15,1 UTR_3_PRIME(MODIFIER||433||351|ATPAF1|protein_coding|CODING|NM_022745.4|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs724309 -0.689466 0.134516 17 S85G 351 Agc/Ggc MODERATE 1 MISSENSE CODING ATPAF1 C protein_coding NM_022745.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47133811 T C 0 100 0 0.8631 0.8347 0.8818 0.9345 0.7853 0.7106 0 . 0 2 144 5359 55 117 0 1385 61 3597 2 178 7298 70 130 0 1772 86 5062 0 . 0 . 0 4 0,0,1,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S85G|351|ATPAF1|protein_coding|CODING|NM_022745.4|1|C),UPSTREAM(MODIFIER||3694||206|TEX38|protein_coding|CODING|NM_001145474.3||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs11211337 -0.511536 0.732596 4 D104E 206 gaT/gaG MODERATE 2 MISSENSE CODING TEX38 G protein_coding NM_001145474.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47138819 T G 0 222 0 0.6513 0.5393 0.4625 0.7996 0.3121 0.408 0.590318 0.369032 0.272784 1 1287 7961 176 474 447 2568 82 2927 2 2184 21580 408 622 1502 8730 240 7894 0.611624 0 . 0 . 137 28,32,33,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D104E|206|TEX38|protein_coding|CODING|NM_001145474.3|2|G),UPSTREAM(MODIFIER||4720||351|ATPAF1|protein_coding|CODING|NM_022745.4||G),DOWNSTREAM(MODIFIER||2012||495|EFCAB14|protein_coding|CODING|NM_014774.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.854039 rs386601751,rs614486 -0.693147 0.10873 137 A199V 206 gCc/gTc MODERATE 2 MISSENSE CODING TEX38 T protein_coding NM_001145474.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47139103 C T 0 222 0 0.1785 0.2662 0.3545 0.3353 0.2972 0.2188 0.186416 0.242444 0.266813 1 450 5821 148 203 432 2664 60 1864 2 2260 21560 408 618 1684 9146 238 7206 0.994294 0 . 0 COSM1343165,COSM1343164 95 21,18,23,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A199V|206|TEX38|protein_coding|CODING|NM_001145474.3|2|T),DOWNSTREAM(MODIFIER||1728||495|EFCAB14|protein_coding|CODING|NM_014774.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.285055 rs1025806,rs386511516 -0.693143 0.0907178 95 495 2415 MODIFIER 11 CODING EFCAB14 C protein_coding NM_014774.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47141718 T C 0 9.7 0 0.8472 0.8299 0.8818 0.9345 0.7843 0.7086 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2415||495|EFCAB14|protein_coding|CODING|NM_014774.2|11|C),DOWNSTREAM(MODIFIER||2462||206|TEX38|protein_coding|CODING|NM_001145474.3||C),INTRAGENIC(MODIFIER|||||EFCAB14-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12794 -0.379885 0 1 495 1595 MODIFIER 11 CODING EFCAB14 A protein_coding NM_014774.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47142538 G A 0 136 0 0.1362 0.2548 0.3545 0.3343 0.2972 0.2188 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.6555 0 . 0 . 43 19,7,16,1 UTR_3_PRIME(MODIFIER||1595||495|EFCAB14|protein_coding|CODING|NM_014774.2|11|A),DOWNSTREAM(MODIFIER||3282||206|TEX38|protein_coding|CODING|NM_001145474.3||A),INTRAGENIC(MODIFIER|||||EFCAB14-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998074 rs1048380 -0.690438 0.0140488 43 495 653 MODIFIER 11 CODING EFCAB14 T protein_coding NM_014774.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47143480 C T 0 104 0 0.1793 0.2662 0.3545 0.3353 0.2962 0.2188 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.707715 0 . 0 . 20 10,0,10,0 UTR_3_PRIME(MODIFIER||653||495|EFCAB14|protein_coding|CODING|NM_014774.2|11|T),DOWNSTREAM(MODIFIER||4224||206|TEX38|protein_coding|CODING|NM_001145474.3||T),INTRAGENIC(MODIFIER|||||EFCAB14-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.965605 rs1048351 -0.670168 0.142559 20 495 586 MODIFIER 11 CODING EFCAB14 G protein_coding NM_014774.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47143547 A G 0 147 0 0.649 0.5387 0.4625 0.7996 0.3121 0.408 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992545 0 . 0 . 42 22,0,17,1 UTR_3_PRIME(MODIFIER||586||495|EFCAB14|protein_coding|CODING|NM_014774.2|11|G),DOWNSTREAM(MODIFIER||4291||206|TEX38|protein_coding|CODING|NM_001145474.3||G),INTRAGENIC(MODIFIER|||||EFCAB14-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.95627 rs13417 -0.691153 0.526397 42 495 810 MODIFIER 1 CODING EFCAB14 C protein_coding NM_014774.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47184569 G C 0 56 0 0.1369 0.2552 0.3545 0.3353 0.2972 0.2188 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.406082 0 . 0 . 9 5,0,4,0 UTR_5_PRIME(MODIFIER||810||495|EFCAB14|protein_coding|CODING|NM_014774.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 0 . 0.406082 rs8851 -0.556411 0.308689 9 R173W 512 Cgg/Tgg MODERATE 5 MISSENSE CODING CYP4B1 T protein_coding NM_001099772.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47279175 C T 0 222 0 0.2027 0.1845 0.1138 0.2123 0.1372 0.2301 0.186337 0.148547 0.129186 1 1919 18172 1411 1656 682 8035 120 4349 2 10400 121302 11568 8620 6610 66688 908 16508 0.929551 0 . 0 . 132 29,30,25,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R173W|512|CYP4B1|protein_coding|CODING|NM_001099772.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.127646 rs4646487 -0.693147 0.165189 132 512 40 MODIFIER 12 CODING CYP4B1 A protein_coding NM_001099772.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47284526 C A 0 113 0 0.0477 0.1316 0.1009 0.2192 0.1203 0.1881 0.0642306 0.099877 0.11814 1 596 14698 1240 1611 643 7340 104 3164 2 10096 117878 11378 8360 6508 65010 880 15646 0.352227 0 . 0 . 22 1,10,1,10 UTR_3_PRIME(MODIFIER||40||512|CYP4B1|protein_coding|CODING|NM_001099772.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986616 rs3766196 -0.676189 0.765622 22 512 86 MODIFIER 12 CODING CYP4B1 A protein_coding NM_001099772.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47284572 G A 0 51 0 0.3064 0.2184 0.1254 0.2192 0.1402 0.2454 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.236382 0 . 0 . 12 0,8,0,4 UTR_3_PRIME(MODIFIER||86||512|CYP4B1|protein_coding|CODING|NM_001099772.1|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3766195 -0.556411 0.0238972 12 I458 519 atC/atT LOW 12 SILENT CODING CYP4A11 A protein_coding NM_000778.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47395973 G A 0 222 0 0.3449 0.5715 0.683 0.495 0.7773 0.6656 0.424194 0.660234 0.781163 1 4289 85002 8083 4476 5121 52136 647 10250 2 10398 120882 11570 8638 6614 66624 900 16138 0.804276 0 . 0 . 110 18,41,7,37 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I458|519|CYP4A11|protein_coding|CODING|NM_000778.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.819991 rs1126743 -0.693146 0.177114 110 F434S 519 tTc/tCc MODERATE 11 MISSENSE CODING CYP4A11 G protein_coding NM_000778.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47398496 A G 0 222 0 0.3336 0.2414 0.1542 0.2579 0.1451 0.2607 0.288924 0.183608 0.129651 1 3286 21428 1593 2017 823 8802 151 4756 2 10404 121398 11576 8652 6612 66734 908 16512 0.552179 0 . 0 . 226 60,45,57,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F434S|519|CYP4A11|protein_coding|CODING|NM_000778.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.00603441 0.290597 0 0.803606 rs1126742 -0.693147 0.491279 226 H323 519 caC/caT LOW 8 SILENT CODING CYP4A11 A protein_coding NM_000778.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47399967 G A 0 203 0 0.528 0.3942 0.3112 0.504 0.2237 0.3344 0.472525 0.304938 0.218677 1 4966 34483 3348 4050 1472 14279 248 6120 2 10224 118740 11254 8400 6492 65214 888 16268 0.867099 0 . 0 . 71 27,18,9,13 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H323|519|CYP4A11|protein_coding|CODING|NM_000778.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 51 0 0.922919 0.924547 0 0.896569 rs28451040 -0.692562 0.663751 71 I390 505 atC/atT LOW 9 SILENT CODING CYP4Z1 T protein_coding NM_178134.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47571902 C T 0 222 0 0.5121 0.5897 0.4683 0.9563 0.34 0.6595 0.49478 0.383438 0.326395 1 5069 51351 4958 7225 2589 21823 387 9300 2 10368 120374 11484 8428 6584 66356 904 16250 0.729814 0 . 0 . 203 23,75,17,77 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I390|505|CYP4Z1|protein_coding|CODING|NM_178134.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.163534 0.989926 0 0.00514974 rs4926802 -0.693147 5.91691e-06 203 T391 505 acC/acT LOW 9 SILENT CODING CYP4Z1 T protein_coding NM_178134.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47571905 C T 0 222 0 0.4766 0.5795 0.4654 0.9563 0.339 0.6585 0 . 0 1 4803 51045 4940 7231 2584 21804 387 9296 2 10372 120370 11492 8432 6580 66346 904 16244 0.972746 0 . 0 . 198 23,70,17,77 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T391|505|CYP4Z1|protein_coding|CODING|NM_178134.2|9|T) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.173645 0.985431 0 0.0233445 rs28463559 -0.693147 5.90223e-06 198 R126W 519 Cgg/Tgg MODERATE 3 MISSENSE CODING CYP4A22 T protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47607281 C T 0 222 0 0.2254 0.3712 0.2867 0.6141 0.2058 0.5481 0.249433 0.223051 0.209535 1 2502 35414 3373 5253 1366 13981 251 8688 2 10404 121338 11572 8634 6612 66704 908 16504 0.676489 0 . 0 . 299 77,81,53,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R126W|519|CYP4A22|protein_coding|CODING|NM_001010969.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913422 rs12564525 -0.693147 5.6017e-05 299 G130S 519 Ggc/Agc MODERATE 4 MISSENSE CODING CYP4A22 A protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47607785 G A 0 222 0 0.2073 0.3363 0.232 0.5546 0.1928 0.5072 0.228098 0.210518 0.201512 1 2307 32296 2669 4739 1284 13402 223 7672 2 10388 119880 11560 8606 6606 66128 886 15706 0.971344 0 . 0 . 155 52,15,57,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G130S|519|CYP4A22|protein_coding|CODING|NM_001010969.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.580861 0.797611 0 0.964631 rs2056900 -0.693147 0.0292728 155 N152Y 519 Aat/Tat MODERATE 4 MISSENSE CODING CYP4A22 T protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47607851 A T 0 222 0 0.944 0.7308 0.5072 0.9802 0.4036 0.681 0.848162 0.542903 0.386512 1 8998 64171 5756 8493 2911 26357 472 11184 2 10404 121058 11564 8642 6598 66580 902 16368 0.370548 0 . 0 . 198 69,26,70,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N152Y|519|CYP4A22|protein_coding|CODING|NM_001010969.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.00260784 0.174741 0 0.945822 rs2056899,rs55910803 -0.693147 0.695784 198 V185F 519 Gtc/Ttc MODERATE 5 MISSENSE CODING CYP4A22 T protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47608983 G T 0 222 0 0.2057 0.3357 0.232 0.5536 0.1928 0.5072 0.228325 0.210506 0.201373 1 2308 32469 2673 4730 1285 13416 224 7833 2 10402 121200 11558 8608 6606 66626 904 16496 0.639111 0 . 0 . 154 37,27,40,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ttc|V185F|519|CYP4A22|protein_coding|CODING|NM_001010969.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 43 0 0.749228 7.49947e-05 0 0.82772 rs113777592 -0.693147 0.9633 154 C231R 519 Tgt/Cgt MODERATE 6 MISSENSE CODING CYP4A22 C protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47609489 T C 0 222 0 0.5015 0.5807 0.464 0.9335 0.3489 0.6452 0.496369 0.391665 0.338023 1 5132 55083 5320 8096 2475 23188 392 10480 2 10404 121288 11568 8650 6612 66652 906 16496 0.999232 0 . 0 . 164 44,29,36,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C231R|519|CYP4A22|protein_coding|CODING|NM_001010969.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.727088 rs10789501,rs386515250 -0.693147 0.146643 164 K276T 519 aAg/aCg MODERATE 7 MISSENSE CODING CYP4A22 C protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47610065 A C 0 222 0 0.0121 0.1418 0.1009 0.3075 0.0775 0.2413 0.0256468 0.0666615 0.0876744 1 261 13978 1260 2624 353 5650 91 3739 2 10406 121276 11576 8636 6612 66678 906 16462 0.965476 0 . 0 . 226 88,22,74,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K276T|519|CYP4A22|protein_coding|CODING|NM_001010969.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 52 0 0.901354 0.988738 0 0.973327 rs149718343 -0.693147 0.853678 226 L428P 519 cTa/cCa MODERATE 10 MISSENSE CODING CYP4A22 C protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47611598 T C 0 222 0 0.2239 0.3758 0.2896 0.6141 0.2237 0.5532 0.253518 0.234353 0.224535 1 2524 36720 3457 5268 1485 14963 268 8755 2 10404 121362 11576 8636 6614 66720 908 16504 0.969355 0 . 0 . 339 94,74,65,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L428P|519|CYP4A22|protein_coding|CODING|NM_001010969.3|10|C) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.113955 0.556264 0 0.999028 rs2405599 -0.693147 0.159764 339 L509F 519 Ctc/Ttc MODERATE 12 MISSENSE CODING CYP4A22 T protein_coding NM_001010969.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47614434 C T 0 222 0 0.0401 0.1526 0.1023 0.3065 0.0805 0.2556 0.0522015 0.076 0.0882011 1 502 14526 1291 2627 353 5717 93 3943 2 10360 118648 11530 8596 6604 65852 868 14838 0.378613 0 . 0 . 204 37,57,36,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L509F|519|CYP4A22|protein_coding|CODING|NM_001010969.3|12|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.993675 0.9797 0 0.18695 rs4926600 -0.693147 0.0120539 204 114 78 MODIFIER 1 CODING PDZK1IP1 T protein_coding NM_005764.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47655682 C T 0 163 0 0.0083 0.0089856 0 0.0258 0 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.927041 0 . 0 . 28 3,12,3,8 UTR_5_PRIME(MODIFIER||78||114|PDZK1IP1|protein_coding|CODING|NM_005764.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.978682 rs386438802,rs77893010 -0.676189 0.119057 28 331 3375 MODIFIER 5 CODING TAL1 G protein_coding NM_001287347.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47682017 T G 0 121 0 0.3238 0.3662 0.4222 0.0357 0.6103 0.4734 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.887472 0 . 0 . 27 11,1,14,0 UTR_3_PRIME(MODIFIER||3375||331|TAL1|protein_coding|CODING|NM_001287347.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.682307 rs7664 -0.686358 0.0117032 27 331 1928 MODIFIER 5 CODING TAL1 A protein_coding NM_001287347.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47683464 G A 0 9.7 0 0.0038 0.1268 0.0403 0.3274 0.0795 0.1963 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1928||331|TAL1|protein_coding|CODING|NM_001287347.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2070930 -0.379885 0 1 331 743 MODIFIER 5 CODING TAL1 A protein_coding NM_001287347.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47684649 G A 0 103 0 0 0.0045927 0 0.0208 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.962588 0 . 0 . 29 17,0,9,1 UTR_3_PRIME(MODIFIER||743||331|TAL1|protein_coding|CODING|NM_001287347.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.974798 rs75550682 -0.670168 0.788314 29 331 715 MODIFIER 5 CODING TAL1 G protein_coding NM_001287347.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47684677 T G 0 151 0 0.3033 0.3596 0.4207 0.0357 0.6054 0.4734 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.747144 0 . 0 . 40 22,2,10,3 UTR_3_PRIME(MODIFIER||715||331|TAL1|protein_coding|CODING|NM_001287347.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.816744 rs977747 -0.683931 0.0426568 40 331 459 MODIFIER 5 CODING TAL1 C protein_coding NM_001287347.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47684933 T C 0 222 0 0 0.004393 0 0.0198 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.716507 0 . 0 . 100 28,21,23,17 UTR_3_PRIME(MODIFIER||459||331|TAL1|protein_coding|CODING|NM_001287347.2|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.838344 rs116910567 -0.693145 0.66905 100 K311 331 aaA/aaG LOW 5 SILENT CODING TAL1 C protein_coding NM_001287347.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47685455 T C 0 170 0 1 1 1 1 1 1 0 . 0 2 9400 116367 11370 8366 6354 63637 846 16394 2 9400 116368 11370 8366 6354 63638 846 16394 0 . 0 . 0 34 0,0,0,34 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K311|331|TAL1|protein_coding|CODING|NM_001287347.2|5|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs927462 -0.693132 0.0196187 34 P1162 1288 ccT/ccC LOW 17 SILENT CODING STIL G protein_coding NM_001048166.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47717189 A G 0 222 0 0.1218 0.3934 0.4078 0.4296 0.5427 0.5593 0.181117 0.408504 0.525 1 1679 60422 5211 3886 4322 36015 501 8808 2 10386 121360 11572 8648 6614 66726 906 16508 0.961309 2|2 benign|benign 0 . 49 10,7,13,15 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1162|1288|STIL|protein_coding|CODING|NM_001048166.1|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.830905 rs2758735 -0.693054 0.804903 49 S484 1288 tcC/tcG LOW 12 SILENT CODING STIL C protein_coding NM_001048166.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47746678 G C 0 222 0 0.3911 0.232 0.0677 0.3095 0.0905 0.1994 0.337721 0.165001 0.0765116 1 3621 15397 524 2680 357 5248 95 2872 2 10402 121370 11576 8640 6614 66724 908 16506 0.988783 2 benign 0 . 128 36,22,34,22 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S484|1288|STIL|protein_coding|CODING|NM_001048166.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980515 rs10789505 -0.693147 0.328924 128 A86V 1288 gCa/gTa MODERATE 4 MISSENSE CODING STIL A protein_coding NM_001048166.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47767914 G A 0 222 0 0.8805 0.6064 0.5937 0.5675 0.4553 0.4407 0.819791 0.593111 0.476977 1 8726 60901 6312 4745 2294 30719 403 7702 2 10386 120968 11518 8628 6586 66468 902 16480 0.935452 2|3 benign|likely-benign 0 . 158 52,17,51,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A86V|1288|STIL|protein_coding|CODING|NM_001048166.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97142 rs3125630 -0.693147 0.155085 158 228 10 MODIFIER 1 CODING CMPK1 C protein_coding NM_016308.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47799608 G C 0 23.2 0 0 0.0057907 0.0029 0.0169 0.006 0.0041 0.000954198 0.00319642 0.00432588 1 2 230 8 51 1 108 1 59 2 760 14812 486 708 140 5698 140 6880 0 0 . 0 . 4 2,0,2,0 UTR_5_PRIME(MODIFIER||10||228|CMPK1|protein_coding|CODING|NM_016308.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.5 rs66904716 -0.453602 0.18 4 G8R 228 Ggg/Cgg MODERATE 1 MISSENSE CODING CMPK1 C protein_coding NM_016308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47799639 G C 0 86 0 0.8245 0.5964 0.5893 0.5843 0.4602 0.4458 0.762333 0.56907 0.470484 2 3348 28554 2818 2471 533 14072 188 5124 2 4202 50566 4554 3898 1096 26176 354 10286 0 . 0 . 0 4 0,0,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Cgg|G8R|228|CMPK1|protein_coding|CODING|NM_016308.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs7543016 -0.556411 0.0257451 4 N115S 228 aAt/aGt MODERATE 3 MISSENSE CODING CMPK1 G protein_coding NM_016308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47838652 A G 0 222 0 0 0.0057907 0.0029 0.0169 0.006 0.0041 0.00136178 0.00492081 0.00674419 1 21 774 41 262 11 349 1 89 2 10290 119984 11440 8520 6578 65944 898 16314 0.466384 0 . 0 COSM146505 98 35,9,33,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N115S|228|CMPK1|protein_coding|CODING|NM_016308.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.648614 rs72553947 -0.693146 0.0116739 98 228 14 MODIFIER 6 CODING CMPK1 A protein_coding NM_016308.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47842431 G A 0 228 0 0.8381 0.9537 0.9769 1 0.998 1 0.847935 0.947316 0.998255 2 8711 119489 11494 8654 6614 66619 896 16501 2 10378 121342 11570 8654 6614 66710 906 16510 0 . 0 . 0 77 0,0,46,24 UTR_3_PRIME(MODIFIER||14||228|CMPK1|protein_coding|CODING|NM_016308.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3125648 -0.693147 0.0739696 77 228 249 MODIFIER 6 CODING CMPK1 T protein_coding NM_016308.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47842666 A T 0 228 0 0.9213 0.9772 0.987 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 110 0,0,62,34 UTR_3_PRIME(MODIFIER||249||228|CMPK1|protein_coding|CODING|NM_016308.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2820981 -0.693147 0.39758 110 228 1106 MODIFIER 6 CODING CMPK1 G protein_coding NM_016308.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47843523 A G 0 222 0 0 0.0059904 0.0029 0.0169 0.006 0.0051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.88368 0 . 0 . 71 9,25,11,13 UTR_3_PRIME(MODIFIER||1106||228|CMPK1|protein_coding|CODING|NM_016308.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.72314 rs78590846 -0.692831 0.0383141 71 319 72 MODIFIER 1 CODING FOXE3 C protein_coding NM_012186.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47883019 T C 0 228 0 0.6619 0.7969 0.7709 0.7163 0.9264 0.9479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,28,6 UTR_3_PRIME(MODIFIER||72||319|FOXE3|protein_coding|CODING|NM_012186.2|1|C),INTRAGENIC(MODIFIER|||||LINC01389||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6666370 -0.693132 0.154797 36 319 77 MODIFIER 1 CODING FOXE3 G protein_coding NM_012186.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47883024 A G 0 228 0 0.9811 0.9948 1 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,30,6 UTR_3_PRIME(MODIFIER||77||319|FOXE3|protein_coding|CODING|NM_012186.2|1|G),INTRAGENIC(MODIFIER|||||LINC01389||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2820969 -0.693139 0.298574 38 495 1522 MODIFIER 1 CODING FOXD2 A protein_coding NM_004474.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47902286 G A 0 46.3 0 0.3359 0.4671 0.5259 0.3958 0.5636 0.5767 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||1522||495|FOXD2|protein_coding|CODING|NM_004474.3|1|A),INTRAGENIC(MODIFIER|||||LINC01389||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2622917 -0.453602 0.32 2 495 1043 MODIFIER 1 CODING FOXD2 A protein_coding NM_004474.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 47906338 G A 0 228 0 0.9622 0.989 0.9942 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 0,0,24,66 UTR_3_PRIME(MODIFIER||1043||495|FOXD2|protein_coding|CODING|NM_004474.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2820966 -0.693147 0.00176532 99 517 3631 MODIFIER 7 CODING TRABD2B T protein_coding NM_001194986.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48227943 C T 0 59 0 0.5408 0.4469 0.5245 0.4435 0.4473 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,1 UTR_3_PRIME(MODIFIER||3631||517|TRABD2B|protein_coding|CODING|NM_001194986.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1561573,rs386538048 -0.511536 0.0941127 4 517 1428 MODIFIER 7 CODING TRABD2B A protein_coding NM_001194986.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48230146 T A 0 6.3 0 0.028 0.2288 0.1988 0.5248 0.1372 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1428||517|TRABD2B|protein_coding|CODING|NM_001194986.1|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs34205788 -0.379885 0 1 A155 517 gcG/gcA LOW 2 SILENT CODING TRABD2B T protein_coding NM_001194986.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48459907 C T 0 222 0 0.0144 0.1657 0.2233 0.253 0.2793 0.1227 0 . 0 1 82 5744 260 393 218 3391 54 1346 2 868 19130 610 862 390 8428 170 7802 0.648393 0 . 0 COSM426409 105 27,25,31,12 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A155|517|TRABD2B|protein_coding|CODING|NM_001194986.1|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.970908 rs3814006 -0.693146 0.386534 105 I294M 706 atT/atG MODERATE 8 MISSENSE CODING SLC5A9 G protein_coding NM_001135181.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48697733 T G 0 228 0 1 0.9994 0.9986 1 0.998 1 1 0.999077 0.998605 2 10404 121317 11562 8653 6614 66666 907 16511 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 101 0,0,41,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I294M|706|SLC5A9|protein_coding|CODING|NM_001135181.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs212991 -0.693147 0.373116 101 706 179 MODIFIER 15 CODING SLC5A9 T protein_coding NM_001135181.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48713394 C T 0 181 0 0.4425 0.6737 0.8343 0.751 0.8062 0.6564 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,1,13 UTR_3_PRIME(MODIFIER||179||706|SLC5A9|protein_coding|CODING|NM_001135181.1|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs986027 -0.686358 0.0923728 14 C478Y 488 tGt/tAt MODERATE 13 MISSENSE CODING SPATA6 T protein_coding NM_019073.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48764419 C T 0 222 0 0.025 0.274 0.3329 0.3492 0.4254 0.3354 0.0889696 0.308781 0.421395 1 785 44100 3967 3078 2459 27618 366 5827 2 10406 121296 11556 8646 6612 66680 906 16490 0.544789 0 . 0 COSM146506 137 50,19,38,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C478Y|488|SPATA6|protein_coding|CODING|NM_019073.3|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988928 rs1056042,rs386514401 -0.693147 0.336782 137 488 11 MODIFIER 1 CODING SPATA6 T protein_coding NM_019073.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48937691 A T 0 222 0 0.025 0.2734 0.3386 0.3452 0.4284 0.3292 0.0829064 0.288089 0.392976 1 451 25871 1899 1943 1083 16933 186 3376 2 4324 59516 4320 4664 2430 35506 394 7878 0.273973 0 . 0 . 94 6,35,6,42 UTR_5_PRIME(MODIFIER||11||488|SPATA6|protein_coding|CODING|NM_019073.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0626077 rs2275309 -0.693147 0.172547 94 503 290 MODIFIER 14 CODING AGBL4 C protein_coding NM_032785.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 48999555 T C 0 130 0 0.2753 0.3221 0.2622 0.3929 0.3419 0.3344 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||290||503|AGBL4|protein_coding|CODING|NM_032785.3|14|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2798111 -0.662043 0.644699 9 421 164 MODIFIER 6 CODING BEND5 T protein_coding NM_024603.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 49193394 G T 0 152 0 0.6384 0.7706 0.7853 0.7589 0.8588 0.8599 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.86097 0 . 0 . 57 28,0,27,0 UTR_3_PRIME(MODIFIER||164||421|BEND5|protein_coding|CODING|NM_024603.3|6|T),INTRON(MODIFIER||||503|AGBL4|protein_coding|CODING|NM_032785.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.367879 rs1385152 -0.693021 0.376535 57 R245 421 Cgg/Agg LOW 3 SILENT CODING BEND5 T protein_coding NM_024603.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 49224584 G T 0 222 0 0.6082 0.6899 0.7795 0.5327 0.8847 0.6984 0.652065 0.80609 0.885 1 6535 89619 8652 4192 5615 56791 664 7170 2 10164 111910 11472 8464 6608 64132 820 10250 0.684402 0 . 0 . 61 25,4,19,10 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R245|421|BEND5|protein_coding|CODING|NM_024603.3|3|T),INTRON(MODIFIER||||503|AGBL4|protein_coding|CODING|NM_032785.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.273805 rs1128934 -0.693079 0.0188474 61 H142 503 caT/caC LOW 5 SILENT CODING AGBL4 G protein_coding NM_032785.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 49511424 A G 0 222 0 0.0401 0.225 0.2608 0.4246 0.1889 0.2812 0.074422 0.176522 0.22093 1 176 5394 124 323 366 2268 58 2079 2 2382 23570 460 666 1652 10230 256 7924 0.895056 0 . 0 COSM146507 127 17,40,15,41 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H142|503|AGBL4|protein_coding|CODING|NM_032785.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.511978 rs386589706,rs3934240 -0.693147 9.03097e-07 127 P265 402 ccC/ccT LOW 5 SILENT CODING ELAVL4 T protein_coding NM_001144775.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 50661411 C T 0 228 0 0.3729 0.8165 0.9366 0.999 0.9712 0.9836 0.459601 0.796632 0.969302 2 4549 112680 11187 8636 6436 64723 867 16282 2 10402 121392 11578 8646 6614 66732 908 16512 0 . 0 . 0 132 0,0,39,72 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P265|402|ELAVL4|protein_coding|CODING|NM_001144775.2|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2480683 -0.693147 0.000719957 132 402 LOW 6 CODING ELAVL4 T protein_coding NM_001144775.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 50666515 C T 0 222 0 0.3442 0.6971 0.8804 0.6528 0.9006 0.8804 0.429187 0.754113 0.920581 1 4224 101255 10101 5644 5549 60812 782 14143 2 10382 120566 11576 8632 6614 66546 906 15910 0.999856 0 . 0 . 214 74,37,50,32 SPLICE_SITE_REGION+INTRON(LOW||||402|ELAVL4|protein_coding|CODING|NM_001144775.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890214 rs2494876 -0.693147 0.0228849 214 402 2108 MODIFIER 7 CODING ELAVL4 C protein_coding NM_001144775.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 50668958 T C 0 36.3 0 0.0182 0.118 0.0533 0.3581 0.0696 0.1012 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2108||402|ELAVL4|protein_coding|CODING|NM_001144775.2|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17106016 -0.453602 0.68 2 542 107 MODIFIER 3 CODING DMRTA2 C protein_coding NM_032110.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 50884230 G C 0 23.3 0 0.9841 0.8912 0.9467 0.9435 0.9125 0.6503 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,0,2,0 UTR_3_PRIME(MODIFIER||107||542|DMRTA2|protein_coding|CODING|NM_032110.2|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs1296714 -0.453602 0.5 5 G114 168 ggC/ggT LOW 3 SILENT CODING CDKN2C T protein_coding NM_001262.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 51439777 C T 0 222 0 0.0038 0.0439 0.0591 0.0417 0.0964 0.0358 0.0199728 0.0665078 0.0903488 1 156 8397 443 484 357 6252 51 654 2 10394 121308 11568 8644 6612 66674 906 16510 0.850516 0 . 0 . 97 23,23,29,15 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G114|168|CDKN2C|protein_coding|CODING|NM_001262.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.933391 rs1043141 -0.693146 0.00984477 97 168 151 MODIFIER 3 CODING CDKN2C T protein_coding NM_001262.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 51440093 C T 0 222 0 0.3563 0.1548 0.0922 0.0784 0.0974 0.0644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.575134 0 . 0 . 105 28,19,25,15 UTR_3_PRIME(MODIFIER||151||168|CDKN2C|protein_coding|CODING|NM_001262.2|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.883279 rs12855 -0.693145 0.0622806 105 154 342 MODIFIER 1 CODING RNF11 G protein_coding NM_014372.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 51702087 C G 0 32.6 0 0.1309 0.0687 0.0187 0.0903 0.0249 0.0429 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||342||154|RNF11|protein_coding|CODING|NM_014372.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs139814203 -0.379885 0 2 613 107 MODIFIER 18 CODING TTC39A A protein_coding NM_001297665.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 51753722 G A 0 222 0 0.1044 0.0839 0.0533 0.0903 0.0795 0.0757 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.601391 0 . 0 . 58 15,19,13,10 UTR_3_PRIME(MODIFIER||107||613|TTC39A|protein_coding|CODING|NM_001297665.1|18|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.461084 rs3748615,rs386585383 -0.692717 0.360718 58 Y443 896 taC/taT LOW 15 SILENT CODING EPS15 A protein_coding NM_001981.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 51873951 G A 0 228 0 0.8941 0.8227 0.7622 0.9921 0.6223 0.8006 0.874716 0.729279 0.654767 2 9146 89169 9414 8596 4695 43998 617 12703 2 10404 121370 11574 8652 6612 66710 908 16510 0 . 0 . 0 124 0,0,37,77 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y443|896|EPS15|protein_coding|CODING|NM_001981.2|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1065754 -0.693147 0.411569 124 P877 1219 ccC/ccT LOW 23 SILENT CODING NRDC A protein_coding NM_002525.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52266242 G A 0 228 0 0.2224 0.489 0.5937 0.8234 0.5298 0.3885 0.278711 0.426649 0.502442 2 2745 61059 6986 7183 3457 33466 463 6759 2 10400 121352 11574 8650 6612 66710 908 16498 0 . 0 . 0 83 0,0,31,45 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P877|1219|NRDC|protein_coding|CODING|NM_002525.2|23|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8375 -0.693147 0.0767998 83 G405 1219 ggA/ggC LOW 8 SILENT CODING NRDC G protein_coding NM_002525.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52290984 T G 0 228 0 0.2496 0.4984 0.6009 0.8313 0.5239 0.3926 0.291875 0.43034 0.501279 2 2946 61010 6988 7183 3384 33276 463 6770 2 10286 121086 11544 8654 6608 66598 906 16490 0 . 0 . 0 159 0,0,82,54 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G405|1219|NRDC|protein_coding|CODING|NM_002525.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11205896 -0.693147 0.0027251 159 1219 127 MODIFIER 1 CODING NRDC C protein_coding NM_002525.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52344414 A C 0 168 0 0.2496 0.4998 0.6066 0.8313 0.5268 0.3926 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,1,7 UTR_5_PRIME(MODIFIER||127||1219|NRDC|protein_coding|CODING|NM_002525.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs736756 -0.651104 0.50952 8 172 442 MODIFIER 7 CODING TXNDC12 C protein_coding NM_015913.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52486163 T C 0 222 0 0.003 0.0407 0.049 0.1379 0.001 0.0266 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.602319 0 . 0 . 64 9,27,11,16 UTR_3_PRIME(MODIFIER||442||172|TXNDC12|protein_coding|CODING|NM_015913.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.986207 rs76000153 -0.693021 0.0328267 64 *355 354 tGa/tAa LOW 1 SILENT CODING KTI12 T protein_coding NM_138417.2 SYNONYMOUS_STOP outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52498370 C T 0 222 0 0.4092 0.22 0.1354 0.1786 0.0855 0.2055 0.358602 0.19614 0.112907 1 3855 17821 1799 1557 520 7313 113 2664 2 10234 113766 11500 8582 6614 64358 832 11646 0.488329 0 . 0 COSM146509 41 14,4,15,6 SYNONYMOUS_STOP(LOW|SILENT|tGa/tAa|*355|354|KTI12|protein_coding|CODING|NM_138417.2|1|T),INTRON(MODIFIER||||172|TXNDC12|protein_coding|CODING|NM_015913.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.732632 rs2809917 -0.692352 0.149883 41 D191E 354 gaT/gaA MODERATE 1 MISSENSE CODING KTI12 T protein_coding NM_138417.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52498861 A T 0 222 0 0.0802 0.0709 0.0735 0.1379 0.0268 0.0327 0.0724013 0.0551284 0.0462791 1 809 7212 1400 1262 143 2941 59 598 2 10246 120682 11568 8628 6614 66216 902 16508 0.446868 0 . 0 COSM146510 116 32,18,33,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D191E|354|KTI12|protein_coding|CODING|NM_138417.2|1|T),INTRON(MODIFIER||||172|TXNDC12|protein_coding|CODING|NM_015913.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.574053 rs2783175 -0.693147 0.0457222 116 172 1008 MODIFIER 1 CODING TXNDC12 T protein_coding NM_015913.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52521776 C T 0 9.7 0 0.9561 0.988 0.9971 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1008||172|TXNDC12|protein_coding|CODING|NM_015913.3|1|T),UPSTREAM(MODIFIER||81||158|BTF3L4|protein_coding|CODING|NM_152265.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2783189 -0.379885 0 1 172 1030 MODIFIER 1 CODING TXNDC12 T protein_coding NM_015913.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52521798 G T 0 9.7 0 0.7269 0.885 0.9265 0.8641 0.999 0.9734 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1030||172|TXNDC12|protein_coding|CODING|NM_015913.3|1|T),UPSTREAM(MODIFIER||59||158|BTF3L4|protein_coding|CODING|NM_152265.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2809954 -0.379885 0 1 158 207 MODIFIER 6 CODING BTF3L4 C protein_coding NM_152265.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52552637 T C 0 105 0 0.003 0.0403 0.049 0.1359 0.001 0.0266 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.245279 0 . 0 . 37 12,11,7,2 UTR_3_PRIME(MODIFIER||207||158|BTF3L4|protein_coding|CODING|NM_152265.4|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.137824 rs59771676 -0.662043 0.771133 37 158 328 MODIFIER 6 CODING BTF3L4 A protein_coding NM_152265.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52552758 G A 0 222 0 0.2738 0.1148 0.0706 0.1359 0.001 0.0266 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.719784 0 . 0 . 72 25,11,24,8 UTR_3_PRIME(MODIFIER||328||158|BTF3L4|protein_coding|CODING|NM_152265.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.498749 rs3015303 -0.69312 0.133978 72 158 515 MODIFIER 6 CODING BTF3L4 G protein_coding NM_152265.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52552945 C G 0 222 0 0.2738 0.1148 0.0706 0.1359 0.001 0.0266 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.822366 0 . 0 . 53 3,25,3,19 UTR_3_PRIME(MODIFIER||515||158|BTF3L4|protein_coding|CODING|NM_152265.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.955153 rs3015302 -0.692562 0.0341728 53 858 1003 MODIFIER 24 CODING CC2D1B A protein_coding NM_032449.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52818188 G A 0 222 0 0.9115 0.525 0.3876 0.1657 0.4761 0.5204 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.936138 0 . 0 . 164 18,66,16,51 UTR_3_PRIME(MODIFIER||1003||858|CC2D1B|protein_coding|CODING|NM_032449.2|24|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.494202 rs7513934 -0.693147 1.26945e-05 164 T466M 861 aCg/aTg MODERATE 9 MISSENSE CODING ORC1 A protein_coding NM_001190818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52851608 G A 0 222 0 0.0008 0.0371 0.0476 0.125 0.001 0.0256 0.00204267 0.00169153 0.00151163 1 19 2816 1076 1209 2 78 15 417 2 10094 118264 11260 8524 6102 65366 866 16052 0.330996 3 likely-benign 0 . 155 46,30,39,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T466M|861|ORC1|protein_coding|CODING|NM_001190818.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.804914 rs3087481 -0.693147 0.442086 155 312 LOW 5 CODING PRPF38A A protein_coding NM_032864.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52878300 T A 0 222 0 0.7852 0.3788 0.1888 0.2321 0.1948 0.3047 0.687472 0.37575 0.216047 1 7323 32311 2171 2185 1303 14230 180 4919 2 10352 119704 11274 8470 6572 65784 906 16346 0.722107 0 . 0 COSM146513 145 22,50,19,37 SPLICE_SITE_REGION+INTRON(LOW||||312|PRPF38A|protein_coding|CODING|NM_032864.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.423273 rs4319263 -0.693147 0.00197628 145 312 44 MODIFIER 10 CODING PRPF38A G protein_coding NM_032864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52882406 A G 0 222 0 0.7852 0.3808 0.1888 0.2361 0.1948 0.3108 0.687926 0.376057 0.216279 1 7318 32329 2186 2173 1302 14212 180 4958 2 10362 117722 11162 8350 6440 64360 892 16156 0.567832 0 . 0 COSN163082 131 27,34,25,25 UTR_3_PRIME(MODIFIER||44||312|PRPF38A|protein_coding|CODING|NM_032864.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.132063 rs6677047 -0.693147 0.14362 131 312 608 MODIFIER 10 CODING PRPF38A G protein_coding NM_032864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 52882970 A G 0 60 0 0.0076 0.0996 0.0821 0.2054 0.1064 0.1207 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992367 0 . 0 . 8 0,4,0,4 UTR_3_PRIME(MODIFIER||608||312|PRPF38A|protein_coding|CODING|NM_032864.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 0 . 0.868321 rs17131760 -0.556411 0.598008 8 F79 187 ttT/ttC LOW 2 SILENT CODING GPX7 C protein_coding NM_015696.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53072454 T C 0 222 0 0.9743 0.878 0.879 0.7996 0.841 0.8661 0.952565 0.875903 0.836628 1 9954 102916 9892 6759 5634 55656 782 14239 2 10406 121396 11576 8646 6614 66734 908 16512 0.757935 0 . 0 . 136 49,14,44,14 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F79|187|GPX7|protein_coding|CODING|NM_015696.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.45613 rs1970951 -0.693147 0.0730049 136 187 435 MODIFIER 3 CODING GPX7 A protein_coding NM_015696.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53074532 C A 0 222 0 0.3238 0.5747 0.6671 0.7669 0.5805 0.6442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.695301 0 . 0 . 66 16,18,13,11 UTR_3_PRIME(MODIFIER||435||187|GPX7|protein_coding|CODING|NM_015696.4|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.77259 rs1047635 -0.692831 0.170967 66 G398 744 ggG/ggA LOW 5 SILENT CODING ZYG11B A protein_coding NM_024646.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53250650 G A 0 228 0 0.9077 0.7149 0.6729 0.9792 0.4284 0.5061 0.825011 0.573658 0.444884 2 8738 66294 8393 8366 3266 29204 500 7827 2 10404 121374 11558 8648 6614 66730 908 16512 0 . 0 . 0 211 0,0,91,104 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G398|744|ZYG11B|protein_coding|CODING|NM_024646.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6588443 -0.693147 0.142901 211 744 4899 MODIFIER 14 CODING ZYG11B C protein_coding NM_024646.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53292200 T C 0 32.6 0 0.0008 0.0563 0.255 0.0823 0.0109 0.0102 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||4899||744|ZYG11B|protein_coding|CODING|NM_024646.2|14|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17107426 -0.379885 0 2 547 161 MODIFIER 1 CODING SCP2 G protein_coding NM_002979.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53392908 A G 0 32.3 0 0.9811 0.8009 0.7666 0.755 0.6521 0.7822 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||161||547|SCP2|protein_coding|CODING|NM_002979.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1242331 -0.453602 0.18 2 547 907 MODIFIER 16 CODING SCP2 A protein_coding NM_002979.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53517283 C A 0 9.7 0 0.0703 0.0978 0.2695 0.1171 0.0229 0.0706 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||907||547|SCP2|protein_coding|CODING|NM_002979.4|16|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3820200 -0.379885 0 1 P19 661 ccT/ccG LOW 1 SILENT CODING PODN G protein_coding NM_153703.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53527948 T G 0 214 0 0.8154 0.4073 0.3934 0.3819 0.1024 0.2055 0.575208 0.261065 0.103993 1 2170 6267 524 1046 67 1955 30 475 2 2854 16450 1036 2320 342 8430 96 1372 0.751254 0 . 0 . 31 3,9,2,13 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P19|661|PODN|protein_coding|CODING|NM_153703.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.187475 rs7513730 -0.688148 0.00418402 31 T172 661 acG/acA LOW 3 SILENT CODING PODN A protein_coding NM_153703.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53537266 G A 0 228 0 0.4977 0.5561 0.6499 0.7371 0.4652 0.4755 0.522707 0.487235 0.46907 2 5203 61096 8499 6505 3277 29808 472 7332 2 10158 119426 11468 8588 6468 65444 892 16408 1 0 . 0 . 102 1,0,41,50 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T172|661|PODN|protein_coding|CODING|NM_153703.4|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1769316 -0.693147 0.215268 102 N417 661 aaC/aaT LOW 8 SILENT CODING PODN T protein_coding NM_153703.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53544289 C T 0 228 0 0.0575 0.128 0.2752 0.2222 0.0477 0.1043 0.0721743 0.0558973 0.0475581 2 729 11004 3521 2030 307 2852 63 1502 2 10294 120270 11512 8552 6606 65922 892 16492 0 . 0 . 0 67 0,0,30,36 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N417|661|PODN|protein_coding|CODING|NM_153703.4|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11206087 -0.693147 0.828334 67 S613 619 agT/agC LOW 11 SILENT CODING SLC1A7 G protein_coding NM_001287595.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53553702 A G 0 228 0 0.7867 0.9429 0.9942 1 1 1 0.833409 0.942796 0.998837 2 8462 113261 11425 8622 6599 65050 838 12265 2 10288 115242 11522 8624 6602 65092 846 12268 0 . 0 . 0 49 0,0,34,10 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S613|619|SLC1A7|protein_coding|CODING|NM_001287595.1|11|G),DOWNSTREAM(MODIFIER||2528||661|PODN|protein_coding|CODING|NM_153703.4||G) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.990244 0 . rs1288400 -0.693146 0.00264762 49 R329 619 cgT/cgC LOW 7 SILENT CODING SLC1A7 G protein_coding NM_001287595.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53558270 A G 0 228 0 0.7383 0.846 0.9207 0.9544 0.835 0.8384 0.761462 0.813548 0.840233 2 7832 101728 10737 8298 5730 54771 763 13597 2 10390 121268 11572 8648 6606 66634 906 16512 0 . 0 . 0 191 0,0,107,68 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R329|619|SLC1A7|protein_coding|CODING|NM_001287595.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1288406,rs386422448 -0.693147 0.00951028 191 S297 619 tcA/tcG LOW 7 SILENT CODING SLC1A7 C protein_coding NM_001287595.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53558366 T C 0 228 0 0.0779 0.1456 0.2839 0.247 0.0487 0.1339 0.0828416 0.0605874 0.049186 2 857 11888 3574 2075 318 2987 72 2005 2 10398 121302 11566 8630 6612 66682 902 16512 0.220583 0 . 0 . 144 1,2,38,90 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S297|619|SLC1A7|protein_coding|CODING|NM_001287595.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.778432 rs12129653 -0.693147 0.0462868 144 P53 619 ccT/ccC LOW 2 SILENT CODING SLC1A7 G protein_coding NM_001287595.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53600078 A G 0 222 0 0.1293 0.1881 0.3718 0.2907 0.159 0.0613 0.139355 0.158312 0.168023 1 1482 21458 3957 2648 1025 11117 147 1082 2 9402 111770 10794 8440 5922 62116 814 14282 0.835127 0 . 0 . 215 49,48,56,34 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P53|619|SLC1A7|protein_coding|CODING|NM_001287595.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89636 rs3737989 -0.693147 0.24415 215 V368I 658 Gtc/Atc MODERATE 4 MISSENSE CODING CPT2 A protein_coding NM_000098.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53676448 G A 0 228 0 0.2564 0.4131 0.3818 0.7242 0.5179 0.2188 0.290059 0.456405 0.541628 2 2941 58647 4947 6325 3504 36217 408 4305 2 10370 121140 11528 8634 6596 66604 908 16500 0 255|2|2 other|benign|benign 0 . 62 0,0,34,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V368I|658|CPT2|protein_coding|CODING|NM_000098.2|4|A),DOWNSTREAM(MODIFIER||3324||160|C1orf123|protein_coding|CODING|NM_017887.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1799821 -0.693147 0.000648449 62 160 453 MODIFIER 8 CODING C1orf123 C protein_coding NM_017887.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53679878 T C 0 9.7 0 0.0567 0.2282 0.1772 0.4921 0.3111 0.1391 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||453||160|C1orf123|protein_coding|CODING|NM_017887.2|8|C),DOWNSTREAM(MODIFIER||9||658|CPT2|protein_coding|CODING|NM_000098.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1056438 -0.379885 0 1 160 241 MODIFIER 8 CODING C1orf123 A protein_coding NM_017887.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53680090 G A 0 151 0 0.0575 0.2236 0.1772 0.4663 0.3111 0.1411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,11,0 UTR_3_PRIME(MODIFIER||241||160|C1orf123|protein_coding|CODING|NM_017887.2|8|A),DOWNSTREAM(MODIFIER||221||658|CPT2|protein_coding|CODING|NM_000098.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1056425 -0.676189 0.50116 11 963 955 MODIFIER 19 CODING LRP8 C protein_coding NM_004631.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53711735 G C 0 203 0 0.0688 0.2724 0.2363 0.5268 0.4016 0.1779 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,1,10 UTR_3_PRIME(MODIFIER||955||963|LRP8|protein_coding|CODING|NM_004631.4|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5177 -0.676189 0.606998 12 R952Q 963 cGa/cAa MODERATE 19 MISSENSE CODING LRP8 T protein_coding NM_004631.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53712727 C T 0 222 0 0.0166 0.1444 0.1772 0.0327 0.3956 0.1503 0.0828416 0.289559 0.395465 1 731 35645 2105 258 2801 26793 252 2705 2 10368 120710 11486 8642 6564 66446 900 16304 0.877954 255 other 0 . 114 28,27,26,21 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGa/cAa|R952Q|963|LRP8|protein_coding|CODING|NM_004631.4|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.332664 rs5174 -0.693147 0.702779 114 D874 963 gaC/gaT LOW 17 SILENT CODING LRP8 A protein_coding NM_004631.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53716416 G A 0 228 0 0.2466 0.3708 0.2867 0.6984 0.4076 0.2229 0.267363 0.362448 0.411163 2 2776 48730 4294 6280 3046 28214 344 3776 2 10406 121364 11568 8646 6614 66712 908 16510 0 . 0 . 0 120 0,0,72,37 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D874|963|LRP8|protein_coding|CODING|NM_004631.4|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3737983,rs386585100 -0.693147 0.14729 120 G419 963 ggC/ggA LOW 9 SILENT CODING LRP8 T protein_coding NM_004631.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 53732315 G T 0 228 0 0.2042 0.3353 0.2824 0.6319 0.3956 0.182 0.227871 0.342534 0.401279 2 2349 46060 4253 5564 2888 27496 321 3189 2 10402 121286 11574 8634 6612 66680 908 16476 1 0 . 0 . 109 0,1,23,77 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G419|963|LRP8|protein_coding|CODING|NM_004631.4|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2297660 -0.693147 0.00460733 109 620 5203 MODIFIER 2 CODING GLIS1 T protein_coding NM_147193.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54065778 C T 0 222 0 0.3283 0.7017 0.8775 0.5764 0.9831 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.741649 0 . 0 . 107 24,33,25,15 UTR_5_PRIME(MODIFIER||5203||620|GLIS1|protein_coding|CODING|NM_147193.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.993976 rs12723437 -0.693145 0.127114 107 620 5256 MODIFIER 2 CODING GLIS1 T protein_coding NM_147193.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54065831 G T 0 222 0 0.3283 0.7017 0.8775 0.5764 0.9831 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.777332 0 . 0 . 88 21,22,23,15 UTR_5_PRIME(MODIFIER||5256||620|GLIS1|protein_coding|CODING|NM_147193.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999821 rs12723875 -0.693143 0.457766 88 620 5349 MODIFIER 2 CODING GLIS1 A protein_coding NM_147193.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54065924 G A 0 222 0 0.3283 0.7017 0.8775 0.5764 0.9831 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998891 0 . 0 . 61 6,19,7,26 START_GAINED(LOW||||620|GLIS1|protein_coding|CODING|NM_147193.2|2|A),UTR_5_PRIME(MODIFIER||5349||620|GLIS1|protein_coding|CODING|NM_147193.2|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.721132 rs12723911 -0.693127 0.0227354 61 306 8040 MODIFIER 11 CODING YIPF1 C protein_coding NM_018982.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54317697 T C 0 9.7 0 0.8631 0.9617 0.9841 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||8040||306|YIPF1|protein_coding|CODING|NM_018982.4|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1127922 -0.379885 0 1 249 29 MODIFIER 4 CODING DIO1 T protein_coding NM_000792.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54375701 C T 0 222 0 0.1589 0.3125 0.5173 0.1468 0.3678 0.4888 0.218112 0.299246 0.340814 1 2095 42896 6790 1257 2213 22557 293 7691 2 10388 121162 11546 8622 6602 66602 906 16496 0.998694 0 . 0 . 75 15,25,6,21 UTR_3_PRIME(MODIFIER||29||249|DIO1|protein_coding|CODING|NM_000792.5|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.155233 rs11206244 -0.693021 0.117594 75 324 783 MODIFIER 8 CODING TMEM59 C protein_coding NM_001305043.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54497040 T C 0 79 0 0.9017 0.5942 0.5821 0.6081 0.4364 0.3354 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924584 0 . 0 . 9 2,1,6,0 UTR_3_PRIME(MODIFIER||783||324|TMEM59|protein_coding|CODING|NM_001305043.1|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 1 0 0.577865 rs1547467 -0.616816 0.551573 9 324 246 MODIFIER 1 CODING TMEM59 C protein_coding NM_001305043.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54519107 G C 0 70 0 0.0318 0.119 0.2608 0.3105 0.0149 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.600535 0 . 0 . 8 0,3,0,5 UTR_5_PRIME(MODIFIER||246||324|TMEM59|protein_coding|CODING|NM_001305043.1|1|C),UPSTREAM(MODIFIER||138||208|TCEANC2|protein_coding|CODING|NM_153035.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 0 . 0.600535 rs2236512 -0.590765 0.345017 8 208 893 MODIFIER 5 CODING TCEANC2 A protein_coding NM_153035.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54563039 G A 0 61 0 0.9985 0.9657 0.9885 0.9921 0.9702 0.8732 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||893||208|TCEANC2|protein_coding|CODING|NM_153035.2|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1181088,rs386521379 -0.511536 0.148533 3 G244R 449 Gga/Aga MODERATE 3 MISSENSE CODING CDCP2 T protein_coding NM_201546.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54606804 C T 0 228 0 0.7723 0.8241 0.7939 0.8681 0.8509 0.8425 0.777475 0.824846 0.849116 2 7593 90609 9342 7572 5067 52755 630 7650 2 9784 109354 11444 8512 6590 62962 792 9270 1 0 . 0 . 233 1,0,124,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G244R|449|CDCP2|protein_coding|CODING|NM_201546.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3766465 -0.693147 0.00107847 233 Y161 449 taT/taC LOW 3 SILENT CODING CDCP2 G protein_coding NM_201546.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54607051 A G 0 228 0 0.9871 0.9966 1 1 1 1 0.991148 0.997001 1 2 10296 121142 11566 8654 6602 66640 902 16482 2 10388 121238 11568 8654 6602 66642 902 16482 0 . 0 . 0 115 0,0,45,58 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y161|449|CDCP2|protein_coding|CODING|NM_201546.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs671103 -0.693147 0.0346843 115 315 763 MODIFIER 8 CODING CYB5RL A protein_coding NM_001031672.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54639529 G A 0 222 0 0 0.0025959 0 0.0129 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.115801 0 . 0 . 110 31,26,12,21 UTR_3_PRIME(MODIFIER||763||315|CYB5RL|protein_coding|CODING|NM_001031672.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0574321 rs143220154 -0.693127 0.0239569 110 G402 423 ggC/ggG LOW 7 SILENT CODING MRPL37 G protein_coding NM_016491.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54683856 C G 0 228 0 0.3502 0.4056 0.3545 0.5942 0.2078 0.5256 0.307535 0.247347 0.216512 2 3406 38483 4487 4991 1967 15046 275 8311 2 10406 121406 11578 8652 6614 66738 908 16510 0 . 0 . COSM1162165 94 0,0,31,54 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G402|423|MRPL37|protein_coding|CODING|NM_016491.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs15921 -0.693147 0.0147758 94 423 3 MODIFIER 7 CODING MRPL37 A protein_coding NM_016491.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 54683925 G A 0 228 0 0.1165 0.2298 0.2176 0.4683 0.1282 0.2505 0.122787 0.132554 0.137558 2 1315 23323 2816 4092 1147 9570 159 4224 2 10406 121394 11578 8646 6614 66730 908 16512 0 . 0 . COSN503912 41 0,0,8,31 UTR_3_PRIME(MODIFIER||3||423|MRPL37|protein_coding|CODING|NM_016491.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6621 -0.693144 0.154332 41 607 LOW 5 CODING ACOT11 A protein_coding NM_015547.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55060224 G A 0 222 0 0.3328 0.1991 0.111 0.1815 0.0398 0.2628 0.272129 0.110564 0.0277907 1 2770 11670 1764 1704 230 1905 79 3218 2 9752 111128 10744 8174 5864 62096 760 13738 0.842829 0 . 0 . 62 14,17,5,21 SPLICE_SITE_REGION+INTRON(LOW||||607|ACOT11|protein_coding|CODING|NM_015547.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.858331 rs1755591 -0.692976 0.608243 62 G202D 607 gGc/gAc MODERATE 6 MISSENSE CODING ACOT11 A protein_coding NM_015547.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55060362 G A 0 222 0 0.5371 0.2554 0.1239 0.1825 0.0417 0.2628 0.448479 0.171536 0.0296512 1 4758 14108 1932 1732 236 2049 97 3304 2 10250 118130 11508 8590 6542 65328 866 15046 0.682853 0 . 0 . 30 6,8,5,8 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gGc/gAc|G202D|607|ACOT11|protein_coding|CODING|NM_015547.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970994 rs1702003 -0.683931 0.0187886 30 A416V 585 gCg/gTg MODERATE 8 MISSENSE CODING FAM151A A protein_coding NM_176782.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55075452 G A 0 222 0 0.1959 0.3023 0.3588 0.1815 0.5388 0.2873 0.248979 0.428725 0.520814 1 2436 49844 2970 1511 2919 34228 364 5416 2 10356 121090 11550 8626 6564 66584 898 16512 0.547121 0 . 0 . 79 23,25,16,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A416V|585|FAM151A|protein_coding|CODING|NM_176782.2|8|A),INTRON(MODIFIER||||607|ACOT11|protein_coding|CODING|NM_015547.3|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.820438 rs1368883,rs386428202 -0.693021 0.0603168 79 S352 585 agC/agT LOW 7 SILENT CODING FAM151A A protein_coding NM_176782.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55076113 G A 0 222 0 0.0567 0.1296 0.0893 0.2083 0.0408 0.2669 0.0533364 0.0355221 0.0263953 1 573 9916 1688 2002 239 1932 70 3412 2 10406 121122 11568 8632 6614 66600 904 16398 0.797991 0 . 0 COSM146518 155 32,38,34,42 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S352|585|FAM151A|protein_coding|CODING|NM_176782.2|7|A),INTRON(MODIFIER||||607|ACOT11|protein_coding|CODING|NM_015547.3|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.929662 rs4926650 -0.693147 0.00861972 155 1323 34 MODIFIER 3 CODING MROH7 G protein_coding NM_001039464.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55118566 C G 0 228 0 0.8116 0.9487 0.9914 1 0.998 1 0.861931 0.954082 0.998204 2 8106 109120 11403 8534 6614 64072 794 9597 2 9626 110806 11486 8534 6614 64150 798 9598 0 . 0 . 0 61 0,0,27,29 UTR_5_PRIME(MODIFIER||34||1323|MROH7|protein_coding|CODING|NM_001039464.3|3|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1655520 -0.693147 0.284289 61 P91 1323 ccA/ccG LOW 3 SILENT CODING MROH7 G protein_coding NM_001039464.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55118872 A G 0 222 0 0.0008 0.0276 0.1254 0.0397 0 0.0102 0.00280612 0.00122911 0.000482859 1 20 2484 1864 352 0 36 21 191 2 9786 120660 11566 8608 6612 66682 898 16508 0.968709 0 . 0 . 39 9,8,9,7 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P91|1323|MROH7|protein_coding|CODING|NM_001039464.3|3|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.557713 rs386440392,rs75579421 -0.689466 0.836076 39 H182R 1323 cAt/cGt MODERATE 3 MISSENSE CODING MROH7 G protein_coding NM_001039464.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55119144 A G 0 222 0 0.1596 0.3107 0.268 0.5188 0.3708 0.2689 0.185722 0.291764 0.340567 1 1736 39292 2629 4620 2580 23292 255 4180 2 9766 120586 11560 8596 6606 66662 896 16500 0.873319 0 . 0 COSM1343517,COSM1343516 96 31,23,24,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H182R|1323|MROH7|protein_coding|CODING|NM_001039464.3|3|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.833466 rs11206407 -0.693127 0.178887 96 L230 1323 ctG/ctC LOW 3 SILENT CODING MROH7 C protein_coding NM_001039464.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55119289 G C 0 222 0 0.2716 0.4205 0.4063 0.5208 0.5944 0.3497 0.367723 0.519145 0.589601 1 3166 61147 3966 4629 3822 38996 434 6134 2 9770 120602 11556 8596 6608 66674 898 16500 0.841388 0 . 0 . 81 27,16,23,12 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L230|1323|MROH7|protein_coding|CODING|NM_001039464.3|3|C),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.138288 rs9332417 -0.693136 0.0600391 81 E316G 1323 gAg/gGg MODERATE 3 MISSENSE CODING MROH7 G protein_coding NM_001039464.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55119546 A G 0 228 0 0.8283 0.9531 0.9914 1 0.998 1 0.881403 0.95882 0.998238 2 8464 119264 11501 8634 6614 66645 896 16510 2 9826 120802 11576 8634 6614 66740 900 16512 0 . 0 . 0 105 0,0,49,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E316G|1323|MROH7|protein_coding|CODING|NM_001039464.3|3|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1655518 -0.693147 0.555724 105 H618R 1323 cAc/cGc MODERATE 10 MISSENSE CODING MROH7 G protein_coding NM_001039464.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55139741 A G 0 228 0 0.9259 0.9097 0.8559 0.998 0.8032 0.9448 0.905293 0.826698 0.790222 2 8921 101933 10393 8623 5603 52387 756 15250 2 9800 120762 11576 8626 6614 66734 900 16512 0 . 0 . 0 76 0,0,40,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H618R|1323|MROH7|protein_coding|CODING|NM_001039464.3|10|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs570218 -0.693147 0.322267 76 H941 1323 caC/caT LOW 16 SILENT CODING MROH7 T protein_coding NM_001039464.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55158208 C T 0 228 0 0.0507 0.0645 0.0072 0.1776 0.001 0.0726 0.0575025 0.019491 0.00107604 2 569 3475 145 1690 0 114 26 931 2 9764 120234 11530 8590 6490 66496 890 16474 1 0 . 0 . 68 0,1,8,55 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H941|1323|MROH7|protein_coding|CODING|NM_001039464.3|16|T),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2304313 -0.693147 0.00557856 68 L947 1323 Ttg/Ctg LOW 16 SILENT CODING MROH7 C protein_coding NM_001039464.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55158224 T C 0 228 0 0.1543 0.0929 0.0144 0.1776 0.001 0.0726 0.155572 0.0510337 0.00120192 2 1561 4527 184 1684 0 130 30 938 2 9696 119312 11436 8522 6370 66106 872 16310 0 . 0 . 0 40 0,0,3,35 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L947|1323|MROH7|protein_coding|CODING|NM_001039464.3|16|C),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2304312 -0.693143 0.116633 40 1323 LOW 16 CODING MROH7 T protein_coding NM_001039464.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55161043 C T 0 228 0 0 0.0501 0.0014 0.1776 0 0.0726 0.00123092 0.00056397 0.000239521 2 7 2608 105 1590 0 44 22 840 2 5082 65932 5460 5588 3122 35752 514 10414 0.767123 0 . 0 . 81 1,1,49,24 SPLICE_SITE_REGION+INTRON(LOW||||1323|MROH7|protein_coding|CODING|NM_001039464.3|16|T),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.705479 rs75529143 -0.693147 0.145091 81 V1099D 1323 gTc/gAc MODERATE 20 MISSENSE CODING MROH7 A protein_coding NM_001039464.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55167773 T A 0 228 0 0.9871 0.9179 0.9251 0.9365 0.832 0.8885 0.967539 0.878312 0.834484 2 9421 103527 10801 8021 5357 55281 754 13892 2 9702 118624 11466 8566 6428 65830 884 15748 1 0 . 0 . 80 1,0,48,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V1099D|1323|MROH7|protein_coding|CODING|NM_001039464.3|20|A),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs646356 -0.693147 0.0299576 80 1323 LOW 20 CODING MROH7 C protein_coding NM_001039464.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55167924 T C 0 228 0 0.0598 0.0757 0.0029 0.1994 0 0.0992 0.0395683 0.0136768 0.000832739 2 197 1198 11 513 0 20 5 452 2 2954 20282 560 1722 348 10848 152 3698 1 0 . 0 . 80 0,1,29,41 SPLICE_SITE_REGION+INTRON(LOW||||1323|MROH7|protein_coding|CODING|NM_001039464.3|20|C),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3816070 -0.693147 0.0470634 80 K1148 1323 aaG/aaA LOW 21 SILENT CODING MROH7 A protein_coding NM_001039464.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55168298 G A 0 228 0 0.0809 0.0817 0.0072 0.1984 0 0.0992 0.061735 0.0201599 0.00121271 2 626 4009 148 1870 0 97 25 1243 2 9798 120154 11576 8624 6614 66530 888 16124 0 . 0 . COSM146519,COSM146520 93 0,0,66,19 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1148|1323|MROH7|protein_coding|CODING|NM_001039464.3|21|A),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3765018 -0.693147 0.0371528 93 T1180 1323 acA/acG LOW 21 SILENT CODING MROH7 G protein_coding NM_001039464.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55168394 A G 0 228 0 0.0809 0.0819 0.0072 0.1994 0 0.0992 0.0593705 0.0206389 0.00141978 2 627 4034 147 1891 0 98 25 1246 2 9800 120582 11576 8618 6614 66656 894 16424 0 . 0 . COSM146521,COSM146522 153 0,0,80,54 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1180|1323|MROH7|protein_coding|CODING|NM_001039464.3|21|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3765017 -0.693147 0.330341 153 S1294R 1323 agC/agG MODERATE 24 MISSENSE CODING MROH7 G protein_coding NM_001039464.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55175770 C G 0 222 0 0 0.0019968 0 0.0099 0 0 0 . 0 1 1 74 0 73 0 0 0 0 2 9726 120084 11508 8590 6536 66384 888 16452 0.919864 0 . 0 . 92 24,18,22,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agG|S1294R|1323|MROH7|protein_coding|CODING|NM_001039464.3|24|G),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.934125 rs139751339 -0.693146 0.141407 92 S47T 387 Tcg/Acg MODERATE 2 MISSENSE CODING TTC4 A protein_coding NM_004623.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55182300 T A 0 228 0 0.5038 0.6683 0.6081 0.9683 0.5477 0.7485 0.551975 0.524912 0.511047 2 5616 72601 7342 8310 3550 35303 505 11975 2 10370 121196 11556 8624 6602 66634 908 16502 0 . 0 . 0 131 0,0,55,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcg/Acg|S47T|387|TTC4|protein_coding|CODING|NM_004623.4|2|A),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1147990 -0.693147 0.46453 131 A168 387 gcC/gcT LOW 5 SILENT CODING TTC4 T protein_coding NM_004623.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55188382 C T 0 222 0 0.1694 0.1294 0.0288 0.128 0.0616 0.2178 0.180663 0.0947255 0.0506977 1 1845 10715 437 1258 350 3711 65 3049 2 10406 121360 11550 8652 6614 66718 908 16512 0.477889 0 . 0 COSM146523 187 44,32,55,43 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A168|387|TTC4|protein_coding|CODING|NM_004623.4|5|T),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.993375 0.993528 0 0.119378 rs11550481 -0.693147 0.0395889 187 387 30 MODIFIER 10 CODING TTC4 C protein_coding NM_004623.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55207216 T C 0 222 0 0.2799 0.1601 0.0331 0.1319 0.0626 0.2178 0.264412 0.123328 0.0510465 1 2767 11698 483 1264 350 3724 71 3039 2 10220 120332 11482 8506 6596 66176 900 16452 0.41009 0 . 0 . 60 5,30,4,19 UTR_3_PRIME(MODIFIER||30||387|TTC4|protein_coding|CODING|NM_004623.4|10|C),INTRAGENIC(MODIFIER|||||MROH7-TTC4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841184 rs41297863 -0.692717 0.0425452 60 475 217 MODIFIER 2 CODING PARS2 T protein_coding NM_152268.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55223190 C T 0 64 0 0.1694 0.3027 0.3573 0.5843 0.1799 0.2802 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||217||475|PARS2|protein_coding|CODING|NM_152268.3|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2240396 -0.511536 0.301053 3 K351E 569 Aag/Gag MODERATE 6 MISSENSE CODING TTC22 C protein_coding NM_001114108.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55248120 T C 0 222 0 0.0008 0.0284 0.0144 0.0804 0 0.0511 0.00433526 0.00131406 0 1 8 385 9 63 0 3 4 298 2 2148 19354 410 614 70 8318 182 7612 0.138458 0 . 0 COSM146524 80 10,25,14,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K351E|569|TTC22|protein_coding|CODING|NM_001114108.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.828186 rs61733130 -0.693141 0.448795 80 E329 569 gaA/gaG LOW 5 SILENT CODING TTC22 C protein_coding NM_001114108.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55251689 T C 0 228 0 0.997 0.999 0.9986 1 1 1 0.991602 0.997155 1 2 10327 121260 11556 8654 6610 66698 907 16508 2 10404 121348 11566 8654 6610 66698 908 16508 0 . 0 . 0 115 0,0,64,45 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E329|569|TTC22|protein_coding|CODING|NM_001114108.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs586462 -0.693147 0.793173 115 R229H 569 cGc/cAc MODERATE 3 MISSENSE CODING TTC22 T protein_coding NM_001114108.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55253437 C T 0 222 0 0 0.0226 0.013 0.0784 0 0.0256 0.00068089 0.000384438 0.000232558 1 7 1281 270 607 0 21 4 372 2 8604 106062 10222 7964 5552 58274 804 14642 0.816128 0 . 0 . 199 44,37,46,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R229H|569|TTC22|protein_coding|CODING|NM_001114108.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.745995 rs80076000 -0.693147 0.124919 199 L14V 569 Ctc/Gtc MODERATE 1 MISSENSE CODING TTC22 C protein_coding NM_001114108.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55266797 G C 0 222 0 0.0265 0.1536 0.2334 0.2639 0.2356 0.0706 0.0571494 0.153146 0.202309 1 530 22947 2307 2451 1600 14324 187 1548 2 9084 115422 11366 8442 6516 62824 854 16336 0.959739 0 . 0 . 52 11,14,9,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L14V|569|TTC22|protein_coding|CODING|NM_001114108.1|1|C),UPSTREAM(MODIFIER||4939||418|LEXM|protein_coding|CODING|NM_001110533.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.624528 rs671108 -0.692352 0.162032 52 418 16 MODIFIER 1 CODING LEXM G protein_coding NM_001110533.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55271774 A G 0 127 0 0.5847 0.5501 0.4741 0.3988 0.5964 0.6656 0.58117 0.583076 0.584047 1 678 9977 217 330 69 3883 88 4712 2 1152 15978 402 718 104 6342 136 7124 0.885987 0 . 0 . 15 5,2,6,1 UTR_5_PRIME(MODIFIER||16||418|LEXM|protein_coding|CODING|NM_001110533.1|1|G),UPSTREAM(MODIFIER||4833||569|TTC22|protein_coding|CODING|NM_001114108.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.966012 1 0 0.240074 rs757581 -0.636426 0.76204 15 T19M 418 aCg/aTg MODERATE 1 MISSENSE CODING LEXM T protein_coding NM_001110533.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55271845 C T 0 137 0 0.0658 0.0449 0.013 0.119 0.003 0.0061 0.0568182 0.0199718 0.00118259 1 347 1099 85 576 0 62 3 26 2 2872 28048 1258 2742 264 12350 194 8368 0.991121 0 . 0 . 24 9,4,6,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T19M|418|LEXM|protein_coding|CODING|NM_001110533.1|1|T),UPSTREAM(MODIFIER||4904||569|TTC22|protein_coding|CODING|NM_001114108.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.705828 rs72895754 -0.662043 0.257627 24 Y205H 418 Tat/Cat MODERATE 5 MISSENSE CODING LEXM C protein_coding NM_001110533.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55277599 T C 0 228 0 1 1 1 1 1 1 0.999773 0.999923 1 2 10399 121396 11576 8654 6612 66735 908 16512 2 10404 121402 11576 8654 6612 66736 908 16512 0 . 0 . 0 77 0,0,29,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y205H|418|LEXM|protein_coding|CODING|NM_001110533.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386601006,rs600499 -0.693147 0.00518954 77 C343Y 418 tGc/tAc MODERATE 8 MISSENSE CODING LEXM A protein_coding NM_001110533.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55280690 G A 0 213 0 0.0416 0.0325 0.0029 0.1002 0.001 0.0041 0.0383568 0.0132247 0.000348837 1 384 1306 16 851 0 22 6 27 2 10402 121364 11578 8650 6614 66706 908 16506 0.605076 0 . 0 . 52 13,18,4,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C343Y|418|LEXM|protein_coding|CODING|NM_001110533.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.708644 rs75191355 -0.690438 0.736632 52 G404 418 ggA/ggG LOW 10 SILENT CODING LEXM G protein_coding NM_001110533.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55307501 A G 0 222 0 0.1498 0.2304 0.281 0.4405 0.2316 0.0859 0.171243 0.194919 0.205217 1 586 6555 293 764 298 3505 69 1040 2 3134 28854 878 1498 1022 13662 274 8386 0.354502 0 . 0 . 98 22,15,30,22 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G404|418|LEXM|protein_coding|CODING|NM_001110533.1|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96186 rs41297871 -0.693147 0.107875 98 418 94 MODIFIER 10 CODING LEXM T protein_coding NM_001110533.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55307640 C T 0 222 0 0.1528 0.2282 0.2795 0.4395 0.2227 0.0818 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957051 0 . 0 . 71 13,24,8,22 UTR_3_PRIME(MODIFIER||94||418|LEXM|protein_coding|CODING|NM_001110533.1|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.71473 rs59138759 -0.693097 0.701764 71 418 147 MODIFIER 10 CODING LEXM A protein_coding NM_001110533.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55307693 C A 0 191 0 0.1498 0.2268 0.2767 0.4405 0.2207 0.0818 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.228827 0 . 0 . 43 7,14,4,13 UTR_3_PRIME(MODIFIER||147||418|LEXM|protein_coding|CODING|NM_001110533.1|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.961854 rs17111100 -0.690438 0.139535 43 516 2555 MODIFIER 9 CODING DHCR24 C protein_coding NM_014762.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55315351 T C 0 228 0 0.9992 0.9998 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,48,15 UTR_3_PRIME(MODIFIER||2555||516|DHCR24|protein_coding|CODING|NM_014762.3|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs657688 -0.693147 0.515577 68 516 2295 MODIFIER 9 CODING DHCR24 G protein_coding NM_014762.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55315611 C G 0 228 0 0.6021 0.4359 0.4337 0.5833 0.3231 0.1769 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 48 0,0,5,41 UTR_3_PRIME(MODIFIER||2295||516|DHCR24|protein_coding|CODING|NM_014762.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7373 -0.693147 0.0540557 48 516 221 MODIFIER 9 CODING DHCR24 A protein_coding NM_014762.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55317685 G A 0 222 0 0.1483 0.226 0.2738 0.4425 0.2217 0.0787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.547319 0 . 0 . 59 9,14,17,11 UTR_3_PRIME(MODIFIER||221||516|DHCR24|protein_coding|CODING|NM_014762.3|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.864564 rs1138030 -0.693054 0.243822 59 516 51 MODIFIER 1 CODING DHCR24 A protein_coding NM_014762.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55352843 C A 0 166 0 0 0.017173 0 0.0833 0 0.002 0.000861079 0.000294406 0 1 1 38 0 26 0 0 1 10 2 614 10614 124 184 4 3160 116 6412 0.999948 0 . 0 . 50 0,29,1,19 START_GAINED(LOW||||516|DHCR24|protein_coding|CODING|NM_014762.3|1|A),UTR_5_PRIME(MODIFIER||51||516|DHCR24|protein_coding|CODING|NM_014762.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.657727 rs17552526 -0.692067 0.155226 50 210 75 MODIFIER 1 CODING TMEM61 C protein_coding NM_182532.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55446664 G C 0 222 0 0.4107 0.609 0.7522 0.4891 0.7724 0.7311 0.468931 0.691853 0.788812 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.716496 0 . 0 . 67 29,2,28,3 UTR_5_PRIME(MODIFIER||75||210|TMEM61|protein_coding|CODING|NM_182532.2|1|C) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.740976 rs2253467 -0.69311 0.493308 67 210 68 MODIFIER 1 CODING TMEM61 T protein_coding NM_182532.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55446671 C T 0 222 0 0.4107 0.6086 0.7522 0.4871 0.7724 0.7311 0.468931 0.691853 0.788812 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.661426 0 . 0 . 71 30,4,28,5 UTR_5_PRIME(MODIFIER||68||210|TMEM61|protein_coding|CODING|NM_182532.2|1|T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.861734 rs2253466 -0.693127 0.182267 71 210 42 MODIFIER 1 CODING TMEM61 A protein_coding NM_182532.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55446697 G A 0 222 0 0.41 0.6084 0.7522 0.4861 0.7724 0.7321 0.47044 0.689618 0.801331 1 1643 22657 1384 894 430 12286 163 5857 2 3498 30820 1806 1606 508 15282 248 7872 0.905797 0 . 0 . 95 36,13,31,6 UTR_5_PRIME(MODIFIER||42||210|TMEM61|protein_coding|CODING|NM_182532.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.153395 rs2253465 -0.693141 0.125369 95 A189 210 gcG/gcA LOW 3 SILENT CODING TMEM61 A protein_coding NM_182532.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55457710 G A 0 222 0 0.8162 0.7875 0.8876 0.6379 0.8002 0.819 0.823423 0.813548 0.808488 1 8522 96312 10411 5402 5046 53170 671 13090 2 10390 121274 11576 8622 6614 66656 904 16512 0.991801 0 . 0 . 115 37,18,17,33 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A189|210|TMEM61|protein_coding|CODING|NM_182532.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.878016 rs2500326,rs386489103 -0.693147 0.252377 115 210 39 MODIFIER 3 CODING TMEM61 T protein_coding NM_182532.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55457815 C T 0 222 0 0.8162 0.7875 0.889 0.6379 0.8002 0.818 0.821526 0.813615 0.809563 1 7910 91962 10357 5330 5043 50962 643 11717 2 9652 115748 11510 8504 6608 63840 864 14770 0.199146 0 . 0 . 60 6,25,5,20 UTR_3_PRIME(MODIFIER||39||210|TMEM61|protein_coding|CODING|NM_182532.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.736054 rs2495513 -0.692914 0.565883 60 Q342 692 caA/caG LOW 7 SILENT CODING PCSK9 G protein_coding NM_174936.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55523033 A G 0 228 0 0.9319 0.9818 0.9986 1 1 1 0.940536 0.979702 0.999767 2 9789 120680 11557 8652 6612 66658 902 16510 2 10392 121342 11578 8652 6614 66688 906 16512 0 . 0 . 0 76 0,0,40,21 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q342|692|PCSK9|protein_coding|CODING|NM_174936.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs509504 -0.693147 0.84175 76 V460 692 gtA/gtG LOW 9 SILENT CODING PCSK9 G protein_coding NM_174936.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55524197 A G 0 228 0 0.7746 0.8692 0.8948 0.9881 0.8211 0.9059 0.787108 0.817776 0.833488 2 8167 103705 10704 8576 5461 55552 795 14450 2 10402 121378 11578 8650 6614 66718 904 16512 0 2 benign 0 . 104 0,0,39,51 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V460|692|PCSK9|protein_coding|CODING|NM_174936.3|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs540796 -0.693147 0.000796639 104 V474I 692 Gtc/Atc MODERATE 9 MISSENSE CODING PCSK9 A protein_coding NM_174936.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55524237 G A 0 228 0 0.7746 0.869 0.8948 0.9881 0.8211 0.9049 0.787108 0.817776 0.833488 2 8155 103643 10699 8572 5460 55512 795 14450 2 10384 121300 11574 8646 6614 66666 904 16512 0 2 benign 0 . 88 0,0,20,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V474I|692|PCSK9|protein_coding|CODING|NM_174936.3|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386599232,rs562556 -0.693147 0.524085 88 G670E 692 gGg/gAg MODERATE 12 MISSENSE CODING PCSK9 A protein_coding NM_174936.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55529187 G A 0 228 0 0.7118 0.899 0.964 0.9603 0.9652 0.9744 0.742624 0.889436 0.964651 2 7607 113911 11281 8151 6237 63680 854 16101 2 10260 120760 11566 8616 6604 66312 894 16508 0 2 benign 0 . 132 0,0,38,83 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G670E|692|PCSK9|protein_coding|CODING|NM_174936.3|12|A),DOWNSTREAM(MODIFIER||2845||2620|USP24|protein_coding|CODING|NM_015306.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs505151 -0.693147 0.000616514 132 692 571 MODIFIER 12 CODING PCSK9 T protein_coding NM_174936.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55529828 C T 0 46.3 0 0.3888 0.7242 0.8559 0.9147 0.7674 0.8436 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||571||692|PCSK9|protein_coding|CODING|NM_174936.3|12|T),DOWNSTREAM(MODIFIER||2204||2620|USP24|protein_coding|CODING|NM_015306.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs662145 -0.453602 0.18 2 V2468A 2620 gTa/gCa MODERATE 63 MISSENSE CODING USP24 G protein_coding NM_015306.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55541174 A G 0 228 0 0.2648 0.6923 0.8473 0.9187 0.7714 0.8456 0.356754 0.640088 0.76709 2 2751 78822 8472 6878 4590 43989 612 11530 2 7650 102404 9488 7608 5886 57158 766 13848 1 0 . 0 . 65 0,1,13,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V2468A|2620|USP24|protein_coding|CODING|NM_015306.2|63|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386596053,rs487230 -0.693147 0.0217582 65 T226I 2620 aCt/aTt MODERATE 4 MISSENSE CODING USP24 A protein_coding NM_015306.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 55638075 G A 0 228 0 0.8729 0.9071 0.9164 0.995 0.837 0.9284 0.865395 0.850633 0.84401 2 8461 105234 10767 8515 5765 56109 805 14812 2 9774 120094 11460 8556 6584 66350 894 16476 0 . 0 . 0 94 0,0,56,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T226I|2620|USP24|protein_coding|CODING|NM_015306.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1165222 -0.693147 0.0356404 94 311 1172 MODIFIER 6 CODING PLPP3 A protein_coding NM_003713.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 56961051 G A 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 0,0,33,40 UTR_3_PRIME(MODIFIER||1172||311|PLPP3|protein_coding|CODING|NM_003713.4|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7519755 -0.693147 0.712291 73 311 869 MODIFIER 6 CODING PLPP3 C protein_coding NM_003713.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 56961354 T C 0 222 0 0.8132 0.7905 0.8271 0.5734 0.9692 0.774 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.956358 0 . 0 . 48 11,15,9,10 UTR_3_PRIME(MODIFIER||869||311|PLPP3|protein_coding|CODING|NM_003713.4|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.613726 rs10888976 -0.69168 0.994039 48 311 467 MODIFIER 6 CODING PLPP3 G protein_coding NM_003713.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 56961756 A G 0 222 0 0.4546 0.4125 0.3473 0.4177 0.4801 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.671614 0 . 0 . 68 4,28,4,29 UTR_3_PRIME(MODIFIER||467||311|PLPP3|protein_coding|CODING|NM_003713.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.91051 rs4628 -0.693127 0.679658 68 A99 311 gcG/gcA LOW 2 SILENT CODING PLPP3 T protein_coding NM_003713.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57002627 C T 0 222 0 0.2337 0.1094 0.0159 0.1756 0.0119 0.0399 0.182251 0.0729663 0.0169767 1 1922 5126 166 1361 57 1108 17 495 2 10404 121096 11562 8638 6614 66584 904 16390 0.619392 0 . 0 . 144 52,20,47,17 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A99|311|PLPP3|protein_coding|CODING|NM_003713.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.520789 rs1136164 -0.693147 0.228591 144 R117 552 agG/agA LOW 4 SILENT CODING PRKAA2 A protein_coding NM_006252.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57158051 G A 0 222 0 0.2231 0.1737 0.0677 0.2252 0.0437 0.2628 0.181798 0.0941104 0.049186 1 2115 11999 498 2187 498 3311 105 3285 2 10406 121396 11576 8646 6614 66734 908 16512 0.719537 0 . 0 . 51 19,4,20,6 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R117|552|PRKAA2|protein_coding|CODING|NM_006252.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937052 rs17848595 -0.692976 0.274958 51 H150 552 caC/caT LOW 4 SILENT CODING PRKAA2 T protein_coding NM_006252.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57158150 C T 0 222 0 0.1399 0.0931 0.0389 0.1062 0.0179 0.1319 0.104857 0.0467477 0.0169767 1 1272 5775 299 987 202 1341 51 1623 2 10406 121356 11574 8652 6614 66712 906 16492 0.914257 0 . 0 . 123 34,18,37,17 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H150|552|PRKAA2|protein_coding|CODING|NM_006252.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931744 rs17848596 -0.693147 0.00216161 123 L467 552 Ttg/Ctg LOW 8 SILENT CODING PRKAA2 C protein_coding NM_006252.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57171870 T C 0 222 0 0 0.0081869 0 0.0387 0 0.002 0.000226963 7.6888e-05 0 1 2 241 0 226 0 2 2 9 2 10390 121246 11566 8644 6614 66648 908 16476 0.888163 0 . 0 . 141 38,20,37,27 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L467|552|PRKAA2|protein_coding|CODING|NM_006252.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99366 rs17848599 -0.693147 0.415936 141 552 3007 MODIFIER 9 CODING PRKAA2 C protein_coding NM_006252.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57176393 T C 0 9.7 0 0.1392 0.0931 0.0389 0.1062 0.0179 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3007||552|PRKAA2|protein_coding|CODING|NM_006252.3|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs78810070 -0.379885 0 1 552 4002 MODIFIER 9 CODING PRKAA2 A protein_coding NM_006252.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57177388 T A 0 9.7 0 0.3116 0.1975 0.072 0.2212 0.0437 0.2658 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4002||552|PRKAA2|protein_coding|CODING|NM_006252.3|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1342382 -0.379885 0 1 552 5540 MODIFIER 9 CODING PRKAA2 G protein_coding NM_006252.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57178926 T G 0 32.6 0 0.7511 0.5343 0.3501 0.5437 0.2654 0.6391 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||5540||552|PRKAA2|protein_coding|CODING|NM_006252.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3738567 -0.379885 0 2 Q93K 584 Caa/Aaa MODERATE 3 MISSENSE CODING C8A A protein_coding NM_000562.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57340727 C A 0 228 0 0.1755 0.3437 0.2507 0.496 0.3439 0.4796 0.212211 0.320929 0.376628 2 2194 44343 2402 3881 2284 25085 345 8152 2 10350 120374 11408 8524 6548 66238 896 16410 1 2 benign 0 . 175 1,0,60,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q93K|584|C8A|protein_coding|CODING|NM_000562.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs652785 -0.693147 0.0555109 175 591 57 MODIFIER 12 CODING C8B G protein_coding NM_000066.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57395020 A G 0 228 0 0.1861 0.3672 0.4107 0.5218 0.2913 0.5 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 83 0,0,60,16 UTR_3_PRIME(MODIFIER||57||591|C8B|protein_coding|CODING|NM_000066.3|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2795 -0.693147 0.561413 83 G117R 591 Gga/Aga MODERATE 3 MISSENSE CODING C8B T protein_coding NM_000066.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 57422484 C T 0 228 0 0.9992 0.9864 0.9683 1 0.9652 0.9898 0.99251 0.97578 0.967209 2 10340 118659 11316 8653 6505 64626 881 16338 2 10406 121410 11578 8654 6614 66740 908 16510 0 . 0 . 0 212 0,0,90,111 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G117R|591|C8B|protein_coding|CODING|NM_000066.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1013579,rs386510210 -0.693147 0.0238553 212 555 959434 MODIFIER 1 CODING DAB1 T protein_coding NM_021080.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 58716136 C T 0 191 0 0.0091 0.1186 0.2594 0.0813 0.1322 0.1912 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994922 0 . 0 . 71 32,2,29,1 UTR_5_PRIME(MODIFIER||959434||555|DAB1|protein_coding|CODING|NM_021080.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.967858 rs79902981 -0.693097 0.124638 71 524 13 MODIFIER 2 CODING OMA1 T protein_coding NM_145243.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59004979 C T 0 228 0 0.9115 0.9754 0.9928 1 0.999 1 0.927298 0.975085 0.999418 2 8827 114485 11406 8530 6594 64574 864 13690 2 9572 115300 11448 8530 6594 64596 868 13692 0 . 0 . 0 41 0,0,7,31 UTR_5_PRIME(MODIFIER||13||524|OMA1|protein_coding|CODING|NM_145243.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs902925 -0.693143 0.256944 41 524 7465 MODIFIER 1 CODING OMA1 T protein_coding NM_145243.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59012431 C T 0 9.7 0 0.3359 0.6871 0.7752 0.9474 0.7068 0.8108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||7465||524|OMA1|protein_coding|CODING|NM_145243.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1109895 -0.379885 0 1 828 5090 MODIFIER 20 CODING MYSM1 A protein_coding NM_001085487.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59120579 G A 0 9.7 0 0.9198 0.9145 0.9121 0.9365 0.8738 0.9284 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5090||828|MYSM1|protein_coding|CODING|NM_001085487.2|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs15307 -0.379885 0 1 828 5019 MODIFIER 20 CODING MYSM1 T protein_coding NM_001085487.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59120650 C T 0 32.6 0 0.9198 0.9137 0.9092 0.9365 0.8718 0.9284 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||5019||828|MYSM1|protein_coding|CODING|NM_001085487.2|20|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs232857 -0.379885 0 2 E825K 828 Gaa/Aaa MODERATE 20 MISSENSE CODING MYSM1 T protein_coding NM_001085487.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59125683 C T 0 222 0 0.4599 0.3025 0.2666 0.2143 0.2018 0.3098 0.389474 0.238387 0.171415 1 3984 28218 3136 2080 2253 12121 226 4418 2 9696 117114 11368 8550 6560 65340 850 14750 0.999974 0 . 0 COSM146527 115 42,11,37,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E825K|828|MYSM1|protein_coding|CODING|NM_001085487.2|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.839973 rs232777 -0.693146 0.316964 115 L754 828 ctC/ctT LOW 18 SILENT CODING MYSM1 A protein_coding NM_001085487.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59127086 G A 0 222 0 0.1339 0.2478 0.2421 0.3095 0.2843 0.3047 0.173203 0.257186 0.294998 1 1618 33443 3284 2365 1303 19262 240 5371 2 9728 118542 11258 8478 6506 65592 886 16094 0.40904 0 . 0 . 90 34,13,30,10 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L754|828|MYSM1|protein_coding|CODING|NM_001085487.2|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.451856 rs7523134 -0.693145 0.022373 90 828 LOW 16 CODING MYSM1 T protein_coding NM_001085487.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59131311 G T 0 228 0 0.8495 0.8952 0.9092 0.9365 0.8718 0.9284 0.844875 0.864798 0.873647 2 8338 107452 10843 8004 6065 58163 797 15242 2 9778 120286 11530 8604 6604 66450 896 16424 0 . 0 . 0 97 0,0,28,59 SPLICE_SITE_REGION+INTRON(LOW||||828|MYSM1|protein_coding|CODING|NM_001085487.2|16|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs232790 -0.693147 0.0499333 97 P425 828 ccA/ccG LOW 9 SILENT CODING MYSM1 C protein_coding NM_001085487.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59142713 T C 0 222 0 0.7133 0.6474 0.6686 0.629 0.5875 0.6237 0.669551 0.607137 0.578934 1 6723 73862 7509 5629 4756 38827 550 9868 2 9796 120738 11576 8618 6614 66726 900 16508 0.920256 0 . 0 . 87 4,40,6,31 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P425|828|MYSM1|protein_coding|CODING|NM_001085487.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.872878 rs579110 -0.693141 7.27935e-05 87 T264A 828 Act/Gct MODERATE 8 MISSENSE CODING MYSM1 C protein_coding NM_001085487.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59147926 T C 0 222 0 0.6589 0.632 0.6643 0.629 0.5875 0.6217 0.620219 0.591938 0.579276 1 6212 73306 7490 5626 4763 38841 547 9827 2 9794 120612 11572 8620 6612 66674 900 16440 0.764948 0 . 0 . 79 23,13,24,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T264A|828|MYSM1|protein_coding|CODING|NM_001085487.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.477245 rs12139511 -0.693139 0.0280219 79 C200S 828 Tgt/Agt MODERATE 8 MISSENSE CODING MYSM1 T protein_coding NM_001085487.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59148118 A T 0 222 0 0.0076 0.1558 0.1527 0.2143 0.1859 0.2669 0.031051 0.11293 0.150536 1 241 21571 1934 2094 2169 10897 188 4048 2 9776 120708 11574 8624 6614 66710 900 16510 0.954657 0 . 0 COSM146528 125 22,32,26,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C200S|828|MYSM1|protein_coding|CODING|NM_001085487.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0509534 rs17118103 -0.693147 0.00126244 125 828 LOW 1 CODING MYSM1 G protein_coding NM_001085487.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59160885 A G 0 222 0 0.3411 0.3682 0.3357 0.372 0.4125 0.3783 0.380321 0.407789 0.420034 1 3539 46717 4037 2968 1843 27391 347 6592 2 9300 115126 11204 8304 6408 62958 868 16084 0.908067 0 . 0 . 213 56,29,58,38 SPLICE_SITE_REGION+INTRON(LOW||||828|MYSM1|protein_coding|CODING|NM_001085487.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.630303 rs2064374 -0.693147 0.746694 213 331 71 MODIFIER 1 CODING JUN C protein_coding NM_002228.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59248813 G C 0 228 0 0.8268 0.9519 0.9841 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 47 0,0,16,28 UTR_5_PRIME(MODIFIER||71||331|JUN|protein_coding|CODING|NM_002228.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2760499 -0.693146 0.0265629 47 331 289 MODIFIER 1 CODING JUN G protein_coding NM_002228.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59249031 T G 0 228 0 0.854 0.9601 0.9914 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 0,0,30,54 UTR_5_PRIME(MODIFIER||289||331|JUN|protein_coding|CODING|NM_002228.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2811894,rs386574184 -0.693147 0.064657 99 331 605 MODIFIER 1 CODING JUN C protein_coding NM_002228.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 59249347 G C 0 228 0 0.9788 0.994 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 190 0,0,89,82 UTR_5_PRIME(MODIFIER||605||331|JUN|protein_coding|CODING|NM_002228.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1407816 -0.693147 0.000565491 190 728 40 MODIFIER 1 CODING HOOK1 G protein_coding NM_015888.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 60280749 GT G 0 198 0 1 1 1 1 1 1 1 0.999636 0.999447 2 678 12672 182 186 2 3852 134 7638 2 678 12672 182 186 2 3852 134 7638 0 . 0 . 0 16 0,0,11,2 UTR_5_PRIME(MODIFIER||40||728|HOOK1|protein_coding|CODING|NM_015888.4|1|G) 1 0 . 14 0.875 1 1 1 1 0 60 0 0 1 0 . rs113730234 -0.683931 0.671308 16 K403E 546 Aaa/Gaa MODERATE 10 MISSENSE CODING C1orf87 C protein_coding NM_152377.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 60466814 T C 0 222 0 0.6135 0.5511 0.6167 0.628 0.4483 0.4468 0.602814 0.508381 0.46 1 6263 59730 7087 5459 2817 30474 461 7169 2 10312 118570 11268 8464 6402 65190 878 16056 0.593335 0 . 0 . 47 6,16,6,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K403E|546|C1orf87|protein_coding|CODING|NM_152377.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.924092 rs386602107,rs626251 -0.692717 0.0183013 47 P406 554 ccG/ccA LOW 9 SILENT CODING NFIA A protein_coding NM_001145512.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 61869783 G A 0 228 0 0.289 0.3538 0.3761 0.5625 0.2853 0.2812 0.285747 0.273566 0.267326 2 2946 38633 4619 4996 2249 18472 280 5071 2 10404 121302 11576 8634 6614 66678 908 16488 1 0 . 0 . 84 1,0,46,30 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P406|554|NFIA|protein_coding|CODING|NM_001145512.1|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2236059 -0.693147 0.351239 84 554 LOW 9 CODING NFIA T protein_coding NM_001145512.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 61872228 C T 0 11.4 0 0.6747 0.4796 0.4006 0.5526 0.2664 0.4162 0 . 0 1 1515 15798 1226 2015 675 8282 109 1976 2 6528 74170 7928 5052 3206 41308 510 9638 0.699302 0 . 0 . 55 18,3,1,4 SPLICE_SITE_REGION+INTRON(LOW||||554|NFIA|protein_coding|CODING|NM_001145512.1|9|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0509867 rs2474380,rs28641100 -0.590765 0.24063 55 I90 1801 atC/atT LOW 4 SILENT CODING INADL T protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62232031 C T 0 228 0 0.6989 0.9101 0.9654 1 0.9791 0.9928 0.750567 0.903583 0.981977 2 7671 116984 11374 8652 6516 65531 883 16357 2 10404 121408 11576 8654 6614 66740 908 16512 0 . 0 . 0 80 0,0,47,22 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I90|1801|INADL|protein_coding|CODING|NM_176877.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1286835 -0.693147 0.18549 80 I400V 1801 Ata/Gta MODERATE 10 MISSENSE CODING INADL G protein_coding NM_176877.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62261168 A G 0 222 0 0.1808 0.4349 0.5634 0.4514 0.493 0.6104 0.243759 0.403122 0.484767 1 2267 59557 7168 3599 3320 32380 468 10355 2 10404 121334 11552 8642 6610 66706 908 16512 0.952908 0 . 0 COSM1126971 97 27,21,16,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I400V|1801|INADL|protein_coding|CODING|NM_176877.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.399118 rs7516332 -0.693132 0.530544 97 I870M 1801 atT/atG MODERATE 20 MISSENSE CODING INADL G protein_coding NM_176877.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62330080 T G 0 228 0 0.966 0.9908 0.9986 1 1 1 0.963232 0.987467 0.999884 2 10035 121018 11569 8654 6614 66728 908 16510 2 10406 121406 11578 8654 6614 66736 908 16510 0 . 0 . 0 94 0,0,33,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I870M|1801|INADL|protein_coding|CODING|NM_176877.2|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2799627 -0.693147 0.867606 94 P1066 1801 ccG/ccA LOW 23 SILENT CODING INADL A protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62365321 G A 0 222 0 0.0023 0.0035942 0 0.0139 0 0.001 0.00136178 0.000768876 0.000465116 1 13 125 0 94 0 13 2 3 2 10406 121286 11576 8654 6614 66674 906 16456 0.982539 0 . 0 . 128 32,25,26,25 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1066|1801|INADL|protein_coding|CODING|NM_176877.2|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999617 rs116844048 -0.693147 0.0516272 128 N1168 1801 aaC/aaT LOW 26 SILENT CODING INADL T protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62380270 C T 0 228 0 0.888 0.777 0.8357 0.7431 0.7247 0.6738 0.881979 0.792173 0.746163 2 9184 90354 9406 6372 4973 48610 636 11173 2 10338 120800 11486 8588 6606 66404 894 16484 1 0 . 0 . 103 1,0,31,56 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1168|1801|INADL|protein_coding|CODING|NM_176877.2|26|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1134766,rs386477469 -0.693147 0.0538281 103 G1178S 1801 Ggt/Agt MODERATE 26 MISSENSE CODING INADL A protein_coding NM_176877.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62380298 G A 0 222 0 0.0862 0.4451 0.5231 0.5655 0.6282 0.5624 0.162052 0.485238 0.650814 1 1540 68224 5602 4869 4121 42298 529 9265 2 10292 120890 11504 8604 6612 66484 904 16490 0.96105 0 . 0 . 92 9,34,12,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1178S|1801|INADL|protein_coding|CODING|NM_176877.2|26|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969097 rs1056513 -0.693145 0.00445397 92 1801 LOW 26 CODING INADL G protein_coding NM_176877.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62393394 A G 0 228 0 0.8707 0.8466 0.9193 0.8125 0.8499 0.7945 0.874943 0.868907 0.865814 2 9103 103612 10267 7184 5509 56964 777 13808 2 10398 121024 11496 8626 6602 66560 904 16438 0 . 0 . 0 72 0,0,47,19 SPLICE_SITE_REGION+INTRON(LOW||||1801|INADL|protein_coding|CODING|NM_176877.2|26|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2251182 -0.693147 0.267315 72 R1282H 1801 cGt/cAt MODERATE 28 MISSENSE CODING INADL A protein_coding NM_176877.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62456014 G A 0 222 0 0.553 0.4748 0.3199 0.4683 0.4066 0.5562 0.490694 0.445333 0.422093 1 5359 51313 3062 3960 2027 28176 386 8343 2 10406 121114 11532 8592 6604 66630 902 16448 0.901664 0 . 0 . 115 20,32,16,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1282H|1801|INADL|protein_coding|CODING|NM_176877.2|28|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.582811 rs1134767 -0.693147 0.00026897 115 V1360L 1801 Gtc/Ctc MODERATE 31 MISSENSE CODING INADL C protein_coding NM_176877.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62516683 G C 0 222 0 0.767 0.5709 0.5591 0.2778 0.5467 0.6411 0.708125 0.607028 0.555233 1 7499 67180 6089 2353 3129 37112 540 10458 2 10400 120794 11544 8566 6594 66294 908 16488 0.599551 0 . 0 COSM146531 149 38,35,33,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V1360L|1801|INADL|protein_coding|CODING|NM_176877.2|31|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.837767 rs2498982 -0.693147 0.127206 149 E1520 1801 gaG/gaA LOW 35 SILENT CODING INADL A protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62579823 G A 0 222 0 0.4206 0.609 0.7161 0.754 0.66 0.5859 0.467998 0.620406 0.698488 1 4759 80262 8854 6750 3729 45573 596 10001 2 10386 121220 11552 8636 6578 66652 906 16510 0.550384 0 . 0 . 113 32,24,30,16 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E1520|1801|INADL|protein_coding|CODING|NM_176877.2|35|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.802999 rs1475563 -0.693147 0.557248 113 I1548 1801 atC/atT LOW 35 SILENT CODING INADL T protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62579907 C T 0 222 0 0.2791 0.2975 0.2291 0.7113 0.0696 0.1789 0.258057 0.14601 0.0886047 1 2731 21013 3235 6324 392 5469 111 2751 2 10380 120628 11480 8608 6478 66378 904 16400 0.980129 0 . 0 . 92 28,19,14,19 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1548|1801|INADL|protein_coding|CODING|NM_176877.2|35|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.643942 rs7418709 -0.693127 0.059768 92 N1749 1801 aaC/aaT LOW 41 SILENT CODING INADL T protein_coding NM_176877.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62594593 C T 0 222 0 0.1362 0.3309 0.4741 0.0754 0.5358 0.545 0.171066 0.426057 0.548376 1 1640 57209 5572 613 2946 36749 479 9210 2 9766 120658 11566 8612 6612 66708 900 16494 0.920218 0 . 0 . 55 10,16,9,15 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1749|1801|INADL|protein_coding|CODING|NM_176877.2|41|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.281472 rs2476194 -0.692831 0.392992 55 1801 634 MODIFIER 43 CODING INADL T protein_coding NM_176877.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62627241 C T 0 9.7 0 0.3495 0.3013 0.2363 0.6359 0.0606 0.1851 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||634||1801|INADL|protein_coding|CODING|NM_176877.2|43|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12059368 -0.379885 0 1 G82 865 ggG/ggA LOW 4 SILENT CODING L1TD1 A protein_coding NM_001164835.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62672546 G A 0 228 0 0.9879 0.8808 0.9352 0.8522 0.841 0.7679 0.966348 0.884124 0.842026 2 9704 103451 10812 7132 5537 56259 798 13209 2 10006 120362 11542 8536 6596 66298 902 16482 0 . 0 . 0 124 0,0,69,45 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G82|865|L1TD1|protein_coding|CODING|NM_001164835.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2457829 -0.693147 0.963895 124 V246A 865 gTa/gCa MODERATE 4 MISSENSE CODING L1TD1 C protein_coding NM_001164835.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62673037 T C 0 222 0 0.6747 0.5763 0.647 0.3234 0.675 0.5521 0.702955 0.702273 0.701891 1 1851 12858 221 230 23 5877 129 4527 2 2726 20606 384 636 34 8746 194 7886 0.684277 0 . 0 COSM426542 47 19,6,17,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V246A|865|L1TD1|protein_coding|CODING|NM_001164835.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.111411 rs7542665 -0.692352 0.828622 47 V309M 865 Gtg/Atg MODERATE 4 MISSENSE CODING L1TD1 A protein_coding NM_001164835.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62673225 G A 0 222 0 0.5961 0.5377 0.6239 0.3194 0.6491 0.5082 0.621753 0.644957 0.658128 1 1421 11688 221 230 23 5520 123 4150 2 2364 20146 400 638 32 8620 198 7894 0.955789 0 . 0 . 101 34,16,21,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V309M|865|L1TD1|protein_coding|CODING|NM_001164835.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.808744 rs7533274 -0.693132 0.467797 101 A421 865 gcT/gcC LOW 5 SILENT CODING L1TD1 C protein_coding NM_001164835.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62675709 T C 0 222 0 0.1785 0.1585 0.1037 0.2103 0.0765 0.2014 0.147299 0.099877 0.0755814 1 1542 14103 1146 1754 704 5675 106 3176 2 9960 119372 11408 8348 6596 65730 902 16428 0.612626 0 . 0 . 44 10,14,10,10 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A421|865|L1TD1|protein_coding|CODING|NM_001164835.1|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.399156 rs7551777 -0.692067 0.00408962 44 E482 865 gaA/gaG LOW 5 SILENT CODING L1TD1 G protein_coding NM_001164835.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62675892 A G 0 222 0 0.5166 0.5076 0.6254 0.251 0.6481 0.5317 0.537676 0.616408 0.656744 1 5456 73153 7229 2059 4338 44588 571 8912 2 10196 120682 11530 8580 6610 66430 900 16436 0.998374 0 . 0 . 53 13,9,19,10 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E482|865|L1TD1|protein_coding|CODING|NM_001164835.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.785887 rs2481694 -0.693079 0.416368 53 P549T 865 Ccc/Acc MODERATE 5 MISSENSE CODING L1TD1 A protein_coding NM_001164835.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62676091 C A 0 222 0 0.1876 0.1885 0.1196 0.2798 0.1183 0.2168 0.16296 0.136629 0.12314 1 1713 19572 1405 2462 1150 9209 147 3486 2 10384 121278 11568 8638 6614 66662 908 16504 0.993045 0 . 0 . 101 19,21,30,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P549T|865|L1TD1|protein_coding|CODING|NM_001164835.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.445302 rs11207933 -0.693147 0.668848 101 995 1312 MODIFIER 10 CODING KANK4 T protein_coding NM_181712.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62702637 C T 0 9.7 0 0.9236 0.9523 0.9841 1 0.9592 0.9121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1312||995|KANK4|protein_coding|CODING|NM_181712.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2481688 -0.379885 0 1 A987V 995 gCg/gTg MODERATE 10 MISSENSE CODING KANK4 A protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62703977 G A 0 222 0 0.0038 0.0485 0.0346 0.0942 0.0258 0.0951 0.00658193 0.0202214 0.0272093 1 59 4336 230 759 104 1711 30 1443 2 10180 120350 11506 8624 6584 66122 900 16434 0.589611 0 . 0 . 50 5,15,10,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A987V|995|KANK4|protein_coding|CODING|NM_181712.4|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.267918 rs34591898 -0.692067 0.148642 50 V935L 995 Gtg/Ctg MODERATE 9 MISSENSE CODING KANK4 G protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62713224 C G 0 228 0 0.9962 0.9862 0.9914 1 0.9672 0.9744 0.992283 0.970783 0.959767 2 10294 118147 11431 8646 6519 64300 889 16068 2 10366 121252 11568 8648 6614 66640 906 16510 0 . 0 . 0 27 0,0,17,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V935L|995|KANK4|protein_coding|CODING|NM_181712.4|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2941679 -0.692914 0.211327 27 V840A 995 gTg/gCg MODERATE 7 MISSENSE CODING KANK4 G protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62728784 A G 0 228 0 0.5484 0.7159 0.7882 0.8433 0.7396 0.7352 0.558103 0.674304 0.733837 2 5683 88460 9775 7160 5408 48430 650 11354 2 10166 118832 11298 8518 6370 65508 886 16086 0 . 0 . 0 85 0,0,66,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V840A|995|KANK4|protein_coding|CODING|NM_181712.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2666472 -0.693147 0.0142436 85 H822R 995 cAc/cGc MODERATE 7 MISSENSE CODING KANK4 C protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62728838 T C 0 228 0 0.5484 0.7163 0.7896 0.8442 0.7396 0.7352 0.558783 0.674612 0.733953 2 5744 89485 9917 7209 5543 48917 659 11496 2 10336 120506 11490 8582 6534 66314 900 16350 0 . 0 . 0 94 0,0,53,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H822R|995|KANK4|protein_coding|CODING|NM_181712.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2258470 -0.693147 0.0517006 94 K814 995 aaA/aaG LOW 7 SILENT CODING KANK4 C protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62728861 T C 0 228 0 0.5492 0.7163 0.7896 0.8433 0.7396 0.7352 0.558783 0.674535 0.733837 2 5740 89493 9916 7221 5525 48906 663 11522 2 10334 120506 11488 8592 6514 66264 904 16410 0 . 0 . 0 111 0,0,54,45 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K814|995|KANK4|protein_coding|CODING|NM_181712.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2260581 -0.693147 0.579306 111 P795 995 ccC/ccT LOW 7 SILENT CODING KANK4 A protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62728918 G A 0 228 0 0.5484 0.7161 0.7896 0.8433 0.7396 0.7352 0.558783 0.674535 0.733837 2 5756 89812 9950 7253 5545 49109 664 11535 2 10318 120762 11514 8606 6530 66458 900 16436 0 . 0 . 0 103 0,0,29,67 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P795|995|KANK4|protein_coding|CODING|NM_181712.4|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2262110 -0.693147 0.0348687 103 T768A 995 Acc/Gcc MODERATE 6 MISSENSE CODING KANK4 C protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62732421 T C 0 222 0 0.2095 0.3055 0.3977 0.5873 0.2654 0.1207 0.222878 0.237429 0.244884 1 2280 34522 5793 5100 2351 16367 262 2369 2 10346 121138 11566 8638 6612 66588 906 16482 0.994911 0 . 0 . 61 7,21,5,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T768A|995|KANK4|protein_coding|CODING|NM_181712.4|6|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.972604 0.992553 0 0.898365 rs11207949 -0.693021 0.11271 61 G701S 995 Ggc/Agc MODERATE 5 MISSENSE CODING KANK4 T protein_coding NM_181712.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62734089 C T 0 222 0 0.2095 0.1286 0.0418 0.1369 0.0358 0.1677 0.187699 0.0888052 0.0381395 1 2007 8996 318 1100 261 2727 64 2519 2 10400 121274 11576 8636 6600 66646 906 16510 0.929257 0 . 0 . 49 12,12,12,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G701S|995|KANK4|protein_coding|CODING|NM_181712.4|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991881 rs17123306 -0.692717 0.0188261 49 P624 995 ccA/ccG LOW 3 SILENT CODING KANK4 C protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62738904 T C 0 228 0 0.8782 0.8005 0.7911 0.8403 0.7018 0.7628 0.854318 0.734575 0.673296 2 7996 81601 9712 7220 5288 43516 572 7297 2 9314 109242 11450 8542 6542 62898 786 9710 0 . 0 . 0 108 0,0,62,31 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P624|995|KANK4|protein_coding|CODING|NM_181712.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7516290 -0.693147 0.0372051 108 S605 995 agC/agT LOW 3 SILENT CODING KANK4 A protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62738961 G A 0 222 0 0.2368 0.1394 0.1182 0.1369 0.0437 0.1237 0.225148 0.105122 0.0436148 1 2339 9780 1225 1106 262 3116 72 1660 2 9652 112952 11480 8546 6566 63560 832 12316 0.214261 0 . 0 . 106 17,33,19,26 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S605|995|KANK4|protein_coding|CODING|NM_181712.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980682 rs61623093 -0.693147 0.197295 106 G237 995 ggT/ggC LOW 3 SILENT CODING KANK4 G protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62740065 A G 0 222 0 0.6437 0.4822 0.3948 0.248 0.4394 0.6115 0.607808 0.488313 0.427093 1 6410 54591 3948 2181 2973 29331 394 9354 2 10376 120898 11494 8618 6584 66434 902 16490 0.354085 0 . 0 . 79 17,18,20,18 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G237|995|KANK4|protein_coding|CODING|NM_181712.4|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.772928 rs12127930 -0.693143 0.141044 79 P110 995 ccA/ccG LOW 3 SILENT CODING KANK4 C protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62740446 T C 0 228 0 0.8812 0.8045 0.7911 0.8522 0.7038 0.7648 0.854545 0.735267 0.674227 2 8678 90103 9786 7467 5330 45918 661 12263 2 10104 120980 11562 8648 6604 66642 908 16512 0 . 0 . 0 63 0,0,23,35 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P110|995|KANK4|protein_coding|CODING|NM_181712.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2666506 -0.693147 0.0128887 63 S109 995 tcA/tcG LOW 3 SILENT CODING KANK4 C protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62740449 T C 0 228 0 0.798 0.781 0.7795 0.8522 0.7038 0.7648 0.772955 0.707109 0.673412 2 7861 89214 9748 7464 5328 45897 657 12259 2 10114 120982 11562 8644 6604 66638 908 16512 0 . 0 . 0 63 0,0,23,35 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S109|995|KANK4|protein_coding|CODING|NM_181712.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2666507 -0.693147 0.0128887 63 D8 995 gaC/gaT LOW 3 SILENT CODING KANK4 A protein_coding NM_181712.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 62740752 G A 0 222 0 0.0053 0.0705 0.0836 0.1349 0.0338 0.1207 0.012256 0.0293711 0.0381395 1 111 7085 1097 1095 261 2775 56 1690 2 10242 120306 11522 8564 6598 66214 906 16260 0.569275 0 . 0 . 61 14,14,15,14 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D8|995|KANK4|protein_coding|CODING|NM_181712.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89167 rs17123318 -0.693079 0.175671 61 S304F 507 tCt/tTt MODERATE 11 MISSENSE CODING ALG6 T protein_coding NM_013339.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 63881552 C T 0 228 0 0.9032 0.8305 0.7608 0.8571 0.6859 0.9029 0.855813 0.736996 0.676094 2 8822 90263 9559 7384 4387 45349 671 14091 2 10224 120122 11464 8590 6536 65958 898 16452 1 255 other 0 . 101 1,0,60,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S304F|507|ALG6|protein_coding|CODING|NM_013339.3|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4630153 -0.693147 0.294001 101 D8 629 gaT/gaC LOW 2 SILENT CODING EFCAB7 C protein_coding NM_032437.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 63991267 T C 0 222 0 0.3026 0.4018 0.4741 0.4812 0.326 0.4806 0.327735 0.32139 0.31814 1 3352 45495 6156 4100 1948 22005 330 7604 2 10276 120924 11572 8644 6612 66524 904 16392 0.868498 0 . 0 . 156 43,19,51,21 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D8|629|EFCAB7|protein_coding|CODING|NM_032437.3|2|C),UPSTREAM(MODIFIER||2323||216|ITGB3BP|protein_coding|CODING|NM_001206739.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.86122 rs217478 -0.693147 0.0941519 156 R347 580 cgC/cgT LOW 6 SILENT CODING PGM1 T protein_coding NM_001172818.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64102018 C T 0 222 0 0 0.005591 0 0.0278 0 0 0 . 0 1 0 158 0 145 1 10 0 2 2 10406 121396 11578 8642 6614 66736 908 16512 0.896986 0 . 0 . 120 45,18,30,16 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R347|580|PGM1|protein_coding|CODING|NM_001172818.1|6|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.422333 rs79097301 -0.693147 0.283214 120 Y438H 580 Tat/Cat MODERATE 8 MISSENSE CODING PGM1 C protein_coding NM_001172818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64114301 T C 0 228 0 0.1967 0.2258 0.3963 0.2083 0.2237 0.1646 0.172492 0.180148 0.18407 2 1847 27153 5142 1718 2180 12743 202 3321 2 10392 121232 11558 8606 6602 66666 906 16502 1 0 . 0 COSM426572,COSM1474137 62 0,1,9,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y438H|580|PGM1|protein_coding|CODING|NM_001172818.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11208257 -0.693147 0.633228 62 580 22 MODIFIER 11 CODING PGM1 T protein_coding NM_001172818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64125368 C T 0 228 0 0.0635 0.1845 0.3329 0.2212 0.2336 0.1544 0.0871539 0.149931 0.182093 2 896 23870 3932 1681 1826 12232 181 3122 2 10306 120016 11420 8504 6498 66082 898 16308 0 . 0 . 0 73 0,0,39,26 UTR_3_PRIME(MODIFIER||22||580|PGM1|protein_coding|CODING|NM_001172818.1|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8294 -0.693147 0.111748 73 580 93 MODIFIER 11 CODING PGM1 C protein_coding NM_001172818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64125439 A C 0 228 0 0.0635 0.1847 0.3329 0.2212 0.2336 0.1554 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 69 0,0,27,39 UTR_3_PRIME(MODIFIER||93||580|PGM1|protein_coding|CODING|NM_001172818.1|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4643 -0.693147 0.176894 69 L60 937 ctC/ctT LOW 3 SILENT CODING ROR1 T protein_coding NM_005012.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64515379 C T 0 228 0 0.5545 0.7788 0.8602 0.9415 0.831 0.8027 0.631866 0.779794 0.855581 2 6546 101773 10279 8293 5750 56882 762 13261 2 10404 121386 11576 8652 6612 66728 908 16506 0 . 0 . 0 114 0,0,54,52 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L60|937|ROR1|protein_coding|CODING|NM_005012.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1772626,rs386544384 -0.693147 2.07257e-05 114 A390 937 gcG/gcT LOW 7 SILENT CODING ROR1 T protein_coding NM_005012.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64608329 G T 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121316 11568 8614 6610 66702 904 16512 2 10406 121316 11568 8614 6610 66702 904 16512 0 . 0 . 0 84 0,0,28,46 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A390|937|ROR1|protein_coding|CODING|NM_005012.3|7|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2762833 -0.693147 0.00295054 84 226 75 MODIFIER 9 CODING UBE2U G protein_coding NM_152489.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 64709891 A G 0 209 0 0.1664 0.2414 0.1801 0.3294 0.2684 0.2679 0.17341 0.227113 0.250471 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972155 0 . 0 . 40 4,13,2,17 UTR_3_PRIME(MODIFIER||75||226|UBE2U|protein_coding|CODING|NM_152489.1|9|G) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.62686 rs10789152 -0.69168 0.0296173 40 L127 1223 ctG/ctA LOW 5 SILENT CODING CACHD1 A protein_coding NM_020925.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65095054 G A 0 222 0 0.0068 0.0609 0.1585 0.0496 0.0746 0.0624 0.018469 0.0490065 0.0628488 1 151 8349 1740 359 502 4403 66 1128 2 9802 120644 11554 8592 6612 66690 900 16494 0.988918 0 . 0 . 156 54,19,45,20 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L127|1223|CACHD1|protein_coding|CODING|NM_020925.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.575361 rs17383227 -0.693147 0.322385 156 M363T 1223 aTg/aCg MODERATE 9 MISSENSE CODING CACHD1 C protein_coding NM_020925.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65113568 T C 0 228 0 0.9917 0.9978 1 1 1 1 0.990014 0.996617 1 2 10302 121252 11567 8646 6612 66714 904 16507 2 10406 121376 11570 8646 6612 66730 904 16508 0 . 0 . 0 110 0,0,70,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M363T|1223|CACHD1|protein_coding|CODING|NM_020925.2|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6588100 -0.693147 0.853049 110 H1105 1223 caC/caT LOW 25 SILENT CODING CACHD1 T protein_coding NM_020925.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65147002 C T 0 222 0 0.1815 0.1276 0.0879 0.1935 0.0457 0.0992 0.16364 0.0858834 0.0460465 1 1720 8442 740 1778 114 2762 69 1259 2 10402 121370 11576 8640 6614 66722 908 16508 0.822827 0 . 0 . 65 20,5,14,15 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H1105|1223|CACHD1|protein_coding|CODING|NM_020925.2|25|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.260869 rs3828064,rs386587368 -0.693079 0.663055 65 1223 1480 MODIFIER 27 CODING CACHD1 T protein_coding NM_020925.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65158724 C T 0 228 0 0.9947 0.9567 0.9251 0.999 0.8738 0.9693 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 151 0,0,62,76 UTR_3_PRIME(MODIFIER||1480||1223|CACHD1|protein_coding|CODING|NM_020925.2|27|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1926303 -0.693147 0.128718 151 678 572 MODIFIER 12 CODING RAVER2 G protein_coding NM_018211.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65297240 A G 0 74 0 0.907 0.5883 0.5432 0.6369 0.3857 0.3476 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.750668 0 . 0 . 8 2,1,0,5 UTR_3_PRIME(MODIFIER||572||678|RAVER2|protein_coding|CODING|NM_018211.3|12|G),DOWNSTREAM(MODIFIER||1666||1154|JAK1|protein_coding|CODING|NM_002227.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.600535 rs1048007 -0.590765 0.0815962 8 678 1315 MODIFIER 12 CODING RAVER2 T protein_coding NM_018211.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65297983 A T 0 222 0 0.882 0.5693 0.5259 0.625 0.3588 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.123692 0 . 0 . 170 33,51,30,36 UTR_3_PRIME(MODIFIER||1315||678|RAVER2|protein_coding|CODING|NM_018211.3|12|T),DOWNSTREAM(MODIFIER||923||1154|JAK1|protein_coding|CODING|NM_002227.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997807 rs1556561 -0.693147 0.000134024 170 678 2123 MODIFIER 12 CODING RAVER2 T protein_coding NM_018211.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65298791 A T 0 111 0 0.8933 0.5573 0.4078 0.625 0.3618 0.3405 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960777 0 . 0 . 27 17,1,8,1 UTR_3_PRIME(MODIFIER||2123||678|RAVER2|protein_coding|CODING|NM_018211.3|12|T),DOWNSTREAM(MODIFIER||115||1154|JAK1|protein_coding|CODING|NM_002227.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.108225 rs373360328,rs2780889 -0.662043 0.201452 27 S683 1154 agC/agT LOW 15 SILENT CODING JAK1 A protein_coding NM_002227.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65311262 G A 0 222 0 0.2035 0.1983 0.2046 0.3165 0.1153 0.1503 0.189224 0.135553 0.110255 1 1981 18194 2186 2793 800 7734 140 2560 2 9802 120748 11574 8606 6614 66740 900 16512 0.998038 0 . 0 . 82 24,18,22,12 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S683|1154|JAK1|protein_coding|CODING|NM_002227.2|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.409004 rs2230587 -0.693132 0.430271 82 P155 223 ccG/ccA LOW 5 SILENT CODING AK4 A protein_coding NM_001005353.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65690461 G A 0 222 0 0.3298 0.37 0.3314 0.6726 0.1769 0.3384 0.312982 0.244503 0.209419 1 3197 34096 4259 5565 1232 13945 256 5642 2 10406 121350 11566 8638 6610 66712 908 16510 0.999246 0 . 0 . 159 41,32,35,29 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P155|223|AK4|protein_coding|CODING|NM_001005353.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414802 rs4915685 -0.693147 0.64002 159 E500 970 gaG/gaA LOW 12 SILENT CODING DNAJC6 A protein_coding NM_001256864.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65858145 G A 0 222 0 0.2784 0.354 0.4323 0.1885 0.5338 0.3865 0.320472 0.461633 0.533953 1 3143 54263 5240 1557 2752 34777 412 6382 2 10310 118218 11440 8590 6562 65716 866 14734 0.51685 0 . 0 . 86 27,16,17,17 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E500|970|DNAJC6|protein_coding|CODING|NM_001256864.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.4453 rs4325172 -0.693132 0.151931 86 H502 970 caC/caT LOW 12 SILENT CODING DNAJC6 T protein_coding NM_001256864.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65858151 C T 0 222 0 0.5144 0.3139 0.1571 0.5873 0.0318 0.1626 0.427826 0.156697 0.0177907 1 4706 16703 1819 4987 887 1567 109 2628 2 10372 119518 11490 8604 6592 66108 884 15468 0.313641 0 . 0 . 85 19,18,23,19 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H502|970|DNAJC6|protein_coding|CODING|NM_001256864.1|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.623117 rs11208644 -0.693146 0.537374 85 S661 970 agT/agC LOW 13 SILENT CODING DNAJC6 C protein_coding NM_001256864.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65860660 T C 0 222 0 0.5151 0.3143 0.1571 0.5883 0.0318 0.1626 0.42828 0.156774 0.0176744 1 4710 16816 1829 5020 888 1577 109 2683 2 10402 121322 11574 8646 6614 66690 906 16490 0.955505 0 . 0 . 57 10,17,7,16 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S661|970|DNAJC6|protein_coding|CODING|NM_001256864.1|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975257 rs12077111 -0.692717 0.175486 57 P670 970 ccA/ccC LOW 13 SILENT CODING DNAJC6 C protein_coding NM_001256864.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65860687 A C 0 228 0 0.9811 0.7578 0.6282 0.7927 0.5924 0.682 0.912846 0.695448 0.58407 2 9648 78496 7411 6729 3777 39057 584 11290 2 10402 121368 11578 8650 6614 66716 908 16500 0 . 0 . 0 48 0,0,8,37 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P670|970|DNAJC6|protein_coding|CODING|NM_001256864.1|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4582839 -0.693147 0.015368 48 S728N 970 aGc/aAc MODERATE 15 MISSENSE CODING DNAJC6 A protein_coding NM_001256864.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65867519 G A 0 222 0 0.5552 0.3602 0.1787 0.6042 0.0477 0.2955 0.464367 0.1833 0.0393023 1 5105 20959 2002 5152 954 2981 150 4615 2 10398 121312 11544 8628 6612 66712 906 16512 0.674023 0 . 0 . 118 33,23,30,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S728N|970|DNAJC6|protein_coding|CODING|NM_001256864.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.51949 rs4915691 -0.693147 0.324441 118 1165 144851 MODIFIER 1 CODING LEPR C protein_coding NM_002303.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65886398 T C 0 228 0 0.4811 0.5679 0.4697 0.8681 0.4453 0.5716 0.441489 0.441844 0.442026 2 2660 31376 1386 3826 497 16630 194 6183 2 5318 56888 2436 4490 952 32642 366 10684 0 . 0 . 0 48 0,0,39,4 UTR_5_PRIME(MODIFIER||144851||1165|LEPR|protein_coding|CODING|NM_002303.5|1|C),UPSTREAM(MODIFIER||1||140|LEPROT|protein_coding|CODING|NM_001198681.1||C),DOWNSTREAM(MODIFIER||4846||970|DNAJC6|protein_coding|CODING|NM_001256864.1||C),INTRAGENIC(MODIFIER|||||LEPROT||CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3790435 -0.693146 0.00477128 48 140 LOW 2 CODING LEPROT C protein_coding NM_001198681.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65887013 A C 0 228 0 0.3873 0.5419 0.4611 0.8681 0.4443 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 196 0,0,141,26 SPLICE_SITE_REGION(LOW||||140|LEPROT|protein_coding|CODING|NM_001198681.1|2|C),UTR_5_PRIME(MODIFIER||87||140|LEPROT|protein_coding|CODING|NM_001198681.1|2|C),INTRON(MODIFIER||||1165|LEPR|protein_coding|CODING|NM_002303.5|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12145690 -0.693147 0.0105888 196 140 87 MODIFIER 2 CODING LEPROT C protein_coding NM_001198681.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65887013 A C 0 228 0 0.3873 0.5419 0.4611 0.8681 0.4443 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 196 0,0,141,26 SPLICE_SITE_REGION(LOW||||140|LEPROT|protein_coding|CODING|NM_001198681.1|2|C),UTR_5_PRIME(MODIFIER||87||140|LEPROT|protein_coding|CODING|NM_001198681.1|2|C),INTRON(MODIFIER||||1165|LEPR|protein_coding|CODING|NM_002303.5|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12145690 -0.693147 0.0105888 196 140 1370 MODIFIER 5 CODING LEPROT A protein_coding NM_001198681.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 65898972 G A 0 6.3 0 1 0.9988 0.9957 1 0.998 0.999 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1370||140|LEPROT|protein_coding|CODING|NM_001198681.1|5|A),INTRON(MODIFIER||||1165|LEPR|protein_coding|CODING|NM_002303.5|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1536466 -0.379885 0 1 K109R 1165 aAg/aGg MODERATE 4 MISSENSE CODING LEPR G protein_coding NM_002303.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 66036441 A G 0 228 0 0.1528 0.3203 0.2378 0.8046 0.2704 0.1575 0.172946 0.233354 0.264302 2 1677 34397 3617 7096 2417 16989 234 2367 2 10278 116932 11486 8632 6600 65624 870 13442 0 2 benign 0 . 72 0,0,15,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K109R|1165|LEPR|protein_coding|CODING|NM_002303.5|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1137100 -0.693147 0.00841545 72 Q223R 1165 cAg/cGg MODERATE 6 MISSENSE CODING LEPR G protein_coding NM_002303.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 66058513 A G 0 228 0 0.5923 0.5843 0.4366 0.869 0.4692 0.5031 0.560826 0.490312 0.454186 2 5769 61749 5356 7590 4014 30734 461 7825 2 10388 121004 11446 8642 6598 66534 908 16488 0 2 benign 0 . 78 0,0,22,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q223R|1165|LEPR|protein_coding|CODING|NM_002303.5|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1137101 -0.693147 0.338672 78 P1019 1165 ccG/ccA LOW 20 SILENT CODING LEPR A protein_coding NM_002303.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 66102257 G A 0 228 0 0.4478 0.5298 0.4841 0.869 0.3797 0.4775 0.470922 0.407496 0.375 2 4496 54506 5924 7517 3188 25289 396 7696 2 9876 120424 11518 8634 6610 66398 900 16488 0 . 0 . 0 34 0,0,15,18 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1019|1165|LEPR|protein_coding|CODING|NM_002303.5|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1805096 -0.693127 0.786156 34 736 LOW 12 CODING PDE4B G protein_coding NM_001037341.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 66829262 A G 0 228 0 0.9349 0.869 0.7839 0.9454 0.7416 0.8926 0.910803 0.790943 0.729535 2 9525 95392 8598 8171 4486 49452 726 14434 2 10394 120492 11446 8622 6554 66322 900 16254 1 0 . 0 . 74 0,1,19,43 SPLICE_SITE_REGION+INTRON(LOW||||736|PDE4B|protein_coding|CODING|NM_001037341.1|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs783039 -0.693147 3.78641e-05 74 Q50L 135 cAg/cTg MODERATE 1 MISSENSE CODING INSL5 A protein_coding NM_005478.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67266756 T A 0 228 0 0.7821 0.8712 0.8919 0.9901 0.83 0.8967 0.807989 0.842611 0.860349 2 8368 106360 10061 8612 6049 57810 782 14678 2 10406 121364 11576 8654 6614 66708 908 16498 0 . 0 . 0 81 0,0,50,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q50L|135|INSL5|protein_coding|CODING|NM_005478.4|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs549148 -0.693147 0.0107449 81 R832Q 848 cGg/cAg MODERATE 16 MISSENSE CODING WDR78 T protein_coding NM_024763.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67288045 C T 0 228 0 0.5537 0.5148 0.5447 0.6419 0.4761 0.3497 0.562869 0.516146 0.492209 2 5854 60248 6933 5632 2325 32586 443 6475 2 10354 120278 11568 8636 6614 66474 896 15736 0 . 0 . 0 56 0,0,38,14 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGg/cAg|R832Q|848|WDR78|protein_coding|CODING|NM_024763.4|16|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs482082 -0.693147 0.481101 56 D403 848 gaC/gaT LOW 8 SILENT CODING WDR78 A protein_coding NM_024763.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67313249 G A 0 228 0 0.0613 0.2212 0.1787 0.5466 0.0338 0.3252 0.0646845 0.0448255 0.0346512 2 693 15478 2761 4620 270 2571 104 4459 2 10314 120950 11490 8622 6592 66550 898 16484 0 . 0 . 0 79 0,0,39,27 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D403|848|WDR78|protein_coding|CODING|NM_024763.4|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs57010209 -0.693147 0.00890766 79 C33W 848 tgC/tgG MODERATE 1 MISSENSE CODING WDR78 C protein_coding NM_024763.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67390416 G C 0 228 0 0.8449 0.8379 0.8343 0.8829 0.7326 0.8926 0.839537 0.768415 0.731977 2 8651 95234 10249 7569 4195 49559 710 14301 2 10406 121400 11576 8648 6614 66736 908 16512 0.552273 0 . 0 . 244 1,1,134,86 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgC/tgG|C33W|848|WDR78|protein_coding|CODING|NM_024763.4|1|C),UPSTREAM(MODIFIER||162||565|MIER1|protein_coding|CODING|NM_001077700.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.813636 rs3008858 -0.693147 2.67725e-07 244 G16A 848 gGa/gCa MODERATE 1 MISSENSE CODING WDR78 G protein_coding NM_024763.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67390468 C G 0 228 0 0.8608 0.8427 0.8372 0.8829 0.7336 0.8926 0.851339 0.772413 0.731977 2 8787 95393 10256 7571 4195 49573 710 14301 2 10402 121388 11578 8646 6614 66728 908 16512 0.956186 0 . 0 . 224 2,0,90,104 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gCa|G16A|848|WDR78|protein_coding|CODING|NM_024763.4|1|G),UPSTREAM(MODIFIER||110||565|MIER1|protein_coding|CODING|NM_001077700.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.610825 rs1886686 -0.693147 0.0328759 224 565 2452 MODIFIER 14 CODING MIER1 G protein_coding NM_001077700.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67453035 A G 0 228 0 0.9924 0.9403 0.8934 0.999 0.8966 0.8875 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 86 0,0,39,44 UTR_3_PRIME(MODIFIER||2452||565|MIER1|protein_coding|CODING|NM_001077700.2|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7516251 -0.693147 0.356985 86 400 519 MODIFIER 8 CODING C1orf141 C protein_coding NM_001276351.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67558169 T C 0 116 0 0.9879 0.9385 0.915 0.9722 0.8141 0.9816 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_3_PRIME(MODIFIER||519||400|C1orf141|protein_coding|CODING|NM_001276351.1|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6687611 -0.616816 0.12166 6 T384 400 acG/acA LOW 8 SILENT CODING C1orf141 T protein_coding NM_001276351.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67558739 C T 0 228 0 0.9228 0.9207 0.9107 0.9722 0.8141 0.9816 0.915077 0.876827 0.857226 2 9160 107096 10860 8412 5092 56815 800 15957 2 10076 120710 11550 8650 6600 66426 906 16502 0 . 0 . 0 16 0,0,5,11 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T384|400|C1orf141|protein_coding|CODING|NM_001276351.1|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6588237 -0.689466 0.586065 16 V189I 400 Gtc/Atc MODERATE 7 MISSENSE CODING C1orf141 T protein_coding NM_001276351.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67560956 C T 0 228 0 0.9879 0.9385 0.915 0.9722 0.8141 0.9816 0.965016 0.893555 0.856977 2 10045 107952 10832 8404 5088 56917 803 15863 2 10396 120982 11498 8646 6600 66542 906 16394 0 . 0 . 0 67 0,0,43,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V189I|400|C1orf141|protein_coding|CODING|NM_001276351.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11208997,rs386517519 -0.693147 0.369744 67 Q3H 629 caG/caT MODERATE 2 MISSENSE CODING IL23R T protein_coding NM_144701.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67633812 G T 0 222 0 0.4713 0.5302 0.3689 0.6369 0.5239 0.6207 0.5 0.518453 0.527907 1 5105 64137 3936 5613 3305 35328 470 10380 2 10398 121356 11572 8638 6612 66716 908 16512 0.837223 0 . 0 . 51 16,6,15,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q3H|629|IL23R|protein_coding|CODING|NM_144701.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.780737 rs1884444 -0.693054 0.44026 51 L310P 629 cTg/cCg MODERATE 7 MISSENSE CODING IL23R C protein_coding NM_144701.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67685387 T C 0 228 0 0.7632 0.876 0.8501 0.9871 0.8569 0.9519 0.762823 0.834 0.870465 2 7989 106540 10673 8506 5593 57568 798 15413 2 10402 121394 11576 8652 6610 66734 908 16512 0 . 0 . 0 69 0,0,22,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L310P|629|IL23R|protein_coding|CODING|NM_144701.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7530511 -0.693147 5.09705e-05 69 629 309 MODIFIER 11 CODING IL23R A protein_coding NM_144701.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67725120 C A 0 9.7 0 0.1324 0.3926 0.245 0.7312 0.2982 0.5971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||309||629|IL23R|protein_coding|CODING|NM_144701.2|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10889677 -0.379885 0 1 N271Y 862 Aat/Tat MODERATE 7 MISSENSE CODING IL12RB2 T protein_coding NM_001559.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67796346 A T 0 222 0 0 0.0011981 0 0.006 0 0 0 . 0 1 0 56 0 55 0 0 1 0 2 10256 121092 11556 8626 6608 66632 906 16508 0.864849 0 . 0 . 114 44,6,43,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N271Y|862|IL12RB2|protein_coding|CODING|NM_001559.2|7|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.891444 rs78198420 -0.693147 0.0174051 114 862 LOW 9 CODING IL12RB2 A protein_coding NM_001559.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 67833501 G A 0 228 0 0.1944 0.1262 0.0937 0.1944 0.0209 0.0951 0.160917 0.0640474 0.0144186 2 1730 7603 1518 1829 120 967 48 1391 2 10286 120780 11554 8632 6614 66288 906 16500 0 . 0 . 0 21 0,0,18,1 SPLICE_SITE_REGION+INTRON(LOW||||862|IL12RB2|protein_coding|CODING|NM_001559.2|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2252596 -0.69168 0.0249786 21 I330 543 atC/atT LOW 7 SILENT CODING WLS A protein_coding NM_001002292.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 68614320 G A 0 222 0 0.0847 0.0601 0.0461 0.0625 0.0477 0.047 0.0855651 0.0582039 0.044186 1 850 5594 348 356 148 3041 35 816 2 10064 117942 11210 8560 6412 65278 878 15540 0.299497 0 . 0 . 96 15,33,12,30 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I330|543|WLS|protein_coding|CODING|NM_001002292.3|7|A),INTRAGENIC(MODIFIER|||||GNG12-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930302 rs17130529 -0.693146 0.0655075 96 A142 543 gcG/gcA LOW 3 SILENT CODING WLS T protein_coding NM_001002292.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 68624878 C T 0 222 0 0.2368 0.3496 0.4524 0.4127 0.3648 0.3487 0.252837 0.313317 0.344302 1 2584 44148 4651 3972 3033 23565 363 5980 2 10404 121362 11566 8632 6614 66726 908 16512 0.280298 0 . 0 . 217 45,49,36,54 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A142|543|WLS|protein_coding|CODING|NM_001002292.3|3|T),INTRAGENIC(MODIFIER|||||GNG12-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.73483 rs3748705,rs386585386 -0.693147 0.178303 217 533 915 MODIFIER 14 CODING RPE65 C protein_coding NM_000329.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 68894544 G C 0 6.3 0 0.6293 0.5655 0.4481 0.745 0.3509 0.5982 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||915||533|RPE65|protein_coding|CODING|NM_000329.2|14|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3118416 -0.379885 0 1 602 275 MODIFIER 15 CODING LRRC40 T protein_coding NM_017768.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 70611208 A T 0 39.3 0 0.416 0.3407 0.2795 0.375 0.1769 0.4151 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||275||602|LRRC40|protein_coding|CODING|NM_017768.4|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs676753 -0.453602 0.22 2 602 136 MODIFIER 15 CODING LRRC40 G protein_coding NM_017768.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 70611347 A G 0 157 0 0.9985 0.979 0.9741 1 0.9314 0.9836 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,13,0 UTR_3_PRIME(MODIFIER||136||602|LRRC40|protein_coding|CODING|NM_017768.4|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs595662 -0.683931 0.165646 13 354 3002 MODIFIER 7 CODING NEGR1 A protein_coding NM_173808.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 71870127 G A 0 228 0 0.8759 0.9661 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,8,28 UTR_3_PRIME(MODIFIER||3002||354|NEGR1|protein_coding|CODING|NM_173808.2|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12123586 -0.693139 0.880914 36 T296 354 acC/acT LOW 6 SILENT CODING NEGR1 A protein_coding NM_173808.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 72058552 G A 0 228 0 0.6634 0.8496 0.928 0.8472 0.996 0.8978 0.701316 0.89674 0.99686 2 7141 114490 10759 7541 6593 66547 877 15032 2 10404 121370 11558 8644 6614 66730 908 16512 0 . 0 . 0 144 0,0,74,54 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T296|354|NEGR1|protein_coding|CODING|NM_173808.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1413368 -0.693147 0.0735354 144 A255T 624 Gca/Aca MODERATE 5 MISSENSE CODING LRRIQ3 T protein_coding NM_001105659.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74575182 C T 0 222 0 0.5053 0.8049 0.8876 0.9573 0.9085 0.8875 0.590223 0.822553 0.925136 1 5575 106170 9938 8250 5565 61031 805 15006 2 9766 119930 11326 8528 6560 66366 890 16494 0.547072 0 . 0 . 127 38,25,31,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A255T|624|LRRIQ3|protein_coding|CODING|NM_001105659.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.485355 rs1340472 -0.693147 0.765603 127 624 14341 MODIFIER 1 CODING LRRIQ3 A protein_coding NM_001105659.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74663709 G A 0 9.7 0 0.1528 0.4445 0.389 0.7391 0.4652 0.5532 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||14341||624|LRRIQ3|protein_coding|CODING|NM_001105659.1|1|A),UPSTREAM(MODIFIER||187||607|FPGT|protein_coding|CODING|NM_003838.4||A),UPSTREAM(MODIFIER||187||949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11806946 -0.379885 0 1 624 14446 MODIFIER 1 CODING LRRIQ3 G protein_coding NM_001105659.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74663814 C G 0 83 0 0.1528 0.4443 0.389 0.7391 0.4652 0.5521 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.695312 0 . 0 . 13 7,0,6,0 START_GAINED(LOW||||624|LRRIQ3|protein_coding|CODING|NM_001105659.1|1|G),UTR_5_PRIME(MODIFIER||14446||624|LRRIQ3|protein_coding|CODING|NM_001105659.1|1|G),UPSTREAM(MODIFIER||82||607|FPGT|protein_coding|CODING|NM_003838.4||G),UPSTREAM(MODIFIER||82||949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.0715762 rs1412825 -0.616816 0.638458 13 V89 607 gtG/gtA LOW 2 SILENT CODING FPGT A protein_coding NM_003838.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74665493 G A 0 222 0 0.1619 0.4467 0.389 0.7391 0.4642 0.5532 0.228098 0.396894 0.483372 1 2201 58113 5245 6389 3175 31460 482 9161 2 10354 121228 11564 8644 6612 66652 908 16494 0.973187 0 . 0 . 79 17,16,16,19 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V89|607|FPGT|protein_coding|CODING|NM_003838.4|2|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V89|949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2|2|A),UPSTREAM(MODIFIER||1622||624|LRRIQ3|protein_coding|CODING|NM_001105659.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.248451 rs792310 -0.693136 0.0600391 79 V89 949 gtG/gtA LOW 2 SILENT CODING FPGT-TNNI3K A protein_coding NM_001112808.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74665493 G A 0 222 0 0.1619 0.4467 0.389 0.7391 0.4642 0.5532 0.228098 0.396894 0.483372 1 2201 58113 5245 6389 3175 31460 482 9161 2 10354 121228 11564 8644 6612 66652 908 16494 0.973187 0 . 0 . 79 17,16,16,19 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V89|607|FPGT|protein_coding|CODING|NM_003838.4|2|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V89|949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2|2|A),UPSTREAM(MODIFIER||1622||624|LRRIQ3|protein_coding|CODING|NM_001105659.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.248451 rs792310 -0.693136 0.0600391 79 607 3 MODIFIER 4 CODING FPGT G protein_coding NM_003838.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74671519 A G 0 222 0 0.1528 0.4445 0.389 0.7391 0.4652 0.5532 0.219818 0.390425 0.477921 1 1956 54863 5154 6307 3159 30011 451 7825 2 9164 113046 11316 8534 6562 63180 848 13442 0.988845 0 . 0 . 53 12,14,9,12 UTR_3_PRIME(MODIFIER||3||607|FPGT|protein_coding|CODING|NM_003838.4|4|G),INTRON(MODIFIER||||949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.26651 rs571848 -0.692352 0.197045 53 607 807 MODIFIER 4 CODING FPGT A protein_coding NM_003838.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 74672323 C A 0 9.7 0 0.1528 0.4443 0.389 0.7391 0.4642 0.5532 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||807||607|FPGT|protein_coding|CODING|NM_003838.4|4|A),INTRON(MODIFIER||||949|FPGT-TNNI3K|protein_coding|CODING|NM_001112808.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs489941 -0.379885 0 1 1530 LOW 14 CODING ERICH3 C protein_coding NM_001002912.4 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75036783 T C 0 228 0 0.907 0.975 0.9971 1 1 1 0.91852 0.97232 0.999884 2 9418 118546 11531 8630 6612 66050 887 15418 2 10364 119540 11566 8630 6612 66056 892 15420 0 . 0 . 0 32 0,0,27,1 SPLICE_SITE_REGION(LOW||||1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|C),UTR_3_PRIME(MODIFIER||18||1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9326115 -0.693054 0.303638 32 1530 18 MODIFIER 14 CODING ERICH3 C protein_coding NM_001002912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75036783 T C 0 228 0 0.907 0.975 0.9971 1 1 1 0.91852 0.97232 0.999884 2 9418 118546 11531 8630 6612 66050 887 15418 2 10364 119540 11566 8630 6612 66056 892 15420 0 . 0 . 0 32 0,0,27,1 SPLICE_SITE_REGION(LOW||||1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|C),UTR_3_PRIME(MODIFIER||18||1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9326115 -0.693054 0.303638 32 V1528M 1530 Gtg/Atg MODERATE 14 MISSENSE CODING ERICH3 T protein_coding NM_001002912.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75036812 C T 0 228 0 0.907 0.9748 0.9957 1 1 1 0.918293 0.972244 0.999884 2 9449 120279 11542 8650 6614 66647 901 16476 2 10398 121278 11578 8650 6614 66654 906 16478 0 . 0 . 0 38 0,0,31,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V1528M|1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9326116 -0.693132 0.512319 38 S1183 1530 agT/agC LOW 14 SILENT CODING ERICH3 G protein_coding NM_001002912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75037845 A G 0 228 0 0.2466 0.3752 0.3314 0.5843 0.3549 0.3855 0.25034 0.329079 0.369419 2 2573 45655 3843 5023 2826 24768 380 6242 2 10402 121388 11576 8648 6612 66734 908 16508 0 . 0 . 0 39 0,0,20,15 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1183|1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12723334 -0.693136 0.407347 39 L1056V 1530 Tta/Gta MODERATE 14 MISSENSE CODING ERICH3 C protein_coding NM_001002912.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75038228 A C 0 228 0 0.2466 0.3758 0.33 0.5794 0.3579 0.3916 0.251248 0.331232 0.372209 2 2569 45933 3860 4976 2842 25045 380 6261 2 10388 121350 11574 8622 6614 66736 908 16508 1 0 . 0 . 103 0,1,39,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Gta|L1056V|1530|ERICH3|protein_coding|CODING|NM_001002912.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11580409 -0.693147 0.00860195 103 329 769 MODIFIER 10 CODING CRYZ A protein_coding NM_001130042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75171211 G A 0 9.7 0 0.0348 0.2167 0.3674 0.1101 0.4592 0.2157 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||769||329|CRYZ|protein_coding|CODING|NM_001130042.1|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6673 -0.379885 0 1 329 229 MODIFIER 10 CODING CRYZ C protein_coding NM_001130042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75171751 T C 0 140 0 0.5136 0.6054 0.7161 0.6895 0.6054 0.5644 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||229||329|CRYZ|protein_coding|CODING|NM_001130042.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17459 -0.662043 0.23154 9 G323 329 ggA/ggT LOW 10 SILENT CODING CRYZ A protein_coding NM_001130042.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75172001 T A 0 228 0 0.0348 0.2165 0.3674 0.1091 0.4592 0.2157 0.106673 0.341126 0.46127 2 944 43102 4123 930 2364 30275 359 4107 2 10340 120628 11540 8644 6606 66478 896 16124 1 0 . 0 . 100 1,0,55,33 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G323|329|CRYZ|protein_coding|CODING|NM_001130042.1|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7527057 -0.693147 0.0215997 100 329 8258 MODIFIER 1 CODING CRYZ C protein_coding NM_001130042.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75198763 A C 0 161 0 0.9856 0.996 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_5_PRIME(MODIFIER||8258||329|CRYZ|protein_coding|CODING|NM_001130042.1|1|C),UPSTREAM(MODIFIER||77||259|TYW3|protein_coding|CODING|NM_138467.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs277372 -0.651104 0.578041 8 259 809 MODIFIER 6 CODING TYW3 T protein_coding NM_138467.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75230606 C T 0 32.6 0 0.1407 0.2183 0.2003 0.2262 0.2545 0.2904 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||809||259|TYW3|protein_coding|CODING|NM_138467.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs277368,rs386573612 -0.379885 0 2 H283 356 caC/caT LOW 9 SILENT CODING LHX8 T protein_coding NM_001001933.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75622616 C T 0 222 0 0.4758 0.394 0.3026 0.2063 0.3907 0.545 0.463913 0.430186 0.412907 1 4891 49832 3513 1725 2375 28280 346 8702 2 10406 121404 11578 8648 6614 66738 908 16512 0.470055 0 . 0 . 161 50,17,46,26 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H283|356|LHX8|protein_coding|CODING|NM_001001933.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.819908 rs941032 -0.693147 0.417199 161 S692 719 tcT/tcC LOW 24 SILENT CODING SLC44A5 G protein_coding NM_152697.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75672376 A G 0 222 0 0.177 0.4407 0.4669 0.8323 0.3966 0.4202 0.207217 0.319852 0.377558 1 2038 49137 5878 7079 2723 24679 347 6393 2 10404 121208 11504 8616 6606 66666 906 16506 0.966344 0 . 0 . 99 15,34,9,28 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S692|719|SLC44A5|protein_coding|CODING|NM_152697.4|24|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.818776 rs1948874 -0.693141 0.207686 99 Q552 719 caA/caG LOW 19 SILENT CODING SLC44A5 C protein_coding NM_152697.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75681511 T C 0 228 0 0.8767 0.8966 0.8862 0.996 0.83 0.8967 0.860191 0.8492 0.843568 2 8949 105060 10263 8551 5578 56256 761 14702 2 10342 121040 11444 8598 6604 66644 906 16502 0 . 0 . 0 162 0,0,61,76 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q552|719|SLC44A5|protein_coding|CODING|NM_152697.4|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs595009 -0.693147 0.103145 162 V105 719 gtG/gtA LOW 7 SILENT CODING SLC44A5 T protein_coding NM_152697.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 75716925 C T 0 228 0 0.5424 0.7446 0.7637 0.9494 0.7316 0.8067 0.574671 0.678225 0.731279 2 5863 89740 9725 8038 4775 48178 652 12509 2 10404 121302 11550 8628 6610 66700 906 16504 0 . 0 . 0 218 0,0,115,68 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V105|719|SLC44A5|protein_coding|CODING|NM_152697.4|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs588098 -0.693147 0.00626873 218 A202 331 gcA/gcT LOW 7 SILENT CODING RABGGTB T protein_coding NM_004582.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 76257892 A T 0 222 0 0.9939 0.8972 0.8055 0.7371 0.9374 0.955 0.973445 0.949946 0.937907 1 10160 109105 8448 6360 5920 61800 840 15577 2 10404 121348 11552 8642 6614 66716 908 16512 0.577187 0 . 0 . 112 41,14,35,7 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcT|A202|331|RABGGTB|protein_coding|CODING|NM_004582.3|7|T),UPSTREAM(MODIFIER||4664||936|MSH4|protein_coding|CODING|NM_002440.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998881 rs12703 -0.693146 0.765751 112 936 LOW 11 CODING MSH4 A protein_coding NM_002440.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 76344011 C A 0 228 0 0.6846 0.7927 0.7781 0.9851 0.7515 0.7935 0.705402 0.74112 0.759419 2 7384 95931 9605 8526 5321 51175 741 13179 2 10388 120416 11476 8634 6602 66318 902 16096 1 0 . 0 . 248 1,0,92,122 SPLICE_SITE_REGION+INTRON(LOW||||936|MSH4|protein_coding|CODING|NM_002440.3|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1493367,rs386500456 -0.693147 0.00263448 248 Y523 936 taT/taC LOW 12 SILENT CODING MSH4 C protein_coding NM_002440.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 76344705 T C 0 222 0 0.0242 0.3375 0.2349 0.6964 0.3022 0.5 0.086246 0.24331 0.323796 1 797 41714 3045 6030 1885 21520 290 8147 2 10314 120894 11432 8632 6588 66530 902 16496 0.969532 0 . 0 . 175 61,26,53,24 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y523|936|MSH4|protein_coding|CODING|NM_002440.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978686 rs5745448 -0.693147 0.00301914 175 L525 936 ctA/ctT LOW 12 SILENT CODING MSH4 T protein_coding NM_002440.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 76344711 A T 0 228 0 0.6846 0.7927 0.7781 0.9851 0.7515 0.7935 0.705856 0.741541 0.759828 2 7381 96451 9602 8536 5318 51401 745 13468 2 10384 121128 11470 8646 6598 66622 906 16502 0 . 0 . 0 177 0,0,119,47 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctT|L525|936|MSH4|protein_coding|CODING|NM_002440.3|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5745449 -0.693147 0.0709104 177 S2N 295 aGt/aAt MODERATE 1 MISSENSE CODING ASB17 T protein_coding NM_080868.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 76397972 C T 0 222 0 0.1884 0.3966 0.2983 0.7073 0.3221 0.5041 0.19877 0.300077 0.351886 1 1984 45264 4071 6107 2058 23029 308 7707 2 9728 117380 11508 8608 6604 65338 876 14718 0.972227 0 . 0 . 143 19,52,9,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S2N|295|ASB17|protein_coding|CODING|NM_080868.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0297145 rs3795251 -0.693147 0.196569 143 395 3284 MODIFIER 11 CODING PIGK G protein_coding NM_005482.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 77554775 A G 0 9.7 0 0.0091 0.0948 0.0231 0.1558 0.0388 0.2566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3284||395|PIGK|protein_coding|CODING|NM_005482.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17099885 -0.379885 0 1 395 2578 MODIFIER 11 CODING PIGK T protein_coding NM_005482.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 77555481 C T 0 228 0 0.8442 0.6929 0.6585 0.5893 0.6193 0.6953 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,4,33 UTR_3_PRIME(MODIFIER||2578||395|PIGK|protein_coding|CODING|NM_005482.2|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs169216,rs386494617 -0.693141 0.962813 37 395 LOW 7 CODING PIGK A protein_coding NM_005482.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 77627096 G A 0 228 0 0.9584 0.9886 0.9971 1 1 1 0.963636 0.987613 0.999884 2 9785 120542 11517 8638 6600 66605 901 16496 2 10144 120944 11536 8638 6600 66628 902 16496 0 . 0 . 0 101 0,0,48,45 SPLICE_SITE_REGION+INTRON(LOW||||395|PIGK|protein_coding|CODING|NM_005482.2|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs839825 -0.693147 0.0289087 101 Y124 395 taC/taT LOW 4 SILENT CODING PIGK A protein_coding NM_005482.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 77634948 G A 0 228 0 0.9508 0.9866 0.9971 1 1 1 0.950522 0.983159 0.999884 2 9894 120741 11541 8644 6606 66664 903 16489 2 10386 121282 11562 8644 6606 66686 906 16492 0 . 0 . 0 68 0,0,39,20 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y124|395|PIGK|protein_coding|CODING|NM_005482.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1779199 -0.693147 0.351086 68 K203 562 aaG/aaA LOW 5 SILENT CODING AK5 A protein_coding NM_174858.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 77763542 G A 0 228 0 0.9251 0.9788 0.9899 1 1 1 0.952792 0.98393 0.999884 2 9873 120760 11510 8650 6614 66698 907 16508 2 10388 121302 11534 8650 6614 66700 908 16508 0 . 0 . 0 65 0,0,22,35 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K203|562|AK5|protein_coding|CODING|NM_174858.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1167206 -0.693147 0.924062 65 562 LOW 13 CODING AK5 C protein_coding NM_174858.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78024284 T C 0 228 0 0.5401 0.6853 0.8357 0.7411 0.7614 0.6391 0.600772 0.716823 0.776279 2 6000 90404 9782 6422 4792 51557 659 11192 2 10368 121154 11552 8640 6604 66600 908 16482 0 . 0 . 0 70 0,0,50,15 SPLICE_SITE_REGION+INTRON(LOW||||562|AK5|protein_coding|CODING|NM_174858.2|13|C),DOWNSTREAM(MODIFIER||3817||903|ZZZ3|protein_coding|CODING|NM_015534.5||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6675743 -0.693147 0.150954 70 562 247 MODIFIER 14 CODING AK5 G protein_coding NM_174858.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78024602 A G 0 151 0 0.5567 0.6873 0.8343 0.7401 0.7614 0.6288 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,0,12 UTR_3_PRIME(MODIFIER||247||562|AK5|protein_coding|CODING|NM_174858.2|14|G),DOWNSTREAM(MODIFIER||3499||903|ZZZ3|protein_coding|CODING|NM_015534.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10873950 -0.680642 0.0436431 13 562 1099 MODIFIER 14 CODING AK5 T protein_coding NM_174858.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78025454 G T 0 192 0 0.5598 0.6879 0.8343 0.7411 0.7604 0.6278 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,30,0 UTR_3_PRIME(MODIFIER||1099||562|AK5|protein_coding|CODING|NM_174858.2|14|T),DOWNSTREAM(MODIFIER||2647||903|ZZZ3|protein_coding|CODING|NM_015534.5||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4949811 -0.693097 0.205771 31 562 1196 MODIFIER 14 CODING AK5 T protein_coding NM_174858.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78025551 C T 0 228 0 0.385 0.6124 0.8012 0.7391 0.7445 0.5194 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,54,11 UTR_3_PRIME(MODIFIER||1196||562|AK5|protein_coding|CODING|NM_174858.2|14|T),DOWNSTREAM(MODIFIER||2550||903|ZZZ3|protein_coding|CODING|NM_015534.5||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3509 -0.693147 0.248846 68 903 1960 MODIFIER 15 CODING ZZZ3 G protein_coding NM_015534.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78029365 A G 0 32.6 0 0.4546 0.6374 0.8055 0.7401 0.7495 0.544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1960||903|ZZZ3|protein_coding|CODING|NM_015534.5|15|G),DOWNSTREAM(MODIFIER||3711||562|AK5|protein_coding|CODING|NM_174858.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs728741 -0.379885 0 2 903 1420 MODIFIER 15 CODING ZZZ3 A protein_coding NM_015534.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78029905 T A 0 46.3 0 0.4592 0.6374 0.8055 0.7391 0.7495 0.5389 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1420||903|ZZZ3|protein_coding|CODING|NM_015534.5|15|A),DOWNSTREAM(MODIFIER||4251||562|AK5|protein_coding|CODING|NM_174858.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1962523 -0.453602 0.28 2 L596 942 Ttg/Ctg LOW 17 SILENT CODING USP33 G protein_coding NM_015017.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78184325 A G 0 222 0 0.4433 0.3556 0.1988 0.2698 0.2744 0.5204 0.401136 0.299923 0.248019 1 4242 35559 2079 2301 1931 16862 296 7848 2 10082 120644 11560 8626 6610 66360 904 16502 0.0278852 0 . 0 . 122 18,41,20,30 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L596|942|USP33|protein_coding|CODING|NM_015017.4|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.608166 rs12142671 -0.693147 0.766817 122 A181 942 gcC/gcA LOW 7 SILENT CODING USP33 T protein_coding NM_015017.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78201745 G T 0 222 0 0.7451 0.4894 0.2608 0.4077 0.332 0.5521 0.67635 0.428571 0.301628 1 7191 44411 2486 3282 2219 20529 352 8352 2 10398 121332 11566 8644 6614 66694 908 16508 0.589066 0 . 0 . 81 27,10,24,8 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A181|942|USP33|protein_coding|CODING|NM_015017.4|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.218257 rs2296227 -0.69312 0.0789195 81 G245R 675 Gga/Aga MODERATE 8 MISSENSE CODING NEXN A protein_coding NM_144573.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78392446 G A 0 222 0 0.0106 0.1508 0.1167 0.38 0.2107 0.0665 0.0465821 0.15781 0.207311 1 356 22222 1647 3398 1127 14251 156 1287 2 9726 120388 11532 8608 6614 66530 898 16480 0.996408 2|2 benign|benign 0 . 101 33,17,21,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G245R|675|NEXN|protein_coding|CODING|NM_144573.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.933643 rs1166698 -0.693136 0.00109299 101 675 22 MODIFIER 13 CODING NEXN G protein_coding NM_144573.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78408536 C G 0 222 0 0.1271 0.122 0.1988 0.0903 0.0775 0.1391 0.0980447 0.0889613 0.0849406 1 761 10369 2358 462 889 4183 93 1623 2 5856 71164 7632 3550 4346 36920 604 12256 0.686067 0 . 0 . 57 19,5,21,6 UTR_3_PRIME(MODIFIER||22||675|NEXN|protein_coding|CODING|NM_144573.3|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.566419 rs3767028 -0.693021 0.539738 57 665 LOW 13 CODING FUBP1 C protein_coding NM_001303433.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78429408 G C 0 222 0 0.0507 0.1016 0.1945 0.0903 0.0795 0.1391 0.0515207 0.0730432 0.0840698 1 520 12649 2806 715 1057 5509 111 1931 2 10356 120592 11474 8612 6598 66292 902 16358 0.782423 0 . 0 . 118 24,38,8,35 SPLICE_SITE_REGION+INTRON(LOW||||665|FUBP1|protein_coding|CODING|NM_001303433.1|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989309 rs2274257 -0.693146 0.00859843 118 L206P 315 cTg/cCg MODERATE 4 MISSENSE CODING GIPC2 C protein_coding NM_017655.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78585086 T C 0 228 0 0.2186 0.3071 0.1758 0.6637 0.2266 0.2352 0.224694 0.220514 0.218372 2 2263 30159 1991 5727 1094 14941 210 3933 2 10218 119176 11286 8574 6570 65940 878 15710 1 0 . 0 . 131 0,1,101,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L206P|315|GIPC2|protein_coding|CODING|NM_017655.5|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs540742 -0.693147 0.471076 131 315 2362 MODIFIER 6 CODING GIPC2 T protein_coding NM_017655.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78603789 C T 0 9.7 0 0.2088 0.3293 0.1974 0.7649 0.2376 0.2311 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2362||315|GIPC2|protein_coding|CODING|NM_017655.5|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs584660 -0.379885 0 1 315 2669 MODIFIER 6 CODING GIPC2 T protein_coding NM_017655.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 78604096 C T 0 9.7 0 0.2088 0.3285 0.1945 0.7649 0.2376 0.229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2669||315|GIPC2|protein_coding|CODING|NM_017655.5|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs580426 -0.379885 0 1 H73R 452 cAt/cGt MODERATE 2 MISSENSE CODING IFI44L G protein_coding NM_006820.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79093818 A G 0 228 0 0.3608 0.4449 0.3545 0.751 0.3449 0.41 0.376305 0.343688 0.326977 2 3765 45996 4218 6451 2579 21725 365 6893 2 10200 120418 11398 8520 6564 66356 900 16480 0 . 0 . 0 84 0,0,45,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H73R|452|IFI44L|protein_coding|CODING|NM_006820.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs273259 -0.693147 0.199132 84 A104T 452 Gca/Aca MODERATE 2 MISSENSE CODING IFI44L A protein_coding NM_006820.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79093910 G A 0 222 0 0.0091 0.0383 0.0144 0.0823 0.0388 0.0491 0.0115751 0.022 0.0273447 1 119 3640 199 780 42 1713 25 762 2 10186 119394 11274 8392 6514 65698 888 16442 0.790383 0 . 0 COSM146547 90 28,21,17,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A104T|452|IFI44L|protein_coding|CODING|NM_006820.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.798194 rs34932081 -0.69312 0.502 90 452 LOW 2 CODING IFI44L A protein_coding NM_006820.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79094081 T A 0 228 0 0.3011 0.4285 0.3516 0.751 0.3439 0.41 0.302507 0.311878 0.316576 2 2813 43102 4184 6399 2578 20855 349 5924 2 9012 112702 11360 8458 6568 63072 852 13380 1 0 . 0 . 94 1,0,47,33 SPLICE_SITE_REGION+INTRON(LOW||||452|IFI44L|protein_coding|CODING|NM_006820.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1333973 -0.693147 0.0162959 94 V217I 452 Gtc/Atc MODERATE 4 MISSENSE CODING IFI44L A protein_coding NM_006820.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79095526 G A 0 222 0 0.0613 0.1464 0.0591 0.4157 0.0686 0.1258 0.0719473 0.0696602 0.0684884 1 667 13340 1151 3591 536 5357 104 1934 2 10400 121114 11510 8570 6590 66636 906 16502 0.641135 0 . 0 . 53 15,11,7,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V217I|452|IFI44L|protein_coding|CODING|NM_006820.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.469716 rs3820093 -0.691153 0.367594 53 R296C 452 Cgt/Tgt MODERATE 6 MISSENSE CODING IFI44L T protein_coding NM_006820.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79102726 C T 0 222 0 0.0537 0.13 0.0519 0.4147 0.0487 0.0787 0.0578756 0.0545133 0.0527907 1 572 10822 1091 3604 347 3959 81 1168 2 10360 121120 11558 8618 6604 66614 906 16460 0.834521 0 . 0 . 99 32,8,32,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R296C|452|IFI44L|protein_coding|CODING|NM_006820.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.695551 rs1981071 -0.693146 0.684792 99 452 2121 MODIFIER 9 CODING IFI44L C protein_coding NM_006820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79109615 T C 0 32.6 0 0.6263 0.8442 0.8948 0.9752 0.8738 0.9376 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2121||452|IFI44L|protein_coding|CODING|NM_006820.3|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs166642,rs386540566 -0.379885 0 2 W9R 444 Tgg/Cgg MODERATE 2 MISSENSE CODING IFI44 C protein_coding NM_006417.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79115905 T C 0 222 0 0.1346 0.1218 0.1138 0.131 0.0775 0.1462 0.133908 0.0994157 0.0817442 1 1363 11335 1041 1065 401 5102 99 2264 2 10396 121014 11564 8602 6612 66562 904 16374 0.739316 0 . 0 . 95 39,6,39,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W9R|444|IFI44|protein_coding|CODING|NM_006417.4|2|C),DOWNSTREAM(MODIFIER||4075||452|IFI44L|protein_coding|CODING|NM_006820.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992444 rs2070123 -0.693146 0.00498553 95 444 LOW 8 CODING IFI44 GT protein_coding NM_006417.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79128570 G GT 0 228 0 0.4781 0.4291 0.3228 0.4266 0.4225 0.4479 0.492034 0.451126 0.429973 2 5102 49623 3331 3236 2573 27514 396 7471 2 10376 121252 11508 8622 6610 66718 908 16510 0 . 0 . 0 161 0,0,75,74 SPLICE_SITE_REGION+INTRON(LOW||||444|IFI44|protein_coding|CODING|NM_006417.4|8|GT) 1 0 . 155 0.962733 1 1 1 1 0 60 0 0 1 0 . rs368139253 -0.693147 0.0678353 161 444 198 MODIFIER 9 CODING IFI44 G protein_coding NM_006417.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79129694 A G 0 128 0 0.0242 0.0835 0.0994 0.131 0.0636 0.1237 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.807887 0 . 0 . 19 1,9,1,8 UTR_3_PRIME(MODIFIER||198||444|IFI44|protein_coding|CODING|NM_006417.4|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.520308 rs1051047 -0.662043 0.0171185 19 690 1243 MODIFIER 15 CODING ADGRL4 G protein_coding NM_022159.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79355596 A G 0 228 0 0.7617 0.7584 0.8213 0.6458 0.7793 0.8037 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 60 0,1,14,40 UTR_3_PRIME(MODIFIER||1243||690|ADGRL4|protein_coding|CODING|NM_022159.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1061728 -0.693147 0.621226 60 A620G 690 gCc/gGc MODERATE 14 MISSENSE CODING ADGRL4 C protein_coding NM_022159.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 79357360 G C 0 228 0 0.2905 0.2528 0.2046 0.2312 0.3091 0.2004 0.260406 0.283295 0.294182 2 2728 31865 2116 1999 1772 19412 253 3585 2 9734 119652 11348 8492 6554 66214 888 16422 0 . 0 . 0 110 0,0,38,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A620G|690|ADGRL4|protein_coding|CODING|NM_022159.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275902 -0.693147 0.0578525 110 P606 1403 ccC/ccT LOW 10 SILENT CODING ADGRL2 T protein_coding NM_001297704.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 82421596 C T 0 228 0 0.9803 0.994 0.9942 1 1 1 0.976396 0.992004 1 2 10165 121011 11563 8646 6612 66657 908 16460 2 10404 121266 11578 8646 6612 66658 908 16460 0 . 0 . 0 179 0,0,82,75 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P606|1403|ADGRL2|protein_coding|CODING|NM_001297704.1|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11163397 -0.693147 0.000395856 179 1403 833 MODIFIER 21 CODING ADGRL2 A protein_coding NM_001297704.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 82457662 G A 0 228 0 0.9909 0.9972 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 117 0,0,47,64 UTR_3_PRIME(MODIFIER||833||1403|ADGRL2|protein_coding|CODING|NM_001297704.1|21|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7523178 -0.693147 0.580881 117 1403 1341 MODIFIER 21 CODING ADGRL2 T protein_coding NM_001297704.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 82458170 C T 0 179 0 0.2148 0.3243 0.3199 0.5873 0.165 0.3681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.993857 0 . 0 . 94 4,50,2,36 UTR_3_PRIME(MODIFIER||1341||1403|ADGRL2|protein_coding|CODING|NM_001297704.1|21|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.819786 rs3790868 -0.693143 0.112875 94 887 233 MODIFIER 21 CODING TTLL7 T protein_coding NM_024686.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84335412 C T 0 222 0 0.4803 0.4 0.3098 0.6022 0.1859 0.3671 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999013 0 . 0 . 99 22,27,18,13 UTR_3_PRIME(MODIFIER||233||887|TTLL7|protein_coding|CODING|NM_024686.4|21|T),INTRAGENIC(MODIFIER|||||MIR548AP||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99989 rs1132122 -0.69311 0.224659 99 398 263 MODIFIER 10 CODING PRKACB C protein_coding NM_182948.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84701251 T C 0 228 0 0.8427 0.7889 0.8084 0.7808 0.7883 0.7117 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 91 0,0,58,30 UTR_3_PRIME(MODIFIER||263||398|PRKACB|protein_coding|CODING|NM_182948.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs600674 -0.693147 0.0468607 91 116 666 MODIFIER 4 CODING SAMD13 T protein_coding NM_001010971.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84816123 C T 0 86 0 0.9735 0.9892 0.9841 1 0.997 0.9949 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||666||116|SAMD13|protein_coding|CODING|NM_001010971.2|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs814152 -0.556411 0.977157 4 Q3H 361 caG/caC MODERATE 1 MISSENSE CODING DNASE2B C protein_coding NM_021233.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84864256 G C 0 222 0 0.1755 0.2941 0.3156 0.4038 0.334 0.2853 0.188195 0.292031 0.342891 1 1895 37571 3147 3417 2037 22630 304 4141 2 9802 120596 11564 8594 6612 66694 898 16432 0.395801 0 . 0 . 133 37,19,41,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q3H|361|DNASE2B|protein_coding|CODING|NM_021233.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.428209 rs111191093,rs3738573 -0.693147 0.0578255 133 R51K 361 aGa/aAa MODERATE 2 MISSENSE CODING DNASE2B A protein_coding NM_021233.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84867610 G A 0 222 0 0.0401 0.2246 0.245 0.369 0.2744 0.2597 0.0737927 0.216563 0.280959 1 412 16019 1026 1513 988 9684 125 2271 2 3430 44488 2288 3054 2962 23842 376 8536 0.406691 0 . 0 . 129 52,18,33,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R51K|361|DNASE2B|protein_coding|CODING|NM_021233.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.383762 rs3754274 -0.693147 0.283932 129 H305 361 caT/caC LOW 6 SILENT CODING DNASE2B C protein_coding NM_021233.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84880380 T C 0 222 0 0.2065 0.3239 0.3573 0.4554 0.334 0.3129 0.235361 0.312932 0.352674 1 2463 40025 3721 3920 1784 23041 291 4805 2 10398 121276 11548 8624 6614 66680 906 16506 0.84819 0 . 0 . 100 40,20,25,7 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H305|361|DNASE2B|protein_coding|CODING|NM_021233.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948923 rs3768250 -0.69312 0.0629005 100 S9G 349 Agc/Ggc MODERATE 1 MISSENSE CODING RPF1 G protein_coding NM_025065.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84944989 A G 0 222 0 0.2005 0.4904 0.4625 0.7331 0.6571 0.4806 0.265788 0.509078 0.633667 1 2494 67431 5693 6346 4446 40327 514 7611 2 9986 116622 11156 8272 6368 64070 876 15894 0.480073 0 . 0 . 175 50,24,44,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S9G|349|RPF1|protein_coding|CODING|NM_025065.6|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.773873 rs2292191 -0.693147 0.0156504 175 459 LOW 1 CODING SPATA1 T protein_coding NM_001310156.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84972099 G T 0 15.2 0 0.1868 0.2244 0.2565 0.2143 0.172 0.317 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,2,1,0 SPLICE_SITE_REGION(LOW||||459|SPATA1|protein_coding|CODING|NM_001310156.1|1|T),UTR_5_PRIME(MODIFIER||9878||459|SPATA1|protein_coding|CODING|NM_001310156.1|1|T),INTRON(MODIFIER||||68|GNG5|protein_coding|CODING|NM_005274.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs111154854,rs2271620 -0.379885 0 5 459 9878 MODIFIER 1 CODING SPATA1 T protein_coding NM_001310156.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 84972099 G T 0 15.2 0 0.1868 0.2244 0.2565 0.2143 0.172 0.317 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,2,1,0 SPLICE_SITE_REGION(LOW||||459|SPATA1|protein_coding|CODING|NM_001310156.1|1|T),UTR_5_PRIME(MODIFIER||9878||459|SPATA1|protein_coding|CODING|NM_001310156.1|1|T),INTRON(MODIFIER||||68|GNG5|protein_coding|CODING|NM_005274.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs111154854,rs2271620 -0.379885 0 5 K265E 459 Aaa/Gaa MODERATE 9 MISSENSE CODING SPATA1 G protein_coding NM_001310156.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85009894 A G 0 222 0 0.2307 0.2358 0.1614 0.1984 0.2147 0.3558 0.247163 0.231929 0.224122 1 2093 21436 770 1177 962 11667 167 4600 2 6920 66368 3430 4776 3762 35686 546 11248 0.967741 0 . 0 COSM1126937 169 49,33,46,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K265E|459|SPATA1|protein_coding|CODING|NM_001310156.1|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.902968 rs12143652 -0.693147 0.100395 169 L418 459 ctA/ctG LOW 12 SILENT CODING SPATA1 G protein_coding NM_001310156.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85016177 A G 0 222 0 0.7617 0.4762 0.4063 0.2619 0.3489 0.4918 0.683803 0.460634 0.361173 1 4529 29219 1998 1178 1182 14489 210 5633 2 6152 58168 4246 3264 2678 31148 452 10228 0.943131 0 . 0 . 290 60,58,65,57 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L418|459|SPATA1|protein_coding|CODING|NM_001310156.1|12|G),DOWNSTREAM(MODIFIER||2627||385|CTBS|protein_coding|CODING|NM_004388.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952914 rs1400777 -0.693147 0.00592929 290 614 2791 MODIFIER 14 CODING SSX2IP A protein_coding NM_001166293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85110325 C A 0 9.7 0 0.7874 0.8478 0.9078 0.7927 0.9523 0.8364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2791||614|SSX2IP|protein_coding|CODING|NM_001166293.1|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3782,rs386586181 -0.379885 0 1 614 172 MODIFIER 14 CODING SSX2IP A protein_coding NM_001166293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85112944 C A 0 222 0 0 0.0019968 0 0.0099 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.799628 0 . 0 . 119 37,28,30,15 UTR_3_PRIME(MODIFIER||172||614|SSX2IP|protein_coding|CODING|NM_001166293.1|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.667119 rs145168208 -0.693147 0.479915 119 A586 614 gcA/gcG LOW 14 SILENT CODING SSX2IP C protein_coding NM_001166293.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85113203 T C 0 228 0 0.6135 0.7626 0.8588 0.7917 0.8787 0.7464 0.640263 0.777453 0.847755 2 6609 98763 10171 7049 5571 56127 741 12495 2 10406 121392 11578 8652 6614 66728 908 16506 0 . 0 . 0 144 0,0,47,86 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A586|614|SSX2IP|protein_coding|CODING|NM_001166293.1|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2994949,rs386578354 -0.693147 0.0338268 144 C578R 614 Tgt/Cgt MODERATE 14 MISSENSE CODING SSX2IP G protein_coding NM_001166293.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85113229 A G 0 228 0 0.2458 0.5126 0.5346 0.7034 0.6521 0.5174 0.294371 0.516838 0.630814 2 2936 70856 6592 6156 4226 41953 534 8459 2 10404 121362 11576 8652 6610 66708 908 16504 0 . 0 . 0 114 0,0,24,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C578R|614|SSX2IP|protein_coding|CODING|NM_001166293.1|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1057746 -0.693147 0.105568 114 566 469 MODIFIER 14 CODING MCOLN2 G protein_coding NM_153259.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85391899 A G 0 9.7 0 0.9985 0.997 0.9986 1 0.9881 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||469||566|MCOLN2|protein_coding|CODING|NM_153259.3|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2389791 -0.379885 0 1 566 44 MODIFIER 14 CODING MCOLN2 T protein_coding NM_153259.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85392324 C T 0 222 0 0.1377 0.2632 0.2983 0.371 0.33 0.228 0.16296 0.238813 0.277674 1 1504 33052 3332 3294 2135 19099 238 3450 2 9500 115178 11020 8444 6404 63564 848 15398 0.994002 0 . 0 . 85 25,17,16,18 UTR_3_PRIME(MODIFIER||44||566|MCOLN2|protein_coding|CODING|NM_153259.3|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.510521 rs6681025 -0.693132 0.178648 85 566 LOW 8 CODING MCOLN2 G protein_coding NM_153259.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85405389 T G 0 222 0 0.1581 0.0575 0.0432 0.0397 0.006 0.0031 0.122333 0.0462863 0.00732558 1 1356 2970 570 381 98 492 11 62 2 10380 121210 11566 8586 6600 66670 906 16502 0.998207 0 . 0 . 72 22,16,9,18 SPLICE_SITE_REGION+INTRON(LOW||||566|MCOLN2|protein_coding|CODING|NM_153259.3|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.808365 rs12064092 -0.693021 0.346885 72 566 27 MODIFIER 1 CODING MCOLN2 G protein_coding NM_153259.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85462582 C G 0 222 0 0.2496 0.4521 0.5029 0.63 0.4662 0.4918 0.308897 0.420114 0.477093 1 3083 56910 6385 5321 2537 31401 422 7761 2 10348 120724 11478 8586 6566 66370 906 16470 0.867819 0 . 0 . 275 44,70,55,71 UTR_5_PRIME(MODIFIER||27||566|MCOLN2|protein_coding|CODING|NM_153259.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7755 rs11161503 -0.693147 0.0216061 275 566 97 MODIFIER 1 CODING MCOLN2 T protein_coding NM_153259.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85462652 G T 0 222 0 0.2489 0.4515 0.5029 0.629 0.4662 0.4908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994269 0 . 0 . 154 8,62,11,60 UTR_5_PRIME(MODIFIER||97||566|MCOLN2|protein_coding|CODING|NM_153259.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.331249 rs11161504 -0.693147 0.000500504 154 566 110 MODIFIER 1 CODING MCOLN2 G protein_coding NM_153259.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85462665 T G 0 222 0 0.2489 0.4515 0.5029 0.629 0.4662 0.4908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.963578 0 . 0 . 119 3,57,5,49 UTR_5_PRIME(MODIFIER||110||566|MCOLN2|protein_coding|CODING|NM_153259.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.962074 rs11161505 -0.693147 0.173619 119 566 195 MODIFIER 1 CODING MCOLN2 C protein_coding NM_153259.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85462750 T C 0 171 0 0.7564 0.9187 0.9726 0.994 0.9791 0.9601 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 34 0,0,0,34 UTR_5_PRIME(MODIFIER||195||566|MCOLN2|protein_coding|CODING|NM_153259.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs920340 -0.693132 0.101969 34 553 530 MODIFIER 13 CODING MCOLN3 T protein_coding NM_018298.10 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85484276 C T 0 31.9 0 0.4569 0.4411 0.4697 0.3006 0.5139 0.4693 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||530||553|MCOLN3|protein_coding|CODING|NM_018298.10|13|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10782536 -0.453602 0.26 3 553 440 MODIFIER 13 CODING MCOLN3 G protein_coding NM_018298.10 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85484366 A G 0 52 0 0.8298 0.7961 0.7522 0.7331 0.84 0.8016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.25 0 . 0 . 5 1,1,1,1 UTR_3_PRIME(MODIFIER||440||553|MCOLN3|protein_coding|CODING|NM_018298.10|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs7522239 -0.453602 0.18 5 L383 553 ctC/ctT LOW 10 SILENT CODING MCOLN3 A protein_coding NM_018298.10 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85488030 G A 0 222 0 0.8298 0.7961 0.7522 0.7331 0.84 0.8016 0.834544 0.850454 0.858605 1 8663 99854 8358 6366 5362 57012 748 13345 2 10388 121270 11528 8640 6612 66690 908 16504 0.994945 0 . 0 . 122 26,40,20,24 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L383|553|MCOLN3|protein_coding|CODING|NM_018298.10|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.878289 rs2028304 -0.693146 0.104556 122 1194 10 MODIFIER 7 CODING SYDE2 C protein_coding NM_032184.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85624423 A C 0 115 0 0.0023 0.0571 0.0418 0.1746 0.0586 0.0194 0.00445931 0.019747 0.0265105 1 78 4060 137 870 202 2460 22 291 2 5626 58584 3718 4606 3652 30100 464 10418 0.760829 0 . 0 . 21 8,2,11,0 UTR_3_PRIME(MODIFIER||10||1194|SYDE2|protein_coding|CODING|NM_032184.1|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.239764 rs79898762 -0.676189 0.0508436 21 V1157I 1194 Gtt/Att MODERATE 7 MISSENSE CODING SYDE2 T protein_coding NM_032184.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85624549 C T 0 228 0 0.997 0.9992 1 1 1 1 0.997579 0.998908 0.999512 2 9738 120284 11529 8598 6604 66450 896 16469 2 9776 120348 11530 8598 6604 66474 896 16470 0 . 0 . 0 100 0,0,72,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1157I|1194|SYDE2|protein_coding|CODING|NM_032184.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs709786 -0.693147 0.0685264 100 L1052 1194 Ctg/Ttg LOW 7 SILENT CODING SYDE2 A protein_coding NM_032184.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85624864 G A 0 228 0 0.9319 0.981 0.9942 1 0.999 1 0.953099 0.985351 0.999755 2 9282 120121 11555 8626 6614 66639 896 16509 2 9784 120654 11576 8626 6614 66646 898 16510 0 . 0 . 0 76 0,0,14,56 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1052|1194|SYDE2|protein_coding|CODING|NM_032184.1|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs817412 -0.693147 0.197054 76 V569I 1194 Gtt/Att MODERATE 3 MISSENSE CODING SYDE2 T protein_coding NM_032184.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85648620 C T 0 228 0 0.9259 0.9794 0.9942 1 0.999 1 0.949919 0.984188 0.999634 2 9266 120178 11549 8626 6614 66720 896 16507 2 9800 120750 11574 8626 6614 66730 898 16508 0 . 0 . 0 68 0,0,34,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V569I|1194|SYDE2|protein_coding|CODING|NM_032184.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs817443 -0.693147 0.0288461 68 S422L 1194 tCa/tTa MODERATE 2 MISSENSE CODING SYDE2 A protein_coding NM_032184.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85655916 G A 0 222 0 0.0023 0.0571 0.0418 0.1756 0.0577 0.0194 0.0101185 0.0429468 0.0588165 1 107 6762 281 1517 282 4121 45 409 2 9806 120736 11558 8618 6614 66730 898 16512 0.616291 0 . 0 . 98 18,40,13,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S422L|1194|SYDE2|protein_coding|CODING|NM_032184.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.747888 rs56191061 -0.693139 0.914065 98 Q175P 1194 cAg/cCg MODERATE 1 MISSENSE CODING SYDE2 G protein_coding NM_032184.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85666156 T G 0 146 0 0.1543 0.3045 0.379 0.4683 0.2376 0.3548 0.162358 0.214168 0.238354 1 1636 34380 5223 4113 1399 16215 260 5534 2 9686 120148 11542 8588 6610 66324 890 16508 0.572451 0 . 0 . 31 8,10,2,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cCg|Q175P|1194|SYDE2|protein_coding|CODING|NM_032184.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.921439 rs12121540 -0.676189 0.420136 31 233 369 MODIFIER 3 CODING BCL10 C protein_coding NM_003921.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85732941 A C 0 57 0 0.3669 0.4505 0.3631 0.4395 0.4543 0.6329 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||369||233|BCL10|protein_coding|CODING|NM_003921.4|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs962409 -0.511536 0.617121 3 G213E 233 gGa/gAa MODERATE 3 MISSENSE CODING BCL10 T protein_coding NM_003921.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85733374 C T 0 222 0 0.0023 0.0721 0.0447 0.1538 0.0527 0.1217 0.0131639 0.0419037 0.0566279 1 113 7754 950 1313 299 3474 52 1553 2 10380 121124 11560 8642 6614 66528 904 16496 0.35432 0 . 0 COSM146549 126 23,38,12,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G213E|233|BCL10|protein_coding|CODING|NM_003921.4|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0332218 rs3768235 -0.693147 0.687414 126 L8 233 ctC/ctG LOW 1 SILENT CODING BCL10 C protein_coding NM_003921.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85742012 G C 0 222 0 0.2663 0.2282 0.2032 0.0744 0.3111 0.2679 0.248071 0.286791 0.306628 1 2597 33276 2153 666 2070 20905 276 4609 2 10348 120788 11540 8618 6510 66366 898 16508 0.535922 0 . 0 . 108 23,38,9,24 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L8|233|BCL10|protein_coding|CODING|NM_003921.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.535922 rs11576939 -0.693127 0.0134447 108 233 303 MODIFIER 1 CODING BCL10 C protein_coding NM_003921.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85742338 G C 0 152 0 0.8442 0.7704 0.6873 0.7173 0.7903 0.7638 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,4 UTR_5_PRIME(MODIFIER||303||233|BCL10|protein_coding|CODING|NM_003921.4|1|C),INTRAGENIC(MODIFIER|||||LOC646626||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2735593 -0.616816 0.438189 6 285 1480 MODIFIER 6 CODING DDAH1 C protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85785655 T C 0 9.7 0 0.6732 0.7113 0.6686 0.6567 0.7127 0.8476 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1480||285|DDAH1|protein_coding|CODING|NM_012137.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs233111 -0.379885 0 1 285 1384 MODIFIER 6 CODING DDAH1 C protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85785751 T C 0 46.2 0 0.3177 0.3728 0.3343 0.4147 0.3827 0.4213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,0,3,0 UTR_3_PRIME(MODIFIER||1384||285|DDAH1|protein_coding|CODING|NM_012137.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.666667 rs233112 -0.511536 0.607612 5 285 836 MODIFIER 6 CODING DDAH1 A protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85786299 T A 0 75 0 0.3154 0.3403 0.3199 0.2927 0.3648 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868321 0 . 0 . 8 0,4,1,3 UTR_3_PRIME(MODIFIER||836||285|DDAH1|protein_coding|CODING|NM_012137.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.124046 rs233113 -0.556411 0.658104 8 285 178 MODIFIER 6 CODING DDAH1 G protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85786957 T G 0 208 0 0.3154 0.3407 0.3199 0.2927 0.3648 0.4141 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.46726 0 . 0 . 25 6,1,14,1 UTR_3_PRIME(MODIFIER||178||285|DDAH1|protein_coding|CODING|NM_012137.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.799136 rs233114 -0.688148 0.133364 25 285 158 MODIFIER 6 CODING DDAH1 A protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85786977 G A 0 222 0 0.298 0.3353 0.3184 0.2927 0.3638 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.750989 0 . 0 . 39 11,1,20,2 UTR_3_PRIME(MODIFIER||158||285|DDAH1|protein_coding|CODING|NM_012137.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666414 rs233115 -0.692562 0.991392 39 285 21 MODIFIER 6 CODING DDAH1 T protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85787114 A T 0 228 0 1 1 1 1 1 1 0 . 0 2 10397 121325 11576 8650 6614 66680 908 16500 2 10398 121330 11576 8650 6614 66684 908 16500 0 . 0 . 0 93 0,0,43,36 UTR_3_PRIME(MODIFIER||21||285|DDAH1|protein_coding|CODING|NM_012137.3|6|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs233116 -0.693147 0.0146669 93 285 17 MODIFIER 6 CODING DDAH1 C protein_coding NM_012137.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 85787118 G C 0 222 0 0.0968 0.2806 0.3084 0.2927 0.3628 0.4121 0.113936 0.266339 0.344419 1 1175 41032 3890 2479 2571 23929 304 6684 2 10370 121060 11540 8626 6604 66578 906 16436 0.646573 0 . 0 . 97 21,16,21,23 UTR_3_PRIME(MODIFIER||17||285|DDAH1|protein_coding|CODING|NM_012137.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.118129 rs3087894 -0.693146 0.512569 97 381 107 MODIFIER 1 CODING CYR61 A protein_coding NM_001554.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86046561 C A 0 99 0 0.5893 0.5857 0.5375 0.5784 0.5278 0.682 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_5_PRIME(MODIFIER||107||381|CYR61|protein_coding|CODING|NM_001554.4|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2297140 -0.616816 0.706942 6 1714 1232 MODIFIER 60 CODING COL24A1 T protein_coding NM_152890.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86194997 C T 0 40.4 0 0.1483 0.3826 0.3689 0.4345 0.4533 0.5828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992367 0 . 0 . 8 3,1,4,0 UTR_3_PRIME(MODIFIER||1232||1714|COL24A1|protein_coding|CODING|NM_152890.5|60|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.992367 rs1047895 -0.556411 0.585652 8 1714 1182 MODIFIER 60 CODING COL24A1 C protein_coding NM_152890.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86195047 T C 0 141 0 0.2337 0.4087 0.5216 0.5099 0.5149 0.3517 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.637085 0 . 0 . 19 7,1,10,1 UTR_3_PRIME(MODIFIER||1182||1714|COL24A1|protein_coding|CODING|NM_152890.5|60|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.959099 rs1047893 -0.676189 0.0789411 19 1714 1163 MODIFIER 60 CODING COL24A1 C protein_coding NM_152890.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86195066 A C 0 126 0 0.4024 0.4531 0.3905 0.4355 0.4543 0.5828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.933359 0 . 0 . 28 15,1,11,1 UTR_3_PRIME(MODIFIER||1163||1714|COL24A1|protein_coding|CODING|NM_152890.5|60|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982906 rs1047892 -0.680642 0.527393 28 1714 LOW 37 CODING COL24A1 G protein_coding NM_152890.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86315095 A G 0 222 0 0.0008 0.014377 0 0.005 0 0.0675 0.000278087 0.000170736 0.000123183 1 5 1045 2 44 0 20 3 971 2 9768 120438 11536 8614 6608 66504 900 16508 0.832824 0 . 0 . 132 26,35,20,32 SPLICE_SITE_REGION+INTRON(LOW||||1714|COL24A1|protein_coding|CODING|NM_152890.5|37|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.648709 rs200588907 -0.693147 0.202571 132 1714 LOW 36 CODING COL24A1 C protein_coding NM_152890.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86334316 T C 0 228 0 0.3253 0.4659 0.3948 0.5942 0.4145 0.6268 0.325633 0.396932 0.428694 2 3200 55063 4898 4989 3185 28898 436 9457 2 9732 119940 11362 8578 6560 66320 900 16488 0 . 0 . 0 81 0,0,35,38 SPLICE_SITE_REGION+INTRON(LOW||||1714|COL24A1|protein_coding|CODING|NM_152890.5|36|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs17411495 -0.693147 0.636609 81 P883 1714 ccG/ccC LOW 26 SILENT CODING COL24A1 G protein_coding NM_152890.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86375654 C G 0 228 0 0.5696 0.6919 0.7795 0.8026 0.7008 0.6718 0.621483 0.674423 0.698384 2 5904 85013 9314 6895 4553 46942 639 10766 2 9794 120680 11558 8622 6614 66692 900 16500 1 0 . 0 . 57 1,0,16,35 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P883|1714|COL24A1|protein_coding|CODING|NM_152890.5|26|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1502657 -0.693147 0.00254837 57 1714 LOW 17 CODING COL24A1 A protein_coding NM_152890.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86487981 G A 0 228 0 0.9327 0.7877 0.7536 0.872 0.6431 0.6779 0.89158 0.699729 0.61431 2 8842 80359 7623 7150 3274 41839 602 11029 2 9796 120464 11488 8580 6602 66608 894 16496 1 0 . 0 . 297 0,1,175,86 SPLICE_SITE_REGION+INTRON(LOW||||1714|COL24A1|protein_coding|CODING|NM_152890.5|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs516213 -0.693147 0.123904 297 P731S 1714 Cct/Tct MODERATE 17 MISSENSE CODING COL24A1 A protein_coding NM_152890.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86488232 G A 0 222 0 0.4168 0.2909 0.2997 0.1329 0.3022 0.2658 0.394565 0.318243 0.283824 1 3953 33994 2873 1058 1480 19622 260 4748 2 9742 119368 11380 8450 6540 65994 894 16368 0.700261 0 . 0 . 127 33,24,29,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P731S|1714|COL24A1|protein_coding|CODING|NM_152890.5|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996539 rs641712 -0.693147 0.00718994 127 P546S 1714 Cct/Tct MODERATE 6 MISSENSE CODING COL24A1 A protein_coding NM_152890.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86557967 G A 0 222 0 0.3563 0.3702 0.4467 0.3849 0.3767 0.3129 0.354992 0.37376 0.382063 1 3477 43470 4525 3401 1761 24921 333 5052 2 9760 120280 11526 8610 6592 66432 892 16468 0.329454 0 . 0 . 162 53,36,33,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P546S|1714|COL24A1|protein_coding|CODING|NM_152890.5|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.831063 rs11161732 -0.693147 0.120489 162 S368 1714 agC/agT LOW 3 SILENT CODING COL24A1 A protein_coding NM_152890.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86590915 G A 0 228 0 0.8941 0.9645 0.987 0.9722 0.999 1 0.92001 0.974085 0.999272 2 8902 119252 11384 8357 6612 66596 898 16503 2 9800 120548 11438 8622 6612 66670 900 16506 0 . 0 . 0 95 0,0,33,50 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S368|1714|COL24A1|protein_coding|CODING|NM_152890.5|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2174767 -0.693147 0.0827 95 L222 1714 Tta/Cta LOW 3 SILENT CODING COL24A1 G protein_coding NM_152890.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86591355 A G 0 222 0 0 0.01897 0.0245 0.0685 0 0.0092 0 0.000166362 0.000243072 1 5 958 199 593 0 27 5 129 2 9716 119020 11284 8528 6512 65834 894 16252 0.804407 0 . 0 . 46 12,12,15,6 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L222|1714|COL24A1|protein_coding|CODING|NM_152890.5|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.892142 rs117871299 -0.692352 0.478119 46 A152 1714 gcA/gcG LOW 3 SILENT CODING COL24A1 C protein_coding NM_152890.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86591563 T C 0 222 0 0.0121 0.0228 0.0159 0.0675 0.006 0.0133 0.00812568 0.00496968 0.00354523 1 104 1346 70 642 5 346 8 171 2 9720 119556 11302 8570 6516 66152 884 16412 0.451264 0 . 0 . 65 24,11,13,13 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A152|1714|COL24A1|protein_coding|CODING|NM_152890.5|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.352646 rs77448813 -0.692976 0.260414 65 R7K 1714 aGa/aAa MODERATE 1 MISSENSE CODING COL24A1 T protein_coding NM_152890.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86622060 C T 0 222 0 0.0424 0.0381 0.0173 0.0903 0.006 0.0266 0.0368421 0.0140272 0.003516 1 368 1985 78 880 5 338 12 304 2 9798 120384 11576 8624 6614 66594 898 16280 0.989179 0 . 0 COSM146550 125 32,28,35,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R7K|1714|COL24A1|protein_coding|CODING|NM_152890.5|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91047 rs77549850 -0.693147 0.191005 125 E621 636 gaA/gaG LOW 17 SILENT CODING ODF2L C protein_coding NM_001007022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86818572 T C 0 228 0 0.7557 0.7412 0.6585 0.8284 0.6451 0.7894 0.758299 0.686528 0.649791 2 7781 82681 7168 7167 4603 42834 639 12489 2 10276 119562 11370 8610 6546 65452 892 16416 0.632184 0 . 0 . 90 0,2,65,22 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E621|636|ODF2L|protein_coding|CODING|NM_001007022.2|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.902299 rs272496 -0.693147 0.552311 90 E571 636 gaG/gaA LOW 16 SILENT CODING ODF2L T protein_coding NM_001007022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86820267 C T 0 228 0 0.7821 0.7546 0.67 0.8284 0.6551 0.8037 0.774626 0.697755 0.658372 2 8065 85138 7347 7191 4792 44184 657 12902 2 10388 121284 11536 8650 6606 66688 906 16510 1 0 . 0 . 70 0,1,43,18 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E571|636|ODF2L|protein_coding|CODING|NM_001007022.2|16|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1182098 -0.693147 0.0309032 70 V292 636 gtG/gtA LOW 9 SILENT CODING ODF2L T protein_coding NM_001007022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86838158 C T 0 228 0 0.7821 0.7546 0.67 0.8284 0.6551 0.8037 0.773059 0.696881 0.657956 2 6206 62538 5868 5997 3676 29911 502 10378 2 7990 87326 9018 7182 5008 44130 690 13308 0.665254 0 . 0 . 146 2,0,98,20 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V292|636|ODF2L|protein_coding|CODING|NM_001007022.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.415254 rs386591710,rs421105 -0.693147 0.000801384 146 A198 636 gcC/gcT LOW 7 SILENT CODING ODF2L A protein_coding NM_001007022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86847955 G A 0 222 0 0.5371 0.388 0.3977 0.2897 0.326 0.3446 0.500681 0.375077 0.310726 1 5186 40904 3632 2709 2333 20847 326 5871 2 10374 120942 11460 8630 6584 66510 902 16482 0.982148 0 . 0 . 117 41,22,28,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A198|636|ODF2L|protein_coding|CODING|NM_001007022.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97353 rs272516,rs386572679 -0.693146 0.56357 117 C30 636 tgT/tgC LOW 2 SILENT CODING ODF2L G protein_coding NM_001007022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86852621 A G 0 222 0 0.2352 0.3147 0.2637 0.4167 0.3181 0.3497 0.268271 0.315624 0.339884 1 2805 40076 3394 3489 2160 22383 296 5549 2 10394 121310 11540 8644 6614 66702 908 16508 0.210678 0 . 0 COSM146551 199 47,34,51,39 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C30|636|ODF2L|protein_coding|CODING|NM_001007022.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.768637 rs2390096 -0.693147 0.00321241 199 943 LOW 3 CODING CLCA2 A protein_coding NM_006536.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86896541 G A 0 222 0 0.2678 0.3662 0.2738 0.5288 0.3191 0.4458 0.311394 0.331001 0.341047 1 3181 43110 3673 4333 2299 22616 323 6685 2 10406 121362 11564 8646 6614 66724 908 16500 0.90637 0 . 0 . 174 61,19,59,19 SPLICE_SITE_REGION+INTRON(LOW||||943|CLCA2|protein_coding|CODING|NM_006536.5|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.627703 rs3737672 -0.693147 0.468243 174 R596 943 cgC/cgT LOW 11 SILENT CODING CLCA2 T protein_coding NM_006536.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86913265 C T 0 222 0 0.0908 0.2546 0.2032 0.3889 0.2634 0.365 0.131866 0.225511 0.273488 1 1297 33848 2954 3270 1988 18476 261 5602 2 10404 121326 11546 8612 6614 66730 908 16512 0.938211 0 . 0 . 86 27,15,23,17 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R596|943|CLCA2|protein_coding|CODING|NM_006536.5|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.880023 rs2275001 -0.693145 0.649504 86 Q842 943 caA/caG LOW 14 SILENT CODING CLCA2 G protein_coding NM_006536.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86920904 A G 0 222 0 0.2057 0.3289 0.2435 0.4405 0.335 0.4346 0.246255 0.304552 0.334419 1 2564 41629 3451 3619 2318 22482 320 6875 2 10396 121314 11566 8632 6612 66692 908 16508 0.99882 0 . 0 COSM146552 137 45,25,32,17 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q842|943|CLCA2|protein_coding|CODING|NM_006536.5|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.694956 rs2390057,rs386566297 -0.693147 0.057121 137 L65F 914 Ctt/Ttt MODERATE 2 MISSENSE CODING CLCA1 T protein_coding NM_001285.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86939130 C T 0 228 0 0.6725 0.8822 0.9308 0.9871 0.9513 0.9519 0.732183 0.884438 0.962442 2 7493 114077 11242 8540 5817 64370 849 15766 2 10318 121302 11578 8650 6612 66728 908 16508 0 . 0 . 0 110 0,0,87,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L65F|914|CLCA1|protein_coding|CODING|NM_001285.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2145412 -0.693147 0.234205 110 V215 914 gtA/gtT LOW 5 SILENT CODING CLCA1 T protein_coding NM_001285.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86947975 A T 0 222 0 0.2443 0.3676 0.2939 0.505 0.3728 0.4397 0.253291 0.319852 0.353953 1 2731 44982 4054 4095 2743 23773 368 7218 2 10400 121276 11546 8640 6608 66670 908 16504 0.976918 0 . 0 . 155 23,49,28,35 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtT|V215|914|CLCA1|protein_coding|CODING|NM_001285.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.963303 rs1321694 -0.693147 0.0396188 155 N357S 914 aAt/aGt MODERATE 7 MISSENSE CODING CLCA1 G protein_coding NM_001285.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86952324 A G 0 228 0 0.9425 0.887 0.9078 0.8472 0.835 0.8916 0.932365 0.869137 0.836744 2 9716 104738 10613 7542 5713 55614 781 14759 2 10404 121384 11566 8650 6614 66732 908 16510 0 . 0 . 0 87 0,0,39,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N357S|914|CLCA1|protein_coding|CODING|NM_001285.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2734705 -0.693147 0.0118347 87 M524T 914 aTg/aCg MODERATE 10 MISSENSE CODING CLCA1 C protein_coding NM_001285.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 86959173 T C 0 228 0 0.7753 0.8496 0.8761 0.9058 0.8241 0.8998 0.770086 0.801707 0.817907 2 8081 102185 10439 7971 5641 54510 768 14775 2 10402 121376 11574 8652 6614 66718 908 16508 0 . 0 . 0 104 0,0,64,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M524T|914|CLCA1|protein_coding|CODING|NM_001285.3|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2791494 -0.693147 0.204405 104 S303R 919 Agt/Cgt MODERATE 6 MISSENSE CODING CLCA4 C protein_coding NM_012128.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87031656 A C 0 222 0 0.053 0.0697 0.0303 0.2054 0.0179 0.0337 0.0472937 0.0229495 0.0117377 1 460 4458 533 1809 299 898 38 421 2 9798 120682 11568 8620 6612 66682 900 16502 0.250201 0 . 0 . 184 49,44,28,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S303R|919|CLCA4|protein_coding|CODING|NM_012128.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943472 rs2231592 -0.693147 0.112498 184 356 19 MODIFIER 7 CODING HS2ST1 A protein_coding NM_012262.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87570398 G A 0 228 0 0.3079 0.7079 0.8084 0.9653 0.7843 0.8333 0.409504 0.655196 0.780959 2 3674 90389 9709 7867 5100 50169 675 13195 2 8956 115302 11200 8084 6448 63660 864 16090 0 . 0 . 0 76 0,0,30,38 UTR_3_PRIME(MODIFIER||19||356|HS2ST1|protein_coding|CODING|NM_012262.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1621247 -0.693147 0.113283 76 356 34 MODIFIER 7 CODING HS2ST1 T protein_coding NM_012262.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87570413 A T 0 222 0 0.0008 0.0475 0 0.2252 0.001 0.0092 0.00296262 0.00131112 0.000466309 1 14 1646 7 1495 11 46 8 65 2 7616 96504 9558 6572 5900 52350 772 13736 0.689761 0 . 0 . 71 11,18,15,19 UTR_3_PRIME(MODIFIER||34||356|HS2ST1|protein_coding|CODING|NM_012262.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.769459 rs3766018 -0.693132 0.483872 71 356 3584 MODIFIER 7 CODING HS2ST1 C protein_coding NM_012262.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87573963 T C 0 32.6 0 0.3449 0.7186 0.8112 0.9692 0.7843 0.8323 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3584||356|HS2ST1|protein_coding|CODING|NM_012262.3|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2798682 -0.379885 0 2 356 3609 MODIFIER 7 CODING HS2ST1 C protein_coding NM_012262.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87573988 T C 0 9.7 0 0.7519 0.8564 0.879 0.9702 0.829 0.8926 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3609||356|HS2ST1|protein_coding|CODING|NM_012262.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2798683 -0.379885 0 1 356 3838 MODIFIER 7 CODING HS2ST1 G protein_coding NM_012262.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87574217 A G 0 32.6 0 0.3517 0.7208 0.8112 0.9692 0.7853 0.8333 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3838||356|HS2ST1|protein_coding|CODING|NM_012262.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2798684 -0.379885 0 2 115 7 MODIFIER 4 CODING LOC101927844 C protein_coding NM_001290053.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87716515 T C 0 45.1 0 0.0847 0.2416 0.4236 0.2282 0.332 0.2454 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,2,0 UTR_3_PRIME(MODIFIER||7||115|LOC101927844|protein_coding|CODING|NM_001290053.1|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs111758073 -0.453602 0.1 4 165 3180 MODIFIER 1 CODING LMO4 G protein_coding NM_006769.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 87794519 C G 0 46.3 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||3180||165|LMO4|protein_coding|CODING|NM_006769.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4369208 -0.453602 0.92 2 L141 984 Tta/Cta LOW 3 SILENT CODING PKN2 C protein_coding NM_006256.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89225976 T C 0 222 0 0.9304 0.7506 0.5807 0.6498 0.6561 0.8292 0.893212 0.715293 0.63614 1 8762 83622 7140 5542 4796 43317 637 13428 2 9800 120676 11554 8626 6614 66674 900 16508 0.985525 0 . 0 . 130 31,29,30,25 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L141|984|PKN2|protein_coding|CODING|NM_006256.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999338 rs430600 -0.693147 0.870423 130 984 1992 MODIFIER 22 CODING PKN2 T protein_coding NM_006256.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89301123 C T 0 222 0 0.9266 0.7498 0.5807 0.6498 0.6561 0.8303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.916121 0 . 0 . 87 13,23,11,30 UTR_3_PRIME(MODIFIER||1992||984|PKN2|protein_coding|CODING|NM_006256.2|22|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.991231 rs786912 -0.693145 0.142732 87 L242 316 Ctg/Ttg LOW 6 SILENT CODING GTF2B A protein_coding NM_001514.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89322982 G A 0 228 0 0.9493 0.986 0.9957 1 1 1 0.948479 0.98247 0.999884 2 9877 120852 11557 8653 6614 66735 906 16510 2 10406 121406 11574 8654 6614 66738 908 16512 0 . 0 . 0 80 0,0,40,31 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L242|316|GTF2B|protein_coding|CODING|NM_001514.5|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2794318 -0.693147 0.20265 80 R290C 595 Cgt/Tgt MODERATE 6 MISSENSE CODING GBP3 A protein_coding NM_018284.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89478868 G A 0 222 0 0.0098 0.135 0.1513 0.1677 0.1879 0.2045 0.0419882 0.141934 0.19314 1 341 21523 2224 1768 1716 12406 174 2894 2 10406 121358 11564 8648 6614 66714 908 16504 0.694436 0 . 0 COSM146555 88 25,18,29,8 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Cgt/Tgt|R290C|595|GBP3|protein_coding|CODING|NM_018284.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966629 rs113490655 -0.693141 0.299496 88 R225W 595 Cgg/Tgg MODERATE 6 MISSENSE CODING GBP3 A protein_coding NM_018284.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89479063 G A 0 228 0 0.1793 0.3337 0.2925 0.3075 0.4404 0.4888 0.261008 0.388436 0.453721 2 2455 50547 3449 2854 3510 30287 394 7598 2 10198 121148 11568 8640 6612 66710 908 16512 0.985915 0 . 0 . 81 2,0,35,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R225W|595|GBP3|protein_coding|CODING|NM_018284.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.359155 rs4656077 -0.693147 0.435984 81 R221Q 595 cGa/cAa MODERATE 6 MISSENSE CODING GBP3 T protein_coding NM_018284.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89479074 C T 0 228 0 0.1793 0.3339 0.2925 0.3075 0.4404 0.4898 0.260218 0.387804 0.45314 2 2418 50498 3450 2855 3508 30278 394 7595 2 9954 120744 11556 8618 6610 66596 908 16502 0.697183 0 . 0 . 79 2,0,31,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R221Q|595|GBP3|protein_coding|CODING|NM_018284.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.549296 rs4656078 -0.693147 0.0982302 79 595 LOW 5 CODING GBP3 C protein_coding NM_018284.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89479758 T C 0 228 0 0.6165 0.6434 0.5692 0.5188 0.7614 0.7393 0.667726 0.736506 0.771744 2 6864 86564 5995 4579 5010 51599 667 11850 2 10400 121362 11562 8638 6608 66734 908 16512 0.864987 0 . 0 . 101 3,0,82,7 SPLICE_SITE_REGION+INTRON(LOW||||595|GBP3|protein_coding|CODING|NM_018284.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.928671 rs3795543 -0.693147 0.0900484 101 592 415 MODIFIER 11 CODING GBP1 T protein_coding NM_002053.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89518623 C T 0 138 0 0.8298 0.7202 0.6801 0.7421 0.6173 0.684 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||415||592|GBP1|protein_coding|CODING|NM_002053.2|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2624 -0.616816 0.80389 6 T349S 592 aCc/aGc MODERATE 7 MISSENSE CODING GBP1 C protein_coding NM_002053.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89522646 G C 0 228 0 0.7958 0.7183 0.6138 0.5595 0.7654 0.8027 0.812755 0.794018 0.784419 2 8401 90438 6570 4930 4982 52016 677 12862 2 10406 121380 11566 8642 6608 66740 908 16510 1 0 . 0 COSM1344744 129 0,1,84,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aGc|T349S|592|GBP1|protein_coding|CODING|NM_002053.2|7|C) 1 0 . 0 . 1 0 1 1 0 59 0 1 1 0 1 rs1048425 -0.693147 0.184842 129 591 1071 MODIFIER 11 CODING GBP2 C protein_coding NM_004120.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89572787 G C 0 6.3 0 0.4924 0.6346 0.6816 0.7728 0.6431 0.6421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1071||591|GBP2|protein_coding|CODING|NM_004120.4|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs997160 -0.379885 0 1 S303G 591 Agc/Ggc MODERATE 7 MISSENSE CODING GBP2 C protein_coding NM_004120.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89579941 T C 0 228 0 0.4614 0.627 0.6801 0.7758 0.6441 0.6421 0.519065 0.614178 0.662907 2 5277 81332 8339 6715 5234 44251 607 10909 2 10402 121362 11562 8650 6608 66720 908 16512 0 . 0 . 0 97 0,0,23,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S303G|591|GBP2|protein_coding|CODING|NM_004120.4|7|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs2230338 -0.693147 1.96021e-05 97 P285A 591 Cca/Gca MODERATE 6 MISSENSE CODING GBP2 C protein_coding NM_004120.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89582690 G C 0 228 0 0.4622 0.627 0.6801 0.7758 0.6431 0.6421 0.519292 0.614255 0.662907 2 5273 81293 8324 6714 5240 44227 606 10909 2 10398 121302 11536 8630 6614 66704 908 16512 0 . 0 . 0 65 0,0,43,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P285A|591|GBP2|protein_coding|CODING|NM_004120.4|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1803632 -0.693147 0.00823152 65 638 77 MODIFIER 11 CODING GBP7 C protein_coding NM_207398.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89597755 T C 0 228 0 0.4697 0.6288 0.6787 0.7728 0.6451 0.6431 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 98 0,0,67,19 UTR_3_PRIME(MODIFIER||77||638|GBP7|protein_coding|CODING|NM_207398.2|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs942442 -0.693147 0.0503371 98 T14I 638 aCt/aTt MODERATE 2 MISSENSE CODING GBP7 A protein_coding NM_207398.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89637578 G A 0 228 0 0.7776 0.7147 0.7046 0.7718 0.6431 0.6513 0.793236 0.706443 0.661977 2 8244 84589 8505 6724 5255 44291 618 10952 2 10406 121356 11570 8634 6614 66716 908 16508 0 . 0 . 0 142 0,0,23,111 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T14I|638|GBP7|protein_coding|CODING|NM_207398.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs676913 -0.693147 0.0771848 142 640 3551 MODIFIER 11 CODING GBP4 A protein_coding NM_052941.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89647386 G A 0 32.6 0 0.7995 0.7472 0.732 0.7837 0.6948 0.7035 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3551||640|GBP4|protein_coding|CODING|NM_052941.4|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs627125 -0.379885 0 2 640 414 MODIFIER 11 CODING GBP4 C protein_coding NM_052941.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89650523 T C 0 32.6 0 0 0.0017971 0 0.0089 0 0 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||414||640|GBP4|protein_coding|CODING|NM_052941.4|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs149700649 -0.379885 0 2 640 87 MODIFIER 11 CODING GBP4 T protein_coding NM_052941.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89650850 A T 0 228 0 0.2685 0.3944 0.3271 0.3998 0.4901 0.5082 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,15,2 UTR_3_PRIME(MODIFIER||87||640|GBP4|protein_coding|CODING|NM_052941.4|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs623134 -0.690438 0.892681 19 E551G 640 gAg/gGg MODERATE 10 MISSENSE CODING GBP4 C protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652071 T C 0 228 0 0.143 0.3574 0.3141 0.3978 0.4881 0.502 0.00771675 0.0169153 0.0216279 2 1980 52082 3465 3191 3519 31535 418 7974 2 10288 120576 11558 8586 6556 66208 902 16478 0.909091 0 . 0 . 37 2,0,21,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E551G|640|GBP4|protein_coding|CODING|NM_052941.4|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.681818 rs386599180,rs561042 -0.693127 0.0277741 37 E551K 640 Gag/Aag MODERATE 10 MISSENSE CODING GBP4 T protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652072 C T 0 228 0 0.1445 0.3588 0.3141 0.3978 0.4891 0.5061 0.00476623 0.0106874 0.0137209 2 1980 52060 3459 3195 3513 31522 418 7973 2 10286 120544 11552 8584 6560 66184 902 16476 0.818182 0 . 0 . 37 2,0,21,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E551K|640|GBP4|protein_coding|CODING|NM_052941.4|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.681818 rs561037 -0.693127 0.0310211 37 L549M 640 Ttg/Atg MODERATE 10 MISSENSE CODING GBP4 T protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652078 A T 0 228 0 0.1445 0.3594 0.3141 0.3988 0.4891 0.5082 0.20177 0.378538 0.469165 2 1979 52038 3467 3190 3524 31490 419 7969 2 10288 120574 11560 8588 6572 66188 902 16476 0.8125 0 . 0 . 37 2,0,20,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L549M|640|GBP4|protein_coding|CODING|NM_052941.4|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.640625 rs608339 -0.69312 0.0329381 37 E546K 640 Gag/Aag MODERATE 10 MISSENSE CODING GBP4 T protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652087 C T 0 228 0 0.1445 0.359 0.3141 0.3988 0.4881 0.5072 0.0347727 0.105308 0.142212 2 1982 51955 3462 3190 3522 31439 416 7944 2 10288 120500 11554 8586 6560 66158 902 16452 1 0 . 0 COSM146556 20 1,0,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E546K|640|GBP4|protein_coding|CODING|NM_052941.4|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1142890,rs386518179 -0.69168 1.2045e-07 20 M545I 640 atG/atC MODERATE 10 MISSENSE CODING GBP4 G protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652088 C G 0 228 0 0.1445 0.359 0.3141 0.3988 0.4881 0.5072 0.0357143 0.105164 0.141579 2 1982 51954 3456 3189 3515 31464 415 7933 2 10292 120496 11546 8586 6560 66170 902 16440 1 0 . 0 COSM146557 20 1,0,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atC|M545I|640|GBP4|protein_coding|CODING|NM_052941.4|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1142889 -0.69168 1.2045e-07 20 M545L 640 Atg/Ctg MODERATE 10 MISSENSE CODING GBP4 G protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652090 T G 0 228 0 0.1445 0.359 0.3141 0.3988 0.4881 0.5072 0.0381818 0.119415 0.161733 2 1979 51986 3464 3191 3518 31472 415 7947 2 10288 120506 11562 8584 6554 66164 902 16452 1 0 . 0 . 20 1,0,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ctg|M545L|640|GBP4|protein_coding|CODING|NM_052941.4|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1142888,rs386518178 -0.69168 1.2045e-07 20 A543 640 gcC/gcT LOW 10 SILENT CODING GBP4 A protein_coding NM_052941.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652094 G A 0 228 0 0.1445 0.359 0.3141 0.3988 0.4881 0.5072 0.0826897 0.228236 0.303329 2 1976 51945 3459 3187 3523 31437 414 7949 2 10292 120510 11554 8578 6564 66168 900 16454 1 0 . 0 . 20 1,0,10,9 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A543|640|GBP4|protein_coding|CODING|NM_052941.4|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1142887 -0.69168 1.2045e-07 20 M542I 640 atG/atA MODERATE 10 MISSENSE CODING GBP4 T protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652097 C T 0 220 0 0.1445 0.3596 0.3141 0.3998 0.4891 0.5082 0.101226 0.261572 0.343721 1 1974 51985 3461 3187 3527 31457 417 7962 2 10290 120518 11552 8580 6560 66170 902 16464 0.842105 0 . 0 . 21 1,1,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M542I|640|GBP4|protein_coding|CODING|NM_052941.4|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.842105 rs1142886 -0.69168 1.2045e-07 21 Y541N 640 Tac/Aac MODERATE 10 MISSENSE CODING GBP4 T protein_coding NM_052941.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89652102 A T 0 228 0 0.1445 0.3596 0.3141 0.3998 0.4891 0.5082 0.098729 0.26088 0.343953 2 1925 51812 3461 3181 3521 31341 418 7965 2 10206 120214 11552 8580 6568 65934 904 16470 0.84375 0 . 0 . 34 1,1,16,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y541N|640|GBP4|protein_coding|CODING|NM_052941.4|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.6875 rs655260 -0.69312 0.999992 34 586 2994 MODIFIER 1 CODING GBP5 C protein_coding NM_001134486.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89738232 G C 0 46.3 0 0.3238 0.4151 0.3732 0.3075 0.5636 0.5266 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||2994||586|GBP5|protein_coding|CODING|NM_001134486.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2147309 -0.453602 0.56 2 A331S 633 Gct/Tct MODERATE 7 MISSENSE CODING GBP6 T protein_coding NM_198460.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89847372 G T 0 228 0 0.9092 0.8059 0.8415 0.7262 0.7465 0.7843 0.880163 0.791096 0.745465 2 9213 94271 10028 6469 5382 49295 717 13167 2 10406 121348 11570 8632 6612 66708 908 16512 0 . 0 . 0 61 0,0,30,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A331S|633|GBP6|protein_coding|CODING|NM_198460.2|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386594465,rs4658359 -0.693147 0.219385 61 L344F 633 Ctc/Ttc MODERATE 7 MISSENSE CODING GBP6 T protein_coding NM_198460.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89847411 C T 0 228 0 0.9092 0.8059 0.8415 0.7262 0.7465 0.7843 0.880163 0.791096 0.745465 2 9211 94305 10031 6470 5382 49326 717 13168 2 10402 121348 11576 8626 6612 66712 908 16512 0 . 0 . 0 63 0,0,34,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L344F|633|GBP6|protein_coding|CODING|NM_198460.2|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386594466,rs4658360 -0.693147 0.0447596 63 M355V 633 Atg/Gtg MODERATE 7 MISSENSE CODING GBP6 G protein_coding NM_198460.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89847444 A G 0 228 0 0.91 0.8065 0.8429 0.7252 0.7485 0.7843 0.880163 0.791096 0.745465 2 9211 94300 10031 6470 5382 49330 717 13159 2 10402 121356 11576 8630 6614 66718 906 16510 0 . 0 . 0 61 0,0,36,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M355V|633|GBP6|protein_coding|CODING|NM_198460.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4658146 -0.693147 0.771044 61 D520V 633 gAt/gTt MODERATE 10 MISSENSE CODING GBP6 T protein_coding NM_198460.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89849742 A T 0 228 0 0.916 0.8606 0.9193 0.7272 0.8897 0.8517 0.909215 0.897355 0.891279 2 9448 107022 10594 6450 6012 59338 820 14360 2 10402 121224 11540 8594 6614 66672 908 16494 0 . 0 . 0 66 0,0,32,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D520V|633|GBP6|protein_coding|CODING|NM_198460.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs959460 -0.693147 0.58318 66 633 1382 MODIFIER 11 CODING GBP6 G protein_coding NM_198460.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89852410 A G 0 6.3 0 0.9206 0.8618 0.9179 0.7282 0.8897 0.8517 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1382||633|GBP6|protein_coding|CODING|NM_198460.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6669782 -0.379885 0 1 633 1491 MODIFIER 11 CODING GBP6 C protein_coding NM_198460.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89852519 T C 0 9.7 0 0.9796 0.8776 0.9207 0.7292 0.8897 0.8497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1491||633|GBP6|protein_coding|CODING|NM_198460.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7526896 -0.379885 0 1 633 1526 MODIFIER 11 CODING GBP6 C protein_coding NM_198460.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89852554 T C 0 60 0 0.9206 0.8614 0.9193 0.7282 0.8887 0.8497 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1526||633|GBP6|protein_coding|CODING|NM_198460.2|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7526910 -0.453602 0.76 3 633 2285 MODIFIER 11 CODING GBP6 A protein_coding NM_198460.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 89853313 G A 0 76 0 0.9206 0.862 0.9193 0.7282 0.8897 0.8517 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||2285||633|GBP6|protein_coding|CODING|NM_198460.2|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1977667 -0.511536 0.519801 3 803 2222 MODIFIER 8 CODING LRRC8B T protein_coding NM_001134476.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 90060824 C T 0 9.7 0 0.997 0.9934 0.9899 1 0.9821 0.9959 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2222||803|LRRC8B|protein_coding|CODING|NM_001134476.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs359906 -0.379885 0 1 D205G 803 gAc/gGc MODERATE 3 MISSENSE CODING LRRC8C G protein_coding NM_032270.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 90178743 A G 0 228 0 0.9523 0.986 0.9899 1 1 1 0.953926 0.984161 0.999651 2 9857 120801 11543 8654 6614 66717 906 16510 2 10390 121380 11576 8654 6614 66726 908 16512 0 . 0 . 0 81 0,0,46,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D205G|803|LRRC8C|protein_coding|CODING|NM_032270.4|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs474536 -0.693147 0.0360689 81 N468S 803 aAt/aGt MODERATE 3 MISSENSE CODING LRRC8C G protein_coding NM_032270.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 90179532 A G 0 222 0 0.0325 0.1506 0.2089 0.25 0.1531 0.1636 0.0460735 0.110564 0.143605 1 437 19054 2848 2318 1101 9352 135 2863 2 10366 121230 11560 8602 6612 66686 908 16496 0.960043 0 . 0 . 53 15,14,13,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N468S|803|LRRC8C|protein_coding|CODING|NM_032270.4|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.840465 rs12032393 -0.692717 0.409738 53 387 222 MODIFIER 3 CODING BARHL2 C protein_coding NM_020063.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91177647 A C 0 64 0 0.3245 0.4782 0.6095 0.4752 0.5447 0.5276 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.857112 0 . 0 . 11 5,0,5,0 UTR_3_PRIME(MODIFIER||222||387|BARHL2|protein_coding|CODING|NM_020063.1|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 0 . 0.952347 rs2390606 -0.590765 0.669454 11 1327 1250 MODIFIER 6 CODING ZNF644 A protein_coding NM_201269.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91381105 T A 0 222 0 0.0166 0.0569 0.0677 0.0754 0.0696 0.0716 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.920573 0 . 0 . 51 6,23,6,14 UTR_3_PRIME(MODIFIER||1250||1327|ZNF644|protein_coding|CODING|NM_201269.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.620835 rs17131232 -0.692067 0.000283124 51 A1357 1435 gcC/gcT LOW 37 SILENT CODING HFM1 A protein_coding NM_001017975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91728053 G A 0 228 0 0.997 0.9992 1 1 1 1 0.997049 0.999 1 2 10353 121256 11568 8650 6612 66661 908 16504 2 10386 121292 11570 8650 6612 66662 908 16504 0 . 0 . 0 61 0,0,3,58 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1357|1435|HFM1|protein_coding|CODING|NM_001017975.4|37|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs585898 -0.693147 0.16205 61 I1033 1435 atA/atC LOW 28 SILENT CODING HFM1 G protein_coding NM_001017975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91781413 T G 0 228 0 0.7489 0.763 0.7233 0.8244 0.6928 0.819 0.729791 0.688106 0.666744 2 7723 85251 7944 7262 4600 43895 654 13173 2 10348 120774 11478 8620 6592 66348 902 16486 0 . 0 . 0 77 0,0,41,27 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I1033|1435|HFM1|protein_coding|CODING|NM_001017975.4|28|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs281992 -0.693147 0.35595 77 Q211 1435 caA/caG LOW 5 SILENT CODING HFM1 C protein_coding NM_001017975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91851253 T C 0 228 0 0.997 0.9992 1 1 1 1 0.997049 0.999 1 2 10361 121235 11542 8650 6606 66664 904 16508 2 10394 121270 11544 8650 6606 66664 904 16508 0 . 0 . 0 94 0,0,54,34 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q211|1435|HFM1|protein_coding|CODING|NM_001017975.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs282026 -0.693147 0.367086 94 I117V 1435 Att/Gtt MODERATE 4 MISSENSE CODING HFM1 C protein_coding NM_001017975.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91859795 T C 0 228 0 0.997 0.9992 1 1 1 1 0.997276 0.999077 1 2 10370 121254 11516 8652 6610 66690 908 16508 2 10402 121288 11518 8652 6610 66690 908 16508 0 . 0 . 0 93 0,0,63,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I117V|1435|HFM1|protein_coding|CODING|NM_001017975.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs282009 -0.693147 0.51569 93 T330 574 acA/acG LOW 9 SILENT CODING CDC7 G protein_coding NM_001134419.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91980447 A G 0 228 0 0.7837 0.769 0.7824 0.7579 0.7942 0.7249 0.771448 0.779179 0.78314 2 8174 94275 9554 6548 4926 51863 692 12518 2 10406 121282 11538 8648 6602 66674 908 16506 0 . 0 . 0 111 0,0,57,42 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T330|574|CDC7|protein_coding|CODING|NM_001134419.1|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386595781,rs483532 -0.693147 0.252423 111 574 453 MODIFIER 12 CODING CDC7 T protein_coding NM_001134419.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 91990444 TAAA T 0 32.2 0 0.2995 0.3377 0.2839 0.4861 0.2664 0.3476 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||453||574|CDC7|protein_coding|CODING|NM_001134419.1|12|T) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs13447559 -0.379885 0 1 851 1069 MODIFIER 17 CODING TGFBR3 G protein_coding NM_003243.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92148227 C G 0 9.7 0 0.8941 0.8421 0.781 0.9821 0.7117 0.8047 0 . 0 1 159 8434 75 131 2 1980 99 5988 2 190 10768 92 132 2 2728 118 7506 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1069||851|TGFBR3|protein_coding|CODING|NM_003243.4|17|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs902 -0.379885 0 1 T749 851 acT/acC LOW 14 SILENT CODING TGFBR3 G protein_coding NM_003243.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92174260 A G 0 228 0 0.9418 0.9067 0.9712 0.7351 0.9433 0.953 0.935315 0.939413 0.941512 2 9760 113353 11233 6686 6426 62705 850 15693 2 10406 121396 11568 8648 6614 66740 908 16512 0 . 0 . 0 118 0,0,54,50 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T749|851|TGFBR3|protein_coding|CODING|NM_003243.4|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs284878 -0.693147 0.00550987 118 P402 851 ccG/ccA LOW 9 SILENT CODING TGFBR3 T protein_coding NM_003243.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92185657 C T 0 188 0 0.2814 0.4062 0.2824 0.5308 0.4592 0.4796 0.317295 0.38167 0.414651 1 3184 50606 3090 4582 3191 29131 382 7046 2 10368 121162 11560 8604 6598 66616 908 16508 0.198683 0 . 0 . 66 12,27,4,17 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P402|851|TGFBR3|protein_coding|CODING|NM_003243.4|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990319 rs1805112 -0.692352 0.0133977 66 A72 851 gcA/gcG LOW 3 SILENT CODING TGFBR3 C protein_coding NM_003243.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92262874 T C 0 222 0 0.7761 0.7153 0.7176 0.7748 0.6322 0.6554 0.750794 0.67861 0.641628 1 7832 80354 7339 6836 4009 42520 619 11199 2 10372 121182 11564 8630 6614 66582 908 16512 0.822298 0 . 0 . 74 30,4,26,8 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A72|851|TGFBR3|protein_coding|CODING|NM_003243.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.606747 rs2810904 -0.693132 0.0922654 74 951 13319 MODIFIER 1 CODING BRDT C protein_coding NM_001242806.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92414993 T C 0 39.3 0 0.4183 0.6396 0.7205 0.6101 0.7952 0.7515 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||13319||951|BRDT|protein_coding|CODING|NM_001242806.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1887812 -0.453602 0.06 2 Q62K 951 Cag/Aag MODERATE 2 MISSENSE CODING BRDT A protein_coding NM_001242806.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92428495 C A 0 228 0 0.6551 0.756 0.8415 0.6141 0.9235 0.8057 0.69882 0.859219 0.941395 2 7203 105769 10316 5214 6299 62392 798 13547 2 10380 120694 11578 8642 6614 66556 896 16028 0 . 0 . 0 69 0,0,9,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q62K|951|BRDT|protein_coding|CODING|NM_001242806.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10783071 -0.693147 0.00943154 69 P700L 951 cCg/cTg MODERATE 14 MISSENSE CODING BRDT T protein_coding NM_001242806.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92457843 C T 0 228 0 0.5908 0.7101 0.7738 0.6081 0.8429 0.7945 0.627553 0.778205 0.855496 2 6324 96866 9739 5161 5881 55664 742 13355 2 9950 118614 11442 8446 6530 65110 894 16242 0 . 0 . 0 165 0,0,95,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P700L|951|BRDT|protein_coding|CODING|NM_001242806.2|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10747493 -0.693147 0.139867 165 K489 1354 aaG/aaA LOW 8 SILENT CODING KIAA1107 A protein_coding NM_015237.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92646021 G A 0 228 0 0.6059 0.7109 0.6066 0.9732 0.6223 0.7474 0 . 0 2 1290 14627 252 603 831 5574 166 5911 2 2152 21714 408 622 1616 8766 244 7906 0 . 0 . 0 67 0,0,30,30 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K489|1354|KIAA1107|protein_coding|CODING|NM_015237.2|8|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1483022 -0.693147 0.727094 67 N890S 1354 aAt/aGt MODERATE 8 MISSENSE CODING KIAA1107 G protein_coding NM_015237.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92647223 A G 0 228 0 0.9713 0.8313 0.6614 0.9752 0.6779 0.772 0.916907 0.751096 0.678931 2 1972 15872 277 602 939 5846 167 6069 2 2108 21486 400 616 1612 8612 238 7900 0 . 0 . 0 144 0,0,52,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N890S|1354|KIAA1107|protein_coding|CODING|NM_015237.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs560389 -0.693147 3.82657e-05 144 T993N 1354 aCt/aAt MODERATE 8 MISSENSE CODING KIAA1107 A protein_coding NM_015237.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92647532 C A 0 228 0 0.9992 0.9956 0.9899 1 0.9861 1 0.998555 0.98664 0.981458 2 2225 21961 409 622 1619 8940 247 7899 2 2228 22142 412 622 1630 9096 250 7904 0 . 0 . 0 93 0,0,56,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T993N|1354|KIAA1107|protein_coding|CODING|NM_015237.2|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs565156 -0.693147 0.123995 93 594 115 MODIFIER 19 CODING GLMN G protein_coding NM_053274.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92711972 C G 0 112 0 0.4599 0.616 0.4856 0.9732 0.4553 0.7168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_3_PRIME(MODIFIER||115||594|GLMN|protein_coding|CODING|NM_053274.2|19|G),DOWNSTREAM(MODIFIER||605||180|C1orf146|protein_coding|CODING|NM_001012425.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2046620 -0.616816 0.878339 6 422 229 MODIFIER 7 CODING GFI1 G protein_coding NM_001127215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92941357 A G 0 142 0 0.8169 0.8083 0.745 0.9613 0.6312 0.8661 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.815018 0 . 0 . 21 9,0,11,1 UTR_3_PRIME(MODIFIER||229||422|GFI1|protein_coding|CODING|NM_001127215.1|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994334 rs4970714 -0.680642 0.543455 21 821 4618 MODIFIER 19 CODING EVI5 A protein_coding NM_001308248.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92974595 G A 0 99 0 0.9508 0.9203 0.8905 0.9752 0.8072 0.9601 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.442128 0 . 0 . 11 4,0,7,0 UTR_3_PRIME(MODIFIER||4618||821|EVI5|protein_coding|CODING|NM_001308248.1|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 0 . 0.964642 rs10782922 -0.636426 0.101802 11 G775 821 ggT/ggC LOW 19 SILENT CODING EVI5 G protein_coding NM_001308248.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 92979354 A G 0 222 0 0.9508 0.9203 0.8905 0.9752 0.8072 0.9601 0.924648 0.838382 0.794186 1 9671 103402 10614 8336 5126 53191 780 15684 2 10404 121368 11568 8654 6610 66716 908 16508 0.998962 0 . 0 . 40 11,7,13,6 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G775|821|EVI5|protein_coding|CODING|NM_001308248.1|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.40082 rs6603979 -0.69168 0.50865 40 Q574 821 caA/caG LOW 15 SILENT CODING EVI5 C protein_coding NM_001308248.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93089823 T C 0 222 0 0.9554 0.9491 0.9395 0.9752 0.9026 0.9683 0.943713 0.913194 0.897558 1 9834 111865 11064 8338 5827 59977 847 15978 2 10404 121384 11568 8654 6614 66730 906 16508 0.925916 0 . 0 . 93 30,17,17,17 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q574|821|EVI5|protein_coding|CODING|NM_001308248.1|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.423411 rs7514716 -0.693132 0.589927 93 I336V 821 Att/Gtt MODERATE 7 MISSENSE CODING EVI5 C protein_coding NM_001308248.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93160902 T C 0 222 0 0.9546 0.9503 0.9452 0.9752 0.9056 0.9683 0.942124 0.912963 0.898023 1 9821 111837 11075 8335 5826 59977 847 15956 2 10406 121354 11578 8652 6614 66706 908 16490 0.76835 0 . 0 . 129 35,32,28,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I336V|821|EVI5|protein_coding|CODING|NM_001308248.1|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.535701 rs2391199 -0.693147 0.587305 129 428 1032 MODIFIER 5 CODING FAM69A A protein_coding NM_001006605.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93307908 T A 0 9.7 0 0.7655 0.8874 0.9063 0.9702 0.8976 0.9427 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1032||428|FAM69A|protein_coding|CODING|NM_001006605.4|5|A),DOWNSTREAM(MODIFIER||427||297|RPL5|protein_coding|CODING|NM_000969.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4240962 -0.379885 0 1 428 142 MODIFIER 5 CODING FAM69A A protein_coding NM_001006605.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93308798 G A 0 225 0 0.9977 0.973 0.9553 0.999 0.9145 0.9857 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 60 0,0,58,0 UTR_3_PRIME(MODIFIER||142||428|FAM69A|protein_coding|CODING|NM_001006605.4|5|A),DOWNSTREAM(MODIFIER||1317||297|RPL5|protein_coding|CODING|NM_000969.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2244588 -0.693147 0.259772 60 428 87 MODIFIER 5 CODING FAM69A A protein_coding NM_001006605.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93308853 C A 0 222 0 0.9909 0.9595 0.9496 0.9752 0.9076 0.9611 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.26136 0 . 0 . 117 42,7,52,6 UTR_3_PRIME(MODIFIER||87||428|FAM69A|protein_coding|CODING|NM_001006605.4|5|A),DOWNSTREAM(MODIFIER||1372||297|RPL5|protein_coding|CODING|NM_000969.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.949475 rs2244496 -0.693147 0.204423 117 C140S 593 tGc/tCc MODERATE 5 MISSENSE CODING MTF2 C protein_coding NM_007358.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93580581 G C 0 228 0 0.997 0.9992 1 1 1 1 0.996142 0.998693 1 2 10357 121301 11558 8654 6606 66712 908 16506 2 10402 121348 11560 8654 6606 66712 908 16506 0 . 0 . 0 74 0,0,43,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tCc|C140S|593|MTF2|protein_coding|CODING|NM_007358.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2815427 -0.693147 0.281113 74 593 600 MODIFIER 15 CODING MTF2 CAT protein_coding NM_007358.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93603183 C CAT 0 182 0 0.9599 0.8458 0.8213 0.7024 0.9115 0.7894 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,11,0,7 UTR_3_PRIME(MODIFIER||600||593|MTF2|protein_coding|CODING|NM_007358.3|15|CAT) 0 0.5 1 7 0.368421 1 1 0 . 0 60 0 0 . 0 . rs3066513 -0.636426 0.252793 19 229 2681 MODIFIER 4 CODING TMED5 C protein_coding NM_016040.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93617546 T C 0 228 0 0.7867 0.8856 0.8862 0.999 0.8091 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,34,1 UTR_3_PRIME(MODIFIER||2681||229|TMED5|protein_coding|CODING|NM_016040.4|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs546 -0.693136 0.257553 37 229 800 MODIFIER 4 CODING TMED5 G protein_coding NM_016040.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93619427 C G 0 58 0 0.1188 0.0405 0.0159 0.0218 0.002 0.0112 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.965069 0 . 0 . 14 9,0,5,0 UTR_3_PRIME(MODIFIER||800||229|TMED5|protein_coding|CODING|NM_016040.4|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.89683 rs75625538 -0.590765 0.345017 14 1454 2486 MODIFIER 1 CODING CCDC18 C protein_coding NM_001306076.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93646433 T C 0 222 0 0.0333 0.1458 0.1599 0.2927 0.0716 0.2127 0.0474074 0.0766694 0.0908115 1 467 15213 3126 2478 486 5357 105 3194 2 8700 114274 11220 8350 6140 62788 822 16254 0.96355 0 . 0 COSM426847 133 26,45,26,25 START_GAINED(LOW||||1454|CCDC18|protein_coding|CODING|NM_001306076.1|1|C),UTR_5_PRIME(MODIFIER||2486||1454|CCDC18|protein_coding|CODING|NM_001306076.1|1|C),UPSTREAM(MODIFIER||187||229|TMED5|protein_coding|CODING|NM_016040.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971897 rs2255722,rs386562741 -0.693147 0.0580327 133 N314 1454 aaC/aaT LOW 9 SILENT CODING CCDC18 T protein_coding NM_001306076.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93672688 C T 0 222 0 0.1974 0.2322 0.2392 0.3175 0.1511 0.2699 0.18465 0.169911 0.163381 1 1781 24542 4206 2649 1121 10130 184 4471 2 8996 111902 10966 8110 6410 61288 846 15286 0.948139 0 . 0 . 115 53,8,37,3 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N314|1454|CCDC18|protein_coding|CODING|NM_001306076.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.663275 rs2783499 -0.693145 0.106241 115 N326T 1454 aAt/aCt MODERATE 9 MISSENSE CODING CCDC18 C protein_coding NM_001306076.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93672723 A C 0 222 0 0.3313 0.748 0.8415 0.9623 0.8052 0.9652 0.42314 0.698543 0.822086 1 3781 98836 10361 8235 5610 54344 752 15753 2 9610 119876 11476 8584 6588 66244 898 16476 0.776768 0 . 0 . 152 57,14,52,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aCt|N326T|1454|CCDC18|protein_coding|CODING|NM_001306076.1|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.260006 rs2815413 -0.693147 0.0886195 152 L1080V 1454 Ctt/Gtt MODERATE 24 MISSENSE CODING CCDC18 G protein_coding NM_001306076.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93720070 C G 0 222 0 0.1974 0.2322 0.2392 0.3175 0.1511 0.2699 0.184268 0.170175 0.163884 1 1841 25282 4395 2741 1143 10425 190 4547 2 9718 119830 11456 8502 6604 66200 894 16456 0.445053 0 . 0 . 108 34,16,30,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Gtt|L1080V|1454|CCDC18|protein_coding|CODING|NM_001306076.1|24|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.430609 rs12030843 -0.693147 0.872543 108 1454 21 MODIFIER 29 CODING CCDC18 A protein_coding NM_001306076.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93744055 G A 0 222 0 0.3321 0.1548 0.1297 0.0218 0.1928 0.0307 0.274103 0.204584 0.173886 1 2965 17835 1005 272 982 11834 134 643 2 9698 117980 11556 8606 6612 65910 876 14722 0.976131 0 . 0 . 156 32,40,30,23 UTR_3_PRIME(MODIFIER||21||1454|CCDC18|protein_coding|CODING|NM_001306076.1|29|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.480067 rs10874767 -0.693147 0.0890668 156 176 406 MODIFIER 3 CODING DR1 T protein_coding NM_001938.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93826602 G T 0 222 0 0.3321 0.0982 0.0317 0.0238 0.003 0.0041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.647924 0 . 0 . 184 41,21,66,32 UTR_3_PRIME(MODIFIER||406||176|DR1|protein_coding|CODING|NM_001938.2|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.9923 rs74104014 -0.693147 0.137284 184 176 1156 MODIFIER 3 CODING DR1 G protein_coding NM_001938.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93827352 A G 0 222 0 0.1286 0.0443 0.0173 0.0268 0.002 0.0112 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.672702 0 . 0 . 141 36,27,40,23 UTR_3_PRIME(MODIFIER||1156||176|DR1|protein_coding|CODING|NM_001938.2|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.786614 rs115794714 -0.693147 0.589018 141 176 1260 MODIFIER 3 CODING DR1 A protein_coding NM_001938.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 93827456 T A 0 228 0 0.8238 0.8958 0.8876 1 0.8091 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 104 0,0,33,63 UTR_3_PRIME(MODIFIER||1260||176|DR1|protein_coding|CODING|NM_001938.2|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs771457 -0.693147 0.702588 104 756 213 MODIFIER 7 CODING DNTTIP2 T protein_coding NM_014597.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94335194 A T 0 133 0 0.5469 0.5363 0.4337 0.621 0.4225 0.6247 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998031 0 . 0 . 30 15,2,12,1 UTR_3_PRIME(MODIFIER||213||756|DNTTIP2|protein_coding|CODING|NM_014597.4|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.951931 rs1051394 -0.683931 0.575716 30 F580 756 ttT/ttC LOW 3 SILENT CODING DNTTIP2 G protein_coding NM_014597.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94341267 A G 0 222 0 0.5378 0.5337 0.4337 0.621 0.4225 0.6237 0.514387 0.455496 0.428973 1 5139 56706 5458 5357 2653 28062 418 9619 2 9722 119274 11356 8538 6560 65786 894 16418 0.692144 0 . 0 . 134 26,35,29,24 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F580|756|DNTTIP2|protein_coding|CODING|NM_014597.4|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.809311 rs2273165 -0.693147 0.027458 134 E309D 756 gaG/gaT MODERATE 2 MISSENSE CODING DNTTIP2 A protein_coding NM_014597.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94342564 C A 0 209 0 0.0817 0.3448 0.33 0.5565 0.325 0.5133 0.138205 0.274526 0.335496 1 1250 42201 4374 4751 1906 21929 308 7683 2 9716 119286 11356 8434 6576 65864 882 16458 0.999213 0 . 0 . 32 10,7,9,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E309D|756|DNTTIP2|protein_coding|CODING|NM_014597.4|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916809 rs3747965 -0.686358 0.760547 32 P156 756 ccT/ccC LOW 2 SILENT CODING DNTTIP2 G protein_coding NM_014597.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94343023 A G 0 222 0 0.3782 0.4369 0.3718 0.5585 0.3499 0.5266 0.380524 0.364434 0.35723 1 3781 47433 4839 4932 2039 23551 336 7955 2 9794 120652 11558 8608 6614 66676 896 16506 0.987282 0 . 0 . 53 22,3,19,5 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P156|756|DNTTIP2|protein_coding|CODING|NM_014597.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947006 rs2391322 -0.692831 0.48759 53 E86 756 gaA/gaG LOW 2 SILENT CODING DNTTIP2 C protein_coding NM_014597.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94343233 T C 0 222 0 0.8094 0.7592 0.8069 0.7857 0.662 0.7301 0.789666 0.725601 0.6958 1 7766 86547 10153 6711 4271 45512 630 11504 2 9798 120714 11576 8620 6610 66706 898 16506 0.96475 0 . 0 . 152 33,27,42,37 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E86|756|DNTTIP2|protein_coding|CODING|NM_014597.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.803621 rs3789457 -0.693147 0.154085 152 756 12 MODIFIER 1 CODING DNTTIP2 T protein_coding NM_014597.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94344716 C T 0 222 0 0.093 0.3482 0.3329 0.5565 0.325 0.5133 0.145478 0.273731 0.333777 1 1359 42898 4494 4846 1913 22265 319 7702 2 9754 119932 11470 8530 6566 66286 898 16428 0.835096 0 . 0 . 175 40,47,30,40 UTR_5_PRIME(MODIFIER||12||756|DNTTIP2|protein_coding|CODING|NM_014597.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.544985 rs2235971 -0.693147 0.575514 175 I2023 2273 atT/atC LOW 44 SILENT CODING ABCA4 G protein_coding NM_000350.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94471075 A G 0 228 0 0.3744 0.77 0.9006 0.8968 0.9394 0.907 0.468225 0.775719 0.933256 2 4654 107973 10897 7689 6328 62485 824 15096 2 10402 121402 11576 8654 6614 66736 908 16512 0 2|2 benign|benign 0 . 102 0,0,48,48 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I2023|2273|ABCA4|protein_coding|CODING|NM_000350.2|44|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1762114 -0.693147 0.0151938 102 H423R 2273 cAc/cGc MODERATE 10 MISSENSE CODING ABCA4 C protein_coding NM_000350.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94544234 T C 0 222 0 0.1316 0.2208 0.3026 0.254 0.2913 0.1769 0.165456 0.260649 0.309419 1 1690 30988 2380 2142 1705 20039 199 2833 2 10406 121400 11576 8646 6614 66738 908 16512 0.717424 255|2 other|benign 0 . 240 71,21,83,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H423R|2273|ABCA4|protein_coding|CODING|NM_000350.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.957308 rs3112831 -0.693147 0.0540547 240 P47 2273 ccA/ccG LOW 2 SILENT CODING ABCA4 C protein_coding NM_000350.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94578548 T C 0 228 0 0.9531 0.987 0.9957 1 1 1 0.963913 0.987698 0.999884 2 9989 120946 11555 8652 6614 66727 907 16502 2 10402 121388 11574 8652 6614 66732 908 16506 0 1,2 not-provided,benign 0 . 81 0,0,41,34 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P47|2273|ABCA4|protein_coding|CODING|NM_000350.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4847281 -0.693147 0.0124754 81 1261 3254 MODIFIER 23 CODING ARHGAP29 C protein_coding NM_004815.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94636171 T C 0 9.7 0 0.0023 0.01857 0.0202 0.0149 0.0447 0.0164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3254||1261|ARHGAP29|protein_coding|CODING|NM_004815.3|23|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs78481476 -0.379885 0 1 1261 88 MODIFIER 23 CODING ARHGAP29 G protein_coding NM_004815.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94639337 A G 0 228 0 0.8986 0.972 0.9928 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 163 0,0,71,74 UTR_3_PRIME(MODIFIER||88||1261|ARHGAP29|protein_coding|CODING|NM_004815.3|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1330858 -0.693147 0.139265 163 G1255D 1261 gGt/gAt MODERATE 23 MISSENSE CODING ARHGAP29 T protein_coding NM_004815.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94639447 C T 0 228 0 0.798 0.9439 0.9827 1 0.998 1 0.836813 0.94418 0.999186 2 8679 119319 11510 8652 6614 66596 902 16366 2 10402 121144 11578 8652 6614 66624 904 16370 0 . 0 . 0 85 0,0,21,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G1255D|1261|ARHGAP29|protein_coding|CODING|NM_004815.3|23|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1999272 -0.693147 0.159136 85 659 100 MODIFIER 23 CODING ABCD3 T protein_coding NM_002858.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94982785 A T 0 214 0 0.2723 0.2831 0.134 0.4077 0.2217 0.3384 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.425913 0 . 0 . 47 3,17,5,14 UTR_3_PRIME(MODIFIER||100||659|ABCD3|protein_coding|CODING|NM_002858.3|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.87363 rs662813 -0.69168 0.219176 47 659 125 MODIFIER 23 CODING ABCD3 G protein_coding NM_002858.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94982810 A G 0 222 0 0.1331 0.11 0.0461 0.1429 0.0666 0.135 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972828 0 . 0 . 44 7,15,8,14 UTR_3_PRIME(MODIFIER||125||659|ABCD3|protein_coding|CODING|NM_002858.3|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999931 rs337592 -0.692562 0.172037 44 659 518 MODIFIER 23 CODING ABCD3 T protein_coding NM_002858.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94983203 C T 0 222 0 0.5938 0.4111 0.1931 0.506 0.2346 0.4029 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969881 0 . 0 . 83 9,26,17,28 UTR_3_PRIME(MODIFIER||518||659|ABCD3|protein_coding|CODING|NM_002858.3|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.493733 rs698951 -0.693147 0.863577 83 295 605 MODIFIER 6 CODING F3 A protein_coding NM_001993.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94995411 C A 0 26.2 0 0.4281 0.4077 0.2522 0.499 0.2843 0.5235 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,2,1,1 UTR_3_PRIME(MODIFIER||605||295|F3|protein_coding|CODING|NM_001993.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs841691 -0.453602 0.8 5 295 525 MODIFIER 6 CODING F3 T protein_coding NM_001993.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94995491 C T 0 129 0 0.5643 0.6138 0.5605 0.7738 0.4901 0.681 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,8,0 UTR_3_PRIME(MODIFIER||525||295|F3|protein_coding|CODING|NM_001993.4|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs841692 -0.651104 0.698141 8 295 431 MODIFIER 6 CODING F3 A protein_coding NM_001993.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94995585 G A 0 89 0 0.1036 0.1935 0.304 0.2569 0.2068 0.1575 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.921243 0 . 0 . 15 7,0,8,0 UTR_3_PRIME(MODIFIER||431||295|F3|protein_coding|CODING|NM_001993.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.87319 rs3917633 -0.651104 0.824003 15 295 197 MODIFIER 6 CODING F3 T protein_coding NM_001993.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 94995819 C T 0 222 0 0.2405 0.3558 0.2378 0.499 0.2833 0.5225 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.340396 0 . 0 . 141 26,47,30,25 UTR_3_PRIME(MODIFIER||197||295|F3|protein_coding|CODING|NM_001993.4|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.898739 rs3354 -0.693147 0.227097 141 P111 295 ccT/ccG LOW 3 SILENT CODING F3 C protein_coding NM_001993.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95001600 A C 0 228 0 0.9365 0.9826 0.9957 1 1 1 0.951884 0.9837 1 2 9818 120800 11557 8654 6614 66738 907 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 76 0,0,30,39 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P111|295|F3|protein_coding|CODING|NM_001993.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs698946 -0.693147 0.50188 76 V438I 653 Gtt/Att MODERATE 11 MISSENSE CODING SLC44A3 A protein_coding NM_001114106.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95330372 G A 0 228 0 0.4841 0.7546 0.8141 0.9831 0.7813 0.8149 0.547662 0.679686 0.747326 2 5615 93497 10215 8491 5297 50467 685 12727 2 10406 121406 11576 8654 6612 66740 908 16510 0 . 0 . 0 139 0,0,78,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V438I|653|SLC44A3|protein_coding|CODING|NM_001114106.2|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs859098 -0.693147 0.100694 139 R472M 653 aGg/aTg MODERATE 12 MISSENSE CODING SLC44A3 T protein_coding NM_001114106.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95332906 G T 0 222 0 0 0.0017971 0 0.0089 0 0 0 . 0 1 0 51 0 51 0 0 0 0 2 10400 120428 11554 8650 6608 66466 904 15846 0.772599 0 . 0 . 137 37,31,30,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aTg|R472M|653|SLC44A3|protein_coding|CODING|NM_001114106.2|12|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.998037 rs181145758 -0.693147 0.362581 137 329 143 MODIFIER 1 CODING CNN3 T protein_coding NM_001839.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95392593 C T 0 197 0 0.0144 0.0839 0.1354 0.1012 0.1441 0.0613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969481 0 . 0 COSN394710 64 4,31,2,26 UTR_5_PRIME(MODIFIER||143||329|CNN3|protein_coding|CODING|NM_001839.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.395285 rs11540278 -0.693054 0.620523 64 263 51221 MODIFIER 1 CODING TMEM56 T protein_coding NM_001199679.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95558237 C T 0 9.7 0 0.441 0.471 0.5908 0.2917 0.5815 0.498 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 START_GAINED(LOW||||263|TMEM56|protein_coding|CODING|NM_001199679.1|1|T),UTR_5_PRIME(MODIFIER||51221||263|TMEM56|protein_coding|CODING|NM_001199679.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs113662180,rs7546710 -0.379885 0 1 V47A 267 gTg/gCg MODERATE 2 MISSENSE CODING RWDD3 C protein_coding NM_015485.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95709821 T C 0 228 0 0.944 0.9846 0.9957 1 1 1 0.956406 0.985995 0.999514 2 9320 120230 11553 8626 6614 66710 898 16509 2 9802 120770 11576 8626 6614 66740 900 16512 0 . 0 . 0 139 0,0,86,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V47A|267|RWDD3|protein_coding|CODING|NM_015485.4|2|C),UTR_3_PRIME(MODIFIER||15||201|TMEM56-RWDD3|protein_coding|CODING|NM_001199691.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs259358 -0.693147 0.0821027 139 201 15 MODIFIER 8 CODING TMEM56-RWDD3 C protein_coding NM_001199691.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95709821 T C 0 228 0 0.944 0.9846 0.9957 1 1 1 0.956406 0.985995 0.999514 2 9320 120230 11553 8626 6614 66710 898 16509 2 9802 120770 11576 8626 6614 66740 900 16512 0 . 0 . 0 139 0,0,86,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V47A|267|RWDD3|protein_coding|CODING|NM_015485.4|2|C),UTR_3_PRIME(MODIFIER||15||201|TMEM56-RWDD3|protein_coding|CODING|NM_001199691.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs259358 -0.693147 0.0821027 139 N86K 267 aaT/aaG MODERATE 2 MISSENSE CODING RWDD3 G protein_coding NM_015485.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95709939 T G 0 228 0 0.6823 0.8173 0.8487 0.8036 0.8728 0.9346 0.722424 0.820053 0.865556 2 6946 103205 9660 6659 5813 57691 806 15630 2 9798 120734 11568 8616 6612 66728 900 16512 1 0 . 0 . 123 1,0,45,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N86K|267|RWDD3|protein_coding|CODING|NM_015485.4|2|G),UTR_3_PRIME(MODIFIER||133||201|TMEM56-RWDD3|protein_coding|CODING|NM_001199691.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2296308 -0.693147 0.018932 123 201 133 MODIFIER 8 CODING TMEM56-RWDD3 G protein_coding NM_001199691.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 95709939 T G 0 228 0 0.6823 0.8173 0.8487 0.8036 0.8728 0.9346 0.722424 0.820053 0.865556 2 6946 103205 9660 6659 5813 57691 806 15630 2 9798 120734 11568 8616 6612 66728 900 16512 1 0 . 0 . 123 1,0,45,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N86K|267|RWDD3|protein_coding|CODING|NM_015485.4|2|G),UTR_3_PRIME(MODIFIER||133||201|TMEM56-RWDD3|protein_coding|CODING|NM_001199691.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2296308 -0.693147 0.018932 123 548 27997 MODIFIER 1 CODING PTBP2 G protein_coding NM_001300987.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 97187174 A G 0 6.3 0 0.6581 0.595 0.4582 0.6131 0.5348 0.6503 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||27997||548|PTBP2|protein_coding|CODING|NM_001300987.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3748784 -0.379885 0 1 L387 548 ttA/ttG LOW 12 SILENT CODING PTBP2 G protein_coding NM_001300987.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 97272456 A G 0 222 0 0.5408 0.278 0.1499 0.2103 0.2117 0.1513 0.497957 0.292019 0.186512 1 5222 25761 1581 1829 1288 12999 184 2658 2 10392 121314 11556 8644 6614 66692 908 16508 0.280217 0 . 0 . 119 44,15,24,18 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L387|548|PTBP2|protein_coding|CODING|NM_001300987.1|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.596631 rs6699932 -0.693146 0.195454 119 548 731 MODIFIER 15 CODING PTBP2 T protein_coding NM_001300987.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 97279692 C T 0 228 0 0.7352 0.6312 0.549 0.6339 0.5358 0.6442 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 178 0,0,87,71 UTR_3_PRIME(MODIFIER||731||548|PTBP2|protein_coding|CODING|NM_001300987.1|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs273885 -0.693147 0.041835 178 A683 1025 gcC/gcG LOW 16 SILENT CODING DPYD C protein_coding NM_000110.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 97839126 G C 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 28 0 27 0 0 0 1 2 10262 120414 11474 8566 6534 66272 902 16404 0.679387 1 not-provided 0 . 62 20,5,29,4 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A683|1025|DPYD|protein_coding|CODING|NM_000110.3|16|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.598805 rs183475941 -0.693127 0.279398 62 R29C 1025 Cgt/Tgt MODERATE 2 MISSENSE CODING DPYD A protein_coding NM_000110.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 98348885 G A 0 228 0 0.5582 0.7398 0.7752 0.9137 0.7853 0.7342 0.600318 0.7159 0.775116 2 6072 92673 9119 7969 4639 51864 701 12309 2 10404 121114 11502 8608 6594 66592 906 16508 0 5,1 pathogenic,not-provided 0 . 111 0,0,57,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R29C|1025|DPYD|protein_coding|CODING|NM_000110.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1801265 -0.693147 0.102768 111 S35 451 agT/agC LOW 1 SILENT CODING SNX7 C protein_coding NM_015976.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 99127392 T C 0 228 0 0.9841 0.9954 0.9971 1 1 1 0 . 0 2 1392 6750 290 410 28 4184 54 392 2 1406 6764 290 410 28 4184 54 392 0 . 0 . 0 24 0,0,22,1 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S35|451|SNX7|protein_coding|CODING|NM_015976.4|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs9728148 -0.692717 0.751436 24 S123T 451 Tct/Act MODERATE 3 MISSENSE CODING SNX7 A protein_coding NM_015976.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 99156634 T A 0 222 0 0.0083 0.0905 0.0793 0.3264 0.008 0.0511 0.0138448 0.0130709 0.0126744 1 153 6665 1758 3059 145 821 41 688 2 10286 119704 11372 8578 6574 65790 882 16222 0.993731 0 . 0 . 79 27,13,21,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Act|S123T|451|SNX7|protein_coding|CODING|NM_015976.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991477 rs35296149 -0.693054 0.192908 79 E432 451 gaG/gaA LOW 9 SILENT CODING SNX7 A protein_coding NM_015976.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 99225627 G A 0 222 0 0.8661 0.8754 0.9078 0.6657 0.9871 0.9663 0.901498 0.957789 0.986628 1 9278 113484 9613 5520 6429 65734 862 16048 2 10398 121010 11412 8552 6600 66636 906 16506 0.957504 0 . 0 . 119 38,11,39,14 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E432|451|SNX7|protein_coding|CODING|NM_015976.4|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.816738 rs2019213,rs386552824 -0.693147 0.106232 119 321 270 MODIFIER 6 CODING PLPPR5 T protein_coding NM_001037317.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 99358358 G T 0 174 0 0.3722 0.5671 0.5965 0.747 0.6392 0.5501 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,9,2 UTR_3_PRIME(MODIFIER||270||321|PLPPR5|protein_coding|CODING|NM_001037317.1|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386625262,rs984271 -0.676189 0.688637 11 Q251 626 caG/caA LOW 7 SILENT CODING FRRS1 T protein_coding NM_001013660.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100203648 C T 0 222 0 0.9402 0.5583 0.4928 0.3909 0.3082 0.5184 0.835225 0.507074 0.338953 1 8932 51113 6054 3369 1772 21934 380 8672 2 10404 120748 11574 8638 6612 66478 900 16142 0.974021 0 . 0 . 58 15,13,14,10 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q251|626|FRRS1|protein_coding|CODING|NM_001013660.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998948 rs7537296 -0.692831 0.455708 58 S236 626 agC/agT LOW 7 SILENT CODING FRRS1 A protein_coding NM_001013660.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100203693 G A 0 222 0 0.9402 0.5583 0.4928 0.3909 0.3082 0.5184 0.835225 0.507074 0.338953 1 8925 51177 6054 3372 1772 21949 385 8720 2 10394 121300 11576 8636 6614 66666 908 16506 0.776672 0 . 0 . 65 13,18,17,14 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S236|626|FRRS1|protein_coding|CODING|NM_001013660.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.301451 rs7514021 -0.69311 0.727623 65 626 163 MODIFIER 2 CODING FRRS1 T protein_coding NM_001013660.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100214487 C T 0 80 0 0.9402 0.5587 0.4942 0.3909 0.3082 0.5194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 1,4,0,6 UTR_5_PRIME(MODIFIER||163||626|FRRS1|protein_coding|CODING|NM_001013660.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.564628 rs1416236 -0.616816 0.348672 11 1532 10 MODIFIER 2 CODING AGL G protein_coding NM_000028.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100316589 A G 0 228 0 0.2231 0.4271 0.4726 0.5198 0.4573 0.544 0.277349 0.415731 0.486628 2 2697 56824 5117 4616 2891 32227 421 8855 2 10252 121250 11578 8650 6614 66736 908 16512 0 2 benign 0 . 76 0,0,49,23 START_GAINED(LOW||||1532|AGL|protein_coding|CODING|NM_000028.2|2|G),UTR_5_PRIME(MODIFIER||10||1532|AGL|protein_coding|CODING|NM_000028.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2307130 -0.693147 0.0535861 76 L298 1532 ctC/ctT LOW 7 SILENT CODING AGL T protein_coding NM_000028.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100336361 C T 0 228 0 0.9334 0.7626 0.7017 0.6835 0.6759 0.7454 0.908272 0.767106 0.695749 2 8970 86850 7973 5879 4486 46544 634 12364 2 9810 120390 11554 8632 6602 66388 906 16498 0 2 benign 0 . 201 0,0,144,35 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L298|1532|AGL|protein_coding|CODING|NM_000028.2|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2230306 -0.693147 0.852992 201 R387Q 1532 cGa/cAa MODERATE 9 MISSENSE CODING AGL A protein_coding NM_000028.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100340787 G A 0 222 0 0.0023 0.0797 0.111 0.1766 0.005 0.1391 0.00317748 0.00238352 0.00197674 1 37 5734 2048 1533 69 183 32 1832 2 9954 120552 11522 8626 6608 66472 902 16468 0.926598 2 benign 0 . 80 31,9,21,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R387Q|1532|AGL|protein_coding|CODING|NM_000028.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.270917 rs17121464 -0.693132 0.680192 80 1532 LOW 15 CODING AGL C protein_coding NM_000028.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100346741 T C 0 228 0 0.4206 0.5585 0.6095 0.6796 0.5338 0.6094 0.437585 0.504152 0.538256 2 4487 66849 7285 5744 3377 35726 486 9744 2 10396 121168 11494 8640 6600 66630 906 16502 1 0 . 0 . 77 0,1,19,53 SPLICE_SITE_REGION+INTRON(LOW||||1532|AGL|protein_coding|CODING|NM_000028.2|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3736296 -0.693147 0.00114917 77 1532 272 MODIFIER 34 CODING AGL T protein_coding NM_000028.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100387479 G T 0 30.7 0 0.0651 0.3321 0.5 0.5496 0.3698 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_3_PRIME(MODIFIER||272||1532|AGL|protein_coding|CODING|NM_000028.2|34|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1804808 -0.511536 0.988818 4 490 229 MODIFIER 12 CODING MFSD14A C protein_coding NM_033055.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100547994 T C 0 222 0 0.0658 0.352 0.5576 0.5833 0.3897 0.316 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.903196 0 . 0 . 58 7,21,12,18 UTR_3_PRIME(MODIFIER||229||490|MFSD14A|protein_coding|CODING|NM_033055.2|12|C),DOWNSTREAM(MODIFIER||1107||657|SASS6|protein_coding|CODING|NM_194292.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.961534 rs5876 -0.693097 0.568121 58 A259V 657 gCg/gTg MODERATE 8 MISSENSE CODING SASS6 A protein_coding NM_194292.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100575933 G A 0 222 0 0.0658 0.3502 0.5562 0.5813 0.3867 0.3129 0.130731 0.306474 0.396512 1 1183 48326 7543 5057 2761 26159 359 5264 2 10332 120988 11514 8628 6592 66524 902 16496 0.934939 0 . 0 . 67 17,16,14,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A259V|657|SASS6|protein_coding|CODING|NM_194292.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977857 rs13375867 -0.693079 0.254117 67 A48T 481 Gcg/Acg MODERATE 1 MISSENSE CODING TRMT13 A protein_coding NM_019083.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100598866 G A 0 228 0 0.3752 0.7564 0.8905 0.9286 0.8519 0.9008 0.45665 0.713748 0.845465 2 4557 100836 10650 8189 5790 56154 764 14732 2 10206 120014 11412 8564 6512 65976 888 16456 0 . 0 . 0 93 0,0,29,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A48T|481|TRMT13|protein_coding|CODING|NM_019083.2|1|A),UPSTREAM(MODIFIER||215||657|SASS6|protein_coding|CODING|NM_194292.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs472498 -0.693147 0.01303 93 A48V 481 gCg/gTg MODERATE 1 MISSENSE CODING TRMT13 T protein_coding NM_019083.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100598867 C T 0 228 0 0.3752 0.7564 0.8905 0.9286 0.8519 0.9008 0.455969 0.713286 0.845116 2 4557 100825 10652 8187 5784 56150 766 14729 2 10202 119994 11414 8562 6506 65968 890 16452 0 . 0 . 0 93 0,0,29,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A48V|481|TRMT13|protein_coding|CODING|NM_019083.2|1|T),UPSTREAM(MODIFIER||216||657|SASS6|protein_coding|CODING|NM_194292.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs687513 -0.693147 0.01303 93 482 5546 MODIFIER 11 CODING DBT T protein_coding NM_001918.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100656265 C T 0 6.3 0 0.5151 0.8007 0.9107 0.9296 0.8757 0.8988 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5546||482|DBT|protein_coding|CODING|NM_001918.3|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs111175244,rs11166412 -0.379885 0 1 S384G 482 Agt/Ggt MODERATE 9 MISSENSE CODING DBT C protein_coding NM_001918.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100672060 T C 0 228 0 0.7443 0.8918 0.9481 0.9494 0.9215 0.9611 0.774852 0.859219 0.902442 2 7952 110942 11147 8397 6176 60704 845 15721 2 10406 121412 11578 8654 6614 66740 908 16512 0 5,255 pathogenic,other 0 . 83 0,0,44,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S384G|482|DBT|protein_coding|CODING|NM_001918.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12021720 -0.693147 0.0819943 83 379 112 MODIFIER 1 CODING RTCA CA protein_coding NM_001130841.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100731819 C CA 0 228 0 0.0015 0.00079872 0 0.001 0.001 0 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,17,3 UTR_5_PRIME(MODIFIER||112||379|RTCA|protein_coding|CODING|NM_001130841.1|1|CA) 0 . 0 19 0.95 1 1 0 . 0 60 0 0 1 0 . rs57195277 -0.692067 0.447401 20 379 111 MODIFIER 1 CODING RTCA GA protein_coding NM_001130841.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100731820 G GA 0 149 0 0.0008 0.00059904 0 0 0 0.002 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,17,3 UTR_5_PRIME(MODIFIER||111||379|RTCA|protein_coding|CODING|NM_001130841.1|1|GA) 0 . 0 1 0.05 1 1 0 . 0 60 0 0 1 0 . rs11406239 -0.692067 0.452943 20 379 703 MODIFIER 12 CODING RTCA C protein_coding NM_001130841.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100757763 T C 0 31.3 0 0.503 0.7903 0.8847 0.9345 0.8748 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||703||379|RTCA|protein_coding|CODING|NM_001130841.1|12|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6704125 -0.453602 0.6 2 623 333 MODIFIER 1 CODING CDC14A C protein_coding NM_033312.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100818178 G C 0 9.7 0 0.2027 0.3732 0.4193 0.4762 0.3767 0.4611 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||333||623|CDC14A|protein_coding|CODING|NM_033312.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs529224 -0.379885 0 1 623 225 MODIFIER 1 CODING CDC14A T protein_coding NM_033312.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100818286 A T 0 144 0 0.6029 0.8171 0.8602 0.9276 0.9105 0.8661 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,10,0 UTR_5_PRIME(MODIFIER||225||623|CDC14A|protein_coding|CODING|NM_033312.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs527644 -0.670168 0.185182 10 623 47 MODIFIER 1 CODING CDC14A C protein_coding NM_033312.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 100818464 T C 0 228 0 1 0.9834 0.9712 0.9812 0.9801 0.9755 0.995915 0.984469 0.978605 2 10297 118391 11147 8500 6393 65176 883 15995 2 10340 120994 11518 8648 6562 66522 904 16500 0 . 0 . 0 93 0,0,53,28 UTR_5_PRIME(MODIFIER||47||623|CDC14A|protein_coding|CODING|NM_033312.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs594529 -0.693147 0.0348251 93 384 761 MODIFIER 1 CODING GPR88 A protein_coding NM_022049.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101003762 C A 0 77 0 0.2118 0.496 0.6369 0.6835 0.493 0.59 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_5_PRIME(MODIFIER||761||384|GPR88|protein_coding|CODING|NM_022049.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2809823 -0.511536 0.0822145 3 384 513 MODIFIER 1 CODING GPR88 T protein_coding NM_022049.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101004010 C T 0 9.7 0 0.9607 0.9892 0.9971 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 START_GAINED(LOW||||384|GPR88|protein_coding|CODING|NM_022049.2|1|T),UTR_5_PRIME(MODIFIER||513||384|GPR88|protein_coding|CODING|NM_022049.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2809822 -0.379885 0 1 V190I 384 Gtc/Atc MODERATE 2 MISSENSE CODING GPR88 A protein_coding NM_022049.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101005090 G A 0 92 0 0.1445 0.4832 0.6412 0.6915 0.5129 0.5838 0.167458 0.359383 0.444405 2 91 7586 327 279 124 2587 82 4096 2 282 12672 412 346 178 4134 120 7200 0 . 0 . 0 4 0,0,2,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V190I|384|GPR88|protein_coding|CODING|NM_022049.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2809819 -0.556411 0.265379 4 384 178 MODIFIER 2 CODING GPR88 C protein_coding NM_022049.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101005855 T C 0 228 0 0.4092 0.7528 0.8718 0.8155 0.9145 0.9018 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,24,21 UTR_3_PRIME(MODIFIER||178||384|GPR88|protein_coding|CODING|NM_022049.2|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2809818 -0.693147 0.244124 53 384 900 MODIFIER 2 CODING GPR88 G protein_coding NM_022049.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101006577 A G 0 228 0 0.0998 0.3948 0.5389 0.6042 0.3608 0.5102 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 48 1,0,23,21 UTR_3_PRIME(MODIFIER||900||384|GPR88|protein_coding|CODING|NM_022049.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2030048 -0.693146 0.131365 48 384 1359 MODIFIER 2 CODING GPR88 C protein_coding NM_022049.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101007036 T C 0 222 0 0.0121 0.1571 0.2046 0.1111 0.1958 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.973216 0 . 0 . 54 10,14,14,12 UTR_3_PRIME(MODIFIER||1359||384|GPR88|protein_coding|CODING|NM_022049.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998305 rs2809817 -0.692976 0.305899 54 384 1378 MODIFIER 2 CODING GPR88 T protein_coding NM_022049.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101007055 C T 0 228 0 0.4614 0.7634 0.8761 0.8006 0.9145 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.836735 0 . 0 . 52 0,2,22,27 UTR_3_PRIME(MODIFIER||1378||384|GPR88|protein_coding|CODING|NM_022049.2|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.510204 rs2030049 -0.693147 0.840656 52 K736 739 aaG/aaA LOW 9 SILENT CODING VCAM1 A protein_coding NM_001078.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101203827 G A 0 228 0 0.6929 0.8712 0.9625 0.8512 0.9702 0.9663 0.720381 0.884574 0.968714 2 7376 113770 11189 7186 6404 64823 867 15925 2 10396 121366 11576 8652 6614 66716 908 16504 0 . 0 . 0 109 0,0,48,56 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K736|739|VCAM1|protein_coding|CODING|NM_001078.3|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3176879 -0.693147 0.235677 109 739 656 MODIFIER 9 CODING VCAM1 A protein_coding NM_001078.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101204495 C A 0 39.3 0 0.0204 0.0739 0.0389 0.125 0.0298 0.1636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||656||739|VCAM1|protein_coding|CODING|NM_001078.3|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3783621 -0.453602 0.74 2 338 1174 MODIFIER 6 CODING EXTL2 C protein_coding NM_001261441.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101338324 T C 0 56 0 0.3903 0.4798 0.4841 0.381 0.5905 0.5859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.597928 0 . 0 . 14 0,10,1,2 UTR_3_PRIME(MODIFIER||1174||338|EXTL2|protein_coding|CODING|NM_001261441.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.699673 rs8888 -0.511536 0.868052 14 338 1016 MODIFIER 6 CODING EXTL2 G protein_coding NM_001261441.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 101338482 A G 0 9.7 0 0.2284 0.4345 0.4683 0.3968 0.5895 0.5685 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1016||338|EXTL2|protein_coding|CODING|NM_001261441.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3188491 -0.379885 0 1 1818 1183 MODIFIER 67 CODING COL11A1 C protein_coding NM_080629.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 103342392 T C 0 222 0 0.1672 0.2244 0.2277 0.247 0.1809 0.3211 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999042 0 . 0 . 39 4,15,5,14 UTR_3_PRIME(MODIFIER||1183||1818|COL11A1|protein_coding|CODING|NM_080629.2|67|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.757967 rs9659030 -0.69168 0.702791 39 I1602 1818 atT/atC LOW 63 SILENT CODING COL11A1 G protein_coding NM_080629.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 103352451 A G 0 222 0 0.0499 0.4846 0.7478 0.6647 0.6064 0.5746 0.139582 0.448408 0.606628 1 1314 70409 8681 5567 4311 40490 565 9481 2 10402 121364 11562 8638 6610 66734 908 16510 0.525513 0 . 0 . 136 34,34,22,33 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I1602|1818|COL11A1|protein_coding|CODING|NM_080629.2|63|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.479061 rs2229783 -0.693147 0.245838 136 S1547P 1818 Tct/Cct MODERATE 62 MISSENSE CODING COL11A1 G protein_coding NM_080629.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 103354138 A G 0 222 0 0.8048 0.7829 0.8948 0.748 0.83 0.6616 0.798684 0.807012 0.811279 1 8348 96088 10077 6300 5693 53847 751 11072 2 10302 120994 11476 8626 6594 66580 906 16510 0.98414 255 other 0 . 118 30,21,39,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S1547P|1818|COL11A1|protein_coding|CODING|NM_080629.2|62|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.196331 rs1676486 -0.693147 0.294204 118 G1516 1818 ggT/ggC LOW 60 SILENT CODING COL11A1 G protein_coding NM_080629.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 103354428 A G 0 222 0 0.2587 0.6226 0.8401 0.746 0.8042 0.6462 0.319791 0.622943 0.778256 1 3222 87776 9613 6263 5363 51900 699 10716 2 10352 121260 11524 8638 6614 66716 908 16508 0.650798 0 . 0 COSM423330,COSM423331 152 41,30,32,30 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1516|1818|COL11A1|protein_coding|CODING|NM_080629.2|60|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.560687 rs1763347 -0.693147 0.0758432 152 P1335L 1818 cCt/cTt MODERATE 52 MISSENSE CODING COL11A1 A protein_coding NM_080629.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 103379918 G A 0 222 0 0.0492 0.4966 0.755 0.7034 0.6123 0.5859 0.139582 0.451715 0.611628 1 1271 70874 8696 5941 4397 40226 577 9766 2 10058 119810 11416 8620 6560 65798 898 16460 0.903775 0 . 0 . 120 26,27,19,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P1335L|1818|COL11A1|protein_coding|CODING|NM_080629.2|52|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997098 rs3753841 -0.693145 0.136394 120 375 404 MODIFIER 1 CODING PRMT6 A protein_coding NM_018137.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 107600869 G A 0 222 0 0.0098 0.133 0.1427 0.1498 0.2097 0.1963 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.565957 0 . 0 . 101 29,24,22,18 UTR_3_PRIME(MODIFIER||404||375|PRMT6|protein_coding|CODING|NM_018137.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0815949 rs3791185 -0.693145 0.621973 101 G455 539 ggA/ggC LOW 6 SILENT CODING NTNG1 C protein_coding NM_001113226.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 107979396 A C 0 228 0 0.8185 0.9503 0.987 1 1 1 0.85236 0.95466 0.999442 2 8191 118344 11415 8518 6610 66213 892 16505 2 9752 120048 11508 8518 6610 66252 898 16510 0 . 0 . 0 245 0,0,91,127 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G455|539|NTNG1|protein_coding|CODING|NM_001113226.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs480392 -0.693147 0.00654047 245 539 1406 MODIFIER 7 CODING NTNG1 T protein_coding NM_001113226.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 108024868 C T 0 9.7 0 0.2436 0.3728 0.3718 0.5675 0.3946 0.3252 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1406||539|NTNG1|protein_coding|CODING|NM_001113226.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs597332 -0.379885 0 1 847 808 MODIFIER 27 CODING VAV3 C protein_coding NM_006113.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 108115145 T C 0 228 0 0.7769 0.9097 0.9452 0.998 0.9384 0.9438 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 43 0,0,38,3 UTR_3_PRIME(MODIFIER||808||847|VAV3|protein_coding|CODING|NM_006113.4|27|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2769668 -0.693145 0.124083 43 K216 847 aaG/aaA LOW 6 SILENT CODING VAV3 T protein_coding NM_006113.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 108313258 C T 0 228 0 0.6876 0.6709 0.6196 0.6776 0.7753 0.5706 0.708314 0.759695 0.786013 2 7298 88263 7183 5815 5320 52279 628 9740 2 10370 121264 11576 8646 6614 66646 906 16506 0 . 0 . 0 86 0,0,38,38 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K216|847|VAV3|protein_coding|CODING|NM_006113.4|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6583048 -0.693147 0.0669174 86 R224L 733 cGg/cTg MODERATE 5 MISSENSE CODING FNDC7 T protein_coding NM_001144937.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109265029 G T 0 228 0 0.2496 0.5787 0.6657 0.8621 0.6044 0.6431 0.310486 0.505767 0.605814 2 3043 73525 8040 7573 4314 40165 526 9864 2 10396 121280 11560 8646 6600 66672 908 16498 0 . 0 . 0 123 0,0,58,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R224L|733|FNDC7|protein_coding|CODING|NM_001144937.1|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4423040 -0.693147 0.0207398 123 S309N 733 aGt/aAt MODERATE 6 MISSENSE CODING FNDC7 A protein_coding NM_001144937.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109268441 G A 0 222 0 0.3215 0.1695 0.0865 0.0992 0.1412 0.1247 0.296868 0.2006 0.151279 1 3183 17935 788 823 1420 9634 135 1952 2 10404 121386 11574 8646 6612 66734 906 16510 0.683078 0 . 0 COSM146569 216 73,33,58,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S309N|733|FNDC7|protein_coding|CODING|NM_001144937.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981687 rs11582005 -0.693147 0.0588373 216 V353A 733 gTc/gCc MODERATE 6 MISSENSE CODING FNDC7 C protein_coding NM_001144937.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109268573 T C 0 222 0 0.7958 0.5929 0.5346 0.2341 0.7127 0.6063 0.790059 0.73912 0.713023 1 8263 79158 6183 2032 4500 47405 588 10187 2 10406 121396 11576 8652 6610 66734 908 16510 0.41451 0 . 0 . 219 72,43,49,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V353A|733|FNDC7|protein_coding|CODING|NM_001144937.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.250329 rs4494160 -0.693147 0.320243 219 G595 733 ggA/ggG LOW 9 SILENT CODING FNDC7 G protein_coding NM_001144937.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109273456 A G 0 222 0 0.5628 0.4503 0.4352 0.2014 0.5388 0.4744 0.561734 0.550592 0.544884 1 5965 59875 5277 1804 3290 35484 439 7616 2 10406 121340 11560 8628 6606 66722 908 16510 0.731232 0 . 0 . 189 45,58,29,44 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G595|733|FNDC7|protein_coding|CODING|NM_001144937.1|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939654 rs4970809 -0.693147 0.465125 189 592 7 MODIFIER 1 CODING STXBP3 G protein_coding NM_007269.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109289353 C G 0 222 0 0.7012 0.5731 0.5173 0.2232 0.7416 0.6268 0.725969 0.772093 0.796097 1 1864 14197 260 154 27 6622 124 5146 2 2664 20730 430 660 44 8816 196 7920 0.960648 0 . 0 . 87 40,7,22,7 UTR_5_PRIME(MODIFIER||7||592|STXBP3|protein_coding|CODING|NM_007269.2|1|G),DOWNSTREAM(MODIFIER||3986||733|FNDC7|protein_coding|CODING|NM_001144937.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948207 rs1124427 -0.693079 0.617504 87 L372 592 ctG/ctC LOW 14 SILENT CODING STXBP3 C protein_coding NM_007269.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109338861 G C 0 222 0 0.2731 0.3295 0.3213 0.1925 0.4334 0.4458 0.302996 0.396202 0.443953 1 3036 47709 4043 1725 2693 28929 354 6929 2 10274 120838 11544 8620 6598 66454 906 16442 0.773054 0 . 0 . 185 57,33,52,21 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L372|592|STXBP3|protein_coding|CODING|NM_007269.2|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.648261 rs1127635 -0.693147 0.204449 185 592 2 MODIFIER 19 CODING STXBP3 G protein_coding NM_007269.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109351501 A G 0 222 0 0.2315 0.4073 0.4741 0.7768 0.2575 0.3712 0.247844 0.237044 0.231512 1 2594 38639 5517 6654 1801 15919 276 5878 2 10240 121088 11560 8644 6612 66622 906 16504 0.737652 0 . 0 . 119 30,18,37,18 UTR_3_PRIME(MODIFIER||2||592|STXBP3|protein_coding|CODING|NM_007269.2|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.92067 rs1149154 -0.693147 0.326781 119 K728 836 aaA/aaG LOW 14 SILENT CODING AKNAD1 C protein_coding NM_152763.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109363232 T C 0 222 0 0.2617 0.3864 0.3919 0.6974 0.2565 0.364 0.275987 0.245963 0.230581 1 2950 37610 4830 6049 1821 15841 275 5844 2 10322 121146 11560 8640 6612 66616 908 16488 0.868377 0 . 0 . 68 8,20,9,22 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K728|836|AKNAD1|protein_coding|CODING|NM_152763.4|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.559473 rs1333130 -0.69311 0.00284232 68 C654Y 836 tGt/tAt MODERATE 12 MISSENSE CODING AKNAD1 T protein_coding NM_152763.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109366286 C T 0 222 0 0.0598 0.1657 0.1787 0.1121 0.2873 0.2301 0.107581 0.244503 0.314651 1 1080 30995 1964 1037 2045 20828 238 3803 2 10402 121384 11572 8652 6610 66732 908 16508 0.685489 0 . 0 COSM146570 51 8,14,5,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C654Y|836|AKNAD1|protein_coding|CODING|NM_152763.4|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.763545 rs7522157 -0.692976 0.0133247 51 N616K 836 aaC/aaA MODERATE 11 MISSENSE CODING AKNAD1 T protein_coding NM_152763.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109369915 G T 0 222 0 0.6331 0.5032 0.5288 0.2649 0.5805 0.4755 0.635951 0.614965 0.60421 1 6557 66841 5639 2321 3254 40137 507 8426 2 10394 121168 11548 8568 6612 66658 904 16484 0.844049 0 . 0 COSM146571 102 21,27,13,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N616K|836|AKNAD1|protein_coding|CODING|NM_152763.4|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988263 rs7551421 -0.693146 0.205085 102 S61N 836 aGt/aAt MODERATE 2 MISSENSE CODING AKNAD1 T protein_coding NM_152763.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109395105 C T 0 228 0 0.8797 0.867 0.879 0.9395 0.7903 0.8456 0.866319 0.833231 0.816279 2 9071 101031 9957 8116 5445 54024 735 13683 2 10404 121368 11578 8650 6614 66718 908 16496 0 . 0 . 0 128 0,0,68,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S61N|836|AKNAD1|protein_coding|CODING|NM_152763.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1277207 -0.693147 0.261694 128 684 211 MODIFIER 15 CODING GPSM2 A protein_coding NM_013296.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109472773 G A 0 222 0 0.3707 0.3682 0.3775 0.3681 0.3658 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.776457 0 . 0 . 238 59,46,54,38 UTR_3_PRIME(MODIFIER||211||684|GPSM2|protein_coding|CODING|NM_013296.4|15|A),UTR_3_PRIME(MODIFIER||4519||551|CLCC1|protein_coding|CODING|NM_001048210.2|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992648 rs1051868 -0.693147 0.0780679 238 551 4519 MODIFIER 12 CODING CLCC1 A protein_coding NM_001048210.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109472773 G A 0 222 0 0.3707 0.3682 0.3775 0.3681 0.3658 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.776457 0 . 0 . 238 59,46,54,38 UTR_3_PRIME(MODIFIER||211||684|GPSM2|protein_coding|CODING|NM_013296.4|15|A),UTR_3_PRIME(MODIFIER||4519||551|CLCC1|protein_coding|CODING|NM_001048210.2|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992648 rs1051868 -0.693147 0.0780679 238 684 251 MODIFIER 15 CODING GPSM2 C protein_coding NM_013296.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109472813 T C 0 222 0 0.1089 0.2095 0.2695 0.3442 0.2137 0.1595 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.892315 0 . 0 . 216 34,65,34,48 UTR_3_PRIME(MODIFIER||251||684|GPSM2|protein_coding|CODING|NM_013296.4|15|C),UTR_3_PRIME(MODIFIER||4479||551|CLCC1|protein_coding|CODING|NM_001048210.2|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.648619 rs12030 -0.693147 0.00628442 216 551 4479 MODIFIER 12 CODING CLCC1 C protein_coding NM_001048210.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109472813 T C 0 222 0 0.1089 0.2095 0.2695 0.3442 0.2137 0.1595 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.892315 0 . 0 . 216 34,65,34,48 UTR_3_PRIME(MODIFIER||251||684|GPSM2|protein_coding|CODING|NM_013296.4|15|C),UTR_3_PRIME(MODIFIER||4479||551|CLCC1|protein_coding|CODING|NM_001048210.2|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.648619 rs12030 -0.693147 0.00628442 216 T201 551 acT/acC LOW 6 SILENT CODING CLCC1 G protein_coding NM_001048210.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109486196 A G 0 222 0 0.7579 0.5383 0.5101 0.3958 0.5219 0.4254 0.725828 0.594802 0.527674 1 7539 64084 6458 3504 3188 35361 492 7542 2 10386 121214 11564 8636 6568 66658 906 16496 0.839544 0 . 0 . 217 45,68,44,43 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T201|551|CLCC1|protein_coding|CODING|NM_001048210.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841376 rs338466 -0.693147 0.113317 217 927 555 MODIFIER 15 CODING WDR47 T protein_coding NM_001142550.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109513497 C T 0 222 0 0.8775 0.8141 0.7435 0.7837 0.7922 0.8323 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.740489 0 . 0 . 25 1,8,3,12 UTR_3_PRIME(MODIFIER||555||927|WDR47|protein_coding|CODING|NM_001142550.1|15|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0936263 rs507776 -0.688148 0.0183137 25 74 108 MODIFIER 3 CODING TMEM167B G protein_coding NM_020141.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109637229 C G 0 222 0 0.267 0.1673 0.0951 0.0308 0.173 0.2188 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98689 0 . 0 . 57 8,23,3,19 UTR_3_PRIME(MODIFIER||108||74|TMEM167B|protein_coding|CODING|NM_020141.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.760433 rs551001 -0.692562 0.00284423 57 157 121 MODIFIER 1 CODING C1orf194 C protein_coding NM_001122961.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109656420 T C 0 222 0 0.7504 0.5371 0.4841 0.4821 0.3718 0.5133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.777086 0 . 0 . 149 22,39,20,40 UTR_5_PRIME(MODIFIER||121||157|C1orf194|protein_coding|CODING|NM_001122961.1|1|C),UPSTREAM(MODIFIER||165||1013|KIAA1324|protein_coding|CODING|NM_020775.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.109757 rs536176 -0.693147 0.000522708 149 H47 1013 caT/caC LOW 1 SILENT CODING KIAA1324 C protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109656946 T C 0 222 0 0.7511 0.5371 0.4841 0.4812 0.3718 0.5133 0.6734 0.465077 0.358273 1 5339 37597 3790 3233 1404 17349 226 6256 2 7418 74482 6504 6090 2792 39070 500 12108 0.688419 0 . 0 . 152 35,28,28,34 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H47|1013|KIAA1324|protein_coding|CODING|NM_020775.4|1|C),UPSTREAM(MODIFIER||467||157|C1orf194|protein_coding|CODING|NM_001122961.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.860529 rs667524 -0.693147 0.00989885 152 I86V 1013 Atc/Gtc MODERATE 2 MISSENSE CODING KIAA1324 G protein_coding NM_020775.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109704618 A G 0 228 0 0.9849 0.9956 0.9986 0.999 1 1 0.986836 0.995464 0.999884 2 10136 120433 11544 8600 6608 66165 900 16480 2 10272 120590 11550 8612 6608 66168 900 16480 1 0 . 0 . 43 0,1,15,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I86V|1013|KIAA1324|protein_coding|CODING|NM_020775.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs678238 -0.693145 0.497039 43 G583 1013 ggT/ggC LOW 14 SILENT CODING KIAA1324 C protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109735298 T C 0 228 0 0.3593 0.7416 0.8055 0.999 0.7565 0.9325 0.411938 0.636475 0.751512 2 4296 95073 10155 8647 5564 50678 727 15006 2 10394 121384 11576 8654 6614 66728 908 16510 0 . 0 . 0 69 0,0,24,37 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G583|1013|KIAA1324|protein_coding|CODING|NM_020775.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs658779 -0.693147 0.153867 69 T623P 1013 Act/Cct MODERATE 14 MISSENSE CODING KIAA1324 C protein_coding NM_020775.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109735416 A C 0 228 0 0.3593 0.74 0.8055 0.998 0.7565 0.9254 0.411938 0.636322 0.751279 2 4286 94935 10147 8628 5564 50639 725 14946 2 10356 121258 11564 8650 6614 66672 906 16496 1 0 . 0 . 45 1,0,27,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T623P|1013|KIAA1324|protein_coding|CODING|NM_020775.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs659543 -0.693146 0.0672265 45 1013 LOW 14 CODING KIAA1324 C protein_coding NM_020775.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109735504 T C 0 228 0 0.3593 0.7414 0.8055 0.998 0.7565 0.9325 0.412165 0.636552 0.751512 2 4293 94982 10154 8628 5564 50633 723 14987 2 10388 121224 11572 8650 6612 66626 902 16474 1 0 . 0 . 80 0,1,38,28 SPLICE_SITE_REGION+INTRON(LOW||||1013|KIAA1324|protein_coding|CODING|NM_020775.4|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs659659 -0.693147 0.0342748 80 N656 1013 aaC/aaT LOW 15 SILENT CODING KIAA1324 T protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109737063 C T 0 228 0 0.3033 0.7137 0.7968 0.9702 0.7634 0.8937 0.368361 0.626634 0.758954 2 3825 94340 10142 8421 5593 51197 723 14439 2 10400 121386 11576 8654 6614 66726 908 16508 0 . 0 . 0 101 0,0,58,29 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N656|1013|KIAA1324|protein_coding|CODING|NM_020775.4|15|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2359246,rs386565601 -0.693147 0.592664 101 P665 1013 ccG/ccA LOW 15 SILENT CODING KIAA1324 A protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109737090 G A 0 228 0 0.3101 0.7153 0.7954 0.9702 0.7634 0.8937 0.371312 0.627403 0.758605 2 3840 94352 10139 8419 5593 51207 719 14435 2 10404 121402 11578 8654 6614 66734 906 16512 0 . 0 . 0 102 0,0,45,44 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P665|1013|KIAA1324|protein_coding|CODING|NM_020775.4|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2359245,rs386565600 -0.693147 0.0496997 102 T679 1013 acT/acC LOW 15 SILENT CODING KIAA1324 C protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109737132 T C 0 228 0 0.4667 0.7666 0.8127 0.9702 0.7654 0.9305 0.48729 0.667999 0.760581 2 5115 96479 10221 8421 5591 51331 727 15073 2 10404 121394 11578 8654 6612 66728 906 16512 0 . 0 . 0 96 0,0,34,53 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T679|1013|KIAA1324|protein_coding|CODING|NM_020775.4|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2359244,rs386565599 -0.693147 0.342044 96 L693 1013 Ctg/Ttg LOW 15 SILENT CODING KIAA1324 T protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109737172 C T 0 228 0 0.3048 0.7141 0.7968 0.9702 0.7634 0.8937 0.368588 0.626711 0.758954 2 3826 94341 10143 8419 5593 51200 721 14439 2 10396 121382 11576 8652 6614 66724 908 16512 0 . 0 . 0 73 0,0,28,37 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L693|1013|KIAA1324|protein_coding|CODING|NM_020775.4|15|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2359243,rs386565598 -0.693147 0.166226 73 S837 1013 tcG/tcA LOW 19 SILENT CODING KIAA1324 A protein_coding NM_020775.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109742485 G A 0 228 0 0.4713 0.7588 0.8055 0.9593 0.7893 0.8763 0.5202 0.700984 0.793605 2 5358 97328 9985 8368 5646 52903 732 14336 2 10386 121300 11568 8648 6610 66672 908 16508 0 . 0 . 0 70 0,0,55,12 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S837|1013|KIAA1324|protein_coding|CODING|NM_020775.4|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs913179 -0.693147 0.450395 70 L1009P 1013 cTa/cCa MODERATE 22 MISSENSE CODING KIAA1324 C protein_coding NM_020775.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109745618 T C 0 228 0 0.7761 0.8904 0.9049 0.9593 0.8996 0.954 0.755334 0.852914 0.902907 2 7971 109914 10742 8375 6221 59997 820 15788 2 10402 121366 11578 8650 6614 66708 908 16506 0 . 0 . 0 63 0,0,27,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L1009P|1013|KIAA1324|protein_coding|CODING|NM_020775.4|22|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1052878 -0.693147 0.82843 63 1013 2913 MODIFIER 22 CODING KIAA1324 T protein_coding NM_020775.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109748547 C T 0 9.7 0 0.7776 0.891 0.9049 0.9603 0.8996 0.954 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2913||1013|KIAA1324|protein_coding|CODING|NM_020775.4|22|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4970827 -0.379885 0 1 1013 3437 MODIFIER 22 CODING KIAA1324 C protein_coding NM_020775.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109749071 T C 0 9.7 0 0.7776 0.8888 0.9049 0.9494 0.8996 0.954 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3437||1013|KIAA1324|protein_coding|CODING|NM_020775.4|22|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3197233 -0.379885 0 1 1013 3461 MODIFIER 22 CODING KIAA1324 G protein_coding NM_020775.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109749095 A G 0 9.7 0 0.1573 0.2452 0.2709 0.4286 0.1829 0.2209 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3461||1013|KIAA1324|protein_coding|CODING|NM_020775.4|22|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3814307 -0.379885 0 1 S517 2923 agT/agC LOW 1 SILENT CODING CELSR2 C protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109794252 T C 0 228 0 0.7186 0.902 0.9625 0.997 0.9672 0.9417 0.778257 0.9002 0.962674 2 7886 114902 11307 8648 6301 64264 879 15617 2 10406 121390 11576 8654 6614 66722 906 16512 0 . 0 . 0 82 0,0,39,40 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S517|2923|CELSR2|protein_coding|CODING|NM_001408.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs454107 -0.693147 0.501162 82 Y775 2923 taT/taC LOW 1 SILENT CODING CELSR2 C protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109795026 T C 0 228 0 0.7194 0.902 0.9611 0.997 0.9672 0.9417 0.77803 0.900123 0.962674 2 7851 114597 11291 8634 6301 64022 877 15621 2 10360 121064 11564 8640 6614 66472 904 16510 0 . 0 . 0 104 0,0,73,27 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y775|2923|CELSR2|protein_coding|CODING|NM_001408.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs413380 -0.693147 0.371685 104 F969 2923 ttT/ttC LOW 1 SILENT CODING CELSR2 C protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109795608 T C 0 228 0 0.7648 0.9143 0.9654 0.997 0.9662 0.9417 0.817749 0.913501 0.962558 2 8336 115014 11318 8646 6301 64082 876 15455 2 10402 121002 11574 8652 6614 66532 904 16324 0 . 0 . 0 97 0,0,42,49 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F969|2923|CELSR2|protein_coding|CODING|NM_001408.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs437444 -0.693147 0.383881 97 P1712 2923 ccC/ccT LOW 10 SILENT CODING CELSR2 T protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109806834 C T 0 222 0 0.0764 0.3534 0.4654 0.498 0.4751 0.3742 0.133227 0.353914 0.466977 1 1270 51744 5927 4044 2876 30629 426 6572 2 9994 120012 11528 8584 6580 65934 890 16502 0.820746 0 . 0 . 99 23,17,32,21 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1712|2923|CELSR2|protein_coding|CODING|NM_001408.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952968 rs6698843 -0.693147 0.00168372 99 P1771 2923 ccG/ccA LOW 11 SILENT CODING CELSR2 A protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109807099 G A 0 222 0 0.0764 0.353 0.4654 0.497 0.4751 0.3732 0.132093 0.352683 0.465698 1 1280 51914 5916 4035 2880 30808 430 6565 2 10368 121136 11554 8584 6606 66612 908 16504 0.882714 0 . 0 COSM1178398 74 22,6,29,9 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1771|2923|CELSR2|protein_coding|CODING|NM_001408.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.792961 rs6689614 -0.693143 0.947707 74 G2876 2923 ggA/ggC LOW 33 SILENT CODING CELSR2 C protein_coding NM_001408.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109816176 A C 0 135 0 0.8926 0.9698 0.987 1 1 1 0.9264 0.97516 0.9994 2 3741 56547 5129 3412 1872 31013 456 10924 2 4082 56916 5146 3412 1872 31018 458 10928 0 . 0 . 0 6 0,0,3,3 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G2876|2923|CELSR2|protein_coding|CODING|NM_001408.2|33|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.861511 0 . rs441853 -0.616816 0.275478 6 2923 521 MODIFIER 34 CODING CELSR2 G protein_coding NM_001408.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109817192 A G 0 222 0 0.2663 0.2009 0.2046 0.0437 0.2127 0.2597 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.637061 0 . 0 . 98 37,18,28,8 UTR_3_PRIME(MODIFIER||521||2923|CELSR2|protein_coding|CODING|NM_001408.2|34|G),DOWNSTREAM(MODIFIER||4984||333|PSRC1|protein_coding|CODING|NM_001032291.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976274 rs7528419 -0.693139 0.66179 98 2923 574 MODIFIER 34 CODING CELSR2 T protein_coding NM_001408.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109817245 C T 0 222 0 0.177 0.6088 0.6816 0.9534 0.665 0.728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.827347 0 . 0 . 137 34,17,45,32 UTR_3_PRIME(MODIFIER||574||2923|CELSR2|protein_coding|CODING|NM_001408.2|34|T),DOWNSTREAM(MODIFIER||4931||333|PSRC1|protein_coding|CODING|NM_001032291.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.857336 rs11102967 -0.693147 0.229794 137 2923 808 MODIFIER 34 CODING CELSR2 C protein_coding NM_001408.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109817479 G C 0 222 0 0.2216 0.137 0.1787 0.0109 0.1501 0.1094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.914829 0 . 0 . 95 25,26,24,11 UTR_3_PRIME(MODIFIER||808||2923|CELSR2|protein_coding|CODING|NM_001408.2|34|C),DOWNSTREAM(MODIFIER||4697||333|PSRC1|protein_coding|CODING|NM_001032291.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.507476 rs1277917 -0.693136 0.586667 95 2923 919 MODIFIER 34 CODING CELSR2 T protein_coding NM_001408.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109817590 G T 0 222 0 0.2474 0.1955 0.2046 0.0427 0.2127 0.2587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.764498 255 other 0 . 116 36,15,34,17 UTR_3_PRIME(MODIFIER||919||2923|CELSR2|protein_coding|CODING|NM_001408.2|34|T),DOWNSTREAM(MODIFIER||4586||333|PSRC1|protein_coding|CODING|NM_001032291.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.777522 rs12740374 -0.693147 0.352123 116 2923 1167 MODIFIER 34 CODING CELSR2 C protein_coding NM_001408.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109817838 T C 0 7.9 0 0.6127 0.7692 0.7896 0.9563 0.8012 0.7403 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,0,2 UTR_3_PRIME(MODIFIER||1167||2923|CELSR2|protein_coding|CODING|NM_001408.2|34|C),DOWNSTREAM(MODIFIER||4338||333|PSRC1|protein_coding|CODING|NM_001032291.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs660240 -0.453602 0.42 3 N170 333 aaC/aaT LOW 4 SILENT CODING PSRC1 A protein_coding NM_001032291.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109824250 G A 0 222 0 0.0166 0.0427 0.0303 0.0308 0.0835 0.0573 0.0261008 0.0575208 0.0736218 1 242 7987 234 315 881 5464 63 788 2 9816 116690 11540 8606 6614 64522 876 14716 0.940301 0 . 0 . 91 27,13,33,10 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N170|333|PSRC1|protein_coding|CODING|NM_001032291.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.123312 rs35358959 -0.693146 0.308942 91 333 HIGH 1 CODING PSRC1 T protein_coding NM_001032291.2 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109825360 C T 0 228 0 0.8979 0.971 0.9856 1 1 1 0.921628 0.971122 0.999567 2 2731 24076 497 744 1676 10221 260 7947 2 2984 24338 500 744 1676 10222 260 7952 0 . 0 . 0 62 0,0,21,39 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||333|PSRC1|protein_coding|CODING|NM_001032291.2|1|T) 1 0 . 0 . 1 0 1 1 (PSRC1|PSRC1|1|1.00) 60 0 0 1 0 . rs643457 -0.693147 0.153841 62 354 19 MODIFIER 8 CODING MYBPHL G protein_coding NM_001010985.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109836842 C G 0 228 0 0.4531 0.5228 0.5879 0.5357 0.6074 0.4703 0.473218 0.573274 0.624535 2 4929 71100 7257 4689 4031 41313 567 8314 2 10402 121280 11556 8632 6608 66672 908 16502 0.910569 0 . 0 . 146 1,1,56,67 UTR_3_PRIME(MODIFIER||19||354|MYBPHL|protein_coding|CODING|NM_001010985.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.898374 rs646335 -0.693147 0.201141 146 D269N 354 Gac/Aac MODERATE 6 MISSENSE CODING MYBPHL T protein_coding NM_001010985.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109838918 C T 0 228 0 0.6558 0.8746 0.9452 1 0.9284 0.9356 0.71448 0.859988 0.934535 2 7256 111931 11125 8653 6365 62033 856 15643 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 121 0,0,59,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D269N|354|MYBPHL|protein_coding|CODING|NM_001010985.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs629001 -0.693147 0.145939 121 354 LOW 5 CODING MYBPHL T protein_coding NM_001010985.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109839400 C T 0 222 0 0.1188 0.0651 0.0346 0.0278 0.0805 0.0368 0.0953246 0.0832693 0.077093 1 1006 8158 274 278 617 5361 51 571 2 10406 121402 11578 8654 6608 66736 908 16512 0.956933 0 . 0 . 161 62,19,48,13 SPLICE_SITE_REGION+INTRON(LOW||||354|MYBPHL|protein_coding|CODING|NM_001010985.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.345018 rs55660224 -0.693147 0.0551014 161 T234 354 acT/acC LOW 5 SILENT CODING MYBPHL G protein_coding NM_001010985.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109839433 A G 0 228 0 0.733 0.9253 0.9697 1 1 1 0.778938 0.924189 0.998605 2 7923 118734 11471 8654 6614 66667 899 16506 2 10402 121408 11578 8654 6614 66740 908 16512 0 . 0 . 0 190 0,0,115,47 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T234|354|MYBPHL|protein_coding|CODING|NM_001010985.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1278285 -0.693147 0.00335048 190 831 1261 MODIFIER 20 CODING SORT1 A protein_coding NM_002959.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109855404 G A 0 198 0 0.5734 0.7444 0.8429 0.9563 0.7137 0.7188 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,1,13 UTR_3_PRIME(MODIFIER||1261||831|SORT1|protein_coding|CODING|NM_002959.6|20|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs461200 -0.686358 0.863595 14 831 359 MODIFIER 20 CODING SORT1 A protein_coding NM_002959.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109856306 G A 0 104 0 0.1036 0.4291 0.5562 0.6329 0.5388 0.456 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.640533 0 . 0 . 29 0,18,0,11 UTR_3_PRIME(MODIFIER||359||831|SORT1|protein_coding|CODING|NM_002959.6|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.937399 rs464218 -0.676189 0.206418 29 T323 831 acA/acC LOW 9 SILENT CODING SORT1 G protein_coding NM_002959.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109884775 T G 0 228 0 0.3593 0.6855 0.8271 0.9563 0.7127 0.7188 0.419882 0.62302 0.727093 2 4268 88355 10200 8298 4661 48274 703 11951 2 10358 121200 11562 8634 6598 66638 906 16504 0 . 0 . 0 134 0,0,47,63 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T323|831|SORT1|protein_coding|CODING|NM_002959.6|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2228604,rs386564431 -0.693147 0.0388935 134 F198 831 ttT/ttC LOW 5 SILENT CODING SORT1 G protein_coding NM_002959.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 109897103 A G 0 228 0 0.6884 0.7764 0.853 0.9563 0.7147 0.7188 0.668407 0.707673 0.727791 2 7074 91428 10323 8316 4666 48376 714 11959 2 10404 121380 11574 8652 6614 66718 908 16510 0 . 0 . COSM1332444 114 0,0,51,55 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F198|831|SORT1|protein_coding|CODING|NM_002959.6|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11142 -0.693147 0.363437 114 272 360 MODIFIER 1 CODING SYPL2 G protein_coding NM_001040709.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110009106 C G 0 54 0 0.031 0.3774 0.4986 0.622 0.4632 0.4192 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,1 UTR_5_PRIME(MODIFIER||360||272|SYPL2|protein_coding|CODING|NM_001040709.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs4970764 -0.453602 0.38 4 272 295 MODIFIER 1 CODING SYPL2 T protein_coding NM_001040709.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110009171 C T 0 9.7 0 0.5325 0.7272 0.8372 0.9573 0.6899 0.7137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||295||272|SYPL2|protein_coding|CODING|NM_001040709.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386423624,rs4970765 -0.379885 0 1 272 32 MODIFIER 1 CODING SYPL2 C protein_coding NM_001040709.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110009434 A C 0 113 0 0.5991 0.7476 0.8487 0.9633 0.6899 0.7137 0 . 0 2 127 7674 75 110 0 2128 93 5141 2 206 10438 94 118 0 2874 118 7028 0 . 0 . 0 5 0,0,2,3 UTR_5_PRIME(MODIFIER||32||272|SYPL2|protein_coding|CODING|NM_001040709.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2787015,rs386481909 -0.590765 0.116872 5 S269 451 tcG/tcA LOW 2 SILENT CODING GPR61 A protein_coding NM_031936.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110086451 G A 0 222 0 0.1142 0.2169 0.1441 0.3621 0.171 0.3047 0.117847 0.170178 0.196977 1 1192 25102 2110 3068 1321 12686 194 4531 2 9862 120448 11538 8576 6598 66474 904 16496 0.732614 0 . 0 . 48 16,6,18,7 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S269|451|GPR61|protein_coding|CODING|NM_031936.4|2|A),UPSTREAM(MODIFIER||4735||354|GNAI3|protein_coding|CODING|NM_006496.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979698 rs17575798 -0.692914 0.0206213 48 354 72 MODIFIER 1 CODING GNAI3 T protein_coding NM_006496.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110091271 C T 0 222 0 0.1415 0.227 0.147 0.3661 0.172 0.3129 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999668 0 . 0 . 104 50,3,41,2 UTR_5_PRIME(MODIFIER||72||354|GNAI3|protein_coding|CODING|NM_006496.3|1|T),DOWNSTREAM(MODIFIER||2816||451|GPR61|protein_coding|CODING|NM_031936.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.408974 rs3737182 -0.693146 0.316047 104 354 453 MODIFIER 9 CODING GNAI3 A protein_coding NM_006496.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110135308 G A 0 222 0 0.1407 0.2228 0.1513 0.3373 0.169 0.3221 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.423244 0 . 0 . 123 30,32,29,23 UTR_3_PRIME(MODIFIER||453||354|GNAI3|protein_coding|CODING|NM_006496.3|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.460173 rs111155096,rs7371 -0.693147 0.00566333 123 354 1603 MODIFIER 9 CODING GNAI3 G protein_coding NM_006496.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110136458 A G 0 222 0 0.174 0.4427 0.5951 0.6389 0.5278 0.408 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.693254 0 . 0 . 94 35,10,18,23 UTR_3_PRIME(MODIFIER||1603||354|GNAI3|protein_coding|CODING|NM_006496.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.986597 rs2301230 -0.693145 0.358784 94 354 1823 MODIFIER 9 CODING GNAI3 T protein_coding NM_006496.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110136678 C T 0 222 0 0.1687 0.2324 0.1556 0.3383 0.17 0.3282 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.964617 0 . 0 . 78 10,32,7,23 UTR_3_PRIME(MODIFIER||1823||354|GNAI3|protein_coding|CODING|NM_006496.3|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.665571 rs2301229,rs386502532 -0.693097 0.144251 78 354 3254 MODIFIER 9 CODING GNAI3 T protein_coding NM_006496.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110138109 C T 0 46.3 0 0.5242 0.3405 0.1859 0.3393 0.1759 0.3722 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3254||354|GNAI3|protein_coding|CODING|NM_006496.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11810577 -0.453602 0.32 2 T182 354 acG/acA LOW 5 SILENT CODING GNAT2 T protein_coding NM_005272.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110148974 C T 0 222 0 0.056 0.3786 0.5375 0.626 0.4602 0.363 0.112347 0.330617 0.442442 1 1069 54513 7335 5535 3326 30208 425 6615 2 10406 121398 11574 8650 6614 66734 908 16512 0.48237 0 . 0 . 234 57,49,41,55 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T182|354|GNAT2|protein_coding|CODING|NM_005272.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986464 rs1799875,rs386545556 -0.693147 0.0300896 234 L107I 354 Ctc/Atc MODERATE 4 MISSENSE CODING GNAT2 T protein_coding NM_005272.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110151395 G T 0 222 0 0.0015 0.0887 0.0303 0.244 0.0348 0.1431 0.00476623 0.0171459 0.0234884 1 57 6077 336 1972 256 1509 50 1897 2 10394 121212 11532 8636 6600 66658 906 16486 0.905352 0 . 0 . 95 18,38,8,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Atc|L107I|354|GNAT2|protein_coding|CODING|NM_005272.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.292877 rs3738766 -0.693127 0.109692 95 879 1088 MODIFIER 1 CODING AMPD2 T protein_coding NM_001257360.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110162548 C T 0 110 0 0.3056 0.2292 0.0778 0.3026 0.0825 0.3088 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.962269 0 . 0 . 12 3,0,9,0 START_GAINED(LOW||||879|AMPD2|protein_coding|CODING|NM_001257360.1|1|T),UTR_5_PRIME(MODIFIER||1088||879|AMPD2|protein_coding|CODING|NM_001257360.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.382304 rs55646629 -0.662043 0.219793 12 A82T 879 Gca/Aca MODERATE 2 MISSENSE CODING AMPD2 A protein_coding NM_001257360.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110163879 G A 0 86 0 0.3343 0.2362 0.0793 0.3095 0.0785 0.3016 0.274216 0.129253 0.0550512 1 2645 13562 704 2527 290 3274 112 4010 2 8424 100864 9870 7998 4468 54614 728 14762 0.939743 0 . 0 . 35 3,20,0,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A82T|879|AMPD2|protein_coding|CODING|NM_001257360.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996936 rs28362581 -0.670168 0.317028 35 H478 879 caT/caC LOW 11 SILENT CODING AMPD2 C protein_coding NM_001257360.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110170896 T C 0 228 0 0.7337 0.8077 0.7695 0.9802 0.6769 0.8916 0.756015 0.684223 0.647442 2 7844 89072 9152 8494 4759 43949 695 14179 2 10400 121130 11548 8650 6598 66548 906 16480 0 . 0 . 0 77 0,0,35,35 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H478|879|AMPD2|protein_coding|CODING|NM_001257360.1|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs863978 -0.693147 0.153982 77 218 285 MODIFIER 1 CODING GSTM4 G protein_coding NM_000850.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110198727 C G 0 41.4 0 0.2519 0.4213 0.5937 0.6389 0.4095 0.316 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 7 4,0,3,0 UTR_5_PRIME(MODIFIER||285||218|GSTM4|protein_coding|CODING|NM_000850.4|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.607698 rs1010167 -0.511536 0.0681597 7 F178 218 ttT/ttC LOW 7 SILENT CODING GSTM4 C protein_coding NM_000850.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110201699 T C 0 228 0 0.5681 0.8053 0.8732 0.9702 0.8598 0.8517 0.613709 0.785462 0.873516 2 6304 104384 10705 8448 5827 57943 793 14364 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 296 0,0,147,134 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F178|218|GSTM4|protein_coding|CODING|NM_000850.4|7|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.289014 0 . rs506008 -0.693147 0.0167633 296 218 LOW 1 CODING GSTM2 G protein_coding NM_000848.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110210780 C G 0 228 0 0.8949 0.9048 0.938 0.9702 0.8976 0.8344 0.896278 0.911733 0.919651 2 9186 109626 11114 8420 5706 60201 815 14184 2 10208 120582 11554 8622 6610 66188 900 16500 0 . 0 . 0 37 0,0,6,30 SPLICE_SITE_REGION+INTRON(LOW||||218|GSTM2|protein_coding|CODING|NM_000848.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs530021 -0.693139 1.22727e-05 37 225 2290 MODIFIER 9 CODING GSTM3 C protein_coding NM_000849.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110277403 T C 0 9.7 0 0.0635 0.3662 0.4092 0.7341 0.2992 0.4346 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2290||225|GSTM3|protein_coding|CODING|NM_000849.4|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3814309 -0.379885 0 1 225 1744 MODIFIER 9 CODING GSTM3 C protein_coding NM_000849.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110277949 T C 0 9.7 0 0.907 0.7598 0.67 0.8651 0.5596 0.7219 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1744||225|GSTM3|protein_coding|CODING|NM_000849.4|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1109138 -0.379885 0 1 V224I 225 Gta/Ata MODERATE 9 MISSENSE CODING GSTM3 T protein_coding NM_000849.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110279701 C T 0 228 0 0.0628 0.3606 0.4035 0.7252 0.2962 0.4233 0.111893 0.233969 0.296512 2 1036 41425 5265 6372 1952 19480 302 7018 2 10400 121314 11566 8636 6612 66692 908 16500 0 . 0 . 0 85 0,0,61,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V224I|225|GSTM3|protein_coding|CODING|NM_000849.4|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386610559,rs7483 -0.693147 0.158575 85 225 63 MODIFIER 2 CODING GSTM3 T protein_coding NM_000849.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110282972 G T 0 228 0 0.8638 0.7414 0.6556 0.8611 0.5507 0.7096 0.820809 0.649146 0.574481 2 5696 53488 5122 4723 2327 26030 379 9211 2 6752 79140 7272 5514 3858 42490 596 12658 0 . 0 . 0 95 0,0,27,58 UTR_5_PRIME(MODIFIER||63||225|GSTM3|protein_coding|CODING|NM_000849.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1332018 -0.693147 0.118846 95 594 157 MODIFIER 19 CODING EPS8L3 C protein_coding NM_139053.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110292856 G C 0 228 0 0.0182 0.3478 0.3919 0.744 0.3002 0.4029 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 66 0,0,53,9 UTR_3_PRIME(MODIFIER||157||594|EPS8L3|protein_coding|CODING|NM_139053.2|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs15864 -0.693147 3.40449e-05 66 S390 594 tcA/tcG LOW 13 SILENT CODING EPS8L3 C protein_coding NM_139053.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110295772 T C 0 228 0 0.9123 0.7702 0.6816 0.8601 0.5795 0.7444 0.865638 0.689297 0.598953 2 9132 80006 7742 7255 3728 39879 542 11728 2 10402 120972 11568 8648 6594 66620 906 16234 0 . 0 . 0 67 0,0,34,28 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S390|594|EPS8L3|protein_coding|CODING|NM_139053.2|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1887547 -0.693147 0.00450596 67 H294Y 594 Cac/Tac MODERATE 10 MISSENSE CODING EPS8L3 A protein_coding NM_139053.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110300441 G A 0 228 0 0.1596 0.4732 0.4366 0.7907 0.4712 0.5982 0.232183 0.403429 0.491163 2 2240 58767 4890 6719 2685 32374 415 9444 2 10382 121338 11574 8642 6610 66716 904 16510 0 . 0 . 0 20 0,0,14,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H294Y|594|EPS8L3|protein_coding|CODING|NM_139053.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3818562 -0.692067 0.135025 20 594 2098 MODIFIER 1 CODING EPS8L3 G protein_coding NM_139053.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110306469 C G 0 222 0 0.0961 0.1755 0.1499 0.2302 0.2087 0.2106 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999315 0 . 0 . 343 81,67,80,77 UTR_5_PRIME(MODIFIER||2098||594|EPS8L3|protein_coding|CODING|NM_139053.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.896132 rs878605 -0.693147 0.0415133 343 594 2160 MODIFIER 1 CODING EPS8L3 G protein_coding NM_139053.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110306531 A G 0 222 0 0.0983 0.1775 0.1513 0.2302 0.2127 0.2127 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.774074 0 . 0 . 284 42,81,38,83 UTR_5_PRIME(MODIFIER||2160||594|EPS8L3|protein_coding|CODING|NM_139053.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.844488 rs943641 -0.693147 9.89701e-09 284 T365 554 acC/acA LOW 6 SILENT CODING CSF1 A protein_coding NM_000757.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110466338 C A 0 222 0 0.1067 0.4301 0.5749 0.4018 0.6213 0.5971 0.19133 0.464632 0.604651 1 1894 67287 7100 3722 4233 40024 528 9786 2 10370 120734 11562 8624 6610 66492 896 16180 0.225785 0 . 0 . 109 24,23,26,24 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T365|554|CSF1|protein_coding|CODING|NM_000757.5|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97448 rs333970 -0.693147 0.23282 109 L408P 554 cTg/cCg MODERATE 6 MISSENSE CODING CSF1 C protein_coding NM_000757.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110466466 T C 0 228 0 0.4554 0.4215 0.3271 0.5972 0.336 0.3497 0.440309 0.39551 0.372558 2 4518 46030 3831 5065 1801 24588 322 5905 2 10306 120642 11570 8622 6610 66282 896 16356 0 . 0 . 0 92 0,0,41,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L408P|554|CSF1|protein_coding|CODING|NM_000757.5|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058885 -0.693147 0.237279 92 F489S 554 tTc/tCc MODERATE 6 MISSENSE CODING CSF1 C protein_coding NM_000757.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110466709 T C 0 228 0 0.9887 0.9968 0.9986 1 1 1 0.990695 0.996848 1 2 10280 121103 11566 8638 6614 66592 901 16512 2 10382 121210 11568 8638 6614 66594 902 16512 0 . 0 . 0 83 0,0,49,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F489S|554|CSF1|protein_coding|CODING|NM_000757.5|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs333971 -0.693147 0.195948 83 R523 554 Cgg/Agg LOW 6 SILENT CODING CSF1 A protein_coding NM_000757.5 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110466810 C A 0 222 0 0.4259 0.3165 0.2176 0.5268 0.1362 0.2076 0.386301 0.236472 0.159771 1 3658 25538 2748 4315 1091 10054 167 3505 2 9038 109282 11090 8376 6272 60568 802 13136 0.181462 0 . 0 . 116 19,31,28,22 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R523|554|CSF1|protein_coding|CODING|NM_000757.5|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874885 rs2229166 -0.693147 0.00809541 116 554 4917 MODIFIER 9 CODING CSF1 G protein_coding NM_000757.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110472728 A G 0 63 0 0.9894 0.9972 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||4917||554|CSF1|protein_coding|CODING|NM_000757.5|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs333946 -0.453602 0.06 3 530 222 MODIFIER 1 CODING AHCYL1 GC protein_coding NM_006621.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110527452 G GC 0 45.3 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||222||530|AHCYL1|protein_coding|CODING|NM_006621.5|1|GC) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs11424431 -0.453602 0.26 2 343 69 MODIFIER 4 CODING ALX3 G protein_coding NM_006492.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110603286 A G 0 167 0 0.0015 0.0013978 0 0.003 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0239507 0 . 0 . 38 18,1,11,3 UTR_3_PRIME(MODIFIER||69||343|ALX3|protein_coding|CODING|NM_006492.2|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 8.0062e-06 rs4520416 -0.686358 4.63377e-08 38 727 16105 MODIFIER 1 CODING SLC6A17 C protein_coding NM_001010898.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110693447 T C 0 23 0 0.9054 0.8458 0.6052 0.9048 0.8012 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_5_PRIME(MODIFIER||16105||727|SLC6A17|protein_coding|CODING|NM_001010898.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7538131 -0.453602 0.76 3 S527 727 tcG/tcA LOW 10 SILENT CODING SLC6A17 A protein_coding NM_001010898.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110738296 G A 0 222 0 0.0439 0.2897 0.3847 0.3016 0.4543 0.3732 0.114616 0.3676 0.497209 1 1038 50220 3612 2368 3385 32963 375 6479 2 10394 121270 11564 8610 6606 66682 904 16510 0.891671 0 . 0 COSM146574 84 22,17,29,9 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S527|727|SLC6A17|protein_coding|CODING|NM_001010898.2|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94009 rs2784140 -0.693143 0.106014 84 727 517 MODIFIER 12 CODING SLC6A17 G protein_coding NM_001010898.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110741583 C G 0 9.7 0 0.792 0.5447 0.5115 0.3492 0.5746 0.4049 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||517||727|SLC6A17|protein_coding|CODING|NM_001010898.2|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2784141 -0.379885 0 1 727 1926 MODIFIER 12 CODING SLC6A17 G protein_coding NM_001010898.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110742992 T G 0 9.7 0 0.1203 0.3079 0.3963 0.3026 0.4543 0.3538 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1926||727|SLC6A17|protein_coding|CODING|NM_001010898.2|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2784142 -0.379885 0 1 635 70 MODIFIER 1 CODING KCNC4 T protein_coding NM_004978.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110754052 A T 0 222 0 0.3903 0.124 0.0288 0.0308 0.0298 0.0245 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.226501 0 . 0 . 57 23,9,16,7 UTR_5_PRIME(MODIFIER||70||635|KCNC4|protein_coding|CODING|NM_004978.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.7398 rs114915950 -0.692717 0.765839 57 C520Y 635 tGc/tAc MODERATE 2 MISSENSE CODING KCNC4 A protein_coding NM_004978.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110766466 G A 0 222 0 0.152 0.0749 0.0447 0.0893 0.0328 0.0204 0.126192 0.0484392 0.00860465 1 1374 4360 779 877 182 730 33 385 2 10318 117812 11550 8628 6598 65770 866 14082 0.852055 0 . 0 . 131 24,38,24,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C520Y|635|KCNC4|protein_coding|CODING|NM_004978.4|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.410837 rs12411176 -0.693147 0.0850845 131 635 264 MODIFIER 4 CODING KCNC4 T protein_coding NM_004978.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110775195 C T 0 26.4 0 0.1604 0.098 0.0793 0.1131 0.0149 0.0971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979382 0 . 0 . 11 1,7,0,3 UTR_3_PRIME(MODIFIER||264||635|KCNC4|protein_coding|CODING|NM_004978.4|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.829029 rs17025562,rs386541925 -0.511536 0.82085 11 E139 977 gaA/gaG LOW 1 SILENT CODING RBM15 G protein_coding NM_022768.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110882444 A G 0 222 0 0.9516 0.8229 0.8545 0.7738 0.6879 0.816 0.928071 0.791817 0.723176 1 8516 88158 9699 6409 4426 45924 632 12552 2 9152 115798 11432 8530 6390 63590 868 15836 0.960774 0 . 0 . 64 21,13,17,11 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E139|977|RBM15|protein_coding|CODING|NM_022768.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.57393 rs814771 -0.693054 0.932967 64 P71L 173 cCg/cTg MODERATE 1 MISSENSE CODING LAMTOR5 A protein_coding NM_006402.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110950277 G A 0 222 0 0.1377 0.0976 0.0562 0.0476 0.1083 0.1135 0.132093 0.127557 0.125233 1 1492 13195 629 425 592 8244 103 1710 2 10370 121152 11562 8636 6574 66612 892 16506 0.765759 0 . 0 . 128 45,17,37,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P71L|173|LAMTOR5|protein_coding|CODING|NM_006402.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.607114 rs6698159 -0.693147 0.367334 128 S17N 173 aGc/aAc MODERATE 1 MISSENSE CODING LAMTOR5 T protein_coding NM_006402.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 110950439 C T 0 222 0 0.3056 0.3634 0.379 0.2758 0.4453 0.4366 0.348162 0.444333 0.493605 1 3567 52379 4480 2152 3089 31751 386 6954 2 10276 120172 11474 8564 6464 66054 884 16456 0.996154 0 . 0 COSM1332599 79 13,20,14,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S17N|173|LAMTOR5|protein_coding|CODING|NM_006402.2|1|T),INTRAGENIC(MODIFIER|||||LAMTOR5-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.801795 rs6674775 -0.693132 0.528403 79 L247 511 ctA/ctG LOW 1 SILENT CODING KCNA10 C protein_coding NM_005549.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111060669 T C 0 228 0 0.5144 0.6242 0.7839 0.5853 0.7336 0.5869 0.556287 0.671536 0.730581 2 5807 85556 9543 4952 4610 49793 626 10225 2 10406 121366 11574 8622 6612 66732 908 16512 1 0 . 0 . 139 1,0,60,66 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L247|511|KCNA10|protein_coding|CODING|NM_005549.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1281175 -0.693147 0.336675 139 R133 511 cgG/cgT LOW 1 SILENT CODING KCNA10 A protein_coding NM_005549.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111061011 C A 0 204 0 0.1868 0.1819 0.2478 0.1736 0.1978 0.1207 0.189287 0.212056 0.223721 1 1983 25663 2805 1439 1402 15106 184 2744 2 10322 121220 11564 8628 6606 66692 906 16502 0.943731 0 . 0 . 58 15,19,4,16 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgT|R133|511|KCNA10|protein_coding|CODING|NM_005549.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.486674 rs3748731 -0.692067 0.527285 58 E116 511 gaA/gaG LOW 1 SILENT CODING KCNA10 C protein_coding NM_005549.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111061062 T C 0 228 0 0.5144 0.6242 0.7839 0.5853 0.7336 0.5869 0.555152 0.671152 0.730581 2 5795 85510 9543 4949 4604 49771 626 10222 2 10376 121294 11572 8618 6608 66710 908 16502 1 0 . 0 . 38 1,0,12,24 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E116|511|KCNA10|protein_coding|CODING|NM_005549.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1281174 -0.693139 0.184376 38 S47F 511 tCc/tTc MODERATE 1 MISSENSE CODING KCNA10 A protein_coding NM_005549.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111061270 G A 0 154 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 35 4 31 0 0 0 0 2 10294 121104 11556 8644 6604 66640 906 16460 0.99688 0 . 0 . 26 9,7,5,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S47F|511|KCNA10|protein_coding|CODING|NM_005549.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.951229 rs201611587 -0.670168 0.705725 26 575 232 MODIFIER 1 CODING KCNA3 C protein_coding NM_002232.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111215472 A C 0 146 0 0.68 0.6294 0.6268 0.5645 0.7117 0.545 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.989673 0 . 0 . 34 17,0,16,0 UTR_3_PRIME(MODIFIER||232||575|KCNA3|protein_coding|CODING|NM_002232.4|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.451687 rs1058184 -0.689466 0.0115509 34 219 18190 MODIFIER 1 CODING CD53 A protein_coding NM_000560.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111415841 G A 0 228 0 0.0711 0.2554 0.2954 0.3323 0.2734 0.3783 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 206 0,3,123,56 UTR_5_PRIME(MODIFIER||18190||219|CD53|protein_coding|CODING|NM_000560.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.539735 rs1494324,rs386534370 -0.693147 0.035925 206 219 12 MODIFIER 8 CODING CD53 T protein_coding NM_000560.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111441829 C T 0 222 0 0.3169 0.5567 0.7349 0.501 0.7614 0.6012 0.388334 0.636399 0.763488 1 3957 82975 9095 4148 4779 50009 649 10338 2 10356 120754 11462 8588 6576 66442 908 16422 0.671206 0 . 0 . 97 29,15,24,20 UTR_3_PRIME(MODIFIER||12||219|CD53|protein_coding|CODING|NM_000560.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.430844 rs1803259 -0.693146 0.30885 97 219 738 MODIFIER 8 CODING CD53 C protein_coding NM_000560.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111442555 G C 0 228 0 0.4062 0.6693 0.817 0.6915 0.8459 0.7157 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,8,51 UTR_3_PRIME(MODIFIER||738||219|CD53|protein_coding|CODING|NM_000560.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1936939 -0.693147 0.236363 62 266 242 MODIFIER 9 CODING DRAM2 C protein_coding NM_178454.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111660540 T C 0 190 0 0.4667 0.3281 0.2536 0.2808 0.1521 0.4233 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98001 0 . 0 . 55 25,5,19,2 UTR_3_PRIME(MODIFIER||242||266|DRAM2|protein_coding|CODING|NM_178454.4|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.988347 rs11002,rs386516256 -0.692352 0.150961 55 416 LOW 8 CODING CEPT1 G protein_coding NM_001007794.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111726213 A G 0 222 0 0.8548 0.755 0.7954 0.6458 0.6431 0.819 0.816841 0.710057 0.655349 1 8680 85005 9876 5593 4499 42951 636 12770 2 10404 121376 11576 8646 6612 66724 908 16506 0.620236 0 . 0 . 102 21,26,18,25 SPLICE_SITE_REGION+INTRON(LOW||||416|CEPT1|protein_coding|CODING|NM_001007794.1|8|G),DOWNSTREAM(MODIFIER||2378||471|DENND2D|protein_coding|CODING|NM_024901.4||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990058 rs694180 -0.693146 0.134823 102 390 LOW 3 CODING CHI3L2 C protein_coding NM_004000.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111773568 G C 0 228 0 0.2542 0.405 0.3329 0.5575 0.4513 0.455 0.285066 0.386975 0.439186 2 2842 51158 2988 4608 3558 29718 409 7035 2 10030 117698 11020 8412 6492 64780 888 16076 1 0 . 0 . 65 1,0,24,32 SPLICE_SITE_REGION+INTRON(LOW||||390|CHI3L2|protein_coding|CODING|NM_004000.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2255089 -0.693147 0.0273928 65 390 LOW 8 CODING CHI3L2 T protein_coding NM_004000.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111783942 C T 0 222 0 0.0212 0.149 0.1239 0.3601 0.0895 0.183 0.0329097 0.0634323 0.0790698 1 323 13885 1086 3110 1085 5519 93 2669 2 10402 121382 11574 8636 6614 66736 908 16512 0.766352 0 . 0 . 160 56,24,46,19 SPLICE_SITE_REGION+INTRON(LOW||||390|CHI3L2|protein_coding|CODING|NM_004000.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.949469 rs56403938 -0.693147 0.562012 160 R318 390 Cgg/Agg LOW 9 SILENT CODING CHI3L2 A protein_coding NM_004000.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111783982 C A 0 222 0 0.0507 0.1903 0.1729 0.1974 0.333 0.2372 0.103949 0.232969 0.29907 1 946 33512 1566 1621 2214 23025 293 3847 2 10404 121368 11558 8646 6606 66734 908 16512 0.972491 0 . 0 . 169 54,29,52,24 PROTEIN_INTERACTION_LOCUS(HIGH||||390|CHI3L2|protein_coding|CODING||9|A),SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R318|390|CHI3L2|protein_coding|CODING|NM_004000.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.480749 rs13721 -0.693147 0.105302 169 Q322 390 caA/caG LOW 9 SILENT CODING CHI3L2 G protein_coding NM_004000.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111783996 A G 0 228 0 0.9977 0.9994 1 1 1 1 0.998184 0.999385 1 2 10387 121378 11565 8654 6614 66740 908 16510 2 10406 121398 11566 8654 6614 66740 908 16510 0 . 0 . 0 178 0,0,107,57 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q322|390|CHI3L2|protein_coding|CODING|NM_004000.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2494007 -0.693147 0.166963 178 390 944 MODIFIER 11 CODING CHI3L2 C protein_coding NM_004000.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111785930 T C 0 39.3 0 0.1944 0.5433 0.6153 0.6567 0.664 0.7229 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||944||390|CHI3L2|protein_coding|CODING|NM_004000.2|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1056825 -0.453602 0.8 2 476 19573 MODIFIER 1 CODING CHIA A protein_coding NM_201653.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111833517 G A 0 228 0 0.2209 0.4655 0.6282 0.7411 0.4592 0.4029 0 . 0 2 192 6676 131 264 656 2269 83 3081 2 768 15314 230 350 1564 4700 194 7508 1 0 . 0 . 32 0,1,5,24 UTR_5_PRIME(MODIFIER||19573||476|CHIA|protein_coding|CODING|NM_201653.3|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs12026825 -0.693079 0.0104047 32 E676Q 678 Gaa/Caa MODERATE 11 MISSENSE CODING OVGP1 G protein_coding NM_002557.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111957097 C G 0 222 0 0.7315 0.6224 0.353 0.7589 0.4364 0.7168 0.686876 0.524685 0.441628 1 7081 61923 3452 6528 3116 29939 447 11360 2 10246 120784 11546 8626 6608 66444 904 16410 0.804097 0 . 0 . 97 24,39,14,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E676Q|678|OVGP1|protein_coding|CODING|NM_002557.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.535159 rs7825 -0.693021 0.156651 97 H604Q 678 caC/caG MODERATE 11 MISSENSE CODING OVGP1 C protein_coding NM_002557.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111957311 G C 0 222 0 0.4539 0.2949 0.1628 0.3919 0.1103 0.2638 0.385837 0.185222 0.0824419 1 4236 19989 1839 3471 971 5697 140 3635 2 10394 121220 11568 8622 6614 66658 908 16456 0.984845 0 . 0 COSM146579 50 11,15,9,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H604Q|678|OVGP1|protein_coding|CODING|NM_002557.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0647253 rs10067 -0.692831 0.0112426 50 M477T 678 aTg/aCg MODERATE 11 MISSENSE CODING OVGP1 G protein_coding NM_002557.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111957693 A G 0 222 0 0.7572 0.6318 0.3573 0.7718 0.4364 0.7137 0.707671 0.531831 0.441744 1 7430 62357 3436 6612 3117 29958 450 11354 2 10406 121382 11566 8650 6614 66726 908 16512 0.719913 0 . 0 . 113 35,28,21,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M477T|678|OVGP1|protein_coding|CODING|NM_002557.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.449665 rs2485319 -0.693146 0.0673302 113 678 LOW 1 CODING OVGP1 G protein_coding NM_002557.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111969719 A G 0 222 0 0.7035 0.5815 0.3271 0.744 0.3986 0.6176 0.655016 0.48739 0.401512 1 6882 56932 2980 6402 2992 27229 410 10037 2 10376 121050 11498 8626 6596 66564 902 16488 0.792375 0 . 0 . 204 73,51,33,16 SPLICE_SITE_REGION+INTRON(LOW||||678|OVGP1|protein_coding|CODING|NM_002557.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.921527 rs1264894 -0.693147 0.115401 204 354 700 MODIFIER 10 CODING WDR77 G protein_coding NM_001317062.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111983152 A G 0 9.7 0 0.174 0.2228 0.1311 0.4395 0.1113 0.2454 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||700||354|WDR77|protein_coding|CODING|NM_001317062.1|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1264904 -0.379885 0 1 354 54 MODIFIER 1 CODING WDR77 A protein_coding NM_001317062.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111991845 C A 0 222 0 0.5272 0.5321 0.3098 0.744 0.3946 0.6196 0 . 0 1 554 8915 199 464 207 2586 74 4831 2 1004 16066 456 616 372 5668 140 7810 0.857714 0 . 0 . 76 30,10,16,5 START_GAINED(LOW||||354|WDR77|protein_coding|CODING|NM_001317062.1|1|A),UTR_5_PRIME(MODIFIER||54||354|WDR77|protein_coding|CODING|NM_001317062.1|1|A),UTR_5_PRIME(MODIFIER||319||256|ATP5F1|protein_coding|CODING|NM_001688.4|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.435016 rs1270853 -0.692352 0.197046 76 256 319 MODIFIER 1 CODING ATP5F1 A protein_coding NM_001688.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111991845 C A 0 222 0 0.5272 0.5321 0.3098 0.744 0.3946 0.6196 0 . 0 1 554 8915 199 464 207 2586 74 4831 2 1004 16066 456 616 372 5668 140 7810 0.857714 0 . 0 . 76 30,10,16,5 START_GAINED(LOW||||354|WDR77|protein_coding|CODING|NM_001317062.1|1|A),UTR_5_PRIME(MODIFIER||54||354|WDR77|protein_coding|CODING|NM_001317062.1|1|A),UTR_5_PRIME(MODIFIER||319||256|ATP5F1|protein_coding|CODING|NM_001688.4|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.435016 rs1270853 -0.692352 0.197046 76 256 69 MODIFIER 1 CODING ATP5F1 T protein_coding NM_001688.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 111992095 C T 0 222 0 0.3888 0.4924 0.2896 0.744 0.3936 0.6186 0.402457 0.403636 0.404148 1 4220 54130 2816 6425 3017 27229 393 10030 2 10376 121198 11556 8638 6604 66608 906 16510 0.95765 0 . 0 . 62 25,12,13,6 UTR_5_PRIME(MODIFIER||69||256|ATP5F1|protein_coding|CODING|NM_001688.4|1|T),UPSTREAM(MODIFIER||165||354|WDR77|protein_coding|CODING|NM_001317062.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969009 rs1264899 -0.69168 0.366434 62 318 441 MODIFIER 2 CODING ADORA3 C protein_coding NM_000677.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112042131 T C 0 21.4 0 0.7352 0.7736 0.8602 0.7579 0.834 0.7178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,0 UTR_3_PRIME(MODIFIER||441||318|ADORA3|protein_coding|CODING|NM_000677.3|2|C),INTRON(MODIFIER||||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3394 -0.379885 0 4 318 336 MODIFIER 2 CODING ADORA3 A protein_coding NM_000677.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112042236 G A 0 63 0 0.7352 0.7734 0.8588 0.7579 0.834 0.7178 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||336||318|ADORA3|protein_coding|CODING|NM_000677.3|2|A),INTRON(MODIFIER||||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1415793,rs386531087 -0.453602 0.58 3 318 189 MODIFIER 2 CODING ADORA3 A protein_coding NM_000677.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112042383 G A 0 81 0 0.7352 0.7734 0.8602 0.7569 0.834 0.7178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974597 0 . 0 . 12 4,1,4,0 UTR_3_PRIME(MODIFIER||189||318|ADORA3|protein_coding|CODING|NM_000677.3|2|A),INTRON(MODIFIER||||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.487298 rs923 -0.556411 0.87268 12 A299 318 gcT/gcC LOW 2 SILENT CODING ADORA3 G protein_coding NM_000677.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112042632 A G 0 222 0 0.7352 0.7736 0.8602 0.7579 0.834 0.7178 0.741943 0.79002 0.814651 1 7675 97843 9839 6632 5625 54645 753 12674 2 10402 121312 11568 8632 6610 66684 908 16508 0.826383 0 . 0 . 206 66,21,63,37 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A299|318|ADORA3|protein_coding|CODING|NM_000677.3|2|G),INTRON(MODIFIER||||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.047941 rs2229155,rs386437584 -0.693147 0.0884153 206 347 564 MODIFIER 1 CODING TMIGD3 G protein_coding NM_020683.6 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112046540 A G 0 21.4 0 0.6195 0.6925 0.8026 0.6746 0.7614 0.6605 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,0 UTR_5_PRIME(MODIFIER||564||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|G),UTR_5_PRIME(MODIFIER||564||318|ADORA3|protein_coding|CODING|NM_000677.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1544224 -0.379885 0 4 318 564 MODIFIER 1 CODING ADORA3 G protein_coding NM_000677.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112046540 A G 0 21.4 0 0.6195 0.6925 0.8026 0.6746 0.7614 0.6605 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,0 UTR_5_PRIME(MODIFIER||564||347|TMIGD3|protein_coding|CODING|NM_020683.6|1|G),UTR_5_PRIME(MODIFIER||564||318|ADORA3|protein_coding|CODING|NM_000677.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1544224 -0.379885 0 4 297 3290 MODIFIER 2 CODING FAM212B G protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112266300 A G 0 6.3 0 0.27 0.4089 0.4395 0.501 0.4364 0.4519 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3290||297|FAM212B|protein_coding|CODING|NM_019099.4|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs197426 -0.379885 0 1 297 3224 MODIFIER 2 CODING FAM212B C protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112266366 T C 0 63 0 0.27 0.4095 0.4395 0.502 0.4374 0.453 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||3224||297|FAM212B|protein_coding|CODING|NM_019099.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs197427 -0.453602 0.14 3 297 2090 MODIFIER 2 CODING FAM212B T protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112267500 C T 0 21.2 0 0.4546 0.3315 0.2867 0.2956 0.2604 0.3067 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_3_PRIME(MODIFIER||2090||297|FAM212B|protein_coding|CODING|NM_019099.4|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs197429 -0.379885 0 3 297 1687 MODIFIER 2 CODING FAM212B A protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112267903 G A 0 6.3 0 0.0257 0.0282 0.049 0.0595 0.0099 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1687||297|FAM212B|protein_coding|CODING|NM_019099.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs115199584 -0.379885 0 1 297 1543 MODIFIER 2 CODING FAM212B C protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112268047 G C 0 9.7 0 0.6362 0.6895 0.6499 0.7321 0.67 0.7658 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1543||297|FAM212B|protein_coding|CODING|NM_019099.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs197430 -0.379885 0 1 297 1306 MODIFIER 2 CODING FAM212B A protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112268284 G A 0 9.7 0 0.0908 0.3343 0.3703 0.4335 0.4215 0.4458 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1306||297|FAM212B|protein_coding|CODING|NM_019099.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11102327 -0.379885 0 1 297 1165 MODIFIER 2 CODING FAM212B G protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112268425 C G 0 36.6 0 0.8699 0.8359 0.7378 0.8244 0.8211 0.8865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1165||297|FAM212B|protein_coding|CODING|NM_019099.4|2|G) 0 . 0 . 0 1 0 . 0 . 43 0 0 1 0 . rs197431 -0.453602 0.58 3 297 924 MODIFIER 2 CODING FAM212B C protein_coding NM_019099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112268666 T C 0 46.3 0 0.9652 0.8642 0.7478 0.8353 0.8191 0.8865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||924||297|FAM212B|protein_coding|CODING|NM_019099.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs197433 -0.453602 0.78 2 F204 297 ttC/ttT LOW 2 SILENT CODING FAM212B A protein_coding NM_019099.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112269872 G A 0 228 0 0.9607 0.8606 0.7464 0.8254 0.8191 0.8855 0.933046 0.85745 0.818721 2 9763 99966 8061 7137 5336 54534 732 14403 2 10406 121358 11572 8648 6612 66702 908 16510 0 . 0 . 0 67 0,0,43,21 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F204|297|FAM212B|protein_coding|CODING|NM_019099.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs197434 -0.693147 0.0531105 67 L95 824 Ttg/Ctg LOW 1 SILENT CODING DDX20 C protein_coding NM_007204.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112298829 T C 0 17.9 0 0.7254 0.4722 0.5014 0.3403 0.4105 0.3088 0.508839 0.359007 0.286406 1 169 2360 108 56 24 1011 32 960 2 244 5260 186 166 54 2162 60 2388 1 0 . 0 . 3 0,1,0,2 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L95|824|DDX20|protein_coding|CODING|NM_007204.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 1 rs197393 -0.453602 0.64 3 I636T 824 aTt/aCt MODERATE 11 MISSENSE CODING DDX20 C protein_coding NM_007204.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112308953 T C 0 222 0 0.7247 0.4744 0.5072 0.3403 0.4185 0.3088 0.669542 0.484007 0.388953 1 7062 51735 6329 3027 3010 26396 366 5545 2 10392 121130 11546 8618 6604 66554 908 16508 0.718072 0 . 0 . 99 33,16,17,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I636T|824|DDX20|protein_coding|CODING|NM_007204.4|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939878 rs197412 -0.693146 0.808065 99 V642 824 gtG/gtA LOW 11 SILENT CODING DDX20 A protein_coding NM_007204.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112308972 G A 0 222 0 0.7428 0.4798 0.5115 0.3403 0.4185 0.3088 0.679074 0.487544 0.389419 1 7161 51788 6326 3029 3010 26352 366 5544 2 10382 121164 11544 8630 6606 66584 908 16510 0.986077 0 . 0 . 104 33,22,19,23 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V642|824|DDX20|protein_coding|CODING|NM_007204.4|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.849315 rs197413 -0.693146 0.59147 104 655 215 MODIFIER 8 CODING KCND3 G protein_coding NM_004980.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112318484 A G 0 228 0 0.208 0.4315 0.3847 0.6815 0.3817 0.5603 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,23,1 UTR_3_PRIME(MODIFIER||215||655|KCND3|protein_coding|CODING|NM_004980.4|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12033257 -0.692831 2.236e-08 27 I102V 125 Ata/Gta MODERATE 2 MISSENSE CODING LOC643355 G protein_coding NM_001270945.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112539061 A G 0 222 0 0.2375 0.3435 0.4885 0.6002 0.1213 0.3476 0 . 0 1 131 2962 59 105 2 544 29 2092 2 558 12304 186 198 4 3610 132 7616 0.845795 0 . 0 . 92 35,14,20,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I102V|125|LOC643355|protein_coding|CODING|NM_001270945.1|2|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.195872 rs2366125 -0.693132 0.063997 92 125 275 MODIFIER 2 CODING LOC643355 G protein_coding NM_001270945.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112539410 A G 0 81 0 0.0855 0.2143 0.1657 0.2192 0.3588 0.2689 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 0,2,1,3 UTR_3_PRIME(MODIFIER||275||125|LOC643355|protein_coding|CODING|NM_001270945.1|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7528073 -0.556411 0.184775 6 125 706 MODIFIER 2 CODING LOC643355 C protein_coding NM_001270945.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112539841 T C 0 9.7 0 0.9917 0.9978 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||706||125|LOC643355|protein_coding|CODING|NM_001270945.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3000748 -0.379885 0 1 125 2201 MODIFIER 2 CODING LOC643355 A protein_coding NM_001270945.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112541336 G A 0 9.7 0 0.9917 0.9978 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2201||125|LOC643355|protein_coding|CODING|NM_001270945.1|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3008529 -0.379885 0 1 N78 639 aaT/aaC LOW 4 SILENT CODING CTTNBP2NL C protein_coding NM_018704.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112991698 T C 0 222 0 0.3238 0.5254 0.5692 0.4464 0.66 0.7096 0.385384 0.559127 0.64814 1 3954 72543 6078 3678 3807 42735 542 11749 2 10398 121168 11518 8600 6600 66638 906 16508 0.996335 0 . 0 COSM146582 84 21,22,13,19 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N78|639|CTTNBP2NL|protein_coding|CODING|NM_018704.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7085 rs2256883 -0.69312 0.477164 84 Q371 639 caG/caA LOW 6 SILENT CODING CTTNBP2NL A protein_coding NM_018704.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 112999227 G A 0 228 0 0.9561 0.9397 0.9366 1 0.8608 0.9387 0.932592 0.883054 0.857674 2 9752 108236 11075 8640 5683 56850 809 15427 2 10394 121382 11576 8654 6614 66726 908 16510 0 . 0 . 0 63 0,0,34,24 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q371|639|CTTNBP2NL|protein_coding|CODING|NM_018704.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1175641 -0.693147 0.87169 63 639 531 MODIFIER 6 CODING CTTNBP2NL G protein_coding NM_018704.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113000565 A G 0 222 0 0.0915 0.2648 0.3184 0.5536 0.2008 0.229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861754 0 . 0 . 55 16,16,8,11 UTR_3_PRIME(MODIFIER||531||639|CTTNBP2NL|protein_coding|CODING|NM_018704.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.499258 rs3795821 -0.69168 0.447926 55 391 155 MODIFIER 1 CODING WNT2B G protein_coding NM_024494.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113051730 C G 0 76 0 0.09 0.2594 0.33 0.3958 0.331 0.2239 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 START_GAINED(LOW||||391|WNT2B|protein_coding|CODING|NM_024494.2|1|G),UTR_5_PRIME(MODIFIER||155||391|WNT2B|protein_coding|CODING|NM_024494.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11102484 -0.511536 0.807564 3 Q390 391 caA/caG LOW 5 SILENT CODING WNT2B G protein_coding NM_024494.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113063125 A G 0 228 0 0.5371 0.4834 0.4438 0.6151 0.4612 0.3262 0.514526 0.47578 0.45593 2 5435 56266 5468 5527 3227 30704 406 5499 2 10140 118394 11198 8494 6384 65138 878 16162 0.545455 0 . 0 . 142 1,1,79,42 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q390|391|WNT2B|protein_coding|CODING|NM_024494.2|5|G),DOWNSTREAM(MODIFIER||3016||575|ST7L|protein_coding|CODING|NM_017744.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.243802 rs910697 -0.693147 0.581238 142 575 58 MODIFIER 15 CODING ST7L T protein_coding NM_017744.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113068577 C T 0 228 0 0.0628 0.227 0.2767 0.4266 0.2266 0.2086 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,37,1 UTR_3_PRIME(MODIFIER||58||575|ST7L|protein_coding|CODING|NM_017744.4|15|T),DOWNSTREAM(MODIFIER||4667||391|WNT2B|protein_coding|CODING|NM_024494.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs35147679 -0.693143 0.0430717 41 286 1343 MODIFIER 10 CODING CAPZA1 A protein_coding NM_006135.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113214097 G A 0 228 0 0.8404 0.8295 0.8732 0.8105 0.7555 0.8793 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 0,0,14,57 UTR_3_PRIME(MODIFIER||1343||286|CAPZA1|protein_coding|CODING|NM_006135.2|10|A),UPSTREAM(MODIFIER||2998||1003|MOV10|protein_coding|CODING|NM_001130079.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1238 -0.693147 0.00260487 73 G394 1003 ggC/ggT LOW 8 SILENT CODING MOV10 T protein_coding NM_001130079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113236681 C T 0 228 0 0.1672 0.2847 0.2911 0.5427 0.2346 0.2249 0.182705 0.197832 0.205581 2 1874 32132 4406 4912 2449 14546 229 3716 2 10390 121324 11570 8634 6608 66704 908 16510 0 . 0 . 0 51 0,0,39,10 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G394|1003|MOV10|protein_coding|CODING|NM_001130079.2|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748656 -0.693147 0.813697 51 T464 1003 acA/acG LOW 9 SILENT CODING MOV10 G protein_coding NM_001130079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113237171 A G 0 228 0 0.1672 0.2847 0.2911 0.5427 0.2346 0.2249 0.182251 0.197294 0.205 2 1871 32087 4396 4920 2443 14516 228 3713 2 10292 120516 11528 8606 6596 66260 904 16330 1 0 . 0 COSM423475 108 0,1,30,72 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T464|1003|MOV10|protein_coding|CODING|NM_001130079.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs883593 -0.693147 0.473896 108 E704 1003 gaG/gaA LOW 14 SILENT CODING MOV10 A protein_coding NM_001130079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113239382 G A 0 228 0 0.0787 0.2346 0.281 0.4425 0.2346 0.1984 0.0964594 0.167077 0.203256 2 801 25246 3533 3740 1747 12328 183 2914 2 7326 88842 8266 7380 3928 48270 642 13030 0 . 0 . 0 54 0,0,21,29 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E704|1003|MOV10|protein_coding|CODING|NM_001130079.2|14|A),DOWNSTREAM(MODIFIER||4367||193|RHOC|protein_coding|CODING|NM_001042678.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs17030651 -0.693147 0.0221218 54 A820 1003 gcT/gcC LOW 16 SILENT CODING MOV10 C protein_coding NM_001130079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113241052 T C 0 228 0 0.1762 0.2871 0.2911 0.5417 0.2346 0.226 0.187699 0.19937 0.205349 2 1935 32160 4409 4915 2444 14513 230 3714 2 10336 120858 11562 8620 6600 66326 908 16506 0 . 0 . 0 76 0,0,18,55 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A820|1003|MOV10|protein_coding|CODING|NM_001130079.2|16|C),DOWNSTREAM(MODIFIER||2697||193|RHOC|protein_coding|CODING|NM_001042678.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2306940 -0.693147 0.259341 76 S977 1003 agC/agT LOW 21 SILENT CODING MOV10 T protein_coding NM_001130079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113243048 C T 0 228 0 0.1702 0.2839 0.2911 0.5407 0.2346 0.2188 0.186564 0.199216 0.205698 2 1910 32029 4406 4892 2450 14527 229 3615 2 10398 120896 11558 8618 6602 66580 904 16236 0 . 0 . 0 87 0,0,43,38 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S977|1003|MOV10|protein_coding|CODING|NM_001130079.2|21|T),DOWNSTREAM(MODIFIER||701||193|RHOC|protein_coding|CODING|NM_001042678.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6679 -0.693147 0.423521 87 V236I 505 Gtt/Att MODERATE 3 MISSENSE CODING PPM1J T protein_coding NM_005167.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113255389 C T 0 228 0 0.8835 0.9679 0.9899 1 1 1 0.885157 0.960864 0.999651 2 9253 119881 11523 8654 6614 66582 900 16355 2 10404 121134 11578 8654 6614 66616 906 16362 0 . 0 . 0 69 0,0,34,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V236I|505|PPM1J|protein_coding|CODING|NM_005167.5|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10857971,rs386481312 -0.693147 0.153597 69 D490E 500 gaT/gaA MODERATE 5 MISSENSE CODING SLC16A1 T protein_coding NM_001166496.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113456546 A T 0 222 0 0.9085 0.6767 0.5519 0.6647 0.5626 0.5818 0.84453 0.666231 0.574884 1 8953 72494 6003 5736 3794 38487 540 8981 2 10406 121388 11576 8648 6612 66732 908 16506 0.890221 2 benign 0 . 105 39,13,32,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D490E|500|SLC16A1|protein_coding|CODING|NM_001166496.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976767 rs1049434 -0.693146 0.84904 105 T708 1065 acA/acC LOW 15 SILENT CODING LRIG2 C protein_coding NM_014813.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113657092 A C 0 228 0 0.7027 0.9018 0.9669 0.9504 0.9891 0.9847 0.7399 0.903122 0.986744 2 7661 116874 11362 8369 6541 65765 895 16281 2 10400 121326 11576 8648 6614 66682 908 16498 0 . 0 . 0 64 0,0,46,12 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T708|1065|LRIG2|protein_coding|CODING|NM_014813.2|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1216793 -0.693147 5.81926e-07 64 1481 174 MODIFIER 1 CODING MAGI3 G protein_coding NM_001142782.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113933482 C G 0 9.7 0 0.1536 0.2905 0.3343 0.6071 0.2386 0.1718 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||174||1481|MAGI3|protein_coding|CODING|NM_001142782.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10857994 -0.379885 0 1 1481 86 MODIFIER 1 CODING MAGI3 A protein_coding NM_001142782.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 113933570 G A 0 178 0 0.0091 0.226 0.3026 0.5972 0.1779 0.1319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,11,1 UTR_5_PRIME(MODIFIER||86||1481|MAGI3|protein_coding|CODING|NM_001142782.1|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12568854 -0.680642 0.00873016 12 762 10 MODIFIER 1 CODING PHTF1 T protein_coding NM_006608.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114301335 C T 0 228 0 0.0113 0.2494 0.3314 0.5863 0.2376 0.1779 0.0497049 0.16254 0.220349 2 425 29354 4298 5057 2026 14585 188 2775 2 10182 117852 11370 8530 6430 64342 888 16110 0 . 0 . 0 51 0,0,28,21 UTR_5_PRIME(MODIFIER||10||762|PHTF1|protein_coding|CODING|NM_006608.2|1|T),DOWNSTREAM(MODIFIER||3119||802|RSBN1|protein_coding|CODING|NM_018364.4||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs61817589 -0.693147 0.0202442 51 W620R 807 Tgg/Cgg MODERATE 14 MISSENSE CODING PTPN22 G protein_coding NM_015967.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114377568 A G 0 228 0 0.997 0.9726 0.964 1 0.9056 0.9867 0.981843 0.931647 0.90593 2 10262 113289 11288 8654 5655 60289 858 16283 2 10404 121404 11578 8654 6612 66736 908 16512 0 255|255|255|255|255 other|other|other|other|other 0 . 72 0,0,25,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W620R|807|PTPN22|protein_coding|CODING|NM_015967.6|14|G),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2476601 -0.693147 0.0389313 72 163 3985 MODIFIER 4 CODING BCL2L15 C protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114419760 G C 0 9.7 0 0.9924 0.8027 0.7939 0.9008 0.667 0.591 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3985||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|C),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1217384 -0.379885 0 1 163 3417 MODIFIER 4 CODING BCL2L15 T protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114420328 C T 0 70 0 0.031 0.2819 0.4135 0.6121 0.2505 0.2198 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||3417||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|T),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12566340 -0.453602 0.22 3 163 3283 MODIFIER 4 CODING BCL2L15 A protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114420462 G A 0 9.7 0 0.2201 0.3357 0.438 0.6121 0.2525 0.2198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3283||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|A),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7529353 -0.379885 0 1 163 769 MODIFIER 4 CODING BCL2L15 C protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114422976 T C 0 9.7 0 0.1823 0.0986 0.0548 0.1111 0.0477 0.0562 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||769||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|C),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1217383 -0.379885 0 1 163 686 MODIFIER 4 CODING BCL2L15 C protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114423059 T C 0 9.7 0 0 0.0017971 0 0.0079 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||686||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|C),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs180806255 -0.379885 0 1 163 581 MODIFIER 4 CODING BCL2L15 C protein_coding NM_001010922.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114423164 A C 0 70 0 0 0.009984 0 0.0476 0 0.002 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||581||163|BCL2L15|protein_coding|CODING|NM_001010922.2|4|C),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111634401 -0.453602 0.66 3 D90N 163 Gac/Aac MODERATE 3 MISSENSE CODING BCL2L15 T protein_coding NM_001010922.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114424601 C T 0 228 0 1 0.9994 1 1 0.997 1 0.999773 0.999846 0.999884 2 10391 121272 11552 8654 6612 66677 908 16478 2 10392 121284 11552 8654 6612 66688 908 16478 0 . 0 . 0 48 0,0,9,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D90N|163|BCL2L15|protein_coding|CODING|NM_001010922.2|3|T),INTRAGENIC(MODIFIER|||||AP4B1-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1217381 -0.693146 0.16125 48 H61Y 532 Cac/Tac MODERATE 1 MISSENSE CODING DCLRE1B T protein_coding NM_022836.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114448389 C T 0 228 0 0.0151 0.2422 0.3833 0.5873 0.1909 0.1462 0.0419882 0.129171 0.173837 2 402 25481 5154 5070 1249 11193 137 2276 2 10336 120298 11500 8598 6518 66308 892 16146 1 0 . 0 . 54 0,1,18,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H61Y|532|DCLRE1B|protein_coding|CODING|NM_022836.3|1|T),UPSTREAM(MODIFIER||844||739|AP4B1|protein_coding|CODING|NM_001253852.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11552449 -0.693147 0.0625863 54 H78 532 caT/caC LOW 2 SILENT CODING DCLRE1B C protein_coding NM_022836.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114449662 T C 0 228 0 0.0151 0.2434 0.3833 0.5903 0.1928 0.1472 0.0419882 0.129556 0.174419 2 402 25698 5199 5115 1258 11286 137 2301 2 10406 121386 11576 8638 6614 66732 908 16512 1 0 . 0 . 85 0,1,43,29 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H78|532|DCLRE1B|protein_coding|CODING|NM_022836.3|2|C),UPSTREAM(MODIFIER||2117||739|AP4B1|protein_coding|CODING|NM_001253852.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3761936 -0.693147 0.106119 85 A1072 1210 gcG/gcA LOW 16 SILENT CODING HIPK1 A protein_coding NM_198268.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114515717 G A 0 222 0 0.5469 0.4862 0.4366 0.5238 0.4314 0.4571 0.509759 0.44764 0.415814 1 5232 46131 4071 4134 2416 25889 341 4048 2 10222 110988 11482 8496 6614 64084 796 9294 0.999013 0 . 0 . 188 44,43,58,23 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1072|1210|HIPK1|protein_coding|CODING|NM_198268.2|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.750831 rs2358996 -0.693147 0.27891 188 1210 106 MODIFIER 16 CODING HIPK1 G protein_coding NM_198268.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114516240 C G 0 222 0 0 0.0013978 0 0.0069 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.55071 0 . 0 . 85 15,24,21,15 UTR_3_PRIME(MODIFIER||106||1210|HIPK1|protein_coding|CODING|NM_198268.2|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.691476 rs369820212 -0.693139 0.143833 85 1210 3217 MODIFIER 16 CODING HIPK1 G protein_coding NM_198268.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114519351 T G 0 222 0 0.5968 0.5427 0.549 0.622 0.4592 0.4693 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935603 0 . 0 . 123 22,28,22,37 UTR_3_PRIME(MODIFIER||3217||1210|HIPK1|protein_coding|CODING|NM_198268.2|16|G),UPSTREAM(MODIFIER||2662||406|OLFML3|protein_coding|CODING|NM_020190.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998153 rs10732635 -0.693147 0.216316 123 425 4428 MODIFIER 8 CODING SYT6 T protein_coding NM_001270805.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114631980 C T 0 228 0 0.1452 0.5048 0.5101 0.9127 0.4622 0.6104 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 105 0,0,43,52 UTR_3_PRIME(MODIFIER||4428||425|SYT6|protein_coding|CODING|NM_001270805.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2432 -0.693147 0.156549 105 425 1923 MODIFIER 8 CODING SYT6 C protein_coding NM_001270805.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114634485 T C 0 228 0 0.3351 0.3744 0.3573 0.5198 0.3698 0.2945 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 55 0,0,53,1 UTR_3_PRIME(MODIFIER||1923||425|SYT6|protein_coding|CODING|NM_001270805.1|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1053135 -0.693147 0.0666224 55 S131 425 tcG/tcA LOW 3 SILENT CODING SYT6 T protein_coding NM_001270805.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114680540 C T 0 222 0 0.2247 0.2077 0.1628 0.2579 0.2078 0.1646 0.189741 0.203983 0.211279 1 2052 23290 2196 2127 720 13437 159 2599 2 10406 121382 11574 8638 6614 66732 908 16510 0.354411 0 . 0 COSM146587 221 49,48,66,41 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S131|425|SYT6|protein_coding|CODING|NM_001270805.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622486 rs17032441 -0.693147 1.97801e-06 221 1127 531 MODIFIER 20 CODING TRIM33 C protein_coding NM_015906.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114939739 T C 0 41.9 0 0.4032 0.3301 0.1988 0.3988 0.1213 0.4683 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,0,2,0 UTR_3_PRIME(MODIFIER||531||1127|TRIM33|protein_coding|CODING|NM_015906.3|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs12057251 -0.453602 0.6 5 I840T 1127 aTt/aCt MODERATE 15 MISSENSE CODING TRIM33 G protein_coding NM_015906.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 114948281 A G 0 228 0 0.9803 0.8564 0.8012 0.5823 0.9364 0.9284 0.971403 0.942334 0.927442 2 10103 108296 8790 5247 6390 61732 805 15229 2 10406 121390 11572 8638 6614 66740 908 16512 0 . 0 . 0 85 0,0,39,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I840T|1127|TRIM33|protein_coding|CODING|NM_015906.3|15|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6537825 -0.693147 0.819126 85 928 134 MODIFIER 21 CODING DENND2C G protein_coding NM_001256404.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115128087 A G 0 228 0 0.9871 0.8283 0.7824 0.5159 0.8668 0.9284 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,44,6 UTR_3_PRIME(MODIFIER||134||928|DENND2C|protein_coding|CODING|NM_001256404.1|21|G),UPSTREAM(MODIFIER||3822||225|BCAS2|protein_coding|CODING|NM_005872.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs222493,rs386561521 -0.693147 0.320088 54 844 1240 MODIFIER 21 CODING CSDE1 G protein_coding NM_001242891.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115259550 A G 0 222 0 0 0.016573 0.0677 0.0288 0.007 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994554 0 . 0 . 75 28,14,19,8 UTR_3_PRIME(MODIFIER||1240||844|CSDE1|protein_coding|CODING|NM_001242891.1|21|G),UPSTREAM(MODIFIER||35||189|NRAS|protein_coding|CODING|NM_002524.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.553216 rs9724615 -0.693021 0.699672 75 976 293 MODIFIER 32 CODING SYCP1 G protein_coding NM_001282541.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115537933 A G 0 222 0 0.329 0.4551 0.5072 0.5446 0.5686 0.3793 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.607243 0 . 0 . 82 16,18,20,16 UTR_3_PRIME(MODIFIER||293||976|SYCP1|protein_coding|CODING|NM_001282541.1|32|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.420606 rs11084 -0.693139 0.435494 82 T14A 138 Aca/Gca MODERATE 2 MISSENSE CODING TSHB G protein_coding NM_000549.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115576023 A G 0 228 0 1 0.9836 0.9942 1 0.9622 0.9591 0.994326 0.975242 0.965465 2 10359 117788 11462 8654 6238 64349 880 15846 2 10406 121348 11544 8654 6608 66720 908 16508 0 . 0 . 0 96 0,0,65,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T14A|138|TSHB|protein_coding|CODING|NM_000549.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10776792,rs386515121 -0.693147 0.00335911 96 221 291 MODIFIER 8 CODING TSPAN2 C protein_coding NM_005725.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115592820 T C 0 222 0 0.4629 0.4788 0.5043 0.4563 0.4085 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.881234 0 . 0 . 40 5,15,6,11 UTR_3_PRIME(MODIFIER||291||221|TSPAN2|protein_coding|CODING|NM_005725.5|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.520452 rs3738706 -0.690438 0.0534721 40 G76 221 ggG/ggA LOW 3 SILENT CODING TSPAN2 T protein_coding NM_005725.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 115604798 C T 0 222 0 0.3018 0.3201 0.3343 0.4921 0.3012 0.1769 0.293236 0.292615 0.292297 1 2308 25610 2444 2913 663 14515 188 2579 2 6896 74842 6238 6058 2116 41476 540 11518 0.956368 0 . 0 COSM423531 100 29,11,35,11 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G76|221|TSPAN2|protein_coding|CODING|NM_005725.5|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.146186 rs10776795 -0.693147 0.0925381 100 524 313 MODIFIER 8 CODING VANGL1 G protein_coding NM_001172412.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116234313 A G 0 228 0 0.8563 0.7394 0.745 0.7371 0.6223 0.7004 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 92 1,0,71,11 UTR_3_PRIME(MODIFIER||313||524|VANGL1|protein_coding|CODING|NM_001172412.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3811012 -0.693147 0.569022 92 524 505 MODIFIER 8 CODING VANGL1 G protein_coding NM_001172412.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116234505 A G 0 228 0 0.8563 0.7394 0.745 0.7371 0.6233 0.6994 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 178 0,1,63,91 UTR_3_PRIME(MODIFIER||505||524|VANGL1|protein_coding|CODING|NM_001172412.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs6700610 -0.693147 0.0923727 178 524 5633 MODIFIER 8 CODING VANGL1 G protein_coding NM_001172412.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116239633 T G 0 32.6 0 0.2988 0.2746 0.2666 0.3651 0.2018 0.229 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||5633||524|VANGL1|protein_coding|CODING|NM_001172412.1|8|G),DOWNSTREAM(MODIFIER||2993||399|CASQ2|protein_coding|CODING|NM_001232.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4348723 -0.379885 0 2 524 6026 MODIFIER 8 CODING VANGL1 A protein_coding NM_001172412.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116240026 G A 0 9.7 0 0.3003 0.2746 0.268 0.3621 0.2018 0.229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||6026||524|VANGL1|protein_coding|CODING|NM_001172412.1|8|A),DOWNSTREAM(MODIFIER||2600||399|CASQ2|protein_coding|CODING|NM_001232.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6428677 -0.379885 0 1 399 632 MODIFIER 11 CODING CASQ2 G protein_coding NM_001232.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116243230 C G 0 62 0 0.8026 0.7179 0.7363 0.7401 0.6074 0.681 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||632||399|CASQ2|protein_coding|CODING|NM_001232.3|11|G),DOWNSTREAM(MODIFIER||2385||524|VANGL1|protein_coding|CODING|NM_001172412.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1140238 -0.556411 0.784982 4 399 482 MODIFIER 11 CODING CASQ2 A protein_coding NM_001232.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116243380 G A 0 31.3 0 0.7421 0.7009 0.732 0.7381 0.6074 0.681 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||482||399|CASQ2|protein_coding|CODING|NM_001232.3|11|A),DOWNSTREAM(MODIFIER||2535||524|VANGL1|protein_coding|CODING|NM_001172412.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7521023 -0.453602 0.84 2 399 138 MODIFIER 11 CODING CASQ2 G protein_coding NM_001232.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116243724 A G 0 222 0 0.1868 0.1036 0.0576 0.1022 0.0895 0.0399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0487285 0 . 0 . 147 60,16,55,8 UTR_3_PRIME(MODIFIER||138||399|CASQ2|protein_coding|CODING|NM_001232.3|11|G),DOWNSTREAM(MODIFIER||2879||524|VANGL1|protein_coding|CODING|NM_001172412.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.513192 rs28730710 -0.693147 0.00926615 147 D395 399 gaC/gaT LOW 11 SILENT CODING CASQ2 A protein_coding NM_001232.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116243877 G A 0 222 0 0.4599 0.4257 0.464 0.3224 0.4135 0.4714 0.447798 0.387975 0.357326 1 4724 46084 5172 2581 2662 23798 358 6789 2 10364 120076 11480 8588 6526 65762 908 16448 0.687457 2 benign 0 . 167 41,59,12,46 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D395|399|CASQ2|protein_coding|CODING|NM_001232.3|11|A),DOWNSTREAM(MODIFIER||3032||524|VANGL1|protein_coding|CODING|NM_001172412.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.951407 rs7413162 -0.693147 0.00851482 167 399 LOW 3 CODING CASQ2 G protein_coding NM_001232.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116283343 A G 0 222 0 0.2814 0.6436 0.7608 0.7431 0.8738 0.7106 0.37744 0.708442 0.878023 1 3720 95236 8838 6530 5384 57847 724 12193 2 10328 120986 11550 8562 6598 66572 906 16470 0.624037 2 benign 0 . 94 28,9,34,12 SPLICE_SITE_REGION+INTRON(LOW||||399|CASQ2|protein_coding|CODING|NM_001232.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.500085 rs9428083 -0.693147 0.456344 94 T66A 399 Acg/Gcg MODERATE 1 MISSENSE CODING CASQ2 C protein_coding NM_001232.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116310967 T C 0 228 0 0.4856 0.4012 0.3674 0.5159 0.2922 0.3047 0.437585 0.339382 0.28907 2 4722 39634 4208 4735 1806 18935 276 4952 2 10406 121390 11576 8636 6614 66738 908 16512 0.887755 2 benign 0 COSM1332993 106 2,0,55,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T66A|399|CASQ2|protein_coding|CODING|NM_001232.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.52551 rs4074536 -0.693147 0.532802 106 399 36 MODIFIER 1 CODING CASQ2 C protein_coding NM_001232.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116311198 T C 0 228 0 0.8631 0.9625 0.9914 1 0.999 1 0.874489 0.957077 0.999418 2 7302 95165 8522 6176 5780 52090 764 14531 2 8362 96344 8580 6176 5780 52142 768 14536 0 . 0 . 0 64 0,0,10,47 UTR_5_PRIME(MODIFIER||36||399|CASQ2|protein_coding|CODING|NM_001232.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4074537 -0.693147 0.487154 64 135 644 MODIFIER 2 CODING NHLH2 C protein_coding NM_001111061.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116379942 T C 0 222 0 0.0318 0.0817 0.196 0.1042 0.0437 0.0838 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991898 0 . 0 . 87 15,23,20,21 UTR_3_PRIME(MODIFIER||644||135|NHLH2|protein_coding|CODING|NM_001111061.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.991898 rs11805084 -0.693145 0.0133071 87 135 414 MODIFIER 2 CODING NHLH2 T protein_coding NM_001111061.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116380172 C T 0 228 0 0.2927 0.4541 0.5317 0.5903 0.3976 0.5348 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 98 0,0,42,42 UTR_3_PRIME(MODIFIER||414||135|NHLH2|protein_coding|CODING|NM_001111061.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10754377 -0.693147 0.467046 98 135 2307 MODIFIER 1 CODING NHLH2 C protein_coding NM_001111061.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116383300 T C 0 228 0 0.8896 0.9694 0.9899 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 119 0,0,38,72 UTR_5_PRIME(MODIFIER||2307||135|NHLH2|protein_coding|CODING|NM_001111061.1|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2811569 -0.693147 0.00106432 119 135 2340 MODIFIER 1 CODING NHLH2 A protein_coding NM_001111061.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116383333 C A 0 222 0 0.0356 0.2248 0.2219 0.375 0.2256 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 98 14,43,13,27 UTR_5_PRIME(MODIFIER||2340||135|NHLH2|protein_coding|CODING|NM_001111061.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666139 rs4839047 -0.693145 2.67598e-05 98 S96 547 tcC/tcT LOW 2 SILENT CODING SLC22A15 T protein_coding NM_018420.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116534852 C T 0 222 0 0.1362 0.4353 0.4827 0.4196 0.6441 0.6074 0.201894 0.486248 0.622874 1 1155 41015 2438 1865 2129 25753 334 7341 2 4992 68432 4682 3958 3510 39154 552 11584 0.558816 0 . 0 . 61 6,26,4,22 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S96|547|SLC22A15|protein_coding|CODING|NM_018420.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.367479 rs4046190 -0.692976 0.0133247 61 L205 547 ctG/ctC LOW 5 SILENT CODING SLC22A15 C protein_coding NM_018420.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116569530 G C 0 222 0 0.8495 0.9034 0.8674 0.874 0.9543 0.9796 0.877755 0.927104 0.950399 1 8466 112112 9618 7723 5936 63439 830 16100 2 9802 120768 11574 8626 6614 66740 900 16512 0.966482 0 . 0 . 111 30,15,20,29 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L205|547|SLC22A15|protein_coding|CODING|NM_018420.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999971 rs2488429 -0.693147 0.025725 111 S404 547 tcC/tcT LOW 9 SILENT CODING SLC22A15 T protein_coding NM_018420.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116605423 C T 0 222 0 0.2655 0.1276 0.1398 0.126 0.0437 0.0204 0.230642 0.108278 0.0470963 1 2360 9665 1998 905 679 3248 63 412 2 9822 120752 11558 8618 6614 66728 900 16512 0.881506 0 . 0 . 168 45,36,46,25 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S404|547|SLC22A15|protein_coding|CODING|NM_018420.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.906474 rs3748743 -0.693147 0.111473 168 547 498 MODIFIER 12 CODING SLC22A15 A protein_coding NM_018420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116610227 G A 0 63 0 0.3101 0.7232 0.7925 0.872 0.8877 0.91 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||498||547|SLC22A15|protein_coding|CODING|NM_018420.2|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1281744,rs386526126 -0.453602 0.66 3 G223 362 ggA/ggG LOW 6 SILENT CODING MAB21L3 G protein_coding NM_152367.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116670774 A G 0 222 0 0.9009 0.4175 0.2983 0.2748 0.2227 0.1963 0.773718 0.404352 0.215116 1 8279 34430 3447 2175 1898 14704 267 3660 2 10398 120236 11548 8634 6614 66400 898 15744 0.956292 0 . 0 . 65 30,5,20,6 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G223|362|MAB21L3|protein_coding|CODING|NM_152367.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.646883 rs10754431 -0.692976 0.226471 65 362 49 MODIFIER 7 CODING MAB21L3 C protein_coding NM_152367.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116676035 A C 0 228 0 0.9009 0.4209 0.3055 0.2798 0.2266 0.1994 0.771344 0.406168 0.219121 2 7348 32065 3269 1976 1780 13879 253 3560 2 9198 111564 10634 7680 6284 60902 850 16016 0 . 0 . 0 83 0,0,17,59 UTR_3_PRIME(MODIFIER||49||362|MAB21L3|protein_coding|CODING|NM_152367.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10802159 -0.693147 0.05659 83 362 157 MODIFIER 7 CODING MAB21L3 G protein_coding NM_152367.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116676143 A G 0 167 0 0.1074 0.0946 0.147 0.1548 0.0537 0.0204 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,0,23 UTR_3_PRIME(MODIFIER||157||362|MAB21L3|protein_coding|CODING|NM_152367.2|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs41313286 -0.692717 0.480631 23 362 682 MODIFIER 7 CODING MAB21L3 C protein_coding NM_152367.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 116676668 G C 0 36.3 0 0.9009 0.4215 0.3055 0.2798 0.2296 0.1994 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||682||362|MAB21L3|protein_coding|CODING|NM_152367.2|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs983760 -0.453602 0.02 2 P276 879 ccA/ccG LOW 3 SILENT CODING PTGFRN G protein_coding NM_020440.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117487710 A G 0 228 0 0.7549 0.8594 0.9222 0.8452 0.8966 0.9325 0.529732 0.644802 0.703768 2 7764 106391 10461 7258 5533 59448 791 15136 2 9868 119328 11506 8572 6578 65596 888 16320 0.525 0 . 0 . 47 1,1,17,23 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P276|879|PTGFRN|protein_coding|CODING|NM_020440.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.9375 rs10159095 -0.693145 0.038906 47 S277T 879 Tca/Aca MODERATE 3 MISSENSE CODING PTGFRN A protein_coding NM_020440.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117487711 T A 0 228 0 0.7549 0.8594 0.9222 0.8452 0.8966 0.9325 0.521562 0.640363 0.701256 2 7758 106363 10466 7257 5534 59440 791 15117 2 9862 119296 11508 8574 6580 65586 888 16298 0.925 0 . 0 . 47 1,1,17,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Aca|S277T|879|PTGFRN|protein_coding|CODING|NM_020440.3|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.9375 rs4546904 -0.693145 0.038906 47 R430Q 879 cGg/cAg MODERATE 5 MISSENSE CODING PTGFRN A protein_coding NM_020440.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117503940 G A 0 222 0 0.0136 0.1222 0.0591 0.3839 0.0437 0.1247 0.0177031 0.0276026 0.0326744 1 167 8043 484 3400 628 2338 50 976 2 10232 110906 11486 8518 6614 64090 794 9172 0.828141 0 . 0 . 95 23,10,38,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R430Q|879|PTGFRN|protein_coding|CODING|NM_020440.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.793983 rs34625170 -0.693147 0.407251 95 V837I 879 Gtc/Atc MODERATE 9 MISSENSE CODING PTGFRN A protein_coding NM_020440.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117529458 G A 0 228 0 0.3018 0.498 0.5951 0.6597 0.4364 0.591 0.312755 0.400046 0.444767 2 3148 59429 8005 5726 2876 29513 438 9723 2 10298 121004 11554 8628 6602 66524 904 16494 0 . 0 . 0 35 0,0,23,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V837I|879|PTGFRN|protein_coding|CODING|NM_020440.3|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10801922 -0.693136 0.0943504 35 879 684 MODIFIER 9 CODING PTGFRN G protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117530273 A G 0 228 0 0.5144 0.5877 0.6527 0.6607 0.507 0.6483 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 61 1,0,47,9 UTR_3_PRIME(MODIFIER||684||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3885 -0.693147 3.13053e-05 61 879 888 MODIFIER 9 CODING PTGFRN A protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117530477 G A 0 218 0 0.5113 0.5861 0.6527 0.6597 0.507 0.6452 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,1,28 UTR_3_PRIME(MODIFIER||888||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10801923 -0.693079 0.448733 29 879 918 MODIFIER 9 CODING PTGFRN T protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117530507 C T 0 192 0 0.4697 0.5747 0.6484 0.6597 0.507 0.6462 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,1,13 UTR_3_PRIME(MODIFIER||918||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1127655 -0.686358 0.000251246 14 879 922 MODIFIER 9 CODING PTGFRN T protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117530511 C T 0 199 0 0.5113 0.5863 0.6527 0.6597 0.507 0.6462 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,1,13 UTR_3_PRIME(MODIFIER||922||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1127656 -0.686358 0.000270463 14 879 2031 MODIFIER 9 CODING PTGFRN A protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117531620 G A 0 46.3 0 0.2852 0.502 0.5922 0.6597 0.4364 0.636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2031||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13951 -0.453602 0.5 2 879 2224 MODIFIER 9 CODING PTGFRN C protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117531813 T C 0 80 0 0.5151 0.5879 0.6527 0.6607 0.507 0.6483 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||2224||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3829881,rs386587403 -0.556411 0.348933 4 879 2322 MODIFIER 9 CODING PTGFRN G protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117531911 A G 0 183 0 0.2935 0.5196 0.6369 0.6617 0.505 0.6104 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,5,3 UTR_3_PRIME(MODIFIER||2322||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.900802 0 . rs10923191 -0.651104 0.0694872 8 879 2702 MODIFIER 9 CODING PTGFRN G protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117532291 A G 0 222 0 0.0877 0.2378 0.3934 0.2073 0.2306 0.3691 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.719697 0 . 0 . 74 12,24,14,17 UTR_3_PRIME(MODIFIER||2702||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.42872 rs8254 -0.69311 0.112712 74 879 2783 MODIFIER 9 CODING PTGFRN T protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117532372 G T 0 203 0 0.3699 0.3337 0.255 0.4514 0.2763 0.2781 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997424 0 . 0 . 49 5,25,4,15 UTR_3_PRIME(MODIFIER||2783||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999526 rs11836 -0.69168 0.456833 49 879 3201 MODIFIER 9 CODING PTGFRN T protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117532790 C T 0 222 0 0.3351 0.3974 0.5403 0.256 0.3926 0.5307 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.807085 0 . 0 . 81 20,19,27,10 UTR_3_PRIME(MODIFIER||3201||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.326363 rs1127215 -0.693141 0.755623 81 879 3209 MODIFIER 9 CODING PTGFRN G protein_coding NM_020440.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117532798 C G 0 222 0 0.0439 0.2254 0.389 0.2073 0.2296 0.3691 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.676955 0 . 0 . 84 18,19,30,9 UTR_3_PRIME(MODIFIER||3209||879|PTGFRN|protein_coding|CODING|NM_020440.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0428776 rs944 -0.693144 0.504136 84 M415V 1021 Atg/Gtg MODERATE 5 MISSENSE CODING CD101 G protein_coding NM_001256106.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117559726 A G 0 228 0 0.969 0.9353 0.9625 0.8462 0.9602 0.9366 0.97231 0.975088 0.976512 2 10100 115399 10895 7265 6000 64728 857 15554 2 10400 121248 11576 8648 6614 66666 908 16436 1 0 . 0 . 112 1,0,75,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M415V|1021|CD101|protein_coding|CODING|NM_001256106.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2249265 -0.693147 0.118883 112 Q551 1021 caA/caG LOW 6 SILENT CODING CD101 G protein_coding NM_001256106.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117560818 A G 0 228 0 0.0408 0.3444 0.4438 0.6181 0.2813 0.4673 0.0832955 0.210057 0.275 2 716 40856 6547 5259 2388 18594 298 7054 2 10378 120260 11506 8630 6584 66210 898 16054 1 0 . 0 . 116 1,0,79,23 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q551|1021|CD101|protein_coding|CODING|NM_001256106.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3736908 -0.693147 0.125335 116 I588 1021 atC/atA LOW 6 SILENT CODING CD101 A protein_coding NM_001256106.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117560929 C A 0 222 0 0.0129 0.2097 0.3876 0.2054 0.2326 0.3303 0.0544712 0.175765 0.237907 1 451 31316 6004 1669 1770 15961 237 5224 2 10406 121336 11560 8642 6610 66698 908 16512 0.935923 0 . 0 . 132 35,25,14,41 SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I588|1021|CD101|protein_coding|CODING|NM_001256106.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982564 rs3736907 -0.693147 0.71824 132 V938M 1021 Gtg/Atg MODERATE 8 MISSENSE CODING CD101 A protein_coding NM_001256106.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117568514 G A 0 222 0 0 0.00079872 0 0.004 0 0 0 7.6888e-05 0.000116279 1 0 42 0 41 0 0 0 1 2 10292 117708 11508 8616 6606 65636 872 14178 0.961315 0 . 0 . 63 1,29,5,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V938M|1021|CD101|protein_coding|CODING|NM_001256106.2|8|A),INTRAGENIC(MODIFIER|||||LOC101929099||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.388584 rs142603483 -0.693097 0.54327 63 1162 9 MODIFIER 1 CODING TTF2 A protein_coding NM_003594.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117602960 C A 0 228 0 0.3835 0.7326 0.8631 0.9018 0.8757 0.7904 0.470722 0.729509 0.862093 2 4755 97418 10286 7611 5332 56639 712 12083 2 10354 119004 11554 8650 6612 66070 876 14888 0 . 0 . 0 93 0,0,49,35 UTR_5_PRIME(MODIFIER||9||1162|TTF2|protein_coding|CODING|NM_003594.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2244501 -0.693147 0.236858 93 K167E 1162 Aaa/Gaa MODERATE 5 MISSENSE CODING TTF2 G protein_coding NM_003594.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117617705 A G 0 228 0 0.1157 0.5146 0.6671 0.7679 0.5934 0.6033 0.206537 0.469322 0.603953 2 1939 69734 8042 6413 3475 39667 526 9672 2 10316 121172 11558 8638 6612 66638 908 16502 1 0 . 0 . 83 1,0,43,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K167E|1162|TTF2|protein_coding|CODING|NM_003594.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs998532 -0.693147 0.142385 83 N287 1162 aaC/aaT LOW 5 SILENT CODING TTF2 T protein_coding NM_003594.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117618067 C T 0 228 0 0.112 0.5138 0.6686 0.7679 0.5934 0.6033 0.20404 0.468553 0.60407 2 1909 69703 8035 6413 3475 39682 525 9664 2 10346 121288 11574 8646 6614 66696 906 16506 0 . 0 . 0 79 0,0,41,34 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N287|1162|TTF2|protein_coding|CODING|NM_003594.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1289673 -0.693147 0.0515384 79 580 69 MODIFIER 6 CODING TRIM45 A protein_coding NM_025188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117654858 G A 0 187 0 0.034 0.0609 0.0749 0.0724 0.0577 0.0787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.931606 0 . 0 . 55 26,2,19,1 UTR_3_PRIME(MODIFIER||69||580|TRIM45|protein_coding|CODING|NM_025188.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.899577 rs1048635 -0.692067 0.901948 55 M496T 580 aTg/aCg MODERATE 5 MISSENSE CODING TRIM45 G protein_coding NM_025188.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117656088 A G 0 222 0 0.6793 0.4451 0.4755 0.1865 0.4364 0.3824 0.620064 0.475704 0.401744 1 6633 50101 4870 1814 2443 27542 385 6414 2 10378 120872 11516 8622 6594 66422 906 16434 0.908944 0 . 0 . 110 30,19,22,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M496T|580|TRIM45|protein_coding|CODING|NM_025188.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992732 rs1289658 -0.693147 0.357339 110 580 90 MODIFIER 1 CODING TRIM45 T protein_coding NM_025188.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117663913 C T 0 145 0 0.7625 0.7666 0.6282 0.9673 0.6441 0.7894 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,1,6 UTR_5_PRIME(MODIFIER||90||580|TRIM45|protein_coding|CODING|NM_025188.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3795655 -0.636426 0.034401 7 282 3788 MODIFIER 6 CODING VTCN1 A protein_coding NM_024626.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117686492 C A 0 32.6 0 0.8359 0.7899 0.7896 0.9018 0.7157 0.6892 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3788||282|VTCN1|protein_coding|CODING|NM_024626.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13505 -0.379885 0 2 282 3453 MODIFIER 6 CODING VTCN1 T protein_coding NM_024626.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117686827 C T 0 9.7 0 0.8366 0.7897 0.7896 0.9018 0.7147 0.6881 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3453||282|VTCN1|protein_coding|CODING|NM_024626.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6428679 -0.379885 0 1 282 3366 MODIFIER 6 CODING VTCN1 T protein_coding NM_024626.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117686914 C T 0 46.3 0 0.8359 0.7897 0.7896 0.9028 0.7147 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3366||282|VTCN1|protein_coding|CODING|NM_024626.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6664759 -0.453602 0.36 2 282 3155 MODIFIER 6 CODING VTCN1 T protein_coding NM_024626.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117687125 A T 0 76 0 0.8359 0.7901 0.7896 0.9038 0.7157 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||3155||282|VTCN1|protein_coding|CODING|NM_024626.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1937956 -0.511536 0.862672 3 282 8 MODIFIER 5 CODING VTCN1 A protein_coding NM_024626.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117690272 G A 0 228 0 0.2897 0.7346 0.8718 0.9206 0.9225 0.8538 0.415116 0.751269 0.923488 2 3937 105749 10749 7723 6331 61741 810 14458 2 10390 121202 11492 8640 6612 66658 908 16502 0 . 0 . 0 108 0,0,72,25 UTR_3_PRIME(MODIFIER||8||282|VTCN1|protein_coding|CODING|NM_024626.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10754339 -0.693147 0.071459 108 641 124 MODIFIER 1 CODING MAN1A2 A protein_coding NM_006699.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 117910682 G A 0 175 0 0.9539 0.7802 0.6772 0.623 0.7555 0.8057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 31 11,1,15,2 UTR_5_PRIME(MODIFIER||124||641|MAN1A2|protein_coding|CODING|NM_006699.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.595337 rs1146297 -0.690438 0.877517 31 641 262 MODIFIER 13 CODING MAN1A2 G protein_coding NM_006699.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118065841 A G 0 222 0 0.4009 0.4171 0.5706 0.4464 0.3678 0.3507 0 . 0 1 450 6715 193 230 562 2275 85 2920 2 1032 17378 346 538 1616 5958 216 7672 0.984215 0 . 0 . 168 47,31,38,27 UTR_3_PRIME(MODIFIER||262||641|MAN1A2|protein_coding|CODING|NM_006699.3|13|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.859943 rs1290558 -0.693147 0.235601 168 641 2455 MODIFIER 13 CODING MAN1A2 G protein_coding NM_006699.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118068034 A G 0 72 0 0.1074 0.2813 0.2032 0.4851 0.2863 0.3569 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.705554 0 . 0 . 23 0,16,0,7 UTR_3_PRIME(MODIFIER||2455||641|MAN1A2|protein_coding|CODING|NM_006699.3|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.665772 rs41312696 -0.636426 0.00429645 23 L29 391 ctC/ctG LOW 2 SILENT CODING FAM46C G protein_coding NM_017709.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118165577 C G 0 222 0 0.2617 0.1268 0.085 0.122 0.0626 0.045 0.215161 0.11141 0.0582558 1 2288 9594 760 1022 417 3950 74 1083 2 10400 121380 11576 8642 6612 66732 908 16510 0.833461 0 . 0 . 117 32,27,25,20 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L29|391|FAM46C|protein_coding|CODING|NM_017709.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999914 rs865443 -0.693147 0.0159476 117 H67Q 391 caC/caG MODERATE 2 MISSENSE CODING FAM46C G protein_coding NM_017709.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118165691 C G 0 222 0 0.2617 0.1268 0.085 0.122 0.0626 0.045 0 . 0 1 2293 9598 760 1023 417 3949 74 1082 2 10402 121360 11570 8638 6612 66720 908 16510 0.776578 1 not-provided 0 . 100 33,29,21,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H67Q|391|FAM46C|protein_coding|CODING|NM_017709.3|2|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.842303 rs1630312 -0.693139 0.0321944 100 N161 391 aaC/aaT LOW 2 SILENT CODING FAM46C T protein_coding NM_017709.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118165973 C T 0 169 0 0.3419 0.2798 0.3127 0.2391 0.2266 0.2689 0.323196 0.257497 0.223837 1 3351 31008 3585 1811 1451 15502 244 5064 2 10380 121304 11570 8640 6614 66682 908 16510 0.965069 0 . 0 . 36 5,15,2,13 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N161|391|FAM46C|protein_coding|CODING|NM_017709.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993218 rs1627787 -0.688148 0.91179 36 391 84 MODIFIER 2 CODING FAM46C G protein_coding NM_017709.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118166750 A G 0 222 0 0.1936 0.2398 0.3098 0.2391 0.2237 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.970649 0 . 0 . 82 27,19,18,13 UTR_3_PRIME(MODIFIER||84||391|FAM46C|protein_coding|CODING|NM_017709.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.880832 rs2066411,rs386556095 -0.69311 0.00709911 82 391 987 MODIFIER 2 CODING FAM46C T protein_coding NM_017709.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118167653 C T 0 222 0 0.4478 0.2344 0.111 0.2748 0.1103 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.954196 0 . 0 . 59 9,21,6,15 UTR_3_PRIME(MODIFIER||987||391|FAM46C|protein_coding|CODING|NM_017709.3|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.219442 rs386617900,rs866111 -0.692352 0.046444 59 Q1851 2223 caG/caA LOW 39 SILENT CODING SPAG17 T protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118530796 C T 0 222 0 0.0522 0.1384 0.0461 0.3403 0.0626 0.1902 0.0490241 0.054744 0.0576744 1 534 10129 428 2727 249 3755 80 2356 2 9860 111434 10830 8332 6336 61414 832 13830 0.0972184 0 . 0 . 145 45,18,37,28 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1851|2223|SPAG17|protein_coding|CODING|NM_206996.2|39|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846797 rs12040811 -0.693147 0.134662 145 P1711 2223 ccT/ccC LOW 35 SILENT CODING SPAG17 G protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118537074 A G 0 222 0 0.034 0.1284 0.0418 0.3204 0.0616 0.1881 0.0413073 0.0517533 0.0571063 1 436 10298 436 2792 252 3830 80 2472 2 10402 121020 11434 8596 6602 66598 906 16482 0.243861 0 . 0 . 134 49,18,40,15 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1711|2223|SPAG17|protein_coding|CODING|NM_206996.2|35|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.412894 rs12031260 -0.693147 0.347973 134 P1348L 2223 cCa/cTa MODERATE 28 MISSENSE CODING SPAG17 A protein_coding NM_206996.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118565953 G A 0 222 0 0.1551 0.2873 0.4107 0.1567 0.4314 0.365 0.203586 0.365524 0.448488 1 2083 47702 4065 1314 3147 30164 358 6571 2 10374 120826 11414 8582 6574 66506 902 16474 0.961426 0 . 0 . 104 29,4,43,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1348L|2223|SPAG17|protein_coding|CODING|NM_206996.2|28|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.253041 rs10923472 -0.693147 0.0177002 104 Y1037 2223 taC/taT LOW 22 SILENT CODING SPAG17 A protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118583408 G A 0 222 0 0.1573 0.2885 0.4135 0.1567 0.4324 0.365 0.202905 0.370368 0.456163 1 2092 48341 4104 1311 3207 30666 365 6596 2 10402 121216 11492 8640 6596 66678 908 16500 0.480318 0 . 0 . 188 55,36,29,40 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1037|2223|SPAG17|protein_coding|CODING|NM_206996.2|22|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.470332 rs10923477 -0.693147 0.0396205 188 P635 2223 ccG/ccA LOW 14 SILENT CODING SPAG17 T protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118624123 C T 0 222 0 0.053 0.1264 0.0447 0.2877 0.0596 0.1861 0.0585565 0.057435 0.0568605 1 631 10030 452 2424 250 3779 79 2415 2 10406 121398 11578 8646 6614 66736 908 16510 0.983346 0 . 0 . 111 31,23,33,13 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P635|2223|SPAG17|protein_coding|CODING|NM_206996.2|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.490842 rs2298176 -0.693147 0.529264 111 P464 2223 ccC/ccT LOW 11 SILENT CODING SPAG17 A protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118629599 G A 0 222 0 0.0749 0.1318 0.0461 0.2847 0.0596 0.1861 0.0769405 0.0636629 0.0568605 1 833 10200 454 2417 250 3767 76 2403 2 10376 119324 11562 8632 6614 66180 882 15078 0.979491 0 . 0 . 77 19,15,19,12 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P464|2223|SPAG17|protein_coding|CODING|NM_206996.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0969086 rs12142616 -0.69311 0.549044 77 N189 2223 aaT/aaC LOW 5 SILENT CODING SPAG17 G protein_coding NM_206996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118644430 A G 0 228 0 0.6906 0.5639 0.5072 0.4534 0.5477 0.5634 0.68611 0.604875 0.563256 2 7241 66984 4998 3765 3806 37551 485 9138 2 10406 121352 11550 8638 6610 66728 908 16512 0 . 0 . 0 156 0,0,56,80 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N189|2223|SPAG17|protein_coding|CODING|NM_206996.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10754367 -0.693147 0.0158796 156 R143Q 2223 cGa/cAa MODERATE 4 MISSENSE CODING SPAG17 T protein_coding NM_206996.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 118657952 C T 0 222 0 0.0038 0.106 0.0346 0.2728 0.0586 0.1718 0.0152134 0.0412181 0.0545349 1 135 8985 400 2273 250 3675 70 2182 2 10396 121358 11576 8632 6614 66724 908 16508 0.526953 0 . 0 . 106 36,20,27,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R143Q|2223|SPAG17|protein_coding|CODING|NM_206996.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.360894 rs12133381 -0.693145 0.369299 106 360 947 MODIFIER 6 CODING WARS2 T protein_coding NM_015836.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 119574587 C T 0 120 0 0.6097 0.5715 0.696 0.6042 0.5656 0.4039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,1 UTR_3_PRIME(MODIFIER||947||360|WARS2|protein_coding|CODING|NM_015836.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2645294 -0.511536 0.0785113 5 L19 364 Ttg/Ctg LOW 3 SILENT CODING HAO2 C protein_coding NM_001005783.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 119923724 T C 0 222 0 0.0817 0.3582 0.5216 0.4504 0.5298 0.3446 0.185202 0.404659 0.517093 1 1466 58663 7206 3992 3890 35330 415 6364 2 10404 121346 11564 8634 6610 66718 908 16508 0.999542 0 . 0 . 227 102,17,67,22 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L19|364|HAO2|protein_coding|CODING|NM_001005783.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987362 rs2275607 -0.693147 0.713096 227 364 LOW 5 CODING HAO2 G protein_coding NM_001005783.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 119927680 A G 0 222 0 0.7042 0.6675 0.7291 0.6726 0.6203 0.6176 0.68906 0.645856 0.623721 1 7266 79284 8922 5907 4426 41916 550 10297 2 10360 120380 11506 8466 6590 66312 898 16248 0.988712 0 . 0 . 264 60,54,66,53 SPLICE_SITE_REGION+INTRON(LOW||||364|HAO2|protein_coding|CODING|NM_001005783.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.72045 rs6667679 -0.693147 0.0079848 264 L338 373 Ctg/Ttg LOW 4 SILENT CODING HSD3B1 T protein_coding NM_000862.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120057158 C T 0 228 0 0.0333 0.3668 0.4813 0.6528 0.4254 0.3814 0.103722 0.321928 0.433721 2 907 53217 6705 5754 3616 29040 420 6775 2 10394 121266 11538 8604 6606 66706 906 16512 0.991304 0 . 0 . 134 1,1,54,61 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L338|373|HSD3B1|protein_coding|CODING|NM_000862.2|4|T) 1 0 . 0 . 1 0 1 1 0 59 0 0.991304 0.985772 0 0.326087 rs6203 -0.693147 0.170241 134 T367N 373 aCc/aAc MODERATE 4 MISSENSE CODING HSD3B1 A protein_coding NM_000862.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120057246 C A 0 228 0 0.9145 0.8335 0.7954 0.9177 0.66 0.8425 0.88079 0.749154 0.681712 2 9041 90646 9863 7977 4942 44776 659 13388 2 10162 119996 11470 8508 6590 65874 900 16492 0 . 0 . 0 82 0,0,20,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T367N|373|HSD3B1|protein_coding|CODING|NM_000862.2|4|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.870274 0 . rs1047303 -0.693147 1.94261e-05 82 533 140 MODIFIER 1 CODING PHGDH G protein_coding NM_006623.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120254506 A G 0 173 0 0.5825 0.6983 0.6844 0.9256 0.5835 0.7485 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,9,1 UTR_5_PRIME(MODIFIER||140||533|PHGDH|protein_coding|CODING|NM_006623.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs561931 -0.670168 0.359729 11 533 101 MODIFIER 1 CODING PHGDH C protein_coding NM_006623.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120254545 G C 0 213 0 0.9077 0.8175 0.755 0.9266 0.6859 0.7628 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,12,2 UTR_5_PRIME(MODIFIER||101||533|PHGDH|protein_coding|CODING|NM_006623.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs562038 -0.686358 0.103041 14 T442 533 acG/acA LOW 11 SILENT CODING PHGDH A protein_coding NM_006623.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120285546 G A 0 222 0 0.7716 0.7222 0.7478 0.622 0.668 0.7965 0.751929 0.706059 0.682558 1 7834 83957 7804 5212 3826 45387 640 13254 2 10400 121254 11558 8616 6600 66666 906 16508 0.375536 0 . 0 . 92 31,11,25,19 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T442|533|PHGDH|protein_coding|CODING|NM_006623.3|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973161 rs543703 -0.693146 0.0239732 92 158 365 MODIFIER 7 CODING REG4 G protein_coding NM_001159352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120336876 T G 0 228 0 0.2133 0.4583 0.5821 0.7589 0.4394 0.411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 64 0,1,20,34 UTR_3_PRIME(MODIFIER||365||158|REG4|protein_coding|CODING|NM_001159352.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs699778 -0.693147 0.0892151 64 D414 790 gaC/gaT LOW 1 SILENT CODING ADAM30 A protein_coding NM_021794.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120437718 G A 0 222 0 0.7171 0.3307 0.2133 0.1052 0.1322 0.3282 0.585338 0.282254 0.126977 1 6396 23881 2209 815 1222 8193 175 4871 2 10378 121254 11568 8642 6614 66650 906 16496 0.989431 0 . 0 . 112 40,11,35,12 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D414|790|ADAM30|protein_coding|CODING|NM_021794.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988912 rs2793823 -0.693147 0.812524 112 2471 2834 MODIFIER 34 CODING NOTCH2 C protein_coding NM_024408.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120455095 T C 0 222 0 0.1127 0.0773 0.072 0.0635 0.0199 0.1063 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.358017 0 . 0 . 46 2,19,4,20 UTR_3_PRIME(MODIFIER||2834||2471|NOTCH2|protein_coding|CODING|NM_024408.3|34|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.55771 rs1043964 -0.692831 0.466002 46 2471 2488 MODIFIER 34 CODING NOTCH2 G protein_coding NM_024408.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120455441 A G 0 222 0 0.8555 0.3754 0.2176 0.1131 0.1322 0.3589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.977871 0 . 0 . 69 26,9,16,5 UTR_3_PRIME(MODIFIER||2488||2471|NOTCH2|protein_coding|CODING|NM_024408.3|34|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.602289 rs386606490,rs699780 -0.692352 0.0407607 69 L2141 2471 Ctg/Ttg LOW 34 SILENT CODING NOTCH2 A protein_coding NM_024408.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120458924 G A 0 222 0 0.0106 0.0483 0.0605 0.0625 0.0199 0.1053 0.0154335 0.0179148 0.019186 1 152 5044 1023 584 222 1261 47 1755 2 10404 121402 11576 8654 6614 66736 908 16510 0.86104 0 . 0 . 103 33,23,19,19 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L2141|2471|NOTCH2|protein_coding|CODING|NM_024408.3|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.323498 rs3795666 -0.693143 0.203875 103 R5 2471 cgC/cgT LOW 1 SILENT CODING NOTCH2 A protein_coding NM_024408.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120612006 G A 0 13.1 0 0.2632 0.394 0.4049 0.4315 0.4423 0.4744 0 . 0 1 1917 44605 4696 3638 2397 24595 335 7027 2 5584 96182 10132 7610 5038 52230 702 14886 0.970786 0 . 0 COSM1320072 67 45,6,10,0 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R5|2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|A) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.888167 0.936147 0 0.669303 rs4021006 -0.670168 0.275189 67 2471 23 MODIFIER 1 CODING NOTCH2 T protein_coding NM_024408.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120612043 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 198 1127 239 192 17 224 10 247 2 572 8564 1088 898 506 3704 60 1736 0.29177 0 . 0 . 111 52,6,31,7 UTR_5_PRIME(MODIFIER||23||2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|T) 0 0.5 1 0 . 0 . 0 1 0 53 0 0.472251 0.967519 0 0.0337408 rs57122008 -0.693143 0.10386 111 2471 134 MODIFIER 1 CODING NOTCH2 G protein_coding NM_024408.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120612154 C G 0 127 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.341146 0 . 0 . 312 136,69,49,20 UTR_5_PRIME(MODIFIER||134||2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|G) 0 0.5 1 0 . 0 . 0 . 0 52 0 0.000231646 6.46932e-05 0 0.452501 rs56375229 -0.693147 0.0232167 312 2471 143 MODIFIER 1 CODING NOTCH2 A protein_coding NM_024408.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120612163 C A 0 204 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.516491 0 . 0 . 326 136,77,52,21 UTR_5_PRIME(MODIFIER||143||2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|A) 0 0.5 1 0 . 0 . 0 . 0 51 0 6.28414e-05 0.000376521 0 0.122152 rs55899574 -0.693147 0.20171 326 2471 245 MODIFIER 1 CODING NOTCH2 G protein_coding NM_024408.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120612265 A G 0 4.4 0 0.3079 0.2272 0.255 0.127 0.1501 0.2812 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.522773 0 . 0 . 163 23,57,0,71 START_GAINED(LOW||||2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|G),UTR_5_PRIME(MODIFIER||245||2471|NOTCH2|protein_coding|CODING|NM_024408.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 35 0 1.2599e-24 0.08725 0 0.985086 rs375584849 -0.693147 0.142324 163 280 56 MODIFIER 5 CODING FCGR1B T protein_coding NM_001017986.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 120927081 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 105 0,0,73,22 UTR_3_PRIME(MODIFIER||56||280|FCGR1B|protein_coding|CODING|NM_001017986.3|5|T) 0 . 0 . 0 . 0 . 0 . 44 0 0 0.492011 0 . rs76856338 -0.693147 0.454697 105 C64R 318 Tgc/Cgc MODERATE 2 MISSENSE CODING SRGAP2B C protein_coding NM_001271870.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121115958 T C 0 26.8 0 0.2126 0.1653 0.1052 0.2748 0.1382 0.0593 0 . 0 2 5 48 1 6 3 28 2 3 2 1526 23006 788 524 1014 12174 204 6776 0 . 0 . 0 6 0,0,1,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C64R|318|SRGAP2B|protein_coding|CODING|NM_001271870.2|2|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||C),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 12 0 0 1 0 . rs200236715,rs2289361 -0.616816 0.203362 6 N71 318 aaC/aaT LOW 2 SILENT CODING SRGAP2B T protein_coding NM_001271870.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121115981 C T 0 74 0 . 0 . 0 . 0 . 0 . 1 240 2149 50 131 77 890 24 737 2 1750 23272 658 614 880 11182 222 7966 0.995413 0 . 0 . 28 10,8,5,5 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N71|318|SRGAP2B|protein_coding|CODING|NM_001271870.2|2|T|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||T),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.920309 0.461407 0 0.296983 rs201138873 -0.670168 0.0682888 28 H94R 318 cAc/cGc MODERATE 3 MISSENSE CODING SRGAP2B G protein_coding NM_001271870.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121116688 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 5482 63030 5912 4555 3684 34822 466 8109 2 9714 119448 11490 8556 6586 66062 886 16154 0.68254 0 . 0 . 134 2,0,94,32 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAc/cGc|H94R|318|SRGAP2B|protein_coding|CODING|NM_001271870.2|3|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||G),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||G) 0 . 0 . 0 . 0 . 1 0 51 0 0.384921 0.799709 0 0.769841 rs61806690 -0.693147 0.281149 134 F266 318 ttT/ttC LOW 6 SILENT CODING SRGAP2B C protein_coding NM_001271870.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121129557 T C 0 75 0 . 0 . 0 . 0 . 0 . 1 1019 11705 442 552 630 5804 114 3144 2 2040 23434 884 1106 1260 11622 228 6294 0.869989 0 . 0 . 63 15,21,0,27 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F266|318|SRGAP2B|protein_coding|CODING|NM_001271870.2|6|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||C),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.993846 0.999479 0 0.163608 rs200881439,rs2580438 -0.693021 0.0482567 63 318 3006 MODIFIER 6 CODING SRGAP2B A protein_coding NM_001271870.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121132722 T A 0 36.3 0 0.5287 0.5557 0.572 0.6756 0.5716 0.4407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3006||318|SRGAP2B|protein_coding|CODING|NM_001271870.2|6|A|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 54 0 0 . 0 . rs1137590 -0.453602 0.5 2 318 4063 MODIFIER 6 CODING SRGAP2B G protein_coding NM_001271870.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 121133779 C G 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4063||318|SRGAP2B|protein_coding|CODING|NM_001271870.2|6|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2-AS1||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 . 0 51 0 0 . 0 . rs2919067 -0.379885 0 1 164 119 MODIFIER 1 CODING PPIAL4G A protein_coding NM_001123068.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767235 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666902 0 . 0 . 194 93,18,55,15 UTR_3_PRIME(MODIFIER||119||164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|A) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.190135 0.000754905 0 0.112905 rs200645759,rs61824236 -0.693147 3.79459e-07 194 F112L 164 ttT/ttA MODERATE 1 MISSENSE CODING PPIAL4G T protein_coding NM_001123068.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767513 A T 0 204 0 . 0 . 0 . 0 . 0 . 1 4151 55336 5477 4077 3080 30333 418 7800 2 8944 116094 11376 8532 6518 63522 890 16312 0.0582471 0 . 0 . 1699 574,518,220,245 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F112L|164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 47 0 2.56386e-07 0.441108 0 0.276465 rs6604511 -0.693147 0.000124867 1699 G109 164 ggT/ggC LOW 1 SILENT CODING PPIAL4G G protein_coding NM_001123068.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767522 A G 0 187 0 . 0 . 0 . 0 . 0 . 1 4200 55159 5434 4046 3012 30294 417 7756 2 8724 115406 11354 8502 6428 63242 880 16276 0.0263475 0 . 0 . 1627 556,486,199,233 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G109|164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 46 0 6.18767e-06 1.90331e-05 0 0.0488816 rs6604512 -0.693147 2.38109e-06 1627 A101V 164 gCa/gTa MODERATE 1 MISSENSE CODING PPIAL4G A protein_coding NM_001123068.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767547 G A 0 169 0 0.4092 0.3748 0.379 0.3284 0.326 0.4233 0 . 0 1 3982 51533 5037 3750 2852 28189 388 7335 2 8416 110126 10752 8124 6198 60138 832 15666 0.672578 0 . 0 . 1527 512,469,131,194 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A101V|164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 42 0 0.236277 4.33039e-13 0 0.052515 rs2490183 -0.693147 0.000294869 1527 H69R 164 cAc/cGc MODERATE 1 MISSENSE CODING PPIAL4G C protein_coding NM_001123068.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767643 T C 0 163 0 0.3033 0.3251 0.3357 0.3274 0.3807 0.2873 0 . 0 1 1155 14576 583 937 776 6450 134 4541 2 7614 98500 9758 7062 5066 54220 754 14026 0.0797031 0 . 0 . 1040 322,347,101,169 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H69R|164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 42 0 0 0.000154369 0 0.0624141 rs61824238 -0.693147 0.00380379 1040 Q24L 164 cAg/cTg MODERATE 1 MISSENSE CODING PPIAL4G A protein_coding NM_001123068.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 143767778 T A 0 190 0 . 0 . 0 . 0 . 0 . 1 108 449 29 30 4 264 2 12 2 9754 120148 11522 8620 6610 66276 898 16468 0.0556361 0 . 0 . 1131 443,226,155,186 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q24L|164|PPIAL4G|protein_coding|CODING|NM_001123068.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 49 0 0 3.43649e-10 0 1.30476e-05 rs6604516 -0.693147 3.29092e-25 1131 941 51 MODIFIER 1 CODING NBPF8 G protein_coding NM_001037501.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615080 A G 0 228 0 0.3933 0.5885 0.5937 0.9266 0.4443 0.6483 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 171 1,0,13,157 UTR_5_PRIME(MODIFIER||51||941|NBPF8|protein_coding|CODING|NM_001037501.2|1|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|1|G) 0 . 0 . 0 1 0 . 0 . 23 0 1 9.92376e-06 0 1 rs201657770,rs3896864 -0.693147 0.842498 171 941 29 MODIFIER 1 CODING NBPF8 G protein_coding NM_001037501.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615102 A G 0 49.8 0 0.1346 0.2776 0.2925 0.4375 0.2386 0.3354 0 . 0 1 2099 30267 2451 2180 1981 16475 232 4849 2 6942 80682 5920 4544 5140 46460 632 11044 0.17811 0 . 0 . 243 103,77,12,51 UTR_5_PRIME(MODIFIER||29||941|NBPF8|protein_coding|CODING|NM_001037501.2|1|G),UTR_5_PRIME(MODIFIER||29||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 1 0 . 1 0 21 0 0.0053542 4.01996e-13 0 0.000528016 rs201543878 -0.693147 0.807471 243 1110 29 MODIFIER 2 CODING NBPF9 G protein_coding NM_001277444.1.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615102 A G 0 49.8 0 0.1346 0.2776 0.2925 0.4375 0.2386 0.3354 0 . 0 1 2099 30267 2451 2180 1981 16475 232 4849 2 6942 80682 5920 4544 5140 46460 632 11044 0.17811 0 . 0 . 243 103,77,12,51 UTR_5_PRIME(MODIFIER||29||941|NBPF8|protein_coding|CODING|NM_001037501.2|1|G),UTR_5_PRIME(MODIFIER||29||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 1 0 . 1 0 21 0 0.0053542 4.01996e-13 0 0.000528016 rs201543878 -0.693147 0.807471 243 941 27 MODIFIER 1 CODING NBPF8 C protein_coding NM_001037501.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615104 T C 0 34.7 0 0.1346 0.2776 0.2925 0.4375 0.2386 0.3354 0 . 0 1 2118 31132 2610 2312 2027 16847 236 4982 2 6490 79308 6082 4782 4914 45240 602 11198 0.262158 0 . 0 . 249 110,76,12,51 UTR_5_PRIME(MODIFIER||27||941|NBPF8|protein_coding|CODING|NM_001037501.2|1|C),UTR_5_PRIME(MODIFIER||27||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 1 0 . 1 0 21 0 0.0051633 4.35967e-13 0 5.92622e-05 rs199745076 -0.693147 0.807471 249 1110 27 MODIFIER 2 CODING NBPF9 C protein_coding NM_001277444.1.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615104 T C 0 34.7 0 0.1346 0.2776 0.2925 0.4375 0.2386 0.3354 0 . 0 1 2118 31132 2610 2312 2027 16847 236 4982 2 6490 79308 6082 4782 4914 45240 602 11198 0.262158 0 . 0 . 249 110,76,12,51 UTR_5_PRIME(MODIFIER||27||941|NBPF8|protein_coding|CODING|NM_001037501.2|1|C),UTR_5_PRIME(MODIFIER||27||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 1 0 . 1 0 21 0 0.0051633 4.35967e-13 0 5.92622e-05 rs199745076 -0.693147 0.807471 249 V3G 941 gTa/gGa MODERATE 1 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615138 T G 0 145 0 . 0 . 0 . 0 . 0 . 1 559 15753 2700 2985 934 6288 118 2169 2 8036 99790 9200 6896 5962 55804 748 13144 0.558438 0 . 0 . 365 143,88,108,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V3G|941|NBPF8|protein_coding|CODING|NM_001037501.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V3G|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 0 . 0 1 0 22 0 0.0010416 1.84574e-21 0 0.614179 rs9441132 -0.693147 4.04436e-08 365 V3G 1110 gTa/gGa MODERATE 2 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144615138 T G 0 145 0 . 0 . 0 . 0 . 0 . 1 559 15753 2700 2985 934 6288 118 2169 2 8036 99790 9200 6896 5962 55804 748 13144 0.558438 0 . 0 . 365 143,88,108,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V3G|941|NBPF8|protein_coding|CODING|NM_001037501.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gGa|V3G|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|2|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 0 . 0 1 0 22 0 0.0010416 1.84574e-21 0 0.614179 rs9441132 -0.693147 4.04436e-08 365 F68L 941 Ttt/Ctt MODERATE 2 MISSENSE CODING NBPF8 C protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144617179 T C 0 222 0 0.0877 0.0757 0.0937 0.1468 0.003 0.0481 0 . 0 1 628 3913 1383 1129 0 228 21 524 2 9288 118028 11478 8364 6588 64960 886 16464 0.989892 0 . 0 COSN163208 272 104,30,69,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F68L|941|NBPF8|protein_coding|CODING|NM_001037501.2|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F68L|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|3|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.784887 3.34921e-16 0 0.820941 rs12059286 -0.693147 0.0610483 272 F68L 1110 Ttt/Ctt MODERATE 3 MISSENSE CODING NBPF9 C protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144617179 T C 0 222 0 0.0877 0.0757 0.0937 0.1468 0.003 0.0481 0 . 0 1 628 3913 1383 1129 0 228 21 524 2 9288 118028 11478 8364 6588 64960 886 16464 0.989892 0 . 0 COSN163208 272 104,30,69,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F68L|941|NBPF8|protein_coding|CODING|NM_001037501.2|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F68L|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|3|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.784887 3.34921e-16 0 0.820941 rs12059286 -0.693147 0.0610483 272 R92G 941 Agg/Ggg MODERATE 2 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144617251 A G 0 222 0 0.1263 0.3053 0.3429 0.6766 0.1948 0.2515 0 . 0 1 1322 30302 5354 5791 1599 12176 219 3841 2 9396 118414 11476 8370 6586 65238 886 16462 0.949108 0 . 0 . 263 63,82,40,55 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Agg/Ggg|R92G|941|NBPF8|protein_coding|CODING|NM_001037501.2|2|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Agg/Ggg|R92G|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|3|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.918415 0.00789702 0 0.701952 rs12057989 -0.693147 0.0899289 263 R92G 1110 Agg/Ggg MODERATE 3 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144617251 A G 0 222 0 0.1263 0.3053 0.3429 0.6766 0.1948 0.2515 0 . 0 1 1322 30302 5354 5791 1599 12176 219 3841 2 9396 118414 11476 8370 6586 65238 886 16462 0.949108 0 . 0 . 263 63,82,40,55 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Agg/Ggg|R92G|941|NBPF8|protein_coding|CODING|NM_001037501.2|2|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Agg/Ggg|R92G|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|3|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.918415 0.00789702 0 0.701952 rs12057989 -0.693147 0.0899289 263 Q113R 941 cAg/cGg MODERATE 3 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144618144 A G 0 228 0 0.7496 0.8237 0.879 0.8512 0.9076 0.7699 0 . 0 2 6739 102603 10372 7357 6211 58872 790 12262 2 9054 117490 11520 8562 6600 64742 890 16122 0 . 0 . 0 682 0,0,265,337 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q113R|941|NBPF8|protein_coding|CODING|NM_001037501.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q113R|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 1 0 . 1 0 35 0 0 1.16686e-06 0 . rs28691033,rs61809736 -0.693147 9.34194e-07 682 Q113R 1110 cAg/cGg MODERATE 4 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144618144 A G 0 228 0 0.7496 0.8237 0.879 0.8512 0.9076 0.7699 0 . 0 2 6739 102603 10372 7357 6211 58872 790 12262 2 9054 117490 11520 8562 6600 64742 890 16122 0 . 0 . 0 682 0,0,265,337 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q113R|941|NBPF8|protein_coding|CODING|NM_001037501.2|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q113R|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 1 0 . 1 0 35 0 0 1.16686e-06 0 . rs28691033,rs61809736 -0.693147 9.34194e-07 682 L132P 941 cTg/cCg MODERATE 3 MISSENSE CODING NBPF8 C protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144618201 T C 0 55 0 . 0 . 0 . 0 . 0 . 1 4116 57132 5668 4147 3289 31772 431 7709 2 8610 116360 11472 8474 6590 64162 882 16170 0.142388 0 . 0 . 367 82,152,6,96 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L132P|941|NBPF8|protein_coding|CODING|NM_001037501.2|3|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L132P|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 0 . 0 1 0 35 0 6.37944e-13 0.259182 0 0.375439 rs61809737 -0.693147 0.112847 367 L132P 1110 cTg/cCg MODERATE 4 MISSENSE CODING NBPF9 C protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144618201 T C 0 55 0 . 0 . 0 . 0 . 0 . 1 4116 57132 5668 4147 3289 31772 431 7709 2 8610 116360 11472 8474 6590 64162 882 16170 0.142388 0 . 0 . 367 82,152,6,96 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L132P|941|NBPF8|protein_coding|CODING|NM_001037501.2|3|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L132P|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|C) 0 0.5 1 0 . 0 . 0 1 0 35 0 6.37944e-13 0.259182 0 0.375439 rs61809737 -0.693147 0.112847 367 941 HIGH 3 CODING NBPF8 A protein_coding NM_001037501.2 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619346 G A 0 228 0 0.2436 0.5609 0.6196 0.7986 0.5288 0.7362 0 . 0 2 2527 69320 8359 7161 3771 35232 522 11748 2 9098 117742 11436 8506 6598 64884 886 16334 0.0139108 0 . 0 . 742 102,2,461,116 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||941|NBPF8|protein_coding|CODING|NM_001037501.2|3|A),SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 . 0 . 0 1 0 . 1 (NBPF8|NBPF8|1|1.00),(NBPF9|NBPF9.2|1|1.00) 46 0 1.15204e-05 1.19753e-09 0 0.883063 rs4649563 -0.693147 0.222989 742 1110 HIGH 4 CODING NBPF9 A protein_coding NM_001277444.1.2 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619346 G A 0 228 0 0.2436 0.5609 0.6196 0.7986 0.5288 0.7362 0 . 0 2 2527 69320 8359 7161 3771 35232 522 11748 2 9098 117742 11436 8506 6598 64884 886 16334 0.0139108 0 . 0 . 742 102,2,461,116 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||941|NBPF8|protein_coding|CODING|NM_001037501.2|3|A),SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|4|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 . 0 . 0 1 0 . 1 (NBPF8|NBPF8|1|1.00),(NBPF9|NBPF9.2|1|1.00) 46 0 1.15204e-05 1.19753e-09 0 0.883063 rs4649563 -0.693147 0.222989 742 D166 941 gaC/gaT LOW 4 SILENT CODING NBPF8 T protein_coding NM_001037501.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619354 C T 0 222 0 0.1634 0.2907 0.3156 0.5903 0.1909 0.2393 0 . 0 1 1497 28756 4762 5190 1551 11881 215 3660 2 9210 118356 11508 8538 6604 65176 896 16424 0.920297 0 . 0 . 881 413,95,238,53 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D166|941|NBPF8|protein_coding|CODING|NM_001037501.2|4|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D166|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|5|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|T) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.194766 1.56472e-08 0 0.528568 rs4067644 -0.693147 0.00134308 881 D166 1110 gaC/gaT LOW 5 SILENT CODING NBPF9 T protein_coding NM_001277444.1.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619354 C T 0 222 0 0.1634 0.2907 0.3156 0.5903 0.1909 0.2393 0 . 0 1 1497 28756 4762 5190 1551 11881 215 3660 2 9210 118356 11508 8538 6604 65176 896 16424 0.920297 0 . 0 . 881 413,95,238,53 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D166|941|NBPF8|protein_coding|CODING|NM_001037501.2|4|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D166|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|5|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|T) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.194766 1.56472e-08 0 0.528568 rs4067644 -0.693147 0.00134308 881 Q182R 941 cAg/cGg MODERATE 4 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619401 A G 0 63 0 . 0 . 0 . 0 . 0 . 1 736 5990 1069 1312 238 1567 54 1014 2 8632 99706 9088 6940 4970 54994 732 14350 0.0148524 0 . 0 . 1363 624,315,211,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q182R|941|NBPF8|protein_coding|CODING|NM_001037501.2|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q182R|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|5|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 0 . 0 1 0 52 0 6.47822e-09 2.93239e-15 0 2.23419e-14 rs61676308 -0.693147 7.98921e-06 1363 Q182R 1110 cAg/cGg MODERATE 5 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619401 A G 0 63 0 . 0 . 0 . 0 . 0 . 1 736 5990 1069 1312 238 1567 54 1014 2 8632 99706 9088 6940 4970 54994 732 14350 0.0148524 0 . 0 . 1363 624,315,211,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q182R|941|NBPF8|protein_coding|CODING|NM_001037501.2|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q182R|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|5|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 0.5 1 0 . 0 . 0 1 0 52 0 6.47822e-09 2.93239e-15 0 2.23419e-14 rs61676308 -0.693147 7.98921e-06 1363 V195E 941 gTg/gAg MODERATE 5 MISSENSE CODING NBPF8 A protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619903 T A 0 228 0 . 0 . 0 . 0 . 0 . 2 2370 50464 5511 6275 2811 22084 377 11036 2 7162 93252 7938 6714 5394 50648 718 14678 0 . 0 . 0 52 0,0,5,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V195E|941|NBPF8|protein_coding|CODING|NM_001037501.2|5|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V195E|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|6|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 . 0 . 0 . 0 . 1 0 34 0 0 0.0307911 0 . rs71527379 -0.693147 0.0585708 52 V195E 1110 gTg/gAg MODERATE 6 MISSENSE CODING NBPF9 A protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144619903 T A 0 228 0 . 0 . 0 . 0 . 0 . 2 2370 50464 5511 6275 2811 22084 377 11036 2 7162 93252 7938 6714 5394 50648 718 14678 0 . 0 . 0 52 0,0,5,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V195E|941|NBPF8|protein_coding|CODING|NM_001037501.2|5|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V195E|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|6|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 . 0 . 0 . 0 . 1 0 34 0 0 0.0307911 0 . rs71527379 -0.693147 0.0585708 52 P258S 941 Cca/Tca MODERATE 5 MISSENSE CODING NBPF8 T protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144620091 C T 0 222 0 0.0666 0.2784 0.3256 0.2411 0.3469 0.499 0 . 0 1 201 8708 388 498 201 4461 76 2883 2 1860 21530 938 1238 590 11658 198 5048 0.922495 0 . 0 . 503 144,85,106,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P258S|941|NBPF8|protein_coding|CODING|NM_001037501.2|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P258S|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|6|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|T) 0 0.5 1 0 . 1 0 . 1 0 31 0 0.927731 0.853476 0 0.604481 rs151155946,rs61810898 -0.693147 0.287204 503 P258S 1110 Cca/Tca MODERATE 6 MISSENSE CODING NBPF9 T protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144620091 C T 0 222 0 0.0666 0.2784 0.3256 0.2411 0.3469 0.499 0 . 0 1 201 8708 388 498 201 4461 76 2883 2 1860 21530 938 1238 590 11658 198 5048 0.922495 0 . 0 . 503 144,85,106,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P258S|941|NBPF8|protein_coding|CODING|NM_001037501.2|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P258S|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|6|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|T) 0 0.5 1 0 . 1 0 . 1 0 31 0 0.927731 0.853476 0 0.604481 rs151155946,rs61810898 -0.693147 0.287204 503 N441D 941 Aat/Gat MODERATE 9 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144815953 A G 0 228 0 0.388 0.481 0.4496 0.755 0.4533 0.3753 0 . 0 2 3293 43503 3995 3140 2682 24290 342 5761 2 8024 103208 10170 5012 6202 58782 798 14220 0.974756 0 . 0 COSM462807,COSM1719623 120 6,3,77,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N441D|941|NBPF8|protein_coding|CODING|NM_001037501.2|9|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N441D|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|10|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 1 0 . 1 0 31 0 0.442818 2.72876e-06 0 0.228363 rs199822480 -0.693147 0.0987875 120 N441D 1110 Aat/Gat MODERATE 10 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144815953 A G 0 228 0 0.388 0.481 0.4496 0.755 0.4533 0.3753 0 . 0 2 3293 43503 3995 3140 2682 24290 342 5761 2 8024 103208 10170 5012 6202 58782 798 14220 0.974756 0 . 0 COSM462807,COSM1719623 120 6,3,77,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N441D|941|NBPF8|protein_coding|CODING|NM_001037501.2|9|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N441D|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|10|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 1 0 . 1 0 31 0 0.442818 2.72876e-06 0 0.228363 rs199822480 -0.693147 0.0987875 120 V446I 941 Gtt/Att MODERATE 9 MISSENSE CODING NBPF8 A protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144815968 G A 0 212 0 0.084 0.3011 0.3847 0.374 0.4264 0.3313 0 . 0 1 1298 42027 4143 2898 2715 25083 332 5558 2 8144 104410 10438 4994 6268 59434 804 14328 0.971149 0 . 0 COSM1134674 134 13,21,85,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V446I|941|NBPF8|protein_coding|CODING|NM_001037501.2|9|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V446I|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|10|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 0.5 1 0 . 1 0 . 1 0 34 0 0.00126562 0.000248327 0 0.934026 rs200833830 -0.693147 0.0963923 134 V446I 1110 Gtt/Att MODERATE 10 MISSENSE CODING NBPF9 A protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144815968 G A 0 212 0 0.084 0.3011 0.3847 0.374 0.4264 0.3313 0 . 0 1 1298 42027 4143 2898 2715 25083 332 5558 2 8144 104410 10438 4994 6268 59434 804 14328 0.971149 0 . 0 COSM1134674 134 13,21,85,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V446I|941|NBPF8|protein_coding|CODING|NM_001037501.2|9|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V446I|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|10|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|A) 0 0.5 1 0 . 1 0 . 1 0 34 0 0.00126562 0.000248327 0 0.934026 rs200833830 -0.693147 0.0963923 134 Y636D 941 Tat/Gat MODERATE 14 MISSENSE CODING NBPF8 G protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144823868 T G 0 34.2 0 . 0 . 0 . 0 . 0 . 2 78 752 40 38 78 486 6 26 2 166 1834 88 48 260 1178 24 70 1 0 . 0 COSM1472511 8 1,0,4,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y636D|941|NBPF8|protein_coding|CODING|NM_001037501.2|14|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y636D|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|15|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 . 0 . 1 0 11 0 1 0.300267 0 1 rs201438627,rs61807127 -0.636426 0.519566 8 Y636D 1110 Tat/Gat MODERATE 15 MISSENSE CODING NBPF9 G protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144823868 T G 0 34.2 0 . 0 . 0 . 0 . 0 . 2 78 752 40 38 78 486 6 26 2 166 1834 88 48 260 1178 24 70 1 0 . 0 COSM1472511 8 1,0,4,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y636D|941|NBPF8|protein_coding|CODING|NM_001037501.2|14|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y636D|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|15|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|52|G) 0 . 0 . 0 . 0 . 1 0 11 0 1 0.300267 0 1 rs201438627,rs61807127 -0.636426 0.519566 8 L748M 941 Ttg/Atg MODERATE 16 MISSENSE CODING NBPF8 A protein_coding NM_001037501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144825519 T A 0 166 0 0.0197 0.1382 0.0793 0.4563 0.0378 0.1155 0 . 0 1 46 1833 97 614 117 372 18 569 2 7716 106488 10718 5392 6200 61082 812 14568 0.908623 0 . 0 . 54 7,17,21,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L748M|941|NBPF8|protein_coding|CODING|NM_001037501.2|16|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L748M|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|17|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A) 0 0.5 1 0 . 1 0 . 1 0 41 0 1.34559e-06 0.245971 0 0.359978 rs678781 -0.693079 0.246927 54 L748M 1110 Ttg/Atg MODERATE 17 MISSENSE CODING NBPF9 A protein_coding NM_001277444.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144825519 T A 0 166 0 0.0197 0.1382 0.0793 0.4563 0.0378 0.1155 0 . 0 1 46 1833 97 614 117 372 18 569 2 7716 106488 10718 5392 6200 61082 812 14568 0.908623 0 . 0 . 54 7,17,21,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L748M|941|NBPF8|protein_coding|CODING|NM_001037501.2|16|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L748M|1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|17|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A) 0 0.5 1 0 . 1 0 . 1 0 41 0 1.34559e-06 0.245971 0 0.359978 rs678781 -0.693079 0.246927 54 941 61 MODIFIER 20 CODING NBPF8 T protein_coding NM_001037501.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144828845 A T 0 22.2 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.767302 0 . 0 . 581 153,266,11,93 UTR_3_PRIME(MODIFIER||61||941|NBPF8|protein_coding|CODING|NM_001037501.2|20|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 . 0 42 0 0.0195966 0.00226972 0 0.667188 rs61807990 -0.693147 0.37032 581 941 73 MODIFIER 20 CODING NBPF8 G protein_coding NM_001037501.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144828857 C G 0 65 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.158159 0 . 0 . 525 125,197,8,149 UTR_3_PRIME(MODIFIER||73||941|NBPF8|protein_coding|CODING|NM_001037501.2|20|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 . 0 40 0 1.12566e-13 3.60708e-06 0 0.950206 rs201893749 -0.693147 0.828628 525 941 126 MODIFIER 20 CODING NBPF8 T protein_coding NM_001037501.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144828910 A T 0 128 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.506605 0 . 0 . 292 19,184,12,68 UTR_3_PRIME(MODIFIER||126||941|NBPF8|protein_coding|CODING|NM_001037501.2|20|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 . 0 38 0 0.000801243 0.30405 0 0.613826 rs12124435 -0.693147 0.00174004 292 941 241 MODIFIER 20 CODING NBPF8 G protein_coding NM_001037501.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144829025 A G 0 27.9 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.401379 0 . 0 . 52 11,29,0,11 UTR_3_PRIME(MODIFIER||241||941|NBPF8|protein_coding|CODING|NM_001037501.2|20|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 . 0 34 0 0.758063 0.995813 0 0.976611 rs368796109 -0.676189 0.0170963 52 2362 870 MODIFIER 44 CODING PDE4DIP G protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144851484 A G 0 46.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||870||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 . 0 . 0 . 0 . 0 . 60 0 0 1 0 . rs8947 -0.453602 0.06 2 2362 506 MODIFIER 44 CODING PDE4DIP A protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144851848 G A 0 89 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 7 1,1,1,4 UTR_3_PRIME(MODIFIER||506||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 . 0 55 0 0.8 0.5 0 0.6 rs1055360 -0.590765 0.391905 7 2362 451 MODIFIER 44 CODING PDE4DIP A protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144851903 G A 0 81 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||451||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 . 0 . 0 . 0 . 0 . 51 0 0 1 0 . rs1055339 -0.556411 0.692431 4 2362 355 MODIFIER 44 CODING PDE4DIP C protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144851999 A C 0 104 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979382 0 . 0 . 11 2,1,8,0 UTR_3_PRIME(MODIFIER||355||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 57 0 0.716531 1 0 0.716531 rs1699761 -0.651104 0.523788 11 2362 274 MODIFIER 44 CODING PDE4DIP C protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852080 T C 0 200 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.307032 0 . 0 . 24 5,2,14,2 UTR_3_PRIME(MODIFIER||274||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 53 0 0.763311 0.622704 0 0.0816738 rs1619391 -0.689466 0.253463 24 2362 187 MODIFIER 44 CODING PDE4DIP T protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852167 G T 0 162 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0780817 0 . 0 . 47 28,2,12,5 UTR_3_PRIME(MODIFIER||187||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 . 0 47 0 0.0310911 0.421352 0 0.0237946 rs113514538 -0.690438 0.122076 47 2362 151 MODIFIER 44 CODING PDE4DIP G protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852203 T G 0 83 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.451184 0 . 0 . 66 46,1,15,2 UTR_3_PRIME(MODIFIER||151||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 . 0 50 0 3.50253e-05 0.67337 0 0.563151 rs74872612 -0.690438 0.952566 66 2362 119 MODIFIER 44 CODING PDE4DIP C protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852235 T C 0 124 0 0.4334 0.4349 0.3919 0.4484 0.4284 0.4601 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.977708 0 . 0 . 130 76,3,40,2 UTR_3_PRIME(MODIFIER||119||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 1 0 . 0 . 50 0 1.46373e-09 0.890402 0 0.281355 rs75842891 -0.693146 1.56693e-08 130 2362 118 MODIFIER 44 CODING PDE4DIP G protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852236 C G 0 120 0 0.4334 0.4349 0.3919 0.4484 0.4284 0.4601 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.451605 0 . 0 . 130 77,3,40,2 UTR_3_PRIME(MODIFIER||118||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 1 0 . 0 . 51 0 1.26285e-09 0.883735 0 0.281474 rs78034674 -0.693146 1.56693e-08 130 2362 105 MODIFIER 44 CODING PDE4DIP T protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852249 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.95914 0 . 0 . 175 63,1,92,7 UTR_3_PRIME(MODIFIER||105||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 . 0 50 0 5.5235e-11 0.783233 0 0.374368 rs1055317 -0.693147 1.34968e-05 175 2362 100 MODIFIER 44 CODING PDE4DIP C protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852254 G C 0 184 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.716098 0 . 0 . 191 98,7,69,5 UTR_3_PRIME(MODIFIER||100||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 51 0 1.41131e-12 0.991982 0 0.17974 rs77608804 -0.693147 4.66588e-06 191 2362 33 MODIFIER 44 CODING PDE4DIP A protein_coding NM_001198834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852321 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 2958 37236 2853 2539 2085 20503 303 5995 2 5966 75156 5762 5104 4218 41454 608 12044 0.984959 0 . 0 . 394 149,43,144,24 UTR_3_PRIME(MODIFIER||33||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 52 0 4.9911e-23 0.190474 0 0.999868 rs1055315 -0.693147 0.0143011 394 W2351* 2362 tgG/tgA HIGH 44 NONSENSE CODING PDE4DIP T protein_coding NM_001198834.3 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144852390 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5198 60646 5780 4303 3305 33355 454 8251 2 10394 121288 11560 8606 6610 66710 908 16500 0.847645 0 . 0 . 606 182,92,183,86 STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W2351*|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|44|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 56 0 1.84587e-06 0.429735 0 0.919582 rs61804988 -0.693147 0.00377341 606 A2328 2362 gcA/gcG LOW 43 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854180 T C 0 221 0 . 0 . 0 . 0 . 0 . 1 5081 58911 5597 4163 3211 32360 441 8058 2 10216 118534 11284 8426 6456 65074 884 16194 0.880626 0 . 0 . 1009 373,258,167,76 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A2328|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|43|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.0236661 0.990913 0 0.785911 rs4997148 -0.693147 0.121404 1009 I2314 2362 atT/atC LOW 42 SILENT CODING PDE4DIP G protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854528 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 4677 49818 4623 3954 2590 26055 379 7540 2 10172 112128 10288 8420 5844 60516 850 16038 0.620383 0 . 0 . 370 148,56,96,43 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I2314|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.00142566 0.803787 0 0.987846 rs78461771 -0.693147 0.000731362 370 E2311 2362 gaA/gaG LOW 42 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854537 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 4691 51321 4656 3927 2789 27271 398 7589 2 10036 112508 10172 8332 5990 61034 870 16074 0.782261 0 . 0 . 383 152,57,98,49 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E2311|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.00220464 0.876703 0 0.999999 rs3851872 -0.693147 0.00406153 383 T2297A 2362 Act/Gct MODERATE 42 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854581 T C 0 193 0 . 0 . 0 . 0 . 0 . 1 4653 48318 4383 3635 2396 25277 357 7617 2 9878 103348 9304 7652 5288 54870 776 15580 0.98017 0 . 0 . 438 205,81,68,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T2297A|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 58 0 7.11142e-05 0.798656 0 0.591446 rs78371650 -0.693147 0.504853 438 L2292 2362 ctC/ctA LOW 42 SILENT CODING PDE4DIP T protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854594 G T 0 147 0 0.5408 0.4411 0.3804 0.4464 0.3191 0.4693 0 . 0 1 4956 58060 5508 4122 3185 31893 436 7960 2 10286 119314 11258 8396 6490 65644 890 16350 0.312903 0 . 0 . 452 200,94,73,43 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L2292|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.000137871 0.971329 0 0.0184058 rs79028512 -0.693147 0.219295 452 R2291 2362 cgA/cgG LOW 42 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854597 T C 0 220 0 0.5408 0.4411 0.3804 0.4464 0.3191 0.4693 0 . 0 1 5257 61936 5828 5235 3326 33434 458 8398 2 10406 121390 11578 8636 6614 66738 908 16510 0.041376 0 . 0 . 417 48,29,200,107 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R2291|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.390984 0.937251 0 0.463161 rs3851873 -0.693147 0.0846975 417 R2291Q 2362 cGa/cAa MODERATE 42 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144854598 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60705 5789 4326 3307 33370 454 8256 2 10406 121410 11578 8652 6614 66740 908 16512 0.947398 0 . 0 . 435 160,89,91,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R2291Q|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|42|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.0918995 0.987392 0 0.979829 rs3863691 -0.693147 0.23365 435 A2257 2362 gcG/gcA LOW 41 SILENT CODING PDE4DIP T protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144855782 C T 0 114 0 . 0 . 0 . 0 0.0229233 0.0246961 0.0256052 1 260 8812 819 3002 433 2526 77 1695 2 10374 120976 11538 8524 6600 66588 908 16444 0.690301 0 . 0 . 455 153,172,37,43 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2257|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|41|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 0 57 0 0.870969 0.0180602 0 0.371716 rs71246352 -0.693147 0.247443 455 S2247 2362 tcA/tcG LOW 41 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144855812 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5076 60042 5612 5105 3200 32369 445 8235 2 10118 118432 11238 8474 6398 65066 888 16250 0.778151 0 . 0 . 397 45,63,89,170 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S2247|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|41|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 55 0 1.08792e-05 0.089868 0 0.770077 rs1699754 -0.693147 0.406902 397 G2229 2362 ggT/ggC LOW 41 SILENT CODING PDE4DIP G protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144855866 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 4536 54025 5037 3742 3134 29659 412 7505 2 9476 112376 10630 7956 6344 61744 850 15376 0.982085 0 . 0 . 288 44,110,39,80 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G2229|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|41|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 53 0 3.06754e-13 0.996324 0 0.00982142 rs1698582 -0.693147 0.0216599 288 L2199 2362 ctG/ctA LOW 40 SILENT CODING PDE4DIP T protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144856888 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 333 3227 1168 1042 0 203 18 463 2 9666 114824 10832 8248 6416 63248 860 15554 0.755375 0 . 0 . 850 259,141,235,150 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L2199|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|40|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 51 0 0.0643012 1.69993e-16 0 0.998117 rs3853915 -0.693147 0.0102597 850 R2052Q 2362 cGa/cAa MODERATE 38 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144859929 C T 0 222 0 . 0 . 0 . 0 0.0517476 0.0191509 0.002443 1 672 3869 1299 1138 0 228 23 509 2 10368 121234 11578 8638 6614 66622 908 16506 0.980887 0 . 0 . 75 22,10,27,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R2052Q|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|38|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.727669 rs2798851 -0.693144 0.784556 75 D1910E 2362 gaC/gaA MODERATE 35 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144865850 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60705 5789 4327 3307 33369 454 8256 2 10406 121410 11578 8654 6614 66738 908 16512 0.637951 0 . 0 . 237 61,67,43,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1910E|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|35|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 59 0 1 1 0 0.99982 rs1613780 -0.693147 0.0319361 237 R1867C 2362 Cgc/Tgc MODERATE 34 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144866643 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.999918 0 . 0 . 137 22,40,22,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R1867C|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|34|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.86895 rs1620560 -0.693147 0.0857552 137 E1860 2362 gaA/gaG LOW 34 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144866662 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5254 61957 5826 5267 3325 33431 458 8396 2 10406 121412 11578 8654 6614 66740 908 16512 0.0291449 0 . 0 . 127 13,17,27,60 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1860|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|34|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.224289 rs1064044 -0.693147 0.386575 127 R1852W 2362 Cgg/Tgg MODERATE 34 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144866688 G A 0 222 0 0.0832 0.0709 0.0879 0.1349 0.003 0.046 0.0406264 0.01531 0.00232775 1 669 3863 1297 1138 0 228 23 508 2 10398 121358 11574 8630 6614 66728 908 16506 0.782388 0 . 0 . 98 18,31,15,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R1852W|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|34|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973701 rs1698597 -0.693146 0.0195701 98 A1757T 2362 Gcc/Acc MODERATE 33 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144868170 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60703 5789 4324 3307 33370 454 8256 2 10406 121406 11578 8648 6614 66740 908 16512 0.658015 0 . 0 . 107 12,52,7,28 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gcc/Acc|A1757T|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|33|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.90661 rs1628310 -0.693136 0.0126218 107 A1742S 2362 Gct/Tct MODERATE 32 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144871738 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60700 5788 4325 3307 33367 454 8256 2 10406 121404 11576 8654 6614 66734 908 16512 0.390559 0 . 0 . 138 60,20,41,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A1742S|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|32|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.517962 rs1698605 -0.693147 0.317961 138 V1736E 2362 gTg/gAg MODERATE 32 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144871755 A T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60700 5788 4324 3307 33368 454 8256 2 10406 121406 11576 8652 6614 66738 908 16512 0.997665 0 . 0 . 147 65,22,36,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V1736E|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|32|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.888949 rs1778159 -0.693147 0.286537 147 L1727P 2362 cTc/cCc MODERATE 32 MISSENSE CODING PDE4DIP G protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144871782 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 5202 60702 5789 4325 3307 33369 454 8256 2 10404 121404 11578 8650 6614 66738 908 16512 0.997841 0 . 0 . 171 67,26,38,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L1727P|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|32|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.940978 rs1778158 -0.693147 0.743978 171 2362 LOW 31 CODING PDE4DIP C protein_coding NM_001198834.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144871889 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 5198 60617 5779 4316 3307 33323 452 8242 2 10396 121238 11560 8632 6614 66646 904 16486 0.745371 0 . 0 . 164 34,43,27,41 SPLICE_SITE_REGION+INTRON(LOW||||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|31|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.899773 rs1698606 -0.693147 0.00994525 164 Q1690 2362 caG/caA LOW 31 SILENT CODING PDE4DIP T protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144873887 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60684 5789 4326 3307 33349 454 8256 2 10406 121368 11578 8652 6614 66698 908 16512 0.938452 0 . 0 . 182 67,23,51,17 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1690|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|31|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.691699 rs1699787 -0.693147 0.294294 182 E1616 2362 gaA/gaG LOW 30 SILENT CODING PDE4DIP C protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144874760 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.757903 0 . 0 . 222 53,58,41,55 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1616|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|30|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.9529 rs1610774 -0.693147 0.203452 222 H1598R 2362 cAt/cGt MODERATE 30 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144874815 T C 0 222 0 . 0 . 0 . 0 0.202905 0.26958 0.303771 1 2630 49032 5440 4295 2714 26004 375 7574 2 10404 121378 11576 8648 6612 66718 908 16512 0.94783 0 . 0 . 186 34,59,37,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H1598R|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|30|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.467029 rs1778155 -0.693147 0.0202906 186 R1504Q 2362 cGg/cAg MODERATE 28 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144877176 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5181 60665 5789 4324 3306 33355 454 8256 2 10366 121338 11578 8648 6612 66714 908 16512 0.125805 0 . 0 . 818 190,131,244,154 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1504Q|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|28|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 58 0 1.27994e-08 0.000290272 0 0.943123 rs2762875 -0.693147 0.247384 818 K1454E 2362 Aaa/Gaa MODERATE 27 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144879090 T C 0 222 0 . 0 . 0 . 0 0.110077 0.124712 0.132209 1 2292 35653 3871 2584 1806 18728 254 6118 2 10094 120980 11578 8648 6614 66662 904 16480 0.963914 0 . 0 . 104 31,17,27,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K1454E|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|27|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.983361 rs1778120 -0.693147 0.347453 104 W1396R 2362 Tgg/Cgg MODERATE 27 MISSENSE CODING PDE4DIP G protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144879264 A G 0 228 0 0.5378 0.7101 0.7248 0.9296 0.6451 0.773 0 . 0 2 5679 83478 9353 8033 4417 42859 621 12516 2 10402 121348 11576 8652 6614 66684 908 16512 0 . 0 . 0 147 0,0,79,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W1396R|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|27|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2798901 -0.693147 0.00414561 147 K1359E 2362 Aaa/Gaa MODERATE 27 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144879375 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.999401 0 . 0 . 220 59,31,68,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K1359E|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|27|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 1 1 0 0.699577 rs1747958 -0.693147 0.215296 220 L1272F 2362 Ctc/Ttc MODERATE 26 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144880814 G A 0 222 0 . 0 . 0 . 0 0.0344984 0.0126154 0.00139632 1 672 3875 1299 1143 0 227 23 511 2 10406 121402 11576 8652 6614 66736 908 16510 0.988063 0 . 0 . 214 68,36,45,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L1272F|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|26|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.230561 rs1747960 -0.693147 0.316137 214 2362 LOW 25 CODING PDE4DIP A protein_coding NM_001198834.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144880864 T A 0 221 0 . 0 . 0 . 0 0.0206537 0.0250808 0.027351 1 252 9022 839 3096 439 2571 76 1749 2 10406 121386 11576 8644 6614 66730 908 16508 0.772949 0 . 0 . 190 46,76,11,31 SPLICE_SITE_REGION+INTRON(LOW||||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|25|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.934114 rs71664011 -0.693146 0.576258 190 S1205P 2362 Tca/Cca MODERATE 25 MISSENSE CODING PDE4DIP G protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144881583 A G 0 222 0 0.0832 0.0707 0.0879 0.1339 0.003 0.046 0.043123 0.0159255 0.00197859 1 673 3870 1297 1140 0 226 23 511 2 10406 121384 11576 8644 6614 66724 908 16512 0.932539 0 . 0 . 109 27,30,13,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S1205P|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|25|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.526774 rs2762877 -0.693145 0.50409 109 I1146 2362 atT/atC LOW 24 SILENT CODING PDE4DIP G protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144882581 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60703 5789 4327 3306 33369 454 8255 2 10406 121412 11578 8654 6614 66740 908 16512 0.998934 0 . 0 . 250 75,41,81,31 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I1146|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|24|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.568728 rs1699836 -0.693147 0.264319 250 A1066T 2362 Gca/Aca MODERATE 24 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144882823 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60703 5789 4327 3306 33369 454 8255 2 10406 121412 11578 8654 6614 66740 908 16512 0.834988 0 . 0 . 188 15,79,21,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1066T|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|24|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.013547 rs1698647 -0.693147 0.122199 188 2362 LOW 23 CODING PDE4DIP T protein_coding NM_001198834.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144886092 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60700 5789 4325 3306 33368 454 8255 2 10406 121406 11578 8650 6614 66738 908 16512 0.856183 0 . 0 . 133 51,14,48,5 SPLICE_SITE_REGION+INTRON(LOW||||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|23|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.87748 rs1343472 -0.693147 0.0897582 133 F1013I 2362 Ttc/Atc MODERATE 23 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144886197 A T 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60703 5789 4327 3306 33369 454 8255 2 10406 121412 11578 8654 6614 66740 908 16512 0.47789 0 . 0 . 144 34,34,22,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Atc|F1013I|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|23|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.768447 rs1698624 -0.693147 0.036961 144 D744 2362 gaC/gaT LOW 17 SILENT CODING PDE4DIP A protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144909956 G A 0 222 0 . 0 . 0 . 0 0.223559 0.225511 0.226512 1 2821 32999 3658 2849 1785 17237 221 4428 2 10308 121092 11568 8624 6610 66570 908 16504 0.631825 0 . 0 . 215 57,44,43,41 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D744|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|17|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.838821 rs638260 -0.693147 0.0278803 215 C708R 2362 Tgt/Cgt MODERATE 15 MISSENSE CODING PDE4DIP G protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144912153 A G 0 228 0 0.9236 0.8838 0.8934 0.9395 0.8022 0.8497 0.893554 0.826618 0.792326 2 9407 100224 10608 8032 5115 52672 754 13636 2 10406 121404 11578 8654 6614 66734 908 16510 1 0 . 0 . 177 1,0,98,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C708R|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|15|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1628172 -0.693147 0.203877 177 R681H 2362 cGc/cAc MODERATE 15 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144912233 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5202 60701 5788 4327 3307 33367 454 8256 2 10404 121402 11576 8654 6614 66734 908 16512 0.921335 0 . 0 . 149 30,41,21,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R681H|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|15|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.547031 rs1629011 -0.693147 0.00618993 149 R622* 2362 Cga/Tga HIGH 14 NONSENSE CODING PDE4DIP A protein_coding NM_001198834.3 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144915561 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.686823 0 . 0 . 240 47,51,69,56 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R622*|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|14|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 (PDE4DIP|PDE4DIP|1|1.00) 58 0 0.591555 0.53919 (PDE4DIP|PDE4DIP|1|1.00) 0.805513 rs1778111 -0.693147 0.18949 240 L601 2362 Ctg/Ttg LOW 14 SILENT CODING PDE4DIP A protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144915624 G A 0 222 0 0.5 0.4573 0.4625 0.3621 0.4761 0.4744 0 . 0 1 5174 56303 4997 2841 3090 31945 423 7833 2 10352 112908 10034 5788 6184 64016 846 15688 0.975428 0 . 0 . 226 43,56,58,47 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L601|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|14|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.370297 0.341461 0 0.978914 rs1778112 -0.693147 1.01582e-05 226 S536T 2362 aGt/aCt MODERATE 13 MISSENSE CODING PDE4DIP G protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144916748 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 5185 60685 5789 4327 3307 33368 454 8255 2 10370 121370 11578 8654 6614 66736 908 16510 0.408055 0 . 0 . 149 9,61,13,53 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|aGt/aCt|S536T|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|13|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.689604 rs1747930 -0.693147 0.000716476 149 L520 2362 Tta/Cta LOW 12 SILENT CODING PDE4DIP G protein_coding NM_001198834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144917546 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.785521 0 . 0 . 139 38,19,37,29 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L520|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|12|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.269022 rs1698682 -0.693147 0.0174993 139 H482R 2362 cAt/cGt MODERATE 11 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144917841 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5200 60702 5789 4327 3307 33370 454 8255 2 10400 121404 11578 8654 6614 66740 908 16510 0.999948 0 . 0 . 708 202,87,213,113 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H482R|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|11|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.863703 0.000144736 0 0.348991 rs1698681 -0.693147 0.172209 708 E410V 2362 gAa/gTa MODERATE 10 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144918957 T A 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60706 5789 4327 3307 33370 454 8256 2 10406 121412 11578 8654 6614 66740 908 16512 0.99812 0 . 0 . 541 52,194,60,192 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E410V|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|10|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.00029659 0.0926664 0 0.844796 rs1061308 -0.693147 2.68736e-07 541 2362 LOW 9 CODING PDE4DIP T protein_coding NM_001198834.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144918994 G T 0 222 0 . 0 . 0 . 0 0.0383568 0.0140791 0.00162942 1 669 3845 1298 1123 0 223 23 509 2 10374 121328 11578 8622 6614 66724 908 16508 0.285738 0 . 0 . 371 26,147,29,144 SPLICE_SITE_REGION+INTRON(LOW||||2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|9|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 0 59 0 0.0124823 0.545927 0 0.1727 rs2134388 -0.693147 0.185262 371 S275L 2362 tCg/tTg MODERATE 7 MISSENSE CODING PDE4DIP A protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144922583 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 5203 60705 5789 4327 3307 33370 454 8255 2 10406 121410 11578 8654 6614 66740 908 16510 0.884437 0 . 0 . 249 40,57,39,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S275L|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|7|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.258347 rs1359300 -0.693147 0.384019 249 A167T 2362 Gcc/Acc MODERATE 4 MISSENSE CODING PDE4DIP T protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144952220 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 5200 60678 5781 4322 3307 33359 454 8255 2 10400 121368 11566 8648 6614 66722 908 16510 0.576632 0 . 0 . 1273 208,448,159,357 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A167T|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|4|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 41 0 0.757264 1.15485e-28 0 0.0145336 rs139438772,rs2590120 -0.693147 3.84333e-07 1273 I109M 2362 atC/atG MODERATE 3 MISSENSE CODING PDE4DIP C protein_coding NM_001198834.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 144952581 G C 0 61 0 . 0 . 0 . 0 . 0 . 1 20 182 4 9 0 145 1 3 2 40 366 8 18 0 292 2 6 0.94925 0 . 0 . 14 0,8,0,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I109M|2362|PDE4DIP|protein_coding|CODING|NM_001198834.3|3|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.77718 0 . 0.586646 rs149078147 -0.616816 0.293058 14 Q32 215 caG/caA LOW 2 SILENT CODING SEC22B A protein_coding NM_004892.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145103928 G A 0 222 0 0.1112 0.3401 0.4352 0.4454 0.4155 0.3957 0 . 0 1 1136 40214 4537 3384 2369 23198 308 5282 2 8518 105454 10070 7828 5844 58260 766 14168 0.757955 0 . 0 COSN231320,COSN231319 247 87,56,40,32 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q32|215|SEC22B|protein_coding|CODING|NM_004892.5|2|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.991724 rs2596251 -0.693147 0.150001 247 *39Q 215 Taa/Caa HIGH 2 MISSENSE CODING SEC22B C protein_coding NM_004892.5 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145103947 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 4771 58449 5498 4210 3206 32367 432 7965 2 9556 117342 11052 8476 6446 64972 868 15972 0.986604 0 . 0 . 251 80,65,30,45 STOP_LOST(HIGH|MISSENSE|Taa/Caa|*39Q|215|SEC22B|protein_coding|CODING|NM_004892.5|2|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.57948 rs2794062 -0.693147 0.267298 251 D71Y 215 Gat/Tat MODERATE 3 MISSENSE CODING SEC22B T protein_coding NM_004892.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145109549 G T 0 141 0 . 0 . 0 . 0 0.315169 0.3091 0.306152 1 4901 60245 5783 4272 3303 33298 449 8239 2 9804 120562 11568 8564 6610 66622 898 16496 0.587122 0 . 0 . 361 174,89,41,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D71Y|215|SEC22B|protein_coding|CODING|NM_004892.5|3|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.886145 rs2596331 -0.693147 0.00678306 361 T82K 215 aCg/aAg MODERATE 3 MISSENSE CODING SEC22B A protein_coding NM_004892.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145109583 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 4912 60393 5788 4312 3307 33369 449 8256 2 9824 120786 11576 8624 6614 66738 898 16512 0.918112 0 . 0 . 398 114,69,106,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T82K|215|SEC22B|protein_coding|CODING|NM_004892.5|3|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.913705 rs2794053 -0.693147 0.89747 398 R108Q 215 cGa/cAa MODERATE 3 MISSENSE CODING SEC22B A protein_coding NM_004892.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145109661 G A 0 221 0 . 0 . 0 . 0 0.396673 0.38122 0.37386 1 4872 59683 5741 4270 3289 32873 445 8193 2 9778 120116 11526 8570 6588 66310 892 16452 0.323224 0 . 0 . 417 109,149,50,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R108Q|215|SEC22B|protein_coding|CODING|NM_004892.5|3|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.0860297 rs2655551 -0.693147 0.0997218 417 C130R 215 Tgt/Cgt MODERATE 4 MISSENSE CODING SEC22B C protein_coding NM_004892.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145112414 T C 0 172 0 . 0 . 0 . 0 0.353298 0.372946 0.382577 1 4885 59949 5729 4237 3286 33140 448 8224 2 9788 120204 11488 8548 6586 66432 896 16466 0.986548 0 . 0 . 450 270,35,68,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C130R|215|SEC22B|protein_coding|CODING|NM_004892.5|4|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.99891 rs2590131 -0.693147 0.90792 450 R132* 215 Cga/Tga HIGH 4 NONSENSE CODING SEC22B T protein_coding NM_004892.5 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145112420 C T 0 222 0 . 0 . 0 . 0 0.393082 0.399395 0.402494 1 4850 59023 5673 4211 3272 32397 443 8177 2 9764 119564 11456 8520 6578 65912 894 16440 0.999023 0 . 0 . 477 233,48,109,15 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R132*|215|SEC22B|protein_coding|CODING|NM_004892.5|4|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 (SEC22B|SEC22B|1|1.00) 60 0 1 1 (SEC22B|SEC22B|1|1.00) 0.999679 rs2794041 -0.693147 0.0256485 477 N134 215 aaC/aaT LOW 4 SILENT CODING SEC22B T protein_coding NM_004892.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145112428 C T 0 157 0 . 0 . 0 . 0 . 0 . 1 4896 60127 5752 4248 3294 33255 447 8235 2 9802 120446 11522 8556 6598 66596 894 16478 0.450196 0 . 0 . 512 285,57,65,24 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N134|215|SEC22B|protein_coding|CODING|NM_004892.5|4|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.143551 rs2794040 -0.693147 0.0454595 512 I153 215 atC/atT LOW 4 SILENT CODING SEC22B T protein_coding NM_004892.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145112485 C T 0 81 0 . 0 . 0 . 0 0.400189 0.422732 0.433993 1 4909 60263 5768 4276 3301 33315 447 8247 2 9828 120652 11550 8588 6610 66678 898 16500 0.688443 0 . 0 . 563 210,171,52,45 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I153|215|SEC22B|protein_coding|CODING|NM_004892.5|4|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.845772 rs2794039 -0.693147 0.0602226 563 H190R 215 cAt/cGt MODERATE 5 MISSENSE CODING SEC22B G protein_coding NM_004892.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145115810 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 4920 60404 5788 4314 3307 33370 449 8256 2 9838 120798 11572 8626 6614 66738 898 16512 0.622534 0 . 0 . 509 150,84,151,72 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H190R|215|SEC22B|protein_coding|CODING|NM_004892.5|5|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.942311 rs2655557 -0.693147 0.470758 509 Y193 215 taT/taC LOW 5 SILENT CODING SEC22B C protein_coding NM_004892.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145115820 T C 0 222 0 . 0 . 0 . 0 0.451549 0.456714 0.459218 1 4871 58827 5712 4232 3271 32530 438 7773 2 9808 119742 11512 8546 6594 66168 892 16222 0.995256 0 . 0 . 515 202,130,96,44 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y193|215|SEC22B|protein_coding|CODING|NM_004892.5|5|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.876662 rs2655558 -0.693147 0.814335 515 215 138 MODIFIER 5 CODING SEC22B C protein_coding NM_004892.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145116027 T C 0 74 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.805049 0 . 0 . 222 16,149,6,42 UTR_3_PRIME(MODIFIER||138||215|SEC22B|protein_coding|CODING|NM_004892.5|5|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.959916 rs7550440 -0.693147 0.712003 222 215 540 MODIFIER 6 CODING SEC22B G protein_coding NM_004892.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145116429 A G 0 228 0 0.702 0.8217 0.8545 0.8978 0.8499 0.8528 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.11344 0 . 0 . 376 35,3,206,69 UTR_3_PRIME(MODIFIER||540||215|SEC22B|protein_coding|CODING|NM_004892.5|6|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.982592 rs2794025 -0.693147 0.988105 376 215 790 MODIFIER 6 CODING SEC22B C protein_coding NM_004892.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145116679 T C 0 83 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.296513 0 . 0 . 108 7,75,3,17 UTR_3_PRIME(MODIFIER||790||215|SEC22B|protein_coding|CODING|NM_004892.5|6|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.996799 rs10797635 -0.692067 0.168963 108 215 909 MODIFIER 6 CODING SEC22B A protein_coding NM_004892.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145116798 G A 0 126 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957526 0 . 0 . 17 2,7,2,4 UTR_3_PRIME(MODIFIER||909||215|SEC22B|protein_coding|CODING|NM_004892.5|6|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.134399 rs2655559 -0.616816 0.0321945 17 215 1031 MODIFIER 6 CODING SEC22B C protein_coding NM_004892.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145116920 T C 0 29.4 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,2,1,1 UTR_3_PRIME(MODIFIER||1031||215|SEC22B|protein_coding|CODING|NM_004892.5|6|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0 rs1838550 -0.453602 0.5 4 T158I 236 aCc/aTc MODERATE 4 MISSENSE CODING NOTCH2NL T protein_coding NM_203458.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145281543 C T 0 204 0 . 0 . 0 . 0 . 0 . 1 4526 57426 5615 4211 3187 31515 430 7942 2 10278 119442 11440 8538 6552 65416 898 16320 0.998333 0 . 0 . 442 111,183,46,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T158I|236|NOTCH2NL|protein_coding|CODING|NM_203458.4|4|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.981543 0.672194 0 0.308375 rs8002 -0.693147 0.0538122 442 236 569 MODIFIER 5 CODING NOTCH2NL C protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145282600 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.620217 0 . 0 . 126 13,24,16,67 UTR_3_PRIME(MODIFIER||569||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C) 0 0.5 1 0 . 0 . 0 . 0 58 0 0.469148 0.928136 0 0.546308 rs711761 -0.693147 0.0205754 126 236 768 MODIFIER 5 CODING NOTCH2NL A protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145282799 G A 0 121 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 20 1,10,1,7 UTR_3_PRIME(MODIFIER||768||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 . 0 59 0 1 1 0 0.686704 rs71664089 -0.651104 0.547491 20 236 1668 MODIFIER 5 CODING NOTCH2NL A protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145283699 G A 0 23.3 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 1,1,0,2 UTR_3_PRIME(MODIFIER||1668||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 . 0 59 0 1 1 0 0.5 rs79434913 -0.453602 0.14 5 236 1687 MODIFIER 5 CODING NOTCH2NL A protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145283718 G A 0 23.4 0 0.3828 0.4427 0.451 0.4742 0.4692 0.4581 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,2,0,2 UTR_3_PRIME(MODIFIER||1687||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 0 . 0.5 rs75738573 -0.453602 0.14 4 236 2139 MODIFIER 5 CODING NOTCH2NL A protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145284170 G A 0 8 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,2,0,2 UTR_3_PRIME(MODIFIER||2139||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A) 0 0.5 1 0 . 0 . 0 . 0 48 0 1 1 0 0.666667 rs61814565,rs76317236 -0.453602 0.06 6 236 3795 MODIFIER 5 CODING NOTCH2NL G protein_coding NM_203458.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145285826 A G 0 39.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||3795||236|NOTCH2NL|protein_coding|CODING|NM_203458.4|5|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs368852902 -0.453602 0.7 2 P7H 3795 cCt/cAt MODERATE 1 MISSENSE CODING NBPF10 A protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145293425 C A 0 168 0 . 0 . 0 . 0 . 0 . 1 2409 41104 4140 3900 2286 22336 326 5707 2 8910 108752 10284 8240 5878 58884 842 15714 0.250386 0 . 0 . 1163 549,232,158,75 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P7H|3795|NBPF10|protein_coding|CODING|NM_001302371.1|1|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.209648 2.0721e-20 0 0.852184 rs7366490 -0.693147 0.00138994 1163 K31N 3795 aaG/aaC MODERATE 1 MISSENSE CODING NBPF10 C protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145293498 G C 0 190 0 . 0 . 0 . 0 . 0 . 1 2146 42757 4119 3797 2581 24465 338 5311 2 9086 114322 10470 8238 6248 63418 874 15988 0.595433 0 . 0 . 1391 544,399,152,135 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K31N|3795|NBPF10|protein_coding|CODING|NM_001302371.1|1|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.000330868 0.0195556 0 0.610224 rs4409714 -0.693147 0.0258592 1391 F35L 3795 ttC/ttG MODERATE 1 MISSENSE CODING NBPF10 G protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145293510 C G 0 185 0 . 0 . 0 . 0 . 0 . 1 1584 33476 3512 3515 2034 18864 276 3691 2 8790 109254 10030 7952 5892 59862 854 15874 0.992352 0 . 0 . 1389 531,430,138,133 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttC/ttG|F35L|3795|NBPF10|protein_coding|CODING|NM_001302371.1|1|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.00336205 0.000375599 0 0.30186 rs4356110 -0.693147 0.0203199 1389 L98 3795 ctA/ctG LOW 3 SILENT CODING NBPF10 G protein_coding NM_001302371.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145296372 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 4840 63309 5934 5085 3498 34273 469 9210 2 9372 114272 11180 8504 6252 62044 868 16052 0.00850628 0 . 0 . 617 147,167,78,162 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L98|3795|NBPF10|protein_coding|CODING|NM_001302371.1|3|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 51 0 3.65904e-34 0.00147987 0 0.978526 rs4068113 -0.693147 0.870802 617 D134Y 3795 Gat/Tat MODERATE 3 MISSENSE CODING NBPF10 T protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145296478 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 4308 58409 6278 4831 3205 31150 438 8199 2 8792 114442 11236 8364 6464 62564 870 16152 0.908095 0 . 0 . 416 109,116,58,87 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D134Y|3795|NBPF10|protein_coding|CODING|NM_001302371.1|3|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|T),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 1 0 43 0 0.3244 6.05649e-09 0 0.987546 rs6663523 -0.693147 0.120515 416 P200A 3795 Cct/Gct MODERATE 5 MISSENSE CODING NBPF10 G protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145298186 C G 0 120 0 . 0 . 0 . 0 . 0 . 1 4375 57090 5644 4082 3255 31113 435 8186 2 8766 114568 11308 8184 6528 62508 870 16404 0.551463 0 . 0 . 836 478,87,218,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P200A|3795|NBPF10|protein_coding|CODING|NM_001302371.1|5|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.748146 0 0 0.667196 rs28507779,rs61814623 -0.693147 1.8588e-06 836 A354 3795 gcA/gcG LOW 7 SILENT CODING NBPF10 G protein_coding NM_001302371.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145301793 A G 0 210 0 . 0 . 0 . 0 . 0 . 1 3784 56720 5711 4255 3248 31404 433 7885 2 8688 116832 11518 8516 6608 64206 886 16410 0.988441 0 . 0 COSM1333553,COSM1333554 264 70,100,22,59 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A354|3795|NBPF10|protein_coding|CODING|NM_001302371.1|7|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 44 0 0.306051 0.188819 0 0.848718 rs5020524,rs75332562 -0.693147 0.276454 264 L357 3795 ctC/ctG LOW 7 SILENT CODING NBPF10 G protein_coding NM_001302371.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145301802 C G 0 187 0 . 0 . 0 . 0 . 0 . 1 4794 58252 5785 4259 3275 31521 436 8182 2 8678 116746 11514 8482 6604 64126 884 16458 0.962694 0 . 0 COSM1132960,COSM1132959 241 69,87,17,54 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L357|3795|NBPF10|protein_coding|CODING|NM_001302371.1|7|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 42 0 0.150685 0.0831608 0 0.987247 rs6690575 -0.693147 0.332592 241 S456 3795 tcA/tcG LOW 9 SILENT CODING NBPF10 G protein_coding NM_001302371.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145303971 A G 0 220 0 0.7156 0.528 0.5994 0.38 0.4821 0.4233 0 . 0 1 6874 57410 7079 2848 3175 30030 428 6976 2 10036 118490 11436 8346 6554 65024 890 16204 0.0012611 0 . 0 . 588 178,126,119,114 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S456|3795|NBPF10|protein_coding|CODING|NM_001302371.1|9|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 42 0 0 0.97335 0 0.0260417 rs146037073 -0.693147 0.10469 588 3795 HIGH 13 CODING NBPF10 G protein_coding NM_001302371.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145311785 C G 0 34.8 0 . 0 . 0 . 0 . 0 . 1 141 1026 63 37 115 522 9 139 2 3010 62770 3892 5676 3788 35996 500 9908 0.784723 0 . 0 . 31 20,2,8,1 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|13|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 (NBPF10|NBPF10|1|1.00) 44 0 0.00135696 0.910002 0 0.0294909 rs61816394 -0.662043 0.90234 31 F632L 3795 ttC/ttG MODERATE 14 MISSENSE CODING NBPF10 G protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145311828 C G 0 228 0 0.9448 0.9802 0.9986 0.9881 0.999 0.9877 0 . 0 2 3541 81883 6003 6824 4808 47988 632 12087 2 4126 83308 6048 7026 4928 48106 644 12430 0 . 0 . 0 49 0,0,36,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttC/ttG|F632L|3795|NBPF10|protein_coding|CODING|NM_001302371.1|14|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|53|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|20|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 38 0 0 0.83567 0 . rs12135693 -0.693147 0.124386 49 I1240F 3795 Att/Ttt MODERATE 29 MISSENSE CODING NBPF10 T protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145323656 A T 0 36.2 0 . 0 . 0 . 0 . 0 . 1 1041 27174 1927 2094 1888 16658 210 3356 2 8374 105374 10020 7978 5988 56682 796 15536 0.865613 0 . 0 COSM895149 135 78,25,10,5 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Att/Ttt|I1240F|3795|NBPF10|protein_coding|CODING|NM_001302371.1|29|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|63|T),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|T),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 1 0 45 0 0.941443 0.168222 0 0.848309 rs75252120 -0.688148 0.163725 135 Y2221S 4963 tAt/tCt MODERATE 64 MISSENSE CODING NBPF20 C protein_coding NM_001278267.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145330748 A C 0 29.4 0 . 0 . 0 . 0 . 0 . 1 0 1 0 0 0 1 0 0 2 28 480 36 30 0 370 8 8 0.994413 0 . 0 . 16 0,7,0,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y2221S|4963|NBPF20|protein_coding|CODING|NM_001278267.1|64|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|32|C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 1 0 24 0 0.03464 0 . 0.146993 rs201711193,rs61816441 -0.662043 0.00667785 16 Y3197S 4963 tAt/tCt MODERATE 88 MISSENSE CODING NBPF20 C protein_coding NM_001278267.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145349628 A C 0 45.5 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 6 0,2,0,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y3197S|4963|NBPF20|protein_coding|CODING|NM_001278267.1|88|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y2348S|3795|NBPF10|protein_coding|CODING|NM_001302371.1|56|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 . 0 32 0 0.5 0 . 1 rs200087380 -0.556411 0.244943 6 Y2348S 3795 tAt/tCt MODERATE 56 MISSENSE CODING NBPF10 C protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145349628 A C 0 45.5 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 6 0,2,0,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y3197S|4963|NBPF20|protein_coding|CODING|NM_001278267.1|88|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y2348S|3795|NBPF10|protein_coding|CODING|NM_001302371.1|56|C),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 . 0 32 0 0.5 0 . 1 rs200087380 -0.556411 0.244943 6 G3429E 4963 gGg/gAg MODERATE 94 MISSENSE CODING NBPF20 A protein_coding NM_001278267.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145354324 G A 0 6.4 0 . 0 . 0 . 0 . 0 . 1 47 1456 41 49 302 659 19 339 2 362 4566 146 118 876 1806 68 1190 0.977751 0 . 0 . 14 0,10,0,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G3429E|4963|NBPF20|protein_coding|CODING|NM_001278267.1|94|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G2580E|3795|NBPF10|protein_coding|CODING|NM_001302371.1|62|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 1 0 37 0 0.997503 0 . 0.697676 rs372557852 -0.556411 0.168287 14 G2580E 3795 gGg/gAg MODERATE 62 MISSENSE CODING NBPF10 A protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145354324 G A 0 6.4 0 . 0 . 0 . 0 . 0 . 1 47 1456 41 49 302 659 19 339 2 362 4566 146 118 876 1806 68 1190 0.977751 0 . 0 . 14 0,10,0,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G3429E|4963|NBPF20|protein_coding|CODING|NM_001278267.1|94|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G2580E|3795|NBPF10|protein_coding|CODING|NM_001302371.1|62|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 1 0 37 0 0.997503 0 . 0.697676 rs372557852 -0.556411 0.168287 14 H3468R 4963 cAt/cGt MODERATE 94 MISSENSE CODING NBPF20 G protein_coding NM_001278267.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145354441 A G 0 46.1 0 0.8404 0.9165 0.9553 0.8978 0.9732 0.953 0 . 0 1 110 830 44 40 4 596 12 24 2 148 898 52 48 4 608 12 26 1 0 . 0 . 6 0,1,0,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H3468R|4963|NBPF20|protein_coding|CODING|NM_001278267.1|94|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H2619R|3795|NBPF10|protein_coding|CODING|NM_001302371.1|62|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 35 0 1 0 . 1 rs199712346 -0.590765 0.320361 6 H2619R 3795 cAt/cGt MODERATE 62 MISSENSE CODING NBPF10 G protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145354441 A G 0 46.1 0 0.8404 0.9165 0.9553 0.8978 0.9732 0.953 0 . 0 1 110 830 44 40 4 596 12 24 2 148 898 52 48 4 608 12 26 1 0 . 0 . 6 0,1,0,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H3468R|4963|NBPF20|protein_coding|CODING|NM_001278267.1|94|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H2619R|3795|NBPF10|protein_coding|CODING|NM_001302371.1|62|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 35 0 1 0 . 1 rs199712346 -0.590765 0.320361 6 G2824E 3795 gGg/gAg MODERATE 68 MISSENSE CODING NBPF10 A protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145365316 G A 0 174 0 0.1369 0.242 0.3674 0.1617 0.3867 0.229 0 . 0 1 1389 37334 4123 1478 2583 23262 289 4210 2 7536 109280 10708 8082 6314 60512 820 15308 0.771623 0 . 0 . 29 9,0,16,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G2824E|3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 1 0 40 0 0.0157936 0.6 0 0.188813 rs368121891,rs61813408 -0.691153 0.0131189 29 L2843V 3795 Ctt/Gtt MODERATE 68 MISSENSE CODING NBPF10 G protein_coding NM_001302371.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145365372 C G 0 219 0 0.1377 0.2432 0.3674 0.1627 0.3887 0.2311 0 . 0 1 1502 38803 4342 1515 2639 24157 306 4342 2 8660 115468 11310 8418 6528 63448 872 16232 0.864129 0 . 0 . 50 4,2,24,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Gtt|L2843V|3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|G),INTRON(MODIFIER||||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|24|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 46 0 0.0395192 0.510136 0 0.0415737 rs4126496,rs61813409 -0.69312 0.822484 50 1110 153 MODIFIER 25 CODING NBPF9 A protein_coding NM_001277444.1.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145368837 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.926536 0 . 0 . 167 8,57,13,81 UTR_3_PRIME(MODIFIER||153||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|25|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 . 0 48 0 0.235353 9.32078e-08 0 0.00799628 rs7414890 -0.693147 0.178836 167 1110 187 MODIFIER 25 CODING NBPF9 G protein_coding NM_001277444.1.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145368871 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 85 0,0,7,78 UTR_3_PRIME(MODIFIER||187||1110|NBPF9|protein_coding|CODING|NM_001277444.1.2|25|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|G),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 . 0 . 0 . 0 . 0 . 44 0 0 0.00109344 0 . rs7416122 -0.693147 0.0117035 85 391 225 MODIFIER 1 CODING TXNIP A protein_coding NM_006472.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145438578 C A 0 57 0 1 0.9992 0.9986 1 0.999 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||225||391|TXNIP|protein_coding|CODING|NM_006472.5|1|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs833392 -0.511536 0.292464 3 391 222 MODIFIER 1 CODING TXNIP A protein_coding NM_006472.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145438581 C A 0 25.9 0 0.0726 0.1112 0.0605 0.2073 0.0944 0.1176 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_5_PRIME(MODIFIER||222||391|TXNIP|protein_coding|CODING|NM_006472.5|1|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs9245 -0.453602 0.56 3 391 402 MODIFIER 8 CODING TXNIP C protein_coding NM_006472.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145441620 T C 0 9.7 0 0.41 0.7398 0.8026 0.8125 0.9533 0.8466 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||402||391|TXNIP|protein_coding|CODING|NM_006472.5|8|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7211 -0.379885 0 1 391 1036 MODIFIER 8 CODING TXNIP C protein_coding NM_006472.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145442254 G C 0 228 0 0.5794 0.7893 0.8156 0.8165 0.9553 0.8558 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,46,11 UTR_3_PRIME(MODIFIER||1036||391|TXNIP|protein_coding|CODING|NM_006472.5|8|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7212 -0.693147 0.89465 59 391 1046 MODIFIER 8 CODING TXNIP A protein_coding NM_006472.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145442264 T A 0 228 0 0.5794 0.7893 0.8156 0.8165 0.9553 0.8558 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,46,13 UTR_3_PRIME(MODIFIER||1046||391|TXNIP|protein_coding|CODING|NM_006472.5|8|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4755 -0.693147 0.816623 62 A33 337 gcT/gcC LOW 1 SILENT CODING LIX1L C protein_coding NM_153713.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145477257 T C 0 9.7 0 0.0825 0.1142 0.0562 0.2123 0.0964 0.1155 0 . 0 1 3 392 6 8 0 88 3 284 2 64 3216 36 72 4 664 30 2346 0 . 0 . 0 1 0,0,0,1 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A33|337|LIX1L|protein_coding|CODING|NM_153713.2|1|C),DOWNSTREAM(MODIFIER||1610||496|ANKRD34A|protein_coding|CODING|NM_001039888.3||C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2282013 -0.379885 0 1 174 1165 MODIFIER 6 CODING RBM8A G protein_coding NM_005105.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145510376 A G 0 228 0 0.6415 0.7971 0.8156 0.8274 0.9553 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 108 0,0,14,90 UTR_3_PRIME(MODIFIER||1165||174|RBM8A|protein_coding|CODING|NM_005105.4|6|G),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|G),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|G),INTRAGENIC(MODIFIER|||||GNRHR2||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 34 0 0 0.000632717 0 . rs147038428 -0.693147 8.06589e-05 108 F334 1167 ttT/ttC LOW 9 SILENT CODING ITGA10 C protein_coding NM_003637.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145532549 T C 0 228 0 0.9554 0.988 0.9986 1 1 1 0.965048 0.988159 1 2 10032 120976 11556 8654 6614 66706 908 16506 2 10402 121376 11578 8654 6614 66714 908 16506 0 . 0 . 0 119 0,0,49,58 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F334|1167|ITGA10|protein_coding|CODING|NM_003637.4|9|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1328584 -0.693147 0.657208 119 P428S 1001 Ccc/Tcc MODERATE 10 MISSENSE CODING ANKRD35 T protein_coding NM_144698.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145561594 C T 0 228 0 0.5794 0.5647 0.5043 0.7252 0.3797 0.6125 0.527916 0.422036 0.367791 2 5518 55519 6356 6308 2547 25163 464 9163 2 10242 121024 11558 8644 6606 66568 904 16502 0 . 0 . 0 53 0,0,23,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P428S|1001|ANKRD35|protein_coding|CODING|NM_144698.4|10|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|T),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6670984 -0.693147 0.00254439 53 L857 1001 Ttg/Ctg LOW 10 SILENT CODING ANKRD35 C protein_coding NM_144698.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145562881 T C 0 228 0 0.6059 0.5889 0.5389 0.7252 0.4384 0.6155 0.543884 0.455735 0.410615 2 5192 54001 5848 5642 2405 25500 443 8971 2 9096 107184 9978 7682 5518 58330 810 15770 0.963636 0 . 0 . 181 1,1,101,64 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L857|1001|ANKRD35|protein_coding|CODING|NM_144698.4|10|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.766667 rs10910824 -0.693147 0.0158643 181 628 687 MODIFIER 14 CODING PIAS3 T protein_coding NM_006099.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145586309 C T 0 228 0 0.975 0.9932 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,32,41 UTR_3_PRIME(MODIFIER||687||628|PIAS3|protein_coding|CODING|NM_006099.3|14|T),DOWNSTREAM(MODIFIER||184||328|NUDT17|protein_coding|CODING|NM_001012758.2||T),DOWNSTREAM(MODIFIER||4358||547|POLR3C|protein_coding|CODING|NM_001303456.1||T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|T),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1983954 -0.693147 0.762782 81 628 781 MODIFIER 14 CODING PIAS3 T protein_coding NM_006099.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145586403 G T 0 228 0 0.6657 0.9091 0.9827 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 102 0,0,58,34 UTR_3_PRIME(MODIFIER||781||628|PIAS3|protein_coding|CODING|NM_006099.3|14|T),DOWNSTREAM(MODIFIER||90||328|NUDT17|protein_coding|CODING|NM_001012758.2||T),DOWNSTREAM(MODIFIER||4264||547|POLR3C|protein_coding|CODING|NM_001303456.1||T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|T),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1050057 -0.693147 0.28975 102 547 617 MODIFIER 16 CODING POLR3C T protein_coding NM_001303456.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145592073 A T 0 9.7 0 0.6324 0.7099 0.6455 0.8522 0.6372 0.7883 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||617||547|POLR3C|protein_coding|CODING|NM_001303456.1|16|T),UPSTREAM(MODIFIER||2638||328|NUDT17|protein_coding|CODING|NM_001012758.2||T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|T),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9729027 -0.379885 0 1 547 LOW 15 CODING POLR3C CT protein_coding NM_001303456.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 145592261 C CT 0 5.6 0 0.5643 0.854 0.9424 0.9246 0.9771 0.9836 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 SPLICE_SITE_REGION+INTRON(LOW||||547|POLR3C|protein_coding|CODING|NM_001303456.1|15|CT),UPSTREAM(MODIFIER||2827||328|NUDT17|protein_coding|CODING|NM_001012758.2||CT),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|CT),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|CT) 0 0.5 1 1 1 1 1 0 . 0 32 0 0 . 0 . rs11370032 -0.379885 0 1 1457 21127 MODIFIER 1 CODING NBPF12 T protein_coding NM_001278141.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146374215 C T 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||21127||1457|NBPF12|protein_coding|CODING|NM_001278141.1|1|T),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|T),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|T),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 . 0 55 0 0 . 0 . rs368248123 -0.379885 0 1 A129T 1457 Gcc/Acc MODERATE 9 MISSENSE CODING NBPF12 A protein_coding NM_001278141.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146398399 G A 0 216 0 0.0582 0.0944 0.1297 0.1925 0.0795 0.0327 0 . 0 1 382 7923 888 1416 672 4000 71 494 2 4228 54446 2636 4182 3804 28458 458 10680 0.891375 0 . 0 COSM462863,COSM1134688 283 54,94,73,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A129T|1457|NBPF12|protein_coding|CODING|NM_001278141.1|9|A),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|A),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.615548 6.10607e-05 0 0.307108 rs377655940 -0.693147 0.0367521 283 Y517S 1457 tAc/tCc MODERATE 16 MISSENSE CODING NBPF12 C protein_coding NM_001278141.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146406560 A C 0 6.4 0 0.6921 0.7356 0.745 0.7302 0.7893 0.7382 0 . 0 1 0 0 0 0 0 0 0 0 2 70 108 12 2 0 24 0 0 0 0 . 0 . 4 1,1,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tCc|Y517S|1457|NBPF12|protein_coding|CODING|NM_001278141.1|16|C),INTRON(MODIFIER||||4963|NBPF20|protein_coding|CODING|NM_001278267.1|99|C),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 22 0 0 1 0 0.25 rs186645718 -0.453602 0.42 4 C3684W 4963 tgT/tgG MODERATE 100 MISSENSE CODING NBPF20 G protein_coding NM_001278267.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146420082 T G 0 222 0 0.1059 0.3001 0.2666 0.3919 0.2744 0.5184 0 . 0 1 74 779 36 76 5 479 12 97 2 838 4812 206 300 34 3146 44 244 0.896166 0 . 0 . 375 158,43,101,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C3684W|4963|NBPF20|protein_coding|CODING|NM_001278267.1|100|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C910W|1457|NBPF12|protein_coding|CODING|NM_001278141.1|25|G),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 36 0 5.03315e-21 0.98435 0 0.885275 rs150070080 -0.693147 0.00147048 375 C910W 1457 tgT/tgG MODERATE 25 MISSENSE CODING NBPF12 G protein_coding NM_001278141.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146420082 T G 0 222 0 0.1059 0.3001 0.2666 0.3919 0.2744 0.5184 0 . 0 1 74 779 36 76 5 479 12 97 2 838 4812 206 300 34 3146 44 244 0.896166 0 . 0 . 375 158,43,101,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C3684W|4963|NBPF20|protein_coding|CODING|NM_001278267.1|100|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C910W|1457|NBPF12|protein_coding|CODING|NM_001278141.1|25|G),INTRON(MODIFIER||||3795|NBPF10|protein_coding|CODING|NM_001302371.1|68|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 36 0 5.03315e-21 0.98435 0 0.885275 rs150070080 -0.693147 0.00147048 375 4963 8 MODIFIER 131 CODING NBPF20 G protein_coding NM_001278267.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466129 T G 0 114 0 0.1452 0.1567 0.2248 0.246 0.1252 0.0644 0 . 0 1 545 8021 922 1321 589 4189 57 398 2 6922 98106 7532 6944 5666 56766 746 13530 0.0722767 0 . 0 . 266 43,128,33,32 UTR_3_PRIME(MODIFIER||8||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|G),UTR_3_PRIME(MODIFIER||8||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|G),DOWNSTREAM(MODIFIER||8||3795|NBPF10|protein_coding|CODING|NM_001302371.1||G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 41 0 4.6644e-05 2.48542e-15 0 2.03056e-05 rs202035412 -0.693147 5.68591e-17 266 1457 8 MODIFIER 37 CODING NBPF12 G protein_coding NM_001278141.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466129 T G 0 114 0 0.1452 0.1567 0.2248 0.246 0.1252 0.0644 0 . 0 1 545 8021 922 1321 589 4189 57 398 2 6922 98106 7532 6944 5666 56766 746 13530 0.0722767 0 . 0 . 266 43,128,33,32 UTR_3_PRIME(MODIFIER||8||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|G),UTR_3_PRIME(MODIFIER||8||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|G),DOWNSTREAM(MODIFIER||8||3795|NBPF10|protein_coding|CODING|NM_001302371.1||G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 41 0 4.6644e-05 2.48542e-15 0 2.03056e-05 rs202035412 -0.693147 5.68591e-17 266 4963 201 MODIFIER 131 CODING NBPF20 G protein_coding NM_001278267.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466322 A G 0 186 0 0.7791 0.7732 0.8357 0.7361 0.7863 0.7454 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,2,12 UTR_3_PRIME(MODIFIER||201||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|G),UTR_3_PRIME(MODIFIER||201||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|G),DOWNSTREAM(MODIFIER||201||3795|NBPF10|protein_coding|CODING|NM_001302371.1||G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 35 0 0 0 0 . rs1284539 -0.686358 0.0310342 14 1457 201 MODIFIER 37 CODING NBPF12 G protein_coding NM_001278141.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466322 A G 0 186 0 0.7791 0.7732 0.8357 0.7361 0.7863 0.7454 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,2,12 UTR_3_PRIME(MODIFIER||201||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|G),UTR_3_PRIME(MODIFIER||201||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|G),DOWNSTREAM(MODIFIER||201||3795|NBPF10|protein_coding|CODING|NM_001302371.1||G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 35 0 0 0 0 . rs1284539 -0.686358 0.0310342 14 4963 373 MODIFIER 131 CODING NBPF20 A protein_coding NM_001278267.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466494 G A 0 49.3 0 0.1112 0.1258 0.1643 0.2063 0.1093 0.0521 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 2,3,1,2 UTR_3_PRIME(MODIFIER||373||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|A),UTR_3_PRIME(MODIFIER||373||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|A),DOWNSTREAM(MODIFIER||373||3795|NBPF10|protein_coding|CODING|NM_001302371.1||A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 53 0 0.300267 0.600535 0 0.900802 rs11581296 -0.511536 0.116687 8 1457 373 MODIFIER 37 CODING NBPF12 A protein_coding NM_001278141.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466494 G A 0 49.3 0 0.1112 0.1258 0.1643 0.2063 0.1093 0.0521 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 2,3,1,2 UTR_3_PRIME(MODIFIER||373||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|A),UTR_3_PRIME(MODIFIER||373||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|A),DOWNSTREAM(MODIFIER||373||3795|NBPF10|protein_coding|CODING|NM_001302371.1||A),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 53 0 0.300267 0.600535 0 0.900802 rs11581296 -0.511536 0.116687 8 4963 607 MODIFIER 131 CODING NBPF20 C protein_coding NM_001278267.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466728 A C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||607||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|C),UTR_3_PRIME(MODIFIER||607||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|C),DOWNSTREAM(MODIFIER||607||3795|NBPF10|protein_coding|CODING|NM_001302371.1||C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 . 0 56 0 0 . 0 . rs201047664 -0.379885 0 1 1457 607 MODIFIER 37 CODING NBPF12 C protein_coding NM_001278141.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146466728 A C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||607||4963|NBPF20|protein_coding|CODING|NM_001278267.1|131|C),UTR_3_PRIME(MODIFIER||607||1457|NBPF12|protein_coding|CODING|NM_001278141.1|37|C),DOWNSTREAM(MODIFIER||607||3795|NBPF10|protein_coding|CODING|NM_001302371.1||C),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 . 0 56 0 0 . 0 . rs201047664 -0.379885 0 1 272 4222 MODIFIER 8 CODING PRKAB2 C protein_coding NM_005399.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146626922 T C 0 222 0 0.1074 0.2594 0.281 0.5268 0.1511 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.527993 0 . 0 . 99 28,21,21,20 UTR_3_PRIME(MODIFIER||4222||272|PRKAB2|protein_coding|CODING|NM_005399.4|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.684362 rs386606051,rs6937 -0.693145 0.467861 99 272 3739 MODIFIER 8 CODING PRKAB2 G protein_coding NM_005399.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146627405 C G 0 228 0 0.9115 0.7169 0.5879 0.8532 0.4443 0.6851 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 105 0,0,14,85 UTR_3_PRIME(MODIFIER||3739||272|PRKAB2|protein_coding|CODING|NM_005399.4|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047140 -0.693147 0.00496344 105 272 2737 MODIFIER 8 CODING PRKAB2 C protein_coding NM_005399.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146628407 T C 0 39.3 0 0.9047 0.7145 0.5879 0.8532 0.4433 0.683 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2737||272|PRKAB2|protein_coding|CODING|NM_005399.4|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1442760 -0.453602 0.1 2 272 228 MODIFIER 8 CODING PRKAB2 C protein_coding NM_005399.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146630916 T C 0 65 0 0.0023 0.1653 0.17 0.3968 0.0875 0.2239 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.800737 0 . 0 . 14 9,0,5,0 UTR_3_PRIME(MODIFIER||228||272|PRKAB2|protein_coding|CODING|NM_005399.4|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.965069 rs2304893 -0.590765 0.530437 14 P337 533 ccG/ccA LOW 7 SILENT CODING FMO5 T protein_coding NM_001461.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146672906 C T 0 228 0 0.8253 0.8958 0.9467 0.9871 0.9085 0.8476 0.849069 0.894972 0.918488 2 8812 111792 11069 8509 6299 61926 835 14342 2 10404 121394 11576 8654 6612 66728 908 16512 0 . 0 . 0 83 0,0,30,49 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P337|533|FMO5|protein_coding|CODING|NM_001461.3|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386619855,rs894469 -0.693147 0.715194 83 I541 897 atA/atC LOW 15 SILENT CODING CHD1L C protein_coding NM_004284.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146751782 A C 0 228 0 0.9433 0.9679 0.9885 0.9881 0.9592 0.9744 0.943259 0.953714 0.95907 2 9803 117227 11419 8519 6328 64314 869 15975 2 10404 121378 11578 8654 6614 66714 908 16506 0 . 0 . 0 93 0,0,42,48 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I541|897|CHD1L|protein_coding|CODING|NM_004284.4|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7547279 -0.693147 0.0124307 93 A885S 897 Gca/Tca MODERATE 23 MISSENSE CODING CHD1L T protein_coding NM_004284.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146767149 G T 0 228 0 0.944 0.9681 0.9885 0.9881 0.9592 0.9744 0.943032 0.954559 0.960465 2 9805 117252 11380 8512 6340 64367 869 15979 2 10402 121304 11538 8648 6608 66696 906 16506 0 . 0 . 0 38 0,0,21,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A885S|897|CHD1L|protein_coding|CODING|NM_004284.4|23|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4950394 -0.693127 0.2806 38 897 130 MODIFIER 23 CODING CHD1L G protein_coding NM_004284.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 146767320 A G 0 126 0 0.9342 0.8239 0.7954 0.8958 0.7276 0.7198 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||130||897|CHD1L|protein_coding|CODING|NM_004284.4|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6537 -0.651104 0.261612 8 1426 34 MODIFIER 10 CODING BCL9 G protein_coding NM_004326.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147096794 A G 0 222 0 0.8585 0.8383 0.8862 0.7093 0.8847 0.862 0.856786 0.886059 0.901071 1 8355 98097 9553 5625 5506 56816 734 11508 2 9742 113266 11356 8420 6370 63244 850 13284 0.968423 0 . 0 . 101 31,16,33,14 UTR_3_PRIME(MODIFIER||34||1426|BCL9|protein_coding|CODING|NM_004326.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.694141 rs386617925,rs867270 -0.693147 0.0643151 101 1426 68 MODIFIER 10 CODING BCL9 G protein_coding NM_004326.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147096828 C G 0 228 0 0.8638 0.9635 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 99 0,0,64,27 UTR_3_PRIME(MODIFIER||68||1426|BCL9|protein_coding|CODING|NM_004326.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs946902 -0.693147 0.589727 99 1426 506 MODIFIER 10 CODING BCL9 C protein_coding NM_004326.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147097266 T C 0 222 0 0.469 0.3043 0.3329 0.3056 0.171 0.1973 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.946881 0 . 0 . 60 8,20,6,18 UTR_3_PRIME(MODIFIER||506||1426|BCL9|protein_coding|CODING|NM_004326.3|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.940997 rs946903 -0.692831 0.346322 60 1426 875 MODIFIER 10 CODING BCL9 T protein_coding NM_004326.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147097635 C T 0 222 0 0.8321 0.8191 0.879 0.6984 0.8847 0.816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.662197 0 . 0 . 141 35,28,33,25 UTR_3_PRIME(MODIFIER||875||1426|BCL9|protein_coding|CODING|NM_004326.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.507452 rs3766512 -0.693147 0.272319 141 H413 428 caC/caT LOW 10 SILENT CODING ACP6 A protein_coding NM_016361.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147119273 G A 0 222 0 0.4281 0.4792 0.6254 0.4226 0.5765 0.4029 0.458239 0.531139 0.568488 1 4716 64847 7506 3226 3876 38383 472 6668 2 10402 121392 11574 8652 6614 66734 908 16508 0.784803 0 . 0 . 123 33,23,25,25 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H413|428|ACP6|protein_coding|CODING|NM_016361.4|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.487159 rs1344,rs386528725 -0.693147 0.227049 123 V316M 428 Gtg/Atg MODERATE 8 MISSENSE CODING ACP6 T protein_coding NM_016361.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147121977 C T 0 228 0 0.9418 0.9844 0.9986 1 1 1 0.957558 0.985468 0.999767 2 9925 120905 11563 8654 6614 66731 906 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 98 0,0,60,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V316M|428|ACP6|protein_coding|CODING|NM_016361.4|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6593795 -0.693147 0.156818 98 R275 428 Agg/Cgg LOW 7 SILENT CODING ACP6 G protein_coding NM_016361.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147124310 T G 0 228 0 . 0 . 0 . 0 0.761689 0.725665 0.707209 2 7946 86206 9586 6166 4852 47484 626 9546 2 10402 121294 11564 8640 6610 66698 908 16472 1 0 . 0 . 109 0,1,43,58 SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R275|428|ACP6|protein_coding|CODING|NM_016361.4|7|G) 1 0 . 0 . 0 . 1 1 0 60 0 1 1 0 1 rs2153463 -0.693147 0.136509 109 428 126 MODIFIER 1 CODING ACP6 C protein_coding NM_016361.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147142296 T C 0 9.7 0 0.6498 0.4832 0.415 0.6141 0.332 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||126||428|ACP6|protein_coding|CODING|NM_016361.4|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2883202 -0.379885 0 1 358 888 MODIFIER 2 CODING GJA5 A protein_coding NM_005266.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147229382 G A 0 39.3 0 0.9584 0.9886 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||888||358|GJA5|protein_coding|CODING|NM_005266.6|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10900395 -0.453602 0.78 2 358 707 MODIFIER 2 CODING GJA5 A protein_coding NM_005266.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147229563 G A 0 9.7 0 0.4138 0.3191 0.3213 0.2718 0.2087 0.3517 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||707||358|GJA5|protein_coding|CODING|NM_005266.6|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1043802 -0.379885 0 1 358 53 MODIFIER 2 CODING GJA5 C protein_coding NM_005266.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147230217 T C 0 222 0 0.9017 0.8804 0.8804 0.9018 0.7584 0.955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.240105 0 . 0 . 73 26,3,33,3 UTR_3_PRIME(MODIFIER||53||358|GJA5|protein_coding|CODING|NM_005266.6|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.90953 rs1692141 -0.693139 0.224114 73 E222K 919 Gaa/Aaa MODERATE 8 MISSENSE CODING NBPF11 T protein_coding NM_183372.5.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147595076 C T 0 117 0 0.1097 0.0803 0.0447 0.004 0.0706 0.1544 0 . 0 2 39 172 2 0 2 102 1 26 2 184 1004 60 42 6 656 6 50 0.961482 0 . 0 . 51 4,0,47,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E222K|919|NBPF11|protein_coding|CODING|NM_183372.5.2|8|T),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|T) 0 . 0 . 0 1 0 . 1 0 57 0 0.0841811 0 . 0.533403 rs200675471 -0.693147 0.162054 51 H70P 164 cAt/cCt MODERATE 1 MISSENSE CODING PPIAL4C G protein_coding NM_001135789.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955136 T G 0 20.7 0 0.3109 0.1098 0.0533 0.0208 0.0298 0.0521 0 . 0 2 0 3 0 0 0 2 0 1 2 42 544 32 38 0 380 2 50 0 . 0 . 0 4 0,0,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H70P|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H70P|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 15 0 0 . 0 . rs372484895 -0.556411 0.998069 4 H70P 164 cAt/cCt MODERATE 1 MISSENSE CODING PPIAL4A G protein_coding NM_001143883.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955136 T G 0 20.7 0 0.3109 0.1098 0.0533 0.0208 0.0298 0.0521 0 . 0 2 0 3 0 0 0 2 0 1 2 42 544 32 38 0 380 2 50 0 . 0 . 0 4 0,0,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H70P|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H70P|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 15 0 0 . 0 . rs372484895 -0.556411 0.998069 4 A33 164 gcG/gcA LOW 1 SILENT CODING PPIAL4C T protein_coding NM_001135789.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955246 C T 0 66 0 0.5401 0.347 0.3098 0.1974 0.2117 0.4059 0 . 0 2 0 20 2 2 0 12 0 4 2 274 4628 232 382 406 2990 66 278 1 0 . 0 . 15 1,0,14,0 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A33|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A33|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|T),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|T) 0 . 0 . 0 1 0 . 1 0 20 0 1 0 . 1 rs202020039 -0.686358 0.00136404 15 A33 164 gcG/gcA LOW 1 SILENT CODING PPIAL4A T protein_coding NM_001143883.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955246 C T 0 66 0 0.5401 0.347 0.3098 0.1974 0.2117 0.4059 0 . 0 2 0 20 2 2 0 12 0 4 2 274 4628 232 382 406 2990 66 278 1 0 . 0 . 15 1,0,14,0 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A33|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A33|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|T),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|T) 0 . 0 . 0 1 0 . 1 0 20 0 1 0 . 1 rs202020039 -0.686358 0.00136404 15 L30P 164 cTa/cCa MODERATE 1 MISSENSE CODING PPIAL4C G protein_coding NM_001135789.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955256 A G 0 79 0 0.6188 0.4665 0.4568 0.3234 0.34 0.545 0 . 0 2 0 21 2 1 0 14 0 4 2 312 5346 262 446 548 3408 70 300 1 0 . 0 . 29 1,0,28,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L30P|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L30P|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 21 0 1 0 . 1 rs199950315 -0.693054 1.4315e-06 29 L30P 164 cTa/cCa MODERATE 1 MISSENSE CODING PPIAL4A G protein_coding NM_001143883.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955256 A G 0 79 0 0.6188 0.4665 0.4568 0.3234 0.34 0.545 0 . 0 2 0 21 2 1 0 14 0 4 2 312 5346 262 446 548 3408 70 300 1 0 . 0 . 29 1,0,28,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L30P|164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L30P|164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 21 0 1 0 . 1 rs199950315 -0.693054 1.4315e-06 29 164 24 MODIFIER 1 CODING PPIAL4C C protein_coding NM_001135789.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955368 T C 0 139 0 0.525 0.3295 0.2824 0.1905 0.1978 0.3773 0 . 0 2 8 117 13 2 1 73 5 15 2 3672 87758 8482 6644 5434 52180 696 10650 1 0 . 0 . 67 0,1,61,4 UTR_5_PRIME(MODIFIER||24||164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|C),UTR_5_PRIME(MODIFIER||24||164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|C),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|C) 0 . 0 . 0 1 0 . 1 0 22 0 1 0.781196 0 1 rs76383089 -0.693147 1.94955e-05 67 164 24 MODIFIER 1 CODING PPIAL4A C protein_coding NM_001143883.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955368 T C 0 139 0 0.525 0.3295 0.2824 0.1905 0.1978 0.3773 0 . 0 2 8 117 13 2 1 73 5 15 2 3672 87758 8482 6644 5434 52180 696 10650 1 0 . 0 . 67 0,1,61,4 UTR_5_PRIME(MODIFIER||24||164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|C),UTR_5_PRIME(MODIFIER||24||164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|C),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|C) 0 . 0 . 0 1 0 . 1 0 22 0 1 0.781196 0 1 rs76383089 -0.693147 1.94955e-05 67 164 34 MODIFIER 1 CODING PPIAL4C G protein_coding NM_001135789.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955378 A G 0 139 0 0.4803 0.2716 0.2233 0.1359 0.1342 0.3047 0 . 0 2 16 23 0 1 1 4 0 1 2 3696 88048 8502 6670 5448 52358 698 10676 0.80303 0 . 0 . 68 0,2,60,6 UTR_5_PRIME(MODIFIER||34||164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),UTR_5_PRIME(MODIFIER||34||164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 21 0 0.0454545 0.0989417 0 0 rs201998677 -0.693147 6.27808e-13 68 164 34 MODIFIER 1 CODING PPIAL4A G protein_coding NM_001143883.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 147955378 A G 0 139 0 0.4803 0.2716 0.2233 0.1359 0.1342 0.3047 0 . 0 2 16 23 0 1 1 4 0 1 2 3696 88048 8502 6670 5448 52358 698 10676 0.80303 0 . 0 . 68 0,2,60,6 UTR_5_PRIME(MODIFIER||34||164|PPIAL4C|protein_coding|CODING|NM_001135789.3|1|G),UTR_5_PRIME(MODIFIER||34||164|PPIAL4A|protein_coding|CODING|NM_001143883.2|1|G),INTRON(MODIFIER||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|18|G) 0 . 0 . 0 1 0 . 1 0 21 0 0.0454545 0.0989417 0 0 rs201998677 -0.693147 6.27808e-13 68 R667C 942 Cgt/Tgt MODERATE 14 MISSENSE CODING NBPF8 A protein_coding NM_001037501.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148010911 G A 0 98 0 . 0 . 0 . 0 . 0 . 1 229 1427 92 73 15 886 20 112 2 400 2706 176 142 26 1712 36 214 0.332988 0 . 0 . 1148 130,48,585,260 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R667C|942|NBPF8|protein_coding|CODING|NM_001037501.2.2|14|A) 0 0.5 1 0 . 0 . 0 1 0 23 0 0.730855 0.764744 0 0.925627 rs111868263,rs201061774,rs61810210 -0.693147 2.48237e-05 1148 H612Q 942 caC/caA MODERATE 13 MISSENSE CODING NBPF8 T protein_coding NM_001037501.2.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148016426 G T 0 29.5 0 0.118 0.0469 0.0418 0.0337 0.005 0.0112 0 . 0 1 10 14 2 0 0 0 0 2 2 4504 99434 9742 7894 5756 57104 774 13660 0.793923 0 . 0 . 19 8,5,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caA|H612Q|942|NBPF8|protein_coding|CODING|NM_001037501.2.2|13|T) 0 0.5 1 0 . 1 0 . 1 0 29 0 0.310905 0.149361 0 1 rs139529628,rs28452263 -0.556411 0.622417 19 R603 942 cgG/cgA LOW 13 SILENT CODING NBPF8 T protein_coding NM_001037501.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148016453 C T 0 163 0 0.0885 0.0367 0.0274 0.0387 0.004 0.0051 0 . 0 1 16 77 3 40 1 5 1 11 2 4412 98364 9676 7864 5710 56678 770 13254 0.938702 0 . 0 . 49 11,20,7,10 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R603|942|NBPF8|protein_coding|CODING|NM_001037501.2.2|13|T) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.0314828 0.55444 0 0.88434 rs199586770 -0.690438 0.122076 49 942 LOW 12 CODING NBPF8 A protein_coding NM_001037501.2.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148016463 G A 0 193 0 . 0 . 0 . 0 0.0060506 0.0017948 0.000205423 1 21 44 3 5 1 4 1 9 2 4350 97786 9630 7842 5690 56466 764 13044 0.620881 0 . 0 . 63 12,27,11,12 SPLICE_SITE_REGION+INTRON(LOW||||942|NBPF8|protein_coding|CODING|NM_001037501.2.2|12|A) 1 0.5 1 0 . 0 . 1 1 0 29 0 0.00263584 0.173224 0 0.493993 rs149662472 -0.692717 0.00239878 63 S566 942 tcG/tcA LOW 12 SILENT CODING NBPF8 T protein_coding NM_001037501.2.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148017605 C T 0 161 0 . 0 . 0 . 0 0.0762769 0.0297633 0.00408163 1 853 3371 905 821 45 344 22 381 2 6324 106714 10212 8122 6030 59886 840 15300 0.778097 0 . 0 . 1213 123,610,137,187 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S566|942|NBPF8|protein_coding|CODING|NM_001037501.2.2|12|T) 1 0.5 1 0 . 0 . 1 1 0 26 0 0.331595 0.00202353 0 1.88966e-07 rs148099814 -0.693147 0.0515339 1213 670 19381 MODIFIER 1 CODING NBPF15 G protein_coding NM_001170755.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148558269 A G 0 4.5 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||19381||670|NBPF15|protein_coding|CODING|NM_001170755.2|1|G),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||G) 0 . 0 . 0 . 0 . 0 . 30 0 0 . 0 . rs200896600 -0.379885 0 2 670 54 MODIFIER 22 CODING NBPF15 T protein_coding NM_001170755.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 148594694 C T 0 228 0 0 0.0077875 0.0043 0.0347 0 0.001 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.118539 0 . 0 . 155 1,3,33,118 UTR_3_PRIME(MODIFIER||54||670|NBPF15|protein_coding|CODING|NM_001170755.2|22|T),INTRAGENIC(MODIFIER|||||NBPF25P||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 45 0 0.655101 1.19149e-08 0 0.600449 rs200131555 -0.693147 0.0830886 155 742 1565 MODIFIER 13 CODING SV2A T protein_coding NM_014849.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 149875001 C T 0 12.5 0 0 0.0025959 0 0.0129 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_3_PRIME(MODIFIER||1565||742|SV2A|protein_coding|CODING|NM_014849.4|13|T),DOWNSTREAM(MODIFIER||2653||137|BOLA1|protein_coding|CODING|NM_016074.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3820447 -0.379885 0 3 M159V 709 Atg/Gtg MODERATE 6 MISSENSE CODING MTMR11 C protein_coding NM_001145862.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 149906413 T C 0 228 0 0.0151 0.2286 0.2637 0.2837 0.3688 0.2914 0.0869269 0.296479 0.403837 2 763 40604 2695 2762 2107 26610 333 5334 2 10396 121110 11518 8622 6592 66574 906 16502 0.545455 0 . 0 COSM146598 88 1,1,31,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M159V|709|MTMR11|protein_coding|CODING|NM_001145862.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.506494 rs11205303 -0.693147 0.607881 88 843 2974 MODIFIER 12 CODING OTUD7B G protein_coding NM_020205.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 149912782 A G 0 9.7 0 0.9849 0.9958 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2974||843|OTUD7B|protein_coding|CODING|NM_020205.3|12|G),UPSTREAM(MODIFIER||3991||709|MTMR11|protein_coding|CODING|NM_001145862.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4926398 -0.379885 0 1 843 1073 MODIFIER 12 CODING OTUD7B A protein_coding NM_020205.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 149914683 G A 0 228 0 0.9644 0.9902 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,7,33 UTR_3_PRIME(MODIFIER||1073||843|OTUD7B|protein_coding|CODING|NM_020205.3|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3930079 -0.693145 0.0866616 51 570 237 MODIFIER 1 CODING VPS45 A protein_coding NM_007259.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150039678 G A 0 114 0 0.329 0.7646 0.8746 0.999 0.8231 0.9734 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_5_PRIME(MODIFIER||237||570|VPS45|protein_coding|CODING|NM_007259.4|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2027349 -0.590765 0.717074 6 G166 268 ggC/ggA LOW 5 SILENT CODING ANP32E T protein_coding NM_030920.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150199123 G T 0 222 0 0.9228 0.602 0.4683 0.5456 0.4304 0.498 0.821834 0.553514 0.416047 1 8766 55528 5109 4216 2604 27139 385 7309 2 10368 120222 11444 8568 6570 66026 894 16352 0.97688 0 . 0 COSM1179736 62 9,22,10,16 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G166|268|ANP32E|protein_coding|CODING|NM_030920.4|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.453432 rs7522034 -0.692976 0.0604691 62 385 LOW 5 CODING CIART G protein_coding NM_001300838.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150258838 C G 0 160 0 0.9667 0.7478 0.719 0.7738 0.5497 0.6493 0.883568 0.636629 0.510116 1 9360 72209 8912 6618 3202 33591 515 10011 2 10394 120818 11574 8642 6612 66496 898 16202 1 0 . 0 . 49 26,5,12,3 SPLICE_SITE_REGION+INTRON(LOW||||385|CIART|protein_coding|CODING|NM_001300838.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517284 rs1122967 -0.688148 0.0352989 49 385 34 MODIFIER 6 CODING CIART C protein_coding NM_001300838.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150259400 A C 0 162 0 0.3601 0.514 0.513 0.7163 0.4056 0.6258 0.399001 0.386898 0.380698 1 3955 48112 5998 6093 2221 24107 348 5390 2 9960 109352 11358 8480 6594 63056 786 9118 0.812241 0 . 0 . 30 1,14,1,12 UTR_3_PRIME(MODIFIER||34||385|CIART|protein_coding|CODING|NM_001300838.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.140605 rs386508040,rs9126 -0.683931 0.484574 30 87 449 MODIFIER 1 CODING MRPS21 A protein_coding NM_018997.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150266338 T A 0 145 0 0.2784 0.4924 0.5043 0.7183 0.4076 0.6278 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957193 0 . 0 . 19 7,0,11,1 START_GAINED(LOW||||87|MRPS21|protein_coding|CODING|NM_018997.3|1|A),UTR_5_PRIME(MODIFIER||449||87|MRPS21|protein_coding|CODING|NM_018997.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.52158 rs3818978 -0.680642 0.106561 19 87 540 MODIFIER 2 CODING MRPS21 C protein_coding NM_018997.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150281202 A C 0 25.9 0 0.972 0.774 0.7493 0.7768 0.6193 0.68 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||540||87|MRPS21|protein_coding|CODING|NM_018997.3|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs580060 -0.453602 0.44 3 1461 9 MODIFIER 11 CODING RPRD2 G protein_coding NM_015203.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150445819 A G 0 222 0 0.034 0.2296 0.2536 0.2242 0.3857 0.3221 0.095457 0.301855 0.395369 1 773 39811 2469 2017 2809 25934 328 5481 2 8886 113908 11512 8554 6614 63544 848 13950 0.852719 0 . 0 . 59 8,15,6,21 UTR_3_PRIME(MODIFIER||9||1461|RPRD2|protein_coding|CODING|NM_015203.4|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.552055 rs7002 -0.693021 0.131146 59 1461 2209 MODIFIER 11 CODING RPRD2 A protein_coding NM_015203.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150448019 G A 0 228 0 0.9803 0.9946 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 92 0,0,54,31 UTR_3_PRIME(MODIFIER||2209||1461|RPRD2|protein_coding|CODING|NM_015203.4|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6587754 -0.693147 0.0314836 92 A193P 1097 Gct/Cct MODERATE 6 MISSENSE CODING ADAMTSL4 C protein_coding NM_001288608.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150526044 G C 0 222 0 0.6074 0.5284 0.4337 0.5675 0.5338 0.4427 0.590104 0.547055 0.525 1 6214 63465 5915 4728 4323 35071 462 6752 2 10402 121332 11574 8618 6610 66712 908 16508 0.873214 0 . 0 . 119 37,23,32,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A193P|1097|ADAMTSL4|protein_coding|CODING|NM_001288608.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975681 rs41317515 -0.693147 0.579966 119 N837 1097 aaT/aaC LOW 16 SILENT CODING ADAMTSL4 C protein_coding NM_001288608.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150531008 T C 0 222 0 0.6475 0.8145 0.9049 0.8373 0.9314 0.8323 0.702224 0.867523 0.952209 1 7194 109847 10548 7299 6466 63063 841 14436 2 10378 121152 11574 8640 6612 66530 906 16512 0.795196 0 . 0 . 99 34,11,26,18 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N837|1097|ADAMTSL4|protein_coding|CODING|NM_001288608.1|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.808315 rs10888382 -0.693146 0.323318 99 P851 1097 ccG/ccA LOW 16 SILENT CODING ADAMTSL4 A protein_coding NM_001288608.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150531050 G A 0 228 0 0.829 0.8784 0.8444 0.9831 0.839 0.9018 0.839083 0.843534 0.845814 2 8691 105097 10213 8422 5793 56230 796 14952 2 10378 121140 11574 8642 6598 66532 906 16510 0 . 0 . COSM423780 106 0,0,70,21 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P851|1097|ADAMTSL4|protein_coding|CODING|NM_001288608.1|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10749657 -0.693147 0.0755656 106 350 2104 MODIFIER 3 CODING MCL1 A protein_coding NM_021960.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150547747 G A 0 222 0 0.2595 0.395 0.402 0.4544 0.5716 0.3303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.90625 0 . 0 . 80 28,15,12,19 UTR_3_PRIME(MODIFIER||2104||350|MCL1|protein_coding|CODING|NM_021960.4|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.9674 rs878471 -0.69311 0.0402279 80 285 1836 MODIFIER 5 CODING GOLPH3L G protein_coding NM_018178.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150618961 T G 0 32.6 0 0.0976 0.4832 0.6484 0.7252 0.5795 0.5389 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1836||285|GOLPH3L|protein_coding|CODING|NM_018178.5|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9733 -0.379885 0 2 285 228 MODIFIER 5 CODING GOLPH3L G protein_coding NM_018178.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150620569 C G 0 14.4 0 0.2852 0.4085 0.4597 0.3571 0.4314 0.5685 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||228||285|GOLPH3L|protein_coding|CODING|NM_018178.5|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3087960 -0.453602 0.9 3 T267I 394 aCa/aTa MODERATE 10 MISSENSE CODING HORMAD1 A protein_coding NM_032132.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150679033 G A 0 222 0 0.2269 0.3856 0.4467 0.3571 0.4095 0.5613 0.262596 0.347047 0.390323 1 2623 48394 4695 2844 2675 26341 366 8850 2 10322 120902 11546 8642 6604 66524 902 16362 0.979418 0 . 0 . 102 29,6,48,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T267I|394|HORMAD1|protein_coding|CODING|NM_032132.4|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.475358 rs1336900 -0.693147 0.000852796 102 R113W 331 Cgg/Tgg MODERATE 4 MISSENSE CODING CTSS A protein_coding NM_004079.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150727539 G A 0 222 0 0.261 0.3824 0.4366 0.3532 0.3698 0.5511 0.278938 0.329156 0.354884 1 2881 45678 4663 2861 2340 23908 331 8694 2 10380 121304 11570 8638 6614 66690 908 16504 0.948601 0 . 0 COSM146600 269 51,70,53,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R113W|331|CTSS|protein_coding|CODING|NM_004079.4|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.49573 rs2230061 -0.693147 0.0068351 269 331 961 MODIFIER 1 CODING CTSS G protein_coding NM_004079.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150738200 A G 0 39.3 0 0.2579 0.3932 0.438 0.4058 0.3718 0.5532 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||961||331|CTSS|protein_coding|CODING|NM_004079.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3754212 -0.453602 0.72 2 A277 329 gcA/gcG LOW 7 SILENT CODING CTSK C protein_coding NM_000396.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150771703 T C 0 228 0 0.8986 0.9633 0.987 0.9931 0.998 0.9673 0.937358 0.977856 0.998605 2 9631 120029 11506 8607 6614 66641 898 16132 2 10404 121402 11576 8654 6614 66736 908 16510 1 0 . 0 . 137 0,1,42,86 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A277|329|CTSK|protein_coding|CODING|NM_000396.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10788796 -0.693147 0.00132337 137 789 1700 MODIFIER 22 CODING ARNT T protein_coding NM_001668.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150782797 C T 0 222 0 0.0159 0.1761 0.2565 0.2262 0.2744 0.183 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.766721 0 . 0 . 71 29,8,15,7 UTR_3_PRIME(MODIFIER||1700||789|ARNT|protein_coding|CODING|NM_001668.3|22|T),UPSTREAM(MODIFIER||1880||329|CTSK|protein_coding|CODING|NM_000396.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998895 rs10847 -0.692562 0.575857 71 789 512 MODIFIER 22 CODING ARNT C protein_coding NM_001668.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150783985 T C 0 155 0 0.2579 0.3936 0.438 0.3998 0.3738 0.5593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.461785 0 . 0 . 72 1,33,0,37 UTR_3_PRIME(MODIFIER||512||789|ARNT|protein_coding|CODING|NM_001668.3|22|C),UPSTREAM(MODIFIER||3068||329|CTSK|protein_coding|CODING|NM_000396.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.981038 rs11552229,rs386519101 -0.693141 0.788873 72 V189 789 gtG/gtC LOW 7 SILENT CODING ARNT G protein_coding NM_001668.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150808889 C G 0 222 0 0.5174 0.471 0.4625 0.4018 0.3926 0.5665 0.508171 0.415424 0.367907 1 5209 49457 4862 3141 2335 24624 346 8940 2 10326 120838 11464 8606 6592 66468 908 16474 0.882086 0 . 0 COSM146601 131 44,12,46,20 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V189|789|ARNT|protein_coding|CODING|NM_001668.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999789 rs2228099 -0.693147 0.657491 131 380 963 MODIFIER 11 CODING CERS2 G protein_coding NM_022075.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150937661 A G 0 222 0 0.2814 0.4075 0.5159 0.4335 0.3688 0.5143 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968597 0 . 0 . 110 28,23,19,13 UTR_3_PRIME(MODIFIER||963||380|CERS2|protein_coding|CODING|NM_022075.4|11|G),DOWNSTREAM(MODIFIER||441||1291|SETDB1|protein_coding|CODING|NM_001145415.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.978086 rs1546376,rs386536884 -0.69312 0.00723427 110 380 853 MODIFIER 11 CODING CERS2 A protein_coding NM_022075.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150937771 T A 0 228 0 0.8986 0.9583 0.9885 0.9931 0.998 0.9407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,4,12 UTR_3_PRIME(MODIFIER||853||380|CERS2|protein_coding|CODING|NM_022075.4|11|A),DOWNSTREAM(MODIFIER||551||1291|SETDB1|protein_coding|CODING|NM_001145415.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8544 -0.689466 0.192221 18 380 53 MODIFIER 11 CODING CERS2 A protein_coding NM_022075.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150938571 G A 0 222 0 0.2693 0.4042 0.5144 0.4345 0.3668 0.5153 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.976248 0 . 0 . 29 10,3,9,7 UTR_3_PRIME(MODIFIER||53||380|CERS2|protein_coding|CODING|NM_022075.4|11|A),DOWNSTREAM(MODIFIER||1351||1291|SETDB1|protein_coding|CODING|NM_001145415.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.850016 rs8444 -0.689466 0.226718 29 380 8 MODIFIER 11 CODING CERS2 A protein_coding NM_022075.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150938616 G A 0 228 0 0.9251 0.9792 0.9928 1 1 1 0.940082 0.979702 1 2 9735 120542 11537 8654 6614 66690 904 16408 2 10406 121266 11578 8654 6614 66696 908 16410 0 . 0 . 0 48 0,0,30,14 UTR_3_PRIME(MODIFIER||8||380|CERS2|protein_coding|CODING|NM_022075.4|11|A),DOWNSTREAM(MODIFIER||1396||1291|SETDB1|protein_coding|CODING|NM_001145415.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs267739 -0.693146 0.133669 48 380 LOW 4 CODING CERS2 T protein_coding NM_022075.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150940357 G T 0 222 0 0.2194 0.3912 0.513 0.4345 0.3688 0.5153 0.245801 0.316392 0.352558 1 2520 47466 6993 3255 2326 23666 339 8367 2 10398 121170 11530 8608 6604 66626 904 16500 0.964147 0 . 0 . 80 22,16,16,21 SPLICE_SITE_REGION+INTRON(LOW||||380|CERS2|protein_coding|CODING|NM_022075.4|4|T),DOWNSTREAM(MODIFIER||3137||1291|SETDB1|protein_coding|CODING|NM_001145415.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.206931 rs6656535 -0.693141 0.0888318 80 380 LOW 4 CODING CERS2 T protein_coding NM_022075.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150940358 C T 0 222 0 0.2194 0.3912 0.513 0.4345 0.3688 0.5153 0.245801 0.316392 0.352558 1 2520 47461 6988 3251 2326 23670 339 8367 2 10396 121178 11530 8612 6604 66630 906 16500 0.987446 0 . 0 . 79 21,17,16,21 SPLICE_SITE_REGION+INTRON(LOW||||380|CERS2|protein_coding|CODING|NM_022075.4|4|T),DOWNSTREAM(MODIFIER||3138||1291|SETDB1|protein_coding|CODING|NM_001145415.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.255004 rs59988025,rs6681742 -0.693141 0.0888318 79 A205 345 gcA/gcC LOW 10 SILENT CODING ANXA9 C protein_coding NM_003568.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150960350 A C 0 222 0 0.5106 0.4918 0.4092 0.5813 0.3429 0.5859 0.449841 0.353145 0.303605 1 4685 47520 5417 4957 1725 20813 360 9563 2 10400 121028 11524 8612 6572 66566 902 16452 0.999837 0 . 0 . 107 47,11,29,11 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A205|345|ANXA9|protein_coding|CODING|NM_003568.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.619012 rs7532008 -0.693145 0.412764 107 517 196 MODIFIER 11 CODING FAM63A G protein_coding NM_001163258.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150969567 A G 0 195 0 0.7935 0.9431 0.9856 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,21,1 UTR_3_PRIME(MODIFIER||196||517|FAM63A|protein_coding|CODING|NM_001163258.1|11|G),DOWNSTREAM(MODIFIER||1453||345|ANXA9|protein_coding|CODING|NM_003568.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs771202 -0.692562 0.00468406 22 T433K 517 aCg/aAg MODERATE 9 MISSENSE CODING FAM63A T protein_coding NM_001163258.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150970577 G T 0 228 0 0.7943 0.9433 0.9856 1 0.998 1 0.831139 0.942411 0.999419 2 8480 119180 11483 8652 6614 66598 900 16453 2 10406 121246 11578 8652 6614 66630 908 16458 0 . 0 . 0 56 0,0,34,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T433K|517|FAM63A|protein_coding|CODING|NM_001163258.1|9|T),DOWNSTREAM(MODIFIER||2463||345|ANXA9|protein_coding|CODING|NM_003568.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2925741 -0.693147 0.00150236 56 K44E 517 Aag/Gag MODERATE 3 MISSENSE CODING FAM63A C protein_coding NM_001163258.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150975108 T C 0 228 0 0.3192 0.759 0.9424 0.8492 0.9692 0.9141 0.454834 0.802014 0.979884 2 4320 109267 11151 6954 6285 64801 834 14922 2 10074 120764 11574 8636 6614 66448 906 16512 0.900826 0 . 0 . 133 2,0,65,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K44E|517|FAM63A|protein_coding|CODING|NM_001163258.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.867769 rs771205 -0.693147 0.31839 133 K236 453 aaA/aaG LOW 6 SILENT CODING PRUNE G protein_coding NM_021222.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 150999737 A G 0 222 0 0.2474 0.2758 0.1974 0.4613 0.2107 0.2454 0.258738 0.236737 0.225465 1 2576 30592 2413 4330 1449 15346 213 4265 2 10388 120924 11526 8624 6598 66412 904 16472 0.986826 0 . 0 . 119 27,26,26,29 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K236|453|PRUNE|protein_coding|CODING|NM_021222.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975156 rs11204762 -0.693147 0.0370491 119 G397S 453 Ggc/Agc MODERATE 8 MISSENSE CODING PRUNE A protein_coding NM_021222.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151006537 G A 0 222 0 0 0.0817 0.0677 0.3383 0.003 0.0184 0.00113482 0.00176841 0.00209302 1 8 4446 781 3158 15 151 23 310 2 10398 121362 11576 8632 6614 66724 906 16512 0.718002 0 . 0 . 54 17,11,14,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G397S|453|PRUNE|protein_coding|CODING|NM_021222.2|8|A),UPSTREAM(MODIFIER||2492||357|BNIPL|protein_coding|CODING|NM_138278.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.723523 rs3738477 -0.692717 0.0170163 54 G397 453 ggC/ggA LOW 8 SILENT CODING PRUNE A protein_coding NM_021222.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151006539 C A 0 228 0 0.4387 0.5094 0.5187 0.5952 0.503 0.5164 0.824784 0.854529 0.869767 2 8526 102659 10075 7523 5467 57119 757 13192 2 10404 121388 11576 8644 6614 66730 908 16512 0 . 0 . 0 53 0,0,30,21 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G397|453|PRUNE|protein_coding|CODING|NM_021222.2|8|A),UPSTREAM(MODIFIER||2490||357|BNIPL|protein_coding|CODING|NM_138278.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3738476 -0.693147 0.00146893 53 357 17 MODIFIER 10 CODING BNIPL G protein_coding NM_138278.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151019180 A G 0 228 0 0.7118 0.8115 0.8228 0.9077 0.8111 0.8395 0.718112 0.777872 0.808488 2 7542 98673 9782 7994 5123 53809 745 13678 2 10404 121366 11574 8648 6610 66712 908 16510 0 . 0 . 0 207 0,0,86,91 UTR_3_PRIME(MODIFIER||17||357|BNIPL|protein_coding|CODING|NM_138278.3|10|G),UPSTREAM(MODIFIER||1079||341|C1orf56|protein_coding|CODING|NM_017860.3||G),DOWNSTREAM(MODIFIER||4267||79|CDC42SE1|protein_coding|CODING|NM_001038707.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587553 -0.693147 0.00118674 207 79 2035 MODIFIER 6 CODING CDC42SE1 G protein_coding NM_001038707.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151024688 T G 0 128 0 0.9297 0.9808 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,1 UTR_3_PRIME(MODIFIER||2035||79|CDC42SE1|protein_coding|CODING|NM_001038707.1|6|G),DOWNSTREAM(MODIFIER||4612||357|BNIPL|protein_coding|CODING|NM_138278.3||G),DOWNSTREAM(MODIFIER||817||341|C1orf56|protein_coding|CODING|NM_017860.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10888402 -0.590765 0.096133 6 79 28 MODIFIER 3 CODING CDC42SE1 T protein_coding NM_001038707.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151028234 G T 0 228 0 1 1 1 1 1 1 0 . 0 2 9796 114314 11104 8402 5544 62996 840 15632 2 9796 114314 11104 8402 5544 62996 840 15632 0 . 0 . 0 47 0,0,11,33 UTR_5_PRIME(MODIFIER||28||79|CDC42SE1|protein_coding|CODING|NM_001038707.1|3|T),UPSTREAM(MODIFIER||3917||90|MLLT11|protein_coding|CODING|NM_006818.3||T),DOWNSTREAM(MODIFIER||4363||341|C1orf56|protein_coding|CODING|NM_017860.3||T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs11204767 -0.693146 0.427186 47 90 462 MODIFIER 2 CODING MLLT11 A protein_coding NM_006818.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151040435 G A 0 222 0 0.4478 0.7043 0.7853 0.8631 0.7883 0.7434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999065 0 . 0 . 60 15,12,11,16 UTR_3_PRIME(MODIFIER||462||90|MLLT11|protein_coding|CODING|NM_006818.3|2|A),UPSTREAM(MODIFIER||2645||448|GABPB2|protein_coding|CODING|NM_144618.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.41179 rs15740 -0.693021 0.0433369 60 962 362 MODIFIER 20 CODING SEMA6C G protein_coding NM_001178061.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151104598 A G 0 170 0 0.6316 0.7881 0.804 0.9048 0.8201 0.8354 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,10,0 UTR_3_PRIME(MODIFIER||362||962|SEMA6C|protein_coding|CODING|NM_001178061.1|20|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4971005 -0.670168 0.218005 11 962 10 MODIFIER 20 CODING SEMA6C A protein_coding NM_001178061.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151104950 G A 0 228 0 0.2103 0.622 0.7334 0.877 0.7237 0.7321 0.410937 0.633506 0.744099 2 273 10053 212 376 96 3659 105 5332 2 858 14034 278 424 144 4972 148 7210 0 . 0 . 0 89 0,0,77,10 UTR_3_PRIME(MODIFIER||10||962|SEMA6C|protein_coding|CODING|NM_001178061.1|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10788800 -0.693147 0.502468 89 P675 962 ccG/ccC LOW 20 SILENT CODING SEMA6C G protein_coding NM_001178061.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151105824 C G 0 152 0 0.5371 0.7582 0.7939 0.9028 0.8121 0.8272 0.592779 0.734307 0.806659 2 4116 77038 8347 6871 3041 42002 548 12113 2 6426 93730 9786 7446 3786 51040 662 14584 0 . 0 . 0 11 0,0,0,11 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P675|962|SEMA6C|protein_coding|CODING|NM_001178061.1|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs4971006 -0.676189 0.0120951 11 T455P 962 Acc/Ccc MODERATE 14 MISSENSE CODING SEMA6C G protein_coding NM_001178061.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151108137 T G 0 228 0 0.7632 0.8235 0.8084 0.9048 0.8201 0.8354 0.778484 0.798862 0.809302 2 8029 99378 9756 7951 5127 54022 744 13749 2 10400 121362 11576 8646 6608 66712 908 16512 0 . 0 . 0 70 0,0,28,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T455P|962|SEMA6C|protein_coding|CODING|NM_001178061.1|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4971007 -0.693147 0.226024 70 562 255 MODIFIER 16 CODING PIP5K1A C protein_coding NM_001135638.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151220596 T C 0 228 0 0.9191 0.978 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 43 0,0,32,9 UTR_3_PRIME(MODIFIER||255||562|PIP5K1A|protein_coding|CODING|NM_001135638.1|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6661347 -0.693145 0.400154 43 828 815 MODIFIER 13 CODING PI4KB G protein_coding NM_002651.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151264513 A G 0 224 0 0.9085 0.9752 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,2,9 UTR_3_PRIME(MODIFIER||815||828|PI4KB|protein_coding|CODING|NM_002651.2|13|G),DOWNSTREAM(MODIFIER||132||1237|ZNF687|protein_coding|CODING|NM_001304763.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2864115 -0.676189 0.486768 12 D201 828 gaT/gaC LOW 3 SILENT CODING PI4KB G protein_coding NM_002651.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151288391 A G 0 228 0 0.9198 0.9782 0.9957 1 1 1 0.928053 0.975473 0.999767 2 9649 120512 11543 8654 6614 66702 905 16445 2 10406 121316 11578 8654 6614 66708 908 16448 0 . 0 . 0 101 0,0,40,46 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D201|828|PI4KB|protein_coding|CODING|NM_002651.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1752379 -0.693147 0.399036 101 616 283 MODIFIER 11 CODING RFX5 C protein_coding NM_000449.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151314379 T C 0 185 0 0.848 0.7644 0.7536 0.7014 0.7684 0.7198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.860923 0 . 0 . 55 23,4,24,0 UTR_3_PRIME(MODIFIER||283||616|RFX5|protein_coding|CODING|NM_000449.3|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.509932 rs1752387,rs386543871 -0.692831 0.555114 55 L251 616 ctC/ctT LOW 9 SILENT CODING RFX5 A protein_coding NM_000449.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151316161 G A 0 228 0 0.9191 0.978 0.9957 1 1 1 0.927372 0.975242 0.999767 2 9571 120176 11507 8638 6604 66492 899 16465 2 10328 120980 11542 8638 6604 66498 902 16468 0 . 0 . 0 59 0,0,29,23 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L251|616|RFX5|protein_coding|CODING|NM_000449.3|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1752386 -0.693147 0.212235 59 264 17 MODIFIER 1 CODING PSMB4 T protein_coding NM_002796.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151372047 C T 0 222 0 0.1278 0.1841 0.2133 0.4544 0.0189 0.1309 0.104498 0.0379406 0.00384078 1 1170 11124 3968 3449 482 463 63 1529 2 9364 117994 11554 8632 6614 64526 894 16410 0.878264 0 . 0 . 52 13,11,10,17 START_GAINED(LOW||||264|PSMB4|protein_coding|CODING|NM_002796.2|1|T),UTR_5_PRIME(MODIFIER||17||264|PSMB4|protein_coding|CODING|NM_002796.2|1|T),DOWNSTREAM(MODIFIER||3153||1410|POGZ|protein_coding|CODING|NM_015100.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.583542 rs111189169,rs2296840 -0.693021 0.53678 52 P25 264 ccG/ccA LOW 1 SILENT CODING PSMB4 A protein_coding NM_002796.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151372138 G A 0 222 0 0.3321 0.493 0.4669 0.2123 0.835 0.6667 0.38788 0.674074 0.820698 1 3789 81723 4280 1946 5112 54554 650 11392 2 10298 121142 11572 8636 6614 66604 908 16510 0.806403 0 . 0 . 45 11,10,8,14 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P25|264|PSMB4|protein_coding|CODING|NM_002796.2|1|A),DOWNSTREAM(MODIFIER||3062||1410|POGZ|protein_coding|CODING|NM_015100.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.861203 rs7172 -0.692562 0.124308 45 1410 1211 MODIFIER 19 CODING POGZ G protein_coding NM_015100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151376067 A G 0 222 0 0.1089 0.1801 0.2133 0.4593 0.0169 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 64 14,13,14,15 UTR_3_PRIME(MODIFIER||1211||1410|POGZ|protein_coding|CODING|NM_015100.3|19|G),DOWNSTREAM(MODIFIER||1655||264|PSMB4|protein_coding|CODING|NM_002796.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.271355 rs12566457 -0.693079 0.191974 64 1410 1203 MODIFIER 19 CODING POGZ C protein_coding NM_015100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151376075 T C 0 222 0 0.084 0.1729 0.2118 0.4593 0.0169 0.1309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.961955 0 . 0 . 60 12,12,13,17 UTR_3_PRIME(MODIFIER||1203||1410|POGZ|protein_coding|CODING|NM_015100.3|19|C),DOWNSTREAM(MODIFIER||1663||264|PSMB4|protein_coding|CODING|NM_002796.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.182241 rs12566673 -0.693097 0.0830284 60 1410 30 MODIFIER 19 CODING POGZ C protein_coding NM_015100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151377248 T C 0 228 0 0.91 0.9758 0.9971 1 1 1 0.913221 0.970385 0.999651 2 8970 111130 11407 8552 6604 64218 802 10577 2 9802 112012 11446 8552 6604 64224 806 10578 0 . 0 . 0 19 0,0,4,15 UTR_3_PRIME(MODIFIER||30||1410|POGZ|protein_coding|CODING|NM_015100.3|19|C),DOWNSTREAM(MODIFIER||2836||264|PSMB4|protein_coding|CODING|NM_002796.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6667714 -0.69168 0.669191 19 T1368 1410 acT/acG LOW 19 SILENT CODING POGZ C protein_coding NM_015100.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151377407 A C 0 221 0 0.2716 0.2242 0.219 0.4593 0.0189 0.1329 0.23695 0.0836537 0.00511628 1 2670 12755 4004 3492 482 487 75 1545 2 10406 121378 11574 8632 6614 66734 908 16510 0.541982 0 . 0 . 62 24,5,25,2 SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T1368|1410|POGZ|protein_coding|CODING|NM_015100.3|19|C),DOWNSTREAM(MODIFIER||2995||264|PSMB4|protein_coding|CODING|NM_002796.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947646 rs1571294 -0.693021 0.166221 62 1203 204 MODIFIER 21 CODING CGN G protein_coding NM_020770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151510026 A G 0 228 0 0.6301 0.7931 0.8833 0.7688 0.9742 0.7883 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 48 0,0,44,3 UTR_3_PRIME(MODIFIER||204||1203|CGN|protein_coding|CODING|NM_020770.2|21|G),UPSTREAM(MODIFIER||2759||409|TUFT1|protein_coding|CODING|NM_001301317.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1418823,rs386531193 -0.693147 0.000217582 48 528 1641 MODIFIER 12 CODING SNX27 G protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151667718 A G 0 153 0 0.2413 0.2039 0.121 0.3185 0.004 0.2996 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||1641||528|SNX27|protein_coding|CODING|NM_030918.5|12|G),DOWNSTREAM(MODIFIER||4816||465|CELF3|protein_coding|CODING|NM_007185.6||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1308135 -0.676189 0.0583733 11 528 2004 MODIFIER 12 CODING SNX27 G protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151668081 T G 0 9.7 0 0.0635 0.1538 0.1052 0.3175 0.003 0.2965 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2004||528|SNX27|protein_coding|CODING|NM_030918.5|12|G),DOWNSTREAM(MODIFIER||4453||465|CELF3|protein_coding|CODING|NM_007185.6||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1308136 -0.379885 0 1 528 3365 MODIFIER 12 CODING SNX27 T protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151669442 C T 0 32.6 0 0.5946 0.524 0.5115 0.6062 0.335 0.547 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3365||528|SNX27|protein_coding|CODING|NM_030918.5|12|T),DOWNSTREAM(MODIFIER||3092||465|CELF3|protein_coding|CODING|NM_007185.6||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1308139 -0.379885 0 2 528 3920 MODIFIER 12 CODING SNX27 A protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151669997 C A 0 228 0 0.6793 0.5521 0.513 0.6319 0.335 0.5491 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,30,4 UTR_3_PRIME(MODIFIER||3920||528|SNX27|protein_coding|CODING|NM_030918.5|12|A),DOWNSTREAM(MODIFIER||2537||465|CELF3|protein_coding|CODING|NM_007185.6||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1048694 -0.693132 0.0370644 36 528 4514 MODIFIER 12 CODING SNX27 C protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151670590 CAG C 0 228 0 0.2398 0.2025 0.121 0.3175 0.004 0.2955 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,13,0 UTR_3_PRIME(MODIFIER||4514||528|SNX27|protein_coding|CODING|NM_030918.5|12|C),DOWNSTREAM(MODIFIER||1943||465|CELF3|protein_coding|CODING|NM_007185.6||C) 0 . 0 13 0.866667 1 1 0 . 0 60 0 0 . 0 . rs145768222 -0.683931 0.846922 15 528 5150 MODIFIER 12 CODING SNX27 A protein_coding NM_030918.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151671227 G A 0 228 0 0.1248 0.1705 0.1095 0.3175 0.003 0.2965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 50 0,0,39,4 UTR_3_PRIME(MODIFIER||5150||528|SNX27|protein_coding|CODING|NM_030918.5|12|A),DOWNSTREAM(MODIFIER||1307||465|CELF3|protein_coding|CODING|NM_007185.6||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1308142 -0.693146 0.161728 50 465 3284 MODIFIER 13 CODING CELF3 C protein_coding NM_007185.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151674233 A C 0 6.3 0 0.593 0.5224 0.5101 0.6062 0.33 0.547 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3284||465|CELF3|protein_coding|CODING|NM_007185.6|13|C),DOWNSTREAM(MODIFIER||2674||528|SNX27|protein_coding|CODING|NM_030918.5||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1308147 -0.379885 0 1 465 2594 MODIFIER 13 CODING CELF3 G protein_coding NM_007185.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151674923 C G 0 9.7 0 0.0635 0.154 0.1052 0.3175 0.003 0.2975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2594||465|CELF3|protein_coding|CODING|NM_007185.6|13|G),DOWNSTREAM(MODIFIER||3364||528|SNX27|protein_coding|CODING|NM_030918.5||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1308149,rs386439442 -0.379885 0 1 465 2103 MODIFIER 13 CODING CELF3 G protein_coding NM_007185.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151675414 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,25,34 UTR_3_PRIME(MODIFIER||2103||465|CELF3|protein_coding|CODING|NM_007185.6|13|G),DOWNSTREAM(MODIFIER||3855||528|SNX27|protein_coding|CODING|NM_030918.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4845326 -0.693147 0.624078 62 465 1899 MODIFIER 13 CODING CELF3 C protein_coding NM_007185.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151675618 T C 0 228 0 0.8941 0.9716 0.9971 1 1 1 0.917544 0.974561 0.999742 2 981 20338 758 630 1246 8646 220 7857 2 1090 20456 760 630 1246 8652 220 7858 0 . 0 . 0 210 0,0,116,75 UTR_3_PRIME(MODIFIER||1899||465|CELF3|protein_coding|CODING|NM_007185.6|13|C),DOWNSTREAM(MODIFIER||4059||528|SNX27|protein_coding|CODING|NM_030918.5||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1308150 -0.693147 0.000495002 210 H77 267 caT/caC LOW 2 SILENT CODING MRPL9 G protein_coding NM_031420.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151735545 A G 0 228 0 0.1422 0.1743 0.1037 0.3611 0.003 0.2515 0.127099 0.0455175 0.00372093 2 1396 10356 1755 3415 2 285 35 3468 2 10368 120980 11566 8620 6612 66418 906 16490 0 . 0 . 0 115 0,0,23,78 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H77|267|MRPL9|protein_coding|CODING|NM_031420.3|2|G),UPSTREAM(MODIFIER||3586||234|OAZ3|protein_coding|CODING|NM_016178.2||G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),INTRAGENIC(MODIFIER|||||OAZ3||CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1196455 -0.693147 0.000362282 115 W146R 234 Tgg/Cgg MODERATE 3 MISSENSE CODING OAZ3 C protein_coding NM_016178.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151740666 T C 0 228 0 0.9985 0.9996 1 1 1 1 0.998203 0.999424 1 2 9741 120411 11522 8612 6606 66562 896 16472 2 9764 120436 11524 8612 6606 66562 896 16472 0 . 0 . 0 78 0,0,24,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W146R|234|OAZ3|protein_coding|CODING|NM_016178.2|3|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),UPSTREAM(MODIFIER||4274||267|MRPL9|protein_coding|CODING|NM_031420.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2495397 -0.693147 0.152096 78 593 247 MODIFIER 2 CODING LINGO4 G protein_coding NM_001004432.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151773152 A G 0 100 0 0.9569 0.9882 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,5,0 UTR_3_PRIME(MODIFIER||247||593|LINGO4|protein_coding|CODING|NM_001004432.3|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1521180 -0.590765 0.121375 5 593 12 MODIFIER 2 CODING LINGO4 A protein_coding NM_001004432.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151773387 G A 0 228 0 0.0976 0.1801 0.2147 0.3462 0.002 0.2791 0.0819709 0.0294615 0.00255933 2 862 10752 3139 3328 3 184 28 3208 2 9072 110262 11456 8546 6614 62270 802 11502 1 0 . 0 COSN163240 77 1,0,36,31 UTR_3_PRIME(MODIFIER||12||593|LINGO4|protein_coding|CODING|NM_001004432.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1521179 -0.693147 6.60551e-05 77 T444S 593 Act/Tct MODERATE 2 MISSENSE CODING LINGO4 A protein_coding NM_001004432.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151773851 T A 0 228 0 0.0968 0.1801 0.2147 0.3462 0.002 0.2802 0.0848842 0.0304475 0.00255814 2 918 11492 3148 3349 3 191 34 3849 2 10404 121334 11578 8646 6614 66676 908 16508 1 0 . 0 COSM146605 36 0,1,20,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Tct|T444S|593|LINGO4|protein_coding|CODING|NM_001004432.3|2|A),DOWNSTREAM(MODIFIER||4696||518|RORC|protein_coding|CODING|NM_005060.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs61746299 -0.693097 0.401914 36 C80 353 tgC/tgT LOW 2 SILENT CODING C2CD4D A protein_coding NM_001136003.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151811226 G A 0 46.3 0 0.7496 0.9317 0.9841 1 1 1 0 . 0 2 20 335 8 8 0 78 2 219 2 24 340 8 8 0 78 2 220 0 . 0 . 0 2 0,0,1,1 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C80|353|C2CD4D|protein_coding|CODING|NM_001136003.1|2|A),INTRAGENIC(MODIFIER|||||LOC100132111||NON_CODING|||A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6673556 -0.453602 0.76 2 L206V 247 Ctg/Gtg MODERATE 5 MISSENSE CODING THEM5 C protein_coding NM_182578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151820298 G C 0 228 0 0.9879 0.9966 0.9986 1 1 1 0.986155 0.99531 1 2 10259 121259 11574 8654 6614 66738 908 16512 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 79 0,0,52,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L206V|247|THEM5|protein_coding|CODING|NM_182578.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587624 -0.693147 0.00240806 79 D197G 247 gAc/gGc MODERATE 5 MISSENSE CODING THEM5 C protein_coding NM_182578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151820324 T C 0 228 0 0.8752 0.778 0.8674 0.6815 0.833 0.6258 0.858375 0.825465 0.808605 2 9102 95410 10213 5627 5974 53503 712 10279 2 10404 121372 11578 8640 6614 66716 908 16512 0 . 0 . 0 71 0,0,36,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D197G|247|THEM5|protein_coding|CODING|NM_182578.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587625 -0.693147 0.384592 71 G17 247 ggC/ggA LOW 1 SILENT CODING THEM5 T protein_coding NM_182578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151825991 G T 0 228 0 0.7421 0.6266 0.562 0.6567 0.6859 0.4243 0.721289 0.691988 0.676977 2 7701 78150 6754 5401 5466 44926 597 7305 2 10400 121286 11576 8638 6614 66696 908 16454 1 0 . 0 . 87 0,1,41,37 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G17|247|THEM5|protein_coding|CODING|NM_182578.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7556386 -0.693147 0.798616 87 240 1795 MODIFIER 6 CODING THEM4 G protein_coding NM_053055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151845569 A G 0 118 0 0.9002 0.9197 0.9078 0.9405 0.9175 0.9356 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,3 UTR_3_PRIME(MODIFIER||1795||240|THEM4|protein_coding|CODING|NM_053055.4|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2338200 -0.590765 0.561811 5 240 1714 MODIFIER 6 CODING THEM4 C protein_coding NM_053055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151845650 G C 0 73 0 0.5492 0.5569 0.6988 0.5972 0.6054 0.3753 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||1714||240|THEM4|protein_coding|CODING|NM_053055.4|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2338201 -0.511536 0.607612 3 240 1651 MODIFIER 6 CODING THEM4 T protein_coding NM_053055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151845713 G T 0 145 0 0.7814 0.8806 0.9078 0.9048 0.9165 0.9335 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,1 UTR_3_PRIME(MODIFIER||1651||240|THEM4|protein_coding|CODING|NM_053055.4|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2171917 -0.590765 0.665344 6 240 645 MODIFIER 6 CODING THEM4 G protein_coding NM_053055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151846719 A G 0 9.7 0 0.9062 0.9213 0.9078 0.9405 0.9175 0.9356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||645||240|THEM4|protein_coding|CODING|NM_053055.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4845385 -0.379885 0 1 240 184 MODIFIER 6 CODING THEM4 G protein_coding NM_053055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151847180 A G 0 199 0 0.9062 0.9213 0.9078 0.9405 0.9175 0.9356 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,18,1 UTR_3_PRIME(MODIFIER||184||240|THEM4|protein_coding|CODING|NM_053055.4|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10749666 -0.69168 0.144739 19 D70 240 gaC/gaT LOW 2 SILENT CODING THEM4 A protein_coding NM_053055.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151867560 G A 0 228 0 0.9047 0.9231 0.9092 0.9504 0.9175 0.9356 0.909215 0.911475 0.912634 2 9494 111063 10558 8179 6044 60839 806 15143 2 10404 121402 11576 8652 6614 66736 908 16512 0 . 0 . 0 156 0,0,90,44 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|240|THEM4|protein_coding|CODING|NM_053055.4|2|A) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.873015 0 . rs3762427 -0.693147 0.0342227 156 L17R 240 cTg/cGg MODERATE 1 MISSENSE CODING THEM4 C protein_coding NM_053055.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151881885 A C 0 228 0 0.8986 0.9229 0.9092 0.9494 0.9155 0.9458 0 . 0 2 506 10216 158 199 4 3044 112 6193 2 554 11182 180 206 4 3396 120 6722 0 . 0 . 0 88 0,0,8,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L17R|240|THEM4|protein_coding|CODING|NM_053055.4|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs3748805 -0.693147 0.235862 88 97 7642 MODIFIER 1 CODING S100A10 T protein_coding NM_002966.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 151966348 C T 0 6.3 0 0.3676 0.514 0.6844 0.6448 0.5994 0.3681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||7642||97|S100A10|protein_coding|CODING|NM_002966.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11542015 -0.379885 0 1 1943 38 MODIFIER 3 CODING TCHH G protein_coding NM_007113.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152079823 C G 0 222 0 0.2806 0.4702 0.585 0.496 0.3688 0.7229 0.274728 0.357838 0.396706 1 2748 48077 6703 4353 2307 25360 331 6275 2 9584 110152 11484 8500 6610 64034 780 9160 0.485595 0 . 0 . 90 30,11,27,11 UTR_3_PRIME(MODIFIER||38||1943|TCHH|protein_coding|CODING|NM_007113.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.333668 rs1131473 -0.693143 0.624091 90 K1902Q 1943 Aaa/Caa MODERATE 3 MISSENSE CODING TCHH G protein_coding NM_007113.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152079989 T G 0 222 0 0.5136 0.5781 0.6484 0.5992 0.4016 0.7751 0.463868 0.447429 0.439628 1 4713 61472 7507 4984 2540 29228 458 12042 2 9794 120692 11570 8606 6610 66708 898 16506 0.550698 0 . 0 . 123 40,22,29,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K1902Q|1943|TCHH|protein_coding|CODING|NM_007113.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.468353 rs1131471 -0.693147 0.95482 123 L1258V 1943 Ctg/Gtg MODERATE 3 MISSENSE CODING TCHH C protein_coding NM_007113.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152081921 G C 0 146 0 0.4781 0.5685 0.647 0.5992 0.4016 0.7751 0.440394 0.439958 0.439746 1 4433 61158 7496 4985 2541 29204 457 12042 2 9768 120610 11556 8600 6612 66666 900 16508 0.894801 0 . 0 . 25 8,7,5,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L1258V|1943|TCHH|protein_coding|CODING|NM_007113.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.9171 rs2496253 -0.670168 0.860346 25 L63R 1943 cTt/cGt MODERATE 3 MISSENSE CODING TCHH C protein_coding NM_007113.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152085505 A C 0 228 0 0.9614 0.9892 0.9957 1 1 1 0.969067 0.990155 0.999757 2 9454 120272 11550 8622 6614 66658 899 16475 2 9788 120632 11568 8622 6614 66662 900 16478 0 . 0 . 0 90 0,0,25,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cGt|L63R|1943|TCHH|protein_coding|CODING|NM_007113.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2515663 -0.693147 0.0281758 90 G410D 784 gGc/gAc MODERATE 3 MISSENSE CODING RPTN T protein_coding NM_001122965.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152128346 C T 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 23 3 19 0 0 1 0 2 9746 120292 11572 8626 6614 66322 900 16512 0.712763 0 . 0 . 332 99,69,65,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G410D|784|RPTN|protein_coding|CODING|NM_001122965.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.987188 rs199724746 -0.693147 9.91408e-05 332 K163R 784 aAa/aGa MODERATE 3 MISSENSE CODING RPTN C protein_coding NM_001122965.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152129087 T C 0 222 0 0.2216 0.2748 0.4741 0.2996 0.1779 0.2791 0.0705619 0.060724 0.056411 1 8 21 5 0 0 6 0 2 2 7420 88432 5690 5932 5494 51574 674 11648 0.7686 0 . 0 . 140 61,29,27,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K163R|784|RPTN|protein_coding|CODING|NM_001122965.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.305988 0.908026 0 0.89066 rs78544048 -0.693146 0.411262 140 S161P 784 Tct/Cct MODERATE 3 MISSENSE CODING RPTN G protein_coding NM_001122965.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152129094 A G 0 219 0 0.2216 0.2748 0.4741 0.2996 0.1779 0.2791 0.0569418 0.0483337 0.0445628 1 8 21 5 0 0 6 0 2 2 7306 86542 5400 5740 5422 50636 652 11386 0.99798 0 . 0 . 146 63,31,28,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S161P|784|RPTN|protein_coding|CODING|NM_001122965.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.300974 0.912554 0 0.608828 rs76015112 -0.693146 0.847459 146 2850 52 MODIFIER 3 CODING HRNR G protein_coding NM_001009931.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152185500 C G 0 228 0 0.2428 0.3774 0.4265 0.619 0.17 0.4888 0.248284 0.192455 0.167924 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 55 0,0,38,12 UTR_3_PRIME(MODIFIER||52||2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs12726613 -0.693147 0.00397186 55 Y2785 2850 taC/taT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152185750 G A 0 228 0 0.1172 0.3427 0.415 0.6181 0.17 0.4898 0 . 0 2 1297 31920 5469 5172 1176 11629 232 6945 2 10378 120388 11406 8548 6568 66174 896 16418 0 . 0 . COSM1334092 295 0,0,170,102 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y2785|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.996709 0 . rs12729662 -0.693147 0.0024681 295 L2688S 2850 tTg/tCg MODERATE 3 MISSENSE CODING HRNR G protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152186042 A G 0 213 0 0.3336 0.4551 0.5908 0.6181 0.3718 0.4407 0 . 0 2 1908 24285 2727 3309 1016 9827 178 5320 2 4254 51760 4316 5686 2414 25336 378 9376 0 . 0 . COSM1127393 34 0,0,2,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L2688S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 0 . 0 . 0 1 0 . 1 0 55 0 0 0 0 . rs12751022 -0.693132 0.336287 34 L2662S 2850 tTg/tCg MODERATE 3 MISSENSE CODING HRNR G protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152186120 A G 0 33.5 0 . 0 . 0 . 0 . 0 . 1 68 491 31 17 6 265 6 98 2 612 3438 216 250 42 1708 36 574 0.68039 0 . 0 . 114 64,12,38,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L2662S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 0 0.5 1 0 . 0 . 0 1 0 32 0 3.95153e-11 3.59119e-05 0 0.885614 rs79071169 -0.693143 0.00905008 114 S2561 2850 tcT/tcC LOW 3 SILENT CODING HRNR G protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152186422 A G 0 17.2 0 . 0 . 0 . 0 . 0 . 1 0 5 1 3 0 1 0 0 2 0 16 2 6 0 6 0 2 0.249352 0 . 0 . 26 6,12,6,2 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2561|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 0 0.5 1 0 . 0 . 0 1 0 24 0 0.381171 0.466776 0 0.916855 rs202168784 -0.651104 0.674881 26 G2539S 2850 Ggc/Agc MODERATE 3 MISSENSE CODING HRNR T protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152186490 C T 0 94 0 0.1203 0.1773 0.2147 0.2679 0.0934 0.2209 0 . 0 1 0 1 0 0 0 0 0 1 2 0 2 0 0 0 0 0 2 0.904666 0 . 0 COSM1472626 32 16,4,9,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G2539S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|T) 0 0.5 1 0 . 1 0 . 1 0 24 0 0.738577 0.322572 0 0.888366 rs201463788 -0.680642 0.137841 32 G2277S 2850 Ggt/Agt MODERATE 3 MISSENSE CODING HRNR T protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152187276 C T 0 200 0 . 0 . 0 . 0 . 0 . 1 77 3860 437 509 164 1589 29 1055 2 2604 48892 2472 2428 3668 30448 390 6882 0.861691 0 . 0 COSM1319985 131 29,47,14,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G2277S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|T) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.92444 0.760414 0 0.958412 rs199952550 -0.693147 0.677809 131 H2181Q 2850 caT/caG MODERATE 3 MISSENSE CODING HRNR C protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152187562 A C 0 228 0 0.857 0.9607 0.9885 1 1 1 0 . 0 2 109 859 35 138 78 450 6 43 2 1748 2768 102 168 92 582 10 66 0 . 0 . 0 276 0,0,205,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H2181Q|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|C) 0 . 0 . 0 1 0 . 1 0 24 0 0 5.79952e-05 0 . rs61814936 -0.693147 0.323475 276 H2172 2850 caC/caT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152187589 G A 0 222 0 . 0 . 0 . 0 0.0330159 0.0598388 0.0727858 1 229 12087 2284 1773 549 4533 90 2629 2 8910 100882 8840 6294 5814 57582 726 12716 0.452665 0 . 0 . 500 168,68,147,71 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H2172|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 1 0.5 1 0 . 0 . 1 1 0 28 0 0.781598 5.58045e-06 0 0.72858 rs143684430 -0.693147 0.300372 500 Y2159 2850 taT/taC LOW 3 SILENT CODING HRNR G protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152187628 A G 0 222 0 . 0 . 0 . 0 0.133758 0.0869095 0.0628505 1 1560 20261 3331 2512 872 7450 158 4378 2 9536 117176 11162 8296 6530 64552 876 16224 0.973898 0 . 0 . 856 251,129,224,148 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y2159|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 1 0.5 1 0 . 0 . 1 1 0 29 0 0.973822 9.78547e-21 0 0.435537 rs75639578 -0.693147 1.07648e-09 856 P2099S 2850 Cct/Tct MODERATE 3 MISSENSE CODING HRNR A protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152187810 G A 0 203 0 . 0 . 0 . 0 . 0 . 2 33 327 8 62 31 161 4 28 2 1724 2136 66 72 34 194 10 36 0 . 0 . 0 101 0,0,53,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P2099S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 0 . 0 . 0 . 0 . 1 0 21 0 0 0.0122091 0 . rs145371085 -0.693147 1.58621e-12 101 G2030 2850 ggC/ggT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152188015 G A 0 52 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89167 0 . 0 . 57 11,17,0,29 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G2030|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 0 0.5 1 0 . 0 . 0 . 0 24 0 0.232563 0.00357554 0 0.950317 rs202175827 -0.693079 7.69304e-08 57 A2022T 2850 Gca/Aca MODERATE 3 MISSENSE CODING HRNR T protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152188041 C T 0 5.2 0 . 0 . 0 . 0 . 0 . 2 0 21 1 4 4 8 0 4 2 9970 107482 9094 6050 6166 62276 816 13110 0 . 0 . 0 4 0,0,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2022T|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|T) 0 . 0 . 0 . 0 . 1 0 9 0 0 1 0 . rs200444708 -0.556411 0.658104 4 E1898K 2850 Gaa/Aaa MODERATE 3 MISSENSE CODING HRNR T protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152188413 C T 0 222 0 . 0 . 0 . 0 0.0248619 0.03641 0.0422486 1 315 14798 2503 1632 676 6017 130 3525 2 9564 116744 11158 8242 6392 64718 870 15800 0.586379 0 . 0 . 822 221,146,192,172 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E1898K|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|T) 1 0.5 1 0 . 0 . 1 1 0 42 0 0.728019 2.54643e-14 0 0.82116 rs200760332 -0.693147 0.166319 822 L1722S 2850 tTg/tCg MODERATE 3 MISSENSE CODING HRNR G protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152188940 A G 0 49.4 0 . 0 . 0 . 0 . 0 . 1 5 13 2 0 0 5 0 1 2 1356 8450 226 224 268 4668 76 1632 0.34744 0 . 0 . 77 8,40,13,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L1722S|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 0 0.5 1 0 . 0 . 0 1 0 23 0 0.19802 0.533172 0 0.611918 rs34655925 -0.692352 0.000115272 77 H1702 2850 caC/caT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152188999 G A 0 196 0 . 0 . 0 . 0 0.0273241 0.0464113 0.0560304 1 267 13984 2677 2100 580 5199 118 3043 2 9078 112302 10620 7856 6280 62098 838 15532 0.917954 0 . 0 COSM128194 162 31,54,37,30 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H1702|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 1 0.5 1 0 . 0 . 1 1 0 23 0 0.413733 0.0104596 0 0.22779 rs149648668 -0.693147 5.25355e-21 162 Y1689 2850 taT/taC LOW 3 SILENT CODING HRNR G protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152189038 A G 0 205 0 . 0 . 0 . 0 0.0972727 0.070327 0.0564893 1 1345 15624 2747 2097 587 5515 126 3207 2 5204 45026 6734 5212 1622 17730 346 8178 0.849166 0 . 0 COSM1472634 125 32,25,40,22 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1689|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 1 0.5 1 0 . 0 . 1 1 0 22 0 0.832043 0.00012473 0 0.950342 rs145118416 -0.693147 7.34507e-10 125 R1684G 2850 Cgt/Ggt MODERATE 3 MISSENSE CODING HRNR C protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152189055 G C 0 55 0 . 0 . 0 . 0 . 0 . 2 0 2 0 0 2 0 0 0 2 1846 1926 58 0 2 14 4 2 0 . 0 . 0 31 0,0,24,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Ggt|R1684G|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|C) 0 . 0 . 0 . 0 . 1 0 10 0 0 0.0489059 0 . rs4845749 -0.69311 0.689043 31 S1621 2850 tcT/tcC LOW 3 SILENT CODING HRNR G protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152189242 A G 0 4.1 0 0.0257 0.1775 0.2507 0.3393 0.0934 0.2505 0 . 0 1 0 2 1 0 0 0 0 1 2 608 662 20 6 0 22 2 4 0.475199 0 . 0 COSM1472635 22 0,12,0,10 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1621|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 0 0.5 1 0 . 1 0 . 1 0 16 0 0.204992 0 . 0.366084 rs201431455 -0.670168 0.525878 22 Y1141 2850 taC/taT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152190682 G A 0 146 0 0.1778 0.3678 0.4222 0.6558 0.17 0.4928 0 . 0 2 77 951 105 78 11 232 7 441 2 252 2192 208 114 44 762 20 792 0 . 0 . 0 72 0,0,72,0 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1141|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 0 . 0 . 0 1 0 . 1 0 27 0 0 . 0 . rs71625163 -0.693147 0.645241 72 G1090 2850 ggC/ggT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152190835 G A 0 228 0 0.0242 0.3003 0.3919 0.6319 0.1412 0.4305 0.0521165 0.113472 0.144835 2 439 27894 5195 5026 1117 9910 214 5993 2 10102 120850 11572 8592 6614 66554 908 16508 0.592988 0 . 0 . 516 2,1,321,125 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1090|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 1 0 . 0 . 1 0 1 1 0 38 0 0.975395 1.21297e-23 0 0.165307 rs144383071 -0.693147 0.00291467 516 E1054K 2850 Gag/Aag MODERATE 3 MISSENSE CODING HRNR T protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152190945 C T 0 228 0 0.0242 0.2961 0.3905 0.619 0.1402 0.4243 0.0474353 0.111385 0.14417 2 409 27728 5177 4914 1113 9913 211 5991 2 10370 121292 11576 8606 6612 66714 908 16506 0.694293 0 . 0 . 408 1,1,164,204 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1054K|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|T) 1 0 . 0 . 1 0 1 1 0 46 0 0.861413 4.56417e-17 0 0.421196 rs77376932 -0.693147 0.170164 408 Y517C 2850 tAt/tGt MODERATE 3 MISSENSE CODING HRNR C protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152192555 T C 0 228 0 0.0242 0.2923 0.3905 0.5962 0.1412 0.4274 0.0467544 0.111256 0.144302 2 412 27737 5181 4913 1113 9906 212 6000 2 10406 121360 11576 8610 6614 66734 908 16512 0 . 0 . 0 446 0,0,274,133 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y517C|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.992455 0 . rs41266134 -0.693147 0.258398 446 E473G 2850 gAg/gGg MODERATE 3 MISSENSE CODING HRNR C protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152192687 T C 0 228 0 0.7905 0.9425 0.9841 1 1 1 0.854063 0.950331 0.999651 2 8776 119678 11517 8651 6614 66713 899 16508 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 561 0,0,249,252 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E473G|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587648 -0.693147 0.0839568 561 Q376R 2850 cAa/cGa MODERATE 3 MISSENSE CODING HRNR C protein_coding NM_001009931.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152192978 T C 0 228 0 0.7905 0.9423 0.9841 0.999 1 1 0.854063 0.950331 0.999651 2 8776 119675 11517 8654 6614 66707 899 16508 2 10406 121404 11578 8654 6614 66732 908 16512 0.226496 0 . 0 . 257 1,1,132,102 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q376R|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6587649 -0.693147 0.00311574 257 H351 2850 caT/caC LOW 3 SILENT CODING HRNR G protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152193052 A G 0 228 0 0.6891 0.9147 0.9784 1 1 0.999 0.756242 0.917038 0.999419 2 7737 118549 11480 8642 6614 66699 894 16483 2 10406 121406 11578 8654 6614 66734 908 16512 0 . 0 . 0 227 0,0,97,118 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H351|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587650 -0.693147 0.00575488 227 S186 2850 tcC/tcT LOW 3 SILENT CODING HRNR A protein_coding NM_001009931.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152193547 G A 0 228 0 0.7905 0.9423 0.9841 1 0.999 1 0.854063 0.950331 0.999651 2 8764 119665 11517 8654 6614 66711 897 16508 2 10394 121394 11578 8654 6614 66736 906 16512 0 . 0 . 0 196 0,0,74,110 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S186|2850|HRNR|protein_coding|CODING|NM_001009931.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587653 -0.693147 0.273877 196 R3738H 4061 cGc/cAc MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276149 C T 0 228 0 0.0113 0.2869 0.3919 0.5804 0.1421 0.4315 0.036995 0.107873 0.144186 2 331 27768 5181 4828 1143 9963 208 6114 2 10406 121370 11572 8626 6614 66732 908 16512 0 . 0 . 0 301 0,0,152,130 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R3738H|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.991912 0 . rs77422831 -0.693147 0.297283 301 S3662T 4061 aGt/aCt MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276377 C G 0 55 0 . 0 . 0 . 0 . 0 . 1 26 4013 924 1085 145 1064 25 744 2 8782 104838 9308 6592 5974 59236 818 14128 0.9446 0 . 0 COSM226460 344 141,79,123,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S3662T|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 0 0.5 1 0 . 0 . 0 1 0 35 0 0.00177538 1.65201e-23 0 0.664296 rs139284720 -0.693147 0.00293047 344 D3635N 4061 Gac/Aac MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276459 C T 0 222 0 . 0 . 0 . 0 0.026806 0.0770952 0.102969 1 297 22883 3938 3444 934 9373 167 4730 2 9496 117498 11504 8576 6520 64538 882 15982 0.624367 0 . 0 . 559 118,155,67,135 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D3635N|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0.5 1 0 . 0 . 1 1 0 36 0 0.444845 0.000647931 0 0.20912 rs75448155 -0.693147 1.12765e-06 559 E3593D 4061 gaG/gaC MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276583 C G 0 187 0 0.4796 0.3614 0.3213 0.4732 0.1233 0.3599 0.379483 0.149669 0.0318753 1 4033 10286 1441 1642 133 1471 60 1506 2 10062 117350 11186 8104 6544 65706 886 14862 0.0964583 0 . 0 . 52 11,19,9,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E3593D|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 32 0 0.793886 0.736934 0 0.102595 rs12083389 -0.692352 0.0595275 52 H3588 4061 caC/caT LOW 3 SILENT CODING FLG A protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276598 G A 0 228 0 0.0227 0.0887 0.0965 0.1984 0.0199 0.1299 0 . 0 2 63 3881 970 1051 108 771 22 896 2 10102 116364 10810 7596 6566 65846 886 14558 0 . 0 . 0 29 0,0,19,10 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H3588|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 0 . 0 . 0 1 0 . 1 0 31 0 0 0.84834 0 . rs12742178 -0.693079 0.891178 29 T3579R 4061 aCg/aGg MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276626 G C 0 228 0 0.6074 0.4778 0.4395 0.6498 0.1561 0.4836 0.25479 0.0976249 0.0173579 2 3647 5813 560 705 52 508 32 309 2 9124 111084 9634 6390 6442 65042 862 13590 0 . 0 . 0 43 0,0,22,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aGg|T3579R|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 34 0 0 0.034072 0 . rs3126075 -0.693146 0.240579 43 Q3568R 4061 cAg/cGg MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276659 T C 0 53 0 0.2133 0.2067 0.1916 0.3403 0.0696 0.2117 0 . 0 1 3027 22350 3217 2952 878 7375 177 4724 2 10106 119258 11086 8368 6544 65888 888 16378 0.870938 0 . 0 . 87 20,41,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q3568R|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.00469191 0.965626 0 0.000916877 rs7532285 -0.692067 1.67101e-08 87 Q3568E 4061 Cag/Gag MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276660 G C 0 53 0 0.2133 0.2067 0.1916 0.3403 0.0696 0.2117 0 . 0 1 2996 22308 3213 2953 875 7370 178 4723 2 10098 119050 11042 8326 6544 65778 890 16372 0.290823 0 . 0 . 90 20,41,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q3568E|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.00469191 0.965626 0 0.000916877 rs7540123 -0.692067 1.67101e-08 90 R3564H 4061 cGt/cAt MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276671 C T 0 106 0 0.2685 0.2564 0.2608 0.38 0.0875 0.2832 0 . 0 1 3062 23079 3383 3042 932 7714 179 4767 2 9992 118348 10944 8128 6546 65516 884 16338 0.345401 0 . 0 . 115 18,45,38,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3564H|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 46 0 0.00110137 0.674023 0 1.54002e-07 rs7518080 -0.693143 2.09556e-06 115 W3555R 4061 Tgg/Cgg MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276699 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 3218 22404 3326 3133 693 7256 175 4603 2 10200 116174 10792 8124 6296 63932 874 15956 0.121633 0 . 0 . 153 84,1,13,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W3555R|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 0 0.5 1 0 . 0 . 0 1 0 51 0 2.6938e-06 0.0034352 0 5.34013e-11 rs12728605 -0.693147 4.98961e-05 153 R3530S 4061 agG/agT MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276772 C A 0 228 0 0.0113 0.2905 0.3919 0.5853 0.1421 0.4448 0.0365411 0.109565 0.146977 2 327 28416 5246 4875 1145 10173 213 6437 2 10406 121260 11570 8630 6606 66708 908 16432 0.5603 0 . 0 . 174 0,4,121,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R3530S|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 59 0 0.00311738 0.0183774 0 0.0117084 rs72697000 -0.693147 0.254575 174 D3497 4061 gaT/gaC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276871 A G 0 228 0 0.5204 0.4471 0.4395 0.6448 0.1471 0.4581 0.463005 0.255077 0.148476 2 4979 33700 5437 5120 1150 10295 236 6483 2 10406 121274 11570 8636 6612 66706 908 16436 0 . 0 . 0 247 0,0,150,74 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D3497|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.996716 0 . rs3126066 -0.693147 0.0139042 247 N3491 4061 aaT/aaC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152276889 A G 0 228 0 0.7912 0.5226 0.4553 0.6498 0.1511 0.4581 0.68906 0.333385 0.151036 2 7426 36470 5585 5140 1151 10427 250 6491 2 10406 121272 11568 8632 6612 66714 908 16432 0 . 0 . 0 276 0,0,169,86 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N3491|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.997023 0 . rs3126067 -0.693147 0.525248 276 G3436A 4061 gGa/gCa MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277055 C G 0 228 0 0.7882 0.5142 0.4481 0.6349 0.1481 0.4427 0.684748 0.331462 0.150465 2 7380 36221 5569 5106 1150 10381 248 6387 2 10402 121250 11564 8608 6612 66722 908 16434 0.887955 0 . 0 . 268 4,2,116,130 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gCa|G3436A|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 57 0 0.00597586 0.052714 0 0.00039839 rs2065955 -0.693147 0.0014701 268 S3398 4061 tcT/tcC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277168 A G 0 228 0 0.5567 0.4736 0.4539 0.6587 0.173 0.4939 0.487744 0.262729 0.147394 2 5366 34437 5473 5162 1159 10474 239 6564 2 10360 118928 11488 8550 6562 65144 898 15926 1 0 . 0 . 273 0,1,143,103 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S3398|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 57 0 1 0.392707 0 1 rs3091276 -0.693147 0.529958 273 Q3339 4061 caG/caA LOW 3 SILENT CODING FLG T protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277345 C T 0 228 0 0.0113 0.2875 0.3905 0.5823 0.1421 0.4335 0.0365411 0.108027 0.144651 2 325 27829 5185 4828 1144 9976 210 6161 2 10406 121356 11574 8622 6612 66728 908 16506 1 0 . 0 . 257 0,1,130,109 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q3339|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.935942 0 1 rs2065956 -0.693147 0.0502103 257 Q3322 4061 caA/caG LOW 3 SILENT CODING FLG C protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277396 T C 0 228 0 0.115 0.3411 0.4193 0.6062 0.171 0.4928 0.132093 0.156005 0.168256 2 1318 31688 5370 5005 1197 11474 228 7096 2 10406 121356 11578 8608 6614 66734 908 16508 0 . 0 . 0 264 0,0,138,107 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q3322|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs6681433 -0.693147 0.0369086 264 V3215 4061 gtG/gtT LOW 3 SILENT CODING FLG A protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277717 C A 0 228 0 0.5212 0.4696 0.4524 0.6835 0.173 0.4969 0.44891 0.251771 0.150583 2 4964 36299 5530 5566 1234 11620 254 7131 2 10368 121324 11578 8642 6614 66710 908 16504 0 . 0 . 0 109 0,0,25,78 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtT|V3215|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 52 0 0 1.48553e-11 0 . rs9436066 -0.693147 0.0259485 109 S3180 4061 tcA/tcG LOW 3 SILENT CODING FLG C protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277822 T C 0 161 0 0.0378 0.2238 0.2709 0.4831 0.0944 0.3078 0 . 0 2 212 10861 1710 2125 290 2606 74 3844 2 10266 118478 11178 8116 6496 65724 886 15812 1 0 . 0 . 24 1,0,0,22 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S3180|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 . 0 . 0 1 0 . 1 0 50 0 1 1 0 1 rs3126069 -0.692562 0.251031 24 V3179G 4061 gTg/gGg MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152277826 A C 0 159 0 0.4894 0.3936 0.3674 0.5883 0.1123 0.3712 0.392808 0.148844 0.0239925 2 4348 15603 1917 2387 290 2691 99 3871 2 10246 117338 10968 7970 6406 65296 878 15574 0 . 0 . 0 23 0,0,0,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V3179G|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 50 0 0 . 0 . rs2065957 -0.692717 0.384017 23 D2936G 4061 gAc/gGc MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152278555 T C 0 139 0 . 0 . 0 . 0 0.0733517 0.0894282 0.0964013 1 727 24679 3977 3455 1050 9948 190 5332 2 6776 114920 11430 8472 6562 64336 890 16454 0.978186 0 . 0 COSM1317676 160 83,0,77,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D2936G|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0.5 1 0 . 0 . 1 1 0 57 0 0.997897 0 . 0.952352 rs80221306 -0.693147 0.371321 160 V2891 4061 gtG/gtT LOW 3 SILENT CODING FLG A protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152278689 C A 0 228 0 0.3147 0.3964 0.4337 0.6101 0.171 0.4918 0.208313 0.180231 0.166938 2 1831 32205 5422 5028 1194 11459 230 7041 2 8760 119638 11570 8616 6612 66666 906 16508 0 . 0 . 0 448 0,0,256,173 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtT|V2891|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 52 0 0 4.92902e-12 0 . rs57672167 -0.693147 0.373578 448 G2850S 4061 Ggc/Agc MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152278814 C T 0 221 0 . 0 . 0 . 0 0.0767616 0.060298 0.052093 1 521 10043 1823 1959 360 2963 74 2343 2 8606 90080 7182 5598 5220 52424 656 10394 0.421732 0 . 0 . 892 365,215,149,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G2850S|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0.5 1 0 . 0 . 1 1 0 51 0 1.34497e-41 0.636482 0 0.177197 rs2184952 -0.693147 8.95179e-08 892 S2836R 4061 Agt/Cgt MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152278856 T G 0 222 0 . 0 . 0 . 0 0.0313798 0.0840811 0.110659 1 334 22820 3925 3435 1023 9120 185 4798 2 9626 120530 11572 8634 6610 66716 906 16466 0.193674 0 . 0 . 791 246,206,128,122 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S2836R|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 0 . 1 1 0 48 0 3.20205e-08 4.70128e-09 0 0.778122 rs11582087 -0.693147 0.0511894 791 D2781 4061 gaC/gaT LOW 3 SILENT CODING FLG A protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152279019 G A 0 222 0 . 0 . 0 . 0 0.0197997 0.0574881 0.0767442 1 287 21990 3836 3328 1002 8576 178 4783 2 10346 120616 11454 8568 6590 66330 900 16428 0.413659 0 . 0 COSM1319976 854 291,252,133,120 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D2781|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0.5 1 0 . 0 . 1 1 0 35 0 0.423076 0.0223759 0 0.621916 rs57670307 -0.693147 0.299709 854 G2545R 4061 Gga/Aga MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152279729 C T 0 228 0 0.5658 0.4748 0.451 0.6548 0.173 0.4939 0.499545 0.281154 0.169419 2 5303 36070 5530 5212 1204 11511 248 7062 2 10326 121294 11566 8634 6614 66734 908 16512 0 . 0 . 0 187 0,0,117,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G2545R|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3126072 -0.693147 0.424547 187 H2507Q 4061 caC/caG MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152279841 G C 0 228 0 0.5189 0.4623 0.451 0.6548 0.172 0.4939 0.465956 0.269799 0.169302 2 4990 35712 5517 5204 1193 11499 247 7062 2 10406 121342 11574 8614 6612 66718 906 16512 0 . 0 . 0 363 0,0,211,115 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H2507Q|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.816679 0 . rs3126074 -0.693147 0.165007 363 L2481S 4061 tTg/tCg MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152279920 A G 0 228 0 0.1203 0.3425 0.4207 0.6071 0.171 0.4908 0.137994 0.15762 0.167674 2 1363 31656 5370 5015 1194 11451 227 7036 2 10404 121366 11576 8614 6614 66740 908 16510 0 . 0 . 0 369 0,0,170,163 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L2481S|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.97887 0 . rs55650366 -0.693147 0.0898635 369 K2444E 4061 Aag/Gag MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280032 T C 0 228 0 0.1218 0.3431 0.4222 0.6071 0.171 0.4908 0.135951 0.15426 0.163643 2 1368 31652 5372 5012 1194 11445 227 7034 2 10404 121374 11578 8618 6614 66740 908 16512 0 . 0 . 0 302 0,0,149,134 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K2444E|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.993082 0 . rs71625200 -0.693147 0.00630027 302 E2398Q 4061 Gag/Cag MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280170 C G 0 228 0 0.1135 0.3305 0.4092 0.5665 0.169 0.4908 0.132607 0.154475 0.165732 2 1298 31251 5332 4821 1191 11382 227 7000 2 10192 120880 11558 8578 6612 66534 908 16498 0.856664 0 . 0 . 158 6,0,24,120 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E2398Q|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 54 0 0.0430721 4.58306e-12 0 0.406002 rs71625201 -0.693147 0.0209858 158 S2366T 4061 aGt/aCt MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280265 C G 0 221 0 . 0 . 0 . 0 0.0347985 0.0997211 0.132935 1 320 24367 4004 3386 1062 9983 194 5418 2 9394 118200 11464 8392 6604 65220 898 16228 0.587442 0 . 0 . 122 29,0,28,65 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S2366T|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 0 . 1 1 0 46 0 0.0321207 0.00112784 0 0.00247674 rs71625202 -0.693147 0.329933 122 D2339N 4061 Gac/Aac MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280347 C T 0 222 0 . 0 . 0 . 0 0.018451 0.0279532 0.032806 1 265 16666 2322 2512 748 6012 140 4667 2 9774 110250 9024 7498 6246 61112 850 15746 0.929497 0 . 0 COSM146618 139 50,1,65,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D2339N|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0.5 1 0 . 0 . 1 1 0 40 0 7.46043e-07 0.00035288 0 0.778325 rs139476473 -0.693147 0.554108 139 H2330 4061 caC/caT LOW 3 SILENT CODING FLG A protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280372 G A 0 228 0 0.4902 0.4535 0.4524 0.6567 0.173 0.4836 0 . 0 2 4093 33358 5220 4874 1204 10710 239 7018 2 9606 119666 11404 8476 6604 66196 902 16478 0.0928571 0 . 0 . 142 1,1,127,13 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H2330|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 0 . 0 . 0 1 0 . 1 0 41 0 0.882143 0.0125285 0 0.635714 rs142776569 -0.693147 0.122274 142 E2297D 4061 gaG/gaC MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280471 C G 0 130 0 . 0 . 0 . 0 0.0914662 0.101799 0.107093 1 1006 25232 4018 3424 1056 10082 198 5448 2 10368 120978 11558 8564 6592 66510 906 16480 0.862471 0 . 0 . 320 108,118,22,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E2297D|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 0 . 1 1 0 51 0 0.00594023 0.000232578 0 0.227256 rs78179835 -0.693147 0.000660471 320 H2209R 4061 cAt/cGt MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280736 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 3712 28561 4147 3557 1065 10384 217 5479 2 10324 121176 11566 8590 6610 66682 908 16496 0.903183 0 . 0 . 404 159,80,117,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H2209R|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.883042 0.979077 0 0.00551948 rs66977240,rs78974621 -0.693147 5.55056e-14 404 D2201 4061 gaT/gaC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280759 A G 0 222 0 0.472 0.3672 0.3501 0.4454 0.1531 0.3773 0.387199 0.203829 0.109884 1 4417 29286 4151 3591 1064 10366 217 5480 2 10382 121216 11572 8584 6608 66666 908 16496 0.483364 0 . 0 . 465 164,85,163,13 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D2201|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.923388 0.983258 0 0.774583 rs2338554 -0.693147 0.205104 465 Y2194H 4061 Tat/Cat MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280782 A G 0 228 0 0.7897 0.5397 0.4683 0.6607 0.1759 0.502 0 . 0 2 7406 38520 5664 5229 1195 11649 258 7119 2 10402 121266 11544 8596 6614 66704 906 16500 0 . 0 . 0 491 0,0,333,110 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y2194H|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.99089 0 . rs2184953 -0.693147 0.10443 491 K2192Q 4061 Aaa/Caa MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280788 T G 0 222 0 . 0 . 0 . 0 0.238084 0.143626 0.0952326 1 3775 28764 4156 3609 1069 10422 217 5516 2 10402 121320 11576 8620 6612 66696 908 16506 0.0382388 0 . 0 . 513 180,94,153,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K2192Q|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 0 . 1 1 0 59 0 0.596561 0.956912 0 0.993051 rs66954353 -0.693147 0.00838582 513 S2166 4061 tcT/tcC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280864 A G 0 228 0 0.5204 0.4637 0.4524 0.6577 0.172 0.4949 0.466636 0.26984 0.168993 2 4999 35735 5521 5210 1194 11499 246 7066 2 10402 121308 11558 8604 6614 66716 906 16508 0 . 0 . 0 583 0,0,302,242 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2166|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.3581 0 . rs2184954 -0.693147 0.0148434 583 Q2154H 4061 caA/caC MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152280900 T G 0 222 0 0.3843 0.3438 0.3487 0.4444 0.1541 0.3773 0 . 0 1 3765 28718 4150 3617 1067 10417 216 5486 2 10402 121366 11578 8634 6612 66720 908 16512 0.988313 0 . 0 . 590 148,144,139,112 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q2154H|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.263386 0.776985 0 0.132768 rs74129452 -0.693147 0.0211514 590 Y2119H 4061 Tat/Cat MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281007 A G 0 222 0 0.3843 0.3277 0.3357 0.4355 0.1282 0.3395 0.329324 0.195294 0.126628 1 3754 26782 4075 3547 1025 9219 207 4955 2 10404 121358 11568 8618 6614 66734 908 16512 0.791905 0 . 0 . 527 119,128,127,116 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y2119H|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.858852 0.859915 0 0.435186 rs7512553 -0.693147 0.00307474 527 H2118 4061 caT/caC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281008 A G 0 222 0 0.3843 0.3277 0.3357 0.4355 0.1282 0.3395 0.328189 0.194449 0.12593 1 3754 26782 4075 3547 1025 9219 207 4955 2 10404 121358 11570 8618 6614 66732 908 16512 0.0196903 0 . 0 . 525 119,125,127,117 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H2118|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.860444 0.858309 0 0.600336 rs7512554 -0.693147 0.00250588 525 A2108V 4061 gCg/gTg MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281039 G A 0 222 0 . 0 . 0 . 0 0.356786 0.209519 0.13407 1 3767 26793 4076 3540 1025 9224 206 4955 2 10404 121364 11576 8610 6614 66740 908 16512 0.456284 0 . 0 . 508 127,100,125,115 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A2108V|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.603261 rs7522925 -0.693147 0.134484 508 S2045T 4061 aGt/aCt MODERATE 3 MISSENSE CODING FLG G protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281228 C G 0 222 0 . 0 . 0 . 0 0.327962 0.197846 0.131138 1 3652 26549 4053 3464 1024 9202 205 4949 2 10400 121268 11560 8560 6612 66716 908 16512 0.816007 0 . 0 . 692 227,127,173,113 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S2045T|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 0 . 1 1 0 57 0 0.0106533 0.100243 0 0.912784 rs7546186 -0.693147 0.654086 692 H2024 4061 caT/caC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281290 A G 0 222 0 0.385 0.3281 0.3343 0.4355 0.1292 0.3405 0.262369 0.172305 0.126163 1 3723 26758 4076 3535 1025 9229 206 4964 2 10358 121340 11576 8636 6614 66736 908 16512 0.977853 0 . 0 . 729 224,163,164,123 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H2024|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.000750603 0.57812 0 0.826411 rs80353812 -0.693147 0.371301 729 S2020A 4061 Tca/Gca MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281304 A C 0 222 0 . 0 . 0 . 0 0.326827 0.198601 0.132907 1 3526 26525 4066 3545 1025 9210 204 4949 2 10350 121336 11578 8640 6614 66734 908 16512 0.573974 0 . 0 . 754 218,165,166,138 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S2020A|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0.5 1 0 . 0 . 1 1 0 58 0 0.00384 0.953277 0 0.381059 rs7512857 -0.693147 0.500348 754 H1961Q 4061 caC/caA MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281479 G T 0 228 0 0.7897 0.5381 0.4683 0.6607 0.1759 0.4939 0.688152 0.346917 0.172093 2 7408 38492 5663 5232 1195 11660 260 7074 2 10402 121312 11556 8608 6614 66716 908 16508 0 . 0 . 0 408 0,0,167,209 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caA|H1961Q|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.998163 0 . rs3126079 -0.693147 0.0321475 408 W1947G 4061 Tgg/Ggg MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281523 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 3679 26636 4064 3527 1008 9205 205 4948 2 10314 121218 11568 8624 6596 66706 906 16504 0.0500435 0 . 0 . 352 100,92,39,96 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W1947G|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.590474 0.916242 0 0.407397 rs80059102 -0.693147 0.00154272 352 L1943H 4061 cTt/cAt MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281534 A T 0 222 0 0.3336 0.3135 0.3285 0.4335 0.1302 0.3405 0 . 0 1 3177 26094 4045 3506 1011 9190 203 4962 2 10140 120978 11536 8610 6602 66680 906 16504 0.0247206 0 . 0 . 331 101,84,30,88 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cAt|L1943H|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.579354 0.868006 0 0.00329883 rs113544881 -0.693147 9.15252e-07 331 R1891Q 4061 cGg/cAg MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281690 C T 0 228 0 0.0113 0.2875 0.3905 0.5843 0.1421 0.4315 0.036768 0.10795 0.144419 2 327 27751 5178 4828 1143 9962 208 6105 2 10406 121378 11576 8622 6614 66740 908 16512 0 . 0 . 0 228 0,0,117,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1891Q|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12407748 -0.693147 0.0715331 228 A1805V 4061 gCg/gTg MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152281948 G A 0 228 0 0.0113 0.2875 0.3905 0.5843 0.1421 0.4315 0.0365411 0.107753 0.144253 2 325 27768 5176 4840 1143 9965 208 6111 2 10406 121370 11576 8618 6614 66736 908 16512 1 0 . 0 . 294 0,1,140,137 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A1805V|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12405241 -0.693147 0.0910138 294 R1699C 4061 Cgc/Tgc MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152282267 G A 0 228 0 0.0121 0.2877 0.3905 0.5843 0.1421 0.4315 0.0365411 0.10772 0.144186 2 325 27771 5177 4842 1143 9964 208 6112 2 10406 121366 11570 8618 6614 66738 908 16512 1 0 . 0 . 207 1,0,108,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R1699C|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12405278 -0.693147 0.113183 207 R1684H 4061 cGc/cAc MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152282311 C T 0 228 0 0.0461 0.2967 0.3905 0.5843 0.1421 0.4315 0.0687699 0.118714 0.144302 2 694 28161 5188 4842 1143 9971 209 6114 2 10406 121362 11576 8612 6614 66734 908 16512 1 0 . 0 . 247 1,0,122,107 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R1684H|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12407807 -0.693147 0.423214 247 S1482Y 4061 tCc/tAc MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152282917 G T 0 228 0 0.0113 0.2871 0.3905 0.5823 0.1421 0.4315 0.0365411 0.10772 0.144186 2 325 27763 5177 4836 1143 9964 208 6110 2 10406 121376 11576 8624 6614 66736 908 16512 0 . 0 . 0 233 0,0,112,110 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S1482Y|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11204978 -0.693147 0.140861 233 R1376G 4061 Aga/Gga MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152283236 T C 0 228 0 0.1218 0.3431 0.4236 0.6062 0.171 0.4908 0.137767 0.15713 0.167054 2 1363 31729 5434 5000 1196 11466 233 7037 2 10402 121390 11578 8640 6614 66736 908 16512 0 . 0 . 0 357 0,0,188,154 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R1376G|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.939823 0 . rs11581433 -0.693147 0.00183504 357 R1360H 4061 cGc/cAc MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152283283 C T 0 228 0 0.0144 0.2877 0.389 0.5823 0.1421 0.4315 0.036995 0.107676 0.143904 2 347 27783 5178 4829 1143 9968 208 6110 2 10378 121358 11578 8634 6614 66734 908 16512 0 . 0 . 0 388 0,0,186,166 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R1360H|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.331357 0 . rs11586631 -0.693147 0.140459 388 A1167G 4061 gCa/gGa MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152283862 G C 0 228 0 0.7806 0.5341 0.4611 0.6577 0.1759 0.4939 0.599637 0.310165 0.16186 2 6812 36703 5430 4948 1178 11408 254 6673 2 10186 120732 11490 8532 6604 66640 904 16376 0.95597 0 . 0 COSM1600315 240 4,1,90,129 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A1167G|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 1 0 . 0 . 1 0 1 1 0 56 0 0.0199205 0.229718 0 0.00336919 rs58001094 -0.693147 0.0124386 240 S1129 4061 tcT/tcC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152283975 A G 0 228 0 0.5204 0.4631 0.4524 0.6558 0.172 0.4939 0.456423 0.263611 0.164806 2 4989 35714 5516 5204 1194 11505 247 7059 2 10390 121366 11578 8648 6612 66720 908 16510 0 . 0 . 0 225 0,0,123,85 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1129|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.426601 0 . rs66831674 -0.693147 0.299738 225 A974V 4061 gCt/gTt MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152284441 G A 0 222 0 0.0008 0.0017971 0 0.0079 0 0 0 . 0 1 6 98 4 79 0 6 1 2 2 10406 121412 11578 8654 6614 66740 908 16512 0.967321 0 . 0 . 242 87,38,50,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A974V|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.99778 0.0851356 0 0.959438 rs143643121 -0.693147 0.339652 242 D836 4061 gaT/gaC LOW 3 SILENT CODING FLG G protein_coding NM_002016.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152284854 A G 0 228 0 0.5567 0.4732 0.4553 0.6558 0.173 0.4939 0.501135 0.282177 0.17 2 5389 36149 5532 5212 1194 11540 248 7034 2 10404 121376 11578 8630 6614 66734 908 16508 0 . 0 . 0 284 0,0,156,102 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D836|4061|FLG|protein_coding|CODING|NM_002016.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3120653 -0.693147 0.0820142 284 K801E 4061 Aaa/Gaa MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152284961 T C 0 222 0 0.0068 0.0021965 0 0.002 0 0 0 . 0 1 9 105 7 16 0 52 2 19 2 10400 121404 11578 8654 6614 66740 908 16510 0.741128 0 . 0 COSM1252502 357 109,74,90,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K801E|4061|FLG|protein_coding|CODING|NM_002016.1|3|C) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.994319 0.993066 0 0.355678 rs147472105 -0.693147 0.0665943 357 E755K 4061 Gaa/Aaa MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152285099 C T 0 228 0 0.0681 0.3277 0.415 0.6062 0.171 0.4908 0.0835225 0.139243 0.167791 2 797 31056 5346 5014 1194 11451 225 7029 2 10406 121372 11578 8622 6614 66734 908 16510 0.958482 0 . 0 . 388 6,2,183,170 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E755K|4061|FLG|protein_coding|CODING|NM_002016.1|3|T) 1 0 . 0 . 1 0 1 1 0 59 0 0.0105099 0.873058 0 0.0670744 rs74129461 -0.693147 0.513352 388 P478S 4061 Cct/Tct MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152285930 G A 0 228 0 0.1286 0.3446 0.4222 0.6062 0.171 0.4908 0.139582 0.158312 0.167907 2 1419 31704 5374 5010 1194 11445 227 7035 2 10400 121352 11578 8608 6612 66734 908 16512 0 . 0 . 0 315 0,0,163,119 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P478S|4061|FLG|protein_coding|CODING|NM_002016.1|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11584340 -0.693147 0.165801 315 T454A 4061 Aca/Gca MODERATE 3 MISSENSE CODING FLG C protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152286002 T C 0 228 0 0.5204 0.4641 0.4539 0.6587 0.173 0.4939 0.46709 0.270567 0.169884 2 5016 35797 5522 5223 1194 11531 247 7064 2 10404 121380 11576 8626 6614 66740 908 16512 0 . 0 . 0 258 0,0,114,123 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T454A|4061|FLG|protein_coding|CODING|NM_002016.1|3|C),INTRAGENIC(MODIFIER|||||FLG-AS1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2011331 -0.693147 0.166821 258 G444R 4061 Ggg/Agg MODERATE 3 MISSENSE CODING FLG T protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152286032 C T 0 228 0 0.0113 0.2871 0.3905 0.5823 0.1421 0.4315 0.0365411 0.107796 0.144302 2 325 27756 5179 4836 1143 9958 208 6107 2 10406 121376 11574 8622 6614 66740 908 16512 0 . 0 . 0 235 0,0,95,131 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G444R|4061|FLG|protein_coding|CODING|NM_002016.1|3|T),INTRAGENIC(MODIFIER|||||FLG-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11588170 -0.693147 0.331786 235 G332V 4061 gGc/gTc MODERATE 3 MISSENSE CODING FLG A protein_coding NM_002016.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152286367 C A 0 228 0 0.115 0.3407 0.4193 0.6062 0.171 0.4908 0.132093 0.155774 0.167907 2 1316 31596 5365 5013 1194 11445 227 7036 2 10406 121396 11578 8638 6614 66740 908 16512 1 0 . 0 . 159 1,0,58,83 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G332V|4061|FLG|protein_coding|CODING|NM_002016.1|3|A),INTRAGENIC(MODIFIER|||||FLG-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs41267154 -0.693147 0.656338 159 2391 836 MODIFIER 3 CODING FLG2 A protein_coding NM_001014342.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152322250 G A 0 222 0 0 0.0228 0 0.0972 0.0099 0.0061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.817948 0 . 0 . 174 41,47,27,36 UTR_3_PRIME(MODIFIER||836||2391|FLG2|protein_coding|CODING|NM_001014342.2|3|A),INTRAGENIC(MODIFIER|||||FLG-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994823 rs79507400 -0.693147 0.051163 174 C40Y 118 tGt/tAt MODERATE 2 MISSENSE CODING LCE5A A protein_coding NM_178438.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152484129 G A 0 228 0 0.3132 0.522 0.5346 0.6111 0.6223 0.6002 0.351566 0.536214 0.630814 2 3511 74066 6633 5719 4838 43395 586 9384 2 10406 121358 11570 8628 6612 66724 908 16510 0 . 0 . 0 58 0,0,28,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C40Y|118|LCE5A|protein_coding|CODING|NM_178438.4|2|A),UPSTREAM(MODIFIER||2849||99|CRCT1|protein_coding|CODING|NM_019060.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2105117 -0.693147 0.161366 58 C40 99 tgC/tgT LOW 2 SILENT CODING CRCT1 T protein_coding NM_019060.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152487979 C T 0 228 0 0.1611 0.4796 0.5245 0.6081 0.6213 0.6002 0.328075 0.567326 0.68225 2 1481 61392 5869 4961 3935 35747 479 8920 2 5602 95620 9644 7140 5172 52360 712 14990 1 0 . 0 . 29 1,0,10,16 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C40|99|CRCT1|protein_coding|CODING|NM_019060.2|2|T),DOWNSTREAM(MODIFIER||3326||118|LCE5A|protein_coding|CODING|NM_178438.4||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2282296 -0.692976 0.0554648 29 R68 99 cgC/cgT LOW 2 SILENT CODING CRCT1 T protein_coding NM_019060.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152488063 C T 0 228 0 0.5151 0.5851 0.5476 0.6478 0.6213 0.6043 0.573423 0.640156 0.672723 2 3335 60948 5688 5001 3234 34725 441 8524 2 5338 87706 8580 6774 4062 48520 626 13806 1 0 . 0 . 36 1,0,24,9 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R68|99|CRCT1|protein_coding|CODING|NM_019060.2|2|T),DOWNSTREAM(MODIFIER||3410||118|LCE5A|protein_coding|CODING|NM_178438.4||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1053588 -0.693127 0.0434745 36 99 269 MODIFIER 2 CODING CRCT1 C protein_coding NM_019060.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152488428 T C 0 228 0 0.6286 0.6176 0.5591 0.6498 0.6252 0.6033 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,18,20 UTR_3_PRIME(MODIFIER||269||99|CRCT1|protein_coding|CODING|NM_019060.2|2|C),DOWNSTREAM(MODIFIER||3775||118|LCE5A|protein_coding|CODING|NM_178438.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1053590 -0.693143 0.0665157 45 92 48 MODIFIER 2 CODING LCE3E C protein_coding NM_178435.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152538358 G C 0 222 0 0.2141 0.2586 0.3343 0.244 0.2187 0.3211 0.210036 0.223958 0.231091 1 2157 30695 5269 1736 1643 14898 213 4779 2 9626 115842 11390 8584 6610 64660 858 14114 0.901704 0 . 0 . 37 14,6,8,6 UTR_3_PRIME(MODIFIER||48||92|LCE3E|protein_coding|CODING|NM_178435.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.209847 rs17659359 -0.686358 0.419688 37 G43V 92 gGc/gTc MODERATE 2 MISSENSE CODING LCE3D A protein_coding NM_032563.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152552285 C A 0 222 0 0.1384 0.2768 0.2853 0.3264 0.3827 0.2975 0.179074 0.302123 0.365223 1 1726 38591 2711 2747 2440 24024 276 4667 2 10362 121190 11472 8626 6614 66702 906 16508 0.0250188 0 . 0 COSM146624 112 35,19,23,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G43V|92|LCE3D|protein_coding|CODING|NM_032563.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.951331 0.872457 0 0.956645 rs512208 -0.693146 0.67622 112 I51S 110 aTc/aGc MODERATE 2 MISSENSE CODING LCE2B G protein_coding NM_014357.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152659471 T G 0 222 0 0.3071 0.2063 0.1556 0.2946 0.0875 0.137 0.286655 0.15093 0.0813954 1 2924 15410 1264 2491 996 5396 114 2225 2 10396 121374 11576 8636 6612 66734 908 16512 0.941686 0 . 0 COSM146625 75 13,21,12,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aGc|I51S|110|LCE2B|protein_coding|CODING|NM_014357.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98927 rs3737859 -0.693139 0.0136299 75 106 215 MODIFIER 2 CODING LCE2A G protein_coding NM_178428.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152671913 C G 0 39.9 0 0.2905 0.2009 0.1499 0.2937 0.0875 0.137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924449 0 . 0 . 11 1,6,0,4 UTR_3_PRIME(MODIFIER||215||106|LCE2A|protein_coding|CODING|NM_178428.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.763675 rs3908717 -0.556411 0.709006 11 99 9 MODIFIER 1 CODING LCE4A C protein_coding NM_178356.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152681543 T C 0 228 0 1 0.9998 1 1 1 0.999 1 0.999616 0.999419 2 10404 120755 11574 8654 6614 66477 904 16128 2 10404 120806 11576 8654 6614 66520 904 16134 0 . 0 . 0 41 0,0,35,3 UTR_5_PRIME(MODIFIER||9||99|LCE4A|protein_coding|CODING|NM_178356.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1332496 -0.693143 0.0360478 41 G95V 99 gGa/gTa MODERATE 1 MISSENSE CODING LCE4A T protein_coding NM_178356.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152681835 G T 0 222 0 0.2693 0.124 0.1037 0.129 0.0139 0.0501 0.216493 0.0841287 0.016298 1 2368 6324 914 1095 227 1154 46 520 2 9446 112368 11476 8572 6402 63324 812 12336 0.880292 0 . 0 . 58 16,16,14,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G95V|99|LCE4A|protein_coding|CODING|NM_178356.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904912 rs10888510 -0.692831 0.653767 58 S26T 250 aGc/aCc MODERATE 1 MISSENSE CODING C1orf68 C protein_coding NM_001024679.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152692074 G C 0 222 0 0.5461 0.3492 0.3804 0.1716 0.3608 0.2321 0 . 0 1 1224 6880 144 92 496 3084 53 1787 2 2308 22424 414 624 1642 9280 244 7912 0.101225 0 . 0 COSM146626 172 70,22,49,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S26T|250|C1orf68|protein_coding|CODING|NM_001024679.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.87804 rs1332500 -0.693147 0.496613 172 T159P 250 Act/Cct MODERATE 1 MISSENSE CODING C1orf68 C protein_coding NM_001024679.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152692472 A C 0 222 0 0.5461 0.3492 0.3804 0.1716 0.3608 0.2321 0.500723 0.395751 0.350094 1 1173 6679 142 93 492 2938 53 1788 2 2228 21936 410 626 1634 8882 242 7914 0.845852 0 . 0 COSM146627 102 22,38,20,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T159P|250|C1orf68|protein_coding|CODING|NM_001024679.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.523349 rs386618453,rs873775 -0.693136 0.0306528 102 S197 250 tcA/tcG LOW 1 SILENT CODING C1orf68 G protein_coding NM_001024679.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152692588 A G 0 222 0 0.5461 0.3492 0.3804 0.1716 0.3608 0.2321 0.500723 0.395532 0.34978 1 1124 6570 142 91 481 2891 53 1788 2 2154 21720 410 622 1604 8776 244 7910 0.748368 0 . 0 COSM146628 91 40,15,19,13 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S197|250|C1orf68|protein_coding|CODING|NM_001024679.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.4936 rs944682 -0.69312 0.157574 91 250 31 MODIFIER 1 CODING C1orf68 T protein_coding NM_001024679.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152692781 G T 0 222 0 0.5461 0.3492 0.3804 0.1716 0.3608 0.2321 0.499277 0.394656 0.349151 1 1056 4461 129 81 483 2230 32 450 2 1966 12236 342 528 1622 6204 140 1434 0.782888 0 . 0 . 102 22,29,19,21 UTR_3_PRIME(MODIFIER||31||250|C1orf68|protein_coding|CODING|NM_001024679.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991334 rs3814350 -0.693145 0.219434 102 250 112 MODIFIER 1 CODING C1orf68 C protein_coding NM_001024679.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152692862 G C 0 222 0 0.5469 0.3494 0.3804 0.1716 0.3608 0.2321 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.657898 0 . 0 . 50 7,16,5,19 UTR_3_PRIME(MODIFIER||112||250|C1orf68|protein_coding|CODING|NM_001024679.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.757751 rs3814351 -0.692831 0.49323 50 Q14H 579 caA/caT MODERATE 2 MISSENSE CODING KPRP T protein_coding NM_001025231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152732106 A T 0 222 0 0.0106 0.1771 0.1441 0.2262 0.2256 0.3252 0.04335 0.16823 0.232209 1 404 27263 1842 1771 1587 15969 213 5477 2 10394 121222 11570 8626 6612 66632 908 16480 0.845635 0 . 0 . 102 37,13,34,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q14H|579|KPRP|protein_coding|CODING|NM_001025231.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0864232 rs17612167 -0.693147 0.723271 102 V37A 579 gTt/gCt MODERATE 2 MISSENSE CODING KPRP C protein_coding NM_001025231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152732174 T C 0 222 0 0.1445 0.1899 0.2147 0.3452 0.1083 0.1575 0.141852 0.119868 0.108605 1 1469 18093 3206 3014 833 6650 138 2783 2 10406 121378 11572 8628 6614 66738 908 16512 0.287599 0 . 0 . 161 55,24,47,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V37A|579|KPRP|protein_coding|CODING|NM_001025231.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.906226 rs944683 -0.693147 0.25662 161 A124 579 gcG/gcC LOW 2 SILENT CODING KPRP C protein_coding NM_001025231.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152732436 G C 0 222 0 0.5787 0.4904 0.4914 0.4187 0.5159 0.4182 0.553563 0.519837 0.502558 1 5687 58414 5389 3623 2978 33087 423 7227 2 10404 121368 11570 8632 6612 66730 908 16512 0.999163 0 . 0 . 80 22,20,16,19 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A124|579|KPRP|protein_coding|CODING|NM_001025231.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0598128 rs4845480 -0.693136 0.0487286 80 R168H 579 cGt/cAt MODERATE 2 MISSENSE CODING KPRP A protein_coding NM_001025231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152732567 G A 0 222 0 0.3585 0.2526 0.2464 0.3442 0.1123 0.1636 0.299591 0.175611 0.112093 1 3147 20240 3321 3014 836 6837 155 2930 2 10404 121390 11574 8646 6614 66732 908 16512 0.989609 0 . 0 . 118 38,20,36,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R168H|579|KPRP|protein_coding|CODING|NM_001025231.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966581 rs16834461 -0.693147 0.170956 118 C413S 579 Tgc/Agc MODERATE 2 MISSENSE CODING KPRP A protein_coding NM_001025231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152733301 T A 0 222 0 0.5787 0.4902 0.4914 0.4177 0.5159 0.4182 0.553563 0.519914 0.502674 1 5677 58363 5387 3622 2978 33051 422 7226 2 10384 121244 11562 8628 6606 66654 906 16504 0.985685 0 . 0 . 79 19,24,12,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Agc|C413S|579|KPRP|protein_coding|CODING|NM_001025231.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.298155 rs4329520 -0.69311 0.132229 79 579 586 MODIFIER 2 CODING KPRP T protein_coding NM_001025231.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152734390 C T 0 222 0 0.3585 0.2524 0.2464 0.3433 0.1123 0.1636 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.949162 0 . 0 . 131 36,17,35,22 UTR_3_PRIME(MODIFIER||586||579|KPRP|protein_coding|CODING|NM_001025231.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.305318 rs2297487 -0.693147 0.414316 131 R82W 118 Cgg/Tgg MODERATE 1 MISSENSE CODING LCE1F T protein_coding NM_178354.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152749091 C T 0 222 0 0.0053 0.0909 0.1311 0.0278 0.2117 0.1186 0.0365743 0.154456 0.214851 1 329 20081 1224 142 1325 14608 158 2295 2 9612 118746 11484 8572 6592 65286 898 16302 0.794587 0 . 0 . 56 14,15,11,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R82W|118|LCE1F|protein_coding|CODING|NM_178354.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980867 rs41268480 -0.692352 0.58672 56 118 124 MODIFIER 1 CODING LCE1F T protein_coding NM_178354.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152749328 C T 0 14.8 0 0.177 0.1981 0.2219 0.3363 0.1113 0.1564 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8 0 . 0 . 7 0,5,0,2 UTR_3_PRIME(MODIFIER||124||118|LCE1F|protein_coding|CODING|NM_178354.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs872180 -0.453602 0.02 7 S59G 118 Agc/Ggc MODERATE 2 MISSENSE CODING LCE1E G protein_coding NM_178353.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152759950 A G 0 222 0 0.7625 0.5357 0.5058 0.4097 0.5 0.4172 0.703678 0.561385 0.488483 1 7358 59244 5401 3454 2960 32422 423 7226 2 10220 120736 11566 8628 6612 66304 902 16504 0.578325 0 . 0 . 48 14,10,7,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S59G|118|LCE1E|protein_coding|CODING|NM_178353.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.773528 rs11205106 -0.692352 0.0162778 48 S100 118 tcA/tcG LOW 2 SILENT CODING LCE1E G protein_coding NM_178353.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760075 A G 0 104 0 0.3654 0.2662 0.2406 0.3313 0.1064 0.2474 0.0843631 0.0418371 0.0208039 1 2078 14301 1858 1678 648 4998 118 2923 2 8056 107384 10206 7342 6116 60732 790 14142 0.934726 0 . 0 . 53 30,8,9,4 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S100|118|LCE1E|protein_coding|CODING|NM_178353.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.0480505 0.726493 0 0.0923039 rs201660535 -0.683931 0.00603695 53 G107 118 ggA/ggT LOW 2 SILENT CODING LCE1E T protein_coding NM_178353.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760096 A T 0 26.3 0 0.239 0.1761 0.1383 0.2639 0.0616 0.1452 0.0933678 0.0483871 0.025939 1 932 5941 813 717 204 2286 42 947 2 7936 106302 10486 7516 6228 61668 766 11702 0.300616 0 . 0 COSM1600836 56 32,7,7,3 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G107|118|LCE1E|protein_coding|CODING|NM_178353.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 54 0 0.000559761 0.924253 0 0.470517 rs115864544 -0.670168 0.947685 56 118 220 MODIFIER 2 CODING LCE1E A protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760352 T A 0 221 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.952173 0 . 0 . 187 59,67,24,22 UTR_3_PRIME(MODIFIER||220||118|LCE1E|protein_coding|CODING|NM_178353.1|2|A) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.940215 3.8099e-08 0 0.707439 rs61814474 -0.693147 0.284228 187 118 496 MODIFIER 2 CODING LCE1E C protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760628 T C 0 222 0 0.6331 0.3754 0.3184 0.3542 0.1859 0.2843 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.425359 0 . 0 . 187 62,42,46,22 UTR_3_PRIME(MODIFIER||496||118|LCE1E|protein_coding|CODING|NM_178353.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 56 0 0.213646 0.0247698 0 0.985801 rs12038374,rs78035972 -0.693147 0.999859 187 118 510 MODIFIER 2 CODING LCE1E T protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760642 C T 0 222 0 0.6346 0.3774 0.3184 0.3562 0.1909 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.574107 0 . 0 . 155 51,38,33,21 UTR_3_PRIME(MODIFIER||510||118|LCE1E|protein_coding|CODING|NM_178353.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.446418 0.0546514 0 0.00350647 rs150561698 -0.693147 3.17276e-05 155 118 512 MODIFIER 2 CODING LCE1E T protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760644 C T 0 222 0 0.6362 0.3778 0.3184 0.3562 0.1909 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.411943 0 . 0 . 152 53,34,32,21 UTR_3_PRIME(MODIFIER||512||118|LCE1E|protein_coding|CODING|NM_178353.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.573377 0.0937143 0 0.0294626 rs138431239 -0.693147 5.82457e-05 152 118 515 MODIFIER 2 CODING LCE1E A protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760647 C A 0 222 0 0.6362 0.3788 0.3199 0.3581 0.1909 0.2873 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.982927 0 . 0 . 154 56,33,32,21 UTR_3_PRIME(MODIFIER||515||118|LCE1E|protein_coding|CODING|NM_178353.1|2|A) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.587576 0.0853036 0 0.0971218 rs148505679 -0.693147 5.82457e-05 154 118 519 MODIFIER 2 CODING LCE1E T protein_coding NM_178353.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152760651 C T 0 222 0 0.6362 0.3792 0.3199 0.3591 0.1918 0.2873 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.883508 0 . 0 . 156 56,33,32,21 UTR_3_PRIME(MODIFIER||519||118|LCE1E|protein_coding|CODING|NM_178353.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.653985 0.126391 0 0.443102 rs12048712 -0.693147 5.82457e-05 156 R84H 114 cGc/cAc MODERATE 2 MISSENSE CODING LCE1D A protein_coding NM_178352.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152770521 G A 0 222 0 0.4455 0.3373 0.3127 0.3502 0.1938 0.3425 0.301411 0.2129 0.165908 1 3029 26123 3907 3005 1143 10043 216 4780 2 7306 100068 10768 8180 5662 52812 774 14566 0.817915 0 . 0 COSM1334238 79 29,14,21,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R84H|114|LCE1D|protein_coding|CODING|NM_178352.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.0258549 0.687918 0 0.653607 rs41268492 -0.693127 0.120937 79 S88N 114 aGc/aAc MODERATE 2 MISSENSE CODING LCE1D A protein_coding NM_178352.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152770533 G A 0 222 0 . 0 . 0 . 0 0.141687 0.119076 0.106982 1 1468 17565 2825 2341 790 6465 146 3530 2 8588 105046 11040 8544 5976 54974 808 15116 0.817427 0 . 0 . 87 37,16,22,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S88N|114|LCE1D|protein_coding|CODING|NM_178352.2|2|A) 1 0.5 1 0 . 0 . 1 1 0 55 0 0.978485 0.684497 0 0.930325 rs41268494 -0.69311 0.69104 87 S107G 114 Agc/Ggc MODERATE 2 MISSENSE CODING LCE1D G protein_coding NM_178352.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152770589 A G 0 222 0 . 0 . 0 . 0 0.377363 0.264803 0.203903 1 3746 28981 3998 3194 1322 11325 239 5157 2 8750 102946 11074 8500 6022 54602 786 13212 0.999719 0 . 0 . 115 32,18,47,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S107G|114|LCE1D|protein_coding|CODING|NM_178352.2|2|G) 1 0.5 1 0 . 0 . 1 1 0 53 0 0.00172004 0.413998 0 0.987277 rs11485496 -0.693147 0.00145213 115 118 257 MODIFIER 2 CODING LCE1C T protein_coding NM_178351.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152777341 C T 0 83 0 0.1838 0.2113 0.2205 0.3135 0.1123 0.2382 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.891517 0 . 0 . 11 4,1,6,0 UTR_3_PRIME(MODIFIER||257||118|LCE1C|protein_coding|CODING|NM_178351.3|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.891517 rs4845487 -0.616816 0.64169 11 118 24 MODIFIER 2 CODING LCE1C A protein_coding NM_178351.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152777574 G A 0 222 0 0.1399 0.1997 0.2205 0.3135 0.1123 0.2382 0.134939 0.120769 0.113515 1 1359 17722 3274 2765 848 6876 139 2461 2 9476 110310 11484 8540 6614 63592 796 9808 0.626449 0 . 0 . 101 26,22,19,17 UTR_3_PRIME(MODIFIER||24||118|LCE1C|protein_coding|CODING|NM_178351.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.933636 rs1048534 -0.693139 0.099131 101 C16Y 118 tGc/tAc MODERATE 2 MISSENSE CODING LCE1C T protein_coding NM_178351.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152777908 C T 0 222 0 0.2163 0.2206 0.2248 0.3135 0.1133 0.2382 0.196185 0.142648 0.115233 1 2044 20157 3314 2764 848 7149 160 3878 2 10276 120906 11544 8612 6606 66454 904 16510 0.654036 0 . 0 . 72 24,12,16,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C16Y|118|LCE1C|protein_coding|CODING|NM_178351.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.232606 rs2006940 -0.69312 0.662943 72 T113A 585 Aca/Gca MODERATE 2 MISSENSE CODING IVL G protein_coding NM_005547.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152882610 A G 0 222 0 0.6808 0.4137 0.2997 0.5615 0.1083 0.2955 0.575125 0.255497 0.0917442 1 6244 26411 3975 5079 399 6548 137 4029 2 10358 120922 11520 8568 6590 66510 904 16472 0.805913 0 . 0 . 87 21,28,12,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T113A|585|IVL|protein_coding|CODING|NM_005547.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.641716 rs2229496 -0.69312 0.119011 87 P236S 585 Cca/Tca MODERATE 2 MISSENSE CODING IVL T protein_coding NM_005547.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152882979 C T 0 61 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.554404 0 . 0 COSM1334251 31 20,1,9,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P236S|585|IVL|protein_coding|CODING|NM_005547.2|2|T) 0 0.5 1 0 . 0 . 0 . 0 47 0 0.957656 1 0 0.327847 rs17855670 -0.662043 0.000491352 31 P236 585 ccA/ccT LOW 2 SILENT CODING IVL T protein_coding NM_005547.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152882981 A T 0 62 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.629927 0 . 0 . 31 21,1,8,0 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P236|585|IVL|protein_coding|CODING|NM_005547.2|2|T) 0 0.5 1 0 . 0 . 0 . 0 47 0 0.982559 1 0 0.27011 rs62637699 -0.651104 0.000550189 31 Q237E 585 Cag/Gag MODERATE 2 MISSENSE CODING IVL G protein_coding NM_005547.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152882982 C G 0 124 0 0.6944 0.4243 0.3112 0.5625 0.1342 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.097233 0 . 0 . 31 11,1,18,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q237E|585|IVL|protein_coding|CODING|NM_005547.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 47 0 0.977848 1 0 0.138153 rs7520711 -0.691153 6.05121e-05 31 Q248R 585 cAg/cGg MODERATE 2 MISSENSE CODING IVL G protein_coding NM_005547.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152883016 A G 0 180 0 0 0.0067891 0 0.0327 0 0.001 0 . 0 1 0 19 0 18 0 0 0 1 2 1544 13614 368 630 36 6338 148 4550 0.882297 0 . 0 . 54 30,0,17,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q248R|585|IVL|protein_coding|CODING|NM_005547.2|2|G) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.516219 1 0 0.644679 rs184035162 -0.691153 0.637787 54 Q445 585 caG/caA LOW 2 SILENT CODING IVL A protein_coding NM_005547.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152883608 G A 0 222 0 0.6808 0.4123 0.2997 0.5615 0.1083 0.2883 0.550735 0.244846 0.0889305 1 2489 7664 221 1315 27 1539 41 2032 2 4016 26384 628 2028 128 11064 212 8308 0.784063 0 . 0 . 101 26,19,24,20 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q445|585|IVL|protein_coding|CODING|NM_005547.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995934 rs7545413 -0.693146 0.0293511 101 Q469 585 caA/caG LOW 2 SILENT CODING IVL G protein_coding NM_005547.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152883680 A G 0 222 0 0.6808 0.4135 0.2997 0.5615 0.1083 0.2945 0.552208 0.244798 0.0881388 1 2664 8559 238 1552 30 1835 49 2191 2 4314 29818 684 2474 222 13260 230 8634 0.673846 0 . 0 . 85 18,21,16,21 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q469|585|IVL|protein_coding|CODING|NM_005547.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846764 rs7535306 -0.693141 0.0314498 85 V480L 585 Gtg/Ctg MODERATE 2 MISSENSE CODING IVL C protein_coding NM_005547.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152883711 G C 0 222 0 0.6808 0.4123 0.2997 0.5615 0.1083 0.2883 0.54961 0.243329 0.0871398 1 2457 7742 210 1291 27 1663 47 2047 2 4060 28894 638 2126 250 13070 232 8518 0.899586 0 . 0 . 78 11,25,15,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V480L|585|IVL|protein_coding|CODING|NM_005547.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.887399 rs7545520 -0.693136 0.707678 78 585 80 MODIFIER 2 CODING IVL A protein_coding NM_005547.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152884111 G A 0 222 0 0.6785 0.4117 0.2997 0.5615 0.1083 0.2883 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.897113 0 . 0 . 83 27,20,17,10 UTR_3_PRIME(MODIFIER||80||585|IVL|protein_coding|CODING|NM_005547.2|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.880153 rs913996 -0.693021 0.40116 83 585 215 MODIFIER 2 CODING IVL T protein_coding NM_005547.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152884246 G T 0 222 0 0.6808 0.4123 0.2997 0.5615 0.1083 0.2883 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0379419 0 . 0 . 61 12,20,9,11 UTR_3_PRIME(MODIFIER||215||585|IVL|protein_coding|CODING|NM_005547.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.879017 rs12407682 -0.692067 0.07183 61 585 216 MODIFIER 2 CODING IVL G protein_coding NM_005547.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152884247 A G 0 222 0 0.6808 0.4123 0.2997 0.5615 0.1083 0.2883 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.540687 0 . 0 . 63 12,21,10,11 UTR_3_PRIME(MODIFIER||216||585|IVL|protein_coding|CODING|NM_005547.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.488099 rs12406539 -0.692352 0.0816513 63 S76 79 agC/agT LOW 2 SILENT CODING SPRR4 T protein_coding NM_173080.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152944594 C T 0 222 0 0.8306 0.6252 0.4986 0.6319 0.5656 0.4918 0.777349 0.641012 0.571163 1 8303 68991 5591 5799 2841 37922 469 8066 2 10404 121344 11568 8640 6608 66708 906 16510 0.881938 0 . 0 . 145 40,36,30,29 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S76|79|SPRR4|protein_coding|CODING|NM_173080.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.651994 rs3170863 -0.693147 0.357121 145 H42Q 89 caC/caA MODERATE 2 MISSENSE CODING SPRR1A A protein_coding NM_001199828.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152957832 C A 0 222 0 0.4523 0.5054 0.4395 0.5972 0.5348 0.499 0 . 0 1 4726 58269 4633 4761 3068 32855 420 7806 2 9570 118400 11374 8362 6554 65532 886 16122 0.4313 0 . 0 . 111 19,19,28,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caA|H42Q|89|SPRR1A|protein_coding|CODING|NM_001199828.1|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.983527 rs1611762 -0.693147 0.0841866 111 V61I 89 Gtt/Att MODERATE 2 MISSENSE CODING SPRR1A A protein_coding NM_001199828.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152957887 G A 0 222 0 0.6278 0.5611 0.4524 0.6319 0.5348 0.502 0.636632 0.575042 0.543488 1 6410 64550 5063 5686 3210 35297 452 8432 2 10374 120764 11510 8560 6596 66396 898 16430 0.991767 0 . 0 . 99 25,21,22,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V61I|89|SPRR1A|protein_coding|CODING|NM_001199828.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976231 rs1611764 -0.693147 0.514665 99 89 262 MODIFIER 2 CODING SPRR1A G protein_coding NM_001199828.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152958238 A G 0 222 0 0.7239 0.5881 0.4597 0.6319 0.5348 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.59791 0 . 0 . 106 13,36,17,28 UTR_3_PRIME(MODIFIER||262||89|SPRR1A|protein_coding|CODING|NM_001199828.1|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.930896 rs1129654 -0.693147 0.0545048 106 89 291 MODIFIER 2 CODING SPRR1A C protein_coding NM_001199828.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152958267 T C 0 222 0 0.7943 0.6084 0.4697 0.6319 0.5368 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99807 0 . 0 . 82 7,32,8,25 UTR_3_PRIME(MODIFIER||291||89|SPRR1A|protein_coding|CODING|NM_001199828.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.779217 rs1129655 -0.693127 0.441928 82 169 2 MODIFIER 2 CODING SPRR3 A protein_coding NM_001097589.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152975495 G A 0 222 0 0.5 0.525 0.4337 0.6319 0.5328 0.5051 0.524966 0.537214 0.543488 1 5409 64139 5087 5816 3279 35674 456 8418 2 10396 120188 11520 8622 6614 66452 896 15688 0.606778 0 . 0 . 97 36,11,32,9 UTR_5_PRIME(MODIFIER||2||169|SPRR3|protein_coding|CODING|NM_001097589.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.921002 0.923751 0 0.576362 rs2075739 -0.693145 0.157288 97 G73 169 ggC/ggT LOW 2 SILENT CODING SPRR3 T protein_coding NM_001097589.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152975715 C T 0 171 0 0.0015 0.00039936 0 0 0 0 0 . 0 1 264 1906 107 228 89 982 16 220 2 9450 113426 11324 8342 6490 63286 858 13676 0.571593 0 . 0 COSM1334263 143 44,52,10,26 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G73|169|SPRR3|protein_coding|CODING|NM_001097589.1|2|T) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.988321 0.999997 0 0.000216489 rs28989168 -0.693139 6.48495e-05 143 G89 169 ggC/ggA LOW 2 SILENT CODING SPRR3 A protein_coding NM_001097589.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152975763 C A 0 222 0 0.5 0.5246 0.4323 0.6319 0.5318 0.5051 0.524512 0.536835 0.54315 1 816 5807 260 537 82 3424 53 635 2 3650 36376 4094 1776 1848 19852 316 4840 0.215187 0 . 0 . 130 47,28,26,14 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G89|169|SPRR3|protein_coding|CODING|NM_001097589.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.983038 0.535182 0 0.0908291 rs1977734 -0.693145 0.0426742 130 E111 169 gaA/gaG LOW 2 SILENT CODING SPRR3 G protein_coding NM_001097589.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152975829 A G 0 222 0 0.5 0.525 0.4337 0.6319 0.5328 0.5051 0.524966 0.537137 0.543372 1 5399 64138 5049 5763 3263 35676 458 8530 2 10392 121096 11490 8568 6600 66634 906 16506 0.940796 0 . 0 . 135 33,33,34,22 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E111|169|SPRR3|protein_coding|CODING|NM_001097589.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.980126 0.87485 0 0.888818 rs1970328 -0.693147 0.0242648 135 L149V 169 Cta/Gta MODERATE 2 MISSENSE CODING SPRR3 G protein_coding NM_001097589.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152975941 C G 0 222 0 0.7133 0.5835 0.4496 0.6319 0.5328 0.5051 0.684748 0.591881 0.544302 1 7114 65676 5091 5717 3240 35531 463 8520 2 10370 120554 11414 8520 6546 66342 900 16462 0.994919 0 . 0 . 108 21,34,20,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Gta|L149V|169|SPRR3|protein_coding|CODING|NM_001097589.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.984093 0.990746 0 0.99947 rs1055935 -0.693147 0.28246 108 169 102 MODIFIER 2 CODING SPRR3 T protein_coding NM_001097589.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152976108 C T 0 222 0 0.5 0.525 0.4337 0.6319 0.5328 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.975427 0 . 0 . 113 35,24,32,13 UTR_3_PRIME(MODIFIER||102||169|SPRR3|protein_coding|CODING|NM_001097589.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99343 rs1015996 -0.693147 0.396919 113 169 108 MODIFIER 2 CODING SPRR3 C protein_coding NM_001097589.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152976114 G C 0 222 0 0.5 0.525 0.4337 0.6319 0.5328 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.73631 0 . 0 . 112 36,24,30,13 UTR_3_PRIME(MODIFIER||108||169|SPRR3|protein_coding|CODING|NM_001097589.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.96656 rs1015995 -0.693146 0.112464 112 169 300 MODIFIER 2 CODING SPRR3 G protein_coding NM_001097589.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 152976306 T G 0 222 0 0.5 0.525 0.4337 0.6319 0.5328 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.295821 0 . 0 . 81 8,37,7,25 UTR_3_PRIME(MODIFIER||300||169|SPRR3|protein_coding|CODING|NM_001097589.1|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997746 rs1134220 -0.69312 0.0112865 81 89 13 MODIFIER 2 CODING SPRR1B C protein_coding NM_003125.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153004809 T C 0 189 0 0.4402 0.494 0.4251 0.5913 0.5099 0.499 0.468679 0.49654 0.510814 1 4830 60795 5025 5456 3065 33706 430 8283 2 10392 120184 11558 8630 6612 66380 892 15720 0.991692 0 . 0 . 80 46,3,21,3 UTR_5_PRIME(MODIFIER||13||89|SPRR1B|protein_coding|CODING|NM_003125.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994431 rs3181787 -0.692831 0.175799 80 P9 89 ccT/ccC LOW 2 SILENT CODING SPRR1B C protein_coding NM_003125.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153004848 T C 0 222 0 0.4402 0.494 0.4251 0.5913 0.5099 0.499 0.46936 0.496694 0.510698 1 4839 60929 5004 5435 3063 33740 435 8413 2 10402 121242 11568 8630 6612 66650 904 16476 0.534032 0 . 0 . 117 42,19,27,9 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P9|89|SPRR1B|protein_coding|CODING|NM_003125.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.920525 rs3795381 -0.693139 0.720257 117 T11I 89 aCc/aTc MODERATE 2 MISSENSE CODING SPRR1B T protein_coding NM_003125.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153004853 C T 0 222 0 0.4402 0.494 0.4251 0.5913 0.5099 0.499 0.46936 0.496694 0.510698 1 4840 60945 5004 5439 3063 33748 435 8416 2 10406 121280 11568 8632 6612 66672 906 16484 0.667712 0 . 0 COSM1180658 123 42,23,27,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T11I|89|SPRR1B|protein_coding|CODING|NM_003125.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998314 rs3795382 -0.693143 0.726682 123 P54 89 ccC/ccT LOW 2 SILENT CODING SPRR1B T protein_coding NM_003125.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153004983 C T 0 222 0 0.441 0.4976 0.4265 0.5923 0.5179 0.5061 0.471176 0.505307 0.522801 1 4845 61016 5022 5464 3064 33768 435 8418 2 10374 119780 11444 8646 6534 65494 892 16396 0.938909 0 . 0 . 92 24,21,25,20 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P54|89|SPRR1B|protein_coding|CODING|NM_003125.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.936193 0.924225 0 0.535489 rs12195 -0.693147 0.188242 92 89 65 MODIFIER 2 CODING SPRR1B T protein_coding NM_003125.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153005156 C T 0 222 0 0.4402 0.494 0.4251 0.5913 0.5099 0.499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987992 0 . 0 . 136 35,19,36,33 UTR_3_PRIME(MODIFIER||65||89|SPRR1B|protein_coding|CODING|NM_003125.2|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.562464 rs2711 -0.693147 0.0961734 136 72 364 MODIFIER 2 CODING SPRR2D C protein_coding NM_006945.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153012240 A C 0 24.4 0 0.441 0.4938 0.4251 0.5913 0.5089 0.498 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 3,0,3,0 UTR_3_PRIME(MODIFIER||364||72|SPRR2D|protein_coding|CODING|NM_006945.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 0 . 0.861511 rs1048296,rs386513272 -0.511536 0.961028 6 72 250 MODIFIER 2 CODING SPRR2D G protein_coding NM_006945.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153012354 T G 0 62 0 0.7663 0.5917 0.451 0.63 0.5109 0.499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98568 0 . 0 . 12 7,1,3,1 UTR_3_PRIME(MODIFIER||250||72|SPRR2D|protein_coding|CODING|NM_006945.4|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.98568 rs682472 -0.556411 0.573211 12 72 248 MODIFIER 2 CODING SPRR2D T protein_coding NM_006945.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153012356 C T 0 45.8 0 0.7663 0.5917 0.451 0.63 0.5109 0.499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968069 0 . 0 . 12 7,1,3,1 UTR_3_PRIME(MODIFIER||248||72|SPRR2D|protein_coding|CODING|NM_006945.4|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.98568 rs682473 -0.556411 0.573211 12 T20A 72 Acg/Gcg MODERATE 2 MISSENSE CODING SPRR2D C protein_coding NM_006945.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153012765 T C 0 222 0 0.0537 0.1799 0.1383 0.5149 0.003 0.2168 0.0473804 0.0169505 0.00128957 1 496 10816 2469 4672 2 146 54 2977 2 9614 118876 11550 8612 6612 65088 900 16500 0.567743 0 . 0 . 184 31,51,43,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T20A|72|SPRR2D|protein_coding|CODING|NM_006945.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 50 0 0.345595 0.612904 0 0.965238 rs1846857 -0.693147 0.585375 184 Q52 72 caA/caG LOW 2 SILENT CODING SPRR2E C protein_coding NM_001024209.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153066072 T C 0 222 0 0.2156 0.2442 0.1729 0.4375 0.1014 0.2812 0.0608261 0.0295248 0.0134884 1 1888 15832 2310 3776 383 3213 117 4145 2 10364 119588 11494 8520 6582 65914 896 15818 0.0787465 0 . 0 . 218 54,48,44,51 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q52|72|SPRR2E|protein_coding|CODING|NM_001024209.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.0271276 1.36963e-05 0 0.410621 rs3737865 -0.693147 0.324969 218 P61T 72 Cca/Aca MODERATE 2 MISSENSE CODING SPRR2F T protein_coding NM_001014450.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153085029 G T 0 222 0 0.0477 0.1384 0.1023 0.3393 0.008 0.2137 0.0413073 0.0175358 0.00535133 1 502 8569 1651 2929 117 457 50 2863 2 10404 120838 11566 8570 6614 66582 904 16198 0.283744 0 . 0 . 246 58,49,58,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P61T|72|SPRR2F|protein_coding|CODING|NM_001014450.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.994227 0.950659 0 0.633427 rs74133286 -0.693147 0.511872 246 72 LOW 1 CODING SPRR2F C protein_coding NM_001014450.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153085232 A C 0 222 0 0.0855 0.1544 0.1066 0.3542 0.008 0.226 0.068347 0.0266923 0.00535133 1 750 9601 1766 3256 119 464 54 3192 2 9606 118436 11512 8554 6598 64770 898 16498 0.990796 0 . 0 . 74 8,32,4,28 SPLICE_SITE_REGION+INTRON(LOW||||72|SPRR2F|protein_coding|CODING|NM_001014450.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89049 rs72480208 -0.69312 0.0639398 74 73 194 MODIFIER 2 CODING SPRR2G A protein_coding NM_001014291.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153122171 G A 0 83 0 0.4682 0.5238 0.4957 0.6091 0.5537 0.5 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.961166 0 . 0 . 13 7,0,6,0 UTR_3_PRIME(MODIFIER||194||73|SPRR2G|protein_coding|CODING|NM_001014291.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.920266 rs386597598,rs509194 -0.616816 0.247382 13 73 55 MODIFIER 2 CODING SPRR2G A protein_coding NM_001014291.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153122310 G A 0 222 0 0.208 0.4265 0.4294 0.5149 0.5517 0.5 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.97922 0 . 0 . 89 36,6,34,7 UTR_3_PRIME(MODIFIER||55||73|SPRR2G|protein_coding|CODING|NM_001014291.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.301564 rs386597631,rs510277 -0.693145 0.678376 89 341 70 MODIFIER 7 CODING PGLYRP3 G protein_coding NM_052891.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153270362 C G 0 175 0 0.5658 0.5413 0.4841 0.7282 0.3598 0.5429 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,42,0 UTR_3_PRIME(MODIFIER||70||341|PGLYRP3|protein_coding|CODING|NM_052891.2|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2771110 -0.693146 0.370701 42 G126S 341 Ggc/Agc MODERATE 3 MISSENSE CODING PGLYRP3 T protein_coding NM_052891.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153277423 C T 0 228 0 0.385 0.4698 0.4553 0.5833 0.3996 0.5501 0.383568 0.384899 0.385581 2 3969 51100 5752 4574 2548 25192 405 8660 2 10390 120656 11542 8628 6606 66432 902 16156 0.988586 0 . 0 . 246 2,1,134,95 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Ggc/Agc|G126S|341|PGLYRP3|protein_coding|CODING|NM_052891.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.394624 rs843971 -0.693147 0.712486 246 G192V 373 gGg/gTg MODERATE 6 MISSENSE CODING PGLYRP4 A protein_coding NM_020393.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153314153 C A 0 228 0 0.7466 0.8444 0.866 0.9058 0.8767 0.865 0.769859 0.823851 0.851512 2 7977 102539 9305 7561 5888 57103 772 13933 2 10406 121398 11574 8650 6614 66736 908 16510 0 . 0 . 0 138 0,0,63,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G192V|373|PGLYRP4|protein_coding|CODING|NM_020393.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3006448,rs386578468 -0.693147 0.259713 138 F153 373 ttT/ttC LOW 5 SILENT CODING PGLYRP4 G protein_coding NM_020393.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153315579 A G 0 228 0 0.9864 0.9271 0.9135 0.9058 0.9165 0.8896 0.975488 0.933415 0.91186 2 10169 109949 9801 7565 6012 60879 826 14697 2 10404 121366 11564 8650 6614 66720 908 16506 0 . 0 . 0 317 0,0,149,151 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F153|373|PGLYRP4|protein_coding|CODING|NM_020393.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3014863 -0.693147 0.663145 317 I13L 373 Atc/Ctc MODERATE 2 MISSENSE CODING PGLYRP4 G protein_coding NM_020393.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153320372 T G 0 228 0 0.7027 0.7941 0.8588 0.7411 0.8728 0.8456 0.731502 0.808242 0.847558 2 7518 99312 9016 6178 5749 56384 746 13721 2 10312 120546 11430 8554 6574 66354 900 16422 0 . 0 . 0 75 0,0,38,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I13L|373|PGLYRP4|protein_coding|CODING|NM_020393.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3006458 -0.693147 0.632329 75 373 789 MODIFIER 1 CODING PGLYRP4 G protein_coding NM_020393.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153321197 T G 0 32.3 0 0.7451 0.8433 0.8646 0.9058 0.8757 0.863 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||789||373|PGLYRP4|protein_coding|CODING|NM_020393.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3006461 -0.453602 0.06 2 G6V 112 gGc/gTc MODERATE 2 MISSENSE CODING S100A7L2 A protein_coding NM_001045479.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153410822 C A 0 228 0 0.5 0.6142 0.7061 0.6042 0.7376 0.5869 0.533137 0.667384 0.736163 2 5446 83822 8648 4876 5305 49012 629 9906 2 10360 121082 11538 8634 6610 66574 902 16464 0 . 0 . 0 65 0,0,14,48 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gGc/gTc|G6V|112|S100A7L2|protein_coding|CODING|NM_001045479.1|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888561 -0.693147 0.175506 65 E28D 101 gaG/gaC MODERATE 2 MISSENSE CODING S100A7 G protein_coding NM_002963.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153431406 C G 0 228 0 0.9879 0.9834 0.9856 1 0.9573 0.9857 0.985247 0.957942 0.943954 2 10210 116656 11339 8654 6383 63010 870 16190 2 10402 121406 11578 8654 6614 66738 908 16512 0 . 0 . 0 177 0,0,79,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E28D|101|S100A7|protein_coding|CODING|NM_002963.3|2|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.991586 0 . rs3014837 -0.693147 0.168479 177 104 105 MODIFIER 4 CODING S100A14 T protein_coding NM_020672.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153587256 A T 0 118 0 0.0772 0.4227 0.5994 0.6736 0.4612 0.4663 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.282063 0 . 0 . 16 8,1,5,1 UTR_3_PRIME(MODIFIER||105||104|S100A14|protein_coding|CODING|NM_020672.2|4|T),DOWNSTREAM(MODIFIER||4020||98|S100A13|protein_coding|CODING|NM_001024210.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.810528 rs11548102 -0.616816 0.810983 16 104 53 MODIFIER 4 CODING S100A14 T protein_coding NM_020672.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153587308 C T 0 222 0 0.77 0.6621 0.7032 0.6776 0.5149 0.6227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.863215 0 . 0 . 41 18,2,9,5 UTR_3_PRIME(MODIFIER||53||104|S100A14|protein_coding|CODING|NM_020672.2|4|T),DOWNSTREAM(MODIFIER||3968||98|S100A13|protein_coding|CODING|NM_001024210.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.597562 rs11548104 -0.686358 0.00864269 41 104 6 MODIFIER 2 CODING S100A14 T protein_coding NM_020672.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153588340 C T 0 222 0 0.23 0.3377 0.2983 0.3224 0.4851 0.3753 0.281434 0.405659 0.469302 1 2807 49341 2659 2792 3262 31438 367 6016 2 10344 120494 11518 8614 6546 66092 896 16484 0.755418 0 . 0 . 143 27,37,25,40 UTR_5_PRIME(MODIFIER||6||104|S100A14|protein_coding|CODING|NM_020672.2|2|T),DOWNSTREAM(MODIFIER||2936||98|S100A13|protein_coding|CODING|NM_001024210.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.793216 rs11548103 -0.693147 0.144454 143 136 281 MODIFIER 4 CODING SNAPIN T protein_coding NM_012437.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153634058 G T 0 39.3 0 0.7753 0.6755 0.7104 0.6954 0.5199 0.6554 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||281||136|SNAPIN|protein_coding|CODING|NM_012437.5|4|T),DOWNSTREAM(MODIFIER||206||390|ILF2|protein_coding|CODING|NM_004515.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7345 -0.453602 0.44 2 1042 270 MODIFIER 1 CODING INTS3 G protein_coding NM_023015.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153700841 A G 0 116 0 0.944 0.9842 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_5_PRIME(MODIFIER||270||1042|INTS3|protein_coding|CODING|NM_023015.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4411157 -0.616816 0.0846985 6 593 3241 MODIFIER 11 CODING GATAD2B G protein_coding NM_020699.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153779412 A G 0 72 0 0.2557 0.3317 0.4409 0.1607 0.5159 0.3436 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.298022 0 . 0 . 24 0,17,0,7 UTR_3_PRIME(MODIFIER||3241||593|GATAD2B|protein_coding|CODING|NM_020699.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.833587 rs1127091 -0.636426 0.207027 24 593 2355 MODIFIER 11 CODING GATAD2B T protein_coding NM_020699.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153780298 C T 0 222 0 0.2557 0.2961 0.3213 0.0694 0.5149 0.3415 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.95952 0 . 0 . 142 49,32,23,25 UTR_3_PRIME(MODIFIER||2355||593|GATAD2B|protein_coding|CODING|NM_020699.2|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.9387 rs9426938 -0.693147 0.0240702 142 593 1273 MODIFIER 11 CODING GATAD2B T protein_coding NM_020699.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153781380 C T 0 54 0 0 0.0029952 0 0.0149 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 2,1,2,1 UTR_3_PRIME(MODIFIER||1273||593|GATAD2B|protein_coding|CODING|NM_020699.2|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.861511 rs376180866 -0.511536 0.740702 6 593 765 MODIFIER 11 CODING GATAD2B A protein_coding NM_020699.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153781888 G A 0 50 0 0.2716 0.3363 0.4424 0.1607 0.5169 0.3436 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.00775 0 . 0 . 10 5,1,4,0 UTR_3_PRIME(MODIFIER||765||593|GATAD2B|protein_coding|CODING|NM_020699.2|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.895781 rs6700115 -0.556411 0.658104 10 A796 1496 gcC/gcG LOW 16 SILENT CODING DENND4B C protein_coding NM_014856.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153909069 G C 0 222 0 0.0991 0.2628 0.4063 0.2847 0.2913 0.3303 0.133001 0.239347 0.292406 1 1293 36588 4707 2255 2169 20612 336 5216 2 7954 103344 9696 7256 5612 57540 812 14474 0.962151 0 . 0 . 64 14,13,13,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A796|1496|DENND4B|protein_coding|CODING|NM_014856.2|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.499352 rs1043608 -0.693054 0.550435 64 1496 LOW 8 CODING DENND4B G protein_coding NM_014856.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153913699 T G 0 222 0 0.115 0.2674 0.4092 0.2837 0.2922 0.3303 0.138375 0.240626 0.290549 1 1400 38058 5029 2337 2174 21401 339 5378 2 9384 118642 11292 8570 6308 65946 878 16264 0.502212 0 . 0 . 120 39,20,27,23 SPLICE_SITE_REGION+INTRON(LOW||||1496|DENND4B|protein_coding|CODING|NM_014856.2|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.757702 rs1110165 -0.693147 0.2648 120 1496 LOW 7 CODING DENND4B G protein_coding NM_014856.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153913770 A G 0 222 0 0.7443 0.7051 0.6816 0.9315 0.4791 0.6677 0.713527 0.551211 0.471364 1 6935 69745 8234 8092 3592 31960 549 10383 2 9772 120242 11508 8616 6524 66464 888 16470 0.968286 0 . 0 . 131 32,32,30,24 SPLICE_SITE_REGION+INTRON(LOW||||1496|DENND4B|protein_coding|CODING|NM_014856.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993279 rs2252508 -0.693147 0.0114348 131 693 299 MODIFIER 14 CODING CRTC2 A protein_coding NM_181715.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153920286 G A 0 222 0 0.0991 0.2628 0.4063 0.2847 0.2913 0.3303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.572685 0 . 0 . 79 33,3,23,2 UTR_3_PRIME(MODIFIER||299||693|CRTC2|protein_coding|CODING|NM_181715.2|14|A),UPSTREAM(MODIFIER||1132||1496|DENND4B|protein_coding|CODING|NM_014856.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994745 rs8450 -0.692914 0.355454 79 693 21 MODIFIER 14 CODING CRTC2 G protein_coding NM_181715.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153920564 A G 0 198 0 0.0991 0.2626 0.4063 0.2847 0.2903 0.3303 0.131017 0.235312 0.288721 1 1401 37933 4969 2326 2223 21279 347 5388 2 9944 117784 11140 8394 6362 64818 880 16246 0.888719 0 . 0 . 56 23,13,11,5 UTR_3_PRIME(MODIFIER||21||693|CRTC2|protein_coding|CODING|NM_181715.2|14|G),UPSTREAM(MODIFIER||1410||1496|DENND4B|protein_coding|CODING|NM_014856.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.857197 rs10559 -0.689466 0.0396008 56 M147V 693 Atg/Gtg MODERATE 5 MISSENSE CODING CRTC2 C protein_coding NM_181715.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153926078 T C 0 222 0 0.0991 0.263 0.4078 0.2847 0.2913 0.3303 0.138448 0.242042 0.295116 1 1402 38098 5034 2335 2232 21410 351 5334 2 9924 117892 11282 8516 6408 65004 882 15876 0.305336 0 . 0 . 108 22,32,13,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M147V|693|CRTC2|protein_coding|CODING|NM_181715.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.301814 rs11264680 -0.693145 0.701545 108 324 362 MODIFIER 4 CODING SLC39A1 C protein_coding NM_001271957.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153932212 G C 0 15.4 0 0.2133 0.2915 0.4121 0.2847 0.2843 0.3262 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.28717 0 . 0 . 6 0,3,0,3 UTR_3_PRIME(MODIFIER||362||324|SLC39A1|protein_coding|CODING|NM_001271957.1|4|C),UPSTREAM(MODIFIER||1080||693|CRTC2|protein_coding|CODING|NM_181715.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 0 . 0.861511 rs386483310,rs6724 -0.511536 0.28399 6 P95S 395 Ccc/Tcc MODERATE 3 MISSENSE CODING CREB3L4 T protein_coding NM_001255978.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153941514 C T 0 222 0 0.0832 0.257 0.4107 0.2837 0.2853 0.3262 0.123468 0.229125 0.283256 1 1273 37334 5101 2310 2225 20882 345 5198 2 10402 121356 11568 8644 6610 66720 908 16504 0.577792 0 . 0 . 76 14,19,13,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P95S|395|CREB3L4|protein_coding|CODING|NM_001255978.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836009 rs11264743,rs386517960 -0.693145 0.132202 76 V1491I 1888 Gtt/Att MODERATE 32 MISSENSE CODING NUP210L T protein_coding NM_207308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 153994647 C T 0 222 0 0.1407 0.2702 0.4035 0.2817 0.2793 0.3292 0.161171 0.237045 0.273912 1 1661 37197 5089 2283 2237 20285 329 5313 2 9808 120756 11566 8620 6614 66736 900 16512 0.452421 0 . 0 . 136 44,20,34,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1491I|1888|NUP210L|protein_coding|CODING|NM_207308.2|32|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.787359 rs11264875 -0.693147 0.00394315 136 N304 1888 aaC/aaT LOW 7 SILENT CODING NUP210L A protein_coding NM_207308.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154108387 G A 0 228 0 0.8858 0.969 0.9942 1 1 1 0.914324 0.972815 0.999635 2 8839 119740 11544 8626 6614 66709 897 16511 2 9802 120770 11576 8626 6614 66740 900 16512 0 . 0 . 0 83 0,0,28,44 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N304|1888|NUP210L|protein_coding|CODING|NM_207308.2|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3001361 -0.693147 0.0388986 83 1087 344 MODIFIER 27 CODING UBAP2L T protein_coding NM_014847.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154243115 C T 0 34.4 0 0.6619 0.4892 0.3545 0.4752 0.5497 0.3037 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 1,1,2,1 UTR_3_PRIME(MODIFIER||344||1087|UBAP2L|protein_coding|CODING|NM_014847.3|27|T),UPSTREAM(MODIFIER||1924||279|HAX1|protein_coding|CODING|NM_006118.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs1044013 -0.511536 0.892765 5 279 58 MODIFIER 1 CODING HAX1 G protein_coding NM_006118.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154245142 T G 0 222 0 0.0159 0.2077 0.1599 0.4226 0.328 0.1554 0.0563584 0.212659 0.280641 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.584591 0 . 0 . 40 8,12,10,7 START_GAINED(LOW||||279|HAX1|protein_coding|CODING|NM_006118.3|1|G),UTR_5_PRIME(MODIFIER||58||279|HAX1|protein_coding|CODING|NM_006118.3|1|G),DOWNSTREAM(MODIFIER||1813||1087|UBAP2L|protein_coding|CODING|NM_014847.3||G) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.988457 rs11265425 -0.690438 0.0620431 40 R15Q 301 cGg/cAg MODERATE 1 MISSENSE CODING AQP10 A protein_coding NM_080429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154293675 G A 0 222 0 0.2685 0.2732 0.2349 0.2093 0.3181 0.3262 0.264185 0.284715 0.295233 1 2760 35398 2465 1943 2463 19772 281 5714 2 10384 121176 11568 8632 6600 66618 906 16468 0.906972 0 . 0 . 126 28,30,28,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R15Q|301|AQP10|protein_coding|CODING|NM_080429.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.503241 rs6668968 -0.693147 0.0305171 126 H123Y 301 Cat/Tat MODERATE 3 MISSENSE CODING AQP10 T protein_coding NM_080429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154295592 C T 0 222 0 0.3434 0.2933 0.2363 0.2103 0.3181 0.3262 0.308216 0.299862 0.295581 1 3309 36074 2503 1962 2467 19801 283 5749 2 10406 121394 11578 8650 6608 66734 908 16510 0.994168 0 . 0 . 115 30,38,22,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H123Y|301|AQP10|protein_coding|CODING|NM_080429.2|3|T),UPSTREAM(MODIFIER||4684||1223|ATP8B2|protein_coding|CODING|NM_020452.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992334 rs6685323 -0.693145 0.165018 115 N153 1223 aaT/aaC LOW 6 SILENT CODING ATP8B2 C protein_coding NM_020452.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154303976 T C 0 222 0 0.3396 0.2913 0.2363 0.2103 0.3181 0.3211 0.308897 0.299862 0.295233 1 3298 36003 2500 1965 2471 19776 284 5709 2 10404 121378 11568 8640 6614 66732 908 16512 0.649429 0 . 0 . 126 39,19,33,18 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N153|1223|ATP8B2|protein_coding|CODING|NM_020452.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996392 rs6702754 -0.693147 0.000149536 126 Y641 1223 taC/taT LOW 18 SILENT CODING ATP8B2 T protein_coding NM_020452.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154316434 C T 0 222 0 0.2549 0.1963 0.1657 0.125 0.2525 0.1544 0.224013 0.239582 0.247558 1 2365 25428 1206 1126 2287 15814 199 2431 2 10348 120830 11550 8638 6534 66432 904 16424 0.777346 0 . 0 COSM1334422 56 11,22,12,9 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y641|1223|ATP8B2|protein_coding|CODING|NM_020452.3|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.647987 rs2274988,rs386431994 -0.692352 0.547388 56 S759 1223 tcC/tcT LOW 21 SILENT CODING ATP8B2 T protein_coding NM_020452.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154317153 C T 0 222 0 0.1203 0.4199 0.4899 0.624 0.4523 0.5317 0.179074 0.373135 0.472558 1 1697 56340 5804 5222 2746 32285 429 8157 2 10398 121304 11574 8622 6608 66702 908 16492 0.625274 0 . 0 . 58 12,11,15,15 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S759|1223|ATP8B2|protein_coding|CODING|NM_020452.3|21|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.825582 rs1194587,rs386522144 -0.693097 0.0887945 58 T1107 1223 acA/acG LOW 27 SILENT CODING ATP8B2 G protein_coding NM_020452.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154320942 A G 0 222 0 0.2867 0.1983 0.1499 0.126 0.2366 0.1483 0.24966 0.234968 0.227442 1 2640 23891 963 1123 2244 14393 180 2348 2 10364 120978 11532 8624 6562 66514 902 16480 0.949871 0 . 0 . 60 13,15,9,16 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1107|1223|ATP8B2|protein_coding|CODING|NM_020452.3|27|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.586274 rs2297607 -0.692914 0.0393148 60 1223 69 MODIFIER 28 CODING ATP8B2 T protein_coding NM_020452.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154321663 C T 0 165 0 0.1778 0.13 0.0821 0.0933 0.1372 0.1299 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.831101 0 . 0 . 62 3,36,2,20 UTR_3_PRIME(MODIFIER||69||1223|ATP8B2|protein_coding|CODING|NM_020452.3|28|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.864005 rs12729561 -0.692562 0.0539028 62 1223 208 MODIFIER 28 CODING ATP8B2 T protein_coding NM_020452.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154321802 C T 0 194 0 0.2352 0.1512 0.1081 0.0923 0.1471 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.366604 0 . 0 . 36 10,5,17,3 UTR_3_PRIME(MODIFIER||208||1223|ATP8B2|protein_coding|CODING|NM_020452.3|28|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.889758 rs3811452 -0.692067 0.428398 36 468 208 MODIFIER 1 CODING IL6R A protein_coding NM_000565.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154377898 G A 0 46.6 0 0.3245 0.3804 0.4697 0.4226 0.3966 0.3323 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||208||468|IL6R|protein_coding|CODING|NM_000565.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4845617 -0.453602 0.06 3 495 4407 MODIFIER 6 CODING SHE T protein_coding NM_001010846.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154452218 C T 0 39.3 0 0.6346 0.9 0.9784 1 0.997 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||4407||495|SHE|protein_coding|CODING|NM_001010846.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4393148 -0.453602 0.38 2 495 1951 MODIFIER 6 CODING SHE G protein_coding NM_001010846.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154454674 C G 0 6.3 0 0.6422 0.902 0.9784 1 0.997 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1951||495|SHE|protein_coding|CODING|NM_001010846.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11265623 -0.379885 0 1 R124 495 cgG/cgC LOW 1 SILENT CODING SHE G protein_coding NM_001010846.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154474131 C G 0 228 0 0.5635 0.777 0.879 0.9117 0.8241 0.8057 0.621253 0.760458 0.831744 2 6161 99118 10454 7852 5367 54713 761 13810 2 10126 119714 11462 8602 6408 65746 892 16478 0 . 0 . 0 62 0,0,15,41 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R124|495|SHE|protein_coding|CODING|NM_001010846.2|1|G),UPSTREAM(MODIFIER||564||366|TDRD10|protein_coding|CODING|NM_001098475.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4845635 -0.693147 0.0467928 62 A212 366 gcT/gcC LOW 9 SILENT CODING TDRD10 C protein_coding NM_001098475.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154516571 T C 0 228 0 0.6362 0.9004 0.9784 1 0.997 1 0.720608 0.904813 0.999186 2 7332 118103 11418 8654 6613 66692 893 16501 2 10402 121406 11576 8654 6614 66740 908 16512 0 . 0 . 0 97 0,0,15,77 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A212|366|TDRD10|protein_coding|CODING|NM_001098475.1|9|C),DOWNSTREAM(MODIFIER||4480||422|UBE2Q1|protein_coding|CODING|NM_017582.6||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386604306,rs6678164 -0.693147 0.609873 97 V215I 366 Gtc/Atc MODERATE 9 MISSENSE CODING TDRD10 A protein_coding NM_001098475.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154516578 G A 0 222 0 0.1384 0.1811 0.1455 0.1706 0.2256 0.229 0.137313 0.176841 0.197093 1 1461 24806 1919 1190 2165 13982 201 3888 2 10394 121268 11556 8638 6598 66668 908 16506 0.807289 0 . 0 . 83 10,30,4,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V215I|366|TDRD10|protein_coding|CODING|NM_001098475.1|9|A),DOWNSTREAM(MODIFIER||4473||422|UBE2Q1|protein_coding|CODING|NM_017582.6||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.398353 rs3811448,rs386586944 -0.693145 0.659143 83 422 1330 MODIFIER 13 CODING UBE2Q1 A protein_coding NM_017582.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154521584 T A 0 121 0 0.1589 0.1885 0.147 0.1776 0.2266 0.2301 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.32741 0 . 0 . 18 0,7,0,11 UTR_3_PRIME(MODIFIER||1330||422|UBE2Q1|protein_coding|CODING|NM_017582.6|13|A),DOWNSTREAM(MODIFIER||961||366|TDRD10|protein_coding|CODING|NM_001098475.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.817948 rs41269915 -0.676189 0.204138 18 422 666 MODIFIER 13 CODING UBE2Q1 G protein_coding NM_017582.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154522248 A G 0 228 0 0.1301 0.6438 0.7795 0.9018 0.8141 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 122 0,0,57,53 UTR_3_PRIME(MODIFIER||666||422|UBE2Q1|protein_coding|CODING|NM_017582.6|13|G),DOWNSTREAM(MODIFIER||1625||366|TDRD10|protein_coding|CODING|NM_001098475.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11265634 -0.693147 0.814444 122 502 113 MODIFIER 6 CODING CHRNB2 G protein_coding NM_000748.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154548521 C G 0 148 0 0.0469 0.1176 0.0663 0.2262 0.1014 0.1544 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999026 0 . 0 . 18 3,6,2,7 UTR_3_PRIME(MODIFIER||113||502|CHRNB2|protein_coding|CODING|NM_000748.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0299337 rs2072659 -0.662043 0.536808 18 502 313 MODIFIER 6 CODING CHRNB2 C protein_coding NM_000748.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154548721 T C 0 70 0 0.534 0.6927 0.7594 0.6964 0.7435 0.8037 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||313||502|CHRNB2|protein_coding|CODING|NM_000748.2|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2072660 -0.453602 0.84 3 1226 1790 MODIFIER 15 CODING ADAR C protein_coding NM_001111.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154555492 T C 0 83 0 0.2791 0.598 0.755 0.6687 0.672 0.7689 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,0 UTR_3_PRIME(MODIFIER||1790||1226|ADAR|protein_coding|CODING|NM_001111.4|15|C),DOWNSTREAM(MODIFIER||3139||502|CHRNB2|protein_coding|CODING|NM_000748.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1127326 -0.453602 0.02 4 1226 1549 MODIFIER 15 CODING ADAR T protein_coding NM_001111.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154555733 A T 0 50 0 0.0113 0.1947 0.3343 0.2907 0.2873 0.1493 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99361 0 . 0 . 18 5,8,2,2 UTR_3_PRIME(MODIFIER||1549||1226|ADAR|protein_coding|CODING|NM_001111.4|15|T),DOWNSTREAM(MODIFIER||3380||502|CHRNB2|protein_coding|CODING|NM_000748.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.66348 rs9616 -0.556411 0.168287 18 1226 857 MODIFIER 15 CODING ADAR A protein_coding NM_001111.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154556425 G A 0 9.7 0 0.2088 0.395 0.4784 0.5159 0.4712 0.3845 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||857||1226|ADAR|protein_coding|CODING|NM_001111.4|15|A),DOWNSTREAM(MODIFIER||4072||502|CHRNB2|protein_coding|CODING|NM_000748.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1127313,rs386517983 -0.379885 0 1 1226 LOW 14 CODING ADAR T protein_coding NM_001111.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154557685 C T 0 228 0 0.1997 0.3888 0.4769 0.499 0.4712 0.3834 0.251929 0.403199 0.480698 2 2484 56195 6110 4639 2972 32790 375 6825 2 10406 121372 11574 8632 6610 66730 908 16512 0.474227 0 . 0 . 107 1,1,57,40 SPLICE_SITE_REGION+INTRON(LOW||||1226|ADAR|protein_coding|CODING|NM_001111.4|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.309278 rs9427094 -0.693147 0.382437 107 K384R 1226 aAa/aGa MODERATE 2 MISSENSE CODING ADAR C protein_coding NM_001111.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154573967 T C 0 228 0 0.3691 0.6226 0.7579 0.6687 0.673 0.7699 0.428507 0.607873 0.699767 2 4309 84446 9615 6194 4385 46860 594 12489 2 10406 121398 11578 8644 6614 66736 908 16512 0.522244 2 benign 0 . 92 1,2,38,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K384R|1226|ADAR|protein_coding|CODING|NM_001111.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.515331 rs2229857,rs386561757 -0.693147 0.308389 92 R100G 1226 Aga/Gga MODERATE 2 MISSENSE CODING ADAR C protein_coding NM_001111.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154574820 T C 0 228 0 0.9856 0.9962 1 1 1 1 0.987517 0.995694 0.999884 2 10265 120257 11571 8650 6614 66414 897 15846 2 10400 120406 11578 8650 6614 66416 900 15848 0 . 0 . 0 96 0,0,65,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R100G|1226|ADAR|protein_coding|CODING|NM_001111.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1466731,rs386454752 -0.693147 0.485536 96 R26 1226 agG/agA LOW 2 SILENT CODING ADAR T protein_coding NM_001111.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154575040 C T 0 228 0 0.9887 0.997 1 1 1 1 0.991602 0.997155 1 2 10228 121022 11573 8652 6614 66541 905 16509 2 10322 121124 11578 8652 6614 66542 906 16510 0 . 0 . 0 65 0,0,23,37 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R26|1226|ADAR|protein_coding|CODING|NM_001111.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1802645 -0.693147 0.0504155 65 746 2202 MODIFIER 9 CODING KCNN3 A protein_coding NM_001204087.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154678250 G A 0 54 0 0.9939 0.9984 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2202||746|KCNN3|protein_coding|CODING|NM_001204087.1|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1506984 -0.511536 0.0860477 3 746 1466 MODIFIER 9 CODING KCNN3 T protein_coding NM_001204087.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154678986 C T 0 46.3 0 0.8313 0.9121 0.9179 0.9812 0.9006 0.9581 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1466||746|KCNN3|protein_coding|CODING|NM_001204087.1|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7543897 -0.453602 0.56 2 746 885 MODIFIER 9 CODING KCNN3 T protein_coding NM_001204087.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154679567 C T 0 9.7 0 0.7277 0.8838 0.9107 0.9812 0.9006 0.9581 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||885||746|KCNN3|protein_coding|CODING|NM_001204087.1|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1995662 -0.379885 0 1 N349 746 aaT/aaC LOW 3 SILENT CODING KCNN3 G protein_coding NM_001204087.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154744852 A G 0 228 0 0.593 0.7792 0.8401 0.9831 0.7445 0.8129 0.64049 0.705136 0.738256 2 6404 91742 10190 8510 4531 47750 688 13669 2 10288 120464 11502 8628 6528 66158 896 16464 0 . 0 . 0 73 0,0,36,32 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N349|746|KCNN3|protein_coding|CODING|NM_001204087.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1131820 -0.693147 0.0688995 73 192 107 MODIFIER 1 CODING PMVK G protein_coding NM_006556.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154909268 A G 0 228 0 0.6392 0.6538 0.6715 0.8929 0.4384 0.636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 0,0,12,73 UTR_5_PRIME(MODIFIER||107||192|PMVK|protein_coding|CODING|NM_006556.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1109815 -0.693147 0.000539354 90 731 186 MODIFIER 11 CODING PBXIP1 A protein_coding NM_020524.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154917314 G A 0 228 0 0.1437 0.5136 0.6326 0.8919 0.4324 0.6227 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,57,12 UTR_3_PRIME(MODIFIER||186||731|PBXIP1|protein_coding|CODING|NM_020524.2|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs705094 -0.693147 0.512352 75 G357D 731 gGt/gAt MODERATE 10 MISSENSE CODING PBXIP1 T protein_coding NM_020524.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154919080 C T 0 228 0 0.1498 0.516 0.6297 0.8958 0.4334 0.6237 0.202678 0.35622 0.434884 2 1958 59958 7824 7616 2887 28902 460 10311 2 10194 120460 11530 8602 6588 66240 898 16408 0 . 0 . 0 31 0,0,12,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G357D|731|PBXIP1|protein_coding|CODING|NM_020524.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2061690 -0.693079 0.157537 31 I164 573 atC/atT LOW 4 SILENT CODING ZBTB7B T protein_coding NM_001252406.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154987526 C T 0 222 0 0.4592 0.6178 0.6671 0.9058 0.4513 0.6718 0.470949 0.440258 0.424535 1 4766 63313 8052 7703 2947 28604 474 10767 2 10148 120032 11544 8592 6596 65756 898 16498 0.684536 0 . 0 COSM424019 91 29,16,27,15 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I164|573|ZBTB7B|protein_coding|CODING|NM_001252406.2|4|T),DOWNSTREAM(MODIFIER||3477||773|DCST2|protein_coding|CODING|NM_144622.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.724583 rs11264295 -0.693146 0.723945 91 P506 573 ccA/ccG LOW 5 SILENT CODING ZBTB7B G protein_coding NM_001252406.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154988957 A G 0 222 0 0.4811 0.6735 0.7478 0.9127 0.5785 0.7321 0.51271 0.54175 0.556628 1 5187 74922 8837 7762 3583 37297 565 11691 2 10340 120992 11548 8626 6532 66540 902 16504 0.0494885 0 . 0 . 108 20,23,18,40 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P506|573|ZBTB7B|protein_coding|CODING|NM_001252406.2|5|G),DOWNSTREAM(MODIFIER||2046||773|DCST2|protein_coding|CODING|NM_144622.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799144 rs2242195 -0.693147 0.339597 108 573 1136 MODIFIER 5 CODING ZBTB7B G protein_coding NM_001252406.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 154990297 C G 0 9.7 0 0.388 0.5721 0.6023 0.9087 0.4085 0.6207 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1136||573|ZBTB7B|protein_coding|CODING|NM_001252406.2|5|G),DOWNSTREAM(MODIFIER||706||773|DCST2|protein_coding|CODING|NM_144622.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2242194 -0.379885 0 1 G29 773 ggT/ggC LOW 1 SILENT CODING DCST2 G protein_coding NM_144622.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155006091 A G 0 222 0 0.5416 0.5988 0.6052 0.881 0.3608 0.6258 0.531548 0.410503 0.348488 1 5512 56698 7440 7438 2704 23469 417 9718 2 10380 121120 11552 8642 6604 66530 904 16508 0.264151 0 . 0 . 68 10,25,11,20 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G29|773|DCST2|protein_coding|CODING|NM_144622.2|1|G),UPSTREAM(MODIFIER||191||706|DCST1|protein_coding|CODING|NM_152494.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987186 rs10908453 -0.69311 0.514293 68 L50 706 ctC/ctT LOW 3 SILENT CODING DCST1 T protein_coding NM_152494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155006999 C T 0 222 0 0.4266 0.5657 0.5922 0.8819 0.3579 0.6227 0.430549 0.373597 0.344419 1 4356 55170 7354 7442 2701 23270 411 9636 2 10300 121206 11576 8640 6612 66660 906 16512 0.805876 0 . 0 . 75 16,22,16,19 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L50|706|DCST1|protein_coding|CODING|NM_152494.3|3|T),UPSTREAM(MODIFIER||742||773|DCST2|protein_coding|CODING|NM_144622.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.956531 rs6680600 -0.693136 0.0607997 75 R369G 706 Cgg/Ggg MODERATE 10 MISSENSE CODING DCST1 G protein_coding NM_152494.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155015918 C G 0 222 0 0 0.0047923 0 0.0089 0 0.0153 0.000226963 7.6899e-05 0 1 1 319 1 82 1 15 1 218 2 10154 118704 11530 8608 6434 65568 872 15538 0.431349 0 . 0 . 50 5,16,7,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Ggg|R369G|706|DCST1|protein_coding|CODING|NM_152494.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.896945 rs141437613 -0.692831 0.419039 50 M512L 706 Atg/Ctg MODERATE 14 MISSENSE CODING DCST1 C protein_coding NM_152494.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155019710 A C 0 222 0 0.3858 0.5545 0.5865 0.8849 0.3569 0.6227 0.40808 0.367676 0.346977 1 4086 54898 7331 7508 2707 23253 401 9612 2 10400 121358 11572 8642 6612 66714 906 16512 0.516839 0 . 0 COSM1559945 237 59,52,61,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ctg|M512L|706|DCST1|protein_coding|CODING|NM_152494.3|14|C),UPSTREAM(MODIFIER||4038||863|ADAM15|protein_coding|CODING|NM_207197.2||C),INTRAGENIC(MODIFIER|||||LOC100505666||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999897 rs11264300 -0.693147 0.023567 237 K191T 863 aAg/aCg MODERATE 6 MISSENSE CODING ADAM15 C protein_coding NM_207197.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155026942 A C 0 222 0 0.8676 0.902 0.9308 0.9901 0.8439 0.8967 0.897413 0.87229 0.859419 1 9284 107144 10813 8576 5856 57393 775 14447 2 10324 120648 11576 8646 6614 66308 904 16276 0.727774 0 . 0 . 102 15,27,15,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K191T|863|ADAM15|protein_coding|CODING|NM_207197.2|6|C),DOWNSTREAM(MODIFIER||3536||706|DCST1|protein_coding|CODING|NM_152494.3||C),INTRAGENIC(MODIFIER|||||LOC100505666||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998347 rs6427128 -0.693147 0.371446 102 K759 863 aaG/aaA LOW 19 SILENT CODING ADAM15 A protein_coding NM_207197.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155033308 G A 0 222 0 0.0045 0.0751 0.0951 0.0089 0.1819 0.1145 0.0320018 0.122789 0.169302 1 255 15616 904 76 914 11364 143 1960 2 10324 120992 11552 8618 6600 66486 902 16510 0.778155 0 . 0 . 75 18,22,10,22 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K759|863|ADAM15|protein_coding|CODING|NM_207197.2|19|A),UPSTREAM(MODIFIER||2905||207|EFNA4|protein_coding|CODING|NM_182689.1||A),INTRAGENIC(MODIFIER|||||LOC100505666||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.543124 rs11589479 -0.69312 0.179538 75 238 832 MODIFIER 5 CODING EFNA3 G protein_coding NM_004952.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155059851 A G 0 222 0 0.2943 0.5571 0.6441 0.9167 0.5189 0.5194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8585 0 . 0 . 139 50,25,27,20 UTR_3_PRIME(MODIFIER||832||238|EFNA3|protein_coding|CODING|NM_004952.4|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0850595 rs2306124 -0.693147 0.0238712 139 D159V 205 gAc/gTc MODERATE 4 MISSENSE CODING EFNA1 T protein_coding NM_004428.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155106227 A T 0 222 0 0.152 0.3199 0.3141 0.1964 0.5209 0.4714 0.173854 0.408504 0.528721 1 1757 54430 3658 1695 3388 35737 428 7767 2 10404 121364 11572 8642 6612 66716 908 16510 0.341433 0 . 0 . 114 28,24,20,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D159V|205|EFNA1|protein_coding|CODING|NM_004428.2|4|T),UPSTREAM(MODIFIER||2061||221|SLC50A1|protein_coding|CODING|NM_018845.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7395 rs4745 -0.693147 0.0305523 114 205 7 MODIFIER 5 CODING EFNA1 G protein_coding NM_004428.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155106550 A G 0 222 0 0.2352 0.4842 0.5937 0.8046 0.4105 0.4888 0.295052 0.365216 0.401163 1 2970 54944 7154 6811 3004 26651 409 7945 2 9524 114456 10950 8494 5980 62832 840 15836 0.99277 0 . 0 . 111 38,13,35,16 UTR_3_PRIME(MODIFIER||7||205|EFNA1|protein_coding|CODING|NM_004428.2|5|G),UPSTREAM(MODIFIER||1738||221|SLC50A1|protein_coding|CODING|NM_018845.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.860199 rs9297 -0.693147 0.388943 111 205 154 MODIFIER 5 CODING EFNA1 A protein_coding NM_004428.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155106697 G A 0 222 0 0.2519 0.4888 0.5965 0.8046 0.4105 0.4877 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.934774 0 . 0 . 125 42,25,34,19 UTR_3_PRIME(MODIFIER||154||205|EFNA1|protein_coding|CODING|NM_004428.2|5|A),UPSTREAM(MODIFIER||1591||221|SLC50A1|protein_coding|CODING|NM_018845.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.98624 rs12904 -0.693147 0.550477 125 T287 759 acG/acA LOW 5 SILENT CODING TRIM46 A protein_coding NM_025058.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155149718 G A 0 222 0 0.2194 0.4459 0.5706 0.7629 0.3579 0.4274 0.273491 0.327926 0.355814 1 2873 51156 7162 6638 3028 23700 373 7382 2 10396 121346 11568 8638 6614 66722 906 16502 0.978958 0 . 0 COSM1334562 95 13,35,7,35 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T287|759|TRIM46|protein_coding|CODING|NM_025058.4|5|A),UPSTREAM(MODIFIER||3914||162|KRTCAP2|protein_coding|CODING|NM_173852.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982848 rs3814316 -0.693146 0.960476 95 T31 484 acG/acA LOW 2 SILENT CODING MUC1 T protein_coding NM_001204286.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155162067 C T 0 222 0 0.6044 0.6288 0.7133 0.7619 0.5477 0.5481 0.644349 0.572351 0.535465 1 6689 70125 8263 6780 3687 35059 503 9144 2 10392 121120 11570 8650 6610 66486 902 16510 0.914216 0 . 0 . 148 30,21,32,40 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T31|484|MUC1|protein_coding|CODING|NM_001204286.1|2|T),DOWNSTREAM(MODIFIER||4620||759|TRIM46|protein_coding|CODING|NM_025058.4||T),DOWNSTREAM(MODIFIER||3312||956|THBS3|protein_coding|CODING|NM_007112.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.899826 rs4072037 -0.693147 0.0447334 148 T63S 466 Act/Tct MODERATE 1 MISSENSE CODING MTX1 T protein_coding NM_002455.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155178782 A T 0 160 0 0.6331 0.6667 0.7608 0.7738 0.6054 0.5982 0.676416 0.629415 0.605561 1 4247 57577 7387 5465 2395 28965 379 8739 2 6074 86084 8848 6712 3562 46422 562 13904 0.993326 0 . 0 . 17 3,4,5,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Tct|T63S|466|MTX1|protein_coding|CODING|NM_002455.4|1|T),UPSTREAM(MODIFIER||1010||956|THBS3|protein_coding|CODING|NM_007112.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97357 rs760077 -0.651104 0.672731 17 T1771A 2964 Aca/Gca MODERATE 5 MISSENSE CODING ASH1L C protein_coding NM_018489.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155408635 T C 0 228 0 0.8147 0.9487 0.9827 1 1 1 0.85951 0.952099 0.999535 2 8895 119817 11521 8654 6614 66727 901 16505 2 10404 121410 11578 8654 6614 66740 908 16512 0 . 0 . 0 116 0,0,67,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T1771A|2964|ASH1L|protein_coding|CODING|NM_018489.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4971053 -0.693147 0.00303433 116 2964 41006 MODIFIER 1 CODING ASH1L C protein_coding NM_018489.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155532316 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 344 11932 132 184 470 3374 146 7282 2 344 11932 132 184 470 3374 146 7282 0 . 0 . 0 33 0,0,19,9 UTR_5_PRIME(MODIFIER||41006||2964|ASH1L|protein_coding|CODING|NM_018489.2|1|C),INTRAGENIC(MODIFIER|||||ASH1L-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12403379 -0.693054 0.584471 33 2241 5569 MODIFIER 1 CODING GON4L G protein_coding NM_001282856.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155829140 C G 0 9.7 0 0.8283 0.9525 0.9841 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||5569||2241|GON4L|protein_coding|CODING|NM_001282856.1|1|G),UPSTREAM(MODIFIER||120||431|SYT11|protein_coding|CODING|NM_152280.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1625821 -0.379885 0 1 431 193 MODIFIER 1 CODING SYT11 A protein_coding NM_152280.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155829360 C A 0 167 0 0.7352 0.9273 0.9813 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,26,0 UTR_5_PRIME(MODIFIER||193||431|SYT11|protein_coding|CODING|NM_152280.4|1|A),UPSTREAM(MODIFIER||169||2241|GON4L|protein_coding|CODING|NM_001282856.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1749412 -0.692976 0.379545 26 Q48H 431 caG/caC MODERATE 2 MISSENSE CODING SYT11 C protein_coding NM_152280.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155837865 G C 0 228 0 0.8374 0.9547 0.9827 1 1 1 0.867226 0.95479 0.999651 2 9008 119929 11523 8654 6614 66726 901 16503 2 10390 121390 11576 8654 6614 66736 908 16512 0 . 0 . 0 51 0,0,36,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q48H|431|SYT11|protein_coding|CODING|NM_152280.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs822522 -0.693147 0.131944 51 H182 431 caT/caC LOW 2 SILENT CODING SYT11 C protein_coding NM_152280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155838267 T C 0 228 0 0.7466 0.9311 0.9856 1 1 1 0.78098 0.925342 0.999302 2 8084 118873 11471 8648 6614 66654 898 16504 2 10372 121308 11576 8650 6614 66676 908 16512 0 . 0 . 0 54 0,0,29,22 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H182|431|SYT11|protein_coding|CODING|NM_152280.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386497363,rs822521 -0.693147 0.588439 54 236 1195 MODIFIER 6 CODING RIT1 C protein_coding NM_001256821.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155868984 T C 0 228 0 0.4327 0.7798 0.9078 0.9405 0.8926 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 97 0,0,54,36 UTR_3_PRIME(MODIFIER||1195||236|RIT1|protein_coding|CODING|NM_001256821.1|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1055184 -0.693147 0.0322867 97 236 LOW 5 CODING RIT1 A protein_coding NM_001256821.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155870416 G A 0 228 0 0.4327 0.7798 0.9078 0.9405 0.8926 0.8763 0.545847 0.793403 0.920233 2 5543 106445 10949 8097 5854 61020 779 14203 2 10384 121348 11572 8650 6614 66712 908 16508 0 2|2 benign|benign 0 . 73 0,0,16,52 SPLICE_SITE_REGION+INTRON(LOW||||236|RIT1|protein_coding|CODING|NM_001256821.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1749409 -0.693147 0.0410342 73 E11Q 236 Gag/Cag MODERATE 2 MISSENSE CODING RIT1 G protein_coding NM_001256821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155880573 C G 0 228 0 0.4334 0.78 0.9078 0.9405 0.8926 0.8763 0.54857 0.795248 0.921628 2 5533 106437 10947 8091 5854 61030 779 14203 2 10328 121302 11570 8650 6614 66724 908 16508 0 . 0 . 0 57 0,0,22,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E11Q|236|RIT1|protein_coding|CODING|NM_001256821.1|2|G),DOWNSTREAM(MODIFIER||2261||614|KIAA0907|protein_coding|CODING|NM_014949.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs493446 -0.693147 0.0012029 57 614 13 MODIFIER 1 CODING KIAA0907 C protein_coding NM_014949.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155904177 T C 0 228 0 0.4334 0.7796 0.9063 0.9395 0.8926 0.8763 0.548819 0.793507 0.918897 2 5283 103970 10832 8006 5612 59338 757 14142 2 9838 118532 11472 8560 6352 64996 876 16438 0 . 0 . 0 156 0,0,68,70 UTR_5_PRIME(MODIFIER||13||614|KIAA0907|protein_coding|CODING|NM_014949.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275079 -0.693147 0.00385825 156 L329S 374 tTg/tCg MODERATE 1 MISSENSE CODING RXFP4 C protein_coding NM_181885.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 155912486 T C 0 228 0 0.7383 0.9241 0.9813 0.999 1 0.9796 0.815395 0.937096 0.999419 2 8336 118302 11477 8641 6614 66263 886 16085 2 10268 120748 11572 8644 6614 66294 900 16456 0 . 0 . 0 169 0,0,92,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L329S|374|RXFP4|protein_coding|CODING|NM_181885.2|1|C),DOWNSTREAM(MODIFIER||4144||986|ARHGEF2|protein_coding|CODING|NM_001162383.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2152051 -0.693147 0.0443902 169 H566 664 caC/caT LOW 10 SILENT CODING LMNA T protein_coding NM_170707.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156107534 C T 0 228 0 0.0658 0.2202 0.3012 0.2738 0.2247 0.3119 0.0881364 0.197012 0.253093 2 267 5377 142 228 10 2343 60 2327 2 2676 20252 388 740 40 8318 182 7908 0 255|2 other|benign 0 . 161 0,0,47,91 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H566|664|LMNA|protein_coding|CODING|NM_170707.3|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4641 -0.693147 0.0935118 161 100 198 MODIFIER 1 CODING BGLAP C protein_coding NM_199173.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156211825 T C 0 42.1 0 0.1944 0.2224 0.17 0.2778 0.2276 0.2352 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.895781 0 . 0 . 10 5,1,4,0 START_GAINED(LOW||||100|BGLAP|protein_coding|CODING|NM_199173.5|1|C),UTR_5_PRIME(MODIFIER||198||100|BGLAP|protein_coding|CODING|NM_199173.5|1|C),DOWNSTREAM(MODIFIER||1957||207|PMF1|protein_coding|CODING|NM_001199654.1||C),DOWNSTREAM(MODIFIER||1287||351|PAQR6|protein_coding|CODING|NM_024897.3||C),INTRON(MODIFIER||||220|PMF1-BGLAP|protein_coding|CODING|NM_001199661.1|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.895781 rs1800247 -0.556411 0.794163 10 351 395 MODIFIER 7 CODING PAQR6 A protein_coding NM_024897.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156213257 G A 0 166 0 0.8321 0.773 0.8228 0.75 0.6938 0.7628 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 255 other 0 . 8 0,0,5,2 UTR_3_PRIME(MODIFIER||395||351|PAQR6|protein_coding|CODING|NM_024897.3|7|A),DOWNSTREAM(MODIFIER||3389||207|PMF1|protein_coding|CODING|NM_001199654.1||A),DOWNSTREAM(MODIFIER||134||220|PMF1-BGLAP|protein_coding|CODING|NM_001199661.1||A),DOWNSTREAM(MODIFIER||134||100|BGLAP|protein_coding|CODING|NM_199173.5||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386611756,rs759330 -0.636426 0.920072 8 E263K 351 Gag/Aag MODERATE 7 MISSENSE CODING PAQR6 T protein_coding NM_024897.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156213921 C T 0 222 0 0.1604 0.2192 0.3026 0.256 0.1481 0.2751 0.15842 0.16231 0.164302 1 1620 22902 3738 2148 517 10727 156 3996 2 10378 119672 11552 8626 6610 66218 890 15398 0.907278 0 . 0 . 61 15,12,11,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E263K|351|PAQR6|protein_coding|CODING|NM_024897.3|7|T),DOWNSTREAM(MODIFIER||4053||207|PMF1|protein_coding|CODING|NM_001199654.1||T),DOWNSTREAM(MODIFIER||798||220|PMF1-BGLAP|protein_coding|CODING|NM_001199661.1||T),DOWNSTREAM(MODIFIER||798||100|BGLAP|protein_coding|CODING|NM_199173.5||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997609 rs7513351 -0.693021 0.665171 61 351 260 MODIFIER 3 CODING PAQR6 A protein_coding NM_024897.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156215899 G A 0 222 0 0.3858 0.4798 0.6369 0.4812 0.4592 0.5153 0.409215 0.473781 0.50686 1 4027 60818 7834 4226 2655 33098 442 8536 2 9832 118066 11398 8386 6462 64786 878 16324 0.998292 0 . 0 . 38 17,1,13,7 START_GAINED(LOW||||351|PAQR6|protein_coding|CODING|NM_024897.3|3|A),UTR_5_PRIME(MODIFIER||260||351|PAQR6|protein_coding|CODING|NM_024897.3|3|A),DOWNSTREAM(MODIFIER||2776||220|PMF1-BGLAP|protein_coding|CODING|NM_001199661.1||A),DOWNSTREAM(MODIFIER||2776||100|BGLAP|protein_coding|CODING|NM_199173.5||A),DOWNSTREAM(MODIFIER||3116||1016|SMG5|protein_coding|CODING|NM_015327.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976248 rs2075165 -0.692067 0.530999 38 1016 928 MODIFIER 22 CODING SMG5 G protein_coding NM_015327.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156219450 A G 0 222 0 0.3843 0.4828 0.6455 0.4821 0.4642 0.5204 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.682718 0 . 0 . 33 5,9,9,9 UTR_3_PRIME(MODIFIER||928||1016|SMG5|protein_coding|CODING|NM_015327.2|22|G),UPSTREAM(MODIFIER||1542||351|PAQR6|protein_coding|CODING|NM_024897.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.176873 rs1804999 -0.691153 0.390055 33 1016 322 MODIFIER 22 CODING SMG5 C protein_coding NM_015327.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156220056 T C 0 222 0 0.2905 0.4577 0.6412 0.4831 0.4642 0.5204 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.591871 0 . 0 . 77 30,4,24,10 UTR_3_PRIME(MODIFIER||322||1016|SMG5|protein_coding|CODING|NM_015327.2|22|C),UPSTREAM(MODIFIER||2148||351|PAQR6|protein_coding|CODING|NM_024897.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.960989 rs1043165 -0.693132 0.614838 77 394 102 MODIFIER 4 CODING TMEM79 C protein_coding NM_032323.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156261491 G C 0 222 0 0.1944 0.2486 0.3617 0.245 0.1948 0.3006 0 . 0 1 671 11636 1360 608 333 5489 95 3080 2 3224 43348 3052 2224 2404 22440 362 9642 0.999629 0 . 0 . 116 20,34,15,32 UTR_3_PRIME(MODIFIER||102||394|TMEM79|protein_coding|CODING|NM_032323.2|4|C),DOWNSTREAM(MODIFIER||987||406|GLMP|protein_coding|CODING|NM_144580.2||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.29974 rs3795728 -0.693147 0.185039 116 G315R 458 Ggg/Agg MODERATE 6 MISSENSE CODING RHBG A protein_coding NM_020407.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156351699 G A 0 228 0 0.5719 0.5447 0.6037 0.7014 0.4095 0.4438 0.526125 0.458533 0.425291 2 5377 57926 7230 6092 2815 28778 401 7233 2 9804 120688 11564 8616 6594 66700 900 16510 0 . 0 . 0 146 0,0,80,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G315R|458|RHBG|protein_coding|CODING|NM_020407.4|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748569 -0.693147 0.0208452 146 H428R 458 cAc/cGc MODERATE 10 MISSENSE CODING RHBG G protein_coding NM_020407.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156354367 A G 0 228 0 0.8956 0.733 0.6686 0.8978 0.5149 0.6135 0.84921 0.633355 0.528807 2 8362 71317 7926 7851 3515 34773 508 8382 2 9774 116496 11528 8612 6608 65602 860 13512 0 . 0 . 0 82 0,0,31,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H428R|458|RHBG|protein_coding|CODING|NM_020407.4|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6668857 -0.693147 0.531389 82 P252 521 ccA/ccG LOW 7 SILENT CODING MEF2D C protein_coding NM_005920.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156446903 T C 0 222 0 0.2368 0.5717 0.5951 0.756 0.672 0.7147 0.315252 0.541289 0.657093 1 3098 75315 6425 6240 3767 43961 557 11267 2 10398 121220 11552 8638 6548 66680 904 16500 0.112203 0 . 0 . 98 34,13,32,10 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P252|521|MEF2D|protein_coding|CODING|NM_005920.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.216056 rs2274317 -0.693146 0.111582 98 P101 521 ccC/ccT LOW 4 SILENT CODING MEF2D A protein_coding NM_005920.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156450719 G A 0 222 0 0.1808 0.2326 0.2983 0.245 0.2386 0.2372 0.211626 0.224504 0.2311 1 2146 30436 4320 2415 2274 14789 229 4263 2 10208 119960 11556 8592 6614 65860 894 16236 0.985153 0 . 0 . 149 41,24,44,23 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P101|521|MEF2D|protein_coding|CODING|NM_005920.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983152 rs1185700 -0.693147 0.137909 149 N94 521 aaC/aaT LOW 4 SILENT CODING MEF2D A protein_coding NM_005920.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156450740 G A 0 222 0 0.2368 0.5723 0.5951 0.756 0.673 0.7168 0.314344 0.541455 0.657864 1 3072 75076 6423 6221 3778 43751 559 11272 2 10248 120764 11562 8622 6614 66310 906 16502 0.233847 0 . 0 . 169 40,34,39,31 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N94|521|MEF2D|protein_coding|CODING|NM_005920.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.777493 rs1925950 -0.693147 0.0271922 169 1631 90 MODIFIER 38 CODING IQGAP3 G protein_coding NM_178229.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156496188 A G 0 228 0 0.7746 0.9383 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 105 0,0,76,20 UTR_3_PRIME(MODIFIER||90||1631|IQGAP3|protein_coding|CODING|NM_178229.4|38|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6427315 -0.693147 0.211816 105 L1444 1631 ctA/ctG LOW 34 SILENT CODING IQGAP3 C protein_coding NM_178229.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156499969 T C 0 222 0 0.8449 0.6056 0.4424 0.6022 0.33 0.6851 0.732183 0.46294 0.325 1 7296 48430 4394 4673 1539 20514 330 9684 2 9604 105846 9480 7840 4618 58346 764 15194 0.232741 0 . 0 COSM424125 117 30,29,19,28 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1444|1631|IQGAP3|protein_coding|CODING|NM_178229.4|34|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.377462 rs1171566 -0.693147 0.23058 117 R663C 1631 Cgt/Tgt MODERATE 17 MISSENSE CODING IQGAP3 A protein_coding NM_178229.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156518379 G A 0 222 0 0.2958 0.4071 0.3646 0.5724 0.2575 0.5716 0.298684 0.283408 0.275581 1 3109 40290 4441 4764 1656 18465 279 7576 2 10362 118414 11548 8612 6614 65862 882 14534 0.959459 0 . 0 . 64 13,16,13,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R663C|1631|IQGAP3|protein_coding|CODING|NM_178229.4|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.12161 rs744224 -0.693079 0.00799613 64 V410L 1631 Gtg/Ctg MODERATE 12 MISSENSE CODING IQGAP3 G protein_coding NM_178229.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156526387 C G 0 222 0 0.1407 0.3782 0.5519 0.4286 0.6272 0.2679 0.237177 0.50246 0.638372 1 2208 64927 6410 3903 4476 41847 503 5580 2 10332 120764 11536 8594 6596 66392 904 16410 0.34666 0 . 0 . 86 22,17,21,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V410L|1631|IQGAP3|protein_coding|CODING|NM_178229.4|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.136861 rs11264498 -0.693146 0.00497812 86 R391G 1631 Aga/Gga MODERATE 12 MISSENSE CODING IQGAP3 C protein_coding NM_178229.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156526444 T C 0 228 0 0.8548 0.9601 0.9885 1 1 1 0.875397 0.957558 0.999651 2 8903 118887 11512 8640 6598 66297 894 16043 2 10286 120350 11564 8640 6598 66314 900 16048 0 . 0 . 0 95 0,0,37,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R391G|1631|IQGAP3|protein_coding|CODING|NM_178229.4|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2488269 -0.693147 0.388207 95 Q249 1631 caA/caG LOW 8 SILENT CODING IQGAP3 C protein_coding NM_178229.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156532977 T C 0 228 0 0.854 0.9599 0.9885 1 1 1 0.87517 0.957481 0.999651 2 8994 119763 11526 8654 6614 66686 902 16387 2 10402 121246 11578 8654 6614 66698 908 16392 0 . 0 . 0 50 0,0,31,11 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q249|1631|IQGAP3|protein_coding|CODING|NM_178229.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1171547 -0.693146 0.0926898 50 P81 1631 ccC/ccG LOW 3 SILENT CODING IQGAP3 C protein_coding NM_178229.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156536221 G C 0 228 0 0.854 0.9599 0.9885 1 1 1 0.87517 0.957481 0.999651 2 8989 119854 11518 8652 6606 66686 898 16505 2 10396 121336 11570 8652 6606 66698 904 16510 0 . 0 . 0 82 0,0,42,32 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P81|1631|IQGAP3|protein_coding|CODING|NM_178229.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2066377 -0.693147 0.0285899 82 L71 1631 ctA/ctG LOW 3 SILENT CODING IQGAP3 C protein_coding NM_178229.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156536251 T C 0 228 0 0.854 0.9599 0.9885 1 1 1 0.87517 0.957481 0.999651 2 8989 119828 11514 8650 6610 66672 898 16495 2 10396 121310 11566 8650 6610 66684 904 16500 1 0 . 0 . 93 0,1,43,44 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L71|1631|IQGAP3|protein_coding|CODING|NM_178229.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs947662 -0.693147 0.0747544 93 E231G 582 gAg/gGg MODERATE 2 MISSENSE CODING TTC24 G protein_coding NM_001105669.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156551848 A G 0 222 0 0.0825 0.35 0.4553 0.2877 0.7018 0.3395 0.193478 0.559185 0.717788 1 224 4568 151 149 27 3599 39 379 2 1292 7910 292 474 36 4918 72 826 0.991234 0 . 0 COSM424131 77 25,13,18,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E231G|582|TTC24|protein_coding|CODING|NM_001105669.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.772906 rs6682716 -0.69311 0.0952063 77 S576 582 tcG/tcA LOW 11 SILENT CODING TTC24 A protein_coding NM_001105669.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156556321 G A 0 228 0 0.2859 0.768 0.9063 0.9692 0.9573 0.9192 0.449564 0.796491 0.966492 2 3679 109194 10964 8360 6236 64088 821 15046 2 9372 119254 11468 8586 6368 66198 882 16380 0 . 0 . 0 140 0,0,58,72 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S576|582|TTC24|protein_coding|CODING|NM_001105669.2|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10796961 -0.693147 0.309605 140 V19L 288 Gtg/Ctg MODERATE 1 MISSENSE CODING APOA1BP C protein_coding NM_144772.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156561651 G C 0 217 0 0.8638 0.9287 0.9568 0.9722 0.9592 0.9202 0.888889 0.947721 0.977 2 6864 106817 11007 8084 6169 58910 773 15010 2 7970 111558 11236 8298 6298 60658 812 16286 0 . 0 . 0 42 0,0,39,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V19L|288|APOA1BP|protein_coding|CODING|NM_144772.2|1|C),DOWNSTREAM(MODIFIER||2449||375|GPATCH4|protein_coding|CODING|NM_015590.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs7516274 -0.693144 0.29411 42 288 LOW 2 CODING APOA1BP A protein_coding NM_144772.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156562008 G A 0 228 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0.857694 0.931647 0.969535 2 8887 115946 11332 8433 6470 64757 864 15203 2 10400 121388 11576 8654 6610 66730 908 16510 0 . 0 . 0 140 0,0,62,71 SPLICE_SITE_REGION+INTRON(LOW||||288|APOA1BP|protein_coding|CODING|NM_144772.2|2|A),DOWNSTREAM(MODIFIER||2092||375|GPATCH4|protein_coding|CODING|NM_015590.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1925949 -0.693147 0.813951 140 I239 288 atA/atC LOW 6 SILENT CODING APOA1BP C protein_coding NM_144772.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156563726 A C 0 228 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0.857694 0.931801 0.969767 2 8894 115966 11334 8433 6473 64765 864 15203 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 236 0,0,151,64 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I239|288|APOA1BP|protein_coding|CODING|NM_144772.2|6|C),DOWNSTREAM(MODIFIER||374||375|GPATCH4|protein_coding|CODING|NM_015590.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6427322 -0.693147 0.0816051 236 E268 288 gaG/gaA LOW 6 SILENT CODING APOA1BP A protein_coding NM_144772.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156563813 G A 0 228 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0.857694 0.931801 0.969767 2 8890 115963 11334 8433 6473 64766 864 15203 2 10404 121408 11578 8654 6614 66740 908 16510 0 . 0 . 0 284 0,0,109,141 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E268|288|APOA1BP|protein_coding|CODING|NM_144772.2|6|A),DOWNSTREAM(MODIFIER||287||375|GPATCH4|protein_coding|CODING|NM_015590.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386604248,rs6668178 -0.693147 0.00852401 284 T281 288 acC/acT LOW 6 SILENT CODING APOA1BP T protein_coding NM_144772.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156563852 C T 0 228 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0.857694 0.931801 0.969767 2 8890 115954 11334 8433 6473 64757 864 15203 2 10406 121400 11578 8654 6614 66730 908 16510 0 . 0 . 0 228 0,0,69,129 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T281|288|APOA1BP|protein_coding|CODING|NM_144772.2|6|T),DOWNSTREAM(MODIFIER||248||375|GPATCH4|protein_coding|CODING|NM_015590.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs942963 -0.693147 0.000212059 228 288 22 MODIFIER 6 CODING APOA1BP C protein_coding NM_144772.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156563898 T C 0 228 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0.852928 0.929648 0.968953 2 8875 115841 11327 8427 6471 64682 862 15197 2 10388 121282 11572 8648 6612 66654 906 16502 0 . 0 . 0 120 0,0,13,101 UTR_3_PRIME(MODIFIER||22||288|APOA1BP|protein_coding|CODING|NM_144772.2|6|C),DOWNSTREAM(MODIFIER||202||375|GPATCH4|protein_coding|CODING|NM_015590.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1270 -0.693147 9.09247e-05 120 288 116 MODIFIER 6 CODING APOA1BP G protein_coding NM_144772.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156563992 C G 0 212 0 0.8638 0.9285 0.9568 0.9722 0.9592 0.9192 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 0,0,1,27 UTR_3_PRIME(MODIFIER||116||288|APOA1BP|protein_coding|CODING|NM_144772.2|6|G),DOWNSTREAM(MODIFIER||108||375|GPATCH4|protein_coding|CODING|NM_015590.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1271 -0.693054 0.742067 28 375 365 MODIFIER 8 CODING GPATCH4 A protein_coding NM_015590.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156564640 G A 0 114 0 0.4304 0.5236 0.6657 0.5169 0.7127 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997118 0 . 0 . 20 8,1,11,0 UTR_3_PRIME(MODIFIER||365||375|GPATCH4|protein_coding|CODING|NM_015590.3|8|A),DOWNSTREAM(MODIFIER||549||288|APOA1BP|protein_coding|CODING|NM_144772.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.372419 rs3795732 -0.676189 0.00186863 20 375 83 MODIFIER 8 CODING GPATCH4 T protein_coding NM_015590.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156564922 C T 0 222 0 0.1596 0.4355 0.6239 0.4911 0.7048 0.3405 0 . 0 1 2365 73815 7903 4558 4975 46736 584 6694 2 9508 118936 11542 8606 6608 65392 896 16384 0.842469 0 . 0 . 107 27,27,17,30 UTR_3_PRIME(MODIFIER||83||375|GPATCH4|protein_coding|CODING|NM_015590.3|8|T),DOWNSTREAM(MODIFIER||831||288|APOA1BP|protein_coding|CODING|NM_144772.2||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.987282 rs3795733 -0.693147 0.0251187 107 T43 375 acT/acC LOW 3 SILENT CODING GPATCH4 G protein_coding NM_015590.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156568252 A G 0 222 0 0.1036 0.0681 0.0418 0.0536 0.0417 0.0808 0.11507 0.0587421 0.0298837 1 1183 5394 229 518 141 1972 41 1310 2 10394 121370 11576 8654 6614 66714 908 16510 0.919571 0 . 0 . 103 16,38,20,21 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T43|375|GPATCH4|protein_coding|CODING|NM_015590.3|3|G),DOWNSTREAM(MODIFIER||4161||288|APOA1BP|protein_coding|CODING|NM_144772.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.500873 rs11264505 -0.693145 0.0238998 103 375 12 MODIFIER 1 CODING GPATCH4 C protein_coding NM_015590.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156571243 G C 0 222 0 0.1044 0.0683 0.0418 0.0536 0.0417 0.0808 0.111111 0.0550116 0.0290189 1 1049 5162 223 513 132 1925 39 1281 2 8648 112884 10884 8432 5586 62968 784 15582 0.668866 0 . 0 . 158 44,29,37,30 UTR_5_PRIME(MODIFIER||12||375|GPATCH4|protein_coding|CODING|NM_015590.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913458 rs16837546 -0.693147 0.485418 158 E504K 911 Gag/Aag MODERATE 8 MISSENSE CODING BCAN A protein_coding NM_021948.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156622252 G A 0 222 0 0.2595 0.3742 0.3718 0.3532 0.3926 0.5337 0.265107 0.338953 0.376805 1 2122 34773 2567 2090 1179 19101 276 7438 2 7106 87972 7640 5936 4276 48138 680 14196 0.888358 0 . 0 . 75 11,29,10,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E504K|911|BCAN|protein_coding|CODING|NM_021948.4|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.536734 rs1056695 -0.693097 0.880164 75 H790 911 caT/caC LOW 12 SILENT CODING BCAN C protein_coding NM_021948.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156627996 T C 0 222 0 0.0219 0.1468 0.1441 0.2937 0.0408 0.2751 0.0256468 0.0334461 0.0374419 1 284 10906 1601 2291 221 2845 66 3598 2 10404 121340 11570 8638 6608 66706 902 16512 0.457146 0 . 0 . 79 17,19,18,13 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H790|911|BCAN|protein_coding|CODING|NM_021948.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.820649 rs2298135 -0.69311 0.0303882 79 911 111 MODIFIER 14 CODING BCAN G protein_coding NM_021948.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156629037 A G 0 143 0 0.6611 0.5433 0.4726 0.4077 0.4483 0.6718 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.981336 0 . 0 . 39 7,16,1,14 UTR_3_PRIME(MODIFIER||111||911|BCAN|protein_coding|CODING|NM_021948.4|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.865471 rs11360 -0.688148 0.0504127 39 1621 114 MODIFIER 4 CODING NES G protein_coding NM_006617.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156639000 A G 0 91 0 0.0189 0.2268 0.2911 0.2946 0.3062 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.834543 0 . 0 . 14 7,0,7,0 UTR_3_PRIME(MODIFIER||114||1621|NES|protein_coding|CODING|NM_006617.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 0 . 0.428703 rs1046650 -0.636426 0.164651 14 A1448 1621 gcC/gcT LOW 4 SILENT CODING NES A protein_coding NM_006617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156639636 G A 0 222 0 0.0204 0.224 0.2882 0.2946 0.3032 0.2996 0.0681508 0.211538 0.28495 1 583 31232 2958 2314 1542 19224 232 4379 2 9720 119962 11520 8602 6566 66152 898 16504 0.666503 0 . 0 COSM1127348 62 10,23,8,18 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1448|1621|NES|protein_coding|CODING|NM_006617.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7939 rs11549292 -0.692976 0.842498 62 S1409 1621 tcC/tcT LOW 4 SILENT CODING NES A protein_coding NM_006617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156639753 G A 0 228 0 0.385 0.6184 0.6787 0.8611 0.6312 0.6278 0.399001 0.544776 0.61953 2 3784 73860 7853 7319 3943 40744 526 9691 2 9456 118564 11488 8618 6502 65140 882 16478 1 0 . 0 . 70 1,0,37,20 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1409|1621|NES|protein_coding|CODING|NM_006617.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11582300 -0.693147 0.0540022 70 P1275L 1621 cCc/cTc MODERATE 4 MISSENSE CODING NES A protein_coding NM_006617.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156640156 G A 0 228 0 0.711 0.7244 0.7104 0.87 0.6551 0.6738 0.693373 0.659849 0.642674 2 7206 80762 8224 7409 4343 43191 593 9796 2 10382 119732 11558 8650 6606 66300 898 15338 0 . 0 . 0 69 0,0,29,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P1275L|1621|NES|protein_coding|CODING|NM_006617.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748570 -0.693147 0.255527 69 T1224 1621 acG/acA LOW 4 SILENT CODING NES T protein_coding NM_006617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156640308 C T 0 222 0 0.0159 0.2242 0.2882 0.2946 0.3032 0.3067 0.0630958 0.210134 0.285465 1 537 30593 2947 2308 1547 19074 230 3950 2 10248 116260 11520 8598 6612 65194 856 13232 0.930069 0 . 0 COSM1559925 86 30,16,18,11 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1224|1621|NES|protein_coding|CODING|NM_006617.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.232527 rs3748571 -0.693079 0.0915067 86 G1159 1621 ggG/ggA LOW 4 SILENT CODING NES T protein_coding NM_006617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156640503 C T 0 222 0 0.0159 0.2238 0.2867 0.2946 0.3022 0.3067 0.0633227 0.210441 0.285814 1 541 31303 2960 2318 1547 19300 233 4404 2 10374 121202 11566 8628 6606 66614 904 16510 0.824769 0 . 0 . 92 27,19,31,10 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1159|1621|NES|protein_coding|CODING|NM_006617.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.545381 rs3828043 -0.693145 0.0580893 92 P1101L 1621 cCg/cTg MODERATE 4 MISSENSE CODING NES A protein_coding NM_006617.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156640678 G A 0 228 0 0.3858 0.6222 0.67 0.8621 0.6481 0.6339 0.408219 0.558878 0.63595 2 3680 74990 7920 7277 4265 41498 551 9799 2 9198 117370 11492 8586 6486 64252 876 16480 0 . 0 . COSM424142 29 0,0,13,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1101L|1621|NES|protein_coding|CODING|NM_006617.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2886443 -0.693054 0.823659 29 V130A 1621 gTg/gCg MODERATE 1 MISSENSE CODING NES G protein_coding NM_006617.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156646668 A G 0 70 0 0.9939 0.9984 1 1 1 1 0.994479 0.998122 0.999837 2 3321 52911 4227 3959 1850 29592 360 9602 2 3340 52934 4228 3960 1850 29594 360 9602 0 . 0 . 0 3 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V130A|1621|NES|protein_coding|CODING|NM_006617.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4278369 -0.453602 0.88 3 353 463 MODIFIER 4 CODING ISG20L2 C protein_coding NM_001303095.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156692678 T C 0 27.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||463||353|ISG20L2|protein_coding|CODING|NM_001303095.1|4|C) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs4593815 -0.453602 0.38 2 V400L 475 Gtg/Ctg MODERATE 7 MISSENSE CODING RRNAD1 C protein_coding NM_015997.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156705593 G C 0 228 0 0.8933 0.971 0.9942 1 1 1 0.920336 0.972628 0.999419 2 9511 120457 11531 8654 6614 66732 905 16510 2 10406 121410 11578 8654 6614 66738 908 16512 1 0 . 0 . 100 0,1,57,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V400L|475|RRNAD1|protein_coding|CODING|NM_015997.3|7|C),DOWNSTREAM(MODIFIER||1501||216|MRPL24|protein_coding|CODING|NM_024540.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4311877 -0.693147 0.379197 100 475 14 MODIFIER 8 CODING RRNAD1 C protein_coding NM_015997.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156706559 A C 0 228 0 0.1536 0.3209 0.1715 0.6865 0.326 0.271 1 1 1 2 1946 38201 1775 5741 2406 20917 311 5105 2 10256 119376 11366 8368 6558 65540 898 16390 0 . 0 . 0 64 0,0,16,44 UTR_3_PRIME(MODIFIER||14||475|RRNAD1|protein_coding|CODING|NM_015997.3|8|C),DOWNSTREAM(MODIFIER||535||216|MRPL24|protein_coding|CODING|NM_024540.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386617896,rs8658 -0.693147 0.226338 64 E232 256 gaG/gaA LOW 5 SILENT CODING HDGF T protein_coding NM_001126050.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156713512 C T 0 228 0 0.8616 0.9621 0.9899 1 1 1 0.899001 0.965247 0.999186 2 8585 109458 10409 7732 6076 61228 808 14620 2 9662 110610 10464 7732 6076 61240 812 14624 0 . 0 . 0 71 0,0,35,35 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E232|256|HDGF|protein_coding|CODING|NM_001126050.1|5|T),UPSTREAM(MODIFIER||2589||216|MRPL24|protein_coding|CODING|NM_024540.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4437869 -0.693147 0.248107 71 N52S 399 aAc/aGc MODERATE 3 MISSENSE CODING SH2D2A C protein_coding NM_001161441.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156784982 T C 0 228 0 0.3192 0.5936 0.6297 0.8155 0.662 0.6401 0.38266 0.552899 0.640116 2 3310 63540 6102 6250 2936 35976 454 8512 2 7906 96100 8766 7520 4474 54298 670 12466 0 . 0 . COSM1472774,COSM424151 72 0,0,13,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N52S|399|SH2D2A|protein_coding|CODING|NM_001161441.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs926103 -0.693147 0.0860932 72 A629 796 gcC/gcT LOW 15 SILENT CODING NTRK1 T protein_coding NM_002529.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156848995 C T 0 222 0 0.1384 0.3341 0.5735 0.0437 0.7127 0.3384 0.226158 0.556829 0.726163 1 2073 68625 6502 314 4722 48048 549 6417 2 10116 119898 11410 8604 6444 65950 894 16480 0.636258 2 benign 0 . 107 33,21,31,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A629|796|NTRK1|protein_coding|CODING|NM_002529.3|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.492868 rs6337 -0.693147 0.293139 107 1037 10102 MODIFIER 1 CODING PEAR1 T protein_coding NM_001080471.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156863617 G T 0 9.7 0 0.8003 0.7983 0.8372 0.6885 0.8777 0.7996 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||10102||1037|PEAR1|protein_coding|CODING|NM_001080471.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4661072 -0.379885 0 1 S234P 1037 Tct/Cct MODERATE 7 MISSENSE CODING PEAR1 C protein_coding NM_001080471.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156877457 T C 0 228 0 0.91 0.9758 0.9971 1 1 1 0.932365 0.97678 0.999535 2 9679 120586 11551 8654 6614 66705 906 16477 2 10406 121362 11578 8654 6614 66720 908 16482 0 . 0 . 0 61 0,0,25,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S234P|1037|PEAR1|protein_coding|CODING|NM_001080471.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1952294 -0.693147 0.116522 61 A751 1037 gcG/gcA LOW 18 SILENT CODING PEAR1 A protein_coding NM_001080471.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156882605 G A 0 222 0 0 0.0009984 0 0.003 0 0.002 0.000226963 7.6888e-05 0 1 1 31 0 14 0 5 1 10 2 10404 121408 11578 8654 6614 66740 906 16512 0.910976 0 . 0 . 146 41,24,45,24 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A751|1037|PEAR1|protein_coding|CODING|NM_001080471.1|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82802 rs118002868 -0.693147 0.592592 146 N903D 1037 Aat/Gat MODERATE 21 MISSENSE CODING PEAR1 G protein_coding NM_001080471.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156883546 A G 0 222 0 0.2557 0.4511 0.5591 0.5913 0.3926 0.5542 0.257149 0.354913 0.405 1 2686 52483 7077 5064 2695 26463 366 8132 2 10360 121006 11554 8626 6596 66560 906 16404 0.870583 0 . 0 . 177 51,22,61,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N903D|1037|PEAR1|protein_coding|CODING|NM_001080471.1|21|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943214 rs12137505 -0.693147 0.0701005 177 1037 901 MODIFIER 23 CODING PEAR1 G protein_coding NM_001080471.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156885491 T G 0 100 0 0.2897 0.4451 0.5043 0.5675 0.3588 0.5757 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||901||1037|PEAR1|protein_coding|CODING|NM_001080471.1|23|G),UPSTREAM(MODIFIER||4933||559|LRRC71|protein_coding|CODING|NM_144702.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4661012 -0.511536 0.470313 4 T495 559 acG/acA LOW 14 SILENT CODING LRRC71 A protein_coding NM_144702.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156902259 G A 0 228 0 0.888 0.7548 0.7061 0.8492 0.5318 0.7413 0.837894 0.640352 0.540376 2 8293 75543 8623 7467 3648 35438 533 11541 2 9818 120638 11554 8618 6604 66638 896 16510 0 . 0 . 0 78 0,0,32,40 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T495|559|LRRC71|protein_coding|CODING|NM_144702.2|14|A),DOWNSTREAM(MODIFIER||2373||1562|ARHGEF11|protein_coding|CODING|NM_198236.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs822430 -0.693147 0.0578326 78 H1467R 1562 cAt/cGt MODERATE 39 MISSENSE CODING ARHGEF11 C protein_coding NM_198236.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156907081 T C 0 228 0 0.888 0.7624 0.7233 0.8512 0.5517 0.7454 0.839991 0.650315 0.55314 2 8805 77536 8723 7498 3736 36563 553 11658 2 10386 121282 11568 8640 6610 66664 908 16506 0 . 0 . 0 99 0,0,40,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H1467R|1562|ARHGEF11|protein_coding|CODING|NM_198236.2|39|C),DOWNSTREAM(MODIFIER||4201||559|LRRC71|protein_coding|CODING|NM_144702.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386622704,rs945508 -0.693147 0.16026 99 S1456G 1562 Agc/Ggc MODERATE 39 MISSENSE CODING ARHGEF11 C protein_coding NM_198236.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 156907115 T C 0 228 0 0.2284 0.4065 0.5014 0.5169 0.3569 0.5174 0.224013 0.311702 0.356628 2 2384 47748 6695 4231 2479 23698 342 7919 2 10362 121094 11554 8618 6608 66570 908 16474 0.896782 0 . 0 . 94 1,2,38,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S1456G|1562|ARHGEF11|protein_coding|CODING|NM_198236.2|39|C),DOWNSTREAM(MODIFIER||4235||559|LRRC71|protein_coding|CODING|NM_144702.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.506165 rs868188 -0.693147 0.557908 94 1562 755 MODIFIER 1 CODING ARHGEF11 T protein_coding NM_198236.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157014877 A T 0 9.7 0 0.0416 0.2346 0.3127 0.4504 0.1968 0.2566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||755||1562|ARHGEF11|protein_coding|CODING|NM_198236.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3806421 -0.379885 0 1 1562 904 MODIFIER 1 CODING ARHGEF11 A protein_coding NM_198236.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157015026 C A 0 32.4 0 0.0393 0.234 0.3127 0.4504 0.1968 0.2566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,1 UTR_5_PRIME(MODIFIER||904||1562|ARHGEF11|protein_coding|CODING|NM_198236.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3806422 -0.453602 0.74 4 F234 512 ttT/ttC LOW 5 SILENT CODING ETV3 G protein_coding NM_001145312.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157095470 A G 0 222 0 0.0129 0.242 0.2882 0.5565 0.1123 0.3282 0.0274566 0.0744634 0.0949089 1 52 3822 111 337 88 950 43 2241 2 2162 20922 410 622 952 8654 218 7904 0.199298 0 . 0 . 167 42,46,23,36 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F234|512|ETV3|protein_coding|CODING|NM_001145312.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.550483 rs2231856,rs386561844 -0.693147 0.00443977 167 998 117 MODIFIER 17 CODING FCRL5 G protein_coding NM_001195388.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157485275 T G 0 131 0 0.4864 0.2131 0.0908 0.1409 0.0924 0.1288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.793923 0 . 0 . 12 4,0,7,1 UTR_3_PRIME(MODIFIER||117||998|FCRL5|protein_coding|CODING|NM_001195388.1|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.94394 rs3811036 -0.651104 0.674881 12 998 LOW 16 CODING FCRL5 A protein_coding NM_001195388.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157485561 G A 0 222 0 0.09 0.5048 0.6484 0.6558 0.6252 0.684 0.172038 0.481547 0.640116 1 1675 75843 8483 5666 4532 43871 586 11030 2 10354 121258 11566 8640 6612 66682 906 16498 0.956947 0 . 0 . 60 10,21,12,13 SPLICE_SITE_REGION+INTRON(LOW||||998|FCRL5|protein_coding|CODING|NM_001195388.1|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.383517 rs3811035 -0.692914 0.666736 60 V466I 998 Gtc/Atc MODERATE 7 MISSENSE CODING FCRL5 T protein_coding NM_001195388.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157508882 C T 0 228 0 0.3222 0.6933 0.8098 0.7887 0.8539 0.8487 0.407626 0.699216 0.848605 2 4151 98366 9558 6696 5817 57349 762 14033 2 10340 120810 11528 8616 6606 66516 904 16300 0 . 0 . 0 97 0,0,50,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V466I|998|FCRL5|protein_coding|CODING|NM_001195388.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6427384 -0.693147 0.0682392 97 G418D 998 gGt/gAt MODERATE 7 MISSENSE CODING FCRL5 T protein_coding NM_001195388.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157509025 C T 0 228 0 0.7345 0.8411 0.8357 0.878 0.8648 0.9264 0.760781 0.824389 0.856977 2 7891 105137 9835 7525 5838 58093 791 15164 2 10400 121308 11538 8634 6608 66712 904 16512 1 0 . 0 . 73 0,1,23,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G418D|998|FCRL5|protein_coding|CODING|NM_001195388.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2012199 -0.693147 0.00440358 73 Y267H 998 Tac/Cac MODERATE 5 MISSENSE CODING FCRL5 G protein_coding NM_001195388.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157514097 A G 0 228 0 0.4115 0.7073 0.7334 0.9067 0.8221 0.7648 0.474126 0.698062 0.812791 2 4845 94845 8402 7809 5564 54805 717 12703 2 10402 121386 11570 8648 6614 66734 908 16510 0 . 0 . 0 92 0,0,61,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y267H|998|FCRL5|protein_coding|CODING|NM_001195388.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6679793 -0.693147 0.0484848 92 D172 515 gaC/gaT LOW 4 SILENT CODING FCRL4 A protein_coding NM_031282.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157557701 G A 0 228 0 0.3623 0.4984 0.5375 0.6806 0.4284 0.5389 0.377213 0.410734 0.427907 2 3816 55086 5886 5690 3264 27758 409 8263 2 9986 114464 10908 8254 6374 62176 860 15906 0 . 0 . 0 113 0,0,49,59 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D172|515|FCRL4|protein_coding|CODING|NM_031282.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2777962,rs386573674 -0.693147 0.78756 113 515 17 MODIFIER 1 CODING FCRL4 G protein_coding NM_031282.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157567751 A G 0 228 0 0.6694 0.7961 0.8501 0.9008 0.7823 0.8354 0.694054 0.736968 0.758954 2 6904 92067 8878 7719 5081 49492 684 13309 2 10038 118544 11216 8546 6416 65416 876 16036 1 0 . 0 . 62 0,1,22,28 UTR_5_PRIME(MODIFIER||17||515|FCRL4|protein_coding|CODING|NM_031282.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1361889 -0.693147 0.0123457 62 V93G 734 gTg/gGg MODERATE 4 MISSENSE CODING FCRL3 C protein_coding NM_052939.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157668194 A C 0 222 0 0 0.0206 0.0014 0.1012 0 0 0.000226963 0.000153775 0.000116279 1 4 850 29 792 0 12 2 11 2 10404 121352 11570 8648 6614 66702 908 16506 0.861306 0 . 0 . 53 16,8,7,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V93G|734|FCRL3|protein_coding|CODING|NM_052939.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.183094 rs79895668 -0.691153 0.563978 53 P237 429 ccG/ccA LOW 5 SILENT CODING FCRL1 T protein_coding NM_052938.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157771880 C T 0 228 0 0.0643 0.3896 0.5072 0.5238 0.493 0.501 0.135043 0.386053 0.514651 2 1306 59123 5838 4695 3867 34498 484 8435 2 10362 121182 11550 8622 6598 66642 904 16504 1 0 . 0 . 102 1,0,58,34 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P237|429|FCRL1|protein_coding|CODING|NM_052938.4|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4971154 -0.693147 0.593104 102 347 LOW 5 CODING CD5L T protein_coding NM_005894.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157802979 C T 0 228 0 0.8427 0.8039 0.7622 0.8095 0.7197 0.862 0.796187 0.743195 0.716047 2 8422 90961 8737 7126 5003 47514 722 13437 2 10378 120188 11558 8640 6612 66338 898 15764 0 . 0 . 0 69 0,0,39,16 SPLICE_SITE_REGION+INTRON(LOW||||347|CD5L|protein_coding|CODING|NM_005894.2|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2261295 -0.693147 0.136941 69 D117E 347 gaT/gaA MODERATE 3 MISSENSE CODING CD5L T protein_coding NM_005894.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 157805650 A T 0 222 0 0.1619 0.1202 0.2147 0.1736 0.007 0.0583 0.137313 0.0514378 0.00744186 1 1583 7469 2940 1565 10 472 42 857 2 10392 119704 11562 8644 6614 66292 896 15304 0.886041 0 . 0 . 62 26,1,21,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D117E|347|CD5L|protein_coding|CODING|NM_005894.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.665865 rs11537583 -0.693079 0.715434 62 757 LOW 7 CODING KIRREL A protein_coding NM_018240.6 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158058109 C A 0 228 0 0.0257 0.4525 0.5836 0.6974 0.5149 0.6196 0.122333 0.3839 0.517907 2 1077 62919 7931 5916 3841 34398 484 9272 2 10388 120042 11566 8640 6612 66302 894 15640 0 . 0 . 0 171 0,0,124,29 SPLICE_SITE_REGION+INTRON(LOW||||757|KIRREL|protein_coding|CODING|NM_018240.6|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6427419 -0.693147 0.409553 171 757 852 MODIFIER 15 CODING KIRREL T protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158065762 C T 0 9.7 0 0.0091 0.273 0.3775 0.4812 0.3469 0.2648 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||852||757|KIRREL|protein_coding|CODING|NM_018240.6|15|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12749808 -0.379885 0 1 757 1132 MODIFIER 15 CODING KIRREL G protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158066042 A G 0 60 0 0.2874 0.5266 0.6167 0.6994 0.5179 0.6166 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1132||757|KIRREL|protein_coding|CODING|NM_018240.6|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3768538 -0.453602 0.92 3 757 1924 MODIFIER 15 CODING KIRREL G protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158066834 A G 0 228 0 0.2095 0.503 0.6009 0.6954 0.5179 0.6166 0 . 0 2 170 7799 106 128 980 1977 98 4340 2 606 14728 198 206 1620 4290 188 7620 0 . 0 . 0 60 0,0,30,27 UTR_3_PRIME(MODIFIER||1924||757|KIRREL|protein_coding|CODING|NM_018240.6|15|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6427420 -0.693147 0.0111661 60 757 2137 MODIFIER 15 CODING KIRREL C protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158067047 A C 0 150 0 0.0272 0.4541 0.5865 0.6954 0.5229 0.6176 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||2137||757|KIRREL|protein_coding|CODING|NM_018240.6|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs386618542,rs874844 -0.676189 0.115897 11 757 3434 MODIFIER 15 CODING KIRREL G protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158068344 A G 0 9.7 0 0.0272 0.4557 0.5865 0.6964 0.5229 0.6247 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3434||757|KIRREL|protein_coding|CODING|NM_018240.6|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3820677 -0.379885 0 1 757 4189 MODIFIER 15 CODING KIRREL A protein_coding NM_018240.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158069099 G A 0 67 0 0.5832 0.7127 0.7233 0.749 0.7445 0.8098 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||4189||757|KIRREL|protein_coding|CODING|NM_018240.6|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11897 -0.511536 0.635923 3 335 56 MODIFIER 7 CODING CD1D C protein_coding NM_001766.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158153996 T C 0 228 0 0.9758 0.9936 1 1 1 1 0.983382 0.994744 0.999686 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 82 0,0,5,75 UTR_3_PRIME(MODIFIER||56||335|CD1D|protein_coding|CODING|NM_001766.3|7|C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs426336 -0.693147 0.0142606 82 327 178 MODIFIER 1 CODING CD1A G protein_coding NM_001763.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158224282 A G 0 144 0 0.562 0.3464 0.2954 0.2659 0.2028 0.3221 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.869318 0 . 0 . 17 7,1,7,2 UTR_5_PRIME(MODIFIER||178||327|CD1A|protein_coding|CODING|NM_001763.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.156946 rs366316 -0.662043 0.21691 17 T30I 327 aCc/aTc MODERATE 2 MISSENSE CODING CD1A T protein_coding NM_001763.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158224904 C T 0 222 0 0.0363 0.1643 0.0908 0.3948 0.0577 0.2618 0.0508398 0.0553591 0.0576744 1 525 13306 1298 3162 458 3853 98 3912 2 10406 121384 11578 8650 6614 66718 908 16510 0.999975 0 . 0 . 69 24,8,21,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T30I|327|CD1A|protein_coding|CODING|NM_001763.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.367141 rs2269714 -0.693097 0.0387871 69 C68W 327 tgC/tgG MODERATE 2 MISSENSE CODING CD1A G protein_coding NM_001763.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158225019 C G 0 222 0 0.0363 0.1643 0.0908 0.3948 0.0577 0.2618 0.0508398 0.0553591 0.0576744 1 525 13307 1298 3162 458 3854 98 3912 2 10404 121374 11570 8630 6614 66736 908 16512 0.661657 0 . 0 . 68 9,21,13,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgC/tgG|C68W|327|CD1A|protein_coding|CODING|NM_001763.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.237722 rs2269715 -0.69311 0.16276 68 Q106R 388 cAg/cGg MODERATE 2 MISSENSE CODING CD1E G protein_coding NM_030893.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158324425 A G 0 228 0 0.8964 0.6164 0.415 0.6617 0.3579 0.6002 0.781185 0.482269 0.344252 2 8033 54044 4731 5689 2648 23273 412 9258 2 9760 120066 11524 8608 6606 66348 892 16328 0 . 0 . 0 39 0,0,5,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q106R|388|CD1E|protein_coding|CODING|NM_030893.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1065457 -0.693143 0.749987 39 S314 314 agC/agT LOW 1 SILENT CODING OR10T2 A protein_coding NM_001004475.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158368315 G A 0 90 0 0.1021 0.1262 0.1513 0.0893 0.0736 0.2331 0.098502 0.0798985 0.0703652 1 890 11315 1691 757 540 4240 98 3099 2 5972 68824 6688 5172 4306 35030 568 11088 0.319301 0 . 0 . 36 25,0,11,0 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S314|314|OR10T2|protein_coding|CODING|NM_001004475.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.990609 rs60530245 -0.676189 0.0479773 36 V239A 314 gTc/gCc MODERATE 1 MISSENSE CODING OR10T2 G protein_coding NM_001004475.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158368541 A G 0 222 0 0.4191 0.3652 0.3055 0.2262 0.3131 0.5317 0.392873 0.33869 0.31093 1 4154 41175 3393 1969 2287 20704 343 8325 2 10398 121174 11534 8624 6608 66606 908 16496 0.870421 0 . 0 . 137 34,35,24,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V239A|314|OR10T2|protein_coding|CODING|NM_001004475.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.719793 rs34465440 -0.693147 0.00469088 137 I137M 314 atA/atG MODERATE 1 MISSENSE CODING OR10T2 C protein_coding NM_001004475.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158368846 T C 0 222 0 0.4191 0.3652 0.3055 0.2262 0.3131 0.5317 0.3931 0.338767 0.31093 1 4154 41189 3395 1974 2287 20710 343 8326 2 10364 121194 11564 8622 6608 66634 908 16494 0.265984 0 . 0 . 39 11,5,14,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I137M|314|OR10T2|protein_coding|CODING|NM_001004475.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.169391 rs6662382 -0.692717 0.829212 39 S192 313 tcC/tcA LOW 1 SILENT CODING OR10K1 A protein_coding NM_001004473.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158435927 C A 0 222 0 0 0.0315 0.0548 0.1091 0.002 0.0082 0.00158874 0.00215285 0.00244186 1 12 1988 1028 794 0 93 8 53 2 10404 121140 11564 8646 6614 66602 906 16404 0.907204 0 . 0 . 181 36,40,50,39 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcA|S192|313|OR10K1|protein_coding|CODING|NM_001004473.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.759303 rs16840204 -0.693147 0.438504 181 N294T 313 aAt/aCt MODERATE 1 MISSENSE CODING OR10Z1 C protein_coding NM_001004478.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158577109 A C 0 222 0 0.0658 0.2422 0.2983 0.495 0.2634 0.1585 0.0980481 0.200062 0.252326 1 971 31984 4035 4015 2292 17608 267 2796 2 10390 121302 11550 8638 6612 66694 908 16510 0.276189 0 . 0 . 74 14,30,11,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aCt|N294T|313|OR10Z1|protein_coding|CODING|NM_001004478.1|1|C),DOWNSTREAM(MODIFIER||3387||2419|SPTA1|protein_coding|CODING|NM_003126.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90896 rs857685 -0.692914 0.109802 74 A2365 2419 gcA/gcG LOW 51 SILENT CODING SPTA1 C protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158582646 T C 0 222 0 0.4183 0.5048 0.5202 0.6319 0.5626 0.4202 0.43685 0.509482 0.543237 1 4149 64951 6150 5228 4288 37578 517 7041 2 9800 120618 11506 8612 6608 66684 900 16508 0.931567 0 . 0 . 87 30,21,18,12 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A2365|2419|SPTA1|protein_coding|CODING|NM_003126.2|51|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997313 rs2251969 -0.693097 0.683677 87 I2265T 2419 aTc/aCc MODERATE 49 MISSENSE CODING SPTA1 G protein_coding NM_003126.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158584091 A G 0 222 0 0.4228 0.5062 0.5202 0.6319 0.5636 0.4202 0.430471 0.506814 0.540713 1 4146 64566 6109 5172 4268 37330 511 7030 2 9766 120156 11458 8550 6590 66408 890 16494 0.318484 0 . 0 . 104 27,33,16,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I2265T|2419|SPTA1|protein_coding|CODING|NM_003126.2|49|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.238905 rs952094 -0.693145 0.557069 104 K1693Q 2419 Aag/Cag MODERATE 36 MISSENSE CODING SPTA1 G protein_coding NM_003126.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158607935 T G 0 222 0 0.1036 0.2456 0.3026 0.4365 0.2763 0.1687 0.122959 0.21836 0.262397 1 1177 32987 4181 3683 2287 18445 283 2931 2 9798 120532 11458 8604 6602 66662 900 16508 0.963083 0 . 0 . 41 6,11,9,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K1693Q|2419|SPTA1|protein_coding|CODING|NM_003126.2|36|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.950089 rs857725 -0.692067 0.12166 41 C1568R 2419 Tgt/Cgt MODERATE 33 MISSENSE CODING SPTA1 G protein_coding NM_003126.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158612236 A G 0 222 0 0.6853 0.594 0.5605 0.6359 0.5865 0.4591 0.678445 0.599561 0.562095 1 6516 69834 6403 5288 4328 38863 550 7886 2 9796 120634 11506 8608 6608 66708 898 16510 0.64341 0 . 0 . 41 19,2,11,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1568R|2419|SPTA1|protein_coding|CODING|NM_003126.2|33|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.632692 rs863931 -0.683931 0.200599 41 S1163A 2419 Tcc/Gcc MODERATE 25 MISSENSE CODING SPTA1 C protein_coding NM_003126.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158619728 A C 0 228 0 0.9796 0.9946 1 1 1 1 0.980614 0.993966 1 2 9281 118805 11337 8574 6518 65962 878 16255 2 9480 119012 11344 8574 6518 65962 878 16256 0 . 0 . 0 77 0,0,34,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S1163A|2419|SPTA1|protein_coding|CODING|NM_003126.2|25|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2482965 -0.693147 0.119021 77 L958 2419 ctG/ctA LOW 20 SILENT CODING SPTA1 T protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158626378 C T 0 228 0 0.7935 0.4235 0.3588 0.4087 0.2495 0.1636 0.696929 0.386956 0.246396 2 6996 37337 4283 3551 2214 17454 282 2557 2 9800 120726 11566 8614 6612 66724 900 16510 0.856895 0 . 0 . 87 2,1,52,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L958|2419|SPTA1|protein_coding|CODING|NM_003126.2|20|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.71462 rs386436992,rs857691 -0.693147 0.00349305 87 L831 2419 ctT/ctG LOW 18 SILENT CODING SPTA1 C protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158631171 A C 0 228 0 0.1407 0.2436 0.3026 0.4087 0.2525 0.1616 0.183386 0.225358 0.244541 2 1726 31657 3973 3550 2243 17396 258 2511 2 9802 120644 11532 8588 6600 66712 900 16510 0 . 0 . 0 87 0,0,25,54 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L831|2419|SPTA1|protein_coding|CODING|NM_003126.2|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2518493,rs386568707 -0.693147 0.00391248 87 A314 2419 gcT/gcA LOW 7 SILENT CODING SPTA1 T protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158647495 A T 0 228 0 0.8442 0.9569 0.9914 1 0.996 1 0.875634 0.958048 0.997113 2 8426 118462 11330 8592 6475 66268 891 16480 2 9792 120270 11416 8592 6562 66520 898 16490 0 . 0 . 0 101 0,0,60,31 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A314|2419|SPTA1|protein_coding|CODING|NM_003126.2|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs325996 -0.693147 0.242504 101 S305 2419 agT/agC LOW 7 SILENT CODING SPTA1 G protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158647522 A G 0 228 0 0.2262 0.4539 0.5058 0.5833 0.6153 0.4254 0.275166 0.477734 0.573235 2 2687 65529 6183 4692 4170 39831 525 7441 2 9792 120256 11430 8568 6574 66496 896 16500 0.517241 0 . 0 . 97 2,0,49,38 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S305|2419|SPTA1|protein_coding|CODING|NM_003126.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.867816 rs703121 -0.693147 0.153882 97 2419 LOW 6 CODING SPTA1 A protein_coding NM_003126.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158647631 T A 0 228 0 0.8442 0.9569 0.9914 1 0.996 1 0.876568 0.95811 0.99712 2 8432 118845 11435 8616 6519 66450 891 16502 2 9804 120662 11522 8616 6608 66702 898 16512 0 . 0 . 0 71 0,0,23,43 SPLICE_SITE_REGION+INTRON(LOW||||2419|SPTA1|protein_coding|CODING|NM_003126.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs325995 -0.693147 0.545134 71 V42 2419 gtC/gtT LOW 2 SILENT CODING SPTA1 A protein_coding NM_003126.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158655036 G A 0 228 0 0.888 0.9698 0.9957 1 1 1 0.916364 0.973189 0.999637 2 8909 119747 11489 8624 6610 66710 898 16507 2 9802 120716 11542 8624 6610 66726 900 16512 0 . 0 . 0 128 0,0,49,61 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V42|2419|SPTA1|protein_coding|CODING|NM_003126.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs435080 -0.693147 0.0182125 128 2419 LOW 1 CODING SPTA1 C protein_coding NM_003126.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158656281 T C 0 228 0 0.888 0.9698 0.9957 1 1 1 0.913043 0.973127 0.999631 2 8891 119593 11473 8622 6596 66612 896 16503 2 9786 120564 11526 8622 6596 66628 898 16508 0 . 0 . 0 225 0,0,100,95 SPLICE_SITE_REGION+INTRON(LOW||||2419|SPTA1|protein_coding|CODING|NM_003126.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2564858 -0.693147 0.0048743 225 P248L 315 cCg/cTg MODERATE 1 MISSENSE CODING OR6K3 A protein_coding NM_001005327.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158687163 G A 0 228 0 0.4773 0.389 0.4323 0.4474 0.3966 0.1708 0.475715 0.411502 0.378605 2 4975 47097 4842 3688 3177 26524 371 3520 2 10400 121126 11472 8612 6604 66628 906 16504 1 0 . 0 . 140 1,0,61,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P248L|315|OR6K3|protein_coding|CODING|NM_001005327.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs28568406 -0.693147 0.350081 140 P228S 315 Ccc/Tcc MODERATE 1 MISSENSE CODING OR6K3 A protein_coding NM_001005327.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158687224 G A 0 228 0 0.09 0.2804 0.389 0.4474 0.3946 0.1708 0.133681 0.294941 0.377558 2 1315 43129 4665 3680 3171 26441 355 3502 2 10386 121062 11470 8610 6602 66588 906 16500 0.90625 0 . 0 COSM146654 140 2,0,59,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P228S|315|OR6K3|protein_coding|CODING|NM_001005327.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.632812 rs857703 -0.693147 0.39962 140 R293H 312 cGc/cAc MODERATE 1 MISSENSE CODING OR6N1 T protein_coding NM_001005185.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158735595 C T 0 228 0 0.7784 0.6679 0.7839 0.6171 0.7217 0.4335 0.779619 0.737967 0.716628 2 8094 82480 9176 5352 4781 46921 611 7545 2 10406 121386 11574 8640 6614 66734 908 16510 0 . 0 . COSM1179737 98 0,0,65,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R293H|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs857824 -0.693147 0.523566 98 Q261R 312 cAg/cGg MODERATE 1 MISSENSE CODING OR6N1 C protein_coding NM_001005185.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158735691 T C 0 228 0 0.7784 0.6679 0.7839 0.6171 0.7217 0.4335 0.779846 0.737967 0.716512 2 8095 82478 9180 5353 4777 46926 611 7536 2 10406 121380 11578 8632 6612 66736 908 16508 0 . 0 . COSM1179738 93 0,0,40,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q261R|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs857825 -0.693147 0.2356 93 F245L 312 Ttc/Ctc MODERATE 1 MISSENSE CODING OR6N1 G protein_coding NM_001005185.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158735740 A G 0 228 0 0.7784 0.6679 0.7839 0.6171 0.7217 0.4335 0.779846 0.737967 0.716512 2 8093 82476 9176 5352 4777 46922 611 7545 2 10402 121352 11574 8628 6612 66720 908 16508 0 . 0 . COSM1127314 88 0,0,32,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F245L|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs857826 -0.693147 0.0277274 88 I194T 312 aTa/aCa MODERATE 1 MISSENSE CODING OR6N1 G protein_coding NM_001005185.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158735892 A G 0 228 0 0.7784 0.6679 0.7839 0.6171 0.7217 0.4335 0.779846 0.737967 0.716512 2 8084 82452 9176 5351 4777 46908 611 7545 2 10396 121332 11568 8640 6614 66702 908 16504 0 . 0 . COSM1559899 66 0,0,37,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I194T|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs857827 -0.693147 0.858091 66 L86 312 ctC/ctT LOW 1 SILENT CODING OR6N1 A protein_coding NM_001005185.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158736215 G A 0 228 0 0.73 0.8125 0.9308 0.9087 0.9473 0.6022 0.739446 0.86437 0.928372 2 7734 105616 11068 7944 6120 61414 779 10557 2 10400 121384 11574 8650 6612 66734 908 16506 0 . 0 . 0 69 0,0,35,29 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L86|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6666753 -0.693147 0.572606 69 A10T 312 Gca/Aca MODERATE 1 MISSENSE CODING OR6N1 T protein_coding NM_001005185.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158736445 C T 0 228 0 0.0182 0.2462 0.3314 0.4246 0.334 0.2198 0.0635497 0.233431 0.320465 2 562 35147 4112 3646 2435 20583 295 3514 2 9532 114928 11004 8326 6486 63596 868 15116 0 . 0 . 0 30 0,0,4,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A10T|312|OR6N1|protein_coding|CODING|NM_001005185.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1864346 -0.693079 0.761829 30 A204V 317 gCt/gTt MODERATE 1 MISSENSE CODING OR6N2 A protein_coding NM_001005278.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158746815 G A 0 222 0 0 0.0095847 0 0.0476 0 0 0 . 0 1 0 494 0 483 0 4 1 6 2 10290 121168 11562 8634 6614 66654 908 16506 0.913032 0 . 0 . 55 10,13,10,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A204V|317|OR6N2|protein_coding|CODING|NM_001005278.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.96563 rs12027473 -0.69312 0.299993 55 P159 407 ccA/ccG LOW 4 SILENT CODING MNDA G protein_coding NM_002432.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158813819 A G 0 228 0 0.3071 0.5282 0.5447 0.6954 0.5825 0.5869 0.369496 0.50469 0.573954 2 3813 67974 5776 5787 4183 38500 501 9414 2 10400 121368 11574 8648 6612 66716 908 16510 0 . 0 . 0 73 0,0,51,16 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P159|407|MNDA|protein_coding|CODING|NM_002432.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs857870 -0.693147 0.426648 73 Q307 729 caA/caG LOW 5 SILENT CODING IFI16 G protein_coding NM_001206567.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 158990247 A G 0 222 0 0.7776 0.4091 0.1427 0.4742 0.1362 0.3139 0.669315 0.319391 0.140116 1 7138 28004 1452 3821 915 9748 165 4765 2 10374 121224 11550 8638 6614 66642 908 16498 0.988008 0 . 0 COSM146657 110 16,34,18,26 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q307|729|IFI16|protein_coding|CODING|NM_001206567.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.417208 rs1057024 -0.693146 0.020744 110 R353S 729 Cgt/Agt MODERATE 6 MISSENSE CODING IFI16 A protein_coding NM_001206567.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159002377 C A 0 228 0 0.3207 0.631 0.8689 0.5883 0.838 0.7127 0.430095 0.686068 0.817209 2 4181 93105 10305 5510 5684 54632 742 12051 2 10398 121324 11562 8634 6612 66700 908 16510 0.608696 0 . 0 . 100 1,1,62,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Agt|R353S|729|IFI16|protein_coding|CODING|NM_001206567.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.804348 rs1057027 -0.693147 0.522392 100 Y357N 729 Tat/Aat MODERATE 6 MISSENSE CODING IFI16 A protein_coding NM_001206567.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159002389 T A 0 228 0 0.3207 0.6308 0.8689 0.5873 0.838 0.7127 0.430322 0.686145 0.817209 2 4186 93128 10311 5513 5684 54641 742 12051 2 10404 121358 11570 8646 6614 66706 908 16510 0.94898 0 . 0 . 107 1,1,70,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y357N|729|IFI16|protein_coding|CODING|NM_001206567.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.918367 rs1057028 -0.693147 0.0864469 107 E32K 343 Gag/Aag MODERATE 2 MISSENSE CODING AIM2 T protein_coding NM_004833.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159043196 C T 0 222 0 0.0295 0.0262 0.0144 0.0625 0.004 0.0153 0.0299591 0.0134553 0.005 1 286 1841 276 596 91 382 12 198 2 10396 121344 11548 8648 6614 66720 908 16510 0.998566 0 . 0 . 114 31,23,16,28 PROTEIN_INTERACTION_LOCUS(HIGH||||343|AIM2|protein_coding|CODING||2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E32K|343|AIM2|protein_coding|CODING|NM_004833.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998566 rs2276405 -0.693146 0.120065 114 L385 432 ctT/ctC LOW 9 SILENT CODING CADM3 C protein_coding NM_021189.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159169641 T C 0 228 0 0.9123 0.8311 0.7205 0.9276 0.7425 0.7914 0.881979 0.789636 0.742326 2 9231 93813 8970 8034 5013 49139 698 12728 2 10390 121152 11540 8642 6586 66586 904 16504 1 0 . 0 . 59 0,1,29,19 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L385|432|CADM3|protein_coding|CODING|NM_021189.3|9|C),INTRAGENIC(MODIFIER|||||CADM3-AS1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386617840,rs862999 -0.693147 0.138748 59 432 274 MODIFIER 10 CODING CADM3 G protein_coding NM_021189.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159170986 T G 0 228 0 0.0424 0.4149 0.4481 0.6905 0.5517 0.4703 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,15,2 UTR_3_PRIME(MODIFIER||274||432|CADM3|protein_coding|CODING|NM_021189.3|10|G),UPSTREAM(MODIFIER||4063||338|ACKR1|protein_coding|CODING|NM_001122951.2||G),INTRAGENIC(MODIFIER|||||CADM3-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs863000 -0.690438 0.000118187 22 432 891 MODIFIER 10 CODING CADM3 A protein_coding NM_021189.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159171603 C A 0 176 0 0.0061 0.2192 0.1888 0.5843 0.1193 0.2556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,21,0 UTR_3_PRIME(MODIFIER||891||432|CADM3|protein_coding|CODING|NM_021189.3|10|A),UPSTREAM(MODIFIER||3446||338|ACKR1|protein_coding|CODING|NM_001122951.2||A),INTRAGENIC(MODIFIER|||||CADM3-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3845622 -0.692352 0.838232 22 E319G 329 gAa/gGa MODERATE 1 MISSENSE CODING OR10J3 C protein_coding NM_001004467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159283494 T C 0 228 0 0.0038 0.1248 0.1009 0.3621 0.0746 0.1125 0.0161144 0.0427495 0.0563953 2 129 11633 1430 3540 610 4202 93 1629 2 9984 120084 11504 8638 6614 66006 906 16432 1 0 . 0 . 132 0,1,64,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E319G|329|OR10J3|protein_coding|CODING|NM_001004467.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs58037016 -0.693147 0.00500315 132 Q235R 329 cAg/cGg MODERATE 1 MISSENSE CODING OR10J3 C protein_coding NM_001004467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159283746 T C 0 228 0 0.1793 0.1959 0.1326 0.4236 0.0964 0.1309 0.152065 0.103414 0.0784884 2 1633 15877 1641 4022 687 5645 138 2111 2 10404 121322 11532 8632 6614 66722 908 16510 0.975959 0 . 0 . 156 2,1,84,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q235R|329|OR10J3|protein_coding|CODING|NM_001004467.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.38456 rs11265165 -0.693147 0.31113 156 320 16 MODIFIER 1 CODING OR10J1 A protein_coding NM_012351.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159409533 G A 0 228 0 0.7088 0.9107 0.9654 1 0.9761 0.9857 0.778711 0.910272 0.977674 2 7953 116340 11270 8649 6538 65105 864 15961 2 10316 120914 11522 8650 6612 66574 906 16334 0 . 0 . 0 123 0,0,73,36 UTR_5_PRIME(MODIFIER||16||320|OR10J1|protein_coding|CODING|NM_012351.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10908721 -0.693147 0.00206152 123 M62I 320 atG/atT MODERATE 1 MISSENSE CODING OR10J1 T protein_coding NM_012351.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159409734 G T 0 228 0 0.9569 0.9882 0.9971 1 1 1 0.968452 0.989236 0.999884 2 10048 121008 11540 8654 6614 66736 907 16509 2 10406 121388 11558 8654 6614 66738 908 16510 0 . 0 . 0 87 0,0,44,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atT|M62I|320|OR10J1|protein_coding|CODING|NM_012351.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10908722 -0.693147 0.41146 87 V144 223 gtA/gtG LOW 2 SILENT CODING APCS G protein_coding NM_001639.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159558258 A G 0 228 0 0.9834 0.9004 0.9063 0.9921 0.839 0.7526 0.963686 0.866677 0.816977 2 10053 102628 10647 8544 5976 54431 756 12221 2 10406 121284 11522 8648 6612 66684 906 16506 0 . 0 . 0 102 0,0,48,43 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V144|223|APCS|protein_coding|CODING|NM_001639.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2808661 -0.693147 0.0159841 102 P184 434 ccT/ccC LOW 4 SILENT CODING FCRL6 C protein_coding NM_001004310.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159778983 T C 0 222 0 0.5265 0.2716 0.2363 0.1855 0.1998 0.1145 0.455949 0.279299 0.188837 1 4948 25066 2480 1902 1002 12748 167 1819 2 10146 116220 11536 8604 6586 65370 870 13108 0.97074 0 . 0 . 57 16,8,16,14 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P184|434|FCRL6|protein_coding|CODING|NM_001004310.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.229917 rs12083967 -0.693097 0.876367 57 S408 434 agT/agC LOW 10 SILENT CODING FCRL6 C protein_coding NM_001004310.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159785370 T C 0 222 0 0.4402 0.1917 0.1499 0.1567 0.0616 0.0552 0.39764 0.175073 0.0610465 1 4215 13071 1826 1676 300 4004 75 975 2 10406 121388 11574 8634 6614 66740 908 16512 0.53137 0 . 0 COSM146662 44 7,12,6,17 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S408|434|FCRL6|protein_coding|CODING|NM_001004310.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.554112 rs4301626 -0.692717 0.677553 44 S427G 434 Agc/Ggc MODERATE 10 MISSENSE CODING FCRL6 G protein_coding NM_001004310.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159785425 A G 0 215 0 0.4622 0.2532 0.2334 0.1716 0.2018 0.1217 0.435996 0.278718 0.19814 1 4577 25138 2494 1813 972 13145 173 1964 2 10402 121340 11568 8636 6612 66714 908 16500 0.980167 0 . 0 COSM146663 31 4,9,4,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S427G|434|FCRL6|protein_coding|CODING|NM_001004310.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.251577 rs4443889 -0.691153 0.0781893 31 R65* 285 Cga/Tga HIGH 2 NONSENSE CODING SLAMF8 T protein_coding NM_020125.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159799808 C T 0 222 0 0 0.0063898 0 0.0317 0 0 0 7.6888e-05 0.000116279 1 0 406 1 375 0 17 3 10 2 10398 121346 11574 8650 6614 66694 906 16510 0.941056 0 . 0 . 72 16,22,17,9 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R65*|285|SLAMF8|protein_coding|CODING|NM_020125.2|2|T),DOWNSTREAM(MODIFIER||4456||235|C1orf204|protein_coding|CODING|NM_001134233.1||T) 1 0.5 1 0 . 1 0 1 1 (SLAMF8|SLAMF8|1|1.00) 60 0 1 1 (SLAMF8|SLAMF8|1|1.00) 0.99916 rs10430458 -0.692976 0.0877033 72 235 3426 MODIFIER 6 CODING C1orf204 G protein_coding NM_001134233.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159804282 C G 0 9.7 0 0.7186 0.4521 0.2723 0.5308 0.2833 0.3119 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3426||235|C1orf204|protein_coding|CODING|NM_001134233.1|6|G),INTRON(MODIFIER||||285|SLAMF8|protein_coding|CODING|NM_020125.2|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2494490 -0.379885 0 1 Q21E 235 Caa/Gaa MODERATE 1 MISSENSE CODING C1orf204 C protein_coding NM_001134233.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159824967 G C 0 228 0 0.9939 0.9311 0.9063 0.9474 0.8598 0.9202 0.968931 0.899255 0.86895 2 2089 18772 375 597 649 7506 184 7372 2 2158 20726 414 628 780 8626 206 7914 0 . 0 . 0 70 0,0,31,25 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Caa/Gaa|Q21E|235|C1orf204|protein_coding|CODING|NM_001134233.1|1|C),INTRON(MODIFIER||||414|VSIG8|protein_coding|CODING|NM_001013661.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2501340 -0.693147 0.000224864 70 235 34 MODIFIER 1 CODING C1orf204 C protein_coding NM_001134233.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159825061 G C 0 222 0 0.9667 0.6324 0.4568 0.6161 0.4433 0.5164 0.879335 0.602278 0.481772 1 1899 11026 192 351 266 3964 107 4247 2 2130 20408 404 616 690 8462 204 7902 0.763662 0 . 0 . 33 4,13,6,8 START_GAINED(LOW||||235|C1orf204|protein_coding|CODING|NM_001134233.1|1|C),UTR_5_PRIME(MODIFIER||34||235|C1orf204|protein_coding|CODING|NM_001134233.1|1|C),INTRON(MODIFIER||||414|VSIG8|protein_coding|CODING|NM_001013661.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.866252 rs2501339 -0.686358 0.439122 33 414 114 MODIFIER 1 CODING VSIG8 A protein_coding NM_001013661.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159832425 G A 0 141 0 0.233 0.495 0.5778 0.499 0.662 0.6145 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 21 0,1,0,20 UTR_5_PRIME(MODIFIER||114||414|VSIG8|protein_coding|CODING|NM_001013661.1|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs2494507 -0.692067 0.74324 21 1179 9 MODIFIER 21 CODING IGSF9 T protein_coding NM_001135050.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159897126 C T 0 222 0 0.7663 0.6673 0.6268 0.7143 0.5547 0.6299 0.728682 0.598718 0.532126 1 7040 69358 7252 6223 3304 34755 492 10292 2 9634 118408 11540 8578 6606 64670 886 16494 0.205046 0 . 0 . 71 19,14,20,8 UTR_3_PRIME(MODIFIER||9||1179|IGSF9|protein_coding|CODING|NM_001135050.1|21|T),UPSTREAM(MODIFIER||3619||220|TAGLN2|protein_coding|CODING|NM_001277224.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997881 rs13052 -0.693054 0.384032 71 1179 3 MODIFIER 21 CODING IGSF9 C protein_coding NM_001135050.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159897132 T C 0 222 0 0.3427 0.131 0.0461 0.0625 0.0477 0.0613 0.283045 0.124497 0.0430712 1 2771 7702 495 311 154 2754 72 1145 2 9642 118388 11544 8592 6614 64614 886 16496 0.97797 0 . 0 . 69 18,14,21,5 UTR_3_PRIME(MODIFIER||3||1179|IGSF9|protein_coding|CODING|NM_001135050.1|21|C),UPSTREAM(MODIFIER||3625||220|TAGLN2|protein_coding|CODING|NM_001277224.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976328 rs2153209 -0.692976 0.41164 69 S1090 1179 tcA/tcG LOW 20 SILENT CODING IGSF9 C protein_coding NM_001135050.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159897638 T C 0 157 0 0.1619 0.0775 0.0288 0.0625 0.0318 0.0603 0.126872 0.0625096 0.0295349 1 1360 5226 285 314 145 2018 52 1052 2 10332 120902 11572 8642 6610 66330 906 16510 0.927661 0 . 0 . 44 8,17,1,15 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1090|1179|IGSF9|protein_coding|CODING|NM_001135050.1|20|C),UPSTREAM(MODIFIER||4131||220|TAGLN2|protein_coding|CODING|NM_001277224.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.763311 rs77570237 -0.689466 0.00531145 44 G34E 1179 gGg/gAg MODERATE 3 MISSENSE CODING IGSF9 T protein_coding NM_001135050.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159912899 C T 0 222 0 0.0212 0.0785 0.1023 0.1528 0.0656 0.0757 0.0267817 0.0456084 0.0552583 1 240 7424 822 1029 313 3968 55 997 2 8798 109690 10386 8088 5298 60872 792 15456 0.994801 0 . 0 . 107 18,37,22,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G34E|1179|IGSF9|protein_coding|CODING|NM_001135050.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987527 rs3747617 -0.693146 0.0243985 107 1179 144 MODIFIER 2 CODING IGSF9 A protein_coding NM_001135050.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159913388 G A 0 188 0 0.2821 0.5513 0.5807 0.8452 0.5189 0.6247 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.745744 0 . 0 . 29 2,10,2,14 START_GAINED(LOW||||1179|IGSF9|protein_coding|CODING|NM_001135050.1|2|A),UTR_5_PRIME(MODIFIER||144||1179|IGSF9|protein_coding|CODING|NM_001135050.1|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.00437385 rs1316275 -0.689466 0.463906 29 I127L 289 Ata/Cta MODERATE 2 MISSENSE CODING SLAMF9 G protein_coding NM_033438.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 159923111 T G 0 228 0 0.7474 0.8902 0.9409 1 0.8966 0.9274 0.756468 0.858604 0.91093 2 7805 109421 11149 8652 5803 60362 823 14827 2 10398 121178 11578 8654 6614 66628 904 16402 0 . 0 . 0 45 0,0,42,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I127L|289|SLAMF9|protein_coding|CODING|NM_033438.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2789417 -0.693146 0.136717 45 379 2062 MODIFIER 2 CODING KCNJ10 C protein_coding NM_002241.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160009121 A C 0 131 0 0.6604 0.481 0.4251 0.3313 0.4175 0.498 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.995386 0 . 0 . 53 2,32,1,17 UTR_3_PRIME(MODIFIER||2062||379|KCNJ10|protein_coding|CODING|NM_002241.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.704669 rs1053074 -0.691153 0.331828 53 379 2040 MODIFIER 2 CODING KCNJ10 C protein_coding NM_002241.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160009143 G C 0 228 0 0.9939 0.9982 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,2,29 UTR_3_PRIME(MODIFIER||2040||379|KCNJ10|protein_coding|CODING|NM_002241.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2486254 -0.69311 0.0902353 31 379 1764 MODIFIER 2 CODING KCNJ10 C protein_coding NM_002241.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160009419 A C 0 61 0 0.8207 0.8628 0.853 0.9603 0.8579 0.8313 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1764||379|KCNJ10|protein_coding|CODING|NM_002241.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2486253 -0.511536 0.235765 3 1029 343 MODIFIER 1 CODING ATP1A4 T protein_coding NM_144699.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160121488 G T 0 9.7 0 0.112 0.2664 0.2795 0.3125 0.3022 0.3814 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||343||1029|ATP1A4|protein_coding|CODING|NM_144699.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2369476,rs386565857 -0.379885 0 1 1029 85 MODIFIER 1 CODING ATP1A4 T protein_coding NM_144699.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160121746 C T 0 126 0 0.1316 0.2704 0.2738 0.3125 0.3012 0.3804 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.531709 0 . 0 . 16 7,0,6,0 START_GAINED(LOW||||1029|ATP1A4|protein_coding|CODING|NM_144699.3|1|T),UTR_5_PRIME(MODIFIER||85||1029|ATP1A4|protein_coding|CODING|NM_144699.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.828239 rs746362 -0.616816 0.80389 16 G83D 1029 gGt/gAt MODERATE 3 MISSENSE CODING ATP1A4 A protein_coding NM_144699.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160124875 G A 0 222 0 0.7458 0.6931 0.7104 0.6835 0.6958 0.6166 0.750113 0.727126 0.715349 1 7895 84683 7732 5783 4292 47600 651 10730 2 10406 121382 11572 8638 6614 66732 908 16512 0.898296 0 . 0 . 157 53,21,44,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G83D|1029|ATP1A4|protein_coding|CODING|NM_144699.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999046 rs6427504 -0.693147 0.0529211 157 A346 1029 gcC/gcT LOW 7 SILENT CODING ATP1A4 T protein_coding NM_144699.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160134205 C T 0 222 0 0.357 0.5288 0.6758 0.5417 0.6421 0.5266 0.40808 0.550515 0.623488 1 4132 73478 8416 5066 4285 41900 557 9122 2 10402 121350 11574 8630 6614 66724 908 16498 0.808269 0 . 0 . 78 7,26,3,38 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A346|1029|ATP1A4|protein_coding|CODING|NM_144699.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.168658 rs11265338 -0.693145 0.0233893 78 A360 1029 gcG/gcA LOW 8 SILENT CODING ATP1A4 A protein_coding NM_144699.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160136350 G A 0 222 0 0.2806 0.4683 0.5375 0.4851 0.5457 0.5757 0.334771 0.487621 0.56593 1 3355 64232 6139 3897 3285 37506 538 9512 2 10402 121326 11572 8620 6608 66708 906 16510 0.730492 0 . 0 . 114 44,7,48,10 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A360|1029|ATP1A4|protein_coding|CODING|NM_144699.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999885 rs55710009,rs7529215 -0.693147 0.0149947 114 Y549 1029 taC/taT LOW 11 SILENT CODING ATP1A4 T protein_coding NM_144699.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160141196 C T 0 228 0 0.9758 0.993 0.9957 1 1 1 0.976169 0.991927 1 2 10159 121138 11559 8654 6614 66734 906 16512 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 121 0,0,56,53 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y549|1029|ATP1A4|protein_coding|CODING|NM_144699.3|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386487977,rs625549 -0.693147 0.0714126 121 151 39 MODIFIER 3 CODING PEA15 G protein_coding NM_001297576.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160178356 A G 0 228 0 0.9644 0.9904 0.9986 1 1 1 0 . 0 2 811 16000 254 382 1600 5110 206 7637 2 842 16032 254 382 1600 5110 206 7638 0 . 0 . 0 57 0,0,40,15 UTR_5_PRIME(MODIFIER||39||151|PEA15|protein_coding|CODING|NM_001297576.1|3|G),INTRAGENIC(MODIFIER|||||LOC729867||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs667306 -0.693147 0.268123 57 597 209 MODIFIER 14 CODING DCAF8 G protein_coding NM_015726.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160187173 A G 0 228 0 0.9955 0.9631 0.9654 1 0.8986 0.9458 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,28,21 UTR_3_PRIME(MODIFIER||209||597|DCAF8|protein_coding|CODING|NM_015726.3|14|G),DOWNSTREAM(MODIFIER||2007||151|PEA15|protein_coding|CODING|NM_001297576.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11265357 -0.693147 0.128669 52 521 2086 MODIFIER 8 CODING VANGL2 T protein_coding NM_020335.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160397254 G T 0 228 0 0.9992 0.9922 0.9899 1 0.9732 0.9959 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,9,22 UTR_3_PRIME(MODIFIER||2086||521|VANGL2|protein_coding|CODING|NM_020335.2|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1324739 -0.69311 0.523001 36 332 921 MODIFIER 8 CODING SLAMF6 G protein_coding NM_001184714.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160455576 A G 0 222 0 0 0.0317 0 0.1022 0 0.0573 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.653738 0 . 0 . 119 49,9,45,7 UTR_3_PRIME(MODIFIER||921||332|SLAMF6|protein_coding|CODING|NM_001184714.1|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.568549 rs149534223 -0.693147 0.0221864 119 345 4863 MODIFIER 8 CODING CD84 G protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160513183 A G 0 9.7 0 0.646 0.7969 0.7695 0.9038 0.9215 0.7822 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4863||345|CD84|protein_coding|CODING|NM_001184879.1|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1503859 -0.379885 0 1 345 3959 MODIFIER 8 CODING CD84 A protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160514087 G A 0 36.3 0 0.1536 0.4679 0.4669 0.6756 0.5696 0.5746 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3959||345|CD84|protein_coding|CODING|NM_001184879.1|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1138323 -0.453602 0.22 2 345 3948 MODIFIER 8 CODING CD84 T protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160514098 C T 0 32.3 0 0.525 0.746 0.745 0.8839 0.8966 0.7485 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3948||345|CD84|protein_coding|CODING|NM_001184879.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1138322 -0.453602 0.22 2 345 3187 MODIFIER 8 CODING CD84 A protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160514859 G A 0 9.7 0 0.5885 0.7734 0.7536 0.9038 0.9066 0.7658 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3187||345|CD84|protein_coding|CODING|NM_001184879.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10797077 -0.379885 0 1 345 2780 MODIFIER 8 CODING CD84 A protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160515266 G A 0 6.3 0 0.3404 0.6695 0.6671 0.8234 0.8767 0.7444 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2780||345|CD84|protein_coding|CODING|NM_001184879.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3737792 -0.379885 0 1 345 2412 MODIFIER 8 CODING CD84 C protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160515634 A C 0 6.3 0 0.5825 0.7726 0.7536 0.9048 0.9076 0.7679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2412||345|CD84|protein_coding|CODING|NM_001184879.1|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3737789 -0.379885 0 1 345 2382 MODIFIER 8 CODING CD84 T protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160515664 C T 0 39.3 0 0.5802 0.772 0.7536 0.9048 0.9076 0.7679 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2382||345|CD84|protein_coding|CODING|NM_001184879.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3737788 -0.453602 0.14 2 345 2242 MODIFIER 8 CODING CD84 A protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160515804 T A 0 9.7 0 0.5257 0.7468 0.745 0.8839 0.8976 0.7505 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2242||345|CD84|protein_coding|CODING|NM_001184879.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6677895 -0.379885 0 1 345 2233 MODIFIER 8 CODING CD84 C protein_coding NM_001184879.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160515813 G C 0 9.7 0 0.5802 0.7718 0.7536 0.9038 0.9076 0.7679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2233||345|CD84|protein_coding|CODING|NM_001184879.1|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6686346 -0.379885 0 1 335 523 MODIFIER 7 CODING SLAMF1 G protein_coding NM_003037.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160580015 A G 0 228 0 0.1657 0.4694 0.4669 0.6895 0.5656 0.5562 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 76 0,0,63,7 UTR_3_PRIME(MODIFIER||523||335|SLAMF1|protein_coding|CODING|NM_003037.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1061217 -0.693147 0.192056 76 I244T 252 aTt/aCt MODERATE 3 MISSENSE CODING CD48 G protein_coding NM_001256030.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160650913 A G 0 228 0 0.3767 0.8287 0.9539 1 0.998 1 0 . 0 2 4201 104496 9985 7697 5873 60382 796 15562 2 7882 108616 10212 7700 5874 60542 816 15590 0 . 0 . 0 102 0,0,69,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I244T|252|CD48|protein_coding|CODING|NM_001256030.1|3|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4656926 -0.693147 0.0893403 102 335 289 MODIFIER 7 CODING SLAMF7 G protein_coding NM_021181.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160723256 A G 0 6.3 0 0.4856 0.6897 0.8084 0.7976 0.6869 0.773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||289||335|SLAMF7|protein_coding|CODING|NM_021181.4|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs495706 -0.379885 0 1 335 550 MODIFIER 7 CODING SLAMF7 G protein_coding NM_021181.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160723517 A G 0 36.3 0 0.4856 0.6897 0.8084 0.7976 0.6869 0.773 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||550||335|SLAMF7|protein_coding|CODING|NM_021181.4|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs518721 -0.453602 0.44 2 335 990 MODIFIER 7 CODING SLAMF7 C protein_coding NM_021181.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160723957 T C 0 70 0 0.0113 0.3059 0.4784 0.4315 0.3668 0.3896 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||990||335|SLAMF7|protein_coding|CODING|NM_021181.4|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs523130 -0.453602 0.22 3 V562 655 gtA/gtG LOW 8 SILENT CODING LY9 G protein_coding NM_002348.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160793442 A G 0 228 0 0.6884 0.6322 0.6643 0.7034 0.4493 0.6483 0.636632 0.494387 0.421512 2 6780 64258 8532 6314 3183 29118 443 9888 2 10398 121358 11572 8644 6610 66714 908 16512 0 . 0 . 0 53 0,0,22,29 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V562|655|LY9|protein_coding|CODING|NM_002348.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs474131 -0.693147 0.363339 53 M602V 655 Atg/Gtg MODERATE 8 MISSENSE CODING LY9 G protein_coding NM_002348.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160793560 A G 0 228 0 0.7912 0.6601 0.6686 0.7034 0.4503 0.6483 0.735588 0.52791 0.421512 2 7781 65293 8576 6315 3183 29107 447 9884 2 10376 121172 11572 8646 6612 66600 904 16462 0 . 0 . 0 40 0,0,9,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M602V|655|LY9|protein_coding|CODING|NM_002348.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs509749 -0.693141 0.40184 40 655 78 MODIFIER 10 CODING LY9 G protein_coding NM_002348.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160797684 A G 0 149 0 0.5613 0.6014 0.6571 0.6954 0.4672 0.6575 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 17 0,1,0,16 UTR_3_PRIME(MODIFIER||78||655|LY9|protein_coding|CODING|NM_002348.3|10|G),DOWNSTREAM(MODIFIER||2266||370|CD244|protein_coding|CODING|NM_001166663.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs574610 -0.689466 0.385941 17 370 657 MODIFIER 9 CODING CD244 C protein_coding NM_001166663.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160800480 T C 0 9.7 0 0.6762 0.6316 0.6657 0.6984 0.4682 0.6462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||657||370|CD244|protein_coding|CODING|NM_001166663.1|9|C),DOWNSTREAM(MODIFIER||2435||655|LY9|protein_coding|CODING|NM_002348.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs485618 -0.379885 0 1 370 91 MODIFIER 9 CODING CD244 G protein_coding NM_001166663.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160801046 C G 0 157 0 0.1725 0.2568 0.2248 0.376 0.2008 0.3282 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.821886 0 . 0 . 34 17,3,11,2 UTR_3_PRIME(MODIFIER||91||370|CD244|protein_coding|CODING|NM_001166663.1|9|G),DOWNSTREAM(MODIFIER||3001||655|LY9|protein_coding|CODING|NM_002348.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.5762 rs480104 -0.683931 0.129369 34 370 179 MODIFIER 1 CODING CD244 G protein_coding NM_001166663.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160832646 A G 0 110 0 0.3601 0.3099 0.232 0.3839 0.1968 0.3374 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.571429 0 . 0 . 9 0,2,1,6 UTR_5_PRIME(MODIFIER||179||370|CD244|protein_coding|CODING|NM_001166663.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.857143 rs12036607 -0.636426 0.757551 9 313 LOW 5 CODING ITLN1 C protein_coding NM_017625.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160850936 T C 0 222 0 0.5968 0.6723 0.7277 0.6974 0.6799 0.7014 0.610304 0.661233 0.687326 1 6302 80995 8598 5941 4528 44859 621 10146 2 10368 118590 11554 8634 6612 66098 886 14438 0.73394 0 . 0 . 95 29,6,35,11 SPLICE_SITE_REGION+INTRON(LOW||||313|ITLN1|protein_coding|CODING|NM_017625.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.310136 rs2236515 -0.693147 0.859428 95 V109D 313 gTc/gAc MODERATE 4 MISSENSE CODING ITLN1 T protein_coding NM_017625.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160851826 A T 0 222 0 0.3275 0.5813 0.696 0.6935 0.6779 0.6278 0.376759 0.578502 0.68186 1 3894 78730 8472 5942 4528 44871 613 10410 2 10406 121364 11570 8632 6614 66722 908 16512 0.905237 0 . 0 . 166 35,39,34,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V109D|313|ITLN1|protein_coding|CODING|NM_017625.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.958918 0.955473 0 0.998041 rs2274907 -0.693147 0.338401 166 H86 313 caC/caT LOW 4 SILENT CODING ITLN1 A protein_coding NM_017625.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160851894 G A 0 222 0 0.3147 0.5779 0.6945 0.6944 0.6779 0.6278 0.368815 0.575273 0.681046 1 3799 78515 8462 5937 4528 44772 611 10406 2 10402 121252 11568 8626 6612 66682 908 16454 0.957094 0 . 0 . 132 14,50,9,50 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H86|313|ITLN1|protein_coding|CODING|NM_017625.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.986964 0.997222 0 0.591278 rs2274908,rs55974765 -0.693147 0.0664222 132 R103H 325 cGt/cAt MODERATE 4 MISSENSE CODING ITLN2 T protein_coding NM_080878.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160920966 C T 0 222 0 0.3101 0.4882 0.6066 0.5635 0.5736 0.4796 0.355878 0.49085 0.56 1 3582 64961 7316 4740 4121 36883 526 7793 2 10404 121284 11572 8608 6608 66686 906 16500 0.537694 0 . 0 . 237 30,91,30,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R103H|325|ITLN2|protein_coding|CODING|NM_080878.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.465858 rs6680969 -0.693147 0.672793 237 299 3326 MODIFIER 10 CODING F11R A protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160965335 G A 0 82 0 0.0507 0.1725 0.2421 0.1944 0.3022 0.1319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,2,1 UTR_3_PRIME(MODIFIER||3326||299|F11R|protein_coding|CODING|NM_016946.4|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs61803665 -0.511536 0.578719 5 299 2229 MODIFIER 10 CODING F11R T protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160966432 C T 0 38.3 0 0.0514 0.1785 0.2752 0.2024 0.2992 0.1329 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2229||299|F11R|protein_coding|CODING|NM_016946.4|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs41267947 -0.453602 0.96 2 299 2062 MODIFIER 10 CODING F11R C protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160966599 T C 0 31.9 0 0.0514 0.1785 0.2752 0.2024 0.2992 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||2062||299|F11R|protein_coding|CODING|NM_016946.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs41267951 -0.453602 0.48 3 299 1817 MODIFIER 10 CODING F11R T protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160966844 C T 0 9.7 0 0.0514 0.1787 0.2752 0.2024 0.3002 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1817||299|F11R|protein_coding|CODING|NM_016946.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1062827 -0.379885 0 1 299 1206 MODIFIER 10 CODING F11R C protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160967455 T C 0 222 0 0.0514 0.1785 0.2752 0.2024 0.2992 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.507368 0 . 0 . 224 67,51,55,28 UTR_3_PRIME(MODIFIER||1206||299|F11R|protein_coding|CODING|NM_016946.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.562594 rs12565932 -0.693147 0.0859387 224 299 656 MODIFIER 10 CODING F11R C protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160968005 G C 0 31.9 0 0.0514 0.1785 0.2752 0.2024 0.2992 0.1329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||656||299|F11R|protein_coding|CODING|NM_016946.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1062826 -0.453602 0.48 3 299 437 MODIFIER 10 CODING F11R A protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160968224 G A 0 64 0 0.0514 0.1787 0.2767 0.2024 0.2992 0.1329 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||437||299|F11R|protein_coding|CODING|NM_016946.4|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs836 -0.511536 0.450604 3 299 52 MODIFIER 10 CODING F11R A protein_coding NM_016946.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160968609 G A 0 222 0 0.0393 0.1749 0.2723 0.2024 0.2992 0.1329 0.067602 0.216019 0.280988 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.837046 0 . 0 . 232 72,47,51,35 UTR_3_PRIME(MODIFIER||52||299|F11R|protein_coding|CODING|NM_016946.4|10|A) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.568445 rs41269993 -0.693147 0.243832 232 299 LOW 5 CODING F11R C protein_coding NM_016946.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160969930 A C 0 222 0 0.0514 0.1785 0.2752 0.2014 0.2992 0.1339 0.0830685 0.214516 0.28186 1 810 29785 3115 1625 2289 19492 243 2211 2 10404 121350 11572 8626 6608 66722 906 16512 0.754061 0 . 0 . 315 97,79,75,41 SPLICE_SITE_REGION+INTRON(LOW||||299|F11R|protein_coding|CODING|NM_016946.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913132 rs869985 -0.693147 0.213598 315 299 LOW 1 CODING F11R G protein_coding NM_016946.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160971146 A G 0 228 0 0.9206 0.8299 0.804 0.8343 0.7913 0.7607 0.886064 0.82239 0.789767 2 9211 97558 9605 7410 5108 52732 729 12763 2 10400 121206 11556 8634 6602 66600 906 16508 1 0 . 0 . 188 1,0,89,75 SPLICE_SITE_REGION+INTRON(LOW||||299|F11R|protein_coding|CODING|NM_016946.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs790055 -0.693147 0.1142 188 299 12 MODIFIER 1 CODING F11R C protein_coding NM_016946.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160990875 T C 0 222 0 0.7678 0.626 0.5231 0.6339 0.499 0.6299 0.177258 0.125557 0.0990698 1 7293 66191 6246 5628 2804 33206 481 10533 2 10240 118794 11306 8476 6122 65322 880 16448 0.664019 0 . 0 . 263 47,87,33,59 UTR_5_PRIME(MODIFIER||12||299|F11R|protein_coding|CODING|NM_016946.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.00260349 rs28365980 -0.693147 0.00197752 263 299 13 MODIFIER 1 CODING F11R A protein_coding NM_016946.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160990876 C A 0 222 0 0.767 0.6252 0.5216 0.6329 0.498 0.6299 0.0628688 0.045825 0.037093 1 7295 66221 6252 5631 2815 33215 483 10530 2 10296 119836 11388 8500 6390 65916 890 16456 0.781613 0 . 0 . 260 44,90,33,59 UTR_5_PRIME(MODIFIER||13||299|F11R|protein_coding|CODING|NM_016946.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0072678 rs28365979 -0.693147 0.0019369 260 299 15 MODIFIER 1 CODING F11R T protein_coding NM_016946.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160990878 C T 0 222 0 0.767 0.6252 0.5216 0.6329 0.498 0.6299 0.460054 0.3167 0.243256 1 7286 66188 6245 5628 2811 33206 484 10528 2 10284 119756 11366 8498 6386 65876 894 16452 0.976197 0 . 0 . 260 43,91,33,59 UTR_5_PRIME(MODIFIER||15||299|F11R|protein_coding|CODING|NM_016946.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.022345 rs28365978 -0.693147 0.0018579 260 299 43 MODIFIER 1 CODING F11R A protein_coding NM_016946.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 160990906 G A 0 222 0 0.1513 0.2045 0.2839 0.2024 0.2922 0.1319 0.172038 0.23666 0.269767 1 1755 29540 3080 1634 2096 18540 235 2200 2 10130 119298 11298 8502 6422 65648 886 16412 0.566812 0 . 0 . 217 27,65,20,81 UTR_5_PRIME(MODIFIER||43||299|F11R|protein_coding|CODING|NM_016946.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.714961 rs2481085 -0.693147 4.0444e-05 217 310 187 MODIFIER 11 CODING USF1 A protein_coding NM_001276373.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161009523 G A 0 56 0 0.0371 0.1703 0.2637 0.1925 0.2942 0.1339 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 255 other 0 . 22 17,0,4,1 UTR_3_PRIME(MODIFIER||187||310|USF1|protein_coding|CODING|NM_001276373.1|11|A),UPSTREAM(MODIFIER||749||115|TSTD1|protein_coding|CODING|NM_001113207.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.779897 rs3737787 -0.590765 0.831179 22 310 163 MODIFIER 11 CODING USF1 T protein_coding NM_001276373.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161009547 C T 0 135 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.862013 0 . 0 . 26 15,0,9,2 UTR_3_PRIME(MODIFIER||163||310|USF1|protein_coding|CODING|NM_001276373.1|11|T),UPSTREAM(MODIFIER||773||115|TSTD1|protein_coding|CODING|NM_001113207.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.1098 rs34985495 -0.676189 0.034293 26 310 56 MODIFIER 2 CODING USF1 T protein_coding NM_001276373.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161013121 C T 0 228 0 0.1846 0.3968 0.4654 0.3333 0.6292 0.4611 0.268064 0.507884 0.612194 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 0,0,21,44 UTR_5_PRIME(MODIFIER||56||310|USF1|protein_coding|CODING|NM_001276373.1|2|T),UPSTREAM(MODIFIER||4347||115|TSTD1|protein_coding|CODING|NM_001113207.1||T),DOWNSTREAM(MODIFIER||3611||1101|ARHGAP30|protein_coding|CODING|NM_001025598.1||T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2516839 -0.693147 0.302944 73 310 1662 MODIFIER 1 CODING USF1 G protein_coding NM_001276373.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161014727 A G 0 32.6 0 0.1884 0.398 0.4654 0.3343 0.6292 0.4611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 START_GAINED(LOW||||310|USF1|protein_coding|CODING|NM_001276373.1|1|G),UTR_5_PRIME(MODIFIER||1662||310|USF1|protein_coding|CODING|NM_001276373.1|1|G),DOWNSTREAM(MODIFIER||2005||1101|ARHGAP30|protein_coding|CODING|NM_001025598.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2516837 -0.379885 0 2 1101 423 MODIFIER 12 CODING ARHGAP30 C protein_coding NM_001025598.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161017082 T C 0 84 0 0 0.010982 0 0.0536 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.857112 0 . 0 . 10 0,5,1,4 UTR_3_PRIME(MODIFIER||423||1101|ARHGAP30|protein_coding|CODING|NM_001025598.1|12|C),UPSTREAM(MODIFIER||2355||310|USF1|protein_coding|CODING|NM_001276373.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.428556 rs35251010 -0.590765 0.387565 10 R1085 1101 agG/agA LOW 12 SILENT CODING ARHGAP30 T protein_coding NM_001025598.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161017556 C T 0 222 0 0.1422 0.2183 0.2003 0.1389 0.333 0.2975 0.192011 0.284638 0.332093 1 1891 31291 1766 1261 1718 20928 213 3514 2 10248 112894 11488 8570 6612 64518 818 10640 0.532874 0 . 0 . 75 17,23,15,11 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R1085|1101|ARHGAP30|protein_coding|CODING|NM_001025598.1|12|T),UPSTREAM(MODIFIER||2829||310|USF1|protein_coding|CODING|NM_001276373.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.927803 rs2774279 -0.692976 0.199079 75 L591V 1101 Ctg/Gtg MODERATE 12 MISSENSE CODING ARHGAP30 C protein_coding NM_001025598.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161019040 G C 0 228 0 0.1815 0.396 0.4654 0.3333 0.6292 0.4611 0.262823 0.490543 0.607209 2 2592 62965 4784 2859 4063 40525 468 7674 2 10332 121192 11568 8628 6608 66654 904 16498 0.750377 0 . 0 . 39 0,3,14,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L591V|1101|ARHGAP30|protein_coding|CODING|NM_001025598.1|12|C),UPSTREAM(MODIFIER||4313||310|USF1|protein_coding|CODING|NM_001276373.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.605643 rs3813609 -0.693136 0.786659 39 349 86 MODIFIER 1 CODING KLHDC9 A protein_coding NM_152366.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161068240 G A 0 101 0 0.2194 0.344 0.3761 0.4375 0.4274 0.3078 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994135 0 . 0 . 17 8,2,4,2 UTR_5_PRIME(MODIFIER||86||349|KLHDC9|protein_coding|CODING|NM_152366.4|1|A),DOWNSTREAM(MODIFIER||2106||154|PFDN2|protein_coding|CODING|NM_012394.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.588086 rs3813611 -0.616816 0.114818 17 S171R 349 Agc/Cgc MODERATE 1 MISSENSE CODING KLHDC9 C protein_coding NM_152366.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161068836 A C 0 51 0 0.0666 0.2392 0.2968 0.371 0.339 0.1933 0.0927107 0.218026 0.282309 1 806 29051 3322 2698 1803 17069 211 3142 2 6546 94924 9736 6972 5006 52322 704 13638 0.991513 0 . 0 COSM424365,COSM424364 15 0,11,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Cgc|S171R|349|KLHDC9|protein_coding|CODING|NM_152366.4|1|C),DOWNSTREAM(MODIFIER||1510||154|PFDN2|protein_coding|CODING|NM_012394.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991513 rs11576830 -0.556411 0.725151 15 393 174 MODIFIER 8 CODING B4GALT3 G protein_coding NM_001199873.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161141432 C G 0 222 0 0.0658 0.228 0.2968 0.375 0.2942 0.1789 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.577074 0 . 0 . 82 25,22,20,12 UTR_3_PRIME(MODIFIER||174||393|B4GALT3|protein_coding|CODING|NM_001199873.1|8|G),DOWNSTREAM(MODIFIER||422||477|PPOX|protein_coding|CODING|NM_000309.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.986515 rs6779 -0.69312 0.273369 82 837 56 MODIFIER 9 CODING ADAMTS4 C protein_coding NM_005099.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161160872 T C 0 222 0 0.0333 0.1647 0.2305 0.3621 0.1551 0.1022 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.70981 0 . 0 . 84 25,22,8,17 UTR_3_PRIME(MODIFIER||56||837|ADAMTS4|protein_coding|CODING|NM_005099.4|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.90151 rs34884997 -0.692914 0.0680568 84 Q626R 837 cAg/cGg MODERATE 7 MISSENSE CODING ADAMTS4 C protein_coding NM_005099.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161163037 T C 0 228 0 0.5893 0.7069 0.7089 0.8859 0.6093 0.7802 0.607808 0.602799 0.600233 2 6320 79644 9180 7788 3824 39594 573 12365 2 10288 120252 11500 8618 6322 66134 894 16496 0 . 0 . COSM424371,COSM1472886 116 0,0,92,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q626R|837|ADAMTS4|protein_coding|CODING|NM_005099.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4233367 -0.693147 0.587942 116 S138 837 tcG/tcA LOW 1 SILENT CODING ADAMTS4 T protein_coding NM_005099.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161168004 C T 0 222 0 0.4145 0.365 0.3141 0.4494 0.2087 0.408 0.360191 0.258573 0.206512 1 3877 34022 4324 4282 1451 13890 246 5952 2 10314 120696 11546 8590 6610 66242 898 16496 0.610757 0 . 0 . 102 14,26,12,36 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S138|837|ADAMTS4|protein_coding|CODING|NM_005099.4|1|T),UPSTREAM(MODIFIER||1101||463|NDUFS2|protein_coding|CODING|NM_004550.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999921 rs33941127 -0.693147 0.0238485 102 463 3011 MODIFIER 1 CODING NDUFS2 T protein_coding NM_004550.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161169165 G T 0 63 0 0.0356 0.1589 0.232 0.3522 0.1382 0.0961 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 START_GAINED(LOW||||463|NDUFS2|protein_coding|CODING|NM_004550.4|1|T),UTR_5_PRIME(MODIFIER||3011||463|NDUFS2|protein_coding|CODING|NM_004550.4|1|T),UPSTREAM(MODIFIER||320||837|ADAMTS4|protein_coding|CODING|NM_005099.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3813623 -0.453602 0.42 3 A430 463 gcC/gcT LOW 13 SILENT CODING NDUFS2 T protein_coding NM_004550.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161183516 C T 0 222 0 0.0348 0.1581 0.2291 0.3562 0.1392 0.09 0.0506128 0.105951 0.134302 1 503 18491 3101 2883 742 9393 124 1745 2 10404 121388 11570 8646 6614 66734 908 16512 0.845496 3 likely-benign 0 . 97 29,26,21,14 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A430|463|NDUFS2|protein_coding|CODING|NM_004550.4|13|T),UPSTREAM(MODIFIER||1571||86|FCER1G|protein_coding|CODING|NM_004106.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.687953 rs1136207 -0.693136 0.506808 97 463 114 MODIFIER 15 CODING NDUFS2 G protein_coding NM_004550.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161184097 A G 0 202 0 0.0287 0.1821 0.2176 0.2758 0.1521 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.985816 0 . 0 . 39 0,18,3,18 UTR_3_PRIME(MODIFIER||114||463|NDUFS2|protein_coding|CODING|NM_004550.4|15|G),UPSTREAM(MODIFIER||990||86|FCER1G|protein_coding|CODING|NM_004106.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666078 rs1136224 -0.692352 0.854978 39 86 203 MODIFIER 5 CODING FCER1G C protein_coding NM_004106.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161188936 T C 0 95 0 0.0938 0.1961 0.2349 0.4018 0.1471 0.1452 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.828239 0 . 0 . 13 0,6,0,7 UTR_3_PRIME(MODIFIER||203||86|FCER1G|protein_coding|CODING|NM_004106.1|5|C),DOWNSTREAM(MODIFIER||4752||463|NDUFS2|protein_coding|CODING|NM_004550.4||C),DOWNSTREAM(MODIFIER||3147||100|APOA2|protein_coding|CODING|NM_001643.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.695312 rs11421 -0.636426 0.0269308 13 100 LOW 3 CODING APOA2 A protein_coding NM_001643.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161192316 G A 0 222 0 0.0121 0.103 0.0735 0.1696 0.1083 0.1728 0.030867 0.0821928 0.108488 1 312 13782 1433 1487 646 7427 86 2391 2 10406 121402 11576 8652 6614 66734 908 16512 0.945925 0 . 0 . 106 21,36,13,27 SPLICE_SITE_REGION+INTRON(LOW||||100|APOA2|protein_coding|CODING|NM_001643.1|3|A),UPSTREAM(MODIFIER||3413||308|TOMM40L|protein_coding|CODING|NM_032174.5||A),DOWNSTREAM(MODIFIER||3278||86|FCER1G|protein_coding|CODING|NM_004106.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.907855 rs6413453 -0.693145 0.172245 106 308 114 MODIFIER 2 CODING TOMM40L C protein_coding NM_032174.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161196166 A C 0 197 0 0.0741 0.3137 0.3473 0.5367 0.3449 0.3517 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 0,0,27,1 UTR_5_PRIME(MODIFIER||114||308|TOMM40L|protein_coding|CODING|NM_032174.5|2|C),UPSTREAM(MODIFIER||2748||100|APOA2|protein_coding|CODING|NM_001643.1||C),DOWNSTREAM(MODIFIER||3290||357|NR1I3|protein_coding|CODING|NM_001077482.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3813628 -0.693054 0.229928 28 308 1602 MODIFIER 10 CODING TOMM40L A protein_coding NM_032174.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161200487 C A 0 228 0 0.7829 0.7654 0.719 0.8998 0.6183 0.7873 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,4,23 UTR_3_PRIME(MODIFIER||1602||308|TOMM40L|protein_coding|CODING|NM_032174.5|10|A),INTRON(MODIFIER||||357|NR1I3|protein_coding|CODING|NM_001077482.2|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386590491,rs4073054 -0.693021 0.449668 27 P180 357 ccC/ccT LOW 5 SILENT CODING NR1I3 A protein_coding NM_001077482.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161202605 G A 0 228 0 0.1067 0.3363 0.3256 0.5188 0.3489 0.453 0.143441 0.269875 0.334651 2 1471 42888 4572 4630 2101 23219 307 6588 2 10400 121348 11574 8634 6614 66706 908 16512 1 2 benign 0 . 109 1,0,62,35 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P180|357|NR1I3|protein_coding|CODING|NM_001077482.2|5|A),DOWNSTREAM(MODIFIER||2069||308|TOMM40L|protein_coding|CODING|NM_032174.5||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2307424 -0.693147 0.201166 109 H167R 317 cAt/cGt MODERATE 4 MISSENSE CODING FCGR2A G protein_coding NM_001136219.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161479745 A G 0 222 0 0.5257 0.4417 0.451 0.2778 0.5109 0.4192 0.55833 0.530986 0.516977 1 5680 58144 6030 2827 3360 32979 412 6856 2 10406 121362 11572 8634 6600 66734 908 16508 0.985558 255|255|255 other|other|other 0 . 234 62,29,63,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H167R|317|FCGR2A|protein_coding|CODING|NM_001136219.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.377523 rs1801274 -0.693147 0.0875628 234 T343 643 acA/acT LOW 1 SILENT CODING HSPA6 T protein_coding NM_002155.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161495477 A T 0 222 0 . 0 . 0 . 0 0.667726 0.653083 0.645581 1 6850 77190 7365 5900 4127 42742 576 9630 2 10248 120002 11388 8580 6516 65948 900 16422 0.772673 0 . 0 . 196 67,65,18,35 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T343|643|HSPA6|protein_coding|CODING|NM_002155.4|1|T) 1 0.5 1 0 . 0 . 1 1 0 57 0 0.855467 0.521806 0 0.148617 rs72633678 -0.693147 0.00220156 196 A375S 643 Gct/Tct MODERATE 1 MISSENSE CODING HSPA6 T protein_coding NM_002155.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161495571 G T 0 51 0 . 0 . 0 . 0 . 0 . 1 151 3164 647 1683 32 80 13 558 2 5604 78520 6414 6144 4162 43124 606 12466 0.340816 0 . 0 . 86 19,45,0,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A375S|643|HSPA6|protein_coding|CODING|NM_002155.4|1|T) 0 0.5 1 0 . 0 . 0 1 0 48 0 0.0619152 0.0773185 0 0.69633 rs140052915,rs9659608 -0.692352 0.0544242 86 T479 643 acT/acC LOW 1 SILENT CODING HSPA6 C protein_coding NM_002155.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161495885 T C 0 222 0 0.7791 0.8011 0.7233 0.9117 0.7883 0.7853 0.793236 0.76557 0.751395 1 8266 93427 8556 8047 4861 50241 678 12778 2 10396 121262 11538 8640 6604 66676 906 16502 0.28801 0 . 0 . 117 38,21,36,18 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T479|643|HSPA6|protein_coding|CODING|NM_002155.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.866859 0.909791 0 0.997624 rs404508 -0.693147 0.134433 117 643 150 MODIFIER 1 CODING HSPA6 G protein_coding NM_002155.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161496530 C G 0 222 0 0.4508 0.3928 0.4193 0.372 0.3579 0.3528 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.703827 0 . 0 . 85 15,28,16,15 UTR_3_PRIME(MODIFIER||150||643|HSPA6|protein_coding|CODING|NM_002155.4|1|G) 0 0.5 1 0 . 1 0 . 0 . 58 0 0.998501 0.998501 0 0.999265 rs1042881 -0.69311 0.101233 85 I142V 290 Atc/Gtc MODERATE 3 MISSENSE CODING FCGR3A C protein_coding NM_000569.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161518214 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 2174 35843 4843 3771 1838 17707 250 5260 2 10210 119978 11444 8524 6502 65972 906 16420 0.282514 1 not-provided 0 . 290 135,21,88,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I142V|290|FCGR3A|protein_coding|CODING|NM_000569.6|3|C) 0 0.5 1 0 . 0 . 0 1 0 42 0 0.00413669 0.325158 0 0.714584 rs148181339 -0.693147 0.0338565 290 S101N 290 aGc/aAc MODERATE 3 MISSENSE CODING FCGR3A T protein_coding NM_000569.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161518336 C T 0 104 0 . 0 . 0 . 0 . 0 . 1 764 11304 1910 1538 419 4692 85 1896 2 9794 111330 9788 7410 6188 62268 838 15044 0.934334 1 not-provided 0 . 305 93,109,43,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S101N|290|FCGR3A|protein_coding|CODING|NM_000569.6|3|T) 0 0.5 1 0 . 0 . 0 1 0 49 0 2.07798e-11 0.0768025 0 0.978316 rs77144485 -0.693147 0.103586 305 T118I 323 aCc/aTc MODERATE 3 MISSENSE CODING FCGR2C T protein_coding NM_201563.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161559571 C T 0 222 0 0.0121 0.1939 0.3718 0.1716 0.2714 0.2566 0.0669456 0.210807 0.285697 1 577 30372 4581 1430 2011 17305 232 4236 2 9266 110480 10836 8456 5720 59842 802 15558 0.65707 0 . 0 COSN163305 146 35,49,26,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T118I|323|FCGR2C|protein_coding|CODING|NM_201563.5|3|T) 1 0.5 1 0 . 1 0 1 1 0 50 0 0.697505 0.391556 0 0.979201 rs138747765 -0.693147 0.603468 146 T203 323 acG/acA LOW 4 SILENT CODING FCGR2C A protein_coding NM_201563.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161561151 G A 0 222 0 0.1573 0.1989 0.1542 0.4067 0.0944 0.18 0.144901 0.0909522 0.0628901 1 1418 13206 1292 3330 757 4465 94 1850 2 9080 105420 9778 7900 5556 58318 772 14016 0.752161 0 . 0 . 198 38,45,43,43 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T203|323|FCGR2C|protein_coding|CODING|NM_201563.5|4|A) 1 0.5 1 0 . 1 0 1 1 0 50 0 0.915043 0.6886 0 0.708493 rs74341264 -0.693147 0.333922 198 323 236 MODIFIER 7 CODING FCGR2C C protein_coding NM_201563.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161569829 G C 0 58 0 0.025 0.0823 0.0533 0.2847 0 0.0562 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,1,2 UTR_3_PRIME(MODIFIER||236||323|FCGR2C|protein_coding|CODING|NM_201563.5|7|C) 0 . 0 . 0 1 0 . 0 . 41 0 1 1 0 1 rs138527633 -0.511536 0.37344 5 269 956 MODIFIER 5 CODING FCGR3B T protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593349 C T 0 7.9 0 0.8737 0.896 0.9452 0.7411 0.999 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||956||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 35 0 0 . 0 . rs61803002 -0.379885 0 1 269 837 MODIFIER 5 CODING FCGR3B G protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593468 A G 0 6.3 0 0.8759 0.8966 0.9467 0.7401 0.999 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||837||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|G) 0 0.5 1 0 . 1 0 . 0 . 54 0 0 . 0 . rs61803003 -0.379885 0 1 269 754 MODIFIER 5 CODING FCGR3B G protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593551 T G 0 9.7 0 0.8601 0.892 0.9424 0.7411 0.999 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||754||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs61803004 -0.379885 0 1 269 734 MODIFIER 5 CODING FCGR3B G protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593571 A G 0 9.7 0 0.8601 0.8918 0.9424 0.7411 0.999 0.9438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||734||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs61803005 -0.379885 0 1 269 347 MODIFIER 5 CODING FCGR3B T protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593958 C T 0 17.3 0 0.7769 0.8205 0.8617 0.7411 0.8598 0.8916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 3,0,2,0 UTR_3_PRIME(MODIFIER||347||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 0 . 0.666667 rs67167367 -0.453602 0.94 5 269 343 MODIFIER 5 CODING FCGR3B A protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161593962 G A 0 20.3 0 0.8669 0.8452 0.8674 0.7411 0.8608 0.8916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 3,0,2,0 UTR_3_PRIME(MODIFIER||343||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 0 . 0.666667 rs67411091 -0.453602 0.94 5 269 274 MODIFIER 5 CODING FCGR3B T protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161594031 G T 0 27.8 0 0.0749 0.0899 0.049 0.2589 0.001 0.0562 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.641538 0 . 0 . 10 7,0,3,0 UTR_3_PRIME(MODIFIER||274||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 53 0 0.916482 0 . 0.916482 rs138053195 -0.511536 0.243476 10 269 79 MODIFIER 5 CODING FCGR3B T protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161594226 C T 0 222 0 0.8737 0.896 0.9452 0.7411 0.999 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998774 0 . 0 . 146 49,15,58,11 UTR_3_PRIME(MODIFIER||79||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 56 0 0.0925364 0.687765 0 0.999959 rs61803008 -0.693147 0.00230046 146 269 59 MODIFIER 5 CODING FCGR3B T protein_coding NM_001244753.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161594246 G T 0 222 0 0.8737 0.896 0.9452 0.7411 0.999 0.9448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996866 0 . 0 . 177 60,19,64,16 UTR_3_PRIME(MODIFIER||59||269|FCGR3B|protein_coding|CODING|NM_001244753.1|5|T) 0 0.5 1 0 . 1 0 . 0 . 57 0 0.0934807 0.873708 0 0.851664 rs61803009 -0.693147 0.0159476 177 I142V 269 Atc/Gtc MODERATE 3 MISSENSE CODING FCGR3B C protein_coding NM_001244753.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161599571 T C 0 97 0 . 0 . 0 . 0 . 0 . 2 1810 35197 4691 3864 1958 16861 241 5772 2 7502 104306 9502 6914 5934 59114 770 14570 1 5 pathogenic 0 . 16 1,0,15,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I142V|269|FCGR3B|protein_coding|CODING|NM_001244753.1|3|C) 0 . 0 . 0 . 0 . 1 0 29 0 1 0 . 1 rs199890941,rs2290834 -0.688148 0.0447362 16 N118D 269 Aac/Gac MODERATE 3 MISSENSE CODING FCGR3B C protein_coding NM_001244753.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161599643 T C 0 70 0 0.3328 0.2835 0.2709 0.4177 0.1332 0.2423 0 . 0 2 841 8057 1170 1400 167 2874 51 1554 2 7950 100822 8712 6184 5686 58246 760 13284 1 5 pathogenic 0 . 11 1,0,9,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N118D|269|FCGR3B|protein_coding|CODING|NM_001244753.1|3|C) 0 . 0 . 0 1 0 . 1 0 25 0 1 0 . 1 rs147574249 -0.662043 0.0383488 11 269 3 MODIFIER 1 CODING FCGR3B T protein_coding NM_001244753.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161600995 C T 0 228 0 0.357 0.4451 0.5086 0.6627 0.336 0.407 0 . 0 2 3175 43778 5697 4828 2341 21036 298 6403 2 8608 103630 10082 7614 5738 56808 754 14026 0 . 0 . 0 128 0,0,41,79 UTR_5_PRIME(MODIFIER||3||269|FCGR3B|protein_coding|CODING|NM_001244753.1|1|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs34085961 -0.693147 0.0079237 128 269 126 MODIFIER 1 CODING FCGR3B C protein_coding NM_001244753.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161601118 G C 0 208 0 0.3964 0.4874 0.5994 0.7202 0.3638 0.4182 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,1,30 UTR_5_PRIME(MODIFIER||126||269|FCGR3B|protein_coding|CODING|NM_001244753.1|1|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs61803026 -0.69311 0.549365 31 269 141 MODIFIER 1 CODING FCGR3B C protein_coding NM_001244753.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161601133 T C 0 214 0 0.8873 0.969 0.9928 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 30 0,0,1,29 UTR_5_PRIME(MODIFIER||141||269|FCGR3B|protein_coding|CODING|NM_001244753.1|1|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs61803027 -0.693097 0.485334 30 269 181 MODIFIER 1 CODING FCGR3B T protein_coding NM_001244753.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161601173 A T 0 228 0 0.3555 0.4435 0.5072 0.6617 0.335 0.4039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,2,17 UTR_5_PRIME(MODIFIER||181||269|FCGR3B|protein_coding|CODING|NM_001244753.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs34322334 -0.69168 0.0214553 19 269 239 MODIFIER 1 CODING FCGR3B G protein_coding NM_001244753.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161601231 A G 0 147 0 0.3555 0.4437 0.5086 0.6617 0.335 0.4039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,1,5 UTR_5_PRIME(MODIFIER||239||269|FCGR3B|protein_coding|CODING|NM_001244753.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs35293629 -0.616816 0.881796 7 310 190 MODIFIER 8 CODING FCGR2B G protein_coding NM_004001.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161647533 A G 0 36.3 0 0.705 0.7041 0.7565 0.7232 0.6968 0.6534 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.600535 0 . 0 . 8 1,4,0,3 UTR_3_PRIME(MODIFIER||190||310|FCGR2B|protein_coding|CODING|NM_004001.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.600535 rs844 -0.511536 0.62656 8 382 100 MODIFIER 1 CODING FCRLA C protein_coding NM_001184866.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161676904 T C 0 222 0 0.4977 0.616 0.5029 0.8254 0.6978 0.5562 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.986471 0 . 0 . 82 25,7,30,8 UTR_5_PRIME(MODIFIER||100||382|FCRLA|protein_coding|CODING|NM_001184866.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.834637 rs1340977 -0.693143 0.0439664 82 382 34 MODIFIER 1 CODING FCRLA G protein_coding NM_001184866.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161676970 A G 0 222 0 0.5953 0.6392 0.5101 0.8254 0.6879 0.5481 0.601906 0.636245 0.653837 1 6270 76661 5410 7189 4370 43818 574 9030 2 10392 121112 11536 8644 6600 66602 906 16432 0.978777 0 . 0 . 105 25,19,39,15 UTR_5_PRIME(MODIFIER||34||382|FCRLA|protein_coding|CODING|NM_001184866.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960009 rs1340978 -0.693147 0.720278 105 382 LOW 1 CODING FCRLA A protein_coding NM_001184866.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161680258 G A 0 222 0 0.1838 0.4431 0.4827 0.3601 0.6561 0.6319 0 . 0 1 337 10784 168 176 1122 4219 128 4634 2 1180 18058 322 498 1710 6462 220 7666 0.833603 0 . 0 . 93 22,16,28,21 SPLICE_SITE_REGION+INTRON(LOW||||382|FCRLA|protein_coding|CODING|NM_001184866.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.8687 rs6427618 -0.693147 0.68504 93 S209G 382 Agc/Ggc MODERATE 5 MISSENSE CODING FCRLA G protein_coding NM_001184866.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161681780 A G 0 222 0 0.764 0.477 0.4553 0.5734 0.2078 0.2822 0.658874 0.367907 0.218837 1 7006 38064 5535 4991 1285 14376 257 4614 2 10386 121266 11578 8636 6614 66670 908 16474 0.966847 0 . 0 . 65 12,18,16,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S209G|382|FCRLA|protein_coding|CODING|NM_001184866.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987488 rs2275603 -0.69311 0.532665 65 426 1030 MODIFIER 1 CODING FCRLB T protein_coding NM_001002901.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161691433 C T 0 9.7 0 0.3154 0.5785 0.8314 0.5198 0.7624 0.6258 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||426|FCRLB|protein_coding|CODING|NM_001002901.3|1|T),UTR_5_PRIME(MODIFIER||1030||426|FCRLB|protein_coding|CODING|NM_001002901.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1891019 -0.379885 0 1 426 877 MODIFIER 2 CODING FCRLB A protein_coding NM_001002901.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161691586 G A 0 21.2 0 0.0061 0.0709 0.1037 0.124 0.0994 0.0511 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 UTR_5_PRIME(MODIFIER||877||426|FCRLB|protein_coding|CODING|NM_001002901.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs6700369 -0.379885 0 3 A112 426 gcG/gcT LOW 6 SILENT CODING FCRLB T protein_coding NM_001002901.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161695639 G T 0 228 0 0.9894 0.9277 0.9352 1 0.8797 0.8139 0.969587 0.901584 0.866744 2 10132 107133 10641 8632 5605 58043 806 13274 2 10404 121068 11568 8650 6610 66628 908 16300 1 0 . 0 . 155 0,1,110,34 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A112|426|FCRLB|protein_coding|CODING|NM_001002901.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7520519 -0.693147 0.0400751 155 G383D 426 gGc/gAc MODERATE 8 MISSENSE CODING FCRLB A protein_coding NM_001002901.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161697319 G A 0 222 0 0.0061 0.0579 0.0735 0.0883 0.0944 0.0481 0.0161144 0.0638167 0.0882558 1 156 8617 876 625 474 5615 63 808 2 9688 118940 11530 8562 6612 65152 898 16498 0.928255 0 . 0 . 118 23,28,27,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G383D|426|FCRLB|protein_coding|CODING|NM_001002901.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999652 rs34868416 -0.693147 0.034122 118 Y170 340 taC/taT LOW 3 SILENT CODING DUSP12 T protein_coding NM_007240.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161721707 C T 0 222 0 0.407 0.36 0.2464 0.4831 0.2922 0.32 0.389242 0.35399 0.33593 1 4064 41241 2779 4134 2011 22296 310 5647 2 10370 121318 11568 8648 6614 66700 908 16510 0.854924 0 . 0 . 122 47,21,31,8 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y170|340|DUSP12|protein_coding|CODING|NM_007240.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.630046 rs1063178 -0.693144 0.00744429 122 670 116 MODIFIER 1 CODING ATF6 G protein_coding NM_007348.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161736035 A G 0 228 0 0.9766 0.9123 0.9121 0.875 0.8897 0.8875 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 85 0,0,71,6 UTR_5_PRIME(MODIFIER||116||670|ATF6|protein_coding|CODING|NM_007348.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2298019 -0.693147 0.0631555 85 L35 670 ctC/ctT LOW 2 SILENT CODING ATF6 T protein_coding NM_007348.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161748056 C T 0 228 0 0.1558 0.1899 0.3646 0.3284 0.0706 0.092 0.139128 0.0960326 0.0739535 2 1548 16735 5551 2671 455 4982 93 1435 2 10366 120830 11484 8618 6578 66428 904 16452 1 0 . 0 . 109 0,1,62,37 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L35|670|ATF6|protein_coding|CODING|NM_007348.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2070151 -0.693147 0.00171499 109 P90 670 ccT/ccC LOW 4 SILENT CODING ATF6 C protein_coding NM_007348.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161753802 T C 0 228 0 0.0446 0.1591 0.3545 0.3284 0.0706 0.092 0.0587835 0.0680455 0.0727907 2 615 15823 5548 2696 456 4981 89 1438 2 10406 121384 11578 8646 6614 66722 908 16510 0 . 0 . 0 61 0,0,28,20 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P90|670|ATF6|protein_coding|CODING|NM_007348.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2271013 -0.693147 0.00682414 61 S103 670 tcG/tcA LOW 4 SILENT CODING ATF6 A protein_coding NM_007348.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161753841 G A 0 228 0 0.1452 0.1869 0.3631 0.3284 0.0706 0.092 0.13005 0.0927264 0.0736047 2 1441 16716 5599 2695 456 4992 92 1441 2 10406 121406 11578 8652 6614 66736 908 16512 0 . 0 . 0 64 0,0,16,39 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S103|670|ATF6|protein_coding|CODING|NM_007348.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2271012 -0.693147 0.718509 64 A145P 670 Gcg/Ccg MODERATE 5 MISSENSE CODING ATF6 C protein_coding NM_007348.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161761276 G C 0 228 0 0.0446 0.1591 0.3545 0.3284 0.0706 0.092 0.0592374 0.06843 0.0731395 2 615 15789 5527 2691 456 4979 89 1432 2 10396 121236 11532 8636 6614 66674 908 16476 0 . 0 . 0 81 0,0,43,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Ccg|A145P|670|ATF6|protein_coding|CODING|NM_007348.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2070150 -0.693147 0.101309 81 P157S 670 Cct/Tct MODERATE 5 MISSENSE CODING ATF6 T protein_coding NM_007348.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161761312 C T 0 228 0 0.1452 0.1869 0.3631 0.3284 0.0706 0.092 0.13005 0.0927264 0.0736047 2 1442 16653 5567 2679 456 4983 92 1434 2 10386 120838 11532 8618 6606 66532 902 16262 1 0 . 0 COSM1335712 78 1,0,34,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P157S|670|ATF6|protein_coding|CODING|NM_007348.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1135983 -0.693147 0.0853145 78 751 357 MODIFIER 8 CODING OLFML2B T protein_coding NM_001297713.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161953108 C T 0 173 0 0.003 0.0599 0.0548 0.2341 0.004 0.0184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.904912 0 . 0 . 60 32,0,23,1 UTR_3_PRIME(MODIFIER||357||751|OLFML2B|protein_coding|CODING|NM_001297713.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.575414 rs16834849 -0.692831 0.139027 60 751 65 MODIFIER 8 CODING OLFML2B A protein_coding NM_001297713.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161953400 G A 0 222 0 0.2443 0.111 0.0648 0.125 0.0219 0.0409 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.981387 0 . 0 . 109 49,8,45,6 UTR_3_PRIME(MODIFIER||65||751|OLFML2B|protein_coding|CODING|NM_001297713.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.842911 rs12039519 -0.693147 0.000164611 109 751 63 MODIFIER 8 CODING OLFML2B A protein_coding NM_001297713.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161953402 G A 0 222 0 0.0144 0.0773 0.1513 0.2411 0.005 0.0153 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.681136 0 . 0 . 115 50,8,47,7 UTR_3_PRIME(MODIFIER||63||751|OLFML2B|protein_coding|CODING|NM_001297713.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.644395 rs12407643 -0.693147 1.96874e-09 115 W471R 751 Tgg/Cgg MODERATE 6 MISSENSE CODING OLFML2B G protein_coding NM_001297713.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161967681 A G 0 228 0 0.5756 0.6332 0.6816 0.6587 0.671 0.6115 0.602133 0.65416 0.680814 2 6281 79803 7852 5644 4049 45422 594 9961 2 10406 121342 11574 8626 6612 66734 908 16482 1 0 . 0 . 66 1,0,31,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W471R|751|OLFML2B|protein_coding|CODING|NM_001297713.1|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2499836,rs386568299 -0.693147 0.0150633 66 N192 751 aaT/aaC LOW 4 SILENT CODING OLFML2B G protein_coding NM_001297713.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 161976234 A G 0 222 0 0.4418 0.5907 0.7925 0.4583 0.8201 0.5491 0.510894 0.717438 0.823256 1 5217 88652 9281 4118 5451 54588 664 9333 2 10404 120974 11574 8634 6614 66618 902 16228 0.188372 0 . 0 . 40 5,13,8,12 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N192|751|OLFML2B|protein_coding|CODING|NM_001297713.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925071 rs12022536 -0.692067 0.00735919 40 S188 506 agC/agT LOW 6 SILENT CODING NOS1AP T protein_coding NM_014697.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162313735 C T 0 222 0 0.2829 0.4309 0.451 0.6339 0.3549 0.4857 0.289832 0.334307 0.357093 1 3002 49383 5691 5226 3078 24320 394 7672 2 10398 121262 11536 8632 6598 66678 908 16512 0.582491 0 . 0 . 55 15,15,10,10 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S188|506|NOS1AP|protein_coding|CODING|NM_014697.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.366997 rs3751284 -0.692067 0.721744 55 R334 506 cgC/cgT LOW 9 SILENT CODING NOS1AP T protein_coding NM_014697.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162335256 C T 0 222 0 0.4342 0.2508 0.2161 0.123 0.1193 0.2945 0.399682 0.21467 0.119884 1 4313 20944 2415 1111 694 7950 143 4318 2 10360 121076 11562 8622 6588 66534 904 16506 0.92079 0 . 0 . 44 10,11,11,8 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R334|506|NOS1AP|protein_coding|CODING|NM_014697.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.588831 rs348624 -0.69168 0.347861 44 506 1705 MODIFIER 10 CODING NOS1AP T protein_coding NM_014697.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162338962 C T 0 39.3 0 0.4894 0.7141 0.7824 0.8681 0.8419 0.6789 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1705||506|NOS1AP|protein_coding|CODING|NM_014697.2|10|T),DOWNSTREAM(MODIFIER||4553||261|C1orf111|protein_coding|CODING|NM_182581.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs164151 -0.453602 0.92 2 506 1846 MODIFIER 10 CODING NOS1AP T protein_coding NM_014697.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162339103 C T 0 9.7 0 0.3427 0.3011 0.2824 0.1736 0.333 0.3569 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1846||506|NOS1AP|protein_coding|CODING|NM_014697.2|10|T),DOWNSTREAM(MODIFIER||4412||261|C1orf111|protein_coding|CODING|NM_182581.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs164152 -0.379885 0 1 506 2497 MODIFIER 10 CODING NOS1AP T protein_coding NM_014697.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162339754 C T 0 9.7 0 0.2035 0.1376 0.1311 0.1121 0.0577 0.1616 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2497||506|NOS1AP|protein_coding|CODING|NM_014697.2|10|T),DOWNSTREAM(MODIFIER||3761||261|C1orf111|protein_coding|CODING|NM_182581.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1504424 -0.379885 0 1 261 64 MODIFIER 3 CODING C1orf111 G protein_coding NM_182581.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162343774 A G 0 222 0 0.1861 0.353 0.4337 0.5099 0.4115 0.2996 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.883013 0 . 0 . 62 25,2,26,5 UTR_3_PRIME(MODIFIER||64||261|C1orf111|protein_coding|CODING|NM_182581.3|3|G),UPSTREAM(MODIFIER||4922||315|C1orf226|protein_coding|CODING|NM_001135240.1||G),DOWNSTREAM(MODIFIER||3961||506|NOS1AP|protein_coding|CODING|NM_014697.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.27555 rs7512126 -0.69311 0.304567 62 R174 261 agG/agA LOW 3 SILENT CODING C1orf111 T protein_coding NM_182581.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162344102 C T 0 222 0 0.1634 0.3405 0.4222 0.5089 0.3817 0.3057 0.21902 0.32239 0.375349 1 2066 44586 4941 4334 2887 24881 348 5129 2 10404 121342 11576 8624 6614 66710 908 16506 0.847637 0 . 0 . 94 30,15,25,16 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R174|261|C1orf111|protein_coding|CODING|NM_182581.3|3|T),UPSTREAM(MODIFIER||4594||315|C1orf226|protein_coding|CODING|NM_001135240.1||T),DOWNSTREAM(MODIFIER||4289||506|NOS1AP|protein_coding|CODING|NM_014697.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894915 rs2282397,rs386563531 -0.693145 0.0320458 94 D78 261 gaT/gaC LOW 3 SILENT CODING C1orf111 G protein_coding NM_182581.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162344390 A G 0 228 0 0.9871 0.9962 0.9971 1 1 1 0.987063 0.995464 0.999767 2 10248 120181 11570 8652 6614 66297 900 15900 2 10372 120312 11574 8652 6614 66300 900 15900 0 . 0 . 0 59 0,0,26,27 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D78|261|C1orf111|protein_coding|CODING|NM_182581.3|3|G),UPSTREAM(MODIFIER||4306||315|C1orf226|protein_coding|CODING|NM_001135240.1||G),DOWNSTREAM(MODIFIER||4577||506|NOS1AP|protein_coding|CODING|NM_014697.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs164159 -0.693147 0.000489973 59 A69V 261 gCg/gTg MODERATE 2 MISSENSE CODING C1orf111 A protein_coding NM_182581.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162345091 G A 0 228 0 0.7874 0.9385 0.9755 1 0.998 0.9918 0.816614 0.935338 0.996163 2 8495 118843 11480 8654 6605 66320 889 16400 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 84 0,0,49,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A69V|261|C1orf111|protein_coding|CODING|NM_182581.3|2|A),UPSTREAM(MODIFIER||3605||315|C1orf226|protein_coding|CODING|NM_001135240.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs164181 -0.693147 0.668578 84 419 669 MODIFIER 8 CODING UHMK1 T protein_coding NM_175866.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162493009 C T 0 222 0 0.3502 0.4205 0.4308 0.4633 0.4443 0.4397 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.9999 0 . 0 . 66 20,9,19,14 UTR_3_PRIME(MODIFIER||669||419|UHMK1|protein_coding|CODING|NM_175866.4|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994418 rs1062174 -0.693127 0.301659 66 419 783 MODIFIER 8 CODING UHMK1 G protein_coding NM_175866.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162493123 A G 0 222 0 0.438 0.4475 0.4352 0.4782 0.4443 0.4407 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999904 0 . 0 . 111 35,20,33,12 UTR_3_PRIME(MODIFIER||783||419|UHMK1|protein_coding|CODING|NM_175866.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994614 rs2236581 -0.693147 0.268727 111 419 5323 MODIFIER 8 CODING UHMK1 A protein_coding NM_175866.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162497663 G A 0 9.7 0 0.4372 0.4475 0.4352 0.4792 0.4443 0.4407 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5323||419|UHMK1|protein_coding|CODING|NM_175866.4|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4657201 -0.379885 0 1 505 4365 MODIFIER 1 CODING UAP1 T protein_coding NM_003115.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162531494 C T 0 9.7 0 0.0083 0.1546 0.2305 0.3006 0.1352 0.1677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||4365||505|UAP1|protein_coding|CODING|NM_003115.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs28384483 -0.379885 0 1 855 63834 MODIFIER 2 CODING DDR2 A protein_coding NM_001014796.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162625020 G A 0 63 0 0.7693 0.8832 0.9582 0.8968 0.9742 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_5_PRIME(MODIFIER||63834||855|DDR2|protein_coding|CODING|NM_001014796.1|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3795641,rs386586487 -0.453602 0.06 3 855 172 MODIFIER 19 CODING DDR2 T protein_coding NM_001014796.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162750208 C T 0 228 0 0.8033 0.9455 0.9827 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 39 0,0,4,33 UTR_3_PRIME(MODIFIER||172||855|DDR2|protein_coding|CODING|NM_001014796.1|19|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1972086 -0.693141 9.05803e-05 39 341 40 MODIFIER 1 CODING HSD17B7 T protein_coding NM_016371.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162760551 C T 0 228 0 0.1944 0.5314 0.562 0.5764 0.7813 0.6616 0 . 0 2 1800 52404 3265 2990 2215 34059 408 7667 2 6366 73390 6254 4828 2576 41712 534 11120 1 0 . 0 . 81 0,1,60,13 UTR_5_PRIME(MODIFIER||40||341|HSD17B7|protein_coding|CODING|NM_016371.3|1|T) 0 . 0 . 0 1 0 . 1 0 52 0 1 0.309305 0 1 rs1704754 -0.693147 0.801698 81 341 37 MODIFIER 1 CODING HSD17B7 C protein_coding NM_016371.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 162760554 T C 0 228 0 0.8048 0.9459 0.9827 1 0.999 1 0 . 0 2 5605 77619 7349 5471 2750 44263 540 11641 2 6932 79150 7432 5476 2760 44354 546 11650 0 . 0 . 0 81 0,0,60,14 UTR_5_PRIME(MODIFIER||37||341|HSD17B7|protein_coding|CODING|NM_016371.3|1|C) 0 . 0 . 0 1 0 . 1 0 52 0 0 0.309305 0 . rs71519246 -0.693147 0.797528 81 302 112 MODIFIER 1 CODING RGS4 A protein_coding NM_001102445.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163038613 C A 0 228 0 0.4796 0.4549 0.3847 0.4335 0.4254 0.5235 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 133 1,0,119,10 UTR_5_PRIME(MODIFIER||112||302|RGS4|protein_coding|CODING|NM_001102445.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7515900 -0.693147 0.017929 133 302 1207 MODIFIER 6 CODING RGS4 C protein_coding NM_001102445.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163045557 T C 0 176 0 0.8654 0.9639 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 15 1,0,13,1 UTR_3_PRIME(MODIFIER||1207||302|RGS4|protein_coding|CODING|NM_001102445.2|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2661318 -0.686358 0.274696 15 185 3254 MODIFIER 5 CODING RGS5 A protein_coding NM_001254749.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163113878 G A 0 6.3 0 0.5091 0.2546 0.098 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3254||185|RGS5|protein_coding|CODING|NM_001254749.1|5|A),UTR_3_PRIME(MODIFIER||3254||73|RGS5|protein_coding|CODING|NM_001254748.1|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3806368,rs386586758 -0.379885 0 1 73 3254 MODIFIER 6 CODING RGS5 A protein_coding NM_001254748.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163113878 G A 0 6.3 0 0.5091 0.2546 0.098 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3254||185|RGS5|protein_coding|CODING|NM_001254749.1|5|A),UTR_3_PRIME(MODIFIER||3254||73|RGS5|protein_coding|CODING|NM_001254748.1|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3806368,rs386586758 -0.379885 0 1 185 2774 MODIFIER 5 CODING RGS5 T protein_coding NM_001254749.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163114358 G T 0 132 0 0.5098 0.2548 0.098 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997429 0 . 0 . 85 38,1,45,0 UTR_3_PRIME(MODIFIER||2774||185|RGS5|protein_coding|CODING|NM_001254749.1|5|T),UTR_3_PRIME(MODIFIER||2774||73|RGS5|protein_coding|CODING|NM_001254748.1|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.493549 rs3820487,rs386587205 -0.693147 0.317878 85 73 2774 MODIFIER 6 CODING RGS5 T protein_coding NM_001254748.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163114358 G T 0 132 0 0.5098 0.2548 0.098 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997429 0 . 0 . 85 38,1,45,0 UTR_3_PRIME(MODIFIER||2774||185|RGS5|protein_coding|CODING|NM_001254749.1|5|T),UTR_3_PRIME(MODIFIER||2774||73|RGS5|protein_coding|CODING|NM_001254748.1|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.493549 rs3820487,rs386587205 -0.693147 0.317878 85 185 2527 MODIFIER 5 CODING RGS5 A protein_coding NM_001254749.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163114605 G A 0 228 0 0.8207 0.8357 0.8242 0.8829 0.7376 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,0,7,45 UTR_3_PRIME(MODIFIER||2527||185|RGS5|protein_coding|CODING|NM_001254749.1|5|A),UTR_3_PRIME(MODIFIER||2527||73|RGS5|protein_coding|CODING|NM_001254748.1|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2815274 -0.693147 0.000728049 57 73 2527 MODIFIER 6 CODING RGS5 A protein_coding NM_001254748.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163114605 G A 0 228 0 0.8207 0.8357 0.8242 0.8829 0.7376 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,0,7,45 UTR_3_PRIME(MODIFIER||2527||185|RGS5|protein_coding|CODING|NM_001254749.1|5|A),UTR_3_PRIME(MODIFIER||2527||73|RGS5|protein_coding|CODING|NM_001254748.1|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2815274 -0.693147 0.000728049 57 185 1811 MODIFIER 5 CODING RGS5 G protein_coding NM_001254749.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163115321 A G 0 9.7 0 0.5582 0.2678 0.0994 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1811||185|RGS5|protein_coding|CODING|NM_001254749.1|5|G),UTR_3_PRIME(MODIFIER||1811||73|RGS5|protein_coding|CODING|NM_001254748.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3806366,rs386586757 -0.379885 0 1 73 1811 MODIFIER 6 CODING RGS5 G protein_coding NM_001254748.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163115321 A G 0 9.7 0 0.5582 0.2678 0.0994 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1811||185|RGS5|protein_coding|CODING|NM_001254749.1|5|G),UTR_3_PRIME(MODIFIER||1811||73|RGS5|protein_coding|CODING|NM_001254748.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3806366,rs386586757 -0.379885 0 1 185 254 MODIFIER 5 CODING RGS5 G protein_coding NM_001254749.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163116878 T G 0 81 0 0.5265 0.2594 0.0994 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.509156 0 . 0 . 14 8,0,6,0 UTR_3_PRIME(MODIFIER||254||185|RGS5|protein_coding|CODING|NM_001254749.1|5|G),UTR_3_PRIME(MODIFIER||254||73|RGS5|protein_coding|CODING|NM_001254748.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.77718 rs15049,rs386534797 -0.616816 0.191363 14 73 254 MODIFIER 6 CODING RGS5 G protein_coding NM_001254748.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163116878 T G 0 81 0 0.5265 0.2594 0.0994 0.2629 0.0944 0.1779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.509156 0 . 0 . 14 8,0,6,0 UTR_3_PRIME(MODIFIER||254||185|RGS5|protein_coding|CODING|NM_001254749.1|5|G),UTR_3_PRIME(MODIFIER||254||73|RGS5|protein_coding|CODING|NM_001254748.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.77718 rs15049,rs386534797 -0.616816 0.191363 14 G186 464 ggA/ggT LOW 8 SILENT CODING NUF2 T protein_coding NM_031423.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 163309219 A T 0 222 0 0.32 0.4285 0.4352 0.3512 0.4374 0.6411 0.343849 0.416885 0.454302 1 3520 53503 4550 2701 2485 30211 405 9631 2 10388 121264 11562 8638 6602 66668 908 16498 0.188836 0 . 0 . 102 30,15,29,15 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G186|464|NUF2|protein_coding|CODING|NM_031423.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.116872 rs1509022 -0.693146 0.245437 102 430 190 MODIFIER 1 CODING PBX1 C protein_coding NM_002585.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 164528870 T C 0 9.7 0 0.9955 0.981 0.9611 1 0.9503 0.9877 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||190||430|PBX1|protein_coding|CODING|NM_002585.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12033962 -0.379885 0 1 G21S 430 Ggc/Agc MODERATE 1 MISSENSE CODING PBX1 A protein_coding NM_002585.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 164529120 G A 0 222 0 0.0159 0.3073 0.4308 0.6101 0.1968 0.4151 0.0408362 0.138099 0.188204 1 97 5543 169 396 11 1923 55 2892 2 1998 18618 410 636 34 7616 180 7744 0.963721 0 . 0 COSM1335879 51 11,17,7,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G21S|430|PBX1|protein_coding|CODING|NM_002585.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.141893 rs2275558 -0.692067 0.585597 51 430 2994 MODIFIER 9 CODING PBX1 T protein_coding NM_002585.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 164818907 C T 0 70 0 0.792 0.9431 0.9856 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2994||430|PBX1|protein_coding|CODING|NM_002585.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1213289 -0.453602 0.32 3 D350 382 gaT/gaC LOW 9 SILENT CODING LMX1A G protein_coding NM_001174069.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165173216 A G 0 228 0 0.9955 0.9988 1 1 1 1 0.997503 0.999154 1 2 10367 121370 11575 8654 6614 66740 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 116 0,0,70,40 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D350|382|LMX1A|protein_coding|CODING|NM_001174069.1|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1354509 -0.693147 0.00883047 116 L117 382 Ctg/Ttg LOW 4 SILENT CODING LMX1A A protein_coding NM_001174069.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165218792 G A 0 222 0 0.1263 0.3247 0.3545 0.5605 0.2406 0.4151 0.160917 0.215055 0.242791 1 1550 36830 4631 4845 2043 16891 250 6620 2 10394 121208 11540 8624 6598 66642 908 16502 0.99952 0 . 0 . 75 25,14,17,12 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L117|382|LMX1A|protein_coding|CODING|NM_001174069.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928777 rs10753668 -0.693079 0.126758 75 463 132 MODIFIER 10 CODING RXRG TA protein_coding NM_006917.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165370367 T TA 0 41.3 0 0.4191 0.2492 0.2378 0.3046 0.0954 0.1288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 9,1,8,0 UTR_3_PRIME(MODIFIER||132||463|RXRG|protein_coding|CODING|NM_006917.4|10|TA) 0 0.5 1 8 0.444444 1 1 0 . 0 60 0 0 1 0 . rs3215856 -0.651104 0.1893 18 463 LOW 9 CODING RXRG C protein_coding NM_006917.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165376043 T C 0 228 0 0.8805 0.872 0.83 0.9276 0.7962 0.911 0.877894 0.813394 0.780349 2 9103 100636 9699 8006 5787 52360 764 14917 2 10404 121394 11578 8650 6614 66730 908 16510 0 . 0 . 0 163 0,0,93,45 SPLICE_SITE_REGION+INTRON(LOW||||463|RXRG|protein_coding|CODING|NM_006917.4|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs283696 -0.693147 0.727423 163 V350 463 gtC/gtT LOW 8 SILENT CODING RXRG A protein_coding NM_006917.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165377552 G A 0 222 0 0.2284 0.4788 0.6023 0.5079 0.671 0.502 0.309578 0.554436 0.679884 1 3081 74094 7010 4589 4353 45830 563 8668 2 10402 121372 11570 8640 6612 66730 908 16510 0.992661 0 . 0 . 118 21,38,10,35 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V350|463|RXRG|protein_coding|CODING|NM_006917.4|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994505 rs2134095 -0.693147 0.341005 118 152 18818 MODIFIER 1 CODING MGST3 A protein_coding NM_004528.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165600267 T A 0 39.3 0 0.1498 0.4467 0.5043 0.7798 0.4553 0.455 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||18818||152|MGST3|protein_coding|CODING|NM_004528.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4147593 -0.453602 0.26 2 152 282 MODIFIER 6 CODING MGST3 T protein_coding NM_004528.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165625023 G T 0 102 0 0.3283 0.4221 0.4308 0.8175 0.1292 0.4366 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_3_PRIME(MODIFIER||282||152|MGST3|protein_coding|CODING|NM_004528.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4147611 -0.590765 0.819532 5 152 396 MODIFIER 6 CODING MGST3 A protein_coding NM_004528.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165625137 T A 0 57 0 0.3283 0.4219 0.4308 0.8175 0.1282 0.4366 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||396||152|MGST3|protein_coding|CODING|NM_004528.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9333489 -0.511536 0.943964 3 518 617 MODIFIER 11 CODING ALDH9A1 G protein_coding NM_000696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165631670 T G 0 130 0 0.2617 0.3814 0.3847 0.8185 0.1223 0.3569 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,2 UTR_3_PRIME(MODIFIER||617||518|ALDH9A1|protein_coding|CODING|NM_000696.3|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12670,rs386525546 -0.590765 0.308315 5 I134 518 atT/atC LOW 3 SILENT CODING ALDH9A1 G protein_coding NM_000696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165652273 A G 0 228 0 0.6074 0.7462 0.7723 0.9881 0.6372 0.7781 0.63005 0.650161 0.660465 2 6433 87038 9779 8490 4644 44832 625 12235 2 10402 121362 11566 8654 6610 66712 906 16512 0 . 0 . 0 93 0,0,46,40 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I134|518|ALDH9A1|protein_coding|CODING|NM_000696.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1143659,rs386518189 -0.693147 0.815613 93 261 1960 MODIFIER 7 CODING UCK2 C protein_coding NM_012474.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165879020 T C 0 9.7 0 0.9894 0.9972 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1960||261|UCK2|protein_coding|CODING|NM_012474.4|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs480813 -0.379885 0 1 261 2002 MODIFIER 7 CODING UCK2 C protein_coding NM_012474.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165879062 T C 0 36.3 0 0.9894 0.9972 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2002||261|UCK2|protein_coding|CODING|NM_012474.4|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs480050 -0.453602 0.78 2 261 3051 MODIFIER 7 CODING UCK2 C protein_coding NM_012474.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 165880111 T C 0 9.7 0 0.941 0.9838 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3051||261|UCK2|protein_coding|CODING|NM_012474.4|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs526374 -0.379885 0 1 A250 609 gcA/gcG LOW 5 SILENT CODING POGK G protein_coding NM_017542.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 166818566 A G 0 222 0 0.152 0.2768 0.17 0.5565 0.162 0.3507 0.174535 0.181608 0.185233 1 1778 26954 1925 4936 1091 12049 173 5002 2 10118 120378 11558 8626 6608 66060 904 16504 0.916702 0 . 0 . 82 25,21,18,9 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A250|609|POGK|protein_coding|CODING|NM_017542.4|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.273109 rs2075946 -0.693021 0.285377 82 609 2920 MODIFIER 6 CODING POGK G protein_coding NM_017542.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 166822566 A G 0 222 0 0.0038 0.0657 0.049 0.1806 0.0487 0.0603 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979382 0 . 0 . 77 14,22,8,29 UTR_3_PRIME(MODIFIER||2920||609|POGK|protein_coding|CODING|NM_017542.4|6|G),DOWNSTREAM(MODIFIER||3183||335|TADA1|protein_coding|CODING|NM_053053.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.959686 rs2232526 -0.693141 0.502375 77 609 5200 MODIFIER 6 CODING POGK C protein_coding NM_017542.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 166824846 T C 0 15.1 0 0.3858 0.3538 0.3127 0.3006 0.4175 0.3292 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 3,0,1,0 UTR_3_PRIME(MODIFIER||5200||609|POGK|protein_coding|CODING|NM_017542.4|6|C),DOWNSTREAM(MODIFIER||903||335|TADA1|protein_coding|CODING|NM_053053.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10800269 -0.379885 0 5 R198Q 335 cGg/cAg MODERATE 6 MISSENSE CODING TADA1 T protein_coding NM_053053.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 166829522 C T 0 222 0 0 0.0351 0.0187 0.1171 0.0099 0.0358 0.00136178 0.00845763 0.012093 1 20 2542 244 971 64 813 10 420 2 10404 121342 11562 8654 6612 66698 908 16504 0.985856 0 . 0 . 171 44,39,33,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R198Q|335|TADA1|protein_coding|CODING|NM_053053.3|6|T),DOWNSTREAM(MODIFIER||3941||609|POGK|protein_coding|CODING|NM_017542.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.783789 rs2272792 -0.693147 0.560788 171 639 5540 MODIFIER 10 CODING ILDR2 C protein_coding NM_199351.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 166883052 G C 0 66 0 1 0.9938 0.9928 1 0.9821 0.9918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||5540||639|ILDR2|protein_coding|CODING|NM_199351.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6427045 -0.453602 0.14 3 319 651 MODIFIER 7 CODING GPA33 G protein_coding NM_005814.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167022920 C G 0 9.7 0 0.3275 0.4533 0.585 0.4554 0.4016 0.5808 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||651||319|GPA33|protein_coding|CODING|NM_005814.2|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12076250 -0.379885 0 1 319 145 MODIFIER 7 CODING GPA33 T protein_coding NM_005814.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167023426 C T 0 60 0 0.1823 0.4075 0.5663 0.4554 0.3807 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.418638 0 . 0 . 21 11,3,6,0 UTR_3_PRIME(MODIFIER||145||319|GPA33|protein_coding|CODING|NM_005814.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.846482 rs3820388 -0.616816 0.758048 21 E265D 1158 gaG/gaC MODERATE 5 MISSENSE CODING DUSP27 C protein_coding NM_001080426.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167095163 G C 0 228 0 0.888 0.642 0.4597 0.872 0.4751 0.3732 0.834544 0.60203 0.482907 2 8754 60800 4128 7616 2836 31112 428 5926 2 10400 121354 11566 8652 6610 66712 906 16508 1 0 . 0 . 60 0,1,28,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E265D|1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs267745 -0.693147 0.0167017 60 R466H 1158 cGc/cAc MODERATE 5 MISSENSE CODING DUSP27 A protein_coding NM_001080426.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167095765 G A 0 228 0 0.2716 0.3291 0.2003 0.7421 0.168 0.2382 0.257493 0.200246 0.17093 2 2501 26808 2229 6301 1064 11053 162 3498 2 8782 104728 9664 8334 4954 57134 732 15128 0.950054 0 . 0 . 82 2,1,42,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R466H|1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.996803 rs6668826 -0.693147 0.205667 82 A505T 1158 Gca/Aca MODERATE 5 MISSENSE CODING DUSP27 A protein_coding NM_001080426.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167095881 G A 0 228 0 0.2716 0.3293 0.2003 0.7431 0.168 0.2382 0.257603 0.199831 0.170233 2 2618 27598 2288 6478 1157 11349 171 3537 2 10328 120802 11532 8628 6608 66308 900 16498 0.818182 0 . 0 . 81 0,2,40,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A505T|1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.980519 rs3795605 -0.693147 0.752935 81 R625W 1158 Cgg/Tgg MODERATE 5 MISSENSE CODING DUSP27 T protein_coding NM_001080426.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167096241 C T 0 222 0 0 0.0019968 0 0.0099 0 0 0.000226963 7.6888e-05 0 1 0 49 1 45 0 1 1 1 2 10168 116288 11412 8544 6162 64990 844 14168 0.388441 0 . 0 . 101 30,27,11,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R625W|1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.362633 rs188895908 -0.693097 0.372512 101 T1124N 1158 aCt/aAt MODERATE 5 MISSENSE CODING DUSP27 A protein_coding NM_001080426.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167097739 C A 0 228 0 0.2776 0.3822 0.2867 0.7431 0.3141 0.2894 0.28325 0.301092 0.310233 2 2774 39314 2989 6390 1901 20397 288 4575 2 10086 119888 11450 8542 6584 65932 898 16396 0.4375 0 . 0 . 62 1,1,20,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T1124N|1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.714286 rs2281959 -0.693147 0.417949 62 1158 250 MODIFIER 5 CODING DUSP27 A protein_coding NM_001080426.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167098095 G A 0 64 0 0.2776 0.3866 0.2867 0.7679 0.3141 0.2863 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||250||1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs66619221 -0.511536 0.0618664 3 1158 284 MODIFIER 5 CODING DUSP27 C protein_coding NM_001080426.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167098129 T C 0 64 0 0.2776 0.3884 0.2867 0.7679 0.3141 0.2955 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||284||1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs72691538 -0.511536 0.0618664 3 1158 286 MODIFIER 5 CODING DUSP27 A protein_coding NM_001080426.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167098131 G A 0 48.5 0 0.9773 0.8089 0.6354 0.9276 0.7873 0.6043 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||286||1158|DUSP27|protein_coding|CODING|NM_001080426.1|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs267748 -0.511536 0.0618664 3 766 4775 MODIFIER 16 CODING POU2F1 T protein_coding NM_002697.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167389822 C T 0 9.7 0 0.6407 0.8886 0.9553 0.996 0.9742 0.9775 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4775||766|POU2F1|protein_coding|CODING|NM_002697.3|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1612096 -0.379885 0 1 766 6857 MODIFIER 16 CODING POU2F1 T protein_coding NM_002697.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167391904 C T 0 54 0 0.6074 0.8758 0.9352 0.9762 0.9791 0.9867 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||6857||766|POU2F1|protein_coding|CODING|NM_002697.3|16|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2949664 -0.453602 0.78 3 766 7169 MODIFIER 16 CODING POU2F1 G protein_coding NM_002697.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167392216 C G 0 9.7 0 0.6278 0.8816 0.938 0.9762 0.9791 0.9867 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||7169||766|POU2F1|protein_coding|CODING|NM_002697.3|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2949665 -0.379885 0 1 766 7295 MODIFIER 16 CODING POU2F1 G protein_coding NM_002697.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167392342 A G 0 9.7 0 0.59 0.8622 0.9251 0.9762 0.9592 0.9683 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||7295||766|POU2F1|protein_coding|CODING|NM_002697.3|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2995094 -0.379885 0 1 164 956 MODIFIER 8 CODING CD247 C protein_coding NM_198053.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167399962 T C 0 9.7 0 0.9569 0.9874 0.9914 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||956||164|CD247|protein_coding|CODING|NM_198053.2|8|C),DOWNSTREAM(MODIFIER||3380||766|POU2F1|protein_coding|CODING|NM_002697.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs947480 -0.379885 0 1 164 844 MODIFIER 8 CODING CD247 A protein_coding NM_198053.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167400074 T A 0 39.3 0 0.7595 0.8111 0.866 0.7431 0.831 0.8916 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||844||164|CD247|protein_coding|CODING|NM_198053.2|8|A),DOWNSTREAM(MODIFIER||3492||766|POU2F1|protein_coding|CODING|NM_002697.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1052231 -0.453602 0.18 2 220 539 MODIFIER 4 CODING CREG1 A protein_coding NM_003851.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167510996 G A 0 139 0 0.8427 0.9383 0.9553 0.997 0.9453 0.9877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,6,0 UTR_3_PRIME(MODIFIER||539||220|CREG1|protein_coding|CODING|NM_003851.2|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2143300 -0.616816 0.348672 7 416 78 MODIFIER 1 CODING RCSD1 A protein_coding NM_052862.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167599583 G A 0 111 0 0.0098 0.126 0.2334 0.1696 0.1928 0.093 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870857 0 . 0 . 39 22,0,15,0 UTR_5_PRIME(MODIFIER||78||416|RCSD1|protein_coding|CODING|NM_052862.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.938683 rs3738221 -0.688148 0.276014 39 269 2123 MODIFIER 6 CODING MPZL1 C protein_coding NM_003953.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167759281 T C 0 9.7 0 0.4455 0.5162 0.6239 0.6141 0.5298 0.4202 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2123||269|MPZL1|protein_coding|CODING|NM_003953.5|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7605 -0.379885 0 1 G799 1610 ggT/ggC LOW 19 SILENT CODING ADCY10 G protein_coding NM_018417.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167817639 A G 0 228 0 0.9297 0.8221 0.8372 0.8571 0.7137 0.7413 0.897413 0.773259 0.709651 2 9421 91691 10089 7465 5017 47476 663 11560 2 10406 121360 11574 8650 6610 66708 904 16508 0 . 0 . COSM424500 74 0,0,56,9 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G799|1610|ADCY10|protein_coding|CODING|NM_018417.5|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs203795,rs386554022 -0.693147 0.041487 74 I697V 1610 Att/Gtt MODERATE 17 MISSENSE CODING ADCY10 C protein_coding NM_018417.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167825485 T C 0 228 0 0.4599 0.5046 0.5749 0.7113 0.4105 0.3988 0.461189 0.420421 0.399535 2 4911 55329 7891 6120 3154 26714 418 6121 2 10406 121402 11576 8652 6614 66736 908 16510 0 . 0 . 0 132 0,0,82,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I697V|1610|ADCY10|protein_coding|CODING|NM_018417.5|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2071921 -0.693147 0.400811 132 F656 1610 ttT/ttC LOW 17 SILENT CODING ADCY10 G protein_coding NM_018417.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167825606 A G 0 222 0 0.0756 0.2083 0.2752 0.4177 0.1272 0.2076 0.0946437 0.106182 0.112093 1 998 21480 4131 3731 1355 8008 188 3069 2 10404 121390 11574 8646 6614 66734 908 16510 0.623305 0 . 0 . 120 8,38,26,36 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F656|1610|ADCY10|protein_coding|CODING|NM_018417.5|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856754 rs2071922 -0.693147 0.00167305 120 V511 1610 gtC/gtT LOW 14 SILENT CODING ADCY10 A protein_coding NM_018417.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167839578 G A 0 222 0 0.0356 0.1256 0.2161 0.126 0.2068 0.0992 0.0728552 0.161156 0.206395 1 707 22419 3494 1139 1236 13738 173 1932 2 10374 120770 11526 8594 6590 66350 908 16428 0.85598 0 . 0 COSM1559273 89 15,26,20,25 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V511|1610|ADCY10|protein_coding|CODING|NM_018417.5|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.00687469 rs67878347 -0.693147 0.0887023 89 G385 1610 ggT/ggC LOW 11 SILENT CODING ADCY10 G protein_coding NM_018417.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167849414 A G 0 222 0 0.6687 0.4932 0.4597 0.3224 0.504 0.4448 0.641398 0.534297 0.479414 1 6408 56002 5272 2798 2845 30943 462 7274 2 10050 117286 11026 8492 6434 64920 872 15492 0.19598 0 . 0 COSM146675 88 23,14,28,9 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G385|1610|ADCY10|protein_coding|CODING|NM_018417.5|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.843326 rs203849 -0.693141 0.636928 88 R30 951 cgA/cgC LOW 1 SILENT CODING DCAF6 C protein_coding NM_001198956.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167906239 A C 0 228 0 1 1 1 1 1 1 0 . 0 2 8936 109276 10564 8100 5150 60542 754 15230 2 8936 109276 10564 8100 5150 60542 754 15230 0 . 0 . 0 24 0,0,15,7 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgC|R30|951|DCAF6|protein_coding|CODING|NM_001198956.1|1|C),UTR_5_PRIME(MODIFIER||1160||127|MPC2|protein_coding|CODING|NM_001143674.3|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs203788 -0.692562 0.906639 24 127 1160 MODIFIER 1 CODING MPC2 C protein_coding NM_001143674.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 167906239 A C 0 228 0 1 1 1 1 1 1 0 . 0 2 8936 109276 10564 8100 5150 60542 754 15230 2 8936 109276 10564 8100 5150 60542 754 15230 0 . 0 . 0 24 0,0,15,7 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgC|R30|951|DCAF6|protein_coding|CODING|NM_001198956.1|1|C),UTR_5_PRIME(MODIFIER||1160||127|MPC2|protein_coding|CODING|NM_001143674.3|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs203788 -0.692562 0.906639 24 V624A 951 gTg/gCg MODERATE 15 MISSENSE CODING DCAF6 C protein_coding NM_001198956.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168013850 T C 0 222 0 0.0545 0.1845 0.1383 0.2044 0.2823 0.272 0.0869269 0.21121 0.274884 1 850 29823 1203 1701 2139 19174 231 4525 2 10384 121176 11490 8644 6612 66644 906 16496 0.989081 0 . 0 . 137 32,37,26,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V624A|951|DCAF6|protein_coding|CODING|NM_001198956.1|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.219162 rs11558511 -0.693147 0.0103866 137 G400 549 ggT/ggC LOW 5 SILENT CODING GPR161 G protein_coding NM_001267609.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168059866 A G 0 222 0 0.5257 0.3205 0.4063 0.1518 0.2634 0.2147 0.618021 0.431647 0.336163 1 5315 37628 5542 1557 1925 19405 268 3616 2 8606 106314 10148 7718 5328 58482 776 15256 0.999298 0 . 0 COSM424503 139 18,61,6,51 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G400|549|GPR161|protein_coding|CODING|NM_001267609.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.715574 rs275149 -0.693147 0.152275 139 549 2557 MODIFIER 1 CODING GPR161 C protein_coding NM_001267609.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168106716 T C 0 228 0 0.9932 0.8516 0.866 0.8065 0.8052 0.7444 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 60 0,0,16,36 UTR_5_PRIME(MODIFIER||2557||549|GPR161|protein_coding|CODING|NM_001267609.1|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6664903 -0.693147 0.000768169 60 549 2624 MODIFIER 1 CODING GPR161 T protein_coding NM_001267609.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168106783 C T 0 148 0 0.0953 0.1382 0.3458 0.1508 0.1054 0.0695 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.97965 0 . 0 . 24 0,11,1,12 UTR_5_PRIME(MODIFIER||2624||549|GPR161|protein_coding|CODING|NM_001267609.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.668167 rs41271651 -0.683931 0.109379 24 272 168 MODIFIER 7 CODING TIPRL A protein_coding NM_152902.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168169452 G A 0 222 0 0.9077 0.5383 0.6614 0.4415 0.3588 0.2362 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.344897 0 . 0 . 129 27,37,31,26 UTR_3_PRIME(MODIFIER||168||272|TIPRL|protein_coding|CODING|NM_152902.4|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.230356 rs2072776 -0.693147 0.000327708 129 448 21 MODIFIER 8 CODING TBX19 A protein_coding NM_005149.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168282261 T A 0 222 0 0.5726 0.4894 0.4452 0.4504 0.4185 0.5215 0.53064 0.456391 0.418334 1 5224 52881 5742 3728 2430 26988 395 8374 2 9682 118750 11482 8538 6422 65270 872 16484 0.615989 0 . 0 . 88 16,19,27,18 UTR_3_PRIME(MODIFIER||21||448|TBX19|protein_coding|CODING|NM_005149.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982275 rs3885717 -0.693147 0.27645 88 448 251 MODIFIER 8 CODING TBX19 C protein_coding NM_005149.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168282491 T C 0 76 0 0.0431 0.1901 0.1816 0.2768 0.3509 0.1401 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.442128 0 . 0 . 12 1,6,0,4 UTR_3_PRIME(MODIFIER||251||448|TBX19|protein_coding|CODING|NM_005149.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.803868 rs1000533 -0.556411 0.337235 12 114 68 MODIFIER 3 CODING XCL2 A protein_coding NM_003175.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168510122 T A 0 142 0 0.4818 0.6276 0.6499 0.8671 0.5398 0.6524 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999923 0 . 0 . 145 65,2,74,0 UTR_3_PRIME(MODIFIER||68||114|XCL2|protein_coding|CODING|NM_003175.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 50 0 3.68568e-09 0.654676 0 0.960238 rs470733,rs61801312 -0.693147 0.00144025 145 114 118 MODIFIER 1 CODING XCL1 T protein_coding NM_002995.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168545758 C T 0 228 0 0.2436 0.4042 0.4294 0.3641 0.5746 0.4693 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,39,1 UTR_5_PRIME(MODIFIER||118||114|XCL1|protein_coding|CODING|NM_002995.2|1|T) 0 . 0 . 0 1 0 . 0 . 56 0 0 1 0 . rs28433337 -0.693145 4.30208e-05 42 114 LOW 2 CODING XCL1 T protein_coding NM_002995.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168549422 C T 0 222 0 0.5393 0.4243 0.3847 0.1935 0.5706 0.3845 0.521335 0.537675 0.546046 1 5403 56787 4053 1462 3402 35601 430 6436 2 10352 120856 11506 8628 6592 66464 900 16414 0.785716 0 . 0 . 149 35,30,27,42 SPLICE_SITE_REGION+INTRON(LOW||||114|XCL1|protein_coding|CODING|NM_002995.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.425865 rs6427130 -0.693147 0.0431065 149 114 54 MODIFIER 3 CODING XCL1 C protein_coding NM_002995.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168550512 G C 0 222 0 0.1679 0.1492 0.1527 0.1915 0.1014 0.1268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.763856 0 . 0 . 177 8,76,7,79 UTR_3_PRIME(MODIFIER||54||114|XCL1|protein_coding|CODING|NM_002995.2|3|C) 0 0.5 1 0 . 1 0 . 0 . 50 0 2.11758e-11 0.728113 0 0.903556 rs200980747 -0.693147 0.00232019 177 T80 201 acG/acA LOW 1 SILENT CODING DPT T protein_coding NM_001937.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 168698173 C T 0 222 0 0.2519 0.3175 0.3141 0.1637 0.5129 0.3661 0.326373 0.468707 0.541628 1 3237 52231 2738 1335 3046 35516 361 5998 2 10406 121400 11578 8650 6610 66740 906 16510 0.986797 0 . 0 COSM1560468 102 26,18,29,24 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T80|201|DPT|protein_coding|CODING|NM_001937.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.752794 rs1052591,rs386514304 -0.693147 0.067566 102 303 480 MODIFIER 6 CODING ATP1B1 G protein_coding NM_001677.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169101273 T G 0 11.6 0 0.1778 0.1358 0.2637 0.0258 0.1352 0.1022 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.236382 0 . 0 . 32 7,1,2,2 UTR_3_PRIME(MODIFIER||480||303|ATP1B1|protein_coding|CODING|NM_001677.3|6|G),DOWNSTREAM(MODIFIER||495||376|NME7|protein_coding|CODING|NM_013330.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.493254 rs1779796 -0.556411 0.89732 32 F7 376 ttC/ttT LOW 2 SILENT CODING NME7 A protein_coding NM_013330.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169293721 G A 0 222 0 0.1732 0.227 0.389 0.0238 0.4394 0.1759 0.226736 0.359526 0.427558 1 2184 42076 4206 279 2919 28638 331 3519 2 10350 120688 11492 8616 6576 66310 898 16446 0.711834 0 . 0 . 152 42,37,22,40 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F7|376|NME7|protein_coding|CODING|NM_013330.4|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.770141 rs1140523 -0.693147 0.0923115 152 F172S 509 tTt/tCt MODERATE 3 MISSENSE CODING CCDC181 G protein_coding NM_001300969.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169391154 A G 0 228 0 0.6422 0.6889 0.7176 0.9236 0.669 0.5102 0.642079 0.644362 0.645533 2 6591 81391 8965 8025 4738 44012 584 8476 2 10326 120976 11474 8644 6608 66538 908 16478 0 . 0 . 0 37 0,0,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F172S|509|CCDC181|protein_coding|CODING|NM_001300969.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3820059 -0.693136 0.587161 37 497 967 MODIFIER 6 CODING SLC19A2 C protein_coding NM_006996.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169434120 T C 0 222 0 0.413 0.2408 0.2305 0.1468 0.1869 0.1677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.659818 0 . 0 . 105 11,44,6,38 UTR_3_PRIME(MODIFIER||967||497|SLC19A2|protein_coding|CODING|NM_006996.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.6023 rs16862199 -0.693146 0.111673 105 497 60 MODIFIER 6 CODING SLC19A2 T protein_coding NM_006996.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169435027 C T 0 227 0 1 0.9976 0.9942 1 0.993 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 0,0,26,2 UTR_3_PRIME(MODIFIER||60||497|SLC19A2|protein_coding|CODING|NM_006996.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2678166 -0.693054 0.0887264 28 T360 497 acT/acC LOW 4 SILENT CODING SLC19A2 G protein_coding NM_006996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169438025 A G 0 222 0 0.0015 0.0236 0.0029 0.1091 0.001 0.0031 0 7.6888e-05 0.000116279 1 7 957 133 751 0 24 7 35 2 10380 121246 11542 8646 6614 66662 906 16496 0.730581 255 other 0 . 108 14,42,9,32 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T360|497|SLC19A2|protein_coding|CODING|NM_006996.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904063 rs3737682 -0.693145 0.219582 108 L1397F 2224 Ctc/Ttc MODERATE 13 MISSENSE CODING F5 A protein_coding NM_000130.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169510139 G A 0 222 0 0.0008 0.1723 0.0908 0.6022 0.0239 0.1718 0.00544712 0.00722743 0.00813953 1 73 10900 1584 5535 543 890 70 2205 2 10406 121336 11548 8640 6610 66712 908 16512 0.947304 0 . 0 . 164 57,19,51,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L1397F|2224|F5|protein_coding|CODING|NM_000130.4|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965647 rs13306334 -0.693147 0.327468 164 L1285I 2224 Ctt/Att MODERATE 13 MISSENSE CODING F5 T protein_coding NM_000130.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169510475 G T 0 222 0 0.1611 0.1647 0.1441 0.1131 0.1819 0.2198 0.175897 0.175073 0.174651 1 1742 21690 1504 878 1363 12594 154 3455 2 10390 121304 11546 8644 6612 66692 908 16512 0.248858 0 . 0 . 300 77,69,55,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L1285I|2224|F5|protein_coding|CODING|NM_000130.4|13|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.993769 0.982164 0 0.804811 rs1046712 -0.693147 0.000310911 300 Q534R 2224 cAa/cGa MODERATE 10 MISSENSE CODING F5 C protein_coding NM_000130.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169519049 T C 0 228 0 1 0.994 0.9899 1 0.9881 0.9888 0.995688 0.978625 0.969884 2 10358 118714 11493 8618 6469 64629 880 16267 2 10404 121322 11564 8618 6606 66714 906 16510 0 5|255|255|255|5 pathogenic|other|other|other|pathogenic 0 . 130 0,0,84,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q534R|2224|F5|protein_coding|CODING|NM_000130.4|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6025 -0.693147 0.000991071 130 R513K 2224 aGa/aAa MODERATE 10 MISSENSE CODING F5 T protein_coding NM_000130.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169519112 C T 0 222 0 0.3238 0.2636 0.1052 0.627 0.0239 0.1667 0.268497 0.0981086 0.010814 1 3035 13587 1418 5601 384 981 72 2096 2 10406 121370 11566 8636 6610 66734 908 16510 0.956876 0 . 0 . 167 52,24,44,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R513K|2224|F5|protein_coding|CODING|NM_000130.4|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.187059 rs6020 -0.693147 0.752978 167 K414 2224 aaA/aaG LOW 8 SILENT CODING F5 C protein_coding NM_000130.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169521849 T C 0 222 0 0.0847 0.0831 0.0735 0.0714 0.0865 0.0961 0.0905583 0.0878056 0.0863953 1 910 10468 1154 542 371 5728 66 1697 2 10406 121378 11576 8644 6614 66720 908 16510 0.522855 0 . 0 . 116 36,20,26,18 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K414|2224|F5|protein_coding|CODING|NM_000130.4|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984445 rs6035 -0.693146 0.272666 116 D603N 830 Gac/Aac MODERATE 11 MISSENSE CODING SELP T protein_coding NM_003005.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169566313 C T 0 228 0 0.8729 0.7508 0.7003 0.9573 0.5905 0.5736 0.815479 0.645471 0.558372 2 8606 77390 8927 8401 4276 37372 547 9261 2 10398 121178 11480 8642 6594 66654 904 16506 1 0 . 0 . 128 0,1,75,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D603N|830|SELP|protein_coding|CODING|NM_003005.3|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386601660,rs6127 -0.693147 0.0329752 128 P340L 830 cCg/cTg MODERATE 7 MISSENSE CODING SELP A protein_coding NM_003005.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169580858 G A 0 222 0 0 0.00039936 0 0.002 0 0 0.000453926 0.000153775 0 1 2 19 0 16 0 1 0 0 2 10404 121344 11554 8646 6614 66712 908 16506 0.999944 0 . 0 . 84 17,18,24,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P340L|830|SELP|protein_coding|CODING|NM_003005.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799462 rs140055915 -0.693145 0.258494 84 S331N 830 aGt/aAt MODERATE 7 MISSENSE CODING SELP T protein_coding NM_003005.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169580885 C T 0 222 0 0.3389 0.239 0.1412 0.2024 0.1859 0.2658 0.303223 0.227126 0.18814 1 3320 24952 1034 1839 1353 13082 194 4130 2 10396 121242 11550 8632 6612 66656 906 16490 0.193225 0 . 0 . 81 16,20,17,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S331N|830|SELP|protein_coding|CODING|NM_003005.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.884458 rs386601678,rs6131 -0.693139 0.0135256 81 E10D 372 gaA/gaC MODERATE 2 MISSENSE CODING METTL18 G protein_coding NM_033418.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169762807 T G 0 222 0 0.2693 0.2183 0.196 0.1657 0.164 0.2751 0.236496 0.184146 0.157326 1 2515 22167 2459 1447 972 10470 165 4139 2 10246 119652 11552 8640 6612 66096 890 15616 0.85885 0 . 0 . 71 20,14,15,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E10D|372|METTL18|protein_coding|CODING|NM_033418.2|2|G),UPSTREAM(MODIFIER||1743||853|C1orf112|protein_coding|CODING|NM_018186.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.74698 rs10489177,rs386513441 -0.693054 0.224704 71 853 5479 MODIFIER 1 CODING C1orf112 G protein_coding NM_018186.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169764568 C G 0 125 0 0.9607 0.7875 0.7637 0.6716 0.6799 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_5_PRIME(MODIFIER||5479||853|C1orf112|protein_coding|CODING|NM_018186.2|1|G),UPSTREAM(MODIFIER||507||372|METTL18|protein_coding|CODING|NM_033418.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3766132 -0.651104 0.575705 8 853 2014 MODIFIER 2 CODING C1orf112 C protein_coding NM_018186.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169768033 T C 0 228 0 0.7209 0.6801 0.7032 0.6607 0.5825 0.729 0 . 0 2 1281 10900 213 214 4 3978 97 5113 2 1764 16202 290 320 6 6568 154 7100 0 . 0 . 0 75 0,0,68,5 UTR_5_PRIME(MODIFIER||2014||853|C1orf112|protein_coding|CODING|NM_018186.2|2|C),UPSTREAM(MODIFIER||3972||372|METTL18|protein_coding|CODING|NM_033418.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6680938 -0.693147 0.000248457 75 853 1967 MODIFIER 2 CODING C1orf112 A protein_coding NM_018186.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169768080 C A 0 228 0 0.7209 0.6801 0.7032 0.6607 0.5825 0.729 0 . 0 2 1309 11663 225 216 4 4203 105 5601 2 1802 17194 306 328 6 6914 164 7674 0 . 0 . 0 122 0,0,87,19 UTR_5_PRIME(MODIFIER||1967||853|C1orf112|protein_coding|CODING|NM_018186.2|2|A),UPSTREAM(MODIFIER||4019||372|METTL18|protein_coding|CODING|NM_033418.2||A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6668114 -0.693147 0.0600064 122 Q621R 742 cAa/cGa MODERATE 13 MISSENSE CODING SCYL3 C protein_coding NM_181093.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169823718 T C 0 228 0 0.7148 0.6797 0.7032 0.6607 0.5875 0.7301 0.710849 0.626634 0.583488 2 7394 78064 8673 5750 3701 39947 579 12020 2 10402 121346 11558 8646 6614 66712 908 16506 0 . 0 . COSM146679,COSM1336135 137 0,0,56,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q621R|742|SCYL3|protein_coding|CODING|NM_181093.3|13|C),DOWNSTREAM(MODIFIER||1489||853|C1orf112|protein_coding|CODING|NM_018186.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4656197 -0.693147 0.0149346 137 792 243 MODIFIER 20 CODING KIFAP3 A protein_coding NM_014970.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169890574 T A 0 228 0 0.9992 0.9565 0.9568 0.9901 0.8966 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 72 0,0,41,24 UTR_3_PRIME(MODIFIER||243||792|KIFAP3|protein_coding|CODING|NM_014970.3|20|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4519 -0.693147 0.24071 72 792 194 MODIFIER 20 CODING KIFAP3 G protein_coding NM_014970.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 169890623 A G 0 222 0 0.1241 0.0667 0.0115 0.122 0 0.0399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.368417 0 . 0 . 83 16,17,16,24 UTR_3_PRIME(MODIFIER||194||792|KIFAP3|protein_coding|CODING|NM_014970.3|20|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.962337 rs386612410,rs7674 -0.693145 0.0770535 83 792 243 MODIFIER 1 CODING KIFAP3 T protein_coding NM_014970.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170043851 C T 0 116 0 0.3699 0.2849 0.2608 0.3423 0.1113 0.3067 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.640197 0 . 0 . 14 0,7,1,6 START_GAINED(LOW||||792|KIFAP3|protein_coding|CODING|NM_014970.3|1|T),UTR_5_PRIME(MODIFIER||243||792|KIFAP3|protein_coding|CODING|NM_014970.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 1 0 0.360111 rs1360294 -0.636426 0.542521 14 C119 283 tgC/tgT LOW 3 SILENT CODING METTL11B T protein_coding NM_001136107.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170135669 C T 0 222 0 0.5076 0.2911 0.2421 0.1349 0.2724 0.2137 0.474711 0.337714 0.278127 1 1228 6449 117 100 533 2817 68 1586 2 2566 23930 476 630 1812 10274 258 7914 0.999583 0 . 0 . 72 22,10,23,6 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C119|283|METTL11B|protein_coding|CODING|NM_001136107.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992494 rs6427234 -0.693079 0.399135 72 S150P 283 Tcc/Ccc MODERATE 3 MISSENSE CODING METTL11B C protein_coding NM_001136107.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170135760 T C 0 222 0 0.5076 0.2913 0.2435 0.1349 0.2724 0.2137 0.474711 0.337714 0.278127 1 1134 6189 108 98 516 2683 68 1582 2 2394 23182 430 628 1744 9814 260 7912 0.994298 0 . 0 . 111 30,18,31,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S150P|283|METTL11B|protein_coding|CODING|NM_001136107.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999144 rs6427235 -0.693147 0.026606 111 F151 283 ttT/ttC LOW 3 SILENT CODING METTL11B C protein_coding NM_001136107.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170135765 T C 0 222 0 0.4758 0.2656 0.2219 0.1349 0.2207 0.1933 0.432803 0.295883 0.236329 1 1049 5414 101 98 447 2258 55 1406 2 2392 23114 426 628 1742 9756 258 7912 0.977387 0 . 0 . 113 31,17,32,20 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F151|283|METTL11B|protein_coding|CODING|NM_001136107.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.857072 rs6669514 -0.693147 0.028176 113 G32 394 ggA/ggC LOW 1 SILENT CODING GORAB C protein_coding NM_152281.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170501385 A C 0 228 0 0.7322 0.9275 0.987 1 1 1 0.814571 0.935491 0.997442 2 8301 118946 11414 8654 6614 66557 901 16505 2 10404 121406 11578 8654 6614 66736 908 16512 0 . 0 . 0 189 0,0,66,104 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G32|394|GORAB|protein_coding|CODING|NM_152281.2|1|C),INTRAGENIC(MODIFIER|||||LOC101928650||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7531125 -0.693147 0.133736 189 E320K 394 Gaa/Aaa MODERATE 5 MISSENSE CODING GORAB A protein_coding NM_152281.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170521376 G A 0 222 0 0.5257 0.5927 0.5865 0.877 0.4692 0.5215 0.531094 0.485853 0.462674 1 5488 65419 7854 7888 3736 31842 473 8138 2 10398 121270 11538 8648 6608 66670 906 16502 0.47726 0 . 0 . 181 30,53,34,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E320K|394|GORAB|protein_coding|CODING|NM_152281.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961108 rs913257 -0.693147 0.389748 181 394 47 MODIFIER 5 CODING GORAB G protein_coding NM_152281.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170521650 T G 0 70 0 0.2322 0.1971 0.1153 0.119 0.1382 0.3487 0.218207 0.167181 0.141193 1 2114 18717 1074 766 754 8708 164 5137 2 9310 117182 11286 8304 6548 64546 874 16314 0.952347 0 . 0 . 10 0,5,0,5 UTR_3_PRIME(MODIFIER||47||394|GORAB|protein_coding|CODING|NM_152281.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.952347 0 . 0.666643 rs7552922 -0.590765 0.945612 10 245 291 MODIFIER 4 CODING PRRX1 C protein_coding NM_022716.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 170705618 A C 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 117 0,0,34,72 UTR_3_PRIME(MODIFIER||291||245|PRRX1|protein_coding|CODING|NM_022716.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6666030 -0.693147 0.00272356 117 S195L 535 tCa/tTa MODERATE 5 MISSENSE CODING FMO2 T protein_coding NM_001460.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171168584 C T 0 222 0 0.5265 0.4728 0.4827 0.5456 0.2962 0.5 0.493418 0.378825 0.320116 1 5277 47986 6071 4837 1865 21560 337 8039 2 10402 121190 11512 8626 6610 66668 908 16464 0.945634 0 . 0 COSM146682 184 45,45,37,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S195L|535|FMO2|protein_coding|CODING|NM_001460.4|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.172958 rs2020862 -0.693147 0.00594667 184 S195 535 tcA/tcG LOW 5 SILENT CODING FMO2 G protein_coding NM_001460.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171168585 A G 0 222 0 0.7209 0.5893 0.6167 0.6032 0.3877 0.5849 0.669769 0.502845 0.417326 1 7157 60854 7831 5212 2600 27918 443 9693 2 10400 121190 11514 8630 6606 66668 908 16464 0.652547 0 . 0 COSM146683 187 45,45,37,48 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S195|535|FMO2|protein_coding|CODING|NM_001460.4|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.172958 rs2020861 -0.693147 0.00594667 187 E314G 535 gAg/gGg MODERATE 7 MISSENSE CODING FMO2 G protein_coding NM_001460.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171174531 A G 0 222 0 0.0424 0.1597 0.2277 0.2371 0.0905 0.2618 0.0624149 0.0818853 0.0918605 1 572 16070 2816 2165 505 5980 107 3925 2 10406 121046 11454 8580 6594 66608 902 16502 0.480215 0 . 0 COSM146684 98 30,19,23,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E314G|535|FMO2|protein_coding|CODING|NM_001460.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975486 rs2020863 -0.693145 0.27167 98 535 206 MODIFIER 9 CODING FMO2 T protein_coding NM_001460.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171178490 C T 0 57 0 0.0968 0.1745 0.2305 0.2371 0.0905 0.2618 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||206||535|FMO2|protein_coding|CODING|NM_001460.4|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs28369914 -0.511536 0.292464 3 A906T 2817 Gct/Act MODERATE 16 MISSENSE CODING PRRC2C A protein_coding NM_015172.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171509327 G A 0 222 0 0.7179 0.8009 0.7248 0.8958 0.8151 0.8548 0.760554 0.794787 0.812326 1 7836 99058 7984 7681 5647 54660 748 14502 2 10326 121186 11546 8634 6612 66656 902 16510 0.245889 0 . 0 COSM1158681,COSM1158680 77 7,27,12,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A906T|2817|PRRC2C|protein_coding|CODING|NM_015172.3|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.587072 rs760644 -0.693143 0.160431 77 S1476 2817 tcC/tcG LOW 16 SILENT CODING PRRC2C G protein_coding NM_015172.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171511039 C G 0 222 0 0.7474 0.8103 0.7349 0.8958 0.8161 0.8548 0.772129 0.797478 0.810465 1 7975 98899 7999 7664 5651 54385 745 14480 2 10240 120718 11544 8618 6614 66324 902 16476 0.998157 0 . 0 . 48 15,6,15,7 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S1476|2817|PRRC2C|protein_coding|CODING|NM_015172.3|16|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987607 rs1687064 -0.692562 0.816201 48 S1624C 2817 tCt/tGt MODERATE 17 MISSENSE CODING PRRC2C G protein_coding NM_015172.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171514731 C G 0 222 0 0.7277 0.8047 0.7305 0.8968 0.8161 0.8548 0.757376 0.792865 0.811047 1 7561 94563 7566 7266 5485 52301 711 13673 2 9874 114878 10730 8130 6406 63370 852 15516 0.994347 0 . 0 . 54 12,18,9,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S1624C|2817|PRRC2C|protein_coding|CODING|NM_015172.3|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987326 rs235468 -0.691153 0.0552092 54 P1771 2817 ccG/ccA LOW 19 SILENT CODING PRRC2C A protein_coding NM_015172.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171526570 G A 0 222 0 0.7474 0.8103 0.7349 0.8958 0.8161 0.8548 0.782738 0.810011 0.825207 1 2175 18479 314 568 745 7494 191 6992 2 2820 22016 412 650 884 9106 230 7914 0.750535 0 . 0 . 111 23,25,23,31 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1771|2817|PRRC2C|protein_coding|CODING|NM_015172.3|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.707824 rs1687057 -0.693147 0.0416851 111 S2589 2817 tcG/tcC LOW 31 SILENT CODING PRRC2C C protein_coding NM_015172.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171556165 G C 0 222 0 0.7088 0.7931 0.732 0.8958 0.8151 0.8221 0.743985 0.788021 0.810581 1 7294 90845 7004 7120 5360 50500 683 12884 2 9650 110916 9864 8002 6270 61362 828 14940 0.901606 0 . 0 . 51 25,4,12,5 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S2589|2817|PRRC2C|protein_coding|CODING|NM_015172.3|31|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.792114 rs235501 -0.690438 0.0817507 51 2817 239 MODIFIER 34 CODING PRRC2C T protein_coding NM_015172.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171561225 C T 0 20.3 0 0.6823 0.7847 0.7233 0.8958 0.8151 0.8211 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,3,0,2 UTR_3_PRIME(MODIFIER||239||2817|PRRC2C|protein_coding|CODING|NM_015172.3|34|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.666667 rs235907 -0.453602 0.1 5 R76K 504 aGa/aAa MODERATE 1 MISSENSE CODING MYOC T protein_coding NM_000261.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171621525 C T 0 222 0 0.0068 0.1362 0.1023 0.0794 0.1412 0.3885 0.0276895 0.0981854 0.134302 1 239 18206 1151 721 1105 9099 145 5746 2 10406 121294 11578 8650 6608 66670 908 16474 0.747154 2 benign 0 . 83 23,12,29,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R76K|504|MYOC|protein_coding|CODING|NM_000261.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.154119 rs2234926 -0.693146 0.847314 83 141 1033 MODIFIER 8 CODING VAMP4 C protein_coding NM_003762.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171672613 A C 0 168 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,27,0 UTR_3_PRIME(MODIFIER||1033||141|VAMP4|protein_coding|CODING|NM_003762.4|8|C) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs236896 -0.693021 1.26438e-11 27 141 LOW 4 CODING VAMP4 A protein_coding NM_003762.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171679958 G A 0 222 0 0.5083 0.351 0.2695 0.3829 0.2883 0.228 0.469133 0.362483 0.307818 1 4918 37989 2907 3418 1716 20381 283 4366 2 10384 120928 11440 8640 6598 66530 906 16430 0.31298 0 . 0 . 82 10,30,9,23 SPLICE_SITE_REGION+INTRON(LOW||||141|VAMP4|protein_coding|CODING|NM_003762.4|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.820542 rs10913530 -0.69312 0.320361 82 699 57 MODIFIER 1 CODING METTL13 G protein_coding NM_015935.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171751051 A G 0 220 0 0.5666 0.4856 0.4092 0.6567 0.4423 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.908864 0 . 0 COSN163337 69 28,9,22,6 UTR_5_PRIME(MODIFIER||57||699|METTL13|protein_coding|CODING|NM_015935.4|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.332626 rs2294719 -0.693054 0.261527 69 H43 699 caT/caC LOW 1 SILENT CODING METTL13 C protein_coding NM_015935.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171751236 T C 0 222 0 0.73 0.5337 0.4395 0.6577 0.4443 0.2996 0.699047 0.547901 0.470465 1 7273 57100 4339 5566 3090 31252 432 5148 2 10390 121342 11572 8640 6606 66718 908 16508 0.805236 0 . 0 COSM146685 115 20,27,33,26 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H43|699|METTL13|protein_coding|CODING|NM_015935.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.810271 rs2294720,rs386564054 -0.693147 0.293456 115 M105V 699 Atg/Gtg MODERATE 2 MISSENSE CODING METTL13 G protein_coding NM_015935.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171753039 A G 0 222 0 0.2829 0.3069 0.2867 0.5238 0.2445 0.1943 0.309578 0.284792 0.272093 1 3249 34679 3149 4641 1939 18162 264 3275 2 10400 121356 11568 8638 6612 66720 906 16512 0.885631 0 . 0 . 219 56,37,63,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M105V|699|METTL13|protein_coding|CODING|NM_015935.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.88784 rs2232816 -0.693147 0.939608 219 S355 699 tcG/tcA LOW 3 SILENT CODING METTL13 A protein_coding NM_015935.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171755170 G A 0 222 0 0.323 0.3181 0.2911 0.5238 0.2445 0.1943 0.3468 0.297478 0.272209 1 3582 34713 3122 4566 1907 18005 264 3267 2 10228 119516 11394 8542 6402 65796 890 16264 0.789084 0 . 0 . 61 15,20,4,15 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S355|699|METTL13|protein_coding|CODING|NM_015935.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976654 rs2232818 -0.69168 0.363416 61 699 800 MODIFIER 8 CODING METTL13 G protein_coding NM_015935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171766696 A G 0 9.7 0 0.2723 0.3027 0.281 0.5228 0.2425 0.1943 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||800||699|METTL13|protein_coding|CODING|NM_015935.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7860 -0.379885 0 1 863 LOW 1 CODING DNM3 G protein_coding NM_015569.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 171810960 A G 0 228 0 0.6838 0.6328 0.5821 0.7907 0.5437 0.5286 0.693192 0.610879 0.569146 2 5535 62914 6054 6279 2924 34090 413 7619 2 7948 105190 10022 7878 4824 58770 754 14994 1 0 . 0 . 178 0,1,31,135 SPLICE_SITE_REGION+INTRON(LOW||||863|DNM3|protein_coding|CODING|NM_015569.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12239702 -0.693147 0.00951102 178 T741 863 acA/acG LOW 19 SILENT CODING DNM3 G protein_coding NM_015569.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172356437 A G 0 228 0 1 0.9966 0.9942 1 0.9871 1 0.997087 0.989368 0.985578 2 9784 119710 11532 8600 6595 65827 888 16484 2 9800 120692 11568 8600 6614 66700 898 16512 0 . 0 . 0 66 0,0,20,36 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T741|863|DNM3|protein_coding|CODING|NM_015569.4|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6688654 -0.693147 0.0373274 66 863 3894 MODIFIER 21 CODING DNM3 A protein_coding NM_015569.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172380875 C A 0 136 0 0.9039 0.9377 0.9251 0.996 0.9195 0.9509 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||3894||863|DNM3|protein_coding|CODING|NM_015569.4|21|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4916255 -0.616816 0.348672 6 863 4402 MODIFIER 21 CODING DNM3 C protein_coding NM_015569.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172381383 T C 0 54 0 0.0189 0.2927 0.3862 0.5109 0.3986 0.2628 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 0,3,1,2 UTR_3_PRIME(MODIFIER||4402||863|DNM3|protein_coding|CODING|NM_015569.4|21|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.28717 rs7528296 -0.511536 0.192436 6 P266S 297 Cca/Tca MODERATE 2 MISSENSE CODING PIGC A protein_coding NM_002642.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172410967 G A 0 222 0 0.0605 0.4543 0.536 0.6597 0.5994 0.5675 0.150931 0.419652 0.557326 1 1413 66463 7358 5508 3926 38391 519 9348 2 10394 121228 11574 8642 6612 66648 908 16450 0.761276 0 . 0 . 101 23,24,17,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P266S|297|PIGC|protein_coding|CODING|NM_002642.3|2|A),INTRON(MODIFIER||||183|C1orf105|protein_coding|CODING|NM_139240.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999803 rs1063412 -0.693146 0.517788 101 G89 297 ggT/ggC LOW 2 SILENT CODING PIGC G protein_coding NM_002642.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172411496 A G 0 228 0 0.9047 0.9241 0.9092 1 0.8499 0.9591 0.892646 0.85376 0.833837 2 9304 106178 10497 8650 5128 56322 785 15492 2 10402 121388 11578 8654 6614 66720 908 16512 0 . 0 . 0 71 0,0,42,26 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G89|297|PIGC|protein_coding|CODING|NM_002642.3|2|G),INTRON(MODIFIER||||183|C1orf105|protein_coding|CODING|NM_139240.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2230471 -0.693147 0.226502 71 297 6 MODIFIER 2 CODING PIGC C protein_coding NM_002642.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172411768 T C 0 222 0 0.1301 0.2524 0.268 0.3403 0.2048 0.365 0.150477 0.197524 0.221628 1 1548 28644 2528 3140 1001 14729 199 5499 2 10336 120120 11560 8626 6614 66270 896 15818 0.601211 0 . 0 . 132 26,33,21,33 UTR_5_PRIME(MODIFIER||6||297|PIGC|protein_coding|CODING|NM_002642.3|2|C),INTRON(MODIFIER||||183|C1orf105|protein_coding|CODING|NM_139240.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998663 rs13932,rs386530368 -0.693147 0.484192 132 S137N 183 aGc/aAc MODERATE 7 MISSENSE CODING C1orf105 A protein_coding NM_139240.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172437592 G A 0 228 0 0.671 0.8413 0.8516 1 0.8072 0.9356 0.708125 0.75888 0.784884 2 7315 100027 10172 8647 4888 53392 750 14863 2 10376 121236 11540 8654 6614 66674 908 16470 0 . 0 . 0 108 0,0,67,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S137N|183|C1orf105|protein_coding|CODING|NM_139240.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1129942 -0.693147 0.797416 108 S11P 1405 Tct/Cct MODERATE 1 MISSENSE CODING SUCO C protein_coding NM_016227.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172501643 T C 0 222 0 0.2118 0.2498 0.2104 0.1885 0.2515 0.3906 0.204948 0.234623 0.248425 1 1969 29963 2298 1596 1298 16481 242 6079 2 8908 116128 10952 8416 6402 64804 866 15780 0.145026 0 . 0 COSM146688 148 57,16,54,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S11P|1405|SUCO|protein_coding|CODING|NM_016227.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740932 rs2239816 -0.693147 0.0048474 148 L117P 1405 cTg/cCg MODERATE 2 MISSENSE CODING SUCO C protein_coding NM_016227.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172502340 T C 0 173 0 0.6006 0.3636 0.2493 0.1895 0.2545 0.4162 0 . 0 1 275 3128 31 48 0 723 27 2024 2 442 6370 84 134 4 1686 64 3956 0.252539 0 . 0 . 18 4,3,7,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L117P|1405|SUCO|protein_coding|CODING|NM_016227.3|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.970677 rs2285143 -0.670168 0.855481 18 I163 1405 atT/atC LOW 2 SILENT CODING SUCO C protein_coding NM_016227.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172502479 T C 0 228 0 0.7171 0.5895 0.4611 0.379 0.5835 0.7311 0.690656 0.625825 0.588566 2 1937 13717 194 258 473 5258 130 5467 2 2764 21566 414 632 732 8904 206 7914 1 0 . 0 . 76 1,0,64,9 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I163|1405|SUCO|protein_coding|CODING|NM_016227.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2285144 -0.693147 0.40612 76 E607 1405 gaA/gaG LOW 13 SILENT CODING SUCO G protein_coding NM_016227.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 172547465 A G 0 222 0 0.2368 0.2542 0.2089 0.2024 0.2296 0.3885 0.232637 0.23789 0.240581 1 2383 29513 2345 1647 1068 15750 243 6077 2 10370 121014 11504 8634 6588 66534 908 16476 0.842903 0 . 0 . 131 27,32,29,31 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E607|1405|SUCO|protein_coding|CODING|NM_016227.3|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.413636 rs2285664 -0.693147 0.253938 131 183 1418 MODIFIER 3 CODING TNFSF4 G protein_coding NM_003326.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173154237 A G 0 9.7 0 0.1619 0.1022 0.1398 0.0784 0.0696 0.0532 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1418||183|TNFSF4|protein_coding|CODING|NM_003326.4|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs60818642 -0.379885 0 1 183 1351 MODIFIER 3 CODING TNFSF4 T protein_coding NM_003326.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173154304 G T 0 9.7 0 0.7292 0.3792 0.353 0.1151 0.3131 0.2648 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1351||183|TNFSF4|protein_coding|CODING|NM_003326.4|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7514229 -0.379885 0 1 224 15 MODIFIER 5 CODING PRDX6 T protein_coding NM_004905.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173457017 C T 0 222 0 0.6921 0.4161 0.2565 0.5853 0.2058 0.1984 0.621425 0.369829 0.24093 1 6533 35409 2078 5358 1362 16335 234 3509 2 10294 120832 11518 8616 6592 66474 902 16436 0.804167 0 . 0 . 55 10,16,7,17 UTR_3_PRIME(MODIFIER||15||224|PRDX6|protein_coding|CODING|NM_004905.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986471 rs4611,rs78495657 -0.692831 0.101881 55 Q1089 1124 caA/caG LOW 26 SILENT CODING SLC9C2 C protein_coding NM_178527.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173474429 T C 0 228 0 0.0136 0.3043 0.3213 0.6448 0.2087 0.4325 0.0481162 0.153314 0.207209 2 486 32685 4929 5598 1419 14189 221 5843 2 10382 120954 11488 8628 6588 66492 908 16468 0 . 0 . 0 88 0,0,33,42 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1089|1124|SLC9C2|protein_coding|CODING|NM_178527.3|26|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12026637 -0.693147 0.0170153 88 A505G 1124 gCt/gGt MODERATE 13 MISSENSE CODING SLC9C2 C protein_coding NM_178527.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173516871 G C 0 228 0 0.1293 0.3347 0.3256 0.6448 0.2107 0.4264 0.132547 0.18107 0.20593 2 1357 33594 5001 5613 1414 14138 227 5844 2 10402 121246 11518 8646 6602 66670 908 16500 1 0 . 0 . 115 0,1,57,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A505G|1124|SLC9C2|protein_coding|CODING|NM_178527.3|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs16846206 -0.693147 0.010783 115 N494 1124 aaT/aaC LOW 13 SILENT CODING SLC9C2 G protein_coding NM_178527.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173516903 A G 0 228 0 0.671 0.4852 0.3732 0.6448 0.2147 0.4274 0.591693 0.338613 0.208953 2 6345 39018 5257 5595 1414 14303 246 5858 2 10400 121166 11498 8618 6604 66642 908 16496 0 . 0 . 0 110 0,0,38,57 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N494|1124|SLC9C2|protein_coding|CODING|NM_178527.3|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10494490 -0.693147 0.0307253 110 177 32 MODIFIER 2 CODING LOC730159 A protein_coding NM_001195190.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173606207 T A 0 92 0 0.826 0.4744 0.3112 0.5962 0.2664 0.2035 0 . 0 1 140 3031 28 87 0 1047 41 1688 2 202 10646 92 132 0 2704 118 7398 0.950952 0 . 0 . 11 0,5,1,5 UTR_3_PRIME(MODIFIER||32||177|LOC730159|protein_coding|CODING|NM_001195190.1|2|A),INTRON(MODIFIER||||266|ANKRD45|protein_coding|CODING|NM_198493.2|3|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.950952 1 0 0.891517 rs12067170 -0.616816 0.712859 11 503 36 MODIFIER 5 CODING ZBTB37 T protein_coding NM_001122770.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173855298 A T 0 193 0 0.8442 0.5351 0.3718 0.5913 0.341 0.3753 0.742129 0.45541 0.331388 1 858 4972 121 280 213 1668 57 1775 2 1064 10948 300 464 704 4012 122 4282 0.854299 0 . 0 . 31 5,11,5,9 UTR_3_PRIME(MODIFIER||36||503|ZBTB37|protein_coding|CODING|NM_001122770.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.00370047 rs1322775 -0.686358 0.116505 31 Q337 464 caA/caG LOW 5 SILENT CODING SERPINC1 C protein_coding NM_000488.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173878832 T C 0 222 0 0.8442 0.5357 0.3732 0.5923 0.3469 0.3701 0.762143 0.488236 0.347907 1 8120 48896 3075 5601 1982 23504 356 6258 2 10406 121372 11576 8626 6614 66732 908 16510 0.665828 0 . 0 . 62 12,14,15,14 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q337|464|SERPINC1|protein_coding|CODING|NM_000488.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.454441 rs386600221,rs5878 -0.693079 0.743471 62 V327 464 gtA/gtG LOW 5 SILENT CODING SERPINC1 C protein_coding NM_000488.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 173878862 T C 0 222 0 0.8366 0.5453 0.4251 0.619 0.34 0.3722 0.75488 0.483623 0.344651 1 8035 49503 3847 5817 1906 23267 362 6269 2 10406 121368 11574 8626 6614 66730 908 16510 0.994475 0 . 0 . 58 9,12,12,18 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V327|464|SERPINC1|protein_coding|CODING|NM_000488.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98001 rs5877 -0.693097 0.0539116 58 361 19 MODIFIER 1 CODING GPR52 A protein_coding NM_005684.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 174417231 G A 0 228 0 0.9977 0.9852 0.9769 1 0.9543 0.9908 0.993872 0.96863 0.955698 2 10306 113727 11303 8622 6320 62751 844 13581 2 10368 117524 11538 8624 6614 65768 876 13736 0 . 0 . 0 47 0,0,44,1 UTR_5_PRIME(MODIFIER||19||361|GPR52|protein_coding|CODING|NM_005684.4|1|A),INTRON(MODIFIER||||815|RABGAP1L|protein_coding|CODING|NM_014857.4|13|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7516240 -0.693147 0.189692 47 D289N 1299 Gat/Aat MODERATE 4 MISSENSE CODING TNN A protein_coding NM_022093.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175049379 G A 0 222 0 0.0053 0.1276 0.0735 0.251 0.1272 0.2045 0.0272356 0.108181 0.149651 1 243 17837 952 1948 1151 10435 134 2974 2 10404 121318 11564 8620 6606 66708 904 16512 0.939413 0 . 0 . 51 18,2,18,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D289N|1299|TNN|protein_coding|CODING|NM_022093.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.957526 rs16847812 -0.692831 0.850866 51 G858 1299 ggC/ggT LOW 11 SILENT CODING TNN T protein_coding NM_022093.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175087884 C T 0 222 0 0.0424 0.1729 0.17 0.3452 0.1292 0.2188 0.0483432 0.0941104 0.117558 1 614 21164 2289 2814 1257 10730 148 3312 2 10378 121252 11550 8622 6600 66692 900 16510 0.767138 0 . 0 COSM146690 149 38,37,26,25 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G858|1299|TNN|protein_coding|CODING|NM_022093.1|11|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.892409 rs2269654 -0.693147 0.148522 149 M859V 1299 Atg/Gtg MODERATE 11 MISSENSE CODING TNN G protein_coding NM_022093.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175087885 A G 0 222 0 0.0424 0.1729 0.17 0.3462 0.1292 0.2178 0.0503858 0.0989543 0.123837 1 614 21178 2293 2818 1257 10738 148 3310 2 10378 121244 11546 8616 6600 66694 900 16510 0.998862 0 . 0 COSM146691 148 37,37,26,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M859V|1299|TNN|protein_coding|CODING|NM_022093.1|11|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.832592 rs6694078 -0.693147 0.148522 148 P930L 1299 cCg/cTg MODERATE 12 MISSENSE CODING TNN T protein_coding NM_022093.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175092674 C T 0 222 0 0.6203 0.5982 0.6671 0.4921 0.6421 0.5838 0.605765 0.62302 0.63186 1 6339 73223 7683 4360 4012 41312 522 8995 2 10406 121374 11578 8630 6608 66732 908 16512 0.918278 0 . 0 COSM146692 168 62,31,39,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P930L|1299|TNN|protein_coding|CODING|NM_022093.1|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94967 rs2285215 -0.693147 0.0324561 168 T1104 1299 acG/acA LOW 15 SILENT CODING TNN A protein_coding NM_022093.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175097864 G A 0 222 0 0.1082 0.1755 0.1643 0.2609 0.1948 0.1667 0.119156 0.183069 0.215814 1 1257 25998 2258 1950 1842 15167 204 3320 2 10394 120232 11554 8634 6602 66416 896 15736 0.999773 0 . 0 . 97 16,31,17,23 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1104|1299|TNN|protein_coding|CODING|NM_022093.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.788244 rs12022593 -0.693145 0.0786962 97 A1156V 1299 gCg/gTg MODERATE 17 MISSENSE CODING TNN T protein_coding NM_022093.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175105996 C T 0 208 0 0.0961 0.1214 0.1052 0.2123 0.0905 0.1053 0.0919201 0.0903429 0.0895349 1 1015 13893 1387 1739 1097 6507 96 2052 2 10404 121268 11540 8646 6606 66674 904 16494 0.941484 0 . 0 . 60 24,7,19,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A1156V|1299|TNN|protein_coding|CODING|NM_022093.1|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.686011 rs2072036 -0.692067 0.586203 60 N1217 1299 aaT/aaC LOW 18 SILENT CODING TNN C protein_coding NM_022093.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175113578 T C 0 228 0 0.9962 0.986 0.9741 0.997 0.9602 0.9959 0.990468 0.971321 0.961512 2 10326 118367 11381 8603 6500 64262 884 16411 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 112 0,0,72,26 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N1217|1299|TNN|protein_coding|CODING|NM_022093.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10912897 -0.693147 0.507819 112 1299 45 MODIFIER 19 CODING TNN G protein_coding NM_022093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175116252 C G 0 228 0 0.9947 0.851 0.9049 0.7331 0.8459 0.7454 0.963232 0.887898 0.849302 2 9651 93718 10246 5930 5654 53154 645 8438 2 9918 109826 11068 8252 6148 62444 772 11224 0 . 0 . 0 87 0,0,23,56 UTR_3_PRIME(MODIFIER||45||1299|TNN|protein_coding|CODING|NM_022093.1|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4651335 -0.693147 0.0132031 87 99 159 MODIFIER 5 CODING KIAA0040 T protein_coding NM_001162893.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175129691 G T 0 228 0 0.3449 0.4251 0.5519 0.5169 0.3559 0.4202 0.322977 0.349978 0.361722 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 73 0,1,10,61 UTR_3_PRIME(MODIFIER||159||99|KIAA0040|protein_coding|CODING|NM_001162893.1|5|T) 1 0 . 0 . 1 0 1 0 . 60 0 1 1 0 1 rs2269650 -0.693147 0.236757 73 K68 99 aaG/aaA LOW 5 SILENT CODING KIAA0040 T protein_coding NM_001162893.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175129946 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 1074 8675 213 305 15 3509 74 3485 2 1644 14686 334 554 24 5860 138 6132 0 . 0 . 0 62 0,0,52,7 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K68|99|KIAA0040|protein_coding|CODING|NM_001162893.1|5|T) 0 . 0 . 0 . 0 . 1 0 60 0 0 1 0 . rs2072035 -0.693147 0.0455002 62 99 127 MODIFIER 5 CODING KIAA0040 A protein_coding NM_001162893.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175130276 G A 0 228 0 0.9962 0.9842 0.9726 0.996 0.9612 0.9877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,3,35 UTR_5_PRIME(MODIFIER||127||99|KIAA0040|protein_coding|CODING|NM_001162893.1|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1135289 -0.693143 0.0316777 38 99 5680 MODIFIER 4 CODING KIAA0040 A protein_coding NM_001162893.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175135829 G A 0 9.7 0 0.0166 0.2372 0.438 0.2946 0.2555 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||5680||99|KIAA0040|protein_coding|CODING|NM_001162893.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2861158 -0.379885 0 1 Q1234 1358 caA/caG LOW 21 SILENT CODING TNR C protein_coding NM_003285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175299301 T C 0 228 0 0.8419 0.766 0.7637 0.7887 0.7187 0.6902 0.806173 0.751038 0.722791 2 8428 90317 9776 7075 4807 48222 655 11354 2 10398 121192 11566 8626 6612 66632 904 16454 0 . 0 . 0 45 0,0,9,34 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1234|1358|TNR|protein_coding|CODING|NM_003285.2|21|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2027867 -0.693146 0.0292141 45 D1079 1358 gaT/gaC LOW 17 SILENT CODING TNR G protein_coding NM_003285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175324651 A G 0 228 0 0.5197 0.6657 0.7104 0.7946 0.6819 0.682 0.536995 0.635476 0.68593 2 5659 83602 8801 7103 4714 45503 619 11203 2 10404 121308 11562 8638 6610 66696 908 16490 0 . 0 . 0 94 0,0,41,45 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1079|1358|TNR|protein_coding|CODING|NM_003285.2|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2228359,rs386561685 -0.693147 0.154697 94 R643K 1358 aGg/aAg MODERATE 9 MISSENSE CODING TNR T protein_coding NM_003285.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175348723 C T 0 228 0 0.646 0.6963 0.7147 0.8065 0.6491 0.6861 0.677258 0.662079 0.654302 2 6917 81585 8931 7101 3994 42908 566 11168 2 10398 121268 11564 8636 6604 66656 908 16502 0 . 0 . 0 172 0,0,100,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R643K|1358|TNR|protein_coding|CODING|NM_003285.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs859427 -0.693147 0.237943 172 T518 1358 acT/acC LOW 8 SILENT CODING TNR G protein_coding NM_003285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175355391 A G 0 228 0 0.8018 0.8329 0.8631 0.8919 0.7724 0.8548 0.817975 0.798401 0.788372 2 8389 97549 10247 7799 5225 52168 688 13033 2 10288 119820 11538 8626 6598 66218 894 15658 0 . 0 . 0 134 0,0,82,38 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T518|1358|TNR|protein_coding|CODING|NM_003285.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386492433,rs859437 -0.693147 0.000221913 134 A128S 1358 Gcc/Tcc MODERATE 3 MISSENSE CODING TNR A protein_coding NM_003285.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175375469 C A 0 228 0 0.0885 0.2871 0.3617 0.5179 0.2525 0.3006 0.132093 0.223974 0.271047 2 1274 35593 5634 4509 2006 17189 228 4753 2 10406 121366 11576 8628 6604 66734 908 16510 0 . 0 . 0 70 0,0,41,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A128S|1358|TNR|protein_coding|CODING|NM_003285.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2239819 -0.693147 0.818917 70 T56 1358 acA/acG LOW 3 SILENT CODING TNR C protein_coding NM_003285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175375683 T C 0 228 0 0.7625 0.7268 0.7781 0.8194 0.6302 0.6462 0.756695 0.680993 0.642209 2 7858 82041 9682 7258 3931 42027 563 10722 2 10402 121398 11576 8648 6614 66738 908 16512 0 . 0 . 0 138 0,0,97,30 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T56|1358|TNR|protein_coding|CODING|NM_003285.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386617745,rs859399 -0.693147 0.00433455 138 I17V 1358 Atc/Gtc MODERATE 3 MISSENSE CODING TNR C protein_coding NM_003285.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 175375802 T C 0 228 0 0.7443 0.722 0.7781 0.8194 0.6302 0.6462 0.740581 0.675381 0.641977 2 7692 81875 9679 7260 3932 42029 563 10720 2 10406 121388 11578 8648 6614 66724 908 16510 0 . 0 . 0 130 0,0,54,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I17V|1358|TNR|protein_coding|CODING|NM_003285.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs859398 -0.693147 0.00265999 130 R230T 1791 aGg/aCg MODERATE 2 MISSENSE CODING PAPPA2 C protein_coding NM_020318.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 176526147 G C 0 222 0 0 0.0017971 0 0.0089 0 0 0 . 0 1 0 118 1 117 0 0 0 0 2 9796 120738 11576 8618 6614 66722 900 16512 0.711449 0 . 0 . 113 38,17,38,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aCg|R230T|1791|PAPPA2|protein_coding|CODING|NM_020318.2|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.161498 rs146412325 -0.693147 0.231172 113 C475 1294 tgT/tgC LOW 7 SILENT CODING ASTN1 G protein_coding NM_004319.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 176992553 A G 0 222 0 0.792 0.5142 0.4957 0.2054 0.5895 0.3926 0.732743 0.642033 0.595581 1 5710 49391 3813 1258 2743 29228 377 6262 2 7596 81626 7016 4366 3978 45680 614 12376 0.851524 0 . 0 . 81 25,11,31,9 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C475|1294|ASTN1|protein_coding|CODING|NM_004319.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.616783 rs172917 -0.693145 0.203708 81 P187 1294 ccG/ccC LOW 3 SILENT CODING ASTN1 G protein_coding NM_004319.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177001896 C G 0 222 0 0.0272 0.15 0.2118 0.2599 0.1471 0.1616 0.0517476 0.126557 0.164884 1 497 20432 2938 2129 1569 10642 135 2522 2 10114 119912 11528 8566 6590 65752 896 16466 0.967104 0 . 0 . 68 21,11,10,17 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P187|1294|ASTN1|protein_coding|CODING|NM_004319.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99262 rs2076069 -0.693021 0.158896 68 L390V 783 Cta/Gta MODERATE 7 MISSENSE CODING BRINP2 G protein_coding NM_021165.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177247854 C G 0 228 0 0.4017 0.2646 0.2061 0.2113 0.2187 0.2229 0.381298 0.265954 0.20686 2 3965 26395 2230 1532 986 13513 211 3958 2 10374 121168 11570 8634 6614 66562 906 16508 1 0 . 0 . 66 1,0,23,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Gta|L390V|783|BRINP2|protein_coding|CODING|NM_021165.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3176443 -0.693147 0.140005 66 1060 414 MODIFIER 26 CODING SEC16B C protein_coding NM_033127.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177898579 G C 0 132 0 0.0189 0.1456 0.1873 0.3482 0.1074 0.1176 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980199 0 . 0 . 14 1,4,1,8 UTR_3_PRIME(MODIFIER||414||1060|SEC16B|protein_coding|CODING|NM_033127.2|26|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.686908 rs16852158 -0.662043 0.834562 14 1060 194 MODIFIER 26 CODING SEC16B T protein_coding NM_033127.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177898799 C T 0 148 0 0.4576 0.5755 0.6412 0.7143 0.5875 0.5327 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.556947 0 . 0 . 30 17,0,10,1 UTR_3_PRIME(MODIFIER||194||1060|SEC16B|protein_coding|CODING|NM_033127.2|26|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.357283 rs623479 -0.676189 0.78249 30 G730R 1060 Gga/Aga MODERATE 18 MISSENSE CODING SEC16B T protein_coding NM_033127.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177908852 C T 0 222 0 0.0545 0.1615 0.1844 0.3294 0.1233 0.1564 0.0637513 0.0964956 0.111569 1 485 12062 1727 2255 588 5232 70 1705 2 4874 55758 4730 5104 3212 27600 452 9786 0.994844 0 . 0 . 108 21,14,43,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G730R|1060|SEC16B|protein_coding|CODING|NM_033127.2|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.767567 rs943762 -0.693147 0.0152746 108 H292R 1060 cAt/cGt MODERATE 7 MISSENSE CODING SEC16B C protein_coding NM_033127.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 177929987 T C 0 222 0 0.8941 0.8099 0.7882 0.8075 0.7485 0.7771 0.869738 0.805216 0.772727 1 8491 92791 8915 6865 4687 50202 685 12946 2 9802 120148 11500 8560 6582 66370 894 16440 0.853441 0 . 0 . 124 41,19,31,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H292R|1060|SEC16B|protein_coding|CODING|NM_033127.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82744 rs12040910 -0.693147 0.50415 124 1280 77 MODIFIER 1 CODING RASAL2 C protein_coding NM_170692.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 178063551 A C 0 123 0 1 0.9998 1 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_5_PRIME(MODIFIER||77||1280|RASAL2|protein_coding|CODING|NM_170692.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs316255 -0.590765 0.471814 6 L171R 233 cTg/cGg MODERATE 7 MISSENSE CODING TEX35 G protein_coding NM_032126.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 178489978 T G 0 222 0 0.2247 0.369 0.4827 0.4077 0.4543 0.3558 0.282796 0.368599 0.412558 1 2678 48647 4914 3425 2999 27665 392 6574 2 10382 121118 11528 8628 6596 66594 902 16488 0.0891194 0 . 0 . 114 17,37,26,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L171R|233|TEX35|protein_coding|CODING|NM_032126.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.674062 rs3813636 -0.693147 0.328799 114 491 105 MODIFIER 6 CODING ANGPTL1 A protein_coding NM_004673.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 178820159 C A 0 180 0 0.8094 0.6008 0.5677 0.5397 0.5775 0.4294 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.982906 0 . 0 . 29 9,7,8,4 UTR_3_PRIME(MODIFIER||105||491|ANGPTL1|protein_coding|CODING|NM_004673.3|6|A),INTRON(MODIFIER||||583|RALGPS2|protein_coding|CODING|NM_152663.4|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.130151 rs1544124 -0.680642 0.400793 29 583 3362 MODIFIER 20 CODING RALGPS2 G protein_coding NM_152663.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 178888856 A G 0 9.7 0 0.708 0.4008 0.2896 0.2183 0.4294 0.2229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3362||583|RALGPS2|protein_coding|CODING|NM_152663.4|20|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386489140,rs9515 -0.379885 0 1 409 36 MODIFIER 2 CODING FAM20B G protein_coding NM_014864.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179012947 C G 0 222 0 0.0575 0.1376 0.0764 0.3036 0.17 0.0849 0.0832955 0.132862 0.158256 1 854 17044 900 2571 1448 10277 116 878 2 10218 110832 11478 8506 6600 64000 792 9238 0.611845 0 . 0 . 139 51,18,37,17 UTR_5_PRIME(MODIFIER||36||409|FAM20B|protein_coding|CODING|NM_014864.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.277926 rs72707294 -0.693147 0.0317888 139 409 119 MODIFIER 8 CODING FAM20B G protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179041398 A G 0 222 0 0.9274 0.6911 0.5288 0.626 0.6372 0.6094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996451 0 . 0 . 51 8,21,7,12 UTR_3_PRIME(MODIFIER||119||409|FAM20B|protein_coding|CODING|NM_014864.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.922908 rs2025584 -0.69168 0.0908514 51 409 1702 MODIFIER 8 CODING FAM20B C protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179042981 G C 0 57 0 0.0567 0.1344 0.0706 0.3026 0.162 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,0,2,1 UTR_3_PRIME(MODIFIER||1702||409|FAM20B|protein_coding|CODING|NM_014864.3|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs56006430 -0.511536 0.917786 5 409 2260 MODIFIER 8 CODING FAM20B G protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179043539 T G 0 119 0 0.9274 0.6911 0.5288 0.626 0.6362 0.6104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.984335 0 . 0 . 45 2,23,0,19 UTR_3_PRIME(MODIFIER||2260||409|FAM20B|protein_coding|CODING|NM_014864.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.488772 rs3766626 -0.69168 0.692141 45 409 2274 MODIFIER 8 CODING FAM20B A protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179043553 G A 0 97 0 0.0726 0.1386 0.072 0.3016 0.162 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.915545 0 . 0 . 34 2,20,0,11 UTR_3_PRIME(MODIFIER||2274||409|FAM20B|protein_coding|CODING|NM_014864.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.768552 rs3766625 -0.676189 0.284215 34 409 4194 MODIFIER 8 CODING FAM20B A protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179045473 G A 0 81 0 0.0726 0.1388 0.072 0.3026 0.162 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.673638 0 . 0 . 26 17,1,8,0 UTR_3_PRIME(MODIFIER||4194||409|FAM20B|protein_coding|CODING|NM_014864.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998458 rs9249 -0.651104 0.116387 26 409 4221 MODIFIER 8 CODING FAM20B A protein_coding NM_014864.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179045500 C A 0 136 0 0.9259 0.6869 0.4971 0.6647 0.6024 0.6084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.981336 0 . 0 . 41 22,1,15,0 UTR_3_PRIME(MODIFIER||4221||409|FAM20B|protein_coding|CODING|NM_014864.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.844032 rs1220 -0.688148 0.937409 41 F13L 397 Ttc/Ctc MODERATE 1 MISSENSE CODING TOR3A C protein_coding NM_022371.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179051300 T C 0 18.5 0 0.9879 0.7672 0.6441 0.6677 0.7117 0.7157 0.94936 0.818501 0.755208 1 1697 20616 1396 1348 491 10269 132 5283 2 1794 27296 2088 1938 572 13680 170 7054 0.25 0 . 0 COSM424690 8 3,1,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F13L|397|TOR3A|protein_coding|CODING|NM_022371.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.5 rs2296377 -0.453602 0.18 8 L211 397 Ctg/Ttg LOW 3 SILENT CODING TOR3A T protein_coding NM_022371.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179055020 C T 0 222 0 0.1112 0.1324 0.0663 0.255 0.1402 0.0736 0.105765 0.117407 0.123372 1 1128 15314 816 2125 1121 8578 114 1432 2 10304 120500 11554 8606 6590 66160 896 16390 0.819088 0 . 0 . 44 3,16,2,21 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L211|397|TOR3A|protein_coding|CODING|NM_022371.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.407824 rs2296376 -0.692717 0.610236 44 397 522 MODIFIER 6 CODING TOR3A G protein_coding NM_022371.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179064875 A G 0 171 0 0.9652 0.762 0.6412 0.6776 0.7087 0.7147 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,1,8 UTR_3_PRIME(MODIFIER||522||397|TOR3A|protein_coding|CODING|NM_022371.3|6|G),DOWNSTREAM(MODIFIER||3587||1182|ABL2|protein_coding|CODING|NM_007314.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046385 -0.662043 0.795511 9 397 772 MODIFIER 6 CODING TOR3A T protein_coding NM_022371.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179065125 C T 0 9.7 0 0.5121 0.3636 0.3228 0.2887 0.2833 0.3517 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||772||397|TOR3A|protein_coding|CODING|NM_022371.3|6|T),DOWNSTREAM(MODIFIER||3337||1182|ABL2|protein_coding|CODING|NM_007314.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1128952 -0.379885 0 1 1182 8002 MODIFIER 12 CODING ABL2 G protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179068851 A G 0 9.7 0 0.4758 0.509 0.4193 0.5347 0.506 0.5941 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||8002||1182|ABL2|protein_coding|CODING|NM_007314.3|12|G),DOWNSTREAM(MODIFIER||3722||397|TOR3A|protein_coding|CODING|NM_022371.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9662858 -0.379885 0 1 1182 4988 MODIFIER 12 CODING ABL2 A protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179071865 G A 0 9.7 0 0.6982 0.6242 0.5259 0.5446 0.6183 0.682 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4988||1182|ABL2|protein_coding|CODING|NM_007314.3|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4651012 -0.379885 0 1 1182 4935 MODIFIER 12 CODING ABL2 T protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179071918 G T 0 9.7 0 0.9864 0.7686 0.6484 0.6766 0.7167 0.7076 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4935||1182|ABL2|protein_coding|CODING|NM_007314.3|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1325194 -0.379885 0 1 1182 4125 MODIFIER 12 CODING ABL2 C protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179072728 T C 0 147 0 0.4773 0.508 0.4164 0.5347 0.504 0.591 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,6,1 UTR_3_PRIME(MODIFIER||4125||1182|ABL2|protein_coding|CODING|NM_007314.3|12|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3829794 -0.636426 0.750734 7 1182 3887 MODIFIER 12 CODING ABL2 T protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179072966 C T 0 228 0 0.6679 0.6156 0.5231 0.5437 0.6183 0.682 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 106 0,0,62,35 UTR_3_PRIME(MODIFIER||3887||1182|ABL2|protein_coding|CODING|NM_007314.3|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4651013 -0.693147 0.0326702 106 1182 3814 MODIFIER 12 CODING ABL2 G protein_coding NM_007314.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179073039 C G 0 228 0 0.9864 0.7682 0.6484 0.6756 0.7167 0.7065 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 111 0,0,42,57 UTR_3_PRIME(MODIFIER||3814||1182|ABL2|protein_coding|CODING|NM_007314.3|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4651014 -0.693147 0.114515 111 P199 550 ccC/ccT LOW 7 SILENT CODING SOAT1 T protein_coding NM_003101.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179310262 C T 0 222 0 0.1354 0.2823 0.2406 0.4782 0.2406 0.3517 0.13527 0.185914 0.21186 1 1390 29321 3107 4121 1444 13794 234 5231 2 10406 121400 11578 8644 6614 66740 908 16510 0.962215 0 . 0 COSM146697 151 35,38,32,37 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P199|550|SOAT1|protein_coding|CODING|NM_003101.5|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.701027 rs11576517 -0.693147 0.227552 151 550 962 MODIFIER 16 CODING SOAT1 A protein_coding NM_003101.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179323738 C A 0 39.3 0 0.7307 0.7326 0.7205 0.869 0.673 0.6646 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||962||550|SOAT1|protein_coding|CODING|NM_003101.5|16|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1044925 -0.453602 0.52 2 550 1143 MODIFIER 16 CODING SOAT1 G protein_coding NM_003101.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179323919 A G 0 9.7 0 0.6573 0.5503 0.4885 0.4851 0.5984 0.4673 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1143||550|SOAT1|protein_coding|CODING|NM_003101.5|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4652366 -0.379885 0 1 550 3621 MODIFIER 16 CODING SOAT1 G protein_coding NM_003101.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179326397 C G 0 25.9 0 0.7307 0.7326 0.7205 0.869 0.673 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||3621||550|SOAT1|protein_coding|CODING|NM_003101.5|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs7536854 -0.453602 0.02 3 1012 728 MODIFIER 1 CODING AXDND1 C protein_coding NM_144696.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179334917 G C 0 9.7 0 0.3903 0.4792 0.4942 0.5377 0.5437 0.4622 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||728||1012|AXDND1|protein_coding|CODING|NM_144696.5|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs16853998 -0.379885 0 1 V145 1012 gtT/gtC LOW 5 SILENT CODING AXDND1 C protein_coding NM_144696.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179347832 T C 0 222 0 0.2799 0.5118 0.5274 0.6974 0.5159 0.6186 0.320699 0.415501 0.46407 1 3160 58804 6297 6262 2588 30357 424 9716 2 10406 121362 11572 8646 6610 66710 908 16510 0.805242 0 . 0 . 141 52,24,30,8 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V145|1012|AXDND1|protein_coding|CODING|NM_144696.5|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999711 rs10798674 -0.693143 0.035245 141 I522L 1012 Atc/Ctc MODERATE 16 MISSENSE CODING AXDND1 C protein_coding NM_144696.5 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179414105 A C 0 222 0 0.2882 0.2129 0.2435 0.0526 0.2783 0.1871 0.280327 0.297846 0.306816 1 3009 34329 3029 396 2511 21510 238 3636 2 10132 120474 11502 8608 6596 66452 902 16282 0.69164 0 . 0 COSM146698 58 19,10,18,7 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Atc/Ctc|I522L|1012|AXDND1|protein_coding|CODING|NM_144696.5|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.123052 rs11577579 -0.692914 0.0079921 58 Q993E 1012 Caa/Gaa MODERATE 25 MISSENSE CODING AXDND1 G protein_coding NM_144696.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179504043 C G 0 222 0 0.2496 0.3814 0.4035 0.4256 0.4115 0.4673 0.265159 0.330534 0.363244 1 2518 42512 4641 3449 1906 23219 324 6455 2 9718 117594 11098 8284 6578 64994 882 16040 0.949192 0 . 0 . 101 31,20,17,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q993E|1012|AXDND1|protein_coding|CODING|NM_144696.5|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.879466 rs6658180 -0.693132 0.119084 101 383 428 MODIFIER 8 CODING NPHS2 C protein_coding NM_014625.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179519880 T C 0 23.4 0 0.826 0.9018 0.938 0.9692 0.9254 0.8845 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||428||383|NPHS2|protein_coding|CODING|NM_014625.3|8|C),INTRON(MODIFIER||||1012|AXDND1|protein_coding|CODING|NM_144696.5|25|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1060775 -0.453602 0.82 2 383 258 MODIFIER 8 CODING NPHS2 C protein_coding NM_014625.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179520050 T C 0 23 0 0.1059 0.2831 0.2867 0.371 0.3121 0.3998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||258||383|NPHS2|protein_coding|CODING|NM_014625.3|8|C),INTRON(MODIFIER||||1012|AXDND1|protein_coding|CODING|NM_144696.5|25|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2274622 -0.453602 0.94 3 383 157 MODIFIER 8 CODING NPHS2 T protein_coding NM_014625.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179520151 C T 0 201 0 0.8389 0.9052 0.938 0.9692 0.9254 0.8845 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 24 0,0,23,1 UTR_3_PRIME(MODIFIER||157||383|NPHS2|protein_coding|CODING|NM_014625.3|8|T),INTRON(MODIFIER||||1012|AXDND1|protein_coding|CODING|NM_144696.5|25|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1410590 -0.692831 0.0288563 24 383 54 MODIFIER 8 CODING NPHS2 G protein_coding NM_014625.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179520254 C G 0 228 0 0.5946 0.5879 0.6354 0.4911 0.6153 0.6166 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 69 0,0,49,11 UTR_3_PRIME(MODIFIER||54||383|NPHS2|protein_coding|CODING|NM_014625.3|8|G),INTRON(MODIFIER||||1012|AXDND1|protein_coding|CODING|NM_144696.5|25|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1410591 -0.693147 0.888409 69 A318 383 gcC/gcT LOW 8 SILENT CODING NPHS2 A protein_coding NM_014625.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179520506 G A 0 228 0 0.5946 0.5877 0.634 0.4911 0.6153 0.6166 0.599637 0.617177 0.626163 2 6213 75096 7693 4141 4124 42396 555 9974 2 10404 121278 11554 8616 6608 66680 908 16508 0 . 0 . COSM146700 71 0,0,19,49 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A318|383|NPHS2|protein_coding|CODING|NM_014625.3|8|A),INTRON(MODIFIER||||1012|AXDND1|protein_coding|CODING|NM_144696.5|25|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1410592 -0.693147 0.324147 71 G34 383 ggA/ggG LOW 1 SILENT CODING NPHS2 C protein_coding NM_014625.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179544898 T C 0 145 0 0.823 0.9309 0.9683 0.9812 0.992 0.9356 0.903069 0.966324 0.993297 2 258 10158 241 261 21 3225 113 6039 2 310 10564 246 266 22 3250 116 6354 0 . 0 . 0 10 0,0,1,9 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G34|383|NPHS2|protein_coding|CODING|NM_014625.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1079292 -0.670168 0.741871 10 R126S 1035 agG/agC MODERATE 3 MISSENSE CODING TDRD5 C protein_coding NM_001199085.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179562740 G C 0 222 0 0.0877 0.3077 0.4092 0.371 0.3897 0.3834 0.149342 0.290789 0.363256 1 1329 42044 5395 3280 2316 23639 324 5761 2 10406 121382 11572 8640 6612 66732 908 16512 0.84944 0 . 0 . 202 58,32,53,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agC|R126S|1035|TDRD5|protein_coding|CODING|NM_001199085.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940004 rs61310274 -0.693147 0.0367617 202 D454 1035 gaC/gaT LOW 9 SILENT CODING TDRD5 T protein_coding NM_001199085.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179604864 C T 0 228 0 0.7163 0.7969 0.8631 0.9048 0.7773 0.7679 0.731729 0.746425 0.753954 2 7464 92686 10200 7721 4639 49462 685 12515 2 10364 121120 11552 8644 6608 66556 904 16492 0 . 0 . 0 18 0,0,12,4 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D454|1035|TDRD5|protein_coding|CODING|NM_001199085.1|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4628468 -0.689466 0.440585 18 P134A 167 Ccc/Gcc MODERATE 5 MISSENSE CODING FAM163A G protein_coding NM_173509.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179783220 C G 0 222 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 19 0 15 0 0 0 4 2 10366 120880 11568 8640 6614 66442 904 16346 0.985737 0 . 0 . 102 24,22,17,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P134A|167|FAM163A|protein_coding|CODING|NM_173509.2|5|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.852465 rs202166334 -0.693146 0.449665 102 470 3211 MODIFIER 7 CODING TOR1AIP2 T protein_coding NM_001199260.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179811995 C T 0 9.7 0 0 0.0009984 0 0.005 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3211||470|TOR1AIP2|protein_coding|CODING|NM_001199260.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs181723310 -0.379885 0 1 470 508 MODIFIER 7 CODING TOR1AIP2 G protein_coding NM_001199260.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179814698 A G 0 9.7 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||508||470|TOR1AIP2|protein_coding|CODING|NM_001199260.1|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs186380424 -0.379885 0 1 M146T 584 aTg/aCg MODERATE 1 MISSENSE CODING TOR1AIP1 C protein_coding NM_001267578.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179852074 T C 0 228 0 0.3812 0.6088 0.6758 0.7778 0.6133 0.6902 0.444268 0.569205 0.633217 2 4074 76222 8950 6511 3664 41431 523 11069 2 9174 117218 11406 8522 6452 64368 880 16416 0 . 0 . 0 109 0,0,4,103 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M146T|584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1281378,rs386526120 -0.693147 0.489143 109 584 HIGH 2 CODING TOR1AIP1 A protein_coding NM_001267578.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179858444 G A 0 228 0 0.4644 0.6354 0.6916 0.7778 0.6064 0.7096 0.503631 0.583064 0.623779 2 5148 78446 9042 6577 3647 42125 552 11355 2 10398 121322 11576 8650 6612 66686 906 16494 0 . 0 . 0 101 0,0,76,13 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|2|A) 1 0 . 0 . 1 0 1 1 (TOR1AIP1|TOR1AIP1|1|1.00) 60 0 0 1 0 . rs2245425 -0.693147 0.199743 101 P277R 584 cCt/cGt MODERATE 7 MISSENSE CODING TOR1AIP1 G protein_coding NM_001267578.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179876988 C G 0 228 0 0.3041 0.5841 0.6715 0.7778 0.6093 0.6748 0.366092 0.540212 0.629419 2 3662 76393 8945 6551 3658 42067 533 10977 2 10356 120710 11512 8624 6584 66288 904 16442 0 . 0 . 0 41 0,0,9,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cGt|P277R|584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs609521 -0.693132 0.00823991 41 A502 584 gcG/gcA LOW 10 SILENT CODING TOR1AIP1 A protein_coding NM_001267578.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179887125 G A 0 228 0 0.8449 0.9185 0.951 0.9147 0.9523 0.9642 0.874716 0.927495 0.954535 2 9108 115153 11170 7794 6476 63930 856 15819 2 10404 121406 11576 8652 6614 66740 908 16512 1 0 . 0 . 80 1,0,24,47 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A502|584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs627897 -0.693147 0.162009 80 584 282 MODIFIER 10 CODING TOR1AIP1 G protein_coding NM_001267578.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179887656 A G 0 222 0 0 0.0009984 0 0.005 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.795173 0 . 0 . 66 14,18,11,16 UTR_3_PRIME(MODIFIER||282||584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.269076 rs188262171 -0.693021 0.309558 66 584 307 MODIFIER 10 CODING TOR1AIP1 C protein_coding NM_001267578.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179887681 G C 0 228 0 0.2375 0.5639 0.6614 0.7778 0.6034 0.6748 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 62 0,1,20,34 UTR_3_PRIME(MODIFIER||307||584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs530854 -0.693147 0.00470002 62 584 414 MODIFIER 10 CODING TOR1AIP1 T protein_coding NM_001267578.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179887788 C T 0 205 0 0.031 0.4589 0.6182 0.7163 0.5596 0.5552 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,1,18 UTR_3_PRIME(MODIFIER||414||584|TOR1AIP1|protein_coding|CODING|NM_001267578.1|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386598323,rs531814 -0.69168 0.196641 19 E945Q 3117 Gaa/Caa MODERATE 12 MISSENSE CODING CEP350 C protein_coding NM_014810.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 179989742 G C 0 222 0 0.2436 0.5643 0.7349 0.7044 0.6461 0.6483 0.332955 0.538136 0.643256 1 3333 77705 9441 6106 4357 43556 544 10368 2 10376 121290 11570 8642 6612 66692 904 16494 0.80977 0 . 0 . 43 10,5,11,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E945Q|3117|CEP350|protein_coding|CODING|NM_014810.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99988 rs2477120 -0.692562 0.323956 43 T1446A 3117 Aca/Gca MODERATE 19 MISSENSE CODING CEP350 G protein_coding NM_014810.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180010911 A G 0 222 0 0.0923 0.1102 0.0389 0.2153 0.0686 0.1196 0.0921471 0.0771183 0.0694186 1 946 10047 534 1826 359 4230 87 2065 2 9552 108760 9716 7996 6040 59792 818 14846 0.839273 0 . 0 . 70 11,34,6,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T1446A|3117|CEP350|protein_coding|CODING|NM_014810.4|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996594 rs16855164 -0.692352 0.265675 70 T145 747 acA/acG LOW 4 SILENT CODING QSOX1 G protein_coding NM_002826.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180145088 A G 0 222 0 0.8094 0.8856 0.9669 0.8472 0.9563 0.8978 0.837955 0.91727 0.957878 1 6308 82054 7010 5387 2582 48220 546 12001 2 7556 88440 7322 6624 2688 50562 588 13100 0.611808 0 . 0 . 91 26,9,30,18 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T145|747|QSOX1|protein_coding|CODING|NM_002826.4|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999479 rs2298206,rs386564179 -0.693147 0.0910001 91 N591H 747 Aac/Cac MODERATE 12 MISSENSE CODING QSOX1 C protein_coding NM_002826.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180165699 A C 0 222 0 0.003 0.0657 0.0375 0.252 0.0189 0.0266 0.00226963 0.00607412 0.00802326 1 32 3979 369 2161 284 663 34 436 2 10384 121272 11578 8624 6614 66656 904 16512 0.895004 0 . 0 . 142 38,33,30,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N591H|747|QSOX1|protein_coding|CODING|NM_002826.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959121 rs3738115 -0.693147 0.0924123 142 747 918 MODIFIER 12 CODING QSOX1 T protein_coding NM_002826.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180167090 C T 0 228 0 0.1127 0.1795 0.0735 0.4534 0.0646 0.181 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 66 0,0,34,30 UTR_3_PRIME(MODIFIER||918||747|QSOX1|protein_coding|CODING|NM_002826.4|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386428925,rs7597 -0.693147 0.0460257 66 N328S 390 aAt/aGt MODERATE 6 MISSENSE CODING LHX4 G protein_coding NM_033343.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180243524 A G 0 228 0 0.1165 0.4263 0.3256 0.5942 0.5487 0.6176 0.204948 0.410657 0.516047 2 1951 58860 2764 5036 3744 35048 443 9874 2 10406 121356 11566 8628 6614 66726 906 16510 0.536458 0 . 0 . 106 1,1,55,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N328S|390|LHX4|protein_coding|CODING|NM_033343.3|6|G),INTRAGENIC(MODIFIER|||||LHX4-AS1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.265625 rs7536561 -0.693147 0.195001 106 696 865 MODIFIER 15 CODING XPR1 G protein_coding NM_004736.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180854067 A G 0 205 0 0.9766 0.9936 1 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,1,13 UTR_3_PRIME(MODIFIER||865||696|XPR1|protein_coding|CODING|NM_004736.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3856061 -0.686358 0.0199928 14 L64P 1190 cTg/cCg MODERATE 2 MISSENSE CODING KIAA1614 C protein_coding NM_020950.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180885430 T C 0 228 0 0.9773 0.994 1 1 1 1 0.988177 0.996008 0.999635 2 9587 120124 11536 8620 6589 66435 892 16465 2 9726 120322 11546 8620 6590 66468 894 16478 0 . 0 . 0 57 0,0,30,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L64P|1190|KIAA1614|protein_coding|CODING|NM_020950.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10732273 -0.693147 0.60728 57 T355 1190 acC/acT LOW 4 SILENT CODING KIAA1614 T protein_coding NM_020950.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180897569 C T 0 228 0 0.2731 0.39 0.4063 0.5516 0.4135 0.3456 0.280079 0.367224 0.409373 2 2864 49542 4615 4836 3016 27959 392 5860 2 9612 118786 11560 8556 6614 65790 882 15772 1 0 . 0 . 65 1,0,42,17 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T355|1190|KIAA1614|protein_coding|CODING|NM_020950.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3747958 -0.693147 0.532705 65 P360 1190 ccG/ccA LOW 4 SILENT CODING KIAA1614 A protein_coding NM_020950.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180897584 G A 0 222 0 0 0.00039936 0 0.001 0 0.001 0.000246427 8.0438e-05 0 1 1 23 1 12 0 3 0 6 2 9568 119032 11558 8564 6614 65596 882 16250 0.979555 0 . 0 . 65 27,5,16,10 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P360|1190|KIAA1614|protein_coding|CODING|NM_020950.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.956834 rs374620585 -0.692976 0.040174 65 N883 1190 aaC/aaT LOW 5 SILENT CODING KIAA1614 T protein_coding NM_020950.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180905694 C T 0 81 0 0.1316 0.2887 0.2738 0.495 0.3012 0.2863 0.166168 0.25864 0.303296 1 1594 36802 3057 4041 2473 20915 283 4439 2 9316 118156 11426 8514 6408 65384 864 16244 0.783012 0 . 0 . 35 4,19,0,11 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N883|1190|KIAA1614|protein_coding|CODING|NM_020950.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.53242 rs3795503 -0.676189 0.617745 35 N1078D 1190 Aac/Gac MODERATE 8 MISSENSE CODING KIAA1614 G protein_coding NM_020950.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180913597 A G 0 228 0 0.9871 0.9964 0.9986 1 1 1 0.988608 0.996248 0.99988 2 9639 120507 11568 8626 6614 66650 898 16512 2 9780 120654 11574 8626 6614 66650 898 16512 0 . 0 . 0 96 0,0,58,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N1078D|1190|KIAA1614|protein_coding|CODING|NM_020950.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2331995 -0.693147 0.554248 96 255 2177 MODIFIER 8 CODING STX6 T protein_coding NM_005819.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180943529 C T 0 228 0 0.4614 0.5298 0.6412 0.63 0.5736 0.3947 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,31,0 UTR_3_PRIME(MODIFIER||2177||255|STX6|protein_coding|CODING|NM_005819.5|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1044595 -0.69311 0.410128 35 N217 255 aaT/aaC LOW 7 SILENT CODING STX6 G protein_coding NM_005819.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 180953853 A G 0 228 0 0.4486 0.5244 0.6282 0.631 0.5686 0.3978 0.483432 0.552591 0.588023 2 4953 69624 7796 5335 4421 39392 514 7213 2 10396 121200 11558 8628 6602 66652 908 16456 0 . 0 . 0 90 0,0,47,32 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N217|255|STX6|protein_coding|CODING|NM_005819.5|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3747957 -0.693147 0.0432811 90 H39R 341 cAt/cGt MODERATE 3 MISSENSE CODING MR1 G protein_coding NM_001531.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181018236 A G 0 222 0 0.1263 0.1929 0.2161 0.3502 0.1372 0.1616 0.134589 0.148547 0.155698 1 1405 20977 2907 2994 858 9795 143 2875 2 10396 121192 11548 8624 6594 66618 908 16504 0.782086 3 likely-benign 0 COSM146702 100 32,21,20,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H39R|341|MR1|protein_coding|CODING|NM_001531.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.869464 0.655533 0 0.893055 rs2236410 -0.693141 0.728663 100 341 3 MODIFIER 7 CODING MR1 A protein_coding NM_001531.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181024404 G A 0 222 0 0.534 0.5224 0.5058 0.7609 0.2942 0.5072 0.526101 0.371444 0.292209 1 5500 48182 6696 6437 1799 19393 343 8014 2 10406 121394 11578 8644 6614 66734 908 16510 0.340156 0 . 0 . 191 28,55,43,43 UTR_3_PRIME(MODIFIER||3||341|MR1|protein_coding|CODING|NM_001531.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.655055 rs3747956 -0.693147 0.0297653 191 341 2157 MODIFIER 7 CODING MR1 A protein_coding NM_001531.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181026558 G A 0 9.7 0 0.6263 0.7109 0.7147 0.8919 0.5646 0.7863 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2157||341|MR1|protein_coding|CODING|NM_001531.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4652552 -0.379885 0 1 341 2926 MODIFIER 7 CODING MR1 A protein_coding NM_001531.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181027327 T A 0 23.4 0 0.7874 0.7644 0.7406 0.9137 0.5716 0.7945 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2926||341|MR1|protein_coding|CODING|NM_001531.2|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6688275 -0.453602 0.94 2 341 3440 MODIFIER 7 CODING MR1 G protein_coding NM_001531.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181027841 A G 0 36.3 0 0.8442 0.7891 0.7594 0.9137 0.5905 0.8119 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3440||341|MR1|protein_coding|CODING|NM_001531.2|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6686208 -0.453602 0.56 2 341 4332 MODIFIER 7 CODING MR1 C protein_coding NM_001531.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181028733 T C 0 39.3 0 0.6399 0.7186 0.7219 0.8919 0.5726 0.7945 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||4332||341|MR1|protein_coding|CODING|NM_001531.2|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10797667 -0.453602 0.78 2 327 165 MODIFIER 1 CODING IER5 G protein_coding NM_016545.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181057874 T G 0 142 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.984304 0 . 0 . 32 16,0,15,0 UTR_5_PRIME(MODIFIER||165||327|IER5|protein_coding|CODING|NM_016545.4|1|G) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 0 . 0.637628 rs6425663 -0.688148 0.240532 32 Q202R 327 cAa/cGa MODERATE 1 MISSENSE CODING IER5 G protein_coding NM_016545.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181058643 A G 0 9.7 0 0.8797 0.9661 0.9856 1 0.999 1 0 . 0 1 67 3453 30 40 163 608 46 2499 2 76 3474 30 40 164 610 46 2508 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q202R|327|IER5|protein_coding|CODING|NM_016545.4|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs1361365 -0.379885 0 1 A1955T 2313 Gcc/Acc MODERATE 44 MISSENSE CODING CACNA1E A protein_coding NM_001205293.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181759657 G A 0 222 0 0.1203 0.2764 0.3242 0.3879 0.4314 0.1789 0.1552 0.359744 0.454501 1 1498 46573 3700 3415 2829 31232 360 3539 2 9798 120678 11562 8596 6612 66710 898 16502 0.501837 0 . 0 . 178 44,45,30,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1955T|2313|CACNA1E|protein_coding|CODING|NM_001205293.1|44|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.463897 rs704326 -0.693147 0.018401 178 2313 216 MODIFIER 48 CODING CACNA1E C protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181768186 T C 0 228 0 0.0832 0.1388 0.1585 0.3075 0.0497 0.1176 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 206 0,0,102,82 UTR_3_PRIME(MODIFIER||216||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2280869,rs386563493 -0.693147 0.0104112 206 2313 1015 MODIFIER 48 CODING CACNA1E A protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181768985 G A 0 152 0 0.736 0.7386 0.6369 0.7401 0.7316 0.82 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,2 UTR_3_PRIME(MODIFIER||1015||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs638132 -0.616816 0.0989217 6 2313 1317 MODIFIER 48 CODING CACNA1E A protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181769287 G A 0 228 0 0.0643 0.118 0.0533 0.3026 0.0497 0.1166 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 69 0,1,40,23 UTR_3_PRIME(MODIFIER||1317||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs41315713 -0.693147 0.498424 69 2313 2018 MODIFIER 48 CODING CACNA1E T protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181769988 C T 0 222 0 0 0.0071885 0 0.0337 0.001 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.830297 0 . 0 . 67 22,15,15,10 UTR_3_PRIME(MODIFIER||2018||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.972358 rs143995568 -0.692914 0.355454 67 2313 4589 MODIFIER 48 CODING CACNA1E C protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181772559 T C 0 9.7 0 0.0983 0.1068 0.0548 0.2698 0.0348 0.0613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4589||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9943168 -0.379885 0 1 2313 6301 MODIFIER 48 CODING CACNA1E G protein_coding NM_001205293.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 181774271 C G 0 32.6 0 0.3548 0.4637 0.4265 0.3512 0.665 0.546 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||6301||2313|CACNA1E|protein_coding|CODING|NM_001205293.1|48|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs685859 -0.379885 0 2 568 586 MODIFIER 2 CODING ZNF648 G protein_coding NM_001009992.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182024853 C G 0 32.6 0 0.0386 0.1042 0.0836 0.1935 0.0984 0.1217 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||586||568|ZNF648|protein_coding|CODING|NM_001009992.1|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs16858474 -0.379885 0 2 N111K 568 aaC/aaG MODERATE 2 MISSENSE CODING ZNF648 C protein_coding NM_001009992.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182026813 G C 0 222 0 0.09 0.1769 0.121 0.2837 0.1471 0.2546 0.0973672 0.123558 0.136977 1 996 20426 2019 2298 1289 9272 164 4388 2 10404 121354 11572 8628 6604 66730 908 16508 0.986202 0 . 0 . 62 14,16,10,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaG|N111K|568|ZNF648|protein_coding|CODING|NM_001009992.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.381045 rs12568050 -0.692562 0.274814 62 E42K 568 Gag/Aag MODERATE 2 MISSENSE CODING ZNF648 T protein_coding NM_001009992.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182027022 C T 0 222 0 0.0862 0.1757 0.121 0.2827 0.1471 0.2546 0.0935089 0.122097 0.136744 1 949 20378 2013 2294 1293 9276 164 4389 2 10378 121244 11576 8636 6614 66624 904 16512 0.597645 0 . 0 . 90 30,21,15,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E42K|568|ZNF648|protein_coding|CODING|NM_001009992.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.367802 rs12564283 -0.693054 0.442993 90 373 4913 MODIFIER 7 CODING GLUL A protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182348627 G A 0 76 0 0.3525 0.3093 0.3429 0.3839 0.2137 0.2485 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||4913||373|GLUL|protein_coding|CODING|NM_001033044.3|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6424852 -0.511536 0.0532881 3 373 4811 MODIFIER 7 CODING GLUL G protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182348729 A G 0 73 0 0.7496 0.6757 0.6167 0.8323 0.5408 0.5951 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||4811||373|GLUL|protein_coding|CODING|NM_001033044.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7541101 -0.511536 0.382879 3 373 3591 MODIFIER 7 CODING GLUL G protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182349949 A G 0 9.7 0 0.7466 0.6749 0.6167 0.8323 0.5408 0.5951 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3591||373|GLUL|protein_coding|CODING|NM_001033044.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6691339 -0.379885 0 1 373 3433 MODIFIER 7 CODING GLUL A protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182350107 G A 0 42.3 0 0.7405 0.6733 0.6167 0.8323 0.5408 0.5951 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3433||373|GLUL|protein_coding|CODING|NM_001033044.3|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10429835 -0.453602 0.88 2 373 2644 MODIFIER 7 CODING GLUL G protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182350896 C G 0 9.7 0 0.7496 0.6757 0.6167 0.8323 0.5408 0.5951 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2644||373|GLUL|protein_coding|CODING|NM_001033044.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2296523 -0.379885 0 1 373 2631 MODIFIER 7 CODING GLUL T protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182350909 C T 0 9.7 0 0.0129 0.1931 0.2882 0.373 0.1938 0.183 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2631||373|GLUL|protein_coding|CODING|NM_001033044.3|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2296522 -0.379885 0 1 373 2307 MODIFIER 7 CODING GLUL A protein_coding NM_001033044.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182351233 G A 0 6.3 0 0.8873 0.7135 0.6268 0.8323 0.5408 0.5951 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2307||373|GLUL|protein_coding|CODING|NM_001033044.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2296521 -0.379885 0 1 S65 373 tcT/tcC LOW 3 SILENT CODING GLUL G protein_coding NM_001033044.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182356399 A G 0 228 0 0.7496 0.6757 0.6167 0.8323 0.5408 0.5951 0.735134 0.590497 0.516395 2 7674 69765 6696 7296 3201 34423 525 9950 2 10398 121370 11572 8650 6612 66718 908 16512 0 . 0 . 0 130 0,0,32,91 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S65|373|GLUL|protein_coding|CODING|NM_001033044.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058111,rs386496061 -0.693147 0.00393816 130 373 2971 MODIFIER 1 CODING GLUL G protein_coding NM_001033044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182360843 C G 0 101 0 0.9697 0.8574 0.8184 0.8373 0.8161 0.7965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_5_PRIME(MODIFIER||2971||373|GLUL|protein_coding|CODING|NM_001033044.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs912901 -0.590765 0.431509 5 373 3058 MODIFIER 1 CODING GLUL G protein_coding NM_001033044.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182360930 A G 0 9.7 0 0.9675 0.8566 0.817 0.8383 0.8151 0.7965 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||3058||373|GLUL|protein_coding|CODING|NM_001033044.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs912902 -0.379885 0 1 P181 273 ccC/ccT LOW 1 SILENT CODING TEDDM1 A protein_coding NM_172000.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182369078 G A 0 228 0 0.9569 0.8536 0.8156 0.8373 0.8171 0.7955 0.926464 0.838152 0.792907 2 9695 98920 9377 7360 5154 53423 739 13172 2 10398 121360 11566 8652 6610 66718 908 16508 0 . 0 . 0 49 0,0,22,25 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P181|273|TEDDM1|protein_coding|CODING|NM_172000.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6698722 -0.693147 0.59621 49 Y130H 273 Tat/Cat MODERATE 1 MISSENSE CODING TEDDM1 G protein_coding NM_172000.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182369233 A G 0 228 0 0.761 0.6781 0.6124 0.8294 0.5417 0.5971 0.744666 0.594034 0.51686 2 7778 69795 6696 7277 3193 34366 524 9961 2 10398 121360 11566 8648 6612 66720 908 16508 0 . 0 . 0 82 0,0,37,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y130H|273|TEDDM1|protein_coding|CODING|NM_172000.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6674281 -0.693147 0.244884 82 273 118 MODIFIER 1 CODING TEDDM1 A protein_coding NM_172000.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182369738 G A 0 228 0 0.9576 0.8526 0.8156 0.8373 0.8171 0.7894 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,9,11 UTR_5_PRIME(MODIFIER||118||273|TEDDM1|protein_coding|CODING|NM_172000.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7551829 -0.692067 0.847723 22 L406 1076 Ttg/Ctg LOW 6 SILENT CODING RGSL1 C protein_coding NM_001137669.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182443462 T C 0 228 0 0.5484 0.4738 0.5274 0.4593 0.3489 0.4785 0.504335 0.389838 0.340038 2 1527 9329 209 321 428 3152 101 3591 2 2844 22772 416 650 1626 9074 254 7908 0 . 0 . 0 64 0,0,24,38 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L406|1076|RGSL1|protein_coding|CODING|NM_001137669.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs649437 -0.693147 0.0277543 64 741 861 MODIFIER 7 CODING RNASEL G protein_coding NM_021133.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182543666 T G 0 109 0 0.1694 0.2644 0.3213 0.2044 0.3032 0.3742 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,0 UTR_3_PRIME(MODIFIER||861||741|RNASEL|protein_coding|CODING|NM_021133.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1048254 -0.556411 0.962096 5 D541E 741 gaT/gaG MODERATE 4 MISSENSE CODING RNASEL C protein_coding NM_021133.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182551337 A C 0 228 0 0.2632 0.4798 0.4424 0.7093 0.5686 0.4714 0.329324 0.472167 0.545349 2 3316 65302 5627 6242 4036 37318 520 8243 2 10398 121382 11576 8650 6612 66728 908 16510 1 0 . 0 . 53 0,1,29,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D541E|741|RNASEL|protein_coding|CODING|NM_021133.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386602167,rs627928 -0.693147 0.268388 53 202 1223 MODIFIER 5 CODING RGS16 C protein_coding NM_002928.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182568204 G C 0 83 0 0.8903 0.9617 0.9755 1 0.9771 0.9928 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||1223||202|RGS16|protein_coding|CODING|NM_002928.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs694383 -0.556411 0.60415 4 202 698 MODIFIER 5 CODING RGS16 G protein_coding NM_002928.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182568729 C G 0 228 0 0.354 0.5877 0.7176 0.7143 0.6024 0.6656 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 47 1,0,35,6 UTR_3_PRIME(MODIFIER||698||202|RGS16|protein_coding|CODING|NM_002928.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs680431 -0.693145 0.417513 47 H137R 202 cAc/cGc MODERATE 5 MISSENSE CODING RGS16 C protein_coding NM_002928.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182569626 T C 0 228 0 0.9766 0.986 0.9856 1 0.9781 0.9928 0.980027 0.975012 0.972442 2 10178 119277 11480 8654 6523 65132 893 16417 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 99 0,0,24,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H137R|202|RGS16|protein_coding|CODING|NM_002928.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1144566 -0.693147 0.0606484 99 T953 1270 acT/acC LOW 24 SILENT CODING DHX9 C protein_coding NM_001357.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182850727 T C 0 228 0 0.947 0.9846 0.9899 1 1 1 0.9592 0.987388 1 2 9383 120310 11557 8626 6614 66727 899 16504 2 9802 120756 11576 8626 6614 66732 900 16506 0 . 0 . 0 147 0,0,77,61 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T953|1270|DHX9|protein_coding|CODING|NM_001357.4|24|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6677840 -0.693147 0.104479 147 A58 1609 gcC/gcT LOW 1 SILENT CODING LAMC1 T protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 182993025 C T 0 211 0 0.3192 0.5196 0.611 0.628 0.5338 0.5992 0.356559 0.480547 0.54407 1 3454 65526 7737 5342 3751 34147 495 10600 2 9760 117434 11340 8460 6344 64322 846 16362 0.940894 0 . 0 . 118 61,1,49,2 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A58|1609|LAMC1|protein_coding|CODING|NM_002293.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.590149 rs10911194 -0.693147 0.439877 118 C182 1609 tgT/tgC LOW 2 SILENT CODING LAMC1 C protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183072590 T C 0 222 0 0.3321 0.5319 0.6268 0.628 0.5646 0.6022 0.376078 0.505151 0.571279 1 3789 69614 7989 5433 3945 37085 544 10829 2 10404 121350 11572 8630 6612 66718 904 16510 0.946229 0 . 0 . 194 45,38,44,45 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C182|1609|LAMC1|protein_coding|CODING|NM_002293.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975955 rs2296288 -0.693147 0.0963685 194 I458V 1609 Att/Gtt MODERATE 7 MISSENSE CODING LAMC1 G protein_coding NM_002293.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183085755 A G 0 222 0 0.3321 0.5317 0.6254 0.628 0.5636 0.6033 0.374489 0.50346 0.569535 1 3786 69468 7961 5430 3952 36927 542 10870 2 10402 121342 11570 8626 6612 66714 908 16510 0.829569 0 . 0 . 105 30,11,29,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I458V|1609|LAMC1|protein_coding|CODING|NM_002293.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.507568 rs20563 -0.693147 0.0304908 105 A592 1609 gcA/gcC LOW 10 SILENT CODING LAMC1 C protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183086757 A C 0 222 0 0.3321 0.5317 0.6254 0.628 0.5636 0.6033 0.374716 0.503537 0.569535 1 3787 69473 7962 5427 3952 36933 542 10870 2 10406 121366 11568 8628 6614 66730 908 16512 0.985339 0 . 0 . 128 32,24,36,25 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A592|1609|LAMC1|protein_coding|CODING|NM_002293.3|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.127472 rs2296292 -0.693147 0.361725 128 N837 1609 aaT/aaC LOW 14 SILENT CODING LAMC1 C protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183093875 T C 0 222 0 0.3321 0.5317 0.6254 0.628 0.5636 0.6033 0.374489 0.50346 0.569535 1 3784 69411 7958 5410 3948 36899 542 10870 2 10396 121268 11566 8618 6602 66666 908 16512 0.877169 0 . 0 . 100 25,27,18,19 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N837|1609|LAMC1|protein_coding|CODING|NM_002293.3|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982611 rs20557 -0.693141 0.105085 100 L888P 1609 cTg/cCg MODERATE 15 MISSENSE CODING LAMC1 C protein_coding NM_002293.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183094547 T C 0 222 0 0.3321 0.5317 0.6254 0.628 0.5636 0.6033 0.374489 0.50346 0.569535 1 3786 69465 7959 5427 3952 36929 542 10870 2 10406 121376 11572 8632 6612 66734 908 16512 0.846322 0 . 0 . 95 38,6,33,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L888P|1609|LAMC1|protein_coding|CODING|NM_002293.3|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.307391 rs20558 -0.693145 0.144185 95 L1103 1609 ctA/ctG LOW 19 SILENT CODING LAMC1 G protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183099507 A G 0 222 0 0 0.0011981 0 0.006 0 0 0.00068089 0.00030755 0.000116279 1 3 98 0 93 0 1 1 0 2 10392 121372 11572 8644 6614 66734 908 16508 0.749519 0 . 0 . 81 21,10,34,6 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1103|1609|LAMC1|protein_coding|CODING|NM_002293.3|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.781934 rs145396708 -0.693145 0.129695 81 R1376 1609 cgT/cgC LOW 25 SILENT CODING LAMC1 C protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183105534 T C 0 222 0 0.4539 0.5605 0.6354 0.625 0.5666 0.5787 0.480481 0.539905 0.570349 1 4945 70364 8009 5412 3952 36818 544 10684 2 10372 121144 11560 8624 6602 66574 906 16506 0.105896 0 . 0 . 72 27,12,21,4 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R1376|1609|LAMC1|protein_coding|CODING|NM_002293.3|25|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.150229 rs20560 -0.692914 0.738382 72 A1433 1609 gcG/gcA LOW 25 SILENT CODING LAMC1 A protein_coding NM_002293.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183105705 G A 0 222 0 0.1702 0.3518 0.3833 0.5109 0.4433 0.317 0.216523 0.358757 0.431628 1 1911 42648 3430 3536 2861 24640 356 5914 2 7784 94812 7942 6682 5226 52228 724 14226 0.901066 0 . 0 . 72 14,21,14,14 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1433|1609|LAMC1|protein_coding|CODING|NM_002293.3|25|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999617 rs20561 -0.693054 0.0285346 72 1609 116 MODIFIER 28 CODING LAMC1 C protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183112041 G C 0 222 0 0.5038 0.5763 0.6455 0.622 0.5666 0.5879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.765794 0 . 0 . 40 12,8,10,9 UTR_3_PRIME(MODIFIER||116||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.85394 rs3359 -0.69168 0.246155 40 1609 487 MODIFIER 28 CODING LAMC1 G protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183112412 A G 0 222 0 0.3986 0.5473 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.645139 0 . 0 . 91 26,26,15,19 UTR_3_PRIME(MODIFIER||487||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.783921 rs1062044 -0.693132 0.663663 91 1609 580 MODIFIER 28 CODING LAMC1 C protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183112505 T C 0 222 0 0.3986 0.5473 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.91089 0 . 0 . 64 15,20,8,16 UTR_3_PRIME(MODIFIER||580||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.901585 rs944971 -0.692831 0.69615 64 1609 641 MODIFIER 28 CODING LAMC1 C protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183112566 T C 0 188 0 0.3986 0.5473 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.619454 0 . 0 . 45 8,18,3,15 UTR_3_PRIME(MODIFIER||641||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.684163 rs944970 -0.691153 0.0438859 45 1609 839 MODIFIER 28 CODING LAMC1 G protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183112764 A G 0 222 0 0.3986 0.5473 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.835879 0 . 0 . 36 2,10,6,15 UTR_3_PRIME(MODIFIER||839||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.871748 rs6424890 -0.692352 0.0975678 36 1609 1937 MODIFIER 28 CODING LAMC1 T protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183113862 C T 0 9.7 0 0.4032 0.5485 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1937||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3738829 -0.379885 0 1 1609 2709 MODIFIER 28 CODING LAMC1 A protein_coding NM_002293.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183114634 G A 0 222 0 0.3986 0.5473 0.6354 0.622 0.5666 0.589 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.875371 0 . 0 . 62 9,17,13,19 UTR_3_PRIME(MODIFIER||2709||1609|LAMC1|protein_coding|CODING|NM_002293.3|28|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.932017 rs386610462,rs7473 -0.69312 0.481098 62 L72 1178 ctG/ctA LOW 4 SILENT CODING SMG7 A protein_coding NM_201569.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183486859 G A 0 228 0 0.9584 0.9419 0.9135 0.998 0.8698 0.956 0.948706 0.89674 0.870116 2 9894 109668 10818 8641 6019 57976 801 15519 2 10404 121358 11552 8648 6614 66720 908 16512 0 . 0 . 0 64 0,0,41,17 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L72|1178|SMG7|protein_coding|CODING|NM_201569.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs789169 -0.693147 0.243035 64 526 398 MODIFIER 15 CODING NCF2 A protein_coding NM_000433.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183524855 C A 0 36.3 0 0.9531 0.9393 0.9078 0.998 0.8688 0.955 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||398||526|NCF2|protein_coding|CODING|NM_000433.3|15|A),DOWNSTREAM(MODIFIER||1527||1178|SMG7|protein_coding|CODING|NM_201569.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs369000587,rs796860 -0.453602 0.58 2 K181R 526 aAg/aGg MODERATE 5 MISSENSE CODING NCF2 C protein_coding NM_000433.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183542387 T C 0 228 0 0.3306 0.4916 0.598 0.621 0.4672 0.5256 0.358829 0.430032 0.466512 2 3773 59410 7605 5425 3140 30577 432 8458 2 10406 121372 11570 8630 6612 66734 908 16512 1 0 . 0 . 62 0,1,22,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K181R|526|NCF2|protein_coding|CODING|NM_000433.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274064 -0.693147 0.368731 62 803 295 MODIFIER 19 CODING RGL1 A protein_coding NM_015149.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183895721 C A 0 228 0 0.5772 0.5633 0.5576 0.5774 0.5596 0.5378 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 50 0,0,40,8 UTR_3_PRIME(MODIFIER||295||803|RGL1|protein_coding|CODING|NM_015149.4|19|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4634865 -0.693147 0.0811936 50 803 1535 MODIFIER 19 CODING RGL1 C protein_coding NM_015149.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183896961 T C 0 228 0 0.6263 0.5833 0.5605 0.5675 0.5646 0.5767 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 46 0,0,12,29 UTR_3_PRIME(MODIFIER||1535||803|RGL1|protein_coding|CODING|NM_015149.4|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4650 -0.693145 0.0837297 46 626 2707 MODIFIER 12 CODING COLGALT2 C protein_coding NM_015101.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183905188 G C 0 39.3 0 0.32 0.3415 0.2622 0.497 0.2565 0.3538 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2707||626|COLGALT2|protein_coding|CODING|NM_015101.3|12|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1053092 -0.453602 0.7 2 626 1886 MODIFIER 12 CODING COLGALT2 G protein_coding NM_015101.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183906009 A G 0 9.7 0 0.5983 0.727 0.7911 0.75 0.7604 0.7975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1886||626|COLGALT2|protein_coding|CODING|NM_015101.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2986573 -0.379885 0 1 626 1806 MODIFIER 12 CODING COLGALT2 G protein_coding NM_015101.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183906089 A G 0 9.7 0 0.5083 0.5485 0.5432 0.5734 0.5567 0.5726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1806||626|COLGALT2|protein_coding|CODING|NM_015101.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1112363 -0.379885 0 1 626 1524 MODIFIER 12 CODING COLGALT2 A protein_coding NM_015101.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183906371 G A 0 32.6 0 0.5893 0.5735 0.5548 0.5734 0.5636 0.5757 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1524||626|COLGALT2|protein_coding|CODING|NM_015101.3|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs60147949 -0.379885 0 2 626 225 MODIFIER 12 CODING COLGALT2 G protein_coding NM_015101.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 183907670 A G 0 9.7 0 0.6717 0.7486 0.7983 0.752 0.7624 0.7996 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||225||626|COLGALT2|protein_coding|CODING|NM_015101.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2986575 -0.379885 0 1 626 401 MODIFIER 1 CODING COLGALT2 A protein_coding NM_015101.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184006892 T A 0 21 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.179237 0 . 0 . 40 1,9,2,5 UTR_5_PRIME(MODIFIER||401||626|COLGALT2|protein_coding|CODING|NM_015101.3|1|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.0182286 rs1887281 -0.636426 0.0322593 40 G19D 175 gGc/gAc MODERATE 1 MISSENSE CODING TSEN15 A protein_coding NM_001300764.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184020945 G A 0 214 0 0.1233 0.3039 0.304 0.4504 0.327 0.3732 0.136229 0.242286 0.295977 1 232 5711 187 276 25 2286 56 2649 2 1192 16436 440 474 38 6294 160 7838 0.781193 0 . 0 . 34 9,9,11,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G19D|175|TSEN15|protein_coding|CODING|NM_001300764.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82166 rs2274432 -0.686358 0.694132 34 Q59H 175 caA/caC MODERATE 2 MISSENSE CODING TSEN15 C protein_coding NM_001300764.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184023529 A C 0 222 0 0.1233 0.3029 0.3026 0.4504 0.327 0.3691 0.162733 0.284945 0.347558 1 1580 40648 3643 4203 2787 22555 331 5549 2 10398 121360 11578 8646 6610 66714 906 16508 0.325496 0 . 0 . 221 74,20,77,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q59H|175|TSEN15|protein_coding|CODING|NM_001300764.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.676729 rs1046934,rs386513147 -0.693147 0.000421887 221 932 2992 MODIFIER 20 CODING EDEM3 A protein_coding NM_025191.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184660205 T A 0 222 0 0.7065 0.6108 0.4899 0.7004 0.4732 0.6166 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.826466 0 . 0 . 187 63,27,56,14 UTR_3_PRIME(MODIFIER||2992||932|EDEM3|protein_coding|CODING|NM_025191.3|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.827343 rs1046239 -0.693147 0.0463921 187 932 1016 MODIFIER 20 CODING EDEM3 T protein_coding NM_025191.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184662181 C T 0 222 0 0.1936 0.4347 0.3977 0.63 0.4344 0.5859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.681055 0 . 0 . 94 26,17,23,22 UTR_3_PRIME(MODIFIER||1016||932|EDEM3|protein_coding|CODING|NM_025191.3|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994571 rs1061508 -0.693147 0.480807 94 I820S 932 aTt/aGt MODERATE 20 MISSENSE CODING EDEM3 C protein_coding NM_025191.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184663537 A C 0 182 0 0.0356 0.3534 0.3401 0.5784 0.3698 0.544 0.0960054 0.286373 0.383926 1 902 46307 3860 4676 2737 24961 355 8816 2 9922 118406 11158 8514 6488 65074 896 16354 0.650542 0 . 0 . 36 1,13,1,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I820S|932|EDEM3|protein_coding|CODING|NM_025191.3|20|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.76338 rs9425343 -0.692067 0.132675 36 Q805 932 caA/caG LOW 20 SILENT CODING EDEM3 C protein_coding NM_025191.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184663581 T C 0 116 0 0.1906 0.4221 0.3963 0.5873 0.4324 0.5726 0.240455 0.375173 0.444147 1 2315 52161 4458 4758 2836 28274 403 9117 2 9478 114524 10902 8384 6414 62830 854 15662 0.887766 0 . 0 . 17 0,7,0,10 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q805|932|EDEM3|protein_coding|CODING|NM_025191.3|20|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.887766 rs9425634 -0.670168 0.282457 17 N722 932 aaC/aaT LOW 18 SILENT CODING EDEM3 A protein_coding NM_025191.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184675814 G A 0 222 0 0.0257 0.3506 0.3372 0.5784 0.3708 0.544 0.0887426 0.284484 0.384767 1 831 46858 3955 4720 2793 25336 361 8862 2 10402 121184 11522 8628 6598 66618 906 16510 0.579227 0 . 0 . 80 40,1,29,3 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N722|932|EDEM3|protein_coding|CODING|NM_025191.3|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.905852 rs1062994 -0.69312 0.193598 80 I620 932 atC/atT LOW 17 SILENT CODING EDEM3 A protein_coding NM_025191.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184677464 G A 0 222 0 0.8525 0.652 0.5101 0.7004 0.4761 0.6125 0.790967 0.58259 0.475808 1 8363 64868 5406 5879 3321 31341 493 10065 2 10402 121186 11520 8626 6594 66634 906 16504 0.790532 0 . 0 . 78 10,29,7,27 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I620|932|EDEM3|protein_coding|CODING|NM_025191.3|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966795 rs3736757 -0.693132 0.536697 78 928 3678 MODIFIER 14 CODING FAM129A T protein_coding NM_052966.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184760433 C T 0 142 0 0.7118 0.5561 0.4539 0.6042 0.4264 0.502 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,9 UTR_3_PRIME(MODIFIER||3678||928|FAM129A|protein_coding|CODING|NM_052966.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7360 -0.662043 0.137712 9 928 2746 MODIFIER 14 CODING FAM129A G protein_coding NM_052966.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184761365 A G 0 6.3 0 0.7322 0.5727 0.4582 0.6458 0.4284 0.5112 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2746||928|FAM129A|protein_coding|CODING|NM_052966.3|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs682331 -0.379885 0 1 928 586 MODIFIER 14 CODING FAM129A G protein_coding NM_052966.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184763525 A G 0 39.6 0 0.7284 0.5725 0.4568 0.6508 0.4284 0.5112 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||586||928|FAM129A|protein_coding|CODING|NM_052966.3|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs14426 -0.453602 0.56 3 928 515 MODIFIER 14 CODING FAM129A T protein_coding NM_052966.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184763596 C T 0 46.3 0 0.1876 0.3712 0.3646 0.5635 0.3469 0.4509 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||515||928|FAM129A|protein_coding|CODING|NM_052966.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs14023 -0.453602 0.06 2 928 44 MODIFIER 14 CODING FAM129A G protein_coding NM_052966.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184764067 C G 0 228 0 0.1868 0.371 0.366 0.5635 0.3459 0.4509 0.217204 0.323235 0.377558 2 2172 45831 4187 4244 2877 24583 350 7418 2 9684 119148 11480 8406 6576 65646 896 16460 0 . 0 . 0 100 0,0,73,17 UTR_3_PRIME(MODIFIER||44||928|FAM129A|protein_coding|CODING|NM_052966.3|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs581100 -0.693147 0.0675744 100 Q211 928 caA/caG LOW 6 SILENT CODING FAM129A C protein_coding NM_052966.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 184801065 T C 0 222 0 0.3812 0.2837 0.2363 0.1558 0.3429 0.2566 0.366773 0.3493 0.340349 1 3855 36015 1987 1446 1953 21636 270 4868 2 10384 121314 11562 8640 6612 66700 908 16508 0.970501 0 . 0 COSM1337073 87 29,19,15,19 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q211|928|FAM129A|protein_coding|CODING|NM_052966.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997512 rs487675 -0.693132 0.553231 87 336 128 MODIFIER 7 CODING RNF2 G protein_coding NM_007212.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 185069561 A G 0 222 0 0.2436 0.1929 0.1441 0.3542 0.0636 0.1258 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.852107 0 . 0 . 74 15,12,20,18 UTR_3_PRIME(MODIFIER||128||336|RNF2|protein_coding|CODING|NM_007212.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.72302 rs1046592,rs41346252 -0.693143 0.179217 74 K136 733 aaG/aaA LOW 3 SILENT CODING TRMT1L T protein_coding NM_030934.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 185119563 C T 0 222 0 0 0.024 0 0.0883 0.003 0.0286 0.00181571 0.0018453 0.00186047 1 17 1453 26 681 4 152 14 559 2 10196 119690 11262 8608 6514 65926 898 16286 0.999677 0 . 0 . 226 57,45,45,48 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K136|733|TRMT1L|protein_coding|CODING|NM_030934.4|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966343 rs117998090 -0.693147 0.205332 226 900 136 MODIFIER 19 CODING SWT1 G protein_coding NM_001105518.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 185260071 A G 0 222 0 0.0144 0.0292 0.0014 0.0982 0.003 0.0245 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.63816 0 . 0 . 46 7,11,10,15 UTR_3_PRIME(MODIFIER||136||900|SWT1|protein_coding|CODING|NM_001105518.1|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.283461 rs76543075 -0.692914 0.892526 46 I2418T 5635 aTa/aCa MODERATE 46 MISSENSE CODING HMCN1 C protein_coding NM_031935.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186026474 T C 0 228 0 0.5393 0.53 0.6124 0.5675 0.496 0.455 0.555152 0.525373 0.510116 2 5711 65267 7834 5228 3251 34421 492 8330 2 10402 121112 11476 8574 6592 66656 908 16504 0 . 0 . 0 96 0,0,31,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2418T|5635|HMCN1|protein_coding|CODING|NM_031935.2|46|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12129650 -0.693147 0.0455468 96 C2457 5635 tgC/tgT LOW 47 SILENT CODING HMCN1 T protein_coding NM_031935.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186031041 C T 0 228 0 0.8495 0.6544 0.647 0.5903 0.5348 0.5849 0.810486 0.628402 0.535116 2 8437 72445 8112 5450 3480 36084 558 10324 2 10402 121152 11528 8596 6594 66628 904 16500 0 . 0 . 0 144 0,0,71,46 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C2457|5635|HMCN1|protein_coding|CODING|NM_031935.2|47|T),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7522627 -0.693147 0.0141125 144 E2893G 5635 gAg/gGg MODERATE 56 MISSENSE CODING HMCN1 G protein_coding NM_031935.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186050417 A G 0 228 0 0.6952 0.5827 0.6311 0.5694 0.499 0.4959 0.667045 0.554975 0.497558 2 6953 66156 7780 5284 3457 33676 474 8532 2 10404 121324 11552 8628 6614 66708 906 16512 0 2 benign 0 COSM424810 90 0,0,40,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E2893G|5635|HMCN1|protein_coding|CODING|NM_031935.2|56|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10798035 -0.693147 0.482553 90 5635 LOW 57 CODING HMCN1 G protein_coding NM_031935.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186055371 A G 0 228 0 0.9213 0.6613 0.6599 0.5794 0.5169 0.544 0.856721 0.628114 0.511047 2 9002 69961 7875 5343 3540 34524 520 9157 2 10400 120972 11442 8616 6586 66510 908 16510 0 . 0 . 0 105 0,0,68,25 SPLICE_SITE_REGION+INTRON(LOW||||5635|HMCN1|protein_coding|CODING|NM_031935.2|57|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6425017 -0.693147 0.3322 105 5635 LOW 80 CODING HMCN1 C protein_coding NM_031935.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186092076 A C 0 228 0 0.885 0.5994 0.5663 0.5724 0.3559 0.5153 0.797549 0.50915 0.361395 2 8434 57019 7227 5285 2705 24406 415 8547 2 10372 120908 11536 8620 6596 66376 908 16500 0 . 0 . 0 51 0,0,45,3 SPLICE_SITE_REGION+INTRON(LOW||||5635|HMCN1|protein_coding|CODING|NM_031935.2|80|C),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2057388 -0.693147 0.245845 51 Q4437R 5635 cAa/cGa MODERATE 86 MISSENSE CODING HMCN1 G protein_coding NM_031935.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186101539 A G 0 228 0 0.6498 0.4844 0.4841 0.5685 0.2634 0.4018 0.579437 0.369963 0.262619 2 5927 43041 6301 4942 2177 17183 315 6196 2 9680 105430 10238 7854 5758 56310 802 14788 0 . 0 . 0 120 0,0,37,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4437R|5635|HMCN1|protein_coding|CODING|NM_031935.2|86|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10911825 -0.693147 7.86919e-05 120 5635 825 MODIFIER 107 CODING HMCN1 G protein_coding NM_031935.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186159835 A G 0 228 0 1 0.9938 0.9827 1 0.9851 0.9959 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 110 0,0,76,16 UTR_3_PRIME(MODIFIER||825||5635|HMCN1|protein_coding|CODING|NM_031935.2|107|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs628748 -0.693147 0.0025828 110 R180W 1404 Cgg/Tgg MODERATE 6 MISSENSE CODING PRG4 T protein_coding NM_005807.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186273994 C T 0 222 0 0.149 0.2316 0.4063 0.129 0.33 0.2239 0.186903 0.296476 0.352524 1 1767 36765 5054 1199 1950 22757 272 3766 2 9940 120542 11540 8614 6600 66458 898 16492 0.686022 0 . 0 . 89 25,14,27,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R180W|1404|PRG4|protein_coding|CODING|NM_005807.4|6|T),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.409077 rs2273779 -0.693146 0.741687 89 T604A 1404 Act/Gct MODERATE 7 MISSENSE CODING PRG4 G protein_coding NM_005807.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186276661 A G 0 222 0 0.1415 0.2294 0.4078 0.125 0.33 0.226 0.187472 0.297017 0.35314 1 1785 36696 5047 1163 1940 22702 270 3789 2 10218 120190 11442 8498 6582 66070 892 16488 0.916741 0 . 0 COSM1599884 54 12,11,9,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T604A|1404|PRG4|protein_coding|CODING|NM_005807.4|7|G),DOWNSTREAM(MODIFIER||4125||2363|TPR|protein_coding|CODING|NM_003292.2||G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.9822 0.959019 0 0.926156 rs111205635,rs61831150 -0.69168 0.60543 54 C746S 1404 tGt/tCt MODERATE 7 MISSENSE CODING PRG4 C protein_coding NM_005807.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186277088 G C 0 228 0 1 1 1 1 1 1 1 0.999923 0.999884 2 10382 121279 11577 8652 6613 66643 904 16508 2 10384 121298 11578 8652 6614 66656 904 16510 0 . 0 . 0 186 0,0,86,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C746S|1404|PRG4|protein_coding|CODING|NM_005807.4|7|C),DOWNSTREAM(MODIFIER||3698||2363|TPR|protein_coding|CODING|NM_003292.2||C),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.499668 0 . rs68069719 -0.693147 0.212307 186 P1046 1404 ccA/ccG LOW 7 SILENT CODING PRG4 G protein_coding NM_005807.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186277989 A G 0 222 0 0.1142 0.2212 0.402 0.125 0.33 0.2249 0.149342 0.284638 0.353953 1 1475 36546 5055 1173 1950 22845 273 3775 2 10332 121178 11564 8636 6614 66628 904 16500 0.376956 0 . 0 . 178 56,29,58,19 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1046|1404|PRG4|protein_coding|CODING|NM_005807.4|7|G),DOWNSTREAM(MODIFIER||2797||2363|TPR|protein_coding|CODING|NM_003292.2||G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.83426 rs3737940 -0.693147 0.0126762 178 2363 1407 MODIFIER 51 CODING TPR G protein_coding NM_003292.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186281696 T G 0 194 0 0.6172 0.6062 0.6023 0.6567 0.6213 0.5266 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,5,3 UTR_3_PRIME(MODIFIER||1407||2363|TPR|protein_coding|CODING|NM_003292.2|51|G),INTRON(MODIFIER||||1404|PRG4|protein_coding|CODING|NM_005807.4|11|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.900802 0 . rs7756 -0.651104 0.112921 8 1404 512 MODIFIER 13 CODING PRG4 T protein_coding NM_005807.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186283422 C T 0 104 0 0.149 0.231 0.4063 0.127 0.33 0.2229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.760054 0 . 0 . 13 3,2,1,6 UTR_3_PRIME(MODIFIER||512||1404|PRG4|protein_coding|CODING|NM_005807.4|13|T),INTRON(MODIFIER||||2363|TPR|protein_coding|CODING|NM_003292.2|50|T),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 1 0 0.0584657 rs61831151 -0.636426 0.293704 13 V779I 2363 Gta/Ata MODERATE 19 MISSENSE CODING TPR T protein_coding NM_003292.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186321242 C T 0 222 0 0.0234 0.0871 0.121 0.0714 0.1849 0.0644 0.0524417 0.141203 0.180511 1 428 15901 822 614 1061 11592 122 1262 2 9730 119292 11444 8468 6558 65862 888 16342 0.692718 0 . 0 COSM146711,COSM328079 108 17,34,16,31 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gta/Ata|V779I|2363|TPR|protein_coding|CODING|NM_003292.2|19|T),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.707431 rs61744267 -0.693147 0.205142 108 S251C 454 tCt/tGt MODERATE 9 MISSENSE CODING C1orf27 G protein_coding NM_017847.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186363119 C G 0 222 0 0.149 0.2324 0.4078 0.127 0.335 0.2239 0.173123 0.273294 0.317833 1 418 6547 174 69 478 3448 71 1889 2 2290 22858 442 640 1634 9682 248 7922 0.569783 0 . 0 COSM424842,COSM424841 59 13,14,10,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S251C|454|C1orf27|protein_coding|CODING|NM_017847.5|9|G),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976333 rs12084264 -0.693054 0.185179 59 454 2095 MODIFIER 14 CODING C1orf27 C protein_coding NM_017847.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186390303 A C 0 9.7 0 0.5424 0.5615 0.5807 0.6349 0.5835 0.4755 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2095||454|C1orf27|protein_coding|CODING|NM_017847.5|14|C),INTRAGENIC(MODIFIER|||||MIR548F1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8824 -0.379885 0 1 604 1859 MODIFIER 10 CODING PTGS2 A protein_coding NM_000963.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186641626 G A 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 82 0,0,64,11 UTR_3_PRIME(MODIFIER||1859||604|PTGS2|protein_coding|CODING|NM_000963.3|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2853805 -0.693147 0.00255063 82 604 1056 MODIFIER 10 CODING PTGS2 G protein_coding NM_000963.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186642429 A G 0 39.3 0 0.9962 0.9629 0.9539 1 0.9105 0.9397 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1056||604|PTGS2|protein_coding|CODING|NM_000963.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2206593 -0.453602 0.22 2 R651K 749 aGg/aAg MODERATE 16 MISSENSE CODING PLA2G4A A protein_coding NM_024420.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 186946912 G A 0 228 0 0.9985 0.9882 0.9841 0.998 0.9742 0.9816 0.995461 0.985622 0.980581 2 10358 119024 11299 8651 6487 65163 891 16175 2 10404 121406 11578 8654 6614 66736 908 16512 0 . 0 . 0 182 0,0,55,112 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R651K|749|PLA2G4A|protein_coding|CODING|NM_024420.2|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2307198 -0.693147 0.00675192 182 235 131 MODIFIER 1 CODING RGS18 G protein_coding NM_130782.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 192127637 T G 0 228 0 0.171 0.4397 0.5504 0.7202 0.493 0.3804 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 71 1,0,63,1 START_GAINED(LOW||||235|RGS18|protein_coding|CODING|NM_130782.2|1|G),UTR_5_PRIME(MODIFIER||131||235|RGS18|protein_coding|CODING|NM_130782.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs4495675 -0.693147 0.474915 71 211 446 MODIFIER 5 CODING RGS2 G protein_coding NM_002923.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 192781172 C G 0 222 0 0.3207 0.3488 0.3141 0.5308 0.2763 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.897654 0 . 0 . 165 36,38,40,40 UTR_3_PRIME(MODIFIER||446||211|RGS2|protein_coding|CODING|NM_002923.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.820396 rs4606 -0.693147 0.0341916 165 538 LOW 7 CODING TROVE2 A protein_coding NM_001173524.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 193051685 G A 0 222 0 0.5242 0.5935 0.6614 0.4435 0.6849 0.6994 0.544085 0.668503 0.724282 1 5156 81406 7458 3821 4292 48216 606 11857 2 9792 120414 11468 8596 6592 66562 900 16504 0.741241 0 . 0 . 135 48,29,29,22 SPLICE_SITE_REGION+INTRON(LOW||||538|TROVE2|protein_coding|CODING|NM_001173524.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982147 rs2275444 -0.693147 0.072319 135 538 293 MODIFIER 9 CODING TROVE2 A protein_coding NM_001173524.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 193054154 G A 0 222 0 0.0227 0.2925 0.3631 0.3423 0.3817 0.4642 0 . 0 1 80 6704 116 178 661 2164 78 3427 2 900 16108 294 466 1598 5248 206 7396 0.370483 0 . 0 . 186 51,40,46,30 UTR_3_PRIME(MODIFIER||293||538|TROVE2|protein_coding|CODING|NM_001173524.1|9|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.926601 rs10921309 -0.693147 0.323498 186 538 624 MODIFIER 9 CODING TROVE2 C protein_coding NM_001173524.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 193054485 T C 0 115 0 0.4803 0.5691 0.6297 0.4435 0.6541 0.6881 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.916482 0 . 0 . 10 0,3,1,6 UTR_3_PRIME(MODIFIER||624||538|TROVE2|protein_coding|CODING|NM_001173524.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.916482 1 0 0.458241 rs10801173 -0.636426 0.402545 10 R40W 165 Agg/Tgg MODERATE 1 MISSENSE CODING GLRX2 A protein_coding NM_016066.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 193074651 T A 0 113 0 0.7458 0.6807 0.696 0.4454 0.6928 0.8119 0.735991 0.736931 0.737413 1 4531 46743 3045 2333 1686 24646 325 10177 2 5990 61212 4104 4294 2344 31830 434 12216 0.875318 0 . 0 . 37 20,0,11,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Tgg|R40W|165|GLRX2|protein_coding|CODING|NM_016066.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.933295 rs10921310 -0.676189 0.427987 37 D1003 1135 gaT/gaC LOW 26 SILENT CODING KCNT2 G protein_coding NM_198503.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196227526 A G 0 228 0 0.9561 0.9872 0.9914 1 1 1 0.960508 0.986468 0.999767 2 9972 120893 11523 8642 6614 66725 905 16512 2 10406 121362 11550 8642 6614 66730 908 16512 0 . 0 . 0 111 0,0,67,35 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1003|1135|KCNT2|protein_coding|CODING|NM_198503.3|26|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs977157 -0.693147 0.956416 111 1231 195 MODIFIER 1 CODING CFH C protein_coding NM_000186.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196621053 T C 0 92 0 0.1543 0.0741 0.0288 0.0456 0.005 0.0982 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924449 0 . 0 . 11 4,0,7,0 UTR_5_PRIME(MODIFIER||195||1231|CFH|protein_coding|CODING|NM_000186.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 0 . 0.562708 rs35836460 -0.636426 0.453474 11 V62I 1231 Gta/Ata MODERATE 2 MISSENSE CODING CFH A protein_coding NM_000186.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196642233 G A 0 228 0 0.7912 0.4681 0.4193 0.4067 0.2604 0.3425 0.707898 0.386591 0.221977 2 7430 38814 4362 3611 2004 15878 284 5245 2 10366 120934 11550 8618 6614 66416 904 16466 0 255|1 other|not-provided 0 COSM146716 36 0,0,9,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V62I|1231|CFH|protein_coding|CODING|NM_000186.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs800292 -0.693127 0.570432 36 A307 1231 gcA/gcC LOW 7 SILENT CODING CFH C protein_coding NM_000186.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196654324 A C 0 228 0 0.5688 0.7131 0.7565 0.9504 0.6382 0.7096 0.590331 0.608104 0.617209 2 5967 80828 9676 8207 3673 41143 600 11562 2 10406 121250 11472 8630 6610 66714 908 16510 0 . 0 . 0 98 0,0,37,56 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A307|1231|CFH|protein_coding|CODING|NM_000186.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1061147 -0.693147 0.755903 98 H402Y 1231 Cat/Tat MODERATE 9 MISSENSE CODING CFH T protein_coding NM_000186.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196659237 C T 0 228 0 0.6377 0.7334 0.7666 0.9514 0.6382 0.7127 0.637313 0.624327 0.617674 2 6530 80806 9618 8126 3646 40747 593 11546 2 10354 120234 11372 8548 6532 66052 900 16476 1 255|5 other|pathogenic 0 COSM424915 164 1,0,117,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H402Y|1231|CFH|protein_coding|CODING|NM_000186.3|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1061170 -0.693147 0.0137062 164 A473 1231 gcG/gcA LOW 10 SILENT CODING CFH A protein_coding NM_000186.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196682947 G A 0 228 0 0.4735 0.479 0.5389 0.4246 0.4235 0.5573 0.468906 0.426188 0.404302 2 4776 53468 5125 3720 2614 27778 413 9042 2 10396 120670 11344 8534 6578 66416 904 16498 1 0 . 0 . 121 1,0,79,28 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A473|1231|CFH|protein_coding|CODING|NM_000186.3|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274700 -0.693147 0.448715 121 1231 LOW 19 CODING CFH C protein_coding NM_000186.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196712577 T C 0 58 0 . 0 . 0 . 0 . 0 . 1 2349 30718 3645 2972 1656 16208 233 3655 2 10058 118830 11264 8420 6492 65402 884 16310 0.971297 0 . 0 . 162 85,26,35,2 SPLICE_SITE_REGION+INTRON(LOW||||1231|CFH|protein_coding|CODING|NM_000186.3|19|C) 0 0.5 1 0 . 0 . 0 1 0 55 0 1.69422e-07 0.412024 0 1.6255e-05 rs513699 -0.693141 6.77873e-07 162 T1046 1231 acC/acT LOW 20 SILENT CODING CFH T protein_coding NM_000186.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196712586 C T 0 183 0 . 0 . 0 . 0 . 0 . 1 2359 30798 3662 2978 1658 16229 233 3679 2 9684 115916 11100 8278 6378 63552 872 16052 0.875628 0 . 0 . 187 91,24,49,4 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1046|1231|CFH|protein_coding|CODING|NM_000186.3|20|T) 0 0.5 1 0 . 0 . 0 1 0 56 0 9.65806e-06 0.666887 0 5.60477e-07 rs61822181 -0.693147 4.0933e-09 187 S159 330 tcC/tcT LOW 4 SILENT CODING CFHR3 T protein_coding NM_021023.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196757392 C T 0 228 0 0.646 0.6494 0.6657 0.9484 0.501 0.4867 0 . 0 2 2935 40062 6965 6039 2006 17172 308 4637 2 4614 80396 8848 6444 5040 44348 622 10480 0 . 0 . COSM424924 59 0,0,17,40 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S159|330|CFHR3|protein_coding|CODING|NM_021023.5|4|T) 0 . 0 . 0 1 0 . 1 0 54 0 0 0.0208538 0 . rs400344 -0.693147 0.53346 59 H157Y 330 Cat/Tat MODERATE 4 MISSENSE CODING CFHR1 T protein_coding NM_002113.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196797238 C T 0 210 0 . 0 . 0 . 0 0.444077 0.30586 0.244764 2 2078 22976 2716 2430 1224 11132 186 3210 2 5788 88140 8774 6720 5328 49154 660 11716 0.967742 0 . 0 . 34 2,0,3,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H157Y|330|CFHR1|protein_coding|CODING|NM_002113.2|4|T) 1 0 . 0 . 0 . 1 1 0 51 0 0.548387 0.940104 0 0.306452 rs425757 -0.69311 5.84726e-05 34 L159V 330 Ctg/Gtg MODERATE 4 MISSENSE CODING CFHR1 G protein_coding NM_002113.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196797244 C G 0 158 0 . 0 . 0 . 0 0.420056 0.288929 0.231436 2 1541 18106 2187 1920 982 8873 131 2472 2 5342 86156 8544 6394 5260 48606 634 11376 0.931035 0 . 0 . 31 2,0,1,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L159V|330|CFHR1|protein_coding|CODING|NM_002113.2|4|G) 1 0 . 0 . 0 . 1 1 0 52 0 0.551724 0.42794 0 0.327586 rs113811987 -0.693079 1.97326e-05 31 E175Q 330 Gaa/Caa MODERATE 4 MISSENSE CODING CFHR1 C protein_coding NM_002113.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196797292 G C 0 152 0 . 0 . 0 . 0 . 0 . 1 744 6385 425 430 342 2786 59 1599 2 4714 79870 7764 5548 4876 45752 606 10610 0.505697 0 . 0 . 14 2,1,2,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E175Q|330|CFHR1|protein_coding|CODING|NM_002113.2|4|C) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.646383 0.997503 0 0.862013 rs388862 -0.676189 0.814039 14 T196 330 acA/acG LOW 4 SILENT CODING CFHR1 G protein_coding NM_002113.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196797357 A G 0 210 0 . 0 . 0 . 0 0.372394 0.252221 0.199926 1 1335 11949 1020 950 674 5435 115 2420 2 5326 85478 8530 6166 5158 48312 638 11348 0.733333 0 . 0 COSM1626718 17 1,1,5,10 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T196|330|CFHR1|protein_coding|CODING|NM_002113.2|4|G) 1 0.5 1 0 . 0 . 1 1 0 49 0 0.466667 0.23233 0 0.2 rs3201739 -0.688148 0.118074 17 R302 330 cgG/cgT LOW 6 SILENT CODING CFHR1 T protein_coding NM_002113.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196801042 G T 0 228 0 0.6157 0.5074 0.5187 0.5437 0.4463 0.3783 0.647059 0.481808 0.406341 2 5645 51789 5784 4690 2494 26513 390 6273 2 8458 113652 11402 8586 6442 63316 848 14600 0.614385 0 . 0 . 259 1,2,121,108 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgT|R302|330|CFHR1|protein_coding|CODING|NM_002113.2|6|T) 1 0 . 0 . 1 0 1 1 0 57 0 0.192983 0.89864 0 0.664097 rs4230 -0.693147 0.133023 259 R314 330 cgA/cgT LOW 6 SILENT CODING CFHR1 T protein_coding NM_002113.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196801078 A T 0 222 0 0.326 0.4237 0.5072 0.5228 0.4433 0.3742 0.379595 0.397034 0.40497 1 3186 48533 5660 4496 2482 26119 379 6211 2 8276 112792 11358 8556 6432 62812 848 14510 0.990869 0 . 0 . 245 40,71,43,65 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgT|R314|330|CFHR1|protein_coding|CODING|NM_002113.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 54 0 0.657906 0.605749 0 0.499972 rs414628 -0.693147 0.683483 245 330 61 MODIFIER 6 CODING CFHR1 A protein_coding NM_002113.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196801190 C A 0 228 0 0.3253 0.4235 0.5072 0.5228 0.4433 0.3742 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 73 0,1,6,63 UTR_3_PRIME(MODIFIER||61||330|CFHR1|protein_coding|CODING|NM_002113.2|6|A) 0 . 0 . 0 1 0 . 0 . 59 0 1 1 0 1 rs390679 -0.693147 0.313621 73 E125D 578 gaG/gaT MODERATE 3 MISSENSE CODING CFHR4 T protein_coding NM_001201550.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196874356 G T 0 228 0 0.9796 0.9944 0.9986 1 1 1 0 . 0 2 9993 120901 11546 8644 6608 66699 905 16506 2 10212 121138 11560 8644 6608 66702 906 16506 0 . 0 . 0 157 0,0,80,66 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E125D|578|CFHR4|protein_coding|CODING|NM_001201550.2|3|T) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.987708 0 . rs10801578 -0.693147 0.134282 157 N210S 578 aAc/aGc MODERATE 5 MISSENSE CODING CFHR4 G protein_coding NM_001201550.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196876458 A G 0 228 0 0.2095 0.5891 0.7305 0.8304 0.6839 0.6554 0 . 0 2 2812 82387 9377 7018 5388 46226 631 10935 2 9678 120234 11534 8622 6600 66408 898 16494 1 0 . 0 . 98 1,0,66,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N210S|578|CFHR4|protein_coding|CODING|NM_001201550.2|5|G) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs7417769 -0.693147 0.137284 98 C140 270 tgC/tgT LOW 3 SILENT CODING CFHR2 T protein_coding NM_005666.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 196920148 C T 0 228 0 0.0272 0.3249 0.464 0.7024 0.2505 0.316 0.0705856 0.170306 0.221395 2 657 35918 6158 6233 2014 15754 274 4828 2 10406 121248 11476 8636 6608 66702 908 16512 1 0 . 0 . 160 0,1,35,110 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C140|270|CFHR2|protein_coding|CODING|NM_005666.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4085749 -0.693147 2.48021e-06 160 N602 661 aaT/aaC LOW 11 SILENT CODING F13B G protein_coding NM_001994.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197009798 A G 0 228 0 0.1921 0.525 0.6455 0.8194 0.501 0.6104 0.229545 0.388607 0.470081 2 2428 63194 8576 7021 3670 31209 506 9784 2 10234 119910 11436 8586 6562 65722 902 16468 0 . 0 . 0 99 0,0,31,55 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N602|661|F13B|protein_coding|CODING|NM_001994.2|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5998 -0.693147 0.685575 99 T152 661 acA/acG LOW 4 SILENT CODING F13B C protein_coding NM_001994.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197030201 T C 0 153 0 0.382 0.7837 0.8804 1 0.9125 0.9029 0.461643 0.756152 0.907071 2 4617 105218 10648 8531 6088 59693 811 14830 2 9972 119496 11282 8534 6508 65854 902 16444 0 . 0 . 0 11 0,0,0,11 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T152|661|F13B|protein_coding|CODING|NM_001994.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs5997 -0.676189 0.00129862 11 R115H 661 cGt/cAt MODERATE 3 MISSENSE CODING F13B T protein_coding NM_001994.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197031021 C T 0 228 0 0.3162 0.7618 0.879 0.9831 0.9115 0.8988 0.409442 0.738505 0.907093 2 4144 105395 10733 8466 6156 60239 807 14850 2 10372 120870 11404 8606 6582 66504 902 16500 0 255 other 0 . 96 0,0,34,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R115H|661|F13B|protein_coding|CODING|NM_001994.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6003 -0.693147 0.0812263 96 3477 81 MODIFIER 28 CODING ASPM A protein_coding NM_018136.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197053373 G A 0 228 0 0.3782 0.7823 0.8804 1 0.9125 0.9008 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 74 0,0,54,16 UTR_3_PRIME(MODIFIER||81||3477|ASPM|protein_coding|CODING|NM_018136.4|28|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12677,rs386424794 -0.693147 0.000669395 74 3477 LOW 27 CODING ASPM C protein_coding NM_018136.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197055925 T C 0 228 0 0.379 0.7827 0.8804 1 0.9135 0.9008 0.457519 0.755118 0.907588 2 4622 106448 10911 8631 6184 60417 817 14866 2 10228 121152 11572 8634 6614 66690 908 16506 0 255 other 0 . 61 0,0,49,6 SPLICE_SITE_REGION+INTRON(LOW||||3477|ASPM|protein_coding|CODING|NM_018136.4|27|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10754213 -0.693147 0.0582269 61 V2535 3477 gtG/gtA LOW 18 SILENT CODING ASPM T protein_coding NM_018136.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197070776 C T 0 228 0 0.0159 0.2949 0.428 0.6696 0.172 0.318 0.0442779 0.114864 0.151036 2 451 28959 5635 6046 1636 10383 210 4598 2 10330 120864 11406 8614 6590 66520 902 16502 0 2|2|2 benign|benign|benign 0 . 114 0,0,60,46 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V2535|3477|ASPM|protein_coding|CODING|NM_018136.4|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10922162 -0.693147 0.0381047 114 L2522 3477 ttA/ttG LOW 18 SILENT CODING ASPM C protein_coding NM_018136.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197070815 T C 0 228 0 0.497 0.8159 0.8934 1 0.9125 0.9029 0.551294 0.786923 0.907726 2 5663 107343 10815 8614 6176 60387 815 14873 2 10308 120942 11412 8618 6604 66592 904 16504 0 2|255 benign|other 0 . 122 0,0,72,41 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L2522|3477|ASPM|protein_coding|CODING|NM_018136.4|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1412640 -0.693147 0.908595 122 Y2494H 3477 Tac/Cac MODERATE 18 MISSENSE CODING ASPM G protein_coding NM_018136.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197070901 A G 0 228 0 1 0.9974 0.9942 1 0.995 0.9959 0.998865 0.995693 0.994067 2 10375 120633 11436 8636 6593 66214 907 16472 2 10386 121166 11448 8636 6602 66678 908 16508 0 2|2|2 benign|benign|benign 0 . 157 0,0,78,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y2494H|3477|ASPM|protein_coding|CODING|NM_018136.4|18|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs964201 -0.693147 0.145256 157 S1193 3477 tcT/tcA LOW 14 SILENT CODING ASPM T protein_coding NM_018136.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197091537 A T 0 228 0 0.379 0.7825 0.8804 1 0.9125 0.9008 0.45665 0.754729 0.907442 2 4672 106375 10831 8639 6174 60374 817 14868 2 10372 121172 11486 8642 6602 66656 908 16506 0 2|3 benign|likely-benign 0 . 139 0,0,78,38 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S1193|3477|ASPM|protein_coding|CODING|NM_018136.4|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4915337 -0.693147 0.108104 139 S283 3477 tcC/tcT LOW 3 SILENT CODING ASPM A protein_coding NM_018136.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197112533 G A 0 228 0 0.295 0.7556 0.8746 0.9831 0.9095 0.9008 0.387199 0.730775 0.906839 2 3864 105485 10867 8510 6180 60391 806 14867 2 10322 121278 11576 8654 6610 66704 904 16508 0 255 other 0 . 137 0,0,52,71 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S283|3477|ASPM|protein_coding|CODING|NM_018136.4|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6677082 -0.693147 0.000140864 137 909 1840 MODIFIER 10 CODING ZBTB41 A protein_coding NM_194314.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197126649 G A 0 225 0 0.0265 0.2973 0.4251 0.6716 0.168 0.32 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,19,2 UTR_3_PRIME(MODIFIER||1840||909|ZBTB41|protein_coding|CODING|NM_194314.2|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4639796 -0.692352 0.70939 21 909 998 MODIFIER 10 CODING ZBTB41 C protein_coding NM_194314.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197127491 A C 0 228 0 0.0265 0.2983 0.4251 0.6726 0.17 0.3221 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.907895 0 . 0 . 140 2,0,62,52 UTR_3_PRIME(MODIFIER||998||909|ZBTB41|protein_coding|CODING|NM_194314.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.464912 rs12028827 -0.693147 0.5648 140 L831 909 ctC/ctT LOW 10 SILENT CODING ZBTB41 A protein_coding NM_194314.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197128726 G A 0 228 0 0.0265 0.2977 0.4251 0.6716 0.17 0.32 0.0447118 0.115101 0.151163 2 477 29019 5702 6081 1641 10298 214 4606 2 10404 121308 11538 8638 6610 66698 908 16512 0 . 0 . 0 158 0,0,114,42 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L831|909|ZBTB41|protein_coding|CODING|NM_194314.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12128631 -0.693147 0.0562265 158 D397H 1406 Gac/Cac MODERATE 6 MISSENSE CODING CRB1 C protein_coding NM_201253.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197390147 G C 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 23 0 23 0 0 0 0 2 10394 121304 11578 8654 6612 66648 908 16510 0.606414 0 . 0 . 81 23,16,31,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Cac|D397H|1406|CRB1|protein_coding|CODING|NM_201253.2|6|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.970399 rs114264441 -0.693145 0.109089 81 L470 1406 ctA/ctG LOW 6 SILENT CODING CRB1 G protein_coding NM_201253.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197390368 A G 0 228 0 0.7065 0.9197 0.9813 1 0.999 1 0.769632 0.921036 0.998605 2 7948 118742 11437 8650 6614 66678 905 16510 2 10404 121406 11578 8654 6614 66736 908 16512 0 2 benign 0 . 128 0,0,68,49 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L470|1406|CRB1|protein_coding|CODING|NM_201253.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3902057 -0.693147 0.531193 128 775 5025 MODIFIER 23 CODING DENND1B G protein_coding NM_001195215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197474565 A G 0 9.7 0 0.8026 0.9453 0.9827 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5025||775|DENND1B|protein_coding|CODING|NM_001195215.1|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7553327 -0.379885 0 1 775 4773 MODIFIER 23 CODING DENND1B G protein_coding NM_001195215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197474817 A G 0 109 0 0.9501 0.986 0.9957 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,1 UTR_3_PRIME(MODIFIER||4773||775|DENND1B|protein_coding|CODING|NM_001195215.1|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7553626 -0.556411 0.303109 5 775 4505 MODIFIER 23 CODING DENND1B C protein_coding NM_001195215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197475085 T C 0 9.7 0 0.8018 0.9433 0.9841 0.9901 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4505||775|DENND1B|protein_coding|CODING|NM_001195215.1|23|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6428408 -0.379885 0 1 775 2353 MODIFIER 23 CODING DENND1B C protein_coding NM_001195215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197477237 T C 0 32.6 0 0.8018 0.9453 0.9841 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2353||775|DENND1B|protein_coding|CODING|NM_001195215.1|23|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10922241 -0.379885 0 2 775 212 MODIFIER 23 CODING DENND1B A protein_coding NM_001195215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197479378 C A 0 228 0 0.8018 0.9433 0.9841 0.9901 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,22,33 UTR_3_PRIME(MODIFIER||212||775|DENND1B|protein_coding|CODING|NM_001195215.1|23|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1421389 -0.693147 0.2771 62 D96 145 gaT/gaC LOW 2 SILENT CODING C1orf53 C protein_coding NM_001024594.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197874949 T C 0 222 0 0.4123 0.3596 0.3948 0.2619 0.3668 0.3569 0.402377 0.366949 0.350156 1 3934 42413 4755 2316 1978 23067 310 6053 2 9796 120718 11566 8608 6614 66724 898 16512 0.629967 0 . 0 . 76 35,11,17,9 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D96|145|C1orf53|protein_coding|CODING|NM_001024594.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.368666 rs2270763 -0.692976 0.797312 76 N247 397 aaT/aaC LOW 4 SILENT CODING LHX9 C protein_coding NM_020204.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 197896728 T C 0 222 0 0.1959 0.268 0.3545 0.4067 0.1859 0.2454 0.185883 0.187913 0.188953 1 1965 28675 4260 3826 1823 12787 199 3815 2 10406 121364 11572 8620 6614 66734 908 16510 0.882868 0 . 0 COSM146721 174 58,29,49,17 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N247|397|LHX9|protein_coding|CODING|NM_020204.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.416058 rs12046958 -0.693147 0.143133 174 302 57 MODIFIER 10 CODING NEK7 G protein_coding NM_133494.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 198288709 A G 0 228 0 0.764 0.6941 0.6599 0.8988 0.3777 0.7382 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 58 0,0,9,45 UTR_3_PRIME(MODIFIER||57||302|NEK7|protein_coding|CODING|NM_133494.2|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6679100 -0.693147 0.00557774 58 T193A 1306 Acc/Gcc MODERATE 6 MISSENSE CODING PTPRC G protein_coding NM_002838.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 198671653 A G 0 222 0 0.0015 0.0563 0.0692 0.1687 0.003 0.0603 0.00567408 0.00668922 0.0072093 1 64 4772 1587 1777 7 553 19 765 2 10406 121388 11570 8640 6614 66738 908 16512 0.996631 0 . 0 . 155 25,56,23,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T193A|1306|PTPRC|protein_coding|CODING|NM_002838.4|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.760803 rs4915154 -0.693147 0.171304 155 T216P 1306 Acc/Ccc MODERATE 7 MISSENSE CODING PTPRC C protein_coding NM_002838.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 198672489 A C 0 222 0 0 0.0019968 0 0.0089 0 0.001 0.000453926 0.000153775 0 1 6 59 0 51 0 0 0 2 2 10378 121248 11550 8626 6606 66668 908 16512 0.99942 0 . 0 . 51 15,7,10,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T216P|1306|PTPRC|protein_coding|CODING|NM_002838.4|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994794 rs148561683 -0.692717 0.42426 51 G772 1306 ggC/ggT LOW 23 SILENT CODING PTPRC T protein_coding NM_002838.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 198704294 C T 0 228 0 0.2738 0.2262 0.2968 0.2361 0.1163 0.2147 0.245801 0.163873 0.121889 2 2540 19985 3416 2234 476 7789 138 3392 2 10250 118736 11230 8414 6488 65136 892 16326 0 . 0 . 0 26 0,0,23,1 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G772|1306|PTPRC|protein_coding|CODING|NM_002838.4|23|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7540378 -0.692831 0.000284014 26 541 104 MODIFIER 8 CODING NR5A2 C protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200143442 T C 0 222 0 0.6899 0.4633 0.5144 0.0883 0.5666 0.4008 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.823447 0 . 0 . 176 45,47,32,32 UTR_3_PRIME(MODIFIER||104||541|NR5A2|protein_coding|CODING|NM_205860.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.95313 rs1060061 -0.693147 0.663987 176 541 506 MODIFIER 8 CODING NR5A2 G protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200143844 C G 0 222 0 0.5749 0.5871 0.6729 0.3284 0.6978 0.6953 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.68321 0 . 0 . 62 8,23,15,16 UTR_3_PRIME(MODIFIER||506||541|NR5A2|protein_coding|CODING|NM_205860.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992865 rs2690034 -0.69311 0.0630687 62 541 751 MODIFIER 8 CODING NR5A2 G protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200144089 T G 0 222 0 0.649 0.6156 0.6787 0.3214 0.6988 0.7434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99963 0 . 0 . 123 30,23,22,26 UTR_3_PRIME(MODIFIER||751||541|NR5A2|protein_coding|CODING|NM_205860.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.983893 rs2816912 -0.693147 0.029504 123 541 2171 MODIFIER 8 CODING NR5A2 A protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200145509 G A 0 222 0 0.6422 0.5982 0.6484 0.3393 0.6561 0.7106 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.9884 0 . 0 . 76 7,29,7,27 UTR_3_PRIME(MODIFIER||2171||541|NR5A2|protein_coding|CODING|NM_205860.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.726695 rs2246210 -0.693132 0.0912677 76 541 2195 MODIFIER 8 CODING NR5A2 A protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200145533 G A 0 222 0 0.6437 0.6028 0.6484 0.3373 0.6541 0.7362 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.604009 0 . 0 . 66 5,27,5,22 UTR_3_PRIME(MODIFIER||2195||541|NR5A2|protein_coding|CODING|NM_205860.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982078 rs2246209 -0.693021 0.228761 66 541 2324 MODIFIER 8 CODING NR5A2 T protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200145662 G T 0 24.7 0 0.6422 0.6022 0.6484 0.3433 0.6551 0.728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.462292 0 . 0 . 9 0,6,0,3 UTR_3_PRIME(MODIFIER||2324||541|NR5A2|protein_coding|CODING|NM_205860.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 0 . 0.924584 rs2690033 -0.511536 0.392388 9 541 2555 MODIFIER 8 CODING NR5A2 G protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200145893 A G 0 9.7 0 0.6452 0.6128 0.6744 0.3423 0.6968 0.7178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2555||541|NR5A2|protein_coding|CODING|NM_205860.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2690032 -0.379885 0 1 541 3065 MODIFIER 8 CODING NR5A2 C protein_coding NM_205860.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200146403 T C 0 222 0 0.0605 0.1538 0.1657 0.2599 0.0765 0.2413 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.195031 0 . 0 . 59 16,5,19,8 UTR_3_PRIME(MODIFIER||3065||541|NR5A2|protein_coding|CODING|NM_205860.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.459575 rs1056426 -0.693021 0.212202 59 1648 247 MODIFIER 30 CODING KIF14 A protein_coding NM_014875.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200522269 G A 0 150 0 0.4962 0.5471 0.4986 0.631 0.493 0.6196 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,11,0 UTR_3_PRIME(MODIFIER||247||1648|KIF14|protein_coding|CODING|NM_014875.2|30|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6667775 -0.676189 0.443772 11 1648 165 MODIFIER 30 CODING KIF14 T protein_coding NM_014875.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200522351 A T 0 228 0 0.3805 0.5553 0.5403 0.6885 0.5755 0.6442 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,20,2 UTR_3_PRIME(MODIFIER||165||1648|KIF14|protein_coding|CODING|NM_014875.2|30|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10800708 -0.692562 0.788551 23 P1633A 1648 Cca/Gca MODERATE 30 MISSENSE CODING KIF14 C protein_coding NM_014875.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200522566 G C 0 222 0 0.0424 0.2196 0.2017 0.2302 0.3917 0.2843 0.103041 0.305782 0.409651 1 923 38789 2029 1990 1746 26660 292 5149 2 10406 121106 11572 8634 6614 66660 906 16314 0.7631 0 . 0 . 75 23,20,15,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P1633A|1648|KIF14|protein_coding|CODING|NM_014875.2|30|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.804886 rs12120084 -0.693054 0.169213 75 E1340 1648 gaG/gaA LOW 25 SILENT CODING KIF14 T protein_coding NM_014875.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200534248 C T 0 228 0 0.4077 0.5635 0.5461 0.6895 0.5765 0.6431 0.429414 0.535906 0.590465 2 4354 69389 5730 5887 3442 38937 556 10483 2 10400 121366 11574 8644 6612 66716 908 16512 0 . 0 . 0 76 0,0,44,27 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E1340|1648|KIF14|protein_coding|CODING|NM_014875.2|25|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7543730 -0.693147 0.564988 76 E1032 1648 gaA/gaG LOW 18 SILENT CODING KIF14 C protein_coding NM_014875.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200558363 T C 0 228 0 0.9032 0.7666 0.67 0.6875 0.7475 0.7515 0.876703 0.806675 0.770814 2 9170 91135 6838 5881 4918 51165 695 12468 2 10398 121268 11544 8644 6608 66668 906 16500 0 . 0 . 0 92 0,0,57,21 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1032|1648|KIF14|protein_coding|CODING|NM_014875.2|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386604231,rs6665951 -0.693147 0.0719562 92 S477 619 tcA/tcG LOW 6 SILENT CODING DDX59 C protein_coding NM_001031725.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200618238 T C 0 228 0 0.9092 0.9575 0.9654 1 0.9543 0.9765 0.92374 0.949562 0.962791 2 9564 117190 11320 8654 6524 64096 888 16144 2 10400 121396 11578 8654 6614 66732 908 16510 0 . 0 . 0 53 0,0,30,17 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S477|619|DDX59|protein_coding|CODING|NM_001031725.4|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6665604 -0.693147 0.0638017 53 I107V 619 Atc/Gtc MODERATE 2 MISSENSE CODING DDX59 C protein_coding NM_001031725.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200635550 T C 0 222 0 0.1664 0.2184 0.2392 0.4365 0.0696 0.2025 0.14503 0.090266 0.0622093 1 1524 15654 3032 3509 803 4056 134 2596 2 10406 121288 11546 8600 6614 66708 904 16510 0.971974 0 . 0 . 83 22,15,20,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I107V|619|DDX59|protein_coding|CODING|NM_001031725.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995951 rs3795634 -0.693143 0.770563 83 P103 619 ccA/ccG LOW 2 SILENT CODING DDX59 C protein_coding NM_001031725.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200635560 T C 0 222 0 0.1664 0.2184 0.2392 0.4365 0.0696 0.2025 0.14503 0.090266 0.0622093 1 1522 15657 3030 3515 803 4057 134 2596 2 10402 121272 11530 8602 6614 66714 904 16506 0.829708 0 . 0 . 82 20,16,22,16 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P103|619|DDX59|protein_coding|CODING|NM_001031725.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.635804 rs3795633 -0.693143 0.532007 82 V157 1489 gtA/gtT LOW 3 SILENT CODING CAMSAP2 T protein_coding NM_001297707.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200776575 A T 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 40 1 39 0 0 0 0 2 10390 121278 11568 8654 6608 66670 908 16480 0.820971 0 . 0 . 130 48,5,45,12 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtT|V157|1489|CAMSAP2|protein_coding|CODING|NM_001297707.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.972469 rs144271144 -0.693147 0.00243152 130 D179 1489 gaC/gaT LOW 3 SILENT CODING CAMSAP2 T protein_coding NM_001297707.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200776641 C T 0 222 0 0.2216 0.2514 0.2738 0.3552 0.0994 0.3252 0.205175 0.123174 0.0811628 1 2200 21013 3688 3070 1378 5948 156 4573 2 10396 121064 11570 8632 6614 66624 908 16320 0.555693 0 . 0 . 121 21,30,27,31 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D179|1489|CAMSAP2|protein_coding|CODING|NM_001297707.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.918268 rs7552353 -0.693147 0.0161111 121 1489 1080 MODIFIER 18 CODING CAMSAP2 T protein_coding NM_001297707.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200828267 A T 0 222 0 0.4713 0.4247 0.4179 0.5347 0.2376 0.4458 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.818973 0 . 0 . 127 47,11,39,17 UTR_3_PRIME(MODIFIER||1080||1489|CAMSAP2|protein_coding|CODING|NM_001297707.1|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.961405 rs7520696 -0.693147 0.199381 127 1489 1765 MODIFIER 18 CODING CAMSAP2 A protein_coding NM_001297707.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200828952 G A 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1765||1489|CAMSAP2|protein_coding|CODING|NM_001297707.1|18|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs192335434 -0.379885 0 1 P87 677 ccC/ccG LOW 2 SILENT CODING C1orf106 G protein_coding NM_018265.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200867492 C G 0 222 0 0.115 0.1983 0.3112 0.1577 0.2495 0.2198 0.155016 0.208212 0.235465 1 1509 28251 3831 1397 1557 15988 234 3735 2 10406 121388 11576 8648 6614 66726 908 16510 0.984286 0 . 0 . 158 47,24,45,29 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P87|677|C1orf106|protein_coding|CODING|NM_018265.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.245892 rs2271018 -0.693147 0.000351927 158 S107 677 agC/agT LOW 2 SILENT CODING C1orf106 T protein_coding NM_018265.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200867552 C T 0 222 0 0.0174 0.0515 0.0159 0.1478 0.0378 0.0378 0.0190649 0.031447 0.0377907 1 197 5205 182 1181 249 2643 28 725 2 10406 121324 11578 8644 6614 66684 908 16490 0.650205 0 . 0 COSM146723 157 52,31,33,28 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S107|677|C1orf106|protein_coding|CODING|NM_018265.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.545045 rs2271017 -0.693147 0.346466 157 R515S 677 agA/agC MODERATE 9 MISSENSE CODING C1orf106 C protein_coding NM_018265.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200880869 A C 0 222 0 0.0091 0.0595 0.0461 0.1091 0.1054 0.0389 0.0256585 0.0848723 0.115223 1 229 11595 464 977 1116 7880 85 844 2 9674 117832 11492 8570 6552 64550 882 16112 0.822079 0 . 0 COSM1337743 112 11,45,14,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R515S|677|C1orf106|protein_coding|CODING|NM_018265.3|9|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.935507 0.834793 0 0.751222 rs45547233 -0.693147 0.140932 112 R552C 677 Cgc/Tgc MODERATE 9 MISSENSE CODING C1orf106 T protein_coding NM_018265.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200880978 C T 0 228 0 0.6089 0.7919 0.8213 0.997 0.7256 0.8753 0.628889 0.678286 0.703475 2 4031 68735 7735 6129 3239 34851 498 12252 2 6446 89852 8846 6154 4162 49016 628 14600 0 . 0 . 0 33 0,0,7,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R552C|677|C1orf106|protein_coding|CODING|NM_018265.3|9|T) 1 0 . 0 . 1 0 1 1 0 55 0 0 0.333737 0 . rs296520 -0.69312 0.256212 33 R616 677 cgC/cgA LOW 9 SILENT CODING C1orf106 A protein_coding NM_018265.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200881172 C A 0 222 0 0.0923 0.3259 0.5432 0.2688 0.5298 0.3364 0 . 0 1 143 5618 125 87 1 2174 77 3011 2 628 12582 232 270 2 3984 142 7324 0.563601 0 . 0 . 46 14,4,17,8 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R616|677|C1orf106|protein_coding|CODING|NM_018265.3|9|A) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.950077 0.0025824 0 0.754354 rs296521 -0.692914 0.527601 46 677 91 MODIFIER 10 CODING C1orf106 G protein_coding NM_018265.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200882848 C G 0 222 0 0.0008 0.023 0.1081 0.0357 0.003 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996287 0 . 0 . 74 16,20,15,20 UTR_3_PRIME(MODIFIER||91||677|C1orf106|protein_coding|CODING|NM_018265.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 41 0 0.696164 0.0906631 0 0.932526 rs146611802 -0.693136 0.274428 74 677 159 MODIFIER 10 CODING C1orf106 A protein_coding NM_018265.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200882916 G A 0 122 0 0.0227 0.0599 0.0461 0.0992 0.0994 0.0389 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.929717 0 . 0 . 41 13,11,10,3 UTR_3_PRIME(MODIFIER||159||677|C1orf106|protein_coding|CODING|NM_018265.3|10|A) 0 0.5 1 0 . 1 0 . 0 . 39 0 0.728844 0.605243 0 0.978845 rs113596582,rs139127452 -0.683931 0.534909 41 677 173 MODIFIER 10 CODING C1orf106 T protein_coding NM_018265.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200882930 A T 0 187 0 0.0234 0.0601 0.0461 0.0992 0.0994 0.0389 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924152 0 . 0 . 42 10,15,8,9 UTR_3_PRIME(MODIFIER||173||677|C1orf106|protein_coding|CODING|NM_018265.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 41 0 0.893717 0.271877 0 0.101357 rs112931859,rs141450714 -0.690438 0.411493 42 677 948 MODIFIER 10 CODING C1orf106 T protein_coding NM_018265.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200883705 C T 0 4.9 0 0.1611 0.3518 0.5605 0.2728 0.5268 0.363 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||948||677|C1orf106|protein_coding|CODING|NM_018265.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 31 0 0 . 0 . rs199579810,rs296524 -0.379885 0 1 1637 3043 MODIFIER 35 CODING KIF21B A protein_coding NM_001252100.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200940180 G A 0 222 0 0.1014 0.2915 0.4179 0.2361 0.3529 0.453 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.939299 0 . 0 . 106 29,29,21,15 UTR_3_PRIME(MODIFIER||3043||1637|KIF21B|protein_coding|CODING|NM_001252100.1|35|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.990779 rs3198583 -0.693139 0.0101864 106 1637 1674 MODIFIER 35 CODING KIF21B C protein_coding NM_001252100.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200941549 T C 0 132 0 0.9486 0.9243 0.9568 0.7937 0.9891 0.9366 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||1674||1637|KIF21B|protein_coding|CODING|NM_001252100.1|35|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs296570 -0.616816 0.149847 6 1637 1507 MODIFIER 35 CODING KIF21B A protein_coding NM_001252100.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200941716 G A 0 222 0 0.1014 0.2895 0.415 0.2371 0.3479 0.4489 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.122407 0 . 0 . 119 39,6,45,8 UTR_3_PRIME(MODIFIER||1507||1637|KIF21B|protein_coding|CODING|NM_001252100.1|35|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999232 rs3738255 -0.693147 0.162858 119 A1150 1637 gcT/gcC LOW 25 SILENT CODING KIF21B G protein_coding NM_001252100.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200956288 A G 0 163 0 0.4531 0.262 0.2032 0.2897 0.1541 0.1278 0.42374 0.261802 0.178837 1 4429 24471 2059 2542 1520 11985 158 1778 2 10232 120524 11532 8620 6612 66234 898 16396 0.999286 0 . 0 . 34 0,10,1,23 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1150|1637|KIF21B|protein_coding|CODING|NM_001252100.1|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943785 rs2275485 -0.692831 0.334657 34 D998 1637 gaC/gaT LOW 20 SILENT CODING KIF21B A protein_coding NM_001252100.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200959302 G A 0 222 0 0.4531 0.2638 0.2032 0.2976 0.1541 0.1288 0.423059 0.261341 0.178488 1 4465 24615 2063 2633 1521 11993 158 1782 2 10396 121106 11572 8622 6612 66602 904 16398 0.182064 0 . 0 . 92 21,22,21,26 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D998|1637|KIF21B|protein_coding|CODING|NM_001252100.1|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992686 rs2297911 -0.693147 0.203517 92 1637 64 MODIFIER 1 CODING KIF21B A protein_coding NM_001252100.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 200992575 G A 0 54 0 0.0862 0.0749 0.0476 0.1379 0.005 0.0859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.50373 0 . 0 . 13 0,8,0,5 UTR_5_PRIME(MODIFIER||64||1637|KIF21B|protein_coding|CODING|NM_001252100.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.41985 rs10920096 -0.590765 0.471814 13 L1800S 1873 tTg/tCg MODERATE 44 MISSENSE CODING CACNA1S G protein_coding NM_000069.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201009182 A G 0 222 0 0.6059 0.2292 0.1023 0.1091 0.1054 0.0613 0.541307 0.269799 0.130698 1 5783 18783 963 1089 928 8745 122 1153 2 10388 121260 11574 8626 6614 66638 908 16512 0.560753 0 . 0 . 80 25,13,28,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L1800S|1873|CACNA1S|protein_coding|CODING|NM_000069.2|44|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0850554 rs12139527 -0.693141 0.0718452 80 1873 LOW 37 CODING CACNA1S T protein_coding NM_000069.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201016646 C T 0 222 0 0.3971 0.1719 0.0951 0.1141 0.1034 0.0521 0.360191 0.205213 0.125814 1 3785 16117 803 1156 923 8312 113 1025 2 10254 119840 11336 8576 6532 66086 896 16160 0.598773 0 . 0 . 83 26,16,22,13 SPLICE_SITE_REGION+INTRON(LOW||||1873|CACNA1S|protein_coding|CODING|NM_000069.2|37|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958387 rs2297905 -0.693136 0.845903 83 1873 LOW 33 CODING CACNA1S G protein_coding NM_000069.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201020105 A G 0 228 0 0.9735 0.8804 0.8213 0.9931 0.67 0.8967 0.923286 0.754805 0.668488 2 9713 93540 10237 8606 5087 44889 713 14295 2 10406 121404 11578 8652 6614 66734 908 16512 0 2 benign 0 . 129 0,0,88,31 SPLICE_SITE_REGION+INTRON(LOW||||1873|CACNA1S|protein_coding|CODING|NM_000069.2|33|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6702590 -0.693147 0.0691803 129 1873 LOW 12 CODING CACNA1S G protein_coding NM_000069.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201044748 A G 0 228 0 0.4955 0.7596 0.7536 0.9643 0.7604 0.909 0.559464 0.703291 0.776977 2 5685 94858 8310 8282 5185 51943 708 14745 2 10402 121400 11574 8654 6612 66740 906 16512 0 . 0 . 0 119 0,0,40,71 SPLICE_SITE_REGION+INTRON(LOW||||1873|CACNA1S|protein_coding|CODING|NM_000069.2|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1998721 -0.693147 0.0012685 119 G517 1873 ggT/ggC LOW 11 SILENT CODING CACNA1S G protein_coding NM_000069.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201047075 A G 0 222 0 0.9433 0.5711 0.6484 0.2302 0.6571 0.2761 0.883568 0.736045 0.660465 1 9332 70806 6605 1933 3519 43681 506 5230 2 10404 121258 11560 8612 6606 66658 908 16510 0.424865 0 . 0 . 145 45,20,42,23 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G517|1873|CACNA1S|protein_coding|CODING|NM_000069.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.941606 rs4915477 -0.693147 0.0523246 145 N497 1873 aaC/aaT LOW 11 SILENT CODING CACNA1S A protein_coding NM_000069.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201047135 G A 0 222 0 0.1664 0.122 0.1282 0.1944 0.0646 0.0419 0.152065 0.0844226 0.0497674 1 1605 10292 1614 1539 644 3835 76 979 2 10406 121370 11570 8636 6614 66724 908 16512 0.991139 0 . 0 . 165 42,30,46,22 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N497|1873|CACNA1S|protein_coding|CODING|NM_000069.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.902743 rs16847674 -0.693147 0.269029 165 1873 LOW 10 CODING CACNA1S A protein_coding NM_000069.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201052283 G A 0 222 0 0.0015 0.0551 0.085 0.1796 0.0179 0.0164 0.00567408 0.0152237 0.0201163 1 64 4841 1306 1438 266 1395 37 335 2 10196 119232 11372 8560 6236 65666 882 16320 0.965073 0 . 0 . 82 37,3,26,5 SPLICE_SITE_REGION+INTRON(LOW||||1873|CACNA1S|protein_coding|CODING|NM_000069.2|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.946876 rs3767512,rs386585875 -0.69311 0.744031 82 I199 1873 atC/atT LOW 5 SILENT CODING CACNA1S A protein_coding NM_000069.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201060865 G A 0 222 0 0.0522 0.3051 0.3963 0.3929 0.4105 0.3834 0.111212 0.329771 0.441744 1 1066 47024 4083 3084 2425 28627 345 7394 2 10356 120988 11528 8596 6592 66514 902 16500 0.903159 0 . 0 . 80 25,15,14,21 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I199|1873|CACNA1S|protein_coding|CODING|NM_000069.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.813504 rs2296383 -0.693136 0.105132 80 206 537 MODIFIER 1 CODING ASCL5 G protein_coding NM_001270601.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201083343 A G 0 46.3 0 0.8275 0.639 0.5418 0.7728 0.4105 0.5501 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||537||206|ASCL5|protein_coding|CODING|NM_001270601.1|1|G),UPSTREAM(MODIFIER||1649||1873|CACNA1S|protein_coding|CODING|NM_000069.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3738262 -0.453602 0.14 2 Y147 208 taT/taC LOW 5 SILENT CODING TMEM9 G protein_coding NM_001288571.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201112981 A G 0 228 0 0.6362 0.6931 0.7133 0.626 0.7644 0.7515 0.660463 0.732047 0.768721 2 6806 90710 8712 5431 5206 51578 652 12325 2 10388 121254 11552 8632 6602 66666 904 16510 0 . 0 . COSM146726 95 0,0,56,36 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y147|208|TMEM9|protein_coding|CODING|NM_001288571.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8158 -0.693147 0.785936 95 T35 208 acA/acC LOW 2 SILENT CODING TMEM9 G protein_coding NM_001288571.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201122947 T G 0 228 0 0.9455 0.9395 0.9625 0.875 0.9543 0.9663 0.938947 0.947563 0.951977 2 9460 111322 10594 7290 6009 61678 807 15484 2 10044 117894 11278 8376 6442 64860 864 16030 1 0 . 0 . 114 0,1,53,53 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T35|208|TMEM9|protein_coding|CODING|NM_001288571.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1925361 -0.693147 0.0022908 114 R102H 3708 cGc/cAc MODERATE 5 MISSENSE CODING IGFN1 A protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201166383 G A 0 228 0 0.8101 0.7326 0.5735 0.8562 0.5547 0.7965 0.769509 0.630092 0.569453 2 1689 14454 246 525 885 5044 171 5894 2 2176 21466 410 622 1380 8728 236 7914 1 0 . 0 . 136 0,1,50,72 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R102H|3708|IGFN1|protein_coding|CODING|NM_001164586.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4915221 -0.693147 0.0974121 136 T119 3708 acT/acC LOW 5 SILENT CODING IGFN1 C protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201166435 T C 0 228 0 0.8623 0.8676 0.7939 0.8552 0.9364 0.8691 0.856936 0.905388 0.926461 2 1860 19171 348 525 1249 8017 212 6960 2 2172 21404 410 624 1320 8732 232 7914 0 . 0 . 0 112 0,0,35,70 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T119|3708|IGFN1|protein_coding|CODING|NM_001164586.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11589317 -0.693147 8.5259e-05 112 P135 3708 ccG/ccA LOW 6 SILENT CODING IGFN1 A protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201168499 G A 0 228 0 0.1498 0.1985 0.2075 0.256 0.1501 0.2485 0.132948 0.140385 0.14362 2 314 4410 97 151 159 1686 51 1952 2 2312 22636 426 624 1666 9442 252 7914 1 0 . 0 . 83 0,1,23,55 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P135|3708|IGFN1|protein_coding|CODING|NM_001164586.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1534057 -0.693147 0.784502 83 3708 LOW 10 CODING IGFN1 T protein_coding NM_001164586.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201174204 C T 0 222 0 0.0113 0.155 0.1787 0.2639 0.2545 0.1176 0.0470333 0.168276 0.221033 1 88 3381 80 162 369 1790 50 842 2 1480 14848 358 576 1606 6542 190 4096 0.996124 0 . 0 . 91 32,10,27,13 SPLICE_SITE_REGION+INTRON(LOW||||3708|IGFN1|protein_coding|CODING|NM_001164586.1|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.636306 rs12725611 -0.693145 0.26249 91 D402E 3708 gaC/gaA MODERATE 12 MISSENSE CODING IGFN1 A protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201175227 C A 0 222 0 0.8775 0.763 0.745 0.6687 0.7217 0.7607 0.836705 0.750548 0.713074 1 1753 15690 300 421 1011 6082 159 5964 2 2052 20992 406 608 1506 8288 226 7906 0.997598 0 . 0 . 75 20,17,14,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D402E|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.813217 rs386616758,rs832156 -0.693097 0.376849 75 Q418R 3708 cAg/cGg MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201175274 A G 0 228 0 0.1467 0.3758 0.4063 0.5903 0.4821 0.3333 0.20159 0.384363 0.463859 2 416 8500 179 360 783 3870 111 2781 2 2060 21078 408 622 1388 8464 230 7906 0 . 0 . 0 45 0,0,20,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q418R|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9651057 -0.693146 0.13795 45 R565L 3708 cGg/cTg MODERATE 12 MISSENSE CODING IGFN1 T protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201175715 G T 0 222 0 0.8775 0.764 0.745 0.6736 0.7217 0.7607 0.837428 0.750109 0.712131 1 1758 14491 261 366 27 6009 133 5937 2 2082 19284 352 508 50 8230 186 7876 0.953227 0 . 0 . 105 34,18,25,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R565L|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.553772 rs1341631 -0.693145 0.119405 105 D666G 3708 gAc/gGc MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201176018 A G 0 222 0 0.8775 0.7638 0.7464 0.6716 0.7217 0.7607 0.837428 0.750986 0.713388 1 1535 13098 224 239 9 5094 121 5876 2 1824 17430 304 342 12 7016 170 7762 0.976129 0 . 0 . 65 27,6,16,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D666G|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414719 rs10753895 -0.692914 0.0626649 65 G1589 3708 ggA/ggG LOW 12 SILENT CODING IGFN1 G protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201178788 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 347 2302 21 14 8 1056 18 838 2 730 4978 46 54 16 2338 40 1754 0.819277 0 . 0 . 385 108,117,60,44 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G1589|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.000474334 0.0835849 0 0.0724471 rs66922684 -0.693147 4.03872e-11 385 E1628G 3708 gAa/gGa MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201178904 A G 0 28.3 0 . 0 . 0 . 0 . 0 . 1 23 831 14 21 0 277 6 490 2 570 6050 84 90 2 2264 58 2982 0.919201 0 . 0 . 236 55,97,41,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E1628G|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 0 . 0 1 0 53 0 2.57035e-15 4.144e-06 0 3.20153e-16 rs201227267 -0.693147 5.33042e-09 236 K1635E 3708 Aag/Gag MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201178924 A G 0 206 0 0.444 0.4419 0.4222 0.4544 0.4225 0.4601 0 . 0 1 20 687 13 13 0 201 5 435 2 374 4852 78 74 2 1696 50 2578 0.910672 0 . 0 . 229 41,79,70,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K1635E|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 1 0 . 1 0 51 0 3.5577e-12 1.33533e-05 0 1.13186e-19 rs6678538 -0.693147 4.79924e-08 229 K1635 3708 aaG/aaA LOW 12 SILENT CODING IGFN1 A protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201178926 G A 0 193 0 0.444 0.4423 0.4222 0.4554 0.4225 0.4611 0 . 0 1 20 685 13 13 0 199 5 435 2 300 3926 62 56 2 1452 42 2012 0.651063 0 . 0 . 225 44,76,69,9 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1635|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|A) 0 0.5 1 0 . 1 0 . 1 0 51 0 2.78438e-12 4.76602e-05 0 3.63838e-19 rs6702960 -0.693147 1.35353e-08 225 I1648M 3708 atA/atG MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201178965 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 326 3037 44 47 2 1208 26 1384 2 666 6212 90 96 4 2484 52 2820 0.787252 0 . 0 . 295 78,33,75,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I1648M|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 0 . 0 1 0 48 0 3.05232e-06 0.0321371 0 0.048252 rs12758143 -0.693147 0.862947 295 N1677D 3708 Aat/Gat MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201179050 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 136 1106 38 54 0 735 12 131 2 882 11244 140 214 0 4380 102 5526 0.189843 0 . 0 . 277 104,52,25,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N1677D|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 0 . 0 1 0 52 0 1.54279e-15 0.599759 0 1.24972e-05 rs1722732 -0.693147 2.40223e-08 277 G1683R 3708 Gga/Aga MODERATE 12 MISSENSE CODING IGFN1 A protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201179068 G A 0 75 0 . 0 . 0 . 0 . 0 . 1 126 1099 40 54 0 735 11 133 2 1142 14026 220 248 2 5204 130 7080 0.674547 0 . 0 . 271 123,56,9,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G1683R|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|A) 0 0.5 1 0 . 0 . 0 1 0 52 0 9.58275e-08 0.941648 0 0.00162847 rs199816935 -0.693147 0.0785282 271 A1860P 3708 Gct/Cct MODERATE 12 MISSENSE CODING IGFN1 C protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201179599 G C 0 180 0 0.0741 0.1392 0.1527 0.2004 0.1769 0.1155 0 . 0 1 38 479 19 30 1 300 4 87 2 402 2332 110 102 4 1226 26 462 0.0199835 0 . 0 . 41 7,12,10,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A1860P|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|C) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.916227 0.00322541 0 0.994547 rs12021954 -0.692562 0.609594 41 E2042K 3708 Gag/Aag MODERATE 12 MISSENSE CODING IGFN1 A protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201180145 G A 0 222 0 0.4418 0.4171 0.402 0.3601 0.3976 0.4734 0 . 0 1 311 3674 76 89 2 1469 40 1687 2 914 10106 180 208 4 3962 106 4732 0.953428 0 . 0 . 197 102,10,12,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2042K|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|A) 0 0.5 1 0 . 1 0 . 1 0 51 0 0.478352 0.731009 0 3.25011e-17 rs12022767 -0.693147 7.21785e-15 197 R2043G 3708 Aga/Gga MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201180148 A G 0 222 0 0.4433 0.4193 0.4035 0.3661 0.3996 0.4734 0 . 0 1 303 3573 77 85 2 1424 40 1642 2 1048 11112 186 214 4 4402 118 5140 0.82052 0 . 0 COSM1626736 207 109,10,13,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R2043G|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.421945 0.598181 0 3.86005e-18 rs145517342 -0.693147 4.26024e-15 207 I2044M 3708 atA/atG MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201180153 A G 0 192 0 . 0 . 0 . 0 . 0 . 1 298 3351 74 84 2 1347 39 1507 2 1022 12620 202 226 4 4710 136 6320 0.963865 0 . 0 . 219 123,9,12,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I2044M|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 0 0.5 1 0 . 0 . 0 1 0 52 0 0.437751 0.61043 0 2.63926e-19 rs12029808 -0.693147 4.92183e-17 219 G2047 3708 ggA/ggC LOW 12 SILENT CODING IGFN1 C protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201180162 A C 0 135 0 0.3313 0.3077 0.3012 0.2173 0.2604 0.4223 0 . 0 1 270 2918 66 72 2 1195 37 1276 2 924 13104 204 226 4 4696 136 6914 0.629489 0 . 0 . 236 135,9,12,42 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G2047|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|C) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.176333 0.15701 0 2.35014e-16 rs12029809 -0.693147 1.05426e-15 236 G2051S 3708 Ggt/Agt MODERATE 12 MISSENSE CODING IGFN1 A protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201180172 G A 0 8.7 0 . 0 . 0 . 0 . 0 . 1 220 1481 51 50 2 774 19 365 2 880 13418 204 224 4 4706 138 7262 0.0647613 0 . 0 . 243 147,17,6,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G2051S|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|A) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.104543 0.00419936 0 2.20813e-12 rs12022770,rs201264013 -0.693146 1.48866e-06 243 N2401S 3708 aAc/aGc MODERATE 12 MISSENSE CODING IGFN1 G protein_coding NM_001164586.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201181223 A G 0 228 0 0.9947 0.998 0.9971 1 0.999 1 0.986272 0.994744 0.998429 2 1801 17552 304 336 14 7062 167 7868 2 1824 17608 304 336 14 7094 168 7868 0 . 0 . 0 78 0,0,20,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N2401S|3708|IGFN1|protein_coding|CODING|NM_001164586.1|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12070919 -0.693147 0.00943714 78 A3292 3708 gcT/gcC LOW 18 SILENT CODING IGFN1 C protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201187764 T C 0 228 0 0.9592 0.9297 0.8501 0.998 0.8946 0.9121 0.949841 0.901276 0.876395 2 9832 107281 9308 8618 6074 58274 793 14382 2 10308 120318 11424 8624 6464 66214 900 16384 0 . 0 . 0 124 0,0,59,46 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A3292|3708|IGFN1|protein_coding|CODING|NM_001164586.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10920144 -0.693147 0.946524 124 V3353 3708 gtG/gtA LOW 19 SILENT CODING IGFN1 A protein_coding NM_001164586.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201190732 G A 0 222 0 0.1135 0.2206 0.2464 0.255 0.2694 0.2618 0.150477 0.233431 0.27593 1 1478 31501 3005 2063 2152 18287 226 4290 2 10266 120348 11480 8606 6434 66194 890 16478 0.57479 0 . 0 COSM424997,COSM424996 138 40,26,40,14 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V3353|3708|IGFN1|protein_coding|CODING|NM_001164586.1|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999875 rs3738269 -0.693147 0.105958 138 747 130 MODIFIER 1 CODING PKP1 T protein_coding NM_000299.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201252701 A T 0 208 0 0.0825 0.6136 0.7378 0.9127 0.7893 0.7546 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,11,1 UTR_5_PRIME(MODIFIER||130||747|PKP1|protein_coding|CODING|NM_000299.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs861275 -0.680642 0.419124 13 K260 747 aaA/aaG LOW 4 SILENT CODING PKP1 G protein_coding NM_000299.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201285759 A G 0 228 0 0.8926 0.9694 0.9885 1 1 0.9969 0.907172 0.966554 0.996977 2 9265 119076 11379 8636 6552 66208 889 16147 2 10234 120372 11424 8636 6552 66378 898 16250 0 . 0 . 0 51 0,0,25,23 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K260|747|PKP1|protein_coding|CODING|NM_000299.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1779297 -0.693147 0.00576039 51 747 1506 MODIFIER 15 CODING PKP1 C protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201299470 A C 0 64 0 0.1959 0.6719 0.8285 0.9375 0.837 0.7607 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||1506||747|PKP1|protein_coding|CODING|NM_000299.3|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs947376 -0.511536 0.37344 3 747 1784 MODIFIER 15 CODING PKP1 A protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201299748 G A 0 39.3 0 0.1884 0.6294 0.7795 0.871 0.7972 0.6973 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1784||747|PKP1|protein_coding|CODING|NM_000299.3|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10920174 -0.453602 0.26 2 747 2878 MODIFIER 15 CODING PKP1 C protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201300842 T C 0 9.7 0 0.8041 0.9042 0.938 0.9335 0.9553 0.9325 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2878||747|PKP1|protein_coding|CODING|NM_000299.3|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10920175 -0.379885 0 1 747 2894 MODIFIER 15 CODING PKP1 A protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201300858 C A 0 6.3 0 0.8116 0.9467 0.9841 1 0.994 0.999 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2894||747|PKP1|protein_coding|CODING|NM_000299.3|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10800772 -0.379885 0 1 747 3909 MODIFIER 15 CODING PKP1 G protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201301873 A G 0 9.7 0 0.7852 0.8423 0.8473 0.8631 0.8211 0.9162 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3909||747|PKP1|protein_coding|CODING|NM_000299.3|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1046962 -0.379885 0 1 747 3942 MODIFIER 15 CODING PKP1 G protein_coding NM_000299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201301906 C G 0 46.3 0 0.8616 0.8642 0.8588 0.8611 0.8241 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3942||747|PKP1|protein_coding|CODING|NM_000299.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046970 -0.453602 0.74 2 I116 298 atC/atT LOW 10 SILENT CODING TNNT2 A protein_coding NM_001276345.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201334382 G A 0 222 0 0.6293 0.6951 0.7997 0.5268 0.7416 0.8354 0.613255 0.682762 0.718372 1 6496 87325 8904 4730 5272 47699 706 13518 2 10406 121386 11578 8632 6614 66736 908 16512 0.859923 2|2 benign|benign 0 COSM1337831 104 19,31,14,35 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I116|298|TNNT2|protein_coding|CODING|NM_001276345.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999388 rs3729547 -0.693147 0.0769909 104 K323E 517 Aag/Gag MODERATE 3 MISSENSE CODING LAD1 C protein_coding NM_005558.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201355522 T C 0 228 0 0.8775 0.5531 0.3847 0.5188 0.4612 0.364 0.802135 0.595293 0.489419 2 8015 51626 3539 4085 2957 29377 342 3311 2 9746 98722 9778 7588 5800 57052 668 8090 0.95 0 . 0 . 92 1,1,54,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K323E|517|LAD1|protein_coding|CODING|NM_005558.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.7375 rs386591087,rs4128458 -0.693147 0.122259 92 P279Q 517 cCg/cAg MODERATE 3 MISSENSE CODING LAD1 T protein_coding NM_005558.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201355653 G T 0 222 0 0.2466 0.0869 0.0389 0.0377 0.0288 0.0153 0.21902 0.0933415 0.0289535 1 2339 5434 236 208 224 1929 41 457 2 10110 115038 11528 8630 6614 65062 858 12236 0.629711 0 . 0 . 65 14,25,15,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cAg|P279Q|517|LAD1|protein_coding|CODING|NM_005558.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890811 rs11805972 -0.692717 0.291935 65 L243P 517 cTg/cCg MODERATE 3 MISSENSE CODING LAD1 G protein_coding NM_005558.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201355761 A G 0 222 0 0.3729 0.1212 0.0447 0.0387 0.0288 0.0153 0.330005 0.131093 0.029186 1 3458 6699 292 211 224 1966 46 502 2 10158 120966 11576 8654 6614 66546 906 16512 0.914217 0 . 0 . 61 14,16,10,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L243P|517|LAD1|protein_coding|CODING|NM_005558.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994619 rs12088790 -0.693021 0.213013 61 K182 517 aaG/aaA LOW 3 SILENT CODING LAD1 T protein_coding NM_005558.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201355943 C T 0 228 0 0.7474 0.5176 0.3775 0.5179 0.4622 0.363 0.690422 0.556743 0.488256 2 7342 58341 3775 4443 3211 32850 426 6294 2 10348 121200 11576 8642 6614 66608 908 16504 0 . 0 . 0 39 0,0,15,21 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K182|517|LAD1|protein_coding|CODING|NM_005558.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2799677 -0.693139 0.184696 39 517 30 MODIFIER 1 CODING LAD1 GT protein_coding NM_005558.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201368463 G GT 0 33.4 0 . 0 . 0 . 0 0.0941846 0.230068 0.283649 1 23 1931 22 48 1 875 21 941 2 232 10964 110 184 2 2986 122 7328 0 . 0 . 0 10 4,0,5,0 UTR_5_PRIME(MODIFIER||30||517|LAD1|protein_coding|CODING|NM_005558.3|1|GT),DOWNSTREAM(MODIFIER||4431||187|TNNI1|protein_coding|CODING|NM_003281.3||GT) 1 0.5 1 5 0.5 0 1 1 1 0 60 0 0 . 0 . rs28364652 -0.590765 0.211211 10 187 5233 MODIFIER 8 CODING TNNI1 A protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201374223 C A 0 102 0 0.0522 0.0495 0.0043 0.1508 0.001 0.0235 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.875173 0 . 0 . 14 6,0,8,0 UTR_3_PRIME(MODIFIER||5233||187|TNNI1|protein_coding|CODING|NM_003281.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs77176971 -0.651104 0.424295 14 187 4803 MODIFIER 8 CODING TNNI1 T protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201374653 C T 0 228 0 0.5696 0.4329 0.3401 0.4663 0.3946 0.319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.88456 0 . 0 . 341 2,2,148,145 UTR_3_PRIME(MODIFIER||4803||187|TNNI1|protein_coding|CODING|NM_003281.3|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.940028 rs1256944 -0.693147 1.56243e-05 341 187 4779 MODIFIER 8 CODING TNNI1 C protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201374677 A C 0 228 0 0.6952 0.4758 0.3631 0.4702 0.4135 0.3292 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.420759 0 . 0 . 328 3,2,145,144 UTR_3_PRIME(MODIFIER||4779||187|TNNI1|protein_coding|CODING|NM_003281.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.351626 rs2799680,rs386573961 -0.693147 0.00697947 328 187 4069 MODIFIER 8 CODING TNNI1 T protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201375370 TCCTCATCTGTAAATTTG T 0 32.2 0 0.5908 0.4477 0.3573 0.4752 0.4125 0.3262 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4069||187|TNNI1|protein_coding|CODING|NM_003281.3|8|T) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs142666675 -0.379885 0 1 187 3798 MODIFIER 8 CODING TNNI1 G protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201375658 A G 0 39.3 0 0.6944 0.4758 0.3617 0.4762 0.4125 0.3262 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3798||187|TNNI1|protein_coding|CODING|NM_003281.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1256945 -0.453602 0.1 2 187 3705 MODIFIER 8 CODING TNNI1 C protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201375751 T C 0 70 0 0.6944 0.4788 0.3602 0.4911 0.4125 0.3272 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||3705||187|TNNI1|protein_coding|CODING|NM_003281.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1256946 -0.453602 0.48 3 187 3643 MODIFIER 8 CODING TNNI1 G protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201375813 A G 0 39.3 0 0.6944 0.4756 0.3617 0.4752 0.4125 0.3262 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3643||187|TNNI1|protein_coding|CODING|NM_003281.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1256947 -0.453602 0.06 2 187 3195 MODIFIER 8 CODING TNNI1 G protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201376261 A G 0 9.7 0 0.7617 0.5008 0.3732 0.4752 0.4254 0.3425 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3195||187|TNNI1|protein_coding|CODING|NM_003281.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1256948,rs386524969 -0.379885 0 1 187 2907 MODIFIER 8 CODING TNNI1 A protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201376549 G A 0 32.6 0 0.0008 0.0214 0.0144 0.0694 0.0179 0.0082 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2907||187|TNNI1|protein_coding|CODING|NM_003281.3|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs41270951 -0.379885 0 2 187 2018 MODIFIER 8 CODING TNNI1 G protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201377438 A G 0 131 0 0.6225 0.7458 0.7017 0.7996 0.8658 0.7648 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,2 UTR_3_PRIME(MODIFIER||2018||187|TNNI1|protein_coding|CODING|NM_003281.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1262295 -0.556411 0.740842 5 187 1571 MODIFIER 8 CODING TNNI1 A protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201377885 G A 0 31.3 0 0.4667 0.5731 0.5476 0.6518 0.6163 0.6094 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1571||187|TNNI1|protein_coding|CODING|NM_003281.3|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4915521 -0.453602 0.1 2 187 1562 MODIFIER 8 CODING TNNI1 T protein_coding NM_003281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201377894 A T 0 46.3 0 0.4667 0.5781 0.5749 0.6567 0.6173 0.6094 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1562||187|TNNI1|protein_coding|CODING|NM_003281.3|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4915522 -0.453602 0.1 2 187 LOW 4 CODING TNNI1 C protein_coding NM_003281.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201383643 A C 0 222 0 0.7277 0.7782 0.853 0.7222 0.8618 0.7648 0.757039 0.820939 0.853715 1 6102 82361 8138 5290 4021 47188 604 11018 2 7942 96882 9038 6918 4712 54046 716 13510 0.913216 0 . 0 . 127 19,51,14,32 SPLICE_SITE_REGION+INTRON(LOW||||187|TNNI1|protein_coding|CODING|NM_003281.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.717099 rs2026594 -0.693147 0.81107 127 127 54 MODIFIER 1 CODING PHLDA3 T protein_coding NM_012396.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201437477 A T 0 222 0 0.2625 0.3818 0.3818 0.6786 0.2356 0.3875 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.937727 0 . 0 . 127 51,9,41,7 UTR_3_PRIME(MODIFIER||54||127|PHLDA3|protein_coding|CODING|NM_012396.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.91895 rs1256930 -0.693147 0.0142825 127 193 552 MODIFIER 6 CODING CSRP1 C protein_coding NM_001193571.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201453289 T C 0 9.7 0 0.8858 0.8646 0.9251 0.8185 0.8907 0.8139 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||552||193|CSRP1|protein_coding|CODING|NM_001193571.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs576697 -0.379885 0 1 S1273L 1877 tCg/tTg MODERATE 18 MISSENSE CODING NAV1 T protein_coding NM_020443.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201777250 C T 0 222 0 0.0023 0.0857 0.1398 0.1756 0.0636 0.09 0.0179301 0.0546671 0.0734884 1 147 10079 1743 1640 293 4625 69 1562 2 10406 121368 11578 8638 6614 66716 908 16508 0.957449 0 . 0 . 124 25,31,29,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S1273L|1877|NAV1|protein_coding|CODING|NM_020443.4|18|T),INTRAGENIC(MODIFIER|||||IPO9-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.730045 rs2820289 -0.693147 0.0741097 124 H1290D 1877 Cac/Gac MODERATE 19 MISSENSE CODING NAV1 G protein_coding NM_020443.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201777568 C G 0 184 0 0 0.0567 0.0058 0.248 0.005 0.0256 0.00181571 0.00276795 0.00325581 1 21 3172 93 2092 189 384 27 366 2 10342 119498 11510 8564 6594 66050 896 15542 0.999357 0 . 0 COSM146729 67 32,5,22,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H1290D|1877|NAV1|protein_coding|CODING|NM_020443.4|19|G),INTRAGENIC(MODIFIER|||||IPO9-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.871823 rs2292822 -0.692914 0.246822 67 1877 1210 MODIFIER 30 CODING NAV1 G protein_coding NM_020443.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201790270 A G 0 222 0 0.5038 0.3385 0.2032 0.3552 0.3111 0.2219 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.657545 0 . 0 . 64 32,2,16,8 UTR_3_PRIME(MODIFIER||1210||1877|NAV1|protein_coding|CODING|NM_020443.4|30|G),INTRAGENIC(MODIFIER|||||IPO9-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.785625 rs1022361,rs386511158 -0.692831 0.0268224 64 1877 4704 MODIFIER 30 CODING NAV1 A protein_coding NM_020443.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201793764 G A 0 9.7 0 0.9395 0.9836 0.9971 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4704||1877|NAV1|protein_coding|CODING|NM_020443.4|30|A),UPSTREAM(MODIFIER||4524||1041|IPO9|protein_coding|CODING|NM_018085.4||A),INTRAGENIC(MODIFIER|||||IPO9-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1517811 -0.379885 0 1 1041 1305 MODIFIER 24 CODING IPO9 A protein_coding NM_018085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201846487 G A 0 59 0 0.1165 0.106 0.0288 0.2669 0.0189 0.0706 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,2,1 UTR_3_PRIME(MODIFIER||1305||1041|IPO9|protein_coding|CODING|NM_018085.4|24|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12023470 -0.511536 0.121629 4 1041 7983 MODIFIER 24 CODING IPO9 T protein_coding NM_018085.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201853165 G T 0 39.3 0 0.1286 0.2957 0.3919 0.4206 0.3648 0.2536 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||7983||1041|IPO9|protein_coding|CODING|NM_018085.4|24|T),UPSTREAM(MODIFIER||4640||197|SHISA4|protein_coding|CODING|NM_198149.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs41299585 -0.453602 0.26 2 I159M 197 atA/atG MODERATE 4 MISSENSE CODING SHISA4 G protein_coding NM_198149.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201860626 A G 0 228 0 0.8041 0.7843 0.7767 0.8978 0.6988 0.7342 0.787789 0.718361 0.682791 2 8188 87782 8561 7765 4628 46052 672 11916 2 10402 121358 11568 8648 6612 66716 908 16504 0 . 0 . 0 80 0,0,19,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I159M|197|SHISA4|protein_coding|CODING|NM_198149.2|4|G),DOWNSTREAM(MODIFIER||4958||600|LMOD1|protein_coding|CODING|NM_012134.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2250377 -0.693147 0.00486678 80 197 42 MODIFIER 5 CODING SHISA4 G protein_coding NM_198149.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201861016 C G 0 222 0 0.2806 0.2985 0.2262 0.3552 0.3618 0.2505 0.286201 0.329848 0.352209 1 3017 39125 2502 3146 2190 23571 284 4415 2 10402 121310 11572 8620 6608 66694 908 16506 0.730372 0 . 0 . 86 14,31,11,20 UTR_3_PRIME(MODIFIER||42||197|SHISA4|protein_coding|CODING|NM_198149.2|5|G),DOWNSTREAM(MODIFIER||4568||600|LMOD1|protein_coding|CODING|NM_012134.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.250166 rs2279681 -0.69311 0.0275032 86 600 1737 MODIFIER 3 CODING LMOD1 G protein_coding NM_012134.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201865763 A G 0 228 0 0.8026 0.7841 0.7738 0.8998 0.6978 0.7362 0 . 0 2 455 10395 129 183 1108 2955 141 5424 2 582 14276 188 200 1588 3914 184 7620 0 . 0 . 0 130 0,0,44,73 UTR_3_PRIME(MODIFIER||1737||600|LMOD1|protein_coding|CODING|NM_012134.2|3|G),DOWNSTREAM(MODIFIER||4048||197|SHISA4|protein_coding|CODING|NM_198149.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs8028 -0.693147 0.565109 130 600 190 MODIFIER 1 CODING LMOD1 C protein_coding NM_012134.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201915658 A C 0 175 0 0.705 0.9197 0.9841 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,1,12 START_GAINED(LOW||||600|LMOD1|protein_coding|CODING|NM_012134.2|1|C),UTR_5_PRIME(MODIFIER||190||600|LMOD1|protein_coding|CODING|NM_012134.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2819371 -0.683931 0.263425 13 171 313 MODIFIER 6 CODING TIMM17A T protein_coding NM_006335.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201938995 C T 0 222 0 0.2451 0.3614 0.2666 0.3343 0.4672 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.750667 0 . 0 . 187 38,55,31,41 UTR_3_PRIME(MODIFIER||313||171|TIMM17A|protein_coding|CODING|NM_006335.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.403575 rs7513 -0.693147 0.00253037 187 Q381 650 caG/caA LOW 6 SILENT CODING RNPEP A protein_coding NM_020216.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201969082 G A 0 228 0 0.1558 0.3085 0.438 0.3978 0.4284 0.2076 0.182025 0.347916 0.432907 2 1778 46766 4878 3726 2613 29509 337 3925 2 10262 120216 11462 8594 6502 66250 894 16252 0 . 0 . COSM146734 125 0,0,82,35 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q381|650|RNPEP|protein_coding|CODING|NM_020216.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1130790 -0.693147 0.000310569 125 V421 650 gtT/gtC LOW 7 SILENT CODING RNPEP C protein_coding NM_020216.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201970562 T C 0 228 0 0.9228 0.9786 0.9942 1 0.999 1 0.939401 0.97924 0.999651 2 9704 120654 11537 8654 6614 66727 906 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 89 0,0,38,45 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V421|650|RNPEP|protein_coding|CODING|NM_020216.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4332408 -0.693147 0.845265 89 G99 371 ggC/ggG LOW 3 SILENT CODING ELF3 G protein_coding NM_001114309.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201981218 C G 0 222 0 0.5424 0.3383 0.2363 0.3363 0.2396 0.2382 0.445983 0.295556 0.218488 1 4757 30910 2343 3026 1194 14923 239 4428 2 10388 121232 11564 8624 6608 66636 906 16506 0.86009 0 . 0 COSM146735 46 11,8,10,12 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G99|371|ELF3|protein_coding|CODING|NM_001114309.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.375983 rs11543979 -0.692562 0.0193123 46 P191 371 ccT/ccC LOW 5 SILENT CODING ELF3 C protein_coding NM_001114309.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 201981862 T C 0 228 0 0.8464 0.7043 0.6009 0.7758 0.5467 0.6738 0.776441 0.605891 0.518493 2 7778 69074 7243 6674 3846 33797 504 9232 2 9774 114220 11438 8550 6578 63818 832 13230 0 . 0 . 0 18 0,0,15,1 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P191|371|ELF3|protein_coding|CODING|NM_001114309.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2819362 -0.689466 0.836076 18 481 46 MODIFIER 1 CODING GPR37L1 T protein_coding NM_004767.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202092046 C T 0 222 0 0.3873 0.5996 0.5634 0.4901 0.8449 0.773 0.49172 0.719116 0.836013 1 4214 86770 5778 4060 5715 53880 682 12441 2 9400 117274 11314 8494 6508 64638 878 16042 0.838801 0 . 0 . 33 13,2,12,4 UTR_5_PRIME(MODIFIER||46||481|GPR37L1|protein_coding|CODING|NM_004767.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.102476 rs3795593 -0.689466 0.853356 33 P81A 481 Ccc/Gcc MODERATE 1 MISSENSE CODING GPR37L1 G protein_coding NM_004767.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202092332 C G 0 222 0 0.3094 0.2232 0.2579 0.3423 0.0606 0.1268 0.279165 0.135322 0.0616279 1 2982 16976 3600 3001 462 4595 116 2220 2 10260 119478 11308 8558 6304 65788 884 16376 0.444227 0 . 0 . 78 21,17,19,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P81A|481|GPR37L1|protein_coding|CODING|NM_004767.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.879277 rs3795594 -0.693127 0.358489 78 G90D 481 gGc/gAc MODERATE 1 MISSENSE CODING GPR37L1 A protein_coding NM_004767.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202092360 G A 0 228 0 0.7769 0.8504 0.83 0.8353 0.9066 0.9223 0.811848 0.865831 0.893488 2 8219 107205 9542 7091 6244 60106 815 15188 2 10352 120988 11492 8604 6592 66540 900 16508 0 . 0 . 0 66 0,0,36,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G90D|481|GPR37L1|protein_coding|CODING|NM_004767.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3795595 -0.693147 0.076067 66 G108 481 ggA/ggG LOW 1 SILENT CODING GPR37L1 G protein_coding NM_004767.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202092415 A G 0 228 0 0.7814 0.8516 0.8285 0.8363 0.9066 0.9223 0.817295 0.867753 0.893605 2 8327 107632 9615 7152 6258 60263 820 15197 2 10398 121344 11564 8644 6608 66712 906 16512 0 . 0 . 0 85 0,0,43,35 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G108|481|GPR37L1|protein_coding|CODING|NM_004767.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3795596 -0.693147 0.0907248 85 S163 481 agT/agC LOW 1 SILENT CODING GPR37L1 C protein_coding NM_004767.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202092580 T C 0 228 0 0.7088 0.8315 0.8228 0.8353 0.9066 0.9223 0.76305 0.849531 0.893837 2 7718 106951 9577 7148 6247 60247 820 15194 2 10398 121272 11556 8614 6594 66696 906 16508 0 . 0 . 0 120 0,0,73,37 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S163|481|GPR37L1|protein_coding|CODING|NM_004767.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7516762 -0.693147 0.138992 120 186 135 MODIFIER 1 CODING ARL8A G protein_coding NM_138795.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202113835 T G 0 9.7 0 0.8623 0.7105 0.7334 0.5933 0.5984 0.7249 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||135||186|ARL8A|protein_coding|CODING|NM_138795.3|1|G),DOWNSTREAM(MODIFIER||2306||465|PTPN7|protein_coding|CODING|NM_002832.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4989100 -0.379885 0 1 Q37R 465 cAg/cGg MODERATE 1 MISSENSE CODING PTPN7 C protein_coding NM_002832.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202129826 T C 0 222 0 0.1006 0.4233 0.5231 0.5387 0.4344 0.6585 0.125551 0.288623 0.358999 1 147 8231 152 282 239 2373 78 4960 2 908 15346 294 514 536 5262 166 7666 0.861408 0 . 0 . 227 25,85,28,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q37R|465|PTPN7|protein_coding|CODING|NM_002832.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.615472 rs4309039 -0.693147 0.000874303 227 465 71 MODIFIER 1 CODING PTPN7 A protein_coding NM_002832.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202130006 C A 0 147 0 0.0212 0.0946 0.1974 0.2272 0.0626 0.0174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999418 0 . 0 . 24 3,11,2,6 UTR_5_PRIME(MODIFIER||71||465|PTPN7|protein_coding|CODING|NM_002832.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.979255 rs4259724 -0.651104 0.220756 24 465 231 MODIFIER 1 CODING PTPN7 A protein_coding NM_002832.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202130166 G A 0 90 0 0.5772 0.6605 0.7277 0.5913 0.7316 0.7239 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 11 0,1,3,2 UTR_5_PRIME(MODIFIER||231||465|PTPN7|protein_coding|CODING|NM_002832.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.861511 0 1 rs4420146 -0.590765 0.968834 11 465 456 MODIFIER 1 CODING PTPN7 T protein_coding NM_002832.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202130391 G T 0 148 0 0.2421 0.11 0.0504 0.1766 0.0119 0.0061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.93568 0 . 0 . 37 18,1,17,1 UTR_5_PRIME(MODIFIER||456||465|PTPN7|protein_coding|CODING|NM_002832.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.924942 rs10920346 -0.691153 0.254512 37 P415 967 ccC/ccT LOW 14 SILENT CODING LGR6 T protein_coding NM_001017403.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202276494 C T 0 228 0 0.2738 0.5339 0.6427 0.7173 0.5447 0.6084 0.314344 0.438029 0.501395 2 3162 65526 8451 6093 3685 33828 472 9835 2 10404 121376 11576 8642 6612 66728 906 16508 0 . 0 . 0 39 0,0,27,9 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P415|967|LGR6|protein_coding|CODING|NM_001017403.1|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs896551 -0.693139 0.405232 39 V592A 967 gTc/gCc MODERATE 18 MISSENSE CODING LGR6 C protein_coding NM_001017403.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202287206 T C 0 228 0 0.3381 0.61 0.7219 0.7679 0.6392 0.7055 0.369269 0.528141 0.609535 2 3786 76925 9051 6497 4325 41120 578 11568 2 10402 121336 11574 8638 6596 66712 908 16506 0 . 0 . 0 120 0,0,68,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V592A|967|LGR6|protein_coding|CODING|NM_001017403.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs788795 -0.693147 0.00533191 120 A702 967 gcG/gcA LOW 18 SILENT CODING LGR6 A protein_coding NM_001017403.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202287537 G A 0 228 0 0.2791 0.528 0.6182 0.7163 0.5268 0.6074 0.314175 0.422899 0.47859 2 2860 59292 8037 5918 2753 30151 399 9174 2 8640 108652 11036 8342 4840 60342 730 14722 0 . 0 . 0 64 0,0,26,35 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A702|967|LGR6|protein_coding|CODING|NM_001017403.1|18|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs788794 -0.693147 0.866339 64 F794 967 ttT/ttC LOW 18 SILENT CODING LGR6 C protein_coding NM_001017403.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202287813 T C 0 228 0 0.3389 0.6104 0.7233 0.7679 0.6392 0.7055 0.373128 0.530832 0.611628 2 3811 76925 9054 6491 4316 41109 576 11568 2 10404 121342 11576 8642 6596 66708 906 16510 0 . 0 . 0 88 0,0,31,54 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F794|967|LGR6|protein_coding|CODING|NM_001017403.1|18|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs788793 -0.693147 0.0475657 88 967 127 MODIFIER 18 CODING LGR6 A protein_coding NM_001017403.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202288462 C A 0 228 0 0.3389 0.6102 0.7233 0.7679 0.6382 0.7055 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 24 0,0,2,22 UTR_3_PRIME(MODIFIER||127||967|LGR6|protein_coding|CODING|NM_001017403.1|18|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs788792 -0.692831 0.182582 24 982 584 MODIFIER 24 CODING PPP1R12B A protein_coding NM_002481.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202550272 G A 0 228 0 0.5166 0.6753 0.7637 0.7897 0.664 0.7209 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 159 0,0,76,63 UTR_3_PRIME(MODIFIER||584||982|PPP1R12B|protein_coding|CODING|NM_002481.3|24|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2008455 -0.693147 0.278988 159 982 859 MODIFIER 24 CODING PPP1R12B A protein_coding NM_002481.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202550547 G A 0 205 0 0.1415 0.529 0.696 0.7113 0.6153 0.6575 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,1,14 UTR_3_PRIME(MODIFIER||859||982|PPP1R12B|protein_coding|CODING|NM_002481.3|24|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2362941 -0.688148 0.0680606 16 982 2250 MODIFIER 24 CODING PPP1R12B A protein_coding NM_002481.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202551938 G A 0 9.7 0 0.1415 0.5272 0.696 0.7063 0.6143 0.6544 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2250||982|PPP1R12B|protein_coding|CODING|NM_002481.3|24|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4950857 -0.379885 0 1 982 2614 MODIFIER 24 CODING PPP1R12B C protein_coding NM_002481.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202552302 T C 0 46.3 0 1 0.9974 0.9986 1 0.998 0.9898 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2614||982|PPP1R12B|protein_coding|CODING|NM_002481.3|24|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs705752 -0.453602 0.84 2 982 7329 MODIFIER 24 CODING PPP1R12B T protein_coding NM_002481.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202557017 C T 0 36.3 0 0.115 0.5212 0.696 0.7063 0.6173 0.6564 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||7329||982|PPP1R12B|protein_coding|CODING|NM_002481.3|24|T),DOWNSTREAM(MODIFIER||2708||419|SYT2|protein_coding|CODING|NM_001136504.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs8288 -0.453602 0.06 2 419 5473 MODIFIER 9 CODING SYT2 C protein_coding NM_001136504.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202560412 T C 0 60 0 0.4939 0.6406 0.7262 0.7183 0.6461 0.6922 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||5473||419|SYT2|protein_coding|CODING|NM_001136504.1|9|C),DOWNSTREAM(MODIFIER||2715||982|PPP1R12B|protein_coding|CODING|NM_002481.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1040010 -0.511536 0.724364 3 419 5227 MODIFIER 9 CODING SYT2 G protein_coding NM_001136504.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202560658 A G 0 42.3 0 0.1543 0.5465 0.7017 0.7183 0.6421 0.6912 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||5227||419|SYT2|protein_coding|CODING|NM_001136504.1|9|G),DOWNSTREAM(MODIFIER||2961||982|PPP1R12B|protein_coding|CODING|NM_002481.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4950780 -0.453602 0.84 2 419 5204 MODIFIER 9 CODING SYT2 G protein_coding NM_001136504.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202560681 T G 0 102 0 0.1536 0.5461 0.7003 0.7183 0.6421 0.6912 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||5204||419|SYT2|protein_coding|CODING|NM_001136504.1|9|G),DOWNSTREAM(MODIFIER||2984||982|PPP1R12B|protein_coding|CODING|NM_002481.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4950781 -0.556411 0.106137 4 419 1555 MODIFIER 9 CODING SYT2 T protein_coding NM_001136504.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202564330 A T 0 9.7 0 0.5174 0.6364 0.7277 0.6964 0.6471 0.6595 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1555||419|SYT2|protein_coding|CODING|NM_001136504.1|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6427958 -0.379885 0 1 S39 419 agC/agT LOW 2 SILENT CODING SYT2 A protein_coding NM_001136504.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202574784 G A 0 222 0 0.0794 0.3588 0.4597 0.3621 0.5746 0.4397 0.157286 0.403045 0.528953 1 1487 57022 5543 2966 3426 35596 452 7552 2 10406 121358 11562 8628 6610 66734 908 16510 0.0452504 0 . 0 . 198 61,39,43,25 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S39|419|SYT2|protein_coding|CODING|NM_001136504.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.808977 rs1968583 -0.693147 0.000648342 198 1580 3187 MODIFIER 28 CODING KDM5B C protein_coding NM_001314042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202694977 T C 0 63 0 0.5537 0.7378 0.8689 0.8165 0.831 0.7168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||3187||1580|KDM5B|protein_coding|CODING|NM_001314042.1|28|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4950790 -0.453602 0.22 3 1580 1286 MODIFIER 28 CODING KDM5B T protein_coding NM_001314042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202696878 C T 0 222 0 0.0893 0.1196 0.1643 0.2629 0.0288 0.0746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.995522 0 . 0 . 85 30,16,21,7 UTR_3_PRIME(MODIFIER||1286||1580|KDM5B|protein_coding|CODING|NM_001314042.1|28|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996961 rs10494836 -0.693054 0.167906 85 1580 617 MODIFIER 28 CODING KDM5B G protein_coding NM_001314042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202697547 C G 0 222 0 0.003 0.0966 0.1643 0.2619 0.0288 0.0746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.795737 0 . 0 . 78 27,10,27,8 UTR_3_PRIME(MODIFIER||617||1580|KDM5B|protein_coding|CODING|NM_001314042.1|28|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.896454 rs10920464 -0.693136 0.552253 78 P1086 1580 ccC/ccG LOW 22 SILENT CODING KDM5B C protein_coding NM_001314042.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202705455 G C 0 228 0 0.323 0.6396 0.8343 0.7837 0.7714 0.6452 0.376532 0.641627 0.777442 2 3790 89716 9902 6691 5357 51923 704 11349 2 10398 121342 11570 8648 6612 66708 906 16500 1 0 . 0 . 105 1,0,31,62 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P1086|1580|KDM5B|protein_coding|CODING|NM_001314042.1|22|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1141109 -0.693147 0.734633 105 Y764 1580 taC/taT LOW 16 SILENT CODING KDM5B A protein_coding NM_001314042.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202715284 G A 0 228 0 0.3222 0.6392 0.8343 0.7837 0.7714 0.6442 0.376305 0.641627 0.777558 2 3791 89688 9905 6691 5356 51911 702 11332 2 10398 121194 11570 8650 6612 66644 904 16416 1 0 . 0 . 112 0,1,53,46 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y764|1580|KDM5B|protein_coding|CODING|NM_001314042.1|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1141108,rs386518161 -0.693147 0.816027 112 H665 1580 caC/caT LOW 15 SILENT CODING KDM5B A protein_coding NM_001314042.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202718202 G A 0 222 0 0.2352 0.5202 0.6715 0.5208 0.7425 0.5685 0.308897 0.598416 0.746744 1 3105 81191 7361 4597 5209 49848 663 10408 2 10396 121344 11560 8650 6612 66712 906 16508 0.788872 0 . 0 . 104 23,26,17,23 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H665|1580|KDM5B|protein_coding|CODING|NM_001314042.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.908878 rs1892164 -0.693145 0.33337 104 T285 1580 acG/acA LOW 7 SILENT CODING KDM5B T protein_coding NM_001314042.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202733238 C T 0 228 0 0.323 0.6354 0.8343 0.7679 0.7714 0.6401 0.376759 0.642088 0.778023 2 3785 89443 9873 6529 5348 51915 703 11290 2 10386 121350 11570 8646 6612 66722 908 16506 1 0 . 0 . 54 1,0,17,29 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T285|1580|KDM5B|protein_coding|CODING|NM_001314042.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3196669 -0.693147 0.00336537 54 1580 528 MODIFIER 1 CODING KDM5B G protein_coding NM_001314042.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202777961 C G 0 222 0 0.2065 0.1522 0.1715 0.2639 0.0298 0.0757 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.993122 0 . 0 . 45 0,23,4,17 UTR_5_PRIME(MODIFIER||528||1580|KDM5B|protein_coding|CODING|NM_001314042.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.664195 rs10920486 -0.692352 0.166221 45 1580 628 MODIFIER 1 CODING KDM5B T protein_coding NM_001314042.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202778061 C T 0 165 0 0.2874 0.2103 0.196 0.2966 0.0875 0.1534 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.9 0 . 0 . 13 0,2,1,9 UTR_5_PRIME(MODIFIER||628||1580|KDM5B|protein_coding|CODING|NM_001314042.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.35 rs41302113 -0.670168 0.364597 13 123 500 MODIFIER 2 CODING RABIF T protein_coding NM_002871.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202849606 C T 0 228 0 0.8351 0.9543 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 132 0,0,69,50 UTR_3_PRIME(MODIFIER||500||123|RABIF|protein_coding|CODING|NM_002871.4|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10753924 -0.693147 0.632848 132 123 383 MODIFIER 2 CODING RABIF A protein_coding NM_002871.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202849723 G A 0 222 0 0.4675 0.5088 0.5303 0.4067 0.6511 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.764086 0 . 0 . 82 7,31,7,32 UTR_3_PRIME(MODIFIER||383||123|RABIF|protein_coding|CODING|NM_002871.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.256099 rs1131906 -0.693144 0.660883 82 123 336 MODIFIER 2 CODING RABIF C protein_coding NM_002871.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202849770 T C 0 191 0 0.4675 0.5088 0.5303 0.4067 0.6511 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.773528 0 . 0 . 45 2,19,2,22 UTR_3_PRIME(MODIFIER||336||123|RABIF|protein_coding|CODING|NM_002871.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.773528 rs1131905,rs386518054 -0.692831 0.203229 45 606 195 MODIFIER 12 CODING KLHL12 T protein_coding NM_001303051.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202861463 TCTG T 0 221 0 0.4266 0.4503 0.5259 0.3155 0.6133 0.3998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 1,0,16,0 UTR_3_PRIME(MODIFIER||195||606|KLHL12|protein_coding|CODING|NM_001303051.1|12|T),UPSTREAM(MODIFIER||3079||123|RABIF|protein_coding|CODING|NM_002871.4||T) 0 0.5 1 16 0.941176 1 1 0 . 0 60 0 0 . 0 . rs201067798 -0.689466 0.382874 17 606 96 MODIFIER 12 CODING KLHL12 G protein_coding NM_001303051.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202861565 C G 0 141 0 0.0008 0.0635 0.121 0.1002 0.0149 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.728793 0 . 0 . 77 36,6,29,0 UTR_3_PRIME(MODIFIER||96||606|KLHL12|protein_coding|CODING|NM_001303051.1|12|G),UPSTREAM(MODIFIER||3180||123|RABIF|protein_coding|CODING|NM_002871.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.928201 rs4950869 -0.693079 0.0351339 77 606 95 MODIFIER 12 CODING KLHL12 G protein_coding NM_001303051.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202861566 A G 0 228 0 0.4266 0.4501 0.5259 0.3155 0.6133 0.3988 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 74 0,1,62,7 UTR_3_PRIME(MODIFIER||95||606|KLHL12|protein_coding|CODING|NM_001303051.1|12|G),UPSTREAM(MODIFIER||3181||123|RABIF|protein_coding|CODING|NM_002871.4||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1042990 -0.693147 0.10903 74 606 LOW 4 CODING KLHL12 A protein_coding NM_001303051.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202887295 G A 0 228 0 0.3949 0.4383 0.5058 0.3085 0.6153 0.4008 0.412846 0.545133 0.612907 2 4172 65802 5936 2801 4324 41114 528 6927 2 10388 121078 11574 8628 6614 66670 902 16302 1 0 . 0 COSM146736 96 1,0,59,24 SPLICE_SITE_REGION+INTRON(LOW||||606|KLHL12|protein_coding|CODING|NM_001303051.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2275734 -0.693147 0.453773 96 375 727 MODIFIER 8 CODING ADIPOR1 C protein_coding NM_001290553.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202909974 G C 0 228 0 0.357 0.4694 0.5663 0.3661 0.6779 0.4448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,21,9 UTR_3_PRIME(MODIFIER||727||375|ADIPOR1|protein_coding|CODING|NM_001290553.1|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7539542 -0.693097 0.0899824 35 375 LOW 1 CODING ADIPOR1 C protein_coding NM_001290553.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202920300 A C 0 156 0 0.5598 0.6362 0.67 0.8274 0.5507 0.6063 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.878264 0 . 0 . 26 2,14,2,7 SPLICE_SITE_REGION+INTRON(LOW||||375|ADIPOR1|protein_coding|CODING|NM_001290553.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.974685 rs2275737 -0.662043 0.206995 26 N44S 305 aAt/aGt MODERATE 2 MISSENSE CODING CYB5R1 C protein_coding NM_016243.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 202935911 T C 0 222 0 0.1392 0.1925 0.2161 0.4117 0.0278 0.1912 0.147072 0.0680455 0.0275581 1 1502 13189 2820 3652 486 2130 88 2511 2 10362 120922 11540 8630 6530 66474 902 16484 0.841547 0 . 0 . 137 39,33,33,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N44S|305|CYB5R1|protein_coding|CODING|NM_016243.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.777803 rs2232842 -0.693147 0.0119536 137 R13P 1207 cGc/cCc MODERATE 2 MISSENSE CODING PPFIA4 C protein_coding NM_001304331.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203008174 G C 0 228 0 1 1 1 1 1 1 0 . 0 2 5442 81900 7642 5596 4856 44560 608 13196 2 5442 81900 7642 5596 4856 44560 608 13196 0 . 0 . 0 42 0,0,22,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R13P|1207|PPFIA4|protein_coding|CODING|NM_001304331.1|2|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs61821060 -0.693145 0.285591 42 T50 1207 acC/acG LOW 2 SILENT CODING PPFIA4 G protein_coding NM_001304331.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203008286 C G 0 222 0 0.3109 0.504 0.5115 0.5863 0.6163 0.5593 0.335616 0.51762 0.597739 1 2364 56122 4793 4216 3474 32598 426 8251 2 6248 96278 9332 7102 5276 53142 704 14474 0.943731 0 . 0 COSM425038 92 34,10,28,12 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T50|1207|PPFIA4|protein_coding|CODING|NM_001304331.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.188418 rs10920553 -0.693145 0.145939 92 1207 1841 MODIFIER 30 CODING PPFIA4 A protein_coding NM_001304331.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203047359 G A 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1841||1207|PPFIA4|protein_coding|CODING|NM_001304331.1|30|A),DOWNSTREAM(MODIFIER||4898||224|MYOG|protein_coding|CODING|NM_002479.5||A) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs371546095 -0.379885 0 1 1207 2103 MODIFIER 30 CODING PPFIA4 A protein_coding NM_001304331.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203047621 C A 0 227 0 0.8933 0.7867 0.7723 0.745 0.7187 0.7658 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,23,2 UTR_3_PRIME(MODIFIER||2103||1207|PPFIA4|protein_coding|CODING|NM_001304331.1|30|A),DOWNSTREAM(MODIFIER||4636||224|MYOG|protein_coding|CODING|NM_002479.5||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3087949 -0.692914 0.706735 25 224 LOW 2 CODING MYOG C protein_coding NM_002479.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203053768 T C 0 222 0 0.9992 0.9561 0.9827 0.8819 0.9742 0.9366 0.990468 0.973089 0.964186 1 9408 106531 10532 7210 5308 59211 764 14098 2 9472 110468 10698 7984 5466 61262 794 14792 0.91561 0 . 0 . 101 27,19,20,20 SPLICE_SITE_REGION+INTRON(LOW||||224|MYOG|protein_coding|CODING|NM_002479.5|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953862 rs903356 -0.693145 0.213569 101 326 297 MODIFIER 4 CODING ADORA1 C protein_coding NM_000674.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203135325 A C 0 100 0 0.9077 0.9008 0.8516 0.8046 0.9761 0.9479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||297||326|ADORA1|protein_coding|CODING|NM_000674.2|4|C),DOWNSTREAM(MODIFIER||1614||477|MYBPH|protein_coding|CODING|NM_004997.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6427994 -0.511536 0.0860477 4 326 424 MODIFIER 4 CODING ADORA1 T protein_coding NM_000674.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203135452 C T 0 9.7 0 0.1142 0.1532 0.1009 0.3958 0.0368 0.1125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||424||326|ADORA1|protein_coding|CODING|NM_000674.2|4|T),DOWNSTREAM(MODIFIER||1487||477|MYBPH|protein_coding|CODING|NM_004997.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs16851030 -0.379885 0 1 326 646 MODIFIER 4 CODING ADORA1 T protein_coding NM_000674.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203135674 G T 0 25.9 0 0.0817 0.1018 0.0533 0.0784 0.0646 0.226 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_3_PRIME(MODIFIER||646||326|ADORA1|protein_coding|CODING|NM_000674.2|4|T),DOWNSTREAM(MODIFIER||1265||477|MYBPH|protein_coding|CODING|NM_004997.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12744240 -0.453602 0.44 3 477 804 MODIFIER 11 CODING MYBPH T protein_coding NM_004997.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203136983 A T 0 68 0 0.8502 0.7005 0.6052 0.6905 0.5567 0.7239 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||804||477|MYBPH|protein_coding|CODING|NM_004997.2|11|T),DOWNSTREAM(MODIFIER||450||326|ADORA1|protein_coding|CODING|NM_000674.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1042295,rs386512883 -0.511536 0.764235 3 477 697 MODIFIER 11 CODING MYBPH T protein_coding NM_004997.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203137090 C T 0 9.7 0 0.0998 0.1328 0.0965 0.3631 0.0368 0.0644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||697||477|MYBPH|protein_coding|CODING|NM_004997.2|11|T),DOWNSTREAM(MODIFIER||557||326|ADORA1|protein_coding|CODING|NM_000674.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs73075725 -0.379885 0 1 N211 477 aaC/aaT LOW 5 SILENT CODING MYBPH A protein_coding NM_004997.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203140671 G A 0 222 0 0.1021 0.1693 0.1153 0.3968 0.0944 0.1411 0.0955515 0.0947255 0.0943023 1 1026 15400 1760 3066 842 6427 130 2149 2 9976 116624 11228 8468 5666 64456 848 15982 0.843765 0 . 0 . 86 11,31,17,21 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N211|477|MYBPH|protein_coding|CODING|NM_004997.2|5|A),DOWNSTREAM(MODIFIER||4138||326|ADORA1|protein_coding|CODING|NM_000674.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.843765 rs3737875 -0.693143 0.201141 86 T17 477 acC/acT LOW 1 SILENT CODING MYBPH A protein_coding NM_004997.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203144833 G A 0 222 0 0.0825 0.1312 0.0951 0.375 0.0368 0.0685 0.0762596 0.0528987 0.0409302 1 828 9751 1599 3052 419 2884 97 872 2 10348 121304 11576 8642 6612 66706 908 16512 0.92271 0 . 0 . 141 21,46,18,39 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T17|477|MYBPH|protein_coding|CODING|NM_004997.2|1|A),DOWNSTREAM(MODIFIER||3226||383|CHI3L1|protein_coding|CODING|NM_001276.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.398656 rs12145010 -0.693147 0.141975 141 C364 383 tgT/tgC LOW 10 SILENT CODING CHI3L1 G protein_coding NM_001276.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203148633 A G 0 228 0 1 0.9996 1 1 0.999 0.999 0.999773 0.998155 0.997326 2 10352 117481 11540 8640 6612 65612 869 13856 2 10354 117626 11542 8642 6612 65728 870 13878 0 . 0 . 0 102 0,0,47,45 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C364|383|CHI3L1|protein_coding|CODING|NM_001276.2|10|G),UPSTREAM(MODIFIER||3691||477|MYBPH|protein_coding|CODING|NM_004997.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4950927 -0.693147 0.0498393 102 R145G 383 Aga/Gga MODERATE 5 MISSENSE CODING CHI3L1 C protein_coding NM_001276.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203152801 T C 0 228 0 0.1747 0.373 0.3343 0.3839 0.5417 0.4836 0.2197 0.414424 0.514186 2 2228 55222 2904 3180 3616 35183 458 7653 2 10404 121292 11558 8594 6604 66712 908 16512 0 . 0 . 0 119 0,0,68,37 PROTEIN_INTERACTION_LOCUS(HIGH||||383|CHI3L1|protein_coding|CODING||5|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R145G|383|CHI3L1|protein_coding|CODING|NM_001276.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs880633 -0.693147 0.511282 119 383 131 MODIFIER 1 CODING CHI3L1 C protein_coding NM_001276.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203155882 G C 0 228 0 0.6626 0.7855 0.8271 0.8512 0.8191 0.82 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,8,23 UTR_5_PRIME(MODIFIER||131||383|CHI3L1|protein_coding|CODING|NM_001276.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4950928 -0.69311 0.564386 36 376 1591 MODIFIER 3 CODING FMOD A protein_coding NM_002023.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203309880 G A 0 9.7 0 0.0303 0.248 0.3804 0.4841 0.1799 0.2751 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1591||376|FMOD|protein_coding|CODING|NM_002023.4|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7208 -0.379885 0 1 376 255 MODIFIER 3 CODING FMOD C protein_coding NM_002023.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203311216 T C 0 94 0 0.0658 0.2578 0.3876 0.4841 0.1799 0.272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.945784 0 . 0 . 22 12,1,9,0 UTR_3_PRIME(MODIFIER||255||376|FMOD|protein_coding|CODING|NM_002023.4|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.356772 rs3738022 -0.662043 0.395707 22 E79 376 gaG/gaA LOW 2 SILENT CODING FMOD T protein_coding NM_002023.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203317162 C T 0 222 0 0.2708 0.6184 0.7925 0.6528 0.8608 0.68 0.339764 0.668615 0.837093 1 3406 90722 8510 5408 5618 55249 708 11823 2 10220 119448 11330 8462 6458 65928 888 16162 0.969269 0 . 0 . 102 24,24,29,16 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E79|376|FMOD|protein_coding|CODING|NM_002023.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.646465 rs7543148 -0.693147 0.882351 102 376 3010 MODIFIER 1 CODING FMOD C protein_coding NM_002023.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203320408 G C 0 31.3 0 0.3623 0.6689 0.7997 0.6716 0.8797 0.771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||3010||376|FMOD|protein_coding|CODING|NM_002023.4|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4971252 -0.453602 0.48 2 382 89 MODIFIER 3 CODING PRELP C protein_coding NM_002725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203456098 T C 0 147 0 0.115 0.1538 0.0865 0.2411 0.1441 0.1738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997325 0 . 0 . 28 0,15,1,11 UTR_3_PRIME(MODIFIER||89||382|PRELP|protein_coding|CODING|NM_002725.3|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.489396 rs1050083 -0.680642 0.302434 28 382 212 MODIFIER 3 CODING PRELP A protein_coding NM_002725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203456221 C A 0 142 0 0.1543 0.1647 0.0908 0.2411 0.1441 0.1738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.833333 0 . 0 . 9 0,2,4,2 UTR_3_PRIME(MODIFIER||212||382|PRELP|protein_coding|CODING|NM_002725.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.992367 0 0.833333 rs1166 -0.616816 0.329692 9 382 2028 MODIFIER 3 CODING PRELP T protein_coding NM_002725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203458037 A T 0 42.4 0 0.1596 0.1851 0.1282 0.2609 0.1521 0.2157 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,3,0 UTR_3_PRIME(MODIFIER||2028||382|PRELP|protein_coding|CODING|NM_002725.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2242203 -0.511536 0.0941127 4 382 2192 MODIFIER 3 CODING PRELP G protein_coding NM_002725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203458201 A G 0 222 0 0.0174 0.1024 0.196 0.2014 0.0447 0.1084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987411 0 . 0 . 40 17,3,10,6 UTR_3_PRIME(MODIFIER||2192||382|PRELP|protein_coding|CODING|NM_002725.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.133812 rs2242202 -0.689466 0.107686 40 1205 407 MODIFIER 2 CODING ATP2B4 C protein_coding NM_001684.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203651927 T C 0 138 0 0.6346 0.8498 0.9366 0.999 0.8976 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_5_PRIME(MODIFIER||407||1205|ATP2B4|protein_coding|CODING|NM_001684.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1541252 -0.616816 0.906964 6 1205 294 MODIFIER 2 CODING ATP2B4 C protein_coding NM_001684.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203652040 T C 0 163 0 0.6346 0.8498 0.9366 0.999 0.8976 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,2 UTR_5_PRIME(MODIFIER||294||1205|ATP2B4|protein_coding|CODING|NM_001684.4|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1541253 -0.636426 0.571008 7 1205 194 MODIFIER 2 CODING ATP2B4 G protein_coding NM_001684.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203652140 C G 0 137 0 0.6346 0.8498 0.9366 0.999 0.8976 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_5_PRIME(MODIFIER||194||1205|ATP2B4|protein_coding|CODING|NM_001684.4|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1541254 -0.662043 0.15334 9 1205 193 MODIFIER 2 CODING ATP2B4 A protein_coding NM_001684.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203652141 G A 0 127 0 0.6346 0.8498 0.9366 0.999 0.8976 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_5_PRIME(MODIFIER||193||1205|ATP2B4|protein_coding|CODING|NM_001684.4|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1541255 -0.662043 0.15334 9 S37 1205 tcA/tcG LOW 2 SILENT CODING ATP2B4 G protein_coding NM_001684.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203652444 A G 0 228 0 0.6354 0.85 0.9366 0.999 0.8976 0.8763 0.694734 0.828925 0.897674 2 7048 106304 10940 8650 5477 59143 794 14252 2 10406 121406 11576 8654 6614 66738 908 16510 0 . 0 . 0 75 0,0,22,50 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S37|1205|ATP2B4|protein_coding|CODING|NM_001684.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1419114 -0.693147 0.564052 75 L106 1205 ctT/ctC LOW 3 SILENT CODING ATP2B4 C protein_coding NM_001684.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203667409 T C 0 228 0 0.6725 0.8598 0.9395 0.999 0.8976 0.8742 0.741943 0.844841 0.897558 2 7564 106846 10964 8650 5477 59139 796 14256 2 10406 121402 11576 8654 6614 66736 906 16510 0 . 0 . 0 72 0,0,47,22 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L106|1205|ATP2B4|protein_coding|CODING|NM_001684.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2228445 -0.693147 0.0353519 72 1205 52 MODIFIER 21 CODING ATP2B4 G protein_coding NM_001684.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203709034 A G 0 228 0 0.6694 0.6006 0.7334 0.499 0.5805 0.5389 0.675961 0.616199 0.581854 2 6479 59611 7371 3882 2811 33691 404 4973 2 9546 102162 10170 7614 6150 58714 734 9234 0 . 0 . 0 52 0,0,16,31 UTR_3_PRIME(MODIFIER||52||1205|ATP2B4|protein_coding|CODING|NM_001684.4|21|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs955865 -0.693147 0.000406756 52 1205 86 MODIFIER 21 CODING ATP2B4 C protein_coding NM_001684.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203709068 T C 0 228 0 0.6717 0.602 0.7334 0.502 0.5805 0.5399 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 39 0,0,7,29 UTR_3_PRIME(MODIFIER||86||1205|ATP2B4|protein_coding|CODING|NM_001684.4|21|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs955866 -0.693139 0.695948 39 1205 4014 MODIFIER 21 CODING ATP2B4 C protein_coding NM_001684.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203712996 T C 0 151 0 0.2269 0.2396 0.4308 0.1845 0.2197 0.1984 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980133 0 . 0 . 22 12,1,6,3 UTR_3_PRIME(MODIFIER||4014||1205|ATP2B4|protein_coding|CODING|NM_001684.4|21|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994996 rs970 -0.662043 0.978735 22 1205 4151 MODIFIER 21 CODING ATP2B4 A protein_coding NM_001684.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203713133 G A 0 222 0 0.2284 0.2388 0.4265 0.1825 0.2197 0.1973 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.233225 0 . 0 . 68 22,9,16,10 UTR_3_PRIME(MODIFIER||4151||1205|ATP2B4|protein_coding|CODING|NM_001684.4|21|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.748574 rs568 -0.692976 0.868055 68 398 1539 MODIFIER 5 CODING LAX1 A protein_coding NM_017773.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203745348 C A 0 6.3 0 0.8631 0.9625 0.9899 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1539||398|LAX1|protein_coding|CODING|NM_017773.3|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9792973 -0.379885 0 1 F560L 979 Ttc/Ctc MODERATE 1 MISSENSE CODING ZBED6 C protein_coding NM_001174108.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203768328 T C 0 222 0 0.0484 0.1837 0.3213 0.2887 0.1173 0.229 0 . 0 1 28 2010 30 56 0 421 13 1462 2 548 12282 184 198 2 3604 132 7614 0.81165 0 . 0 . 57 13,23,5,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F560L|979|ZBED6|protein_coding|CODING|NM_001174108.1|1|C),INTRON(MODIFIER||||810|ZC3H11A|protein_coding|CODING|NM_014827.4|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.950514 rs7552670 -0.69168 0.0758566 57 S961N 979 aGc/aAc MODERATE 1 MISSENSE CODING ZBED6 A protein_coding NM_001174108.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203769532 G A 0 222 0 0.0499 0.1837 0.3199 0.2887 0.1183 0.227 0 . 0 1 28 1985 30 56 0 421 14 1436 2 550 11114 180 196 2 3230 116 6840 0.861121 0 . 0 . 100 15,33,17,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S961N|979|ZBED6|protein_coding|CODING|NM_001174108.1|1|A),INTRON(MODIFIER||||810|ZC3H11A|protein_coding|CODING|NM_014827.4|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.991448 rs7540041 -0.693139 0.287018 100 G19 810 ggT/ggC LOW 6 SILENT CODING ZC3H11A C protein_coding NM_014827.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203787700 T C 0 228 0 0.9228 0.9788 0.9942 1 1 1 0.929868 0.975704 0.999186 2 9683 120622 11547 8654 6612 66718 901 16507 2 10404 121404 11576 8654 6612 66738 908 16512 0 . 0 . 0 51 0,0,26,21 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G19|810|ZC3H11A|protein_coding|CODING|NM_014827.4|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4951260 -0.693147 0.730646 51 A586 810 gcC/gcA LOW 17 SILENT CODING ZC3H11A A protein_coding NM_014827.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203818973 C A 0 222 0 0.1112 0.1751 0.183 0.1558 0.2197 0.2301 0.129142 0.181839 0.208837 1 1312 23801 2400 1659 1127 13392 194 3717 2 10406 121376 11570 8638 6614 66728 908 16512 0.74412 0 . 0 . 213 71,25,60,36 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A586|810|ZC3H11A|protein_coding|CODING|NM_014827.4|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.447101 rs41299639 -0.693147 0.423188 213 P740 810 ccG/ccA LOW 20 SILENT CODING ZC3H11A A protein_coding NM_014827.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203821314 G A 0 222 0 0.112 0.1753 0.183 0.1558 0.2197 0.2301 0.11958 0.174313 0.202311 1 1148 23264 2396 1652 1126 13033 193 3716 2 8994 117918 11558 8638 6608 64716 896 16508 0.790758 0 . 0 . 195 76,15,71,19 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P740|810|ZC3H11A|protein_coding|CODING|NM_014827.4|20|A) 1 0.5 1 0 . 1 0 1 1 0 53 0 0.24165 0.000657115 0 0.266089 rs41264265 -0.693147 0.0153807 195 810 777 MODIFIER 20 CODING ZC3H11A C protein_coding NM_014827.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203822304 T C 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,20,6 UTR_3_PRIME(MODIFIER||777||810|ZC3H11A|protein_coding|CODING|NM_014827.4|20|C) 0 . 0 . 0 . 0 . 0 . 42 0 0 0.0969271 0 . rs4019811 -0.692976 0.191597 26 810 1539 MODIFIER 20 CODING ZC3H11A C protein_coding NM_014827.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203823066 G C 0 222 0 0.6846 0.7127 0.755 0.8085 0.6521 0.684 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.404132 0 . 0 . 73 9,27,8,29 UTR_3_PRIME(MODIFIER||1539||810|ZC3H11A|protein_coding|CODING|NM_014827.4|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.049118 rs7311 -0.693141 0.240283 73 92 213 MODIFIER 5 CODING SNRPE T protein_coding NM_003094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203839273 C T 0 206 0 0.7042 0.7656 0.7867 0.8343 0.7575 0.771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.49212 0 . 0 . 32 1,16,3,11 UTR_3_PRIME(MODIFIER||213||92|SNRPE|protein_coding|CODING|NM_003094.3|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.29253 rs2298870 -0.686358 0.0133034 32 92 445 MODIFIER 5 CODING SNRPE C protein_coding NM_003094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 203839505 T C 0 125 0 0.9365 0.9826 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,4 UTR_3_PRIME(MODIFIER||445||92|SNRPE|protein_coding|CODING|NM_003094.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5003874 -0.590765 0.877481 5 622 425 MODIFIER 14 CODING SOX13 A protein_coding NM_005686.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204095687 C A 0 222 0 0.031 0.1558 0.0879 0.3482 0.1014 0.2301 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.222383 0 . 0 . 150 45,38,17,35 UTR_3_PRIME(MODIFIER||425||622|SOX13|protein_coding|CODING|NM_005686.2|14|A),DOWNSTREAM(MODIFIER||4502||394|ETNK2|protein_coding|CODING|NM_001297760.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.211243 rs3737659 -0.693147 0.000102325 150 622 1368 MODIFIER 14 CODING SOX13 C protein_coding NM_005686.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204096630 T C 0 228 0 0.5953 0.8572 0.9092 1 0.9215 0.9611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,50,10 UTR_3_PRIME(MODIFIER||1368||622|SOX13|protein_coding|CODING|NM_005686.2|14|C),DOWNSTREAM(MODIFIER||3559||394|ETNK2|protein_coding|CODING|NM_001297760.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1138617 -0.693147 0.0264125 68 *139 138 tga/ HIGH 3 CODING KISS1 C protein_coding NM_002256.3 FRAME_SHIFT+STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204159611 CT C 0 39.2 0 0.0809 0.2218 0.2464 0.4147 0.2167 0.2014 0.0848783 0.16706 0.204576 1 556 20914 2847 2903 809 10830 134 2835 2 3864 70110 8182 6164 2626 37316 496 11462 0 . 0 . COSM425060 9 5,0,3,0 FRAME_SHIFT+STOP_LOST(HIGH||tga/|*139|138|KISS1|protein_coding|CODING|NM_002256.3|3|C) 1 0.5 1 4 0.444444 1 1 1 1 0 60 0 0 . 0 . rs71745629 -0.511536 0.00809987 9 P81R 138 cCc/cGc MODERATE 3 MISSENSE CODING KISS1 C protein_coding NM_002256.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204159787 G C 0 222 0 0.4009 0.3299 0.3156 0.4216 0.2545 0.227 0.260247 0.208957 0.18768 1 1368 16936 1932 1870 424 8412 98 2832 2 3254 49628 4268 3964 1360 25850 314 10618 0.703584 0 . 0 . 42 10,4,20,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P81R|138|KISS1|protein_coding|CODING|NM_002256.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.804377 rs4889 -0.693021 0.19431 42 1048 2186 MODIFIER 23 CODING PLEKHA6 G protein_coding NM_014935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204190412 C G 0 222 0 0.5976 0.4896 0.5346 0.4841 0.4533 0.3548 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.841538 0 . 0 . 147 40,47,29,25 UTR_3_PRIME(MODIFIER||2186||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.121616 rs11793 -0.693147 0.0425747 147 1048 2090 MODIFIER 23 CODING PLEKHA6 T protein_coding NM_014935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204190508 C T 0 222 0 0.3593 0.3866 0.4568 0.4841 0.3499 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998107 0 . 0 . 186 62,41,32,31 UTR_3_PRIME(MODIFIER||2090||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.587379 rs4631764 -0.693147 0.0767286 186 1048 2022 MODIFIER 23 CODING PLEKHA6 T protein_coding NM_014935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204190576 C T 0 222 0 0.3593 0.3872 0.4611 0.4841 0.3499 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.898843 0 . 0 . 161 34,52,25,28 UTR_3_PRIME(MODIFIER||2022||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.759616 rs4489623 -0.693147 0.0596249 161 1048 1725 MODIFIER 23 CODING PLEKHA6 G protein_coding NM_014935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204190873 A G 0 121 0 0.6157 0.4968 0.5375 0.4851 0.4612 0.3558 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0916482 0 . 0 . 11 0,3,0,7 UTR_3_PRIME(MODIFIER||1725||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.916482 0 . 0.366593 rs10793758 -0.636426 0.134494 11 1048 1189 MODIFIER 23 CODING PLEKHA6 C protein_coding NM_014935.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204191409 T C 0 222 0 0.6936 0.5166 0.5403 0.4861 0.4543 0.3558 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.906642 0 . 0 . 105 22,37,18,21 UTR_3_PRIME(MODIFIER||1189||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|23|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.192783 rs3795572 -0.693144 0.0150548 105 R929W 1048 Cgg/Tgg MODERATE 20 MISSENSE CODING PLEKHA6 A protein_coding NM_014935.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204197956 G A 0 222 0 0 0.00019968 0 0 0.001 0 0 7.6888e-05 0.000116279 1 0 8 0 0 0 6 0 2 2 10406 121392 11570 8654 6614 66728 908 16512 0.828541 0 . 0 . 287 70,91,38,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R929W|1048|PLEKHA6|protein_coding|CODING|NM_014935.4|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.912266 rs148649544 -0.693147 0.0308409 287 H869 1048 caT/caC LOW 19 SILENT CODING PLEKHA6 G protein_coding NM_014935.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204198209 A G 0 222 0 0.6967 0.5124 0.5389 0.4802 0.4344 0.3579 0.660917 0.52668 0.457907 1 6967 59091 6431 4317 2849 31457 388 6682 2 10366 120964 11520 8600 6538 66540 902 16498 0.541846 0 . 0 . 79 11,39,5,20 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H869|1048|PLEKHA6|protein_coding|CODING|NM_014935.4|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.753131 rs3795571,rs386586481 -0.692914 0.130191 79 R837K 1048 aGg/aAg MODERATE 18 MISSENSE CODING PLEKHA6 T protein_coding NM_014935.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204199614 C T 0 222 0 0.6914 0.5106 0.5375 0.4802 0.4334 0.3579 0.657656 0.52411 0.455594 1 4112 31719 2469 2586 844 16975 194 4539 2 6004 58934 3940 4766 1518 31650 396 10660 0.82664 0 . 0 COSM1338061 119 33,32,25,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R837K|1048|PLEKHA6|protein_coding|CODING|NM_014935.4|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.422231 rs10900562,rs386487419 -0.693147 0.0283154 119 1048 LOW 6 CODING PLEKHA6 A protein_coding NM_014935.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204230581 G A 0 222 0 0.5068 0.5976 0.696 0.8095 0.5268 0.5051 0.564911 0.556897 0.552791 1 5729 71706 8737 7039 4567 37139 512 7983 2 10222 118360 11526 8628 6518 65760 884 14822 0.435176 0 . 0 . 63 23,13,9,14 SPLICE_SITE_REGION+INTRON(LOW||||1048|PLEKHA6|protein_coding|CODING|NM_014935.4|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.927295 rs3795569 -0.692717 0.580911 63 V43I 1048 Gtc/Atc MODERATE 4 MISSENSE CODING PLEKHA6 T protein_coding NM_014935.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204237416 C T 0 222 0 0.475 0.6326 0.7637 0.8046 0.661 0.546 0.503858 0.616254 0.673837 1 5177 82295 9473 7040 4948 45374 604 9679 2 10362 120842 11550 8622 6558 66448 900 16402 0.832978 0 . 0 COSM1179739 90 16,25,10,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V43I|1048|PLEKHA6|protein_coding|CODING|NM_014935.4|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.77544 rs10900571 -0.693145 0.0572891 90 713 850 MODIFIER 2 CODING PPP1R15B C protein_coding NM_032833.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204374370 T C 0 184 0 0 0.0095847 0 0.0456 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.763541 0 . 0 . 26 2,11,2,7 UTR_3_PRIME(MODIFIER||850||713|PPP1R15B|protein_coding|CODING|NM_032833.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.973056 rs117124850 -0.662043 0.0933471 26 N308S 713 aAc/aGc MODERATE 1 MISSENSE CODING PPP1R15B C protein_coding NM_032833.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204379617 T C 0 228 0 0.888 0.9689 0.9914 1 0.998 1 0.908988 0.96863 0.999186 2 9490 120367 11527 8654 6613 66670 902 16511 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 107 0,0,42,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N308S|713|PPP1R15B|protein_coding|CODING|NM_032833.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3014626 -0.693147 0.0069773 107 N1198 1634 aaT/aaC LOW 25 SILENT CODING PIK3C2B G protein_coding NM_002646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204403659 A G 0 222 0 0.525 0.405 0.2666 0.5089 0.2594 0.3834 0.477531 0.306013 0.21814 1 5045 36206 3233 4479 2140 15162 298 5849 2 10322 120326 11430 8592 6492 66222 892 16376 0.289788 0 . 0 . 87 21,18,28,16 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N1198|1634|PIK3C2B|protein_coding|CODING|NM_002646.3|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.384663 rs3747636 -0.693146 0.111763 87 1634 LOW 18 CODING PIK3C2B T protein_coding NM_002646.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204413297 C T 0 222 0 0.4236 0.6108 0.7723 0.494 0.7753 0.7004 0.510894 0.710518 0.812791 1 5170 88201 8608 4143 4742 53347 640 11551 2 10400 121050 11496 8614 6590 66552 904 16494 0.462663 0 . 0 . 167 37,46,28,41 SPLICE_SITE_REGION+INTRON(LOW||||1634|PIK3C2B|protein_coding|CODING|NM_002646.3|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.121335 rs2292459 -0.693147 0.00195563 167 F633 1634 ttC/ttT LOW 12 SILENT CODING PIK3C2B A protein_coding NM_002646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204425028 G A 0 222 0 0.0582 0.2033 0.0865 0.3998 0.2078 0.2751 0.0712665 0.138936 0.173605 1 707 23085 755 3490 1324 12030 205 4574 2 10364 120602 11538 8616 6548 66428 896 16212 0.95905 0 . 0 . 114 29,17,43,13 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F633|1634|PIK3C2B|protein_coding|CODING|NM_002646.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948197 rs3765156 -0.693147 0.893832 114 P199 1634 ccG/ccA LOW 3 SILENT CODING PIK3C2B T protein_coding NM_002646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204438334 C T 0 228 0 0.2413 0.728 0.8948 0.8194 0.9841 0.91 0.374262 0.776718 0.982907 2 3581 107837 9904 6780 6379 65424 832 14937 2 10366 120954 11576 8642 6614 66586 902 16268 0 . 0 . 0 51 0,0,39,2 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P199|1634|PIK3C2B|protein_coding|CODING|NM_002646.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1124777 -0.693145 0.115796 51 L96 1634 ctC/ctA LOW 3 SILENT CODING PIK3C2B T protein_coding NM_002646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204438643 G T 0 228 0 0.2368 0.7272 0.8963 0.8194 0.9841 0.911 0.372901 0.776257 0.982907 2 3560 106323 9891 6760 6379 65045 823 13865 2 10372 119430 11566 8628 6614 66202 892 15156 0 . 0 . 0 95 0,0,53,35 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L96|1634|PIK3C2B|protein_coding|CODING|NM_002646.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1553921,rs386537453 -0.693147 0.449445 95 490 32 MODIFIER 11 CODING MDM4 A protein_coding NM_002393.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204518842 C A 0 228 0 0.7685 0.7859 0.7147 0.9504 0.7396 0.7382 0.796126 0.767792 0.754119 2 6398 79245 8490 7887 5528 43719 575 6648 2 8256 102998 11090 8154 6528 59258 746 8966 0 . 0 . 0 60 0,0,12,42 UTR_3_PRIME(MODIFIER||32||490|MDM4|protein_coding|CODING|NM_002393.4|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4245739 -0.693147 1.5324e-05 60 490 7911 MODIFIER 11 CODING MDM4 A protein_coding NM_002393.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204526721 G A 0 20.4 0 0.0658 0.3113 0.5058 0.3026 0.4573 0.364 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||7911||490|MDM4|protein_coding|CODING|NM_002393.4|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12118859 -0.453602 0.44 2 713 174 MODIFIER 3 CODING LRRN2 A protein_coding NM_006338.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204586805 G A 0 222 0 0.0492 0.2985 0.5029 0.3373 0.4294 0.316 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999623 0 . 0 . 57 15,11,8,18 UTR_3_PRIME(MODIFIER||174||713|LRRN2|protein_coding|CODING|NM_006338.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.928808 rs3789046 -0.692976 0.830356 57 713 167 MODIFIER 3 CODING LRRN2 T protein_coding NM_006338.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204586812 C T 0 222 0 0.0575 0.1843 0.0922 0.3075 0.2237 0.2536 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972393 0 . 0 . 55 8,20,13,10 UTR_3_PRIME(MODIFIER||167||713|LRRN2|protein_coding|CODING|NM_006338.2|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992459 rs3789045 -0.692717 0.353536 55 P692S 713 Cca/Tca MODERATE 3 MISSENSE CODING LRRN2 A protein_coding NM_006338.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204587047 G A 0 222 0 0.0575 0.1843 0.0922 0.3075 0.2237 0.2536 0.0810259 0.168307 0.213023 1 777 24089 778 2759 1454 14084 188 4049 2 10328 121060 11566 8628 6614 66510 902 16512 0.667862 0 . 0 . 86 17,30,10,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P692S|713|LRRN2|protein_coding|CODING|NM_006338.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.839158 rs11588857 -0.69311 0.131537 86 D627 713 gaC/gaT LOW 3 SILENT CODING LRRN2 A protein_coding NM_006338.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204587240 G A 0 187 0 0.0318 0.2941 0.5014 0.3383 0.4294 0.317 0.0962324 0.331386 0.45186 1 908 49005 6036 2600 3399 30206 374 5482 2 10248 119744 11356 8540 6370 65878 884 16468 0.841147 0 . 0 . 60 24,3,26,1 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D627|713|LRRN2|protein_coding|CODING|NM_006338.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.866054 rs3747632 -0.693021 0.423996 60 L518V 713 Ctc/Gtc MODERATE 3 MISSENSE CODING LRRN2 C protein_coding NM_006338.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204587569 G C 0 222 0 0.0575 0.1847 0.0922 0.3095 0.2237 0.2536 0.0812528 0.168614 0.213372 1 778 24103 782 2758 1437 14112 187 4049 2 10394 121054 11560 8578 6564 66564 904 16490 0.912719 0 . 0 . 96 17,23,23,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L518V|713|LRRN2|protein_coding|CODING|NM_006338.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.691495 rs3747631 -0.693147 0.0559652 96 H327 713 caC/caT LOW 3 SILENT CODING LRRN2 A protein_coding NM_006338.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204588140 G A 0 222 0 0.0847 0.2107 0.1153 0.3234 0.2545 0.2873 0.110304 0.199523 0.245233 1 1128 27662 983 2894 1651 16225 227 4554 2 10338 119616 11492 8572 6566 66006 894 15748 0.769125 0 . 0 . 152 25,45,33,36 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H327|713|LRRN2|protein_coding|CODING|NM_006338.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.899073 rs3747630 -0.693147 0.633266 152 P7L 713 cCa/cTa MODERATE 3 MISSENSE CODING LRRN2 A protein_coding NM_006338.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204589101 G A 0 222 0 0.0446 0.1787 0.0908 0.3085 0.2247 0.2413 0.0700229 0.167104 0.216515 1 606 22435 740 2554 1170 13370 164 3831 2 7428 95192 7408 7344 4392 53712 670 14238 0.905792 0 . 0 . 55 20,8,18,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P7L|713|LRRN2|protein_coding|CODING|NM_006338.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970174 rs3789044 -0.692717 0.186636 55 1240 86 MODIFIER 3 CODING NFASC T protein_coding NM_001005388.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204913358 G T 0 197 0 0 0.012979 0.0562 0.0238 0 0.002 0 . 0 1 10 362 252 78 2 9 0 11 2 1580 20890 1016 906 276 8832 196 8084 0.806037 0 . 0 . 42 18,5,11,5 START_GAINED(LOW||||1240|NFASC|protein_coding|CODING|NM_001005388.2|3|T),UTR_5_PRIME(MODIFIER||86||1240|NFASC|protein_coding|CODING|NM_001005388.2|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.742935 rs79130984 -0.689466 0.997681 42 V518 1240 gtC/gtA LOW 14 SILENT CODING NFASC A protein_coding NM_001005388.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204943947 C A 0 228 0 0.1952 0.4677 0.5403 0.6716 0.4125 0.6309 0.217431 0.330309 0.38814 2 2194 55077 7137 5871 3366 26511 442 9556 2 10402 121360 11568 8640 6614 66716 908 16512 0 . 0 . 0 77 0,0,22,48 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtA|V518|1240|NFASC|protein_coding|CODING|NM_001005388.2|14|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2246662 -0.693147 0.000201221 77 I971M 1240 atC/atG MODERATE 25 MISSENSE CODING NFASC G protein_coding NM_001005388.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204966428 C G 0 222 0 0.208 0.3105 0.2867 0.4345 0.2545 0.3957 0.215837 0.26302 0.283659 1 1622 29211 2629 2763 1528 15619 215 4835 2 6540 85128 7412 5680 4412 46490 686 13908 0.862358 0 . 0 COSM1338137,COSM1338138 225 64,46,61,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I971M|1240|NFASC|protein_coding|CODING|NM_001005388.2|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.806839 rs2802808 -0.693147 0.0193122 225 P1008 1240 ccT/ccC LOW 26 SILENT CODING NFASC C protein_coding NM_001005388.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204970302 T C 0 222 0 0.1573 0.2306 0.1787 0.2401 0.2575 0.3292 0.181992 0.226204 0.245533 1 1473 25906 1931 1716 1448 14681 197 4460 2 6412 84178 6822 5742 4612 47134 676 12780 0.451673 0 . 0 COSM425087 117 27,25,37,17 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1008|1240|NFASC|protein_coding|CODING|NM_001005388.2|26|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97718 rs4951151 -0.693147 0.124776 117 1240 919 MODIFIER 30 CODING NFASC C protein_coding NM_001005388.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204986586 T C 0 228 0 0.9418 0.9673 0.9726 1 0.9732 0.9581 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 32 0,0,27,3 UTR_3_PRIME(MODIFIER||919||1240|NFASC|protein_coding|CODING|NM_001005388.2|30|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2595966 -0.693097 0.613807 32 1240 2516 MODIFIER 30 CODING NFASC A protein_coding NM_001005388.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204988183 C A 0 77 0 0.4175 0.6378 0.7176 0.749 0.7575 0.6411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2516||1240|NFASC|protein_coding|CODING|NM_001005388.2|30|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs868512 -0.511536 0.833544 3 1240 3496 MODIFIER 30 CODING NFASC G protein_coding NM_001005388.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204989163 T G 0 9.7 0 0.1566 0.5335 0.6801 0.75 0.7117 0.5327 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3496||1240|NFASC|protein_coding|CODING|NM_001005388.2|30|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2841633,rs386464179 -0.379885 0 1 1240 5193 MODIFIER 30 CODING NFASC C protein_coding NM_001005388.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 204990860 G C 0 228 0 0.9402 0.9685 0.9813 1 0.9742 0.9591 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 118 0,0,105,12 UTR_3_PRIME(MODIFIER||5193||1240|NFASC|protein_coding|CODING|NM_001005388.2|30|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2802848 -0.693147 8.69649e-06 118 P366L 1040 cCt/cTt MODERATE 9 MISSENSE CODING CNTN2 T protein_coding NM_005076.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205031116 C T 0 222 0 0.323 0.5511 0.5591 0.876 0.339 0.7372 0.336058 0.341052 0.343612 1 3137 54326 7045 7474 2480 22414 392 11384 2 9114 114286 11196 8496 6374 61890 866 16350 0.999913 0 . 0 . 168 31,41,37,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P366L|1040|CNTN2|protein_coding|CODING|NM_005076.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993862 rs2229866 -0.693147 0.557858 168 S876 1040 agC/agT LOW 20 SILENT CODING CNTN2 T protein_coding NM_005076.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205041158 C T 0 222 0 0.2405 0.3566 0.3242 0.5486 0.1988 0.501 0.243078 0.222974 0.212674 1 2536 35641 4329 4678 1742 14412 271 7673 2 10386 121224 11564 8626 6602 66630 906 16510 0.99196 0 . 0 . 104 28,30,23,20 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S876|1040|CNTN2|protein_coding|CODING|NM_005076.3|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.465712 rs2229868 -0.693146 0.176032 104 1040 1446 MODIFIER 23 CODING CNTN2 G protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205044339 A G 0 65 0 0.4183 0.6066 0.5994 0.873 0.4056 0.7986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 0 . 0 . 6 2,0,2,0 UTR_3_PRIME(MODIFIER||1446||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs11240351 -0.453602 0.42 6 1040 1461 MODIFIER 23 CODING CNTN2 A protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205044354 G A 0 145 0 0.5953 0.8287 0.8948 0.9752 0.8489 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,1 UTR_3_PRIME(MODIFIER||1461||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10900443 -0.590765 0.636041 6 1040 1523 MODIFIER 23 CODING CNTN2 A protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205044416 C A 0 150 0 0.9902 0.9435 0.9251 1 0.8559 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,8,0 UTR_3_PRIME(MODIFIER||1523||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10900444 -0.651104 0.784517 9 1040 1949 MODIFIER 23 CODING CNTN2 C protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205044842 T C 0 50 0 0.1172 0.2418 0.2767 0.3938 0.1928 0.2791 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_3_PRIME(MODIFIER||1949||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs28447128 -0.511536 0.607612 4 1040 1973 MODIFIER 23 CODING CNTN2 C protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205044866 G C 0 125 0 0.5961 0.8293 0.8948 0.9762 0.8499 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||1973||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7518906 -0.556411 0.331443 5 1040 2194 MODIFIER 23 CODING CNTN2 A protein_coding NM_005076.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205045087 G A 0 39.3 0 0.4463 0.6378 0.6282 0.9315 0.4175 0.8272 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2194||1040|CNTN2|protein_coding|CODING|NM_005076.3|23|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1572993,rs386538953 -0.453602 0.44 2 L170 255 ctC/ctT LOW 1 SILENT CODING TMEM81 A protein_coding NM_203376.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205052939 G A 0 228 0 0.5008 0.7987 0.8718 0.9762 0.84 0.9243 0.561961 0.757343 0.857442 2 5755 103744 10673 8404 5858 57335 755 14964 2 10372 121360 11576 8654 6614 66724 908 16512 0 . 0 . 0 64 0,0,14,49 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L170|255|TMEM81|protein_coding|CODING|NM_203376.1|1|A),DOWNSTREAM(MODIFIER||2331||538|RBBP5|protein_coding|CODING|NM_005057.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4950979 -0.693147 0.0280344 64 R77Q 255 cGg/cAg MODERATE 1 MISSENSE CODING TMEM81 T protein_coding NM_203376.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205053219 C T 0 228 0 0.5545 0.8173 0.889 0.9762 0.8489 0.9254 0.603041 0.775104 0.863256 2 6175 104930 10767 8404 5902 57883 768 15031 2 10406 121392 11572 8654 6614 66728 908 16510 0 . 0 . 0 138 0,0,73,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R77Q|255|TMEM81|protein_coding|CODING|NM_203376.1|1|T),DOWNSTREAM(MODIFIER||2051||538|RBBP5|protein_coding|CODING|NM_005057.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4951168 -0.693147 0.012692 138 538 2286 MODIFIER 14 CODING RBBP5 C protein_coding NM_005057.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205055629 T C 0 9.7 0 0.028 0.0321 0.0288 0.0595 0.0139 0.0307 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2286||538|RBBP5|protein_coding|CODING|NM_005057.3|14|C),UPSTREAM(MODIFIER||2041||255|TMEM81|protein_coding|CODING|NM_203376.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs147327244 -0.379885 0 1 538 1966 MODIFIER 14 CODING RBBP5 A protein_coding NM_005057.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205055949 G A 0 32.6 0 0.5552 0.8173 0.889 0.9742 0.8499 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1966||538|RBBP5|protein_coding|CODING|NM_005057.3|14|A),UPSTREAM(MODIFIER||2361||255|TMEM81|protein_coding|CODING|NM_203376.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7537322 -0.379885 0 2 538 510 MODIFIER 14 CODING RBBP5 G protein_coding NM_005057.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205057405 C G 0 131 0 0.028 0.0321 0.0288 0.0595 0.0139 0.0307 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992997 0 . 0 . 46 27,2,15,1 UTR_3_PRIME(MODIFIER||510||538|RBBP5|protein_coding|CODING|NM_005057.3|14|G),UPSTREAM(MODIFIER||3817||255|TMEM81|protein_coding|CODING|NM_203376.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.763268 rs16855072 -0.689466 0.0300602 46 538 104 MODIFIER 1 CODING RBBP5 C protein_coding NM_005057.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205091105 G C 0 194 0 0.0469 0.2726 0.3127 0.5159 0.1809 0.3926 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997439 0 . 0 . 46 3,23,3,15 UTR_5_PRIME(MODIFIER||104||538|RBBP5|protein_coding|CODING|NM_005057.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.907096 rs12033568 -0.691153 0.00895123 46 929 3775 MODIFIER 13 CODING DSTYK C protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205112911 T C 0 185 0 0.4175 0.3718 0.3184 0.4008 0.2575 0.4356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.84697 0 . 0 . 33 4,13,2,14 UTR_3_PRIME(MODIFIER||3775||929|DSTYK|protein_coding|CODING|NM_015375.2|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.451687 rs3795556 -0.689466 0.697216 33 929 3091 MODIFIER 13 CODING DSTYK C protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205113595 A C 0 222 0 0.0477 0.2728 0.3112 0.5179 0.1809 0.3916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.671057 0 . 0 . 88 20,22,15,19 UTR_3_PRIME(MODIFIER||3091||929|DSTYK|protein_coding|CODING|NM_015375.2|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.573131 rs12037322 -0.693132 0.0010525 88 929 3090 MODIFIER 13 CODING DSTYK A protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205113596 G A 0 222 0 0.0477 0.2726 0.3112 0.5169 0.1809 0.3916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.440938 0 . 0 . 89 20,22,15,19 UTR_3_PRIME(MODIFIER||3090||929|DSTYK|protein_coding|CODING|NM_015375.2|13|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.369913 rs12040428,rs79993851 -0.693132 0.0010525 89 929 2853 MODIFIER 13 CODING DSTYK G protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205113833 A G 0 78 0 0.4168 0.3714 0.3184 0.4008 0.2565 0.4356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 0,5,0,6 UTR_3_PRIME(MODIFIER||2853||929|DSTYK|protein_coding|CODING|NM_015375.2|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.683497 rs3183297 -0.616816 0.87834 11 929 1536 MODIFIER 13 CODING DSTYK A protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205115150 C A 0 9.7 0 0.4175 0.3684 0.317 0.4008 0.2416 0.4356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1536||929|DSTYK|protein_coding|CODING|NM_015375.2|13|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1061132 -0.379885 0 1 929 947 MODIFIER 13 CODING DSTYK A protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205115739 G A 0 9.7 0 0.4191 0.3688 0.317 0.4008 0.2416 0.4356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||947||929|DSTYK|protein_coding|CODING|NM_015375.2|13|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11808879 -0.379885 0 1 929 51 MODIFIER 13 CODING DSTYK T protein_coding NM_015375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205116635 A T 0 222 0 0.0477 0.273 0.3112 0.5188 0.1809 0.3916 0.0764866 0.162079 0.20593 1 770 28931 4134 4393 1121 13134 216 5163 2 10292 117712 11502 8600 6606 65568 868 14276 0.253156 0 . 0 . 106 31,18,24,21 UTR_3_PRIME(MODIFIER||51||929|DSTYK|protein_coding|CODING|NM_015375.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988035 rs11367 -0.693147 0.124726 106 F676 929 ttC/ttT LOW 8 SILENT CODING DSTYK A protein_coding NM_015375.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205129319 G A 0 222 0 0.4175 0.3714 0.3184 0.4008 0.2565 0.4346 0.382206 0.285637 0.236163 1 3964 36524 4018 3561 2063 15840 258 6820 2 10404 121358 11572 8620 6614 66734 908 16506 0.998987 0 . 0 . 84 18,23,22,15 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F676|929|DSTYK|protein_coding|CODING|NM_015375.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.983011 0.982124 0 0.751724 rs1062715 -0.693141 0.0720789 84 C641R 929 Tgt/Cgt MODERATE 7 MISSENSE CODING DSTYK G protein_coding NM_015375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205130413 A G 0 228 0 0.9947 0.9611 0.9424 1 0.8946 0.9571 0.9798 0.930186 0.904767 2 10248 113101 11209 8654 6120 60387 821 15662 2 10404 121396 11578 8654 6614 66726 908 16512 0 . 0 . 0 49 0,0,32,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C641R|929|DSTYK|protein_coding|CODING|NM_015375.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3851294 -0.693147 0.00385256 49 L64F 929 Ctc/Ttc MODERATE 1 MISSENSE CODING DSTYK A protein_coding NM_015375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205180474 G A 0 222 0 0.0295 0.0347 0.0274 0.0625 0.0159 0.0378 0.0270209 0.0215318 0.0187209 1 290 3164 320 508 175 1227 37 607 2 8564 106216 10466 7864 4934 58448 774 15166 0.3073 0 . 0 . 144 42,24,32,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L64F|929|DSTYK|protein_coding|CODING|NM_015375.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.20691 rs78212113 -0.693147 0.927894 144 709 336 MODIFIER 1 CODING TMCC2 T protein_coding NM_014858.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205197357 G T 0 43.4 0 0.0303 0.0351 0.0274 0.0625 0.0169 0.0378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.333333 0 . 0 . 6 3,0,2,0 UTR_5_PRIME(MODIFIER||336||709|TMCC2|protein_coding|CODING|NM_014858.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs77230573 -0.453602 0.28 6 709 254 MODIFIER 1 CODING TMCC2 A protein_coding NM_014858.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205197439 G A 0 114 0 0.0303 0.0349 0.0274 0.0625 0.0159 0.0378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.834543 0 . 0 . 16 6,1,7,0 UTR_5_PRIME(MODIFIER||254||709|TMCC2|protein_coding|CODING|NM_014858.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 1 0 0.925999 rs78966833 -0.636426 0.0992599 16 T39M 709 aCg/aTg MODERATE 1 MISSENSE CODING TMCC2 T protein_coding NM_014858.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205197808 C T 0 222 0 0.0303 0.0351 0.0274 0.0625 0.0159 0.0389 0.0270209 0.0215385 0.0187296 1 299 3211 322 519 183 1241 34 613 2 8978 110304 10732 8030 5630 60334 802 15798 0.73042 0 . 0 . 119 20,34,23,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T39M|709|TMCC2|protein_coding|CODING|NM_014858.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970976 rs112979653 -0.693147 0.0613576 119 709 407 MODIFIER 5 CODING TMCC2 C protein_coding NM_014858.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205241659 T C 0 61 0 0.9947 0.9619 0.9424 1 0.8986 0.9571 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||407||709|TMCC2|protein_coding|CODING|NM_014858.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17728 -0.511536 0.450604 3 672 286 MODIFIER 7 CODING NUAK2 T protein_coding NM_030952.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205272292 C T 0 9.7 0 0.4145 0.2131 0.1254 0.1151 0.1302 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||286||672|NUAK2|protein_coding|CODING|NM_030952.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7550061 -0.379885 0 1 G239 672 ggT/ggC LOW 5 SILENT CODING NUAK2 G protein_coding NM_030952.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205275421 A G 0 228 0 0.9259 0.9792 0.9928 1 0.999 1 0.941217 0.979471 0.99907 2 9792 120579 11516 8654 6614 66616 899 16488 2 10406 121328 11578 8654 6614 66676 908 16492 0 . 0 . 0 97 0,0,37,49 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G239|672|NUAK2|protein_coding|CODING|NM_030952.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4951197 -0.693147 0.069563 97 T32I 672 aCt/aTt MODERATE 1 MISSENSE CODING NUAK2 A protein_coding NM_030952.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205290794 G A 0 79 0 0.4879 0.2899 0.1974 0.0913 0.2972 0.2853 0.447768 0.362519 0.319004 1 2748 24618 1419 475 1122 14872 161 3821 2 5622 75634 6374 5352 3160 42366 546 12214 0.974597 0 . 0 . 10 0,5,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T32I|672|NUAK2|protein_coding|CODING|NM_030952.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.974597 1 0 0.649731 rs3738746 -0.556411 0.0550934 10 350 1078 MODIFIER 9 CODING KLHDC8A T protein_coding NM_001271863.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205305449 C T 0 61 0 0.2776 0.1727 0.111 0.0258 0.2594 0.137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.923116 0 . 0 . 14 9,0,5,0 UTR_3_PRIME(MODIFIER||1078||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.945959 rs10900480 -0.590765 0.575151 14 350 602 MODIFIER 9 CODING KLHDC8A A protein_coding NM_001271863.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205305925 G A 0 157 0 0.1989 0.1516 0.1081 0.0258 0.2594 0.137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.953497 0 . 0 . 14 0,4,1,8 UTR_3_PRIME(MODIFIER||602||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.651439 rs10900481 -0.662043 0.778467 14 350 82 MODIFIER 9 CODING KLHDC8A T protein_coding NM_001271863.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205306445 C T 0 146 0 0.202 0.1546 0.1095 0.0268 0.2674 0.138 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.937601 0 . 0 . 26 13,0,12,1 UTR_3_PRIME(MODIFIER||82||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.898967 rs72747066 -0.683931 0.123415 26 A330 350 gcC/gcT LOW 9 SILENT CODING KLHDC8A A protein_coding NM_001271863.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205306590 G A 0 222 0 0.0219 0.1785 0.17 0.3383 0.2127 0.1963 0.0460735 0.138936 0.186512 1 463 22393 2054 2872 1276 12421 175 3132 2 10406 121364 11578 8624 6614 66724 908 16510 0.998641 0 . 0 . 89 27,17,19,18 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A330|350|KLHDC8A|protein_coding|CODING|NM_001271863.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.70885 rs3210952 -0.693141 0.410876 89 F248 350 ttC/ttT LOW 7 SILENT CODING KLHDC8A A protein_coding NM_001271863.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205308335 G A 0 157 0 0.2247 0.1833 0.1354 0.0317 0.2942 0.2035 0.224013 0.276795 0.303837 1 2265 30175 1299 259 1994 20267 210 3881 2 10130 119924 11432 8590 6524 66006 884 16358 0.332145 0 . 0 . 101 51,1,48,1 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F248|350|KLHDC8A|protein_coding|CODING|NM_001271863.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988889 rs1105385 -0.693147 0.181731 101 R237 350 cgG/cgA LOW 7 SILENT CODING KLHDC8A T protein_coding NM_001271863.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205308368 C T 0 222 0 0.2247 0.1801 0.134 0.0308 0.2813 0.2025 0.223332 0.272336 0.297442 1 2270 29582 1276 256 1887 19834 207 3852 2 10332 120866 11526 8622 6584 66444 898 16460 0.850435 0 . 0 . 150 66,6,63,7 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R237|350|KLHDC8A|protein_coding|CODING|NM_001271863.1|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974683 rs1105387 -0.693147 0.308571 150 350 35 MODIFIER 5 CODING KLHDC8A T protein_coding NM_001271863.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205312767 G T 0 8.2 0 0.1989 0.3193 0.402 0.3522 0.4374 0.2679 0.21421 0.316145 0.365528 1 1546 32719 3641 2578 1552 20282 244 2876 2 5808 81868 8944 6670 3718 47364 522 8842 0.833333 0 . 0 . 8 0,6,0,2 UTR_5_PRIME(MODIFIER||35||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.333333 rs7526603 -0.453602 0.1 8 350 HIGH 3 CODING KLHDC8A T protein_coding NM_001271863.1 SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205317503 C T 0 46.3 0 0.1399 0.1947 0.0893 0.2143 0.172 0.3466 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 SPLICE_SITE_DONOR+INTRON(HIGH||||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|3|T) 0 . 0 . 0 1 0 . 0 (KLHDC8A|KLHDC8A|1|1.00) 60 0 0 1 0 . rs12059162 -0.453602 0.22 2 350 4944 MODIFIER 3 CODING KLHDC8A C protein_coding NM_001271863.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205317676 T C 0 9.7 0 0.4992 0.6919 0.768 0.6875 0.7674 0.8252 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||4944||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7517617 -0.379885 0 1 350 4952 MODIFIER 3 CODING KLHDC8A A protein_coding NM_001271863.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205317684 C A 0 9.7 0 0.9902 0.9974 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 START_GAINED(LOW||||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|3|A),UTR_5_PRIME(MODIFIER||4952||350|KLHDC8A|protein_coding|CODING|NM_001271863.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7548748 -0.379885 0 1 V92 504 gtA/gtG LOW 3 SILENT CODING CDK18 G protein_coding NM_212503.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205492756 A G 0 222 0 0.9531 0.9213 0.9352 0.7659 0.9642 0.9847 0.947053 0.959382 0.965659 1 3897 38462 2018 1829 966 20378 319 9055 2 4134 40396 2206 2404 1004 21116 338 9194 0.916303 0 . 0 . 121 39,13,38,18 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V92|504|CDK18|protein_coding|CODING|NM_212503.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850663 rs7529442 -0.693147 0.0750576 121 504 675 MODIFIER 16 CODING CDK18 C protein_coding NM_212503.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205501181 T C 0 222 0 0.4592 0.4914 0.4496 0.5833 0.5109 0.4499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.840105 0 . 0 . 59 17,10,23,6 UTR_3_PRIME(MODIFIER||675||504|CDK18|protein_coding|CODING|NM_212503.2|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99916 rs3820377 -0.693079 0.508162 59 504 963 MODIFIER 16 CODING CDK18 G protein_coding NM_212503.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205501469 A G 0 222 0 0.2716 0.3884 0.4409 0.3899 0.332 0.5654 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.938105 0 . 0 . 140 30,57,8,33 UTR_3_PRIME(MODIFIER||963||504|CDK18|protein_coding|CODING|NM_212503.2|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.366368 rs1042832 -0.693145 0.0953005 140 504 1015 MODIFIER 16 CODING CDK18 G protein_coding NM_212503.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205501521 A G 0 219 0 0.2315 0.3444 0.3458 0.3631 0.3131 0.5092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.709834 0 . 0 . 88 17,35,4,26 UTR_3_PRIME(MODIFIER||1015||504|CDK18|protein_coding|CODING|NM_212503.2|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.5131 rs14028 -0.693097 0.286445 88 504 1337 MODIFIER 16 CODING CDK18 G protein_coding NM_212503.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205501843 A G 0 222 0 0.233 0.3772 0.438 0.3899 0.331 0.5634 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950379 0 . 0 . 76 29,6,28,5 UTR_3_PRIME(MODIFIER||1337||504|CDK18|protein_coding|CODING|NM_212503.2|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.779644 rs8027 -0.693127 0.668852 76 514 1370 MODIFIER 10 CODING MFSD4 C protein_coding NM_181644.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205570959 T C 0 9.7 0 0.1536 0.3512 0.3948 0.6399 0.1849 0.4611 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1370||514|MFSD4|protein_coding|CODING|NM_181644.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7555438 -0.379885 0 1 514 1878 MODIFIER 10 CODING MFSD4 T protein_coding NM_181644.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205571467 C T 0 228 0 0.1528 0.351 0.3948 0.6399 0.1849 0.4611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 139 1,0,113,18 UTR_3_PRIME(MODIFIER||1878||514|MFSD4|protein_coding|CODING|NM_181644.4|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs16856019 -0.693147 0.220023 139 514 2204 MODIFIER 10 CODING MFSD4 G protein_coding NM_181644.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205571793 A G 0 228 0 0.1536 0.3514 0.3948 0.6399 0.1859 0.4611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 34 0,0,2,30 UTR_3_PRIME(MODIFIER||2204||514|MFSD4|protein_coding|CODING|NM_181644.4|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4951014 -0.69312 0.603537 34 431 5358 MODIFIER 5 CODING ELK4 C protein_coding NM_001973.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205580316 T C 0 9.7 0 0.4372 0.4219 0.3919 0.625 0.166 0.4765 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5358||431|ELK4|protein_coding|CODING|NM_001973.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4573566 -0.379885 0 1 431 1287 MODIFIER 5 CODING ELK4 A protein_coding NM_001973.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205584387 C A 0 9.7 0 0.0454 0.1685 0.1095 0.371 0.0696 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1287||431|ELK4|protein_coding|CODING|NM_001973.3|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs35219050 -0.379885 0 1 P200 431 ccG/ccA LOW 3 SILENT CODING ELK4 T protein_coding NM_001973.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205589574 C T 0 228 0 0.146 0.1959 0.1153 0.37 0.0706 0.2699 0.130277 0.104106 0.0906977 2 1337 15858 1764 2983 755 5528 111 3380 2 10398 121386 11578 8644 6612 66734 908 16512 0 . 0 . 0 96 0,0,38,50 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P200|431|ELK4|protein_coding|CODING|NM_001973.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1064406 -0.693147 0.0832826 96 553 1367 MODIFIER 5 CODING SLC45A3 G protein_coding NM_033102.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205626995 C G 0 228 0 0.0575 0.1665 0.098 0.3819 0.0557 0.2546 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.705714 0 . 0 . 194 1,1,134,41 UTR_3_PRIME(MODIFIER||1367||553|SLC45A3|protein_coding|CODING|NM_033102.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.677143 rs34244565 -0.693147 0.31437 194 553 289 MODIFIER 5 CODING SLC45A3 A protein_coding NM_033102.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205628073 G A 0 160 0 0.0567 0.0853 0.0331 0.2014 0.0219 0.1063 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.562558 0 . 0 . 60 4,28,1,26 UTR_3_PRIME(MODIFIER||289||553|SLC45A3|protein_coding|CODING|NM_033102.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.795173 rs2275753 -0.693021 0.0966798 60 243 4128 MODIFIER 7 CODING NUCKS1 C protein_coding NM_022731.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205683280 T C 0 9.7 0 0.9932 0.998 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4128||243|NUCKS1|protein_coding|CODING|NM_022731.4|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6593965 -0.379885 0 1 203 2020 MODIFIER 6 CODING RAB29 C protein_coding NM_001135662.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205737450 T C 0 32.6 0 0.6263 0.8209 0.8444 0.8552 0.9662 0.8824 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2020||203|RAB29|protein_coding|CODING|NM_001135662.1|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs844005 -0.379885 0 2 203 278 MODIFIER 6 CODING RAB29 C protein_coding NM_001135662.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205739192 T C 0 22.7 0 0.6263 0.8211 0.8444 0.8552 0.9662 0.8834 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||278||203|RAB29|protein_coding|CODING|NM_001135662.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs823138 -0.453602 0.6 3 203 204 MODIFIER 6 CODING RAB29 T protein_coding NM_001135662.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205739266 C T 0 54 0 0.1672 0.4147 0.379 0.5079 0.5318 0.5583 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 9 4,1,3,0 UTR_3_PRIME(MODIFIER||204||203|RAB29|protein_coding|CODING|NM_001135662.1|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.900802 rs708723 -0.511536 0.645206 9 203 74 MODIFIER 6 CODING RAB29 G protein_coding NM_001135662.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205739396 T G 0 136 0 0.441 0.721 0.7767 0.8462 0.8579 0.7904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980497 0 . 0 . 31 13,1,16,1 UTR_3_PRIME(MODIFIER||74||203|RAB29|protein_coding|CODING|NM_001135662.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.611167 rs823139 -0.690438 0.194975 31 203 462 MODIFIER 1 CODING RAB29 A protein_coding NM_001135662.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205744546 C A 0 9.7 0 0.3563 0.5367 0.4798 0.5089 0.7515 0.6288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||462||203|RAB29|protein_coding|CODING|NM_001135662.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs823144 -0.379885 0 1 T113 513 acC/acT LOW 2 SILENT CODING SLC41A1 A protein_coding NM_173854.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205779231 G A 0 222 0 0.0174 0.2766 0.1873 0.5198 0.2883 0.4274 0.0635497 0.211133 0.286744 1 555 35745 2187 4919 1936 19635 276 6237 2 10376 121226 11564 8630 6574 66676 902 16504 0.975197 0 . 0 COSM146744 120 44,12,38,17 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T113|513|SLC41A1|protein_coding|CODING|NM_173854.5|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.726624 rs11240569 -0.693147 0.853531 120 T293 502 acT/acA LOW 7 SILENT CODING PM20D1 T protein_coding NM_152491.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205811828 A T 0 222 0 0.4183 0.2845 0.2421 0.2917 0.1352 0.2802 0.367227 0.212825 0.133721 1 3819 23981 3448 2402 828 8818 157 4509 2 10406 121392 11574 8644 6614 66734 908 16512 0.306898 0 . 0 COSM146745 147 37,33,33,33 SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T293|502|PM20D1|protein_coding|CODING|NM_152491.4|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997869 rs4951025 -0.693147 0.630343 147 R153W 502 Cgg/Tgg MODERATE 3 MISSENSE CODING PM20D1 A protein_coding NM_152491.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205814485 G A 0 222 0 0.1868 0.2498 0.2536 0.255 0.2515 0.3252 0.203132 0.233738 0.249419 1 2011 31966 3211 2237 1658 17152 243 5454 2 10402 121376 11574 8634 6612 66734 908 16512 0.331402 0 . 0 . 107 42,16,26,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R153W|502|PM20D1|protein_coding|CODING|NM_152491.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.130098 rs1104899 -0.693144 0.140548 107 I149V 502 Atc/Gtc MODERATE 3 MISSENSE CODING PM20D1 C protein_coding NM_152491.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205814497 T C 0 228 0 0.8744 0.8385 0.8386 0.7411 0.9344 0.7914 0.884022 0.924958 0.94593 2 9170 107224 8324 6400 6072 63041 819 13398 2 10406 121396 11576 8642 6614 66738 908 16512 0 . 0 . 0 107 0,0,64,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I149V|502|PM20D1|protein_coding|CODING|NM_152491.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1891460 -0.693147 0.050245 107 H84R 502 cAt/cGt MODERATE 2 MISSENSE CODING PM20D1 C protein_coding NM_152491.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205817018 T C 0 222 0 0.0545 0.1556 0.062 0.3978 0.0964 0.1697 0.0572467 0.0670628 0.0721131 1 647 12779 510 3630 501 5038 92 2361 2 9602 118106 11338 8444 6532 65140 876 16174 0.995735 0 . 0 . 104 41,16,28,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H84R|502|PM20D1|protein_coding|CODING|NM_152491.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 49 0 0.990662 1.05619e-11 0 0.952604 rs11540015,rs201477375 -0.693146 0.0238154 104 A54 502 gcG/gcA LOW 1 SILENT CODING PM20D1 T protein_coding NM_152491.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205819039 C T 0 222 0 0.053 0.1601 0.0605 0.4246 0.0964 0.1687 0.0601453 0.0701215 0.0752326 1 656 12979 513 3813 503 5059 99 2336 2 10348 119390 11556 8624 6608 66168 884 15202 0.903041 0 . 0 . 115 38,13,31,18 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A54|502|PM20D1|protein_coding|CODING|NM_152491.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.842188 rs11540016 -0.693147 0.00730494 115 H33Y 502 Cat/Tat MODERATE 1 MISSENSE CODING PM20D1 A protein_coding NM_152491.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205819104 G A 0 222 0 0.053 0.1609 0.0605 0.4266 0.0974 0.1697 0.0603722 0.0702753 0.0753488 1 658 13048 515 3804 501 5084 100 2386 2 10402 121308 11568 8628 6608 66690 906 16506 0.776734 0 . 0 . 93 20,23,14,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H33Y|502|PM20D1|protein_coding|CODING|NM_152491.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.461273 rs11540014 -0.693145 0.136753 93 887 1566 MODIFIER 22 CODING SLC26A9 T protein_coding NM_134325.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205882454 C T 0 142 0 0.062 0.1653 0.0634 0.4296 0.0984 0.1738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996401 0 . 0 . 27 9,0,16,0 UTR_3_PRIME(MODIFIER||1566||887|SLC26A9|protein_coding|CODING|NM_134325.2|22|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.493254 rs2282430 -0.689466 0.120349 27 887 130 MODIFIER 22 CODING SLC26A9 C protein_coding NM_134325.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205883890 G C 0 222 0 0.0499 0.1166 0.0187 0.4494 0.003 0.0501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.897025 0 . 0 . 158 59,20,47,21 UTR_3_PRIME(MODIFIER||130||887|SLC26A9|protein_coding|CODING|NM_134325.2|22|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.934827 rs11240589 -0.693147 0.104079 158 Y222 887 taC/taT LOW 6 SILENT CODING SLC26A9 A protein_coding NM_134325.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 205899071 G A 0 222 0 0 0.0011981 0 0.006 0 0 0 . 0 1 0 69 0 69 0 0 0 0 2 10380 121084 11568 8646 6592 66606 900 16392 0.542914 0 . 0 . 110 33,17,35,18 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y222|887|SLC26A9|protein_coding|CODING|NM_134325.2|6|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.985391 rs146581591 -0.693147 0.0593713 110 R21W 371 Cgg/Tgg MODERATE 1 MISSENSE CODING SRGAP2C T protein_coding NM_001271872.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206516261 C T 0 132 0 . 0 . 0 . 0 . 0 . 1 3871 46550 3902 3135 2807 25559 372 6904 2 7744 93164 7808 6272 5618 51158 744 13820 0.233316 0 . 0 . 114 53,5,56,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R21W|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R21W|984|SRGAP2|protein_coding|CODING|NM_015326.4|1|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 1 0 49 0 0.921161 0.00105922 0 0.999803 rs201036189 -0.693147 0.382416 114 R21W 984 Cgg/Tgg MODERATE 1 MISSENSE CODING SRGAP2 T protein_coding NM_015326.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206516261 C T 0 132 0 . 0 . 0 . 0 . 0 . 1 3871 46550 3902 3135 2807 25559 372 6904 2 7744 93164 7808 6272 5618 51158 744 13820 0.233316 0 . 0 . 114 53,5,56,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R21W|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R21W|984|SRGAP2|protein_coding|CODING|NM_015326.4|1|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 0 . 0 1 0 49 0 0.921161 0.00105922 0 0.999803 rs201036189 -0.693147 0.382416 114 N125 371 aaC/aaT LOW 3 SILENT CODING SRGAP2C T protein_coding NM_001271872.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206566195 C T 0 115 0 . 0 . 0 . 0 . 0 . 1 2053 27641 2705 2669 1716 15162 214 3122 2 7502 92004 8390 6832 4984 50760 678 12858 0.847449 0 . 0 COSM1127171 329 99,127,30,35 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N125|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|3|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N125|984|SRGAP2|protein_coding|CODING|NM_015326.4|3|T|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 1 0 40 0 0.574479 0.123668 0 0.983965 rs12090039,rs200978831 -0.693147 0.107742 329 N125 984 aaC/aaT LOW 3 SILENT CODING SRGAP2 T protein_coding NM_015326.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206566195 C T 0 115 0 . 0 . 0 . 0 . 0 . 1 2053 27641 2705 2669 1716 15162 214 3122 2 7502 92004 8390 6832 4984 50760 678 12858 0.847449 0 . 0 COSM1127171 329 99,127,30,35 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N125|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|3|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N125|984|SRGAP2|protein_coding|CODING|NM_015326.4|3|T|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 1 0 40 0 0.574479 0.123668 0 0.983965 rs12090039,rs200978831 -0.693147 0.107742 329 R148 371 cgT/cgC LOW 4 SILENT CODING SRGAP2C C protein_coding NM_001271872.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206566904 T C 0 222 0 0.497 0.4944 0.4942 0.4851 0.495 0.5 0 . 0 1 4890 60219 5756 4300 3306 33282 447 8238 2 9782 120516 11532 8612 6612 66600 896 16482 0.595702 0 . 0 . 247 104,26,89,17 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R148|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|4|C|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R148|984|SRGAP2|protein_coding|CODING|NM_015326.4|4|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 53 0 5.34351e-08 0.204784 0 0.342681 rs2919105 -0.693147 2.58846e-06 247 R148 984 cgT/cgC LOW 4 SILENT CODING SRGAP2 C protein_coding NM_015326.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206566904 T C 0 222 0 0.497 0.4944 0.4942 0.4851 0.495 0.5 0 . 0 1 4890 60219 5756 4300 3306 33282 447 8238 2 9782 120516 11532 8612 6612 66600 896 16482 0.595702 0 . 0 . 247 104,26,89,17 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R148|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|4|C|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R148|984|SRGAP2|protein_coding|CODING|NM_015326.4|4|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 53 0 5.34351e-08 0.204784 0 0.342681 rs2919105 -0.693147 2.58846e-06 247 F319 371 ttT/ttC LOW 7 SILENT CODING SRGAP2C C protein_coding NM_001271872.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206579798 T C 0 44.7 0 . 0 . 0 . 0 . 0 . 1 2109 26554 1466 1512 1714 14160 239 5354 2 4206 53040 2930 3016 3424 28290 478 10696 0.957518 0 . 0 . 62 9,35,18,0 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F319|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|7|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F320|984|SRGAP2|protein_coding|CODING|NM_015326.4|7|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.91607 0.847634 0 0.0363845 rs200703951 -0.691153 0.394181 62 F320 984 ttT/ttC LOW 7 SILENT CODING SRGAP2 C protein_coding NM_015326.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206579798 T C 0 44.7 0 . 0 . 0 . 0 . 0 . 1 2109 26554 1466 1512 1714 14160 239 5354 2 4206 53040 2930 3016 3424 28290 478 10696 0.957518 0 . 0 . 62 9,35,18,0 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F319|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|7|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F320|984|SRGAP2|protein_coding|CODING|NM_015326.4|7|C|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.91607 0.847634 0 0.0363845 rs200703951 -0.691153 0.394181 62 984 LOW 7 CODING SRGAP2 G protein_coding NM_015326.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206579936 A G 0 78 0 . 0 . 0 . 0 . 0 . 1 3053 42334 3676 2840 2532 23377 327 6529 2 6474 86062 7510 5734 5110 47404 666 13164 0.923654 0 . 0 . 37 20,1,16,0 SPLICE_SITE_REGION+INTRON(LOW||||984|SRGAP2|protein_coding|CODING|NM_015326.4|7|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V365|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|7|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 30 0 0.858769 1 0 0.36996 rs201644221,rs2772061 -0.689466 0.244131 37 V365 371 gtA/gtG LOW 7 SILENT CODING SRGAP2C G protein_coding NM_001271872.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206579936 A G 0 78 0 . 0 . 0 . 0 . 0 . 1 3053 42334 3676 2840 2532 23377 327 6529 2 6474 86062 7510 5734 5110 47404 666 13164 0.923654 0 . 0 . 37 20,1,16,0 SPLICE_SITE_REGION+INTRON(LOW||||984|SRGAP2|protein_coding|CODING|NM_015326.4|7|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V365|371|SRGAP2C|protein_coding|CODING|NM_001271872.1|7|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 30 0 0.858769 1 0 0.36996 rs201644221,rs2772061 -0.689466 0.244131 37 371 127 MODIFIER 7 CODING SRGAP2C G protein_coding NM_001271872.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206580084 C G 0 121 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994676 0 . 0 . 36 1,16,1,16 UTR_3_PRIME(MODIFIER||127||371|SRGAP2C|protein_coding|CODING|NM_001271872.1|7|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRON(MODIFIER||||984|SRGAP2|protein_coding|CODING|NM_015326.4|7|G|WARNING_TRANSCRIPT_NO_START_CODON),INTRAGENIC(MODIFIER|||||SRGAP2D||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 . 0 33 0 0.967184 0.609375 0 0.415099 rs143665212,rs2772060 -0.690438 0.00855081 36 L419 984 ctG/ctA LOW 11 SILENT CODING SRGAP2 A protein_coding NM_015326.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206603535 G A 0 222 0 0.4175 0.525 0.5634 0.7024 0.4334 0.5542 0.404524 0.436899 0.451804 1 4095 59519 6047 6125 3452 30818 398 8584 2 9800 120746 11572 8616 6614 66734 898 16512 0.790967 0 . 0 COSM1338270 189 44,36,55,34 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L419|984|SRGAP2|protein_coding|CODING|NM_015326.4|11|A|WARNING_TRANSCRIPT_NO_START_CODON) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981426 rs2297539 -0.693147 0.5285 189 984 805 MODIFIER 20 CODING SRGAP2 T protein_coding NM_015326.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206635570 C T 0 228 0 0.0817 0.2933 0.3588 0.6508 0.1889 0.272 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 82 0,0,58,15 UTR_3_PRIME(MODIFIER||805||984|SRGAP2|protein_coding|CODING|NM_015326.4|20|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11576488 -0.693147 0.2518 82 716 2799 MODIFIER 1 CODING IKBKE G protein_coding NM_014002.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206643772 C G 0 9.7 0 0.0968 0.2376 0.3026 0.5188 0.1133 0.2198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2799||716|IKBKE|protein_coding|CODING|NM_014002.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2297550 -0.379885 0 1 Q52 716 caA/caG LOW 4 SILENT CODING IKBKE G protein_coding NM_014002.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206647742 A G 0 228 0 1 0.9994 1 1 0.997 1 1 0.998385 0.997558 2 10401 121207 11560 8650 6609 66585 906 16496 2 10406 121374 11570 8650 6614 66718 906 16510 0 . 0 . 0 73 0,0,31,38 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q52|716|IKBKE|protein_coding|CODING|NM_014002.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1539242 -0.693147 0.366194 73 I67 716 atT/atC LOW 4 SILENT CODING IKBKE C protein_coding NM_014002.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206647787 T C 0 228 0 0.8797 0.8992 0.9207 0.9732 0.835 0.8998 0.86995 0.845917 0.833605 2 9079 103781 10775 8436 5481 54883 784 14343 2 10372 120802 11544 8640 6558 66324 904 16460 0 . 0 . 0 55 0,0,15,36 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I67|716|IKBKE|protein_coding|CODING|NM_014002.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1539243 -0.693147 0.573272 55 T239 716 acG/acA LOW 8 SILENT CODING IKBKE A protein_coding NM_014002.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206651107 G A 0 222 0 0.1558 0.3155 0.402 0.6131 0.2286 0.2526 0.163995 0.19416 0.209572 1 633 8917 798 1292 176 4016 73 1929 2 2738 27450 1658 1900 390 12474 240 8050 0.851808 0 . 0 COSM425146 83 14,25,23,14 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T239|716|IKBKE|protein_coding|CODING|NM_014002.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.831269 rs2297545 -0.693141 0.185503 83 P713L 716 cCt/cTt MODERATE 22 MISSENSE CODING IKBKE T protein_coding NM_014002.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206669465 C T 0 222 0 0.0182 0.1482 0.3256 0.1935 0.2326 0.0644 0.0442578 0.159234 0.21814 1 398 23420 3162 1841 1829 14633 188 1369 2 10400 121352 11568 8644 6608 66714 908 16510 0.570878 0 . 0 COSM1178403 205 76,28,57,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P713L|716|IKBKE|protein_coding|CODING|NM_014002.3|22|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.718378 rs3748022 -0.693147 0.0339876 205 716 691 MODIFIER 22 CODING IKBKE C protein_coding NM_014002.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206670169 G C 0 9.7 0 0.3411 0.4283 0.3991 0.3393 0.4881 0.5971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||691||716|IKBKE|protein_coding|CODING|NM_014002.3|22|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10836 -0.379885 0 1 L16 418 ctA/ctC LOW 1 SILENT CODING RASSF5 C protein_coding NM_182663.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206680983 A C 0 228 0 0.9955 0.9537 0.9323 1 0.8519 0.9693 0.972635 0.888293 0.850214 2 2092 36802 5142 3126 694 16925 238 8585 2 2158 41792 5502 3128 854 20788 272 9090 0 . 0 . COSM1338281 59 0,0,30,22 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctC|L16|418|RASSF5|protein_coding|CODING|NM_182663.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2095124 -0.693147 0.373006 59 418 164 MODIFIER 6 CODING RASSF5 C protein_coding NM_182663.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206760474 T C 0 89 0 0.8321 0.7764 0.7954 0.6964 0.831 0.7137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.783809 0 . 0 . 11 0,6,1,3 UTR_3_PRIME(MODIFIER||164||418|RASSF5|protein_coding|CODING|NM_182663.3|6|C),DOWNSTREAM(MODIFIER||4500||584|EIF2D|protein_coding|CODING|NM_006893.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.727822 rs7541244 -0.556411 0.745967 11 P302 584 ccT/ccC LOW 8 SILENT CODING EIF2D G protein_coding NM_006893.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206773659 A G 0 228 0 0.9992 0.9998 1 1 1 1 0.999092 0.999616 0.999884 2 10403 121392 11578 8654 6614 66727 908 16508 2 10406 121396 11578 8654 6614 66728 908 16508 0 . 0 . 0 125 0,0,47,61 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P302|584|EIF2D|protein_coding|CODING|NM_006893.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6662929 -0.693147 0.00145594 125 L72 400 ctG/ctC LOW 1 SILENT CODING MAPKAPK2 C protein_coding NM_032960.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 206858790 G C 0 222 0 0 0.0021965 0 0.0099 0 0.001 0.000226963 7.6888e-05 0 1 0 81 2 74 0 1 0 4 2 10048 118670 11396 8528 6574 64998 878 16248 0.678993 0 . 0 . 137 46,15,33,14 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L72|400|MAPKAPK2|protein_coding|CODING|NM_032960.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997005 rs144830172 -0.693147 0.112321 137 F213S 215 tTc/tCc MODERATE 6 MISSENSE CODING IL19 C protein_coding NM_153758.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207015957 T C 0 222 0 0.8185 0.6729 0.6729 0.3363 0.7724 0.7209 0.831744 0.796259 0.778062 1 4319 33533 1712 1152 1025 18695 247 6383 2 5188 44834 2540 2644 1352 23506 348 9256 0.932177 0 . 0 . 125 22,36,24,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F213S|215|IL19|protein_coding|CODING|NM_153758.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.318291 rs2243191 -0.693147 0.115381 125 215 258 MODIFIER 6 CODING IL19 G protein_coding NM_153758.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207016225 A G 0 76 0 0.5431 0.5887 0.6441 0.3333 0.7575 0.7004 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 0,3,0,5 UTR_3_PRIME(MODIFIER||258||215|IL19|protein_coding|CODING|NM_153758.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 0 . 0.300267 rs2243193 -0.590765 0.400625 8 Y125H 207 Tac/Cac MODERATE 5 MISSENSE CODING IL24 C protein_coding NM_001185156.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207074905 T C 0 228 0 0.2905 0.3157 0.438 0.2123 0.4533 0.228 0.295733 0.411964 0.471512 2 3036 48235 5317 1860 2499 31015 385 4123 2 10398 121304 11558 8622 6610 66702 906 16508 0 . 0 . 0 108 0,0,49,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y125H|207|IL24|protein_coding|CODING|NM_001185156.1|5|C),DOWNSTREAM(MODIFIER||1726||390|FCMR|protein_coding|CODING|NM_005449.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1150258,rs386518535 -0.693147 0.110746 108 S14 390 tcG/tcA LOW 2 SILENT CODING FCMR T protein_coding NM_005449.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207087435 C T 0 228 0 0.1717 0.2442 0.3069 0.1339 0.4543 0.1953 0.20177 0.376442 0.46593 2 2026 43768 3259 1254 2518 30623 368 3720 2 10300 120788 11556 8614 6604 66458 908 16348 0 . 0 . 0 34 0,0,6,25 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S14|390|FCMR|protein_coding|CODING|NM_005449.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs167082 -0.69311 0.00948348 34 764 1370 MODIFIER 11 CODING PIGR T protein_coding NM_002644.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207102293 A T 0 151 0 0.1619 0.2875 0.3256 0.3294 0.4543 0.2157 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||1370||764|PIGR|protein_coding|CODING|NM_002644.3|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13190 -0.676189 0.159794 11 G365S 764 Ggc/Agc MODERATE 5 MISSENSE CODING PIGR T protein_coding NM_002644.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207109116 C T 0 228 0 0.1944 0.2963 0.3271 0.3284 0.4563 0.2147 0.218665 0.376884 0.457907 2 2203 45674 3388 2736 2655 30235 379 4078 2 9778 119166 11502 8578 6540 65868 888 16012 0 . 0 . COSM425158 96 0,0,40,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G365S|764|PIGR|protein_coding|CODING|NM_002644.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275531,rs386563268 -0.693147 0.459815 96 764 LOW 4 CODING PIGR A protein_coding NM_002644.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207109167 G A 0 228 0 0.1596 0.2867 0.3242 0.3284 0.4563 0.2147 0.18457 0.361021 0.45147 2 1678 42999 3267 2671 2594 28870 356 3563 2 8742 111382 11172 8410 6388 62946 822 12902 0 . 0 . 0 87 0,0,18,58 SPLICE_SITE_REGION+INTRON(LOW||||764|PIGR|protein_coding|CODING|NM_002644.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6695632 -0.693147 0.0159127 87 V183 764 gtA/gtG LOW 4 SILENT CODING PIGR C protein_coding NM_002644.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207110936 T C 0 228 0 0.9319 0.5509 0.5115 0.4474 0.4682 0.2556 0.848616 0.596725 0.467674 2 8946 57276 5798 3727 2534 31118 422 4731 2 10372 120080 11370 8530 6534 66038 896 16340 1 0 . 0 . 131 0,1,78,37 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V183|764|PIGR|protein_coding|CODING|NM_002644.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs291096 -0.693147 0.522958 131 A42 577 gcG/gcA LOW 3 SILENT CODING FCAMR T protein_coding NM_001170631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207140440 C T 0 228 0 0.3797 0.2366 0.1715 0.3165 0.165 0.0808 0.326531 0.23 0.187744 2 3268 23568 1928 2706 1290 12290 170 1916 2 9622 118416 11398 8520 6370 65594 882 16030 1 0 . 0 COSM146750 70 0,1,36,25 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A42|577|FCAMR|protein_coding|CODING|NM_001170631.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11119933 -0.693147 0.862542 70 577 80 MODIFIER 1 CODING FCAMR T protein_coding NM_001170631.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207143550 C T 0 228 0 0.2141 0.1729 0.1499 0.244 0.1551 0.0787 0.177023 0.183749 0.186675 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 86 0,0,18,63 UTR_5_PRIME(MODIFIER||80||577|FCAMR|protein_coding|CODING|NM_001170631.1|1|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs1340232 -0.693147 0.000235732 86 601 3123 MODIFIER 4 CODING C1orf116 T protein_coding NM_023938.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207192180 C T 0 26.4 0 0.3389 0.2396 0.1729 0.248 0.2117 0.1728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,0,2 UTR_3_PRIME(MODIFIER||3123||601|C1orf116|protein_coding|CODING|NM_023938.5|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10877 -0.453602 0.66 4 S444P 601 Tct/Cct MODERATE 4 MISSENSE CODING C1orf116 G protein_coding NM_023938.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207195779 A G 0 228 0 0.9985 0.9952 0.9914 1 0.9891 0.9949 0.997503 0.988698 0.984186 2 10264 119711 11507 8654 6393 65584 891 16418 2 10286 121132 11574 8654 6604 66600 908 16506 0 . 0 . 0 49 0,0,34,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S444P|601|C1orf116|protein_coding|CODING|NM_023938.5|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2842726 -0.693147 0.504639 49 348 5006 MODIFIER 2 CODING YOD1 C protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207217359 T C 0 228 0 0.8533 0.5321 0.5014 0.2411 0.5835 0.3671 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 144 0,0,46,85 UTR_3_PRIME(MODIFIER||5006||348|YOD1|protein_coding|CODING|NM_018566.3|2|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.827801 0 . rs1044145 -0.693147 0.0367351 144 348 3706 MODIFIER 2 CODING YOD1 G protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207218659 A G 0 222 0 0 0.027 0.0965 0.0298 0.005 0.0337 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999996 0 . 0 . 124 53,16,37,14 UTR_3_PRIME(MODIFIER||3706||348|YOD1|protein_coding|CODING|NM_018566.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.413035 rs78516387 -0.693147 0.934443 124 348 2083 MODIFIER 2 CODING YOD1 A protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207220282 G A 0 124 0 0.2345 0.2656 0.255 0.1677 0.4125 0.2648 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.594978 0 . 0 . 12 3,1,7,1 UTR_3_PRIME(MODIFIER||2083||348|YOD1|protein_coding|CODING|NM_018566.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.878264 rs12123107 -0.651104 0.761142 12 348 1565 MODIFIER 2 CODING YOD1 A protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207220800 C A 0 222 0 0.6641 0.3872 0.2968 0.1696 0.4205 0.2669 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998845 0 . 0 . 210 72,23,67,23 UTR_3_PRIME(MODIFIER||1565||348|YOD1|protein_coding|CODING|NM_018566.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.979001 rs2629665 -0.693147 0.264657 210 348 956 MODIFIER 2 CODING YOD1 C protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207221409 T C 0 228 0 0.9992 0.9958 0.9914 1 0.9891 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 131 0,0,92,24 UTR_3_PRIME(MODIFIER||956||348|YOD1|protein_coding|CODING|NM_018566.3|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1385611 -0.693147 0.101421 131 348 753 MODIFIER 2 CODING YOD1 T protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207221612 C T 0 222 0 0.0628 0.1094 0.1931 0.0714 0.16 0.1002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.664965 0 . 0 . 143 22,42,25,46 UTR_3_PRIME(MODIFIER||753||348|YOD1|protein_coding|CODING|NM_018566.3|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.891993 rs2054780,rs386555216 -0.693147 0.295889 143 348 436 MODIFIER 2 CODING YOD1 G protein_coding NM_018566.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207221929 T G 0 222 0 0.3684 0.3023 0.2637 0.1677 0.4135 0.2648 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.146149 0 . 0 . 120 30,23,19,33 UTR_3_PRIME(MODIFIER||436||348|YOD1|protein_coding|CODING|NM_018566.3|2|G),UPSTREAM(MODIFIER||4691||505|PFKFB2|protein_coding|CODING|NM_006212.2||G) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.999995 0.951678 0 0.0735148 rs3790619 -0.693147 0.0397497 120 P16 348 ccT/ccC LOW 1 SILENT CODING YOD1 G protein_coding NM_018566.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207224328 A G 0 63 0 0 0.0222 0.0058 0.0724 0.0109 0.0235 0.00113122 0.00605458 0.00836653 1 2 475 8 57 4 126 10 268 2 742 14016 410 502 126 4904 150 7182 0.902783 0 . 0 . 17 0,11,0,6 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P16|348|YOD1|protein_coding|CODING|NM_018566.3|1|G),UPSTREAM(MODIFIER||2292||505|PFKFB2|protein_coding|CODING|NM_006212.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.603475 rs78043860 -0.616816 0.329692 17 252 LOW 2 CODING C4BPB G protein_coding NM_000716.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207263829 A G 0 222 0 0.0658 0.4435 0.536 0.747 0.4702 0.5481 0.143895 0.370752 0.486977 1 1308 60222 7338 6679 3409 32443 441 8604 2 10368 120036 11546 8634 6604 66262 894 15728 0.769041 0 . 0 . 141 10,52,14,52 SPLICE_SITE_REGION+INTRON(LOW||||252|C4BPB|protein_coding|CODING|NM_000716.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96799 rs6690037 -0.693147 0.101697 141 N154 252 aaC/aaT LOW 4 SILENT CODING C4BPB T protein_coding NM_000716.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207269919 C T 0 222 0 0.885 0.3898 0.2867 0.1617 0.1769 0.2474 0.763958 0.3829 0.187674 1 8206 29482 2334 1454 739 12290 181 4278 2 10394 120114 11534 8602 6612 66364 904 15704 0.887498 0 . 0 . 80 17,21,15,16 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N154|252|C4BPB|protein_coding|CODING|NM_000716.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.276071 rs8942 -0.69311 0.440574 80 G225 597 ggT/ggC LOW 6 SILENT CODING C4BPA C protein_coding NM_000715.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207297680 T C 0 228 0 0.9198 0.8578 0.8646 0.7639 0.829 0.8957 0.911938 0.860987 0.834884 2 9448 103555 10445 6965 5813 55631 765 14488 2 10394 121190 11508 8596 6606 66672 908 16506 0 . 0 . 0 54 0,0,8,41 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G225|597|C4BPA|protein_coding|CODING|NM_000715.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1126618 -0.693147 0.048449 54 I300T 597 aTt/aCt MODERATE 8 MISSENSE CODING C4BPA C protein_coding NM_000715.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207304900 T C 0 222 0 0.8374 0.4898 0.4625 0.2679 0.3767 0.3845 0.75261 0.484084 0.346512 1 7937 47780 4893 2530 3056 23226 367 5771 2 10364 119030 11348 8428 6522 65498 896 15974 0.527091 0 . 0 . 190 75,15,65,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I300T|597|C4BPA|protein_coding|CODING|NM_000715.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.520582 rs4844573 -0.693147 0.109618 190 A1062E 1092 gCa/gAa MODERATE 18 MISSENSE CODING CR2 A protein_coding NM_001006658.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207653395 C A 0 228 0 0.9962 0.9429 0.9121 1 0.837 0.9427 0.975715 0.878788 0.829107 2 10141 107041 10579 8647 5669 55951 797 15257 2 10382 121150 11512 8648 6600 66598 904 16506 0 . 0 . 0 180 0,0,65,96 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gAa|A1062E|1092|CR2|protein_coding|CODING|NM_001006658.2|18|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs17617 -0.693147 0.0458176 180 E60 2489 gaA/gaG LOW 2 SILENT CODING CR1 G protein_coding NM_000651.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207679307 A G 0 222 0 0.9523 0.8504 0.9078 0.6488 0.8111 0.9202 0.938606 0.849294 0.808539 1 9181 99191 10502 5460 5298 53278 725 14747 2 9800 120720 11546 8618 6614 66732 898 16512 0.930624 0 . 0 . 213 71,29,57,30 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E60|2489|CR1|protein_coding|CODING|NM_000651.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.990871 0.996329 0 0.96327 rs4844600 -0.693147 0.680231 213 Q1022H 2489 caG/caT MODERATE 19 MISSENSE CODING CR1 T protein_coding NM_000651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207726161 G T 0 51 0 . 0 . 0 . 0 . 0 . 1 0 0 0 0 0 0 0 0 2 4 24 0 0 0 18 2 0 0.55055 0 . 0 . 112 0,61,0,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q1022H|2489|CR1|protein_coding|CODING|NM_000651.4|19|T) 0 0.5 1 0 . 0 . 0 1 0 25 0 0.84739 0 . 0.989807 rs200082366 -0.693147 0.0599887 112 H1658R 2489 cAt/cGt MODERATE 30 MISSENSE CODING CR1 G protein_coding NM_000651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207753621 A G 0 222 0 0.2186 0.2943 0.2709 0.3274 0.1819 0.4949 0.222987 0.196061 0.183349 1 2168 30288 3807 2424 1245 13380 210 7054 2 9800 120690 11572 8594 6614 66706 898 16506 0.185339 0 . 0 . 255 75,40,65,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H1658R|2489|CR1|protein_coding|CODING|NM_000651.4|30|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.711024 rs2274567 -0.693147 0.0402099 255 T2060S 2489 Acc/Tcc MODERATE 37 MISSENSE CODING CR1 T protein_coding NM_000651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207782916 A T 0 228 0 1 0.995 0.9942 1 0.9801 0.999 0.995827 0.981543 0.974903 2 9695 118229 11399 8550 6506 64838 877 16364 2 9736 119990 11462 8550 6602 66318 892 16430 0 . 0 . 0 125 0,0,49,66 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Tcc|T2060S|2489|CR1|protein_coding|CODING|NM_000651.4|37|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4844609 -0.693147 0.018628 125 I2065V 2489 Atc/Gtc MODERATE 37 MISSENSE CODING CR1 G protein_coding NM_000651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207782931 A G 0 222 0 0.8722 0.4934 0.3761 0.3433 0.2256 0.4949 0.751169 0.384291 0.213248 1 7553 38745 4621 2479 1633 15104 254 7101 2 9570 115966 10918 8226 6448 63946 870 15988 0.46217 0 . 0 . 126 30,37,22,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I2065V|2489|CR1|protein_coding|CODING|NM_000651.4|37|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.905213 rs6691117 -0.693147 0.684713 126 P2277R 2489 cCt/cGt MODERATE 41 MISSENSE CODING CR1 G protein_coding NM_000651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207790088 C G 0 222 0 0.1172 0.2628 0.2608 0.3224 0.1809 0.4836 0.127301 0.164669 0.182346 1 1258 29017 3743 2397 1239 13219 206 6955 2 9802 120760 11574 8622 6614 66738 898 16512 0.940922 0 . 0 . 332 93,71,64,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cGt|P2277R|2489|CR1|protein_coding|CODING|NM_000651.4|41|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.169367 rs3811381 -0.693147 0.00414842 332 T2419A 2489 Aca/Gca MODERATE 44 MISSENSE CODING CR1 G protein_coding NM_000651.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207795320 A G 0 222 0 0.8162 0.8281 0.9207 0.6885 0.8221 0.9284 0.817464 0.817006 0.816796 1 7105 82035 8266 4906 4632 43746 633 12747 2 8780 100542 9102 7466 5750 54574 768 14102 0.999747 0 . 0 . 251 83,40,61,29 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Aca/Gca|T2419A|2489|CR1|protein_coding|CODING|NM_000651.4|44|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998884 rs2296160,rs386451653 -0.693147 0.217789 251 2489 300 MODIFIER 47 CODING CR1 C protein_coding NM_000651.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207813054 A C 0 14.7 0 0 0.0009984 0 0.005 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 7 0,5,0,2 UTR_3_PRIME(MODIFIER||300||2489|CR1|protein_coding|CODING|NM_000651.4|47|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.8 rs192021844 -0.453602 0.02 7 2489 1697 MODIFIER 47 CODING CR1 C protein_coding NM_000651.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207814451 T C 0 9.7 0 0.6604 0.5827 0.3977 0.6806 0.5 0.593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1697||2489|CR1|protein_coding|CODING|NM_000651.4|47|C),UPSTREAM(MODIFIER||4007||569|CR1L|protein_coding|CODING|NM_175710.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10779339 -0.379885 0 1 R116G 569 Aga/Gga MODERATE 3 MISSENSE CODING CR1L G protein_coding NM_175710.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207851611 A G 0 228 0 0.4493 0.5266 0.379 0.6984 0.492 0.5941 0.478967 0.508746 0.522303 2 4459 62421 4786 5957 3150 34336 463 9270 2 9800 120720 11562 8612 6614 66722 898 16512 0 . 0 . 0 173 0,0,73,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R116G|569|CR1L|protein_coding|CODING|NM_175710.1|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs2296158 -0.693147 0.000898501 173 I455V 569 Atc/Gtc MODERATE 10 MISSENSE CODING CR1L G protein_coding NM_175710.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207881557 A G 0 228 0 0.7753 0.7053 0.4755 0.8819 0.5626 0.7382 0.725738 0.61726 0.567242 2 7260 73499 5521 7581 3290 37532 566 11749 2 9804 120758 11570 8624 6614 66736 898 16512 0.944882 0 . 0 . 281 1,1,170,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I455V|569|CR1L|protein_coding|CODING|NM_175710.1|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.903543 rs6683902 -0.693147 0.000113051 281 S13F 399 tCc/tTc MODERATE 1 MISSENSE CODING CD46 T protein_coding NM_172359.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207925595 C T 0 222 0 0.0061 0.0085863 0.0101 0.0228 0 0.0051 0.00408534 0.00146086 0.000116279 1 35 607 211 289 0 16 2 54 2 10398 121330 11568 8640 6614 66690 908 16512 0.989748 0 . 0 . 77 17,27,10,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S13F|399|CD46|protein_coding|CODING|NM_172359.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999981 rs138843816 -0.692914 0.226393 77 S151 399 agC/agT LOW 4 SILENT CODING CD46 T protein_coding NM_172359.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207933047 C T 0 222 0 0.0068 0.010184 0.0173 0.0228 0.002 0.0051 0.00771675 0.00346207 0.00128026 1 60 661 219 287 0 37 3 55 2 9230 110712 11018 8428 6366 59362 822 15486 0.599558 0 . 0 COSM1338466 147 22,40,32,36 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S151|399|CD46|protein_coding|CODING|NM_172359.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.686711 rs145041158 -0.693147 0.0196313 147 399 389 MODIFIER 13 CODING CD46 G protein_coding NM_172359.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 207967325 A G 0 32.6 0 0.0635 0.0266 0.0317 0.0228 0 0.0041 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||389||399|CD46|protein_coding|CODING|NM_172359.2|13|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2724390 -0.379885 0 2 385 1074 MODIFIER 8 CODING CD34 T protein_coding NM_001025109.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208060009 C T 0 222 0 0.2284 0.2973 0.2867 0.5089 0.2018 0.2781 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.367561 0 . 0 . 85 26,14,26,10 UTR_3_PRIME(MODIFIER||1074||385|CD34|protein_coding|CODING|NM_001025109.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.432247 rs7572 -0.693139 0.0815756 85 385 LOW 4 CODING CD34 T protein_coding NM_001025109.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208062973 A T 0 222 0 0.1014 0.1458 0.1816 0.0228 0.3181 0.1299 0.129369 0.232893 0.28593 1 1309 25737 1403 196 1372 18625 190 2642 2 10386 121112 11564 8650 6610 66620 904 16378 0.222043 0 . 0 . 124 34,26,29,21 SPLICE_SITE_REGION+INTRON(LOW||||385|CD34|protein_coding|CODING|NM_001025109.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990099 rs2745953 -0.693147 0.091515 124 1894 4507 MODIFIER 32 CODING PLXNA2 C protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208196081 T C 0 163 0 0.7973 0.8964 0.8545 0.9077 0.9751 0.9673 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935507 0 . 0 . 41 0,20,1,20 UTR_3_PRIME(MODIFIER||4507||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.765928 rs2767567 -0.692352 0.0482681 41 1894 3032 MODIFIER 32 CODING PLXNA2 G protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208197556 C G 0 9.7 0 0.0287 0.0727 0.0648 0.0645 0.0994 0.1186 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3032||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11583070 -0.379885 0 1 1894 2706 MODIFIER 32 CODING PLXNA2 C protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208197882 G C 0 32.6 0 0.7844 0.9401 0.9798 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2706||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs591305 -0.379885 0 2 1894 1959 MODIFIER 32 CODING PLXNA2 A protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208198629 C A 0 222 0 0.0023 0.0519 0.1326 0.1052 0.0229 0.0368 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.978799 0 . 0 . 36 1,15,2,16 UTR_3_PRIME(MODIFIER||1959||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.841959 rs72731345 -0.691153 0.112499 36 1894 1953 MODIFIER 32 CODING PLXNA2 T protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208198635 C T 0 155 0 0.0287 0.0693 0.062 0.0635 0.0905 0.1135 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999493 0 . 0 . 39 2,18,1,15 UTR_3_PRIME(MODIFIER||1953||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996838 rs11118974 -0.689466 0.0165314 39 1894 1794 MODIFIER 32 CODING PLXNA2 G protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208198794 A G 0 122 0 0.0023 0.0519 0.1326 0.1052 0.0229 0.0368 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 8 0,2,3,3 UTR_3_PRIME(MODIFIER||1794||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.900802 0 0 rs72731347 -0.616816 0.434785 8 1894 1685 MODIFIER 32 CODING PLXNA2 C protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208198901 CCT C 0 86 0 0.0015 0.0375 0.1066 0.1032 0.001 0.0072 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 1,1,0,5 UTR_3_PRIME(MODIFIER||1685||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|C) 0 0.5 1 5 0.555556 1 1 0 . 0 60 0 0 1 0 . rs140757737 -0.590765 0.118055 9 1894 473 MODIFIER 32 CODING PLXNA2 C protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208200115 T C 0 222 0 0.174 0.2622 0.3631 0.3403 0.2187 0.274 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.889585 0 . 0 . 111 35,4,39,11 UTR_3_PRIME(MODIFIER||473||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.792397 rs55877527 -0.693147 0.366352 111 1894 461 MODIFIER 32 CODING PLXNA2 A protein_coding NM_025179.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208200127 T A 0 228 0 0.8064 0.9469 0.987 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 109 0,0,62,28 UTR_3_PRIME(MODIFIER||461||1894|PLXNA2|protein_coding|CODING|NM_025179.3|32|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs866833 -0.693147 0.0224858 109 Y1621 1894 taC/taT LOW 27 SILENT CODING PLXNA2 A protein_coding NM_025179.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208207839 G A 0 222 0 0.5401 0.4427 0.4539 0.2579 0.6203 0.3108 0.551521 0.566738 0.574535 1 5742 62050 4905 2231 3867 39139 477 5689 2 10396 121192 11540 8614 6556 66672 906 16508 0.883512 0 . 0 . 82 43,6,18,10 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1621|1894|PLXNA2|protein_coding|CODING|NM_025179.3|27|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.685923 rs3736963 -0.693054 0.015693 82 A805G 1894 gCa/gGa MODERATE 12 MISSENSE CODING PLXNA2 C protein_coding NM_025179.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208252777 G C 0 222 0 0.0015 0.0455 0.098 0.1022 0.0189 0.0368 0.00658492 0.0136881 0.0173256 1 53 4127 1283 741 46 1226 35 743 2 6100 67728 6042 4746 2550 36372 474 11444 0.644067 0 . 0 . 78 15,18,19,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A805G|1894|PLXNA2|protein_coding|CODING|NM_025179.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.881205 rs17011882 -0.693144 0.172747 78 T394 1894 acC/acG LOW 2 SILENT CODING PLXNA2 C protein_coding NM_025179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208390086 G C 0 96 0 0.3623 0.3672 0.3343 0.4048 0.3042 0.4233 0.35202 0.335307 0.326744 1 3634 41317 4063 3583 2101 21095 288 6553 2 10206 118856 11522 8566 6562 65606 880 15514 0.712528 0 . 0 . 34 18,3,12,0 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T394|1894|PLXNA2|protein_coding|CODING|NM_025179.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985919 rs1664227 -0.680642 0.350982 34 L371 1894 ctG/ctA LOW 2 SILENT CODING PLXNA2 T protein_coding NM_025179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208390155 C T 0 222 0 0.0461 0.1276 0.2046 0.1429 0.2078 0.0849 0.0585565 0.146394 0.191395 1 582 20933 2481 1192 1921 12766 189 1802 2 10358 121102 11546 8640 6592 66552 904 16510 0.605264 0 . 0 . 64 22,2,22,11 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L371|1894|PLXNA2|protein_coding|CODING|NM_025179.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.749363 rs4844657 -0.693127 0.127524 64 E369G 1894 gAg/gGg MODERATE 2 MISSENSE CODING PLXNA2 C protein_coding NM_025179.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208390162 T C 0 222 0 0.0121 0.1186 0.2032 0.1429 0.2087 0.0849 0.0335906 0.137936 0.191395 1 318 20662 2473 1194 1921 12765 188 1803 2 10372 121134 11546 8642 6588 66572 906 16508 0.807786 0 . 0 . 62 22,2,19,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E369G|1894|PLXNA2|protein_coding|CODING|NM_025179.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985702 rs386595842,rs4844658 -0.69311 0.0201454 62 A61 1894 gcC/gcT LOW 2 SILENT CODING PLXNA2 A protein_coding NM_025179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208391085 G A 0 222 0 0.0129 0.0825 0.1412 0.0159 0.159 0.1247 0.0447118 0.125404 0.166744 1 360 16079 1734 155 821 10642 110 2257 2 10394 121366 11578 8650 6614 66712 906 16512 0.9175 0 . 0 . 142 28,44,18,39 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A61|1894|PLXNA2|protein_coding|CODING|NM_025179.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.633424 rs12120681,rs386522929 -0.693147 0.215108 142 R5Q 1894 cGg/cAg MODERATE 2 MISSENSE CODING PLXNA2 T protein_coding NM_025179.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208391254 C T 0 155 0 0.3601 0.3646 0.3314 0.4018 0.3022 0.4202 0.346244 0.33093 0.323128 1 3132 39692 4002 3536 2072 20112 275 6563 2 8466 112728 11168 8298 6192 61522 834 16248 0.953497 0 . 0 COSM1127155 27 2,12,1,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R5Q|1894|PLXNA2|protein_coding|CODING|NM_025179.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.666915 rs2782948 -0.680642 0.378827 27 1894 25760 MODIFIER 1 CODING PLXNA2 C protein_coding NM_025179.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 208417027 G C 0 23.4 0 0.1445 0.153 0.0735 0.2421 0.0795 0.2045 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,2,0 UTR_5_PRIME(MODIFIER||25760||1894|PLXNA2|protein_coding|CODING|NM_025179.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs58657209 -0.453602 0.98 4 102 262 MODIFIER 1 CODING MIR205HG A protein_coding NM_001104548.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209602381 G A 0 9.7 0 0.5613 0.6893 0.7507 0.7946 0.6829 0.7168 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||262||102|MIR205HG|protein_coding|CODING|NM_001104548.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10779505 -0.379885 0 1 P218 476 ccA/ccG LOW 8 SILENT CODING CAMK1G G protein_coding NM_020439.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209782343 A G 0 228 0 0.7073 0.5455 0.5476 0.5714 0.3867 0.4622 0.660236 0.480932 0.38907 2 6967 55019 7312 5014 2089 25515 406 7716 2 10406 121382 11576 8644 6610 66728 908 16510 1 0 . 0 COSM146752 103 0,1,54,36 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P218|476|CAMK1G|protein_coding|CODING|NM_020439.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11119314 -0.693147 0.0213223 103 S1144 1172 tcA/tcG LOW 23 SILENT CODING LAMB3 C protein_coding NM_000228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209788703 T C 0 222 0 0.6694 0.4633 0.3689 0.381 0.3648 0.4376 0.600545 0.440873 0.35907 1 6441 48624 4501 3579 2593 24509 369 6632 2 10400 120984 11568 8604 6596 66564 904 16348 0.982548 0 . 0 . 77 21,20,14,17 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1144|1172|LAMB3|protein_coding|CODING|NM_000228.2|23|C),DOWNSTREAM(MODIFIER||1419||476|CAMK1G|protein_coding|CODING|NM_020439.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978111 rs1049607 -0.69311 0.156468 77 A926D 1172 gCt/gAt MODERATE 19 MISSENSE CODING LAMB3 T protein_coding NM_000228.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209791929 G T 0 222 0 0.0023 0.0891 0.0764 0.2669 0.0209 0.1022 0.00839764 0.0176841 0.0224419 1 90 6768 1206 2271 94 1476 42 1589 2 10392 121260 11560 8620 6596 66676 904 16512 0.998218 0 . 0 . 58 14,18,9,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A926D|1172|LAMB3|protein_coding|CODING|NM_000228.2|19|T),DOWNSTREAM(MODIFIER||4645||476|CAMK1G|protein_coding|CODING|NM_020439.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985548 rs2076222 -0.692717 0.597876 58 S708 1172 agT/agC LOW 15 SILENT CODING LAMB3 G protein_coding NM_000228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209797198 A G 0 222 0 0.0023 0.0887 0.0764 0.2649 0.0209 0.1022 0.00839764 0.0176841 0.0224419 1 90 6753 1222 2236 94 1476 42 1593 2 10382 121318 11568 8640 6612 66702 908 16506 0.199983 0 . 0 . 35 11,5,14,4 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S708|1172|LAMB3|protein_coding|CODING|NM_000228.2|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.699568 rs2072937 -0.691153 0.854484 35 N690S 1172 aAt/aGt MODERATE 15 MISSENSE CODING LAMB3 C protein_coding NM_000228.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209797253 T C 0 222 0 0.0045 0.0895 0.0778 0.2649 0.0209 0.1022 0.00635497 0.0169922 0.0224419 1 72 6742 1221 2244 94 1476 42 1593 2 10394 121358 11574 8640 6614 66718 908 16510 0.435232 0 . 0 . 48 16,6,18,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N690S|1172|LAMB3|protein_coding|CODING|NM_000228.2|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.637592 rs2229466 -0.692914 0.566311 48 Y588 1172 taT/taC LOW 14 SILENT CODING LAMB3 G protein_coding NM_000228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209799205 A G 0 222 0 0.0015 0.094 0.0793 0.2966 0.0219 0.0951 0.00567408 0.0169948 0.022796 1 70 7069 1223 2496 117 1612 47 1504 2 10196 119648 11404 8532 6330 65838 878 16470 0.969112 0 . 0 . 121 25,31,22,27 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y588|1172|LAMB3|protein_coding|CODING|NM_000228.2|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995965 rs2229465 -0.693147 0.409829 121 C572 1172 tgT/tgC LOW 14 SILENT CODING LAMB3 G protein_coding NM_000228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209799253 A G 0 228 0 0.7837 0.765 0.7075 0.8304 0.7326 0.7464 0.767484 0.746001 0.735 2 7861 90237 8822 7070 4682 48892 661 12249 2 10162 119290 11376 8560 6354 65462 878 16498 0.942529 0 . 0 . 94 0,2,27,60 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C572|1172|LAMB3|protein_coding|CODING|NM_000228.2|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.994253 rs2179402 -0.693147 0.0805699 94 V527M 1172 Gtg/Atg MODERATE 13 MISSENSE CODING LAMB3 T protein_coding NM_000228.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209800230 C T 0 228 0 0.3169 0.2552 0.2061 0.5794 0.0278 0.1063 0.253972 0.103952 0.027093 2 2781 15043 3597 4928 139 1784 75 1739 2 9964 117660 11440 8552 6122 64570 854 16158 0.842524 0 . 0 COSM1338510 123 4,0,57,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V527M|1172|LAMB3|protein_coding|CODING|NM_000228.2|13|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.857847 rs2076349 -0.693147 0.101469 123 N181D 1172 Aat/Gat MODERATE 6 MISSENSE CODING LAMB3 C protein_coding NM_000228.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209807815 T C 0 222 0 0.0023 0.0851 0.0735 0.249 0.0219 0.1012 0.00544712 0.0163002 0.0218605 1 65 6497 1006 2184 183 1511 46 1502 2 10394 121358 11576 8634 6614 66724 906 16510 0.995893 0 . 0 . 102 29,20,21,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N181D|1172|LAMB3|protein_coding|CODING|NM_000228.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.810908 rs2235542 -0.693145 0.410769 102 S97 1172 tcA/tcC LOW 4 SILENT CODING LAMB3 G protein_coding NM_000228.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209811886 T G 0 222 0 0.3517 0.4325 0.4582 0.2847 0.6412 0.4611 0.435089 0.574581 0.646047 1 4307 69224 5073 2523 4664 43967 543 8147 2 10398 121246 11536 8620 6610 66674 908 16500 0.519026 0 . 0 COSM146753 60 24,4,16,7 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S97|1172|LAMB3|protein_coding|CODING|NM_000228.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970174 rs2076356 -0.692717 0.753869 60 103 28 MODIFIER 2 CODING G0S2 C protein_coding NM_015714.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209849002 T C 0 222 0 0.466 0.6066 0.6182 0.5387 0.7356 0.726 0.507998 0.660151 0.737862 1 1704 23134 1177 1030 556 12126 185 6356 2 3246 31966 1764 1644 708 15778 242 8584 0.674435 0 . 0 . 65 23,6,26,5 UTR_5_PRIME(MODIFIER||28||103|G0S2|protein_coding|CODING|NM_015714.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.80127 rs3817870 -0.69311 0.433559 65 103 59 MODIFIER 2 CODING G0S2 A protein_coding NM_015714.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209849399 AG A 0 222 0 0.4349 0.5978 0.6167 0.5377 0.7346 0.726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 15,27,10,17 UTR_3_PRIME(MODIFIER||59||103|G0S2|protein_coding|CODING|NM_015714.3|2|A) 0 0.5 1 27 0.369863 1 1 0 . 0 60 0 0 1 0 . rs3830766 -0.693021 0.183405 73 103 65 MODIFIER 2 CODING G0S2 G protein_coding NM_015714.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209849406 T G 0 228 0 0.9985 0.9193 0.8948 0.7381 0.9871 0.9468 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 68 1,0,25,39 UTR_3_PRIME(MODIFIER||65||103|G0S2|protein_coding|CODING|NM_015714.3|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1473683 -0.693147 0.0855163 68 551 54 MODIFIER 3 CODING TRAF3IP3 G protein_coding NM_025228.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209933331 A G 0 222 0 0.7443 0.3732 0.2795 0.2133 0.2386 0.2413 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999568 0 . 0 . 73 33,4,25,8 UTR_5_PRIME(MODIFIER||54||551|TRAF3IP3|protein_coding|CODING|NM_025228.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.975324 rs6685077 -0.693127 0.236318 73 Q52 551 caA/caG LOW 3 SILENT CODING TRAF3IP3 G protein_coding NM_025228.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209933540 A G 0 222 0 0.7436 0.373 0.2795 0.2133 0.2386 0.2413 0.680436 0.377826 0.222791 1 7191 33969 2875 1894 1837 15857 228 4087 2 10354 120902 11538 8630 6540 66434 900 16506 0.983765 0 . 0 . 82 21,28,11,18 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q52|551|TRAF3IP3|protein_coding|CODING|NM_025228.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.286173 rs2076150 -0.693079 0.235605 82 A228 551 gcC/gcT LOW 8 SILENT CODING TRAF3IP3 T protein_coding NM_025228.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209936914 C T 0 222 0 0.6906 0.3806 0.2752 0.3075 0.2306 0.2658 0.638901 0.362525 0.22093 1 6703 34721 2781 2842 1902 15821 233 4439 2 10358 120640 11446 8570 6576 66342 902 16446 0.643792 0 . 0 . 87 13,26,14,27 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A228|551|TRAF3IP3|protein_coding|CODING|NM_025228.3|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.92856 rs17015169 -0.693145 0.00271072 87 G264 551 ggA/ggC LOW 10 SILENT CODING TRAF3IP3 C protein_coding NM_025228.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209948711 A C 0 228 0 0.2784 0.2095 0.1052 0.247 0.1441 0.2188 0.268724 0.196986 0.160233 2 2681 20535 882 2123 828 10300 145 3576 2 8924 101822 8346 7230 5702 55968 778 14874 1 0 . 0 . 68 1,0,31,26 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G264|551|TRAF3IP3|protein_coding|CODING|NM_025228.3|10|C),DOWNSTREAM(MODIFIER||3842||269|C1orf74|protein_coding|CODING|NM_152485.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs17015183 -0.693147 0.0160727 68 Q373E 551 Caa/Gaa MODERATE 12 MISSENSE CODING TRAF3IP3 G protein_coding NM_025228.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209950760 C G 0 228 0 0.8828 0.8123 0.7781 0.8135 0.7674 0.7863 0.857467 0.818699 0.798837 2 9008 95840 9062 6986 4908 52231 706 12939 2 10400 121308 11556 8640 6610 66684 906 16512 0 . 0 . COSM1127153 69 0,0,23,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q373E|551|TRAF3IP3|protein_coding|CODING|NM_025228.3|12|G),DOWNSTREAM(MODIFIER||1793||269|C1orf74|protein_coding|CODING|NM_152485.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs669694 -0.693147 0.0181803 69 L146F 269 ttG/ttT MODERATE 2 MISSENSE CODING C1orf74 A protein_coding NM_152485.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209956542 C A 0 96 0 0.2231 0.1552 0.1009 0.0744 0.1412 0.1994 0.231276 0.184453 0.160465 1 2324 18664 891 566 754 10494 138 3497 2 10380 121304 11562 8644 6610 66690 908 16510 0.751519 0 . 0 . 29 14,8,3,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L146F|269|C1orf74|protein_coding|CODING|NM_152485.3|2|A),DOWNSTREAM(MODIFIER||874||551|TRAF3IP3|protein_coding|CODING|NM_025228.3||A),DOWNSTREAM(MODIFIER||2426||467|IRF6|protein_coding|CODING|NM_006147.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.09218 rs7550857 -0.616816 0.218338 29 467 2597 MODIFIER 9 CODING IRF6 T protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209959168 C T 0 21.2 0 0.0015 0.1324 0.1801 0.4286 0.0139 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_3_PRIME(MODIFIER||2597||467|IRF6|protein_coding|CODING|NM_006147.3|9|T),UPSTREAM(MODIFIER||1093||269|C1orf74|protein_coding|CODING|NM_152485.3||T),DOWNSTREAM(MODIFIER||3500||551|TRAF3IP3|protein_coding|CODING|NM_025228.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1856161 -0.379885 0 3 467 2151 MODIFIER 9 CODING IRF6 T protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209959614 G T 0 9.7 0 0.2504 0.3099 0.2853 0.5635 0.1551 0.3057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2151||467|IRF6|protein_coding|CODING|NM_006147.3|9|T),UPSTREAM(MODIFIER||1539||269|C1orf74|protein_coding|CODING|NM_152485.3||T),DOWNSTREAM(MODIFIER||3946||551|TRAF3IP3|protein_coding|CODING|NM_025228.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044516 -0.379885 0 1 467 1893 MODIFIER 9 CODING IRF6 A protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209959872 G A 0 32.6 0 0.8722 0.8081 0.7795 0.8095 0.7724 0.7771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1893||467|IRF6|protein_coding|CODING|NM_006147.3|9|A),UPSTREAM(MODIFIER||1797||269|C1orf74|protein_coding|CODING|NM_152485.3||A),DOWNSTREAM(MODIFIER||4204||551|TRAF3IP3|protein_coding|CODING|NM_025228.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs680331 -0.379885 0 2 467 1329 MODIFIER 9 CODING IRF6 A protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209960436 G A 0 9.7 0 0.2564 0.2991 0.2882 0.503 0.1531 0.3047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1329||467|IRF6|protein_coding|CODING|NM_006147.3|9|A),UPSTREAM(MODIFIER||2361||269|C1orf74|protein_coding|CODING|NM_152485.3||A),DOWNSTREAM(MODIFIER||4768||551|TRAF3IP3|protein_coding|CODING|NM_025228.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2235372 -0.379885 0 1 467 840 MODIFIER 9 CODING IRF6 C protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209960925 T C 0 108 0 0.2504 0.2971 0.2853 0.503 0.1531 0.3047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_3_PRIME(MODIFIER||840||467|IRF6|protein_coding|CODING|NM_006147.3|9|C),UPSTREAM(MODIFIER||2850||269|C1orf74|protein_coding|CODING|NM_152485.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs742214 -0.590765 0.948062 6 467 451 MODIFIER 9 CODING IRF6 C protein_coding NM_006147.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209961314 T C 0 222 0 0.0091 0.0875 0.0908 0.0456 0.1332 0.1871 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.367611 0 . 0 . 105 42,12,30,10 UTR_3_PRIME(MODIFIER||451||467|IRF6|protein_coding|CODING|NM_006147.3|9|C),UPSTREAM(MODIFIER||3239||269|C1orf74|protein_coding|CODING|NM_152485.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.739904 rs17317411 -0.693145 0.652728 105 V274I 467 Gtc/Atc MODERATE 7 MISSENSE CODING IRF6 T protein_coding NM_006147.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209964080 C T 0 199 0 0.0015 0.1326 0.1801 0.4296 0.0139 0.092 0.00771675 0.0117638 0.0138372 1 63 9280 3104 3601 107 1023 53 1329 2 10348 121178 11572 8628 6612 66610 902 16506 0.728944 0 . 0 . 31 10,7,6,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V274I|467|IRF6|protein_coding|CODING|NM_006147.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994541 rs2235371 -0.683931 0.767474 31 S153 467 tcG/tcT LOW 5 SILENT CODING IRF6 A protein_coding NM_006147.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209968684 C A 0 228 0 0.2428 0.4038 0.4769 0.5843 0.3608 0.4274 0.291421 0.34238 0.368488 2 2858 48785 6517 4971 2448 24758 335 6898 2 10406 121348 11574 8634 6610 66706 908 16510 1 0 . 0 . 147 0,1,38,97 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcT|S153|467|IRF6|protein_coding|CODING|NM_006147.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2013162 -0.693147 0.00509653 147 467 LOW 3 CODING IRF6 C protein_coding NM_006147.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 209969902 G C 0 222 0 0.2413 0.271 0.2968 0.1548 0.3469 0.3344 0.282569 0.33054 0.355116 1 2781 39154 3383 1318 2330 23563 279 5500 2 10294 120102 11376 8546 6530 66024 902 16430 0.0872823 0 . 0 . 78 6,28,10,25 SPLICE_SITE_REGION+INTRON(LOW||||467|IRF6|protein_coding|CODING|NM_006147.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988809 rs7552506 -0.693136 0.304822 78 Q67E 756 Caa/Gaa MODERATE 3 MISSENSE CODING DIEXF G protein_coding NM_014388.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210004199 C G 0 222 0 0.6074 0.5901 0.5418 0.3859 0.7286 0.6687 0.588516 0.703137 0.76186 1 6183 81636 5593 3386 4856 49803 626 11189 2 10388 121298 11562 8642 6608 66682 908 16508 0.735969 0 . 0 COSM1338527 99 35,8,41,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q67E|756|DIEXF|protein_coding|CODING|NM_014388.6|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.175949 rs585627 -0.693147 0.107497 99 G111D 756 gGt/gAt MODERATE 3 MISSENSE CODING DIEXF A protein_coding NM_014388.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210004332 G A 0 222 0 0.0847 0.1168 0.085 0.0784 0.1312 0.2076 0.0882887 0.131555 0.153721 1 879 16556 745 620 738 9967 123 3484 2 10406 121394 11578 8652 6614 66726 906 16512 0.87716 0 . 0 . 190 51,30,52,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G111D|756|DIEXF|protein_coding|CODING|NM_014388.6|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.764314 rs61747285 -0.693147 0.907906 190 P154 756 ccC/ccT LOW 4 SILENT CODING DIEXF T protein_coding NM_014388.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210006603 C T 0 222 0 0.6082 0.5903 0.5418 0.3859 0.7286 0.6687 0.598275 0.706443 0.76186 1 6263 81778 5599 3393 4860 49842 626 11195 2 10404 121306 11558 8618 6610 66702 906 16508 0.994496 0 . 0 COSM146755 95 31,10,29,8 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P154|756|DIEXF|protein_coding|CODING|NM_014388.6|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966722 rs656566 -0.693141 0.0633857 95 756 959 MODIFIER 12 CODING DIEXF A protein_coding NM_014388.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210025751 G A 0 6.3 0 0.4032 0.2087 0.1225 0.0774 0.1461 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||959||756|DIEXF|protein_coding|CODING|NM_014388.6|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7539638 -0.379885 0 1 756 2024 MODIFIER 12 CODING DIEXF T protein_coding NM_014388.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210026816 C T 0 32.6 0 0.0862 0.1196 0.0908 0.0764 0.1451 0.2035 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2024||756|DIEXF|protein_coding|CODING|NM_014388.6|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs112972438 -0.379885 0 2 756 5847 MODIFIER 12 CODING DIEXF C protein_coding NM_014388.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210030639 T C 0 9.7 0 0.0106 0.0823 0.0893 0.0466 0.1342 0.1575 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5847||756|DIEXF|protein_coding|CODING|NM_014388.6|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs75308488 -0.379885 0 1 756 5938 MODIFIER 12 CODING DIEXF A protein_coding NM_014388.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210030730 C A 0 9.7 0 0.2489 0.1488 0.1081 0.0466 0.1402 0.1564 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5938||756|DIEXF|protein_coding|CODING|NM_014388.6|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs59435160 -0.379885 0 1 L179 494 ctG/ctC LOW 5 SILENT CODING HHAT C protein_coding NM_001170587.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210577873 G C 0 228 0 0.8517 0.76 0.8444 0.628 0.7634 0.7086 0.811167 0.778948 0.762442 2 8580 93525 10046 5360 5299 51591 697 11952 2 10406 121374 11578 8636 6612 66724 908 16510 0 . 0 . 0 120 0,0,54,54 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L179|494|HHAT|protein_coding|CODING|NM_001170587.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2066721 -0.693147 0.475962 120 494 503 MODIFIER 11 CODING HHAT G protein_coding NM_001170587.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210848224 A G 0 39.3 0 0.854 0.7664 0.6974 0.6677 0.7266 0.8395 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||503||494|HHAT|protein_coding|CODING|NM_001170587.2|11|G),DOWNSTREAM(MODIFIER||3433||989|KCNH1|protein_coding|CODING|NM_172362.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10863850 -0.453602 0.36 2 989 3641 MODIFIER 11 CODING KCNH1 T protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210852982 G T 0 81 0 0.1142 0.2927 0.3026 0.1042 0.4712 0.5378 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,0 UTR_3_PRIME(MODIFIER||3641||989|KCNH1|protein_coding|CODING|NM_172362.2|11|T),DOWNSTREAM(MODIFIER||3344||494|HHAT|protein_coding|CODING|NM_001170587.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12126038 -0.511536 0.901652 4 989 3250 MODIFIER 11 CODING KCNH1 T protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210853373 C T 0 9.7 0 0 0.014177 0.0014 0.0585 0.001 0.0102 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3250||989|KCNH1|protein_coding|CODING|NM_172362.2|11|T),DOWNSTREAM(MODIFIER||3735||494|HHAT|protein_coding|CODING|NM_001170587.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs116945771 -0.379885 0 1 989 2919 MODIFIER 11 CODING KCNH1 C protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210853703 CA C 0 9.7 0 0.1142 0.2905 0.3012 0.1052 0.4712 0.5266 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2919||989|KCNH1|protein_coding|CODING|NM_172362.2|11|C),DOWNSTREAM(MODIFIER||4066||494|HHAT|protein_coding|CODING|NM_001170587.2||C) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs56001969 -0.379885 0 1 989 772 MODIFIER 11 CODING KCNH1 G protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210855851 A G 0 51 0 0.8079 0.7396 0.6801 0.6617 0.6918 0.819 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||772||989|KCNH1|protein_coding|CODING|NM_172362.2|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1890841 -0.453602 0.06 3 989 503 MODIFIER 11 CODING KCNH1 C protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210856120 T C 0 9.7 0 0.8086 0.7398 0.6801 0.6617 0.6918 0.819 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||503||989|KCNH1|protein_coding|CODING|NM_172362.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12126648 -0.379885 0 1 989 38 MODIFIER 11 CODING KCNH1 T protein_coding NM_172362.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210856585 G T 0 228 0 0.8744 0.7568 0.6844 0.6617 0.6909 0.8149 0.858671 0.758243 0.706848 2 7918 81465 7277 5499 3787 44886 628 11470 2 9228 114894 11480 8492 6590 64100 864 14140 0 . 0 . 0 52 0,0,27,20 UTR_3_PRIME(MODIFIER||38||989|KCNH1|protein_coding|CODING|NM_172362.2|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3135473 -0.693147 0.514612 52 D712 989 gaT/gaC LOW 11 SILENT CODING KCNH1 G protein_coding NM_172362.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 210857457 A G 0 228 0 0.8071 0.7394 0.6888 0.6528 0.7117 0.8016 0.795506 0.741387 0.713654 2 8076 78316 7425 5483 4181 45345 587 7219 2 10130 110082 11452 8464 6602 63642 790 9002 1 0 . 0 . 66 0,1,22,37 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D712|989|KCNH1|protein_coding|CODING|NM_172362.2|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1135317 -0.693147 0.207314 66 553 966 MODIFIER 12 CODING RCOR3 G protein_coding NM_001136223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211488076 A G 0 39.3 0 0.9365 0.9696 0.9798 0.997 0.9682 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||966||553|RCOR3|protein_coding|CODING|NM_001136223.1|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1533219 -0.453602 0.56 2 553 1428 MODIFIER 12 CODING RCOR3 A protein_coding NM_001136223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211488538 C A 0 31.3 0 0.8843 0.9549 0.9741 0.997 0.9672 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1428||553|RCOR3|protein_coding|CODING|NM_001136223.1|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6663627 -0.453602 0.66 2 553 2077 MODIFIER 12 CODING RCOR3 G protein_coding NM_001136223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211489187 T G 0 46.3 0 0.8828 0.9545 0.9741 0.997 0.9672 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2077||553|RCOR3|protein_coding|CODING|NM_001136223.1|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3855878 -0.453602 0.42 2 195 10542 MODIFIER 1 CODING RD3 AG protein_coding NM_001164688.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211665298 A AG 0 32.3 0 0.8162 0.739 0.6844 0.9355 0.6103 0.6033 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||10542||195|RD3|protein_coding|CODING|NM_001164688.1|1|AG) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs11463656 -0.453602 0.78 2 H168 445 caT/caC LOW 3 SILENT CODING NEK2 G protein_coding NM_002497.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211846876 A G 0 228 0 0.5454 0.603 0.6671 0.7252 0.4732 0.6431 0.534045 0.501461 0.484767 2 5676 67722 8587 6294 3864 32348 534 10419 2 10374 121288 11568 8640 6614 66678 908 16506 0.63253 0 . 0 . 103 2,0,61,22 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H168|445|NEK2|protein_coding|CODING|NM_002497.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.253012 rs56500874,rs701929 -0.693147 0.785545 103 370 5126 MODIFIER 8 CODING LPGAT1 T protein_coding NM_014873.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211918115 C T 0 72 0 0.5401 0.4507 0.4352 0.7083 0.2386 0.2935 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991701 0 . 0 . 15 8,0,6,0 UTR_3_PRIME(MODIFIER||5126||370|LPGAT1|protein_coding|CODING|NM_014873.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.875173 rs4480424 -0.616816 0.631962 15 370 2012 MODIFIER 8 CODING LPGAT1 A protein_coding NM_014873.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211921229 C A 0 222 0 0.5401 0.4511 0.4366 0.7093 0.2386 0.2935 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.946265 0 . 0 . 115 28,11,51,14 UTR_3_PRIME(MODIFIER||2012||370|LPGAT1|protein_coding|CODING|NM_014873.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998558 rs11119806 -0.693147 0.0009197 115 370 1474 MODIFIER 8 CODING LPGAT1 T protein_coding NM_014873.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211921767 C T 0 15.2 0 0.0348 0.1885 0.1902 0.0605 0.3867 0.3231 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,1,1,0 UTR_3_PRIME(MODIFIER||1474||370|LPGAT1|protein_coding|CODING|NM_014873.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs11119807 -0.379885 0 5 370 886 MODIFIER 8 CODING LPGAT1 T protein_coding NM_014873.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211922355 C T 0 170 0 0.0348 0.1887 0.1902 0.0605 0.3867 0.3241 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.849331 0 . 0 . 30 16,2,9,3 UTR_3_PRIME(MODIFIER||886||370|LPGAT1|protein_coding|CODING|NM_014873.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.264959 rs61828259 -0.680642 0.338575 30 370 638 MODIFIER 8 CODING LPGAT1 A protein_coding NM_014873.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 211922603 G A 0 222 0 0.5401 0.4505 0.4366 0.7083 0.2386 0.2914 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.706599 0 . 0 . 94 27,19,23,16 UTR_3_PRIME(MODIFIER||638||370|LPGAT1|protein_coding|CODING|NM_014873.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.595238 rs28368551 -0.693144 0.279141 94 962 306 MODIFIER 20 CODING INTS7 C protein_coding NM_015434.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212114860 T C 0 9.7 0 0.5053 0.5473 0.5346 0.4196 0.667 0.6217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||306||962|INTS7|protein_coding|CODING|NM_015434.3|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2808385 -0.379885 0 1 A436V 730 gCa/gTa MODERATE 14 MISSENSE CODING DTL T protein_coding NM_016448.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212273639 C T 0 228 0 0.9115 0.9595 0.9957 1 0.9592 0.9571 0.919201 0.949331 0.964767 2 9575 115056 11364 8647 6431 63807 841 14391 2 10390 119512 11564 8652 6614 66256 880 15156 0 . 0 . 0 69 0,0,55,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A436V|730|DTL|protein_coding|CODING|NM_016448.3|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3135474 -0.693147 0.0298856 69 K694T 730 aAa/aCa MODERATE 14 MISSENSE CODING DTL C protein_coding NM_016448.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212274413 A C 0 228 0 1 0.9966 0.9971 1 0.9891 0.9959 0.99773 0.99062 0.986977 2 10292 117279 11365 8566 6495 64808 881 14872 2 10314 118614 11442 8566 6592 65864 892 14944 0 . 0 . 0 118 0,0,34,65 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K694T|730|DTL|protein_coding|CODING|NM_016448.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6540718 -0.693147 0.690726 118 486 336 MODIFIER 13 CODING PPP2R5A C protein_coding NM_006243.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212534448 T C 0 228 0 0.4501 0.276 0.2262 0.3968 0.1859 0.044 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 0,0,38,27 UTR_3_PRIME(MODIFIER||336||486|PPP2R5A|protein_coding|CODING|NM_006243.3|13|C),DOWNSTREAM(MODIFIER||3368||411|TMEM206|protein_coding|CODING|NM_001198862.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs14123 -0.693147 0.384911 71 486 920 MODIFIER 13 CODING PPP2R5A G protein_coding NM_006243.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212535032 T G 0 228 0 0.0045 0.1542 0.196 0.3978 0.1839 0.045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 109 0,0,47,50 UTR_3_PRIME(MODIFIER||920||486|PPP2R5A|protein_coding|CODING|NM_006243.3|13|G),DOWNSTREAM(MODIFIER||2784||411|TMEM206|protein_coding|CODING|NM_001198862.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1056985 -0.693147 0.0171529 109 F144 411 ttT/ttC LOW 4 SILENT CODING TMEM206 G protein_coding NM_001198862.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212560327 A G 0 228 0 0.997 0.9938 0.9899 1 0.9811 0.999 0.997049 0.986468 0.981046 2 10370 119840 11515 8653 6320 65660 895 16427 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 65 0,0,34,27 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F144|411|TMEM206|protein_coding|CODING|NM_001198862.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs792449 -0.693147 0.112408 65 D170 172 gaT/gaC LOW 4 SILENT CODING NENF C protein_coding NM_013349.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212619339 T C 0 228 0 0.4939 0.4792 0.5605 0.6746 0.3807 0.3016 0.493418 0.432339 0.401047 2 5212 52006 7497 5872 1816 26335 349 4925 2 10402 121316 11572 8630 6610 66698 906 16498 0 . 0 . 0 42 0,0,9,32 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D170|172|NENF|protein_coding|CODING|NM_013349.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4804 -0.693145 0.0363265 42 181 716 MODIFIER 4 CODING ATF3 C protein_coding NM_001030287.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212793613 T C 0 170 0 0.73 0.6661 0.7003 0.4335 0.7644 0.6943 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.874808 0 . 0 . 59 30,3,22,2 UTR_3_PRIME(MODIFIER||716||181|ATF3|protein_coding|CODING|NM_001030287.3|4|C),UPSTREAM(MODIFIER||4176||594|FAM71A|protein_coding|CODING|NM_153606.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982874 rs10475 -0.692831 0.125901 59 594 330 MODIFIER 1 CODING FAM71A G protein_coding NM_153606.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212797890 A G 0 9.7 0 0.7231 0.6464 0.6758 0.4405 0.7266 0.6513 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||330||594|FAM71A|protein_coding|CODING|NM_153606.3|1|G),DOWNSTREAM(MODIFIER||3771||181|ATF3|protein_coding|CODING|NM_001030287.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7533306 -0.379885 0 1 N551D 594 Aac/Gac MODERATE 1 MISSENSE CODING FAM71A G protein_coding NM_153606.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212799870 A G 0 222 0 0.7731 0.7841 0.755 0.6796 0.841 0.8691 0.790513 0.840766 0.866512 1 8207 101144 9174 5602 5829 57278 761 14293 2 10402 121354 11568 8620 6614 66730 908 16512 0.890964 0 . 0 . 93 17,29,12,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N551D|594|FAM71A|protein_coding|CODING|NM_153606.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982023 rs3122713 -0.693145 0.0595618 93 T577M 594 aCg/aTg MODERATE 1 MISSENSE CODING FAM71A T protein_coding NM_153606.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212799949 C T 0 89 0 0.3359 0.485 0.3156 0.4514 0.6451 0.6769 0.39015 0.551438 0.63407 1 3867 69577 3186 3758 4831 42532 551 10852 2 10364 120922 11558 8622 6612 66552 902 16312 0.619422 0 . 0 . 37 3,22,0,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T577M|594|FAM71A|protein_coding|CODING|NM_153606.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.242726 rs3795842 -0.676189 0.736405 37 V11I 127 Gtc/Atc MODERATE 1 MISSENSE CODING BATF3 T protein_coding NM_018664.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212873074 C T 0 25.9 0 0.2239 0.2019 0.1052 0.1875 0.1233 0.3364 0 . 0 1 9 323 3 12 0 39 2 258 2 24 1092 12 40 0 168 8 840 1 0 . 0 . 3 0,1,0,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V11I|127|BATF3|protein_coding|CODING|NM_018664.2|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 1 rs2202683 -0.453602 0.26 3 Q3 127 caA/caG LOW 1 SILENT CODING BATF3 C protein_coding NM_018664.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212873096 T C 0 8 0 0.2262 0.2039 0.1052 0.1895 0.1272 0.3374 0 . 0 1 2 80 0 3 0 10 0 65 2 8 420 2 16 0 62 2 330 1 0 . 0 . 3 0,1,0,2 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q3|127|BATF3|protein_coding|CODING|NM_018664.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 1 rs2202682 -0.453602 0.26 3 281 11439 MODIFIER 6 CODING NSL1 C protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212900311 G C 0 126 0 0.652 0.6094 0.4496 0.5308 0.6909 0.6626 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.95253 0 . 0 . 55 28,1,26,0 UTR_3_PRIME(MODIFIER||11439||281|NSL1|protein_coding|CODING|NM_015471.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.801147 rs2292214 -0.692976 0.0249071 55 281 11315 MODIFIER 6 CODING NSL1 CG protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212900434 C CG 0 222 0 . 0 . 0 . 0 0.679583 0.691899 0.698109 1 1557 19247 460 876 1855 9497 186 4816 2 2298 29026 1066 1614 2480 13634 286 7648 0 . 0 . 0 181 64,30,55,21 UTR_3_PRIME(MODIFIER||11315||281|NSL1|protein_coding|CODING|NM_015471.3|6|CG) 1 0.5 1 80 0.441989 0 1 1 1 0 60 0 0 1 0 . rs3835160 -0.693147 0.0652203 181 281 11263 MODIFIER 6 CODING NSL1 G protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212900487 A G 0 228 0 0.907 0.9099 0.9611 0.8938 0.9155 0.8885 0.916667 0.914341 0.913317 2 5461 71663 6516 5592 4559 39336 531 9668 2 5940 78290 6738 6198 4948 43058 584 10824 0 . 0 . 0 220 0,0,109,81 UTR_3_PRIME(MODIFIER||11263||281|NSL1|protein_coding|CODING|NM_015471.3|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2244935,rs386562366 -0.693147 0.0483237 220 281 8939 MODIFIER 6 CODING NSL1 G protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212902811 A G 0 9.7 0 0.4002 0.2356 0.1326 0.1538 0.1809 0.227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||8939||281|NSL1|protein_coding|CODING|NM_015471.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11120006 -0.379885 0 1 281 8849 MODIFIER 6 CODING NSL1 A protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212902901 G A 0 9.7 0 0.2965 0.1877 0.1081 0.1419 0.1441 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||8849||281|NSL1|protein_coding|CODING|NM_015471.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11120007 -0.379885 0 1 281 8347 MODIFIER 6 CODING NSL1 G protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212903403 A G 0 9.7 0 0.9039 0.9087 0.9611 0.8938 0.9155 0.8865 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||8347||281|NSL1|protein_coding|CODING|NM_015471.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2492786 -0.379885 0 1 281 6064 MODIFIER 6 CODING NSL1 C protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212905686 T C 0 9.7 0 0.9062 0.9095 0.9611 0.8938 0.9155 0.8875 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||6064||281|NSL1|protein_coding|CODING|NM_015471.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2492787 -0.379885 0 1 281 5852 MODIFIER 6 CODING NSL1 A protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212905898 G A 0 54 0 0.6778 0.8454 0.9337 0.8938 0.9155 0.8875 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||5852||281|NSL1|protein_coding|CODING|NM_015471.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2501836 -0.453602 0.88 3 281 2821 MODIFIER 6 CODING NSL1 C protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212908929 T C 0 9.7 0 0.6513 0.6072 0.4438 0.5308 0.6859 0.6616 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2821||281|NSL1|protein_coding|CODING|NM_015471.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6700465 -0.379885 0 1 281 135 MODIFIER 6 CODING NSL1 T protein_coding NM_015471.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212911615 C T 0 53 0 0.3986 0.2153 0.1124 0.1419 0.1441 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.964642 0 . 0 . 12 6,1,4,0 UTR_3_PRIME(MODIFIER||135||281|NSL1|protein_coding|CODING|NM_015471.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.924449 rs1046083 -0.556411 0.38486 12 M254V 281 Atg/Gtg MODERATE 6 MISSENSE CODING NSL1 C protein_coding NM_015471.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212911836 T C 0 222 0 0.6513 0.6074 0.4438 0.5308 0.6859 0.6626 0.682478 0.678533 0.676512 1 6996 77703 4189 4525 4930 46186 568 10309 2 10406 121370 11558 8646 6612 66732 908 16508 0.837729 0 . 0 . 95 23,18,30,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M254V|281|NSL1|protein_coding|CODING|NM_015471.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910118 rs15702 -0.693146 0.65249 95 S4F 281 tCt/tTt MODERATE 1 MISSENSE CODING NSL1 A protein_coding NM_015471.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212965095 G A 0 222 0 0.2943 0.1873 0.1081 0.1429 0.1441 0.1892 0.267136 0.179754 0.134902 1 2569 16155 938 1123 599 8454 102 2370 2 8648 103688 9492 7498 5668 56290 774 15318 0.652195 0 . 0 . 158 54,29,32,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S4F|281|NSL1|protein_coding|CODING|NM_015471.3|1|A),UPSTREAM(MODIFIER||75||281|TATDN3|protein_coding|CODING|NM_001146171.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.573232 rs17856201 -0.693147 0.0802338 158 G7 281 ggC/ggG LOW 1 SILENT CODING TATDN3 G protein_coding NM_001146171.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212965284 C G 0 222 0 0.3986 0.2278 0.1196 0.1538 0.1541 0.226 0.362171 0.224239 0.153605 1 3683 20352 1075 1349 649 10320 133 3143 2 9658 116212 11212 8446 5858 63824 848 16366 0.948766 0 . 0 COSM425259 148 42,34,27,33 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G7|281|TATDN3|protein_coding|CODING|NM_001146171.1|1|G),UPSTREAM(MODIFIER||145||281|NSL1|protein_coding|CODING|NM_015471.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.659997 rs61736926 -0.693147 0.281295 148 281 491 MODIFIER 10 CODING TATDN3 A protein_coding NM_001146171.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 212988989 C A 0 57 0 0.6006 0.8095 0.8919 0.9861 0.8191 0.8415 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||491||281|TATDN3|protein_coding|CODING|NM_001146171.1|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6700544 -0.511536 0.0714862 3 I8T 98 aTt/aCt MODERATE 2 MISSENSE CODING SPATA45 G protein_coding NM_001024601.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213009469 A G 0 222 0 0.7943 0.6605 0.464 0.5407 0.7366 0.6646 0.796868 0.737615 0.707238 1 8258 81317 4383 4654 5290 48108 592 10032 2 10406 121012 11564 8636 6614 66558 908 16326 0.903423 0 . 0 . 115 27,30,25,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I8T|98|SPATA45|protein_coding|CODING|NM_001024601.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.804521 rs10864004 -0.693145 0.528812 115 A52P 555 Gcc/Ccc MODERATE 1 MISSENSE CODING FLVCR1 C protein_coding NM_014053.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213031948 G C 0 68 0 0.2269 0.4445 0.3084 0.5476 0.5646 0.6053 0.256995 0.394563 0.46394 1 248 4804 86 206 21 2013 52 2178 2 728 8368 196 326 28 3446 78 3566 0.800737 3 likely-benign 0 . 14 4,5,2,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Ccc|A52P|555|FLVCR1|protein_coding|CODING|NM_014053.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.526122 rs11120047 -0.590765 0.340858 14 T544M 555 aCg/aTg MODERATE 10 MISSENSE CODING FLVCR1 T protein_coding NM_014053.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213068595 C T 0 222 0 0.1316 0.3794 0.2781 0.4583 0.5 0.5808 0.208806 0.384899 0.475116 1 2019 54464 3090 4127 3882 32630 425 8291 2 10386 121238 11560 8622 6614 66646 908 16502 0.428183 3 likely-benign 0 COSM1560294 102 29,15,27,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T544M|555|FLVCR1|protein_coding|CODING|NM_014053.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.9642 rs3207090 -0.693147 0.0797973 102 555 339 MODIFIER 10 CODING FLVCR1 G protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213068971 T G 0 9.7 0 0.3018 0.6637 0.7695 0.9038 0.6879 0.8057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||339||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12074192 -0.379885 0 1 555 931 MODIFIER 10 CODING FLVCR1 T protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213069563 C T 0 6.3 0 0.1702 0.2843 0.4914 0.4454 0.1879 0.2249 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||931||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12567713 -0.379885 0 1 555 1106 MODIFIER 10 CODING FLVCR1 T protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213069738 C T 0 39.3 0 0.1702 0.2841 0.4914 0.4444 0.1879 0.2249 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1106||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12567728 -0.453602 0.66 2 555 1151 MODIFIER 10 CODING FLVCR1 G protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213069783 A G 0 9.7 0 0.3018 0.6637 0.7695 0.9038 0.6879 0.8057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1151||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6682947 -0.379885 0 1 555 1793 MODIFIER 10 CODING FLVCR1 T protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213070425 C T 0 46.3 0 0.1309 0.3792 0.2781 0.4583 0.5 0.5808 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1793||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12567975 -0.453602 0.14 2 555 1826 MODIFIER 10 CODING FLVCR1 T protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213070458 C T 0 70 0 0.1309 0.3792 0.2781 0.4583 0.5 0.5808 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1826||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12567976 -0.453602 0.36 3 555 2578 MODIFIER 10 CODING FLVCR1 A protein_coding NM_014053.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213071210 G A 0 9.7 0 0.6445 0.475 0.5807 0.5357 0.3191 0.2689 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2578||555|FLVCR1|protein_coding|CODING|NM_014053.3|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1284856 -0.379885 0 1 355 2157 MODIFIER 8 CODING VASH2 G protein_coding NM_001301056.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213164083 A G 0 9.7 0 0.0439 0.4143 0.3732 0.5278 0.6471 0.5879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2157||355|VASH2|protein_coding|CODING|NM_001301056.1|8|G),DOWNSTREAM(MODIFIER||1441||544|ANGEL2|protein_coding|CODING|NM_144567.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10864033 -0.379885 0 1 1066 28 MODIFIER 1 CODING RPS6KC1 C protein_coding NM_012424.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 213224719 T C 0 228 0 0.9002 0.7218 0.5735 0.6161 0.7197 0.6973 0.850656 0.750936 0.700685 2 6706 72046 5486 4951 3166 40292 519 10926 2 7786 104658 10712 7940 4704 57028 742 15746 0 . 0 . 0 23 0,0,17,4 UTR_5_PRIME(MODIFIER||28||1066|RPS6KC1|protein_coding|CODING|NM_012424.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4951476 -0.692352 0.153863 23 G165E 433 gGa/gAa MODERATE 5 MISSENSE CODING SMYD2 A protein_coding NM_020197.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214492286 G A 0 228 0 0.9962 0.8307 0.755 0.623 0.9076 0.7955 0.979119 0.938336 0.917442 2 10212 104147 8133 5324 5722 60672 772 13312 2 10406 121382 11578 8626 6612 66740 908 16512 0 . 0 . 0 71 0,0,30,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G165E|433|SMYD2|protein_coding|CODING|NM_020197.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1134647,rs386518089 -0.693147 0.493301 71 1187 7583 MODIFIER 19 CODING PTPN14 C protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214523682 T C 0 36.3 0 0.0061 0.1352 0.1671 0.2599 0.2038 0.0879 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||7583||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs77502835 -0.453602 0.88 2 1187 5662 MODIFIER 19 CODING PTPN14 G protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214525603 A G 0 9.7 0 0.9909 0.7917 0.6772 0.6458 0.7694 0.7771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5662||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1472439 -0.379885 0 1 1187 5295 MODIFIER 19 CODING PTPN14 T protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214525970 C T 0 9.7 0 0.0787 0.153 0.1772 0.251 0.1998 0.0869 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5295||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17022675 -0.379885 0 1 1187 4933 MODIFIER 19 CODING PTPN14 G protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214526332 A G 0 9.7 0 0.4372 0.2963 0.2608 0.0585 0.3211 0.3507 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4933||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9429919 -0.379885 0 1 1187 4301 MODIFIER 19 CODING PTPN14 C protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214526964 T C 0 9.7 0 0.9909 0.7931 0.6772 0.6458 0.7773 0.7761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4301||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1472443 -0.379885 0 1 1187 3979 MODIFIER 19 CODING PTPN14 C protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214527286 T C 0 32.6 0 0.0908 0.1581 0.1787 0.256 0.1998 0.091 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3979||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs59134396 -0.379885 0 2 1187 3579 MODIFIER 19 CODING PTPN14 T protein_coding NM_005401.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214527686 C T 0 9.7 0 0.0575 0.1454 0.1758 0.2421 0.1998 0.0869 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3579||1187|PTPN14|protein_coding|CODING|NM_005401.4|19|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4655339 -0.379885 0 1 E1084 1187 gaA/gaG LOW 17 SILENT CODING PTPN14 C protein_coding NM_005401.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214542819 T C 0 228 0 0.9569 0.7839 0.6744 0.6488 0.7763 0.7751 0.926237 0.826695 0.775698 2 9742 93403 7407 5336 5201 52187 672 12858 2 10406 121378 11574 8626 6612 66740 908 16512 0 . 0 . COSM146762 72 0,0,48,17 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1084|1187|PTPN14|protein_coding|CODING|NM_005401.4|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1135352 -0.693147 0.355588 72 R326 1187 cgA/cgG LOW 11 SILENT CODING PTPN14 C protein_coding NM_005401.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214564340 T C 0 228 0 0.9909 0.7863 0.6772 0.6349 0.7704 0.7597 0.953246 0.839228 0.780814 2 10013 93454 7401 5290 5115 52376 658 12601 2 10394 120980 11520 8620 6584 66558 908 16396 0 . 0 . 0 58 0,0,35,19 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R326|1187|PTPN14|protein_coding|CODING|NM_005401.4|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7550799 -0.693147 0.116098 58 1187 LOW 8 CODING PTPN14 C protein_coding NM_005401.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214571251 A C 0 228 0 0.3389 0.3504 0.3977 0.4365 0.4046 0.1881 0.330005 0.37106 0.392093 2 3553 45105 4751 3807 2514 26677 382 3421 2 10370 120804 11526 8616 6588 66386 904 16414 0 . 0 . 0 98 0,0,86,7 SPLICE_SITE_REGION+INTRON(LOW||||1187|PTPN14|protein_coding|CODING|NM_005401.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11580603 -0.693147 0.0679846 98 1187 26 MODIFIER 2 CODING PTPN14 T protein_coding NM_005401.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214638172 C T 0 222 0 0.9206 0.8261 0.8141 0.7847 0.7992 0.7771 0.891462 0.83441 0.805187 1 9193 96971 9871 6666 5014 52769 701 12757 2 10250 120000 11538 8586 6446 65910 884 16386 0.771425 0 . 0 . 42 3,15,4,18 UTR_5_PRIME(MODIFIER||26||1187|PTPN14|protein_coding|CODING|NM_005401.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930129 rs10864100 -0.692562 0.208539 42 R2729Q 3114 cGa/cAa MODERATE 16 MISSENSE CODING CENPF A protein_coding NM_016343.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214826196 G A 0 228 0 0.2874 0.5611 0.5893 0.8849 0.4443 0.6973 0.317749 0.391435 0.429186 2 3285 62245 8052 7667 3265 29077 465 10434 2 10282 120300 11558 8642 6612 66288 904 16014 0 . 0 . 0 76 0,0,51,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R2729Q|3114|CENPF|protein_coding|CODING|NM_016343.3|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs335524,rs386581845 -0.693147 0.180286 76 R2943G 3114 Aga/Gga MODERATE 18 MISSENSE CODING CENPF G protein_coding NM_016343.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214830617 A G 0 228 0 0.354 0.6184 0.6383 0.8879 0.5606 0.7434 0.397186 0.492004 0.540581 2 4090 72526 8489 7638 3803 36281 534 11691 2 10358 121148 11540 8642 6610 66594 906 16498 0 . 0 . 0 93 0,0,41,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R2943G|3114|CENPF|protein_coding|CODING|NM_016343.3|18|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386592781,rs438034 -0.693147 0.118225 93 N3106K 3114 aaC/aaG MODERATE 20 MISSENSE CODING CENPF G protein_coding NM_016343.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 214837110 C G 0 228 0 0.3775 0.631 0.6772 0.8889 0.5606 0.7474 0.418747 0.503921 0.547558 2 4302 73031 8699 7544 3766 36433 537 11750 2 10216 120110 11472 8566 6538 66020 880 16418 0 . 0 . 0 85 0,0,34,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaG|N3106K|3114|CENPF|protein_coding|CODING|NM_016343.3|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7289 -0.693147 0.0236292 85 426 912 MODIFIER 7 CODING KCNK2 C protein_coding NM_001017425.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215409399 CT C 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 155 8,45,8,34 UTR_3_PRIME(MODIFIER||912||426|KCNK2|protein_coding|CODING|NM_001017425.2|7|C) 0 0.5 1 42 0.270968 0 1 0 . 0 60 0 0 1 0 . rs71762246 -0.693146 0.503482 155 426 1618 MODIFIER 7 CODING KCNK2 C protein_coding NM_001017425.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215410106 G C 0 110 0 0.6165 0.6593 0.755 0.6895 0.7644 0.5102 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998622 0 . 0 . 16 7,1,7,1 UTR_3_PRIME(MODIFIER||1618||426|KCNK2|protein_coding|CODING|NM_001017425.2|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.987669 rs6686529 -0.651104 0.930513 16 A774 815 gcG/gcA LOW 18 SILENT CODING KCTD3 A protein_coding NM_016121.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215793834 G A 0 222 0 0.2867 0.4143 0.6124 0.3492 0.6372 0.2843 0.317522 0.54075 0.655116 1 3291 67280 7294 3131 4564 43301 511 5188 2 10322 121282 11570 8638 6610 66726 908 16508 0.74272 0 . 0 . 242 61,52,57,38 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A774|815|KCTD3|protein_coding|CODING|NM_016121.3|18|A),DOWNSTREAM(MODIFIER||2402||5202|USH2A|protein_coding|CODING|NM_206933.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.14222 rs14137 -0.693147 0.00437248 242 T4222 5202 acA/acG LOW 63 SILENT CODING USH2A C protein_coding NM_206933.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215848587 T C 0 192 0 0.1793 0.3031 0.4539 0.3155 0.3738 0.2781 0.223105 0.333692 0.390349 1 2217 44162 5511 2753 2622 25705 330 5024 2 10334 120962 11532 8600 6606 66498 906 16486 1 2|2 benign|benign 0 COSM146764 28 5,10,3,10 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4222|5202|USH2A|protein_coding|CODING|NM_206933.2|63|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.216082 rs2797234 -0.683931 0.039133 28 T4204 5202 acA/acG LOW 63 SILENT CODING USH2A C protein_coding NM_206933.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215848641 T C 0 228 0 0.6127 0.6897 0.7954 0.6429 0.8091 0.6442 0.638221 0.754421 0.813953 2 6478 92480 9449 5561 4877 54002 707 11406 2 10244 120702 11512 8598 6608 66364 906 16470 0 2|2,2 benign|benign,benign 0 COSM146765 18 0,0,9,9 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T4204|5202|USH2A|protein_coding|CODING|NM_206933.2|63|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2797235 -0.691153 0.431797 18 Y4031 5202 taC/taT LOW 62 SILENT CODING USH2A A protein_coding NM_206933.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215853692 G A 0 222 0 0 0.00079872 0.0029 0 0.002 0 0.000907853 0.00292173 0.00395349 1 4 357 25 1 3 308 5 11 2 10234 121154 11544 8646 6614 66700 908 16508 0.251577 255|2 other|benign 0 . 34 4,9,6,12 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y4031|5202|USH2A|protein_coding|CODING|NM_206933.2|62|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966712 rs55921307 -0.691153 0.00679643 34 E3411A 5202 gAa/gCa MODERATE 52 MISSENSE CODING USH2A G protein_coding NM_206933.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 215960167 T G 0 222 0 0.7057 0.5887 0.4899 0.6518 0.5358 0.4898 0.671584 0.570583 0.518837 1 7070 66076 6559 5532 3672 34595 515 8133 2 10372 120822 11446 8638 6540 66414 906 16506 0.583385 2,2|2 benign,benign|benign 0 . 151 20,50,14,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E3411A|5202|USH2A|protein_coding|CODING|NM_206933.2|52|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971086 rs10864198 -0.693147 0.331804 151 I2169T 5202 aTa/aCa MODERATE 34 MISSENSE CODING USH2A G protein_coding NM_206933.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216172380 A G 0 228 0 0.4206 0.5935 0.6513 0.8343 0.497 0.637 0.438493 0.480932 0.502674 2 4499 67418 7957 7197 3814 33551 482 9918 2 10396 121106 11502 8618 6596 66586 908 16500 0 2|2 benign|benign 0 . 108 0,0,38,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2169T|5202|USH2A|protein_coding|CODING|NM_206933.2|34|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10864219 -0.693147 0.0489929 108 R1486K 5202 aGg/aAg MODERATE 21 MISSENSE CODING USH2A T protein_coding NM_206933.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216348764 C T 0 228 0 0.5537 0.6623 0.7017 0.7788 0.6143 0.7106 0.596005 0.606412 0.611744 2 5999 79489 8519 6699 4675 41478 615 11504 2 10396 120802 11466 8546 6592 66396 906 16500 0 2|2,2 benign|benign,benign 0 . 138 0,0,59,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R1486K|5202|USH2A|protein_coding|CODING|NM_206933.2|21|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1805049 -0.693147 0.000656061 138 T473 5202 acC/acT LOW 8 SILENT CODING USH2A A protein_coding NM_206933.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216496947 G A 0 222 0 0.3911 0.263 0.2824 0.129 0.2386 0.2393 0.384476 0.295479 0.249884 1 3999 30552 2958 1159 1194 16612 204 4426 2 10396 121204 11516 8586 6614 66678 908 16506 0.998174 2|2 benign|benign 0 . 130 24,42,21,30 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T473|5202|USH2A|protein_coding|CODING|NM_206933.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980613 rs1805050 -0.693147 0.0244787 130 T168 5202 acA/acG LOW 3 SILENT CODING USH2A C protein_coding NM_206933.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216592003 T C 0 228 0 0.4531 0.6328 0.6614 0.8175 0.664 0.6329 0.504993 0.59634 0.64314 2 5134 78618 8023 7252 4550 43095 594 9970 2 10402 121236 11478 8644 6602 66692 908 16510 0 2|2 benign|benign 0 . 108 0,0,48,53 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T168|5202|USH2A|protein_coding|CODING|NM_206933.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4253963 -0.693147 0.000604215 108 A125T 5202 Gca/Aca MODERATE 2 MISSENSE CODING USH2A T protein_coding NM_206933.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216595306 C T 0 228 0 0.764 0.7612 0.7089 0.8125 0.7326 0.771 0.75783 0.718976 0.69907 2 7828 88418 8422 7209 5093 47062 669 12135 2 10400 121238 11504 8636 6604 66674 908 16512 0 2|2 benign|benign 0 . 97 0,0,56,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A125T|5202|USH2A|protein_coding|CODING|NM_206933.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10779261 -0.693147 0.300402 97 470 2931 MODIFIER 8 CODING ESRRG T protein_coding NM_001243518.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216677350 C T 0 228 0 0.8873 0.8772 0.804 0.8294 0.9225 0.9182 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 65 0,0,15,47 UTR_3_PRIME(MODIFIER||2931||470|ESRRG|protein_coding|CODING|NM_001243518.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2809287 -0.693147 0.00609609 65 470 638 MODIFIER 8 CODING ESRRG G protein_coding NM_001243518.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216679643 A G 0 228 0 0.9508 0.896 0.817 0.8294 0.9264 0.9151 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 0,0,40,29 UTR_3_PRIME(MODIFIER||638||470|ESRRG|protein_coding|CODING|NM_001243518.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2809288 -0.693147 0.196416 73 S331 470 tcG/tcA LOW 7 SILENT CODING ESRRG T protein_coding NM_001243518.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 216692669 C T 0 228 0 0.733 0.6326 0.6354 0.7381 0.4344 0.59 0.661598 0.498078 0.414302 2 6991 60905 7256 6199 2527 27824 465 9643 2 10392 121080 11454 8630 6596 66596 908 16504 0.999362 0 . 0 . 92 2,1,51,31 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S331|470|ESRRG|protein_coding|CODING|NM_001243518.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.929969 rs945453 -0.693147 0.588321 92 282 5043 MODIFIER 5 CODING RRP15 T protein_coding NM_016052.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 218509476 A T 0 39.3 0 0 0.013379 0 0.0605 0 0.0061 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||5043||282|RRP15|protein_coding|CODING|NM_016052.3|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs76564318 -0.453602 0.36 2 442 784 MODIFIER 1 CODING TGFB2 C protein_coding NM_001135599.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 218519260 A C 0 9.7 0 0.9992 0.9994 0.9986 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||784||442|TGFB2|protein_coding|CODING|NM_001135599.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1557153 -0.379885 0 1 442 201 MODIFIER 8 CODING TGFB2 T protein_coding NM_001135599.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 218614905 A T 0 222 0 0.3472 0.4189 0.487 0.6865 0.2803 0.3344 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.743533 0 . 0 . 93 17,19,15,30 UTR_3_PRIME(MODIFIER||201||442|TGFB2|protein_coding|CODING|NM_001135599.2|8|T),INTRAGENIC(MODIFIER|||||MIR548F3||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.935243 rs900 -0.693147 0.087701 93 237 LOW 3 CODING LYPLAL1 C protein_coding NM_138794.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 219383867 T C 0 228 0 0.8517 0.9603 0.9957 1 1 1 0.881752 0.959698 0.999651 2 8872 119452 11368 8640 6606 66576 903 16487 2 10152 120830 11444 8640 6606 66592 906 16490 0 . 0 . 0 152 0,0,111,26 SPLICE_SITE_REGION+INTRON(LOW||||237|LYPLAL1|protein_coding|CODING|NM_138794.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386622404,rs940571 -0.693147 0.0928018 152 I131M 237 atA/atG MODERATE 4 MISSENSE CODING LYPLAL1 G protein_coding NM_138794.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 219383905 A G 0 228 0 0.8631 0.9633 0.9957 1 1 1 0.895824 0.964549 0.999767 2 9222 120061 11471 8654 6610 66698 905 16501 2 10404 121336 11544 8654 6610 66714 908 16502 0 . 0 . 0 175 0,0,96,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I131M|237|LYPLAL1|protein_coding|CODING|NM_138794.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs940570 -0.693147 0.00606039 175 1512 125 MODIFIER 32 CODING EPRS T protein_coding NM_004446.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220142023 C T 0 195 0 0.3873 0.4764 0.3674 0.5804 0.496 0.547 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,43,0 UTR_3_PRIME(MODIFIER||125||1512|EPRS|protein_coding|CODING|NM_004446.2|32|T),INTRAGENIC(MODIFIER|||||RNU5F-1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1061248 -0.693146 0.00880647 44 1512 78 MODIFIER 32 CODING EPRS T protein_coding NM_004446.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220142070 C T 0 228 0 0.3865 0.4762 0.3674 0.5804 0.496 0.547 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 0,0,87,2 UTR_3_PRIME(MODIFIER||78||1512|EPRS|protein_coding|CODING|NM_004446.2|32|T),INTRAGENIC(MODIFIER|||||RNU5F-1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1061242 -0.693147 0.764788 90 D308E 1512 gaC/gaA MODERATE 8 MISSENSE CODING EPRS T protein_coding NM_004446.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220197625 G T 0 222 0 0.9902 0.899 0.8732 0.9395 0.7932 0.8609 0.956877 0.859065 0.808953 1 10065 102014 10669 8068 5359 53346 739 13768 2 10394 120728 11564 8648 6600 66344 900 16278 0.555373 0 . 0 . 113 53,12,33,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D308E|1512|EPRS|protein_coding|CODING|NM_004446.2|8|T),INTRAGENIC(MODIFIER|||||RNU5F-1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.814207 rs2230301 -0.693146 0.0358487 113 308 739 MODIFIER 9 CODING BPNT1 A protein_coding NM_006085.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220231447 G A 0 218 0 0.8101 0.7608 0.7839 0.6121 0.8698 0.7188 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.675694 0 . 0 . 56 20,7,25,4 UTR_3_PRIME(MODIFIER||739||308|BPNT1|protein_coding|CODING|NM_006085.5|9|A),INTRAGENIC(MODIFIER|||||RNU5F-1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998354 rs2647465 -0.693079 0.55787 56 1012 LOW 1 CODING IARS2 T protein_coding NM_018060.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220269439 A T 0 222 0 0.0204 0.0713 0.0548 0.0516 0.0855 0.1575 0.0138573 0.0345385 0.0451268 1 225 8941 437 403 433 5360 75 2008 2 9108 110566 11064 7978 6290 60112 850 15164 0.999896 0 . 0 . 93 18,34,10,20 SPLICE_SITE_REGION+INTRON(LOW||||1012|IARS2|protein_coding|CODING|NM_018060.3|1|T),INTRAGENIC(MODIFIER|||||RNU5F-1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943274 rs78836180 -0.693097 0.758372 93 1393 404 MODIFIER 35 CODING RAB3GAP2 G protein_coding NM_012414.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220324189 A G 0 15.5 0 0.0076 0.0627 0.0548 0.0496 0.0845 0.1339 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 7 1,4,1,1 UTR_3_PRIME(MODIFIER||404||1393|RAB3GAP2|protein_coding|CODING|NM_012414.3|35|G),DOWNSTREAM(MODIFIER||2806||1012|IARS2|protein_coding|CODING|NM_018060.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.9 rs1059140 -0.453602 0.5 7 L1165 1393 ttG/ttA LOW 31 SILENT CODING RAB3GAP2 T protein_coding NM_012414.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220330672 C T 0 222 0 0.0076 0.0605 0.0519 0.0496 0.0885 0.1207 0.0215615 0.0691988 0.0936047 1 181 10621 515 496 497 6642 89 2201 2 10396 121198 11506 8632 6600 66660 908 16496 0.997733 3|2 likely-benign|benign 0 . 118 34,28,26,15 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L1165|1393|RAB3GAP2|protein_coding|CODING|NM_012414.3|31|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.77491 rs11547779,rs386518982 -0.693145 0.551456 118 S1092T 1393 aGt/aCt MODERATE 30 MISSENSE CODING RAB3GAP2 G protein_coding NM_012414.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220331205 C G 0 222 0 0.0076 0.0603 0.0519 0.0486 0.0885 0.1207 0.0215615 0.0691988 0.0936047 1 181 10514 490 492 499 6575 89 2188 2 10114 117536 11166 8420 6482 64608 890 15856 0.901576 3|2 likely-benign|benign 0 . 168 48,32,33,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S1092T|1393|RAB3GAP2|protein_coding|CODING|NM_012414.3|30|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.294132 rs2289189 -0.693147 0.243734 168 142 1050 MODIFIER 2 CODING C1orf115 G protein_coding NM_024709.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220871123 A G 0 6.3 0 0.5106 0.4968 0.4726 0.8304 0.2455 0.41 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1050||142|C1orf115|protein_coding|CODING|NM_024709.4|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs337154 -0.379885 0 1 T165A 337 Acc/Gcc MODERATE 3 MISSENSE CODING MARC1 G protein_coding NM_022746.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 220970028 A G 0 228 0 0.9508 0.8095 0.7767 0.7679 0.7217 0.7751 0.919882 0.776642 0.703256 2 9595 91424 9685 6864 4711 47146 663 12760 2 10394 121218 11560 8636 6586 66632 904 16506 1 0 . 0 . 70 1,0,43,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T165A|337|MARC1|protein_coding|CODING|NM_022746.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2642438 -0.693147 0.245164 70 488 263 MODIFIER 1 CODING HLX C protein_coding NM_021958.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 221052937 A C 0 6.3 0 0.7859 0.6645 0.6427 0.5982 0.671 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||263||488|HLX|protein_coding|CODING|NM_021958.3|1|C),INTRAGENIC(MODIFIER|||||HLX-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2738754 -0.379885 0 1 E242 482 gaA/gaG LOW 2 SILENT CODING DUSP10 C protein_coding NM_007207.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 221912361 T C 0 228 0 0.8313 0.7202 0.6816 0.6736 0.6412 0.727 0.819564 0.708442 0.651512 2 8600 81764 7862 5912 3897 43371 589 11533 2 10404 121368 11574 8644 6604 66722 908 16512 0 . 0 . 0 106 0,0,39,59 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E242|482|DUSP10|protein_coding|CODING|NM_007207.5|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1141714 -0.693147 0.467513 106 Q93 482 caA/caG LOW 2 SILENT CODING DUSP10 C protein_coding NM_007207.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 221912808 T C 0 228 0 0.0961 0.3433 0.4179 0.4484 0.3777 0.4806 0.144803 0.318622 0.407674 2 1427 47225 4372 4062 2124 27403 364 7473 2 10398 121122 11522 8604 6558 66630 904 16506 1 0 . 0 . 138 1,0,82,46 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q93|482|DUSP10|protein_coding|CODING|NM_007207.5|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1136448 -0.693147 0.0002381 138 T433 724 acG/acC LOW 4 SILENT CODING HHIPL2 G protein_coding NM_024746.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222713503 C G 0 228 0 0.3434 0.3756 0.5058 0.5089 0.2604 0.3078 0.328189 0.303783 0.291279 2 3395 41419 6943 4661 2543 18995 297 4585 2 10404 121348 11568 8622 6610 66724 908 16512 1 0 . 0 . 84 1,0,47,33 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T433|724|HHIPL2|protein_coding|CODING|NM_024746.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3748664 -0.693147 0.0183628 84 H391D 724 Cat/Gat MODERATE 4 MISSENSE CODING HHIPL2 C protein_coding NM_024746.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222713631 G C 0 228 0 0.3434 0.3756 0.5058 0.5089 0.2604 0.3078 0.328643 0.303937 0.291279 2 3393 41417 6942 4663 2539 18996 298 4586 2 10390 121178 11572 8626 6606 66662 908 16414 1 0 . 0 . 55 0,1,10,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H391D|724|HHIPL2|protein_coding|CODING|NM_024746.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3748666 -0.693147 0.00678506 55 V241M 724 Gtg/Atg MODERATE 2 MISSENSE CODING HHIPL2 T protein_coding NM_024746.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222717132 C T 0 222 0 0.0008 0.0984 0.2219 0.2669 0.003 0.0675 0.00476623 0.00415193 0.00383721 1 58 7294 3451 2374 111 282 61 957 2 10394 121298 11544 8622 6608 66722 908 16500 0.644989 0 . 0 COSM146779 91 26,19,19,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V241M|724|HHIPL2|protein_coding|CODING|NM_024746.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.912224 rs3811466 -0.693141 0.0977326 91 L33 724 ttG/ttA LOW 1 SILENT CODING HHIPL2 T protein_coding NM_024746.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222721288 C T 0 228 0 0.3124 0.5819 0.7205 0.6379 0.6044 0.7669 0.381449 0.541956 0.616663 2 3431 76173 9296 5514 4221 40725 577 12409 2 9588 119600 11530 8568 6562 66004 884 16464 1 0 . 0 . 28 0,1,13,12 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L33|724|HHIPL2|protein_coding|CODING|NM_024746.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386595854,rs4846382 -0.692914 0.282337 28 G381 450 ggC/ggG LOW 10 SILENT CODING TAF1A C protein_coding NM_001201536.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222734803 G C 0 222 0 0.0234 0.3125 0.353 0.3671 0.5119 0.4131 0.103949 0.355836 0.484884 1 907 52447 3917 3098 3562 32797 425 7741 2 10362 121188 11548 8614 6606 66656 908 16494 0.512582 0 . 0 . 151 28,45,20,38 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G381|450|TAF1A|protein_coding|CODING|NM_001201536.1|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998045 rs1134898 -0.693147 0.357568 151 450 1330 MODIFIER 1 CODING TAF1A G protein_coding NM_001201536.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222763235 T G 0 70 0 0.7859 0.7959 0.8372 0.88 0.7734 0.7168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||1330||450|TAF1A|protein_coding|CODING|NM_001201536.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3008651 -0.453602 0.06 3 450 1344 MODIFIER 1 CODING TAF1A T protein_coding NM_001201536.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222763249 C T 0 61 0 0.9856 0.9962 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||1344||450|TAF1A|protein_coding|CODING|NM_001201536.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3008652 -0.453602 0.06 3 1907 LOW 2 CODING MIA3 A protein_coding NM_198551.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222798106 G A 0 228 0 0.9939 0.9984 1 1 1 1 0.987514 0.996119 1 2 9454 118765 11458 8596 6562 65590 881 16224 2 9540 118856 11460 8596 6562 65592 882 16224 0 . 0 . 0 117 0,0,76,32 SPLICE_SITE_REGION+INTRON(LOW||||1907|MIA3|protein_coding|CODING|NM_198551.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3008617 -0.693147 0.0961435 117 K482E 1907 Aag/Gag MODERATE 4 MISSENSE CODING MIA3 G protein_coding NM_198551.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222802006 A G 0 228 0 0.9834 0.9956 1 1 1 1 0.977273 0.992691 0.999878 2 9369 119846 11563 8624 6614 66271 895 16510 2 9560 120046 11568 8624 6614 66274 896 16510 0 . 0 . 0 99 0,0,43,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K482E|1907|MIA3|protein_coding|CODING|NM_198551.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2936053 -0.693147 0.600623 99 K605R 1907 aAa/aGa MODERATE 4 MISSENSE CODING MIA3 G protein_coding NM_198551.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222802376 A G 0 222 0 0.3222 0.2939 0.3977 0.3085 0.168 0.2965 0.284478 0.210887 0.175245 1 2941 28390 5551 2639 1185 11816 208 4050 2 9766 120532 11544 8594 6612 66626 900 16490 0.735694 0 . 0 COSM146780 82 16,18,20,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K605R|1907|MIA3|protein_coding|CODING|NM_198551.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999509 rs2936052 -0.693146 0.574653 82 P747 1907 ccT/ccG LOW 4 SILENT CODING MIA3 G protein_coding NM_198551.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222802803 T G 0 159 0 0.2504 0.5074 0.5072 0.5823 0.7296 0.5491 0.314815 0.585178 0.706812 1 2869 76221 5349 5001 4933 47471 611 9987 2 9690 120284 11540 8598 6612 66464 898 16482 0.780117 0 . 0 COSM146781 36 10,14,7,5 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P747|1907|MIA3|protein_coding|CODING|NM_198551.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.84161 rs3748626 -0.680642 0.51263 36 S788 1907 agC/agT LOW 4 SILENT CODING MIA3 T protein_coding NM_198551.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222802926 C T 0 228 0 0.5711 0.8005 0.9035 0.8899 0.8976 0.8456 0.614026 0.79995 0.884494 2 5788 104502 10898 7637 6120 59230 817 14012 2 9708 120320 11554 8608 6614 66462 896 16478 0 . 0 . 0 87 0,0,66,14 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S788|1907|MIA3|protein_coding|CODING|NM_198551.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3008620 -0.693147 0.187057 87 E881G 1907 gAg/gGg MODERATE 4 MISSENSE CODING MIA3 G protein_coding NM_198551.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222803204 A G 0 222 0 0.3374 0.3213 0.4236 0.3998 0.168 0.3037 0.296373 0.214675 0.176478 1 3011 29881 6391 3283 1179 11723 212 4082 2 9508 118968 11442 8456 6600 65656 886 16420 0.986415 0 . 0 . 46 4,17,10,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E881G|1907|MIA3|protein_coding|CODING|NM_198551.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.797558 rs2936051 -0.692914 0.783133 46 N1333 1907 aaT/aaC LOW 13 SILENT CODING MIA3 C protein_coding NM_198551.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222825587 T C 0 222 0 0 0.0021965 0 0.0109 0 0 0 . 0 1 0 67 0 67 0 0 0 0 2 9788 120594 11570 8626 6612 66594 900 16504 0.968615 0 . 0 . 66 16,12,13,14 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N1333|1907|MIA3|protein_coding|CODING|NM_198551.3|13|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.711573 rs181422930 -0.693021 0.214368 66 P1686 1907 ccT/ccC LOW 24 SILENT CODING MIA3 C protein_coding NM_198551.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222833601 T C 0 228 0 0.9826 0.995 0.9986 1 0.999 1 0.976203 0.992351 0.999757 2 9607 120530 11564 8626 6612 66710 899 16512 2 9804 120746 11570 8626 6612 66722 900 16512 0 . 0 . 0 90 0,0,48,30 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1686|1907|MIA3|protein_coding|CODING|NM_198551.3|24|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3002153 -0.693147 0.202625 90 1907 877 MODIFIER 28 CODING MIA3 G protein_coding NM_198551.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222839838 A G 0 9.7 0 0.3775 0.7446 0.889 0.881 0.8936 0.8446 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||877||1907|MIA3|protein_coding|CODING|NM_198551.3|28|G),DOWNSTREAM(MODIFIER||1517||306|AIDA|protein_coding|CODING|NM_022831.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1053316 -0.379885 0 1 411 2923 MODIFIER 1 CODING BROX G protein_coding NM_144695.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222886119 A G 0 23.3 0 0.8109 0.7572 0.6268 0.7262 0.8479 0.7157 0 . 0 1 192 8526 74 108 2 2310 99 5741 2 236 10904 94 140 2 2814 118 7500 0.5 0 . 0 . 4 1,1,0,2 START_GAINED(LOW||||411|BROX|protein_coding|CODING|NM_144695.3|1|G),UTR_5_PRIME(MODIFIER||2923||411|BROX|protein_coding|CODING|NM_144695.3|1|G),UPSTREAM(MODIFIER||255||306|AIDA|protein_coding|CODING|NM_022831.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.5 rs3811465 -0.453602 0.7 4 411 238 MODIFIER 13 CODING BROX G protein_coding NM_144695.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222906294 A G 0 44.3 0 0.2239 0.4844 0.4942 0.5764 0.6998 0.5133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.28717 0 . 0 . 6 0,3,0,3 UTR_3_PRIME(MODIFIER||238||411|BROX|protein_coding|CODING|NM_144695.3|13|G),UPSTREAM(MODIFIER||4264||158|FAM177B|protein_coding|CODING|NM_207468.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 0 . 0.861511 rs12043288 -0.511536 0.074936 6 I3S 158 aTt/aGt MODERATE 3 MISSENSE CODING FAM177B G protein_coding NM_207468.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222919895 T G 0 228 0 0.2375 0.5893 0.7378 0.7708 0.6998 0.6585 0.296414 0.547901 0.676744 2 2989 81435 9240 6681 4870 45800 646 11209 2 10354 120864 11562 8648 6612 66548 902 16238 0 . 0 . 0 82 0,0,35,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I3S|158|FAM177B|protein_coding|CODING|NM_207468.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2378607,rs386473884 -0.693147 0.988205 82 Q143R 158 cAa/cGa MODERATE 6 MISSENSE CODING FAM177B G protein_coding NM_207468.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222923351 A G 0 228 0 0.7481 0.7915 0.8545 0.8006 0.826 0.7607 0.767037 0.796332 0.810213 2 7504 96953 9891 6831 5317 53902 709 12799 2 9804 120708 11536 8618 6614 66728 898 16510 0.544872 0 . 0 COSM146785 91 1,1,39,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q143R|158|FAM177B|protein_coding|CODING|NM_207468.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.230769 rs6683071 -0.693147 0.0239838 91 158 439 MODIFIER 6 CODING FAM177B G protein_coding NM_207468.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 222923839 A G 0 73 0 0.9652 0.9363 0.9438 0.996 0.8738 0.8947 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||439||158|FAM177B|protein_coding|CODING|NM_207468.2|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2378608 -0.511536 0.470313 3 E103K 1524 Gag/Aag MODERATE 4 MISSENSE CODING DISP1 A protein_coding NM_032890.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223116472 G A 0 228 0 0.1566 0.2117 0.1715 0.2907 0.1352 0.3119 0.167499 0.147163 0.136744 2 1755 21661 2306 2582 985 9182 156 4695 2 10402 121338 11574 8630 6612 66712 908 16500 0.886376 0 . 0 . 115 1,2,66,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E103K|1524|DISP1|protein_coding|CODING|NM_032890.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.999362 rs2609383 -0.693147 0.00510157 115 E103D 1524 gaG/gaT MODERATE 4 MISSENSE CODING DISP1 T protein_coding NM_032890.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223116474 G T 0 228 0 0.1566 0.2117 0.1715 0.2907 0.1352 0.3119 0.167499 0.147163 0.136744 2 1755 21661 2306 2583 985 9182 156 4694 2 10402 121330 11572 8630 6612 66706 908 16500 0.261694 0 . 0 . 116 1,2,66,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E103D|1524|DISP1|protein_coding|CODING|NM_032890.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.95315 rs2789975 -0.693147 0.00665201 116 P1274 1524 ccA/ccC LOW 10 SILENT CODING DISP1 C protein_coding NM_032890.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223178561 A C 0 222 0 0.4153 0.498 0.5346 0.4782 0.6163 0.4826 0.453246 0.534907 0.576744 1 4627 66055 6135 4445 3929 38531 511 7877 2 10324 121128 11558 8600 6612 66628 908 16498 0.836025 0 . 0 COSM146786 41 7,12,5,14 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P1274|1524|DISP1|protein_coding|CODING|NM_032890.3|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.566793 rs9441941 -0.69168 0.016628 41 F822L 858 Ttc/Ctc MODERATE 6 MISSENSE CODING TLR5 G protein_coding NM_003268.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223283910 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10404 121385 11566 8652 6614 66731 908 16510 2 10404 121386 11566 8652 6614 66732 908 16510 0 . 0 . 0 116 0,0,78,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F822L|858|TLR5|protein_coding|CODING|NM_003268.5|6|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7512943 -0.693147 0.0133171 116 N592S 858 aAt/aGt MODERATE 6 MISSENSE CODING TLR5 C protein_coding NM_003268.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223284599 T C 0 222 0 0.0045 0.1402 0.2089 0.2728 0.162 0.1155 0.0326827 0.116638 0.159651 1 281 17998 2615 2125 924 9837 135 2081 2 10358 121018 11466 8618 6598 66578 906 16494 0.997048 255 other 0 COSM146787 89 16,17,17,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N592S|858|TLR5|protein_coding|CODING|NM_003268.5|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937105 rs2072493 -0.693147 0.26787 89 L549 594 ctC/ctT LOW 15 SILENT CODING CAPN8 A protein_coding NM_001143962.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223717484 G A 0 222 0 0.5356 0.6747 0.7493 0.6687 0.7555 0.7331 0.565029 0.705431 0.766499 1 1215 15597 318 418 661 6751 173 6061 2 2188 20926 410 622 876 8700 218 7912 0.91089 0 . 0 . 121 21,31,26,35 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L549|594|CAPN8|protein_coding|CODING|NM_001143962.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999896 rs34158997 -0.693147 0.664829 121 T483M 594 aCg/aTg MODERATE 13 MISSENSE CODING CAPN8 A protein_coding NM_001143962.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223718651 G A 0 222 0 0.2042 0.4411 0.5692 0.5397 0.5586 0.4479 0.252168 0.455979 0.544626 1 519 10895 231 336 893 4936 140 3840 2 2148 21708 410 622 1618 8756 242 7912 0.84406 0 . 0 . 122 29,29,27,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T483M|594|CAPN8|protein_coding|CODING|NM_001143962.1|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94549 rs61823553 -0.693147 0.00373116 122 S245Y 594 tCc/tAc MODERATE 6 MISSENSE CODING CAPN8 T protein_coding NM_001143962.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223813586 G T 0 222 0 0.674 0.6042 0.5432 0.5675 0.5229 0.6748 0.663295 0.57972 0.543369 1 1428 12855 237 334 646 4969 133 5108 2 2182 21808 410 622 1576 8868 236 7914 0.970833 0 . 0 . 87 24,22,17,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S245Y|594|CAPN8|protein_coding|CODING|NM_001143962.1|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.921669 rs35539373 -0.693132 0.318077 87 D22E 700 gaC/gaG MODERATE 1 MISSENSE CODING CAPN2 G protein_coding NM_001748.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223900408 C G 0 228 0 0.9539 0.9874 0.9971 1 1 1 0.954483 0.98444 0.999767 2 7566 96004 9033 7160 4034 54137 642 13432 2 7926 96396 9048 7160 4034 54146 644 13438 1 0 . 0 . 94 1,0,66,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D22E|700|CAPN2|protein_coding|CODING|NM_001748.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs25655 -0.693147 0.725477 94 L102 700 ctG/ctA LOW 2 SILENT CODING CAPN2 A protein_coding NM_001748.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223905532 G A 0 228 0 0.351 0.5954 0.6354 0.5823 0.7634 0.7382 0.436904 0.66254 0.77814 2 4372 86782 7187 4792 5580 51981 676 12194 2 10352 120978 11490 8604 6598 66554 904 16476 0 . 0 . COSM146789 51 0,0,18,25 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L102|700|CAPN2|protein_coding|CODING|NM_001748.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs17596 -0.693146 0.15792 51 L166 700 ctC/ctT LOW 4 SILENT CODING CAPN2 T protein_coding NM_001748.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223933079 C T 0 222 0 0.6437 0.2752 0.268 0.1905 0.0984 0.0511 0.529959 0.241658 0.0939535 1 5771 18684 3198 1813 596 6240 108 958 2 10400 121362 11572 8640 6612 66720 906 16512 0.926889 0 . 0 . 113 27,26,24,18 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L166|700|CAPN2|protein_coding|CODING|NM_001748.4|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.92278 rs17598 -0.693146 0.343905 113 A194 700 gcG/gcA LOW 5 SILENT CODING CAPN2 A protein_coding NM_001748.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223934720 G A 0 222 0 0.289 0.6839 0.7233 0.7143 0.9016 0.9346 0.404222 0.735737 0.905581 1 3951 100775 8338 5870 6018 60456 788 15354 2 10404 121370 11578 8646 6614 66714 908 16506 0.691319 0 . 0 . 98 30,20,25,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A194|700|CAPN2|protein_coding|CODING|NM_001748.4|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.119897 rs17600 -0.693143 0.311261 98 700 370 MODIFIER 21 CODING CAPN2 A protein_coding NM_001748.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223962929 G A 0 222 0 0.8812 0.5433 0.4841 0.4673 0.4235 0.3303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.897845 0 . 0 . 159 45,21,46,30 UTR_3_PRIME(MODIFIER||370||700|CAPN2|protein_coding|CODING|NM_001748.4|21|A),DOWNSTREAM(MODIFIER||4666||1134|TP53BP2|protein_coding|CODING|NM_001031685.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.857632 rs10961 -0.693147 0.35232 159 L960 1134 ctC/ctG LOW 15 SILENT CODING TP53BP2 C protein_coding NM_001031685.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223980207 G C 0 222 0 0.4198 0.2139 0.2133 0.1935 0.0944 0.0798 0.352474 0.165231 0.0693023 1 3853 14836 2502 1861 255 4982 101 1282 2 10372 120632 11416 8608 6564 66488 904 16280 0.878159 0 . 0 . 133 22,41,22,37 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L960|1134|TP53BP2|protein_coding|CODING|NM_001031685.2|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.320391 rs1153936 -0.693147 0.136198 133 S359 1134 tcG/tcA LOW 9 SILENT CODING TP53BP2 T protein_coding NM_001031685.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 223989966 C T 0 222 0 0.416 0.2129 0.2147 0.1935 0.0934 0.0798 0.346573 0.162463 0.0681395 1 3810 14772 2515 1865 256 4944 102 1280 2 10380 121236 11572 8630 6614 66620 908 16512 0.994887 0 . 0 . 147 39,27,40,27 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S359|1134|TP53BP2|protein_coding|CODING|NM_001031685.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.521678 rs1153933,rs386518747 -0.693147 0.424548 147 368 1843 MODIFIER 5 CODING FBXO28 A protein_coding NM_015176.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224347291 G A 0 228 0 0.7156 0.9155 0.9597 0.997 0.996 0.9877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 69 0,0,14,49 UTR_3_PRIME(MODIFIER||1843||368|FBXO28|protein_coding|CODING|NM_015176.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10916388 -0.693147 0.0926264 69 368 1943 MODIFIER 5 CODING FBXO28 T protein_coding NM_015176.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224347391 C T 0 171 0 0.7156 0.9155 0.9597 0.997 0.996 0.9877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,1,12 UTR_3_PRIME(MODIFIER||1943||368|FBXO28|protein_coding|CODING|NM_015176.3|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11804140 -0.683931 0.126964 13 368 1985 MODIFIER 5 CODING FBXO28 T protein_coding NM_015176.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224347433 C T 0 187 0 0.9478 0.985 0.9928 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,1,10 UTR_3_PRIME(MODIFIER||1985||368|FBXO28|protein_coding|CODING|NM_015176.3|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11804144 -0.676189 0.355721 11 368 2470 MODIFIER 5 CODING FBXO28 C protein_coding NM_015176.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224347918 G C 0 9.7 0 0.7156 0.9155 0.9597 0.997 0.996 0.9877 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2470||368|FBXO28|protein_coding|CODING|NM_015176.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2048994 -0.379885 0 1 323 54 MODIFIER 3 CODING DEGS1 G protein_coding NM_003676.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224380234 A G 0 222 0 0.2065 0.1913 0.2248 0.3581 0.0944 0.0746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.887852 0 . 0 . 53 5,14,8,20 UTR_3_PRIME(MODIFIER||54||323|DEGS1|protein_coding|CODING|NM_003676.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.393543 rs386620455,rs908804 -0.693054 0.0746299 53 323 298 MODIFIER 3 CODING DEGS1 G protein_coding NM_003676.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224380478 A G 0 18.2 0 0.2905 0.2342 0.2608 0.3681 0.1282 0.1104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||298||323|DEGS1|protein_coding|CODING|NM_003676.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1060386 -0.453602 0.92 3 L246 856 ctG/ctA LOW 7 SILENT CODING NVL T protein_coding NM_002533.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224492746 C T 0 228 0 0.5242 0.8201 0.9337 0.8899 0.9672 0.9162 0.594417 0.825235 0.943488 2 6029 110907 11127 7773 6455 63294 862 15367 2 10404 121376 11578 8654 6614 66714 908 16504 0 . 0 . 0 89 0,0,51,30 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L246|856|NVL|protein_coding|CODING|NM_002533.3|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3754090 -0.693147 0.0392709 89 R152 856 cgG/cgA LOW 6 SILENT CODING NVL T protein_coding NM_002533.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224495852 C T 0 228 0 0.5295 0.8217 0.9337 0.8899 0.9672 0.9172 0.600091 0.827157 0.943488 2 6085 110999 11128 7775 6455 63321 862 15373 2 10404 121408 11578 8652 6614 66740 908 16512 0 . 0 . 0 104 0,0,52,38 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R152|856|NVL|protein_coding|CODING|NM_002533.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7534447 -0.693147 0.794519 104 856 13 MODIFIER 1 CODING NVL T protein_coding NM_002533.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224517842 C T 0 228 0 0.5605 0.8299 0.9337 0.8899 0.9672 0.9172 0.618475 0.833308 0.943372 2 6261 110950 11119 7754 6408 63182 854 15372 2 10330 121072 11558 8630 6562 66582 900 16510 1 0 . 0 . 115 0,1,47,54 UTR_5_PRIME(MODIFIER||13||856|NVL|protein_coding|CODING|NM_002533.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2896990 -0.693147 0.00917053 115 139 98 MODIFIER 1 CODING CNIH4 G protein_coding NM_014184.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224544529 A G 0 228 0 0.3616 0.7316 0.8141 0.9891 0.7505 0.8885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,14,4 UTR_5_PRIME(MODIFIER||98||139|CNIH4|protein_coding|CODING|NM_014184.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7517754 -0.691153 0.22938 18 661 2164 MODIFIER 14 CODING WDR26 A protein_coding NM_025160.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224575373 G A 0 228 0 0.5446 0.8686 0.9395 0.994 0.994 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 46 0,0,28,18 UTR_3_PRIME(MODIFIER||2164||661|WDR26|protein_coding|CODING|NM_025160.6|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4653586 -0.693147 0.669254 46 160 159 MODIFIER 6 CODING CNIH3 T protein_coding NM_152495.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 224927217 C T 0 228 0 0.0159 0.1424 0.1671 0.0714 0.3121 0.1943 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,2,11 UTR_3_PRIME(MODIFIER||159||160|CNIH3|protein_coding|CODING|NM_152495.1|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3738362 -0.683931 0.266244 14 4515 LOW 6 CODING DNAH14 A protein_coding NM_001373.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225156457 G A 0 222 0 0.0023 0.1336 0.1671 0.3036 0.1044 0.1421 0 . 0 1 43 2369 61 192 115 837 25 1096 2 2144 21438 406 622 1622 8602 240 7802 0.917927 0 . 0 . 134 44,15,35,19 SPLICE_SITE_REGION+INTRON(LOW||||4515|DNAH14|protein_coding|CODING|NM_001373.1|6|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.689567 rs16858926 -0.693147 0.0019096 134 C520 4515 tgC/tgT LOW 13 SILENT CODING DNAH14 T protein_coding NM_001373.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225230608 C T 0 222 0 0.3616 0.7013 0.7651 0.7212 0.9553 0.8333 0.510838 0.824354 0.960717 1 1065 19251 333 425 1585 8738 214 6891 2 2200 22232 418 622 1634 9196 248 7914 0.972937 0 . 0 . 113 39,28,20,17 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C520|4515|DNAH14|protein_coding|CODING|NM_001373.1|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.656981 rs2501107 -0.693141 0.205092 113 L828V 4515 Ctg/Gtg MODERATE 18 MISSENSE CODING DNAH14 G protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225266966 C G 0 222 0 0.3654 0.7023 0.7651 0.7212 0.9553 0.8333 0.518786 0.826611 0.960667 1 1039 18761 328 425 1575 8295 208 6891 2 2136 21678 408 622 1622 8734 242 7914 0.845431 0 . 0 . 67 14,13,14,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L828V|4515|DNAH14|protein_coding|CODING|NM_001373.1|18|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.25662 rs3105559 -0.693127 0.000328852 67 K1010R 4515 aAg/aGg MODERATE 19 MISSENSE CODING DNAH14 G protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225268343 A G 0 222 0 0.3654 0.7033 0.7651 0.7262 0.9553 0.8333 0.518786 0.826763 0.960717 1 1158 19872 340 421 1658 9199 215 6881 2 2362 22962 428 614 1708 9696 250 7904 0.996215 0 . 0 . 96 23,28,19,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1010R|4515|DNAH14|protein_coding|CODING|NM_001373.1|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.716229 rs3128651 -0.693143 0.0849636 96 R1011Q 4515 cGa/cAa MODERATE 19 MISSENSE CODING DNAH14 A protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225268346 G A 0 222 0 0.3654 0.7027 0.7651 0.7262 0.9523 0.8333 0.518786 0.826763 0.960717 1 1177 20131 351 421 1694 9388 219 6881 2 2388 23238 442 614 1746 9890 254 7904 0.683199 0 . 0 . 94 23,26,19,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R1011Q|4515|DNAH14|protein_coding|CODING|NM_001373.1|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.900497 rs3128652 -0.693143 0.0849636 94 N1099Y 4515 Aac/Tac MODERATE 20 MISSENSE CODING DNAH14 T protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225270409 A T 0 202 0 0.3366 0.6621 0.7277 0.7133 0.8817 0.7771 0.468931 0.761717 0.889063 1 950 17371 307 419 1418 7724 192 6361 2 2124 21660 404 618 1624 8742 242 7906 0.99928 0 . 0 . 62 6,25,2,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Tac|N1099Y|4515|DNAH14|protein_coding|CODING|NM_001373.1|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.223748 rs3128655 -0.693054 0.00595274 62 M1110I 4515 atG/atT MODERATE 21 MISSENSE CODING DNAH14 T protein_coding NM_001373.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225273248 G T 0 222 0 0.3654 0.7021 0.7651 0.7202 0.9553 0.8333 0.515896 0.825132 0.960227 1 1031 18510 328 425 1578 8205 206 6737 2 2132 21360 410 620 1626 8634 240 7698 0.978512 0 . 0 . 208 73,34,42,23 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|atG/atT|M1110I|4515|DNAH14|protein_coding|CODING|NM_001373.1|21|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99998 rs3128658 -0.693147 0.00177524 208 E1272A 4515 gAa/gCa MODERATE 23 MISSENSE CODING DNAH14 C protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225288534 A C 0 222 0 0.0764 0.1242 0.1916 0.2232 0.0427 0.1227 0.0686416 0.045614 0.0355793 1 159 1609 65 164 48 383 23 767 2 2130 21512 406 614 1622 8592 240 7908 0.597075 0 . 0 . 225 66,41,41,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E1272A|4515|DNAH14|protein_coding|CODING|NM_001373.1|23|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.888079 rs3105571 -0.693147 0.0260774 225 4515 LOW 29 CODING DNAH14 A protein_coding NM_001373.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225334800 T A 0 88 0 0.0779 0.1248 0.1931 0.2232 0.0427 0.1227 0.025289 0.0140228 0.0091195 1 143 1487 43 130 48 355 21 747 2 1830 19464 280 440 1586 7632 224 7472 0.899815 0 . 0 . 15 5,1,7,0 SPLICE_SITE_REGION+INTRON(LOW||||4515|DNAH14|protein_coding|CODING|NM_001373.1|29|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.961166 1 0 0.777113 rs1480104 -0.636426 0.226073 15 T1850M 4515 aCg/aTg MODERATE 36 MISSENSE CODING DNAH14 T protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225373072 C T 0 222 0 0.1331 0.1751 0.1902 0.3125 0.1133 0.1431 0.129335 0.122646 0.119736 1 323 2993 69 203 135 1021 29 1213 2 2158 21798 406 620 1624 8838 242 7910 0.972414 0 . 0 . 84 16,30,9,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1850M|4515|DNAH14|protein_coding|CODING|NM_001373.1|36|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980979 rs61851487 -0.692352 0.821884 84 N2991D 4515 Aat/Gat MODERATE 59 MISSENSE CODING DNAH14 G protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225506294 A G 0 222 0 0.1422 0.1492 0.1988 0.2569 0.0775 0.0859 0.153179 0.0930793 0.066939 1 309 1997 67 183 189 653 28 568 2 2250 22244 418 620 1634 9220 248 7854 0.987671 0 . 0 . 97 34,13,26,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N2991D|4515|DNAH14|protein_coding|CODING|NM_001373.1|59|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.809438 rs10495237 -0.693146 0.0176705 97 D3393E 4515 gaC/gaA MODERATE 67 MISSENSE CODING DNAH14 A protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225528183 C A 0 222 0 0.643 0.5298 0.4697 0.5089 0.4046 0.5695 0.611272 0.492554 0.440918 1 1339 9761 199 313 11 3441 100 4358 2 2148 19782 410 622 34 8470 190 7908 0.841221 0 . 0 . 220 83,24,61,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D3393E|4515|DNAH14|protein_coding|CODING|NM_001373.1|67|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.137446 rs3856145 -0.693147 0.00195178 220 K3474E 4515 Aaa/Gaa MODERATE 68 MISSENSE CODING DNAH14 G protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225533684 A G 0 222 0 0.6399 0.529 0.4697 0.5089 0.4046 0.5695 0.608382 0.492335 0.44186 1 1326 10176 199 309 428 3475 114 4325 2 2106 20072 390 614 944 8264 216 7538 0.830049 0 . 0 . 88 21,13,26,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K3474E|4515|DNAH14|protein_coding|CODING|NM_001373.1|68|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.800677 rs6667999 -0.693146 0.022426 88 I3489 4515 atT/atA LOW 68 SILENT CODING DNAH14 A protein_coding NM_001373.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225533731 T A 0 222 0 0.1573 0.1524 0.2003 0.253 0.0765 0.0859 0.147399 0.0917652 0.0675676 1 279 1801 67 180 100 583 22 570 2 2132 20270 400 616 518 8514 200 7890 0.877421 0 . 0 . 86 22,19,19,13 SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I3489|4515|DNAH14|protein_coding|CODING|NM_001373.1|68|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.745107 rs12742757 -0.69312 0.799915 86 V3627A 4515 gTa/gCa MODERATE 69 MISSENSE CODING DNAH14 C protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225534219 T C 0 222 0 0.6407 0.5292 0.4697 0.5089 0.4046 0.5695 0.608382 0.49276 0.442344 1 1332 9748 199 313 11 3432 100 4361 2 2140 19750 410 622 34 8440 190 7914 0.125538 0 . 0 . 198 62,25,50,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3627A|4515|DNAH14|protein_coding|CODING|NM_001373.1|69|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.195579 rs7527925 -0.693147 0.640987 198 R3670K 4515 aGa/aAa MODERATE 69 MISSENSE CODING DNAH14 A protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225534348 G A 0 222 0 0.6407 0.5292 0.4697 0.5089 0.4046 0.5695 0 . 0 1 1313 9525 196 303 11 3340 98 4264 2 2072 18592 380 598 34 7884 174 7450 0.76515 0 . 0 . 94 5,33,7,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R3670K|4515|DNAH14|protein_coding|CODING|NM_001373.1|69|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.804845 rs7535953 -0.693147 0.35903 94 4515 LOW 75 CODING DNAH14 T protein_coding NM_001373.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225562385 C T 0 228 0 0.357 0.7097 0.8631 0.9663 0.841 0.6779 0.455202 0.72339 0.840038 2 935 14716 354 588 31 7166 155 5487 2 2144 19658 410 620 38 8434 188 7824 0 . 0 . 0 152 0,0,110,26 SPLICE_SITE_REGION+INTRON(LOW||||4515|DNAH14|protein_coding|CODING|NM_001373.1|75|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10915816 -0.693147 0.0231498 152 L4096P 4515 cTt/cCt MODERATE 77 MISSENSE CODING DNAH14 C protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225565015 T C 0 222 0 0.295 0.5563 0.7507 0.7619 0.659 0.454 0.342486 0.561761 0.657134 1 722 11025 297 453 22 5692 122 3717 2 2142 19786 408 622 34 8484 190 7906 0.943789 0 . 0 . 135 37,22,36,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L4096P|4515|DNAH14|protein_coding|CODING|NM_001373.1|77|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.70129 rs3856154 -0.693147 0.674287 135 G4115 4515 ggC/ggT LOW 77 SILENT CODING DNAH14 T protein_coding NM_001373.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225565073 C T 0 222 0 0.171 0.4918 0.7118 0.7411 0.6123 0.3885 0.227601 0.490145 0.604337 1 502 9877 288 436 22 5270 97 3262 2 2132 19744 410 618 34 8462 190 7898 0.500197 0 . 0 . 138 29,30,35,33 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G4115|4515|DNAH14|protein_coding|CODING|NM_001373.1|77|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.818318 rs3856155 -0.693147 0.321721 138 F4244C 4515 tTt/tGt MODERATE 79 MISSENSE CODING DNAH14 G protein_coding NM_001373.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225569241 T G 0 222 0 0.1936 0.5284 0.7435 0.7639 0.6561 0.454 0.244942 0.531975 0.65682 1 536 10847 299 454 22 5678 122 3736 2 2144 19782 410 622 34 8474 190 7908 0.90722 0 . 0 . 218 55,37,44,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F4244C|4515|DNAH14|protein_coding|CODING|NM_001373.1|79|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916292 rs950210 -0.693147 0.0698863 218 S154N 615 aGt/aAt MODERATE 5 MISSENSE CODING LBR T protein_coding NM_002296.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225607144 C T 0 165 0 0.3631 0.7123 0.8602 0.9633 0.8419 0.6871 0.437131 0.703291 0.839651 2 4279 96789 10096 8261 5704 56209 755 11485 2 10164 120848 11538 8640 6612 66498 906 16490 0 . 0 . 0 16 0,0,0,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S154N|615|LBR|protein_coding|CODING|NM_002296.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs2230419 -0.689466 0.557628 16 P87 615 ccT/ccC LOW 3 SILENT CODING LBR G protein_coding NM_002296.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225609884 A G 0 228 0 0.3328 0.6709 0.8329 0.9018 0.8022 0.6401 0.401952 0.659157 0.79093 2 3972 91035 9855 7775 5146 52785 688 10814 2 10388 121340 11574 8648 6610 66702 908 16510 1 0 . 0 . 146 0,1,61,72 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P87|615|LBR|protein_coding|CODING|NM_002296.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1056608 -0.693147 0.127561 146 V39 615 gtG/gtA LOW 2 SILENT CODING LBR T protein_coding NM_002296.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225611661 C T 0 228 0 0.6286 0.6571 0.7839 0.744 0.7058 0.4663 0.635951 0.698985 0.731279 2 6589 86339 9119 6641 5202 49504 678 8606 2 10402 121394 11578 8652 6614 66728 908 16512 0 . 0 . 0 96 0,0,26,65 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V39|615|LBR|protein_coding|CODING|NM_002296.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1056607 -0.693147 0.143514 96 591 6936 MODIFIER 15 CODING ENAH G protein_coding NM_001008493.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225678541 A G 0 9.7 0 0.8873 0.9692 0.9942 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6936||591|ENAH|protein_coding|CODING|NM_001008493.1|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1764344 -0.379885 0 1 591 4497 MODIFIER 15 CODING ENAH C protein_coding NM_001008493.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225680980 A C 0 6.3 0 0.8722 0.9179 0.9726 0.9097 0.9583 0.908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4497||591|ENAH|protein_coding|CODING|NM_001008493.1|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1771316 -0.379885 0 1 591 2917 MODIFIER 15 CODING ENAH A protein_coding NM_001008493.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225682560 G A 0 228 0 0.5734 0.6006 0.6398 0.7004 0.6829 0.4223 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 149 0,1,88,39 UTR_3_PRIME(MODIFIER||2917||591|ENAH|protein_coding|CODING|NM_001008493.1|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs6751 -0.693147 0.00668934 149 86 212 MODIFIER 3 CODING SRP9 G protein_coding NM_003133.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 225977273 C G 0 147 0 0 0.004992 0 0.0248 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.88901 0 . 0 . 16 0,4,1,11 UTR_3_PRIME(MODIFIER||212||86|SRP9|protein_coding|CODING|NM_003133.5|3|G) 0 0.5 1 0 . 1 0 . 0 . 46 0 0.152231 1 0 0.288619 rs74604368 -0.680642 0.233838 16 K119 455 aaG/aaA LOW 3 SILENT CODING EPHX1 A protein_coding NM_000120.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226019653 G A 0 222 0 0.1165 0.1911 0.1484 0.2867 0.162 0.2536 0.145937 0.144472 0.143721 1 1360 19418 1227 2641 696 9619 126 3749 2 10398 121302 11562 8634 6612 66688 906 16502 0.898143 0 . 0 . 86 13,31,16,18 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K119|455|EPHX1|protein_coding|CODING|NM_000120.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.964976 rs1131873,rs386563972 -0.693132 0.0243703 86 H139R 455 cAt/cGt MODERATE 4 MISSENSE CODING EPHX1 G protein_coding NM_000120.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226026406 A G 0 222 0 0.3533 0.2155 0.1427 0.1181 0.164 0.2342 0.336813 0.249654 0.205 1 3601 23810 948 1109 1042 13086 174 3850 2 10388 121306 11570 8640 6612 66676 908 16512 0.976011 2 benign 0 . 51 19,7,18,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H139R|455|EPHX1|protein_coding|CODING|NM_000120.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.400798 rs2234922 -0.692717 0.516965 51 N357 455 aaC/aaT LOW 8 SILENT CODING EPHX1 T protein_coding NM_000120.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226032229 C T 0 222 0 0.1051 0.1264 0.0591 0.1141 0.0895 0.2536 0.113028 0.106566 0.103256 1 1129 13579 442 1075 362 6684 102 3785 2 10406 121368 11574 8640 6612 66716 908 16512 0.97435 0 . 0 COSM146794 190 41,59,27,43 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N357|455|EPHX1|protein_coding|CODING|NM_000120.3|8|T),DOWNSTREAM(MODIFIER||1004||807|TMEM63A|protein_coding|CODING|NM_014698.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850862 rs1051741 -0.693147 0.480361 190 807 772 MODIFIER 25 CODING TMEM63A G protein_coding NM_014698.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226033969 A G 0 32.6 0 0.1074 0.1342 0.062 0.129 0.0964 0.2658 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||772||807|TMEM63A|protein_coding|CODING|NM_014698.2|25|G),DOWNSTREAM(MODIFIER||707||455|EPHX1|protein_coding|CODING|NM_000120.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2740174 -0.379885 0 2 Y752 807 taC/taT LOW 24 SILENT CODING TMEM63A A protein_coding NM_014698.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226034909 G A 0 222 0 0.003 0.0226 0.0029 0.0863 0.0119 0.0082 0.00931395 0.0137713 0.016054 1 72 2084 61 914 19 917 11 90 2 10038 118128 11534 8556 6596 64696 864 15844 0.802602 0 . 0 . 84 10,32,13,24 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y752|807|TMEM63A|protein_coding|CODING|NM_014698.2|24|A),DOWNSTREAM(MODIFIER||1647||455|EPHX1|protein_coding|CODING|NM_000120.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910796 rs41441645 -0.693141 0.47587 84 N368S 807 aAt/aGt MODERATE 14 MISSENSE CODING TMEM63A C protein_coding NM_014698.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226048680 T C 0 222 0 0 0.0051917 0 0.0258 0 0 0 . 0 1 0 199 0 157 5 32 2 3 2 10376 120278 11574 8644 6614 66372 894 15804 0.556347 0 . 0 . 48 11,11,9,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N368S|807|TMEM63A|protein_coding|CODING|NM_014698.2|14|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.880866 rs116013256 -0.692067 0.167399 48 D169 807 gaC/gaT LOW 7 SILENT CODING TMEM63A A protein_coding NM_014698.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226055595 G A 0 222 0 0.5189 0.4301 0.3127 0.5188 0.2624 0.4744 0.439401 0.339997 0.28907 1 4813 40627 3772 4671 1189 18203 272 7707 2 10386 121184 11536 8632 6602 66632 904 16492 0.860864 0 . 0 COSM146795 198 69,29,52,27 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D169|807|TMEM63A|protein_coding|CODING|NM_014698.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.658093 rs2292564 -0.693147 0.07489 198 D322A 366 gAc/gCc MODERATE 4 MISSENSE CODING LEFTY1 G protein_coding NM_020997.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226074563 T G 0 222 0 0.1407 0.2548 0.3415 0.2073 0.3946 0.2526 0.185429 0.300938 0.360116 1 1883 40438 4804 1553 2734 24385 327 4752 2 10256 120374 11486 8610 6550 66064 902 16506 0.559327 0 . 0 COSM1339274 115 21,25,28,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D322A|366|LEFTY1|protein_coding|CODING|NM_020997.3|4|G),UPSTREAM(MODIFIER||4143||807|TMEM63A|protein_coding|CODING|NM_014698.2||G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.756935 0.900039 0 0.67362 rs360057 -0.693147 0.425887 115 D381G 451 gAt/gGt MODERATE 7 MISSENSE CODING SDE2 C protein_coding NM_152608.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226173217 T C 0 222 0 0 0.0097844 0 0.0476 0 0.001 0.000542888 0.000506671 0.000490316 1 4 413 0 358 0 40 4 7 2 9630 120060 11542 8588 6610 66298 898 16494 0.887697 0 . 0 . 92 10,34,8,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D381G|451|SDE2|protein_coding|CODING|NM_152608.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0536807 rs76285584 -0.693145 0.200351 92 C191 240 tgC/tgT LOW 2 SILENT CODING MIXL1 T protein_coding NM_001282402.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226413363 C T 0 222 0 0 0.0079872 0 0.0377 0 0.002 0.000226963 0.000461326 0.000581395 1 2 296 1 226 0 40 3 24 2 10406 121406 11576 8652 6614 66738 908 16512 0.638064 0 . 0 . 158 41,35,47,23 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C191|240|MIXL1|protein_coding|CODING|NM_001282402.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969063 rs3738796 -0.693147 0.392338 158 558 1036 MODIFIER 15 CODING LIN9 C protein_coding NM_173083.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226419166 G C 0 228 0 0.7549 0.7079 0.6628 0.745 0.6809 0.6656 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 72 0,0,30,39 UTR_3_PRIME(MODIFIER||1036||558|LIN9|protein_coding|CODING|NM_173083.3|15|C),DOWNSTREAM(MODIFIER||4410||240|MIXL1|protein_coding|CODING|NM_001282402.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2377029 -0.693147 0.970858 72 558 965 MODIFIER 15 CODING LIN9 G protein_coding NM_173083.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226419237 C G 0 228 0 0.7549 0.7083 0.6628 0.745 0.6819 0.6667 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 94 0,0,49,34 UTR_3_PRIME(MODIFIER||965||558|LIN9|protein_coding|CODING|NM_173083.3|15|G),DOWNSTREAM(MODIFIER||4481||240|MIXL1|protein_coding|CODING|NM_001282402.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2377028 -0.693147 0.871479 94 F158 558 ttC/ttT LOW 6 SILENT CODING LIN9 A protein_coding NM_173083.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226474132 G A 0 228 0 0.7542 0.7075 0.6657 0.745 0.6799 0.6636 0.740917 0.704615 0.686017 2 7610 85602 9206 6380 5119 45442 609 11236 2 10328 121072 11570 8632 6608 66590 896 16448 1 0 . 0 . 118 0,1,64,35 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F158|558|LIN9|protein_coding|CODING|NM_173083.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10799347 -0.693147 0.749972 118 1014 95 MODIFIER 23 CODING PARP1 T protein_coding NM_001618.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226549066 C T 0 228 0 0 0.0268 0 0.0466 0 0.089 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 43 0,0,33,8 UTR_3_PRIME(MODIFIER||95||1014|PARP1|protein_coding|CODING|NM_001618.3|23|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13306133 -0.693145 0.281215 43 K940R 1014 aAg/aGg MODERATE 21 MISSENSE CODING PARP1 C protein_coding NM_001618.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226550829 T C 0 228 0 0.0008 0.0272 0 0.0466 0 0.09 0.00158874 0.000999539 0.000697674 2 25 1634 12 260 0 50 7 1280 2 10406 121400 11578 8650 6614 66736 906 16510 0.4875 0 . 0 . 92 2,0,58,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K940R|1014|PARP1|protein_coding|CODING|NM_001618.3|21|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.725 rs3219145 -0.693147 0.0768575 92 F638 1014 ttC/ttT LOW 13 SILENT CODING PARP1 A protein_coding NM_001618.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226564836 G A 0 222 0 0 0.0067891 0 0.0327 0 0.001 0 0.000461326 0.000697674 1 1 247 1 189 0 41 2 13 2 10406 121412 11578 8654 6614 66740 908 16512 0.997702 0 . 0 . 173 41,40,43,34 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F638|1014|PARP1|protein_coding|CODING|NM_001618.3|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997583 rs13306137 -0.693147 0.0737912 173 K352 1014 aaA/aaG LOW 8 SILENT CODING PARP1 C protein_coding NM_001618.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226570840 T C 0 228 0 0.9123 0.7893 0.6455 0.5635 0.8459 0.8998 0.89764 0.860065 0.840814 2 9336 96342 6382 4882 5047 55116 746 14833 2 10402 121360 11574 8642 6612 66710 908 16512 1 0 . 0 . 142 0,1,60,68 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K352|1014|PARP1|protein_coding|CODING|NM_001618.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1805415 -0.693147 0.000265726 142 A284 1014 gcT/gcC LOW 7 SILENT CODING PARP1 G protein_coding NM_001618.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226573364 A G 0 228 0 0.5582 0.5166 0.5029 0.7946 0.329 0.3763 0.536995 0.407735 0.341512 2 5689 51280 6679 6959 2637 22999 330 5987 2 10392 121286 11564 8642 6602 66672 908 16506 0 . 0 . 0 88 0,0,34,40 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A284|1014|PARP1|protein_coding|CODING|NM_001618.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1805414 -0.693147 0.157821 88 A220V 1014 gCg/gTg MODERATE 5 MISSENSE CODING PARP1 A protein_coding NM_001618.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226576415 G A 0 222 0 0 0.0025959 0 0.0119 0 0.001 0 . 0 1 0 73 0 62 0 1 0 10 2 10360 121284 11568 8650 6614 66690 908 16494 0.995347 0 . 0 COSM1339298 65 18,15,14,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A220V|1014|PARP1|protein_coding|CODING|NM_001618.3|5|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.342643 rs139232092 -0.693021 0.344824 65 141 1210 MODIFIER 4 CODING C1orf95 G protein_coding NM_001003665.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226790951 A G 0 70 0 0.2557 0.2382 0.196 0.2659 0.2018 0.2536 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1210||141|C1orf95|protein_coding|CODING|NM_001003665.3|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3820632 -0.453602 0.64 3 946 1872 MODIFIER 8 CODING ITPKB A protein_coding NM_002221.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226820500 G A 0 129 0 0.7806 0.5134 0.4539 0.6071 0.2773 0.3405 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.988967 0 . 0 . 40 2,24,1,12 UTR_3_PRIME(MODIFIER||1872||946|ITPKB|protein_coding|CODING|NM_002221.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.367404 rs1050492 -0.683931 0.0372282 40 946 452 MODIFIER 8 CODING ITPKB A protein_coding NM_002221.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226821920 G A 0 9.7 0 0.0106 0.0527 0.1484 0.0655 0.0089 0.0736 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||452||946|ITPKB|protein_coding|CODING|NM_002221.3|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs41268731 -0.379885 0 1 A632 946 gcC/gcT LOW 2 SILENT CODING ITPKB A protein_coding NM_002221.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226923264 G A 0 222 0 0.2428 0.2815 0.317 0.2639 0.3141 0.2935 0.25488 0.28087 0.294186 1 2593 32352 3329 2285 1838 18520 259 3528 2 10260 113206 11504 8574 6612 64626 824 10806 0.832321 0 . 0 COSM146796 57 11,17,11,11 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A632|946|ITPKB|protein_coding|CODING|NM_002221.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.758978 rs708775 -0.692562 0.0404417 57 P552Q 946 cCg/cAg MODERATE 2 MISSENSE CODING ITPKB T protein_coding NM_002221.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226923505 G T 0 228 0 0.9962 0.9798 0.9553 1 0.9423 0.9928 0.991375 0.958788 0.942093 2 10294 116702 11321 8651 6275 63073 871 16217 2 10378 120980 11560 8652 6588 66528 904 16370 0 . 0 . 0 73 0,0,46,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cAg|P552Q|946|ITPKB|protein_coding|CODING|NM_002221.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs708776 -0.693147 0.784401 73 S408A 946 Tcc/Gcc MODERATE 2 MISSENSE CODING ITPKB C protein_coding NM_002221.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 226923938 A C 0 222 0 0.6067 0.6104 0.6599 0.6786 0.5258 0.5971 0.576888 0.514237 0.482205 1 5618 58249 8437 5669 2867 29883 414 5361 2 9612 109790 11466 8480 6596 63314 788 9534 0.994371 0 . 0 COSM425464 70 19,12,19,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S408A|946|ITPKB|protein_coding|CODING|NM_002221.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.628421 rs6667260 -0.693054 0.499102 70 1719 3021 MODIFIER 36 CODING CDC42BPA A protein_coding NM_003607.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227178948 G A 0 222 0 0.8094 0.6859 0.7075 0.7143 0.7227 0.4366 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.392427 0 . 0 . 53 8,10,5,24 UTR_3_PRIME(MODIFIER||3021||1719|CDC42BPA|protein_coding|CODING|NM_003607.3|36|A),DOWNSTREAM(MODIFIER||3702||647|ADCK3|protein_coding|CODING|NM_020247.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995163 rs2989946 -0.693079 0.601706 53 1719 2922 MODIFIER 36 CODING CDC42BPA T protein_coding NM_003607.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227179047 C T 0 158 0 0.0197 0.1645 0.1513 0.1726 0.1501 0.3763 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.476686 0 . 0 . 17 1,6,1,8 UTR_3_PRIME(MODIFIER||2922||1719|CDC42BPA|protein_coding|CODING|NM_003607.3|36|T),DOWNSTREAM(MODIFIER||3801||647|ADCK3|protein_coding|CODING|NM_020247.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.965592 rs3768431 -0.662043 0.675141 17 A1699V 1719 gCt/gTt MODERATE 36 MISSENSE CODING CDC42BPA A protein_coding NM_003607.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227182033 G A 0 228 0 0.9259 0.8782 0.8718 0.8869 0.8738 0.8139 0.9203 0.903337 0.894651 2 7345 83994 8268 6539 3858 46347 620 11017 2 8038 94560 9272 7334 4130 51650 682 13454 0.948718 0 . 0 . 93 0,2,39,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A1699V|1719|CDC42BPA|protein_coding|CODING|NM_003607.3|36|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.858974 rs2802269 -0.693147 0.399991 93 S1659 1719 tcT/tcC LOW 35 SILENT CODING CDC42BPA G protein_coding NM_003607.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227182575 A G 0 222 0 0.9803 0.8269 0.8372 0.8274 0.826 0.6125 0.943713 0.855528 0.810349 1 9889 96886 9362 7281 4883 54139 715 10617 2 10404 121358 11576 8640 6612 66714 908 16504 0.999925 0 . 0 . 77 21,20,16,12 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1659|1719|CDC42BPA|protein_coding|CODING|NM_003607.3|35|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.897794 rs1045247 -0.693054 0.098717 77 1719 LOW 3 CODING CDC42BPA G protein_coding NM_003607.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227387361 A G 0 228 0 0.9168 0.7993 0.7291 0.6577 0.8519 0.7822 0.892143 0.870191 0.858939 2 9331 97081 7100 5275 5023 56466 734 13152 2 10380 120906 11492 8572 6592 66486 906 16478 0 . 0 . 0 117 0,0,20,84 SPLICE_SITE_REGION+INTRON(LOW||||1719|CDC42BPA|protein_coding|CODING|NM_003607.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3768434 -0.693147 0.000910212 117 580 1366 MODIFIER 4 CODING ZNF678 A protein_coding NM_178549.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227844895 T A 0 9.7 0 0.1899 0.2157 0.2853 0.2431 0.17 0.2198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1366||580|ZNF678|protein_coding|CODING|NM_178549.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1951729 -0.379885 0 1 580 1754 MODIFIER 4 CODING ZNF678 A protein_coding NM_178549.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227845283 C A 0 9.7 0 0.1354 0.2702 0.2968 0.4484 0.2157 0.3057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1754||580|ZNF678|protein_coding|CODING|NM_178549.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs16848029 -0.379885 0 1 580 2255 MODIFIER 4 CODING ZNF678 G protein_coding NM_178549.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227845784 A G 0 9.7 0 0.9198 0.7742 0.719 0.8254 0.5746 0.7689 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2255||580|ZNF678|protein_coding|CODING|NM_178549.3|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10916191 -0.379885 0 1 463 32 MODIFIER 6 CODING JMJD4 G protein_coding NM_023007.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227920061 T G 0 228 0 0.9531 0.7488 0.7104 0.7907 0.5557 0.6554 0.895587 0.682196 0.572992 2 8948 75455 8470 6680 3725 36837 560 10235 2 9864 118910 11528 8590 6596 65082 892 16358 0 . 0 . 0 23 0,0,15,7 UTR_3_PRIME(MODIFIER||32||463|JMJD4|protein_coding|CODING|NM_023007.2|6|G),UPSTREAM(MODIFIER||2636||464|SNAP47|protein_coding|CODING|NM_053052.3||G),INTRAGENIC(MODIFIER|||||LOC100130093||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1060295 -0.692562 0.794986 23 A461V 463 gCg/gTg MODERATE 6 MISSENSE CODING JMJD4 A protein_coding NM_023007.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227920103 G A 0 222 0 0.1445 0.1759 0.2723 0.2093 0.1531 0.1391 0.151611 0.175996 0.188488 1 1499 20812 2418 2048 734 11689 161 2263 2 10074 119810 11548 8600 6602 65578 902 16506 0.88059 0 . 0 . 34 14,2,12,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A461V|463|JMJD4|protein_coding|CODING|NM_023007.2|6|A),UPSTREAM(MODIFIER||2594||464|SNAP47|protein_coding|CODING|NM_053052.3||A),INTRAGENIC(MODIFIER|||||LOC100130093||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997408 rs3087908 -0.690438 0.00591908 34 D65E 463 gaT/gaG MODERATE 1 MISSENSE CODING JMJD4 C protein_coding NM_023007.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227922918 A C 0 131 0 0.4682 0.4153 0.4914 0.3671 0.3976 0.3579 0.379447 0.379091 0.378912 1 1911 26834 2967 1722 952 14790 210 4282 2 3676 57926 5884 3784 1882 31258 450 10992 0.838008 0 . 0 . 12 2,3,2,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D65E|463|JMJD4|protein_coding|CODING|NM_023007.2|1|C),UTR_5_PRIME(MODIFIER||193||464|SNAP47|protein_coding|CODING|NM_053052.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.95494 1 0 0.13642 rs2295994 -0.636426 0.255255 12 464 193 MODIFIER 1 CODING SNAP47 C protein_coding NM_053052.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227922918 A C 0 131 0 0.4682 0.4153 0.4914 0.3671 0.3976 0.3579 0.379447 0.379091 0.378912 1 1911 26834 2967 1722 952 14790 210 4282 2 3676 57926 5884 3784 1882 31258 450 10992 0.838008 0 . 0 . 12 2,3,2,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D65E|463|JMJD4|protein_coding|CODING|NM_023007.2|1|C),UTR_5_PRIME(MODIFIER||193||464|SNAP47|protein_coding|CODING|NM_053052.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.95494 1 0 0.13642 rs2295994 -0.636426 0.255255 12 A11V 463 gCg/gTg MODERATE 1 MISSENSE CODING JMJD4 A protein_coding NM_023007.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227923081 G A 0 228 0 1 1 1 1 1 1 0.999752 0.999917 1 2 6306 96476 10329 7492 4642 52223 668 14816 2 6306 96494 10334 7492 4642 52236 668 14816 0 . 0 . 0 19 0,0,4,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A11V|463|JMJD4|protein_coding|CODING|NM_023007.2|1|A),UTR_5_PRIME(MODIFIER||30||464|SNAP47|protein_coding|CODING|NM_053052.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7419238 -0.691153 0.419171 19 464 30 MODIFIER 1 CODING SNAP47 A protein_coding NM_053052.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227923081 G A 0 228 0 1 1 1 1 1 1 0.999752 0.999917 1 2 6306 96476 10329 7492 4642 52223 668 14816 2 6306 96494 10334 7492 4642 52236 668 14816 0 . 0 . 0 19 0,0,4,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A11V|463|JMJD4|protein_coding|CODING|NM_023007.2|1|A),UTR_5_PRIME(MODIFIER||30||464|SNAP47|protein_coding|CODING|NM_053052.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7419238 -0.691153 0.419171 19 R48G 464 Agg/Ggg MODERATE 2 MISSENSE CODING SNAP47 G protein_coding NM_053052.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227935444 A G 0 222 0 0.4826 0.4193 0.4928 0.3651 0.3996 0.3579 0.439628 0.421882 0.412791 1 4667 48488 4884 3307 2597 26852 363 5818 2 10374 120678 11540 8604 6584 66448 906 16222 0.424373 0 . 0 . 83 18,27,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R48G|464|SNAP47|protein_coding|CODING|NM_053052.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.265164 rs2236359 -0.693136 0.0496336 83 V154M 464 Gtg/Atg MODERATE 2 MISSENSE CODING SNAP47 A protein_coding NM_053052.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 227935762 G A 0 222 0 0.0998 0.1474 0.1311 0.3462 0.0457 0.1227 0.108715 0.0668153 0.0453488 1 1120 12124 2828 2799 397 3054 67 1859 2 10280 120568 11542 8598 6588 66218 902 16440 0.656171 0 . 0 . 103 30,23,23,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V154M|464|SNAP47|protein_coding|CODING|NM_053052.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.474267 rs2236358 -0.693146 0.728387 103 M204V 326 Atg/Gtg MODERATE 4 MISSENSE CODING PRSS38 G protein_coding NM_183062.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228033197 A G 0 222 0 0.7738 0.7973 0.7637 0.6915 0.8439 0.9141 0.795506 0.83769 0.859302 1 8137 98722 7232 6080 5194 56445 750 14884 2 10254 119274 11158 8476 6352 65786 878 16370 0.141368 0 . 0 . 117 31,21,30,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M204V|326|PRSS38|protein_coding|CODING|NM_183062.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.950706 rs9426581 -0.693147 0.0348249 117 A51 365 gcT/gcC LOW 2 SILENT CODING WNT9A G protein_coding NM_003395.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228113163 A G 0 228 0 0.8752 0.6877 0.6499 0.6091 0.67 0.5603 0.8356 0.753507 0.711963 2 3421 41480 4003 2351 1118 23736 280 6571 2 4088 60178 6086 3628 1590 33540 394 10852 0 . 0 . COSM425495 28 0,0,7,19 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A51|365|WNT9A|protein_coding|CODING|NM_003395.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3795768 -0.692976 0.0237598 28 439 573 MODIFIER 2 CODING GJC2 G protein_coding NM_020435.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228347352 A G 0 222 0 0.5938 0.8043 0.8703 0.7589 0.9583 0.9305 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.64072 0 . 0 . 73 18,11,27,9 UTR_3_PRIME(MODIFIER||573||439|GJC2|protein_coding|CODING|NM_020435.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.953049 rs6668719 -0.693139 0.00294962 73 356 3073 MODIFIER 3 CODING IBA57 C protein_coding NM_001010867.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228366286 CAAA C 0 21.4 0 0.2534 0.3207 0.3746 0.371 0.3668 0.274 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,1,0,1 UTR_3_PRIME(MODIFIER||3073||356|IBA57|protein_coding|CODING|NM_001010867.3|3|C) 0 0.5 1 1 0.5 1 1 0 . 0 60 0 0 . 0 . rs10565504 -0.379885 0.18 2 356 3312 MODIFIER 3 CODING IBA57 G protein_coding NM_001010867.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228366526 A G 0 9.7 0 0.8116 0.9469 0.9769 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3312||356|IBA57|protein_coding|CODING|NM_001010867.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6667424 -0.379885 0 1 356 5016 MODIFIER 3 CODING IBA57 A protein_coding NM_001010867.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228368230 G A 0 9.7 0 0.8661 0.9629 0.9885 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5016||356|IBA57|protein_coding|CODING|NM_001010867.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6666843 -0.379885 0 1 8923 3 MODIFIER 2 CODING OBSCN G protein_coding NM_001271223.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228399482 C G 0 228 0 0.6815 0.721 0.6427 0.8313 0.6362 0.8037 0.678775 0.634161 0.612859 2 4441 57787 5910 6100 3206 31930 404 5796 2 6644 87954 9744 7388 4788 51446 592 7352 0.490323 0 . 0 . 170 1,1,95,60 UTR_5_PRIME(MODIFIER||3||8923|OBSCN|protein_coding|CODING|NM_001271223.2|2|G),INTRAGENIC(MODIFIER|||||C1orf145||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.406452 rs11804508 -0.693147 0.0140442 170 A94 8923 gcT/gcC LOW 2 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228399766 T C 0 145 0 0.7057 0.7262 0.6441 0.8244 0.6372 0.8027 0.688853 0.640864 0.617823 2 1015 13495 455 662 98 5127 92 6046 2 1454 19454 710 794 130 8226 146 7994 0 . 0 . COSM1339475,COSM425503,COSM425502,COSM1339474 10 0,0,0,10 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A94|8923|OBSCN|protein_coding|CODING|NM_001271223.2|2|C),INTRAGENIC(MODIFIER|||||C1orf145||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs55971985 -0.670168 0.133033 10 L477 8923 ctA/ctG LOW 4 SILENT CODING OBSCN G protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228402047 A G 0 228 0 0.6808 0.7198 0.6427 0.8244 0.6372 0.8047 0.672123 0.630541 0.609493 2 6405 78363 6964 6963 4366 40404 593 12668 2 9730 119746 11548 8562 6606 65894 894 16512 0 . 0 . COSM1339494,COSM1339493,COSM1339492 110 0,0,55,52 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L477|8923|OBSCN|protein_coding|CODING|NM_001271223.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1620111 -0.693147 0.030272 110 Q502R 8923 cAg/cGg MODERATE 4 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228402121 A G 0 228 0 0.6815 0.7196 0.6427 0.8244 0.6362 0.8037 0.66319 0.625665 0.606544 2 6380 78346 6974 6973 4376 40385 593 12665 2 9700 119820 11562 8576 6614 65964 894 16510 0 . 0 . 0 112 0,0,41,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q502R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1771487 -0.693147 0.0675558 112 S999 8923 agT/agC LOW 10 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228412227 T C 0 228 0 0.5885 0.4125 0.402 0.3849 0.3668 0.2577 0 . 0 2 5732 48044 5476 3567 2292 25970 324 4683 2 9746 120118 11486 8568 6572 66358 896 16492 0.995456 0 . 0 . 201 2,2,139,40 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S999|8923|OBSCN|protein_coding|CODING|NM_001271223.2|10|C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.524698 rs1771480 -0.693147 0.0871782 201 S1026 8923 tcG/tcA LOW 10 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228412308 G A 0 228 0 0.5885 0.4125 0.402 0.3839 0.3678 0.2577 0.556824 0.44714 0.392544 2 5764 48364 5495 3557 2308 26212 327 4701 2 9824 120608 11544 8584 6604 66648 898 16506 0.382441 0 . 0 . 218 1,4,62,130 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1026|8923|OBSCN|protein_coding|CODING|NM_001271223.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.345457 rs1757152 -0.693147 0.00177691 218 C1054 8923 tgC/tgT LOW 10 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228412392 C T 0 222 0 0.0008 0.0087859 0.0274 0.0169 0 0.0072 0.000496524 0.000323729 0.000240154 1 8 1068 749 161 0 2 2 146 2 9674 119596 11490 8608 6588 66132 890 16214 0.778841 0 . 0 . 119 12,44,15,41 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1054|8923|OBSCN|protein_coding|CODING|NM_001271223.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.455525 rs12040506 -0.693147 0.111257 119 K1119R 8923 aAa/aGa MODERATE 11 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228431034 A G 0 222 0 0.0121 0.011582 0.0288 0.0159 0 0.0061 0.0111216 0.00379087 0.00011854 1 142 1188 764 133 0 2 2 145 2 9746 120346 11508 8620 6602 66530 892 16448 0.190435 0 . 0 . 212 41,56,43,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1119R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997586 rs55760713 -0.693147 0.0220945 212 T1139 8923 acA/acG LOW 11 SILENT CODING OBSCN G protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228431095 A G 0 222 0 0.7095 0.6166 0.6542 0.5992 0.6412 0.4571 0.735492 0.700254 0.682791 1 6896 78165 7693 4957 4621 45174 556 8268 2 9780 120264 11482 8572 6588 66458 896 16488 0.804592 0 . 0 . 138 21,44,21,47 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1139|8923|OBSCN|protein_coding|CODING|NM_001271223.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962409 rs1771455 -0.693147 0.015188 138 T1287 8923 acA/acG LOW 13 SILENT CODING OBSCN G protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228433217 A G 0 222 0 0.7095 0.6166 0.6542 0.5992 0.6412 0.4571 0.731473 0.69874 0.682523 1 6913 78502 7747 4993 4636 45339 557 8317 2 9818 120740 11572 8600 6610 66732 900 16508 0.775444 0 . 0 . 298 85,40,83,53 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1287|8923|OBSCN|protein_coding|CODING|NM_001271223.2|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.917073 rs2487384 -0.693147 0.062755 298 C1330 8923 tgC/tgT LOW 13 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228433346 C T 0 222 0 0.028 0.0587 0.0058 0.1964 0.003 0.0532 0.0258366 0.0103093 0.00275383 1 273 3103 56 1867 31 261 18 597 2 9804 120494 11574 8608 6614 66632 898 16364 0.99972 0 . 0 . 148 21,58,10,49 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1330|8923|OBSCN|protein_coding|CODING|NM_001271223.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0638802 rs75801409 -0.693147 0.507667 148 A1400 8923 gcT/gcC LOW 14 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228434395 T C 0 222 0 0.7133 0.6176 0.6542 0.5992 0.6412 0.4571 0.730937 0.698947 0.683298 1 6925 78445 7745 4980 4636 45328 557 8274 2 9820 120720 11568 8600 6608 66718 900 16506 0.927301 0 . 0 COSM146810 250 47,73,35,60 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1400|8923|OBSCN|protein_coding|CODING|NM_001271223.2|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.807761 rs7517088 -0.693147 0.104711 250 A1424 8923 gcT/gcC LOW 14 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228434467 T C 0 228 0 0.848 0.6625 0.6902 0.6151 0.6421 0.4622 0.827595 0.729456 0.682384 2 8047 80681 8569 5123 4636 45337 562 8407 2 9794 120620 11574 8604 6614 66654 898 16482 0 . 0 . 0 113 0,0,31,79 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1424|8923|OBSCN|protein_coding|CODING|NM_001271223.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7517108 -0.693147 0.00293094 113 E1472 8923 gaG/gaA LOW 15 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228437772 G A 0 222 0 0.0537 0.0611 0.0072 0.1746 0.003 0.0521 0.0534074 0.0193075 0.00250119 1 533 3087 68 1664 31 186 15 590 2 9782 120606 11572 8604 6614 66626 896 16512 0.994013 0 . 0 . 274 86,68,54,41 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E1472|8923|OBSCN|protein_coding|CODING|NM_001271223.2|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928923 rs12080655 -0.693147 0.209887 274 C1514 8923 tgC/tgT LOW 15 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228437898 C T 0 222 0 0 0.016773 0.0014 0.0813 0 0.001 0.000244978 0.00032175 0.000359281 1 3 931 2 881 0 16 1 28 2 9776 120512 11572 8600 6614 66566 896 16488 0.750027 0 . 0 . 171 25,63,26,39 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1514|8923|OBSCN|protein_coding|CODING|NM_001271223.2|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975777 rs117627593 -0.693147 0.96679 171 V1600D 8923 gTc/gAc MODERATE 16 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228444565 T A 0 228 0 1 1 1 1 1 1 0 . 0 2 9798 120590 11560 8616 6614 66608 896 16498 2 9798 120590 11560 8616 6614 66608 896 16498 0 . 0 . 0 128 0,0,44,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V1600D|8923|OBSCN|protein_coding|CODING|NM_001271223.2|16|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7532342 -0.693147 0.636571 128 A1716V 8923 gCg/gTg MODERATE 18 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228451826 C T 0 222 0 0.2761 0.3063 0.2983 0.4226 0.2823 0.2577 0.241859 0.267897 0.280961 1 2441 35442 3163 3468 2374 19427 259 4310 2 9744 120384 11554 8580 6614 66490 894 16508 0.999846 0 . 0 . 195 67,23,64,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A1716V|8923|OBSCN|protein_coding|CODING|NM_001271223.2|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961231 rs453140 -0.693147 0.166227 195 A1719 8923 gcC/gcT LOW 18 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228451836 C T 0 222 0 0.0106 0.014776 0.0288 0.0317 0 0.0082 0.0113208 0.00417586 0.000591576 1 144 1440 770 278 16 38 2 192 2 9752 120478 11566 8624 6614 66516 896 16510 0.663841 0 . 0 . 196 73,33,62,19 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1719|8923|OBSCN|protein_coding|CODING|NM_001271223.2|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.723627 rs118114493 -0.693147 0.665616 196 A1785T 8923 Gcc/Acc MODERATE 18 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228452032 G A 0 222 0 0.0234 0.0571 0.0043 0.1935 0.005 0.0532 0.0236407 0.0108061 0.00437973 1 242 3146 54 1896 39 285 20 610 2 9732 120044 11546 8578 6612 66182 896 16498 0.596031 0 . 0 . 220 51,59,35,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1785T|8923|OBSCN|protein_coding|CODING|NM_001271223.2|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.620708 rs55706639 -0.693147 0.0866733 220 P1914L 8923 cCg/cTg MODERATE 20 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228459677 C T 0 222 0 0.0008 0.01258 0.0303 0.0298 0 0.0112 0.00171233 0.000871992 0.00050226 1 16 1306 766 265 16 38 2 203 2 9220 118088 11470 8584 6610 64928 876 16400 0.967646 0 . 0 . 190 64,24,57,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1914L|8923|OBSCN|protein_coding|CODING|NM_001271223.2|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.85405 rs117651701 -0.693147 0.445219 190 H2048R 8923 cAc/cGc MODERATE 21 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228461129 A G 0 228 0 0.8442 0.6935 0.6974 0.75 0.663 0.4601 0.816881 0.735737 0.695348 2 7935 82834 8539 6251 4954 46084 575 8496 2 9758 119912 11508 8580 6590 66088 894 16494 0 . 0 . 0 201 0,0,82,102 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H2048R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|21|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188724 -0.693147 0.172752 201 R2136H 8923 cGc/cAc MODERATE 22 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228461615 G A 0 222 0 0.0008 0.009385 0.0303 0.0159 0 0.0092 0.000709891 0.000394571 0.000236798 1 8 888 603 116 0 1 2 158 2 6632 91036 8094 6368 4278 51162 606 13896 0.45178 0 . 0 . 131 23,42,17,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R2136H|8923|OBSCN|protein_coding|CODING|NM_001271223.2|22|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996712 rs28603121 -0.693147 0.133342 131 E2290K 8923 Gag/Aag MODERATE 24 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228462332 G A 0 222 0 0.0023 0.012979 0.0303 0.0298 0 0.0112 0.00234852 0.00117943 0.000591017 1 30 1270 713 265 14 37 2 209 2 7070 96330 8876 7256 4486 54444 670 13528 0.961605 0 . 0 . 132 44,20,35,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2290K|8923|OBSCN|protein_coding|CODING|NM_001271223.2|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.32967 rs12023551 -0.693147 0.0618736 132 D2481E 8923 gaT/gaG MODERATE 26 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228464248 T G 0 228 0 0.8495 0.6955 0.7003 0.75 0.664 0.4601 0.820785 0.738366 0.696479 2 7753 81362 8468 6128 4769 45205 556 8483 2 9466 117408 11364 8418 6312 64600 846 16402 0 . 0 . COSM1339606,COSM1339607,COSM1339608 61 0,0,33,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D2481E|8923|OBSCN|protein_coding|CODING|NM_001271223.2|26|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188721 -0.693147 0.469537 61 F2491L 8923 Ttc/Ctc MODERATE 26 MISSENSE CODING OBSCN C protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228464276 T C 0 228 0 0.733 0.6635 0.6931 0.75 0.663 0.4601 0.734574 0.708851 0.695965 2 6667 79219 8285 6096 4606 44571 544 8450 2 9250 115762 11196 8354 6098 63738 834 16292 0 . 0 . 0 53 0,0,23,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F2491L|8923|OBSCN|protein_coding|CODING|NM_001271223.2|26|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188722 -0.693147 0.0253895 53 P2504R 8923 cCc/cGc MODERATE 26 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228464316 C G 0 222 0 0.0023 0.012979 0.0303 0.0298 0 0.0112 0.00144509 0.000878173 0.000597086 1 27 1252 705 253 11 39 2 215 2 7374 97014 9254 7034 4290 53702 684 14676 0.998265 0 . 0 . 49 4,16,6,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P2504R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|26|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.655406 rs142776685 -0.692831 0.698618 49 8923 LOW 29 CODING OBSCN G protein_coding NM_001271223.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228465370 T G 0 228 0 0.7542 0.6695 0.6988 0.744 0.67 0.4571 0 . 0 2 5155 64239 6300 4856 3886 36211 446 7385 2 6750 89108 8090 6186 4846 49260 640 13336 0 . 0 . 0 297 0,0,159,117 SPLICE_SITE_REGION+INTRON(LOW||||8923|OBSCN|protein_coding|CODING|NM_001271223.2|29|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs386617952,rs867599 -0.693147 0.136349 297 T2875 8923 acC/acT LOW 32 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228467087 C T 0 222 0 0.0008 0.010783 0.0303 0.0228 0 0.0092 0.000479157 0.000317712 0.000237643 1 8 1164 758 204 0 8 2 184 2 9530 118274 11474 8500 6494 65052 868 16356 0.253305 0 . 0 . 208 50,43,44,42 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T2875|8923|OBSCN|protein_coding|CODING|NM_001271223.2|32|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.196831 rs12030528 -0.693147 0.0097857 208 R2958Q 8923 cGg/cAg MODERATE 33 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228467711 G A 0 222 0 0.0166 0.0837 0.0115 0.3056 0.0258 0.0562 0.0183072 0.0183486 0.0183693 1 151 4638 61 2192 279 1251 30 674 2 5014 62116 3660 5294 2886 33780 494 10988 0.95149 0 . 0 . 79 9,24,14,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R2958Q|8923|OBSCN|protein_coding|CODING|NM_001271223.2|33|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.426799 rs3795783 -0.693145 0.322091 79 S3047N 8923 aGc/aAc MODERATE 34 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228468069 G A 0 222 0 0.0023 0.013179 0.0303 0.0308 0 0.0112 0.00259067 0.00142046 0.000830762 1 26 692 328 146 9 22 2 159 2 4490 52438 3244 2976 1882 28872 422 10552 0.936356 0 . 0 . 128 40,18,24,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S3047N|8923|OBSCN|protein_coding|CODING|NM_001271223.2|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999687 rs56384735 -0.693147 0.0381631 128 V3077 8923 gtG/gtA LOW 35 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228468244 G A 0 222 0 0.115 0.1136 0.0173 0.3185 0.0268 0.0583 0.10434 0.0472931 0.0183013 1 1051 6760 119 2901 370 1507 36 776 2 9482 118438 11348 8480 6454 65484 876 16314 0.848136 0 . 0 . 145 43,22,45,17 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V3077|8923|OBSCN|protein_coding|CODING|NM_001271223.2|35|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.501747 rs12061320 -0.693147 0.0120437 145 R3252* 8923 Aga/Tga HIGH 36 NONSENSE CODING OBSCN T protein_coding NM_001271223.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228469903 A T 0 181 0 0.0166 0.0767 0.0058 0.2927 0.007 0.0573 0.0108978 0.00520919 0.00254854 1 149 4124 63 2539 207 384 27 755 2 9048 115560 11274 8450 5764 64060 822 16142 0.870697 0 . 0 . 38 1,17,2,18 STOP_GAINED(HIGH|NONSENSE|Aga/Tga|R3252*|8923|OBSCN|protein_coding|CODING|NM_001271223.2|36|T) 1 0.5 1 0 . 1 0 1 1 (OBSCN|OBSCN|1|1.00) 60 0 1 1 (OBSCN|OBSCN|1|1.00) 0.919651 rs3795786 -0.692067 0.386158 38 R3252I 8923 aGa/aTa MODERATE 36 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228469904 G T 0 186 0 0.0166 0.0767 0.0058 0.2927 0.007 0.0573 0.0114167 0.00529276 0.00242777 1 147 4118 63 2535 206 385 27 755 2 9038 115520 11272 8452 5762 64036 820 16140 0.42089 0 . 0 . 38 1,17,2,18 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|aGa/aTa|R3252I|8923|OBSCN|protein_coding|CODING|NM_001271223.2|36|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.919651 rs3795787 -0.692067 0.386158 38 A3764V 8923 gCc/gTc MODERATE 42 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228475954 C T 0 222 0 0.0008 0.009385 0.0303 0.0159 0 0.0092 0.000464468 0.000312744 0.000235738 1 8 1085 761 134 0 7 2 173 2 9808 120564 11574 8620 6614 66630 898 16420 0.939558 0 . 0 . 201 40,43,53,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A3764V|8923|OBSCN|protein_coding|CODING|NM_001271223.2|42|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952027 rs55946300 -0.693147 0.0271292 201 E3801D 8923 gaG/gaT MODERATE 43 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228476366 G T 0 222 0 0.0514 0.0958 0.0144 0.3165 0.0258 0.0583 0.0452335 0.0248442 0.0148703 1 532 6201 101 2889 369 1497 36 777 2 9796 120682 11572 8582 6614 66704 902 16512 0.964837 0 . 0 . 127 37,22,36,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E3801D|8923|OBSCN|protein_coding|CODING|NM_001271223.2|43|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.193595 rs3795789 -0.693147 0.0568544 127 S3802C 8923 Agc/Tgc MODERATE 43 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228476367 A T 0 222 0 0.0514 0.0958 0.0144 0.3165 0.0258 0.0583 0.0442607 0.0240492 0.0141599 1 532 6207 101 2895 369 1497 36 777 2 9796 120688 11570 8586 6614 66708 902 16512 0.812791 0 . 0 . 126 37,21,36,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S3802C|8923|OBSCN|protein_coding|CODING|NM_001271223.2|43|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.241751 rs3795790 -0.693147 0.0568544 126 A3817 8923 gcG/gcA LOW 43 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228476414 G A 0 222 0 0.0439 0.0938 0.013 0.3175 0.0258 0.0583 0.0462386 0.0277822 0.018598 1 440 6158 98 2931 372 1501 36 780 2 9810 120734 11574 8598 6614 66724 902 16512 0.963888 0 . 0 . 161 46,26,51,29 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A3817|8923|OBSCN|protein_coding|CODING|NM_001271223.2|43|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.686611 rs3795791 -0.693147 0.264237 161 T3983 8923 acA/acG LOW 45 SILENT CODING OBSCN G protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228480282 A G 0 228 0 0.8669 0.6989 0.7147 0.749 0.672 0.4366 0.831733 0.743825 0.702156 2 8106 83848 8661 6287 5106 46895 588 8205 2 9804 120712 11568 8602 6612 66718 900 16508 0 . 0 . 0 149 0,0,82,63 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T3983|8923|OBSCN|protein_coding|CODING|NM_001271223.2|45|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1150908 -0.693147 0.0367417 149 L4198 8923 ctG/ctC LOW 47 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228482028 G C 0 222 0 0.3139 0.2125 0.2795 0.1835 0.164 0.1074 0.29912 0.217829 0.176581 1 3096 24584 4499 1564 1006 12262 167 1990 2 9838 120774 11572 8602 6614 66736 900 16512 0.962474 0 . 0 . 258 77,55,70,37 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L4198|8923|OBSCN|protein_coding|CODING|NM_001271223.2|47|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.000521498 rs4653547 -0.693147 0.0733559 258 A4964 8923 gcG/gcA LOW 56 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228494696 G A 0 228 0 0.3714 0.3085 0.2925 0.497 0.1869 0.1656 0.372311 0.254686 0.194496 2 3397 28374 4067 4173 1126 12810 182 2619 2 7714 89052 8310 7296 3670 48594 614 12854 0 . 0 . 0 65 0,0,27,36 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4964|8923|OBSCN|protein_coding|CODING|NM_001271223.2|56|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4653939 -0.693147 0.596306 65 T5180 8923 acG/acA LOW 58 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228496014 G A 0 222 0 0.32 0.2131 0.2781 0.1825 0.161 0.1074 0.318974 0.22461 0.177194 1 3107 23932 4301 1540 930 11924 160 1970 2 8528 100280 9802 7044 4630 55398 720 14158 0.720457 0 . 0 COSM425523,COSM1473532,COSM1473531 189 43,33,62,33 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T5180|8923|OBSCN|protein_coding|CODING|NM_001271223.2|58|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.796513 rs386446522,rs876180 -0.693147 0.221741 189 H5338R 8923 cAc/cGc MODERATE 61 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228503677 A G 0 228 0 0.8722 0.7009 0.7147 0.748 0.674 0.4387 0.838263 0.74988 0.705552 2 5399 61756 6266 4881 2581 35769 379 6481 2 6486 88048 8258 6654 3272 50304 564 12510 0 . 0 . 0 167 0,0,96,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H5338R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|61|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1150912 -0.693147 0.560694 167 C5407R 8923 Tgc/Cgc MODERATE 62 MISSENSE CODING OBSCN C protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228504472 T C 0 228 0 0.8661 0.6993 0.7147 0.748 0.674 0.4387 0.831097 0.744069 0.700763 2 7278 78604 8277 5987 4655 43843 515 8049 2 8812 113122 11028 8220 5998 62274 796 15994 0 . 0 . 0 73 0,0,19,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C5407R|8923|OBSCN|protein_coding|CODING|NM_001271223.2|62|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188732 -0.693147 0.600165 73 H5445D 8923 Cac/Gac MODERATE 62 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228504586 C G 0 222 0 0.0008 0.0061901 0.0288 0.0099 0 0 0.000467071 0.000236332 0.000118878 1 4 341 318 18 0 0 1 0 2 2960 41836 3792 2368 1216 21862 314 9324 0.473814 0 . 0 . 44 10,10,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H5445D|8923|OBSCN|protein_coding|CODING|NM_001271223.2|62|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.599548 rs188287808 -0.69168 0.371282 44 R5466H 8923 cGc/cAc MODERATE 62 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228504650 G A 0 186 0 0.0023 0.0097844 0.0303 0.0159 0 0.0092 0.000248262 0.000166889 0.000125691 1 1 100 15 10 0 1 1 72 2 1042 13842 274 298 60 5088 140 6940 0.980497 0 . 0 . 31 4,10,2,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5466H|8923|OBSCN|protein_coding|CODING|NM_001271223.2|62|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.706504 rs193004966 -0.690438 0.0478316 31 R5491H 8923 cGc/cAc MODERATE 63 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228505204 G A 0 228 0 0.3941 0.3153 0.2954 0.499 0.1869 0.1656 0.376582 0.254239 0.194378 2 3782 30590 4550 4461 1325 13513 197 2762 2 9270 116794 11338 8506 6086 64490 840 16264 0.147436 0 . 0 . 172 2,0,58,98 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5491H|8923|OBSCN|protein_coding|CODING|NM_001271223.2|63|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.615385 rs4653942 -0.693147 0.0601921 172 S5599C 8923 tCt/tGt MODERATE 64 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228505668 C G 0 228 0 0.8661 0.6993 0.7147 0.748 0.674 0.4387 0.832546 0.745307 0.701563 2 8096 83715 8647 6265 5090 46848 583 8186 2 9810 120622 11560 8590 6584 66670 900 16508 0 . 0 . 0 129 0,0,96,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S5599C|8923|OBSCN|protein_coding|CODING|NM_001271223.2|64|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188729 -0.693147 0.601255 129 G5609 8923 ggT/ggC LOW 64 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228505699 T C 0 228 0 0.8888 0.7059 0.719 0.748 0.674 0.4387 0.856674 0.753062 0.700803 2 8329 84032 8667 6279 5108 46876 585 8188 2 9804 120488 11564 8602 6570 66542 900 16506 0 . 0 . 0 154 0,0,98,40 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G5609|8923|OBSCN|protein_coding|CODING|NM_001271223.2|64|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1188728 -0.693147 8.47619e-05 154 R5619C 8923 Cgc/Tgc MODERATE 64 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228505727 C T 0 222 0 0.0166 0.0863 0.0115 0.3165 0.0258 0.0583 0.0177487 0.0183328 0.0186277 1 182 5884 82 2930 373 1505 36 776 2 9806 120688 11574 8586 6612 66700 900 16510 0.977624 0 . 0 . 178 50,33,53,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R5619C|8923|OBSCN|protein_coding|CODING|NM_001271223.2|64|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.438804 rs3795800 -0.693147 0.0232613 178 D5919G 8923 gAc/gGc MODERATE 66 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228509427 A G 0 228 0 0.8684 0.6847 0.6758 0.7044 0.674 0.4335 0.824399 0.739736 0.696789 2 8108 82705 8126 5898 5105 46726 579 8163 2 9820 120518 11564 8572 6612 66548 898 16504 0 . 0 . 0 90 0,0,41,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D5919G|8923|OBSCN|protein_coding|CODING|NM_001271223.2|66|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs373610 -0.693147 0.208693 90 A6689 8923 gcT/gcC LOW 80 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228526665 T C 0 222 0 0.5522 0.4944 0.4294 0.5665 0.5209 0.3609 0.552383 0.55544 0.556947 1 1058 8928 145 348 130 4109 74 3064 2 2022 18230 356 578 178 7726 180 7190 0.496128 0 . 0 . 62 4,24,5,26 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A6689|8923|OBSCN|protein_coding|CODING|NM_001271223.2|80|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904603 rs505629 -0.69311 0.0227628 62 Q6848E 8923 Cag/Gag MODERATE 83 MISSENSE CODING OBSCN G protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228528563 C G 0 228 0 0.6679 0.5387 0.4654 0.5942 0.5229 0.3753 0.608026 0.548757 0.520334 2 3758 42467 3192 3450 2216 24322 280 5249 2 5902 77662 6650 5654 3312 43608 548 11988 0.84 0 . 0 COSM1473554,COSM1473555 52 0,2,5,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q6848E|8923|OBSCN|protein_coding|CODING|NM_001271223.2|83|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.84 rs1188710 -0.693147 0.00573355 52 P7228S 8923 Ccc/Tcc MODERATE 91 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228550426 C T 0 228 0 0.0825 0.147 0.0764 0.3264 0.0984 0.1493 0.0937664 0.0866567 0.0833536 2 569 9894 673 1735 807 4220 72 1818 2 4392 58368 4484 4282 3022 30940 438 10810 0.88535 0 . 0 . 181 2,0,93,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P7228S|8923|OBSCN|protein_coding|CODING|NM_001271223.2|91|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.350318 rs35155240 -0.693147 0.0465431 181 L7733 8923 ctC/ctT LOW 105 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228558807 C T 0 222 0 0.0008 0.009984 0.0317 0.0188 0 0.0082 0.000486145 0.000319591 0.000238039 1 7 968 662 135 0 8 2 154 2 9396 118052 11452 8538 6584 64968 874 16240 0.757727 0 . 0 . 112 17,28,24,30 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L7733|8923|OBSCN|protein_coding|CODING|NM_001271223.2|105|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.803986 rs147052901 -0.693147 0.279542 112 A8129V 8923 gCg/gTg MODERATE 105 MISSENSE CODING OBSCN T protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228559994 C T 0 228 0 0.708 0.5891 0.389 0.5625 0.504 0.6851 0.659333 0.55496 0.503348 2 3228 31770 1587 2451 819 16983 217 6485 2 4562 51312 3026 3726 1318 28422 374 9884 1 0 . 0 COSM425535,COSM1473567 156 1,0,85,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A8129V|8923|OBSCN|protein_coding|CODING|NM_001271223.2|105|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs500049 -0.693147 0.0092699 156 Y8142 8923 taC/taT LOW 105 SILENT CODING OBSCN T protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228560034 C T 0 222 0 0 0.013778 0 0.0575 0.001 0.0102 0.00049456 0.000485044 0.000480423 1 6 298 1 229 3 27 0 32 2 3044 32812 1422 2270 512 16742 256 8566 0.770048 0 . 0 . 158 33,34,51,21 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y8142|8923|OBSCN|protein_coding|CODING|NM_001271223.2|105|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0107903 rs36119328 -0.693147 0.669098 158 S8177 8923 tcA/tcG LOW 105 SILENT CODING OBSCN G protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228560139 A G 0 228 0 0.9962 0.9742 0.964 1 0.9066 0.9949 0.983471 0.94489 0.925886 2 3823 39910 2021 2906 796 21025 312 9027 2 3876 42000 2104 2906 892 22758 328 9136 0 . 0 . 0 165 0,0,66,73 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S8177|8923|OBSCN|protein_coding|CODING|NM_001271223.2|105|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs498382 -0.693147 0.152739 165 D8364 8923 gaT/gaC LOW 105 SILENT CODING OBSCN C protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228560700 T C 0 228 0 0.9365 0.758 0.6398 0.752 0.5636 0.8067 0.863442 0.653542 0.548517 2 7822 67302 7562 6684 3289 33868 486 7591 2 8802 106534 11194 8378 6426 61028 750 9956 0.515111 0 . 0 COSM1473568 96 1,3,41,43 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D8364|8923|OBSCN|protein_coding|CODING|NM_001271223.2|105|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.736993 rs512253 -0.693147 0.201518 96 E8613 8923 gaG/gaA LOW 111 SILENT CODING OBSCN A protein_coding NM_001271223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228564504 G A 0 222 0 0.0008 0.010982 0.0317 0.0248 0 0.0072 0.000259471 0.000250459 0.000246184 1 3 123 29 26 0 1 2 62 2 2234 20300 450 722 74 8768 192 7860 0.920309 0 . 0 . 66 14,13,19,11 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E8613|8923|OBSCN|protein_coding|CODING|NM_001271223.2|111|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0503048 rs139209300 -0.693097 0.0585339 66 R8681H 8923 cGc/cAc MODERATE 112 MISSENSE CODING OBSCN A protein_coding NM_001271223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228564884 G A 0 222 0 0.0983 0.1408 0.0432 0.3085 0.0974 0.1391 0.0978952 0.0890455 0.0847417 1 620 9555 260 1719 787 4369 80 1720 2 3932 56960 4076 4100 3026 30792 422 10612 0.836847 0 . 0 . 56 23,4,22,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R8681H|8923|OBSCN|protein_coding|CODING|NM_001271223.2|112|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.171761 rs56174824 -0.693021 0.528265 56 A240 468 gcT/gcG LOW 3 SILENT CODING TRIM11 C protein_coding NM_145214.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228588680 A C 0 207 0 0.2648 0.2173 0.1282 0.377 0.1133 0.1585 0.200197 0.128658 0.0928712 2 1676 14141 1283 2582 846 5817 110 1827 2 4930 63324 6366 5750 2884 35756 452 7186 1 0 . 0 . 42 2,0,37,2 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A240|468|TRIM11|protein_coding|CODING|NM_145214.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.512821 rs11555960 -0.693144 0.131728 42 A38 477 gcC/gcG LOW 2 SILENT CODING TRIM17 C protein_coding NM_001024940.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228602660 G C 0 222 0 0.6513 0.2959 0.098 0.3095 0.1014 0.1421 0.535179 0.244656 0.095814 1 5688 19728 700 2891 1305 6673 134 2337 2 10184 119204 11452 8554 6552 65138 886 16438 0.995914 0 . 0 . 95 7,44,7,29 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A38|477|TRIM17|protein_coding|CODING|NM_001024940.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995914 rs503203 -0.693139 0.0410134 95 I63 136 atC/atA LOW 1 SILENT CODING HIST3H3 T protein_coding NM_003493.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228612838 G T 0 222 0 0.3116 0.6903 0.8977 0.6895 0.8847 0.8558 0.417158 0.726665 0.885233 1 4142 99629 10806 5711 5258 58846 761 14105 2 10404 121378 11578 8632 6614 66730 908 16512 0.999156 0 . 0 . 254 58,59,59,56 SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I63|136|HIST3H3|protein_coding|CODING|NM_003493.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.704849 rs2230656 -0.693147 0.000822974 254 T121 130 acG/acT LOW 1 SILENT CODING HIST3H2A A protein_coding NM_033445.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228645156 C A 0 222 0 0 0.0095847 0.0317 0.0208 0 0.0051 0.000453926 0.000230698 0.000116306 1 8 916 612 169 0 6 3 118 2 10176 120716 11560 8632 6596 66356 896 16500 0.324036 0 . 0 . 196 69,17,62,27 SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T121|130|HIST3H2A|protein_coding|CODING|NM_033445.2|1|A),UPSTREAM(MODIFIER||652||126|HIST3H2BB|protein_coding|CODING|NM_175055.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.499107 rs183360027 -0.693147 0.00266845 196 235 163 MODIFIER 4 CODING RNF187 T protein_coding NM_001010858.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228681749 C T 0 94 0 0.1838 0.4535 0.6023 0.4385 0.5457 0.6329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.931639 0 . 0 . 29 2,15,0,11 UTR_3_PRIME(MODIFIER||163||235|RNF187|protein_coding|CODING|NM_001010858.2|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982453 rs3795817 -0.676189 0.0374523 29 235 744 MODIFIER 4 CODING RNF187 G protein_coding NM_001010858.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228682330 C G 0 9.7 0 0.9523 0.9219 0.928 1 0.8091 0.9121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||744||235|RNF187|protein_coding|CODING|NM_001010858.2|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12542 -0.379885 0 1 H61R 208 cAc/cGc MODERATE 2 MISSENSE CODING BTNL10 C protein_coding NM_001287262.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 228699477 T C 0 222 0 0.2958 0.5024 0.6412 0.4444 0.5905 0.6524 0 . 0 1 393 10626 183 211 1170 3731 132 4806 2 1112 17642 302 492 1692 6166 214 7664 0.505636 0 . 0 . 132 17,37,27,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H61R|208|BTNL10|protein_coding|CODING|NM_001287262.1|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.99925 rs6665115 -0.693147 0.00976752 132 270 3774 MODIFIER 4 CODING CCSAP A protein_coding NM_145257.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229457208 C A 0 46.3 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3774||270|CCSAP|protein_coding|CODING|NM_145257.4|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs237796 -0.453602 0.72 2 377 941 MODIFIER 1 CODING ACTA1 G protein_coding NM_001100.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229569803 A G 0 9.7 0 0.7625 0.6302 0.6383 0.4514 0.5994 0.6616 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||941||377|ACTA1|protein_coding|CODING|NM_001100.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs605430 -0.379885 0 1 377 942 MODIFIER 1 CODING ACTA1 A protein_coding NM_001100.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229569804 G A 0 9.7 0 0.789 0.6436 0.6527 0.4623 0.6004 0.6718 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||942||377|ACTA1|protein_coding|CODING|NM_001100.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs605428 -0.379885 0 1 S454 589 agC/agT LOW 5 SILENT CODING TAF5L A protein_coding NM_014409.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229730452 G A 0 222 0 0.0938 0.3035 0.2666 0.3254 0.4612 0.4284 0.147299 0.356451 0.463605 1 1386 48315 2896 2840 3078 30882 383 6850 2 10342 121226 11566 8624 6612 66666 908 16508 0.546378 0 . 0 . 112 35,19,26,23 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S454|589|TAF5L|protein_coding|CODING|NM_014409.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930449 rs2295625 -0.693147 0.185637 112 R248 589 cgA/cgC LOW 4 SILENT CODING TAF5L G protein_coding NM_014409.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229738170 T G 0 228 0 0.4887 0.5737 0.5447 0.7639 0.5179 0.5706 0.509759 0.511533 0.512442 2 5331 66841 7692 6604 3691 33847 500 9176 2 10396 121362 11568 8646 6614 66718 908 16512 0 . 0 . 0 35 0,0,19,16 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgC|R248|589|TAF5L|protein_coding|CODING|NM_014409.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3753886 -0.693136 0.812276 35 P226 589 ccC/ccT LOW 4 SILENT CODING TAF5L A protein_coding NM_014409.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229738236 G A 0 228 0 0.9281 0.8421 0.7219 0.9415 0.7614 0.7914 0.915797 0.807473 0.751977 2 9517 95853 9056 8217 4898 50281 721 13163 2 10398 121368 11564 8654 6612 66720 908 16512 0 . 0 . COSM1339965,COSM1339966 69 0,0,54,15 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P226|589|TAF5L|protein_coding|CODING|NM_014409.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4925500 -0.693147 0.294807 69 V778G 1524 gTc/gGc MODERATE 4 MISSENSE CODING URB2 G protein_coding NM_001314021.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229772693 T G 0 228 0 0.4796 0.5719 0.5432 0.7649 0.5189 0.5726 0.504539 0.509995 0.512791 2 5285 66772 7696 6604 3692 33843 501 9151 2 10392 121082 11566 8644 6610 66594 906 16370 1 0 . 0 . 94 0,1,23,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gGc|V778G|1524|URB2|protein_coding|CODING|NM_001314021.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3811473 -0.693147 0.0204472 94 K858E 1524 Aaa/Gaa MODERATE 4 MISSENSE CODING URB2 G protein_coding NM_001314021.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229772932 A G 0 222 0 0.1952 0.1993 0.2421 0.4315 0.0636 0.0746 0.191557 0.107412 0.0643023 1 2095 16398 4348 3755 513 4099 109 1479 2 10400 121112 11570 8622 6614 66652 906 16348 0.999169 0 . 0 . 84 28,9,32,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K858E|1524|URB2|protein_coding|CODING|NM_001314021.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856947 rs3811474 -0.693145 0.06588 84 T1027 1524 acC/acT LOW 4 SILENT CODING URB2 T protein_coding NM_001314021.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229773441 C T 0 222 0 0.2156 0.2051 0.2464 0.4315 0.0626 0.0746 0.21153 0.114332 0.0645349 1 2333 16642 4352 3738 513 4103 111 1492 2 10382 121240 11562 8640 6614 66648 906 16488 0.597036 0 . 0 . 159 39,34,39,34 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1027|1524|URB2|protein_coding|CODING|NM_001314021.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0753602 rs3811475 -0.693147 0.0168063 159 R1430 1524 agA/agG LOW 9 SILENT CODING URB2 G protein_coding NM_001314021.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229790048 A G 0 228 0 0.503 0.604 0.5778 0.8502 0.5457 0.5654 0.524739 0.519068 0.516163 2 5535 68404 8066 7546 3451 34223 513 9070 2 10404 121386 11574 8646 6614 66730 906 16512 0 . 0 . 0 330 0,0,182,115 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R1430|1524|URB2|protein_coding|CODING|NM_001314021.1|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7521953 -0.693147 0.203559 330 T1523M 1524 aCg/aTg MODERATE 10 MISSENSE CODING URB2 T protein_coding NM_001314021.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229795037 C T 0 222 0 . 0 . 0 . 0 0.000453926 0.000153775 0 1 1 3 0 1 0 0 0 1 2 10322 120880 11556 8632 6612 66388 906 16464 0.849606 0 . 0 . 68 9,24,8,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1523M|1524|URB2|protein_coding|CODING|NM_001314021.1|10|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.90641 rs139372652 -0.69311 0.447928 68 1524 26 MODIFIER 10 CODING URB2 G protein_coding NM_001314021.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 229795070 T G 0 228 0 0.5083 0.602 0.5778 0.8343 0.5457 0.5644 0.53586 0.522682 0.51593 2 5548 67862 8049 7368 3447 33924 512 9014 2 10252 120394 11524 8600 6600 66096 904 16418 0 . 0 . 0 41 0,0,7,31 UTR_3_PRIME(MODIFIER||26||1524|URB2|protein_coding|CODING|NM_001314021.1|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1048306 -0.693143 0.0135509 41 D275 571 gaT/gaC LOW 9 SILENT CODING GALNT2 C protein_coding NM_004481.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230384937 T C 0 228 0 0.1906 0.2536 0.3458 0.5992 0.0547 0.1217 0.17113 0.0910349 0.05 2 1915 17613 4839 5157 467 3584 81 1570 2 10406 121312 11578 8632 6614 66678 906 16498 0 . 0 . 0 81 0,0,38,36 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D275|571|GALNT2|protein_coding|CODING|NM_004481.4|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748006 -0.693147 0.00252411 81 V554M 571 Gtg/Atg MODERATE 16 MISSENSE CODING GALNT2 A protein_coding NM_004481.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230415148 G A 0 222 0 0.0121 0.1134 0.1427 0.3115 0.0437 0.0971 0.0242851 0.0419037 0.0509302 1 244 10311 2616 2727 325 2982 54 1363 2 10356 120870 11556 8612 6544 66410 898 16494 0.871833 0 . 0 . 91 22,18,29,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V554M|571|GALNT2|protein_coding|CODING|NM_004481.4|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841937 rs2273970 -0.693147 0.91649 91 571 40 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230415244 T C 0 222 0 0.2474 0.2276 0.2363 0.4435 0.1064 0.0971 0.202224 0.131478 0.0952326 1 2158 17202 2156 3788 781 6655 113 1551 2 10100 117432 11366 8504 6322 65164 862 15114 0.473654 0 . 0 . 144 33,32,50,13 UTR_3_PRIME(MODIFIER||40||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.706209 rs2273968 -0.693147 0.573045 144 571 1014 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230416218 T C 0 36.3 0 0.4985 0.4119 0.4121 0.756 0.159 0.2004 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1014||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13728 -0.453602 0.92 2 571 1195 MODIFIER 16 CODING GALNT2 T protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230416399 G T 0 23.4 0 0.6528 0.6056 0.585 0.872 0.4056 0.4877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1195||571|GALNT2|protein_coding|CODING|NM_004481.4|16|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1043897 -0.453602 0.84 2 571 1556 MODIFIER 16 CODING GALNT2 G protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230416760 A G 0 46.3 0 0.6914 0.5132 0.4654 0.8462 0.1918 0.2935 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1556||571|GALNT2|protein_coding|CODING|NM_004481.4|16|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13490 -0.453602 0.72 2 571 1749 MODIFIER 16 CODING GALNT2 G protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230416953 A G 0 39.3 0 0.8979 0.7161 0.6297 0.9613 0.4205 0.5828 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1749||571|GALNT2|protein_coding|CODING|NM_004481.4|16|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10005 -0.453602 0.36 2 571 1852 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417056 G C 0 54 0 0.4085 0.2881 0.2781 0.3899 0.1451 0.1748 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,1 UTR_3_PRIME(MODIFIER||1852||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7544606 -0.453602 0.88 4 571 2167 MODIFIER 16 CODING GALNT2 T protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417371 C T 0 90 0 0.0182 0.1945 0.2277 0.3413 0.2107 0.2413 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.990401 0 . 0 . 28 16,2,7,1 UTR_3_PRIME(MODIFIER||2167||571|GALNT2|protein_coding|CODING|NM_004481.4|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.261067 rs1043909 -0.651104 0.454873 28 571 2190 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417394 T C 0 221 0 0.3714 0.269 0.2579 0.4683 0.1014 0.1053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991242 0 . 0 . 31 5,2,15,6 UTR_3_PRIME(MODIFIER||2190||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.649836 rs3088075,rs386579113 -0.692352 0.246363 31 571 2204 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417408 T C 0 131 0 0.5711 0.5008 0.4452 0.5109 0.4404 0.4969 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.986577 0 . 0 . 40 20,7,6,3 UTR_3_PRIME(MODIFIER||2204||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.947381 rs11620 -0.662043 0.841751 40 571 2353 MODIFIER 16 CODING GALNT2 C protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417557 T C 0 228 0 0.9191 0.8812 0.8516 0.9841 0.8062 0.8221 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,37,21 UTR_3_PRIME(MODIFIER||2353||571|GALNT2|protein_coding|CODING|NM_004481.4|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1043941 -0.693147 0.0095509 68 571 2356 MODIFIER 16 CODING GALNT2 G protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417560 A G 0 228 0 0.9191 0.8818 0.8516 0.9841 0.8062 0.8252 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,37,21 UTR_3_PRIME(MODIFIER||2356||571|GALNT2|protein_coding|CODING|NM_004481.4|16|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1043944 -0.693147 0.0095509 68 571 2460 MODIFIER 16 CODING GALNT2 G protein_coding NM_004481.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230417664 C G 0 223 0 0.7723 0.4984 0.4409 0.5694 0.329 0.2699 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 32 0,0,1,30 UTR_3_PRIME(MODIFIER||2460||571|GALNT2|protein_coding|CODING|NM_004481.4|16|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7022 -0.69311 0.353407 32 524 441 MODIFIER 7 CODING PGBD5 C protein_coding NM_001258311.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230458730 T C 0 28.1 0 0 0.0069888 0.0115 0.0268 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.485537 0 . 0 . 14 2,8,0,4 UTR_3_PRIME(MODIFIER||441||524|PGBD5|protein_coding|CODING|NM_001258311.1|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99005 rs3748014 -0.556411 0.865924 14 *739 738 taA/taG LOW 18 SILENT CODING COG2 G protein_coding NM_007357.2 SYNONYMOUS_STOP outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230829139 A G 0 222 0 0.2345 0.3446 0.4352 0.5913 0.2087 0.3149 0.201316 0.213594 0.219884 1 2238 34939 6452 5044 1828 14345 244 4788 2 10322 120602 11510 8590 6606 66374 902 16298 0.990358 0 . 0 . 40 4,11,14,8 SYNONYMOUS_STOP(LOW|SILENT|taA/taG|*739|738|COG2|protein_coding|CODING|NM_007357.2|18|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.640763 rs1051038 -0.692562 0.786108 40 738 589 MODIFIER 18 CODING COG2 C protein_coding NM_007357.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230829727 CA C 0 30.4 0 0.1823 0.2352 0.2594 0.4802 0.0696 0.2076 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,2,1,1 UTR_3_PRIME(MODIFIER||589||738|COG2|protein_coding|CODING|NM_007357.2|18|C) 0 0.5 1 2 0.5 1 1 0 . 0 60 0 0 1 0 . rs66582779 -0.453602 0.202231 4 L372 485 ctA/ctG LOW 3 SILENT CODING AGT C protein_coding NM_000029.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230841687 T C 0 228 0 0.9962 0.9726 0.951 1 0.9155 0.9867 0.984113 0.940873 0.918721 2 10263 114569 11218 8650 6273 61102 858 16205 2 10398 121356 11576 8650 6614 66700 906 16512 0 . 0 . 0 90 0,0,66,17 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L372|485|AGT|protein_coding|CODING|NM_000029.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386567962,rs7080 -0.693147 0.00527189 90 M268T 485 aTg/aCg MODERATE 2 MISSENSE CODING AGT G protein_coding NM_000029.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230845794 A G 0 228 0 0.9032 0.7051 0.6354 0.8532 0.4115 0.636 0.826827 0.561664 0.425814 2 8783 66516 8582 7235 2879 28281 471 10285 2 10398 121284 11572 8636 6610 66648 908 16512 0 255|255|255 other|other|other 0 COSM425562 79 0,0,23,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M268T|485|AGT|protein_coding|CODING|NM_000029.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs699 -0.693147 0.287955 79 485 3276 MODIFIER 1 CODING AGT T protein_coding NM_000029.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230849872 C T 0 9.7 0 0.916 0.7105 0.6455 0.8512 0.4125 0.6401 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||3276||485|AGT|protein_coding|CODING|NM_000029.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs5051 -0.379885 0 1 485 3487 MODIFIER 1 CODING AGT T protein_coding NM_000029.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230850083 C T 0 31.6 0 0.2912 0.1895 0.0908 0.1786 0.1054 0.2198 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_5_PRIME(MODIFIER||3487||485|AGT|protein_coding|CODING|NM_000029.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs5049 -0.453602 0.88 3 N166 690 aaC/aaT LOW 4 SILENT CODING CAPN9 T protein_coding NM_006615.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230898494 C T 0 222 0 0.2716 0.3329 0.4452 0.4385 0.3797 0.1789 0.266909 0.337306 0.373372 1 2789 42056 5210 3820 2183 24905 307 2842 2 10374 121022 11514 8614 6584 66556 908 16472 0.776502 0 . 0 COSM146818 102 22,32,13,21 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N166|690|CAPN9|protein_coding|CODING|NM_006615.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.866379 rs2282319 -0.693132 0.360666 102 K322Q 690 Aag/Cag MODERATE 9 MISSENSE CODING CAPN9 C protein_coding NM_006615.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230914729 A C 0 222 0 0.3888 0.3313 0.2075 0.1875 0.3201 0.501 0.378802 0.34092 0.321512 1 3883 39993 2350 1532 2671 21095 301 8161 2 10158 118544 11166 8432 6456 65446 880 16006 0.545224 0 . 0 . 164 63,18,41,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K322Q|690|CAPN9|protein_coding|CODING|NM_006615.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.838268 rs1933631 -0.693147 0.127647 164 D429 690 gaC/gaT LOW 11 SILENT CODING CAPN9 T protein_coding NM_006615.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230916260 C T 0 222 0 0.087 0.1078 0.1297 0.0813 0.1481 0.1063 0.0962324 0.13463 0.154302 1 993 16514 1595 647 1114 10155 126 1884 2 10406 121378 11574 8652 6614 66720 906 16506 0.961315 0 . 0 . 66 13,17,19,11 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D429|690|CAPN9|protein_coding|CODING|NM_006615.2|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94143 rs28359687 -0.693097 0.704027 66 R522W 690 Cgg/Tgg MODERATE 13 MISSENSE CODING CAPN9 T protein_coding NM_006615.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230923313 C T 0 222 0 0.3207 0.1961 0.1542 0.0813 0.1819 0.1902 0.284839 0.224204 0.19314 1 2997 23205 1865 649 1253 12722 174 3545 2 10406 121378 11574 8648 6612 66720 908 16510 0.142557 0 . 0 . 113 35,22,26,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R522W|690|CAPN9|protein_coding|CODING|NM_006615.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.790446 rs12731961,rs386525850 -0.693146 0.065002 113 327 2191 MODIFIER 4 CODING C1orf198 T protein_coding NM_032800.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230973407 G T 0 46.3 0 0.8911 0.8628 0.8343 0.9325 0.7107 0.9294 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2191||327|C1orf198|protein_coding|CODING|NM_032800.2|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12699 -0.453602 0.32 2 327 1337 MODIFIER 4 CODING C1orf198 T protein_coding NM_032800.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230974261 A T 0 119 0 0.2413 0.3444 0.5 0.4821 0.334 0.2423 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.885813 0 . 0 . 60 22,7,12,2 UTR_3_PRIME(MODIFIER||1337||327|C1orf198|protein_coding|CODING|NM_032800.2|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.948873 rs1010189 -0.686358 0.679222 60 327 989 MODIFIER 4 CODING C1orf198 T protein_coding NM_032800.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230974609 C T 0 107 0 0.0424 0.1979 0.072 0.3343 0.165 0.3906 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.720273 0 . 0 . 21 1,11,1,7 UTR_3_PRIME(MODIFIER||989||327|C1orf198|protein_coding|CODING|NM_032800.2|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.133734 rs1555294 -0.651104 0.020653 21 327 824 MODIFIER 4 CODING C1orf198 C protein_coding NM_032800.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230974774 T C 0 125 0 0.9622 0.8826 0.8357 0.9325 0.7147 0.9294 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,4 UTR_3_PRIME(MODIFIER||824||327|C1orf198|protein_coding|CODING|NM_032800.2|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1202549 -0.590765 0.37035 5 327 144 MODIFIER 4 CODING C1orf198 G protein_coding NM_032800.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 230975454 A G 0 169 0 0.5318 0.7564 0.7925 0.9325 0.7018 0.909 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,21,0 UTR_3_PRIME(MODIFIER||144||327|C1orf198|protein_coding|CODING|NM_032800.2|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1202550 -0.692352 0.0190206 21 G606 860 ggT/ggA LOW 16 SILENT CODING TTC13 T protein_coding NM_024525.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231057247 A T 0 228 0 0.1354 0.2145 0.1167 0.3879 0.17 0.2577 0.151243 0.168843 0.177817 2 1417 23497 1429 3522 1196 11777 170 3986 2 9566 118260 11428 8568 6568 64872 890 16368 1 0 . 0 . 104 0,1,13,86 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G606|860|TTC13|protein_coding|CODING|NM_024525.4|16|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2275333 -0.693147 0.0146925 104 G38R 860 Ggg/Cgg MODERATE 1 MISSENSE CODING TTC13 G protein_coding NM_024525.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231114465 C G 0 19.7 0 0.1498 0.2572 0.1729 0.3899 0.2396 0.3436 0 . 0 2 40 3411 33 49 1 722 28 2538 2 176 9816 88 122 2 2346 110 6972 0 . 0 . COSM1320392 2 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Cgg|G38R|860|TTC13|protein_coding|CODING|NM_024525.4|1|G),UPSTREAM(MODIFIER||358||271|ARV1|protein_coding|CODING|NM_022786.1||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs76376323 -0.379885 0 2 860 19 MODIFIER 1 CODING TTC13 T protein_coding NM_024525.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231114595 C T 0 164 0 0.4183 0.5112 0.3631 0.6458 0.4274 0.6892 0 . 0 2 151 2377 56 68 2 492 24 1584 2 286 3664 90 98 4 928 40 2218 0 . 0 . 0 21 0,0,21,0 UTR_5_PRIME(MODIFIER||19||860|TTC13|protein_coding|CODING|NM_024525.4|1|T),UPSTREAM(MODIFIER||228||271|ARV1|protein_coding|CODING|NM_022786.1||T) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs11122174 -0.692352 0.731136 21 783 17 MODIFIER 1 CODING TRIM67 G protein_coding NM_001004342.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231298699 T G 0 121 0 0.2012 0.1524 0.1268 0.2569 0.0755 0.0757 0.170015 0.0972862 0.0631795 1 1510 11307 1723 2173 647 4032 82 1140 2 7104 89592 8142 6736 3766 49940 634 13270 0.993528 0 . 0 . 21 9,2,8,1 UTR_5_PRIME(MODIFIER||17||783|TRIM67|protein_coding|CODING|NM_001004342.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.39256 rs112692510 -0.662043 0.838183 21 A61 783 gcC/gcA LOW 1 SILENT CODING TRIM67 A protein_coding NM_001004342.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231298898 C A 0 109 0 0.0189 0.0861 0.1052 0.2282 0.0477 0.0562 0 . 0 1 18 749 36 65 11 228 8 383 2 526 9810 210 244 124 3182 118 5406 0.829029 0 . 0 COSM425567,COSM1473598 24 7,9,2,6 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A61|783|TRIM67|protein_coding|CODING|NM_001004342.3|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.35506 rs61750990 -0.651104 0.612706 24 680 44 MODIFIER 1 CODING GNPAT T protein_coding NM_014236.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231377081 C T 0 222 0 0.531 0.5819 0.621 0.63 0.5229 0.6339 0.575579 0.5509 0.538256 1 5918 66620 7115 5129 2853 34804 500 10301 2 10398 121346 11572 8640 6608 66712 904 16512 0.472928 0 . 0 . 99 37,14,28,8 UTR_5_PRIME(MODIFIER||44||680|GNPAT|protein_coding|CODING|NM_014236.3|1|T),UPSTREAM(MODIFIER||148||293|C1orf131|protein_coding|CODING|NM_152379.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.310361 rs518686 -0.693139 0.473298 99 E305 680 gaG/gaA LOW 7 SILENT CODING GNPAT A protein_coding NM_014236.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231401902 G A 0 222 0 0.7012 0.6286 0.6254 0.6339 0.5318 0.6268 0.685429 0.594802 0.548372 1 7194 68890 7220 5161 2905 35619 506 10285 2 10384 121366 11578 8646 6614 66728 906 16510 0.75415 0 . 0 . 131 42,25,25,22 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E305|680|GNPAT|protein_coding|CODING|NM_014236.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939257 rs574553 -0.693147 0.879813 131 680 18 MODIFIER 16 CODING GNPAT C protein_coding NM_014236.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231413306 T C 0 222 0 0 0.0035942 0 0.0179 0 0 0.000453926 0.000153775 0 1 2 222 3 216 0 0 1 0 2 10394 121344 11572 8648 6612 66704 908 16506 0.938232 0 . 0 . 79 21,16,15,16 UTR_3_PRIME(MODIFIER||18||680|GNPAT|protein_coding|CODING|NM_014236.3|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.623041 rs150776112 -0.69311 0.0165494 79 725 542 MODIFIER 1 CODING EXOC8 G protein_coding NM_175876.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231470772 A G 0 9.7 0 0.2678 0.485 0.4957 0.5179 0.6561 0.5613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||542||725|EXOC8|protein_coding|CODING|NM_175876.4|1|G),UPSTREAM(MODIFIER||2910||489|SPRTN|protein_coding|CODING|NM_032018.6||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11122272 -0.379885 0 1 P296L 489 cCt/cTt MODERATE 5 MISSENSE CODING SPRTN T protein_coding NM_032018.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231488524 C T 0 222 0 0.4402 0.5329 0.5216 0.5248 0.6511 0.5532 0.467771 0.579271 0.636395 1 4687 72495 5656 4936 4593 42807 549 9267 2 10336 121068 11538 8626 6606 66572 898 16492 0.991484 0 . 0 . 76 15,26,10,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P296L|489|SPRTN|protein_coding|CODING|NM_032018.6|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997272 rs2437150 -0.69311 0.891648 76 489 246 MODIFIER 5 CODING SPRTN T protein_coding NM_032018.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231489353 G T 0 25.9 0 0.5197 0.5595 0.5245 0.5298 0.661 0.5644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||246||489|SPRTN|protein_coding|CODING|NM_032018.6|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2749717 -0.453602 0.22 3 C127S 426 tGt/tCt MODERATE 1 MISSENSE CODING EGLN1 G protein_coding NM_022051.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231557255 C G 0 22.1 0 0.3366 0.2604 0.1239 0.4593 0.0596 0.2556 0 . 0 1 10 32 0 9 0 11 0 2 2 20 108 4 14 2 66 0 2 1 0 . 0 . 3 0,1,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C127S|426|EGLN1|protein_coding|CODING|NM_022051.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs12097901 -0.453602 0.22 3 R264Q 886 cGg/cAg MODERATE 2 MISSENSE CODING DISC1 A protein_coding NM_001164537.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 231830295 G A 0 222 0 0.1172 0.2322 0.3329 0.2173 0.339 0.2219 0.147072 0.260034 0.317907 1 1449 35391 4328 2095 1956 20947 272 4344 2 10364 121062 11520 8616 6582 66566 904 16510 0.37613 1 not-provided 0 . 90 34,11,29,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R264Q|886|DISC1|protein_coding|CODING|NM_001164537.1|2|A),INTRAGENIC(MODIFIER|||||TSNAX-DISC1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.814909 rs3738401 -0.693143 0.662437 90 S736C 886 Agc/Tgc MODERATE 12 MISSENSE CODING DISC1 T protein_coding NM_001164537.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232144598 A T 0 222 0 0.3782 0.2502 0.1369 0.1052 0.2873 0.2689 0.32706 0.299068 0.285817 1 3301 31815 1323 1006 2175 19382 248 4380 2 9780 119032 11492 8564 6602 66150 884 15560 0.956358 0 . 0 . 77 25,19,16,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S736C|886|DISC1|protein_coding|CODING|NM_001164537.1|12|T),INTRAGENIC(MODIFIER|||||TSNAX-DISC1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.828003 rs821616 -0.693079 0.136397 77 R1695 1722 agA/agG LOW 21 SILENT CODING SIPA1L2 C protein_coding NM_020808.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232534957 T C 0 228 0 0.2564 0.4016 0.4697 0.7371 0.2654 0.3436 0.250597 0.253229 0.254524 2 2494 40341 6734 6355 1942 17015 286 5515 2 9812 120692 11560 8602 6604 66702 902 16510 0 . 0 . 0 162 0,0,56,95 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R1695|1722|SIPA1L2|protein_coding|CODING|NM_020808.4|21|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12043251 -0.693147 0.139965 162 G1639S 1722 Ggc/Agc MODERATE 19 MISSENSE CODING SIPA1L2 T protein_coding NM_020808.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232539219 C T 0 228 0 0 0.1232 0.072 0.4593 0.0089 0.0971 0.00452716 0.00569106 0.006247 2 48 7794 1357 4193 175 598 62 1361 2 9790 120188 11572 8598 6604 66516 898 16210 1 0 . 0 . 119 1,0,56,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1639S|1722|SIPA1L2|protein_coding|CODING|NM_020808.4|19|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2275303 -0.693147 0.575559 119 T1322A 1722 Acc/Gcc MODERATE 13 MISSENSE CODING SIPA1L2 C protein_coding NM_020808.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232574921 T C 0 222 0 0.41 0.3522 0.3473 0.4643 0.2008 0.318 0.385893 0.271991 0.215944 1 3852 33318 4532 4069 1538 14174 242 4911 2 9338 118086 11496 8514 6586 64820 890 16442 0.795195 0 . 0 . 91 35,17,22,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T1322A|1722|SIPA1L2|protein_coding|CODING|NM_020808.4|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94209 rs2275307 -0.69312 0.825237 91 S112 1722 tcT/tcC LOW 1 SILENT CODING SIPA1L2 G protein_coding NM_020808.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232650750 A G 0 222 0 0.9917 0.8351 0.8429 0.504 0.9463 0.8446 0.983366 0.948408 0.931424 1 9690 105177 8956 3961 5775 62034 787 13974 2 9824 120750 11570 8594 6614 66734 902 16512 0.996833 0 . 0 . 121 31,26,27,27 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S112|1722|SIPA1L2|protein_coding|CODING|NM_020808.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.344334 rs3795366 -0.693147 0.844128 121 F128 1047 ttC/ttT LOW 1 SILENT CODING MAP10 T protein_coding NM_019090.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232941153 C T 0 228 0 0.084 0.5274 0.5879 0.6607 0.7097 0.7587 0.190476 0.531032 0.689186 2 1482 76857 6797 5417 4699 45395 598 12469 2 8978 117564 11274 8412 6484 65104 874 16438 0 . 0 . 0 71 0,0,26,40 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F128|1047|MAP10|protein_coding|CODING|NM_019090.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12409898 -0.693147 0.00674742 71 1047 656 MODIFIER 1 CODING MAP10 T protein_coding NM_019090.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 232944569 C T 0 228 0 0.1717 0.5615 0.6671 0.6677 0.7376 0.7229 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,48,40 UTR_3_PRIME(MODIFIER||656||1047|MAP10|protein_coding|CODING|NM_019090.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1845789 -0.693147 0.0208957 95 R4P 1036 cGg/cCg MODERATE 1 MISSENSE CODING KIAA1804 C protein_coding NM_032435.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233463785 G C 0 9.7 0 0.0847 0.1008 0.0793 0.0665 0.1133 0.1605 0 . 0 1 7 53 4 1 0 28 2 11 2 12 110 10 2 2 60 4 20 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R4P|1036|KIAA1804|protein_coding|CODING|NM_032435.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs78916182 -0.379885 0 1 T12 1036 acC/acG LOW 1 SILENT CODING KIAA1804 G protein_coding NM_032435.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233463810 C G 0 32.6 0 0 0.0242 0.0202 0.0635 0.003 0.0409 0 . 0 2 0 16 4 6 1 1 1 3 2 20 222 16 28 2 80 6 70 0 . 0 . 0 2 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T12|1036|KIAA1804|protein_coding|CODING|NM_032435.2|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs199635611 -0.379885 0 2 E54D 1036 gaG/gaC MODERATE 1 MISSENSE CODING KIAA1804 C protein_coding NM_032435.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233463936 G C 0 127 0 0 0.0242 0.0202 0.0635 0.003 0.0409 0 . 0 2 0 297 5 18 0 8 4 262 2 176 8706 82 134 4 2034 90 6186 0 . 0 . 0 7 0,0,7,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E54D|1036|KIAA1804|protein_coding|CODING|NM_032435.2|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs189326455 -0.636426 0.629475 7 V257 1036 gtG/gtC LOW 1 SILENT CODING KIAA1804 C protein_coding NM_032435.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233464545 G C 0 228 0 0 0.0242 0.0202 0.0635 0.003 0.0409 0.000772002 0.000257998 0 2 2 758 114 261 5 26 10 340 2 1774 21810 1164 1720 394 9172 202 7384 1 0 . 0 . 31 0,1,24,2 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V257|1036|KIAA1804|protein_coding|CODING|NM_032435.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs79952117 -0.692976 0.306251 31 1036 225 MODIFIER 10 CODING KIAA1804 A protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233518682 G A 0 125 0 0.5038 0.4147 0.3761 0.4048 0.4026 0.3446 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||225||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1294236 -0.636426 0.834632 7 1036 296 MODIFIER 10 CODING KIAA1804 C protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233518753 T C 0 165 0 0.5121 0.4171 0.3761 0.4048 0.4036 0.3446 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,21,0 UTR_3_PRIME(MODIFIER||296||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1294235 -0.692352 0.273302 21 1036 428 MODIFIER 10 CODING KIAA1804 C protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233518885 T C 0 228 0 0.798 0.6801 0.6931 0.748 0.494 0.6329 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0045079 0 . 0 . 86 7,0,54,16 UTR_3_PRIME(MODIFIER||428||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.0748559 rs1294234 -0.693147 0.000527398 86 1036 541 MODIFIER 10 CODING KIAA1804 T protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233518998 C T 0 228 0 0.5045 0.4143 0.3761 0.4048 0.4026 0.3415 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 232 1,0,138,58 UTR_3_PRIME(MODIFIER||541||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1294233,rs386526669 -0.693147 0.8279 232 1036 820 MODIFIER 10 CODING KIAA1804 G protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233519277 A G 0 165 0 0.5121 0.4169 0.3775 0.4048 0.4026 0.3436 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,18 UTR_3_PRIME(MODIFIER||820||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1294232 -0.691153 0.00856894 18 1036 936 MODIFIER 10 CODING KIAA1804 T protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233519393 C T 0 39.3 0 0.8003 0.7061 0.7262 0.748 0.5755 0.6554 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||936||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1294231 -0.453602 0.48 2 1036 1368 MODIFIER 10 CODING KIAA1804 T protein_coding NM_032435.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233519825 C T 0 9.7 0 0.5045 0.4141 0.3761 0.4048 0.4016 0.3415 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1368||1036|KIAA1804|protein_coding|CODING|NM_032435.2|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1294230 -0.379885 0 1 336 63 MODIFIER 1 CODING KCNK1 G protein_coding NM_002245.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 233749855 A G 0 9.7 0 0.6914 0.6755 0.6686 0.744 0.674 0.59 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||63||336|KCNK1|protein_coding|CODING|NM_002245.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2795294 -0.379885 0 1 490 82 MODIFIER 1 CODING SLC35F3 C protein_coding NM_173508.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234040742 A C 0 96 0 0.4304 0.4495 0.3098 0.4464 0.4831 0.5429 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935451 0 . 0 . 12 5,0,7,0 UTR_5_PRIME(MODIFIER||82||490|SLC35F3|protein_coding|CODING|NM_173508.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 0 . 0.935451 rs12136133 -0.636426 0.903975 12 S32 490 tcC/tcT LOW 2 SILENT CODING SLC35F3 T protein_coding NM_173508.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234041317 C T 0 222 0 0.0015 0.0589 0.0346 0.1508 0.0258 0.093 0.00544712 0.0189912 0.0259302 1 59 5023 360 1363 90 1654 45 1452 2 10002 118418 11446 8480 6160 64998 878 16454 0.706826 0 . 0 . 137 43,24,47,13 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S32|490|SLC35F3|protein_coding|CODING|NM_173508.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.614072 rs79244900 -0.693147 0.0277473 137 P67 490 ccG/ccC LOW 2 SILENT CODING SLC35F3 C protein_coding NM_173508.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234041422 G C 0 222 0 0.4387 0.4507 0.3127 0.4474 0.4742 0.544 0.453019 0.496309 0.518488 1 4672 58708 3200 3777 3392 34057 435 9175 2 10368 120978 11554 8596 6606 66448 902 16504 0.650743 0 . 0 . 153 40,30,32,33 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P67|490|SLC35F3|protein_coding|CODING|NM_173508.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.242948 rs57010808 -0.693147 0.00131967 153 S16T 155 aGt/aCt MODERATE 1 MISSENSE CODING COA6 C protein_coding NM_001206641.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234509259 G C 0 228 0 0.8865 0.6064 0.6614 0.4871 0.495 0.4264 0 . 0 2 6574 54627 6556 3635 2652 27891 382 6937 2 7744 97760 9752 6822 5840 52202 736 14664 0.852299 0 . 0 . 165 3,2,101,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S16T|155|COA6|protein_coding|CODING|NM_001206641.2|1|C),INTRAGENIC(MODIFIER|||||LOC101927765||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.346828 rs10910420 -0.693147 0.142987 165 A1425 1621 gcG/gcA LOW 27 SILENT CODING TARBP1 T protein_coding NM_005646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234529552 C T 0 228 0 0.6225 0.51 0.5692 0.495 0.4384 0.4049 0.588743 0.486775 0.434535 2 6114 55656 6728 4310 2988 28633 377 6506 2 10358 121140 11560 8630 6610 66590 906 16486 0 . 0 . 0 57 0,0,18,33 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1425|1621|TARBP1|protein_coding|CODING|NM_005646.3|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2175594 -0.693147 0.665772 57 V1419 1621 gtC/gtT LOW 27 SILENT CODING TARBP1 A protein_coding NM_005646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234529570 G A 0 228 0 0.6089 0.504 0.5677 0.494 0.4334 0.3998 0.567635 0.474858 0.427326 2 5944 54900 6694 4308 2939 28210 374 6431 2 10316 120942 11562 8630 6608 66480 904 16442 0 . 0 . 0 47 0,0,12,32 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V1419|1621|TARBP1|protein_coding|CODING|NM_005646.3|27|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2175593 -0.693146 0.0114196 47 T1246 1621 acG/acA LOW 23 SILENT CODING TARBP1 T protein_coding NM_005646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234546245 C T 0 222 0 0.211 0.3371 0.3847 0.3958 0.3907 0.3579 0.240227 0.336207 0.385358 1 2322 43772 4338 3604 2304 25255 314 5635 2 10032 120316 11508 8602 6586 66192 898 16498 0.890534 0 . 0 . 204 50,42,49,36 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1246|1621|TARBP1|protein_coding|CODING|NM_005646.3|23|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.493109 rs1141264 -0.693147 0.509896 204 1621 LOW 19 CODING TARBP1 C protein_coding NM_005646.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234563060 T C 0 222 0 0.4773 0.4151 0.2723 0.4464 0.335 0.4826 0.450954 0.388 0.355747 1 4711 44078 3396 3686 2106 22310 304 7565 2 10320 118978 11362 8558 6542 65016 894 16286 0.845007 0 . 0 . 78 26,13,17,10 SPLICE_SITE_REGION+INTRON(LOW||||1621|TARBP1|protein_coding|CODING|NM_005646.3|19|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959674 rs443685 -0.693021 0.00099315 78 S678G 1621 Agt/Ggt MODERATE 12 MISSENSE CODING TARBP1 C protein_coding NM_005646.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234582651 T C 0 222 0 0.3101 0.3031 0.3804 0.3036 0.2932 0.2485 0.329551 0.291865 0.272558 1 3458 36298 5005 2716 2028 18564 290 4237 2 10406 121350 11550 8632 6614 66728 908 16512 0.912924 0 . 0 . 69 7,24,13,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S678G|1621|TARBP1|protein_coding|CODING|NM_005646.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.67504 rs4920246 -0.693132 0.0169935 69 Q652 1621 caG/caA LOW 11 SILENT CODING TARBP1 T protein_coding NM_005646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234584231 C T 0 222 0 0.2564 0.2871 0.3732 0.3036 0.2893 0.2485 0.284839 0.274489 0.269186 1 2980 35392 4932 2700 1969 18298 285 4228 2 10380 121154 11498 8626 6612 66628 908 16502 0.956383 0 . 0 . 95 26,18,19,18 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q652|1621|TARBP1|protein_coding|CODING|NM_005646.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.773988 rs2102596 -0.693141 0.170843 95 H345 1621 caT/caC LOW 3 SILENT CODING TARBP1 G protein_coding NM_005646.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234606998 A G 0 222 0 0.1157 0.2939 0.2522 0.749 0.0487 0.3476 0.112903 0.0684129 0.0455817 1 1169 19826 3506 6512 894 3079 138 4528 2 10020 119820 11500 8640 6568 65798 898 16396 0.760394 0 . 0 . 150 37,24,39,20 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H345|1621|TARBP1|protein_coding|CODING|NM_005646.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.830775 rs3754307 -0.693147 0.00103712 150 S51N 1621 aGc/aAc MODERATE 1 MISSENSE CODING TARBP1 T protein_coding NM_005646.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234614698 C T 0 39.3 0 0.1831 0.0891 0.0634 0.0804 0.0249 0.0552 0.0961538 0.0378634 0.0140476 2 43 508 9 16 0 66 2 372 2 148 5066 64 102 0 1080 40 3632 0 . 0 . 0 2 0,0,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S51N|1621|TARBP1|protein_coding|CODING|NM_005646.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs941965 -0.453602 0.48 2 L331 587 Ctg/Ttg LOW 1 SILENT CODING IRF2BP2 A protein_coding NM_182972.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234744250 G A 0 222 0 0.0129 0.1358 0.1398 0.2034 0.2455 0.1166 0.0452067 0.16782 0.230581 1 346 22117 1330 1778 1614 15278 160 1611 2 8032 103904 10544 7766 5286 58562 738 12976 0.934263 0 . 0 . 90 19,14,26,23 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L331|587|IRF2BP2|protein_coding|CODING|NM_182972.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.869187 rs8722 -0.693147 0.324855 90 A276 587 gcG/gcT LOW 1 SILENT CODING IRF2BP2 A protein_coding NM_182972.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234744413 C A 0 179 0 0.1619 0.2608 0.2896 0.2083 0.4185 0.2658 0.156724 0.282225 0.342409 1 556 16881 1412 762 629 10628 113 2781 2 1868 38790 3514 2032 1268 21624 266 8218 0.544635 0 . 0 . 24 1,8,1,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A276|587|IRF2BP2|protein_coding|CODING|NM_182972.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.733432 rs4636 -0.686358 0.0643404 24 S78P 587 Tcg/Ccg MODERATE 1 MISSENSE CODING IRF2BP2 G protein_coding NM_182972.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 234745009 A G 0 52 0 0.8729 0.6038 0.549 0.2679 0.7734 0.4509 0 . 0 1 25 970 8 2 16 174 9 736 2 30 1524 14 10 20 232 14 1204 0.89338 0 . 0 . 10 5,0,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcg/Ccg|S78P|587|IRF2BP2|protein_coding|CODING|NM_182972.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.974597 0 . 0.649731 rs7545855 -0.556411 0.314313 10 500 1201 MODIFIER 12 CODING B3GALNT2 T protein_coding NM_152490.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235612320 C T 0 64 0 0.9735 0.7446 0.719 0.6756 0.6481 0.6237 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1201||500|B3GALNT2|protein_coding|CODING|NM_152490.4|12|T),DOWNSTREAM(MODIFIER||37||578|TBCE|protein_coding|CODING|NM_001287801.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs704705 -0.511536 0.235765 3 500 LOW 4 CODING B3GALNT2 T protein_coding NM_152490.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235647631 G T 0 228 0 0.5893 0.6783 0.7104 0.8403 0.5129 0.7791 0.564685 0.520913 0.498488 2 5881 70760 8939 7440 3150 32848 511 11991 2 10400 121022 11542 8642 6614 66538 904 16382 0 . 0 . 0 53 0,0,41,7 SPLICE_SITE_REGION+INTRON(LOW||||500|B3GALNT2|protein_coding|CODING|NM_152490.4|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs291387 -0.693147 0.295847 53 E107 500 gaA/gaG LOW 3 SILENT CODING B3GALNT2 C protein_coding NM_152490.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235652513 T C 0 228 0 0.5893 0.6787 0.7104 0.8413 0.5139 0.7791 0.564685 0.520913 0.498488 2 5883 70880 8958 7447 3150 32908 511 12023 2 10406 121374 11572 8650 6610 66718 908 16510 0 . 0 . 0 139 0,0,60,59 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E107|500|B3GALNT2|protein_coding|CODING|NM_152490.4|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs291396 -0.693147 0.00984513 139 500 138 MODIFIER 1 CODING B3GALNT2 G protein_coding NM_152490.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235667690 A G 0 9.7 0 0.5946 0.6787 0.7075 0.8433 0.507 0.7791 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||138||500|B3GALNT2|protein_coding|CODING|NM_152490.4|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs291348 -0.379885 0 1 500 190 MODIFIER 1 CODING B3GALNT2 T protein_coding NM_152490.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235667742 G T 0 9.7 0 0.0492 0.2254 0.3055 0.4831 0.0577 0.3139 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||190||500|B3GALNT2|protein_coding|CODING|NM_152490.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs75700660 -0.379885 0 1 75 4003 MODIFIER 4 CODING GNG4 A protein_coding NM_001098721.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235711406 G A 0 6.3 0 0.4047 0.5583 0.6239 0.8244 0.5606 0.4427 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4003||75|GNG4|protein_coding|CODING|NM_001098721.1|4|A),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10925973 -0.379885 0 1 75 2622 MODIFIER 4 CODING GNG4 T protein_coding NM_001098721.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235712787 C T 0 46.3 0 0.4395 0.5729 0.6297 0.8194 0.5547 0.4775 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2622||75|GNG4|protein_coding|CODING|NM_001098721.1|4|T),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10754679 -0.453602 0.22 2 75 1247 MODIFIER 4 CODING GNG4 A protein_coding NM_001098721.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235714162 G A 0 9.7 0 0.5658 0.4461 0.3905 0.6766 0.2028 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1247||75|GNG4|protein_coding|CODING|NM_001098721.1|4|A),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12756717 -0.379885 0 1 75 380 MODIFIER 4 CODING GNG4 A protein_coding NM_001098721.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235715029 G A 0 39.3 0 0.298 0.3788 0.4813 0.6647 0.1571 0.3487 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||380||75|GNG4|protein_coding|CODING|NM_001098721.1|4|A),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs923942 -0.453602 0.28 2 75 345 MODIFIER 4 CODING GNG4 T protein_coding NM_001098721.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235715064 A T 0 39.3 0 0.9713 0.8023 0.7983 0.8373 0.6819 0.6646 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||345||75|GNG4|protein_coding|CODING|NM_001098721.1|4|T),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs589175 -0.453602 0.52 2 A38 75 gcT/gcC LOW 4 SILENT CODING GNG4 G protein_coding NM_001098721.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235715523 A G 0 228 0 0.5893 0.6312 0.6599 0.8383 0.495 0.5941 0.598275 0.539136 0.508837 2 6214 70573 8270 7444 4076 34554 525 9490 2 10396 121356 11576 8652 6612 66700 908 16512 0 . 0 . 0 82 0,0,27,50 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A38|75|GNG4|protein_coding|CODING|NM_001098721.1|4|G),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs14326 -0.693147 0.174692 82 75 LOW 2 CODING GNG4 G protein_coding NM_001098721.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 235747154 A G 0 228 0 0.3722 0.4948 0.5231 0.7996 0.3767 0.4479 0.375624 0.364601 0.358953 2 3801 53587 7011 6952 3542 24695 406 7180 2 10400 121258 11572 8648 6612 66672 906 16448 0 . 0 . 0 86 0,0,32,44 SPLICE_SITE_REGION+INTRON(LOW||||75|GNG4|protein_coding|CODING|NM_001098721.1|2|G),INTRAGENIC(MODIFIER|||||MIR5096||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2774336 -0.693147 0.0675677 86 1247 2026 MODIFIER 20 CODING NID1 T protein_coding NM_002508.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236139141 A T 0 222 0 0.2814 0.3143 0.245 0.6121 0.1441 0.2761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.758217 0 . 0 . 102 36,10,30,11 UTR_3_PRIME(MODIFIER||2026||1247|NID1|protein_coding|CODING|NM_002508.2|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0723894 rs4660135 -0.693145 0.233686 102 1247 1736 MODIFIER 20 CODING NID1 A protein_coding NM_002508.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236139431 G A 0 97 0 0 0.0015974 0.0029 0.006 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868815 0 . 0 . 15 2,7,1,5 UTR_3_PRIME(MODIFIER||1736||1247|NID1|protein_coding|CODING|NM_002508.2|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.939413 rs184667370 -0.616816 0.177551 15 1247 901 MODIFIER 20 CODING NID1 C protein_coding NM_002508.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236140266 A C 0 9.7 0 0.5499 0.39 0.2781 0.6131 0.1441 0.2761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||901||1247|NID1|protein_coding|CODING|NM_002508.2|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1048253 -0.379885 0 1 Q1246R 1247 cAg/cGg MODERATE 20 MISSENSE CODING NID1 C protein_coding NM_002508.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236141174 T C 0 164 0 0.385 0.3442 0.2608 0.6131 0.1451 0.2761 0.349296 0.233969 0.174884 1 3700 28772 2946 5187 970 11527 213 4229 2 10400 121216 11568 8638 6606 66652 906 16446 0.90464 0 . 0 . 54 19,8,23,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1246R|1247|NID1|protein_coding|CODING|NM_002508.2|20|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.86652 rs3213190 -0.692717 0.121497 54 L1063 1247 Ttg/Ctg LOW 16 SILENT CODING NID1 G protein_coding NM_002508.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236144951 A G 0 222 0 0.3555 0.3345 0.2579 0.6151 0.1402 0.271 0.336133 0.22751 0.17186 1 3533 28454 2904 5196 969 11372 206 4274 2 10404 121272 11566 8638 6614 66670 906 16474 0.985137 0 . 0 . 92 18,23,31,11 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L1063|1247|NID1|protein_coding|CODING|NM_002508.2|16|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997669 rs3738525 -0.693146 0.511636 92 1247 LOW 13 CODING NID1 T protein_coding NM_002508.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236154365 G T 0 202 0 0.382 0.3478 0.2608 0.6429 0.1412 0.272 0.370631 0.239736 0.172674 1 3742 26582 2756 5157 883 10804 192 3048 2 9598 102308 9974 8184 5406 58298 752 10096 0.576555 0 . 0 . 86 16,32,3,31 SPLICE_SITE_REGION+INTRON(LOW||||1247|NID1|protein_coding|CODING|NM_002508.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.857109 rs4660137 -0.693132 0.000410686 86 Q807H 1247 caG/caT MODERATE 12 MISSENSE CODING NID1 A protein_coding NM_002508.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236175327 C A 0 222 0 0.1104 0.1945 0.3127 0.2589 0.0885 0.2669 0.110077 0.102337 0.0983721 1 1100 20054 3827 2411 1253 6994 141 4328 2 10400 121148 11522 8612 6548 66662 906 16498 0.4482 0 . 0 . 89 10,26,17,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q807H|1247|NID1|protein_coding|CODING|NM_002508.2|12|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.913442 0.962967 0 0.833042 rs3738531 -0.693146 0.172897 89 V803 1247 gtA/gtG LOW 12 SILENT CODING NID1 C protein_coding NM_002508.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236175339 T C 0 228 0 0.795 0.6967 0.6427 0.7698 0.5 0.729 0.760554 0.585115 0.495233 2 7949 71591 8110 6605 4116 33340 522 10949 2 10388 121024 11526 8636 6592 66474 904 16504 0 . 0 . 0 80 0,0,20,54 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V803|1247|NID1|protein_coding|CODING|NM_002508.2|12|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.970805 0 . rs2031487 -0.693147 0.00334877 80 1247 LOW 9 CODING NID1 G protein_coding NM_002508.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236180580 C G 0 228 0 0.3585 0.4044 0.4366 0.6706 0.1093 0.4724 0.331366 0.188528 0.115349 2 3473 32400 6188 5907 1504 8111 222 6995 2 10292 120836 11544 8600 6604 66402 906 16488 0 . 0 . 0 42 0,0,9,30 SPLICE_SITE_REGION+INTRON(LOW||||1247|NID1|protein_coding|CODING|NM_002508.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3768081 -0.693144 0.912096 42 1247 LOW 9 CODING NID1 C protein_coding NM_002508.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236187365 T C 0 222 0 0.2103 0.2348 0.3343 0.2728 0.1193 0.2771 0.200409 0.151238 0.126047 1 2030 23402 4004 2510 1309 8773 180 4596 2 10394 120980 11546 8624 6608 66544 908 16356 0.700495 0 . 0 . 160 37,22,50,30 SPLICE_SITE_REGION+INTRON(LOW||||1247|NID1|protein_coding|CODING|NM_002508.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.435671 rs3738533 -0.693147 0.176839 160 V246I 1247 Gtt/Att MODERATE 3 MISSENSE CODING NID1 T protein_coding NM_002508.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236208773 C T 0 228 0 0.6369 0.5873 0.5562 0.7063 0.4334 0.5777 0.616659 0.493311 0.430116 2 6435 58918 6732 5871 2449 28040 400 8991 2 10396 121290 11562 8634 6612 66676 908 16502 0 . 0 . 0 191 0,0,98,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V246I|1247|NID1|protein_coding|CODING|NM_002508.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10733133 -0.693147 0.0143021 191 399 373 MODIFIER 7 CODING GPR137B C protein_coding NM_003272.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236371831 T C 0 222 0 0.4841 0.2686 0.2824 0.2073 0.1342 0.1687 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974389 0 . 0 . 106 22,30,25,21 UTR_3_PRIME(MODIFIER||373||399|GPR137B|protein_coding|CODING|NM_003272.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996358 rs5873 -0.693147 0.0517945 106 467 3146 MODIFIER 16 CODING ERO1B A protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236378670 T A 0 9.7 0 0.5371 0.2776 0.2767 0.2083 0.1133 0.1677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3146||467|ERO1B|protein_coding|CODING|NM_019891.3|16|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12046588 -0.379885 0 1 467 2900 MODIFIER 16 CODING ERO1B C protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236378916 T C 0 9.7 0 0.5371 0.2837 0.2853 0.2083 0.1362 0.1697 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2900||467|ERO1B|protein_coding|CODING|NM_019891.3|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1111667 -0.379885 0 1 467 2667 MODIFIER 16 CODING ERO1B C protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236379149 A C 0 9.7 0 0.1278 0.3187 0.3357 0.626 0.2604 0.3078 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2667||467|ERO1B|protein_coding|CODING|NM_019891.3|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2449 -0.379885 0 1 467 1205 MODIFIER 16 CODING ERO1B T protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236380611 C T 0 185 0 0.4887 0.5723 0.5793 0.8849 0.4046 0.5307 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,22,1 UTR_3_PRIME(MODIFIER||1205||467|ERO1B|protein_coding|CODING|NM_019891.3|16|T) 0 . 0 . 0 1 0 . 0 . 57 0 0 1 0 . rs1726631 -0.692717 0.140581 23 467 1072 MODIFIER 16 CODING ERO1B G protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236380744 T G 0 228 0 0.4909 0.5741 0.5821 0.878 0.4085 0.5378 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 69 0,0,49,9 UTR_3_PRIME(MODIFIER||1072||467|ERO1B|protein_coding|CODING|NM_019891.3|16|G) 0 . 0 . 0 1 0 . 0 . 56 0 0 0.928008 0 . rs2950396 -0.693147 0.348408 69 467 903 MODIFIER 16 CODING ERO1B C protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236380913 T C 0 228 0 0.4803 0.5699 0.5821 0.8869 0.3996 0.5307 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 92 0,0,35,48 UTR_3_PRIME(MODIFIER||903||467|ERO1B|protein_coding|CODING|NM_019891.3|16|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.889418 0 . rs1749596 -0.693147 0.01609 92 467 467 MODIFIER 16 CODING ERO1B G protein_coding NM_019891.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236381349 C G 0 9.7 0 0.4803 0.5691 0.5821 0.8829 0.4006 0.5297 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||467||467|ERO1B|protein_coding|CODING|NM_019891.3|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1726630 -0.379885 0 1 H465Q 467 caC/caG MODERATE 16 MISSENSE CODING ERO1B C protein_coding NM_019891.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236381825 G C 0 228 0 0.4803 0.5693 0.5821 0.8839 0.4006 0.5297 0.488176 0.431327 0.402126 2 4970 59376 7953 7615 3127 27115 413 8183 2 10196 119676 11366 8582 6550 65804 896 16282 1 0 . 0 . 173 1,0,100,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H465Q|467|ERO1B|protein_coding|CODING|NM_019891.3|16|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1055851 -0.693147 0.0109479 173 S251 467 tcG/tcA LOW 11 SILENT CODING ERO1B T protein_coding NM_019891.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236389999 C T 0 222 0 0.1006 0.144 0.0778 0.373 0.0318 0.1288 0.0938636 0.0512623 0.029446 1 952 9226 968 3341 179 1932 62 1792 2 10080 120852 11552 8634 6606 66572 904 16504 0.489444 0 . 0 . 193 51,51,36,26 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S251|467|ERO1B|protein_coding|CODING|NM_019891.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.601145 rs10924790 -0.693147 0.0246763 193 467 LOW 4 CODING ERO1B C protein_coding NM_019891.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236415347 T C 0 222 0 0.1929 0.2608 0.3112 0.3968 0.2475 0.1902 0.194734 0.229202 0.24686 1 2089 32564 4005 3463 2297 17311 242 3157 2 10392 121240 11544 8642 6610 66654 908 16490 0.908778 0 . 0 . 233 52,33,54,54 SPLICE_SITE_REGION+INTRON(LOW||||467|ERO1B|protein_coding|CODING|NM_019891.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841273 rs1749589 -0.693147 0.00030006 233 467 129 MODIFIER 1 CODING ERO1B G protein_coding NM_019891.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236445212 A G 0 77 0 0.8911 0.9657 0.9827 0.999 1 0.9847 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_5_PRIME(MODIFIER||129||467|ERO1B|protein_coding|CODING|NM_019891.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2764567 -0.511536 0.588406 3 M9I 215 atG/atA MODERATE 1 MISSENSE CODING EDARADD A protein_coding NM_145861.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236557771 G A 0 228 0 0.4682 0.7768 0.8631 0.9187 0.825 0.9366 0.540399 0.738352 0.839767 2 5549 100864 10569 7954 5355 55579 770 15088 2 10406 121406 11578 8654 6614 66736 906 16512 0 . 0 . 0 130 0,0,70,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M9I|215|EDARADD|protein_coding|CODING|NM_145861.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs966365 -0.693147 0.0296099 130 E20 215 gaG/gaA LOW 1 SILENT CODING EDARADD A protein_coding NM_145861.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236557804 G A 0 222 0 0.0015 0.0911 0.0605 0.3065 0.002 0.1033 0.00476623 0.00615101 0.00686046 1 52 5341 999 2687 75 438 38 1052 2 10406 121374 11576 8646 6614 66714 908 16510 0.822891 0 . 0 COSM146829 118 18,34,21,27 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E20|215|EDARADD|protein_coding|CODING|NM_145861.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.433122 rs60808129 -0.693147 0.236902 118 D123 215 gaC/gaT LOW 6 SILENT CODING EDARADD T protein_coding NM_145861.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236645670 C T 0 222 0 0.0545 0.1332 0.1095 0.1062 0.2753 0.138 0.080345 0.189682 0.245698 1 731 24568 1170 771 1917 17313 212 2454 2 10406 121388 11576 8644 6612 66732 908 16510 0.502218 0 . 0 . 133 33,38,22,25 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D123|215|EDARADD|protein_coding|CODING|NM_145861.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.221182 rs604070 -0.693147 0.520491 133 F19Y 359 tTt/tAt MODERATE 4 MISSENSE CODING LGALS8 A protein_coding NM_006499.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236700807 T A 0 222 0 0.4448 0.4998 0.5072 0.4762 0.6759 0.4121 0.493191 0.618407 0.682558 1 5056 73566 5927 4197 4840 45262 544 7740 2 10390 120552 11492 8614 6592 66238 900 16326 0.527869 0 . 0 COSM146350 120 61,11,29,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F19Y|359|LGALS8|protein_coding|CODING|NM_006499.4|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.110919 rs1126407 -0.693144 0.430636 120 P24 359 ccT/ccC LOW 4 SILENT CODING LGALS8 C protein_coding NM_006499.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236700823 T C 0 222 0 0.4455 0.5 0.5072 0.4762 0.6759 0.4121 0.492283 0.618022 0.682442 1 5060 73707 5927 4205 4848 45367 546 7754 2 10394 120828 11506 8620 6602 66414 902 16390 0.999767 0 . 0 COSM146830 136 58,16,35,11 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P24|359|LGALS8|protein_coding|CODING|NM_006499.4|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986975 rs1041934 -0.693147 0.870117 136 R36C 359 Cgt/Tgt MODERATE 4 MISSENSE CODING LGALS8 T protein_coding NM_006499.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236700857 C T 0 222 0 0.4455 0.5 0.5072 0.4762 0.6759 0.4121 0.493418 0.61833 0.682326 1 5056 73790 5951 4216 4846 45428 546 7747 2 10394 120870 11518 8632 6592 66472 900 16362 0.923276 0 . 0 COSM146351 156 53,27,34,23 PROTEIN_INTERACTION_LOCUS(HIGH||||359|LGALS8|protein_coding|CODING||4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R36C|359|LGALS8|protein_coding|CODING|NM_006499.4|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0676451 rs1041935 -0.693147 0.00412449 156 S55 359 agC/agT LOW 5 SILENT CODING LGALS8 T protein_coding NM_006499.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236702209 C T 0 222 0 0.2231 0.4171 0.464 0.4732 0.6014 0.3988 0.278711 0.479932 0.583023 1 2973 66020 5511 4143 4285 41147 497 7464 2 10386 120840 11488 8614 6558 66400 906 16488 0.902739 0 . 0 COSM146831 74 20,11,24,14 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S55|359|LGALS8|protein_coding|CODING|NM_006499.4|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738813 rs1041936 -0.693143 0.538855 74 M56V 359 Atg/Gtg MODERATE 5 MISSENSE CODING LGALS8 G protein_coding NM_006499.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236702210 A G 0 228 0 0.6657 0.6304 0.6311 0.6577 0.7048 0.4775 0.679755 0.697524 0.706628 2 7072 81612 7240 5462 4864 47526 601 8847 2 10390 120838 11482 8620 6552 66390 906 16498 0 . 0 . COSM146352 72 0,0,43,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M56V|359|LGALS8|protein_coding|CODING|NM_006499.4|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1041937 -0.693147 0.708157 72 L110 359 ctG/ctA LOW 5 SILENT CODING LGALS8 A protein_coding NM_006499.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236702374 G A 0 222 0 0.2738 0.4333 0.464 0.4752 0.6173 0.3947 0.411257 0.566123 0.645465 1 3405 67781 5616 4208 4539 42073 499 7441 2 10400 121368 11576 8642 6610 66730 904 16506 0.925403 0 . 0 . 68 15,20,10,16 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L110|359|LGALS8|protein_coding|CODING|NM_006499.4|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982188 rs2472126 -0.692976 0.227076 68 D205Y 359 Gat/Tat MODERATE 9 MISSENSE CODING LGALS8 T protein_coding NM_006499.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236706278 G T 0 222 0 0.2209 0.1312 0.1225 0.1806 0.0318 0.0675 0.193827 0.09165 0.0393023 1 2029 8232 1370 1270 78 2315 56 1114 2 10402 121396 11578 8646 6614 66738 908 16510 0.971137 0 . 0 . 100 23,28,29,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D205Y|359|LGALS8|protein_coding|CODING|NM_006499.4|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.497758 rs2273863 -0.693147 0.197049 100 L212* 359 tTg/tAg HIGH 9 NONSENSE CODING LGALS8 A protein_coding NM_006499.4 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236706300 T A 0 222 0 0.2209 0.1312 0.1225 0.1806 0.0318 0.0675 0.193827 0.09165 0.0393023 1 2029 8227 1364 1270 78 2316 56 1114 2 10402 121388 11576 8648 6614 66730 908 16510 0.0513273 0 . 0 . 102 22,23,32,16 STOP_GAINED(HIGH|NONSENSE|tTg/tAg|L212*|359|LGALS8|protein_coding|CODING|NM_006499.4|9|A) 1 0.5 1 0 . 1 0 1 1 (LGALS8|LGALS8|1|1.00) 60 0 1 1 (LGALS8|LGALS8|1|1.00) 0.735322 rs2273865 -0.693147 0.561749 102 R226S 359 agG/agC MODERATE 10 MISSENSE CODING LGALS8 C protein_coding NM_006499.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236706862 G C 0 228 0 0.7005 0.6777 0.7622 0.6865 0.7396 0.5143 0.722651 0.742657 0.752907 2 7441 87147 8973 5678 5083 49832 640 9500 2 10380 121244 11562 8618 6606 66674 904 16500 0 . 0 . 0 102 0,0,76,20 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|agG/agC|R226S|359|LGALS8|protein_coding|CODING|NM_006499.4|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2243525 -0.693147 0.00258981 102 Y314 359 taT/taC LOW 12 SILENT CODING LGALS8 C protein_coding NM_006499.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711323 T C 0 222 0 0.4448 0.5004 0.5101 0.4772 0.6759 0.4121 0.492737 0.618176 0.682442 1 5056 74039 5977 4241 4855 45598 546 7766 2 10396 121284 11572 8636 6612 66674 904 16490 0.611887 0 . 0 . 99 36,13,31,8 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y314|359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),DOWNSTREAM(MODIFIER||982||2144|HEATR1|protein_coding|CODING|NM_018072.5||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.867406 rs15701 -0.693144 0.437679 99 359 125 MODIFIER 12 CODING LGALS8 A protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711586 G A 0 103 0 0.4448 0.5002 0.5086 0.4772 0.6759 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 1,4,1,5 UTR_3_PRIME(MODIFIER||125||359|LGALS8|protein_coding|CODING|NM_006499.4|12|A),DOWNSTREAM(MODIFIER||719||2144|HEATR1|protein_coding|CODING|NM_018072.5||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.297172 rs1160 -0.616816 0.503448 11 359 157 MODIFIER 12 CODING LGALS8 C protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711618 A C 0 64 0 0.2216 0.138 0.1225 0.1806 0.0318 0.1012 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.562708 0 . 0 . 11 1,6,1,3 UTR_3_PRIME(MODIFIER||157||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),DOWNSTREAM(MODIFIER||687||2144|HEATR1|protein_coding|CODING|NM_018072.5||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.643095 rs1041939 -0.556411 0.95353 11 359 349 MODIFIER 12 CODING LGALS8 G protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711810 A G 0 70 0 0.6906 0.6817 0.7622 0.6855 0.7406 0.5481 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||349||359|LGALS8|protein_coding|CODING|NM_006499.4|12|G),DOWNSTREAM(MODIFIER||495||2144|HEATR1|protein_coding|CODING|NM_018072.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2758997 -0.453602 0.82 3 359 490 MODIFIER 12 CODING LGALS8 A protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711951 T A 0 9.7 0 0.4463 0.5006 0.5086 0.4772 0.6759 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||490||359|LGALS8|protein_coding|CODING|NM_006499.4|12|A),DOWNSTREAM(MODIFIER||354||2144|HEATR1|protein_coding|CODING|NM_018072.5||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1041942 -0.379885 0 1 359 495 MODIFIER 12 CODING LGALS8 C protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711956 A C 0 9.7 0 0.4463 0.5006 0.5086 0.4772 0.6759 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||495||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),DOWNSTREAM(MODIFIER||349||2144|HEATR1|protein_coding|CODING|NM_018072.5||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1041943 -0.379885 0 1 359 520 MODIFIER 12 CODING LGALS8 T protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236711981 C T 0 39.3 0 0.4455 0.5004 0.5086 0.4772 0.6759 0.4121 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||520||359|LGALS8|protein_coding|CODING|NM_006499.4|12|T),DOWNSTREAM(MODIFIER||324||2144|HEATR1|protein_coding|CODING|NM_018072.5||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1041944 -0.453602 0.52 2 359 2367 MODIFIER 12 CODING LGALS8 A protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236713828 G A 0 39.3 0 0.4334 0.4974 0.5101 0.4772 0.6759 0.4121 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2367||359|LGALS8|protein_coding|CODING|NM_006499.4|12|A),UTR_3_PRIME(MODIFIER||374||2144|HEATR1|protein_coding|CODING|NM_018072.5|45|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2758998 -0.453602 0.52 2 2144 374 MODIFIER 45 CODING HEATR1 A protein_coding NM_018072.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236713828 G A 0 39.3 0 0.4334 0.4974 0.5101 0.4772 0.6759 0.4121 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2367||359|LGALS8|protein_coding|CODING|NM_006499.4|12|A),UTR_3_PRIME(MODIFIER||374||2144|HEATR1|protein_coding|CODING|NM_018072.5|45|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2758998 -0.453602 0.52 2 359 2603 MODIFIER 12 CODING LGALS8 C protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236714064 A C 0 222 0 0.4342 0.497 0.5086 0.4762 0.675 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.553388 0 . 0 . 68 25,2,26,6 UTR_3_PRIME(MODIFIER||2603||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),UTR_3_PRIME(MODIFIER||138||2144|HEATR1|protein_coding|CODING|NM_018072.5|45|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.243358 rs6989 -0.69312 0.311177 68 2144 138 MODIFIER 45 CODING HEATR1 C protein_coding NM_018072.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236714064 A C 0 222 0 0.4342 0.497 0.5086 0.4762 0.675 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.553388 0 . 0 . 68 25,2,26,6 UTR_3_PRIME(MODIFIER||2603||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),UTR_3_PRIME(MODIFIER||138||2144|HEATR1|protein_coding|CODING|NM_018072.5|45|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.243358 rs6989 -0.69312 0.311177 68 359 3455 MODIFIER 12 CODING LGALS8 C protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236714916 T C 0 46.4 0 0.4448 0.5002 0.5086 0.4772 0.6759 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 1,1,3,0 UTR_3_PRIME(MODIFIER||3455||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),INTRON(MODIFIER||||2144|HEATR1|protein_coding|CODING|NM_018072.5|44|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.833333 rs2540 -0.511536 0.220755 6 359 4056 MODIFIER 12 CODING LGALS8 C protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236715517 T C 0 154 0 0.4334 0.4972 0.5086 0.4772 0.6759 0.4121 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994015 0 . 0 . 43 1,22,1,19 UTR_3_PRIME(MODIFIER||4056||359|LGALS8|protein_coding|CODING|NM_006499.4|12|C),INTRON(MODIFIER||||2144|HEATR1|protein_coding|CODING|NM_018072.5|43|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.60755 rs3189 -0.692067 0.815301 43 359 4249 MODIFIER 12 CODING LGALS8 A protein_coding NM_006499.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236715710 G A 0 31.3 0 0.2194 0.4263 0.4741 0.4772 0.6362 0.4039 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,2,0,3 UTR_3_PRIME(MODIFIER||4249||359|LGALS8|protein_coding|CODING|NM_006499.4|12|A),INTRON(MODIFIER||||2144|HEATR1|protein_coding|CODING|NM_018072.5|43|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2758999 -0.511536 0.354794 5 S2053 2144 tcG/tcA LOW 43 SILENT CODING HEATR1 T protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236716959 C T 0 222 0 0.3865 0.4846 0.5072 0.4772 0.6759 0.4121 0.442805 0.601261 0.682442 1 4477 73477 5958 4239 4856 45629 547 7771 2 10406 121354 11566 8640 6608 66716 908 16510 0.652599 0 . 0 COSM146832 106 26,27,22,22 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S2053|2144|HEATR1|protein_coding|CODING|NM_018072.5|43|T),DOWNSTREAM(MODIFIER||680||359|LGALS8|protein_coding|CODING|NM_006499.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.725736 rs2275685 -0.693146 0.210314 106 E2017G 2144 gAa/gGa MODERATE 42 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236717926 T C 0 222 0 0.3865 0.4848 0.5086 0.4772 0.6759 0.4121 0.442805 0.601415 0.682674 1 4476 73503 5960 4239 4855 45651 548 7774 2 10396 121364 11576 8638 6614 66722 908 16510 0.909689 0 . 0 . 67 16,10,23,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E2017G|2144|HEATR1|protein_coding|CODING|NM_018072.5|42|C),DOWNSTREAM(MODIFIER||1647||359|LGALS8|protein_coding|CODING|NM_006499.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991792 rs2275687 -0.693139 0.0326297 67 2144 LOW 41 CODING HEATR1 T protein_coding NM_018072.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236718060 C T 0 222 0 0.2148 0.1226 0.1153 0.1766 0.0169 0.0562 0.185656 0.0715055 0.0130233 1 1944 6197 1258 1222 23 790 42 918 2 10264 120566 11550 8632 6608 66430 904 16178 0.856859 0 . 0 . 87 14,30,13,20 SPLICE_SITE_REGION+INTRON(LOW||||2144|HEATR1|protein_coding|CODING|NM_018072.5|41|T),DOWNSTREAM(MODIFIER||1781||359|LGALS8|protein_coding|CODING|NM_006499.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.762744 rs73113054 -0.693127 0.403088 87 N1967D 2144 Aac/Gac MODERATE 41 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236718620 T C 0 222 0 0.3858 0.4848 0.5086 0.4782 0.6759 0.4121 0.443032 0.601492 0.682674 1 4476 73509 5963 4243 4855 45652 548 7772 2 10404 121334 11578 8642 6614 66716 908 16472 0.970545 0 . 0 . 81 24,14,25,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N1967D|2144|HEATR1|protein_coding|CODING|NM_018072.5|41|C),DOWNSTREAM(MODIFIER||2341||359|LGALS8|protein_coding|CODING|NM_006499.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.301432 rs1126627 -0.693144 0.593636 81 E1873 2144 gaA/gaG LOW 39 SILENT CODING HEATR1 C protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236719135 T C 0 228 0 0.8775 0.873 0.8833 0.9593 0.8022 0.8436 0.87744 0.840766 0.821977 2 9111 102147 10629 8322 5580 54103 737 13665 2 10406 121400 11576 8652 6610 66736 908 16512 0 . 0 . 0 62 0,0,25,36 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E1873|2144|HEATR1|protein_coding|CODING|NM_018072.5|39|C),DOWNSTREAM(MODIFIER||2856||359|LGALS8|protein_coding|CODING|NM_006499.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1885532 -0.693147 0.611492 62 V1854A 2144 gTg/gCg MODERATE 39 MISSENSE CODING HEATR1 G protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236719193 A G 0 222 0 0.3865 0.485 0.5086 0.4782 0.6759 0.4121 0.442805 0.601415 0.682674 1 4477 73506 5958 4236 4855 45659 548 7773 2 10404 121388 11574 8642 6614 66736 908 16510 0.426293 0 . 0 . 88 17,24,24,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V1854A|2144|HEATR1|protein_coding|CODING|NM_018072.5|39|G),DOWNSTREAM(MODIFIER||2914||359|LGALS8|protein_coding|CODING|NM_006499.4||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.451654 rs1885533 -0.693141 0.294579 88 L1711 2144 Ctg/Ttg LOW 36 SILENT CODING HEATR1 A protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236721610 G A 0 227 0 0.6074 0.6148 0.6297 0.6538 0.7078 0.4785 0.636632 0.692911 0.721744 2 6516 81677 7332 5455 4929 47961 604 8880 2 10402 121350 11574 8622 6604 66732 908 16508 0 . 0 . 0 46 0,0,44,2 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1711|2144|HEATR1|protein_coding|CODING|NM_018072.5|36|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275688 -0.693147 0.504717 46 N1694S 2144 aAc/aGc MODERATE 36 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236721660 T C 0 228 0 0.702 0.6773 0.7622 0.6825 0.7406 0.5133 0.723332 0.742888 0.752907 2 7472 87239 8986 5646 5091 49905 641 9498 2 10406 121390 11576 8642 6612 66736 906 16512 1 0 . 0 . 90 0,1,71,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1694S|2144|HEATR1|protein_coding|CODING|NM_018072.5|36|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2275689 -0.693147 0.00107867 90 A1670 2144 gcA/gcG LOW 36 SILENT CODING HEATR1 C protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236721731 T C 0 228 0 0.9985 0.9996 1 1 1 1 0.996142 0.998693 1 2 10362 121355 11576 8653 6614 66730 908 16512 2 10406 121406 11578 8654 6614 66734 908 16512 0 . 0 . 0 160 0,0,89,52 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1670|2144|HEATR1|protein_coding|CODING|NM_018072.5|36|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs819431 -0.693147 0.0092952 160 D1570E 2144 gaC/gaG MODERATE 34 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236723074 G C 0 222 0 0.0356 0.0685 0.0951 0.1756 0.0139 0.0399 0.0285974 0.0168384 0.010814 1 315 3993 1117 1222 21 690 26 602 2 10400 121352 11576 8630 6614 66718 908 16506 0.755978 0 . 0 . 138 24,35,34,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D1570E|2144|HEATR1|protein_coding|CODING|NM_018072.5|34|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.988644 0.986633 0 0.855626 rs77776078 -0.693147 0.123149 138 S1559N 2144 aGt/aAt MODERATE 34 MISSENSE CODING HEATR1 T protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236723108 C T 0 222 0 0.3684 0.1717 0.1398 0.1766 0.0328 0.0665 0.317068 0.133477 0.0394186 1 3356 9648 1463 1223 78 2351 62 1115 2 10386 121284 11570 8630 6614 66672 908 16504 0.891819 0 . 0 . 113 15,41,18,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S1559N|2144|HEATR1|protein_coding|CODING|NM_018072.5|34|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.983958 0.969597 0 0.407891 rs6661946 -0.693147 0.090301 113 2144 LOW 28 CODING HEATR1 A protein_coding NM_018072.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236732427 G A 0 222 0 0.0356 0.0675 0.0879 0.1756 0.0139 0.0399 0.0279165 0.0165334 0.0107002 1 311 3958 1109 1213 21 684 22 598 2 10038 117492 11352 8510 6550 64682 884 15476 0.939093 0 . 0 . 107 15,36,10,34 SPLICE_SITE_REGION+INTRON(LOW||||2144|HEATR1|protein_coding|CODING|NM_018072.5|28|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.656145 rs79830964 -0.693146 0.000363176 107 I1102T 2144 aTt/aCt MODERATE 23 MISSENSE CODING HEATR1 G protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236737983 A G 0 222 0 0.0356 0.0675 0.0879 0.1756 0.0139 0.0399 0.0283833 0.0166897 0.0107002 1 314 3974 1115 1227 21 673 23 601 2 10356 121082 11572 8648 6612 66520 908 16466 0.692372 0 . 0 . 94 29,13,22,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I1102T|2144|HEATR1|protein_coding|CODING|NM_018072.5|23|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.576128 rs79225714 -0.693143 0.170885 94 V855 2144 gtG/gtT LOW 20 SILENT CODING HEATR1 A protein_coding NM_018072.5 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236744712 C A 0 154 0 0.1316 0.4147 0.4957 0.4762 0.671 0.4131 0.217204 0.521452 0.677326 1 2051 66384 5730 4165 4767 43780 499 5392 2 9842 112584 11404 8478 6584 64434 838 11004 0.560575 0 . 0 COSM146833 31 3,16,2,9 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtT|V855|2144|HEATR1|protein_coding|CODING|NM_018072.5|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.573571 rs4518892 -0.676189 0.0336882 31 V765 2144 gtG/gtA LOW 18 SILENT CODING HEATR1 T protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236746443 C T 0 228 0 0.3003 0.5186 0.5922 0.6518 0.6849 0.453 0.367907 0.580271 0.68907 2 3686 75695 6995 5448 4807 45801 564 8394 2 10394 121360 11576 8638 6614 66734 906 16498 0 . 0 . 0 98 0,0,64,29 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V765|2144|HEATR1|protein_coding|CODING|NM_018072.5|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2794768 -0.693147 0.0644806 98 L711 2144 ctC/ctT LOW 17 SILENT CODING HEATR1 A protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236748433 G A 0 222 0 0.0703 0.0883 0.1052 0.1756 0.0527 0.047 0.0628688 0.0556666 0.0519767 1 660 7367 1339 1223 92 3141 52 860 2 10368 121238 11568 8622 6614 66656 908 16502 0.789103 0 . 0 . 84 17,16,22,15 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L711|2144|HEATR1|protein_coding|CODING|NM_018072.5|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990889 rs3738535 -0.693141 0.0974395 84 L687 2144 ttA/ttG LOW 17 SILENT CODING HEATR1 C protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236748505 T C 0 228 0 0.3003 0.5186 0.5922 0.6518 0.6849 0.453 0.368134 0.580194 0.688837 2 3663 75437 6975 5432 4803 45620 563 8381 2 10264 120742 11532 8596 6604 66420 902 16424 0 . 0 . 0 49 0,0,9,37 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L687|2144|HEATR1|protein_coding|CODING|NM_018072.5|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1006456 -0.693147 0.303524 49 T614 2144 acG/acA LOW 15 SILENT CODING HEATR1 T protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236749626 C T 0 222 0 0.0703 0.0891 0.1052 0.1766 0.0557 0.047 0.0628688 0.0556068 0.0518846 1 659 7361 1338 1220 91 3143 51 859 2 10260 121116 11550 8628 6606 66670 906 16496 0.424926 0 . 0 . 91 25,15,28,13 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T614|2144|HEATR1|protein_coding|CODING|NM_018072.5|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.279631 rs3738541 -0.693145 0.222138 91 M607V 2144 Atg/Gtg MODERATE 15 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236749649 T C 0 222 0 0.0348 0.369 0.464 0.4712 0.6223 0.3875 0.127326 0.456167 0.62468 1 1157 65060 5504 4219 4693 41772 498 7217 2 10294 121210 11564 8630 6602 66708 908 16504 0.990175 0 . 0 . 98 28,19,24,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M607V|2144|HEATR1|protein_coding|CODING|NM_018072.5|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.437393 rs2794763,rs386573897 -0.693145 0.0737031 98 A580T 2144 Gct/Act MODERATE 15 MISSENSE CODING HEATR1 T protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236749730 C T 0 222 0 0.0454 0.0701 0.0879 0.1756 0.0139 0.0399 0.0365577 0.0195355 0.0108165 1 398 4053 1110 1222 21 677 23 602 2 10152 120854 11564 8634 6610 66612 904 16378 0.356868 0 . 0 . 75 8,23,10,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A580T|2144|HEATR1|protein_coding|CODING|NM_018072.5|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.613083 rs60920266 -0.693143 0.647155 75 L535 2144 ttG/ttA LOW 13 SILENT CODING HEATR1 T protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236751269 C T 0 222 0 0.0356 0.0673 0.0879 0.1756 0.0139 0.0389 0.0283704 0.0166128 0.0105863 1 314 3953 1105 1217 21 676 22 598 2 10374 120952 11504 8616 6590 66518 904 16446 0.989952 0 . 0 . 142 48,28,28,17 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L535|2144|HEATR1|protein_coding|CODING|NM_018072.5|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.695207 rs78459283 -0.693147 0.0750642 142 R430 2144 agG/agA LOW 10 SILENT CODING HEATR1 T protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236755837 C T 0 228 0 0.329 0.5595 0.6009 0.7242 0.6998 0.5276 0.386612 0.601728 0.71192 2 3238 61044 5900 5357 4135 33908 473 8033 2 8436 95144 9794 7486 5702 48730 738 14258 0 . 0 . COSM146834 149 0,0,52,75 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R430|2144|HEATR1|protein_coding|CODING|NM_018072.5|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2564739 -0.693147 0.000599327 149 H348R 2144 cAt/cGt MODERATE 8 MISSENSE CODING HEATR1 C protein_coding NM_018072.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236758887 T C 0 228 0 0.329 0.5595 0.6009 0.7242 0.6998 0.5276 0.391058 0.605567 0.715465 2 3922 79301 7121 6281 4861 47266 589 9261 2 10372 121090 11534 8602 6606 66576 906 16494 0.592105 0 . 0 . 172 1,1,81,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H348R|2144|HEATR1|protein_coding|CODING|NM_018072.5|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.930921 rs2794751 -0.693147 0.0620978 172 S22 2144 tcT/tcC LOW 2 SILENT CODING HEATR1 G protein_coding NM_018072.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236767330 A G 0 228 0 0.329 0.5833 0.7205 0.752 0.6928 0.5429 0.398547 0.601338 0.705233 2 3996 80780 8528 6475 4950 46759 598 9474 2 10402 121328 11568 8628 6614 66698 908 16510 0 . 0 . 0 145 0,0,66,58 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S22|2144|HEATR1|protein_coding|CODING|NM_018072.5|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10802551 -0.693147 0.608375 145 I117 894 atT/atC LOW 3 SILENT CODING ACTN2 C protein_coding NM_001103.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236882303 T C 0 228 0 0.975 0.9926 0.9957 1 0.999 1 0.977531 0.992234 0.999767 2 10169 121158 11567 8654 6614 66734 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 2|2,2 benign|benign,benign 0 . 133 0,0,49,75 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I117|894|ACTN2|protein_coding|CODING|NM_001103.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1341864 -0.693147 0.00119156 133 N126 894 aaC/aaT LOW 4 SILENT CODING ACTN2 T protein_coding NM_001103.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236883421 C T 0 228 0 0.8139 0.9207 0.8559 0.9831 0.996 0.9693 0.825238 0.937721 0.995349 2 8516 116845 9978 8491 6527 66425 886 16022 2 10406 121412 11578 8654 6614 66740 908 16512 0 2|2|2|2,2 benign|benign|benign|benign,benign 0 . 106 0,0,71,27 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N126|894|ACTN2|protein_coding|CODING|NM_001103.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1341863 -0.693147 0.000589705 106 894 LOW 9 CODING ACTN2 G protein_coding NM_001103.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236902594 C G 0 228 0 0.764 0.7676 0.7853 0.7837 0.7753 0.7352 0.779846 0.777487 0.776279 2 8104 94042 8637 6912 5340 51695 718 12636 2 10340 121304 11574 8646 6612 66714 908 16510 0 2,2|2 benign,benign|benign 0 . 34 0,0,19,14 SPLICE_SITE_REGION+INTRON(LOW||||894|ACTN2|protein_coding|CODING|NM_001103.3|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2288601 -0.693127 0.219071 34 S870 894 tcG/tcA LOW 21 SILENT CODING ACTN2 A protein_coding NM_001103.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236925844 G A 0 222 0 0.2057 0.1961 0.1729 0.2183 0.171 0.2025 0.187926 0.155697 0.139186 1 1992 20422 2325 1602 1458 9623 138 3284 2 10380 120974 11526 8614 6568 66492 898 16496 0.970054 2|2 benign|benign 0 . 91 16,30,20,21 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S870|894|ACTN2|protein_coding|CODING|NM_001103.3|21|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0745304 rs12063382 -0.693145 0.0180658 91 894 111 MODIFIER 21 CODING ACTN2 G protein_coding NM_001103.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236926030 A G 0 19.9 0 0.0287 0.3498 0.5231 0.3532 0.5586 0.4427 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.809011 0 . 0 . 9 1,5,0,3 UTR_3_PRIME(MODIFIER||111||894|ACTN2|protein_coding|CODING|NM_001103.3|21|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 1 0 0.231146 rs1051251 -0.511536 0.5 9 894 748 MODIFIER 21 CODING ACTN2 G protein_coding NM_001103.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 236926667 A G 0 6.3 0 0.031 0.3992 0.5893 0.4167 0.6531 0.4826 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||748||894|ACTN2|protein_coding|CODING|NM_001103.3|21|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7522310 -0.379885 0 1 A1048 1265 gcA/gcG LOW 29 SILENT CODING MTR G protein_coding NM_000254.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237054569 A G 0 222 0 0.149 0.3233 0.4323 0.4276 0.3857 0.3098 0.198366 0.340535 0.413372 1 2020 46528 5204 3862 2967 26757 356 5362 2 10404 121386 11574 8642 6614 66732 908 16512 0.469743 2 benign 0 . 61 10,20,10,18 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1048|1265|MTR|protein_coding|CODING|NM_000254.2|29|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.119379 rs2229276 -0.693054 0.485633 61 R1164 1265 cgC/cgA LOW 31 SILENT CODING MTR A protein_coding NM_000254.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237058744 C A 0 222 0 0.1543 0.3215 0.438 0.4196 0.3857 0.2975 0.207217 0.341664 0.410561 1 1588 35927 4011 3153 1888 20749 265 4273 2 6592 82978 7978 6654 3526 45342 596 12290 0.790095 2 benign 0 . 68 26,13,14,10 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R1164|1265|MTR|protein_coding|CODING|NM_000254.2|31|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999099 rs12070777 -0.692831 0.599375 68 L1192 1265 ctC/ctT LOW 31 SILENT CODING MTR T protein_coding NM_000254.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237058828 C T 0 222 0 0.4342 0.5292 0.5922 0.5198 0.5358 0.6155 0.466136 0.546064 0.587043 1 2771 37861 4064 2643 1582 19704 278 6819 2 5394 61138 6074 4352 2288 31950 440 10640 0.780783 2 benign 0 COSM425684 79 18,21,15,16 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1192|1265|MTR|protein_coding|CODING|NM_000254.2|31|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.642894 rs1131449 -0.69311 0.262668 79 1265 112 MODIFIER 33 CODING MTR C protein_coding NM_000254.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237061056 A C 0 222 0 0.438 0.5401 0.6124 0.5258 0.5596 0.6217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868595 0 . 0 . 46 12,13,10,5 UTR_3_PRIME(MODIFIER||112||1265|MTR|protein_coding|CODING|NM_000254.2|33|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.993776 rs2853522 -0.688148 0.400989 46 1265 3682 MODIFIER 33 CODING MTR G protein_coding NM_000254.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237064626 T G 0 43.3 0 0.4402 0.5397 0.6124 0.5238 0.5606 0.6176 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,2,0,3 UTR_3_PRIME(MODIFIER||3682||1265|MTR|protein_coding|CODING|NM_000254.2|33|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.666667 rs6676866 -0.511536 0.771809 5 S453 4967 agC/agT LOW 15 SILENT CODING RYR2 T protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237617757 C T 0 228 0 0.2769 0.5357 0.5447 0.7391 0.5994 0.6043 0.32141 0.511932 0.60051 2 2989 69363 6897 6331 3954 39384 522 9286 2 9800 120522 11446 8594 6606 66670 898 16508 0 2 benign 0 . 118 0,0,52,55 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S453|4967|RYR2|protein_coding|CODING|NM_001035.2|15|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3765097 -0.693147 0.991625 118 S991 4967 tcA/tcG LOW 26 SILENT CODING RYR2 G protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237711797 A G 0 228 0 0.5378 0.8303 0.951 0.872 0.9583 0.9652 0.620313 0.851108 0.958454 2 5863 111675 11055 7601 6420 63958 853 15925 2 9782 120576 11546 8590 6612 66668 898 16480 0 2 benign 0 . 146 0,0,83,49 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S991|4967|RYR2|protein_coding|CODING|NM_001035.2|26|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2253273 -0.693147 0.111891 146 K1800 4967 aaA/aaG LOW 37 SILENT CODING RYR2 G protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237777828 A G 0 222 0 0.1233 0.0623 0.0245 0.0635 0.001 0.0685 0.0995872 0.0326373 0.00132722 1 1050 2537 77 681 0 47 11 671 2 9768 120642 11554 8618 6614 66678 900 16510 0.902857 2 benign 0 . 83 12,31,20,15 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1800|4967|RYR2|protein_coding|CODING|NM_001035.2|37|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.709301 rs3820216 -0.693136 0.0199191 83 G1886S 4967 Ggc/Agc MODERATE 37 MISSENSE CODING RYR2 A protein_coding NM_001035.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237778084 G A 0 222 0 0.1551 0.0763 0.0303 0.0635 0.0268 0.0665 0.128943 0.0628451 0.0311223 1 1341 5099 200 674 149 1994 30 711 2 9464 116288 11410 8516 6600 64970 850 14478 0.38009 2|2 benign|benign 0 . 48 8,10,11,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1886S|4967|RYR2|protein_coding|CODING|NM_001035.2|37|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82746 rs3766871 -0.692914 0.74991 48 L2302 4967 ctT/ctC LOW 45 SILENT CODING RYR2 C protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237801770 T C 0 228 0 0.8359 0.9549 0.987 1 1 1 0.870639 0.959206 0.999391 2 8495 119368 11516 8626 6612 66718 892 16509 2 9802 120770 11576 8626 6614 66740 900 16512 0 2 benign 0 . 127 0,0,44,75 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L2302|4967|RYR2|protein_coding|CODING|NM_001035.2|45|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs707189 -0.693147 0.164037 127 H2602 4967 caC/caT LOW 51 SILENT CODING RYR2 T protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237814783 C T 0 228 0 0.4864 0.5549 0.5029 0.7956 0.4324 0.5624 0.483406 0.450733 0.436082 2 2839 31367 2474 3739 1975 14894 234 5212 2 5498 60342 4382 4740 3874 31430 478 9940 0 2 benign 0 . 52 0,0,16,30 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H2602|4967|RYR2|protein_coding|CODING|NM_001035.2|51|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386605488,rs684923 -0.693147 0.140791 52 S3106 4967 tcT/tcG LOW 65 SILENT CODING RYR2 G protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237863718 T G 0 228 0 0.888 0.9692 0.9914 1 1 1 0.911312 0.971824 0.999514 2 8473 115037 10869 8442 6426 64405 868 15554 2 9332 116000 10920 8442 6426 64442 872 15566 0 2 benign 0 . 119 0,0,38,67 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S3106|4967|RYR2|protein_coding|CODING|NM_001035.2|65|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2797436 -0.693147 0.00633244 119 T3501 4967 acC/acT LOW 73 SILENT CODING RYR2 T protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237881770 C T 0 228 0 0.8555 0.9605 0.9899 1 1 1 0.877446 0.961616 0.999511 2 8502 119064 11471 8606 6614 66530 890 16451 2 9766 120438 11526 8606 6614 66566 896 16464 0 2 benign 0 . 134 0,0,70,47 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T3501|4967|RYR2|protein_coding|CODING|NM_001035.2|73|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2797441 -0.693147 0.728489 134 S3592 4967 tcC/tcT LOW 76 SILENT CODING RYR2 T protein_coding NM_001035.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237890437 C T 0 228 0 0.8548 0.9603 0.9899 1 1 1 0.875405 0.960779 0.99951 2 8531 119296 11459 8624 6614 66681 894 16493 2 9800 120680 11518 8624 6614 66718 900 16506 0 2 benign 0 . 139 0,0,72,45 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S3592|4967|RYR2|protein_coding|CODING|NM_001035.2|76|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2685301 -0.693147 0.118032 139 4967 LOW 94 CODING RYR2 G protein_coding NM_001035.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237957161 A G 0 228 0 0.5688 0.7576 0.804 0.9494 0.6501 0.8926 0.590255 0.651379 0.678501 2 5630 85204 9259 7808 4610 43385 621 13891 2 9448 115158 10976 8270 6440 63122 858 16044 0 2 benign 0 . 69 0,0,45,17 SPLICE_SITE_REGION+INTRON(LOW||||4967|RYR2|protein_coding|CODING|NM_001035.2|94|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs790901 -0.693147 0.623304 69 4967 129 MODIFIER 105 CODING RYR2 G protein_coding NM_001035.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237996076 C G 0 184 0 0.0938 0.0485 0.0159 0.0397 0.0199 0.0491 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924849 0 . 0 . 32 1,15,2,13 UTR_3_PRIME(MODIFIER||129||4967|RYR2|protein_coding|CODING|NM_001035.2|105|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.984304 rs16835891 -0.688148 0.70368 32 4967 1307 MODIFIER 105 CODING RYR2 T protein_coding NM_001035.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 237997254 C T 0 163 0 0.379 0.242 0.111 0.2639 0.0775 0.2965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,0,15 UTR_3_PRIME(MODIFIER||1307||4967|RYR2|protein_coding|CODING|NM_001035.2|105|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs16835904 -0.688148 0.157895 15 T140A 540 Act/Gct MODERATE 4 MISSENSE CODING ZP4 C protein_coding NM_021186.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 238051793 T C 0 222 0 0 0.0053914 0 0.0268 0 0 0 . 0 1 0 263 2 261 0 0 0 0 2 10402 120916 11574 8642 6614 66568 898 16218 0.998963 0 . 0 . 135 30,29,23,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T140A|540|ZP4|protein_coding|CODING|NM_021186.3|4|C),INTRAGENIC(MODIFIER|||||LOC100130331||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.985296 rs141504911 -0.693147 0.78607 135 1726 207 MODIFIER 1 CODING FMN2 T protein_coding NM_001305424.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240255203 G T 0 163 0 0.0908 0.3333 0.3372 0.3016 0.5348 0.4836 0 . 0 1 8 121 6 2 4 79 4 18 2 40 238 8 4 4 142 4 36 0.629414 0 . 0 . 27 3,8,1,15 START_GAINED(LOW||||1726|FMN2|protein_coding|CODING|NM_001305424.1|1|T),UTR_5_PRIME(MODIFIER||207||1726|FMN2|protein_coding|CODING|NM_001305424.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.989102 rs12727981 -0.689466 0.000449413 27 A471 1726 gcC/gcA LOW 1 SILENT CODING FMN2 A protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240256822 C A 0 222 0 0.09 0.3299 0.3357 0.3006 0.5249 0.4796 0.163479 0.39721 0.517527 1 1334 50785 4203 2612 2857 31624 374 7781 2 7664 106306 10700 7758 6028 59136 768 14252 0.576299 0 . 0 . 65 7,17,7,27 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A471|1726|FMN2|protein_coding|CODING|NM_001305424.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.576299 rs10926124 -0.693132 0.136802 65 G945A 1726 gGa/gCa MODERATE 6 MISSENSE CODING FMN2 C protein_coding NM_001305424.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240370934 G C 0 89 0 0.3616 0.2766 0.1902 0.3115 0.2276 0.2372 0 . 0 1 51 454 13 19 20 270 4 77 2 4396 68014 8380 4448 4092 37080 442 9176 0.999481 0 . 0 COSM1502036 58 16,27,5,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gCa|G945A|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|C) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.870716 0.999961 0 0.0461091 rs4997328 -0.676189 0.000489651 58 G945 1726 ggA/ggC LOW 6 SILENT CODING FMN2 C protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240370935 A C 0 6.3 0 . 0 . 0 . 0 . 0 . 1 0 50 5 2 2 38 2 1 2 4478 67870 8376 4450 4084 36912 442 9128 0.421293 0 . 0 . 58 17,29,3,5 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G945|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|C) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.308331 0.999358 0 0.006419 rs188083977 -0.651104 0.0719087 58 P947 1726 ccT/ccC LOW 6 SILENT CODING FMN2 C protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240370941 T C 0 152 0 0.357 0.2746 0.1902 0.3105 0.2286 0.2331 0.0866822 0.0603557 0.0469862 1 47 470 17 22 24 286 5 69 2 4328 67410 8364 4442 4082 36520 436 9238 0.981361 0 . 0 COSM1340567 52 11,21,7,8 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P947|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.188876 1 0 0.454862 rs4997329 -0.688148 0.978464 52 P949L 1726 cCg/cTg MODERATE 6 MISSENSE CODING FMN2 T protein_coding NM_001305424.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240370946 C T 0 22.4 0 . 0 . 0 . 0 . 0 . 1 0 44 2 2 2 37 1 0 2 4302 66748 8294 4418 4066 36118 432 9118 0.859336 0 . 0 COSM425735 49 15,23,2,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P949L|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|T) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.335462 0.999418 0 0.00102796 rs193049501 -0.651104 0.00108242 49 P962L 1726 cCt/cTt MODERATE 6 MISSENSE CODING FMN2 T protein_coding NM_001305424.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240370985 C T 0 164 0 . 0 . 0 . 0 . 0 . 1 1217 22278 1322 1724 1094 13805 208 2908 2 9342 113432 11342 8362 6418 62512 838 14618 0.965852 0 . 0 . 38 7,12,4,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P962L|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|T) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.430803 0.524909 0 0.896947 rs111896385 -0.680642 0.0768001 38 P992L 1726 cCt/cTt MODERATE 6 MISSENSE CODING FMN2 T protein_coding NM_001305424.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240371075 C T 0 44.6 0 . 0 . 0 . 0 . 0 . 1 1012 8908 627 711 456 5160 82 860 2 5236 75404 9414 5782 4230 40698 522 9522 0.544711 0 . 0 . 18 2,8,1,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P992L|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|T) 0 0.5 1 0 . 0 . 0 1 0 56 0 1 0.91051 0 0.79702 rs71646825 -0.590765 0.029231 18 P995 1726 ccA/ccT LOW 6 SILENT CODING FMN2 T protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240371085 A T 0 14.5 0 0.2678 0.2053 0.1427 0.2054 0.1769 0.1943 0 . 0 1 854 7622 527 627 418 4277 74 845 2 4642 72394 9356 5552 4122 40120 480 8122 0.618783 0 . 0 . 16 2,8,0,5 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P995|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|T) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.655816 0.576923 0 0.983267 rs71646826 -0.590765 0.0588947 16 P1004 1726 ccG/ccT LOW 6 SILENT CODING FMN2 T protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240371112 G T 0 21.3 0 0.357 0.2678 0.1873 0.2927 0.2008 0.2474 0 . 0 1 338 4159 452 513 116 2412 19 309 2 2234 49736 7942 3920 2534 27738 284 5084 0.62023 0 . 0 COSM1127092 9 1,3,0,4 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1004|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|T) 0 0.5 1 0 . 1 0 . 1 0 40 0 0.868321 1 0 0.992367 rs71646889 -0.556411 0.851686 9 P1017 1726 ccT/ccA LOW 6 SILENT CODING FMN2 A protein_coding NM_001305424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240371151 T A 0 6.5 0 . 0 . 0 . 0 . 0 . 1 18 258 30 46 2 147 1 14 2 482 14158 2872 1032 416 8532 80 744 0.666667 0 . 0 . 5 0,2,1,2 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccA|P1017|1726|FMN2|protein_coding|CODING|NM_001305424.1|6|A) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.666667 1 0 0.333333 rs71646892 -0.511536 0.539554 5 R1472H 1726 cGt/cAt MODERATE 11 MISSENSE CODING FMN2 A protein_coding NM_001305424.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240492734 G A 0 222 0 0.3381 0.3209 0.3588 0.3185 0.2883 0.3067 0.313209 0.28779 0.274767 1 3266 36659 4541 2681 1741 18919 275 5236 2 10348 121106 11552 8618 6608 66588 908 16484 0.834078 0 . 0 . 51 13,14,7,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1472H|1726|FMN2|protein_coding|CODING|NM_001305424.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.779062 rs3795677 -0.691153 0.720792 51 1726 117 MODIFIER 19 CODING FMN2 G protein_coding NM_001305424.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240637571 A G 0 222 0 0.093 0.3001 0.4092 0.4851 0.326 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.749948 0 . 0 . 65 8,18,13,16 UTR_3_PRIME(MODIFIER||117||1726|FMN2|protein_coding|CODING|NM_001305424.1|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976271 rs111189604,rs882869 -0.693079 0.092707 65 168 1254 MODIFIER 2 CODING GREM2 T protein_coding NM_022469.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240655015 C T 0 222 0 0.4516 0.6182 0.6484 0.7907 0.6113 0.6513 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.975075 0 . 0 . 55 20,6,15,6 UTR_3_PRIME(MODIFIER||1254||168|GREM2|protein_coding|CODING|NM_022469.3|2|T),INTRAGENIC(MODIFIER|||||MIR1273E||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.680557 rs3748535 -0.692352 0.10079 55 168 939 MODIFIER 2 CODING GREM2 A protein_coding NM_022469.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240655330 G A 0 97 0 0.7269 0.7274 0.7075 0.8145 0.66 0.7219 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.94925 0 . 0 . 15 2,4,0,8 UTR_3_PRIME(MODIFIER||939||168|GREM2|protein_coding|CODING|NM_022469.3|2|A),INTRAGENIC(MODIFIER|||||MIR1273E||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs111175419,rs9287248 -0.651104 0.360182 15 487 LOW 14 CODING RGS7 C protein_coding NM_002924.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 240975213 T C 0 228 0 0.2148 0.4046 0.428 0.4683 0.5557 0.4233 0.272356 0.473547 0.576646 2 2640 61280 4734 3934 4197 38151 467 7157 2 10170 121096 11566 8636 6604 66702 908 16510 0 . 0 . COSM146839 98 0,0,57,32 SPLICE_SITE_REGION+INTRON(LOW||||487|RGS7|protein_coding|CODING|NM_002924.5|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275742 -0.693147 0.00313515 98 487 22 MODIFIER 2 CODING RGS7 A protein_coding NM_002924.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241519098 T A 0 228 0 0.8321 0.9483 0.9899 0.9921 0.9881 0.9898 0.882206 0.9511 0.986395 2 8938 118294 11436 8606 6577 65568 889 16280 2 10292 120974 11556 8636 6614 66500 902 16474 0 . 0 . 0 48 0,0,6,39 UTR_5_PRIME(MODIFIER||22||487|RGS7|protein_coding|CODING|NM_002924.5|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4659599 -0.693147 0.0133954 48 T393 486 acC/acA LOW 13 SILENT CODING KMO A protein_coding NM_003679.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241753394 C A 0 222 0 0 0.004393 0 0.0218 0 0 0 . 0 1 1 253 0 252 0 0 0 0 2 10406 121326 11574 8610 6608 66714 908 16506 0.269529 0 . 0 . 100 19,37,19,16 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T393|486|KMO|protein_coding|CODING|NM_003679.4|13|A),DOWNSTREAM(MODIFIER||3058||402|OPN3|protein_coding|CODING|NM_014322.2||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.707382 rs118152617 -0.693136 0.4643 100 I442M 486 atA/atG MODERATE 15 MISSENSE CODING KMO G protein_coding NM_003679.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241755320 A G 0 222 0 0 0.004393 0 0.0218 0 0 0 . 0 1 1 231 0 230 0 0 0 0 2 10406 121378 11574 8636 6612 66732 908 16510 0.148799 0 . 0 . 160 44,29,39,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I442M|486|KMO|protein_coding|CODING|NM_003679.4|15|G),DOWNSTREAM(MODIFIER||1132||402|OPN3|protein_coding|CODING|NM_014322.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.386642 rs117220986 -0.693147 0.524639 160 486 5 MODIFIER 15 CODING KMO G protein_coding NM_003679.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241755460 A G 0 222 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 25 0 25 0 0 0 0 2 9940 114268 10662 7860 6272 62738 842 15954 0.901227 0 . 0 . 154 29,43,11,50 UTR_3_PRIME(MODIFIER||5||486|KMO|protein_coding|CODING|NM_003679.4|15|G),DOWNSTREAM(MODIFIER||992||402|OPN3|protein_coding|CODING|NM_014322.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.82121 rs201483365 -0.693147 0.00630843 154 486 112 MODIFIER 15 CODING KMO C protein_coding NM_003679.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241755567 T C 0 35.8 0 0.0076 0.135 0.1023 0.255 0.1421 0.1994 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950129 0 . 0 . 24 2,17,0,5 UTR_3_PRIME(MODIFIER||112||486|KMO|protein_coding|CODING|NM_003679.4|15|C),DOWNSTREAM(MODIFIER||885||402|OPN3|protein_coding|CODING|NM_014322.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.441081 rs1053221 -0.590765 0.176043 24 S146 656 tcG/tcA LOW 1 SILENT CODING CHML T protein_coding NM_001821.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241798631 C T 0 222 0 0.2254 0.2766 0.2565 0.2232 0.3241 0.3661 0.256695 0.31821 0.349732 1 2634 39244 2514 2033 2624 23244 307 5888 2 10268 121116 11572 8642 6614 66618 908 16494 0.743397 0 . 0 COSM146840 40 10,5,17,4 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S146|656|CHML|protein_coding|CODING|NM_001821.3|1|T),INTRON(MODIFIER||||402|OPN3|protein_coding|CODING|NM_014322.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.336446 rs3737604 -0.692352 0.384584 40 1081 LOW 11 CODING WDR64 G protein_coding NM_144625.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241907691 A G 0 228 0 0.121 0.3504 0.4222 0.5119 0.3121 0.4826 0.152973 0.289405 0.359302 2 1577 45382 5609 4506 2066 23737 331 7556 2 10388 121258 11566 8630 6600 66666 906 16502 1 0 . 0 . 107 0,1,75,22 SPLICE_SITE_REGION+INTRON(LOW||||1081|WDR64|protein_coding|CODING|NM_144625.4|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7418599 -0.693147 0.227914 107 N521 1081 aaT/aaC LOW 12 SILENT CODING WDR64 C protein_coding NM_144625.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241907817 T C 0 228 0 0.8185 0.5909 0.572 0.5149 0.4672 0.502 0.774172 0.608488 0.523605 2 8196 64948 6633 4517 2667 34410 443 8082 2 10406 121304 11570 8626 6598 66692 906 16506 0 . 0 . 0 131 0,0,49,69 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N521|1081|WDR64|protein_coding|CODING|NM_144625.4|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10802990 -0.693147 0.0206409 131 1081 42 MODIFIER 27 CODING WDR64 T protein_coding NM_144625.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 241964559 C T 0 228 0 0.1899 0.3814 0.3934 0.4077 0.506 0.4765 0.228098 0.469014 0.592442 2 2156 57065 3953 3743 3133 35330 451 8299 2 10016 120320 11450 8556 6584 66336 904 16474 0 . 0 . 0 63 0,0,17,38 UTR_3_PRIME(MODIFIER||42||1081|WDR64|protein_coding|CODING|NM_144625.4|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4658661 -0.693147 0.0148135 63 H354R 846 cAt/cGt MODERATE 9 MISSENSE CODING EXO1 G protein_coding NM_006027.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242030151 A G 0 222 0 0.615 0.637 0.6902 0.7956 0.5716 0.5327 0.621652 0.56743 0.539651 1 6442 71974 8379 6918 4004 36834 533 8864 2 10404 121380 11570 8652 6612 66722 908 16512 0.992723 0 . 0 . 79 34,3,29,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H354R|846|EXO1|protein_coding|CODING|NM_006027.4|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.429191 rs735943 -0.693132 0.00568141 79 E589K 846 Gag/Aag MODERATE 11 MISSENSE CODING EXO1 A protein_coding NM_006027.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242042301 G A 0 222 0 0.4781 0.3516 0.3876 0.2312 0.3688 0.2618 0.475034 0.408734 0.374767 1 4984 43822 4234 1643 2697 25126 322 4816 2 10404 121390 11578 8646 6610 66734 906 16512 0.818277 0 . 0 COSM146843 75 15,19,15,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E589K|846|EXO1|protein_coding|CODING|NM_006027.4|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.484443 rs1047840 -0.693127 0.168805 75 E670G 846 gAg/gGg MODERATE 11 MISSENSE CODING EXO1 G protein_coding NM_006027.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242042545 A G 0 228 0 0.6884 0.6819 0.6859 0.8085 0.6511 0.5716 0.700409 0.655005 0.631744 2 7245 78749 8485 7020 4025 42156 585 9233 2 10376 119810 11552 8646 6610 66196 890 15540 0 . 0 . 0 38 0,0,19,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E670G|846|EXO1|protein_coding|CODING|NM_006027.4|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1776148 -0.69312 0.203333 38 R723C 846 Cgt/Tgt MODERATE 12 MISSENSE CODING EXO1 T protein_coding NM_006027.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242045275 C T 0 222 0 0.8714 0.9153 0.9784 0.869 0.9672 0.9243 0.885559 0.945197 0.97578 1 9121 115994 11311 7532 6552 65013 877 15588 2 10342 121286 11574 8650 6612 66690 908 16510 0.661202 0 . 0 . 101 26,15,21,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R723C|846|EXO1|protein_coding|CODING|NM_006027.4|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931964 rs1635498 -0.693144 0.0477593 101 S725 846 tcT/tcA LOW 12 SILENT CODING EXO1 A protein_coding NM_006027.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242045283 T A 0 222 0 0.003 0.0499 0.0159 0.131 0.0288 0.0757 0.00975942 0.0189318 0.0236376 1 99 4024 192 1117 59 1613 26 918 2 10244 120900 11552 8630 6602 66468 906 16498 0.336617 0 . 0 . 92 19,18,20,17 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S725|846|EXO1|protein_coding|CODING|NM_006027.4|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.440174 rs4149984 -0.693141 0.00998445 92 P757L 846 cCt/cTt MODERATE 13 MISSENSE CODING EXO1 T protein_coding NM_006027.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242048674 C T 0 222 0 0.1808 0.2516 0.3199 0.4683 0.1521 0.1779 0.18384 0.167384 0.158953 1 1927 24531 4669 3593 999 10387 183 2773 2 10292 120512 11450 8546 6602 66252 900 16470 0.879037 0 . 0 . 58 27,1,21,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P757L|846|EXO1|protein_coding|CODING|NM_006027.4|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.459426 rs9350 -0.692914 0.600206 58 536 132 MODIFIER 11 CODING PLD5 C protein_coding NM_152666.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242253024 T C 0 222 0 0.4523 0.3381 0.3069 0.2153 0.337 0.3333 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.133556 0 . 0 . 94 26,22,27,9 UTR_3_PRIME(MODIFIER||132||536|PLD5|protein_coding|CODING|NM_152666.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.75982 rs7523793 -0.693139 0.145061 94 H63 536 caC/caT LOW 2 SILENT CODING PLD5 A protein_coding NM_152666.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 242687390 G A 0 159 0 0.3684 0.2893 0.3141 0.1577 0.33 0.2587 0 . 0 1 190 3394 70 26 0 1206 33 1869 2 552 11804 186 196 2 3418 126 7324 0.151919 0 . 0 . 50 18,5,20,2 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H63|536|PLD5|protein_coding|CODING|NM_152666.2|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.742309 rs2810008 -0.692562 0.786924 50 T738I 1584 aCt/aTt MODERATE 13 MISSENSE CODING CEP170 A protein_coding NM_014812.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243329049 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 3047 39689 2065 3305 2740 23098 320 5114 2 9762 120524 11562 8616 6612 66572 898 16502 0.998533 0 . 0 . 292 89,89,39,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T738I|1584|CEP170|protein_coding|CODING|NM_014812.2|13|A) 0 0.5 1 0 . 0 . 0 1 0 53 0 2.89195e-15 0.297096 0 0.00101351 rs3766664 -0.693147 6.66824e-05 292 K729 1584 aaA/aaG LOW 13 SILENT CODING CEP170 C protein_coding NM_014812.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243329075 T C 0 53 0 . 0 . 0 . 0 . 0 . 1 2687 34103 1780 3016 2485 20184 272 3679 2 9582 116684 11310 8354 6342 64458 858 15780 0.563149 0 . 0 . 237 89,81,18,32 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K729|1584|CEP170|protein_coding|CODING|NM_014812.2|13|C) 0 0.5 1 0 . 0 . 0 1 0 50 0 8.77507e-14 0.890739 0 0.190941 rs61833876 -0.693147 0.000957539 237 G213S 1584 Ggc/Agc MODERATE 8 MISSENSE CODING CEP170 T protein_coding NM_014812.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243354791 C T 0 166 0 0.7428 0.8474 0.8386 0.9335 0.8787 0.8742 0 . 0 2 43 335 16 18 0 203 2 53 2 1348 9454 472 322 646 4818 76 1772 0 . 0 . 0 12 0,0,2,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G213S|1584|CEP170|protein_coding|CODING|NM_014812.2|8|T) 0 . 0 . 0 1 0 . 1 0 29 0 0 0.7 0 . rs144272877 -0.680642 0.15006 12 713 47 MODIFIER 1 CODING SDCCAG8 A protein_coding NM_006642.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243419429 T A 0 222 0 0.0635 0.4121 0.5548 0.7381 0.5209 0.3344 0.131185 0.384054 0.513605 1 1264 58792 7281 6290 3609 34182 458 5708 2 10376 121164 11542 8630 6604 66602 904 16506 0.519128 0 . 0 . 97 28,11,25,19 UTR_5_PRIME(MODIFIER||47||713|SDCCAG8|protein_coding|CODING|NM_006642.3|1|A),UPSTREAM(MODIFIER||721||1584|CEP170|protein_coding|CODING|NM_014812.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.665001 rs3904682 -0.693146 0.459115 97 E378D 713 gaA/gaT MODERATE 10 MISSENSE CODING SDCCAG8 T protein_coding NM_006642.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243493907 A T 0 222 0 0.1702 0.2714 0.2147 0.1935 0.3231 0.4755 0.19133 0.268184 0.307558 1 2004 36087 2241 1728 1822 20472 282 7538 2 10392 121278 11562 8642 6610 66654 908 16510 0.995636 0 . 0 . 141 35,36,36,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E378D|713|SDCCAG8|protein_coding|CODING|NM_006642.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.630189 rs2275155 -0.693147 0.0436489 141 E575 713 gaG/gaA LOW 14 SILENT CODING SDCCAG8 A protein_coding NM_006642.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 243579112 G A 0 222 0 0.0938 0.4395 0.5403 0.7847 0.498 0.4192 0.164321 0.392204 0.508954 1 1545 58624 6608 6524 3422 33267 437 6821 2 10184 119904 11270 8520 6568 66008 906 16448 0.910203 0 . 0 . 89 22,24,12,23 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E575|713|SDCCAG8|protein_coding|CODING|NM_006642.3|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.860483 rs10927011 -0.693136 0.153006 89 531 891 MODIFIER 2 CODING ZBTB18 G protein_coding NM_205768.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244219563 A G 0 228 0 0.9977 0.9992 1 1 1 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 86 0,0,35,40 UTR_3_PRIME(MODIFIER||891||531|ZBTB18|protein_coding|CODING|NM_205768.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2486536 -0.693147 0.00523773 86 456 307 MODIFIER 13 CODING ADSS C protein_coding NM_001126.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244572581 T C 0 222 0 0.0446 0.1755 0.1441 0.2292 0.168 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.788578 0 . 0 . 188 46,42,33,51 UTR_3_PRIME(MODIFIER||307||456|ADSS|protein_coding|CODING|NM_001126.3|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.886155 rs3087609 -0.693147 0.0602201 188 S384 951 tcG/tcA LOW 10 SILENT CODING C1orf101 A protein_coding NM_001130957.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244724092 G A 0 222 0 0.4334 0.2732 0.2435 0.376 0.0775 0.1728 0.381298 0.187913 0.0888372 1 4076 20075 3348 3504 700 5754 112 2581 2 10406 121308 11520 8636 6612 66714 908 16512 0.787371 0 . 0 . 227 68,32,63,33 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S384|951|C1orf101|protein_coding|CODING|NM_001130957.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977863 rs7544794 -0.693147 0.208807 227 T578 951 acA/acG LOW 11 SILENT CODING C1orf101 G protein_coding NM_001130957.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244735858 A G 0 222 0 0.4289 0.272 0.2464 0.373 0.0785 0.1728 0.384249 0.18899 0.0889535 1 4077 20120 3388 3495 702 5758 110 2590 2 10406 121352 11566 8626 6612 66724 908 16510 0.679008 0 . 0 COSM1473723,COSM425808 174 57,38,37,29 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T578|951|C1orf101|protein_coding|CODING|NM_001130957.1|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.607444 rs10927267 -0.693147 0.443695 174 194 388 MODIFIER 5 CODING DESI2 G protein_coding NM_016076.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244869479 A G 0 180 0 0.3941 0.3281 0.2406 0.3353 0.2654 0.3579 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.711573 0 . 0 . 16 1,5,2,7 UTR_3_PRIME(MODIFIER||388||194|DESI2|protein_coding|CODING|NM_016076.4|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.894839 rs2242448 -0.662043 0.380722 16 194 1950 MODIFIER 5 CODING DESI2 A protein_coding NM_016076.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 244871041 T A 0 65 0 0.413 0.3247 0.2363 0.3065 0.2604 0.3528 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 0,2,0,4 UTR_3_PRIME(MODIFIER||1950||194|DESI2|protein_coding|CODING|NM_016076.4|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.75 rs3795479 -0.556411 0.634447 6 130 LOW 3 CODING COX20 TG protein_coding NM_001312872.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245005492 T TG 0 222 0 0.1536 0.1168 0.1009 0.0109 0.174 0.1288 0.148313 0.14798 0.147807 1 1611 15655 838 88 636 10130 138 2214 2 10382 121302 11566 8654 6612 66674 908 16506 0 2 benign 0 . 78 17,21,10,16 SPLICE_SITE_REGION+INTRON(LOW||||130|COX20|protein_coding|CODING|NM_001312872.1|3|TG) 1 0.5 1 27 0.346154 1 1 1 1 0 60 0 0 1 0 . rs150123625 -0.692976 0.684808 78 825 3975 MODIFIER 14 CODING HNRNPU C protein_coding NM_031844.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245013776 CA C 0 8.8 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3975||825|HNRNPU|protein_coding|CODING|NM_031844.2|14|C) 0 0.5 1 1 1 0 1 0 . 0 60 0 0 . 0 . rs397841417,rs57229249 -0.379885 0 1 E87 825 gaG/gaA LOW 1 SILENT CODING HNRNPU T protein_coding NM_031844.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245027349 C T 0 211 0 0.4017 0.2851 0.3919 0.1706 0.2644 0.1912 0.334211 0.258886 0.22151 1 2474 25079 4132 1237 1800 12000 190 3246 2 6400 89550 9166 6248 4790 47968 678 14300 0.50086 0 . 0 . 42 9,16,8,8 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E87|825|HNRNPU|protein_coding|CODING|NM_031844.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.597074 rs6675421 -0.689466 0.0344743 42 172 31818 MODIFIER 1 CODING EFCAB2 C protein_coding NM_001290327.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245133662 G C 0 228 0 0.0144 0.3712 0.3501 0.5903 0.4712 0.5399 0 . 0 2 99 7149 87 177 16 2528 74 4168 2 942 13966 198 266 22 4628 144 7766 1 0 . 0 . 30 1,0,22,1 UTR_5_PRIME(MODIFIER||31818||172|EFCAB2|protein_coding|CODING|NM_001290327.1|1|C),INTRAGENIC(MODIFIER|||||LOC101928068||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs61844237 -0.692717 0.659398 30 2108 342 MODIFIER 1 CODING KIF26B C protein_coding NM_018012.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245318385 G C 0 161 0 0.8986 0.9387 0.9236 0.9643 0.9533 0.9622 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_5_PRIME(MODIFIER||342||2108|KIF26B|protein_coding|CODING|NM_018012.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4658708 -0.651104 0.405689 8 2108 39 MODIFIER 1 CODING KIF26B T protein_coding NM_018012.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245318688 C T 0 222 0 0.2148 0.4056 0.3718 0.5823 0.3499 0.5624 0.23154 0.342565 0.393707 1 1493 33601 2143 3053 1927 18392 252 6341 2 5652 74342 5434 5086 4164 41788 570 11648 0.223142 0 . 0 . 298 87,39,99,42 START_GAINED(LOW||||2108|KIF26B|protein_coding|CODING|NM_018012.3|1|T),UTR_5_PRIME(MODIFIER||39||2108|KIF26B|protein_coding|CODING|NM_018012.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.703763 rs12409851 -0.693147 0.121046 298 A410P 2108 Gct/Cct MODERATE 5 MISSENSE CODING KIF26B C protein_coding NM_018012.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245704130 G C 0 222 0 0.0091 0.127 0.1744 0.2262 0.1292 0.1483 0.0237333 0.0805993 0.106611 1 182 15046 2918 2002 678 6852 112 2302 2 9798 120742 11572 8612 6614 66736 898 16512 0.999923 0 . 0 COSM146847 99 16,33,20,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A410P|2108|KIF26B|protein_coding|CODING|NM_018012.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.557826 rs61754898 -0.693145 0.281713 99 T1673 2108 acA/acG LOW 12 SILENT CODING KIF26B G protein_coding NM_018012.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245851304 A G 0 228 0 0.9985 0.9898 0.9784 1 0.9722 0.9939 0.997197 0.984823 0.978805 2 2311 37262 2426 2077 1256 19884 283 9025 2 2320 37856 2454 2078 1262 20324 288 9130 0 . 0 . 0 14 0,0,4,10 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1673|2108|KIF26B|protein_coding|CODING|NM_018012.3|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6701084 -0.686358 0.550319 14 D1996 2108 gaC/gaT LOW 13 SILENT CODING KIF26B T protein_coding NM_018012.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 245861571 C T 0 222 0 0.3298 0.4004 0.4481 0.378 0.5537 0.3272 0.403103 0.526423 0.584901 1 3496 59161 4238 3347 3267 38099 455 6259 2 9594 119710 11492 8514 6576 66188 892 16454 0.297849 0 . 0 . 135 38,27,24,31 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1996|2108|KIF26B|protein_coding|CODING|NM_018012.3|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999653 rs3205034 -0.693147 0.0356242 135 A311 428 gcA/gcG LOW 10 SILENT CODING SMYD3 C protein_coding NM_001167740.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246021941 T C 0 228 0 0.2224 0.3894 0.5173 0.1925 0.7177 0.3896 0.289151 0.573043 0.718488 2 2926 68809 4635 1483 4246 47992 522 7005 2 10400 121320 11570 8650 6610 66710 908 16472 0.991228 0 . 0 . 134 1,1,48,66 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A311|428|SMYD3|protein_coding|CODING|NM_001167740.1|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.596491 rs2362587 -0.693147 1.4515e-06 134 K13N 428 aaG/aaC MODERATE 1 MISSENSE CODING SMYD3 G protein_coding NM_001167740.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246670481 C G 0 228 0 0.472 0.7486 0.8329 0.9028 0.8618 0.7873 0.546965 0.77661 0.876493 2 1096 15686 342 520 255 6839 161 6473 2 2052 19368 396 578 294 7976 188 7884 0 . 0 . 0 142 0,0,44,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K13N|428|SMYD3|protein_coding|CODING|NM_001167740.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7520453 -0.693147 0.0491155 142 396 371 MODIFIER 8 CODING TFB2M G protein_coding NM_022366.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246703962 A G 0 222 0 0 0.010583 0 0.0476 0.005 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.914856 0 . 0 . 107 27,19,27,15 UTR_3_PRIME(MODIFIER||371||396|TFB2M|protein_coding|CODING|NM_022366.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.572131 rs78470425 -0.693146 0.0224411 107 I147 396 atC/atT LOW 3 SILENT CODING TFB2M A protein_coding NM_022366.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246720798 G A 0 228 0 1 1 1 1 1 1 0.999773 0.999923 1 2 10397 121391 11576 8654 6614 66732 908 16510 2 10398 121392 11576 8654 6614 66732 908 16510 0 . 0 . 0 97 0,0,24,67 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I147|396|TFB2M|protein_coding|CODING|NM_022366.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3124071 -0.693147 0.040908 97 L87S 725 tTg/tCg MODERATE 2 MISSENSE CODING CNST C protein_coding NM_152609.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246755124 T C 0 222 0 0.795 0.8834 0.9236 0.8919 0.9056 0.9427 0.8468 0.884592 0.903953 1 8614 110204 10780 7801 6120 60541 815 15533 2 10392 121262 11540 8638 6608 66672 906 16506 0.839373 0 . 0 . 187 68,34,50,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L87S|725|CNST|protein_coding|CODING|NM_152609.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.45374 rs386604501,rs6702823 -0.693147 0.26262 187 725 409 MODIFIER 11 CODING CNST C protein_coding NM_152609.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246829616 T C 0 228 0 0.6112 0.6266 0.621 0.6964 0.6203 0.5859 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.54918 0 . 0 . 135 0,2,71,51 UTR_3_PRIME(MODIFIER||409||725|CNST|protein_coding|CODING|NM_152609.2|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.938525 rs386591158,rs4130648 -0.693147 0.13379 135 725 535 MODIFIER 11 CODING CNST C protein_coding NM_152609.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246829742 T C 0 228 0 0.9425 0.7186 0.6513 0.6964 0.6213 0.5869 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,8,64 UTR_3_PRIME(MODIFIER||535||725|CNST|protein_coding|CODING|NM_152609.2|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1135644 -0.693147 0.116672 75 725 666 MODIFIER 11 CODING CNST A protein_coding NM_152609.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246829873 G A 0 140 0 0.6097 0.6246 0.621 0.6865 0.6213 0.5869 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,9 UTR_3_PRIME(MODIFIER||666||725|CNST|protein_coding|CODING|NM_152609.2|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3795472,rs386586479 -0.662043 0.0448628 9 G250 429 ggA/ggG LOW 7 SILENT CODING SCCPDH G protein_coding NM_016002.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 246922390 A G 0 222 0 0.093 0.096 0.1585 0.1736 0.0268 0.047 0.0842034 0.0496694 0.0319767 1 894 8243 3518 1403 82 1700 44 602 2 10404 121394 11572 8652 6614 66734 908 16510 0.77628 0 . 0 . 79 25,12,32,4 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G250|429|SCCPDH|protein_coding|CODING|NM_016002.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.573978 rs1127098 -0.693139 0.733822 79 N883S 2275 aAc/aGc MODERATE 21 MISSENSE CODING AHCTF1 C protein_coding NM_015446.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247048834 T C 0 222 0 0.9803 0.6817 0.6311 0.622 0.5159 0.546 0.892873 0.630268 0.495697 1 9476 68396 7618 5160 3898 32735 507 9002 2 10394 120806 11510 8620 6590 66350 902 16440 0.921685 0 . 0 . 174 53,37,42,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N883S|2275|AHCTF1|protein_coding|CODING|NM_015446.4|21|C) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.766103 0.374149 0 0.983908 rs2642990 -0.693147 0.0164794 174 515 351 MODIFIER 4 CODING ZNF695 A protein_coding NM_020394.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247149918 G A 0 46.3 0 0.3374 0.6452 0.7493 0.9722 0.663 0.6319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||351||515|ZNF695|protein_coding|CODING|NM_020394.4|4|A),INTRAGENIC(MODIFIER|||||ZNF670-ZNF695||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4971306 -0.453602 0.06 2 515 273 MODIFIER 4 CODING ZNF695 G protein_coding NM_020394.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247149996 A G 0 9.7 0 0.1634 0.5891 0.7205 0.9722 0.6372 0.6268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||273||515|ZNF695|protein_coding|CODING|NM_020394.4|4|G),INTRAGENIC(MODIFIER|||||ZNF670-ZNF695||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4971310 -0.379885 0 1 K359 515 aaA/aaG LOW 4 SILENT CODING ZNF695 C protein_coding NM_020394.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247150740 T C 0 228 0 0.1634 0.5889 0.719 0.9722 0.6362 0.6278 0.247319 0.511295 0.643776 2 2166 77538 9410 8407 4547 42421 599 9988 2 9596 118596 11354 8560 6560 65322 888 16316 0 . 0 . 0 69 0,0,33,27 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K359|515|ZNF695|protein_coding|CODING|NM_020394.4|4|C),INTRAGENIC(MODIFIER|||||ZNF670-ZNF695||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3749427 -0.693147 0.592664 69 V87A 515 gTt/gCt MODERATE 4 MISSENSE CODING ZNF695 G protein_coding NM_020394.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247151557 A G 0 228 0 0.2882 0.6256 0.7392 0.9712 0.6412 0.6288 0.332967 0.548721 0.64494 2 3124 75062 9591 8366 4578 41738 563 7102 2 9454 112402 11466 8520 6610 64258 824 11270 0 . 0 . COSM1127064 41 0,0,8,30 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gTt/gCt|V87A|515|ZNF695|protein_coding|CODING|NM_020394.4|4|G),INTRAGENIC(MODIFIER|||||ZNF670-ZNF695||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2642992 -0.693143 0.0208181 41 R84K 515 aGa/aAa MODERATE 3 MISSENSE CODING ZNF695 T protein_coding NM_020394.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247162658 C T 0 228 0 0.8268 0.8311 0.9265 0.9742 0.833 0.6196 0.825672 0.829752 0.831721 2 8082 99872 10792 8478 5749 55625 757 10389 2 9816 120760 11574 8632 6614 66716 902 16506 0 . 0 . 0 138 0,0,74,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R84K|515|ZNF695|protein_coding|CODING|NM_020394.4|3|T),INTRAGENIC(MODIFIER|||||ZNF670-ZNF695||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2642973 -0.693147 0.0177777 138 *46Q 357 Taa/Caa HIGH 1 MISSENSE CODING VN1R5 C protein_coding NM_173858.1 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247419509 T C 0 222 0 0.5582 0.7819 0.8919 0.8353 0.8877 0.8425 0.611806 0.812796 0.903384 1 5909 103806 10050 7309 5457 60301 776 14004 2 9794 120738 11576 8620 6614 66728 896 16510 0.519766 0 . 0 . 99 38,8,34,12 STOP_LOST(HIGH|MISSENSE|Taa/Caa|*46Q|357|VN1R5|protein_coding|CODING|NM_173858.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.618647 rs1778540 -0.693147 0.0122769 99 T97 357 acC/acT LOW 1 SILENT CODING VN1R5 T protein_coding NM_173858.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247419664 C T 0 222 0 0.5151 0.772 0.889 0.8353 0.8887 0.8507 0.591182 0.803028 0.904187 1 5600 103565 10023 7312 5457 60288 774 14111 2 9804 120760 11574 8620 6614 66740 896 16512 0.456225 0 . 0 . 96 20,20,21,27 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T97|357|VN1R5|protein_coding|CODING|NM_173858.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945369 rs1778541 -0.693147 0.420851 96 R350C 357 Cgc/Tgc MODERATE 1 MISSENSE CODING VN1R5 T protein_coding NM_173858.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247420421 C T 0 228 0 0.0673 0.2248 0.17 0.4058 0.2406 0.274 0.096463 0.172001 0.206363 2 695 20235 1204 2283 1242 10349 197 4265 2 4794 66280 4180 4886 3820 35642 558 12400 1 0 . 0 . 25 0,1,3,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R350C|357|VN1R5|protein_coding|CODING|NM_173858.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386499259,rs41308154 -0.692717 0.0277047 25 D161N 587 Gac/Aac MODERATE 4 MISSENSE CODING ZNF496 T protein_coding NM_032752.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247492078 C T 0 222 0 0 0.004992 0 0.0248 0 0 0 . 0 1 0 248 2 96 79 64 5 2 2 10404 120484 11574 8652 6614 66444 894 15902 0.930021 0 . 0 . 69 12,17,16,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D161N|587|ZNF496|protein_coding|CODING|NM_032752.1|4|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.934939 rs74634615 -0.693127 0.706985 69 T221 1036 acC/acT LOW 5 SILENT CODING NLRP3 T protein_coding NM_001079821.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247587408 C T 0 222 0 0.2277 0.1166 0.0879 0.131 0.0547 0.0358 0.2197 0.115254 0.0617442 1 2265 9913 967 1269 547 4044 74 747 2 10400 121306 11548 8638 6594 66712 906 16508 0.673419 0 . 0 . 54 12,16,9,13 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T221|1036|NLRP3|protein_coding|CODING|NM_001079821.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.61443 rs7525979 -0.692562 0.410894 54 A244 1036 gcG/gcA LOW 5 SILENT CODING NLRP3 A protein_coding NM_001079821.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247587477 G A 0 222 0 0.0348 0.3874 0.3617 0.5437 0.5487 0.5552 0.119837 0.405966 0.552558 1 1098 60597 4620 4651 3651 37130 458 8989 2 10394 121286 11566 8636 6604 66678 906 16502 0.371609 2 benign 0 COSM146848 48 12,8,15,11 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A244|1036|NLRP3|protein_coding|CODING|NM_001079821.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.857755 rs3806268 -0.692976 0.149235 48 R262 1036 cgA/cgG LOW 5 SILENT CODING NLRP3 G protein_coding NM_001079821.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247587531 A G 0 228 0 0.8434 0.9199 0.951 0.998 0.9592 0.8804 0.850885 0.918807 0.953605 2 8823 114429 11215 8642 6310 64023 860 14556 2 10404 121398 11574 8654 6614 66734 908 16510 0 2 benign 0 . 50 0,0,29,17 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R262|1036|NLRP3|protein_coding|CODING|NM_001079821.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4925543 -0.693147 0.695773 50 1036 230 MODIFIER 11 CODING NLRP3 C protein_coding NM_001079821.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247612036 G C 0 222 0 0.7526 0.6536 0.7536 0.5873 0.5427 0.6309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.962671 0 . 0 . 43 16,2,19,4 UTR_3_PRIME(MODIFIER||230||1036|NLRP3|protein_coding|CODING|NM_001079821.2|11|C),DOWNSTREAM(MODIFIER||2295||317|OR2B11|protein_coding|CODING|NM_001004492.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.393349 rs10754558 -0.692717 0.92686 43 1036 489 MODIFIER 11 CODING NLRP3 T protein_coding NM_001079821.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247612295 C T 0 138 0 0.5083 0.4884 0.3689 0.4653 0.5676 0.4888 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.92764 0 . 0 . 25 1,14,2,7 UTR_3_PRIME(MODIFIER||489||1036|NLRP3|protein_coding|CODING|NM_001079821.2|11|T),DOWNSTREAM(MODIFIER||2036||317|OR2B11|protein_coding|CODING|NM_001004492.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.652391 rs10802502 -0.662043 0.205601 25 G223D 317 gGc/gAc MODERATE 1 MISSENSE CODING OR2B11 T protein_coding NM_001004492.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247614617 C T 0 222 0 0.1785 0.3992 0.4856 0.503 0.4105 0.5174 0.236042 0.337537 0.389535 1 2401 48691 5658 4383 2885 25625 345 7394 2 10400 121322 11564 8634 6602 66706 906 16510 0.71112 0 . 0 . 108 23,37,22,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G223D|317|OR2B11|protein_coding|CODING|NM_001004492.1|1|T),DOWNSTREAM(MODIFIER||2211||1036|NLRP3|protein_coding|CODING|NM_001079821.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.670088 rs4925663 -0.693146 0.247352 108 V198M 317 Gtg/Atg MODERATE 1 MISSENSE CODING OR2B11 T protein_coding NM_001004492.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247614693 C T 0 228 0 0.6203 0.8956 0.9741 1 0.998 0.999 0.700409 0.896817 0.997442 2 7044 117627 11365 8654 6614 66585 885 16480 2 10378 121328 11566 8654 6614 66700 904 16512 0 . 0 . 0 125 0,0,53,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V198M|317|OR2B11|protein_coding|CODING|NM_001004492.1|1|T),DOWNSTREAM(MODIFIER||2287||1036|NLRP3|protein_coding|CODING|NM_001079821.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6695302 -0.693147 0.0154298 125 I130S 317 aTc/aGc MODERATE 1 MISSENSE CODING OR2B11 C protein_coding NM_001004492.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247614896 A C 0 222 0 0.1165 0.3696 0.3401 0.4474 0.4742 0.545 0.165456 0.361602 0.462093 1 1668 52400 4110 3934 2535 30287 410 9456 2 10392 121270 11564 8634 6606 66674 906 16494 0.953997 0 . 0 . 80 19,23,18,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aGc|I130S|317|OR2B11|protein_coding|CODING|NM_001004492.1|1|C),DOWNSTREAM(MODIFIER||2490||1036|NLRP3|protein_coding|CODING|NM_001079821.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.42636 rs11583410 -0.69311 0.0542706 80 320 885 MODIFIER 2 CODING OR2C3 C protein_coding NM_198074.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247693966 T C 0 69 0 0.9614 0.9882 0.9899 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||885||320|OR2C3|protein_coding|CODING|NM_198074.4|2|C),INTRON(MODIFIER||||135|GCSAML|protein_coding|CODING|NM_001281853.1|2|C),INTRAGENIC(MODIFIER|||||GCSAML-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6690833 -0.556411 0.360777 4 320 744 MODIFIER 2 CODING OR2C3 CTCCGTGGCCTAAACGGGCAGCCGAGCCCG protein_coding NM_198074.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247694106 C CTCCGTGGCCTAAACGGGCAGCCGAGCCCG 0 185 0 0.5189 0.7296 0.7248 0.9692 0.7008 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,5 UTR_3_PRIME(MODIFIER||744||320|OR2C3|protein_coding|CODING|NM_198074.4|2|CTCCGTGGCCTAAACGGGCAGCCGAGCCCG),INTRON(MODIFIER||||135|GCSAML|protein_coding|CODING|NM_001281853.1|2|CTCCGTGGCCTAAACGGGCAGCCGAGCCCG) 0 . 0 5 0.454545 1 1 0 . 0 60 0 0 . 0 . rs60288064 -0.590765 0.150948 11 P68S 320 Ccc/Tcc MODERATE 2 MISSENSE CODING OR2C3 A protein_coding NM_198074.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247695612 G A 0 228 0 0.9947 0.9984 0.9986 1 1 1 0.994553 0.998078 0.999884 2 10353 121346 11569 8654 6614 66736 908 16512 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 193 0,0,122,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P68S|320|OR2C3|protein_coding|CODING|NM_198074.4|2|A),INTRON(MODIFIER||||135|GCSAML|protein_coding|CODING|NM_001281853.1|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6657127 -0.693147 0.775774 193 T20A 320 Aca/Gca MODERATE 2 MISSENSE CODING OR2C3 C protein_coding NM_198074.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247695756 T C 0 228 0 0.9198 0.977 0.9885 1 0.999 1 0.926237 0.973858 0.998256 2 9653 120494 11514 8653 6614 66661 897 16502 2 10404 121410 11578 8654 6614 66740 908 16512 0 . 0 . 0 124 0,0,41,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T20A|320|OR2C3|protein_coding|CODING|NM_198074.4|2|C),INTRON(MODIFIER||||135|GCSAML|protein_coding|CODING|NM_001281853.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6697472 -0.693147 0.00818151 124 320 1044 MODIFIER 1 CODING OR2C3 C protein_coding NM_198074.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247696857 G C 0 39.3 0 0.7897 0.8976 0.9409 0.9048 0.9602 0.9407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||1044||320|OR2C3|protein_coding|CODING|NM_198074.4|1|C),INTRON(MODIFIER||||135|GCSAML|protein_coding|CODING|NM_001281853.1|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12563814 -0.453602 0.36 2 V120L 317 Gtg/Ctg MODERATE 1 MISSENSE CODING OR2G2 C protein_coding NM_001001915.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247752019 G C 0 162 0 0.1641 0.5795 0.6686 0.7599 0.7147 0.7526 0.251248 0.55336 0.70814 1 2432 82275 8410 6849 4508 46988 618 12470 2 10400 121360 11572 8646 6606 66716 908 16512 0.99046 0 . 0 COSM1178405 41 14,11,3,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V120L|317|OR2G2|protein_coding|CODING|NM_001001915.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928705 rs1151687 -0.683931 0.917408 41 L167P 317 cTg/cCg MODERATE 1 MISSENSE CODING OR2G2 C protein_coding NM_001001915.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247752161 T C 0 222 0 0.0582 0.3075 0.3501 0.5228 0.4125 0.2843 0.105538 0.302091 0.402791 1 972 43964 4347 4511 2432 26677 337 4688 2 10404 121350 11570 8618 6614 66726 906 16512 0.177194 0 . 0 . 80 37,9,25,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L167P|317|OR2G2|protein_coding|CODING|NM_001001915.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.75753 rs10925085 -0.693079 0.19619 80 R236G 317 Agg/Ggg MODERATE 1 MISSENSE CODING OR2G2 G protein_coding NM_001001915.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247752367 A G 0 222 0 0.3116 0.3888 0.3444 0.4444 0.5159 0.3364 0.312528 0.435722 0.498837 1 3304 55145 3409 4009 3631 33832 443 6517 2 10404 121342 11570 8618 6610 66724 908 16508 0.999662 0 . 0 . 354 91,80,84,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R236G|317|OR2G2|protein_coding|CODING|NM_001001915.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.610335 rs869111 -0.693147 0.00196408 354 H235 309 caC/caT LOW 1 SILENT CODING OR2G3 T protein_coding NM_001001914.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247769592 C T 0 222 0 0.3048 0.3099 0.3689 0.3413 0.2217 0.3333 0.304585 0.256805 0.232326 1 3163 33646 5207 3015 1483 15164 220 5394 2 10402 121192 11510 8618 6606 66646 908 16502 0.827286 0 . 0 . 113 23,39,16,27 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H235|309|OR2G3|protein_coding|CODING|NM_001001914.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.848387 rs1151683 -0.693146 0.0104978 113 I289V 309 Atc/Gtc MODERATE 1 MISSENSE CODING OR2G3 G protein_coding NM_001001914.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247769752 A G 0 138 0 0.2307 0.3381 0.3127 0.4325 0.4394 0.2996 0.2399 0.361602 0.423953 1 2494 47862 3059 3902 3212 28896 385 5914 2 10138 120282 11504 8598 6606 66122 904 16410 0.770381 0 . 0 . 23 1,10,1,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I289V|309|OR2G3|protein_coding|CODING|NM_001001914.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.751921 rs61730407 -0.676189 0.698487 23 I132V 307 Att/Gtt MODERATE 1 MISSENSE CODING OR13G1 C protein_coding NM_001005487.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247835950 T C 0 228 0 0.1286 0.406 0.5937 0.6032 0.4195 0.4305 0.167726 0.337767 0.424884 2 1691 53928 7843 5205 2650 28922 387 7230 2 10400 121104 11478 8624 6596 66604 904 16498 1 0 . 0 COSM1341001 245 0,1,120,110 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I132V|307|OR13G1|protein_coding|CODING|NM_001005487.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1151640 -0.693147 0.0320447 245 G203 314 ggA/ggC LOW 1 SILENT CODING OR1C1 G protein_coding NM_012353.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247921100 T G 0 228 0 0.4523 0.7324 0.8775 0.7659 0.9115 0.7894 0.518084 0.769182 0.891211 2 4794 101771 10578 6484 6257 59538 776 13344 2 9716 120250 11460 8564 6610 66530 898 16472 0 . 0 . 0 52 0,0,27,22 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G203|314|OR1C1|protein_coding|CODING|NM_012353.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1552812 -0.693147 0.032671 52 A119 314 gcG/gcA LOW 1 SILENT CODING OR1C1 T protein_coding NM_012353.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247921352 C T 0 228 0 0.5825 0.844 0.9236 0.9851 0.9573 0.8793 0.634817 0.841388 0.940485 2 6075 110970 11077 8519 6457 63013 849 14980 2 9804 120688 11530 8604 6614 66728 900 16508 0 . 0 . 0 162 0,0,110,44 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A119|314|OR1C1|protein_coding|CODING|NM_012353.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1552813 -0.693147 0.0955259 162 I238T 309 aTt/aCt MODERATE 1 MISSENSE CODING OR14A16 G protein_coding NM_001001966.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247978319 A G 0 228 0 0.9955 0.9988 1 1 1 1 0.996596 0.99877 0.999884 2 10372 121297 11566 8604 6614 66721 908 16512 2 10406 121338 11572 8604 6614 66722 908 16512 0 . 0 . 0 176 0,0,66,95 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I238T|309|OR14A16|protein_coding|CODING|NM_001001966.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6695283 -0.693147 0.202224 176 L12 309 ctT/ctC LOW 1 SILENT CODING OR14A16 G protein_coding NM_001001966.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 247978996 A G 0 228 0 0.5424 0.8468 0.9035 1 0.9175 0.9877 0.611212 0.821363 0.929053 2 5841 109370 10770 8450 6265 61215 825 16004 2 9758 119664 11490 8454 6586 66106 898 16372 0 . 0 . 0 94 0,0,23,61 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L12|309|OR14A16|protein_coding|CODING|NM_001001966.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888249 -0.693147 0.00577339 94 T195 322 acC/acT LOW 1 SILENT CODING OR11L1 A protein_coding NM_001001959.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004614 G A 0 228 0 0.6233 0.8468 0.8703 0.996 0.8986 0.9254 0.654108 0.804782 0.881977 2 6798 108201 10840 8630 6115 59578 833 15407 2 10394 121376 11576 8652 6614 66724 906 16510 0 . 0 . 0 91 0,0,60,26 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T195|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6667389 -0.693147 0.0825135 91 R171P 322 cGc/cCc MODERATE 1 MISSENSE CODING OR11L1 G protein_coding NM_001001959.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004687 C G 0 228 0 0.7103 0.8704 0.8732 0.996 0.8986 0.9264 0.727871 0.829925 0.882209 2 7558 109018 10887 8632 6115 59577 839 15410 2 10396 121366 11576 8654 6614 66708 908 16510 0 . 0 . 0 111 0,0,51,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R171P|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888255 -0.693147 0.226128 111 A142T 322 Gcc/Acc MODERATE 1 MISSENSE CODING OR11L1 T protein_coding NM_001001959.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004775 C T 0 228 0 0.7829 0.8906 0.8804 0.996 0.8986 0.9264 0.781661 0.848224 0.882326 2 8107 109559 10916 8630 6114 59543 838 15411 2 10386 121294 11570 8652 6614 66654 906 16512 0 . 0 . 0 95 0,0,36,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A142T|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888256 -0.693147 0.899319 95 F117L 322 ttC/ttG MODERATE 1 MISSENSE CODING OR11L1 C protein_coding NM_001001959.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004848 G C 0 228 0 0.7821 0.8904 0.8804 0.996 0.8986 0.9264 0.781434 0.848147 0.882326 2 8101 109249 10890 8593 6103 59350 832 15380 2 10372 120938 11540 8616 6600 66410 900 16500 0 . 0 . 0 86 0,0,53,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttC/ttG|F117L|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4607924 -0.693147 0.625223 86 G108S 322 Ggc/Agc MODERATE 1 MISSENSE CODING OR11L1 T protein_coding NM_001001959.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004877 C T 0 228 0 0.7126 0.871 0.8732 0.996 0.8986 0.9264 0.728325 0.830002 0.882093 2 7530 108631 10837 8602 6091 59359 834 15378 2 10352 120926 11520 8624 6588 66436 904 16502 0 . 0 . 0 81 0,0,59,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G108S|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888257 -0.693147 0.0452712 81 V105 322 gtA/gtG LOW 1 SILENT CODING OR11L1 C protein_coding NM_001001959.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248004884 T C 0 228 0 0.8926 0.9563 0.951 1 0.9592 0.998 0.904675 0.944103 0.964302 2 9370 117295 11220 8642 6513 64297 882 16371 2 10364 121034 11530 8642 6578 66524 900 16496 0 . 0 . 0 84 0,0,63,19 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V105|322|OR11L1|protein_coding|CODING|NM_001001959.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1339845 -0.693147 0.160577 84 W3S 486 tGg/tCg MODERATE 1 MISSENSE CODING TRIM58 C protein_coding NM_015431.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248020556 G C 0 199 0 0.4168 0.6801 0.7262 0.7897 0.7614 0.8067 0.50675 0.678015 0.765753 2 535 5420 297 417 164 3480 34 493 2 994 7076 372 528 210 4338 42 592 1 0 . 0 COSM425890 41 1,0,37,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W3S|486|TRIM58|protein_coding|CODING|NM_015431.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 0 . 1 rs11204523 -0.693141 0.599467 41 P243 486 ccG/ccA LOW 3 SILENT CODING TRIM58 A protein_coding NM_015431.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248028219 G A 0 209 0 0.0499 0.4157 0.4409 0.5744 0.5716 0.5685 0.132461 0.415091 0.559051 1 710 36045 2045 2718 1535 21974 262 6801 2 3930 61564 3684 4538 2326 34990 456 11640 0.94769 0 . 0 . 18 1,5,4,8 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P243|486|TRIM58|protein_coding|CODING|NM_015431.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998904 rs946696 -0.680642 0.122176 18 486 502 MODIFIER 6 CODING TRIM58 C protein_coding NM_015431.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248040293 T C 0 9.7 0 0.9387 0.9822 0.9885 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||502||486|TRIM58|protein_coding|CODING|NM_015431.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9661539 -0.379885 0 1 R179C 314 Cgt/Tgt MODERATE 1 MISSENSE CODING OR2W3 T protein_coding NM_001001957.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248059423 C T 0 228 0 0.1422 0.389 0.3487 0.5714 0.5308 0.4172 0.230595 0.429955 0.532093 2 2278 57935 3995 4778 3753 35745 450 6936 2 10406 121336 11570 8614 6606 66726 908 16506 0 . 0 . 0 110 0,0,55,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R179C|314|OR2W3|protein_coding|CODING|NM_001001957.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10888267 -0.693147 0.175829 110 V190I 314 Gtc/Atc MODERATE 1 MISSENSE CODING OR2W3 A protein_coding NM_001001957.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248059456 G A 0 228 0 0.0545 0.3636 0.3357 0.5327 0.5507 0.4346 0.135497 0.399969 0.535465 2 1284 55974 3402 4465 3716 35561 419 7127 2 10406 121348 11568 8616 6612 66726 908 16512 0 . 0 . COSM1600163 118 0,0,60,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V190I|314|OR2W3|protein_coding|CODING|NM_001001957.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12135078 -0.693147 0.904792 118 E196D 314 gaA/gaC MODERATE 1 MISSENSE CODING OR2W3 C protein_coding NM_001001957.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248059476 A C 0 228 0 0.2602 0.5761 0.5965 0.5833 0.7962 0.7546 0.363822 0.655851 0.805465 2 3545 86815 5953 4832 5349 53993 671 12472 2 10404 121340 11566 8614 6612 66724 908 16512 0 . 0 . 0 116 0,0,58,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E196D|314|OR2W3|protein_coding|CODING|NM_001001957.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12139390 -0.693147 0.00358587 116 M272K 314 aTg/aAg MODERATE 1 MISSENSE CODING OR2W3 A protein_coding NM_001001957.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248059703 T A 0 228 0 0.2648 0.478 0.4553 0.5893 0.665 0.4755 0.35724 0.5499 0.648605 2 3538 69728 4769 4937 4295 43553 549 8087 2 10404 121328 11562 8640 6606 66702 904 16510 1 0 . 0 . 75 0,1,31,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M272K|314|OR2W3|protein_coding|CODING|NM_001001957.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11204545 -0.693147 0.419596 75 M275T 314 aTg/aCg MODERATE 1 MISSENSE CODING OR2W3 C protein_coding NM_001001957.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248059712 T C 0 228 0 0.264 0.4798 0.4568 0.5903 0.667 0.4816 0.358148 0.553206 0.65314 2 3555 70351 4777 4942 4408 43882 556 8231 2 10404 121324 11562 8630 6602 66714 904 16508 0 . 0 . 0 64 0,0,28,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M275T|314|OR2W3|protein_coding|CODING|NM_001001957.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11204546 -0.693147 0.097333 64 G39S 312 Ggc/Agc MODERATE 1 MISSENSE CODING OR2T8 A protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084434 G A 0 228 0 0.1415 0.4629 0.6686 0.372 0.7813 0.5174 0 . 0 2 2308 76497 8011 3186 4801 49894 603 7694 2 10256 119136 11526 8572 6606 65938 884 15354 0.26179 0 . 0 . 277 22,2,118,116 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G39S|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|A) 0 . 0 . 0 1 0 . 1 0 45 0 7.44766e-07 2.53126e-33 0 0.957182 rs11204563 -0.693147 0.689993 277 W49R 312 Tgg/Cgg MODERATE 1 MISSENSE CODING OR2T8 C protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084464 T C 0 228 0 . 0 . 0 . 0 . 0 . 2 7046 82311 8277 5743 4678 45145 616 10806 2 9856 110298 10508 7976 5930 60780 822 14426 0.959678 0 . 0 . 306 16,1,139,104 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W49R|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|C) 0 . 0 . 0 . 0 . 1 0 43 0 0.00474833 7.53468e-22 0 0.00512387 rs11204564 -0.693147 0.00783497 306 A97V 312 gCg/gTg MODERATE 1 MISSENSE CODING OR2T8 T protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084609 C T 0 226 0 0.9539 0.987 0.9942 1 1 1 0 . 0 2 1649 10582 583 486 395 6005 125 1339 2 2282 11356 622 498 396 6084 130 1344 0 . 0 . 0 36 0,0,3,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A97V|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 . 0 . 0 1 0 . 1 0 41 0 0 0.0556076 0 . rs140703773 -0.693139 0.651861 36 L102 312 ctC/ctG LOW 1 SILENT CODING OR2T8 G protein_coding NM_001005522.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084625 C G 0 181 0 0.4622 0.5825 0.6816 0.5357 0.7644 0.5358 0 . 0 2 524 5321 301 199 216 3436 50 595 2 1938 8816 490 386 294 4636 78 994 0.653165 0 . 0 . 26 1,2,2,21 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L102|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|G) 0 . 0 . 0 1 0 . 1 0 35 0 0.168877 0.210393 0 0.907172 rs6692365 -0.692717 0.635095 26 P103L 312 cCc/cTc MODERATE 1 MISSENSE CODING OR2T8 T protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084627 C T 0 179 0 0.4622 0.5831 0.6859 0.5357 0.7644 0.5358 0 . 0 2 515 5189 288 194 197 3362 56 577 2 1916 8628 470 380 274 4528 86 974 0.813736 0 . 0 . 26 1,2,2,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P103L|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 . 0 . 0 1 0 . 1 0 35 0 0.168877 0.210393 0 0.907172 rs61857490 -0.692717 0.635095 26 T104 312 acA/acC LOW 1 SILENT CODING OR2T8 C protein_coding NM_001005522.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084631 A C 0 186 0 0.6717 0.6587 0.732 0.5536 0.7903 0.5624 0 . 0 2 796 6122 324 202 221 3872 65 642 2 1852 9198 502 370 298 5058 92 1026 0.791667 0 . 0 . 26 0,2,2,22 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T104|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|C) 0 . 0 . 0 1 0 . 1 0 37 0 0.3125 0.375 0 0.333333 rs28689982 -0.692831 0.685352 26 N143T 312 aAc/aCc MODERATE 1 MISSENSE CODING OR2T8 C protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084747 A C 0 58 0 0.8086 0.9429 0.9798 0.9901 0.992 0.999 0 . 0 2 39 267 7 10 0 203 4 4 2 1390 1742 94 10 0 228 12 8 0 . 0 . 0 6 0,0,2,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N143T|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|C) 0 . 0 . 0 1 0 . 1 0 24 0 0 0.75 0 . rs4523549 -0.616816 0.496552 6 L144M 312 Ctg/Atg MODERATE 1 MISSENSE CODING OR2T8 A protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084749 C A 0 66 0 0.8124 0.9439 0.9813 0.9881 0.993 0.999 0 . 0 2 144 1074 44 34 12 782 14 44 2 1482 2530 126 34 12 810 20 46 0 . 0 . COSM302809 6 0,0,2,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L144M|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|A) 0 . 0 . 0 1 0 . 1 0 24 0 0 0.75 0 . rs12142488 -0.616816 0.496552 6 A169V 312 gCa/gTa MODERATE 1 MISSENSE CODING OR2T8 T protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084825 C T 0 112 0 0.4758 0.476 0.4827 0.4702 0.4642 0.4898 0 . 0 1 4906 56369 5303 4127 3070 30624 421 7918 2 9754 114884 10990 8442 6242 62506 856 16094 0.125835 0 . 0 . 52 10,15,20,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A169V|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 31 0 0.637592 0.986308 0 0.000455304 rs61857492 -0.692562 0.000141394 52 H174Y 312 Cac/Tac MODERATE 1 MISSENSE CODING OR2T8 T protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084839 C T 0 197 0 . 0 . 0 . 0 . 0 . 1 0 13 0 12 0 0 0 1 2 9868 114062 10878 8566 6024 61638 826 16262 0.888727 0 . 0 . 48 23,2,7,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H174Y|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.481858 0.863513 0 0.0793939 rs200305171 -0.69168 0.828139 48 T179A 312 Acc/Gcc MODERATE 1 MISSENSE CODING OR2T8 G protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084854 A G 0 115 0 . 0 . 0 . 0 . 0 . 1 524 17367 1772 568 854 12032 120 1497 2 8622 96704 8760 7798 4626 51764 670 14464 0.538829 0 . 0 . 39 19,4,7,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T179A|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 30 0 0.051874 0.997155 0 0.888378 rs4584426 -0.680642 0.022591 39 M197R 312 aTg/aGg MODERATE 1 MISSENSE CODING OR2T8 G protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084909 T G 0 182 0 0.1029 0.3017 0.4337 0.2778 0.4652 0.3333 0 . 0 1 220 6570 311 241 165 4220 63 1350 2 1626 13970 648 860 304 7628 126 2778 0.877345 0 . 0 . 39 6,12,13,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aGg|M197R|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 37 0 0.000508585 0.00131519 0 0.0214263 rs34508376 -0.690438 0.244097 39 A221S 312 Gct/Tct MODERATE 1 MISSENSE CODING OR2T8 T protein_coding NM_001005522.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248084980 G T 0 109 0 0.1377 0.3556 0.5072 0.3244 0.5507 0.3742 0 . 0 1 961 28577 1669 1120 1775 19007 259 3786 2 3266 44662 2606 2458 2562 26116 396 7258 0.495941 0 . 0 . 41 0,8,33,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A221S|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 49 0 0.000362452 0.000362452 0 0.120782 rs111275277,rs113479553,rs4362017 -0.693127 0.253144 41 H263 312 caC/caT LOW 1 SILENT CODING OR2T8 T protein_coding NM_001005522.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248085108 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 4492 82024 8204 3831 4845 51421 647 8584 2 10310 121082 11556 8608 6610 66604 908 16486 1 0 . 0 . 188 0,1,181,3 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H263|312|OR2T8|protein_coding|CODING|NM_001005522.1|1|T) 0 . 0 . 0 . 0 . 1 0 56 0 1 0.00597397 0 1 rs4625315 -0.693147 0.484769 188 312 162309 MODIFIER 1 CODING OR2L13 C protein_coding NM_001304535.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248100369 T C 0 39.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||162309||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|C) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs72761090 -0.453602 0.36 2 C156 312 tgT/tgC LOW 1 SILENT CODING OR2L8 C protein_coding NM_001001963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112627 T C 0 228 0 0.0893 0.4119 0.549 0.4385 0.6103 0.5194 0.187472 0.461633 0.602093 2 1718 64221 6683 3697 3935 39362 502 8324 2 10400 121326 11542 8632 6612 66724 908 16508 0.966019 0 . 0 . 231 0,2,90,116 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C156|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|C),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|C) 1 0 . 0 . 1 0 1 1 0 58 0 0.946602 0.870506 0 0.975728 rs4925787 -0.693147 0.0356459 231 G196C 312 Ggc/Tgc MODERATE 1 MISSENSE CODING OR2L8 T protein_coding NM_001001963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112745 G T 0 228 0 0.3283 0.7228 0.8746 0.7808 0.8767 0.9305 0 . 0 2 3772 95274 10260 6195 5714 56153 725 12455 2 10056 115244 11214 8322 6504 64396 864 13888 0 . 0 . 0 136 0,0,73,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G196C|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|T),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|T) 0 . 0 . 0 1 0 . 1 0 52 0 0 0.210854 0 . rs4925788 -0.693147 0.999956 136 S201 312 agT/agC LOW 1 SILENT CODING OR2L8 C protein_coding NM_001001963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112762 T C 0 228 0 0.2708 0.7298 0.8991 0.8165 0.9294 0.9356 0.118636 0.555538 0.780482 2 3441 92399 10053 6053 5599 54068 699 12486 2 10316 116856 11298 8484 6482 64880 874 14522 0 . 0 . 0 118 0,0,70,48 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S201|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|C),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|C) 1 0 . 0 . 1 0 1 1 0 51 0 0 0.397353 0 . rs4925789 -0.693147 2.94973e-06 118 A202T 312 Gcc/Acc MODERATE 1 MISSENSE CODING OR2L8 A protein_coding NM_001001963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112763 G A 0 228 0 0.3177 0.7432 0.9049 0.8165 0.9294 0.9366 0.178328 0.57937 0.785848 2 3795 93067 10086 6059 5610 54196 707 12614 2 10318 117088 11300 8500 6494 64948 878 14650 0 . 0 . 0 118 0,0,70,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A202T|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|A),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|A) 1 0 . 0 . 1 0 1 1 0 51 0 0 0.397353 0 . rs4925790 -0.693147 2.94973e-06 118 I204 312 atC/atT LOW 1 SILENT CODING OR2L8 T protein_coding NM_001001963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112771 C T 0 228 0 . 0 . 0 . 0 0.202678 0.632554 0.852791 2 3466 94692 10120 6077 5648 54797 725 13859 2 10334 119180 11364 8504 6534 65620 902 15922 0 . 0 . 0 147 0,0,89,54 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I204|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|T),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|T) 1 0 . 0 . 0 . 1 1 0 53 0 0 0.427687 0 . rs4925791 -0.693147 0.00472073 147 Y217C 312 tAt/tGt MODERATE 1 MISSENSE CODING OR2L8 G protein_coding NM_001001963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112809 A G 0 228 0 0.2753 0.756 0.9251 0.8829 0.9513 0.954 0.380844 0.753652 0.944651 2 3564 104492 10760 6769 6356 61029 798 15216 2 10392 121178 11518 8634 6602 66622 908 16502 0 . 0 . 0 224 0,0,137,75 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y217C|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|G),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|G) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.985299 0 . rs4925583 -0.693147 0.0342857 224 H226R 312 cAc/cGc MODERATE 1 MISSENSE CODING OR2L8 G protein_coding NM_001001963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248112836 A G 0 228 0 0.2965 0.762 0.9265 0.8849 0.9503 0.954 0.412619 0.765877 0.94686 2 4067 108597 10991 7494 6472 63090 826 15657 2 10392 121132 11540 8618 6610 66644 906 16422 0 . 0 . 0 259 0,0,159,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H226R|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|G),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.989295 0 . rs4925792 -0.693147 0.00725428 259 Y289* 312 taT/taA HIGH 1 NONSENSE CODING OR2L8 A protein_coding NM_001001963.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248113026 T A 0 228 0 0.2867 0.7458 0.9135 0.8532 0.9453 0.9315 0.395143 0.747654 0.928339 2 3670 103835 10750 6701 6345 60459 799 15111 2 10220 120074 11504 8578 6582 65972 902 16316 0 . 0 . 0 205 0,0,78,105 STOP_GAINED(HIGH|NONSENSE|taT/taA|Y289*|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|A),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|A) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.406479 0 . rs10888281 -0.693147 0.314507 205 K294R 312 aAg/aGg MODERATE 1 MISSENSE CODING OR2L8 G protein_coding NM_001001963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248113040 A G 0 228 0 0.8359 0.9381 0.9784 0.9603 0.993 0.9683 0 . 0 2 7667 111897 11103 7382 6429 62774 860 15682 2 9728 118854 11466 8482 6580 65446 898 16254 0 . 0 . 0 183 0,0,66,100 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K294R|312|OR2L8|protein_coding|CODING|NM_001001963.1|1|G),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|G) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.264176 0 . rs10888282 -0.693147 0.158162 183 V203M 335 Gtg/Atg MODERATE 1 MISSENSE CODING OR2AK2 A protein_coding NM_001004491.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248129240 G A 0 228 0 0.0915 0.4313 0.5706 0.4623 0.6531 0.5317 0.194281 0.489466 0.640698 2 1793 67622 6858 3930 4290 42064 538 8149 2 10376 119526 11502 8614 6596 66186 894 15358 0.542735 0 . 0 . 126 1,1,82,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V203M|335|OR2AK2|protein_coding|CODING|NM_001004491.1|1|A),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.641026 rs4478844 -0.693147 0.669547 126 V259L 312 Gta/Cta MODERATE 1 MISSENSE CODING OR2L2 C protein_coding NM_001004686.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248202344 G C 0 222 0 0.7799 0.345 0.1484 0.3036 0.1551 0.135 0.682025 0.32708 0.145233 1 7231 23947 1075 2754 962 9734 170 2021 2 10404 121352 11572 8626 6612 66722 908 16508 0.990387 0 . 0 . 212 38,56,42,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V259L|312|OR2L2|protein_coding|CODING|NM_001004686.2|1|C),INTRON(MODIFIER||||312|OR2L13|protein_coding|CODING|NM_001304535.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.22433 rs6658141 -0.693147 0.242052 212 312 402 MODIFIER 2 CODING OR2L13 T protein_coding NM_001304535.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248264018 C T 0 228 0 0.2073 0.6456 0.8429 0.7202 0.7992 0.863 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 144 0,0,86,50 UTR_3_PRIME(MODIFIER||402||312|OR2L13|protein_coding|CODING|NM_001304535.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10749643 -0.693147 0.0983976 144 C141 312 tgT/tgC LOW 1 SILENT CODING OR2M3 C protein_coding NM_001004689.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248366792 T C 0 222 0 0.171 0.246 0.255 0.3542 0.1451 0.3333 0.156151 0.149623 0.146279 1 1667 23861 3506 3178 916 9476 144 4974 2 10406 121366 11554 8640 6614 66736 908 16508 0.984857 0 . 0 . 417 103,126,68,80 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C141|312|OR2M3|protein_coding|CODING|NM_001004689.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.838387 rs12562957 -0.693147 0.201008 417 H176 311 caC/caT LOW 1 SILENT CODING OR2M4 T protein_coding NM_017504.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248402758 C T 0 222 0 0.4266 0.7029 0.7522 0.7966 0.7346 0.9121 0.500908 0.663924 0.747442 1 5141 90908 8856 6932 5185 49483 697 14614 2 10406 121400 11576 8650 6612 66736 908 16512 0.930046 0 . 0 . 107 32,20,30,16 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H176|311|OR2M4|protein_coding|CODING|NM_017504.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999234 rs386604235,rs6666148 -0.693147 0.382254 107 A221S 320 Gct/Tct MODERATE 1 MISSENSE CODING OR2T33 A protein_coding NM_001004695.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436456 C A 0 3.8 0 . 0 . 0 . 0 . 0 . 1 116 4933 349 140 273 3340 53 662 2 7950 86880 7990 6566 4720 45966 678 13010 0.876583 0 . 0 . 132 15,96,9,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A221S|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 50 0 1.10277e-05 0.000107751 0 0.222886 rs142107755 -0.692352 0.376376 132 M197R 320 aTg/aGg MODERATE 1 MISSENSE CODING OR2T33 C protein_coding NM_001004695.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436527 A C 0 27.9 0 . 0 . 0 . 0 . 0 . 1 874 31973 3228 1448 1997 20389 253 3784 2 7828 92092 8440 6124 4966 50672 682 13380 0.289331 0 . 0 . 122 60,40,14,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aGg|M197R|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|C) 0 0.5 1 0 . 0 . 0 1 0 44 0 0.000146512 0.857009 0 0.999645 rs142669752 -0.692562 0.144949 122 A169V 320 gCa/gTa MODERATE 1 MISSENSE CODING OR2T33 A protein_coding NM_001004695.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436611 G A 0 228 0 0.5461 0.6522 0.6009 0.7798 0.5855 0.7689 0 . 0 2 5494 66414 6060 5487 3461 34101 527 11284 2 9706 113408 10778 7976 6114 62634 868 15332 0.245782 0 . 0 . 125 14,1,82,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A169V|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|A) 0 . 0 . 0 1 0 . 1 0 44 0 1.78776e-05 0.966947 0 0.00961446 rs10888338 -0.693147 0.636155 125 C167 320 tgT/tgC LOW 1 SILENT CODING OR2T33 G protein_coding NM_001004695.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436616 A G 0 228 0 0.8041 0.8133 0.7767 0.8601 0.7227 0.8967 0 . 0 2 8072 88848 8310 6938 4844 46274 684 13726 2 10010 116870 11064 8292 6274 64346 878 16006 0 . 0 . 0 131 0,0,95,28 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C167|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|G) 0 . 0 . 0 1 0 . 1 0 45 0 0 0.98914 0 . rs71538179 -0.693147 0.596305 131 T104 320 acA/acC LOW 1 SILENT CODING OR2T33 G protein_coding NM_001004695.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436805 T G 0 228 0 . 0 . 0 . 0 . 0 . 2 7084 86316 8245 6379 5123 47147 671 11667 2 9738 116270 11094 8142 6424 64730 880 15262 0.962106 0 . 0 . 340 3,0,189,122 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T104|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|G) 0 . 0 . 0 . 0 . 1 0 38 0 0.0177089 0.00112048 0 0.207605 rs28399248 -0.693147 5.99102e-06 340 P103L 320 cCc/cTc MODERATE 1 MISSENSE CODING OR2T33 A protein_coding NM_001004695.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436809 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 3850 52542 5192 3095 3025 30815 402 6163 2 9860 119272 11406 8466 6564 65804 900 16272 0.134455 0 . 0 . 362 129,67,76,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P103L|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 38 0 0.000724682 0.00067893 0 0.792831 rs61832700 -0.693147 4.72506e-09 362 L102 320 ctC/ctG LOW 1 SILENT CODING OR2T33 C protein_coding NM_001004695.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436811 G C 0 222 0 . 0 . 0 . 0 . 0 . 1 3849 52544 5194 3096 3024 30817 401 6163 2 9840 119216 11410 8460 6560 65796 898 16252 0.0735209 0 . 0 . 364 130,68,77,59 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L102|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|C) 0 0.5 1 0 . 0 . 0 1 0 38 0 0.000726088 0.00118423 0 0.586272 rs61832701 -0.693147 9.24841e-09 364 W49R 320 Tgg/Cgg MODERATE 1 MISSENSE CODING OR2T33 G protein_coding NM_001004695.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248436972 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 3868 31971 3932 3215 1515 13426 216 5799 2 9108 113174 11146 8414 6292 61790 840 15584 0.919764 0 . 0 . 312 68,81,46,97 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W49R|320|OR2T33|protein_coding|CODING|NM_001004695.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 42 0 3.0154e-05 1.83771e-16 0 0.038353 rs112084843 -0.693147 1.87873e-05 312 R301L 320 cGg/cTg MODERATE 1 MISSENSE CODING OR2T12 A protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248457979 C A 0 228 0 0.7496 0.7947 0.7608 0.8591 0.7177 0.8926 0.76759 0.754729 0.74814 2 7990 94071 8972 7430 5298 49424 714 14243 2 10404 121404 11576 8654 6614 66736 908 16512 0 . 0 . 0 245 0,0,145,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R301L|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6667171 -0.693147 0.59767 245 K296N 320 aaG/aaC MODERATE 1 MISSENSE CODING OR2T12 G protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248457993 C G 0 222 0 0.0091 0.2131 0.2464 0.3591 0.174 0.3548 0.0440309 0.128248 0.171395 1 367 25395 3641 3187 1385 11145 182 5488 2 10406 121388 11576 8638 6614 66734 908 16512 0.292461 0 . 0 . 274 76,53,74,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K296N|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.620915 rs11204625,rs56024759 -0.693147 0.357728 274 T104S 320 Aca/Tca MODERATE 1 MISSENSE CODING OR2T12 A protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458571 T A 0 222 0 0.0711 0.3886 0.4481 0.498 0.5139 0.5337 0 . 0 1 1104 46334 3359 3182 2837 27849 381 7622 2 7562 97404 8746 6788 5200 53702 742 14664 0.212493 0 . 0 . 137 41,34,27,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Tca|T104S|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 38 0 0.189169 5.69344e-05 0 0.817056 rs12137982 -0.693147 0.0635231 137 M69V 320 Atg/Gtg MODERATE 1 MISSENSE CODING OR2T12 C protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458676 T C 0 221 0 . 0 . 0 . 0 . 0 . 1 5408 24492 1922 1681 1194 11650 178 2459 2 9024 81972 8358 6000 4126 44858 574 9032 0.391823 0 . 0 COSM1600062 128 3,35,80,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M69V|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|C) 0 0.5 1 0 . 0 . 0 1 0 45 0 1.2775e-06 9.68942e-09 0 8.8945e-09 rs6678138 -0.693147 0.841042 128 L64 320 ctT/ctC LOW 1 SILENT CODING OR2T12 G protein_coding NM_001004692.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458689 A G 0 218 0 . 0 . 0 . 0 . 0 . 1 5493 19548 1285 989 724 9798 155 1104 2 8718 66774 6100 3816 3148 38998 508 5486 0.947127 0 . 0 COSM146853 144 2,24,94,21 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L64|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 49 0 1.88042e-05 3.29791e-06 0 2.20168e-07 rs6674940 -0.693147 0.744607 144 R55T 320 aGg/aCg MODERATE 1 MISSENSE CODING OR2T12 G protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458717 C G 0 228 0 . 0 . 0 . 0 . 0 . 2 3595 84090 8245 7238 4914 45980 641 13477 2 10118 118328 11218 8510 6422 65358 868 15834 0 . 0 . 0 165 0,0,102,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aCg|R55T|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|G) 0 . 0 . 0 . 0 . 1 0 54 0 0 0.00847532 0 . rs12745228 -0.693147 6.72662e-08 165 W49R 320 Tgg/Cgg MODERATE 1 MISSENSE CODING OR2T12 G protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458736 A G 0 222 0 0.0567 0.2272 0.2522 0.3601 0.1769 0.3548 0.0633227 0.115331 0.141977 1 776 24624 3457 3101 1317 10662 171 5140 2 10296 119450 11338 8522 6518 65986 884 15906 0.58901 0 . 0 . 233 75,56,51,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W49R|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.637448 0.0349097 0 0.194164 rs28409263 -0.693147 0.140739 233 A41S 320 Gcc/Tcc MODERATE 1 MISSENSE CODING OR2T12 A protein_coding NM_001004692.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458760 C A 0 222 0 0.1316 0.2512 0.2651 0.3591 0.1849 0.3599 0.131866 0.164616 0.181395 1 1380 26190 3589 3090 1321 11372 180 5258 2 10312 119506 11354 8522 6522 66014 882 15900 0.999775 0 . 0 COSM1341134 283 79,69,59,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A41S|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.651161 0.0912226 0 0.000776445 rs12135684 -0.693147 0.0158312 283 E2 320 gag/ HIGH 1 CODING OR2T12 C protein_coding NM_001004692.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248458875 CT C 0 222 0 0.0159 0.2147 0.245 0.3591 0.174 0.3548 0.047329 0.130251 0.173128 1 394 22605 3608 3133 1385 10737 154 3194 2 9888 111100 11486 8520 6614 64224 800 9568 0 . 0 . COSM327981 221 51,67,42,48 FRAME_SHIFT(HIGH||gag/|E2|320|OR2T12|protein_coding|CODING|NM_001004692.1|1|C) 1 0.5 1 99 0.447964 1 1 1 1 0 55 0 0 0.710273 0 . rs11339452 -0.693147 0.721069 221 L285 312 ctG/ctA LOW 1 SILENT CODING OR2M7 T protein_coding NM_001004691.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248487016 C T 0 222 0 0.0091 0.2137 0.245 0.3641 0.172 0.3558 0.0440309 0.12648 0.168721 1 367 25186 3593 3254 1377 10929 181 5485 2 10396 120648 11442 8642 6610 66478 904 16176 0.828081 0 . 0 . 197 82,26,59,17 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L285|312|OR2M7|protein_coding|CODING|NM_001004691.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.476719 rs4451579 -0.693147 0.51134 197 D191N 312 Gac/Aac MODERATE 1 MISSENSE CODING OR2M7 T protein_coding NM_001004691.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248487300 C T 0 222 0 0.1377 0.4065 0.4539 0.494 0.5159 0.5337 0.221289 0.438779 0.550256 1 2184 60920 4967 4179 3827 36626 499 8638 2 10404 121364 11560 8650 6612 66718 908 16512 0.840045 0 . 0 . 343 103,63,84,65 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D191N|312|OR2M7|protein_coding|CODING|NM_001004691.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.989278 0.56148 0 0.102796 rs4916129 -0.693147 0.342892 343 C178F 312 tGc/tTc MODERATE 1 MISSENSE CODING OR2M7 A protein_coding NM_001004691.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248487338 C A 0 228 0 0.8661 0.8275 0.7709 0.8621 0.7137 0.8967 0.848162 0.776573 0.739879 2 8867 94994 9005 7442 5298 49403 724 14255 2 10398 121364 11560 8650 6614 66722 908 16512 0 . 0 . 0 324 0,0,171,132 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tTc|C178F|312|OR2M7|protein_coding|CODING|NM_001004691.1|1|A) 1 0 . 0 . 1 0 1 1 0 56 0 0 0.22021 0 . rs4916130 -0.693147 0.00616175 324 V78A 312 gTa/gCa MODERATE 1 MISSENSE CODING OR2M7 G protein_coding NM_001004691.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248487638 A G 0 228 0 0.77 0.8005 0.7651 0.8601 0.7117 0.8967 0.776214 0.756574 0.746512 2 8060 94152 8985 7445 5298 49393 721 14250 2 10404 121370 11566 8648 6612 66724 908 16508 0 . 0 . 0 271 0,0,131,125 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V78A|312|OR2M7|protein_coding|CODING|NM_001004691.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs7555310 -0.693147 0.185188 271 F35L 312 Ttt/Ctt MODERATE 1 MISSENSE CODING OR2M7 G protein_coding NM_001004691.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248487768 A G 0 228 0 0.7693 0.8009 0.7651 0.8621 0.7137 0.8957 0.776214 0.756497 0.746395 2 8061 94149 8984 7446 5298 49393 722 14245 2 10406 121372 11564 8648 6610 66728 908 16508 0 . 0 . 0 218 0,0,92,109 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F35L|312|OR2M7|protein_coding|CODING|NM_001004691.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.993752 0 . rs7555424 -0.693147 0.157574 218 T6 312 acC/acT LOW 1 SILENT CODING OR14C36 T protein_coding NM_001001918.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512094 C T 0 222 0 0.3744 0.4643 0.4885 0.4315 0.5239 0.5409 0.416931 0.517838 0.569535 1 4206 61831 5371 3627 3735 37261 490 7141 2 10324 116128 11490 8588 6608 65398 858 12862 0.81232 0 . 0 . 89 27,16,22,14 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T6|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940768 rs28728105 -0.693139 0.0544884 89 Q141R 312 cAg/cGg MODERATE 1 MISSENSE CODING OR14C36 G protein_coding NM_001001918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512498 A G 0 222 0 0.0923 0.2544 0.2594 0.4276 0.1938 0.3538 0.10985 0.163079 0.190349 1 1126 28136 3539 3698 1458 12576 203 5536 2 10404 121208 11516 8592 6610 66680 908 16498 0.792163 0 . 0 . 127 36,26,22,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q141R|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.379232 rs28448343 -0.693147 0.0229546 127 C187 312 tgC/tgT LOW 1 SILENT CODING OR14C36 T protein_coding NM_001001918.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512637 C T 0 222 0 0.3601 0.4605 0.4885 0.4315 0.5239 0.5409 0.400363 0.511918 0.56907 1 4054 63825 5390 3631 3732 37813 512 8693 2 10400 121238 11530 8624 6604 66672 908 16500 0.720903 0 . 0 . 72 16,22,5,25 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C187|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.602507 rs2039824 -0.693097 0.00833045 72 F211 312 ttT/ttC LOW 1 SILENT CODING OR14C36 C protein_coding NM_001001918.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512709 T C 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 1 0 1 0 0 0 0 2 10388 121272 11536 8640 6608 66688 908 16504 0.836883 0 . 0 . 54 12,9,22,9 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F211|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.126681 rs200640574 -0.69311 0.384538 54 G225R 312 Ggg/Agg MODERATE 1 MISSENSE CODING OR14C36 A protein_coding NM_001001918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512749 G A 0 222 0 0.3601 0.4605 0.4885 0.4315 0.5239 0.5409 0.400363 0.511918 0.56907 1 4046 63813 5392 3634 3735 37797 512 8697 2 10374 121228 11532 8624 6608 66678 906 16506 0.551678 0 . 0 COSM1178408 71 31,11,14,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G225R|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.626414 rs28377739 -0.692717 0.0540935 71 D231Y 312 Gac/Tac MODERATE 1 MISSENSE CODING OR14C36 T protein_coding NM_001001918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248512767 G T 0 222 0 0.3608 0.4609 0.4885 0.4315 0.5249 0.5409 0.401271 0.512225 0.56907 1 4042 63787 5388 3633 3735 37778 513 8698 2 10368 121200 11536 8618 6610 66654 906 16508 0.894571 0 . 0 COSM1178409 79 37,13,15,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D231Y|312|OR14C36|protein_coding|CODING|NM_001001918.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.33829 rs28545014 -0.692914 0.369709 79 A57 348 gcA/gcT LOW 1 SILENT CODING OR2T4 T protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525053 A T 0 80 0 0.2398 0.2941 0.2709 0.4276 0.1799 0.364 0 . 0 1 2408 25499 3203 3267 1257 9935 175 5254 2 10378 119960 11340 8366 6544 66140 902 16290 0.862186 0 . 0 . 167 76,50,10,21 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcT|A57|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.021095 0.769019 0 0.924272 rs28415565 -0.69311 0.051735 167 C60S 348 Tgt/Agt MODERATE 1 MISSENSE CODING OR2T4 A protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525060 T A 0 110 0 0.2421 0.2949 0.2709 0.4276 0.1809 0.364 0 . 0 1 2386 25456 3201 3262 1256 9924 176 5251 2 10362 120018 11382 8388 6548 66126 902 16310 0.950662 0 . 0 . 188 83,51,18,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C60S|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.000201748 0.301537 0 0.224944 rs28491677 -0.693146 0.798983 188 I63 348 atT/atC LOW 1 SILENT CODING OR2T4 C protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525071 T C 0 207 0 0.3926 0.3462 0.2896 0.4385 0.1948 0.3845 0 . 0 1 2384 23190 2796 3045 1121 8597 162 5085 2 10258 117958 11020 8154 6424 65068 882 16152 0.999974 0 . 0 COSM1626979 203 85,46,31,27 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I63|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 56 0 1.07251e-07 0.0433143 0 0.292961 rs28499298 -0.693147 0.990342 203 A85T 348 Gcc/Acc MODERATE 1 MISSENSE CODING OR2T4 A protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525135 G A 0 63 0 0.3374 0.3083 0.2392 0.3819 0.2207 0.3323 0 . 0 1 3845 34455 3521 3340 1901 16452 249 5147 2 10226 120428 11486 8516 6574 66372 902 16352 0.0286838 0 . 0 . 350 144,93,67,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A85T|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 55 0 3.73568e-12 9.27259e-07 0 0.719652 rs76721536 -0.693147 0.000849192 350 H86Y 348 Cac/Tac MODERATE 1 MISSENSE CODING OR2T4 T protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525138 C T 0 6.1 0 0.3343 0.3075 0.2392 0.3819 0.2207 0.3323 0 . 0 1 3701 34280 3502 3340 1901 16441 246 5149 2 10232 120364 11472 8506 6570 66342 902 16340 0.00121829 0 . 0 . 354 146,98,68,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H86Y|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 55 0 1.77213e-12 7.08259e-07 0 0.976165 rs75096121 -0.693147 0.00168085 354 H88 348 caC/caT LOW 1 SILENT CODING OR2T4 T protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525146 C T 0 139 0 . 0 . 0 . 0 0.193373 0.167231 0.153837 1 2181 24660 3195 2956 1257 10194 167 4710 2 10404 121366 11574 8622 6612 66736 908 16510 0.451511 0 . 0 . 366 170,70,47,30 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H88|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 55 0 0.146329 6.96764e-08 0 0.995761 rs28482938 -0.693147 0.00246176 366 A104V 348 gCg/gTg MODERATE 1 MISSENSE CODING OR2T4 T protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525193 C T 0 177 0 . 0 . 0 . 0 0.0295052 0.0920628 0.124127 1 322 21976 3097 2897 1233 9605 158 4664 2 10394 121276 11566 8594 6612 66694 908 16508 0.358371 0 . 0 . 354 117,104,40,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A104V|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 55 0 0.117214 0.112726 0 0.597046 rs28655275 -0.693147 0.956656 354 F135L 348 Ttc/Ctc MODERATE 1 MISSENSE CODING OR2T4 C protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525285 T C 0 62 0 0.3464 0.3353 0.2824 0.4514 0.1928 0.3845 0 . 0 1 3259 29777 3616 3645 1569 11655 204 5829 2 9624 117074 11028 8280 6346 64682 882 16232 0.169259 0 . 0 . 207 74,72,43,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F135L|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.00103524 0.942132 0 0.118138 rs28637620 -0.693147 0.0727212 207 Y136 348 taC/taT LOW 1 SILENT CODING OR2T4 T protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525290 C T 0 55 0 0.2678 0.3093 0.2752 0.4405 0.1899 0.3773 0 . 0 1 2663 29138 3588 3647 1568 11645 201 5826 2 9478 119098 11286 8468 6512 66028 896 16430 0.964848 0 . 0 . 203 74,69,40,7 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y136|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.000434296 0.885071 0 0.104938 rs202028348 -0.693147 0.0223256 203 V137L 348 Gtg/Ctg MODERATE 1 MISSENSE CODING OR2T4 C protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525291 G C 0 58 0 0.1551 0.2692 0.2622 0.4266 0.1779 0.3599 0 . 0 1 2661 29131 3580 3643 1567 11655 202 5823 2 9292 117980 11138 8380 6418 65558 888 16306 0.872954 0 . 0 . 204 75,68,40,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V137L|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.000434296 0.895024 0 0.185365 rs28540568 -0.693147 0.0223256 204 T149T? 348 acc/acTAc HIGH 1 CODING OR2T4 CTA protein_coding NM_001004696.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525328 C CTA 0 84 0 0.2284 0.2712 0.2637 0.381 0.1779 0.317 0 . 0 1 2288 25406 3330 3131 1284 10359 173 4841 2 10378 121046 11518 8556 6600 66666 908 16420 0 . 0 . 0 236 75,82,21,20 FRAME_SHIFT(HIGH||acc/acTAc|T149T?|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|CTA) 0 0.5 1 64 0.271186 1 1 0 1 (OR2T4|OR2T4|1|1.00) 59 0 0 0.248955 0 . rs61248663 -0.693145 0.922088 236 M150T? 348 atg/aCGtg HIGH 1 CODING OR2T4 ACG protein_coding NM_001004696.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525330 A ACG 0 84 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 235 82,81,21,20 FRAME_SHIFT(HIGH||atg/aCGtg|M150T?|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|ACG) 0 0.5 1 3 0.012766 0 1 0 . (OR2T4|OR2T4|1|1.00) 59 0 0 0.231646 0 . rs376643959 -0.693145 0.921019 235 L255 348 ctC/ctA LOW 1 SILENT CODING OR2T4 A protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525647 C A 0 222 0 0.239 0.2931 0.2709 0.4256 0.1799 0.362 0.240808 0.188836 0.162209 1 2463 27392 3608 3636 1355 10705 182 5443 2 10402 121318 11556 8614 6614 66714 908 16510 0.115456 0 . 0 . 343 112,65,96,45 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L255|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.00932958 0.162992 0 0.972318 rs28405645 -0.693147 0.295724 343 T256 348 acC/acT LOW 1 SILENT CODING OR2T4 T protein_coding NM_001004696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525650 C T 0 222 0 0.2398 0.2941 0.2709 0.4276 0.1799 0.364 0.240808 0.188759 0.162093 1 2465 27393 3611 3643 1355 10697 181 5441 2 10402 121334 11564 8626 6614 66714 908 16506 0.699549 0 . 0 . 337 111,63,95,45 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T256|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.00924278 0.162233 0 0.359396 rs28602650 -0.693147 0.231507 337 G259R 348 Ggg/Agg MODERATE 1 MISSENSE CODING OR2T4 A protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525657 G A 0 222 0 0.2405 0.2947 0.2709 0.4296 0.1799 0.364 0.239673 0.187759 0.161163 1 2468 27410 3610 3650 1355 10703 182 5442 2 10400 121326 11558 8620 6614 66718 908 16508 0.894379 0 . 0 . 347 111,62,98,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G259R|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.00098783 0.063648 0 0.998288 rs28718027 -0.693147 0.712117 347 P300S 348 Cct/Tct MODERATE 1 MISSENSE CODING OR2T4 T protein_coding NM_001004696.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248525780 C T 0 222 0 0.2405 0.2943 0.2709 0.4276 0.1799 0.364 0.241262 0.189374 0.162791 1 2468 27568 3661 3684 1360 10757 183 5455 2 10406 121388 11576 8636 6614 66736 908 16512 0.00719493 0 . 0 . 501 123,111,110,110 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P300S|348|OR2T4|protein_coding|CODING|NM_001004696.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.141791 0.00571256 0 0.372297 rs28698997 -0.693147 0.248329 501 N21D 308 Aat/Gat MODERATE 1 MISSENSE CODING OR2T6 G protein_coding NM_001005471.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248550970 A G 0 222 0 0.5234 0.3774 0.3156 0.4375 0.1769 0.3681 0.454607 0.253883 0.151047 1 4817 29673 3942 3702 1348 10130 189 5545 2 10402 120916 11572 8610 6608 66572 906 16246 0.936251 0 . 0 . 81 18,14,28,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N21D|308|OR2T6|protein_coding|CODING|NM_001005471.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.8962 rs7417616 -0.693146 0.566165 81 C23G 308 Tgc/Ggc MODERATE 1 MISSENSE CODING OR2T6 G protein_coding NM_001005471.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248550976 T G 0 228 0 0.8684 0.7728 0.7406 0.749 0.66 0.8067 0.849523 0.751115 0.700698 2 8905 87470 8316 6132 4534 46317 648 12618 2 10402 121278 11574 8618 6608 66694 906 16476 0 . 0 . 0 78 0,0,43,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C23G|308|OR2T6|protein_coding|CODING|NM_001005471.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6587467 -0.693147 0.445856 78 T98 308 acT/acC LOW 1 SILENT CODING OR2T6 C protein_coding NM_001005471.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248551203 T C 0 222 0 0.4962 0.3694 0.3127 0.4365 0.1769 0.3671 0.429641 0.245271 0.150814 1 4566 28422 3927 3704 1347 10009 184 4685 2 10340 116868 11546 8604 6612 65548 878 13340 0.900149 0 . 0 . 90 21,21,24,21 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T98|308|OR2T6|protein_coding|CODING|NM_001005471.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0573451 rs6700947 -0.693147 0.273912 90 S217 308 tcC/tcT LOW 1 SILENT CODING OR2T6 T protein_coding NM_001005471.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248551560 C T 0 222 0 0.2247 0.2937 0.2867 0.4365 0.175 0.3671 0.22424 0.174842 0.149535 1 2319 26975 3799 3703 1347 10093 176 5538 2 10404 121300 11566 8594 6612 66710 908 16506 0.997814 0 . 0 . 233 72,34,65,36 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S217|308|OR2T6|protein_coding|CODING|NM_001005471.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.018187 rs954474 -0.693147 0.00011336 233 S243A 308 Tca/Gca MODERATE 1 MISSENSE CODING OR2T6 G protein_coding NM_001005471.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248551636 T G 0 222 0 0.4962 0.3696 0.3127 0.4365 0.1769 0.3681 0.435996 0.247424 0.150814 1 4590 29415 3930 3709 1347 10130 188 5521 2 10402 121078 11568 8604 6612 66632 904 16356 0.96924 0 . 0 . 199 39,51,48,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S243A|308|OR2T6|protein_coding|CODING|NM_001005471.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987388 rs386623335,rs954475 -0.693147 0.16686 199 H25R 369 cAt/cGt MODERATE 1 MISSENSE CODING OR2T1 G protein_coding NM_030904.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248569369 A G 0 222 0 0.0424 0.3263 0.4078 0.3135 0.503 0.4836 0.137994 0.418269 0.56186 1 1277 56265 4282 2452 3234 36967 453 7600 2 10346 121258 11558 8636 6612 66690 908 16508 0.785755 0 . 0 . 80 35,4,24,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H25R|369|OR2T1|protein_coding|CODING|NM_030904.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992341 rs28599722 -0.693079 0.328938 80 V217 324 gtC/gtG LOW 1 SILENT CODING OR2T2 G protein_coding NM_001004136.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248616749 C G 0 105 0 . 0 . 0 . 0 . 0 . 1 17 648 69 94 31 240 12 185 2 10222 114904 10300 7504 6360 65022 874 14622 0.979382 0 . 0 COSM425928 11 0,3,5,3 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V217|324|OR2T2|protein_coding|CODING|NM_001004136.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.829029 0.356607 0 0.655816 rs151176830 -0.651104 0.770293 11 I222 324 atC/atT LOW 1 SILENT CODING OR2T2 T protein_coding NM_001004136.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248616764 C T 0 39.4 0 . 0 . 0 . 0 . 0 . 1 2 218 24 45 11 69 4 63 2 10252 115530 10338 7542 6382 65334 884 14798 0.992367 0 . 0 COSM1320257 8 1,3,4,0 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I222|324|OR2T2|protein_coding|CODING|NM_001004136.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 39 0 0.868321 0.450401 0 0.372138 rs376553658 -0.556411 0.348933 8 C132Y 318 tGc/tAc MODERATE 1 MISSENSE CODING OR2T3 A protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637046 G A 0 228 0 . 0 . 0 . 0 . 0 . 2 2347 31717 4280 3602 1772 14098 204 5414 2 9298 110796 10834 8094 5934 62248 798 13590 1 0 . 0 . 87 1,0,27,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C132Y|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|A) 0 . 0 . 0 . 0 . 1 0 33 0 1 0.235191 0 1 rs148025314 -0.693147 0.000498745 87 V155A 318 gTt/gCt MODERATE 1 MISSENSE CODING OR2T3 C protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637115 T C 0 227 0 . 0 . 0 . 0 . 0 . 2 2441 23525 2679 2338 1375 11085 156 3451 2 7876 90866 8238 5976 4978 52620 676 10502 0.987156 0 . 0 . 51 6,0,12,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V155A|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|C) 0 . 0 . 0 . 0 . 1 0 29 0 0.470553 0.999951 0 0.0472932 rs139558207,rs79056151 -0.693147 0.0944353 51 M204T 318 aTg/aCg MODERATE 1 MISSENSE CODING OR2T3 C protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637262 T C 0 104 0 0.0333 0.0952 0.0893 0.1944 0.0378 0.1401 0.0144578 0.0105499 0.00861038 2 24 564 108 88 73 193 4 74 2 9366 109068 9790 6820 5976 63202 828 13086 0 . 0 . 0 9 0,0,7,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M204T|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|C) 1 0 . 0 . 1 0 1 1 0 21 0 0 0.428571 0 . rs1770110 -0.662043 0.0387577 9 A214T 318 Gcc/Acc MODERATE 1 MISSENSE CODING OR2T3 A protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637291 G A 0 121 0 0.1263 0.1905 0.1916 0.2867 0.1064 0.2638 0 . 0 2 74 451 39 83 12 177 8 58 2 9338 108672 9672 6746 5964 63044 820 13088 0 . 0 . COSM225832 20 0,0,19,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A214T|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|A) 0 . 0 . 0 1 0 . 1 0 28 0 0 1 0 . rs1770109 -0.692067 1.03615e-06 20 A237 318 gcC/gcT LOW 1 SILENT CODING OR2T3 T protein_coding NM_001005495.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637362 C T 0 228 0 0.3124 0.3824 0.3775 0.503 0.2604 0.4816 0 . 0 2 3230 38304 4988 4271 2156 16054 260 7345 2 10316 120610 11530 8618 6544 66262 894 16446 0.163889 0 . 0 . 135 13,1,92,20 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A237|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|T) 0 . 0 . 0 1 0 . 1 0 41 0 0.0015021 0.0584932 0 2.99098e-05 rs77686526 -0.693147 1.25212e-07 135 L255 318 ctG/ctC LOW 1 SILENT CODING OR2T3 C protein_coding NM_001005495.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637416 G C 0 222 0 0.2572 0.2901 0.2853 0.3661 0.2097 0.3425 0 . 0 1 2423 26857 3380 2865 1429 11381 188 5191 2 9212 114226 11116 8184 6118 62864 854 15878 0.148286 0 . 0 . 326 141,6,112,39 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L255|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 42 0 0.000445597 0.48088 0 5.15073e-06 rs75924848 -0.693147 0.0121098 326 L256F 318 Ctc/Ttc MODERATE 1 MISSENSE CODING OR2T3 T protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637417 C T 0 222 0 0.2572 0.2901 0.2853 0.3661 0.2097 0.3425 0 . 0 1 2638 28623 3545 2966 1545 12405 196 5328 2 9488 116444 11318 8318 6272 64156 862 16030 0.836103 0 . 0 . 332 147,6,111,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L256F|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 42 0 0.000263605 0.603463 0 6.40291e-07 rs74711605 -0.693147 0.0177792 332 R298C 318 Cgc/Tgc MODERATE 1 MISSENSE CODING OR2T3 T protein_coding NM_001005495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248637543 C T 0 222 0 . 0 . 0 . 0 0.121935 0.0931486 0.0783834 1 2770 32487 4040 3313 1866 14546 225 5727 2 10368 121188 11564 8606 6606 66662 908 16474 0.721339 0 . 0 . 470 106,119,75,117 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R298C|318|OR2T3|protein_coding|CODING|NM_001005495.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 35 0 0.897498 0.520728 0 0.989702 rs139993642 -0.693147 0.0359073 470 K13R 315 aAg/aGg MODERATE 1 MISSENSE CODING OR2T5 G protein_coding NM_001004697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248651927 A G 0 228 0 0.9803 0.9165 0.8401 0.997 0.7614 0.9611 0 . 0 2 1791 22646 1861 2085 832 11618 180 4279 2 2166 40706 3208 2100 2748 24946 324 5214 0 . 0 . 0 102 0,0,43,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K13R|315|OR2T5|protein_coding|CODING|NM_001004697.1|1|G) 0 . 0 . 0 1 0 . 1 0 28 0 0 0.000974951 0 . rs1770043,rs201060805 -0.693147 4.00955e-16 102 K41M 315 aAg/aTg MODERATE 1 MISSENSE CODING OR2T5 T protein_coding NM_001004697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248652011 A T 0 83 0 0.7307 0.3916 0.2147 0.3542 0.1889 0.3057 0.487363 0.212643 0.0784816 1 6284 33151 3392 3243 1618 13422 224 4968 2 9648 118578 11358 8440 6538 65530 894 16170 0.507883 0 . 0 COSM249005 238 70,87,37,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aTg|K41M|315|OR2T5|protein_coding|CODING|NM_001004697.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 32 0 0.335468 0.216635 0 0.999092 rs150528589 -0.693147 2.87167e-22 238 G45E 315 gGa/gAa MODERATE 1 MISSENSE CODING OR2T5 A protein_coding NM_001004697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248652023 G A 0 92 0 . 0 . 0 . 0 . 0 . 1 6157 30287 2976 3008 1453 12004 204 4485 2 9782 115776 10934 8196 6378 63954 870 15662 0.98391 0 . 0 . 238 67,83,36,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G45E|315|OR2T5|protein_coding|CODING|NM_001004697.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.280653 0.233058 0 0.707424 rs139516854 -0.693147 1.94085e-20 238 V96I 315 Gtc/Atc MODERATE 1 MISSENSE CODING OR2T5 A protein_coding NM_001004697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248652175 G A 0 52 0 . 0 . 0 . 0 . 0 . 1 500 2219 152 217 119 930 23 278 2 1186 20720 1196 952 1534 13802 214 1836 0.741343 0 . 0 . 32 0,21,0,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V96I|315|OR2T5|protein_coding|CODING|NM_001004697.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 28 0 0.381293 0 . 0.611444 rs199519459 -0.676189 0.256378 32 Y102 316 taT/taC LOW 1 SILENT CODING OR2G6 C protein_coding NM_001013355.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248685253 T C 0 228 0 0.823 0.9519 0.9899 1 1 1 0.851112 0.9491 0.999302 2 8783 119659 11482 8652 6614 66716 902 16510 2 10398 121400 11578 8652 6614 66738 908 16512 0 . 0 . 0 69 0,0,21,46 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y102|316|OR2G6|protein_coding|CODING|NM_001013355.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9727474 -0.693147 0.715833 69 S114 315 tcG/tcA LOW 1 SILENT CODING OR2T29 T protein_coding NM_001004694.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722451 C T 0 49.4 0 . 0 . 0 . 0 . 0 . 1 2 109 3 23 0 67 1 13 2 164 708 20 66 2 406 6 44 0.547344 0 . 0 . 13 8,0,5,0 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S114|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|T) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.50373 0 . 0.50373 rs376895464 -0.590765 0.797968 13 V96I 315 Gtc/Atc MODERATE 1 MISSENSE CODING OR2T29 T protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722507 C T 0 84 0 . 0 . 0 . 0 . 0 . 1 288 2153 97 193 92 1141 22 320 2 678 4244 192 318 146 2316 46 548 0.606531 0 . 0 . 19 4,0,15,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V96I|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|T) 0 0.5 1 0 . 0 . 0 1 0 28 0 0.486752 0 . 0.546074 rs199706827 -0.688148 0.483806 19 A76V 315 gCg/gTg MODERATE 1 MISSENSE CODING OR2T29 A protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722566 G A 0 46.9 0 . 0 . 0 . 0 . 0 . 1 45 2551 245 360 246 1156 18 481 2 1628 11618 792 1066 696 5856 96 1484 0.906209 0 . 0 . 35 22,0,13,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A76V|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|A) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.00760512 0 . 0.261151 rs200777722 -0.683931 0.267187 35 S61T 315 aGc/aCc MODERATE 1 MISSENSE CODING OR2T29 G protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722611 C G 0 59 0 0.6467 0.4621 0.3833 0.4544 0.3171 0.4254 0 . 0 1 310 8752 725 880 627 4749 62 1399 2 2480 27036 1976 2122 1660 14774 200 3824 0.661933 0 . 0 . 57 14,0,43,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S61T|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 27 0 0.00583997 0 . 0.986177 rs200169450 -0.693146 0.127224 57 H58Y 315 Cac/Tac MODERATE 1 MISSENSE CODING OR2T29 A protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722621 G A 0 81 0 0.295 0.276 0.2233 0.3462 0.2217 0.271 0 . 0 1 346 8369 638 752 555 4632 58 1388 2 3006 36578 2928 2842 2280 19108 276 6138 0.874716 0 . 0 . 69 32,0,37,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H58Y|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.262109 0 . 0.962428 rs201345491 -0.693141 0.0947278 69 A57T 315 Gcc/Acc MODERATE 1 MISSENSE CODING OR2T29 T protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722624 C T 0 81 0 0.3578 0.2931 0.2277 0.3462 0.2217 0.271 0 . 0 1 373 8568 666 774 554 4719 60 1422 2 3074 37036 2960 2862 2258 19374 274 6234 0.96709 0 . 0 . 70 31,1,37,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A57T|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|T) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.187761 1 0 0.985911 rs200919674 -0.693141 0.0947278 70 G45E 315 gGa/gAa MODERATE 1 MISSENSE CODING OR2T29 T protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722659 C T 0 68 0 0.5545 0.3762 0.2795 0.3849 0.2535 0.3211 0 . 0 1 2080 14819 1128 1195 889 7138 105 2284 2 6006 58504 5482 5210 3220 28126 440 10020 0.838602 0 . 0 . 87 30,16,35,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G45E|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|T) 0 0.5 1 0 . 1 0 . 1 0 29 0 0.00168382 0.456392 0 0.00899866 rs201896684 -0.693139 0.0259295 87 K41M 315 aAg/aTg MODERATE 1 MISSENSE CODING OR2T29 A protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722671 T A 0 213 0 0.6399 0.498 0.4222 0.5427 0.338 0.4785 0 . 0 1 3913 37180 4143 4239 1987 16525 239 6134 2 6600 64096 6400 5984 3418 30126 466 11102 0.899563 0 . 0 . 100 20,0,56,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aTg|K41M|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 29 0 0.611156 0.998282 0 0.376181 rs140437806 -0.693147 0.0393696 100 Q24R 315 cAa/cGa MODERATE 1 MISSENSE CODING OR2T29 C protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722722 T C 0 67 0 0.5877 0.5984 0.6455 0.5228 0.7247 0.5276 0 . 0 1 2604 18707 1468 1552 999 9673 137 2274 2 6654 55782 5570 5506 2896 26424 362 8370 0.0645266 0 . 0 . 162 8,27,113,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q24R|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 30 0 0.394506 0.195108 0 1.2133e-14 rs199528787 -0.693147 2.42898e-12 162 Q24* 315 Caa/Taa HIGH 1 NONSENSE CODING OR2T29 A protein_coding NM_001004694.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722723 G A 0 137 0 0.0507 0.0749 0.0519 0.1538 0.0288 0.09 0 . 0 1 277 1894 182 366 96 538 22 413 2 7954 75900 7590 6794 4150 37716 542 11154 0.58216 0 . 0 . 164 31,30,90,4 STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q24*|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 30 0 0.60103 0.142524 0 2.398e-07 rs200037558 -0.693147 1.3266e-07 164 R6W 315 Agg/Tgg MODERATE 1 MISSENSE CODING OR2T29 A protein_coding NM_001004694.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248722777 T A 0 221 0 . 0 . 0 . 0 0.583296 0.353561 0.235807 1 6145 37045 3546 3262 1995 16668 259 5170 2 10296 118574 11182 8294 6506 65350 894 16052 0.402731 0 . 0 . 295 28,35,148,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Tgg|R6W|315|OR2T29|protein_coding|CODING|NM_001004694.2|1|A) 1 0.5 1 0 . 0 . 1 1 0 35 0 0.029068 0.000305317 0 0.758033 rs77589892 -0.693147 0.0291015 295 R298C 318 Cgc/Tgc MODERATE 1 MISSENSE CODING OR2T34 A protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737167 G A 0 34.7 0 . 0 . 0 . 0 . 0 . 1 876 12090 1344 1306 774 5313 89 2388 2 4554 61478 5332 4822 3598 34562 472 8138 0.294867 0 . 0 . 50 39,0,10,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R298C|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 36 0 0.0305032 0 . 0.241046 rs148590921 -0.670168 0.551647 50 R267P 318 cGg/cCg MODERATE 1 MISSENSE CODING OR2T34 G protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737259 C G 0 187 0 . 0 . 0 . 0 . 0 . 2 6891 97056 9922 7216 5717 55384 714 11212 2 7250 97454 9944 7222 5718 55394 714 11212 0 . 0 . 0 46 0,0,45,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R267P|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|G) 0 . 0 . 0 . 0 . 1 0 40 0 0 1 0 . rs1770107,rs189248971 -0.693147 0.980839 46 L256F 318 Ctc/Ttc MODERATE 1 MISSENSE CODING OR2T34 A protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737293 G A 0 72 0 0.379 0.3025 0.2536 0.3194 0.2018 0.32 0 . 0 1 3572 30520 3493 2908 1709 13335 217 5286 2 9740 118458 11326 8422 6552 65690 886 15842 0.999044 0 . 0 . 85 46,11,22,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L256F|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 43 0 0.559743 0.0170589 0 0.165237 rs200427293 -0.692562 0.782824 85 L255 318 ctG/ctC LOW 1 SILENT CODING OR2T34 G protein_coding NM_001001821.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737294 C G 0 63 0 0.379 0.3025 0.2536 0.3194 0.2018 0.32 0 . 0 1 3575 30524 3490 2909 1709 13337 217 5287 2 9792 118614 11312 8416 6552 65790 888 15864 0.793065 0 . 0 . 90 47,14,22,0 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L255|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 42 0 0.461697 0.00847629 0 0.080629 rs201475070 -0.692562 0.782824 90 A244T 318 Gcc/Acc MODERATE 1 MISSENSE CODING OR2T34 T protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737329 C T 0 221 0 . 0 . 0 . 0 0.205517 0.125714 0.0853488 1 2044 17076 2141 2603 721 5907 111 3549 2 10096 120916 11552 8592 6610 66676 906 16484 0.584678 0 . 0 . 137 32,1,60,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A244T|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 41 0 0.997848 0.000166964 0 0.864597 rs75095367 -0.693147 0.0604397 137 R239H 318 cGc/cAc MODERATE 1 MISSENSE CODING OR2T34 T protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737343 C T 0 14.9 0 . 0 . 0 . 0 . 0 . 1 2549 29168 3669 2927 1705 12792 207 5319 2 9978 118262 11170 8252 6448 65290 888 16236 0.160697 0 . 0 . 160 72,36,33,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R239H|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 43 0 0.999769 0.000171587 0 0.843604 rs61833441 -0.693132 0.153838 160 A237 318 gcC/gcT LOW 1 SILENT CODING OR2T34 A protein_coding NM_001001821.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737348 G A 0 8.3 0 0.5098 0.3245 0.2349 0.251 0.2107 0.3303 0 . 0 1 4838 39242 4288 3322 2263 18201 269 6061 2 10112 120026 11434 8418 6576 66214 898 16374 0.197514 0 . 0 . 164 72,40,33,1 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A237|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 43 0 0.820164 3.58885e-05 0 0.996533 rs61833442 -0.693132 0.204118 164 M202T 318 aTg/aCg MODERATE 1 MISSENSE CODING OR2T34 G protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737454 A G 0 222 0 . 0 . 0 . 0 0.0798479 0.0739382 0.0710465 1 971 16562 2134 2574 755 6426 110 3592 2 9732 120496 11560 8604 6588 66610 906 16496 0.729263 0 . 0 . 273 91,71,47,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M202T|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|G) 1 0.5 1 0 . 0 . 1 1 0 50 0 5.14312e-14 0.154126 0 0.0258375 rs79750523 -0.693147 8.72878e-05 273 V155A 318 gTt/gCt MODERATE 1 MISSENSE CODING OR2T34 G protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737595 A G 0 64 0 . 0 . 0 . 0 . 0 . 1 3850 38096 4294 3300 2260 18067 267 6058 2 8416 112748 10938 7950 6246 62678 854 15666 0.472573 0 . 0 COSM120080 130 56,35,0,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V155A|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 38 0 2.15762e-14 1.67469e-05 0 0.997821 rs150601708 -0.693144 0.944604 130 C132Y 318 tGc/tAc MODERATE 1 MISSENSE CODING OR2T34 T protein_coding NM_001001821.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248737664 C T 0 20.2 0 . 0 . 0 . 0 . 0 . 1 1638 16539 1913 1735 1040 7058 116 3039 2 7774 93188 8464 6598 4896 53348 698 11410 0.624781 0 . 0 . 130 60,30,0,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C132Y|318|OR2T34|protein_coding|CODING|NM_001001821.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 37 0 5.3657e-08 0.00364573 0 0.00319876 rs147489167 -0.692976 0.0315044 130 R26C 312 Cgc/Tgc MODERATE 1 MISSENSE CODING OR2T10 A protein_coding NM_001004693.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248756994 G A 0 222 0 0.239 0.0713 0.0274 0.0139 0.007 0.001 0.211557 0.0733301 0.00661782 1 2018 2802 134 88 3 486 10 63 2 8802 114676 11084 8280 6310 63472 858 15870 0.969205 0 . 0 . 85 25,16,21,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R26C|312|OR2T10|protein_coding|CODING|NM_001004693.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998213 rs28405936 -0.693127 0.5819 85 Q309R 316 cAg/cGg MODERATE 1 MISSENSE CODING OR2T11 C protein_coding NM_001001964.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248789504 T C 0 228 0 0.8578 0.9561 0.9841 1 0.9861 0.9928 0.856238 0.946971 0.990913 2 8148 115490 11184 8401 6381 64784 877 15715 2 9510 117784 11280 8406 6384 65376 884 15944 0 . 0 . 0 98 0,0,65,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q309R|316|OR2T11|protein_coding|CODING|NM_001001964.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1892442 -0.693147 0.102901 98 C119R 316 Tgc/Cgc MODERATE 1 MISSENSE CODING OR2T11 G protein_coding NM_001001964.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248790075 A G 0 228 0 0.6997 0.9129 0.9741 1 0.9861 0.9928 0.719863 0.902641 0.991031 2 6759 114341 11119 8398 6377 64860 878 15950 2 9438 118018 11268 8398 6380 65460 888 16186 0 . 0 . 0 146 0,0,83,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C119R|316|OR2T11|protein_coding|CODING|NM_001001964.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1892443 -0.693147 0.299412 146 G323D 323 gGc/gAc MODERATE 1 MISSENSE CODING OR2T35 T protein_coding NM_001001827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801592 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 95 102 1 1 0 4 1 0 2 2760 4934 260 32 34 1186 28 634 0.00196037 0 . 0 COSM291162 133 1,17,87,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G323D|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|T) 0 . 0 . 0 . 0 . 1 0 52 0 0.00139984 3.55862e-05 0 1.91733e-06 rs78622116 -0.693147 0.455837 133 A317V 323 gCg/gTg MODERATE 1 MISSENSE CODING OR2T35 A protein_coding NM_001001827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801610 G A 0 222 0 0.0129 0.0033946 0 0 0 0 0 . 0 1 42 46 0 0 0 4 0 0 2 3836 8394 408 178 184 2094 56 1638 0.00132657 0 . 0 . 142 9,39,58,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A317V|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.0488205 0.212795 0 1.64456e-13 rs150878651 -0.693147 1.66967e-06 142 A317T 323 Gcg/Acg MODERATE 1 MISSENSE CODING OR2T35 T protein_coding NM_001001827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801611 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 0 0 0 0 0 0 0 2 4312 9192 466 194 206 2228 56 1730 0.39025 0 . 0 . 142 9,39,58,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A317T|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 48 0 0.0488205 0.212795 0 1.64456e-13 rs143981271 -0.693147 1.66967e-06 142 G309 323 ggT/ggC LOW 1 SILENT CODING OR2T35 G protein_coding NM_001001827.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801633 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 9 164 8 21 6 76 1 43 2 3506 11122 596 514 364 3264 72 2806 0.0621797 0 . 0 . 167 15,53,53,35 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G309|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 48 0 0.338219 0.805558 0 3.9763e-10 rs74901534 -0.693147 0.0279959 167 L261Q 323 cTg/cAg MODERATE 1 MISSENSE CODING OR2T35 T protein_coding NM_001001827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801778 A T 0 222 0 0.416 0.5807 0.6455 0.5913 0.7137 0.6094 0 . 0 1 1103 13296 714 753 322 5911 125 4368 2 2370 21800 1338 1408 566 8724 194 7200 0.980481 0 . 0 . 180 58,14,85,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cAg|L261Q|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 34 0 0.838165 5.67786e-11 0 0.954938 rs201643849,rs61834268 -0.693147 0.135792 180 I221 323 atC/atT LOW 1 SILENT CODING OR2T35 A protein_coding NM_001001827.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248801897 G A 0 222 0 . 0 . 0 . 0 0.0304878 0.0795364 0.103201 1 264 18526 3011 2554 1058 7281 122 4236 2 8642 113026 10614 8046 6050 62994 844 15836 0.693781 0 . 0 COSM118819 427 78,120,83,108 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I221|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|A) 1 0.5 1 0 . 0 . 1 1 0 33 0 0.820906 0.0016766 0 0.842751 rs79303917 -0.693147 0.034692 427 V31I 323 Gta/Ata MODERATE 1 MISSENSE CODING OR2T35 T protein_coding NM_001001827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248802469 C T 0 42.7 0 . 0 . 0 . 0 . 0 . 2 402 1919 102 169 22 1036 17 171 2 2352 5560 294 176 28 2122 36 552 0 . 0 . 0 5 0,0,5,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V31I|323|OR2T35|protein_coding|CODING|NM_001001827.1|1|T) 0 . 0 . 0 . 0 . 1 0 20 0 0 . 0 . rs199678335 -0.590765 0.697632 5 V213 317 gtC/gtG LOW 1 SILENT CODING OR2T27 C protein_coding NM_001001824.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248813547 G C 0 126 0 . 0 . 0 . 0 . 0 . 2 429 4503 265 258 81 2670 55 745 2 7048 25064 1714 2498 750 10962 212 1880 1 0 . 0 . 27 1,0,1,25 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V213|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|C) 0 . 0 . 0 . 0 . 1 0 34 0 1 0.62 0 1 rs201161767 -0.692976 0.0353879 27 Y120C 317 tAt/tGt MODERATE 1 MISSENSE CODING OR2T27 C protein_coding NM_001001824.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248813827 T C 0 166 0 . 0 . 0 . 0 . 0 . 2 638 18417 1297 950 816 11272 155 3289 2 9216 73546 6298 4854 3318 40082 550 9228 0.608696 0 . 0 . 25 0,2,10,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y120C|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|C) 0 . 0 . 0 . 0 . 1 0 28 0 0.0869565 0.0906831 0 0.73913 rs1782241 -0.692717 0.00682864 25 A95 317 gcT/gcA LOW 1 SILENT CODING OR2T27 T protein_coding NM_001001824.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248813901 A T 0 228 0 . 0 . 0 . 0 . 0 . 2 5585 59321 5610 4932 3106 30575 452 9061 2 9550 102768 9060 6850 5354 56296 790 14868 0 . 0 . 0 65 0,0,50,15 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A95|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|T) 0 . 0 . 0 . 0 . 1 0 30 0 0 0.99891 0 . rs144600224 -0.693147 0.00921724 65 K45M 317 aAg/aTg MODERATE 1 MISSENSE CODING OR2T27 A protein_coding NM_001001824.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248814052 T A 0 209 0 . 0 . 0 . 0 . 0 . 1 5266 64944 6814 4587 3692 33908 492 10185 2 10208 119262 11314 8544 6404 65522 892 16378 0.990351 0 . 0 . 229 44,11,101,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aTg|K45M|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 34 0 0.890048 4.71158e-08 0 0.442123 rs28533004 -0.693147 0.962083 229 L36V 317 Ttg/Gtg MODERATE 1 MISSENSE CODING OR2T27 C protein_coding NM_001001824.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248814080 A C 0 228 0 0.8056 0.9447 0.9769 1 0.996 1 0 . 0 2 8724 119202 11445 8654 6582 66402 895 16500 2 10384 121158 11538 8654 6582 66588 906 16506 0.592342 0 . 0 . 237 1,1,100,122 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L36V|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|C) 0 . 0 . 0 1 0 . 1 0 33 0 0.238739 9.29527e-24 0 0.558559 rs1782242,rs55932833 -0.693147 1.26429e-07 237 N20 317 aaC/aaT LOW 1 SILENT CODING OR2T27 A protein_coding NM_001001824.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248814126 G A 0 228 0 . 0 . 0 . 0 . 0 . 2 5737 69463 7412 7275 3712 34694 524 10109 2 10368 120794 11500 8646 6540 66370 906 16464 1 0 . 0 . 279 0,1,90,155 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N20|317|OR2T27|protein_coding|CODING|NM_001001824.1|1|A) 0 . 0 . 0 . 0 . 1 0 41 0 1 6.25904e-19 0 1 rs28418327 -0.693147 0.181605 279 S170N 311 aGt/aAt MODERATE 1 MISSENSE CODING OR14I1 T protein_coding NM_001004734.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248845097 C T 0 228 0 0.4251 0.7518 0.8703 0.872 0.8777 0.8558 0.49773 0.750192 0.879535 2 5060 100156 9470 7161 5448 58178 757 14082 2 10380 121228 11532 8632 6600 66674 902 16508 0 . 0 . 0 157 0,0,55,91 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S170N|311|OR14I1|protein_coding|CODING|NM_001004734.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2000390 -0.693147 0.00165182 157 S65 311 tcC/tcT LOW 1 SILENT CODING OR14I1 A protein_coding NM_001004734.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248845411 G A 0 228 0 0.503 0.7732 0.8775 0.872 0.8787 0.8538 0.562415 0.77272 0.880465 2 5781 100983 9538 7182 5458 58239 763 14022 2 10402 121360 11572 8646 6612 66712 906 16510 0 . 0 . 0 192 0,0,82,88 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S65|311|OR14I1|protein_coding|CODING|NM_001004734.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11485825 -0.693147 0.32908 192 D50N 311 Gat/Aat MODERATE 1 MISSENSE CODING OR14I1 T protein_coding NM_001004734.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248845458 C T 0 228 0 0.3964 0.7464 0.866 0.872 0.8857 0.862 0.461416 0.740581 0.883605 2 4686 100312 9486 7178 5462 58519 763 14218 2 10404 121382 11574 8644 6614 66728 908 16510 0 . 0 . 0 164 0,0,53,97 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D50N|311|OR14I1|protein_coding|CODING|NM_001004734.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4509608 -0.693147 0.00704286 164 A45 311 gcA/gcG LOW 1 SILENT CODING OR14I1 C protein_coding NM_001004734.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248845471 T C 0 228 0 0.5507 0.874 0.9539 1 0.996 0.999 0.608715 0.863678 0.994302 2 6252 116666 11338 8654 6609 66435 882 16496 2 10404 121406 11578 8654 6614 66738 908 16510 0 . 0 . 0 156 0,0,48,92 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A45|311|OR14I1|protein_coding|CODING|NM_001004734.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4575113 -0.693147 4.20653e-05 156 V36A 311 gTg/gCg MODERATE 1 MISSENSE CODING OR14I1 G protein_coding NM_001004734.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 248845499 A G 0 228 0 0.6679 0.9071 0.9669 1 0.997 1 0.716296 0.901123 0.995814 2 7428 118010 11404 8653 6614 66522 891 16498 2 10402 121398 11578 8654 6614 66732 908 16510 0 . 0 . 0 145 0,0,50,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V36A|311|OR14I1|protein_coding|CODING|NM_001004734.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4462184 -0.693147 0.0267271 145 393 936 MODIFIER 7 CODING SH3BP5L C protein_coding NM_030645.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 249105163 T C 0 222 0 0.8593 0.4643 0.2262 0.5565 0.1451 0.3323 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999991 0 . 0 . 96 28,16,21,21 UTR_3_PRIME(MODIFIER||936||393|SH3BP5L|protein_coding|CODING|NM_030645.1|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.527065 rs386592336,rs4307600 -0.693146 0.228109 96 393 LOW 5 CODING SH3BP5L T protein_coding NM_030645.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 1 249108640 C T 0 200 0 0.5174 0.2616 0.0879 0.3869 0.0934 0.0828 0.463459 0.22405 0.101395 1 4707 16683 768 2733 643 6385 106 1341 2 10078 118138 11212 8462 5996 65378 868 16144 0.701037 0 . 0 . 65 31,3,21,5 SPLICE_SITE_REGION+INTRON(LOW||||393|SH3BP5L|protein_coding|CODING|NM_030645.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947571 rs12031808 -0.692976 0.14325 65 P243 444 ccG/ccA LOW 4 SILENT CODING TUBB8 T protein_coding NM_177987.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93603 C T 0 222 0 0.73 0.6701 0.6715 0.4812 0.8101 0.6391 0 . 0 1 5704 78776 6005 3782 4704 47104 605 10872 2 7906 108970 10606 7758 6266 59464 824 16146 0.906296 0 . 0 . 116 48,17,40,9 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P243|444|TUBB8|protein_coding|CODING|NM_177987.2|4|T) 0 0.5 1 0 . 1 0 . 1 0 47 0 0.974765 0.989515 0 0.974131 rs6560827 -0.693147 0.0318271 116 S172 444 tcG/tcA LOW 4 SILENT CODING TUBB8 T protein_coding NM_177987.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93816 C T 0 222 0 0.2973 0.2879 0.2378 0.2163 0.3549 0.316 0.254314 0.296199 0.317663 1 2934 38118 2517 1928 2336 22407 302 5694 2 9994 119008 11402 8648 6558 65094 888 16424 0.834274 0 . 0 COSM146863 245 71,57,47,46 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S172|444|TUBB8|protein_coding|CODING|NM_177987.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.939353 0.926336 0 0.956171 rs9329305 -0.693147 0.50047 245 C129 444 tgC/tgT LOW 4 SILENT CODING TUBB8 A protein_coding NM_177987.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93945 G A 0 222 0 0.528 0.5228 0.5447 0.4226 0.6103 0.5133 0 . 0 1 4964 64822 5634 3623 3756 37560 500 8785 2 9506 118432 11438 8592 6590 64918 900 16488 0.692348 0 . 0 . 238 64,60,50,48 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C129|444|TUBB8|protein_coding|CODING|NM_177987.2|4|A) 0 0.5 1 0 . 1 0 . 1 0 53 0 0.901855 0.00383713 0 0.998075 rs4431953 -0.693147 0.10301 238 E537 602 gaA/gaG LOW 14 SILENT CODING ZMYND11 G protein_coding NM_006624.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 294953 A G 0 228 0 0.8805 0.9359 0.9164 0.9454 0.9781 0.9714 0.898547 0.95133 0.978372 2 9193 116719 10770 8139 6506 65201 863 16047 2 10402 121394 11578 8646 6614 66734 908 16512 0 . 0 . 0 136 0,0,60,59 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E537|602|ZMYND11|protein_coding|CODING|NM_006624.5|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1017361 -0.693147 0.521991 136 1556 LOW 25 CODING DIP2C C protein_coding NM_014974.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 395266 T C 0 228 0 0.9297 0.9806 0.9942 1 1 1 0.931457 0.976469 0.999535 2 9517 118899 11476 8590 6484 65557 877 16398 2 10194 119646 11514 8590 6484 65582 882 16400 0 . 0 . 0 49 0,0,28,18 SPLICE_SITE_REGION+INTRON(LOW||||1556|DIP2C|protein_coding|CODING|NM_014974.2|25|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4880611 -0.693147 0.302328 49 P416 1556 ccG/ccA LOW 10 SILENT CODING DIP2C T protein_coding NM_014974.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 445061 C T 0 228 0 0.938 0.9794 0.9942 0.9861 0.998 0.999 0.933273 0.975242 0.996744 2 9674 120053 11495 8496 6584 66411 886 16507 2 10368 121250 11572 8650 6584 66660 906 16510 0 . 0 . 0 129 0,0,79,33 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P416|1556|DIP2C|protein_coding|CODING|NM_014974.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6560837 -0.693147 0.0631558 129 A250 634 gcG/gcA LOW 7 SILENT CODING GTPBP4 A protein_coding NM_012341.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1046712 G A 0 222 0 0.407 0.5302 0.5447 0.6111 0.5199 0.6135 0.434862 0.496386 0.527907 1 4431 64341 6374 5028 3706 34922 497 9383 2 10390 119710 11554 8612 6614 66218 896 15426 0.971879 0 . 0 . 131 54,7,50,9 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A250|634|GTPBP4|protein_coding|CODING|NM_012341.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.5652 rs2306409 -0.693147 0.274962 131 R525H 634 cGt/cAt MODERATE 15 MISSENSE CODING GTPBP4 A protein_coding NM_012341.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1060218 G A 0 222 0 0.0477 0.0795 0.0576 0.0972 0.0795 0.1196 0.0658193 0.0861141 0.0965116 1 638 10100 584 971 73 5842 76 1916 2 10404 121398 11572 8654 6614 66734 908 16512 0.9613 0 . 0 . 147 39,19,33,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R525H|634|GTPBP4|protein_coding|CODING|NM_012341.2|15|A),DOWNSTREAM(MODIFIER||4629||227|IDI2|protein_coding|CODING|NM_033261.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994222 rs3207775 -0.693147 2.66085e-05 147 P561 634 ccG/ccA LOW 16 SILENT CODING GTPBP4 A protein_coding NM_012341.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1061767 G A 0 222 0 0.0492 0.0803 0.0576 0.0972 0.0805 0.1207 0.0674081 0.0865754 0.0963954 1 649 10091 584 947 73 5843 77 1918 2 10406 121326 11578 8650 6614 66696 908 16474 0.997866 0 . 0 . 249 74,38,79,25 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P561|634|GTPBP4|protein_coding|CODING|NM_012341.2|16|A),DOWNSTREAM(MODIFIER||3080||227|IDI2|protein_coding|CODING|NM_033261.2||A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.999971 0.935055 0 0.950659 rs2306405 -0.693147 0.342255 249 634 274 MODIFIER 17 CODING GTPBP4 G protein_coding NM_012341.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1063441 T G 0 89 0 0.9811 0.9946 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_3_PRIME(MODIFIER||274||634|GTPBP4|protein_coding|CODING|NM_012341.2|17|G),DOWNSTREAM(MODIFIER||1406||227|IDI2|protein_coding|CODING|NM_033261.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2387218 -0.590765 0.128355 5 634 280 MODIFIER 17 CODING GTPBP4 G protein_coding NM_012341.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1063447 A G 0 91 0 0.9811 0.9946 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_3_PRIME(MODIFIER||280||634|GTPBP4|protein_coding|CODING|NM_012341.2|17|G),DOWNSTREAM(MODIFIER||1400||227|IDI2|protein_coding|CODING|NM_033261.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2387219 -0.590765 0.128355 5 227 517 MODIFIER 5 CODING IDI2 T protein_coding NM_033261.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1064940 C T 0 9.7 0 0.6778 0.7406 0.7507 0.7113 0.8111 0.7761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||517||227|IDI2|protein_coding|CODING|NM_033261.2|5|T),DOWNSTREAM(MODIFIER||1232||634|GTPBP4|protein_coding|CODING|NM_012341.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2170142,rs386492509 -0.379885 0 1 227 325 MODIFIER 5 CODING IDI2 T protein_coding NM_033261.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1065132 C T 0 32.6 0 0.9811 0.9938 0.9971 0.999 1 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||325||227|IDI2|protein_coding|CODING|NM_033261.2|5|T),DOWNSTREAM(MODIFIER||1424||634|GTPBP4|protein_coding|CODING|NM_012341.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2127607 -0.379885 0 2 E121 227 gaG/gaA LOW 4 SILENT CODING IDI2 T protein_coding NM_033261.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1066710 C T 0 222 0 0.0484 0.0849 0.0764 0.0972 0.0905 0.1217 0.0689968 0.092342 0.104302 1 656 10712 679 944 97 6323 80 1933 2 10384 119306 11530 8632 6606 66154 888 15112 0.989168 0 . 0 . 50 13,10,7,15 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E121|227|IDI2|protein_coding|CODING|NM_033261.2|4|T),DOWNSTREAM(MODIFIER||3002||634|GTPBP4|protein_coding|CODING|NM_012341.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.954107 rs34407608 -0.692562 0.0244199 50 494 15300 MODIFIER 1 CODING WDR37 G protein_coding NM_014023.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1102796 C G 0 9.7 0 0.6732 0.5843 0.5029 0.6131 0.4652 0.6145 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||15300||494|WDR37|protein_coding|CODING|NM_014023.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs35656218 -0.379885 0 1 494 655 MODIFIER 14 CODING WDR37 T protein_coding NM_014023.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1175939 C T 0 228 0 0.1732 0.4401 0.4986 0.5347 0.4801 0.6207 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,32,3 UTR_3_PRIME(MODIFIER||655||494|WDR37|protein_coding|CODING|NM_014023.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12359210 -0.693136 0.452458 36 739 4797 MODIFIER 10 CODING ADARB2 C protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1224336 T C 0 125 0 0.7474 0.7754 0.8242 0.7004 0.8201 0.8098 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||4797||739|ADARB2|protein_coding|CODING|NM_018702.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6560716 -0.556411 0.459448 5 739 4674 MODIFIER 10 CODING ADARB2 T protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1224459 C T 0 9.7 0 0.7118 0.7398 0.7781 0.6994 0.7525 0.7791 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4674||739|ADARB2|protein_coding|CODING|NM_018702.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1500966 -0.379885 0 1 739 3376 MODIFIER 10 CODING ADARB2 G protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1225757 A G 0 9.7 0 0.7723 0.9259 0.9769 0.9613 0.999 0.9857 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3376||739|ADARB2|protein_coding|CODING|NM_018702.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1983027,rs386551338 -0.379885 0 1 739 3127 MODIFIER 10 CODING ADARB2 G protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1226006 A G 0 46.3 0 0.6906 0.9036 0.9712 0.9613 0.999 0.9857 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3127||739|ADARB2|protein_coding|CODING|NM_018702.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7081909 -0.453602 0.86 2 739 3060 MODIFIER 10 CODING ADARB2 C protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1226073 G C 0 32.6 0 0.8162 0.9377 0.9784 0.9613 0.999 0.9857 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3060||739|ADARB2|protein_coding|CODING|NM_018702.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7097304 -0.379885 0 2 739 2350 MODIFIER 10 CODING ADARB2 T protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1226783 C T 0 39.3 0 0.0772 0.2993 0.2738 0.3651 0.3748 0.4724 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2350||739|ADARB2|protein_coding|CODING|NM_018702.3|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17293692 -0.453602 0.06 2 739 223 MODIFIER 10 CODING ADARB2 G protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1228910 A G 0 228 0 0.9206 0.9776 0.9899 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,32,2 UTR_3_PRIME(MODIFIER||223||739|ADARB2|protein_coding|CODING|NM_018702.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs904959 -0.693132 0.234516 35 739 124 MODIFIER 10 CODING ADARB2 A protein_coding NM_018702.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1229009 G A 0 228 0 0.5855 0.6494 0.5447 0.7123 0.6819 0.7117 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 98 0,1,74,11 UTR_3_PRIME(MODIFIER||124||739|ADARB2|protein_coding|CODING|NM_018702.3|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs904960 -0.693147 0.00697474 98 A626T 739 Gcc/Acc MODERATE 9 MISSENSE CODING ADARB2 T protein_coding NM_018702.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1230968 C T 0 228 0 0.2504 0.5431 0.5115 0.6696 0.6809 0.6892 0.322742 0.560529 0.68241 2 3062 75459 6449 5774 3983 44344 584 11263 2 9688 117846 11410 8512 6172 64822 872 16370 1 0 . 0 COSM1560925 140 0,1,43,82 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A626T|739|ADARB2|protein_coding|CODING|NM_018702.3|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2271275 -0.693147 0.386814 140 G91S 739 Ggc/Agc MODERATE 3 MISSENSE CODING ADARB2 T protein_coding NM_018702.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1406029 C T 0 222 0 0 0.01218 0.0014 0.0585 0.001 0 0 . 0 1 5 655 127 311 112 80 5 15 2 2600 44284 4104 3332 1842 22074 332 10000 0.867315 0 . 0 . 55 6,19,5,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G91S|739|ADARB2|protein_coding|CODING|NM_018702.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.783525 rs3750673 -0.692914 0.145242 55 A44T 739 Gct/Act MODERATE 2 MISSENSE CODING ADARB2 T protein_coding NM_018702.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1421326 C T 0 222 0 0.0257 0.0503 0.0086 0.12 0.0209 0.0716 0.0240581 0.0173766 0.0139535 1 275 3872 299 969 250 1101 24 954 2 10362 120700 11554 8626 6608 66334 896 16320 0.656519 0 . 0 . 130 21,30,26,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A44T|739|ADARB2|protein_coding|CODING|NM_018702.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.522432 rs3793733,rs386586428 -0.693147 0.0144423 130 739 5 MODIFIER 1 CODING ADARB2 A protein_coding NM_018702.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 1779349 G A 0 222 0 0.4811 0.4459 0.464 0.1647 0.5765 0.5409 0.510667 0.544902 0.562442 1 5217 60078 4908 1358 3271 36123 465 8736 2 10118 119358 11470 8434 6550 65418 886 16482 0.959102 0 . 0 . 107 17,35,12,30 START_GAINED(LOW||||739|ADARB2|protein_coding|CODING|NM_018702.3|1|A),UTR_5_PRIME(MODIFIER||5||739|ADARB2|protein_coding|CODING|NM_018702.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.759643 rs3750684 -0.693146 0.0604314 107 R117 784 cgA/cgC LOW 4 SILENT CODING PFKP C protein_coding NM_002627.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3143643 A C 0 228 0 0.9962 0.9986 1 0.998 1 1 1 1 1 2 9450 113385 11067 8398 5120 62860 794 15696 2 9466 113424 11070 8400 5120 62878 794 15696 0 . 0 . 0 206 0,0,129,46 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgC|R117|784|PFKP|protein_coding|CODING|NM_002627.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4881080 -0.693147 0.0208181 206 784 LOW 7 CODING PFKP G protein_coding NM_002627.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3149402 A G 0 228 0 0.385 0.5954 0.5317 0.8145 0.661 0.6319 0.4075 0.561077 0.639651 2 4041 74094 5030 6893 4361 42692 556 10521 2 10032 120002 11462 8636 6602 65934 900 16436 0 . 0 . 0 76 0,0,52,17 SPLICE_SITE_REGION+INTRON(LOW||||784|PFKP|protein_coding|CODING|NM_002627.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10903967 -0.693147 0.0683778 76 A427 784 gcA/gcG LOW 13 SILENT CODING PFKP G protein_coding NM_002627.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3155620 A G 0 228 0 0.413 0.6062 0.5749 0.8363 0.6471 0.6104 0.446437 0.566738 0.628372 2 4466 73325 6069 7052 4212 41412 534 9580 2 10232 118382 11460 8590 6460 65282 876 15482 0 . 0 . 0 128 0,0,57,60 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A427|784|PFKP|protein_coding|CODING|NM_002627.4|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1052309 -0.693147 0.00419017 128 784 110 MODIFIER 22 CODING PFKP T protein_coding NM_002627.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3178881 C T 0 55 0 0.0144 0.1805 0.1772 0.2153 0.2783 0.271 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.895781 0 . 0 . 11 1,5,1,3 UTR_3_PRIME(MODIFIER||110||784|PFKP|protein_coding|CODING|NM_002627.4|22|T),DOWNSTREAM(MODIFIER||1038||1038|PITRM1|protein_coding|CODING|NM_001242307.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.503877 rs1053000 -0.556411 0.977157 11 784 134 MODIFIER 22 CODING PFKP A protein_coding NM_002627.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3178905 T A 0 115 0 0.8359 0.8842 0.9265 0.8899 0.9304 0.8661 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,0,7 UTR_3_PRIME(MODIFIER||134||784|PFKP|protein_coding|CODING|NM_002627.4|22|A),DOWNSTREAM(MODIFIER||1014||1038|PITRM1|protein_coding|CODING|NM_001242307.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7673 -0.636426 0.0219768 7 784 144 MODIFIER 22 CODING PFKP T protein_coding NM_002627.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3178915 C T 0 38.4 0 0.0318 0.1753 0.1729 0.2153 0.2604 0.2423 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 7 0,4,0,3 UTR_3_PRIME(MODIFIER||144||784|PFKP|protein_coding|CODING|NM_002627.4|22|T),DOWNSTREAM(MODIFIER||1004||1038|PITRM1|protein_coding|CODING|NM_001242307.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 1.01283 rs541 -0.511536 0.206307 7 Q1038R 1038 cAa/cGa MODERATE 27 MISSENSE CODING PITRM1 C protein_coding NM_001242307.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3180227 T C 0 228 0 0.6861 0.7043 0.6527 0.7361 0.7177 0.7188 0.723013 0.714412 0.710218 2 5299 71241 6744 5624 3634 39614 483 9843 2 7304 98936 9136 7404 5080 55788 720 13504 0 . 0 . 0 37 0,0,26,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q1038R|1038|PITRM1|protein_coding|CODING|NM_001242307.1|27|C),DOWNSTREAM(MODIFIER||1230||784|PFKP|protein_coding|CODING|NM_002627.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6901 -0.693136 0.135844 37 P970L 1038 cCt/cTt MODERATE 25 MISSENSE CODING PITRM1 A protein_coding NM_001242307.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3181107 G A 0 222 0 0.0061 0.0357 0.0533 0.1151 0.002 0.0164 0.00198413 0.00161134 0.00143198 1 32 2717 1225 1146 0 72 9 233 2 9800 120764 11576 8624 6614 66740 898 16512 0.598556 0 . 0 . 163 33,48,35,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P970L|1038|PITRM1|protein_coding|CODING|NM_001242307.1|25|A),DOWNSTREAM(MODIFIER||2110||784|PFKP|protein_coding|CODING|NM_002627.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.954747 rs2279218 -0.693147 0.119586 163 P767 1038 ccG/ccA LOW 20 SILENT CODING PITRM1 T protein_coding NM_001242307.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3189380 C T 0 228 0 0.4508 0.5453 0.5403 0.6865 0.5239 0.5532 0.46742 0.484336 0.492131 2 4643 63147 7324 5936 3136 32824 445 8839 2 9798 120720 11572 8614 6614 66724 896 16502 1 0 . 0 . 110 0,1,44,54 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P767|1038|PITRM1|protein_coding|CODING|NM_001242307.1|20|T),INTRAGENIC(MODIFIER|||||PITRM1-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3740607 -0.693147 0.00988381 110 Q516H 1038 caG/caC MODERATE 14 MISSENSE CODING PITRM1 G protein_coding NM_001242307.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3197856 C G 0 222 0 0.031 0.1422 0.1225 0.3145 0.0746 0.1984 0.0301641 0.051883 0.0625444 1 313 12148 1796 2563 772 4060 72 2572 2 9800 120728 11572 8600 6614 66736 894 16512 0.978137 0 . 0 COSM146866 132 36,25,32,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q516H|1038|PITRM1|protein_coding|CODING|NM_001242307.1|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.748931 rs3765101 -0.693147 0.846449 132 A397V 1038 gCg/gTg MODERATE 11 MISSENSE CODING PITRM1 A protein_coding NM_001242307.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3200292 G A 0 222 0 0.5719 0.626 0.5677 0.6022 0.7097 0.6789 0.631647 0.681968 0.705569 1 5940 79386 6241 5086 4629 45641 584 11265 2 9804 120582 11548 8590 6606 66638 898 16498 0.230313 0 . 0 . 157 39,37,22,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A397V|1038|PITRM1|protein_coding|CODING|NM_001242307.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.924353 rs3182535 -0.693147 0.478164 157 I328V 1038 Atc/Gtc MODERATE 9 MISSENSE CODING PITRM1 C protein_coding NM_001242307.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3202065 T C 0 222 0 0.5923 0.6208 0.5591 0.6032 0.671 0.6697 0.679703 0.687322 0.690909 1 5521 68096 5017 4548 4105 39004 490 9411 2 8596 101876 8738 7328 5810 56938 762 13704 0.801679 0 . 0 . 66 17,14,12,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I328V|1038|PITRM1|protein_coding|CODING|NM_001242307.1|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994592 rs4242746 -0.692976 0.363978 66 P227 1038 ccT/ccC LOW 7 SILENT CODING PITRM1 G protein_coding NM_001242307.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3206027 A G 0 222 0 0.5393 0.6242 0.5793 0.6032 0.6988 0.7157 0.604296 0.684015 0.721308 1 5600 80043 6217 5118 4580 46292 585 11651 2 9790 120656 11560 8608 6610 66688 896 16504 0.867859 0 . 0 . 148 42,16,40,29 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P227|1038|PITRM1|protein_coding|CODING|NM_001242307.1|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.64935 rs4609511 -0.693147 0.0390196 148 T94 1038 acT/acC LOW 4 SILENT CODING PITRM1 G protein_coding NM_001242307.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3208557 A G 0 222 0 0.5915 0.6396 0.5807 0.6042 0.7018 0.7188 0.654336 0.700595 0.723193 1 6134 80860 6206 5077 4608 46574 582 11679 2 9794 120456 11554 8578 6612 66572 896 16450 0.668316 0 . 0 . 162 28,58,24,38 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T94|1038|PITRM1|protein_coding|CODING|NM_001242307.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0699334 rs12359035 -0.693147 0.771798 162 283 170 MODIFIER 4 CODING KLF6 A protein_coding NM_001300.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 3821561 G A 0 222 0 0.0265 0.2706 0.2723 0.4821 0.3489 0.3006 0 . 0 1 66 4715 66 184 13 1656 73 2657 2 472 12876 176 324 34 4110 146 7614 0.910073 0 . 0 . 24 6,4,6,7 UTR_3_PRIME(MODIFIER||170||283|KLF6|protein_coding|CODING|NM_001300.5|4|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.573631 rs17731 -0.683931 0.456033 24 320 72 MODIFIER 1 CODING AKR1E2 T protein_coding NM_001040177.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 4868445 G T 0 173 0 0.5045 0.7712 0.8905 0.877 0.8698 0.8364 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,2 UTR_5_PRIME(MODIFIER||72||320|AKR1E2|protein_coding|CODING|NM_001040177.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2924275 -0.651104 0.0804486 8 R51H 320 cGt/cAt MODERATE 2 MISSENSE CODING AKR1E2 A protein_coding NM_001040177.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 4872979 G A 0 222 0 0 0.00019968 0 0.001 0 0 0 7.6888e-05 0.000116279 1 0 33 0 27 1 4 0 1 2 10402 121396 11574 8654 6614 66734 908 16510 0.970454 0 . 0 . 126 36,29,29,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R51H|320|AKR1E2|protein_coding|CODING|NM_001040177.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.457317 rs150563421 -0.693147 0.430532 126 T147 323 acA/acG LOW 4 SILENT CODING AKR1C1 G protein_coding NM_001353.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5010572 A G 0 228 0 0.9917 0.9972 1 1 0.999 0.998 0 . 0 2 6050 69038 6552 6015 4243 36233 529 9416 2 6100 69200 6554 6018 4246 36302 530 9450 0 . 0 . COSM1559317 88 0,0,47,41 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T147|323|AKR1C1|protein_coding|CODING|NM_001353.5|4|G) 0 . 0 . 0 1 0 . 1 0 41 0 0 0.00196899 0 . rs1138600 -0.693147 0.0355918 88 323 LOW 8 CODING AKR1C1 G protein_coding NM_001353.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5018132 A G 0 228 0 0.6808 0.6873 0.7493 0.7937 0.6541 0.5767 0 . 0 2 168 796 47 84 6 435 10 46 2 252 1252 68 112 8 724 14 74 0 . 0 . 0 23 0,0,14,9 SPLICE_SITE_REGION+INTRON(LOW||||323|AKR1C1|protein_coding|CODING|NM_001353.5|8|G) 0 . 0 . 0 1 0 . 1 0 43 0 0 0.167677 0 . rs201420087 -0.692717 0.0245928 23 323 25 MODIFIER 9 CODING AKR1C1 A protein_coding NM_001353.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5019959 G A 0 228 0 0.6346 0.5224 0.6037 0.5526 0.4115 0.3957 0.610808 0.449622 0.366674 2 6111 52586 6978 4695 3643 24226 399 6534 2 10024 116670 11158 8336 6436 63662 884 16170 0 . 0 . 0 66 0,0,28,38 UTR_3_PRIME(MODIFIER||25||323|AKR1C1|protein_coding|CODING|NM_001353.5|9|A) 1 0 . 0 . 1 0 1 1 0 55 0 0 0.192118 0 . rs8483 -0.693147 0.00681543 66 323 311 MODIFIER 11 CODING AKR1C2 T protein_coding NM_001354.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5031877 C T 0 139 0 0.1884 0.3932 0.4251 0.619 0.2694 0.5419 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,0 UTR_3_PRIME(MODIFIER||311||323|AKR1C2|protein_coding|CODING|NM_001354.5|11|T) 0 . 0 . 0 1 0 . 0 . 59 0 0 . 0 . rs10904383 -0.636426 0.408139 8 323 LOW 10 CODING AKR1C2 C protein_coding NM_001354.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5034016 T C 0 228 0 0.0946 0.3213 0.3862 0.5982 0.2028 0.4182 0 . 0 2 40 407 33 90 0 202 7 35 2 210 1222 62 146 2 732 12 58 0 . 0 . 0 21 0,0,3,18 SPLICE_SITE_REGION+INTRON(LOW||||323|AKR1C2|protein_coding|CODING|NM_001354.5|10|C) 0 . 0 . 0 1 0 . 1 0 51 0 0 0.0775511 0 . rs200698968 -0.692352 0.271257 21 K104 323 aaG/aaA LOW 3 SILENT CODING AKR1C3 A protein_coding NM_001253908.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5139685 G A 0 222 0 0.8737 0.8482 0.8084 0.8621 0.8519 0.8241 0.869042 0.843072 0.829767 1 9089 101515 9327 7521 5479 55309 784 14006 2 10406 121394 11574 8648 6614 66734 908 16510 0.865844 0 . 0 . 152 34,30,41,29 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K104|323|AKR1C3|protein_coding|CODING|NM_001253908.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.264761 rs12387 -0.693147 0.0281601 152 C145Y 323 tGt/tAt MODERATE 4 MISSENSE CODING AKR1C3 A protein_coding NM_001253908.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5141058 G A 0 222 0 0 0.004992 0 0.0248 0 0 0 . 0 1 0 306 0 299 0 1 1 5 2 10318 120622 11462 8614 6596 66408 904 16320 0.595707 0 . 0 . 82 12,24,14,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C145Y|323|AKR1C3|protein_coding|CODING|NM_001253908.1|4|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.936482 rs28943579 -0.693136 0.207796 82 Q250R 323 cAa/cGa MODERATE 7 MISSENSE CODING AKR1C4 G protein_coding NM_001818.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5255025 A G 0 228 0 0.9992 0.9998 1 1 1 1 0 . 0 2 10399 121330 11560 8630 6610 66716 904 16511 2 10404 121340 11560 8630 6610 66720 904 16512 0 . 0 . 0 114 0,0,62,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q250R|323|AKR1C4|protein_coding|CODING|NM_001818.3|7|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4880718 -0.693147 0.811392 114 323 89 MODIFIER 9 CODING AKR1C4 G protein_coding NM_001818.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5260812 A G 0 228 0 0.8918 0.9698 0.9899 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,4,19 UTR_3_PRIME(MODIFIER||89||323|AKR1C4|protein_coding|CODING|NM_001818.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2398157 -0.692717 0.0610419 25 A301 446 gcC/gcT LOW 4 SILENT CODING TUBAL3 A protein_coding NM_024803.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5435918 G A 0 228 0 0.7436 0.6681 0.7695 0.6478 0.6561 0.5276 0.727644 0.671229 0.642326 2 7624 79447 9353 5505 4489 43466 587 8423 2 10404 121372 11574 8632 6612 66732 908 16510 0 . 0 . COSM1128035 153 0,0,69,74 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A301|446|TUBAL3|protein_coding|CODING|NM_024803.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7097775 -0.693147 0.796288 153 A187 446 gcT/gcC LOW 4 SILENT CODING TUBAL3 G protein_coding NM_024803.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5436260 A G 0 228 0 0.789 0.7792 0.7997 0.8294 0.7197 0.7607 0.770086 0.720514 0.695116 2 8104 89568 9701 7182 4712 47375 634 11860 2 10400 121352 11574 8648 6610 66704 904 16512 0 . 0 . 0 112 0,0,42,64 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A187|446|TUBAL3|protein_coding|CODING|NM_024803.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7910290 -0.693147 0.445544 112 A107 446 gcT/gcC LOW 3 SILENT CODING TUBAL3 G protein_coding NM_024803.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5437365 A G 0 228 0 0.8238 0.7897 0.8084 0.8294 0.7227 0.7587 0.794825 0.729586 0.696163 2 8337 89722 9767 7183 4710 47395 636 11694 2 10400 120960 11576 8644 6610 66584 906 16240 0 . 0 . 0 58 0,0,34,23 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A107|446|TUBAL3|protein_coding|CODING|NM_024803.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11253156 -0.693147 0.188774 58 596 LOW 3 CODING NET1 T protein_coding NM_001047160.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5471200 C T 0 228 0 0.913 0.9503 0.9928 0.8909 1 0.9806 0.917849 0.974147 0.999388 2 9011 118409 11409 7713 6614 66699 893 16070 2 9802 120760 11574 8626 6614 66734 900 16510 0 . 0 . 0 169 0,0,68,72 SPLICE_SITE_REGION+INTRON(LOW||||596|NET1|protein_coding|CODING|NM_001047160.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4604777 -0.693147 2.86355e-09 169 Y200 596 taT/taC LOW 7 SILENT CODING NET1 C protein_coding NM_001047160.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5495218 T C 0 228 0 0.913 0.9766 0.9986 1 0.999 1 0.918293 0.972167 0.999767 2 9573 120539 11546 8654 6614 66735 905 16512 2 10404 121406 11578 8654 6614 66738 906 16512 0 . 0 . 0 60 0,0,39,12 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y200|596|NET1|protein_coding|CODING|NM_001047160.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4567355 -0.693147 0.537313 60 596 216 MODIFIER 12 CODING NET1 G protein_coding NM_001047160.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5499173 A G 0 228 0 0.6362 0.6474 0.7695 0.6498 0.6541 0.5665 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,6,30 UTR_3_PRIME(MODIFIER||216||596|NET1|protein_coding|CODING|NM_001047160.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11791 -0.693139 0.233931 37 596 748 MODIFIER 12 CODING NET1 T protein_coding NM_001047160.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5499705 A T 0 228 0 0.6536 0.6843 0.7118 0.6925 0.7406 0.6401 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 96 0,0,52,17 UTR_3_PRIME(MODIFIER||748||596|NET1|protein_coding|CODING|NM_001047160.2|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6601972 -0.693147 0.00144045 96 596 1202 MODIFIER 12 CODING NET1 G protein_coding NM_001047160.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5500159 C G 0 127 0 0.913 0.9768 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,8,0 UTR_3_PRIME(MODIFIER||1202||596|NET1|protein_coding|CODING|NM_001047160.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7087584 -0.651104 0.547491 8 K74R 146 aAg/aGg MODERATE 1 MISSENSE CODING CALML5 C protein_coding NM_017422.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5541181 T C 0 222 0 0.5121 0.3532 0.2334 0.3046 0.3221 0.3057 0.120291 0.0764263 0.0539535 1 5181 40347 2303 2576 2477 22161 316 5333 2 10246 120498 11520 8566 6588 66184 904 16490 1 0 . 0 COSM146869 31 9,4,12,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K74R|146|CALML5|protein_coding|CODING|NM_017422.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976053 rs10904516 -0.691153 0.528533 31 A73 146 gcG/gcA LOW 1 SILENT CODING CALML5 T protein_coding NM_017422.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5541183 C T 0 222 0 0.5182 0.3554 0.2334 0.3065 0.3231 0.3057 0.092374 0.0585115 0.0411628 1 5189 40354 2305 2579 2474 22158 316 5333 2 10256 120540 11524 8574 6586 66206 904 16490 0.9998 0 . 0 COSM1561299 31 10,3,12,6 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A73|146|CALML5|protein_coding|CODING|NM_017422.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.88232 rs10904517 -0.691153 0.528533 31 S58G 146 Agc/Ggc MODERATE 1 MISSENSE CODING CALML5 C protein_coding NM_017422.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5541230 T C 0 222 0 0.4493 0.2969 0.2133 0.2014 0.2972 0.2485 0.409442 0.339382 0.303488 1 4393 34593 2115 1781 2073 19376 272 4583 2 10378 121276 11564 8636 6612 66670 906 16510 0.972037 0 . 0 . 42 15,2,20,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S58G|146|CALML5|protein_coding|CODING|NM_017422.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.909077 rs11546426 -0.692831 0.409395 42 A36 146 gcG/gcA LOW 1 SILENT CODING CALML5 T protein_coding NM_017422.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5541294 C T 0 222 0 0.0008 0.0021965 0 0.0099 0 0 0.000226963 0.000153775 0.000116279 1 2 143 0 127 3 2 0 9 2 10404 121388 11574 8654 6614 66722 908 16512 0.707527 0 . 0 . 110 43,16,30,7 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A36|146|CALML5|protein_coding|CODING|NM_017422.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.865146 rs116143222 -0.693141 0.00585646 110 L106 149 ctG/ctA LOW 1 SILENT CODING CALML3 A protein_coding NM_005185.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5567366 G A 0 228 0 0.5076 0.4183 0.3156 0.6091 0.2455 0.3517 0.469133 0.321467 0.245814 2 4855 38967 3902 5268 2062 17194 282 5404 2 10238 119714 11430 8576 6418 65688 884 16480 0.92054 0 . 0 . 235 4,2,121,91 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L106|149|CALML3|protein_coding|CODING|NM_005185.3|1|A),INTRAGENIC(MODIFIER|||||CALML3-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.935808 rs1142825 -0.693147 0.00198527 235 149 197 MODIFIER 1 CODING CALML3 A protein_coding NM_005185.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5567695 G A 0 228 0 0.6679 0.8924 0.9481 1 0.9543 0.9816 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 106 0,0,35,66 UTR_3_PRIME(MODIFIER||197||149|CALML3|protein_coding|CODING|NM_005185.3|1|A),INTRAGENIC(MODIFIER|||||CALML3-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386591852,rs4242797 -0.693147 0.0020263 106 149 469 MODIFIER 1 CODING CALML3 T protein_coding NM_005185.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5567967 G T 0 228 0 0.239 0.3387 0.3069 0.5853 0.2525 0.3303 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0786517 0 . 0 . 99 1,1,58,31 UTR_3_PRIME(MODIFIER||469||149|CALML3|protein_coding|CODING|NM_005185.3|1|T),INTRAGENIC(MODIFIER|||||CALML3-AS1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.870786 rs1131482 -0.693147 0.142919 99 278 1824 MODIFIER 6 CODING ASB13 T protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5680842 C T 0 66 0 0.3101 0.2821 0.1801 0.4365 0.1839 0.2587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.783809 0 . 0 . 10 6,0,3,1 UTR_3_PRIME(MODIFIER||1824||278|ASB13|protein_coding|CODING|NM_024701.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 1.00775 rs2386649 -0.556411 0.220638 10 278 1782 MODIFIER 6 CODING ASB13 A protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5680884 G A 0 120 0 0.3729 0.388 0.3026 0.2758 0.5229 0.4458 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.839457 0 . 0 . 19 6,1,12,0 UTR_3_PRIME(MODIFIER||1782||278|ASB13|protein_coding|CODING|NM_024701.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.914584 rs1132305 -0.680642 0.674631 19 278 1770 MODIFIER 6 CODING ASB13 G protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5680896 A G 0 88 0 0.3147 0.2835 0.1801 0.4375 0.1839 0.2587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.93223 0 . 0 . 18 12,0,5,1 UTR_3_PRIME(MODIFIER||1770||278|ASB13|protein_coding|CODING|NM_024701.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.85394 rs1573 -0.616816 0.368038 18 278 1752 MODIFIER 6 CODING ASB13 A protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5680914 T A 0 85 0 0.3139 0.2831 0.1801 0.4365 0.1839 0.2587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.940317 0 . 0 . 19 12,1,5,1 UTR_3_PRIME(MODIFIER||1752||278|ASB13|protein_coding|CODING|NM_024701.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.732319 rs2386648 -0.616816 0.469001 19 278 1318 MODIFIER 6 CODING ASB13 C protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5681348 T C 0 228 0 0.9009 0.9724 0.9928 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,3,21 UTR_3_PRIME(MODIFIER||1318||278|ASB13|protein_coding|CODING|NM_024701.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7901492 -0.692831 0.152498 25 278 1276 MODIFIER 6 CODING ASB13 G protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5681390 A G 0 195 0 0.879 0.9667 0.9928 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,1,12 UTR_3_PRIME(MODIFIER||1276||278|ASB13|protein_coding|CODING|NM_024701.3|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7908974 -0.683931 0.0766623 13 278 883 MODIFIER 6 CODING ASB13 T protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5681783 C T 0 152 0 0.3041 0.2482 0.1614 0.4107 0.1759 0.1411 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.967472 0 . 0 . 29 9,0,18,0 UTR_3_PRIME(MODIFIER||883||278|ASB13|protein_coding|CODING|NM_024701.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.988166 rs11256474 -0.691153 0.485724 29 278 596 MODIFIER 6 CODING ASB13 T protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5682070 C T 0 222 0 0.1014 0.2198 0.219 0.1399 0.4155 0.2618 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.906216 0 . 0 . 136 22,38,18,41 UTR_3_PRIME(MODIFIER||596||278|ASB13|protein_coding|CODING|NM_024701.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.419496 rs3750645 -0.693147 0.0355536 136 278 25 MODIFIER 6 CODING ASB13 T protein_coding NM_024701.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5682641 C T 0 228 0 0.9153 0.9766 0.9928 1 1 1 0.9335 0.977241 0.999651 2 9723 120597 11540 8654 6612 66668 903 16497 2 10406 121336 11574 8654 6612 66688 904 16498 0 . 0 . 0 72 0,0,52,15 UTR_3_PRIME(MODIFIER||25||278|ASB13|protein_coding|CODING|NM_024701.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7896492 -0.693147 0.435488 72 D212 278 gaC/gaT LOW 5 SILENT CODING ASB13 A protein_coding NM_024701.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5683806 G A 0 222 0 0 0.0035942 0.0014 0.0169 0 0 0 . 0 1 0 153 2 142 0 3 0 6 2 9306 107982 9568 7786 5560 60778 810 14174 0.90905 0 . 0 . 83 37,14,14,11 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D212|278|ASB13|protein_coding|CODING|NM_024701.3|5|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.393708 rs143338473 -0.692914 0.0567403 83 2430 35724 MODIFIER 1 CODING FAM208B T protein_coding NM_017782.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5726882 C T 0 21.2 0 0.0325 0.1785 0.0648 0.506 0.0258 0.2761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 START_GAINED(LOW||||2430|FAM208B|protein_coding|CODING|NM_017782.4|1|T),UTR_5_PRIME(MODIFIER||35724||2430|FAM208B|protein_coding|CODING|NM_017782.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs114003811 -0.379885 0 3 2430 LOW 6 CODING FAM208B T protein_coding NM_017782.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5765637 C T 0 222 0 0.0582 0.1559 0.062 0.4296 0.0199 0.2127 0.0373754 0.0130102 0.00220913 1 445 9210 1508 3708 591 493 62 2403 2 9752 118876 11556 8596 6610 66092 886 15384 0.561082 0 . 0 . 98 32,15,21,15 SPLICE_SITE_REGION+INTRON(LOW||||2430|FAM208B|protein_coding|CODING|NM_017782.4|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.394181 rs3793708 -0.693139 0.00868398 98 C499G 2430 Tgt/Ggt MODERATE 13 MISSENSE CODING FAM208B G protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5781628 T G 0 222 0 0.8865 0.8375 0.8804 0.8135 0.8419 0.7607 0.871436 0.84429 0.831993 1 8617 100970 10577 6995 5751 55387 756 12887 2 9798 120658 11568 8618 6614 66664 896 16500 0.881319 0 . 0 . 113 44,18,24,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C499G|2430|FAM208B|protein_coding|CODING|NM_017782.4|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.728711 rs2254067 -0.693141 0.0439578 113 T612P 2430 Aca/Cca MODERATE 13 MISSENSE CODING FAM208B C protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5781967 A C 0 222 0 0 0.0065895 0 0.0317 0 0.001 0.000794913 0.000249584 0 1 3 265 1 227 2 5 5 22 2 9684 120228 11536 8596 6614 66426 894 16478 0.907693 0 . 0 . 58 19,13,10,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Cca|T612P|2430|FAM208B|protein_coding|CODING|NM_017782.4|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993474 rs75862308 -0.692562 0.0403199 58 T612 2430 acA/acT LOW 13 SILENT CODING FAM208B T protein_coding NM_017782.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5781969 A T 0 222 0 0.8865 0.8371 0.8804 0.8135 0.841 0.7597 0.871618 0.844566 0.832202 1 8546 100650 10540 6977 5749 55230 751 12857 2 9710 120338 11542 8596 6612 66508 894 16476 0.992049 0 . 0 . 55 10,12,16,15 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T612|2430|FAM208B|protein_coding|CODING|NM_017782.4|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.780516 rs2797486 -0.69311 0.110558 55 R1075P 2430 cGt/cCt MODERATE 15 MISSENSE CODING FAM208B C protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5788608 G C 0 222 0 0.8873 0.8361 0.8761 0.8135 0.839 0.7587 0.873724 0.842609 0.82791 1 8626 100747 10566 6991 5728 55194 756 12886 2 9796 120714 11572 8620 6614 66704 900 16508 0.999805 0 . 0 . 159 66,25,37,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R1075P|2430|FAM208B|protein_coding|CODING|NM_017782.4|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.00558897 rs2797491 -0.693147 0.207625 159 S1150C 2430 tCt/tGt MODERATE 15 MISSENSE CODING FAM208B G protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5788833 C G 0 222 0 0 0.0065895 0 0.0317 0 0.001 0.000791139 0.00024946 0 1 3 260 1 223 2 5 5 21 2 9790 120730 11574 8622 6614 66720 900 16510 0.76275 0 . 0 . 104 21,27,24,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S1150C|2430|FAM208B|protein_coding|CODING|NM_017782.4|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981886 rs79826323 -0.693147 0.503341 104 V1679A 2430 gTg/gCg MODERATE 15 MISSENSE CODING FAM208B C protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5790420 T C 0 228 0 0.9478 0.9774 0.9798 1 0.9851 0.9847 0.954714 0.978813 0.990975 2 9376 119291 11454 8626 6563 66039 890 16343 2 9820 120784 11576 8626 6614 66734 902 16512 0 . 0 . 0 69 0,0,39,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V1679A|2430|FAM208B|protein_coding|CODING|NM_017782.4|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2669142 -0.693147 0.004164 69 L1744 2430 ctA/ctG LOW 15 SILENT CODING FAM208B G protein_coding NM_017782.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5790616 A G 0 222 0 0.2723 0.2145 0.0749 0.4315 0.0199 0.2117 0.20143 0.0676849 0.00298187 1 2176 11102 1611 3731 592 508 66 2418 2 9806 120670 11554 8590 6612 66706 898 16504 0.836642 0 . 0 . 57 14,12,20,8 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1744|2430|FAM208B|protein_coding|CODING|NM_017782.4|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998166 rs2797492 -0.693054 0.407041 57 S2404N 2430 aGt/aAt MODERATE 20 MISSENSE CODING FAM208B A protein_coding NM_017782.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5804531 G A 0 222 0 0.8737 0.854 0.9063 0.8204 0.8718 0.8067 0.860302 0.85953 0.85919 1 8520 103440 10739 7018 5781 57099 771 13512 2 9782 120506 11564 8616 6614 66528 896 16506 0.915682 0 . 0 . 114 52,7,42,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S2404N|2430|FAM208B|protein_coding|CODING|NM_017782.4|20|A),DOWNSTREAM(MODIFIER||2655||445|GDI2|protein_coding|CODING|NM_001494.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.957218 rs2797501 -0.693147 9.06595e-07 114 2430 148 MODIFIER 21 CODING FAM208B G protein_coding NM_017782.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5805143 A G 0 93 0 0 0.0065895 0 0.0317 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.966012 0 . 0 . 14 0,7,0,7 UTR_3_PRIME(MODIFIER||148||2430|FAM208B|protein_coding|CODING|NM_017782.4|21|G),DOWNSTREAM(MODIFIER||2043||445|GDI2|protein_coding|CODING|NM_001494.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 0 . 0.966012 rs74861203 -0.636426 0.145738 14 445 156 MODIFIER 11 CODING GDI2 G protein_coding NM_001494.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5807813 A G 0 137 0 0 0.0065895 0 0.0317 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 14 4,1,8,1 UTR_3_PRIME(MODIFIER||156||445|GDI2|protein_coding|CODING|NM_001494.3|11|G),DOWNSTREAM(MODIFIER||2110||2430|FAM208B|protein_coding|CODING|NM_017782.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.945959 rs145662995 -0.662043 0.135572 14 445 155 MODIFIER 11 CODING GDI2 T protein_coding NM_001494.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5807814 A T 0 137 0 0 0.0065895 0 0.0317 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 14 4,1,8,1 UTR_3_PRIME(MODIFIER||155||445|GDI2|protein_coding|CODING|NM_001494.3|11|T),DOWNSTREAM(MODIFIER||2111||2430|FAM208B|protein_coding|CODING|NM_017782.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.945959 rs138453901 -0.662043 0.135572 14 445 4 MODIFIER 1 CODING GDI2 A protein_coding NM_001494.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5855225 G A 0 222 0 0.0144 0.0865 0.0692 0.1528 0.1034 0.1104 0.0345633 0.0840277 0.109123 1 252 11382 530 1137 420 6989 69 1985 2 4098 64564 5096 5474 1828 35820 428 11820 0.898511 0 . 0 . 56 20,3,14,6 START_GAINED(LOW||||445|GDI2|protein_coding|CODING|NM_001494.3|1|A),UTR_5_PRIME(MODIFIER||4||445|GDI2|protein_coding|CODING|NM_001494.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985579 rs3736460 -0.692067 0.782119 56 Q353R 361 cAg/cGg MODERATE 7 MISSENSE CODING ANKRD16 C protein_coding NM_001009941.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5920121 T C 0 228 0 0.6853 0.8039 0.9135 0.8472 0.8638 0.7802 0.715388 0.821544 0.87593 2 7416 103478 10760 7389 5833 58321 775 12984 2 10406 121390 11578 8642 6614 66732 908 16510 0 . 0 . 0 62 0,0,22,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q353R|361|ANKRD16|protein_coding|CODING|NM_001009941.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1052420,rs386514296 -0.693147 0.348825 62 G216 361 ggG/ggT LOW 4 SILENT CODING ANKRD16 A protein_coding NM_001009941.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5925971 C A 0 228 0 0.9523 0.9225 0.9424 0.9504 0.8837 0.8793 0.950295 0.915654 0.897907 2 9906 109995 10967 8282 5926 59628 813 14473 2 10406 121388 11578 8652 6614 66722 908 16508 0 . 0 . COSM427709 135 0,0,86,36 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G216|361|ANKRD16|protein_coding|CODING|NM_001009941.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs631947 -0.693147 0.122152 135 Q195 361 caA/caG LOW 4 SILENT CODING ANKRD16 C protein_coding NM_001009941.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5926034 T C 0 222 0 0.0008 0.0635 0.0346 0.1577 0.0368 0.0992 0.0111212 0.0269107 0.035 1 104 6589 679 1399 454 2546 52 1355 2 10202 119034 11254 8478 6464 65614 882 16140 0.922265 0 . 0 COSM146870 124 37,35,15,23 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q195|361|ANKRD16|protein_coding|CODING|NM_001009941.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940959 rs3750656 -0.693143 0.722004 124 A128G 361 gCc/gGc MODERATE 2 MISSENSE CODING ANKRD16 C protein_coding NM_001009941.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5929962 G C 0 222 0 0.0008 0.0605 0.0346 0.1429 0.0368 0.0992 0.00998638 0.0264493 0.0348837 1 101 6417 680 1243 456 2538 50 1349 2 10400 121386 11578 8644 6614 66730 908 16512 0.0465832 0 . 0 COSM146871 97 27,31,13,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A128G|361|ANKRD16|protein_coding|CODING|NM_001009941.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.944645 rs2296136 -0.692914 0.195063 97 G30R 361 Ggg/Agg MODERATE 1 MISSENSE CODING ANKRD16 T protein_coding NM_001009941.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5931230 C T 0 16.6 0 0.0008 0.0605 0.0346 0.1429 0.0368 0.0992 0.00524781 0.0185438 0.0252347 1 31 2841 301 511 134 1165 19 680 2 1454 28814 2692 2138 856 16390 184 5100 0.666667 0 . 0 . 8 0,6,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G30R|361|ANKRD16|protein_coding|CODING|NM_001009941.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.833333 rs3750659 -0.453602 0.22 8 1094 LOW 5 CODING FBXO18 C protein_coding NM_032807.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5951025 T C 0 222 0 0.1036 0.4085 0.5663 0.6607 0.3897 0.4683 0.155697 0.312394 0.392674 1 1450 51779 7534 5808 2857 26114 386 7630 2 10406 121362 11570 8640 6614 66716 908 16508 0.589766 0 . 0 . 241 39,50,61,67 SPLICE_SITE_REGION+INTRON(LOW||||1094|FBXO18|protein_coding|CODING|NM_032807.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991196 rs595923 -0.693147 0.0787093 241 1094 LOW 20 CODING FBXO18 C protein_coding NM_032807.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5978411 T C 0 228 0 0.8177 0.8299 0.9236 0.8512 0.8588 0.728 0.833409 0.855067 0.866163 2 8632 103567 10706 7418 5898 57665 780 12468 2 10398 121328 11574 8644 6612 66684 906 16510 0 . 0 . 0 103 0,0,78,13 SPLICE_SITE_REGION+INTRON(LOW||||1094|FBXO18|protein_coding|CODING|NM_032807.4|20|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs646406 -0.693147 0.48643 103 L1002 1094 ctG/ctA LOW 21 SILENT CODING FBXO18 A protein_coding NM_032807.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5978442 G A 0 222 0 0 0.0085863 0 0.0417 0 0.001 0.00113482 0.000384438 0 1 8 355 3 323 0 0 2 19 2 10406 121388 11578 8640 6614 66732 908 16510 0.929206 0 . 0 COSM146872 142 48,17,48,13 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L1002|1094|FBXO18|protein_coding|CODING|NM_032807.4|21|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958694 rs117214741 -0.693147 0.885813 142 C1053 1094 tgT/tgC LOW 22 SILENT CODING FBXO18 C protein_coding NM_032807.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5979117 T C 0 222 0 0.0333 0.0719 0.0389 0.1558 0.0358 0.0982 0.0356332 0.0344456 0.0338372 1 370 6913 790 1423 437 2485 51 1357 2 10314 120346 11504 8634 6486 66282 894 16232 0.996015 0 . 0 . 99 17,32,10,36 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C1053|1094|FBXO18|protein_coding|CODING|NM_032807.4|22|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.397114 rs2274033 -0.693147 0.138983 99 353 364 MODIFIER 8 CODING IL15RA C protein_coding NM_001256765.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 5994694 A C 0 228 0 0.7965 0.5667 0.4424 0.4345 0.4891 0.5603 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,4,21 UTR_3_PRIME(MODIFIER||364||353|IL15RA|protein_coding|CODING|NM_001256765.1|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2296135 -0.692914 0.00918116 27 N268T 353 aAc/aCc MODERATE 5 MISSENSE CODING IL15RA G protein_coding NM_001256765.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6002368 T G 0 228 0 0.7549 0.5505 0.4928 0.4266 0.4632 0.5327 0.718793 0.566585 0.488605 2 7547 62154 6231 3652 2974 32544 450 8756 2 10404 121356 11568 8626 6610 66728 908 16512 0.921053 0 . 0 . 85 1,1,46,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N268T|353|IL15RA|protein_coding|CODING|NM_001256765.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.993421 rs2228059,rs386561667 -0.693147 0.312733 85 401 7643 MODIFIER 1 CODING RBM17 G protein_coding NM_001145547.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6131386 T G 0 39.3 0 0.9266 0.98 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||7643||401|RBM17|protein_coding|CODING|NM_001145547.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12261535 -0.453602 0.28 2 401 7402 MODIFIER 1 CODING RBM17 C protein_coding NM_001145547.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6131627 T C 0 85 0 0.9259 0.9798 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,0 UTR_5_PRIME(MODIFIER||7402||401|RBM17|protein_coding|CODING|NM_001145547.1|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4749964 -0.511536 0.235765 4 401 LOW 10 CODING RBM17 C protein_coding NM_001145547.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6156118 T C 0 228 0 0.9289 0.9804 0.9957 1 1 0.999 0.941897 0.980163 0.999767 2 9427 115816 11227 8306 6534 63709 886 15727 2 10036 116464 11258 8306 6534 63712 890 15728 0 . 0 . 0 107 0,0,40,56 SPLICE_SITE_REGION+INTRON(LOW||||401|RBM17|protein_coding|CODING|NM_001145547.1|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10795823 -0.693147 0.00146871 107 534 240 MODIFIER 15 CODING PFKFB3 C protein_coding NM_001282630.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6275145 T C 0 21.1 0 0.4213 0.4245 0.4683 0.2688 0.5855 0.3926 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_3_PRIME(MODIFIER||240||534|PFKFB3|protein_coding|CODING|NM_001282630.2|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1539232 -0.379885 0 3 534 318 MODIFIER 15 CODING PFKFB3 A protein_coding NM_001282630.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6275223 G A 0 152 0 0.9592 0.9886 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,3 UTR_3_PRIME(MODIFIER||318||534|PFKFB3|protein_coding|CODING|NM_001282630.2|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1539233 -0.590765 0.150948 6 534 871 MODIFIER 15 CODING PFKFB3 C protein_coding NM_001282630.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6275776 T C 0 222 0 0.2466 0.2318 0.2752 0.1746 0.2654 0.2055 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.798993 0 . 0 . 54 13,14,6,18 UTR_3_PRIME(MODIFIER||871||534|PFKFB3|protein_coding|CODING|NM_001282630.2|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.963254 rs55643411 -0.692831 0.376778 54 534 1838 MODIFIER 15 CODING PFKFB3 A protein_coding NM_001282630.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6276743 G A 0 19.1 0 0.8472 0.608 0.4524 0.5575 0.5726 0.4836 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 3,1,1,1 UTR_3_PRIME(MODIFIER||1838||534|PFKFB3|protein_coding|CODING|NM_001282630.2|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.75 rs1539234 -0.453602 0.22 6 706 1014 MODIFIER 18 CODING PRKCQ T protein_coding NM_006257.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6469155 G T 0 9.7 0 0.8328 0.5134 0.451 0.255 0.5437 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1014||706|PRKCQ|protein_coding|CODING|NM_006257.4|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs582052 -0.379885 0 1 R616 706 Cga/Aga LOW 17 SILENT CODING PRKCQ T protein_coding NM_006257.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6472891 G T 0 222 0 0.1271 0.1226 0.1124 0.0308 0.2187 0.1196 0.141625 0.194679 0.22186 1 1467 21808 898 315 1737 14800 170 2421 2 10302 120176 11536 8556 6570 66050 890 16272 0.946991 0 . 0 . 66 10,27,6,19 PROTEIN_INTERACTION_LOCUS(HIGH||||706|PRKCQ|protein_coding|CODING||17|T),SYNONYMOUS_CODING(LOW|SILENT|Cga/Aga|R616|706|PRKCQ|protein_coding|CODING|NM_006257.4|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.841074 rs11258747 -0.692914 0.55346 66 I520 706 atC/atT LOW 15 SILENT CODING PRKCQ A protein_coding NM_006257.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 6498723 G A 0 222 0 0.1551 0.1414 0.1153 0.0645 0.2187 0.1411 0.159101 0.197601 0.217326 1 1621 22230 911 535 1735 14644 168 2616 2 10402 121220 11516 8622 6596 66666 908 16510 0.37027 0 . 0 . 127 33,23,29,26 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I520|706|PRKCQ|protein_coding|CODING|NM_006257.4|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.714583 rs11258943 -0.693147 7.20236e-06 127 894 4621 MODIFIER 21 CODING SFMBT2 A protein_coding NM_001018039.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7201111 G A 0 9.7 0 0.2375 0.1795 0.1772 0.1944 0.1243 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4621||894|SFMBT2|protein_coding|CODING|NM_001018039.1|21|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044681 -0.379885 0 1 894 2495 MODIFIER 21 CODING SFMBT2 T protein_coding NM_001018039.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7203237 C T 0 9.7 0 0.2458 0.3834 0.5634 0.3482 0.5219 0.3354 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2495||894|SFMBT2|protein_coding|CODING|NM_001018039.1|21|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9665413 -0.379885 0 1 894 466 MODIFIER 21 CODING SFMBT2 G protein_coding NM_001018039.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7205266 A G 0 228 0 0.9947 0.9986 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 0,0,9,17 UTR_3_PRIME(MODIFIER||466||894|SFMBT2|protein_coding|CODING|NM_001018039.1|21|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3002158 -0.692976 0.0256175 28 D336 894 gaT/gaC LOW 9 SILENT CODING SFMBT2 G protein_coding NM_001018039.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7285632 A G 0 228 0 0.8896 0.9024 0.9582 0.9097 0.9165 0.8579 0.889696 0.901891 0.90814 2 9268 110428 10995 8005 6281 60984 830 14065 2 10396 121316 11552 8642 6612 66698 908 16508 0 . 0 . 0 55 0,0,11,40 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D336|894|SFMBT2|protein_coding|CODING|NM_001018039.1|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2248474,rs386562483 -0.693147 0.00758381 55 942 3337 MODIFIER 15 CODING ITIH5 G protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7601708 A G 0 222 0 0.2413 0.1629 0.1268 0.1131 0.0994 0.1994 0 . 0 1 85 1297 11 28 0 316 13 844 2 432 10928 136 178 0 3238 120 6824 0.997449 0 . 0 . 60 26,3,22,2 UTR_3_PRIME(MODIFIER||3337||942|ITIH5|protein_coding|CODING|NM_030569.6|15|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.803683 rs7092583 -0.692831 0.204564 60 942 3275 MODIFIER 15 CODING ITIH5 C protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7601770 G C 0 222 0 0.2413 0.1629 0.1268 0.1131 0.0994 0.1994 0 . 0 1 117 1712 18 31 0 385 15 1146 2 490 11906 150 186 0 3426 130 7524 0.681807 0 . 0 . 91 26,18,22,14 UTR_3_PRIME(MODIFIER||3275||942|ITIH5|protein_coding|CODING|NM_030569.6|15|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.998318 rs7074077 -0.693139 0.21001 91 942 3043 MODIFIER 15 CODING ITIH5 T protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7602002 C T 0 20.4 0 0.2428 0.1629 0.1268 0.1121 0.0994 0.1984 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,2,0,2 UTR_3_PRIME(MODIFIER||3043||942|ITIH5|protein_coding|CODING|NM_030569.6|15|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs111506888 -0.453602 0.78 4 942 2503 MODIFIER 15 CODING ITIH5 G protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7602542 C G 0 9.7 0 0.8767 0.9659 0.9914 1 0.998 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2503||942|ITIH5|protein_coding|CODING|NM_030569.6|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2050351 -0.379885 0 1 942 1864 MODIFIER 15 CODING ITIH5 G protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7603181 A G 0 16.5 0 0.3396 0.1921 0.1427 0.1171 0.1024 0.1973 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||1864||942|ITIH5|protein_coding|CODING|NM_030569.6|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs7924140 -0.453602 0.7 4 942 1501 MODIFIER 15 CODING ITIH5 C protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7603544 G C 0 22 0 0.2428 0.1536 0.0893 0.1101 0.1054 0.1728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_3_PRIME(MODIFIER||1501||942|ITIH5|protein_coding|CODING|NM_030569.6|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3814699 -0.379885 0 3 942 1194 MODIFIER 15 CODING ITIH5 T protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7603851 C T 0 39.3 0 0.5976 0.8824 0.9597 0.995 0.992 0.9836 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1194||942|ITIH5|protein_coding|CODING|NM_030569.6|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2050353 -0.453602 0.6 2 942 1169 MODIFIER 15 CODING ITIH5 G protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7603876 C G 0 100 0 0.8389 0.9541 0.9813 1 0.996 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,2 UTR_3_PRIME(MODIFIER||1169||942|ITIH5|protein_coding|CODING|NM_030569.6|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2050354 -0.511536 0.519801 4 942 1137 MODIFIER 15 CODING ITIH5 C protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7603908 T C 0 70 0 0.8775 0.9605 0.9856 0.995 0.995 0.9836 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1137||942|ITIH5|protein_coding|CODING|NM_030569.6|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2050355 -0.453602 0.14 3 942 951 MODIFIER 15 CODING ITIH5 A protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7604094 G A 0 16.6 0 0.0386 0.0313 0.0086 0.0397 0.004 0.0573 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 8 4,0,2,0 UTR_3_PRIME(MODIFIER||951||942|ITIH5|protein_coding|CODING|NM_030569.6|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs386454259,rs60587565 -0.453602 0.42 8 942 691 MODIFIER 15 CODING ITIH5 C protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7604354 T C 0 9.7 0 0.5749 0.8758 0.9597 0.995 0.992 0.9806 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||691||942|ITIH5|protein_coding|CODING|NM_030569.6|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10795550 -0.379885 0 1 942 396 MODIFIER 15 CODING ITIH5 G protein_coding NM_030569.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7604649 T G 0 172 0 0.6778 0.9052 0.9741 0.995 0.993 0.9806 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,5,2 UTR_3_PRIME(MODIFIER||396||942|ITIH5|protein_coding|CODING|NM_030569.6|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12024 -0.636426 0.0684004 8 R936Q 942 cGg/cAg MODERATE 15 MISSENSE CODING ITIH5 T protein_coding NM_030569.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7605067 C T 0 222 0 0.407 0.5717 0.6225 0.5179 0.7694 0.6104 0.464594 0.664616 0.767093 1 4755 83759 8017 4054 4823 51002 649 10459 2 10376 120760 11560 8594 6614 66612 902 16102 0.990627 0 . 0 . 432 122,102,91,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R936Q|942|ITIH5|protein_coding|CODING|NM_030569.6|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.327634 rs3824658 -0.693147 0.0963603 432 F925S 942 tTc/tCc MODERATE 14 MISSENSE CODING ITIH5 G protein_coding NM_030569.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7605101 A G 0 228 0 0.8835 0.9667 0.9856 1 0.997 1 0.91035 0.968476 0.998256 2 9471 120307 11510 8654 6614 66648 901 16509 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 403 0,0,182,191 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F925S|942|ITIH5|protein_coding|CODING|NM_030569.6|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10795551 -0.693147 0.0380323 403 D631 942 gaT/gaC LOW 10 SILENT CODING ITIH5 G protein_coding NM_030569.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7618501 A G 0 222 0 0.3646 0.5311 0.5461 0.7679 0.5219 0.5112 0.406945 0.493079 0.537218 1 4058 65376 6302 6554 3809 35360 505 8788 2 9946 119272 11492 8556 6422 65482 888 16486 0.0720627 0 . 0 COSM1349156,COSM427934 212 78,39,58,20 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D631|942|ITIH5|protein_coding|CODING|NM_030569.6|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0737916 rs2275068 -0.693147 0.196933 212 T570P 942 Acc/Ccc MODERATE 10 MISSENSE CODING ITIH5 G protein_coding NM_030569.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7618686 T G 0 222 0 0.3631 0.5306 0.5461 0.7669 0.5209 0.5123 0.407399 0.494003 0.538372 1 4147 66150 6314 6644 3883 35846 513 8803 2 10384 121162 11528 8636 6586 66616 906 16506 0.973248 0 . 0 . 156 18,64,24,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T570P|942|ITIH5|protein_coding|CODING|NM_030569.6|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.636834 rs2275069 -0.693147 0.491802 156 K150 942 aaG/aaA LOW 5 SILENT CODING ITIH5 T protein_coding NM_030569.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7679393 C T 0 228 0 0.6089 0.4489 0.2233 0.4623 0.3121 0.5194 0.565365 0.398662 0.313256 2 5933 44807 1970 4004 2826 21792 335 7947 2 10392 121268 11562 8638 6610 66658 908 16500 1 0 . 0 . 124 1,0,63,44 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K150|942|ITIH5|protein_coding|CODING|NM_030569.6|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6602256 -0.693147 0.297024 124 N263S 946 aAc/aGc MODERATE 8 MISSENSE CODING ITIH2 G protein_coding NM_002216.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7763661 A G 0 228 0 0.969 0.9912 0.9971 1 0.999 1 0.968225 0.988928 0.999535 2 10112 121088 11563 8654 6614 66728 908 16509 2 10406 121410 11578 8654 6614 66740 908 16510 0 . 0 . 0 129 0,0,40,83 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N263S|946|ITIH2|protein_coding|CODING|NM_002216.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7075296 -0.693147 0.290833 129 P674A 946 Cca/Gca MODERATE 16 MISSENSE CODING ITIH2 G protein_coding NM_002216.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7780646 C G 0 228 0 0.0091 0.0841 0.0274 0.2351 0.0626 0.092 0.0208806 0.0469783 0.0603488 2 184 9209 316 2101 655 4251 75 1627 2 10396 121236 11576 8630 6614 66660 908 16452 0 . 0 . 0 220 0,0,73,122 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P674A|946|ITIH2|protein_coding|CODING|NM_002216.2|16|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3740217 -0.693147 0.00522642 220 393 3395 MODIFIER 13 CODING KIN G protein_coding NM_012311.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7794648 T G 0 64 0 0.289 0.4129 0.4942 0.4365 0.5765 0.3303 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||3395||393|KIN|protein_coding|CODING|NM_012311.3|13|G),DOWNSTREAM(MODIFIER||3165||946|ITIH2|protein_coding|CODING|NM_002216.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7907897 -0.511536 0.411594 3 298 745 MODIFIER 10 CODING ATP5C1 C protein_coding NM_001001973.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 7849688 T C 0 222 0 0.329 0.3616 0.3718 0.2659 0.3588 0.5 0.309249 0.346036 0.362036 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.617753 0 . 0 . 45 4,11,7,17 UTR_3_PRIME(MODIFIER||745||298|ATP5C1|protein_coding|CODING|NM_001001973.1|10|C) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.504878 rs4655 -0.692831 0.11618 45 N442S 929 aAt/aGt MODERATE 3 MISSENSE CODING TAF3 G protein_coding NM_031923.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 8006798 A G 0 228 0 0.2632 0.5421 0.7349 0.7103 0.6203 0.5286 0.357999 0.529178 0.608717 2 3171 72905 9173 6057 4306 40450 559 9189 2 9754 120572 11558 8612 6610 66648 896 16494 0.95 0 . 0 COSM427970 87 0,2,44,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N442S|929|TAF3|protein_coding|CODING|NM_031923.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.36875 rs4747647 -0.693147 0.552301 87 V696L 929 Gtg/Ctg MODERATE 3 MISSENSE CODING TAF3 C protein_coding NM_031923.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 8007559 G C 0 228 0 0.3275 0.5773 0.7651 0.7183 0.6372 0.5746 0.395506 0.549301 0.61882 2 3747 75496 9252 6056 4398 41514 575 9954 2 9672 119930 11514 8550 6592 66224 894 16484 0 . 0 . 0 50 0,0,14,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V696L|929|TAF3|protein_coding|CODING|NM_031923.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10795583 -0.693147 0.460993 50 V696A 929 gTg/gCg MODERATE 3 MISSENSE CODING TAF3 C protein_coding NM_031923.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 8007560 T C 0 228 0 0.5477 0.6909 0.8026 0.7272 0.7376 0.7198 0.600758 0.677373 0.711995 2 5703 86831 9691 6158 4804 47393 667 12415 2 9664 119946 11518 8550 6594 66238 894 16488 1 0 . 0 . 50 0,1,14,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V696A|929|TAF3|protein_coding|CODING|NM_031923.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1244229 -0.693147 0.546066 50 444 251 MODIFIER 2 CODING GATA3 A protein_coding NM_001002295.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 8097368 G A 0 32.6 0 0.2141 0.4902 0.4337 0.6716 0.5358 0.6697 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||251||444|GATA3|protein_coding|CODING|NM_001002295.1|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10905277 -0.379885 0 2 444 612 MODIFIER 6 CODING GATA3 A protein_coding NM_001002295.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 8116598 G A 0 228 0 0.7443 0.865 0.8948 0.9762 0.8241 0.9346 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 58 0,0,52,3 UTR_3_PRIME(MODIFIER||612||444|GATA3|protein_coding|CODING|NM_001002295.1|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1058240 -0.693147 0.340804 58 V146 521 gtA/gtT LOW 5 SILENT CODING CELF2 T protein_coding NM_006561.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11299735 A T 0 222 0 0.7352 0.7811 0.7493 0.8611 0.7247 0.8415 0.742828 0.741608 0.741035 1 7212 91457 8546 7290 4914 49178 671 13646 2 9796 120714 11570 8618 6606 66718 898 16508 0.585067 0 . 0 COSM1345794,COSM1345795 68 27,7,20,5 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtT|V146|521|CELF2|protein_coding|CODING|NM_006561.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960535 rs2277212 -0.692914 0.0606821 68 L345 521 ctC/ctT LOW 10 SILENT CODING CELF2 T protein_coding NM_006561.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11356160 C T 0 222 0 0.6377 0.4511 0.2594 0.4871 0.2684 0.4857 0.559771 0.356223 0.26149 1 5866 42178 3194 3865 2011 18811 300 8131 2 9802 120738 11572 8606 6612 66734 900 16512 0.202618 0 . 0 . 129 23,42,21,25 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L345|521|CELF2|protein_coding|CODING|NM_006561.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.563226 rs2246449 -0.693147 0.25499 129 845 127 MODIFIER 14 CODING USP6NL T protein_coding NM_001080491.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11504313 C T 0 228 0 0.9251 0.98 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 116 0,0,84,25 UTR_3_PRIME(MODIFIER||127||845|USP6NL|protein_coding|CODING|NM_001080491.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2440082 -0.693147 0.00493314 116 P601 845 ccT/ccC LOW 14 SILENT CODING USP6NL G protein_coding NM_001080491.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11505175 A G 0 228 0 0.5772 0.4994 0.2997 0.7351 0.3042 0.4939 0.514081 0.378398 0.314592 2 5321 44330 2938 6159 1644 20436 300 7532 2 9688 119902 11504 8528 6586 66234 894 16468 1 0 . 0 . 88 1,0,47,33 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P601|845|USP6NL|protein_coding|CODING|NM_001080491.3|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3740204 -0.693147 0.190307 88 A69T 303 Gcg/Acg MODERATE 2 MISSENSE CODING ECHDC3 A protein_coding NM_024693.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11789382 G A 0 228 0 0.6891 0.9135 0.9741 1 0.997 0.999 0.740581 0.910734 0.997907 2 7604 118304 11444 8653 6612 66597 897 16497 2 10406 121408 11578 8654 6614 66738 908 16510 0 . 0 . 0 147 0,0,52,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A69T|303|ECHDC3|protein_coding|CODING|NM_024693.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4750090 -0.693147 0.0487506 147 K76 303 aaG/aaA LOW 2 SILENT CODING ECHDC3 A protein_coding NM_024693.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11789405 G A 0 228 0 0.7201 0.9223 0.9769 1 0.998 0.999 0.779392 0.924496 0.998837 2 7999 118810 11469 8653 6614 66676 900 16499 2 10406 121410 11578 8654 6614 66740 908 16510 0 . 0 . 0 130 0,0,40,79 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K76|303|ECHDC3|protein_coding|CODING|NM_024693.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4750091 -0.693147 0.0787552 130 V140 303 gtT/gtC LOW 4 SILENT CODING ECHDC3 C protein_coding NM_024693.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11797436 T C 0 228 0 0.7519 0.9313 0.9813 1 0.998 0.999 0.814117 0.936337 0.998953 2 8302 119085 11484 8651 6614 66653 902 16479 2 10394 121350 11576 8652 6614 66716 908 16490 0 . 0 . 0 412 0,0,220,106 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V140|303|ECHDC3|protein_coding|CODING|NM_024693.4|4|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.990525 0 . rs7899215 -0.693147 0.0222663 412 A151T 303 Gcg/Acg MODERATE 4 MISSENSE CODING ECHDC3 A protein_coding NM_024693.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11797467 G A 0 228 0 0.6974 0.9159 0.9755 1 0.997 0.999 0.744212 0.912194 0.998256 2 7639 118243 11439 8641 6596 66537 896 16495 2 10350 121182 11566 8642 6596 66616 906 16506 0 . 0 . 0 308 0,0,77,208 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A151T|303|ECHDC3|protein_coding|CODING|NM_024693.4|4|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.99806 0 . rs7910140 -0.693147 0.0684668 308 A241 303 gcA/gcG LOW 5 SILENT CODING ECHDC3 G protein_coding NM_024693.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11805354 A G 0 228 0 0.3828 0.5152 0.5072 0.5377 0.5875 0.6022 0.444394 0.544825 0.596279 2 4500 66954 5392 4647 3427 38760 490 9738 2 10354 120622 11504 8580 6544 66250 898 16492 0.99274 0 . 0 . 155 2,2,91,50 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A241|303|ECHDC3|protein_coding|CODING|NM_024693.4|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.955481 rs12258196 -0.693147 0.0928051 155 S242 303 tcG/tcA LOW 5 SILENT CODING ECHDC3 A protein_coding NM_024693.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11805357 G A 0 228 0 0.385 0.5158 0.5072 0.5377 0.5875 0.6022 0.444394 0.544518 0.595814 2 4496 66940 5393 4644 3425 38761 490 9731 2 10346 120604 11502 8574 6542 66252 898 16490 0.952584 0 . 0 . 156 2,2,92,50 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S242|303|ECHDC3|protein_coding|CODING|NM_024693.4|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.9627 rs10906011 -0.693147 0.125134 156 303 296 MODIFIER 5 CODING ECHDC3 CT protein_coding NM_024693.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11805838 C CT 0 83 0 0.6974 0.9157 0.9755 0.999 0.997 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||296||303|ECHDC3|protein_coding|CODING|NM_024693.4|5|CT) 0 . 0 4 1 1 1 0 . 0 60 0 0 1 0 . rs34954686 -0.556411 0.292086 4 435 26 MODIFIER 4 CODING PROSER2 T protein_coding NM_153256.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 11912431 C T 0 154 0 0.4387 0.3844 0.3775 0.1607 0.4006 0.5297 0.34555 0.316696 0.301802 1 241 2885 53 67 6 1069 27 1422 2 488 5802 140 340 28 2358 60 2388 0.976745 0 . 0 . 16 2,4,7,3 UTR_3_PRIME(MODIFIER||26||435|PROSER2|protein_coding|CODING|NM_153256.3|4|T),INTRAGENIC(MODIFIER|||||PROSER2-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836992 rs12253600 -0.670168 0.602433 16 F20L 919 Ttc/Ctc MODERATE 1 MISSENSE CODING DHTKD1 C protein_coding NM_018706.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12111090 T C 0 228 0 0.8911 0.9702 0.9928 1 1 1 0.905251 0.967485 0.9993 2 8484 116015 11297 8538 6099 64315 854 16428 2 9480 117102 11366 8538 6104 64328 856 16430 0 . 0 . 0 15 0,0,7,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F20L|919|DHTKD1|protein_coding|CODING|NM_018706.6|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.964642 0 . rs1279138 -0.676189 0.577434 15 P637 919 ccA/ccC LOW 11 SILENT CODING DHTKD1 C protein_coding NM_018706.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12148259 A C 0 228 0 0.8321 0.9541 0.9899 1 0.999 1 0.852701 0.949485 0.99907 2 8819 119683 11491 8654 6614 66703 899 16503 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 74 0,0,41,26 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P637|919|DHTKD1|protein_coding|CODING|NM_018706.6|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1701472 -0.693147 0.072722 74 F646 919 ttT/ttC LOW 11 SILENT CODING DHTKD1 C protein_coding NM_018706.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12148286 T C 0 228 0 0.8699 0.9641 0.9899 1 0.999 1 0.881752 0.95948 0.999302 2 9146 120048 11524 8654 6614 66707 900 16503 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 88 0,0,45,32 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F646|919|DHTKD1|protein_coding|CODING|NM_018706.6|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1615510 -0.693147 0.352931 88 I693 919 atC/atT LOW 12 SILENT CODING DHTKD1 T protein_coding NM_018706.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12149939 C T 0 228 0 0.8048 0.9032 0.938 0.9821 0.9006 0.9325 0.810713 0.862371 0.888837 2 8378 109602 10744 8420 6169 59985 837 15069 2 10404 121392 11574 8654 6614 66726 908 16512 0 . 0 . 0 38 0,0,22,11 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I693|919|DHTKD1|protein_coding|CODING|NM_018706.6|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1722462 -0.693127 0.337114 38 A145 476 gcC/gcT LOW 6 SILENT CODING SEC61A2 T protein_coding NM_018144.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12191933 C T 0 228 0 0.41 0.4243 0.4986 0.5258 0.4056 0.3057 0.41852 0.417269 0.416628 2 4387 50549 5526 4602 2585 28126 354 4969 2 10406 121354 11576 8622 6610 66722 908 16510 1 0 . 0 . 87 0,1,23,53 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A145|476|SEC61A2|protein_coding|CODING|NM_018144.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10466280 -0.693147 0.0020161 87 A203 219 gcA/gcG LOW 10 SILENT CODING NUDT5 C protein_coding NM_014142.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12209752 T C 0 228 0 0.4251 0.4623 0.5245 0.5575 0.4821 0.3497 0.450522 0.481855 0.497907 2 4662 57819 6109 4818 2948 33027 384 5871 2 10406 121384 11576 8644 6612 66728 908 16510 0 . 0 . 0 105 0,0,41,52 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A203|219|NUDT5|protein_coding|CODING|NM_014142.2|10|C),DOWNSTREAM(MODIFIER||2349||476|SEC61A2|protein_coding|CODING|NM_018144.3||C),INTRAGENIC(MODIFIER|||||SEC61A2||CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6686 -0.693147 0.78663 105 336 8 MODIFIER 13 CODING CDC123 G protein_coding NM_006023.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12292344 A G 0 222 0 0.7292 0.6526 0.6052 0.6062 0.5974 0.6871 0.687018 0.628325 0.598256 1 7255 75318 6913 5450 4203 39904 566 11027 2 10402 121226 11510 8630 6604 66688 906 16486 0.847634 0 . 0 . 69 21,14,9,18 UTR_3_PRIME(MODIFIER||8||336|CDC123|protein_coding|CODING|NM_006023.2|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.678818 rs10951 -0.693021 0.480004 69 336 118 MODIFIER 13 CODING CDC123 G protein_coding NM_006023.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12292454 A G 0 222 0 0.7655 0.6909 0.7075 0.5942 0.6561 0.7137 0 . 0 1 4728 55208 3631 3056 3466 30382 453 9492 2 6426 80176 5278 4810 4986 44456 670 13550 0.800085 0 . 0 . 59 15,16,13,9 UTR_3_PRIME(MODIFIER||118||336|CDC123|protein_coding|CODING|NM_006023.2|13|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.972842 rs1051055 -0.692562 0.453331 59 V316 385 gtC/gtG LOW 10 SILENT CODING CAMK1D G protein_coding NM_153498.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12867598 C G 0 222 0 0.6997 0.774 0.7219 0.8542 0.7634 0.8395 0.712438 0.739966 0.75407 1 7318 91869 8200 7285 4881 50246 672 13267 2 10394 121356 11572 8646 6612 66720 904 16508 0.985933 0 . 0 . 55 11,9,16,14 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V316|385|CAMK1D|protein_coding|CODING|NM_153498.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.880293 rs1757051 -0.693097 0.0116563 55 385 3829 MODIFIER 11 CODING CAMK1D G protein_coding NM_153498.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12874715 T G 0 69 0 0.9493 0.7546 0.6398 0.8403 0.4871 0.7597 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||3829||385|CAMK1D|protein_coding|CODING|NM_153498.3|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2431621,rs386567072 -0.511536 0.732596 3 270 1662 MODIFIER 3 CODING CCDC3 T protein_coding NM_031455.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12938754 C T 0 222 0 0.0265 0.1711 0.219 0.2302 0.3241 0.1145 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999862 0 . 0 . 84 23,16,17,17 UTR_3_PRIME(MODIFIER||1662||270|CCDC3|protein_coding|CODING|NM_031455.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0592182 rs3232 -0.693132 0.314008 84 270 1455 MODIFIER 3 CODING CCDC3 T protein_coding NM_031455.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12938961 C T 0 81 0 0.0265 0.1709 0.219 0.2282 0.3241 0.1155 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.730948 0 . 0 . 9 0,4,1,4 UTR_3_PRIME(MODIFIER||1455||270|CCDC3|protein_coding|CODING|NM_031455.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.406082 rs2280076 -0.590765 0.652896 9 270 39 MODIFIER 3 CODING CCDC3 C protein_coding NM_031455.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12940377 T C 0 214 0 0.8896 0.9609 0.987 1 0.9801 0.9785 0.915908 0.966865 0.991563 2 7283 103173 10979 8270 5994 57928 774 11945 2 8022 105154 11104 8272 6182 58590 790 12194 0 . 0 . 0 15 0,0,13,1 UTR_3_PRIME(MODIFIER||39||270|CCDC3|protein_coding|CODING|NM_031455.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10752280 -0.686358 0.0708043 15 N258 270 aaT/aaC LOW 3 SILENT CODING CCDC3 G protein_coding NM_031455.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 12940455 A G 0 228 0 0.969 0.9914 0.9971 1 1 1 0.974106 0.991163 0.999883 2 8870 116443 11437 8436 6578 63844 880 16398 2 9092 116692 11452 8436 6578 63854 880 16400 0 . 0 . 0 18 0,0,12,6 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N258|270|CCDC3|protein_coding|CODING|NM_031455.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10906249 -0.691153 0.0618961 18 M98K 577 aTg/aAg MODERATE 5 MISSENSE CODING OPTN A protein_coding NM_001008211.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13152400 T A 0 228 0 0.1301 0.0787 0.0259 0.1359 0.0308 0.0368 0.117567 0.0611256 0.0322093 2 1235 5447 196 1024 158 2054 39 741 2 10318 120532 11540 8584 6606 66200 898 16386 0 255|5|2 other|pathogenic|benign 0 . 468 0,0,291,118 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M98K|577|OPTN|protein_coding|CODING|NM_001008211.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11258194 -0.693147 0.182882 468 577 LOW 6 CODING OPTN T protein_coding NM_001008211.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13158262 C T 0 228 0 0.829 0.8039 0.8631 0.745 0.8181 0.774 0.812982 0.81893 0.821977 2 8335 98753 10133 6301 4748 54891 742 13603 2 10348 121086 11530 8614 6606 66600 906 16482 0 2 benign 0 . 249 0,0,161,53 SPLICE_SITE_REGION+INTRON(LOW||||577|OPTN|protein_coding|CODING|NM_001008211.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2244380 -0.693147 0.00183581 249 K322E 577 Aaa/Gaa MODERATE 10 MISSENSE CODING OPTN G protein_coding NM_001008211.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13166076 A G 0 228 0 0.9773 0.9934 0.9971 1 0.999 1 0.97458 0.99062 0.998837 2 10016 120046 11401 8516 6598 66287 894 16334 2 10246 120366 11412 8516 6598 66358 896 16340 0 . 0 . 0 296 0,0,57,217 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K322E|577|OPTN|protein_coding|CODING|NM_001008211.1|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs523747 -0.693147 0.00226983 296 R324H 875 cGt/cAt MODERATE 8 MISSENSE CODING MCM10 A protein_coding NM_182751.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13224970 G A 0 222 0 0 0.005591 0.0274 0.0079 0 0.001 0.000226963 0.000230663 0.000232558 1 2 287 167 80 10 18 1 9 2 10402 121306 11554 8650 6610 66676 906 16508 0.862451 0 . 0 . 202 56,31,59,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R324H|875|MCM10|protein_coding|CODING|NM_182751.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.300912 rs149343572 -0.693147 0.000200169 202 138 238 MODIFIER 5 CODING UCMA A protein_coding NM_145314.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13263865 G A 0 9.5 0 0 0.01278 0 0.0327 0 0.0317 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.875 0 . 0 . 6 4,0,2,0 UTR_3_PRIME(MODIFIER||238||138|UCMA|protein_coding|CODING|NM_145314.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs76274665 -0.453602 0.44 6 R69 138 Aga/Cga LOW 3 SILENT CODING UCMA G protein_coding NM_145314.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13275553 T G 0 228 0 0.7186 0.8037 0.9193 0.8393 0.8946 0.7065 0.773037 0.864524 0.911395 2 7980 105673 10782 7080 5884 60629 782 12536 2 10400 121316 11576 8642 6612 66708 908 16470 0 . 0 . 0 89 0,0,54,18 SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R69|138|UCMA|protein_coding|CODING|NM_145314.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3829925 -0.693147 0.0103376 89 N51 338 aaC/aaT LOW 3 SILENT CODING PHYH A protein_coding NM_006214.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13337588 G A 0 228 0 0.9017 0.9724 0.9885 1 1 1 0.900772 0.965928 0.999302 2 9346 120148 11526 8634 6612 66641 903 16486 2 10370 121266 11566 8634 6612 66672 906 16506 0 255 other 0 . 132 0,0,39,81 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N51|338|PHYH|protein_coding|CODING|NM_006214.3|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1747682 -0.693147 0.011008 132 T157 392 acA/acG LOW 5 SILENT CODING SEPHS1 C protein_coding NM_012247.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13375906 T C 0 228 0 0.7012 0.6779 0.745 0.7609 0.5487 0.6462 0.697458 0.622097 0.583488 2 7370 76792 8972 6900 3941 38675 548 10386 2 10406 121358 11578 8650 6608 66698 906 16512 0 . 0 . 0 202 0,0,93,87 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T157|392|SEPHS1|protein_coding|CODING|NM_012247.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10752297 -0.693147 0.154717 202 S384 468 tcA/tcT LOW 9 SILENT CODING BEND7 A protein_coding NM_152751.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13481427 T A 0 195 0 0.0257 0.3331 0.3401 0.6667 0.3559 0.3763 0.080345 0.249423 0.336047 1 725 45182 5060 6112 3599 23089 353 6244 2 10384 121208 11558 8646 6600 66646 908 16466 0.956856 0 . 0 . 55 1,23,2,29 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S384|468|BEND7|protein_coding|CODING|NM_152751.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.907238 rs12415754 -0.69311 0.228559 55 V324 468 gtA/gtG LOW 7 SILENT CODING BEND7 C protein_coding NM_152751.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13494594 T C 0 222 0 0.1218 0.3564 0.3458 0.6696 0.3429 0.3722 0.158193 0.271106 0.328953 1 1594 45269 5048 6125 3465 22504 344 6189 2 10398 121366 11578 8646 6614 66716 908 16506 0.846591 0 . 0 . 100 20,24,19,27 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V324|468|BEND7|protein_coding|CODING|NM_152751.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995701 rs2277222 -0.693147 0.0139638 100 1039 8139 MODIFIER 25 CODING FRMD4A A protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13685766 G A 0 228 0 0.4433 0.5801 0.634 0.7728 0.5785 0.5297 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,23,41 UTR_3_PRIME(MODIFIER||8139||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13005 -0.693147 0.0778099 68 1039 7915 MODIFIER 25 CODING FRMD4A A protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13685990 C A 0 228 0 0.2814 0.3031 0.268 0.5804 0.2137 0.1636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 84 1,0,36,39 UTR_3_PRIME(MODIFIER||7915||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1043648 -0.693147 0.216939 84 1039 6734 MODIFIER 25 CODING FRMD4A C protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13687171 T C 0 63 0 0.5499 0.6304 0.6441 0.8472 0.5855 0.5521 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||6734||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9473 -0.453602 0.68 3 1039 6015 MODIFIER 25 CODING FRMD4A A protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13687890 G A 0 228 0 0.354 0.3111 0.1902 0.5685 0.2237 0.1636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 117 0,0,46,62 UTR_3_PRIME(MODIFIER||6015||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs17153667 -0.693147 3.87496e-05 117 1039 5854 MODIFIER 25 CODING FRMD4A T protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13688051 C T 0 228 0 0.3343 0.3053 0.1888 0.5675 0.2227 0.1636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 30 0,0,11,19 UTR_3_PRIME(MODIFIER||5854||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1060093 -0.693097 0.102959 30 1039 5334 MODIFIER 25 CODING FRMD4A C protein_coding NM_018027.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 13688571 T C 0 224 0 0.3767 0.4615 0.3458 0.7738 0.3529 0.4479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,3,8 UTR_3_PRIME(MODIFIER||5334||1039|FRMD4A|protein_coding|CODING|NM_018027.3|25|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs729435 -0.676189 0.248694 11 306 1214 MODIFIER 5 CODING FAM107B C protein_coding NM_031453.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 14561975 G C 0 209 0 0.0008 0.0485 0.0086 0.131 0.0189 0.0869 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972716 0 . 0 . 55 22,7,13,2 UTR_3_PRIME(MODIFIER||1214||306|FAM107B|protein_coding|CODING|NM_031453.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.716202 rs11542181 -0.688148 0.615537 55 306 92 MODIFIER 5 CODING FAM107B G protein_coding NM_031453.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 14563097 A G 0 88 0 0.677 0.7889 0.6643 0.881 0.8529 0.8681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99361 0 . 0 . 25 13,3,9,0 UTR_3_PRIME(MODIFIER||92||306|FAM107B|protein_coding|CODING|NM_031453.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.697274 rs3780915 -0.662043 0.490055 25 P171R 692 cCa/cGa MODERATE 7 MISSENSE CODING DCLRE1C C protein_coding NM_001033855.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 14976727 G C 0 222 0 0.1362 0.1168 0.1455 0.1815 0.0646 0.0573 0.128007 0.0911887 0.0723256 1 1324 10991 1443 1721 332 5020 74 1077 2 10406 121394 11574 8654 6614 66726 908 16512 0.896779 2 benign 0 COSM146888 160 25,45,18,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P171R|692|DCLRE1C|protein_coding|CODING|NM_001033855.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.988192 0.994858 0 0.873707 rs35441642 -0.693147 0.27953 160 692 407 MODIFIER 1 CODING DCLRE1C G protein_coding NM_001033855.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 14996416 A G 0 39.3 0 0.2655 0.1571 0.1311 0.2778 0.0189 0.047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||407||692|DCLRE1C|protein_coding|CODING|NM_001033855.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3814175,rs386587035 -0.453602 0.32 2 318 287 MODIFIER 9 CODING OLAH T protein_coding NM_018324.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15115515 C T 0 39.3 0 0.5045 0.3744 0.5029 0.3512 0.2763 0.2321 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||287||318|OLAH|protein_coding|CODING|NM_018324.2|9|T),DOWNSTREAM(MODIFIER||1959||88|ACBD7|protein_coding|CODING|NM_001039844.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7917664 -0.453602 0.9 2 498 LOW 9 CODING NMT2 T protein_coding NM_004808.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15161334 G T 0 222 0 0.0408 0.0497 0.0216 0.0823 0.0447 0.0532 0.0485701 0.0550515 0.0583721 1 540 6773 264 711 314 3967 39 938 2 10406 120952 11578 8650 6614 66590 900 16214 0.99523 0 . 0 . 191 70,40,41,22 SPLICE_SITE_REGION+INTRON(LOW||||498|NMT2|protein_coding|CODING|NM_004808.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.746312 rs45582333 -0.693147 0.34365 191 1063 1836 MODIFIER 30 CODING ITGA8 A protein_coding NM_003638.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15557321 G A 0 18.4 0 0.4115 0.2989 0.2349 0.3214 0.1958 0.2751 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,1,0 UTR_3_PRIME(MODIFIER||1836||1063|ITGA8|protein_coding|CODING|NM_003638.2|30|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs386618856,rs878319 -0.379885 0 4 V994A 1063 gTa/gCa MODERATE 28 MISSENSE CODING ITGA8 G protein_coding NM_003638.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15573050 A G 0 222 0 0.8775 0.9139 0.9841 0.7579 1 0.9857 0.89537 0.963786 0.998837 1 9296 118037 11517 6794 6613 66632 896 16289 2 10402 121388 11578 8654 6614 66722 908 16510 0.907761 0 . 0 . 74 22,10,29,2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gTa/gCa|V994A|1063|ITGA8|protein_coding|CODING|NM_003638.2|28|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.637664 rs1041135 -0.69311 0.0365863 74 S577F 1063 tCc/tTc MODERATE 17 MISSENSE CODING ITGA8 A protein_coding NM_003638.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15649710 G A 0 222 0 0.025 0.0349 0.0346 0.0843 0.0268 0.0061 0.024512 0.0176073 0.0140698 1 259 3907 737 670 641 1398 52 150 2 10300 120964 11538 8634 6612 66490 908 16482 0.77575 0 . 0 . 84 29,7,22,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S577F|1063|ITGA8|protein_coding|CODING|NM_003638.2|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.211323 rs2298033,rs386564169 -0.69312 0.231454 84 445 5 MODIFIER 1 CODING FAM188A G protein_coding NM_024948.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 15902303 A G 0 222 0 0.4766 0.3101 0.2997 0.1687 0.2813 0.2679 0.450749 0.327849 0.264884 1 3428 25511 2088 1177 1336 13592 174 3716 2 7122 72258 5534 5004 3034 39512 504 11548 0.503262 0 . 0 . 100 17,25,17,33 UTR_5_PRIME(MODIFIER||5||445|FAM188A|protein_coding|CODING|NM_024948.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.396611 rs2297882 -0.693147 0.00388874 100 349 47377 MODIFIER 1 CODING PTER G protein_coding NM_001001484.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16479007 C G 0 42.3 0 0.8707 0.6637 0.5159 0.6131 0.4911 0.7188 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||47377||349|PTER|protein_coding|CODING|NM_001001484.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7922050 -0.453602 0.38 2 Q246 349 caA/caG LOW 5 SILENT CODING PTER G protein_coding NM_001001484.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16547058 A G 0 228 0 0.6392 0.6564 0.5793 0.8264 0.4771 0.7434 0.593736 0.508458 0.464767 2 6302 67463 6809 7279 3143 31127 523 12280 2 10404 121382 11578 8646 6612 66728 908 16506 0 . 0 . 0 156 0,0,71,68 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q246|349|PTER|protein_coding|CODING|NM_001001484.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7904014 -0.693147 0.73676 156 277 2417 MODIFIER 9 CODING RSU1 C protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16632976 T C 0 9.7 0 0.0356 0.0359 0.0216 0.0913 0.007 0.0194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2417||277|RSU1|protein_coding|CODING|NM_012425.3|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs45470693 -0.379885 0 1 277 2390 MODIFIER 9 CODING RSU1 T protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16633003 C T 0 46.3 0 0.6846 0.2835 0.1729 0.1865 0.1342 0.0736 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2390||277|RSU1|protein_coding|CODING|NM_012425.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs45461296 -0.453602 0.48 2 277 2334 MODIFIER 9 CODING RSU1 C protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16633059 T C 0 70 0 0.6762 0.2957 0.196 0.1925 0.167 0.091 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2334||277|RSU1|protein_coding|CODING|NM_012425.3|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs45514294 -0.453602 0.48 3 277 2024 MODIFIER 9 CODING RSU1 A protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16633369 G A 0 39.3 0 0.1589 0.0679 0.0259 0.0863 0.007 0.0184 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2024||277|RSU1|protein_coding|CODING|NM_012425.3|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs73599177 -0.453602 0.6 2 277 1094 MODIFIER 9 CODING RSU1 T protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16634299 C T 0 9.7 0 0.1059 0.0984 0.1167 0.0923 0.1233 0.0562 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1094||277|RSU1|protein_coding|CODING|NM_012425.3|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7068341 -0.379885 0 1 277 293 MODIFIER 9 CODING RSU1 G protein_coding NM_012425.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16635100 A G 0 23.4 0 0.7254 0.2406 0.0793 0.1052 0.0179 0.0685 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||293||277|RSU1|protein_coding|CODING|NM_012425.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs6977 -0.453602 0.68 4 N3552K 3623 aaC/aaA MODERATE 66 MISSENSE CODING CUBN T protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16870912 G T 0 222 0 0.0061 0.0823 0.036 0.1458 0.1004 0.1339 0.0177031 0.0556666 0.0751163 1 172 10747 359 1272 966 5662 106 2210 2 10406 121382 11574 8638 6610 66734 908 16512 0.32034 0 . 0 . 135 30,27,43,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N3552K|3623|CUBN|protein_coding|CODING|NM_001081.3|66|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988491 rs1801232,rs386545623 -0.693147 0.520674 135 T3281 3623 acA/acG LOW 62 SILENT CODING CUBN C protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16882518 T C 0 228 0 0.6263 0.636 0.7378 0.4772 0.7535 0.6196 0.641398 0.714824 0.752442 2 5454 69721 5914 3396 4467 40833 568 9089 2 8370 97244 8200 6288 5412 54088 760 14126 0 . 0 . COSM146894 144 0,0,43,86 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T3281|3623|CUBN|protein_coding|CODING|NM_001081.3|62|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs56059527,rs703064 -0.693147 0.0063389 144 A3010 3623 gcT/gcC LOW 57 SILENT CODING CUBN G protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16918972 A G 0 222 0 0.354 0.2474 0.2882 0.3065 0.0855 0.18 0.327054 0.148777 0.0574419 1 3399 18544 4769 2601 826 4333 128 2488 2 10402 121382 11574 8646 6612 66728 908 16512 0.998488 0 . 0 COSM146895 210 69,37,51,29 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A3010|3623|CUBN|protein_coding|CODING|NM_001081.3|57|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799041 rs1801241 -0.693147 0.568599 210 S2717W 3623 tCg/tGg MODERATE 52 MISSENSE CODING CUBN C protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16943371 G C 0 228 0 1 1 1 1 1 1 0.999773 0.999923 1 2 10404 121408 11576 8654 6614 66740 908 16512 2 10406 121410 11576 8654 6614 66740 908 16512 0 . 0 . 0 142 0,0,91,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tGg|S2717W|3623|CUBN|protein_coding|CODING|NM_001081.3|52|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2796835 -0.693147 0.0341836 142 P2575R 3623 cCa/cGa MODERATE 50 MISSENSE CODING CUBN C protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16948390 G C 0 222 0 0.0045 0.0675 0.0634 0.1369 0.0219 0.1309 0.00703586 0.012152 0.0147743 1 71 5101 1161 1147 65 1051 24 1582 2 10312 121208 11562 8648 6614 66654 908 16510 0.981625 0 . 0 . 585 156,141,103,108 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P2575R|3623|CUBN|protein_coding|CODING|NM_001081.3|50|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.448904 rs3740168 -0.693147 0.119064 585 C2162Y 3623 tGt/tAt MODERATE 43 MISSENSE CODING CUBN T protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16967401 C T 0 228 0 1 0.9934 0.9539 0.999 1 1 0.999319 0.999616 0.999767 2 10378 120768 11024 8641 6610 66702 905 16508 2 10384 121276 11514 8646 6610 66706 908 16508 0 . 0 . 0 114 0,0,50,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C2162Y|3623|CUBN|protein_coding|CODING|NM_001081.3|43|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1276712 -0.693147 0.170392 114 3623 LOW 40 CODING CUBN A protein_coding NM_001081.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16975078 G A 0 222 0 0.0862 0.1969 0.1614 0.3194 0.1958 0.2464 0.127099 0.171382 0.19407 1 1260 25020 2542 2661 1303 12985 168 4101 2 10404 121172 11516 8624 6596 66624 904 16504 0.926431 0 . 0 . 148 54,19,45,16 SPLICE_SITE_REGION+INTRON(LOW||||3623|CUBN|protein_coding|CODING|NM_001081.3|40|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.453437 rs2271461 -0.693147 0.852578 148 P1971T 3623 Cct/Act MODERATE 39 MISSENSE CODING CUBN T protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16979606 G T 0 222 0 0.0166 0.0795 0.2176 0.1627 0.0189 0.0429 0.0213345 0.017761 0.0159302 1 218 6992 3386 1476 136 1308 36 432 2 10304 120154 11472 8494 6574 66062 900 16348 0.932945 0 . 0 . 159 55,29,36,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P1971T|3623|CUBN|protein_coding|CODING|NM_001081.3|39|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.411234 rs2356590 -0.693147 0.489151 159 S1952 3623 tcA/tcG LOW 39 SILENT CODING CUBN C protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16979661 T C 0 228 0 0.7542 0.5413 0.5548 0.4911 0.4175 0.4233 0.685883 0.510841 0.421163 2 7252 56013 7287 4308 2622 26884 400 7260 2 10384 121102 11536 8588 6596 66590 904 16504 0 . 0 . 0 137 0,0,61,56 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1952|3623|CUBN|protein_coding|CODING|NM_001081.3|39|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1801234 -0.693147 9.68149e-05 137 G1840S 3623 Ggc/Agc MODERATE 37 MISSENSE CODING CUBN T protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16982061 C T 0 222 0 0.1566 0.1176 0.2248 0.1627 0.0199 0.0429 0.137313 0.0572813 0.0162791 1 1472 8399 3464 1492 141 1351 42 437 2 10370 121178 11566 8624 6608 66606 904 16500 0.399844 0 . 0 . 125 49,7,42,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1840S|3623|CUBN|protein_coding|CODING|NM_001081.3|37|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952733 rs2271462 -0.693147 0.708427 125 3623 LOW 36 CODING CUBN T protein_coding NM_001081.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16982244 G T 0 222 0 0.2398 0.2304 0.1585 0.2887 0.1938 0.2464 0.187472 0.170075 0.161163 1 2224 24117 2115 2550 1351 11854 164 3859 2 10020 120404 11524 8576 6600 66302 898 16484 0.940641 0 . 0 . 76 8,30,5,26 SPLICE_SITE_REGION+INTRON(LOW||||3623|CUBN|protein_coding|CODING|NM_001081.3|36|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975405 rs2271463 -0.69311 0.335526 76 L1712 3623 Ctg/Ttg LOW 35 SILENT CODING CUBN A protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 16990552 G A 0 222 0 0.1589 0.1182 0.2248 0.1637 0.0199 0.0419 0.136178 0.0568968 0.0162791 1 1462 8338 3426 1483 141 1352 41 433 2 10328 120538 11414 8604 6550 66412 906 16324 0.921225 0 . 0 . 131 41,31,22,30 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1712|3623|CUBN|protein_coding|CODING|NM_001081.3|35|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.133927 rs2271468 -0.693147 0.0495155 131 S829 3623 tcG/tcA LOW 19 SILENT CODING CUBN T protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17113563 C T 0 222 0 0.0552 0.356 0.4827 0.5407 0.3966 0.4407 0.108261 0.335691 0.452209 1 1075 51367 6104 4717 2431 28957 382 7701 2 10236 120814 11496 8576 6596 66530 908 16472 0.760677 0 . 0 . 126 24,36,15,36 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S829|3623|CUBN|protein_coding|CODING|NM_001081.3|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939902 rs1801225 -0.693147 0.249279 126 G415 3623 ggT/ggC LOW 12 SILENT CODING CUBN G protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17146590 A G 0 221 0 0.0862 0.1168 0.0937 0.25 0.0378 0.1186 0.0914662 0.0479779 0.0256977 1 898 8571 1486 1844 748 1993 59 1543 2 9822 113994 10992 8230 6412 62308 854 15376 0.493452 0 . 0 COSM146896 102 10,49,4,29 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G415|3623|CUBN|protein_coding|CODING|NM_001081.3|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.722695 rs12571671 -0.693127 0.317014 102 P389T 3623 Cca/Aca MODERATE 11 MISSENSE CODING CUBN T protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17147521 G T 0 222 0 0.3676 0.5343 0.6009 0.6558 0.5875 0.5327 0.412846 0.587575 0.677093 1 4227 74470 7358 5769 3852 43626 499 9139 2 10398 121334 11572 8628 6610 66706 908 16512 0.157978 0 . 0 . 254 58,40,65,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P389T|3623|CUBN|protein_coding|CODING|NM_001081.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.210329 rs1801224 -0.693147 0.0213918 254 N313 3623 aaC/aaT LOW 9 SILENT CODING CUBN A protein_coding NM_001081.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17152994 G A 0 222 0 0.1944 0.2149 0.2262 0.25 0.2584 0.1534 0.216977 0.197063 0.18686 1 2203 25489 2498 1869 1778 14115 249 2777 2 10400 121348 11568 8636 6612 66714 906 16512 0.96199 0 . 0 . 76 17,29,12,12 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N313|3623|CUBN|protein_coding|CODING|NM_001081.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986146 rs1801223 -0.692831 0.340685 76 F253S 3623 tTt/tCt MODERATE 8 MISSENSE CODING CUBN G protein_coding NM_001081.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17156151 A G 0 222 0 0.8056 0.7993 0.7997 0.8472 0.7107 0.8323 0.799591 0.698447 0.646628 1 8266 86977 9058 6954 4492 43901 706 13600 2 10262 119502 11360 8554 6446 65714 890 16276 0.988809 0 . 0 . 75 22,12,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F253S|3623|CUBN|protein_coding|CODING|NM_001081.3|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937231 rs1801222,rs386545622 -0.693136 0.580226 75 391 2654 MODIFIER 11 CODING TRDMT1 G protein_coding NM_004412.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17188385 A G 0 9.7 0 0.8994 0.8832 0.8199 0.751 0.996 0.9264 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2654||391|TRDMT1|protein_coding|CODING|NM_004412.5|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2176286,rs386559787 -0.379885 0 1 391 163 MODIFIER 1 CODING TRDMT1 G protein_coding NM_004412.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17243796 A G 0 20.4 0 0.6619 0.729 0.5879 0.7103 0.8459 0.819 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||163||391|TRDMT1|protein_coding|CODING|NM_004412.5|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2281647 -0.453602 0.92 2 H227Y 288 Cat/Tat MODERATE 6 MISSENSE CODING HACD1 A protein_coding NM_014241.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17636309 G A 0 222 0 0.2542 0.1985 0.1744 0.0685 0.3022 0.1677 0.253745 0.271125 0.280042 1 2627 28051 1316 470 1641 19053 198 2746 2 10272 120974 11568 8650 6614 66584 906 16380 0.919136 0 . 0 . 135 27,26,27,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H227Y|288|HACD1|protein_coding|CODING|NM_014241.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.136473 rs1053926,rs386514344 -0.693147 0.0712795 135 V70F 288 Gtc/Ttc MODERATE 1 MISSENSE CODING HACD1 A protein_coding NM_014241.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17659131 C A 0 76 0 1 1 1 1 1 1 0 . 0 2 446 11496 116 152 0 3142 128 7512 2 446 11496 116 152 0 3142 128 7512 0 . 0 . 0 4 0,0,3,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ttc|V70F|288|HACD1|protein_coding|CODING|NM_014241.3|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs11254692 -0.556411 0.0625499 4 E64K 288 Gag/Aag MODERATE 1 MISSENSE CODING HACD1 T protein_coding NM_014241.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17659149 C T 0 84 0 0.9599 0.8916 0.879 0.7679 0.8897 0.9376 1 1 1 2 379 10667 108 127 0 2865 114 7074 2 392 11390 116 150 0 3082 124 7526 0 . 0 . 0 4 0,0,3,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E64K|288|HACD1|protein_coding|CODING|NM_014241.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7895850 -0.556411 0.0587288 4 Y480 540 taT/taC LOW 14 SILENT CODING STAM C protein_coding NM_003473.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17756596 T C 0 222 0 0.0787 0.1524 0.1441 0.2262 0.2058 0.1268 0.109623 0.184223 0.222442 1 1056 23473 1170 1816 1724 15319 197 2191 2 10406 121324 11576 8610 6610 66706 908 16508 0.37164 0 . 0 COSM146897 75 12,19,22,17 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y480|540|STAM|protein_coding|CODING|NM_003473.3|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903993 rs12221 -0.693144 0.839458 75 540 1181 MODIFIER 14 CODING STAM A protein_coding NM_003473.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17757960 C A 0 228 0 0.8737 0.6422 0.6499 0.5903 0.5795 0.4417 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 76 0,0,13,59 UTR_3_PRIME(MODIFIER||1181||540|STAM|protein_coding|CODING|NM_003473.3|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2764805 -0.693147 0.02938 76 T167I 1456 aCc/aTc MODERATE 3 MISSENSE CODING MRC1 T protein_coding NM_002438.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17869577 C T 0 9.7 0 0.0219 0.1589 0.147 0.2837 0.2445 0.136 0 . 0 1 5 304 12 29 1 252 3 2 2 58 818 40 64 2 640 4 10 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T167I|1456|MRC1|protein_coding|CODING|NM_002438.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs370136276 -0.379885 0 1 I260 1456 atT/atA LOW 4 SILENT CODING MRC1 A protein_coding NM_002438.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 17875816 T A 0 80 0 0.0076 0.0707 0.0533 0.1399 0.1143 0.0521 0 . 0 1 0 66 2 12 0 37 2 13 2 8406 90938 9302 6770 5286 46786 704 13684 0.423077 0 . 0 . 17 1,1,0,13 SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I260|1456|MRC1|protein_coding|CODING|NM_002438.3|4|A) 0 0.5 1 0 . 1 0 . 1 0 33 0 0 1 0 0 rs56331215 -0.683931 5.5603e-05 17 351 1799 MODIFIER 4 CODING TMEM236 C protein_coding NM_001098844.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18087289 T C 0 64 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||1799||351|TMEM236|protein_coding|CODING|NM_001098844.2.2|4|C),INTRON(MODIFIER||||1456|MRC1|protein_coding|CODING|NM_002438.3|4|C) 0 . 0 . 0 . 0 . 0 . 30 0 0 . 0 . rs149367816 -0.556411 0.745967 4 351 4115 MODIFIER 4 CODING TMEM236 G protein_coding NM_001098844.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18089605 A G 0 63 0 0.0212 0.1825 0.2017 0.3869 0.1421 0.2178 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||4115||351|TMEM236|protein_coding|CODING|NM_001098844.2.2|4|G),INTRON(MODIFIER||||1456|MRC1|protein_coding|CODING|NM_002438.3|4|G) 0 . 0 . 0 1 0 . 0 . 39 0 0 1 0 . rs149298165 -0.511536 0.0649539 3 351 4192 MODIFIER 4 CODING TMEM236 A protein_coding NM_001098844.2.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18089682 T A 0 9.7 0 0.5174 0.6402 0.5663 0.8373 0.6511 0.6442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4192||351|TMEM236|protein_coding|CODING|NM_001098844.2.2|4|A),INTRON(MODIFIER||||1456|MRC1|protein_coding|CODING|NM_002438.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 0 . 0 . rs78874899 -0.379885 0 1 T399A 1456 Aca/Gca MODERATE 7 MISSENSE CODING MRC1 G protein_coding NM_002438.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18138639 A G 0 128 0 0.475 0.3297 0.1628 0.5595 0.168 0.181 0 . 0 2 2040 4365 109 1966 0 60 20 170 2 5226 39772 2346 2010 1620 24438 262 3870 0 . 0 . 0 9 0,0,3,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T399A|1456|MRC1|protein_coding|CODING|NM_002438.3|7|G) 0 . 0 . 0 1 0 . 1 0 27 0 0 0.810265 0 . rs71497223 -0.636426 0.313883 9 L407F 1456 ttG/ttC MODERATE 7 MISSENSE CODING MRC1 C protein_coding NM_002438.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18138665 G C 0 80 0 0.413 0.2895 0.147 0.5427 0.1163 0.1411 0 . 0 2 259 498 7 224 0 3 5 0 2 3618 35770 2256 254 1622 24290 242 3488 0 . 0 . 0 6 0,0,0,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L407F|1456|MRC1|protein_coding|CODING|NM_002438.3|7|C) 0 . 0 . 0 1 0 . 1 0 27 0 0 . 0 . rs71497225 -0.616816 0.0989217 6 D33 691 gaT/gaC LOW 2 SILENT CODING SLC39A12 C protein_coding NM_001145195.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18242304 T C 0 228 0 0.9939 0.9279 0.9035 0.9087 0.9145 0.8896 0.975488 0.933108 0.911395 2 10219 109985 9953 7993 5845 60758 801 14416 2 10406 121402 11576 8654 6612 66734 908 16512 0 . 0 . 0 40 0,0,27,12 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D33|691|SLC39A12|protein_coding|CODING|NM_001145195.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386605901,rs691112 -0.693144 0.61021 40 S36G 691 Agc/Ggc MODERATE 2 MISSENSE CODING SLC39A12 G protein_coding NM_001145195.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18242311 A G 0 228 0 0.3048 0.2654 0.2017 0.1548 0.2883 0.3476 0.300953 0.299093 0.29814 2 3097 33529 1615 1186 2184 19524 251 5672 2 10404 121374 11574 8642 6612 66722 908 16512 0 . 0 . 0 43 0,0,28,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S36G|691|SLC39A12|protein_coding|CODING|NM_001145195.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10764176 -0.693146 0.680058 43 V304I 691 Gtt/Att MODERATE 5 MISSENSE CODING SLC39A12 A protein_coding NM_001145195.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18266989 G A 0 228 0 0.6195 0.6647 0.6888 0.6627 0.6322 0.7444 0.625965 0.629632 0.631512 2 6453 79752 7976 5822 4551 42364 604 11982 2 10388 121082 11562 8638 6612 66626 904 16352 0.5375 0 . 0 . 91 2,0,22,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V304I|691|SLC39A12|protein_coding|CODING|NM_001145195.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.43125 rs2478568 -0.693147 0.399191 91 691 230 MODIFIER 13 CODING SLC39A12 A protein_coding NM_001145195.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18331992 G A 0 222 0 0.1157 0.105 0.0908 0.2312 0.0557 0.0215 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.495765 0 . 0 . 71 30,6,28,7 UTR_3_PRIME(MODIFIER||230||691|SLC39A12|protein_coding|CODING|NM_001145195.1|13|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.578287 rs11012350 -0.693136 0.0599635 71 691 350 MODIFIER 13 CODING SLC39A12 G protein_coding NM_001145195.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18332112 A G 0 222 0 0.9463 0.7248 0.6441 0.6835 0.7366 0.5133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.976066 0 . 0 . 205 56,30,54,33 UTR_3_PRIME(MODIFIER||350||691|SLC39A12|protein_coding|CODING|NM_001145195.1|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0202246 rs1935502 -0.693147 0.000930073 205 660 10 MODIFIER 14 CODING CACNB2 T protein_coding NM_201596.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18828663 G T 0 228 0 0.612 0.7744 0.7752 0.9613 0.7903 0.7843 0 . 0 2 5917 91531 8809 8290 5147 50101 693 12574 2 8820 116136 11478 8526 6590 63602 874 16246 0 2 benign 0 . 42 0,0,7,34 UTR_3_PRIME(MODIFIER||10||660|CACNB2|protein_coding|CODING|NM_201596.2|14|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4747352 -0.693145 4.19357e-10 42 660 608 MODIFIER 14 CODING CACNB2 A protein_coding NM_201596.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18829261 T A 0 58 0 0.2829 0.3872 0.2867 0.631 0.3549 0.3814 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,3 UTR_3_PRIME(MODIFIER||608||660|CACNB2|protein_coding|CODING|NM_201596.2|14|A),DOWNSTREAM(MODIFIER||4875||469|NSUN6|protein_coding|CODING|NM_182543.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4748484 -0.511536 0.37344 9 660 609 MODIFIER 14 CODING CACNB2 T protein_coding NM_201596.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18829262 A T 0 65 0 0.2829 0.3872 0.2867 0.631 0.3549 0.3814 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,3 UTR_3_PRIME(MODIFIER||609||660|CACNB2|protein_coding|CODING|NM_201596.2|14|T),DOWNSTREAM(MODIFIER||4874||469|NSUN6|protein_coding|CODING|NM_182543.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4748485 -0.511536 0.37344 9 660 1965 MODIFIER 14 CODING CACNB2 T protein_coding NM_201596.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18830618 C T 0 9.7 0 0.2648 0.4056 0.3012 0.7192 0.3757 0.3773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1965||660|CACNB2|protein_coding|CODING|NM_201596.2|14|T),DOWNSTREAM(MODIFIER||3518||469|NSUN6|protein_coding|CODING|NM_182543.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10828872 -0.379885 0 1 660 2016 MODIFIER 14 CODING CACNB2 C protein_coding NM_201596.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18830669 T C 0 9.7 0 0.6036 0.7602 0.755 0.9613 0.7545 0.774 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2016||660|CACNB2|protein_coding|CODING|NM_201596.2|14|C),DOWNSTREAM(MODIFIER||3467||469|NSUN6|protein_coding|CODING|NM_182543.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7079776 -0.379885 0 1 469 25 MODIFIER 1 CODING NSUN6 A protein_coding NM_182543.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18940157 C A 0 228 0 0.267 0.4062 0.2968 0.7272 0.3718 0.3763 0.297457 0.347278 0.372791 2 3184 45948 2906 6347 2189 24669 346 6307 2 10332 120160 11552 8618 6608 66250 902 15898 0 . 0 . 0 59 0,0,11,48 START_GAINED(LOW||||469|NSUN6|protein_coding|CODING|NM_182543.3|1|A),UTR_5_PRIME(MODIFIER||25||469|NSUN6|protein_coding|CODING|NM_182543.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3740102 -0.693147 5.54526e-06 59 179 1015 MODIFIER 6 CODING ARL5B A protein_coding NM_178815.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18965160 G A 0 222 0 0.0038 0.0857 0.0029 0.3641 0.0119 0.044 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.729313 0 . 0 . 56 16,9,15,8 UTR_3_PRIME(MODIFIER||1015||179|ARL5B|protein_coding|CODING|NM_178815.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.61223 rs12571687 -0.692717 0.00936999 56 179 2722 MODIFIER 6 CODING ARL5B C protein_coding NM_178815.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18966867 T C 0 103 0 0.2489 0.4024 0.2983 0.7272 0.3738 0.3783 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||2722||179|ARL5B|protein_coding|CODING|NM_178815.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1055116 -0.556411 0.193383 4 179 2762 MODIFIER 6 CODING ARL5B G protein_coding NM_178815.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 18966907 A G 0 32.6 0 0.2579 0.405 0.2997 0.7272 0.3738 0.3783 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2762||179|ARL5B|protein_coding|CODING|NM_178815.3|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10741129 -0.379885 0 2 S887N 2156 aGc/aAc MODERATE 18 MISSENSE CODING MALRD1 A protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19498278 G A 0 228 0 0.9924 0.9355 0.9164 0.999 0.833 0.9121 0 . 0 2 1188 16046 304 490 1434 5460 187 6983 2 1222 18000 326 490 1690 6386 222 7664 0 . 0 . 0 145 0,0,82,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S887N|2156|MALRD1|protein_coding|CODING|NM_001142308.2|18|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2358355 -0.693147 0.220003 145 2156 LOW 20 CODING MALRD1 G protein_coding NM_001142308.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19571941 A G 0 221 0 0.7042 0.473 0.5749 0.3849 0.3638 0.2914 0 . 0 1 624 6365 129 178 741 2075 85 2533 2 908 15010 250 462 1628 5008 198 6556 0.861977 0 . 0 . 55 21,2,25,2 SPLICE_SITE_REGION+INTRON(LOW||||2156|MALRD1|protein_coding|CODING|NM_001142308.2|20|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.749649 rs2499066 -0.693021 0.160027 55 D1266A 2156 gAt/gCt MODERATE 24 MISSENSE CODING MALRD1 C protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19620407 A C 0 222 0 0.7194 0.5823 0.5432 0.5248 0.6173 0.4479 0 . 0 1 848 9874 178 260 1027 3773 139 3649 2 1146 17604 308 492 1650 6124 218 7666 0.999945 0 . 0 . 286 76,39,94,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D1266A|2156|MALRD1|protein_coding|CODING|NM_001142308.2|24|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.95394 rs7100382 -0.693147 0.0098002 286 I1277V 2156 Att/Gtt MODERATE 24 MISSENSE CODING MALRD1 G protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19620439 A G 0 222 0 0.4871 0.5056 0.5029 0.5248 0.5905 0.4254 0 . 0 1 551 8948 157 260 993 3451 129 3407 2 1032 17172 294 490 1630 5850 210 7666 0.967517 0 . 0 . 307 77,56,74,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I1277V|2156|MALRD1|protein_coding|CODING|NM_001142308.2|24|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.152553 rs7100403 -0.693147 0.0185269 307 K1357N 2156 aaG/aaT MODERATE 25 MISSENSE CODING MALRD1 T protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19636869 G T 0 222 0 0.475 0.5012 0.5058 0.5218 0.5905 0.4202 0 . 0 1 468 8604 155 257 985 3189 125 3425 2 934 16636 292 488 1618 5434 208 7662 0.992522 0 . 0 . 107 20,28,19,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K1357N|2156|MALRD1|protein_coding|CODING|NM_001142308.2|25|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.641858 rs1609746 -0.693147 0.404084 107 V1417A 2156 gTa/gCa MODERATE 26 MISSENSE CODING MALRD1 C protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19641035 T C 0 222 0 0.5454 0.522 0.5072 0.5228 0.5895 0.4305 0 . 0 1 611 9110 162 258 990 3511 129 3449 2 1078 17316 298 488 1644 5928 214 7666 0.972142 0 . 0 . 254 84,25,83,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V1417A|2156|MALRD1|protein_coding|CODING|NM_001142308.2|26|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.902112 rs10827306 -0.693147 0.0248897 254 2156 LOW 26 CODING MALRD1 G protein_coding NM_001142308.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19641231 A G 0 222 0 0.612 0.5507 0.5375 0.5218 0.6143 0.4417 0 . 0 1 551 8737 154 252 991 3131 128 3530 2 834 15792 270 468 1620 5028 204 7368 0.965915 0 . 0 . 99 0,49,5,43 SPLICE_SITE_REGION+INTRON(LOW||||2156|MALRD1|protein_coding|CODING|NM_001142308.2|26|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.481751 rs7092566 -0.693147 0.129496 99 M1586V 2156 Atg/Gtg MODERATE 28 MISSENSE CODING MALRD1 G protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19678449 A G 0 222 0 0.0068 0.0787 0.085 0.1528 0.1103 0.0624 0 . 0 1 19 1730 26 70 293 695 28 599 2 988 17002 298 486 1638 5718 210 7664 0.927663 0 . 0 . 148 39,31,35,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M1586V|2156|MALRD1|protein_coding|CODING|NM_001142308.2|28|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.991597 rs78832888 -0.693147 0.00512867 148 V1602I 2156 Gta/Ata MODERATE 28 MISSENSE CODING MALRD1 A protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19678497 G A 0 228 0 0.9327 0.8393 0.7334 0.8343 0.8907 0.7403 0 . 0 2 1117 14704 244 405 1547 5480 182 5729 2 1212 17960 310 492 1704 6368 214 7660 0 . 0 . 0 139 0,0,55,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1602I|2156|MALRD1|protein_coding|CODING|NM_001142308.2|28|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs10763975 -0.693147 0.905848 139 L1683I 2156 Ctt/Att MODERATE 30 MISSENSE CODING MALRD1 A protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19780463 C A 0 222 0 0.5862 0.2214 0.1225 0.1339 0.0606 0.0542 0 . 0 1 437 1516 35 63 112 402 14 453 2 902 16356 268 462 1616 5244 206 7658 0.448721 0 . 0 . 37 15,4,11,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L1683I|2156|MALRD1|protein_coding|CODING|NM_001142308.2|30|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.346091 rs16918863 -0.688148 0.271244 37 D1709 2156 gaC/gaT LOW 30 SILENT CODING MALRD1 T protein_coding NM_001142308.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19780543 C T 0 222 0 0.0212 0.255 0.4006 0.3016 0.2913 0.3824 0 . 0 1 68 5213 106 156 439 1602 63 2779 2 928 16722 290 484 1624 5526 206 7664 0.489499 0 . 0 . 47 8,10,13,10 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1709|2156|MALRD1|protein_coding|CODING|NM_001142308.2|30|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.71007 rs10827499 -0.692717 0.730251 47 H1721Q 2156 caT/caG MODERATE 31 MISSENSE CODING MALRD1 G protein_coding NM_001142308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19787418 T G 0 222 0 0.6309 0.3181 0.2147 0.245 0.172 0.1943 0 . 0 1 500 3912 61 136 287 1296 37 1595 2 908 16282 288 486 1618 5232 202 7548 0.524544 0 . 0 . 185 46,39,42,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H1721Q|2156|MALRD1|protein_coding|CODING|NM_001142308.2|31|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.650623 rs12256835 -0.693147 0.259236 185 S2023 2156 tcC/tcA LOW 35 SILENT CODING MALRD1 A protein_coding NM_001142308.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19896830 C A 0 222 0 0.7262 0.8201 0.915 0.7768 0.8956 0.8466 0 . 0 1 679 14328 264 379 1509 4695 181 6621 2 914 16528 292 486 1624 5350 206 7656 0.0548129 0 . 0 . 111 25,28,18,28 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|tcC/tcA|S2023|2156|MALRD1|protein_coding|CODING|NM_001142308.2|35|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.262877 rs7909976 -0.693147 0.0363312 111 2156 LOW 36 CODING MALRD1 A protein_coding NM_001142308.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 19981203 C A 0 222 0 0.1051 0.0577 0.0202 0.12 0.001 0.0143 0 . 0 1 33 228 3 13 0 8 3 168 2 550 13960 184 194 1586 3730 184 7532 0.837711 0 . 0 . 95 36,4,37,4 SPLICE_SITE_REGION+INTRON(LOW||||2156|MALRD1|protein_coding|CODING|NM_001142308.2|36|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.422303 rs78991042 -0.693145 0.303973 95 529 LOW 9 CODING PLXDC2 C protein_coding NM_032812.8 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20500592 T C 0 222 0 0.4327 0.2772 0.1787 0.4196 0.1402 0.1309 0.385611 0.221898 0.138023 1 4015 23036 2342 3582 1497 9529 164 1907 2 10386 120532 11424 8538 6532 66356 902 16394 0.945991 0 . 0 . 80 26,10,20,11 SPLICE_SITE_REGION+INTRON(LOW||||529|PLXDC2|protein_coding|CODING|NM_032812.8|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.766461 rs16920092 -0.69311 0.0733897 80 V396I 529 Gta/Ata MODERATE 11 MISSENSE CODING PLXDC2 A protein_coding NM_032812.8 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20506418 G A 0 222 0 0.7095 0.5663 0.4481 0.3085 0.7048 0.5798 0.692238 0.688375 0.686395 1 7315 74602 4263 2501 4049 45494 595 10385 2 10402 121140 11500 8542 6604 66678 906 16508 0.712055 0 . 0 . 133 34,30,17,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V396I|529|PLXDC2|protein_coding|CODING|NM_032812.8|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.23705 rs3817405 -0.693147 0.213338 133 I458V 529 Att/Gtt MODERATE 13 MISSENSE CODING PLXDC2 G protein_coding NM_032812.8 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20534333 A G 0 228 0 0.9304 0.7821 0.6758 0.5536 0.8857 0.7863 0.919882 0.909426 0.90407 2 9561 101562 7062 4777 5520 60181 798 13663 2 10406 121374 11576 8630 6614 66730 908 16510 0 . 0 . 0 156 0,0,104,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I458V|529|PLXDC2|protein_coding|CODING|NM_032812.8|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2778979 -0.693147 0.332081 156 529 712 MODIFIER 14 CODING PLXDC2 G protein_coding NM_032812.8 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20569460 A G 0 39.3 0 0.8548 0.7566 0.6729 0.5556 0.8847 0.7587 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||712||529|PLXDC2|protein_coding|CODING|NM_032812.8|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2778958 -0.453602 0.52 2 529 1956 MODIFIER 14 CODING PLXDC2 G protein_coding NM_032812.8 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20570704 A G 0 32.6 0 0.8366 0.751 0.6729 0.5546 0.8847 0.7556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1956||529|PLXDC2|protein_coding|CODING|NM_032812.8|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2255279 -0.379885 0 2 529 3661 MODIFIER 14 CODING PLXDC2 C protein_coding NM_032812.8 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 20572409 G C 0 9.7 0 0.3124 0.2476 0.2464 0.2798 0.1869 0.1902 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3661||529|PLXDC2|protein_coding|CODING|NM_032812.8|14|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11527716 -0.379885 0 1 1014 5504 MODIFIER 28 CODING NEBL G protein_coding NM_006393.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21069172 T G 0 9.7 0 0.2769 0.3397 0.2233 0.4623 0.2863 0.4356 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5504||1014|NEBL|protein_coding|CODING|NM_006393.2|28|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10828131 -0.379885 0 1 1014 3485 MODIFIER 28 CODING NEBL C protein_coding NM_006393.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21071191 G C 0 228 0 0.4357 0.4419 0.3429 0.498 0.3728 0.5337 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 74 0,0,47,20 UTR_3_PRIME(MODIFIER||3485||1014|NEBL|protein_coding|CODING|NM_006393.2|28|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1043121 -0.693147 0.00906876 74 1014 1155 MODIFIER 28 CODING NEBL C protein_coding NM_006393.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21073521 T C 0 9.7 0 0.3207 0.4133 0.3357 0.498 0.3738 0.547 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1155||1014|NEBL|protein_coding|CODING|NM_006393.2|28|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4748722 -0.379885 0 1 1014 332 MODIFIER 28 CODING NEBL G protein_coding NM_006393.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21074344 A G 0 228 0 0.7587 0.6174 0.4553 0.6954 0.4085 0.6759 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.620301 0 . 0 . 146 1,1,65,68 UTR_3_PRIME(MODIFIER||332||1014|NEBL|protein_coding|CODING|NM_006393.2|28|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.646617 rs2296612 -0.693147 0.0225954 146 1014 221 MODIFIER 28 CODING NEBL C protein_coding NM_006393.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21074455 T C 0 228 0 0.1672 0.2929 0.1974 0.4395 0.2684 0.4049 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 87 0,1,24,56 UTR_3_PRIME(MODIFIER||221||1014|NEBL|protein_coding|CODING|NM_006393.2|28|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2296613 -0.693147 0.0312945 87 1014 LOW 10 CODING NEBL C protein_coding NM_006393.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21141469 T C 0 228 0 0.9811 0.9525 0.8357 0.9117 0.998 0.9918 0.9798 0.992773 0.999419 2 10196 117663 9163 7865 6607 66602 893 16337 2 10398 121186 11536 8578 6608 66646 908 16512 0.989928 2|2 benign|benign 0 . 124 2,2,53,48 SPLICE_SITE_REGION+INTRON(LOW||||1014|NEBL|protein_coding|CODING|NM_006393.2|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.598798 rs703089 -0.693147 0.0558545 124 D110H 155 Gat/Cat MODERATE 2 MISSENSE CODING C10orf113 G protein_coding NM_001010896.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21414892 C G 0 222 0 0.6657 0.5429 0.3847 0.7063 0.3181 0.5521 0.598275 0.425342 0.336744 1 6392 49073 3844 6201 1813 21724 351 8748 2 10404 121320 11564 8616 6612 66708 906 16510 0.997007 0 . 0 . 67 7,24,13,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D110H|155|C10orf113|protein_coding|CODING|NM_001010896.2|2|G),INTRAGENIC(MODIFIER|||||NEBL||CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98583 rs625223 -0.69311 0.527191 67 R72G 155 Agg/Ggg MODERATE 2 MISSENSE CODING C10orf113 C protein_coding NM_001010896.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 21415006 T C 0 222 0 0.0061 0.1498 0.1095 0.3115 0.1342 0.2219 0.024966 0.101892 0.141312 1 250 18305 1194 2635 886 9754 152 3434 2 9870 120356 11556 8612 6614 66306 904 16494 0.720132 0 . 0 . 38 9,6,7,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R72G|155|C10orf113|protein_coding|CODING|NM_001010896.2|2|C),INTRAGENIC(MODIFIER|||||NEBL||CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.449329 rs11591355 -0.689466 0.461207 38 M235T 366 aTg/aCg MODERATE 1 MISSENSE CODING EBLN1 G protein_coding NM_001199938.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22498209 A G 0 42.3 0 0.5598 0.3139 0.3098 0.2202 0.2535 0.1431 0 . 0 2 3551 25012 2511 1399 1273 13713 150 2415 2 6316 71050 5852 4610 4334 38028 526 11384 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M235T|366|EBLN1|protein_coding|CODING|NM_001199938.1|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2243897 -0.453602 0.56 2 V55D 366 gTc/gAc MODERATE 1 MISSENSE CODING EBLN1 T protein_coding NM_001199938.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22498749 A T 0 39.3 0 0.9992 0.9988 0.9957 1 0.998 1 0 . 0 2 306 11343 128 182 22 3346 114 7245 2 306 11348 128 182 22 3350 114 7246 0 . 0 . 0 2 0,0,0,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gAc|V55D|366|EBLN1|protein_coding|CODING|NM_001199938.1|1|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs2478476 -0.453602 0.48 2 469 968 MODIFIER 14 CODING COMMD3-BMI1 A protein_coding NM_001204062.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22619439 G A 0 228 0 1 0.9826 0.8775 0.998 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,4,16 UTR_3_PRIME(MODIFIER||968||469|COMMD3-BMI1|protein_coding|CODING|NM_001204062.1|14|A),UTR_3_PRIME(MODIFIER||968||326|BMI1|protein_coding|CODING|NM_005180.8|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1170546 -0.692067 0.0545442 20 326 968 MODIFIER 10 CODING BMI1 A protein_coding NM_005180.8 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22619439 G A 0 228 0 1 0.9826 0.8775 0.998 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,4,16 UTR_3_PRIME(MODIFIER||968||469|COMMD3-BMI1|protein_coding|CODING|NM_001204062.1|14|A),UTR_3_PRIME(MODIFIER||968||326|BMI1|protein_coding|CODING|NM_005180.8|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1170546 -0.692067 0.0545442 20 406 997 MODIFIER 10 CODING PIP4K2A C protein_coding NM_005028.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22825133 T C 0 9.7 0 0.857 0.7522 0.8098 0.6607 0.6451 0.774 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||997||406|PIP4K2A|protein_coding|CODING|NM_005028.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8341 -0.379885 0 1 406 37 MODIFIER 10 CODING PIP4K2A C protein_coding NM_005028.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 22826093 A C 0 228 0 0.8502 0.748 0.8084 0.6528 0.6382 0.7781 0.822969 0.690989 0.623372 2 5314 49102 6301 3306 2053 22773 392 8963 2 6312 68442 7428 5000 3122 34412 556 11612 1 0 . 0 . 149 1,0,94,42 UTR_3_PRIME(MODIFIER||37||406|PIP4K2A|protein_coding|CODING|NM_005028.4|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1053454 -0.693147 0.0240077 149 R626Q 872 cGa/cAa MODERATE 15 MISSENSE CODING ARMC3 A protein_coding NM_173081.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23297252 G A 0 222 0 0.2821 0.1885 0.0951 0.12 0.1859 0.2014 0.273163 0.212152 0.180839 1 2193 15589 684 932 678 8206 111 2785 2 6518 63392 6612 4788 2932 30744 496 11302 0.914944 0 . 0 . 125 29,20,43,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R626Q|872|ARMC3|protein_coding|CODING|NM_173081.4|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.818725 rs10828395 -0.693147 0.00633194 125 N642 872 aaC/aaT LOW 15 SILENT CODING ARMC3 T protein_coding NM_173081.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23297301 C T 0 222 0 0.2958 0.5 0.5605 0.5476 0.6163 0.5644 0.342466 0.520837 0.612945 1 1701 27797 2673 1812 1707 14152 257 5495 2 4696 48170 5008 3244 2388 22572 412 9850 0.737489 0 . 0 . 127 34,26,25,25 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N642|872|ARMC3|protein_coding|CODING|NM_173081.4|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.822931 rs11817610 -0.693147 0.378035 127 E46G 182 gAg/gGg MODERATE 2 MISSENSE CODING MSRB2 G protein_coding NM_012228.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23393091 A G 0 222 0 0 0.0325 0.0346 0.1359 0 0.002 0.000532481 0.00125104 0.00157882 1 4 1940 549 1201 21 97 14 54 2 9780 120382 11552 8614 6612 66536 898 16390 0.271138 0 . 0 . 92 23,17,29,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E46G|182|MSRB2|protein_coding|CODING|NM_012228.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992432 rs2296466 -0.693147 0.13825 92 S263P 328 Tcc/Ccc MODERATE 2 MISSENSE CODING PTF1A C protein_coding NM_178161.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23482635 T C 0 228 0 0.5983 0.6244 0.6326 0.869 0.4742 0.5562 0.558783 0.510764 0.486163 2 5891 66223 8112 7689 2860 32365 492 8814 2 10340 121062 11552 8636 6610 66542 906 16476 0 3 likely-benign 0 . 70 0,0,59,7 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Tcc/Ccc|S263P|328|PTF1A|protein_coding|CODING|NM_178161.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7918487 -0.693147 0.145452 70 328 15 MODIFIER 2 CODING PTF1A A protein_coding NM_178161.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23482850 G A 0 228 0 0.087 0.2129 0.1354 0.6895 0.0775 0.0859 0.0755788 0.0585883 0.0498837 2 875 15443 2702 5946 646 3725 109 1440 2 10276 120974 11560 8642 6612 66480 902 16502 0 . 0 . 0 67 0,0,19,47 UTR_3_PRIME(MODIFIER||15||328|PTF1A|protein_coding|CODING|NM_178161.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10828415 -0.693147 0.00733079 67 185 2123 MODIFIER 5 CODING C10orf67 A protein_coding NM_153714.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23605716 G A 0 9.7 0 0.5779 0.4619 0.5173 0.6518 0.2137 0.3252 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2123||185|C10orf67|protein_coding|CODING|NM_153714.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4748860 -0.379885 0 1 185 1909 MODIFIER 5 CODING C10orf67 G protein_coding NM_153714.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23605930 A G 0 9.7 0 0.7511 0.6783 0.6657 0.873 0.4602 0.6125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1909||185|C10orf67|protein_coding|CODING|NM_153714.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4326695 -0.379885 0 1 185 1669 MODIFIER 5 CODING C10orf67 T protein_coding NM_153714.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23606170 C T 0 161 0 0.2776 0.3776 0.2334 0.7827 0.2594 0.319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,1 UTR_3_PRIME(MODIFIER||1669||185|C10orf67|protein_coding|CODING|NM_153714.2|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4297364 -0.616816 0.766069 7 185 1448 MODIFIER 5 CODING C10orf67 G protein_coding NM_153714.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23606391 A G 0 64 0 0.7035 0.5389 0.5548 0.7302 0.2465 0.409 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||1448||185|C10orf67|protein_coding|CODING|NM_153714.2|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9888000 -0.511536 0.11189 3 R47 185 cgG/cgT LOW 1 SILENT CODING C10orf67 A protein_coding NM_153714.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 23633566 C A 0 228 0 0.7277 0.6747 0.6599 0.8562 0.4771 0.6299 0.709002 0.557838 0.487037 2 3755 35916 3286 3576 1465 17314 276 6244 2 5198 58280 4506 4132 2856 30952 450 10186 0 . 0 . COSM427396 69 0,0,34,27 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgT|R47|185|C10orf67|protein_coding|CODING|NM_153714.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2036917 -0.693147 0.272635 69 G192 1943 ggA/ggC LOW 4 SILENT CODING KIAA1217 C protein_coding NM_019590.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24721946 A C 0 222 0 0.3124 0.1887 0.121 0.1935 0.1531 0.1012 0.302769 0.207212 0.158256 1 3138 19958 1605 1818 1101 10464 126 1706 2 10402 121136 11514 8598 6606 66654 906 16456 0.322969 0 . 0 . 110 28,12,33,25 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G192|1943|KIAA1217|protein_coding|CODING|NM_019590.4|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874985 rs2274831 -0.693147 0.0896366 110 M621T 1943 aTg/aCg MODERATE 9 MISSENSE CODING KIAA1217 C protein_coding NM_019590.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24790335 T C 0 222 0 0 0.0065895 0 0.0327 0 0 0.000226963 7.6888e-05 0 1 4 188 0 180 0 0 1 3 2 10388 120988 11552 8644 6596 66530 902 16376 0.26221 0 . 0 . 88 19,19,20,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M621T|1943|KIAA1217|protein_coding|CODING|NM_019590.4|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.677138 rs116844906 -0.693143 0.111846 88 T1562 1943 acC/acT LOW 19 SILENT CODING KIAA1217 T protein_coding NM_019590.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24832885 C T 0 222 0 0.3343 0.279 0.2233 0.3988 0.1521 0.2505 0.316387 0.202906 0.144767 1 3376 25020 3208 3660 1465 9781 190 3340 2 10344 121202 11566 8632 6610 66636 906 16508 0.845227 0 . 0 . 265 89,54,71,28 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1562|1943|KIAA1217|protein_coding|CODING|NM_019590.4|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.917634 rs3748218 -0.693147 0.070187 265 I1646 1943 atC/atT LOW 19 SILENT CODING KIAA1217 T protein_coding NM_019590.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24833137 C T 0 222 0 0.2542 0.2612 0.3141 0.1419 0.3956 0.2178 0.275306 0.346994 0.383721 1 2818 38902 2893 1301 2150 25734 302 3704 2 10326 121038 11540 8636 6610 66542 904 16480 0.776402 0 . 0 . 125 34,31,28,25 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1646|1943|KIAA1217|protein_coding|CODING|NM_019590.4|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971434 rs2250411 -0.693147 0.18999 125 1958 381 MODIFIER 26 CODING ARHGAP21 A protein_coding NM_020824.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24872960 T A 0 222 0 0 0.0077875 0 0.0387 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999668 0 . 0 . 192 42,61,25,47 UTR_3_PRIME(MODIFIER||381||1958|ARHGAP21|protein_coding|CODING|NM_020824.3|26|A) 0 0.5 1 0 . 1 0 . 0 . 58 0 0.973798 0.937025 0 0.0410241 rs188146861 -0.693147 0.000267705 192 D1207 1958 gaT/gaC LOW 18 SILENT CODING ARHGAP21 G protein_coding NM_020824.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24884829 A G 0 222 0 0 0.0079872 0 0.0397 0 0 0.000907853 0.000384497 0.000116306 1 5 319 1 290 0 6 2 15 2 10390 121074 11532 8638 6608 66544 906 16456 0.999996 0 . 0 . 126 39,23,35,22 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1207|1958|ARHGAP21|protein_coding|CODING|NM_020824.3|18|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.988574 0.992427 0 0.997965 rs3748220 -0.693147 0.96966 126 P1100 1958 ccG/ccA LOW 16 SILENT CODING ARHGAP21 T protein_coding NM_020824.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24886410 C T 0 222 0 0 0.00079872 0 0.004 0 0 0 7.6888e-05 0.000116279 1 1 41 0 35 0 0 0 5 2 10406 121352 11578 8650 6614 66692 908 16504 0.679942 0 . 0 . 135 53,22,23,23 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1100|1958|ARHGAP21|protein_coding|CODING|NM_020824.3|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904309 rs3762088 -0.693147 0.339364 135 T318 1958 acA/acC LOW 9 SILENT CODING ARHGAP21 G protein_coding NM_020824.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 24909870 T G 0 222 0 0 0.0077875 0 0.0387 0 0 0.000907853 0.000384497 0.000116306 1 5 318 1 289 0 6 2 15 2 10392 121392 11578 8654 6614 66734 908 16512 0.453006 0 . 0 . 435 130,84,98,68 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T318|1958|ARHGAP21|protein_coding|CODING|NM_020824.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.933986 0.994163 0 0.211854 rs184602735 -0.693147 0.112136 435 225 510 MODIFIER 9 CODING PRTFDC1 T protein_coding NM_020200.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25138263 A T 0 222 0 0.1936 0.3592 0.3256 0.379 0.4404 0.5031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.780412 0 . 0 . 63 9,13,9,23 UTR_3_PRIME(MODIFIER||510||225|PRTFDC1|protein_coding|CODING|NM_020200.6|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.158649 rs7912596 -0.69312 0.202904 63 225 493 MODIFIER 9 CODING PRTFDC1 T protein_coding NM_020200.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25138280 C T 0 222 0 0.0083 0.0313 0.0072 0.1091 0.0149 0.0164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.203218 0 . 0 . 53 6,24,5,14 UTR_3_PRIME(MODIFIER||493||225|PRTFDC1|protein_coding|CODING|NM_020200.6|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.965047 rs41279878 -0.69168 0.436514 53 G179 743 ggA/ggG LOW 3 SILENT CODING THNSL1 G protein_coding NM_024838.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25312689 A G 0 222 0 0.0749 0.3079 0.4308 0.4851 0.2714 0.3906 0.0930549 0.219975 0.285 1 992 39098 6020 4341 2045 18735 310 6655 2 10224 121040 11558 8640 6608 66618 904 16488 0.791246 0 . 0 . 83 22,19,17,11 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G179|743|THNSL1|protein_coding|CODING|NM_024838.4|3|G),INTRAGENIC(MODIFIER|||||ENKUR||CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.732992 rs4748997 -0.693054 0.00833935 83 L556 743 Cta/Tta LOW 3 SILENT CODING THNSL1 T protein_coding NM_024838.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25313818 C T 0 222 0 0.6936 0.509 0.5389 0.4861 0.3459 0.4294 0.638448 0.450331 0.353953 1 6733 51030 6548 4331 2397 23336 378 7307 2 10274 120890 11550 8608 6604 66470 904 16480 0.795849 0 . 0 COSM146908 92 38,12,21,9 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L556|743|THNSL1|protein_coding|CODING|NM_024838.4|3|T),INTRAGENIC(MODIFIER|||||ENKUR||CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.757465 rs7086282 -0.693097 0.0811702 92 743 154 MODIFIER 3 CODING THNSL1 C protein_coding NM_024838.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25314538 A C 0 222 0 0.0802 0.3093 0.4308 0.4851 0.2714 0.3906 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.812848 0 . 0 . 61 29,6,17,6 UTR_3_PRIME(MODIFIER||154||743|THNSL1|protein_coding|CODING|NM_024838.4|3|C),INTRAGENIC(MODIFIER|||||ENKUR||CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.500685 rs12249889 -0.692717 0.0693511 61 743 253 MODIFIER 3 CODING THNSL1 C protein_coding NM_024838.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25314637 G C 0 222 0 0.0749 0.3079 0.4308 0.4851 0.2714 0.3906 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.95435 0 . 0 . 130 44,17,45,13 UTR_3_PRIME(MODIFIER||253||743|THNSL1|protein_coding|CODING|NM_024838.4|3|C),INTRAGENIC(MODIFIER|||||ENKUR||CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.92553 rs12256642 -0.693147 0.0147129 130 G523 1215 ggC/ggT LOW 7 SILENT CODING GPR158 T protein_coding NM_020752.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25861632 C T 0 222 0 0 0.0527 0.0029 0.253 0 0.0072 0.0024966 0.00153775 0.00104651 1 15 2736 198 2235 62 126 28 72 2 10402 121344 11548 8648 6612 66716 908 16510 0.879481 0 . 0 . 128 44,22,45,2 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G523|1215|GPR158|protein_coding|CODING|NM_020752.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985343 rs56928458 -0.693147 0.195159 128 I1209V 1215 Atc/Gtc MODERATE 11 MISSENSE CODING GPR158 G protein_coding NM_020752.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25888180 A G 0 228 0 0.9652 0.6635 0.5144 0.7579 0.3956 0.5399 0.866773 0.574131 0.424168 2 8983 61862 6018 6564 3268 28314 445 8270 2 10092 119968 11524 8598 6600 65866 898 16390 0 . 0 . 0 57 0,0,23,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I1209V|1215|GPR158|protein_coding|CODING|NM_020752.2|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10828833 -0.693147 0.0165482 57 1215 289 MODIFIER 11 CODING GPR158 C protein_coding NM_020752.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 25888492 T C 0 48.2 0 0 0.019369 0.0014 0.0933 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 8 3,1,1,2 UTR_3_PRIME(MODIFIER||289||1215|GPR158|protein_coding|CODING|NM_020752.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1.01283 0 0.607698 rs74962027 -0.511536 0.951887 8 I348V 1616 Att/Gtt MODERATE 11 MISSENSE CODING MYO3A G protein_coding NM_017433.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 26355992 A G 0 222 0 0.6929 0.6627 0.6311 0.6181 0.7217 0.6299 0.679982 0.682531 0.683837 1 7058 82249 7139 5339 5092 46607 629 10385 2 10378 121206 11548 8622 6608 66648 908 16494 0.953983 2 benign 0 . 232 34,76,37,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I348V|1616|MYO3A|protein_coding|CODING|NM_017433.4|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961517 rs3824699 -0.693147 0.0638874 232 V369I 1616 Gtc/Atc MODERATE 12 MISSENSE CODING MYO3A A protein_coding NM_017433.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 26357748 G A 0 222 0 0.7133 0.6689 0.6369 0.6181 0.7227 0.6288 0.681798 0.666769 0.65907 1 7295 82310 7134 5331 5086 46458 625 10381 2 10398 121146 11546 8626 6610 66566 904 16496 0.942416 2 benign 0 . 89 21,17,26,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V369I|1616|MYO3A|protein_coding|CODING|NM_017433.4|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.634564 rs3817420 -0.693141 0.794739 89 R1313S 1616 Cgt/Agt MODERATE 30 MISSENSE CODING MYO3A A protein_coding NM_017433.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 26463130 C A 0 222 0 0.5545 0.601 0.634 0.6329 0.6004 0.6084 0.545393 0.56274 0.571628 1 5749 72639 7616 5512 4324 39063 554 9821 2 10384 121332 11576 8642 6610 66710 908 16502 0.947471 2 benign 0 . 125 41,16,46,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Agt|R1313S|1616|MYO3A|protein_coding|CODING|NM_017433.4|30|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.705825 rs1999240 -0.693147 0.220283 125 K1488E 1616 Aaa/Gaa MODERATE 32 MISSENSE CODING MYO3A G protein_coding NM_017433.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 26482157 A G 0 222 0 0 0.0091853 0 0.0437 0 0.002 0.000226963 0.000153775 0.000116279 1 4 457 6 397 0 8 7 35 2 10194 119668 11378 8480 6574 65896 896 16250 0.827859 2 benign 0 . 144 42,18,41,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K1488E|1616|MYO3A|protein_coding|CODING|NM_017433.4|32|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0195089 rs34204285 -0.693147 0.00261535 144 415 76 MODIFIER 12 CODING PDSS1 T protein_coding NM_014317.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27035478 C T 0 222 0 0.0091 0.0899 0.245 0.0327 0.174 0.0613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.967014 0 . 0 . 49 3,13,7,19 UTR_3_PRIME(MODIFIER||76||415|PDSS1|protein_coding|CODING|NM_014317.3|12|T),DOWNSTREAM(MODIFIER||47||508|ABI1|protein_coding|CODING|NM_005470.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997906 rs12776877 -0.692976 0.10554 49 508 116 MODIFIER 1 CODING ABI1 A protein_coding NM_005470.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27149908 G A 0 181 0 0 0.0775 0.0086 0.1438 0.0109 0.2311 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968368 0 . 0 . 14 0,3,3,7 UTR_5_PRIME(MODIFIER||116||508|ABI1|protein_coding|CODING|NM_005470.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.839457 rs2296544 -0.670168 0.439806 14 1710 68 MODIFIER 34 CODING ANKRD26 C protein_coding NM_014915.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27294449 CAT C 0 222 0 0.0461 0.1418 0.1196 0.2768 0.1183 0.1718 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 25,18,22,17 UTR_3_PRIME(MODIFIER||68||1710|ANKRD26|protein_coding|CODING|NM_014915.2|34|C) 0 0.5 1 45 0.5 1 1 0 . 0 60 0 0 1 0 . rs3215884 -0.693144 0.119967 90 F1514L 1710 ttT/ttA MODERATE 31 MISSENSE CODING ANKRD26 T protein_coding NM_014915.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27303605 A T 0 228 0 0.236 0.3173 0.1758 0.5506 0.1928 0.4151 0.232577 0.171734 0.144766 2 2230 26593 1927 4724 1544 10192 212 5764 2 9588 117766 11288 8492 6512 64624 880 16382 1 0 . 0 . 29 0,1,5,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttA|F1514L|1710|ANKRD26|protein_coding|CODING|NM_014915.2|31|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2274741,rs386501511 -0.692914 0.218946 29 1710 LOW 27 CODING ANKRD26 C protein_coding NM_014915.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27317778 T C 0 222 0 0.0477 0.1422 0.1196 0.2768 0.1183 0.1718 0.0651099 0.0795011 0.0859317 1 579 13419 1134 2470 763 5846 102 2525 2 9698 119018 11480 8446 6572 65556 886 16380 0.978554 0 . 0 . 59 20,8,10,13 SPLICE_SITE_REGION+INTRON(LOW||||1710|ANKRD26|protein_coding|CODING|NM_014915.2|27|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.426125 rs72807627 -0.692717 0.00880397 59 V1305I 1710 Gtc/Atc MODERATE 27 MISSENSE CODING ANKRD26 T protein_coding NM_014915.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27317840 C T 0 228 0 0.2352 0.3173 0.1758 0.5516 0.1928 0.4151 0.233056 0.17227 0.14532 2 2230 26560 1935 4693 1542 10181 212 5767 2 9732 119804 11494 8512 6600 66114 892 16460 1 0 . 0 . 42 0,1,7,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1305I|1710|ANKRD26|protein_coding|CODING|NM_014915.2|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10829163 -0.693143 0.0390898 42 V1220L 1710 Gtt/Ctt MODERATE 25 MISSENSE CODING ANKRD26 G protein_coding NM_014915.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27322303 C G 0 222 0 0.0008 0.0673 0.013 0.1488 0.0119 0.1687 0.000272331 0.00160446 0.00220318 1 10 4325 353 1265 385 389 31 1892 2 9798 120698 11572 8610 6608 66704 900 16506 0.367333 0 . 0 . 102 11,40,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V1220L|1710|ANKRD26|protein_coding|CODING|NM_014915.2|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.968029 rs12572862 -0.693136 0.443668 102 1710 LOW 11 CODING ANKRD26 C protein_coding NM_014915.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27355403 CCATAG C 0 222 0 . 0 . 0 . 0 0.00627854 0.00301579 0.0015444 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 93 37,14,22,6 SPLICE_SITE_REGION+INTRON(LOW||||1710|ANKRD26|protein_coding|CODING|NM_014915.2|11|C) 1 0.5 1 28 0.301075 0 1 1 0 . 60 0 0 1 0 . rs199920305 -0.693054 0.573589 93 V208 1710 gtA/gtG LOW 4 SILENT CODING ANKRD26 C protein_coding NM_014915.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27381349 T C 0 228 0 0.3207 0.3466 0.1873 0.5427 0.2137 0.4294 0.309801 0.210105 0.165889 2 3062 28990 2021 4629 1618 11324 247 6089 2 9600 112740 10250 8212 6400 61262 870 16146 0 . 0 . 0 65 0,0,50,11 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V208|1710|ANKRD26|protein_coding|CODING|NM_014915.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2297145 -0.693147 0.0190494 65 Q20R 1710 cAg/cGg MODERATE 1 MISSENSE CODING ANKRD26 C protein_coding NM_014915.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27389197 T C 0 228 0 0.9871 0.9447 0.9337 0.999 0.8628 0.9233 0.973384 0.893455 0.857318 2 8893 104991 10733 8321 6113 55045 783 15103 2 9150 116950 11434 8324 6590 64156 882 16414 0 . 0 . 0 28 0,0,6,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q20R|1710|ANKRD26|protein_coding|CODING|NM_014915.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7897309 -0.692831 0.000276672 28 773 592 MODIFIER 20 CODING YME1L1 T protein_coding NM_139312.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27400314 C T 0 46.3 0 0.3071 0.3472 0.1873 0.5506 0.2247 0.4315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||592||773|YME1L1|protein_coding|CODING|NM_139312.2|20|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4749226 -0.453602 0.52 2 773 518 MODIFIER 20 CODING YME1L1 A protein_coding NM_139312.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27400388 G A 0 9.7 0 0.0023 0.0669 0.0115 0.1488 0.0119 0.1656 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||518||773|YME1L1|protein_coding|CODING|NM_139312.2|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4749227 -0.379885 0 1 773 517 MODIFIER 20 CODING YME1L1 T protein_coding NM_139312.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27400389 C T 0 9.7 0 0.0023 0.0669 0.0115 0.1488 0.0119 0.1656 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||517||773|YME1L1|protein_coding|CODING|NM_139312.2|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs147349217 -0.379885 0 1 773 245 MODIFIER 20 CODING YME1L1 T protein_coding NM_139312.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27400661 C T 0 127 0 0.0113 0.1304 0.1167 0.2798 0.1103 0.1677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.374644 0 . 0 . 25 9,0,15,0 UTR_3_PRIME(MODIFIER||245||773|YME1L1|protein_coding|CODING|NM_139312.2|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.757465 rs3758438 -0.688148 0.844969 25 773 45 MODIFIER 20 CODING YME1L1 A protein_coding NM_139312.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27400861 G A 0 228 0 0.8903 0.8724 0.7161 0.9881 0.829 0.8845 0.893781 0.85153 0.829884 2 9261 103366 8405 8579 6148 55748 759 14466 2 10402 121390 11572 8654 6614 66732 908 16508 0 . 0 . 0 177 0,0,93,65 UTR_3_PRIME(MODIFIER||45||773|YME1L1|protein_coding|CODING|NM_139312.2|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9833 -0.693147 0.425812 177 773 LOW 19 CODING YME1L1 T protein_coding NM_139312.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27401056 C T 0 228 0 0.3071 0.3472 0.1873 0.5506 0.2247 0.4315 0.303904 0.220821 0.178256 2 3175 30644 2090 4839 1734 12450 251 6105 2 10398 120854 11542 8632 6608 66516 902 16256 0 . 0 . 0 114 0,0,32,67 SPLICE_SITE_REGION+INTRON(LOW||||773|YME1L1|protein_coding|CODING|NM_139312.2|19|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11015538,rs111565817 -0.693147 0.502872 114 F318 773 ttC/ttT LOW 9 SILENT CODING YME1L1 A protein_coding NM_139312.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27420863 G A 0 222 0 0 0.0009984 0 0.005 0 0 0 . 0 1 0 13 0 12 0 0 0 1 2 10342 120862 11544 8642 6612 66482 906 16334 0.859937 0 . 0 . 102 16,36,9,30 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F318|773|YME1L1|protein_coding|CODING|NM_139312.2|9|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.425531 rs370179921 -0.693144 0.348441 102 L126 773 Cta/Tta LOW 4 SILENT CODING YME1L1 A protein_coding NM_139312.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27434483 G A 0 228 0 0.3132 0.3488 0.1873 0.5506 0.2247 0.4315 0.310032 0.222855 0.178181 2 3237 30766 2093 4846 1738 12477 253 6122 2 10308 121118 11562 8638 6614 66600 908 16488 0 . 0 . 0 65 0,0,15,43 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L126|773|YME1L1|protein_coding|CODING|NM_139312.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2274634 -0.693147 0.157803 65 T13 773 acA/acG LOW 2 SILENT CODING YME1L1 C protein_coding NM_139312.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27437964 T C 0 222 0 0.0106 0.13 0.1167 0.2798 0.1093 0.1677 0.0292783 0.0645856 0.0826744 1 272 12836 1078 2512 790 5616 101 2467 2 10250 120764 11522 8630 6606 66380 902 16474 0.796394 0 . 0 . 81 9,29,14,26 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T13|773|YME1L1|protein_coding|CODING|NM_139312.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.633999 rs11538750 -0.693145 0.336731 81 879 27 MODIFIER 1 CODING MASTL C protein_coding NM_001172303.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27444329 T C 0 228 0 0.7746 0.8155 0.6873 0.9841 0.7744 0.8303 0.664193 0.632427 0.616274 2 3852 53046 3068 3892 2000 29298 387 10549 2 4832 65252 4060 3948 2276 36912 490 12734 0 . 0 . 0 113 0,0,65,35 UTR_5_PRIME(MODIFIER||27||879|MASTL|protein_coding|CODING|NM_001172303.1|1|C),UPSTREAM(MODIFIER||980||773|YME1L1|protein_coding|CODING|NM_139312.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7907981 -0.693147 0.209114 113 879 12 MODIFIER 1 CODING MASTL G protein_coding NM_001172303.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27444344 T G 0 228 0 0.8411 0.8552 0.7147 0.9881 0.827 0.8661 0.864441 0.840664 0.828488 2 6591 79129 5566 6390 3994 43255 564 12769 2 7616 92328 7240 6454 4282 51226 672 14838 1 0 . 0 . 120 1,0,65,41 UTR_5_PRIME(MODIFIER||12||879|MASTL|protein_coding|CODING|NM_001172303.1|1|G),UPSTREAM(MODIFIER||995||773|YME1L1|protein_coding|CODING|NM_139312.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7907988 -0.693147 0.521223 120 P620A 879 Cca/Gca MODERATE 8 MISSENSE CODING MASTL G protein_coding NM_001172303.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27459746 C G 0 222 0 0.0825 0.1104 0.0432 0.1528 0.0646 0.1994 0.0819337 0.0622789 0.0522093 1 890 10188 780 1313 722 4026 75 2382 2 10286 120930 11548 8602 6608 66476 902 16508 0.95136 0 . 0 . 82 26,24,14,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P620A|879|MASTL|protein_coding|CODING|NM_001172303.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.600141 rs3802526 -0.69311 0.412018 82 T177 525 acC/acT LOW 6 SILENT CODING ACBD5 A protein_coding NM_145698.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27508746 G A 0 222 0 0.0008 0.0689 0.0072 0.13 0.0119 0.2004 0.000453926 0.00153775 0.00209302 1 17 4644 312 1108 375 374 34 2424 2 10400 121374 11568 8650 6614 66726 906 16510 0.413288 0 . 0 . 76 4,30,11,22 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T177|525|ACBD5|protein_coding|CODING|NM_145698.4|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.386139 rs12572325 -0.693127 0.0837467 76 I584M 767 atA/atG MODERATE 4 MISSENSE CODING PTCHD3 C protein_coding NM_001034842.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27687775 T C 0 228 0 0.9622 0.975 0.9769 0.997 0.9612 0.9826 0.968452 0.960403 0.956279 2 10067 117790 11246 8624 6472 64244 881 16256 2 10400 121368 11576 8654 6614 66712 908 16504 0 . 0 . 0 83 0,0,46,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I584M|767|PTCHD3|protein_coding|CODING|NM_001034842.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1638630 -0.693147 0.134333 83 C407G 767 Tgc/Ggc MODERATE 3 MISSENSE CODING PTCHD3 C protein_coding NM_001034842.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27692279 A C 0 222 0 0.4228 0.4319 0.4107 0.5417 0.3907 0.3885 0.458466 0.4165 0.395 1 4477 48255 4435 4468 2342 25834 361 6338 2 10396 121094 11564 8638 6600 66546 902 16448 0.93105 0 . 0 . 90 24,23,14,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Ggc|C407G|767|PTCHD3|protein_coding|CODING|NM_001034842.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988346 rs2484180 -0.693132 0.824983 90 Q186K 767 Cag/Aag MODERATE 1 MISSENSE CODING PTCHD3 T protein_coding NM_001034842.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27702624 G T 0 222 0 0.0008 0.0913 0.0677 0.2252 0.0109 0.1748 0.00272356 0.00292173 0.00302326 1 34 6462 1468 2270 239 404 41 2006 2 10376 121124 11564 8632 6612 66530 906 16504 0.028757 0 . 0 . 96 22,19,24,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q186K|767|PTCHD3|protein_coding|CODING|NM_001034842.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.215005 rs77473776 -0.693146 0.125618 96 767 55 MODIFIER 1 CODING PTCHD3 G protein_coding NM_001034842.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27703234 A G 0 222 0 0.4637 0.4601 0.536 0.247 0.5308 0.5481 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.954575 0 . 0 . 69 18,16,9,18 UTR_5_PRIME(MODIFIER||55||767|PTCHD3|protein_coding|CODING|NM_001034842.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.984934 rs7071851 -0.693021 0.0108344 69 235 504 MODIFIER 8 CODING RAB18 G protein_coding NM_001256410.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27827484 A G 0 179 0 0 0.0907 0.0303 0.2629 0.0099 0.1616 0 . 0 1 3 956 8 55 1 45 10 834 2 468 11918 142 188 2 3394 132 7592 0.496922 0 . 0 . 71 13,22,2,26 UTR_3_PRIME(MODIFIER||504||235|RAB18|protein_coding|CODING|NM_001256410.1|8|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0727853 rs12571836 -0.693054 0.766588 71 235 561 MODIFIER 8 CODING RAB18 G protein_coding NM_001256410.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27827541 A G 0 170 0 0.8759 0.9665 0.9942 1 1 1 0 . 0 2 368 11618 125 168 2 3265 126 7564 2 414 11668 128 168 2 3266 126 7564 0 . 0 . 0 28 0,0,0,26 UTR_3_PRIME(MODIFIER||561||235|RAB18|protein_coding|CODING|NM_001256410.1|8|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs2763306,rs56527804 -0.692976 0.179516 28 235 1542 MODIFIER 8 CODING RAB18 C protein_coding NM_001256410.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27828522 T C 0 75 0 0 0.0909 0.0303 0.2639 0.0099 0.1616 0 . 0 1 3 896 6 40 0 38 9 800 2 178 8158 68 132 0 1996 94 5690 0.981133 0 . 0 . 17 0,10,0,7 UTR_3_PRIME(MODIFIER||1542||235|RAB18|protein_coding|CODING|NM_001256410.1|8|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 0.252539 rs10508724 -0.636426 0.0498254 17 235 3476 MODIFIER 8 CODING RAB18 G protein_coding NM_001256410.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27830456 A G 0 9.7 0 0.1717 0.2338 0.2046 0.3433 0.1879 0.273 0 . 0 1 40 2522 22 36 0 435 24 1965 2 192 10768 92 132 0 2732 118 7502 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3476||235|RAB18|protein_coding|CODING|NM_001256410.1|8|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs11597728 -0.379885 0 1 235 3484 MODIFIER 8 CODING RAB18 C protein_coding NM_001256410.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27830464 T C 0 9.7 0 0.1717 0.2338 0.2046 0.3433 0.1879 0.273 0 . 0 1 40 2521 23 36 0 433 24 1965 2 192 10760 94 132 0 2724 118 7500 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3484||235|RAB18|protein_coding|CODING|NM_001256410.1|8|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs11598268 -0.379885 0 1 352 1444 MODIFIER 7 CODING MKX A protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27962714 G A 0 222 0 0.1241 0.1861 0.2594 0.1042 0.2147 0.273 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.653875 0 . 0 . 87 25,9,20,13 UTR_3_PRIME(MODIFIER||1444||352|MKX|protein_coding|CODING|NM_001242702.1|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.536378 rs2253055 -0.693127 0.799029 87 352 912 MODIFIER 7 CODING MKX G protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27963246 A G 0 228 0 0.4924 0.5891 0.6369 0.8056 0.4195 0.637 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,30,4 UTR_3_PRIME(MODIFIER||912||352|MKX|protein_coding|CODING|NM_001242702.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2492909 -0.693132 0.653293 36 352 486 MODIFIER 7 CODING MKX C protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27963672 A C 0 228 0 0.5023 0.6022 0.647 0.8056 0.4384 0.6646 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,7,5 UTR_3_PRIME(MODIFIER||486||352|MKX|protein_coding|CODING|NM_001242702.1|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.95494 0 . rs2172085 -0.680642 0.598947 12 352 471 MODIFIER 7 CODING MKX T protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27963687 A T 0 125 0 0.0658 0.1713 0.1902 0.4454 0.0696 0.1227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.966012 0 . 0 . 14 5,2,2,5 UTR_3_PRIME(MODIFIER||471||352|MKX|protein_coding|CODING|NM_001242702.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 0.966012 0 0.571605 rs17756619 -0.636426 0.505181 14 352 266 MODIFIER 7 CODING MKX T protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27963892 C T 0 222 0 0.2496 0.272 0.3444 0.121 0.338 0.3384 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.27014 0 . 0 . 72 17,20,16,5 UTR_3_PRIME(MODIFIER||266||352|MKX|protein_coding|CODING|NM_001242702.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997908 rs2130809 -0.692352 0.170479 72 352 24 MODIFIER 7 CODING MKX C protein_coding NM_001242702.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27964134 T C 0 158 0 0.0197 0.1284 0.1729 0.3442 0.0537 0.0982 0.0215615 0.0402122 0.0497674 1 244 11340 2990 2684 623 3261 74 1464 2 10374 118142 11538 8622 6612 65852 884 14260 0.481593 0 . 0 . 42 15,5,21,1 UTR_3_PRIME(MODIFIER||24||352|MKX|protein_coding|CODING|NM_001242702.1|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.765901 rs17756631 -0.692562 0.149144 42 N284 352 aaC/aaT LOW 6 SILENT CODING MKX A protein_coding NM_001242702.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 27964470 G A 0 222 0 0.295 0.2851 0.353 0.121 0.338 0.3384 0.312982 0.325388 0.331744 1 3148 38755 3652 941 2358 23044 251 5361 2 10324 120144 11388 8582 6572 65986 902 16390 0.50037 0 . 0 . 83 2,37,3,39 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N284|352|MKX|protein_coding|CODING|NM_001242702.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.254605 rs2253230 -0.693146 0.00322396 83 352 LOW 1 CODING MKX A protein_coding NM_001242702.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28034629 G A 0 222 0 0.056 0.1575 0.1081 0.3323 0.1103 0.1984 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 39 0,0,36,2 SPLICE_SITE_REGION+INTRON(LOW||||352|MKX|protein_coding|CODING|NM_001242702.1|1|A),INTRAGENIC(MODIFIER|||||MKX-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11006701 -0.693143 0.0734536 39 R787C 1044 Cgt/Tgt MODERATE 16 MISSENSE CODING ARMC4 A protein_coding NM_001290020.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28224075 G A 0 222 0 0.0015 0.0749 0.0893 0.1716 0.0378 0.1022 0.00567408 0.0149931 0.0197674 1 70 6273 1089 1622 454 1586 46 1406 2 10406 121322 11542 8612 6614 66730 908 16510 0.749282 0 . 0 . 225 58,56,49,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R787C|1044|ARMC4|protein_coding|CODING|NM_001290020.1|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.758224 rs35242712 -0.693147 0.285099 225 N686 1044 aaT/aaC LOW 14 SILENT CODING ARMC4 G protein_coding NM_001290020.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28228865 A G 0 222 0 0.469 0.5331 0.5764 0.5 0.5477 0.6084 0.460735 0.508073 0.532326 1 4815 64993 5840 4682 3438 35678 503 10037 2 10400 121176 11526 8586 6606 66658 908 16492 0.90336 0 . 0 . 114 29,21,21,23 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N686|1044|ARMC4|protein_coding|CODING|NM_001290020.1|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991247 rs7893462 -0.693146 0.453738 114 R666Q 1044 cGg/cAg MODERATE 14 MISSENSE CODING ARMC4 T protein_coding NM_001290020.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28228926 C T 0 222 0 0.0015 0.0749 0.0893 0.1746 0.0378 0.0992 0.00567408 0.0153006 0.0202326 1 70 6280 1087 1608 452 1613 46 1404 2 10378 120752 11508 8558 6584 66460 904 16360 0.989598 0 . 0 COSM146914 85 14,29,7,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R666Q|1044|ARMC4|protein_coding|CODING|NM_001290020.1|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.908058 rs35472668 -0.69312 0.559655 85 L370 576 ctC/ctT LOW 14 SILENT CODING MPP7 A protein_coding NM_173496.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28378613 G A 0 222 0 0.1717 0.1526 0.1268 0.253 0.0477 0.1493 0.166137 0.0932646 0.0559302 1 1740 11656 1252 2388 490 3854 67 1865 2 10404 121352 11568 8644 6614 66712 908 16502 0.997994 0 . 0 COSM146915 124 42,7,42,15 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L370|576|MPP7|protein_coding|CODING|NM_173496.3|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.794645 rs11006853 -0.693147 0.383756 124 K322R 576 aAa/aGa MODERATE 14 MISSENSE CODING MPP7 C protein_coding NM_173496.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 28378758 T C 0 228 0 0.9516 0.9317 0.9496 0.9593 0.8757 0.9213 0.947572 0.900738 0.876744 2 9856 110000 11058 8154 6047 58868 831 15186 2 10396 120984 11514 8540 6596 66524 908 16506 1 0 . 0 . 66 0,1,4,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K322R|576|MPP7|protein_coding|CODING|NM_173496.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2997211 -0.693147 1.33094e-10 66 172 790 MODIFIER 1 CODING C10orf126 T protein_coding NM_001278522.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29135380 C T 0 9.7 0 0.0303 0.0899 0.1023 0.1647 0.0378 0.138 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||790||172|C10orf126|protein_coding|CODING|NM_001278522.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12766476 -0.379885 0 1 172 41 MODIFIER 2 CODING C10orf126 G protein_coding NM_001278522.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29136129 A G 0 23.7 0 0.8805 0.9673 0.9914 1 1 1 0 . 0 2 182 10652 92 134 0 2665 117 7462 2 202 10682 92 134 0 2674 118 7462 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||41||172|C10orf126|protein_coding|CODING|NM_001278522.1|2|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs813935 -0.379885 0 2 172 802 MODIFIER 5 CODING C10orf126 T protein_coding NM_001278522.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29170177 C T 0 46.3 0 0.4493 0.1981 0.072 0.2192 0.0169 0.1125 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||802||172|C10orf126|protein_coding|CODING|NM_001278522.1|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7905314 -0.453602 0.18 2 K13R 194 aAg/aGg MODERATE 1 MISSENSE CODING LYZL1 G protein_coding NM_032517.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29578084 A G 0 222 0 0.6006 0.6769 0.7421 0.7897 0.6153 0.681 0 . 0 1 6241 77337 9333 6834 4126 39571 537 10695 2 10278 119596 11396 8556 6486 65744 886 16250 0.510938 0 . 0 . 75 27,13,12,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K13R|194|LYZL1|protein_coding|CODING|NM_032517.4|1|G) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.8485 0.772101 0 0.877646 rs17851935,rs2532753 -0.693054 0.796436 75 194 LOW 2 CODING LYZL1 T protein_coding NM_032517.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29581440 C T 0 222 0 0.1846 0.3768 0.4467 0.5159 0.4056 0.4141 0.216523 0.353222 0.423256 1 2208 49381 5096 4636 2832 27821 350 6438 2 10396 120548 11550 8630 6608 66460 894 16010 0.413353 0 . 0 . 115 43,12,41,6 SPLICE_SITE_REGION+INTRON(LOW||||194|LYZL1|protein_coding|CODING|NM_032517.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.47405 rs3818550 -0.693147 0.185807 115 Q108P 194 cAg/cCg MODERATE 3 MISSENSE CODING LYZL1 C protein_coding NM_032517.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29581493 A C 0 222 0 0.2504 0.2552 0.2795 0.2748 0.2227 0.2577 0.24512 0.224358 0.213721 1 2550 29394 4421 2256 1436 14219 242 4270 2 10404 121326 11564 8634 6612 66696 906 16510 0.980225 0 . 0 . 173 56,24,51,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cCg|Q108P|194|LYZL1|protein_coding|CODING|NM_032517.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.925311 0.93629 0 0.826815 rs3818551 -0.693147 0.0102824 173 P2168 2214 ccG/ccA LOW 37 SILENT CODING SVIL T protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29747417 C T 0 222 0 0.2852 0.3594 0.3746 0.5565 0.2465 0.362 0.295279 0.241811 0.214419 1 3104 34751 5303 4759 2245 14478 264 4598 2 10300 114838 11522 8624 6612 64946 848 11986 0.363675 0 . 0 . 66 11,13,10,23 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P2168|2214|SVIL|protein_coding|CODING|NM_021738.2|37|T),INTRAGENIC(MODIFIER|||||SVIL-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978168 rs1887465 -0.693127 0.0334441 66 T2016 2214 acA/acG LOW 34 SILENT CODING SVIL C protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29754609 T C 0 222 0 0.3638 0.4231 0.4323 0.5625 0.3817 0.3957 0.378348 0.356758 0.345698 1 3978 47888 5816 4776 3254 23270 343 6451 2 10258 120768 11550 8628 6590 66340 902 16500 0.849783 0 . 0 COSM146917 111 20,26,27,27 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T2016|2214|SVIL|protein_coding|CODING|NM_021738.2|34|C),INTRAGENIC(MODIFIER|||||SVIL-AS1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.982717 0.983392 0 0.953745 rs1057952 -0.693147 0.39752 111 P1994 2214 ccT/ccC LOW 34 SILENT CODING SVIL G protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29754675 A G 0 222 0 0.0045 0.0539 0.0476 0.0496 0.0835 0.0992 0.0154335 0.0539065 0.0736218 1 169 7784 376 457 326 4777 69 1610 2 8432 107284 9976 7606 5774 59160 814 15522 0.596532 0 . 0 . 105 19,37,11,26 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1994|2214|SVIL|protein_coding|CODING|NM_021738.2|34|G),INTRAGENIC(MODIFIER|||||SVIL-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.907913 0.991392 0 0.981679 rs56248456 -0.693141 0.176233 105 A1941 2214 gcT/gcC LOW 32 SILENT CODING SVIL G protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29759225 A G 0 222 0 0.2814 0.2472 0.2839 0.2391 0.2286 0.2025 0.268951 0.23097 0.211512 1 2854 27503 3113 2059 1887 14046 183 3361 2 10402 121376 11578 8652 6608 66716 908 16512 0.828692 0 . 0 COSM146918 89 33,12,30,6 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1941|2214|SVIL|protein_coding|CODING|NM_021738.2|32|G),INTRAGENIC(MODIFIER|||||SVIL-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993517 rs11007607 -0.693139 0.0364335 89 V1752I 2214 Gtt/Att MODERATE 29 MISSENSE CODING SVIL T protein_coding NM_021738.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29769589 C T 0 222 0 0.0408 0.0625 0.0533 0.0347 0.0795 0.1094 0.0415343 0.0682762 0.0819767 1 430 8394 402 434 333 4921 70 1804 2 10406 121398 11576 8648 6614 66736 906 16512 0.649363 0 . 0 . 75 15,17,20,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1752I|2214|SVIL|protein_coding|CODING|NM_021738.2|29|T),INTRAGENIC(MODIFIER|||||SVIL-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.502651 rs61737920 -0.693145 0.938533 75 2214 LOW 19 CODING SVIL T protein_coding NM_021738.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29784013 C T 0 169 0 0.0749 0.0461 0.013 0.0258 0.002 0.0971 0.0408534 0.0140704 0.000348837 1 452 2074 31 252 0 88 6 1245 2 8928 110252 10000 7410 6114 61506 820 15474 0.993664 0 . 0 . 88 33,26,13,7 SPLICE_SITE_REGION+INTRON(LOW||||2214|SVIL|protein_coding|CODING|NM_021738.2|19|T) 1 0.5 1 0 . 1 0 1 1 0 50 0 0.801516 0.0124312 0 0.0131712 rs12266126 -0.692067 8.69895e-09 88 2214 LOW 18 CODING SVIL C protein_coding NM_021738.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29784114 T C 0 228 0 0.7421 0.7802 0.8415 0.7014 0.8748 0.772 0 . 0 2 5787 83954 7287 5205 4250 49198 641 11586 2 7676 96782 8310 6518 4852 54278 736 14412 0 . 0 . 0 102 0,0,36,53 SPLICE_SITE_REGION+INTRON(LOW||||2214|SVIL|protein_coding|CODING|NM_021738.2|18|C) 0 . 0 . 0 1 0 . 1 0 53 0 0 0.0646128 0 . rs6481601,rs67361084 -0.693147 0.000989293 102 R981 2214 Cga/Aga LOW 15 SILENT CODING SVIL T protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29812602 G T 0 222 0 0.562 0.3824 0.438 0.0804 0.4284 0.364 0.546754 0.455943 0.409419 1 5753 47431 4377 750 2890 27251 342 6068 2 10404 121344 11564 8644 6612 66708 908 16504 0.615308 0 . 0 COSM1347520 115 31,23,30,16 SYNONYMOUS_CODING(LOW|SILENT|Cga/Aga|R981|2214|SVIL|protein_coding|CODING|NM_021738.2|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97031 rs7070678 -0.693147 0.256641 115 V617 2214 gtG/gtA LOW 9 SILENT CODING SVIL T protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29821089 C T 0 222 0 0.3313 0.2867 0.3617 0.0764 0.3926 0.2812 0.344984 0.388359 0.410581 1 3609 42740 3039 720 2824 27199 303 5046 2 10398 121276 11562 8650 6610 66648 906 16502 0.285978 0 . 0 . 90 23,20,14,21 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V617|2214|SVIL|protein_coding|CODING|NM_021738.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998739 rs17756919 -0.693136 0.515922 90 K591 2214 aaA/aaG LOW 8 SILENT CODING SVIL C protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29821523 T C 0 222 0 0.3351 0.2973 0.3818 0.0764 0.4245 0.2832 0.353155 0.412348 0.442674 1 3678 45875 3168 720 3038 29748 325 5198 2 10396 121230 11548 8636 6596 66642 906 16506 0.999879 0 . 0 . 63 18,12,13,15 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K591|2214|SVIL|protein_coding|CODING|NM_021738.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.756589 rs1328323 -0.693054 0.0609414 63 V422I 2214 Gtc/Atc MODERATE 8 MISSENSE CODING SVIL T protein_coding NM_021738.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29822032 C T 0 228 0 1 0.9932 0.9885 1 0.9791 0.9949 0.997049 0.987621 0.982791 2 10347 119147 11434 8502 6522 65209 886 16247 2 10376 120838 11526 8502 6598 66430 902 16504 0 . 0 . 0 55 0,0,31,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V422I|2214|SVIL|protein_coding|CODING|NM_021738.2|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1247696 -0.693147 0.0174126 55 L379 2214 ctA/ctG LOW 8 SILENT CODING SVIL C protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29822159 T C 0 222 0 0.3502 0.3107 0.3862 0.0823 0.4274 0.319 0.362914 0.418115 0.446395 1 3779 47115 3188 790 3048 29984 329 5997 2 10396 121342 11558 8646 6610 66714 908 16510 0.24321 0 . 0 . 66 21,18,14,7 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L379|2214|SVIL|protein_coding|CODING|NM_021738.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.855861 rs7076239 -0.692352 0.00801055 66 V189A 2214 gTg/gCg MODERATE 6 MISSENSE CODING SVIL G protein_coding NM_021738.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29839787 A G 0 228 0 0.4228 0.3079 0.2651 0.3462 0.2386 0.2147 0.416024 0.313624 0.261163 2 4237 33146 3503 2933 2059 17037 207 3170 2 10402 121378 11578 8648 6610 66722 908 16510 1 0 . 0 COSM146920 54 0,1,31,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V189A|2214|SVIL|protein_coding|CODING|NM_021738.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10160013 -0.693147 0.554899 54 A163 2214 gcT/gcG LOW 6 SILENT CODING SVIL C protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29839864 A C 0 228 0 0.6324 0.7278 0.7075 0.8224 0.7286 0.773 0.663414 0.703752 0.724419 2 6883 89331 8359 7230 5168 48355 660 12676 2 10406 121380 11570 8640 6612 66732 908 16512 1 0 . 0 . 57 0,1,28,21 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A163|2214|SVIL|protein_coding|CODING|NM_021738.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1270874 -0.693147 0.256812 57 I105 2214 atT/atC LOW 6 SILENT CODING SVIL G protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29840038 A G 0 228 0 0.4228 0.3245 0.2666 0.3472 0.2416 0.2945 0.416024 0.315547 0.26407 2 4247 34581 3515 2928 2062 17192 214 4423 2 10406 121396 11574 8650 6614 66732 908 16512 0.943396 0 . 0 COSM146922 61 2,0,20,33 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I105|2214|SVIL|protein_coding|CODING|NM_021738.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.981132 rs3740003 -0.693147 0.674864 61 S63 2214 tcT/tcC LOW 6 SILENT CODING SVIL G protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29840164 A G 0 188 0 0.2337 0.255 0.245 0.3462 0.2376 0.2147 0.263277 0.26088 0.259651 2 2596 31029 3383 2897 2054 16838 197 3064 2 10090 117052 11476 8552 6592 65128 866 14348 0.9 0 . 0 . 23 0,2,2,18 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S63|2214|SVIL|protein_coding|CODING|NM_021738.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.925 rs3740002 -0.692067 0.00355926 23 G13 2214 ggG/ggA LOW 5 SILENT CODING SVIL T protein_coding NM_021738.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 29843833 C T 0 228 0 0.2352 0.2574 0.245 0.3552 0.2386 0.2147 0.263504 0.261187 0.26 2 2649 31451 3399 3016 2044 16975 202 3166 2 10404 120958 11552 8624 6588 66602 898 16290 1 0 . 0 . 71 0,1,35,26 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G13|2214|SVIL|protein_coding|CODING|NM_021738.2|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1547169 -0.693147 0.476513 71 1359 8 MODIFIER 4 CODING KIAA1462 A protein_coding NM_020848.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30306804 G A 0 222 0 0.0862 0.2644 0.4539 0.1964 0.4274 0.273 0.140384 0.340886 0.43261 1 1369 45758 4925 1645 3103 29158 385 5173 2 9632 119920 11508 8574 6602 66306 894 16404 0.730321 0 . 0 . 54 14,12,8,11 UTR_3_PRIME(MODIFIER||8||1359|KIAA1462|protein_coding|CODING|NM_020848.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.909084 rs2478839 -0.69168 0.0192472 54 S1002T 1359 aGt/aCt MODERATE 3 MISSENSE CODING KIAA1462 G protein_coding NM_020848.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30316072 C G 0 222 0 0.0598 0.2518 0.4524 0.1825 0.4215 0.2658 0.119285 0.328218 0.424606 1 1158 44575 4869 1492 3014 28598 374 5070 2 9790 120722 11572 8620 6610 66720 900 16510 0.638901 0 . 0 . 44 10,5,12,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S1002T|1359|KIAA1462|protein_coding|CODING|NM_020848.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.677519 rs3739998 -0.692352 0.0157842 44 P376 1359 ccG/ccA LOW 3 SILENT CODING KIAA1462 T protein_coding NM_020848.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30317949 C T 0 222 0 0.0598 0.2552 0.4524 0.1935 0.4254 0.2679 0.117419 0.32283 0.423461 1 1151 45330 4893 1638 3093 29018 380 5157 2 9764 120602 11572 8614 6610 66632 900 16510 0.938535 0 . 0 . 52 22,4,10,9 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P376|1359|KIAA1462|protein_coding|CODING|NM_020848.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.254419 rs2478835 -0.69168 0.0547385 52 582 3596 MODIFIER 9 CODING MTPAP C protein_coding NM_018109.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30598942 T C 0 46.3 0 0.1936 0.2192 0.147 0.5228 0.0507 0.1656 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3596||582|MTPAP|protein_coding|CODING|NM_018109.3|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11007975 -0.453602 0.36 2 582 2048 MODIFIER 9 CODING MTPAP G protein_coding NM_018109.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30600490 A G 0 51 0 0.9221 0.8033 0.8963 0.7292 0.7565 0.7014 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2048||582|MTPAP|protein_coding|CODING|NM_018109.3|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs608973 -0.453602 0.06 3 582 1980 MODIFIER 9 CODING MTPAP C protein_coding NM_018109.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30600558 T C 0 9.7 0 0.913 0.8005 0.8948 0.7282 0.7565 0.7014 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1980||582|MTPAP|protein_coding|CODING|NM_018109.3|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs608872 -0.379885 0 1 Y78 467 taT/taC LOW 2 SILENT CODING MAP3K8 C protein_coding NM_001244134.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30728101 T C 0 228 0 0.0976 0.3528 0.5187 0.3492 0.6044 0.3252 0.157512 0.452253 0.603256 2 1587 61021 6169 3193 3992 39858 443 5779 2 10406 121352 11566 8620 6612 66728 908 16512 1 0 . 0 . 177 0,1,84,80 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y78|467|MAP3K8|protein_coding|CODING|NM_001244134.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1042058 -0.693147 0.148322 177 467 130 MODIFIER 8 CODING MAP3K8 A protein_coding NM_001244134.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 30749895 G A 0 228 0 0.9508 0.883 0.9006 0.9514 0.8748 0.7168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,43,8 UTR_3_PRIME(MODIFIER||130||467|MAP3K8|protein_coding|CODING|NM_001244134.1|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3034 -0.693147 0.00483606 52 P173S 828 Ccc/Tcc MODERATE 7 MISSENSE CODING ZNF438 A protein_coding NM_001143766.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 31138817 G A 0 228 0 0.326 0.3754 0.4308 0.3978 0.3479 0.408 0.332274 0.361833 0.376977 2 3377 48730 6193 3266 3283 25644 341 6626 2 10406 121388 11578 8636 6614 66734 908 16512 1 0 . 0 . 108 0,1,53,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P173S|828|ZNF438|protein_coding|CODING|NM_001143766.1|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10160116 -0.693147 0.107568 108 846 1835 MODIFIER 20 CODING ARHGAP12 C protein_coding NM_018287.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32094751 T C 0 9.7 0 0.0923 0.2426 0.3012 0.4127 0.2048 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1835||846|ARHGAP12|protein_coding|CODING|NM_018287.6|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044798 -0.379885 0 1 846 1696 MODIFIER 20 CODING ARHGAP12 A protein_coding NM_018287.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32094890 C A 0 9.7 0 0.5991 0.5068 0.5375 0.4187 0.495 0.4632 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1696||846|ARHGAP12|protein_coding|CODING|NM_018287.6|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1023207,rs386511234 -0.379885 0 1 846 1337 MODIFIER 20 CODING ARHGAP12 G protein_coding NM_018287.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32095249 T G 0 222 0 0.32 0.2917 0.2219 0.4544 0.1879 0.2423 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.491954 0 . 0 . 98 40,11,28,7 UTR_3_PRIME(MODIFIER||1337||846|ARHGAP12|protein_coding|CODING|NM_018287.6|20|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.525742 rs1044795 -0.693136 0.304377 98 846 920 MODIFIER 20 CODING ARHGAP12 C protein_coding NM_018287.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32095666 T C 0 222 0 0.0545 0.2334 0.2983 0.4127 0.2107 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.758803 0 . 0 . 150 39,26,30,29 UTR_3_PRIME(MODIFIER||920||846|ARHGAP12|protein_coding|CODING|NM_018287.6|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.280921 rs2799002 -0.693147 0.000918771 150 G479 846 ggG/ggA LOW 10 SILENT CODING ARHGAP12 T protein_coding NM_018287.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32120678 C T 0 222 0 0.0908 0.2418 0.2983 0.4127 0.2048 0.2679 0.108182 0.171053 0.203234 1 1158 26106 2847 3241 1000 13470 196 4194 2 9472 116416 11162 8542 6352 63942 848 16098 0.656133 0 . 0 . 120 49,6,36,9 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G479|846|ARHGAP12|protein_coding|CODING|NM_018287.6|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99425 rs2808100 -0.693147 0.00247779 120 F442S 846 tTt/tCt MODERATE 8 MISSENSE CODING ARHGAP12 G protein_coding NM_018287.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32128611 A G 0 222 0 0.0545 0.2318 0.2954 0.4127 0.2048 0.2679 0.0842034 0.168768 0.212093 1 831 26364 2911 3293 1024 13852 201 4252 2 10380 120998 11528 8628 6598 66472 908 16484 0.480433 0 . 0 . 357 68,67,73,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F442S|846|ARHGAP12|protein_coding|CODING|NM_018287.6|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.480021 rs2808096 -0.693147 1.59118e-05 357 E385 846 gaA/gaG LOW 6 SILENT CODING ARHGAP12 C protein_coding NM_018287.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32141460 T C 0 228 0 0.0545 0.2318 0.2954 0.4127 0.2048 0.2679 0.0842034 0.168922 0.212326 2 831 26414 2917 3323 1025 13864 201 4253 2 10398 121368 11576 8652 6614 66712 908 16508 0 . 0 . 0 29 0,0,16,8 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E385|846|ARHGAP12|protein_coding|CODING|NM_018287.6|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2799021 -0.692831 0.0419791 29 846 19939 MODIFIER 1 CODING ARHGAP12 A protein_coding NM_018287.6 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32217722 C A 0 30.3 0 0.0908 0.257 0.3055 0.4196 0.2346 0.3027 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,2,0,3 START_GAINED(LOW||||846|ARHGAP12|protein_coding|CODING|NM_018287.6|1|A),UTR_5_PRIME(MODIFIER||19939||846|ARHGAP12|protein_coding|CODING|NM_018287.6|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs7099930 -0.511536 0.126715 5 963 LOW 15 CODING KIF5B G protein_coding NM_004521.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32311969 A G 0 228 0 0.8797 0.9671 0.9914 1 1 1 0.905356 0.967707 0.999651 2 9377 119965 11476 8632 6606 66495 898 16481 2 10354 121008 11528 8632 6606 66502 902 16484 0 . 0 . 0 53 0,0,2,49 SPLICE_SITE_REGION+INTRON(LOW||||963|KIF5B|protein_coding|CODING|NM_004521.2|15|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs176924 -0.693147 0.127465 53 L4 836 Ctg/Ttg LOW 1 SILENT CODING EPC1 A protein_coding NM_025209.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32635834 G A 0 222 0 0.062 0.1883 0.2061 0.2103 0.1521 0.3609 0.0812528 0.136629 0.165 1 766 22277 2509 1965 1110 10574 160 5193 2 10210 120308 11534 8598 6596 65970 902 16498 0.693786 0 . 0 . 78 12,19,15,21 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L4|836|EPC1|protein_coding|CODING|NM_025209.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.697513 rs11597888 -0.693139 0.754662 78 I39V 628 Ata/Gta MODERATE 4 MISSENSE CODING CCDC7 G protein_coding NM_024688.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 32974969 A G 0 228 0 0.7103 0.9165 0.9539 1 0.997 1 0.743985 0.91224 0.998602 2 7749 118367 11431 8650 6614 66533 895 16495 2 10372 121248 11572 8650 6614 66626 906 16508 0 . 0 . 0 141 0,0,56,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I39V|628|CCDC7|protein_coding|CODING|NM_024688.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1762526 -0.693147 0.000982618 141 T264 628 acG/acC LOW 10 SILENT CODING CCDC7 C protein_coding NM_024688.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33018351 G C 0 228 0 0.7103 0.9165 0.9539 1 0.997 1 0.74577 0.913151 0.998599 2 7378 117256 11313 8500 6580 66120 889 16476 2 9890 120024 11454 8500 6580 66214 900 16486 0 . 0 . 0 91 0,0,19,61 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T264|628|CCDC7|protein_coding|CODING|NM_024688.2|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1414548 -0.693147 1.05896e-06 91 G388A 628 gGa/gCa MODERATE 14 MISSENSE CODING CCDC7 C protein_coding NM_024688.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33123824 G C 0 228 0 0.9425 0.9836 0.9914 1 1 1 0.94804 0.982278 0.999767 2 8723 107361 10501 8092 6144 57895 814 15192 2 9244 107924 10534 8092 6144 57904 814 15192 0 . 0 . 0 226 0,0,93,106 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gGa/gCa|G388A|628|CCDC7|protein_coding|CODING|NM_024688.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4448627 -0.693147 0.000746757 226 V607I 628 Gtt/Att MODERATE 21 MISSENSE CODING CCDC7 A protein_coding NM_024688.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33143396 G A 0 228 0 0.9425 0.9836 0.9914 1 1 1 0.947548 0.982066 0.999767 2 9773 120223 11442 8572 6578 66478 900 16480 2 10350 120846 11478 8572 6578 66488 900 16480 0 . 0 . 0 138 0,0,72,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V607I|628|CCDC7|protein_coding|CODING|NM_024688.2|21|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1418538 -0.693147 0.727147 138 628 101 MODIFIER 22 CODING CCDC7 A protein_coding NM_024688.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33165422 G A 0 172 0 0.028 0.1536 0.1844 0.245 0.173 0.1871 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.377711 0 . 0 . 66 2,30,1,30 UTR_3_PRIME(MODIFIER||101||628|CCDC7|protein_coding|CODING|NM_024688.2|22|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.100269 rs12217414 -0.69311 0.197091 66 801 6340 MODIFIER 16 CODING ITGB1 T protein_coding NM_033668.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33189657 C T 0 154 0 0.1884 0.6188 0.8012 0.6786 0.8141 0.8088 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.836111 0 . 0 . 25 12,0,5,8 UTR_3_PRIME(MODIFIER||6340||801|ITGB1|protein_coding|CODING|NM_033668.2|16|T) 0 0.5 1 0 . 1 0 . 0 . 38 0 0.038092 0.000391254 0 0.93008 rs17576669,rs7217 -0.683931 0.124591 25 801 5712 MODIFIER 16 CODING ITGB1 A protein_coding NM_033668.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33190285 G A 0 213 0 0.6626 0.7847 0.8963 0.6875 0.8767 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 36 0,1,32,2 UTR_3_PRIME(MODIFIER||5712||801|ITGB1|protein_coding|CODING|NM_033668.2|16|A),INTRAGENIC(MODIFIER|||||SNORA86||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 55 0 1 0.0540199 0 1 rs11557914,rs17468 -0.693132 0.261321 36 801 LOW 15 CODING ITGB1 A protein_coding NM_033668.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33190567 C A 0 228 0 0.1853 0.5112 0.7579 0.501 0.7406 0.5511 0.267817 0.594418 0.761744 2 2598 81839 8984 4336 4879 50638 656 9748 2 10376 121158 11498 8628 6610 66638 908 16500 0 . 0 . 0 62 0,0,11,46 SPLICE_SITE_REGION+INTRON(LOW||||801|ITGB1|protein_coding|CODING|NM_033668.2|15|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs2153875 -0.693147 0.000195601 62 G392 801 ggC/ggA LOW 9 SILENT CODING ITGB1 T protein_coding NM_033668.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33209266 G T 0 228 0 0.6626 0.7845 0.8963 0.6885 0.8767 0.8742 0.682705 0.825542 0.898721 2 7129 104093 10560 5841 5776 59576 804 14407 2 10400 121308 11542 8638 6610 66700 908 16510 1 0 . 0 . 82 0,1,34,35 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G392|801|ITGB1|protein_coding|CODING|NM_033668.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2230396 -0.693147 0.0160492 82 C261 801 tgT/tgC LOW 5 SILENT CODING ITGB1 G protein_coding NM_033668.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33214802 A G 0 222 0 0.0401 0.1566 0.1859 0.245 0.172 0.1861 0.0567408 0.135322 0.175581 1 595 19832 2151 2189 995 11029 174 2699 2 10404 121198 11566 8640 6614 66648 908 16418 0.359146 0 . 0 . 93 36,9,29,4 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C261|801|ITGB1|protein_coding|CODING|NM_033668.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953537 rs2298141 -0.693127 0.519504 93 923 2485 MODIFIER 17 CODING NRP1 C protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33466519 T C 0 222 0 0.1914 0.2426 0.1124 0.4911 0.1223 0.272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.934125 0 . 0 . 177 44,42,38,38 UTR_3_PRIME(MODIFIER||2485||923|NRP1|protein_coding|CODING|NM_003873.5|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982182 rs1044274 -0.693147 0.355184 177 923 2438 MODIFIER 17 CODING NRP1 T protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33466566 C T 0 222 0 0.1921 0.2428 0.1138 0.4901 0.1223 0.272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974534 0 . 0 . 144 41,31,29,34 UTR_3_PRIME(MODIFIER||2438||923|NRP1|protein_coding|CODING|NM_003873.5|17|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.758702 rs1044268 -0.693147 0.186614 144 923 2161 MODIFIER 17 CODING NRP1 C protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33466843 T C 0 222 0 0.1914 0.2426 0.1124 0.4911 0.1223 0.272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.38364 0 . 0 . 66 16,11,21,14 UTR_3_PRIME(MODIFIER||2161||923|NRP1|protein_coding|CODING|NM_003873.5|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.85108 rs1044222 -0.693136 0.00641487 66 923 1896 MODIFIER 17 CODING NRP1 A protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33467108 G A 0 211 0 0.7005 0.5847 0.5 0.7272 0.4314 0.499 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 32 0,0,1,31 UTR_3_PRIME(MODIFIER||1896||923|NRP1|protein_coding|CODING|NM_003873.5|17|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10080,rs386509573 -0.69312 0.151077 32 923 1683 MODIFIER 17 CODING NRP1 T protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33467321 G T 0 111 0 0.5681 0.4345 0.2305 0.5972 0.3052 0.364 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,2 UTR_3_PRIME(MODIFIER||1683||923|NRP1|protein_coding|CODING|NM_003873.5|17|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1044210 -0.556411 0.0107983 5 923 1465 MODIFIER 17 CODING NRP1 G protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33467539 A G 0 65 0 0.3343 0.1793 0.1066 0.1071 0.1829 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868815 0 . 0 . 15 9,0,6,0 UTR_3_PRIME(MODIFIER||1465||923|NRP1|protein_coding|CODING|NM_003873.5|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.778801 rs2506140 -0.616816 0.23129 15 923 1354 MODIFIER 17 CODING NRP1 A protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33467650 G A 0 228 0 0.5681 0.4345 0.2305 0.5972 0.3052 0.364 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 63 0,0,60,3 UTR_3_PRIME(MODIFIER||1354||923|NRP1|protein_coding|CODING|NM_003873.5|17|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13324 -0.693147 0.0887681 63 923 990 MODIFIER 17 CODING NRP1 C protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33468014 T C 0 228 0 0.8797 0.6564 0.5346 0.7272 0.4851 0.544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 245 0,0,144,67 UTR_3_PRIME(MODIFIER||990||923|NRP1|protein_coding|CODING|NM_003873.5|17|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2506141 -0.693147 0.000410379 245 923 882 MODIFIER 17 CODING NRP1 A protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33468122 G A 0 222 0 0.3343 0.1789 0.1066 0.1062 0.1819 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.729916 0 . 0 . 177 33,57,28,53 UTR_3_PRIME(MODIFIER||882||923|NRP1|protein_coding|CODING|NM_003873.5|17|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.911691 rs2474733,rs386482829 -0.693147 0.482549 177 923 880 MODIFIER 17 CODING NRP1 G protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33468124 A G 0 222 0 0.3449 0.1865 0.1124 0.1062 0.1998 0.0941 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.298693 0 . 0 . 175 30,58,28,53 UTR_3_PRIME(MODIFIER||880||923|NRP1|protein_coding|CODING|NM_003873.5|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.486437 rs2506142 -0.693147 0.486055 175 923 835 MODIFIER 17 CODING NRP1 G protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33468169 A G 0 222 0 0.3343 0.1787 0.1066 0.1062 0.1819 0.091 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.500532 0 . 0 . 159 46,38,35,33 UTR_3_PRIME(MODIFIER||835||923|NRP1|protein_coding|CODING|NM_003873.5|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.645508 rs2506143 -0.693147 0.101241 159 923 548 MODIFIER 17 CODING NRP1 T protein_coding NM_003873.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33468456 C T 0 222 0 0.3336 0.1787 0.1066 0.1062 0.1819 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.225668 0 . 0 . 121 15,49,14,37 UTR_3_PRIME(MODIFIER||548||923|NRP1|protein_coding|CODING|NM_003873.5|17|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.545708 rs2506144 -0.693147 0.462383 121 S865 923 agT/agC LOW 17 SILENT CODING NRP1 G protein_coding NM_003873.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33469181 A G 0 228 0 0.5666 0.4243 0.2061 0.622 0.2455 0.3671 0.501589 0.325542 0.235349 2 5478 36184 1525 5659 1227 16210 276 5809 2 10406 121372 11574 8634 6610 66730 908 16510 0 . 0 . COSM146924 233 0,0,130,79 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S865|923|NRP1|protein_coding|CODING|NM_003873.5|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1048804 -0.693147 0.486569 233 Y422 923 taC/taT LOW 8 SILENT CODING NRP1 A protein_coding NM_003873.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33510663 G A 0 228 0 0.1793 0.359 0.4337 0.623 0.2485 0.3906 0.208125 0.246194 0.265698 2 2205 38147 4980 5574 1794 17762 270 5562 2 10406 121392 11574 8648 6608 66736 908 16512 1 0 . 0 . 102 1,0,71,25 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y422|923|NRP1|protein_coding|CODING|NM_003873.5|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2229935 -0.693147 0.0682668 102 P387 923 ccC/ccT LOW 8 SILENT CODING NRP1 A protein_coding NM_003873.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33510768 G A 0 228 0 0.18 0.3592 0.4337 0.623 0.2485 0.3906 0.208125 0.246194 0.265698 2 2206 38142 4981 5570 1794 17759 270 5562 2 10402 121378 11572 8636 6612 66736 908 16512 0.692488 0 . 0 . 134 2,1,47,63 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P387|923|NRP1|protein_coding|CODING|NM_003873.5|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.964751 rs2229934 -0.693147 0.0107322 134 V179 923 gtG/gtA LOW 4 SILENT CODING NRP1 T protein_coding NM_003873.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33552695 C T 0 222 0 0.3222 0.2841 0.2003 0.4623 0.162 0.2342 0.238311 0.158312 0.117326 1 3060 24728 2164 4070 1132 10984 166 3152 2 10406 121392 11578 8642 6610 66736 908 16512 0.998418 0 . 0 . 119 30,26,24,23 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V179|923|NRP1|protein_coding|CODING|NM_003873.5|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.626731 rs2070296 -0.693147 0.374703 119 V179A 923 gTg/gCg MODERATE 4 MISSENSE CODING NRP1 G protein_coding NM_003873.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33552696 A G 0 228 0 1 1 1 1 1 1 0.999773 0.999462 0.999302 2 10406 121393 11577 8654 6614 66722 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 113 0,0,48,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V179A|923|NRP1|protein_coding|CODING|NM_003873.5|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7079053 -0.693147 0.0479199 113 G20 923 ggC/ggT LOW 1 SILENT CODING NRP1 A protein_coding NM_003873.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 33623251 G A 0 228 0 0.0378 0.1244 0.0865 0.2143 0.0885 0.2127 0.0387654 0.0554446 0.0639287 2 70 2009 40 122 3 405 19 1350 2 734 13154 204 370 20 3936 138 7752 1 0 . 0 . 20 0,1,14,3 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G20|923|NRP1|protein_coding|CODING|NM_003873.5|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3750733 -0.690438 0.254279 20 S889 1356 tcG/tcA LOW 19 SILENT CODING PARD3 T protein_coding NM_019619.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 34620220 C T 0 222 0 0.7254 0.5497 0.5173 0.3919 0.4761 0.5736 0.704721 0.54867 0.468721 1 7323 60164 5554 3204 3194 31688 455 8746 2 10402 121244 11512 8630 6610 66672 908 16510 0.986281 0 . 0 . 64 8,12,12,23 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S889|1356|PARD3|protein_coding|CODING|NM_019619.3|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.645262 rs3781128 -0.693136 0.00251347 64 H287 1356 caC/caT LOW 7 SILENT CODING PARD3 A protein_coding NM_019619.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 34688287 G A 0 228 0 0.9992 0.9998 1 1 1 1 0.999773 0.998462 0.997791 2 10395 121244 11567 8652 6609 66611 907 16503 2 10398 121370 11570 8652 6614 66716 908 16512 0 . 0 . 0 75 0,0,26,41 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H287|1356|PARD3|protein_coding|CODING|NM_019619.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2796011 -0.693147 0.11815 75 T75 341 acG/acA LOW 2 SILENT CODING CCNY A protein_coding NM_145012.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 35772402 G A 0 222 0 0.6536 0.4571 0.4539 0.4266 0.3241 0.362 0.61734 0.422267 0.322326 1 6405 44360 4951 3470 1893 21591 307 5743 2 10396 121026 11546 8626 6598 66476 906 16478 0.999213 0 . 0 . 42 8,6,9,8 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T75|341|CCNY|protein_coding|CODING|NM_145012.5|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.104882 rs3802509 -0.690438 0.0708308 42 341 567 MODIFIER 10 CODING CCNY C protein_coding NM_145012.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 35858665 T C 0 159 0 0.5303 0.4131 0.4452 0.4187 0.327 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987886 0 . 0 . 55 22,3,28,1 UTR_3_PRIME(MODIFIER||567||341|CCNY|protein_coding|CODING|NM_145012.5|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.959862 rs1043583 -0.693079 0.836501 55 694 49 MODIFIER 1 CODING FZD8 G protein_coding NM_031866.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 35928224 C G 0 228 0 0.7042 0.8998 0.9467 0.995 0.9871 0.9427 0 . 0 2 633 10579 402 1053 88 4661 96 3646 2 844 10990 424 1066 90 4700 96 3770 0 . 0 . 0 29 0,0,2,26 UTR_3_PRIME(MODIFIER||49||694|FZD8|protein_coding|CODING|NM_031866.2|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs625858 -0.693054 0.00867997 29 T768 1341 acG/acA LOW 25 SILENT CODING ANKRD30A A protein_coding NM_052997.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 37478445 G A 0 228 0 0.9153 0.9317 0.9438 0.9583 0.9195 0.9305 0 . 0 2 471 3728 180 314 58 2449 38 218 2 1212 12108 808 974 624 6814 84 1592 0.929825 0 . 0 . 242 2,0,152,76 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T768|1341|ANKRD30A|protein_coding|CODING|NM_052997.2|25|A) 0 . 0 . 0 1 0 . 1 0 28 0 0.79386 2.77379e-13 0 0.427632 rs143202734,rs61865166 -0.693147 0.0908021 242 A1214 1341 gcA/gcC LOW 34 SILENT CODING ANKRD30A C protein_coding NM_052997.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 37508450 A C 0 228 0 0.382 0.5335 0.5 0.6746 0.4125 0.7413 0.37654 0.408572 0.42318 2 3847 59582 5769 5672 3196 28777 437 11884 2 9706 119224 11254 8476 6554 65916 896 16422 1 0 . 0 . 295 0,1,181,81 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A1214|1341|ANKRD30A|protein_coding|CODING|NM_052997.2|34|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1148259 -0.693147 0.93 295 456 1212 MODIFIER 6 CODING ZNF25 A protein_coding NM_145011.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 38239843 C A 0 32.6 0 0.475 0.5242 0.4841 0.4246 0.507 0.7393 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1212||456|ZNF25|protein_coding|CODING|NM_145011.2|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13503 -0.379885 0 2 Q571E 832 Cag/Gag MODERATE 5 MISSENSE CODING ZNF33A G protein_coding NM_001278177.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 38344700 C G 0 222 0 0.5272 0.477 0.5173 0.5754 0.493 0.2628 0.514753 0.489851 0.477093 1 5371 54133 6245 4870 2141 30581 395 4530 2 10394 121300 11556 8616 6610 66708 908 16508 0.432849 0 . 0 . 95 22,16,23,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q571E|832|ZNF33A|protein_coding|CODING|NM_001278177.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.298615 rs2505232 -0.693147 0.0346599 95 561 1531 MODIFIER 2 CODING ZNF37A G protein_coding NM_001007094.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 38384015 T G 0 9.7 0 0.4924 0.4425 0.4611 0.5595 0.4095 0.2751 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1531||561|ZNF37A|protein_coding|CODING|NM_001007094.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2472177 -0.379885 0 1 T250 561 acA/acG LOW 8 SILENT CODING ZNF37A G protein_coding NM_001007094.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 38406829 A G 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 16 0 16 0 0 0 0 2 9908 120322 11440 8638 6610 66320 902 16504 0.744091 0 . 0 . 66 21,8,18,15 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T250|561|ZNF37A|protein_coding|CODING|NM_001007094.2|8|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.798887 rs184390316 -0.693127 0.214874 66 S480 561 tcA/tcG LOW 8 SILENT CODING ZNF37A G protein_coding NM_001007094.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 38407519 A G 0 222 0 0.4947 0.469 0.513 0.5595 0.4901 0.2883 0.50749 0.495156 0.488837 1 5154 55140 6216 4729 2381 31379 396 4885 2 10322 120926 11432 8620 6596 66580 906 16470 0.670897 0 . 0 . 79 24,14,15,18 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S480|561|ZNF37A|protein_coding|CODING|NM_001007094.2|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.601223 rs176889 -0.693127 0.530594 79 785 412 MODIFIER 4 CODING ZNF33B G protein_coding NM_001305033.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43087649 A G 0 36.3 0 0.6611 0.7933 0.7939 0.9633 0.835 0.7536 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||412||785|ZNF33B|protein_coding|CODING|NM_001305033.1|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs210282 -0.453602 0.7 2 785 298 MODIFIER 4 CODING ZNF33B C protein_coding NM_001305033.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43087763 T C 0 179 0 0.6611 0.7933 0.7939 0.9633 0.835 0.7536 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,2 UTR_3_PRIME(MODIFIER||298||785|ZNF33B|protein_coding|CODING|NM_001305033.1|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs210281 -0.651104 0.360182 8 R152C 785 Cgt/Tgt MODERATE 4 MISSENSE CODING ZNF33B A protein_coding NM_001305033.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43089965 G A 0 228 0 0.5348 0.727 0.7767 0.873 0.835 0.6902 0.622389 0.772615 0.849581 2 6345 96676 9623 7482 4809 56102 706 11609 2 10372 121088 11494 8650 6602 66584 904 16482 0 . 0 . 0 127 0,0,77,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R152C|785|ZNF33B|protein_coding|CODING|NM_001305033.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs210280 -0.693147 0.0104248 127 785 290 MODIFIER 1 CODING ZNF33B GCTCTCCCAGTGC protein_coding NM_001305033.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43134240 G GCTCTCCCAGTGC 0 82 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||290||785|ZNF33B|protein_coding|CODING|NM_001305033.1|1|GCTCTCCCAGTGC) 0 . 0 2 0.222222 0 1 0 . 0 60 0 0 . 0 . rs3078017 -0.453602 0.36 2 T112 1282 acT/acC LOW 3 SILENT CODING BMS1 C protein_coding NM_014753.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43281089 T C 0 222 0 0.6293 0.5611 0.4899 0.6359 0.4185 0.589 0.596459 0.460634 0.391047 1 6187 56308 5942 5582 2672 26232 401 9292 2 10404 121330 11576 8642 6614 66706 908 16480 0.639672 0 . 0 . 362 81,77,91,86 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T112|1282|BMS1|protein_coding|CODING|NM_014753.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.376119 rs7074877 -0.693147 0.241284 362 K652R 1282 aAg/aGg MODERATE 10 MISSENSE CODING BMS1 G protein_coding NM_014753.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43292647 A G 0 222 0 0.1725 0.1805 0.2392 0.1835 0.1571 0.1708 0.168765 0.164043 0.161672 1 1718 21927 2737 1691 1486 11140 186 2969 2 9468 119108 11524 8616 6610 65574 896 16420 0.744779 0 . 0 . 71 23,9,21,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K652R|1282|BMS1|protein_coding|CODING|NM_014753.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89464 rs386613776,rs787795 -0.693097 0.61005 71 P815 1282 ccC/ccT LOW 15 SILENT CODING BMS1 T protein_coding NM_014753.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43312807 C T 0 222 0 0.0333 0.2051 0.1167 0.4018 0.1988 0.3037 0 . 0 1 497 24011 1276 3509 879 12544 186 5120 2 7838 106268 10776 7744 6368 57356 842 15344 0.840132 0 . 0 COSM1162580 266 96,16,108,22 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P815|1282|BMS1|protein_coding|CODING|NM_014753.3|15|T) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.992529 0.798221 0 0.788328 rs11239786 -0.693147 0.0279031 266 V1141I 1282 Gtc/Atc MODERATE 21 MISSENSE CODING BMS1 A protein_coding NM_014753.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43319197 G A 0 222 0 0.0378 0.2049 0.1153 0.4018 0.1918 0.3047 0.064693 0.138708 0.182427 1 484 22969 1248 3511 865 11632 179 5050 2 8754 112858 11352 8212 6582 61240 844 15874 0.839249 0 . 0 . 386 60,111,64,105 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1141I|1282|BMS1|protein_coding|CODING|NM_014753.3|21|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.999999 0.998611 0 0.110516 rs12764004 -0.693147 0.0219182 386 1282 83 MODIFIER 23 CODING BMS1 C protein_coding NM_014753.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43326627 A C 0 66 0 0.5053 0.4914 0.4236 0.626 0.3141 0.5644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.373673 0 . 0 . 24 2,14,1,6 UTR_3_PRIME(MODIFIER||83||1282|BMS1|protein_coding|CODING|NM_014753.3|23|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.980111 rs7133 -0.636426 0.444909 24 A45 1114 gcA/gcG LOW 2 SILENT CODING RET G protein_coding NM_020975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43595968 A G 0 200 0 0.9803 0.7536 0.7493 0.5268 0.7435 0.6943 0.945302 0.809165 0.739419 2 9819 89064 8716 4729 4244 48848 654 12054 2 10318 120924 11552 8612 6606 66452 902 16482 0 255|2|2,2 other|benign|benign,benign 0 . 35 0,0,34,1 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A45|1114|RET|protein_coding|CODING|NM_020975.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1800858 -0.693136 0.244213 35 A432 1114 gcA/gcG LOW 7 SILENT CODING RET G protein_coding NM_020975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43606687 A G 0 228 0 0.8903 0.7752 0.6239 0.8006 0.7237 0.7536 0.86246 0.748578 0.690233 2 8991 85670 6144 6975 4638 46037 650 12235 2 10398 121334 11570 8638 6606 66704 906 16512 0 2|2 benign|benign 0 . 75 0,0,51,18 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A432|1114|RET|protein_coding|CODING|NM_020975.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1800860 -0.693147 0.373342 75 L769 1114 ctG/ctT LOW 13 SILENT CODING RET T protein_coding NM_020975.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43613843 G T 0 228 0 0.9206 0.7125 0.7478 0.4742 0.7644 0.5982 0.875397 0.80263 0.765349 2 9183 89691 8853 4292 5068 51058 654 10583 2 10374 120892 11522 8586 6588 66436 900 16486 0 2|2|2|2,2 benign|benign|benign|benign,benign 0 . 74 0,0,45,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L769|1114|RET|protein_coding|CODING|NM_020975.4|13|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1800861 -0.693147 0.68526 74 1114 95 MODIFIER 20 CODING RET T protein_coding NM_020975.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43623812 C T 0 228 0 0.0083 0.1366 0.1585 0.1994 0.2117 0.1524 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 61 1,0,11,44 UTR_3_PRIME(MODIFIER||95||1114|RET|protein_coding|CODING|NM_020975.4|20|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs17028 -0.693147 0.00981864 61 1114 600 MODIFIER 20 CODING RET T protein_coding NM_020975.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43624317 A T 0 228 0 0.9418 0.7524 0.7781 0.4762 0.8231 0.6902 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 43 1,0,31,8 UTR_3_PRIME(MODIFIER||600||1114|RET|protein_coding|CODING|NM_020975.4|20|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2742240 -0.693144 0.128911 43 1114 1116 MODIFIER 20 CODING RET C protein_coding NM_020975.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43624833 T C 0 228 0 0.1483 0.1899 0.2104 0.2004 0.2356 0.1738 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 119 1,0,65,34 UTR_3_PRIME(MODIFIER||1116||1114|RET|protein_coding|CODING|NM_020975.4|20|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2435355 -0.693147 0.154479 119 1114 1506 MODIFIER 20 CODING RET A protein_coding NM_020975.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43625223 G A 0 228 0 0.9221 0.7472 0.7767 0.4792 0.8231 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 100 1,0,78,15 UTR_3_PRIME(MODIFIER||1506||1114|RET|protein_coding|CODING|NM_020975.4|20|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2742241 -0.693147 0.667897 100 P479S 542 Cct/Tct MODERATE 8 MISSENSE CODING CSGALNACT2 T protein_coding NM_018590.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43678796 C T 0 228 0 0.0204 0.1585 0.1945 0.1974 0.2644 0.1708 0.0694508 0.199831 0.266628 2 678 28127 1845 2006 2098 18427 214 2859 2 10406 121392 11574 8642 6614 66736 908 16512 0.932644 0 . 0 . 170 2,1,85,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P479S|542|CSGALNACT2|protein_coding|CODING|NM_018590.4|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.416854 rs2435381 -0.693147 0.0595528 170 489 1503 MODIFIER 13 CODING RASGEF1A A protein_coding NM_001282862.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 43690189 G A 0 228 0 0.9561 0.9876 0.9957 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 32 0,0,27,3 UTR_3_PRIME(MODIFIER||1503||489|RASGEF1A|protein_coding|CODING|NM_001282862.1|13|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1254966 -0.693097 0.429954 32 458 332 MODIFIER 4 CODING ZNF239 A protein_coding NM_001099282.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44051819 C A 0 23.4 0 0.1142 0.2165 0.2089 0.4444 0.1551 0.1881 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||332||458|ZNF239|protein_coding|CODING|NM_001099282.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10793442 -0.453602 0.92 4 458 250 MODIFIER 4 CODING ZNF239 A protein_coding NM_001099282.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44051901 T A 0 42.3 0 0.4924 0.5441 0.513 0.5516 0.5308 0.6421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 9 5,0,4,0 UTR_3_PRIME(MODIFIER||250||458|ZNF239|protein_coding|CODING|NM_001099282.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 0 . 0.649731 rs2999277 -0.556411 0.390954 9 C209G 458 Tgt/Ggt MODERATE 4 MISSENSE CODING ZNF239 C protein_coding NM_001099282.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44052903 A C 0 222 0 0.4917 0.5449 0.513 0.5506 0.5308 0.6483 0.532512 0.533906 0.534581 1 5049 67261 5952 4784 4188 36647 528 10113 2 9810 120698 11534 8614 6612 66716 902 16510 0.981294 0 . 0 . 96 25,23,18,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C209G|458|ZNF239|protein_coding|CODING|NM_001099282.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960277 rs2230661 -0.693139 0.0435 96 A172G 458 gCt/gGt MODERATE 4 MISSENSE CODING ZNF239 C protein_coding NM_001099282.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44053013 G C 0 222 0 . 0 . 0 . 0 0.528133 0.533355 0.535809 1 5040 67247 5961 4783 4188 36641 523 10111 2 9794 120690 11556 8602 6610 66720 898 16510 0.999663 0 . 0 . 58 15,13,14,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A172G|458|ZNF239|protein_coding|CODING|NM_001099282.1|4|C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.791517 rs2230660 -0.692976 0.0941084 58 458 13 MODIFIER 4 CODING ZNF239 C protein_coding NM_001099282.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44053540 T C 0 222 0 0 0.0047923 0 0.0228 0 0.001 0 0.000333556 0.000487092 1 0 272 0 255 0 8 2 7 2 8336 100098 9442 7464 5830 55532 728 12766 0.861239 0 . 0 . 63 13,22,7,20 START_GAINED(LOW||||458|ZNF239|protein_coding|CODING|NM_001099282.1|4|C),UTR_5_PRIME(MODIFIER||13||458|ZNF239|protein_coding|CODING|NM_001099282.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.584463 rs117513280 -0.693021 0.262134 63 458 58 MODIFIER 4 CODING ZNF239 T protein_coding NM_001099282.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44053585 C T 0 222 0 0.4917 0.5449 0.513 0.5506 0.5308 0.6483 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.606354 0 . 0 . 46 5,22,6,11 UTR_5_PRIME(MODIFIER||58||458|ZNF239|protein_coding|CODING|NM_001099282.1|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.584435 rs2999278 -0.690438 0.324759 46 S84F 130 tCc/tTc MODERATE 2 MISSENSE CODING C10orf142 T protein_coding NM_001258000.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44788826 C T 0 9.7 0 0.0121 0.101 0.1297 0.1121 0.1799 0.1084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S84F|130|C10orf142|protein_coding|CODING|NM_001258000.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386483307,rs58189594 -0.379885 0 1 130 163 MODIFIER 3 CODING C10orf142 A protein_coding NM_001258000.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44789554 G A 0 9.7 0 0.0076 0.0992 0.1282 0.1121 0.1779 0.1084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||163||130|C10orf142|protein_coding|CODING|NM_001258000.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs72788791 -0.379885 0 1 130 598 MODIFIER 3 CODING C10orf142 A protein_coding NM_001258000.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 44789989 T A 0 102 0 0.7141 0.9 0.9337 0.996 0.9761 0.9499 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||598||130|C10orf142|protein_coding|CODING|NM_001258000.1|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs808972 -0.556411 0.610267 4 275 51 MODIFIER 1 CODING TMEM72 T protein_coding NM_001123376.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45406910 C T 0 222 0 0.0076 0.0019968 0 0 0 0 0.00188822 0.000574449 0 1 11 12 0 0 0 1 0 0 2 2072 18744 386 558 34 7906 172 7616 0.96337 0 . 0 . 35 10,4,12,7 START_GAINED(LOW||||275|TMEM72|protein_coding|CODING|NM_001123376.2|1|T),UTR_5_PRIME(MODIFIER||51||275|TMEM72|protein_coding|CODING|NM_001123376.2|1|T),INTRAGENIC(MODIFIER|||||TMEM72-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97236 rs143625079 -0.69168 0.143281 35 A236 275 gcC/gcT LOW 5 SILENT CODING TMEM72 T protein_coding NM_001123376.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45430462 C T 0 222 0 0.3086 0.3335 0.4438 0.3274 0.3986 0.228 0.331633 0.394078 0.421413 1 3058 46388 5754 2604 2333 27867 340 4432 2 9726 120138 11568 8608 6606 66232 896 16502 0.945464 0 . 0 . 78 20,14,17,19 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A236|275|TMEM72|protein_coding|CODING|NM_001123376.2|5|T),INTRAGENIC(MODIFIER|||||TMEM72-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.407683 rs17417442 -0.693139 0.0548874 78 275 117 MODIFIER 5 CODING TMEM72 G protein_coding NM_001123376.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45430699 A G 0 228 0 0.9145 0.7013 0.768 0.4663 0.7545 0.5532 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,4,14 UTR_3_PRIME(MODIFIER||117||275|TMEM72|protein_coding|CODING|NM_001123376.2|5|G),INTRAGENIC(MODIFIER|||||TMEM72-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7067692 -0.691153 0.058061 18 275 834 MODIFIER 5 CODING TMEM72 A protein_coding NM_001123376.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45431416 G A 0 76 0 0.9145 0.7033 0.7723 0.4663 0.7584 0.5562 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||834||275|TMEM72|protein_coding|CODING|NM_001123376.2|5|A),INTRAGENIC(MODIFIER|||||TMEM72-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10900132 -0.511536 0.172729 3 275 1677 MODIFIER 5 CODING TMEM72 T protein_coding NM_001123376.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45432259 A T 0 9.7 0 0.9153 0.7031 0.7723 0.4663 0.7584 0.5542 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1677||275|TMEM72|protein_coding|CODING|NM_001123376.2|5|T),INTRAGENIC(MODIFIER|||||TMEM72-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs914695 -0.379885 0 1 L54 212 ctG/ctA LOW 2 SILENT CODING C10orf10 T protein_coding NM_007021.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45473317 C T 0 222 0 0.0083 0.1476 0.1167 0.3056 0.1581 0.184 0.0367847 0.120597 0.163526 1 346 19282 1116 2547 1067 10877 143 3186 2 9696 117946 11510 8540 6604 64396 892 16308 0.999552 0 . 0 . 147 44,23,35,29 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L54|212|C10orf10|protein_coding|CODING|NM_007021.3|2|T),INTRON(MODIFIER||||321|RASSF4|protein_coding|CODING|NM_032023.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.452515 rs3740094 -0.693147 0.164042 147 R88G 321 Aga/Gga MODERATE 4 MISSENSE CODING RASSF4 G protein_coding NM_032023.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45478092 A G 0 222 0 0.3782 0.2808 0.1412 0.3194 0.171 0.3211 0.336813 0.229356 0.174302 1 3540 24659 1040 2733 1067 11333 175 4771 2 10222 119126 11374 8560 6196 65608 872 16294 0.814142 0 . 0 . 90 20,25,15,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R88G|321|RASSF4|protein_coding|CODING|NM_032023.3|4|G),UPSTREAM(MODIFIER||3762||212|C10orf10|protein_coding|CODING|NM_007021.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.752917 rs870957 -0.693144 0.262214 90 122 271 MODIFIER 2 CODING C10orf25 T protein_coding NM_001039380.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45495555 C T 0 25.9 0 0.0219 0.108 0.0893 0.2589 0.0934 0.0971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_3_PRIME(MODIFIER||271||122|C10orf25|protein_coding|CODING|NM_001039380.3|2|T),UPSTREAM(MODIFIER||718||224|ZNF22|protein_coding|CODING|NM_006963.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12219891 -0.453602 0.14 3 P61L 122 cCa/cTa MODERATE 1 MISSENSE CODING C10orf25 A protein_coding NM_001039380.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45496126 G A 0 222 0 0.0749 0.0551 0.013 0.0972 0.0427 0.0276 0.0551521 0.0497463 0.0469767 1 576 4964 128 693 272 2764 34 497 2 10308 120932 11548 8598 6602 66512 902 16462 0.598415 0 . 0 . 245 75,48,45,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P61L|122|C10orf25|protein_coding|CODING|NM_001039380.3|1|A),UPSTREAM(MODIFIER||147||224|ZNF22|protein_coding|CODING|NM_006963.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.687851 rs41301609 -0.693147 0.348539 245 S65G 224 Agt/Ggt MODERATE 2 MISSENSE CODING ZNF22 G protein_coding NM_006963.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45499009 A G 0 222 0 0.003 0.0343 0.0101 0.0903 0.0427 0.0276 0.0086246 0.034907 0.0483721 1 95 4532 106 654 276 2891 33 477 2 10380 121292 11562 8644 6614 66678 906 16508 0.280781 0 . 0 . 131 37,30,29,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S65G|224|ZNF22|protein_coding|CODING|NM_006963.4|2|G),UPSTREAM(MODIFIER||2651||122|C10orf25|protein_coding|CODING|NM_001039380.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.88327 rs3740093 -0.693147 0.0165618 131 S152 224 tcC/tcG LOW 2 SILENT CODING ZNF22 G protein_coding NM_006963.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45499272 C G 0 222 0 0.0151 0.0373 0.0101 0.0893 0.0427 0.0276 0.0142987 0.036906 0.0484884 1 149 4591 108 652 276 2895 34 477 2 10360 121164 11546 8622 6608 66636 906 16486 0.813188 0 . 0 . 67 21,17,8,16 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S152|224|ZNF22|protein_coding|CODING|NM_006963.4|2|G),UPSTREAM(MODIFIER||2914||122|C10orf25|protein_coding|CODING|NM_001039380.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959089 rs3740092 -0.692831 0.258281 67 224 308 MODIFIER 2 CODING ZNF22 C protein_coding NM_006963.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45499799 T C 0 222 0 0.7761 0.7432 0.8127 0.62 0.7624 0.7566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999992 0 . 0 . 204 60,37,64,26 UTR_3_PRIME(MODIFIER||308||224|ZNF22|protein_coding|CODING|NM_006963.4|2|C),UPSTREAM(MODIFIER||3441||122|C10orf25|protein_coding|CODING|NM_001039380.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.790628 rs11471 -0.693147 0.623826 204 G106 674 ggC/ggT LOW 2 SILENT CODING ALOX5 T protein_coding NM_000698.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 45878098 C T 0 222 0 0 0.0023962 0 0.0109 0 0.001 0 7.6888e-05 0.000116279 1 0 108 0 99 0 3 1 5 2 9212 108934 10220 7806 5274 60414 812 15196 0.633052 0 . 0 COSM189216 128 24,36,23,31 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G106|674|ALOX5|protein_coding|CODING|NM_000698.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925166 rs150281723 -0.693147 0.355599 128 T379M 1320 aCg/aTg MODERATE 13 MISSENSE CODING FAM21C T protein_coding NM_015262.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46248641 C T 0 51 0 0.177 0.1402 0.0951 0.1776 0.0706 0.1554 0 . 0 2 5 28 0 4 0 17 0 2 2 5146 83068 7092 4622 5282 49736 682 10508 0 . 0 . 0 4 0,0,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T379M|1320|FAM21C|protein_coding|CODING|NM_015262.2|13|T) 0 . 0 . 0 1 0 . 1 0 24 0 0 . 0 . rs199748321 -0.556411 0.714437 4 S382P 1320 Tcc/Ccc MODERATE 13 MISSENSE CODING FAM21C C protein_coding NM_015262.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46248649 T C 0 53 0 0.1823 0.1508 0.1196 0.1706 0.0944 0.1677 0 . 0 2 8 66 1 28 0 23 2 4 2 5268 84224 7196 4670 5322 50340 696 10732 0 . 0 . 0 5 0,0,5,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S382P|1320|FAM21C|protein_coding|CODING|NM_015262.2|13|C) 0 . 0 . 0 1 0 . 1 0 22 0 0 . 0 . rs184073575,rs2610452 -0.590765 0.960975 5 R507H 686 cGc/cAc MODERATE 8 MISSENSE CODING AGAP4 T protein_coding NM_001276343.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46321904 C T 0 125 0 . 0 . 0 . 0 . 0 . 1 0 4 0 0 0 2 0 2 2 12 26 0 0 0 12 0 2 0.00235336 0 . 0 . 180 53,16,85,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R507H|686|AGAP4|protein_coding|CODING|NM_001276343.2|8|T) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.000400553 5.45946e-06 0 0.62762 rs202104169 -0.693147 0.0526237 180 686 LOW 1 CODING AGAP4 T protein_coding NM_001276343.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46342570 C T 0 24.9 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969376 0 . 0 . 151 27,69,0,55 SPLICE_SITE_REGION+INTRON(LOW||||686|AGAP4|protein_coding|CODING|NM_001276343.2|1|T) 0 0.5 1 0 . 0 . 0 . 0 26 0 1.30904e-07 0.980847 0 0.0132486 rs199591580 -0.693147 0.0101679 151 421 4016 MODIFIER 8 CODING SYT15 C protein_coding NM_031912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46957954 T C 0 20.7 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||4016||421|SYT15|protein_coding|CODING|NM_031912.4|8|C) 0 . 0 . 0 . 0 . 0 . 48 0 0 . 0 . rs3120440 -0.379885 0 2 421 2026 MODIFIER 8 CODING SYT15 A protein_coding NM_031912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46959944 C A 0 221 0 0.0008 0.005591 0 0.0238 0 0.0031 0 . 0 1 1 200 0 193 0 0 1 5 2 9648 120188 11504 8588 6598 66528 892 16430 0.999152 0 . 0 . 361 180,47,66,18 UTR_3_PRIME(MODIFIER||2026||421|SYT15|protein_coding|CODING|NM_031912.4|8|A) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.949358 0.994932 0 0.379615 rs369013065 -0.693147 0.173793 361 421 1886 MODIFIER 8 CODING SYT15 A protein_coding NM_031912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46960084 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.964829 0 . 0 . 242 37,115,17,49 UTR_3_PRIME(MODIFIER||1886||421|SYT15|protein_coding|CODING|NM_031912.4|8|A) 0 0.5 1 0 . 0 . 0 . 0 59 0 0.956575 0.788698 0 0.518379 rs9422009 -0.693147 0.00417055 242 421 1665 MODIFIER 8 CODING SYT15 A protein_coding NM_031912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46960305 G A 0 17 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,3,0,2 UTR_3_PRIME(MODIFIER||1665||421|SYT15|protein_coding|CODING|NM_031912.4|8|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.75 rs9422010 -0.453602 0.8 6 421 6 MODIFIER 8 CODING SYT15 A protein_coding NM_031912.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46961964 G A 0 213 0 . 0 . 0 . 0 0.0252021 0.0920076 0.125237 1 310 17875 1084 603 1130 11249 145 3354 2 9442 118692 11534 8568 6564 65544 892 16148 0.986542 0 . 0 . 200 78,46,26,24 UTR_3_PRIME(MODIFIER||6||421|SYT15|protein_coding|CODING|NM_031912.4|8|A) 1 0.5 1 0 . 0 . 1 1 0 51 0 0.779025 0.00741205 0 0.998993 rs138447966,rs9422211 -0.693147 0.487285 200 E309D 421 gaG/gaC MODERATE 6 MISSENSE CODING SYT15 G protein_coding NM_031912.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46965018 C G 0 222 0 . 0 . 0 . 0 0.450187 0.467141 0.475664 1 4613 57560 5439 3455 3158 32310 442 8143 2 9774 120082 11502 8580 6560 66358 888 16420 0.317714 0 . 0 COSM146930 244 48,116,20,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E309D|421|SYT15|protein_coding|CODING|NM_031912.4|6|G) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.132088 rs3127785 -0.693147 0.0569835 244 A270 421 gcC/gcT LOW 5 SILENT CODING SYT15 A protein_coding NM_031912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46965727 G A 0 222 0 . 0 . 0 . 0 0.540241 0.5207 0.510791 1 5186 61139 5775 4120 3349 33900 465 8344 2 9820 120602 11562 8604 6608 66654 898 16456 0.896705 0 . 0 . 136 36,21,46,19 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A270|421|SYT15|protein_coding|CODING|NM_031912.4|5|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.662005 rs1889849 -0.693147 0.0334876 136 P135 421 ccG/ccA LOW 4 SILENT CODING SYT15 T protein_coding NM_031912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46967672 C T 0 145 0 . 0 . 0 . 0 0.589024 0.542647 0.520005 1 5319 61358 5830 4330 3362 33607 471 8439 2 9420 119496 11558 8618 6612 65886 898 16504 0.958048 0 . 0 . 28 3,12,1,11 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P135|421|SYT15|protein_coding|CODING|NM_031912.4|4|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.204741 rs2152530 -0.680642 0.180121 28 421 125 MODIFIER 1 CODING SYT15 G protein_coding NM_031912.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46970573 C G 0 44.4 0 . 0 . 0 . 0 . 0 . 1 83 914 22 74 28 395 4 308 2 206 2072 54 148 64 906 12 682 0.577865 0 . 0 . 13 5,1,2,1 UTR_5_PRIME(MODIFIER||125||421|SYT15|protein_coding|CODING|NM_031912.4|1|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 0.924584 1 0 0.809011 rs6587511 -0.511536 0.635923 13 458 LOW 2 CODING GPRIN2 T protein_coding NM_014696.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46995037 C T 0 60 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,1,2 SPLICE_SITE_REGION+INTRON(LOW||||458|GPRIN2|protein_coding|CODING|NM_014696.3|2|T) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 1 rs873876 -0.511536 0.160333 5 R5H 458 cGc/cAc MODERATE 3 MISSENSE CODING GPRIN2 A protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46998894 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 4553 53939 5744 4249 3313 31162 387 4531 2 9062 107462 11454 8466 6608 62098 762 9012 0.875442 0 . 0 COSM427578 91 20,31,14,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R5H|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.834757 rs3127817 -0.693132 0.249217 91 L39V 458 Ctc/Gtc MODERATE 3 MISSENSE CODING GPRIN2 G protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46998995 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 3866 54286 5670 4237 3236 31060 395 5822 2 9606 112330 11456 8528 6588 63454 832 11866 0.904354 0 . 0 . 87 27,17,18,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L39V|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.962334 rs4926045 -0.693132 0.905579 87 R40H 458 cGc/cAc MODERATE 3 MISSENSE CODING GPRIN2 A protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46998999 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 4935 57148 5759 4284 3307 32092 431 6340 2 9792 113670 11480 8560 6602 63864 846 12526 0.7217 0 . 0 COSM1560780 85 19,16,25,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R40H|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.87542 rs3127818 -0.693145 0.0279827 85 V47M 458 Gtg/Atg MODERATE 3 MISSENSE CODING GPRIN2 A protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999019 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 4859 57249 5760 4287 3306 32129 428 6480 2 9776 114044 11482 8566 6598 63968 844 12810 0.867651 0 . 0 COSM1560779 85 16,17,24,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V47M|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.796692 rs3127819 -0.693145 0.662593 85 A50 458 gcC/gcT LOW 3 SILENT CODING GPRIN2 T protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999030 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 3839 54170 5663 4241 3219 30832 386 5990 2 9434 112170 11450 8536 6566 63072 818 12294 0.210312 0 . 0 COSM1560778 86 25,18,11,19 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A50|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.119079 rs4925989 -0.693097 0.291471 86 W91R 458 Tgg/Cgg MODERATE 3 MISSENSE CODING GPRIN2 C protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999151 T C 0 201 0 . 0 . 0 . 0 . 0 . 1 4835 59099 5763 4269 3295 32303 450 8184 2 9610 117800 11500 8538 6576 64396 892 16288 0.5048 0 . 0 . 24 3,4,2,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W91R|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.896394 rs3127820 -0.689466 0.0849445 24 T100P 458 Acc/Ccc MODERATE 3 MISSENSE CODING GPRIN2 C protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999178 A C 0 61 0 . 0 . 0 . 0 . 0 . 1 3939 57014 5692 4238 3206 31549 423 7967 2 9632 117836 11496 8524 6534 64460 890 16300 0.984804 0 . 0 COSM427579 31 6,19,4,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T100P|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.415691 rs7090312 -0.616816 0.676541 31 G103 458 ggC/ggT LOW 3 SILENT CODING GPRIN2 T protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999189 C T 0 221 0 0.4887 0.4936 0.4942 0.497 0.493 0.4969 0 . 0 1 4944 59277 5754 4266 3271 32402 445 8195 2 9832 118176 11488 8536 6528 64592 880 16320 0.872525 0 . 0 . 32 5,3,7,17 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G103|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.2832 rs3127678 -0.692831 0.415818 32 S104G 458 Agt/Ggt MODERATE 3 MISSENSE CODING GPRIN2 G protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999190 A G 0 228 0 0.8192 0.9109 0.9352 0.9603 0.9344 0.9427 0 . 0 2 7381 105390 10776 8080 5790 57723 767 14873 2 9762 117902 11476 8520 6498 64456 878 16312 0 . 0 . 0 32 0,0,12,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S104G|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs3127679 -0.69312 0.625895 32 L106 458 ctG/ctT LOW 3 SILENT CODING GPRIN2 T protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999198 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 4967 59341 5753 4271 3264 32440 446 8200 2 9862 118232 11482 8540 6510 64636 882 16320 0.727604 0 . 0 COSM1285256 37 8,3,9,17 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L106|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.343411 rs3127680 -0.692976 0.392606 37 S195 458 tcA/tcG LOW 3 SILENT CODING GPRIN2 G protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999465 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 5166 59540 5778 4318 3293 33032 448 7505 2 10282 118578 11528 8634 6566 65778 884 14906 0.85084 0 . 0 . 104 29,17,33,17 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S195|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.997314 rs3127682 -0.693147 0.00338949 104 G202W 458 Ggg/Tgg MODERATE 3 MISSENSE CODING GPRIN2 T protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999484 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 4130 57261 5677 4269 3209 32084 416 7476 2 10172 118608 11486 8606 6536 65626 874 15308 0.943977 0 . 0 . 126 48,22,26,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Tgg|G202W|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.848136 rs11204658 -0.693146 0.224865 126 A233S 458 Gct/Tct MODERATE 3 MISSENSE CODING GPRIN2 T protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999577 G T 0 222 0 . 0 . 0 . 0 0.377667 0.439874 0.471744 1 4267 58542 5723 4295 3238 32536 427 8056 2 10214 120696 11564 8640 6582 66380 898 16418 0.987688 0 . 0 . 131 29,36,28,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A233S|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.846112 rs11204659 -0.693147 0.0657081 131 R239K 458 aGg/aAg MODERATE 3 MISSENSE CODING GPRIN2 A protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999596 G A 0 222 0 0.2542 0.394 0.4366 0.4663 0.4374 0.4335 0 . 0 1 4184 58449 5721 4293 3238 32526 428 8059 2 10284 120978 11560 8638 6606 66492 904 16494 0.0480221 0 . 0 . 128 17,17,22,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R239K|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.943928 rs7895979 -0.693147 0.0692472 128 R242G 458 Agg/Ggg MODERATE 3 MISSENSE CODING GPRIN2 G protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999604 A G 0 228 0 0.6513 0.8073 0.8516 0.9137 0.8469 0.8364 0 . 0 2 7259 107194 10814 8201 5845 59287 778 15010 2 10322 121096 11574 8652 6610 66540 900 16498 9.02551e-05 0 . 0 . 116 5,5,27,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R242G|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.286883 rs3127683 -0.693147 0.775432 116 G284 458 ggG/ggA LOW 3 SILENT CODING GPRIN2 A protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999732 G A 0 221 0 . 0 . 0 . 0 0.390604 0.444795 0.472558 1 4263 58710 5733 4299 3247 32665 431 8072 2 10404 121356 11576 8650 6606 66706 906 16508 0.673226 0 . 0 . 102 15,6,57,16 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G284|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.686778 rs4579877 -0.693147 0.792913 102 H289 458 caT/caC LOW 3 SILENT CODING GPRIN2 C protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999747 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5223 60897 5801 4333 3313 33474 459 8294 2 10402 121378 11576 8654 6612 66716 908 16510 0.996794 0 . 0 . 128 44,21,36,13 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H289|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.730353 rs3127821 -0.693147 0.821083 128 V348L 458 Gtg/Ttg MODERATE 3 MISSENSE CODING GPRIN2 T protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 46999922 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 2271 45546 4326 4291 2547 24441 343 7327 2 10242 120342 11524 8630 6542 66022 904 16478 0.622192 0 . 0 COSM1347901 98 20,22,25,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V348L|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.91427 rs4926046 -0.693147 0.461555 98 V375A 458 gTg/gCg MODERATE 3 MISSENSE CODING GPRIN2 C protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000004 T C 0 228 0 0.8101 0.9459 0.9726 0.999 1 1 0.858829 0.951407 0.998837 2 8875 119705 11491 8648 6612 66675 896 16508 2 10406 121388 11578 8652 6612 66720 908 16512 0 . 0 . 0 126 0,0,99,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V375A|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3127822 -0.693147 0.597689 126 A397 458 gcG/gcA LOW 3 SILENT CODING GPRIN2 A protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000071 G A 0 222 0 . 0 . 0 . 0 0.391285 0.446794 0.475233 1 4278 58581 5732 4299 3238 32586 426 8022 2 10384 121058 11568 8646 6592 66556 900 16412 0.988327 0 . 0 . 222 54,38,57,42 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A397|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.475459 rs4244614 -0.693147 0.00122691 222 L400P 458 cTg/cCg MODERATE 3 MISSENSE CODING GPRIN2 C protein_coding NM_014696.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000079 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 5220 60756 5798 4325 3301 33401 458 8253 2 10396 121096 11572 8648 6588 66566 906 16420 0.451403 0 . 0 . 228 62,44,46,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L400P|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.995419 rs3127823 -0.693147 0.00161427 228 P422 458 ccC/ccT LOW 3 SILENT CODING GPRIN2 T protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000146 C T 0 222 0 0.4992 0.5034 0.5058 0.505 0.507 0.502 0 . 0 1 4763 57498 5636 4214 2855 31613 411 8006 2 9540 114624 11238 8428 5698 62978 816 15926 0.116234 0 . 0 . 135 26,48,14,40 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P422|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.986242 rs3127684 -0.693147 0.20086 135 P436 458 ccA/ccG LOW 3 SILENT CODING GPRIN2 G protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000188 A G 0 228 0 0.8275 0.9513 0.9784 1 0.999 1 0.882393 0.959315 0.998595 2 6721 92030 8995 6386 4556 52344 672 12356 2 7768 93178 9056 6386 4556 52374 680 12358 0 . 0 . 0 88 0,0,33,51 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P436|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3127824 -0.693147 0.53168 88 S453 458 tcC/tcT LOW 3 SILENT CODING GPRIN2 T protein_coding NM_014696.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000239 C T 0 222 0 0.5227 0.5164 0.5159 0.5099 0.5159 0.5153 0 . 0 1 1118 10524 692 478 350 6558 83 1245 2 2222 20912 1374 950 698 13042 164 2462 0.999731 0 . 0 . 78 25,15,18,13 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S453|458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.839626 rs7912299 -0.69311 0.196418 78 458 64 MODIFIER 3 CODING GPRIN2 A protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000321 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.179301 0 . 0 . 111 40,22,24,16 UTR_3_PRIME(MODIFIER||64||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.189763 rs28689656 -0.693145 0.156512 111 458 109 MODIFIER 3 CODING GPRIN2 G protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000366 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.580277 0 . 0 . 137 51,29,24,25 UTR_3_PRIME(MODIFIER||109||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|G) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.959843 rs28512259 -0.693147 0.20295 137 458 117 MODIFIER 3 CODING GPRIN2 C protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000374 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.977633 0 . 0 . 139 53,26,24,26 UTR_3_PRIME(MODIFIER||117||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.694892 rs28587692 -0.693147 0.10337 139 458 124 MODIFIER 3 CODING GPRIN2 C protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000381 T C 0 228 0 0.6846 0.8576 0.9092 0.9524 0.8986 0.9151 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 133 0,0,76,48 UTR_3_PRIME(MODIFIER||124||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs28549106 -0.693147 2.33865e-05 133 458 169 MODIFIER 3 CODING GPRIN2 C protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000426 T C 0 228 0 0.9486 0.985 0.9899 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 135 0,0,73,52 UTR_3_PRIME(MODIFIER||169||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs28666990 -0.693147 0.704498 135 458 230 MODIFIER 3 CODING GPRIN2 A protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000487 G A 0 222 0 0.5068 0.5072 0.5086 0.505 0.5099 0.5061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.334209 0 . 0 . 149 42,37,25,26 UTR_3_PRIME(MODIFIER||230||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982419 rs3127825 -0.693147 9.33855e-05 149 458 290 MODIFIER 3 CODING GPRIN2 T protein_coding NM_014696.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47000547 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.888091 0 . 0 . 111 18,45,12,28 UTR_3_PRIME(MODIFIER||290||458|GPRIN2|protein_coding|CODING|NM_014696.3|3|T) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.658863 rs3127685 -0.693145 0.0496582 111 I44 375 atC/atT LOW 2 SILENT CODING NPY4R T protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47086915 C T 0 104 0 . 0 . 0 . 0 0.133681 0.116177 0.107209 1 1916 20846 2297 2942 879 10186 168 2458 2 10406 121278 11560 8626 6608 66682 908 16488 0.712424 0 . 0 . 364 170,84,40,28 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I44|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I44|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.9918 rs59974223 -0.693147 0.0600032 364 I44 375 atC/atT LOW 1 SILENT CODING CH17-360D5.1 T protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47086915 C T 0 104 0 . 0 . 0 . 0 0.133681 0.116177 0.107209 1 1916 20846 2297 2942 879 10186 168 2458 2 10406 121278 11560 8626 6608 66682 908 16488 0.712424 0 . 0 . 364 170,84,40,28 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I44|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I44|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.9918 rs59974223 -0.693147 0.0600032 364 V65 375 gtG/gtA LOW 2 SILENT CODING NPY4R A protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47086978 G A 0 59 0 0.1029 0.1739 0.1369 0.3264 0.1521 0.1616 0.0685429 0.0981086 0.113256 1 1055 20006 2248 2926 876 10222 161 2518 2 10400 121190 11554 8630 6598 66616 906 16486 0.877805 0 . 0 . 372 135,133,26,30 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V65|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V65|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.351845 rs3740294 -0.693147 0.00329279 372 V65 375 gtG/gtA LOW 1 SILENT CODING CH17-360D5.1 A protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47086978 G A 0 59 0 0.1029 0.1739 0.1369 0.3264 0.1521 0.1616 0.0685429 0.0981086 0.113256 1 1055 20006 2248 2926 876 10222 161 2518 2 10400 121190 11554 8630 6598 66616 906 16486 0.877805 0 . 0 . 372 135,133,26,30 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V65|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V65|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.351845 rs3740294 -0.693147 0.00329279 372 L231 375 Ctg/Ttg LOW 2 SILENT CODING NPY4R T protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087474 C T 0 228 0 . 0 . 0 . 0 0.779619 0.729663 0.70407 2 8154 91551 10137 8548 4672 46328 677 13035 2 10402 121384 11576 8654 6612 66720 908 16512 0 . 0 . 0 124 0,0,40,76 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L231|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L231|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs1129838 -0.693147 0.000399053 124 L231 375 Ctg/Ttg LOW 1 SILENT CODING CH17-360D5.1 T protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087474 C T 0 228 0 . 0 . 0 . 0 0.779619 0.729663 0.70407 2 8154 91551 10137 8548 4672 46328 677 13035 2 10402 121384 11576 8654 6612 66720 908 16512 0 . 0 . 0 124 0,0,40,76 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L231|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L231|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs1129838 -0.693147 0.000399053 124 R240C 375 Cgc/Tgc MODERATE 2 MISSENSE CODING NPY4R T protein_coding NM_001278794.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087501 C T 0 198 0 . 0 . 0 . 0 0.120064 0.229048 0.284884 1 1300 37178 4077 4089 1738 19883 287 5804 2 10384 121004 11562 8640 6592 66504 906 16416 0.795003 0 . 0 . 96 24,46,10,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R240C|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R240C|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.599577 rs3824733 -0.692562 0.35215 96 R240C 375 Cgc/Tgc MODERATE 1 MISSENSE CODING CH17-360D5.1 T protein_coding NM_001278795.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087501 C T 0 198 0 . 0 . 0 . 0 0.120064 0.229048 0.284884 1 1300 37178 4077 4089 1738 19883 287 5804 2 10384 121004 11562 8640 6592 66504 906 16416 0.795003 0 . 0 . 96 24,46,10,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R240C|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R240C|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.599577 rs3824733 -0.692562 0.35215 96 A275 375 gcT/gcC LOW 2 SILENT CODING NPY4R C protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087608 T C 0 228 0 0.8737 0.9647 0.9899 0.997 1 1 0.887653 0.961402 0.999186 2 9207 120066 11506 8639 6611 66700 900 16503 2 10400 121402 11576 8654 6612 66740 908 16512 0 . 0 . 0 106 0,0,57,36 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A275|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A275|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1936339 -0.693147 0.982933 106 A275 375 gcT/gcC LOW 1 SILENT CODING CH17-360D5.1 C protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087608 T C 0 228 0 0.8737 0.9647 0.9899 0.997 1 1 0.887653 0.961402 0.999186 2 9207 120066 11506 8639 6611 66700 900 16503 2 10400 121402 11576 8654 6612 66740 908 16512 0 . 0 . 0 106 0,0,57,36 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A275|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A275|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1936339 -0.693147 0.982933 106 H299 375 caC/caT LOW 2 SILENT CODING NPY4R T protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087680 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 8158 91538 10134 8548 4669 46318 677 13034 2 10406 121374 11574 8654 6602 66720 908 16510 0 . 0 . 0 156 0,0,91,54 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H299|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H299|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 0 . 0 . 0 . 0 . 1 0 60 0 0 1 0 . rs1048157 -0.693147 0.0011191 156 H299 375 caC/caT LOW 1 SILENT CODING CH17-360D5.1 T protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087680 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 8158 91538 10134 8548 4669 46318 677 13034 2 10406 121374 11574 8654 6602 66720 908 16510 0 . 0 . 0 156 0,0,91,54 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H299|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H299|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 0 . 0 . 0 . 0 . 1 0 60 0 0 1 0 . rs1048157 -0.693147 0.0011191 156 C316 375 tgC/tgT LOW 2 SILENT CODING NPY4R T protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087731 C T 0 228 0 0.798 0.8267 0.8184 0.9901 0.7177 0.8149 0.780527 0.730663 0.705116 2 8158 91549 10138 8548 4671 46322 677 13035 2 10406 121388 11578 8654 6608 66726 908 16508 0 . 0 . 0 149 0,0,70,67 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C316|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C316|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1048158 -0.693147 0.536823 149 C316 375 tgC/tgT LOW 1 SILENT CODING CH17-360D5.1 T protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087731 C T 0 228 0 0.798 0.8267 0.8184 0.9901 0.7177 0.8149 0.780527 0.730663 0.705116 2 8158 91549 10138 8548 4671 46322 677 13035 2 10406 121388 11578 8654 6608 66726 908 16508 0 . 0 . 0 149 0,0,70,67 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C316|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C316|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1048158 -0.693147 0.536823 149 S349 375 tcG/tcA LOW 2 SILENT CODING NPY4R A protein_coding NM_001278794.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087830 G A 0 228 0 0.798 0.8265 0.8184 0.9891 0.7177 0.8149 0 . 0 2 8156 91523 10136 8548 4660 46311 676 13036 2 10406 121380 11578 8654 6612 66710 908 16512 0 . 0 . 0 146 0,0,78,56 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S349|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S349|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1129839 -0.693147 0.921018 146 S349 375 tcG/tcA LOW 1 SILENT CODING CH17-360D5.1 A protein_coding NM_001278795.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47087830 G A 0 228 0 0.798 0.8265 0.8184 0.9891 0.7177 0.8149 0 . 0 2 8156 91523 10136 8548 4660 46311 676 13036 2 10406 121380 11578 8654 6612 66710 908 16512 0 . 0 . 0 146 0,0,78,56 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S349|375|NPY4R|protein_coding|CODING|NM_001278794.1|2|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S349|375|CH17-360D5.1|protein_coding|CODING|NM_001278795.1|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1129839 -0.693147 0.921018 146 365 LOW 11 CODING ANXA8 T protein_coding NM_001271702.1.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47158904 C T 0 222 0 0.3343 0.5711 0.5576 0.8214 0.5567 0.6575 0.36455 0.505729 0.581197 1 3237 47489 4776 6158 1808 22960 358 8192 2 7934 74922 7690 7462 3034 35824 546 12432 0.852148 0 . 0 . 207 52,48,35,45 SPLICE_SITE_REGION+INTRON(LOW||||365|ANXA8|protein_coding|CODING|NM_001271702.1.2|11|T) 1 0.5 1 0 . 1 0 1 1 0 36 0 0.433717 0.109008 0 0.565336 rs151312129,rs76674881 -0.693147 2.03912e-07 207 631 114 MODIFIER 1 CODING ANTXRL A protein_coding NM_001278688.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47658385 G A 0 68 0 0.0734 0.0731 0.0389 0.123 0.005 0.1155 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998531 0 . 0 . 16 9,1,6,0 UTR_5_PRIME(MODIFIER||114||631|ANTXRL|protein_coding|CODING|NM_001278688.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.65377 rs78924721 -0.616816 0.233931 16 R31P 631 cGg/cCg MODERATE 1 MISSENSE CODING ANTXRL C protein_coding NM_001278688.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47658590 G C 0 161 0 0.0756 0.0737 0.0389 0.123 0.005 0.1155 0 . 0 1 40 779 9 21 17 25 9 658 2 602 14432 184 198 1596 4050 182 7620 0.981911 0 . 0 . 67 29,10,23,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R31P|631|ANTXRL|protein_coding|CODING|NM_001278688.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.845042 rs78797099 -0.692831 0.0647552 67 H33Q 631 caT/caG MODERATE 1 MISSENSE CODING ANTXRL G protein_coding NM_001278688.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47658597 T G 0 222 0 0.0734 0.0731 0.0389 0.123 0.005 0.1155 0 . 0 1 36 776 9 21 17 26 9 658 2 602 14454 186 198 1600 4066 182 7620 0.998458 0 . 0 . 68 27,9,23,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H33Q|631|ANTXRL|protein_coding|CODING|NM_001278688.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.276187 rs78983634 -0.693021 0.343796 68 D217 631 gaT/gaC LOW 7 SILENT CODING ANTXRL C protein_coding NM_001278688.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47668707 T C 0 222 0 0.2844 0.3431 0.4726 0.1597 0.4761 0.3824 0 . 0 1 165 5947 78 31 709 1731 74 3159 2 564 14236 186 198 1600 3886 184 7618 0.379661 0 . 0 . 88 19,26,6,29 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D217|631|ANTXRL|protein_coding|CODING|NM_001278688.2|7|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.740078 rs4409768 -0.693136 0.157398 88 P259A 631 Cct/Gct MODERATE 9 MISSENSE CODING ANTXRL G protein_coding NM_001278688.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47669277 C G 0 222 0 0.2859 0.3429 0.4712 0.1597 0.4751 0.3814 0 . 0 1 168 5565 72 33 607 1644 66 2975 2 590 13928 182 206 1440 3860 172 7478 0.46548 0 . 0 . 71 19,14,10,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P259A|631|ANTXRL|protein_coding|CODING|NM_001278688.2|9|G) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.937663 0.661138 0 0.747235 rs61845226 -0.692976 0.448307 71 P413 631 ccG/ccA LOW 15 SILENT CODING ANTXRL A protein_coding NM_001278688.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47682811 G A 0 195 0 0.1891 0.1446 0.2017 0.0764 0.1441 0.1145 0 . 0 1 163 1976 36 20 309 672 23 753 2 660 14734 196 216 1592 4282 188 7600 0.933441 0 . 0 COSM427583 22 5,1,9,5 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P413|631|ANTXRL|protein_coding|CODING|NM_001278688.2|15|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.441677 rs2999446 -0.686358 0.826571 22 T617 631 acG/acA LOW 17 SILENT CODING ANTXRL A protein_coding NM_001278688.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47701275 G A 0 222 0 0.093 0.276 0.4986 0.2262 0.4205 0.2679 0 . 0 1 77 4778 77 47 754 1587 63 2173 2 560 13246 166 188 1612 3684 178 6858 0.945733 0 . 0 . 74 13,18,14,21 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T617|631|ANTXRL|protein_coding|CODING|NM_001278688.2|17|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.993337 rs10906952 -0.693136 0.151511 74 P626 631 ccG/ccC LOW 17 SILENT CODING ANTXRL C protein_coding NM_001278688.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47701302 G C 0 228 0 0.7231 0.8085 0.8069 0.8929 0.8082 0.8384 0 . 0 2 398 9394 118 161 1291 2596 133 4697 2 516 11468 152 176 1600 3174 162 5688 0 . 0 . 0 56 0,0,13,37 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P626|631|ANTXRL|protein_coding|CODING|NM_001278688.2|17|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7091749 -0.693147 0.14139 56 327 134 MODIFIER 1 CODING ANXA8L1 A protein_coding NM_001098845.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47746978 C A 0 222 0 0.32 0.4906 0.3026 0.8075 0.4274 0.593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999616 0 . 0 . 171 74,7,76,8 UTR_5_PRIME(MODIFIER||134||327|ANXA8L1|protein_coding|CODING|NM_001098845.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 36 0 0.911594 0.035425 0 0.114668 rs138970875,rs61842918 -0.693147 8.02644e-07 171 N192K 327 aaT/aaG MODERATE 8 MISSENSE CODING ANXA8L1 G protein_coding NM_001098845.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 47756662 T G 0 99 0 . 0 . 0 . 0 . 0 . 2 1683 17834 1346 336 1089 11499 126 1755 2 6228 51774 4674 2160 2718 29426 344 6224 0 . 0 . 0 36 0,0,0,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N192K|327|ANXA8L1|protein_coding|CODING|NM_001098845.2|8|G) 0 . 0 . 0 . 0 . 1 0 26 0 0 . 0 . rs202221168 -0.693139 0.155281 36 P220L 658 cCg/cTg MODERATE 8 MISSENSE CODING AGAP9 T protein_coding NM_001190810.1.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48235892 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 0 1 0 0 0 0 1 0 2 0 2 0 0 0 0 2 0 1 0 . 0 . 188 0,1,132,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P220L|658|AGAP9|protein_coding|CODING|NM_001190810.1.2|8|T) 0 . 0 . 0 . 0 . 1 0 23 0 1 3.78756e-08 0 1 rs200283865 -0.693147 0.207235 188 G21 340 ggG/ggA LOW 2 SILENT CODING ZNF488 A protein_coding NM_153034.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48370595 G A 0 222 0 0.3396 0.3668 0.2421 0.4812 0.329 0.4131 0.343324 0.337538 0.334574 1 3401 41012 3142 4268 2005 20803 322 7071 2 9780 117318 11516 8548 6612 64378 882 15602 0.669731 0 . 0 COSM427587 276 91,42,79,44 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G21|340|ZNF488|protein_coding|CODING|NM_153034.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.770423 rs11204210 -0.693147 0.361679 276 1247 13 MODIFIER 1 CODING RBP3 A protein_coding NM_002900.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48390890 G A 0 211 0 0.0182 0.1012 0.085 0.2123 0.0755 0.137 0.0279545 0.0630963 0.0810842 1 260 10968 1355 1608 447 4660 94 2544 2 8642 111370 10936 8028 5852 61198 820 15894 0.403239 0 . 0 . 36 5,9,3,16 UTR_5_PRIME(MODIFIER||13||1247|RBP3|protein_coding|CODING|NM_002900.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.253231 rs41284964 -0.69168 0.0756273 36 478 24 MODIFIER 1 CODING GDF10 T protein_coding NM_004962.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48438734 C T 0 228 0 0.5469 0.6849 0.7896 0.6915 0.7634 0.7096 0.662859 0.75 0.791498 2 4094 78225 9067 5604 4361 44715 553 9831 2 6950 101724 10872 8070 5246 56908 710 12968 1 0 . 0 . 20 0,1,8,11 UTR_5_PRIME(MODIFIER||24||478|GDF10|protein_coding|CODING|NM_004962.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1126827 -0.69168 0.623242 20 478 197 MODIFIER 1 CODING GDF10 T protein_coding NM_004962.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48438907 C T 0 73 0 0.5454 0.6727 0.781 0.6905 0.7535 0.6667 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_5_PRIME(MODIFIER||197||478|GDF10|protein_coding|CODING|NM_004962.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2853839 -0.511536 0.166456 3 478 290 MODIFIER 1 CODING GDF10 T protein_coding NM_004962.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 48439000 C T 0 70 0 0.1853 0.5058 0.6513 0.5992 0.6948 0.545 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||290||478|GDF10|protein_coding|CODING|NM_004962.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1540253 -0.453602 0.6 3 1309 LOW 26 CODING FRMPD2 G protein_coding NM_001018071.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49376743 A G 0 27.4 0 0.1967 0.0673 0.0231 0.0169 0.0348 0.0092 0 . 0 1 0 0 0 0 0 0 0 0 2 5966 79796 8996 6180 3558 41680 562 12854 0.950952 0 . 0 . 11 1,4,0,6 SPLICE_SITE_REGION+INTRON(LOW||||1309|FRMPD2|protein_coding|CODING|NM_001018071.3|26|G),INTRAGENIC(MODIFIER|||||FRMPD2B||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 32 0 0.0594345 1 0 0.356607 rs199688001 -0.616816 0.6577 11 T1021K 1309 aCg/aAg MODERATE 24 MISSENSE CODING FRMPD2 T protein_coding NM_001018071.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49382926 G T 0 16 0 0.7784 0.9215 0.9568 0.9841 0.9573 0.9888 0 . 0 2 58 337 16 27 0 220 6 10 2 1152 1488 42 28 0 244 12 10 1 0 . 0 . 7 1,0,0,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T1021K|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|24|T),INTRAGENIC(MODIFIER|||||FRMPD2B||NON_CODING|||T) 0 . 0 . 0 1 0 . 1 0 13 0 1 1 0 1 rs144837285,rs1898784 -0.616816 0.80389 7 S874G 1309 Agc/Ggc MODERATE 21 MISSENSE CODING FRMPD2 C protein_coding NM_001018071.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49389016 T C 0 168 0 . 0 . 0 . 0 . 0 . 1 500 3264 152 242 31 2150 36 153 2 1074 5730 336 472 52 3394 58 344 0.611616 0 . 0 COSM1474626 119 35,30,22,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S874G|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|21|C) 0 0.5 1 0 . 0 . 0 1 0 27 0 0.999291 0.965594 0 0.703985 rs1346694,rs199919944 -0.693146 0.757103 119 K534E 1309 Aag/Gag MODERATE 13 MISSENSE CODING FRMPD2 C protein_coding NM_001018071.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49420008 T C 0 222 0 0.6074 0.2823 0.183 0.0694 0.2535 0.1626 0.542896 0.327695 0.217442 1 5742 27994 1663 559 1741 14937 189 3163 2 10312 119808 11414 8566 6482 66146 888 16000 0.282786 0 . 0 . 65 19,16,17,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K534E|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953857 rs1864345 -0.692914 0.166522 65 A386 1309 gcG/gcA LOW 10 SILENT CODING FRMPD2 T protein_coding NM_001018071.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49440168 C T 0 222 0 0.1188 0.0451 0.0173 0.0258 0.0109 0.0204 0.0978212 0.0375211 0.00662791 1 1071 2214 101 154 2 463 14 409 2 10406 121396 11576 8650 6614 66734 908 16508 0.815751 0 . 0 . 95 38,10,24,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A386|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0518179 rs11816450 -0.693141 0.19917 95 V57 1309 gtT/gtC LOW 3 SILENT CODING FRMPD2 G protein_coding NM_001018071.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49457202 A G 0 222 0 0.3616 0.1052 0.0331 0.0238 0.002 0 0.3064 0.105259 0.0022093 1 3370 3764 146 153 0 76 11 8 2 10310 120474 11532 8624 6612 66294 890 16212 0.898925 0 . 0 . 63 6,25,9,21 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.950883 rs440943 -0.693097 0.20577 63 S53 1309 tcG/tcA LOW 3 SILENT CODING FRMPD2 T protein_coding NM_001018071.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49457214 C T 0 222 0 0 0.0053914 0.0014 0.0248 0 0.001 0 . 0 1 0 162 1 153 0 3 0 5 2 10196 119610 11522 8620 6608 66010 878 15776 0.868491 0 . 0 . 58 6,23,8,18 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S53|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.997729 rs115963067 -0.692976 0.0730504 58 N50 1309 aaC/aaT LOW 2 SILENT CODING FRMPD2 A protein_coding NM_001018071.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49459610 G A 0 222 0 0.1717 0.0523 0.013 0.0248 0 0.001 0.139809 0.0485161 0.00174419 1 1546 1829 58 150 0 62 7 6 2 10394 121290 11578 8642 6614 66658 904 16500 0.330491 0 . 0 . 85 22,22,24,5 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N50|1309|FRMPD2|protein_coding|CODING|NM_001018071.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.529707 rs166815 -0.693079 0.114763 85 S97 427 tcC/tcT LOW 4 SILENT CODING MAPK8 T protein_coding NM_001278547.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49617960 C T 0 222 0 0 0.0045927 0 0.0218 0 0.001 0 . 0 1 0 155 0 151 0 1 0 3 2 9694 117994 11290 8506 6548 64776 892 16288 0.840174 0 . 0 . 95 32,15,21,16 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S97|427|MAPK8|protein_coding|CODING|NM_001278547.1|4|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.997406 rs55740545 -0.693141 0.0856762 95 427 1630 MODIFIER 12 CODING MAPK8 C protein_coding NM_001278547.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49644702 A C 0 9.7 0 0.0174 0.009385 0.0014 0.0218 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1630||427|MAPK8|protein_coding|CODING|NM_001278547.1|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs73293545 -0.379885 0 1 714 239 MODIFIER 10 CODING ARHGAP22 G protein_coding NM_001256024.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49654195 A G 0 91 0 0.2307 0.3952 0.4769 0.371 0.3867 0.593 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,5,0 UTR_3_PRIME(MODIFIER||239||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs1051509 -0.590765 0.237122 6 714 92 MODIFIER 10 CODING ARHGAP22 T protein_coding NM_001256024.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49654342 C T 0 222 0 0.3336 0.4784 0.4856 0.628 0.6054 0.3845 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.3117 0 . 0 . 63 30,3,25,3 UTR_3_PRIME(MODIFIER||92||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.866424 rs1051508 -0.693054 0.275225 63 714 31 MODIFIER 10 CODING ARHGAP22 T protein_coding NM_001256024.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49654403 C T 0 222 0 0.323 0.4746 0.4856 0.625 0.6044 0.3834 0.360418 0.501307 0.573488 1 3642 63985 5889 5497 3561 38206 503 6687 2 10380 120660 11512 8540 6578 66344 900 16406 0.751759 0 . 0 . 112 48,6,35,10 UTR_3_PRIME(MODIFIER||31||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998791 rs1051507 -0.693147 0.220393 112 714 LOW 8 CODING ARHGAP22 G protein_coding NM_001256024.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49661341 A G 0 228 0 0.5484 0.8249 0.928 0.9891 0.9553 0.8221 0.61734 0.835537 0.947326 2 6227 109213 11049 8581 6337 62513 846 13660 2 10320 120896 11558 8646 6614 66348 902 16508 0 . 0 . 0 93 0,0,60,24 SPLICE_SITE_REGION+INTRON(LOW||||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7092959 -0.693147 0.314049 93 P213 714 ccA/ccG LOW 5 SILENT CODING ARHGAP22 C protein_coding NM_001256024.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49667795 T C 0 228 0 0.6437 0.902 0.9755 1 0.999 0.998 0.6936 0.89551 0.998953 2 7165 117889 11425 8653 6614 66645 897 16490 2 10404 121364 11578 8654 6614 66696 906 16512 0 . 0 . 0 150 0,0,61,75 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P213|714|ARHGAP22|protein_coding|CODING|NM_001256024.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3853761 -0.693147 0.0958444 150 A110 714 gcC/gcT LOW 4 SILENT CODING ARHGAP22 A protein_coding NM_001256024.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49687800 G A 0 228 0 0.4894 0.7893 0.8761 0.9425 0.8678 0.8947 0.55293 0.749654 0.850396 2 4499 85691 9360 7112 4057 49091 615 10957 2 7986 99940 10046 7726 4590 56394 708 12490 0 . 0 . 0 70 0,0,13,53 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A110|714|ARHGAP22|protein_coding|CODING|NM_001256024.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4080665 -0.693147 0.400204 70 714 76 MODIFIER 1 CODING ARHGAP22 C protein_coding NM_001256024.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49812917 T C 0 228 0 0.3177 0.2991 0.2032 0.3254 0.2803 0.3344 0.333815 0.305738 0.293526 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 47 0,1,9,33 START_GAINED(LOW||||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|1|C),UTR_5_PRIME(MODIFIER||76||714|ARHGAP22|protein_coding|CODING|NM_001256024.1|1|C) 1 0 . 0 . 1 0 1 0 . 60 0 1 1 0 1 rs17010948 -0.693146 0.440016 47 V1359I 3184 Gta/Ata MODERATE 23 MISSENSE CODING WDFY4 A protein_coding NM_020945.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 49998780 G A 0 222 0 0.0076 0.1168 0.1354 0.3075 0.0378 0.136 0.015896 0.0328515 0.0402263 1 29 1965 57 173 76 409 19 1202 2 2186 21734 408 618 1632 8842 234 7814 0.936679 0 . 0 . 99 34,9,37,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1359I|3184|WDFY4|protein_coding|CODING|NM_020945.1|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932581 rs41282009 -0.693147 0.119578 99 A1429 3184 gcC/gcT LOW 24 SILENT CODING WDFY4 T protein_coding NM_020945.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50004372 C T 0 222 0 0.0083 0.1174 0.1354 0.3075 0.0378 0.138 0.0130058 0.0326325 0.0411691 1 34 2107 67 175 85 505 23 1218 2 2532 23646 486 630 1778 10086 258 7876 0.794512 0 . 0 . 189 53,29,42,42 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1429|3184|WDFY4|protein_coding|CODING|NM_020945.1|24|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.685615 rs41282011 -0.693147 0.147327 189 S1528P 3184 Tcc/Ccc MODERATE 26 MISSENSE CODING WDFY4 C protein_coding NM_020945.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50013402 T C 0 228 0 0.7905 0.5769 0.3977 0.8304 0.2962 0.4427 0.730491 0.439553 0.313011 2 1646 9378 156 491 539 3037 104 3405 2 2264 21778 388 588 1616 8784 240 7898 0 . 0 . 0 65 0,0,27,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S1528P|3184|WDFY4|protein_coding|CODING|NM_020945.1|26|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2170132 -0.693147 0.979084 65 R1816Q 3184 cGa/cAa MODERATE 32 MISSENSE CODING WDFY4 A protein_coding NM_020945.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50025396 G A 0 228 0 0.0983 0.3586 0.3271 0.6935 0.3956 0.3497 0.129335 0.310337 0.389063 2 280 7773 131 436 487 3482 87 2870 2 2098 20708 402 616 986 8478 220 7908 0.179856 0 . 0 COSM1560763 157 1,1,70,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R1816Q|3184|WDFY4|protein_coding|CODING|NM_020945.1|32|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.845324 rs7097397 -0.693147 0.00455279 157 Q2132 3184 caA/caG LOW 38 SILENT CODING WDFY4 G protein_coding NM_020945.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50038800 A G 0 228 0 0.7216 0.6502 0.5331 0.8115 0.5149 0.6094 0.712428 0.569426 0.507228 2 1618 13032 220 501 851 4829 138 4875 2 2278 22290 410 622 1624 9200 244 7912 1 0 . 0 . 133 0,1,98,27 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q2132|3184|WDFY4|protein_coding|CODING|NM_020945.1|38|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3747874 -0.693147 0.446163 133 3184 LOW 38 CODING WDFY4 G protein_coding NM_020945.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50040610 T G 0 228 0 0.5287 0.5232 0.428 0.8095 0.3658 0.4499 0.524566 0.4159 0.368636 2 1345 9903 201 503 693 3751 114 3296 2 2552 21948 462 622 1758 9634 244 6676 1 0 . 0 . 106 0,1,74,23 SPLICE_SITE_REGION+INTRON(LOW||||3184|WDFY4|protein_coding|CODING|NM_020945.1|38|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3747872 -0.693147 0.576437 106 S2527N 3184 aGt/aAt MODERATE 47 MISSENSE CODING WDFY4 A protein_coding NM_020945.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50109902 G A 0 228 0 0.888 0.9696 0.9942 1 1 1 0.916907 0.974595 0.999686 2 1941 21516 405 622 1624 8769 241 7914 2 2154 21736 410 622 1624 8770 242 7914 0 . 0 . 0 146 0,0,57,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S2527N|3184|WDFY4|protein_coding|CODING|NM_020945.1|47|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2663046 -0.693147 0.302755 146 T139 261 acA/acG LOW 1 SILENT CODING LRRC18 C protein_coding NM_001006939.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50121784 T C 0 228 0 0.68 0.6252 0.5346 0.7292 0.494 0.6431 0.629596 0.540212 0.494419 2 6561 64170 5689 6264 3387 31661 493 10115 2 10360 120852 11476 8612 6542 66484 894 16484 1 0 . 0 . 87 0,1,35,45 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T139|261|LRRC18|protein_coding|CODING|NM_001006939.3|1|C),INTRON(MODIFIER||||3184|WDFY4|protein_coding|CODING|NM_020945.1|47|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10776653 -0.693147 0.000762873 87 G7V 261 gGc/gTc MODERATE 1 MISSENSE CODING LRRC18 A protein_coding NM_001006939.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50122181 C A 0 228 0 0.0772 0.363 0.2925 0.7202 0.339 0.456 0.113255 0.266954 0.345698 2 1046 42821 3404 6197 2256 22681 331 6906 2 10218 120338 11526 8596 6596 66250 902 16250 0 . 0 . 0 72 0,0,25,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G7V|261|LRRC18|protein_coding|CODING|NM_001006939.3|1|A),INTRON(MODIFIER||||3184|WDFY4|protein_coding|CODING|NM_020945.1|47|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7094610 -0.693147 0.0124079 72 320 5110 MODIFIER 8 CODING VSTM4 T protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50222585 G T 0 9.7 0 0.3843 0.603 0.7378 0.6419 0.8429 0.5164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5110||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2254863,rs386562716 -0.379885 0 1 320 4926 MODIFIER 8 CODING VSTM4 G protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50222769 T G 0 9.7 0 0.6392 0.8626 0.9481 0.9077 0.998 0.9182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4926||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2254861 -0.379885 0 1 320 4081 MODIFIER 8 CODING VSTM4 A protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50223614 G A 0 103 0 0.3873 0.6054 0.7464 0.6419 0.8459 0.5153 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||4081||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1996185 -0.556411 0.281254 4 320 1361 MODIFIER 8 CODING VSTM4 G protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50226334 T G 0 9.7 0 0.3623 0.5673 0.7089 0.6419 0.7863 0.4417 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1361||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1055583 -0.379885 0 1 320 843 MODIFIER 8 CODING VSTM4 C protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50226852 T C 0 57 0 0.6808 0.8734 0.9352 0.9702 0.9414 0.9202 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||843||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2244704 -0.511536 0.160332 3 320 180 MODIFIER 8 CODING VSTM4 T protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50227515 C T 0 213 0 0.3374 0.489 0.5418 0.6409 0.5736 0.4131 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.613636 0 . 0 . 46 1,1,41,3 UTR_3_PRIME(MODIFIER||180||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.965909 rs2244575 -0.693146 0.0313747 46 320 136 MODIFIER 8 CODING VSTM4 T protein_coding NM_001031746.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50227559 C T 0 221 0 0 0.022 0.0807 0.0506 0 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998698 0 . 0 . 81 42,3,25,3 UTR_3_PRIME(MODIFIER||136||320|VSTM4|protein_coding|CODING|NM_001031746.4|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.562895 rs3810952 -0.693054 0.0847598 81 E291 320 gaA/gaG LOW 8 SILENT CODING VSTM4 C protein_coding NM_001031746.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50227785 T C 0 228 0 0.7685 0.9353 0.9741 1 1 1 0.825238 0.940489 0.999535 2 8479 119335 11476 8648 6614 66707 904 16507 2 10400 121386 11576 8648 6614 66732 908 16508 0 . 0 . 0 81 0,0,20,58 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E291|320|VSTM4|protein_coding|CODING|NM_001031746.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1913525 -0.693147 0.0134771 81 1435 78 MODIFIER 3 CODING C10orf71 A protein_coding NM_001135196.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50530513 G A 0 222 0 0.0068 0.0964 0.0793 0.2738 0.0845 0.0593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.829616 0 . 0 . 56 20,2,28,2 UTR_5_PRIME(MODIFIER||78||1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982994 rs12416329 -0.693097 0.00415464 56 L338 1435 ctT/ctC LOW 3 SILENT CODING C10orf71 C protein_coding NM_001135196.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50531604 T C 0 228 0 0.8495 0.9571 0.9784 1 0.999 1 0.878371 0.960464 0.999278 2 8504 118305 11505 8624 6613 66382 884 15793 2 9786 119682 11570 8624 6614 66406 888 15794 0 . 0 . 0 64 0,0,35,27 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L338|1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7093235 -0.693147 0.162195 64 F698S 1435 tTc/tCc MODERATE 3 MISSENSE CODING C10orf71 C protein_coding NM_001135196.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50532683 T C 0 228 0 0.8707 0.9629 0.9798 1 0.999 1 0.893858 0.966381 0.999267 2 8490 118965 11453 8618 6608 66450 892 16454 2 9546 120110 11516 8618 6608 66472 896 16454 0 . 0 . 0 63 0,0,17,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F698S|1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7921186 -0.693147 0.00928037 63 G1009 1435 ggT/ggC LOW 3 SILENT CODING C10orf71 C protein_coding NM_001135196.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50533617 T C 0 228 0 0.8071 0.872 0.8775 0.7837 0.9533 0.9632 0.813584 0.912177 0.95506 2 1856 21031 364 503 1671 8693 232 7712 2 2256 22216 412 622 1706 9064 244 7912 1 0 . 0 . 104 0,1,45,48 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1009|1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2377940 -0.693147 0.843203 104 P1062 1435 ccC/ccG LOW 3 SILENT CODING C10orf71 G protein_coding NM_001135196.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50533776 C G 0 222 0 0.2806 0.3468 0.3919 0.1954 0.4334 0.4714 0 . 0 1 531 8559 153 133 505 3588 80 3569 2 1658 19700 362 534 1548 7498 230 7870 0.908478 0 . 0 . 84 27,20,13,15 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P1062|1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.483897 rs10857471 -0.693054 0.610931 84 G1337S 1435 Ggc/Agc MODERATE 3 MISSENSE CODING C10orf71 A protein_coding NM_001135196.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50534599 G A 0 222 0 0.2194 0.3297 0.3818 0.1925 0.4354 0.4744 0.218425 0.379418 0.448784 1 267 7005 114 90 400 2600 66 3468 2 858 15660 258 370 1018 5314 176 7666 0.782223 0 . 0 . 157 35,60,26,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1337S|1435|C10orf71|protein_coding|CODING|NM_001135196.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.60735 rs10857472 -0.693147 0.125645 157 A53 263 gcC/gcT LOW 4 SILENT CODING DRGX A protein_coding NM_001276451.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50598254 G A 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 1 59 0 48 0 8 0 2 2 7526 91992 8280 6680 5414 51044 714 12334 0.999937 0 . 0 . 84 28,15,14,16 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A53|263|DRGX|protein_coding|CODING|NM_001276451.1|4|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.196081 rs188251168 -0.693097 0.145928 84 1493 1830 MODIFIER 21 CODING ERCC6 G protein_coding NM_000124.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50665031 A G 0 9.7 0 0.1188 0.1761 0.2104 0.4107 0.0666 0.1002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1830||1493|ERCC6|protein_coding|CODING|NM_000124.3|21|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11101137 -0.379885 0 1 1493 379 MODIFIER 21 CODING ERCC6 C protein_coding NM_000124.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50666482 G C 0 135 0 0.0893 0.2582 0.3012 0.3165 0.3966 0.2536 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.785785 0 . 0 . 16 8,0,6,1 UTR_3_PRIME(MODIFIER||379||1493|ERCC6|protein_coding|CODING|NM_000124.3|21|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.985046 rs386421478,rs4253234 -0.636426 0.787989 16 G917 1493 ggC/ggT LOW 15 SILENT CODING ERCC6 A protein_coding NM_000124.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50681033 G A 0 222 0 0.0893 0.2542 0.2968 0.3155 0.3926 0.2413 0.149569 0.323774 0.413023 1 1370 40716 3139 2683 2475 26645 337 4067 2 10384 120814 11516 8548 6580 66424 908 16454 0.864255 255 other 0 COSM146934 155 53,16,49,10 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G917|1493|ERCC6|protein_coding|CODING|NM_000124.3|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999589 rs2229760 -0.693147 0.445296 155 1493 LOW 8 CODING ERCC6 A protein_coding NM_000124.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50701156 G A 0 228 0 0.7141 0.877 0.9251 0.999 0.8638 0.9509 0.735361 0.832231 0.88186 2 7522 107530 10857 8571 5918 58365 813 15484 2 10370 121000 11540 8578 6598 66520 906 16488 0 2 benign 0 . 107 0,0,78,24 SPLICE_SITE_REGION+INTRON(LOW||||1493|ERCC6|protein_coding|CODING|NM_000124.3|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386592024,rs4253132 -0.693147 0.114543 107 L493 593 Ctg/Ttg LOW 2 SILENT CODING PGBD3 A protein_coding NM_170753.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50723684 G A 0 228 0 0.7345 0.8934 0.9409 0.999 0.8966 0.9622 0.741262 0.84907 0.904302 2 7596 110115 10960 8647 6142 60294 831 15645 2 10406 121400 11566 8654 6614 66740 908 16512 1 0 . 0 . 140 0,1,51,76 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L493|593|PGBD3|protein_coding|CODING|NM_170753.3|2|A),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L961|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|6|A),INTRON(MODIFIER||||1493|ERCC6|protein_coding|CODING|NM_000124.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4253073 -0.693147 0.130551 140 L961 1061 Ctg/Ttg LOW 6 SILENT CODING ERCC6-PGBD3 A protein_coding NM_001277058.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50723684 G A 0 228 0 0.7345 0.8934 0.9409 0.999 0.8966 0.9622 0.741262 0.84907 0.904302 2 7596 110115 10960 8647 6142 60294 831 15645 2 10406 121400 11566 8654 6614 66740 908 16512 1 0 . 0 . 140 0,1,51,76 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L493|593|PGBD3|protein_coding|CODING|NM_170753.3|2|A),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L961|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|6|A),INTRON(MODIFIER||||1493|ERCC6|protein_coding|CODING|NM_000124.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4253073 -0.693147 0.130551 140 R382K 593 aGa/aAa MODERATE 2 MISSENSE CODING PGBD3 T protein_coding NM_170753.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50724016 C T 0 228 0 0.9856 0.9962 1 1 1 1 0.98207 0.993926 1 2 10225 121176 11541 8654 6614 66724 907 16511 2 10400 121386 11562 8654 6614 66736 908 16512 0 . 0 . 0 84 0,0,44,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R382K|593|PGBD3|protein_coding|CODING|NM_170753.3|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R850K|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|6|T),INTRON(MODIFIER||||1493|ERCC6|protein_coding|CODING|NM_000124.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386592018,rs4253072 -0.693147 0.363511 84 R850K 1061 aGa/aAa MODERATE 6 MISSENSE CODING ERCC6-PGBD3 T protein_coding NM_001277058.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50724016 C T 0 228 0 0.9856 0.9962 1 1 1 1 0.98207 0.993926 1 2 10225 121176 11541 8654 6614 66724 907 16511 2 10400 121386 11562 8654 6614 66736 908 16512 0 . 0 . 0 84 0,0,44,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R382K|593|PGBD3|protein_coding|CODING|NM_170753.3|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R850K|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|6|T),INTRON(MODIFIER||||1493|ERCC6|protein_coding|CODING|NM_000124.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386592018,rs4253072 -0.693147 0.363511 84 G399D 1493 gGt/gAt MODERATE 5 MISSENSE CODING ERCC6 T protein_coding NM_000124.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50732280 C T 0 222 0 0.1793 0.2378 0.2378 0.4911 0.1581 0.138 0.165456 0.16231 0.160698 1 1799 23745 3645 3988 1084 10852 161 2216 2 10404 121284 11540 8636 6598 66690 908 16508 0.924648 255 other 0 . 64 7,20,11,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1493|ERCC6|protein_coding|CODING|NM_000124.3|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|5|T),UTR_5_PRIME(MODIFIER||7120||593|PGBD3|protein_coding|CODING|NM_170753.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738991 rs2228528,rs386561695 -0.693139 0.785955 64 G399D 1061 gGt/gAt MODERATE 5 MISSENSE CODING ERCC6-PGBD3 T protein_coding NM_001277058.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50732280 C T 0 222 0 0.1793 0.2378 0.2378 0.4911 0.1581 0.138 0.165456 0.16231 0.160698 1 1799 23745 3645 3988 1084 10852 161 2216 2 10404 121284 11540 8636 6598 66690 908 16508 0.924648 255 other 0 . 64 7,20,11,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1493|ERCC6|protein_coding|CODING|NM_000124.3|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|5|T),UTR_5_PRIME(MODIFIER||7120||593|PGBD3|protein_coding|CODING|NM_170753.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738991 rs2228528,rs386561695 -0.693139 0.785955 64 593 7120 MODIFIER 1 CODING PGBD3 T protein_coding NM_170753.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50732280 C T 0 222 0 0.1793 0.2378 0.2378 0.4911 0.1581 0.138 0.165456 0.16231 0.160698 1 1799 23745 3645 3988 1084 10852 161 2216 2 10404 121284 11540 8636 6598 66690 908 16508 0.924648 255 other 0 . 64 7,20,11,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1493|ERCC6|protein_coding|CODING|NM_000124.3|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G399D|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|5|T),UTR_5_PRIME(MODIFIER||7120||593|PGBD3|protein_coding|CODING|NM_170753.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738991 rs2228528,rs386561695 -0.693139 0.785955 64 L137 1493 ctG/ctA LOW 2 SILENT CODING ERCC6 T protein_coding NM_000124.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50740600 C T 0 222 0 0.118 0.1757 0.2089 0.4107 0.0666 0.1002 0.107354 0.0788098 0.064186 1 1135 14417 3257 3355 727 4281 106 1556 2 10394 121190 11562 8616 6610 66592 904 16512 0.751492 255 other 0 . 152 48,27,50,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L137|1493|ERCC6|protein_coding|CODING|NM_000124.3|2|T),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L137|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.446854 rs4253013 -0.693147 0.580891 152 L137 1061 ctG/ctA LOW 2 SILENT CODING ERCC6-PGBD3 T protein_coding NM_001277058.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50740600 C T 0 222 0 0.118 0.1757 0.2089 0.4107 0.0666 0.1002 0.107354 0.0788098 0.064186 1 1135 14417 3257 3355 727 4281 106 1556 2 10394 121190 11562 8616 6610 66592 904 16512 0.751492 255 other 0 . 152 48,27,50,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L137|1493|ERCC6|protein_coding|CODING|NM_000124.3|2|T),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L137|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.446854 rs4253013 -0.693147 0.580891 152 L45 1493 ctC/ctG LOW 2 SILENT CODING ERCC6 C protein_coding NM_000124.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50740876 G C 0 222 0 0.3336 0.5909 0.6657 0.5079 0.7346 0.8231 0.404448 0.627557 0.74186 1 3953 84287 7185 4640 5057 49364 660 13428 2 10404 121340 11568 8626 6610 66714 906 16512 0.955809 255 other 0 . 90 26,19,10,25 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L45|1493|ERCC6|protein_coding|CODING|NM_000124.3|2|C),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L45|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.942451 rs2228524 -0.693136 0.0137621 90 L45 1061 ctC/ctG LOW 2 SILENT CODING ERCC6-PGBD3 C protein_coding NM_001277058.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50740876 G C 0 222 0 0.3336 0.5909 0.6657 0.5079 0.7346 0.8231 0.404448 0.627557 0.74186 1 3953 84287 7185 4640 5057 49364 660 13428 2 10404 121340 11568 8626 6610 66714 906 16512 0.955809 255 other 0 . 90 26,19,10,25 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L45|1493|ERCC6|protein_coding|CODING|NM_000124.3|2|C),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L45|1061|ERCC6-PGBD3|protein_coding|CODING|NM_001277058.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.942451 rs2228524 -0.693136 0.0137621 90 532 25 MODIFIER 1 CODING SLC18A3 T protein_coding NM_003055.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50818762 C T 0 140 0 0.8964 0.851 0.9063 0.5694 0.9851 0.9029 0.928608 0.972337 0.994439 1 1187 8908 261 612 226 5655 45 922 2 1292 9476 294 904 228 5698 48 1012 0.367879 0 . 0 . 25 12,1,11,1 UTR_5_PRIME(MODIFIER||25||532|SLC18A3|protein_coding|CODING|NM_003055.2|1|T),UPSTREAM(MODIFIER||3321||748|CHAT|protein_coding|CODING|NM_020549.4||T),INTRAGENIC(MODIFIER|||||CHAT||CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.920158 rs1880675 -0.680642 0.588494 25 A132 532 gcT/gcC LOW 1 SILENT CODING SLC18A3 C protein_coding NM_003055.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50819182 T C 0 222 0 0.0113 0.1136 0.0735 0.4306 0.0089 0.0613 0.0165683 0.00722743 0.00244186 1 161 6847 1817 3539 190 264 36 840 2 10360 121072 11572 8612 6614 66500 904 16510 0.818522 0 . 0 . 62 25,6,17,9 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A132|532|SLC18A3|protein_coding|CODING|NM_003055.2|1|C),UPSTREAM(MODIFIER||2901||748|CHAT|protein_coding|CODING|NM_020549.4||C),INTRAGENIC(MODIFIER|||||CHAT||CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.295199 rs8175353 -0.692976 0.575499 62 A520E 532 gCg/gAg MODERATE 1 MISSENSE CODING SLC18A3 A protein_coding NM_003055.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50820345 C A 0 228 0 0.9902 0.9974 1 1 1 1 0.9875 0.995767 1 2 9938 120318 11561 8624 6614 66393 902 16286 2 10066 120450 11564 8624 6614 66394 902 16286 1 0 . 0 . 127 1,0,56,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A520E|532|SLC18A3|protein_coding|CODING|NM_003055.2|1|A),UPSTREAM(MODIFIER||1738||748|CHAT|protein_coding|CODING|NM_020549.4||A),INTRAGENIC(MODIFIER|||||CHAT||CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs8187730 -0.693147 0.0481674 127 532 39 MODIFIER 1 CODING SLC18A3 T protein_coding NM_003055.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50820424 G T 0 222 0 0.1029 0.1881 0.1455 0.4871 0.1322 0.0828 0.0986969 0.105045 0.108169 1 1009 16775 2451 3931 1246 7165 144 829 2 9420 108874 11446 8472 6602 62946 770 9218 0.702855 0 . 0 . 89 19,31,14,16 UTR_3_PRIME(MODIFIER||39||532|SLC18A3|protein_coding|CODING|NM_003055.2|1|T),UPSTREAM(MODIFIER||1659||748|CHAT|protein_coding|CODING|NM_020549.4||T),INTRAGENIC(MODIFIER|||||CHAT||CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.571146 rs2269338 -0.693097 0.714667 89 532 308 MODIFIER 1 CODING SLC18A3 T protein_coding NM_003055.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50820693 G T 0 222 0 0.0045 0.1104 0.0735 0.4266 0.008 0.0593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.643707 0 . 0 . 93 28,24,19,11 UTR_3_PRIME(MODIFIER||308||532|SLC18A3|protein_coding|CODING|NM_003055.2|1|T),UPSTREAM(MODIFIER||1390||748|CHAT|protein_coding|CODING|NM_020549.4||T),INTRAGENIC(MODIFIER|||||CHAT||CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999259 rs74832669 -0.693097 0.107724 93 748 10 MODIFIER 1 CODING CHAT G protein_coding NM_020549.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50822226 T G 0 149 0 0.91 0.9718 0.9841 1 0.997 0.9918 0 . 0 2 362 12178 119 252 4 3813 137 7491 2 398 12274 120 252 4 3826 138 7536 0 2 benign 0 . 7 0,0,6,1 UTR_5_PRIME(MODIFIER||10||748|CHAT|protein_coding|CODING|NM_020549.4|1|G),DOWNSTREAM(MODIFIER||1460||532|SLC18A3|protein_coding|CODING|NM_003055.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7923716 -0.636426 0.450616 7 D47E 748 gaC/gaG MODERATE 1 MISSENSE CODING CHAT G protein_coding NM_020549.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50822376 C G 0 23.1 0 0.0045 0.1088 0.0735 0.4187 0.008 0.0593 0.00209864 0.00178031 0.00161681 1 8 559 19 188 1 20 11 312 2 1164 14478 254 444 26 4986 148 7456 0.594025 255 other 0 COSM427640 13 2,6,0,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D47E|748|CHAT|protein_coding|CODING|NM_020549.4|1|G),DOWNSTREAM(MODIFIER||1610||532|SLC18A3|protein_coding|CODING|NM_003055.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.184981 rs3810948 -0.511536 0.292464 13 A120T 748 Gca/Aca MODERATE 2 MISSENSE CODING CHAT A protein_coding NM_020549.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50824619 G A 0 222 0 0.0053 0.1605 0.1671 0.1696 0.2316 0.2832 0.0517476 0.182377 0.249302 1 447 24228 1485 1204 1166 15296 193 4437 2 8626 106760 10342 7382 5592 59374 808 14636 0.729926 2 benign 0 . 89 21,19,14,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A120T|748|CHAT|protein_coding|CODING|NM_020549.4|2|A),DOWNSTREAM(MODIFIER||3853||532|SLC18A3|protein_coding|CODING|NM_003055.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.359139 rs3810950 -0.693145 0.0165896 89 V461M 748 Gtg/Atg MODERATE 9 MISSENSE CODING CHAT A protein_coding NM_020549.4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50856652 G A 0 228 0 0.8767 0.9665 0.9928 1 1 1 0.886291 0.961018 0.999302 2 8926 117794 11345 8574 6266 65667 869 16147 2 10068 119030 11402 8574 6266 65700 872 16148 1 2 benign 0 . 47 0,1,8,34 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gtg/Atg|V461M|748|CHAT|protein_coding|CODING|NM_020549.4|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4838544 -0.693146 0.213945 47 H547 748 caT/caC LOW 12 SILENT CODING CHAT C protein_coding NM_020549.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50863147 T C 0 222 0 0.6846 0.7935 0.7378 0.8244 0.8926 0.8466 0.699501 0.839843 0.911744 1 7202 103030 7713 6863 5877 60314 781 14280 2 10390 121336 11578 8636 6612 66704 906 16510 0.996687 2 benign 0 . 79 29,12,15,12 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H547|748|CHAT|protein_coding|CODING|NM_020549.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.650413 rs8178992 -0.693021 0.656307 79 I689 748 atC/atT LOW 15 SILENT CODING CHAT T protein_coding NM_020549.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50872912 C T 0 222 0 0.0015 0.0705 0.0014 0.2907 0.005 0.0532 0.00204267 0.00161464 0.00139535 1 27 3903 34 2668 85 183 22 884 2 10406 121402 11578 8646 6614 66740 908 16510 0.909401 255 other 0 . 112 34,19,33,19 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I689|748|CHAT|protein_coding|CODING|NM_020549.4|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94995 rs3793801 -0.693147 0.950929 112 R99G 157 Agg/Ggg MODERATE 3 MISSENSE CODING C10orf53 G protein_coding NM_182554.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50916484 A G 0 228 0 0.5129 0.8081 0.9121 0.9643 0.9354 0.8415 0.600772 0.82239 0.93593 2 5976 108735 11064 8364 6065 62483 824 13959 2 10404 121408 11578 8652 6614 66740 908 16512 0 . 0 . 0 158 0,0,102,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R99G|157|C10orf53|protein_coding|CODING|NM_182554.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1258236 -0.693147 0.752441 158 157 268 MODIFIER 3 CODING C10orf53 T protein_coding NM_182554.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50916931 C T 0 184 0 0.5333 0.8163 0.9179 0.9663 0.9354 0.8497 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,1,10 UTR_3_PRIME(MODIFIER||268||157|C10orf53|protein_coding|CODING|NM_182554.2|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1270561 -0.676189 0.247426 11 1010 511 MODIFIER 23 CODING OGDHL T protein_coding NM_018245.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50942763 C T 0 9.7 0 0.0666 0.4345 0.4712 0.8948 0.4473 0.4182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||511||1010|OGDHL|protein_coding|CODING|NM_018245.2|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6816 -0.379885 0 1 1010 206 MODIFIER 23 CODING OGDHL C protein_coding NM_018245.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50943068 T C 0 123 0 0.2602 0.5228 0.5403 0.8899 0.4781 0.5327 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||206||1010|OGDHL|protein_coding|CODING|NM_018245.2|23|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13736 -0.636426 0.808291 7 1010 88 MODIFIER 23 CODING OGDHL T protein_coding NM_018245.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50943186 C T 0 228 0 0.0522 0.4297 0.4669 0.8839 0.4423 0.4325 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,34,3 UTR_3_PRIME(MODIFIER||88||1010|OGDHL|protein_coding|CODING|NM_018245.2|23|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1258256 -0.693141 0.311444 41 L188 1010 ctC/ctT LOW 5 SILENT CODING OGDHL A protein_coding NM_018245.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 50960209 G A 0 228 0 0.1407 0.4643 0.4798 0.9107 0.4642 0.4305 0.198593 0.387898 0.484884 2 1955 58273 6390 7671 3284 31761 434 6778 2 10384 121052 11478 8630 6588 66566 908 16498 0 . 0 . 0 99 0,0,49,30 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L188|1010|OGDHL|protein_coding|CODING|NM_018245.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1258184 -0.693147 0.160106 99 976 681 MODIFIER 18 CODING PARG G protein_coding NM_003631.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51026705 C G 0 145 0 0.056 0.399 0.4006 0.6042 0.5427 0.502 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,0,10 UTR_3_PRIME(MODIFIER||681||976|PARG|protein_coding|CODING|NM_003631.3|18|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs8474 -0.670168 0.0421135 10 W485R 976 Tgg/Cgg MODERATE 4 MISSENSE CODING PARG G protein_coding NM_003631.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51361729 A G 0 9.7 0 0.7526 0.7079 0.7248 0.7996 0.6362 0.6145 0 . 0 1 3 31 0 0 1 26 0 1 2 708 10402 206 218 964 5976 90 2240 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W485R|976|PARG|protein_coding|CODING|NM_003631.3|4|G),INTRAGENIC(MODIFIER|||||PARGP1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 56 0 0 . 0 . rs202084750 -0.379885 0 1 Q466R 976 cAg/cGg MODERATE 4 MISSENSE CODING PARG C protein_coding NM_003631.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51361785 T C 0 87 0 0.7761 0.7542 0.7637 0.872 0.6938 0.6585 0 . 0 2 20 92 5 2 0 60 1 4 2 352 6082 116 100 550 3196 66 1702 0 . 0 . 0 5 0,0,5,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q466R|976|PARG|protein_coding|CODING|NM_003631.3|4|C),INTRAGENIC(MODIFIER|||||PARGP1||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 35 0 0 . 0 . rs200401326 -0.590765 0.0537672 5 P444 976 ccG/ccA LOW 4 SILENT CODING PARG T protein_coding NM_003631.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51361850 C T 0 67 0 . 0 . 0 . 0 . 0 . 2 100 728 36 29 3 510 9 41 2 290 3022 80 58 200 1784 32 578 1 0 . 0 . 5 1,0,4,0 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P444|976|PARG|protein_coding|CODING|NM_003631.3|4|T),INTRAGENIC(MODIFIER|||||PARGP1||NON_CODING|||T) 0 . 0 . 0 . 0 . 1 0 54 0 1 0 . 1 rs201204635 -0.556411 0.337235 5 Q427 976 caA/caG LOW 4 SILENT CODING PARG C protein_coding NM_003631.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51361901 T C 0 164 0 0.6982 0.6741 0.7378 0.7202 0.5944 0.6309 0 . 0 2 144 1079 51 56 4 753 12 59 2 302 2310 78 80 90 1562 20 178 0 . 0 . 0 18 0,0,18,0 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q427|976|PARG|protein_coding|CODING|NM_003631.3|4|C),INTRAGENIC(MODIFIER|||||PARGP1||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 49 0 0 . 0 . rs199667579 -0.691153 0.0101891 18 188 LOW 2 CODING TIMM23B C protein_coding NM_001290117.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51374435 T C 0 149 0 0.6339 0.5547 0.67 0.5238 0.5686 0.3834 0 . 0 2 564 6331 261 462 407 3348 60 1229 2 1368 17810 604 1420 1352 9082 160 3824 0 . 0 . 0 11 0,0,1,10 SPLICE_SITE_REGION+INTRON(LOW||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|2|C),UPSTREAM(MODIFIER||3064||976|PARG|protein_coding|CODING|NM_003631.3||C) 0 . 0 . 0 1 0 . 1 0 30 0 0 1 0 . rs201973475 -0.676189 0.749333 11 209 LOW 2 CODING TIMM23 G protein_coding NM_006327.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51620317 A G 0 80 0 0.5514 0.6074 0.5663 0.5952 0.5994 0.7331 0 . 0 1 4672 60604 5417 4355 3596 32726 476 9362 2 8248 102178 10402 7352 6088 55542 802 13744 0.931623 0 . 0 . 116 62,0,54,0 SPLICE_SITE_REGION+INTRON(LOW||||209|TIMM23|protein_coding|CODING|NM_006327.3|2|G),INTRON(MODIFIER||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|6|G) 0 0.5 1 0 . 1 0 . 1 0 29 0 0.936398 0 . 0.21664 rs200147310 -0.693147 0.120671 116 G23E 209 gGa/gAa MODERATE 1 MISSENSE CODING TIMM23 T protein_coding NM_006327.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51623147 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 1857 19754 1821 1242 553 9356 166 4759 2 3716 39358 3662 2492 1106 18674 328 9380 0.794951 0 . 0 . 175 24,57,18,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G23E|209|TIMM23|protein_coding|CODING|NM_006327.3|1|T),INTRON(MODIFIER||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|6|T) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.0903433 0.740238 0 0.147762 rs373071373 -0.693147 0.76578 175 G14V 209 gGa/gTa MODERATE 1 MISSENSE CODING TIMM23 A protein_coding NM_006327.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51623174 C A 0 83 0 . 0 . 0 . 0 . 0 . 1 2302 26355 2777 1770 1059 12926 205 5316 2 4610 52636 5566 3566 2122 25858 410 10504 0.145537 0 . 0 . 105 0,50,0,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G14V|209|TIMM23|protein_coding|CODING|NM_006327.3|1|A),INTRON(MODIFIER||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|6|A) 0 0.5 1 0 . 0 . 0 1 0 28 0 0.00132156 0 . 0.304058 rs141118546,rs61847112 -0.693147 0.141701 105 N9D 209 Aac/Gac MODERATE 1 MISSENSE CODING TIMM23 C protein_coding NM_006327.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51623190 T C 0 83 0 . 0 . 0 . 0 . 0 . 1 1860 21031 2122 1345 757 9843 173 4931 2 3734 42044 4270 2700 1528 19712 346 9754 0.999405 0 . 0 . 100 0,48,0,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N9D|209|TIMM23|protein_coding|CODING|NM_006327.3|1|C),INTRON(MODIFIER||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|6|C) 0 0.5 1 0 . 0 . 0 1 0 29 0 0.00112853 0 . 0.454587 rs137912947 -0.693147 0.0132871 100 209 121 MODIFIER 1 CODING TIMM23 A protein_coding NM_006327.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51623335 C A 0 87 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.644773 0 . 0 . 24 0,10,0,14 START_GAINED(LOW||||209|TIMM23|protein_coding|CODING|NM_006327.3|1|A),UTR_5_PRIME(MODIFIER||121||209|TIMM23|protein_coding|CODING|NM_006327.3|1|A),INTRON(MODIFIER||||188|TIMM23B|protein_coding|CODING|NM_001290117.1|6|A) 0 0.5 1 0 . 0 . 0 . 0 29 0 0.679965 0 . 0.993166 rs369820569 -0.686358 0.881642 24 V25M 1341 Gtg/Atg MODERATE 2 MISSENSE CODING FAM21A A protein_coding NM_001005751.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51827934 G A 0 228 0 0.0681 0.3075 0.3213 0.3304 0.5189 0.3804 0.138636 0.369486 0.471111 2 840 38608 3423 2719 2078 23449 299 5800 2 4970 83504 8186 7112 3608 44850 580 14198 1 0 . 0 COSM427651 24 0,1,4,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V25M|1341|FAM21A|protein_coding|CODING|NM_001005751.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs55875820 -0.692352 0.310262 24 T379M 1341 aCg/aTg MODERATE 13 MISSENSE CODING FAM21A T protein_coding NM_001005751.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 51853633 C T 0 81 0 . 0 . 0 . 0 . 0 . 1 96 381 13 66 2 178 4 22 2 430 2144 70 188 10 1322 14 110 0.755683 0 . 0 COSM1474651 118 71,3,44,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T379M|1341|FAM21A|protein_coding|CODING|NM_001005751.2|13|T) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.00154571 0.0536025 0 0.985698 rs199520696 -0.693146 0.0374927 118 S164 780 tcA/tcC LOW 3 SILENT CODING ASAH2 G protein_coding NM_019893.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52002980 T G 0 222 0 0.4766 0.3043 0.1715 0.4276 0.0924 0.2566 0.4335 0.20898 0.0939535 1 4663 20946 1447 3646 674 6649 137 3730 2 10406 121322 11560 8628 6614 66698 908 16508 0.620366 0 . 0 . 101 34,16,28,10 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S164|780|ASAH2|protein_coding|CODING|NM_019893.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.891116 rs3739979 -0.693143 0.353885 101 A63 780 gcT/gcC LOW 2 SILENT CODING ASAH2 G protein_coding NM_019893.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52005153 A G 0 222 0 0.5719 0.3321 0.1888 0.4276 0.0934 0.2566 0.507036 0.234892 0.0954651 1 5444 21856 1486 3632 674 6728 139 3753 2 10392 120934 11486 8570 6606 66474 904 16502 0.813652 0 . 0 . 84 26,19,13,16 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A63|780|ASAH2|protein_coding|CODING|NM_019893.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925652 rs7097319 -0.693079 0.432176 84 413 1012 MODIFIER 11 CODING SGMS1 C protein_coding NM_147156.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52065890 T C 0 228 0 0.8971 0.7183 0.5965 0.7976 0.5298 0.6748 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,5,26 UTR_3_PRIME(MODIFIER||1012||413|SGMS1|protein_coding|CODING|NM_147156.3|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs14327 -0.69311 0.353707 31 N56 413 aaT/aaC LOW 7 SILENT CODING SGMS1 G protein_coding NM_147156.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52103707 A G 0 183 0 0.5212 0.502 0.6311 0.4861 0.5298 0.3722 0.539946 0.532831 0.529186 1 5526 63113 7793 4448 2801 35470 479 6596 2 10400 121352 11574 8632 6610 66718 908 16510 0.934091 0 . 0 . 24 4,8,2,9 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N56|413|SGMS1|protein_coding|CODING|NM_147156.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.689898 rs10763354 -0.676189 0.342371 24 602 6030 MODIFIER 15 CODING A1CF A protein_coding NM_001198819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52560459 G A 0 39.3 0 0.9985 0.9978 1 1 0.999 0.9918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||6030||602|A1CF|protein_coding|CODING|NM_001198819.1|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6479730 -0.453602 0.86 2 602 549 MODIFIER 15 CODING A1CF C protein_coding NM_001198819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 52565940 A C 0 9.7 0 0.5446 0.7814 0.8804 0.9663 0.839 0.7812 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||549||602|A1CF|protein_coding|CODING|NM_001198819.1|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386590842,rs4078160 -0.379885 0 1 616 2051 MODIFIER 1 CODING CSTF2T G protein_coding NM_015235.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53455408 A G 0 9.7 0 0.3048 0.1561 0.0591 0.1419 0.0795 0.1176 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2051||616|CSTF2T|protein_coding|CODING|NM_015235.2|1|G),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1045767 -0.379885 0 1 616 1897 MODIFIER 1 CODING CSTF2T C protein_coding NM_015235.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53455562 A C 0 9.7 0 0.0756 0.0917 0.0461 0.1409 0.0736 0.1135 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1897||616|CSTF2T|protein_coding|CODING|NM_015235.2|1|C),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs14168 -0.379885 0 1 616 335 MODIFIER 1 CODING CSTF2T A protein_coding NM_015235.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53457124 G A 0 61 0 0.7806 0.4379 0.3689 0.3621 0.2545 0.2904 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||335||616|CSTF2T|protein_coding|CODING|NM_015235.2|1|A),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11601 -0.511536 0.354794 3 R421 616 cgT/cgC LOW 1 SILENT CODING CSTF2T G protein_coding NM_015235.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53458047 A G 0 222 0 0.4501 0.2498 0.1196 0.2173 0.1551 0.2025 0.379256 0.219745 0.138023 1 4118 21258 1083 1703 1290 9384 176 3504 2 10406 121382 11576 8638 6614 66730 908 16510 0.676173 0 . 0 COSM146938 63 13,12,6,29 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R421|616|CSTF2T|protein_coding|CODING|NM_015235.2|1|G),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.571943 rs3740228 -0.693136 0.309283 63 R381 616 agG/agA LOW 1 SILENT CODING CSTF2T T protein_coding NM_015235.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53458167 C T 0 144 0 0.0764 0.0909 0.0461 0.1369 0.0736 0.1125 0.068089 0.0625096 0.0596512 1 770 9021 525 928 724 3907 85 2082 2 10382 121260 11572 8642 6612 66632 908 16512 0.852099 0 . 0 . 28 5,13,3,6 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R381|616|CSTF2T|protein_coding|CODING|NM_015235.2|1|T),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937241 rs3824686 -0.662043 0.862072 28 L104 616 ctT/ctC LOW 1 SILENT CODING CSTF2T G protein_coding NM_015235.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 53458998 A G 0 222 0 0.6831 0.3157 0.1455 0.2123 0.1571 0.2096 0.565819 0.284253 0.14 1 6055 23529 1191 1690 1304 9518 189 3582 2 10406 121396 11576 8650 6614 66730 908 16512 0.921994 0 . 0 COSM146939 58 27,7,14,6 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L104|616|CSTF2T|protein_coding|CODING|NM_015235.2|1|G),INTRON(MODIFIER||||686|PRKG1|protein_coding|CODING|NM_006258.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.848506 rs2292828 -0.692067 0.913762 58 L126 248 ctC/ctG LOW 4 SILENT CODING MBL2 C protein_coding NM_000242.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 54528266 G C 0 228 0 0.6399 0.7388 0.8559 0.7302 0.8032 0.7321 0.664396 0.770609 0.825 2 6711 90269 10309 6530 5265 52978 666 7810 2 10118 112256 11490 8574 6614 64392 826 10242 0 . 0 . COSM1348195 30 0,0,4,24 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L126|248|MBL2|protein_coding|CODING|NM_000242.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs930507 -0.693054 0.183794 30 P1534 1962 ccC/ccA LOW 35 SILENT CODING PCDH15 T protein_coding NM_001142763.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 55582905 G T 0 222 0 0.1755 0.2837 0.2277 0.7014 0.0447 0.2853 0.176577 0.0895878 0.0450105 1 1862 20745 4189 6410 467 3735 125 3957 2 10328 121102 11568 8648 6608 66536 908 16506 0.644387 2 benign 0 . 118 24,34,25,20 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P1534|1962|PCDH15|protein_coding|CODING|NM_001142763.1|35|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.365107 rs10825114 -0.693147 0.723045 118 D440A 1962 gAt/gCt MODERATE 12 MISSENSE CODING PCDH15 G protein_coding NM_001142763.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 55955444 T G 0 228 0 0.1346 0.3452 0.2536 0.8413 0.1312 0.4039 0.131412 0.131632 0.131744 2 1350 28879 3529 7290 974 9755 227 5754 2 10396 121328 11564 8644 6612 66694 908 16510 0 2 benign 0 . 85 0,0,53,21 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gAt/gCt|D440A|1962|PCDH15|protein_coding|CODING|NM_001142763.1|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4935502 -0.693147 0.359161 85 24 135 MODIFIER 1 CODING MTRNR2L5 T protein_coding NM_001190478.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 57359525 C T 0 228 0 0.8911 0.8289 0.804 0.9921 0.672 0.7556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,34,4 UTR_5_PRIME(MODIFIER||135||24|MTRNR2L5|protein_coding|CODING|NM_001190478.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11004927 -0.693143 0.633051 41 R187G 277 Agg/Ggg MODERATE 6 MISSENSE CODING ZWINT C protein_coding NM_007057.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 58118630 T C 0 222 0 0.8026 0.762 0.7781 0.8313 0.6382 0.7515 0.753064 0.672536 0.631279 1 7965 82514 9325 7088 3807 41436 607 12286 2 10376 121256 11566 8638 6612 66660 904 16500 0.657128 0 . 0 . 46 11,10,12,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R187G|277|ZWINT|protein_coding|CODING|NM_007057.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.918934 rs2241666 -0.692717 0.00665928 46 M349I 416 atG/atA MODERATE 6 MISSENSE CODING IPMK T protein_coding NM_152230.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 59956041 C T 0 222 0 0.1059 0.1136 0.0692 0.2808 0.0139 0.0859 0.0807989 0.0342919 0.0104651 1 901 6897 942 2703 285 818 44 1204 2 10388 121378 11578 8648 6614 66732 908 16510 0.9927 0 . 0 . 172 32,45,34,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M349I|416|IPMK|protein_coding|CODING|NM_152230.4|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94849 rs2275443 -0.693147 0.350749 172 108 140 MODIFIER 1 CODING CISD1 T protein_coding NM_018464.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60028894 C T 0 118 0 0.6936 0.3968 0.2493 0.4315 0.2087 0.2577 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996753 0 . 0 . 63 35,1,25,0 UTR_5_PRIME(MODIFIER||140||108|CISD1|protein_coding|CODING|NM_018464.4|1|T),UPSTREAM(MODIFIER||1200||416|IPMK|protein_coding|CODING|NM_152230.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999758 rs2251039 -0.692914 0.0633371 63 108 214 MODIFIER 3 CODING CISD1 T protein_coding NM_018464.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60047623 TG T 0 10.1 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,1 UTR_3_PRIME(MODIFIER||214||108|CISD1|protein_coding|CODING|NM_018464.4|3|T) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs56776648 -0.379885 0 2 246 1594 MODIFIER 7 CODING TFAM A protein_coding NM_003201.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60156428 G A 0 9.7 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1594||246|TFAM|protein_coding|CODING|NM_003201.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs191347684 -0.379885 0 1 246 1750 MODIFIER 7 CODING TFAM A protein_coding NM_003201.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60156584 G A 0 9.7 0 0.8903 0.5665 0.4611 0.4692 0.4423 0.4315 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1750||246|TFAM|protein_coding|CODING|NM_003201.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11006133 -0.379885 0 1 246 1768 MODIFIER 7 CODING TFAM C protein_coding NM_003201.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60156602 T C 0 9.7 0 0.0318 0.1048 0.0807 0.2867 0.0189 0.1217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1768||246|TFAM|protein_coding|CODING|NM_003201.2|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs74827573 -0.379885 0 1 974 LOW 18 CODING BICC1 T protein_coding NM_001080512.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60573753 G T 0 228 0 0.8132 0.7466 0.7867 0.749 0.7008 0.6728 0.808216 0.751192 0.721977 2 8370 90552 9384 6507 4795 48960 674 11862 2 10406 121242 11528 8574 6608 66706 908 16512 0 . 0 . 0 156 0,0,61,82 SPLICE_SITE_REGION+INTRON(LOW||||974|BICC1|protein_coding|CODING|NM_001080512.2|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9416746 -0.693147 0.0516677 156 L869 974 Tta/Cta LOW 19 SILENT CODING BICC1 C protein_coding NM_001080512.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60577393 T C 0 228 0 0.7678 0.7374 0.7781 0.755 0.7018 0.6861 0.763731 0.737967 0.724767 2 7902 90491 9330 6559 4788 49087 675 12150 2 10400 121060 11480 8554 6598 66616 908 16504 0 . 0 . 0 90 0,0,47,30 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L869|974|BICC1|protein_coding|CODING|NM_001080512.2|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4344442 -0.693147 0.0395532 90 S943P 974 Tcg/Ccg MODERATE 21 MISSENSE CODING BICC1 C protein_coding NM_001080512.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 60588553 T C 0 228 0 0.3759 0.6074 0.7334 0.7292 0.6909 0.6196 0.44099 0.620483 0.712442 2 4471 84853 9126 6402 4719 48316 645 11174 2 10396 121164 11526 8586 6592 66654 906 16504 0 . 0 . 0 74 0,0,46,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcg/Ccg|S943P|974|BICC1|protein_coding|CODING|NM_001080512.2|21|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4948550 -0.693147 0.0200698 74 V342L 376 Gtg/Ctg MODERATE 5 MISSENSE CODING PHYHIPL C protein_coding NM_032439.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61005244 G C 0 228 0 0.4781 0.7396 0.8703 0.8829 0.8688 0.7198 0.539265 0.739274 0.841744 2 5511 98356 10002 7857 5907 56495 745 11839 2 10388 121334 11572 8648 6612 66704 906 16504 0 . 0 . 0 32 0,0,16,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V342L|376|PHYHIPL|protein_coding|CODING|NM_032439.3|5|C),DOWNSTREAM(MODIFIER||645||585|FAM13C|protein_coding|CODING|NM_198215.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2452505 -0.693054 0.302429 32 376 LOW 5 CODING PHYHIPL G protein_coding NM_032439.3 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61007534 A G 0 228 0 0.4614 0.7352 0.8718 0.8829 0.8678 0.7198 0.514753 0.731355 0.842326 2 5243 97567 9942 7796 5893 56153 739 11801 2 10342 120644 11498 8580 6596 66278 900 16450 0 . 0 . 0 84 0,0,11,69 SPLICE_SITE_REGION(LOW||||376|PHYHIPL|protein_coding|CODING|NM_032439.3|5|G),UTR_3_PRIME(MODIFIER||2183||376|PHYHIPL|protein_coding|CODING|NM_032439.3|5|G),INTRON(MODIFIER||||585|FAM13C|protein_coding|CODING|NM_198215.3|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1459996,rs386532741 -0.693147 0.000353481 84 376 2183 MODIFIER 5 CODING PHYHIPL G protein_coding NM_032439.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61007534 A G 0 228 0 0.4614 0.7352 0.8718 0.8829 0.8678 0.7198 0.514753 0.731355 0.842326 2 5243 97567 9942 7796 5893 56153 739 11801 2 10342 120644 11498 8580 6596 66278 900 16450 0 . 0 . 0 84 0,0,11,69 SPLICE_SITE_REGION(LOW||||376|PHYHIPL|protein_coding|CODING|NM_032439.3|5|G),UTR_3_PRIME(MODIFIER||2183||376|PHYHIPL|protein_coding|CODING|NM_032439.3|5|G),INTRON(MODIFIER||||585|FAM13C|protein_coding|CODING|NM_198215.3|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1459996,rs386532741 -0.693147 0.000353481 84 509 195 MODIFIER 6 CODING SLC16A9 G protein_coding NM_194298.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61412335 A G 0 109 0 0.0212 0.3191 0.3674 0.5794 0.2217 0.5194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.899815 0 . 0 . 13 6,0,6,1 UTR_3_PRIME(MODIFIER||195||509|SLC16A9|protein_coding|CODING|NM_194298.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 1 0 0.470358 rs111182844,rs3763747 -0.636426 0.278975 13 T258K 509 aCa/aAa MODERATE 5 MISSENSE CODING SLC16A9 T protein_coding NM_194298.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61414011 G T 0 222 0 0.0696 0.345 0.3847 0.5804 0.2664 0.5276 0.106219 0.207827 0.259884 1 1037 40648 5468 4921 3076 18157 305 7684 2 10404 121398 11578 8648 6614 66736 908 16510 0.994147 0 . 0 . 138 46,24,36,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T258K|509|SLC16A9|protein_coding|CODING|NM_194298.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.790674 rs2242206 -0.693147 0.136586 138 509 25489 MODIFIER 1 CODING SLC16A9 C protein_coding NM_194298.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61469538 T C 0 9.7 0 0.7625 0.8413 0.8501 0.999 0.7584 0.864 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||25489||509|SLC16A9|protein_coding|CODING|NM_194298.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1171614 -0.379885 0 1 474 2618 MODIFIER 9 CODING CCDC6 T protein_coding NM_005436.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61550057 C T 0 228 0 0.9977 0.9425 0.9582 0.878 0.9155 0.9509 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 50 0,0,11,37 UTR_3_PRIME(MODIFIER||2618||474|CCDC6|protein_coding|CODING|NM_005436.4|9|T) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.99094 0 . rs3802695 -0.693147 0.095652 50 4377 15200 MODIFIER 44 CODING ANK3 T protein_coding NM_020987.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61787249 C T 0 9.7 0 0.5015 0.3113 0.2305 0.2133 0.2356 0.2904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||15200||4377|ANK3|protein_coding|CODING|NM_020987.3|44|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1050745 -0.379885 0 1 4377 13177 MODIFIER 44 CODING ANK3 A protein_coding NM_020987.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61789272 G A 0 222 0 0.0439 0.2802 0.3314 0.2222 0.497 0.3998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.285482 0 . 0 . 110 22,26,21,31 UTR_3_PRIME(MODIFIER||13177||4377|ANK3|protein_coding|CODING|NM_020987.3|44|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.763417 rs1049862 -0.693147 0.12129 110 K3123R 4377 aAg/aGg MODERATE 37 MISSENSE CODING ANK3 C protein_coding NM_020987.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61831271 T C 0 222 0 0.0204 0.1258 0.2104 0.0347 0.2724 0.1513 0.0512937 0.189912 0.26093 1 477 24501 1708 313 1653 17577 190 2583 2 10398 121356 11564 8652 6612 66718 908 16504 0.929422 3 likely-benign 0 . 216 70,36,64,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K3123R|4377|ANK3|protein_coding|CODING|NM_020987.3|37|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.75658 rs10821668 -0.693147 0.0926426 216 A2965 4377 gcT/gcC LOW 37 SILENT CODING ANK3 G protein_coding NM_020987.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61831744 A G 0 222 0 0.0204 0.126 0.2104 0.0347 0.2724 0.1524 0.0512937 0.190527 0.26186 1 480 24521 1709 312 1651 17580 190 2599 2 10392 121236 11520 8626 6608 66678 908 16504 0.986406 3 likely-benign 0 . 54 7,16,16,11 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2965|4377|ANK3|protein_coding|CODING|NM_020987.3|37|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999574 rs10740006 -0.693021 0.179067 54 F1460 4377 ttC/ttT LOW 36 SILENT CODING ANK3 A protein_coding NM_020987.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61840347 G A 0 222 0 0 0.0218 0 0.0972 0.001 0.0102 0.000226963 0.000384438 0.000465116 1 1 1214 8 886 3 33 5 278 2 10242 119694 11350 8500 6578 66072 886 16066 0.946991 0 . 0 . 67 6,31,3,22 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1460|4377|ANK3|protein_coding|CODING|NM_020987.3|36|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.47111 rs75052415 -0.692914 0.230004 67 T1015 4377 acG/acT LOW 27 SILENT CODING ANK3 A protein_coding NM_020987.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 61868716 C A 0 222 0 0.0272 0.1791 0.2262 0.0704 0.3221 0.316 0.0701316 0.239582 0.326395 1 619 32029 1602 524 2197 21508 275 5304 2 10404 121302 11560 8618 6606 66698 908 16508 0.902974 3 likely-benign 0 . 70 22,13,13,16 SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T1015|4377|ANK3|protein_coding|CODING|NM_020987.3|27|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.736435 rs3750800 -0.693079 0.162248 70 297 30 MODIFIER 8 CODING CDK1 G protein_coding NM_001786.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 62553763 A G 0 228 0 0.6762 0.7714 0.7867 0.8423 0.7942 0.7924 0.704133 0.732558 0.747145 2 7162 93934 8977 7361 5572 50885 712 13265 2 10364 120746 11430 8626 6582 66364 902 16478 0 . 0 . 0 87 0,0,42,39 UTR_3_PRIME(MODIFIER||30||297|CDK1|protein_coding|CODING|NM_001786.4|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1871446 -0.693147 0.0571138 87 696 1677 MODIFIER 12 CODING RHOBTB1 G protein_coding NM_001242359.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 62629563 A G 0 158 0 0.0015 0.0323 0.0187 0.0198 0.0139 0.1155 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.108368 0 . 0 . 26 9,7,7,3 UTR_3_PRIME(MODIFIER||1677||696|RHOBTB1|protein_coding|CODING|NM_001242359.1|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.987578 rs60499252 -0.670168 0.491369 26 696 130 MODIFIER 12 CODING RHOBTB1 A protein_coding NM_001242359.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 62631110 G A 0 187 0 0.1407 0.0689 0.0274 0.0198 0.0139 0.1084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.927743 0 . 0 . 22 6,5,6,4 UTR_3_PRIME(MODIFIER||130||696|RHOBTB1|protein_coding|CODING|NM_001242359.1|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.853271 rs61853326 -0.670168 0.258129 22 F163 208 ttT/ttC LOW 6 SILENT CODING C10orf107 C protein_coding NM_173554.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63520698 T C 0 222 0 0.8638 0.872 0.8948 0.9127 0.8022 0.8967 0.853609 0.81844 0.800419 1 8920 101174 10295 7880 5158 53340 760 14821 2 10400 121140 11442 8648 6596 66640 908 16506 0.667296 0 . 0 COSM1128027 105 27,21,24,21 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F163|208|C10orf107|protein_coding|CODING|NM_173554.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.571955 rs1992625 -0.693147 0.219731 105 1188 129 MODIFIER 1 CODING ARID5B C protein_coding NM_032199.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63661340 T C 0 127 0 0.0424 0.097 0.1599 0.128 0.0885 0.1033 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.982716 0 . 0 . 46 22,1,23,0 UTR_5_PRIME(MODIFIER||129||1188|ARID5B|protein_coding|CODING|NM_032199.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.419471 rs4509706 -0.692717 0.178819 46 T611M 1188 aCg/aTg MODERATE 10 MISSENSE CODING ARID5B T protein_coding NM_032199.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63851054 C T 0 198 0 0 0.0009984 0 0.005 0 0 0 7.6888e-05 0.000116279 1 0 68 2 62 0 2 0 2 2 10392 121292 11564 8626 6612 66694 906 16498 0.998393 0 . 0 . 41 10,16,6,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T611M|1188|ARID5B|protein_coding|CODING|NM_032199.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996388 rs117757404 -0.686358 0.106637 41 1188 176 MODIFIER 10 CODING ARID5B G protein_coding NM_032199.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63852965 C G 0 228 0 0.8079 0.7019 0.549 0.5268 0.8509 0.6943 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,4,8 UTR_3_PRIME(MODIFIER||176||1188|ARID5B|protein_coding|CODING|NM_032199.2|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4948506 -0.680642 0.259327 12 H462R 609 cAt/cGt MODERATE 12 MISSENSE CODING RTKN2 C protein_coding NM_145307.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63958112 T C 0 228 0 0.3132 0.5889 0.7017 0.8998 0.6362 0.5123 0.382887 0.553668 0.641163 2 3892 76906 9139 7954 4016 42495 555 8855 2 10402 121322 11558 8646 6608 66698 908 16502 0 . 0 . 0 127 0,0,34,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H462R|609|RTKN2|protein_coding|CODING|NM_145307.3|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3125734 -0.693147 6.36238e-05 127 609 LOW 8 CODING RTKN2 T protein_coding NM_145307.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63977010 TGAAAA T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 181 37,22,27,51 SPLICE_SITE_REGION+INTRON(LOW||||609|RTKN2|protein_coding|CODING|NM_145307.3|8|T) 0 0.5 1 3 0.0164835 0 1 0 . 0 60 0 0 1 0 . rs369452617 -0.693147 0.992554 181 V176 609 gtG/gtA LOW 6 SILENT CODING RTKN2 T protein_coding NM_145307.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 63995983 C T 0 228 0 0.9342 0.9069 0.8991 0.9881 0.8579 0.8425 0.91644 0.887419 0.872558 2 9574 106834 10491 8485 6009 57496 782 13997 2 10364 120328 11322 8574 6562 66146 896 16464 0 . 0 . 0 123 0,0,48,56 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V176|609|RTKN2|protein_coding|CODING|NM_145307.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3852448 -0.693147 0.00287485 123 609 169 MODIFIER 1 CODING RTKN2 G protein_coding NM_145307.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64028538 C G 0 130 0 0.1853 0.5351 0.6772 0.8829 0.5905 0.4918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,5 UTR_5_PRIME(MODIFIER||169||609|RTKN2|protein_coding|CODING|NM_145307.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1864836 -0.616816 0.250121 6 462 204 MODIFIER 8 CODING ZNF365 A protein_coding NM_199451.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64430265 C A 0 38.2 0 0.0174 0.1312 0.1686 0.1062 0.2843 0.1268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.150134 0 . 0 . 8 1,4,0,3 UTR_3_PRIME(MODIFIER||204||462|ZNF365|protein_coding|CODING|NM_199451.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.900802 rs729738 -0.511536 0.102722 8 462 241 MODIFIER 8 CODING ZNF365 A protein_coding NM_199451.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64430302 G A 0 54 0 0.0174 0.1312 0.1686 0.1062 0.2843 0.1268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,2,1,2 UTR_3_PRIME(MODIFIER||241||462|ZNF365|protein_coding|CODING|NM_199451.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs729739 -0.511536 0.833544 5 E64 270 gaG/gaA LOW 1 SILENT CODING ADO A protein_coding NM_032804.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64565011 G A 0 225 0 0.0053 0.0775 0.0605 0.1875 0.0795 0.0716 0.0129781 0.0516497 0.0714452 2 124 7992 536 1420 408 4425 55 1024 2 7970 108480 10912 8194 5494 59318 770 15822 1 0 . 0 . 47 0,1,43,3 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E64|270|ADO|protein_coding|CODING|NM_032804.5|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs61744064 -0.693147 0.00057506 47 270 940 MODIFIER 1 CODING ADO C protein_coding NM_032804.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64566572 T C 0 228 0 0.3812 0.3251 0.4179 0.4286 0.1461 0.2607 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,28,19 UTR_3_PRIME(MODIFIER||940||270|ADO|protein_coding|CODING|NM_032804.5|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10995312 -0.693147 0.378282 52 270 1732 MODIFIER 1 CODING ADO T protein_coding NM_032804.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64567364 C T 0 228 0 0.3812 0.3247 0.4179 0.4286 0.1461 0.2587 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 61 0,0,54,7 UTR_3_PRIME(MODIFIER||1732||270|ADO|protein_coding|CODING|NM_032804.5|1|T),DOWNSTREAM(MODIFIER||4392||476|EGR2|protein_coding|CODING|NM_000399.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1509964 -0.693147 0.194252 61 270 2306 MODIFIER 1 CODING ADO T protein_coding NM_032804.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64567938 C T 0 228 0 0.3805 0.3243 0.4164 0.4286 0.1461 0.2587 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,50,34 UTR_3_PRIME(MODIFIER||2306||270|ADO|protein_coding|CODING|NM_032804.5|1|T),DOWNSTREAM(MODIFIER||3818||476|EGR2|protein_coding|CODING|NM_000399.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9990 -0.693147 0.476131 95 476 874 MODIFIER 2 CODING EGR2 C protein_coding NM_000399.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64572093 T C 0 228 0 0.0053 0.0751 0.0591 0.1835 0.0785 0.0654 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 121 0,0,28,86 UTR_3_PRIME(MODIFIER||874||476|EGR2|protein_coding|CODING|NM_000399.3|2|C),DOWNSTREAM(MODIFIER||3854||270|ADO|protein_coding|CODING|NM_032804.5||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs61865882 -0.693147 0.0575483 121 476 287 MODIFIER 2 CODING EGR2 T protein_coding NM_000399.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64572680 A T 0 228 0 0.0053 0.0763 0.0605 0.1855 0.0775 0.0695 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,2,24 UTR_3_PRIME(MODIFIER||287||476|EGR2|protein_coding|CODING|NM_000399.3|2|T),DOWNSTREAM(MODIFIER||4441||270|ADO|protein_coding|CODING|NM_032804.5||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs61865883 -0.692976 0.571955 26 P209 476 ccG/ccA LOW 2 SILENT CODING EGR2 T protein_coding NM_000399.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64573771 C T 0 228 0 0.9486 0.986 0.9971 1 1 1 0.947798 0.982162 0.999767 2 9876 120836 11545 8654 6614 66734 906 16507 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 84 0,0,41,39 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P209|476|EGR2|protein_coding|CODING|NM_000399.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs224083 -0.693147 0.610351 84 R1328 2540 cgT/cgA LOW 10 SILENT CODING JMJD1C T protein_coding NM_032776.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 64967445 A T 0 228 0 0.9508 0.9868 0.9986 1 1 1 0.946068 0.983061 1 2 9281 120193 11546 8626 6612 66724 899 16505 2 9802 120750 11572 8626 6612 66728 900 16510 0 . 0 . 0 55 0,0,30,22 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgA|R1328|2540|JMJD1C|protein_coding|CODING|NM_032776.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1904294 -0.693147 0.954735 55 255 3938 MODIFIER 8 CODING REEP3 G protein_coding NM_001001330.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 65384567 A G 0 83 0 0.3949 0.5341 0.6023 0.5704 0.5616 0.6084 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,0 UTR_3_PRIME(MODIFIER||3938||255|REEP3|protein_coding|CODING|NM_001001330.2|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7089698 -0.453602 0.1 4 581 413 MODIFIER 1 CODING LRRTM3 C protein_coding NM_178011.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 68685929 G C 0 228 0 0.8018 0.9042 0.9323 0.9931 0.8966 0.9387 0 . 0 2 470 11533 178 216 2 3462 122 7083 2 572 12404 196 216 2 3708 130 7580 0 . 0 . 0 56 0,0,14,38 UTR_5_PRIME(MODIFIER||413||581|LRRTM3|protein_coding|CODING|NM_178011.4|1|C),INTRON(MODIFIER||||895|CTNNA3|protein_coding|CODING|NM_001127384.2|7|C),INTRAGENIC(MODIFIER|||||LOC101928961||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7902006 -0.693147 0.259217 56 198 55 MODIFIER 1 CODING DNAJC12 T protein_coding NM_021800.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69597824 C T 0 228 0 0 0.117 0.0922 0.4028 0.008 0.1104 0.00578035 0.00459921 0.00408548 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 0,0,11,57 UTR_5_PRIME(MODIFIER||55||198|DNAJC12|protein_coding|CODING|NM_021800.2|1|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2273772 -0.693147 0.054055 71 747 480 MODIFIER 9 CODING SIRT1 C protein_coding NM_012238.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69676830 T C 0 228 0 0 0.1156 0.0937 0.3998 0.008 0.1053 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 92 0,1,29,50 UTR_3_PRIME(MODIFIER||480||747|SIRT1|protein_coding|CODING|NM_012238.4|9|C),DOWNSTREAM(MODIFIER||4826||1057|HERC4|protein_coding|CODING|NM_022079.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs4746720 -0.693147 0.00970692 92 747 710 MODIFIER 9 CODING SIRT1 T protein_coding NM_012238.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69677060 C T 0 228 0 0.8646 0.9621 0.987 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,45,24 UTR_3_PRIME(MODIFIER||710||747|SIRT1|protein_coding|CODING|NM_012238.4|9|T),DOWNSTREAM(MODIFIER||4596||1057|HERC4|protein_coding|CODING|NM_022079.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs752578 -0.693147 0.0638067 81 S337 1057 agC/agT LOW 9 SILENT CODING HERC4 A protein_coding NM_022079.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69773841 G A 0 228 0 0.4039 0.5194 0.4741 0.8413 0.331 0.5695 0.384476 0.347839 0.32907 2 4105 51894 6858 7344 2681 21449 416 9041 2 10372 121196 11552 8650 6604 66616 906 16496 0 . 0 . 0 67 0,0,34,23 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S337|1057|HERC4|protein_coding|CODING|NM_022079.2|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs866255 -0.693147 0.161335 67 V962 1320 gtT/gtC LOW 14 SILENT CODING MYPN C protein_coding NM_001256267.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69948844 T C 0 228 0 0.9425 0.9846 0.9986 1 1 1 0.958239 0.985468 0.999419 2 9899 120792 11522 8642 6614 66697 906 16512 2 10394 121328 11542 8642 6614 66716 908 16512 0 2,1 benign,not-provided 0 . 92 0,0,21,63 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V962|1320|MYPN|protein_coding|CODING|NM_001256267.1|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10733838 -0.693147 0.219153 92 1320 683 MODIFIER 21 CODING MYPN C protein_coding NM_001256267.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69970895 G C 0 42.3 0 0.1452 0.3584 0.2997 0.6558 0.3439 0.3967 0 . 0 2 29 3832 19 87 0 961 40 2696 2 190 10774 92 132 0 2736 118 7506 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||683||1320|MYPN|protein_coding|CODING|NM_001256267.1|21|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs876489 -0.453602 0.92 2 152 419 MODIFIER 1 CODING ATOH7 G protein_coding NM_145178.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 69991853 A G 0 228 0 0.174 0.5599 0.5908 0.6806 0.7435 0.7464 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 79 1,0,23,50 UTR_5_PRIME(MODIFIER||419||152|ATOH7|protein_coding|CODING|NM_145178.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7916697 -0.693147 0.0135777 79 288 18 MODIFIER 10 CODING PBLD A protein_coding NM_022129.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70043916 G A 0 222 0 0.3222 0.2981 0.3847 0.2946 0.1978 0.3108 0.311167 0.232585 0.192326 1 3255 32188 5563 2866 1813 12907 231 5553 2 10400 121238 11564 8628 6614 66654 908 16470 0.684661 0 . 0 . 71 35,4,19,5 UTR_3_PRIME(MODIFIER||18||288|PBLD|protein_coding|CODING|NM_022129.3|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.968069 rs736535 -0.692831 0.421803 71 H257R 288 cAc/cGc MODERATE 10 MISSENSE CODING PBLD C protein_coding NM_022129.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70044031 T C 0 222 0 0.3275 0.2993 0.3847 0.2946 0.1968 0.3108 0.316387 0.234507 0.192558 1 3312 32268 5561 2868 1814 12920 231 5562 2 10402 121316 11564 8636 6614 66686 908 16506 0.84269 0 . 0 . 122 26,30,27,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H257R|288|PBLD|protein_coding|CODING|NM_022129.3|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984024 rs4142048 -0.693146 0.0409316 122 D117 288 gaT/gaC LOW 5 SILENT CODING PBLD G protein_coding NM_022129.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70051928 A G 0 222 0 0.5923 0.739 0.7089 0.8591 0.8211 0.7505 0.627553 0.749039 0.811279 1 6398 93476 7800 7328 4947 54137 700 12166 2 10380 121182 11530 8624 6598 66640 906 16504 0.527863 0 . 0 . 118 36,17,26,18 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D117|288|PBLD|protein_coding|CODING|NM_022129.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.547392 rs10823171 -0.693146 0.496904 118 346 1125 MODIFIER 10 CODING HNRNPH3 A protein_coding NM_012207.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70102936 T A 0 208 0 0.8215 0.9409 0.9669 1 0.9692 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,11,2 UTR_3_PRIME(MODIFIER||1125||346|HNRNPH3|protein_coding|CODING|NM_012207.2|10|A),DOWNSTREAM(MODIFIER||339||641|RUFY2|protein_coding|CODING|NM_017987.4||A),INTRAGENIC(MODIFIER|||||RUFY2||CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1162756 -0.683931 0.604715 13 641 1928 MODIFIER 18 CODING RUFY2 A protein_coding NM_017987.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70103597 C A 0 39.3 0 0.9864 0.9962 1 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1928||641|RUFY2|protein_coding|CODING|NM_017987.4|18|A),DOWNSTREAM(MODIFIER||644||346|HNRNPH3|protein_coding|CODING|NM_012207.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1162754 -0.453602 0.64 2 641 726 MODIFIER 18 CODING RUFY2 G protein_coding NM_017987.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70104799 A G 0 88 0 0.8752 0.9557 0.9712 1 0.9692 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,0 UTR_3_PRIME(MODIFIER||726||641|RUFY2|protein_coding|CODING|NM_017987.4|18|G),DOWNSTREAM(MODIFIER||1846||346|HNRNPH3|protein_coding|CODING|NM_012207.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1177364 -0.511536 0.873285 4 L631 641 Ctg/Ttg LOW 18 SILENT CODING RUFY2 A protein_coding NM_017987.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70105560 G A 0 228 0 0.7965 0.8031 0.7536 0.872 0.8618 0.7157 0.80676 0.83804 0.852637 2 7879 98501 8062 7319 5372 56841 745 12283 2 9804 120748 11574 8624 6612 66722 900 16512 0 . 0 . 0 85 0,0,58,20 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L631|641|RUFY2|protein_coding|CODING|NM_017987.4|18|A),DOWNSTREAM(MODIFIER||2607||346|HNRNPH3|protein_coding|CODING|NM_012207.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1162753 -0.693147 0.0522734 85 641 294 MODIFIER 1 CODING RUFY2 G protein_coding NM_017987.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70166913 T G 0 197 0 0.9902 0.9792 0.9841 0.9861 0.9583 0.9755 0.990244 0.971567 0.963487 2 230 9257 90 138 2 2275 106 6416 2 232 9598 94 138 2 2386 110 6636 0 . 0 . 0 8 0,0,4,3 UTR_5_PRIME(MODIFIER||294||641|RUFY2|protein_coding|CODING|NM_017987.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1.01283 0 . rs59831114 -0.636426 0.712723 8 332 561 MODIFIER 9 CODING SLC25A16 T protein_coding NM_152707.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70242628 C T 0 39.3 0 0.9743 0.9928 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||561||332|SLC25A16|protein_coding|CODING|NM_152707.3|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4529795 -0.453602 0.14 2 2136 30 MODIFIER 2 CODING TET1 T protein_coding NM_030625.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70332066 C T 0 228 0 0.3162 0.4836 0.428 0.5645 0.5716 0.5757 0.361833 0.478909 0.538911 2 3180 55563 4471 4373 3196 33132 391 6820 2 8694 101784 9338 7564 6020 58094 760 11314 0 . 0 . 0 56 0,0,37,14 UTR_5_PRIME(MODIFIER||30||2136|TET1|protein_coding|CODING|NM_030625.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3814177 -0.693147 0.29175 56 D162G 2136 gAc/gGc MODERATE 2 MISSENSE CODING TET1 G protein_coding NM_030625.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70332580 A G 0 228 0 0.0227 0.2586 0.2622 0.3919 0.3877 0.3047 0.0753518 0.286176 0.394186 2 725 39906 2496 3307 1828 26033 288 5229 2 10306 121240 11576 8640 6608 66698 908 16504 1 0 . 0 . 147 0,1,87,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D162G|2136|TET1|protein_coding|CODING|NM_030625.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10823229 -0.693147 0.10397 147 I1123M 2136 atA/atG MODERATE 4 MISSENSE CODING TET1 G protein_coding NM_030625.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70405855 A G 0 228 0 0.4508 0.6933 0.7781 0.8502 0.8091 0.68 0.499319 0.721206 0.834884 2 5079 93598 8343 7229 5292 54789 735 12131 2 10344 120976 11486 8624 6612 66534 904 16472 1 0 . 0 . 104 1,0,45,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I1123M|2136|TET1|protein_coding|CODING|NM_030625.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3998860 -0.693147 0.0749266 104 2136 900 MODIFIER 12 CODING TET1 T protein_coding NM_030625.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70452471 C T 0 158 0 0.7383 0.8908 0.9467 0.9742 0.9374 0.9233 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,1,8 UTR_3_PRIME(MODIFIER||900||2136|TET1|protein_coding|CODING|NM_030625.2|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5030882 -0.662043 0.75912 9 T160 1150 acG/acA LOW 6 SILENT CODING CCAR1 A protein_coding NM_018237.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70502288 G A 0 222 0 0.9297 0.8614 0.9222 0.7401 0.8618 0.8507 0.923059 0.881132 0.859651 1 9614 105123 10835 6385 6117 57247 804 14121 2 10406 121384 11576 8640 6614 66736 908 16504 0.557706 0 . 0 . 165 36,38,21,48 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T160|1150|CCAR1|protein_coding|CODING|NM_018237.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.378597 rs1300253,rs386526856 -0.693147 0.036731 165 Y153H 989 Tac/Cac MODERATE 2 MISSENSE CODING STOX1 C protein_coding NM_001130161.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70641860 T C 0 228 0 0.3835 0.6124 0.6081 0.9008 0.6412 0.5982 0.416304 0.57167 0.641685 2 3955 75244 5978 7799 4530 42474 576 9932 2 9800 120750 11574 8626 6612 66728 900 16510 0 255 other 0 . 68 0,0,24,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y153H|989|STOX1|protein_coding|CODING|NM_001130161.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1341667 -0.693147 0.967757 68 G763 989 ggA/ggG LOW 3 SILENT CODING STOX1 G protein_coding NM_001130161.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70645841 A G 0 222 0 0 0.0035942 0 0.0179 0 0 0 . 0 1 0 114 0 113 0 0 1 0 2 9794 120752 11574 8624 6614 66734 900 16512 0.738371 0 . 0 . 42 7,15,7,10 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G763|989|STOX1|protein_coding|CODING|NM_001130161.2|3|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.993603 rs386453668,rs78258245 -0.690438 0.00630028 42 Y539 737 taC/taT LOW 12 SILENT CODING DDX50 T protein_coding NM_024045.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70696713 C T 0 228 0 0.9834 0.9537 0.9568 0.9871 0.9066 0.9254 0.970722 0.929187 0.907907 2 10147 113160 11074 8592 6352 60748 851 15396 2 10404 121404 11578 8654 6614 66736 908 16510 0 . 0 . 0 58 0,0,42,8 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y539|737|DDX50|protein_coding|CODING|NM_024045.1|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5030895 -0.693147 0.127343 58 G628 737 ggA/ggG LOW 13 SILENT CODING DDX50 G protein_coding NM_024045.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70700944 A G 0 228 0 0.528 0.656 0.6326 0.9038 0.6412 0.6053 0.547435 0.61241 0.645698 2 5564 77147 6000 7835 4516 42538 581 10113 2 10372 121106 11494 8650 6604 66586 904 16496 0 . 0 . 0 83 0,0,20,56 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G628|737|DDX50|protein_coding|CODING|NM_024045.1|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5030900 -0.693147 4.69678e-07 83 783 LOW 4 CODING DDX21 G protein_coding NM_004728.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70725128 A G 0 228 0 0.1263 0.2847 0.3127 0.5605 0.1581 0.3252 0.12778 0.149085 0.16 2 1341 26535 2775 4622 1852 10673 236 5036 2 10324 120994 11554 8628 6606 66510 906 16466 0 . 0 . COSM146949 75 0,0,50,19 SPLICE_SITE_REGION+INTRON(LOW||||783|DDX21|protein_coding|CODING|NM_004728.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3898314 -0.693147 0.638199 75 R31Q 158 cGg/cAg MODERATE 2 MISSENSE CODING SRGN A protein_coding NM_002727.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70856852 G A 0 228 0 0.348 0.5897 0.6066 0.503 0.8499 0.726 0.421017 0.700446 0.843605 2 4184 91104 7027 4731 5716 56218 717 12511 2 10402 121306 11556 8632 6610 66696 908 16502 1 0 . 0 . 136 1,0,84,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R31Q|158|SRGN|protein_coding|CODING|NM_002727.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2229498 -0.693147 0.591452 136 158 189 MODIFIER 3 CODING SRGN C protein_coding NM_002727.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70864065 T C 0 112 0 0.6573 0.6945 0.6729 0.5308 0.8917 0.726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,0,6 UTR_3_PRIME(MODIFIER||189||158|SRGN|protein_coding|CODING|NM_002727.2|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12437 -0.616816 0.87834 6 T114 917 acG/acA LOW 3 SILENT CODING HKDC1 A protein_coding NM_025130.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70992635 G A 0 228 0 0.0219 0.0331 0.0014 0.1319 0 0.0031 0.018611 0.00699677 0.00104651 2 212 1823 59 1316 46 79 11 100 2 10394 121226 11570 8626 6610 66614 904 16508 1 0 . 0 . 132 0,1,55,67 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T114|917|HKDC1|protein_coding|CODING|NM_025130.3|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10998655 -0.693147 0.306286 132 T124I 917 aCa/aTa MODERATE 3 MISSENSE CODING HKDC1 T protein_coding NM_025130.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 70992664 C T 0 228 0 0.5545 0.5339 0.4539 0.7361 0.4135 0.4785 0.528824 0.453483 0.414884 2 5588 56273 5484 6643 3047 27565 436 7510 2 10378 121152 11564 8610 6610 66580 906 16504 0 . 0 . 0 119 0,0,43,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T124I|917|HKDC1|protein_coding|CODING|NM_025130.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs874556 -0.693147 0.0128912 119 W721R 917 Tgg/Cgg MODERATE 15 MISSENSE CODING HKDC1 C protein_coding NM_025130.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71018660 T C 0 228 0 0.9705 0.99 1 0.995 1 0.9939 0.981162 0.993541 0.999884 2 10147 120845 11545 8623 6610 66671 905 16344 2 10398 121262 11566 8652 6610 66682 908 16446 0 . 0 . 0 108 0,0,31,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W721R|917|HKDC1|protein_coding|CODING|NM_025130.3|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1111335 -0.693147 0.386809 108 917 516 MODIFIER 18 CODING HKDC1 G protein_coding NM_025130.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71027029 A G 0 228 0 0.9644 0.9906 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,26,3 UTR_3_PRIME(MODIFIER||516||917|HKDC1|protein_coding|CODING|NM_025130.3|18|G),UPSTREAM(MODIFIER||2727||921|HK1|protein_coding|CODING|NM_033497.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4746832 -0.693079 0.0509373 29 917 718 MODIFIER 18 CODING HKDC1 C protein_coding NM_025130.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71027231 G C 0 228 0 0.5113 0.4121 0.2666 0.3224 0.333 0.5552 0 . 0 2 278 6580 85 58 499 1628 67 3965 2 576 14320 188 208 1590 3954 184 7620 1 0 . 0 . 101 1,0,34,57 UTR_3_PRIME(MODIFIER||718||917|HKDC1|protein_coding|CODING|NM_025130.3|18|C),UPSTREAM(MODIFIER||2525||921|HK1|protein_coding|CODING|NM_033497.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs2611 -0.693147 0.00360656 101 L30 921 ctC/ctG LOW 5 SILENT CODING HK1 G protein_coding NM_033497.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71103597 C G 0 222 0 0.3873 0.2833 0.2334 0.122 0.3728 0.2526 0.393554 0.376211 0.367326 1 4110 39303 1771 1039 2360 25344 253 4426 2 10406 121394 11574 8648 6612 66734 908 16512 0.354326 0 . 0 . 128 25,40,33,22 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L30|921|HK1|protein_coding|CODING|NM_033497.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0467016 rs1133189 -0.693147 0.366055 128 K485 921 aaG/aaA LOW 13 SILENT CODING HK1 A protein_coding NM_033497.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71142420 G A 0 228 0 0.8896 0.7788 0.6254 0.6409 0.7763 0.8824 0.879483 0.820083 0.789651 2 9149 94399 6378 5724 5289 52518 715 14626 2 10356 120536 11374 8566 6566 66336 898 16440 0.732 0 . 0 . 133 1,1,72,53 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K485|921|HK1|protein_coding|CODING|NM_033497.2|13|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.832 rs748235 -0.693147 0.712175 133 M245K 398 aTg/aAg MODERATE 3 MISSENSE CODING TACR2 T protein_coding NM_001057.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71168685 A T 0 210 0 1 1 1 1 1 1 0 . 0 2 6978 86024 7255 6126 3707 48510 592 12856 2 6980 86034 7256 6126 3708 48514 592 12858 0 . 0 . 0 91 0,0,87,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M245K|398|TACR2|protein_coding|CODING|NM_001057.2|3|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs55953810 -0.693147 1.67822e-20 91 F199S 214 tTt/tCt MODERATE 2 MISSENSE CODING NEUROG3 G protein_coding NM_020999.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71332204 A G 0 94 0 0.2572 0.4299 0.611 0.3125 0.666 0.4131 0.394622 0.587754 0.678736 1 1458 40686 3839 1506 2378 25263 331 5911 2 3930 69432 6576 4120 3636 38156 558 12456 0.994135 3 likely-benign 0 . 16 6,4,1,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F199S|214|NEUROG3|protein_coding|CODING|NM_020999.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.620971 rs4536103 -0.616816 0.00873499 16 N36 121 aaC/aaT LOW 4 SILENT CODING C10orf35 T protein_coding NM_145306.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71392557 C T 0 228 0 0.5976 0.7085 0.7392 0.8909 0.665 0.6933 0.619437 0.650385 0.66624 2 6106 82698 9691 7686 4022 43509 573 11111 2 9772 119546 11524 8604 6542 65730 896 16478 0 . 0 . 0 48 0,0,16,27 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N36|121|C10orf35|protein_coding|CODING|NM_145306.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12020,rs386522500 -0.693146 0.497835 48 L81 121 ctT/ctC LOW 4 SILENT CODING C10orf35 C protein_coding NM_145306.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71392692 T C 0 228 0 0.6067 0.7111 0.7406 0.8919 0.665 0.6922 0.626646 0.653237 0.66686 2 6526 83928 9741 7734 4073 44142 580 11132 2 10398 121320 11576 8648 6594 66688 908 16508 0 . 0 . 0 54 0,0,41,11 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L81|121|C10orf35|protein_coding|CODING|NM_145306.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1052152 -0.693147 0.28503 54 121 210 MODIFIER 4 CODING C10orf35 G protein_coding NM_145306.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71393025 A G 0 147 0 0.6006 0.7093 0.7392 0.8909 0.666 0.6922 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||210||121|C10orf35|protein_coding|CODING|NM_145306.2|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1132075 -0.676189 0.574293 11 717 410 MODIFIER 1 CODING COL13A1 A protein_coding NM_001130103.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71561770 G A 0 9.7 0 0.8185 0.8894 0.9726 0.8423 0.9761 0.8855 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||717|COL13A1|protein_coding|CODING|NM_001130103.1|1|A),UTR_5_PRIME(MODIFIER||410||717|COL13A1|protein_coding|CODING|NM_001130103.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2704505,rs386572283 -0.379885 0 1 T86 717 acG/acA LOW 1 SILENT CODING COL13A1 A protein_coding NM_001130103.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71562437 G A 0 228 0 0.3139 0.5272 0.6571 0.7073 0.5686 0.4949 0.301906 0.463492 0.540777 2 3144 66702 7968 6187 3421 36733 495 8754 2 9798 120706 11576 8606 6614 66704 898 16510 1 0 . 0 COSM427823,COSM427824 125 1,0,62,50 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T86|717|COL13A1|protein_coding|CODING|NM_001130103.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10998973 -0.693147 0.0160555 125 717 LOW 5 CODING COL13A1 A protein_coding NM_001130103.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71640255 G A 0 213 0 0.2322 0.2919 0.2435 0.4613 0.164 0.364 0.24601 0.172382 0.139543 1 2232 25139 3591 3746 1404 8745 208 5213 2 8810 112558 10930 8406 5888 61918 814 15792 0.959425 0 . 0 COSM146950 33 10,2,14,3 SPLICE_SITE_REGION+INTRON(LOW||||717|COL13A1|protein_coding|CODING|NM_001130103.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.568527 rs2395272 -0.690438 0.0318091 33 Q233 717 caA/caG LOW 13 SILENT CODING COL13A1 G protein_coding NM_001130103.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71657272 A G 0 228 0 0.9849 0.9954 0.9971 1 0.999 1 0.988189 0.996148 1 2 9658 120589 11559 8626 6614 66727 898 16507 2 9808 120752 11570 8626 6614 66728 898 16508 0 . 0 . 0 100 0,0,44,40 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q233|717|COL13A1|protein_coding|CODING|NM_001130103.1|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1227746 -0.693147 0.0323265 100 T258 717 acG/acA LOW 14 SILENT CODING COL13A1 A protein_coding NM_001130103.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71658512 G A 0 228 0 0.9849 0.9954 0.9971 1 0.999 1 0.987688 0.996013 1 2 9581 119998 11513 8624 6602 66497 894 16287 2 9730 120160 11524 8624 6602 66498 894 16288 0 . 0 . 0 135 0,0,57,59 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T258|717|COL13A1|protein_coding|CODING|NM_001130103.1|14|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1227747 -0.693147 0.0597931 135 717 267 MODIFIER 40 CODING COL13A1 G protein_coding NM_001130103.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71718724 C G 0 222 0 0.1127 0.261 0.3372 0.2927 0.3151 0.319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.780059 0 . 0 . 115 25,31,27,24 UTR_3_PRIME(MODIFIER||267||717|COL13A1|protein_coding|CODING|NM_001130103.1|40|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.967053 rs1061966 -0.693147 0.0973985 115 A255 373 gcG/gcA LOW 7 SILENT CODING AIFM2 T protein_coding NM_001198696.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71876382 C T 0 228 0 0.3661 0.6006 0.6628 0.6409 0.7744 0.6534 0.446891 0.676841 0.794651 2 4507 87307 8149 5500 4989 52717 644 10801 2 10404 121374 11578 8640 6604 66730 906 16512 0.953846 0 . 0 . 74 2,0,37,28 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A255|373|AIFM2|protein_coding|CODING|NM_001198696.1|7|T),DOWNSTREAM(MODIFIER||4342||372|H2AFY2|protein_coding|CODING|NM_018649.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.623077 rs2394656 -0.693147 0.971739 74 566 1674 MODIFIER 4 CODING TYSND1 C protein_coding NM_173555.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71898006 A C 0 63 0 0.0333 0.0351 0.0072 0.0516 0.0368 0.0389 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1674||566|TYSND1|protein_coding|CODING|NM_173555.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs74738400 -0.453602 0.74 3 566 1612 MODIFIER 4 CODING TYSND1 C protein_coding NM_173555.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71898068 T C 0 31.9 0 0.0356 0.0357 0.0072 0.0516 0.0368 0.0389 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||1612||566|TYSND1|protein_coding|CODING|NM_173555.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs75054780 -0.453602 0.06 3 566 1325 MODIFIER 4 CODING TYSND1 T protein_coding NM_173555.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71898355 C T 0 9.7 0 0.9372 0.9441 0.9452 0.9871 0.9245 0.9284 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1325||566|TYSND1|protein_coding|CODING|NM_173555.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2394647 -0.379885 0 1 L258 566 ctG/ctT LOW 1 SILENT CODING TYSND1 A protein_coding NM_173555.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71905569 C A 0 55 0 0.1679 0.3866 0.513 0.5327 0.4115 0.4162 0.200133 0.331769 0.396451 1 74 4357 46 110 3 1227 51 2846 2 230 8812 90 182 4 2368 102 5836 0.875 0 . 0 . 6 2,0,1,3 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L258|566|TYSND1|protein_coding|CODING|NM_173555.3|1|A),DOWNSTREAM(MODIFIER||4392||198|SAR1A|protein_coding|CODING|NM_001142648.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0.861511 0 0 rs3750774 -0.556411 0.100421 6 G216 566 ggT/ggC LOW 1 SILENT CODING TYSND1 G protein_coding NM_173555.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71905695 A G 0 80 0 0.3775 0.3263 0.2911 0.0615 0.4791 0.3978 0.378654 0.408004 0.423049 1 845 9020 212 55 132 4671 78 3027 2 1840 20316 490 474 218 9216 182 7896 0.5 0 . 0 . 6 1,1,1,3 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G216|566|TYSND1|protein_coding|CODING|NM_173555.3|1|G),DOWNSTREAM(MODIFIER||4266||198|SAR1A|protein_coding|CODING|NM_001142648.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0 rs10999158 -0.556411 0.10325 6 P203L 566 cCa/cTa MODERATE 1 MISSENSE CODING TYSND1 A protein_coding NM_173555.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71905735 G A 0 92 0 0.0038 0.0276 0.0072 0.0526 0.0358 0.0399 0.00965074 0.0295807 0.0397514 1 34 1967 50 193 89 1306 12 283 2 2020 24106 782 1002 370 11588 204 8140 1 0 . 0 COSM1162271 6 1,0,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P203L|566|TYSND1|protein_coding|CODING|NM_173555.3|1|A),DOWNSTREAM(MODIFIER||4226||198|SAR1A|protein_coding|CODING|NM_001142648.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11549689 -0.556411 0.10325 6 A111 566 gcG/gcC LOW 1 SILENT CODING TYSND1 G protein_coding NM_173555.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71906010 C G 0 6.3 0 0.0265 0.0337 0.0072 0.0526 0.0368 0.0399 0.0183318 0.0230857 0.0252504 1 4 42 1 2 0 10 0 25 2 32 812 10 8 2 116 6 638 0 . 0 . 0 1 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A111|566|TYSND1|protein_coding|CODING|NM_173555.3|1|G),DOWNSTREAM(MODIFIER||3951||198|SAR1A|protein_coding|CODING|NM_001142648.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0 . 0 . rs11549688 -0.379885 0 1 T65A 566 Acc/Gcc MODERATE 1 MISSENSE CODING TYSND1 C protein_coding NM_173555.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71906150 T C 0 56 0 0.1679 0.3854 0.513 0.5327 0.4115 0.41 0.187852 0.323877 0.393808 1 1013 32574 3779 3216 1035 17867 215 5449 2 3234 62084 5500 5048 1952 34130 416 11804 0.577865 0 . 0 . 10 5,1,3,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T65A|566|TYSND1|protein_coding|CODING|NM_173555.3|1|C),DOWNSTREAM(MODIFIER||3811||198|SAR1A|protein_coding|CODING|NM_001142648.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.924584 1 0 0.115573 rs4746970 -0.511536 0.617121 10 198 1344 MODIFIER 8 CODING SAR1A T protein_coding NM_001142648.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71910888 C T 0 9.7 0 0.9773 0.9603 0.9568 0.998 0.9324 0.9294 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1344||198|SAR1A|protein_coding|CODING|NM_001142648.1|8|T),UPSTREAM(MODIFIER||4392||566|TYSND1|protein_coding|CODING|NM_173555.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7919647 -0.379885 0 1 198 613 MODIFIER 8 CODING SAR1A C protein_coding NM_001142648.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 71911619 T C 0 123 0 0.0023 0.0272 0.0072 0.0526 0.0358 0.0399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.552148 0 . 0 . 26 0,11,0,15 UTR_3_PRIME(MODIFIER||613||198|SAR1A|protein_coding|CODING|NM_001142648.1|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.996974 rs78341510 -0.688148 0.788874 26 R347S 430 Cgc/Agc MODERATE 4 MISSENSE CODING NPFFR1 T protein_coding NM_022146.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72014967 G T 0 104 0 0.0023 0.0298 0.0072 0.0556 0.0388 0.047 0.00747161 0.0254439 0.0333773 1 12 1662 32 120 53 1040 8 397 2 1012 17386 404 692 166 6972 144 7996 0.955563 0 . 0 . 17 8,3,3,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Agc|R347S|430|NPFFR1|protein_coding|CODING|NM_022146.4|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.23233 rs113487866 -0.616816 0.438189 17 184 31 MODIFIER 5 CODING LRRC20 T protein_coding NM_001278211.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72061079 C T 0 228 0 0.9592 0.9878 0.9928 1 0.998 1 0.960856 0.984284 0.996273 2 9287 116365 11492 8574 6586 64263 885 15278 2 9708 117120 11514 8574 6586 64572 888 15278 0 . 0 . 0 84 0,0,73,2 UTR_3_PRIME(MODIFIER||31||184|LRRC20|protein_coding|CODING|NM_001278211.1|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10740336 -0.693147 0.00266078 84 H74 120 caC/caT LOW 2 SILENT CODING EIF4EBP2 T protein_coding NM_004096.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72179746 C T 0 228 0 0.4266 0.5128 0.4712 0.7272 0.4612 0.4908 0.421698 0.466785 0.489884 2 4379 61002 4887 6268 3431 33598 439 8000 2 10402 121338 11570 8646 6614 66708 906 16492 0 . 0 . 0 94 0,0,61,23 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H74|120|EIF4EBP2|protein_coding|CODING|NM_004096.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1043098 -0.693147 0.0177615 94 120 2194 MODIFIER 3 CODING EIF4EBP2 G protein_coding NM_004096.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72183697 T G 0 165 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,18 UTR_3_PRIME(MODIFIER||2194||120|EIF4EBP2|protein_coding|CODING|NM_004096.4|3|G) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs1871596 -0.691153 0.239262 18 120 4816 MODIFIER 3 CODING EIF4EBP2 G protein_coding NM_004096.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72186319 C G 0 9.7 0 0.1415 0.355 0.4179 0.6369 0.4135 0.2485 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4816||120|EIF4EBP2|protein_coding|CODING|NM_004096.4|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7906903 -0.379885 0 1 120 5291 MODIFIER 3 CODING EIF4EBP2 C protein_coding NM_004096.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72186794 G C 0 63 0 0.0386 0.3261 0.4063 0.6369 0.4125 0.2485 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||5291||120|EIF4EBP2|protein_coding|CODING|NM_004096.4|3|C),DOWNSTREAM(MODIFIER||4898||347|NODAL|protein_coding|CODING|NM_018055.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7463 -0.453602 0.06 3 H165R 347 cAc/cGc MODERATE 2 MISSENSE CODING NODAL C protein_coding NM_018055.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72195439 T C 0 228 0 0.5113 0.6657 0.6816 0.9563 0.5308 0.7025 0.506128 0.538598 0.555233 2 5208 74629 7993 8191 3921 37684 520 11112 2 10348 120926 11526 8634 6590 66426 896 16506 0 2 benign 0 . 58 0,0,36,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H165R|347|NODAL|protein_coding|CODING|NM_018055.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1904589 -0.693147 0.167 58 V115 856 gtG/gtA LOW 4 SILENT CODING PALD1 A protein_coding NM_014431.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72289701 G A 0 222 0 0.0166 0.2181 0.2046 0.503 0.1491 0.2771 0.0419882 0.108258 0.142209 1 386 21810 2893 4137 1183 9080 201 3930 2 10326 120748 11538 8626 6594 66474 900 16290 0.988149 0 . 0 . 66 23,9,17,15 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V115|856|PALD1|protein_coding|CODING|NM_014431.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947329 rs2275059 -0.69312 0.342399 66 S141L 856 tCa/tTa MODERATE 4 MISSENSE CODING PALD1 T protein_coding NM_014431.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72289778 C T 0 222 0 0.0113 0.128 0.1816 0.2173 0.2147 0.0665 0.043123 0.146855 0.2 1 377 20708 1887 2011 2141 12863 170 1259 2 10242 115370 11510 8586 6604 65134 848 12446 0.7853 0 . 0 . 68 17,14,11,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S141L|856|PALD1|protein_coding|CODING|NM_014431.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98801 rs2275060 -0.693079 0.28257 68 R721C 856 Cgt/Tgt MODERATE 18 MISSENSE CODING PALD1 T protein_coding NM_014431.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72307101 C T 0 222 0 0.0151 0.2041 0.1686 0.5079 0.1481 0.229 0.0406264 0.107412 0.141628 1 381 20462 2196 4145 1045 9077 183 3435 2 10396 121282 11574 8598 6614 66682 908 16510 0.950649 0 . 0 . 165 17,58,18,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R721C|856|PALD1|protein_coding|CODING|NM_014431.2|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.915815 rs3740447 -0.693147 0.132561 165 Q762 856 caA/caG LOW 19 SILENT CODING PALD1 G protein_coding NM_014431.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72324143 A G 0 228 0 0.8411 0.9561 0.9885 1 0.998 1 0.881752 0.959326 0.99907 2 9100 119759 11461 8650 6614 66566 895 16473 2 10394 121250 11576 8650 6614 66630 906 16480 0 . 0 . 0 170 0,0,92,67 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q762|856|PALD1|protein_coding|CODING|NM_014431.2|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7093516 -0.693147 0.667342 170 856 453 MODIFIER 20 CODING PALD1 T protein_coding NM_014431.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72326942 C T 0 222 0 0.1104 0.1815 0.0677 0.4067 0.1113 0.1984 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.488485 0 . 0 . 133 60,9,48,7 UTR_3_PRIME(MODIFIER||453||856|PALD1|protein_coding|CODING|NM_014431.2|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.933083 rs3740442 -0.693147 0.431624 133 856 463 MODIFIER 20 CODING PALD1 C protein_coding NM_014431.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72326952 G C 0 228 0 0.9584 0.9886 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 142 0,0,110,23 UTR_3_PRIME(MODIFIER||463||856|PALD1|protein_coding|CODING|NM_014431.2|20|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1556613 -0.693147 0.199484 142 555 96 MODIFIER 3 CODING PRF1 T protein_coding NM_001083116.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72357713 C T 0 199 0 0.7927 0.5779 0.4928 0.6101 0.3877 0.5102 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.7501 0 . 0 . 41 20,1,17,2 UTR_3_PRIME(MODIFIER||96||555|PRF1|protein_coding|CODING|NM_001083116.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.316576 rs1889490 -0.69168 0.160645 41 H300 555 caC/caT LOW 3 SILENT CODING PRF1 A protein_coding NM_001083116.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72358577 G A 0 222 0 0.8381 0.6959 0.6427 0.7341 0.5885 0.6125 0.795279 0.662387 0.594302 1 8355 77140 7991 6611 4319 39103 594 10167 2 10404 121356 11564 8644 6606 66718 908 16512 0.908684 0 . 0 . 148 49,14,48,20 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H300|555|PRF1|protein_coding|CODING|NM_001083116.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.557963 rs885822 -0.693147 0.00198475 148 L593P 1226 cTg/cCg MODERATE 12 MISSENSE CODING ADAMTS14 C protein_coding NM_139155.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72500763 T C 0 222 0 0.6657 0.7999 0.7406 0.9097 0.8579 0.8507 0.708579 0.808319 0.859419 1 7324 101820 8004 7966 6153 57444 795 14134 2 10378 121224 11554 8648 6600 66630 906 16508 0.952031 0 . 0 . 107 29,16,26,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L593P|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988691 rs10823607 -0.693147 0.771079 107 S626 1226 tcC/tcG LOW 12 SILENT CODING ADAMTS14 G protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72500863 C G 0 222 0 0.6498 0.6671 0.5663 0.8571 0.6113 0.6237 0.650477 0.618099 0.601512 1 6821 75979 6358 7478 4496 39999 591 10236 2 10388 121060 11544 8636 6578 66506 902 16506 0.181822 0 . 0 . 86 11,23,12,31 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S626|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.950694 rs10999500 -0.693146 0.0572023 86 T658 1226 acG/acA LOW 13 SILENT CODING ADAMTS14 A protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72503344 G A 0 222 0 0.1641 0.3115 0.2089 0.5387 0.2167 0.4468 0.172492 0.198678 0.212093 1 1763 32435 2685 4496 1735 14495 248 7013 2 10348 120530 11550 8618 6542 66222 896 16354 0.992538 0 . 0 COSM1178414 84 28,13,23,11 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T658|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.907068 rs10999502 -0.693132 0.504267 84 C955 1226 tgC/tgT LOW 19 SILENT CODING ADAMTS14 T protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72513682 C T 0 222 0 0.5182 0.5252 0.6614 0.4395 0.5447 0.5061 0.507296 0.546156 0.566044 1 3196 40761 4148 2465 1501 23393 290 5768 2 5656 66514 5732 4708 2300 36854 468 10796 0.972053 0 . 0 . 104 15,31,14,29 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C955|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|19|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.21363 rs2587475 -0.693146 6.18843e-06 104 S1020N 1226 aGc/aAc MODERATE 20 MISSENSE CODING ADAMTS14 A protein_coding NM_139155.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72517830 G A 0 222 0 0.1543 0.2135 0.2262 0.37 0.1849 0.1524 0.174535 0.165539 0.16093 1 1792 22425 2658 3013 1526 10900 172 2364 2 10226 119184 11474 8590 6490 65750 888 15766 0.479514 0 . 0 . 193 55,29,53,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S1020N|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.280614 rs10999516 -0.693147 0.0337127 193 P1022 1226 ccC/ccT LOW 20 SILENT CODING ADAMTS14 T protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72517837 C T 0 222 0 0.5537 0.517 0.611 0.4018 0.5517 0.4836 0.536768 0.570967 0.588488 1 5492 67073 7580 3417 3270 38562 495 8257 2 10324 119606 11446 8560 6468 66006 882 15920 0.422978 0 . 0 COSM1348862 188 52,33,53,30 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1022|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.280638 rs6480463 -0.693147 0.0240056 188 E1052G 1226 gAa/gGa MODERATE 21 MISSENSE CODING ADAMTS14 G protein_coding NM_139155.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72518009 A G 0 222 0 0.1694 0.2181 0.2305 0.37 0.1849 0.1524 0.188379 0.17046 0.161279 1 1939 22835 2703 3026 1545 10996 179 2447 2 10390 120954 11562 8622 6470 66576 900 16434 0.762722 0 . 0 . 157 35,38,39,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E1052G|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|21|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.257578 rs4747096 -0.693147 0.0891232 157 A1134 1226 gcA/gcG LOW 22 SILENT CODING ADAMTS14 G protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72520330 A G 0 222 0 0.4637 0.386 0.3386 0.3075 0.3091 0.4744 0.399455 0.364217 0.346163 1 4219 44271 4412 2599 1636 23083 322 8000 2 10336 120888 11556 8602 6608 66508 904 16374 0.994552 0 . 0 . 58 24,8,13,12 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1134|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414734 rs10823615 -0.692914 0.479968 58 R1213 1226 agA/agG LOW 22 SILENT CODING ADAMTS14 G protein_coding NM_139155.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72520567 A G 0 222 0 0.3283 0.243 0.2709 0.1687 0.1899 0.2393 0.299138 0.253652 0.230349 1 3071 27878 3911 1237 799 14735 209 3916 2 10194 116182 11480 8586 6532 65136 858 13396 0.430328 0 . 0 . 69 16,27,11,12 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R1213|1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.690123 rs10823616 -0.692717 0.580911 69 1226 51 MODIFIER 22 CODING ADAMTS14 C protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72520660 T C 0 222 0 0.1664 0.2186 0.2305 0.371 0.1879 0.1554 0.185967 0.169512 0.161084 1 1687 19445 2460 2736 1336 9805 137 1284 2 8824 98352 9902 7654 5528 57490 684 8270 0.769773 0 . 0 . 93 34,14,33,10 UTR_3_PRIME(MODIFIER||51||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.588664 rs10999519 -0.693146 0.00602427 93 1226 347 MODIFIER 22 CODING ADAMTS14 G protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72520956 A G 0 228 0 0.7428 0.7462 0.8444 0.7718 0.7406 0.6605 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,3,51 UTR_3_PRIME(MODIFIER||347||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7074569 -0.693147 3.23978e-05 56 1226 531 MODIFIER 22 CODING ADAMTS14 C protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521140 G C 0 12.3 0 0.087 0.0697 0.1354 0.0675 0.001 0.0726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.166667 0 . 0 . 5 1,2,1,1 UTR_3_PRIME(MODIFIER||531||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs74437787 -0.453602 0.02 5 1226 546 MODIFIER 22 CODING ADAMTS14 A protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521155 G A 0 94 0 0.5643 0.616 0.4957 0.6974 0.6173 0.6861 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8 0 . 0 . 7 1,1,2,3 UTR_3_PRIME(MODIFIER||546||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1.01283 0 0.8 rs2587469,rs386570025 -0.590765 0.850373 7 1226 566 MODIFIER 22 CODING ADAMTS14 C protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521175 T C 0 104 0 0.584 0.6212 0.4942 0.6974 0.6173 0.6871 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.150134 0 . 0 . 8 2,1,3,2 UTR_3_PRIME(MODIFIER||566||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 0.900802 0 0.900802 rs2688769 -0.590765 0.25494 8 1226 700 MODIFIER 22 CODING ADAMTS14 G protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521309 C G 0 45.3 0 0.3911 0.4095 0.3963 0.4683 0.4394 0.3528 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,0,3 UTR_3_PRIME(MODIFIER||700||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3740440 -0.511536 0.137328 4 1226 1184 MODIFIER 22 CODING ADAMTS14 T protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521793 C T 0 222 0 0.0333 0.0427 0.1254 0.0675 0.001 0.0143 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.905711 0 . 0 . 156 61,17,43,23 UTR_3_PRIME(MODIFIER||1184||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.713342 rs12413137 -0.693147 0.0635269 156 1226 1185 MODIFIER 22 CODING ADAMTS14 A protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521794 G A 0 222 0 0.1672 0.2204 0.2305 0.3671 0.1839 0.1718 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.452228 0 . 0 . 161 46,25,59,17 UTR_3_PRIME(MODIFIER||1185||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.443427 rs3740437 -0.693147 0.0308714 161 1226 1305 MODIFIER 22 CODING ADAMTS14 G protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72521913 GA G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 120 4,44,5,55 UTR_3_PRIME(MODIFIER||1305||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|G) 0 0.5 1 61 0.508333 0 1 0 . 0 60 0 0 1 0 . rs3832690 -0.693147 0.133899 120 1226 1479 MODIFIER 22 CODING ADAMTS14 T protein_coding NM_139155.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72522088 C T 0 86 0 0.7126 0.7037 0.6354 0.7649 0.6233 0.7597 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||1479||1226|ADAMTS14|protein_coding|CODING|NM_139155.2|22|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11572 -0.556411 0.421803 4 R237Q 351 cGg/cAg MODERATE 8 MISSENSE CODING TBATA T protein_coding NM_152710.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72535007 C T 0 222 0 0.7852 0.7716 0.6888 0.627 0.8777 0.8517 0.79596 0.863525 0.89814 1 8207 100017 7012 5008 5593 59659 740 13798 2 10396 121310 11560 8624 6602 66708 908 16512 0.988149 0 . 0 . 72 13,19,15,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R237Q|351|TBATA|protein_coding|CODING|NM_152710.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943069 rs2254174 -0.69312 0.459645 72 E171 351 gaG/gaA LOW 7 SILENT CODING TBATA T protein_coding NM_152710.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72537086 C T 0 222 0 0.0492 0.0929 0.2104 0.1825 0.0368 0.0337 0.0449387 0.0342919 0.0288372 1 460 8775 3790 1703 230 1932 61 599 2 10240 119432 11506 8580 6472 66042 890 15702 0.932593 0 . 0 . 91 20,31,11,24 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E171|351|TBATA|protein_coding|CODING|NM_152710.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994452 rs386595074,rs4747099 -0.693136 0.450447 91 I188 568 atC/atT LOW 7 SILENT CODING SGPL1 T protein_coding NM_003901.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72619205 C T 0 228 0 0.944 0.9848 0.9971 1 1 1 0.948706 0.982547 0.999884 2 9901 120842 11550 8654 6614 66720 906 16497 2 10406 121386 11576 8654 6614 66728 908 16500 0 . 0 . 0 183 0,0,84,72 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I188|568|SGPL1|protein_coding|CODING|NM_003901.3|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs827255 -0.693147 0.315705 183 A241 568 gcC/gcT LOW 9 SILENT CODING SGPL1 T protein_coding NM_003901.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72629567 C T 0 189 0 0.0492 0.0687 0.0807 0.1369 0.0517 0.0337 0.0426691 0.0398278 0.0383721 1 482 6460 1505 1213 112 2509 49 590 2 10382 121012 11558 8628 6598 66572 902 16372 0.695229 0 . 0 . 61 24,3,28,1 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A241|568|SGPL1|protein_coding|CODING|NM_003901.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.87512 rs827249 -0.693079 0.104473 61 V314 568 gtC/gtT LOW 11 SILENT CODING SGPL1 T protein_coding NM_003901.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72631626 C T 0 222 0 0.0779 0.1605 0.1758 0.2163 0.2316 0.1309 0.0907853 0.164463 0.202209 1 962 21417 2310 1923 1119 13022 153 1928 2 10406 121386 11578 8648 6614 66724 908 16508 0.987258 0 . 0 . 131 47,12,46,11 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V314|568|SGPL1|protein_coding|CODING|NM_003901.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.774353 rs865832 -0.693147 0.184109 131 568 2529 MODIFIER 15 CODING SGPL1 T protein_coding NM_003901.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72639621 C T 0 222 0 0.3585 0.2808 0.232 0.2937 0.1819 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.747688 0 . 0 . 99 40,5,37,8 UTR_3_PRIME(MODIFIER||2529||568|SGPL1|protein_coding|CODING|NM_003901.3|15|T),DOWNSTREAM(MODIFIER||3644||104|PCBD1|protein_coding|CODING|NM_000281.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.154486 rs877034 -0.693147 0.12172 99 104 36 MODIFIER 4 CODING PCBD1 T protein_coding NM_000281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 72643671 C T 0 222 0 0.73 0.7654 0.7608 0.7817 0.7157 0.8507 0.72946 0.728314 0.727727 1 6262 74241 6709 5645 3817 39858 572 11378 2 8418 95570 8628 7168 4722 52676 722 13236 0.946448 0 . 0 . 138 49,11,43,18 UTR_3_PRIME(MODIFIER||36||104|PCBD1|protein_coding|CODING|NM_000281.3|4|T),DOWNSTREAM(MODIFIER||2739||568|SGPL1|protein_coding|CODING|NM_003901.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.615645 rs9712 -0.693147 0.00379822 138 A136 945 gcG/gcA LOW 3 SILENT CODING UNC5B A protein_coding NM_170744.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73044580 G A 0 222 0 0.4289 0.498 0.4611 0.3879 0.6948 0.5286 0.46936 0.617869 0.693954 1 4819 75207 5216 3267 4888 46532 583 9902 2 10350 120816 11546 8600 6594 66476 904 16346 0.81806 0 . 0 . 68 15,21,11,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A136|945|UNC5B|protein_coding|CODING|NM_170744.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.654678 rs12770025 -0.692831 0.0021371 68 L860 945 ctG/ctC LOW 16 SILENT CODING UNC5B C protein_coding NM_170744.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73057755 G C 0 222 0 0.0492 0.0659 0.0072 0.1786 0.0089 0.0726 0.04335 0.0282946 0.0205814 1 480 4784 150 1445 113 1548 30 1018 2 10396 121258 11568 8610 6612 66658 906 16508 0.996139 0 . 0 . 89 16,31,14,19 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L860|945|UNC5B|protein_coding|CODING|NM_170744.4|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.558138 rs10823720 -0.693127 0.0047262 89 475 LOW 3 CODING SLC29A3 G protein_coding NM_018344.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73104056 A G 0 228 0 0.8487 0.8143 0.8674 0.6657 0.9036 0.7914 0.848843 0.87944 0.895116 2 8883 105220 10194 5962 5737 59913 776 13755 2 10400 121308 11562 8628 6604 66700 906 16508 0 3 likely-benign 0 . 78 0,0,30,37 SPLICE_SITE_REGION+INTRON(LOW||||475|SLC29A3|protein_coding|CODING|NM_018344.5|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2243540 -0.693147 0.00034469 78 S158F 475 tCc/tTc MODERATE 4 MISSENSE CODING SLC29A3 T protein_coding NM_018344.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73111408 C T 0 228 0 0.2943 0.4798 0.4957 0.4325 0.7644 0.4755 0.366546 0.618253 0.747209 2 3646 77481 5385 3840 4874 50382 621 8733 2 10406 121362 11570 8624 6612 66732 908 16510 0.689368 3 likely-benign 0 . 128 1,2,70,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S158F|475|SLC29A3|protein_coding|CODING|NM_018344.5|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.921731 rs780668 -0.693147 0.0386043 128 T238 475 acT/acC LOW 5 SILENT CODING SLC29A3 C protein_coding NM_018344.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73115941 T C 0 228 0 0.8964 0.7808 0.6599 0.6657 0.8847 0.7219 0.889242 0.889051 0.888954 2 9257 100616 7208 5912 5684 58951 772 12832 2 10396 121312 11556 8622 6604 66720 906 16508 0 3 likely-benign 0 . 98 0,0,44,48 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T238|475|SLC29A3|protein_coding|CODING|NM_018344.5|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2252997 -0.693147 0.0521155 98 V239I 475 Gtc/Atc MODERATE 5 MISSENSE CODING SLC29A3 A protein_coding NM_018344.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73115942 G A 0 228 0 0.8253 0.7602 0.647 0.6657 0.8847 0.7219 0.80867 0.861602 0.888721 2 8426 99694 7174 5904 5684 58920 768 12818 2 10396 121320 11556 8634 6606 66712 906 16510 0 3 likely-benign 0 . 98 0,0,44,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V239I|475|SLC29A3|protein_coding|CODING|NM_018344.5|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2252996 -0.693147 0.0521155 98 I326V 475 Atc/Gtc MODERATE 6 MISSENSE CODING SLC29A3 G protein_coding NM_018344.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73121913 A G 0 228 0 0.9425 0.7927 0.6412 0.6964 0.8608 0.727 0.921925 0.89228 0.877093 2 9612 100096 7172 6126 5648 57905 761 12872 2 10402 121384 11576 8644 6614 66732 908 16508 0 3 likely-benign 0 . 68 0,0,42,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I326V|475|SLC29A3|protein_coding|CODING|NM_018344.5|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2487068 -0.693147 0.604613 68 G336 475 ggT/ggC LOW 6 SILENT CODING SLC29A3 C protein_coding NM_018344.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73121945 T C 0 228 0 0.7466 0.7538 0.6614 0.7153 0.8976 0.7209 0.766909 0.8666 0.917674 2 7870 100760 6957 6230 5532 60633 767 12771 2 10400 121372 11574 8630 6614 66736 908 16510 0 3 likely-benign 0 . 67 0,0,39,23 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G336|475|SLC29A3|protein_coding|CODING|NM_018344.5|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1084004 -0.693147 0.122776 67 V122 3354 gtT/gtC LOW 6 SILENT CODING CDH23 C protein_coding NM_022124.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73270906 T C 0 222 0 0.9856 0.7346 0.5 0.7758 0.6889 0.5665 0.932954 0.749597 0.660881 1 9181 81157 5123 6687 4852 44733 613 9968 2 9808 120756 11574 8612 6614 66736 900 16512 0.959662 2,2 benign,benign 0 . 103 28,17,28,22 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V122|3354|CDH23|protein_coding|CODING|NM_022124.5|6|C),INTRAGENIC(MODIFIER|||||LOC102723377||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999937 rs3802720 -0.693147 0.0172097 103 G490A 3354 gGc/gCc MODERATE 14 MISSENSE CODING CDH23 C protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73434888 G C 0 222 0 0.0113 0.1853 0.1455 0.2887 0.1948 0.3323 0.0354424 0.121193 0.163754 1 322 24074 2041 2677 2151 11957 192 4734 2 9782 120488 11542 8600 6600 66600 894 16470 0.340843 2 benign 0 . 69 23,14,13,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G490A|3354|CDH23|protein_coding|CODING|NM_022124.5|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.898058 rs1227049 -0.692717 0.277567 69 133 3000 MODIFIER 2 CODING C10orf105 A protein_coding NM_001164375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73472693 G A 0 222 0 0.1248 0.1597 0.1398 0.1815 0.1958 0.1616 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996422 0 . 0 . 30 3,9,9,9 UTR_3_PRIME(MODIFIER||3000||133|C10orf105|protein_coding|CODING|NM_001164375.2|2|A),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|27|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.817411 rs11599901 -0.691153 0.880155 30 133 2825 MODIFIER 2 CODING C10orf105 G protein_coding NM_001164375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73472868 C G 0 222 0 0.6536 0.4499 0.3602 0.4544 0.2535 0.4356 0.579909 0.346194 0.243209 1 4140 31399 3857 3063 771 13077 240 6251 2 6458 77844 7568 5984 4138 40002 602 13092 0.805841 0 . 0 . 110 45,19,25,11 UTR_3_PRIME(MODIFIER||2825||133|C10orf105|protein_coding|CODING|NM_001164375.2|2|G),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|27|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.288728 rs2394838 -0.693139 0.0212023 110 133 2811 MODIFIER 2 CODING C10orf105 T protein_coding NM_001164375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73472882 C T 0 222 0 0.6278 0.4413 0.3559 0.4544 0.2505 0.4325 0.570205 0.345496 0.246479 1 4420 33716 4239 3355 810 13994 248 6650 2 7200 91460 9146 6934 4914 48312 692 14262 0.936265 0 . 0 . 117 43,22,28,12 UTR_3_PRIME(MODIFIER||2811||133|C10orf105|protein_coding|CODING|NM_001164375.2|2|T),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|27|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.42776 rs2166631 -0.693145 0.0762417 117 N1351D 3354 Aac/Gac MODERATE 31 MISSENSE CODING CDH23 G protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73492079 A G 0 228 0 0.7262 0.7821 0.7104 0.8194 0.8151 0.8364 0.791063 0.812899 0.823655 2 5952 78310 6806 5487 3986 44287 604 11188 2 7622 95976 8446 6474 5222 53568 740 13904 0 2,2 benign,benign 0 . 116 0,0,47,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N1351D|3354|CDH23|protein_coding|CODING|NM_022124.5|31|G),INTRAGENIC(MODIFIER|||||C10orf105||CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1227065,rs386523539 -0.693147 0.0433554 116 A1575T 3354 Gcc/Acc MODERATE 36 MISSENSE CODING CDH23 A protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73501556 G A 0 228 0 0.5582 0.7288 0.6902 0.8254 0.7903 0.8241 0.633941 0.741081 0.796028 2 5607 89611 8608 6989 4758 50391 666 12592 2 8934 115590 10998 8406 6360 64042 860 15990 0 2,2 benign,benign 0 . 108 0,0,56,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1575T|3354|CDH23|protein_coding|CODING|NM_022124.5|36|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1227051 -0.693147 0.0225532 108 311 3124 MODIFIER 7 CODING C10orf54 G protein_coding NM_022153.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73507886 A G 0 83 0 0.1634 0.1811 0.1297 0.1319 0.1441 0.3303 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,2,2 UTR_3_PRIME(MODIFIER||3124||311|C10orf54|protein_coding|CODING|NM_022153.1|7|G),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs745577 -0.556411 0.292086 6 311 2219 MODIFIER 7 CODING C10orf54 C protein_coding NM_022153.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73508791 T C 0 63 0 0.1293 0.406 0.4395 0.7044 0.4394 0.4141 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 7 0,3,0,4 UTR_3_PRIME(MODIFIER||2219||311|C10orf54|protein_coding|CODING|NM_022153.1|7|C),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.810265 rs748113 -0.556411 0.0308934 7 311 1305 MODIFIER 7 CODING C10orf54 A protein_coding NM_022153.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73509705 G A 0 31.3 0 0.2602 0.2959 0.2594 0.4177 0.2744 0.2669 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1305||311|C10orf54|protein_coding|CODING|NM_022153.1|7|A),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs748504 -0.453602 0.22 2 311 1244 MODIFIER 7 CODING C10orf54 C protein_coding NM_022153.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73509766 T C 0 10.7 0 0.5333 0.3654 0.2939 0.4355 0.2684 0.2168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1244||311|C10orf54|protein_coding|CODING|NM_022153.1|7|C),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs748505 -0.453602 0.28 2 D187E 311 gaT/gaG MODERATE 3 MISSENSE CODING C10orf54 C protein_coding NM_022153.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73520632 A C 0 228 0 0.9849 0.8928 0.7954 0.7827 0.9016 0.9417 0.969587 0.922805 0.898837 2 10122 107625 9386 6991 5346 59481 814 15485 2 10406 121400 11578 8648 6614 66734 908 16512 1 0 . 0 . 220 1,0,95,101 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D187E|311|C10orf54|protein_coding|CODING|NM_022153.1|3|C),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3747869 -0.693147 0.0120395 220 L7P 311 cTg/cCg MODERATE 1 MISSENSE CODING C10orf54 G protein_coding NM_022153.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73533177 A G 0 222 0 0.2557 0.3299 0.2997 0.1895 0.4264 0.4969 0.273355 0.374553 0.426126 1 1934 38663 2450 1469 1881 23220 297 7412 2 5602 82518 6810 5472 4128 45960 618 13928 0.39459 0 . 0 . 87 13,36,6,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L7P|311|C10orf54|protein_coding|CODING|NM_022153.1|1|G),INTRON(MODIFIER||||3354|CDH23|protein_coding|CODING|NM_022124.5|36|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.896451 rs3747862 -0.692976 0.0755909 87 V1675I 3354 Gtc/Atc MODERATE 37 MISSENSE CODING CDH23 A protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73537614 G A 0 222 0 0.0083 0.1322 0.1225 0.1518 0.2177 0.1984 0.0389877 0.14097 0.193224 1 322 21562 1597 1380 1538 13313 155 3257 2 9820 120530 11534 8606 6604 66566 898 16502 0.806116 2|1 benign|not-provided 0 COSM146951 218 59,64,43,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1675I|3354|CDH23|protein_coding|CODING|NM_022124.5|37|A),UPSTREAM(MODIFIER||4277||311|C10orf54|protein_coding|CODING|NM_022153.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916814 rs17712523 -0.693147 0.0945753 218 T1999S 3354 aCc/aGc MODERATE 44 MISSENSE CODING CDH23 G protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73550117 C G 0 222 0 0.2625 0.3452 0.317 0.1597 0.499 0.5102 0.270206 0.414431 0.486098 1 2766 51084 3183 1400 2776 31976 411 8572 2 9556 119038 11396 8536 6378 65854 886 16432 0.999651 2 benign 0 . 76 15,29,9,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aGc|T1999S|3354|CDH23|protein_coding|CODING|NM_022124.5|44|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.459039 rs11592462 -0.692717 0.059508 76 E2044K 3354 Gag/Aag MODERATE 45 MISSENSE CODING CDH23 A protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73550969 G A 0 222 0 0.261 0.3327 0.3473 0.5288 0.2763 0.2751 0.270473 0.265481 0.262925 1 2564 35774 5011 4420 2294 17471 258 3756 2 9054 115004 10978 8414 6200 63966 850 15542 0.994017 2|2 benign|benign 0 COSM146953 113 33,14,25,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2044K|3354|CDH23|protein_coding|CODING|NM_022124.5|45|A),UPSTREAM(MODIFIER||4559||1114|CDH23|protein_coding|CODING|NM_001171933.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.441241 rs10466026 -0.693147 0.35877 113 R2358Q 3354 cGg/cAg MODERATE 49 MISSENSE CODING CDH23 A protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73558886 G A 0 222 0 0.267 0.3413 0.3501 0.5298 0.2783 0.3057 0.263289 0.262008 0.261393 1 2648 37017 5190 4513 2330 17799 268 4269 2 9806 120154 11546 8608 6610 66508 892 16184 0.164079 2|2 benign|benign 0 COSM146954 157 53,18,46,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R2358Q|3354|CDH23|protein_coding|CODING|NM_022124.5|49|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R118Q|1114|CDH23|protein_coding|CODING|NM_001171933.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.321375 rs4747194 -0.693147 0.0468018 157 R118Q 1114 cGg/cAg MODERATE 4 MISSENSE CODING CDH23 A protein_coding NM_001171933.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73558886 G A 0 222 0 0.267 0.3413 0.3501 0.5298 0.2783 0.3057 0.263289 0.262008 0.261393 1 2648 37017 5190 4513 2330 17799 268 4269 2 9806 120154 11546 8608 6610 66508 892 16184 0.164079 2|2 benign|benign 0 COSM146954 157 53,18,46,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R2358Q|3354|CDH23|protein_coding|CODING|NM_022124.5|49|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R118Q|1114|CDH23|protein_coding|CODING|NM_001171933.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.321375 rs4747194 -0.693147 0.0468018 157 P2380L 3354 cCg/cTg MODERATE 49 MISSENSE CODING CDH23 T protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73558952 C T 0 222 0 0.2443 0.3283 0.3473 0.5298 0.2744 0.2761 0.24006 0.254335 0.261241 1 2431 36148 5159 4516 2326 17668 259 3789 2 9798 120620 11560 8586 6608 66666 896 16506 0.97334 2|2 benign|benign 0 COSM146955 171 50,30,43,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P2380L|3354|CDH23|protein_coding|CODING|NM_022124.5|49|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P140L|1114|CDH23|protein_coding|CODING|NM_001171933.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.206972 rs4747195 -0.693147 0.0236594 171 P140L 1114 cCg/cTg MODERATE 4 MISSENSE CODING CDH23 T protein_coding NM_001171933.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73558952 C T 0 222 0 0.2443 0.3283 0.3473 0.5298 0.2744 0.2761 0.24006 0.254335 0.261241 1 2431 36148 5159 4516 2326 17668 259 3789 2 9798 120620 11560 8586 6608 66666 896 16506 0.97334 2|2 benign|benign 0 COSM146955 171 50,30,43,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P2380L|3354|CDH23|protein_coding|CODING|NM_022124.5|49|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P140L|1114|CDH23|protein_coding|CODING|NM_001171933.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.206972 rs4747195 -0.693147 0.0236594 171 A2524 3354 gcG/gcA LOW 52 SILENT CODING CDH23 A protein_coding NM_022124.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73562744 G A 0 222 0 0.2307 0.3285 0.3444 0.5298 0.2783 0.2935 0.223762 0.24883 0.260953 1 2224 36418 5185 4486 2331 17804 268 4120 2 9802 120644 11556 8590 6610 66676 898 16512 0.967192 2|2 benign|benign 0 COSM146956 96 24,22,26,18 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2524|3354|CDH23|protein_coding|CODING|NM_022124.5|52|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A284|1114|CDH23|protein_coding|CODING|NM_001171933.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937528 rs10823849 -0.693146 0.0440272 96 A284 1114 gcG/gcA LOW 7 SILENT CODING CDH23 A protein_coding NM_001171933.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73562744 G A 0 222 0 0.2307 0.3285 0.3444 0.5298 0.2783 0.2935 0.223762 0.24883 0.260953 1 2224 36418 5185 4486 2331 17804 268 4120 2 9802 120644 11556 8590 6610 66676 898 16512 0.967192 2|2 benign|benign 0 COSM146956 96 24,22,26,18 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2524|3354|CDH23|protein_coding|CODING|NM_022124.5|52|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A284|1114|CDH23|protein_coding|CODING|NM_001171933.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937528 rs10823849 -0.693146 0.0440272 96 F3125L 3354 Ttt/Ctt MODERATE 64 MISSENSE CODING CDH23 C protein_coding NM_022124.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73571765 T C 0 222 0 0.0045 0.0954 0.0893 0.251 0.0437 0.1155 0.0106061 0.0255177 0.032627 1 89 8405 1584 2163 620 2558 63 1328 2 9776 120562 11566 8580 6614 66622 894 16510 0.582427 2|2 benign|benign 0 COSM146957 119 33,14,28,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3125L|3354|CDH23|protein_coding|CODING|NM_022124.5|64|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F885L|1114|CDH23|protein_coding|CODING|NM_001171933.1|19|C),DOWNSTREAM(MODIFIER||4290||527|PSAP|protein_coding|CODING|NM_001042465.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.759884 rs45583140 -0.693147 0.0338322 119 F885L 1114 Ttt/Ctt MODERATE 19 MISSENSE CODING CDH23 C protein_coding NM_001171933.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73571765 T C 0 222 0 0.0045 0.0954 0.0893 0.251 0.0437 0.1155 0.0106061 0.0255177 0.032627 1 89 8405 1584 2163 620 2558 63 1328 2 9776 120562 11566 8580 6614 66622 894 16510 0.582427 2|2 benign|benign 0 COSM146957 119 33,14,28,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F3125L|3354|CDH23|protein_coding|CODING|NM_022124.5|64|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F885L|1114|CDH23|protein_coding|CODING|NM_001171933.1|19|C),DOWNSTREAM(MODIFIER||4290||527|PSAP|protein_coding|CODING|NM_001042465.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.759884 rs45583140 -0.693147 0.0338322 119 T3291 3354 acG/acA LOW 68 SILENT CODING CDH23 A protein_coding NM_022124.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73574843 G A 0 222 0 0.0416 0.1398 0.1945 0.2887 0.0765 0.1452 0.0508357 0.0693271 0.0787299 1 410 13788 3565 2389 815 4794 106 1709 2 7452 104658 10286 7830 5710 57466 748 15166 0.732978 2|2 benign|benign 0 . 206 47,50,36,54 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T3291|3354|CDH23|protein_coding|CODING|NM_022124.5|68|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1051|1114|CDH23|protein_coding|CODING|NM_001171933.1|23|A),DOWNSTREAM(MODIFIER||1212||527|PSAP|protein_coding|CODING|NM_001042465.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.516684 rs2290021 -0.693147 0.0143224 206 T1051 1114 acG/acA LOW 23 SILENT CODING CDH23 A protein_coding NM_001171933.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73574843 G A 0 222 0 0.0416 0.1398 0.1945 0.2887 0.0765 0.1452 0.0508357 0.0693271 0.0787299 1 410 13788 3565 2389 815 4794 106 1709 2 7452 104658 10286 7830 5710 57466 748 15166 0.732978 2|2 benign|benign 0 . 206 47,50,36,54 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T3291|3354|CDH23|protein_coding|CODING|NM_022124.5|68|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1051|1114|CDH23|protein_coding|CODING|NM_001171933.1|23|A),DOWNSTREAM(MODIFIER||1212||527|PSAP|protein_coding|CODING|NM_001042465.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.516684 rs2290021 -0.693147 0.0143224 206 3354 204 MODIFIER 68 CODING CDH23 G protein_coding NM_022124.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73575239 A G 0 54 0 0.1997 0.1993 0.2104 0.3552 0.0805 0.1524 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,2,1,2 UTR_3_PRIME(MODIFIER||204||3354|CDH23|protein_coding|CODING|NM_022124.5|68|G),UTR_3_PRIME(MODIFIER||204||1114|CDH23|protein_coding|CODING|NM_001171933.1|23|G),DOWNSTREAM(MODIFIER||816||527|PSAP|protein_coding|CODING|NM_001042465.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.333333 rs2290022 -0.511536 0.539554 5 1114 204 MODIFIER 23 CODING CDH23 G protein_coding NM_001171933.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73575239 A G 0 54 0 0.1997 0.1993 0.2104 0.3552 0.0805 0.1524 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 0,2,1,2 UTR_3_PRIME(MODIFIER||204||3354|CDH23|protein_coding|CODING|NM_022124.5|68|G),UTR_3_PRIME(MODIFIER||204||1114|CDH23|protein_coding|CODING|NM_001171933.1|23|G),DOWNSTREAM(MODIFIER||816||527|PSAP|protein_coding|CODING|NM_001042465.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.333333 rs2290022 -0.511536 0.539554 5 3354 510 MODIFIER 68 CODING CDH23 A protein_coding NM_022124.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73575545 G A 0 6.3 0 0.0091 0.1314 0.1974 0.2887 0.0765 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||510||3354|CDH23|protein_coding|CODING|NM_022124.5|68|A),UTR_3_PRIME(MODIFIER||510||1114|CDH23|protein_coding|CODING|NM_001171933.1|23|A),DOWNSTREAM(MODIFIER||510||527|PSAP|protein_coding|CODING|NM_001042465.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1054635 -0.379885 0 1 1114 510 MODIFIER 23 CODING CDH23 A protein_coding NM_001171933.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73575545 G A 0 6.3 0 0.0091 0.1314 0.1974 0.2887 0.0765 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||510||3354|CDH23|protein_coding|CODING|NM_022124.5|68|A),UTR_3_PRIME(MODIFIER||510||1114|CDH23|protein_coding|CODING|NM_001171933.1|23|A),DOWNSTREAM(MODIFIER||510||527|PSAP|protein_coding|CODING|NM_001042465.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1054635 -0.379885 0 1 527 891 MODIFIER 15 CODING PSAP T protein_coding NM_001042465.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73576307 C T 0 222 0 0.4508 0.404 0.3689 0.5982 0.2793 0.2935 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.616659 0 . 0 . 48 10,9,8,17 UTR_3_PRIME(MODIFIER||891||527|PSAP|protein_coding|CODING|NM_001042465.1|15|T),DOWNSTREAM(MODIFIER||603||3354|CDH23|protein_coding|CODING|NM_022124.5||T),DOWNSTREAM(MODIFIER||603||1114|CDH23|protein_coding|CODING|NM_001171933.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.474976 rs7869 -0.692914 0.836846 48 R357Q 479 cGg/cAg MODERATE 3 MISSENSE CODING CHST3 A protein_coding NM_004273.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73767859 G A 0 220 0 0.2474 0.274 0.3804 0.0893 0.4314 0.2628 0.266705 0.358104 0.405939 1 351 5017 91 31 10 2120 66 2348 2 994 13772 216 256 14 4588 140 7564 0.999947 0 . 0 . 52 22,8,13,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R357Q|479|CHST3|protein_coding|CODING|NM_004273.4|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.837736 rs3740129 -0.69168 0.741017 52 479 1278 MODIFIER 3 CODING CHST3 T protein_coding NM_004273.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73769507 C T 0 72 0 0.407 0.3357 0.4265 0.1121 0.4722 0.2648 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991701 0 . 0 . 17 7,1,6,0 UTR_3_PRIME(MODIFIER||1278||479|CHST3|protein_coding|CODING|NM_004273.4|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs4148943 -0.616816 0.335973 17 479 1361 MODIFIER 3 CODING CHST3 T protein_coding NM_004273.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73769590 C T 0 222 0 0.0658 0.2362 0.389 0.1002 0.4652 0.2628 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.671476 0 . 0 . 51 25,2,12,3 UTR_3_PRIME(MODIFIER||1361||479|CHST3|protein_coding|CODING|NM_004273.4|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.871262 rs4148945 -0.688148 0.328431 51 479 1844 MODIFIER 3 CODING CHST3 T protein_coding NM_004273.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73770073 C T 0 28 0 0.7814 0.5765 0.6153 0.3681 0.5716 0.4918 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||1844||479|CHST3|protein_coding|CODING|NM_004273.4|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs4148946 -0.453602 0.06 3 479 1888 MODIFIER 3 CODING CHST3 C protein_coding NM_004273.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73770117 T C 0 46.6 0 0.2413 0.2871 0.4078 0.1091 0.4662 0.2628 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1888||479|CHST3|protein_coding|CODING|NM_004273.4|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4148947 -0.453602 0.06 3 479 4533 MODIFIER 3 CODING CHST3 T protein_coding NM_004273.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73772762 C T 0 32.6 0 0.4107 0.3373 0.428 0.1131 0.4722 0.2658 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||4533||479|CHST3|protein_coding|CODING|NM_004273.4|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs730720 -0.379885 0 2 424 3585 MODIFIER 11 CODING SPOCK2 A protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73818933 G A 0 222 0 0.1929 0.276 0.4092 0.1161 0.4891 0.2393 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.84752 0 . 0 . 76 14,13,16,24 UTR_3_PRIME(MODIFIER||3585||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.80856 rs7307 -0.693145 0.583641 76 424 2122 MODIFIER 11 CODING SPOCK2 A protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73820396 G A 0 222 0 0.1944 0.2654 0.3876 0.1161 0.4533 0.2352 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997984 0 . 0 . 78 9,19,10,34 UTR_3_PRIME(MODIFIER||2122||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.388781 rs896079 -0.693146 0.749505 78 424 1896 MODIFIER 11 CODING SPOCK2 G protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73820622 A G 0 18.9 0 0.9266 0.6024 0.5937 0.4206 0.5447 0.4172 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 7 1,3,1,1 UTR_3_PRIME(MODIFIER||1896||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs3180 -0.453602 0.52 7 424 885 MODIFIER 11 CODING SPOCK2 T protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73821633 C T 0 9.7 0 0.1944 0.264 0.3804 0.1161 0.4523 0.2342 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||885||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1678623 -0.379885 0 1 424 855 MODIFIER 11 CODING SPOCK2 T protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73821663 C T 0 9.7 0 0.1944 0.264 0.3804 0.1161 0.4523 0.2342 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||855||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1668174 -0.379885 0 1 424 275 MODIFIER 11 CODING SPOCK2 T protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73822243 G T 0 74 0 0.0719 0.2254 0.3588 0.1151 0.4394 0.2321 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.952347 0 . 0 . 11 4,1,5,0 UTR_3_PRIME(MODIFIER||275||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.857112 rs1049245 -0.590765 0.324419 11 424 11 MODIFIER 11 CODING SPOCK2 T protein_coding NM_001244950.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73822507 C T 0 222 0 0.1974 0.266 0.3703 0.1339 0.4473 0.2342 0.21153 0.366523 0.44593 1 2217 45636 3928 1159 2596 30356 397 4983 2 10198 120278 11526 8562 6550 66262 906 16274 0.869825 0 . 0 . 63 22,10,15,7 UTR_3_PRIME(MODIFIER||11||424|SPOCK2|protein_coding|CODING|NM_001244950.1|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.647084 rs1530803,rs386535880 -0.692562 0.464461 63 400 5143 MODIFIER 13 CODING ASCC1 G protein_coding NM_001198799.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73856984 A G 0 228 0 0.6626 0.4696 0.4063 0.2817 0.4155 0.5031 0 . 0 2 6441 55634 4287 2525 2440 30784 436 8721 2 10190 119882 11414 8434 6544 65948 904 16448 0 . 0 . 0 93 0,0,56,31 UTR_3_PRIME(MODIFIER||5143||400|ASCC1|protein_coding|CODING|NM_001198799.2|13|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs3312 -0.693147 0.0173389 93 S78* 400 tCa/tGa HIGH 4 NONSENSE CODING ASCC1 C protein_coding NM_001198799.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73964243 G C 0 222 0 0.2784 0.1164 0.0259 0.123 0.0089 0.0654 0 . 0 1 222 896 10 68 7 55 4 530 2 902 16490 286 484 1620 5328 206 7664 0.853731 0 . 0 . 89 29,14,25,7 STOP_GAINED(HIGH|NONSENSE|tCa/tGa|S78*|400|ASCC1|protein_coding|CODING|NM_001198799.2|4|C) 0 0.5 1 0 . 1 0 . 1 (ASCC1|ASCC1|1|1.00) 60 0 1 1 (ASCC1|ASCC1|1|1.00) 0.804926 rs11000217 -0.69312 0.324994 89 D34N 400 Gac/Aac MODERATE 2 MISSENSE CODING ASCC1 T protein_coding NM_001198799.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73972957 C T 0 222 0 0.2648 0.1126 0.0245 0.123 0.0089 0.0654 0.230595 0.0850377 0.0104651 1 2388 5660 164 1191 38 724 26 1129 2 10396 121320 11568 8648 6608 66690 906 16504 0.420962 0 . 0 . 119 42,16,36,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D34N|400|ASCC1|protein_coding|CODING|NM_001198799.2|2|T),UPSTREAM(MODIFIER||2801||110|ANAPC16|protein_coding|CODING|NM_001242546.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91715 rs11558719 -0.693147 0.00891934 119 110 644 MODIFIER 5 CODING ANAPC16 G protein_coding NM_001242546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73993518 A G 0 222 0 0.2572 0.1072 0.0231 0.122 0.0089 0.0501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868655 0 . 0 . 174 35,42,33,42 UTR_3_PRIME(MODIFIER||644||110|ANAPC16|protein_coding|CODING|NM_001242546.1|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.851253 rs11000229 -0.693147 0.0057762 174 110 1891 MODIFIER 5 CODING ANAPC16 C protein_coding NM_001242546.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 73994765 T C 0 9.7 0 0.9206 0.627 0.5519 0.2738 0.6412 0.6329 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1891||110|ANAPC16|protein_coding|CODING|NM_001242546.1|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6480601 -0.379885 0 1 232 95 MODIFIER 3 CODING DDIT4 A protein_coding NM_019058.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74035041 T A 0 144 0 0.1967 0.4627 0.4798 0.8085 0.3986 0.5194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.656089 0 . 0 . 61 27,8,23,1 UTR_3_PRIME(MODIFIER||95||232|DDIT4|protein_coding|CODING|NM_019058.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.502772 rs1053639 -0.692831 0.0337491 61 232 351 MODIFIER 3 CODING DDIT4 T protein_coding NM_019058.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74035297 C T 0 228 0 0.6301 0.6168 0.5288 0.9157 0.4105 0.5654 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,6,33 UTR_3_PRIME(MODIFIER||351||232|DDIT4|protein_coding|CODING|NM_019058.2|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8316 -0.693144 0.0444971 41 409 2449 MODIFIER 8 CODING DNAJB12 C protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74093119 A C 0 14.3 0 0.0023 0.0218 0.0014 0.0784 0.001 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 2,2,2,0 UTR_3_PRIME(MODIFIER||2449||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs16929769 -0.453602 0.14 6 409 1916 MODIFIER 8 CODING DNAJB12 T protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74093652 C T 0 131 0 0.0809 0.0433 0.0058 0.0784 0.002 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.673228 0 . 0 . 42 15,3,24,0 UTR_3_PRIME(MODIFIER||1916||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.255466 rs16929771 -0.692831 0.16041 42 409 1839 MODIFIER 8 CODING DNAJB12 A protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74093729 G A 0 202 0 0.0809 0.0415 0.0058 0.0694 0.002 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0458621 0 . 0 . 109 55,0,51,2 UTR_3_PRIME(MODIFIER||1839||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.134407 rs74145741 -0.693147 0.058218 109 409 1511 MODIFIER 8 CODING DNAJB12 C protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74094057 T C 0 125 0 0.3835 0.1516 0.0634 0.1101 0.0308 0.0675 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.896474 0 . 0 . 12 0,5,2,5 UTR_3_PRIME(MODIFIER||1511||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 1 0 0.935451 rs41282262 -0.636426 0.551097 12 409 1396 MODIFIER 8 CODING DNAJB12 G protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74094172 C G 0 48.3 0 0.3003 0.1286 0.0576 0.1101 0.0298 0.0675 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 7 2,2,2,1 UTR_3_PRIME(MODIFIER||1396||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1.01283 0 0.810265 rs72808118 -0.511536 0.654404 7 409 903 MODIFIER 8 CODING DNAJB12 C protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74094665 T C 0 211 0 1 0.9998 1 0.999 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,8,3 UTR_3_PRIME(MODIFIER||903||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1879471 -0.676189 0.970155 11 409 515 MODIFIER 8 CODING DNAJB12 A protein_coding NM_001002762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74095053 G A 0 83 0 0.3828 0.1514 0.0634 0.1101 0.0308 0.0675 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.899815 0 . 0 . 13 0,7,0,6 UTR_3_PRIME(MODIFIER||515||409|DNAJB12|protein_coding|CODING|NM_001002762.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.378331 rs7894262 -0.616816 0.0630446 13 478 112 MODIFIER 12 CODING MICU1 T protein_coding NM_006077.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74127841 C T 0 222 0 0.0809 0.0433 0.0058 0.0784 0.002 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.80289 0 . 0 . 77 16,17,17,18 UTR_3_PRIME(MODIFIER||112||478|MICU1|protein_coding|CODING|NM_006077.3|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.786364 rs74145761 -0.693136 0.0150384 77 478 100 MODIFIER 12 CODING MICU1 A protein_coding NM_006077.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74127853 G A 0 222 0 0.4614 0.4263 0.4755 0.1498 0.6044 0.4458 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.426636 0 . 0 . 76 14,17,18,19 UTR_3_PRIME(MODIFIER||100||478|MICU1|protein_coding|CODING|NM_006077.3|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.740153 rs4262652 -0.693141 0.162469 76 195 88 MODIFIER 4 CODING PLA2G12B C protein_coding NM_032562.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74695287 T C 0 228 0 0.9992 0.9998 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 70 0,0,51,10 UTR_3_PRIME(MODIFIER||88||195|PLA2G12B|protein_coding|CODING|NM_032562.3|4|C),DOWNSTREAM(MODIFIER||2493||545|OIT3|protein_coding|CODING|NM_152635.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2461917 -0.693147 0.756505 70 534 645 MODIFIER 15 CODING P4HA1 G protein_coding NM_000917.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74767335 A G 0 41.1 0 0.6157 0.3183 0.1441 0.3621 0.0646 0.2556 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.745722 0 . 0 . 15 1,8,0,6 UTR_3_PRIME(MODIFIER||645||534|P4HA1|protein_coding|CODING|NM_000917.3|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.939413 rs8380 -0.616816 0.387746 15 534 285 MODIFIER 15 CODING P4HA1 T protein_coding NM_000917.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74767695 C T 0 54 0 0.1694 0.1769 0.1009 0.2986 0.0537 0.2423 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.872525 0 . 0 . 15 10,1,3,1 UTR_3_PRIME(MODIFIER||285||534|P4HA1|protein_coding|CODING|NM_000917.3|15|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.948127 rs16930262,rs386541361 -0.556411 0.484771 15 534 LOW 12 CODING P4HA1 A protein_coding NM_000917.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74773975 G A 0 222 0 0.0938 0.026 0.0086 0 0 0 0.0937358 0.0327541 0.00151163 1 928 1092 52 28 0 71 7 6 2 10380 121240 11562 8634 6610 66654 908 16492 0.966699 0 . 0 . 114 25,32,28,16 SPLICE_SITE_REGION+INTRON(LOW||||534|P4HA1|protein_coding|CODING|NM_000917.3|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995735 rs73272315 -0.693146 0.0632441 114 534 10 MODIFIER 2 CODING P4HA1 C protein_coding NM_000917.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74834651 T C 0 222 0 0.3646 0.2348 0.1239 0.3105 0.0596 0.2403 0.32887 0.159203 0.0721769 1 3464 16003 1074 2692 298 4597 75 3803 2 9966 117894 11344 8382 6540 64448 894 16320 0.675694 0 . 0 COSM146958 29 2,7,5,14 UTR_5_PRIME(MODIFIER||10||534|P4HA1|protein_coding|CODING|NM_000917.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.852133 rs4405231 -0.69168 0.337238 29 534 21935 MODIFIER 1 CODING P4HA1 G protein_coding NM_000917.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74856576 C G 0 159 0 0.028 0.1386 0.0821 0.3125 0.0567 0.2331 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870254 0 . 0 . 67 1,34,1,31 START_GAINED(LOW||||534|P4HA1|protein_coding|CODING|NM_000917.3|1|G),UTR_5_PRIME(MODIFIER||21935||534|P4HA1|protein_coding|CODING|NM_000917.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999823 rs28384495 -0.69312 0.0153643 67 D667G 677 gAt/gGt MODERATE 15 MISSENSE CODING ECD C protein_coding NM_001135752.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74894375 T C 0 222 0 0.1664 0.1777 0.0994 0.3145 0.0537 0.2352 0.150931 0.0950331 0.0663953 1 1704 13805 996 2741 281 4247 69 3767 2 10398 121292 11556 8632 6598 66690 906 16512 0.929147 0 . 0 COSM146959 87 40,7,24,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D667G|677|ECD|protein_coding|CODING|NM_001135752.1|15|C),DOWNSTREAM(MODIFIER||2789||352|NUDT13|protein_coding|CODING|NM_015901.5||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.742177 rs2271904 -0.693054 0.0253074 87 N534S 677 aAt/aGt MODERATE 14 MISSENSE CODING ECD C protein_coding NM_001135752.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74896664 T C 0 222 0 0.1657 0.1765 0.0994 0.3145 0.0537 0.2301 0.150704 0.0949562 0.0663953 1 1703 13761 999 2751 281 4248 68 3711 2 10398 121342 11574 8626 6614 66716 906 16508 0.442119 0 . 0 . 80 3,34,5,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N534S|677|ECD|protein_coding|CODING|NM_001135752.1|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.906478 rs36152134 -0.693132 5.04292e-06 80 E511 677 gaG/gaA LOW 13 SILENT CODING ECD T protein_coding NM_001135752.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74897816 C T 0 222 0 0.3676 0.2356 0.1239 0.3145 0.0596 0.2362 0.322742 0.156466 0.0712791 1 3309 15397 1047 2649 295 4407 71 3619 2 9038 101846 9918 7876 5830 53774 792 14618 0.981501 0 . 0 COSM146960 54 9,20,10,10 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E511|677|ECD|protein_coding|CODING|NM_001135752.1|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.352408 rs2271905 -0.692067 0.0495765 54 E485Q 677 Gaa/Caa MODERATE 12 MISSENSE CODING ECD G protein_coding NM_001135752.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74899134 C G 0 222 0 0.3676 0.2356 0.1239 0.3145 0.0596 0.2362 0.325465 0.157696 0.0717442 1 3560 16191 1085 2755 298 4625 74 3794 2 10404 121370 11574 8636 6614 66722 908 16512 0.620485 0 . 0 . 89 35,6,33,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E485Q|677|ECD|protein_coding|CODING|NM_001135752.1|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.812244 rs3736518 -0.693144 0.117152 89 A150 677 gcA/gcT LOW 5 SILENT CODING ECD A protein_coding NM_001135752.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74916173 T A 0 222 0 0.1657 0.1775 0.0994 0.3145 0.0537 0.2352 0.150931 0.0950331 0.0663953 1 1703 13785 1000 2750 279 4243 69 3741 2 10396 120918 11578 8642 6612 66534 908 16248 0.397521 0 . 0 . 58 16,12,11,11 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcT|A150|677|ECD|protein_coding|CODING|NM_001135752.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.725389 rs12241093 -0.692562 0.727893 58 R45Q 677 cGg/cAg MODERATE 2 MISSENSE CODING ECD T protein_coding NM_001135752.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74923562 C T 0 222 0 0.3684 0.2358 0.1239 0.3145 0.0596 0.2362 0.325238 0.15762 0.0717442 1 3559 16203 1085 2757 298 4633 74 3797 2 10406 121396 11576 8650 6614 66730 908 16512 0.999769 0 . 0 . 123 31,24,30,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R45Q|677|ECD|protein_coding|CODING|NM_001135752.1|2|T),UPSTREAM(MODIFIER||4315||582|FAM149B1|protein_coding|CODING|NM_173348.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.440029 rs3812619 -0.693147 0.0344905 123 582 LOW 1 CODING FAM149B1 T protein_coding NM_173348.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 74934442 C T 0 222 0 0.3684 0.2356 0.1239 0.3135 0.0596 0.2362 0.340318 0.153964 0.0729101 1 772 3556 57 206 67 673 23 1758 2 2148 21552 406 622 1624 8688 240 7824 0.795623 0 . 0 COSM146961 108 34,25,27,11 SPLICE_SITE_REGION+INTRON(LOW||||582|FAM149B1|protein_coding|CODING|NM_173348.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846926 rs61290608 -0.693143 0.045542 108 582 LOW 13 CODING FAM149B1 C protein_coding NM_173348.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75000698 T C 0 222 0 0.2186 0.1909 0.1023 0.3175 0.0557 0.2249 0.177746 0.10184 0.0688246 1 426 3132 55 206 72 643 21 1709 2 2186 22150 410 616 1632 9166 238 7902 0.944313 0 . 0 COSM146963 91 25,9,34,9 SPLICE_SITE_REGION+INTRON(LOW||||582|FAM149B1|protein_coding|CODING|NM_173348.1|13|C),DOWNSTREAM(MODIFIER||1016||260|DNAJC9|protein_coding|CODING|NM_015190.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456978 rs11000561 -0.693146 0.382608 91 G571R 582 Gga/Aga MODERATE 14 MISSENSE CODING FAM149B1 A protein_coding NM_173348.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75000739 G A 0 228 0 0.3351 0.24 0.0879 0.4107 0.0606 0.228 0 . 0 2 157 2817 35 203 68 640 20 1694 2 1478 21480 398 562 1572 9332 240 7898 1 0 . 0 . 84 1,0,32,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G571R|582|FAM149B1|protein_coding|CODING|NM_173348.1|14|A),DOWNSTREAM(MODIFIER||975||260|DNAJC9|protein_coding|CODING|NM_015190.4||A) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs12573841 -0.693147 0.124443 84 GRPVS572 582 ggcagaccagtctct/ MODERATE 14 CODING FAM149B1 A protein_coding NM_173348.1 CODON_DELETION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75000741 AGGCAGACCAGTCTCT A 0 222 0 . 0 . 0 . 0 0.163355 0.0581683 0.00252313 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 89 35,27,13,14 CODON_DELETION(MODERATE||ggcagaccagtctct/|GRPVS572|582|FAM149B1|protein_coding|CODING|NM_173348.1|14|A),DOWNSTREAM(MODIFIER||972||260|DNAJC9|protein_coding|CODING|NM_015190.4||A) 1 0.5 1 27 0.303371 0 1 1 0 . 60 0 0 1 0 . rs148222664 -0.693021 0.0549039 89 582 160 MODIFIER 14 CODING FAM149B1 G protein_coding NM_173348.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75000937 A G 0 107 0 0.1747 0.1795 0.1009 0.3185 0.0547 0.227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.703384 0 . 0 . 18 0,9,0,9 UTR_3_PRIME(MODIFIER||160||582|FAM149B1|protein_coding|CODING|NM_173348.1|14|G),DOWNSTREAM(MODIFIER||777||260|DNAJC9|protein_coding|CODING|NM_015190.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.28276 rs3763725 -0.662043 0.639222 18 260 65 MODIFIER 5 CODING DNAJC9 T protein_coding NM_015190.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75003093 C T 0 222 0 0.3517 0.2298 0.1239 0.3135 0.0636 0.2249 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 83 30,16,20,12 UTR_3_PRIME(MODIFIER||65||260|DNAJC9|protein_coding|CODING|NM_015190.4|5|T),DOWNSTREAM(MODIFIER||1154||582|FAM149B1|protein_coding|CODING|NM_173348.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.938751 rs7100458 -0.69312 0.0551377 83 G48 260 ggT/ggC LOW 1 SILENT CODING DNAJC9 G protein_coding NM_015190.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75006804 A G 0 222 0 0.351 0.2312 0.1239 0.3105 0.0636 0.2362 0.271938 0.134648 0.0644143 1 1175 6115 364 947 63 1704 22 1840 2 3120 27540 2158 2442 606 13964 164 5086 0.798881 0 . 0 . 54 16,8,16,8 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G48|260|DNAJC9|protein_coding|CODING|NM_015190.4|1|G),DOWNSTREAM(MODIFIER||4865||582|FAM149B1|protein_coding|CODING|NM_173348.1||G),DOWNSTREAM(MODIFIER||1797||137|MRPS16|protein_coding|CODING|NM_016065.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.537999 rs35302968 -0.692831 0.445445 54 137 1503 MODIFIER 3 CODING MRPS16 A protein_coding NM_016065.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75009107 T A 0 222 0 0.1346 0.1649 0.0937 0.3105 0.0547 0.2198 0 . 0 1 148 2473 40 163 65 406 17 1634 2 912 16624 286 492 1630 5464 206 7634 0.737966 0 . 0 . 90 24,16,14,25 UTR_3_PRIME(MODIFIER||1503||137|MRPS16|protein_coding|CODING|NM_016065.3|3|A),UPSTREAM(MODIFIER||2018||260|DNAJC9|protein_coding|CODING|NM_015190.4||A),DOWNSTREAM(MODIFIER||4409||1121|CFAP70|protein_coding|CODING|NM_145170.3||A),INTRAGENIC(MODIFIER|||||DNAJC9-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.265854 rs2018198 -0.693144 0.0142948 90 N944D 1121 Aac/Gac MODERATE 23 MISSENSE CODING CFAP70 C protein_coding NM_145170.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75035257 T C 0 222 0 0.3525 0.2294 0.1239 0.3105 0.0636 0.2249 0.313663 0.153775 0.0718605 1 3405 15978 1091 2754 305 4654 75 3694 2 10402 120922 11572 8628 6614 66594 908 16204 0.994414 0 . 0 COSM146965 84 10,30,10,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N944D|1121|CFAP70|protein_coding|CODING|NM_145170.3|23|C),INTRAGENIC(MODIFIER|||||DNAJC9-AS1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.142901 rs4294502 -0.693145 0.0776476 84 L597 1121 ctT/ctG LOW 16 SILENT CODING CFAP70 C protein_coding NM_145170.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75056863 A C 0 222 0 0.177 0.1777 0.0994 0.3105 0.0547 0.2239 0.149569 0.0947255 0.0666279 1 1687 13795 1013 2747 288 4295 71 3694 2 10404 121184 11510 8624 6604 66640 908 16494 0.999018 0 . 0 COSM146966 153 40,29,31,30 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L597|1121|CFAP70|protein_coding|CODING|NM_145170.3|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998684 rs6480692 -0.693147 0.371453 153 C274 1121 tgC/tgT LOW 8 SILENT CODING CFAP70 A protein_coding NM_145170.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75095253 G A 0 222 0 0.177 0.1781 0.0994 0.3105 0.0547 0.226 0.149569 0.0947255 0.0666279 1 1687 13856 1016 2728 287 4296 72 3770 2 10396 121188 11552 8628 6614 66606 906 16486 0.998754 0 . 0 COSM146967 94 16,31,11,21 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C274|1121|CFAP70|protein_coding|CODING|NM_145170.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93401 rs7910541 -0.69312 0.382248 94 488 441 MODIFIER 14 CODING ANXA7 GA protein_coding NM_004034.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75135411 G GA 0 45.3 0 0.3495 0.2276 0.1225 0.3026 0.0646 0.228 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||441||488|ANXA7|protein_coding|CODING|NM_004034.2|14|GA) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs11453254 -0.453602 0.82 2 488 407 MODIFIER 14 CODING ANXA7 T protein_coding NM_004034.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75135446 C T 0 89 0 0.9977 0.9806 0.9755 1 0.9334 0.9898 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,5,0 UTR_3_PRIME(MODIFIER||407||488|ANXA7|protein_coding|CODING|NM_004034.2|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6896 -0.590765 0.233642 5 D186 488 gaT/gaC LOW 7 SILENT CODING ANXA7 G protein_coding NM_004034.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75148116 A G 0 222 0 0.1785 0.1765 0.0994 0.3026 0.0557 0.2229 0.149569 0.0940335 0.0655814 1 1704 13660 1002 2718 288 4206 70 3672 2 10400 121308 11548 8644 6610 66696 908 16502 0.978966 0 . 0 COSM146969 57 16,8,17,7 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D186|488|ANXA7|protein_coding|CODING|NM_004034.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.967329 rs2234965,rs386562004 -0.692831 0.330375 57 525 949 MODIFIER 14 CODING PPP3CB T protein_coding NM_001142353.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75197051 C T 0 222 0 0.7746 0.3888 0.1657 0.4435 0.0954 0.271 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.260052 0 . 0 . 93 11,27,17,27 UTR_3_PRIME(MODIFIER||949||525|PPP3CB|protein_coding|CODING|NM_001142353.2|14|T),UPSTREAM(MODIFIER||3732||460|MSS51|protein_coding|CODING|NM_001024593.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995245 rs12644,rs386525368 -0.693146 0.329047 93 L255 299 ctG/ctT LOW 6 SILENT CODING MYOZ1 A protein_coding NM_021245.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75391823 C A 0 222 0 0.0023 0.0643 0.0231 0.1429 0.0408 0.1207 0.0111212 0.033523 0.045 1 98 6240 197 1037 173 2852 30 1853 2 10404 121388 11568 8650 6612 66734 908 16512 0.640883 0 . 0 . 91 26,13,13,28 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L255|299|MYOZ1|protein_coding|CODING|NM_021245.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992788 rs41280400 -0.693145 0.296483 91 977 841 MODIFIER 4 CODING SYNPO2L G protein_coding NM_001114133.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75405635 T G 0 131 0 0.2277 0.1765 0.1124 0.1845 0.1332 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.941883 0 . 0 . 34 1,13,0,19 UTR_3_PRIME(MODIFIER||841||977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|G),UPSTREAM(MODIFIER||4120||299|MYOZ1|protein_coding|CODING|NM_021245.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.834755 rs41280404 -0.69168 0.397665 34 977 335 MODIFIER 4 CODING SYNPO2L C protein_coding NM_001114133.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75406141 A C 0 39.3 0 0.3782 0.2179 0.1254 0.1845 0.1332 0.1881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||335||977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|C),UPSTREAM(MODIFIER||4626||299|MYOZ1|protein_coding|CODING|NM_021245.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3740293 -0.453602 0.32 2 A882 977 gcC/gcG LOW 4 SILENT CODING SYNPO2L C protein_coding NM_001114133.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75406764 G C 0 222 0 0.0061 0.010783 0 0.0427 0 0.0031 0.00385837 0.00161489 0.000465224 1 41 599 7 451 0 19 1 80 2 9902 119610 11570 8638 6614 65800 894 16192 0.894613 0 . 0 . 32 6,5,15,3 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A882|977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874952 rs118159842 -0.691153 0.214995 32 S833Y 977 tCc/tAc MODERATE 4 MISSENSE CODING SYNPO2L T protein_coding NM_001114133.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75406912 G T 0 196 0 0.2065 0.1703 0.111 0.1845 0.1332 0.1871 0.188241 0.161889 0.148428 1 1978 20053 1420 1909 888 9988 153 3717 2 9768 120450 11574 8632 6614 66448 902 16512 0.834552 0 . 0 . 33 7,8,4,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tAc|S833Y|977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.684303 rs34163229 -0.688148 0.43361 33 P707L 977 cCt/cTt MODERATE 4 MISSENSE CODING SYNPO2L A protein_coding NM_001114133.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75407290 G A 0 67 0 0.2073 0.1707 0.111 0.1845 0.1332 0.1881 0.192465 0.163694 0.148953 1 2044 19526 1412 1901 888 9809 146 3326 2 9576 114642 11466 8490 6580 64278 860 13392 0.823561 0 . 0 COSM1599869,COSM1599868 18 5,6,2,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P707L|977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960687 rs3812629 -0.590765 0.383239 18 P587 977 ccT/ccG LOW 4 SILENT CODING SYNPO2L C protein_coding NM_001114133.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75407649 A C 0 190 0 0.1483 0.1546 0.1052 0.1845 0.1332 0.1892 0.13367 0.140242 0.143593 1 1330 16429 1350 1790 856 8911 120 2072 2 8102 100026 10776 7880 5980 57648 702 8938 0.789232 0 . 0 . 18 4,3,5,4 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P587|977|SYNPO2L|protein_coding|CODING|NM_001114133.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95083 rs4746139 -0.662043 0.0408554 18 G2S 977 Ggt/Agt MODERATE 1 MISSENSE CODING SYNPO2L T protein_coding NM_001114133.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75415677 C T 0 222 0 0.2012 0.1647 0.1182 0.1577 0.1372 0.184 0.191474 0.169076 0.159334 1 424 4068 64 116 202 1415 48 1799 2 2142 20976 406 602 1244 8608 220 7754 0.862246 0 . 0 . 49 13,14,11,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G2S|977|SYNPO2L|protein_coding|CODING|NM_001114133.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.497546 rs60632610 -0.691153 0.0469615 49 R653* 686 Cga/Tga HIGH 8 NONSENSE CODING AGAP5 A protein_coding NM_001144000.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75434461 G A 0 222 0 0.0129 0.01238 0 0.0387 0 0.0061 0 . 0 1 78 608 5 419 0 16 0 90 2 7548 106170 10756 8030 4828 58886 760 15362 0.998429 0 . 0 . 313 88,61,72,50 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R653*|686|AGAP5|protein_coding|CODING|NM_001144000.1|8|A) 0 0.5 1 0 . 1 0 . 1 0 32 0 0.648886 0.0412706 0 0.985816 rs200494302 -0.693147 0.321408 313 E136K 686 Gag/Aag MODERATE 5 MISSENSE CODING AGAP5 T protein_coding NM_001144000.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75442543 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 152 1212 37 54 212 459 15 283 2 628 5426 164 188 1408 2192 84 762 0.345226 0 . 0 . 786 208,153,194,120 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E136K|686|AGAP5|protein_coding|CODING|NM_001144000.1|5|T) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.867926 8.88417e-14 0 0.49995 rs200625436 -0.693147 1.06136e-05 786 Y28 1094 taT/taC LOW 3 SILENT CODING SEC24C C protein_coding NM_004922.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75506674 T C 0 222 0 0.1528 0.1528 0.1182 0.1587 0.1332 0.1912 0.148207 0.14501 0.143372 1 1516 18621 1175 1580 876 9754 147 3573 2 10404 121348 11568 8638 6612 66708 908 16510 0.13278 0 . 0 COSM146970 115 37,19,27,20 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y28|1094|SEC24C|protein_coding|CODING|NM_004922.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960281 rs2306325 -0.693147 0.680137 115 T708 1094 acA/acG LOW 16 SILENT CODING SEC24C G protein_coding NM_004922.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75527708 A G 0 222 0 0.1528 0.1444 0.1167 0.1171 0.1332 0.1922 0.148207 0.144933 0.143256 1 1514 18107 1172 1120 877 9726 144 3554 2 10404 121202 11566 8646 6608 66634 906 16438 0.995815 0 . 0 COSM427901 90 12,25,15,34 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T708|1094|SEC24C|protein_coding|CODING|NM_004922.3|16|G),UPSTREAM(MODIFIER||4341||492|FUT11|protein_coding|CODING|NM_173540.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.58352 rs4746147 -0.693147 0.0684007 90 1094 109 MODIFIER 24 CODING SEC24C T protein_coding NM_004922.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75530962 C T 0 222 0 0.1528 0.1444 0.1167 0.1171 0.1332 0.1922 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.770845 0 . 0 . 58 10,19,14,13 UTR_3_PRIME(MODIFIER||109||1094|SEC24C|protein_coding|CODING|NM_004922.3|24|T),UPSTREAM(MODIFIER||1087||492|FUT11|protein_coding|CODING|NM_173540.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.823555 rs11541237 -0.693021 0.632377 58 V920 1892 gtG/gtA LOW 13 SILENT CODING ZSWIM8 A protein_coding NM_001242488.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75554039 G A 0 222 0 0.0129 0.01238 0 0.0387 0 0.0061 0.00553151 0.00206743 0.000356379 1 85 622 5 427 0 15 0 90 2 9802 120706 11576 8622 6614 66700 898 16494 0.495515 0 . 0 . 153 41,37,19,28 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V920|1892|ZSWIM8|protein_coding|CODING|NM_001242488.1|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720086 rs118159663 -0.693147 0.0128737 153 L1423 1892 ctG/ctA LOW 21 SILENT CODING ZSWIM8 A protein_coding NM_001242488.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75558867 G A 0 228 0 0.4887 0.4878 0.4755 0.2351 0.7575 0.4785 0.557454 0.688539 0.751916 2 5163 74140 4222 2187 3813 48957 584 9214 2 9574 118350 10936 8298 6474 65872 890 16306 0 . 0 . COSM146971 63 0,0,20,41 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L1423|1892|ZSWIM8|protein_coding|CODING|NM_001242488.1|21|A),DOWNSTREAM(MODIFIER||2802||883|NDST2|protein_coding|CODING|NM_003635.3||A),INTRAGENIC(MODIFIER|||||ZSWIM8-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2271271 -0.693147 6.05653e-06 63 P1493 1892 ccG/ccA LOW 21 SILENT CODING ZSWIM8 A protein_coding NM_001242488.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75559077 G A 0 214 0 0.0764 0.122 0.0994 0.1181 0.1342 0.1912 0.0805271 0.120234 0.139637 1 677 15530 990 994 791 8743 120 3215 2 6420 88018 7548 6046 4506 49448 650 13400 0.98843 0 . 0 . 29 3,5,17,3 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1493|1892|ZSWIM8|protein_coding|CODING|NM_001242488.1|21|A),DOWNSTREAM(MODIFIER||2592||883|NDST2|protein_coding|CODING|NM_003635.3||A),INTRAGENIC(MODIFIER|||||ZSWIM8-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.867131 rs11000780 -0.692067 0.555672 29 883 101 MODIFIER 15 CODING NDST2 A protein_coding NM_003635.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75562108 G A 0 222 0 0.1218 0.1356 0.1095 0.1181 0.1342 0.1922 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.29625 0 . 0 . 49 10,5,16,13 UTR_3_PRIME(MODIFIER||101||883|NDST2|protein_coding|CODING|NM_003635.3|15|A),DOWNSTREAM(MODIFIER||552||1892|ZSWIM8|protein_coding|CODING|NM_001242488.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.856268 rs2075641 -0.693079 0.473727 49 883 99 MODIFIER 3 CODING NDST2 A protein_coding NM_003635.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75568245 G A 0 127 0 0.0121 0.01218 0 0.0387 0 0.0061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.091033 0 . 0 . 37 17,4,10,2 UTR_5_PRIME(MODIFIER||99||883|NDST2|protein_coding|CODING|NM_003635.3|3|A),DOWNSTREAM(MODIFIER||4014||556|CAMK2G|protein_coding|CODING|NM_172171.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.991458 rs3758492 -0.680642 0.0512963 37 556 995 MODIFIER 21 CODING CAMK2G T protein_coding NM_172171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75573778 A T 0 100 0 0.1203 0.1348 0.111 0.119 0.1332 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.984341 0 . 0 . 22 3,9,0,9 UTR_3_PRIME(MODIFIER||995||556|CAMK2G|protein_coding|CODING|NM_172171.2|21|T),UPSTREAM(MODIFIER||2189||883|NDST2|protein_coding|CODING|NM_003635.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.969539 rs2306327 -0.662043 0.0204797 22 556 694 MODIFIER 21 CODING CAMK2G A protein_coding NM_172171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75574079 G A 0 76 0 0.1437 0.1412 0.1124 0.119 0.1332 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.487298 0 . 0 . 9 3,1,5,0 UTR_3_PRIME(MODIFIER||694||556|CAMK2G|protein_coding|CODING|NM_172171.2|21|A),UPSTREAM(MODIFIER||2490||883|NDST2|protein_coding|CODING|NM_003635.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.487298 rs1057410 -0.590765 0.00506968 9 L141P 431 cTg/cCg MODERATE 6 MISSENSE CODING PLAU C protein_coding NM_002658.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75673101 T C 0 222 0 0.9902 0.7754 0.7536 0.6349 0.7922 0.6278 0.955288 0.83869 0.778953 1 9989 91598 8172 5574 4381 51254 689 11539 2 10404 121386 11574 8642 6610 66736 908 16512 0.468837 255 other 0 . 57 17,14,11,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L141P|431|PLAU|protein_coding|CODING|NM_002658.3|6|C),INTRON(MODIFIER||||151|C10orf55|protein_coding|CODING|NM_001001791.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998914 rs2227564 -0.692352 0.763573 57 P796 1134 ccG/ccA LOW 16 SILENT CODING VCL A protein_coding NM_014000.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75865065 G A 0 222 0 0.0598 0.3247 0.4568 0.254 0.5915 0.3875 0.144349 0.438721 0.589535 1 1308 57706 4321 2256 3592 38992 479 6758 2 10376 121200 11566 8616 6600 66632 902 16508 0.23679 2,2|2 benign,benign|benign 0 . 93 15,16,23,28 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P796|1134|VCL|protein_coding|CODING|NM_014000.2|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.290168 rs767809 -0.693147 0.0446975 93 G938 1134 ggC/ggG LOW 19 SILENT CODING VCL G protein_coding NM_014000.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75871735 C G 0 222 0 0.7753 0.623 0.6744 0.3819 0.7485 0.5 0.782569 0.762417 0.752093 1 8154 81648 6558 3240 4452 49545 639 9060 2 10404 121250 11538 8596 6606 66696 908 16502 0.727519 2,2|2 benign,benign|benign 0 COSM1349106 107 37,17,24,18 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G938|1134|VCL|protein_coding|CODING|NM_014000.2|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.60384 rs2131956 -0.693146 0.494851 107 1134 1584 MODIFIER 22 CODING VCL A protein_coding NM_014000.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75879511 T A 0 178 0 0.7761 0.6254 0.6758 0.3829 0.7555 0.502 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.96027 0 . 0 . 39 14,4,17,1 UTR_3_PRIME(MODIFIER||1584||1134|VCL|protein_coding|CODING|NM_014000.2|22|A),DOWNSTREAM(MODIFIER||504||418|AP3M1|protein_coding|CODING|NM_012095.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.251703 rs703258 -0.691153 0.368269 39 418 1892 MODIFIER 9 CODING AP3M1 A protein_coding NM_012095.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75881676 G A 0 39.3 0 0.7753 0.6232 0.6758 0.381 0.7495 0.5 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1892||418|AP3M1|protein_coding|CODING|NM_012095.4|9|A),DOWNSTREAM(MODIFIER||1762||1134|VCL|protein_coding|CODING|NM_014000.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6688 -0.453602 0.9 2 418 433 MODIFIER 9 CODING AP3M1 CTT protein_coding NM_012095.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 75883134 C CTT 0 222 0 0.7761 0.625 0.6758 0.3819 0.7555 0.501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 55 7,26,7,13 UTR_3_PRIME(MODIFIER||433||418|AP3M1|protein_coding|CODING|NM_012095.4|9|CTT),DOWNSTREAM(MODIFIER||3221||1134|VCL|protein_coding|CODING|NM_014000.2||CTT) 0 0.5 1 21 0.381818 1 1 0 . 0 60 0 0 1 0 . rs3830382 -0.692067 0.153862 55 220 LOW 2 CODING DUPD1 T protein_coding NM_001003892.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76803548 C T 0 93 0 0.1762 0.1168 0.1023 0.1558 0.0089 0.1176 0.14503 0.0546755 0.00837404 1 1533 6502 1555 1266 61 625 45 1417 2 9494 114934 11248 8272 6428 62350 846 16296 0.724199 0 . 0 . 27 17,0,10,0 SPLICE_SITE_REGION+INTRON(LOW||||220|DUPD1|protein_coding|CODING|NM_001003892.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.994971 rs114881123 -0.670168 0.000100675 27 S137R 220 Agc/Cgc MODERATE 2 MISSENSE CODING DUPD1 G protein_coding NM_001003892.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76803567 T G 0 159 0 0.6543 0.3009 0.2061 0.2738 0.0457 0.181 0.555606 0.220898 0.0494186 1 5879 17346 3195 2256 314 3191 119 2392 2 10214 118914 11464 8476 6594 64818 888 16460 0.279445 0 . 0 . 51 29,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Cgc|S137R|220|DUPD1|protein_coding|CODING|NM_001003892.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.874123 rs16931938 -0.692067 8.8742e-05 51 C249Y 291 tGt/tAt MODERATE 6 MISSENSE CODING DUSP13 T protein_coding NM_001007273.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76854564 C T 0 228 0 0.6884 0.6418 0.6844 0.9028 0.4433 0.4836 0.658874 0.504844 0.42593 2 6892 62606 8805 7867 3108 27595 480 7859 2 10338 120610 11500 8632 6488 66276 898 16478 0 . 0 . 0 59 0,0,21,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C249Y|291|DUSP13|protein_coding|CODING|NM_001007273.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3088142 -0.693147 0.373405 59 291 LOW 5 CODING DUSP13 G protein_coding NM_001007273.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76855326 A G 0 222 0 0.4463 0.4263 0.4452 0.6379 0.2773 0.3211 0.430776 0.322467 0.266977 1 4591 41154 5362 5793 2343 17551 298 5216 2 10396 121130 11528 8628 6600 66594 904 16480 0.998283 0 . 0 . 113 40,21,21,16 SPLICE_SITE_REGION+INTRON(LOW||||291|DUSP13|protein_coding|CODING|NM_001007273.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.770643 rs3740318 -0.693141 0.0259826 113 D198 291 gaC/gaT LOW 5 SILENT CODING DUSP13 A protein_coding NM_001007273.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76855412 G A 0 222 0 0.4289 0.4213 0.4424 0.6379 0.2773 0.3211 0.419655 0.318853 0.267209 1 4437 41023 5360 5798 2354 17557 298 5219 2 10402 121374 11572 8634 6614 66736 906 16510 0.639507 0 . 0 COSM146972 90 28,21,16,17 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D198|291|DUSP13|protein_coding|CODING|NM_001007273.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.803275 rs3740317 -0.693127 8.63608e-05 90 I195 291 atC/atT LOW 5 SILENT CODING DUSP13 A protein_coding NM_001007273.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76855421 G A 0 222 0 0.233 0.2133 0.2406 0.2649 0.166 0.1626 0.216069 0.177226 0.157326 1 2232 21547 3472 2080 787 10151 179 2646 2 10404 121378 11570 8638 6614 66734 908 16510 0.731694 0 . 0 . 87 16,19,24,21 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I195|291|DUSP13|protein_coding|CODING|NM_001007273.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.922194 rs3740316 -0.693147 0.148562 87 S75G 291 Agc/Ggc MODERATE 3 MISSENSE CODING DUSP13 C protein_coding NM_001007273.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76861680 T C 0 228 0 0.7829 0.6701 0.6902 0.8998 0.4483 0.4949 0.732864 0.532216 0.429419 2 7790 64189 8918 7882 3148 27982 482 7987 2 10404 121402 11576 8654 6614 66736 908 16510 0 . 0 . 0 73 0,0,22,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S75G|291|DUSP13|protein_coding|CODING|NM_001007273.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6480771 -0.693147 0.189626 73 415 241 MODIFIER 6 CODING SAMD8 G protein_coding NM_001174156.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76936691 T G 0 46.3 0 0.1407 0.0795 0.0476 0.0605 0.0547 0.0644 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||241||415|SAMD8|protein_coding|CODING|NM_001174156.1|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7893833 -0.453602 0.72 2 415 2407 MODIFIER 6 CODING SAMD8 C protein_coding NM_001174156.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76938857 T C 0 9.7 0 0.1407 0.0797 0.0476 0.0615 0.0547 0.0644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2407||415|SAMD8|protein_coding|CODING|NM_001174156.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs143609631 -0.379885 0 1 309 729 MODIFIER 1 CODING VDAC2 C protein_coding NM_001184783.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 76970613 G C 0 228 0 0.9728 0.8411 0.8026 0.9673 0.5517 0.8579 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,10,4 UTR_5_PRIME(MODIFIER||729||309|VDAC2|protein_coding|CODING|NM_001184783.1|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11543 -0.686358 0.297415 16 1236 1957 MODIFIER 28 CODING KCNMA1 A protein_coding NM_001161352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 78645067 G A 0 9.7 0 0.9115 0.7147 0.6988 0.5139 0.8002 0.5787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1957||1236|KCNMA1|protein_coding|CODING|NM_001161352.1|28|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7073015 -0.379885 0 1 1236 1571 MODIFIER 28 CODING KCNMA1 A protein_coding NM_001161352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 78645453 G A 0 46.3 0 0.3472 0.3806 0.3573 0.2956 0.5845 0.32 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1571||1236|KCNMA1|protein_coding|CODING|NM_001161352.1|28|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10762733 -0.453602 0.28 2 1919 558 MODIFIER 32 CODING DLG5 T protein_coding NM_004747.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79551640 C T 0 228 0 0.1369 0.271 0.4755 0.2907 0.2813 0.2761 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987026 0 . 0 . 189 2,2,106,63 UTR_3_PRIME(MODIFIER||558||1919|DLG5|protein_coding|CODING|NM_004747.3|32|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.936029 rs2165047,rs386559359 -0.693147 0.793851 189 1919 91 MODIFIER 32 CODING DLG5 A protein_coding NM_004747.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79552107 G A 0 228 0 0.1369 0.2712 0.4755 0.2907 0.2823 0.2761 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,25,4 UTR_3_PRIME(MODIFIER||91||1919|DLG5|protein_coding|CODING|NM_004747.3|32|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1058203 -0.693079 0.40007 31 1919 47 MODIFIER 32 CODING DLG5 C protein_coding NM_004747.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79552151 T C 0 228 0 0.8419 0.7414 0.781 0.7272 0.661 0.6748 0.816841 0.720744 0.671512 2 8553 84004 9049 6375 4081 44248 579 11119 2 10402 121242 11568 8644 6606 66640 908 16474 0 . 0 . 0 49 0,0,39,7 UTR_3_PRIME(MODIFIER||47||1919|DLG5|protein_coding|CODING|NM_004747.3|32|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058202,rs386514462 -0.693147 0.110574 49 G1176 1919 ggC/ggT LOW 17 SILENT CODING DLG5 A protein_coding NM_004747.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79579222 G A 0 228 0 0.0908 0.2554 0.4625 0.2917 0.2753 0.273 0.129823 0.226895 0.276628 2 1286 33898 5442 2497 1963 17462 233 5015 2 10188 119422 11454 8558 6398 65960 872 15992 1 0 . 0 . 199 1,0,122,51 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1176|1919|DLG5|protein_coding|CODING|NM_004747.3|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1248634 -0.693147 0.510663 199 R782 1919 cgC/cgG LOW 14 SILENT CODING DLG5 C protein_coding NM_004747.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79584178 G C 0 228 0 0.8737 0.7442 0.7795 0.7282 0.6491 0.6585 0.83931 0.716285 0.653256 2 8820 82372 8963 6332 3943 42921 567 10826 2 10382 120920 11538 8610 6544 66468 904 16474 0.979095 0 . 0 . 78 1,2,39,32 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgG|R782|1919|DLG5|protein_coding|CODING|NM_004747.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.879374 rs1248629 -0.693147 0.0388781 78 Q140R 1919 cAg/cGg MODERATE 3 MISSENSE CODING DLG5 C protein_coding NM_004747.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79616605 T C 0 228 0 0.9939 0.9657 0.951 0.998 0.9115 0.9601 0.982751 0.925573 0.896279 2 10185 112431 11127 8621 6072 59827 828 15771 2 10354 120748 11532 8626 6592 66348 900 16396 0 . 0 . 0 101 0,0,42,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q140R|1919|DLG5|protein_coding|CODING|NM_004747.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1248696 -0.693147 0.183777 101 1390 1323 MODIFIER 31 CODING POLR3A A protein_coding NM_007055.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79735913 G A 0 23.4 0 0.1422 0.2746 0.2421 0.5347 0.2147 0.2699 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1323||1390|POLR3A|protein_coding|CODING|NM_007055.3|31|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs45570840 -0.453602 0.56 2 1390 272 MODIFIER 31 CODING POLR3A G protein_coding NM_007055.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79736964 C G 0 75 0 0.351 0.3343 0.2608 0.5446 0.2147 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.936488 0 . 0 . 18 3,8,0,7 UTR_3_PRIME(MODIFIER||272||1390|POLR3A|protein_coding|CODING|NM_007055.3|31|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.554013 rs2241547 -0.636426 0.720054 18 C798 1390 tgT/tgC LOW 18 SILENT CODING POLR3A G protein_coding NM_007055.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79760818 A G 0 222 0 0.0113 0.108 0.1124 0.255 0.0348 0.1595 0.0222424 0.0256805 0.0274419 1 201 7156 1076 1842 221 1522 51 2243 2 10396 121302 11552 8650 6612 66678 908 16506 0.383674 0 . 0 COSM146976 119 33,23,37,17 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C798|1390|POLR3A|protein_coding|CODING|NM_007055.3|18|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96896 rs35536566 -0.693147 0.0267942 119 H762 1390 caC/caT LOW 17 SILENT CODING POLR3A A protein_coding NM_007055.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79762028 G A 0 222 0 0.0113 0.108 0.1124 0.255 0.0348 0.1595 0.0222424 0.0255267 0.0272093 1 174 5670 763 1517 137 1278 43 1758 2 6956 68424 4786 6014 2260 36756 498 11154 0.488518 0 . 0 . 57 17,8,13,10 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H762|1390|POLR3A|protein_coding|CODING|NM_007055.3|17|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95912 rs16935534 -0.692717 0.467861 57 289 109 MODIFIER 1 CODING RPS24 G protein_coding NM_001142285.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79793551 A G 0 222 0 0.025 0.1138 0.1153 0.2629 0.0328 0.1626 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.837558 0 . 0 . 52 17,4,19,6 UTR_5_PRIME(MODIFIER||109||289|RPS24|protein_coding|CODING|NM_001142285.1|1|G),UPSTREAM(MODIFIER||4253||1390|POLR3A|protein_coding|CODING|NM_007055.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0460739 rs3740254 -0.692914 0.00606887 52 L141 289 Ttg/Ctg LOW 5 SILENT CODING RPS24 C protein_coding NM_001142285.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 79814319 T C 0 222 0 0.0234 0.1146 0.1153 0.2599 0.0328 0.1718 0.0260116 0.0291283 0.030484 1 54 1429 40 161 2 192 17 963 2 2142 16736 386 614 38 7516 156 5884 0.602662 0 . 0 COSM146978 170 70,12,62,15 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L141|289|RPS24|protein_coding|CODING|NM_001142285.1|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.266294 rs72642283 -0.693147 0.0674627 170 1067 132416 MODIFIER 1 CODING ZMIZ1 T protein_coding NM_020338.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 80828974 C T 0 9.7 0 0.0053 0.1186 0.17 0.2937 0.0646 0.1104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||1067|ZMIZ1|protein_coding|CODING|NM_020338.3|1|T),UTR_5_PRIME(MODIFIER||132416||1067|ZMIZ1|protein_coding|CODING|NM_020338.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs76908738 -0.379885 0 1 1067 39526 MODIFIER 4 CODING ZMIZ1 G protein_coding NM_020338.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 80921864 A G 0 228 0 0.8759 0.734 0.719 0.6954 0.8091 0.5153 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,0,16,38 UTR_5_PRIME(MODIFIER||39526||1067|ZMIZ1|protein_coding|CODING|NM_020338.3|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs697241 -0.693147 0.000301023 57 1067 1009 MODIFIER 25 CODING ZMIZ1 G protein_coding NM_020338.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81073515 C G 0 145 0 0.329 0.3748 0.3631 0.4603 0.3847 0.3466 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,2 UTR_3_PRIME(MODIFIER||1009||1067|ZMIZ1|protein_coding|CODING|NM_020338.3|25|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3824718 -0.590765 0.768087 6 1067 2310 MODIFIER 25 CODING ZMIZ1 A protein_coding NM_020338.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81074816 G A 0 228 0 0.1589 0.2458 0.1916 0.3075 0.3221 0.2597 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,45,7 UTR_3_PRIME(MODIFIER||2310||1067|ZMIZ1|protein_coding|CODING|NM_020338.3|25|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3740259,rs386585181 -0.693147 0.420964 54 207 462 MODIFIER 6 CODING PPIF A protein_coding NM_005729.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81114060 G A 0 228 0 0.8744 0.6496 0.6657 0.6468 0.5268 0.4632 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 90 0,0,80,9 UTR_3_PRIME(MODIFIER||462||207|PPIF|protein_coding|CODING|NM_005729.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386609330,rs7332 -0.693147 0.0778289 90 207 1215 MODIFIER 6 CODING PPIF G protein_coding NM_005729.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81114813 C G 0 39.3 0 0.9607 0.6899 0.6888 0.6577 0.5577 0.4939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1215||207|PPIF|protein_coding|CODING|NM_005729.3|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs8837 -0.453602 0.66 2 207 1361 MODIFIER 6 CODING PPIF T protein_coding NM_005729.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81114959 C T 0 39.3 0 0.385 0.5122 0.6254 0.6468 0.5159 0.4611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1361||207|PPIF|protein_coding|CODING|NM_005729.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7898 -0.453602 0.1 2 241 3736 MODIFIER 4 CODING ZCCHC24 T protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81142365 C T 0 228 0 0.3525 0.4565 0.5159 0.6171 0.4761 0.3691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 76 1,0,48,26 UTR_3_PRIME(MODIFIER||3736||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs6858 -0.693147 0.339501 76 241 1404 MODIFIER 4 CODING ZCCHC24 T protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81144697 C T 0 193 0 0.1324 0.3103 0.2651 0.5933 0.2932 0.3088 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,1,15 UTR_3_PRIME(MODIFIER||1404||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4979863 -0.689466 0.134516 16 241 835 MODIFIER 4 CODING ZCCHC24 A protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81145266 G A 0 67 0 0.9894 0.8403 0.8545 0.7808 0.7714 0.7607 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||835||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4980069 -0.511536 0.275636 3 241 566 MODIFIER 4 CODING ZCCHC24 C protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81145535 T C 0 58 0 0.8268 0.6178 0.513 0.6071 0.5388 0.502 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 10 5,0,4,0 UTR_3_PRIME(MODIFIER||566||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 0 . 0.89338 rs1063119 -0.556411 0.372756 10 241 459 MODIFIER 4 CODING ZCCHC24 C protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81145642 T C 0 228 0 0.9758 0.9439 0.8588 0.994 0.9245 0.9294 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 48 0,0,45,1 UTR_3_PRIME(MODIFIER||459||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046445 -0.693147 0.193862 48 241 400 MODIFIER 4 CODING ZCCHC24 C protein_coding NM_153367.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81145701 G C 0 228 0 0.1021 0.2857 0.2738 0.6319 0.2177 0.2556 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 88 0,0,56,23 UTR_3_PRIME(MODIFIER||400||241|ZCCHC24|protein_coding|CODING|NM_153367.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046444 -0.693147 0.0196197 88 154 11 MODIFIER 1 CODING EIF5AL1 G protein_coding NM_001099692.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81272881 A G 0 213 0 . 0 . 0 . 0 . 0 . 1 1233 25283 2522 3109 1449 13387 206 3377 2 8148 106290 10290 8032 5810 58262 820 14928 0.62804 0 . 0 . 163 39,58,26,34 UTR_3_PRIME(MODIFIER||11||154|EIF5AL1|protein_coding|CODING|NM_001099692.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.660767 0.621876 0 0.775296 rs199829110 -0.693147 0.0685641 163 154 1192 MODIFIER 1 CODING EIF5AL1 T protein_coding NM_001099692.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81274062 C T 0 45.8 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.243788 0 . 0 . 128 54,43,6,17 UTR_3_PRIME(MODIFIER||1192||154|EIF5AL1|protein_coding|CODING|NM_001099692.1|1|T) 0 0.5 1 0 . 0 . 0 . 0 53 0 1.45846e-08 0.834784 0 0.0139299 rs199493583 -0.692717 1.70203e-05 128 T9N 248 aCc/aAc MODERATE 3 MISSENSE CODING SFTPA2 T protein_coding NM_001098668.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81319214 G T 0 228 0 0.292 0.4485 0.5303 0.4821 0.5855 0.4264 0 . 0 2 1901 36996 2882 2243 1995 22324 264 5387 2 8874 100138 9462 7176 5286 54314 726 14300 1 0 . 0 . 61 1,0,15,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T9N|248|SFTPA2|protein_coding|CODING|NM_001098668.2|3|T) 0 . 0 . 0 1 0 . 1 0 33 0 1 0.999965 0 1 rs1059046 -0.693147 0.00129005 61 248 LOW 2 CODING SFTPA2 T protein_coding NM_001098668.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81319267 C T 0 228 0 0.5802 0.6875 0.6787 0.7282 0.7873 0.6943 0.513403 0.602441 0.648326 2 5224 64066 3801 4466 3648 37253 500 9174 2 9104 97804 8740 7090 5178 53476 742 13474 0 . 0 . 0 35 0,0,13,21 SPLICE_SITE_REGION+INTRON(LOW||||248|SFTPA2|protein_coding|CODING|NM_001098668.2|2|T) 1 0 . 0 . 1 0 1 1 0 34 0 0 0.0154375 0 . rs1650232 -0.693132 0.997958 35 L65V 263 Ctc/Gtc MODERATE 3 MISSENSE CODING SFTPA1 G protein_coding NM_001093770.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81371729 C G 0 157 0 . 0 . 0 . 0 . 0 . 1 4607 58659 4788 2254 3556 36928 426 6100 2 10102 118700 11336 8484 6420 65022 890 16446 0.882518 0 . 0 . 107 16,45,3,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L65V|263|SFTPA1|protein_coding|CODING|NM_001093770.2|3|G) 0 0.5 1 0 . 0 . 0 1 0 50 0 3.21352e-07 0.546524 0 0.94376 rs1136450 -0.693145 0.077797 107 Y199 263 taT/taC LOW 6 SILENT CODING SFTPA1 C protein_coding NM_001093770.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81373674 T C 0 222 0 0.0272 0.0893 0.0663 0.245 0.007 0.1135 0.0261008 0.0118534 0.00454228 1 256 4919 810 2259 2 261 32 1299 2 10330 121238 11578 8640 6614 66658 908 16510 0.165691 2 benign 0 . 175 46,31,49,31 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y199|263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 43 0 0.920395 1.43716e-06 0 0.654967 rs148138544 -0.693147 0.636378 175 263 213 MODIFIER 6 CODING SFTPA1 C protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374082 T C 0 179 0 0.1831 0.3077 0.3386 0.5079 0.17 0.3896 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.431591 0 . 0 . 16 1,5,2,7 UTR_3_PRIME(MODIFIER||213||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.840624 rs2945439 -0.662043 0.0692038 16 263 214 MODIFIER 6 CODING SFTPA1 A protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374083 C A 0 168 0 0.1831 0.3077 0.3386 0.5079 0.17 0.3896 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99308 0 . 0 . 16 1,5,2,7 UTR_3_PRIME(MODIFIER||214||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.840624 rs1650220 -0.662043 0.0692038 16 263 249 MODIFIER 6 CODING SFTPA1 A protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374118 C A 0 164 0 0.1596 0.3021 0.3401 0.5109 0.171 0.3875 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.795669 0 . 0 . 14 0,3,1,9 UTR_3_PRIME(MODIFIER||249||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.699673 rs4253529 -0.670168 0.525878 14 263 424 MODIFIER 6 CODING SFTPA1 G protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374293 A G 0 23.4 0 0.407 0.4075 0.4741 0.2649 0.5746 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||424||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs71493605 -0.453602 0.18 4 263 428 MODIFIER 6 CODING SFTPA1 C protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374297 T C 0 23.4 0 0.407 0.4075 0.4741 0.2649 0.5746 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||428||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs77610008 -0.453602 0.18 4 263 782 MODIFIER 6 CODING SFTPA1 T protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374651 C T 0 198 0 0.9115 0.6685 0.5331 0.7212 0.4205 0.637 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.87342 0 . 0 . 36 15,0,18,1 UTR_3_PRIME(MODIFIER||782||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.242953 rs1250991 -0.69168 0.552074 36 263 1018 MODIFIER 6 CODING SFTPA1 G protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374887 A G 0 222 0 0.0416 0.0935 0.0836 0.25 0.007 0.0982 0.033237 0.0135786 0.00502828 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666643 0 . 0 . 182 48,39,20,40 UTR_3_PRIME(MODIFIER||1018||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|G) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.219309 rs3740271 -0.693147 0.0109248 182 263 1108 MODIFIER 6 CODING SFTPA1 C protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374977 T C 0 94 0 0.0598 0.0978 0.0821 0.248 0.008 0.0982 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.995836 0 . 0 . 52 2,33,0,16 UTR_3_PRIME(MODIFIER||1108||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.793555 rs3740272 -0.689466 0.282545 52 263 1117 MODIFIER 6 CODING SFTPA1 C protein_coding NM_001093770.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81374986 T C 0 149 0 0.6067 0.5887 0.5115 0.7579 0.4016 0.637 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.937555 0 . 0 . 46 2,25,1,17 UTR_3_PRIME(MODIFIER||1117||263|SFTPA1|protein_coding|CODING|NM_001093770.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.993313 rs1059225 -0.691153 0.730927 46 V205 878 gtC/gtA LOW 2 SILENT CODING NUTM2B A protein_coding NM_001278495.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81466030 C A 0 200 0 . 0 . 0 . 0 . 0 . 1 30 101 3 22 0 42 3 1 2 124 890 30 88 2 620 12 14 0.846574 0 . 0 . 196 39,40,35,52 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtA|V205|878|NUTM2B|protein_coding|CODING|NM_001278495.1|2|A),INTRAGENIC(MODIFIER|||||NUTM2B-AS1||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 1 0 26 0 0.954861 0.596297 0 0.0412324 rs201336686,rs61863489 -0.693147 0.000266311 196 Y835H 878 Tac/Cac MODERATE 7 MISSENSE CODING NUTM2B C protein_coding NM_001278495.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81472107 T C 0 88 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,20,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y835H|878|NUTM2B|protein_coding|CODING|NM_001278495.1|7|C),INTRAGENIC(MODIFIER|||||NUTM2B-AS1||NON_CODING|||C) 0 . 0 . 0 . 0 . 0 . 21 0 0 . 0 . rs451438 -0.692067 0.000142956 20 T180A 375 Aca/Gca MODERATE 5 MISSENSE CODING SFTPD C protein_coding NM_003019.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81701722 T C 0 228 0 0.9826 0.7704 0.6196 0.7917 0.6113 0.7321 0.92374 0.716054 0.609651 2 9714 80455 7060 6953 4036 40125 605 11962 2 10400 121258 11564 8646 6608 66644 906 16490 1 2 benign 0 . 39 1,0,31,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T180A|375|SFTPD|protein_coding|CODING|NM_003019.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2243639 -0.693141 0.566884 39 M31T 375 aTg/aCg MODERATE 2 MISSENSE CODING SFTPD G protein_coding NM_003019.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81706324 A G 0 228 0 0.4009 0.5046 0.379 0.6151 0.4205 0.7065 0.401498 0.413578 0.419767 2 4196 56918 5243 5401 2675 27898 417 11088 2 10382 121092 11516 8628 6548 66606 904 16508 0 2 benign 0 . 104 0,0,54,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M31T|375|SFTPD|protein_coding|CODING|NM_003019.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs721917 -0.693147 0.00634903 104 L85 147 ctG/ctT LOW 2 SILENT CODING TMEM254 T protein_coding NM_001270367.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81841692 G T 0 222 0 0.2345 0.4211 0.3372 0.6865 0.4125 0.4683 0.26759 0.373443 0.427674 1 2648 50386 3106 6013 2752 28134 396 7337 2 10396 121348 11570 8642 6612 66716 904 16508 0.4582 0 . 0 . 66 14,21,12,15 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L85|147|TMEM254|protein_coding|CODING|NM_001270367.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.212331 rs1932574 -0.693021 0.367378 66 505 473 MODIFIER 15 CODING ANXA11 C protein_coding NM_001157.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81915136 T C 0 228 0 0.6657 0.8658 0.8919 0.997 0.8986 0.9489 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . COSN407460 57 0,0,26,24 UTR_3_PRIME(MODIFIER||473||505|ANXA11|protein_coding|CODING|NM_001157.2|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2789686 -0.693147 0.00267536 57 R230C 505 Cgc/Tgc MODERATE 6 MISSENSE CODING ANXA11 A protein_coding NM_001157.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 81926702 G A 0 222 0 0.1551 0.3922 0.4654 0.6429 0.4503 0.3425 0.202224 0.339228 0.409419 1 1870 45030 4766 5202 2496 24922 361 5413 2 7718 100742 9562 7600 4788 56546 744 13784 0.848539 0 . 0 . 121 19,40,21,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R230C|505|ANXA11|protein_coding|CODING|NM_001157.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984738 rs1049550 -0.693147 0.102217 121 395 1297 MODIFIER 9 CODING MAT1A G protein_coding NM_000429.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82032240 A G 0 9.7 0 0.329 0.4982 0.4366 0.9474 0.3479 0.4622 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1297||395|MAT1A|protein_coding|CODING|NM_000429.2|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1985908 -0.379885 0 1 A294 395 gcT/gcC LOW 7 SILENT CODING MAT1A G protein_coding NM_000429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82034842 A G 0 228 0 0.9266 0.8405 0.7781 0.9712 0.6412 0.8384 0.869891 0.707032 0.623575 2 5620 55471 5431 4975 2225 26665 416 10139 2 6340 74546 6638 5116 3186 40440 554 12272 0 . 0 . COSM428025 61 0,0,36,18 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A294|395|MAT1A|protein_coding|CODING|NM_000429.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10887711 -0.693147 0.0130854 61 V290 395 gtA/gtG LOW 7 SILENT CODING MAT1A C protein_coding NM_000429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82034854 T C 0 228 0 0.9266 0.8409 0.7781 0.9712 0.6412 0.8405 0.872558 0.70934 0.625756 2 7131 71194 7555 7058 3104 34024 524 11798 2 7992 94870 9128 7232 4368 51260 698 14192 0 . 0 . 0 76 0,0,44,23 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V290|395|MAT1A|protein_coding|CODING|NM_000429.2|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10788546 -0.693147 0.996376 76 A142 395 gcT/gcC LOW 5 SILENT CODING MAT1A G protein_coding NM_000429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82040052 A G 0 228 0 0.9743 0.8634 0.7968 0.9722 0.669 0.8487 0.921017 0.748424 0.66 2 9731 91527 9564 8449 4642 44606 696 13839 2 10402 121340 11566 8652 6610 66692 908 16510 1 0 . 0 . 76 0,1,23,45 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A142|395|MAT1A|protein_coding|CODING|NM_000429.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1143694 -0.693147 0.0089441 76 191 101 MODIFIER 4 CODING DYDC2 G protein_coding NM_001270042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82126808 C G 0 228 0 0.8986 0.8452 0.781 0.9772 0.6769 0.8558 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,3,33 UTR_3_PRIME(MODIFIER||101||191|DYDC2|protein_coding|CODING|NM_001270042.1|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047952 -0.693139 0.533576 38 191 404 MODIFIER 4 CODING DYDC2 G protein_coding NM_001270042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82127111 T G 0 46.3 0 0.8986 0.8452 0.781 0.9772 0.6769 0.8558 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||404||191|DYDC2|protein_coding|CODING|NM_001270042.1|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1972371 -0.453602 0.42 2 191 473 MODIFIER 4 CODING DYDC2 G protein_coding NM_001270042.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82127180 A G 0 6.3 0 0.966 0.8744 0.8055 0.9772 0.7068 0.8661 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||473||191|DYDC2|protein_coding|CODING|NM_001270042.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1972370 -0.379885 0 1 270 34925 MODIFIER 1 CODING TSPAN14 C protein_coding NM_030927.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82214065 G C 0 9.7 0 0.615 0.6815 0.6772 0.9504 0.5696 0.6125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||34925||270|TSPAN14|protein_coding|CODING|NM_030927.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs116857892 -0.379885 0 1 270 2195 MODIFIER 9 CODING TSPAN14 T protein_coding NM_030927.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82279927 C T 0 6.3 0 0.1135 0.4335 0.5014 0.8155 0.4652 0.3916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2195||270|TSPAN14|protein_coding|CODING|NM_030927.2|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386618405,rs873259 -0.379885 0 1 270 2228 MODIFIER 9 CODING TSPAN14 T protein_coding NM_030927.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82279960 C T 0 42.3 0 0.0408 0.3734 0.4438 0.8155 0.3877 0.3027 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2228||270|TSPAN14|protein_coding|CODING|NM_030927.2|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386618404,rs873258 -0.453602 0.32 2 270 2405 MODIFIER 9 CODING TSPAN14 G protein_coding NM_030927.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82280137 T G 0 179 0 0.9682 0.9243 0.889 0.9851 0.8151 0.9397 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,2 UTR_3_PRIME(MODIFIER||2405||270|TSPAN14|protein_coding|CODING|NM_030927.2|9|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1878036 -0.651104 0.612706 8 270 2408 MODIFIER 9 CODING TSPAN14 T protein_coding NM_030927.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82280140 C T 0 179 0 0.1135 0.4335 0.5014 0.8145 0.4652 0.3926 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,6,2 UTR_3_PRIME(MODIFIER||2408||270|TSPAN14|protein_coding|CODING|NM_030927.2|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs873257 -0.651104 0.612706 8 270 4246 MODIFIER 9 CODING TSPAN14 C protein_coding NM_030927.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82281978 T C 0 46.3 0 0.9992 0.9918 0.9928 1 0.9732 0.9918 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||4246||270|TSPAN14|protein_coding|CODING|NM_030927.2|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1878034 -0.453602 0.22 2 R217 357 Cgg/Agg LOW 5 SILENT CODING SH2D4B A protein_coding NM_207372.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82363340 C A 0 228 0 0.5151 0.3742 0.2536 0.5149 0.2386 0.2638 0.460028 0.318196 0.245877 2 1737 9483 326 921 124 3907 76 2392 2 3192 23582 768 1522 246 10416 216 7222 1 0 . 0 . 112 0,1,77,25 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R217|357|SH2D4B|protein_coding|CODING|NM_207372.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7069048 -0.693147 0.241455 112 H238R 357 cAc/cGc MODERATE 5 MISSENSE CODING SH2D4B G protein_coding NM_207372.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82363404 A G 0 228 0 0.4592 0.3606 0.255 0.5188 0.2386 0.2648 0.432894 0.31632 0.256691 2 3594 29068 2775 3407 1229 13754 208 4101 2 7346 75440 6124 6078 2992 40084 530 12286 0 . 0 . COSM428029 126 0,0,77,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H238R|357|SH2D4B|protein_coding|CODING|NM_207372.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7075840 -0.693147 0.00287443 126 D299E 357 gaT/gaA MODERATE 6 MISSENSE CODING SH2D4B A protein_coding NM_207372.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 82369219 T A 0 228 0 0.0242 0.15 0.1239 0.3442 0.171 0.1166 0.0533364 0.130555 0.170116 2 503 20516 1977 3225 1312 11395 167 1937 2 10398 121334 11572 8618 6614 66714 906 16512 0.923077 0 . 0 . 57 0,2,26,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D299E|357|SH2D4B|protein_coding|CODING|NM_207372.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.615385 rs17107368 -0.693147 0.228569 57 S662 696 agC/agT LOW 9 SILENT CODING NRG3 T protein_coding NM_001010848.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 84745256 C T 0 228 0 0.4236 0.4696 0.4438 0.6637 0.3439 0.4796 0.42374 0.340766 0.298256 2 4494 46057 5324 5721 2699 20087 334 7398 2 10394 121132 11528 8576 6602 66618 904 16510 0 . 0 . 0 144 0,0,59,70 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S662|696|NRG3|protein_coding|CODING|NM_001010848.3|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2295933 -0.693147 0.0111218 144 696 1215 MODIFIER 9 CODING NRG3 T protein_coding NM_001010848.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 84746576 C T 0 9.7 0 0.885 0.9307 0.9798 0.9266 0.9423 0.9499 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1215||696|NRG3|protein_coding|CODING|NM_001010848.3|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3763704 -0.379885 0 1 81 333 MODIFIER 3 CODING C10orf99 A protein_coding NM_207373.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85944855 T A 0 9.7 0 0.3858 0.243 0.2046 0.1548 0.2604 0.1503 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||333||81|C10orf99|protein_coding|CODING|NM_207373.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs13697 -0.379885 0 1 A159 859 gcA/gcG LOW 6 SILENT CODING CDHR1 G protein_coding NM_033100.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85960395 A G 0 222 0 0.711 0.516 0.5202 0.3948 0.4612 0.4305 0.669315 0.524912 0.45093 1 6756 54961 6108 3173 2636 29166 365 6757 2 9648 111096 10614 8184 5408 61560 792 14890 0.489292 0 . 0 . 94 24,20,22,18 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A159|859|CDHR1|protein_coding|CODING|NM_033100.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930119 rs4933975 -0.693145 0.78658 94 T813 859 acT/acC LOW 17 SILENT CODING CDHR1 C protein_coding NM_033100.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85974236 T C 0 222 0 0.829 0.5737 0.5692 0.4107 0.5189 0.456 0.766001 0.604875 0.522326 1 8113 64651 6824 3372 3127 35100 456 7659 2 10362 121048 11550 8582 6600 66554 906 16494 0.679406 2 benign 0 . 86 10,41,5,28 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T813|859|CDHR1|protein_coding|CODING|NM_033100.3|17|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.855503 rs3814213,rs386587041 -0.693127 0.0141751 86 859 4 MODIFIER 17 CODING CDHR1 G protein_coding NM_033100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85974381 A G 0 222 0 0.9228 0.6274 0.6412 0.4117 0.6024 0.4663 0.858602 0.680532 0.589302 1 8669 69838 7265 3292 3603 38590 503 7916 2 9854 119034 11472 8378 6582 65406 886 16456 0.976296 2 benign 0 . 85 18,20,23,10 UTR_3_PRIME(MODIFIER||4||859|CDHR1|protein_coding|CODING|NM_033100.3|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.863469 rs3814212,rs386587040 -0.693127 0.144662 85 859 173 MODIFIER 17 CODING CDHR1 A protein_coding NM_033100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85974550 C A 0 163 0 0.0666 0.2069 0.268 0.2907 0.2843 0.1871 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 19 2,6,2,7 UTR_3_PRIME(MODIFIER||173||859|CDHR1|protein_coding|CODING|NM_033100.3|17|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995381 rs386504305,rs41291358 -0.662043 0.295206 19 859 869 MODIFIER 17 CODING CDHR1 G protein_coding NM_033100.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85975246 T G 0 9.7 0 0.8215 0.5717 0.5706 0.4107 0.5159 0.4581 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||869||859|CDHR1|protein_coding|CODING|NM_033100.3|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6585845 -0.379885 0 1 560 325 MODIFIER 4 CODING LRIT2 A protein_coding NM_001284223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85981351 G A 0 9.7 0 0.0575 0.2091 0.2925 0.3452 0.2316 0.1912 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||325||560|LRIT2|protein_coding|CODING|NM_001284223.1|4|A),DOWNSTREAM(MODIFIER||2899||859|CDHR1|protein_coding|CODING|NM_033100.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11817531 -0.379885 0 1 T520P 560 Acc/Ccc MODERATE 4 MISSENSE CODING LRIT2 G protein_coding NM_001284223.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85981801 T G 0 170 0 0.8192 0.5551 0.5346 0.4107 0.4662 0.453 0.748296 0.554077 0.454641 1 7643 58972 6605 3380 2965 30770 412 7197 2 9880 117946 11548 8588 6610 65204 886 15230 0.957561 0 . 0 COSM1349333,COSM1349334 38 9,14,2,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T520P|560|LRIT2|protein_coding|CODING|NM_001284223.1|4|G),DOWNSTREAM(MODIFIER||3349||859|CDHR1|protein_coding|CODING|NM_033100.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.294085 rs6585847 -0.676189 0.525132 38 V506A 560 gTc/gCc MODERATE 4 MISSENSE CODING LRIT2 G protein_coding NM_001284223.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85981842 A G 0 191 0 0.0522 0.2079 0.2911 0.3452 0.2346 0.1902 0.0865123 0.175561 0.221163 1 846 25029 3054 2838 750 14166 155 3220 2 9706 117602 11524 8576 6606 64968 884 15338 0.945355 0 . 0 . 40 10,15,4,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V506A|560|LRIT2|protein_coding|CODING|NM_001284223.1|4|G),DOWNSTREAM(MODIFIER||3390||859|CDHR1|protein_coding|CODING|NM_033100.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.437904 rs12217769 -0.688148 0.417695 40 G490 560 ggC/ggT LOW 4 SILENT CODING LRIT2 A protein_coding NM_001284223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85981889 G A 0 222 0 0.0514 0.1861 0.232 0.2907 0.2316 0.181 0.0860191 0.175688 0.221628 1 862 23522 2067 2308 743 14182 151 3209 2 9984 119242 11538 8598 6598 65634 888 16002 0.598331 0 . 0 . 46 15,9,13,7 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G490|560|LRIT2|protein_coding|CODING|NM_001284223.1|4|A),DOWNSTREAM(MODIFIER||3437||859|CDHR1|protein_coding|CODING|NM_033100.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975242 rs12218853 -0.692067 0.456643 46 L220F 560 Ctc/Ttc MODERATE 2 MISSENSE CODING LRIT2 A protein_coding NM_001284223.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85984323 G A 0 222 0 0.0522 0.1869 0.232 0.2907 0.2346 0.181 0.0860191 0.177764 0.224767 1 873 23830 2069 2319 749 14419 156 3245 2 10400 121238 11572 8640 6614 66656 904 16452 0.999853 0 . 0 . 110 27,30,18,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L220F|560|LRIT2|protein_coding|CODING|NM_001284223.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.701285 rs11200925 -0.693146 0.0150927 110 G186 560 ggG/ggA LOW 2 SILENT CODING LRIT2 T protein_coding NM_001284223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85984423 C T 0 222 0 0.0522 0.2079 0.2911 0.3452 0.2346 0.1902 0.0876078 0.178533 0.225116 1 884 25505 3050 2862 746 14446 162 3355 2 10398 121270 11552 8626 6604 66686 906 16498 0.937947 0 . 0 . 92 14,29,19,22 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G186|560|LRIT2|protein_coding|CODING|NM_001284223.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.715185 rs11200926 -0.693145 0.476647 92 L86 560 ctC/ctT LOW 2 SILENT CODING LRIT2 A protein_coding NM_001284223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85984723 G A 0 222 0 0.0522 0.2081 0.2925 0.3452 0.2346 0.1902 0.0876078 0.17861 0.225233 1 882 25525 3060 2867 750 14448 162 3356 2 10402 121396 11576 8650 6614 66734 908 16512 0.995153 0 . 0 . 61 15,11,18,12 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L86|560|LRIT2|protein_coding|CODING|NM_001284223.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.4216 rs11200928 -0.693097 0.338441 61 N296 623 aaT/aaC LOW 3 SILENT CODING LRIT1 G protein_coding NM_015613.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85993836 A G 0 228 0 0.9992 0.9946 0.9986 1 0.9781 0.9969 0.994326 0.984392 0.979302 2 10034 109392 11409 8515 6303 62403 783 9945 2 10168 111668 11476 8536 6594 64072 808 10014 0 . 0 . 0 71 0,0,37,29 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N296|623|LRIT1|protein_coding|CODING|NM_015613.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4933986 -0.693147 0.241916 71 L272 623 Ctg/Ttg LOW 3 SILENT CODING LRIT1 A protein_coding NM_015613.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85993910 G A 0 222 0 0.8941 0.5725 0.5418 0.4058 0.4722 0.4346 0.813663 0.573735 0.450814 1 8666 60113 6681 3367 3197 30660 444 7098 2 10396 120664 11570 8612 6610 66470 904 16102 0.968095 0 . 0 . 77 16,11,21,23 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L272|623|LRIT1|protein_coding|CODING|NM_015613.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913101 rs3814206 -0.693146 0.477518 77 623 LOW 2 CODING LRIT1 G protein_coding NM_015613.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85994142 A G 0 222 0 0.9236 0.5811 0.5461 0.4058 0.4732 0.4346 0.839764 0.582654 0.45093 1 8788 55813 6663 3330 3196 29408 385 4043 2 10194 110824 11476 8520 6606 63906 788 9334 0.976591 0 . 0 . 76 14,19,18,19 SPLICE_SITE_REGION+INTRON(LOW||||623|LRIT1|protein_coding|CODING|NM_015613.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.265105 rs3829858 -0.693141 0.232055 76 L154M 623 Ctg/Atg MODERATE 2 MISSENSE CODING LRIT1 T protein_coding NM_015613.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 85997105 G T 0 208 0 0.0272 0.0791 0.062 0.1478 0.0746 0.0951 0.0303109 0.0435288 0.0504913 1 99 1517 29 108 0 506 14 761 2 2028 17484 322 458 20 6638 178 7840 0.941237 0 . 0 . 37 9,9,3,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L154M|623|LRIT1|protein_coding|CODING|NM_015613.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996877 rs11200933,rs386517483 -0.691153 0.773863 37 T9 295 acT/acC LOW 1 SILENT CODING RGR C protein_coding NM_002921.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86004873 T C 0 228 0 0.9773 0.6336 0.5879 0.495 0.4911 0.4908 0.89832 0.62056 0.478256 2 9441 64061 6757 3865 3160 31982 501 8355 2 10390 120602 11542 8624 6182 66498 902 16464 0 . 0 . 0 42 0,0,13,24 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T9|295|RGR|protein_coding|CODING|NM_002921.3|1|C),UPSTREAM(MODIFIER||3656||623|LRIT1|protein_coding|CODING|NM_015613.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2279227 -0.693141 0.548943 42 Y157 295 taC/taT LOW 4 SILENT CODING RGR T protein_coding NM_002921.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86012713 C T 0 222 0 0.8548 0.5032 0.4841 0.3313 0.3588 0.3671 0.780073 0.505151 0.364302 1 8251 50713 5975 2565 2988 24195 407 6332 2 10400 121218 11536 8626 6580 66666 904 16506 0.882396 2 benign 0 COSM146980 75 14,16,12,26 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y157|295|RGR|protein_coding|CODING|NM_002921.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.568844 rs1042454,rs386512899 -0.693143 0.270138 75 1047 LOW 5 CODING CCSER2 G protein_coding NM_001284240.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86185654 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 10402 120742 11458 8594 6606 66504 904 16274 2 10402 120780 11458 8632 6606 66504 904 16274 0 . 0 . 0 62 0,0,15,42 SPLICE_SITE_REGION+INTRON(LOW||||1047|CCSER2|protein_coding|CODING|NM_001284240.1|5|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1336202 -0.693147 0.16297 62 1047 279 MODIFIER 10 CODING CCSER2 G protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86274302 C G 0 227 0 0.0545 0.3143 0.2853 0.4028 0.4732 0.4315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,7,4 UTR_3_PRIME(MODIFIER||279||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.964642 0 . rs11915 -0.676189 0.303542 11 1047 631 MODIFIER 10 CODING CCSER2 A protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86274654 G A 0 228 0 0.2065 0.5306 0.6484 0.6329 0.668 0.638 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,21,23 UTR_3_PRIME(MODIFIER||631||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10788344 -0.693146 0.670749 45 1047 709 MODIFIER 10 CODING CCSER2 C protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86274732 T C 0 228 0 0.0552 0.3145 0.2853 0.4028 0.4732 0.4315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,62,7 UTR_3_PRIME(MODIFIER||709||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10887314 -0.693147 8.46682e-05 75 1047 848 MODIFIER 10 CODING CCSER2 T protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86274871 C T 0 228 0 0.798 0.8393 0.8963 0.8224 0.8598 0.8507 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 159 0,0,62,83 UTR_3_PRIME(MODIFIER||848||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2784846 -0.693147 0.00476577 159 1047 1369 MODIFIER 10 CODING CCSER2 G protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86275392 A G 0 39.3 0 0.1944 0.5274 0.647 0.6329 0.668 0.6391 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1369||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11201083 -0.453602 0.78 2 1047 2573 MODIFIER 10 CODING CCSER2 C protein_coding NM_001284240.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 86276596 T C 0 63 0 0.6384 0.6226 0.5346 0.5923 0.666 0.6503 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||2573||1047|CCSER2|protein_coding|CODING|NM_001284240.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2784847 -0.453602 0.32 3 1009 2595 MODIFIER 16 CODING GRID1 C protein_coding NM_017551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 87359435 A C 0 222 0 0.0045 0.0683 0.0879 0.1954 0.0427 0.0358 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.869092 0 . 0 . 88 10,24,7,38 UTR_3_PRIME(MODIFIER||2595||1009|GRID1|protein_coding|CODING|NM_017551.2|16|C),INTRAGENIC(MODIFIER|||||GRID1-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.857507 rs76636418 -0.693147 0.00366324 88 1009 2352 MODIFIER 16 CODING GRID1 T protein_coding NM_017551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 87359678 A T 0 69 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 16 4,0,5,0 UTR_3_PRIME(MODIFIER||2352||1009|GRID1|protein_coding|CODING|NM_017551.2|16|T),INTRAGENIC(MODIFIER|||||GRID1-AS1||NON_CODING|||T) 0 0.5 1 0 . 0 . 0 . 0 60 0 0.974597 0 . 0.649731 rs56731174 -0.590765 0.0942182 16 1009 2204 MODIFIER 16 CODING GRID1 G protein_coding NM_017551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 87359826 A G 0 222 0 0.851 0.65 0.5634 0.6022 0.5706 0.5706 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.233254 0 . 0 . 91 31,16,25,10 UTR_3_PRIME(MODIFIER||2204||1009|GRID1|protein_coding|CODING|NM_017551.2|16|G),INTRAGENIC(MODIFIER|||||GRID1-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.542327 rs2664405 -0.693136 0.506301 91 1009 739 MODIFIER 16 CODING GRID1 G protein_coding NM_017551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 87361291 T G 0 31.3 0 0.2405 0.1456 0.121 0.2133 0.0656 0.047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||739||1009|GRID1|protein_coding|CODING|NM_017551.2|16|G),INTRAGENIC(MODIFIER|||||GRID1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3812651 -0.453602 0.32 2 1009 700 MODIFIER 16 CODING GRID1 A protein_coding NM_017551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 87361330 C A 0 39.3 0 0.1271 0.109 0.1138 0.1954 0.0656 0.0368 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||700||1009|GRID1|protein_coding|CODING|NM_017551.2|16|A),INTRAGENIC(MODIFIER|||||GRID1-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3812650 -0.453602 0.32 2 I26 1009 atC/atT LOW 1 SILENT CODING GRID1 A protein_coding NM_017551.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88126072 G A 0 16.6 0 0.5219 0.3437 0.1398 0.5218 0.172 0.2403 0.445837 0.246331 0.1448 1 1234 5835 175 784 49 1875 46 1672 2 2244 20040 718 1270 134 7468 182 8024 1 0 . 0 . 23 10,5,1,2 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I26|1009|GRID1|protein_coding|CODING|NM_017551.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.957088 rs61856638 -0.511536 0.732596 23 1190 1650 MODIFIER 19 CODING WAPL T protein_coding NM_015045.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88195650 C T 0 228 0 0.997 0.9611 0.8213 0.999 0.9672 0.9663 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,10,9 UTR_3_PRIME(MODIFIER||1650||1190|WAPL|protein_coding|CODING|NM_015045.2|19|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1896513 -0.69168 0.669192 20 T1125 1190 acA/acG LOW 17 SILENT CODING WAPL C protein_coding NM_015045.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88203068 T C 0 222 0 0.8147 0.8139 0.7695 0.629 0.9334 0.9121 0.830912 0.891435 0.922442 1 8622 105710 8461 5116 6299 61287 791 15134 2 10406 121388 11574 8644 6614 66732 908 16510 0.551638 0 . 0 . 274 56,73,54,53 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1125|1190|WAPL|protein_coding|CODING|NM_015045.2|17|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.963943 rs7094132 -0.693147 0.0444426 274 V124I 1190 Gtt/Att MODERATE 2 MISSENSE CODING WAPL T protein_coding NM_015045.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88277457 C T 0 222 0 0.0643 0.1925 0.1239 0.1776 0.2803 0.3395 0.104857 0.222051 0.282093 1 983 30046 1037 1646 1924 18381 215 5860 2 10402 121394 11578 8652 6612 66734 906 16510 0.769969 0 . 0 . 71 14,17,13,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V124I|1190|WAPL|protein_coding|CODING|NM_015045.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910186 rs10887621 -0.693139 0.314372 71 1190 3518 MODIFIER 1 CODING WAPL G protein_coding NM_015045.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88281344 C G 0 126 0 0.0681 0.254 0.2421 0.2302 0.338 0.4519 0 . 0 1 33 4554 38 37 0 1009 54 3383 2 330 11166 110 164 0 3092 122 7348 0.612847 0 . 0 . 47 22,1,24,0 UTR_5_PRIME(MODIFIER||3518||1190|WAPL|protein_coding|CODING|NM_015045.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.497818 rs2289738 -0.692831 0.0647551 47 1190 3520 MODIFIER 1 CODING WAPL G protein_coding NM_015045.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88281346 A G 0 200 0 1 1 1 1 1 1 0 . 0 2 470 11777 130 192 0 3419 132 7434 2 470 11784 130 192 0 3422 132 7438 0 . 0 . 0 45 0,0,44,1 UTR_5_PRIME(MODIFIER||3520||1190|WAPL|protein_coding|CODING|NM_015045.2|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4934218 -0.693147 0.285947 45 P10 489 ccG/ccA LOW 1 SILENT CODING OPN4 A protein_coding NM_001030015.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88414570 G A 0 222 0 0.062 0.236 0.1758 0.2778 0.3022 0.4029 0.0980481 0.249962 0.327791 1 964 35601 1617 2235 2168 21525 253 6839 2 10300 120792 11550 8594 6614 66382 898 16454 0.962359 0 . 0 . 101 28,22,24,15 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P10|489|OPN4|protein_coding|CODING|NM_001030015.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.412224 rs11202106 -0.693144 0.347306 101 T405I 489 aCc/aTc MODERATE 9 MISSENSE CODING OPN4 T protein_coding NM_001030015.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88422116 C T 0 228 0 0.7965 0.7532 0.7565 0.7927 0.6342 0.774 0.767865 0.687057 0.645702 2 5486 53450 4751 4644 1687 27810 335 8737 2 6916 73368 6072 5686 2346 40274 474 11600 1 0 . 0 . 188 0,1,84,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T405I|489|OPN4|protein_coding|CODING|NM_001030015.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1079610 -0.693147 0.590977 188 R417 489 Cgg/Agg LOW 9 SILENT CODING OPN4 A protein_coding NM_001030015.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88422151 C A 0 222 0 0.0386 0.2298 0.1744 0.2798 0.3012 0.4029 0.0820384 0.24034 0.321228 1 366 13565 372 687 390 7788 85 3877 2 3658 36458 1424 1978 842 19332 258 8966 0.160028 0 . 0 . 166 46,46,24,42 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R417|489|OPN4|protein_coding|CODING|NM_001030015.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.556698 rs3740337 -0.693147 0.164984 166 489 246 MODIFIER 11 CODING OPN4 G protein_coding NM_001030015.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88425754 A G 0 178 0 1 0.9986 1 1 1 0.9928 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,1,9 UTR_3_PRIME(MODIFIER||246||489|OPN4|protein_coding|CODING|NM_001030015.2|11|G),UPSTREAM(MODIFIER||2452||732|LDB3|protein_coding|CODING|NM_001171610.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2736687 -0.670168 0.187503 10 489 534 MODIFIER 11 CODING OPN4 A protein_coding NM_001030015.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88426042 G A 0 32.6 0 0.1967 0.2376 0.2608 0.4306 0.1342 0.184 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||534||489|OPN4|protein_coding|CODING|NM_001030015.2|11|A),UPSTREAM(MODIFIER||2164||732|LDB3|protein_coding|CODING|NM_001171610.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3740341 -0.379885 0 2 732 LOW 1 CODING LDB3 C protein_coding NM_001171610.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88428335 T C 0 228 0 0.8502 0.7522 0.6354 0.8095 0.6561 0.7423 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 2 benign 0 . 47 0,0,44,2 SPLICE_SITE_REGION+INTRON(LOW||||732|LDB3|protein_coding|CODING|NM_001171610.1|1|C),DOWNSTREAM(MODIFIER||2119||489|OPN4|protein_coding|CODING|NM_001030015.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2803558 -0.693147 0.182894 47 V55I 732 Gtc/Atc MODERATE 3 MISSENSE CODING LDB3 A protein_coding NM_001171610.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88439193 G A 0 222 0 0 0.01877 0.0072 0.0853 0 0.0031 0.00113482 0.00107643 0.00104651 1 13 876 79 715 0 36 5 28 2 10366 121292 11566 8626 6610 66706 906 16512 0.981107 2 benign 0 . 106 27,25,27,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V55I|732|LDB3|protein_coding|CODING|NM_001171610.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973563 rs3740343 -0.693147 0.764985 106 532 119181 MODIFIER 1 CODING BMPR1A C protein_coding NM_004329.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88516595 T C 0 6.3 0 0.1188 0.3482 0.33 0.6895 0.3201 0.3487 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||119181||532|BMPR1A|protein_coding|CODING|NM_004329.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs34755052 -0.379885 0 1 P2T 532 Cct/Act MODERATE 3 MISSENSE CODING BMPR1A A protein_coding NM_004329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88635779 C A 0 228 0 0.7239 0.4998 0.3617 0.7093 0.2753 0.3098 0.649796 0.389513 0.256163 2 6903 43160 4573 6220 2361 17832 331 4940 2 10394 121298 11564 8646 6608 66672 906 16508 0 2|1|2 benign|not-provided|benign 0 . 113 0,0,59,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P2T|532|BMPR1A|protein_coding|CODING|NM_004329.2|3|A) 1 0 . 0 . 1 0 1 1 0 56 0 0 0.529123 0 . rs11528010,rs3182217 -0.693147 0.00854629 113 532 414 MODIFIER 13 CODING BMPR1A A protein_coding NM_004329.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88683890 T A 0 228 0 0.9818 0.9655 0.9654 0.9573 0.9364 0.9816 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 172 0,0,69,91 UTR_3_PRIME(MODIFIER||414||532|BMPR1A|protein_coding|CODING|NM_004329.2|13|A) 0 . 0 . 0 1 0 . 0 . 50 0 0 0.0516892 0 . rs386607200,rs7078571 -0.693147 0.314572 172 H731D 949 Cac/Gac MODERATE 6 MISSENSE CODING MMRN2 C protein_coding NM_024756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88702350 G C 0 228 0 0.8638 0.9521 0.9683 0.999 0.9781 0.9847 0.882887 0.936952 0.964651 2 9146 116439 11251 8643 6489 63940 855 16115 2 10352 121088 11566 8644 6612 66520 904 16490 0 . 0 . 0 44 0,0,12,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H731D|949|MMRN2|protein_coding|CODING|NM_024756.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4934281 -0.693145 0.287103 44 R270H 949 cGc/cAc MODERATE 6 MISSENSE CODING MMRN2 T protein_coding NM_024756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88703732 C T 0 210 0 0.0015 0.016573 0.0735 0.0288 0 0.001 0.00136178 0.000691988 0.000348837 1 15 1416 1075 253 0 12 11 50 2 10394 121262 11570 8644 6614 66624 904 16512 0.0792615 0 . 0 . 81 33,10,30,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R270H|949|MMRN2|protein_coding|CODING|NM_024756.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.640611 rs79370279 -0.693132 0.197322 81 V53 949 gtA/gtT LOW 1 SILENT CODING MMRN2 A protein_coding NM_024756.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88717140 T A 0 228 0 0.9743 0.9832 0.9827 0.999 0.9791 0.9836 0.976623 0.971244 0.968488 2 10169 118009 11344 8649 6492 64317 873 16165 2 10404 121388 11578 8650 6614 66722 908 16512 0 . 0 . 0 56 0,0,30,24 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtT|V53|949|MMRN2|protein_coding|CODING|NM_024756.2|1|A),UPSTREAM(MODIFIER||1148||127|SNCG|protein_coding|CODING|NM_003087.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4244973 -0.693147 0.458115 56 G49S 949 Ggc/Agc MODERATE 1 MISSENSE CODING MMRN2 T protein_coding NM_024756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88717154 C T 0 222 0 0.1899 0.4235 0.4179 0.7113 0.4742 0.3947 0.226509 0.385514 0.466977 1 2279 54546 4951 5988 3338 30719 411 6860 2 10398 121336 11570 8640 6614 66696 906 16512 0.885075 0 . 0 COSM146986 55 11,15,16,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G49S|949|MMRN2|protein_coding|CODING|NM_024756.2|1|T),UPSTREAM(MODIFIER||1134||127|SNCG|protein_coding|CODING|NM_003087.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.674405 rs3750823 -0.692976 0.726782 55 127 19 MODIFIER 1 CODING SNCG C protein_coding NM_003087.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88718436 A C 0 222 0 0.5151 0.5381 0.4769 0.7123 0.5477 0.4233 0.512256 0.529832 0.538837 1 5211 63940 5457 5895 3757 35605 475 7540 2 10244 119774 11388 8560 6424 65832 882 16444 0.988755 0 . 0 . 131 50,10,46,8 UTR_5_PRIME(MODIFIER||19||127|SNCG|protein_coding|CODING|NM_003087.2|1|C),UPSTREAM(MODIFIER||1011||949|MMRN2|protein_coding|CODING|NM_024756.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993896 rs1800373 -0.693147 0.0729137 131 I68 76 atT/atC LOW 3 SILENT CODING ADIRF C protein_coding NM_006829.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88730312 T C 0 222 0 0.3585 0.5272 0.4308 0.8095 0.6014 0.456 0.377213 0.482239 0.536047 1 3754 63513 4253 6777 4098 36053 492 8086 2 9568 115216 10634 8488 6256 63836 864 15570 0.670155 0 . 0 COSM146987 84 11,27,19,21 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I68|76|ADIRF|protein_coding|CODING|NM_006829.2|3|C),UPSTREAM(MODIFIER||186||550|AGAP11|protein_coding|CODING|NM_133447.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932146 rs4869 -0.693145 0.0432359 84 76 35 MODIFIER 3 CODING ADIRF T protein_coding NM_006829.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88730374 C T 0 208 0 0.2126 0.4032 0.2882 0.6855 0.4751 0.3773 0.241035 0.369502 0.435334 1 1432 27046 1035 3060 1357 15440 209 4513 2 5502 59158 3450 4574 2464 32040 452 10676 0.879499 0 . 0 . 47 11,13,3,17 UTR_3_PRIME(MODIFIER||35||76|ADIRF|protein_coding|CODING|NM_006829.2|3|T),UPSTREAM(MODIFIER||124||550|AGAP11|protein_coding|CODING|NM_133447.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.418486 rs7960 -0.692067 0.246836 47 550 17789 MODIFIER 3 CODING AGAP11 G protein_coding NM_133447.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88743691 A G 0 222 0 0.2383 0.251 0.3919 0.2411 0.2048 0.226 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.843427 0 . 0 . 85 23,15,14,18 START_GAINED(LOW||||550|AGAP11|protein_coding|CODING|NM_133447.1|3|G),UTR_5_PRIME(MODIFIER||17789||550|AGAP11|protein_coding|CODING|NM_133447.1|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.911571 rs11202285 -0.69312 0.743837 85 550 9274 MODIFIER 4 CODING AGAP11 A protein_coding NM_133447.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88752206 G A 0 222 0 0.5477 0.3902 0.5043 0.2381 0.329 0.316 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996674 0 . 0 . 381 125,77,93,50 UTR_5_PRIME(MODIFIER||9274||550|AGAP11|protein_coding|CODING|NM_133447.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.834761 rs1745903 -0.693147 0.236659 381 I82V 550 Att/Gtt MODERATE 12 MISSENSE CODING AGAP11 G protein_coding NM_133447.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88768253 A G 0 222 0 0.8585 0.7911 0.7522 0.9325 0.7048 0.6708 0.833333 0.735376 0.685565 1 8299 88394 8687 7880 4988 46255 692 11593 2 9894 120880 11576 8652 6614 66732 902 16510 0.999916 0 . 0 . 655 205,107,202,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I82V|550|AGAP11|protein_coding|CODING|NM_133447.1|12|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.97521 0.999968 0 0.859014 rs2641563 -0.693147 0.469975 655 D216 550 gaC/gaT LOW 12 SILENT CODING AGAP11 T protein_coding NM_133447.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88768657 C T 0 222 0 0.8116 0.7778 0.7522 0.9286 0.7038 0.6708 0.78325 0.715747 0.681163 1 8235 88290 8664 7876 4988 46237 688 11602 2 10396 121382 11574 8654 6612 66730 906 16510 0.655541 0 . 0 . 441 68,133,74,125 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D216|550|AGAP11|protein_coding|CODING|NM_133447.1|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995022 rs1745901,rs386543705 -0.693147 0.124441 441 E11* 89 Gaa/Taa HIGH 1 NONSENSE CODING FAM25A T protein_coding NM_001146157.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88780112 G T 0 222 0 0.0015 0.0208 0.0735 0.0486 0 0.002 0 . 0 1 2 94 23 27 0 2 5 35 2 1522 18656 396 598 736 7290 206 7908 0.988851 0 . 0 . 308 67,47,88,63 STOP_GAINED(HIGH|NONSENSE|Gaa/Taa|E11*|89|FAM25A|protein_coding|CODING|NM_001146157.2|1|T) 0 0.5 1 0 . 1 0 . 1 (FAM25A|FAM25A|1|1.00) 59 0 0.971706 0.998334 (FAM25A|FAM25A|1|1.00) 0.408565 rs183710110 -0.693147 0.0675867 308 89 50 MODIFIER 3 CODING FAM25A G protein_coding NM_001146157.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88784481 A G 0 222 0 0.5227 0.5367 0.5202 0.7669 0.4443 0.4254 0 . 0 1 982 9513 165 270 864 3537 115 3580 2 1962 20322 312 334 1656 7972 232 7854 0.924674 0 . 0 . 586 67,173,65,215 UTR_3_PRIME(MODIFIER||50||89|FAM25A|protein_coding|CODING|NM_001146157.2|3|G) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.638848 9.85563e-06 0 0.0189383 rs66948676,rs9421557 -0.693147 0.000464611 586 S550C 835 Agt/Tgt MODERATE 5 MISSENSE CODING FAM35A T protein_coding NM_019054.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88930249 A T 0 222 0 0.1785 0.2754 0.255 0.1607 0.3638 0.4479 0.199955 0.324619 0.388488 1 2065 40826 2994 1369 2232 25235 289 6642 2 10272 117894 11506 8624 6610 65626 870 14386 0.977294 0 . 0 . 218 78,12,85,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S550C|835|FAM35A|protein_coding|CODING|NM_019054.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.999943 0.994976 0 0.997961 rs11202365 -0.693147 0.219842 218 E628K 835 Gaa/Aaa MODERATE 6 MISSENSE CODING FAM35A A protein_coding NM_019054.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88930650 G A 0 222 0 0 0.0021965 0 0.0099 0 0.001 0 . 0 1 0 24 1 18 0 0 0 5 2 2318 23472 1652 1214 2246 12862 236 2944 0.996937 0 . 0 . 229 37,69,24,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E628K|835|FAM35A|protein_coding|CODING|NM_019054.2|6|A) 0 0.5 1 0 . 1 0 . 1 0 36 0 0.633126 2.71386e-14 0 0.624089 rs368106548 -0.693147 0.632024 229 G698 835 ggT/ggC LOW 7 SILENT CODING FAM35A C protein_coding NM_019054.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88939962 T C 0 228 0 0.9879 0.7933 0.7968 0.377 0.84 0.909 0.953473 0.884769 0.849546 2 9826 101089 9600 3163 5434 57194 783 15089 2 10222 120972 11552 8606 6612 66570 908 16502 0.267697 0 . 0 . 175 2,1,94,58 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G698|835|FAM35A|protein_coding|CODING|NM_019054.2|7|C) 1 0 . 0 . 1 0 1 1 0 50 0 0.961762 0.147391 0 0.858689 rs7081609 -0.693147 0.714477 175 835 206 MODIFIER 9 CODING FAM35A C protein_coding NM_019054.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88950646 A C 0 39.3 0 0.9879 0.7929 0.7954 0.377 0.839 0.909 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||206||835|FAM35A|protein_coding|CODING|NM_019054.2|9|C) 0 . 0 . 0 1 0 . 0 . 58 0 0 . 0 . rs56065176 -0.453602 0.1 2 835 569 MODIFIER 9 CODING FAM35A G protein_coding NM_019054.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88951009 C G 0 30.3 0 0.9879 0.7925 0.7954 0.375 0.839 0.909 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||569||835|FAM35A|protein_coding|CODING|NM_019054.2|9|G) 0 . 0 . 0 1 0 . 0 . 43 0 0 . 0 . rs61858950,rs6423746 -0.453602 0.38 2 A160T 878 Gca/Aca MODERATE 2 MISSENSE CODING NUTM2A A protein_coding NM_001099338.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88988115 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 943 27116 3331 3328 1192 13704 181 4437 2 6098 89692 9212 7110 4262 48600 658 13752 0.909506 0 . 0 COSM1317421,COSM1317420 161 51,20,52,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A160T|878|NUTM2A|protein_coding|CODING|NM_001099338.1|2|A) 0 0.5 1 0 . 0 . 0 1 0 39 0 0.490975 0.351851 0 0.226164 rs200168540 -0.693147 0.0477575 161 G545S 878 Ggc/Agc MODERATE 5 MISSENSE CODING NUTM2A A protein_coding NM_001099338.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 88992641 G A 0 228 0 0.6974 0.7939 0.8256 0.9563 0.7734 0.7556 0 . 0 2 977 6215 369 965 79 2098 43 1684 2 1282 7340 408 1018 92 2570 52 1918 0 . 0 . 0 233 0,0,87,116 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G545S|878|NUTM2A|protein_coding|CODING|NM_001099338.1|5|A) 0 . 0 . 0 1 0 . 1 0 28 0 0 4.07716e-20 0 . rs145500179 -0.693147 4.23785e-08 233 619 LOW 6 CODING PAPSS2 C protein_coding NM_001015880.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 89475483 T C 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 23 0 23 0 0 0 0 2 10320 119164 11186 8514 6536 65774 884 15950 0.531349 0 . 0 . 111 21,28,32,20 SPLICE_SITE_REGION+INTRON(LOW||||619|PAPSS2|protein_coding|CODING|NM_001015880.1|6|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.989871 rs202210032 -0.693147 3.2612e-08 111 619 146 MODIFIER 13 CODING PAPSS2 T protein_coding NM_001015880.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 89505873 A T 0 30 0 0.5151 0.4874 0.5504 0.3135 0.498 0.5736 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 6 0,2,0,3 UTR_3_PRIME(MODIFIER||146||619|PAPSS2|protein_coding|CODING|NM_001015880.1|13|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs1058801 -0.511536 0.267404 6 576 HIGH 1 CODING PTEN C protein_coding NM_001304717.2 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 89623860 CT C 0 65 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON(HIGH||||576|PTEN|protein_coding|CODING|NM_001304717.2|1|C),UPSTREAM(MODIFIER||667||178|KLLN|protein_coding|CODING|NM_001126049.1||C) 0 . 0 3 1 1 1 0 . (PTEN|PTEN|1|1.00) 60 0 0 . 0 . rs71022512 -0.511536 0.192436 3 C65S 576 tGc/tCc MODERATE 2 MISSENSE CODING PTEN C protein_coding NM_001304717.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 89623901 G C 0 150 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tCc|C65S|576|PTEN|protein_coding|CODING|NM_001304717.2|2|C),UPSTREAM(MODIFIER||707||178|KLLN|protein_coding|CODING|NM_001126049.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2943772 -0.636426 0.462061 8 576 1516 MODIFIER 10 CODING PTEN C protein_coding NM_001304717.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 89726745 T C 0 192 0 0.121 0.3734 0.3588 0.4226 0.3917 0.6554 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.671908 0 . 0 . 33 15,0,13,2 UTR_3_PRIME(MODIFIER||1516||576|PTEN|protein_coding|CODING|NM_001304717.2|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.958725 rs701848 -0.688148 0.133364 33 E37D 342 gaG/gaC MODERATE 1 MISSENSE CODING RNLS G protein_coding NM_001031709.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90342837 C G 0 222 0 0.5408 0.4782 0.3948 0.4484 0.4771 0.4847 0.537222 0.469168 0.434302 1 5522 55688 5486 3712 3526 29277 460 7705 2 10390 121068 11556 8628 6604 66550 906 16434 0.929699 0 . 0 . 122 37,26,30,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E37D|342|RNLS|protein_coding|CODING|NM_001031709.2|1|G),UPSTREAM(MODIFIER||3682||366|LIPJ|protein_coding|CODING|NM_001010939.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93662 rs2296545 -0.693147 0.910868 122 I210V 366 Att/Gtt MODERATE 8 MISSENSE CODING LIPJ G protein_coding NM_001010939.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90356598 A G 0 228 0 0.9788 0.8926 0.8487 0.994 0.7505 0.8487 0.926658 0.789595 0.719325 2 9707 96772 10101 8532 5247 48740 735 13710 2 10310 121062 11526 8640 6596 66588 908 16494 0 . 0 . 0 81 0,0,46,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I210V|366|LIPJ|protein_coding|CODING|NM_001010939.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs111186212,rs1409136 -0.693147 0.0212231 81 L380 398 ctC/ctT LOW 9 SILENT CODING LIPN T protein_coding NM_001102469.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90537942 C T 0 222 0 0.0038 0.1256 0.1455 0.2679 0.0547 0.2025 0.0162407 0.046002 0.0596341 1 139 10938 1120 2205 187 4003 65 3219 2 8954 112440 10360 8018 6240 62256 832 15780 0.940942 0 . 0 . 115 19,34,19,35 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L380|398|LIPN|protein_coding|CODING|NM_001102469.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.833066 rs11202851 -0.693147 0.000295575 115 423 34 MODIFIER 9 CODING LIPM A protein_coding NM_001128215.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90580292 C A 0 168 0 0 0.0579 0.0908 0.1687 0.006 0.0521 0.00433526 0.00328515 0.00282841 1 8 413 28 121 17 39 7 193 2 1800 16464 326 552 1624 7026 202 4934 0.0847736 0 . 0 . 36 4,13,2,15 UTR_3_PRIME(MODIFIER||34||423|LIPM|protein_coding|CODING|NM_001128215.1|9|A),UTR_3_PRIME(MODIFIER||2406||191|ANKRD22|protein_coding|CODING|NM_144590.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.57591 rs78586189 -0.690438 0.429534 36 191 2406 MODIFIER 6 CODING ANKRD22 A protein_coding NM_144590.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90580292 C A 0 168 0 0 0.0579 0.0908 0.1687 0.006 0.0521 0.00433526 0.00328515 0.00282841 1 8 413 28 121 17 39 7 193 2 1800 16464 326 552 1624 7026 202 4934 0.0847736 0 . 0 . 36 4,13,2,15 UTR_3_PRIME(MODIFIER||34||423|LIPM|protein_coding|CODING|NM_001128215.1|9|A),UTR_3_PRIME(MODIFIER||2406||191|ANKRD22|protein_coding|CODING|NM_144590.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.57591 rs78586189 -0.690438 0.429534 36 191 2368 MODIFIER 6 CODING ANKRD22 A protein_coding NM_144590.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90580330 G A 0 148 0 0.0666 0.2638 0.3689 0.374 0.2853 0.32 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997846 0 . 0 . 22 0,11,2,9 UTR_3_PRIME(MODIFIER||2368||191|ANKRD22|protein_coding|CODING|NM_144590.2|6|A),DOWNSTREAM(MODIFIER||27||423|LIPM|protein_coding|CODING|NM_001128215.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.925321 rs1661281 -0.676189 0.4517 22 436 143 MODIFIER 11 CODING STAMBPL1 C protein_coding NM_020799.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90683124 T C 0 206 0 0.5734 0.6791 0.6945 0.8968 0.4871 0.7843 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,1,11 UTR_3_PRIME(MODIFIER||143||436|STAMBPL1|protein_coding|CODING|NM_020799.3|11|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1530281,rs386535822 -0.680642 0.162982 13 377 42222 MODIFIER 1 CODING ACTA2 T protein_coding NM_001141945.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90750909 C T 0 41.5 0 0.1762 0.3622 0.3559 0.5069 0.3897 0.4407 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_5_PRIME(MODIFIER||42222||377|ACTA2|protein_coding|CODING|NM_001141945.1|1|T),INTRON(MODIFIER||||335|FAS|protein_coding|CODING|NM_000043.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12775501 -0.511536 0.598038 4 T214 335 acT/acC LOW 7 SILENT CODING FAS C protein_coding NM_000043.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90771829 T C 0 228 0 0.6475 0.7754 0.7911 0.9573 0.7028 0.8241 0.685429 0.695218 0.700233 2 7014 91637 9972 8508 5242 46565 703 13633 2 10372 121192 11508 8654 6610 66640 906 16502 0 . 0 . 0 66 0,0,15,47 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T214|335|FAS|protein_coding|CODING|NM_000043.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2234978 -0.693147 0.0483621 66 272 523 MODIFIER 1 CODING CH25H T protein_coding NM_003956.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90965708 G T 0 32.6 0 0.0091 0.3013 0.2824 0.744 0.1491 0.41 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||523||272|CH25H|protein_coding|CODING|NM_003956.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3802657 -0.379885 0 2 A168 272 gcG/gcA LOW 1 SILENT CODING CH25H T protein_coding NM_003956.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90966546 C T 0 222 0 0.0083 0.2772 0.2579 0.7351 0.1332 0.3303 0.0256468 0.0836537 0.113372 1 257 25892 3883 6676 1613 8388 187 4888 2 10398 121364 11576 8640 6614 66720 908 16508 0.846335 0 . 0 . 122 15,48,22,34 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A168|272|CH25H|protein_coding|CODING|NM_003956.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856616 rs4078488 -0.693147 0.0783128 122 L18 272 ctG/ctC LOW 1 SILENT CODING CH25H G protein_coding NM_003956.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90966996 C G 0 222 0 0.0083 0.2804 0.2637 0.7371 0.1392 0.3344 0.027475 0.0877557 0.118632 1 207 19535 2418 4840 952 6911 130 4077 2 6204 75148 6074 6260 3068 40470 532 12540 0.964585 0 . 0 . 68 14,18,15,17 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L18|272|CH25H|protein_coding|CODING|NM_003956.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986014 rs10887932 -0.69312 0.149128 68 399 LOW 5 CODING LIPA A protein_coding NM_000235.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 90984990 G A 0 222 0 0.0976 0.3189 0.3674 0.7004 0.2018 0.3108 0.104176 0.165001 0.196163 1 1093 33625 5726 6474 1679 13227 227 5199 2 10258 120928 11544 8626 6612 66502 904 16482 0.603622 0 . 0 . 56 8,22,9,12 SPLICE_SITE_REGION+INTRON(LOW||||399|LIPA|protein_coding|CODING|NM_000235.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978083 rs2297472 -0.692352 0.0602599 56 K121R 472 aAa/aGa MODERATE 2 MISSENSE CODING IFIT2 G protein_coding NM_001547.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91066075 A G 0 222 0 0.27 0.1957 0.1945 0.127 0.2485 0.1125 0.250945 0.244791 0.241739 1 2617 25894 2200 1083 1377 16486 214 1917 2 9840 120700 11542 8598 6610 66696 902 16512 0.968107 0 . 0 . 66 16,12,15,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K121R|472|IFIT2|protein_coding|CODING|NM_001547.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998775 rs2070845,rs386556307 -0.693132 0.396476 66 V249 472 gtT/gtA LOW 2 SILENT CODING IFIT2 A protein_coding NM_001547.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91066460 T A 0 228 0 0.879 0.6813 0.4957 0.8571 0.5089 0.5419 0.826778 0.595088 0.485305 2 8142 67259 6224 7542 3110 32719 502 9020 2 9800 120714 11564 8608 6612 66722 900 16508 0 . 0 . 0 103 0,0,21,75 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V249|472|IFIT2|protein_coding|CODING|NM_001547.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs954439 -0.693147 0.0619761 103 D352E 472 gaC/gaA MODERATE 2 MISSENSE CODING IFIT2 A protein_coding NM_001547.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91066769 C A 0 228 0 0.9871 0.8788 0.6916 0.9921 0.7624 0.8681 0.949377 0.812191 0.748308 2 9355 96626 8181 8502 5338 50542 744 13964 2 9804 120616 11514 8590 6606 66694 900 16508 0 . 0 . 0 61 0,0,36,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D352E|472|IFIT2|protein_coding|CODING|NM_001547.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1727 -0.693147 0.186971 61 S406 490 tcT/tcC LOW 2 SILENT CODING IFIT3 C protein_coding NM_001031683.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91099630 T C 0 222 0 0.2837 0.2171 0.1873 0.2292 0.2376 0.1145 0.270994 0.243119 0.228837 1 2843 25662 2089 1993 1356 15468 202 1711 2 10316 121204 11570 8610 6612 66702 908 16486 0.905568 0 . 0 . 85 27,26,14,10 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S406|490|IFIT3|protein_coding|CODING|NM_001031683.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999622 rs3780878 -0.692831 0.494171 85 490 58 MODIFIER 2 CODING IFIT3 G protein_coding NM_001031683.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91099943 C G 0 164 0 0.9546 0.7306 0.5058 0.9415 0.5318 0.5746 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,0,15 UTR_3_PRIME(MODIFIER||58||490|IFIT3|protein_coding|CODING|NM_001031683.3|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10749607 -0.688148 0.0231874 15 490 373 MODIFIER 2 CODING IFIT3 A protein_coding NM_001031683.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91100258 T A 0 9.7 0 0.2685 0.3678 0.2738 0.6022 0.2455 0.453 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||373||490|IFIT3|protein_coding|CODING|NM_001031683.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1141862 -0.379885 0 1 474 67 MODIFIER 1 CODING IFIT1B C protein_coding NM_001010987.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91137826 T C 0 228 0 0.947 0.7111 0.5144 0.873 0.5258 0.5552 0.86922 0.601402 0.484915 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 91 0,0,56,28 UTR_5_PRIME(MODIFIER||67||474|IFIT1B|protein_coding|CODING|NM_001010987.2|1|C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs304504 -0.693147 0.0275224 91 G153 474 ggT/ggA LOW 2 SILENT CODING IFIT1B A protein_coding NM_001010987.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91143529 T A 0 228 0 0.9493 0.7117 0.5144 0.873 0.5258 0.5552 0.872901 0.619406 0.489535 2 9225 69321 6288 7550 3315 33455 523 8965 2 10402 121350 11562 8650 6612 66712 908 16504 0 . 0 . 0 73 0,0,23,44 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G153|474|IFIT1B|protein_coding|CODING|NM_001010987.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs304494,rs55902039 -0.693147 0.814766 73 K155 478 aaA/aaG LOW 3 SILENT CODING IFIT1 G protein_coding NM_001270927.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91162497 A G 0 228 0 0.9962 0.9766 0.9481 1 0.9433 0.9806 0.989333 0.958558 0.942791 2 10312 116614 11288 8651 6166 63070 874 16253 2 10404 121396 11576 8652 6614 66730 908 16512 0 . 0 . COSM1127983 102 0,0,44,49 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K155|478|IFIT1|protein_coding|CODING|NM_001270927.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs303211,rs386578857 -0.693147 0.170448 102 D215 478 gaC/gaT LOW 3 SILENT CODING IFIT1 T protein_coding NM_001270927.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91162677 C T 0 222 0 0.0318 0.243 0.2522 0.4395 0.2068 0.3569 0.0576487 0.146932 0.192674 1 582 28514 3497 3950 1374 13068 216 5827 2 10352 121320 11576 8642 6612 66718 908 16512 0.881538 0 . 0 . 92 22,24,20,20 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D215|478|IFIT1|protein_coding|CODING|NM_001270927.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.117541 rs303210 -0.693145 0.260156 92 478 701 MODIFIER 3 CODING IFIT1 C protein_coding NM_001270927.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91164170 T C 0 77 0 0.9501 0.7186 0.5274 0.8571 0.5477 0.5746 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||701||478|IFIT1|protein_coding|CODING|NM_001270927.1|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs215493 -0.511536 0.549396 3 478 2364 MODIFIER 3 CODING IFIT1 T protein_coding NM_001270927.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91165833 C T 0 9.7 0 0.2927 0.3934 0.3026 0.621 0.2763 0.4796 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2364||478|IFIT1|protein_coding|CODING|NM_001270927.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs303208,rs386578856 -0.379885 0 1 Y348 482 taC/taT LOW 2 SILENT CODING IFIT5 T protein_coding NM_012420.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91178000 C T 0 228 0 0.7201 0.6508 0.5029 0.8571 0.5358 0.5675 0.688833 0.567738 0.505698 2 7221 68623 6224 7486 3399 34262 531 9500 2 10402 121376 11572 8648 6612 66726 908 16508 0 . 0 . 0 93 0,0,43,47 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y348|482|IFIT5|protein_coding|CODING|NM_012420.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs304448 -0.693147 0.244616 93 598 2918 MODIFIER 7 CODING PANK1 A protein_coding NM_148977.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91341245 G A 0 9.7 0 0.0015 0.0853 0.1643 0.252 0.0199 0.0378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2918||598|PANK1|protein_coding|CODING|NM_148977.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4934487 -0.379885 0 1 C533 598 tgC/tgT LOW 5 SILENT CODING PANK1 A protein_coding NM_148977.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91352966 G A 0 228 0 0.7095 0.7025 0.6326 0.9435 0.5567 0.6442 0.692238 0.594879 0.545 2 7295 74977 8314 8095 3813 36472 534 10454 2 10406 121310 11558 8650 6608 66678 908 16502 0 . 0 . 0 185 0,0,103,64 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C533|598|PANK1|protein_coding|CODING|NM_148977.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2296616 -0.693147 0.11249 185 L204 598 ctG/ctC LOW 1 SILENT CODING PANK1 G protein_coding NM_148977.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91404448 C G 0 175 0 0.4766 0.3608 0.2233 0.2986 0.2604 0.4693 0.37572 0.265233 0.211753 1 1349 13882 1192 967 485 5520 86 4283 2 2450 35204 3424 2650 1142 16018 270 9250 0.943487 0 . 0 . 25 5,8,5,5 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L204|598|PANK1|protein_coding|CODING|NM_148977.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.792397 rs11185826 -0.670168 0.481017 25 A76 598 gcA/gcG LOW 1 SILENT CODING PANK1 C protein_coding NM_148977.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91404832 T C 0 25.9 0 0.4924 0.3648 0.2233 0.2996 0.2594 0.4683 0.375545 0.252639 0.19541 1 3192 29686 2544 2208 1744 13393 195 6410 2 6164 91490 9736 7128 5102 48908 656 13796 1 0 . 0 . 3 0,1,0,2 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A76|598|PANK1|protein_coding|CODING|NM_148977.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 1 rs12769113 -0.453602 0.06 3 R203 1820 Agg/Cgg LOW 6 SILENT CODING KIF20B C protein_coding NM_001284259.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91470834 A C 0 228 0 0.5749 0.4635 0.3847 0.5665 0.2396 0.4928 0.545847 0.344586 0.241452 2 5789 41668 5016 5049 1650 16236 260 7668 2 10318 121080 11530 8642 6602 66604 904 16480 1 0 . 0 COSM146992 207 1,0,112,70 SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R203|1820|KIF20B|protein_coding|CODING|NM_001284259.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1048057,rs386513205 -0.693147 0.13928 207 E622 1820 gaG/gaA LOW 15 SILENT CODING KIF20B A protein_coding NM_001284259.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91484780 G A 0 222 0 0.4796 0.357 0.219 0.3085 0.2326 0.4673 0.453473 0.307627 0.232907 1 4942 35015 2670 2572 1578 15741 225 7287 2 10400 121324 11574 8644 6614 66694 908 16490 0.748073 0 . 0 . 134 49,17,39,14 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E622|1820|KIF20B|protein_coding|CODING|NM_001284259.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.884881 rs8181361 -0.693147 0.666349 134 N870S 1820 aAc/aGc MODERATE 20 MISSENSE CODING KIF20B G protein_coding NM_001284259.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91497207 A G 0 222 0 0.0015 0.0807 0.1585 0.2579 0.007 0.0256 0.00317893 0.00631255 0.00791987 1 41 5829 2311 2471 78 505 36 387 2 9990 119788 11536 8614 6596 66166 898 15988 0.96364 0 . 0 . 113 34,25,25,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N870S|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.28486 rs78963463 -0.693146 0.000854544 113 D1011E 1820 gaT/gaA MODERATE 20 MISSENSE CODING KIF20B A protein_coding NM_001284259.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91497631 T A 0 222 0 0.4697 0.3538 0.2147 0.3085 0.2326 0.4673 0.460054 0.310058 0.233194 1 4783 34818 2661 2573 1578 15715 225 7283 2 10202 120944 11538 8638 6608 66554 908 16496 0.991282 0 . 0 . 107 28,19,26,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D1011E|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.78506 rs1062465 -0.693147 0.445805 107 K1105R 1820 aAg/aGg MODERATE 20 MISSENSE CODING KIF20B G protein_coding NM_001284259.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91497912 A G 0 222 0 0.0015 0.0807 0.1585 0.2579 0.007 0.0256 0.00319197 0.0060938 0.00757752 1 40 5727 2292 2409 78 490 33 385 2 9506 117788 11386 8300 6574 64742 886 16394 0.981964 0 . 0 COSM146993 73 33,10,18,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1105R|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.538314 rs79579856 -0.692914 0.130652 73 C1177R 1820 Tgt/Cgt MODERATE 20 MISSENSE CODING KIF20B C protein_coding NM_001284259.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91498127 T C 0 228 0 0.848 0.8574 0.8026 0.9355 0.7346 0.955 0.842955 0.757156 0.713239 2 8632 95924 10046 7994 5210 47933 721 15388 2 10258 120896 11556 8640 6604 66436 906 16496 0 . 0 . 0 193 0,0,102,70 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1177R|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1886996 -0.693147 0.0160555 193 N1219S 1820 aAt/aGt MODERATE 20 MISSENSE CODING KIF20B G protein_coding NM_001284259.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91498254 A G 0 222 0 0.4796 0.357 0.219 0.3085 0.2326 0.4673 0.455093 0.305603 0.230212 1 4688 34687 2667 2564 1577 15689 225 7277 2 9826 120308 11516 8592 6604 66384 900 16486 0.926104 0 . 0 . 157 27,43,30,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1219S|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.53952 rs1886997 -0.693147 0.00122013 157 K1240 1820 aaA/aaG LOW 20 SILENT CODING KIF20B G protein_coding NM_001284259.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91498318 A G 0 222 0 0.4796 0.357 0.219 0.3085 0.2326 0.4673 0.450314 0.301935 0.22927 1 4609 34349 2650 2543 1571 15570 220 7186 2 9594 118384 11402 8478 6590 65310 884 16126 0.997053 0 . 0 . 95 8,40,7,35 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1240|1820|KIF20B|protein_coding|CODING|NM_001284259.1|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.543691 rs1886998 -0.693146 0.311676 95 K1337 1820 aaA/aaG LOW 22 SILENT CODING KIF20B G protein_coding NM_001284259.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91503660 A G 0 222 0 0.4697 0.3538 0.2147 0.3085 0.2326 0.4673 0.459582 0.309645 0.232845 1 4809 34851 2668 2567 1576 15724 225 7282 2 10302 121170 11568 8626 6606 66656 908 16504 0.396694 0 . 0 COSM1717692,COSM1717691 138 32,33,34,23 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1337|1820|KIF20B|protein_coding|CODING|NM_001284259.1|22|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996842 rs1126480 -0.693147 0.0834434 138 1820 719 MODIFIER 33 CODING KIF20B T protein_coding NM_001284259.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91534524 G T 0 20.4 0 0.4697 0.353 0.2147 0.3065 0.2326 0.4652 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||719||1820|KIF20B|protein_coding|CODING|NM_001284259.1|33|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12948 -0.453602 0.36 2 1820 722 MODIFIER 33 CODING KIF20B A protein_coding NM_001284259.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 91534527 G A 0 20.4 0 0.239 0.2131 0.1671 0.2996 0.2286 0.1053 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||722||1820|KIF20B|protein_coding|CODING|NM_001284259.1|33|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10982 -0.453602 0.36 2 479 1515 MODIFIER 4 CODING HTR7 T protein_coding NM_019859.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 92500724 C T 0 228 0 0.9327 0.6765 0.5115 0.6786 0.5249 0.6012 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 100 1,0,58,41 UTR_3_PRIME(MODIFIER||1515||479|HTR7|protein_coding|CODING|NM_019859.3|4|T) 0 . 0 . 0 1 0 . 0 . 56 0 1 0.285268 0 1 rs1045949,rs56502730 -0.693147 0.933425 100 479 589 MODIFIER 4 CODING HTR7 A protein_coding NM_019859.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 92501650 G A 0 222 0 0.3744 0.2664 0.1902 0.3313 0.1501 0.227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.771112 0 . 0 . 111 29,24,20,24 UTR_3_PRIME(MODIFIER||589||479|HTR7|protein_coding|CODING|NM_019859.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992441 rs1418213 -0.693146 0.784907 111 319 145 MODIFIER 1 CODING ANKRD1 G protein_coding NM_014391.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 92680929 A G 0 161 0 0.6127 0.6623 0.7622 0.6558 0.6769 0.6503 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,0,15 UTR_5_PRIME(MODIFIER||145||319|ANKRD1|protein_coding|CODING|NM_014391.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10881855 -0.688148 0.502859 15 P19A 780 Ccc/Gcc MODERATE 1 MISSENSE CODING HECTD2 G protein_coding NM_001284274.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93170250 C G 0 63 0 1 1 1 1 1 1 0 . 0 2 340 12904 278 290 62 4414 134 7386 2 340 12906 278 290 62 4414 134 7388 0 . 0 . 0 3 0,0,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P19A|780|HECTD2|protein_coding|CODING|NM_001284274.1|1|G),INTRAGENIC(MODIFIER|||||HECTD2-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs7081569 -0.453602 0.7 3 T158 780 acG/acA LOW 4 SILENT CODING HECTD2 A protein_coding NM_001284274.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93221077 G A 0 222 0 0.6702 0.2183 0.0605 0.0853 0.0487 0.0307 0.563153 0.225262 0.0517845 1 6099 11630 556 686 217 3475 62 535 2 10350 121074 11544 8652 6612 66582 902 16432 0.464626 0 . 0 . 75 22,12,12,14 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T158|780|HECTD2|protein_coding|CODING|NM_001284274.1|4|A),INTRAGENIC(MODIFIER|||||HECTD2-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.374126 rs7920604 -0.692976 0.592341 75 780 314 MODIFIER 22 CODING HECTD2 C protein_coding NM_001284274.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93272454 CA C 0 170 0 0.1952 0.0783 0.0245 0.0813 0.0159 0.0194 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 11,3,13,2 UTR_3_PRIME(MODIFIER||314||780|HECTD2|protein_coding|CODING|NM_001284274.1|22|C),INTRAGENIC(MODIFIER|||||HECTD2-AS1||NON_CODING|||C) 0 0.5 1 15 0.483871 1 1 0 . 0 60 0 0 1 0 . rs3834408 -0.688148 0.00837513 31 780 1651 MODIFIER 22 CODING HECTD2 G protein_coding NM_001284274.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93273792 T G 0 222 0 0.6233 0.2051 0.0548 0.0863 0.0477 0.0307 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.902263 0 . 0 . 49 18,8,11,7 UTR_3_PRIME(MODIFIER||1651||780|HECTD2|protein_coding|CODING|NM_001284274.1|22|G),INTRAGENIC(MODIFIER|||||HECTD2-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.907096 rs11186596 -0.691153 0.591982 49 780 2230 MODIFIER 22 CODING HECTD2 G protein_coding NM_001284274.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93274371 A G 0 222 0 0.6725 0.2183 0.0576 0.0853 0.0477 0.0307 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999491 0 . 0 . 54 8,15,16,8 UTR_3_PRIME(MODIFIER||2230||780|HECTD2|protein_coding|CODING|NM_001284274.1|22|G),INTRAGENIC(MODIFIER|||||HECTD2-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.73344 rs11186597 -0.692831 0.656805 54 1166 LOW 11 CODING TNKS2 C protein_coding NM_025235.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93593602 T C 0 222 0 0 0.0023962 0 0.0119 0 0 0.00113482 0.000461326 0.000116279 1 12 148 1 135 0 0 0 0 2 10332 117178 11476 8594 6596 65622 870 13688 0.44668 0 . 0 . 88 24,14,27,13 SPLICE_SITE_REGION+INTRON(LOW||||1166|TNKS2|protein_coding|CODING|NM_025235.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720484 rs142919984 -0.693145 0.0233456 88 1166 1261 MODIFIER 27 CODING TNKS2 G protein_coding NM_025235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93624017 C G 0 222 0 0.4856 0.603 0.5562 0.748 0.498 0.7536 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.724111 0 . 0 . 52 20,9,13,7 UTR_3_PRIME(MODIFIER||1261||1166|TNKS2|protein_coding|CODING|NM_025235.3|27|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.411627 rs1539042 -0.692067 0.389733 52 1166 1269 MODIFIER 27 CODING TNKS2 T protein_coding NM_025235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93624025 C T 0 222 0 0.0499 0.0707 0.0231 0.1825 0.0308 0.0583 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5348 0 . 0 . 56 21,8,13,7 UTR_3_PRIME(MODIFIER||1269||1166|TNKS2|protein_coding|CODING|NM_025235.3|27|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.378776 rs9633689 -0.692067 0.574043 56 258 315 MODIFIER 2 CODING FGFBP3 T protein_coding NM_152429.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93667635 C T 0 183 0 0.9546 0.9876 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,8,1 UTR_3_PRIME(MODIFIER||315||258|FGFBP3|protein_coding|CODING|NM_152429.4|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1890897 -0.662043 0.375148 10 1849 577 MODIFIER 38 CODING BTAF1 C protein_coding NM_003972.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93789267 T C 0 168 0 0.0303 0.2003 0.2363 0.2609 0.3986 0.138 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,0,25 UTR_3_PRIME(MODIFIER||577||1849|BTAF1|protein_coding|CODING|NM_003972.2|38|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1914345 -0.692914 0.0230552 25 Y573 698 taT/taC LOW 9 SILENT CODING CPEB3 G protein_coding NM_014912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93841227 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10404 121397 11572 8654 6614 66733 908 16512 2 10406 121400 11572 8654 6614 66734 908 16512 0 . 0 . 0 82 0,0,14,63 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y573|698|CPEB3|protein_coding|CODING|NM_014912.4|9|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2676811 -0.693147 8.81961e-06 82 P182 698 ccA/ccT LOW 2 SILENT CODING CPEB3 A protein_coding NM_014912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93999562 T A 0 206 0 0.2806 0.2622 0.3991 0.3611 0.1183 0.1861 0 . 0 1 328 2194 266 458 68 783 16 275 2 796 6220 458 794 244 3092 44 792 0.717506 0 . 0 . 39 18,2,15,4 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P182|698|CPEB3|protein_coding|CODING|NM_014912.4|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.574016 rs3740302 -0.69168 0.171861 39 P86 698 ccT/ccC LOW 2 SILENT CODING CPEB3 G protein_coding NM_014912.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 93999850 A G 0 228 0 0.9501 0.6585 0.745 0.499 0.6173 0.41 0.895221 0.708736 0.613165 2 4737 35345 2982 2196 858 19123 272 5177 2 5266 56410 4070 3766 1564 30472 420 10852 0 . 0 . 0 68 0,0,7,59 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P86|698|CPEB3|protein_coding|CODING|NM_014912.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3824734 -0.693147 0.00188333 68 278 264 MODIFIER 1 CODING MARCH5 G protein_coding NM_017824.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94050988 C G 0 44.2 0 0.025 0.1392 0.1729 0.12 0.3221 0.1012 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.760115 0 . 0 . 19 1,13,0,5 START_GAINED(LOW||||278|MARCH5|protein_coding|CODING|NM_017824.4|1|G),UTR_5_PRIME(MODIFIER||264||278|MARCH5|protein_coding|CODING|NM_017824.4|1|G),UPSTREAM(MODIFIER||113||698|CPEB3|protein_coding|CODING|NM_014912.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.962163 rs746842 -0.590765 0.937711 19 278 167 MODIFIER 1 CODING MARCH5 T protein_coding NM_017824.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94051085 C T 0 101 0 0 0.017772 0 0.0853 0 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 9 2,1,5,0 START_GAINED(LOW||||278|MARCH5|protein_coding|CODING|NM_017824.4|1|T),UTR_5_PRIME(MODIFIER||167||278|MARCH5|protein_coding|CODING|NM_017824.4|1|T),UPSTREAM(MODIFIER||210||698|CPEB3|protein_coding|CODING|NM_014912.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.150134 rs2274454 -0.590765 0.618918 9 1019 51 MODIFIER 1 CODING IDE A protein_coding NM_004969.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94333827 G A 0 222 0 0.3941 0.2035 0.1844 0.1349 0.0696 0.1677 0.272727 0.14028 0.072093 1 564 2417 42 36 0 413 13 1349 2 1580 15110 242 274 8 5104 154 7748 0.818 0 . 0 . 23 1,6,4,8 START_GAINED(LOW||||1019|IDE|protein_coding|CODING|NM_004969.3|1|A),UTR_5_PRIME(MODIFIER||51||1019|IDE|protein_coding|CODING|NM_004969.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.257165 rs4646954 -0.680642 0.209801 23 1056 1014 MODIFIER 22 CODING KIF11 T protein_coding NM_004523.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94414567 A T 0 169 0 0.9191 0.8001 0.719 0.9196 0.5755 0.8047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,23,0 UTR_3_PRIME(MODIFIER||1014||1056|KIF11|protein_coding|CODING|NM_004523.3|22|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4933734 -0.692717 0.0278685 23 270 11 MODIFIER 1 CODING HHEX A protein_coding NM_002729.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94449733 G A 0 20.3 0 0.1127 0.102 0.147 0.121 0.0258 0.1145 0 . 0 1 0 42 1 0 0 2 0 39 2 0 106 2 0 0 18 0 86 1 0 . 0 . 5 3,0,2,0 UTR_5_PRIME(MODIFIER||11||270|HHEX|protein_coding|CODING|NM_002729.4|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 0.333333 rs117639730 -0.453602 0.82 5 T396I 804 aCt/aTt MODERATE 12 MISSENSE CODING EXOC6 T protein_coding NM_019053.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94695617 C T 0 228 0 0.9924 0.8886 0.8473 0.996 0.6839 0.8773 0.935996 0.772643 0.688953 2 9852 93464 10155 8608 4121 46196 700 13832 2 10394 120984 11448 8632 6582 66526 908 16494 0 . 0 . 0 119 0,0,61,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T396I|804|EXOC6|protein_coding|CODING|NM_019053.4|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1326331 -0.693147 0.000492898 119 804 270 MODIFIER 22 CODING EXOC6 C protein_coding NM_019053.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 94818382 A C 0 228 0 0.7882 0.879 0.8184 0.9871 0.8936 0.9182 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,2,39 UTR_3_PRIME(MODIFIER||270||804|EXOC6|protein_coding|CODING|NM_019053.4|22|C),UPSTREAM(MODIFIER||2639||522|CYP26C1|protein_coding|CODING|NM_183374.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1339820 -0.693145 0.458664 42 R1920 2061 agA/agG LOW 51 SILENT CODING MYOF C protein_coding NM_013451.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95072906 T C 0 228 0 0.7867 0.8435 0.7795 0.9107 0.8479 0.8916 0.799294 0.836152 0.853697 2 7789 102468 8737 7871 5790 57220 775 14286 2 9804 120764 11572 8626 6614 66738 900 16510 1 0 . 0 . 153 0,1,69,73 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R1920|2061|MYOF|protein_coding|CODING|NM_013451.3|51|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs787666 -0.693147 0.00766093 153 G213 2061 ggT/ggC LOW 7 SILENT CODING MYOF G protein_coding NM_013451.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95168634 A G 0 228 0 0.059 0.2095 0.1499 0.6677 0.0318 0.1656 0.0627837 0.0426155 0.0330132 2 602 14336 2398 5543 491 2873 107 2322 2 9804 120728 11570 8600 6612 66730 900 16512 1 0 . 0 . 310 1,0,102,175 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G213|2061|MYOF|protein_coding|CODING|NM_013451.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2296142 -0.693147 0.0025546 310 2061 35 MODIFIER 1 CODING MYOF A protein_coding NM_013451.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95241986 C A 0 185 0 0.1271 0.2312 0.2205 0.5208 0.172 0.1421 0.122022 0.148457 0.160619 1 1187 23142 2501 4478 1516 10914 192 2354 2 9794 120254 11558 8598 6610 66556 898 16240 0.998315 0 . 0 . 64 7,27,2,25 UTR_5_PRIME(MODIFIER||35||2061|MYOF|protein_coding|CODING|NM_013451.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.747845 rs882873 -0.693021 0.298161 64 2061 48 MODIFIER 1 CODING MYOF C protein_coding NM_013451.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95241999 A C 0 228 0 0.7859 0.9415 0.987 1 1 0.999 0.841645 0.949766 0.999512 2 8077 118205 11453 8617 6606 66463 884 16105 2 9774 120078 11564 8620 6606 66504 894 16116 0 . 0 . 0 50 0,0,4,44 UTR_5_PRIME(MODIFIER||48||2061|MYOF|protein_coding|CODING|NM_013451.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs947597 -0.693147 0.771524 50 T99A 464 Aca/Gca MODERATE 3 MISSENSE CODING CEP55 G protein_coding NM_001127182.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95262981 A G 0 228 0 0.941 0.983 0.9914 1 0.999 1 0.953473 0.984084 0.999767 2 9876 120825 11548 8654 6614 66717 907 16509 2 10406 121408 11576 8654 6614 66740 908 16510 0 . 0 . 0 156 0,0,95,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T99A|464|CEP55|protein_coding|CODING|NM_001127182.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7080916 -0.693147 0.824102 156 H378L 464 cAt/cTt MODERATE 8 MISSENSE CODING CEP55 T protein_coding NM_001127182.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95279506 A T 0 228 0 0.2587 0.5597 0.7118 0.5437 0.7525 0.6769 0.327508 0.610257 0.755116 2 3248 85348 8720 4901 5243 51182 663 11391 2 10398 121350 11570 8636 6614 66716 908 16508 1 0 . 0 . 113 0,1,70,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cTt|H378L|464|CEP55|protein_coding|CODING|NM_001127182.1|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2293277 -0.693147 0.372755 113 I349 377 atT/atA LOW 4 SILENT CODING FFAR4 A protein_coding NM_181745.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95347279 T A 0 222 0 0 0.00079872 0 0.004 0 0 0.00068089 0.000230663 0 1 4 69 0 61 0 0 0 4 2 10398 121402 11578 8654 6614 66738 908 16512 0.662493 0 . 0 . 72 11,17,9,28 SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I349|377|FFAR4|protein_coding|CODING|NM_181745.3|4|A),DOWNSTREAM(MODIFIER||4314||201|RBP4|protein_coding|CODING|NM_006744.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.267992 rs142295722 -0.693141 0.270952 72 L84 858 ctG/ctA LOW 1 SILENT CODING PDE6C A protein_coding NM_006204.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95372734 G A 0 222 0 0.2421 0.1643 0.1643 0.1131 0.167 0.1094 0.240127 0.194526 0.171163 1 2459 19994 1137 951 693 12432 140 2182 2 10342 120886 11534 8608 6586 66404 904 16508 0.837783 2 benign 0 . 80 28,15,16,18 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L84|858|PDE6C|protein_coding|CODING|NM_006204.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.862608 rs1131978 -0.693132 0.114985 80 S270T 858 Tca/Aca MODERATE 4 MISSENSE CODING PDE6C A protein_coding NM_006204.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95381773 T A 0 222 0 0.4803 0.4143 0.4222 0.4861 0.3628 0.2986 0.462778 0.391281 0.354651 1 4856 45262 5076 4146 2154 23383 352 5295 2 10406 121364 11570 8636 6608 66724 908 16512 0.992971 0 . 0 . 171 38,42,28,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Aca|S270T|858|PDE6C|protein_coding|CODING|NM_006204.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.420985 rs701865 -0.693147 0.15311 171 A366 858 gcG/gcA LOW 8 SILENT CODING PDE6C A protein_coding NM_006204.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95389041 G A 0 222 0 0.4493 0.3958 0.389 0.4792 0.3459 0.2935 0.429868 0.366292 0.333721 1 4504 42435 4546 4023 2107 21866 326 5063 2 10406 121376 11576 8634 6612 66730 908 16510 0.890307 0 . 0 . 87 23,20,18,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A366|858|PDE6C|protein_coding|CODING|NM_006204.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.839454 rs714550 -0.69311 0.202983 87 858 LOW 9 CODING PDE6C G protein_coding NM_006204.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95395247 A G 0 222 0 0.7065 0.7288 0.6988 0.6419 0.7416 0.8569 0.720608 0.737506 0.746163 1 7349 89657 7392 5654 4863 49975 683 13741 2 10356 121212 11544 8636 6602 66664 906 16504 0.819801 0 . 0 . 247 71,49,41,60 SPLICE_SITE_REGION+INTRON(LOW||||858|PDE6C|protein_coding|CODING|NM_006204.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999986 rs616522 -0.693147 0.313336 247 T460 858 acC/acG LOW 10 SILENT CODING PDE6C G protein_coding NM_006204.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95395364 C G 0 222 0 0.1112 0.2352 0.3199 0.3661 0.2922 0.1493 0.132093 0.229125 0.278837 1 1384 32083 4249 3040 1791 18459 230 2930 2 10406 121372 11568 8648 6614 66724 906 16506 0.915572 0 . 0 . 311 79,54,79,54 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T460|858|PDE6C|protein_coding|CODING|NM_006204.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.613646 rs3737228 -0.693147 0.109745 311 S251F 315 tCt/tTt MODERATE 11 MISSENSE CODING FRA10AC1 A protein_coding NM_145246.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95441272 G A 0 222 0 0.093 0.0817 0.0965 0.0337 0.1193 0.0665 0.0874205 0.104522 0.113282 1 908 11212 725 324 440 7356 87 1372 2 10336 120248 11368 8562 6560 66058 896 16468 0.75764 0 . 0 . 82 18,26,14,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S251F|315|FRA10AC1|protein_coding|CODING|NM_145246.4|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.849195 rs11187583,rs386517418 -0.693054 0.0117124 82 R16H 315 cGc/cAc MODERATE 2 MISSENSE CODING FRA10AC1 T protein_coding NM_145246.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95459817 C T 0 228 0 0.469 0.6226 0.6729 0.6885 0.7495 0.5961 0.509986 0.663463 0.742093 2 5173 84450 7951 6223 4721 49293 644 10445 2 10280 121008 11538 8624 6604 66584 906 16472 1 0 . 0 . 87 1,0,71,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R16H|315|FRA10AC1|protein_coding|CODING|NM_145246.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs726817 -0.693147 0.0514254 87 F219 557 ttT/ttC LOW 6 SILENT CODING LGI1 C protein_coding NM_005097.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95552653 T C 0 228 0 0.9244 0.9774 0.9856 1 0.997 1 0.935315 0.976934 0.998256 2 9711 120533 11507 8654 6614 66630 906 16511 2 10406 121406 11574 8654 6614 66738 908 16512 0 . 0 . 0 101 0,0,26,65 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F219|557|LGI1|protein_coding|CODING|NM_005097.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1111820 -0.693147 9.88876e-05 101 365 303 MODIFIER 3 CODING SLC35G1 TA protein_coding NM_001134658.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95661549 T TA 0 169 0 0.3654 0.5449 0.5072 0.8611 0.4573 0.5787 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,15,1 UTR_3_PRIME(MODIFIER||303||365|SLC35G1|protein_coding|CODING|NM_001134658.1|3|TA) 0 . 0 16 0.888889 1 1 0 . 0 60 0 0 1 0 . rs11389471 -0.689466 0.0130681 18 365 1149 MODIFIER 3 CODING SLC35G1 C protein_coding NM_001134658.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95662396 T C 0 228 0 0.3654 0.5477 0.5072 0.8611 0.4573 0.593 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 276 0,0,191,64 UTR_3_PRIME(MODIFIER||1149||365|SLC35G1|protein_coding|CODING|NM_001134658.1|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10882363 -0.693147 0.262585 276 2302 36982 MODIFIER 1 CODING PLCE1 G protein_coding NM_016341.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95753822 A G 0 9.7 0 0.677 0.5525 0.3775 0.7044 0.4006 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||2302|PLCE1|protein_coding|CODING|NM_016341.3|1|G),UTR_5_PRIME(MODIFIER||36982||2302|PLCE1|protein_coding|CODING|NM_016341.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2911857 -0.379885 0 1 2302 135 MODIFIER 2 CODING PLCE1 A protein_coding NM_016341.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95790669 G A 0 146 0 0.5 0.367 0.2133 0.4415 0.2873 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.228827 0 . 0 . 39 20,1,17,0 UTR_5_PRIME(MODIFIER||135||2302|PLCE1|protein_coding|CODING|NM_016341.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.484609 rs10882386 -0.690438 0.273955 39 C270 2302 tgT/tgC LOW 2 SILENT CODING PLCE1 C protein_coding NM_016341.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95791613 T C 0 222 0 0.7799 0.4605 0.2608 0.4792 0.3032 0.3129 0.677529 0.39654 0.265826 1 6948 38529 2234 4051 1949 17819 274 5254 2 9798 120516 11510 8590 6588 66632 900 16498 0.973436 0 . 0 COSM1349909,COSM1349910 123 45,15,39,17 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C270|2302|PLCE1|protein_coding|CODING|NM_016341.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.970884 rs17109671 -0.693147 0.460093 123 E320 2302 gaG/gaA LOW 2 SILENT CODING PLCE1 A protein_coding NM_016341.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 95791763 G A 0 222 0 0.5393 0.3782 0.2176 0.4415 0.2883 0.3016 0.458131 0.318235 0.254892 1 4714 34494 1645 3756 1943 17074 256 5106 2 9800 120590 11494 8604 6608 66682 898 16504 0.28398 0 . 0 . 170 41,31,43,37 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E320|2302|PLCE1|protein_coding|CODING|NM_016341.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0927356 rs17109674 -0.693147 0.812336 170 R1575P 2302 cGa/cCa MODERATE 20 MISSENSE CODING PLCE1 C protein_coding NM_016341.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96039597 G C 0 222 0 0.5893 0.4862 0.3487 0.5377 0.4563 0.4223 0.545407 0.475941 0.443945 1 5427 52756 3997 4713 2194 28951 413 7061 2 9794 120502 11512 8576 6592 66618 900 16510 0.817379 0 . 0 . 153 52,16,44,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cCa|R1575P|2302|PLCE1|protein_coding|CODING|NM_016341.3|20|C),INTRAGENIC(MODIFIER|||||PLCE1-AS1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0276594 rs2274224 -0.693147 0.0021704 153 E472A 800 gAg/gCg MODERATE 12 MISSENSE CODING NOC3L G protein_coding NM_022451.10 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96104665 T G 0 222 0 0.1657 0.2069 0.0908 0.2937 0.1213 0.3436 0.165077 0.136671 0.122121 1 1861 19489 1023 2373 923 8101 117 5091 2 10390 121026 11542 8638 6598 66526 902 16430 0.89238 0 . 0 . 75 20,8,17,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E472A|800|NOC3L|protein_coding|CODING|NM_022451.10|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977279 rs3758526 -0.693136 0.0569986 75 P194L 800 cCt/cTt MODERATE 6 MISSENSE CODING NOC3L A protein_coding NM_022451.10 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96114835 G A 0 222 0 0.1649 0.2061 0.0908 0.2917 0.1213 0.3425 0.163034 0.135287 0.121075 1 1847 19412 1026 2369 927 8047 118 5078 2 10396 121276 11576 8652 6614 66670 906 16462 0.880792 0 . 0 . 90 19,19,15,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P194L|800|NOC3L|protein_coding|CODING|NM_022451.10|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.84939 rs12572897 -0.693143 0.476826 90 P223 775 ccC/ccG LOW 1 SILENT CODING TBC1D12 G protein_coding NM_015188.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96163039 C G 0 129 0 0.6165 0.6811 0.5648 0.8373 0.6342 0.7382 0.687092 0.696523 0.700632 2 410 6646 134 330 20 2029 61 3662 2 602 9432 196 384 24 3018 94 5114 0 . 0 . 0 9 0,0,9,0 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P223|775|TBC1D12|protein_coding|CODING|NM_015188.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs2477534 -0.662043 0.74989 9 I77 884 atA/atC LOW 3 SILENT CODING HELLS C protein_coding NM_001289067.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96313960 A C 0 228 0 0.469 0.5306 0.3228 0.746 0.4404 0.6319 0.478212 0.454713 0.442674 2 5026 56923 4102 6167 2422 28962 391 9853 2 10296 121232 11572 8644 6614 66688 908 16510 0 . 0 . 0 87 0,0,21,50 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I77|884|HELLS|protein_coding|CODING|NM_001289067.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11188019 -0.693147 0.376666 87 884 397 MODIFIER 23 CODING HELLS T protein_coding NM_001289067.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96361776 C T 0 169 0 0.174 0.241 0.1225 0.3224 0.2048 0.3691 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.833732 0 . 0 . 58 1,24,1,31 UTR_3_PRIME(MODIFIER||397||884|HELLS|protein_coding|CODING|NM_001289067.1|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.742353 rs1048196 -0.69312 0.0244677 58 T385M 490 aCg/aTg MODERATE 8 MISSENSE CODING CYP2C18 T protein_coding NM_000772.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96493058 C T 0 222 0 0.1611 0.2189 0.1023 0.3135 0.1451 0.3579 0.16364 0.153468 0.148256 1 1822 22209 1149 2675 1190 9771 151 5451 2 10406 120900 11460 8560 6600 66566 904 16404 0.684463 0 . 0 . 73 19,7,33,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T385M|490|CYP2C18|protein_coding|CODING|NM_000772.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.785934 rs1126545 -0.693146 0.294473 73 490 83 MODIFIER 9 CODING CYP2C18 A protein_coding NM_000772.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96495284 G A 0 161 0 0.211 0.2324 0.1066 0.3135 0.1451 0.3569 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.832897 0 . 0 . 48 3,21,1,21 UTR_3_PRIME(MODIFIER||83||490|CYP2C18|protein_coding|CODING|NM_000772.2|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982683 rs1042192 -0.692562 0.543223 48 490 283 MODIFIER 9 CODING CYP2C18 T protein_coding NM_000772.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96495484 G T 0 38.2 0 0.211 0.2328 0.1066 0.3135 0.1461 0.3579 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 1,4,0,3 UTR_3_PRIME(MODIFIER||283||490|CYP2C18|protein_coding|CODING|NM_000772.2|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.900802 rs1042194 -0.511536 0.440791 8 P227 490 ccG/ccA LOW 5 SILENT CODING CYP2C19 A protein_coding NM_000769.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96541616 G A 0 222 0 0.1702 0.2214 0.1052 0.3125 0.1451 0.3579 0.165304 0.15413 0.148407 1 1808 22168 1143 2676 1201 9751 152 5437 2 9990 119422 11340 8624 6576 65998 900 15994 0.939484 6|6|6 drug-response|drug-response|drug-response 0 . 115 44,8,41,8 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P227|490|CYP2C19|protein_coding|CODING|NM_000769.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.922781 rs4244285 -0.693147 0.011869 115 V330 490 gtC/gtT LOW 7 SILENT CODING CYP2C19 T protein_coding NM_000769.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96602622 C T 0 222 0 0.1702 0.2212 0.1037 0.3125 0.1451 0.3579 0.16591 0.15416 0.14814 1 1847 22275 1160 2695 1190 9772 153 5458 2 10406 121380 11578 8636 6614 66732 908 16506 0.539558 0 . 0 . 171 56,25,49,24 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V330|490|CYP2C19|protein_coding|CODING|NM_000769.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.442304 rs3758580 -0.693147 0.013672 171 490 220 MODIFIER 9 CODING CYP2C9 G protein_coding NM_000771.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96749005 A G 0 105 0 0 0.0017971 0 0.0089 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.597145 0 . 0 . 18 0,9,0,9 UTR_3_PRIME(MODIFIER||220||490|CYP2C9|protein_coding|CODING|NM_000771.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.650623 rs9332244 -0.662043 0.74989 18 490 24 MODIFIER 9 CODING CYP2C8 A protein_coding NM_000770.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 96796861 G A 0 222 0 0.3661 0.3011 0.1441 0.38 0.1978 0.3497 0.344984 0.244272 0.192674 1 3697 27770 1490 3367 1288 12299 200 5429 2 10306 120584 11394 8596 6594 66396 902 16396 0.198972 0 . 0 COSN163713 60 18,9,16,10 UTR_3_PRIME(MODIFIER||24||490|CYP2C8|protein_coding|CODING|NM_000770.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850376 rs1058932 -0.692976 0.628531 60 1292 3067 MODIFIER 31 CODING SORBS1 T protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97071749 C T 0 155 0 0.0318 0.141 0.0807 0.4058 0.0567 0.1452 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.989343 0 . 0 . 24 4,10,4,6 UTR_3_PRIME(MODIFIER||3067||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.883506 rs1132810 -0.670168 0.690639 24 1292 2944 MODIFIER 31 CODING SORBS1 T protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97071872 G T 0 222 0 0.0446 0.147 0.0879 0.4107 0.0586 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.863642 0 . 0 . 73 29,3,31,6 UTR_3_PRIME(MODIFIER||2944||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.757083 rs386621604,rs9313 -0.693141 0.364554 73 1292 2808 MODIFIER 31 CODING SORBS1 C protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97072008 T C 0 222 0 0.3631 0.3474 0.2608 0.3313 0.4105 0.3395 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.986043 0 . 0 . 125 39,32,27,20 UTR_3_PRIME(MODIFIER||2808||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.518487 rs3193970 -0.693147 0.299185 125 1292 2776 MODIFIER 31 CODING SORBS1 G protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97072040 A G 0 222 0 0.0461 0.1464 0.0965 0.3909 0.0666 0.1472 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.855796 0 . 0 . 128 26,23,33,32 UTR_3_PRIME(MODIFIER||2776||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.629807 rs14420 -0.693147 0.18755 128 1292 2498 MODIFIER 31 CODING SORBS1 A protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97072318 C A 0 77 0 0.0219 0.1366 0.0951 0.376 0.0666 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666643 0 . 0 . 11 1,4,1,4 UTR_3_PRIME(MODIFIER||2498||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.523791 rs3814155 -0.590765 0.237122 11 1292 392 MODIFIER 31 CODING SORBS1 A protein_coding NM_001034954.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97074424 G A 0 46.3 0 0.0219 0.1394 0.0922 0.3919 0.0666 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,0,2,0 UTR_3_PRIME(MODIFIER||392||1292|SORBS1|protein_coding|CODING|NM_001034954.1|31|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs2296966,rs386564132 -0.453602 0.44 5 L809 1292 ctA/ctG LOW 24 SILENT CODING SORBS1 C protein_coding NM_001034954.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97106165 T C 0 222 0 0.205 0.4079 0.451 0.6696 0.3241 0.4683 0.207671 0.254267 0.27814 1 2228 43031 6026 5744 1939 18905 321 7868 2 10352 121052 11534 8642 6600 66538 904 16482 0.920757 0 . 0 . 80 27,10,24,7 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L809|1292|SORBS1|protein_coding|CODING|NM_001034954.1|24|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.936154 rs726176 -0.69311 0.395407 80 1292 LOW 19 CODING SORBS1 A protein_coding NM_001034954.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97127462 C A 0 195 0 0.8729 0.8251 0.8559 0.7649 0.7495 0.8783 0.832047 0.761725 0.725698 1 8428 91095 9951 6315 4681 47064 691 13965 2 9998 116024 11158 8218 6446 63446 880 15878 0.226411 0 . 0 . 32 0,19,3,9 SPLICE_SITE_REGION+INTRON(LOW||||1292|SORBS1|protein_coding|CODING|NM_001034954.1|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.851135 rs6583998 -0.680642 0.00767469 32 D524 1292 gaC/gaT LOW 16 SILENT CODING SORBS1 A protein_coding NM_001034954.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97141523 G A 0 222 0 0.4289 0.5974 0.7233 0.6498 0.6024 0.6769 0.459374 0.545902 0.590233 1 4677 75200 9305 5497 4209 40134 573 10805 2 10404 121348 11564 8648 6612 66710 908 16502 0.821121 0 . 0 . 109 15,35,10,44 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D524|1292|SORBS1|protein_coding|CODING|NM_001034954.1|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.69545 rs2274490,rs386563225 -0.693147 0.0250557 109 L61P 1292 cTt/cCt MODERATE 4 MISSENSE CODING SORBS1 G protein_coding NM_001034954.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97192324 A G 0 228 0 0.9289 0.9808 0.9971 1 1 1 0.942124 0.980163 0.999651 2 9748 120638 11518 8654 6614 66695 905 16504 2 10406 121398 11578 8654 6614 66734 908 16504 1 0 . 0 . 91 0,1,33,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L61P|1292|SORBS1|protein_coding|CODING|NM_001034954.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs943542 -0.693147 0.0794593 91 795 155 MODIFIER 18 CODING ALDH18A1 T protein_coding NM_002860.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97366364 C T 0 7 0 0.1687 0.2979 0.5648 0.0764 0.508 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 12 9,0,1,1 UTR_3_PRIME(MODIFIER||155||795|ALDH18A1|protein_coding|CODING|NM_002860.3|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs1053905 -0.453602 0.58 12 795 140 MODIFIER 18 CODING ALDH18A1 A protein_coding NM_002860.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97366379 G A 0 148 0 0.0008 0.0481 0.0043 0.2183 0 0.0174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.693041 0 . 0 . 14 2,1,10,1 UTR_3_PRIME(MODIFIER||140||795|ALDH18A1|protein_coding|CODING|NM_002860.3|18|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.927041 rs76824727 -0.676189 0.404531 14 S372Y 795 tCt/tAt MODERATE 10 MISSENSE CODING ALDH18A1 T protein_coding NM_002860.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97386497 G T 0 222 0 0.0106 0.0204 0.0159 0.0337 0.0199 0.0235 0.00635497 0.0149162 0.0193023 1 58 2091 94 296 37 1333 16 257 2 10406 121288 11558 8648 6600 66664 908 16504 0.284196 0 . 0 . 203 56,37,44,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tAt|S372Y|795|ALDH18A1|protein_coding|CODING|NM_002860.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.927772 rs3765571 -0.693147 0.0121359 203 T299I 795 aCc/aTc MODERATE 8 MISSENSE CODING ALDH18A1 A protein_coding NM_002860.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97388162 G A 0 222 0 0.0439 0.0717 0.0922 0.0377 0.1421 0.0573 0.0526555 0.101184 0.126047 1 461 12503 719 328 1044 8832 118 1001 2 10406 121388 11572 8654 6610 66726 908 16512 0.325868 0 . 0 . 177 43,45,38,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T299I|795|ALDH18A1|protein_coding|CODING|NM_002860.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939546 rs2275272 -0.693147 0.0539043 177 A309S 607 Gct/Tct MODERATE 8 MISSENSE CODING TCTN3 A protein_coding NM_015631.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97445357 C A 0 222 0 0.0113 0.0204 0.0159 0.0337 0.0189 0.0235 0.00578035 0.0173018 0.022313 1 20 383 3 16 11 200 4 129 2 2096 21476 396 620 1624 8616 238 7886 0.999561 3 likely-benign 0 . 113 31,24,24,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A309S|607|TCTN3|protein_coding|CODING|NM_015631.5|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.849901 rs55859130 -0.693145 0.00158922 113 T201 607 acT/acA LOW 4 SILENT CODING TCTN3 T protein_coding NM_015631.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97447373 A T 0 222 0 0.4236 0.4247 0.255 0.7133 0.3469 0.3292 0.415116 0.351761 0.319302 1 4259 42990 2423 6134 1911 22055 309 5899 2 10406 121304 11546 8634 6612 66690 908 16508 0.999031 3 likely-benign 0 . 97 15,30,11,29 SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T201|607|TCTN3|protein_coding|CODING|NM_015631.5|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.49342 rs10786229 -0.693145 0.116949 97 176 256 MODIFIER 8 CODING C10orf131 G protein_coding NM_001130446.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97698222 T G 0 228 0 0.323 0.3377 0.1888 0.62 0.1769 0.3374 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,32,0 UTR_3_PRIME(MODIFIER||256||176|C10orf131|protein_coding|CODING|NM_001130446.2|8|G),INTRAGENIC(MODIFIER|||||ENTPD1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1336457 -0.69312 0.190279 37 176 404 MODIFIER 8 CODING C10orf131 T protein_coding NM_001130446.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97698370 C T 0 228 0 0.8253 0.7652 0.768 0.8631 0.5467 0.8057 0 . 0 2 729 11216 212 421 923 3121 125 5685 2 918 16502 284 486 1618 5336 208 7652 0 . 0 . 0 78 0,0,45,27 UTR_3_PRIME(MODIFIER||404||176|C10orf131|protein_coding|CODING|NM_001130446.2|8|T),INTRAGENIC(MODIFIER|||||ENTPD1-AS1||NON_CODING|||T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4918979 -0.693147 0.0666629 78 A268 383 gcG/gcT LOW 6 SILENT CODING CCNJ T protein_coding NM_001134375.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97817650 G T 0 222 0 0.0174 0.1384 0.0159 0.4891 0.0089 0.1605 0.0181571 0.0110718 0.00744186 1 181 7573 133 4249 113 808 50 2039 2 10404 121338 11576 8626 6614 66706 908 16504 0.981148 0 . 0 . 137 61,14,44,14 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A268|383|CCNJ|protein_coding|CODING|NM_001134375.1|6|T),INTRAGENIC(MODIFIER|||||ENTPD1-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.895597 rs17111275 -0.693147 0.0186237 137 383 2293 MODIFIER 6 CODING CCNJ G protein_coding NM_001134375.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97820291 A G 0 222 0 0.0015 0.0369 0.0937 0.0863 0.0139 0.0174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.249455 0 . 0 . 124 30,23,34,28 UTR_3_PRIME(MODIFIER||2293||383|CCNJ|protein_coding|CODING|NM_001134375.1|6|G),INTRAGENIC(MODIFIER|||||ENTPD1-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 59 0 1 1 0 0.744205 rs147123834 -0.693147 0.421866 124 383 2341 MODIFIER 6 CODING CCNJ T protein_coding NM_001134375.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97820339 G T 0 222 0 0.1104 0.3121 0.3559 0.5179 0.3171 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.193322 0 . 0 . 82 39,8,26,7 UTR_3_PRIME(MODIFIER||2341||383|CCNJ|protein_coding|CODING|NM_001134375.1|6|T),INTRAGENIC(MODIFIER|||||ENTPD1-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.983787 rs1047370 -0.693127 0.0824353 82 R1328Q 1482 cGg/cAg MODERATE 7 MISSENSE CODING ZNF518A A protein_coding NM_001278524.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97920062 G A 0 222 0 0.0008 0.1358 0.0144 0.4891 0.0089 0.1708 0.00732501 0.00742992 0.00747732 1 56 7634 127 4213 113 818 49 2258 2 9782 120294 11414 8594 6598 66516 894 16496 0.908557 0 . 0 . 178 62,32,35,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1328Q|1482|ZNF518A|protein_coding|CODING|NM_001278524.1|7|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.146923 rs3814226,rs386587043 -0.693147 0.710639 178 1482 2137 MODIFIER 7 CODING ZNF518A C protein_coding NM_001278524.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97922667 T C 0 228 0 0.1248 0.3678 0.3184 0.6835 0.3419 0.4325 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 73 0,0,30,34 UTR_3_PRIME(MODIFIER||2137||1482|ZNF518A|protein_coding|CODING|NM_001278524.1|7|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10748660 -0.693147 0.0123395 73 1482 2469 MODIFIER 7 CODING ZNF518A A protein_coding NM_001278524.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97922999 T A 0 228 0 0.1248 0.3676 0.3184 0.6835 0.3419 0.4315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,26,32 UTR_3_PRIME(MODIFIER||2469||1482|ZNF518A|protein_coding|CODING|NM_001278524.1|7|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3748226 -0.693147 0.565655 62 P57 456 ccT/ccC LOW 4 SILENT CODING BLNK G protein_coding NM_013314.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 97990583 A G 0 228 0 0.1551 0.4613 0.6571 0.4514 0.7127 0.4877 0.243759 0.558204 0.719302 2 2223 70942 7661 3856 4312 44797 555 7538 2 9010 111128 10488 7986 5818 62534 812 14480 0 . 0 . COSM147002 27 0,0,11,14 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P57|456|BLNK|protein_coding|CODING|NM_013314.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs727852 -0.692914 0.827026 27 I74 509 atC/atT LOW 2 SILENT CODING DNTT T protein_coding NM_004088.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98078127 C T 0 228 0 0.9735 0.9928 0.9986 1 1 1 0.972764 0.990697 0.999884 2 10128 121019 11568 8654 6614 66679 906 16470 2 10404 121310 11578 8654 6614 66682 908 16470 0 . 0 . 0 156 0,0,84,61 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I74|509|DNTT|protein_coding|CODING|NM_004088.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7081385 -0.693147 0.143678 156 R112G 509 Aga/Gga MODERATE 2 MISSENSE CODING DNTT G protein_coding NM_004088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98078239 A G 0 228 0 0.9735 0.9928 0.9986 1 1 1 0.972764 0.990697 0.999884 2 10130 121087 11562 8638 6614 66731 906 16506 2 10406 121378 11572 8638 6614 66734 908 16506 0 . 0 . 0 229 0,0,122,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R112G|509|DNTT|protein_coding|CODING|NM_004088.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6584066 -0.693147 0.728766 229 509 17 MODIFIER 11 CODING DNTT A protein_coding NM_004088.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98097998 T A 0 188 0 0.0045 0.0831 0.0764 0.0883 0.1103 0.1605 0.0265668 0.071132 0.0939535 1 229 12158 923 705 804 6775 88 2634 2 10262 119890 11514 8514 6576 65924 892 16208 0.981818 0 . 0 . 100 13,49,4,26 UTR_3_PRIME(MODIFIER||17||509|DNTT|protein_coding|CODING|NM_004088.3|11|A),DOWNSTREAM(MODIFIER||4977||141|OPALIN|protein_coding|CODING|NM_033207.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.878915 rs2273891 -0.693097 0.209748 100 141 762 MODIFIER 6 CODING OPALIN G protein_coding NM_033207.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98104936 A G 0 21.2 0 0.5938 0.4243 0.2853 0.5317 0.1839 0.4305 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 UTR_3_PRIME(MODIFIER||762||141|OPALIN|protein_coding|CODING|NM_033207.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs11188726 -0.379885 0 3 141 76 MODIFIER 6 CODING OPALIN C protein_coding NM_033207.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98105622 T C 0 222 0 0.0492 0.25 0.2233 0.5317 0.1531 0.3497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999427 0 . 0 . 60 27,8,14,7 UTR_3_PRIME(MODIFIER||76||141|OPALIN|protein_coding|CODING|NM_033207.4|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999678 rs3814224 -0.692352 0.923496 60 1015 3451 MODIFIER 21 CODING TLL2 T protein_coding NM_012465.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98124394 G T 0 228 0 0.9539 0.9874 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 139 0,0,85,37 UTR_3_PRIME(MODIFIER||3451||1015|TLL2|protein_coding|CODING|NM_012465.3|21|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386482006,rs7073904 -0.693147 0.0184369 139 1015 3130 MODIFIER 21 CODING TLL2 C protein_coding NM_012465.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98124715 A C 0 25.8 0 0.1422 0.1314 0.0965 0.0942 0.1213 0.1902 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||3130||1015|TLL2|protein_coding|CODING|NM_012465.3|21|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs7077344 -0.453602 0.14 3 A844 1015 gcC/gcT LOW 19 SILENT CODING TLL2 A protein_coding NM_012465.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98133483 G A 0 222 0 0.1611 0.153 0.1282 0.0933 0.1451 0.229 0.152746 0.144318 0.14 1 1692 17314 946 835 914 8949 122 3856 2 10394 121316 11562 8644 6614 66682 908 16512 0.930159 0 . 0 . 70 5,27,12,21 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A844|1015|TLL2|protein_coding|CODING|NM_012465.3|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.329886 rs61741039 -0.693127 0.450681 70 589 1652 MODIFIER 15 CODING TM9SF3 G protein_coding NM_020123.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98280365 GAAA G 0 82 0 0.3404 0.5992 0.5403 0.8304 0.6392 0.7117 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1652||589|TM9SF3|protein_coding|CODING|NM_020123.3|15|G) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs36006955 -0.453602 0.5 2 589 LOW 12 CODING TM9SF3 C protein_coding NM_020123.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98287261 G C 0 228 0 0.3411 0.601 0.5403 0.8304 0.6471 0.7117 0.392322 0.57278 0.665193 2 3821 79004 6150 7186 4588 44867 599 11793 2 9906 119998 11442 8620 6594 66086 900 16450 0 . 0 . 0 86 0,0,22,54 SPLICE_SITE_REGION+INTRON(LOW||||589|TM9SF3|protein_coding|CODING|NM_020123.3|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3789957 -0.693147 0.011126 86 805 2121 MODIFIER 17 CODING PIK3AP1 T protein_coding NM_152309.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98353213 C T 0 9.7 0 0.3949 0.612 0.5317 0.8284 0.6382 0.7127 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2121||805|PIK3AP1|protein_coding|CODING|NM_152309.2|17|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7448 -0.379885 0 1 S591 805 tcG/tcA LOW 12 SILENT CODING PIK3AP1 T protein_coding NM_152309.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98380277 C T 0 228 0 0.3177 0.5733 0.5058 0.8234 0.5994 0.682 0.347481 0.529679 0.623023 2 3576 75066 5975 7144 4384 42122 569 11296 2 10292 120976 11526 8632 6606 66520 902 16498 0 . 0 . 0 46 0,0,6,37 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S591|805|PIK3AP1|protein_coding|CODING|NM_152309.2|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3748234,rs386585373 -0.693146 0.0216542 46 L526 805 Ctg/Ttg LOW 10 SILENT CODING PIK3AP1 A protein_coding NM_152309.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98386558 G A 0 228 0 0.7133 0.8918 0.951 0.999 0.9344 0.9366 0.746709 0.879748 0.947907 2 7661 112319 11192 8651 5812 62748 841 15414 2 10406 121406 11572 8654 6614 66740 908 16512 0 . 0 . 0 145 0,0,65,67 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L526|805|PIK3AP1|protein_coding|CODING|NM_152309.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4344416 -0.693147 2.32799e-07 145 A83S 805 Gcc/Tcc MODERATE 2 MISSENSE CODING PIK3AP1 A protein_coding NM_152309.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98469507 C A 0 228 0 0.5439 0.4225 0.4092 0.3095 0.3191 0.4908 0.504312 0.37921 0.315116 2 5303 42623 4386 2751 1779 20765 329 7310 2 10348 120760 11546 8608 6608 66330 900 16420 1 0 . 0 . 71 1,0,35,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A83S|805|PIK3AP1|protein_coding|CODING|NM_152309.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3748229 -0.693147 0.201005 71 I535L 1247 Atc/Ctc MODERATE 1 MISSENSE CODING C10orf12 C protein_coding NM_015652.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98742750 A C 0 222 0 0.0832 0.1016 0.0476 0.1915 0.0646 0.1104 0.0755788 0.0642879 0.058502 1 833 8742 355 1689 201 3740 61 1863 2 9976 120710 11570 8650 6614 66514 906 16480 0.870979 0 . 0 . 71 19,16,11,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I535L|1247|C10orf12|protein_coding|CODING|NM_015652.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740818 rs3829856 -0.693054 0.0642459 71 A437 1534 gcG/gcC LOW 14 SILENT CODING SLIT1 G protein_coding NM_003061.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98808866 C G 0 228 0 0.8495 0.9581 0.987 1 0.998 1 0.881979 0.959096 0.998605 2 9138 119769 11497 8652 6614 66505 896 16467 2 10392 121222 11574 8652 6614 66614 906 16470 0 . 0 . 0 57 0,0,12,38 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A437|1534|SLIT1|protein_coding|CODING|NM_003061.2|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2805588 -0.693147 0.0298714 57 494 1101 MODIFIER 12 CODING ARHGAP19 C protein_coding NM_032900.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 98984778 T C 0 9.7 0 0.7874 0.9413 0.9827 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1101||494|ARHGAP19|protein_coding|CODING|NM_032900.5|12|C),INTRAGENIC(MODIFIER|||||ARHGAP19-SLIT1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs701818 -0.379885 0 1 H274 494 caT/caC LOW 5 SILENT CODING ARHGAP19 G protein_coding NM_032900.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99019177 A G 0 228 0 0.7368 0.8444 0.9337 0.8095 0.9692 0.8344 0.764412 0.899508 0.968721 2 7895 111739 10496 7364 6296 64704 857 14127 2 10406 121410 11578 8652 6614 66740 908 16512 0 . 0 . 0 95 0,0,72,14 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H274|494|ARHGAP19|protein_coding|CODING|NM_032900.5|5|G),INTRAGENIC(MODIFIER|||||ARHGAP19-SLIT1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2253301 -0.693147 0.0139249 95 494 LOW 2 CODING ARHGAP19 A protein_coding NM_032900.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99025611 T A 0 228 0 0.1725 0.5038 0.5879 0.7113 0.6342 0.544 0.228325 0.468322 0.591279 2 2328 69285 7545 6341 3887 40203 545 8436 2 10386 121278 11570 8634 6614 66698 908 16468 0 . 0 . 0 88 0,0,50,29 SPLICE_SITE_REGION+INTRON(LOW||||494|ARHGAP19|protein_coding|CODING|NM_032900.5|2|A),INTRAGENIC(MODIFIER|||||ARHGAP19-SLIT1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10882884 -0.693147 0.179675 88 279 535 MODIFIER 1 CODING FRAT1 T protein_coding NM_005479.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99080585 C T 0 228 0 0.4652 0.6024 0.6167 0.6954 0.6501 0.6329 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 70 1,0,36,25 UTR_3_PRIME(MODIFIER||535||279|FRAT1|protein_coding|CODING|NM_005479.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3781373 -0.693147 0.046292 70 279 821 MODIFIER 1 CODING FRAT1 T protein_coding NM_005479.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99080871 G T 0 222 0 0.0371 0.2426 0.3228 0.3552 0.3479 0.2393 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.878533 0 . 0 . 81 29,12,15,10 UTR_3_PRIME(MODIFIER||821||279|FRAT1|protein_coding|CODING|NM_005479.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.752873 rs1334891 -0.692914 0.773444 81 279 931 MODIFIER 1 CODING FRAT1 T protein_coding NM_005479.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99080981 G T 0 228 0 0.4652 0.6026 0.6153 0.6964 0.6501 0.6339 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.640625 0 . 0 . 35 0,2,7,25 UTR_3_PRIME(MODIFIER||931||279|FRAT1|protein_coding|CODING|NM_005479.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.515625 rs1334892 -0.69312 0.00314241 35 R1281Q 1297 cGg/cAg MODERATE 34 MISSENSE CODING RRP12 T protein_coding NM_015179.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99116903 C T 0 222 0 0.1762 0.2833 0.2853 0.3075 0.2813 0.4039 0.174535 0.236276 0.267907 1 1856 33203 2549 2412 2112 18300 287 5687 2 10404 121290 11572 8640 6612 66656 904 16502 0.951607 0 . 0 . 28 4,5,10,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1281Q|1297|RRP12|protein_coding|CODING|NM_015179.3|34|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.851535 rs1048445,rs386513322 -0.686358 0.0261866 28 1297 LOW 32 CODING RRP12 C protein_coding NM_015179.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99118382 T C 0 222 0 0.6316 0.4255 0.353 0.3115 0.335 0.409 0.556741 0.397355 0.315698 1 5919 41735 3354 2469 2344 21438 345 5866 2 10404 121358 11572 8628 6614 66726 908 16506 0.552185 0 . 0 . 72 11,17,12,26 SPLICE_SITE_REGION+INTRON(LOW||||1297|RRP12|protein_coding|CODING|NM_015179.3|32|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931664 rs2297988 -0.693143 0.00609998 72 G1145S 1297 Ggc/Agc MODERATE 29 MISSENSE CODING RRP12 T protein_coding NM_015179.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99125949 C T 0 222 0 0.1271 0.396 0.562 0.3968 0.5934 0.4376 0.210622 0.466246 0.597209 1 2092 64814 6997 3812 3670 39779 481 7983 2 10392 121318 11572 8618 6610 66710 906 16510 0.649676 0 . 0 . 64 12,27,8,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1145S|1297|RRP12|protein_coding|CODING|NM_015179.3|29|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0603132 rs2275580 -0.692067 0.395713 64 D1115 1297 gaC/gaT LOW 28 SILENT CODING RRP12 A protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99126249 G A 0 151 0 0.1815 0.273 0.2622 0.3095 0.2584 0.3814 0.182705 0.227433 0.250349 1 1920 31532 2486 2449 1935 17114 271 5357 2 10370 120910 11564 8634 6614 66568 904 16256 0.63001 0 . 0 . 24 9,4,9,1 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1115|1297|RRP12|protein_coding|CODING|NM_015179.3|28|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.377737 rs2275581 -0.670168 0.0830571 24 A452 1297 gcT/gcC LOW 12 SILENT CODING RRP12 G protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99141205 A G 0 222 0 0.553 0.4048 0.3415 0.3125 0.337 0.4141 0.493872 0.377826 0.318372 1 5094 40298 3264 2424 2172 21264 323 5757 2 10106 117440 11242 8532 5796 65042 846 15876 0.543573 0 . 0 . 70 14,22,6,21 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A452|1297|RRP12|protein_coding|CODING|NM_015179.3|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.726956 rs2275089 -0.693021 0.0909126 70 T436 1297 acG/acA LOW 11 SILENT CODING RRP12 T protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99141484 C T 0 222 0 0.1377 0.2628 0.2579 0.3125 0.2604 0.3865 0.15025 0.218438 0.253372 1 1536 31396 2484 2449 1969 17327 268 5363 2 10336 120810 11514 8624 6492 66482 896 16466 0.986663 0 . 0 COSM1350177 63 22,6,20,8 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T436|1297|RRP12|protein_coding|CODING|NM_015179.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.733928 rs12218483 -0.693054 0.111139 63 F148 1297 ttC/ttT LOW 3 SILENT CODING RRP12 A protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99155984 G A 0 222 0 0.5507 0.4042 0.3429 0.3125 0.337 0.4131 0.493418 0.377979 0.318837 1 5169 41160 3335 2450 2379 21619 338 5870 2 10400 121302 11570 8614 6604 66702 904 16508 0.99816 0 . 0 . 81 23,13,27,10 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F148|1297|RRP12|protein_coding|CODING|NM_015179.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.360295 rs3814553 -0.693141 0.339049 81 G93 1297 ggT/ggC LOW 2 SILENT CODING RRP12 G protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99160152 A G 0 222 0 0.5378 0.4006 0.3444 0.3125 0.336 0.4121 0.497049 0.377672 0.316512 1 5191 41022 3311 2455 2384 21491 336 5854 2 10404 121346 11574 8628 6612 66708 908 16512 0.9543 0 . 0 . 69 13,24,10,17 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G93|1297|RRP12|protein_coding|CODING|NM_015179.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.549484 rs1048442,rs386513318 -0.693021 0.143833 69 P8 1297 ccT/ccC LOW 1 SILENT CODING RRP12 G protein_coding NM_015179.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99160965 A G 0 228 0 0.8896 0.9269 0.9827 0.875 0.9771 0.9397 0.891285 0.949715 0.979651 2 9291 116537 11367 7730 6335 65371 879 15564 2 10402 121384 11576 8654 6614 66718 908 16512 0 . 0 . 0 176 0,0,98,59 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|1297|RRP12|protein_coding|CODING|NM_015179.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2275091 -0.693147 0.00446233 176 A858 1030 gcC/gcT LOW 27 SILENT CODING MMS19 A protein_coding NM_001289405.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99219885 G A 0 220 0 0.4153 0.5252 0.5548 0.5863 0.5189 0.5961 0.422606 0.502614 0.543605 1 4391 65041 5565 4984 3605 36352 518 9626 2 10344 121110 11538 8616 6610 66606 904 16492 0.979222 0 . 0 . 62 17,23,6,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A858|1030|MMS19|protein_coding|CODING|NM_001289405.1|27|A),DOWNSTREAM(MODIFIER||2758||377|ZDHHC16|protein_coding|CODING|NM_032327.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.933184 rs2152092 -0.692352 0.857767 62 G790D 1030 gGc/gAc MODERATE 25 MISSENSE CODING MMS19 T protein_coding NM_001289405.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99220707 C T 0 222 0 0.1793 0.3301 0.4063 0.375 0.4503 0.3098 0.201954 0.342036 0.41389 1 1124 21588 1753 1370 1171 12768 166 3236 2 4672 50344 3288 3052 2694 26992 398 9248 0.774335 0 . 0 COSM147015 112 13,34,16,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G790D|1030|MMS19|protein_coding|CODING|NM_001289405.1|25|T),DOWNSTREAM(MODIFIER||3580||377|ZDHHC16|protein_coding|CODING|NM_032327.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.628726 rs3740526 -0.693147 0.386868 112 A68G 1030 gCa/gGa MODERATE 4 MISSENSE CODING MMS19 C protein_coding NM_001289405.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99240758 G C 0 228 0 0.8797 0.9375 0.9769 0.9613 0.9761 0.9233 0.885384 0.946786 0.978251 2 8804 111702 10740 8167 6128 62805 831 14227 2 9914 115760 10850 8358 6378 64158 850 15252 1 0 . 0 . 162 1,0,67,79 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A68G|1030|MMS19|protein_coding|CODING|NM_001289405.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2275586 -0.693147 0.322279 162 227 533 MODIFIER 3 CODING UBTD1 G protein_coding NM_024954.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99330813 A G 0 228 0 0.9531 0.9814 0.9942 1 0.9871 0.9857 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,37,34 UTR_3_PRIME(MODIFIER||533||227|UBTD1|protein_coding|CODING|NM_024954.4|3|G),UPSTREAM(MODIFIER||1385||446|ANKRD2|protein_coding|CODING|NM_001291218.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10748705 -0.693147 0.153502 81 P6R 446 cCc/cGc MODERATE 1 MISSENSE CODING ANKRD2 G protein_coding NM_001291218.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99332223 C G 0 23.4 0 0.2746 0.362 0.2709 0.5238 0.2783 0.4642 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 4 1,1,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P6R|446|ANKRD2|protein_coding|CODING|NM_001291218.1|1|G),DOWNSTREAM(MODIFIER||1256||227|UBTD1|protein_coding|CODING|NM_024954.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs12219064 -0.453602 0.42 4 A94 446 gcA/gcC LOW 1 SILENT CODING ANKRD2 C protein_coding NM_001291218.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99332488 A C 0 222 0 0.2557 0.3534 0.2666 0.5288 0.2724 0.4499 0.233091 0.248346 0.256166 1 1940 29536 2534 3363 1295 14829 238 5337 2 7334 84498 7310 6662 3136 46928 618 12510 0.950259 0 . 0 . 67 32,3,24,3 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A94|446|ANKRD2|protein_coding|CODING|NM_001291218.1|1|C),DOWNSTREAM(MODIFIER||1521||227|UBTD1|protein_coding|CODING|NM_024954.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890028 rs12221474 -0.693021 0.0192333 67 A148T 446 Gca/Aca MODERATE 2 MISSENSE CODING ANKRD2 A protein_coding NM_001291218.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99337572 G A 0 214 0 0.1921 0.4541 0.6585 0.4018 0.6869 0.4775 0.285227 0.561094 0.702564 1 1357 24359 898 1465 497 15282 167 4693 2 4068 39252 1326 2752 750 21356 284 8716 0.490175 0 . 0 COSM147016 43 17,2,16,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A148T|446|ANKRD2|protein_coding|CODING|NM_001291218.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980844 rs7094973 -0.692067 0.0159056 43 P11 173 ccC/ccG LOW 1 SILENT CODING MARVELD1 G protein_coding NM_031484.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99473666 C G 0 22.6 0 0.5129 0.4635 0.4337 0.6766 0.2117 0.4571 0 . 0 2 12 60 0 2 17 8 0 21 2 18 126 0 2 36 24 2 44 0 . 0 . 0 3 0,0,2,0 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P11|173|MARVELD1|protein_coding|CODING|NM_031484.3|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs11189342 -0.453602 0.02 3 G32 173 ggC/ggG LOW 1 SILENT CODING MARVELD1 G protein_coding NM_031484.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99473729 C G 0 118 0 0.0045 0.0783 0.1167 0.2262 0.0437 0.0337 0.0130246 0.0392372 0.0506289 1 33 819 22 63 44 289 8 360 2 1244 14884 196 256 302 5020 148 7718 0.961166 0 . 0 . 15 6,0,7,0 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G32|173|MARVELD1|protein_coding|CODING|NM_031484.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.961166 0 . 0.0715762 rs71486131 -0.636426 0.0317414 15 G138V 416 gGt/gTt MODERATE 3 MISSENSE CODING ZFYVE27 T protein_coding NM_001002261.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99504630 G T 0 222 0 0.7761 0.6965 0.6023 0.5427 0.7962 0.7117 0.767484 0.763842 0.761977 1 7182 79346 5548 4214 4673 46319 624 10786 2 9322 108340 9574 7704 5780 59856 832 15272 0.609697 3 likely-benign 0 . 48 11,9,11,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G138V|416|ZFYVE27|protein_coding|CODING|NM_001002261.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.403455 rs10882993 -0.692562 0.643049 48 416 40 MODIFIER 12 CODING ZFYVE27 G protein_coding NM_001002261.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99519097 A G 0 222 0 0.6793 0.6797 0.6124 0.5258 0.83 0.7321 0.695869 0.759034 0.791395 1 7037 87965 6368 4230 5320 52399 676 11935 2 10330 120424 11380 8544 6506 66296 896 16472 0.959235 0 . 0 . 63 6,25,5,19 UTR_3_PRIME(MODIFIER||40||416|ZFYVE27|protein_coding|CODING|NM_001002261.3|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.366386 rs1981237,rs386551210 -0.692831 0.275321 63 416 367 MODIFIER 12 CODING ZFYVE27 A protein_coding NM_001002261.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99519424 G A 0 46.3 0 0.8752 0.7342 0.6311 0.5258 0.833 0.7301 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||367||416|ZFYVE27|protein_coding|CODING|NM_001002261.3|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3814560 -0.453602 0.32 2 317 603 MODIFIER 3 CODING SFRP5 A protein_coding NM_003015.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99526668 G A 0 21.2 0 0.3185 0.5569 0.5634 0.4841 0.8072 0.6922 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 UTR_3_PRIME(MODIFIER||603||317|SFRP5|protein_coding|CODING|NM_003015.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2039826,rs386554156 -0.379885 0 3 H656R 792 cAt/cGt MODERATE 7 MISSENSE CODING R3HCC1L G protein_coding NM_001256619.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 99991408 A G 0 228 0 0.9705 0.9918 0.9971 1 1 1 0.972537 0.990389 0.999535 2 10094 120985 11500 8654 6612 66711 906 16508 2 10406 121318 11510 8654 6612 66718 908 16510 0 . 0 . 0 82 0,0,24,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H656R|792|R3HCC1L|protein_coding|CODING|NM_001256619.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1952061,rs386550231 -0.693147 0.906145 82 756 242 MODIFIER 15 CODING LOXL4 A protein_coding NM_032211.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100008436 G A 0 228 0 0.2057 0.3215 0.3285 0.4722 0.3231 0.316 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,5,16 UTR_3_PRIME(MODIFIER||242||756|LOXL4|protein_coding|CODING|NM_032211.6|15|A),DOWNSTREAM(MODIFIER||3782||792|R3HCC1L|protein_coding|CODING|NM_001256619.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3793692 -0.692352 0.319006 22 D405A 756 gAt/gCt MODERATE 8 MISSENSE CODING LOXL4 G protein_coding NM_032211.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100017453 T G 0 222 0 0.0575 0.3622 0.5231 0.6081 0.341 0.4284 0.104857 0.251422 0.326512 1 1049 45322 7006 4905 2247 22526 326 7263 2 10402 121270 11568 8632 6610 66668 908 16482 0.999848 0 . 0 . 112 45,17,26,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D405A|756|LOXL4|protein_coding|CODING|NM_032211.6|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.722865 rs1983864,rs386551399 -0.693144 0.0479122 112 H281 756 caC/caT LOW 6 SILENT CODING LOXL4 A protein_coding NM_032211.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100018844 G A 0 222 0 0.23 0.5016 0.6138 0.752 0.4473 0.5869 0.268182 0.367846 0.418837 1 2096 42976 5607 4543 1756 20728 328 7918 2 6136 75750 7402 6082 3190 39448 568 12924 0.982879 0 . 0 . 58 14,22,9,10 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H281|756|LOXL4|protein_coding|CODING|NM_032211.6|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.353295 rs7077073 -0.69168 0.550167 58 581 31 MODIFIER 1 CODING PYROXD2 C protein_coding NM_032709.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100174923 G C 0 222 0 0 0.0013978 0 0.0069 0 0 0 . 0 1 0 86 0 84 0 1 0 1 2 10180 117444 11288 8348 6458 64874 876 15420 0.910479 0 . 0 . 49 11,17,5,12 UTR_5_PRIME(MODIFIER||31||581|PYROXD2|protein_coding|CODING|NM_032709.2|1|C),DOWNSTREAM(MODIFIER||1032||700|HPS1|protein_coding|CODING|NM_000195.4||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.994466 rs2296437 -0.690438 0.18571 49 700 1326 MODIFIER 20 CODING HPS1 T protein_coding NM_000195.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100175995 G T 0 9.7 0 0 0.016174 0 0.0794 0.001 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1326||700|HPS1|protein_coding|CODING|NM_000195.4|20|T),UPSTREAM(MODIFIER||1017||581|PYROXD2|protein_coding|CODING|NM_032709.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs146022441 -0.379885 0 1 700 706 MODIFIER 20 CODING HPS1 C protein_coding NM_000195.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100176615 G C 0 9.7 0 0.8457 0.5905 0.4611 0.6796 0.326 0.5174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||706||700|HPS1|protein_coding|CODING|NM_000195.4|20|C),UPSTREAM(MODIFIER||1637||581|PYROXD2|protein_coding|CODING|NM_032709.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3830020 -0.379885 0 1 592 1722 MODIFIER 12 CODING HPSE2 C protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100217609 A C 0 9.7 0 0.0045 0.0665 0.0793 0.1151 0.1123 0.044 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1722||592|HPSE2|protein_coding|CODING|NM_021828.4|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs75584607 -0.379885 0 1 592 1639 MODIFIER 12 CODING HPSE2 C protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100217692 T C 0 9.7 0 0.7738 0.5891 0.562 0.5744 0.5169 0.4479 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1639||592|HPSE2|protein_coding|CODING|NM_021828.4|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4917831 -0.379885 0 1 592 799 MODIFIER 12 CODING HPSE2 T protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100218532 C T 0 46.3 0 0.6218 0.5337 0.536 0.5268 0.5099 0.4448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||799||592|HPSE2|protein_coding|CODING|NM_021828.4|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1060447 -0.453602 0.18 2 592 610 MODIFIER 12 CODING HPSE2 G protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100218721 C G 0 9.7 0 0.6218 0.5343 0.536 0.5278 0.5109 0.4458 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||610||592|HPSE2|protein_coding|CODING|NM_021828.4|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1060446 -0.379885 0 1 592 599 MODIFIER 12 CODING HPSE2 G protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100218732 A G 0 9.7 0 0.6218 0.5341 0.536 0.5278 0.5109 0.4448 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||599||592|HPSE2|protein_coding|CODING|NM_021828.4|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3179357 -0.379885 0 1 592 565 MODIFIER 12 CODING HPSE2 T protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100218766 C T 0 9.7 0 0.6203 0.5397 0.536 0.5595 0.5099 0.4438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||565||592|HPSE2|protein_coding|CODING|NM_021828.4|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1060445,rs386514525 -0.379885 0 1 592 436 MODIFIER 12 CODING HPSE2 T protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100218895 G T 0 34.3 0 0.0045 0.0645 0.0764 0.1131 0.1064 0.044 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 7 4,0,3,0 UTR_3_PRIME(MODIFIER||436||592|HPSE2|protein_coding|CODING|NM_021828.4|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.607698 rs17457493 -0.511536 0.045681 7 592 17 MODIFIER 12 CODING HPSE2 A protein_coding NM_021828.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100219314 G A 0 228 0 0.621 0.5298 0.5346 0.5109 0.5099 0.4427 0.620517 0.531216 0.485465 2 6448 60938 5855 4688 3064 33116 457 7310 2 10338 120940 11552 8614 6596 66430 904 16506 0 . 0 . 0 92 0,0,27,56 UTR_3_PRIME(MODIFIER||17||592|HPSE2|protein_coding|CODING|NM_021828.4|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10883099 -0.693147 0.00409021 92 Y579F 592 tAt/tTt MODERATE 12 MISSENSE CODING HPSE2 A protein_coding NM_021828.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 100219374 T A 0 228 0 0.6233 0.5306 0.5346 0.5119 0.5099 0.4427 0.621425 0.532293 0.486628 2 6477 61099 5854 4690 3073 33240 457 7308 2 10366 121074 11546 8616 6600 66550 902 16494 0 . 0 . COSM426898 67 0,0,21,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y579F|592|HPSE2|protein_coding|CODING|NM_021828.4|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10883100 -0.693147 0.290866 67 V428 951 gtT/gtG LOW 1 SILENT CODING CNNM1 G protein_coding NM_020348.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101090428 T G 0 222 0 0.9539 0.8698 0.7435 0.872 0.8201 0.8947 0.937585 0.868292 0.832791 1 9781 101740 8095 7453 5499 55374 753 14785 2 10390 121286 11560 8636 6612 66672 906 16510 0.89811 0 . 0 . 122 16,36,22,41 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtG|V428|951|CNNM1|protein_coding|CODING|NM_020348.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955004 rs2862600 -0.693147 0.616112 122 951 2317 MODIFIER 11 CODING CNNM1 T protein_coding NM_020348.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101153590 A T 0 9.7 0 0.8442 0.8243 0.8919 0.6677 0.9125 0.82 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||2317||951|CNNM1|protein_coding|CODING|NM_020348.2|11|T),DOWNSTREAM(MODIFIER||3037||413|GOT1|protein_coding|CODING|NM_002079.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7914408 -0.453602 0.1 3 413 545 MODIFIER 9 CODING GOT1 T protein_coding NM_002079.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101156759 C T 0 39.3 0 0.2375 0.1052 0.0504 0.0704 0.0358 0.0726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||545||413|GOT1|protein_coding|CODING|NM_002079.2|9|T),DOWNSTREAM(MODIFIER||2672||951|CNNM1|protein_coding|CODING|NM_020348.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2641 -0.453602 0.42 2 413 323 MODIFIER 9 CODING GOT1 G protein_coding NM_002079.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101156981 T G 0 44.7 0 0.2549 0.1098 0.0519 0.0704 0.0348 0.0726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924584 0 . 0 . 11 6,0,2,1 UTR_3_PRIME(MODIFIER||323||413|GOT1|protein_coding|CODING|NM_002079.2|9|G),DOWNSTREAM(MODIFIER||2894||951|CNNM1|protein_coding|CODING|NM_020348.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 1 0 0.809011 rs1126878 -0.511536 0.401962 11 413 144 MODIFIER 9 CODING GOT1 A protein_coding NM_002079.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101157160 G A 0 155 0 0.0681 0.0567 0.0259 0.0704 0.0338 0.0726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.533653 0 . 0 . 72 29,0,41,0 UTR_3_PRIME(MODIFIER||144||413|GOT1|protein_coding|CODING|NM_002079.2|9|A),DOWNSTREAM(MODIFIER||3073||951|CNNM1|protein_coding|CODING|NM_020348.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.0526897 rs11867,rs386521689 -0.693145 0.912516 72 A49 364 gcC/gcA LOW 1 SILENT CODING NKX2-3 A protein_coding NM_145285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101293035 C A 0 228 0 0.5628 0.5513 0.5994 0.5546 0.503 0.5481 0.570657 0.537019 0.520704 2 5415 63921 7222 4593 3520 33735 463 8973 2 9682 118924 11310 8436 6446 65778 882 16390 0.876121 0 . 0 COSM426905 315 2,1,193,85 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A49|364|NKX2-3|protein_coding|CODING|NM_145285.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.331632 rs41290504 -0.693147 0.192869 315 364 385 MODIFIER 2 CODING NKX2-3 G protein_coding NM_145285.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101295863 A G 0 228 0 0.1089 0.2584 0.3242 0.4395 0.2853 0.1994 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 129 0,0,80,33 UTR_3_PRIME(MODIFIER||385||364|NKX2-3|protein_coding|CODING|NM_145285.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs888208 -0.693147 0.087553 129 604 5165 MODIFIER 13 CODING ENTPD7 A protein_coding NM_020354.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101469605 G A 0 60 0 0.7511 0.8263 0.8746 0.7817 0.8787 0.8855 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||5165||604|ENTPD7|protein_coding|CODING|NM_020354.3|13|A),UTR_3_PRIME(MODIFIER||4739||410|COX15|protein_coding|CODING|NM_078470.4|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2300983 -0.453602 0.88 3 410 4739 MODIFIER 9 CODING COX15 A protein_coding NM_078470.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101469605 G A 0 60 0 0.7511 0.8263 0.8746 0.7817 0.8787 0.8855 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||5165||604|ENTPD7|protein_coding|CODING|NM_020354.3|13|A),UTR_3_PRIME(MODIFIER||4739||410|COX15|protein_coding|CODING|NM_078470.4|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2300983 -0.453602 0.88 3 604 6487 MODIFIER 13 CODING ENTPD7 G protein_coding NM_020354.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101470927 A G 0 9.7 0 0.0545 0.1264 0.085 0.2887 0.1004 0.1125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6487||604|ENTPD7|protein_coding|CODING|NM_020354.3|13|G),UTR_3_PRIME(MODIFIER||3417||410|COX15|protein_coding|CODING|NM_078470.4|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10883407 -0.379885 0 1 410 3417 MODIFIER 9 CODING COX15 G protein_coding NM_078470.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101470927 A G 0 9.7 0 0.0545 0.1264 0.085 0.2887 0.1004 0.1125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6487||604|ENTPD7|protein_coding|CODING|NM_020354.3|13|G),UTR_3_PRIME(MODIFIER||3417||410|COX15|protein_coding|CODING|NM_078470.4|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10883407 -0.379885 0 1 410 1126 MODIFIER 9 CODING COX15 G protein_coding NM_078470.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101473218 A G 0 228 0 0.7542 0.8271 0.8746 0.7817 0.8787 0.8855 0.759873 0.834845 0.873256 2 7857 103874 10340 6653 5811 57920 788 14505 2 10314 120642 11498 8592 6550 66296 904 16488 0 255 other 0 . 69 0,0,34,29 UTR_3_PRIME(MODIFIER||1126||410|COX15|protein_coding|CODING|NM_078470.4|9|G),DOWNSTREAM(MODIFIER||2216||604|ENTPD7|protein_coding|CODING|NM_020354.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2231687 -0.693147 0.264753 69 410 435 MODIFIER 1 CODING COX15 A protein_coding NM_078470.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101492241 G A 0 70 0 0.4402 0.5387 0.6527 0.3998 0.5984 0.6728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.475476 0 . 0 . 11 0,6,0,5 UTR_5_PRIME(MODIFIER||435||410|COX15|protein_coding|CODING|NM_078470.4|1|A),INTRON(MODIFIER||||273|CUTC|protein_coding|CODING|NM_015960.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.891517 rs2231675 -0.590765 0.128356 11 410 597 MODIFIER 1 CODING COX15 G protein_coding NM_078470.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101492403 T G 0 130 0 0.4455 0.5401 0.6527 0.3998 0.5984 0.6728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 7 0,1,3,2 START_GAINED(LOW||||410|COX15|protein_coding|CODING|NM_078470.4|1|G),UTR_5_PRIME(MODIFIER||597||410|COX15|protein_coding|CODING|NM_078470.4|1|G),INTRON(MODIFIER||||273|CUTC|protein_coding|CODING|NM_015960.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.861511 0 1 rs2281636,rs386563514 -0.590765 0.0152419 7 Y39F 1545 tAc/tTc MODERATE 2 MISSENSE CODING ABCC2 T protein_coding NM_000392.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101544447 A T 0 228 0 0.9811 0.9946 0.9971 1 1 1 0.980708 0.993465 1 2 10189 121174 11565 8654 6614 66733 907 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 58 0,0,23,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y39F|1545|ABCC2|protein_coding|CODING|NM_000392.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs927344 -0.693147 0.0521183 58 I1324 1545 atC/atT LOW 28 SILENT CODING ABCC2 T protein_coding NM_000392.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101604207 C T 0 222 0 0.2163 0.2881 0.3415 0.247 0.3708 0.3047 0.259873 0.333538 0.371279 1 2684 41476 4005 2090 2285 24740 299 5373 2 10390 121260 11570 8628 6612 66648 906 16506 0.852925 2 benign 0 COSM147024 86 20,27,11,19 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1324|1545|ABCC2|protein_coding|CODING|NM_000392.4|28|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983431 rs3740066 -0.693097 0.0713408 86 S1440 1577 tcC/tcT LOW 16 SILENT CODING DNMBP A protein_coding NM_015221.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101639796 G A 0 222 0 0.5386 0.4645 0.4798 0.2679 0.5388 0.4796 0.534725 0.527372 0.523605 1 5667 59208 5441 2325 2845 34296 438 8196 2 10404 121378 11572 8642 6610 66730 908 16512 0.996597 0 . 0 COSM1179742 77 18,26,14,16 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1440|1577|DNMBP|protein_coding|CODING|NM_015221.2|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.148159 rs2255901 -0.693097 0.00209745 77 C1413W 1577 tgT/tgG MODERATE 16 MISSENSE CODING DNMBP C protein_coding NM_015221.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101639877 A C 0 222 0 0.1437 0.2772 0.3329 0.244 0.3917 0.3344 0.187699 0.315085 0.380349 1 1949 41783 3952 2138 2321 25219 305 5899 2 10406 121396 11578 8638 6614 66740 908 16512 0.77456 0 . 0 . 64 21,14,12,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C1413W|1577|DNMBP|protein_coding|CODING|NM_015221.2|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.628182 rs11190305 -0.693079 0.00944362 64 P1248 1577 ccA/ccG LOW 14 SILENT CODING DNMBP C protein_coding NM_015221.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101645498 T C 0 222 0 0.587 0.4786 0.4827 0.2698 0.5388 0.4826 0.583296 0.543749 0.523488 1 4700 43701 3753 1884 2076 24429 308 6551 2 7382 77388 6648 5128 3856 41556 556 12262 0.999989 0 . 0 . 96 28,21,18,16 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1248|1577|DNMBP|protein_coding|CODING|NM_015221.2|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94595 rs2490763,rs386568151 -0.693132 0.239919 96 1577 LOW 11 CODING DNMBP C protein_coding NM_015221.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101654696 T C 0 222 0 0.4652 0.4561 0.4784 0.2808 0.5736 0.4877 0.492056 0.542596 0.568488 1 5108 62453 5418 2468 3283 37321 452 8403 2 10344 120402 11474 8572 6578 66174 906 16354 0.942794 0 . 0 . 98 35,5,33,9 SPLICE_SITE_REGION+INTRON(LOW||||1577|DNMBP|protein_coding|CODING|NM_015221.2|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.336949 rs3758394,rs386585610 -0.693146 0.195313 98 N961 1577 aaC/aaT LOW 9 SILENT CODING DNMBP A protein_coding NM_015221.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101657880 G A 0 222 0 0.1589 0.2746 0.3256 0.2183 0.3946 0.3292 0.201997 0.323851 0.386279 1 2095 41938 3925 1860 2332 25585 304 5837 2 10406 121400 11576 8648 6610 66740 908 16512 0.964023 0 . 0 . 146 45,14,48,20 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N961|1577|DNMBP|protein_coding|CODING|NM_015221.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.462228 rs7919323 -0.693147 0.921251 146 P444 1577 ccC/ccT LOW 4 SILENT CODING DNMBP A protein_coding NM_015221.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101715899 G A 0 228 0 0.6558 0.4415 0.4352 0.2579 0.4175 0.3701 0.623241 0.492619 0.425698 2 6614 50500 5039 2108 2415 27633 357 6334 2 10392 121374 11576 8646 6614 66726 908 16512 1 0 . 0 . 134 0,2,65,51 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P444|1577|DNMBP|protein_coding|CODING|NM_015221.2|4|A),INTRAGENIC(MODIFIER|||||DNMBP-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.547414 rs2862923 -0.693147 0.0172113 134 G282 458 ggG/ggA LOW 5 SILENT CODING CPN1 T protein_coding NM_001308.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101823396 C T 0 222 0 0.0144 0.0681 0.0159 0.2679 0.006 0.0358 0.0131639 0.00907274 0.00697674 1 151 3873 212 2234 41 562 31 642 2 10360 121160 11558 8642 6614 66582 904 16500 0.867797 0 . 0 . 69 19,10,23,8 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G282|458|CPN1|protein_coding|CODING|NM_001308.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999973 rs17852464 -0.69311 0.302305 69 458 LOW 1 CODING CPN1 G protein_coding NM_001308.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101841153 A G 0 228 0 0.9735 0.893 0.8732 0.9325 0.8857 0.7648 0.955288 0.902507 0.875465 2 9758 102956 10047 7952 5313 56909 738 12239 2 10174 118092 11210 8506 6046 65222 868 16066 0 . 0 . 0 53 0,0,43,4 SPLICE_SITE_REGION+INTRON(LOW||||458|CPN1|protein_coding|CODING|NM_001308.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10883439 -0.693147 0.938462 53 348 746 MODIFIER 12 CODING ERLIN1 G protein_coding NM_001100626.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101911142 A G 0 149 0 0.6762 0.3401 0.1484 0.4117 0.0835 0.2117 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99606 0 . 0 . 18 3,7,4,4 UTR_3_PRIME(MODIFIER||746||348|ERLIN1|protein_coding|CODING|NM_001100626.1|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.952795 rs12806 -0.651104 0.740326 18 V268I 745 Gta/Ata MODERATE 9 MISSENSE CODING CHUK T protein_coding NM_001278.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 101977883 C T 0 222 0 0.7965 0.5457 0.4294 0.5109 0.5179 0.3538 0.743078 0.583039 0.501047 1 7772 58033 3933 4194 3049 33143 453 5489 2 10400 121118 11536 8620 6598 66570 902 16492 0.82152 0 . 0 . 94 15,33,9,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V268I|745|CHUK|protein_coding|CODING|NM_001278.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.542132 rs2230804,rs386561792 -0.693136 0.122867 94 A240 538 gcG/gcA LOW 8 SILENT CODING CWF19L1 T protein_coding NM_018294.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102006681 C T 0 222 0 0.1165 0.1084 0.0216 0.3026 0.0129 0.0573 0.0887426 0.0415962 0.0174419 1 1011 5688 177 2343 74 1242 49 792 2 10390 121112 11560 8638 6608 66572 906 16438 0.862856 3 likely-benign 0 . 72 7,30,9,19 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A240|538|CWF19L1|protein_coding|CODING|NM_018294.5|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.245564 rs17112787 -0.693054 0.27148 72 V393I 805 Gtc/Atc MODERATE 6 MISSENSE CODING PKD2L1 T protein_coding NM_016112.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102056745 C T 0 228 0 0.1006 0.1194 0.1542 0.1101 0.1193 0.1299 0.0882887 0.104029 0.112093 2 960 14033 1728 1035 1022 7381 130 1777 2 9920 117870 11086 8416 6330 65304 870 15944 0 . 0 . 0 78 0,0,59,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V393I|805|PKD2L1|protein_coding|CODING|NM_016112.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2278842 -0.693147 0.206023 78 1179 861 MODIFIER 26 CODING SEC31B T protein_coding NM_015490.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102246512 C T 0 39.3 0 0.0635 0.2528 0.3069 0.3879 0.329 0.2526 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||861||1179|SEC31B|protein_coding|CODING|NM_015490.3|26|T),DOWNSTREAM(MODIFIER||3113||351|WNT8B|protein_coding|CODING|NM_003393.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2970 -0.453602 0.14 2 P41A 349 Ccc/Gcc MODERATE 1 MISSENSE CODING HIF1AN G protein_coding NM_017902.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102295836 C G 0 200 0 0.0182 0.1807 0.2147 0.253 0.2694 0.2106 0.049749 0.18635 0.256311 1 484 28688 2359 2212 1531 17724 230 4148 2 8378 113008 11156 8444 6026 62122 830 16052 0.944904 0 . 0 COSM426936 35 12,1,18,3 PROTEIN_INTERACTION_LOCUS(HIGH||||349|HIF1AN|protein_coding|CODING||1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P41A|349|HIF1AN|protein_coding|CODING|NM_017902.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2295778 -0.692352 0.45609 35 432 203 MODIFIER 1 CODING PAX2 G protein_coding NM_003990.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102505815 A G 0 72 0 0.7209 0.8496 0.8213 0.998 0.8012 0.9407 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,0 UTR_5_PRIME(MODIFIER||203||432|PAX2|protein_coding|CODING|NM_003990.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11190680 -0.511536 0.690245 4 1186 150 MODIFIER 1 CODING SLF2 C protein_coding NM_001136123.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102672718 T C 0 222 0 0.3843 0.3608 0.2752 0.5446 0.1829 0.3834 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.751166 0 . 0 . 214 78,26,67,12 UTR_5_PRIME(MODIFIER||150||1186|SLF2|protein_coding|CODING|NM_001136123.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976743 rs3802724 -0.693147 0.73975 214 S541Y 1186 tCt/tAt MODERATE 5 MISSENSE CODING SLF2 A protein_coding NM_001136123.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102684380 C A 0 218 0 0.1619 0.3187 0.4769 0.0952 0.5746 0.3855 0.207898 0.428187 0.541047 1 2095 55224 4640 781 3582 36608 440 7078 2 10226 120722 11534 8620 6610 66372 900 16460 0.623253 0 . 0 . 43 14,11,5,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tAt|S541Y|1186|SLF2|protein_coding|CODING|NM_001136123.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.246298 rs10883563,rs386515749 -0.691153 0.571717 43 843 326 MODIFIER 14 CODING SEMA4G C protein_coding NM_017893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102744214 T C 0 218 0 0.4312 0.3624 0.2867 0.5278 0.1829 0.3374 0 . 0 1 221 2506 47 115 4 497 31 1591 2 534 7920 152 198 18 2370 102 4546 0.714018 0 . 0 . 43 13,4,20,3 UTR_3_PRIME(MODIFIER||326||843|SEMA4G|protein_coding|CODING|NM_017893.3|14|C),UPSTREAM(MODIFIER||3079||684|C10orf2|protein_coding|CODING|NM_021830.4||C),INTRON(MODIFIER||||235|MRPL43|protein_coding|CODING|NM_176794.1|3|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.988742 rs2295716 -0.692717 0.526677 43 843 443 MODIFIER 14 CODING SEMA4G T protein_coding NM_017893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102744331 A T 0 222 0 0.0885 0.2556 0.3977 0.0675 0.4503 0.3742 0 . 0 1 102 5034 68 10 9 1669 50 3126 2 578 12440 188 200 16 3706 132 7620 0.935341 0 . 0 . 96 26,20,28,13 UTR_3_PRIME(MODIFIER||443||843|SEMA4G|protein_coding|CODING|NM_017893.3|14|T),UPSTREAM(MODIFIER||2962||684|C10orf2|protein_coding|CODING|NM_021830.4||T),INTRON(MODIFIER||||235|MRPL43|protein_coding|CODING|NM_176794.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.256507 rs11591349 -0.693145 0.397246 96 843 1174 MODIFIER 14 CODING SEMA4G T protein_coding NM_017893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102745062 G T 0 222 0 0.4304 0.362 0.2882 0.5258 0.1829 0.3374 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.867351 0 . 0 . 50 5,11,9,20 UTR_3_PRIME(MODIFIER||1174||843|SEMA4G|protein_coding|CODING|NM_017893.3|14|T),UPSTREAM(MODIFIER||2231||684|C10orf2|protein_coding|CODING|NM_021830.4||T),INTRON(MODIFIER||||235|MRPL43|protein_coding|CODING|NM_176794.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.908274 rs722435 -0.693079 0.353813 50 235 LOW 3 CODING MRPL43 T protein_coding NM_176794.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102746503 C T 0 222 0 0.3941 0.3526 0.2882 0.5268 0.1829 0.3374 0.352928 0.256958 0.207791 1 3759 32447 4305 4773 1177 13322 218 4893 2 10388 121146 11564 8618 6600 66564 906 16506 0.677854 0 . 0 . 106 36,23,25,14 SPLICE_SITE_REGION+INTRON(LOW||||235|MRPL43|protein_coding|CODING|NM_176794.1|3|T),UPSTREAM(MODIFIER||790||684|C10orf2|protein_coding|CODING|NM_021830.4||T),DOWNSTREAM(MODIFIER||1130||843|SEMA4G|protein_coding|CODING|NM_017893.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987333 rs2863095 -0.693144 0.0243476 106 684 LOW 3 CODING C10orf2 T protein_coding NM_021830.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102750621 C T 0 222 0 0.4758 0.376 0.2954 0.5298 0.1839 0.3374 0.406037 0.258189 0.182442 1 4650 33399 4346 4769 1181 13340 220 4893 2 10406 121386 11574 8640 6614 66732 908 16512 0.464772 2 benign 0 . 309 87,63,54,67 SPLICE_SITE_REGION+INTRON(LOW||||684|C10orf2|protein_coding|CODING|NM_021830.4|3|T),UPSTREAM(MODIFIER||3349||235|MRPL43|protein_coding|CODING|NM_176794.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.496512 rs3740485 -0.693147 1.75362e-06 309 684 LOW 3 CODING C10orf2 C protein_coding NM_021830.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102750623 T C 0 222 0 0.4758 0.376 0.2954 0.5298 0.1839 0.3374 0.401725 0.255728 0.18093 1 4650 33405 4348 4772 1181 13341 220 4893 2 10404 121386 11578 8638 6614 66732 908 16512 0.981551 2 benign 0 . 307 86,62,54,67 SPLICE_SITE_REGION+INTRON(LOW||||684|C10orf2|protein_coding|CODING|NM_021830.4|3|C),UPSTREAM(MODIFIER||3351||235|MRPL43|protein_coding|CODING|NM_176794.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.802986 rs3740486 -0.693147 1.75362e-06 307 669 5396 MODIFIER 1 CODING LZTS2 G protein_coding NM_032429.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102756900 C G 0 144 0 0.8782 0.7903 0.8285 0.623 0.8171 0.7894 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,1 UTR_5_PRIME(MODIFIER||5396||669|LZTS2|protein_coding|CODING|NM_032429.2|1|G),DOWNSTREAM(MODIFIER||2742||684|C10orf2|protein_coding|CODING|NM_021830.4||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3740491 -0.556411 0.265379 6 669 LOW 2 CODING LZTS2 T protein_coding NM_032429.2 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102762256 C T 0 222 0 0.084 0.275 0.4928 0.0903 0.4891 0.3487 0.138249 0.363658 0.478613 1 1216 45459 5892 776 3513 30363 347 3352 2 8982 105730 11348 8362 6570 60804 758 8906 0.964252 0 . 0 . 185 60,44,48,17 SPLICE_SITE_REGION(LOW||||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T),START_GAINED(LOW||||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T),UTR_5_PRIME(MODIFIER||40||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.898065 rs386611068,rs752974 -0.693147 0.0157579 185 669 40 MODIFIER 2 CODING LZTS2 T protein_coding NM_032429.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102762256 C T 0 222 0 0.084 0.275 0.4928 0.0903 0.4891 0.3487 0.138249 0.363658 0.478613 1 1216 45459 5892 776 3513 30363 347 3352 2 8982 105730 11348 8362 6570 60804 758 8906 0.964252 0 . 0 . 185 60,44,48,17 SPLICE_SITE_REGION(LOW||||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T),START_GAINED(LOW||||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T),UTR_5_PRIME(MODIFIER||40||669|LZTS2|protein_coding|CODING|NM_032429.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.898065 rs386611068,rs752974 -0.693147 0.0157579 185 A553 669 gcA/gcG LOW 5 SILENT CODING LZTS2 G protein_coding NM_032429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102766574 A G 0 222 0 0.385 0.3674 0.3271 0.5387 0.2346 0.3323 0.333105 0.273541 0.243057 1 2548 26432 3400 3902 863 13203 166 2350 2 6880 84450 8712 7024 3820 49992 558 7464 0.210788 0 . 0 . 30 8,3,12,3 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A553|669|LZTS2|protein_coding|CODING|NM_032429.2|5|G),DOWNSTREAM(MODIFIER||866||1033|PDZD7|protein_coding|CODING|NM_001195263.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0828904 rs807024 -0.688148 0.0779875 30 669 192 MODIFIER 5 CODING LZTS2 A protein_coding NM_032429.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102767117 C A 0 222 0 0.3896 0.3634 0.3256 0.5278 0.2147 0.3384 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.4804 0 . 0 . 201 65,29,64,16 UTR_3_PRIME(MODIFIER||192||669|LZTS2|protein_coding|CODING|NM_032429.2|5|A),DOWNSTREAM(MODIFIER||323||1033|PDZD7|protein_coding|CODING|NM_001195263.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995628 rs701836 -0.693147 0.0626806 201 669 230 MODIFIER 5 CODING LZTS2 G protein_coding NM_032429.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102767155 C G 0 222 0 0.3699 0.3576 0.3213 0.5288 0.2157 0.3364 0 . 0 1 137 895 33 79 3 272 11 360 2 400 2632 104 134 6 1156 22 810 0.840077 0 . 0 . 266 58,56,70,44 UTR_3_PRIME(MODIFIER||230||669|LZTS2|protein_coding|CODING|NM_032429.2|5|G),DOWNSTREAM(MODIFIER||285||1033|PDZD7|protein_coding|CODING|NM_001195263.1||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.452105 rs14177 -0.693147 4.24548e-05 266 N855T 1033 aAc/aCc MODERATE 15 MISSENSE CODING PDZD7 G protein_coding NM_001195263.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102770082 T G 0 222 0 0.7595 0.773 0.8429 0.6647 0.833 0.7914 0 . 0 1 598 12318 188 149 1307 3898 157 6021 2 744 15166 214 222 1590 4590 190 7616 0.998286 2 benign 0 . 103 31,16,24,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N855T|1033|PDZD7|protein_coding|CODING|NM_001195263.1|15|G),DOWNSTREAM(MODIFIER||2489||669|LZTS2|protein_coding|CODING|NM_032429.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.917882 rs386615201,rs807023 -0.693147 0.368275 103 R773 1033 cgT/cgC LOW 15 SILENT CODING PDZD7 G protein_coding NM_001195263.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102770327 A G 0 77 0 0.7738 0.7762 0.8429 0.6637 0.833 0.7894 0 . 0 1 415 7773 140 125 5 2416 90 4582 2 514 9586 160 186 6 2860 106 5754 0.998397 2 benign 0 . 17 3,8,2,3 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R773|1033|PDZD7|protein_coding|CODING|NM_001195263.1|15|G),DOWNSTREAM(MODIFIER||2734||669|LZTS2|protein_coding|CODING|NM_032429.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.924401 rs807022 -0.590765 0.288695 17 1033 LOW 3 CODING PDZD7 C protein_coding NM_001195263.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102783678 T C 0 228 0 0.8381 0.596 0.5793 0.3988 0.5775 0.5031 0.786201 0.661464 0.597558 2 8265 70112 5417 3480 3387 40399 527 8637 2 10406 121364 11570 8624 6612 66732 908 16512 1 2 benign 0 COSM147031 84 0,1,37,36 SPLICE_SITE_REGION+INTRON(LOW||||1033|PDZD7|protein_coding|CODING|NM_001195263.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6584410 -0.693147 0.00544733 84 G255A 304 gGc/gCc MODERATE 4 MISSENSE CODING KAZALD1 C protein_coding NM_030929.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102824349 G C 0 222 0 0.6241 0.5956 0.549 0.4921 0.6461 0.6452 0.631185 0.651853 0.662442 1 6496 75868 6135 3702 4143 44389 592 10411 2 10382 121096 11540 8614 6582 66576 902 16500 0.280128 0 . 0 . 39 8,10,9,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G255A|304|KAZALD1|protein_coding|CODING|NM_030929.4|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930403 rs807037 -0.69168 0.739976 39 330 131 MODIFIER 3 CODING TLX1 A protein_coding NM_005521.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102896801 G A 0 78 0 0.1899 0.2326 0.2046 0.3313 0.1581 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 0,5,0,6 UTR_3_PRIME(MODIFIER||131||330|TLX1|protein_coding|CODING|NM_005521.3|3|A),INTRAGENIC(MODIFIER|||||TLX1NB||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.0297172 rs2235128 -0.616816 0.00359632 11 330 417 MODIFIER 3 CODING TLX1 T protein_coding NM_005521.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 102897087 C T 0 45.3 0 0.2065 0.2376 0.2046 0.3313 0.16 0.2863 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,3,0 UTR_3_PRIME(MODIFIER||417||330|TLX1|protein_coding|CODING|NM_005521.3|3|T),INTRAGENIC(MODIFIER|||||TLX1NB||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2742038 -0.511536 0.892765 4 605 LOW 5 CODING BTRC G protein_coding NM_033637.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103281634 C G 0 228 0 0.6172 0.4155 0.2421 0.6171 0.2097 0.2699 0.537449 0.305628 0.18686 2 5591 31281 2935 5330 1068 11846 215 4296 2 10318 118514 11408 8584 6576 65242 886 15500 0 . 0 . 0 45 0,0,7,33 SPLICE_SITE_REGION+INTRON(LOW||||605|BTRC|protein_coding|CODING|NM_033637.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6584429 -0.693145 0.32447 45 605 2982 MODIFIER 15 CODING BTRC T protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103313599 C T 0 227 0 0.8487 0.7412 0.6499 0.8562 0.5288 0.7607 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 48 0,0,1,46 UTR_3_PRIME(MODIFIER||2982||605|BTRC|protein_coding|CODING|NM_033637.3|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3127242 -0.693147 0.0751021 48 605 3003 MODIFIER 15 CODING BTRC G protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103313620 A G 0 167 0 0.8487 0.7414 0.6499 0.8562 0.5288 0.7618 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,0,31 UTR_3_PRIME(MODIFIER||3003||605|BTRC|protein_coding|CODING|NM_033637.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1045324 -0.69311 0.0534733 31 605 3103 MODIFIER 15 CODING BTRC C protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103313719 CAACAGTGGA C 0 228 0 0.6225 0.4527 0.3055 0.6796 0.2177 0.3354 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,8 UTR_3_PRIME(MODIFIER||3103||605|BTRC|protein_coding|CODING|NM_033637.3|15|C) 0 . 0 8 0.888889 1 1 0 . 0 60 0 0 . 0 . rs16405 -0.651104 0.303943 9 605 3111 MODIFIER 15 CODING BTRC C protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103313728 A C 0 4.2 0 0.6142 0.4483 0.304 0.6796 0.2177 0.3252 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3111||605|BTRC|protein_coding|CODING|NM_033637.3|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs79177816 -0.379885 0 1 605 4561 MODIFIER 15 CODING BTRC A protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103315178 G A 0 228 0 0.621 0.4519 0.3055 0.6796 0.2157 0.3354 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,9,30 UTR_3_PRIME(MODIFIER||4561||605|BTRC|protein_coding|CODING|NM_033637.3|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4919552 -0.693144 0.213139 41 605 5184 MODIFIER 15 CODING BTRC T protein_coding NM_033637.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103315801 C T 0 116 0 0.8404 0.7388 0.6499 0.8562 0.5268 0.7618 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||5184||605|BTRC|protein_coding|CODING|NM_033637.3|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1045232 -0.556411 0.409395 5 916 1131 MODIFIER 16 CODING MGEA5 G protein_coding NM_012215.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103545077 A G 0 193 0 0.997 0.999 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,26,0 UTR_3_PRIME(MODIFIER||1131||916|MGEA5|protein_coding|CODING|NM_012215.3|16|G),UPSTREAM(MODIFIER||1907||178|NPM3|protein_coding|CODING|NM_006993.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6584456 -0.692976 0.195178 27 285 681 MODIFIER 10 CODING KCNIP2 T protein_coding NM_014591.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103586429 G T 0 9.7 0 0.1891 0.271 0.1931 0.5179 0.1879 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||681||285|KCNIP2|protein_coding|CODING|NM_014591.4|10|T),INTRAGENIC(MODIFIER|||||KCNIP2-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3209554 -0.379885 0 1 775 178 MODIFIER 1 CODING HPS6 G protein_coding NM_024747.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103827737 T G 0 228 0 0.1997 0.2808 0.2017 0.5149 0.1918 0.2965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 110 0,0,43,54 UTR_3_PRIME(MODIFIER||178||775|HPS6|protein_coding|CODING|NM_024747.5|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3816 -0.693147 0.0082359 110 I95 302 atC/atT LOW 3 SILENT CODING PITX3 A protein_coding NM_005029.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 103991381 G A 0 228 0 0.7753 0.6641 0.6254 0.7718 0.5974 0.499 0.754653 0.663232 0.616395 2 7087 69298 6064 6317 3307 37875 482 8166 2 9284 107112 9810 8070 4986 59312 772 14878 0 2 benign 0 . 109 0,0,82,15 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I95|302|PITX3|protein_coding|CODING|NM_005029.3|3|A),DOWNSTREAM(MODIFIER||2037||270|ELOVL3|protein_coding|CODING|NM_152310.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2281983 -0.693147 0.178187 109 I1399 1859 atT/atC LOW 32 SILENT CODING GBF1 C protein_coding NM_004193.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104136469 T C 0 228 0 0.9856 0.9958 0.9971 1 1 1 0.986836 0.99554 1 2 10207 120910 11564 8626 6612 66492 906 16503 2 10346 121060 11566 8626 6612 66498 906 16506 0 . 0 . 0 46 0,0,13,31 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I1399|1859|GBF1|protein_coding|CODING|NM_004193.2|32|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2180707 -0.693146 0.267564 46 P423 900 ccA/ccG LOW 13 SILENT CODING NFKB2 G protein_coding NM_001077494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104159196 A G 0 213 0 0.9539 0.9868 0.9942 1 0.999 1 0.974255 0.991855 0.999698 2 822 11676 239 348 14 4078 114 6061 2 854 11710 240 348 14 4078 114 6062 0 . 0 . 0 9 0,0,4,3 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P423|900|NFKB2|protein_coding|CODING|NM_001077494.3|13|G),DOWNSTREAM(MODIFIER||3178||1024|PSD|protein_coding|CODING|NM_001270965.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1.01283 0 . rs4919633 -0.636426 0.266982 9 A607 900 gcA/gcG LOW 17 SILENT CODING NFKB2 G protein_coding NM_001077494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104160434 A G 0 228 0 0.9539 0.9868 0.9942 1 0.999 1 0.968312 0.989479 0.999881 2 9390 119917 11534 8622 6518 66489 896 16468 2 9752 120306 11548 8622 6518 66502 896 16468 0 . 0 . 0 135 0,0,57,61 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A607|900|NFKB2|protein_coding|CODING|NM_001077494.3|17|G),DOWNSTREAM(MODIFIER||1940||1024|PSD|protein_coding|CODING|NM_001270965.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4919634 -0.693147 0.876132 135 Y283 1024 taC/taT LOW 5 SILENT CODING PSD A protein_coding NM_001270965.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104174895 G A 0 222 0 0.0061 0.141 0.0821 0.3651 0.0905 0.1861 0.03064 0.074581 0.097093 1 261 14687 1558 3175 613 6481 84 2515 2 10152 119922 11522 8562 6580 65698 902 16506 0.924063 0 . 0 . 74 17,20,9,19 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y283|1024|PSD|protein_coding|CODING|NM_001270965.1|5|A),UPSTREAM(MODIFIER||4676||300|FBXL15|protein_coding|CODING|NM_024326.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99368 rs2282295 -0.693054 0.235751 74 517 2955 MODIFIER 2 CODING MFSD13A C protein_coding NM_024789.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104225832 T C 0 6.3 0 0.1573 0.2602 0.3487 0.2629 0.3052 0.2873 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||2955||517|MFSD13A|protein_coding|CODING|NM_024789.3|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10883723 -0.379885 0 1 517 2950 MODIFIER 2 CODING MFSD13A G protein_coding NM_024789.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104225837 T G 0 6.3 0 0.1573 0.26 0.3487 0.2629 0.3042 0.2873 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||2950||517|MFSD13A|protein_coding|CODING|NM_024789.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11191294 -0.379885 0 1 L89 517 ctC/ctG LOW 5 SILENT CODING MFSD13A G protein_coding NM_024789.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104230437 C G 0 181 0 0.0378 0.2071 0.2421 0.4325 0.1302 0.2577 0.0450782 0.0841884 0.104157 1 434 18937 3216 3642 702 6869 135 3939 2 8982 116290 11494 8500 6608 63544 872 16290 0.741082 0 . 0 . 33 14,3,12,3 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L89|517|MFSD13A|protein_coding|CODING|NM_024789.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.338073 rs3740416 -0.688148 0.00747001 33 517 68 MODIFIER 10 CODING MFSD13A T protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104235809 G T 0 10.3 0 0.2579 0.4898 0.6037 0.7004 0.4384 0.5583 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,1 UTR_3_PRIME(MODIFIER||68||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|T),DOWNSTREAM(MODIFIER||3177||376|ACTR1A|protein_coding|CODING|NM_005736.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7923675 -0.379885 0 3 517 535 MODIFIER 10 CODING MFSD13A T protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236276 C T 0 111 0 0.1974 0.2744 0.3559 0.2629 0.3052 0.3006 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.892753 0 . 0 . 16 7,0,9,0 UTR_3_PRIME(MODIFIER||535||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|T),DOWNSTREAM(MODIFIER||2710||376|ACTR1A|protein_coding|CODING|NM_005736.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.892753 rs10883726 -0.662043 0.137712 16 517 541 MODIFIER 10 CODING MFSD13A T protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236282 C T 0 162 0 1 0.9998 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,17,0 UTR_3_PRIME(MODIFIER||541||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|T),DOWNSTREAM(MODIFIER||2704||376|ACTR1A|protein_coding|CODING|NM_005736.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7101160 -0.690438 0.0352487 17 517 716 MODIFIER 10 CODING MFSD13A T protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236457 C T 0 228 0 0.9902 0.997 0.9986 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 80 0,0,35,33 UTR_3_PRIME(MODIFIER||716||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|T),DOWNSTREAM(MODIFIER||2529||376|ACTR1A|protein_coding|CODING|NM_005736.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7071048 -0.693147 0.00248613 80 517 740 MODIFIER 10 CODING MFSD13A A protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236481 G A 0 222 0 0.1891 0.2722 0.3559 0.2629 0.3052 0.3006 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.57675 0 . 0 . 68 8,15,14,20 UTR_3_PRIME(MODIFIER||740||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|A),DOWNSTREAM(MODIFIER||2505||376|ACTR1A|protein_coding|CODING|NM_005736.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.985521 rs1056738 -0.693132 0.142181 68 517 801 MODIFIER 10 CODING MFSD13A C protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236542 T C 0 222 0 0.1974 0.2744 0.3559 0.2629 0.3052 0.3006 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.949192 0 . 0 . 40 1,16,3,18 UTR_3_PRIME(MODIFIER||801||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|C),DOWNSTREAM(MODIFIER||2444||376|ACTR1A|protein_coding|CODING|NM_005736.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.64321 rs1056739 -0.692352 0.0975678 40 517 811 MODIFIER 10 CODING MFSD13A T protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236552 C T 0 222 0 0.1967 0.2744 0.3559 0.2629 0.3052 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.542674 0 . 0 . 37 1,16,3,15 UTR_3_PRIME(MODIFIER||811||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|T),DOWNSTREAM(MODIFIER||2434||376|ACTR1A|protein_coding|CODING|NM_005736.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.94699 rs1056740 -0.691153 0.205194 37 517 904 MODIFIER 10 CODING MFSD13A A protein_coding NM_024789.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104236645 G A 0 31.5 0 0.0378 0.2053 0.2406 0.4296 0.1272 0.2556 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,0,3 UTR_3_PRIME(MODIFIER||904||517|MFSD13A|protein_coding|CODING|NM_024789.3|10|A),DOWNSTREAM(MODIFIER||2341||376|ACTR1A|protein_coding|CODING|NM_005736.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3740409 -0.511536 0.121629 4 376 639 MODIFIER 11 CODING ACTR1A G protein_coding NM_005736.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104239981 T G 0 228 0 0.9909 0.9972 0.9986 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,18,8 UTR_3_PRIME(MODIFIER||639||376|ACTR1A|protein_coding|CODING|NM_005736.3|11|G),DOWNSTREAM(MODIFIER||3179||517|MFSD13A|protein_coding|CODING|NM_024789.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10748821 -0.692976 0.5939 26 376 617 MODIFIER 11 CODING ACTR1A T protein_coding NM_005736.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104240003 C T 0 192 0 0.1982 0.2716 0.3573 0.256 0.3012 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.976472 0 . 0 . 30 12,3,12,2 UTR_3_PRIME(MODIFIER||617||376|ACTR1A|protein_coding|CODING|NM_005736.3|11|T),DOWNSTREAM(MODIFIER||3201||517|MFSD13A|protein_coding|CODING|NM_024789.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.971601 rs1056857 -0.686358 0.278007 30 376 182 MODIFIER 11 CODING ACTR1A G protein_coding NM_005736.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104240438 A G 0 222 0 0.3767 0.3201 0.366 0.2579 0.3002 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.930473 0 . 0 . 73 26,14,17,15 UTR_3_PRIME(MODIFIER||182||376|ACTR1A|protein_coding|CODING|NM_005736.3|11|G),DOWNSTREAM(MODIFIER||3636||517|MFSD13A|protein_coding|CODING|NM_024789.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.594449 rs13287 -0.69312 0.11062 73 376 122 MODIFIER 11 CODING ACTR1A G protein_coding NM_005736.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104240498 A G 0 222 0 0.3752 0.3195 0.366 0.256 0.3002 0.2965 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957609 0 . 0 . 104 43,13,30,12 UTR_3_PRIME(MODIFIER||122||376|ACTR1A|protein_coding|CODING|NM_005736.3|11|G),DOWNSTREAM(MODIFIER||3696||517|MFSD13A|protein_coding|CODING|NM_024789.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.534145 rs12162 -0.693146 0.0329197 104 376 LOW 5 CODING ACTR1A T protein_coding NM_005736.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104244139 G T 0 222 0 0.1982 0.2714 0.3573 0.256 0.3002 0.2955 0.243305 0.302168 0.332326 1 2355 39129 4666 2221 2423 22545 301 4618 2 10100 118760 11224 8468 6434 65302 882 16350 0.213803 0 . 0 . 80 6,34,7,25 SPLICE_SITE_REGION+INTRON(LOW||||376|ACTR1A|protein_coding|CODING|NM_005736.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.645942 rs2296582 -0.69312 6.0568e-05 80 I433 484 atT/atC LOW 11 SILENT CODING SUFU C protein_coding NM_016169.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104386934 T C 0 222 0 0.2277 0.246 0.2378 0.4335 0.0934 0.2403 0.216523 0.128479 0.0833721 1 2275 19257 3246 3662 530 5646 135 3763 2 10398 121358 11576 8638 6614 66722 908 16502 0.739728 0 . 0 . 343 133,17,134,25 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I433|484|SUFU|protein_coding|CODING|NM_016169.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.744474 rs17114803 -0.693147 0.0165105 343 484 20 MODIFIER 12 CODING SUFU G protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104389932 T G 0 228 0 0.9917 0.9974 0.9986 1 0.999 1 0.993645 0.997847 1 2 10342 121323 11573 8654 6614 66722 906 16512 2 10406 121396 11578 8654 6614 66726 906 16512 1 0 . 0 . 390 0,1,192,166 UTR_3_PRIME(MODIFIER||20||484|SUFU|protein_coding|CODING|NM_016169.3|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4917980 -0.693147 0.323855 390 484 118 MODIFIER 12 CODING SUFU T protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104390030 C T 0 222 0 0 0.0439 0.049 0.1806 0 0.0041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996997 0 . 0 . 371 81,97,50,102 UTR_3_PRIME(MODIFIER||118||484|SUFU|protein_coding|CODING|NM_016169.3|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.300289 rs2298277 -0.693147 0.000571031 371 484 391 MODIFIER 12 CODING SUFU G protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104390303 A G 0 121 0 0.2277 0.2464 0.2378 0.4335 0.0954 0.2403 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.6 0 . 0 . 8 0,2,2,3 UTR_3_PRIME(MODIFIER||391||484|SUFU|protein_coding|CODING|NM_016169.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.5 rs2298278,rs386445757 -0.590765 0.566267 8 484 1373 MODIFIER 12 CODING SUFU T protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104391285 C T 0 41.3 0 0.2277 0.2458 0.2378 0.4335 0.0924 0.2403 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 7 3,1,3,0 UTR_3_PRIME(MODIFIER||1373||484|SUFU|protein_coding|CODING|NM_016169.3|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1 0 0.810265 rs17114808 -0.511536 0.921489 7 484 1633 MODIFIER 12 CODING SUFU T protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104391545 C T 0 56 0 0.2216 0.245 0.2378 0.4365 0.0934 0.2403 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||1633||484|SUFU|protein_coding|CODING|NM_016169.3|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17114810 -0.556411 0.292086 4 484 1715 MODIFIER 12 CODING SUFU G protein_coding NM_016169.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104391627 A G 0 48.3 0 0.2277 0.246 0.2378 0.4335 0.0934 0.2403 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,0 UTR_3_PRIME(MODIFIER||1715||484|SUFU|protein_coding|CODING|NM_016169.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs11818043 -0.453602 0.58 4 551 40 MODIFIER 1 CODING TRIM8 T protein_coding NM_030912.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104404335 A T 0 215 0 0.1687 0.1148 0.1095 0.2063 0.0398 0.0286 0.140449 0.0763959 0.0467706 1 864 5221 575 1052 69 2159 31 471 2 4288 66122 6306 4196 2626 36122 468 12116 0.0153967 0 . 0 . 87 31,2,49,1 UTR_5_PRIME(MODIFIER||40||551|TRIM8|protein_coding|CODING|NM_030912.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.873054 rs4146426 -0.693147 0.0540183 87 182 2457 MODIFIER 6 CODING ARL3 G protein_coding NM_004311.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104434194 A G 0 91 0 0.1657 0.1092 0.0994 0.2123 0.0199 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 8 1,1,0,6 UTR_3_PRIME(MODIFIER||2457||182|ARL3|protein_coding|CODING|NM_004311.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7088470 -0.616816 0.0630446 8 182 905 MODIFIER 6 CODING ARL3 T protein_coding NM_004311.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104435746 C T 0 228 0 0.9917 0.9974 0.9986 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 110 0,0,82,19 UTR_3_PRIME(MODIFIER||905||182|ARL3|protein_coding|CODING|NM_004311.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4146427 -0.693147 0.00131719 110 182 10 MODIFIER 6 CODING ARL3 T protein_coding NM_004311.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104436641 C T 0 222 0 0.0537 0.2065 0.2262 0.4494 0.0974 0.2607 0.0490241 0.0735045 0.0860465 1 558 17424 2945 3664 474 5688 122 3973 2 10404 121362 11578 8644 6614 66708 908 16506 0.990579 0 . 0 . 58 21,8,17,4 UTR_3_PRIME(MODIFIER||10||182|ARL3|protein_coding|CODING|NM_004311.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.563383 rs8354 -0.692352 0.291508 58 182 75 MODIFIER 1 CODING ARL3 A protein_coding NM_004311.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104474107 G A 0 228 0 0.9924 0.9976 0.9986 1 0.999 1 0.990511 0.997139 1 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0227277 0 . 0 . 77 0,3,4,66 UTR_5_PRIME(MODIFIER||75||182|ARL3|protein_coding|CODING|NM_004311.3|1|A),UPSTREAM(MODIFIER||191||322|SFXN2|protein_coding|CODING|NM_178858.4||A) 1 0 . 0 . 1 0 1 0 . 60 0 1 1 0 0.418475 rs2248679 -0.693147 0.852246 77 322 246 MODIFIER 12 CODING SFXN2 GA protein_coding NM_178858.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104497764 G GA 0 48.1 0 0.0915 0.132 0.1427 0.1062 0.2127 0.1227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,7,0,4 UTR_3_PRIME(MODIFIER||246||322|SFXN2|protein_coding|CODING|NM_178858.4|12|GA) 0 0.5 1 4 0.333333 1 1 0 . 0 60 0 0 . 0 . rs59640190 -0.556411 0.432711 12 322 1087 MODIFIER 12 CODING SFXN2 T protein_coding NM_178858.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104498606 G T 0 222 0 0 0.0053914 0 0.0258 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.60186 0 . 0 . 141 57,15,45,15 UTR_3_PRIME(MODIFIER||1087||322|SFXN2|protein_coding|CODING|NM_178858.4|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.111325 rs11191382 -0.693147 0.00854427 141 S323P 363 Tcc/Ccc MODERATE 4 MISSENSE CODING WBP1L C protein_coding NM_001083913.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104572963 T C 0 222 0 0.5212 0.5433 0.5764 0.3988 0.5954 0.6452 0.539946 0.572813 0.589651 1 5473 70529 7009 3624 4040 39408 532 10443 2 10302 120796 11550 8610 6604 66322 900 16508 0.993617 0 . 0 . 66 17,19,17,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S323P|363|WBP1L|protein_coding|CODING|NM_001083913.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.748017 rs284860,rs386575244 -0.692831 0.504983 66 363 315 MODIFIER 4 CODING WBP1L G protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104573403 A G 0 117 0 0.1188 0.1737 0.2464 0.1806 0.2863 0.0736 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.405132 0 . 0 . 9 1,2,2,2 UTR_3_PRIME(MODIFIER||315||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1.01283 0 0.810265 rs11191401 -0.556411 0.235052 9 363 848 MODIFIER 4 CODING WBP1L C protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104573936 T C 0 40.2 0 0.5431 0.5497 0.5807 0.3998 0.5944 0.6452 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 5,0,2,1 UTR_3_PRIME(MODIFIER||848||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.750668 rs284858 -0.511536 0.509904 8 363 975 MODIFIER 4 CODING WBP1L A protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104574063 G A 0 122 0 0.5204 0.5429 0.5764 0.3988 0.5944 0.6452 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.806004 0 . 0 . 41 21,2,18,0 UTR_3_PRIME(MODIFIER||975||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.915453 rs284857 -0.691153 0.254512 41 363 1241 MODIFIER 4 CODING WBP1L T protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104574329 A T 0 222 0 0.5219 0.5439 0.5764 0.4008 0.5944 0.6462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.942527 0 . 0 . 99 40,8,26,4 UTR_3_PRIME(MODIFIER||1241||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.506899 rs284856 -0.693097 0.000828056 99 363 1334 MODIFIER 4 CODING WBP1L G protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104574422 A G 0 222 0 0.5219 0.5435 0.5764 0.3978 0.5944 0.6472 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969195 0 . 0 . 80 16,31,20,11 UTR_3_PRIME(MODIFIER||1334||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.475024 rs284855 -0.69311 0.365207 80 363 1474 MODIFIER 4 CODING WBP1L G protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104574562 T G 0 222 0 0.329 0.4587 0.5591 0.3938 0.5736 0.5112 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.975798 0 . 0 . 115 31,23,15,30 UTR_3_PRIME(MODIFIER||1474||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.202045 rs284854 -0.693147 0.00179667 115 363 1554 MODIFIER 4 CODING WBP1L A protein_coding NM_001083913.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104574642 T A 0 228 0 0.6694 0.724 0.8228 0.5794 0.8807 0.7157 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,31,18 UTR_3_PRIME(MODIFIER||1554||363|WBP1L|protein_coding|CODING|NM_001083913.1|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs284853 -0.693147 0.162513 59 S65 508 tcG/tcT LOW 1 SILENT CODING CYP17A1 A protein_coding NM_000102.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104596924 C A 0 222 0 0.3268 0.4103 0.4179 0.5873 0.3926 0.3538 0.361552 0.383285 0.394419 1 3801 48242 4649 4879 2460 26118 368 5967 2 10406 121390 11576 8638 6612 66738 908 16512 0.575686 0 . 0 . 200 55,49,34,45 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcT|S65|508|CYP17A1|protein_coding|CODING|NM_000102.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986963 rs6163 -0.693147 0.101727 200 H46 508 caC/caT LOW 1 SILENT CODING CYP17A1 A protein_coding NM_000102.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104596981 G A 0 222 0 0.323 0.4425 0.4236 0.5913 0.4115 0.4959 0.364503 0.394895 0.410465 1 3834 51567 4728 4890 2499 27307 399 7910 2 10406 121396 11576 8642 6614 66738 908 16512 0.896757 0 . 0 . 177 51,37,35,34 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H46|508|CYP17A1|protein_coding|CODING|NM_000102.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.832872 rs6162 -0.693147 0.0210981 177 508 34 MODIFIER 1 CODING CYP17A1 G protein_coding NM_000102.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104597152 A G 0 192 0 0.326 0.4105 0.4164 0.5873 0.3936 0.3558 0.360808 0.382344 0.393372 1 3566 47052 4530 4697 2428 25468 365 5998 2 9708 117614 11204 8302 6466 64620 894 16420 0.672617 0 . 0 . 46 1,23,3,19 UTR_5_PRIME(MODIFIER||34||508|CYP17A1|protein_coding|CODING|NM_000102.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992713 rs743572 -0.692562 0.0292824 46 S614 875 agT/agC LOW 3 SILENT CODING CNNM2 C protein_coding NM_017649.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104814162 T C 0 222 0 0.3328 0.4325 0.4135 0.5863 0.4145 0.4407 0.358118 0.39021 0.405454 1 3643 50588 4836 4847 2543 27372 383 6964 2 9780 120472 11508 8586 6608 66604 896 16490 0.991208 0 . 0 . 66 23,9,9,17 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S614|875|CNNM2|protein_coding|CODING|NM_017649.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.457367 rs2275271 -0.692976 0.575106 66 875 3 MODIFIER 8 CODING CNNM2 T protein_coding NM_017649.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104836940 C T 0 222 0 0.0106 0.0771 0.0749 0.1528 0.1382 0.0276 0.033111 0.107793 0.144993 1 292 13609 810 1159 1084 9563 106 595 2 9542 118774 11458 8394 6588 65510 884 16398 0.922617 0 . 0 . 67 8,27,7,23 UTR_3_PRIME(MODIFIER||3||875|CNNM2|protein_coding|CODING|NM_017649.4|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.457771 rs2296568 -0.693097 0.889065 67 875 879 MODIFIER 8 CODING CNNM2 A protein_coding NM_017649.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104837816 G A 0 179 0 0.3033 0.2628 0.2233 0.2242 0.331 0.2055 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.97236 0 . 0 . 34 1,13,1,18 UTR_3_PRIME(MODIFIER||879||875|CNNM2|protein_coding|CODING|NM_017649.4|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.134411 rs1046411 -0.69168 0.298322 34 D549 561 gaC/gaT LOW 18 SILENT CODING NT5C2 A protein_coding NM_001134373.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104849468 G A 0 222 0 0.3442 0.4221 0.4135 0.499 0.4135 0.4632 0.374943 0.396817 0.408023 1 3954 50085 4851 4054 2489 27212 383 7142 2 10392 120078 11552 8620 6610 66376 900 15628 0.956143 0 . 0 . 77 30,9,23,10 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D549|561|NT5C2|protein_coding|CODING|NM_001134373.2|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.585858 rs3740387 -0.693127 0.0897251 77 T3A 561 Acc/Gcc MODERATE 2 MISSENSE CODING NT5C2 C protein_coding NM_001134373.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 104934709 T C 0 222 0 0.0098 0.0767 0.0735 0.1528 0.1382 0.0276 0.0340445 0.110103 0.14907 1 316 13808 818 1211 1088 9669 107 599 2 10386 121330 11570 8644 6612 66700 908 16510 0.636448 0 . 0 . 107 12,41,5,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T3A|561|NT5C2|protein_coding|CODING|NM_001134373.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978094 rs10883841 -0.693147 0.036195 107 228 1088 MODIFIER 1 CODING RPEL1 T protein_coding NM_001143909.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105007528 C T 0 222 0 0.3926 0.36 0.4207 0.373 0.3459 0.274 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.947665 0 . 0 . 147 38,34,39,30 UTR_3_PRIME(MODIFIER||1088||228|RPEL1|protein_coding|CODING|NM_001143909.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.975504 rs4917386 -0.693147 0.000447229 147 S130A 800 Tcc/Gcc MODERATE 1 MISSENSE CODING TAF5 G protein_coding NM_006951.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105128134 T G 0 48.3 0 0.1952 0.3101 0.4078 0.4206 0.329 0.2628 0.17688 0.253215 0.290765 1 599 14042 859 1453 351 7778 91 2911 2 2598 39936 1760 3152 1018 21410 260 9738 0.810265 0 . 0 . 8 3,1,1,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S130A|800|TAF5|protein_coding|CODING|NM_006951.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.01283 1.01283 0 1.01283 rs10883859 -0.511536 0.0649539 8 1871 50 MODIFIER 36 CODING PDCD11 T protein_coding NM_014976.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105205356 C T 0 131 0 0.0068 0.0489 0.0331 0.1419 0.0497 0.0204 0.0172963 0.0491525 0.0654554 1 145 6037 381 960 335 3762 47 407 2 8180 97946 8528 6868 5372 53682 718 14598 0.631923 0 . 0 . 33 4,14,1,14 UTR_3_PRIME(MODIFIER||50||1871|PDCD11|protein_coding|CODING|NM_014976.1|36|T),DOWNSTREAM(MODIFIER||1187||323|CALHM2|protein_coding|CODING|NM_015916.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.739246 rs3740478 -0.688148 0.0482202 33 346 87 MODIFIER 2 CODING CALHM1 C protein_coding NM_001001412.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105214932 T C 0 222 0 0.41 0.3636 0.438 0.4137 0.2932 0.2689 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.562302 0 . 0 . 50 25,3,15,4 UTR_3_PRIME(MODIFIER||87||346|CALHM1|protein_coding|CODING|NM_001001412.3|2|C),UPSTREAM(MODIFIER||2770||323|CALHM2|protein_coding|CODING|NM_015916.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.542733 rs729211 -0.69168 0.463208 50 346 3 MODIFIER 2 CODING CALHM1 G protein_coding NM_001001412.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105215016 A G 0 222 0 0.9788 0.8802 0.8386 0.8849 0.7545 0.9008 0.935315 0.809894 0.745577 1 7268 71911 7227 5874 3214 36792 539 10997 2 7742 87988 8426 6560 3946 48238 648 12428 0.840063 0 . 0 . 106 28,22,29,17 UTR_3_PRIME(MODIFIER||3||346|CALHM1|protein_coding|CODING|NM_001001412.3|2|G),UPSTREAM(MODIFIER||2854||323|CALHM2|protein_coding|CODING|NM_015916.4||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.747603 rs2986016 -0.693147 0.859428 106 L86P 346 cTg/cCg MODERATE 1 MISSENSE CODING CALHM1 G protein_coding NM_001001412.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105218252 A G 0 222 0 0.9705 0.872 0.8343 0.8849 0.7406 0.8875 0.92617 0.796368 0.729865 1 8965 92568 9630 7554 5069 46342 703 14305 2 9602 117448 11432 8524 6376 64148 880 16486 0.949307 0 . 0 . 117 31,12,45,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L86P|346|CALHM1|protein_coding|CODING|NM_001001412.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.519992 rs2986017 -0.693147 0.35056 117 P85 346 ccG/ccA LOW 1 SILENT CODING CALHM1 T protein_coding NM_001001412.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105218254 C T 0 222 0 0.1997 0.3037 0.4063 0.4137 0.2992 0.2628 0.216136 0.28291 0.317113 1 2112 38656 5218 3800 2042 20531 287 4666 2 9434 117066 11408 8504 6384 63978 876 16482 0.28457 0 . 0 . 121 33,18,43,16 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P85|346|CALHM1|protein_coding|CODING|NM_001001412.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99623 rs4918016 -0.693147 0.493203 121 A50 346 gcA/gcG LOW 1 SILENT CODING CALHM1 C protein_coding NM_001001412.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105218359 T C 0 222 0 0.9796 0.8848 0.8444 0.8849 0.7714 0.9018 0.938039 0.818315 0.756977 1 9768 98187 9902 7665 5408 50168 737 14539 2 10362 121090 11568 8636 6604 66502 906 16512 0.97406 0 . 0 . 146 41,24,25,44 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A50|346|CALHM1|protein_coding|CODING|NM_001001412.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894631 rs2986018 -0.693147 0.0406015 146 344 390 MODIFIER 3 CODING CALHM3 A protein_coding NM_001129742.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105232580 G A 0 9.7 0 0.5681 0.74 0.7925 0.7718 0.7555 0.8865 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||390||344|CALHM3|protein_coding|CODING|NM_001129742.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2986034 -0.379885 0 1 D299N 344 Gac/Aac MODERATE 3 MISSENSE CODING CALHM3 T protein_coding NM_001129742.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105233110 C T 0 222 0 0.5681 0.7402 0.7925 0.7728 0.7555 0.8865 0 . 0 1 1150 9146 269 426 73 4721 82 2425 2 1910 11952 340 540 90 6200 102 2770 0.999388 0 . 0 . 188 60,35,55,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D299N|344|CALHM3|protein_coding|CODING|NM_001129742.1|3|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.231129 rs2986035 -0.693147 0.221596 188 574 215 MODIFIER 1 CODING NEURL1 T protein_coding NM_004210.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105253930 C T 0 46.3 0 0.9781 0.9153 0.8343 0.999 0.7932 0.9274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 START_GAINED(LOW||||574|NEURL1|protein_coding|CODING|NM_004210.4|1|T),UTR_5_PRIME(MODIFIER||215||574|NEURL1|protein_coding|CODING|NM_004210.4|1|T),INTRAGENIC(MODIFIER|||||NEURL1-AS1||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3014203 -0.453602 0.44 2 574 214 MODIFIER 1 CODING NEURL1 C protein_coding NM_004210.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105253931 T C 0 46.3 0 0.9781 0.9153 0.8343 0.999 0.7932 0.9274 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||214||574|NEURL1|protein_coding|CODING|NM_004210.4|1|C),INTRAGENIC(MODIFIER|||||NEURL1-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2986040 -0.453602 0.44 2 574 55 MODIFIER 1 CODING NEURL1 T protein_coding NM_004210.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105254090 G T 0 228 0 0.8268 0.8622 0.817 0.999 0.7495 0.9172 0.819767 0.781882 0.765448 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,17,1 UTR_5_PRIME(MODIFIER||55||574|NEURL1|protein_coding|CODING|NM_004210.4|1|T),INTRAGENIC(MODIFIER|||||NEURL1-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2986041 -0.691153 0.0183785 22 P371 574 ccT/ccC LOW 4 SILENT CODING NEURL1 C protein_coding NM_004210.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105344756 T C 0 135 0 0.3964 0.5292 0.5173 0.6478 0.5378 0.5859 0.359868 0.456879 0.505335 1 1651 35580 3675 2953 1175 19098 246 6782 2 3198 57344 5786 4308 1850 30800 390 11012 0.422455 0 . 0 . 18 7,1,5,3 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P371|574|NEURL1|protein_coding|CODING|NM_004210.4|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.915545 rs2236209 -0.651104 0.375922 18 1105 6591 MODIFIER 14 CODING SH3PXD2A C protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105354982 T C 0 9.7 0 0.8124 0.8802 0.8977 0.999 0.8042 0.9151 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||6591||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|C),DOWNSTREAM(MODIFIER||2673||574|NEURL1|protein_coding|CODING|NM_004210.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4918029 -0.379885 0 1 1105 5170 MODIFIER 14 CODING SH3PXD2A G protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105356403 C G 0 90 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.460355 0 . 0 . 23 2,1,3,8 UTR_3_PRIME(MODIFIER||5170||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|G),DOWNSTREAM(MODIFIER||4094||574|NEURL1|protein_coding|CODING|NM_004210.4||G) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 1 0 0.693041 rs10786759 -0.676189 0.0147057 23 1105 5129 MODIFIER 14 CODING SH3PXD2A T protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105356444 A T 0 81 0 0.5635 0.5337 0.536 0.6567 0.4533 0.4479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 26 1,0,7,5 UTR_3_PRIME(MODIFIER||5129||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|T),DOWNSTREAM(MODIFIER||4135||574|NEURL1|protein_coding|CODING|NM_004210.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs10656552,rs28510549 -0.680642 0.169706 26 1105 4392 MODIFIER 14 CODING SH3PXD2A A protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105357181 G A 0 47.2 0 0.1959 0.4225 0.4409 0.5456 0.4334 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,0,3 UTR_3_PRIME(MODIFIER||4392||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|A),DOWNSTREAM(MODIFIER||4872||574|NEURL1|protein_coding|CODING|NM_004210.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10883887 -0.511536 0.793693 4 1105 3597 MODIFIER 14 CODING SH3PXD2A A protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105357976 G A 0 222 0 0.3593 0.4748 0.464 0.5476 0.4533 0.5859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.946997 0 . 0 . 105 12,38,9,37 UTR_3_PRIME(MODIFIER||3597||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.639199 rs11191740 -0.693147 0.444321 105 1105 3586 MODIFIER 14 CODING SH3PXD2A C protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105357987 T C 0 228 0 0.8744 0.874 0.8689 0.999 0.7406 0.8855 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 89 0,0,11,75 UTR_3_PRIME(MODIFIER||3586||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7911638 -0.693147 0.416829 89 1105 3115 MODIFIER 14 CODING SH3PXD2A G protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105358458 C G 0 222 0 0.4682 0.3796 0.3905 0.4514 0.2684 0.2924 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.708576 0 . 0 . 77 28,10,24,9 UTR_3_PRIME(MODIFIER||3115||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.884376 rs9521 -0.693127 0.27129 77 1105 2593 MODIFIER 14 CODING SH3PXD2A G protein_coding NM_014631.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105358980 A G 0 108 0 0.5053 0.3946 0.3977 0.4514 0.2853 0.2965 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.925999 0 . 0 . 14 1,6,1,6 UTR_3_PRIME(MODIFIER||2593||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 1 0 0.571605 rs2281584 -0.636426 0.257579 14 I1025 1105 atA/atC LOW 14 SILENT CODING SH3PXD2A G protein_coding NM_014631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105361816 T G 0 228 0 0.882 0.88 0.8761 0.999 0.7545 0.8865 0.861779 0.801476 0.770581 2 8990 98067 10626 8645 4927 50642 725 13512 2 10376 119390 11562 8652 6610 66198 884 15108 0 . 0 . 0 68 0,0,34,32 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I1025|1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386421130,rs4918031 -0.693147 0.990558 68 R904 1105 cgC/cgT LOW 14 SILENT CODING SH3PXD2A A protein_coding NM_014631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105362179 G A 0 181 0 0.0794 0.1006 0.0937 0.1964 0.1014 0.0348 0.0994099 0.0934184 0.0903488 1 1017 11818 853 1807 905 6456 85 695 2 10270 120904 11554 8628 6614 66468 900 16470 0.845034 0 . 0 . 47 25,4,13,4 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R904|1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.523425 rs3740473 -0.690438 0.117665 47 K894 1105 aaA/aaG LOW 14 SILENT CODING SH3PXD2A C protein_coding NM_014631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105362209 T C 0 228 0 0.9743 0.9125 0.8876 0.999 0.7624 0.9121 0.936223 0.834077 0.781744 2 9822 101827 10710 8647 4933 51916 761 15038 2 10398 121372 11576 8652 6610 66718 908 16510 0 . 0 . 0 60 0,0,48,8 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K894|1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4917396 -0.693147 0.0955619 60 L868 1105 ctG/ctC LOW 14 SILENT CODING SH3PXD2A G protein_coding NM_014631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105362287 C G 0 222 0 0.0227 0.0885 0.0879 0.1994 0.1014 0.0501 0.0283704 0.0693526 0.0903488 1 287 11369 823 1815 906 6485 93 960 2 10406 121364 11574 8640 6612 66714 908 16510 0.769771 0 . 0 . 103 45,21,20,8 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L868|1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999146 rs3740472 -0.693054 0.850279 103 A534 1105 gcA/gcG LOW 14 SILENT CODING SH3PXD2A C protein_coding NM_014631.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105363289 T C 0 222 0 0.0643 0.1356 0.1628 0.1548 0.1998 0.1268 0.0882887 0.177687 0.223488 1 920 22281 1753 1175 1623 14441 189 2180 2 10188 119368 11552 8612 6602 66068 894 15452 0.99984 0 . 0 . 159 70,17,40,10 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A534|1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90758 rs3740471 -0.693147 0.157497 159 1105 50 MODIFIER 1 CODING SH3PXD2A T protein_coding NM_014631.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105615074 C T 0 165 0 0.0726 0.3662 0.4222 0.6419 0.3082 0.499 0.101313 0.234572 0.306298 1 278 6667 135 319 7 2503 68 3357 2 2324 16536 334 500 26 6552 152 6648 0.999633 0 . 0 . 41 0,19,1,20 UTR_5_PRIME(MODIFIER||50||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.564252 rs10883928 -0.692352 0.00874816 41 1105 81 MODIFIER 1 CODING SH3PXD2A C protein_coding NM_014631.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105615105 G C 0 166 0 0.9917 0.9978 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,0,23 UTR_5_PRIME(MODIFIER||81||1105|SH3PXD2A|protein_coding|CODING|NM_014631.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10883929 -0.692717 0.0800207 23 368 4210 MODIFIER 10 CODING OBFC1 C protein_coding NM_024928.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105638232 T C 0 9.7 0 0.9085 0.9401 0.9582 0.9841 0.9433 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4210||368|OBFC1|protein_coding|CODING|NM_024928.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs111165801,rs4917405 -0.379885 0 1 368 3021 MODIFIER 10 CODING OBFC1 A protein_coding NM_024928.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105639421 G A 0 9.7 0 0.4372 0.777 0.8602 0.9782 0.8439 0.9008 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3021||368|OBFC1|protein_coding|CODING|NM_024928.4|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs911547 -0.379885 0 1 368 2831 MODIFIER 10 CODING OBFC1 C protein_coding NM_024928.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105639611 T C 0 46.3 0 0.3555 0.4173 0.4784 0.3403 0.5447 0.4059 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2831||368|OBFC1|protein_coding|CODING|NM_024928.4|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11191841 -0.453602 0.7 2 S248C 368 tCc/tGc MODERATE 7 MISSENSE CODING OBFC1 C protein_coding NM_024928.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105657316 G C 0 228 0 0.6407 0.873 0.9193 1 0.9085 0.9867 0.677939 0.822851 0.897093 2 6980 110111 10988 8654 6099 60307 835 16248 2 10404 121390 11570 8654 6614 66730 908 16510 0 . 0 . 0 109 0,0,61,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tGc|S248C|368|OBFC1|protein_coding|CODING|NM_024928.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10786775 -0.693147 0.0113795 109 T151A 368 Act/Gct MODERATE 5 MISSENSE CODING OBFC1 C protein_coding NM_024928.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105659826 T C 0 228 0 0.6415 0.8736 0.9193 1 0.9085 0.9888 0.677939 0.822774 0.896977 2 6983 110111 10989 8654 6097 60303 835 16250 2 10406 121380 11572 8654 6612 66716 908 16512 0 . 0 . 0 152 0,0,93,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T151A|368|OBFC1|protein_coding|CODING|NM_024928.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2487999 -0.693147 0.208567 152 C552Y 1235 tGt/tAt MODERATE 9 MISSENSE CODING SLK A protein_coding NM_014720.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105762591 G A 0 222 0 0.3616 0.2103 0.2147 0.0962 0.168 0.1636 0.30867 0.214978 0.166977 1 3295 22534 2445 684 1463 11545 164 2938 2 10390 121320 11566 8644 6610 66692 908 16510 0.422114 0 . 0 . 194 48,45,50,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|1235|SLK|protein_coding|CODING|NM_014720.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969828 rs805657 -0.693147 0.0613577 194 1235 435 MODIFIER 19 CODING SLK A protein_coding NM_014720.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105785913 G A 0 222 0 0.0023 0.0845 0.049 0.3641 0.001 0.0184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.945325 0 . 0 . 43 4,13,4,22 UTR_3_PRIME(MODIFIER||435||1235|SLK|protein_coding|CODING|NM_014720.3|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.380031 rs11191898 -0.692976 0.0489336 43 1235 820 MODIFIER 19 CODING SLK T protein_coding NM_014720.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105786298 C T 0 138 0 0.7678 0.9345 0.9813 1 0.992 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,9 UTR_3_PRIME(MODIFIER||820||1235|SLK|protein_coding|CODING|NM_014720.3|19|T),DOWNSTREAM(MODIFIER||4748||1497|COL17A1|protein_coding|CODING|NM_000494.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs805684 -0.662043 0.078067 9 1235 1065 MODIFIER 19 CODING SLK A protein_coding NM_014720.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105786543 G A 0 9.7 0 0.7678 0.9341 0.9813 1 0.9901 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1065||1235|SLK|protein_coding|CODING|NM_014720.3|19|A),DOWNSTREAM(MODIFIER||4503||1497|COL17A1|protein_coding|CODING|NM_000494.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs809303 -0.379885 0 1 1235 2396 MODIFIER 19 CODING SLK G protein_coding NM_014720.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105787874 A G 0 70 0 0.3555 0.2103 0.2161 0.1002 0.168 0.1667 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2396||1235|SLK|protein_coding|CODING|NM_014720.3|19|G),DOWNSTREAM(MODIFIER||3172||1497|COL17A1|protein_coding|CODING|NM_000494.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs809821 -0.453602 0.22 3 1497 638 MODIFIER 56 CODING COL17A1 T protein_coding NM_000494.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105791355 C T 0 67 0 0.2844 0.1885 0.2061 0.0992 0.164 0.1636 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935229 0 . 0 . 14 1,7,0,5 UTR_3_PRIME(MODIFIER||638||1497|COL17A1|protein_coding|CODING|NM_000494.3|56|T),DOWNSTREAM(MODIFIER||2364||1235|SLK|protein_coding|CODING|NM_014720.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.342519 rs9425 -0.590765 0.24773 14 1497 64 MODIFIER 56 CODING COL17A1 G protein_coding NM_000494.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105791929 C G 0 182 0 0.4221 0.2288 0.2248 0.1012 0.167 0.1656 0.373555 0.231932 0.170333 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998651 0 . 0 . 50 21,0,26,1 UTR_3_PRIME(MODIFIER||64||1497|COL17A1|protein_coding|CODING|NM_000494.3|56|G),DOWNSTREAM(MODIFIER||2938||1235|SLK|protein_coding|CODING|NM_014720.3||G) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.868987 rs805687 -0.693021 0.615414 50 I1087 1497 atT/atC LOW 47 SILENT CODING COL17A1 G protein_coding NM_000494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105796819 A G 0 228 0 0.9478 0.986 0.9986 1 1 1 0.959355 0.986235 1 2 8796 111485 10472 8294 5910 62574 817 14622 2 9184 111884 10482 8294 5910 62574 818 14622 0 . 0 . 0 94 0,0,45,34 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I1087|1497|COL17A1|protein_coding|CODING|NM_000494.3|47|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2476958 -0.693147 0.00224204 94 P968 1497 ccA/ccG LOW 44 SILENT CODING COL17A1 C protein_coding NM_000494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105798872 T C 0 222 0 0.4402 0.6815 0.7695 0.7708 0.8171 0.7137 0.507036 0.722513 0.832907 1 5193 94252 9067 6963 5183 55163 713 11970 2 10402 121340 11570 8644 6612 66696 906 16510 0.926245 0 . 0 . 176 49,40,29,39 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P968|1497|COL17A1|protein_coding|CODING|NM_000494.3|44|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999693 rs2274100 -0.693147 0.0423551 176 P961 1497 ccC/ccA LOW 43 SILENT CODING COL17A1 T protein_coding NM_000494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105799216 G T 0 222 0 0.4145 0.6835 0.768 0.8224 0.8171 0.7065 0.487744 0.715131 0.831628 1 5001 94293 9049 7428 5175 55061 715 11864 2 10402 121376 11574 8644 6606 66732 906 16512 0.902327 0 . 0 . 130 33,22,33,28 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P961|1497|COL17A1|protein_coding|CODING|NM_000494.3|43|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.792047 rs2296219 -0.693147 0.716893 130 R865 1497 cgC/cgT LOW 37 SILENT CODING COL17A1 A protein_coding NM_000494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105801253 G A 0 222 0 0.4372 0.6739 0.768 0.7589 0.8131 0.6963 0.50227 0.71813 0.828721 1 5024 92705 8950 6781 5058 54519 702 11671 2 10044 120008 11492 8604 6420 66152 896 16400 0.999907 0 . 0 . 120 25,28,19,29 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R865|1497|COL17A1|protein_coding|CODING|NM_000494.3|37|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856008 rs4918079 -0.693147 0.0924878 120 M703V 1497 Atg/Gtg MODERATE 27 MISSENSE CODING COL17A1 C protein_coding NM_000494.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105810400 T C 0 222 0 0.4728 0.6937 0.7954 0.7659 0.8052 0.7311 0.524966 0.719053 0.818488 1 5477 94732 9582 6829 5010 54665 722 12447 2 10406 121398 11574 8644 6614 66740 908 16512 0.225865 0 . 0 COSM1178415 90 19,23,26,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M703V|1497|COL17A1|protein_coding|CODING|NM_000494.3|27|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995543 rs805722 -0.693144 0.705282 90 G428S 1497 Ggc/Agc MODERATE 17 MISSENSE CODING COL17A1 T protein_coding NM_000494.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105816916 C T 0 228 0 0.4902 0.8185 0.9395 0.8829 0.9841 0.9397 0.567469 0.848869 0.992907 2 5680 113211 10961 7679 6286 66100 863 15642 2 10124 120996 11574 8652 6612 66620 906 16508 0 . 0 . 0 52 0,0,26,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G428S|1497|COL17A1|protein_coding|CODING|NM_000494.3|17|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs805698 -0.693146 0.486462 52 A354 1497 gcC/gcT LOW 14 SILENT CODING COL17A1 A protein_coding NM_000494.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105819956 G A 0 222 0 0.2519 0.5525 0.6902 0.6875 0.6551 0.6166 0.323423 0.555205 0.673953 1 3279 78576 8921 5998 4431 44906 613 10428 2 10406 121386 11570 8646 6610 66734 908 16512 0.463953 0 . 0 . 111 20,19,26,29 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A354|1497|COL17A1|protein_coding|CODING|NM_000494.3|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.193994 rs805701 -0.693147 0.00974611 111 T210M 1497 aCg/aTg MODERATE 10 MISSENSE CODING COL17A1 A protein_coding NM_000494.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105824333 G A 0 222 0 0.2814 0.5649 0.7061 0.6746 0.6799 0.6166 0.35497 0.585115 0.703023 1 3568 79725 8833 5876 4292 46176 613 10367 2 9864 118296 11300 8476 6238 65390 878 16150 0.336826 0 . 0 . 114 14,41,15,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T210M|1497|COL17A1|protein_coding|CODING|NM_000494.3|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.309474 rs805708 -0.693146 0.0046726 114 V634I 1665 Gta/Ata MODERATE 15 MISSENSE CODING CFAP43 T protein_coding NM_025145.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 105945842 C T 0 222 0 0.0008 0.019169 0.0159 0.0823 0 0.001 0.00113482 0.000538213 0.000232558 1 8 1193 466 679 0 18 2 20 2 10364 118346 11550 8644 6614 66032 882 14260 0.979393 0 . 0 . 160 56,37,18,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V634I|1665|CFAP43|protein_coding|CODING|NM_025145.5|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.891948 rs17116635 -0.693147 0.714639 160 547 12839 MODIFIER 1 CODING ITPRIP G protein_coding NM_001272012.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 106088648 A G 0 46.3 0 0.6936 0.3706 0.2522 0.2063 0.3459 0.2127 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||12839||547|ITPRIP|protein_coding|CODING|NM_001272012.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs276216 -0.453602 0.66 2 1222 LOW 2 CODING SORCS3 T protein_coding NM_014978.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 106675585 C T 0 222 0 0.618 0.3103 0.2421 0.1538 0.2445 0.1718 0.535179 0.345533 0.248372 1 5696 30491 1412 1119 1822 17574 243 2625 2 10406 121304 11572 8586 6614 66710 906 16510 0.52407 0 . 0 COSM147039 123 37,21,42,8 SPLICE_SITE_REGION+INTRON(LOW||||1222|SORCS3|protein_coding|CODING|NM_014978.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.956333 rs6584635 -0.693147 0.0283477 123 N456 1222 aaC/aaT LOW 9 SILENT CODING SORCS3 T protein_coding NM_014978.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 106907440 C T 0 228 0 0.4803 0.489 0.6268 0.3492 0.5467 0.4877 0.486382 0.525219 0.545116 2 5122 64332 7131 2829 3337 37087 480 8346 2 10402 121144 11488 8570 6606 66670 908 16500 0.855956 0 . 0 . 254 4,2,156,70 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N456|1222|SORCS3|protein_coding|CODING|NM_014978.2|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.0379824 rs791125 -0.693147 0.00751465 254 A1023 1198 gcG/gcA LOW 23 SILENT CODING SORCS1 T protein_coding NM_001013031.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 108367020 C T 0 222 0 0.323 0.237 0.0994 0.2401 0.0765 0.3804 0.282796 0.151238 0.0838372 1 3055 17774 1039 2007 632 5642 107 5292 2 10382 120834 11482 8570 6514 66484 900 16502 0.941731 0 . 0 . 61 12,18,13,12 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1023|1198|SORCS1|protein_coding|CODING|NM_001013031.2|23|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786515 rs7082289 -0.692914 0.00240246 61 Y923 1198 taC/taT LOW 20 SILENT CODING SORCS1 A protein_coding NM_001013031.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 108380213 G A 0 228 0 0.4682 0.376 0.2435 0.5069 0.171 0.4213 0.427372 0.256266 0.168605 2 4421 30101 2805 4724 1050 10741 220 6140 2 10402 121100 11576 8618 6612 66556 902 16434 0.745098 0 . 0 . 115 0,2,54,48 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y923|1198|SORCS1|protein_coding|CODING|NM_001013031.2|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.323529 rs4917481 -0.693147 0.00457815 115 F837 1198 ttT/ttC LOW 19 SILENT CODING SORCS1 G protein_coding NM_001013031.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 108389111 A G 0 228 0 0.2829 0.232 0.1052 0.3383 0.0815 0.2986 0.258965 0.136706 0.0740698 2 2728 16342 1063 2777 539 4924 111 4200 2 10326 120448 11446 8532 6578 66392 900 16274 1 0 . 0 . 157 0,1,54,82 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F837|1198|SORCS1|protein_coding|CODING|NM_001013031.2|19|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3802553 -0.693147 1.05002e-05 157 A249 666 gcG/gcA LOW 8 SILENT CODING XPNPEP1 T protein_coding NM_020383.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 111646005 C T 0 222 0 0 0.0013978 0 0.0069 0 0 0 . 0 1 0 37 0 35 0 1 0 1 2 9916 117306 11150 8510 6354 64722 878 15776 0.952255 0 . 0 . 185 57,29,42,31 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A249|666|XPNPEP1|protein_coding|CODING|NM_020383.3|8|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0300518 rs190184663 -0.693147 0.0237453 185 706 302 MODIFIER 15 CODING ADD3 G protein_coding NM_016824.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 111893678 A G 0 228 0 0.0023 0.0379 0.0014 0.1399 0 0.046 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,3,14 UTR_3_PRIME(MODIFIER||302||706|ADD3|protein_coding|CODING|NM_016824.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13306103 -0.690438 0.0632791 17 295 1405 MODIFIER 6 CODING MXI1 C protein_coding NM_130439.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112046150 T C 0 228 0 0.6067 0.7452 0.755 0.9137 0.7058 0.7924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 115 0,0,77,22 UTR_3_PRIME(MODIFIER||1405||295|MXI1|protein_coding|CODING|NM_130439.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs17658,rs386544209 -0.693147 0.0918932 115 295 1455 MODIFIER 6 CODING MXI1 T protein_coding NM_130439.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112046200 G T 0 228 0 0.0234 0.1316 0.036 0.2986 0.0328 0.2751 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 140 0,0,71,55 UTR_3_PRIME(MODIFIER||1455||295|MXI1|protein_coding|CODING|NM_130439.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1803997 -0.693147 3.86258e-08 140 238 309 MODIFIER 6 CODING SMNDC1 T protein_coding NM_005871.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112053599 C T 0 228 0 0.059 0.5256 0.621 0.8413 0.5825 0.7045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,45,5 UTR_3_PRIME(MODIFIER||309||238|SMNDC1|protein_coding|CODING|NM_005871.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1050755,rs386513946 -0.693147 0.00675709 53 A220T 384 Gcg/Acg MODERATE 3 MISSENSE CODING DUSP5 A protein_coding NM_004419.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112266822 G A 0 228 0 0.9024 0.9732 0.9928 1 1 1 0.903995 0.967246 0.999651 2 9378 120312 11533 8654 6614 66719 904 16510 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 128 0,0,50,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A220T|384|DUSP5|protein_coding|CODING|NM_004419.3|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1889566 -0.693147 0.00294226 128 A220V 384 gCg/gTg MODERATE 3 MISSENSE CODING DUSP5 T protein_coding NM_004419.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112266823 C T 0 228 0 0.9024 0.9732 0.9928 1 1 1 0.903768 0.967169 0.999651 2 9378 120312 11533 8654 6614 66719 904 16510 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 128 0,0,50,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A220V|384|DUSP5|protein_coding|CODING|NM_004419.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1889565 -0.693147 0.00287719 128 384 491 MODIFIER 4 CODING DUSP5 C protein_coding NM_004419.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112270675 A C 0 202 0 0.5439 0.6573 0.7133 0.6151 0.7008 0.7699 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,7,3 UTR_3_PRIME(MODIFIER||491||384|DUSP5|protein_coding|CODING|NM_004419.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.916482 0 . rs1042606 -0.670168 0.219282 10 384 1073 MODIFIER 4 CODING DUSP5 G protein_coding NM_004419.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112271257 C G 0 222 0 0.0219 0.1036 0.0764 0.2113 0.0825 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.937574 0 . 0 . 112 18,30,18,30 UTR_3_PRIME(MODIFIER||1073||384|DUSP5|protein_coding|CODING|NM_004419.3|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.423074 rs1042641 -0.693147 0.00167809 112 S1013 1217 tcA/tcG LOW 25 SILENT CODING SMC3 G protein_coding NM_005445.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112361870 A G 0 228 0 0.9531 0.9868 0.9986 1 0.997 1 0.971403 0.989851 0.999302 2 9939 120836 11563 8652 6614 66656 905 16507 2 10306 121284 11578 8652 6614 66716 908 16510 0 2 benign 0 . 176 0,0,70,87 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1013|1217|SMC3|protein_coding|CODING|NM_005445.3|25|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2419565 -0.693147 0.0115498 176 W768S 1227 tGg/tCg MODERATE 9 MISSENSE CODING RBM20 C protein_coding NM_001134363.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112572458 G C 0 228 0 0.969 0.991 0.9942 1 1 1 1 1 1 2 2083 21670 406 621 1626 8780 242 7912 2 2148 21740 408 622 1626 8782 242 7912 0 2|2 benign|benign 0 . 165 0,0,67,88 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W768S|1227|RBM20|protein_coding|CODING|NM_001134363.2|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1417635 -0.693147 0.24572 165 E1223Q 1227 Gaa/Caa MODERATE 14 MISSENSE CODING RBM20 C protein_coding NM_001134363.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112595719 G C 0 228 0 0.4334 0.6971 0.7983 0.7956 0.8688 0.7035 0.496387 0.758432 0.872407 2 1031 14542 327 492 31 7193 146 5322 2 2128 19042 404 620 34 8286 184 7386 0 2|2 benign|benign 0 . 33 0,0,12,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E1223Q|1227|RBM20|protein_coding|CODING|NM_001134363.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs942077 -0.693054 0.381059 33 I36V 469 Ata/Gta MODERATE 3 MISSENSE CODING PDCD4 G protein_coding NM_014456.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112641053 A G 0 228 0 0.8389 0.9185 0.9654 0.9901 0.9523 0.8845 0.852474 0.920268 0.955 2 8837 114695 11258 8618 6316 63954 870 14842 2 10386 121322 11572 8650 6614 66690 908 16502 0 . 0 . 0 124 0,0,74,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I36V|469|PDCD4|protein_coding|CODING|NM_014456.4|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7081726 -0.693147 0.82211 124 469 214 MODIFIER 12 CODING PDCD4 A protein_coding NM_014456.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112658060 G A 0 228 0 0.0711 0.1558 0.2046 0.3502 0.0278 0.1667 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 60 0,0,36,22 UTR_3_PRIME(MODIFIER||214||469|PDCD4|protein_coding|CODING|NM_014456.4|12|A),DOWNSTREAM(MODIFIER||428||103|BBIP1|protein_coding|CODING|NM_001195304.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12248739 -0.693147 1.68218e-08 60 465 682 MODIFIER 1 CODING ADRA2A C protein_coding NM_000681.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112837073 G C 0 60 0 0.9312 0.9245 0.9769 0.8919 0.9384 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||682||465|ADRA2A|protein_coding|CODING|NM_000681.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2484516 -0.453602 0.6 3 465 666 MODIFIER 1 CODING ADRA2A C protein_coding NM_000681.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112837089 T C 0 66 0 0.9917 0.9978 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||666||465|ADRA2A|protein_coding|CODING|NM_000681.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2479049 -0.453602 0.6 3 R380 465 Cgg/Agg LOW 1 SILENT CODING ADRA2A A protein_coding NM_000681.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112838892 C A 0 144 0 0.0809 0.132 0.1729 0.3313 0.004 0.0982 0.0776214 0.0296786 0.00511628 2 779 7699 2589 2687 100 368 48 1128 2 9634 110766 11066 8320 6252 61454 824 13216 1 0 . 0 . 20 1,0,19,0 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R380|465|ADRA2A|protein_coding|CODING|NM_000681.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 0 . 1 rs1800038 -0.69168 0.303354 20 465 1019 MODIFIER 1 CODING ADRA2A G protein_coding NM_000681.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 112840171 A G 0 228 0 0.0809 0.1372 0.1758 0.3413 0.0139 0.1022 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,43,25 UTR_3_PRIME(MODIFIER||1019||465|ADRA2A|protein_coding|CODING|NM_000681.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13306146 -0.693147 0.781923 75 828 2587 MODIFIER 22 CODING GPAM G protein_coding NM_001244949.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113910721 A G 0 197 0 0.764 0.7518 0.6455 0.7579 0.6889 0.8691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 27 1,0,24,1 UTR_3_PRIME(MODIFIER||2587||828|GPAM|protein_coding|CODING|NM_001244949.1|22|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1129555 -0.692914 0.191489 27 828 2227 MODIFIER 22 CODING GPAM C protein_coding NM_001244949.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113911080 CG C 0 228 0 0.0242 0.1182 0.0648 0.2381 0.0805 0.1984 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 98 0,0,72,19 UTR_3_PRIME(MODIFIER||2227||828|GPAM|protein_coding|CODING|NM_001244949.1|22|C) 0 . 0 94 0.959184 1 1 0 . 0 60 0 0 1 0 . rs145414051 -0.693147 0.0967071 98 828 86 MODIFIER 22 CODING GPAM C protein_coding NM_001244949.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113913222 T C 0 228 0 0.6936 0.7306 0.647 0.7579 0.6769 0.8671 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 114 0,0,55,47 UTR_3_PRIME(MODIFIER||86||828|GPAM|protein_coding|CODING|NM_001244949.1|22|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2297991 -0.693147 0.0291663 114 P681 828 ccA/ccT LOW 19 SILENT CODING GPAM A protein_coding NM_001244949.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113917085 T A 0 228 0 0.7837 0.7576 0.6499 0.7589 0.6879 0.8691 0.751929 0.721206 0.705465 2 7802 88051 8532 6212 4428 46679 648 13750 2 10406 121348 11568 8632 6608 66714 908 16512 0.518657 0 . 0 . 155 0,2,67,67 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P681|828|GPAM|protein_coding|CODING|NM_001244949.1|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.802239 rs2254537 -0.693147 0.0869621 155 N552 828 aaC/aaT LOW 16 SILENT CODING GPAM A protein_coding NM_001244949.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113920465 G A 0 228 0 0.528 0.5535 0.4553 0.6002 0.5437 0.6196 0.503404 0.558435 0.586628 2 5269 68649 5793 4940 3381 38476 516 10274 2 10406 121280 11556 8620 6600 66682 908 16508 0 . 0 . 0 196 0,0,86,96 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N552|828|GPAM|protein_coding|CODING|NM_001244949.1|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2277207 -0.693147 0.00582112 196 E131G 828 gAa/gGa MODERATE 6 MISSENSE CODING GPAM C protein_coding NM_001244949.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113935379 T C 0 228 0 0.528 0.5547 0.4582 0.6042 0.5437 0.6196 0.503858 0.55928 0.587674 2 5269 68769 5795 4977 3385 38526 516 10301 2 10404 121340 11566 8612 6612 66728 906 16512 0 . 0 . 0 147 0,0,87,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E131G|828|GPAM|protein_coding|CODING|NM_001244949.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10787428 -0.693147 0.408282 147 I43V 828 Atc/Gtc MODERATE 4 MISSENSE CODING GPAM C protein_coding NM_001244949.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 113940329 T C 0 228 0 0.9561 0.8069 0.6671 0.7629 0.6918 0.8681 0.926237 0.780947 0.706512 2 9660 90048 8573 6218 4422 46786 648 13741 2 10404 121232 11526 8638 6596 66666 904 16498 1 0 . 0 . 162 1,0,71,79 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I43V|828|GPAM|protein_coding|CODING|NM_001244949.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2792751 -0.693147 0.110705 162 S178 329 tcC/tcG LOW 5 SILENT CODING TECTB G protein_coding NM_058222.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 114053546 C G 0 228 0 . 0 . 0 . 0 0.556287 0.492619 0.46 2 5877 63620 8206 6395 2507 30873 418 9344 2 10406 121398 11578 8648 6610 66740 906 16510 0 . 0 . 0 180 0,0,87,77 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S178|329|TECTB|protein_coding|CODING|NM_058222.2|5|G) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs726009 -0.693147 0.263338 180 739 LOW 20 CODING ACSL5 A protein_coding NM_016234.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 114186624 G A 0 228 0 0.9803 0.9639 0.964 0.9871 0.9155 0.9673 0.970495 0.933954 0.915233 2 10121 112981 11298 8557 5449 60598 828 16130 2 10398 121384 11578 8652 6614 66724 908 16510 0 . 0 . 0 104 0,0,21,75 SPLICE_SITE_REGION+INTRON(LOW||||739|ACSL5|protein_coding|CODING|NM_016234.3|20|A),DOWNSTREAM(MODIFIER||3424||413|ZDHHC6|protein_coding|CODING|NM_022494.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2256368 -0.693147 0.077053 104 739 671 MODIFIER 21 CODING ACSL5 C protein_coding NM_016234.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 114187787 T C 0 9.7 0 0.5408 0.3678 0.2954 0.3194 0.2982 0.3067 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||671||739|ACSL5|protein_coding|CODING|NM_016234.3|21|C),DOWNSTREAM(MODIFIER||2261||413|ZDHHC6|protein_coding|CODING|NM_022494.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8624 -0.379885 0 1 413 LOW 8 CODING ZDHHC6 A protein_coding NM_022494.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 114192285 G A 0 222 0 0.0393 0.3528 0.4481 0.5466 0.3827 0.4785 0.0946437 0.261495 0.346977 1 935 45843 6914 4344 1963 23542 283 7862 2 10198 121036 11572 8632 6612 66638 906 16478 0.530807 0 . 0 . 123 23,26,29,29 SPLICE_SITE_REGION+INTRON(LOW||||413|ZDHHC6|protein_coding|CODING|NM_022494.2|8|A),DOWNSTREAM(MODIFIER||4147||739|ACSL5|protein_coding|CODING|NM_016234.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.52521 rs2306158 -0.693147 0.00340984 123 217 1611 MODIFIER 8 CODING VTI1A T protein_coding NM_145206.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 114576753 C T 0 6.3 0 0.0582 0.2973 0.2622 0.5139 0.2316 0.4898 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1611||217|VTI1A|protein_coding|CODING|NM_145206.2|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1047468 -0.379885 0 1 H61 560 caC/caT LOW 3 SILENT CODING HABP2 T protein_coding NM_004132.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115334124 C T 0 228 0 0.2965 0.5345 0.6354 0.6042 0.6183 0.6268 0.359737 0.544057 0.638488 2 3682 75672 8608 5757 4294 42703 552 10076 2 10406 121368 11572 8644 6614 66724 908 16500 0 . 0 . 0 131 0,0,48,70 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H61|560|HABP2|protein_coding|CODING|NM_004132.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3740530 -0.693147 0.021871 131 I1189 1731 atT/atC LOW 31 SILENT CODING NRAP G protein_coding NM_001261463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115370254 A G 0 228 0 0.354 0.4694 0.4669 0.6032 0.4652 0.4939 0.360191 0.442334 0.484419 2 3750 56431 5150 5402 2959 31344 444 7382 2 10406 121380 11570 8650 6612 66724 908 16510 1 0 . 0 . 136 1,0,56,54 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I1189|1731|NRAP|protein_coding|CODING|NM_001261463.1|31|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12243176 -0.693147 0.612282 136 I1183V 1731 Att/Gtt MODERATE 31 MISSENSE CODING NRAP C protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115370274 T C 0 228 0 0.3321 0.4629 0.4669 0.5992 0.4652 0.4939 0.33409 0.433262 0.48407 2 3510 56155 5133 5379 2960 31349 444 7380 2 10404 121376 11572 8644 6614 66724 908 16510 1 0 . 0 COSM1180648 119 1,0,34,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I1183V|1731|NRAP|protein_coding|CODING|NM_001261463.1|31|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10749138 -0.693147 0.000147938 119 P1007 1731 ccG/ccT LOW 27 SILENT CODING NRAP A protein_coding NM_001261463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115375528 C A 0 222 0 0.0802 0.2276 0.2507 0.3958 0.2783 0.1851 0.102133 0.212825 0.269535 1 1036 30774 3389 3389 1987 17859 231 2883 2 10316 119990 11424 8576 6436 66160 902 16176 0.959739 0 . 0 COSM147045 97 34,15,23,15 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1007|1731|NRAP|protein_coding|CODING|NM_001261463.1|27|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.127866 rs11196397 -0.693143 0.149274 97 D966G 1731 gAt/gGt MODERATE 26 MISSENSE CODING NRAP C protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115377290 T C 0 222 0 0.0008 0.0701 0.0677 0.1528 0.0825 0.0675 0.0181571 0.0638936 0.0873256 1 169 9003 693 1290 366 5411 71 1003 2 10406 121390 11576 8646 6614 66728 908 16512 0.54345 0 . 0 . 116 19,31,22,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D966G|1731|NRAP|protein_coding|CODING|NM_001261463.1|26|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.572052 rs77678145 -0.693147 0.00866142 116 N519I 1731 aAt/aTt MODERATE 16 MISSENSE CODING NRAP A protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115392919 T A 0 222 0 0.3336 0.2588 0.2248 0.1915 0.2714 0.2382 0.353155 0.30286 0.277093 1 3653 31983 1916 1565 1953 18523 235 4138 2 10390 121228 11546 8634 6602 66658 908 16490 0.993458 0 . 0 . 114 18,38,11,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N519I|1731|NRAP|protein_coding|CODING|NM_001261463.1|16|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989424 rs2270182 -0.693146 0.261292 114 S490L 1731 tCg/tTg MODERATE 15 MISSENSE CODING NRAP A protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115393929 G A 0 222 0 0.1203 0.2907 0.2781 0.4266 0.328 0.3517 0.139355 0.251115 0.308372 1 1410 37154 3477 3780 2167 20591 281 5448 2 10406 121372 11576 8622 6614 66734 908 16512 0.993733 0 . 0 COSM1179743 122 36,15,30,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S490L|1731|NRAP|protein_coding|CODING|NM_001261463.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975166 rs3189030 -0.693147 0.132378 122 D484N 1731 Gac/Aac MODERATE 15 MISSENSE CODING NRAP T protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115393948 C T 0 222 0 0.3094 0.1921 0.1124 0.1677 0.1382 0.1708 0.296187 0.188067 0.132674 1 3121 18725 1069 1351 904 9232 130 2918 2 10406 121382 11576 8636 6614 66732 908 16510 0.794078 0 . 0 . 128 31,24,34,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D484N|1731|NRAP|protein_coding|CODING|NM_001261463.1|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996564 rs11196400 -0.693147 0.458329 128 Q360R 1731 cAg/cGg MODERATE 11 MISSENSE CODING NRAP C protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115405615 T C 0 222 0 0.2965 0.5643 0.6715 0.7103 0.6243 0.638 0.352247 0.525988 0.615 1 3628 74918 8858 6201 4167 41125 562 10377 2 10406 121324 11578 8640 6610 66692 906 16492 0.417523 0 . 0 . 109 15,31,17,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q360R|1731|NRAP|protein_coding|CODING|NM_001261463.1|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.426322 rs3127106 -0.693147 0.16276 109 A344T 1731 Gct/Act MODERATE 11 MISSENSE CODING NRAP T protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115405664 C T 0 222 0 0.2965 0.5643 0.6715 0.7103 0.6243 0.638 0.35202 0.525834 0.614884 1 3628 74921 8852 6203 4169 41132 563 10374 2 10404 121330 11572 8644 6608 66708 908 16486 0.832208 0 . 0 . 58 1,26,6,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A344T|1731|NRAP|protein_coding|CODING|NM_001261463.1|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.390096 rs3121478 -0.693054 0.00134692 58 A282T 1731 Gct/Act MODERATE 9 MISSENSE CODING NRAP T protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115409840 C T 0 222 0 0.3419 0.2678 0.2248 0.2173 0.2684 0.2495 0.362006 0.30632 0.277791 1 3773 32453 1929 1803 1952 18578 236 4182 2 10404 121394 11578 8650 6614 66728 908 16512 0.439322 0 . 0 . 100 30,13,19,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A282T|1731|NRAP|protein_coding|CODING|NM_001261463.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981295 rs2275799 -0.693146 0.0008301 100 Y249C 1731 tAt/tGt MODERATE 8 MISSENSE CODING NRAP C protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115410234 T C 0 222 0 0.0182 0.2035 0.245 0.3343 0.3012 0.1892 0.0581026 0.212825 0.292093 1 554 31509 3195 2829 2100 19290 232 3309 2 10404 121284 11552 8622 6604 66692 908 16502 0.984803 0 . 0 COSM147049 136 46,26,26,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y249C|1731|NRAP|protein_coding|CODING|NM_001261463.1|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.354848 rs2185913,rs386560111 -0.693147 0.0589955 136 L213 1731 ctG/ctT LOW 7 SILENT CODING NRAP A protein_coding NM_001261463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115411598 C A 0 222 0 0.3306 0.2646 0.2248 0.2163 0.2684 0.2495 0.342941 0.299862 0.277791 1 3608 32226 1912 1798 1943 18543 236 4186 2 10404 121220 11544 8622 6598 66640 908 16504 0.18966 0 . 0 . 70 22,11,24,6 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L213|1731|NRAP|protein_coding|CODING|NM_001261463.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.553771 rs4918861 -0.693097 0.766704 70 V208A 1731 gTg/gCg MODERATE 7 MISSENSE CODING NRAP G protein_coding NM_001261463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115411614 A G 0 228 0 0.8086 0.8776 0.9107 0.9038 0.8936 0.9039 0.823423 0.868907 0.892209 2 8578 108663 10850 7775 6126 59691 804 14839 2 10406 121378 11570 8648 6612 66724 908 16510 0 . 0 . 0 77 0,0,43,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V208A|1731|NRAP|protein_coding|CODING|NM_001261463.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2154028 -0.693147 0.538045 77 1731 LOW 6 CODING NRAP A protein_coding NM_001261463.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115412686 G A 0 228 0 0.8109 0.8778 0.9107 0.9038 0.8926 0.9029 0.825919 0.869676 0.892093 2 8610 108696 10839 7779 6124 59702 804 14838 2 10404 121374 11558 8654 6612 66728 908 16510 0 . 0 . 0 53 0,0,39,10 SPLICE_SITE_REGION+INTRON(LOW||||1731|NRAP|protein_coding|CODING|NM_001261463.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3121488 -0.693147 0.662489 53 Y157 1731 taT/taC LOW 6 SILENT CODING NRAP G protein_coding NM_001261463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115412793 A G 0 222 0 0.4887 0.3081 0.2378 0.2173 0.2664 0.2505 0.447094 0.335205 0.277907 1 4717 33467 1971 1803 1955 18593 239 4189 2 10128 120950 11526 8632 6608 66676 908 16472 0.764897 0 . 0 . 98 23,13,20,28 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y157|1731|NRAP|protein_coding|CODING|NM_001261463.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932064 rs3737322 -0.693147 0.178636 98 H100 1731 caC/caT LOW 4 SILENT CODING NRAP A protein_coding NM_001261463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115417289 G A 0 228 0 0.8071 0.8766 0.9092 0.9038 0.8917 0.9039 0.819791 0.867753 0.892326 2 8543 108541 10813 7776 6120 59650 803 14836 2 10402 121290 11532 8646 6608 66688 908 16506 0 . 0 . 0 100 0,0,46,38 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H100|1731|NRAP|protein_coding|CODING|NM_001261463.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1891762 -0.693147 0.493381 100 1731 106 MODIFIER 1 CODING NRAP A protein_coding NM_001261463.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115423747 G A 0 99 0 0.4123 0.3033 0.1801 0.2867 0.2366 0.3292 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.205052 0 . 0 . 18 3,5,0,9 UTR_5_PRIME(MODIFIER||106||1731|NRAP|protein_coding|CODING|NM_001261463.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.959189 rs1109927 -0.662043 0.987721 18 T19I 388 aCc/aTc MODERATE 1 MISSENSE CODING CASP7 T protein_coding NM_001267057.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115439569 C T 0 9.7 0 0.9924 0.8542 0.6816 0.8224 0.8151 0.863 0 . 0 1 131 6094 53 88 0 1457 67 4298 2 146 7036 66 114 0 1678 82 4950 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T19I|388|CASP7|protein_coding|CODING|NM_001267057.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs386479493,rs7921977 -0.379885 0 1 D340E 388 gaC/gaG MODERATE 7 MISSENSE CODING CASP7 G protein_coding NM_001267057.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115489152 C G 0 222 0 0.1278 0.2498 0.2579 0.4157 0.2535 0.2342 0.144803 0.216054 0.252558 1 1480 31539 3298 3645 1835 17112 223 3946 2 10406 121384 11576 8632 6614 66736 908 16512 0.943433 0 . 0 . 60 24,8,14,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D340E|388|CASP7|protein_coding|CODING|NM_001267057.1|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.550861 rs2227310 -0.692717 0.65089 60 Q345 388 caG/caA LOW 7 SILENT CODING CASP7 A protein_coding NM_001267057.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115489167 G A 0 222 0 0.1346 0.2498 0.2579 0.4087 0.2525 0.2331 0.14798 0.217207 0.252674 1 1513 31501 3298 3597 1835 17091 224 3943 2 10404 121384 11576 8632 6614 66738 908 16512 0.800737 0 . 0 . 69 27,9,16,11 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q345|388|CASP7|protein_coding|CODING|NM_001267057.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997592 rs2227309 -0.693021 0.307918 69 388 290 MODIFIER 7 CODING CASP7 C protein_coding NM_001267057.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115489589 T C 0 77 0 0.1346 0.2518 0.2579 0.4157 0.2545 0.2342 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.649731 0 . 0 . 9 0,4,1,4 UTR_3_PRIME(MODIFIER||290||388|CASP7|protein_coding|CODING|NM_001267057.1|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.406082 rs4353229 -0.590765 0.284843 9 388 351 MODIFIER 7 CODING CASP7 G protein_coding NM_001267057.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115489650 T G 0 82 0 0.4387 0.3632 0.4856 0.1964 0.325 0.3855 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,1,2 UTR_3_PRIME(MODIFIER||351||388|CASP7|protein_coding|CODING|NM_001267057.1|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10787498 -0.511536 0.126715 5 388 761 MODIFIER 7 CODING CASP7 A protein_coding NM_001267057.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115490060 G A 0 93 0 0.2617 0.1741 0.1182 0.131 0.1332 0.182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.961166 0 . 0 . 13 6,0,7,0 UTR_3_PRIME(MODIFIER||761||388|CASP7|protein_coding|CODING|NM_001267057.1|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.961166 0 . 0.899815 rs12247479 -0.636426 0.62127 13 465 146 MODIFIER 1 CODING PLEKHS1 C protein_coding NM_182601.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115524994 T C 0 149 0 0 0.0059904 0 0.0298 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.113766 0 . 0 . 43 14,2,25,1 UTR_5_PRIME(MODIFIER||146||465|PLEKHS1|protein_coding|CODING|NM_182601.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.843828 rs182913165 -0.692976 0.818161 43 T861P 1040 Act/Cct MODERATE 7 MISSENSE CODING DCLRE1A G protein_coding NM_001271816.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115602186 T G 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 1 0 1 0 0 0 0 2 10406 121406 11576 8654 6614 66738 908 16510 0.748655 0 . 0 . 147 37,31,36,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T861P|1040|DCLRE1A|protein_coding|CODING|NM_001271816.1|7|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.437221 rs200602494 -0.693147 0.0326168 147 D317H 1040 Gat/Cat MODERATE 3 MISSENSE CODING DCLRE1A G protein_coding NM_001271816.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115609915 C G 0 222 0 0.3086 0.6577 0.817 0.8185 0.7942 0.7106 0.384249 0.637859 0.767791 1 3815 91792 10389 7296 5284 52214 707 12087 2 10400 121384 11576 8650 6606 66736 906 16510 0.988695 0 . 0 . 77 25,13,16,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D317H|1040|DCLRE1A|protein_coding|CODING|NM_001271816.1|3|G),UPSTREAM(MODIFIER||4476||726|NHLRC2|protein_coding|CODING|NM_198514.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.902739 rs3750898 -0.69311 0.873159 77 V314I 726 Gta/Ata MODERATE 5 MISSENSE CODING NHLRC2 A protein_coding NM_198514.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115644040 G A 0 222 0 0.121 0.2234 0.2291 0.3125 0.2932 0.1943 0.155243 0.238813 0.281628 1 1553 32959 3123 2811 2523 19449 242 3258 2 10396 121164 11500 8634 6598 66644 906 16486 0.943525 0 . 0 COSM427091 235 70,38,53,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V314I|726|NHLRC2|protein_coding|CODING|NM_198514.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.535991 rs7913176 -0.693147 0.20333 235 S49G 477 Agc/Ggc MODERATE 1 MISSENSE CODING ADRB1 G protein_coding NM_000684.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115804036 A G 0 94 0 0.239 0.1777 0.2507 0.1409 0.1272 0.1329 0.194366 0.136693 0.107508 1 1312 13194 2372 868 710 6056 78 1798 2 3620 43402 4884 2928 1904 21684 302 8080 0.883506 255 other 0 . 25 14,0,10,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S49G|477|ADRB1|protein_coding|CODING|NM_000684.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.99615 rs1801252 -0.670168 0.906563 25 G389R 477 Gga/Cga MODERATE 1 MISSENSE CODING ADRB1 C protein_coding NM_000684.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115805056 G C 0 228 0 0.5703 0.7017 0.8055 0.7877 0.6849 0.7342 0.627446 0.69967 0.736429 2 5041 82606 9684 6262 4679 44079 604 12257 2 8512 112236 11198 8308 6266 61014 828 16110 0 6 drug-response 0 . 79 0,0,8,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G389R|477|ADRB1|protein_coding|CODING|NM_000684.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1801253 -0.693147 0.0947382 79 A771T 898 Gca/Aca MODERATE 14 MISSENSE CODING CCDC186 T protein_coding NM_018017.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 115887302 C T 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 40 0 40 0 0 0 0 2 10400 121204 11486 8644 6598 66664 906 16506 0.381211 0 . 0 . 114 37,16,25,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A771T|898|CCDC186|protein_coding|CODING|NM_018017.2|14|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.927921 rs79637542 -0.693146 0.0423466 114 E131G 755 gAa/gGa MODERATE 6 MISSENSE CODING VWA2 G protein_coding NM_001272046.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116032519 A G 0 222 0 0.8782 0.5571 0.4741 0.3373 0.4324 0.5368 0.800272 0.55559 0.430233 1 8476 57652 5553 3011 2752 28876 406 8578 2 10406 120858 11570 8632 6612 66526 900 16212 0.587787 0 . 0 . 94 22,21,21,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E131G|755|VWA2|protein_coding|CODING|NM_001272046.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.463799 rs597371 -0.693147 0.357045 94 755 781 MODIFIER 14 CODING VWA2 T protein_coding NM_001272046.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116051777 C T 0 6.3 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||781||755|VWA2|protein_coding|CODING|NM_001272046.1|14|T),DOWNSTREAM(MODIFIER||2806||871|AFAP1L2|protein_coding|CODING|NM_001287824.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs472134 -0.379885 0 1 871 384 MODIFIER 20 CODING AFAP1L2 T protein_coding NM_001287824.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116055417 C T 0 108 0 0.2027 0.597 0.8156 0.6944 0.8221 0.6431 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,2 UTR_3_PRIME(MODIFIER||384||871|AFAP1L2|protein_coding|CODING|NM_001287824.1|20|T),DOWNSTREAM(MODIFIER||1158||755|VWA2|protein_coding|CODING|NM_001272046.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3750821 -0.556411 0.112085 4 R588 871 cgA/cgG LOW 15 SILENT CODING AFAP1L2 C protein_coding NM_001287824.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116060387 T C 0 228 0 0.3003 0.6416 0.8372 0.7054 0.831 0.7035 0.381071 0.681455 0.835349 2 3849 94374 10059 6279 5511 55790 724 12162 2 10398 121138 11572 8636 6606 66628 904 16394 1 0 . 0 . 105 1,0,43,55 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R588|871|AFAP1L2|protein_coding|CODING|NM_001287824.1|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2286396,rs386563639 -0.693147 0.0439544 105 T295 871 acG/acA LOW 8 SILENT CODING AFAP1L2 T protein_coding NM_001287824.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116073696 C T 0 228 0 0.09 0.5849 0.8084 0.8929 0.7614 0.5961 0.192465 0.579809 0.778256 2 1833 87985 9603 7843 5506 52304 681 10215 2 10404 121368 11572 8646 6610 66720 908 16508 0 . 0 . 0 110 0,0,84,23 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T295|871|AFAP1L2|protein_coding|CODING|NM_001287824.1|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3813722 -0.693147 0.874531 110 871 LOW 4 CODING AFAP1L2 C protein_coding NM_001287824.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116091555 T C 0 228 0 0.4909 0.7366 0.7911 0.9405 0.8191 0.7352 0.543274 0.741603 0.843795 2 1393 10614 285 636 37 5977 109 2177 2 2726 14012 354 670 48 7220 128 2866 0 . 0 . 0 64 0,0,38,21 SPLICE_SITE_REGION+INTRON(LOW||||871|AFAP1L2|protein_coding|CODING|NM_001287824.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10787524 -0.693147 0.28215 64 778 3188 MODIFIER 22 CODING ABLIM1 G protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116192831 T G 0 9.7 0 0.8933 0.9517 0.9539 1 0.9414 0.9898 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3188||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7906164 -0.379885 0 1 778 2102 MODIFIER 22 CODING ABLIM1 G protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116193917 A G 0 9.7 0 0.7935 0.6889 0.67 0.7232 0.5885 0.6288 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2102||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10787530 -0.379885 0 1 778 1239 MODIFIER 22 CODING ABLIM1 G protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116194780 C G 0 9.7 0 0.4425 0.4151 0.3818 0.3929 0.4304 0.409 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1239||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4751906 -0.379885 0 1 778 864 MODIFIER 22 CODING ABLIM1 C protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116195155 T C 0 23.4 0 0.8525 0.6571 0.5605 0.6528 0.5706 0.5552 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||864||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1057144 -0.453602 0.18 2 778 420 MODIFIER 22 CODING ABLIM1 A protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116195599 T A 0 86 0 0.8525 0.656 0.5591 0.6508 0.5686 0.5542 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||420||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10978,rs111198697 -0.556411 0.885471 4 778 243 MODIFIER 22 CODING ABLIM1 G protein_coding NM_002313.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116195776 C G 0 228 0 0.8517 0.656 0.5591 0.6508 0.5706 0.5532 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 91 0,0,77,9 UTR_3_PRIME(MODIFIER||243||778|ABLIM1|protein_coding|CODING|NM_002313.5|22|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1057139 -0.693147 0.0914078 91 N235 778 aaT/aaC LOW 5 SILENT CODING ABLIM1 G protein_coding NM_002313.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116307504 A G 0 222 0 0.9584 0.7831 0.745 0.6706 0.7356 0.7382 0.915343 0.791788 0.728488 1 9570 88025 7503 5808 4528 48654 667 11295 2 10374 121034 11542 8582 6592 66540 906 16498 0.987244 0 . 0 . 94 20,28,18,26 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N235|778|ABLIM1|protein_coding|CODING|NM_002313.5|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.405062 rs2247528 -0.693146 0.253 94 E212 765 gaA/gaG LOW 6 SILENT CODING FAM160B1 G protein_coding NM_020940.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116602805 A G 0 222 0 0.0227 0.0986 0.1455 0.1974 0.0875 0.0777 0.0478892 0.0823466 0.1 1 455 13389 2482 1936 809 6154 88 1465 2 10344 121124 11528 8608 6612 66630 904 16498 0.886052 0 . 0 . 119 25,27,24,32 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E212|765|FAM160B1|protein_coding|CODING|NM_020940.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979625 rs17092491 -0.693147 0.104993 119 765 594 MODIFIER 17 CODING FAM160B1 C protein_coding NM_020940.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116621893 A C 0 222 0 0.1566 0.1376 0.1571 0.1994 0.0944 0.0787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.958452 0 . 0 . 131 16,56,9,36 UTR_3_PRIME(MODIFIER||594||765|FAM160B1|protein_coding|CODING|NM_020940.3|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.980416 rs11196957 -0.693147 6.28117e-09 131 765 1978 MODIFIER 17 CODING FAM160B1 C protein_coding NM_020940.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116623277 G C 0 112 0 0.1384 0.1328 0.1571 0.1994 0.0944 0.0787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.895781 0 . 0 . 11 3,1,6,0 UTR_3_PRIME(MODIFIER||1978||765|FAM160B1|protein_coding|CODING|NM_020940.3|17|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.895781 rs2286632 -0.616816 0.733112 11 1379 333 MODIFIER 1 CODING ATRNL1 G protein_coding NM_207303.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 116853177 C G 0 116 0 0.4849 0.6711 0.7781 0.8046 0.7018 0.6779 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 START_GAINED(LOW||||1379|ATRNL1|protein_coding|CODING|NM_207303.4|1|G),UTR_5_PRIME(MODIFIER||333||1379|ATRNL1|protein_coding|CODING|NM_207303.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2484265 -0.616816 0.080746 6 S989N 1379 aGt/aAt MODERATE 18 MISSENSE CODING ATRNL1 A protein_coding NM_207303.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 117075175 G A 0 228 0 0.9425 0.969 0.9798 0.999 0.9722 0.9632 0.957558 0.964785 0.968488 2 9904 118171 11345 8626 6446 64996 886 15968 2 10406 121346 11516 8652 6614 66738 908 16512 0 . 0 . 0 135 0,0,53,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S989N|1379|ATRNL1|protein_coding|CODING|NM_207303.4|18|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1953758 -0.693147 0.00293435 135 1379 335 MODIFIER 29 CODING ATRNL1 T protein_coding NM_207303.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 117704625 G T 0 39.3 0 0.9349 0.982 0.9942 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||335||1379|ATRNL1|protein_coding|CODING|NM_207303.4|29|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs963192 -0.453602 0.44 2 N184 465 aaC/aaT LOW 6 SILENT CODING GFRA1 A protein_coding NM_005264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 117884950 G A 0 222 0 0.2466 0.485 0.6455 0.5546 0.5467 0.5583 0.316841 0.4837 0.569186 1 3162 67308 8128 5077 3753 37519 528 9141 2 10374 120900 11552 8598 6560 66418 906 16492 0.225417 0 . 0 COSM147055 107 31,24,14,26 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N184|465|GFRA1|protein_coding|CODING|NM_005264.4|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.908856 rs2245020 -0.693145 0.741671 107 465 78 MODIFIER 2 CODING GFRA1 A protein_coding NM_005264.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118031619 G A 0 170 0 0.3865 0.4998 0.5548 0.5248 0.659 0.4243 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.50373 0 . 0 . 16 3,2,3,5 START_GAINED(LOW||||465|GFRA1|protein_coding|CODING|NM_005264.4|2|A),UTR_5_PRIME(MODIFIER||78||465|GFRA1|protein_coding|CODING|NM_005264.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.961166 0 0.935229 rs2577360 -0.651104 0.259674 16 465 106 MODIFIER 2 CODING GFRA1 T protein_coding NM_005264.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118031647 C T 0 195 0 0.4274 0.244 0.2003 0.3333 0.0676 0.1166 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.593759 0 . 0 . 23 4,6,9,2 UTR_5_PRIME(MODIFIER||106||465|GFRA1|protein_coding|CODING|NM_005264.4|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.961107 rs8192661 -0.676189 0.855713 23 465 1560 MODIFIER 1 CODING GFRA1 G protein_coding NM_005264.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118033101 T G 0 46.3 0 0.9478 0.9854 0.9942 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||1560||465|GFRA1|protein_coding|CODING|NM_005264.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2577363 -0.453602 0.52 2 258 56 MODIFIER 2 CODING CCDC172 G protein_coding NM_198515.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118084468 A G 0 222 0 0.2118 0.1526 0.1671 0.2024 0.0547 0.1115 0.197977 0.107315 0.0678818 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.495018 0 . 0 . 63 19,4,22,10 UTR_5_PRIME(MODIFIER||56||258|CCDC172|protein_coding|CODING|NM_198515.2|2|G) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.999673 rs41386650 -0.69312 0.141331 63 F332L 467 Ttc/Ctc MODERATE 9 MISSENSE CODING PNLIPRP3 C protein_coding NM_001011709.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118228763 T C 0 222 0 0.3283 0.1797 0.1441 0.2341 0.0557 0.0757 0.314571 0.142055 0.0536296 1 3294 13240 1937 2189 357 4160 61 1242 2 10368 121124 11544 8632 6596 66592 906 16486 0.602616 0 . 0 . 118 28,20,36,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F332L|467|PNLIPRP3|protein_coding|CODING|NM_001011709.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.484614 rs7077408 -0.693147 0.41103 118 K362 467 aaA/aaG LOW 10 SILENT CODING PNLIPRP3 G protein_coding NM_001011709.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118231305 A G 0 222 0 0.3162 0.1797 0.1542 0.2371 0.0606 0.0767 0.308897 0.145241 0.0613954 1 3215 13906 1991 2222 368 4757 71 1282 2 10406 121402 11576 8646 6614 66740 908 16512 0.898166 0 . 0 . 198 60,33,46,36 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K362|467|PNLIPRP3|protein_coding|CODING|NM_001011709.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.749455 rs10510020 -0.693147 0.0492912 198 V381I 467 Gtt/Att MODERATE 10 MISSENSE CODING PNLIPRP3 A protein_coding NM_001011709.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118231360 G A 0 228 0 0.8691 0.9641 0.9899 1 1 1 0.888334 0.961326 0.998721 2 8578 119415 11473 8654 6614 66683 902 16511 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 162 0,0,58,87 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V381I|467|PNLIPRP3|protein_coding|CODING|NM_001011709.2|10|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10736251 -0.693147 0.000206091 162 R382G 467 Agg/Ggg MODERATE 10 MISSENSE CODING PNLIPRP3 G protein_coding NM_001011709.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118231363 A G 0 228 0 0.885 0.9685 0.9914 1 1 1 0.893781 0.963171 0.998721 2 9247 120125 11502 8654 6614 66693 903 16512 2 10400 121406 11578 8654 6614 66740 908 16512 0 . 0 . 0 163 0,0,58,88 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R382G|467|PNLIPRP3|protein_coding|CODING|NM_001011709.2|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1897519 -0.693147 0.00042857 163 F450Y 467 tTc/tAc MODERATE 12 MISSENSE CODING PNLIPRP3 A protein_coding NM_001011709.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118236610 T A 0 222 0 0.1188 0.1468 0.1801 0.3899 0.0258 0.0348 0.109396 0.043749 0.0101163 1 1109 9771 3194 3375 562 1075 61 395 2 10340 120962 11532 8610 6594 66500 906 16480 0.854469 0 . 0 . 134 26,30,30,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tAc|F450Y|467|PNLIPRP3|protein_coding|CODING|NM_001011709.2|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.845052 rs2116286 -0.693147 0.619648 134 N162 465 aaT/aaC LOW 6 SILENT CODING PNLIP C protein_coding NM_000936.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118313265 T C 0 228 0 0.8578 0.8427 0.8444 0.6667 0.9225 0.9202 0.874035 0.904275 0.919767 2 9042 106961 9685 5637 6015 60751 818 15013 2 10404 121326 11558 8622 6604 66724 906 16508 1 0 . 0 . 73 1,0,36,28 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N162|465|PNLIP|protein_coding|CODING|NM_000936.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2915748 -0.693147 0.399304 73 S388 467 agT/agC LOW 11 SILENT CODING PNLIPRP1 C protein_coding NM_001303135.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118363642 T C 0 228 0 0.5363 0.7063 0.7637 0.8988 0.6918 0.7117 0.566954 0.663386 0.712791 2 5800 87066 9288 7785 4093 47581 625 11894 2 10356 121058 11560 8646 6606 66514 904 16472 0 . 0 . 0 142 0,0,66,60 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S388|467|PNLIPRP1|protein_coding|CODING|NM_001303135.1|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3010501 -0.693147 0.0193986 142 E414D 467 gaG/gaC MODERATE 12 MISSENSE CODING PNLIPRP1 C protein_coding NM_001303135.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118364967 G C 0 222 0 0.0091 0.1254 0.0576 0.4107 0.0567 0.1074 0.0188379 0.0517453 0.0686046 1 173 11295 566 3729 453 4541 75 1758 2 10404 121362 11578 8636 6614 66716 908 16506 0.422231 0 . 0 . 143 34,27,31,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E414D|467|PNLIPRP1|protein_coding|CODING|NM_001303135.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.732877 rs2305204 -0.693147 0.24984 143 L158 469 ctA/ctG LOW 6 SILENT CODING PNLIPRP2 G protein_coding NM_005396.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118387282 A G 0 228 0 0.2375 0.3622 0.4193 0.5784 0.338 0.2924 0.238682 0.280989 0.301408 2 576 7760 846 971 188 4844 54 281 2 1482 15204 1400 1562 398 9590 94 678 0 . 0 . COSM427116,COSM427117 15 0,0,9,2 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L158|469|PNLIPRP2|protein_coding|CODING|NM_005396.4|6|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11544712 -0.676189 0.933481 15 A134 625 gcC/gcT LOW 3 SILENT CODING ENO4 T protein_coding NM_001242699.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118616110 C T 0 228 0 0.4319 0.3668 0.3559 0.4454 0.2584 0.317 0 . 0 2 255 3947 52 96 344 983 53 2164 2 594 14016 182 194 1466 3814 180 7586 0 . 0 . 0 84 0,0,38,40 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A134|625|ENO4|protein_coding|CODING|NM_001242699.1|3|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7083543 -0.693147 0.142138 84 625 216 MODIFIER 14 CODING ENO4 T protein_coding NM_001242699.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118641396 G T 0 172 0 0.0461 0.1402 0.2118 0.2044 0.1779 0.1115 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924089 0 . 0 . 19 0,9,2,7 UTR_3_PRIME(MODIFIER||216||625|ENO4|protein_coding|CODING|NM_001242699.1|14|T),DOWNSTREAM(MODIFIER||1492||631|SHTN1|protein_coding|CODING|NM_001127211.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.826105 rs11197843 -0.662043 0.0824373 19 625 897 MODIFIER 14 CODING ENO4 G protein_coding NM_001242699.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118642077 T G 0 9.7 0 0.8366 0.9551 0.987 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||897||625|ENO4|protein_coding|CODING|NM_001242699.1|14|G),DOWNSTREAM(MODIFIER||811||631|SHTN1|protein_coding|CODING|NM_001127211.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2449807 -0.379885 0 1 631 239 MODIFIER 1 CODING SHTN1 G protein_coding NM_001127211.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 118764829 T G 0 164 0 0.6104 0.8844 0.9654 0.9802 0.996 0.9836 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,1,7 UTR_5_PRIME(MODIFIER||239||631|SHTN1|protein_coding|CODING|NM_001127211.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7906476 -0.651104 0.619542 8 514 232 MODIFIER 16 CODING SLC18A2 C protein_coding NM_003054.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119037009 A C 0 228 0 0.2897 0.4521 0.5476 0.5327 0.501 0.4703 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 118 0,1,22,86 UTR_3_PRIME(MODIFIER||232||514|SLC18A2|protein_coding|CODING|NM_003054.4|16|C),DOWNSTREAM(MODIFIER||2991||1154|PDZD8|protein_coding|CODING|NM_173791.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs10377 -0.693147 0.0109768 118 514 294 MODIFIER 16 CODING SLC18A2 C protein_coding NM_003054.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119037071 T C 0 220 0 0.2897 0.4523 0.5476 0.5327 0.502 0.4703 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,1,52 UTR_3_PRIME(MODIFIER||294||514|SLC18A2|protein_coding|CODING|NM_003054.4|16|C),DOWNSTREAM(MODIFIER||2929||1154|PDZD8|protein_coding|CODING|NM_173791.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs14240,rs386491448 -0.693147 0.450188 53 514 891 MODIFIER 16 CODING SLC18A2 A protein_coding NM_003054.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119037668 G A 0 9.7 0 0.6225 0.6909 0.7608 0.5595 0.8489 0.7065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||891||514|SLC18A2|protein_coding|CODING|NM_003054.4|16|A),DOWNSTREAM(MODIFIER||2332||1154|PDZD8|protein_coding|CODING|NM_173791.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs363282 -0.379885 0 1 514 1319 MODIFIER 16 CODING SLC18A2 A protein_coding NM_003054.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119038096 T A 0 9.7 0 0.6225 0.6911 0.7608 0.5595 0.8489 0.7076 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1319||514|SLC18A2|protein_coding|CODING|NM_003054.4|16|A),DOWNSTREAM(MODIFIER||1904||1154|PDZD8|protein_coding|CODING|NM_173791.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs363235 -0.379885 0 1 514 1594 MODIFIER 16 CODING SLC18A2 T protein_coding NM_003054.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119038371 C T 0 32.6 0 0.6225 0.6909 0.7608 0.5595 0.8489 0.7065 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1594||514|SLC18A2|protein_coding|CODING|NM_003054.4|16|T),DOWNSTREAM(MODIFIER||1629||1154|PDZD8|protein_coding|CODING|NM_173791.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs363236 -0.379885 0 2 1154 2161 MODIFIER 5 CODING PDZD8 A protein_coding NM_173791.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119040618 G A 0 9.7 0 0.6225 0.6911 0.7608 0.5585 0.8489 0.7086 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2161||1154|PDZD8|protein_coding|CODING|NM_173791.4|5|A),DOWNSTREAM(MODIFIER||1677||514|SLC18A2|protein_coding|CODING|NM_003054.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2803809 -0.379885 0 1 1154 18 MODIFIER 5 CODING PDZD8 T protein_coding NM_173791.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119042761 C T 0 228 0 0.8116 0.9469 0.9798 1 0.997 1 0.846346 0.946486 0.997791 2 8751 117015 11448 8638 6614 65879 877 14808 2 10370 118846 11558 8638 6614 65976 882 14808 0 . 0 . 0 68 0,0,27,33 UTR_3_PRIME(MODIFIER||18||1154|PDZD8|protein_coding|CODING|NM_173791.4|5|T),DOWNSTREAM(MODIFIER||3820||514|SLC18A2|protein_coding|CODING|NM_003054.4||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs363293 -0.693147 0.104345 68 252 674 MODIFIER 1 CODING EMX2 A protein_coding NM_004098.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119302105 G A 0 222 0 0.2247 0.152 0.1167 0.2312 0.0905 0.0603 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.331772 0 . 0 . 95 31,10,32,11 UTR_5_PRIME(MODIFIER||674||252|EMX2|protein_coding|CODING|NM_004098.3|1|A),INTRAGENIC(MODIFIER|||||EMX2OS||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99999 rs12777466 -0.693146 0.0872423 95 252 179 MODIFIER 1 CODING EMX2 T protein_coding NM_004098.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119302600 C T 0 20.4 0 0 0.0009984 0 0.005 0 0 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||179||252|EMX2|protein_coding|CODING|NM_004098.3|1|T),INTRAGENIC(MODIFIER|||||EMX2OS||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs372863199 -0.453602 0.18 2 512 2658 MODIFIER 5 CODING RAB11FIP2 C protein_coding NM_014904.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119765851 T C 0 222 0 0.0182 0.1865 0.1844 0.1488 0.3559 0.2802 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.932191 0 . 0 . 96 12,33,8,30 UTR_3_PRIME(MODIFIER||2658||512|RAB11FIP2|protein_coding|CODING|NM_014904.2|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0492241 rs11198226 -0.693143 0.312978 96 512 2128 MODIFIER 5 CODING RAB11FIP2 T protein_coding NM_014904.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119766381 C T 0 119 0 0.0121 0.0899 0.0749 0.2927 0.0278 0.0603 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.988657 0 . 0 . 32 17,0,15,0 UTR_3_PRIME(MODIFIER||2128||512|RAB11FIP2|protein_coding|CODING|NM_014904.2|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.594648 rs2928125 -0.688148 0.0582994 32 P499 512 ccG/ccA LOW 5 SILENT CODING RAB11FIP2 T protein_coding NM_014904.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119768551 C T 0 222 0 0.6989 0.7875 0.879 0.5794 0.9602 0.8793 0.729233 0.88513 0.965 1 7535 108831 10220 5052 6133 64108 832 14951 2 10404 121366 11556 8650 6610 66728 908 16510 0.660462 0 . 0 . 80 31,6,18,11 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P499|512|RAB11FIP2|protein_coding|CODING|NM_014904.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.81168 rs7923321 -0.693079 0.036211 80 512 10 MODIFIER 1 CODING RAB11FIP2 C protein_coding NM_014904.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 119805684 T C 0 222 0 0.0938 0.1595 0.1412 0.4732 0.0298 0.0716 0.0844303 0.0475934 0.0287209 1 850 10553 2103 4140 433 2082 68 877 2 10374 119218 11548 8604 6614 66080 888 15110 0.948639 0 . 0 . 126 20,40,23,32 UTR_5_PRIME(MODIFIER||10||512|RAB11FIP2|protein_coding|CODING|NM_014904.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.402379 rs2240778 -0.693147 0.0140991 126 233 LOW 7 CODING FAM204A T protein_coding NM_001134672.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120070427 G T 0 222 0 0.1974 0.4185 0.5346 0.4464 0.5368 0.4847 0.258284 0.430801 0.519186 1 2505 57357 6128 3829 2702 33745 452 7996 2 10320 121042 11552 8616 6610 66560 906 16478 0.791193 0 . 0 . 37 6,11,5,11 SPLICE_SITE_REGION+INTRON(LOW||||233|FAM204A|protein_coding|CODING|NM_001134672.1|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.761357 rs4751651 -0.689466 0.00389177 37 I283V 370 Atc/Gtc MODERATE 2 MISSENSE CODING PRLHR C protein_coding NM_004248.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120353910 T C 0 228 0 0.9244 0.978 0.987 1 0.999 1 0.939235 0.97934 0.999883 2 8927 116198 11356 8334 6572 63890 863 16256 2 9530 116838 11368 8334 6572 63910 864 16260 0 . 0 . 0 172 0,0,71,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I283V|370|PRLHR|protein_coding|CODING|NM_004248.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1613448 -0.693147 0.0125568 172 292 868 MODIFIER 1 CODING NANOS1 C protein_coding NM_199461.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120791060 A C 0 228 0 0.9992 0.9996 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 80 0,0,30,44 UTR_3_PRIME(MODIFIER||868||292|NANOS1|protein_coding|CODING|NM_199461.3|1|C),DOWNSTREAM(MODIFIER||3481||1382|EIF3A|protein_coding|CODING|NM_003750.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs614465 -0.693147 0.126643 80 292 1587 MODIFIER 1 CODING NANOS1 T protein_coding NM_199461.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120791778 TAAATACC T 0 222 0 0.1384 0.3045 0.3674 0.4236 0.3956 0.2679 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 77 5,32,6,30 UTR_3_PRIME(MODIFIER||1587||292|NANOS1|protein_coding|CODING|NM_199461.3|1|T),DOWNSTREAM(MODIFIER||2762||1382|EIF3A|protein_coding|CODING|NM_003750.2||T) 0 0.5 1 36 0.467532 1 1 0 . 0 60 0 0 1 0 . rs3215953 -0.693139 0.903002 77 292 2492 MODIFIER 1 CODING NANOS1 G protein_coding NM_199461.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120792684 A G 0 228 0 0.6498 0.8838 0.9726 0.9415 0.997 0.9611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 66 0,0,55,7 UTR_3_PRIME(MODIFIER||2492||292|NANOS1|protein_coding|CODING|NM_199461.3|1|G),DOWNSTREAM(MODIFIER||1857||1382|EIF3A|protein_coding|CODING|NM_003750.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs546753 -0.693147 0.00716286 66 292 2511 MODIFIER 1 CODING NANOS1 A protein_coding NM_199461.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120792703 C A 0 228 0 0.4175 0.7969 0.9207 0.8839 0.9692 0.955 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 83 0,0,60,11 UTR_3_PRIME(MODIFIER||2511||292|NANOS1|protein_coding|CODING|NM_199461.3|1|A),DOWNSTREAM(MODIFIER||1838||1382|EIF3A|protein_coding|CODING|NM_003750.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386598755,rs546808 -0.693147 0.227369 83 1382 285 MODIFIER 22 CODING EIF3A T protein_coding NM_003750.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120795266 G T 0 228 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,25,15 UTR_3_PRIME(MODIFIER||285||1382|EIF3A|protein_coding|CODING|NM_003750.2|22|T),DOWNSTREAM(MODIFIER||2022||292|NANOS1|protein_coding|CODING|NM_199461.3||T) 0 . 0 . 0 . 0 . 0 . 46 0 0 7.06374e-05 0 . rs1147627 -0.693145 0.0717185 40 D313 1382 gaT/gaC LOW 6 SILENT CODING EIF3A G protein_coding NM_003750.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120828969 A G 0 228 0 0.3949 0.7905 0.9193 0.8829 0.9692 0.955 0.514526 0.818007 0.973488 2 4939 111595 11039 7645 6521 64765 868 15818 2 10242 120798 11510 8596 6608 66462 902 16478 0 . 0 . 0 122 0,0,84,25 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D313|1382|EIF3A|protein_coding|CODING|NM_003750.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7908387 -0.693147 0.0832762 122 357 LOW 6 CODING FAM45A C protein_coding NM_207009.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120889022 T C 0 215 0 0.0772 0.2792 0.2954 0.3919 0.4235 0.2761 0.140263 0.325235 0.42 1 1327 44172 3296 3359 3083 27676 346 5085 2 10232 119678 11264 8560 6556 65986 892 16188 0.898208 0 . 0 . 76 31,8,30,3 SPLICE_SITE_REGION+INTRON(LOW||||357|FAM45A|protein_coding|CODING|NM_207009.3|6|C),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.348359 rs3802739 -0.693127 0.25246 76 P314 357 ccG/ccA LOW 9 SILENT CODING FAM45A A protein_coding NM_207009.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120896027 G A 0 228 0 0.7194 0.9024 0.9236 0.9534 0.9911 0.9908 0 . 0 2 7593 116622 10935 8299 6595 66032 879 16289 2 10080 121016 11576 8654 6614 66682 906 16504 0 . 0 . 0 91 0,0,63,16 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P314|357|FAM45A|protein_coding|CODING|NM_207009.3|9|A),DOWNSTREAM(MODIFIER||4398||337|SFXN4|protein_coding|CODING|NM_213649.1||A),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||A) 0 . 0 . 0 1 0 . 1 0 58 0 0 0.958048 0 . rs11198799 -0.693147 2.08834e-06 91 357 768 MODIFIER 9 CODING FAM45A A protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120896927 G A 0 46.4 0 0.4788 0.5787 0.6196 0.5615 0.5666 0.7147 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.985665 0 . 0 . 16 9,2,3,2 UTR_3_PRIME(MODIFIER||768||357|FAM45A|protein_coding|CODING|NM_207009.3|9|A),DOWNSTREAM(MODIFIER||3498||337|SFXN4|protein_coding|CODING|NM_213649.1||A),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 49 0 0.214015 0.191205 0 0.960687 rs61874337 -0.590765 0.494358 16 357 904 MODIFIER 9 CODING FAM45A T protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120897063 C T 0 222 0 0.702 0.6597 0.6859 0.6081 0.5755 0.7239 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.566573 0 . 0 . 91 32,24,18,11 UTR_3_PRIME(MODIFIER||904||357|FAM45A|protein_coding|CODING|NM_207009.3|9|T),DOWNSTREAM(MODIFIER||3362||337|SFXN4|protein_coding|CODING|NM_213649.1||T),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 54 0 2.9197e-05 0.999004 0 0.636767 rs4751697 -0.693079 0.0500145 91 357 992 MODIFIER 9 CODING FAM45A T protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120897151 C T 0 155 0 0.7012 0.6585 0.6844 0.6052 0.5755 0.7229 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998066 0 . 0 . 51 14,17,9,9 UTR_3_PRIME(MODIFIER||992||357|FAM45A|protein_coding|CODING|NM_207009.3|9|T),DOWNSTREAM(MODIFIER||3274||337|SFXN4|protein_coding|CODING|NM_213649.1||T),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 49 0 4.39283e-06 0.849597 0 0.961565 rs1048713,rs34073025 -0.691153 0.286472 51 357 1020 MODIFIER 9 CODING FAM45A C protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120897179 T C 0 222 0 0.0855 0.2813 0.2954 0.3948 0.4185 0.2781 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.976069 0 . 0 . 66 13,15,13,18 UTR_3_PRIME(MODIFIER||1020||357|FAM45A|protein_coding|CODING|NM_207009.3|9|C),DOWNSTREAM(MODIFIER||3246||337|SFXN4|protein_coding|CODING|NM_213649.1||C),INTRAGENIC(MODIFIER|||||FAM45BP||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 46 0 0.000510688 0.222812 0 0.545769 rs10886401 -0.69311 0.942311 66 357 1223 MODIFIER 9 CODING FAM45A A protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120897382 G A 0 228 0 0.9985 0.9994 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,29,15 UTR_3_PRIME(MODIFIER||1223||357|FAM45A|protein_coding|CODING|NM_207009.3|9|A),DOWNSTREAM(MODIFIER||3043||337|SFXN4|protein_coding|CODING|NM_213649.1||A) 0 . 0 . 0 1 0 . 0 . 50 0 0 0.0031734 0 . rs11198800 -0.693146 0.668208 44 357 1320 MODIFIER 9 CODING FAM45A G protein_coding NM_207009.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120897479 A G 0 222 0 0.7148 0.6633 0.6859 0.6081 0.5765 0.7239 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.890185 0 . 0 . 62 8,27,5,16 UTR_3_PRIME(MODIFIER||1320||357|FAM45A|protein_coding|CODING|NM_207009.3|9|G),DOWNSTREAM(MODIFIER||2946||337|SFXN4|protein_coding|CODING|NM_213649.1||G) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.977871 0.880474 0 0.451635 rs34179455 -0.692352 0.226437 62 337 LOW 7 CODING SFXN4 A protein_coding NM_213649.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120917445 G A 0 222 0 0.4546 0.51 0.4856 0.7123 0.4632 0.4417 0.446664 0.482393 0.500698 1 4555 60234 5289 6206 2937 33492 441 7314 2 10402 121360 11572 8636 6614 66724 908 16504 0.983017 0 . 0 . 99 19,21,24,28 SPLICE_SITE_REGION+INTRON(LOW||||337|SFXN4|protein_coding|CODING|NM_213649.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969692 rs2275111 -0.693147 0.114958 99 A118 337 gcA/gcG LOW 6 SILENT CODING SFXN4 C protein_coding NM_213649.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120919246 T C 0 228 0 0.9418 0.983 0.9885 1 1 1 0.949387 0.982162 0.998953 2 9851 120795 11544 8654 6614 66718 903 16511 2 10406 121408 11576 8654 6614 66740 906 16512 0 . 0 . 0 86 0,0,34,42 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A118|337|SFXN4|protein_coding|CODING|NM_213649.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2181118 -0.693147 0.301908 86 Q86 337 caA/caG LOW 4 SILENT CODING SFXN4 C protein_coding NM_213649.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120920588 T C 0 222 0 0.4349 0.4944 0.4496 0.7163 0.4374 0.4366 0.431457 0.466861 0.485 1 4404 58463 5052 6223 2798 32308 414 7264 2 10380 121312 11558 8648 6614 66696 906 16510 0.967358 0 . 0 . 98 8,36,7,43 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q86|337|SFXN4|protein_coding|CODING|NM_213649.1|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976952 rs10749291 -0.693147 0.000649172 98 256 778 MODIFIER 7 CODING PRDX3 A protein_coding NM_006793.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120927214 C A 0 6.3 0 0.9849 0.9954 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||778||256|PRDX3|protein_coding|CODING|NM_006793.4|7|A),UPSTREAM(MODIFIER||2010||337|SFXN4|protein_coding|CODING|NM_213649.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6585537 -0.379885 0 1 256 199 MODIFIER 7 CODING PRDX3 C protein_coding NM_006793.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120927793 G C 0 228 0 0.4849 0.3916 0.2983 0.5724 0.3072 0.2321 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 0,0,25,3 UTR_3_PRIME(MODIFIER||199||256|PRDX3|protein_coding|CODING|NM_006793.4|7|C),UPSTREAM(MODIFIER||2589||337|SFXN4|protein_coding|CODING|NM_213649.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7768 -0.693054 0.00801056 28 D124 256 gaC/gaT LOW 4 SILENT CODING PRDX3 A protein_coding NM_006793.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 120933324 G A 0 228 0 0.938 0.9533 0.9337 0.9127 0.997 0.9847 0.944167 0.975165 0.991046 2 9824 118148 10443 7964 6607 66189 886 16235 2 10406 121404 11574 8654 6614 66736 908 16512 0 . 0 . 0 202 0,0,106,75 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D124|256|PRDX3|protein_coding|CODING|NM_006793.4|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3758609 -0.693147 0.242341 202 590 LOW 2 CODING GRK5 T protein_coding NM_005308.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121140321 C T 0 11.9 0 0.2057 0.2051 0.0879 0.37 0.1312 0.1933 0.169768 0.147163 0.135581 1 1785 18983 823 3350 714 8842 140 3329 2 10364 120592 11558 8626 6608 66476 900 16060 0.998439 0 . 0 . 21 14,2,3,0 SPLICE_SITE_REGION+INTRON(LOW||||590|GRK5|protein_coding|CODING|NM_005308.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.703588 rs2275036 -0.511536 0.450604 21 R304H 590 cGt/cAt MODERATE 9 MISSENSE CODING GRK5 A protein_coding NM_005308.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121196335 G A 0 222 0 0.0023 0.1258 0.0951 0.2827 0.0755 0.2045 0.0226963 0.0736583 0.0997674 1 206 12870 1165 2244 398 6148 81 2628 2 10158 116318 11446 8580 6528 64954 852 13800 0.702097 0 . 0 . 121 15,50,11,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R304H|590|GRK5|protein_coding|CODING|NM_005308.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.822295 rs2230349 -0.693147 0.00073538 121 P334 575 ccT/ccG LOW 4 SILENT CODING BAG3 G protein_coding NM_004281.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121436068 T G 0 228 0 0.1664 0.1558 0.1744 0.254 0.0964 0.0879 0.170676 0.1161 0.0881395 2 1720 13883 2076 2332 681 5642 123 1309 2 10398 121360 11576 8628 6612 66728 908 16510 0 2 benign 0 . 62 0,0,25,30 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P334|575|BAG3|protein_coding|CODING|NM_004281.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3858339 -0.693147 0.0543998 62 P407L 575 cCt/cTt MODERATE 4 MISSENSE CODING BAG3 T protein_coding NM_004281.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121436286 C T 0 228 0 0.1664 0.1556 0.1744 0.253 0.0964 0.0879 0.170449 0.115716 0.0876744 2 1711 13824 2069 2322 681 5621 123 1297 2 10376 121204 11566 8630 6612 66608 904 16508 0 2 benign 0 . 43 0,0,22,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P407L|575|BAG3|protein_coding|CODING|NM_004281.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3858340 -0.693146 0.170583 43 V432 575 gtA/gtG LOW 4 SILENT CODING BAG3 G protein_coding NM_004281.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121436362 A G 0 228 0 0.7534 0.7065 0.7219 0.4881 0.8012 0.7597 0.753064 0.770337 0.779186 2 7813 89871 7297 4499 4822 52138 693 12609 2 10394 121300 11564 8638 6606 66680 908 16510 0.914894 2 benign 0 . 55 1,1,27,20 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V432|575|BAG3|protein_coding|CODING|NM_004281.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.819149 rs196295 -0.693147 0.0676788 55 575 218 MODIFIER 4 CODING BAG3 C protein_coding NM_004281.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121437012 G C 0 83 0 0.3941 0.3544 0.3501 0.3512 0.3618 0.2996 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||218||575|BAG3|protein_coding|CODING|NM_004281.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs8946 -0.556411 0.26019 4 N997D 1132 Aat/Gat MODERATE 20 MISSENSE CODING INPP5F G protein_coding NM_014937.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121586882 A G 0 222 0 0.2678 0.269 0.2824 0.1796 0.337 0.2832 0.264185 0.30855 0.331279 1 2719 35522 2747 1685 2211 21545 312 4303 2 10404 121358 11556 8650 6614 66720 908 16506 0.928652 0 . 0 COSM147061 94 27,18,26,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N997D|1132|INPP5F|protein_coding|CODING|NM_014937.3|20|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N387D|522|INPP5F|protein_coding|CODING|NM_001243194.1|6|G),DOWNSTREAM(MODIFIER||2034||642|MCMBP|protein_coding|CODING|NM_024834.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948792 rs3188055 -0.693145 0.0444922 94 N387D 522 Aat/Gat MODERATE 6 MISSENSE CODING INPP5F G protein_coding NM_001243194.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121586882 A G 0 222 0 0.2678 0.269 0.2824 0.1796 0.337 0.2832 0.264185 0.30855 0.331279 1 2719 35522 2747 1685 2211 21545 312 4303 2 10404 121358 11556 8650 6614 66720 908 16506 0.928652 0 . 0 COSM147061 94 27,18,26,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N997D|1132|INPP5F|protein_coding|CODING|NM_014937.3|20|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N387D|522|INPP5F|protein_coding|CODING|NM_001243194.1|6|G),DOWNSTREAM(MODIFIER||2034||642|MCMBP|protein_coding|CODING|NM_024834.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948792 rs3188055 -0.693145 0.0444922 94 1132 909 MODIFIER 20 CODING INPP5F C protein_coding NM_014937.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121588201 T C 0 9.7 0 0.6241 0.5252 0.5937 0.6319 0.501 0.2577 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||909||1132|INPP5F|protein_coding|CODING|NM_014937.3|20|C),UTR_3_PRIME(MODIFIER||909||522|INPP5F|protein_coding|CODING|NM_001243194.1|6|C),DOWNSTREAM(MODIFIER||715||642|MCMBP|protein_coding|CODING|NM_024834.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1129793 -0.379885 0 1 522 909 MODIFIER 6 CODING INPP5F C protein_coding NM_001243194.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121588201 T C 0 9.7 0 0.6241 0.5252 0.5937 0.6319 0.501 0.2577 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||909||1132|INPP5F|protein_coding|CODING|NM_014937.3|20|C),UTR_3_PRIME(MODIFIER||909||522|INPP5F|protein_coding|CODING|NM_001243194.1|6|C),DOWNSTREAM(MODIFIER||715||642|MCMBP|protein_coding|CODING|NM_024834.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1129793 -0.379885 0 1 642 1584 MODIFIER 16 CODING MCMBP G protein_coding NM_024834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121589402 T G 0 133 0 0.5038 0.4912 0.5778 0.6319 0.5 0.2587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.208094 0 . 0 . 42 27,0,14,1 UTR_3_PRIME(MODIFIER||1584||642|MCMBP|protein_coding|CODING|NM_024834.3|16|G),DOWNSTREAM(MODIFIER||740||1132|INPP5F|protein_coding|CODING|NM_014937.3||G),DOWNSTREAM(MODIFIER||740||522|INPP5F|protein_coding|CODING|NM_001243194.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.846409 rs6881 -0.688148 0.80042 42 K644E 1000 Aaa/Gaa MODERATE 11 MISSENSE CODING SEC23IP G protein_coding NM_007190.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121679013 A G 0 222 0 0.7821 0.7514 0.7248 0.8363 0.671 0.7239 0.778938 0.708519 0.672442 1 8158 86906 8864 7065 4403 45479 607 12330 2 10392 121314 11564 8640 6612 66690 908 16508 0.950908 0 . 0 . 83 22,18,27,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K644E|1000|SEC23IP|protein_coding|CODING|NM_007190.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.694993 rs2475298 -0.693139 0.55499 83 1000 7881 MODIFIER 19 CODING SEC23IP T protein_coding NM_007190.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 121701160 G T 0 214 0 0.0651 0.1352 0.2262 0.0813 0.2495 0.1033 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.797754 0 . 0 . 70 34,8,17,6 UTR_3_PRIME(MODIFIER||7881||1000|SEC23IP|protein_coding|CODING|NM_007190.3|19|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.470559 rs10686 -0.692717 0.280152 70 271 28 MODIFIER 1 CODING PLPP4 T protein_coding NM_001030059.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122216790 A T 0 228 0 0.5968 0.6947 0.7522 0.625 0.7336 0.818 0.68734 0.744642 0.770779 2 1054 12181 222 252 11 4566 108 5968 2 1618 16506 296 384 14 6314 162 7718 0 . 0 . 0 76 0,0,63,4 UTR_5_PRIME(MODIFIER||28||271|PLPP4|protein_coding|CODING|NM_001030059.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10886691 -0.693147 0.00174232 76 I8 271 atC/atT LOW 1 SILENT CODING PLPP4 T protein_coding NM_001030059.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122216841 C T 0 222 0 0 0.0027955 0 0.0139 0 0 0 . 0 1 0 7 0 7 0 0 0 0 2 1894 17940 356 502 30 7120 172 7866 0.742002 0 . 0 . 121 42,13,33,12 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I8|271|PLPP4|protein_coding|CODING|NM_001030059.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0995963 rs192701942 -0.693147 0.577309 121 1224 LOW 2 CODING WDR11 C protein_coding NM_018117.11 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122618148 G C 0 222 0 0.0257 0.1843 0.2925 0.3472 0.1571 0.182 0.0508398 0.142857 0.19 1 531 23876 4608 2979 764 12153 153 2688 2 10400 121170 11516 8606 6604 66658 908 16478 0.79421 0 . 0 COSM147065 115 44,13,35,8 SPLICE_SITE_REGION+INTRON(LOW||||1224|WDR11|protein_coding|CODING|NM_018117.11|2|C),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.000637148 rs2241846 -0.693146 0.35474 115 T278 1224 acG/acA LOW 6 SILENT CODING WDR11 A protein_coding NM_018117.11 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122624679 G A 0 222 0 0.171 0.3229 0.4063 0.4177 0.333 0.3609 0.179755 0.282793 0.335581 1 1900 41495 6069 3657 1874 22431 310 5254 2 10404 121356 11564 8646 6610 66718 908 16506 0.580197 0 . 0 COSM147066 168 38,37,40,31 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T278|1224|WDR11|protein_coding|CODING|NM_018117.11|6|A),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904394 rs10886789 -0.693147 0.0537459 168 A633 1224 gcA/gcT LOW 15 SILENT CODING WDR11 T protein_coding NM_018117.11 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122645376 A T 0 222 0 0.4297 0.3956 0.4366 0.4177 0.334 0.3609 0.418974 0.364447 0.336512 1 4343 44136 6193 3659 1875 22484 322 5260 2 10406 121362 11558 8634 6612 66734 908 16510 0.407353 0 . 0 COSM147067 138 31,40,31,25 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcT|A633|1224|WDR11|protein_coding|CODING|NM_018117.11|15|T),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.541797 rs7899928 -0.693147 0.125683 138 L986 1224 ctG/ctA LOW 24 SILENT CODING WDR11 A protein_coding NM_018117.11 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122663585 G A 0 116 0 0.8752 0.6765 0.6657 0.5179 0.6511 0.6053 0.859283 0.72382 0.654419 1 8870 80381 7925 4557 4401 44292 585 9751 2 10342 120976 11544 8624 6608 66470 904 16484 0.893388 0 . 0 . 37 17,1,14,0 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L986|1224|WDR11|protein_coding|CODING|NM_018117.11|24|A),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0225417 rs1652727 -0.686358 0.0403175 37 V1121 1224 gtC/gtG LOW 27 SILENT CODING WDR11 G protein_coding NM_018117.11 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122665459 C G 0 222 0 0.0129 0.1552 0.2305 0.3373 0.1093 0.1534 0.0326827 0.096417 0.12907 1 324 18169 3856 2971 422 8262 99 2235 2 10406 121388 11570 8642 6614 66736 908 16512 0.296344 0 . 0 COSM147069 81 16,21,17,17 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V1121|1224|WDR11|protein_coding|CODING|NM_018117.11|27|G),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.602197 rs3740307 -0.693132 0.0479859 81 1224 71 MODIFIER 29 CODING WDR11 A protein_coding NM_018117.11 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122668296 G A 0 222 0 0.4523 0.4016 0.4366 0.4177 0.334 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.84006 0 . 0 COSN163791 82 13,27,13,28 UTR_3_PRIME(MODIFIER||71||1224|WDR11|protein_coding|CODING|NM_018117.11|29|A),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.927743 rs7077126 -0.693145 0.0242656 82 1224 187 MODIFIER 29 CODING WDR11 A protein_coding NM_018117.11 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122668412 G A 0 222 0 0.025 0.1841 0.2925 0.3472 0.1571 0.182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.687798 0 . 0 . 121 41,16,39,9 UTR_3_PRIME(MODIFIER||187||1224|WDR11|protein_coding|CODING|NM_018117.11|29|A),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.284483 rs10886800 -0.693147 0.889657 121 1224 379 MODIFIER 29 CODING WDR11 A protein_coding NM_018117.11 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122668604 G A 0 222 0 0.1921 0.3289 0.4092 0.4177 0.333 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.978165 0 . 0 . 92 19,28,7,26 UTR_3_PRIME(MODIFIER||379||1224|WDR11|protein_coding|CODING|NM_018117.11|29|A),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.777997 rs1045154 -0.693127 0.159096 92 1224 557 MODIFIER 29 CODING WDR11 T protein_coding NM_018117.11 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122668782 G T 0 221 0 0.1921 0.3291 0.4092 0.4187 0.333 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960687 0 . 0 . 33 9,6,13,4 UTR_3_PRIME(MODIFIER||557||1224|WDR11|protein_coding|CODING|NM_018117.11|29|T),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982333 rs1045170 -0.690438 0.30061 33 1224 576 MODIFIER 29 CODING WDR11 C protein_coding NM_018117.11 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 122668801 A C 0 193 0 0.4523 0.4016 0.4366 0.4177 0.334 0.3609 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8246 0 . 0 . 34 13,5,12,4 UTR_3_PRIME(MODIFIER||576||1224|WDR11|protein_coding|CODING|NM_018117.11|29|C),INTRAGENIC(MODIFIER|||||MIR5694||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.627089 rs1045179 -0.689466 0.652411 34 822 259 MODIFIER 18 CODING FGFR2 A protein_coding NM_022970.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123239112 G A 0 222 0 0.0938 0.4143 0.6873 0.3512 0.5099 0.6207 0.171243 0.434516 0.549026 1 350 10843 305 259 27 5017 112 4773 2 2222 20418 446 670 44 8956 196 7884 0.732509 0 . 0 COSM147070 121 27,24,20,36 UTR_3_PRIME(MODIFIER||259||822|FGFR2|protein_coding|CODING|NM_022970.3|18|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.530594 rs1047057,rs386513156 -0.693147 0.151926 121 V232 822 gtA/gtG LOW 6 SILENT CODING FGFR2 C protein_coding NM_022970.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123298158 T C 0 228 0 0.7322 0.7953 0.7997 0.9355 0.7903 0.7382 0.747844 0.766723 0.776395 2 7778 94636 9477 7982 4937 51451 722 12289 2 10402 121378 11574 8644 6614 66724 908 16512 0 . 0 . 0 122 0,0,41,70 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V232|822|FGFR2|protein_coding|CODING|NM_022970.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1047100 -0.693147 0.00434867 122 V12M 822 Gtg/Atg MODERATE 2 MISSENSE CODING FGFR2 T protein_coding NM_022970.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123353298 C T 0 222 0 0.0038 0.0011981 0.0014 0 0 0 0.00136178 0.000538213 0.000116279 1 19 36 1 13 0 3 0 0 2 10370 121204 11538 8652 6614 66612 906 16512 0.98934 1 not-provided 0 COSM1134982,COSM465368,COSM465367,COSM465369 216 80,37,52,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V12M|822|FGFR2|protein_coding|CODING|NM_022970.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.228509 rs143978938 -0.693147 0.615076 216 518 263 MODIFIER 12 CODING ATE1 A protein_coding NM_001001976.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123502932 G A 0 67 0 0.8669 0.9627 0.9914 1 0.995 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||263||518|ATE1|protein_coding|CODING|NM_001001976.2|12|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1219497 -0.511536 0.267404 3 P457 518 ccA/ccC LOW 11 SILENT CODING ATE1 G protein_coding NM_001001976.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123549691 T G 0 222 0 0.4879 0.5016 0.4813 0.5387 0.4284 0.5716 0.479346 0.456482 0.444767 1 4889 56943 5199 4824 3073 29781 423 8754 2 10406 121316 11556 8632 6610 66694 908 16510 0.985705 0 . 0 . 117 26,29,33,21 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P457|518|ATE1|protein_coding|CODING|NM_001001976.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.762528 rs35350755 -0.693147 0.379983 117 S412 518 tcA/tcG LOW 10 SILENT CODING ATE1 C protein_coding NM_001001976.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123596254 T C 0 228 0 0.8828 0.8892 0.7867 0.9256 0.9225 0.8988 0.872098 0.909707 0.928954 2 8709 108535 8648 8046 6100 61515 834 14683 2 10064 120870 11518 8652 6610 66614 902 16510 0 . 0 . 0 151 0,0,87,45 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S412|518|ATE1|protein_coding|CODING|NM_001001976.2|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4237536 -0.693147 0.0417437 151 518 LOW 9 CODING ATE1 G protein_coding NM_001001976.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123600590 A G 0 222 0 0.0401 0.116 0.1369 0.1815 0.167 0.0838 0.0517476 0.133784 0.175814 1 528 17380 1338 1638 884 11290 125 1577 2 9036 105472 10808 7640 6308 59572 790 11318 0.712176 0 . 0 . 427 143,58,136,42 SPLICE_SITE_REGION+INTRON(LOW||||518|ATE1|protein_coding|CODING|NM_001001976.2|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.753407 rs10886994 -0.693147 0.0390029 427 L101 518 ctA/ctG LOW 4 SILENT CODING ATE1 C protein_coding NM_001001976.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123673339 T C 0 228 0 0.9017 0.8992 0.7839 0.9286 0.9245 0.9213 0.889923 0.91527 0.928256 2 9217 109554 8708 8058 6066 61618 839 15048 2 10398 121324 11562 8652 6614 66688 906 16504 0 . 0 . 0 81 0,0,25,48 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L101|518|ATE1|protein_coding|CODING|NM_001001976.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10749435 -0.693147 0.51646 81 385 2121 MODIFIER 11 CODING NSMCE4A A protein_coding NM_017615.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123716730 G A 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 136 0,0,40,83 UTR_3_PRIME(MODIFIER||2121||385|NSMCE4A|protein_coding|CODING|NM_017615.2|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7099895 -0.693147 0.0707994 136 385 LOW 2 CODING NSMCE4A G protein_coding NM_017615.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123733511 C G 0 222 0 0.0408 0.1056 0.1427 0.1458 0.1551 0.0746 0.0496357 0.12373 0.161587 1 306 9353 929 811 480 5696 85 1046 2 4370 46658 4400 3166 2138 22586 404 9594 0.82073 0 . 0 . 53 17,8,10,5 SPLICE_SITE_REGION+INTRON(LOW||||385|NSMCE4A|protein_coding|CODING|NM_017615.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.611522 rs10887034 -0.688148 0.38995 53 V170I 2948 Gtc/Atc MODERATE 4 MISSENSE CODING TACC2 A protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123842523 G A 0 222 0 0.3101 0.2053 0.1902 0.0992 0.2087 0.18 0.341126 0.262956 0.222907 1 3461 25358 1418 912 1413 15119 181 2854 2 10050 118894 11466 8478 6556 64988 886 16470 0.5961 0 . 0 . 47 10,11,13,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V170I|2948|TACC2|protein_coding|CODING|NM_206862.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.866804 rs11200385 -0.692067 0.530999 47 L830F 2948 Ctc/Ttc MODERATE 4 MISSENSE CODING TACC2 T protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123844503 C T 0 222 0 0.2882 0.1841 0.17 0.0982 0.1829 0.1431 0.313436 0.228817 0.185465 1 3281 21792 1251 916 1130 12672 147 2395 2 10402 121366 11576 8642 6614 66714 908 16510 0.818522 0 . 0 . 66 17,14,17,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L830F|2948|TACC2|protein_coding|CODING|NM_206862.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973376 rs10887063 -0.692976 0.233483 66 A1066T 2948 Gcc/Acc MODERATE 4 MISSENSE CODING TACC2 A protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123845211 G A 0 222 0 0.1929 0.1386 0.1499 0.0913 0.17 0.0736 0.225148 0.187096 0.167597 1 2262 18194 1080 851 1062 11442 122 1375 2 10142 120152 11548 8604 6588 65862 902 16506 0.713552 0 . 0 . 103 22,24,28,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1066T|2948|TACC2|protein_coding|CODING|NM_206862.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823536 rs11200387 -0.693147 0.388328 103 W1103R 2948 Tgg/Cgg MODERATE 4 MISSENSE CODING TACC2 C protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123845322 T C 0 228 0 0.9576 0.9882 0.9957 1 1 1 0.966409 0.988313 0.999535 2 10023 120764 11547 8651 6614 66607 903 16419 2 10384 121190 11576 8652 6614 66640 904 16420 0 . 0 . 0 88 0,0,39,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W1103R|2948|TACC2|protein_coding|CODING|NM_206862.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7073433 -0.693147 0.777143 88 L1294 2948 ctG/ctC LOW 4 SILENT CODING TACC2 C protein_coding NM_206862.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123845897 G C 0 222 0 0.2973 0.2045 0.1916 0.1022 0.2167 0.181 0.33182 0.263955 0.229186 1 3401 25869 1405 941 1447 15564 184 2927 2 10214 120062 11472 8574 6550 65882 898 16472 0.99713 0 . 0 . 43 13,10,9,10 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L1294|2948|TACC2|protein_coding|CODING|NM_206862.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99992 rs1106992 -0.69168 0.616514 43 A1425T 2948 Gcc/Acc MODERATE 4 MISSENSE CODING TACC2 A protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123846288 G A 0 222 0 0.3071 0.2047 0.1844 0.1002 0.2117 0.181 0.343849 0.264955 0.224535 1 3558 25736 1406 930 1428 15329 183 2902 2 10376 121050 11542 8630 6606 66502 902 16492 0.787695 0 . 0 . 62 16,17,13,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1425T|2948|TACC2|protein_coding|CODING|NM_206862.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.698063 rs4752642 -0.692914 0.104197 62 Q1490 2948 caA/caG LOW 4 SILENT CODING TACC2 G protein_coding NM_206862.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123846485 A G 0 222 0 0.3071 0.2049 0.1844 0.1012 0.2117 0.181 0.343849 0.264955 0.224535 1 3551 25746 1414 932 1426 15338 184 2901 2 10330 121016 11566 8628 6608 66474 906 16504 0.998263 0 . 0 . 96 29,21,25,13 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1490|2948|TACC2|protein_coding|CODING|NM_206862.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.919926 rs4751871 -0.693143 0.685533 96 P1615 2948 ccC/ccT LOW 4 SILENT CODING TACC2 T protein_coding NM_206862.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123846860 C T 0 222 0 0.2859 0.1989 0.1844 0.1002 0.2107 0.181 0.31911 0.256497 0.224419 1 3302 25438 1389 924 1428 15322 182 2891 2 10368 121120 11566 8632 6612 66530 906 16506 0.99551 0 . 0 COSM1346385 53 22,7,15,4 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1615|2948|TACC2|protein_coding|CODING|NM_206862.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.586504 rs11599291 -0.69168 0.467677 53 G1780 2948 ggG/ggA LOW 4 SILENT CODING TACC2 A protein_coding NM_206862.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123847355 G A 0 222 0 0.2867 0.2007 0.1844 0.1002 0.2187 0.181 0.320699 0.259573 0.228256 1 3222 23710 1391 902 1429 14943 162 1661 2 9916 108622 11346 8386 6538 62612 786 9038 0.872005 0 . 0 COSM1346386 70 14,23,11,16 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1780|2948|TACC2|protein_coding|CODING|NM_206862.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.920204 rs10788237 -0.693021 0.271314 70 A2732T 2948 Gct/Act MODERATE 17 MISSENSE CODING TACC2 A protein_coding NM_206862.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 123996976 G A 0 228 0 0.1286 0.2692 0.2925 0.2351 0.339 0.4059 0.159101 0.253652 0.302093 2 1622 36699 3464 2065 2018 20695 277 6558 2 10388 121184 11544 8620 6600 66624 906 16502 0 . 0 . 0 58 0,0,48,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2732T|2948|TACC2|protein_coding|CODING|NM_206862.3|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2295879 -0.693147 0.26399 58 2948 33 MODIFIER 23 CODING TACC2 A protein_coding NM_206862.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124013604 C A 0 222 0 0.2231 0.2616 0.2622 0.249 0.2575 0.3303 0.243305 0.236276 0.232674 1 2625 32690 3308 2312 1923 16656 213 5653 2 10394 121140 11562 8626 6592 66580 902 16484 0.801667 0 . 0 . 164 32,47,32,27 UTR_3_PRIME(MODIFIER||33||2948|TACC2|protein_coding|CODING|NM_206862.3|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.885667 rs3763763 -0.693147 0.24714 164 R318Q 506 cGg/cAg MODERATE 11 MISSENSE CODING BTBD16 A protein_coding NM_144587.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124089036 G A 0 222 0 0.5976 0.616 0.6037 0.8671 0.5099 0.5 0.605311 0.542903 0.51093 1 6251 68052 7490 7428 3926 34255 497 8205 2 10398 121352 11568 8644 6614 66708 908 16512 0.854206 0 . 0 . 129 31,28,35,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R318Q|506|BTBD16|protein_coding|CODING|NM_144587.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965106 rs2421013 -0.693147 0.0254858 129 G331D 506 gGc/gAc MODERATE 11 MISSENSE CODING BTBD16 A protein_coding NM_144587.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124089075 G A 0 222 0 0.0113 0.0958 0.0764 0.1687 0.1044 0.1401 0.0263277 0.0929571 0.127093 1 239 13345 622 1392 593 8115 106 2278 2 10354 120788 11516 8600 6560 66484 906 16368 0.726068 0 . 0 . 128 23,38,24,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G331D|506|BTBD16|protein_coding|CODING|NM_144587.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.908298 rs986178 -0.693147 0.681328 128 R233 404 cgT/cgC LOW 9 SILENT CODING PLEKHA1 C protein_coding NM_001001974.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124183732 T C 0 228 0 0.9834 0.9403 0.9179 1 0.8181 0.9622 0.960281 0.881747 0.841512 2 9811 105520 10433 8561 5526 55063 762 15364 2 10134 118772 11242 8564 6558 65268 884 16122 0 . 0 . 0 77 0,0,60,13 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R233|404|PLEKHA1|protein_coding|CODING|NM_001001974.2|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4405249 -0.693147 6.52228e-21 77 480 LOW 8 CODING HTRA1 A protein_coding NM_002775.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124271589 G A 0 228 0 0.9977 0.9994 1 1 1 1 0.998184 0.999385 1 2 10368 121365 11576 8654 6614 66733 908 16512 2 10382 121384 11578 8654 6614 66736 908 16512 0 . 0 . 0 68 0,0,34,26 SPLICE_SITE_REGION+INTRON(LOW||||480|HTRA1|protein_coding|CODING|NM_002775.4|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2672586 -0.693147 0.378966 68 2413 93 MODIFIER 1 CODING DMBT1 C protein_coding NM_007329.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124320194 T C 0 148 0 0.5756 0.6991 0.7824 0.752 0.6819 0.7699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.6456 0 . 0 . 62 30,4,21,0 UTR_5_PRIME(MODIFIER||93||2413|DMBT1|protein_coding|CODING|NM_007329.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.321164 rs2981745 -0.692352 0.212334 62 2413 LOW 1 CODING DMBT1 A protein_coding NM_007329.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124320355 G A 0 222 0 0.0424 0.0433 0.0029 0.1389 0.001 0.0184 0.0333519 0.0104149 0.000246427 1 109 430 1 206 0 4 3 107 2 2822 27166 722 1328 1804 12100 284 8106 0.795523 0 . 0 . 80 17,27,9,20 SPLICE_SITE_REGION+INTRON(LOW||||2413|DMBT1|protein_coding|CODING|NM_007329.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.202635 rs79078159 -0.693079 0.00483411 80 2413 LOW 2 CODING DMBT1 C protein_coding NM_007329.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124329672 T C 0 222 0 0.612 0.7057 0.7882 0.7758 0.6789 0.729 0.201787 0.237795 0.254431 1 6148 86417 9959 6775 4873 45753 674 12235 2 9798 120714 11574 8608 6614 66710 898 16512 0.264672 0 . 0 . 129 39,22,27,26 SPLICE_SITE_REGION+INTRON(LOW||||2413|DMBT1|protein_coding|CODING|NM_007329.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973877 rs3740220 -0.693147 0.0101564 129 2413 LOW 2 CODING DMBT1 T protein_coding NM_007329.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124329673 C T 0 222 0 0.612 0.7057 0.7882 0.7758 0.6789 0.729 0.209584 0.247134 0.264442 1 6150 86424 9959 6777 4871 45755 674 12238 2 9800 120716 11574 8610 6612 66710 898 16512 0.896059 0 . 0 . 130 40,22,27,26 SPLICE_SITE_REGION+INTRON(LOW||||2413|DMBT1|protein_coding|CODING|NM_007329.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996696 rs3740221 -0.693147 0.00987099 130 P42T 2413 Cca/Aca MODERATE 3 MISSENSE CODING DMBT1 A protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124329710 C A 0 222 0 0.612 0.7057 0.7882 0.7758 0.6789 0.729 0.641524 0.674323 0.689294 1 6151 86464 9963 6783 4873 45790 674 12230 2 9800 120750 11576 8616 6614 66734 898 16512 0.627215 0 . 0 . 139 29,32,34,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P42T|2413|DMBT1|protein_coding|CODING|NM_007329.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981812 rs11523871 -0.693147 0.689363 139 S54L 2413 tCg/tTg MODERATE 4 MISSENSE CODING DMBT1 T protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124330427 C T 0 222 0 0.612 0.7053 0.7882 0.7738 0.6789 0.729 0.642216 0.67468 0.689626 1 6150 86460 9962 6771 4873 45795 674 12235 2 9800 120750 11576 8616 6614 66736 898 16510 0.905636 0 . 0 . 200 59,22,59,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S54L|2413|DMBT1|protein_coding|CODING|NM_007329.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.842121 rs3013236 -0.693147 0.193257 200 2413 LOW 4 CODING DMBT1 A protein_coding NM_007329.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124330459 G A 0 222 0 0 0.0319 0 0.1379 0.001 0.0204 0.000260824 0.000165508 0.000121212 1 5 1307 4 1051 1 8 6 232 2 9800 120752 11576 8618 6614 66738 898 16508 0.974909 0 . 0 . 186 50,52,33,40 SPLICE_SITE_REGION+INTRON(LOW||||2413|DMBT1|protein_coding|CODING|NM_007329.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.547007 rs3824677 -0.693147 0.857105 186 T75 2413 acC/acT LOW 5 SILENT CODING DMBT1 T protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124331867 C T 0 228 0 0.9561 0.9874 0.9942 1 0.999 1 0.961378 0.987597 0.999758 2 9370 120290 11546 8626 6614 66726 897 16511 2 9802 120768 11576 8626 6614 66740 898 16512 0 . 0 . 0 223 0,0,111,85 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T75|2413|DMBT1|protein_coding|CODING|NM_007329.2|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7084792 -0.693147 0.200421 223 H306 2413 caT/caC LOW 10 SILENT CODING DMBT1 C protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124339332 T C 0 228 0 . 0 . 0 . 0 0.955579 0.985083 0.998661 2 8979 117752 11468 8601 6544 65292 877 15991 2 9536 119696 11558 8616 6584 66124 890 16388 0 . 0 . 0 307 0,0,113,169 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H306|2413|DMBT1|protein_coding|CODING|NM_007329.2|10|C) 1 0 . 0 . 0 . 1 1 0 56 0 0 0.0116306 0 . rs3013245 -0.693147 0.368851 307 S343T 2413 aGc/aCc MODERATE 11 MISSENSE CODING DMBT1 C protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124340406 G C 0 228 0 . 0 . 0 . 0 0.0992147 0.0456435 0.0207115 2 1181 8070 1431 1692 218 2115 39 1394 2 9798 120754 11576 8622 6614 66734 898 16512 0.938734 0 . 0 . 537 2,5,227,244 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S343T|2413|DMBT1|protein_coding|CODING|NM_007329.2|11|C) 1 0 . 0 . 0 . 1 1 0 58 0 0.95058 0.88113 0 0.415959 rs111575923 -0.693147 0.021729 537 R656Q 2413 cGg/cAg MODERATE 17 MISSENSE CODING DMBT1 A protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124348643 G A 0 228 0 0 0.0397 0 0.1736 0.001 0.0235 0.000250878 0.000163773 0.000121566 2 5 1543 4 1294 0 8 6 226 2 9744 118372 11526 8288 6382 65746 876 15810 0.930367 0 . 0 . 383 6,4,167,162 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R656Q|2413|DMBT1|protein_coding|CODING|NM_007329.2|17|A) 1 0 . 0 . 1 0 1 1 0 59 0 0.998794 0.994924 0 0.325404 rs2277236 -0.693147 0.0193965 383 T719M 2413 aCg/aTg MODERATE 19 MISSENSE CODING DMBT1 T protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124351013 C T 0 228 0 0 0.0385 0 0.1657 0.001 0.0256 0.000257599 0.000166085 0.000122549 2 4 1658 5 1312 0 7 6 324 2 9772 118400 11526 8276 6378 65796 878 15774 0.825984 0 . 0 . 257 3,1,143,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T719M|2413|DMBT1|protein_coding|CODING|NM_007329.2|19|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.952762 rs2277238 -0.693147 0.0219336 257 S781 2413 tcG/tcA LOW 20 SILENT CODING DMBT1 A protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124351954 G A 0 228 0 0.5469 0.3722 0.2435 0.4395 0.1511 0.3855 0.471414 0.247918 0.140039 2 4978 28605 3162 3852 1057 9964 179 5413 2 9706 117868 11506 8224 6316 65454 872 15790 0 . 0 . 0 385 0,0,159,180 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S781|2413|DMBT1|protein_coding|CODING|NM_007329.2|20|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.782917 0 . rs4752722 -0.693147 0.313609 385 P839L 2413 cCg/cTg MODERATE 21 MISSENSE CODING DMBT1 T protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124353100 C T 0 228 0 0 0.0405 0 0.1677 0.001 0.0337 0.000262467 0.00025092 0.000245519 2 7 1630 6 1291 0 15 6 305 2 9774 118822 11530 8348 6382 65840 878 16070 0.587815 0 . 0 . 549 5,4,216,259 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P839L|2413|DMBT1|protein_coding|CODING|NM_007329.2|21|T) 1 0 . 0 . 1 0 1 1 0 58 0 0.974488 0.997497 0 0.967411 rs117786926 -0.693147 0.0508259 549 S971R 2413 agT/agG MODERATE 24 MISSENSE CODING DMBT1 G protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124356566 T G 0 123 0 0.3896 0.2282 0.0922 0.1617 0.0676 0.3405 0.104185 0.0430725 0.0199538 2 93 223 7 11 1 65 3 43 2 492 3504 210 186 28 2276 44 268 0.735294 0 . 0 . 19 2,0,17,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S971R|2413|DMBT1|protein_coding|CODING|NM_007329.2|24|G) 1 0 . 0 . 1 0 1 1 0 49 0 0.647059 0 . 0.823529 rs181123368 -0.690438 0.996868 19 2413 LOW 25 CODING DMBT1 A protein_coding NM_007329.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124357536 T A 0 228 0 0 0.0329 0 0.1389 0.001 0.0245 0 . 0 2 4 1420 10 1101 0 10 6 289 2 9800 120762 11576 8622 6614 66740 898 16512 0.384271 0 . 0 . 307 2,2,135,123 SPLICE_SITE_REGION+INTRON(LOW||||2413|DMBT1|protein_coding|CODING|NM_007329.2|25|A) 0 . 0 . 0 1 0 . 1 0 59 0 0.997792 0.941617 0 0.0887451 rs3980982 -0.693147 0.00075355 307 V1029 2413 gtC/gtG LOW 26 SILENT CODING DMBT1 G protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124358420 C G 0 228 0 0.1566 0.1282 0.1052 0.2093 0.0368 0.1166 0.148795 0.0677342 0.0286087 2 1490 8913 1547 1875 222 2161 41 1577 2 9794 120682 11574 8556 6614 66734 898 16512 1 0 . 0 . 441 1,0,202,192 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V1029|2413|DMBT1|protein_coding|CODING|NM_007329.2|26|G) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.996003 0 1 rs2277242 -0.693147 0.00158637 441 Q1050 2413 caG/caA LOW 26 SILENT CODING DMBT1 A protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124358483 G A 0 228 0 0.0378 0.0431 0.0029 0.1389 0.001 0.0235 0.0297351 0.00980075 0.000239693 2 331 1745 24 1099 0 12 6 273 2 9802 120740 11576 8598 6614 66740 898 16512 0.388253 0 . 0 . 351 1,3,128,195 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1050|2413|DMBT1|protein_coding|CODING|NM_007329.2|26|A) 1 0 . 0 . 1 0 1 1 0 59 0 1 1 0 0.35488 rs2277243 -0.693147 0.000383535 351 N1157 2413 aaT/aaC LOW 29 SILENT CODING DMBT1 C protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124361440 T C 0 122 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,0,31 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N1157|2413|DMBT1|protein_coding|CODING|NM_007329.2|29|C) 0 . 0 . 0 . 0 . 0 . 27 0 0 . 0 . rs370733610 -0.69311 6.47544e-13 31 V1159 2413 gtT/gtC LOW 29 SILENT CODING DMBT1 C protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124361446 T C 0 122 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,0,31 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V1159|2413|DMBT1|protein_coding|CODING|NM_007329.2|29|C) 0 . 0 . 0 . 0 . 0 . 27 0 0 . 0 . rs367641389 -0.69311 6.00074e-13 31 Q1527R 2413 cAa/cGa MODERATE 38 MISSENSE CODING DMBT1 G protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124377608 A G 0 228 0 . 0 . 0 . 0 0.0218235 0.00731552 0.00023663 2 356 1772 26 1091 0 19 7 273 2 9788 120746 11576 8620 6614 66738 898 16512 0.79387 0 . 0 . 343 3,4,238,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q1527R|2413|DMBT1|protein_coding|CODING|NM_007329.2|38|G) 1 0 . 0 . 0 . 1 1 0 54 0 0.979259 0.993192 0 0.438145 rs150706313 -0.693147 0.738951 343 D1603 2413 gaT/gaC LOW 38 SILENT CODING DMBT1 C protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124377837 T C 0 228 0 0.0719 0.0535 0.0115 0.1389 0.002 0.0235 0.0729167 0.0234916 0.000602991 2 739 2193 43 1096 0 20 6 289 2 9682 120446 11574 8618 6614 66550 896 16512 0.883495 0 . 0 . 221 1,1,81,125 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D1603|2413|DMBT1|protein_coding|CODING|NM_007329.2|38|C) 1 0 . 0 . 1 0 1 1 0 59 0 0.980583 0.927992 0 0.764563 rs140118852 -0.693147 0.120331 221 P1628 2413 ccG/ccA LOW 40 SILENT CODING DMBT1 A protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124379794 G A 0 228 0 0 0.0325 0 0.1389 0.001 0.0225 0.000266383 0.000167308 0.000121951 2 4 1388 4 1096 0 7 5 272 2 9800 120760 11574 8626 6614 66736 898 16512 0.606501 0 . 0 . 233 0,3,115,85 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1628|2413|DMBT1|protein_coding|CODING|NM_007329.2|40|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.986743 rs2277247 -0.693147 0.0231574 233 D1667E 2413 gaC/gaA MODERATE 41 MISSENSE CODING DMBT1 A protein_coding NM_007329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124380676 C A 0 228 0 0 0.0325 0 0.1389 0.001 0.0225 0.000246063 0.000160668 0.000119275 2 4 1389 4 1097 0 7 5 272 2 9804 120766 11576 8622 6614 66740 898 16512 0.335689 0 . 0 . 431 6,3,181,204 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1667E|2413|DMBT1|protein_coding|CODING|NM_007329.2|41|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.346801 rs150865923 -0.693147 0.00985733 431 P2335 2413 ccA/ccG LOW 53 SILENT CODING DMBT1 G protein_coding NM_007329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124402677 A G 0 222 0 0.8767 0.6438 0.5029 0.6687 0.4125 0.6411 0.814797 0.549707 0.418167 1 8078 62442 6750 5928 2669 28355 409 10253 2 9824 120752 11568 8608 6612 66730 898 16512 0.508455 0 . 0 . 257 53,57,53,68 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P2335|2413|DMBT1|protein_coding|CODING|NM_007329.2|53|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981884 rs1052715 -0.693147 3.5424e-05 257 2413 193 MODIFIER 53 CODING DMBT1 C protein_coding NM_007329.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124403107 T C 0 11.9 0 0.8767 0.644 0.5029 0.6696 0.4125 0.6411 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 8 0,6,0,2 UTR_3_PRIME(MODIFIER||193||2413|DMBT1|protein_coding|CODING|NM_007329.2|53|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.333333 rs7383 -0.453602 0.6 8 A269T 335 Gca/Aca MODERATE 3 MISSENSE CODING C10orf120 T protein_coding NM_001010912.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124457452 C T 0 222 0 0.8359 0.8077 0.7291 0.8095 0.7535 0.8793 0.847027 0.786099 0.754884 1 8799 94981 8773 6922 4629 50906 707 14245 2 10406 121410 11578 8652 6614 66740 908 16512 0.505843 0 . 0 . 127 39,26,24,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A269T|335|C10orf120|protein_coding|CODING|NM_001010912.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890287 rs2947594 -0.693147 0.158103 127 R96S 335 agG/agC MODERATE 3 MISSENSE CODING C10orf120 G protein_coding NM_001010912.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124457969 C G 0 222 0 0 0.0423 0.0692 0.1071 0 0.0573 0.0024966 0.00107643 0.000348837 1 21 2939 1334 896 1 18 13 656 2 10188 120700 11560 8634 6612 66308 906 16492 0.669513 0 . 0 . 79 16,19,8,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agC|R96S|335|C10orf120|protein_coding|CODING|NM_001010912.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.042259 rs74509433 -0.693127 0.0380434 79 P2L 94 cCt/cTt MODERATE 3 MISSENSE CODING FAM24B A protein_coding NM_001204364.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124610027 G A 0 222 0 0.4834 0.5024 0.4597 0.4931 0.5785 0.4898 0.5202 0.543134 0.554884 1 5211 64125 5028 4406 4231 36773 449 8027 2 10402 121360 11570 8634 6612 66724 908 16510 0.800585 0 . 0 . 199 24,74,27,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P2L|94|FAM24B|protein_coding|CODING|NM_001204364.1|3|A),UPSTREAM(MODIFIER||4336||607|CUZD1|protein_coding|CODING|NM_022034.5||A),INTRAGENIC(MODIFIER|||||FAM24B-CUZD1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0271588 rs1891110 -0.693147 0.127093 199 S171 348 tcG/tcA LOW 3 SILENT CODING PSTK A protein_coding NM_153336.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124742792 G A 0 222 0 0.6589 0.5817 0.5576 0.3919 0.7296 0.5378 0.644803 0.688528 0.71093 1 6607 76404 5562 3570 4663 46713 560 8729 2 10222 119952 11376 8504 6570 66108 896 16276 0.824864 0 . 0 COSM147076 64 25,11,20,6 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S171|348|PSTK|protein_coding|CODING|NM_153336.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.954055 rs3736583 -0.692976 0.695579 64 G206R 348 Gga/Cga MODERATE 3 MISSENSE CODING PSTK C protein_coding NM_153336.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124742895 G C 0 222 0 0.6589 0.5817 0.5576 0.3919 0.7296 0.5378 0.645029 0.688451 0.710698 1 6688 76820 5614 3594 4683 46923 564 8754 2 10386 121186 11544 8612 6614 66628 906 16496 0.592565 0 . 0 COSM147077 89 26,20,25,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G206R|348|PSTK|protein_coding|CODING|NM_153336.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.534061 rs3736582 -0.693144 0.383438 89 H213 432 caC/caT LOW 5 SILENT CODING ACADSB T protein_coding NM_001609.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124800853 C T 0 222 0 0.2163 0.2278 0.2176 0.1419 0.2296 0.3374 0.215615 0.228125 0.234535 1 2258 28985 2455 1305 1986 15582 227 5172 2 10406 121402 11578 8652 6612 66738 906 16510 0.184497 0 . 0 . 145 36,30,36,25 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H213|432|ACADSB|protein_coding|CODING|NM_001609.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.602812 rs1140591 -0.693147 0.0327733 145 432 262 MODIFIER 11 CODING ACADSB T protein_coding NM_001609.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124813543 C T 0 39.7 0 0.4085 0.4415 0.4308 0.5833 0.4394 0.3497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_3_PRIME(MODIFIER||262||432|ACADSB|protein_coding|CODING|NM_001609.3|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12248515 -0.511536 0.873285 4 432 1868 MODIFIER 11 CODING ACADSB G protein_coding NM_001609.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124815149 C G 0 9.7 0 0.8903 0.8954 0.8991 0.8611 0.8757 0.955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1868||432|ACADSB|protein_coding|CODING|NM_001609.3|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10902868 -0.379885 0 1 432 3234 MODIFIER 11 CODING ACADSB G protein_coding NM_001609.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 124816515 C G 0 228 0 1 0.9623 0.9784 0.8512 0.9861 0.9898 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 129 0,0,41,74 UTR_3_PRIME(MODIFIER||3234||432|ACADSB|protein_coding|CODING|NM_001609.3|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3763738 -0.693147 0.00200161 129 P163 337 ccA/ccG LOW 1 SILENT CODING GPR26 G protein_coding NM_153442.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125426412 A G 0 222 0 0.618 0.5519 0.5706 0.38 0.6322 0.544 0.63624 0.635811 0.635591 1 5906 66901 5282 3333 3428 39619 463 8870 2 9276 113440 11044 8204 5848 62162 826 16080 1 0 . 0 COSM1346532 50 21,6,8,13 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P163|337|GPR26|protein_coding|CODING|NM_153442.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.887574 rs12263344 -0.692352 0.189032 50 L214 337 ctG/ctC LOW 1 SILENT CODING GPR26 C protein_coding NM_153442.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125426565 G C 0 228 0 0.9955 0.9988 1 1 1 1 0.999773 0.999846 0.999884 2 7703 95657 9342 6776 4448 52980 710 13698 2 7710 95664 9342 6776 4448 52980 710 13698 0 . 0 . 0 33 0,0,8,23 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L214|337|GPR26|protein_coding|CODING|NM_153442.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4980313 -0.69311 0.419278 33 337 1339 MODIFIER 3 CODING GPR26 A protein_coding NM_153442.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125449015 G A 0 32.6 0 0.6558 0.8047 0.8228 0.9385 0.8887 0.7689 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1339||337|GPR26|protein_coding|CODING|NM_153442.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1219822 -0.379885 0 2 337 2175 MODIFIER 3 CODING GPR26 A protein_coding NM_153442.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125449851 G A 0 9.7 0 0.9433 0.9832 0.9928 1 0.996 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2175||337|GPR26|protein_coding|CODING|NM_153442.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1219823 -0.379885 0 1 337 3937 MODIFIER 3 CODING GPR26 G protein_coding NM_153442.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125451613 A G 0 9.7 0 0.0015 0.013978 0.013 0.0317 0.0109 0.0164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3937||337|GPR26|protein_coding|CODING|NM_153442.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17608415 -0.379885 0 1 337 7601 MODIFIER 3 CODING GPR26 C protein_coding NM_153442.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125455277 T C 0 65 0 0.0015 0.013978 0.013 0.0317 0.0109 0.0164 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_3_PRIME(MODIFIER||7601||337|GPR26|protein_coding|CODING|NM_153442.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs17608508 -0.511536 0.131948 4 Q750R 756 cAg/cGg MODERATE 14 MISSENSE CODING CPXM2 C protein_coding NM_198148.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125506302 T C 0 228 0 0.9523 0.9864 0.9957 1 0.998 1 0.950522 0.982239 0.998488 2 9881 120692 11516 8654 6614 66615 902 16510 2 10390 121362 11578 8654 6614 66708 908 16510 0 . 0 . 0 49 0,0,43,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q750R|756|CPXM2|protein_coding|CODING|NM_198148.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7088479 -0.693147 0.204336 49 D544 756 gaC/gaT LOW 11 SILENT CODING CPXM2 A protein_coding NM_198148.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125521533 G A 0 222 0 0.4614 0.6064 0.7277 0.5655 0.7684 0.592 0.508625 0.667846 0.749419 1 5248 85706 8669 4757 5339 50720 633 10340 2 10368 121202 11570 8606 6610 66642 908 16498 0.842452 0 . 0 . 88 19,29,10,25 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D544|756|CPXM2|protein_coding|CODING|NM_198148.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799731 rs10794566 -0.693136 0.122738 88 Y525 756 taC/taT LOW 11 SILENT CODING CPXM2 A protein_coding NM_198148.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125521590 G A 0 222 0 0.6112 0.65 0.7435 0.5665 0.7744 0.5941 0.626192 0.70998 0.752907 1 6507 87487 8812 4768 5338 50995 647 10420 2 10380 121228 11572 8616 6610 66636 906 16508 0.797265 0 . 0 . 67 20,22,11,13 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y525|756|CPXM2|protein_coding|CODING|NM_198148.2|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.756837 rs10794567 -0.692831 0.663282 67 Y431 756 taC/taT LOW 9 SILENT CODING CPXM2 A protein_coding NM_198148.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125528048 G A 0 222 0 0.1528 0.3788 0.4784 0.5992 0.3738 0.3916 0.191557 0.313086 0.375349 1 1964 48492 6217 5594 2437 25115 394 6771 2 10326 119588 11536 8608 6552 66162 894 15510 0.720006 0 . 0 . 89 31,9,26,11 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y431|756|CPXM2|protein_coding|CODING|NM_198148.2|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985949 rs1219725,rs386523245 -0.693141 0.0727838 89 561 1571 MODIFIER 8 CODING CHST15 T protein_coding NM_001270764.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 125768094 C T 0 87 0 0.3116 0.3942 0.389 0.4385 0.4284 0.4284 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,2,2 UTR_3_PRIME(MODIFIER||1571||561|CHST15|protein_coding|CODING|NM_001270764.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12915 -0.556411 0.885471 5 N378 439 aaC/aaT LOW 9 SILENT CODING OAT A protein_coding NM_000274.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126089434 G A 0 222 0 0.1445 0.4099 0.5259 0.6369 0.3648 0.499 0.173627 0.315259 0.387855 1 1679 50214 6880 5063 2370 25910 362 7950 2 10236 120122 11460 8584 6588 65894 896 16464 0.996412 2 benign 0 . 58 21,4,25,1 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N378|439|OAT|protein_coding|CODING|NM_000274.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91767 rs11461 -0.692976 0.416727 58 439 6766 MODIFIER 1 CODING OAT C protein_coding NM_000274.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126107506 A C 0 9.7 0 0.7678 0.863 0.8156 0.9821 0.8141 0.953 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||6766||439|OAT|protein_coding|CODING|NM_000274.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4144117 -0.379885 0 1 270 44 MODIFIER 1 CODING LHPP A protein_coding NM_022126.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126150388 C A 0 101 0 0.3638 0.6318 0.67 0.8591 0.7018 0.6605 0.68172 0.77822 0.822591 1 304 3872 158 683 89 2315 17 306 2 444 4618 178 744 106 2744 24 378 0.759945 0 . 0 . 19 9,0,7,0 UTR_5_PRIME(MODIFIER||44||270|LHPP|protein_coding|CODING|NM_022126.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.698693 rs2491156 -0.636426 0.276556 19 Q94R 270 cAa/cGa MODERATE 2 MISSENSE CODING LHPP G protein_coding NM_022126.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126172863 A G 0 228 0 0.9917 0.898 0.8674 0.9385 0.8479 0.8027 0.975034 0.916039 0.885814 2 10184 107019 9746 8156 5834 59138 779 13182 2 10394 121226 11574 8644 6612 66594 904 16504 1 0 . 0 . 399 0,1,174,185 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q94R|270|LHPP|protein_coding|CODING|NM_022126.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6597801 -0.693147 0.0132356 399 422 2878 MODIFIER 5 CODING FAM53B C protein_coding NM_014661.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126308933 A C 0 167 0 0.5461 0.2804 0.1513 0.2252 0.2028 0.1493 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,0,29 UTR_3_PRIME(MODIFIER||2878||422|FAM53B|protein_coding|CODING|NM_014661.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1057103 -0.693079 0.175255 44 422 1079 MODIFIER 5 CODING FAM53B G protein_coding NM_014661.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126310732 T G 0 60 0 0.0151 0.0312 0.0072 0.0714 0.001 0.0593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868321 0 . 0 . 8 0,4,0,4 UTR_3_PRIME(MODIFIER||1079||422|FAM53B|protein_coding|CODING|NM_014661.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 0 . 0.868321 rs79299099 -0.556411 0.698002 8 422 316 MODIFIER 5 CODING FAM53B C protein_coding NM_014661.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126311495 G C 0 174 0 0.1778 0.2041 0.1499 0.2996 0.2823 0.0992 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.852144 0 . 0 . 15 2,2,3,7 UTR_3_PRIME(MODIFIER||316||422|FAM53B|protein_coding|CODING|NM_014661.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.122151 rs3740536 -0.670168 0.376037 15 H366D 422 Cac/Gac MODERATE 5 MISSENSE CODING FAM53B C protein_coding NM_014661.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126311984 G C 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 11 0 11 0 0 0 0 2 6834 82578 6942 5664 4030 44694 632 13782 0.827304 0 . 0 . 111 24,39,17,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H366D|422|FAM53B|protein_coding|CODING|NM_014661.3|5|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.969144 rs201718461 -0.693145 0.0168171 111 291 2480 MODIFIER 7 CODING METTL10 G protein_coding NM_212554.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126446592 A G 0 9.7 0 0.4206 0.5393 0.5937 0.5149 0.5487 0.6769 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2480||291|METTL10|protein_coding|CODING|NM_212554.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1055256 -0.379885 0 1 V202 415 gtG/gtA LOW 7 SILENT CODING FAM175B A protein_coding NM_032182.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126517989 G A 0 222 0 0.1694 0.483 0.5663 0.5873 0.5457 0.6759 0.236723 0.457327 0.570349 1 2319 66940 7112 5163 3969 37624 507 10246 2 10406 121356 11566 8644 6612 66716 908 16504 0.816306 0 . 0 . 51 14,13,8,10 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V202|415|FAM175B|protein_coding|CODING|NM_032182.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.088729 rs2303611 -0.691153 0.950162 51 708 437 MODIFIER 9 CODING ZRANB1 C protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126673998 A C 0 228 0 0.5303 0.7776 0.683 0.9494 0.8887 0.8875 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 82 0,0,55,21 UTR_3_PRIME(MODIFIER||437||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|C),DOWNSTREAM(MODIFIER||2420||985|CTBP2|protein_coding|CODING|NM_022802.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3906796 -0.693147 0.0416525 82 708 532 MODIFIER 9 CODING ZRANB1 C protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674093 T C 0 228 0 0.3222 0.602 0.4784 0.7808 0.7455 0.7362 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 144 0,0,75,53 UTR_3_PRIME(MODIFIER||532||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|C),DOWNSTREAM(MODIFIER||2325||985|CTBP2|protein_coding|CODING|NM_022802.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3845 -0.693147 0.371151 144 708 1128 MODIFIER 9 CODING ZRANB1 C protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674689 A C 0 228 0 0.3616 0.6138 0.4813 0.7817 0.7485 0.7372 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 71 0,0,56,4 UTR_3_PRIME(MODIFIER||1128||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|C),DOWNSTREAM(MODIFIER||1729||985|CTBP2|protein_coding|CODING|NM_022802.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046373 -0.693147 0.318648 71 708 1291 MODIFIER 9 CODING ZRANB1 A protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674852 G A 0 52 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,2,3 UTR_3_PRIME(MODIFIER||1291||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|A),DOWNSTREAM(MODIFIER||1566||985|CTBP2|protein_coding|CODING|NM_022802.2||A) 0 . 0 . 0 . 0 . 0 . 60 0 0 1 0 . rs11813829 -0.590765 0.409395 12 708 1293 MODIFIER 9 CODING ZRANB1 A protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674854 G A 0 109 0 0.3177 0.6783 0.7435 0.7976 0.8767 0.7924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,2,3 UTR_3_PRIME(MODIFIER||1293||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|A),DOWNSTREAM(MODIFIER||1564||985|CTBP2|protein_coding|CODING|NM_022802.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs148576335 -0.590765 0.41821 14 708 1295 MODIFIER 9 CODING ZRANB1 A protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674856 G A 0 104 0 0.4637 0.5701 0.598 0.5863 0.6412 0.6043 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 33 0,0,2,3 UTR_3_PRIME(MODIFIER||1295||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|A),DOWNSTREAM(MODIFIER||1562||985|CTBP2|protein_coding|CODING|NM_022802.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs143258620 -0.590765 0.405004 33 708 1297 MODIFIER 9 CODING ZRANB1 A protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674858 G A 0 94 0 0.5446 0.7278 0.7392 0.7966 0.8469 0.774 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 43 0,0,1,3 UTR_3_PRIME(MODIFIER||1297||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|A),DOWNSTREAM(MODIFIER||1560||985|CTBP2|protein_coding|CODING|NM_022802.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs145108464 -0.556411 0.421803 43 708 1299 MODIFIER 9 CODING ZRANB1 A protein_coding NM_017580.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126674860 G A 0 95 0 0.6286 0.5994 0.5447 0.6796 0.5487 0.5685 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 65 0,0,1,4 UTR_3_PRIME(MODIFIER||1299||708|ZRANB1|protein_coding|CODING|NM_017580.2|9|A),DOWNSTREAM(MODIFIER||1558||985|CTBP2|protein_coding|CODING|NM_022802.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs142478896 -0.590765 0.273436 65 985 1401 MODIFIER 9 CODING CTBP2 C protein_coding NM_022802.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126676686 T C 0 228 0 0.211 0.5703 0.4654 0.7788 0.7455 0.7352 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 95 1,0,62,20 UTR_3_PRIME(MODIFIER||1401||985|CTBP2|protein_coding|CODING|NM_022802.2|9|C),DOWNSTREAM(MODIFIER||681||708|ZRANB1|protein_coding|CODING|NM_017580.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3740535 -0.693147 0.0244614 95 985 1250 MODIFIER 9 CODING CTBP2 C protein_coding NM_022802.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126676837 T C 0 228 0 0.5703 0.7901 0.6859 0.9514 0.8926 0.8896 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,34,47 UTR_3_PRIME(MODIFIER||1250||985|CTBP2|protein_coding|CODING|NM_022802.2|9|C),DOWNSTREAM(MODIFIER||832||708|ZRANB1|protein_coding|CODING|NM_017580.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7099361 -0.693147 0.251901 95 Q539E 985 Cag/Gag MODERATE 1 MISSENSE CODING CTBP2 C protein_coding NM_022802.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126714714 G C 0 228 0 0.3744 0.4677 0.3357 0.6607 0.4761 0.4796 0.384703 0.458096 0.495698 2 3880 57754 3776 5485 3766 33175 408 7264 2 10300 119026 11550 8618 6602 65898 880 15178 0 . 0 . COSM1346598 38 0,0,25,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q539E|985|CTBP2|protein_coding|CODING|NM_022802.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2946994 -0.693136 0.0482175 38 Y455H 985 Tac/Cac MODERATE 1 MISSENSE CODING CTBP2 G protein_coding NM_022802.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126714966 A G 0 219 0 0.298 0.4479 0.3343 0.6597 0.4811 0.4785 0.329169 0.440317 0.497209 2 3164 56866 3730 5457 3719 32953 401 7442 2 9880 118698 11452 8558 6364 65334 882 16228 0 . 0 . 0 10 0,0,5,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y455H|985|CTBP2|protein_coding|CODING|NM_022802.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.974597 0 . rs3012075 -0.662043 0.868432 10 985 18 MODIFIER 1 CODING CTBP2 T protein_coding NM_022802.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 126716346 C T 0 228 0 0.3238 0.4543 0.3314 0.6597 0.4801 0.4796 0.348901 0.444788 0.493695 2 1728 25226 1131 1776 1744 14460 209 4178 2 4238 47448 2914 2678 2820 26192 392 8214 0 . 0 . 0 38 0,0,3,33 UTR_5_PRIME(MODIFIER||18||985|CTBP2|protein_coding|CODING|NM_022802.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2938006,rs386577494 -0.693139 0.161813 38 A1117T 1238 Gca/Aca MODERATE 23 MISSENSE CODING EDRF1 A protein_coding NM_001202438.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127441439 G A 0 222 0 0.0015 0.0827 0.0403 0.2093 0.0775 0.0971 0.0161144 0.0599723 0.0824419 1 140 11193 615 2274 548 5656 99 1861 2 10370 121274 11558 8638 6610 66682 908 16508 0.955271 0 . 0 COSM147079 98 31,18,28,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1117T|1238|EDRF1|protein_coding|CODING|NM_001202438.1|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856176 rs17153510 -0.693146 0.234674 98 V191A 569 gTg/gCg MODERATE 2 MISSENSE CODING MMP21 G protein_coding NM_147191.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127462525 A G 0 206 0 0.6974 0.7388 0.6282 0.7619 0.8091 0.7771 0.737614 0.790407 0.817101 2 5013 78523 6345 5318 4755 44344 565 12183 2 6898 101108 10376 7504 5594 54426 710 15600 0 . 0 . 0 19 0,0,1,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V191A|569|MMP21|protein_coding|CODING|NM_147191.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10901425 -0.69168 0.205665 19 T247M 265 aCg/aTg MODERATE 10 MISSENSE CODING UROS A protein_coding NM_000375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127477495 G A 0 183 0 0 0.00039936 0 0.002 0 0 0 7.697e-05 0.000116279 1 1 51 0 48 0 1 0 1 2 6434 76656 5050 5294 3190 44234 506 11948 0.95843 0 . 0 . 37 12,7,12,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T247M|265|UROS|protein_coding|CODING|NM_000375.2|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0813306 rs199925121 -0.686358 0.2458 37 265 6688 MODIFIER 1 CODING UROS T protein_coding NM_000375.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127511756 C T 0 73 0 0.357 0.3732 0.3242 0.3006 0.4433 0.4325 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_5_PRIME(MODIFIER||6688||265|UROS|protein_coding|CODING|NM_000375.2|1|T),UPSTREAM(MODIFIER||348||322|BCCIP|protein_coding|CODING|NM_016567.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4256900 -0.511536 0.681436 3 265 6722 MODIFIER 1 CODING UROS T protein_coding NM_000375.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127511790 G T 0 118 0 0.3797 0.3794 0.3285 0.3006 0.4414 0.4325 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,2 UTR_5_PRIME(MODIFIER||6722||265|UROS|protein_coding|CODING|NM_000375.2|1|T),UPSTREAM(MODIFIER||314||322|BCCIP|protein_coding|CODING|NM_016567.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4385801 -0.590765 0.561811 5 743 184 MODIFIER 11 CODING DHX32 C protein_coding NM_018180.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127525072 A C 0 205 0 0.3086 0.3498 0.3055 0.2907 0.4135 0.4325 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . COSN163815 9 0,0,5,4 UTR_3_PRIME(MODIFIER||184||743|DHX32|protein_coding|CODING|NM_018180.2|11|C),INTRON(MODIFIER||||322|BCCIP|protein_coding|CODING|NM_016567.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.974597 0 . rs7320 -0.662043 0.0588085 9 A510 743 gcA/gcG LOW 7 SILENT CODING DHX32 C protein_coding NM_018180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127530325 T C 0 228 0 0.5961 0.4541 0.3487 0.3234 0.4443 0.4816 0.574671 0.498539 0.459535 2 6047 52463 2681 2469 2859 30501 404 7502 2 10324 120908 11538 8616 6598 66464 906 16462 1 0 . 0 COSM147080 63 0,1,48,3 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A510|743|DHX32|protein_coding|CODING|NM_018180.2|7|C),INTRON(MODIFIER||||322|BCCIP|protein_coding|CODING|NM_016567.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3208565 -0.693147 0.861448 63 909 568 MODIFIER 23 CODING ADAM12 C protein_coding NM_003474.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127705280 G C 0 185 0 0.7398 0.7021 0.5634 0.7877 0.6541 0.7106 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 13 0,0,12,1 UTR_3_PRIME(MODIFIER||568||909|ADAM12|protein_coding|CODING|NM_003474.5|23|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10751538 -0.683931 0.797017 13 909 481 MODIFIER 23 CODING ADAM12 C protein_coding NM_003474.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127705367 T C 0 228 0 0.5129 0.639 0.5418 0.7877 0.6531 0.7106 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,37,3 UTR_3_PRIME(MODIFIER||481||909|ADAM12|protein_coding|CODING|NM_003474.5|23|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7916918 -0.693145 0.959603 40 909 444 MODIFIER 23 CODING ADAM12 G protein_coding NM_003474.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127705404 A G 0 228 0 0.4909 0.6326 0.5375 0.7877 0.6531 0.7106 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,50,3 UTR_3_PRIME(MODIFIER||444||909|ADAM12|protein_coding|CODING|NM_003474.5|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7913591 -0.693147 0.000185851 56 T733 909 acC/acT LOW 19 SILENT CODING ADAM12 A protein_coding NM_003474.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 127727913 G A 0 222 0 0 0.013778 0 0.0625 0.004 0.002 0 0.000384438 0.000581395 1 1 939 2 775 46 82 11 22 2 10406 121398 11576 8652 6614 66732 908 16510 0.224885 0 . 0 COSM147082,COSM147081 145 42,22,48,16 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T733|909|ADAM12|protein_coding|CODING|NM_003474.5|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890621 rs56651369 -0.693147 0.129485 145 D558E 699 gaC/gaG MODERATE 5 MISSENSE CODING C10orf90 C protein_coding NM_001004298.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128150015 G C 0 222 0 0.0015 0.0075879 0 0.0317 0 0.0041 0.000453926 0.00030755 0.000232558 1 5 383 1 343 0 4 0 30 2 10384 121244 11552 8632 6584 66688 908 16496 0.749753 0 . 0 . 178 59,40,37,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D558E|699|C10orf90|protein_coding|CODING|NM_001004298.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945272 rs146121361 -0.693147 0.584444 178 D531E 699 gaC/gaA MODERATE 5 MISSENSE CODING C10orf90 T protein_coding NM_001004298.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128150096 G T 0 222 0 0.2095 0.1224 0.1095 0.2163 0.0199 0.0225 0.182932 0.0653545 0.00511628 1 1973 6781 1176 2115 491 727 43 256 2 10302 119982 11418 8552 6406 66082 896 16326 0.162935 0 . 0 . 218 34,38,70,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D531E|699|C10orf90|protein_coding|CODING|NM_001004298.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.657165 rs12412320 -0.693147 0.0411579 218 A32 699 gcA/gcG LOW 2 SILENT CODING C10orf90 C protein_coding NM_001004298.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128202435 T C 0 228 0 0.9145 0.876 0.8631 0.8571 0.8569 0.8722 0.910123 0.870444 0.850116 2 9471 104513 9800 7378 5901 56941 772 14250 2 10406 121402 11578 8652 6614 66734 908 16510 0 . 0 . 0 131 0,0,81,26 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A32|699|C10orf90|protein_coding|CODING|NM_001004298.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1436803,rs386531850 -0.693147 0.0292609 131 699 70 MODIFIER 1 CODING C10orf90 T protein_coding NM_001004298.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128209959 G T 0 228 0 0.9697 0.8906 0.8631 0.8552 0.8579 0.8732 0.952312 0.882121 0.851572 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 63 0,0,14,45 UTR_5_PRIME(MODIFIER||70||699|C10orf90|protein_coding|CODING|NM_001004298.2|1|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs4962342 -0.693147 0.13552 63 R944 1886 cgA/cgG LOW 27 SILENT CODING DOCK1 G protein_coding NM_001290223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128926013 A G 0 228 0 0.438 0.7438 0.7853 0.8423 0.8648 0.9018 0.515261 0.748596 0.857992 2 4827 98901 8720 7144 5944 56690 740 14836 2 9798 120736 11566 8622 6614 66728 898 16510 1 0 . 0 . 98 0,1,27,62 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R944|1886|DOCK1|protein_coding|CODING|NM_001290223.1|27|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1060561 -0.693147 0.00591462 98 479 2275 MODIFIER 6 CODING FAM196A A protein_coding NM_001039762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128933826 C A 0 228 0 0.9372 0.9828 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 108 0,0,64,23 UTR_3_PRIME(MODIFIER||2275||479|FAM196A|protein_coding|CODING|NM_001039762.2|6|A),INTRON(MODIFIER||||1886|DOCK1|protein_coding|CODING|NM_001290223.1|27|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2483856 -0.693147 0.00120081 108 479 2109 MODIFIER 6 CODING FAM196A C protein_coding NM_001039762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128933992 T C 0 228 0 0.2519 0.6917 0.7781 0.8403 0.8608 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 77 0,0,59,17 UTR_3_PRIME(MODIFIER||2109||479|FAM196A|protein_coding|CODING|NM_001039762.2|6|C),INTRON(MODIFIER||||1886|DOCK1|protein_coding|CODING|NM_001290223.1|27|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2483855 -0.693147 0.932438 77 479 659 MODIFIER 6 CODING FAM196A T protein_coding NM_001039762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128935442 C T 0 222 0 0 0.0214 0 0.1062 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.973969 0 . 0 . 115 25,35,23,15 UTR_3_PRIME(MODIFIER||659||479|FAM196A|protein_coding|CODING|NM_001039762.2|6|T),INTRON(MODIFIER||||1886|DOCK1|protein_coding|CODING|NM_001290223.1|27|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.692815 rs75051076 -0.693143 0.145673 115 T13 479 acG/acA LOW 4 SILENT CODING FAM196A T protein_coding NM_001039762.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 128974621 C T 0 228 0 0.2436 0.5286 0.5634 0.7401 0.5875 0.6104 0.286428 0.482467 0.582926 2 2823 68349 6070 6396 3544 38803 514 10199 2 9880 120276 11570 8638 6612 66480 900 16196 0 . 0 . 0 68 0,0,16,46 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T13|479|FAM196A|protein_coding|CODING|NM_001039762.2|4|T),INTRON(MODIFIER||||1886|DOCK1|protein_coding|CODING|NM_001290223.1|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2489386,rs386568115 -0.693147 0.671461 68 R1795 1886 agG/agA LOW 50 SILENT CODING DOCK1 A protein_coding NM_001290223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129242515 G A 0 222 0 0.2133 0.3375 0.2824 0.4653 0.3658 0.3834 0.217319 0.323954 0.377018 1 2242 41148 2677 3778 1845 24565 308 5733 2 9322 116580 11226 8454 6448 65078 870 15182 0.466244 0 . 0 . 166 31,49,22,47 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R1795|1886|DOCK1|protein_coding|CODING|NM_001290223.1|50|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993499 rs11371 -0.693147 0.0253764 166 A1814T 1886 Gcg/Acg MODERATE 51 MISSENSE CODING DOCK1 A protein_coding NM_001290223.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129245684 G A 0 222 0 0.211 0.2047 0.2233 0.12 0.2584 0.2147 0.193313 0.237522 0.25865 1 1997 27516 2134 996 1506 16760 212 3911 2 8684 107250 9768 7382 5802 60008 784 14822 0.00548841 0 . 0 COSM147088 82 25,18,21,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A1814T|1886|DOCK1|protein_coding|CODING|NM_001290223.1|51|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.545438 rs869801 -0.69311 0.468155 82 A1878T 1886 Gca/Aca MODERATE 52 MISSENSE CODING DOCK1 A protein_coding NM_001290223.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249662 G A 0 222 0 0.6452 0.865 0.9409 0.9127 0.9761 0.9448 0.696172 0.876508 0.966033 1 4873 84337 8126 5653 4824 49129 617 11115 2 7126 89658 8360 6112 4878 50678 652 11852 0.736194 0 . 0 . 116 55,16,22,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1878T|1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.755378 rs2229603 -0.693136 0.0916044 116 S1882 1886 tcC/tcT LOW 52 SILENT CODING DOCK1 T protein_coding NM_001290223.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249676 C T 0 222 0 0.2337 0.4225 0.4986 0.4593 0.497 0.5092 0.262817 0.418016 0.494897 1 1628 34116 2698 2174 1621 20408 272 5315 2 5548 69602 5736 4332 3708 39552 544 10182 0.952469 0 . 0 . 113 49,20,23,11 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1882|1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.167611 rs2229604,rs386504439 -0.693132 0.517684 113 1886 2 MODIFIER 52 CODING DOCK1 A protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249693 G A 0 222 0 0.205 0.4309 0.5821 0.4554 0.5169 0.5153 0.238502 0.429034 0.524142 1 1144 26793 1982 1327 1294 15986 221 4839 2 4330 53246 3608 2770 2974 30048 446 9070 0.437846 0 . 0 . 123 50,30,24,10 UTR_3_PRIME(MODIFIER||2||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928919 rs2229605 -0.693132 0.76503 123 1886 10 MODIFIER 52 CODING DOCK1 G protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249701 C G 0 222 0 0.6089 0.855 0.9409 0.9127 0.9761 0.9427 0.668481 0.866762 0.966184 1 2810 43252 2619 2047 2661 24539 380 8196 2 4380 46718 2734 2262 2698 25490 404 8750 0.900098 0 . 0 . 127 50,32,25,11 UTR_3_PRIME(MODIFIER||10||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971697 rs2229606 -0.693139 0.725882 127 1886 223 MODIFIER 52 CODING DOCK1 C protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249914 T C 0 222 0 0.2163 0.4229 0.5821 0.3998 0.5169 0.5164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.976081 0 . 0 . 129 37,30,28,16 UTR_3_PRIME(MODIFIER||223||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.991243 0.990567 0 0.771435 rs3824814 -0.693146 0.236984 129 1886 234 MODIFIER 52 CODING DOCK1 C protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129249925 T C 0 222 0 0.2163 0.4227 0.5836 0.3978 0.5169 0.5164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.86231 0 . 0 . 120 29,32,25,21 UTR_3_PRIME(MODIFIER||234||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.989581 0.986461 0 0.520889 rs10765104 -0.693147 0.0661153 120 1886 384 MODIFIER 52 CODING DOCK1 G protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129250075 A G 0 115 0 0.2179 0.4217 0.5821 0.3899 0.5169 0.5184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.890852 0 . 0 . 36 2,23,1,10 UTR_3_PRIME(MODIFIER||384||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.867907 rs3740543 -0.676189 0.84546 36 1886 806 MODIFIER 52 CODING DOCK1 T protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129250497 C T 0 222 0 0.6074 0.8544 0.9395 0.9127 0.9751 0.9438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924684 0 . 0 . 133 27,39,17,45 UTR_3_PRIME(MODIFIER||806||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.80283 rs4751414 -0.693147 0.124885 133 1886 912 MODIFIER 52 CODING DOCK1 C protein_coding NM_001290223.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129250603 G C 0 222 0 0.205 0.4181 0.5836 0.3909 0.5199 0.5123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.25452 0 . 0 . 127 43,23,29,20 UTR_3_PRIME(MODIFIER||912||1886|DOCK1|protein_coding|CODING|NM_001290223.1|52|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.953605 rs1051039 -0.693147 0.273608 127 P61Q 318 cCg/cAg MODERATE 1 MISSENSE CODING FOXI2 A protein_coding NM_207426.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129535719 C A 0 139 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.777778 0 . 0 . 11 0,2,7,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cAg|P61Q|318|FOXI2|protein_coding|CODING|NM_207426.2|1|A) 0 0.5 1 0 . 0 . 0 . 0 60 0 1 0.964642 0 0.888889 rs118034115 -0.662043 0.577326 11 318 225 MODIFIER 2 CODING FOXI2 G protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129537454 A G 0 73 0 0.9826 0.9952 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||225||318|FOXI2|protein_coding|CODING|NM_207426.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1887006 -0.556411 0.658104 4 318 838 MODIFIER 2 CODING FOXI2 T protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129538067 C T 0 31.3 0 0.6445 0.745 0.7839 0.8125 0.7575 0.771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||838||318|FOXI2|protein_coding|CODING|NM_207426.2|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3890093 -0.453602 0.64 2 318 1188 MODIFIER 2 CODING FOXI2 T protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129538417 C T 0 5 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1188||318|FOXI2|protein_coding|CODING|NM_207426.2|2|T) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs11018307 -0.453602 0.7 2 318 1207 MODIFIER 2 CODING FOXI2 G protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129538436 C G 0 39.3 0 0.6694 0.8385 0.8847 1 0.829 0.8773 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1207||318|FOXI2|protein_coding|CODING|NM_207426.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12413422 -0.453602 0.68 2 318 1226 MODIFIER 2 CODING FOXI2 T protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129538455 C T 0 50 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||1226||318|FOXI2|protein_coding|CODING|NM_207426.2|2|T) 0 . 0 . 0 . 0 . 0 . 60 0 0 1 0 . rs11594501 -0.511536 0.800701 3 318 1244 MODIFIER 2 CODING FOXI2 T protein_coding NM_207426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129538473 C T 0 46.3 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1244||318|FOXI2|protein_coding|CODING|NM_207426.2|2|T) 0 . 0 . 0 . 0 . 0 . 60 0 0 1 0 . rs4992328 -0.453602 0.5 2 711 2610 MODIFIER 22 CODING PTPRE A protein_coding NM_001316676.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129883780 G A 0 222 0 0.1831 0.1318 0.0735 0.1558 0.0865 0.1258 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.359023 0 . 0 . 173 28,52,31,48 UTR_3_PRIME(MODIFIER||2610||711|PTPRE|protein_coding|CODING|NM_001316676.1|22|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.220864 rs12768414 -0.693147 0.0118254 173 3256 1222 MODIFIER 15 CODING MKI67 G protein_coding NM_002417.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129896232 A G 0 25.9 0 0.5787 0.5597 0.5187 0.624 0.5666 0.4898 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_3_PRIME(MODIFIER||1222||3256|MKI67|protein_coding|CODING|NM_002417.4|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7347 -0.453602 0.22 3 T1848 3256 acG/acA LOW 13 SILENT CODING MKI67 T protein_coding NM_002417.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129904560 C T 0 222 0 0.236 0.2875 0.219 0.3819 0.2992 0.2965 0.251248 0.277564 0.291047 1 2517 35312 2510 2990 2177 19616 270 5232 2 10406 121408 11576 8654 6614 66738 908 16512 0.999662 0 . 0 . 212 76,45,46,34 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1848|3256|MKI67|protein_coding|CODING|NM_002417.4|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.197105 rs2853346 -0.693147 0.679794 212 N1729 3256 aaC/aaT LOW 13 SILENT CODING MKI67 A protein_coding NM_002417.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129904917 G A 0 222 0 0.1505 0.1392 0.1556 0.0813 0.1451 0.1656 0.161371 0.159542 0.158605 1 1702 18305 1985 706 906 10186 131 2689 2 10404 121378 11572 8646 6612 66724 908 16512 0.994095 0 . 0 . 168 45,42,31,38 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1729|3256|MKI67|protein_coding|CODING|NM_002417.4|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977342 rs1894410 -0.693147 0.840367 168 N104S 3256 aAt/aGt MODERATE 5 MISSENSE CODING MKI67 C protein_coding NM_002417.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 129917560 T C 0 222 0 0.5802 0.634 0.719 0.6389 0.665 0.6094 0.564062 0.615136 0.641279 1 5795 78414 8317 5208 4532 43326 615 10621 2 10352 121076 11534 8624 6602 66562 902 16500 0.893079 0 . 0 . 249 45,69,39,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N104S|3256|MKI67|protein_coding|CODING|NM_002417.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.648761 rs2071498 -0.693147 1.23939e-08 249 I174V 238 Atc/Gtc MODERATE 5 MISSENSE CODING MGMT G protein_coding NM_002412.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131565064 A G 0 222 0 0.0061 0.0513 0.0519 0.0139 0.1362 0.0634 0.0224796 0.09251 0.128372 1 191 10869 480 66 772 7956 100 1304 2 8998 110006 10792 8096 5448 60858 778 15036 0.942483 0 . 0 . 337 100,54,89,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I174V|238|MGMT|protein_coding|CODING|NM_002412.4|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991333 rs2308321 -0.693147 0.00379144 337 K209R 238 aAg/aGg MODERATE 5 MISSENSE CODING MGMT G protein_coding NM_002412.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131565170 A G 0 222 0 0.0061 0.0513 0.0519 0.0139 0.1362 0.0634 0.0222424 0.0924958 0.128488 1 197 11184 490 66 822 8196 101 1312 2 9938 118058 11398 8568 6142 64866 860 16286 0.609605 0 . 0 . 232 48,72,28,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K209R|238|MGMT|protein_coding|CODING|NM_002412.4|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.951841 rs2308327 -0.693147 0.00188269 232 551 2473 MODIFIER 16 CODING EBF3 C protein_coding NM_001005463.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131633720 T C 0 228 0 0.0204 0.2887 0.4452 0.4355 0.2893 0.3885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,4,22 UTR_3_PRIME(MODIFIER||2473||551|EBF3|protein_coding|CODING|NM_001005463.2|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8217 -0.692976 0.852439 26 551 1292 MODIFIER 16 CODING EBF3 TA protein_coding NM_001005463.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131634900 T TA 0 117 0 0.031 0.3536 0.5115 0.4355 0.4225 0.5225 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 120 0,0,73,22 UTR_3_PRIME(MODIFIER||1292||551|EBF3|protein_coding|CODING|NM_001005463.2|16|TA) 0 . 0 118 0.983333 1 1 0 . 0 60 0 0 1 0 . rs34421686 -0.693147 9.58903e-07 120 335 31 MODIFIER 1 CODING GLRX3 G protein_coding NM_001199868.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131934654 C G 0 14.9 0 0.0303 0.0797 0.0994 0.0813 0.1153 0.0941 0 . 0 1 9 118 4 8 0 80 2 15 2 192 816 32 48 4 432 8 100 0.6 0 . 0 . 7 4,1,2,0 UTR_5_PRIME(MODIFIER||31||335|GLRX3|protein_coding|CODING|NM_001199868.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.7 rs2274218 -0.453602 0.28 7 335 LOW 6 CODING GLRX3 A protein_coding NM_001199868.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 131967693 T A 0 222 0 0.1884 0.2806 0.2291 0.1915 0.4036 0.407 0.204948 0.325004 0.386512 1 2170 41873 2576 1517 2544 25727 360 6979 2 10374 121142 11556 8634 6596 66574 906 16502 0.996805 0 . 0 . 139 38,22,40,24 SPLICE_SITE_REGION+INTRON(LOW||||335|GLRX3|protein_coding|CODING|NM_001199868.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904721 rs17297984 -0.693147 0.316362 139 586 399 MODIFIER 12 CODING TCERG1L G protein_coding NM_174937.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 132891026 A G 0 222 0 0.9834 0.735 0.6974 0.6796 0.5994 0.6227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.956564 0 . 0 . 36 14,5,9,7 UTR_3_PRIME(MODIFIER||399||586|TCERG1L|protein_coding|CODING|NM_174937.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.988959 rs7088377 -0.689466 0.819915 36 586 LOW 8 CODING TCERG1L G protein_coding NM_174937.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 132915202 A G 0 228 0 0.1989 0.2692 0.2622 0.4157 0.2416 0.2464 0.212892 0.217779 0.220284 2 1916 25543 2451 3243 1225 13364 182 3162 2 7716 89694 7670 6838 4812 50062 642 11954 0 . 0 . 0 81 0,0,37,36 SPLICE_SITE_REGION+INTRON(LOW||||586|TCERG1L|protein_coding|CODING|NM_174937.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2298193,rs386564178 -0.693147 0.122447 81 420 15 MODIFIER 7 CODING PPP2R2D C protein_coding NM_018461.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133769482 G C 0 222 0 0.2874 0.3147 0.2622 0.4524 0.2644 0.2986 0.273799 0.266004 0.262055 1 2639 31319 3074 3751 1664 17078 213 2900 2 8856 101702 10168 7936 5868 58998 742 9134 0.725773 0 . 0 . 140 26,36,18,47 UTR_3_PRIME(MODIFIER||15||420|PPP2R2D|protein_coding|CODING|NM_018461.4|7|C|WARNING_TRANSCRIPT_NO_START_CODON) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969621 rs7894 -0.693147 0.0129156 140 420 101 MODIFIER 7 CODING PPP2R2D A protein_coding NM_018461.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133769568 G A 0 164 0 0.087 0.1693 0.1297 0.3601 0.0775 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.916962 0 . 0 . 49 2,26,1,17 UTR_3_PRIME(MODIFIER||101||420|PPP2R2D|protein_coding|CODING|NM_018461.4|7|A|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99943 rs11146336 -0.691153 0.461507 49 420 2856 MODIFIER 7 CODING PPP2R2D T protein_coding NM_018461.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133772323 C T 0 9.7 0 0.8616 0.6917 0.6542 0.6329 0.6034 0.6401 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2856||420|PPP2R2D|protein_coding|CODING|NM_018461.4|7|T|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 38 0 0 . 0 . rs9787525 -0.379885 0 1 420 2962 MODIFIER 7 CODING PPP2R2D G protein_coding NM_018461.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133772429 A G 0 9.7 0 0.6029 0.5761 0.5418 0.631 0.4901 0.5961 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2962||420|PPP2R2D|protein_coding|CODING|NM_018461.4|7|G|WARNING_TRANSCRIPT_NO_START_CODON) 0 0.5 1 0 . 1 0 . 0 . 38 0 0 . 0 . rs9787590 -0.379885 0 1 259 579 MODIFIER 6 CODING BNIP3 T protein_coding NM_004052.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133781449 C T 0 118 0 0.323 0.3245 0.2695 0.4484 0.2654 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.194346 0 . 0 . 14 0,7,1,6 UTR_3_PRIME(MODIFIER||579||259|BNIP3|protein_coding|CODING|NM_004052.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 1 0 0.571605 rs6557 -0.636426 0.499424 14 259 230 MODIFIER 6 CODING BNIP3 T protein_coding NM_004052.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133781798 C T 0 73 0 0.3238 0.3247 0.2695 0.4484 0.2654 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.4 0 . 0 . 7 2,0,5,0 UTR_3_PRIME(MODIFIER||230||259|BNIP3|protein_coding|CODING|NM_004052.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0 rs4550 -0.590765 0.713234 7 S39A 259 Tcc/Gcc MODERATE 1 MISSENSE CODING BNIP3 C protein_coding NM_004052.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133795391 A C 0 79 0 0.1483 0.1897 0.1398 0.3512 0.0865 0.2209 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 0,1,0,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S39A|259|BNIP3|protein_coding|CODING|NM_004052.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs11556626 -0.590765 0.0299925 6 N313 844 aaT/aaC LOW 4 SILENT CODING JAKMIP3 C protein_coding NM_001105521.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133948634 T C 0 228 0 0.9796 0.8606 0.8501 0.9891 0.6958 0.7444 0.950768 0.774557 0.693312 2 9292 91163 10020 8464 4396 46093 655 12243 2 9768 120106 11548 8612 6604 66176 892 16506 0 . 0 . 0 132 0,0,30,87 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N313|844|JAKMIP3|protein_coding|CODING|NM_001105521.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2814182 -0.693147 6.54206e-05 132 D412 844 gaT/gaC LOW 6 SILENT CODING JAKMIP3 C protein_coding NM_001105521.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133950642 T C 0 222 0 0.0023 0.0803 0.0101 0.3016 0.0308 0.0583 0.0075956 0.0257219 0.0341268 1 64 6964 147 2878 313 2588 40 934 2 9790 120540 11568 8606 6614 66560 898 16504 0.944718 0 . 0 . 121 35,23,29,27 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D412|844|JAKMIP3|protein_coding|CODING|NM_001105521.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.502429 rs75996870 -0.693147 0.174779 121 D467 844 gaC/gaT LOW 9 SILENT CODING JAKMIP3 T protein_coding NM_001105521.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133954011 C T 0 222 0 0.4584 0.514 0.5793 0.5883 0.4841 0.4969 0.452345 0.47825 0.490739 1 4450 59681 6636 4698 3150 31878 456 8413 2 9562 118318 11340 8476 6514 65172 882 16372 0.108219 0 . 0 . 408 102,73,96,72 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D467|844|JAKMIP3|protein_coding|CODING|NM_001105521.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.860108 0.891404 0 0.423767 rs2818387 -0.693147 0.300397 408 H596 844 caC/caT LOW 13 SILENT CODING JAKMIP3 T protein_coding NM_001105521.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133961494 C T 0 222 0 0.2821 0.4255 0.7233 0.3065 0.5895 0.362 0.346206 0.518245 0.606428 1 3270 61859 9041 2653 2834 36849 466 6746 2 9306 110714 10870 7620 5950 61038 834 15096 0.967278 0 . 0 . 114 35,8,37,15 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H596|844|JAKMIP3|protein_coding|CODING|NM_001105521.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.450081 rs2818384 -0.693147 0.53249 114 844 LOW 18 CODING JAKMIP3 T protein_coding NM_001105521.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133976706 G T 0 222 0 0.1142 0.3307 0.5317 0.3234 0.4851 0.3292 0.180222 0.403834 0.517639 1 553 11229 417 361 229 6290 103 3276 2 2972 24808 662 938 392 11632 214 7998 0.241425 0 . 0 . 174 46,28,48,28 SPLICE_SITE_REGION+INTRON(LOW||||844|JAKMIP3|protein_coding|CODING|NM_001105521.2|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.486156 rs12776458 -0.693147 0.000716795 174 844 1145 MODIFIER 22 CODING JAKMIP3 A protein_coding NM_001105521.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133981682 G A 0 228 0 0.4463 0.6242 0.6758 0.9365 0.5258 0.6074 0 . 0 2 261 7005 113 184 2 1867 86 4492 2 564 11906 186 200 4 3484 126 7342 0 . 0 . 0 115 0,0,49,61 UTR_3_PRIME(MODIFIER||1145||844|JAKMIP3|protein_coding|CODING|NM_001105521.2|22|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4880338 -0.693147 0.154516 115 844 2890 MODIFIER 23 CODING JAKMIP3 T protein_coding NM_001105521.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 133983427 C T 0 9.7 0 0.3366 0.5942 0.67 0.9365 0.5249 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2890||844|JAKMIP3|protein_coding|CODING|NM_001105521.2|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7096307 -0.379885 0 1 572 146 MODIFIER 1 CODING DPYSL4 T protein_coding NM_006426.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134000422 C T 0 9.7 0 0.3064 0.5403 0.5692 0.9236 0.5149 0.4673 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||572|DPYSL4|protein_coding|CODING|NM_006426.2|1|T),UTR_5_PRIME(MODIFIER||146||572|DPYSL4|protein_coding|CODING|NM_006426.2|1|T),DOWNSTREAM(MODIFIER||2109||844|JAKMIP3|protein_coding|CODING|NM_001105521.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs61865793 -0.379885 0 1 572 LOW 8 CODING DPYSL4 T protein_coding NM_006426.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134013856 G T 0 222 0 0.0492 0.3962 0.5144 0.6845 0.4831 0.3947 0.124603 0.377595 0.507209 1 1145 58702 7959 6024 3036 33028 430 7080 2 10234 120024 11528 8612 6550 65770 888 16442 0.996672 0 . 0 . 284 84,39,67,63 SPLICE_SITE_REGION+INTRON(LOW||||572|DPYSL4|protein_coding|CODING|NM_006426.2|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.624529 rs871883 -0.693147 0.262013 284 A314 572 gcG/gcA LOW 9 SILENT CODING DPYSL4 A protein_coding NM_006426.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134013990 G A 0 228 0 0.8003 0.8546 0.8862 0.9286 0.8131 0.8722 0.804585 0.819622 0.827326 2 8200 102569 10628 8118 5278 55241 758 14346 2 10316 120560 11552 8640 6600 66040 906 16506 0 . 0 . 0 90 0,0,11,77 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A314|572|DPYSL4|protein_coding|CODING|NM_006426.2|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2247705 -0.693147 0.00854667 90 G497 572 ggA/ggG LOW 13 SILENT CODING DPYSL4 G protein_coding NM_006426.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134017295 A G 0 228 0 0.7549 0.8417 0.8718 0.9583 0.8052 0.8548 0.751817 0.790923 0.810959 2 7689 99729 10508 8244 5291 53512 734 13751 2 10152 119466 11494 8552 6572 65412 888 16396 0 . 0 . 0 107 0,0,86,14 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G497|572|DPYSL4|protein_coding|CODING|NM_006426.2|13|G),DOWNSTREAM(MODIFIER||3701||486|STK32C|protein_coding|CODING|NM_173575.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12313 -0.693147 0.00554601 107 572 400 MODIFIER 14 CODING DPYSL4 T protein_coding NM_006426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134018834 C T 0 207 0 0.1362 0.1849 0.0403 0.5665 0.0288 0.1207 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.988657 0 . 0 . 32 10,7,10,5 UTR_3_PRIME(MODIFIER||400||572|DPYSL4|protein_coding|CODING|NM_006426.2|14|T),DOWNSTREAM(MODIFIER||2162||486|STK32C|protein_coding|CODING|NM_173575.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.57178 rs2279523 -0.688148 0.786796 32 486 396 MODIFIER 12 CODING STK32C A protein_coding NM_173575.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134021118 C A 0 9.7 0 0.7685 0.846 0.879 0.9583 0.8052 0.8538 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||396||486|STK32C|protein_coding|CODING|NM_173575.2|12|A),DOWNSTREAM(MODIFIER||1838||572|DPYSL4|protein_coding|CODING|NM_006426.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2818413 -0.379885 0 1 R401 486 cgT/cgC LOW 10 SILENT CODING STK32C G protein_coding NM_173575.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134036193 A G 0 212 0 0.6513 0.7662 0.8573 0.8442 0.7883 0.7536 0.677192 0.752231 0.790649 1 6779 93430 10227 7213 4809 51232 672 12498 2 10082 117882 11334 8422 6076 64780 866 16322 0.782234 0 . 0 . 63 24,13,12,7 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R401|486|STK32C|protein_coding|CODING|NM_173575.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99985 rs2818401 -0.69168 0.739455 63 T192 486 acG/acA LOW 4 SILENT CODING STK32C T protein_coding NM_173575.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134040367 C T 0 222 0 0.0242 0.0853 0.0706 0.1825 0.0805 0.0828 0.0288243 0.0580501 0.0730233 1 313 9100 693 1696 387 4840 54 1117 2 10284 120234 11534 8610 6600 65800 898 16508 0.733766 0 . 0 . 113 41,26,22,16 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T192|486|STK32C|protein_coding|CODING|NM_173575.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.431254 rs12413251 -0.693143 0.757963 113 P233 530 ccA/ccG LOW 6 SILENT CODING LRRC27 G protein_coding NM_001143757.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134161633 A G 0 222 0 0.9834 0.8458 0.7954 0.8651 0.7535 0.771 0.944167 0.816469 0.751047 1 9852 95246 9501 7402 5149 50250 679 12413 2 10400 121244 11560 8632 6610 66624 906 16512 0.999868 0 . 0 . 77 13,23,12,26 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P233|530|LRRC27|protein_coding|CODING|NM_001143757.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.826959 rs2474328 -0.693143 0.47511 77 530 3233 MODIFIER 11 CODING LRRC27 A protein_coding NM_001143757.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134191979 G A 0 32.6 0 0.0098 0.0383 0.1037 0.0565 0.0368 0.0133 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3233||530|LRRC27|protein_coding|CODING|NM_001143757.1|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs61864551 -0.379885 0 2 E344 590 gaG/gaA LOW 2 SILENT CODING PWWP2B A protein_coding NM_138499.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134219036 G A 0 203 0 0.1241 0.103 0.0908 0.0813 0.0875 0.1217 0.0830979 0.0715078 0.0656228 2 806 9031 705 582 648 4299 73 1918 2 7668 109012 11144 8130 6250 58872 788 16160 0 . 0 . 0 12 0,0,10,1 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E344|590|PWWP2B|protein_coding|CODING|NM_138499.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11817589 -0.676189 0.0837689 12 P347 590 ccC/ccT LOW 2 SILENT CODING PWWP2B T protein_coding NM_138499.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134219045 C T 0 205 0 0.2027 0.1637 0.2104 0.1429 0.1074 0.1575 0.149718 0.106231 0.0841501 2 1452 13515 1948 1034 822 5656 113 2490 2 7790 109578 11174 8130 6298 59200 798 16188 0 . 0 . 0 12 0,0,10,1 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P347|590|PWWP2B|protein_coding|CODING|NM_138499.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11146364 -0.676189 0.0837689 12 145 246 MODIFIER 3 CODING C10orf91 G protein_coding NM_173541.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134261811 A G 0 109 0 0.9811 0.9251 0.9063 0.8968 0.9473 0.8691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,4 UTR_3_PRIME(MODIFIER||246||145|C10orf91|protein_coding|CODING|NM_173541.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7081436 -0.590765 0.623223 5 K45R 412 aAg/aGg MODERATE 3 MISSENSE CODING INPP5A G protein_coding NM_005539.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134459388 A G 0 228 0 0.1014 0.2123 0.2565 0.3016 0.2137 0.2372 0.107808 0.17069 0.202907 2 1106 25508 3384 2995 1097 13086 163 3677 2 9732 116476 11146 8466 6190 64244 856 15842 0 . 0 . 0 137 0,0,78,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K45R|412|INPP5A|protein_coding|CODING|NM_005539.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1133400 -0.693147 0.5963 137 V209A 277 gTg/gCg MODERATE 3 MISSENSE CODING NKX6-2 G protein_coding NM_177400.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134598628 A G 0 228 0 0.9985 0.9752 0.9654 1 0.9453 0.956 0.991568 0.955855 0.937616 2 9966 114017 11179 8551 6283 61399 840 15799 2 10044 118998 11424 8552 6498 65148 876 16456 1 0 . 0 . 100 1,0,20,74 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V209A|277|NKX6-2|protein_coding|CODING|NM_177400.2|3|G),DOWNSTREAM(MODIFIER||1644||412|INPP5A|protein_coding|CODING|NM_005539.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2804003 -0.693147 0.0182086 100 R2555 2715 agA/agG LOW 58 SILENT CODING CFAP46 C protein_coding NM_001200049.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134622408 T C 0 228 0 0.9644 0.7426 0.5346 0.7272 0.6779 0.6728 0.928831 0.753116 0.663256 2 8639 72406 4038 5928 3808 40869 514 8610 2 9296 106878 10262 8154 5308 60592 752 12514 0 . 0 . 0 19 0,0,10,7 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R2555|2715|CFAP46|protein_coding|CODING|NM_001200049.2|58|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2767434 -0.690438 0.379052 19 S2540G 2715 Agt/Ggt MODERATE 57 MISSENSE CODING CFAP46 C protein_coding NM_001200049.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134623959 T C 0 228 0 0.9697 0.757 0.5447 0.7381 0.6978 0.7004 0.936904 0.773566 0.689884 2 9733 84012 4509 6356 4859 46265 640 11650 2 10366 120900 11562 8620 6604 66336 902 16510 0.875 0 . 0 . 158 1,1,105,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S2540G|2715|CFAP46|protein_coding|CODING|NM_001200049.2|57|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.385417 rs2254419 -0.693147 0.00169998 158 A2511 2715 gcG/gcA LOW 56 SILENT CODING CFAP46 T protein_coding NM_001200049.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134624504 C T 0 222 0 0.0983 0.3311 0.219 0.6181 0.3419 0.4182 0.142435 0.270804 0.336512 1 1098 34677 2107 4570 1348 19257 236 6061 2 6526 86204 7548 7314 3096 47686 616 13418 0.934592 0 . 0 . 105 19,17,24,29 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A2511|2715|CFAP46|protein_coding|CODING|NM_001200049.2|56|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.397464 rs2274429 -0.693147 0.0012506 105 C2125R 2715 Tgc/Cgc MODERATE 44 MISSENSE CODING CFAP46 G protein_coding NM_001200049.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134659626 A G 0 222 0 0.2867 0.1687 0.1167 0.0744 0.1352 0.1779 0.252615 0.166795 0.122907 1 2464 14556 657 582 650 7530 102 2571 2 8756 104178 10056 7632 4278 58012 744 14700 0.65641 0 . 0 . 239 75,61,53,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C2125R|2715|CFAP46|protein_coding|CODING|NM_001200049.2|44|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.597043 rs10870341 -0.693147 0.0966176 239 P681 2715 ccC/ccT LOW 17 SILENT CODING CFAP46 A protein_coding NM_001200049.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134730130 G A 0 222 0 0 0.0085863 0 0.0427 0 0 0 . 0 1 0 31 0 31 0 0 0 0 2 852 11112 254 474 684 3976 128 4744 0.203279 0 . 0 . 135 32,25,46,28 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P681|2715|CFAP46|protein_coding|CODING|NM_001200049.2|17|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.442657 rs189591112 -0.693147 0.0811334 135 560 100 MODIFIER 2 CODING ADGRA1 G protein_coding NM_001083909.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134902314 A G 0 155 0 0.9213 0.7059 0.5821 0.7222 0.5507 0.6452 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,2 UTR_5_PRIME(MODIFIER||100||560|ADGRA1|protein_coding|CODING|NM_001083909.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10745302 -0.636426 0.427859 7 560 18 MODIFIER 2 CODING ADGRA1 G protein_coding NM_001083909.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134902396 C G 0 228 0 0.6732 0.6182 0.5504 0.6994 0.5219 0.6074 0.662091 0.557922 0.505459 2 1046 5310 408 582 47 2832 43 352 2 1488 8428 644 758 74 4832 72 560 0 . 0 . 0 14 0,0,9,4 UTR_5_PRIME(MODIFIER||18||560|ADGRA1|protein_coding|CODING|NM_001083909.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10776692 -0.683931 0.0834917 14 560 16 MODIFIER 2 CODING ADGRA1 T protein_coding NM_001083909.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134902398 C T 0 228 0 0.9788 0.7428 0.6326 0.6994 0.6103 0.683 0.927163 0.733741 0.636375 2 1547 6935 527 633 66 3691 54 417 2 1630 9480 768 818 98 5482 76 608 0 . 0 . 0 14 0,0,10,4 UTR_5_PRIME(MODIFIER||16||560|ADGRA1|protein_coding|CODING|NM_001083909.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10776693 -0.686358 0.0777558 14 S278 560 tcA/tcG LOW 7 SILENT CODING ADGRA1 G protein_coding NM_001083909.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134942166 A G 0 222 0 0.4826 0.4892 0.621 0.5357 0.4145 0.4335 0.474476 0.410422 0.377679 1 4410 49548 7970 4620 2537 22837 378 6796 2 8554 105642 10784 7952 5256 57022 786 15288 0.997708 0 . 0 . 86 32,9,25,10 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S278|560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.650432 rs2806452 -0.693136 0.773121 86 A336 560 gcC/gcT LOW 7 SILENT CODING ADGRA1 T protein_coding NM_001083909.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134942340 C T 0 191 0 0.2791 0.2806 0.2767 0.4573 0.1312 0.2566 0.233024 0.155482 0.115978 1 1841 20931 3872 3602 890 7129 134 3463 2 5738 82266 9004 7074 3790 42876 562 13222 0.886703 0 . 0 . 36 1,17,3,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A336|560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993888 rs10776696 -0.691153 0.107123 36 P500 560 ccG/ccA LOW 7 SILENT CODING ADGRA1 A protein_coding NM_001083909.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134942832 G A 0 164 0 0.2648 0.2546 0.2421 0.4454 0.0905 0.2219 0.209557 0.119313 0.0735398 1 852 7241 1109 1070 204 2012 60 1934 2 2458 26354 2100 1832 526 10248 236 8954 0.268646 0 . 0 . 54 22,7,22,1 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P500|560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.389838 rs45586231 -0.692717 0.0833146 54 560 70 MODIFIER 7 CODING ADGRA1 A protein_coding NM_001083909.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134943085 G A 0 180 0 0.267 0.2788 0.2767 0.4593 0.1312 0.2618 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.817092 0 . 0 . 68 1,27,1,38 UTR_3_PRIME(MODIFIER||70||560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997095 rs73399158 -0.693144 0.30191 68 560 522 MODIFIER 7 CODING ADGRA1 T protein_coding NM_001083909.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134943537 C T 0 9.7 0 0.3011 0.2865 0.2781 0.4573 0.1312 0.2566 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||522||560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3827689 -0.379885 0 1 560 1305 MODIFIER 7 CODING ADGRA1 T protein_coding NM_001083909.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134944320 C T 0 4.6 0 0.292 0.2839 0.2781 0.4573 0.1312 0.2556 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,1,1,1 UTR_3_PRIME(MODIFIER||1305||560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.333333 rs4838799 -0.453602 0.36 5 560 1412 MODIFIER 7 CODING ADGRA1 A protein_coding NM_001083909.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134944427 G A 0 57 0 0.8056 0.6605 0.7277 0.5367 0.6054 0.6012 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 1,1,1,2 UTR_3_PRIME(MODIFIER||1412||560|ADGRA1|protein_coding|CODING|NM_001083909.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.333333 rs2806454 -0.511536 0.724364 5 F204 1749 ttC/ttT LOW 5 SILENT CODING KNDC1 T protein_coding NM_152643.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134997480 C T 0 222 0 0.118 0.4195 0.3876 0.5843 0.4384 0.6605 0.167272 0.366292 0.468256 1 1687 55735 4904 5030 2915 30640 455 10104 2 10326 119274 11528 8620 6604 65798 886 15512 0.523904 0 . 0 . 74 15,20,12,19 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F204|1749|KNDC1|protein_coding|CODING|NM_152643.6|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456296 rs57510763 -0.69311 0.585319 74 T250 1749 acG/acC LOW 6 SILENT CODING KNDC1 C protein_coding NM_152643.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 134999602 G C 0 185 0 0.7549 0.7821 0.7939 0.6885 0.8618 0.8252 0.80482 0.85935 0.887074 1 4543 71589 6213 4657 3108 41273 505 11290 2 5868 85970 8376 6614 3654 47462 584 13412 0.989637 0 . 0 . 26 5,7,9,3 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T250|1749|KNDC1|protein_coding|CODING|NM_152643.6|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.898825 rs3008393 -0.680642 0.543455 26 A432 1749 gcT/gcC LOW 6 SILENT CODING KNDC1 C protein_coding NM_152643.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135000148 T C 0 222 0 0.118 0.4167 0.3847 0.5764 0.4354 0.6595 0.163335 0.359781 0.460428 1 1510 53915 4816 4853 2875 29168 433 10260 2 9048 115004 11360 8282 6536 63122 840 15816 0.939296 0 . 0 . 93 26,17,13,21 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A432|1749|KNDC1|protein_coding|CODING|NM_152643.6|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850384 rs3810965 -0.693132 0.180234 93 E436G 1749 gAa/gGa MODERATE 6 MISSENSE CODING KNDC1 G protein_coding NM_152643.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135000159 A G 0 222 0 0.118 0.4169 0.3847 0.5774 0.4354 0.6595 0.158864 0.356604 0.457868 1 1488 53354 4791 4844 2868 28935 426 10002 2 8888 113668 11294 8242 6496 62566 830 15352 0.996814 0 . 0 . 94 25,22,11,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E436G|1749|KNDC1|protein_coding|CODING|NM_152643.6|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.589171 rs3810964,rs386586929 -0.69312 0.288995 94 L717P 1749 cTg/cCg MODERATE 14 MISSENSE CODING KNDC1 C protein_coding NM_152643.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135012162 T C 0 121 0 0.5182 0.5579 0.4914 0.6121 0.5308 0.6309 0.549234 0.559684 0.564992 1 3473 50396 4207 4312 1880 27310 356 8858 2 6088 83670 7406 6592 3226 46302 586 13470 0.283839 0 . 0 COSM427278 32 2,19,1,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L717P|1749|KNDC1|protein_coding|CODING|NM_152643.6|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.504107 rs2998139 -0.676189 0.375317 32 V806D 1749 gTt/gAt MODERATE 14 MISSENSE CODING KNDC1 A protein_coding NM_152643.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135012429 T A 0 92 0 0.1604 0.4002 0.3919 0.5476 0.4195 0.5583 0.166456 0.313913 0.37872 1 678 26637 2937 2271 743 13632 183 6193 2 2896 55128 5938 3934 1682 29284 368 11026 0.503877 0 . 0 . 12 3,3,3,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V806D|1749|KNDC1|protein_coding|CODING|NM_152643.6|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.00775 1.00775 0 0.727822 rs3008390 -0.556411 0.354838 12 V806 1749 gtT/gtC LOW 14 SILENT CODING KNDC1 C protein_coding NM_152643.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135012430 T C 0 92 0 0.5166 0.5451 0.4942 0.5486 0.5318 0.6299 0.589093 0.583623 0.581224 1 1751 32127 3174 2229 934 16792 226 7021 2 3094 54970 5820 3850 1680 29166 370 10990 0.783809 0 . 0 . 12 3,3,3,1 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V806|1749|KNDC1|protein_coding|CODING|NM_152643.6|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.00775 1.00775 0 0.727822 rs3008389 -0.556411 0.354838 12 D880 1749 gaT/gaC LOW 14 SILENT CODING KNDC1 C protein_coding NM_152643.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135012652 T C 0 222 0 0.1203 0.4113 0.4049 0.6091 0.4384 0.5777 0 . 0 1 789 26360 2023 1984 541 14362 206 6455 2 4752 61804 5190 3712 1630 34632 424 11464 0.646724 0 . 0 COSM427279 61 24,6,25,3 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D880|1749|KNDC1|protein_coding|CODING|NM_152643.6|14|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.906345 rs3008388 -0.693054 0.531883 61 1749 438 MODIFIER 30 CODING KNDC1 C protein_coding NM_152643.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135038832 G C 0 9.7 0 1 0.9956 0.9813 1 0.993 0.998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||438||1749|KNDC1|protein_coding|CODING|NM_152643.6|30|C),UPSTREAM(MODIFIER||4946||341|UTF1|protein_coding|CODING|NM_003577.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7089153 -0.379885 0 1 1749 592 MODIFIER 30 CODING KNDC1 T protein_coding NM_152643.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135038986 C T 0 9.7 0 0.1967 0.4111 0.3689 0.6002 0.3708 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||592||1749|KNDC1|protein_coding|CODING|NM_152643.6|30|T),UPSTREAM(MODIFIER||4792||341|UTF1|protein_coding|CODING|NM_003577.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3750850 -0.379885 0 1 341 89 MODIFIER 2 CODING UTF1 C protein_coding NM_003577.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135045035 T C 0 9.7 0 0.9909 0.8524 0.8559 0.6677 0.8966 0.8078 0.982906 0.943433 0.927486 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||89||341|UTF1|protein_coding|CODING|NM_003577.2|2|C) 1 0.5 1 0 . 1 0 1 0 . 60 0 0 . 0 . rs3008362 -0.379885 0 1 L42P 258 cTg/cCg MODERATE 1 MISSENSE CODING VENTX C protein_coding NM_014468.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135051543 T C 0 29.7 0 0.2943 0.2438 0.1859 0.376 0.1123 0.2157 0.179057 0.121682 0.0932917 1 1470 15654 2098 2303 535 6116 92 3040 2 5168 77130 8122 6442 2984 41038 502 12874 0.655816 0 . 0 COSM1346923 11 1,7,0,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L42P|258|VENTX|protein_coding|CODING|NM_014468.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.877913 rs2240892 -0.511536 0.480199 11 P48 258 ccA/ccG LOW 1 SILENT CODING VENTX G protein_coding NM_014468.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135051562 A G 0 185 0 0.8268 0.7969 0.6643 0.994 0.6054 0.8446 0.799585 0.660221 0.593897 2 4606 58964 5953 6636 2332 27773 371 11293 2 5588 82148 8136 6680 3440 43988 522 13794 0 . 0 . COSM427282 12 0,0,1,11 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P48|258|VENTX|protein_coding|CODING|NM_014468.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2998143 -0.680642 0.143863 12 258 1046 MODIFIER 3 CODING VENTX C protein_coding NM_014468.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135054856 G C 0 73 0 1 0.9948 0.9942 1 0.9781 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||1046||258|VENTX|protein_coding|CODING|NM_014468.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9418954 -0.511536 0.62656 3 824 137 MODIFIER 23 CODING ADAM8 A protein_coding NM_001109.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135076523 C A 0 222 0 0.6936 0.8289 0.8141 0.9167 0.8926 0.8661 0.723105 0.831155 0.886512 1 7348 103497 9168 8087 5931 58904 798 13261 2 10340 118928 11556 8634 6612 65898 888 15000 0.765498 0 . 0 . 74 24,12,23,9 UTR_3_PRIME(MODIFIER||137||824|ADAM8|protein_coding|CODING|NM_001109.4|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988275 rs2995300 -0.69312 0.483822 74 824 64 MODIFIER 23 CODING ADAM8 C protein_coding NM_001109.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135076596 T C 0 222 0 0.4153 0.737 0.7594 0.9137 0.8698 0.8374 0.452565 0.725819 0.865814 1 4642 100702 8910 8103 5889 58178 778 14202 2 10400 121356 11576 8650 6614 66702 906 16508 0.601781 0 . 0 . 105 32,19,21,25 UTR_3_PRIME(MODIFIER||64||824|ADAM8|protein_coding|CODING|NM_001109.4|23|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98184 rs2230576 -0.693147 0.122119 105 P788 824 ccC/ccT LOW 22 SILENT CODING ADAM8 A protein_coding NM_001109.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135077225 G A 0 222 0 0 0.0041933 0 0.0208 0 0 0 . 0 1 0 40 0 39 0 0 0 1 2 3802 30752 1558 2276 586 15966 242 6322 0.594236 0 . 0 . 219 64,28,68,30 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P788|824|ADAM8|protein_coding|CODING|NM_001109.4|22|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.977123 rs189433072 -0.693147 0.504528 219 V690M 824 Gtg/Atg MODERATE 20 MISSENSE CODING ADAM8 T protein_coding NM_001109.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135081618 C T 0 66 0 0 0.0041933 0 0.0208 0 0 0 . 0 1 0 23 0 23 0 0 0 0 2 1788 10860 710 1020 184 6466 74 618 1 0 . 0 . 6 0,1,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V690M|824|ADAM8|protein_coding|CODING|NM_001109.4|20|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs149418021 -0.556411 0.0751808 6 F657L 824 Ttc/Ctc MODERATE 19 MISSENSE CODING ADAM8 G protein_coding NM_001109.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135082346 A G 0 222 0 0.6921 0.8243 0.8026 0.9286 0.8787 0.8548 0.673785 0.801 0.866132 1 6791 102431 9071 8179 5943 57310 785 14352 2 10028 119034 11400 8570 6536 65180 882 16438 0.55932 0 . 0 . 182 40,56,28,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F657L|824|ADAM8|protein_coding|CODING|NM_001109.4|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.682509 rs2275720 -0.693147 0.00491125 182 A365 824 gcG/gcA LOW 11 SILENT CODING ADAM8 T protein_coding NM_001109.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135085321 C T 0 158 0 0.7489 0.8466 0.8242 0.9167 0.8946 0.8732 0.772624 0.848529 0.887401 1 7407 103579 9139 7996 5899 57739 791 14608 2 9772 118226 11450 8534 6578 64588 878 16426 0.785785 0 . 0 . 27 9,0,17,1 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A365|824|ADAM8|protein_coding|CODING|NM_001109.4|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945647 rs1131720 -0.691153 0.754022 27 C330 824 tgT/tgC LOW 11 SILENT CODING ADAM8 G protein_coding NM_001109.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135085426 A G 0 222 0 0.9932 0.9189 0.8501 0.9286 0.8996 0.8773 0.970949 0.919576 0.893256 1 9996 108246 9391 8213 6027 59080 816 14723 2 10242 120044 11544 8608 6614 65642 890 16504 0.2566 0 . 0 COSM427283 78 27,4,33,6 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C330|824|ADAM8|protein_coding|CODING|NM_001109.4|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720377 rs1131719 -0.693144 0.319058 78 T300 824 acC/acT LOW 10 SILENT CODING ADAM8 A protein_coding NM_001109.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135085754 G A 0 222 0 0.9039 0.8836 0.8184 0.9286 0.8777 0.862 0.898904 0.879025 0.86885 1 2174 16051 295 522 41 6212 164 6643 2 2434 18258 350 560 44 7144 174 7552 0.709064 0 . 0 . 35 5,9,3,12 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T300|824|ADAM8|protein_coding|CODING|NM_001109.4|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997859 rs1131718 -0.688148 0.313043 35 G80 824 ggC/ggT LOW 4 SILENT CODING ADAM8 A protein_coding NM_001109.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135087521 G A 0 205 0 0.4228 0.7242 0.7579 0.9167 0.827 0.8037 0.495879 0.710019 0.818933 1 4330 86451 7497 7465 4356 49767 606 12430 2 8396 106070 9680 7956 4996 59328 716 14998 0.765489 0 . 0 . 56 21,5,26,4 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G80|824|ADAM8|protein_coding|CODING|NM_001109.4|4|A),DOWNSTREAM(MODIFIER||4613||930|TUBGCP2|protein_coding|CODING|NM_001256617.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.157651 rs3008326 -0.693097 0.00554976 56 W35R 824 Tgg/Cgg MODERATE 2 MISSENSE CODING ADAM8 G protein_coding NM_001109.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135089035 A G 0 222 0 0.9387 0.9032 0.8401 0.9286 0.8996 0.8773 0.925263 0.909171 0.901102 1 2576 22954 927 974 180 10735 213 7349 2 2788 25458 1102 1032 198 11914 228 8196 0.557736 0 . 0 . 132 20,39,19,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W35R|824|ADAM8|protein_coding|CODING|NM_001109.4|2|G),DOWNSTREAM(MODIFIER||3099||930|TUBGCP2|protein_coding|CODING|NM_001256617.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988029 rs2275725 -0.693147 0.415268 132 F727 930 ttT/ttC LOW 15 SILENT CODING TUBGCP2 G protein_coding NM_001256617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135097434 A G 0 222 0 0.9175 0.902 0.8401 0.9286 0.8996 0.8998 0.903087 0.895202 0.891163 1 9393 108804 9423 8263 6026 59960 827 14912 2 10406 121400 11576 8654 6614 66730 908 16512 0.702514 0 . 0 . 187 43,38,32,51 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F727|930|TUBGCP2|protein_coding|CODING|NM_001256617.1|15|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.127145 rs2995326 -0.693147 0.113235 187 Y675 930 taC/taT LOW 14 SILENT CODING TUBGCP2 A protein_coding NM_001256617.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135098672 G A 0 222 0 0.882 0.888 0.8415 0.9286 0.8976 0.8773 0.874262 0.885207 0.890814 1 9057 107974 9386 8249 6018 59715 824 14725 2 10390 121088 11552 8640 6604 66484 906 16512 0.930102 0 . 0 . 308 77,43,110,47 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y675|930|TUBGCP2|protein_coding|CODING|NM_001256617.1|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836324 rs3008334 -0.693147 0.049141 308 H101R 151 cAt/cGt MODERATE 5 MISSENSE CODING PRAP1 G protein_coding NM_145202.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135165790 A G 0 228 0 0.9713 0.992 0.9971 1 1 1 0.969133 0.989543 1 2 10080 120772 11561 8652 6613 66454 903 16509 2 10388 121100 11572 8652 6614 66460 904 16510 0 . 0 . 0 115 0,0,65,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H101R|151|PRAP1|protein_coding|CODING|NM_145202.4|5|G),DOWNSTREAM(MODIFIER||2868||154|FUOM|protein_coding|CODING|NM_001098483.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4369319 -0.693147 0.0180973 115 290 281 MODIFIER 8 CODING ECHS1 A protein_coding NM_004092.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135176091 G A 0 178 0 0.3404 0.7334 0.8501 0.9603 0.8509 0.8272 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,4,3 UTR_3_PRIME(MODIFIER||281||290|ECHS1|protein_coding|CODING|NM_004092.3|8|A),UPSTREAM(MODIFIER||4562||154|FUOM|protein_coding|CODING|NM_001098483.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1.01283 0 . rs4604 -0.636426 0.116635 7 T194 290 acT/acC LOW 5 SILENT CODING ECHS1 G protein_coding NM_004092.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135180430 A G 0 228 0 0.8169 0.9479 0.9741 1 0.999 1 0.830005 0.941873 0.999186 2 8542 118711 11479 8634 6614 66036 900 16506 2 10328 120628 11560 8634 6614 66078 906 16508 0 . 0 . 0 165 0,0,72,78 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T194|290|ECHS1|protein_coding|CODING|NM_004092.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2230261 -0.693147 0.0226344 165 T75I 290 aCc/aTc MODERATE 2 MISSENSE CODING ECHS1 A protein_coding NM_004092.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135184126 G A 0 228 0 0.4697 0.8213 0.9135 0.9851 0.9453 0.9346 0.5302 0.801338 0.940219 2 5211 108348 10837 8314 6370 61533 836 15247 2 9956 118662 11350 8532 6558 65070 896 16300 0 . 0 . 0 61 0,0,49,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T75I|290|ECHS1|protein_coding|CODING|NM_004092.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1049951,rs386513787 -0.693147 0.207133 61 V11A 290 gTc/gCc MODERATE 1 MISSENSE CODING ECHS1 G protein_coding NM_004092.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135186806 A G 0 228 0 0.2829 0.6759 0.6988 0.9355 0.7674 0.8292 0.341769 0.604804 0.739262 2 503 12088 498 674 60 4998 98 5257 2 1402 16006 630 706 72 6518 124 6554 0 . 0 . COSM427288 27 0,0,9,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V11A|290|ECHS1|protein_coding|CODING|NM_004092.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10466126 -0.692352 0.518017 27 P509 511 ccC/ccG LOW 7 SILENT CODING PAOX G protein_coding NM_152911.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135204950 C G 0 228 0 0.68 0.845 0.8948 0.9792 0.8738 0.865 0.736723 0.828591 0.875669 2 7102 104347 10636 8312 6178 56966 793 14360 2 9674 118226 11510 8574 6608 64558 890 16412 0 . 0 . COSM427292,COSM427291 56 0,0,25,23 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P509|511|PAOX|protein_coding|CODING|NM_152911.3|7|G),UPSTREAM(MODIFIER||2671||334|MTG1|protein_coding|CODING|NM_138384.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1046175 -0.693147 0.279374 56 511 50 MODIFIER 7 CODING PAOX G protein_coding NM_152911.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135205009 C G 0 228 0 0.6785 0.8458 0.8948 0.9812 0.8777 0.865 0.740861 0.83224 0.878802 2 6369 93066 9918 7621 5748 51394 674 11342 2 8578 105094 10710 7868 6150 58090 758 12940 0 . 0 . 0 61 0,0,23,34 UTR_3_PRIME(MODIFIER||50||511|PAOX|protein_coding|CODING|NM_152911.3|7|G),UPSTREAM(MODIFIER||2612||334|MTG1|protein_coding|CODING|NM_138384.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1046178 -0.693147 0.270035 61 I293V 334 Att/Gtt MODERATE 11 MISSENSE CODING MTG1 G protein_coding NM_138384.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135233541 A G 0 228 0 0.9894 0.9972 1 1 1 1 0.990468 0.996771 1 2 10296 120765 11569 8650 6614 66510 902 16224 2 10390 120862 11570 8650 6614 66512 902 16224 0 . 0 . 0 188 0,0,87,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I293V|334|MTG1|protein_coding|CODING|NM_138384.2|11|G),DOWNSTREAM(MODIFIER||629||151|SPRN|protein_coding|CODING|NM_001012508.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2255246 -0.693147 0.363747 188 334 409 MODIFIER 11 CODING MTG1 G protein_coding NM_138384.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135234078 A G 0 32.6 0 0.9735 0.993 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||409||334|MTG1|protein_coding|CODING|NM_138384.2|11|G),DOWNSTREAM(MODIFIER||92||151|SPRN|protein_coding|CODING|NM_001012508.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2255262 -0.379885 0 2 151 1323 MODIFIER 2 CODING SPRN G protein_coding NM_001012508.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135235407 C G 0 228 0 0.9024 0.9415 0.9438 0.9891 0.9324 0.953 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 122 1,0,60,47 UTR_3_PRIME(MODIFIER||1323||151|SPRN|protein_coding|CODING|NM_001012508.3|2|G),DOWNSTREAM(MODIFIER||1233||334|MTG1|protein_coding|CODING|NM_138384.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7080988 -0.693147 0.0138216 122 G42 151 ggT/ggC LOW 2 SILENT CODING SPRN G protein_coding NM_001012508.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135237060 A G 0 9.7 0 0.9554 0.9876 0.9957 1 1 1 0 . 0 1 57 2190 41 78 32 582 24 1376 2 64 2198 42 78 32 582 24 1376 0 . 0 . 0 1 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G42|151|SPRN|protein_coding|CODING|NM_001012508.3|2|G),DOWNSTREAM(MODIFIER||2886||334|MTG1|protein_coding|CODING|NM_138384.2||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2480253 -0.379885 0 1 151 11 MODIFIER 2 CODING SPRN T protein_coding NM_001012508.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135237196 C T 0 31.3 0 0.1838 0.4866 0.5331 0.628 0.671 0.5276 0.335151 0.567187 0.682672 2 1353 53002 4664 4491 2544 31930 347 7673 2 4300 81080 7908 6724 3394 45676 550 12528 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||11||151|SPRN|protein_coding|CODING|NM_001012508.3|2|T),DOWNSTREAM(MODIFIER||3022||334|MTG1|protein_coding|CODING|NM_138384.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs4838682 -0.453602 0.44 2 I321 493 atT/atC LOW 6 SILENT CODING CYP2E1 C protein_coding NM_000773.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135347397 T C 0 228 0 0.9002 0.9728 0.9942 1 1 1 0.899001 0.965247 0.999186 2 9389 120263 11527 8654 6614 66672 902 16505 2 10400 121336 11574 8654 6614 66682 906 16506 0 . 0 . 0 202 0,0,52,138 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I321|493|CYP2E1|protein_coding|CODING|NM_000773.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs915909 -0.693147 0.00190197 202 F421 493 ttT/ttC LOW 8 SILENT CODING CYP2E1 C protein_coding NM_000773.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135351362 T C 0 228 0 0.3389 0.7009 0.8213 0.7946 0.8718 0.8323 0.397186 0.718207 0.882674 2 4084 100736 9545 7149 6081 59173 765 13939 2 10388 121336 11570 8640 6612 66716 906 16504 0 . 0 . 0 162 0,0,73,77 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F421|493|CYP2E1|protein_coding|CODING|NM_000773.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2515641 -0.693147 0.0180424 162 493 41 MODIFIER 9 CODING CYP2E1 A protein_coding NM_000773.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135352509 T A 0 222 0 0.1293 0.503 0.6369 0.5258 0.7654 0.6196 0.208579 0.594879 0.792791 1 2078 80329 7245 4773 5138 51347 628 9120 2 10060 114966 11050 8390 6514 64334 856 13762 0.989131 0 . 0 . 85 7,34,9,22 UTR_3_PRIME(MODIFIER||41||493|CYP2E1|protein_coding|CODING|NM_000773.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978111 rs2480257 -0.69311 0.0428893 85 493 46 MODIFIER 9 CODING CYP2E1 G protein_coding NM_000773.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135352514 A G 0 222 0 0.2731 0.5423 0.6499 0.5248 0.7654 0.6186 0.316387 0.631478 0.792907 1 3221 80303 7250 4742 5129 50831 621 8509 2 9944 113094 10964 8292 6496 63640 840 12918 0.470131 0 . 0 . 81 6,33,9,21 UTR_3_PRIME(MODIFIER||46||493|CYP2E1|protein_coding|CODING|NM_000773.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95868 rs2480256 -0.693097 0.0436907 81 351 44 MODIFIER 13 CODING SYCE1 G protein_coding NM_001143764.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135368452 A G 0 222 0 0.0454 0.1548 0.1715 0.2698 0.1093 0.2188 0 . 0 1 106 1254 45 145 177 575 8 198 2 2022 12248 340 556 1596 6426 134 1174 0.203926 0 . 0 . 89 32,12,25,7 UTR_3_PRIME(MODIFIER||44||351|SYCE1|protein_coding|CODING|NM_001143764.1|13|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.960458 rs3737029 -0.69312 0.185367 89 351 34 MODIFIER 13 CODING SYCE1 C protein_coding NM_001143764.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135368462 T C 0 222 0 0.1989 0.1971 0.1844 0.2698 0.1093 0.2188 0 . 0 1 371 1647 50 147 179 600 8 292 2 2042 12608 348 566 1602 6502 138 1410 0.777643 0 . 0 . 87 30,12,24,8 UTR_3_PRIME(MODIFIER||34||351|SYCE1|protein_coding|CODING|NM_001143764.1|13|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.68321 rs2183163 -0.69312 0.354194 87 H321R 351 cAc/cGc MODERATE 13 MISSENSE CODING SYCE1 C protein_coding NM_001143764.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135368590 T C 0 222 0 0.0454 0.1548 0.1715 0.2698 0.1093 0.2188 0.0549133 0.0784056 0.0886235 1 123 2804 57 174 176 800 20 1454 2 2170 20990 424 650 1272 8598 230 7646 0.719131 0 . 0 COSM147095 90 16,23,18,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H321R|351|SYCE1|protein_coding|CODING|NM_001143764.1|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.248086 rs3737031 -0.693146 0.138156 90 K183R 351 aAg/aGg MODERATE 9 MISSENSE CODING SYCE1 C protein_coding NM_001143764.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135369532 T C 0 222 0 0.1997 0.1973 0.1844 0.2698 0.1093 0.2188 0.163867 0.117561 0.0938372 1 1922 16275 1909 2209 808 6128 103 3196 2 10390 121196 11574 8628 6606 66626 906 16466 0.910046 0 . 0 . 61 8,25,6,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|NM_001143764.1|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.926491 rs3747881,rs386585367 -0.693054 0.512571 61 K134 351 aaG/aaA LOW 7 SILENT CODING SYCE1 T protein_coding NM_001143764.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135370633 C T 0 222 0 0.0454 0.1548 0.1715 0.2698 0.1093 0.2188 0.0590104 0.0826542 0.0947674 1 600 14892 1853 2209 810 6120 99 3201 2 10404 121398 11578 8650 6614 66738 908 16506 0.956863 0 . 0 COSM147096,COSM147097 120 6,48,9,49 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K134|351|SYCE1|protein_coding|CODING|NM_001143764.1|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973896 rs8181356 -0.693147 0.905182 120 E132D 351 gaG/gaT MODERATE 7 MISSENSE CODING SYCE1 A protein_coding NM_001143764.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135370639 C A 0 222 0 0.0454 0.1548 0.1715 0.2698 0.1093 0.2188 0.0621879 0.0842688 0.0955814 1 600 14897 1853 2210 810 6122 99 3203 2 10404 121402 11578 8650 6614 66740 908 16508 0.993319 0 . 0 COSM147098,COSM147099 111 6,42,5,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E132D|351|SYCE1|protein_coding|CODING|NM_001143764.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986112 rs386616080,rs8181357 -0.693147 0.707623 111 351 LOW 2 CODING SYCE1 G protein_coding NM_001143764.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135372870 C G 0 222 0 0.0454 0.1548 0.1715 0.2698 0.1093 0.2188 0.061734 0.0838844 0.0952326 1 599 14896 1854 2212 810 6119 99 3203 2 10394 121298 11566 8632 6610 66684 908 16504 0.995958 0 . 0 COSM147101,COSM147100 54 4,21,4,20 SPLICE_SITE_REGION+INTRON(LOW||||351|SYCE1|protein_coding|CODING|NM_001143764.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.9998 rs11101825 -0.692831 0.538306 54 351 LOW 2 CODING SYCE1 T protein_coding NM_001143764.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 10 135373591 C T 0 222 0 0.0961 0.1683 0.1729 0.2698 0.1093 0.2188 0.0935089 0.0950331 0.095814 1 1015 15318 1867 2197 809 6124 103 3203 2 10376 121112 11538 8608 6564 66632 908 16486 0.878297 0 . 0 . 240 61,42,59,39 SPLICE_SITE_REGION+INTRON(LOW||||351|SYCE1|protein_coding|CODING|NM_001143764.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.409267 rs3813873 -0.693147 0.193368 240 95 4 MODIFIER 1 CODING SCGB1C2 C protein_coding NM_001097610.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193096 T C 0 222 0 . 0 . 0 . 0 0.442937 0.476016 0.492609 1 4765 59227 4884 3778 3254 34371 451 7724 2 9700 119322 11406 8512 6516 65886 888 16414 0.819204 0 . 0 . 109 20,27,15,26 UTR_5_PRIME(MODIFIER||4||95|SCGB1C2|protein_coding|CODING|NM_001097610.2|1|C),UTR_5_PRIME(MODIFIER||4||95|SCGB1C1|protein_coding|CODING|NM_145651.2|1|C),UPSTREAM(MODIFIER||3665||254|ODF3|protein_coding|CODING|NM_053280.4||C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.899578 rs2280539 -0.693145 0.158326 109 95 4 MODIFIER 1 CODING SCGB1C1 C protein_coding NM_145651.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193096 T C 0 222 0 . 0 . 0 . 0 0.442937 0.476016 0.492609 1 4765 59227 4884 3778 3254 34371 451 7724 2 9700 119322 11406 8512 6516 65886 888 16414 0.819204 0 . 0 . 109 20,27,15,26 UTR_5_PRIME(MODIFIER||4||95|SCGB1C2|protein_coding|CODING|NM_001097610.2|1|C),UTR_5_PRIME(MODIFIER||4||95|SCGB1C1|protein_coding|CODING|NM_145651.2|1|C),UPSTREAM(MODIFIER||3665||254|ODF3|protein_coding|CODING|NM_053280.4||C) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 0.899578 rs2280539 -0.693145 0.158326 109 R5C 95 Cgt/Tgt MODERATE 1 MISSENSE CODING SCGB1C2 T protein_coding NM_001097610.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193112 C T 0 222 0 0.1899 0.2662 0.2709 0.2411 0.3569 0.2986 0.177434 0.273409 0.321521 1 1909 36158 2370 1874 2089 22870 297 4749 2 9674 118810 11408 8492 6484 65464 880 16408 0.95637 0 . 0 . 109 22,43,11,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5C|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5C|95|SCGB1C1|protein_coding|CODING|NM_145651.2|1|T),UPSTREAM(MODIFIER||3649||254|ODF3|protein_coding|CODING|NM_053280.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.188329 rs7951297 -0.692976 0.705694 109 R5C 95 Cgt/Tgt MODERATE 1 MISSENSE CODING SCGB1C1 T protein_coding NM_145651.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193112 C T 0 222 0 0.1899 0.2662 0.2709 0.2411 0.3569 0.2986 0.177434 0.273409 0.321521 1 1909 36158 2370 1874 2089 22870 297 4749 2 9674 118810 11408 8492 6484 65464 880 16408 0.95637 0 . 0 . 109 22,43,11,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5C|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5C|95|SCGB1C1|protein_coding|CODING|NM_145651.2|1|T),UPSTREAM(MODIFIER||3649||254|ODF3|protein_coding|CODING|NM_053280.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.188329 rs7951297 -0.692976 0.705694 109 C69 95 tgT/tgC LOW 2 SILENT CODING SCGB1C2 C protein_coding NM_001097610.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193863 T C 0 222 0 0.6672 0.7508 0.7795 0.8383 0.7008 0.8047 0.588977 0.602769 0.609713 1 5504 76463 8414 6595 4032 40067 556 11295 2 9798 120424 11540 8604 6602 66488 894 16498 0.777741 0 . 0 . 92 7,24,14,42 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C69|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|2|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C69|95|SCGB1C1|protein_coding|CODING|NM_145651.2|2|C),UPSTREAM(MODIFIER||2898||254|ODF3|protein_coding|CODING|NM_053280.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999961 rs2294081 -0.693147 0.0421185 92 C69 95 tgT/tgC LOW 2 SILENT CODING SCGB1C1 C protein_coding NM_145651.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193863 T C 0 222 0 0.6672 0.7508 0.7795 0.8383 0.7008 0.8047 0.588977 0.602769 0.609713 1 5504 76463 8414 6595 4032 40067 556 11295 2 9798 120424 11540 8604 6602 66488 894 16498 0.777741 0 . 0 . 92 7,24,14,42 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C69|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|2|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C69|95|SCGB1C1|protein_coding|CODING|NM_145651.2|2|C),UPSTREAM(MODIFIER||2898||254|ODF3|protein_coding|CODING|NM_053280.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999961 rs2294081 -0.693147 0.0421185 92 I70R 95 aTa/aGa MODERATE 2 MISSENSE CODING SCGB1C2 G protein_coding NM_001097610.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193865 T G 0 222 0 0.4992 0.493 0.4942 0.4812 0.4901 0.499 0 . 0 1 4909 60320 5786 4313 3307 33300 449 8256 2 9818 120638 11572 8626 6614 66598 898 16512 0.823028 0 . 0 . 92 10,41,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aGa|I70R|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aGa|I70R|95|SCGB1C1|protein_coding|CODING|NM_145651.2|2|G),UPSTREAM(MODIFIER||2896||254|ODF3|protein_coding|CODING|NM_053280.4||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.79527 rs2686894 -0.693136 0.0679874 92 I70R 95 aTa/aGa MODERATE 2 MISSENSE CODING SCGB1C1 G protein_coding NM_145651.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 193865 T G 0 222 0 0.4992 0.493 0.4942 0.4812 0.4901 0.499 0 . 0 1 4909 60320 5786 4313 3307 33300 449 8256 2 9818 120638 11572 8626 6614 66598 898 16512 0.823028 0 . 0 . 92 10,41,11,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aGa|I70R|95|SCGB1C2|protein_coding|CODING|NM_001097610.2|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aGa|I70R|95|SCGB1C1|protein_coding|CODING|NM_145651.2|2|G),UPSTREAM(MODIFIER||2896||254|ODF3|protein_coding|CODING|NM_053280.4||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.79527 rs2686894 -0.693136 0.0679874 92 R11 254 agG/agA LOW 2 SILENT CODING ODF3 A protein_coding NM_053280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 197337 G A 0 222 0 0.2685 0.4127 0.3646 0.7034 0.2167 0.544 0.255692 0.23601 0.225938 1 1592 24809 3103 4006 412 9122 173 6401 2 4876 56226 5822 5330 1224 26856 420 11698 0.964328 0 . 0 . 121 51,24,21,14 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R11|254|ODF3|protein_coding|CODING|NM_053280.4|2|A),DOWNSTREAM(MODIFIER||2837||95|SCGB1C2|protein_coding|CODING|NM_001097610.2||A),DOWNSTREAM(MODIFIER||2764||95|SCGB1C1|protein_coding|CODING|NM_145651.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.681352 rs3802984 -0.693136 0.130787 121 254 LOW 2 CODING ODF3 G protein_coding NM_053280.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 197557 A G 0 228 0 0.553 0.8448 0.9049 0.9921 0.9175 0.9703 0.60059 0.81375 0.922907 2 6047 108640 10635 8556 6019 60783 827 15773 2 10272 120046 11524 8612 6488 65880 892 16378 0 . 0 . 0 75 0,0,48,22 SPLICE_SITE_REGION+INTRON(LOW||||254|ODF3|protein_coding|CODING|NM_053280.4|2|G),DOWNSTREAM(MODIFIER||3057||95|SCGB1C2|protein_coding|CODING|NM_001097610.2||G),DOWNSTREAM(MODIFIER||2984||95|SCGB1C1|protein_coding|CODING|NM_145651.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7103852 -0.693147 0.185361 75 111 1514 MODIFIER 4 CODING BET1L T protein_coding NM_001098787.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 203788 C T 0 222 0 0.0651 0.0809 0.0389 0.1548 0.0328 0.1053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.767347 0 . 0 . 56 20,9,14,9 UTR_3_PRIME(MODIFIER||1514||111|BET1L|protein_coding|CODING|NM_001098787.1|4|T),UPSTREAM(MODIFIER||3723||537|RIC8A|protein_coding|CODING|NM_021932.5||T),DOWNSTREAM(MODIFIER||3530||254|ODF3|protein_coding|CODING|NM_053280.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.954843 rs2280543 -0.692717 0.0215138 56 111 1240 MODIFIER 4 CODING BET1L C protein_coding NM_001098787.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 204062 T C 0 228 0 0.4607 0.6741 0.804 0.8651 0.7515 0.5941 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,3,17 UTR_3_PRIME(MODIFIER||1240||111|BET1L|protein_coding|CODING|NM_001098787.1|4|C),UPSTREAM(MODIFIER||3449||537|RIC8A|protein_coding|CODING|NM_021932.5||C),DOWNSTREAM(MODIFIER||3804||254|ODF3|protein_coding|CODING|NM_053280.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2280544,rs386563484 -0.692067 0.260787 21 111 104 MODIFIER 4 CODING BET1L A protein_coding NM_001098787.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 205198 C A 0 170 0 0.3638 0.5118 0.5749 0.4464 0.7207 0.5194 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,11,0 UTR_3_PRIME(MODIFIER||104||111|BET1L|protein_coding|CODING|NM_001098787.1|4|A),UPSTREAM(MODIFIER||2313||537|RIC8A|protein_coding|CODING|NM_021932.5||A),DOWNSTREAM(MODIFIER||4940||254|ODF3|protein_coding|CODING|NM_053280.4||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3782123 -0.676189 0.575864 12 111 79 MODIFIER 1 CODING BET1L G protein_coding NM_001098787.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 207400 A G 0 198 0 0.6029 0.5927 0.6095 0.4514 0.7565 0.544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,3,5 UTR_5_PRIME(MODIFIER||79||111|BET1L|protein_coding|CODING|NM_001098787.1|1|G),UPSTREAM(MODIFIER||111||537|RIC8A|protein_coding|CODING|NM_021932.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.900802 0 . rs71487219 -0.651104 0.340291 8 111 89 MODIFIER 1 CODING BET1L T protein_coding NM_001098787.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 207410 C T 0 64 0 0.326 0.2438 0.1873 0.1935 0.2724 0.1953 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868321 0 . 0 . 8 1,3,1,3 UTR_5_PRIME(MODIFIER||89||111|BET1L|protein_coding|CODING|NM_001098787.1|1|T),UPSTREAM(MODIFIER||101||537|RIC8A|protein_coding|CODING|NM_021932.5||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.248092 rs58692051 -0.556411 0.189048 8 537 194 MODIFIER 10 CODING RIC8A T protein_coding NM_021932.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 214544 C T 0 29.5 0 0.1982 0.2476 0.2651 0.5714 0.0586 0.1626 0 . 0 1 110 1224 33 129 0 171 20 761 2 554 8182 142 210 4 2540 96 4636 0.655816 0 . 0 . 11 0,8,0,3 UTR_3_PRIME(MODIFIER||194||537|RIC8A|protein_coding|CODING|NM_021932.5|10|T),DOWNSTREAM(MODIFIER||486||399|SIRT3|protein_coding|CODING|NM_012239.5||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 0.979382 rs10081,rs386509582 -0.511536 0.748679 11 399 1334 MODIFIER 7 CODING SIRT3 G protein_coding NM_012239.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 215364 A G 0 46.3 0 0.7943 0.7975 0.8847 0.872 0.837 0.6227 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1334||399|SIRT3|protein_coding|CODING|NM_012239.5|7|G),DOWNSTREAM(MODIFIER||189||537|RIC8A|protein_coding|CODING|NM_021932.5||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs570591 -0.453602 0.64 2 399 642 MODIFIER 7 CODING SIRT3 A protein_coding NM_012239.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 216056 G A 0 168 0 0.0688 0.0813 0.0403 0.1548 0.0328 0.1012 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870325 0 . 0 . 30 13,3,9,1 UTR_3_PRIME(MODIFIER||642||399|SIRT3|protein_coding|CODING|NM_012239.5|7|A),DOWNSTREAM(MODIFIER||881||537|RIC8A|protein_coding|CODING|NM_021932.5||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.776371 rs12226697,rs386467696 -0.670168 0.126632 30 399 15 MODIFIER 1 CODING SIRT3 G protein_coding NM_012239.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 236343 A G 0 86 0 1 0.9992 0.9986 1 0.997 1 0.999155 0.997681 0.996957 2 230 3130 110 154 8 1291 34 1303 2 230 3144 110 154 8 1302 34 1306 0 . 0 . 0 4 0,0,0,4 UTR_5_PRIME(MODIFIER||15||399|SIRT3|protein_coding|CODING|NM_012239.5|1|G),UPSTREAM(MODIFIER||465||378|PSMD13|protein_coding|CODING|NM_175932.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs7118852 -0.556411 0.100421 4 378 179 MODIFIER 1 CODING PSMD13 C protein_coding NM_175932.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 236871 T C 0 58 0 0.8918 0.8171 0.83 0.8075 0.7316 0.8047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.649731 0 . 0 . 9 5,0,4,0 UTR_5_PRIME(MODIFIER||179||378|PSMD13|protein_coding|CODING|NM_175932.2|1|C),UPSTREAM(MODIFIER||509||399|SIRT3|protein_coding|CODING|NM_012239.5||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 0 . 0.89338 rs2272563 -0.556411 0.27062 9 N13S 378 aAc/aGc MODERATE 1 MISSENSE CODING PSMD13 G protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 237087 A G 0 222 0 0.8918 0.8171 0.83 0.8075 0.7316 0.8047 0.883341 0.791173 0.743953 1 9103 93809 9766 7030 5003 49195 677 13035 2 10272 120528 11522 8604 6584 66148 904 16494 0.862334 0 . 0 . 116 38,23,15,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N13S|378|PSMD13|protein_coding|CODING|NM_175932.2|1|G),UPSTREAM(MODIFIER||725||399|SIRT3|protein_coding|CODING|NM_012239.5||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0455701 rs1045288 -0.693136 0.038442 116 E54G 378 gAa/gGa MODERATE 2 MISSENSE CODING PSMD13 G protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244106 A G 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.861552 0.761227 0.709816 1 9156 93266 9737 6981 4937 48828 677 12950 2 10364 120758 11534 8612 6554 66304 906 16484 0.963701 0 . 0 . 155 57,36,30,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E54G|378|PSMD13|protein_coding|CODING|NM_175932.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.877497 rs10902112,rs386496482 -0.693147 0.112669 155 N55D 378 Aat/Gat MODERATE 2 MISSENSE CODING PSMD13 G protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244108 A G 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.861325 0.761766 0.710747 1 9159 93271 9736 6978 4940 48826 677 12955 2 10368 120774 11534 8610 6558 66310 906 16488 0.919238 0 . 0 . 156 58,37,30,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N55D|378|PSMD13|protein_coding|CODING|NM_175932.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.615406 rs7107362 -0.693147 0.112669 156 C57Y 378 tGc/tAc MODERATE 2 MISSENSE CODING PSMD13 A protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244115 G A 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.872447 0.773861 0.72327 1 9145 93247 9733 6975 4945 48822 677 12950 2 10356 120764 11532 8606 6560 66318 906 16486 0.766794 0 . 0 COSM85682 160 55,39,33,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C57Y|378|PSMD13|protein_coding|CODING|NM_175932.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.385414 rs7128044 -0.693147 0.0215108 160 R62W 378 Cgg/Tgg MODERATE 2 MISSENSE CODING PSMD13 T protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244129 C T 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.872616 0.777231 0.728362 1 9160 94012 9801 7041 5005 49350 678 12977 2 10362 121182 11570 8632 6598 66614 906 16500 0.979649 0 . 0 . 175 62,44,34,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R62W|378|PSMD13|protein_coding|CODING|NM_175932.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981076 rs7116130 -0.693147 0.116037 175 A66T 378 Gct/Act MODERATE 2 MISSENSE CODING PSMD13 A protein_coding NM_175932.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244141 G A 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.874489 0.778222 0.72889 1 9149 93968 9800 7036 5009 49314 678 12982 2 10352 121144 11570 8630 6604 66576 906 16506 0.542069 0 . 0 . 172 62,39,33,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A66T|378|PSMD13|protein_coding|CODING|NM_175932.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.944936 rs7128029 -0.693147 0.256242 172 N74 378 aaC/aaT LOW 2 SILENT CODING PSMD13 T protein_coding NM_175932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244167 C T 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.874943 0.781716 0.733953 1 9152 93537 9731 7020 4962 49036 676 12960 2 10362 120876 11520 8626 6568 66402 904 16494 0.982246 0 . 0 COSM292491,COSM292492 166 53,41,27,22 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N74|378|PSMD13|protein_coding|CODING|NM_175932.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.260708 rs1128320 -0.693147 0.257785 166 L76 378 Ttg/Ctg LOW 2 SILENT CODING PSMD13 C protein_coding NM_175932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244171 T C 0 222 0 0.8918 0.8151 0.83 0.8026 0.7306 0.8006 0.872901 0.78064 0.733372 1 9147 93545 9728 7024 4966 49043 678 12959 2 10356 120888 11514 8632 6574 66414 906 16492 0.606444 0 . 0 . 169 53,43,27,21 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L76|378|PSMD13|protein_coding|CODING|NM_175932.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.363936 rs1128321 -0.693147 0.186224 169 H84 378 caT/caC LOW 2 SILENT CODING PSMD13 C protein_coding NM_175932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 244197 T C 0 222 0 0.8918 0.8153 0.83 0.8036 0.7306 0.8006 0.880163 0.788911 0.742149 1 9156 94091 9804 7052 5012 49407 679 12981 2 10356 121240 11570 8640 6606 66654 908 16506 0.999955 0 . 0 . 153 35,49,21,27 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H84|378|PSMD13|protein_coding|CODING|NM_175932.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.145588 rs1128322,rs386518002 -0.693147 0.0697025 153 378 133 MODIFIER 11 CODING PSMD13 C protein_coding NM_175932.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 252733 T C 0 102 0 0.2897 0.2262 0.134 0.4891 0.0258 0.1411 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.803082 0 . 0 . 18 1,8,0,9 UTR_3_PRIME(MODIFIER||133||378|PSMD13|protein_coding|CODING|NM_175932.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.984526 rs1045405 -0.662043 0.75912 18 378 135 MODIFIER 11 CODING PSMD13 C protein_coding NM_175932.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 252735 T C 0 99 0 0.2897 0.2266 0.134 0.4891 0.0268 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.623919 0 . 0 . 18 1,8,0,9 UTR_3_PRIME(MODIFIER||135||378|PSMD13|protein_coding|CODING|NM_175932.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.984526 rs2948222 -0.662043 0.75912 18 M163L 892 Atg/Ctg MODERATE 4 MISSENSE CODING NLRP6 C protein_coding NM_138329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 280221 A C 0 104 0 0.8994 0.7198 0.8314 0.2688 0.8787 0.6994 0.916897 0.904052 0.897624 1 623 9970 181 76 17 3556 103 5414 2 698 13214 228 318 20 4160 140 7650 1 0 . 0 . 7 0,2,2,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ctg|M163L|892|NLRP6|protein_coding|CODING|NM_138329.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.5 rs6421985 -0.556411 0.858927 7 S313 892 agC/agT LOW 4 SILENT CODING NLRP6 T protein_coding NM_138329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 280673 C T 0 220 0 0.2209 0.4874 0.7363 0.2579 0.8032 0.5828 0.527817 0.754265 0.858228 2 1081 40091 3611 855 2304 25975 313 5952 2 2214 51792 4686 2176 2870 30810 404 8632 0 . 0 . 0 32 0,0,30,2 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S313|892|NLRP6|protein_coding|CODING|NM_138329.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12807092 -0.69312 0.0160221 32 Y361F 892 tAt/tTt MODERATE 4 MISSENSE CODING NLRP6 T protein_coding NM_138329.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 280816 A T 0 228 0 0.8169 0.7009 0.8228 0.2877 0.8807 0.6984 0.613936 0.671613 0.701163 2 8425 95664 8756 2162 5599 58449 714 11559 2 10310 120588 11556 8576 6612 66132 898 16504 0.558442 0 . 0 . 172 2,0,120,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y361F|892|NLRP6|protein_coding|CODING|NM_138329.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.746753 rs7482965 -0.693147 0.000151436 172 Y361 892 taT/taC LOW 4 SILENT CODING NLRP6 C protein_coding NM_138329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 280817 T C 0 228 0 0.8169 0.7009 0.8228 0.2877 0.8807 0.6984 0.617567 0.67515 0.704651 2 8424 95686 8756 2165 5600 58470 714 11557 2 10310 120610 11556 8576 6614 66154 898 16502 0.12987 0 . 0 . 172 2,0,120,34 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y361|892|NLRP6|protein_coding|CODING|NM_138329.2|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.746753 rs7482279 -0.693147 0.000154641 172 P812 892 ccT/ccC LOW 7 SILENT CODING NLRP6 C protein_coding NM_138329.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 284538 T C 0 17.7 0 0.5908 0.5471 0.6239 0.3274 0.7674 0.4335 0.651384 0.712133 0.743256 1 6412 78035 6670 2850 5384 49211 604 6904 2 9954 118324 11360 8478 6454 64842 872 16364 0.556584 0 . 0 . 15 2,10,0,3 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P812|892|NLRP6|protein_coding|CODING|NM_138329.2|7|C),UPSTREAM(MODIFIER||4600||737|ATHL1|protein_coding|CODING|NM_025092.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959189 rs6598047 -0.511536 0.354794 15 R122C 737 Cgc/Tgc MODERATE 3 MISSENSE CODING ATHL1 T protein_coding NM_025092.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 290494 C T 0 222 0 0.0749 0.0968 0.0144 0.122 0.0189 0.2393 0.0679191 0.0348379 0.0204403 1 146 1952 9 64 1 202 11 1519 2 1700 17392 358 526 68 6680 170 7890 0.812277 0 . 0 . 90 23,17,22,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R122C|737|ATHL1|protein_coding|CODING|NM_025092.4|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.881813 rs3809110 -0.693146 0.0758344 90 A203 737 gcA/gcG LOW 4 SILENT CODING ATHL1 G protein_coding NM_025092.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 290816 A G 0 228 0 0.7292 0.6665 0.6816 0.4504 0.7475 0.7106 0.727871 0.751269 0.763256 2 7491 85693 7518 3692 4626 49901 622 11843 2 10226 119764 11514 8556 6566 65660 894 16348 0 . 0 . 0 149 0,0,76,55 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A203|737|ATHL1|protein_coding|CODING|NM_025092.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10902120 -0.693147 0.361146 149 H432 737 caT/caC LOW 8 SILENT CODING ATHL1 C protein_coding NM_025092.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 293188 T C 0 228 0 0.3585 0.4008 0.3718 0.3998 0.3668 0.5143 0.325465 0.338536 0.345233 2 3437 47221 5185 3323 2951 23661 339 8325 2 10398 121282 11568 8620 6614 66668 908 16506 0 . 0 . 0 82 0,0,27,44 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H432|737|ATHL1|protein_coding|CODING|NM_025092.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12801980 -0.693147 0.387396 82 737 921 MODIFIER 14 CODING ATHL1 A protein_coding NM_025092.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 295670 G A 0 63 0 0.6891 0.651 0.6513 0.4633 0.7435 0.6973 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||921||737|ATHL1|protein_coding|CODING|NM_025092.4|14|A),DOWNSTREAM(MODIFIER||2531||132|IFITM5|protein_coding|CODING|NM_001025295.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs386443214,rs7104019 -0.453602 0.96 3 132 277 MODIFIER 2 CODING IFITM5 T protein_coding NM_001025295.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 298224 C T 0 9.7 0 0.1498 0.0877 0.0173 0.0437 0.0209 0.1677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||277||132|IFITM5|protein_coding|CODING|NM_001025295.2|2|T),DOWNSTREAM(MODIFIER||2536||737|ATHL1|protein_coding|CODING|NM_025092.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2293743 -0.379885 0 1 G27A 132 gGg/gCg MODERATE 1 MISSENSE CODING IFITM5 G protein_coding NM_001025295.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 299411 C G 0 228 0 0.7148 0.5927 0.5922 0.6429 0.3479 0.6278 0.597527 0.388072 0.281192 2 3162 23827 3207 2345 431 9385 164 5133 2 4668 44728 4484 3364 894 22760 318 8240 1 2 benign 0 . 117 1,0,31,74 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G27A|132|IFITM5|protein_coding|CODING|NM_001025295.2|1|G),DOWNSTREAM(MODIFIER||3723||737|ATHL1|protein_coding|CODING|NM_025092.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs57285449 -0.693147 0.518216 117 132 15 MODIFIER 1 CODING IFITM2 C protein_coding NM_006435.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308178 T C 0 228 0 0.4418 0.4736 0.3977 0.6935 0.2664 0.5573 0.349825 0.275057 0.239136 2 4023 42974 5024 5916 1857 17449 332 8373 2 9806 120332 11568 8606 6614 66568 894 16276 0 . 0 . 0 118 0,0,53,52 UTR_5_PRIME(MODIFIER||15||132|IFITM2|protein_coding|CODING|NM_006435.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1058873 -0.693147 0.00197271 118 132 13 MODIFIER 1 CODING IFITM2 G protein_coding NM_006435.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308180 A G 0 228 0 0.3843 0.3964 0.3631 0.626 0.1928 0.409 0.3002 0.223204 0.186194 2 3342 34130 4674 5365 1343 12981 276 6149 2 9802 120376 11568 8606 6614 66592 894 16300 0 . 0 . 0 118 0,0,53,52 UTR_5_PRIME(MODIFIER||13||132|IFITM2|protein_coding|CODING|NM_006435.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10398 -0.693147 0.00208137 118 V33A 132 gTg/gCg MODERATE 1 MISSENSE CODING IFITM2 C protein_coding NM_006435.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308290 T C 0 228 0 0.9637 0.8644 0.7968 0.997 0.5805 0.9335 0.898297 0.693082 0.594666 2 8892 84378 9874 8616 3192 38325 619 14860 2 9806 120708 11572 8624 6612 66684 898 16512 0 . 0 . 0 103 0,0,66,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V33A|132|IFITM2|protein_coding|CODING|NM_006435.2|1|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.835495 0 . rs1058900 -0.693147 0.00105467 103 M41T 132 aTg/aCg MODERATE 1 MISSENSE CODING IFITM2 C protein_coding NM_006435.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308314 T C 0 228 0 0.7617 0.7051 0.6657 0.9593 0.3787 0.7301 0.643514 0.453645 0.363998 2 6831 62607 8458 8323 2276 25130 453 11136 2 9784 120590 11566 8620 6600 66610 898 16512 0 . 0 . COSM1561439 115 0,0,68,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M41T|132|IFITM2|protein_coding|CODING|NM_006435.2|1|C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.535967 0 . rs14408 -0.693147 0.315838 115 V57 132 gtG/gtC LOW 1 SILENT CODING IFITM2 C protein_coding NM_006435.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308363 G C 0 228 0 0.9607 0.8419 0.7839 0.997 0.5388 0.8742 0.880699 0.639759 0.525373 2 8811 79137 9494 8612 2937 34909 582 13792 2 9798 120504 11568 8622 6606 66510 894 16506 0 . 0 . 0 124 0,0,63,58 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V57|132|IFITM2|protein_coding|CODING|NM_006435.2|1|C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.600995 0 . rs1058935 -0.693147 0.0113224 124 A78 132 gcG/gcC LOW 1 SILENT CODING IFITM2 C protein_coding NM_006435.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 308426 G C 0 228 0 0.9523 0.8363 0.7752 0.997 0.5278 0.8742 0.87282 0.632237 0.519572 2 8607 78335 9418 8614 2939 34416 583 13758 2 9682 120370 11568 8624 6610 66478 898 16510 1 0 . 0 . 101 1,0,39,52 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A78|132|IFITM2|protein_coding|CODING|NM_006435.2|1|C) 1 0 . 0 . 1 0 1 1 0 57 0 1 0.988275 0 1 rs1058964 -0.693147 0.0156902 101 I121V 132 Atc/Gtc MODERATE 2 MISSENSE CODING IFITM2 G protein_coding NM_006435.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 309127 A G 0 228 0 0.5976 0.5405 0.4553 0.6944 0.332 0.5798 0.545631 0.400849 0.329548 2 5524 50442 5662 5921 2184 21939 378 8834 2 9798 120522 11550 8610 6612 66544 898 16510 0.496622 0 . 0 . 170 1,1,66,82 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I121V|132|IFITM2|protein_coding|CODING|NM_006435.2|2|G),UPSTREAM(MODIFIER||4864||125|IFITM1|protein_coding|CODING|NM_003641.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.486486 rs1059091 -0.693147 0.191869 170 P13A 125 Cca/Gca MODERATE 1 MISSENSE CODING IFITM1 G protein_coding NM_003641.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 314207 C G 0 228 0 1 1 1 1 1 1 0 . 0 2 9804 120754 11576 8626 6614 66724 898 16512 2 9804 120754 11576 8626 6614 66724 898 16512 0 . 0 . 0 105 0,0,62,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P13A|125|IFITM1|protein_coding|CODING|NM_003641.3|1|G),DOWNSTREAM(MODIFIER||4797||132|IFITM2|protein_coding|CODING|NM_006435.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs9667990 -0.693147 0.491538 105 S14 133 agT/agC LOW 1 SILENT CODING IFITM3 G protein_coding NM_021034.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 320772 A G 0 228 0 0.2602 0.2364 0.1772 0.5278 0.0408 0.1472 0.228696 0.10046 0.0401786 2 2446 15029 2246 4835 520 2893 107 1982 2 9794 120562 11574 8600 6614 66648 900 16432 0 255 other 0 . 75 0,0,39,31 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S14|133|IFITM3|protein_coding|CODING|NM_021034.2|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs12252 -0.693147 0.0996648 75 A67V 1039 gCg/gTg MODERATE 2 MISSENSE CODING B4GALNT4 T protein_coding NM_178537.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 372157 C T 0 222 0 0.4887 0.3756 0.3098 0.3859 0.2952 0.3415 0.453395 0.334134 0.270494 1 1399 6740 127 252 18 2507 62 2375 2 2796 20602 408 642 40 8610 192 7914 0.641664 0 . 0 . 147 44,18,38,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A67V|1039|B4GALNT4|protein_coding|CODING|NM_178537.4|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.68668 rs34063493 -0.693147 0.0247852 147 G98 1039 ggG/ggC LOW 3 SILENT CODING B4GALNT4 C protein_coding NM_178537.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 372700 G C 0 222 0 0.3253 0.3307 0.2997 0.3839 0.2952 0.3415 0.326782 0.294095 0.277388 1 3182 34312 2929 3533 1776 17736 231 4925 2 9086 112660 11084 8370 5646 61966 804 15704 0.531991 0 . 0 COSM1561414 106 12,20,18,29 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G98|1039|B4GALNT4|protein_coding|CODING|NM_178537.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.755404 rs35475866 -0.693147 0.00494719 106 A487 812 gcA/gcG LOW 7 SILENT CODING PKP3 G protein_coding NM_001303029.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 400109 A G 0 228 0 0.9811 0.8974 0.7421 0.998 0.7475 0.9448 0.93588 0.795709 0.724836 2 8030 82049 6894 7746 3499 41403 601 13876 2 8494 103492 9932 7748 4926 56902 718 14772 0 . 0 . 0 60 0,0,16,40 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A487|812|PKP3|protein_coding|CODING|NM_001303029.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8858 -0.693147 0.0681488 60 812 LOW 11 CODING PKP3 G protein_coding NM_001303029.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 403939 A G 0 228 0 0.9826 0.9269 0.8991 0.998 0.7783 0.9509 0.946033 0.823689 0.761688 2 9185 93391 10388 8274 4574 46808 697 13465 2 9596 111234 11142 8276 6200 61076 802 14142 0 . 0 . 0 55 0,0,31,20 SPLICE_SITE_REGION+INTRON(LOW||||812|PKP3|protein_coding|CODING|NM_001303029.1|11|G),DOWNSTREAM(MODIFIER||1777||410|SIGIRR|protein_coding|CODING|NM_001135053.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7479832 -0.693147 0.127176 55 V362 410 gtC/gtT LOW 10 SILENT CODING SIGIRR A protein_coding NM_001135053.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 406043 G A 0 228 0 0.91 0.9067 0.8919 0.998 0.7783 0.9509 0.88833 0.804035 0.761032 2 6167 67400 6377 5308 2812 33747 524 12465 2 6838 80362 6908 5310 3806 43720 604 13176 0 . 0 . 0 91 0,0,34,55 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V362|410|SIGIRR|protein_coding|CODING|NM_001135053.1|10|A),DOWNSTREAM(MODIFIER||1135||812|PKP3|protein_coding|CODING|NM_001303029.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7947 -0.693147 0.00589425 91 P315 410 ccT/ccG LOW 9 SILENT CODING SIGIRR C protein_coding NM_001135053.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 406473 A C 0 228 0 0.9115 0.9071 0.8919 0.998 0.7783 0.9509 0.891542 0.805329 0.761178 2 9270 99568 10724 8611 4818 49730 772 15643 2 10242 119766 11548 8612 6606 65362 890 16506 0 . 0 . 0 90 0,0,35,46 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P315|410|SIGIRR|protein_coding|CODING|NM_001135053.1|9|C),DOWNSTREAM(MODIFIER||1565||812|PKP3|protein_coding|CODING|NM_001303029.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3087588 -0.693147 0.00128732 90 Q312R 410 cAg/cGg MODERATE 9 MISSENSE CODING SIGIRR C protein_coding NM_001135053.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 406483 T C 0 228 0 0.9834 0.9271 0.8977 0.998 0.7793 0.9509 0.946997 0.824503 0.761816 2 9783 100089 10759 8605 4816 49709 773 15644 2 10214 119690 11554 8606 6604 65316 890 16506 0 . 0 . 0 79 0,0,28,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q312R|410|SIGIRR|protein_coding|CODING|NM_001135053.1|9|C),DOWNSTREAM(MODIFIER||1575||812|PKP3|protein_coding|CODING|NM_001303029.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3210908 -0.693147 0.00012774 79 C399R 782 Tgc/Cgc MODERATE 14 MISSENSE CODING ANO9 G protein_coding NM_001012302.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 428385 A G 0 228 0 0.9894 0.9217 0.7464 0.996 0.832 0.9703 0.959773 0.849075 0.792308 2 9802 99707 8168 8628 5103 51429 769 15808 2 10152 119338 11454 8632 6544 65186 876 16494 0 . 0 . COSM1561410 34 0,0,24,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C399R|782|ANO9|protein_coding|CODING|NM_001012302.2|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10794323 -0.69311 0.202526 34 I391V 782 Atc/Gtc MODERATE 13 MISSENSE CODING ANO9 C protein_coding NM_001012302.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 428489 T C 0 228 0 0.9917 0.9189 0.7478 0.997 0.8161 0.9673 0.955869 0.831818 0.76829 2 9678 97600 8233 8590 5039 49664 758 15638 2 10056 118904 11524 8594 6596 64770 880 16484 0 . 0 . 0 97 0,0,73,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I391V|782|ANO9|protein_coding|CODING|NM_001012302.2|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10794324 -0.693147 0.306399 97 R159H 782 cGc/cAc MODERATE 7 MISSENSE CODING ANO9 T protein_coding NM_001012302.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 431757 C T 0 228 0 0.0008 0.0276 0 0.1339 0 0.002 0.000907853 0.000307645 0 2 16 1038 1 986 0 1 9 25 2 10188 119514 11456 8588 6542 65384 886 16470 0.996625 0 . 0 . 86 2,1,43,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R159H|782|ANO9|protein_coding|CODING|NM_001012302.2|7|T) 1 0 . 0 . 1 0 1 1 0 59 0 0.999155 0.969442 0 0.65606 rs78972632 -0.693147 0.521317 86 F93L 782 Ttc/Ctc MODERATE 4 MISSENSE CODING ANO9 G protein_coding NM_001012302.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 433387 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10348 120748 11566 8638 6614 66174 900 16508 2 10348 120752 11566 8642 6614 66174 900 16508 0 . 0 . 0 160 0,0,94,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F93L|782|ANO9|protein_coding|CODING|NM_001012302.2|4|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7395065 -0.693147 0.327474 160 H27 189 caT/caC LOW 2 SILENT CODING HRAS G protein_coding NM_001130442.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 534242 A G 0 222 0 0.3729 0.2971 0.3646 0.1726 0.3121 0.2597 0.374943 0.354529 0.34407 1 3874 37746 4243 1632 1724 21765 253 4255 2 10274 120394 11530 8620 6556 66014 902 16498 0.910436 2|2 benign|benign 0 COSM249860 136 22,36,33,31 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H27|189|HRAS|protein_coding|CODING|NM_001130442.1|2|G),UPSTREAM(MODIFIER||3280||542|LRRC56|protein_coding|CODING|NM_198075.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993072 rs12628 -0.693147 0.0318059 136 542 1039 MODIFIER 3 CODING LRRC56 T protein_coding NM_198075.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 539646 G T 0 8.1 0 0.3986 0.3063 0.3703 0.1716 0.3191 0.2618 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_5_PRIME(MODIFIER||1039||542|LRRC56|protein_coding|CODING|NM_198075.3|3|T),UPSTREAM(MODIFIER||4096||189|HRAS|protein_coding|CODING|NM_001130442.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1870725 -0.453602 0.18 3 L128 542 ctC/ctT LOW 7 SILENT CODING LRRC56 T protein_coding NM_198075.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 549959 C T 0 228 0 0.6203 0.7811 0.8415 0.9196 0.8201 0.773 0.652973 0.764226 0.821238 2 6709 97582 10314 7887 5292 53684 710 12986 2 10256 120180 11562 8620 6592 65750 894 16506 0.847328 0 . 0 . 138 0,2,63,68 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L128|542|LRRC56|protein_coding|CODING|NM_198075.3|7|T),DOWNSTREAM(MODIFIER||4891||634|LMNTD2|protein_coding|CODING|NM_173573.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.438931 rs7942030 -0.693147 0.0168868 138 542 LOW 9 CODING LRRC56 T protein_coding NM_198075.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 551644 C T 0 198 0 0.0514 0.0553 0.049 0.0476 0.0656 0.0624 0.0632105 0.0622691 0.0617873 1 615 5914 487 305 196 3595 39 677 2 9274 106218 11306 8412 6410 60490 740 9586 0.869487 0 . 0 . 43 16,6,17,3 SPLICE_SITE_REGION+INTRON(LOW||||542|LRRC56|protein_coding|CODING|NM_198075.3|9|T),DOWNSTREAM(MODIFIER||3206||634|LMNTD2|protein_coding|CODING|NM_173573.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99715 rs113026126 -0.692067 0.665601 43 R300H 542 cGt/cAt MODERATE 10 MISSENSE CODING LRRC56 A protein_coding NM_198075.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 551753 G A 0 228 0 0.4372 0.6474 0.6369 0.873 0.664 0.6892 0.464725 0.576047 0.632938 2 4541 77232 7359 7329 4422 41578 584 11419 2 9760 117672 11364 8550 6454 64466 876 16202 0 . 0 . 0 127 0,0,90,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R300H|542|LRRC56|protein_coding|CODING|NM_198075.3|10|A),DOWNSTREAM(MODIFIER||3097||634|LMNTD2|protein_coding|CODING|NM_173573.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4963198 -0.693147 0.177353 127 R457 542 agG/agA LOW 14 SILENT CODING LRRC56 A protein_coding NM_198075.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554018 G A 0 222 0 0.0507 0.0549 0.049 0.0466 0.0656 0.0624 0.0621879 0.0618271 0.0616422 1 636 6437 494 302 196 3747 41 1021 2 9842 118314 11498 8556 6612 64546 880 16380 0.772076 0 . 0 . 45 11,10,12,5 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R457|542|LRRC56|protein_coding|CODING|NM_198075.3|14|A),DOWNSTREAM(MODIFIER||832||634|LMNTD2|protein_coding|CODING|NM_173573.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.713296 rs112033363 -0.690438 0.0755689 45 R507G 542 Cgc/Ggc MODERATE 14 MISSENSE CODING LRRC56 G protein_coding NM_198075.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554166 C G 0 187 0 0.7103 0.7939 0.8718 0.874 0.829 0.7331 0.71848 0.787683 0.823057 1 7134 95362 10266 7504 5466 52692 715 11585 2 10004 116730 11422 8540 6528 64202 860 15174 0.888322 0 . 0 . 33 9,10,4,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R507G|542|LRRC56|protein_coding|CODING|NM_198075.3|14|G),DOWNSTREAM(MODIFIER||684||634|LMNTD2|protein_coding|CODING|NM_173573.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965852 rs10902170 -0.680642 0.698506 33 D523H 542 Gat/Cat MODERATE 14 MISSENSE CODING LRRC56 C protein_coding NM_198075.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554214 G C 0 162 0 0.7057 0.7915 0.853 0.873 0.827 0.7434 0.714091 0.78478 0.820963 1 7070 90621 10208 7474 5500 51656 649 8064 2 9958 110902 11440 8506 6582 62968 788 10660 0.893996 0 . 0 . 31 7,12,4,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D523H|542|LRRC56|protein_coding|CODING|NM_198075.3|14|C),DOWNSTREAM(MODIFIER||636||634|LMNTD2|protein_coding|CODING|NM_173573.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.599643 rs10902171 -0.676189 0.469204 31 542 23 MODIFIER 14 CODING LRRC56 G protein_coding NM_198075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554299 C G 0 222 0 0.7685 0.882 0.9568 0.9206 0.9453 0.8773 0.796212 0.890105 0.93798 2 7276 95661 10883 7293 5716 56280 672 7541 2 9196 104146 11154 7986 6364 60142 732 8572 0 . 0 . 0 14 0,0,2,11 UTR_3_PRIME(MODIFIER||23||542|LRRC56|protein_coding|CODING|NM_198075.3|14|G),DOWNSTREAM(MODIFIER||551||634|LMNTD2|protein_coding|CODING|NM_173573.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10902172 -0.683931 0.0754305 14 542 383 MODIFIER 14 CODING LRRC56 A protein_coding NM_198075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554659 G A 0 6.3 0 0.208 0.4752 0.4337 0.6399 0.5567 0.6125 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||383||542|LRRC56|protein_coding|CODING|NM_198075.3|14|A),DOWNSTREAM(MODIFIER||191||634|LMNTD2|protein_coding|CODING|NM_173573.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11246184 -0.379885 0 1 542 522 MODIFIER 14 CODING LRRC56 C protein_coding NM_198075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 554798 T C 0 76 0 0.3185 0.5841 0.5893 0.7698 0.6223 0.7086 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||522||542|LRRC56|protein_coding|CODING|NM_198075.3|14|C),DOWNSTREAM(MODIFIER||52||634|LMNTD2|protein_coding|CODING|NM_173573.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12277611 -0.511536 0.732596 3 P348 634 ccG/ccC LOW 9 SILENT CODING LMNTD2 G protein_coding NM_173573.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 556521 C G 0 228 0 0.6505 0.846 0.9438 0.9067 0.9433 0.8783 0.710796 0.862328 0.939076 2 2417 27249 1344 1518 406 13891 231 7442 2 3412 30414 1404 1652 452 14822 252 8420 0.926909 0 . 0 . 139 3,1,76,46 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P348|634|LMNTD2|protein_coding|CODING|NM_173573.2|9|G),UPSTREAM(MODIFIER||4929||373|RASSF7|protein_coding|CODING|NM_003475.3||G),DOWNSTREAM(MODIFIER||1605||542|LRRC56|protein_coding|CODING|NM_198075.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.313237 rs28406183 -0.693147 0.00635672 139 G318 634 ggC/ggG LOW 8 SILENT CODING LMNTD2 C protein_coding NM_173573.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 556857 G C 0 228 0 0.7655 0.8782 0.9568 0.9067 0.9443 0.8773 0.80879 0.895662 0.939748 2 5174 78948 7920 5965 2861 45648 560 10820 2 6394 85470 8098 6560 3126 48570 604 12118 0 . 0 . 0 37 0,0,20,15 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G318|634|LMNTD2|protein_coding|CODING|NM_173573.2|8|C),UPSTREAM(MODIFIER||4593||373|RASSF7|protein_coding|CODING|NM_003475.3||C),DOWNSTREAM(MODIFIER||1941||542|LRRC56|protein_coding|CODING|NM_198075.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7938269 -0.693136 0.67779 37 A204 634 gcC/gcT LOW 6 SILENT CODING LMNTD2 A protein_coding NM_173573.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 557584 G A 0 222 0 0.0522 0.0543 0.0504 0.0466 0.0606 0.0613 0.0660763 0.0621347 0.0601163 1 667 6408 494 309 195 3690 41 1012 2 10282 120260 11534 8638 6614 65798 894 16500 0.692993 0 . 0 . 67 11,16,14,23 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A204|634|LMNTD2|protein_coding|CODING|NM_173573.2|6|A),UPSTREAM(MODIFIER||3866||373|RASSF7|protein_coding|CODING|NM_003475.3||A),DOWNSTREAM(MODIFIER||2668||542|LRRC56|protein_coding|CODING|NM_198075.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786366 rs11822657 -0.693141 0.450145 67 Q150 634 caG/caA LOW 5 SILENT CODING LMNTD2 T protein_coding NM_173573.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 557989 C T 0 222 0 0.152 0.4718 0.4366 0.6696 0.5746 0.6196 0.21753 0.444 0.560028 1 2089 63922 4723 5783 4225 37851 490 8761 2 9800 115256 11392 8592 6394 63964 854 14260 0.504999 0 . 0 . 70 11,23,11,20 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q150|634|LMNTD2|protein_coding|CODING|NM_173573.2|5|T),UPSTREAM(MODIFIER||3461||373|RASSF7|protein_coding|CODING|NM_003475.3||T),DOWNSTREAM(MODIFIER||3073||542|LRRC56|protein_coding|CODING|NM_198075.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.86196 rs7129811 -0.69311 0.348604 70 A44T 634 Gca/Aca MODERATE 2 MISSENSE CODING LMNTD2 T protein_coding NM_173573.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 558884 C T 0 222 0 0.5643 0.7582 0.8516 0.8591 0.8211 0.7853 0.598502 0.748923 0.826041 1 6089 96685 10368 7445 5239 54058 718 12768 2 10118 119460 11534 8604 6506 65412 894 16392 0.155279 0 . 0 . 120 33,24,23,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A44T|634|LMNTD2|protein_coding|CODING|NM_173573.2|2|T),UPSTREAM(MODIFIER||2566||373|RASSF7|protein_coding|CODING|NM_003475.3||T),DOWNSTREAM(MODIFIER||3968||542|LRRC56|protein_coding|CODING|NM_198075.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.855622 rs2061586 -0.693147 0.512162 120 V1449A 1649 gTg/gCg MODERATE 15 MISSENSE CODING PHRF1 C protein_coding NM_001286581.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 610277 T C 0 222 0 0.7837 0.8037 0.7867 0.7679 0.8748 0.8067 0.816257 0.863371 0.885493 1 2526 28809 1587 1338 936 14967 263 7192 2 3078 33778 2028 1712 1080 17000 298 8582 0.987064 0 . 0 . 91 24,27,17,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V1449A|1649|PHRF1|protein_coding|CODING|NM_001286581.1|15|C),DOWNSTREAM(MODIFIER||2278||516|IRF7|protein_coding|CODING|NM_004031.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.670056 rs11246212 -0.693097 0.185467 91 R122 516 cgG/cgA LOW 2 SILENT CODING IRF7 T protein_coding NM_004031.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 614864 C T 0 158 0 0.8525 0.8167 0.7954 0.749 0.8748 0.7935 0.852474 0.869923 0.878749 1 3441 44401 3737 2457 1240 24942 329 8255 2 3956 51584 4622 3122 1418 28058 368 10040 0.924449 0 . 0 . 12 2,2,4,3 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R122|516|IRF7|protein_coding|CODING|NM_004031.2|2|T),DOWNSTREAM(MODIFIER||2642||1649|PHRF1|protein_coding|CODING|NM_001286581.1||T),DOWNSTREAM(MODIFIER||1701||845|CDHR5|protein_coding|CODING|NM_021924.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.964642 0.950952 0 0.924449 rs1061501 -0.636426 0.565335 12 845 381 MODIFIER 15 CODING CDHR5 T protein_coding NM_021924.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 616970 A T 0 228 0 1 1 1 1 1 1 0 . 0 2 376 3062 96 70 1254 1100 52 114 2 376 3062 96 70 1254 1100 52 114 1 0 . 0 . 146 1,0,73,58 UTR_3_PRIME(MODIFIER||381||845|CDHR5|protein_coding|CODING|NM_021924.4|15|T),UPSTREAM(MODIFIER||1242||516|IRF7|protein_coding|CODING|NM_004031.2||T),DOWNSTREAM(MODIFIER||4748||1649|PHRF1|protein_coding|CODING|NM_001286581.1||T) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs1610161 -0.693147 0.0340073 146 P784 845 ccG/ccA LOW 15 SILENT CODING CDHR5 T protein_coding NM_021924.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 617537 C T 0 222 0 0.1876 0.4848 0.4625 0.7044 0.5596 0.5992 0.255368 0.446324 0.543874 1 2330 63372 4810 5906 4281 36142 482 9421 2 8632 114084 11206 8466 6370 62196 826 16388 0.454185 0 . 0 . 267 37,87,27,85 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P784|845|CDHR5|protein_coding|CODING|NM_021924.4|15|T),UPSTREAM(MODIFIER||1809||516|IRF7|protein_coding|CODING|NM_004031.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.140286 rs2740380 -0.693147 1.90675e-05 267 C702S 845 tGt/tCt MODERATE 14 MISSENSE CODING CDHR5 G protein_coding NM_021924.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 617967 C G 0 228 0 0.9327 0.9808 0.9914 1 0.999 1 0.936364 0.978301 0.999767 2 9085 116566 11268 8576 6086 64539 851 16161 2 9752 117276 11296 8576 6086 64552 852 16162 0 . 0 . 0 51 0,0,42,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C702S|845|CDHR5|protein_coding|CODING|NM_021924.4|14|G),UPSTREAM(MODIFIER||2239||516|IRF7|protein_coding|CODING|NM_004031.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2740379 -0.693147 0.421157 51 P521S 845 Ccc/Tcc MODERATE 13 MISSENSE CODING CDHR5 A protein_coding NM_021924.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 618998 G A 0 222 0 0.2436 0.4998 0.4669 0.7024 0.5586 0.6002 0.288243 0.45363 0.538381 1 2959 65702 4888 5996 4320 37575 511 9453 2 10100 120450 11560 8636 6606 66144 900 16504 0.934944 0 . 0 . 88 12,26,15,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P521S|845|CDHR5|protein_coding|CODING|NM_021924.4|13|A),UPSTREAM(MODIFIER||3270||516|IRF7|protein_coding|CODING|NM_004031.2||A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.979452 0.910773 0 0.558108 rs2740375 -0.693144 0.118871 88 R357S 845 agA/agC MODERATE 10 MISSENSE CODING CDHR5 G protein_coding NM_021924.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 619789 T G 0 73 0 0.4516 0.61 0.5389 0.7292 0.6581 0.7025 0.448362 0.564213 0.623487 1 3918 69361 5027 5678 3697 39256 531 11254 2 8124 106700 9976 7888 5094 58980 760 15878 0.974597 0 . 0 . 10 2,3,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R357S|845|CDHR5|protein_coding|CODING|NM_021924.4|10|G),UPSTREAM(MODIFIER||4061||516|IRF7|protein_coding|CODING|NM_004031.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.974597 0.924584 0 0.89338 rs2246614 -0.556411 0.879194 10 Q529 565 caA/caG LOW 11 SILENT CODING DEAF1 C protein_coding NM_021008.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 653968 T C 0 222 0 0.6263 0.2847 0.1369 0.2202 0.1312 0.1524 0.540853 0.264109 0.122326 1 5722 19049 862 1957 691 7284 134 2399 2 10390 121176 11556 8632 6560 66626 902 16510 0.71462 0 . 0 . 48 11,4,18,4 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q529|565|DEAF1|protein_coding|CODING|NM_021008.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.447398 rs10615,rs386607501 -0.692562 0.442791 48 C504 565 tgC/tgT LOW 11 SILENT CODING DEAF1 A protein_coding NM_021008.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 654043 G A 0 152 0 0.0552 0.1034 0.1729 0.1528 0.0815 0.091 0.0565138 0.073889 0.0827907 1 555 11542 2486 1371 337 5366 70 1357 2 10088 119092 11400 8526 6198 65610 884 16386 0.849331 0 . 0 . 32 7,11,3,9 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C504|565|DEAF1|protein_coding|CODING|NM_021008.3|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.101757 rs10902188 -0.680642 0.0340442 32 T161 565 acC/acT LOW 3 SILENT CODING DEAF1 A protein_coding NM_021008.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 688365 G A 0 222 0 0.0008 0.0029952 0 0.0139 0 0 0 . 0 1 2 82 1 76 0 2 0 1 2 10246 119864 11510 8610 6594 65510 896 16498 0.966125 0 . 0 . 125 30,30,27,25 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T161|565|DEAF1|protein_coding|CODING|NM_021008.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.327812 rs187623972 -0.693147 0.00958532 125 715 7 MODIFIER 2 CODING EPS8L2 G protein_coding NM_022772.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 709401 A G 0 228 0 0.5038 0.3492 0.2622 0.4613 0.1789 0.2618 0.417512 0.257019 0.17559 2 2074 11859 972 1518 203 4980 72 2040 2 4452 42376 2680 3128 808 21736 312 9260 0.0267761 0 . 0 . 129 3,1,87,28 UTR_5_PRIME(MODIFIER||7||715|EPS8L2|protein_coding|CODING|NM_022772.3|2|G),DOWNSTREAM(MODIFIER||4373||283|TMEM80|protein_coding|CODING|NM_001276274.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.319185 rs10902202 -0.693147 0.0933823 129 715 LOW 18 CODING EPS8L2 C protein_coding NM_022772.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 726178 G C 0 206 0 1 1 1 1 1 1 0 . 0 2 7355 104126 10693 7992 5296 56222 744 15824 2 7356 104166 10696 7992 5296 56258 744 15824 0 . 0 . 0 9 0,0,2,5 SPLICE_SITE_REGION+INTRON(LOW||||715|EPS8L2|protein_coding|CODING|NM_022772.3|18|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs28498399 -0.636426 0.200896 9 715 235 MODIFIER 21 CODING EPS8L2 G protein_coding NM_022772.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 727216 C G 0 90 0 0.1271 0.126 0.0144 0.3016 0.006 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.346719 0 . 0 . 9 0,3,0,6 UTR_3_PRIME(MODIFIER||235||715|EPS8L2|protein_coding|CODING|NM_022772.3|21|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 0 . 0.924584 rs61541872 -0.616816 0.025915 9 220 3147 MODIFIER 8 CODING PDDC1 T protein_coding NM_182612.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 767750 C T 0 9.7 0 0.8933 0.7011 0.7767 0.6419 0.666 0.4847 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3147||220|PDDC1|protein_coding|CODING|NM_182612.2|8|T),DOWNSTREAM(MODIFIER||2726||337|TALDO1|protein_coding|CODING|NM_006755.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11606152 -0.379885 0 1 220 890 MODIFIER 8 CODING PDDC1 T protein_coding NM_182612.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 770007 C T 0 34.4 0 0.3056 0.4323 0.6037 0.5605 0.4433 0.3384 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.333333 0 . 0 . 6 2,0,2,1 UTR_3_PRIME(MODIFIER||890||220|PDDC1|protein_coding|CODING|NM_182612.2|8|T),DOWNSTREAM(MODIFIER||4983||337|TALDO1|protein_coding|CODING|NM_006755.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs7940065 -0.511536 0.126715 6 T205 220 acT/acC LOW 7 SILENT CODING PDDC1 G protein_coding NM_182612.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 771034 A G 0 222 0 0.3064 0.4325 0.6037 0.5605 0.4433 0.3384 0.342189 0.440941 0.491512 1 3329 55986 7092 4802 3015 31628 377 5743 2 9810 116152 11122 8408 5980 63872 852 16108 0.926075 0 . 0 . 169 56,29,41,29 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T205|220|PDDC1|protein_coding|CODING|NM_182612.2|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456082 rs7930569 -0.693147 0.618694 169 149 556 MODIFIER 2 CODING CEND1 G protein_coding NM_016564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 787571 T G 0 58 0 0.0605 0.1032 0.0058 0.2728 0.004 0.1575 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.649731 0 . 0 . 9 1,4,0,4 UTR_3_PRIME(MODIFIER||556||149|CEND1|protein_coding|CODING|NM_016564.3|2|G),DOWNSTREAM(MODIFIER||2904||323|SLC25A22|protein_coding|CODING|NM_001191060.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.487298 rs7483022 -0.556411 0.297574 9 149 120 MODIFIER 2 CODING CEND1 A protein_coding NM_016564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 788007 G A 0 111 0 0.6755 0.632 0.7507 0.622 0.6541 0.4765 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.650664 0 . 0 . 28 15,0,12,0 UTR_3_PRIME(MODIFIER||120||149|CEND1|protein_coding|CODING|NM_016564.3|2|A),DOWNSTREAM(MODIFIER||2468||323|SLC25A22|protein_coding|CODING|NM_001191060.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.99881 rs6597982 -0.680642 0.714734 28 L226 504 ctC/ctT LOW 5 SILENT CODING PNPLA2 T protein_coding NM_020376.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 822588 C T 0 222 0 0.0522 0.0978 0.013 0.249 0.006 0.1585 0.0485701 0.0219932 0.00837404 1 444 5345 88 2131 14 521 33 2114 2 10384 121154 11572 8626 6614 66542 906 16510 0.948048 0 . 0 . 120 16,54,7,38 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L226|504|PNPLA2|protein_coding|CODING|NM_020376.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.118364 rs10902224 -0.693147 0.0346268 120 P291 504 ccC/ccG LOW 7 SILENT CODING PNPLA2 G protein_coding NM_020376.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 823809 C G 0 99 0 0.0809 0.2672 0.1888 0.4127 0.2644 0.4274 0.0927198 0.191238 0.241428 1 748 26652 1894 2825 1043 13836 196 6110 2 5220 76974 6838 6314 2740 41894 558 13410 0.916482 0 . 0 . 10 2,1,5,2 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P291|504|PNPLA2|protein_coding|CODING|NM_020376.3|7|G),UPSTREAM(MODIFIER||4451||399|CRACR2B|protein_coding|CODING|NM_001286606.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.916482 0.916482 0 0.916482 rs1135628 -0.636426 0.0593842 10 L389 504 ctG/ctT LOW 9 SILENT CODING PNPLA2 T protein_coding NM_020376.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 824428 G T 0 149 0 0.0522 0.0972 0.013 0.247 0.006 0.1575 0.0428367 0.0189914 0.00696279 1 104 1365 11 202 0 104 9 935 2 1742 16482 308 614 34 5756 144 7884 0.98568 0 . 0 . 13 0,4,1,7 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L389|504|PNPLA2|protein_coding|CODING|NM_020376.3|9|T),UPSTREAM(MODIFIER||3832||399|CRACR2B|protein_coding|CODING|NM_001286606.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94394 rs11554663 -0.651104 0.85452 13 L481P 504 cTg/cCg MODERATE 10 MISSENSE CODING PNPLA2 C protein_coding NM_020376.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 824789 T C 0 75 0 0.7133 0.6544 0.7709 0.6002 0.7058 0.4949 0.704161 0.706844 0.708034 1 405 8645 315 320 79 3655 83 3788 2 540 14594 406 476 100 5316 136 7620 0.8618 0 . 0 . 12 3,3,1,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L481P|504|PNPLA2|protein_coding|CODING|NM_020376.3|10|C),UPSTREAM(MODIFIER||3471||399|CRACR2B|protein_coding|CODING|NM_001286606.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.950952 0.964642 0 0.564628 rs1138693 -0.590765 0.300397 12 P486 504 ccC/ccT LOW 10 SILENT CODING PNPLA2 T protein_coding NM_020376.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 824805 C T 0 28.5 0 0.3684 0.2676 0.121 0.3224 0.1352 0.3149 0.179064 0.1213 0.096083 1 129 2598 31 111 3 506 15 1803 2 306 11426 142 262 14 3196 118 7388 0.13642 0 . 0 . 13 4,3,2,3 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P486|504|PNPLA2|protein_coding|CODING|NM_020376.3|10|T),UPSTREAM(MODIFIER||3455||399|CRACR2B|protein_coding|CODING|NM_001286606.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.95494 0.982603 0 0.935451 rs1138694 -0.590765 0.336719 13 R77Q 399 cGg/cAg MODERATE 2 MISSENSE CODING CRACR2B A protein_coding NM_001286606.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 828916 G A 0 222 0 0.4576 0.5683 0.7695 0.6647 0.6948 0.3456 0.515988 0.645161 0.708671 1 4795 79191 9608 5834 5115 46694 574 6571 2 9742 120048 11556 8568 6610 66188 892 16492 0.554631 0 . 0 . 92 20,24,7,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R77Q|399|CRACR2B|protein_coding|CODING|NM_001286606.1|2|A),UPSTREAM(MODIFIER||4036||253|CD151|protein_coding|CODING|NM_001039490.1||A),DOWNSTREAM(MODIFIER||3345||504|PNPLA2|protein_coding|CODING|NM_020376.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.943145 rs7126805 -0.693144 0.0316041 92 K153E 399 Aag/Gag MODERATE 3 MISSENSE CODING CRACR2B G protein_coding NM_001286606.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 829539 A G 0 222 0 0.5847 0.6655 0.7824 0.8929 0.67 0.453 0.611919 0.66072 0.685299 1 3808 53521 5106 5253 2283 30660 345 6066 2 6106 76334 6096 5820 2880 43548 520 11364 0.992928 0 . 0 . 114 24,35,10,31 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Aag/Gag|K153E|399|CRACR2B|protein_coding|CODING|NM_001286606.1|3|G),UPSTREAM(MODIFIER||3413||253|CD151|protein_coding|CODING|NM_001039490.1||G),DOWNSTREAM(MODIFIER||3968||504|PNPLA2|protein_coding|CODING|NM_020376.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961469 rs28558789 -0.693145 0.404112 114 S248I 399 aGc/aTc MODERATE 6 MISSENSE CODING CRACR2B T protein_coding NM_001286606.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 830670 G T 0 211 0 0.5431 0.6524 0.7767 0.8909 0.667 0.4509 0.62766 0.69143 0.721437 1 596 8003 188 368 34 3129 88 3600 2 996 14344 276 426 46 5070 146 7384 0.54361 0 . 0 COSM1561958 34 11,7,11,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S248I|399|CRACR2B|protein_coding|CODING|NM_001286606.1|6|T),UPSTREAM(MODIFIER||2282||253|CD151|protein_coding|CODING|NM_001039490.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.679055 rs4075289 -0.689466 0.242712 34 399 100 MODIFIER 9 CODING CRACR2B G protein_coding NM_001286606.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 831809 T G 0 222 0 0.8154 0.7434 0.8199 0.8919 0.7177 0.4652 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997279 0 . 0 . 199 74,27,45,25 UTR_3_PRIME(MODIFIER||100||399|CRACR2B|protein_coding|CODING|NM_001286606.1|9|G),UPSTREAM(MODIFIER||1143||253|CD151|protein_coding|CODING|NM_001039490.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.842301 rs1130276 -0.693147 0.296584 199 G193 253 ggG/ggA LOW 6 SILENT CODING CD151 A protein_coding NM_001039490.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 837582 G A 0 222 0 0.5318 0.6422 0.7925 0.8552 0.663 0.4438 0.550909 0.63458 0.677408 1 5617 80350 9561 7394 4935 44375 581 7887 2 10246 119982 11526 8622 6578 65620 894 16496 0.977684 0 . 0 . 192 38,53,26,53 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G193|253|CD151|protein_coding|CODING|NM_001039490.1|6|A),DOWNSTREAM(MODIFIER||2139||67|POLR2L|protein_coding|CODING|NM_021128.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.119692 rs1130663 -0.693147 0.378693 192 67 604 MODIFIER 2 CODING POLR2L CCT protein_coding NM_021128.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 839767 C CCT 0 32.2 0 0.5318 0.6422 0.7925 0.8552 0.663 0.4438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||604||67|POLR2L|protein_coding|CODING|NM_021128.4|2|CCT),UPSTREAM(MODIFIER||4313||238|TSPAN4|protein_coding|CODING|NM_001025234.1||CCT),DOWNSTREAM(MODIFIER||933||253|CD151|protein_coding|CODING|NM_001039490.1||CCT) 0 0.5 1 1 1 1 1 0 . 0 60 0 0 . 0 . rs76892054 -0.379885 0 1 67 121 MODIFIER 2 CODING POLR2L G protein_coding NM_021128.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 840251 C G 0 228 0 0.9418 0.9692 0.9784 0.999 0.9483 0.9908 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,26,2 UTR_3_PRIME(MODIFIER||121||67|POLR2L|protein_coding|CODING|NM_021128.4|2|G),UPSTREAM(MODIFIER||3830||238|TSPAN4|protein_coding|CODING|NM_001025234.1||G),DOWNSTREAM(MODIFIER||1416||253|CD151|protein_coding|CODING|NM_001039490.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11629 -0.693054 0.569557 31 67 70 MODIFIER 2 CODING POLR2L A protein_coding NM_021128.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 840302 G A 0 222 0 0 0.016573 0 0.0794 0 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.83524 0 . 0 . 59 22,3,22,8 UTR_3_PRIME(MODIFIER||70||67|POLR2L|protein_coding|CODING|NM_021128.4|2|A),UPSTREAM(MODIFIER||3779||238|TSPAN4|protein_coding|CODING|NM_001025234.1||A),DOWNSTREAM(MODIFIER||1467||253|CD151|protein_coding|CODING|NM_001039490.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998715 rs56118780 -0.693097 0.0262021 59 67 53 MODIFIER 2 CODING POLR2L T protein_coding NM_021128.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 840319 C T 0 222 0 0.5272 0.641 0.7925 0.8552 0.663 0.4438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.541214 0 . 0 . 63 23,8,22,6 UTR_3_PRIME(MODIFIER||53||67|POLR2L|protein_coding|CODING|NM_021128.4|2|T),UPSTREAM(MODIFIER||3762||238|TSPAN4|protein_coding|CODING|NM_001025234.1||T),DOWNSTREAM(MODIFIER||1484||253|CD151|protein_coding|CODING|NM_001039490.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.754057 rs3059,rs386578955 -0.693054 0.088171 63 D33 67 gaT/gaC LOW 2 SILENT CODING POLR2L G protein_coding NM_021128.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 840477 A G 0 222 0 0.5318 0.6422 0.7925 0.8552 0.663 0.4438 0.54857 0.633826 0.677524 1 5614 80339 9576 7360 4944 44371 578 7896 2 10240 119858 11538 8570 6600 65542 890 16478 0.982189 0 . 0 . 43 5,14,3,18 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D33|67|POLR2L|protein_coding|CODING|NM_021128.4|2|G),UPSTREAM(MODIFIER||3604||238|TSPAN4|protein_coding|CODING|NM_001025234.1||G),DOWNSTREAM(MODIFIER||1642||253|CD151|protein_coding|CODING|NM_001039490.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.291179 rs4895 -0.692352 0.0640284 43 L56 238 Ttg/Ctg LOW 4 SILENT CODING TSPAN4 C protein_coding NM_001025234.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 862652 T C 0 228 0 0.9697 0.9916 0.9971 1 1 1 0.978212 0.992541 0.999884 2 10039 120226 11545 8638 6598 66009 892 16505 2 10316 120514 11554 8638 6598 66010 892 16506 0 . 0 . 0 87 0,0,40,40 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L56|238|TSPAN4|protein_coding|CODING|NM_001025234.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs28505621 -0.693147 0.745138 87 238 164 MODIFIER 9 CODING TSPAN4 G protein_coding NM_001025234.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 866794 A G 0 228 0 0.5756 0.625 0.4207 0.7629 0.502 0.8211 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,5,30 UTR_3_PRIME(MODIFIER||164||238|TSPAN4|protein_coding|CODING|NM_001025234.1|9|G),DOWNSTREAM(MODIFIER||1065||418|CHID1|protein_coding|CODING|NM_001142676.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7091 -0.693136 0.780137 35 418 578 MODIFIER 14 CODING CHID1 T protein_coding NM_001142676.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 869280 C T 0 68 0 0.9682 0.991 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||578||418|CHID1|protein_coding|CODING|NM_001142676.1|14|T),DOWNSTREAM(MODIFIER||2164||238|TSPAN4|protein_coding|CODING|NM_001025234.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs28478730 -0.511536 0.690245 3 A363V 418 gCc/gTc MODERATE 12 MISSENSE CODING CHID1 A protein_coding NM_001142676.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 870446 G A 0 228 0 0.4077 0.5689 0.4092 0.7639 0.4851 0.7853 0.434151 0.476912 0.498836 2 4469 62115 4792 6353 2572 31495 444 11990 2 9644 113636 10756 8460 5600 62384 818 15974 0 . 0 . 0 120 0,0,61,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A363V|418|CHID1|protein_coding|CODING|NM_001142676.1|12|A),DOWNSTREAM(MODIFIER||3330||238|TSPAN4|protein_coding|CODING|NM_001025234.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6682 -0.693147 0.0678685 120 418 LOW 6 CODING CHID1 G protein_coding NM_001142676.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 900929 C G 0 228 0 0.7088 0.6771 0.5418 0.7579 0.5358 0.7924 0.705856 0.602891 0.550128 2 7198 70377 5922 6335 3029 34972 498 12423 2 10146 118018 11264 8518 6140 64726 870 16354 0 . 0 . 0 60 0,0,39,16 SPLICE_SITE_REGION+INTRON(LOW||||418|CHID1|protein_coding|CODING|NM_001142676.1|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10794339 -0.693147 0.517206 60 V76 418 gtC/gtG LOW 4 SILENT CODING CHID1 C protein_coding NM_001142676.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 903070 G C 0 228 0 0.969 0.9914 0.9971 1 1 1 0.974126 0.991157 0.999884 2 10085 120772 11556 8634 6612 66475 902 16508 2 10382 121080 11566 8634 6612 66476 902 16508 0 . 0 . 0 157 0,0,80,64 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V76|418|CHID1|protein_coding|CODING|NM_001142676.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs28380110 -0.693147 0.00280882 157 L569 940 ctC/ctG LOW 13 SILENT CODING AP2A2 G protein_coding NM_001242837.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 993907 C G 0 228 0 0.295 0.1845 0.0533 0.2976 0.0885 0.1104 0.233333 0.130967 0.0789104 2 2385 13238 404 2164 783 5444 98 1960 2 9042 113930 10914 8284 6040 62906 820 15924 0.997273 0 . 0 . 224 3,0,89,112 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L569|940|AP2A2|protein_coding|CODING|NM_001242837.1|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.868024 rs11538725 -0.693147 0.104563 224 S1627I 2439 aGt/aTt MODERATE 31 MISSENSE CODING MUC6 A protein_coding NM_005961.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1017921 C A 0 51 0 . 0 . 0 . 0 . 0 . 1 4588 54008 5657 4182 3281 31349 381 4570 2 9846 120306 11550 8606 6598 66414 900 16392 0.0853467 0 . 0 . 68 0,53,15,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aTt|S1627I|2439|MUC6|protein_coding|CODING|NM_005961.2|31|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.998251 0.998251 0 1.45971e-06 rs112301388 -0.688148 3.22007e-07 68 S1620 2439 tcC/tcA LOW 31 SILENT CODING MUC6 T protein_coding NM_005961.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1017941 G T 0 128 0 . 0 . 0 . 0 . 0 . 1 4613 54413 5681 4209 3291 31552 384 4683 2 9814 120282 11534 8590 6606 66440 896 16402 0.972983 0 . 0 . 70 0,34,35,0 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcA|S1620|2439|MUC6|protein_coding|CODING|NM_005961.2|31|T) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.813699 0.813699 0 2.29904e-09 rs61869007 -0.693136 2.66423e-06 70 P1613L 2439 cCc/cTc MODERATE 31 MISSENSE CODING MUC6 A protein_coding NM_005961.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1017963 G A 0 159 0 . 0 . 0 . 0 . 0 . 1 4631 54721 5712 4223 3293 31719 390 4753 2 9828 119902 11554 8608 6608 66368 896 16040 0.954337 0 . 0 . 77 0,21,53,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P1613L|2439|MUC6|protein_coding|CODING|NM_005961.2|31|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.515599 0.515599 0 4.54135e-08 rs61869008 -0.693147 1.22486e-06 77 T1611 2439 acA/acT LOW 31 SILENT CODING MUC6 A protein_coding NM_005961.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1017968 T A 0 149 0 . 0 . 0 . 0 . 0 . 1 4633 54831 5715 4224 3293 31755 392 4819 2 9800 118462 11542 8588 6608 65960 868 15096 0.859475 0 . 0 . 76 0,18,55,0 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T1611|2439|MUC6|protein_coding|CODING|NM_005961.2|31|A) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.430092 0.430092 0 4.32234e-07 rs61869009 -0.693147 6.13968e-06 76 H1607L 2439 cAc/cTc MODERATE 31 MISSENSE CODING MUC6 A protein_coding NM_005961.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1017981 T A 0 151 0 . 0 . 0 . 0 . 0 . 1 4630 54857 5723 4224 3294 31765 392 4829 2 9660 112964 11478 8488 6588 64494 814 11442 0.800176 0 . 0 . 85 0,13,66,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cTc|H1607L|2439|MUC6|protein_coding|CODING|NM_005961.2|31|A) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.940461 0.940461 0 1.45104e-05 rs61869010 -0.693147 0.0147267 85 A1310 2439 gcG/gcA LOW 30 SILENT CODING MUC6 T protein_coding NM_005961.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1019375 C T 0 228 0 0.9773 0.9233 0.8876 0.881 0.9274 0.9151 0.970615 0.943852 0.930094 2 9543 110360 9821 7480 6040 61608 822 15046 2 9856 120532 11566 8618 6608 66474 898 16512 0 . 0 . 0 286 0,0,179,82 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1310|2439|MUC6|protein_coding|CODING|NM_005961.2|30|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9704308 -0.693147 0.332731 286 L58P 2813 cTc/cCc MODERATE 2 MISSENSE CODING MUC2 C protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1075747 T C 0 228 0 0.4062 0.2714 0.1052 0.4375 0.1362 0.1748 0.336873 0.197262 0.128534 2 3223 20022 1156 3932 1054 7840 138 2679 2 8292 105062 9638 8026 5574 58232 760 14540 0 . 0 . 0 211 0,0,99,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L58P|2813|MUC2|protein_coding|CODING|NM_002457.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2856111 -0.693147 0.867057 211 T1426 2813 acC/acA LOW 30 SILENT CODING MUC2 A protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092459 C A 0 25 0 . 0 . 0 . 0 . 0 . 1 0 5 0 0 0 5 0 0 2 1042 5820 62 194 1440 2562 66 454 0.896626 0 . 0 . 151 47,61,27,3 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T1426|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 0 . 0 1 0 54 0 6.80028e-08 0.012482 0 0.0832147 rs374506032 -0.693097 6.03796e-10 151 T1437 2813 acC/acT LOW 30 SILENT CODING MUC2 T protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092492 C T 0 39.5 0 . 0 . 0 . 0 . 0 . 1 6 35 0 4 0 21 0 4 2 974 4956 38 114 854 2424 48 504 0.788532 0 . 0 . 174 60,46,22,9 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1437|2813|MUC2|protein_coding|CODING|NM_002457.3|30|T) 0 0.5 1 0 . 0 . 0 1 0 53 0 1.71555e-08 0.177457 0 0.00393137 rs111844333 -0.69311 0.000578137 174 I1458T 2813 aTa/aCa MODERATE 30 MISSENSE CODING MUC2 C protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092554 T C 0 209 0 0.3631 0.3397 0.3084 0.2917 0.3181 0.4018 0 . 0 1 38 199 11 6 1 127 1 15 2 466 2310 50 94 56 1300 20 324 0.0335458 0 . 0 COSM231229,COSM231230 234 87,47,55,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I1458T|2813|MUC2|protein_coding|CODING|NM_002457.3|30|C) 0 0.5 1 0 . 1 0 . 1 0 51 0 2.30103e-08 0.842042 0 0.131348 rs199676812 -0.693147 5.87503e-09 234 S1459T 2813 aGc/aCc MODERATE 30 MISSENSE CODING MUC2 C protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092557 G C 0 222 0 0.3676 0.3456 0.3127 0.2966 0.325 0.411 0 . 0 1 53 284 13 13 1 176 1 27 2 440 2264 54 102 54 1262 16 336 0.000149418 0 . 0 COSM1171744,COSM1171745 235 77,40,63,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S1459T|2813|MUC2|protein_coding|CODING|NM_002457.3|30|C) 0 0.5 1 0 . 1 0 . 1 0 52 0 1.12589e-10 0.881805 0 0.941877 rs200605255 -0.693147 5.63244e-06 235 S1501 2813 agC/agT LOW 30 SILENT CODING MUC2 T protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092684 C T 0 92 0 . 0 . 0 . 0 . 0 . 1 91 277 0 0 2 163 1 20 2 244 756 8 4 4 446 2 48 0.00176325 0 . 0 . 467 152,115,50,28 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1501|2813|MUC2|protein_coding|CODING|NM_002457.3|30|T) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.885586 0.26587 0 0.127919 rs111163720,rs201269049 -0.693147 0.121649 467 T1506 2813 acG/acA LOW 30 SILENT CODING MUC2 A protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092699 G A 0 177 0 0.4796 0.4812 0.4841 0.4831 0.4801 0.4806 0 . 0 1 344 972 1 5 10 609 3 0 2 752 2176 12 18 20 1356 6 12 5.59058e-06 0 . 0 . 431 143,91,48,38 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1506|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.767314 0.927046 0 0.567895 rs111210448,rs111218567,rs191524914,rs62651879 -0.693147 0.19855 431 A1512T 2813 Gcc/Acc MODERATE 30 MISSENSE CODING MUC2 A protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092715 G A 0 222 0 0.5061 0.5062 0.5029 0.5069 0.504 0.5102 0 . 0 1 377 1138 3 13 15 717 7 6 2 764 2346 8 32 30 1482 14 16 0.858762 0 . 0 . 424 65,61,88,91 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A1512T|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.791937 0.780609 0 0.212618 rs111155228,rs111163721,rs111210449,rs199926071,rs62637243 -0.693147 0.0912458 424 T1515 2813 acC/acT LOW 30 SILENT CODING MUC2 T protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092726 C T 0 221 0 . 0 . 0 . 0 . 0 . 1 184 513 0 2 6 317 3 1 2 668 1924 12 14 14 1196 12 8 0.00598585 0 . 0 . 448 98,122,35,54 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1515|2813|MUC2|protein_coding|CODING|NM_002457.3|30|T) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.999991 0.372735 0 0.718339 rs111163722,rs111210450,rs147478427 -0.693147 0.0122548 448 T1527P 2813 Aca/Cca MODERATE 30 MISSENSE CODING MUC2 C protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1092760 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 302 886 7 5 6 558 6 2 2 634 1860 16 14 12 1168 12 4 0.0285534 0 . 0 COSM1171747,COSM1171746 342 23,77,38,106 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Cca|T1527P|2813|MUC2|protein_coding|CODING|NM_002457.3|30|C) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.944048 0.933215 0 0.559327 rs111163723,rs111210451,rs77094665 -0.693147 1.06089e-20 342 P1629T 2813 Cca/Aca MODERATE 30 MISSENSE CODING MUC2 A protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093066 C A 0 37.3 0 . 0 . 0 . 0 . 0 . 1 105 378 3 12 48 173 1 36 2 972 7806 142 108 716 4324 70 1474 0.683497 0 . 0 COSM428387,COSM428388 14 5,1,4,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P1629T|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 0 . 0 1 0 32 0 0.742931 0.111111 0 0.0297172 rs111170569,rs111210455,rs56365200 -0.590765 0.312308 14 S1698L 2813 tCg/tTg MODERATE 30 MISSENSE CODING MUC2 T protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093274 C T 0 222 0 0.4826 0.4862 0.4899 0.631 0.3608 0.4683 0 . 0 1 742 5062 102 187 104 1967 45 1915 2 1720 14102 258 386 598 6280 122 4738 0.563164 0 . 0 . 87 26,12,8,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S1698L|2813|MUC2|protein_coding|CODING|NM_002457.3|30|T) 0 0.5 1 0 . 1 0 . 1 0 42 0 0.00500734 0.0565452 0 0.0977484 rs11245949 -0.693021 0.00071125 87 S1725T 2813 Tcc/Acc MODERATE 30 MISSENSE CODING MUC2 A protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093354 T A 0 63 0 . 0 . 0 . 0 . 0 . 1 6 63 1 4 2 40 0 10 2 1932 16638 260 340 920 6728 168 6290 0.63381 0 . 0 COSM147102,COSM147103 46 13,9,9,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Acc|S1725T|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 0 . 0 1 0 37 0 0.0518913 0.48252 0 0.1909 rs56290335 -0.680642 0.637461 46 T1750N 2813 aCc/aAc MODERATE 30 MISSENSE CODING MUC2 A protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093430 C A 0 89 0 0.3865 0.376 0.3401 0.3621 0.3549 0.4233 0 . 0 1 590 5859 118 205 148 2379 53 2366 2 1932 14856 326 488 672 6436 134 4868 0.0185309 0 . 0 COSM220048,COSM220049 92 44,14,17,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T1750N|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 1 0 . 1 0 53 0 0.949532 0.000126428 0 0.733149 rs199573018 -0.692352 0.741694 92 T1777 2813 acC/acA LOW 30 SILENT CODING MUC2 A protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093512 C A 0 222 0 . 0 . 0 . 0 . 0 . 1 1188 10132 193 295 285 4439 97 3635 2 2758 26912 698 844 996 13126 258 8232 0.222848 0 . 0 COSM1127914,COSM1127913 124 54,18,13,18 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T1777|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.739716 0.785381 0 0.992558 rs34493663 -0.69311 0.0752097 124 T1796 2813 acA/acC LOW 30 SILENT CODING MUC2 C protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093569 A C 0 33.4 0 . 0 . 0 . 0 . 0 . 1 509 4532 102 174 33 2066 37 1611 2 6226 80080 5802 4978 4478 45838 574 12184 0.146385 0 . 0 . 121 60,31,1,19 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T1796|2813|MUC2|protein_coding|CODING|NM_002457.3|30|C) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.940882 0.983793 0 0.000473194 rs72842460 -0.692067 0.000194935 121 G1807S 2813 Ggc/Agc MODERATE 30 MISSENSE CODING MUC2 A protein_coding NM_002457.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093600 G A 0 228 0 0.0189 0.144 0.1398 0.4117 0.0358 0.1513 0.0309936 0.027825 0.0261988 2 223 10598 1766 3700 514 2186 64 2145 2 9478 116210 11088 8308 6504 63708 866 16258 0.929842 0 . 0 COSM428392,COSM428391 118 2,11,64,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G1807S|2813|MUC2|protein_coding|CODING|NM_002457.3|30|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.000113481 rs74193969 -0.693147 0.0377935 118 P1839 2813 ccC/ccG LOW 31 SILENT CODING MUC2 G protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1093710 C G 0 228 0 0.9826 0.8958 0.853 0.9931 0.8091 0.7975 0.957447 0.858 0.808112 2 9395 99534 9341 8579 5294 52976 742 13207 2 9802 120498 11570 8628 6614 66606 892 16386 0 . 0 . 0 102 0,0,45,52 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P1839|2813|MUC2|protein_coding|CODING|NM_002457.3|31|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7944723 -0.693147 0.185953 102 T1922 2813 acC/acT LOW 32 SILENT CODING MUC2 T protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1094690 C T 0 228 0 0.848 0.7548 0.7363 0.9325 0.5099 0.7106 0.789436 0.596871 0.500474 2 7684 70652 8063 7940 2998 32403 531 11033 2 9664 117902 11500 8588 6610 65168 872 15500 0 . 0 . 0 102 0,0,56,35 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1922|2813|MUC2|protein_coding|CODING|NM_002457.3|32|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10794291 -0.693147 0.16631 102 P1943 2813 ccA/ccC LOW 32 SILENT CODING MUC2 C protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1094753 A C 0 228 0 0.9357 0.8257 0.7795 0.9901 0.5954 0.7771 0.873216 0.679582 0.583156 2 8630 80506 8498 8555 3708 37995 608 12512 2 9752 120032 11558 8614 6614 66100 890 16504 1 0 . 0 . 84 1,0,42,36 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccC|P1943|2813|MUC2|protein_coding|CODING|NM_002457.3|32|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10794292 -0.693147 0.0591971 84 C2169 2813 tgT/tgC LOW 35 SILENT CODING MUC2 C protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1096494 T C 0 228 0 . 0 . 0 . 0 0.878261 0.684476 0.585151 2 8640 80368 8503 8537 3706 37825 606 12551 2 9748 119620 11538 8600 6610 65730 886 16508 0 . 0 . 0 132 0,0,40,77 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C2169|2813|MUC2|protein_coding|CODING|NM_002457.3|35|C) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs386602630,rs6421972 -0.693147 0.102786 132 2813 LOW 37 CODING MUC2 G protein_coding NM_002457.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1098637 A G 0 228 0 0.7602 0.8133 0.7795 0.9911 0.6461 0.8978 0.747218 0.665842 0.625745 2 5737 72998 7689 7538 3191 35724 541 12578 2 7772 102826 10244 7600 5032 56880 724 14574 0 . 0 . 0 175 0,0,124,35 SPLICE_SITE_REGION+INTRON(LOW||||2813|MUC2|protein_coding|CODING|NM_002457.3|37|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12418069 -0.693147 0.0320918 175 P2550 2813 ccT/ccC LOW 43 SILENT CODING MUC2 C protein_coding NM_002457.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1101649 T C 0 228 0 0.6808 0.6973 0.6196 0.9931 0.5219 0.6503 0.618579 0.550691 0.517102 2 6088 69627 7577 8525 3652 33042 489 10254 2 9728 119650 11542 8596 6612 65780 888 16504 0 . 0 . COSM428399 127 0,0,26,91 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P2550|2813|MUC2|protein_coding|CODING|NM_002457.3|43|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386610535,rs7480563 -0.693147 0.000147756 127 C351 1812 tgT/tgC LOW 9 SILENT CODING MUC5AC C protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1158073 T C 0 228 0 0.8389 0.892 0.9035 0.997 0.7992 0.9427 0.832377 0.804545 0.792358 2 6782 95326 10305 8367 5056 49163 711 14942 2 8080 111530 11136 8398 6436 60620 828 16032 1 0 . 0 . 195 1,0,92,81 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C351|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|9|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs28691231 -0.693147 0.00701693 195 V497A 1812 gTg/gCg MODERATE 12 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1161315 T C 0 228 0 1 0.9786 0.9654 0.999 0.9583 0.9591 0.992938 0.970925 0.961468 2 1009 16552 311 557 1575 5626 202 7272 2 1012 17462 330 558 1642 6046 210 7664 0 . 0 . 0 99 0,0,41,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V497A|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|12|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs28403537 -0.693147 0.540745 99 A632S? 1812 gca/Agca HIGH 16 CODING MUC5AC CA protein_coding NM_001304359.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212784 C CA 0 198 0 1 0.9996 1 1 0.999 0.999 0 . 0 2 59 993 93 91 44 643 7 56 2 60 1008 94 92 44 654 8 56 0 . 0 . 0 39 0,0,31,5 FRAME_SHIFT(HIGH||gca/Agca|A632S?|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 36 0.923077 1 1 0 1 (MUC5AC|MUC5AC|1|1.00) 46 0 0 0.83794 0 . rs146135733 -0.693139 5.98498e-09 39 P660L 1812 cCt/cTt MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212870 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0512779 0 . 0 . 699 232,52,136,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P660L|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 48 0 0.850452 0.0638238 0 0.914853 rs79862170 -0.693147 0.000451614 699 P660 1812 ccT/ccC LOW 16 SILENT CODING MUC5AC C protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212871 T C 0 221 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.00192313 0 . 0 . 711 246,57,111,38 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P660|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 49 0 1.72291e-07 0.00205114 0 0.000284022 rs75826663 -0.693147 0.0700362 711 Q662 1812 caA/caG LOW 16 SILENT CODING MUC5AC G protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212877 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.00968374 0 . 0 . 783 254,52,154,45 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q662|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 48 0 0.00160472 0.0297563 0 2.09849e-06 rs36195734,rs77623982 -0.693147 6.26937e-06 783 A688E 1812 gCa/gAa MODERATE 16 MISSENSE CODING MUC5AC A protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212954 C A 0 137 0 . 0 . 0 . 0 . 0 . 1 58 863 93 37 74 550 8 43 2 236 2786 312 164 212 1648 24 190 0.878485 0 . 0 . 476 147,133,26,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gAa|A688E|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 50 0 0.103413 0.792458 0 0.562572 rs201461932,rs35216491 -0.693147 4.91145e-08 476 Q694 1812 caG/caA LOW 16 SILENT CODING MUC5AC A protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1212973 G A 0 105 0 . 0 . 0 . 0 . 0 . 1 2 10 1 2 0 4 0 1 2 1336 14962 1678 1220 600 7632 110 2386 0.005729 0 . 0 . 273 82,84,7,55 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q694|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 50 0 0.714355 0.9443 0 0.000463576 rs79228823 -0.693147 3.04367e-21 273 L703 1812 ctT/ctA LOW 16 SILENT CODING MUC5AC A protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213000 T A 0 222 0 . 0 . 0 . 0 . 0 . 1 428 4650 444 224 256 2823 36 439 2 2372 26246 2610 1810 1588 15330 160 2376 0.372847 0 . 0 . 130 34,34,18,27 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L703|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 54 0 1.06215e-05 0.530375 0 0.907784 rs75897537 -0.693147 0.971148 130 S705P 1812 Tca/Cca MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213004 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 412 4558 437 222 256 2764 34 433 2 2754 30640 3130 2098 1992 17664 174 2828 0.132997 0 . 0 . 130 36,33,18,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S705P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 54 0 5.29318e-05 0.473393 0 0.321134 rs112704799 -0.693147 0.970822 130 R711P 1812 cGa/cCa MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213023 G C 0 222 0 . 0 . 0 . 0 . 0 . 1 166 1690 173 101 84 982 12 172 2 658 6208 598 376 336 3454 34 752 0.110203 0 . 0 . 155 52,32,23,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cCa|R711P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.00485987 0.057902 0 0.138332 rs202067431,rs28971119 -0.693147 0.462132 155 L719P 1812 cTa/cCa MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213047 T C 0 189 0 . 0 . 0 . 0 . 0 . 1 35 199 9 9 11 112 2 21 2 404 4772 454 348 270 2624 34 638 0.882826 0 . 0 . 202 69,46,21,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L719P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.00580771 0.0469497 0 0.000787516 rs28764936,rs76705130 -0.693145 4.27581e-08 202 Q742* 1812 Caa/Taa HIGH 16 NONSENSE CODING MUC5AC T protein_coding NM_001304359.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213115 C T 0 78 0 . 0 . 0 . 0 . 0 . 1 480 6825 435 401 237 2741 74 2457 2 6086 81640 7858 5502 5172 44686 610 11726 0.979993 0 . 0 . 242 112,55,9,23 STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q742*|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 (MUC5AC|MUC5AC|1|1.00) 53 0 0.565823 0.00135984 (MUC5AC|MUC5AC|1|1.00) 0.0222149 rs113511365 -0.69312 0.000544372 242 R745Q 1812 cGa/cAa MODERATE 16 MISSENSE CODING MUC5AC A protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213125 G A 0 222 0 0.4977 0.5 0.5 0.499 0.499 0.5051 0 . 0 1 1304 15625 1361 873 946 7331 127 3683 2 4136 52622 5136 3472 3180 26954 404 9340 0.0232992 0 . 0 . 212 54,25,57,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R745Q|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.00634915 0.0740442 0 0.49834 rs78716500 -0.693147 0.911467 212 P755L 1812 cCg/cTg MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213155 C T 0 107 0 . 0 . 0 . 0 . 0 . 1 289 3990 156 165 111 1383 47 1839 2 4210 60980 6306 4844 2746 33880 404 8590 0.999238 0 . 0 . 220 111,45,16,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P755L|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.759334 0.0792756 0 2.13118e-05 rs77137100 -0.693145 0.232376 220 Q761 1812 caA/caG LOW 16 SILENT CODING MUC5AC G protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213174 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 454 5809 533 433 311 3495 40 543 2 1504 20792 1522 1140 1032 11648 166 3780 0.574676 0 . 0 . 225 51,44,71,32 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q761|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.645361 0.0803742 0 0.370053 rs74046245 -0.693147 0.00546434 225 P762 1812 ccC/ccT LOW 16 SILENT CODING MUC5AC T protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213177 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 554 7528 571 466 313 3980 60 1584 2 1472 20220 1506 1132 1028 11422 164 3496 0.546737 0 . 0 . 214 52,33,70,32 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P762|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.383872 0.189388 0 0.960229 rs74046246 -0.693147 0.00776616 214 I771M 1812 atC/atG MODERATE 16 MISSENSE CODING MUC5AC G protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213204 C G 0 222 0 . 0 . 0 . 0 . 0 . 1 524 8673 680 444 586 5777 62 600 2 1310 18562 1486 1050 1188 12022 134 1372 0.839011 0 . 0 . 239 52,42,83,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I771M|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.477913 0.206404 0 0.361606 rs72479396 -0.693147 0.026847 239 L773P 1812 cTg/cCg MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213209 T C 0 221 0 . 0 . 0 . 0 . 0 . 1 29 226 9 8 16 117 5 42 2 5608 82110 8566 6434 3338 44880 584 12700 0.978586 0 . 0 . 243 102,57,35,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L773P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.100009 0.225839 0 0.728957 rs377214284 -0.693147 0.0052318 243 V785E 1812 gTg/gAg MODERATE 16 MISSENSE CODING MUC5AC A protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213245 T A 0 222 0 . 0 . 0 . 0 . 0 . 1 1142 16536 1270 1026 1125 10649 116 1208 2 2380 34206 2660 2190 2286 21862 238 2590 0.997556 0 . 0 . 263 53,51,98,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V785E|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.534456 0.748628 0 0.774519 rs67624660 -0.693147 0.115371 263 L789F 1812 Ctc/Ttc MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213256 C T 0 165 0 . 0 . 0 . 0 . 0 . 1 85 816 56 49 36 403 5 182 2 7256 103598 10468 7512 5704 57134 752 14772 0.728386 0 . 0 . 236 98,67,43,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L789F|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.803053 0.92916 0 0.537179 rs370028072 -0.693147 2.38127e-05 236 L789P 1812 cTc/cCc MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213257 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 1137 16532 1270 1026 1124 10647 116 1212 2 2370 34220 2656 2184 2286 21874 238 2612 0.0542003 0 . 0 . 225 50,50,86,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L789P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.624899 0.923896 0 0.999991 rs76779582 -0.693147 1.19991e-10 225 C790G 1812 Tgt/Ggt MODERATE 16 MISSENSE CODING MUC5AC G protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213259 T G 0 222 0 . 0 . 0 . 0 . 0 . 1 1136 16525 1270 1027 1123 10641 116 1212 2 2376 34324 2652 2176 2286 21898 240 2696 0.0403011 0 . 0 . 224 51,48,86,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C790G|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.626505 0.916789 0 0.924927 rs75991767 -0.693147 1.10337e-10 224 A791 1812 gcG/gcA LOW 16 SILENT CODING MUC5AC A protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213264 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 1137 16528 1271 1027 1125 10639 117 1212 2 2386 34258 2654 2174 2290 21892 242 2620 0.927308 0 . 0 . 235 51,40,102,35 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A791|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.590695 0.941837 0 0.997502 rs72846341 -0.693147 0.00987812 235 Q794P 1812 cAa/cCa MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213272 A C 0 222 0 . 0 . 0 . 0 . 0 . 1 1081 15530 1243 1024 1021 9861 112 1188 2 2314 32998 2614 2170 2160 20946 234 2560 0.952227 0 . 0 . 264 57,41,113,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cCa|Q794P|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.477357 0.993056 0 0.998238 rs78252457 -0.693147 0.874668 264 S797L 1812 tCg/tTg MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213281 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 1084 15571 1247 1025 1022 9889 113 1191 2 2314 32946 2614 2172 2156 20916 234 2540 0.827833 0 . 0 . 269 54,42,118,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S797L|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.546609 0.881875 0 0.340381 rs75618268 -0.693147 0.990705 269 W799* 1812 tGg/tAg HIGH 16 NONSENSE CODING MUC5AC A protein_coding NM_001304359.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213287 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 230 1739 89 91 82 945 15 287 2 3712 52778 5238 3984 2092 28754 386 8612 0.667765 0 . 0 . 281 116,61,60,23 STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W799*|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 (MUC5AC|MUC5AC|1|1.00) 58 0 0.919892 0.813351 (MUC5AC|MUC5AC|1|1.00) 0.941658 rs112774721 -0.693147 0.817821 281 S801F 1812 tCc/tTc MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213293 C T 0 221 0 . 0 . 0 . 0 . 0 . 1 1049 15295 1235 1011 998 9707 109 1186 2 2368 33946 2630 2152 2262 21650 246 2638 0.99989 0 . 0 . 294 124,67,56,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S801F|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.174166 0.720001 0 0.578219 rs77207494 -0.693147 0.993186 294 A808V 1812 gCg/gTg MODERATE 16 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213314 C T 0 222 0 . 0 . 0 . 0 . 0 . 1 1065 15588 1265 1039 1001 9883 110 1225 2 2170 31514 2560 2106 2026 19966 222 2464 0.948794 0 . 0 . 309 119,71,52,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A808V|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 58 0 0.0156555 0.20995 0 0.44222 rs73395695 -0.693147 0.00962275 309 T845A 1812 Aca/Gca MODERATE 16 MISSENSE CODING MUC5AC G protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213424 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 4151 56694 5679 4117 3291 30917 423 8116 2 8274 113312 11356 8234 6582 61788 846 16232 0.706966 0 . 0 . 234 60,51,15,86 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T845A|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.0452387 0.731103 0 0.0641537 rs61867531 -0.693147 0.0106697 234 V850A 1812 gTc/gCc MODERATE 16 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1213440 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 4184 56779 5686 4118 3290 30961 427 8113 2 8278 113368 11362 8234 6580 61838 850 16226 0.79962 0 . 0 . 223 65,49,11,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V850A|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|16|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.0520064 0.800622 0 0.282073 rs61867533 -0.693147 0.0647861 223 Y1255 1812 tac/ HIGH 21 CODING MUC5AC T protein_coding NM_001304359.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1216333 TA T 0 228 0 1 1 1 1 1 1 0.999626 0.999872 1 2 3722 64787 6121 4620 2060 36273 436 11555 2 3722 64804 6122 4626 2060 36282 436 11556 0 . 0 . 0 64 0,0,25,7 FRAME_SHIFT(HIGH||tac/|Y1255|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|21|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 63 0.984375 1 1 1 1 (MUC5AC|MUC5AC|1|1.00) 60 0 0 1 0 . rs60138698 -0.69312 0.0938475 64 T1289 1812 acG/acC LOW 22 SILENT CODING MUC5AC C protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1216440 G C 0 228 0 0.2995 0.5128 0.5562 0.6687 0.5885 0.5317 0.330645 0.508575 0.586224 2 2622 64061 6382 5724 3521 35954 488 9370 2 7690 109550 11112 8110 6424 59298 812 16104 0 . 0 . 0 55 0,0,18,29 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T1289|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|22|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.98079 0 . rs28415193 -0.693147 0.0444297 55 Q1306H 1812 caG/caC MODERATE 22 MISSENSE CODING MUC5AC C protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1216491 G C 0 228 0 0.298 0.514 0.5562 0.6687 0.5944 0.5337 0.331808 0.510129 0.588487 2 2677 65119 6491 5774 3602 36645 499 9431 2 7872 111172 11288 8162 6548 60324 822 16156 0 . 0 . 0 32 0,0,8,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caC|Q1306H|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|22|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.981133 0 . rs1132434 -0.693079 0.241356 32 P1679L 1812 cCg/cTg MODERATE 33 MISSENSE CODING MUC5AC T protein_coding NM_001304359.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1220967 C T 0 228 0 0.2943 0.4922 0.5533 0.6508 0.5944 0.4479 0.380892 0.544006 0.613182 2 414 13225 603 613 258 6640 119 4578 2 976 21966 994 874 414 10182 192 8334 0 . 0 . 0 48 0,0,43,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1679L|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|33|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1132436 -0.693147 0.129265 48 R1776 1812 cgG/cgC LOW 35 SILENT CODING MUC5AC C protein_coding NM_001304359.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1221817 G C 0 228 0 0.2927 0.4914 0.5533 0.6498 0.5924 0.4489 0.336605 0.513499 0.590634 2 2627 63277 6415 5629 3544 36190 488 8384 2 7628 109228 11038 8086 6334 59298 804 16040 0 . 0 . 0 162 0,0,84,59 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R1776|1812|MUC5AC|protein_coding|CODING|NM_001304359.1|35|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1132440 -0.693147 0.759058 162 1812 397 MODIFIER 35 CODING MUC5AC C protein_coding NM_001304359.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1222325 T C 0 103 0 0.8011 0.8816 0.902 0.997 0.7952 0.9458 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||397||1812|MUC5AC|protein_coding|CODING|NM_001304359.1|35|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11347 -0.556411 0.692431 4 1812 403 MODIFIER 35 CODING MUC5AC A protein_coding NM_001304359.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1222331 G A 0 95 0 0.8669 0.899 0.9035 0.997 0.7952 0.9448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||403||1812|MUC5AC|protein_coding|CODING|NM_001304359.1|35|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13380 -0.556411 0.692431 4 R1401H 5762 cGc/cAc MODERATE 31 MISSENSE CODING MUC5B A protein_coding NM_002458.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1262312 G A 0 228 0 0.1067 0.136 0.1282 0.3105 0.003 0.138 0.0786623 0.0270738 0.00118203 2 796 7285 1768 2678 23 109 36 1875 2 8976 113188 10854 8320 5886 62438 818 15896 0.913633 0 . 0 . 163 3,0,63,95 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R1401H|5762|MUC5B|protein_coding|CODING|NM_002458.2|31|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.419083 rs10835639 -0.693147 0.0373641 163 M2194T 5762 aTg/aCg MODERATE 31 MISSENSE CODING MUC5B C protein_coding NM_002458.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1264691 T C 0 228 0 0.9448 0.8107 0.7853 0.9593 0.5984 0.7127 0.841878 0.600652 0.488314 2 4923 33160 3232 1241 1400 14372 284 7708 2 5594 63204 4630 1404 2790 36192 524 12070 1 0 . 0 . 123 1,0,55,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M2194T|5762|MUC5B|protein_coding|CODING|NM_002458.2|31|C) 1 0 . 0 . 1 0 1 1 0 43 0 1 0.0236528 0 1 rs2943502 -0.693147 0.154312 123 L2238P 5762 cTa/cCa MODERATE 31 MISSENSE CODING MUC5B C protein_coding NM_002458.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1264823 T C 0 228 0 0.7526 0.7969 0.817 0.9722 0.6889 0.773 0.649156 0.592304 0.563595 2 7282 88846 9856 8470 5057 44957 656 12568 2 9742 119994 11558 8622 6560 66124 892 16496 0 . 0 . COSM1600233,COSM1600234 165 0,0,90,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L2238P|5762|MUC5B|protein_coding|CODING|NM_002458.2|31|C) 1 0 . 0 . 1 0 1 1 0 49 0 0 1.99027e-07 0 . rs4963031 -0.693147 0.000346115 165 T3284A 5762 Acc/Gcc MODERATE 31 MISSENSE CODING MUC5B G protein_coding NM_002458.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1267960 A G 0 228 0 . 0 . 0 . 0 0.874483 0.67401 0.579898 2 8890 91602 10117 8426 4811 45120 677 13561 2 9544 116676 11358 8588 6300 63626 866 16394 0 . 0 . 0 189 0,0,97,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T3284A|5762|MUC5B|protein_coding|CODING|NM_002458.2|31|G) 1 0 . 0 . 0 . 1 1 0 52 0 0 0.00041523 0 . rs2943531 -0.693147 0.125948 189 A5241T 5762 Gcc/Acc MODERATE 36 MISSENSE CODING MUC5B A protein_coding NM_002458.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1276327 G A 0 228 0 0.1089 0.1296 0.1282 0.2768 0.003 0.137 0.0769967 0.0267017 0.00155428 2 560 5023 1265 1674 13 83 31 1397 2 3918 45088 3918 4070 1082 22082 332 9686 0.447368 0 . 0 . 126 1,1,64,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A5241T|5762|MUC5B|protein_coding|CODING|NM_002458.2|36|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.642105 rs3829224 -0.693147 0.0340339 126 P139 274 ccG/ccA LOW 4 SILENT CODING TOLLIP T protein_coding NM_019009.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1309956 C T 0 228 0 0.2761 0.36 0.3415 0.3165 0.4573 0.4315 0.299046 0.391769 0.439274 2 2967 48072 3995 2631 2548 28399 348 7184 2 10262 120046 11540 8584 6586 65678 892 16504 0.4313 0 . 0 COSM428715 163 1,2,59,94 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P139|274|TOLLIP|protein_coding|CODING|NM_019009.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.0747391 rs3750920 -0.693147 0.00452461 163 T760A 766 Acc/Gcc MODERATE 20 MISSENSE CODING BRSK2 G protein_coding NM_001256630.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1481930 A G 0 50 0 . 0 . 0 . 0 . 0 . 1 138 5327 42 50 25 1180 57 3835 2 180 8738 76 110 42 1990 100 6240 0.542126 0 . 0 . 13 1,5,2,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T760A|766|BRSK2|protein_coding|CODING|NM_001256630.1|20|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 0.982603 1 0 0.304946 rs4963048 -0.616816 0.510342 13 766 629 MODIFIER 20 CODING BRSK2 C protein_coding NM_001256630.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1482582 T C 0 100 0 0.9977 0.9802 0.9669 1 0.9543 0.9724 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||629||766|BRSK2|protein_coding|CODING|NM_001256630.1|20|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6578412 -0.511536 0.126715 4 766 767 MODIFIER 20 CODING BRSK2 T protein_coding NM_001256630.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1482720 C T 0 55 0 0.6747 0.5521 0.5101 0.4236 0.5676 0.5327 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,1 UTR_3_PRIME(MODIFIER||767||766|BRSK2|protein_coding|CODING|NM_001256630.1|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs4072884 -0.511536 0.5 4 766 898 MODIFIER 20 CODING BRSK2 C protein_coding NM_001256630.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1482851 T C 0 25.9 0 0.7315 0.619 0.6167 0.4296 0.6879 0.593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||898||766|BRSK2|protein_coding|CODING|NM_001256630.1|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3829225 -0.453602 0.02 3 766 1224 MODIFIER 20 CODING BRSK2 C protein_coding NM_001256630.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1483177 T C 0 46.3 0 0.997 0.978 0.9654 1 0.9523 0.9652 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1224||766|BRSK2|protein_coding|CODING|NM_001256630.1|20|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1881505 -0.453602 0.66 2 268 306 MODIFIER 5 CODING MOB2 A protein_coding NM_001172223.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1491096 G A 0 222 0 0.6997 0.5483 0.5187 0.4058 0.5656 0.4939 0 . 0 1 340 6316 74 77 6 1907 64 3848 2 462 11952 148 180 8 3438 130 7586 0.862186 0 . 0 . 68 14,14,18,16 UTR_3_PRIME(MODIFIER||306||268|MOB2|protein_coding|CODING|NM_001172223.2|5|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.397735 rs9440 -0.693132 0.0413987 68 S106 268 tcC/tcG LOW 3 SILENT CODING MOB2 C protein_coding NM_001172223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1501670 G C 0 228 0 0.9939 0.9401 0.8818 0.998 0.8797 0.911 0.975167 0.914304 0.884096 2 9581 109276 10543 8618 5941 58958 787 14848 2 9814 120736 11576 8624 6614 66698 898 16512 0 . 0 . 0 43 0,0,16,22 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S106|268|MOB2|protein_coding|CODING|NM_001172223.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10742185 -0.693143 0.772194 43 P43 268 ccT/ccC LOW 2 SILENT CODING MOB2 G protein_coding NM_001172223.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1502097 A G 0 228 0 0.972 0.9343 0.8818 0.998 0.8797 0.911 0.954961 0.909571 0.886985 2 3082 29870 1346 1609 627 15365 241 7600 2 3222 32908 1472 1610 684 17166 270 8484 1 0 . 0 . 72 0,1,24,40 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P43|268|MOB2|protein_coding|CODING|NM_001172223.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10767696 -0.693147 0.334323 72 L19P 268 cTg/cCg MODERATE 1 MISSENSE CODING MOB2 G protein_coding NM_001172223.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1507731 A G 0 228 0 0.9939 0.9403 0.8833 0.998 0.8797 0.911 0 . 0 2 546 11133 165 197 6 3299 116 6804 2 564 12334 184 198 6 3630 132 7620 0 . 0 . COSM428748,COSM1133933 36 0,0,13,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L19P|268|MOB2|protein_coding|CODING|NM_001172223.2|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1881503 -0.693079 0.388886 36 268 9 MODIFIER 1 CODING MOB2 A protein_coding NM_001172223.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1507795 G A 0 150 0 0.2352 0.37 0.3588 0.6101 0.3101 0.3742 0 . 0 1 119 4324 68 129 1 1244 49 2714 2 504 12026 176 198 4 3456 128 7560 0.863243 0 . 0 . 18 0,10,3,3 START_GAINED(LOW||||268|MOB2|protein_coding|CODING|NM_001172223.2|1|A),UTR_5_PRIME(MODIFIER||9||268|MOB2|protein_coding|CODING|NM_001172223.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.2016 rs1110206 -0.616816 0.469001 18 268 190 MODIFIER 1 CODING MOB2 C protein_coding NM_001172223.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1507976 T C 0 39.7 0 0.2352 0.3702 0.3588 0.6111 0.3101 0.3742 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_5_PRIME(MODIFIER||190||268|MOB2|protein_coding|CODING|NM_001172223.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12798762 -0.511536 0.160332 4 625 1743 MODIFIER 7 CODING DUSP8 C protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576005 T C 0 112 0 0.5416 0.4934 0.4539 0.4315 0.5328 0.4796 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.983927 0 . 0 . 27 4,14,2,7 UTR_3_PRIME(MODIFIER||1743||625|DUSP8|protein_coding|CODING|NM_004420.2|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.757215 rs59483236 -0.662043 0.521248 27 625 1669 MODIFIER 7 CODING DUSP8 T protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576079 C T 0 222 0 0.5408 0.493 0.4539 0.4315 0.5318 0.4796 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.606846 0 . 0 . 63 24,2,30,4 UTR_3_PRIME(MODIFIER||1669||625|DUSP8|protein_coding|CODING|NM_004420.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875959 rs1982827 -0.693132 0.0546379 63 625 1611 MODIFIER 7 CODING DUSP8 T protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576137 C T 0 222 0 0.5242 0.488 0.4539 0.4365 0.5318 0.4714 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980429 0 . 0 . 100 32,3,34,11 UTR_3_PRIME(MODIFIER||1611||625|DUSP8|protein_coding|CODING|NM_004420.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.780979 rs11604635 -0.693147 0.500769 100 625 1513 MODIFIER 7 CODING DUSP8 C protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576235 T C 0 222 0 0.8359 0.6667 0.6311 0.4355 0.7097 0.6575 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968964 0 . 0 . 103 33,21,27,15 UTR_3_PRIME(MODIFIER||1513||625|DUSP8|protein_coding|CODING|NM_004420.2|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.964317 rs6578504 -0.693146 0.769822 103 625 1465 MODIFIER 7 CODING DUSP8 A protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576283 G A 0 222 0 0.5416 0.4934 0.4539 0.4315 0.5328 0.4796 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.430684 0 . 0 . 125 33,23,37,21 UTR_3_PRIME(MODIFIER||1465||625|DUSP8|protein_coding|CODING|NM_004420.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.387311 rs11603496 -0.693147 0.00278574 125 625 885 MODIFIER 7 CODING DUSP8 G protein_coding NM_004420.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1576863 A G 0 68 0 0.5756 0.6082 0.6268 0.5089 0.7256 0.6207 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.62023 0 . 0 . 8 0,4,1,3 UTR_3_PRIME(MODIFIER||885||625|DUSP8|protein_coding|CODING|NM_004420.2|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.372138 rs12576976 -0.556411 0.27062 8 G117 278 ggT/ggG LOW 1 SILENT CODING KRTAP5-1 C protein_coding NM_001005922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1606129 A C 0 92 0 0.59 0.5385 0.5173 0.4732 0.5626 0.5266 0 . 0 1 152 985 40 38 76 567 16 96 2 2418 30324 3402 3192 1044 15356 254 4658 0.983728 0 . 0 . 40 9,14,0,13 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G117|278|KRTAP5-1|protein_coding|CODING|NM_001005922.1|1|C),INTRAGENIC(MODIFIER|||||KRTAP5-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.250794 rs76191756 -0.683931 0.139304 40 G114 278 ggA/ggC LOW 1 SILENT CODING KRTAP5-1 G protein_coding NM_001005922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1606138 T G 0 97 0 . 0 . 0 . 0 0.143307 0.133399 0.128342 1 90 730 32 26 70 444 12 56 2 2388 30244 3390 3212 1028 15348 252 4626 0.618184 0 . 0 . 33 4,14,1,12 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G114|278|KRTAP5-1|protein_coding|CODING|NM_001005922.1|1|G),INTRAGENIC(MODIFIER|||||KRTAP5-AS1||NON_CODING|||G) 1 0.5 1 0 . 0 . 1 1 0 60 0 1 1 0 1 rs80025267 -0.683931 0.0175094 33 S111 278 tcT/tcC LOW 1 SILENT CODING KRTAP5-1 G protein_coding NM_001005922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1606147 A G 0 101 0 0.5295 0.4443 0.3948 0.3294 0.4563 0.4703 0 . 0 1 54 386 17 14 43 231 10 17 2 2420 30222 3416 3224 1016 15310 252 4584 0.573753 0 . 0 . 27 1,15,0,10 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S111|278|KRTAP5-1|protein_coding|CODING|NM_001005922.1|1|G),INTRAGENIC(MODIFIER|||||KRTAP5-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0529245 rs138363822 -0.670168 0.000231808 27 G93 177 ggC/ggT LOW 1 SILENT CODING KRTAP5-2 A protein_coding NM_001004325.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1619202 G A 0 57 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.936262 0 . 0 . 32 11,13,3,3 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G93|177|KRTAP5-2|protein_coding|CODING|NM_001004325.1|1|A),INTRAGENIC(MODIFIER|||||KRTAP5-AS1||NON_CODING|||A) 0 0.5 1 0 . 0 . 0 . 0 58 0 0.907456 0.998058 0 0.0933903 rs61869706 -0.616816 0.00794932 32 228 1860 MODIFIER 3 CODING IFITM10 G protein_coding NM_001170820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1754650 C G 0 18.5 0 0 0.0029952 0 0.0149 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,2,0 UTR_3_PRIME(MODIFIER||1860||228|IFITM10|protein_coding|CODING|NM_001170820.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3740626 -0.453602 0.84 5 228 219 MODIFIER 3 CODING IFITM10 C protein_coding NM_001170820.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1756291 T C 0 69 0 0.6301 0.4205 0.33 0.251 0.334 0.4652 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.727822 0 . 0 . 11 5,1,3,1 UTR_3_PRIME(MODIFIER||219||228|IFITM10|protein_coding|CODING|NM_001170820.3|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.895781 rs2292958,rs386563986 -0.556411 0.372756 11 412 67 MODIFIER 9 CODING CTSD C protein_coding NM_001909.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1774666 T C 0 222 0 0.1422 0.2005 0.1542 0.1042 0.2972 0.3119 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.740201 0 . 0 . 331 117,58,82,30 UTR_3_PRIME(MODIFIER||67||412|CTSD|protein_coding|CODING|NM_001909.4|9|C),UPSTREAM(MODIFIER||2842||228|IFITM10|protein_coding|CODING|NM_001170820.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999987 rs12214 -0.693147 0.074277 331 A317 412 gcC/gcT LOW 7 SILENT CODING CTSD A protein_coding NM_001909.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1775245 G A 0 222 0 0 0.017971 0 0.0893 0 0 0 7.6982e-05 0.00011636 1 1 589 3 533 10 27 3 12 2 7836 96770 9346 7074 3942 53044 684 14844 0.352866 2 benign 0 . 85 37,3,35,5 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A317|412|CTSD|protein_coding|CODING|NM_001909.4|7|A),UPSTREAM(MODIFIER||3421||228|IFITM10|protein_coding|CODING|NM_001170820.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.655581 rs78306946 -0.693145 0.000179817 85 402 LOW 1 CODING SYT8 C protein_coding NM_001290332.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1855854 G C 0 228 0 0.6967 0.7358 0.7839 0.6399 0.7903 0.7975 0.685447 0.761479 0.800256 2 4095 53975 5670 3250 2102 29331 444 9083 2 5796 68666 6748 4874 2450 36902 552 11344 0 . 0 . 0 23 0,0,9,13 SPLICE_SITE_REGION+INTRON(LOW||||402|SYT8|protein_coding|CODING|NM_001290332.1|1|C),UPSTREAM(MODIFIER||4865||182|TNNI2|protein_coding|CODING|NM_001145829.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2063551 -0.692562 0.170967 23 C121R 402 Tgc/Cgc MODERATE 4 MISSENSE CODING SYT8 C protein_coding NM_001290332.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1857173 T C 0 228 0 0.9395 0.9832 0.9942 1 1 1 0.952997 0.983926 0.999767 2 9845 120133 11532 8642 6610 66106 897 16501 2 10310 120652 11556 8642 6610 66122 902 16510 0 . 0 . 0 87 0,0,22,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C121R|402|SYT8|protein_coding|CODING|NM_001290332.1|4|C),UPSTREAM(MODIFIER||3546||182|TNNI2|protein_coding|CODING|NM_001145829.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs564271 -0.693147 0.0345653 87 T304M 402 aCg/aTg MODERATE 8 MISSENSE CODING SYT8 T protein_coding NM_001290332.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1858262 C T 0 228 0 0.0507 0.1855 0.2262 0.4137 0.1282 0.1626 0.0613079 0.100369 0.120377 2 604 17921 1830 3338 861 8638 123 2527 2 10350 120876 11558 8630 6614 66322 902 16500 0.9 0 . 0 COSM1353012 151 2,0,106,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T304M|402|SYT8|protein_coding|CODING|NM_001290332.1|8|T),UPSTREAM(MODIFIER||2457||182|TNNI2|protein_coding|CODING|NM_001145829.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.657143 rs484955 -0.693147 0.0130622 151 S20 182 agT/agC LOW 4 SILENT CODING TNNI2 C protein_coding NM_001145829.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1861760 T C 0 228 0 0.612 0.8277 0.8703 0.9861 0.8847 0.8671 0.668568 0.803241 0.872085 2 6239 101156 10198 8338 5790 55347 762 14482 2 9332 115472 11248 8440 6202 62984 850 16416 0 255|1 other|not-provided 0 . 80 0,0,53,22 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S20|182|TNNI2|protein_coding|CODING|NM_001145829.1|4|C),DOWNSTREAM(MODIFIER||3009||402|SYT8|protein_coding|CODING|NM_001290332.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs907610 -0.693147 0.0582244 80 H34Q 467 caT/caA MODERATE 2 MISSENSE CODING LSP1 A protein_coding NM_001242932.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1887806 T A 0 228 0 0.531 0.6244 0.7622 0.7688 0.6322 0.4959 0 . 0 2 491 8146 202 349 369 3031 101 3603 2 896 14756 280 478 580 5022 162 7338 0 . 0 . 0 65 0,0,43,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H34Q|467|LSP1|protein_coding|CODING|NM_001242932.1|2|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7938342 -0.693147 0.915803 65 A228T 467 Gcc/Acc MODERATE 4 MISSENSE CODING LSP1 A protein_coding NM_001242932.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1902768 G A 0 222 0 0.2595 0.397 0.5418 0.5863 0.3867 0.2955 0.266744 0.329335 0.3615 1 868 8418 434 809 58 4031 87 2131 2 2862 21340 730 1288 112 9456 186 6706 0.96078 0 . 0 . 35 5,4,11,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A228T|467|LSP1|protein_coding|CODING|NM_001242932.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.926163 rs621679 -0.692562 0.761657 35 R11Q 153 cGg/cAg MODERATE 2 MISSENSE CODING MRPL23 A protein_coding NM_021134.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1972143 G A 0 222 0 0.0976 0.098 0.0303 0.1448 0.0258 0.1728 0.0815168 0.0456853 0.0273319 1 885 6789 395 1192 125 1900 46 2246 2 10342 120552 11512 8618 6498 66216 898 16468 0.65698 0 . 0 . 155 49,27,44,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R11Q|153|MRPL23|protein_coding|CODING|NM_021134.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.9211 rs34134444 -0.693147 0.360865 155 G32S 153 Ggt/Agt MODERATE 2 MISSENSE CODING MRPL23 A protein_coding NM_021134.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 1972205 G A 0 222 0 0.0802 0.0925 0.0288 0.1429 0.0249 0.1718 0.0667878 0.0405385 0.0270993 1 703 6403 373 1135 115 1834 45 2198 2 8372 91328 7816 6836 4364 49174 690 14076 0.815648 0 . 0 . 179 47,26,52,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G32S|153|MRPL23|protein_coding|CODING|NM_021134.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97331 rs2240197 -0.693147 0.837186 179 151 1794 MODIFIER 1 CODING HOTS T protein_coding NM_001293171.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2014633 C T 0 32.6 0 0.1936 0.1042 0.0303 0.1438 0.0139 0.0879 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 START_GAINED(LOW||||151|HOTS|protein_coding|CODING|NM_001293171.2|1|T),UTR_5_PRIME(MODIFIER||1794||151|HOTS|protein_coding|CODING|NM_001293171.2|1|T),INTRAGENIC(MODIFIER|||||LINC01219||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs58781599 -0.379885 0 2 151 758 MODIFIER 1 CODING HOTS T protein_coding NM_001293171.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2015669 G T 0 46.3 0 0.0348 0.0603 0.0187 0.1429 0.0129 0.0879 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||758||151|HOTS|protein_coding|CODING|NM_001293171.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs117154195 -0.453602 0.58 2 151 699 MODIFIER 1 CODING HOTS C protein_coding NM_001293171.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2015728 T C 0 46.3 0 0.236 0.5054 0.5159 0.5417 0.6869 0.638 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||699||151|HOTS|protein_coding|CODING|NM_001293171.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs217232 -0.453602 0.02 2 T65A 151 Aca/Gca MODERATE 1 MISSENSE CODING HOTS G protein_coding NM_001293171.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2016619 A G 0 203 0 0.0825 0.2983 0.4121 0.3343 0.5 0.2648 0.143429 0.396124 0.50729 1 1140 45819 4014 2535 3277 29851 369 4633 2 7706 108892 10858 7926 6220 59344 814 16024 0.97619 0 . 0 . 66 23,17,16,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T65A|151|HOTS|protein_coding|CODING|NM_001293171.2|1|G),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.415655 rs3741219 -0.692067 0.340651 66 V78A 151 gTa/gCa MODERATE 1 MISSENSE CODING HOTS C protein_coding NM_001293171.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2016659 T C 0 222 0 0.0794 0.2688 0.3617 0.3343 0.3976 0.2587 0.120571 0.308834 0.391654 1 936 35973 3506 2495 2121 22230 281 4404 2 7510 106404 10548 7774 5906 58098 780 15788 0.987928 0 . 0 . 86 35,14,20,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V78A|151|HOTS|protein_coding|CODING|NM_001293171.2|1|C),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.96775 rs2839704 -0.692976 0.627771 86 L79P 151 cTg/cCg MODERATE 1 MISSENSE CODING HOTS C protein_coding NM_001293171.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2016662 T C 0 222 0 0.0794 0.269 0.3617 0.3343 0.3986 0.2587 0.120571 0.308834 0.391654 1 947 35953 3505 2494 2117 22204 284 4402 2 7516 106430 10560 7784 5920 58074 788 15788 0.998188 0 . 0 . 87 36,14,20,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L79P|151|HOTS|protein_coding|CODING|NM_001293171.2|1|C),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925258 rs2839703 -0.692976 0.627771 87 I97 151 atT/atA LOW 1 SILENT CODING HOTS A protein_coding NM_001293171.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2016717 T A 0 222 0 0.034 0.0603 0.0187 0.1438 0.0129 0.0879 0.0297143 0.021815 0.0183417 1 244 4346 185 1110 131 1410 36 1230 2 7070 101110 9850 7248 5698 55328 772 15144 0.572991 0 . 0 . 99 28,12,37,16 SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I97|151|HOTS|protein_coding|CODING|NM_001293171.2|1|A),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.387282 rs3741216 -0.693147 0.377283 99 151 42 MODIFIER 1 CODING HOTS G protein_coding NM_001293171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2016924 A G 0 220 0 0.0552 0.2913 0.4135 0.3323 0.5 0.2669 0.121143 0.392147 0.511307 1 930 46697 4128 2586 3336 30688 377 4652 2 7990 111644 11228 8178 6320 60960 826 16142 0.796801 0 . 0 . 52 4,27,3,15 UTR_3_PRIME(MODIFIER||42||151|HOTS|protein_coding|CODING|NM_001293171.2|1|G),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.690474 rs10840159 -0.691153 0.354859 52 151 135 MODIFIER 1 CODING HOTS C protein_coding NM_001293171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2017017 A C 0 209 0 0.0552 0.2901 0.4049 0.3323 0.5 0.2669 0.121281 0.390712 0.509045 1 926 46592 4110 2595 3396 30640 373 4552 2 7926 110632 11136 8120 6396 60660 812 15582 0.447194 0 . 0 . 27 9,3,11,4 UTR_3_PRIME(MODIFIER||135||151|HOTS|protein_coding|CODING|NM_001293171.2|1|C),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.708895 rs2839702 -0.688148 0.538056 27 151 228 MODIFIER 1 CODING HOTS G protein_coding NM_001293171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2017110 C G 0 222 0 0.0552 0.2901 0.4092 0.3313 0.499 0.2658 0.121143 0.388831 0.506533 1 937 46650 4136 2586 3384 30592 382 4633 2 8108 112616 11304 8188 6534 61448 842 16192 0.913423 0 . 0 . 68 25,6,26,4 UTR_3_PRIME(MODIFIER||228||151|HOTS|protein_coding|CODING|NM_001293171.2|1|G),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.500984 rs2839701 -0.693097 0.826934 68 151 557 MODIFIER 1 CODING HOTS G protein_coding NM_001293171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2017439 C G 0 228 0 0.1475 0.3654 0.4337 0.4683 0.5169 0.3497 0.202176 0.424126 0.521641 2 978 33859 2546 2420 1899 21236 283 4497 2 4070 67168 5636 4774 3152 37488 514 11534 1 0 . 0 . 184 1,0,67,105 UTR_3_PRIME(MODIFIER||557||151|HOTS|protein_coding|CODING|NM_001293171.2|1|G),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3024270 -0.693147 0.33138 184 151 582 MODIFIER 1 CODING HOTS A protein_coding NM_001293171.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2017464 G A 0 222 0 0.112 0.0829 0.0259 0.1567 0.0129 0.0798 0.0880322 0.0380568 0.0161453 1 407 2978 112 693 52 804 22 888 2 3182 45296 3388 3330 1370 23746 328 9952 0.75448 0 . 0 . 167 19,55,26,56 UTR_3_PRIME(MODIFIER||582||151|HOTS|protein_coding|CODING|NM_001293171.2|1|A),INTRAGENIC(MODIFIER|||||H19||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.109594 rs3825028 -0.693147 0.128954 167 200 LOW 4 CODING INS-IGF2 A protein_coding NM_001042376.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2167981 G A 0 9.7 0 0.1899 0.3353 0.1859 0.496 0.2982 0.5102 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 SPLICE_SITE_REGION+INTRON(LOW||||200|INS-IGF2|protein_coding|CODING|NM_001042376.2|4|A),INTRAGENIC(MODIFIER|||||IGF2||CODING|||A),INTRAGENIC(MODIFIER|||||IGF2-AS||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2239681 -0.379885 0 1 110 22 MODIFIER 3 CODING INS G protein_coding NM_000207.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2181060 T G 0 228 0 0.1793 0.6492 0.7248 0.9415 0.7256 0.8507 0.26865 0.547553 0.689539 2 2295 80183 8246 7893 4116 44263 577 12793 2 8302 108678 10492 8280 5102 60586 766 15150 0 . 0 . 0 50 0,0,34,12 UTR_3_PRIME(MODIFIER||22||110|INS|protein_coding|CODING|NM_000207.2|3|G),DOWNSTREAM(MODIFIER||4099||528|TH|protein_coding|CODING|NM_199292.2||G),INTRON(MODIFIER||||200|INS-IGF2|protein_coding|CODING|NM_001042376.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3842753 -0.693147 0.0539148 50 200 LOW 1 CODING INS-IGF2 T protein_coding NM_001042376.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2182224 A T 0 228 0 0.1808 0.6496 0.7233 0.9415 0.7256 0.8517 0.28366 0.56714 0.711987 2 2499 84031 8645 8084 4663 45761 632 13747 2 9556 115618 11146 8478 5904 63304 842 16388 0 . 0 . 0 89 0,0,13,73 SPLICE_SITE_REGION+INTRON(LOW||||200|INS-IGF2|protein_coding|CODING|NM_001042376.2|1|T),SPLICE_SITE_REGION+INTRON(LOW||||110|INS|protein_coding|CODING|NM_000207.2|1|T),DOWNSTREAM(MODIFIER||2935||528|TH|protein_coding|CODING|NM_199292.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs689 -0.693147 0.48793 89 110 LOW 1 CODING INS T protein_coding NM_000207.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2182224 A T 0 228 0 0.1808 0.6496 0.7233 0.9415 0.7256 0.8517 0.28366 0.56714 0.711987 2 2499 84031 8645 8084 4663 45761 632 13747 2 9556 115618 11146 8478 5904 63304 842 16388 0 . 0 . 0 89 0,0,13,73 SPLICE_SITE_REGION+INTRON(LOW||||200|INS-IGF2|protein_coding|CODING|NM_001042376.2|1|T),SPLICE_SITE_REGION+INTRON(LOW||||110|INS|protein_coding|CODING|NM_000207.2|1|T),DOWNSTREAM(MODIFIER||2935||528|TH|protein_coding|CODING|NM_199292.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs689 -0.693147 0.48793 89 V112M 528 Gtg/Atg MODERATE 3 MISSENSE CODING TH T protein_coding NM_199292.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2190951 C T 0 228 0 0.1014 0.4305 0.3919 0.7877 0.4026 0.5634 0.141527 0.288 0.362991 2 1396 50951 5239 6847 2955 24882 415 9217 2 10176 119912 11514 8630 6540 65658 890 16504 0 2 benign 0 . 83 0,0,17,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V112M|528|TH|protein_coding|CODING|NM_199292.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6356 -0.693147 0.0153009 83 193 518 MODIFIER 1 CODING ASCL2 A protein_coding NM_005170.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2292080 G A 0 194 0 0.0144 0.1266 0.1441 0.0794 0.2117 0.227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.240661 0 . 0 . 80 2,42,3,31 UTR_5_PRIME(MODIFIER||518||193|ASCL2|protein_coding|CODING|NM_005170.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.975728 0.757891 0 0.393719 rs55930300 -0.693132 0.0182509 80 178 1819 MODIFIER 5 CODING C11orf21 G protein_coding NM_001142946.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2318867 A G 0 81 0 0.6036 0.4149 0.3372 0.1925 0.4066 0.453 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,3,1 UTR_3_PRIME(MODIFIER||1819||178|C11orf21|protein_coding|CODING|NM_001142946.1|5|G),UPSTREAM(MODIFIER||4376||320|TSPAN32|protein_coding|CODING|NM_139022.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2074019 -0.556411 0.0665622 6 178 1818 MODIFIER 5 CODING C11orf21 A protein_coding NM_001142946.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2318868 G A 0 82 0 0.6036 0.4155 0.3386 0.1944 0.4066 0.453 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,3,1 UTR_3_PRIME(MODIFIER||1818||178|C11orf21|protein_coding|CODING|NM_001142946.1|5|A),UPSTREAM(MODIFIER||4375||320|TSPAN32|protein_coding|CODING|NM_139022.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2074020 -0.556411 0.0665622 6 V24M 178 Gtg/Atg MODERATE 1 MISSENSE CODING C11orf21 T protein_coding NM_001142946.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2323022 C T 0 222 0 0.0802 0.2101 0.2637 0.1399 0.3588 0.2669 0.123555 0.27661 0.34318 1 258 5960 86 111 227 3047 58 2173 2 2150 20830 406 626 968 8570 208 7902 0.826949 0 . 0 . 156 28,31,36,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V24M|178|C11orf21|protein_coding|CODING|NM_001142946.1|1|T),UPSTREAM(MODIFIER||221||320|TSPAN32|protein_coding|CODING|NM_139022.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.745215 rs12276847 -0.693147 0.641039 156 G21 178 ggA/ggG LOW 1 SILENT CODING C11orf21 C protein_coding NM_001142946.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2323029 T C 0 228 0 0.9561 0.8067 0.83 0.4058 0.9264 0.8783 0.950867 0.933859 0.926461 2 2058 18457 327 259 842 7891 182 6898 2 2162 20992 408 624 1040 8630 216 7912 0.88311 0 . 0 . 149 1,3,61,72 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G21|178|C11orf21|protein_coding|CODING|NM_001142946.1|1|C),UPSTREAM(MODIFIER||214||320|TSPAN32|protein_coding|CODING|NM_139022.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.794877 rs756924 -0.693147 0.361965 149 C103 320 tgC/tgT LOW 4 SILENT CODING TSPAN32 T protein_coding NM_139022.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2329995 C T 0 228 0 0.6014 0.6312 0.6686 0.2698 0.8996 0.7413 0.644455 0.806576 0.889433 2 3278 47687 3007 1036 2156 30155 377 7678 2 4964 59080 4446 2568 2582 34044 476 10000 0.884376 0 . 0 . 146 3,0,95,18 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C103|320|TSPAN32|protein_coding|CODING|NM_139022.2|4|T) 1 0 . 0 . 1 0 1 1 0 59 0 0.996941 0.533549 0 0.322429 rs11554947 -0.693147 0.158224 146 S199 236 tcC/tcT LOW 7 SILENT CODING CD81 T protein_coding NM_004356.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2417893 C T 0 222 0 0.2617 0.0891 0.0288 0.0317 0.0129 0.0358 0.228429 0.0843077 0.01047 1 2412 4081 321 156 2 630 31 529 2 10222 119800 11548 8592 6612 65430 890 16506 0.994142 0 . 0 . 120 35,30,19,16 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S199|236|CD81|protein_coding|CODING|NM_004356.3|7|T),UPSTREAM(MODIFIER||3825||329|TSSC4|protein_coding|CODING|NM_001297658.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.263495 rs14077 -0.693136 0.0129572 120 A213 236 gcT/gcC LOW 7 SILENT CODING CD81 C protein_coding NM_004356.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2417935 T C 0 222 0 0.3797 0.122 0.0389 0.0317 0.0149 0.0358 0.326975 0.118136 0.0111654 1 3476 5241 375 158 2 665 35 530 2 10232 119838 11540 8590 6612 65474 888 16502 0.626889 0 . 0 . 107 29,32,15,18 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A213|236|CD81|protein_coding|CODING|NM_004356.3|7|C),UPSTREAM(MODIFIER||3783||329|TSSC4|protein_coding|CODING|NM_001297658.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.6699 rs2229751 -0.693127 0.738316 107 236 241 MODIFIER 8 CODING CD81 G protein_coding NM_004356.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2418337 A G 0 118 0 0.261 0.0909 0.0288 0.0317 0.0129 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.25 0 . 0 . 8 0,2,3,1 UTR_3_PRIME(MODIFIER||241||236|CD81|protein_coding|CODING|NM_004356.3|8|G),UPSTREAM(MODIFIER||3381||329|TSSC4|protein_coding|CODING|NM_001297658.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.861511 0 0 rs1049390 -0.556411 0.803107 8 236 462 MODIFIER 8 CODING CD81 T protein_coding NM_004356.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2418558 C T 0 26.4 0 0.2239 0.0889 0.0259 0.0327 0.0129 0.0869 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,0 UTR_3_PRIME(MODIFIER||462||236|CD81|protein_coding|CODING|NM_004356.3|8|T),UPSTREAM(MODIFIER||3160||329|TSSC4|protein_coding|CODING|NM_001297658.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1049652 -0.453602 0.42 4 236 466 MODIFIER 8 CODING CD81 A protein_coding NM_004356.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2418562 G A 0 26.4 0 0.2625 0.0994 0.0288 0.0327 0.0129 0.0869 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,0 UTR_3_PRIME(MODIFIER||466||236|CD81|protein_coding|CODING|NM_004356.3|8|A),UPSTREAM(MODIFIER||3156||329|TSSC4|protein_coding|CODING|NM_001297658.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1049659 -0.453602 0.42 4 G262R 329 Ggg/Agg MODERATE 4 MISSENSE CODING TSSC4 A protein_coding NM_001297658.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2424647 G A 0 222 0 0.2602 0.0863 0.0274 0.0258 0.0119 0.0317 0.20984 0.0773267 0.00989753 1 2118 3475 285 109 1 520 29 413 2 8992 102430 10080 7572 5178 56944 718 12946 0.981417 0 . 0 . 130 39,14,52,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G262R|329|TSSC4|protein_coding|CODING|NM_001297658.1|4|A),DOWNSTREAM(MODIFIER||1099||1165|TRPM5|protein_coding|CODING|NM_014555.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.850951 rs2234281 -0.693147 0.0340923 130 H274P 329 cAc/cCc MODERATE 4 MISSENSE CODING TSSC4 C protein_coding NM_001297658.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2424684 A C 0 228 0 0.9992 0.9966 0.9899 1 0.993 0.998 0.999086 0.993215 0.990226 2 9317 107323 10455 7812 5359 59224 794 14362 2 9332 108012 10490 7812 5456 59714 804 14404 0 . 0 . 0 163 0,0,100,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cCc|H274P|329|TSSC4|protein_coding|CODING|NM_001297658.1|4|C),DOWNSTREAM(MODIFIER||1062||1165|TRPM5|protein_coding|CODING|NM_014555.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2234283,rs386561978 -0.693147 0.148181 163 G1094 1165 ggT/ggG LOW 22 SILENT CODING TRPM5 C protein_coding NM_014555.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2427291 A C 0 228 0 0.91 0.7744 0.6873 0.5387 0.8718 0.7955 0.893733 0.873635 0.86334 2 9313 97959 6822 4714 5531 57740 740 13099 2 10364 120924 11546 8618 6614 66368 906 16508 0.815789 0 . 0 . 42 1,1,19,19 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggG|G1094|1165|TRPM5|protein_coding|CODING|NM_014555.3|22|C),DOWNSTREAM(MODIFIER||2183||329|TSSC4|protein_coding|CODING|NM_001297658.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.973684 rs800342 -0.693143 0.0729296 42 1165 LOW 20 CODING TRPM5 A protein_coding NM_014555.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2428341 G A 0 168 0 0.1104 0.2338 0.2363 0.3125 0.2624 0.2883 0.0959781 0.153233 0.18253 1 606 10605 1319 617 275 6153 84 1551 2 4182 44372 3816 2756 1370 23408 338 8502 0.0869891 0 . 0 COSM1604441 68 24,18,7,11 SPLICE_SITE_REGION+INTRON(LOW||||1165|TRPM5|protein_coding|CODING|NM_014555.3|20|A),DOWNSTREAM(MODIFIER||3233||329|TSSC4|protein_coding|CODING|NM_001297658.1||A) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.978252 0.912092 0 8.44101e-09 rs11022676 -0.691153 2.31898e-11 68 T836 1165 acA/acG LOW 17 SILENT CODING TRPM5 C protein_coding NM_014555.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2432964 T C 0 222 0 0.2027 0.3311 0.366 0.4643 0.3509 0.3221 0.240917 0.313413 0.350547 1 2441 42544 5222 3702 2114 23201 348 5516 2 10224 119828 11530 8586 6582 65514 886 16506 0.898055 0 . 0 . 114 11,36,15,42 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T836|1165|TRPM5|protein_coding|CODING|NM_014555.3|17|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.759741 rs2074234 -0.693147 0.0852753 114 L581 1165 ctT/ctC LOW 11 SILENT CODING TRPM5 G protein_coding NM_014555.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2435946 A G 0 145 0 0.6286 0.7604 0.83 0.9048 0.7117 0.7904 0.7051 0.731559 0.744799 2 720 10918 186 272 8 3768 123 5841 2 1052 14536 226 304 10 5294 150 7500 0 . 0 . 0 6 0,0,4,1 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L581|1165|TRPM5|protein_coding|CODING|NM_014555.3|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4929981 -0.590765 0.754056 6 R578Q 1165 cGg/cAg MODERATE 11 MISSENSE CODING TRPM5 T protein_coding NM_014555.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2435956 C T 0 82 0 0.4924 0.529 0.5663 0.6597 0.4533 0.4949 0.451096 0.431068 0.421039 1 652 7236 129 249 9 2535 83 3579 2 1188 15186 242 350 12 5680 162 7552 1 0 . 0 . 6 0,1,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R578Q|1165|TRPM5|protein_coding|CODING|NM_014555.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4929982 -0.556411 0.756056 6 V254A 1165 gTa/gCa MODERATE 6 MISSENSE CODING TRPM5 G protein_coding NM_014555.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2439542 A G 0 228 0 0.9705 0.8433 0.8444 0.9008 0.6561 0.8037 0.924228 0.750971 0.66284 2 3995 36138 2888 3022 685 17508 263 7777 2 4302 47486 3296 3382 956 25264 348 9938 0 . 0 . COSM428853 24 0,0,11,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V254A|1165|TRPM5|protein_coding|CODING|NM_014555.3|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3986599 -0.692831 0.201237 24 N235S 1165 aAc/aGc MODERATE 5 MISSENSE CODING TRPM5 C protein_coding NM_014555.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2439767 T C 0 222 0 0.6407 0.5373 0.5375 0.6607 0.3678 0.4448 0.612602 0.462279 0.385385 1 5922 50490 5694 5573 2219 24087 355 6640 2 9364 108798 10546 8220 4856 59854 778 15180 0.998956 0 . 0 . 94 25,20,17,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N235S|1165|TRPM5|protein_coding|CODING|NM_014555.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.35949 rs886277 -0.693143 0.80902 94 S546 676 tcG/tcA LOW 13 SILENT CODING KCNQ1 A protein_coding NM_000218.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2797237 G A 0 222 0 0.0106 0.1809 0.33 0.2927 0.1978 0.1728 0.0464481 0.143507 0.193214 1 211 8983 772 1034 185 4958 66 1757 2 3584 34758 1640 2652 520 17482 276 8604 0.922805 2|2 benign|benign 0 COSM1604458 85 17,15,27,11 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S546|676|KCNQ1|protein_coding|CODING|NM_000218.2|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.791533 rs1057128 -0.693143 0.0170219 85 676 875 MODIFIER 16 CODING KCNQ1 G protein_coding NM_000218.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2870108 A G 0 32.6 0 0.4312 0.5218 0.4798 0.8363 0.3588 0.5174 0 . 0 2 89 4838 49 120 4 974 57 3545 2 190 10796 92 140 6 2744 118 7506 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||875||676|KCNQ1|protein_coding|CODING|NM_000218.2|16|G),INTRAGENIC(MODIFIER|||||KCNQ1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs8234 -0.379885 0 2 676 932 MODIFIER 16 CODING KCNQ1 G protein_coding NM_000218.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2870165 A G 0 46.3 0 0.4077 0.5154 0.4784 0.8363 0.3588 0.5174 0 . 0 2 88 4828 49 115 0 975 57 3544 2 194 10790 92 134 0 2746 118 7506 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||932||676|KCNQ1|protein_coding|CODING|NM_000218.2|16|G),INTRAGENIC(MODIFIER|||||KCNQ1-AS1||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs10798 -0.453602 0.86 2 R97Q 509 cGg/cAg MODERATE 2 MISSENSE CODING SLC22A18 A protein_coding NM_001315501.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2924610 G A 0 222 0 0.4516 0.6076 0.5908 0.7579 0.6014 0.682 0.478429 0.542609 0.575483 1 4859 73103 7518 6673 4054 38632 563 10804 2 10282 120100 11546 8616 6610 65654 892 16500 0.804496 0 . 0 . 90 22,22,21,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R97Q|509|SLC22A18|protein_coding|CODING|NM_001315501.1|2|A),INTRON(MODIFIER||||253|SLC22A18AS|protein_coding|CODING|NM_007105.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994898 rs1048047 -0.693145 0.034685 90 V163 509 gtA/gtG LOW 3 SILENT CODING SLC22A18 G protein_coding NM_001315501.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2929552 A G 0 222 0 0.7179 0.7506 0.6902 0.8006 0.7416 0.7955 0.747502 0.73281 0.725285 1 7723 89663 8260 7048 5079 48024 666 12863 2 10284 119786 11484 8614 6542 65642 888 16332 0.99025 0 . 0 . 109 14,29,22,31 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V163|509|SLC22A18|protein_coding|CODING|NM_001315501.1|3|G),UPSTREAM(MODIFIER||4377||253|SLC22A18AS|protein_coding|CODING|NM_007105.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.70059 rs429886 -0.693147 0.643328 109 D297 509 gaC/gaT LOW 6 SILENT CODING SLC22A18 T protein_coding NM_001315501.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2937951 C T 0 222 0 0 0.0063898 0 0.0317 0 0 0.000454133 0.000307645 0.000232612 1 2 285 1 259 0 6 3 14 2 10142 119778 11546 8606 6608 65528 888 16460 0.914627 0 . 0 . 145 44,31,22,29 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D297|509|SLC22A18|protein_coding|CODING|NM_001315501.1|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.508488 rs141958733 -0.693147 0.110659 145 375 LOW 3 CODING NAP1L4 T protein_coding NM_005969.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 2999507 G T 0 228 0 0.118 0.3852 0.5173 0.7014 0.2962 0.4182 0.152313 0.250585 0.295593 2 1513 42107 6843 5798 1503 19841 306 6303 2 9774 120008 11492 8574 6584 66234 896 16454 0 . 0 . 0 75 0,0,35,34 SPLICE_SITE_REGION+INTRON(LOW||||375|NAP1L4|protein_coding|CODING|NM_005969.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3814964 -0.693147 0.207072 75 P706 831 ccC/ccT LOW 19 SILENT CODING CARS A protein_coding NM_001014437.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3028140 G A 0 228 0 0.0303 0.3508 0.4957 0.6627 0.2922 0.4202 0.0756131 0.218231 0.291298 2 734 40664 6830 5460 1503 19449 311 6377 2 10246 120924 11556 8612 6612 66496 906 16496 1 0 . 0 . 20 1,0,10,9 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P706|831|CARS|protein_coding|CODING|NM_001014437.2|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs729662 -0.69168 0.192221 20 879 32 MODIFIER 22 CODING OSBPL5 G protein_coding NM_020896.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3109403 A G 0 222 0 0.7254 0.7588 0.7104 0.8056 0.6859 0.865 0.735922 0.702724 0.685711 1 7065 74294 7561 6519 3979 40604 474 8092 2 9634 105482 10710 8124 6042 60534 738 9700 0.982557 0 . 0 . 199 81,31,52,12 UTR_3_PRIME(MODIFIER||32||879|OSBPL5|protein_coding|CODING|NM_020896.3|22|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998937 rs2289999 -0.693147 0.167696 199 879 27 MODIFIER 22 CODING OSBPL5 T protein_coding NM_020896.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3109408 C T 0 222 0 0.7254 0.7588 0.7104 0.8056 0.6859 0.865 0.736483 0.70337 0.686409 1 7163 75710 7677 6618 4036 41068 482 8666 2 9740 107082 10834 8232 6112 61058 748 10358 0.926323 0 . 0 . 196 81,31,50,12 UTR_3_PRIME(MODIFIER||27||879|OSBPL5|protein_coding|CODING|NM_020896.3|22|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.919943 rs2289998 -0.693147 0.0235247 196 879 9 MODIFIER 22 CODING OSBPL5 C protein_coding NM_020896.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3109426 T C 0 222 0 0.8964 0.8636 0.8919 0.8214 0.8032 0.9049 0.897593 0.832615 0.799325 1 9083 94429 10270 7001 4705 51336 627 11407 2 10062 113202 11286 8410 6342 63516 800 12786 0.747583 0 . 0 . 219 80,38,57,21 UTR_3_PRIME(MODIFIER||9||879|OSBPL5|protein_coding|CODING|NM_020896.3|22|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.582692 rs10160757 -0.693147 0.139139 219 L171 879 ctG/ctA LOW 6 SILENT CODING OSBPL5 T protein_coding NM_020896.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3141744 C T 0 222 0 0.1558 0.122 0.1297 0.0258 0.1451 0.1462 0.152816 0.134538 0.125174 1 1616 16252 1832 226 1153 8712 119 2594 2 10250 119960 11528 8596 6576 65622 882 16506 0.730785 0 . 0 COSM428899 124 39,27,26,22 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L171|879|OSBPL5|protein_coding|CODING|NM_020896.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.676664 rs34950527 -0.693147 0.691989 124 312 10 MODIFIER 2 CODING MRGPRE C protein_coding NM_001039165.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3249081 G C 0 36.7 0 0.0212 0.0761 0.085 0.123 0.0755 0.0961 0.0070922 0.0195825 0.0251509 1 10 220 7 37 2 144 1 19 2 234 1352 50 110 12 816 14 116 0.809011 0 . 0 . 10 5,1,1,2 UTR_3_PRIME(MODIFIER||10||312|MRGPRE|protein_coding|CODING|NM_001039165.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.924584 0.924584 0 0.809011 rs11026035 -0.511536 0.392388 10 G16S 312 Ggc/Agc MODERATE 2 MISSENSE CODING MRGPRE T protein_coding NM_001039165.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3249984 C T 0 222 0 0.0567 0.3315 0.3026 0.4692 0.495 0.4131 0.123344 0.361612 0.474421 1 1111 50385 3465 4154 3189 31555 391 6520 2 9310 118474 11510 8550 6562 65492 882 16168 0.716502 0 . 0 . 55 10,13,10,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G16S|312|MRGPRE|protein_coding|CODING|NM_001039165.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517068 rs12295710 -0.693097 0.743868 55 629 352 MODIFIER 6 CODING ZNF195 CGTGCTCTATTCCTTTCTCCTTCAAATCCTCCATTGTTTACTTAAATTGGATT protein_coding NM_001130520.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3379995 C CGTGCTCTATTCCTTTCTCCTTCAAATCCTCCATTGTTTACTTAAATTGGATT 0 32.6 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||352||629|ZNF195|protein_coding|CODING|NM_001130520.2|6|CGTGCTCTATTCCTTTCTCCTTCAAATCCTCCATTGTTTACTTAAATTGGATT) 0 . 0 1 0.5 0 1 0 . 0 60 0 0 . 0 . rs55873719 -0.379885 0 2 P290R 629 cCt/cGt MODERATE 6 MISSENSE CODING ZNF195 C protein_coding NM_001130520.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3381369 G C 0 222 0 0.1808 0.2238 0.1167 0.4067 0.1093 0.2873 0.16378 0.129352 0.113571 1 1655 20190 1802 3607 702 7747 143 4534 2 9796 120722 11574 8616 6612 66718 900 16506 0.918163 0 . 0 . 78 24,17,19,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cGt|P290R|629|ZNF195|protein_coding|CODING|NM_001130520.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.849616 rs62619253 -0.693127 0.919069 78 629 64 MODIFIER 1 CODING ZNF195 G protein_coding NM_001130520.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3400334 A G 0 228 0 0.702 0.8736 0.8818 0.9871 0.9006 0.955 0.712428 0.844503 0.901948 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 121 0,0,48,55 UTR_5_PRIME(MODIFIER||64||629|ZNF195|protein_coding|CODING|NM_001130520.2|1|G) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs7931660 -0.693147 0.000735911 121 629 152 MODIFIER 1 CODING ZNF195 T protein_coding NM_001130520.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3400422 C T 0 228 0 0.702 0.8736 0.8818 0.9871 0.9006 0.955 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,2,41 UTR_5_PRIME(MODIFIER||152||629|ZNF195|protein_coding|CODING|NM_001130520.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6578342 -0.693146 0.0124182 44 G173 291 ggA/ggG LOW 3 SILENT CODING ART5 C protein_coding NM_001079536.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3661140 T C 0 228 0 0.9652 0.9906 1 1 1 0.999 0.975693 0.991768 1 2 10119 121056 11567 8652 6614 66697 904 16503 2 10400 121350 11578 8652 6614 66698 904 16504 0 . 0 . 0 117 0,0,81,23 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G173|291|ART5|protein_coding|CODING|NM_001079536.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4910876 -0.693147 0.30507 117 A1428 1800 gcG/gcA LOW 27 SILENT CODING NUP98 T protein_coding NM_016320.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3714489 C T 0 222 0 0.3608 0.2758 0.0965 0.3185 0.1938 0.3282 0.328033 0.223804 0.170428 1 3411 25585 968 2656 1787 11638 202 4923 2 10406 121380 11576 8638 6614 66726 908 16512 0.883974 0 . 0 . 99 29,15,29,14 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1428|1800|NUP98|protein_coding|CODING|NM_016320.4|27|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.582295 rs1875 -0.693146 0.213592 99 791 427 MODIFIER 1 CODING STIM1 T protein_coding NM_001277961.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 3877074 C T 0 9.7 0 0.3449 0.4461 0.4049 0.5565 0.4095 0.5358 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||791|STIM1|protein_coding|CODING|NM_001277961.1|1|T),UTR_5_PRIME(MODIFIER||427||791|STIM1|protein_coding|CODING|NM_001277961.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10835206 -0.379885 0 1 Q360 791 caA/caG LOW 8 SILENT CODING STIM1 G protein_coding NM_001277961.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4103524 A G 0 222 0 0.0976 0.389 0.4841 0.4425 0.5676 0.4765 0.173785 0.43876 0.574453 1 1738 60125 5890 3816 3204 37564 455 7458 2 10206 120346 11440 8542 6538 66340 906 16374 0.231151 0 . 0 COSM428967 66 13,15,10,24 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q360|791|STIM1|protein_coding|CODING|NM_001277961.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.301343 rs2304891 -0.693132 0.422094 66 791 367 MODIFIER 12 CODING STIM1 A protein_coding NM_001277961.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4113395 G A 0 61 0 0.295 0.6941 0.7767 0.7669 0.8837 0.9049 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||367||791|STIM1|protein_coding|CODING|NM_001277961.1|12|A),UPSTREAM(MODIFIER||2529||792|RRM1|protein_coding|CODING|NM_001033.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1561876 -0.511536 0.0649539 3 V273 792 gtA/gtC LOW 9 SILENT CODING RRM1 C protein_coding NM_001033.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4141101 A C 0 222 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 53 0 53 0 0 0 0 2 10406 121408 11578 8654 6614 66736 908 16512 0.883102 0 . 0 . 100 43,12,22,7 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtC|V273|792|RRM1|protein_coding|CODING|NM_001033.3|9|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.503597 rs201618632 -0.693079 0.175046 100 R284 792 Cga/Aga LOW 9 SILENT CODING RRM1 A protein_coding NM_001033.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4141132 C A 0 222 0 0.0227 0.3231 0.4366 0.378 0.5229 0.3865 0.105407 0.388521 0.533504 1 965 54476 5344 3294 3034 35389 411 6039 2 10406 121366 11568 8642 6612 66726 908 16504 0.960021 0 . 0 . 119 47,18,22,11 PROTEIN_INTERACTION_LOCUS(HIGH||||792|RRM1|protein_coding|CODING||9|A),SYNONYMOUS_CODING(LOW|SILENT|Cga/Aga|R284|792|RRM1|protein_coding|CODING|NM_001033.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978092 rs183484 -0.693127 0.388505 119 T741 792 acA/acG LOW 19 SILENT CODING RRM1 G protein_coding NM_001033.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4159457 A G 0 222 0 0.0953 0.3446 0.4424 0.3819 0.5239 0.3896 0.166515 0.411217 0.536529 1 1564 55224 5386 3295 3038 35459 409 6073 2 10282 119698 11546 8636 6610 66332 892 15400 0.891969 0 . 0 . 154 66,14,48,9 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T741|792|RRM1|protein_coding|CODING|NM_001033.3|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.692009 rs9937 -0.693147 0.000822381 154 A744 792 gcG/gcA LOW 19 SILENT CODING RRM1 A protein_coding NM_001033.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4159466 G A 0 222 0 0.7965 0.8456 0.8256 0.7619 0.9294 0.9264 0.821672 0.893291 0.929967 1 8461 108170 9345 6407 5884 61757 814 15502 2 10394 121206 11558 8644 6614 66642 902 16452 0.432831 0 . 0 . 170 70,17,54,11 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A744|792|RRM1|protein_coding|CODING|NM_001033.3|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.536846 rs1042858 -0.693147 0.0355075 170 792 151 MODIFIER 19 CODING RRM1 T protein_coding NM_001033.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4159764 A T 0 222 0 0.7965 0.8452 0.8256 0.7599 0.9294 0.9264 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.402573 0 . 0 . 145 14,75,11,37 UTR_3_PRIME(MODIFIER||151||792|RRM1|protein_coding|CODING|NM_001033.3|19|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.22647 rs1042919 -0.693147 0.000504143 145 792 316 MODIFIER 19 CODING RRM1 A protein_coding NM_001033.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4159929 C A 0 43.9 0 0.7973 0.8454 0.8256 0.7599 0.9294 0.9264 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924449 0 . 0 . 11 0,7,1,3 UTR_3_PRIME(MODIFIER||316||792|RRM1|protein_coding|CODING|NM_001033.3|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.924449 rs1042927 -0.556411 0.45314 11 S207 314 tcG/tcA LOW 1 SILENT CODING OR52B4 T protein_coding NM_001005161.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4388905 C T 0 222 0 0.2436 0.2452 0.2709 0.1706 0.3618 0.1861 0.257188 0.31907 0.347747 1 2539 35334 2890 1477 1968 22758 267 3435 2 9750 120348 11488 8578 6604 66550 896 16482 0.377181 0 . 0 . 83 12,29,9,26 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S207|314|OR52B4|protein_coding|CODING|NM_001005161.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.886964 rs11031960 -0.693136 0.00392298 83 314 62 MODIFIER 1 CODING OR52B4 C protein_coding NM_001005161.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4389587 G C 0 222 0 0.2194 0.3488 0.4179 0.2996 0.5 0.3701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.912864 0 . 0 . 57 6,20,6,21 UTR_5_PRIME(MODIFIER||62||314|OR52B4|protein_coding|CODING|NM_001005161.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.528234 rs7929171 -0.693021 0.258507 57 475 36 MODIFIER 7 CODING TRIM21 T protein_coding NM_003141.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4406479 G T 0 168 0 0.1967 0.1601 0.0663 0.2054 0.0954 0.1973 0.1627 0.113527 0.0893921 1 1574 12259 722 1613 442 6006 102 1800 2 8142 93674 8548 7166 5448 54570 688 9112 0.99731 0 . 0 . 41 19,2,16,1 UTR_3_PRIME(MODIFIER||36||475|TRIM21|protein_coding|CODING|NM_003141.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.772076 rs386591346,rs4144331 -0.690438 0.413837 41 475 32 MODIFIER 7 CODING TRIM21 G protein_coding NM_003141.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4406483 A G 0 212 0 0.0053 0.1326 0.134 0.3403 0.0537 0.1708 0.0133885 0.034411 0.0447067 1 117 10028 1383 2832 401 2834 58 2403 2 8316 97832 9054 7646 5612 56102 736 10366 0.532543 0 . 0 . 43 19,1,18,2 UTR_3_PRIME(MODIFIER||32||475|TRIM21|protein_coding|CODING|NM_003141.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996713 rs2269330 -0.692067 0.245855 43 Q133 475 caG/caA LOW 2 SILENT CODING TRIM21 T protein_coding NM_003141.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4411241 C T 0 222 0 0.1921 0.2105 0.1254 0.2837 0.1233 0.3098 0.163049 0.136681 0.124161 1 1727 20400 1383 2415 767 8994 152 4962 2 9660 118974 11316 8522 6562 65822 888 16204 0.971096 0 . 0 . 57 22,5,21,6 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q133|475|TRIM21|protein_coding|CODING|NM_003141.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.748479 rs926101 -0.693021 0.0690087 57 T141M 217 aCg/aTg MODERATE 3 MISSENSE CODING C11orf40 A protein_coding NM_144663.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4593411 G A 0 222 0 0.2103 0.0923 0.072 0.0397 0.0716 0.0225 0.212176 0.11748 0.0689856 1 2167 8291 478 391 315 4438 66 436 2 10400 121324 11570 8632 6614 66700 908 16500 0.900862 0 . 0 . 104 30,18,25,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T141M|217|C11orf40|protein_coding|CODING|NM_144663.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999967 rs34097396 -0.693146 0.00385433 104 T41I 324 aCa/aTa MODERATE 1 MISSENSE CODING OR52I1 T protein_coding NM_001005169.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4615390 C T 0 228 0 0.5643 0.8736 0.9424 0.999 0.9891 0.9949 0.562244 0.836392 0.977241 2 6363 113385 11138 8649 6484 63557 857 16337 2 10342 120508 11524 8650 6566 66062 898 16466 0 . 0 . 0 75 0,0,37,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T41I|324|OR52I1|protein_coding|CODING|NM_001005169.1|1|T),DOWNSTREAM(MODIFIER||4512||485|TRIM68|protein_coding|CODING|NM_018073.7||T) 1 0 . 0 . 1 0 1 1 0 49 0 0 0.304612 0 . rs2010722 -0.693147 0.0333597 75 L201V 324 Ctc/Gtc MODERATE 1 MISSENSE CODING OR52I1 G protein_coding NM_001005169.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4615869 C G 0 222 0 0.0227 0.014976 0 0.0367 0.001 0.0072 0.0170377 0.00592672 0.000232829 1 185 803 13 390 21 60 4 130 2 10406 121378 11576 8652 6610 66716 908 16510 0.936228 0 . 0 . 106 25,21,29,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L201V|324|OR52I1|protein_coding|CODING|NM_001005169.1|1|G),DOWNSTREAM(MODIFIER||4033||485|TRIM68|protein_coding|CODING|NM_018073.7||G) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.69419 0.761297 0 0.970269 rs78745657 -0.693147 0.618649 106 G246V 324 gGc/gTc MODERATE 1 MISSENSE CODING OR52I1 T protein_coding NM_001005169.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4616005 G T 0 222 0 0 0.0027955 0 0.0139 0 0 0 . 0 1 0 106 0 104 0 0 0 2 2 10406 121408 11576 8654 6614 66738 908 16512 0.704767 0 . 0 . 161 46,25,47,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G246V|324|OR52I1|protein_coding|CODING|NM_001005169.1|1|T),DOWNSTREAM(MODIFIER||3897||485|TRIM68|protein_coding|CODING|NM_018073.7||T) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.839608 0.756994 0 0.473863 rs74977190 -0.693147 0.00914112 161 485 183 MODIFIER 7 CODING TRIM68 G protein_coding NM_018073.7 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4621323 T G 0 91 0 0.3033 0.3333 0.2795 0.3998 0.3449 0.3313 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987669 0 . 0 . 16 8,0,8,0 UTR_3_PRIME(MODIFIER||183||485|TRIM68|protein_coding|CODING|NM_018073.7|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.987669 rs3750992 -0.651104 0.357952 16 485 21 MODIFIER 7 CODING TRIM68 G protein_coding NM_018073.7 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4621485 C G 0 222 0 0.584 0.8522 0.9035 0.9633 0.9443 0.9693 0.642662 0.83559 0.934388 1 6208 101637 10859 8151 6444 60201 742 9032 2 9774 110448 11474 8540 6588 64024 790 9258 0.916991 0 . 0 . 107 26,12,35,19 UTR_3_PRIME(MODIFIER||21||485|TRIM68|protein_coding|CODING|NM_018073.7|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.483645 rs2231978 -0.693147 0.118043 107 485 2710 MODIFIER 1 CODING TRIM68 G protein_coding NM_018073.7 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4629444 A G 0 9.7 0 0.9213 0.9786 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2710||485|TRIM68|protein_coding|CODING|NM_018073.7|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6578503 -0.379885 0 1 318 445 MODIFIER 2 CODING OR51E1 A protein_coding NM_152430.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4675158 G A 0 222 0 0.4153 0.5873 0.6542 0.3651 0.8489 0.7321 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.831719 0 . 0 . 113 44,24,24,13 UTR_3_PRIME(MODIFIER||445||318|OR51E1|protein_coding|CODING|NM_152430.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976517 rs721758 -0.693141 0.0602683 113 318 1109 MODIFIER 2 CODING OR51E1 A protein_coding NM_152430.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4675822 G A 0 222 0 0 0.015575 0 0.0764 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.42541 0 . 0 . 156 53,27,48,12 UTR_3_PRIME(MODIFIER||1109||318|OR51E1|protein_coding|CODING|NM_152430.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.836308 rs117543228 -0.693147 0.00110559 156 320 1393 MODIFIER 2 CODING OR51E2 A protein_coding NM_030774.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4701586 G A 0 172 0 0.1112 0.0937 0.1254 0.1944 0.0308 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.142326 0 . 0 . 43 20,0,20,0 UTR_3_PRIME(MODIFIER||1393||320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.996713 rs2292157 -0.692067 0.543357 43 320 1066 MODIFIER 2 CODING OR51E2 A protein_coding NM_030774.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4701913 G A 0 222 0 0.1112 0.0937 0.1254 0.1944 0.0308 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.942176 0 . 0 . 77 4,36,4,31 UTR_3_PRIME(MODIFIER||1066||320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.903159 rs7111883 -0.693136 0.214034 77 320 1036 MODIFIER 2 CODING OR51E2 A protein_coding NM_030774.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4701943 T A 0 126 0 0.0204 0.0689 0.1196 0.1944 0.0308 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.938723 0 . 0 . 55 1,28,0,25 UTR_3_PRIME(MODIFIER||1036||320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99985 rs7101393 -0.692914 0.11775 55 320 186 MODIFIER 2 CODING OR51E2 A protein_coding NM_030774.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4702793 T A 0 126 0 0.1104 0.0935 0.1254 0.1944 0.0308 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.611214 0 . 0 . 23 13,0,9,1 UTR_3_PRIME(MODIFIER||186||320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.536292 rs12575268 -0.670168 0.268014 23 320 141 MODIFIER 2 CODING OR51E2 A protein_coding NM_030774.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4702838 G A 0 129 0 0.1104 0.0935 0.1254 0.1944 0.0308 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.736296 0 . 0 . 41 19,1,21,0 UTR_3_PRIME(MODIFIER||141||320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.765928 rs73388885 -0.692352 0.365326 41 V259 320 gtG/gtT LOW 2 SILENT CODING OR51E2 A protein_coding NM_030774.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4703165 C A 0 228 0 0.5287 0.752 0.768 0.8214 0.83 0.8906 0.571331 0.747346 0.837483 2 5962 99531 8725 6800 5914 57011 752 14367 2 10392 121338 11564 8626 6614 66724 908 16510 0.29852 0 . 0 . 155 2,1,68,76 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtT|V259|320|OR51E2|protein_coding|CODING|NM_030774.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.870141 rs1123991,rs386517725 -0.693147 0.25628 155 L264F 323 Ctc/Ttc MODERATE 1 MISSENSE CODING OR51S1 A protein_coding NM_001004758.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4869649 G A 0 222 0 0.3411 0.2993 0.2608 0.0675 0.4046 0.4008 0.348705 0.402754 0.430433 1 3621 44889 2286 490 3053 28842 372 6225 2 10406 121262 11570 8638 6610 66684 906 16448 0.950794 0 . 0 . 99 20,27,13,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L264F|323|OR51S1|protein_coding|CODING|NM_001004758.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.322232 rs12361955 -0.693146 0.109907 99 L178R 323 cTc/cGc MODERATE 1 MISSENSE CODING OR51S1 C protein_coding NM_001004758.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4869906 A C 0 222 0 0.6233 0.5018 0.4135 0.0942 0.6054 0.7137 0.598137 0.616787 0.626338 1 6306 68529 3628 786 3673 41827 579 11730 2 10398 121212 11570 8650 6608 66668 908 16410 0.310436 0 . 0 . 78 28,12,18,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L178R|323|OR51S1|protein_coding|CODING|NM_001004758.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991194 rs7117260 -0.693127 0.607369 78 V100 323 gtC/gtT LOW 1 SILENT CODING OR51S1 A protein_coding NM_001004758.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4870139 G A 0 222 0 0.1203 0.2386 0.2421 0.0675 0.4046 0.4018 0.170377 0.341591 0.429269 1 1656 42759 2205 490 3052 28771 367 6218 2 10390 121242 11564 8632 6610 66666 908 16472 0.780335 0 . 0 . 97 32,19,17,22 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V100|323|OR51S1|protein_coding|CODING|NM_001004758.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.387989 rs11602455 -0.693144 0.0154875 97 Q60E 323 Cag/Gag MODERATE 1 MISSENSE CODING OR51S1 C protein_coding NM_001004758.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4870261 G C 0 222 0 0.2352 0.2742 0.2579 0.0675 0.4066 0.4151 0.281009 0.379828 0.430433 1 2839 44240 2269 491 3049 28822 373 6397 2 10398 121316 11568 8640 6608 66684 908 16510 0.850432 0 . 0 . 70 21,19,13,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q60E|323|OR51S1|protein_coding|CODING|NM_001004758.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.888721 rs11602499 -0.692352 0.00285481 70 A47 323 gcA/gcC LOW 1 SILENT CODING OR51S1 G protein_coding NM_001004758.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4870298 T G 0 222 0 0.0227 0.1685 0.1441 0.0675 0.2555 0.3978 0.0531577 0.211494 0.292578 1 526 30604 1393 491 2184 19774 259 5977 2 10398 121312 11566 8630 6610 66692 908 16508 0.999568 0 . 0 . 81 17,26,15,13 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A47|323|OR51S1|protein_coding|CODING|NM_001004758.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.795457 rs11601065 -0.693054 0.863572 81 E8K 312 Gaa/Aaa MODERATE 1 MISSENSE CODING OR51A7 A protein_coding NM_001004749.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4928621 G A 0 222 0 0.0703 0.1799 0.1527 0.5427 0.0835 0.0726 0.079055 0.0781659 0.0777106 1 828 15701 2652 4736 692 5369 109 1315 2 10394 120406 11472 8558 6548 66314 902 16218 0.989731 0 . 0 COSM147112 103 33,13,29,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E8K|312|OR51A7|protein_coding|CODING|NM_001004749.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.6774 rs11034596 -0.693146 0.043598 103 A89 312 gcC/gcT LOW 1 SILENT CODING OR51A7 T protein_coding NM_001004749.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4928866 C T 0 222 0 0.2625 0.3984 0.3919 0.0804 0.6143 0.6922 0.302817 0.510463 0.616799 1 3070 64917 3532 705 4172 41761 544 11133 2 10398 121324 11568 8636 6610 66700 902 16510 0.90504 0 . 0 COSM1561380 54 16,8,14,15 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A89|312|OR51A7|protein_coding|CODING|NM_001004749.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.457377 rs7941509 -0.693079 0.139779 54 L154 312 ctC/ctG LOW 1 SILENT CODING OR51A7 G protein_coding NM_001004749.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4929061 C G 0 222 0 0.0613 0.1779 0.1527 0.5437 0.0845 0.0726 0.0761018 0.0772427 0.0778269 1 778 15758 2662 4778 711 5403 111 1315 2 10402 121300 11544 8604 6612 66720 908 16510 0.937677 0 . 0 COSM147113 62 22,15,9,16 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L154|312|OR51A7|protein_coding|CODING|NM_001004749.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.638589 rs10500627,rs386439183 -0.692914 0.58376 62 Y125S 321 tAc/tCc MODERATE 1 MISSENSE CODING OR51G1 G protein_coding NM_001005237.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4945196 T G 0 228 0 0.7231 0.6573 0.6484 0.7222 0.5686 0.5992 0.699228 0.620326 0.579921 2 7361 72643 8409 5823 3426 37693 486 9445 2 10390 121212 11558 8594 6604 66656 906 16504 0 . 0 . 0 29 0,0,20,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tCc|Y125S|321|OR51G1|protein_coding|CODING|NM_001005237.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1378739 -0.693054 0.218016 29 T288M 313 aCg/aTg MODERATE 1 MISSENSE CODING OR51A4 A protein_coding NM_001005329.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4967468 G A 0 228 0 0.7995 0.8488 0.9092 0.9107 0.836 0.8221 0.8 0.83341 0.850512 2 8185 103079 10722 7797 5358 56662 761 13594 2 10398 121370 11556 8652 6612 66732 908 16512 0 . 0 . 0 308 0,0,213,72 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T288M|313|OR51A4|protein_coding|CODING|NM_001005329.1|1|A) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.890972 0 . rs28698374 -0.693147 0.225955 308 L227P 313 cTg/cCg MODERATE 1 MISSENSE CODING OR51A4 G protein_coding NM_001005329.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4967651 A G 0 175 0 . 0 . 0 . 0 . 0 . 1 1189 23898 1112 766 1110 13499 195 6027 2 9848 111190 10732 8314 6056 60388 844 15008 0.597141 0 . 0 . 257 77,90,14,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L227P|313|OR51A4|protein_coding|CODING|NM_001005329.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 51 0 3.2433e-16 0.923313 0 0.591991 rs28673258,rs76895759 -0.693147 0.11979 257 G45C 313 Ggc/Tgc MODERATE 1 MISSENSE CODING OR51A4 A protein_coding NM_001005329.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4968198 C A 0 228 0 0.8374 0.859 0.9107 0.9107 0.836 0.8221 0.82939 0.842778 0.849628 2 8476 103353 10740 7795 5358 56637 762 13585 2 10306 121244 11558 8652 6612 66700 908 16508 0 . 0 . 0 249 0,0,118,112 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G45C|313|OR51A4|protein_coding|CODING|NM_001005329.1|1|A) 1 0 . 0 . 1 0 1 1 0 46 0 0 0.00017357 0 . rs3845246,rs56255038 -0.693147 0.0116608 249 P286 313 ccG/ccA LOW 1 SILENT CODING OR51A2 T protein_coding NM_001004748.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4976086 C T 0 228 0 0.7322 0.7865 0.8458 0.876 0.7535 0.7597 0.682327 0.699638 0.709122 2 5491 59172 6499 5179 2501 29003 406 10093 2 8486 86280 7752 6468 4500 44520 640 13914 0 . 0 . 0 126 0,0,87,34 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P286|313|OR51A2|protein_coding|CODING|NM_001004748.1|1|T) 1 0 . 0 . 1 0 1 1 0 54 0 0 0.296252 0 . rs2570572 -0.693147 0.228153 126 S218F 313 tCt/tTt MODERATE 1 MISSENSE CODING OR51A2 A protein_coding NM_001004748.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4976291 G A 0 222 0 0.3722 0.375 0.3905 0.379 0.4841 0.2515 0.35868 0.430928 0.469373 1 3553 43548 2239 2780 2730 27810 356 4080 2 9850 107708 8940 7478 5812 59178 806 15644 0.964413 0 . 0 . 286 69,93,30,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S218F|313|OR51A2|protein_coding|CODING|NM_001004748.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 53 0 0.813115 0.00261948 0 0.822332 rs55889636 -0.693147 0.00189187 286 N130 313 aaT/aaC LOW 1 SILENT CODING OR51A2 G protein_coding NM_001004748.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4976554 A G 0 228 0 0.4054 0.6038 0.7003 0.8353 0.5278 0.6431 0 . 0 2 2199 37806 5156 3962 1397 17046 250 7796 2 8014 86036 7676 5468 4628 46300 646 13304 0 . 0 . 0 25 0,0,17,8 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N130|313|OR51A2|protein_coding|CODING|NM_001004748.1|1|G) 0 . 0 . 0 1 0 . 1 0 45 0 0 0.00300648 0 . rs2595986 -0.692914 0.178447 25 G45C 313 Ggc/Tgc MODERATE 1 MISSENSE CODING OR51A2 A protein_coding NM_001004748.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 4976811 C A 0 228 0 0.7905 0.8385 0.902 0.8948 0.8191 0.82 0 . 0 2 7586 96384 10383 7340 5204 52957 693 12221 2 9800 115124 11214 8208 6468 63174 842 15418 0 . 0 . 0 126 0,0,80,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G45C|313|OR51A2|protein_coding|CODING|NM_001004748.1|1|A) 0 . 0 . 0 1 0 . 1 0 49 0 0 0.0299097 0 . rs28482315 -0.693147 0.0537142 126 K43E 261 Aag/Gag MODERATE 2 MISSENSE CODING MMP26 G protein_coding NM_021801.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5010905 A G 0 200 0 0.2761 0.1667 0.1614 0.2788 0.0308 0.047 0.245343 0.0974765 0.0217543 1 2605 10095 2334 2493 330 1482 75 776 2 9742 113264 10814 8332 6184 62282 838 15072 0.53521 0 . 0 . 46 23,1,13,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K43E|261|MMP26|protein_coding|CODING|NM_021801.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.895711 rs2499953 -0.689466 0.583416 46 L68 315 ttA/ttG LOW 1 SILENT CODING OR51L1 G protein_coding NM_001004755.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5020416 A G 0 222 0 0.8752 0.8263 0.8271 0.6696 0.8718 0.8742 0.853476 0.85267 0.852257 1 8902 101321 9032 5954 5289 57199 757 14188 2 10406 121376 11566 8638 6612 66734 908 16512 0.797943 0 . 0 . 158 45,34,40,31 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L68|315|OR51L1|protein_coding|CODING|NM_001004755.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.508442 rs2445290 -0.693147 0.099559 158 V304 325 gtG/gtA LOW 1 SILENT CODING OR52E2 T protein_coding NM_001005164.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5079946 C T 0 222 0 0.8956 0.9012 0.9524 0.7708 0.9414 0.9652 0.893458 0.938606 0.961726 1 9281 108502 10463 6754 6334 62783 802 12085 2 10318 115904 11500 8610 6610 65372 852 12642 0.858781 0 . 0 . 145 45,26,37,22 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V304|325|OR52E2|protein_coding|CODING|NM_001005164.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.441371 rs2445332 -0.693147 0.376623 145 N5S 325 aAt/aGt MODERATE 1 MISSENSE CODING OR52E2 C protein_coding NM_001005164.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5080844 T C 0 222 0 0.1853 0.3091 0.353 0.3829 0.3241 0.3538 0.220127 0.306663 0.350977 1 2279 39304 3699 3223 2358 22229 310 5206 2 10292 116656 11448 8572 6602 65440 848 13454 0.751071 0 . 0 . 68 5,25,5,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N5S|325|OR52E2|protein_coding|CODING|NM_001005164.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999221 rs16909440 -0.693136 0.11199 68 F204 316 ttT/ttC LOW 1 SILENT CODING OR52A5 G protein_coding NM_001005160.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5153261 A G 0 222 0 0.0144 0.1987 0.232 0.3929 0.2028 0.2198 0.0499773 0.157178 0.212075 1 458 26643 3084 3174 1512 14323 204 3888 2 10400 121336 11568 8640 6612 66698 906 16512 0.684064 0 . 0 . 132 35,23,36,29 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F204|316|OR52A5|protein_coding|CODING|NM_001005160.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.749175 rs2472530 -0.693147 0.112561 132 S272P 312 Tcc/Ccc MODERATE 1 MISSENSE CODING OR52A1 G protein_coding NM_012375.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5172786 A G 0 228 0 0.888 0.9677 0.9813 1 0.999 1 0.905952 0.967841 0.999535 2 9421 120344 11523 8653 6614 66721 905 16507 2 10406 121410 11578 8654 6614 66740 908 16510 0 . 0 . 0 221 0,0,127,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S272P|312|OR52A1|protein_coding|CODING|NM_012375.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10768611 -0.693147 0.0544635 221 147 55 MODIFIER 3 CODING HBG1 G protein_coding NM_000559.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5269533 GT G 0 228 0 0.0333 0.1817 0.1686 0.4256 0.1272 0.1963 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 70 0,0,50,8 UTR_3_PRIME(MODIFIER||55||147|HBG1|protein_coding|CODING|NM_000559.2|3|G),DOWNSTREAM(MODIFIER||4887||147|HBG2|protein_coding|CODING|NM_000184.2||G) 0 . 0 69 0.985714 1 1 0 . 0 55 0 0 0.665791 0 . rs3841756 -0.693147 1.21596e-06 70 147 6 MODIFIER 3 CODING HBG1 A protein_coding NM_000559.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5269583 G A 0 115 0 0.497 0.4774 0.4798 0.4732 0.4583 0.4734 0 . 0 1 0 1 0 0 0 1 0 0 2 246 5148 348 82 620 3164 36 652 0.5 0 . 0 . 91 2,0,2,4 UTR_3_PRIME(MODIFIER||6||147|HBG1|protein_coding|CODING|NM_000559.2|3|A),DOWNSTREAM(MODIFIER||4838||147|HBG2|protein_coding|CODING|NM_000184.2||A) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.833333 0.868321 0 0.166667 rs5009539,rs76701119 -0.616816 0.0269737 91 147 5 MODIFIER 3 CODING HBG1 G protein_coding NM_000559.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5269584 T G 0 115 0 0.7194 0.7185 0.7017 0.7996 0.668 0.6973 0 . 0 2 0 0 0 0 0 0 0 0 2 9648 118690 11454 8482 6562 65198 894 16452 0 . 0 . 0 6 0,0,2,4 UTR_3_PRIME(MODIFIER||5||147|HBG1|protein_coding|CODING|NM_000559.2|3|G),DOWNSTREAM(MODIFIER||4837||147|HBG2|protein_coding|CODING|NM_000184.2||G) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.5 0 . rs1065686 -0.616816 0.0269737 6 147 4 MODIFIER 3 CODING HBG1 A protein_coding NM_000559.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5269585 G A 0 62 0 0.7194 0.7185 0.7017 0.7996 0.668 0.6973 0 . 0 2 0 0 0 0 0 0 0 0 2 1444 23230 2338 794 2030 13508 144 2972 0 . 0 . 0 6 0,0,2,4 UTR_3_PRIME(MODIFIER||4||147|HBG1|protein_coding|CODING|NM_000559.2|3|A),DOWNSTREAM(MODIFIER||4836||147|HBG2|protein_coding|CODING|NM_000184.2||A) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.5 0 . rs61893083 -0.616816 0.0269737 6 147 3 MODIFIER 3 CODING HBG1 G protein_coding NM_000559.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5269586 A G 0 80 0 0.7194 0.7185 0.7017 0.7996 0.668 0.6973 0 . 0 2 0 1 0 0 0 1 0 0 2 9720 118826 11450 8486 6564 65258 894 16454 0 . 0 . 0 6 0,0,2,2 UTR_3_PRIME(MODIFIER||3||147|HBG1|protein_coding|CODING|NM_000559.2|3|G),DOWNSTREAM(MODIFIER||4835||147|HBG2|protein_coding|CODING|NM_000184.2||G) 0 . 0 . 0 1 0 . 1 0 56 0 0 0.5 0 . rs62755960 -0.556411 0.118267 6 T76I 147 aCa/aTa MODERATE 2 MISSENSE CODING HBG1 A protein_coding NM_000559.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5270686 G A 0 89 0 . 0 . 0 . 0 . 0 . 2 2091 3679 161 157 8 949 30 283 2 3976 44856 3724 1866 3410 25824 316 5740 0 2|255|255|255 benign|other|other|other 0 . 8 0,0,0,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T76I|147|HBG1|protein_coding|CODING|NM_000559.2|2|A),DOWNSTREAM(MODIFIER||3735||147|HBG2|protein_coding|CODING|NM_000184.2||A) 0 . 0 . 0 . 0 . 1 0 34 0 0 . 0 . rs1061234 -0.651104 0.0795616 8 M147T 310 aTg/aCg MODERATE 1 MISSENSE CODING OR51B4 G protein_coding NM_033179.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5322737 A G 0 228 0 0.1195 0.4423 0.4582 0.747 0.4473 0.5481 0.165834 0.344337 0.435769 2 1716 55356 5323 6500 2883 29574 454 8906 2 10406 121354 11550 8638 6614 66728 908 16510 1 0 . 0 . 132 0,1,76,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M147T|310|OR51B4|protein_coding|CODING|NM_033179.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10837771 -0.693147 0.153609 132 V36I 310 Gtc/Atc MODERATE 1 MISSENSE CODING OR51B4 T protein_coding NM_033179.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5323071 C T 0 228 0 0.4191 0.6805 0.7392 0.878 0.6918 0.7771 0.456611 0.621884 0.706539 2 4734 86534 9417 7605 4158 47273 677 12670 2 10364 121224 11546 8652 6612 66670 906 16474 0 . 0 . 0 86 0,0,19,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V36I|310|OR51B4|protein_coding|CODING|NM_033179.2|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7118113 -0.693147 0.0158278 86 312 37 MODIFIER 1 CODING OR51B2 T protein_coding NM_033180.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344552 C T 0 222 0 0.7829 0.7552 0.7651 0.5407 0.9076 0.7751 0.803859 0.875967 0.912567 1 7518 90631 7533 4106 5629 56404 691 8750 2 9462 107824 10798 7882 6242 61812 792 10836 0.928167 0 . 0 . 69 26,8,25,4 UTR_3_PRIME(MODIFIER||37||312|OR51B2|protein_coding|CODING|NM_033180.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.845588 rs7934105 -0.693079 0.116335 69 312 28 MODIFIER 1 CODING OR51B2 A protein_coding NM_033180.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344561 G A 0 222 0 0.7821 0.7546 0.7651 0.5407 0.9076 0.773 0.803645 0.875944 0.912902 1 7729 94110 7630 4229 5746 58269 715 9792 2 9706 111880 10950 8140 6370 63826 822 12066 0.629191 0 . 0 . 77 28,9,27,5 UTR_3_PRIME(MODIFIER||28||312|OR51B2|protein_coding|CODING|NM_033180.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.346484 rs7933257 -0.69312 0.173826 77 P283S 312 Cct/Tct MODERATE 1 MISSENSE CODING OR51B2 A protein_coding NM_033180.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344681 G A 0 222 0 0.2897 0.2648 0.2954 0.2173 0.2853 0.2372 0.300545 0.291782 0.287293 1 3045 32998 3061 1846 1759 18951 249 4087 2 10398 121250 11514 8640 6604 66684 908 16502 0.988537 0 . 0 . 206 68,40,55,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P283S|312|OR51B2|protein_coding|CODING|NM_033180.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.564829 rs11036815 -0.693147 0.1047 206 T252 312 acA/acG LOW 1 SILENT CODING OR51B2 C protein_coding NM_033180.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344772 T C 0 222 0 0.7829 0.755 0.7651 0.5407 0.9066 0.7751 0.806679 0.877193 0.913312 1 8315 101995 8125 4489 5961 61014 785 13306 2 10404 121256 11502 8638 6610 66688 908 16506 0.45781 0 . 0 . 154 29,53,27,38 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T252|312|OR51B2|protein_coding|CODING|NM_033180.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517017 rs10742622,rs386485636 -0.693147 0.384693 154 A227 312 gcT/gcC LOW 1 SILENT CODING OR51B2 G protein_coding NM_033180.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344847 A G 0 222 0 0.7829 0.7552 0.7651 0.5407 0.9076 0.7751 0.806679 0.877193 0.913312 1 8306 101842 8094 4469 5953 60935 783 13302 2 10388 121066 11462 8604 6602 66604 906 16500 0.800226 0 . 0 . 120 32,38,18,27 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A227|312|OR51B2|protein_coding|CODING|NM_033180.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.780029 rs10768793,rs386515038 -0.693147 0.862302 120 C209S 312 tGt/tCt MODERATE 1 MISSENSE CODING OR51B2 G protein_coding NM_033180.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5344902 C G 0 222 0 0.7829 0.7552 0.7651 0.5407 0.9076 0.7751 0.806679 0.877193 0.913312 1 8290 101730 8075 4465 5955 60868 785 13292 2 10372 120936 11432 8600 6602 66534 908 16488 0.455643 0 . 0 . 107 33,32,21,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C209S|312|OR51B2|protein_coding|CODING|NM_033180.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.879896 rs7937237 -0.693136 0.715267 107 C120R 312 Tgt/Cgt MODERATE 1 MISSENSE CODING OR51B2 G protein_coding NM_033180.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5345170 A G 0 222 0 0.7852 0.756 0.7651 0.5407 0.9076 0.7761 0.808042 0.877655 0.913312 1 8279 101905 8125 4483 5965 60968 783 13302 2 10344 121118 11500 8622 6614 66634 906 16498 0.663264 0 . 0 . 70 8,26,10,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C120R|312|OR51B2|protein_coding|CODING|NM_033180.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.554364 rs7952293 -0.693136 0.132141 70 G14 312 ggC/ggT LOW 1 SILENT CODING OR51B2 A protein_coding NM_033180.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5345486 G A 0 222 0 0.7844 0.7556 0.7651 0.5397 0.9085 0.7751 0.808723 0.877655 0.912963 1 8285 101441 8020 4446 5957 60668 778 13287 2 10358 120562 11368 8564 6604 66310 902 16456 0.299169 0 . 0 . 69 14,18,13,18 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G14|312|OR51B2|protein_coding|CODING|NM_033180.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.57518 rs4910750 -0.69311 0.0673897 69 P160L 312 cCc/cTc MODERATE 5 MISSENSE CODING OR51B5 A protein_coding NM_001005567.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5364276 G A 0 222 0 0.2595 0.3249 0.402 0.1786 0.4404 0.3906 0.278055 0.389504 0.446591 1 2845 49786 4762 1431 3263 30630 346 6509 2 10198 120536 11514 8578 6610 66294 902 16440 0.997477 0 . 0 . 45 12,7,17,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P160L|312|OR51B5|protein_coding|CODING|NM_001005567.2|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98634 rs4910551 -0.692914 0.953517 45 I102T 312 aTa/aCa MODERATE 5 MISSENSE CODING OR51B5 G protein_coding NM_001005567.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5364450 A G 0 222 0 0.2595 0.3257 0.4035 0.1796 0.4404 0.3926 0.279191 0.390274 0.447172 1 2874 49963 4762 1432 3265 30726 347 6557 2 10302 120708 11498 8538 6606 66414 906 16444 0.97443 0 . 0 . 97 16,19,30,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I102T|312|OR51B5|protein_coding|CODING|NM_001005567.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.219218 rs11036912 -0.693147 0.783905 97 G5S 312 Ggc/Agc MODERATE 5 MISSENSE CODING OR51B5 T protein_coding NM_001005567.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5364742 C T 0 222 0 0.0847 0.2977 0.438 0.2391 0.4304 0.41 0.152214 0.348109 0.447246 1 1293 43138 5127 1994 2624 26932 355 4813 2 8866 107758 11024 7994 6414 62088 788 10584 0.984404 0 . 0 . 256 63,58,45,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G5S|312|OR51B5|protein_coding|CODING|NM_001005567.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.917838 rs11036913 -0.693147 0.00616547 256 R48 312 agG/agA LOW 1 SILENT CODING OR51B6 A protein_coding NM_001004750.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5372881 G A 0 222 0 0.0303 0.1056 0.1614 0.0754 0.1541 0.1493 0.0547478 0.119267 0.152316 1 553 17782 2370 710 953 10585 129 2482 2 10406 121330 11548 8646 6610 66704 908 16508 0.557939 0 . 0 . 175 42,48,36,36 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R48|312|OR51B6|protein_coding|CODING|NM_001004750.1|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.651792 rs77135024 -0.693147 0.0869671 175 S126N 312 aGc/aAc MODERATE 1 MISSENSE CODING OR51B6 A protein_coding NM_001004750.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5373114 G A 0 222 0 0.587 0.6064 0.5692 0.5446 0.6054 0.7239 0.581554 0.587104 0.589946 1 6145 73008 6609 4528 3641 39631 547 11907 2 10390 121170 11530 8624 6598 66622 908 16498 0.713356 0 . 0 . 176 44,37,45,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S126N|312|OR51B6|protein_coding|CODING|NM_001004750.1|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.879928 rs5006888 -0.693147 0.0117431 176 V254L 312 Gtt/Ctt MODERATE 1 MISSENSE CODING OR51B6 C protein_coding NM_001004750.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5373497 G C 0 222 0 0.0303 0.1054 0.1599 0.0754 0.1541 0.1493 0.0547478 0.119037 0.151966 1 553 17743 2355 722 953 10550 128 2482 2 10406 121380 11568 8646 6614 66728 908 16510 0.969766 0 . 0 . 136 34,23,54,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V254L|312|OR51B6|protein_coding|CODING|NM_001004750.1|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.563694 rs7106330 -0.693147 0.216138 136 R303 312 cgT/cgC LOW 1 SILENT CODING OR51B6 C protein_coding NM_001004750.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5373646 T C 0 222 0 0.5764 0.6036 0.5692 0.5466 0.6054 0.7219 0.579773 0.590685 0.596275 1 5837 72591 6665 4562 3669 39711 544 11603 2 9952 120224 11560 8618 6610 66464 894 16126 0.714449 0 . 0 . 147 22,41,23,46 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R303|312|OR51B6|protein_coding|CODING|NM_001004750.1|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90697 rs5024041 -0.693147 0.605672 147 H102Q 326 caT/caG MODERATE 1 MISSENSE CODING OR51M1 G protein_coding NM_001004756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5410934 T G 0 222 0 0.6815 0.6981 0.7277 0.5476 0.8241 0.7249 0.736368 0.797542 0.826762 1 6922 92784 7767 4405 5565 54991 710 12424 2 9804 120736 11568 8600 6614 66738 900 16512 0.724449 0 . 0 . 88 21,23,20,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H102Q|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|G),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.684114 rs1498467 -0.693144 0.484963 88 L135F 326 Ctt/Ttt MODERATE 1 MISSENSE CODING OR51M1 T protein_coding NM_001004756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5411031 C T 0 222 0 0.6815 0.6987 0.7277 0.5486 0.8231 0.728 0.738234 0.798794 0.828224 1 6924 92773 7763 4404 5564 54983 711 12424 2 9806 120738 11566 8604 6612 66736 902 16512 0.97867 0 . 0 . 112 38,16,30,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L135F|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|T),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97279 rs1498468 -0.693147 0.805159 112 I204T 326 aTc/aCc MODERATE 1 MISSENSE CODING OR51M1 C protein_coding NM_001004756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5411239 T C 0 222 0 0.7383 0.7145 0.7349 0.5476 0.8231 0.728 0.784585 0.813806 0.827894 1 7429 93316 7789 4403 5564 54995 710 12426 2 9818 120734 11572 8602 6614 66718 898 16512 0.188145 0 . 0 . 174 52,41,33,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I204T|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.115289 rs1498469 -0.693147 0.57754 174 P256H 326 cCt/cAt MODERATE 1 MISSENSE CODING OR51M1 A protein_coding NM_001004756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5411395 C A 0 222 0 0.7368 0.7123 0.7349 0.5387 0.8231 0.728 0.780659 0.81261 0.828296 1 7407 93191 7780 4338 5562 54982 708 12414 2 9814 120652 11548 8586 6610 66696 896 16502 0.460018 0 . 0 . 135 42,28,35,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P256H|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955615 rs9783355 -0.693147 0.688908 135 K317 326 aaG/aaA LOW 1 SILENT CODING OR51M1 A protein_coding NM_001004756.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5411579 G A 0 155 0 0.7383 0.7145 0.7349 0.5476 0.8231 0.728 0.777147 0.810403 0.82549 1 6367 83337 6720 3908 5242 49094 647 11359 2 8358 107192 9822 7340 6252 59678 820 14922 0.131442 0 . 0 . 84 4,48,2,27 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K317|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.131442 rs10768906 -0.693079 0.0706223 84 F318L 326 Ttc/Ctc MODERATE 1 MISSENSE CODING OR51M1 C protein_coding NM_001004756.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5411580 T C 0 186 0 0.7383 0.7145 0.7349 0.5476 0.8231 0.728 0.776906 0.811014 0.826471 1 6349 82992 6674 3897 5244 48877 641 11310 2 8312 106556 9718 7258 6242 59372 812 14842 0.991433 0 . 0 . 84 4,46,2,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F318L|326|OR51M1|protein_coding|CODING|NM_001004756.2|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0324307 rs10768907 -0.69311 0.0902353 84 L204F 317 Ctt/Ttt MODERATE 1 MISSENSE CODING OR51Q1 T protein_coding NM_001004757.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5444040 C T 0 222 0 0.0015 0.024 0.085 0.0526 0.005 0.001 0.0022717 0.00338566 0.00395625 1 34 2802 1727 447 114 441 15 24 2 10406 121394 11578 8648 6614 66730 908 16510 0.767555 0 . 0 COSM147119 105 28,29,26,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L204F|317|OR51Q1|protein_coding|CODING|NM_001004757.2|1|T),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.470534 rs78214713 -0.693145 0.674314 105 A252S 314 Gcc/Tcc MODERATE 1 MISSENSE CODING OR51I1 A protein_coding NM_001005288.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5461991 C A 0 228 0 0.1437 0.3033 0.464 0.1319 0.5368 0.3415 0.202181 0.429825 0.546428 2 2126 55940 5720 1108 3740 36765 425 6056 2 10396 121086 11428 8634 6598 66626 902 16502 1 0 . 0 . 68 0,1,29,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A252S|314|OR51I1|protein_coding|CODING|NM_001005288.2|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1498486 -0.693147 0.250865 68 T134A 312 Act/Gct MODERATE 1 MISSENSE CODING OR51I2 G protein_coding NM_001004754.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5475118 A G 0 222 0 0.0666 0.1927 0.1628 0.3581 0.1282 0.2802 0.069741 0.107572 0.126949 1 817 20187 2106 3183 731 8749 171 4430 2 10406 121374 11578 8626 6612 66736 908 16508 0.809946 0 . 0 . 133 32,29,25,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T134A|312|OR51I2|protein_coding|CODING|NM_001004754.2|1|G),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999967 rs12577167 -0.693147 0.0104012 133 S116 318 tcA/tcG LOW 1 SILENT CODING OR52D1 G protein_coding NM_001005163.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5510284 A G 0 228 0 0.9175 0.9505 0.9726 0.9246 0.9742 0.9816 0.94298 0.961142 0.970445 2 9787 117669 11336 7946 6389 65065 867 16279 2 10406 121386 11554 8654 6614 66738 908 16512 0 . 0 . 0 110 0,0,58,48 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S116|318|OR52D1|protein_coding|CODING|NM_001005163.2|1|G),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs417425 -0.693147 0.000957824 110 Y135 318 taC/taT LOW 1 SILENT CODING OR52D1 T protein_coding NM_001005163.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5510341 C T 0 222 0 0.323 0.5254 0.5836 0.6071 0.5944 0.6022 0.383689 0.542398 0.623691 1 3953 71076 6314 5305 3602 41207 542 10153 2 10404 121352 11546 8640 6614 66730 908 16510 0.39219 0 . 0 . 105 26,24,16,24 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y135|318|OR52D1|protein_coding|CODING|NM_001005163.2|1|T),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.131651 rs404280 -0.693145 0.0131126 105 I187 318 atT/atC LOW 1 SILENT CODING OR52D1 C protein_coding NM_001005163.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5510497 T C 0 228 0 0.9107 0.9483 0.9712 0.9246 0.9742 0.9806 0.938437 0.959526 0.970328 2 9741 117628 11350 7947 6389 65058 867 16276 2 10406 121400 11574 8652 6614 66736 908 16510 0 . 0 . 0 47 0,0,27,19 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I187|318|OR52D1|protein_coding|CODING|NM_001005163.2|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2467219 -0.693147 0.00437927 47 H230 318 caT/caC LOW 1 SILENT CODING OR52D1 C protein_coding NM_001005163.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5510626 T C 0 228 0 0.9107 0.9485 0.9712 0.9246 0.9742 0.9816 0.93821 0.959449 0.970328 2 9741 117633 11356 7944 6389 65057 867 16279 2 10406 121406 11576 8654 6614 66736 908 16512 0 . 0 . 0 69 0,0,36,29 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H230|318|OR52D1|protein_coding|CODING|NM_001005163.2|1|C),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs444878 -0.693147 0.0615123 69 318 35 MODIFIER 1 CODING OR52D1 A protein_coding NM_001005163.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5510928 G A 0 228 0 0.9107 0.9485 0.9712 0.9246 0.9742 0.9816 0.938412 0.959753 0.97065 2 9113 113581 11266 7913 6387 63754 826 14322 2 9740 117246 11486 8620 6612 65390 864 14534 0 . 0 . 0 39 0,0,12,25 UTR_3_PRIME(MODIFIER||35||318|OR52D1|protein_coding|CODING|NM_001005163.2|1|A),INTRON(MODIFIER||||312|OR51B5|protein_coding|CODING|NM_001005567.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs392296 -0.693141 0.286599 39 M546T 655 aTg/aCg MODERATE 2 MISSENSE CODING UBQLN3 G protein_coding NM_017481.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5529152 A G 0 193 0 0.0098 0.1158 0.2363 0.0933 0.2127 0.0971 0.0397547 0.135349 0.184315 1 348 21198 3754 628 1663 12902 163 1740 2 10192 120604 11526 8588 6610 66308 900 16480 0.520252 0 . 0 . 30 5,11,9,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M546T|655|UBQLN3|protein_coding|CODING|NM_017481.2|2|G),UPSTREAM(MODIFIER||2270||312|OR51B5|protein_coding|CODING|NM_001005567.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939481 rs2234455 -0.686358 0.502073 30 S308 655 tcC/tcT LOW 2 SILENT CODING UBQLN3 A protein_coding NM_017481.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5529865 G A 0 228 0 0.9478 0.9862 1 1 1 1 0.969105 0.989227 0.999535 2 10063 121039 11570 8652 6614 66720 908 16512 2 10406 121408 11578 8652 6614 66738 908 16512 0 . 0 . 0 69 0,0,43,23 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S308|655|UBQLN3|protein_coding|CODING|NM_017481.2|2|A),UPSTREAM(MODIFIER||2983||312|OR51B5|protein_coding|CODING|NM_001005567.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs186434,rs386443301 -0.693147 5.37273e-06 69 475 573 MODIFIER 1 CODING UBQLNL G protein_coding NM_145053.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5535671 A G 0 125 0 0.4478 0.4189 0.3732 0.6091 0.2684 0.3712 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.813291 0 . 0 . 30 15,0,15,0 UTR_3_PRIME(MODIFIER||573||475|UBQLNL|protein_coding|CODING|NM_145053.4|1|G),UPSTREAM(MODIFIER||4518||655|UBQLN3|protein_coding|CODING|NM_017481.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.634414 rs1044392 -0.688148 0.269663 30 W379G 475 Tgg/Ggg MODERATE 1 MISSENSE CODING UBQLNL C protein_coding NM_145053.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5536537 A C 0 228 0 0.8896 0.9698 0.9942 1 1 0.999 0.934121 0.976762 0.998604 2 9614 120494 11540 8652 6614 66658 908 16508 2 10406 121410 11578 8652 6614 66740 908 16512 0 . 0 . 0 44 0,0,17,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W379G|475|UBQLNL|protein_coding|CODING|NM_145053.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs393044 -0.693143 0.883388 44 A275V 475 gCt/gTt MODERATE 1 MISSENSE CODING UBQLNL A protein_coding NM_145053.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5536848 G A 0 222 0 0.3707 0.5321 0.6138 0.3988 0.7266 0.6299 0.436165 0.618652 0.712125 1 4459 75825 6567 3218 3871 47064 551 10095 2 10406 121272 11542 8610 6612 66694 904 16504 0.999052 0 . 0 COSM147120 69 19,15,16,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A275V|475|UBQLNL|protein_coding|CODING|NM_145053.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.539595 rs2017433 -0.693021 0.0656129 69 Q143K 475 Caa/Aaa MODERATE 1 MISSENSE CODING UBQLNL T protein_coding NM_145053.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5537245 G T 0 222 0 0.0908 0.0931 0.0187 0.2252 0.008 0.1002 0.0904135 0.0377809 0.0108215 1 893 5712 361 2107 39 783 28 1501 2 10352 121176 11566 8620 6612 66628 906 16492 0.734582 0 . 0 . 45 14,7,11,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q143K|475|UBQLNL|protein_coding|CODING|NM_145053.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994149 rs3802978 -0.69168 0.0673076 45 C242R 320 Tgc/Cgc MODERATE 1 MISSENSE CODING OR52H1 G protein_coding NM_001005289.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5566030 A G 0 222 0 0.941 0.891 0.8415 0.9196 0.8002 0.9223 0.927079 0.848107 0.807657 1 9660 101424 9182 8049 4965 53873 754 14941 2 10400 121300 11544 8650 6610 66676 908 16512 0.987091 0 . 0 . 67 6,25,8,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C242R|320|OR52H1|protein_coding|CODING|NM_001005289.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.349074 rs1995158,rs386551804 -0.693127 0.181702 67 H130R 320 cAc/cGc MODERATE 1 MISSENSE CODING OR52H1 C protein_coding NM_001005289.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5566365 T C 0 222 0 0.9349 0.8894 0.8415 0.9196 0.8002 0.9223 0.918446 0.84526 0.807773 1 9567 101380 9200 8050 4965 53906 753 14939 2 10388 121346 11570 8648 6614 66708 908 16510 0.953537 0 . 0 . 80 23,10,34,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H130R|320|OR52H1|protein_coding|CODING|NM_001005289.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.46709 rs1566275,rs386538462 -0.693147 0.0692912 80 T57A 335 Act/Gct MODERATE 1 MISSENSE CODING OR52B6 G protein_coding NM_001005162.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602275 A G 0 228 0 0.6362 0.5723 0.5692 0.7669 0.331 0.5358 0.560465 0.395126 0.311915 2 5751 51712 7577 6686 2310 21022 362 8004 2 9834 120624 11560 8626 6606 66628 896 16474 1 0 . 0 . 56 0,1,32,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T57A|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1077126 -0.693147 0.0683461 56 L111H 335 cTc/cAc MODERATE 1 MISSENSE CODING OR52B6 A protein_coding NM_001005162.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602438 T A 0 228 0 0.7352 0.7151 0.67 0.9802 0.4761 0.6922 0.697632 0.54591 0.468335 2 7008 69254 8265 8459 3243 31509 481 10289 2 9930 120550 11574 8652 6612 66562 904 16316 0 . 0 . 0 73 0,0,50,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L111H|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2341432 -0.693147 0.482749 73 A167T 335 Gcc/Acc MODERATE 1 MISSENSE CODING OR52B6 A protein_coding NM_001005162.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602605 G A 0 228 0 0.6142 0.5653 0.562 0.7659 0.331 0.5358 0.547024 0.392643 0.313547 2 5698 51538 7564 6698 2312 20968 361 7937 2 10154 120708 11572 8640 6614 66578 902 16248 1 0 . 0 . 88 0,1,39,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A167T|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2341433 -0.693147 0.131714 88 H170R 335 cAc/cGc MODERATE 1 MISSENSE CODING OR52B6 G protein_coding NM_001005162.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602615 A G 0 228 0 0.7413 0.7167 0.67 0.9802 0.4761 0.6922 0.696274 0.545252 0.467877 2 7156 69435 8266 8455 3243 31534 479 10302 2 10088 120844 11574 8650 6614 66642 904 16372 0 . 0 . 0 96 0,0,39,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H170R|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2341434 -0.693147 0.393807 96 N191 335 aaT/aaC LOW 1 SILENT CODING OR52B6 C protein_coding NM_001005162.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602679 T C 0 228 0 0.7413 0.7165 0.67 0.9792 0.4761 0.6922 0.703204 0.549258 0.470684 2 7032 69408 8267 8455 3243 31574 482 10355 2 9918 120830 11566 8648 6614 66694 902 16488 0 . 0 . 0 90 0,0,36,48 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N191|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs892336 -0.693147 0.0190443 90 L228 335 ctA/ctG LOW 1 SILENT CODING OR52B6 G protein_coding NM_001005162.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602790 A G 0 228 0 0.7413 0.7169 0.67 0.9802 0.4761 0.6933 0.708724 0.551808 0.472682 2 6956 69328 8263 8442 3243 31579 478 10367 2 9822 120752 11566 8634 6608 66716 900 16506 0 . 0 . 0 71 0,0,47,21 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L228|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2163946 -0.693147 0.567033 71 A274 335 gcG/gcC LOW 1 SILENT CODING OR52B6 C protein_coding NM_001005162.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602928 G C 0 228 0 0.7383 0.7159 0.67 0.9792 0.4761 0.6933 0.706511 0.548327 0.473551 2 6917 69256 8264 8433 3243 31560 478 10361 2 9800 120702 11570 8626 6614 66694 900 16498 0 . 0 . 0 131 0,0,72,43 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A274|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10838375 -0.693147 4.78693e-05 131 V288I 335 Gtc/Atc MODERATE 1 MISSENSE CODING OR52B6 A protein_coding NM_001005162.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5602968 G A 0 228 0 0.969 0.8946 0.8833 0.9931 0.7604 0.8384 0.949597 0.816748 0.753481 2 9323 97815 10478 8547 5222 50012 724 13509 2 9802 120740 11576 8626 6614 66714 900 16508 0 . 0 . 0 157 0,0,78,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V288I|335|OR52B6|protein_coding|CODING|NM_001005162.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769086 -0.693147 0.662887 157 516 232 MODIFIER 1 CODING TRIM6 G protein_coding NM_001003818.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5617896 A G 0 17.3 0 0.1808 0.1328 0.0461 0.1825 0.0686 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 3,0,2,0 UTR_5_PRIME(MODIFIER||232||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|G),UTR_5_PRIME(MODIFIER||232||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10838406 -0.453602 0.64 5 842 232 MODIFIER 1 CODING TRIM6-TRIM34 G protein_coding NM_001003819.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5617896 A G 0 17.3 0 0.1808 0.1328 0.0461 0.1825 0.0686 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 3,0,2,0 UTR_5_PRIME(MODIFIER||232||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|G),UTR_5_PRIME(MODIFIER||232||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10838406 -0.453602 0.64 5 516 141 MODIFIER 1 CODING TRIM6 A protein_coding NM_001003818.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5617987 G A 0 128 0 0.4236 0.4535 0.5245 0.4881 0.5099 0.3497 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,8,0 START_GAINED(LOW||||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|A),START_GAINED(LOW||||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|A),UTR_5_PRIME(MODIFIER||141||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|A),UTR_5_PRIME(MODIFIER||141||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12272467 -0.651104 0.519034 8 842 141 MODIFIER 1 CODING TRIM6-TRIM34 A protein_coding NM_001003819.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5617987 G A 0 128 0 0.4236 0.4535 0.5245 0.4881 0.5099 0.3497 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,8,0 START_GAINED(LOW||||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|A),START_GAINED(LOW||||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|A),UTR_5_PRIME(MODIFIER||141||516|TRIM6|protein_coding|CODING|NM_001003818.2|1|A),UTR_5_PRIME(MODIFIER||141||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12272467 -0.651104 0.519034 8 K197 516 aaA/aaG LOW 3 SILENT CODING TRIM6 G protein_coding NM_001003818.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5625847 A G 0 228 0 0.7171 0.6999 0.6556 0.7212 0.5865 0.8027 0.720582 0.655048 0.62148 2 7531 79562 8448 6357 3256 40812 566 12592 2 10402 121292 11568 8646 6608 66696 908 16464 0 . 0 . 0 65 0,0,28,31 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K197|516|TRIM6|protein_coding|CODING|NM_001003818.2|3|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K197|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3751006 -0.693147 0.0292119 65 K197 842 aaA/aaG LOW 3 SILENT CODING TRIM6-TRIM34 G protein_coding NM_001003819.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5625847 A G 0 228 0 0.7171 0.6999 0.6556 0.7212 0.5865 0.8027 0.720582 0.655048 0.62148 2 7531 79562 8448 6357 3256 40812 566 12592 2 10402 121292 11568 8646 6608 66696 908 16464 0 . 0 . 0 65 0,0,28,31 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K197|516|TRIM6|protein_coding|CODING|NM_001003818.2|3|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K197|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3751006 -0.693147 0.0292119 65 V280 516 gtG/gtA LOW 5 SILENT CODING TRIM6 A protein_coding NM_001003818.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5629607 G A 0 228 0 0.5643 0.3968 0.3559 0.4335 0.2326 0.3303 0.505225 0.334872 0.247615 2 5451 36382 4344 4047 1268 15528 288 5456 2 10390 121036 11510 8630 6608 66544 906 16448 0.423784 0 . 0 COSM147121,COSM147122 198 3,2,88,84 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V280|516|TRIM6|protein_coding|CODING|NM_001003818.2|5|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V280|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.709884 rs10769121 -0.693147 0.0424907 198 V280 842 gtG/gtA LOW 5 SILENT CODING TRIM6-TRIM34 A protein_coding NM_001003819.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5629607 G A 0 228 0 0.5643 0.3968 0.3559 0.4335 0.2326 0.3303 0.505225 0.334872 0.247615 2 5451 36382 4344 4047 1268 15528 288 5456 2 10390 121036 11510 8630 6608 66544 906 16448 0.423784 0 . 0 COSM147121,COSM147122 198 3,2,88,84 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V280|516|TRIM6|protein_coding|CODING|NM_001003818.2|5|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V280|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.709884 rs10769121 -0.693147 0.0424907 198 L397 516 ctG/ctA LOW 8 SILENT CODING TRIM6 A protein_coding NM_001003818.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5632212 G A 0 228 0 0.6044 0.7891 0.7622 0.998 0.662 0.9734 0.634484 0.687135 0.714103 2 6453 92894 9945 8616 4472 47161 696 15551 2 10402 121392 11578 8652 6612 66728 908 16512 0 . 0 . 0 102 0,0,39,56 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L397|516|TRIM6|protein_coding|CODING|NM_001003818.2|8|A),INTRON(MODIFIER||||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769124 -0.693147 0.057958 102 516 1473 MODIFIER 8 CODING TRIM6 A protein_coding NM_001003818.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5634045 T A 0 9.7 0 0.1331 0.1783 0.1542 0.2907 0.1491 0.1708 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1473||516|TRIM6|protein_coding|CODING|NM_001003818.2|8|A),INTRON(MODIFIER||||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11038346 -0.379885 0 1 D636H 842 Gat/Cat MODERATE 12 MISSENSE CODING TRIM6-TRIM34 C protein_coding NM_001003819.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5663706 G C 0 222 0 0.0098 0.0665 0.1167 0.1597 0.0278 0.0511 0.016129 0.0228532 0.0262974 1 163 5523 1453 1290 96 1560 42 919 2 10380 121096 11528 8628 6612 66562 908 16478 0.9775 0 . 0 COSM147123,COSM147124 127 24,28,32,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D636H|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|12|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D282H|488|TRIM34|protein_coding|CODING|NM_001003827.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.899266 rs3740997 -0.693147 0.504822 127 D282H 488 Gat/Cat MODERATE 6 MISSENSE CODING TRIM34 C protein_coding NM_001003827.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5663706 G C 0 222 0 0.0098 0.0665 0.1167 0.1597 0.0278 0.0511 0.016129 0.0228532 0.0262974 1 163 5523 1453 1290 96 1560 42 919 2 10380 121096 11528 8628 6612 66562 908 16478 0.9775 0 . 0 COSM147123,COSM147124 127 24,28,32,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D636H|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|12|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D282H|488|TRIM34|protein_coding|CODING|NM_001003827.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.899266 rs3740997 -0.693147 0.504822 127 G807 842 ggC/ggA LOW 14 SILENT CODING TRIM6-TRIM34 A protein_coding NM_001003819.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5664831 C A 0 222 0 0.2103 0.3778 0.438 0.6458 0.2306 0.4366 0.237165 0.237458 0.237608 1 2403 39270 6288 5356 1845 16367 272 6739 2 10406 121390 11570 8648 6614 66732 908 16512 0.944562 0 . 0 . 211 43,51,57,40 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G807|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|A),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G453|488|TRIM34|protein_coding|CODING|NM_001003827.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.642144 rs3740998 -0.693147 0.136445 211 G453 488 ggC/ggA LOW 8 SILENT CODING TRIM34 A protein_coding NM_001003827.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5664831 C A 0 222 0 0.2103 0.3778 0.438 0.6458 0.2306 0.4366 0.237165 0.237458 0.237608 1 2403 39270 6288 5356 1845 16367 272 6739 2 10406 121390 11570 8648 6614 66732 908 16512 0.944562 0 . 0 . 211 43,51,57,40 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G807|842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|A),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G453|488|TRIM34|protein_coding|CODING|NM_001003827.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.642144 rs3740998 -0.693147 0.136445 211 842 35 MODIFIER 14 CODING TRIM6-TRIM34 C protein_coding NM_001003819.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5664974 T C 0 228 0 0.6732 0.8744 0.9352 0.997 0.9503 0.8988 0.717727 0.875116 0.955752 2 6744 103737 11056 8541 6559 61432 756 8649 2 9588 110718 11486 8554 6614 64044 796 9636 0 . 0 . 0 115 0,0,28,75 UTR_3_PRIME(MODIFIER||35||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|C),UTR_3_PRIME(MODIFIER||35||488|TRIM34|protein_coding|CODING|NM_001003827.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7109861 -0.693147 0.0238892 115 488 35 MODIFIER 8 CODING TRIM34 C protein_coding NM_001003827.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5664974 T C 0 228 0 0.6732 0.8744 0.9352 0.997 0.9503 0.8988 0.717727 0.875116 0.955752 2 6744 103737 11056 8541 6559 61432 756 8649 2 9588 110718 11486 8554 6614 64044 796 9636 0 . 0 . 0 115 0,0,28,75 UTR_3_PRIME(MODIFIER||35||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|C),UTR_3_PRIME(MODIFIER||35||488|TRIM34|protein_coding|CODING|NM_001003827.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7109861 -0.693147 0.0238892 115 842 286 MODIFIER 14 CODING TRIM6-TRIM34 G protein_coding NM_001003819.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5665225 A G 0 155 0 0.6725 0.8752 0.9352 0.997 0.9503 0.9039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,4 UTR_3_PRIME(MODIFIER||286||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|G),UTR_3_PRIME(MODIFIER||286||488|TRIM34|protein_coding|CODING|NM_001003827.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7106798 -0.616816 0.111502 6 488 286 MODIFIER 8 CODING TRIM34 G protein_coding NM_001003827.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5665225 A G 0 155 0 0.6725 0.8752 0.9352 0.997 0.9503 0.9039 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,2,4 UTR_3_PRIME(MODIFIER||286||842|TRIM6-TRIM34|protein_coding|CODING|NM_001003819.3|14|G),UTR_3_PRIME(MODIFIER||286||488|TRIM34|protein_coding|CODING|NM_001003827.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7106798 -0.616816 0.111502 6 G249D 493 gGt/gAt MODERATE 5 MISSENSE CODING TRIM5 T protein_coding NM_033034.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5688940 C T 0 222 0 0.3124 0.2452 0.2291 0.4256 0.0586 0.1718 0.254884 0.124962 0.0584128 1 2776 17125 3467 3860 394 4051 117 2460 2 10406 121338 11562 8642 6614 66698 908 16508 0.415837 0 . 0 . 203 63,43,37,38 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gGt/gAt|G249D|493|TRIM5|protein_coding|CODING|NM_033034.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952783 rs11038628 -0.693147 0.732289 203 L159 493 ttA/ttG LOW 3 SILENT CODING TRIM5 C protein_coding NM_033034.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5700340 T C 0 228 0 0.733 0.8119 0.8012 0.8304 0.8559 0.862 0.713994 0.806556 0.853968 2 7540 101790 9497 7102 5825 57150 779 13897 2 10404 121406 11578 8652 6614 66738 908 16512 1 0 . 0 . 149 1,0,74,62 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L159|493|TRIM5|protein_coding|CODING|NM_033034.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3740995 -0.693147 0.32111 149 R59Q 493 cGg/cAg MODERATE 2 MISSENSE CODING TRIM5 T protein_coding NM_033034.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5701232 C T 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 19 0 14 0 3 0 2 2 10406 121336 11578 8632 6614 66704 908 16494 0.663106 0 . 0 . 132 24,46,22,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R59Q|493|TRIM5|protein_coding|CODING|NM_033034.2|2|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.995312 rs200209793 -0.693147 0.0563538 132 493 2 MODIFIER 2 CODING TRIM5 C protein_coding NM_033034.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5701409 G C 0 222 0 0.1051 0.3998 0.4741 0.4355 0.5348 0.5695 0.186221 0.433852 0.560666 1 1745 59092 5702 3835 3443 35930 435 8002 2 10068 115856 11518 8582 6592 65080 850 13166 0.865112 0 . 0 . 95 13,26,10,34 UTR_5_PRIME(MODIFIER||2||493|TRIM5|protein_coding|CODING|NM_033034.2|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998742 rs3824949 -0.693146 0.11618 95 R242T 498 aGg/aCg MODERATE 4 MISSENSE CODING TRIM22 C protein_coding NM_006074.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5719750 G C 0 222 0 0.3722 0.4269 0.4553 0.2054 0.5398 0.593 0.395349 0.513264 0.570017 1 3735 60535 3960 1633 4048 37600 463 9096 2 9666 118366 11010 8228 6488 65834 890 16250 0.246706 0 . 0 COSM147127 199 61,45,33,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aCg|R242T|498|TRIM22|protein_coding|CODING|NM_006074.4|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.892945 rs1063303,rs386487822 -0.693147 0.0142712 199 S13 324 agC/agT LOW 1 SILENT CODING OR56B1 T protein_coding NM_001005180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5757785 C T 0 222 0 0.09 0.113 0.1268 0.1399 0.1133 0.1063 0.0920036 0.0979532 0.101001 1 945 11562 893 1108 279 6546 81 1710 2 10388 121182 11490 8616 6606 66662 908 16512 0.516184 0 . 0 . 84 25,20,23,13 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S13|324|OR56B1|protein_coding|CODING|NM_001005180.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.553136 rs12792180 -0.693139 0.313733 84 C106R 324 Tgc/Cgc MODERATE 1 MISSENSE CODING OR56B1 C protein_coding NM_001005180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5758062 T C 0 222 0 0.6611 0.7396 0.6571 0.748 0.833 0.7996 0.677192 0.796784 0.858041 1 7029 98868 7751 6380 6021 57269 761 13657 2 10400 121000 11430 8560 6582 66612 906 16510 0.89027 0 . 0 . 120 36,27,30,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C106R|324|OR56B1|protein_coding|CODING|NM_001005180.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.178264 rs7397032 -0.693147 0.0470233 120 L124 324 ctA/ctC LOW 1 SILENT CODING OR56B1 C protein_coding NM_001005180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5758118 A C 0 228 0 0.7481 0.8518 0.7839 0.8909 0.9433 0.9059 0.76488 0.890813 0.955318 2 7935 110350 8664 7542 6316 63646 843 15404 2 10406 121202 11482 8598 6604 66692 908 16512 0 . 0 . 0 113 0,0,49,54 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctC|L124|324|OR56B1|protein_coding|CODING|NM_001005180.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7396766 -0.693147 0.0967509 113 T106I 321 aCc/aTc MODERATE 1 MISSENSE CODING OR52N4 T protein_coding NM_001005175.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5776287 C T 0 228 0 0.8843 0.9221 0.8746 0.9067 0.9712 0.9724 0.897092 0.946291 0.971492 2 9280 114579 10076 7704 6185 64414 877 16043 2 10386 121294 11530 8620 6614 66726 908 16510 0 . 0 . 0 196 0,0,59,124 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T106I|321|OR52N4|protein_coding|CODING|NM_001005175.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7936512 -0.693147 0.00403447 196 L167R 321 cTc/cGc MODERATE 1 MISSENSE CODING OR52N4 G protein_coding NM_001005175.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5776470 T G 0 228 0 0.7738 0.8918 0.8703 0.9067 0.9682 0.9724 0.8121 0.917515 0.971252 2 7896 113137 10023 7713 6185 64390 869 16061 2 9948 120874 11538 8630 6614 66728 906 16510 0 . 0 . 0 123 0,0,74,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L167R|321|OR52N4|protein_coding|CODING|NM_001005175.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7394584 -0.693147 0.256759 123 N218I 321 aAc/aTc MODERATE 1 MISSENSE CODING OR52N4 T protein_coding NM_001005175.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5776623 A T 0 228 0 0.7874 0.8958 0.8703 0.9067 0.9702 0.9724 0.822506 0.921535 0.971385 2 7960 113186 10019 7699 6185 64392 868 16063 2 9896 120786 11520 8614 6614 66726 904 16512 0 . 0 . 0 154 0,0,107,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aTc|N218I|321|OR52N4|protein_coding|CODING|NM_001005175.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7396938 -0.693147 0.604425 154 R243W 324 Cgg/Tgg MODERATE 1 MISSENSE CODING OR52N5 A protein_coding NM_001001922.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5799138 G A 0 222 0 0.003 0.0027955 0 0.0069 0.003 0 0.00733207 0.00257981 0.000122309 1 63 117 8 42 0 4 0 0 2 9878 113162 10750 8080 6108 62254 844 15248 0.439721 0 . 0 . 203 51,47,43,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R243W|324|OR52N5|protein_coding|CODING|NM_001001922.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972077 rs117500523 -0.693147 0.0136152 203 F247I 320 Ttc/Atc MODERATE 1 MISSENSE CODING OR52N1 T protein_coding NM_001001913.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5809308 A T 0 228 0 0.885 0.9239 0.8804 0.9067 0.9712 0.9765 0.885961 0.939357 0.966713 2 9252 114338 10019 7674 6158 64251 882 16102 2 10346 120912 11450 8564 6586 66568 906 16492 1 0 . 0 . 191 1,0,74,113 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Atc|F247I|320|OR52N1|protein_coding|CODING|NM_001001913.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7934670 -0.693147 0.052948 191 R167C 320 Cgc/Tgc MODERATE 1 MISSENSE CODING OR52N1 A protein_coding NM_001001913.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5809548 G A 0 228 0 0.2458 0.5517 0.5908 0.7054 0.6382 0.6902 0.326215 0.548099 0.661778 2 3184 76444 6972 5841 4141 44019 607 11680 2 10380 121030 11466 8556 6606 66606 908 16508 0 . 0 . 0 126 0,0,70,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R167C|320|OR52N1|protein_coding|CODING|NM_001001913.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7948009 -0.693147 0.0865639 126 N97 321 aaC/aaT LOW 1 SILENT CODING OR52N2 T protein_coding NM_001005174.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5841856 C T 0 228 0 0.7231 0.7386 0.7133 0.6687 0.8191 0.7669 0.74557 0.786902 0.808077 2 7624 93636 7830 5538 5374 53991 717 12562 2 10402 121338 11566 8634 6612 66706 908 16510 0 . 0 . 0 61 0,0,44,17 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N97|321|OR52N2|protein_coding|CODING|NM_001005174.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4758435 -0.693147 0.760233 61 S249A 321 Tcc/Gcc MODERATE 1 MISSENSE CODING OR52N2 G protein_coding NM_001005174.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5842310 T G 0 228 0 0.447 0.503 0.5086 0.4702 0.5845 0.5245 0.47274 0.570417 0.620461 2 4802 68177 5314 3758 3705 40938 511 9149 2 10406 121292 11560 8606 6606 66702 908 16504 0 . 0 . 0 204 0,0,117,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S249A|321|OR52N2|protein_coding|CODING|NM_001005174.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8181529 -0.693147 0.515462 204 H264R 321 cAt/cGt MODERATE 1 MISSENSE CODING OR52N2 G protein_coding NM_001005174.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5842356 A G 0 228 0 0.3411 0.4543 0.4813 0.4692 0.5368 0.4877 0.374602 0.492843 0.553422 2 3768 62135 5128 3756 3467 37085 473 8458 2 10406 121342 11564 8618 6610 66726 908 16510 0 . 0 . 0 186 0,0,92,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H264R|321|OR52N2|protein_coding|CODING|NM_001005174.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs8181512 -0.693147 0.0227024 186 M199R 313 aTg/aGg MODERATE 1 MISSENSE CODING OR52E6 C protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862532 A C 0 222 0 0.2224 0.3283 0.304 0.4593 0.3439 0.3374 0.234212 0.294828 0.325885 1 2378 40879 4060 4015 2612 21993 329 5492 2 10260 121018 11472 8570 6614 66682 908 16512 0.543641 0 . 0 . 276 87,74,47,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aGg|M199R|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.987396 0.995089 0 0.769352 rs10742809 -0.693147 0.615235 276 I159V 313 Att/Gtt MODERATE 1 MISSENSE CODING OR52E6 C protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862653 T C 0 222 0 0.3782 0.3842 0.3184 0.4593 0.3728 0.3732 0.366879 0.355857 0.35021 1 3885 44788 4245 4030 2774 23549 352 5953 2 10402 121292 11544 8608 6614 66706 908 16510 0.525769 0 . 0 . 240 86,61,50,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I159V|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.89691 0.961156 0 0.690266 rs4357719 -0.693147 0.0783302 240 W133R 313 Tgg/Cgg MODERATE 1 MISSENSE CODING OR52E6 G protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862731 A G 0 222 0 0.2352 0.3874 0.389 0.4593 0.5258 0.3753 0.273966 0.426735 0.505005 1 2701 55284 4851 4015 3431 33367 425 6494 2 10402 121316 11560 8628 6612 66708 908 16498 0.685729 0 . 0 . 268 73,66,39,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W133R|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.419476 0.997849 0 0.993546 rs10838719,rs61743084 -0.693147 0.00602779 268 V116 313 gtA/gtG LOW 1 SILENT CODING OR52E6 C protein_coding NM_001005167.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862780 T C 0 222 0 0.3782 0.3842 0.3184 0.4603 0.3728 0.3722 0.368015 0.356241 0.35021 1 3888 44809 4250 4037 2774 23555 352 5953 2 10404 121318 11548 8620 6612 66716 908 16510 0.308836 0 . 0 . 243 60,85,32,48 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V116|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.740265 0.99998 0 0.68319 rs4362172 -0.693147 0.0484199 243 S95P 313 Tct/Cct MODERATE 1 MISSENSE CODING OR52E6 G protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862845 A G 0 222 0 0.3782 0.384 0.3184 0.4593 0.3728 0.3722 0.367787 0.356164 0.35021 1 3882 44796 4247 4034 2774 23555 352 5952 2 10368 121270 11550 8608 6614 66714 908 16508 0.146286 0 . 0 . 169 51,49,33,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S95P|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953048 rs4592451 -0.693147 0.494841 169 C64F 313 tGc/tTc MODERATE 1 MISSENSE CODING OR52E6 A protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862937 C A 0 222 0 0.379 0.3842 0.3184 0.4593 0.3728 0.3722 0.368015 0.356164 0.350093 1 3887 44710 4247 4036 2773 23511 352 5904 2 10358 121092 11534 8620 6612 66638 908 16422 0.923634 0 . 0 . 246 83,43,70,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tTc|C64F|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.991826 0.98649 0 0.982836 rs4495918 -0.693147 0.160237 246 F48L 313 ttC/ttG MODERATE 1 MISSENSE CODING OR52E6 C protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5862984 G C 0 222 0 0.379 0.3842 0.3184 0.4593 0.3728 0.3722 0.368015 0.356318 0.350326 1 3885 44759 4241 4030 2773 23538 350 5942 2 10298 121086 11516 8600 6608 66664 906 16494 0.768368 0 . 0 COSM1127733 285 77,69,74,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttC/ttG|F48L|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.992382 0.991752 0 0.840057 rs10769272 -0.693147 0.44643 285 I39V 313 Att/Gtt MODERATE 1 MISSENSE CODING OR52E6 C protein_coding NM_001005167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5863013 T C 0 222 0 0.379 0.3842 0.3184 0.4593 0.3728 0.3722 0.369318 0.356835 0.350442 1 3852 44734 4243 4027 2773 23545 350 5944 2 10162 120932 11502 8590 6608 66666 904 16500 0.788925 0 . 0 . 299 72,79,73,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I39V|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.803357 rs4362173 -0.693147 0.366208 299 N5 313 aaC/aaT LOW 1 SILENT CODING OR52E6 A protein_coding NM_001005167.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5863113 G A 0 222 0 0.379 0.3842 0.3184 0.4593 0.3728 0.3722 0.360932 0.353524 0.349778 1 3695 44529 4235 4004 2773 23530 349 5943 2 9820 120300 11460 8542 6612 66490 898 16478 0.302252 0 . 0 COSM429318 240 51,65,31,72 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5|313|OR52E6|protein_coding|CODING|NM_001005167.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517764 rs10742810 -0.693147 0.540601 240 *318Y 317 taA/taT HIGH 1 MISSENSE CODING OR52E8 A protein_coding NM_001005168.1 STOP_LOST+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5877979 T A 0 222 0 0.3737 0.3748 0.4135 0.373 0.4085 0.316 0.385173 0.410631 0.423301 1 3558 44886 4164 3151 2670 27440 343 3560 2 9276 110556 11404 8502 6602 63928 822 10022 0.677376 0 . 0 . 96 31,7,37,11 STOP_LOST+SPLICE_SITE_REGION(HIGH|MISSENSE|taA/taT|*318Y|317|OR52E8|protein_coding|CODING|NM_001005168.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874715 rs12419602 -0.693147 0.0323819 96 V176I 312 Gta/Ata MODERATE 1 MISSENSE CODING OR52E4 A protein_coding NM_001005165.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906048 G A 0 228 0 0.8101 0.7796 0.7536 0.8254 0.7992 0.6892 0.81304 0.796214 0.787593 2 8410 94808 8549 7086 5538 52899 723 11603 2 10404 121248 11464 8640 6612 66710 908 16510 0 . 0 . 0 70 0,0,40,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V176I|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4758168 -0.693147 0.263656 70 R184M 312 aGg/aTg MODERATE 1 MISSENSE CODING OR52E4 T protein_coding NM_001005165.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906073 G T 0 228 0 0.8094 0.7802 0.7536 0.8254 0.7992 0.6933 0.812812 0.796214 0.787709 2 8405 94801 8550 7082 5538 52887 723 11616 2 10402 121228 11464 8638 6612 66696 908 16508 0 . 0 . 0 72 0,0,46,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aTg|R184M|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4757986 -0.693147 0.0318498 72 Y207 312 taT/taC LOW 1 SILENT CODING OR52E4 C protein_coding NM_001005165.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906143 T C 0 222 0 0.3222 0.3578 0.402 0.3641 0.4085 0.316 0.341209 0.394567 0.421904 1 3432 47307 4135 3045 2598 28155 351 5591 2 10402 121226 11472 8628 6614 66696 908 16506 0.821254 0 . 0 . 80 24,16,25,14 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y207|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.305731 rs11823809 -0.693144 0.365992 80 R224 312 Aga/Cga LOW 1 SILENT CODING OR52E4 C protein_coding NM_001005165.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906192 A C 0 228 0 0.8835 0.8003 0.7579 0.8254 0.7992 0.6933 0.869605 0.815684 0.788059 2 9074 95543 8588 7089 5538 52908 724 11622 2 10404 121284 11484 8640 6614 66722 908 16512 0 . 0 . 0 114 0,0,63,40 SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R224|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1453435,rs386532499 -0.693147 0.0455332 114 F227L 312 ttT/ttG MODERATE 1 MISSENSE CODING OR52E4 G protein_coding NM_001005165.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906203 T G 0 222 0 0.3207 0.3578 0.402 0.3641 0.4085 0.318 0.339618 0.394028 0.421904 1 3423 47331 4136 3045 2596 28153 351 5627 2 10404 121270 11484 8630 6610 66722 908 16512 0.999674 0 . 0 . 127 34,25,34,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F227L|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.313763 rs11823828 -0.693147 0.0461023 127 R228H 312 cGc/cAc MODERATE 1 MISSENSE CODING OR52E4 A protein_coding NM_001005165.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906205 G A 0 222 0 0.4894 0.4223 0.3516 0.4613 0.3907 0.3742 0.473194 0.402109 0.365689 1 4987 47538 4436 4039 2940 24747 372 6017 2 10404 121278 11488 8636 6614 66716 908 16512 0.572754 0 . 0 . 123 35,21,32,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R228H|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.674379 rs4757987 -0.693147 0.0390541 123 F257L 312 Ttt/Ctt MODERATE 1 MISSENSE CODING OR52E4 C protein_coding NM_001005165.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5906291 T C 0 222 0 0.3207 0.3574 0.402 0.3641 0.4085 0.316 0.339618 0.393951 0.421788 1 3424 47283 4129 3047 2598 28144 351 5590 2 10400 121182 11456 8636 6606 66672 908 16504 0.994081 0 . 0 . 107 21,25,20,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F257L|312|OR52E4|protein_coding|CODING|NM_001005165.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.892796 rs11823842 -0.693146 0.0119183 107 M51T 315 aTg/aCg MODERATE 1 MISSENSE CODING OR56A3 C protein_coding NM_001003443.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5968728 T C 0 222 0 0.4871 0.5609 0.6412 0.6548 0.5408 0.5276 0.509995 0.543482 0.560638 1 5156 68687 7405 5550 3613 37413 510 9040 2 10406 121380 11572 8638 6610 66734 908 16512 0.972862 0 . 0 . 104 28,24,31,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M51T|315|OR56A3|protein_coding|CODING|NM_001003443.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.739912 rs1840178,rs386546370 -0.693147 0.290039 104 V144 313 gtC/gtT LOW 1 SILENT CODING OR56A5 A protein_coding NM_001146033.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5989293 G A 0 222 0 0.1989 0.2282 0.2233 0.2133 0.2883 0.2249 0.214595 0.259308 0.278755 1 2135 29489 2525 1680 1820 17246 227 3856 2 8188 98102 8254 6600 5828 54030 784 14418 0.739124 0 . 0 . 140 34,21,44,31 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V144|313|OR56A5|protein_coding|CODING|NM_001146033.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.56289 rs7113548 -0.693147 0.43718 140 V104M 313 Gtg/Atg MODERATE 1 MISSENSE CODING OR56A5 T protein_coding NM_001146033.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 5989415 C T 0 222 0 0.733 0.4718 0.3444 0.3194 0.3897 0.4509 0.718931 0.541174 0.463859 1 7099 48488 3977 2764 2537 24681 348 7082 2 10398 121138 11532 8620 6610 66578 906 16494 0.643294 0 . 0 . 159 41,29,36,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V104M|313|OR56A5|protein_coding|CODING|NM_001146033.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985338 rs7114672 -0.693147 0.931809 159 W297R 329 Tgg/Cgg MODERATE 1 MISSENSE CODING OR52L1 G protein_coding NM_001005173.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007272 A G 0 222 0 0.7821 0.8291 0.8703 0.8681 0.8489 0.8027 0.787901 0.812332 0.824375 1 7579 100438 10487 7471 5388 55290 741 13482 2 9688 119880 11456 8578 6574 66264 890 16430 0.990212 0 . 0 . 192 57,30,57,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W297R|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.852945 rs4237768 -0.693147 0.0364272 192 A255 329 gcG/gcA LOW 1 SILENT CODING OR52L1 T protein_coding NM_001005173.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007396 C T 0 222 0 0.0091 0.0825 0.0764 0.1171 0.0706 0.1626 0.0221687 0.0682504 0.0909199 1 203 10231 549 944 435 5680 74 2346 2 9804 120762 11574 8620 6614 66738 900 16512 0.434709 0 . 0 . 163 28,52,30,45 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A255|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.991026 0.984048 0 0.0867894 rs61732631 -0.693147 0.0631014 163 K183T 329 aAa/aCa MODERATE 1 MISSENSE CODING OR52L1 G protein_coding NM_001005173.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007613 T G 0 222 0 0.4206 0.7123 0.8228 0.8671 0.8171 0.7607 0.515703 0.70214 0.791977 1 4796 94861 10298 7506 5159 53538 700 12864 2 9810 120754 11572 8620 6614 66728 898 16512 0.912804 0 . 0 . 149 32,39,43,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K183T|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.990191 0.989053 0 0.709424 rs4354673 -0.693147 0.577093 149 C161R 329 Tgc/Cgc MODERATE 1 MISSENSE CODING OR52L1 G protein_coding NM_001005173.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007680 A G 0 222 0 0.562 0.7506 0.8357 0.8631 0.8171 0.7607 0.625984 0.739193 0.794083 1 5901 96004 10354 7472 5159 53545 708 12865 2 9812 120738 11566 8620 6614 66718 896 16512 0.793082 0 . 0 COSM429356,COSM429357 170 45,19,66,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C161R|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.9054 0.997782 0 0.795897 rs4436524 -0.693147 0.688437 170 C140R 329 Tgc/Cgc MODERATE 1 MISSENSE CODING OR52L1 G protein_coding NM_001005173.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007743 A G 0 222 0 0.7428 0.8009 0.853 0.8681 0.7863 0.7883 0.738813 0.755714 0.763985 1 7221 95253 10228 7452 4947 51607 692 13106 2 9778 120252 11482 8570 6588 66440 896 16498 0.990213 0 . 0 . 209 58,25,73,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C140R|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.808113 0.958406 0 0.993519 rs4436525 -0.693147 0.135889 209 S130L 329 tCa/tTa MODERATE 1 MISSENSE CODING OR52L1 A protein_coding NM_001005173.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6007772 G A 0 222 0 0.1543 0.1228 0.085 0.1171 0.0746 0.1626 0.137643 0.106923 0.091755 1 1467 11602 611 944 433 5724 79 2344 2 9778 120198 11452 8582 6590 66450 894 16452 0.52698 0 . 0 . 224 80,47,55,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S130L|329|OR52L1|protein_coding|CODING|NM_001005173.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.932018 0.912555 0 0.515962 rs61750896 -0.693147 0.0853916 224 V180 318 gtC/gtG LOW 1 SILENT CODING OR56A1 C protein_coding NM_001001917.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6048395 G C 0 222 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 27 0 27 0 0 0 0 2 10404 121380 11572 8652 6612 66724 908 16508 0.990929 0 . 0 . 135 33,31,33,27 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V180|318|OR56A1|protein_coding|CODING|NM_001001917.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.713015 rs200181037 -0.693147 0.362942 135 P277S 319 Cct/Tct MODERATE 1 MISSENSE CODING OR56B4 T protein_coding NM_001005181.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6129837 C T 0 222 0 0.1029 0.504 0.6023 0.8839 0.4463 0.6442 0.17174 0.357627 0.452863 1 1703 61624 8375 7360 3319 30420 465 9982 2 10404 121376 11566 8648 6610 66730 908 16510 0.683477 0 . 0 . 111 39,22,23,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P277S|319|OR56B4|protein_coding|CODING|NM_001005181.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.883989 rs1462983 -0.693146 0.756845 111 H239R 320 cAt/cGt MODERATE 1 MISSENSE CODING OR52W1 G protein_coding NM_001005178.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6221169 A G 0 228 0 0.2481 0.6783 0.7522 0.9593 0.7932 0.7996 0.329169 0.622749 0.773161 2 3261 91764 9635 8359 5008 51654 698 13149 2 10406 121402 11576 8654 6612 66734 908 16512 0 . 0 . 0 112 0,0,50,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H239R|320|OR52W1|protein_coding|CODING|NM_001005178.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10839531 -0.693147 0.30142 112 L254Q 320 cTg/cAg MODERATE 1 MISSENSE CODING OR52W1 A protein_coding NM_001005178.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6221214 T A 0 228 0 0.2133 0.5699 0.598 0.7976 0.7475 0.6145 0.302135 0.589118 0.73615 2 2989 82483 7052 6944 4759 49725 648 10366 2 10406 121380 11566 8642 6612 66734 908 16512 0 . 0 . 0 123 0,0,59,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cAg|L254Q|320|OR52W1|protein_coding|CODING|NM_001005178.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11040799 -0.693147 0.00875938 123 P242S 333 Cct/Tct MODERATE 2 MISSENSE CODING C11orf42 T protein_coding NM_173525.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6231731 C T 0 228 0 0.3555 0.6172 0.719 0.8135 0.7535 0.5562 0.440482 0.640834 0.743482 2 4447 85347 9374 6869 4757 49814 665 9421 2 10360 121134 11574 8640 6612 66586 906 16456 0 . 0 . 0 88 0,0,57,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P242S|333|C11orf42|protein_coding|CODING|NM_173525.2|2|T),DOWNSTREAM(MODIFIER||833||986|FAM160A2|protein_coding|CODING|NM_032127.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769671,rs386515044 -0.693147 0.779374 88 Y353 986 taT/taC LOW 6 SILENT CODING FAM160A2 G protein_coding NM_032127.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6243804 A G 0 228 0 0.3555 0.728 0.8055 0.9593 0.8161 0.8476 0.417765 0.675543 0.807612 2 4209 96184 10296 8352 5084 53826 729 13688 2 10396 121390 11578 8654 6612 66730 908 16512 0 . 0 . 0 160 0,0,40,112 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y353|986|FAM160A2|protein_coding|CODING|NM_032127.3|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3750945 -0.693147 0.000223271 160 986 LOW 5 CODING FAM160A2 G protein_coding NM_032127.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6243843 C G 0 228 0 0.4682 0.7602 0.8228 0.9593 0.8161 0.8476 0.529305 0.713791 0.80831 2 5370 97394 10343 8348 5082 53823 739 13689 2 10394 121318 11564 8650 6608 66684 908 16510 0 . 0 . 0 102 0,0,19,76 SPLICE_SITE_REGION+INTRON(LOW||||986|FAM160A2|protein_coding|CODING|NM_032127.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3750946 -0.693147 0.607723 102 447 51 MODIFIER 1 CODING CCKBR G protein_coding NM_176875.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6281108 T G 0 153 0 0.6604 0.8233 0.8559 0.9653 0.8469 0.8497 0.747117 0.804423 0.833093 2 398 3424 148 198 54 1606 36 984 2 594 4230 170 208 64 1952 42 1200 0 . 0 . 0 8 0,0,7,1 UTR_5_PRIME(MODIFIER||51||447|CCKBR|protein_coding|CODING|NM_176875.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2929180 -0.651104 0.480966 8 447 64 MODIFIER 5 CODING CCKBR G protein_coding NM_176875.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6292837 C G 0 228 0 0.6346 0.8197 0.8617 0.9504 0.8648 0.8589 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,3,18 UTR_3_PRIME(MODIFIER||64||447|CCKBR|protein_coding|CODING|NM_176875.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10839535 -0.692352 0.129063 21 447 65 MODIFIER 5 CODING CCKBR A protein_coding NM_176875.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6292838 G A 0 228 0 0.6362 0.8339 0.8804 0.9504 0.9125 0.8671 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,3,18 UTR_3_PRIME(MODIFIER||65||447|CCKBR|protein_coding|CODING|NM_176875.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10839536 -0.692352 0.129063 21 447 377 MODIFIER 5 CODING CCKBR C protein_coding NM_176875.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6293150 T C 0 228 0 0.9576 0.9888 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 130 0,0,95,24 UTR_3_PRIME(MODIFIER||377||447|CCKBR|protein_coding|CODING|NM_176875.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7944010 -0.693147 0.00317881 130 447 409 MODIFIER 5 CODING CCKBR C protein_coding NM_176875.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6293182 A C 0 222 0 0.5877 0.477 0.5447 0.4563 0.3847 0.3957 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999138 0 . 0 . 169 59,29,42,25 UTR_3_PRIME(MODIFIER||409||447|CCKBR|protein_coding|CODING|NM_176875.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.857526 rs1042047 -0.693147 0.39644 169 A218 261 gcT/gcA LOW 2 SILENT CODING PRKCDBP T protein_coding NM_145040.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6340525 A T 0 228 0 0.5537 0.6548 0.5937 0.7341 0.7097 0.6963 0.559573 0.643638 0.686699 2 5368 80937 6288 6456 4976 45825 617 11407 2 9608 117844 11472 8466 6592 65026 886 15794 0 . 0 . COSM1162642 52 0,0,9,41 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A218|261|PRKCDBP|protein_coding|CODING|NM_145040.2|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12570 -0.693147 0.21529 52 L158P 261 cTg/cCg MODERATE 2 MISSENSE CODING PRKCDBP G protein_coding NM_145040.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6340706 A G 0 222 0 0.3873 0.528 0.4726 0.623 0.5805 0.6053 0.395624 0.491363 0.540326 1 3569 63298 4979 5423 3905 35189 471 9762 2 8576 112028 11006 8300 6014 61584 824 15724 0.598743 0 . 0 COSM429498 69 29,7,20,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L158P|261|PRKCDBP|protein_coding|CODING|NM_145040.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994293 rs1051992 -0.692976 0.65921 69 G114 261 ggG/ggA LOW 1 SILENT CODING PRKCDBP T protein_coding NM_145040.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6341365 C T 0 222 0 0.0416 0.0865 0.0951 0.1438 0.1064 0.0613 0.0488383 0.0882447 0.108179 1 350 9502 863 1015 420 5985 66 803 2 4888 74544 7418 5740 3052 42196 524 10726 0.872811 0 . 0 COSM429499 70 5,18,13,31 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G114|261|PRKCDBP|protein_coding|CODING|NM_145040.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.684001 rs11544764 -0.693146 0.0352563 70 R8P 261 cGg/cCg MODERATE 1 MISSENSE CODING PRKCDBP G protein_coding NM_145040.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6341684 C G 0 181 0 0.8578 0.9465 0.9683 1 0.9682 0.9734 0.890837 0.943959 0.971332 2 6953 96727 10769 8208 5215 55816 659 9107 2 7926 99826 10942 8210 5242 57346 680 9480 0 . 0 . 0 9 0,0,6,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R8P|261|PRKCDBP|protein_coding|CODING|NM_145040.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2682123 -0.651104 0.169891 9 V36A 631 gTg/gCg MODERATE 1 MISSENSE CODING SMPD1 C protein_coding NM_000543.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6411935 T C 0 228 0 0.202 0.5613 0.6729 0.8075 0.5905 0.684 0.240512 0.454595 0.564915 2 1947 61590 8324 6365 3348 31853 455 9298 2 8382 110368 11062 8132 5824 60060 812 16096 0 2 benign 0 COSM1561695,COSM1561696 38 0,0,18,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V36A|631|SMPD1|protein_coding|CODING|NM_000543.4|1|C),DOWNSTREAM(MODIFIER||4419||710|APBB1|protein_coding|CODING|NM_001164.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1050228 -0.693136 0.587161 38 P332R 631 cCc/cGc MODERATE 2 MISSENSE CODING SMPD1 G protein_coding NM_000543.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6413290 C G 0 222 0 0 0.0017971 0 0.0089 0 0 0 . 0 1 1 52 2 45 0 2 0 2 2 10380 121280 11570 8644 6600 66668 908 16510 0.831669 0 . 0 . 78 19,19,19,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P332R|631|SMPD1|protein_coding|CODING|NM_000543.4|2|G),DOWNSTREAM(MODIFIER||3064||710|APBB1|protein_coding|CODING|NM_001164.4||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.461392 rs202081954 -0.69312 0.783805 78 4753 83 MODIFIER 3 CODING DNHD1 G protein_coding NM_144666.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6519363 C G 0 201 0 0.7542 0.5038 0.5274 0.1627 0.5606 0.4417 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.536915 0 . 0 . 34 16,3,9,3 UTR_5_PRIME(MODIFIER||83||4753|DNHD1|protein_coding|CODING|NM_144666.2|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.979651 rs2723645,rs386426010 -0.680642 0.850567 34 R66Q 4753 cGa/cAa MODERATE 3 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6519642 G A 0 222 0 0.3306 0.3806 0.4942 0.1587 0.5378 0.4346 0.347796 0.46406 0.523627 1 3588 55964 6012 1386 2765 34540 393 7280 2 10374 121302 11570 8628 6612 66702 906 16510 0.998896 0 . 0 . 48 11,12,6,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R66Q|4753|DNHD1|protein_coding|CODING|NM_144666.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786443 rs11604149 -0.692352 0.4348 48 L190 4753 ctG/ctT LOW 3 SILENT CODING DNHD1 T protein_coding NM_144666.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6520015 G T 0 222 0 0.3238 0.3774 0.4928 0.1587 0.5378 0.4284 0.345979 0.463291 0.523394 1 3567 55911 6010 1386 2765 34540 393 7250 2 10406 121354 11570 8640 6608 66714 906 16510 0.999646 0 . 0 . 68 19,8,29,9 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L190|4753|DNHD1|protein_coding|CODING|NM_144666.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958022 rs11040899 -0.693143 0.0236384 68 V240E 4753 gTg/gAg MODERATE 3 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6520164 T A 0 222 0 0.6982 0.4884 0.5231 0.1627 0.5606 0.4417 0.645616 0.579498 0.545624 1 6823 61084 6259 1416 2955 35802 414 7415 2 10392 119846 11554 8628 6602 66320 894 15456 0.96482 0 . 0 . 69 9,21,5,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V240E|4753|DNHD1|protein_coding|CODING|NM_144666.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0394718 rs2555158 -0.69312 0.125633 69 F363 4753 ttC/ttT LOW 5 SILENT CODING DNHD1 T protein_coding NM_144666.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6530278 C T 0 222 0 0.1377 0.2192 0.3199 0.128 0.3519 0.2157 0.166515 0.27428 0.329493 1 1716 35509 4587 1167 1927 22257 245 3610 2 10406 121406 11574 8654 6612 66740 908 16512 0.999928 0 . 0 . 192 43,50,31,51 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F363|4753|DNHD1|protein_coding|CODING|NM_144666.2|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999972 rs10839568 -0.693147 0.373238 192 H418Y 4753 Cac/Tac MODERATE 7 MISSENSE CODING DNHD1 T protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6532519 C T 0 222 0 0.1377 0.2204 0.3199 0.128 0.3549 0.2188 0.166742 0.274357 0.329493 1 1717 35539 4594 1168 1929 22274 244 3613 2 10406 121338 11574 8652 6612 66694 908 16492 0.852288 0 . 0 COSM1179744,COSM1179745 140 35,27,31,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H418Y|4753|DNHD1|protein_coding|CODING|NM_144666.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930269 rs4758423 -0.693147 0.216215 140 D622A 4753 gAc/gCc MODERATE 11 MISSENSE CODING DNHD1 C protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6549779 A C 0 222 0 0.6944 0.73 0.6585 0.874 0.6302 0.7832 0.689306 0.677179 0.671904 1 1489 14349 278 545 24 5785 148 6080 2 2172 19842 410 622 36 8510 190 7902 0.952992 0 . 0 . 110 28,21,24,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D622A|4753|DNHD1|protein_coding|CODING|NM_144666.2|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.655186 rs4633449 -0.693147 0.156036 110 N694S 4753 aAt/aGt MODERATE 11 MISSENSE CODING DNHD1 G protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6549995 A G 0 222 0 0.6831 0.7254 0.6571 0.87 0.6302 0.7802 0.677023 0.674113 0.672847 1 1473 14326 278 539 23 5815 149 6049 2 2192 19900 410 620 34 8538 192 7914 0.621463 0 . 0 COSM1355950 67 13,21,10,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N694S|4753|DNHD1|protein_coding|CODING|NM_144666.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.678237 rs7480644 -0.693097 0.265959 67 Q697R 4753 cAg/cGg MODERATE 11 MISSENSE CODING DNHD1 G protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6550004 A G 0 222 0 0.6944 0.73 0.6585 0.874 0.6302 0.7832 0.690029 0.678055 0.672847 1 1491 14359 278 541 23 5801 148 6077 2 2180 19864 410 618 34 8518 190 7914 0.891505 0 . 0 COSM1355951 62 10,22,11,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q697R|4753|DNHD1|protein_coding|CODING|NM_144666.2|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.881578 rs2344828 -0.693021 0.14257 62 G769R 4753 Ggg/Agg MODERATE 12 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6550309 G A 0 222 0 0.6422 0.7153 0.6527 0.874 0.6292 0.7832 0.645954 0.66382 0.67159 1 1389 14253 276 545 23 5791 148 6081 2 2190 19896 410 622 34 8536 190 7914 0.158332 0 . 0 . 110 19,32,15,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G769R|4753|DNHD1|protein_coding|CODING|NM_144666.2|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.871284 rs2344829,rs386488570 -0.693147 0.0131214 110 D987G 4753 gAc/gGc MODERATE 14 MISSENSE CODING DNHD1 G protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6555365 A G 0 228 0 0.7806 0.867 0.9107 0.9167 0.8877 0.8804 0.770231 0.839685 0.869893 2 1653 16668 353 560 32 7124 160 6786 2 2092 19372 396 608 34 8164 190 7888 0 . 0 . 0 60 0,0,20,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D987G|4753|DNHD1|protein_coding|CODING|NM_144666.2|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7103810 -0.693147 0.163249 60 V2374M 4753 Gtg/Atg MODERATE 24 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6569896 G A 0 222 0 0.0832 0.127 0.1729 0.0228 0.1829 0.2035 0.0982659 0.165353 0.194532 1 202 3910 65 18 4 1753 40 1828 2 2140 19800 410 622 34 8492 190 7912 0.922451 0 . 0 . 70 25,12,16,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V2374M|4753|DNHD1|protein_coding|CODING|NM_144666.2|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.765061 rs11606889 -0.692914 0.525439 70 H2861N 4753 Cac/Aac MODERATE 25 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6579106 C A 0 222 0 0.0582 0.2386 0.304 0.2242 0.3897 0.2955 0 . 0 1 190 5793 122 122 6 3022 50 2281 2 1902 18802 378 534 26 7880 186 7896 0.970968 0 . 0 . 77 17,19,17,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H2861N|4753|DNHD1|protein_coding|CODING|NM_144666.2|25|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.928145 rs11040920 -0.693141 0.0348919 77 D3313N 4753 Gat/Aat MODERATE 31 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6585007 G A 0 222 0 0.0734 0.4357 0.4654 0.7212 0.4742 0.5706 0.139451 0.382173 0.487744 1 263 9736 201 439 15 4137 111 4570 2 2090 19576 402 602 28 8380 190 7884 0.719884 0 . 0 . 89 25,18,26,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D3313N|4753|DNHD1|protein_coding|CODING|NM_144666.2|31|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.84024 rs11040923,rs386516391 -0.693146 0.556028 89 R3830H 4753 cGt/cAt MODERATE 36 MISSENSE CODING DNHD1 A protein_coding NM_144666.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6588228 G A 0 222 0 0.0734 0.233 0.3098 0.2222 0.4095 0.2239 0.110891 0.295433 0.384698 1 1062 39837 4204 2108 1952 26503 279 3729 2 9800 120556 11518 8596 6604 66644 896 16498 0.932598 0 . 0 . 146 39,30,40,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R3830H|4753|DNHD1|protein_coding|CODING|NM_144666.2|36|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99476 rs10769699 -0.693147 0.62096 146 N194 456 aaC/aaT LOW 3 SILENT CODING RRP8 A protein_coding NM_015324.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6622714 G A 0 222 0 0.3911 0.739 0.7925 0.9137 0.8598 0.8671 0.475239 0.729414 0.859637 1 4608 99307 9868 7576 5154 57196 746 14159 2 10286 121148 11574 8648 6614 66610 906 16510 0.064389 0 . 0 . 43 11,11,12,8 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N194|456|RRP8|protein_coding|CODING|NM_015324.3|3|A),UPSTREAM(MODIFIER||2224||452|ILK|protein_coding|CODING|NM_001014794.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984581 rs2288283 -0.692067 0.555673 43 A306 452 gcC/gcT LOW 10 SILENT CODING ILK T protein_coding NM_001014794.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6631016 C T 0 222 0 0.1256 0.1601 0.2219 0.0833 0.2575 0.1421 0.154475 0.227336 0.264665 1 1583 27542 2829 956 1926 17308 204 2736 2 10404 121394 11578 8648 6612 66734 908 16510 0.846371 2 benign 0 . 117 26,26,23,26 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A306|452|ILK|protein_coding|CODING|NM_001014794.2|10|T),DOWNSTREAM(MODIFIER||1032||218|TAF10|protein_coding|CODING|NM_006284.3||T),DOWNSTREAM(MODIFIER||2981||563|TPP1|protein_coding|CODING|NM_000391.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.447988 rs2292195 -0.693147 0.00670256 117 T179 218 acG/acA LOW 4 SILENT CODING TAF10 T protein_coding NM_006284.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6632450 C T 0 222 0 0.0825 0.1414 0.1974 0.0833 0.2406 0.1391 0.125625 0.200631 0.23906 1 1249 25438 2658 956 1882 15818 194 2681 2 10280 121142 11562 8650 6606 66632 906 16506 0.921781 0 . 0 . 92 20,25,24,15 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T179|218|TAF10|protein_coding|CODING|NM_006284.3|4|T),DOWNSTREAM(MODIFIER||345||452|ILK|protein_coding|CODING|NM_001014794.2||T),DOWNSTREAM(MODIFIER||1547||563|TPP1|protein_coding|CODING|NM_000391.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974185 rs12451 -0.693144 0.00668156 92 563 1628 MODIFIER 13 CODING TPP1 T protein_coding NM_000391.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6634149 C T 0 222 0 0.7988 0.8103 0.7839 0.9087 0.7535 0.8016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980544 0 . 0 . 109 31,22,20,21 UTR_3_PRIME(MODIFIER||1628||563|TPP1|protein_coding|CODING|NM_000391.3|13|T),UPSTREAM(MODIFIER||674||218|TAF10|protein_coding|CODING|NM_006284.3||T),DOWNSTREAM(MODIFIER||2044||452|ILK|protein_coding|CODING|NM_001014794.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.951175 rs7488 -0.693145 0.547191 109 563 1588 MODIFIER 13 CODING TPP1 A protein_coding NM_000391.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6634189 G A 0 222 0 0.1672 0.4489 0.5432 0.5486 0.5736 0.5317 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999824 0 . 0 . 105 15,39,13,28 UTR_3_PRIME(MODIFIER||1588||563|TPP1|protein_coding|CODING|NM_000391.3|13|A),UPSTREAM(MODIFIER||714||218|TAF10|protein_coding|CODING|NM_006284.3||A),DOWNSTREAM(MODIFIER||2084||452|ILK|protein_coding|CODING|NM_001014794.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997962 rs7487 -0.693145 0.0595416 105 H634 3298 caC/caT LOW 3 SILENT CODING DCHS1 A protein_coding NM_003737.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6655433 G A 0 222 0 0.2572 0.3464 0.3631 0.4296 0.3777 0.3374 0.290095 0.347468 0.376862 1 2892 45423 4047 3892 2553 26330 329 5380 2 10400 121134 11566 8610 6612 66658 904 16384 0.998034 0 . 0 . 51 12,8,16,12 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H634|3298|DCHS1|protein_coding|CODING|NM_003737.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990804 rs997263 -0.693054 0.0738999 51 R353Q 3298 cGa/cAa MODERATE 2 MISSENSE CODING DCHS1 T protein_coding NM_003737.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6661787 C T 0 222 0 0 0.011382 0 0.0546 0 0.002 0.000681508 0.000230876 0 1 5 366 1 331 0 7 4 18 2 10346 120884 11566 8596 6610 66358 900 16508 0.965119 0 . 0 . 63 20,13,13,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R353Q|3298|DCHS1|protein_coding|CODING|NM_003737.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984826 rs139223913 -0.692717 0.843773 63 R299G 316 Cgg/Ggg MODERATE 1 MISSENSE CODING OR2AG2 C protein_coding NM_001004490.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6789294 G C 0 228 0 0.4887 0.2562 0.0836 0.1538 0.1024 0.3282 0.42617 0.207865 0.0960196 2 4457 17445 670 1252 359 6267 110 4330 2 10404 121236 11576 8624 6614 66652 908 16458 0.982906 0 . 0 . 135 1,1,88,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Ggg|R299G|316|OR2AG2|protein_coding|CODING|NM_001004490.1|1|C) 1 0 . 0 . 1 0 1 1 0 59 0 0.991453 0.995795 0 0.611111 rs7924459 -0.693147 0.0627756 135 R54P 316 cGg/cCg MODERATE 1 MISSENSE CODING OR2AG2 G protein_coding NM_001004490.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6790028 C G 0 228 0 0.3654 0.2885 0.1671 0.2143 0.2157 0.4223 0.340981 0.260967 0.219972 2 3547 28999 1544 1761 932 14331 211 6673 2 10404 121376 11574 8634 6612 66734 908 16510 0 . 0 . 0 103 0,0,37,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R54P|316|OR2AG2|protein_coding|CODING|NM_001004490.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.975178 0 . rs10839616 -0.693147 0.123289 103 Y28C 316 tAt/tGt MODERATE 1 MISSENSE CODING OR2AG2 C protein_coding NM_001004490.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6790106 T C 0 228 0 0.9002 0.8772 0.8415 0.9286 0.8141 0.8834 0.901636 0.855857 0.832402 2 9372 103623 9683 8163 5534 55494 781 14596 2 10406 121374 11572 8644 6612 66724 908 16508 0 . 0 . 0 87 0,0,36,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y28C|316|OR2AG2|protein_coding|CODING|NM_001004490.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386607438,rs7102536 -0.693147 0.131211 87 316 LOW 1 CODING OR2AG1 A protein_coding NM_001004489.2 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6807243 G A 0 222 0 0.534 0.5659 0.4928 0.6329 0.6312 0.5245 0.544525 0.579113 0.596834 1 5674 66134 4750 5507 4273 38466 521 6943 2 10230 114756 11308 8468 6532 64662 848 12708 0.918688 0 . 0 . 68 11,26,5,21 SPLICE_SITE_REGION(LOW||||316|OR2AG1|protein_coding|CODING|NM_001004489.2|1|A),UTR_3_PRIME(MODIFIER||24||316|OR2AG1|protein_coding|CODING|NM_001004489.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.64567 rs497681 -0.692976 0.0068 68 316 24 MODIFIER 1 CODING OR2AG1 A protein_coding NM_001004489.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6807243 G A 0 222 0 0.534 0.5659 0.4928 0.6329 0.6312 0.5245 0.544525 0.579113 0.596834 1 5674 66134 4750 5507 4273 38466 521 6943 2 10230 114756 11308 8468 6532 64662 848 12708 0.918688 0 . 0 . 68 11,26,5,21 SPLICE_SITE_REGION(LOW||||316|OR2AG1|protein_coding|CODING|NM_001004489.2|1|A),UTR_3_PRIME(MODIFIER||24||316|OR2AG1|protein_coding|CODING|NM_001004489.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.64567 rs497681 -0.692976 0.0068 68 S54 327 tcT/tcC LOW 1 SILENT CODING OR6A2 G protein_coding NM_003696.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6816778 A G 0 228 0 0.4781 0.6943 0.5922 0.8224 0.8032 0.8149 0.521808 0.685008 0.768622 2 5488 88639 6053 7229 4977 50821 714 13357 2 10404 121330 11528 8642 6610 66726 908 16512 0 . 0 . COSM1179746 240 0,0,134,86 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S54|327|OR6A2|protein_coding|CODING|NM_003696.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs866347 -0.693147 0.0715107 240 A22V 327 gCg/gTg MODERATE 1 MISSENSE CODING OR6A2 A protein_coding NM_003696.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6816875 G A 0 228 0 0.1906 0.3129 0.2695 0.4623 0.2932 0.3753 0.222172 0.261274 0.281308 2 2332 36271 3254 4169 1520 18685 266 6045 2 10406 121268 11518 8616 6608 66700 908 16512 1 0 . 0 . 286 1,0,139,113 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A22V|327|OR6A2|protein_coding|CODING|NM_003696.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7122644 -0.693147 0.0244784 286 I240T 303 aTa/aCa MODERATE 1 MISSENSE CODING OR10A2 C protein_coding NM_001004460.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6891704 T C 0 228 0 0.205 0.3109 0.2882 0.4067 0.325 0.3569 0.236483 0.268509 0.284916 2 2401 36640 3259 3729 2217 19212 263 5559 2 10406 121382 11570 8642 6612 66732 908 16512 0.934615 0 . 0 . 281 1,1,90,170 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I240T|303|OR10A2|protein_coding|CODING|NM_001004460.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.855769 rs10839632 -0.693147 0.000305097 281 R262Q 315 cGa/cAa MODERATE 1 MISSENSE CODING OR10A4 A protein_coding NM_207186.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6898663 G A 0 228 0 0.2042 0.3091 0.2882 0.3988 0.325 0.3569 0.236256 0.26797 0.284218 2 2398 36480 3249 3694 2216 19143 261 5519 2 10388 121304 11560 8638 6612 66694 906 16506 0 . 0 . 0 78 0,0,31,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R262Q|315|OR10A4|protein_coding|CODING|NM_207186.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10839635 -0.693147 0.724471 78 I163T 308 aTa/aCa MODERATE 1 MISSENSE CODING OR2D2 G protein_coding NM_003700.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6913244 A G 0 228 0 0.7995 0.9445 0.9841 1 0.998 1 0.845525 0.945898 0.997323 2 8674 119204 11364 8638 6612 66509 897 16510 2 10394 121212 11460 8638 6612 66688 908 16512 0 . 0 . 0 82 0,0,55,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I163T|308|OR2D2|protein_coding|CODING|NM_003700.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1965208 -0.693147 0.145067 82 R155W 330 Cgg/Tgg MODERATE 1 MISSENSE CODING OR2D3 T protein_coding NM_001004684.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6942695 C T 0 228 0 0.0408 0.1709 0.17 0.2143 0.1581 0.316 0.0695139 0.14145 0.178305 2 677 22875 2157 1784 1167 12038 173 4879 2 10402 120754 11570 8640 6614 66490 908 16130 0 . 0 . COSM147132 52 0,0,29,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R155W|330|OR2D3|protein_coding|CODING|NM_001004684.1|1|T),UPSTREAM(MODIFIER||4959||517|ZNF215|protein_coding|CODING|NM_013250.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12806437 -0.693147 0.279345 52 G260 517 ggA/ggT LOW 7 SILENT CODING ZNF215 T protein_coding NM_013250.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6976988 A T 0 228 0 0.4418 0.6761 0.7911 0.7133 0.7227 0.8252 0.494548 0.657842 0.741504 2 5080 88771 9529 6349 4800 49049 656 13308 2 10312 120898 11570 8644 6614 66554 904 16300 0 . 0 . 0 53 0,0,44,9 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G260|517|ZNF215|protein_coding|CODING|NM_013250.2|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2239731 -0.693147 0.216331 53 517 686 MODIFIER 7 CODING ZNF215 G protein_coding NM_013250.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 6978448 A G 0 9.7 0 0.2194 0.3618 0.4265 0.3641 0.3549 0.5133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||686||517|ZNF215|protein_coding|CODING|NM_013250.2|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10742995,rs386427592 -0.379885 0 1 606 464 MODIFIER 3 CODING ZNF214 G protein_coding NM_013249.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7020629 A G 0 109 0 0.7345 0.9179 0.9741 1 0.9751 0.9826 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,0 UTR_3_PRIME(MODIFIER||464||606|ZNF214|protein_coding|CODING|NM_013249.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1388526 -0.556411 0.077463 5 606 406 MODIFIER 3 CODING ZNF214 T protein_coding NM_013249.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7020687 C T 0 9.7 0 0.7254 0.9093 0.964 1 0.9712 0.9622 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||406||606|ZNF214|protein_coding|CODING|NM_013249.2|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1352860 -0.379885 0 1 606 173 MODIFIER 3 CODING ZNF214 A protein_coding NM_013249.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7020920 T A 0 135 0 0.143 0.2113 0.2939 0.1458 0.3191 0.2014 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.00606994 0 . 0 . 48 29,0,18,0 UTR_3_PRIME(MODIFIER||173||606|ZNF214|protein_coding|CODING|NM_013249.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.478257 rs2252765 -0.691153 0.0608116 48 C252R 606 Tgt/Cgt MODERATE 3 MISSENSE CODING ZNF214 G protein_coding NM_013249.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7022160 A G 0 228 0 0.7269 0.9095 0.964 1 0.9712 0.9611 0.745797 0.893489 0.969157 2 7678 115160 11048 8639 6563 64562 864 15806 2 10336 121070 11476 8644 6610 66598 908 16498 0 . 0 . 0 28 0,0,13,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C252R|606|ZNF214|protein_coding|CODING|NM_013249.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2857919,rs386575530 -0.693021 0.184973 28 I185R 606 aTa/aGa MODERATE 3 MISSENSE CODING ZNF214 C protein_coding NM_013249.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7022360 A C 0 222 0 0.0378 0.1042 0.1542 0.128 0.1083 0.1299 0.0595455 0.0850785 0.0981602 1 571 12642 2640 911 734 6044 78 1664 2 10134 120878 11442 8640 6606 66640 908 16508 0.808782 0 . 0 . 85 23,19,19,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aGa|I185R|606|ZNF214|protein_coding|CODING|NM_013249.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988005 rs2239734 -0.693139 0.746663 85 L128H 606 cTc/cAc MODERATE 3 MISSENSE CODING ZNF214 T protein_coding NM_013249.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7022531 A T 0 222 0 0.357 0.5757 0.6268 0.7073 0.6223 0.6513 0.4005 0.554649 0.633644 1 3862 76003 6989 6447 4826 42376 582 10921 2 10396 121294 11518 8648 6612 66704 908 16508 0.423576 0 . 0 . 50 19,7,7,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cAc|L128H|606|ZNF214|protein_coding|CODING|NM_013249.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.73959 rs1156525 -0.692831 0.36166 50 Y66C 606 tAc/tGc MODERATE 3 MISSENSE CODING ZNF214 C protein_coding NM_013249.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7022717 T C 0 222 0 0.416 0.5927 0.6354 0.7073 0.6223 0.6524 0.412994 0.550031 0.620256 1 4317 76436 7024 6447 4826 42312 581 10929 2 10284 120886 11512 8636 6610 66432 906 16506 0.999277 0 . 0 . 57 8,21,9,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y66C|606|ZNF214|protein_coding|CODING|NM_013249.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.897127 rs1156526 -0.692562 0.191273 57 N48T 1093 aAt/aCt MODERATE 2 MISSENSE CODING NLRP14 C protein_coding NM_176822.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7059960 A C 0 228 0 0.8752 0.9661 0.9928 1 1 1 0.893685 0.963676 0.999534 2 9194 120105 11519 8654 6614 66712 902 16510 2 10366 121366 11578 8654 6614 66736 908 16510 0 . 0 . 0 71 0,0,25,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aCt|N48T|1093|NLRP14|protein_coding|CODING|NM_176822.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12801277 -0.693147 0.0099249 71 K92R 1093 aAa/aGa MODERATE 2 MISSENSE CODING NLRP14 G protein_coding NM_176822.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7060092 A G 0 222 0 0.0038 0.0815 0.0533 0.2133 0.0258 0.1278 0.00840527 0.0246268 0.0329376 1 98 7658 1083 1720 334 2373 39 2011 2 9886 119370 11454 8588 6576 65956 884 16026 0.923539 0 . 0 COSM147135,COSM147134 52 12,14,14,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K92R|1093|NLRP14|protein_coding|CODING|NM_176822.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.923539 rs16921697 -0.692067 0.0382082 52 F166 1093 ttC/ttT LOW 4 SILENT CODING NLRP14 T protein_coding NM_176822.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7063755 C T 0 228 0 0.8533 0.9593 0.9885 1 0.998 1 0.871876 0.955056 0.997672 2 8953 119698 11489 8654 6614 66577 901 16510 2 10346 121352 11578 8654 6614 66740 908 16512 0 . 0 . 0 77 0,0,30,44 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F166|1093|NLRP14|protein_coding|CODING|NM_176822.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7123944 -0.693147 0.274555 77 E751 1093 gaG/gaA LOW 6 SILENT CODING NLRP14 A protein_coding NM_176822.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7071031 G A 0 228 0 0.764 0.9351 0.9827 1 0.999 1 0.794866 0.929737 0.998836 2 8190 119005 11469 8654 6614 66679 894 16505 2 10406 121406 11578 8654 6614 66734 908 16512 0 . 0 . 0 127 0,0,57,54 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E751|1093|NLRP14|protein_coding|CODING|NM_176822.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1552726,rs386537365 -0.693147 0.00772175 127 E808K 1093 Gag/Aag MODERATE 7 MISSENSE CODING NLRP14 A protein_coding NM_176822.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7079038 G A 0 222 0 0.3502 0.5659 0.6124 0.7063 0.6024 0.6421 0.360745 0.511236 0.588338 1 3787 73429 7008 6475 4677 40233 563 10686 2 10404 121342 11548 8650 6608 66716 908 16508 0.972148 0 . 0 . 231 80,28,64,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E808K|1093|NLRP14|protein_coding|CODING|NM_176822.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.41715 rs10839708 -0.693147 0.0935223 231 A4 392 gcG/gcA LOW 1 SILENT CODING RBMXL2 A protein_coding NM_014469.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7110363 G A 0 222 0 0.1437 0.3173 0.2954 0.4385 0.3648 0.3937 0.152204 0.273973 0.336359 1 1514 41911 3833 3912 3097 23249 332 5974 2 8930 112826 10748 8332 6228 62142 842 15604 0.789832 0 . 0 . 281 96,42,80,29 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4|392|RBMXL2|protein_coding|CODING|NM_014469.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622904 rs4758158 -0.693147 0.0465589 281 D117 491 gaT/gaC LOW 2 SILENT CODING SYT9 C protein_coding NM_175733.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7324475 T C 0 228 0 0.9168 0.9778 0.9986 1 1 1 0.941617 0.980068 0.999767 2 9716 120688 11558 8654 6614 66734 903 16509 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 123 0,0,49,64 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D117|491|SYT9|protein_coding|CODING|NM_175733.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4412741 -0.693147 0.245727 123 491 310 MODIFIER 7 CODING SYT9 G protein_coding NM_175733.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7488341 A G 0 228 0 0.941 0.862 0.8458 0.7917 0.8449 0.8569 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 80 0,0,58,13 UTR_3_PRIME(MODIFIER||310||491|SYT9|protein_coding|CODING|NM_175733.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4344466 -0.693147 0.318424 80 491 841 MODIFIER 7 CODING SYT9 T protein_coding NM_175733.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7488872 C T 0 31.9 0 0.4342 0.4748 0.6239 0.3056 0.5179 0.5542 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||841||491|SYT9|protein_coding|CODING|NM_175733.3|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10732509 -0.453602 0.1 3 491 896 MODIFIER 7 CODING SYT9 C protein_coding NM_175733.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7488927 A C 0 59 0 0.4357 0.4762 0.6254 0.3095 0.5179 0.5542 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,1 UTR_3_PRIME(MODIFIER||896||491|SYT9|protein_coding|CODING|NM_175733.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10732510 -0.511536 0.748679 4 491 1409 MODIFIER 7 CODING SYT9 T protein_coding NM_175733.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7489440 C T 0 177 0 0.851 0.8195 0.8184 0.7887 0.7883 0.8415 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,2,7 UTR_3_PRIME(MODIFIER||1409||491|SYT9|protein_coding|CODING|NM_175733.3|7|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4408288 -0.662043 0.286826 9 491 1788 MODIFIER 7 CODING SYT9 C protein_coding NM_175733.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7489819 A C 0 228 0 0.6248 0.5439 0.6542 0.3145 0.5706 0.5654 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,26,18 UTR_3_PRIME(MODIFIER||1788||491|SYT9|protein_coding|CODING|NM_175733.3|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4351800 -0.693146 0.168626 51 E113V 402 gAa/gTa MODERATE 2 MISSENSE CODING OLFML1 T protein_coding NM_198474.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7509566 A T 0 222 0 0.1271 0.1663 0.2219 0.1558 0.1889 0.1677 0.131531 0.156534 0.169344 1 1374 21494 3077 1387 1381 11767 138 2370 2 10394 121184 11540 8616 6608 66648 908 16470 0.579128 0 . 0 . 170 33,41,31,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E113V|402|OLFML1|protein_coding|CODING|NM_198474.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974139 rs12805648 -0.693147 0.0918824 170 402 89 MODIFIER 3 CODING OLFML1 G protein_coding NM_198474.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7531508 C G 0 156 0 0.1165 0.1196 0.1513 0.0843 0.0507 0.2086 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.620251 0 . 0 . 19 1,9,2,6 UTR_3_PRIME(MODIFIER||89||402|OLFML1|protein_coding|CODING|NM_198474.3|3|G),UPSTREAM(MODIFIER||3488||876|PPFIBP2|protein_coding|CODING|NM_003621.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.513192 rs77933621 -0.651104 0.325119 19 402 525 MODIFIER 3 CODING OLFML1 G protein_coding NM_198474.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7531944 A G 0 9.7 0 0.1392 0.1258 0.1542 0.0843 0.0507 0.2076 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||525||402|OLFML1|protein_coding|CODING|NM_198474.3|3|G),UPSTREAM(MODIFIER||3052||876|PPFIBP2|protein_coding|CODING|NM_003621.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs116974989 -0.379885 0 1 876 35607 MODIFIER 1 CODING PPFIBP2 T protein_coding NM_003621.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7535100 C T 0 23.7 0 0.031 0.0867 0.1282 0.0813 0.0278 0.1984 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||35607||876|PPFIBP2|protein_coding|CODING|NM_003621.3|1|T),DOWNSTREAM(MODIFIER||2494||402|OLFML1|protein_coding|CODING|NM_198474.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs76835853 -0.379885 0 2 876 35593 MODIFIER 1 CODING PPFIBP2 T protein_coding NM_003621.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7535114 C T 0 23.7 0 0.0098 0.0797 0.1254 0.0774 0.0268 0.1984 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 START_GAINED(LOW||||876|PPFIBP2|protein_coding|CODING|NM_003621.3|1|T),UTR_5_PRIME(MODIFIER||35593||876|PPFIBP2|protein_coding|CODING|NM_003621.3|1|T),DOWNSTREAM(MODIFIER||2508||402|OLFML1|protein_coding|CODING|NM_198474.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs117105713 -0.379885 0 2 D466 876 gaC/gaT LOW 16 SILENT CODING PPFIBP2 T protein_coding NM_003621.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7662732 C T 0 222 0 0.7905 0.6665 0.6182 0.5813 0.6431 0.6452 0.788505 0.707711 0.666318 1 8122 80374 6906 4785 4419 44361 609 11172 2 10406 121358 11574 8638 6610 66716 906 16508 0.928449 0 . 0 . 90 35,8,34,5 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D466|876|PPFIBP2|protein_coding|CODING|NM_003621.3|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.826441 rs4643071 -0.693144 0.0591275 90 876 LOW 18 CODING PPFIBP2 C protein_coding NM_003621.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7669775 G C 0 222 0 0.2088 0.1488 0.0807 0.126 0.1362 0.1524 0.193776 0.158073 0.139781 1 1965 16534 912 1216 691 9323 135 2292 2 10404 121288 11574 8642 6612 66684 908 16464 0.984508 0 . 0 . 42 9,13,9,9 SPLICE_SITE_REGION+INTRON(LOW||||876|PPFIBP2|protein_coding|CODING|NM_003621.3|18|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.881193 rs4758007 -0.691153 0.0122969 42 R658G 876 Aga/Gga MODERATE 20 MISSENSE CODING PPFIBP2 G protein_coding NM_003621.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7670440 A G 0 228 0 0.9977 0.9994 1 1 1 1 0.995002 0.998307 1 2 10369 121372 11578 8654 6614 66737 908 16512 2 10404 121408 11578 8654 6614 66738 908 16512 0 . 0 . 0 67 0,0,22,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R658G|876|PPFIBP2|protein_coding|CODING|NM_003621.3|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4758209 -0.693147 0.000356841 67 E792 876 gaG/gaA LOW 23 SILENT CODING PPFIBP2 A protein_coding NM_003621.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7673015 G A 0 222 0 0.7466 0.6605 0.6138 0.6012 0.6392 0.6605 0.734893 0.689934 0.666899 1 7598 80209 6860 4997 4417 44389 606 11342 2 10404 121368 11574 8638 6610 66728 908 16506 0.645528 0 . 0 . 139 34,24,39,25 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E792|876|PPFIBP2|protein_coding|CODING|NM_003621.3|23|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.815712 rs5864 -0.693147 0.0490482 139 276 112 MODIFIER 9 CODING CYB5R2 C protein_coding NM_001302826.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7686493 G C 0 115 0 0.2458 0.1735 0.1196 0.12 0.1869 0.1554 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.447858 0 . 0 . 61 35,1,24,0 UTR_3_PRIME(MODIFIER||112||276|CYB5R2|protein_coding|CODING|NM_001302826.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.636453 rs11758 -0.692831 0.0105325 61 276 9 MODIFIER 9 CODING CYB5R2 A protein_coding NM_001302826.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7686596 G A 0 228 0 0.8381 0.7684 0.6686 0.7708 0.7604 0.7505 0.828033 0.779591 0.754772 2 6342 55934 3397 3940 3046 32412 407 6390 2 7640 72668 5190 5280 3734 42100 528 8196 0.198936 0 . 0 . 142 2,1,86,40 UTR_3_PRIME(MODIFIER||9||276|CYB5R2|protein_coding|CODING|NM_001302826.1|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.363815 rs13172 -0.693147 0.00175439 142 L254 276 ctA/ctG LOW 9 SILENT CODING CYB5R2 C protein_coding NM_001302826.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7686674 T C 0 228 0 0.854 0.7736 0.67 0.7728 0.7604 0.7526 0.853476 0.796829 0.767807 2 8698 91816 7244 6490 5195 50808 701 12680 2 10278 118862 11106 8510 6342 65622 884 16120 0.515789 0 . 0 . 104 1,1,19,76 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L254|276|CYB5R2|protein_coding|CODING|NM_001302826.1|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.821053 rs13854 -0.693147 0.101676 104 N209D 276 Aac/Gac MODERATE 8 MISSENSE CODING CYB5R2 C protein_coding NM_001302826.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7687715 T C 0 228 0 0.8525 0.7863 0.6787 0.8165 0.7634 0.7658 0.852113 0.798215 0.770601 2 8770 93866 7450 6835 5400 51585 717 13109 2 10406 121376 11568 8652 6612 66720 906 16512 0 . 0 . 0 88 0,0,35,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N209D|276|CYB5R2|protein_coding|CODING|NM_001302826.1|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12801394 -0.693147 0.370214 88 276 1199 MODIFIER 1 CODING CYB5R2 C protein_coding NM_001302826.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7695255 T C 0 9.7 0 0.348 0.143 0.0461 0.1052 0.0467 0.0726 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1199||276|CYB5R2|protein_coding|CODING|NM_001302826.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4536203 -0.379885 0 1 E559 565 gaA/gaG LOW 16 SILENT CODING OVCH2 C protein_coding NM_198185.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7711207 T C 0 222 0 0.2784 0.1727 0.1383 0.1587 0.1392 0.1033 0 . 0 1 136 1633 28 31 0 673 14 751 2 528 12152 180 188 2 3514 132 7608 0.962921 0 . 0 . 82 18,24,13,16 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E559|565|OVCH2|protein_coding|CODING|NM_198185.4|16|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.898751 rs35699890 -0.693079 0.577545 82 T539I 565 aCa/aTa MODERATE 15 MISSENSE CODING OVCH2 A protein_coding NM_198185.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7712523 G A 0 222 0 0.2791 0.1683 0.1369 0.1577 0.1382 0.0828 0.251058 0.17969 0.146887 1 2507 17409 1478 1324 1109 9369 144 1478 2 8988 106552 9620 7348 6060 59394 800 14342 0.749748 0 . 0 . 65 10,18,17,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T539I|565|OVCH2|protein_coding|CODING|NM_198185.4|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.596208 rs4633461 -0.69311 0.854437 65 Q526H 565 caA/caT MODERATE 15 MISSENSE CODING OVCH2 A protein_coding NM_198185.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7712561 T A 0 222 0 0.2776 0.1719 0.1383 0.1627 0.1382 0.0971 0.247673 0.178689 0.146448 1 2556 18063 1520 1393 1143 9584 149 1718 2 9772 120132 11442 8598 6572 66486 890 16372 0.990063 0 . 0 . 71 13,18,18,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q526H|565|OVCH2|protein_coding|CODING|NM_198185.4|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.858464 rs4519083 -0.693136 0.00816466 71 N410Y 565 Aat/Tat MODERATE 12 MISSENSE CODING OVCH2 A protein_coding NM_198185.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7716855 T A 0 228 0 0.8517 0.9563 0.9697 1 0.998 1 0.872259 0.96002 0.999265 2 8446 119138 11457 8622 6614 66614 885 16500 2 9788 120660 11548 8622 6614 66690 896 16502 0 . 0 . 0 97 0,0,40,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N410Y|565|OVCH2|protein_coding|CODING|NM_198185.4|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4528317 -0.693147 0.0275244 97 P292S 565 Ccc/Tcc MODERATE 7 MISSENSE CODING OVCH2 A protein_coding NM_198185.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7721870 G A 0 228 0 0.5666 0.8444 0.9063 0.999 0.9513 0.907 0.64856 0.849902 0.945524 2 6066 110334 11023 8611 6218 62716 819 14881 2 9776 120502 11492 8612 6604 66638 896 16484 0 . 0 . 0 119 0,0,59,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P292S|565|OVCH2|protein_coding|CODING|NM_198185.4|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10839849 -0.693147 0.00708466 119 R19Q 565 cGa/cAa MODERATE 1 MISSENSE CODING OVCH2 T protein_coding NM_198185.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7727886 C T 0 222 0 0.205 0.4032 0.5144 0.4157 0.3728 0.6104 0.243982 0.328736 0.366699 1 1851 34928 3910 2564 2241 17237 298 6827 2 6176 74058 6364 5414 4460 39356 608 11680 0.973538 0 . 0 COSM429902 76 22,19,13,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R19Q|565|OVCH2|protein_coding|CODING|NM_198185.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.415559 rs7927138 -0.692976 0.135672 76 V104 311 gtA/gtG LOW 1 SILENT CODING OR5P3 C protein_coding NM_153445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7847208 T C 0 222 0 0.0711 0.4435 0.5937 0.4762 0.6292 0.6155 0.169488 0.474622 0.629888 1 1586 70351 7459 4192 4396 42045 563 10110 2 10330 121304 11578 8624 6614 66740 908 16510 0.891132 0 . 0 . 203 55,50,45,41 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V104|311|OR5P3|protein_coding|CODING|NM_153445.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.533641 rs1482791 -0.693147 0.222168 203 S18 311 tcT/tcC LOW 1 SILENT CODING OR5P3 G protein_coding NM_153445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7847466 A G 0 158 0 0.7292 0.8065 0.938 0.6091 0.9553 0.8681 0.786633 0.899536 0.956923 1 6887 106270 11031 5322 6531 61438 811 14250 2 8860 116546 11496 8540 6606 64136 878 16030 0.982233 0 . 0 . 40 0,20,1,19 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S18|311|OR5P3|protein_coding|CODING|NM_153445.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.430449 rs1482792 -0.692067 0.69615 40 G16 311 ggG/ggA LOW 1 SILENT CODING OR5P3 T protein_coding NM_153445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7847472 C T 0 159 0 0.0726 0.4439 0.5937 0.4762 0.6292 0.6155 0.166667 0.465023 0.616293 1 1306 67667 7381 4109 4391 40239 545 9696 2 8482 114998 11446 8526 6606 63592 862 15484 0.838087 0 . 0 . 33 0,16,1,16 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G16|311|OR5P3|protein_coding|CODING|NM_153445.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983911 rs1482793 -0.690438 0.65404 33 L287P 314 cTg/cCg MODERATE 1 MISSENSE CODING OR10A6 G protein_coding NM_001004461.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7949350 A G 0 228 0 0.7504 0.7877 0.8545 0.7619 0.7982 0.8067 0.737392 0.765507 0.779912 2 7760 96050 9760 6901 5478 52274 699 13178 2 10406 121282 11490 8638 6610 66718 908 16512 1 0 . 0 . 225 0,1,127,87 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L287P|314|OR10A6|protein_coding|CODING|NM_001004461.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4758258 -0.693147 0.364666 225 V140G 314 gTt/gGt MODERATE 1 MISSENSE CODING OR10A6 C protein_coding NM_001004461.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7949791 A C 0 222 0 0.3351 0.4131 0.3833 0.494 0.4264 0.4427 0.331967 0.377388 0.400605 1 3385 50166 4187 4460 2844 27258 391 7641 2 9876 120180 11388 8600 6600 66338 902 16476 0.768436 0 . 0 . 127 45,28,30,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V140G|314|OR10A6|protein_coding|CODING|NM_001004461.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.734863 rs7933807 -0.693147 0.344979 127 A117V 314 gCa/gTa MODERATE 1 MISSENSE CODING OR10A6 A protein_coding NM_001004461.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7949860 G A 0 222 0 0.2685 0.3944 0.3761 0.494 0.4254 0.4427 0.278055 0.360705 0.403049 1 2901 49795 4202 4470 2845 27337 392 7648 2 10272 121080 11492 8634 6610 66654 908 16510 0.954434 0 . 0 . 224 81,25,58,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A117V|314|OR10A6|protein_coding|CODING|NM_001004461.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999996 rs7928451 -0.693147 0.0250204 224 F62 314 ttT/ttC LOW 1 SILENT CODING OR10A6 G protein_coding NM_001004461.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 7950024 A G 0 222 0 0.2617 0.3333 0.4568 0.2698 0.3718 0.3681 0.285552 0.345544 0.37628 1 2930 44196 5472 2428 2635 24871 298 5562 2 10384 121200 11504 8634 6612 66656 906 16504 0.597719 0 . 0 . 159 31,32,42,38 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F62|314|OR10A6|protein_coding|CODING|NM_001004461.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.250839 rs12272735 -0.693147 0.022651 159 H187 357 caC/caT LOW 4 SILENT CODING EIF3F T protein_coding NM_003754.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8014479 C T 0 222 0 0.4909 0.6883 0.8112 0.8353 0.7207 0.683 0.516811 0.655687 0.726839 1 5283 86730 9311 7224 4532 48312 636 11432 2 10392 121346 11574 8644 6610 66716 906 16504 0.531734 0 . 0 . 83 17,30,8,25 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H187|357|EIF3F|protein_coding|CODING|NM_003754.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.261862 rs4758267 -0.693127 0.65475 83 G175 561 ggT/ggC LOW 5 SILENT CODING TUB C protein_coding NM_003320.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8115699 T C 0 222 0 0.3805 0.3988 0.4467 0.5258 0.2555 0.4059 0.345298 0.314992 0.299465 1 3608 43142 6587 4642 1752 19385 308 6860 2 10310 120454 11516 8610 6526 66236 894 16362 0.625784 0 . 0 . 67 25,10,19,9 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G175|561|TUB|protein_coding|CODING|NM_003320.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.421742 rs4758289 -0.693054 0.331404 67 369 2949 MODIFIER 6 CODING RIC3 A protein_coding NM_001206671.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8129296 C A 0 70 0 0.0325 0.3908 0.4164 0.4702 0.6789 0.4785 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2949||369|RIC3|protein_coding|CODING|NM_001206671.2|6|A),DOWNSTREAM(MODIFIER||1642||561|TUB|protein_coding|CODING|NM_003320.4||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4758042 -0.453602 0.98 3 369 1320 MODIFIER 6 CODING RIC3 A protein_coding NM_001206671.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8130925 G A 0 9.7 0 0.997 0.999 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1320||369|RIC3|protein_coding|CODING|NM_001206671.2|6|A),DOWNSTREAM(MODIFIER||3271||561|TUB|protein_coding|CODING|NM_003320.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7481825 -0.379885 0 1 L118 369 ctC/ctA LOW 3 SILENT CODING RIC3 T protein_coding NM_001206671.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8159892 G T 0 222 0 0.2799 0.3035 0.3444 0.4196 0.2197 0.273 0.270104 0.24596 0.233589 1 2753 32662 4070 3895 1584 15679 236 4445 2 10406 121366 11556 8640 6612 66732 908 16512 0.733441 0 . 0 . 94 13,32,8,29 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L118|369|RIC3|protein_coding|CODING|NM_001206671.2|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966534 rs10839976 -0.693141 0.0901181 94 156 72 MODIFIER 1 CODING LMO1 C protein_coding NM_002315.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8284981 A C 0 228 0 0.9501 0.9864 0.9971 1 1 1 0.953788 0.985014 0.998379 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 174 0,0,111,38 UTR_5_PRIME(MODIFIER||72||156|LMO1|protein_coding|CODING|NM_002315.2|1|C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs176083 -0.693147 0.00201871 174 156 86 MODIFIER 1 CODING LMO1 C protein_coding NM_002315.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8284995 T C 0 228 0 0.5635 0.866 0.951 1 0.9732 0.9663 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 190 0,0,113,54 UTR_5_PRIME(MODIFIER||86||156|LMO1|protein_coding|CODING|NM_002315.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs204929 -0.693147 0.012561 190 156 215 MODIFIER 1 CODING LMO1 C protein_coding NM_002315.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8285124 A C 0 228 0 0.3699 0.6627 0.7219 0.7649 0.7664 0.8047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 93 0,0,3,88 UTR_5_PRIME(MODIFIER||215||156|LMO1|protein_coding|CODING|NM_002315.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2071458 -0.693147 0.199574 93 514 187 MODIFIER 13 CODING STK33 C protein_coding NM_001289061.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8413870 T C 0 67 0 0.8056 0.646 0.4452 0.5883 0.5427 0.7382 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.765017 0 . 0 . 13 7,1,5,0 UTR_3_PRIME(MODIFIER||187||514|STK33|protein_coding|CODING|NM_001289061.1|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.989343 rs749263 -0.590765 0.181959 13 A437T 514 Gcc/Acc MODERATE 12 MISSENSE CODING STK33 T protein_coding NM_001289061.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8435077 C T 0 222 0 0.1142 0.2496 0.2565 0.2877 0.2545 0.3834 0.0113585 0.0263968 0.0341015 1 1511 31156 3129 2735 1128 16493 239 5921 2 10406 121382 11572 8650 6614 66724 908 16508 0.473288 0 . 0 . 101 39,3,36,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A437T|514|STK33|protein_coding|CODING|NM_001289061.1|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.196123 rs3751095 -0.693147 0.563091 101 D436E 514 gaT/gaG MODERATE 12 MISSENSE CODING STK33 C protein_coding NM_001289061.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8435078 A C 0 222 0 0.1142 0.2496 0.2565 0.2877 0.2545 0.3834 0.0154475 0.0286286 0.0353817 1 1511 31154 3127 2737 1128 16490 239 5922 2 10406 121390 11568 8652 6614 66732 908 16510 0.590908 0 . 0 . 103 41,3,35,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D436E|514|STK33|protein_coding|CODING|NM_001289061.1|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.375763 rs3751096 -0.693147 0.503978 103 A133 514 gcG/gcT LOW 4 SILENT CODING STK33 A protein_coding NM_001289061.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8486310 C A 0 222 0 0.3411 0.4451 0.3703 0.4871 0.4245 0.6166 0.329169 0.382253 0.409451 1 3385 52290 4534 4601 2207 27905 417 9241 2 10402 121342 11552 8654 6608 66708 908 16510 0.773538 0 . 0 COSM147138 137 12,30,27,49 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A133|514|STK33|protein_coding|CODING|NM_001289061.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.865834 rs1446464 -0.693147 1.70869e-06 137 514 64 MODIFIER 2 CODING STK33 A protein_coding NM_001289061.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8496516 G A 0 213 0 0.6354 0.5467 0.6167 0.5149 0.5736 0.3824 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999368 0 . 0 . 49 2,27,3,13 UTR_5_PRIME(MODIFIER||64||514|STK33|protein_coding|CODING|NM_001289061.1|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99993 rs2289923 -0.689466 0.413935 49 514 LOW 2 CODING STK33 C protein_coding NM_001289061.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8496611 G C 0 110 0 0.2912 0.4028 0.5216 0.4593 0.496 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.888889 0 . 0 . 11 0,2,0,9 SPLICE_SITE_REGION(LOW||||514|STK33|protein_coding|CODING|NM_001289061.1|2|C),START_GAINED(LOW||||514|STK33|protein_coding|CODING|NM_001289061.1|2|C),UTR_5_PRIME(MODIFIER||159||514|STK33|protein_coding|CODING|NM_001289061.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.444444 rs2289921 -0.662043 0.0046443 11 514 159 MODIFIER 2 CODING STK33 C protein_coding NM_001289061.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8496611 G C 0 110 0 0.2912 0.4028 0.5216 0.4593 0.496 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.888889 0 . 0 . 11 0,2,0,9 SPLICE_SITE_REGION(LOW||||514|STK33|protein_coding|CODING|NM_001289061.1|2|C),START_GAINED(LOW||||514|STK33|protein_coding|CODING|NM_001289061.1|2|C),UTR_5_PRIME(MODIFIER||159||514|STK33|protein_coding|CODING|NM_001289061.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.444444 rs2289921 -0.662043 0.0046443 11 1216 3335 MODIFIER 20 CODING TRIM66 A protein_coding NM_014818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8636156 T A 0 83 0 0.7557 0.8237 0.8372 0.7649 0.8728 0.9162 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,0 UTR_3_PRIME(MODIFIER||3335||1216|TRIM66|protein_coding|CODING|NM_014818.1|20|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10734634 -0.453602 0.52 4 1216 2300 MODIFIER 20 CODING TRIM66 C protein_coding NM_014818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8637191 G C 0 63 0 0.7526 0.7913 0.7839 0.7639 0.8151 0.8528 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||2300||1216|TRIM66|protein_coding|CODING|NM_014818.1|20|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1128559 -0.453602 0.84 3 1216 166 MODIFIER 20 CODING TRIM66 A protein_coding NM_014818.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8639325 G A 0 129 0 0.4705 0.5114 0.5778 0.4038 0.6223 0.5164 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.884621 0 . 0 . 25 8,0,17,0 UTR_3_PRIME(MODIFIER||166||1216|TRIM66|protein_coding|CODING|NM_014818.1|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.228397 rs4929924 -0.690438 0.0363542 25 N661H 1216 Aac/Cac MODERATE 11 MISSENSE CODING TRIM66 G protein_coding NM_014818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8646670 T G 0 222 0 0.2587 0.275 0.2061 0.3621 0.1928 0.3405 0.24422 0.200175 0.181018 1 524 4937 84 221 186 1616 46 2260 2 2094 20204 404 614 1028 8286 216 7562 0.62768 0 . 0 . 70 18,23,7,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N661H|1216|TRIM66|protein_coding|CODING|NM_014818.1|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.313829 rs7947230 -0.692831 0.132857 70 L630V 1216 Ctg/Gtg MODERATE 11 MISSENSE CODING TRIM66 C protein_coding NM_014818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8646763 G C 0 222 0 0.2746 0.3099 0.2608 0.3621 0.2505 0.3998 0 . 0 1 423 2798 77 184 394 1337 26 357 2 1390 9076 274 464 1430 4618 120 780 0.743248 0 . 0 . 48 4,20,9,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L630V|1216|TRIM66|protein_coding|CODING|NM_014818.1|11|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs7935453 -0.69168 0.318674 48 H466R 1216 cAt/cGt MODERATE 9 MISSENSE CODING TRIM66 C protein_coding NM_014818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8662090 T C 0 129 0 0.7398 0.7662 0.8256 0.7202 0.8529 0.7178 0 . 0 2 1258 14608 216 275 97 5695 135 6932 2 1426 16210 254 356 106 6344 160 7564 0 . 0 . 0 9 0,0,9,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H466R|1216|TRIM66|protein_coding|CODING|NM_014818.1|9|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs11042022 -0.662043 0.00012995 9 H324R 1216 cAc/cGc MODERATE 9 MISSENSE CODING TRIM66 C protein_coding NM_014818.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8662516 T C 0 222 0 0.5166 0.5252 0.5836 0.4028 0.6302 0.5133 0.53396 0.619361 0.656505 1 1167 12337 233 246 565 5606 125 4395 2 2176 20774 408 618 800 8658 202 7912 0.0289715 0 . 0 COSM1561936 65 24,10,19,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H324R|1216|TRIM66|protein_coding|CODING|NM_014818.1|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.431698 rs11042023 -0.692914 0.568874 65 L25 1216 ctG/ctA LOW 3 SILENT CODING TRIM66 T protein_coding NM_014818.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8671369 C T 0 222 0 0.0076 0.1482 0.2003 0.1329 0.2744 0.1871 0.050578 0.224266 0.299811 1 105 4755 79 71 391 2331 68 1710 2 2144 21680 408 618 1616 8738 242 7914 0.998103 0 . 0 . 90 24,20,18,19 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L25|1216|TRIM66|protein_coding|CODING|NM_014818.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.807361 rs10840101 -0.693141 0.33635 90 D399E 1137 gaC/gaG MODERATE 6 MISSENSE CODING ST5 C protein_coding NM_005418.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8751640 G C 0 222 0 0.121 0.2654 0.3429 0.253 0.341 0.3405 0.150613 0.258581 0.313897 1 1582 37858 3882 1968 1983 22462 304 5677 2 10406 121376 11566 8636 6614 66734 908 16512 0.684812 0 . 0 . 164 28,54,26,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D399E|1137|ST5|protein_coding|CODING|NM_005418.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947491 rs3812762 -0.693147 0.0271347 164 K316N 1137 aaG/aaC MODERATE 6 MISSENSE CODING ST5 G protein_coding NM_005418.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8751889 C G 0 186 0 0.0159 0.2802 0.4539 0.3472 0.4354 0.2853 0.0907433 0.321021 0.438709 1 731 46293 5913 3086 3655 27983 332 4593 2 8908 115628 11454 8356 6582 63890 864 15574 0.999286 0 . 0 . 21 7,3,7,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K316N|1137|ST5|protein_coding|CODING|NM_005418.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.772706 rs3794153 -0.670168 0.297266 21 210 264 MODIFIER 1 CODING AKIP1 G protein_coding NM_020642.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8932733 A G 0 108 0 0.6218 0.8952 0.9669 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,1 UTR_5_PRIME(MODIFIER||264||210|AKIP1|protein_coding|CODING|NM_020642.3|1|G),UPSTREAM(MODIFIER||235||1137|ST5|protein_coding|CODING|NM_005418.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2568026 -0.590765 0.383239 5 210 170 MODIFIER 6 CODING AKIP1 G protein_coding NM_020642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8941197 T G 0 111 0 0.1634 0.2997 0.4582 0.3155 0.4026 0.2495 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.635221 0 . 0 . 18 2,5,0,9 UTR_3_PRIME(MODIFIER||170||210|AKIP1|protein_coding|CODING|NM_020642.3|6|G),DOWNSTREAM(MODIFIER||426||467|C11orf16|protein_coding|CODING|NM_020643.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0396807 rs4910156 -0.662043 0.130321 18 210 188 MODIFIER 6 CODING AKIP1 G protein_coding NM_020642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8941215 A G 0 96 0 0.1679 0.3275 0.5086 0.3343 0.4553 0.2761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.760054 0 . 0 . 12 0,5,0,7 UTR_3_PRIME(MODIFIER||188||210|AKIP1|protein_coding|CODING|NM_020642.3|6|G),DOWNSTREAM(MODIFIER||408||467|C11orf16|protein_coding|CODING|NM_020643.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 0 . 0.6821 rs4910157 -0.636426 0.0168868 12 210 233 MODIFIER 6 CODING AKIP1 C protein_coding NM_020642.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8941260 T C 0 62 0 0.1672 0.3135 0.4942 0.3323 0.4195 0.2546 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 6 0,2,0,4 UTR_3_PRIME(MODIFIER||233||210|AKIP1|protein_coding|CODING|NM_020642.3|6|C),DOWNSTREAM(MODIFIER||363||467|C11orf16|protein_coding|CODING|NM_020643.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs4910158 -0.556411 0.573211 6 A423V 467 gCa/gTa MODERATE 6 MISSENSE CODING C11orf16 A protein_coding NM_020643.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8942999 G A 0 228 0 0.7186 0.9217 0.9741 1 0.998 1 0.761699 0.918039 0.998138 2 7882 118600 11442 8652 6614 66612 896 16502 2 10404 121406 11578 8654 6614 66738 908 16510 0 . 0 . 0 124 0,0,46,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A423V|467|C11orf16|protein_coding|CODING|NM_020643.2|6|A),DOWNSTREAM(MODIFIER||1373||210|AKIP1|protein_coding|CODING|NM_020642.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2568023 -0.693147 0.00184418 124 L398P 467 cTt/cCt MODERATE 5 MISSENSE CODING C11orf16 G protein_coding NM_020643.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8947021 A G 0 228 0 0.6029 0.8898 0.964 1 0.998 1 0.638573 0.876097 0.997789 2 6615 116915 11378 8642 6614 66302 892 16472 2 10300 120952 11578 8644 6614 66428 908 16480 0 . 0 . 0 37 0,0,28,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L398P|467|C11orf16|protein_coding|CODING|NM_020643.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2653588 -0.693132 0.0427272 37 P311A 467 Ccc/Gcc MODERATE 5 MISSENSE CODING C11orf16 C protein_coding NM_020643.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8947283 G C 0 228 0 0.2935 0.5308 0.6787 0.7093 0.6044 0.4867 0.347796 0.519701 0.607775 2 3619 71561 8656 5895 4538 39995 557 8301 2 10402 121384 11570 8650 6612 66730 908 16512 0 . 0 . 0 67 0,0,30,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P311A|467|C11orf16|protein_coding|CODING|NM_020643.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3751066 -0.693147 0.0792294 67 V210L 467 Gtc/Ctc MODERATE 5 MISSENSE CODING C11orf16 G protein_coding NM_020643.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8947586 C G 0 185 0 0.2307 0.2486 0.2003 0.377 0.1918 0.2331 0.21831 0.193012 0.180051 1 2360 25688 2667 2894 1173 12214 217 4163 2 10238 120784 11556 8624 6610 66376 904 16476 0.947528 0 . 0 . 26 5,6,2,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V210L|467|C11orf16|protein_coding|CODING|NM_020643.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0712875 rs11042127 -0.676189 0.567998 26 P122 467 ccT/ccA LOW 4 SILENT CODING C11orf16 T protein_coding NM_020643.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8948680 A T 0 228 0 0.2821 0.5276 0.6772 0.7093 0.6044 0.4867 0.333485 0.514622 0.607426 2 3478 71085 8595 5865 4516 39781 556 8294 2 10322 120816 11508 8618 6570 66414 906 16478 0 . 0 . 0 47 0,0,18,23 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccA|P122|467|C11orf16|protein_coding|CODING|NM_020643.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3751065,rs386423588 -0.693145 0.337098 47 G66 181 ggA/ggC LOW 2 SILENT CODING ASCL3 G protein_coding NM_020646.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8959511 T G 0 228 0 0.3215 0.6607 0.7176 0.9306 0.6819 0.7791 0.382326 0.596829 0.706752 2 3946 85653 9008 7832 5109 46774 660 12324 2 10392 121358 11578 8650 6610 66712 908 16508 0 . 0 . 0 80 0,0,47,28 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G66|181|ASCL3|protein_coding|CODING|NM_020646.2|2|G),UPSTREAM(MODIFIER||4958||467|C11orf16|protein_coding|CODING|NM_020643.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4910179 -0.693147 0.00553826 80 R55L 181 cGg/cTg MODERATE 2 MISSENSE CODING ASCL3 A protein_coding NM_020646.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8959545 C A 0 228 0 0.3003 0.5457 0.6916 0.7113 0.6392 0.5072 0.35711 0.546875 0.644121 2 3713 74829 8805 5890 4611 42443 567 8800 2 10402 121374 11574 8646 6612 66722 908 16510 0 . 0 . 0 80 0,0,48,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R55L|181|ASCL3|protein_coding|CODING|NM_020646.2|2|A),UPSTREAM(MODIFIER||4992||467|C11orf16|protein_coding|CODING|NM_020643.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4909951 -0.693147 0.680071 80 198 558 MODIFIER 5 CODING TMEM9B C protein_coding NM_020644.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8969309 T C 0 222 0 0.2375 0.258 0.2118 0.3829 0.2058 0.2434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.91491 0 . 0 . 63 15,15,10,13 UTR_3_PRIME(MODIFIER||558||198|TMEM9B|protein_coding|CODING|NM_020644.2|5|C),UPSTREAM(MODIFIER||4729||181|ASCL3|protein_coding|CODING|NM_020646.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.2753 rs10279 -0.692717 0.873859 63 V71 198 gtT/gtC LOW 3 SILENT CODING TMEM9B G protein_coding NM_020644.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8977830 A G 0 222 0 0.4395 0.3349 0.2363 0.4494 0.2097 0.274 0.378691 0.265969 0.208217 1 4122 30985 2842 3750 1305 14009 237 4720 2 10352 120846 11496 8604 6600 66452 908 16434 0.97289 0 . 0 . 95 25,27,17,16 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V71|198|TMEM9B|protein_coding|CODING|NM_020644.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903352 rs2568068 -0.693127 0.0286047 95 198 188 MODIFIER 1 CODING TMEM9B A protein_coding NM_020644.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 8986048 C A 0 75 0 0.4743 0.3417 0.232 0.4474 0.2068 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.62023 0 . 0 . 8 1,3,1,3 UTR_5_PRIME(MODIFIER||188||198|TMEM9B|protein_coding|CODING|NM_020644.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.868321 rs2568091 -0.556411 0.152777 8 241 2691 MODIFIER 7 CODING NRIP3 A protein_coding NM_020645.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9002401 G A 0 9.7 0 0.736 0.9261 0.9726 1 0.998 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2691||241|NRIP3|protein_coding|CODING|NM_020645.2|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2653608 -0.379885 0 1 241 1139 MODIFIER 7 CODING NRIP3 T protein_coding NM_020645.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9003953 C T 0 6.3 0 0.5885 0.6286 0.4986 0.6796 0.5795 0.773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1139||241|NRIP3|protein_coding|CODING|NM_020645.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2742471 -0.379885 0 1 241 1090 MODIFIER 7 CODING NRIP3 T protein_coding NM_020645.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9004002 C T 0 25.9 0 0.4508 0.5509 0.4726 0.6101 0.5408 0.6912 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||1090||241|NRIP3|protein_coding|CODING|NM_020645.2|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2742470 -0.453602 0.58 3 241 56 MODIFIER 7 CODING NRIP3 A protein_coding NM_020645.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9005036 T A 0 228 0 0.764 0.9339 0.9755 1 0.998 1 0.781792 0.932764 0.998429 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,21,27 UTR_3_PRIME(MODIFIER||56||241|NRIP3|protein_coding|CODING|NM_020645.2|7|A) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2568046 -0.693147 0.153501 53 971 261 MODIFIER 22 CODING SCUBE2 T protein_coding NM_020974.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9042331 G T 0 138 0 0.7844 0.8187 0.7666 0.997 0.7256 0.8139 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,1 UTR_3_PRIME(MODIFIER||261||971|SCUBE2|protein_coding|CODING|NM_020974.2|22|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1136966 -0.616816 0.763412 6 H684Q 971 caT/caG MODERATE 17 MISSENSE CODING SCUBE2 C protein_coding NM_020974.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9052423 A C 0 228 0 0.9894 0.997 0.9986 1 1 1 0.993185 0.997614 0.999884 2 10311 121248 11574 8652 6614 66690 903 16504 2 10394 121338 11576 8652 6614 66694 904 16504 0 . 0 . 0 83 0,0,17,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H684Q|971|SCUBE2|protein_coding|CODING|NM_020974.2|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7395988 -0.693147 0.00994644 83 971 LOW 6 CODING SCUBE2 G protein_coding NM_020974.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9087533 A G 0 222 0 0.3207 0.3421 0.2867 0.4137 0.2346 0.4468 0.302135 0.269201 0.252328 1 3104 36281 3267 4107 1438 16741 256 7368 2 9998 118502 11178 8548 6486 65238 882 16172 0.459693 0 . 0 . 92 7,43,9,29 SPLICE_SITE_REGION+INTRON(LOW||||971|SCUBE2|protein_coding|CODING|NM_020974.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.921502 rs2003906 -0.693143 0.743264 92 291 548 MODIFIER 7 CODING TMEM41B A protein_coding NM_015012.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9304423 G A 0 9.7 0 0.4448 0.4161 0.3646 0.5149 0.4493 0.2781 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||548||291|TMEM41B|protein_coding|CODING|NM_015012.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4343026 -0.379885 0 1 291 543 MODIFIER 7 CODING TMEM41B C protein_coding NM_015012.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9304428 T C 0 6.3 0 0.8185 0.9487 0.9784 1 0.998 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||543||291|TMEM41B|protein_coding|CODING|NM_015012.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4384389 -0.379885 0 1 I266V 291 Ata/Gta MODERATE 7 MISSENSE CODING TMEM41B C protein_coding NM_015012.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9305051 T C 0 222 0 0.0023 0.0475 0.0288 0.2123 0 0.001 0.00204452 0.00115438 0.000698324 1 19 2135 342 1689 3 26 9 47 2 10106 118264 11272 8488 6560 64724 892 16222 0.604728 0 . 0 . 65 10,25,8,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I266V|291|TMEM41B|protein_coding|CODING|NM_015012.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.590693 rs78813996 -0.692831 0.14139 65 291 LOW 2 CODING TMEM41B A protein_coding NM_015012.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9316937 G A 0 228 0 0.8101 0.9463 0.9784 0.999 0.998 1 0.827649 0.940777 0.998833 2 7253 107835 10535 8422 5990 59356 796 15483 2 8776 109540 10624 8422 5990 59438 802 15488 0 . 0 . 0 77 0,0,26,45 SPLICE_SITE_REGION+INTRON(LOW||||291|TMEM41B|protein_coding|CODING|NM_015012.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4601780 -0.693147 0.955594 77 291 83 MODIFIER 1 CODING TMEM41B G protein_coding NM_015012.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9336071 A G 0 222 0 0.2194 0.359 0.3746 0.5089 0.4533 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.96209 0 . 0 . 48 4,23,3,15 UTR_5_PRIME(MODIFIER||83||291|TMEM41B|protein_coding|CODING|NM_015012.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.191312 rs4325312 -0.691153 0.440254 48 T13 1038 acT/acC LOW 1 SILENT CODING IPO7 C protein_coding NM_006391.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9406349 T C 0 228 0 0.9349 0.9822 0.9957 1 1 1 0.949818 0.982955 0.999883 2 8127 107205 10517 8095 4706 59927 758 15075 2 8570 107692 10550 8096 4706 59934 760 15076 0 . 0 . 0 134 0,0,43,79 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T13|1038|IPO7|protein_coding|CODING|NM_006391.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4606477 -0.693147 0.0154296 134 E561Q 638 Gaa/Caa MODERATE 14 MISSENSE CODING ZNF143 C protein_coding NM_003442.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9537904 G C 0 228 0 0.9864 0.9012 0.8617 0.7788 0.9732 0.8661 0.977965 0.977906 0.977876 2 9787 108781 8120 6235 6170 63371 828 14270 2 9988 117462 10640 8334 6500 64984 880 16136 0 . 0 . 0 28 0,0,3,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E561Q|638|ZNF143|protein_coding|CODING|NM_003442.5|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10743108 -0.693054 0.482182 28 1849 963 MODIFIER 40 CODING SBF2 A protein_coding NM_030962.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 9801002 G A 0 222 0 0 0.0013978 0 0.0069 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.923907 0 . 0 . 64 23,12,19,10 UTR_3_PRIME(MODIFIER||963||1849|SBF2|protein_coding|CODING|NM_030962.3|40|A),INTRAGENIC(MODIFIER|||||SBF2-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.951017 rs144512459 -0.693079 0.114295 64 776 694 MODIFIER 15 CODING AMPD3 G protein_coding NM_000480.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10528125 A G 0 228 0 0.9092 0.9748 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 65 0,0,25,27 UTR_3_PRIME(MODIFIER||694||776|AMPD3|protein_coding|CODING|NM_000480.2|15|G),DOWNSTREAM(MODIFIER||1309||24|MTRNR2L8|protein_coding|CODING|NM_001190702.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2169594 -0.693147 0.0936892 65 776 1052 MODIFIER 15 CODING AMPD3 G protein_coding NM_000480.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10528483 A G 0 228 0 0.8238 0.9473 0.9741 1 0.9891 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,17,4 UTR_3_PRIME(MODIFIER||1052||776|AMPD3|protein_coding|CODING|NM_000480.2|15|G),DOWNSTREAM(MODIFIER||951||24|MTRNR2L8|protein_coding|CODING|NM_001190702.1||G),DOWNSTREAM(MODIFIER||4742||230|RNF141|protein_coding|CODING|NM_016422.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9292 -0.692352 0.533948 23 776 1090 MODIFIER 15 CODING AMPD3 G protein_coding NM_000480.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10528521 A G 0 228 0 0.9773 0.9934 0.9986 1 1 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,28,7 UTR_3_PRIME(MODIFIER||1090||776|AMPD3|protein_coding|CODING|NM_000480.2|15|G),DOWNSTREAM(MODIFIER||913||24|MTRNR2L8|protein_coding|CODING|NM_001190702.1||G),DOWNSTREAM(MODIFIER||4704||230|RNF141|protein_coding|CODING|NM_016422.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1037998 -0.693136 0.0546408 38 24 49 MODIFIER 1 CODING MTRNR2L8 G protein_coding NM_001190702.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10529822 A G 0 228 0 0.4501 0.2716 0.1599 0.1597 0.17 0.3292 0 . 0 2 188 3292 35 32 0 707 43 2287 2 470 10974 124 158 0 3050 128 7044 0 . 0 . 0 42 0,0,16,23 UTR_5_PRIME(MODIFIER||49||24|MTRNR2L8|protein_coding|CODING|NM_001190702.1|1|G),DOWNSTREAM(MODIFIER||696||776|AMPD3|protein_coding|CODING|NM_000480.2||G),DOWNSTREAM(MODIFIER||3403||230|RNF141|protein_coding|CODING|NM_016422.3||G),INTRAGENIC(MODIFIER|||||MIR4485||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.615601 0 . rs7350542 -0.693144 0.238323 42 230 1114 MODIFIER 6 CODING RNF141 A protein_coding NM_016422.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10535349 G A 0 9.7 0 0.4175 0.25 0.1326 0.1508 0.1471 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1114||230|RNF141|protein_coding|CODING|NM_016422.3|6|A),UPSTREAM(MODIFIER||4626||24|MTRNR2L8|protein_coding|CODING|NM_001190702.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7929890 -0.379885 0 1 230 347 MODIFIER 6 CODING RNF141 G protein_coding NM_016422.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10536116 A G 0 228 0 0.6097 0.7157 0.7277 0.8502 0.6571 0.772 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 94 0,0,47,35 UTR_3_PRIME(MODIFIER||347||230|RNF141|protein_coding|CODING|NM_016422.3|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4146830 -0.693147 0.941806 94 230 165 MODIFIER 6 CODING RNF141 C protein_coding NM_016422.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10536298 T C 0 228 0 0.388 0.243 0.1311 0.1538 0.1471 0.317 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,21,49 UTR_3_PRIME(MODIFIER||165||230|RNF141|protein_coding|CODING|NM_016422.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047730 -0.693147 0.00489461 81 A79T 912 Gcc/Acc MODERATE 3 MISSENSE CODING MRVI1 T protein_coding NM_130385.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10655609 C T 0 228 0 0.8956 0.969 0.9928 1 0.994 0.9939 0.914353 0.963291 0.985939 2 8562 112874 10983 8326 6132 62689 826 15356 2 9418 115416 11078 8330 6340 63952 850 15448 0 . 0 . 0 41 0,0,10,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A79T|912|MRVI1|protein_coding|CODING|NM_130385.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2162044 -0.693144 0.245025 41 H487 1173 caC/caT LOW 12 SILENT CODING CTR9 T protein_coding NM_014633.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10786142 C T 0 228 0 0.3154 0.6116 0.7608 0.7847 0.6014 0.7382 0.358928 0.511085 0.589078 2 3699 76041 8777 7116 4167 39297 571 12414 2 10294 119240 11372 8560 6500 65280 886 16348 0 . 0 . 0 213 0,0,132,56 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H487|1173|CTR9|protein_coding|CODING|NM_014633.4|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3736326 -0.693147 0.0263981 213 907 LOW 16 CODING EIF4G2 A protein_coding NM_001172705.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10822202 G A 0 222 0 0.1293 0.4944 0.6614 0.5764 0.5626 0.7147 0.189459 0.438645 0.566372 1 1938 69799 8052 4917 3871 38955 510 11556 2 10382 121318 11558 8648 6612 66704 908 16506 0.998046 0 . 0 . 56 19,10,15,9 SPLICE_SITE_REGION+INTRON(LOW||||907|EIF4G2|protein_coding|CODING|NM_001172705.1|16|A|WARNING_TRANSCRIPT_NO_START_CODON) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962372 rs4910190 -0.692831 0.804737 56 P524 907 ccG/ccA LOW 16 SILENT CODING EIF4G2 T protein_coding NM_001172705.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10822350 C T 0 228 0 0.9576 0.9888 1 1 1 1 0.967515 0.988992 1 2 10084 121077 11566 8654 6614 66739 908 16512 2 10404 121410 11578 8654 6614 66740 908 16512 0 . 0 . 0 72 0,0,32,31 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P524|907|EIF4G2|protein_coding|CODING|NM_001172705.1|16|T|WARNING_TRANSCRIPT_NO_START_CODON) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7951708 -0.693147 0.000464882 72 907 LOW 3 CODING EIF4G2 A protein_coding NM_001172705.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 10828361 C A 0 222 0 0.1241 0.493 0.6614 0.5734 0.5606 0.7198 0.188551 0.437875 0.565673 1 1924 69731 8043 4913 3871 38886 510 11584 2 10398 121372 11574 8652 6610 66728 906 16504 0.620809 0 . 0 . 82 24,11,9,22 SPLICE_SITE_REGION+INTRON(LOW||||907|EIF4G2|protein_coding|CODING|NM_001172705.1|3|A|WARNING_TRANSCRIPT_NO_START_CODON) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973613 rs10743151 -0.69311 0.649162 82 A437 607 gcA/gcG LOW 8 SILENT CODING GALNT18 C protein_coding NM_198516.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11354346 T C 0 222 0 0.3381 0.4347 0.4452 0.5764 0.3559 0.4928 0.341436 0.36759 0.380997 1 3513 50396 6432 5028 2742 25212 370 7099 2 10396 121290 11574 8630 6606 66670 906 16508 0.998642 0 . 0 COSM428439 98 19,30,14,32 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A437|607|GALNT18|protein_coding|CODING|NM_198516.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0222304 rs386620164,rs901553 -0.693147 0.0021067 98 T387A 391 Act/Gct MODERATE 1 MISSENSE CODING CSNK2A3 C protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373508 T C 0 228 0 0.826 0.9517 0.9856 1 0.998 1 0 . 0 2 6296 91895 8763 6246 4898 50625 674 14393 2 7504 93374 8878 6246 4898 50758 688 14402 0 . 0 . 0 67 0,0,56,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T387A|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|C),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|C) 0 . 0 . 0 1 0 . 1 0 56 0 0 0.293585 0 . rs7948121 -0.693147 0.304368 67 T360 391 acT/acC LOW 1 SILENT CODING CSNK2A3 G protein_coding NM_001256686.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373587 A G 0 228 0 0.8245 0.9513 0.9856 1 0.998 1 0 . 0 2 8932 119548 11447 8616 6612 66557 891 16493 2 10382 121270 11568 8616 6612 66682 908 16502 0 . 0 . 0 119 0,0,70,41 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T360|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|G),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|G) 0 . 0 . 0 1 0 . 1 0 58 0 0 0.326141 0 . rs7945066 -0.693147 0.496712 119 T344 391 acG/acA LOW 1 SILENT CODING CSNK2A3 T protein_coding NM_001256686.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373635 C T 0 228 0 0.8185 0.9497 0.9856 1 0.998 1 0 . 0 2 8886 119590 11455 8634 6614 66607 891 16503 2 10404 121380 11576 8634 6614 66732 908 16512 0 . 0 . 0 146 0,0,92,45 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T344|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|T),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1056963 -0.693147 0.247138 146 S287R 391 Agt/Cgt MODERATE 1 MISSENSE CODING CSNK2A3 G protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373808 T G 0 228 0 0.8124 0.9481 0.9856 1 0.998 1 0 . 0 2 8825 119532 11453 8634 6614 66611 892 16503 2 10406 121388 11576 8634 6614 66738 908 16512 0 . 0 . 0 208 0,0,91,101 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S287R|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|G),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|G) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.839404 0 . rs1056951 -0.693147 0.340089 208 F248V 391 Ttt/Gtt MODERATE 1 MISSENSE CODING CSNK2A3 C protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373925 A C 0 228 0 0.8041 0.9459 0.9856 1 0.998 1 0 . 0 2 8757 119480 11452 8650 6613 66615 892 16501 2 10404 121404 11578 8650 6614 66740 908 16510 0 . 0 . 0 282 0,0,183,83 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F248V|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|C),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4243927 -0.693147 0.602768 282 R236H 391 cGt/cAt MODERATE 1 MISSENSE CODING CSNK2A3 T protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11373960 C T 0 228 0 0.4123 0.625 0.6326 0.6607 0.7256 0.7669 0 . 0 2 4945 85497 7619 5908 5129 48430 670 12796 2 10404 121382 11578 8634 6614 66734 908 16510 0.983548 0 . 0 . 304 2,1,179,99 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R236H|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|T),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|T) 0 . 0 . 0 1 0 . 1 0 59 0 0.999943 0.997066 0 0.177069 rs2071461,rs386556348 -0.693147 0.175594 304 R217S 391 agA/agT MODERATE 1 MISSENSE CODING CSNK2A3 A protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11374016 T A 0 228 0 0.8018 0.9443 0.9856 1 0.998 0.9949 0 . 0 2 8760 119351 11452 8646 6614 66615 892 16372 2 10406 121404 11578 8646 6614 66740 908 16512 1 0 . 0 . 333 0,1,159,137 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agT|R217S|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|A),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|A) 0 . 0 . 0 1 0 . 1 0 59 0 1 0.995641 0 1 rs2896586,rs41488951 -0.693147 0.141095 333 I133T 391 aTt/aCt MODERATE 1 MISSENSE CODING CSNK2A3 G protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11374269 A G 0 228 0 0.1906 0.4205 0.4553 0.5248 0.4791 0.5389 0 . 0 2 2387 57421 5975 4883 3805 31179 441 8751 2 10406 121376 11576 8634 6612 66730 908 16510 1 0 . 0 COSN405261 203 0,1,99,86 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I133T|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|G),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|G) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs2071460,rs41334347 -0.693147 0.668199 203 L128F 391 ttA/ttC MODERATE 1 MISSENSE CODING CSNK2A3 G protein_coding NM_001256686.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11374283 T G 0 228 0 0.8048 0.9461 0.9856 1 0.998 1 0 . 0 2 8770 119489 11452 8644 6614 66616 892 16501 2 10406 121400 11578 8644 6614 66740 908 16510 0 . 0 . 0 205 0,0,108,79 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttA/ttC|L128F|391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|G),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2896585,rs41359350 -0.693147 0.349013 205 391 148 MODIFIER 1 CODING CSNK2A3 C protein_coding NM_001256686.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11374814 T C 0 169 0 0.8026 0.9453 0.9841 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,0,25 UTR_5_PRIME(MODIFIER||148||391|CSNK2A3|protein_coding|CODING|NM_001256686.1|1|C),INTRON(MODIFIER||||607|GALNT18|protein_coding|CODING|NM_198516.2|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2129524 -0.692914 0.0400588 25 G143V 1355 gGg/gTg MODERATE 4 MISSENSE CODING USP47 T protein_coding NM_001282659.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11913585 G T 0 228 0 0.9637 0.8237 0.7608 0.8562 0.7018 0.771 0.924 0.779007 0.712521 2 9130 90565 8614 7452 4877 47193 669 12630 2 9802 120728 11546 8624 6612 66732 900 16512 0 . 0 . 0 145 0,0,51,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G143V|1355|USP47|protein_coding|CODING|NM_001282659.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11022079 -0.693147 3.49859e-06 145 Q1270 1355 caG/caA LOW 27 SILENT CODING USP47 A protein_coding NM_001282659.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11976628 G A 0 222 0 0.8654 0.7143 0.8429 0.4861 0.6879 0.681 0.855234 0.726874 0.669315 1 8313 82684 10203 4171 3887 44014 636 11460 2 9798 120708 11568 8616 6608 66708 900 16510 0.833882 0 . 0 . 79 21,14,7,30 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1270|1355|USP47|protein_coding|CODING|NM_001282659.1|27|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.896454 rs7933089 -0.693141 0.387189 79 R335G 350 Agg/Ggg MODERATE 7 MISSENSE CODING DKK3 C protein_coding NM_001018057.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 11986061 T C 0 228 0 0.8154 0.8121 0.8761 0.7907 0.7575 0.8405 0.810995 0.771824 0.751747 2 8244 93418 10527 6868 4100 49179 717 13783 2 10184 120054 11548 8590 6416 65916 894 16506 0 . 0 . 0 75 0,0,50,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R335G|350|DKK3|protein_coding|CODING|NM_001018057.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3206824 -0.693147 0.700561 75 R138 1124 cgT/cgG LOW 4 SILENT CODING MICAL2 G protein_coding NM_001282663.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12225946 T G 0 222 0 0.8911 0.7011 0.7089 0.6508 0.5905 0.6043 0.836665 0.653349 0.559385 1 8785 74777 7879 5800 4315 37745 537 9716 2 10404 121376 11572 8636 6612 66734 908 16510 0.193415 0 . 0 COSM1352045 91 19,27,13,23 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgG|R138|1124|MICAL2|protein_coding|CODING|NM_001282663.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.589666 rs3763823 -0.693139 0.281524 91 R518 1124 cgG/cgC LOW 13 SILENT CODING MICAL2 C protein_coding NM_001282663.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12246233 G C 0 78 0 0.0159 0.2746 0.4035 0.5387 0.1382 0.4008 0.0452067 0.103233 0.132976 1 435 27972 5788 4569 1320 9739 188 5933 2 10314 120964 11560 8612 6608 66480 902 16488 0.935507 0 . 0 . 29 17,3,4,2 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R518|1124|MICAL2|protein_coding|CODING|NM_001282663.1|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.188876 rs3816921 -0.616816 0.0549273 29 L889 1124 ctA/ctG LOW 21 SILENT CODING MICAL2 G protein_coding NM_001282663.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12265542 A G 0 222 0 0.1551 0.2091 0.2651 0.2103 0.168 0.2832 0.180373 0.162587 0.15347 1 1785 22663 2787 1695 1245 10418 174 4559 2 10404 121384 11578 8642 6614 66730 908 16508 0.340937 0 . 0 . 83 18,17,25,14 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L889|1124|MICAL2|protein_coding|CODING|NM_001282663.1|21|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.895027 rs2270511,rs386563021 -0.693144 0.753936 83 695 5216 MODIFIER 1 CODING MICALCL G protein_coding NM_032867.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12308500 A G 0 228 0 0.6884 0.848 0.915 0.9306 0.9135 0.864 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,20,3 UTR_5_PRIME(MODIFIER||5216||695|MICALCL|protein_coding|CODING|NM_032867.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs903209 -0.692717 0.0794499 23 V70I 695 Gta/Ata MODERATE 3 MISSENSE CODING MICALCL A protein_coding NM_032867.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315186 G A 0 228 0 0.6377 0.5337 0.585 0.5952 0.3658 0.4663 0.565789 0.42427 0.357749 2 5934 53340 7814 5485 2650 23616 377 7464 2 9800 120718 11574 8610 6614 66708 900 16512 1 0 . 0 . 129 1,0,52,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V70I|695|MICALCL|protein_coding|CODING|NM_032867.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10741578 -0.693147 0.638497 129 G143 695 ggG/ggC LOW 3 SILENT CODING MICALCL C protein_coding NM_032867.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315407 G C 0 228 0 0.9191 0.9217 0.951 0.9415 0.9463 0.8589 0.926251 0.928312 0.929282 2 8999 109944 10750 8108 6356 61792 823 13116 2 9750 118666 11540 8596 6606 66162 882 15130 0 . 0 . 0 64 0,0,40,21 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G143|695|MICALCL|protein_coding|CODING|NM_032867.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10741579 -0.693147 0.31924 64 A246 695 gcC/gcT LOW 3 SILENT CODING MICALCL T protein_coding NM_032867.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315716 C T 0 228 0 0.9085 0.9227 0.9496 0.9415 0.9463 0.8793 0.916268 0.925263 0.92939 2 8753 110809 10740 8053 6351 61552 828 14532 2 9576 119546 11536 8534 6602 65914 890 16494 0 . 0 . 0 77 0,0,21,48 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A246|695|MICALCL|protein_coding|CODING|NM_032867.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1493951 -0.693147 0.0605297 77 G290 695 ggC/ggT LOW 3 SILENT CODING MICALCL T protein_coding NM_032867.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315848 C T 0 228 0 . 0 . 0 . 0 0.517986 0.381824 0.317464 2 5405 45794 6043 4583 2059 20786 317 6601 2 9726 120222 11518 8548 6604 66456 894 16476 0 . 0 . 0 50 0,0,35,11 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G290|695|MICALCL|protein_coding|CODING|NM_032867.2|3|T) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs1493952 -0.693147 0.429326 50 A305T 695 Gca/Aca MODERATE 3 MISSENSE CODING MICALCL A protein_coding NM_032867.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315891 G A 0 228 0 0.9077 0.9225 0.9496 0.9415 0.9463 0.8793 0.918321 0.925738 0.929262 2 8935 111821 10767 8124 6359 62267 835 14534 2 9786 120646 11564 8606 6610 66684 898 16498 0 . 0 . 0 65 0,0,48,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A305T|695|MICALCL|protein_coding|CODING|NM_032867.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1493953,rs386534354 -0.693147 0.226253 65 S313G 695 Agc/Ggc MODERATE 3 MISSENSE CODING MICALCL G protein_coding NM_032867.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12315915 A G 0 228 0 0.618 0.531 0.4755 0.6786 0.3429 0.4939 0.545059 0.402956 0.335871 2 5715 50194 6212 5727 2121 22253 342 7824 2 9786 120646 11560 8598 6610 66696 898 16498 0 . 0 . 0 86 0,0,61,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S313G|695|MICALCL|protein_coding|CODING|NM_032867.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1493954 -0.693147 0.260021 86 695 107 MODIFIER 9 CODING MICALCL TAA protein_coding NM_032867.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12380132 T TAA 0 228 0 0.9032 0.9018 0.9438 0.9306 0.9006 0.8415 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,4,24 UTR_3_PRIME(MODIFIER||107||695|MICALCL|protein_coding|CODING|NM_032867.2|9|TAA) 0 . 0 28 0.8 1 1 0 . 0 60 0 0 1 0 . rs3045408,rs72520150 -0.693054 0.0137588 35 R242 412 cgC/cgT LOW 6 SILENT CODING PARVA T protein_coding NM_018222.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12525925 C T 0 222 0 0.1679 0.1408 0.0778 0.1518 0.1133 0.1656 0.141945 0.13199 0.127129 1 1543 15940 607 1352 706 8906 103 2723 2 9722 119766 11422 8558 6596 66426 884 16158 0.96389 0 . 0 . 159 46,22,44,25 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R242|412|PARVA|protein_coding|CODING|NM_018222.4|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.339366 rs11547363 -0.693147 0.100729 159 412 4002 MODIFIER 13 CODING PARVA C protein_coding NM_018222.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12553474 A C 0 32.6 0 0.9115 0.9752 0.9914 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||4002||412|PARVA|protein_coding|CODING|NM_018222.4|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10734200 -0.379885 0 2 412 4509 MODIFIER 13 CODING PARVA C protein_coding NM_018222.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12553981 T C 0 46.3 0 0.8003 0.9441 0.9813 1 0.997 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||4509||412|PARVA|protein_coding|CODING|NM_018222.4|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12802339 -0.453602 0.5 2 412 5884 MODIFIER 13 CODING PARVA CTGA protein_coding NM_018222.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12555355 C CTGA 0 32.2 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5884||412|PARVA|protein_coding|CODING|NM_018222.4|13|CTGA) 0 0.5 1 1 1 0 1 0 . 0 60 0 0 . 0 . rs56689985 -0.379885 0 1 412 6136 MODIFIER 13 CODING PARVA G protein_coding NM_018222.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12555608 A G 0 9.7 0 0.8472 0.7993 0.8098 0.8105 0.6869 0.8313 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6136||412|PARVA|protein_coding|CODING|NM_018222.4|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7104689 -0.379885 0 1 D171 426 gaC/gaT LOW 8 SILENT CODING TEAD1 T protein_coding NM_021961.5 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 12903443 C T 0 228 0 0.2973 0.4337 0.2925 0.8393 0.4195 0.3149 0.315909 0.379273 0.411737 2 3277 51537 4306 7259 3431 27403 367 5494 2 10406 121372 11572 8652 6604 66720 908 16510 0 . 0 . 0 69 0,0,45,14 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D171|426|TEAD1|protein_coding|CODING|NM_021961.5|8|T|WARNING_TRANSCRIPT_NO_START_CODON) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2304733 -0.693147 0.0121615 69 515 1184 MODIFIER 12 CODING FAR1 G protein_coding NM_032228.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 13751505 A G 0 222 0 0.8139 0.7506 0.6571 0.5496 0.8111 0.8763 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.69034 0 . 0 . 136 37,19,33,20 UTR_3_PRIME(MODIFIER||1184||515|FAR1|protein_coding|CODING|NM_032228.5|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.229497 rs10766106 -0.693147 9.23261e-05 136 806 88 MODIFIER 1 CODING SPON1 T protein_coding NM_006108.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 13984364 G T 0 42.8 0 0.2216 0.2123 0.2522 0.2103 0.2167 0.1687 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.635922 0 . 0 . 13 7,1,5,0 UTR_5_PRIME(MODIFIER||88||806|SPON1|protein_coding|CODING|NM_006108.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.989343 rs7122836 -0.590765 0.618918 13 806 895 MODIFIER 16 CODING SPON1 T protein_coding NM_006108.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14288128 G T 0 9.7 0 0.0847 0.2784 0.2781 0.3998 0.341 0.3507 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||895||806|SPON1|protein_coding|CODING|NM_006108.3|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11238 -0.379885 0 1 806 1820 MODIFIER 16 CODING SPON1 T protein_coding NM_006108.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14289053 A T 0 9.7 0 0.0817 0.277 0.2767 0.3998 0.3429 0.3466 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1820||806|SPON1|protein_coding|CODING|NM_006108.3|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1043237 -0.379885 0 1 204 124 MODIFIER 6 CODING RRAS2 G protein_coding NM_012250.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14300759 C G 0 228 0 0.0817 0.2706 0.2767 0.369 0.338 0.3507 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 100 0,0,87,12 UTR_3_PRIME(MODIFIER||124||204|RRAS2|protein_coding|CODING|NM_012250.5|6|G) 0 . 0 . 0 1 0 . 0 . 45 0 0 0.0447492 0 . rs8570 -0.693147 0.103656 100 953 880 MODIFIER 1 CODING COPB1 A protein_coding NM_001144061.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14521354 C A 0 32.6 0 0.7451 0.6933 0.7262 0.6944 0.6501 0.6431 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||880||953|COPB1|protein_coding|CODING|NM_001144061.1|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2575823 -0.379885 0 2 269 38 MODIFIER 2 CODING PSMA1 C protein_coding NM_148976.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14632570 A C 0 228 0 0.6914 0.6484 0.6729 0.6786 0.5706 0.6217 0.660682 0.578688 0.536679 2 6914 71062 6977 5650 3993 36505 553 10470 2 10394 120836 11414 8600 6586 66444 906 16492 0.548872 0 . 0 . 154 1,1,83,50 UTR_5_PRIME(MODIFIER||38||269|PSMA1|protein_coding|CODING|NM_148976.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.319549 rs1403247 -0.693147 1.6063e-05 154 R463 1112 agA/agG LOW 4 SILENT CODING PDE3B G protein_coding NM_000922.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14810762 A G 0 228 0 0.708 0.6713 0.7017 0.6806 0.6173 0.6462 0.677045 0.630736 0.60701 2 7100 76033 7193 5627 4226 40423 598 10866 2 10388 120854 11404 8578 6596 66516 906 16466 0 . 0 . COSM147149 158 0,0,50,90 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R463|1112|PDE3B|protein_coding|CODING|NM_000922.3|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4757268 -0.693147 0.00155133 158 1112 840 MODIFIER 16 CODING PDE3B A protein_coding NM_000922.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14892046 G A 0 228 0 0.9569 0.9882 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,16,31 UTR_3_PRIME(MODIFIER||840||1112|PDE3B|protein_coding|CODING|NM_000922.3|16|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1247720 -0.693147 0.126353 56 1112 859 MODIFIER 16 CODING PDE3B C protein_coding NM_000922.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14892065 T C 0 228 0 0.9569 0.9882 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,7,27 UTR_3_PRIME(MODIFIER||859||1112|PDE3B|protein_coding|CODING|NM_000922.3|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1247719 -0.693132 0.216735 38 S59 501 tcC/tcT LOW 1 SILENT CODING CYP2R1 A protein_coding NM_024514.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14913575 G A 0 228 0 0.1029 0.3492 0.5144 0.3681 0.4473 0.4448 0.145455 0.341623 0.442129 2 1428 48785 5253 3144 2611 28467 385 7497 2 9862 118808 11412 8522 6478 65230 872 16432 1 0 . 0 . 22 0,1,9,12 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S59|501|CYP2R1|protein_coding|CODING|NM_024514.4|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12794714 -0.692352 0.473828 22 N57D 141 Aac/Gac MODERATE 3 MISSENSE CODING CALCA C protein_coding NM_001033952.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 14991539 T C 0 228 0 0.9508 0.9868 0.9986 1 1 1 0.952045 0.983677 0.999884 2 9872 120800 11553 8650 6614 66692 908 16511 2 10400 121366 11576 8650 6614 66706 908 16512 0 . 0 . 0 59 0,0,37,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N57D|141|CALCA|protein_coding|CODING|NM_001033952.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs5239 -0.693147 0.0631939 59 G228 579 ggT/ggC LOW 5 SILENT CODING INSC C protein_coding NM_001031853.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15199957 T C 0 228 0 0.8389 0.8932 0.8991 0.9762 0.8588 0.9121 0.835794 0.84 0.841997 2 8115 104208 10618 8498 5392 55794 780 15011 2 9800 120696 11568 8620 6610 66690 898 16510 0 . 0 . 0 71 0,0,21,46 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G228|579|INSC|protein_coding|CODING|NM_001031853.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1714376 -0.693147 0.644384 71 579 141 MODIFIER 13 CODING INSC G protein_coding NM_001031853.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15267727 A G 0 228 0 0.7806 0.7698 0.7262 0.8681 0.6133 0.8456 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,12,8 UTR_3_PRIME(MODIFIER||141||579|INSC|protein_coding|CODING|NM_001031853.4|13|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1945624 -0.692067 0.237602 20 112 65 MODIFIER 3 CODING LOC102724957 A protein_coding NM_001293172.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15726892 G A 0 19.7 0 0.1051 0.2628 0.3458 0.3869 0.2316 0.3211 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||65||112|LOC102724957|protein_coding|CODING|NM_001293172.1|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10741683 -0.379885 0 2 841 5005 MODIFIER 16 CODING SOX6 G protein_coding NM_001145819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15989350 A G 0 9.7 0 0.5651 0.3506 0.2305 0.5228 0.1362 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5005||841|SOX6|protein_coding|CODING|NM_001145819.1|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1065024 -0.379885 0 1 841 2036 MODIFIER 16 CODING SOX6 C protein_coding NM_001145819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15992319 A C 0 222 0 0.1218 0.1388 0.1427 0.3661 0.0199 0.047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994927 0 . 0 . 130 25,34,29,29 UTR_3_PRIME(MODIFIER||2036||841|SOX6|protein_coding|CODING|NM_001145819.1|16|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.820187 rs11023803 -0.693147 0.386484 130 841 1298 MODIFIER 16 CODING SOX6 G protein_coding NM_001145819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15993057 A G 0 222 0 0.034 0.2568 0.4294 0.246 0.4085 0.2904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.519238 0 . 0 . 71 16,23,7,19 UTR_3_PRIME(MODIFIER||1298||841|SOX6|protein_coding|CODING|NM_001145819.1|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.893163 rs4539287 -0.692976 0.619001 71 841 788 MODIFIER 16 CODING SOX6 T protein_coding NM_001145819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15993567 A T 0 222 0 0.1225 0.1384 0.1441 0.3611 0.0219 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.923285 0 . 0 . 219 60,50,56,27 UTR_3_PRIME(MODIFIER||788||841|SOX6|protein_coding|CODING|NM_001145819.1|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.676757 rs59859401 -0.693147 0.00499312 219 841 787 MODIFIER 16 CODING SOX6 G protein_coding NM_001145819.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 15993568 C G 0 222 0 0.1225 0.1384 0.1441 0.3611 0.0219 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.903304 0 . 0 . 220 61,50,56,27 UTR_3_PRIME(MODIFIER||787||841|SOX6|protein_coding|CODING|NM_001145819.1|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.738905 rs59410528 -0.693147 0.00499312 220 T291 841 acT/acC LOW 7 SILENT CODING SOX6 G protein_coding NM_001145819.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 16133413 A G 0 228 0 0.4569 0.5058 0.647 0.6121 0.5119 0.3558 0.502045 0.510471 0.514788 2 5116 63920 8370 5269 3617 34689 459 6400 2 10406 121210 11492 8620 6608 66666 908 16510 0 . 0 . 0 132 0,0,53,67 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T291|841|SOX6|protein_coding|CODING|NM_001145819.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4617548 -0.693147 0.531467 132 183 82 MODIFIER 1 CODING C11orf58 G protein_coding NM_014267.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 16760244 T G 0 228 0 0.8676 0.863 0.8617 0.9048 0.8052 0.8742 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 66 0,0,41,18 UTR_5_PRIME(MODIFIER||82||183|C11orf58|protein_coding|CODING|NM_014267.5|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1846936 -0.693147 0.619742 66 183 691 MODIFIER 5 CODING C11orf58 A protein_coding NM_014267.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 16777342 G A 0 228 0 0.9788 0.9936 0.9957 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 148 0,0,87,44 UTR_3_PRIME(MODIFIER||691||183|C11orf58|protein_coding|CODING|NM_014267.5|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386495610,rs4576801 -0.693147 0.102441 148 1121 1061 MODIFIER 23 CODING PLEKHA7 A protein_coding NM_175058.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 16809573 G A 0 89 0 0.087 0.1761 0.255 0.2718 0.1561 0.1626 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.295105 0 . 0 . 15 7,1,7,0 UTR_3_PRIME(MODIFIER||1061||1121|PLEKHA7|protein_coding|CODING|NM_175058.4|23|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.845852 rs1557875 -0.636426 0.144094 15 H39 1121 caT/caC LOW 2 SILENT CODING PLEKHA7 G protein_coding NM_175058.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17035718 A G 0 116 0 0.5408 0.7079 0.7334 0.9653 0.6143 0.7464 0.5684 0.629753 0.660025 2 3877 72511 8906 7612 3125 36976 489 11526 2 7056 104446 10824 7950 5324 56908 738 15646 0 . 0 . 0 6 0,0,0,6 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H39|1121|PLEKHA7|protein_coding|CODING|NM_175058.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs61881311 -0.616816 0.220895 6 1686 13 MODIFIER 32 CODING PIK3C2A G protein_coding NM_002645.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17111272 A G 0 228 0 0.6248 0.6326 0.6196 0.8115 0.5 0.6043 0.617273 0.564444 0.537378 2 6467 70832 7557 7286 3307 35985 506 9724 2 10392 120198 11558 8646 6608 66336 900 15758 0 . 0 . 0 36 0,0,25,2 UTR_3_PRIME(MODIFIER||13||1686|PIK3C2A|protein_coding|CODING|NM_002645.2|32|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10832733 -0.693021 0.114682 36 A413 1686 gcA/gcG LOW 3 SILENT CODING PIK3C2A C protein_coding NM_002645.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17172133 T C 0 222 0 0.8714 0.8486 0.9438 0.5923 0.998 0.8609 0.888409 0.959341 0.995691 1 9170 113246 10451 4876 6544 66437 872 14896 2 10404 121336 11562 8636 6612 66708 908 16506 0.624931 0 . 0 . 162 32,46,28,36 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A413|1686|PIK3C2A|protein_coding|CODING|NM_002645.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.732377 rs2302511 -0.693147 0.481227 162 420 HIGH 10 CODING NUCB2 A protein_coding NM_005013.2 SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17333663 G A 0 228 0 1 1 1 1 1 1 0.999722 0.999915 1 2 9796 120469 11572 8626 6612 66585 900 16378 2 9798 120472 11572 8626 6612 66586 900 16378 0 . 0 . 0 262 0,0,79,147 SPLICE_SITE_DONOR+INTRON(HIGH||||420|NUCB2|protein_coding|CODING|NM_005013.2|10|A) 1 0 . 0 . 1 0 1 1 (NUCB2|NUCB2|1|1.00) 60 0 0 1 0 . rs2521998 -0.693147 0.00433003 262 Q338E 420 Cag/Gag MODERATE 12 MISSENSE CODING NUCB2 G protein_coding NM_005013.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17351683 C G 0 222 0 0.0182 0.2378 0.2795 0.3552 0.3111 0.3088 0.0583333 0.23998 0.320453 1 447 28785 3029 2304 1866 16604 222 4313 2 6026 78540 6968 5740 5232 42300 638 11636 0.650828 0 . 0 . 58 30,4,17,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q338E|420|NUCB2|protein_coding|CODING|NM_005013.2|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999963 rs757081 -0.692352 0.447556 58 454 14 MODIFIER 5 CODING NCR3LG1 G protein_coding NM_001202439.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17394073 C G 0 222 0 0.9758 0.7324 0.6902 0.6637 0.6412 0.5982 0 . 0 1 856 7628 146 117 988 2531 98 2892 2 916 11396 208 182 1690 3948 150 4302 0.855419 0 . 0 . 80 6,22,9,34 UTR_3_PRIME(MODIFIER||14||454|NCR3LG1|protein_coding|CODING|NM_001202439.2|5|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.7631 rs10832778 -0.693146 0.397821 80 390 215 MODIFIER 1 CODING KCNJ11 A protein_coding NM_000525.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17408251 G A 0 222 0 0.5893 0.4677 0.389 0.5813 0.3757 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.839245 0 . 0 . 93 37,5,34,7 UTR_3_PRIME(MODIFIER||215||390|KCNJ11|protein_coding|CODING|NM_000525.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0369328 rs5210 -0.693145 0.00538803 93 390 62 MODIFIER 1 CODING KCNJ11 T protein_coding NM_000525.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17408404 C T 0 222 0 0.9607 0.7358 0.7118 0.6617 0.6581 0.6053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.522394 0 . 0 . 116 18,39,12,41 UTR_3_PRIME(MODIFIER||62||390|KCNJ11|protein_coding|CODING|NM_000525.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.931447 rs5213 -0.693147 0.207162 116 V337I 390 Gtc/Atc MODERATE 1 MISSENSE CODING KCNJ11 T protein_coding NM_000525.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17408630 C T 0 222 0 0.9546 0.7306 0.7032 0.6617 0.6471 0.6043 0.913182 0.732019 0.63918 1 9516 78250 7054 5515 3467 41767 578 10353 2 10404 121348 11570 8622 6612 66722 908 16510 0.999455 2 benign 0 . 178 60,30,47,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V337I|390|KCNJ11|protein_coding|CODING|NM_000525.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995926 rs5215 -0.693147 0.0768806 178 A190 390 gcC/gcT LOW 1 SILENT CODING KCNJ11 A protein_coding NM_000525.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17409069 G A 0 222 0 0.0257 0.2274 0.1816 0.5129 0.3221 0.1411 0.0752273 0.222855 0.298509 1 648 30431 1475 4115 2120 19205 203 2665 2 10036 117854 11218 8434 6052 64920 858 16336 0.908324 2 benign 0 . 42 14,4,9,11 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A190|390|KCNJ11|protein_coding|CODING|NM_000525.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.671969 rs5218 -0.692067 0.108963 42 K23E 390 Aag/Gag MODERATE 1 MISSENSE CODING KCNJ11 C protein_coding NM_000525.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17409572 T C 0 222 0 0.9766 0.737 0.7075 0.6617 0.6471 0.6043 0.930682 0.738103 0.639413 1 9719 78371 7067 5505 3475 41667 578 10360 2 10376 121112 11566 8600 6606 66546 908 16510 0.41102 255|6|2|2 other|drug-response|benign|benign 0 . 36 8,4,11,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K23E|390|KCNJ11|protein_coding|CODING|NM_000525.3|1|C),DOWNSTREAM(MODIFIER||4860||1582|ABCC8|protein_coding|CODING|NM_001287174.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.323274 rs5219 -0.691153 0.928632 36 A1370S 1582 Gcc/Tcc MODERATE 33 MISSENSE CODING ABCC8 A protein_coding NM_001287174.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17418477 C A 0 222 0 0.975 0.7264 0.6931 0.6389 0.6481 0.5849 0.932045 0.738565 0.639413 1 9755 77880 7040 5338 3408 41604 575 10160 2 10398 121110 11552 8602 6534 66610 906 16508 0.597809 3 likely-benign 0 . 89 28,19,24,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A1370S|1582|ABCC8|protein_coding|CODING|NM_001287174.1|33|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958299 rs386611540,rs757110 -0.693132 0.022222 89 1582 LOW 15 CODING ABCC8 A protein_coding NM_001287174.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17448704 G A 0 201 0 0.1384 0.3684 0.536 0.5506 0.4205 0.319 0.179318 0.353612 0.44293 1 1681 51409 7139 5121 2789 29021 374 5284 2 9894 118292 11398 8540 6470 65138 880 15972 0.956162 255 other 0 . 29 0,13,2,13 SPLICE_SITE_REGION+INTRON(LOW||||1582|ABCC8|protein_coding|CODING|NM_001287174.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.626313 rs1799854 -0.688148 0.774801 29 K649 1582 aaG/aaA LOW 14 SILENT CODING ABCC8 T protein_coding NM_001287174.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17449929 C T 0 222 0 0.171 0.2021 0.1499 0.2024 0.1511 0.3333 0.18 0.156707 0.144771 1 1863 21509 1389 1439 1297 10506 151 4864 2 10258 120504 11554 8612 6550 66216 894 16420 0.948512 255 other 0 . 73 24,15,20,11 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K649|1582|ABCC8|protein_coding|CODING|NM_001287174.1|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.827782 rs1799858 -0.69311 0.240231 73 H562 1582 caC/caT LOW 12 SILENT CODING ABCC8 A protein_coding NM_001287174.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17452492 G A 0 222 0 0.4841 0.4299 0.3516 0.3125 0.4404 0.5225 0.472955 0.458725 0.451433 1 4964 51749 3438 2382 2752 29500 411 8302 2 10316 120034 11382 8376 6584 66002 904 16470 0.927628 3 likely-benign 0 . 161 33,42,34,37 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H562|1582|ABCC8|protein_coding|CODING|NM_001287174.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.276553 rs1799857 -0.693147 0.0253416 161 899 211 MODIFIER 27 CODING USH1C C protein_coding NM_153676.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17515668 T C 0 102 0 0.4327 0.3826 0.3228 0.2956 0.4583 0.3691 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.546428 0 . 0 . 15 7,0,8,0 UTR_3_PRIME(MODIFIER||211||899|USH1C|protein_coding|CODING|NM_153676.3|27|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.993326 rs1055581 -0.651104 0.749902 15 899 186 MODIFIER 27 CODING USH1C A protein_coding NM_153676.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17515693 G A 0 132 0 0.3858 0.3666 0.3184 0.2887 0.4592 0.3599 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960505 0 . 0 . 31 12,0,19,0 UTR_3_PRIME(MODIFIER||186||899|USH1C|protein_coding|CODING|NM_153676.3|27|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.999178 rs1055577 -0.69168 0.00493554 31 899 46 MODIFIER 27 CODING USH1C G protein_coding NM_153676.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17515833 A G 0 222 0 0.3873 0.3704 0.3199 0.2946 0.4602 0.3691 0.414545 0.45241 0.471815 1 3185 37596 2455 2009 2017 22952 254 4724 2 7358 82888 7020 6018 3836 46060 606 11990 0.157292 0 . 0 . 132 48,14,32,22 UTR_3_PRIME(MODIFIER||46||899|USH1C|protein_coding|CODING|NM_153676.3|27|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.774999 rs1055574 -0.693147 0.0021062 132 E819D 899 gaG/gaC MODERATE 24 MISSENSE CODING USH1C G protein_coding NM_153676.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17519742 C G 0 222 0 0.4168 0.4209 0.3718 0.3026 0.5636 0.4366 0.428636 0.515093 0.559399 1 4383 59175 4090 2651 3498 36683 446 7424 2 10404 121392 11578 8642 6614 66734 908 16512 0.871134 2 benign 0 . 53 17,4,19,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E819D|899|USH1C|protein_coding|CODING|NM_153676.3|24|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.035307 rs1064074 -0.693054 0.349815 53 P396 899 ccA/ccG LOW 14 SILENT CODING USH1C C protein_coding NM_153676.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17542439 T C 0 228 0 0.3018 0.5164 0.6527 0.6716 0.5338 0.5317 0.356591 0.504004 0.579548 2 3537 69050 7849 5737 3807 39035 504 8581 2 10404 121382 11578 8638 6614 66730 908 16510 1 2 benign 0 . 172 1,0,92,65 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P396|899|USH1C|protein_coding|CODING|NM_153676.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2240487 -0.693147 0.157441 172 S692P 2925 Tct/Cct MODERATE 17 MISSENSE CODING OTOG C protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17593709 T C 0 222 0 0.6664 0.4409 0.3242 0.3204 0.4155 0.3691 0 . 0 1 621 6170 101 160 63 2218 55 2952 2 964 14820 292 490 122 5132 154 7666 0.467128 0 . 0 . 60 13,15,8,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S692P|2925|OTOG|protein_coding|CODING|NM_001277269.1|17|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.876998 rs7106548 -0.692067 0.246836 60 P792 2925 ccG/ccA LOW 19 SILENT CODING OTOG A protein_coding NM_001277269.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17596313 G A 0 222 0 0.3759 0.3339 0.2435 0.2986 0.3976 0.3119 0 . 0 1 360 5888 81 155 646 2150 63 2433 2 970 16578 294 500 1522 5486 198 7608 0.600723 0 . 0 . 166 53,20,42,28 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P792|2925|OTOG|protein_coding|CODING|NM_001277269.1|19|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.984338 rs4757548 -0.693147 0.23585 166 A919T 2925 Gcc/Acc MODERATE 22 MISSENSE CODING OTOG A protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17600033 G A 0 222 0 0.1914 0.2762 0.2133 0.2579 0.3946 0.3323 0 . 0 1 199 5163 75 125 308 1917 47 2492 2 812 14396 262 408 584 4812 158 7360 0.303971 0 . 0 . 87 20,19,18,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A919T|2925|OTOG|protein_coding|CODING|NM_001277269.1|22|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.44177 rs2355466 -0.693141 0.224156 87 R1075Q 2925 cGa/cAa MODERATE 26 MISSENSE CODING OTOG A protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17615203 G A 0 222 0 0.0779 0.1566 0.0922 0.2242 0.165 0.2301 0 . 0 1 93 2726 30 127 85 894 21 1476 2 912 14938 292 486 292 5130 160 7666 0.902362 0 . 0 . 79 19,21,15,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R1075Q|2925|OTOG|protein_coding|CODING|NM_001277269.1|26|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.249683 rs11024333 -0.69312 0.178149 79 S1218 2925 tcC/tcT LOW 29 SILENT CODING OTOG T protein_coding NM_001277269.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17618490 C T 0 222 0 0.0015 0.014577 0 0.0675 0 0.0031 0 . 0 1 2 45 0 34 0 1 1 7 2 930 16802 292 486 1638 5584 208 7664 0.112219 0 . 0 . 92 17,26,21,19 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1218|2925|OTOG|protein_coding|CODING|NM_001277269.1|29|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.9051 rs143393149 -0.693145 0.526975 92 A1375P 2925 Gcg/Ccg MODERATE 32 MISSENSE CODING OTOG C protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17627613 G C 0 228 0 0.9894 0.8261 0.7305 0.8294 0.7157 0.7832 0 . 0 2 875 11673 214 405 382 3903 125 5769 2 914 15200 290 486 534 5162 166 7648 0.56635 0 . 0 . 186 1,2,83,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Ccg|A1375P|2925|OTOG|protein_coding|CODING|NM_001277269.1|32|C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.664767 rs7934079 -0.693147 0.450948 186 P1647L 2925 cCa/cTa MODERATE 35 MISSENSE CODING OTOG T protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17631751 C T 0 222 0 0.649 0.4347 0.2695 0.2222 0.3767 0.5409 0 . 0 1 596 6716 83 134 539 1917 63 3384 2 964 16600 290 498 1608 5396 206 7638 0.570642 0 . 0 . 85 30,7,25,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P1647L|2925|OTOG|protein_coding|CODING|NM_001277269.1|35|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.797317 rs2041028 -0.693139 0.764742 85 T1947M 2925 aCg/aTg MODERATE 35 MISSENSE CODING OTOG T protein_coding NM_001277269.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17632651 C T 0 179 0 0.5325 0.4032 0.2637 0.2222 0.3767 0.5409 0 . 0 1 427 6393 80 124 478 1843 58 3383 2 842 15774 276 470 1220 5122 188 7656 0.982422 0 . 0 . 30 13,4,10,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1947M|2925|OTOG|protein_coding|CODING|NM_001277269.1|35|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.968964 rs7111528 -0.683931 0.474283 30 C2759 2925 tgC/tgT LOW 51 SILENT CODING OTOG T protein_coding NM_001277269.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17663444 C T 0 222 0 0.5106 0.3431 0.2017 0.1657 0.3201 0.4233 0 . 0 1 429 5234 68 95 357 1618 51 2616 2 910 15636 290 486 904 5214 182 7650 0.995212 0 . 0 . 112 26,31,19,28 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C2759|2925|OTOG|protein_coding|CODING|NM_001277269.1|51|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0312989 rs10832824 -0.693147 0.455373 112 L2800 2925 ctG/ctC LOW 52 SILENT CODING OTOG C protein_coding NM_001277269.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17663742 G C 0 222 0 0.5424 0.3662 0.2017 0.1835 0.3091 0.4918 0 . 0 1 460 5389 71 102 217 1448 46 3045 2 932 15108 290 484 562 5114 162 7564 0.984966 0 . 0 . 114 12,29,11,53 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L2800|2925|OTOG|protein_coding|CODING|NM_001277269.1|52|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.483665 rs2023483 -0.693147 0.0705631 114 S327 458 tcG/tcA LOW 9 SILENT CODING SERGEF T protein_coding NM_012139.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 17981047 C T 0 222 0 0.9221 0.6885 0.5836 0.4881 0.6044 0.7403 0.866136 0.69883 0.613091 1 9128 74060 6265 4237 3550 39346 510 11024 2 10402 121298 11566 8626 6606 66682 906 16510 0.992444 0 . 0 . 100 32,13,25,17 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S327|458|SERGEF|protein_coding|CODING|NM_012139.3|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.473288 rs211146,rs386557547 -0.693146 0.115429 100 458 35 MODIFIER 1 CODING SERGEF C protein_coding NM_012139.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18034592 G C 0 6.3 0 0.205 0.4561 0.5576 0.6131 0.5706 0.4438 0 . 0 1 0 109 2 0 2 3 1 101 2 0 174 2 0 2 6 2 162 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||35||458|SERGEF|protein_coding|CODING|NM_012139.3|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs3741202 -0.379885 0 1 458 48 MODIFIER 1 CODING SERGEF G protein_coding NM_012139.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18034605 C G 0 9.7 0 0.1997 0.4547 0.5576 0.6131 0.5706 0.4438 0 . 0 1 0 24 0 0 2 0 0 22 2 0 36 0 0 2 0 0 34 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||48||458|SERGEF|protein_coding|CODING|NM_012139.3|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs3741201 -0.379885 0 1 458 139 MODIFIER 1 CODING SERGEF G protein_coding NM_012139.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18034696 A G 0 70 0 0.1906 0.4529 0.5591 0.6151 0.5706 0.4438 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||139||458|SERGEF|protein_coding|CODING|NM_012139.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3741200 -0.453602 0.22 3 444 LOW 6 CODING TPH1 T protein_coding NM_004179.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18047255 G T 0 222 0 0.1626 0.3211 0.3718 0.4752 0.3907 0.2689 0.182273 0.315802 0.38423 1 1832 46498 4583 4010 3028 27077 388 5580 2 10372 121228 11530 8638 6612 66664 908 16504 0.896626 0 . 0 COSM147151 205 28,69,27,60 SPLICE_SITE_REGION+INTRON(LOW||||444|TPH1|protein_coding|CODING|NM_004179.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947894 rs1799913 -0.693147 0.0101663 205 322 4527 MODIFIER 2 CODING MRGPRX3 G protein_coding NM_054031.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18154223 T G 0 9.7 0 0.7542 0.8019 0.8473 0.874 0.7773 0.7853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||4527||322|MRGPRX3|protein_coding|CODING|NM_054031.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1975777 -0.379885 0 1 S140 322 tcA/tcG LOW 3 SILENT CODING MRGPRX3 G protein_coding NM_054031.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18159169 A G 0 228 0 0.8351 0.9545 0.9899 1 0.997 1 0.855682 0.950485 0.999068 2 8865 119715 11511 8633 6614 66682 902 16508 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 155 0,0,118,28 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S140|322|MRGPRX3|protein_coding|CODING|NM_054031.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2468839 -0.693147 0.830255 155 N169D 322 Aat/Gat MODERATE 3 MISSENSE CODING MRGPRX3 G protein_coding NM_054031.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18159254 A G 0 228 0 0.5371 0.743 0.8357 0.874 0.7773 0.7853 0.579545 0.70422 0.768111 2 5913 93440 9945 7576 5034 51307 735 12930 2 10404 121396 11574 8650 6614 66734 908 16512 1 0 . 0 . 277 1,0,140,99 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N169D|322|MRGPRX3|protein_coding|CODING|NM_054031.3|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.995639 0 1 rs4274188 -0.693147 0.0259073 277 322 11 MODIFIER 1 CODING MRGPRX4 A protein_coding NM_054032.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18194793 G A 0 228 0 0.0658 0.2688 0.3602 0.505 0.2724 0.2311 0.105957 0.209258 0.262171 2 970 32081 4753 4506 1683 17070 239 2860 2 10262 112302 11500 8566 6614 64512 810 10038 1 0 . 0 . 146 0,1,79,44 UTR_5_PRIME(MODIFIER||11||322|MRGPRX4|protein_coding|CODING|NM_054032.3|1|A) 1 0 . 0 . 1 0 1 1 0 59 0 1 1 0 1 rs11024530 -0.693147 0.341002 146 V47 322 gtT/gtA LOW 1 SILENT CODING MRGPRX4 A protein_coding NM_054032.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18194944 T A 0 228 0 0.0862 0.2744 0.3617 0.504 0.2734 0.2311 0.121419 0.214495 0.262171 2 1131 34280 4770 4539 1683 17570 274 4313 2 10406 121374 11572 8630 6614 66732 908 16512 1 0 . 0 . 161 1,0,75,74 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V47|322|MRGPRX4|protein_coding|CODING|NM_054032.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11024531 -0.693147 0.694957 161 L83S 322 tTg/tCg MODERATE 1 MISSENSE CODING MRGPRX4 C protein_coding NM_054032.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18195051 T C 0 228 0 0.8744 0.9657 0.9914 1 1 1 0.899954 0.965496 0.999068 2 9343 120250 11532 8654 6614 66693 904 16510 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 106 0,0,32,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L83S|322|MRGPRX4|protein_coding|CODING|NM_054032.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2445179 -0.693147 0.129658 106 C89Y 130 tGc/tAc MODERATE 4 MISSENSE CODING SAA4 T protein_coding NM_006512.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18253176 C T 0 228 0 0.6997 0.8806 0.9553 0.8948 0.9732 0.9622 0.745111 0.895256 0.972164 2 7647 114965 11277 7804 6522 64952 864 15899 2 10404 121388 11574 8652 6614 66726 908 16510 0 . 0 . 0 51 0,0,25,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C89Y|130|SAA4|protein_coding|CODING|NM_006512.3|4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C167Y|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2460827 -0.693147 0.474702 51 C167Y 208 tGc/tAc MODERATE 6 MISSENSE CODING SAA2-SAA4 T protein_coding NM_001199744.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18253176 C T 0 228 0 0.6997 0.8806 0.9553 0.8948 0.9732 0.9622 0.745111 0.895256 0.972164 2 7647 114965 11277 7804 6522 64952 864 15899 2 10404 121388 11574 8652 6614 66726 908 16510 0 . 0 . 0 51 0,0,25,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C89Y|130|SAA4|protein_coding|CODING|NM_006512.3|4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C167Y|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2460827 -0.693147 0.474702 51 130 809 MODIFIER 1 CODING SAA4 C protein_coding NM_006512.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18258282 A C 0 23.7 0 0.7027 0.883 0.9553 0.9018 0.9742 0.9622 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||809||130|SAA4|protein_coding|CODING|NM_006512.3|1|C),INTRON(MODIFIER||||208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1378609 -0.379885 0 2 R89H 122 cGt/cAt MODERATE 4 MISSENSE CODING SAA2 T protein_coding NM_030754.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18267027 C T 0 228 0 0.6089 0.771 0.7839 0.9276 0.8857 0.7014 0.683038 0.799908 0.859772 2 6788 100918 8749 8087 6117 58190 775 12212 2 10400 121388 11576 8654 6612 66730 908 16508 0 . 0 . 0 92 0,0,28,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R89H|122|SAA2|protein_coding|CODING|NM_030754.4|4|T),INTRON(MODIFIER||||208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2468844,rs386567783 -0.693147 0.212791 92 V75A 208 gTg/gCg MODERATE 3 MISSENSE CODING SAA2-SAA4 G protein_coding NM_001199744.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18267463 A G 0 44.1 0 . 0 . 0 . 0 . 0 . 1 3314 44193 3776 3369 2668 24978 313 5775 2 9768 114834 10812 8180 6320 63366 868 15520 0.675983 0 . 0 . 228 131,23,33,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V75A|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V75A|122|SAA2|protein_coding|CODING|NM_030754.4|3|G) 0 0.5 1 0 . 0 . 0 1 0 39 0 0.1907 3.17444e-06 0 0.0141881 rs74872559 -0.693143 0.0757315 228 V75A 122 gTg/gCg MODERATE 3 MISSENSE CODING SAA2 G protein_coding NM_030754.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18267463 A G 0 44.1 0 . 0 . 0 . 0 . 0 . 1 3314 44193 3776 3369 2668 24978 313 5775 2 9768 114834 10812 8180 6320 63366 868 15520 0.675983 0 . 0 . 228 131,23,33,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V75A|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V75A|122|SAA2|protein_coding|CODING|NM_030754.4|3|G) 0 0.5 1 0 . 0 . 0 1 0 39 0 0.1907 3.17444e-06 0 0.0141881 rs74872559 -0.693143 0.0757315 228 A72 208 gcT/gcC LOW 3 SILENT CODING SAA2-SAA4 G protein_coding NM_001199744.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18267471 A G 0 222 0 . 0 . 0 . 0 0.438154 0.459181 0.469951 1 4651 57839 5205 4232 3268 32445 441 7597 2 10326 120572 11370 8596 6596 66356 904 16424 0.82461 0 . 0 . 207 72,13,66,28 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A72|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A72|122|SAA2|protein_coding|CODING|NM_030754.4|3|G) 1 0.5 1 0 . 0 . 1 1 0 40 0 0.0109256 1.04808e-08 0 0.999896 rs1136766 -0.693147 0.00296118 207 A72 122 gcT/gcC LOW 3 SILENT CODING SAA2 G protein_coding NM_030754.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18267471 A G 0 222 0 . 0 . 0 . 0 0.438154 0.459181 0.469951 1 4651 57839 5205 4232 3268 32445 441 7597 2 10326 120572 11370 8596 6596 66356 904 16424 0.82461 0 . 0 . 207 72,13,66,28 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A72|208|SAA2-SAA4|protein_coding|CODING|NM_001199744.1|3|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A72|122|SAA2|protein_coding|CODING|NM_030754.4|3|G) 1 0.5 1 0 . 0 . 1 1 0 40 0 0.0109256 1.04808e-08 0 0.999896 rs1136766 -0.693147 0.00296118 207 V75A 122 gTg/gCg MODERATE 3 MISSENSE CODING SAA1 C protein_coding NM_000331.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18290874 T C 0 159 0 . 0 . 0 . 0 . 0 . 1 2516 25779 1632 1359 1783 16250 206 2033 2 4992 47632 3514 2958 2774 28814 402 4178 0.996225 0 . 0 . 61 38,5,13,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V75A|122|SAA1|protein_coding|CODING|NM_000331.4|3|C) 0 0.5 1 0 . 0 . 0 1 0 51 0 0.647113 0.00428918 0 0.975792 rs1136747 -0.691153 0.413586 61 122 HIGH 3 CODING SAA1 G protein_coding NM_000331.4 SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18290880 C G 0 228 0 0.975 0.9928 0.9957 1 1 1 0 . 0 2 4238 39936 2989 2452 2172 24292 331 3462 2 4512 40658 3030 2472 2210 24612 338 3484 0 . 0 . 0 59 0,0,49,10 SPLICE_SITE_DONOR+INTRON(HIGH||||122|SAA1|protein_coding|CODING|NM_000331.4|3|G) 0 . 0 . 0 1 0 . 1 (SAA1|SAA1|1|1.00) 51 0 0 0.0055615 0 . rs1671926,rs28720026 -0.693147 0.119187 59 1129 475 MODIFIER 23 CODING HPS5 A protein_coding NM_181507.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18300954 G A 0 6.3 0 0.4198 0.3552 0.3026 0.3849 0.3151 0.316 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||475||1129|HPS5|protein_coding|CODING|NM_181507.1|23|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1046615 -0.379885 0 1 L274 1129 ctC/ctA LOW 7 SILENT CODING HPS5 T protein_coding NM_181507.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18327684 G T 0 228 0 0.7852 0.8047 0.7536 0.9722 0.7107 0.7914 0.765575 0.712261 0.684952 2 7939 88485 9473 8434 4666 45298 595 12080 2 10404 121386 11578 8652 6610 66724 908 16510 0 2 benign 0 . 66 0,0,39,17 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ctC/ctA|L274|1129|HPS5|protein_coding|CODING|NM_181507.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1140047 -0.693147 0.207622 66 548 10800 MODIFIER 1 CODING GTF2H1 G protein_coding NM_001142307.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18343822 C G 0 9.7 0 0.7829 0.8049 0.7579 0.9712 0.7127 0.7914 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||548|GTF2H1|protein_coding|CODING|NM_001142307.1|1|G),UTR_5_PRIME(MODIFIER||10800||548|GTF2H1|protein_coding|CODING|NM_001142307.1|1|G),UPSTREAM(MODIFIER||101||1129|HPS5|protein_coding|CODING|NM_181507.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3825025 -0.379885 0 1 548 10744 MODIFIER 1 CODING GTF2H1 G protein_coding NM_001142307.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18343878 A G 0 32.6 0 0.7829 0.8049 0.7579 0.9712 0.7127 0.7914 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||10744||548|GTF2H1|protein_coding|CODING|NM_001142307.1|1|G),UPSTREAM(MODIFIER||157||1129|HPS5|protein_coding|CODING|NM_181507.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3802968 -0.379885 0 2 548 10558 MODIFIER 1 CODING GTF2H1 C protein_coding NM_001142307.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18344064 T C 0 27.5 0 0.0673 0.3928 0.5115 0.5883 0.5378 0.3978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 START_GAINED(LOW||||548|GTF2H1|protein_coding|CODING|NM_001142307.1|1|C),UTR_5_PRIME(MODIFIER||10558||548|GTF2H1|protein_coding|CODING|NM_001142307.1|1|C),UPSTREAM(MODIFIER||343||1129|HPS5|protein_coding|CODING|NM_181507.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3802967 -0.511536 0.578719 3 548 712 MODIFIER 16 CODING GTF2H1 C protein_coding NM_001142307.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18388128 G C 0 228 0 0.0666 0.3916 0.5101 0.5853 0.5368 0.3978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 91 0,0,41,40 UTR_3_PRIME(MODIFIER||712||548|GTF2H1|protein_coding|CODING|NM_001142307.1|16|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4596 -0.693147 0.304241 91 S190 361 agC/agT LOW 5 SILENT CODING LDHA T protein_coding NM_001165414.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18424451 C T 0 222 0 0.4183 0.6346 0.7334 0.6478 0.7336 0.7413 0.478627 0.63228 0.711023 1 4897 84703 8455 5686 5231 47438 662 12334 2 10406 121388 11578 8646 6610 66732 908 16508 0.858667 0 . 0 . 97 33,19,22,12 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S190|361|LDHA|protein_coding|CODING|NM_001165414.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.788737 0.916255 0 0.981297 rs5030621 -0.693132 0.0224366 97 L202 361 ctA/ctG LOW 5 SILENT CODING LDHA G protein_coding NM_001165414.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18424487 A G 0 222 0 0.4183 0.6346 0.7334 0.6478 0.7336 0.7413 0.475898 0.629801 0.7088 1 4857 84627 8455 5672 5231 47417 662 12333 2 10348 121290 11574 8636 6610 66706 908 16508 0.928102 0 . 0 . 96 22,31,14,19 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L202|361|LDHA|protein_coding|CODING|NM_001165414.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.779411 0.894291 0 0.996448 rs4820 -0.693127 0.659475 96 L259 332 Ttg/Ctg LOW 7 SILENT CODING LDHC C protein_coding NM_002301.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18467821 T C 0 228 0 0.9955 0.9988 1 1 1 1 0.996135 0.998691 1 2 10372 121371 11575 8654 6614 66737 908 16511 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 172 0,0,72,76 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L259|332|LDHC|protein_coding|CODING|NM_002301.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2658565 -0.693147 0.00912636 172 332 722 MODIFIER 8 CODING LDHAL6A C protein_coding NM_001144071.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18501139 A C 0 9.7 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||722||332|LDHAL6A|protein_coding|CODING|NM_001144071.1|8|C),DOWNSTREAM(MODIFIER||719||390|TSG101|protein_coding|CODING|NM_006292.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2658557 -0.379885 0 1 471 728 MODIFIER 12 CODING UEVLD C protein_coding NM_001040697.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18553139 T C 0 46.3 0 0.9546 0.987 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||728||471|UEVLD|protein_coding|CODING|NM_001040697.2|12|C),UPSTREAM(MODIFIER||4636||390|TSG101|protein_coding|CODING|NM_006292.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4757670 -0.453602 0.84 2 685 2678 MODIFIER 6 CODING SPTY2D1 A protein_coding NM_194285.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18628730 G A 0 222 0 0.0446 0.2849 0.4352 0.3462 0.3688 0.3538 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.985606 0 . 0 . 80 30,4,39,2 UTR_3_PRIME(MODIFIER||2678||685|SPTY2D1|protein_coding|CODING|NM_194285.2|6|A),INTRAGENIC(MODIFIER|||||SPTY2D1-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.769608 rs10832948 -0.693145 0.0605684 80 685 2104 MODIFIER 6 CODING SPTY2D1 T protein_coding NM_194285.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18629304 C T 0 58 0 0.4395 0.4177 0.487 0.3681 0.4394 0.3681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 9 1,4,0,4 UTR_3_PRIME(MODIFIER||2104||685|SPTY2D1|protein_coding|CODING|NM_194285.2|6|T),INTRAGENIC(MODIFIER|||||SPTY2D1-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.487298 rs7934205 -0.556411 0.598008 9 K617R 685 aAg/aGg MODERATE 4 MISSENSE CODING SPTY2D1 C protein_coding NM_194285.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18633897 T C 0 222 0 0.0091 0.1026 0.0605 0.2232 0.0974 0.1401 0.0213734 0.0622304 0.0831586 1 190 11369 671 1981 949 5618 81 1879 2 10380 121266 11576 8646 6614 66652 906 16492 0.74561 0 . 0 COSM147159 79 27,9,18,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K617R|685|SPTY2D1|protein_coding|CODING|NM_194285.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999482 rs35411689,rs386444461 -0.693097 0.826725 79 D592 685 gaC/gaT LOW 4 SILENT CODING SPTY2D1 A protein_coding NM_194285.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18633971 G A 0 222 0 0.0794 0.3083 0.451 0.3472 0.4195 0.362 0.138017 0.351201 0.460401 1 1367 50378 5228 3222 2765 30723 385 6688 2 10398 121316 11578 8632 6608 66692 906 16502 0.443568 0 . 0 . 66 12,16,10,21 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D592|685|SPTY2D1|protein_coding|CODING|NM_194285.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925075 rs11605097 -0.69311 0.944611 66 240 130 MODIFIER 1 CODING TMEM86A G protein_coding NM_153347.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18720304 C G 0 61 0 0.941 0.9675 0.9654 1 0.9423 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||130||240|TMEM86A|protein_coding|CODING|NM_153347.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7946446 -0.511536 0.0411132 3 R976 1326 cgG/cgC LOW 18 SILENT CODING IGSF22 G protein_coding NM_173588.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18731004 C G 0 222 0 0.0371 0.1552 0.1859 0.129 0.1849 0.2894 0.0625641 0.153966 0.197028 1 608 22766 2648 1142 993 12488 184 4703 2 9798 120712 11574 8606 6614 66712 900 16508 0.964605 0 . 0 . 111 34,21,27,16 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R976|1326|IGSF22|protein_coding|CODING|NM_173588.3|18|G),DOWNSTREAM(MODIFIER||4672||240|TMEM86A|protein_coding|CODING|NM_153347.2||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.235633 rs72880717 -0.693146 0.32164 111 1326 LOW 14 CODING IGSF22 T protein_coding NM_173588.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18735396 G T 0 207 0 0.8502 0.7564 0.7118 0.8125 0.7803 0.5787 0.820123 0.775723 0.753555 1 7509 83332 6761 6491 4726 47562 595 9688 2 9158 110512 10112 7892 5714 61762 810 15064 0.0696609 0 . 0 . 84 28,1,51,2 SPLICE_SITE_REGION+INTRON(LOW||||1326|IGSF22|protein_coding|CODING|NM_173588.3|14|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.40041 rs10741752 -0.693147 0.438354 84 M559V 1326 Atg/Gtg MODERATE 13 MISSENSE CODING IGSF22 C protein_coding NM_173588.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18735947 T C 0 222 0 0.851 0.7562 0.7075 0.8125 0.7783 0.5818 0.815929 0.771301 0.749226 1 7999 89526 7504 7054 5423 50526 651 10369 2 9822 120762 11576 8616 6614 66722 900 16512 0.911865 0 . 0 . 113 33,18,37,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M559V|1326|IGSF22|protein_coding|CODING|NM_173588.3|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740136 rs7125943 -0.693147 0.124776 113 R472Q 1326 cGa/cAa MODERATE 11 MISSENSE CODING IGSF22 T protein_coding NM_173588.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18737095 C T 0 222 0 0.829 0.7494 0.7032 0.8125 0.7734 0.5849 0.789354 0.757632 0.741371 1 8020 88944 7453 7054 5341 50135 651 10290 2 10102 121036 11568 8620 6608 66720 906 16512 0.997274 0 . 0 . 172 35,34,42,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R472Q|1326|IGSF22|protein_coding|CODING|NM_173588.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.700916 rs4424652 -0.693147 0.286821 172 V414I 1326 Gtt/Att MODERATE 10 MISSENSE CODING IGSF22 T protein_coding NM_173588.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18738281 C T 0 222 0 0.8298 0.749 0.7032 0.8125 0.7724 0.5828 0.797753 0.760475 0.742895 1 7787 88723 7461 7054 5343 50162 645 10271 2 9806 120724 11572 8616 6614 66726 900 16490 0.98914 0 . 0 . 195 46,39,54,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V414I|1326|IGSF22|protein_coding|CODING|NM_173588.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945634 rs10766494 -0.693147 0.346306 195 E398K 1326 Gag/Aag MODERATE 10 MISSENSE CODING IGSF22 T protein_coding NM_173588.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18738329 C T 0 222 0 0.034 0.1504 0.1844 0.127 0.166 0.2914 0.0584416 0.142684 0.183137 1 570 21906 2608 1128 1078 11777 175 4570 2 9806 120754 11576 8610 6614 66736 900 16512 0.994908 0 . 0 . 174 45,44,42,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E398K|1326|IGSF22|protein_coding|CODING|NM_173588.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.64684 rs61886891 -0.693147 0.967347 174 A94P 1326 Gcc/Ccc MODERATE 4 MISSENSE CODING IGSF22 G protein_coding NM_173588.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18743180 C G 0 222 0 0.171 0.36 0.5187 0.3224 0.3897 0.5112 0.217118 0.336452 0.393691 1 2204 49524 7000 2753 2516 26588 362 8101 2 9806 120736 11568 8610 6612 66730 900 16510 0.885904 0 . 0 COSM428799,COSM428800 121 21,32,11,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Ccc|A94P|1326|IGSF22|protein_coding|CODING|NM_173588.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.986964 rs10832975 -0.693147 0.11788 121 P170A 565 Cca/Gca MODERATE 7 MISSENSE CODING PTPN5 C protein_coding NM_006906.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18764026 G C 0 222 0 0.0242 0.2973 0.4899 0.3194 0.3857 0.4162 0.0952706 0.291975 0.392732 1 876 45060 6266 2558 2017 25964 336 7043 2 10274 120784 11540 8602 6462 66502 898 16506 0.863973 0 . 0 COSM143742,COSM1353095 61 10,18,13,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P170A|565|PTPN5|protein_coding|CODING|NM_006906.1|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989184 rs4757707 -0.693054 0.595578 61 L196 322 ctG/ctA LOW 1 SILENT CODING MRGPRX1 T protein_coding NM_147199.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18955744 C T 0 222 0 0.2769 0.2953 0.2695 0.3879 0.2237 0.317 0.275524 0.23696 0.217219 1 2894 30979 4065 3076 1419 14720 230 4575 2 10378 120756 11348 8598 6592 66492 908 16440 0.956299 0 . 0 COSM147160 174 53,36,40,27 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L196|322|MRGPRX1|protein_coding|CODING|NM_147199.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.761877 rs11599929 -0.693147 0.127179 174 E157 322 gaG/gaA LOW 1 SILENT CODING MRGPRX1 T protein_coding NM_147199.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 18955861 C T 0 222 0 0.0076 0.0996 0.0865 0.2073 0.1292 0.092 0.0257521 0.089429 0.122025 1 237 12749 610 1794 517 7891 97 1603 2 10386 120932 11436 8594 6596 66554 904 16462 0.983392 0 . 0 . 112 21,32,15,32 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E157|322|MRGPRX1|protein_coding|CODING|NM_147199.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.672429 rs72890000 -0.693147 0.475074 112 330 3487 MODIFIER 1 CODING MRGPRX2 G protein_coding NM_001303615.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19081436 T G 0 9.7 0 0.1135 0.4501 0.6239 0.5357 0.5895 0.5501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||3487||330|MRGPRX2|protein_coding|CODING|NM_001303615.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12804585 -0.379885 0 1 330 3495 MODIFIER 1 CODING MRGPRX2 A protein_coding NM_001303615.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19081444 G A 0 9.7 0 0.1135 0.4501 0.6239 0.5357 0.5895 0.5501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||3495||330|MRGPRX2|protein_coding|CODING|NM_001303615.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12803552 -0.379885 0 1 330 3507 MODIFIER 1 CODING MRGPRX2 A protein_coding NM_001303615.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19081456 T A 0 9.7 0 0.1135 0.4501 0.6239 0.5357 0.5895 0.5501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||3507||330|MRGPRX2|protein_coding|CODING|NM_001303615.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12804592 -0.379885 0 1 K99R 622 aAg/aGg MODERATE 3 MISSENSE CODING ZDHHC13 G protein_coding NM_019028.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19167850 A G 0 228 0 0.326 0.6076 0.7752 0.7262 0.6978 0.6544 0.40956 0.623099 0.719524 2 3729 82420 9716 6152 4194 46992 616 11021 2 9658 119112 11388 8490 6560 65842 886 16288 0 . 0 . 0 213 0,0,91,101 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|aAg/aGg|K99R|622|ZDHHC13|protein_coding|CODING|NM_019028.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2271001,rs386563046 -0.693147 0.165693 213 867 351 MODIFIER 13 CODING E2F8 C protein_coding NM_001256371.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19245854 T C 0 228 0 0.7943 0.7674 0.6844 0.7768 0.832 0.7137 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 145 0,1,53,84 UTR_3_PRIME(MODIFIER||351||867|E2F8|protein_coding|CODING|NM_001256371.1|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs386614178,rs793278 -0.693147 0.360231 145 867 163 MODIFIER 13 CODING E2F8 A protein_coding NM_001256371.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19246042 G A 0 228 0 0.2572 0.3421 0.3775 0.3393 0.3857 0.3896 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 36 0,1,14,10 UTR_3_PRIME(MODIFIER||163||867|E2F8|protein_coding|CODING|NM_001256371.1|13|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs61876765 -0.692831 0.00674375 36 867 161 MODIFIER 13 CODING E2F8 A protein_coding NM_001256371.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19246044 G A 0 228 0 0.4289 0.5016 0.5303 0.4772 0.5567 0.5481 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,14,10 UTR_3_PRIME(MODIFIER||161||867|E2F8|protein_coding|CODING|NM_001256371.1|13|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs793277 -0.692831 0.00646026 36 R109K 2488 aGg/aAg MODERATE 2 MISSENSE CODING NAV2 A protein_coding NM_001244963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19854088 G A 0 222 0 0.6672 0.4058 0.3804 0.3542 0.337 0.1943 0.656207 0.43284 0.318425 1 6733 42201 4411 3568 2053 21691 304 3441 2 10406 121394 11574 8642 6614 66738 908 16512 0.997905 0 . 0 . 160 30,35,43,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R109K|2488|NAV2|protein_coding|CODING|NM_001244963.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948923 rs6483617 -0.693147 0.845125 160 K593 2488 aaA/aaG LOW 8 SILENT CODING NAV2 G protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19955500 A G 0 228 0 0.6452 0.7334 0.7911 0.6438 0.9066 0.726 0.675307 0.837954 0.921267 2 6900 96960 8027 5413 5360 60079 722 10459 2 10300 117604 11532 8566 6602 65582 876 14146 0 . 0 . 0 163 0,0,59,88 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K593|2488|NAV2|protein_coding|CODING|NM_001244963.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1372989 -0.693147 0.000197752 163 D865 2488 gaC/gaT LOW 11 SILENT CODING NAV2 T protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19970507 C T 0 176 0 0.003 0.0749 0.0937 0.0188 0.0775 0.2137 0.0138699 0.0579945 0.0805963 1 146 11351 1348 217 583 5790 68 3199 2 10346 121124 11566 8632 6612 66566 902 16500 0.53895 0 . 0 . 55 30,9,10,6 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D865|2488|NAV2|protein_coding|CODING|NM_001244963.1|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990388 rs12284679 -0.689466 0.791925 55 D882 2488 gaT/gaC LOW 11 SILENT CODING NAV2 C protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19970558 T C 0 228 0 0.8661 0.9631 0.9885 1 1 1 0.899954 0.96565 0.999301 2 9330 120125 11520 8646 6614 66610 900 16505 2 10384 121260 11570 8646 6614 66630 904 16512 0 . 0 . 0 67 0,0,33,23 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D882|2488|NAV2|protein_coding|CODING|NM_001244963.1|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2585773 -0.693147 0.825537 67 D889 2488 gaC/gaT LOW 11 SILENT CODING NAV2 T protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 19970579 C T 0 228 0 0.7958 0.9431 0.9813 1 0.999 0.999 0.843793 0.94655 0.999185 2 8609 119167 11486 8634 6614 66452 900 16472 2 10352 121030 11568 8634 6614 66476 904 16482 0 . 0 . 0 70 0,0,29,32 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D889|2488|NAV2|protein_coding|CODING|NM_001244963.1|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2707084 -0.693147 0.089524 70 E1041D 2488 gaG/gaT MODERATE 14 MISSENSE CODING NAV2 T protein_coding NM_001244963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20065673 G T 0 222 0 0.0242 0.2704 0.2709 0.4504 0.2227 0.4663 0.0540172 0.147701 0.195698 1 516 30386 3968 3912 2249 12124 265 7352 2 10398 121322 11564 8620 6608 66712 908 16512 0.726597 0 . 0 . 145 30,30,35,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E1041D|2488|NAV2|protein_coding|CODING|NM_001244963.1|14|T),INTRAGENIC(MODIFIER|||||NAV2-AS2||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.373802 rs3802799 -0.693147 0.0628107 145 P1077A 2488 Cct/Gct MODERATE 14 MISSENSE CODING NAV2 G protein_coding NM_001244963.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20065779 C G 0 228 0 0.6664 0.8814 0.8876 0.9484 0.9861 0.9908 0.711757 0.891281 0.983256 2 7223 115194 10544 8089 6597 65473 876 16392 2 10344 121138 11566 8620 6614 66578 906 16510 0 . 0 . 0 51 0,0,4,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P1077A|2488|NAV2|protein_coding|CODING|NM_001244963.1|14|G),INTRAGENIC(MODIFIER|||||NAV2-AS2||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3802800 -0.693147 0.229108 51 D1273 2488 gaC/gaT LOW 15 SILENT CODING NAV2 T protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20067064 C T 0 228 0 0.5983 0.6623 0.6628 0.8313 0.5378 0.7025 0.611893 0.566508 0.543256 2 6321 74184 8489 7402 4055 35887 568 11462 2 10386 121256 11572 8632 6606 66644 906 16510 1 0 . 0 . 58 1,0,26,29 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1273|2488|NAV2|protein_coding|CODING|NM_001244963.1|15|T),INTRAGENIC(MODIFIER|||||NAV2-AS2||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7125647 -0.693147 0.18105 58 N1717 2488 aaT/aaC LOW 24 SILENT CODING NAV2 C protein_coding NM_001244963.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20089944 T C 0 228 0 0.348 0.3141 0.2853 0.5526 0.1928 0.1677 0.316387 0.229356 0.184767 2 3377 29257 4258 4845 1492 12607 199 2479 2 10344 121040 11528 8622 6610 66550 904 16482 0 . 0 . 0 68 0,0,10,54 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N1717|2488|NAV2|protein_coding|CODING|NM_001244963.1|24|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1442710 -0.693147 0.416051 68 A1722 2488 gcA/gcT LOW 25 SILENT CODING NAV2 T protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20099112 A T 0 228 0 0.8782 0.9085 0.8977 0.9514 0.8917 0.9305 0.869042 0.874289 0.876977 2 9027 108681 10870 8260 6003 58396 825 15300 2 10396 121338 11572 8640 6610 66706 908 16506 0 . 0 . 0 144 0,0,78,44 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcT|A1722|2488|NAV2|protein_coding|CODING|NM_001244963.1|25|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4757028 -0.693147 0.0093731 144 D1746 2488 gaC/gaT LOW 26 SILENT CODING NAV2 T protein_coding NM_001244963.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20099541 C T 0 228 0 0.8835 0.9083 0.8919 0.9573 0.8887 0.9233 0.867907 0.865908 0.864884 2 8997 107364 10782 8147 6244 57332 817 15045 2 10330 120596 11520 8546 6600 66258 906 16436 0 . 0 . 0 83 0,0,52,25 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1746|2488|NAV2|protein_coding|CODING|NM_001244963.1|26|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6483642 -0.693147 0.206164 83 S1814 2488 agC/agT LOW 27 SILENT CODING NAV2 T protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20101704 C T 0 228 0 0.885 0.9064 0.8847 0.9563 0.8787 0.9274 0.865411 0.862141 0.860465 2 9006 107560 10750 8182 6239 57391 810 15182 2 10354 121116 11548 8602 6600 66604 902 16506 0 . 0 . 0 68 0,0,27,35 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1814|2488|NAV2|protein_coding|CODING|NM_001244963.1|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1867114 -0.693147 0.557516 68 R1828 2488 Cgg/Agg LOW 27 SILENT CODING NAV2 A protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20101744 C A 0 228 0 0.9607 0.9317 0.889 0.9583 0.8797 0.9489 0.940536 0.887898 0.86093 2 9665 108070 10726 8142 6217 57085 811 15424 2 10268 120486 11496 8548 6578 66254 898 16444 0 . 0 . 0 62 0,0,23,32 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R1828|2488|NAV2|protein_coding|CODING|NM_001244963.1|27|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1867115,rs386547104 -0.693147 0.00971487 62 S1894 2488 tcA/tcC LOW 29 SILENT CODING NAV2 C protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20112417 A C 0 228 0 0.4592 0.4069 0.4467 0.6349 0.3101 0.1728 0.409669 0.350069 0.319535 2 4407 42249 5774 5643 2220 21339 259 2607 2 10384 120840 11534 8596 6586 66448 900 16392 1 0 . 0 . 120 0,1,54,47 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S1894|2488|NAV2|protein_coding|CODING|NM_001244963.1|29|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2243624 -0.693147 0.0343431 120 H2036 2488 caT/caC LOW 32 SILENT CODING NAV2 C protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20117232 T C 0 228 0 0.2239 0.4535 0.438 0.8899 0.3012 0.4816 0.220835 0.257112 0.275698 2 2331 45850 6700 7832 2358 18400 342 7887 2 10406 121376 11578 8650 6612 66712 908 16510 0 . 0 . 0 257 0,0,158,71 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H2036|2488|NAV2|protein_coding|CODING|NM_001244963.1|32|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2289566 -0.693147 0.0977289 257 G2236 2488 ggA/ggC LOW 35 SILENT CODING NAV2 C protein_coding NM_001244963.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20124914 A C 0 228 0 0.7814 0.9173 0.9669 0.9573 0.9881 0.9519 0.824103 0.933262 0.989186 2 8490 117485 11399 8176 6604 66075 877 15864 2 10404 121376 11578 8650 6614 66722 908 16500 1 0 . 0 . 92 0,1,41,40 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G2236|2488|NAV2|protein_coding|CODING|NM_001244963.1|35|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2243411,rs386562333 -0.693147 0.0305856 92 2488 133 MODIFIER 40 CODING NAV2 T protein_coding NM_001244963.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20139937 C T 0 222 0 0.1362 0.1779 0.232 0.374 0.0974 0.0767 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.803979 0 . 0 . 67 5,28,3,27 UTR_3_PRIME(MODIFIER||133||2488|NAV2|protein_coding|CODING|NM_001244963.1|40|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.29844 rs3802803 -0.693097 0.0515385 67 2488 583 MODIFIER 40 CODING NAV2 G protein_coding NM_001244963.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20140387 A G 0 222 0 0.3858 0.7189 0.8329 0.746 0.8946 0.8793 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969171 0 . 0 . 144 48,22,26,27 UTR_3_PRIME(MODIFIER||583||2488|NAV2|protein_coding|CODING|NM_001244963.1|40|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.935499 rs3087788 -0.693147 0.214953 144 2488 667 MODIFIER 40 CODING NAV2 G protein_coding NM_001244963.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20140471 A G 0 222 0 0.4372 0.7404 0.8444 0.751 0.9135 0.8875 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.527607 0 . 0 . 103 23,31,15,26 UTR_3_PRIME(MODIFIER||667||2488|NAV2|protein_coding|CODING|NM_001244963.1|40|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.884292 rs894445 -0.693145 0.0157844 103 2488 2035 MODIFIER 40 CODING NAV2 A protein_coding NM_001244963.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20141839 G A 0 142 0 0.6051 0.4499 0.379 0.7698 0.2058 0.2117 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||2035||2488|NAV2|protein_coding|CODING|NM_001244963.1|40|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2246192 -0.662043 0.369599 9 2488 2644 MODIFIER 40 CODING NAV2 C protein_coding NM_001244963.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20142448 T C 0 222 0 0.0151 0.1248 0.2032 0.373 0.0368 0.0521 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.701231 0 . 0 . 77 24,12,15,16 UTR_3_PRIME(MODIFIER||2644||2488|NAV2|protein_coding|CODING|NM_001244963.1|40|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.917502 rs78606106 -0.69311 0.0103615 77 343 LOW 3 CODING DBX1 A protein_coding NM_001029865.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20178575 G A 0 148 0 0 0.0063898 0 0.0288 0 0.0031 0.000226963 7.6888e-05 0 1 2 200 0 195 0 0 0 3 2 9920 118516 11456 8494 6550 64814 876 16406 0.999893 0 . 0 . 39 18,1,18,1 SPLICE_SITE_REGION+INTRON(LOW||||343|DBX1|protein_coding|CODING|NM_001029865.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.337283 rs77814312 -0.69168 6.84713e-06 39 S231R 276 agT/agG MODERATE 6 MISSENSE CODING HTATIP2 G protein_coding NM_001098520.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20404613 T G 0 222 0 0.587 0.7121 0.7205 0.4673 0.9433 0.8896 0.641398 0.84561 0.950233 1 6634 103737 7495 4265 6298 63393 801 14851 2 10354 120996 11430 8568 6606 66628 908 16502 0.966137 0 . 0 . 203 81,12,61,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S231R|276|HTATIP2|protein_coding|CODING|NM_001098520.1|6|G),UPSTREAM(MODIFIER||4463||531|PRMT3|protein_coding|CODING|NM_005788.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.211202 rs3824886 -0.693147 0.0504521 203 276 6 MODIFIER 6 CODING HTATIP2 C protein_coding NM_001098520.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20404757 T C 0 222 0 0.5855 0.7107 0.7176 0.4673 0.9404 0.8896 0.64049 0.843995 0.948256 1 6461 101586 7143 4158 6144 62280 786 14614 2 9882 117608 10604 7948 6462 65610 888 16214 0.870195 0 . 0 . 98 6,48,5,33 UTR_3_PRIME(MODIFIER||6||276|HTATIP2|protein_coding|CODING|NM_001098520.1|6|C),UPSTREAM(MODIFIER||4319||531|PRMT3|protein_coding|CODING|NM_005788.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930122 rs3781679 -0.693143 0.0425813 98 531 124 MODIFIER 1 CODING PRMT3 C protein_coding NM_005788.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20409169 G C 0 81 0 0.7209 0.8387 0.8646 0.7748 0.9473 0.9335 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 2,0,1,3 UTR_5_PRIME(MODIFIER||124||531|PRMT3|protein_coding|CODING|NM_005788.3|1|C),DOWNSTREAM(MODIFIER||3840||276|HTATIP2|protein_coding|CODING|NM_001098520.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.861511 0 0.25 rs2270678 -0.556411 0.292086 6 531 LOW 8 CODING PRMT3 C protein_coding NM_005788.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20429454 T C 0 228 0 0.9977 0.9101 0.8617 0.6964 0.995 0.9591 0.995007 0.99554 0.995814 2 10351 115136 8950 6032 6551 66406 878 15968 2 10404 121342 11544 8644 6612 66720 908 16510 1 0 . 0 . 67 1,0,55,6 SPLICE_SITE_REGION+INTRON(LOW||||531|PRMT3|protein_coding|CODING|NM_005788.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10741836 -0.693147 0.0297939 67 S508N 531 aGt/aAt MODERATE 16 MISSENSE CODING PRMT3 A protein_coding NM_005788.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20529886 G A 0 228 0 1 0.9914 1 0.9573 1 1 0.999546 0.999846 1 2 10383 120921 11569 8245 6612 66707 906 16499 2 10388 121316 11570 8628 6612 66708 908 16502 1 0 . 0 . 101 1,0,63,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S508N|531|PRMT3|protein_coding|CODING|NM_005788.3|16|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6483700 -0.693147 0.385238 101 A162G 797 gCc/gGc MODERATE 2 MISSENSE CODING SLC6A5 G protein_coding NM_004211.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20623156 C G 0 228 0 0.9758 0.9936 1 1 1 1 0.980481 0.993234 0.999767 2 10106 120344 11518 8632 6408 66302 886 16492 2 10292 120546 11522 8632 6408 66312 888 16492 0 . 0 . 0 109 0,0,44,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gGc|A162G|797|SLC6A5|protein_coding|CODING|NM_004211.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1443549 -0.693147 0.0945941 109 S410 797 tcA/tcG LOW 7 SILENT CODING SLC6A5 G protein_coding NM_004211.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20639400 A G 0 228 0 0.9902 0.9974 1 1 1 1 0.985474 0.995002 0.999884 2 10288 121276 11575 8654 6614 66729 905 16511 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 124 0,0,46,66 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S410|797|SLC6A5|protein_coding|CODING|NM_004211.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7925597 -0.693147 0.000169814 124 K457N 797 aaG/aaC MODERATE 8 MISSENSE CODING SLC6A5 C protein_coding NM_004211.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20648364 G C 0 222 0 0.0091 0.0905 0.0922 0.0744 0.1392 0.1656 0.0304131 0.116715 0.16093 1 276 16254 850 596 1276 10771 116 2369 2 10406 121408 11578 8654 6612 66738 908 16512 0.841269 0 . 0 COSM1353176 99 20,25,17,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K457N|797|SLC6A5|protein_coding|CODING|NM_004211.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.377213 rs3740870 -0.693145 0.00199901 99 D463N 797 Gat/Aat MODERATE 8 MISSENSE CODING SLC6A5 A protein_coding NM_004211.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20648380 G A 0 222 0 0.1165 0.1627 0.1787 0.0883 0.2505 0.2004 0.125057 0.232277 0.287209 1 1246 27408 1402 662 1949 18752 219 3178 2 10404 121390 11578 8654 6612 66722 908 16512 0.448436 0 . 0 COSM1353177 86 11,23,10,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D463N|797|SLC6A5|protein_coding|CODING|NM_004211.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999306 rs1805091 -0.693145 0.387312 86 E701 797 gaG/gaA LOW 15 SILENT CODING SLC6A5 A protein_coding NM_004211.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20673867 G A 0 228 0 0.1543 0.4782 0.5562 0.8234 0.4414 0.5429 0.185202 0.323774 0.394767 2 1933 54696 7697 7275 2701 26146 434 8510 2 10406 121390 11576 8646 6612 66730 908 16512 0 . 0 . 0 170 0,0,95,63 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E701|797|SLC6A5|protein_coding|CODING|NM_004211.3|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276433 -0.693147 0.69582 170 R110Q 838 cGg/cAg MODERATE 4 MISSENSE CODING NELL1 A protein_coding NM_001288713.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20805286 G A 0 222 0 0.2269 0.6372 0.8256 0.8393 0.7396 0.7444 0.302088 0.602414 0.756279 1 3059 89357 10288 7473 4380 51053 678 12426 2 10394 121382 11574 8654 6614 66728 908 16510 0.928549 0 . 0 . 79 23,17,16,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R110Q|838|NELL1|protein_coding|CODING|NM_001288713.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903654 rs8176785 -0.693132 0.222306 79 S126 838 tcC/tcT LOW 4 SILENT CODING NELL1 T protein_coding NM_001288713.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 20805335 C T 0 222 0 0.4523 0.2744 0.1513 0.1607 0.2575 0.2556 0.438947 0.308012 0.24093 1 4499 28885 1121 1179 2234 15576 211 4065 2 10406 121376 11574 8648 6614 66720 908 16506 0.932337 0 . 0 COSM428830 84 21,23,13,17 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S126|838|NELL1|protein_coding|CODING|NM_001288713.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.978359 rs2280363 -0.693097 0.14932 84 G647 838 ggC/ggT LOW 18 SILENT CODING NELL1 T protein_coding NM_001288713.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 21581805 C T 0 222 0 0.2481 0.5431 0.634 0.5774 0.8101 0.5675 0.36995 0.666615 0.818605 1 3551 85640 6304 5407 5155 54454 653 10116 2 10404 121172 11528 8536 6606 66680 908 16510 0.380979 0 . 0 . 79 27,16,13,16 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G647|838|NELL1|protein_coding|CODING|NM_001288713.1|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.801134 rs8176789 -0.693079 0.870997 79 582 838 MODIFIER 12 CODING SLC17A6 A protein_coding NM_020346.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22400124 C A 0 222 0 0.4123 0.2692 0.2046 0.2698 0.172 0.2209 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.6254 0 . 0 . 156 57,24,34,16 UTR_3_PRIME(MODIFIER||838||582|SLC17A6|protein_coding|CODING|NM_020346.2|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.219636 rs1979072 -0.693147 0.350965 156 582 983 MODIFIER 12 CODING SLC17A6 G protein_coding NM_020346.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22400269 A G 0 161 0 0.4123 0.269 0.2046 0.2688 0.172 0.2209 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.769584 0 . 0 . 65 1,34,1,29 UTR_3_PRIME(MODIFIER||983||582|SLC17A6|protein_coding|CODING|NM_020346.2|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.941011 rs1979073 -0.693097 0.135528 65 582 1416 MODIFIER 12 CODING SLC17A6 G protein_coding NM_020346.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22400702 A G 0 222 0 0 0.0057907 0 0.0228 0.003 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.832491 0 . 0 . 55 12,8,17,16 UTR_3_PRIME(MODIFIER||1416||582|SLC17A6|protein_coding|CODING|NM_020346.2|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.896309 rs149858476 -0.693127 0.900152 55 374 819 MODIFIER 1 CODING FANCF A protein_coding NM_022725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22645413 G A 0 23.7 0 0.8971 0.9491 0.9928 0.9157 1 0.9703 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||819||374|FANCF|protein_coding|CODING|NM_022725.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs450946 -0.379885 0 2 374 207 MODIFIER 1 CODING FANCF A protein_coding NM_022725.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22646025 G A 0 190 0 0.3442 0.7037 0.7565 0.878 0.8549 0.817 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,21,0 UTR_3_PRIME(MODIFIER||207||374|FANCF|protein_coding|CODING|NM_022725.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4447177 -0.692352 0.207456 22 374 10 MODIFIER 1 CODING FANCF A protein_coding NM_022725.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22647366 G A 0 222 0 0.0424 0.1138 0.0937 0.1964 0.2028 0.0481 0.0633227 0.146625 0.189302 1 652 18746 865 1855 1902 12219 166 1087 2 10176 119642 11504 8532 6558 65560 894 16418 0.735419 0 . 0 . 359 63,96,64,89 START_GAINED(LOW||||374|FANCF|protein_coding|CODING|NM_022725.3|1|A),UTR_5_PRIME(MODIFIER||10||374|FANCF|protein_coding|CODING|NM_022725.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972964 rs3740615 -0.693147 0.0109799 359 G12 313 ggA/ggG LOW 2 SILENT CODING GAS2 G protein_coding NM_001143830.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22696451 A G 0 222 0 0.1747 0.5242 0.6095 0.749 0.67 0.5542 0.256922 0.54398 0.691047 1 2517 75055 7248 6567 4434 44647 564 9078 2 10394 121108 11462 8638 6588 66630 908 16488 0.883894 0 . 0 COSM147166 170 58,11,72,12 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G12|313|GAS2|protein_coding|CODING|NM_001143830.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.706164 rs922571 -0.693147 0.0268491 170 313 627 MODIFIER 8 CODING GAS2 T protein_coding NM_001143830.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 22834189 C T 0 222 0 0.0363 0.2632 0.3372 0.4583 0.2773 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.715873 0 . 0 . 57 15,14,11,15 UTR_3_PRIME(MODIFIER||627||313|GAS2|protein_coding|CODING|NM_001143830.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.584233 rs1055320 -0.692976 0.649584 57 346 LOW 4 CODING LUZP2 A protein_coding NM_001009909.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 24759855 G A 0 222 0 0.1082 0.3442 0.379 0.5774 0.3191 0.4243 0.14503 0.255882 0.312674 1 1459 42322 4807 5108 2837 20852 340 6919 2 10264 119774 11260 8550 6552 65836 894 16418 0.768875 0 . 0 . 116 25,30,24,26 SPLICE_SITE_REGION+INTRON(LOW||||346|LUZP2|protein_coding|CODING|NM_001009909.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.950817 rs1564992 -0.693147 0.0553331 116 346 LOW 5 CODING LUZP2 T protein_coding NM_001009909.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 24784862 A T 0 222 0 0.6566 0.5948 0.5476 0.4643 0.671 0.6012 0.641947 0.663627 0.674783 1 6228 75813 5581 3885 4604 44566 554 10395 2 9842 118124 11260 8500 6488 64982 892 16160 0.800166 0 . 0 . 161 23,62,16,39 SPLICE_SITE_REGION+INTRON(LOW||||346|LUZP2|protein_coding|CODING|NM_001009909.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.606205 rs2716532 -0.693147 0.0585515 161 E308Q 346 Gag/Cag MODERATE 11 MISSENSE CODING LUZP2 C protein_coding NM_001009909.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 25098938 G C 0 228 0 0.1195 0.4383 0.4712 0.7808 0.4553 0.4755 0.16818 0.335384 0.421047 2 1622 52867 5078 6972 3197 27993 427 7578 2 10406 121400 11576 8650 6614 66734 908 16512 1 0 . 0 . 128 1,0,23,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E308Q|346|LUZP2|protein_coding|CODING|NM_001009909.3|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7930185 -0.693147 0.65782 128 346 25 MODIFIER 12 CODING LUZP2 A protein_coding NM_001009909.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 25100229 G A 0 228 0 0.0628 0.4213 0.4625 0.7748 0.4553 0.4775 0.125284 0.320852 0.421047 2 1163 51192 4905 6594 3152 27418 417 7543 2 9896 117328 11096 8264 6512 64442 880 16238 0 . 0 . 0 128 0,0,72,47 UTR_3_PRIME(MODIFIER||25||346|LUZP2|protein_coding|CODING|NM_001009909.3|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10500994 -0.693147 0.671878 128 346 2127 MODIFIER 12 CODING LUZP2 G protein_coding NM_001009909.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 25102331 A G 0 9.7 0 0.2352 0.4944 0.4784 0.8671 0.4632 0.5041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2127||346|LUZP2|protein_coding|CODING|NM_001009909.3|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17050 -0.379885 0 1 346 2211 MODIFIER 12 CODING LUZP2 T protein_coding NM_001009909.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 25102415 C T 0 9.7 0 0.1884 0.4812 0.4741 0.8661 0.4632 0.5041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2211||346|LUZP2|protein_coding|CODING|NM_001009909.3|12|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1374133 -0.379885 0 1 346 3337 MODIFIER 12 CODING LUZP2 T protein_coding NM_001009909.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 25103541 A T 0 36.8 0 0.2292 0.489 0.4784 0.8671 0.4642 0.4836 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,0 UTR_3_PRIME(MODIFIER||3337||346|LUZP2|protein_coding|CODING|NM_001009909.3|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7946603 -0.453602 0.5 4 L447 1042 ctA/ctG LOW 13 SILENT CODING ANO3 G protein_coding NM_001313726.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26568966 A G 0 222 0 0.5522 0.6751 0.7061 0.8135 0.666 0.6861 0.5867 0.6507 0.683488 1 6066 83246 8177 7043 4854 44901 625 11580 2 10404 121306 11556 8634 6614 66686 908 16504 0.147145 0 . 0 . 293 87,58,63,52 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L447|1042|ANO3|protein_coding|CODING|NM_001313726.1|13|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999833 rs2663168 -0.693147 0.173906 293 361 945 MODIFIER 5 CODING MUC15 G protein_coding NM_001135091.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26581667 A G 0 125 0 0.1505 0.2053 0.17 0.1944 0.2495 0.2699 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||945||361|MUC15|protein_coding|CODING|NM_001135091.1|5|G),INTRON(MODIFIER||||1042|ANO3|protein_coding|CODING|NM_001313726.1|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs17243454 -0.556411 0.891512 5 I22V 361 Ata/Gta MODERATE 3 MISSENSE CODING MUC15 C protein_coding NM_001135091.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26587423 T C 0 222 0 0 0.0073882 0 0.0367 0 0 0.000228728 7.7387e-05 0 1 1 242 0 236 0 0 2 3 2 9226 115300 11160 8230 6516 63520 864 15784 0.662581 0 . 0 . 42 7,9,3,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I22V|361|MUC15|protein_coding|CODING|NM_001135091.1|3|C),INTRON(MODIFIER||||1042|ANO3|protein_coding|CODING|NM_001313726.1|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.198356 rs141903076 -0.692067 0.444328 42 F724 1042 ttC/ttT LOW 21 SILENT CODING ANO3 T protein_coding NM_001313726.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26656563 C T 0 228 0 0.2277 0.3413 0.2507 0.3552 0.4165 0.4673 0.234226 0.355352 0.417423 2 2385 46227 2551 3085 2209 27791 335 7871 2 10400 121312 11546 8636 6612 66704 906 16508 1 0 . 0 . 80 0,1,41,29 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F724|1042|ANO3|protein_coding|CODING|NM_001313726.1|21|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7946841 -0.693147 0.0249365 80 P955 1042 ccC/ccT LOW 27 SILENT CODING ANO3 T protein_coding NM_001313726.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26677947 C T 0 228 0 0.3268 0.5585 0.5519 0.5655 0.666 0.7587 0.360872 0.561058 0.663643 2 3655 76999 6108 4844 4352 45028 588 12424 2 10402 121324 11548 8640 6610 66706 908 16510 0 . 0 . 0 80 0,0,33,35 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P955|1042|ANO3|protein_coding|CODING|NM_001313726.1|27|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10835051 -0.693147 0.108902 80 1042 843 MODIFIER 28 CODING ANO3 A protein_coding NM_001313726.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26682834 T A 0 228 0 0.6377 0.8021 0.7536 0.8938 0.8996 0.864 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 64 0,0,54,9 UTR_3_PRIME(MODIFIER||843||1042|ANO3|protein_coding|CODING|NM_001313726.1|28|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3802755 -0.693147 0.04056 64 1042 2626 MODIFIER 28 CODING ANO3 T protein_coding NM_001313726.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26684617 G T 0 228 0 0.0265 0.2881 0.2392 0.3552 0.4304 0.4611 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,4,16 UTR_3_PRIME(MODIFIER||2626||1042|ANO3|protein_coding|CODING|NM_001313726.1|28|T),DOWNSTREAM(MODIFIER||3949||618|SLC5A12|protein_coding|CODING|NM_178498.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3550 -0.692067 0.229976 21 618 1332 MODIFIER 15 CODING SLC5A12 G protein_coding NM_178498.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26691317 T G 0 32.6 0 0.236 0.3464 0.2608 0.3532 0.4314 0.4622 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1332||618|SLC5A12|protein_coding|CODING|NM_178498.3|15|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4615979 -0.379885 0 2 618 384 MODIFIER 15 CODING SLC5A12 A protein_coding NM_178498.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26692265 G A 0 64 0 0.1808 0.3319 0.2565 0.3562 0.4314 0.4622 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||384||618|SLC5A12|protein_coding|CODING|NM_178498.3|15|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10835055 -0.511536 0.126715 3 618 214 MODIFIER 15 CODING SLC5A12 C protein_coding NM_178498.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26692435 T C 0 165 0 0.2753 0.3702 0.2853 0.3532 0.4672 0.4765 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,21,0 UTR_3_PRIME(MODIFIER||214||618|SLC5A12|protein_coding|CODING|NM_178498.3|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11029666 -0.692352 0.800253 21 C559 618 tgT/tgC LOW 14 SILENT CODING SLC5A12 G protein_coding NM_178498.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26694979 A G 0 228 0 0.4448 0.4229 0.3127 0.3502 0.4881 0.4796 0.435531 0.481779 0.504383 2 4315 55151 3064 3074 2633 33354 411 8300 2 9798 120094 11518 8612 6612 66504 894 16156 1 0 . 0 . 159 0,1,47,94 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C559|618|SLC5A12|protein_coding|CODING|NM_178498.3|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4369354 -0.693147 0.00198423 159 L471 618 ctG/ctA LOW 12 SILENT CODING SLC5A12 T protein_coding NM_178498.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26702664 C T 0 228 0 0.9682 0.9912 0.9971 1 1 1 0.972164 0.991095 0.999879 2 9510 120081 11399 8586 6590 66597 898 16501 2 9794 120386 11416 8586 6590 66600 898 16502 0 . 0 . 0 185 0,0,96,72 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L471|618|SLC5A12|protein_coding|CODING|NM_178498.3|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10734383 -0.693147 0.0440057 185 N434 618 aaT/aaC LOW 11 SILENT CODING SLC5A12 G protein_coding NM_178498.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26705310 A G 0 228 0 0.3185 0.4351 0.3689 0.3472 0.6342 0.5256 0.377054 0.542235 0.617761 2 2310 39468 1618 1878 1818 25480 273 6091 2 5756 66912 3476 4446 2986 38976 492 10780 0 . 0 . 0 189 0,0,104,59 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N434|618|SLC5A12|protein_coding|CODING|NM_178498.3|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3924551 -0.693147 0.00482221 189 T128 618 acG/acA LOW 2 SILENT CODING SLC5A12 T protein_coding NM_178498.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 26734209 C T 0 228 0 0.3956 0.7704 0.8963 0.8631 0.9592 0.8978 0.48434 0.796678 0.956734 2 5001 108260 10491 7530 6046 63747 839 14606 2 10398 121360 11566 8648 6614 66716 908 16510 0 . 0 . 0 128 0,0,71,43 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T128|618|SLC5A12|protein_coding|CODING|NM_178498.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10742156 -0.693147 0.0253126 128 387 1 MODIFIER 3 CODING BBOX1 T protein_coding NM_003986.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27076977 C T 0 222 0 0.0083 0.1406 0.232 0.2619 0.1233 0.1472 0.0365577 0.104369 0.139102 1 316 17873 3214 2444 759 8714 134 2292 2 10400 121264 11566 8634 6606 66664 904 16490 0.840493 0 . 0 . 73 26,11,16,12 UTR_5_PRIME(MODIFIER||1||387|BBOX1|protein_coding|CODING|NM_003986.2|3|T),INTRAGENIC(MODIFIER|||||BBOX1-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.221822 rs2305095 -0.693054 0.0573721 73 S47 387 tcC/tcT LOW 3 SILENT CODING BBOX1 T protein_coding NM_003986.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27077118 C T 0 228 0 1 1 1 1 1 1 0.999773 0.999923 1 2 10400 121392 11578 8650 6610 66734 908 16512 2 10406 121398 11578 8650 6610 66734 908 16512 0 . 0 . 0 63 0,0,28,33 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S47|387|BBOX1|protein_coding|CODING|NM_003986.2|3|T),INTRAGENIC(MODIFIER|||||BBOX1-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10767598 -0.693147 0.0105987 63 373 188 MODIFIER 6 CODING CCDC34 G protein_coding NM_030771.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27360180 A G 0 56 0 0.9523 0.9872 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||188||373|CCDC34|protein_coding|CODING|NM_030771.1|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10835167 -0.556411 0.681156 4 951 1782 MODIFIER 18 CODING LGR4 A protein_coding NM_018490.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27387632 G A 0 228 0 0.5787 0.6308 0.7839 0.5784 0.7028 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 191 0,1,121,43 UTR_3_PRIME(MODIFIER||1782||951|LGR4|protein_coding|CODING|NM_018490.2|18|A),UPSTREAM(MODIFIER||2837||373|CCDC34|protein_coding|CODING|NM_030771.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs8290 -0.693147 0.0775052 191 951 910 MODIFIER 18 CODING LGR4 A protein_coding NM_018490.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27388504 G A 0 76 0 0.5802 0.6312 0.7839 0.5784 0.7028 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||910||951|LGR4|protein_coding|CODING|NM_018490.2|18|A),UPSTREAM(MODIFIER||3709||373|CCDC34|protein_coding|CODING|NM_030771.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046568 -0.511536 0.148533 3 K727 951 aaA/aaG LOW 18 SILENT CODING LGR4 C protein_coding NM_018490.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27390089 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 10401 121405 11576 8654 6614 66740 908 16512 2 10404 121408 11576 8654 6614 66740 908 16512 0 . 0 . 0 78 0,0,30,42 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K727|951|LGR4|protein_coding|CODING|NM_018490.2|18|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2447997 -0.693147 0.219623 78 197 3479 MODIFIER 5 CODING LIN7C C protein_coding NM_018362.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27516717 T C 0 179 0 0.0688 0.3648 0.304 0.4425 0.5447 0.5429 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.788445 0 . 0 . 24 1,10,2,9 UTR_3_PRIME(MODIFIER||3479||197|LIN7C|protein_coding|CODING|NM_018362.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.751921 rs3209593 -0.676189 0.690053 24 197 3411 MODIFIER 5 CODING LIN7C G protein_coding NM_018362.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27516785 C G 0 8.7 0 0.7005 0.7504 0.6354 0.7629 0.7793 0.8569 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.571429 0 . 0 . 9 0,7,0,2 UTR_3_PRIME(MODIFIER||3411||197|LIN7C|protein_coding|CODING|NM_018362.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.428571 rs11030034 -0.453602 0.92 9 329 2327 MODIFIER 3 CODING BDNF T protein_coding NM_001143810.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27677041 C T 0 152 0 0.4887 0.6701 0.7262 0.9058 0.7068 0.5951 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,1,6 UTR_3_PRIME(MODIFIER||2327||329|BDNF|protein_coding|CODING|NM_001143810.1|3|T),INTRAGENIC(MODIFIER|||||BDNF-AS||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7124442 -0.636426 0.416565 7 329 1785 MODIFIER 3 CODING BDNF A protein_coding NM_001143810.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27677583 C A 0 23.4 0 0.0499 0.229 0.1729 0.4772 0.2217 0.2628 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1785||329|BDNF|protein_coding|CODING|NM_001143810.1|3|A),INTRAGENIC(MODIFIER|||||BDNF-AS||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11030099 -0.453602 0.18 2 329 1782 MODIFIER 3 CODING BDNF T protein_coding NM_001143810.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27677586 G T 0 23.4 0 0.0499 0.2284 0.17 0.4762 0.2217 0.2628 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1782||329|BDNF|protein_coding|CODING|NM_001143810.1|3|T),INTRAGENIC(MODIFIER|||||BDNF-AS||NON_CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11030100 -0.453602 0.18 2 A232 329 gcA/gcG LOW 3 SILENT CODING BDNF C protein_coding NM_001143810.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27679662 T C 0 228 0 0.9826 0.9952 0.9986 1 1 1 0.98842 0.996078 1 2 10282 121280 11573 8654 6614 66737 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 2 benign 0 . 72 0,0,29,36 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A232|329|BDNF|protein_coding|CODING|NM_001143810.1|3|C),INTRAGENIC(MODIFIER|||||BDNF-AS||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2353512 -0.693147 0.0026208 72 V148M 329 Gtg/Atg MODERATE 3 MISSENSE CODING BDNF T protein_coding NM_001143810.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 27679916 C T 0 222 0 0.0106 0.2013 0.1527 0.4881 0.1968 0.2025 0.0417802 0.140286 0.190742 1 360 23511 1736 4206 1006 12852 148 3203 2 10384 121350 11576 8646 6612 66712 908 16512 0.950257 255|255|255|255|255|255|2 other|other|other|other|other|other|benign 0 . 63 7,27,7,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V148M|329|BDNF|protein_coding|CODING|NM_001143810.1|3|T),INTRAGENIC(MODIFIER|||||BDNF-AS||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.359588 rs6265 -0.693021 0.0370624 63 I735V 898 Atc/Gtc MODERATE 14 MISSENSE CODING KIF18A C protein_coding NM_031217.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28057957 T C 0 228 0 0.6384 0.3974 0.2046 0.4762 0.2962 0.2311 0.597411 0.395231 0.291647 2 6192 38792 1871 3827 2127 19690 279 4806 2 10384 120768 11352 8616 6564 66464 906 16482 0 . 0 . 0 74 0,0,34,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I735V|898|KIF18A|protein_coding|CODING|NM_031217.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10458896 -0.693147 0.336464 74 Q458 898 caA/caG LOW 10 SILENT CODING KIF18A C protein_coding NM_031217.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28098605 T C 0 228 0 0 0.0469 0.0014 0.2242 0.003 0.0051 0.00272727 0.00161713 0.00104822 2 10 1975 7 1674 44 136 12 92 2 9954 116128 11172 8342 6496 63270 880 16014 0 . 0 . 0 80 0,0,58,5 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q458|898|KIF18A|protein_coding|CODING|NM_031217.3|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7941488 -0.693147 0.0101957 80 T273A 898 Acc/Gcc MODERATE 6 MISSENSE CODING KIF18A C protein_coding NM_031217.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28110151 T C 0 228 0 0.1634 0.1631 0.036 0.3988 0.0487 0.1278 0.150318 0.0790648 0.042568 2 1576 10881 292 3156 271 2912 57 2617 2 10392 121120 11522 8630 6602 66584 902 16488 0.520833 0 . 0 . 110 2,0,65,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T273A|898|KIF18A|protein_coding|CODING|NM_031217.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.869792 rs12272419 -0.693147 0.157029 110 407 4900 MODIFIER 1 CODING METTL15 A protein_coding NM_001113528.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28129982 C A 0 9.7 0 0.643 0.3976 0.2017 0.4742 0.2962 0.2301 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||4900||407|METTL15|protein_coding|CODING|NM_001113528.1|1|A),UPSTREAM(MODIFIER||236||898|KIF18A|protein_coding|CODING|NM_031217.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3812738 -0.379885 0 1 N31K 407 aaC/aaA MODERATE 3 MISSENSE CODING METTL15 A protein_coding NM_001113528.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28134974 C A 0 228 0 0.764 0.604 0.3905 0.756 0.4364 0.5552 0 . 0 2 6670 56099 4031 5937 2475 27953 384 8649 2 9360 117476 11398 8418 6568 64890 884 15958 0 . 0 . 0 54 0,0,29,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N31K|407|METTL15|protein_coding|CODING|NM_001113528.1|3|A) 0 . 0 . 0 1 0 . 1 0 54 0 0 0.473372 0 . rs60970073 -0.693147 0.186269 54 T67A 407 Act/Gct MODERATE 3 MISSENSE CODING METTL15 G protein_coding NM_001113528.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28135080 A G 0 222 0 0 0.0091853 0.0014 0.0427 0 0.002 0.000908265 0.000307692 0 1 3 318 4 293 0 0 2 16 2 10088 120960 11570 8650 6608 66630 906 16508 0.997716 0 . 0 . 88 25,15,19,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T67A|407|METTL15|protein_coding|CODING|NM_001113528.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 54 0 0.998054 0.0332474 0 0.267969 rs141648004 -0.693139 0.59658 88 407 215 MODIFIER 7 CODING METTL15 G protein_coding NM_001113528.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 28352603 A G 0 74 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||215||407|METTL15|protein_coding|CODING|NM_001113528.1|7|G) 0 . 0 . 0 . 0 . 0 . 37 0 0 . 0 . rs144938816 -0.556411 0.421803 4 Y76 129 taC/taT LOW 3 SILENT CODING FSHB T protein_coding NM_000510.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30255185 C T 0 228 0 0.7572 0.6148 0.5317 0.6696 0.4503 0.5941 0.709355 0.528457 0.435799 2 7424 62307 6250 5795 3236 29702 416 9484 2 10398 121172 11496 8590 6608 66664 906 16510 1 0 . 0 . 153 0,1,71,77 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y76|129|FSHB|protein_coding|CODING|NM_000510.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386601843,rs6169 -0.693147 0.720076 153 129 476 MODIFIER 3 CODING FSHB G protein_coding NM_000510.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30255823 A G 0 23.4 0 0.5613 0.5585 0.5202 0.6696 0.4473 0.5818 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||476||129|FSHB|protein_coding|CODING|NM_000510.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs506197 -0.453602 0.92 2 129 520 MODIFIER 3 CODING FSHB G protein_coding NM_000510.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30255867 C G 0 64 0 0.5613 0.5587 0.5202 0.6696 0.4483 0.5818 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||520||129|FSHB|protein_coding|CODING|NM_000510.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs506306 -0.511536 0.509904 3 129 635 MODIFIER 3 CODING FSHB G protein_coding NM_000510.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30255982 A G 0 77 0 0.5567 0.5573 0.5187 0.6696 0.4473 0.5828 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||635||129|FSHB|protein_coding|CODING|NM_000510.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs676349 -0.511536 0.748679 3 260 7771 MODIFIER 1 CODING ARL14EP T protein_coding NM_152316.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30344725 C T 0 22.9 0 0.0446 0.0869 0.1182 0.0308 0.161 0.1033 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,0,3 START_GAINED(LOW||||260|ARL14EP|protein_coding|CODING|NM_152316.2|1|T),UTR_5_PRIME(MODIFIER||7771||260|ARL14EP|protein_coding|CODING|NM_152316.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs4071559 -0.511536 0.857144 4 260 22 MODIFIER 2 CODING ARL14EP CAG protein_coding NM_152316.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30352473 C CAG 0 228 0 . 0 . 0 . 0 . 0 . 2 8068 81823 7038 7659 4395 42840 588 11235 2 10030 118900 11252 8514 6546 65314 892 16352 0 . 0 . 0 26 0,0,23,1 UTR_5_PRIME(MODIFIER||22||260|ARL14EP|protein_coding|CODING|NM_152316.2|2|CAG) 0 . 0 24 0.923077 0 1 0 1 0 60 0 0 1 0 . rs35824273,rs72516301 -0.692831 0.00345013 26 260 133 MODIFIER 4 CODING ARL14EP T protein_coding NM_152316.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30358475 A T 0 124 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||133||260|ARL14EP|protein_coding|CODING|NM_152316.2|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1222206 -0.651104 0.414968 8 294 839 MODIFIER 6 CODING MPPED2 C protein_coding NM_001584.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30432176 T C 0 222 0 0.5545 0.5733 0.6398 0.4107 0.7087 0.5798 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.994286 0 . 0 . 52 19,8,10,13 UTR_3_PRIME(MODIFIER||839||294|MPPED2|protein_coding|CODING|NM_001584.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.749649 rs553951 -0.692717 0.268183 52 294 795 MODIFIER 6 CODING MPPED2 T protein_coding NM_001584.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30432220 A T 0 222 0 0.1899 0.2887 0.3444 0.3462 0.3529 0.2577 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998657 0 . 0 . 52 24,7,6,12 UTR_3_PRIME(MODIFIER||795||294|MPPED2|protein_coding|CODING|NM_001584.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.839728 rs13642 -0.691153 0.0880389 52 890 LOW 2 CODING DCDC5 A protein_coding NM_020869.3 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30974115 C A 0 222 0 0.0446 0.113 0.2089 0.1607 0.0934 0.1084 0.0486799 0.0871225 0.104269 1 388 11240 2309 969 695 5254 103 1522 2 5862 70212 6258 4822 4638 37082 570 10980 0.17664 0 . 0 COSM147170 157 9,66,15,58 SPLICE_SITE_REGION(LOW||||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A),START_GAINED(LOW||||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A),UTR_5_PRIME(MODIFIER||88||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99991 rs158633 -0.693147 0.067856 157 890 88 MODIFIER 2 CODING DCDC5 A protein_coding NM_020869.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 30974115 C A 0 222 0 0.0446 0.113 0.2089 0.1607 0.0934 0.1084 0.0486799 0.0871225 0.104269 1 388 11240 2309 969 695 5254 103 1522 2 5862 70212 6258 4822 4638 37082 570 10980 0.17664 0 . 0 COSM147170 157 9,66,15,58 SPLICE_SITE_REGION(LOW||||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A),START_GAINED(LOW||||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A),UTR_5_PRIME(MODIFIER||88||890|DCDC5|protein_coding|CODING|NM_020869.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99991 rs158633 -0.693147 0.067856 157 535 LOW 7 CODING ELP4 A protein_coding NM_001288726.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 31653956 C A 0 228 0 0.9387 0.9822 0.9899 1 0.999 1 0.959893 0.987227 0.999636 2 9351 120118 11518 8604 6610 66649 898 16488 2 9800 120606 11544 8604 6610 66660 900 16488 0 . 0 . 0 51 0,0,16,31 SPLICE_SITE_REGION+INTRON(LOW||||535|ELP4|protein_coding|CODING|NM_001288726.1|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4922872 -0.693147 0.44791 51 436 2412 MODIFIER 14 CODING PAX6 T protein_coding NM_001258462.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 31809070 C T 0 18.4 0 0.3275 0.1733 0.1599 0.1756 0.0626 0.0859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,1,0 UTR_3_PRIME(MODIFIER||2412||436|PAX6|protein_coding|CODING|NM_001258462.1|14|T),DOWNSTREAM(MODIFIER||2997||535|ELP4|protein_coding|CODING|NM_001288726.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs662702 -0.379885 0 4 436 1063 MODIFIER 14 CODING PAX6 C protein_coding NM_001258462.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 31810419 T C 0 222 0 0.0008 0.016573 0 0.0794 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.543376 0 . 0 . 162 47,42,38,29 UTR_3_PRIME(MODIFIER||1063||436|PAX6|protein_coding|CODING|NM_001258462.1|14|C),DOWNSTREAM(MODIFIER||4346||535|ELP4|protein_coding|CODING|NM_001288726.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.991728 rs117590302 -0.693147 0.0558597 162 H280 331 caT/caC LOW 5 SILENT CODING RCN1 C protein_coding NM_002901.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32124978 T C 0 228 0 0.23 0.479 0.464 0.6776 0.501 0.5992 0.258629 0.43301 0.522331 2 2653 62209 5845 5917 3263 34783 480 9268 2 10378 121334 11568 8634 6608 66730 906 16510 0 . 0 . 0 172 0,0,58,96 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H280|331|RCN1|protein_coding|CODING|NM_002901.2|5|C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.773922 0 . rs4876 -0.693147 0.000598949 172 V313 331 gtC/gtT LOW 6 SILENT CODING RCN1 T protein_coding NM_002901.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32125961 C T 0 228 0 0.3207 0.5046 0.4683 0.6776 0.505 0.6002 0.316303 0.441624 0.505815 2 3439 62198 5798 5790 3330 34205 484 9152 2 10350 120184 11468 8532 6546 66054 896 16338 0 . 0 . 0 125 0,0,54,51 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V313|331|RCN1|protein_coding|CODING|NM_002901.2|6|T) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.26277 0 . rs11529889 -0.693147 5.81156e-05 125 331 920 MODIFIER 6 CODING RCN1 C protein_coding NM_002901.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32126938 T C 0 228 0 0.3064 0.65 0.6354 0.9613 0.663 0.7904 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,2,12 UTR_3_PRIME(MODIFIER||920||331|RCN1|protein_coding|CODING|NM_002901.2|6|C) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs386604567,rs6711 -0.686358 0.103486 15 331 1239 MODIFIER 6 CODING RCN1 A protein_coding NM_002901.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32127257 G A 0 97 0 0.5968 0.7332 0.6556 0.9613 0.6759 0.7965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||1239||331|RCN1|protein_coding|CODING|NM_002901.2|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs223056 -0.511536 0.946712 4 517 602 MODIFIER 10 CODING WT1 C protein_coding NM_024426.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32410002 T C 0 149 0 0.7927 0.5849 0.4251 0.7202 0.329 0.5409 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.726149 0 . 0 . 14 5,0,7,2 UTR_3_PRIME(MODIFIER||602||517|WT1|protein_coding|CODING|NM_024426.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.764228 rs386597371,rs5030320 -0.662043 0.766668 14 517 267 MODIFIER 10 CODING WT1 G protein_coding NM_024426.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32410337 C G 0 174 0 0.8396 0.5879 0.4135 0.7192 0.2942 0.5378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.898956 0 . 0 . 22 4,8,4,6 UTR_3_PRIME(MODIFIER||267||517|WT1|protein_coding|CODING|NM_024426.4|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.912244 rs5030317 -0.670168 0.807803 22 R369 517 cgA/cgG LOW 7 SILENT CODING WT1 C protein_coding NM_024426.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32417945 T C 0 222 0 0.121 0.3315 0.3156 0.6984 0.172 0.4131 0.112852 0.130288 0.139218 1 1207 28265 4495 5975 1141 9328 193 5926 2 10374 121072 11528 8620 6574 66568 904 16504 0.992148 2 benign 0 COSM1353507,COSM1353508 101 17,22,21,24 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R369|517|WT1|protein_coding|CODING|NM_024426.4|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.830288 rs16754,rs386540677 -0.693147 0.642225 101 S227 517 agC/agT LOW 2 SILENT CODING WT1 A protein_coding NM_024426.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32450131 G A 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 29 0 29 0 0 0 0 2 10252 119614 11436 8576 6144 65916 866 16424 0.460345 0 . 0 . 164 35,42,25,42 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S227|517|WT1|protein_coding|CODING|NM_024426.4|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.891777 rs9332974 -0.693147 0.0379478 164 K644 1079 aaA/aaG LOW 16 SILENT CODING CCDC73 C protein_coding NM_001008391.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32635932 T C 0 222 0 0 0.011382 0.013 0.0466 0.001 0 0.000277316 0.000680967 0.00085974 1 2 738 266 392 31 37 2 8 2 9650 118200 11244 8422 6508 65066 888 16422 0.982456 0 . 0 . 68 15,13,18,15 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K644|1079|CCDC73|protein_coding|CODING|NM_001008391.3|16|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0861455 rs117983166 -0.693127 0.0394224 68 1079 LOW 15 CODING CCDC73 C protein_coding NM_001008391.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32636495 T C 0 122 0 0 0.0077875 0.0014 0.0377 0 0 0 . 0 1 1 220 4 214 0 0 1 0 2 9048 110942 11136 8228 6510 62534 830 12656 0.85666 0 . 0 . 24 0,10,0,14 SPLICE_SITE_REGION+INTRON(LOW||||1079|CCDC73|protein_coding|CODING|NM_001008391.3|15|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 0.919431 rs145888197 -0.686358 0.52378 24 T387 1079 acA/acG LOW 14 SILENT CODING CCDC73 C protein_coding NM_001008391.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32657266 T C 0 191 0 0.792 0.6338 0.6282 0.2302 0.7594 0.7106 0.764507 0.744872 0.736215 1 7494 80354 6804 1730 5604 48866 608 9248 2 9614 113784 11248 8338 6560 64334 830 12860 0.886895 0 . 0 COSM147172 45 10,17,4,12 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T387|1079|CCDC73|protein_coding|CODING|NM_001008391.3|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.679309 rs201854 -0.689466 0.0170033 45 P178 226 ccG/ccA LOW 6 SILENT CODING PRRG4 A protein_coding NM_024081.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32874926 G A 0 228 0 0.3464 0.4054 0.4841 0.4127 0.3986 0.4284 0.37307 0.378403 0.381135 2 3741 48545 5132 3336 2802 25614 396 7524 2 10404 121362 11572 8640 6608 66718 908 16512 0.516393 0 . 0 COSM1353552 203 2,0,125,58 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P178|226|PRRG4|protein_coding|CODING|NM_024081.5|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.54918 rs11032025 -0.693147 0.16688 203 226 524 MODIFIER 6 CODING PRRG4 C protein_coding NM_024081.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32875597 T C 0 32.6 0 0.7254 0.6212 0.6744 0.4871 0.5229 0.682 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||524||226|PRRG4|protein_coding|CODING|NM_024081.5|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7933966 -0.379885 0 2 226 1865 MODIFIER 6 CODING PRRG4 C protein_coding NM_024081.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32876937 CT C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1865||226|PRRG4|protein_coding|CODING|NM_024081.5|6|C) 0 0.5 1 1 1 0 1 0 . 0 60 0 0 . 0 . rs5790906 -0.379885 0 1 226 2789 MODIFIER 6 CODING PRRG4 T protein_coding NM_024081.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32877862 C T 0 9.7 0 0.8427 0.8387 0.8357 0.995 0.7117 0.8047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2789||226|PRRG4|protein_coding|CODING|NM_024081.5|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs761284 -0.379885 0 1 226 3236 MODIFIER 6 CODING PRRG4 T protein_coding NM_024081.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32878309 C T 0 32.6 0 0.9297 0.9161 0.8862 0.995 0.831 0.9254 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3236||226|PRRG4|protein_coding|CODING|NM_024081.5|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2419773 -0.379885 0 2 226 3777 MODIFIER 6 CODING PRRG4 C protein_coding NM_024081.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32878850 G C 0 6.3 0 0.9962 0.9343 0.889 0.995 0.832 0.9254 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3777||226|PRRG4|protein_coding|CODING|NM_024081.5|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11032026 -0.379885 0 1 V385I 1735 Gta/Ata MODERATE 4 MISSENSE CODING QSER1 A protein_coding NM_001076786.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32954344 G A 0 228 0 0.8941 0.9712 0.9942 1 1 1 0.912405 0.972715 0.999877 2 8940 119686 11437 8626 6614 66680 892 16497 2 9798 120714 11560 8626 6614 66716 900 16500 0 . 0 . 0 79 0,0,25,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V385I|1735|QSER1|protein_coding|CODING|NM_001076786.2|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1022586 -0.693147 0.135295 79 Q644R 1735 cAa/cGa MODERATE 4 MISSENSE CODING QSER1 G protein_coding NM_001076786.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32955122 A G 0 222 0 0.0772 0.0789 0.0778 0.0595 0.0577 0.1237 0.0727322 0.0670691 0.0644965 1 710 8737 1187 506 309 4039 73 1913 2 9758 120292 11478 8604 6612 66542 900 16398 0.532393 0 . 0 COSM147173 136 36,20,27,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q644R|1735|QSER1|protein_coding|CODING|NM_001076786.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.768797 rs2297781 -0.693147 0.512094 136 N1018S 1735 aAt/aGt MODERATE 4 MISSENSE CODING QSER1 G protein_coding NM_001076786.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32956244 A G 0 228 0 0.8964 0.9718 0.9942 1 1 1 0.91491 0.973063 0.999879 2 8898 119356 11354 8620 6610 66535 888 16451 2 9742 120370 11476 8620 6610 66572 896 16454 0 . 0 . 0 72 0,0,56,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1018S|1735|QSER1|protein_coding|CODING|NM_001076786.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7940077 -0.693147 0.00104744 72 P1143 1735 ccA/ccG LOW 4 SILENT CODING QSER1 G protein_coding NM_001076786.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32956620 A G 0 228 0 0.5522 0.7979 0.8458 0.995 0.8082 0.8824 0.588749 0.750084 0.822364 2 5619 99452 10202 8591 5429 54503 747 14361 2 9754 120558 11494 8620 6612 66674 894 16510 0 . 0 . 0 50 0,0,22,25 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P1143|1735|QSER1|protein_coding|CODING|NM_001076786.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7481878 -0.693147 0.437556 50 1735 422 MODIFIER 13 CODING QSER1 T protein_coding NM_001076786.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 32998442 C T 0 126 0 0 0.019768 0.0173 0.0804 0 0.0061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.633483 0 . 0 . 22 11,3,6,2 UTR_3_PRIME(MODIFIER||422||1735|QSER1|protein_coding|CODING|NM_001076786.2|13|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.792218 rs80196731 -0.651104 0.00796861 22 A192T 511 Gca/Aca MODERATE 3 MISSENSE CODING DEPDC7 A protein_coding NM_001077242.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33049341 G A 0 222 0 0.0053 0.0703 0.1282 0.0456 0.0616 0.1513 0.0117486 0.0510342 0.068707 1 119 8732 1275 375 708 4096 59 2100 2 6688 78184 6520 5000 4802 41476 632 13066 0.950718 0 . 0 . 46 4,15,7,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A192T|511|DEPDC7|protein_coding|CODING|NM_001077242.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.912487 rs34161108 -0.692831 0.000779166 46 G72 509 ggT/ggC LOW 3 SILENT CODING TCP11L1 C protein_coding NM_001145541.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33076191 T C 0 222 0 0.6536 0.7171 0.67 0.881 0.7356 0.6483 0.672343 0.710077 0.729409 1 6996 85475 7142 7609 4423 48167 641 10497 2 10402 121364 11562 8652 6612 66722 908 16506 0.980157 0 . 0 . 90 33,13,25,10 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G72|509|TCP11L1|protein_coding|CODING|NM_001145541.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.34993 rs2273544,rs386563169 -0.693136 0.494902 90 L78 509 ctA/ctG LOW 3 SILENT CODING TCP11L1 G protein_coding NM_001145541.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33076209 A G 0 222 0 0 0.0222 0.0173 0.0923 0.001 0.0051 0.00181653 0.00223077 0.002443 1 14 1426 408 846 1 107 7 43 2 10400 121388 11572 8652 6612 66734 908 16510 0.872257 0 . 0 . 92 31,19,22,10 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L78|509|TCP11L1|protein_coding|CODING|NM_001145541.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962716 rs78690604 -0.69312 0.559655 92 K178R 509 aAg/aGg MODERATE 5 MISSENSE CODING TCP11L1 G protein_coding NM_001145541.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33079580 A G 0 222 0 0.0696 0.1192 0.1297 0.122 0.1948 0.0982 0.100363 0.152077 0.178571 1 962 18131 1360 1024 1071 11648 175 1891 2 10400 121270 11538 8640 6610 66674 906 16502 0.686822 0 . 0 . 96 33,15,16,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K178R|509|TCP11L1|protein_coding|CODING|NM_001145541.1|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998715 rs2273549,rs386563170 -0.693136 0.217194 96 717 70 MODIFIER 1 CODING CSTF3 G protein_coding NM_001326.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33182941 A G 0 222 0 0 0.014776 0.0173 0.0595 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.801759 0 . 0 . 87 17,26,11,17 UTR_5_PRIME(MODIFIER||70||717|CSTF3|protein_coding|CODING|NM_001326.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.945332 rs117854987 -0.693054 0.0881711 87 G41 1849 ggT/ggC LOW 1 SILENT CODING KIAA1549L C protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33564123 T C 0 222 0 0.8918 0.6969 0.6095 0.6617 0.6153 0.6155 0.856484 0.709051 0.639706 1 8398 78715 7132 5706 4275 42444 605 10155 2 9796 120698 11572 8584 6610 66726 898 16512 0.995893 0 . 0 . 113 34,29,17,17 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G41|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.550561 rs2076623 -0.693132 0.421566 113 S531 1849 tcC/tcT LOW 1 SILENT CODING KIAA1549L T protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33565593 C T 0 222 0 0.0983 0.1354 0.0764 0.3085 0.0577 0.1288 0.100391 0.06942 0.0543685 1 973 12116 1183 2695 761 4327 105 2072 2 9804 120734 11574 8594 6614 66740 898 16510 0.767617 0 . 0 . 200 52,68,34,32 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S531|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.308887 rs2235944 -0.693147 0.0895689 200 T992 1849 acG/acA LOW 6 SILENT CODING KIAA1549L A protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33581306 G A 0 222 0 0.469 0.389 0.3213 0.3264 0.3887 0.3937 0.459227 0.410269 0.386015 1 4641 46775 3708 2841 2907 25541 374 6763 2 9808 120646 11564 8576 6604 66696 896 16502 0.971918 0 . 0 . 106 29,20,24,19 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T992|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999074 rs2281380 -0.693146 0.0971905 106 P1171 1849 ccC/ccT LOW 10 SILENT CODING KIAA1549L T protein_coding NM_012194.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33604885 C T 0 222 0 0.0764 0.1943 0.2378 0.3591 0.2197 0.1268 0.0903818 0.185406 0.231906 1 755 21952 2452 2471 1173 13429 156 1516 2 6140 76784 6494 5858 4206 43150 598 10338 0.99706 0 . 0 . 97 34,13,28,15 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1171|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.517969 rs2273117 -0.693146 0.208217 97 I1196 1849 atC/atT LOW 10 SILENT CODING KIAA1549L T protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33604960 C T 0 222 0 0.0166 0.1773 0.2334 0.3591 0.2187 0.1247 0.0419385 0.167422 0.230679 1 310 20175 2185 2260 1113 12644 152 1511 2 5594 73582 5946 5402 4132 41318 574 10616 0.0755352 0 . 0 . 116 29,29,31,22 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1196|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.749939 rs2273115 -0.693147 0.3465 116 K1433 1849 aaG/aaA LOW 14 SILENT CODING KIAA1549L A protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33631423 G A 0 222 0 0.5605 0.4517 0.3818 0.3839 0.3857 0.4918 0.526684 0.432321 0.388203 1 5300 50067 4381 3422 2853 25912 404 7795 2 9790 120678 11566 8614 6610 66696 896 16506 0.729999 0 . 0 . 172 37,35,36,44 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1433|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999939 rs2076622 -0.693147 0.447401 172 R1472 1849 Aga/Cga LOW 15 SILENT CODING KIAA1549L C protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33640104 A C 0 222 0 0.9728 0.7456 0.6441 0.747 0.6292 0.6288 0.915501 0.733026 0.650475 1 8800 80563 7397 6487 4460 42671 612 10136 2 9584 117358 11136 8468 6454 64924 862 15930 0.484971 0 . 0 . 75 19,24,10,14 SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R1472|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999466 rs768474 -0.692831 0.765202 75 T1540 1849 acA/acG LOW 16 SILENT CODING KIAA1549L G protein_coding NM_012194.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33667333 A G 0 222 0 0.938 0.7077 0.6066 0.7232 0.6004 0.5624 0.881494 0.711608 0.625324 1 8629 78726 7544 6252 4525 41681 617 9478 2 9810 120480 11560 8588 6614 66506 894 16508 0.961777 0 . 0 . 119 46,21,28,19 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T1540|1849|KIAA1549L|protein_coding|CODING|NM_012194.2|16|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983694 rs1033543 -0.693147 0.00939576 119 128 7059 MODIFIER 4 CODING CD59 G protein_coding NM_000611.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33724613 T G 0 22.7 0 0 0.01238 0.0014 0.0565 0.003 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,0,2 UTR_3_PRIME(MODIFIER||7059||128|CD59|protein_coding|CODING|NM_000611.5|4|G),UPSTREAM(MODIFIER||2327||193|C11orf91|protein_coding|CODING|NM_001166692.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs77762316 -0.453602 0.5 3 128 4692 MODIFIER 4 CODING CD59 G protein_coding NM_000611.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33726980 A G 0 25.6 0 0.8389 0.641 0.4697 0.5377 0.6223 0.6207 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,0,2 UTR_3_PRIME(MODIFIER||4692||128|CD59|protein_coding|CODING|NM_000611.5|4|G),UPSTREAM(MODIFIER||4694||193|C11orf91|protein_coding|CODING|NM_001166692.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7046 -0.453602 0.68 3 471 LOW 6 CODING FBXO3 C protein_coding NM_012175.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33773161 G C 0 228 0 0.8858 0.9681 0.9914 1 1 0.9969 0.907088 0.967913 0.999069 2 9277 119832 11422 8633 6602 66543 897 16458 2 10242 120958 11484 8634 6602 66600 904 16492 0 . 0 . 0 119 0,0,29,80 SPLICE_SITE_REGION+INTRON(LOW||||471|FBXO3|protein_coding|CODING|NM_012175.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7479064 -0.693147 9.95795e-06 119 K190 227 aaA/aaG LOW 6 SILENT CODING LMO2 C protein_coding NM_005574.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 33881016 T C 0 222 0 0.4682 0.5625 0.7291 0.4921 0.5954 0.6104 0.506585 0.572154 0.605747 1 5234 72799 9070 4440 3175 40110 513 10257 2 10404 121304 11570 8630 6608 66680 908 16504 0.981057 0 . 0 COSM147176 152 40,37,36,22 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K190|227|LMO2|protein_coding|CODING|NM_005574.3|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.349989 rs3740617 -0.693147 0.0270861 152 709 608 MODIFIER 1 CODING CAPRIN1 G protein_coding NM_005898.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34073360 A G 0 20.4 0 0.969 0.9918 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||608||709|CAPRIN1|protein_coding|CODING|NM_005898.4|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7950888 -0.453602 0.36 2 709 1455 MODIFIER 19 CODING CAPRIN1 T protein_coding NM_005898.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34122369 G T 0 228 0 0.997 0.9992 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 106 0,0,53,37 UTR_3_PRIME(MODIFIER||1455||709|CAPRIN1|protein_coding|CODING|NM_005898.4|19|T),UPSTREAM(MODIFIER||4742||1025|NAT10|protein_coding|CODING|NM_024662.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2982590 -0.693147 0.17127 106 Y461H 1025 Tat/Cat MODERATE 14 MISSENSE CODING NAT10 C protein_coding NM_024662.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34152939 T C 0 228 0 0.9917 0.9978 1 1 1 1 0.992507 0.997462 1 2 10323 121276 11575 8654 6614 66696 908 16506 2 10406 121362 11578 8654 6614 66696 908 16506 0 . 0 . 0 148 0,0,85,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Cat|Y461H|1025|NAT10|protein_coding|CODING|NM_024662.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2957516 -0.693147 0.0166295 148 P562 1025 ccC/ccT LOW 16 SILENT CODING NAT10 T protein_coding NM_024662.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34154641 C T 0 228 0 0.5696 0.8604 0.9553 1 0.9592 0.9407 0.637375 0.848692 0.956957 2 6659 113356 11234 8653 6313 63958 864 15675 2 10404 121406 11576 8654 6614 66738 908 16512 0 . 0 . 0 58 0,0,22,31 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P562|1025|NAT10|protein_coding|CODING|NM_024662.2|16|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2957518 -0.693147 0.00411172 58 P564S 1025 Ccc/Tcc MODERATE 16 MISSENSE CODING NAT10 T protein_coding NM_024662.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34154645 C T 0 222 0 0.0008 0.0242 0.0086 0.0724 0.0169 0.0245 0.00317893 0.0171538 0.0243136 1 33 2630 90 559 32 1397 23 496 2 10406 121380 11574 8644 6614 66726 908 16508 0.853052 0 . 0 . 60 12,17,10,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P564S|1025|NAT10|protein_coding|CODING|NM_024662.2|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.608054 rs61735311 -0.692914 0.0265837 60 1025 273 MODIFIER 17 CODING ABTB2 A protein_coding NM_145804.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34173661 C A 0 162 0 0.969 0.9918 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,18 UTR_3_PRIME(MODIFIER||273||1025|ABTB2|protein_coding|CODING|NM_145804.2|17|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2982609 -0.691153 0.303136 18 322 156 MODIFIER 9 CODING EHF A protein_coding NM_001206616.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34680634 G A 0 228 0 0.9735 0.9924 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 124 0,0,90,28 UTR_3_PRIME(MODIFIER||156||322|EHF|protein_coding|CODING|NM_001206616.1|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs286890 -0.693147 0.512914 124 322 375 MODIFIER 9 CODING EHF T protein_coding NM_001206616.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34680853 G T 0 222 0 0.2988 0.3794 0.317 0.5387 0.2783 0.4724 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.490123 0 . 0 . 196 36,61,31,48 UTR_3_PRIME(MODIFIER||375||322|EHF|protein_coding|CODING|NM_001206616.1|9|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.422205 rs286889 -0.693147 0.166709 196 322 2069 MODIFIER 9 CODING EHF C protein_coding NM_001206616.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34682547 T C 0 61 0 0.7912 0.9427 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||2069||322|EHF|protein_coding|CODING|NM_001206616.1|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs286888 -0.511536 0.172729 3 322 4065 MODIFIER 9 CODING EHF A protein_coding NM_001206616.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34684543 C A 0 36.3 0 0.1195 0.2183 0.2334 0.4117 0.159 0.2025 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||4065||322|EHF|protein_coding|CODING|NM_001206616.1|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1048904 -0.453602 0.68 2 T125 242 acA/acC LOW 5 SILENT CODING APIP G protein_coding NM_015957.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34909926 T G 0 222 0 0.3533 0.5795 0.5692 0.7371 0.6839 0.6227 0.414169 0.598154 0.692415 1 4257 77490 6028 6469 4285 45538 580 10333 2 10390 121306 11510 8654 6612 66722 908 16510 0.985015 0 . 0 . 335 69,90,52,79 SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T125|242|APIP|protein_coding|CODING|NM_015957.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932601 rs1571133 -0.693147 0.00761305 335 C76Y 242 tGt/tAt MODERATE 4 MISSENSE CODING APIP T protein_coding NM_015957.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34910397 C T 0 222 0 0.3056 0.4575 0.4035 0.7371 0.3559 0.5174 0.30895 0.340976 0.357376 1 3251 48553 4643 6422 2602 23494 340 7801 2 10334 120130 11408 8614 6580 66248 900 16046 0.993886 0 . 0 . 116 21,35,23,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C76Y|242|APIP|protein_coding|CODING|NM_015957.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.972956 rs1977420 -0.693147 0.0562241 116 501 506 MODIFIER 1 CODING PDHX C protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937697 T C 0 39.3 0 0.7927 0.7722 0.6744 0.8244 0.8012 0.7301 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||506||501|PDHX|protein_coding|CODING|NM_003477.2|1|C),INTRON(MODIFIER||||242|APIP|protein_coding|CODING|NM_015957.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2016814 -0.453602 0.94 2 R7W 242 Cgg/Tgg MODERATE 1 MISSENSE CODING APIP A protein_coding NM_015957.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937813 G A 0 57 0 0.2239 0.4347 0.3977 0.7371 0.3539 0.5174 0.242721 0.316697 0.354565 1 2303 45402 4465 6240 2252 22106 294 7742 2 8024 107672 10746 8322 5042 59128 740 15670 0.810265 0 . 0 . 11 4,0,3,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R7W|242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||390||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.01283 0 . 0.607698 rs2956114 -0.511536 0.663511 11 501 390 MODIFIER 1 CODING PDHX A protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937813 G A 0 57 0 0.2239 0.4347 0.3977 0.7371 0.3539 0.5174 0.242721 0.316697 0.354565 1 2303 45402 4465 6240 2252 22106 294 7742 2 8024 107672 10746 8322 5042 59128 740 15670 0.810265 0 . 0 . 11 4,0,3,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R7W|242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||390||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1.01283 0 . 0.607698 rs2956114 -0.511536 0.663511 11 242 53 MODIFIER 1 CODING APIP A protein_coding NM_015957.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937884 G A 0 142 0 0.2239 0.4347 0.3977 0.7371 0.3539 0.5174 0.259045 0.33231 0.364151 1 1608 36173 3600 4978 1488 17500 223 6776 2 5500 82210 7860 6558 3278 44826 576 13612 0.208021 0 . 0 . 12 1,4,4,2 START_GAINED(LOW||||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||53||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||319||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.950952 0.950952 0 0.475476 rs2956113 -0.616816 0.972484 12 501 319 MODIFIER 1 CODING PDHX A protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937884 G A 0 142 0 0.2239 0.4347 0.3977 0.7371 0.3539 0.5174 0.259045 0.33231 0.364151 1 1608 36173 3600 4978 1488 17500 223 6776 2 5500 82210 7860 6558 3278 44826 576 13612 0.208021 0 . 0 . 12 1,4,4,2 START_GAINED(LOW||||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||53||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||319||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.950952 0.950952 0 0.475476 rs2956113 -0.616816 0.972484 12 242 70 MODIFIER 1 CODING APIP G protein_coding NM_015957.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937901 A G 0 180 0 0.7579 0.7626 0.6715 0.8244 0.8012 0.7301 0.782923 0.80057 0.808249 2 3548 52598 3736 3928 1922 29934 388 9142 2 4446 66402 5782 4592 2434 36544 484 12120 0 . 0 . 0 7 0,0,3,4 START_GAINED(LOW||||501|PDHX|protein_coding|CODING|NM_003477.2|1|G),UTR_5_PRIME(MODIFIER||70||242|APIP|protein_coding|CODING|NM_015957.3|1|G),UTR_5_PRIME(MODIFIER||302||501|PDHX|protein_coding|CODING|NM_003477.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1.01283 0 . rs2956112 -0.636426 0.536793 7 501 302 MODIFIER 1 CODING PDHX G protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937901 A G 0 180 0 0.7579 0.7626 0.6715 0.8244 0.8012 0.7301 0.782923 0.80057 0.808249 2 3548 52598 3736 3928 1922 29934 388 9142 2 4446 66402 5782 4592 2434 36544 484 12120 0 . 0 . 0 7 0,0,3,4 START_GAINED(LOW||||501|PDHX|protein_coding|CODING|NM_003477.2|1|G),UTR_5_PRIME(MODIFIER||70||242|APIP|protein_coding|CODING|NM_015957.3|1|G),UTR_5_PRIME(MODIFIER||302||501|PDHX|protein_coding|CODING|NM_003477.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1.01283 0 . rs2956112 -0.636426 0.536793 7 242 100 MODIFIER 1 CODING APIP A protein_coding NM_015957.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937931 G A 0 83 0 0.3056 0.4573 0.4035 0.7371 0.3559 0.5164 0 . 0 1 447 10058 516 753 186 4165 80 3911 2 1114 20018 986 972 350 8676 178 7742 1 0 . 0 . 5 0,1,2,2 START_GAINED(LOW||||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||100||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||272||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs2956111 -0.556411 0.0162466 5 501 272 MODIFIER 1 CODING PDHX A protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34937931 G A 0 83 0 0.3056 0.4573 0.4035 0.7371 0.3559 0.5164 0 . 0 1 447 10058 516 753 186 4165 80 3911 2 1114 20018 986 972 350 8676 178 7742 1 0 . 0 . 5 0,1,2,2 START_GAINED(LOW||||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||100||242|APIP|protein_coding|CODING|NM_015957.3|1|A),UTR_5_PRIME(MODIFIER||272||501|PDHX|protein_coding|CODING|NM_003477.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs2956111 -0.556411 0.0162466 5 501 202 MODIFIER 1 CODING PDHX G protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938001 A G 0 24.1 0 0.4395 0.1927 0.1037 0.0873 0.1173 0.1084 0 . 0 1 162 280 6 3 2 59 2 46 2 356 1214 72 46 8 358 14 360 0.450401 0 . 0 . 8 1,4,3,0 UTR_5_PRIME(MODIFIER||202||501|PDHX|protein_coding|CODING|NM_003477.2|1|G),UPSTREAM(MODIFIER||43||242|APIP|protein_coding|CODING|NM_015957.3||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.900802 0.992367 0 0.900802 rs113073242 -0.511536 0.490096 8 501 88 MODIFIER 1 CODING PDHX A protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938115 C A 0 156 0 0.326 0.5719 0.5677 0.7371 0.6839 0.6217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.622437 0 . 0 . 65 32,3,29,1 START_GAINED(LOW||||501|PDHX|protein_coding|CODING|NM_003477.2|1|A),UTR_5_PRIME(MODIFIER||88||501|PDHX|protein_coding|CODING|NM_003477.2|1|A),UPSTREAM(MODIFIER||157||242|APIP|protein_coding|CODING|NM_015957.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.302599 rs2956110 -0.693097 0.0401805 65 501 4 MODIFIER 1 CODING PDHX G protein_coding NM_003477.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938199 C G 0 222 0 0.4395 0.1925 0.1037 0.0873 0.1173 0.1074 0.39396 0.206538 0.110517 1 3951 16031 752 849 751 7725 132 1871 2 9716 116102 11200 8452 5796 63844 840 16254 0.985044 0 . 0 . 179 59,20,61,15 UTR_5_PRIME(MODIFIER||4||501|PDHX|protein_coding|CODING|NM_003477.2|1|G),UPSTREAM(MODIFIER||241||242|APIP|protein_coding|CODING|NM_015957.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.820939 rs3818401 -0.693147 0.303362 179 P21 501 ccC/ccT LOW 1 SILENT CODING PDHX T protein_coding NM_003477.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938265 C T 0 228 0 0.7655 0.7646 0.6715 0.8244 0.8012 0.7301 0.785876 0.796769 0.80235 2 7793 92033 6714 7253 4845 52527 692 12209 2 9948 118850 11338 8560 6232 65462 868 16442 0 . 0 . 0 185 0,0,78,79 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P21|501|PDHX|protein_coding|CODING|NM_003477.2|1|T),UPSTREAM(MODIFIER||307||242|APIP|protein_coding|CODING|NM_015957.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2956109 -0.693147 0.0321063 185 R23C 501 Cgc/Tgc MODERATE 1 MISSENSE CODING PDHX T protein_coding NM_003477.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938269 C T 0 222 0 0.4395 0.1925 0.1037 0.0873 0.1173 0.1074 0.392144 0.205692 0.110168 1 3888 15947 750 845 739 7716 130 1879 2 9722 115218 11052 8328 5692 63638 826 15960 0.999188 0 . 0 . 191 42,45,40,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R23C|501|PDHX|protein_coding|CODING|NM_003477.2|1|T),UPSTREAM(MODIFIER||311||242|APIP|protein_coding|CODING|NM_015957.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994766 rs1049306 -0.693147 0.0579517 191 S36 501 tcT/tcC LOW 1 SILENT CODING PDHX C protein_coding NM_003477.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34938310 T C 0 222 0 0.4395 0.1927 0.1052 0.0873 0.1173 0.1074 0.390504 0.205032 0.110051 1 3481 14395 657 771 604 6978 116 1788 2 8278 85836 6940 5814 3632 47270 606 13296 0.823201 0 . 0 . 158 34,43,18,43 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S36|501|PDHX|protein_coding|CODING|NM_003477.2|1|C),UPSTREAM(MODIFIER||352||242|APIP|protein_coding|CODING|NM_015957.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90013 rs1049307,rs386513636 -0.693147 0.000595604 158 I169 501 atC/atT LOW 4 SILENT CODING PDHX T protein_coding NM_003477.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34979095 C T 0 222 0 0.0083 0.0323 0.0403 0.0159 0.0318 0.0767 0.00726612 0.0226923 0.0305956 1 78 4446 427 156 128 2260 56 1341 2 10380 121256 11558 8652 6614 66652 904 16496 0.815396 2 benign 0 . 137 22,41,22,34 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I169|501|PDHX|protein_coding|CODING|NM_003477.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0705789 rs79170416 -0.693147 0.000428845 137 501 LOW 5 CODING PDHX C protein_coding NM_003477.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34982069 T C 0 222 0 0.0008 0.0783 0.0591 0.3185 0.0109 0.0184 0.00408719 0.00884615 0.0112843 1 41 5766 1266 3048 156 903 30 322 2 10106 119526 11442 8604 6492 65634 896 16352 0.404886 0 . 0 . 68 13,20,5,22 SPLICE_SITE_REGION+INTRON(LOW||||501|PDHX|protein_coding|CODING|NM_003477.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.711742 rs2767035 -0.693021 0.0416515 68 P266 501 ccT/ccC LOW 6 SILENT CODING PDHX C protein_coding NM_003477.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34988343 T C 0 222 0 0.3177 0.117 0.062 0.0159 0.0318 0.0767 0.273388 0.114231 0.0326896 1 2829 7519 625 156 129 2361 75 1344 2 10404 121386 11568 8650 6614 66738 908 16504 0.941706 2 benign 0 . 92 12,37,5,33 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P266|501|PDHX|protein_coding|CODING|NM_003477.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.274114 rs61760973 -0.693143 0.227189 92 V286 501 gtT/gtC LOW 7 SILENT CODING PDHX C protein_coding NM_003477.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 34991727 T C 0 222 0 0.3169 0.5705 0.5562 0.7421 0.7058 0.6074 0.387148 0.597231 0.704863 1 3926 78035 5885 6516 4473 46622 572 10041 2 10392 121208 11518 8634 6600 66652 908 16504 0.483951 0 . 0 . 173 69,10,66,8 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V286|501|PDHX|protein_coding|CODING|NM_003477.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.915634 rs386596900,rs497582 -0.693147 0.227582 173 501 486 MODIFIER 11 CODING PDHX T protein_coding NM_003477.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35017205 G T 0 222 0 0.5151 0.6248 0.5706 0.7421 0.7058 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.104779 0 . 0 . 106 21,31,23,18 UTR_3_PRIME(MODIFIER||486||501|PDHX|protein_coding|CODING|NM_003477.2|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.966959 rs9326 -0.693145 0.338082 106 501 644 MODIFIER 11 CODING PDHX A protein_coding NM_003477.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35017363 C A 0 210 0 0.8449 0.7815 0.6873 0.8065 0.8101 0.7076 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 34 0,0,1,33 UTR_3_PRIME(MODIFIER||644||501|PDHX|protein_coding|CODING|NM_003477.2|11|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7808 -0.693132 0.0202029 34 H85 742 caC/caT LOW 3 SILENT CODING CD44 T protein_coding NM_000610.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35201842 C T 0 222 0 0.149 0.1394 0.2205 0.0714 0.173 0.1043 0.161671 0.168385 0.171824 1 1644 19522 2404 692 699 11595 159 2329 2 10404 121288 11550 8628 6606 66688 908 16504 0.596829 0 . 0 COSM1353673 283 55,66,54,85 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H85|742|CD44|protein_coding|CODING|NM_000610.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.69935 rs1071695 -0.693147 0.278372 283 K417R 742 aAa/aGa MODERATE 10 MISSENSE CODING CD44 G protein_coding NM_000610.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35226155 A G 0 222 0 0.9221 0.8303 0.6859 0.9306 0.6839 0.8558 0.867393 0.752385 0.693462 1 9094 90697 7895 8029 4926 46501 671 13581 2 10404 121290 11530 8616 6608 66712 908 16512 0.375295 0 . 0 . 335 87,65,87,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K417R|742|CD44|protein_coding|CODING|NM_000610.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.817868 rs9666607 -0.693147 0.0304894 335 I479T 742 aTa/aCa MODERATE 12 MISSENSE CODING CD44 C protein_coding NM_000610.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35229673 T C 0 228 0 0.9939 0.9391 0.8919 0.999 0.8141 0.9652 0.960036 0.863231 0.813634 2 10038 106848 10844 8615 5613 55195 806 15737 2 10406 121328 11556 8616 6614 66718 908 16510 0 . 0 . 0 137 0,0,94,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I479T|742|CD44|protein_coding|CODING|NM_000610.3|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1467558 -0.693147 0.084884 137 742 138 MODIFIER 18 CODING CD44 C protein_coding NM_000610.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35251018 T C 0 25.9 0 0.0908 0.0323 0.0086 0.0298 0.001 0.0051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||138||742|CD44|protein_coding|CODING|NM_000610.3|18|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2295755 -0.453602 0.22 3 742 2392 MODIFIER 18 CODING CD44 T protein_coding NM_000610.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35253272 C T 0 9.7 0 0.6952 0.375 0.3501 0.3393 0.2157 0.1605 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2392||742|CD44|protein_coding|CODING|NM_000610.3|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs13347,rs386528223 -0.379885 0 1 574 3482 MODIFIER 11 CODING SLC1A2 T protein_coding NM_004171.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35278959 C T 0 9.7 0 0.9902 0.9024 0.8689 0.9663 0.7296 0.9192 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3482||574|SLC1A2|protein_coding|CODING|NM_004171.3|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7936950 -0.379885 0 1 574 3140 MODIFIER 11 CODING SLC1A2 T protein_coding NM_004171.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35279301 C T 0 9.7 0 0.1619 0.1965 0.2781 0.2331 0.1859 0.1585 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3140||574|SLC1A2|protein_coding|CODING|NM_004171.3|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12294045 -0.379885 0 1 737 185 MODIFIER 12 CODING PAMR1 T protein_coding NM_015430.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35453719 C T 0 197 0 0.295 0.5214 0.513 0.7242 0.5567 0.5879 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,16,1 UTR_3_PRIME(MODIFIER||185||737|PAMR1|protein_coding|CODING|NM_015430.3|12|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7767 -0.690438 0.000775479 17 E100 437 gaG/gaA LOW 1 SILENT CODING FJX1 A protein_coding NM_014344.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 35640484 G A 0 26.4 0 0.0204 0.0697 0.0346 0.119 0.0408 0.1401 0 . 0 1 7 1049 6 14 0 92 6 924 2 112 6486 46 104 0 1326 74 4824 1 0 . 0 . 4 1,0,0,2 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E100|437|FJX1|protein_coding|CODING|NM_014344.3|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 1 rs143163205 -0.453602 0.44 4 345 99 MODIFIER 6 CODING LDLRAD3 A protein_coding NM_174902.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36251046 G A 0 199 0 0.3396 0.5831 0.5519 0.7292 0.6909 0.6728 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,1,18 UTR_3_PRIME(MODIFIER||99||345|LDLRAD3|protein_coding|CODING|NM_174902.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4755444 -0.69168 0.0284476 19 345 2350 MODIFIER 6 CODING LDLRAD3 T protein_coding NM_174902.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36253297 G T 0 37.3 0 0.3949 0.5992 0.5548 0.7351 0.6909 0.6728 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2350||345|LDLRAD3|protein_coding|CODING|NM_174902.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2084221 -0.453602 0.22 2 A41T 368 Gct/Act MODERATE 2 MISSENSE CODING PRR5L A protein_coding NM_001160167.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36422792 G A 0 228 0 0.5794 0.8337 0.9308 0.9673 0.9125 0.8896 0.643279 0.819769 0.910191 2 6541 107713 11122 8269 5775 60452 810 14744 2 10268 120930 11562 8630 6608 66448 904 16510 1 0 . 0 . 69 0,1,21,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A41T|368|PRR5L|protein_coding|CODING|NM_001160167.1|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs330261,rs386581571 -0.693147 0.0885748 69 Q209 368 caA/caG LOW 8 SILENT CODING PRR5L G protein_coding NM_001160167.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36472800 A G 0 222 0 0.1679 0.2047 0.111 0.377 0.1282 0.2219 0.163488 0.140846 0.129246 1 1669 19158 1603 3283 434 8456 142 3571 2 10406 121362 11578 8626 6614 66718 908 16512 0.760142 0 . 0 . 196 50,59,28,34 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q209|368|PRR5L|protein_coding|CODING|NM_001160167.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.363957 rs3740958 -0.693147 0.025279 196 T343 368 acT/acC LOW 9 SILENT CODING PRR5L C protein_coding NM_001160167.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36484208 T C 0 228 0 0.9803 0.9948 1 1 1 1 0.986136 0.995073 0.999651 2 9649 117785 11507 8564 6596 64373 878 16218 2 9826 117996 11524 8566 6596 64388 878 16218 0 . 0 . 0 71 0,0,21,44 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T343|368|PRR5L|protein_coding|CODING|NM_001160167.1|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs514352 -0.693147 0.205756 71 368 1059 MODIFIER 9 CODING PRR5L C protein_coding NM_001160167.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36485345 G C 0 228 0 0.8245 0.7973 0.7046 0.8413 0.7286 0.8517 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,7,32 UTR_3_PRIME(MODIFIER||1059||368|PRR5L|protein_coding|CODING|NM_001160167.1|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs331439 -0.693144 0.0597926 44 368 1609 MODIFIER 9 CODING PRR5L T protein_coding NM_001160167.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36485895 G T 0 31.3 0 0.9849 0.996 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1609||368|PRR5L|protein_coding|CODING|NM_001160167.1|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs331437 -0.453602 0.48 2 368 1778 MODIFIER 9 CODING PRR5L A protein_coding NM_001160167.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36486064 G A 0 46.3 0 0.4675 0.6256 0.6153 0.7976 0.5915 0.7045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1778||368|PRR5L|protein_coding|CODING|NM_001160167.1|9|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111175243,rs331436 -0.453602 0.06 2 368 2021 MODIFIER 9 CODING PRR5L A protein_coding NM_001160167.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36486307 G A 0 9.7 0 0.3222 0.5709 0.5937 0.7748 0.5785 0.6728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2021||368|PRR5L|protein_coding|CODING|NM_001160167.1|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs331435 -0.379885 0 1 522 2768 MODIFIER 7 CODING TRAF6 A protein_coding NM_004620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36508620 G A 0 13.8 0 0.202 0.527 0.585 0.7708 0.5775 0.6217 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2768||522|TRAF6|protein_coding|CODING|NM_004620.3|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs5030487 -0.379885 0 2 522 2248 MODIFIER 7 CODING TRAF6 G protein_coding NM_004620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36509140 T G 0 9.7 0 0.9561 0.988 0.9971 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2248||522|TRAF6|protein_coding|CODING|NM_004620.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs580653 -0.379885 0 1 H249R 1043 cAc/cGc MODERATE 2 MISSENSE CODING RAG1 G protein_coding NM_000448.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36595600 A G 0 222 0 0.7708 0.6134 0.6052 0.756 0.3648 0.5153 0.726612 0.468308 0.33597 1 7537 54214 8044 6743 1900 21890 348 7752 2 10394 121280 11560 8636 6610 66664 906 16510 0.527133 2 benign 0 . 67 16,13,14,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H249R|1043|RAG1|protein_coding|CODING|NM_000448.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999562 rs3740955 -0.69311 0.697568 67 K820R 1043 aAg/aGg MODERATE 2 MISSENSE CODING RAG1 G protein_coding NM_000448.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36597313 A G 0 222 0 0.0847 0.258 0.2795 0.5665 0.1193 0.3016 0.107629 0.111923 0.114123 1 1015 22610 4211 5173 538 7211 141 4321 2 10358 121170 11554 8630 6614 66606 906 16502 0.977259 0 . 0 . 62 15,14,18,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K820R|1043|RAG1|protein_coding|CODING|NM_000448.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.923337 rs2227973 -0.69311 0.0837031 62 1043 3184 MODIFIER 2 CODING RAG1 A protein_coding NM_000448.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36601170 G A 0 222 0 0.77 0.6126 0.6037 0.754 0.3648 0.5153 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.623185 0 . 0 . 64 12,18,12,16 UTR_3_PRIME(MODIFIER||3184||1043|RAG1|protein_coding|CODING|NM_000448.2|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.557231 rs1056403 -0.693054 0.130241 64 527 328 MODIFIER 2 CODING RAG2 C protein_coding NM_000536.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 36613807 T C 0 21.2 0 0.7655 0.6132 0.6037 0.7589 0.3688 0.5153 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 UTR_3_PRIME(MODIFIER||328||527|RAG2|protein_coding|CODING|NM_000536.3|2|C),UPSTREAM(MODIFIER||2236||221|C11orf74|protein_coding|CODING|NM_001276722.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10836573 -0.379885 0 3 R100 640 agA/agG LOW 7 SILENT CODING LRRC4C C protein_coding NM_001258419.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 40137543 T C 0 228 0 0.7027 0.4994 0.5058 0.6052 0.3728 0.2413 0.662052 0.498155 0.414186 2 6855 52128 5840 5369 2050 27257 387 4370 2 10402 121256 11548 8600 6608 66680 906 16512 1 0 . 0 COSM147178 91 0,1,48,36 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R100|640|LRRC4C|protein_coding|CODING|NM_001258419.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2953310 -0.693147 0.333264 91 524 1236 MODIFIER 14 CODING API5 C protein_coding NM_001142930.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43365296 G C 0 228 0 0.9175 0.9774 0.9957 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 110 0,0,48,59 UTR_3_PRIME(MODIFIER||1236||524|API5|protein_coding|CODING|NM_001142930.1|14|C) 0 . 0 . 0 1 0 . 0 . 42 0 0 0.236763 0 . rs5743258 -0.693147 0.0292507 110 1141 41 MODIFIER 24 CODING TTC17 T protein_coding NM_018259.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43515495 A T 0 222 0 0 0.019768 0 0.0942 0 0.0041 0.00068089 0.000230663 0 1 5 821 1 786 0 10 2 17 2 10250 112688 11488 8560 6614 64498 816 10462 0.815183 0 . 0 . 59 4,23,4,26 UTR_3_PRIME(MODIFIER||41||1141|TTC17|protein_coding|CODING|NM_018259.5|24|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999968 rs3740980 -0.693097 0.0153703 59 T119 286 acT/acC LOW 6 SILENT CODING ALKBH3 C protein_coding NM_139178.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43911365 T C 0 228 0 0.9909 0.9976 1 1 1 1 0.990468 0.996771 1 2 10285 121283 11575 8654 6613 66736 908 16512 2 10406 121406 11576 8654 6614 66736 908 16512 0 . 0 . 0 75 0,0,23,43 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T119|286|ALKBH3|protein_coding|CODING|NM_139178.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2434478 -0.693147 0.00108288 75 D228E 286 gaC/gaG MODERATE 9 MISSENSE CODING ALKBH3 G protein_coding NM_139178.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43940602 C G 0 222 0 0.0802 0.139 0.1398 0.0933 0.2575 0.1431 0.0978212 0.205751 0.261046 1 1033 24090 1196 651 1498 17019 185 2508 2 10406 121386 11576 8654 6614 66724 908 16504 0.924501 0 . 0 COSM1127789 116 48,15,27,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D228E|286|ALKBH3|protein_coding|CODING|NM_139178.3|9|G),INTRAGENIC(MODIFIER|||||ALKBH3-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.222045 rs1130290,rs386494362 -0.693141 0.624925 116 G242 286 ggG/ggT LOW 9 SILENT CODING ALKBH3 T protein_coding NM_139178.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43940644 G T 0 222 0 0.2958 0.6162 0.6542 0.8373 0.6243 0.7863 0.362233 0.535445 0.624186 1 3656 79073 8648 7311 4344 41973 599 12542 2 10406 121398 11576 8650 6612 66734 908 16512 0.83088 0 . 0 . 120 29,23,33,23 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G242|286|ALKBH3|protein_coding|CODING|NM_139178.3|9|T),INTRAGENIC(MODIFIER|||||ALKBH3-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.542015 rs1048928 -0.693147 0.450672 120 286 217 MODIFIER 10 CODING ALKBH3 G protein_coding NM_139178.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43941777 C G 0 58 0 0.1846 0.1685 0.1484 0.0933 0.2604 0.1442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992367 0 . 0 . 8 0,4,0,4 UTR_3_PRIME(MODIFIER||217||286|ALKBH3|protein_coding|CODING|NM_139178.3|10|G),INTRAGENIC(MODIFIER|||||ALKBH3-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 0 . 0.62023 rs2292889 -0.556411 0.0422968 8 P39S 122 Ccc/Tcc MODERATE 1 MISSENSE CODING C11orf96 T protein_coding NM_001145033.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 43964569 C T 0 97 0 0.1589 0.0881 0.0403 0.0992 0.0795 0.0235 0 . 0 1 135 714 5 28 1 304 7 234 2 848 9738 170 202 6 3296 100 5116 1.01283 0 . 0 . 8 0,3,3,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P39S|122|C11orf96|protein_coding|CODING|NM_001145033.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1.01283 1.01283 0 0.202566 rs2434483 -0.556411 0.0707707 8 C529R 568 Tgc/Cgc MODERATE 13 MISSENSE CODING ACCSL C protein_coding NM_001031854.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44080210 T C 0 228 0 0.8964 0.7943 0.5893 0.8433 0.7803 0.7658 0.864267 0.794437 0.762588 2 8484 91142 6511 7376 5098 50620 668 12385 2 9800 120734 11570 8626 6612 66730 900 16496 1 0 . 0 . 105 1,0,60,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C529R|568|ACCSL|protein_coding|CODING|NM_001031854.2|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2074051 -0.693147 0.0348706 105 501 LOW 5 CODING ACCS A protein_coding NM_001127219.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44096238 G A 0 228 0 0.649 0.7712 0.8314 0.9077 0.7425 0.7822 0.672719 0.692065 0.701977 2 6941 89676 10006 7958 4926 46673 657 12515 2 10406 121328 11566 8652 6604 66684 908 16508 0 . 0 . 0 78 0,0,18,52 SPLICE_SITE_REGION+INTRON(LOW||||501|ACCS|protein_coding|CODING|NM_001127219.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs178521 -0.693147 0.00317013 78 L291 501 Ctg/Ttg LOW 10 SILENT CODING ACCS T protein_coding NM_001127219.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44101118 C T 0 228 0 0.1203 0.1142 0.0937 0.1151 0.1223 0.1115 0.131639 0.130632 0.130116 2 1315 13244 721 939 487 8215 97 1470 2 9078 102858 9498 7938 4570 57702 736 13336 1 0 . 0 . 147 0,1,90,35 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L291|501|ACCS|protein_coding|CODING|NM_001127219.1|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7950395 -0.693147 0.302456 147 P421L 501 cCc/cTc MODERATE 14 MISSENSE CODING ACCS T protein_coding NM_001127219.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44104981 C T 0 228 0 0.4054 0.4038 0.304 0.4692 0.4612 0.3456 0.416478 0.415116 0.414419 2 4305 47857 2635 4009 2871 27942 372 5723 2 10360 120760 11492 8600 6572 66342 902 16492 0 . 0 . 0 50 0,0,13,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P421L|501|ACCS|protein_coding|CODING|NM_001127219.1|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3107275 -0.693147 0.0397676 50 411 3107 MODIFIER 4 CODING ALX4 C protein_coding NM_021926.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44283297 T C 0 46.3 0 0.8722 0.9073 0.9524 0.9812 0.8936 0.8609 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||3107||411|ALX4|protein_coding|CODING|NM_021926.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4755239 -0.453602 0.28 2 411 2110 MODIFIER 4 CODING ALX4 C protein_coding NM_021926.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44284294 T C 0 9.7 0 0.969 0.9918 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2110||411|ALX4|protein_coding|CODING|NM_021926.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7105993 -0.379885 0 1 411 1699 MODIFIER 4 CODING ALX4 A protein_coding NM_021926.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44284705 C A 0 9.7 0 0.0915 0.1392 0.0706 0.2927 0.0666 0.1687 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1699||411|ALX4|protein_coding|CODING|NM_021926.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7942612 -0.379885 0 1 411 973 MODIFIER 4 CODING ALX4 T protein_coding NM_021926.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44285431 C T 0 63 0 0.0832 0.0919 0.0706 0.1151 0.0676 0.1196 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||973||411|ALX4|protein_coding|CODING|NM_021926.3|4|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs117526668 -0.453602 0.14 3 H358 411 caC/caT LOW 4 SILENT CODING ALX4 A protein_coding NM_021926.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44286566 G A 0 228 0 0.1248 0.3584 0.5202 0.5258 0.334 0.4121 0.166364 0.274608 0.330077 2 1622 43101 6780 4727 2274 20942 312 6444 2 10064 119118 11494 8530 6514 65148 876 16492 0.935305 0 . 0 COSM1178421 186 2,1,45,128 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H358|411|ALX4|protein_coding|CODING|NM_021926.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.893608 rs3802805 -0.693147 0.210938 186 S207 411 tcA/tcG LOW 2 SILENT CODING ALX4 C protein_coding NM_021926.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44297054 T C 0 228 0 0.9697 0.9916 0.9986 0.999 1 1 0.97458 0.991233 0.999767 2 10121 121104 11570 8653 6614 66731 908 16507 2 10404 121406 11576 8654 6614 66738 908 16512 0 . 0 . 0 40 0,0,24,14 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S207|411|ALX4|protein_coding|CODING|NM_021926.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769028 -0.693143 0.652343 40 P102S 411 Ccg/Tcg MODERATE 1 MISSENSE CODING ALX4 A protein_coding NM_021926.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44331309 G A 0 222 0 0.0287 0.372 0.3473 0.506 0.4364 0.6493 0 . 0 1 94 9878 318 337 125 3461 91 5452 2 656 16386 522 520 206 6102 160 8220 0.781715 0 . 0 . 39 9,6,16,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccg/Tcg|P102S|411|ALX4|protein_coding|CODING|NM_021926.3|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.991011 rs12421995 -0.692717 0.320286 39 R35T 411 aGg/aCg MODERATE 1 MISSENSE CODING ALX4 G protein_coding NM_021926.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44331509 C G 0 222 0 0.2443 0.4726 0.3833 0.5079 0.4682 0.8129 0.300909 0.424207 0.48732 1 1948 41610 3059 3097 1337 22129 269 9771 2 5222 70354 5924 5252 2268 38666 486 12536 0.437168 0 . 0 . 311 95,54,84,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aCg|R35T|411|ALX4|protein_coding|CODING|NM_021926.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.589475 rs3824915 -0.693147 0.166556 311 E116 267 gaG/gaA LOW 7 SILENT CODING CD82 A protein_coding NM_002231.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44636833 G A 0 228 0 0.0129 0.2458 0.3141 0.4653 0.1322 0.4029 0.0354063 0.101046 0.134682 2 346 25551 4729 3946 1034 9338 201 5957 2 10368 120912 11530 8606 6596 66432 904 16476 1 0 . 0 . 177 0,1,57,95 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E116|267|CD82|protein_coding|CODING|NM_002231.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2303865 -0.693147 0.0908246 177 V256 267 gtC/gtG LOW 10 SILENT CODING CD82 G protein_coding NM_002231.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44640640 C G 0 222 0 0.0825 0.1697 0.1081 0.3899 0.1978 0.0757 0.101453 0.157798 0.186671 1 968 21002 800 3359 1575 12989 145 1166 2 10402 121340 11576 8622 6612 66710 908 16510 0.934727 0 . 0 . 66 16,16,15,11 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V256|267|CD82|protein_coding|CODING|NM_002231.3|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97797 rs7107335 -0.692976 0.141442 66 267 116 MODIFIER 10 CODING CD82 C protein_coding NM_002231.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44640792 T C 0 151 0 0.9123 0.9758 0.9957 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,0,12 UTR_3_PRIME(MODIFIER||116||267|CD82|protein_coding|CODING|NM_002231.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4755266 -0.680642 0.674631 12 V133I 248 Gtc/Atc MODERATE 6 MISSENSE CODING TSPAN18 A protein_coding NM_130783.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44940828 G A 0 228 0 0.034 0.347 0.415 0.5575 0.329 0.5235 0.0998638 0.259689 0.341591 2 928 44897 5085 5158 2325 23460 327 7614 2 10388 121314 11570 8624 6612 66710 904 16506 1 0 . 0 . 134 0,1,67,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V133I|248|TSPAN18|protein_coding|CODING|NM_130783.4|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2291334 -0.693147 0.795224 134 248 55 MODIFIER 9 CODING TSPAN18 A protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44950784 G A 0 228 0 0.8949 0.875 0.928 0.7837 0.8907 0.8885 0.906069 0.878668 0.86675 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 88 0,0,25,50 UTR_3_PRIME(MODIFIER||55||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|A),DOWNSTREAM(MODIFIER||3115||189|TP53I11|protein_coding|CODING|NM_001258320.1||A) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs835990 -0.693147 0.398149 88 248 248 MODIFIER 9 CODING TSPAN18 C protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44950977 A C 0 76 0 0.8964 0.8323 0.8501 0.6438 0.8936 0.864 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||248||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|C),DOWNSTREAM(MODIFIER||2922||189|TP53I11|protein_coding|CODING|NM_001258320.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs704671 -0.511536 0.235765 3 248 888 MODIFIER 9 CODING TSPAN18 C protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44951617 G C 0 100 0 0.211 0.5016 0.5764 0.62 0.4881 0.7331 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||888||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|C),DOWNSTREAM(MODIFIER||2282||189|TP53I11|protein_coding|CODING|NM_001258320.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs860694 -0.511536 0.549396 4 248 1556 MODIFIER 9 CODING TSPAN18 T protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44952285 C T 0 190 0 0.1263 0.4716 0.5634 0.5972 0.4861 0.729 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,22,0 UTR_3_PRIME(MODIFIER||1556||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|T),DOWNSTREAM(MODIFIER||1614||189|TP53I11|protein_coding|CODING|NM_001258320.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10838390 -0.692562 0.819538 23 248 1940 MODIFIER 9 CODING TSPAN18 C protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44952669 G C 0 134 0 0.8956 0.8756 0.9337 0.7788 0.8936 0.8885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,0,9 UTR_3_PRIME(MODIFIER||1940||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|C),DOWNSTREAM(MODIFIER||1230||189|TP53I11|protein_coding|CODING|NM_001258320.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs836001 -0.662043 0.499805 9 248 1997 MODIFIER 9 CODING TSPAN18 C protein_coding NM_130783.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44952726 G C 0 64 0 0.8994 0.878 0.9337 0.7847 0.8946 0.8885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1997||248|TSPAN18|protein_coding|CODING|NM_130783.4|9|C),DOWNSTREAM(MODIFIER||1173||189|TP53I11|protein_coding|CODING|NM_001258320.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs836002 -0.511536 0.0714862 3 189 1321 MODIFIER 10 CODING TP53I11 T protein_coding NM_001258320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44955114 C T 0 69 0 0.2912 0.513 0.5648 0.7044 0.4205 0.6738 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,1 UTR_3_PRIME(MODIFIER||1321||189|TP53I11|protein_coding|CODING|NM_001258320.1|10|T),DOWNSTREAM(MODIFIER||1137||248|TSPAN18|protein_coding|CODING|NM_130783.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2592187 -0.556411 0.522837 5 189 314 MODIFIER 10 CODING TP53I11 T protein_coding NM_001258320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44956121 C T 0 212 0 0.9826 0.9952 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,7,2 UTR_3_PRIME(MODIFIER||314||189|TP53I11|protein_coding|CODING|NM_001258320.1|10|T),DOWNSTREAM(MODIFIER||2144||248|TSPAN18|protein_coding|CODING|NM_130783.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs835992 -0.662043 0.0991864 10 189 LOW 4 CODING TP53I11 A protein_coding NM_001258320.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44959924 G A 0 228 0 0.3752 0.5553 0.5504 0.6825 0.4751 0.7536 0.388056 0.450392 0.482321 2 2512 37952 4238 3703 1393 20362 243 5501 2 5746 64134 6412 5114 2434 36716 406 7306 1 0 . 0 . 55 1,0,10,40 SPLICE_SITE_REGION+INTRON(LOW||||189|TP53I11|protein_coding|CODING|NM_001258320.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2306666 -0.693147 0.0517971 55 189 803 MODIFIER 4 CODING TP53I11 G protein_coding NM_001258320.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 44960689 A G 0 6.3 0 1 0.9998 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||803||189|TP53I11|protein_coding|CODING|NM_001258320.1|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs835995 -0.379885 0 1 D732 1177 gaT/gaC LOW 8 SILENT CODING PRDM11 C protein_coding NM_001256695.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45248372 T C 0 222 0 0.7753 0.7786 0.9006 0.4563 0.9702 0.8313 0 . 0 1 487 10917 171 87 2 3419 113 6638 2 602 12380 186 196 2 3642 132 7620 0.272107 0 . 0 . 163 27,54,30,31 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D732|1177|PRDM11|protein_coding|CODING|NM_001256695.1|8|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.136797 rs11038361 -0.693147 0.000189695 163 A1046 1177 gcT/gcC LOW 8 SILENT CODING PRDM11 C protein_coding NM_001256695.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45249314 T C 0 222 0 0.7753 0.7796 0.9006 0.4563 0.9702 0.8364 0 . 0 1 462 10941 174 91 2 3447 113 6652 2 566 12382 188 204 2 3670 132 7620 0.727265 0 . 0 . 135 40,25,40,20 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A1046|1177|PRDM11|protein_coding|CODING|NM_001256695.1|8|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.298885 rs746555 -0.693147 0.432257 135 1177 737 MODIFIER 8 CODING PRDM11 A protein_coding NM_001256695.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45250447 C A 0 18.2 0 0.0877 0.2961 0.3876 0.2728 0.4274 0.4018 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,0,1,0 UTR_3_PRIME(MODIFIER||737||1177|PRDM11|protein_coding|CODING|NM_001256695.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3758719 -0.379885 0 5 1177 2150 MODIFIER 8 CODING PRDM11 A protein_coding NM_001256695.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45251860 C A 0 9.7 0 0.3011 0.4621 0.4323 0.3155 0.671 0.637 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2150||1177|PRDM11|protein_coding|CODING|NM_001256695.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10769130 -0.379885 0 1 1177 6216 MODIFIER 8 CODING PRDM11 T protein_coding NM_001256695.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45255926 C T 0 21.2 0 0.4002 0.4958 0.451 0.2946 0.7097 0.6442 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,0 UTR_3_PRIME(MODIFIER||6216||1177|PRDM11|protein_coding|CODING|NM_001256695.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3740781 -0.379885 0 3 426 3477 MODIFIER 6 CODING SYT13 T protein_coding NM_020826.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45262126 C T 0 87 0 0.3321 0.3922 0.3516 0.2956 0.5109 0.4796 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.986852 0 . 0 . 16 0,10,1,5 UTR_3_PRIME(MODIFIER||3477||426|SYT13|protein_coding|CODING|NM_020826.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.315707 rs8929 -0.616816 0.0959456 16 426 3361 MODIFIER 6 CODING SYT13 A protein_coding NM_020826.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45262242 G A 0 83 0 0.559 0.6444 0.5706 0.4008 0.8519 0.8497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,1,2 UTR_3_PRIME(MODIFIER||3361||426|SYT13|protein_coding|CODING|NM_020826.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2863173 -0.511536 0.460446 6 426 3347 MODIFIER 6 CODING SYT13 G protein_coding NM_020826.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45262256 A G 0 55 0 0.6256 0.6629 0.5764 0.4008 0.8529 0.8497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,1,1 UTR_3_PRIME(MODIFIER||3347||426|SYT13|protein_coding|CODING|NM_020826.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2902427 -0.453602 0.56 5 411 232 MODIFIER 4 CODING CHST1 T protein_coding NM_003654.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45671006 G T 0 5.7 0 0.997 0.9992 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 95 1,3,2,3 UTR_3_PRIME(MODIFIER||232||411|CHST1|protein_coding|CODING|NM_003654.5|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 0.924584 0 0.89338 rs115499615 -0.590765 0.825417 95 S71 411 agT/agC LOW 4 SILENT CODING CHST1 G protein_coding NM_003654.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45672261 A G 0 228 0 0.3986 0.6871 0.7795 0.6716 0.828 0.8824 0.452792 0.716933 0.852291 2 4542 97179 9741 5877 5117 56479 746 14677 2 10392 121340 11576 8638 6604 66712 906 16512 0.949686 0 . 0 . 176 0,2,88,71 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S71|411|CHST1|protein_coding|CODING|NM_003654.5|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.100629 rs3802762,rs386586649 -0.693147 0.763083 176 364 3 MODIFIER 1 CODING SLC35C1 G protein_coding NM_018389.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45827350 A G 0 222 0 0.4478 0.25 0.1657 0.1389 0.2535 0.1534 0.411938 0.276915 0.207723 1 4237 25223 1409 1081 1827 14070 191 2408 2 9808 119330 11522 8534 6588 65496 894 16488 0.917466 2 benign 0 . 87 24,10,27,14 START_GAINED(LOW||||364|SLC35C1|protein_coding|CODING|NM_018389.4|1|G),UTR_5_PRIME(MODIFIER||3||364|SLC35C1|protein_coding|CODING|NM_018389.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.76366 rs3808976 -0.693145 0.514864 87 364 49 MODIFIER 2 CODING SLC35C1 A protein_coding NM_018389.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45832935 G A 0 228 0 0.1051 0.4513 0.6081 0.3393 0.7187 0.6483 0.328616 0.640213 0.791645 2 244 6241 266 260 193 4589 41 648 2 976 9258 394 730 260 5898 64 936 1 0 . 0 . 201 0,1,146,49 UTR_3_PRIME(MODIFIER||49||364|SLC35C1|protein_coding|CODING|NM_018389.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1139266 -0.693147 0.791472 201 364 1312 MODIFIER 2 CODING SLC35C1 C protein_coding NM_018389.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45834198 T C 0 9.7 0 0.5446 0.6538 0.8256 0.4058 0.8827 0.6994 0 . 0 1 123 8353 75 39 2 2448 92 5574 2 194 10788 92 132 2 2744 118 7506 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1312||364|SLC35C1|protein_coding|CODING|NM_018389.4|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs7943306 -0.379885 0 1 614 LOW 1 CODING CRY2 G protein_coding NM_021117.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45877529 A G 0 228 0 0.8215 0.7949 0.879 0.4831 0.9334 0.8783 0.851112 0.909028 0.938707 2 8749 106634 10008 3921 6290 62387 816 14463 2 10404 121384 11578 8638 6614 66732 908 16510 0 . 0 . 0 90 0,0,66,18 SPLICE_SITE_REGION+INTRON(LOW||||614|CRY2|protein_coding|CODING|NM_021117.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2292913 -0.693147 0.00830185 90 614 9831 MODIFIER 12 CODING CRY2 C protein_coding NM_021117.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45903613 A C 0 124 0 0.6301 0.5841 0.7291 0.3343 0.6809 0.5767 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.998823 0 . 0 . 28 12,1,14,0 UTR_3_PRIME(MODIFIER||9831||614|CRY2|protein_coding|CODING|NM_021117.3|12|C),UPSTREAM(MODIFIER||3434||711|MAPK8IP1|protein_coding|CODING|NM_005456.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.94394 rs2292910 -0.686358 0.427441 28 614 10695 MODIFIER 12 CODING CRY2 C protein_coding NM_021117.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45904477 T C 0 228 0 0.7617 0.7602 0.8588 0.4831 0.8936 0.8364 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,12,2 UTR_3_PRIME(MODIFIER||10695||614|CRY2|protein_coding|CODING|NM_021117.3|12|C),UPSTREAM(MODIFIER||2570||711|MAPK8IP1|protein_coding|CODING|NM_005456.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6798 -0.686358 0.0572 15 346 273 MODIFIER 11 CODING PEX16 A protein_coding NM_057174.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45931367 G A 0 18.4 0 0.0772 0.0405 0.0072 0.0347 0.001 0.0613 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,1,0 UTR_3_PRIME(MODIFIER||273||346|PEX16|protein_coding|CODING|NM_057174.2|11|A),UPSTREAM(MODIFIER||2534||98|C11orf94|protein_coding|CODING|NM_001080446.2||A),DOWNSTREAM(MODIFIER||3351||711|MAPK8IP1|protein_coding|CODING|NM_005456.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2280328 -0.379885 0 4 346 138 MODIFIER 11 CODING PEX16 A protein_coding NM_057174.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45931502 G A 0 70 0 0.0847 0.3936 0.5576 0.2054 0.7276 0.545 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.422245 0 . 0 . 30 21,1,8,0 UTR_3_PRIME(MODIFIER||138||346|PEX16|protein_coding|CODING|NM_057174.2|11|A),UPSTREAM(MODIFIER||2669||98|C11orf94|protein_coding|CODING|NM_001080446.2||A),DOWNSTREAM(MODIFIER||3486||711|MAPK8IP1|protein_coding|CODING|NM_005456.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.658255 rs10838529 -0.651104 0.0231463 30 Y291 346 taT/taC LOW 9 SILENT CODING PEX16 G protein_coding NM_057174.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45935384 A G 0 228 0 0.559 0.6891 0.6643 0.4653 0.9215 0.8742 0.601226 0.811366 0.919051 2 6100 98425 6403 3713 6265 60781 764 14399 2 10326 120700 11526 8598 6602 66244 896 16508 1 0 . 0 . 141 1,0,68,63 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y291|346|PEX16|protein_coding|CODING|NM_057174.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1132349 -0.693147 0.070542 141 V116I 346 Gtc/Atc MODERATE 4 MISSENSE CODING PEX16 T protein_coding NM_057174.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45937267 C T 0 228 0 1 1 1 1 1 1 0 . 0 2 10404 121390 11578 8654 6614 66724 904 16512 2 10404 121390 11578 8654 6614 66724 904 16512 0 . 0 . 0 87 0,0,23,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V116I|346|PEX16|protein_coding|CODING|NM_057174.2|4|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs10742772 -0.693147 0.239472 87 F556 721 ttC/ttT LOW 12 SILENT CODING GYLTL1B T protein_coding NM_001300721.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45949534 C T 0 222 0 0.3419 0.5843 0.6326 0.4038 0.8996 0.7393 0.401952 0.725161 0.890789 1 4032 91323 5923 3221 5975 59184 724 12264 2 10368 121078 11552 8604 6602 66538 906 16508 0.667651 0 . 0 . 71 29,12,11,14 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F556|721|GYLTL1B|protein_coding|CODING|NM_001300721.1|12|T),DOWNSTREAM(MODIFIER||1336||680|PHF21A|protein_coding|CODING|NM_001101802.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.167531 rs939105 -0.692914 0.24648 71 680 1816 MODIFIER 18 CODING PHF21A C protein_coding NM_001101802.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 45953698 CAGCCT C 0 83 0 0.7254 0.8744 0.9294 0.998 0.9016 0.8814 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||1816||680|PHF21A|protein_coding|CODING|NM_001101802.1|18|C),DOWNSTREAM(MODIFIER||3052||721|GYLTL1B|protein_coding|CODING|NM_001300721.1||C) 0 . 0 2 0.666667 1 1 0 . 0 60 0 0 . 0 . rs141686809 -0.453602 0.1 3 519 538 MODIFIER 12 CODING CREB3L1 C protein_coding NM_052854.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46342834 A C 0 222 0 0.9433 0.4944 0.2334 0.245 0.325 0.5041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.335753 0 . 0 . 170 42,40,28,31 UTR_3_PRIME(MODIFIER||538||519|CREB3L1|protein_coding|CODING|NM_052854.3|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.96042 rs7476 -0.693147 0.000101962 170 1117 20 MODIFIER 32 CODING DGKZ G protein_coding NM_001105540.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46401517 A G 0 3.7 0 . 0 . 0 . 0 . 0 . 1 848 19352 2191 1717 680 12200 116 1600 2 3400 49604 4908 3970 1610 28694 316 6706 0.140178 0 . 0 . 447 124,183,71,1 UTR_3_PRIME(MODIFIER||20||1117|DGKZ|protein_coding|CODING|NM_001105540.1|32|G),UPSTREAM(MODIFIER||1744||143|MDK|protein_coding|CODING|NM_001012333.2||G),DOWNSTREAM(MODIFIER||4825||479|CHRM4|protein_coding|CODING|NM_000741.3||G) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.000179392 1.8732e-05 0 0.547008 rs61882687 -0.693147 0.000226278 447 550 432 MODIFIER 18 CODING ATG13 G protein_coding NM_001205119.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46694313 GTC G 0 228 0 0.9977 0.9992 0.9986 1 1 1 0.994276 0.997829 0.999654 2 7947 110665 11046 8078 6508 60448 816 15822 2 7968 110686 11046 8078 6508 60448 816 15822 0 . 0 . 0 106 0,0,23,72 UTR_3_PRIME(MODIFIER||432||550|ATG13|protein_coding|CODING|NM_001205119.1|18|G),DOWNSTREAM(MODIFIER||4311||439|ARHGAP1|protein_coding|CODING|NM_004308.3||G) 1 0 . 96 0.90566 1 1 1 1 0 60 0 0 1 0 . rs67065551 -0.693147 0.0567325 106 K153 439 aaA/aaG LOW 6 SILENT CODING ARHGAP1 C protein_coding NM_004308.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46702920 T C 0 228 0 0.9977 0.9992 0.9986 1 1 1 0.995911 0.998615 1 2 10376 121381 11577 8654 6614 66740 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 79 0,0,37,33 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K153|439|ARHGAP1|protein_coding|CODING|NM_004308.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4268467 -0.693147 0.0794074 79 622 LOW 5 CODING F2 C protein_coding NM_000506.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46744925 G C 0 222 0 0.1263 0.4553 0.5836 0.3026 0.7078 0.7065 0.230577 0.538385 0.695976 1 2206 73067 5586 2533 4188 46985 596 10973 2 10388 121250 11564 8612 6606 66664 904 16512 0.795315 0 . 0 COSM147179 77 22,16,22,12 SPLICE_SITE_REGION+INTRON(LOW||||622|F2|protein_coding|CODING|NM_000506.4|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836359 rs2070852 -0.693132 0.0709295 77 T165M 622 aCg/aTg MODERATE 6 MISSENSE CODING F2 T protein_coding NM_000506.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46745003 C T 0 222 0 0.0053 0.2192 0.281 0.6002 0.1213 0.1728 0.0343026 0.096 0.127588 1 328 23878 4921 5230 1613 8297 149 3340 2 10320 120828 11528 8610 6546 66436 902 16486 0.84006 0 . 0 COSM147180 87 13,27,14,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T165M|622|F2|protein_coding|CODING|NM_000506.4|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.953967 rs5896 -0.693145 0.144929 87 1905 1805 MODIFIER 38 CODING LRP4 A protein_coding NM_002334.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46878729 G A 0 228 0 0.9743 0.9926 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,11,44 UTR_3_PRIME(MODIFIER||1805||1905|LRP4|protein_coding|CODING|NM_002334.3|38|A),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6485701 -0.693147 4.11097e-05 62 1905 1017 MODIFIER 38 CODING LRP4 A protein_coding NM_002334.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46879517 G A 0 222 0 0.0008 0.0611 0.0014 0.2887 0.001 0.0123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.831723 0 . 0 . 68 3,33,4,25 UTR_3_PRIME(MODIFIER||1017||1905|LRP4|protein_coding|CODING|NM_002334.3|38|A),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.572755 rs10838623 -0.693079 0.44076 68 1905 561 MODIFIER 38 CODING LRP4 G protein_coding NM_002334.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46879973 A G 0 222 0 0.4092 0.5827 0.6484 0.3889 0.7863 0.7607 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.948346 0 . 0 . 129 33,27,31,13 UTR_3_PRIME(MODIFIER||561||1905|LRP4|protein_coding|CODING|NM_002334.3|38|G),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.726491 rs3829940 -0.693146 0.0638848 129 1905 544 MODIFIER 38 CODING LRP4 C protein_coding NM_002334.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46879990 T C 0 228 0 0.9743 0.9926 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 115 0,0,47,51 UTR_3_PRIME(MODIFIER||544||1905|LRP4|protein_coding|CODING|NM_002334.3|38|C),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7950924 -0.693147 0.00713253 115 R1646Q 1905 cGg/cAg MODERATE 33 MISSENSE CODING LRP4 T protein_coding NM_002334.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46890165 C T 0 222 0 0.3986 0.5797 0.6484 0.3889 0.7863 0.7597 0.442299 0.660077 0.771575 1 4464 83044 6030 3272 4507 51950 668 12153 2 10400 121294 11568 8602 6610 66702 906 16506 0.826211 0 . 0 . 40 14,3,10,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1646Q|1905|LRP4|protein_coding|CODING|NM_002334.3|33|T),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93576 rs3816614 -0.69168 0.564119 40 F1635 1905 ttC/ttT LOW 33 SILENT CODING LRP4 A protein_coding NM_002334.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46890197 G A 0 222 0 0.0045 0.2192 0.2781 0.6101 0.1193 0.1677 0.0336211 0.0923077 0.122354 1 319 23633 4933 5365 1613 8047 143 3213 2 10400 121342 11566 8634 6604 66720 906 16512 0.930496 0 . 0 . 57 17,10,15,8 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1635|1905|LRP4|protein_coding|CODING|NM_002334.3|33|A),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.798125 rs2290883 -0.692717 0.300808 57 S1554G 1905 Agc/Ggc MODERATE 31 MISSENSE CODING LRP4 C protein_coding NM_002334.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46893108 T C 0 222 0 0.1142 0.3676 0.4841 0.2569 0.5417 0.5624 0.194911 0.425308 0.543266 1 1780 56277 4386 1977 3578 35698 459 8399 2 9336 113884 10750 8072 5918 63512 826 15470 0.836692 0 . 0 . 101 22,23,33,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S1554G|1905|LRP4|protein_coding|CODING|NM_002334.3|31|C),INTRAGENIC(MODIFIER|||||LRP4-AS1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.862128 rs2306029,rs386491782 -0.693147 0.0822781 101 A1203V 1905 gCg/gTg MODERATE 26 MISSENSE CODING LRP4 A protein_coding NM_002334.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46897446 G A 0 222 0 0.0045 0.2192 0.2781 0.6101 0.1193 0.1677 0.0336211 0.0922308 0.122238 1 319 23566 4901 5352 1607 8037 142 3208 2 10398 121184 11536 8618 6602 66644 904 16482 0.833248 0 . 0 . 155 35,25,37,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A1203V|1905|LRP4|protein_coding|CODING|NM_002334.3|26|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.656885 rs2306033 -0.693147 0.332978 155 I1086V 1905 Att/Gtt MODERATE 23 MISSENSE CODING LRP4 C protein_coding NM_002334.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46898771 T C 0 222 0 0.1256 0.4459 0.572 0.2927 0.6769 0.7096 0.221945 0.516154 0.666783 1 2091 70992 5520 2430 4147 45147 594 11063 2 10406 121374 11574 8632 6614 66728 908 16512 0.788489 0 . 0 COSM147182 142 26,43,26,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I1086V|1905|LRP4|protein_coding|CODING|NM_002334.3|23|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.485743 rs6485702 -0.693147 0.018781 142 K546 1905 aaA/aaG LOW 13 SILENT CODING LRP4 C protein_coding NM_002334.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46914583 T C 0 228 0 0.938 0.9808 0.9928 1 0.993 0.998 0.964107 0.979231 0.986974 2 9992 119806 11448 8645 6583 65821 900 16417 2 10372 121160 11554 8646 6602 66602 906 16478 0 . 0 . 0 74 0,0,33,37 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K546|1905|LRP4|protein_coding|CODING|NM_002334.3|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10838631 -0.693147 0.0462017 74 D541 1905 gaT/gaC LOW 13 SILENT CODING LRP4 G protein_coding NM_002334.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 46914598 A G 0 228 0 0.9803 0.9946 0.9986 1 1 1 0.987506 0.995769 1 2 10248 121037 11547 8648 6606 66606 906 16476 2 10380 121174 11550 8648 6606 66608 906 16476 0 . 0 . 0 77 0,0,33,38 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D541|1905|LRP4|protein_coding|CODING|NM_002334.3|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769215 -0.693147 0.345156 77 521 609 MODIFIER 16 CODING ARFGAP2 A protein_coding NM_032389.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47186424 C A 0 26.2 0 0.4781 0.492 0.5072 0.2708 0.5288 0.6902 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,2,1,1 UTR_3_PRIME(MODIFIER||609||521|ARFGAP2|protein_coding|CODING|NM_032389.4|16|A),DOWNSTREAM(MODIFIER||2626||337|C11orf49|protein_coding|CODING|NM_001003677.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs1055447 -0.453602 0.14 5 A443 521 gcA/gcG LOW 13 SILENT CODING ARFGAP2 C protein_coding NM_032389.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47188314 T C 0 228 0 0.9962 0.9988 0.9986 1 1 1 0.994548 0.998154 1 2 10357 121293 11575 8650 6614 66688 908 16501 2 10402 121342 11578 8650 6614 66688 908 16502 0 . 0 . 0 78 0,0,32,39 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A443|521|ARFGAP2|protein_coding|CODING|NM_032389.4|13|C),DOWNSTREAM(MODIFIER||4516||337|C11orf49|protein_coding|CODING|NM_001003677.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4752820 -0.693147 0.608519 78 S411N 521 aGc/aAc MODERATE 13 MISSENSE CODING ARFGAP2 T protein_coding NM_032389.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47188411 C T 0 222 0 0.6853 0.3886 0.2435 0.124 0.335 0.4182 0.612676 0.417385 0.317399 1 6499 39419 2074 1127 1485 21384 272 6578 2 10392 121206 11570 8642 6612 66600 906 16484 0.71462 0 . 0 . 41 9,13,5,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S411N|521|ARFGAP2|protein_coding|CODING|NM_032389.4|13|T),DOWNSTREAM(MODIFIER||4613||337|C11orf49|protein_coding|CODING|NM_001003677.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.79328 rs3740691,rs386585197 -0.688148 0.592534 41 T126 427 acT/acC LOW 3 SILENT CODING DDB2 C protein_coding NM_000107.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47238522 T C 0 228 0 0.9788 0.9942 0.9986 1 1 1 0.986143 0.995307 1 2 10256 121251 11570 8654 6614 66738 908 16511 2 10404 121404 11574 8654 6614 66738 908 16512 0 . 0 . 0 58 0,0,31,21 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T126|427|DDB2|protein_coding|CODING|NM_000107.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs326212,rs386486167 -0.693147 0.00475816 58 427 77 MODIFIER 10 CODING DDB2 T protein_coding NM_000107.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47260477 C T 0 213 0 0.0136 0.0489 0.0072 0.0506 0.0378 0.136 0.0245665 0.0337276 0.0377121 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992713 0 . 0 . 47 3,21,3,19 UTR_3_PRIME(MODIFIER||77||427|DDB2|protein_coding|CODING|NM_000107.2|10|T),DOWNSTREAM(MODIFIER||376||423|ACP2|protein_coding|CODING|NM_001610.3||T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.221143 rs1050244 -0.692562 0.0474748 47 L165 423 ctG/ctA LOW 5 SILENT CODING ACP2 T protein_coding NM_001610.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47267079 C T 0 222 0 0.0136 0.0489 0.0072 0.0506 0.0378 0.136 0.0229441 0.0315433 0.035947 1 235 5643 150 353 310 2582 21 1992 2 10400 121388 11578 8648 6612 66730 908 16512 0.996749 0 . 0 . 77 16,17,19,19 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L165|423|ACP2|protein_coding|CODING|NM_001610.3|5|T),UPSTREAM(MODIFIER||2772||453|NR1H3|protein_coding|CODING|NM_001251934.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.393307 rs10838677 -0.693143 0.151665 77 R29Q 423 cGg/cAg MODERATE 1 MISSENSE CODING ACP2 T protein_coding NM_001610.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47270255 C T 0 228 0 0.6203 0.517 0.3458 0.7768 0.3002 0.454 0.559052 0.379874 0.288408 2 5345 43746 4671 6175 2151 18041 250 7113 2 9034 104650 9898 8136 4594 57442 720 14826 1 0 . 0 . 122 0,1,66,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R29Q|423|ACP2|protein_coding|CODING|NM_001610.3|1|T),START_GAINED(LOW||||453|NR1H3|protein_coding|CODING|NM_001251934.1|2|T),UTR_5_PRIME(MODIFIER||100||453|NR1H3|protein_coding|CODING|NM_001251934.1|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2167079 -0.693147 0.00602327 122 453 100 MODIFIER 2 CODING NR1H3 T protein_coding NM_001251934.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47270255 C T 0 228 0 0.6203 0.517 0.3458 0.7768 0.3002 0.454 0.559052 0.379874 0.288408 2 5345 43746 4671 6175 2151 18041 250 7113 2 9034 104650 9898 8136 4594 57442 720 14826 1 0 . 0 . 122 0,1,66,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R29Q|423|ACP2|protein_coding|CODING|NM_001610.3|1|T),START_GAINED(LOW||||453|NR1H3|protein_coding|CODING|NM_001251934.1|2|T),UTR_5_PRIME(MODIFIER||100||453|NR1H3|protein_coding|CODING|NM_001251934.1|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2167079 -0.693147 0.00602327 122 S105 453 agC/agT LOW 4 SILENT CODING NR1H3 T protein_coding NM_001251934.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47282024 C T 0 222 0 0.4228 0.3538 0.2622 0.6726 0.1521 0.2045 0.366197 0.222573 0.149023 1 3954 29969 4610 5778 1877 9797 181 3772 2 10386 121208 11552 8632 6614 66610 906 16508 0.87488 0 . 0 . 105 25,25,21,25 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S105|453|NR1H3|protein_coding|CODING|NM_001251934.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93244 rs2279238 -0.693147 0.0434516 105 V751M 1647 Gtg/Atg MODERATE 13 MISSENSE CODING MADD A protein_coding NM_003682.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47306585 G A 0 170 0 0.3873 0.3351 0.2608 0.622 0.162 0.1994 0.344616 0.225496 0.164495 1 3707 30210 4635 5277 1895 10766 184 3746 2 10364 121166 11558 8630 6610 66606 902 16496 0.810649 0 . 0 . 44 21,0,17,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V751M|1647|MADD|protein_coding|CODING|NM_003682.3|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974923 rs1051006 -0.691153 0.263198 44 1647 LOW 20 CODING MADD G protein_coding NM_003682.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47312374 A G 0 214 0 0.0053 0.23 0.2349 0.624 0.1571 0.1994 0.0427079 0.121096 0.161238 1 374 25941 4337 5078 1866 10400 169 3717 2 9612 114172 10822 8250 6364 62400 872 15852 0.966558 0 . 0 . 43 8,12,3,18 SPLICE_SITE_REGION+INTRON(LOW||||1647|MADD|protein_coding|CODING|NM_003682.3|20|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.494521 rs386452214,rs58023804 -0.692352 0.00367136 43 L1371 1647 Ttg/Ctg LOW 28 SILENT CODING MADD C protein_coding NM_003682.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47331116 T C 0 228 0 0.9773 0.9938 0.9986 1 1 1 0.985461 0.995076 1 2 10256 121258 11574 8654 6614 66740 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 129 0,0,34,86 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L1371|1647|MADD|protein_coding|CODING|NM_003682.3|28|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1017594 -0.693147 0.421526 129 1647 619 MODIFIER 36 CODING MADD C protein_coding NM_003682.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47351320 T C 0 228 0 0.9697 0.991 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,6,6 UTR_3_PRIME(MODIFIER||619||1647|MADD|protein_coding|CODING|NM_003682.3|36|C),DOWNSTREAM(MODIFIER||1637||1274|MYBPC3|protein_coding|CODING|NM_000256.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.982603 0 . rs3021055 -0.680642 0.723817 12 E1096 1274 gaG/gaA LOW 29 SILENT CODING MYBPC3 T protein_coding NM_000256.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47354787 C T 0 228 0 0.5083 0.4762 0.3329 0.7202 0.3072 0.4571 0.462179 0.355036 0.303877 2 3341 32406 3251 4246 1663 14010 172 5723 2 6168 68846 5912 5858 3170 35830 466 11442 1 2|2 benign|benign 0 . 91 0,1,61,22 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E1096|1274|MYBPC3|protein_coding|CODING|NM_000256.3|29|T),DOWNSTREAM(MODIFIER||3205||1647|MADD|protein_coding|CODING|NM_003682.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1052373 -0.693147 0.883207 91 V849 1274 gtC/gtT LOW 24 SILENT CODING MYBPC3 A protein_coding NM_000256.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47358997 G A 0 202 0 0.0136 0.0481 0.0058 0.0506 0.0378 0.1329 0.0200186 0.0300375 0.0351084 1 215 5535 152 348 309 2537 21 1953 2 9654 119194 11516 8578 6604 65950 884 16008 0.955854 2 benign 0 . 25 8,1,11,2 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V849|1274|MYBPC3|protein_coding|CODING|NM_000256.3|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.851213 rs3729953 -0.683931 0.648169 25 E28G 371 gAa/gGa MODERATE 2 MISSENSE CODING SLC39A13 G protein_coding NM_001128225.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47431728 A G 0 228 0 0.7791 0.9405 0.9928 1 0.999 1 0.83667 0.944128 0.999184 2 8002 117369 11483 8622 6614 65256 891 16501 2 9634 119114 11564 8622 6614 65278 896 16506 0 . 0 . 0 62 0,0,18,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E28G|371|SLC39A13|protein_coding|CODING|NM_001128225.2|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2010519 -0.693147 0.41086 62 A191 371 gcG/gcA LOW 5 SILENT CODING SLC39A13 A protein_coding NM_001128225.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47434986 G A 0 228 0 0.0136 0.2706 0.2147 0.3988 0.3111 0.4836 0.0695139 0.245807 0.336087 2 652 37569 2117 3176 1677 22038 279 7630 2 10216 120562 11518 8610 6548 66258 904 16508 0.923094 0 . 0 . 128 2,1,53,60 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A191|371|SLC39A13|protein_coding|CODING|NM_001128225.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.906317 rs2293576 -0.693147 0.0072453 128 371 288 MODIFIER 10 CODING SLC39A13 T protein_coding NM_001128225.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47437202 C T 0 228 0 0.584 0.6464 0.562 0.7411 0.666 0.6728 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,6,30 UTR_3_PRIME(MODIFIER||288||371|SLC39A13|protein_coding|CODING|NM_001128225.2|10|T),DOWNSTREAM(MODIFIER||3118||439|PSMC3|protein_coding|CODING|NM_002804.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2293577 -0.693139 0.211223 38 R397W 412 Cgg/Tgg MODERATE 8 MISSENSE CODING RAPSN A protein_coding NM_005055.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47459576 G A 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 0 0 0 0 0 0 0 2 2804 20870 410 640 34 8870 198 7914 0.525393 0 . 0 . 96 27,23,19,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R397W|412|RAPSN|protein_coding|CODING|NM_005055.4|8|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.35467 rs201796294 -0.693132 0.0340123 96 P381 412 ccT/ccC LOW 7 SILENT CODING RAPSN G protein_coding NM_005055.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47460306 A G 0 228 0 0.348 0.6248 0.6902 0.6567 0.7058 0.8364 0.422866 0.612314 0.709455 2 2169 32049 2200 2362 580 17611 249 6878 2 4820 46874 3520 3780 930 24618 340 8866 1 3 likely-benign 0 . 87 1,0,37,43 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P381|412|RAPSN|protein_coding|CODING|NM_005055.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386607679,rs7126210 -0.693147 0.0987241 87 Y152 412 taT/taC LOW 2 SILENT CODING RAPSN G protein_coding NM_005055.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47469439 A G 0 228 0 0.3472 0.6256 0.6902 0.6587 0.7068 0.8384 0.426851 0.620114 0.719106 2 4246 80478 6754 5436 3721 46917 628 12776 2 9938 117542 11076 8428 6042 64860 866 16332 1 3 likely-benign 0 . 57 1,0,36,16 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y152|412|RAPSN|protein_coding|CODING|NM_005055.4|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7111873 -0.693147 0.104936 57 512 6042 MODIFIER 16 CODING CELF1 A protein_coding NM_001172639.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47487740 G A 0 9.7 0 0.3215 0.6761 0.7752 0.7054 0.8519 0.8742 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6042||512|CELF1|protein_coding|CODING|NM_001172639.1|16|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044269 -0.379885 0 1 201 113 MODIFIER 1 CODING PTPMT1 A protein_coding NM_175732.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47587062 G A 0 9.7 0 0.3661 0.6887 0.7795 0.7073 0.8519 0.8732 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||113||201|PTPMT1|protein_coding|CODING|NM_175732.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11039300 -0.379885 0 1 201 764 MODIFIER 4 CODING PTPMT1 C protein_coding NM_175732.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47593945 A C 0 228 0 0.9493 0.9846 0.9914 1 0.996 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 206 0,0,109,74 UTR_3_PRIME(MODIFIER||764||201|PTPMT1|protein_coding|CODING|NM_175732.2|4|C),UTR_3_PRIME(MODIFIER||537||534|KBTBD4|protein_coding|CODING|NM_018095.4|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6416137 -0.693147 0.63259 206 534 537 MODIFIER 4 CODING KBTBD4 C protein_coding NM_018095.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47593945 A C 0 228 0 0.9493 0.9846 0.9914 1 0.996 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 206 0,0,109,74 UTR_3_PRIME(MODIFIER||764||201|PTPMT1|protein_coding|CODING|NM_175732.2|4|C),UTR_3_PRIME(MODIFIER||537||534|KBTBD4|protein_coding|CODING|NM_018095.4|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6416137 -0.693147 0.63259 206 A145T 183 Gcc/Acc MODERATE 3 MISSENSE CODING FAM180B A protein_coding NM_001164379.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47609867 G A 0 228 0 0.9501 0.9848 0.9914 1 0.996 1 0.953035 0.982917 0.995915 2 1717 19315 303 334 1605 7299 221 7836 2 1806 19478 306 334 1608 7336 222 7866 0 . 0 . 0 156 0,0,55,90 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A145T|183|FAM180B|protein_coding|CODING|NM_001164379.1|3|A),DOWNSTREAM(MODIFIER||3752||264|NDUFS3|protein_coding|CODING|NM_004551.2||A),DOWNSTREAM(MODIFIER||1349||329|C1QTNF4|protein_coding|CODING|NM_031909.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4486587 -0.693147 0.0299675 156 329 57 MODIFIER 2 CODING C1QTNF4 G protein_coding NM_031909.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47611316 C G 0 225 0 0.9501 0.9856 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,39,2 UTR_3_PRIME(MODIFIER||57||329|C1QTNF4|protein_coding|CODING|NM_031909.2|2|G),DOWNSTREAM(MODIFIER||570||183|FAM180B|protein_coding|CODING|NM_001164379.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10769279 -0.693145 0.039893 41 D598 1436 gaC/gaT LOW 15 SILENT CODING NUP160 A protein_coding NM_015231.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47834592 G A 0 228 0 0.9766 0.9936 0.9986 1 1 1 0.984098 0.994615 1 2 10161 121107 11564 8652 6612 66704 908 16506 2 10326 121276 11568 8652 6612 66704 908 16506 0 . 0 . 0 81 0,0,26,46 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D598|1436|NUP160|protein_coding|CODING|NM_015231.1|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7110289 -0.693147 0.208273 81 T351A 1436 Acc/Gcc MODERATE 7 MISSENSE CODING NUP160 C protein_coding NM_015231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47857253 T C 0 228 0 0.0847 0.3458 0.3242 0.4355 0.4344 0.5307 0.158337 0.357132 0.458934 2 1614 49837 2840 3337 2289 30572 359 8826 2 10312 119682 11364 8552 6390 66210 892 15962 1 0 . 0 . 90 1,0,51,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T351A|1436|NUP160|protein_coding|CODING|NM_015231.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3816605 -0.693147 0.0506428 90 A40T 1436 Gcc/Acc MODERATE 1 MISSENSE CODING NUP160 T protein_coding NM_015231.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 47869855 C T 0 222 0 0 0.0489 0 0.2341 0 0.0092 0 . 0 1 21 1843 5 1727 1 12 5 72 2 9444 117534 11468 8532 6424 64298 872 16496 0.982397 0 . 0 . 78 13,29,13,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A40T|1436|NUP160|protein_coding|CODING|NM_015231.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.39703 rs2305984 -0.693097 0.262484 78 Q276P 1337 cAa/cCa MODERATE 5 MISSENSE CODING PTPRJ C protein_coding NM_002843.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48145375 A C 0 228 0 0.1051 0.1899 0.1239 0.3185 0.161 0.2485 0.119945 0.147484 0.161587 2 1253 20511 1068 2292 652 10717 158 4371 2 10340 121116 11550 8632 6614 66578 908 16494 0.116667 5 pathogenic 0 COSM1127775,COSM1127776 69 1,1,23,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cCa|Q276P|1337|PTPRJ|protein_coding|CODING|NM_002843.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.366667 rs1566734 -0.693147 0.142568 69 R326Q 1337 cGa/cAa MODERATE 6 MISSENSE CODING PTPRJ A protein_coding NM_002843.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48146622 G A 0 228 0 0.3056 0.2428 0.1297 0.3165 0.162 0.2454 0.252385 0.192183 0.161354 2 2614 21917 1149 2283 652 10691 167 4361 2 10392 121294 11572 8628 6614 66672 906 16510 0.906521 0 . 0 . 77 3,0,46,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R326Q|1337|PTPRJ|protein_coding|CODING|NM_002843.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.580294 rs1503185,rs386534741 -0.693147 0.43745 77 1337 1613 MODIFIER 25 CODING PTPRJ C protein_coding NM_002843.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48190527 T C 0 9.7 0 0.9213 0.9786 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1613||1337|PTPRJ|protein_coding|CODING|NM_002843.3|25|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2174127 -0.379885 0 1 1337 2761 MODIFIER 25 CODING PTPRJ G protein_coding NM_002843.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48191675 A G 0 9.7 0 0.9213 0.9784 0.9957 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2761||1337|PTPRJ|protein_coding|CODING|NM_002843.3|25|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4752912 -0.379885 0 1 A20 309 gcT/gcG LOW 1 SILENT CODING OR4B1 G protein_coding NM_001005470.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48238421 T G 0 228 0 0.9191 0.9778 0.9942 1 1 1 0.931849 0.976612 0.999535 2 9717 120640 11509 8654 6614 66731 905 16510 2 10406 121380 11550 8654 6614 66736 908 16512 0 . 0 . 0 117 0,0,76,29 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A20|309|OR4B1|protein_coding|CODING|NM_001005470.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10769329 -0.693147 0.024208 117 C63Y 309 tGc/tAc MODERATE 1 MISSENSE CODING OR4B1 A protein_coding NM_001005470.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48238549 G A 0 228 0 0.171 0.2742 0.1916 0.3869 0.174 0.4591 0.174693 0.176258 0.177059 2 1828 26776 1698 3035 893 11992 194 7136 2 10406 121354 11552 8632 6614 66734 908 16508 1 0 . 0 . 127 1,0,57,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C63Y|309|OR4B1|protein_coding|CODING|NM_001005470.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11606506 -0.693147 0.00241264 127 T274K 309 aCg/aAg MODERATE 1 MISSENSE CODING OR4B1 A protein_coding NM_001005470.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48239182 C A 0 228 0 0.1293 0.2622 0.1844 0.3869 0.174 0.4591 0.140845 0.160025 0.169846 2 1496 26411 1675 3036 893 11981 193 7137 2 10404 121310 11532 8630 6612 66714 908 16510 0.778462 0 . 0 . 125 2,2,56,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T274K|309|OR4B1|protein_coding|CODING|NM_001005470.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.217331 rs7130086 -0.693147 0.110216 125 R144G 305 Agg/Ggg MODERATE 1 MISSENSE CODING OR4X1 G protein_coding NM_001004726.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48285842 A G 0 228 0 0.9584 0.9886 0.9971 1 1 1 0.967288 0.988768 0.999767 2 10055 120990 11554 8620 6614 66728 907 16512 2 10406 121356 11568 8620 6614 66728 908 16512 0 . 0 . 0 78 0,0,27,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R144G|305|OR4X1|protein_coding|CODING|NM_001004726.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1503193 -0.693147 0.774059 78 N290 309 aaC/aaT LOW 1 SILENT CODING OR4S1 T protein_coding NM_001004725.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48328644 C T 0 228 0 0.5113 0.4313 0.2911 0.4544 0.3042 0.5297 0.48796 0.362748 0.298627 2 5213 40969 2448 3545 1487 19684 284 8308 2 10388 121198 11556 8626 6610 66604 908 16506 0 . 0 . 0 172 0,0,56,98 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N290|309|OR4S1|protein_coding|CODING|NM_001004725.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs753095 -0.693147 0.163732 172 N216 329 aaT/aaC LOW 1 SILENT CODING OR4C3 C protein_coding NM_001004702.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48347140 T C 0 228 0 0.4539 0.3972 0.2594 0.4583 0.2555 0.501 0.442072 0.313279 0.247324 2 6233 66695 5979 5078 3426 35340 488 10151 2 10406 121288 11556 8636 6612 66670 906 16502 0.534375 0 . 0 . 178 2,0,118,42 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N216|329|OR4C3|protein_coding|CODING|NM_001004702.1|1|C) 1 0 . 0 . 1 0 1 1 0 59 0 0.98125 0.971428 0 0.496875 rs10838874 -0.693147 0.0111643 178 F249C 305 tTt/tGt MODERATE 2 MISSENSE CODING OR4C45 C protein_coding NM_001005513.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48367073 A C 0 228 0 0.677 0.7955 0.8473 0.8353 0.8241 0.8487 0 . 0 2 1775 19046 351 563 1394 8102 219 6642 2 2356 22842 424 640 1694 9564 250 7914 0 . 0 . 0 175 0,0,96,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F249C|305|OR4C45|protein_coding|CODING|NM_001005513.1|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.937938 0 . rs7941588 -0.693147 0.00067575 175 L18 305 ctG/ctT LOW 1 SILENT CODING OR4C45 A protein_coding NM_001005513.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 48373946 C A 0 228 0 0.1256 0.27 0.2378 0.3978 0.174 0.455 0 . 0 2 271 4916 80 213 206 1552 58 2536 2 2136 21636 406 620 1624 8738 242 7870 0 . 0 . 0 71 0,0,11,55 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L18|305|OR4C45|protein_coding|CODING|NM_001005513.1|1|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12797020 -0.693147 0.351857 71 P187 452 ccT/ccC LOW 3 SILENT CODING TRIM49B C protein_coding NM_001206626.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49055751 T C 0 222 0 0.3631 0.488 0.6167 0.4415 0.6889 0.407 0 . 0 1 4212 72996 7770 4015 4194 45345 562 6898 2 9552 119998 11578 8650 6612 66196 900 16510 0.846734 0 . 0 . 1063 306,195,249,180 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P187|452|TRIM49B|protein_coding|CODING|NM_001206626.1|3|C) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.134673 2.29235e-07 0 0.892241 rs2727042 -0.693147 0.296033 1063 L398M 452 Ctg/Atg MODERATE 6 MISSENSE CODING TRIM49B A protein_coding NM_001206626.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49059362 C A 0 222 0 0.882 0.723 0.7579 0.6022 0.8221 0.5061 0 . 0 1 8934 93228 9289 5443 5608 54272 697 8985 2 10366 121300 11568 8644 6612 66690 908 16512 0.598157 0 . 0 . 471 138,82,106,90 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L398M|452|TRIM49B|protein_coding|CODING|NM_001206626.1|6|A) 0 0.5 1 0 . 1 0 . 1 0 54 0 2.17959e-07 2.36989e-05 0 0.440023 rs2696914 -0.693147 0.000581001 471 S338 450 tcC/tcT LOW 6 SILENT CODING TRIM64C A protein_coding NM_001206631.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49075605 G A 0 222 0 0.8495 0.7147 0.7565 0.6032 0.8231 0.5061 0 . 0 1 1821 15730 314 343 1388 7239 182 4443 2 2146 22002 410 622 1640 9020 250 7914 0.949722 0 . 0 . 181 52,36,56,26 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S338|450|TRIM64C|protein_coding|CODING|NM_001206631.1|6|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0174436 rs2851535 -0.693147 0.0660489 181 I17V 450 Att/Gtt MODERATE 1 MISSENSE CODING TRIM64C C protein_coding NM_001206631.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49080616 T C 0 222 0 0.087 0.3299 0.5115 0.3651 0.498 0.32 0 . 0 1 447 11233 416 400 885 6246 137 2702 2 2506 25768 738 958 1764 11544 272 7986 0.628315 0 . 0 . 166 18,56,14,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I17V|450|TRIM64C|protein_coding|CODING|NM_001206631.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.982488 rs60452246 -0.693147 0.000643404 166 V133I 309 Gtc/Atc MODERATE 1 MISSENSE CODING OR4C13 A protein_coding NM_001001955.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49974371 G A 0 228 0 0.9902 0.9974 1 1 1 1 0.992503 0.997306 0.999767 2 10333 121304 11556 8652 6614 66730 908 16511 2 10406 121386 11564 8652 6614 66730 908 16512 0 . 0 . 0 340 0,0,148,166 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V133I|309|OR4C13|protein_coding|CODING|NM_001001955.2|1|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.995763 0 . rs28662375 -0.693147 0.164216 340 309 27 MODIFIER 1 CODING OR4C13 A protein_coding NM_001001955.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 49974931 G A 0 222 0 0.9123 0.9034 0.9207 0.9147 0.8439 0.9284 0 . 0 1 4583 53578 4693 3448 3667 31949 447 4791 2 5168 62198 5094 3854 4156 38190 516 5220 0.888623 0 . 0 . 145 8,65,13,54 UTR_3_PRIME(MODIFIER||27||309|OR4C13|protein_coding|CODING|NM_001001955.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.00578947 0.999655 0 0.966585 rs12791255 -0.693147 0.000134141 145 V283L 309 Gtg/Ttg MODERATE 1 MISSENSE CODING OR4C12 A protein_coding NM_001005270.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 50003191 C A 0 222 0 0.2912 0.4922 0.634 0.5565 0.5924 0.4939 0.348478 0.515853 0.601606 1 3518 70322 7865 4567 3959 40851 581 8981 2 10340 121146 11514 8634 6598 66652 906 16502 0.985125 0 . 0 . 77 21,12,18,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V283L|309|OR4C12|protein_coding|CODING|NM_001005270.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.977861 0.968179 0 0.820827 rs4598671 -0.693127 0.225452 77 S312 315 tcC/tcT LOW 1 SILENT CODING OR4A5 A protein_coding NM_001005272.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51411460 G A 0 222 0 0.0938 0.0931 0.0706 0.0863 0.1262 0.0808 0.0884651 0.109409 0.120042 1 823 9963 489 599 583 6632 85 752 2 5546 54426 4612 4012 3686 31440 454 4676 0.925333 0 . 0 . 88 30,19,21,9 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S312|315|OR4A5|protein_coding|CODING|NM_001005272.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.627935 rs34285763 -0.693097 0.777807 88 L219Q 315 cTa/cAa MODERATE 1 MISSENSE CODING OR4A5 T protein_coding NM_001005272.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51411740 A T 0 222 0 0.056 0.0811 0.0591 0.0863 0.1252 0.0798 0.0545207 0.0985222 0.121071 1 584 11917 511 719 646 8138 89 1230 2 10288 120652 11434 8482 6596 66442 904 16506 0.989475 0 . 0 . 101 32,25,21,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cAa|L219Q|315|OR4A5|protein_coding|CODING|NM_001005272.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928858 rs35083184 -0.693144 0.956007 101 K23N 315 aaA/aaT MODERATE 1 MISSENSE CODING OR4A5 A protein_coding NM_001005272.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51412327 T A 0 222 0 0.0401 0.0761 0.0591 0.0853 0.1223 0.0798 0.0484091 0.0953664 0.119413 1 504 11690 464 683 646 8084 85 1224 2 10140 119896 11346 8434 6568 66080 902 16426 0.613638 0 . 0 . 106 27,18,24,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K23N|315|OR4A5|protein_coding|CODING|NM_001005272.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.553587 rs56302591 -0.693147 0.196931 106 S240F 309 tCc/tTc MODERATE 1 MISSENSE CODING OR4C46 T protein_coding NM_001004703.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51516000 C T 0 222 0 0.202 0.4333 0.5893 0.5427 0.5467 0.4059 0.261018 0.449207 0.545624 1 2637 62881 7577 4452 3539 36781 512 7383 2 10404 121326 11572 8610 6610 66716 908 16506 0.999079 0 . 0 . 235 48,64,43,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S240F|309|OR4C46|protein_coding|CODING|NM_001004703.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.999908 0.934636 0 0.0441809 rs11246607 -0.693147 0.0635619 235 C252Y 309 tGc/tAc MODERATE 1 MISSENSE CODING OR4C46 A protein_coding NM_001004703.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51516036 G A 0 222 0 0.2171 0.4375 0.5908 0.5427 0.5467 0.4059 0.275102 0.453979 0.545624 1 2803 63060 7585 4453 3539 36783 513 7384 2 10406 121332 11574 8612 6608 66718 908 16506 0.670955 0 . 0 . 217 47,63,27,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C252Y|309|OR4C46|protein_coding|CODING|NM_001004703.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.977382 0.153322 0 0.885465 rs11246608 -0.693147 0.377489 217 K288R 309 aAg/aGg MODERATE 1 MISSENSE CODING OR4C46 G protein_coding NM_001004703.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 51516144 A G 0 222 0 0.5333 0.6981 0.8012 0.7698 0.7028 0.7689 0 . 0 1 5101 78700 9023 6024 4196 43821 611 9924 2 9422 111950 11080 8082 6492 62462 836 13576 0.994296 0 . 0 . 107 26,33,19,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K288R|309|OR4C46|protein_coding|CODING|NM_001004703.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.35986 0.152455 0 0.813888 rs11246609 -0.693145 0.565154 107 R15Q 224 cGa/cAa MODERATE 1 MISSENSE CODING TRIM48 A protein_coding NM_024114.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55029787 G A 0 222 0 0.1505 0.099 0.049 0.0853 0.1113 0.0665 0.148121 0.120018 0.107794 1 342 1983 27 68 114 872 12 548 2 2108 21588 410 622 1624 8668 242 7914 0.933276 0 . 0 COSM147198 842 136,268,103,244 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGa/cAa|R15Q|224|TRIM48|protein_coding|CODING|NM_024114.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.510119 3.43012e-13 0 0.548379 rs12799381 -0.693147 0.000975744 842 224 1114 MODIFIER 6 CODING TRIM48 G protein_coding NM_024114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55037928 A G 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.932649 0 . 0 . 528 202,29,229,31 UTR_3_PRIME(MODIFIER||1114||224|TRIM48|protein_coding|CODING|NM_024114.3|6|G) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.957586 0.993232 0 0.155597 rs187754982 -0.693147 0.000262204 528 224 1561 MODIFIER 6 CODING TRIM48 C protein_coding NM_024114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55038375 T C 0 222 0 0.3283 0.5819 0.7104 0.7054 0.6143 0.6728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957005 0 . 0 . 1123 220,264,217,311 UTR_3_PRIME(MODIFIER||1561||224|TRIM48|protein_coding|CODING|NM_024114.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.998644 0.998054 0 0.783384 rs3213870 -0.693147 0.0104448 1123 224 1760 MODIFIER 6 CODING TRIM48 C protein_coding NM_024114.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55038574 T C 0 222 0 0.0477 0.0759 0.0447 0.0913 0.1163 0.0787 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.521756 0 . 0 . 288 18,119,25,106 UTR_3_PRIME(MODIFIER||1760||224|TRIM48|protein_coding|CODING|NM_024114.3|6|C) 0 0.5 1 0 . 1 0 . 0 . 59 0 0.994682 0.998935 0 0.246502 rs35264107 -0.693147 0.000674577 288 L188I 328 Ctt/Att MODERATE 1 MISSENSE CODING OR4A16 A protein_coding NM_001005274.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55111238 C A 0 222 0 0.1853 0.4145 0.5548 0.5387 0.494 0.4151 0.231259 0.400108 0.486615 1 2355 58469 7216 4486 3509 33007 484 7412 2 10396 121276 11538 8612 6606 66704 908 16512 0.516633 0 . 0 . 108 28,30,16,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L188I|328|OR4A16|protein_coding|CODING|NM_001005274.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.876615 rs11229158 -0.693145 0.183458 108 K303M 328 aAg/aTg MODERATE 1 MISSENSE CODING OR4A16 T protein_coding NM_001005274.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55111584 A T 0 222 0 0.1853 0.4125 0.5504 0.5387 0.494 0.408 0.231031 0.3994 0.485681 1 2326 57612 7113 4358 3460 32609 471 7275 2 9974 119306 11386 8342 6552 65784 894 16374 0.991484 0 . 0 . 78 16,25,9,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aTg|K303M|328|OR4A16|protein_coding|CODING|NM_001005274.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945278 rs10896659 -0.69311 0.311687 78 P26S 344 Cct/Tct MODERATE 1 MISSENSE CODING OR4A15 T protein_coding NM_001005275.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55135435 C T 0 222 0 0.0159 0.2274 0.3141 0.3869 0.2823 0.2311 0.0624716 0.196706 0.26548 1 560 32875 4839 3211 2159 17824 277 4005 2 10388 120536 11388 8426 6576 66376 898 16484 0.98939 0 . 0 . 156 39,37,32,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P26S|344|OR4A15|protein_coding|CODING|NM_001005275.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955961 rs1425193 -0.693147 0.291968 156 K143 370 aaA/aaG LOW 1 SILENT CODING OR4C15 G protein_coding NM_001001920.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55322211 A G 0 222 0 0.1014 0.2526 0.3242 0.3919 0.2833 0.2311 0.127442 0.219255 0.266294 1 1299 33877 4926 3288 2170 17915 283 3996 2 10406 121302 11532 8630 6610 66704 908 16512 0.262012 0 . 0 . 75 10,29,8,26 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K143|370|OR4C15|protein_coding|CODING|NM_001001920.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.885957 rs9804659 -0.693132 0.176198 75 Q17* 310 Cag/Tag HIGH 1 NONSENSE CODING OR4C16 T protein_coding NM_001004701.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55339652 C T 0 222 0 0.1014 0.2526 0.3242 0.3909 0.2843 0.2311 0.127442 0.219409 0.266527 1 1294 33806 4929 3274 2169 17882 284 3974 2 10390 120544 11558 8646 6610 66414 898 16028 0.930953 0 . 0 . 92 36,12,25,13 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q17*|310|OR4C16|protein_coding|CODING|NM_001004701.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969756 rs1459101 -0.693143 0.0083024 92 S65 310 tcC/tcT LOW 1 SILENT CODING OR4C16 T protein_coding NM_001004701.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55339798 C T 0 222 0 0.1188 0.2572 0.3242 0.3909 0.2843 0.2311 0.141072 0.22395 0.266411 1 1463 34047 4948 3275 2171 17918 285 3987 2 10406 121384 11572 8652 6614 66724 908 16508 0.505593 0 . 0 . 161 26,52,29,38 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S65|310|OR4C16|protein_coding|CODING|NM_001004701.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991728 rs557667 -0.693147 0.0862891 161 T76A 310 Acc/Gcc MODERATE 1 MISSENSE CODING OR4C16 G protein_coding NM_001004701.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55339829 A G 0 228 0 0.7171 0.8914 0.9294 1 0.8917 0.9877 0.738982 0.836771 0.886872 2 7638 109488 10966 8648 6013 59244 836 16143 2 10406 121400 11576 8654 6614 66732 908 16510 0 . 0 . 0 131 0,0,43,82 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T76A|310|OR4C16|protein_coding|CODING|NM_001004701.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs557590 -0.693147 0.0297234 131 L259P 310 cTt/cCt MODERATE 1 MISSENSE CODING OR4C16 C protein_coding NM_001004701.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55340379 T C 0 222 0 0.3275 0.4788 0.5951 0.5446 0.5547 0.455 0.348932 0.48153 0.549465 1 3637 65166 7568 4486 3893 37044 525 8013 2 10404 121244 11560 8632 6610 66684 908 16446 0.909316 0 . 0 . 185 28,54,27,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L259P|310|OR4C16|protein_coding|CODING|NM_001004701.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.727438 rs559449 -0.693147 0.0684171 185 I133T 309 aTc/aCc MODERATE 1 MISSENSE CODING OR4C6 C protein_coding NM_001004704.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55433040 T C 0 222 0 0.1029 0.253 0.3242 0.3909 0.2843 0.2311 0.128864 0.219982 0.266643 1 1302 33857 4931 3276 2170 17909 284 3985 2 10392 121274 11510 8630 6608 66714 908 16512 0.718364 0 . 0 . 95 42,11,19,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I133T|309|OR4C6|protein_coding|CODING|NM_001004704.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.608932 rs11230600 -0.693132 0.628653 95 C62Y 314 tGc/tAc MODERATE 1 MISSENSE CODING OR5D13 A protein_coding NM_001001967.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55541098 G A 0 228 0 0.8971 0.9712 0.9899 1 0.999 1 0.916591 0.97129 0.999302 2 9487 120314 11468 8646 6612 66696 902 16503 2 10400 121308 11514 8646 6612 66720 908 16508 0 . 0 . 0 116 0,0,68,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C62Y|314|OR5D13|protein_coding|CODING|NM_001001967.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs297118 -0.693147 0.378249 116 G191S 314 Ggc/Agc MODERATE 1 MISSENSE CODING OR5D14 A protein_coding NM_001004735.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55563602 G A 0 222 0 0.1884 0.1048 0.0461 0.0813 0.0924 0.0706 0.152273 0.107528 0.0846136 1 1687 9857 374 678 412 5610 72 1024 2 10398 121370 11560 8648 6614 66732 908 16510 0.977308 0 . 0 COSM147202 235 57,47,61,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G191S|314|OR5D14|protein_coding|CODING|NM_001004735.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.346553 rs68042892 -0.693147 0.34419 235 R236H 314 cGc/cAc MODERATE 1 MISSENSE CODING OR5D14 A protein_coding NM_001004735.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55563738 G A 0 222 0 0.1301 0.0893 0.0432 0.0823 0.0924 0.0706 0.119545 0.0960591 0.0840317 1 1316 9451 348 681 412 5600 71 1023 2 10398 121312 11534 8652 6614 66702 908 16504 0.739562 0 . 0 COSM147203 206 44,42,47,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R236H|314|OR5D14|protein_coding|CODING|NM_001004735.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988005 rs67863827 -0.693147 0.225038 206 S249A 314 Tct/Gct MODERATE 1 MISSENSE CODING OR5D14 G protein_coding NM_001004735.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55563776 T G 0 228 0 0.8956 0.9706 0.9885 1 1 0.999 0.916364 0.971213 0.999302 2 9494 120370 11500 8654 6614 66699 902 16507 2 10400 121356 11546 8654 6614 66722 908 16512 1 0 . 0 . 170 0,1,65,85 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S249A|314|OR5D14|protein_coding|CODING|NM_001004735.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs297054 -0.693147 0.0250207 170 L15 311 ctT/ctC LOW 1 SILENT CODING OR5L1 C protein_coding NM_001004738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55578987 T C 0 222 0 0.1884 0.1048 0.0461 0.0813 0.0924 0.0706 0.152273 0.107346 0.0843233 1 1670 9788 374 675 411 5581 71 1006 2 10394 120896 11562 8646 6614 66504 902 16274 0.999998 0 . 0 COSM147205 153 66,11,60,2 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L15|311|OR5L1|protein_coding|CODING|NM_001004738.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.899711 0.931696 0 0.945514 rs67727364 -0.693147 0.166375 153 L17 311 Cta/Tta LOW 1 SILENT CODING OR5L1 T protein_coding NM_001004738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55578991 C T 0 222 0 0.1884 0.1048 0.0461 0.0813 0.0924 0.0706 0.152273 0.107346 0.0843233 1 1670 9792 374 676 411 5584 71 1006 2 10392 121002 11562 8646 6614 66544 902 16342 0.971561 0 . 0 COSM147206 155 68,11,61,2 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L17|311|OR5L1|protein_coding|CODING|NM_001004738.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.903858 0.934584 0 0.617824 rs61732387,rs66537410 -0.693147 0.252893 155 R54W 311 Cgg/Tgg MODERATE 1 MISSENSE CODING OR5L1 T protein_coding NM_001004738.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55579102 C T 0 222 0 0.1309 0.0895 0.0432 0.0813 0.0924 0.0716 0.117727 0.0949815 0.0833333 1 1280 9299 356 672 406 5523 70 992 2 10398 121358 11574 8650 6614 66712 908 16502 0.420774 0 . 0 . 274 88,49,66,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R54W|311|OR5L1|protein_coding|CODING|NM_001004738.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.680263 0.749929 0 0.469732 rs34961497 -0.693147 0.00102284 274 H159 311 caT/caC LOW 1 SILENT CODING OR5L1 C protein_coding NM_001004738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55579419 T C 0 222 0 0.1884 0.1048 0.0461 0.0813 0.0924 0.0706 0.152273 0.107374 0.0843808 1 1688 9863 375 680 412 5612 72 1024 2 10400 121392 11578 8648 6614 66732 908 16512 0.775738 0 . 0 COSM147207 240 59,47,40,69 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H159|311|OR5L1|protein_coding|CODING|NM_001004738.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940309 rs34948392 -0.693147 0.37321 240 S287P 311 Tct/Cct MODERATE 1 MISSENSE CODING OR5L1 C protein_coding NM_001004738.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55579801 T C 0 222 0 0.1884 0.1048 0.0461 0.0813 0.0924 0.0706 0.152045 0.107374 0.0844972 1 1685 9851 375 679 412 5606 72 1022 2 10290 120732 11488 8640 6614 66418 904 16378 0.97734 0 . 0 COSM147208 151 25,39,17,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S287P|311|OR5L1|protein_coding|CODING|NM_001004738.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.794037 rs12790505 -0.693147 0.00187395 151 T4 313 acT/acA LOW 1 SILENT CODING OR5D18 A protein_coding NM_001001952.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55587117 T A 0 228 0 0.9871 0.9966 1 1 1 1 0.989773 0.996536 1 2 10257 119473 11569 8652 6614 66137 889 15355 2 10382 119606 11574 8652 6614 66138 890 15356 0 . 0 . 0 43 0,0,39,3 SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T4|313|OR5D18|protein_coding|CODING|NM_001001952.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs297082 -0.693146 0.0353664 43 N136D 313 Aac/Gac MODERATE 1 MISSENSE CODING OR5D18 G protein_coding NM_001001952.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55587511 A G 0 228 0 0.9871 0.9966 1 1 1 1 0.989773 0.996536 1 2 10275 121271 11573 8654 6614 66737 907 16511 2 10400 121404 11578 8654 6614 66738 908 16512 0 . 0 . 0 184 0,0,99,69 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N136D|313|OR5D18|protein_coding|CODING|NM_001001952.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs297081 -0.693147 0.393305 184 H270R 313 cAc/cGc MODERATE 1 MISSENSE CODING OR5D18 G protein_coding NM_001001952.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55587914 A G 0 222 0 0.0204 0.233 0.3228 0.3889 0.2903 0.2372 0.0654545 0.204434 0.275605 1 598 34094 4967 3312 2174 18605 289 4149 2 10398 121320 11556 8628 6612 66708 908 16510 0.897835 0 . 0 . 172 23,55,31,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H270R|313|OR5D18|protein_coding|CODING|NM_001001952.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.180567 rs55832853 -0.693147 0.0492915 172 V59M 311 Gtg/Atg MODERATE 1 MISSENSE CODING OR5L2 A protein_coding NM_001004739.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55594869 G A 0 222 0 0.1952 0.1072 0.0461 0.0843 0.0924 0.0706 0.149545 0.10468 0.0817039 1 1711 9926 376 710 413 5619 72 1025 2 10400 121384 11566 8652 6614 66732 908 16512 0.156374 0 . 0 COSM147210 221 59,39,48,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V59M|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.311363 0.780874 0 0.99622 rs56711116 -0.693147 0.034213 221 T106 311 acA/acT LOW 1 SILENT CODING OR5L2 T protein_coding NM_001004739.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595012 A T 0 69 0 . 0 . 0 . 0 . 0 . 1 216 891 24 68 7 523 8 45 2 10178 120004 11494 8574 6566 66010 900 16282 0.548127 0 . 0 . 151 61,48,18,7 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T106|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.646618 0.974251 0 0.22482 rs35645945 -0.692914 0.97601 151 G108V 311 gGa/gTa MODERATE 1 MISSENSE CODING OR5L2 T protein_coding NM_001004739.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595017 G T 0 55 0 0.0938 0.0683 0.036 0.0704 0.0736 0.0491 0 . 0 1 206 845 26 66 16 476 9 46 2 10006 118444 11456 8480 6468 64960 890 16184 0.919978 0 . 0 COSM147211 148 60,52,14,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G108V|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.601042 0.883969 0 0.0184449 rs117277709 -0.692562 0.0058481 148 G108 311 ggA/ggG LOW 1 SILENT CODING OR5L2 G protein_coding NM_001004739.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595018 A G 0 57 0 0.0938 0.0683 0.036 0.0704 0.0736 0.0491 0 . 0 1 206 850 25 66 18 480 9 46 2 9670 115718 11324 8224 6338 63362 854 15946 0.686678 0 . 0 COSM147212 145 59,51,14,8 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G108|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.601987 0.881977 0 0.0473518 rs61745634 -0.692562 0.0058481 145 L140 311 ctG/ctT LOW 1 SILENT CODING OR5L2 T protein_coding NM_001004739.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595114 G T 0 222 0 0.1309 0.0897 0.0403 0.0853 0.0924 0.0706 0 . 0 1 1315 9417 344 707 411 5548 71 1021 2 10400 121346 11554 8654 6614 66704 908 16512 0.963765 0 . 0 . 136 37,39,23,29 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L140|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.123572 rs34929168 -0.693147 0.0621891 136 R141C 311 Cgt/Tgt MODERATE 1 MISSENSE CODING OR5L2 T protein_coding NM_001004739.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595115 C T 0 222 0 0.1309 0.0897 0.0403 0.0853 0.0924 0.0706 0 . 0 1 1315 9422 344 707 410 5551 71 1024 2 10400 121334 11552 8654 6614 66696 908 16510 0.998445 0 . 0 COSM147213 137 38,38,23,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R141C|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.20052 rs71490506 -0.693147 0.0621891 137 R141P 311 cGt/cCt MODERATE 1 MISSENSE CODING OR5L2 C protein_coding NM_001004739.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55595116 G C 0 222 0 0.1293 0.0891 0.0403 0.0843 0.0924 0.0706 0 . 0 1 1315 9416 344 705 409 5551 71 1021 2 10400 121342 11550 8652 6612 66708 908 16512 0.998547 0 . 0 . 136 37,38,23,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R141P|311|OR5L2|protein_coding|CODING|NM_001004739.1|1|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.358865 rs75822385 -0.693147 0.0621891 136 L25 328 ctG/ctT LOW 1 SILENT CODING OR5D16 T protein_coding NM_001005496.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55606302 G T 0 222 0 0.6112 0.6731 0.683 0.7718 0.6163 0.7065 0.633348 0.62929 0.627211 1 6482 79667 8544 6791 4241 41574 572 11463 2 10404 121308 11536 8640 6610 66700 906 16512 0.990681 0 . 0 . 126 36,18,39,19 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L25|328|OR5D16|protein_coding|CODING|NM_001005496.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.443485 rs6591699 -0.693147 0.0636444 126 S197 328 agC/agT LOW 1 SILENT CODING OR5D16 T protein_coding NM_001005496.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55606818 C T 0 222 0 0.2746 0.4531 0.4957 0.626 0.3638 0.5777 0.304861 0.347545 0.369413 1 3115 51455 6529 5426 2327 24672 382 9004 2 10398 121274 11522 8646 6612 66680 906 16510 0.936632 0 . 0 COSM1179679 167 43,38,37,36 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S197|328|OR5D16|protein_coding|CODING|NM_001005496.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.827625 rs11231253 -0.693147 0.266109 167 N20S 452 aAc/aGc MODERATE 2 MISSENSE CODING TRIM51 G protein_coding NM_032681.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55652963 A G 0 222 0 0.6452 0.6817 0.683 0.7649 0.6153 0.7127 0.648121 0.629181 0.620886 1 6314 78963 8540 6705 4240 41088 564 11512 2 9672 119804 11520 8648 6602 65956 896 16510 0.916519 0 . 0 . 796 238,171,180,129 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N20S|452|TRIM51|protein_coding|CODING|NM_032681.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.857389 0.881456 0 0.718406 rs2063276 -0.693147 0.101516 796 L23I 452 Cta/Ata MODERATE 2 MISSENSE CODING TRIM51 A protein_coding NM_032681.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55652971 C A 0 228 0 0.9274 0.979 0.9914 1 0.999 0.998 0 . 0 2 9241 117647 11366 8648 6503 64664 889 16336 2 9768 119226 11468 8650 6566 65470 900 16404 1 0 . 0 . 752 0,1,386,301 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L23I|452|TRIM51|protein_coding|CODING|NM_032681.3|2|A) 0 . 0 . 0 1 0 . 1 0 58 0 1 0.551147 0 1 rs2063277 -0.693147 0.0269938 752 S87N 452 aGc/aAc MODERATE 2 MISSENSE CODING TRIM51 A protein_coding NM_032681.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55653164 G A 0 222 0 0.1672 0.4243 0.4928 0.621 0.3628 0.5838 0.200867 0.30894 0.355975 1 1951 48426 6204 5152 2272 23471 372 9004 2 9136 115268 11050 8274 6456 63066 882 16404 0.86921 0 . 0 . 459 138,111,107,73 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S87N|452|TRIM51|protein_coding|CODING|NM_032681.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.994089 0.91882 0 0.981933 rs10897403 -0.693147 0.557389 459 452 LOW 5 CODING TRIM51 A protein_coding NM_032681.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55656483 T A 0 222 0 0.6982 0.8297 0.9078 0.9087 0.8151 0.8855 0.740118 0.803063 0.835312 1 7318 96899 10422 7598 5324 53113 708 12416 2 10228 119624 11398 8542 6572 65938 894 16052 0.878017 0 . 0 . 223 61,64,45,37 SPLICE_SITE_REGION+INTRON(LOW||||452|TRIM51|protein_coding|CODING|NM_032681.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.886399 rs7483200 -0.693147 0.0062559 223 452 39 MODIFIER 7 CODING TRIM51 T protein_coding NM_032681.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55659147 A T 0 222 0 0.1278 0.0907 0.0403 0.0903 0.0944 0.0726 0.105325 0.0873157 0.077882 1 1123 9195 346 757 412 5449 74 1034 2 9228 117870 11486 8478 6588 64852 896 16342 0.731455 0 . 0 . 359 36,135,33,135 UTR_3_PRIME(MODIFIER||39||452|TRIM51|protein_coding|CODING|NM_032681.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.864944 0.466659 0 0.999569 rs35149540 -0.693147 0.0656026 359 F310Y 310 tTt/tAt MODERATE 1 MISSENSE CODING OR5W2 T protein_coding NM_001001960.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55681130 A T 0 222 0 0.1278 0.0907 0.0403 0.0903 0.0944 0.0726 0.0970546 0.0812738 0.0735676 1 975 8320 338 675 398 4885 71 978 2 7498 101312 11030 7616 6028 55884 784 12472 0.998506 0 . 0 . 99 15,30,20,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tAt|F310Y|310|OR5W2|protein_coding|CODING|NM_001001960.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.79383 rs34573569 -0.693147 0.0297145 99 R189C 310 Cgc/Tgc MODERATE 1 MISSENSE CODING OR5W2 A protein_coding NM_001001960.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55681494 G A 0 228 0 0.9962 0.999 1 1 1 1 0.998183 0.999384 1 2 10288 121070 11570 8650 6614 66538 908 16502 2 10312 121094 11570 8650 6614 66538 908 16502 0 . 0 . 0 76 0,0,44,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R189C|310|OR5W2|protein_coding|CODING|NM_001001960.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2457239 -0.693147 0.000898717 76 R165C 310 Cgc/Tgc MODERATE 1 MISSENSE CODING OR5W2 A protein_coding NM_001001960.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55681566 G A 0 222 0 0.1392 0.0937 0.0403 0.0903 0.0944 0.0726 0.126306 0.0983531 0.0840317 1 1353 9591 348 768 412 5598 74 1038 2 10232 120610 11550 8632 6614 66240 902 16440 0.251238 0 . 0 COSM287895 61 17,13,10,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R165C|310|OR5W2|protein_coding|CODING|NM_001001960.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.947743 rs61749302 -0.693021 0.27503 61 I210 314 atC/atT LOW 1 SILENT CODING OR5I1 A protein_coding NM_006637.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55703247 G A 0 222 0 0.2958 0.1683 0.0893 0.0913 0.1849 0.1145 0.249432 0.192764 0.163717 1 2558 17608 728 732 1195 10616 140 1639 2 9464 110174 10384 7266 6294 60306 854 15606 0.970195 0 . 0 . 156 50,28,41,23 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I210|314|OR5I1|protein_coding|CODING|NM_006637.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.680506 rs4465383 -0.693147 0.601285 156 L50S 314 tTg/tCg MODERATE 1 MISSENSE CODING OR5I1 G protein_coding NM_006637.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55703728 A G 0 222 0 0.1286 0.0913 0.0418 0.0903 0.0954 0.0726 0.114039 0.0940434 0.0837989 1 1246 9437 343 762 412 5580 74 1020 2 10342 120420 11324 8552 6570 66274 904 16454 0.986156 0 . 0 COSM147217 140 42,19,46,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L50S|314|OR5I1|protein_coding|CODING|NM_006637.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980591 rs4367963 -0.693147 0.907744 140 S294N 314 aGt/aAt MODERATE 1 MISSENSE CODING OR5F1 T protein_coding NM_003697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55761221 C T 0 228 0 0.9024 0.9728 0.9899 1 1 1 0.921172 0.972834 0.999302 2 9457 120236 11482 8652 6614 66650 901 16480 2 10294 121146 11524 8652 6614 66672 906 16484 0 . 0 . 0 103 0,0,56,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S294N|314|OR5F1|protein_coding|CODING|NM_003697.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2449134 -0.693147 0.257854 103 T192A 314 Aca/Gca MODERATE 1 MISSENSE CODING OR5F1 C protein_coding NM_003697.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55761528 T C 0 222 0 0.1293 0.0913 0.0403 0.0913 0.0944 0.0726 0.116765 0.0953517 0.0843808 1 1273 9569 350 778 411 5651 74 1032 2 10394 121276 11518 8644 6614 66686 908 16512 0.440777 0 . 0 . 123 38,17,30,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T192A|314|OR5F1|protein_coding|CODING|NM_003697.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.530483 rs35607186 -0.693147 0.547517 123 R122 314 Agg/Cgg LOW 1 SILENT CODING OR5F1 G protein_coding NM_003697.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55761738 T G 0 228 0 0.9939 0.9984 1 1 1 1 0.993412 0.997768 1 2 10334 121287 11550 8652 6614 66719 908 16510 2 10400 121356 11552 8652 6614 66720 908 16510 0 . 0 . 0 176 0,0,129,36 SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R122|314|OR5F1|protein_coding|CODING|NM_003697.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.989964 0 . rs2128152 -0.693147 0.0508496 176 L86 324 ttG/ttA LOW 1 SILENT CODING OR5AS1 A protein_coding NM_001001921.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55798152 G A 0 228 0 0.8979 0.9714 0.9885 1 1 1 0.917083 0.971448 0.999302 2 9499 117255 11499 8616 6610 65782 865 14384 2 10382 118210 11542 8616 6610 65802 870 14388 0 . 0 . 0 126 0,0,64,49 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L86|324|OR5AS1|protein_coding|CODING|NM_001001921.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1482011 -0.693147 0.0919015 126 I47L 312 Ata/Cta MODERATE 1 MISSENSE CODING OR8H2 C protein_coding NM_001005200.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55872657 A C 0 222 0 0.1604 0.1903 0.1354 0.2351 0.2187 0.1943 0.141072 0.179418 0.199069 1 1620 23567 1525 2097 1703 13258 182 3182 2 10400 121350 11564 8630 6612 66724 908 16512 0.995648 0 . 0 COSM147219 210 67,38,50,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I47L|312|OR8H2|protein_coding|CODING|NM_001005200.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.435652 0.065093 0 0.461047 rs28681529 -0.693147 0.155938 210 H120Y 312 Cat/Tat MODERATE 1 MISSENSE CODING OR8H2 T protein_coding NM_001005200.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55872876 C T 0 228 0 0.9818 0.9595 0.9553 0.999 0.9056 0.9468 0.971377 0.936952 0.919306 2 10109 113402 11210 8654 5787 61118 842 15682 2 10406 121408 11578 8654 6612 66740 908 16510 0 . 0 . 0 157 0,0,64,81 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H120Y|312|OR8H2|protein_coding|CODING|NM_001005200.1|1|T) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.816325 0 . rs2512961 -0.693147 0.189521 157 Y169C 312 tAc/tGc MODERATE 1 MISSENSE CODING OR8H2 G protein_coding NM_001005200.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55873024 A G 0 228 0 0.9939 0.9984 1 1 1 1 0.993639 0.997845 1 2 10341 121337 11576 8654 6614 66734 908 16510 2 10406 121404 11578 8654 6614 66734 908 16510 0 . 0 . 0 141 0,0,84,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y169C|312|OR8H2|protein_coding|CODING|NM_001005200.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.979895 0 . rs2449148 -0.693147 0.484546 141 V284M 312 Gtg/Atg MODERATE 1 MISSENSE CODING OR8H2 A protein_coding NM_001005200.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55873368 G A 0 228 0 0.9939 0.9984 1 1 1 1 0.993633 0.997844 1 2 10141 121079 11574 8654 6614 66682 908 16506 2 10206 121146 11576 8654 6614 66682 908 16506 0 . 0 . 0 96 0,0,48,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V284M|312|OR8H2|protein_coding|CODING|NM_001005200.1|1|A) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs1842696 -0.693147 0.655364 96 P137S 312 Ccc/Tcc MODERATE 1 MISSENSE CODING OR8H3 T protein_coding NM_001005201.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 55890257 C T 0 228 0 0.9939 0.9984 1 1 1 1 0.993639 0.997844 1 2 10334 121268 11538 8654 6612 66712 908 16510 2 10400 121336 11540 8654 6612 66712 908 16510 0 . 0 . 0 140 0,0,59,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P137S|312|OR8H3|protein_coding|CODING|NM_001005201.1|1|T) 1 0 . 0 . 1 0 1 1 0 56 0 0 0.959283 0 . rs1842691,rs61763009 -0.693147 0.197328 140 V87L 359 Gtg/Ctg MODERATE 1 MISSENSE CODING OR5T2 G protein_coding NM_001004746.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56000403 C G 0 228 0 0.795 0.9065 0.915 1 0.8787 0.9836 0.790777 0.84716 0.876047 2 8181 108662 10773 8631 6208 58169 829 15871 2 10374 120748 11526 8636 6612 66442 906 16252 0 . 0 . 0 64 0,0,18,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V87L|359|OR5T2|protein_coding|CODING|NM_001004746.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10791893 -0.693147 0.504913 64 S21Y 359 tCt/tAt MODERATE 1 MISSENSE CODING OR5T2 T protein_coding NM_001004746.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56000600 G T 0 222 0 0.0265 0.2097 0.2954 0.378 0.2286 0.2035 0.065652 0.168231 0.220787 1 591 28698 4821 3206 2001 14600 223 3256 2 10252 116470 11526 8620 6612 65308 862 13290 0.875413 0 . 0 . 117 28,28,24,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tAt|S21Y|359|OR5T2|protein_coding|CODING|NM_001004746.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.283139 rs386589364,rs3919907 -0.693147 0.655483 117 S164G 326 Agc/Ggc MODERATE 1 MISSENSE CODING OR5T1 G protein_coding NM_001004745.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56043604 A G 0 222 0 0.1649 0.4413 0.5821 0.6478 0.3708 0.5746 0.201499 0.31376 0.371276 1 2124 52472 7580 5597 2612 25131 389 9039 2 10406 121386 11576 8644 6612 66730 908 16510 0.800537 0 . 0 . 236 70,35,50,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S164G|326|OR5T1|protein_coding|CODING|NM_001004745.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.832843 0.87671 0 0.953115 rs12360890 -0.693147 0.185452 236 L196 326 ctG/ctC LOW 1 SILENT CODING OR5T1 C protein_coding NM_001004745.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56043702 G C 0 228 0 0.7587 0.7658 0.7233 0.8343 0.6779 0.8252 0.722399 0.679698 0.657821 2 7564 86462 8706 7369 5161 44033 633 12996 2 10404 121376 11570 8648 6614 66726 906 16508 0.494652 0 . 0 . 204 2,0,81,106 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L196|326|OR5T1|protein_coding|CODING|NM_001004745.1|1|C) 1 0 . 0 . 1 0 1 1 0 59 0 0.989305 0.975576 0 0.804813 rs7125697 -0.693147 0.113245 204 V226F 326 Gtc/Ttc MODERATE 1 MISSENSE CODING OR5T1 T protein_coding NM_001004745.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56043790 G T 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 33 0 33 0 0 0 0 2 10406 121404 11574 8650 6614 66740 908 16512 0.754898 0 . 0 . 179 46,35,41,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ttc|V226F|326|OR5T1|protein_coding|CODING|NM_001004745.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.571741 rs202156360 -0.693147 0.443353 179 L114 311 ctC/ctT LOW 1 SILENT CODING OR8H1 A protein_coding NM_001005199.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56058197 G A 0 222 0 0.1861 0.4293 0.5072 0.6151 0.3708 0.5716 0.213994 0.318301 0.371741 1 2278 51353 6624 5349 2611 25106 378 9007 2 10406 121382 11576 8652 6612 66720 908 16508 0.85117 0 . 0 . 184 50,40,52,32 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L114|311|OR8H1|protein_coding|CODING|NM_001005199.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.920671 rs1842674 -0.693147 0.579301 184 L122R 312 cTc/cGc MODERATE 1 MISSENSE CODING OR8K3 G protein_coding NM_001005202.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56086147 T G 0 228 0 0.7625 0.7855 0.8156 0.8651 0.675 0.8272 0.728305 0.681622 0.657705 2 7614 87577 9663 7603 5126 43920 646 13005 2 10404 121338 11556 8650 6610 66702 906 16510 0 . 0 . 0 78 0,0,45,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L122R|312|OR8K3|protein_coding|CODING|NM_001005202.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386623697,rs960193 -0.693147 0.847474 78 M21V 319 Atg/Gtg MODERATE 1 MISSENSE CODING OR8K1 G protein_coding NM_001002907.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56113575 A G 0 222 0 0.2292 0.4609 0.6052 0.6438 0.3708 0.5757 0.252385 0.33123 0.371625 1 2691 52936 7571 5586 2607 25088 393 9000 2 10404 121108 11510 8636 6608 66580 904 16466 0.985351 0 . 0 . 110 37,9,36,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M21V|319|OR8K1|protein_coding|CODING|NM_001002907.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.637567 rs10896271 -0.693147 0.00447919 110 P27T 319 Cct/Act MODERATE 1 MISSENSE CODING OR8K1 A protein_coding NM_001002907.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56113593 C A 0 222 0 0.2133 0.4557 0.598 0.6438 0.3708 0.5757 0.248069 0.329845 0.371741 1 2598 52851 7573 5584 2607 25097 392 9000 2 10406 121228 11522 8638 6604 66646 908 16504 0.720219 0 . 0 . 120 37,12,37,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P27T|319|OR8K1|protein_coding|CODING|NM_001002907.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.914012 rs10896272 -0.693147 0.517449 120 R8 316 agA/agG LOW 1 SILENT CODING OR8J1 G protein_coding NM_001005205.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56127746 A G 0 51 0 0.9365 0.8984 0.8991 0.875 0.8837 0.8855 0.936818 0.90077 0.882305 1 9568 105429 10340 7346 5325 58585 785 13480 2 10164 119066 11526 8630 6604 65990 880 15272 0.909649 0 . 0 . 35 24,0,8,0 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R8|316|OR8J1|protein_coding|CODING|NM_001005205.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.872525 0 . 0.981007 rs7942390 -0.651104 0.00721959 35 L268 316 Ctg/Ttg LOW 1 SILENT CODING OR8J1 T protein_coding NM_001005205.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56128524 C T 0 222 0 0.9365 0.8984 0.8991 0.875 0.8837 0.8855 0.936847 0.901108 0.882798 1 9621 98547 10289 7262 5328 56912 706 8429 2 10222 111320 11464 8532 6612 64170 794 9526 0.918704 0 . 0 . 93 14,22,21,33 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L268|316|OR8J1|protein_coding|CODING|NM_001005205.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0120335 rs7928704 -0.693147 0.341573 93 D19 287 gaC/gaT LOW 1 SILENT CODING OR8U8 T protein_coding NM_001013356.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143156 C T 0 150 0 0.2133 0.4557 0.598 0.6438 0.3708 0.5757 0 . 0 1 4067 61663 7852 5731 3145 30966 463 9439 2 9304 116150 11318 8534 6350 63584 860 16200 0.740081 0 . 0 . 68 28,5,33,0 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D19|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D19|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.5559 rs11228165 -0.693127 0.365987 68 D19 309 gaC/gaT LOW 1 SILENT CODING OR8U1 T protein_coding NM_001005204.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143156 C T 0 150 0 0.2133 0.4557 0.598 0.6438 0.3708 0.5757 0 . 0 1 4067 61663 7852 5731 3145 30966 463 9439 2 9304 116150 11318 8534 6350 63584 860 16200 0.740081 0 . 0 . 68 28,5,33,0 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D19|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D19|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.5559 rs11228165 -0.693127 0.365987 68 H20R 287 cAt/cGt MODERATE 1 MISSENSE CODING OR8U8 G protein_coding NM_001013356.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143158 A G 0 154 0 0.2133 0.4557 0.598 0.6438 0.3708 0.5757 0 . 0 1 4097 61923 7860 5731 3154 31165 464 9452 2 9366 116820 11342 8518 6360 64094 860 16280 0.923039 0 . 0 . 67 27,5,33,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.415536 rs11228166 -0.693127 0.365987 67 H20R 309 cAt/cGt MODERATE 1 MISSENSE CODING OR8U1 G protein_coding NM_001005204.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143158 A G 0 154 0 0.2133 0.4557 0.598 0.6438 0.3708 0.5757 0 . 0 1 4097 61923 7860 5731 3154 31165 464 9452 2 9366 116820 11342 8518 6360 64094 860 16280 0.923039 0 . 0 . 67 27,5,33,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.415536 rs11228166 -0.693127 0.365987 67 L157 287 ctA/ctG LOW 1 SILENT CODING OR8U8 G protein_coding NM_001013356.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143570 A G 0 56 0 . 0 . 0 . 0 . 0 . 1 4644 54838 5646 4126 2956 31255 397 5814 2 9566 117040 11504 8554 6386 65078 862 15090 0.715 0 . 0 . 94 38,33,15,2 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L157|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L157|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 1.07739e-06 rs11228169 -0.690438 1.2407e-08 94 L157 309 ctA/ctG LOW 1 SILENT CODING OR8U1 G protein_coding NM_001005204.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143570 A G 0 56 0 . 0 . 0 . 0 . 0 . 1 4644 54838 5646 4126 2956 31255 397 5814 2 9566 117040 11504 8554 6386 65078 862 15090 0.715 0 . 0 . 94 38,33,15,2 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L157|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L157|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 1.07739e-06 rs11228169 -0.690438 1.2407e-08 94 R165C 287 Cgc/Tgc MODERATE 1 MISSENSE CODING OR8U8 T protein_coding NM_001013356.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143592 C T 0 136 0 . 0 . 0 . 0 . 0 . 1 2027 40012 5027 3766 2108 20285 300 6499 2 9822 120690 11552 8628 6614 66680 904 16490 0.983488 0 . 0 COSM1354638 113 63,19,4,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R165C|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R165C|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.0265605 rs17150411 -0.69168 0.301673 113 R165C 309 Cgc/Tgc MODERATE 1 MISSENSE CODING OR8U1 T protein_coding NM_001005204.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56143592 C T 0 136 0 . 0 . 0 . 0 . 0 . 1 2027 40012 5027 3766 2108 20285 300 6499 2 9822 120690 11552 8628 6614 66680 904 16490 0.983488 0 . 0 COSM1354638 113 63,19,4,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R165C|287|OR8U8|protein_coding|CODING|NM_001013356.2|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R165C|309|OR8U1|protein_coding|CODING|NM_001005204.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 0.0265605 rs17150411 -0.69168 0.301673 113 A274V 324 gCt/gTt MODERATE 1 MISSENSE CODING OR5R1 A protein_coding NM_001004744.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56184888 G A 0 222 0 0.1838 0.4469 0.5922 0.6429 0.3708 0.5757 0.215811 0.318532 0.371159 1 2264 52481 7557 5591 2607 25075 391 8996 2 10388 121304 11534 8650 6614 66700 908 16510 0.854228 0 . 0 . 97 27,31,17,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A274V|324|OR5R1|protein_coding|CODING|NM_001004744.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622231 rs386626408,rs998544 -0.693127 0.0336039 97 C122R 324 Tgc/Cgc MODERATE 1 MISSENSE CODING OR5R1 G protein_coding NM_001004744.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56185345 A G 0 222 0 0.7443 0.7698 0.8285 0.7798 0.7247 0.7986 0.763971 0.750808 0.744064 1 8018 92851 9710 6634 4736 49809 702 13242 2 10402 121292 11516 8644 6610 66704 908 16508 0.896736 0 . 0 . 156 50,25,42,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C122R|324|OR5R1|protein_coding|CODING|NM_001004744.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.42527 rs6591324 -0.693147 0.0203333 156 T37M 311 aCg/aTg MODERATE 1 MISSENSE CODING OR5M8 A protein_coding NM_001005282.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56258737 G A 0 222 0 0 0.00059904 0 0.003 0 0 0.000227169 7.6959e-05 0 1 3 35 0 31 0 1 0 0 2 10046 120422 11570 8630 6614 66160 900 16502 0.867154 0 . 0 . 102 9,32,13,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T37M|311|OR5M8|protein_coding|CODING|NM_001005282.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.856241 rs192749813 -0.693147 0.0277199 102 S171N 305 aGt/aAt MODERATE 1 MISSENSE CODING OR5M11 T protein_coding NM_001005245.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56310222 C T 0 222 0 0.3608 0.6939 0.7651 0.875 0.7455 0.8538 0.439532 0.645626 0.747576 1 4046 89399 9194 7297 4890 49686 676 13610 2 9772 120012 11344 8574 6588 66348 896 16490 0.990893 0 . 0 . 113 29,27,30,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S171N|305|OR5M11|protein_coding|CODING|NM_001005245.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.826194 rs386602187,rs628524 -0.693147 0.571163 113 V69L 315 Gta/Tta MODERATE 1 MISSENSE CODING OR5M10 A protein_coding NM_001004741.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56344993 C A 0 222 0 0.3517 0.6538 0.719 0.874 0.6501 0.7924 0.412731 0.584579 0.665419 1 3835 81861 8999 7334 3982 44407 611 12693 2 9800 120754 11574 8622 6614 66734 898 16512 0.748114 0 . 0 . 240 52,36,77,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Tta|V69L|315|OR5M10|protein_coding|CODING|NM_001004741.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.999998 0.977706 0 0.335192 rs10792043 -0.693147 0.522046 240 S282T 315 aGc/aCc MODERATE 1 MISSENSE CODING OR5M1 G protein_coding NM_001004740.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56380134 C G 0 222 0 0.1815 0.4183 0.5605 0.622 0.3141 0.5348 0.198144 0.26796 0.29917 1 1971 45736 7209 5365 2336 20357 340 8158 2 9798 120704 11548 8620 6614 66716 898 16510 0.95146 0 . 0 . 166 49,33,45,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S282T|315|OR5M1|protein_coding|CODING|NM_001004740.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 54 0 0.807348 0.00248764 0 0.976756 rs4939078 -0.693147 0.95403 166 Q19* 310 Cag/Tag HIGH 1 NONSENSE CODING OR5AR1 T protein_coding NM_001004730.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56431216 C T 0 129 0 0.2716 0.623 0.7406 0.7857 0.6879 0.7802 0.337801 0.57034 0.689479 1 3429 83508 9137 6685 4731 46328 636 12562 2 10394 121260 11566 8648 6612 66658 906 16476 0.527032 0 . 0 . 74 37,1,35,0 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q19*|310|OR5AR1|protein_coding|CODING|NM_001004730.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.260702 rs11228710 -0.693136 0.157398 74 C53R 305 Tgc/Cgc MODERATE 1 MISSENSE CODING OR9G1 C protein_coding NM_001005213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468020 T C 0 222 0 0.7163 0.4121 0.3098 0.2312 0.4105 0.2618 0 . 0 1 7565 70149 6153 4583 3880 38479 515 8974 2 10400 121256 11544 8628 6592 66686 908 16498 0.41647 0 . 0 . 148 33,34,39,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C53R|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C53R|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 53 0 0.867477 0.938535 0 0.656866 rs532637 -0.693147 0.183608 148 C53R 305 Tgc/Cgc MODERATE 1 MISSENSE CODING OR9G9 C protein_coding NM_001013358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468020 T C 0 222 0 0.7163 0.4121 0.3098 0.2312 0.4105 0.2618 0 . 0 1 7565 70149 6153 4583 3880 38479 515 8974 2 10400 121256 11544 8628 6592 66686 908 16498 0.41647 0 . 0 . 148 33,34,39,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C53R|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C53R|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|C) 0 0.5 1 0 . 1 0 . 1 0 53 0 0.867477 0.938535 0 0.656866 rs532637 -0.693147 0.183608 148 F61V 305 Ttc/Gtc MODERATE 1 MISSENSE CODING OR9G1 G protein_coding NM_001005213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468044 T G 0 222 0 0.2602 0.5815 0.6888 0.7688 0.5885 0.7393 0 . 0 1 5074 82195 8973 6665 4215 44181 619 12468 2 10106 119928 11474 8604 6506 65890 900 16448 0.150568 0 . 0 . 119 38,25,18,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F61V|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F61V|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.0116995 0.531667 0 0.0825124 rs3975155 -0.693146 0.0431876 119 F61V 305 Ttc/Gtc MODERATE 1 MISSENSE CODING OR9G9 G protein_coding NM_001013358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468044 T G 0 222 0 0.2602 0.5815 0.6888 0.7688 0.5885 0.7393 0 . 0 1 5074 82195 8973 6665 4215 44181 619 12468 2 10106 119928 11474 8604 6506 65890 900 16448 0.150568 0 . 0 . 119 38,25,18,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F61V|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F61V|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.0116995 0.531667 0 0.0825124 rs3975155 -0.693146 0.0431876 119 T62A 305 Act/Gct MODERATE 1 MISSENSE CODING OR9G1 G protein_coding NM_001005213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468047 A G 0 222 0 0.2564 0.5803 0.6873 0.7688 0.5885 0.7393 0 . 0 1 5072 82136 8952 6661 4211 44163 619 12458 2 10100 119876 11476 8602 6506 65844 900 16448 0.759546 0 . 0 . 116 36,27,18,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T62A|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T62A|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.00651565 0.705065 0 0.436781 rs2865519 -0.693145 0.0272645 116 T62A 305 Act/Gct MODERATE 1 MISSENSE CODING OR9G9 G protein_coding NM_001013358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468047 A G 0 222 0 0.2564 0.5803 0.6873 0.7688 0.5885 0.7393 0 . 0 1 5072 82136 8952 6661 4211 44163 619 12458 2 10100 119876 11476 8602 6506 65844 900 16448 0.759546 0 . 0 . 116 36,27,18,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T62A|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T62A|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 52 0 0.00651565 0.705065 0 0.436781 rs2865519 -0.693145 0.0272645 116 T62I 305 aCt/aTt MODERATE 1 MISSENSE CODING OR9G1 T protein_coding NM_001005213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468048 C T 0 228 0 0.9939 0.9982 1 1 0.999 1 0.993639 0.997614 0.999651 2 10337 121210 11551 8648 6612 66662 907 16493 2 10404 121362 11558 8654 6612 66714 908 16512 0 . 0 . 0 111 0,0,51,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T62I|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T62I|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|T) 1 0 . 0 . 1 0 1 1 0 53 0 0 0.671059 0 . rs2865520 -0.693147 0.0378208 111 T62I 305 aCt/aTt MODERATE 1 MISSENSE CODING OR9G9 T protein_coding NM_001013358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468048 C T 0 228 0 0.9939 0.9982 1 1 0.999 1 0.993639 0.997614 0.999651 2 10337 121210 11551 8648 6612 66662 907 16493 2 10404 121362 11558 8654 6612 66714 908 16512 0 . 0 . 0 111 0,0,51,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T62I|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T62I|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|T) 1 0 . 0 . 1 0 1 1 0 53 0 0 0.671059 0 . rs2865520 -0.693147 0.0378208 111 C98G 305 Tgt/Ggt MODERATE 1 MISSENSE CODING OR9G1 G protein_coding NM_001005213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468155 T G 0 222 0 0.6778 0.3618 0.2507 0.2292 0.3091 0.2045 0 . 0 1 4502 30787 2121 1879 1610 17209 228 3238 2 10392 121284 11550 8644 6610 66674 908 16506 0.31435 0 . 0 . 107 22,37,18,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C98G|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C98G|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.59653 0.922761 0 0.984005 rs11228732 -0.693146 0.722342 107 C98G 305 Tgt/Ggt MODERATE 1 MISSENSE CODING OR9G9 G protein_coding NM_001013358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468155 T G 0 222 0 0.6778 0.3618 0.2507 0.2292 0.3091 0.2045 0 . 0 1 4502 30787 2121 1879 1610 17209 228 3238 2 10392 121284 11550 8644 6610 66674 908 16506 0.31435 0 . 0 . 107 22,37,18,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C98G|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Ggt|C98G|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.59653 0.922761 0 0.984005 rs11228732 -0.693146 0.722342 107 A132 305 gcC/gcT LOW 1 SILENT CODING OR9G1 T protein_coding NM_001005213.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468259 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 5202 60672 5787 4325 3305 33347 454 8252 2 10406 121400 11572 8650 6614 66738 908 16512 0 . 0 . 0 85 0,0,45,31 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A132|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A132|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|T) 0 . 0 . 0 . 0 . 1 0 51 0 0 0.947736 0 . rs503776 -0.693147 0.0621435 85 A132 305 gcC/gcT LOW 1 SILENT CODING OR9G9 T protein_coding NM_001013358.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468259 C T 0 228 0 . 0 . 0 . 0 . 0 . 2 5202 60672 5787 4325 3305 33347 454 8252 2 10406 121400 11572 8650 6614 66738 908 16512 0 . 0 . 0 85 0,0,45,31 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A132|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A132|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|T) 0 . 0 . 0 . 0 . 1 0 51 0 0 0.947736 0 . rs503776 -0.693147 0.0621435 85 A210 305 gcA/gcG LOW 1 SILENT CODING OR9G1 G protein_coding NM_001005213.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468493 A G 0 218 0 0.2693 0.1581 0.121 0.122 0.1163 0.1145 0 . 0 1 5474 61112 5856 4285 3401 33386 454 8256 2 10388 121244 11576 8604 6614 66664 904 16494 0.966929 0 . 0 . 86 31,24,8,14 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A210|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A210|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.95306 0.981437 0 0.933111 rs10792053 -0.692562 0.00062624 86 A210 305 gcA/gcG LOW 1 SILENT CODING OR9G9 G protein_coding NM_001013358.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56468493 A G 0 218 0 0.2693 0.1581 0.121 0.122 0.1163 0.1145 0 . 0 1 5474 61112 5856 4285 3401 33386 454 8256 2 10388 121244 11576 8604 6614 66664 904 16494 0.966929 0 . 0 . 86 31,24,8,14 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A210|305|OR9G1|protein_coding|CODING|NM_001005213.1|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A210|305|OR9G9|protein_coding|CODING|NM_001013358.2|1|G) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.95306 0.981437 0 0.933111 rs10792053 -0.692562 0.00062624 86 N206D 327 Aac/Gac MODERATE 1 MISSENSE CODING OR9G4 C protein_coding NM_001005284.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56510672 T C 0 228 0 0.9539 0.9878 1 1 1 1 0.970468 0.989841 0.999767 2 10088 120995 11538 8640 6614 66704 905 16506 2 10400 121368 11566 8642 6614 66732 906 16508 0 . 0 . 0 103 0,0,43,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N206D|327|OR9G4|protein_coding|CODING|NM_001005284.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs577576 -0.693147 0.26712 103 F43S 327 tTt/tCt MODERATE 1 MISSENSE CODING OR9G4 G protein_coding NM_001005284.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56511160 A G 0 222 0 0.084 0.1006 0.0994 0.119 0.1004 0.1053 0.0915493 0.0871171 0.0848464 1 875 12231 1205 1272 1150 5715 91 1923 2 10402 121340 11570 8634 6612 66710 908 16504 0.91014 0 . 0 COSM147235 117 30,27,26,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F43S|327|OR9G4|protein_coding|CODING|NM_001005284.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.109282 rs11228763 -0.693147 0.57219 117 G4V 309 gGa/gTa MODERATE 1 MISSENSE CODING OR5AK2 T protein_coding NM_001005323.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56756399 G T 0 222 0 0.025 0.1366 0.0778 0.3879 0.0746 0.1339 0.025443 0.0554102 0.0707635 1 282 11488 937 3241 601 4568 70 1789 2 10058 115172 11508 8646 6614 65028 832 12486 0.162073 0 . 0 . 167 64,12,59,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G4V|309|OR5AK2|protein_coding|CODING|NM_001005323.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.968321 rs10896563 -0.693147 0.0151297 167 M92I 309 atG/atA MODERATE 1 MISSENSE CODING OR5AK2 A protein_coding NM_001005323.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56756664 G A 0 222 0 0.9508 0.7095 0.562 0.7093 0.6183 0.5818 0.889141 0.698199 0.600349 1 9364 77106 6977 6155 3703 40406 550 9951 2 10402 121322 11546 8646 6612 66702 906 16508 0.973268 0 . 0 . 146 34,47,26,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M92I|309|OR5AK2|protein_coding|CODING|NM_001005323.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999261 rs2853083,rs386575343 -0.693147 0.0474636 146 F306 341 ttC/ttT LOW 2 SILENT CODING LRRC55 T protein_coding NM_001005210.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56954846 C T 0 222 0 0.1422 0.2418 0.255 0.1925 0.3817 0.274 0.179464 0.311913 0.379772 1 1907 38234 2854 1500 1969 25246 294 4464 2 10390 121300 11566 8640 6606 66680 906 16512 0.862847 0 . 0 . 85 24,23,17,13 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F306|341|LRRC55|protein_coding|CODING|NM_001005210.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.051728 rs386608044,rs716745 -0.693097 0.158228 85 341 1128 MODIFIER 2 CODING LRRC55 A protein_coding NM_001005210.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 56956082 G A 0 23 0 0.2995 0.5645 0.6196 0.749 0.5686 0.6892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||1128||341|LRRC55|protein_coding|CODING|NM_001005210.2|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs111133185,rs1124847 -0.453602 0.18 3 380 1185 MODIFIER 1 CODING APLNR A protein_coding NM_005161.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57002151 G A 0 9.7 0 0.9599 0.9892 1 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1185||380|APLNR|protein_coding|CODING|NM_005161.4|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs948846 -0.379885 0 1 G45 380 ggC/ggA LOW 1 SILENT CODING APLNR T protein_coding NM_005161.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57004344 G T 0 228 0 0.3835 0.5847 0.6412 0.7113 0.5577 0.7137 0.442526 0.515623 0.553073 2 4448 71121 7434 6094 3969 37452 549 11175 2 10352 121064 11562 8632 6612 66494 906 16506 0 . 0 . COSM292362 60 0,0,26,32 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G45|380|APLNR|protein_coding|CODING|NM_005161.4|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs948847 -0.693147 0.221125 60 T322S 1729 aCt/aGt MODERATE 5 MISSENSE CODING TNKS1BP1 C protein_coding NM_033396.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57081197 G C 0 228 0 0.0711 0.4868 0.6268 0.7063 0.5457 0.6626 0.147541 0.398799 0.527235 2 1042 46924 4966 4298 2058 26272 324 7964 2 5216 77700 6808 5908 3228 44054 562 11924 1 0 . 0 . 103 1,0,84,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T322S|1729|TNKS1BP1|protein_coding|CODING|NM_033396.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4939134 -0.693147 0.722002 103 T365 397 acG/acA LOW 12 SILENT CODING P2RX3 A protein_coding NM_002559.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57137371 G A 0 228 0 0.0756 0.4113 0.4813 0.6319 0.3847 0.6155 0.129941 0.290288 0.372439 2 1201 50687 5952 5523 3108 25351 402 9150 2 10200 119836 11428 8502 6544 65868 892 16402 1 0 . 0 COSM1178422 112 0,1,57,44 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T365|397|P2RX3|protein_coding|CODING|NM_002559.3|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2276039 -0.693147 0.122955 112 A383V 397 gCg/gTg MODERATE 12 MISSENSE CODING P2RX3 T protein_coding NM_002559.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57137424 C T 0 228 0 0.0696 0.4319 0.4914 0.7163 0.3926 0.6268 0.124035 0.297445 0.38629 2 1153 52426 6069 6190 3113 26168 409 9324 2 10272 120474 11476 8578 6572 66192 896 16488 0 . 0 . 0 93 0,0,31,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A383V|397|P2RX3|protein_coding|CODING|NM_002559.3|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276038 -0.693147 0.0191569 93 I109T 225 aTc/aCc MODERATE 3 MISSENSE CODING PRG3 G protein_coding NM_006093.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57147016 A G 0 228 0 0.8593 0.9585 0.9841 0.996 1 0.9928 0.868469 0.954748 0.998953 2 9017 119730 11519 8641 6614 66578 901 16460 2 10394 121240 11576 8654 6614 66592 904 16506 0 . 0 . 0 128 0,0,79,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I109T|225|PRG3|protein_coding|CODING|NM_006093.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs540687 -0.693147 0.0824079 128 C3R 225 Tgc/Cgc MODERATE 2 MISSENSE CODING PRG3 G protein_coding NM_006093.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57148175 A G 0 228 0 0.8593 0.9579 0.9841 0.996 1 0.9898 0.867045 0.95428 0.998953 2 7464 101119 10171 7727 5125 55998 759 13875 2 8600 102406 10224 7740 5126 56014 762 13940 0 . 0 . 0 171 0,0,73,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C3R|225|PRG3|protein_coding|CODING|NM_006093.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs669661 -0.693147 7.19394e-06 171 222 418 MODIFIER 6 CODING PRG2 C protein_coding NM_001302926.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57154530 G C 0 9.7 0 0.593 0.8856 0.9697 0.996 0.997 0.9928 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||418||222|PRG2|protein_coding|CODING|NM_001302926.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs536352 -0.379885 0 1 H206Y 222 Cac/Tac MODERATE 6 MISSENSE CODING PRG2 A protein_coding NM_001302926.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57155001 G A 0 228 0 0.5908 0.885 0.9697 0.996 0.997 0.9928 0.648115 0.879406 0.997905 2 6688 117193 11384 8631 6614 66542 892 16442 2 10332 121146 11556 8644 6614 66602 906 16492 0 . 0 . 0 62 0,0,15,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H206Y|222|PRG2|protein_coding|CODING|NM_001302926.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386598475,rs536455 -0.693147 0.481845 62 A183 222 gcA/gcG LOW 5 SILENT CODING PRG2 C protein_coding NM_001302926.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57155288 T C 0 228 0 0.7973 0.9411 0.9784 0.996 0.999 0.9928 0.839627 0.944719 0.9986 2 5810 75340 5484 5885 2468 43784 514 11395 2 7042 76696 5532 5896 2468 43812 516 11430 0 . 0 . 0 180 0,0,103,55 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A183|222|PRG2|protein_coding|CODING|NM_001302926.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs630396 -0.693147 0.038287 180 L5 222 Tta/Cta LOW 2 SILENT CODING PRG2 G protein_coding NM_001302926.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57157405 A G 0 228 0 0.6241 0.7522 0.8343 0.7718 0.7406 0.8589 0.627896 0.696091 0.731029 2 6505 91443 10295 6690 5080 48572 695 13606 2 10254 120814 11534 8616 6612 66416 904 16478 0 . 0 . 0 87 0,0,36,39 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L5|222|PRG2|protein_coding|CODING|NM_001302926.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386596304,rs490358 -0.693147 0.000259304 87 504 150 MODIFIER 3 CODING SLC43A3 G protein_coding NM_001278206.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57193795 C G 0 72 0 0.0091 0.1474 0.1369 0.3175 0.2087 0.1033 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.857112 0 . 0 . 10 1,4,0,5 UTR_5_PRIME(MODIFIER||150||504|SLC43A3|protein_coding|CODING|NM_001278206.1|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.761877 rs12420590 -0.590765 0.431509 10 559 241 MODIFIER 15 CODING SLC43A1 A protein_coding NM_001198810.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57252328 G A 0 36.5 0 0.7322 0.7827 0.7478 0.8919 0.7684 0.7781 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,2,1 UTR_3_PRIME(MODIFIER||241||559|SLC43A1|protein_coding|CODING|NM_001198810.1|15|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2848634 -0.511536 0.943964 4 R345G 494 Cgg/Ggg MODERATE 4 MISSENSE CODING SMTNL1 G protein_coding NM_001105565.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57313469 C G 0 222 0 0.3563 0.5076 0.5086 0.752 0.4414 0.5276 0.376757 0.398234 0.407937 1 3691 55739 6043 6270 3389 28334 416 7596 2 9412 116316 11322 8518 6538 64408 868 15250 0.999878 0 . 0 . 126 34,37,28,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Ggg|R345G|494|SMTNL1|protein_coding|CODING|NM_001105565.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.951435 rs12223229 -0.693144 0.266396 126 L332 715 Ttg/Ctg LOW 9 SILENT CODING ZDHHC5 C protein_coding NM_015457.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57463500 T C 0 222 0 0.5832 0.6601 0.6556 0.8968 0.5596 0.6268 0.560654 0.569263 0.573673 1 5870 74686 7925 7755 4519 38182 555 9880 2 10386 121072 11536 8648 6578 66554 904 16466 0.61667 0 . 0 . 122 30,25,22,31 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L332|715|ZDHHC5|protein_coding|CODING|NM_015457.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.659398 rs1783978 -0.693147 0.392986 122 715 626 MODIFIER 12 CODING ZDHHC5 C protein_coding NM_015457.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57468129 T C 0 222 0 0.8245 0.7266 0.6686 0.8968 0.5636 0.6278 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.519403 0 . 0 . 83 19,19,31,9 UTR_3_PRIME(MODIFIER||626||715|ZDHHC5|protein_coding|CODING|NM_015457.2|12|C),DOWNSTREAM(MODIFIER||3052||261|MED19|protein_coding|CODING|NM_001317078.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999201 rs1783979 -0.693145 0.241715 83 261 30 MODIFIER 1 CODING MED19 C protein_coding NM_001317078.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57479731 CG C 0 87 0 0.2519 0.3902 0.4078 0.626 0.328 0.3855 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 61 2,34,0,19 UTR_5_PRIME(MODIFIER||30||261|MED19|protein_coding|CODING|NM_001317078.1|1|C),UPSTREAM(MODIFIER||263||296|TMX2|protein_coding|CODING|NM_015959.3||C) 0 0.5 1 18 0.285714 1 1 0 . 0 60 0 0 1 0 . rs141274831 -0.69168 0.202734 61 A12 122 gcC/gcT LOW 1 SILENT CODING C11orf31 T protein_coding NM_170746.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57509103 C T 0 222 0 0 0.0081869 0 0.0407 0 0 0 . 0 1 0 149 0 147 0 0 2 0 2 2332 14442 810 1368 146 8748 84 954 0.950772 0 . 0 . 39 4,10,19,5 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A12|122|C11orf31|protein_coding|CODING|NM_170746.2|1|T),DOWNSTREAM(MODIFIER||658||296|TMX2|protein_coding|CODING|NM_015959.3||T),DOWNSTREAM(MODIFIER||1883||712|BTBD18|protein_coding|CODING|NM_001145101.1||T),INTRAGENIC(MODIFIER|||||TMX2-CTNND1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0102677 rs3741078 -0.692831 0.375436 39 122 LOW 2 CODING C11orf31 G protein_coding NM_170746.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57509429 A G 0 228 0 0.7708 0.9341 0.9885 0.999 0.999 0.9826 0.838331 0.946196 0.998193 2 6421 106210 10328 8058 5862 60583 758 14200 2 7806 107910 10414 8058 5864 60630 766 14372 0 . 0 . 0 38 0,0,24,13 SPLICE_SITE_REGION+INTRON(LOW||||122|C11orf31|protein_coding|CODING|NM_170746.2|2|G),DOWNSTREAM(MODIFIER||984||296|TMX2|protein_coding|CODING|NM_015959.3||G),DOWNSTREAM(MODIFIER||1557||712|BTBD18|protein_coding|CODING|NM_001145101.1||G),INTRAGENIC(MODIFIER|||||TMX2-CTNND1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs635663 -0.693141 0.202518 38 968 29522 MODIFIER 1 CODING CTNND1 G protein_coding NM_001085458.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57529429 A G 0 9.7 0 0.1762 0.2716 0.3285 0.1042 0.4284 0.3712 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||29522||968|CTNND1|protein_coding|CODING|NM_001085458.1|1|G),INTRAGENIC(MODIFIER|||||TMX2-CTNND1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11570176 -0.379885 0 1 D161 968 gaC/gaT LOW 6 SILENT CODING CTNND1 T protein_coding NM_001085458.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57563991 C T 0 222 0 0.1762 0.2714 0.3314 0.1012 0.4284 0.3712 0.225733 0.350024 0.408938 1 2207 42917 3505 893 1933 27479 334 6566 2 9790 120574 11568 8622 6610 66670 900 16414 0.869205 0 . 0 . 81 22,9,24,13 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D161|968|CTNND1|protein_coding|CODING|NM_001085458.1|6|T),INTRAGENIC(MODIFIER|||||TMX2-CTNND1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.936154 rs10896644 -0.693141 0.794091 81 H520 968 caC/caT LOW 8 SILENT CODING CTNND1 T protein_coding NM_001085458.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57571232 C T 0 228 0 0.9856 0.9962 1 1 1 1 0.993722 0.997888 0.99988 2 9695 120304 11507 8610 6602 66594 898 16398 2 9780 120398 11514 8610 6602 66596 898 16398 0 . 0 . 0 100 0,0,32,51 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H520|968|CTNND1|protein_coding|CODING|NM_001085458.1|8|T),INTRAGENIC(MODIFIER|||||TMX2-CTNND1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11229137 -0.693147 0.0443523 100 310 155418 MODIFIER 1 CODING OR9Q1 C protein_coding NM_001005212.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57791499 T C 0 9.7 0 0.8933 0.9702 0.9928 1 0.998 0.999 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||155418||310|OR9Q1|protein_coding|CODING|NM_001005212.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2513723 -0.379885 0 1 D100G 317 gAt/gGt MODERATE 1 MISSENSE CODING OR6Q1 G protein_coding NM_001005186.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57798723 A G 0 222 0 0.3238 0.4081 0.2651 0.6825 0.2913 0.4611 0.336665 0.311451 0.298534 1 3475 42696 3251 5898 2731 19953 292 7096 2 10406 121388 11574 8644 6610 66734 908 16512 0.990803 0 . 0 . 102 32,19,31,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D100G|317|OR6Q1|protein_coding|CODING|NM_001005186.2|1|G),INTRON(MODIFIER||||310|OR9Q1|protein_coding|CODING|NM_001005212.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.875465 rs921135 -0.693145 0.18537 102 Y173C 317 tAt/tGt MODERATE 1 MISSENSE CODING OR6Q1 G protein_coding NM_001005186.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57798942 A G 0 222 0 0.3238 0.4081 0.2651 0.6825 0.2913 0.4611 0.336665 0.311451 0.298534 1 3476 42704 3253 5899 2733 19955 292 7096 2 10400 121386 11576 8644 6612 66736 908 16510 0.992056 0 . 0 . 60 9,25,11,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y173C|317|OR6Q1|protein_coding|CODING|NM_001005186.2|1|G),INTRON(MODIFIER||||310|OR9Q1|protein_coding|CODING|NM_001005212.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.129785 rs2513726 -0.692831 0.314313 60 310 123564 MODIFIER 2 CODING OR9Q1 G protein_coding NM_001005212.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57823353 C G 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||123564||310|OR9Q1|protein_coding|CODING|NM_001005212.3|2|G) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs975831 -0.379885 0 1 310 1103 MODIFIER 3 CODING OR9Q1 A protein_coding NM_001005212.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57948952 G A 0 228 0 0.8109 0.7867 0.8098 0.869 0.662 0.7812 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 94 0,0,15,67 UTR_3_PRIME(MODIFIER||1103||310|OR9Q1|protein_coding|CODING|NM_001005212.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2443443 -0.693147 0.519011 94 314 3 MODIFIER 1 CODING OR9Q2 C protein_coding NM_001005283.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57957960 T C 0 222 0 0.0779 0.1462 0.2637 0.0744 0.2396 0.1329 0.110404 0.209097 0.25966 1 1093 26718 3682 627 1511 17102 183 2520 2 10352 117544 11522 8606 6600 65660 876 13928 0.572252 0 . 0 . 143 50,25,41,11 UTR_5_PRIME(MODIFIER||3||314|OR9Q2|protein_coding|CODING|NM_001005283.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932077 rs61902821 -0.693147 0.00110776 143 C179R 314 Tgt/Cgt MODERATE 1 MISSENSE CODING OR9Q2 C protein_coding NM_001005283.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57958497 T C 0 222 0 0.2806 0.2039 0.2939 0.0734 0.2406 0.1329 0.282826 0.269124 0.262104 1 2999 29053 3780 630 1515 17283 193 2653 2 10400 121236 11542 8612 6612 66656 908 16506 0.995432 0 . 0 . 89 18,22,25,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C179R|314|OR9Q2|protein_coding|CODING|NM_001005283.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.176097 rs34337292 -0.693146 0.28556 89 D271 314 gaC/gaT LOW 1 SILENT CODING OR9Q2 T protein_coding NM_001005283.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57958775 C T 0 222 0 0.2209 0.4239 0.3847 0.752 0.3082 0.5072 0.242617 0.293751 0.319949 1 2457 45068 4366 6443 2452 21353 338 7659 2 10406 121386 11574 8644 6612 66730 908 16512 0.685938 0 . 0 COSM147237 102 21,35,12,31 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D271|314|OR9Q2|protein_coding|CODING|NM_001005283.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.551687 rs7120468 -0.693146 0.177811 102 314 65 MODIFIER 1 CODING OR9Q2 A protein_coding NM_001005283.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57958972 C A 0 90 0 0.2179 0.4231 0.3847 0.752 0.3072 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8618 0 . 0 . 11 0,6,1,4 UTR_3_PRIME(MODIFIER||65||314|OR9Q2|protein_coding|CODING|NM_001005283.2|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.297172 rs1451317 -0.590765 0.148314 11 F153 325 ttC/ttT LOW 1 SILENT CODING OR1S2 A protein_coding NM_001004459.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57971195 G A 0 222 0 0.2239 0.4267 0.3876 0.752 0.3161 0.5072 0.248978 0.300139 0.32635 1 2506 44961 4313 6273 2433 21487 335 7614 2 10396 121114 11522 8598 6604 66620 906 16468 0.319171 0 . 0 COSM147238 252 57,59,58,58 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F153|325|OR1S2|protein_coding|CODING|NM_001004459.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.662313 0.666994 0 0.557565 rs11229279 -0.693147 0.115468 252 A151 325 gcC/gcT LOW 1 SILENT CODING OR1S2 A protein_coding NM_001004459.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57971201 G A 0 222 0 0.2806 0.5142 0.4971 0.7927 0.4245 0.6472 0.301454 0.382176 0.423534 1 3084 57221 5877 6667 3110 28021 444 10018 2 10402 121126 11522 8598 6606 66626 906 16466 0.165828 0 . 0 COSM147239 240 53,54,56,59 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A151|325|OR1S2|protein_coding|CODING|NM_001004459.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.992797 0.993533 0 0.94655 rs11229280 -0.693147 0.0568124 240 S5G 325 Agt/Ggt MODERATE 1 MISSENSE CODING OR1S1 G protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982229 A G 0 228 0 0.3759 0.6649 0.7622 0.8681 0.662 0.7802 0.417992 0.593428 0.68331 2 4267 84825 9635 7526 4646 45427 635 12689 2 10394 121158 11536 8646 6608 66606 906 16462 0 . 0 . 0 113 0,0,81,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S5G|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1966836,rs386550684 -0.693147 0.378715 113 I123T 325 aTt/aCt MODERATE 1 MISSENSE CODING OR1S1 C protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982584 T C 0 222 0 0.2844 0.5232 0.5418 0.8036 0.4225 0.6472 0.300545 0.382176 0.423999 1 3122 59204 7164 6960 3131 28297 454 10076 2 10406 121388 11566 8650 6614 66732 908 16512 0.546423 0 . 0 . 190 39,47,46,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I123T|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.704145 rs1966835 -0.693147 0.136296 190 H135R 325 cAc/cGc MODERATE 1 MISSENSE CODING OR1S1 G protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982620 A G 0 222 0 0.2844 0.5188 0.5418 0.8036 0.4205 0.6268 0.300772 0.38056 0.421439 1 3120 58780 7140 6958 3127 28161 453 9821 2 10406 121384 11562 8648 6612 66736 908 16512 0.991427 0 . 0 . 171 48,37,36,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H135R|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.32388 rs1966834 -0.693147 0.12129 171 L170 325 ctG/ctT LOW 1 SILENT CODING OR1S1 T protein_coding NM_001004458.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982726 G T 0 222 0 0.2844 0.5232 0.5418 0.8036 0.4225 0.6472 0.263062 0.3497 0.394088 1 3104 59063 7151 6928 3118 28245 454 10063 2 10382 121284 11568 8640 6606 66688 908 16492 0.998711 0 . 0 COSM147240 174 55,43,24,38 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L170|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.168317 0.7857 0 0.0045585 rs1993089 -0.693147 0.0394365 174 N183D 325 Aac/Gac MODERATE 1 MISSENSE CODING OR1S1 G protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982763 A G 0 215 0 . 0 . 0 . 0 0.190595 0.260283 0.296037 1 2979 57289 6867 6697 3059 27273 442 9972 2 10304 119946 11348 8456 6570 65960 896 16412 0.895919 0 . 0 COSM147241 152 54,46,18,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N183D|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|G) 1 0.5 1 0 . 0 . 1 1 0 57 0 8.09061e-06 0.221557 0 0.311376 rs1993088,rs61763008 -0.693146 0.126409 152 L206M 325 Ttg/Atg MODERATE 1 MISSENSE CODING OR1S1 A protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982832 T A 0 222 0 0.2829 0.525 0.5403 0.8046 0.4225 0.6585 0 . 0 1 3077 58746 7034 6833 3108 27987 455 10252 2 10386 120872 11458 8572 6598 66452 908 16498 0.927699 0 . 0 COSM147242 148 38,48,39,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L206M|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 57 0 0.00747363 0.271548 0 0.316155 rs2867400 -0.693147 0.214309 148 S227I 325 aGc/aTc MODERATE 1 MISSENSE CODING OR1S1 T protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57982896 G T 0 222 0 0.2814 0.5224 0.5418 0.8036 0.4225 0.6472 0.295093 0.380234 0.423865 1 3081 59088 7136 6954 3120 28268 454 10075 2 10382 121266 11522 8646 6602 66696 906 16512 0.73646 0 . 0 . 167 42,40,48,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S227I|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.204519 0.140904 0 0.2408 rs2903566 -0.693147 0.408533 167 K316E 325 Aag/Gag MODERATE 1 MISSENSE CODING OR1S1 G protein_coding NM_001004458.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57983162 A G 0 222 0 0.0772 0.1376 0.2205 0.0635 0.2386 0.1329 0.107905 0.20773 0.25891 1 1067 25548 2493 538 1505 17144 183 2618 2 10400 121002 11568 8654 6614 66600 904 16262 0.619051 0 . 0 COSM1127737 173 36,40,33,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K316E|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.989083 0.943933 0 0.880668 rs7103026 -0.693147 0.764515 173 *326W 325 tgA/tgG HIGH 1 MISSENSE CODING OR1S1 G protein_coding NM_001004458.1 STOP_LOST+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57983194 A G 0 222 0 0.2224 0.4335 0.428 0.7619 0.3141 0.5072 0.241708 0.297876 0.326659 1 2480 46445 5460 6542 2457 21697 343 7466 2 10372 119790 11516 8650 6614 66198 890 15550 0.999452 0 . 0 . 146 30,43,24,38 STOP_LOST+SPLICE_SITE_REGION(HIGH|MISSENSE|tgA/tgG|*326W|325|OR1S1|protein_coding|CODING|NM_001004458.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.982138 0.998425 0 0.906238 rs7103033 -0.693147 0.00588377 146 R191C 319 Cgc/Tgc MODERATE 1 MISSENSE CODING OR10Q1 A protein_coding NM_001004471.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57995777 G A 0 222 0 0.1513 0.155 0.1873 0.123 0.163 0.1616 0.141754 0.140317 0.139581 1 1467 18394 1978 1228 1144 9604 139 2834 2 10358 121106 11548 8626 6546 66620 898 16510 0.77872 0 . 0 . 85 27,13,16,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R191C|319|OR10Q1|protein_coding|CODING|NM_001004471.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.576923 rs11229301 -0.693145 0.751191 85 E12D 319 gaG/gaC MODERATE 1 MISSENSE CODING OR10Q1 G protein_coding NM_001004471.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 57996312 C G 0 228 0 0.8359 0.9413 0.9784 0.9593 0.9851 0.9939 0.859796 0.942911 0.984966 2 8332 117362 11463 8223 6486 65579 887 16392 2 9834 120760 11578 8652 6614 66666 904 16512 0 . 0 . 0 89 0,0,29,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E12D|319|OR10Q1|protein_coding|CODING|NM_001004471.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4245219 -0.693147 0.239902 89 R263Q 305 cGg/cAg MODERATE 1 MISSENSE CODING OR10W1 T protein_coding NM_207374.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58034543 C T 0 222 0 0.4841 0.5136 0.4942 0.6954 0.3787 0.5184 0.495229 0.435884 0.405471 1 5215 55661 6685 5804 2703 26614 412 8228 2 10404 121188 11554 8634 6608 66676 906 16406 0.868453 0 . 0 . 88 24,23,23,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R263Q|305|OR10W1|protein_coding|CODING|NM_207374.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740506 rs10792156 -0.693132 0.0194272 88 Y308C 314 tAt/tGt MODERATE 1 MISSENSE CODING OR5B17 C protein_coding NM_001005489.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58125620 T C 0 177 0 0.7307 0.7308 0.7334 0.8562 0.6312 0.7025 0.736029 0.668796 0.634342 2 7684 82402 9104 7425 4420 41688 597 11484 2 10290 119942 11554 8624 6610 66172 892 15800 0 . 0 . COSM1179749 46 0,0,46,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y308C|314|OR5B17|protein_coding|CODING|NM_001005489.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs4127353 -0.693147 0.201351 46 L80I 314 Tta/Ata MODERATE 1 MISSENSE CODING OR5B17 T protein_coding NM_001005489.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58126305 A T 0 228 0 0.6793 0.7167 0.7305 0.8552 0.6312 0.7025 0.698092 0.655634 0.633877 2 7309 82325 9057 7379 4413 41827 599 11741 2 10392 121168 11524 8616 6598 66628 904 16506 0 . 0 . 0 67 0,0,21,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L80I|314|OR5B17|protein_coding|CODING|NM_001005489.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4939208 -0.693147 0.274054 67 Q22* 314 Cag/Tag HIGH 1 NONSENSE CODING OR5B17 A protein_coding NM_001005489.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58126479 G A 0 222 0 0 0.011182 0.0014 0.0526 0 0.002 0 . 0 1 0 562 1 533 1 2 0 25 2 10132 118632 11450 8496 6596 65352 894 15712 0.79735 0 . 0 . 73 17,16,12,16 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q22*|314|OR5B17|protein_coding|CODING|NM_001005489.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.67725 rs79337234 -0.693054 0.13734 73 M200T 309 aTg/aCg MODERATE 1 MISSENSE CODING OR5B2 G protein_coding NM_001005566.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58190136 A G 0 222 0 0.7413 0.4914 0.4481 0.2738 0.4394 0.4622 0.660382 0.500308 0.418277 1 6899 53860 4215 2597 3361 28731 415 7642 2 10390 120804 11392 8566 6594 66460 904 16498 0.583312 0 . 0 . 151 33,31,38,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M200T|309|OR5B2|protein_coding|CODING|NM_001005566.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.830188 rs4298923 -0.693147 0.766682 151 T107M 309 aCg/aTg MODERATE 1 MISSENSE CODING OR5B2 A protein_coding NM_001005566.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58190415 G A 0 222 0 0 0.0047923 0.0014 0.0218 0 0.001 0.000227169 0.000153941 0.000116414 1 1 311 3 268 0 4 0 35 2 10406 121224 11442 8646 6612 66700 908 16510 0.104472 0 . 0 . 213 50,52,52,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T107M|309|OR5B2|protein_coding|CODING|NM_001005566.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.491395 rs118052160 -0.693147 0.0219616 213 C141R 314 Tgc/Cgc MODERATE 1 MISSENSE CODING OR5B12 G protein_coding NM_001004733.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58207204 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121405 11578 8653 6614 66738 908 16508 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 199 0,0,115,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C141R|314|OR5B12|protein_coding|CODING|NM_001004733.2|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4938895 -0.693147 0.374658 199 T310A 391 Act/Gct MODERATE 9 MISSENSE CODING LPXN C protein_coding NM_001143995.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58295175 T C 0 107 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 43 0 42 0 1 0 0 2 9922 119380 11402 8542 6590 65696 888 16340 0.299732 0 . 0 . 30 2,15,0,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T310A|391|LPXN|protein_coding|CODING|NM_001143995.2|9|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.267967 rs181781366 -0.676189 0.181116 30 L140 391 ctG/ctC LOW 5 SILENT CODING LPXN G protein_coding NM_001143995.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58318619 C G 0 222 0 0.2753 0.5082 0.5576 0.6905 0.5616 0.545 0.348478 0.502848 0.581956 1 3603 67134 7278 5776 3248 37830 496 8903 2 10394 121036 11530 8628 6584 66502 904 16494 0.999474 0 . 0 . 83 21,16,21,16 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L140|391|LPXN|protein_coding|CODING|NM_001143995.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.801699 rs1047979 -0.693141 0.116459 83 570 573 MODIFIER 11 CODING ZFP91 C protein_coding NM_053023.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58385752 T C 0 222 0 0.0469 0.1324 0.1859 0.119 0.1819 0.1728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870029 0 . 0 . 59 14,14,7,15 UTR_3_PRIME(MODIFIER||573||570|ZFP91|protein_coding|CODING|NM_053023.4|11|C),UPSTREAM(MODIFIER||4394||200|CNTF|protein_coding|CODING|NM_000614.3||C),INTRAGENIC(MODIFIER|||||ZFP91-CNTF||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.235612 rs11541682 -0.692562 0.417453 59 200 LOW 1 CODING CNTF A protein_coding NM_000614.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58391501 G A 0 222 0 0.0363 0.1234 0.1772 0.119 0.16 0.1697 0.056338 0.113377 0.142608 1 543 17683 1980 1233 1170 9684 142 2931 2 10372 119122 11560 8624 6614 66116 890 14946 0.790552 0 . 0 . 123 36,25,34,15 SPLICE_SITE_REGION+INTRON(LOW||||200|CNTF|protein_coding|CODING|NM_000614.3|1|A),DOWNSTREAM(MODIFIER||2478||570|ZFP91|protein_coding|CODING|NM_053023.4||A),INTRAGENIC(MODIFIER|||||ZFP91-CNTF||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937983 rs1800169,rs386427934 -0.693147 0.0351391 123 N156S 296 aAt/aGt MODERATE 5 MISSENSE CODING GLYAT C protein_coding NM_201648.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58478084 T C 0 228 0 0.9985 0.9265 0.9568 0.8046 0.9761 0.8824 0.992503 0.985376 0.981723 2 10350 115370 10836 6704 6479 65358 878 14765 2 10406 121374 11568 8642 6614 66726 908 16510 0 . 0 . 0 100 0,0,60,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N156S|296|GLYAT|protein_coding|CODING|NM_201648.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs675815 -0.693147 0.233295 100 S17T 296 Tcc/Acc MODERATE 2 MISSENSE CODING GLYAT T protein_coding NM_201648.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58491921 A T 0 222 0 0.1997 0.2183 0.2695 0.2609 0.161 0.2219 0.188551 0.160175 0.145634 1 2019 23420 3649 2324 1960 10000 162 3306 2 10394 121020 11476 8640 6604 66554 908 16444 0.662594 0 . 0 . 71 12,29,5,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Acc|S17T|296|GLYAT|protein_coding|CODING|NM_201648.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.905243 rs10896818 -0.692352 0.307009 71 E160K 294 Gaa/Aaa MODERATE 6 MISSENSE CODING GLYATL2 T protein_coding NM_145016.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58602309 C T 0 97 0 0.2852 0.3335 0.3242 0.4841 0.2018 0.3855 0.258182 0.20998 0.187606 1 2682 32040 4478 4474 2136 12922 203 5145 2 9354 113426 11318 8484 6552 63588 826 13304 0.986538 0 . 0 COSM147251 28 1,16,0,11 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gaa/Aaa|E160K|294|GLYATL2|protein_coding|CODING|NM_145016.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.585378 rs11229651 -0.676189 0.0174388 28 294 4864 MODIFIER 1 CODING GLYATL2 C protein_coding NM_145016.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58611949 G C 0 9.7 0 0.3185 0.3423 0.3242 0.4841 0.2008 0.3865 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||4864||294|GLYATL2|protein_coding|CODING|NM_145016.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1943281 -0.379885 0 1 294 4909 MODIFIER 1 CODING GLYATL2 T protein_coding NM_145016.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58611994 C T 0 9.7 0 0.3101 0.3401 0.3242 0.4841 0.2008 0.3865 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||4909||294|GLYATL2|protein_coding|CODING|NM_145016.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1943282 -0.379885 0 1 333 476 MODIFIER 7 CODING GLYATL1 G protein_coding NM_080661.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58723976 A G 0 32.6 0 0.8782 0.9655 0.9885 1 0.998 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||476||333|GLYATL1|protein_coding|CODING|NM_080661.4|7|G),INTRAGENIC(MODIFIER|||||LOC283194||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs518154 -0.379885 0 2 L330 734 Cta/Tta LOW 4 SILENT CODING FAM111B T protein_coding NM_198947.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58892558 C T 0 222 0 0.2005 0.1074 0.0605 0.1786 0.004 0.0481 0.135597 0.0477879 0.00291172 1 1429 5068 1094 1671 22 256 27 569 2 9788 119960 11486 8602 6604 66116 904 16460 0.474999 0 . 0 . 91 21,20,21,25 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L330|734|FAM111B|protein_coding|CODING|NM_198947.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.653387 rs35732637 -0.693147 0.920872 91 734 478 MODIFIER 4 CODING FAM111B C protein_coding NM_198947.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58894253 T C 0 222 0 0.3956 0.28 0.2507 0.2897 0.2048 0.2117 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.944074 0 . 0 . 110 28,19,19,31 UTR_3_PRIME(MODIFIER||478||734|FAM111B|protein_coding|CODING|NM_198947.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.966799 rs1938589 -0.693147 0.891486 110 734 528 MODIFIER 4 CODING FAM111B T protein_coding NM_198947.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58894303 G T 0 222 0 0.2005 0.1074 0.0605 0.1786 0.004 0.0481 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.719795 0 . 0 . 96 20,27,15,22 UTR_3_PRIME(MODIFIER||528||734|FAM111B|protein_coding|CODING|NM_198947.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.132846 rs2154626 -0.693141 0.102625 96 734 593 MODIFIER 4 CODING FAM111B A protein_coding NM_198947.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58894368 G A 0 222 0 0.2005 0.1074 0.0605 0.1786 0.004 0.0481 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.549964 0 . 0 . 80 22,26,14,9 UTR_3_PRIME(MODIFIER||593||734|FAM111B|protein_coding|CODING|NM_198947.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.260467 rs2154627 -0.692717 0.0492069 80 A224 611 gcA/gcG LOW 5 SILENT CODING FAM111A G protein_coding NM_001142519.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58919813 A G 0 222 0 0.3971 0.2812 0.2507 0.2917 0.2028 0.2157 0.336438 0.254541 0.212573 1 3573 27899 2782 2588 1324 13556 192 3884 2 10400 121346 11544 8644 6614 66728 908 16508 0.117448 0 . 0 . 189 36,49,44,34 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A224|611|FAM111A|protein_coding|CODING|NM_001142519.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991427 rs10896928 -0.693147 0.12536 189 619 287 MODIFIER 9 CODING DTX4 A protein_coding NM_015177.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58972669 C A 0 125 0 0.0144 0.1266 0.0519 0.3165 0.1153 0.1472 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,1 UTR_3_PRIME(MODIFIER||287||619|DTX4|protein_coding|CODING|NM_015177.1|9|A),DOWNSTREAM(MODIFIER||3314||716|MPEG1|protein_coding|CODING|NM_001039396.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3740946 -0.556411 0.836469 5 619 1061 MODIFIER 9 CODING DTX4 T protein_coding NM_015177.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58973443 C T 0 180 0 0 0.011582 0 0.0486 0 0.0092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979382 0 . 0 . 13 1,2,3,5 UTR_3_PRIME(MODIFIER||1061||619|DTX4|protein_coding|CODING|NM_015177.1|9|T),DOWNSTREAM(MODIFIER||2540||716|MPEG1|protein_coding|CODING|NM_001039396.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0.964642 0 0.979382 rs181580991 -0.651104 0.83311 13 619 1349 MODIFIER 9 CODING DTX4 G protein_coding NM_015177.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58973731 A G 0 228 0 0.5076 0.5837 0.4914 0.6617 0.6322 0.6217 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 83 0,0,80,2 UTR_3_PRIME(MODIFIER||1349||619|DTX4|protein_coding|CODING|NM_015177.1|9|G),DOWNSTREAM(MODIFIER||2252||716|MPEG1|protein_coding|CODING|NM_001039396.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1048444 -0.693147 0.0247293 83 619 1478 MODIFIER 9 CODING DTX4 C protein_coding NM_015177.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58973860 G C 0 228 0 0.0144 0.1192 0.0519 0.3165 0.1173 0.1074 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 292 0,0,126,108 UTR_3_PRIME(MODIFIER||1478||619|DTX4|protein_coding|CODING|NM_015177.1|9|C),DOWNSTREAM(MODIFIER||2123||716|MPEG1|protein_coding|CODING|NM_001039396.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3781796 -0.693147 0.00222952 292 619 2702 MODIFIER 9 CODING DTX4 T protein_coding NM_015177.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58975084 G T 0 228 0 0.0144 0.127 0.0533 0.3165 0.1153 0.1483 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 45 1,0,36,5 UTR_3_PRIME(MODIFIER||2702||619|DTX4|protein_coding|CODING|NM_015177.1|9|T),DOWNSTREAM(MODIFIER||899||716|MPEG1|protein_coding|CODING|NM_001039396.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs146231532 -0.693145 0.893724 45 P552L 716 cCg/cTg MODERATE 1 MISSENSE CODING MPEG1 A protein_coding NM_001039396.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 58978684 G A 0 228 0 0.0144 0.1148 0.0403 0.3046 0.1153 0.1074 0.0235672 0.0869675 0.115873 2 215 13751 514 2437 672 8002 103 1808 2 9274 118962 11550 8586 6602 65572 892 16486 0 . 0 . 0 31 0,0,20,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P552L|716|MPEG1|protein_coding|CODING|NM_001039396.1|1|A),DOWNSTREAM(MODIFIER||2624||619|DTX4|protein_coding|CODING|NM_015177.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7926933 -0.693054 0.888665 31 L289F 311 ttG/ttC MODERATE 1 MISSENSE CODING OR5AN1 C protein_coding NM_001004729.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59132798 G C 0 228 0 0.5061 0.6733 0.7363 0.744 0.7227 0.7311 0.531577 0.639701 0.695111 2 5509 83260 8581 6136 4652 45897 616 11869 2 10352 121014 11504 8568 6610 66596 908 16476 0 . 0 . 0 50 0,0,20,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L289F|311|OR5AN1|protein_coding|CODING|NM_001004729.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7941190 -0.693147 0.382879 50 G171E 324 gGg/gAg MODERATE 1 MISSENSE CODING OR5A2 T protein_coding NM_001001954.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59189915 C T 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 5 0 5 0 0 0 0 2 10402 121362 11568 8638 6614 66724 908 16508 0.999242 0 . 0 . 117 31,20,36,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G171E|324|OR5A2|protein_coding|CODING|NM_001001954.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.812077 rs188592274 -0.693147 0.398025 117 D183N 315 Gac/Aac MODERATE 1 MISSENSE CODING OR5A1 A protein_coding NM_001004728.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59211188 G A 0 228 0 0.4433 0.6354 0.5836 0.7609 0.6938 0.7423 0.4791 0.607605 0.673458 2 4962 80117 6495 6419 4405 44848 591 12397 2 10406 121386 11568 8650 6614 66732 908 16508 1 0 . 0 . 109 1,0,62,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D183N|315|OR5A1|protein_coding|CODING|NM_001004728.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6591536 -0.693147 0.37384 109 T208 315 acT/acC LOW 1 SILENT CODING OR5A1 C protein_coding NM_001004728.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59211265 T C 0 228 0 0.4433 0.6354 0.5836 0.7609 0.6938 0.7423 0.479328 0.607682 0.673458 2 4965 80126 6496 6419 4405 44851 591 12399 2 10406 121394 11566 8652 6614 66736 908 16512 1 0 . 0 . 139 1,0,85,43 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T208|315|OR5A1|protein_coding|CODING|NM_001004728.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7941591 -0.693147 0.661196 139 D96G 314 gAc/gGc MODERATE 1 MISSENSE CODING OR4D6 G protein_coding NM_001004708.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59224720 A G 0 228 0 0.7511 0.8958 0.853 0.9435 0.9901 0.9755 0.790095 0.921028 0.988126 2 8231 115123 9309 8150 6565 65900 871 16097 2 10406 121336 11576 8654 6614 66708 908 16470 0.901099 0 . 0 . 98 0,2,30,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D96G|314|OR4D6|protein_coding|CODING|NM_001004708.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.346154 rs1453543 -0.693147 0.31594 98 F197L 311 Ttc/Ctc MODERATE 1 MISSENSE CODING OR4D11 C protein_coding NM_001004706.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59271637 T C 0 222 0 0.289 0.3025 0.2219 0.2758 0.3091 0.3988 0.278283 0.294027 0.302095 1 2973 36000 1899 2378 1673 19774 294 7009 2 10404 121372 11574 8632 6612 66730 908 16512 0.999238 0 . 0 COSM147254 221 56,36,58,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F197L|311|OR4D11|protein_coding|CODING|NM_001004706.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.985976 rs7120079 -0.693147 0.00239784 221 R230W 309 Cgg/Tgg MODERATE 1 MISSENSE CODING OR10V1 A protein_coding NM_001005324.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59480631 G A 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 22 1 21 0 0 0 0 2 10314 121034 11510 8638 6614 66570 904 16484 0.818797 0 . 0 . 89 16,22,11,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R230W|309|OR10V1|protein_coding|CODING|NM_001005324.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.977388 rs200659739 -0.693146 0.373578 89 Q123R 309 cAg/cGg MODERATE 1 MISSENSE CODING OR10V1 C protein_coding NM_001005324.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59480951 T C 0 228 0 0.9977 0.9738 0.9582 1 0.9165 0.9847 0.982508 0.936345 0.912689 2 10212 112808 10933 8500 6084 60120 837 16122 2 10362 120318 11324 8500 6592 66204 900 16436 0 . 0 . 0 76 0,0,48,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q123R|309|OR10V1|protein_coding|CODING|NM_001005324.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs499033 -0.693147 0.426978 76 G193R 251 Ggg/Agg MODERATE 4 MISSENSE CODING MRPL16 T protein_coding NM_017840.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59573999 C T 0 222 0 0 0.016573 0.0504 0.0476 0 0 0.00113585 0.000692734 0.000465658 1 11 1430 919 467 0 18 3 12 2 10406 121410 11578 8652 6614 66740 908 16512 0.934859 0 . 0 . 141 28,34,36,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G193R|251|MRPL16|protein_coding|CODING|NM_017840.3|4|T),DOWNSTREAM(MODIFIER||644||289|STX3|protein_coding|CODING|NM_004177.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414688 rs147545257 -0.693147 0.39366 141 158 593 MODIFIER 4 CODING OOSP2 T protein_coding NM_173801.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59815139 C T 0 9.7 0 0.1014 0.2408 0.4409 0.4097 0.1948 0.1605 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||593||158|OOSP2|protein_coding|CODING|NM_173801.4|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10501381 -0.379885 0 1 T188 214 acC/acT LOW 6 SILENT CODING MS4A3 T protein_coding NM_006138.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59837097 C T 0 222 0 0.2859 0.3007 0.1844 0.2272 0.2724 0.5082 0.250114 0.268858 0.278463 1 2673 35055 1827 1875 1374 18986 263 8057 2 10400 121386 11578 8648 6614 66734 908 16504 0.977723 0 . 0 . 66 11,19,12,17 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T188|214|MS4A3|protein_coding|CODING|NM_006138.4|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.872136 rs386598209,rs528823 -0.693079 0.346338 66 253 78 MODIFIER 7 CODING MS4A6A G protein_coding NM_001247999.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59940396 A G 0 228 0 0.9902 0.9974 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,48,6 UTR_3_PRIME(MODIFIER||78||253|MS4A6A|protein_coding|CODING|NM_001247999.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs595718 -0.693147 0.00234196 62 253 74 MODIFIER 7 CODING MS4A6A T protein_coding NM_001247999.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59940400 C T 0 228 0 0.9902 0.9974 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,48,6 UTR_3_PRIME(MODIFIER||74||253|MS4A6A|protein_coding|CODING|NM_001247999.1|7|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2044979 -0.693147 0.0022589 62 253 71 MODIFIER 7 CODING MS4A6A G protein_coding NM_001247999.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59940403 A G 0 228 0 0.9902 0.9974 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,48,6 UTR_3_PRIME(MODIFIER||71||253|MS4A6A|protein_coding|CODING|NM_001247999.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2044978 -0.693147 0.0022589 62 253 67 MODIFIER 7 CODING MS4A6A G protein_coding NM_001247999.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59940407 A G 0 228 0 0.9902 0.9974 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 63 0,0,49,6 UTR_3_PRIME(MODIFIER||67||253|MS4A6A|protein_coding|CODING|NM_001247999.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs592346 -0.693147 0.00712635 63 T213S 253 Act/Tct MODERATE 7 MISSENSE CODING MS4A6A A protein_coding NM_001247999.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59940599 T A 0 222 0 0.0401 0.2141 0.2277 0.0575 0.3608 0.4499 0.0972285 0.277709 0.370198 1 989 37988 1832 546 1891 24879 316 7535 2 10390 121324 11564 8640 6612 66698 908 16512 0.566816 0 . 0 . 88 18,30,10,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Tct|T213S|253|MS4A6A|protein_coding|CODING|NM_001247999.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966701 rs7232 -0.69312 0.0938475 88 L137 253 ttA/ttG LOW 5 SILENT CODING MS4A6A C protein_coding NM_001247999.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 59945745 T C 0 222 0 0.1581 0.3073 0.2723 0.2252 0.4046 0.5184 0.200363 0.331974 0.399418 1 2122 43576 2364 1839 1948 26717 359 8227 2 10398 121332 11566 8644 6608 66702 906 16508 0.239563 0 . 0 COSM1162170,COSM147256 109 32,15,24,22 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L137|253|MS4A6A|protein_coding|CODING|NM_001247999.1|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99997 rs12453 -0.693147 0.134672 109 L191 239 Cta/Tta LOW 6 SILENT CODING MS4A4A T protein_coding NM_148975.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60073597 C T 0 222 0 0.8858 0.9263 0.9899 0.8403 0.999 0.9499 0.884249 0.960403 0.999419 1 9272 117918 11476 7314 6609 66644 898 15705 2 10406 121398 11578 8644 6614 66738 908 16510 0.497465 0 . 0 . 158 52,16,56,13 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L191|239|MS4A4A|protein_coding|CODING|NM_148975.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977997 rs4644658,rs56604262 -0.693147 0.0916472 158 L83 147 Ttg/Ctg LOW 2 SILENT CODING MS4A6E C protein_coding NM_139249.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60105313 T C 0 222 0 0 0.0071885 0 0.0278 0 0.0082 0 . 0 1 0 188 2 152 1 2 3 28 2 10406 121402 11576 8652 6614 66734 908 16512 0.616309 0 . 0 . 138 22,44,21,35 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L83|147|MS4A6E|protein_coding|CODING|NM_139249.2|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.958743 rs140696222 -0.693147 0.34037 138 147 850 MODIFIER 4 CODING MS4A6E C protein_coding NM_139249.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60108278 T C 0 228 0 0.5598 0.3452 0.2507 0.3829 0.2445 0.1871 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,3,11 UTR_3_PRIME(MODIFIER||850||147|MS4A6E|protein_coding|CODING|NM_139249.2|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10212 -0.686358 0.309523 15 T50 240 acT/acA LOW 3 SILENT CODING MS4A7 A protein_coding NM_021201.4 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60152563 T A 0 228 0 0.4939 0.5927 0.7061 0.5972 0.6501 0.5818 0.489333 0.592419 0.645233 2 5122 77553 8635 5621 4100 43893 584 9598 2 10406 121386 11574 8648 6614 66726 908 16510 1 0 . 0 . 126 1,0,87,24 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T50|240|MS4A7|protein_coding|CODING|NM_021201.4|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs950803 -0.693147 0.000205276 126 L57 240 ctG/ctA LOW 3 SILENT CODING MS4A7 A protein_coding NM_021201.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60152584 G A 0 228 0 0.4569 0.4028 0.3646 0.4375 0.339 0.3865 0.410803 0.359911 0.333837 2 4399 42824 3827 4283 1555 22340 328 6092 2 10406 121380 11562 8646 6614 66734 908 16510 1 0 . 0 . 131 1,0,76,32 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L57|240|MS4A7|protein_coding|CODING|NM_021201.4|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs950802 -0.693147 0.000407135 131 240 317 MODIFIER 7 CODING MS4A7 C protein_coding NM_021201.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60161651 T C 0 36.3 0 0.8396 0.7849 0.8357 0.7183 0.7296 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||317||240|MS4A7|protein_coding|CODING|NM_021201.4|7|C),UPSTREAM(MODIFIER||1836||712|MS4A14|protein_coding|CODING|NM_001261828.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1892 -0.453602 0.64 2 240 1055 MODIFIER 7 CODING MS4A7 T protein_coding NM_021201.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60162389 C T 0 87 0 0 0.0039936 0 0.0198 0 0 0 . 0 1 0 7 0 5 0 0 0 2 2 534 12018 184 194 2 3472 130 7502 0.94925 0 . 0 . 23 15,0,8,0 UTR_3_PRIME(MODIFIER||1055||240|MS4A7|protein_coding|CODING|NM_021201.4|7|T),UPSTREAM(MODIFIER||1098||712|MS4A14|protein_coding|CODING|NM_001261828.1||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 0.902954 rs147113699 -0.651104 0.13615 23 712 417 MODIFIER 1 CODING MS4A14 C protein_coding NM_001261828.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60163635 T C 0 95 0 0.8631 0.7909 0.8343 0.7183 0.7296 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_5_PRIME(MODIFIER||417||712|MS4A14|protein_coding|CODING|NM_001261828.1|1|C),DOWNSTREAM(MODIFIER||209||240|MS4A7|protein_coding|CODING|NM_021201.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3816270 -0.590765 0.530437 6 712 94 MODIFIER 1 CODING MS4A14 A protein_coding NM_001261828.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60163958 G A 0 228 0 0.9803 0.9948 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 135 0,0,120,11 UTR_5_PRIME(MODIFIER||94||712|MS4A14|protein_coding|CODING|NM_001261828.1|1|A),DOWNSTREAM(MODIFIER||532||240|MS4A7|protein_coding|CODING|NM_021201.4||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6591579 -0.693147 0.00078264 135 I56 712 att/ HIGH 2 CODING MS4A14 A protein_coding NM_001261828.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60165352 ATT A 0 228 0 0.4788 0.5871 0.7089 0.5942 0.6551 0.5695 0.479137 0.591933 0.65023 2 5019 77493 8582 5653 4036 44187 584 9432 2 10404 121204 11542 8630 6596 66624 904 16504 0 . 0 . COSM1684267 124 4,2,61,45 FRAME_SHIFT(HIGH||att/|I56|712|MS4A14|protein_coding|CODING|NM_001261828.1|2|A),DOWNSTREAM(MODIFIER||1927||240|MS4A7|protein_coding|CODING|NM_021201.4||A) 1 0 . 110 0.887097 1 1 1 1 (MS4A14|MS4A14|1|1.00) 60 0 0 1 0 . rs3217518 -0.693147 0.00423126 124 712 HIGH 4 CODING MS4A14 G protein_coding NM_001261828.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60173360 A G 0 228 0 0.4803 0.6054 0.7118 0.6399 0.6551 0.6125 0.49422 0.600307 0.646449 2 878 10810 199 232 3 4709 111 4678 2 1780 17218 302 332 6 6920 164 7714 0 . 0 . 0 36 0,0,16,17 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||712|MS4A14|protein_coding|CODING|NM_001261828.1|4|G) 1 0 . 0 . 1 0 1 1 (MS4A14|MS4A14|1|1.00) 60 0 0 1 0 . rs4938941 -0.693127 0.412238 36 N210Y 712 Aat/Tat MODERATE 6 MISSENSE CODING MS4A14 T protein_coding NM_001261828.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60182970 A T 0 222 0 0.5492 0.5779 0.6902 0.4097 0.7018 0.5828 0.533818 0.64032 0.694884 1 5656 78624 8168 3692 4177 46607 593 9731 2 10394 121146 11500 8630 6602 66630 908 16482 0.999865 0 . 0 . 167 50,35,31,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N210Y|712|MS4A14|protein_coding|CODING|NM_001261828.1|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999789 rs7131283 -0.693147 0.0416247 167 G617R 712 Gga/Aga MODERATE 6 MISSENSE CODING MS4A14 A protein_coding NM_001261828.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60184191 G A 0 222 0 0.5182 0.4982 0.6513 0.3433 0.6262 0.3906 0.489106 0.575042 0.61907 1 5173 68858 7754 3195 3811 41649 522 6754 2 10312 120192 11358 8442 6574 66206 904 16396 0.664759 0 . 0 . 173 59,48,25,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G617R|712|MS4A14|protein_coding|CODING|NM_001261828.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.644592 rs3825020 -0.693147 0.321595 173 Q645H 712 caA/caC MODERATE 6 MISSENSE CODING MS4A14 C protein_coding NM_001261828.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60184277 A C 0 222 0 0.0363 0.0915 0.0389 0.247 0.0169 0.1196 0.0340445 0.0241427 0.0190698 1 357 6237 589 2291 148 1187 48 1617 2 10342 120496 11342 8492 6590 66358 904 16468 0.702931 0 . 0 . 130 30,22,26,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q645H|712|MS4A14|protein_coding|CODING|NM_001261828.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992479 rs73481226 -0.693147 0.181052 130 T71 200 acC/acT LOW 2 SILENT CODING MS4A5 T protein_coding NM_023945.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60198328 C T 0 222 0 0.4796 0.3137 0.3069 0.2004 0.3131 0.2117 0.416705 0.346278 0.310188 1 4575 35183 3082 2032 1360 20429 275 3430 2 10400 121376 11572 8648 6614 66726 908 16508 0.998701 0 . 0 . 110 31,33,29,10 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T71|200|MS4A5|protein_coding|CODING|NM_023945.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.676634 rs708229 -0.693144 0.202305 110 297 331 MODIFIER 7 CODING MS4A1 G protein_coding NM_021950.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60236272 A G 0 9.7 0 0.7368 0.638 0.6729 0.6647 0.5129 0.5808 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||331||297|MS4A1|protein_coding|CODING|NM_021950.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1051756,rs386514170 -0.379885 0 1 297 2050 MODIFIER 7 CODING MS4A1 C protein_coding NM_021950.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60237991 T C 0 9.7 0 0.5666 0.4756 0.5029 0.4603 0.4344 0.3916 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2050||297|MS4A1|protein_coding|CODING|NM_021950.3|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1051593 -0.379885 0 1 Y52 267 taC/taT LOW 2 SILENT CODING MS4A12 T protein_coding NM_017716.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60264947 C T 0 222 0 0.6626 0.6154 0.6599 0.6607 0.5099 0.5818 0.596459 0.550669 0.527209 1 6412 69544 8113 5475 3268 35988 505 9783 2 10404 121380 11574 8646 6610 66726 908 16512 0.260723 0 . 0 . 139 20,57,18,34 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y52|267|MS4A12|protein_coding|CODING|NM_017716.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.194308 rs2298552 -0.693147 0.769921 139 Q71* 267 Caa/Taa HIGH 2 NONSENSE CODING MS4A12 T protein_coding NM_017716.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60265002 C T 0 222 0 0.534 0.4782 0.4914 0.4802 0.4334 0.4376 0.468225 0.452407 0.444302 1 5116 57732 6762 4086 3005 30807 428 7528 2 10386 121290 11562 8642 6606 66680 908 16506 0.393876 0 . 0 . 87 17,29,17,20 STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q71*|267|MS4A12|protein_coding|CODING|NM_017716.2|2|T) 1 0.5 1 0 . 1 0 1 1 (MS4A12|MS4A12|1|1.00) 60 0 1 1 (MS4A12|MS4A12|1|1.00) 0.25095 rs2298553 -0.693141 0.129398 87 I7V 152 Att/Gtt MODERATE 3 MISSENSE CODING MS4A13 G protein_coding NM_001012417.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60285575 A G 0 228 0 0.8071 0.9473 0.9885 0.999 1 1 0.846346 0.947409 0.999186 2 8733 119468 11463 8650 6612 66629 895 16486 2 10392 121286 11562 8650 6612 66672 902 16496 0 . 0 . 0 158 0,0,101,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I7V|152|MS4A13|protein_coding|CODING|NM_001012417.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10736706 -0.693147 0.00135075 158 P58L 152 cCg/cTg MODERATE 4 MISSENSE CODING MS4A13 T protein_coding NM_001012417.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60291413 C T 0 222 0 0.6059 0.7288 0.6859 0.7242 0.8787 0.7761 0.640781 0.790544 0.867397 1 6554 99095 8376 6224 6106 58209 765 12861 2 10326 121076 11548 8648 6608 66554 904 16488 0.882701 0 . 0 . 105 22,23,23,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P58L|152|MS4A13|protein_coding|CODING|NM_001012417.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998598 rs6591595 -0.693147 0.465486 105 152 LOW 5 CODING MS4A13 G protein_coding NM_001012417.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60296834 A G 0 222 0 0.003 0.0575 0.036 0.128 0.0666 0.0644 0.00885157 0.0365216 0.0506977 1 90 7054 307 1248 551 3978 51 829 2 10346 118838 11540 8626 6608 66022 888 14808 0.983179 0 . 0 . 139 48,2,56,1 SPLICE_SITE_REGION+INTRON(LOW||||152|MS4A13|protein_coding|CODING|NM_001012417.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.133339 rs12802514 -0.693147 0.0207249 139 Y116 152 taC/taT LOW 6 SILENT CODING MS4A13 T protein_coding NM_001012417.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60296879 C T 0 222 0 0.0613 0.1076 0.098 0.129 0.0825 0.181 0.0667272 0.081821 0.0895557 1 711 12359 1556 1210 315 5796 74 2697 2 10392 121218 11564 8652 6608 66634 904 16464 0.863321 0 . 0 . 124 28,27,32,18 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y116|152|MS4A13|protein_coding|CODING|NM_001012417.2|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.737968 rs11230364 -0.693147 0.00140285 124 L47R 240 cTg/cGg MODERATE 2 MISSENSE CODING MS4A15 G protein_coding NM_001098835.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60531346 T G 0 228 0 0.0628 0.406 0.4769 0.628 0.4841 0.5102 0.14261 0.354922 0.458343 2 1346 55343 6315 5466 3169 30744 398 7905 2 9738 120388 11532 8598 6598 66518 896 16508 0 . 0 . 0 102 0,0,57,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L47R|240|MS4A15|protein_coding|CODING|NM_001098835.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1032939,rs386512193 -0.693147 0.58639 102 240 179 MODIFIER 7 CODING MS4A15 G protein_coding NM_001098835.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60543367 C G 0 77 0 0.2345 0.268 0.2536 0.1171 0.4235 0.319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||179||240|MS4A15|protein_coding|CODING|NM_001098835.1|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs17628721 -0.511536 0.0681597 3 267 144 MODIFIER 8 CODING MS4A10 C protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567525 CCTGGG C 0 228 0 0.1891 0.5088 0.4813 0.8095 0.4453 0.7157 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,6,31 UTR_3_PRIME(MODIFIER||144||267|MS4A10|protein_coding|CODING|NM_206893.3|8|C) 0 . 0 37 0.925 1 1 0 . 0 60 0 0 1 0 . rs71997819 -0.693141 0.0270642 40 267 152 MODIFIER 8 CODING MS4A10 C protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567534 G C 0 228 0 0.2897 0.5453 0.4942 0.8105 0.4523 0.7495 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,6,29 UTR_3_PRIME(MODIFIER||152||267|MS4A10|protein_coding|CODING|NM_206893.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs74932478 -0.693136 0.00706045 37 267 207 MODIFIER 8 CODING MS4A10 A protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567589 G A 0 221 0 0.289 0.5451 0.4942 0.8105 0.4523 0.7495 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,1,17 UTR_3_PRIME(MODIFIER||207||267|MS4A10|protein_coding|CODING|NM_206893.3|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10792292 -0.691153 0.0629959 19 267 323 MODIFIER 8 CODING MS4A10 C protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567705 T C 0 80 0 0.9198 0.9784 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||323||267|MS4A10|protein_coding|CODING|NM_206893.3|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs539800 -0.556411 0.472095 4 267 337 MODIFIER 8 CODING MS4A10 A protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567719 G A 0 39.3 0 0.289 0.5451 0.4942 0.8105 0.4523 0.7495 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||337||267|MS4A10|protein_coding|CODING|NM_206893.3|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10750942 -0.453602 0.68 2 267 354 MODIFIER 8 CODING MS4A10 G protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60567736 A G 0 9.7 0 0.27 0.5397 0.4928 0.8105 0.4513 0.7495 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||354||267|MS4A10|protein_coding|CODING|NM_206893.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10750943 -0.379885 0 1 267 1386 MODIFIER 8 CODING MS4A10 T protein_coding NM_206893.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60568768 G T 0 39.3 0 0.2504 0.5433 0.4885 0.8532 0.4523 0.7526 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1386||267|MS4A10|protein_coding|CODING|NM_206893.3|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10750945 -0.453602 0.06 2 P156 360 ccG/ccA LOW 1 SILENT CODING CCDC86 A protein_coding NM_024098.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60610065 G A 0 228 0 0.1664 0.3409 0.2752 0.6806 0.1899 0.4284 0 . 0 2 1555 31802 3599 6169 1954 12709 206 5610 2 9620 118406 11540 8608 6602 64640 888 16508 0 . 0 . COSM429370 72 0,0,52,15 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P156|360|CCDC86|protein_coding|CODING|NM_024098.3|1|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2074420 -0.693147 0.345093 72 360 36 MODIFIER 4 CODING CCDC86 A protein_coding NM_024098.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60617834 C A 0 228 0 0.5567 0.6787 0.6931 0.9196 0.5517 0.7157 0.55495 0.562077 0.565728 2 5628 74312 8823 7865 3942 36557 487 11010 2 9958 118990 11458 8590 6462 65310 872 16340 0 . 0 . 0 44 0,0,11,32 UTR_3_PRIME(MODIFIER||36||360|CCDC86|protein_coding|CODING|NM_024098.3|4|A),DOWNSTREAM(MODIFIER||564||395|PTGDR2|protein_coding|CODING|NM_004778.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs530963 -0.693146 0.156039 44 360 144 MODIFIER 4 CODING CCDC86 A protein_coding NM_024098.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60617942 G A 0 228 0 0.7201 0.732 0.7133 0.9236 0.5716 0.729 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 33 0,0,21,12 UTR_3_PRIME(MODIFIER||144||360|CCDC86|protein_coding|CODING|NM_024098.3|4|A),DOWNSTREAM(MODIFIER||456||395|PTGDR2|protein_coding|CODING|NM_004778.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs493176 -0.693127 0.210519 33 360 336 MODIFIER 4 CODING CCDC86 G protein_coding NM_024098.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60618134 A G 0 222 0 0.0877 0.3415 0.33 0.7054 0.2197 0.4427 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.714241 0 . 0 . 70 10,24,9,19 UTR_3_PRIME(MODIFIER||336||360|CCDC86|protein_coding|CODING|NM_024098.3|4|G),DOWNSTREAM(MODIFIER||264||395|PTGDR2|protein_coding|CODING|NM_004778.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.990046 rs386608040,rs7167 -0.693054 0.0498313 70 360 471 MODIFIER 4 CODING CCDC86 A protein_coding NM_024098.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60618269 G A 0 174 0 0.9448 0.9846 0.9942 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,1,8 UTR_3_PRIME(MODIFIER||471||360|CCDC86|protein_coding|CODING|NM_024098.3|4|A),DOWNSTREAM(MODIFIER||129||395|PTGDR2|protein_coding|CODING|NM_004778.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs634933 -0.662043 0.0261122 9 395 244 MODIFIER 2 CODING PTGDR2 G protein_coding NM_004778.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60619764 C G 0 9.7 0 0.2352 0.2496 0.3184 0.1567 0.3151 0.2485 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||244||395|PTGDR2|protein_coding|CODING|NM_004778.2|2|G),DOWNSTREAM(MODIFIER||1203||360|CCDC86|protein_coding|CODING|NM_024098.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11571288 -0.379885 0 1 V204A 395 gTg/gCg MODERATE 2 MISSENSE CODING PTGDR2 G protein_coding NM_004778.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60620585 A G 0 223 0 0.9448 0.9846 0.9942 1 1 1 0.957292 0.985457 0.999884 2 8479 112410 11086 8180 5810 61972 805 16078 2 8878 112860 11124 8180 5810 61982 806 16080 0 . 0 . 0 41 0,0,39,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V204A|395|PTGDR2|protein_coding|CODING|NM_004778.2|2|G),DOWNSTREAM(MODIFIER||2024||360|CCDC86|protein_coding|CODING|NM_024098.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2467642 -0.693145 0.314578 41 R202 395 cgG/cgC LOW 2 SILENT CODING PTGDR2 G protein_coding NM_004778.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60620590 C G 0 215 0 0.9448 0.9846 0.9942 1 1 1 0.956176 0.985154 1 2 8708 113920 11184 8260 6008 62762 825 16173 2 9116 114378 11222 8260 6008 62772 826 16174 0 . 0 . 0 43 0,0,41,1 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R202|395|PTGDR2|protein_coding|CODING|NM_004778.2|2|G),DOWNSTREAM(MODIFIER||2029||360|CCDC86|protein_coding|CODING|NM_024098.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2428461 -0.693146 0.382781 43 V19 638 gtT/gtC LOW 1 SILENT CODING ZP1 C protein_coding NM_207341.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60635091 T C 0 228 0 0.8669 0.9633 0.9899 1 0.999 1 0.912619 0.970009 0.999418 2 9351 119311 11457 8630 6362 66128 888 16495 2 10328 120398 11518 8630 6362 66168 892 16500 0 . 0 . 0 170 0,0,91,64 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V19|638|ZP1|protein_coding|CODING|NM_207341.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs550479 -0.693147 0.227188 170 T158I 638 aCc/aTc MODERATE 3 MISSENSE CODING ZP1 T protein_coding NM_207341.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60637164 C T 0 228 0 0.8359 0.6933 0.8213 0.4038 0.8161 0.5818 0.842941 0.82813 0.82054 2 8739 91901 9413 3402 4765 54402 712 10468 2 10402 121282 11572 8622 6580 66702 906 16498 0.948351 0 . 0 . 93 2,1,48,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T158I|638|ZP1|protein_coding|CODING|NM_207341.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.578169 rs386430946,rs489172 -0.693147 0.062115 93 V289 638 gtA/gtG LOW 5 SILENT CODING ZP1 G protein_coding NM_207341.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60638470 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121396 11578 8654 6614 66730 906 16508 2 10406 121396 11578 8654 6614 66730 906 16508 0 . 0 . 0 112 0,0,78,28 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V289|638|ZP1|protein_coding|CODING|NM_207341.3|5|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs566411 -0.693147 0.343008 112 S349 504 tcC/tcT LOW 12 SILENT CODING PRPF19 A protein_coding NM_014502.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60666341 G A 0 228 0 0.1422 0.3085 0.3905 0.3194 0.3887 0.3814 0.183386 0.326515 0.39986 2 1497 35738 3752 2343 1880 20628 257 5381 2 6538 82824 7454 6078 3944 45826 594 12390 1 0 . 0 . 78 1,0,61,9 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S349|504|PRPF19|protein_coding|CODING|NM_014502.4|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3763840 -0.693147 0.00114127 78 504 14 MODIFIER 1 CODING PRPF19 C protein_coding NM_014502.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60673868 T C 0 228 0 0.3109 0.3574 0.4006 0.3254 0.3897 0.3896 0.29386 0.358501 0.391437 2 1407 24309 2527 1550 645 13118 173 4889 2 3774 54338 5076 3896 1336 28854 396 11006 0 . 0 . 0 35 0,0,17,16 UTR_5_PRIME(MODIFIER||14||504|PRPF19|protein_coding|CODING|NM_014502.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs17155470 -0.693127 0.0202388 35 P180 243 ccT/ccC LOW 4 SILENT CODING TMEM109 C protein_coding NM_024092.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60689445 T C 0 228 0 0.5756 0.7408 0.7363 0.9534 0.6103 0.8824 0.562869 0.608966 0.632589 2 5994 83818 9248 8325 4631 41089 594 13937 2 10402 121338 11574 8650 6604 66692 908 16508 0 . 0 . 0 126 0,0,34,79 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P180|243|TMEM109|protein_coding|CODING|NM_024092.2|4|C),UPSTREAM(MODIFIER||2468||1024|TMEM132A|protein_coding|CODING|NM_017870.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs555835 -0.693147 0.000112991 126 A168 1024 gcC/gcA LOW 3 SILENT CODING TMEM132A A protein_coding NM_017870.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60695301 C A 0 228 0 0.5272 0.7392 0.7608 0.9514 0.6451 0.8885 0.550705 0.62448 0.662313 2 5388 83770 9362 8249 4637 41489 596 14049 2 9700 117776 11486 8576 6484 64204 870 16456 0 . 0 . COSM429373,COSM1475612 52 0,0,4,45 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A168|1024|TMEM132A|protein_coding|CODING|NM_017870.3|3|A),DOWNSTREAM(MODIFIER||4386||243|TMEM109|protein_coding|CODING|NM_024092.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs575123 -0.693147 0.643141 52 L313 1024 ctG/ctA LOW 5 SILENT CODING TMEM132A A protein_coding NM_017870.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60698054 G A 0 228 0 0.0961 0.2961 0.3862 0.3204 0.3897 0.3814 0.150023 0.315826 0.400791 2 1484 44496 4950 2733 2601 25695 346 6687 2 10328 120970 11558 8584 6610 66520 906 16464 1 0 . 0 . 53 0,1,16,31 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L313|1024|TMEM132A|protein_coding|CODING|NM_017870.3|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2074416 -0.693147 0.172099 53 P494 1024 ccC/ccG LOW 8 SILENT CODING TMEM132A G protein_coding NM_017870.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60701136 C G 0 228 0 0.4713 0.4211 0.4452 0.3165 0.4225 0.4427 0.45672 0.432299 0.41978 2 3944 44784 4690 2445 1944 24090 321 7350 2 7970 99024 9634 7100 4282 54226 690 15122 0 . 0 . 0 40 0,0,23,10 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P494|1024|TMEM132A|protein_coding|CODING|NM_017870.3|8|G),DOWNSTREAM(MODIFIER||3419||581|SLC15A3|protein_coding|CODING|NM_016582.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9513 -0.693127 0.461444 40 S530 1024 tcG/tcA LOW 9 SILENT CODING TMEM132A A protein_coding NM_017870.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60701987 G A 0 201 0 0.4713 0.4215 0.4467 0.3165 0.4225 0.4438 0.38449 0.376456 0.372954 2 109 1593 94 62 16 588 14 710 2 176 2542 142 104 30 952 20 1118 0 . 0 . 0 9 0,0,5,3 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S530|1024|TMEM132A|protein_coding|CODING|NM_017870.3|9|A),DOWNSTREAM(MODIFIER||2568||581|SLC15A3|protein_coding|CODING|NM_016582.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.900802 0 . rs7715 -0.651104 0.360182 9 A970V 1024 gCg/gTg MODERATE 11 MISSENSE CODING TMEM132A T protein_coding NM_017870.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60704213 C T 0 228 0 0.4735 0.4219 0.4467 0.3165 0.4225 0.4427 0.466863 0.442864 0.430565 2 4706 49967 5180 2652 2559 26992 379 7499 2 9884 116082 11262 8426 6204 64098 848 15360 0.6 0 . 0 . 88 2,0,67,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A970V|1024|TMEM132A|protein_coding|CODING|NM_017870.3|11|T),DOWNSTREAM(MODIFIER||342||581|SLC15A3|protein_coding|CODING|NM_016582.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.7375 rs2469887 -0.693147 0.0359065 88 G493 581 ggT/ggC LOW 7 SILENT CODING SLC15A3 G protein_coding NM_016582.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60705454 A G 0 228 0 0.9781 0.9942 1 1 1 1 0.971176 0.990157 0.999884 2 10088 120501 11541 8642 6426 66422 892 16490 2 10340 120762 11548 8642 6426 66424 892 16490 1 0 . 0 . 105 1,0,64,28 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G493|581|SLC15A3|protein_coding|CODING|NM_016582.2|7|G),DOWNSTREAM(MODIFIER||823||1024|TMEM132A|protein_coding|CODING|NM_017870.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2905692 -0.693147 0.665251 105 A257V 668 gCg/gTg MODERATE 4 MISSENSE CODING CD6 T protein_coding NM_006725.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60776306 C T 0 222 0 0.6702 0.5363 0.4438 0.4067 0.6243 0.4642 0.549225 0.548449 0.548052 1 5353 53834 3907 3616 2312 34193 368 4085 2 8404 97928 10426 7956 5046 56906 640 8550 0.961498 0 . 0 . 33 8,5,10,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A257V|668|CD6|protein_coding|CODING|NM_006725.4|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.85466 rs2074225 -0.691153 0.116657 33 H461R 495 cAc/cGc MODERATE 9 MISSENSE CODING CD5 G protein_coding NM_014207.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60892606 A G 0 228 0 0.9947 0.9679 0.9524 0.997 0.9205 0.9611 0.983659 0.936635 0.912538 2 10224 113765 11168 8649 6157 61016 831 15720 2 10396 121290 11554 8650 6596 66678 906 16510 0 . 0 . 0 93 0,0,37,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H461R|495|CD5|protein_coding|CODING|NM_014207.3|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs637186 -0.693147 0.0421593 93 A471V 495 gCt/gTt MODERATE 10 MISSENSE CODING CD5 T protein_coding NM_014207.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60893235 C T 0 228 0 0.5083 0.6911 0.6628 0.9881 0.5517 0.7955 0.530413 0.512535 0.503373 2 5358 73783 8409 8591 4075 34685 517 12148 2 10378 120858 11540 8650 6588 66466 898 16338 0 . 0 . COSM1355182 60 0,0,27,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A471V|495|CD5|protein_coding|CODING|NM_014207.3|10|T),DOWNSTREAM(MODIFIER||4493||355|VPS37C|protein_coding|CODING|NM_017966.4||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2229177 -0.693147 0.163047 60 495 1181 MODIFIER 11 CODING CD5 T protein_coding NM_014207.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60894492 G T 0 9.7 0 0.9735 0.8724 0.7752 0.996 0.6561 0.8998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1181||495|CD5|protein_coding|CODING|NM_014207.3|11|T),DOWNSTREAM(MODIFIER||3236||355|VPS37C|protein_coding|CODING|NM_017966.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2186409,rs386481274 -0.379885 0 1 495 1495 MODIFIER 11 CODING CD5 C protein_coding NM_014207.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60894805 CGGCT C 0 32.2 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1495||495|CD5|protein_coding|CODING|NM_014207.3|11|C),DOWNSTREAM(MODIFIER||2922||355|VPS37C|protein_coding|CODING|NM_017966.4||C) 0 0.5 1 1 1 0 1 0 . 0 60 0 0 . 0 . rs202166881 -0.379885 0 1 355 1380 MODIFIER 5 CODING VPS37C G protein_coding NM_017966.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60897912 A G 0 228 0 0.888 0.8167 0.7017 0.994 0.5666 0.8763 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,50,3 UTR_3_PRIME(MODIFIER||1380||355|VPS37C|protein_coding|CODING|NM_017966.4|5|G),DOWNSTREAM(MODIFIER||2589||495|CD5|protein_coding|CODING|NM_014207.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7876 -0.693147 0.0158377 59 L198S 355 tTa/tCa MODERATE 5 MISSENSE CODING VPS37C G protein_coding NM_017966.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 60899767 A G 0 228 0 0.9183 0.8532 0.7767 0.9891 0.6889 0.8487 0.869091 0.728721 0.656854 2 8113 79450 8316 8180 3486 40283 487 10585 2 9270 105012 10384 8232 4610 58872 714 12930 0 . 0 . 0 31 0,0,11,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L198S|355|VPS37C|protein_coding|CODING|NM_017966.4|5|G),DOWNSTREAM(MODIFIER||4444||495|CD5|protein_coding|CODING|NM_014207.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs754382 -0.693097 0.158623 31 T157 575 acG/acC LOW 5 SILENT CODING TKFC C protein_coding NM_015533.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61106892 G C 0 228 0 0.3132 0.7676 0.9308 0.9702 0.9841 0.8344 0.437045 0.803695 0.991502 2 3884 108174 11182 8214 6476 63578 832 14008 2 9530 117336 11498 8560 6578 64102 878 16190 0 . 0 . 0 184 0,0,75,91 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T157|575|TKFC|protein_coding|CODING|NM_015533.3|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2513329 -0.693147 0.0050614 184 A185T 575 Gcc/Acc MODERATE 6 MISSENSE CODING TKFC A protein_coding NM_015533.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61108974 G A 0 228 0 0.3956 0.7907 0.9366 0.9712 0.9861 0.8344 0.512318 0.828742 0.991216 2 1559 24706 870 1226 366 13166 238 7281 2 3224 27616 910 1272 376 13306 250 8278 0 . 0 . 0 78 0,0,28,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A185T|575|TKFC|protein_coding|CODING|NM_015533.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2260655 -0.693147 0.165129 78 V437 575 gtC/gtT LOW 14 SILENT CODING TKFC T protein_coding NM_015533.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61112802 C T 0 228 0 0.3956 0.7907 0.938 0.9712 0.9861 0.8333 0.487517 0.820671 0.991393 2 4885 110864 11261 8311 6503 65517 847 13540 2 10302 119740 11556 8634 6602 66036 890 15720 0 . 0 . 0 102 0,0,62,32 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V437|575|TKFC|protein_coding|CODING|NM_015533.3|14|T),DOWNSTREAM(MODIFIER||3418||263|CYB561A3|protein_coding|CODING|NM_001300763.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2305465 -0.693147 0.0125331 102 575 641 MODIFIER 18 CODING TKFC C protein_coding NM_015533.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61114616 T C 0 9.7 0 0.4418 0.8069 0.9424 0.9722 0.9911 0.8446 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||641||575|TKFC|protein_coding|CODING|NM_015533.3|18|C),DOWNSTREAM(MODIFIER||1604||263|CYB561A3|protein_coding|CODING|NM_001300763.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3972757 -0.379885 0 1 263 684 MODIFIER 7 CODING CYB561A3 C protein_coding NM_001300763.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61116345 T C 0 73 0 0.9508 0.986 0.9942 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||684||263|CYB561A3|protein_coding|CODING|NM_001300763.1|7|C),DOWNSTREAM(MODIFIER||114||575|TKFC|protein_coding|CODING|NM_015533.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4939516 -0.511536 0.645206 3 P88 148 ccG/ccA LOW 4 SILENT CODING TMEM216 A protein_coding NM_001173991.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61165280 G A 0 228 0 0.7443 0.8558 0.879 0.9762 0.8678 0.8538 0.774038 0.832275 0.860966 2 7438 104584 10250 8333 5822 57723 797 14221 2 9820 120784 11576 8626 6614 66738 898 16512 0 3 likely-benign 0 . 117 0,0,59,44 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P88|148|TMEM216|protein_coding|CODING|NM_001173991.2|4|A),DOWNSTREAM(MODIFIER||4840||514|CPSF7|protein_coding|CODING|NM_024811.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3741265 -0.693147 0.142827 117 148 HIGH 4 CODING TMEM216 CA protein_coding NM_001173991.2 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61165731 C CA 0 228 0 0.7436 0.8558 0.879 0.9762 0.8688 0.8538 0.761551 0.827907 0.859277 2 7180 100404 9544 8116 5600 55385 773 13806 2 9514 116840 10936 8432 6414 64594 874 16076 0 2 benign 0 . 58 0,0,21,31 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||148|TMEM216|protein_coding|CODING|NM_001173991.2|4|CA),DOWNSTREAM(MODIFIER||4388||514|CPSF7|protein_coding|CODING|NM_024811.3||CA) 1 0 . 53 0.913793 1 1 1 1 (TMEM216|TMEM216|1|1.00) 60 0 0 1 0 . rs11382548 -0.693147 0.490849 58 R147T 148 aGg/aCg MODERATE 5 MISSENSE CODING TMEM216 C protein_coding NM_001173991.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61165741 G C 0 228 0 0.295 0.7196 0.8386 0.9712 0.8549 0.8108 0.391996 0.70388 0.85 2 3407 95665 9366 8154 5609 55028 759 13342 2 9432 117336 11004 8504 6452 64910 884 16150 0 2|2 benign|benign 0 COSM1582850 55 0,0,22,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aCg|R147T|148|TMEM216|protein_coding|CODING|NM_001173991.2|5|C),DOWNSTREAM(MODIFIER||4379||514|CPSF7|protein_coding|CODING|NM_024811.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10897158 -0.693147 0.398722 55 148 558 MODIFIER 5 CODING TMEM216 A protein_coding NM_001173991.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61166306 G A 0 228 0 0.295 0.7196 0.8386 0.9712 0.8549 0.8108 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,16,12 UTR_3_PRIME(MODIFIER||558||148|TMEM216|protein_coding|CODING|NM_001173991.2|5|A),DOWNSTREAM(MODIFIER||3814||514|CPSF7|protein_coding|CODING|NM_024811.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7607 -0.693054 0.999665 29 514 8023 MODIFIER 10 CODING CPSF7 A protein_coding NM_024811.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61170392 G A 0 228 0 0 0.013578 0 0.0645 0 0.0031 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,6,20 UTR_3_PRIME(MODIFIER||8023||514|CPSF7|protein_coding|CODING|NM_024811.3|10|A),DOWNSTREAM(MODIFIER||4057||148|TMEM216|protein_coding|CODING|NM_001173991.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs117565407 -0.692976 0.151109 26 I446 514 atC/atT LOW 8 SILENT CODING CPSF7 A protein_coding NM_024811.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61179285 G A 0 228 0 0.295 0.7196 0.8386 0.9712 0.8549 0.8108 0.373751 0.688279 0.849384 2 3762 99381 10001 8325 5796 57039 781 13677 2 10392 121360 11568 8652 6612 66716 908 16512 0 . 0 . 0 109 0,0,57,41 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I446|514|CPSF7|protein_coding|CODING|NM_024811.3|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3019198 -0.693147 0.167852 109 T34 425 acC/acA LOW 2 SILENT CODING PPP1R32 A protein_coding NM_145017.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61249383 C A 0 228 0 0.5008 0.7756 0.8458 0.9732 0.826 0.8415 0.534514 0.721504 0.817283 2 5501 98211 9995 8322 5316 54459 744 13874 2 10244 120664 11516 8610 6568 66368 898 16460 0 . 0 . 0 89 0,0,31,50 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T34|425|PPP1R32|protein_coding|CODING|NM_145017.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3019200 -0.693147 0.0366393 89 L187 292 ctC/ctT LOW 1 SILENT CODING LRRC10B T protein_coding NM_001145077.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61277031 C T 0 189 0 0.0068 0.1969 0.2637 0.4474 0.0636 0.2853 0 . 0 1 13 2115 31 64 6 187 19 1795 2 312 11112 130 152 24 2882 116 7496 0.555556 0 . 0 . 13 1,1,7,2 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L187|292|LRRC10B|protein_coding|CODING|NM_001145077.1|1|T),DOWNSTREAM(MODIFIER||4157||478|SYT7|protein_coding|CODING|NM_001252065.1||T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.444444 rs1139011 -0.662043 0.583058 13 292 349 MODIFIER 1 CODING LRRC10B G protein_coding NM_001145077.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61277698 A G 0 228 0 0.0741 0.2348 0.2795 0.4603 0.1083 0.318 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 68 1,0,35,28 UTR_3_PRIME(MODIFIER||349||292|LRRC10B|protein_coding|CODING|NM_001145077.1|1|G),DOWNSTREAM(MODIFIER||3490||478|SYT7|protein_coding|CODING|NM_001252065.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs11230728 -0.693147 0.330379 68 292 426 MODIFIER 1 CODING LRRC10B G protein_coding NM_001145077.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61277775 A G 0 228 0 0.0726 0.2346 0.2795 0.4603 0.1093 0.318 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.654762 0 . 0 . 86 1,1,69,15 UTR_3_PRIME(MODIFIER||426||292|LRRC10B|protein_coding|CODING|NM_001145077.1|1|G),DOWNSTREAM(MODIFIER||3413||478|SYT7|protein_coding|CODING|NM_001252065.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.47619 rs10897164 -0.693147 0.340481 86 292 536 MODIFIER 1 CODING LRRC10B A protein_coding NM_001145077.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61277885 G A 0 228 0 0.0719 0.2328 0.2795 0.4544 0.1074 0.318 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 168 1,0,68,76 UTR_3_PRIME(MODIFIER||536||292|LRRC10B|protein_coding|CODING|NM_001145077.1|1|A),DOWNSTREAM(MODIFIER||3303||478|SYT7|protein_coding|CODING|NM_001252065.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs10897165 -0.693147 0.000101774 168 292 897 MODIFIER 1 CODING LRRC10B C protein_coding NM_001145077.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61278246 T C 0 228 0 0.1929 0.271 0.2853 0.4623 0.1183 0.3262 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.587719 0 . 0 . 62 1,1,42,15 UTR_3_PRIME(MODIFIER||897||292|LRRC10B|protein_coding|CODING|NM_001145077.1|1|C),DOWNSTREAM(MODIFIER||2942||478|SYT7|protein_coding|CODING|NM_001252065.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.0789474 rs751984 -0.693147 0.422554 62 478 4726 MODIFIER 10 CODING SYT7 T protein_coding NM_001252065.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61281373 C T 0 9.7 0 0.1679 0.2792 0.3804 0.4623 0.161 0.2904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4726||478|SYT7|protein_coding|CODING|NM_001252065.1|10|T),DOWNSTREAM(MODIFIER||2883||292|LRRC10B|protein_coding|CODING|NM_001145077.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1057544 -0.379885 0 1 478 4336 MODIFIER 10 CODING SYT7 G protein_coding NM_001252065.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61281763 C G 0 39.3 0 0.3487 0.3233 0.3674 0.4554 0.164 0.2853 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||4336||478|SYT7|protein_coding|CODING|NM_001252065.1|10|G),DOWNSTREAM(MODIFIER||3273||292|LRRC10B|protein_coding|CODING|NM_001145077.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12808337 -0.453602 0.58 2 P21 1042 ccG/ccA LOW 2 SILENT CODING DAGLA A protein_coding NM_006133.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61487690 G A 0 222 0 0.2269 0.3001 0.3213 0.4643 0.2416 0.2751 0.225023 0.243809 0.253431 1 2246 32731 3501 3881 1656 16882 238 4327 2 10394 121262 11564 8624 6598 66664 908 16510 0.602532 0 . 0 COSM429407 63 15,19,9,13 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P21|1042|DAGLA|protein_coding|CODING|NM_006133.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997751 rs198430 -0.692562 0.663751 63 A508 1042 gcG/gcA LOW 15 SILENT CODING DAGLA A protein_coding NM_006133.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61505168 G A 0 228 0 0.3631 0.4914 0.4986 0.7986 0.4284 0.408 0.360127 0.411706 0.438125 2 3654 54992 5352 7013 3001 28713 436 6823 2 10404 121370 11572 8650 6612 66716 908 16508 0 . 0 . 0 79 0,0,31,38 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A508|1042|DAGLA|protein_coding|CODING|NM_006133.2|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs198444 -0.693147 0.415101 79 P889L 1042 cCg/cTg MODERATE 20 MISSENSE CODING DAGLA T protein_coding NM_006133.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61511498 C T 0 185 0 0.3086 0.1789 0.0504 0.2569 0.0954 0.1002 0.24349 0.126141 0.0660664 1 2513 12305 509 2467 951 4145 103 1617 2 9010 113574 11358 8278 6544 61168 830 16386 0.961136 0 . 0 . 52 19,7,22,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P889L|1042|DAGLA|protein_coding|CODING|NM_006133.2|20|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3741252 -0.692831 0.246985 52 1042 1711 MODIFIER 20 CODING DAGLA C protein_coding NM_006133.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61513671 CAGAG C 0 63 0 0.1944 0.3415 0.4395 0.5327 0.3131 0.3027 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 3,0,2,0 UTR_3_PRIME(MODIFIER||1711||1042|DAGLA|protein_coding|CODING|NM_006133.2|20|C) 0 0.5 1 3 0.5 1 1 0 . 0 60 0 0 . 0 . rs139937518 -0.453602 0.732182 6 1042 2124 MODIFIER 20 CODING DAGLA T protein_coding NM_006133.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61514085 C T 0 222 0 0.2163 0.4926 0.6427 0.5774 0.6521 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935502 0 . 0 . 84 15,29,11,24 UTR_3_PRIME(MODIFIER||2124||1042|DAGLA|protein_coding|CODING|NM_006133.2|20|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0194114 rs2852786 -0.693136 0.42742 84 S1051 1151 agT/agC LOW 24 SILENT CODING MYRF C protein_coding NM_001127392.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61551356 T C 0 222 0 0.1467 0.3401 0.6037 0.5694 0.3549 0.1626 0.202997 0.288725 0.332635 1 1725 39445 7366 4470 2342 20461 284 2797 2 7888 98478 10134 7978 4828 53494 742 13414 0.742127 0 . 0 COSM1355261 89 30,15,20,14 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1051|1151|MYRF|protein_coding|CODING|NM_001127392.2|24|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.753416 rs174535 -0.693132 0.0421193 89 79 51 MODIFIER 1 CODING TMEM258 A protein_coding NM_014206.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61560081 G A 0 222 0 0.0204 0.2821 0.572 0.5556 0.3131 0.1166 0.0812897 0.22335 0.296115 1 722 38047 7892 4638 2296 19830 281 2388 2 10304 120740 11550 8592 6602 66294 900 16498 0.659902 0 . 0 . 167 25,44,20,55 UTR_5_PRIME(MODIFIER||51||79|TMEM258|protein_coding|CODING|NM_014206.3|1|A),UPSTREAM(MODIFIER||28||380|FEN1|protein_coding|CODING|NM_004111.5||A),DOWNSTREAM(MODIFIER||4091||1151|MYRF|protein_coding|CODING|NM_001127392.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.52232 rs174538 -0.693147 0.00047431 167 380 323 MODIFIER 2 CODING FEN1 T protein_coding NM_004111.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61564299 G T 0 222 0 0.0219 0.3031 0.5908 0.5655 0.3698 0.1401 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.983204 0 . 0 . 227 61,50,47,48 UTR_3_PRIME(MODIFIER||323||380|FEN1|protein_coding|CODING|NM_004111.5|2|T),UPSTREAM(MODIFIER||4214||79|TMEM258|protein_coding|CODING|NM_014206.3||T),DOWNSTREAM(MODIFIER||2798||501|FADS1|protein_coding|CODING|NM_013402.4||T) 0 0.5 1 0 . 1 0 . 0 . 58 0 0.906479 0.663544 0 0.639914 rs4246215 -0.693147 0.0266113 227 501 2130 MODIFIER 12 CODING FADS1 A protein_coding NM_013402.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61567753 C A 0 28 0 0.0204 0.2804 0.5692 0.5476 0.3042 0.1268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,1,1 UTR_3_PRIME(MODIFIER||2130||501|FADS1|protein_coding|CODING|NM_013402.4|12|A),DOWNSTREAM(MODIFIER||3039||380|FEN1|protein_coding|CODING|NM_004111.5||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs174544 -0.453602 0.02 3 501 53 MODIFIER 12 CODING FADS1 T protein_coding NM_013402.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61569830 C T 0 222 0 0.0219 0.2975 0.5865 0.5665 0.3469 0.137 0.0816474 0.260841 0.338781 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.753102 0 . 0 . 66 24,2,23,5 UTR_3_PRIME(MODIFIER||53||501|FADS1|protein_coding|CODING|NM_013402.4|12|T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.435306 rs174546 -0.693054 0.0472162 66 445 75 MODIFIER 12 CODING FADS3 G protein_coding NM_021727.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61641211 A G 0 228 0 0.9584 0.9888 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,31,6 UTR_3_PRIME(MODIFIER||75||445|FADS3|protein_coding|CODING|NM_021727.4|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6591665 -0.693141 0.0678103 40 A18 445 gcG/gcA LOW 1 SILENT CODING FADS3 T protein_coding NM_021727.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61658800 C T 0 136 0 0.1067 0.4716 0.3631 0.6875 0.6829 0.6022 0.411883 0.646471 0.756082 2 81 7124 80 188 22 2344 72 4337 2 298 11294 150 262 26 3236 118 7204 0 . 0 . 0 6 0,0,2,4 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A18|445|FADS3|protein_coding|CODING|NM_021727.4|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs174465 -0.616816 0.0347691 6 382 758 MODIFIER 10 CODING RAB3IL1 C protein_coding NM_013401.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61664992 T C 0 157 0 0.4758 0.632 0.6412 0.8581 0.5189 0.7198 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,0,12 UTR_3_PRIME(MODIFIER||758||382|RAB3IL1|protein_coding|CODING|NM_013401.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13966 -0.680642 0.290783 12 382 628 MODIFIER 10 CODING RAB3IL1 G protein_coding NM_013401.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61665122 A G 0 61 0 0.4365 0.623 0.6427 0.8562 0.5169 0.7301 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||628||382|RAB3IL1|protein_coding|CODING|NM_013401.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2235093 -0.511536 0.116687 3 604 5000 MODIFIER 1 CODING BEST1 T protein_coding NM_001139443.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61717607 C T 0 74 0 0.1657 0.349 0.304 0.6567 0.0934 0.5746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.952347 0 . 0 . 10 5,0,5,0 UTR_5_PRIME(MODIFIER||5000||604|BEST1|protein_coding|CODING|NM_001139443.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 0 . 0.857112 rs972354 -0.590765 0.784982 10 604 4892 MODIFIER 1 CODING BEST1 C protein_coding NM_001139443.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61717715 T C 0 222 0 0.7943 0.6793 0.5893 0.8978 0.3052 0.7474 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810878 0 . 0 . 67 18,2,37,5 UTR_5_PRIME(MODIFIER||4892||604|BEST1|protein_coding|CODING|NM_001139443.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.95347 rs972353 -0.693146 0.0738762 67 I13 604 atC/atA LOW 2 SILENT CODING BEST1 A protein_coding NM_001139443.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61722645 C A 0 222 0 0.0825 0.3175 0.2839 0.6498 0.0726 0.5685 0.0831063 0.0765267 0.0731566 1 879 24527 3735 5862 443 4951 143 8514 2 10388 121200 11558 8628 6606 66608 906 16506 0.737241 1|2 not-provided|benign 0 . 54 11,16,7,12 SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I13|604|BEST1|protein_coding|CODING|NM_001139443.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989541 rs1109748 -0.69168 0.0700704 54 T476 604 acT/acC LOW 9 SILENT CODING BEST1 C protein_coding NM_001139443.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61730234 T C 0 228 0 0.5348 0.5915 0.4899 0.8552 0.3539 0.7127 0.491826 0.399323 0.351942 2 5220 55621 5940 7412 2493 22925 379 11252 2 10404 121352 11556 8646 6612 66718 906 16510 0 1|2 not-provided|benign 0 . 194 0,0,132,47 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T476|604|BEST1|protein_coding|CODING|NM_001139443.1|9|C),DOWNSTREAM(MODIFIER||1523||183|FTH1|protein_coding|CODING|NM_002032.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1800009 -0.693147 0.0180563 194 183 222 MODIFIER 4 CODING FTH1 A protein_coding NM_002032.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61731977 G A 0 124 0 0.0053 0.1432 0.1009 0.2272 0.0398 0.3793 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.758384 0 . 0 . 49 27,0,22,0 UTR_3_PRIME(MODIFIER||222||183|FTH1|protein_coding|CODING|NM_002032.2|4|A),DOWNSTREAM(MODIFIER||911||604|BEST1|protein_coding|CODING|NM_001139443.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.929667 rs17156609 -0.692562 0.213403 49 E36 918 gaA/gaG LOW 2 SILENT CODING INCENP G protein_coding NM_001040694.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61895741 A G 0 222 0 0.329 0.3514 0.3818 0.131 0.6859 0.2434 0.367847 0.578911 0.68702 1 3775 62919 3247 914 4036 45581 517 4849 2 10398 121214 11546 8630 6570 66658 906 16506 0.983921 0 . 0 . 89 12,34,13,21 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E36|918|INCENP|protein_coding|CODING|NM_001040694.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.525814 rs1675131 -0.693132 0.453106 89 R697Q 918 cGg/cAg MODERATE 15 MISSENSE CODING INCENP A protein_coding NM_001040694.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 61914260 G A 0 225 0 0.0068 0.1877 0.0893 0.495 0.0974 0.2781 0.0174322 0.0551899 0.0746226 2 32 2454 24 163 1 479 20 1735 2 990 13992 228 302 6 4720 144 7602 0.636851 0 . 0 . 43 2,1,18,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R697Q|918|INCENP|protein_coding|CODING|NM_001040694.1|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.259232 rs116873148 -0.693141 0.0216558 43 P53L 90 cCg/cTg MODERATE 2 MISSENSE CODING SCGB1D2 T protein_coding NM_006551.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62010863 C T 0 222 0 0.2322 0.471 0.4251 0.7927 0.337 0.6329 0.235922 0.296262 0.327169 1 2379 50756 6400 6884 2688 22323 372 9710 2 10406 121384 11572 8646 6614 66730 908 16508 0.531656 0 . 0 . 206 53,47,46,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P53L|90|SCGB1D2|protein_coding|CODING|NM_006551.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.485635 rs2232950 -0.693147 0.110867 206 308 513 MODIFIER 1 CODING ASRGL1 G protein_coding NM_001083926.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62104937 T G 0 70 0 0.6967 0.8688 0.8905 0.9901 0.8827 0.9468 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_5_PRIME(MODIFIER||513||308|ASRGL1|protein_coding|CODING|NM_001083926.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2246920,rs386562428 -0.453602 0.06 3 308 59 MODIFIER 2 CODING ASRGL1 T protein_coding NM_001083926.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62105391 C T 0 228 0 0.6959 0.8686 0.889 0.9901 0.8837 0.9468 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 68 1,0,57,4 UTR_5_PRIME(MODIFIER||59||308|ASRGL1|protein_coding|CODING|NM_001083926.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2513749 -0.693147 0.050746 68 308 210 MODIFIER 7 CODING ASRGL1 T protein_coding NM_001083926.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62159966 A T 0 80 0 0.7239 0.7504 0.7233 0.627 0.8091 0.8722 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||210||308|ASRGL1|protein_coding|CODING|NM_001083926.1|7|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs15810 -0.556411 0.106137 4 L4414V 5890 Ctc/Gtc MODERATE 5 MISSENSE CODING AHNAK C protein_coding NM_001620.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62288649 G C 0 222 0 0 0.0327 0.0014 0.1597 0.001 0.001 0.000681199 0.0013844 0.00174459 1 7 1488 11 1327 14 71 8 50 2 10358 121308 11578 8648 6614 66694 908 16508 0.433628 0 . 0 . 156 52,19,50,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L4414V|5890|AHNAK|protein_coding|CODING|NM_001620.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.920825 rs77865984 -0.693147 0.0231608 156 Q3003K 5890 Caa/Aaa MODERATE 5 MISSENSE CODING AHNAK T protein_coding NM_001620.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62292882 G T 0 228 0 1 1 1 1 1 1 0 . 0 2 10402 121406 11578 8654 6614 66738 908 16512 2 10402 121406 11578 8654 6614 66738 908 16512 0 . 0 . 0 169 0,0,82,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q3003K|5890|AHNAK|protein_coding|CODING|NM_001620.2|5|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs566144 -0.693147 0.24116 169 L86 5890 ctG/ctA LOW 4 SILENT CODING AHNAK T protein_coding NM_001620.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62302559 C T 0 222 0 0 0.0065895 0.0029 0.0308 0 0 0 . 0 1 0 192 2 188 0 1 0 1 2 10284 120384 11534 8610 6478 66078 892 16508 0.98017 0 . 0 . 98 31,21,24,14 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L86|5890|AHNAK|protein_coding|CODING|NM_001620.2|4|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.694627 rs79854453 -0.693143 0.399465 98 351 22 MODIFIER 1 CODING ROM1 C protein_coding NM_000327.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62380732 T C 0 228 0 0.7784 0.9369 0.9755 1 0.995 0.999 0.826967 0.940022 0.997905 2 4624 61027 4678 4107 2254 33913 470 10981 2 5720 62252 4728 4108 2254 33976 476 10990 0 . 0 . 0 32 0,0,23,7 UTR_5_PRIME(MODIFIER||22||351|ROM1|protein_coding|CODING|NM_000327.3|1|C),UPSTREAM(MODIFIER||495||918|EML3|protein_coding|CODING|NM_001300793.1||C),DOWNSTREAM(MODIFIER||2036||335|B3GAT3|protein_coding|CODING|NM_012200.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386505813,rs4387351 -0.693097 0.552653 32 G118A 351 gGc/gCc MODERATE 1 MISSENSE CODING ROM1 C protein_coding NM_000327.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62381106 G C 0 228 0 0.7723 0.9353 0.9755 1 0.995 0.999 0.822434 0.938471 0.997907 2 8187 117513 11409 8575 6456 65524 880 16482 2 10084 119642 11498 8576 6456 65642 888 16498 0 2 benign 0 . 82 0,0,42,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G118A|351|ROM1|protein_coding|CODING|NM_000327.3|1|C),UPSTREAM(MODIFIER||869||918|EML3|protein_coding|CODING|NM_001300793.1||C),DOWNSTREAM(MODIFIER||1662||335|B3GAT3|protein_coding|CODING|NM_012200.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1799959 -0.693147 0.179238 82 335 199 MODIFIER 1 CODING B3GAT3 T protein_coding NM_012200.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62389618 C T 0 91 0 0.8003 0.9435 0.9813 1 0.995 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,0,5 UTR_5_PRIME(MODIFIER||199||335|B3GAT3|protein_coding|CODING|NM_012200.3|1|T),DOWNSTREAM(MODIFIER||2680||966|GANAB|protein_coding|CODING|NM_198335.3||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4343028 -0.590765 0.316324 5 G89S 93 Ggc/Agc MODERATE 2 MISSENSE CODING UQCC3 A protein_coding NM_001085372.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62439569 G A 0 228 0 0.584 0.7494 0.7522 0.9385 0.7296 0.7965 0.627719 0.679591 0.705979 2 3530 53732 4216 4943 2089 28261 418 10275 2 5536 70834 5190 5324 2572 38880 528 12804 0 . 0 . COSM429461 74 0,0,35,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G89S|93|UQCC3|protein_coding|CODING|NM_001085372.2|2|A),UPSTREAM(MODIFIER||328||263|LBHD1|protein_coding|CODING|NM_024099.3||A),DOWNSTREAM(MODIFIER||4646||240|METTL12|protein_coding|CODING|NM_001043229.1||A),DOWNSTREAM(MODIFIER||4401||312|UBXN1|protein_coding|CODING|NM_015853.4||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs13941 -0.693147 0.0384924 74 238 1312 MODIFIER 2 CODING LRRN4CL A protein_coding NM_203422.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62453952 G A 0 9.7 0 0.6868 0.7586 0.8199 0.7619 0.7893 0.7771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1312||238|LRRN4CL|protein_coding|CODING|NM_203422.3|2|A),DOWNSTREAM(MODIFIER||3782||462|BSCL2|protein_coding|CODING|NM_001122955.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2512561 -0.379885 0 1 75 515 MODIFIER 1 CODING GNG3 C protein_coding NM_012202.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62475253 G C 0 9.7 0 0.8986 0.9708 0.9856 1 0.998 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||515||75|GNG3|protein_coding|CODING|NM_012202.4|1|C),UPSTREAM(MODIFIER||74||462|BSCL2|protein_coding|CODING|NM_001122955.3||C),DOWNSTREAM(MODIFIER||4844||747|HNRNPUL2|protein_coding|CODING|NM_001079559.2||C),INTRAGENIC(MODIFIER|||||BSCL2||CODING|||C),INTRAGENIC(MODIFIER|||||HNRNPUL2-BSCL2||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs560618 -0.379885 0 1 L67 171 Ttg/Ctg LOW 1 SILENT CODING TTC9C C protein_coding NM_173810.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62496519 T C 0 222 0 0.4947 0.2927 0.2061 0.2391 0.2127 0.2188 0.455722 0.316182 0.244708 1 4865 29157 1834 1990 1004 15966 177 3321 2 10402 121300 11564 8620 6610 66688 908 16508 0.951431 0 . 0 . 165 48,32,45,31 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L67|171|TTC9C|protein_coding|CODING|NM_173810.3|1|C),UPSTREAM(MODIFIER||1662||747|HNRNPUL2|protein_coding|CODING|NM_001079559.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.911385 rs584845 -0.693147 0.11213 165 I574M 574 atC/atG MODERATE 2 MISSENSE CODING ZBTB3 C protein_coding NM_024784.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62519565 G C 0 222 0 0.2504 0.1128 0.0303 0.1518 0.0189 0.0419 0.206403 0.08491 0.0226797 1 2238 5780 184 1246 135 1405 39 533 2 10304 114478 11494 8576 6608 64826 836 11834 0.821265 0 . 0 . 81 20,10,33,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I574M|574|ZBTB3|protein_coding|CODING|NM_024784.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.63542 rs544641 -0.693146 0.0452599 81 T28A 202 Acg/Gcg MODERATE 1 MISSENSE CODING TMEM223 C protein_coding NM_001080501.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62559385 T C 0 159 0 0.2405 0.1348 0.0634 0.1558 0.0457 0.1125 0.176531 0.0932384 0.0538814 1 1378 6910 225 1021 218 2763 46 1259 2 5014 55820 3380 4520 1454 30474 396 10582 0.871097 0 . 0 . 67 4,30,1,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T28A|202|TMEM223|protein_coding|CODING|NM_001080501.2|1|C),DOWNSTREAM(MODIFIER||4572||622|TAF6L|protein_coding|CODING|NM_006473.3||C),DOWNSTREAM(MODIFIER||1513||219|TMEM179B|protein_coding|CODING|NM_199337.2||C),DOWNSTREAM(MODIFIER||213||619|NXF1|protein_coding|CODING|NM_006362.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.868078 rs2584918 -0.69311 0.670515 67 R403 619 cgA/cgG LOW 14 SILENT CODING NXF1 C protein_coding NM_006362.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62564009 T C 0 228 0 0.5348 0.5082 0.4179 0.5496 0.6233 0.3753 0.550204 0.609 0.639102 2 5742 66823 3773 4612 3768 42148 496 6284 2 10402 121350 11566 8634 6610 66724 906 16508 0 . 0 . 0 64 0,0,11,47 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R403|619|NXF1|protein_coding|CODING|NM_006362.4|14|C),UPSTREAM(MODIFIER||4523||202|TMEM223|protein_coding|CODING|NM_001080501.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386594698,rs4693 -0.693147 0.000588517 64 S328 355 tcT/tcA LOW 11 SILENT CODING STX5 T protein_coding NM_003164.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62575025 A T 0 222 0 0.1634 0.109 0.0548 0.1558 0.0437 0.093 0.141754 0.0860769 0.0575715 1 1499 8822 296 1330 468 3777 65 1387 2 10230 120108 11348 8584 6570 66138 900 16338 0.979212 0 . 0 . 94 29,20,19,18 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S328|355|STX5|protein_coding|CODING|NM_003164.4|11|T),UPSTREAM(MODIFIER||2061||619|NXF1|protein_coding|CODING|NM_006362.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989067 rs2228626 -0.693141 0.144073 94 R158 355 agA/agG LOW 6 SILENT CODING STX5 C protein_coding NM_003164.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62592961 T C 0 215 0 0.1641 0.1132 0.0548 0.1558 0.0447 0.1125 0.142208 0.0862308 0.0575715 1 1510 9086 301 1337 469 3790 66 1613 2 10334 121088 11556 8626 6614 66566 906 16486 0.740233 0 . 0 . 37 1,17,3,14 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R158|355|STX5|protein_coding|CODING|NM_003164.4|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.235845 rs2228627 -0.690438 0.0401878 37 L180 385 Ttg/Ctg LOW 7 SILENT CODING WDR74 G protein_coding NM_018093.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62602983 A G 0 222 0 0.1634 0.1124 0.0548 0.1558 0.0437 0.1104 0.131247 0.0801887 0.0559155 1 1426 8951 301 1329 469 3792 64 1570 2 9798 120696 11568 8608 6612 66702 896 16512 0.967526 0 . 0 . 90 26,20,19,17 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L180|385|WDR74|protein_coding|CODING|NM_018093.3|7|G),UPSTREAM(MODIFIER||3420||355|STX5|protein_coding|CODING|NM_003164.4||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995644 rs2298636 -0.693139 0.609769 90 385 26 MODIFIER 2 CODING WDR74 G protein_coding NM_018093.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62607068 A G 0 222 0 0.1634 0.1124 0.0548 0.1558 0.0437 0.1104 0.133487 0.0821928 0.0561547 1 1415 8698 298 1322 469 3698 61 1435 2 9626 116104 11516 8548 6602 65050 854 13908 0.775572 0 . 0 . 85 7,35,3,35 UTR_5_PRIME(MODIFIER||26||385|WDR74|protein_coding|CODING|NM_018093.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.960414 rs7102434 -0.693143 0.0398706 85 385 526 MODIFIER 1 CODING WDR74 C protein_coding NM_018093.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62607568 G C 0 9.7 0 0.1634 0.1124 0.0548 0.1558 0.0437 0.1104 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||526||385|WDR74|protein_coding|CODING|NM_018093.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10897296 -0.379885 0 1 563 20 MODIFIER 1 CODING SLC22A6 C protein_coding NM_004790.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62752182 T C 0 222 0 0.3646 0.2284 0.1484 0.2351 0.1481 0.1769 0.312843 0.206414 0.152032 1 2917 20273 1851 2031 1005 9598 157 2714 2 8418 101960 10146 7492 5110 56734 746 13314 0.999864 0 . 0 . 111 15,37,8,43 UTR_5_PRIME(MODIFIER||20||563|SLC22A6|protein_coding|CODING|NM_004790.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.684514 rs4149171 -0.693147 0.0133542 111 563 127 MODIFIER 1 CODING SLC22A6 T protein_coding NM_004790.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62752289 C T 0 189 0 0.3744 0.2101 0.121 0.2312 0.0815 0.1616 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.7675 0 . 0 . 31 0,16,2,12 UTR_5_PRIME(MODIFIER||127||563|SLC22A6|protein_coding|CODING|NM_004790.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.844209 rs4149170 -0.686358 0.0376046 31 I540V 552 Ata/Gta MODERATE 10 MISSENSE CODING SLC22A24 C protein_coding NM_001136506.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62847453 T C 0 222 0 0.5794 0.7542 0.8357 0.8234 0.7922 0.8221 0.620665 0.747043 0.802011 1 1319 15340 348 512 32 6664 151 6314 2 2148 19816 410 622 34 8498 190 7914 0.634421 0 . 0 . 77 9,23,10,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I540V|552|SLC22A24|protein_coding|CODING|NM_001136506.2|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994971 rs7945121 -0.693136 0.0749122 77 L515 552 ctT/ctC LOW 9 SILENT CODING SLC22A24 G protein_coding NM_001136506.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62848445 A G 0 222 0 0.3442 0.4437 0.4914 0.4196 0.5109 0.5 0.354769 0.478099 0.531741 1 926 11652 283 324 88 5964 119 3948 2 2456 23134 538 732 154 11078 228 7948 0.07604 0 . 0 COSM467168 184 69,26,34,36 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L515|552|SLC22A24|protein_coding|CODING|NM_001136506.2|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.819285 rs11231340 -0.693147 0.00942692 184 Y501* 552 taT/taG HIGH 9 NONSENSE CODING SLC22A24 C protein_coding NM_001136506.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62848487 A C 0 222 0 0.5794 0.754 0.8343 0.8234 0.7922 0.8221 0.620665 0.746605 0.801383 1 1396 16299 384 549 80 7403 162 6325 2 2282 21066 450 668 88 9450 202 7926 0.590414 0 . 0 . 189 65,30,27,51 STOP_GAINED(HIGH|NONSENSE|taT/taG|Y501*|552|SLC22A24|protein_coding|CODING|NM_001136506.2|9|C) 1 0.5 1 0 . 1 0 1 1 (SLC22A24|SLC22A24|1|1.00) 60 0 1 1 (SLC22A24|SLC22A24|1|1.00) 0.999833 rs11231341 -0.693147 0.224879 189 V474 552 gtG/gtC LOW 9 SILENT CODING SLC22A24 G protein_coding NM_001136506.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62848568 C G 0 222 0 0.3442 0.4437 0.4914 0.4196 0.5109 0.5 0.354769 0.478099 0.531741 1 789 9828 217 274 16 4505 95 3932 2 2170 19996 428 640 36 8618 190 7914 0.824304 0 . 0 . 173 28,64,22,37 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V474|552|SLC22A24|protein_coding|CODING|NM_001136506.2|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.909819 rs11231342 -0.693147 0.09131 173 Q409* 552 Cag/Tag HIGH 7 NONSENSE CODING SLC22A24 A protein_coding NM_001136506.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62850775 G A 0 222 0 0 0.0313 0.0274 0.0903 0.0229 0.0245 0.00433526 0.0157687 0.0207417 1 6 541 9 42 1 262 8 213 2 2550 23766 548 888 134 11450 214 7982 0.993435 0 . 0 . 138 34,26,33,22 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q409*|552|SLC22A24|protein_coding|CODING|NM_001136506.2|7|A) 1 0.5 1 0 . 1 0 1 1 (SLC22A24|SLC22A24|1|1.00) 60 0 1 1 (SLC22A24|SLC22A24|1|1.00) 0.303013 rs77002186 -0.693147 0.128918 138 S339P 552 Tcc/Ccc MODERATE 6 MISSENSE CODING SLC22A24 G protein_coding NM_001136506.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62863518 A G 0 228 0 0.4319 0.4868 0.5014 0.504 0.5109 0.5082 0.419075 0.49562 0.528913 2 927 10010 204 309 15 4445 96 4014 2 2144 19800 410 622 34 8490 190 7910 0.97973 0 . 0 . 173 1,1,86,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S339P|552|SLC22A24|protein_coding|CODING|NM_001136506.2|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.557432 rs7113279 -0.693147 0.0220882 173 L157 552 ctT/ctG LOW 2 SILENT CODING SLC22A24 C protein_coding NM_001136506.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62902172 A C 0 228 0 0.9713 0.9918 0.9957 1 1 1 0.978324 0.99343 1 2 3299 34680 1339 1624 2252 17414 344 8408 2 3358 34740 1340 1624 2252 17414 344 8408 0 . 0 . 0 126 0,0,63,47 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L157|552|SLC22A24|protein_coding|CODING|NM_001136506.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1939782 -0.693147 0.000297282 126 552 HIGH 1 CODING SLC22A24 C protein_coding NM_001136506.2 SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62910849 T C 0 228 0 0.4766 0.754 0.8559 0.8899 0.825 0.8436 0.518786 0.734341 0.828096 2 5208 90285 10185 7663 5801 53340 676 7412 2 9212 107470 11242 8344 6564 62522 780 8806 0 . 0 . 0 94 0,0,57,29 SPLICE_SITE_DONOR+INTRON(HIGH||||552|SLC22A24|protein_coding|CODING|NM_001136506.2|1|C) 1 0 . 0 . 1 0 1 1 (SLC22A24|SLC22A24|1|1.00) 60 0 0 1 0 . rs1939749 -0.693147 0.663337 94 T58S 552 aCt/aGt MODERATE 1 MISSENSE CODING SLC22A24 C protein_coding NM_001136506.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62911079 G C 0 228 0 0.4766 0.754 0.8559 0.8899 0.825 0.8436 0.518064 0.734122 0.828096 2 5406 96338 10277 7771 5799 55051 727 11307 2 9998 115966 11408 8482 6572 65102 852 13552 0 . 0 . 0 108 0,0,47,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T58S|552|SLC22A24|protein_coding|CODING|NM_001136506.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1939748 -0.693147 0.461381 108 M486V 547 Atg/Gtg MODERATE 9 MISSENSE CODING SLC22A25 C protein_coding NM_199352.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62931484 T C 0 228 0 0.6377 0.5431 0.5 0.5337 0.4473 0.5542 0.621536 0.499154 0.436482 2 6420 58309 5710 4989 2416 29330 378 9066 2 10402 121202 11544 8634 6614 66678 906 16424 1 0 . 0 . 88 0,1,27,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M486V|547|SLC22A25|protein_coding|CODING|NM_199352.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6591771 -0.693147 0.293049 88 R300T 547 aGa/aCa MODERATE 5 MISSENSE CODING SLC22A25 G protein_coding NM_199352.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62951221 C G 0 228 0 0.2617 0.4203 0.4438 0.5317 0.3946 0.5297 0.296683 0.349723 0.376891 2 2942 49316 5287 4959 2175 25090 335 8528 2 10406 121284 11502 8632 6610 66714 908 16512 0 . 0 . 0 246 0,0,108,107 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R300T|547|SLC22A25|protein_coding|CODING|NM_199352.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11231397 -0.693147 0.40673 246 S250G 547 Agc/Ggc MODERATE 4 MISSENSE CODING SLC22A25 C protein_coding NM_199352.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 62984868 T C 0 228 0 0.2859 0.4283 0.451 0.5288 0.3966 0.5337 0.31781 0.358363 0.37913 2 3143 49597 5277 4935 2179 25165 342 8556 2 10402 120994 11408 8566 6596 66610 906 16506 0 . 0 . 0 83 0,0,50,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S250G|547|SLC22A25|protein_coding|CODING|NM_199352.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11231409 -0.693147 0.110014 83 S31G 279 Agt/Ggt MODERATE 1 MISSENSE CODING HRASLS5 C protein_coding NM_054108.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63258416 T C 0 228 0 0.9448 0.9842 0.9914 1 1 1 0.954028 0.983978 0.999301 2 7811 101475 9627 7580 4170 56865 718 14704 2 8198 101892 9646 7580 4170 56876 718 14704 0 . 0 . 0 117 0,0,30,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S31G|279|HRASLS5|protein_coding|CODING|NM_054108.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10897424 -0.693147 0.000440365 117 V137 164 gtT/gtC LOW 4 SILENT CODING RARRES3 C protein_coding NM_004585.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63313644 T C 0 228 0 1 1 1 1 1 1 0.999756 0.99992 1 2 9809 120774 11573 8626 6614 66740 900 16512 2 9810 120778 11576 8626 6614 66740 900 16512 0 . 0 . 0 143 0,0,62,59 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V137|164|RARRES3|protein_coding|CODING|NM_004585.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs584905 -0.693147 0.0207494 143 162 391 MODIFIER 1 CODING PLA2G16 T protein_coding NM_001128203.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63381877 G T 0 54 0 0.2655 0.3822 0.4813 0.5694 0.3201 0.3405 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||391||162|PLA2G16|protein_coding|CODING|NM_001128203.1|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3809073 -0.511536 0.421281 3 V471A 1032 gTt/gCt MODERATE 3 MISSENSE CODING RTN3 C protein_coding NM_001265589.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63487386 T C 0 228 0 0.4221 0.737 0.879 0.9921 0.8082 0.726 0.479782 0.692645 0.801652 2 4826 96343 10514 8555 5897 53819 736 11996 2 10402 121404 11578 8654 6614 66738 908 16510 0 . 0 . 0 57 0,0,35,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V471A|1032|RTN3|protein_coding|CODING|NM_001265589.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs542998 -0.693147 0.819151 57 R192 381 Cgg/Agg LOW 3 SILENT CODING C11orf84 A protein_coding NM_138471.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63585804 C A 0 228 0 0.0734 0.3926 0.6354 0.6944 0.4225 0.3098 0.138346 0.355208 0.466263 2 1300 54219 8289 5995 2905 29885 396 5449 2 10272 121056 11572 8634 6604 66574 906 16494 0 . 0 . 0 88 0,0,34,47 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R192|381|C11orf84|protein_coding|CODING|NM_138471.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386602740,rs643634 -0.693147 0.77269 88 381 461 MODIFIER 6 CODING C11orf84 A protein_coding NM_138471.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63595072 C A 0 228 0 0.0741 0.4131 0.6628 0.6954 0.4891 0.3252 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 70 0,0,31,23 UTR_3_PRIME(MODIFIER||461||381|C11orf84|protein_coding|CODING|NM_138471.2|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8995 -0.693147 0.263417 70 788 187 MODIFIER 19 CODING MARK2 C protein_coding NM_001039469.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63676896 A C 0 228 0 0.8321 0.9533 0.9827 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,35,17 UTR_3_PRIME(MODIFIER||187||788|MARK2|protein_coding|CODING|NM_001039469.2|19|C),DOWNSTREAM(MODIFIER||1797||523|RCOR2|protein_coding|CODING|NM_173587.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs182664 -0.693147 0.305432 52 788 1223 MODIFIER 19 CODING MARK2 T protein_coding NM_001039469.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63677932 C T 0 6.3 0 0.1982 0.5282 0.7147 0.8829 0.5398 0.4642 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1223||788|MARK2|protein_coding|CODING|NM_001039469.2|19|T),DOWNSTREAM(MODIFIER||761||523|RCOR2|protein_coding|CODING|NM_173587.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10736731,rs386431087 -0.379885 0 1 T514A 523 Acc/Gcc MODERATE 12 MISSENSE CODING RCOR2 C protein_coding NM_173587.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63679369 T C 0 89 0 0.8064 0.9463 0.9813 1 1 1 0 . 0 2 282 9497 97 202 2 2969 108 5837 2 334 9556 98 202 2 2972 108 5840 0 . 0 . 0 5 0,0,0,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T514A|523|RCOR2|protein_coding|CODING|NM_173587.3|12|C),DOWNSTREAM(MODIFIER||877||788|MARK2|protein_coding|CODING|NM_001039469.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs320108 -0.590765 0.713234 5 E268 523 gaA/gaG LOW 8 SILENT CODING RCOR2 C protein_coding NM_173587.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63681513 T C 0 228 0 0.9168 0.9764 0.9885 1 1 1 0.928896 0.975685 0.999651 2 9646 120524 11537 8652 6614 66665 902 16508 2 10402 121356 11576 8652 6614 66694 906 16512 0 . 0 . 0 90 0,0,59,24 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E268|523|RCOR2|protein_coding|CODING|NM_173587.3|8|C),DOWNSTREAM(MODIFIER||3021||788|MARK2|protein_coding|CODING|NM_001039469.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10897461 -0.693147 0.161559 90 523 LOW 7 CODING RCOR2 A protein_coding NM_173587.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63681648 G A 0 228 0 0.1944 0.5284 0.7161 0.8829 0.5427 0.4663 0.259882 0.450062 0.547475 2 2611 67952 9275 7685 3704 36601 472 7604 2 10348 121000 11558 8646 6582 66464 902 16500 0 . 0 . 0 110 0,0,50,47 SPLICE_SITE_REGION+INTRON(LOW||||523|RCOR2|protein_coding|CODING|NM_173587.3|7|A),DOWNSTREAM(MODIFIER||3156||788|MARK2|protein_coding|CODING|NM_001039469.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4980533 -0.693147 0.150758 110 237 1994 MODIFIER 8 CODING NAA40 G protein_coding NM_024771.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63723945 A G 0 218 0 0.9539 0.9868 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,16,2 UTR_3_PRIME(MODIFIER||1994||237|NAA40|protein_coding|CODING|NM_024771.3|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs320127 -0.691153 0.167824 18 237 2349 MODIFIER 8 CODING NAA40 T protein_coding NM_024771.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63724300 C T 0 112 0 0.9539 0.9868 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,0,6 UTR_3_PRIME(MODIFIER||2349||237|NAA40|protein_coding|CODING|NM_024771.3|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs320126 -0.616816 0.0769344 6 674 12207 MODIFIER 1 CODING FLRT1 T protein_coding NM_013280.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63871533 G T 0 9.7 0 0.2224 0.4696 0.4078 0.5913 0.6342 0.5532 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||12207||674|FLRT1|protein_coding|CODING|NM_013280.4|1|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs687581 -0.379885 0 1 D82 674 gaT/gaC LOW 2 SILENT CODING FLRT1 C protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63883985 T C 0 222 0 0.2035 0.5258 0.6686 0.4167 0.8519 0.637 0.315993 0.675746 0.860019 1 3097 88143 6848 3625 5579 56981 702 11311 2 10366 121194 11540 8598 6608 66680 904 16498 0.283323 0 . 0 . 145 42,35,33,23 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D82|674|FLRT1|protein_coding|CODING|NM_013280.4|2|C),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.735502 rs614397 -0.693147 0.148348 145 A96 674 gcC/gcT LOW 2 SILENT CODING FLRT1 T protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63884027 C T 0 222 0 0.1475 0.4062 0.5519 0.3254 0.6968 0.4366 0.231259 0.53024 0.683384 1 2320 70233 5714 2805 4731 45823 563 8277 2 10352 121062 11536 8592 6588 66586 906 16502 0.478056 0 . 0 . 158 39,44,26,34 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A96|674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.164438 rs614035 -0.693147 0.0221901 158 R238 674 cgC/cgT LOW 2 SILENT CODING FLRT1 T protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63884453 C T 0 222 0 0.6014 0.353 0.1873 0.5377 0.0865 0.2188 0.497728 0.21599 0.0716779 1 5223 21415 2558 4538 667 5174 129 3126 2 9972 115788 11176 8424 5868 63266 844 16238 0.866392 0 . 0 . 273 73,62,58,52 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R238|674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.268304 rs3751120 -0.693147 0.00755196 273 S245 674 agC/agT LOW 2 SILENT CODING FLRT1 T protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63884474 C T 0 222 0 0.0008 0.1162 0.1138 0.4782 0.0179 0.002 0.0113585 0.0117729 0.0119851 1 84 7328 2007 3997 133 968 31 108 2 8916 109426 10570 8146 5254 60300 800 15440 0.955251 0 . 0 . 243 65,59,48,45 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S245|674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.70462 rs3751121 -0.693147 0.00598205 243 P522 674 ccC/ccT LOW 2 SILENT CODING FLRT1 T protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63885305 C T 0 222 0 0.0673 0.1456 0.3055 0.1815 0.174 0.0716 0.0883689 0.145045 0.174075 1 901 20549 3495 1727 1177 11484 168 1597 2 10330 120920 11516 8602 6592 66482 904 16494 0.794872 0 . 0 . 67 9,17,13,23 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P522|674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95612 rs3824854 -0.693139 0.459463 67 E631 674 gaA/gaG LOW 2 SILENT CODING FLRT1 G protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63885632 A G 0 228 0 0.8343 0.9543 0.9856 1 1 1 0.855066 0.950446 0.999302 2 8832 119457 11516 8628 6614 66472 895 16500 2 10370 121066 11570 8628 6614 66478 902 16504 0 . 0 . 0 346 0,0,139,175 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E631|674|FLRT1|protein_coding|CODING|NM_013280.4|2|G),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4379854 -0.693147 0.816552 346 Y655 674 taC/taT LOW 2 SILENT CODING FLRT1 T protein_coding NM_013280.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63885704 C T 0 222 0 0.1309 0.3986 0.5346 0.3254 0.6958 0.4335 0.219091 0.525785 0.682845 1 2143 69213 5669 2798 4718 45140 552 8193 2 9962 119028 11512 8544 6578 65564 892 15976 0.905508 0 . 0 . 308 51,89,42,95 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y655|674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.283095 rs386605003,rs677447 -0.693147 0.00021051 308 674 775 MODIFIER 2 CODING FLRT1 T protein_coding NM_013280.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63886539 C T 0 222 0 0.1293 0.4016 0.5533 0.3254 0.6968 0.4366 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.565085 0 . 0 . 227 61,38,72,32 UTR_3_PRIME(MODIFIER||775||674|FLRT1|protein_coding|CODING|NM_013280.4|2|T),INTRON(MODIFIER||||325|MACROD1|protein_coding|CODING|NM_014067.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.479845 rs386604005,rs663149 -0.693147 0.284087 227 590 176 MODIFIER 1 CODING STIP1 T protein_coding NM_001282652.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63953121 G T 0 90 0 0.1619 0.2059 0.1816 0.4891 0.0855 0.1145 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.559863 0 . 0 . 10 3,1,3,3 START_GAINED(LOW||||590|STIP1|protein_coding|CODING|NM_001282652.1|1|T),UTR_5_PRIME(MODIFIER||176||590|STIP1|protein_coding|CODING|NM_001282652.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1.00775 0 0.895781 rs3751122 -0.616816 0.69494 10 590 LOW 10 CODING STIP1 G protein_coding NM_001282652.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63967770 C G 0 222 0 0.3185 0.3856 0.5807 0.3105 0.3857 0.4151 0.348478 0.393967 0.417268 1 3531 49056 6700 2772 2328 26851 376 6498 2 10336 119866 11546 8626 6612 66190 894 15662 0.68205 0 . 0 . 38 3,11,7,13 SPLICE_SITE_REGION+INTRON(LOW||||590|STIP1|protein_coding|CODING|NM_001282652.1|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0783091 rs11231722 -0.692067 0.00133941 38 P487 667 ccG/ccA LOW 12 SILENT CODING FERMT3 A protein_coding NM_178443.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63988045 G A 0 222 0 0.1172 0.1653 0.147 0.4762 0.0726 0.0184 0.0983569 0.0703692 0.0560486 1 894 11589 2144 3866 543 3694 70 378 2 6636 88872 8756 7258 3976 47630 674 13942 0.974465 0 . 0 COSM429519,COSM429520 75 29,12,19,12 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P487|667|FERMT3|protein_coding|CODING|NM_178443.2|12|A),DOWNSTREAM(MODIFIER||3226||255|TRPT1|protein_coding|CODING|NM_001160389.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.361128 rs3802932 -0.69311 0.133271 75 L506 667 ctC/ctT LOW 12 SILENT CODING FERMT3 T protein_coding NM_178443.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63988102 C T 0 222 0 0.1278 0.1629 0.3271 0.1756 0.17 0.0736 0.136529 0.158503 0.169774 1 1230 18938 3257 1537 987 10244 152 1531 2 7606 99732 10158 7798 4868 54100 738 14464 0.680408 0 . 0 . 132 31,21,36,23 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L506|667|FERMT3|protein_coding|CODING|NM_178443.2|12|T),DOWNSTREAM(MODIFIER||3169||255|TRPT1|protein_coding|CODING|NM_001160389.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.429502 rs3802933 -0.693147 0.53696 132 H174R 255 cAt/cGt MODERATE 6 MISSENSE CODING TRPT1 C protein_coding NM_001160389.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63991801 T C 0 196 0 0.0915 0.1534 0.3242 0.1766 0.171 0.0736 0.105407 0.149815 0.172562 1 1084 20517 3559 1618 1147 11331 170 1608 2 10336 120860 11542 8598 6612 66370 902 16500 0.652615 0 . 0 . 23 3,9,3,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H174R|255|TRPT1|protein_coding|CODING|NM_001160389.1|6|C),UPSTREAM(MODIFIER||1929||303|NUDT22|protein_coding|CODING|NM_001128612.2||C),DOWNSTREAM(MODIFIER||438||667|FERMT3|protein_coding|CODING|NM_178443.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.833227 rs1059440 -0.662043 0.317505 23 255 202 MODIFIER 1 CODING TRPT1 C protein_coding NM_001160389.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63993534 G C 0 107 0 0.8404 0.9557 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,0,6 UTR_5_PRIME(MODIFIER||202||255|TRPT1|protein_coding|CODING|NM_001160389.1|1|C),UPSTREAM(MODIFIER||196||303|NUDT22|protein_coding|CODING|NM_001128612.2||C),UPSTREAM(MODIFIER||4370||249|DNAJC4|protein_coding|CODING|NM_001307980.1||C),DOWNSTREAM(MODIFIER||2171||667|FERMT3|protein_coding|CODING|NM_178443.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2429457 -0.616816 0.679639 6 Q260R 303 cAg/cGg MODERATE 6 MISSENSE CODING NUDT22 G protein_coding NM_001128612.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63997329 A G 0 228 0 0.8147 0.9439 0.9827 0.9861 0.998 0.9918 0.83712 0.941828 0.995462 2 8597 118355 11474 8437 6599 66049 887 16312 2 10336 120872 11556 8626 6614 66332 898 16510 0 . 0 . 0 48 0,0,24,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q260R|303|NUDT22|protein_coding|CODING|NM_001128612.2|6|G),UPSTREAM(MODIFIER||3603||255|TRPT1|protein_coding|CODING|NM_001160389.1||G),UPSTREAM(MODIFIER||575||249|DNAJC4|protein_coding|CODING|NM_001307980.1||G),UPSTREAM(MODIFIER||4727||207|VEGFB|protein_coding|CODING|NM_003377.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386602342,rs633561 -0.693147 0.211848 48 L263P 303 cTc/cCc MODERATE 6 MISSENSE CODING NUDT22 C protein_coding NM_001128612.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 63997338 T C 0 228 0 0.8321 0.9535 0.9841 1 1 1 0.858928 0.951754 0.999302 2 8809 119286 11503 8630 6614 66331 891 16508 2 10328 120876 11556 8630 6614 66340 898 16510 0 . 0 . 0 47 0,0,27,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L263P|303|NUDT22|protein_coding|CODING|NM_001128612.2|6|C),UPSTREAM(MODIFIER||3612||255|TRPT1|protein_coding|CODING|NM_001160389.1||C),UPSTREAM(MODIFIER||566||249|DNAJC4|protein_coding|CODING|NM_001307980.1||C),UPSTREAM(MODIFIER||4718||207|VEGFB|protein_coding|CODING|NM_003377.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs633557 -0.693147 0.155501 47 207 1187 MODIFIER 7 CODING VEGFB C protein_coding NM_003377.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64006292 T C 0 209 0 0.6936 0.7121 0.5778 0.755 0.664 0.8374 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.518841 0 . 0 . 116 19,56,8,22 UTR_3_PRIME(MODIFIER||1187||207|VEGFB|protein_coding|CODING|NM_003377.4|7|C),UPSTREAM(MODIFIER||2312||142|FKBP2|protein_coding|CODING|NM_001135208.1||C),DOWNSTREAM(MODIFIER||4539||249|DNAJC4|protein_coding|CODING|NM_001307980.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.979773 rs594942 -0.693097 0.0404639 116 207 1361 MODIFIER 7 CODING VEGFB G protein_coding NM_003377.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64006466 T G 0 45.3 0 0.6936 0.7121 0.5778 0.755 0.664 0.8374 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.89338 0 . 0 . 9 2,3,0,4 UTR_3_PRIME(MODIFIER||1361||207|VEGFB|protein_coding|CODING|NM_003377.4|7|G),UPSTREAM(MODIFIER||2138||142|FKBP2|protein_coding|CODING|NM_001135208.1||G),DOWNSTREAM(MODIFIER||4713||249|DNAJC4|protein_coding|CODING|NM_001307980.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.730948 rs595880 -0.556411 0.372756 9 207 1379 MODIFIER 7 CODING VEGFB T protein_coding NM_003377.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64006484 C T 0 118 0 0.0915 0.1556 0.3199 0.1815 0.1789 0.0746 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 9 0,3,2,3 UTR_3_PRIME(MODIFIER||1379||207|VEGFB|protein_coding|CODING|NM_003377.4|7|T),UPSTREAM(MODIFIER||2120||142|FKBP2|protein_coding|CODING|NM_001135208.1||T),DOWNSTREAM(MODIFIER||4731||249|DNAJC4|protein_coding|CODING|NM_001307980.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.900802 rs12794145 -0.590765 0.689691 9 G123 142 ggT/ggC LOW 6 SILENT CODING FKBP2 C protein_coding NM_001135208.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64011441 T C 0 228 0 0.9153 0.9768 0.9942 1 1 1 0.940027 0.979609 0.999884 2 9743 120707 11553 8651 6614 66731 904 16511 2 10404 121402 11578 8654 6614 66732 908 16512 0 . 0 . 0 50 0,0,17,30 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G123|142|FKBP2|protein_coding|CODING|NM_001135208.1|6|C),DOWNSTREAM(MODIFIER||4705||207|VEGFB|protein_coding|CODING|NM_003377.4||C),DOWNSTREAM(MODIFIER||510||147|PPP1R14B|protein_coding|CODING|NM_138689.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs654573 -0.693147 0.00115883 50 147 1 MODIFIER 4 CODING PPP1R14B C protein_coding NM_138689.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64012225 G C 0 228 0 0.8321 0.9535 0.9841 1 1 1 0 . 0 2 8780 119181 11508 8644 6596 66246 897 16510 2 10286 120758 11562 8644 6596 66254 904 16512 0 . 0 . 0 38 0,0,21,12 UTR_3_PRIME(MODIFIER||1||147|PPP1R14B|protein_coding|CODING|NM_138689.2|4|C),DOWNSTREAM(MODIFIER||618||142|FKBP2|protein_coding|CODING|NM_001135208.1||C) 0 . 0 . 0 1 0 . 1 0 53 0 0 0.668071 0 . rs605187 -0.693127 0.298183 38 P112 1234 ccA/ccG LOW 4 SILENT CODING PLCB3 G protein_coding NM_000932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64022459 A G 0 228 0 0.8313 0.9539 0.9885 1 1 1 0.864834 0.953755 0.999302 2 8823 114210 11462 8622 6596 64907 849 12951 2 10250 115698 11508 8622 6596 64912 854 12956 0 . 0 . 0 69 0,0,38,30 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P112|1234|PLCB3|protein_coding|CODING|NM_000932.2|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs632439 -0.693147 0.0100145 69 A1181 1234 gcG/gcA LOW 31 SILENT CODING PLCB3 A protein_coding NM_000932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64034866 G A 0 222 0 0.0234 0.0897 0.1239 0.1052 0.165 0.0613 0.0459447 0.112419 0.146535 1 112 2734 126 127 35 1737 24 573 2 1644 15184 510 670 92 6772 150 5346 0.674458 0 . 0 . 26 0,10,3,12 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1181|1234|PLCB3|protein_coding|CODING|NM_000932.2|31|A),DOWNSTREAM(MODIFIER||2434||168|BAD|protein_coding|CODING|NM_004322.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.815902 rs7938380 -0.688148 0.0414578 26 P1196 1234 ccG/ccA LOW 31 SILENT CODING PLCB3 A protein_coding NM_000932.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64034911 G A 0 87 0 0.0023 0.1202 0.1182 0.4861 0.0219 0.0051 0.0106736 0.0118971 0.0125243 1 19 1574 304 878 11 289 12 61 2 1116 15026 840 1498 94 5548 134 5796 0.655816 0 . 0 COSM1355661 15 4,6,2,3 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P1196|1234|PLCB3|protein_coding|CODING|NM_000932.2|31|A),DOWNSTREAM(MODIFIER||2389||168|BAD|protein_coding|CODING|NM_004322.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.934728 rs28395877 -0.590765 0.781662 15 1234 699 MODIFIER 31 CODING PLCB3 C protein_coding NM_000932.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64035727 T C 0 39.3 0 0.4788 0.8041 0.9496 0.9375 0.994 0.8078 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||699||1234|PLCB3|protein_coding|CODING|NM_000932.2|31|C),DOWNSTREAM(MODIFIER||1573||168|BAD|protein_coding|CODING|NM_004322.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs621816 -0.453602 0.96 2 T281 393 acG/acA LOW 7 SILENT CODING KCNK4 A protein_coding NM_001317090.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64066859 G A 0 228 0 0.4728 0.7917 0.9481 0.9177 0.994 0.774 0.653415 0.882029 0.996496 2 2002 58355 5685 4429 1883 34362 413 9581 2 3310 62354 5808 4778 1884 34460 434 11680 0 . 0 . 0 18 0,0,9,8 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T281|393|KCNK4|protein_coding|CODING|NM_001317090.1|7|A),UPSTREAM(MODIFIER||1004||200|TEX40|protein_coding|CODING|NM_001039496.1||A),INTRAGENIC(MODIFIER|||||KCNK4-TEX40||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2232417 -0.690438 0.0568264 18 P328L 393 cCg/cTg MODERATE 7 MISSENSE CODING KCNK4 T protein_coding NM_001317090.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64066999 C T 0 113 0 0.2383 0.2808 0.2939 0.5437 0.1561 0.1861 0.200552 0.162954 0.143698 1 1908 23765 4250 4561 1040 9241 155 2610 2 8216 111442 11166 8254 6444 60378 832 16152 0.144298 0 . 0 . 33 13,6,7,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P328L|393|KCNK4|protein_coding|CODING|NM_001317090.1|7|T),UPSTREAM(MODIFIER||864||200|TEX40|protein_coding|CODING|NM_001039496.1||T),INTRAGENIC(MODIFIER|||||KCNK4-TEX40||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997281 rs953778 -0.662043 0.787088 33 R389C 423 Cgc/Tgc MODERATE 7 MISSENSE CODING ESRRA T protein_coding NM_001282450.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64083331 C T 0 16.7 0 . 0 . 0 . 0 . 0 . 1 154 3648 289 352 205 2153 31 464 2 7370 70520 6422 4186 3174 37562 560 11246 0.925855 0 . 0 . 440 244,78,50,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R389C|423|ESRRA|protein_coding|CODING|NM_001282450.1|7|T),UPSTREAM(MODIFIER||2229||214|PRDX5|protein_coding|CODING|NM_012094.4||T),DOWNSTREAM(MODIFIER||633||125|TRMT112|protein_coding|CODING|NM_016404.2||T) 0 0.5 1 0 . 0 . 0 1 0 56 0 2.01788e-06 0.00187336 0 0.0834267 rs80310817 -0.693147 0.339037 440 423 675 MODIFIER 7 CODING ESRRA G protein_coding NM_001282450.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64084113 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,17,25 UTR_3_PRIME(MODIFIER||675||423|ESRRA|protein_coding|CODING|NM_001282450.1|7|G),UTR_3_PRIME(MODIFIER||220||125|TRMT112|protein_coding|CODING|NM_016404.2|4|G),UPSTREAM(MODIFIER||1447||214|PRDX5|protein_coding|CODING|NM_012094.4||G) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs679730 -0.693146 0.216947 45 125 220 MODIFIER 4 CODING TRMT112 G protein_coding NM_016404.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64084113 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,17,25 UTR_3_PRIME(MODIFIER||675||423|ESRRA|protein_coding|CODING|NM_001282450.1|7|G),UTR_3_PRIME(MODIFIER||220||125|TRMT112|protein_coding|CODING|NM_016404.2|4|G),UPSTREAM(MODIFIER||1447||214|PRDX5|protein_coding|CODING|NM_012094.4||G) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs679730 -0.693146 0.216947 45 125 76 MODIFIER 1 CODING TRMT112 A protein_coding NM_016404.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64085074 T A 0 228 0 0.8517 0.9589 0.9856 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 115 0,0,19,89 UTR_5_PRIME(MODIFIER||76||125|TRMT112|protein_coding|CODING|NM_016404.2|1|A),UPSTREAM(MODIFIER||486||214|PRDX5|protein_coding|CODING|NM_012094.4||A),DOWNSTREAM(MODIFIER||862||423|ESRRA|protein_coding|CODING|NM_001282450.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs550819 -0.693147 0.166621 115 125 150 MODIFIER 1 CODING TRMT112 C protein_coding NM_016404.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64085148 A C 0 180 0 0.0174 0.1665 0.1527 0.1062 0.3012 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968885 0 . 0 . 41 0,15,1,24 UTR_5_PRIME(MODIFIER||150||125|TRMT112|protein_coding|CODING|NM_016404.2|1|C),UPSTREAM(MODIFIER||412||214|PRDX5|protein_coding|CODING|NM_012094.4||C),DOWNSTREAM(MODIFIER||936||423|ESRRA|protein_coding|CODING|NM_001282450.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.855476 rs28364831 -0.692914 0.37012 41 125 300 MODIFIER 1 CODING TRMT112 T protein_coding NM_016404.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64085298 C T 0 83 0 0.025 0.1683 0.1527 0.1062 0.3002 0.3016 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.750668 0 . 0 . 8 1,2,1,4 UTR_5_PRIME(MODIFIER||300||125|TRMT112|protein_coding|CODING|NM_016404.2|1|T),UPSTREAM(MODIFIER||262||214|PRDX5|protein_coding|CODING|NM_012094.4||T),DOWNSTREAM(MODIFIER||1086||423|ESRRA|protein_coding|CODING|NM_001282450.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.300267 rs9787810 -0.590765 0.677613 8 Y33C 214 tAc/tGc MODERATE 1 MISSENSE CODING PRDX5 G protein_coding NM_012094.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64085785 A G 0 228 0 0.7784 0.9389 0.9813 1 1 1 0.809686 0.935017 0.999185 2 7897 115339 11262 8534 5856 64498 829 16463 2 9784 117314 11328 8534 5856 64510 834 16468 0 . 0 . COSM429533 147 0,0,107,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y33C|214|PRDX5|protein_coding|CODING|NM_012094.4|1|G),UPSTREAM(MODIFIER||229||125|TRMT112|protein_coding|CODING|NM_016404.2||G),DOWNSTREAM(MODIFIER||1573||423|ESRRA|protein_coding|CODING|NM_001282450.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7938623 -0.693147 0.0140771 147 W639R 1476 Tgg/Cgg MODERATE 14 MISSENSE CODING CCDC88B C protein_coding NM_032251.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64111928 T C 0 222 0 0.3843 0.5337 0.562 0.3492 0.6769 0.7587 0.433409 0.605125 0.693042 1 4290 73868 5687 2902 4184 44436 551 11818 2 9714 114340 10892 8004 6056 63362 858 15454 0.989884 0 . 0 COSM429538 122 31,28,37,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W639R|1476|CCDC88B|protein_coding|CODING|NM_032251.5|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.483471 rs685870 -0.693147 0.0989498 122 D886A 1476 gAc/gCc MODERATE 15 MISSENSE CODING CCDC88B C protein_coding NM_032251.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64116843 A C 0 228 0 0.8631 0.9619 0.9856 1 1 1 0.884493 0.960277 0.999069 2 8673 117207 11379 8586 6058 65294 859 16358 2 9826 118412 11420 8586 6058 65300 862 16360 0 . 0 . 0 80 0,0,36,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D886A|1476|CCDC88B|protein_coding|CODING|NM_032251.5|15|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1318165 -0.693147 0.0844921 80 S758A 772 Tcc/Gcc MODERATE 17 MISSENSE CODING RPS6KA4 G protein_coding NM_003942.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64138905 T G 0 15.7 0 0.0514 0.253 0.3833 0.2123 0.3708 0.3538 0.0627209 0.19611 0.263922 1 549 28438 2972 1362 1563 16588 203 5201 2 5274 81480 7840 5894 3768 43924 604 14176 0.333333 0 . 0 . 16 4,8,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Gcc|S758A|772|RPS6KA4|protein_coding|CODING|NM_003942.2|17|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.458333 rs17857342 -0.453602 0.22 16 553 424 MODIFIER 1 CODING SLC22A12 C protein_coding NM_144585.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64358605 T C 0 9.7 0 0.7504 0.5719 0.5548 0.7808 0.2932 0.4141 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||424||553|SLC22A12|protein_coding|CODING|NM_144585.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs559946 -0.379885 0 1 N82 553 aaC/aaT LOW 1 SILENT CODING SLC22A12 T protein_coding NM_144585.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64359274 C T 0 228 0 0.0038 0.0707 0.0634 0.2956 0.004 0.0031 0.0052249 0.00330871 0.0023272 2 47 3850 1090 2266 110 262 18 57 2 9928 119058 11468 8452 6550 65294 884 16482 0 . 0 . 0 107 0,0,29,71 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N82|553|SLC22A12|protein_coding|CODING|NM_144585.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3825017 -0.693147 0.311407 107 A416 553 gcA/gcG LOW 7 SILENT CODING SLC22A12 G protein_coding NM_144585.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64367325 A G 0 228 0 0.9244 0.9768 0.9942 1 1 0.9877 0.930196 0.976282 0.999884 2 9245 117952 11441 8530 6592 64877 888 16379 2 9934 118800 11478 8530 6592 64894 888 16484 0 . 0 . 0 65 0,0,24,38 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A416|553|SLC22A12|protein_coding|CODING|NM_144585.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1630320 -0.693147 0.019433 65 L437 553 Ttg/Ctg LOW 8 SILENT CODING SLC22A12 C protein_coding NM_144585.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64367862 T C 0 228 0 0.674 0.3974 0.255 0.5129 0.2018 0.2065 0.579727 0.318819 0.185418 2 5537 29238 2626 3852 1585 12286 192 3160 2 8640 96398 8964 7842 4304 53096 650 12902 0.857773 0 . 0 . 63 2,1,37,17 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L437|553|SLC22A12|protein_coding|CODING|NM_144585.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.90504 rs7932775 -0.693147 0.742298 63 1712 1012 MODIFIER 23 CODING NRXN2 C protein_coding NM_015080.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64373656 G C 0 228 0 0.0038 0.0703 0.0677 0.2907 0.004 0.0031 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 70 1,0,52,10 UTR_3_PRIME(MODIFIER||1012||1712|NRXN2|protein_coding|CODING|NM_015080.3|23|C),DOWNSTREAM(MODIFIER||3831||553|SLC22A12|protein_coding|CODING|NM_144585.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs11231840 -0.693147 0.00749271 70 1712 427 MODIFIER 23 CODING NRXN2 A protein_coding NM_015080.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64374241 G A 0 228 0 0.2345 0.1653 0.1282 0.3185 0.0467 0.0624 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 45 0,0,2,43 UTR_3_PRIME(MODIFIER||427||1712|NRXN2|protein_coding|CODING|NM_015080.3|23|A),DOWNSTREAM(MODIFIER||4416||553|SLC22A12|protein_coding|CODING|NM_144585.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3741399 -0.693147 0.00726588 45 G177 1712 ggC/ggT LOW 2 SILENT CODING NRXN2 A protein_coding NM_015080.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64480641 G A 0 63 0 0.2216 0.5335 0.5403 0.5407 0.7604 0.7096 0.438667 0.6844 0.804192 2 109 8011 73 77 4 2288 96 5364 2 252 11060 116 144 6 2914 124 7504 0 3 likely-benign 0 . 3 0,0,2,0 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G177|1712|NRXN2|protein_coding|CODING|NM_015080.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs2518907 -0.453602 0.18 3 673 347 MODIFIER 13 CODING SF1 A protein_coding NM_001178030.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64532579 C A 0 228 0 0.0991 0.5829 0.6268 0.6468 0.9066 0.8067 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,53,2 UTR_3_PRIME(MODIFIER||347||673|SF1|protein_coding|CODING|NM_001178030.1|13|A),UPSTREAM(MODIFIER||4392||842|PYGM|protein_coding|CODING|NM_005609.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs523200 -0.693147 0.041995 56 820 LOW 24 CODING MAP4K2 C protein_coding NM_004579.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64559898 T C 0 228 0 0.2474 0.4233 0.4798 0.7351 0.2475 0.4806 0.240682 0.255619 0.263268 2 1463 23981 2627 3637 763 9981 164 5346 2 4962 54330 4600 4820 1600 27464 398 10486 0 . 0 . 0 50 0,0,26,15 SPLICE_SITE_REGION+INTRON(LOW||||820|MAP4K2|protein_coding|CODING|NM_004579.4|24|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10897526 -0.693145 0.00465451 50 820 LOW 11 CODING MAP4K2 C protein_coding NM_004579.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64567692 G C 0 228 0 0.2247 0.136 0.0922 0.3036 0.0089 0.0051 0.179691 0.0634041 0.00383989 2 2031 6489 1345 2580 100 318 43 72 2 9880 118120 11392 8482 6470 64680 878 16338 0 . 0 . 0 101 0,0,59,36 SPLICE_SITE_REGION+INTRON(LOW||||820|MAP4K2|protein_coding|CODING|NM_004579.4|11|C),DOWNSTREAM(MODIFIER||3294||615|MEN1|protein_coding|CODING|NM_000244.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2301564 -0.693147 0.383861 101 H438 615 caT/caC LOW 9 SILENT CODING MEN1 G protein_coding NM_000244.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64572557 A G 0 228 0 0.9115 0.976 0.9957 1 1 1 0.930259 0.976147 0.999651 2 9548 120337 11518 8648 6604 66603 905 16511 2 10376 121216 11562 8648 6604 66608 906 16512 0 2,2 benign,benign 0 . 112 0,0,55,49 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H438|615|MEN1|protein_coding|CODING|NM_000244.3|9|G),UPSTREAM(MODIFIER||1831||820|MAP4K2|protein_coding|CODING|NM_004579.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs540012 -0.693147 0.0447304 112 1551 266 MODIFIER 37 CODING CDC42BPG A protein_coding NM_017525.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64591679 G A 0 39.3 0 0.0749 0.2111 0.3386 0.4593 0.1262 0.136 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||266||1551|CDC42BPG|protein_coding|CODING|NM_017525.2|37|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs670358 -0.453602 0.06 2 G358 1551 ggG/ggA LOW 8 SILENT CODING CDC42BPG T protein_coding NM_017525.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64606177 C T 0 228 0 0.2829 0.2682 0.366 0.4544 0.1233 0.136 0.254884 0.149508 0.0955318 2 2626 23071 4708 3615 2293 7351 161 2317 2 10276 120306 11542 8612 6610 65872 894 16500 0 . 0 . 0 64 0,0,29,29 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G358|1551|CDC42BPG|protein_coding|CODING|NM_017525.2|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386431611,rs653343 -0.693147 0.149924 64 1551 LOW 5 CODING CDC42BPG T protein_coding NM_017525.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64607587 C T 0 228 0 0.2814 0.2676 0.3646 0.4544 0.1233 0.136 0.251933 0.148345 0.0953212 2 2421 21269 4319 3371 1911 6846 144 2257 2 8686 99832 9744 7486 4964 53902 724 14326 0.661765 0 . 0 . 73 2,0,61,7 SPLICE_SITE_REGION+INTRON(LOW||||1551|CDC42BPG|protein_coding|CODING|NM_017525.2|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.830882 rs589984 -0.693147 0.586876 73 548 1287 MODIFIER 6 CODING EHD1 A protein_coding NM_001282445.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64620518 G A 0 39.3 0 0.4849 0.6633 0.7795 0.5536 0.8121 0.7822 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||1287||548|EHD1|protein_coding|CODING|NM_001282445.1|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12573 -0.453602 0.5 2 548 335 MODIFIER 6 CODING EHD1 A protein_coding NM_001282445.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64621470 G A 0 228 0 0.3275 0.6432 0.8112 0.5506 0.8757 0.8067 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,20,6 UTR_3_PRIME(MODIFIER||335||548|EHD1|protein_coding|CODING|NM_001282445.1|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3741391 -0.692976 0.109252 27 P532 548 ccT/ccC LOW 6 SILENT CODING EHD1 G protein_coding NM_001282445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64621856 A G 0 228 0 1 1 1 1 1 1 1 0.999923 0.999884 2 10252 120170 11496 8586 6550 65909 896 16481 2 10252 120172 11496 8586 6550 65910 896 16482 0 . 0 . 0 146 0,0,64,72 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P532|548|EHD1|protein_coding|CODING|NM_001282445.1|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3897618 -0.693147 0.0486096 146 L349 548 ctC/ctG LOW 5 SILENT CODING EHD1 C protein_coding NM_001282445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64622869 G C 0 228 0 0.5076 0.6961 0.8256 0.5625 0.8797 0.8078 0.585643 0.779471 0.878753 2 5948 99586 9745 4453 6332 58784 738 13586 2 10402 121354 11570 8634 6614 66716 906 16512 0 . 0 . 0 71 0,0,33,29 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L349|548|EHD1|protein_coding|CODING|NM_001282445.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10897533 -0.693147 0.212843 71 A36 548 gcT/gcC LOW 2 SILENT CODING EHD1 G protein_coding NM_001282445.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64645871 A G 0 228 0 0.3396 0.6498 0.817 0.5615 0.8777 0.8067 0.451159 0.734072 0.878985 2 4480 97656 9654 4425 6288 58508 734 13567 2 10294 120780 11550 8586 6600 66346 902 16502 1 0 . 0 . 249 0,1,46,182 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A36|548|EHD1|protein_coding|CODING|NM_001282445.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1211284 -0.693147 0.0661461 249 P656R 1938 cCg/cGg MODERATE 14 MISSENSE CODING ATG2A C protein_coding NM_015104.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64677293 G C 0 228 0 0.9955 0.9986 0.9986 1 1 1 0.998405 0.99946 1 2 9559 116991 11434 8424 6558 63722 872 16422 2 9580 117018 11436 8424 6558 63726 872 16422 0 . 0 . 0 69 0,0,17,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cGg|P656R|1938|ATG2A|protein_coding|CODING|NM_015104.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs656195 -0.693147 0.0329434 69 D215 1938 gaC/gaT LOW 5 SILENT CODING ATG2A A protein_coding NM_015104.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64680819 G A 0 228 0 0.4054 0.5517 0.4697 0.5427 0.7217 0.6421 0.469077 0.639205 0.72631 2 3763 66239 4470 3668 3417 40631 484 9806 2 7856 98238 8654 7036 4332 55182 692 14486 0.933333 0 . 0 . 35 0,2,15,15 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D215|1938|ATG2A|protein_coding|CODING|NM_015104.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.45 rs618006 -0.693097 0.297952 35 S161 497 tcG/tcA LOW 4 SILENT CODING PPP2R5B A protein_coding NM_006244.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64695360 G A 0 228 0 0.0008 0.0347 0.0014 0.1637 0.004 0.0031 0.000681508 0.000769468 0.000814522 2 4 1590 48 1348 17 105 8 60 2 10404 121358 11562 8640 6614 66720 906 16512 0 . 0 . 0 99 0,0,55,40 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S161|497|PPP2R5B|protein_coding|CODING|NM_006244.3|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs117110422 -0.693147 0.620917 99 129 45 MODIFIER 4 CODING GPHA2 T protein_coding NM_130769.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64702200 C T 0 228 0 0.7799 0.6901 0.7622 0.5784 0.6928 0.6299 0.784189 0.727301 0.698161 2 7991 84845 9593 4744 4670 46307 645 10895 2 10366 121110 11558 8608 6578 66590 902 16508 1 0 . 0 . 106 1,0,73,20 UTR_3_PRIME(MODIFIER||45||129|GPHA2|protein_coding|CODING|NM_130769.3|4|T),DOWNSTREAM(MODIFIER||250||497|PPP2R5B|protein_coding|CODING|NM_006244.3||T),DOWNSTREAM(MODIFIER||3502||216|C11orf85|protein_coding|CODING|NM_001037225.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs673995 -0.693147 0.066376 106 V141A 184 gTc/gCc MODERATE 5 MISSENSE CODING ARL2 C protein_coding NM_001667.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64789194 T C 0 228 0 0.7088 0.4577 0.3905 0.1806 0.6064 0.2986 0.706724 0.654379 0.62756 2 7097 61482 3267 1368 3523 39647 476 6104 2 10070 117360 11212 8388 6096 64974 856 15764 0.99719 0 . 0 COSM1132962 96 2,1,53,25 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gTc/gCc|V141A|184|ARL2|protein_coding|CODING|NM_001667.3|5|C),INTRAGENIC(MODIFIER|||||ARL2-SNX15||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.501203 rs664226 -0.693147 0.103116 96 P77 342 ccT/ccC LOW 3 SILENT CODING SNX15 C protein_coding NM_013306.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64799998 T C 0 228 0 0.2148 0.3746 0.6052 0.1825 0.6213 0.3712 0.28896 0.525085 0.646032 2 2893 64830 6472 1426 4108 41886 522 7523 2 10404 121278 11552 8618 6598 66690 904 16512 1 0 . 0 . 110 0,1,42,56 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P77|342|SNX15|protein_coding|CODING|NM_013306.4|3|C),INTRAGENIC(MODIFIER|||||ARL2-SNX15||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs534236 -0.693147 0.222457 110 342 30 MODIFIER 8 CODING SNX15 A protein_coding NM_013306.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64807294 G A 0 228 0 0.1838 0.3662 0.6138 0.1806 0.6173 0.3701 0.269545 0.514858 0.640512 2 1770 42878 3774 938 2068 28308 345 5675 2 6062 75066 6142 4358 3174 43224 570 11536 0.718391 0 . 0 . 97 1,1,50,37 UTR_3_PRIME(MODIFIER||30||342|SNX15|protein_coding|CODING|NM_013306.4|8|A),UPSTREAM(MODIFIER||1082||358|SAC3D1|protein_coding|CODING|NM_013299.3||A),INTRAGENIC(MODIFIER|||||ARL2-SNX15||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.816092 rs653111 -0.693147 0.276743 97 342 183 MODIFIER 8 CODING SNX15 C protein_coding NM_013306.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64807447 A C 0 228 0 0.7655 0.8403 0.8862 0.9435 0.9165 0.7239 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 93 0,0,23,58 UTR_3_PRIME(MODIFIER||183||342|SNX15|protein_coding|CODING|NM_013306.4|8|C),UPSTREAM(MODIFIER||929||358|SAC3D1|protein_coding|CODING|NM_013299.3||C),DOWNSTREAM(MODIFIER||4848||740|NAALADL1|protein_coding|CODING|NM_005468.2||C),INTRAGENIC(MODIFIER|||||ARL2-SNX15||NON_CODING|||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs664118 -0.693147 0.0450646 93 342 277 MODIFIER 8 CODING SNX15 A protein_coding NM_013306.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64807541 G A 0 164 0 0.1838 0.366 0.6138 0.1796 0.6173 0.3701 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,0,22 UTR_3_PRIME(MODIFIER||277||342|SNX15|protein_coding|CODING|NM_013306.4|8|A),UPSTREAM(MODIFIER||835||358|SAC3D1|protein_coding|CODING|NM_013299.3||A),DOWNSTREAM(MODIFIER||4754||740|NAALADL1|protein_coding|CODING|NM_005468.2||A),INTRAGENIC(MODIFIER|||||ARL2-SNX15||NON_CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs498636 -0.692562 0.794188 22 358 118 MODIFIER 1 CODING SAC3D1 C protein_coding NM_013299.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64808647 A C 0 143 0 0.8132 0.853 0.8862 0.9435 0.9175 0.7239 0 . 0 2 142 7543 69 118 0 2030 98 5086 2 164 9054 78 126 0 2144 108 6434 0 . 0 . 0 9 0,0,0,9 UTR_5_PRIME(MODIFIER||118||358|SAC3D1|protein_coding|CODING|NM_013299.3|1|C),DOWNSTREAM(MODIFIER||603||342|SNX15|protein_coding|CODING|NM_013306.4||C),DOWNSTREAM(MODIFIER||3648||740|NAALADL1|protein_coding|CODING|NM_005468.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs10160811 -0.662043 0.00254187 9 L109R 358 cTc/cGc MODERATE 1 MISSENSE CODING SAC3D1 G protein_coding NM_013299.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64809090 T G 0 180 0 0.9909 0.9974 0.9986 1 1 1 0.996229 0.998681 0.999824 2 222 10565 110 148 10 2734 120 7221 2 224 10584 110 148 10 2734 120 7238 0 . 0 . 0 8 0,0,3,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L109R|358|SAC3D1|protein_coding|CODING|NM_013299.3|1|G),DOWNSTREAM(MODIFIER||1046||342|SNX15|protein_coding|CODING|NM_013306.4||G),DOWNSTREAM(MODIFIER||3205||740|NAALADL1|protein_coding|CODING|NM_005468.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1.01283 0 . rs12271134 -0.636426 0.87105 8 A123 358 gcT/gcG LOW 1 SILENT CODING SAC3D1 G protein_coding NM_013299.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64809133 T G 0 134 0 0.7663 0.8403 0.8847 0.9435 0.9165 0.7239 0.875788 0.922787 0.945159 2 144 6786 68 114 0 1833 88 4539 2 178 8136 80 124 0 1934 96 5724 0 . 0 . 0 6 0,0,3,2 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A123|358|SAC3D1|protein_coding|CODING|NM_013299.3|1|G),DOWNSTREAM(MODIFIER||1089||342|SNX15|protein_coding|CODING|NM_013306.4||G),DOWNSTREAM(MODIFIER||3162||740|NAALADL1|protein_coding|CODING|NM_005468.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10792455 -0.590765 0.251321 6 T135A 358 Acc/Gcc MODERATE 1 MISSENSE CODING SAC3D1 G protein_coding NM_013299.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64809167 A G 0 147 0 0.854 0.9427 0.9669 0.9752 0.9722 0.9816 0 . 0 2 28 1529 17 33 2 168 16 1265 2 32 1578 18 34 2 172 16 1304 0 . 0 . 0 6 0,0,2,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T135A|358|SAC3D1|protein_coding|CODING|NM_013299.3|1|G),DOWNSTREAM(MODIFIER||1123||342|SNX15|protein_coding|CODING|NM_013306.4||G),DOWNSTREAM(MODIFIER||3128||740|NAALADL1|protein_coding|CODING|NM_005468.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs10792456 -0.556411 0.675454 6 252 1141 MODIFIER 6 CODING CDCA5 A protein_coding NM_080668.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64845438 C A 0 9.7 0 0.0976 0.3403 0.6009 0.1786 0.6083 0.3742 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1141||252|CDCA5|protein_coding|CODING|NM_080668.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs489489 -0.379885 0 1 F98L 116 Ttc/Ctc MODERATE 3 MISSENSE CODING TMEM262 G protein_coding NM_001282448.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64855986 A G 0 228 0 0.0477 0.241 0.4856 0.1756 0.3837 0.2495 0 . 0 2 63 4702 66 26 571 1557 69 2350 2 560 14226 188 198 1582 3896 182 7620 0.920072 0 . 0 . 200 4,1,104,79 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F98L|116|TMEM262|protein_coding|CODING|NM_001282448.1|3|G),UPSTREAM(MODIFIER||4371||252|CDCA5|protein_coding|CODING|NM_080668.3||G),DOWNSTREAM(MODIFIER||112||310|ZFPL1|protein_coding|CODING|NM_006782.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.96824 rs2282498 -0.693147 0.302252 200 W2R 116 Tgg/Cgg MODERATE 1 MISSENSE CODING TMEM262 G protein_coding NM_001282448.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64856500 A G 0 122 0 0.9894 0.997 0.9986 1 1 1 0 . 0 2 216 10801 92 136 16 2736 118 7487 2 216 10802 92 136 16 2736 118 7488 0 . 0 . 0 5 0,0,3,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W2R|116|TMEM262|protein_coding|CODING|NM_001282448.1|1|G),UPSTREAM(MODIFIER||4885||252|CDCA5|protein_coding|CODING|NM_080668.3||G),DOWNSTREAM(MODIFIER||626||310|ZFPL1|protein_coding|CODING|NM_006782.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs525781 -0.556411 0.0452455 5 P52 418 ccG/ccC LOW 2 SILENT CODING TM7SF2 C protein_coding NM_003273.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64880090 G C 0 205 0 0.9879 0.9964 0.9986 1 0.999 1 0.997271 0.999145 1 2 405 12467 412 408 88 4538 122 6494 2 408 12470 412 408 88 4538 122 6494 0 . 0 . 0 11 0,0,9,2 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P52|418|TM7SF2|protein_coding|CODING|NM_003273.3|2|C),DOWNSTREAM(MODIFIER||758||782|VPS51|protein_coding|CODING|NM_013265.3||C),DOWNSTREAM(MODIFIER||3785||403|ZNHIT2|protein_coding|CODING|NM_014205.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4930284 -0.676189 0.0408454 11 T299I 418 aCt/aTt MODERATE 8 MISSENSE CODING TM7SF2 T protein_coding NM_003273.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64882789 C T 0 228 0 0.3268 0.3652 0.5821 0.2728 0.4463 0.2751 0.326098 0.403881 0.440588 2 3359 50455 6432 2437 3004 29492 394 5337 2 9800 120724 11572 8602 6614 66728 898 16510 0 . 0 . 0 65 0,0,41,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T299I|418|TM7SF2|protein_coding|CODING|NM_003273.3|8|T),DOWNSTREAM(MODIFIER||3457||782|VPS51|protein_coding|CODING|NM_013265.3||T),DOWNSTREAM(MODIFIER||1086||403|ZNHIT2|protein_coding|CODING|NM_014205.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1129195 -0.693147 0.130703 65 A358 403 gcC/gcT LOW 1 SILENT CODING ZNHIT2 A protein_coding NM_014205.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64884052 G A 0 228 0 0.9002 0.8868 0.9164 0.9325 0.9423 0.7434 0.913448 0.932826 0.942751 2 9516 109327 9952 8118 6359 62396 817 12169 2 10368 119206 11548 8644 6612 66092 882 15060 1 0 . 0 . 86 0,1,48,25 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A358|403|ZNHIT2|protein_coding|CODING|NM_014205.3|1|A),DOWNSTREAM(MODIFIER||4720||782|VPS51|protein_coding|CODING|NM_013265.3||A),DOWNSTREAM(MODIFIER||345||418|TM7SF2|protein_coding|CODING|NM_003273.3||A),DOWNSTREAM(MODIFIER||4047||133|FAU|protein_coding|CODING|NM_001997.4||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1546532 -0.693147 0.0190849 86 617 652 MODIFIER 16 CODING SYVN1 G protein_coding NM_172230.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64895202 A G 0 154 0 0.6649 0.8217 0.902 0.9335 0.9394 0.7403 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_3_PRIME(MODIFIER||652||617|SYVN1|protein_coding|CODING|NM_172230.2|16|G),DOWNSTREAM(MODIFIER||361||166|MRPL49|protein_coding|CODING|NM_004927.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10088 -0.651104 0.696057 8 617 930 MODIFIER 1 CODING SYVN1 A protein_coding NM_172230.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64902002 C A 0 228 0 0.0197 0.1482 0.3559 0.1458 0.1819 0.1421 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.313931 0 . 0 . 155 1,2,62,72 UTR_5_PRIME(MODIFIER||930||617|SYVN1|protein_coding|CODING|NM_172230.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.575271 rs10895986 -0.693147 5.1464e-06 155 R433P 714 cGc/cCc MODERATE 11 MISSENSE CODING CAPN1 C protein_coding NM_001198868.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64972286 G C 0 228 0 0.0068 0.0725 0.0476 0.2044 0.0835 0.0317 0.0197754 0.0606304 0.0806954 2 177 9137 525 1820 484 5343 75 713 2 9384 117796 11464 8498 6612 64552 864 16422 0.850746 0 . 0 . 146 0,2,40,94 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R433P|714|CAPN1|protein_coding|CODING|NM_001198868.1|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.880597 rs10895991 -0.693147 0.0223688 146 T43 349 acG/acC LOW 1 SILENT CODING SLC22A20 C protein_coding NM_001004326.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64981472 G C 0 228 0 0.233 0.3466 0.2939 0.3929 0.4553 0.3783 0.217447 0.375165 0.449599 2 1845 43142 2870 3073 1943 26615 299 6497 2 6648 99440 9628 7506 4322 55766 672 14898 1 0 . 0 COSM429595,COSM429594 155 1,0,68,68 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T43|349|SLC22A20|protein_coding|CODING|NM_001004326.4|1|C),DOWNSTREAM(MODIFIER||1995||714|CAPN1|protein_coding|CODING|NM_001198868.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs239258 -0.693147 0.00389576 155 M146I 349 atG/atT MODERATE 2 MISSENSE CODING SLC22A20 T protein_coding NM_001004326.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64981853 G T 0 228 0 0.1082 0.2973 0.268 0.3889 0.4115 0.362 0.151225 0.336548 0.426949 2 1452 45045 2970 3318 2515 27938 332 6520 2 9436 117900 11412 8528 6222 65080 854 16368 0 . 0 . COSM429602,COSM429603 80 0,0,50,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atT|M146I|349|SLC22A20|protein_coding|CODING|NM_001004326.4|2|T),DOWNSTREAM(MODIFIER||2376||714|CAPN1|protein_coding|CODING|NM_001198868.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs239259 -0.693147 0.365939 80 G246A 349 gGa/gCa MODERATE 4 MISSENSE CODING SLC22A20 C protein_coding NM_001004326.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64990041 G C 0 228 0 0.1876 0.5721 0.719 0.6776 0.7783 0.6667 0.307973 0.628172 0.784696 2 2648 85953 8540 5711 4783 52092 667 11512 2 9804 120646 11556 8598 6610 66686 894 16498 0 . 0 . 0 188 0,0,91,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gCa|G246A|349|SLC22A20|protein_coding|CODING|NM_001004326.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs514076 -0.693147 0.104351 188 349 190 MODIFIER 6 CODING SLC22A20 G protein_coding NM_001004326.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 64993357 A G 0 228 0 0.8608 0.8736 0.9063 0.9236 0.9215 0.7669 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 24 0,0,4,18 UTR_3_PRIME(MODIFIER||190||349|SLC22A20|protein_coding|CODING|NM_001004326.4|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs239261 -0.692562 0.497426 24 210 790 MODIFIER 2 CODING CDC42EP2 C protein_coding NM_006779.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65089792 G C 0 228 0 0.6929 0.8197 0.8746 0.7738 0.8946 0.9223 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,21,26 UTR_3_PRIME(MODIFIER||790||210|CDC42EP2|protein_coding|CODING|NM_006779.3|2|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs525141 -0.693147 0.0185739 51 M224V 288 Atg/Gtg MODERATE 7 MISSENSE CODING SLC25A45 C protein_coding NM_182556.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65144075 T C 0 228 0 0.8994 0.9714 0.9856 1 1 1 0.92365 0.974289 0.999882 2 9046 119904 11509 8626 6614 66702 898 16509 2 9830 120790 11574 8626 6614 66734 900 16512 0 . 0 . 0 47 0,0,35,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M224V|288|SLC25A45|protein_coding|CODING|NM_182556.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs624307 -0.693145 0.366256 47 D113 464 gaC/gaT LOW 4 SILENT CODING FRMD8 T protein_coding NM_031904.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65161129 C T 0 228 0 0.028 0.2879 0.2911 0.2698 0.5467 0.3896 0.115402 0.408727 0.559008 2 1017 54576 2764 2381 3891 37051 441 7031 2 9576 117580 11210 8360 6266 65146 864 16158 0.881434 0 . 0 . 177 2,2,55,108 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D113|464|FRMD8|protein_coding|CODING|NM_031904.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.922016 rs2073800,rs386556457 -0.693147 0.00498833 177 464 224 MODIFIER 11 CODING FRMD8 G protein_coding NM_031904.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65179055 C G 0 114 0 0.8275 0.9523 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||224||464|FRMD8|protein_coding|CODING|NM_031904.3|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2957273 -0.556411 0.703527 5 V133L 1523 Gtg/Ctg MODERATE 5 MISSENSE CODING EHBP1L1 C protein_coding NM_001099409.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65347636 G C 0 228 0 0.9992 0.9998 1 1 1 1 0.998142 0.999374 1 2 9757 120242 11551 8614 6612 66302 894 16512 2 9770 120256 11552 8614 6612 66302 894 16512 0 . 0 . 0 55 0,0,27,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V133L|1523|EHBP1L1|protein_coding|CODING|NM_001099409.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1194100 -0.693147 0.195353 55 R307Q 1523 cGg/cAg MODERATE 9 MISSENSE CODING EHBP1L1 A protein_coding NM_001099409.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65349063 G A 0 222 0 0.4501 0.4599 0.3876 0.4504 0.4881 0.5051 0.453876 0.459734 0.462398 1 1725 19085 1059 1453 942 11204 142 2560 2 3166 32482 2078 2568 1470 18976 234 3990 0.639686 0 . 0 . 64 15,11,17,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R307Q|1523|EHBP1L1|protein_coding|CODING|NM_001099409.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99539 rs3741380 -0.69311 0.0551672 64 V538G 1523 gTg/gGg MODERATE 9 MISSENSE CODING EHBP1L1 G protein_coding NM_001099409.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65349756 T G 0 104 0 0.3101 0.4259 0.3775 0.4514 0.506 0.5082 0.315339 0.424197 0.474214 1 2767 46774 3426 3589 3487 28498 370 4637 2 7906 96652 9912 7638 5624 56314 692 8566 0.605689 0 . 0 . 19 8,4,3,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V538G|1523|EHBP1L1|protein_coding|CODING|NM_001099409.1|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.818731 rs6591182 -0.590765 0.130743 19 D569V 1523 gAc/gTc MODERATE 9 MISSENSE CODING EHBP1L1 T protein_coding NM_001099409.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65349849 A T 0 228 0 0.8048 0.9437 0.9798 0.9921 0.998 1 0.847304 0.950729 0.998046 2 7652 113611 11387 8508 6596 63715 847 14906 2 9106 115282 11482 8556 6598 63768 852 14920 0 . 0 . 0 44 0,0,33,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D569V|1523|EHBP1L1|protein_coding|CODING|NM_001099409.1|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1194099 -0.693143 0.275509 44 A977 1523 gcG/gcA LOW 9 SILENT CODING EHBP1L1 A protein_coding NM_001099409.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65351074 G A 0 222 0 0.0658 0.2778 0.4524 0.4504 0.2654 0.2751 0.0978378 0.226821 0.285121 1 817 32938 5247 3466 1641 17279 227 4261 2 7040 97388 9406 7220 5514 53230 740 14238 0.382535 0 . 0 . 113 35,20,30,17 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A977|1523|EHBP1L1|protein_coding|CODING|NM_001099409.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.347755 rs10896018 -0.693147 0.01863 113 307 120 MODIFIER 3 CODING KCNK7 C protein_coding NM_033347.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65360356 T C 0 134 0 0.9818 0.9952 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||120||307|KCNK7|protein_coding|CODING|NM_033347.1|3|C),DOWNSTREAM(MODIFIER||240||1523|EHBP1L1|protein_coding|CODING|NM_001099409.1||C),DOWNSTREAM(MODIFIER||4870||847|MAP3K11|protein_coding|CODING|NM_002419.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2510077 -0.662043 0.0421576 9 G104 847 ggC/ggT LOW 1 SILENT CODING MAP3K11 A protein_coding NM_002419.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65380916 G A 0 222 0 0.1195 0.3544 0.2925 0.3244 0.4404 0.6585 0.185539 0.34555 0.427474 1 1722 50352 3101 2879 3663 28597 398 9992 2 9738 118126 11484 8520 6582 64464 882 16456 0.816999 0 . 0 . 164 17,65,20,50 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G104|847|MAP3K11|protein_coding|CODING|NM_002419.3|1|A),UPSTREAM(MODIFIER||2867||2034|PCNXL3|protein_coding|CODING|NM_032223.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.586421 rs2004649 -0.693147 0.464545 164 V38 2034 gtG/gtC LOW 1 SILENT CODING PCNXL3 C protein_coding NM_032223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65383896 G C 0 228 0 1 1 1 1 1 1 0 . 0 2 9640 119251 11519 8592 6584 65557 878 16481 2 9640 119254 11520 8592 6584 65558 878 16482 0 . 0 . 0 133 0,0,67,49 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V38|2034|PCNXL3|protein_coding|CODING|NM_032223.3|1|C),UPSTREAM(MODIFIER||2176||847|MAP3K11|protein_coding|CODING|NM_002419.3||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7947140 -0.693147 0.0809643 133 P116 2034 ccC/ccT LOW 3 SILENT CODING PCNXL3 T protein_coding NM_032223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65384727 C T 0 222 0 0.2648 0.2959 0.4236 0.4226 0.1968 0.2188 0.238072 0.210236 0.19678 1 1889 23852 4107 2882 972 10720 160 3122 2 6474 78344 7770 6136 3970 41268 620 12106 0.580823 0 . 0 COSM147270 71 23,5,37,2 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P116|2034|PCNXL3|protein_coding|CODING|NM_032223.3|3|T),UPSTREAM(MODIFIER||3007||847|MAP3K11|protein_coding|CODING|NM_002419.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999495 rs12790427 -0.693144 0.674255 71 Q258R 2034 cAg/cGg MODERATE 6 MISSENSE CODING PCNXL3 G protein_coding NM_032223.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65385606 A G 0 228 0 0.9856 0.9962 1 1 1 1 0.985721 0.995288 0.99988 2 9140 117250 11391 8542 6562 64358 872 16385 2 9274 117406 11402 8542 6562 64368 872 16386 0 . 0 . 0 93 0,0,39,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q258R|2034|PCNXL3|protein_coding|CODING|NM_032223.3|6|G),UPSTREAM(MODIFIER||3886||847|MAP3K11|protein_coding|CODING|NM_002419.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1151489 -0.693147 0.0105742 93 A570 2034 gcC/gcT LOW 7 SILENT CODING PCNXL3 T protein_coding NM_032223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65387012 C T 0 222 0 0.1278 0.1092 0.3055 0.1577 0.004 0.0031 0.10878 0.0378339 0.00263284 1 1083 6806 4037 1328 55 209 24 70 2 8458 110956 10996 8312 5566 61322 802 15500 0.336633 0 . 0 . 75 17,22,17,12 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A570|2034|PCNXL3|protein_coding|CODING|NM_032223.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.812291 rs57318451 -0.693079 0.390434 75 A661 2034 gcT/gcA LOW 8 SILENT CODING PCNXL3 A protein_coding NM_032223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65387378 T A 0 20.6 0 0.2065 0.4117 0.3228 0.4355 0.4672 0.6708 0.23947 0.374763 0.44265 1 2232 53479 3201 3963 3649 29778 417 10239 2 8880 115858 11086 8418 6412 64124 850 16088 0.375 0 . 0 . 15 2,10,1,1 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A661|2034|PCNXL3|protein_coding|CODING|NM_032223.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.75 rs61744384 -0.453602 0.38 15 A342 1042 gcG/gcA LOW 5 SILENT CODING SIPA1 A protein_coding NM_006747.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65412467 G A 0 222 0 0.3321 0.3534 0.2579 0.251 0.4364 0.4703 0.335756 0.39112 0.419479 1 3538 48613 2204 2198 3472 28466 384 8351 2 10396 121260 11570 8624 6608 66654 904 16504 0.691476 0 . 0 . 95 25,11,27,12 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A342|1042|SIPA1|protein_coding|CODING|NM_006747.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.996842 rs2306364 -0.693144 0.373714 95 T735 1042 acT/acG LOW 9 SILENT CODING SIPA1 G protein_coding NM_006747.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65415028 T G 0 100 0 0.9864 0.9964 1 1 1 1 0.988538 0.995768 0.999241 2 538 7050 561 616 222 3057 48 2008 2 546 7060 562 616 222 3058 48 2008 0 . 0 . 0 5 0,0,4,0 SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T735|1042|SIPA1|protein_coding|CODING|NM_006747.3|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs4930157 -0.556411 0.658104 5 A920 1042 gcG/gcA LOW 13 SILENT CODING SIPA1 A protein_coding NM_006747.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65417434 G A 0 222 0 0.1392 0.2364 0.1974 0.2123 0.3569 0.2965 0.191958 0.295476 0.348499 1 1878 37986 1659 1906 3131 23707 315 5390 2 10386 121282 11574 8636 6596 66678 906 16506 0.995791 0 . 0 . 65 22,11,24,8 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A920|1042|SIPA1|protein_coding|CODING|NM_006747.3|13|A),DOWNSTREAM(MODIFIER||3633||551|RELA|protein_coding|CODING|NM_021975.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.486387 rs746429 -0.69312 0.602072 65 546 149 MODIFIER 1 CODING KAT5 T protein_coding NM_182710.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65479590 A T 0 49.4 0 0 0.0031949 0 0.0159 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 7 3,0,4,0 START_GAINED(LOW||||546|KAT5|protein_coding|CODING|NM_182710.2|1|T),UTR_5_PRIME(MODIFIER||149||546|KAT5|protein_coding|CODING|NM_182710.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.405132 rs4645911 -0.556411 0.152777 7 164 1527 MODIFIER 4 CODING RNASEH2C G protein_coding NM_032193.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65485727 T G 0 9.7 0 0.8011 0.8249 0.8963 0.9018 0.9145 0.635 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1527||164|RNASEH2C|protein_coding|CODING|NM_032193.3|4|G),INTRON(MODIFIER||||546|KAT5|protein_coding|CODING|NM_182710.2|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386597989,rs521678 -0.379885 0 1 878 3901 MODIFIER 2 CODING AP5B1 C protein_coding NM_138368.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65541426 T C 0 9.7 0 0.969 0.9918 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3901||878|AP5B1|protein_coding|CODING|NM_138368.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2508302 -0.379885 0 1 878 1715 MODIFIER 2 CODING AP5B1 T protein_coding NM_138368.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65543612 G T 0 39.3 0 0.9614 0.9896 1 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1715||878|AP5B1|protein_coding|CODING|NM_138368.4|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2508299 -0.453602 0.7 2 267 165 MODIFIER 1 CODING OVOL1 G protein_coding NM_004561.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65554680 C G 0 110 0 0.7141 0.6915 0.5836 0.6101 0.8817 0.6258 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.821542 0 . 0 . 51 31,0,20,0 UTR_5_PRIME(MODIFIER||165||267|OVOL1|protein_coding|CODING|NM_004561.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.886021 rs10896044 -0.692067 0.223882 51 267 40 MODIFIER 4 CODING OVOL1 C protein_coding NM_004561.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65562852 G C 0 222 0 0.0424 0.1881 0.3588 0.1577 0.1153 0.3701 0.062096 0.0933354 0.10929 1 170 4405 289 115 35 1596 29 2171 2 2588 20886 696 712 232 9998 174 6486 0.456205 0 . 0 . 69 8,35,10,15 UTR_3_PRIME(MODIFIER||40||267|OVOL1|protein_coding|CODING|NM_004561.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.642138 rs72922786 -0.692914 0.24648 69 267 691 MODIFIER 4 CODING OVOL1 T protein_coding NM_004561.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65563502 TA T 0 222 0 0.0666 0.2175 0.3905 0.1885 0.1451 0.4029 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 129 29,26,27,30 UTR_3_PRIME(MODIFIER||691||267|OVOL1|protein_coding|CODING|NM_004561.3|4|T) 0 0.5 1 61 0.462121 1 1 0 . 0 60 0 0 1 0 . rs78712280 -0.693147 0.0320409 129 403 71 MODIFIER 1 CODING SNX32 T protein_coding NM_152760.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65601466 C T 0 222 0 0.0507 0.2117 0.3602 0.253 0.1352 0.3599 0.0715318 0.117389 0.137335 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987531 0 . 0 . 193 84,16,69,16 UTR_5_PRIME(MODIFIER||71||403|SNX32|protein_coding|CODING|NM_152760.2|1|T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.990557 rs59416249 -0.693147 4.61717e-05 193 403 251 MODIFIER 13 CODING SNX32 C protein_coding NM_152760.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65621057 T C 0 60 0 0.2035 0.4283 0.4063 0.3294 0.668 0.6033 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.62023 0 . 0 . 8 1,3,0,4 UTR_3_PRIME(MODIFIER||251||403|SNX32|protein_coding|CODING|NM_152760.2|13|C),DOWNSTREAM(MODIFIER||1228||166|CFL1|protein_coding|CODING|NM_005507.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.868321 rs656040 -0.556411 0.134765 8 D66 166 gaC/gaT LOW 2 SILENT CODING CFL1 A protein_coding NM_005507.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65623519 G A 0 222 0 0.2012 0.4279 0.4063 0.3313 0.668 0.6022 0.261699 0.530163 0.667675 1 2645 70236 4131 2815 4653 44927 585 10480 2 10406 121378 11574 8632 6614 66736 908 16508 0.279298 0 . 0 . 190 51,37,47,38 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D66|166|CFL1|protein_coding|CODING|NM_005507.2|2|A),UPSTREAM(MODIFIER||4353||551|MUS81|protein_coding|CODING|NM_025128.4||A),DOWNSTREAM(MODIFIER||2347||403|SNX32|protein_coding|CODING|NM_152760.2||A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.991115 0.993424 0 0.993538 rs4621 -0.693147 0.0463902 190 R37H 551 cGc/cAc MODERATE 1 MISSENSE CODING MUS81 A protein_coding NM_025128.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65628334 G A 0 16.7 0 0.2012 0.4279 0.4063 0.3323 0.667 0.6022 0.300378 0.552553 0.679539 1 635 16076 366 491 358 8530 152 5544 2 1594 24114 668 990 472 11768 216 8406 0.938795 0 . 0 . 22 11,4,2,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R37H|551|MUS81|protein_coding|CODING|NM_025128.4|1|A),UPSTREAM(MODIFIER||2530||166|CFL1|protein_coding|CODING|NM_005507.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.709028 rs13817 -0.511536 0.635923 22 A179 551 gcT/gcC LOW 6 SILENT CODING MUS81 C protein_coding NM_025128.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65629932 T C 0 222 0 0.2012 0.4281 0.4063 0.3323 0.668 0.6022 0.253748 0.524704 0.663524 1 2619 69492 4054 2773 4607 44427 577 10435 2 10358 120808 11532 8626 6592 66318 900 16482 0.980506 0 . 0 . 120 27,30,19,24 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A179|551|MUS81|protein_coding|CODING|NM_025128.4|6|C),UPSTREAM(MODIFIER||4128||166|CFL1|protein_coding|CODING|NM_005507.2||C),DOWNSTREAM(MODIFIER||3980||443|EFEMP2|protein_coding|CODING|NM_016938.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846224 rs659857 -0.693146 0.0204659 120 R180P 551 cGa/cCa MODERATE 6 MISSENSE CODING MUS81 C protein_coding NM_025128.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65629934 G C 0 222 0 0.2012 0.4281 0.4063 0.3323 0.668 0.6022 0.255338 0.526166 0.664921 1 2621 69483 4056 2766 4605 44427 578 10430 2 10358 120804 11538 8620 6590 66320 902 16476 0.960805 0 . 0 . 117 25,30,19,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cCa|R180P|551|MUS81|protein_coding|CODING|NM_025128.4|6|C),UPSTREAM(MODIFIER||4130||166|CFL1|protein_coding|CODING|NM_005507.2||C),DOWNSTREAM(MODIFIER||3978||443|EFEMP2|protein_coding|CODING|NM_016938.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962728 rs545500 -0.693146 0.0204659 117 A312 551 gcC/gcT LOW 9 SILENT CODING MUS81 T protein_coding NM_025128.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65631167 C T 0 222 0 0.2012 0.4281 0.4063 0.3323 0.668 0.6022 0.261245 0.530168 0.667947 1 2645 70123 4116 2814 4652 44838 583 10475 2 10384 121128 11534 8624 6594 66580 906 16506 0.967523 0 . 0 . 119 43,21,34,16 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A312|551|MUS81|protein_coding|CODING|NM_025128.4|9|T),DOWNSTREAM(MODIFIER||2745||443|EFEMP2|protein_coding|CODING|NM_016938.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.963882 rs648732 -0.693147 0.528332 119 R355 551 cgG/cgA LOW 11 SILENT CODING MUS81 A protein_coding NM_025128.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65631973 G A 0 222 0 0.208 0.4299 0.4063 0.3323 0.668 0.6022 0.263062 0.530783 0.667947 1 2673 70228 4125 2819 4650 44900 582 10479 2 10388 121234 11542 8614 6606 66674 906 16504 0.54134 0 . 0 COSM1179750 100 28,19,27,17 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R355|551|MUS81|protein_coding|CODING|NM_025128.4|11|A),DOWNSTREAM(MODIFIER||1939||443|EFEMP2|protein_coding|CODING|NM_016938.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916748 rs630303 -0.693146 0.744722 100 T416 551 acG/acT LOW 12 SILENT CODING MUS81 T protein_coding NM_025128.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65632262 G T 0 222 0 0.202 0.4283 0.4063 0.3323 0.668 0.6022 0.261018 0.52986 0.667598 1 2631 69969 4100 2797 4630 44757 581 10473 2 10252 120860 11520 8606 6586 66498 904 16494 0.799943 0 . 0 . 57 8,17,7,21 SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T416|551|MUS81|protein_coding|CODING|NM_025128.4|12|T),DOWNSTREAM(MODIFIER||1650||443|EFEMP2|protein_coding|CODING|NM_016938.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0542406 rs558114 -0.693054 0.103464 57 I259V 443 Atc/Gtc MODERATE 8 MISSENSE CODING EFEMP2 C protein_coding NM_016938.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65636053 T C 0 228 0 0.6248 0.8946 0.9597 1 0.997 0.999 0.691504 0.89449 0.998487 2 7029 117556 11391 8644 6612 66498 894 16488 2 10378 121254 11574 8644 6614 66626 906 16512 0 2|2 benign|benign 0 . 173 0,0,137,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I259V|443|EFEMP2|protein_coding|CODING|NM_016938.4|8|C),DOWNSTREAM(MODIFIER||2139||551|MUS81|protein_coding|CODING|NM_025128.4||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs601314 -0.693147 0.253062 173 H92 443 caC/caT LOW 4 SILENT CODING EFEMP2 A protein_coding NM_016938.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65638719 G A 0 222 0 0.0953 0.3211 0.3127 0.2262 0.503 0.5429 0.1597 0.396645 0.51804 1 1594 54595 3163 1735 3768 34428 468 9439 2 10392 121254 11562 8612 6612 66656 908 16512 0.103352 2 benign 0 . 204 61,37,45,34 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H92|443|EFEMP2|protein_coding|CODING|NM_016938.4|4|A),DOWNSTREAM(MODIFIER||4805||551|MUS81|protein_coding|CODING|NM_025128.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.634039 rs633800 -0.693147 0.295114 204 443 379 MODIFIER 1 CODING EFEMP2 T protein_coding NM_016938.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65640204 C T 0 16.4 0 0.4902 0.6206 0.7089 0.4812 0.6521 0.8456 0 . 0 2 107 7556 64 52 0 1539 74 5720 2 160 9544 82 116 0 2202 104 6880 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||379||443|EFEMP2|protein_coding|CODING|NM_016938.4|1|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs2303384 -0.453602 0.66 2 S139G 376 Agc/Ggc MODERATE 4 MISSENSE CODING CTSW G protein_coding NM_001335.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65649774 A G 0 228 0 0.7451 0.9273 0.964 1 0.998 1 0.805089 0.933431 0.999185 2 8187 118938 11462 8652 6612 66627 899 16499 2 10406 121390 11576 8654 6614 66724 906 16510 0 . 0 . 0 105 0,0,49,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S139G|376|CTSW|protein_coding|CODING|NM_001335.3|4|G),DOWNSTREAM(MODIFIER||1437||364|FIBP|protein_coding|CODING|NM_198897.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs604630 -0.693147 0.219286 105 D175 376 gaT/gaC LOW 5 SILENT CODING CTSW C protein_coding NM_001335.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65649984 T C 0 228 0 0.4947 0.6967 0.7839 0.5903 0.8111 0.8998 0.565198 0.724719 0.806448 2 5720 95641 9766 5019 5547 54199 729 14661 2 10398 121362 11572 8638 6608 66726 908 16512 1 0 . 0 . 92 1,0,45,40 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D175|376|CTSW|protein_coding|CODING|NM_001335.3|5|C),DOWNSTREAM(MODIFIER||1227||364|FIBP|protein_coding|CODING|NM_198897.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs687672 -0.693147 0.00449257 92 Q77 271 caA/caG LOW 2 SILENT CODING FOSL1 C protein_coding NM_005438.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65664346 T C 0 222 0 0.559 0.5685 0.6412 0.746 0.4523 0.4663 0.561563 0.483993 0.44425 1 5831 61426 8398 6615 2596 29772 421 7793 2 10374 120986 11562 8634 6588 66422 902 16504 0.96134 0 . 0 . 109 25,32,23,21 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q77|271|FOSL1|protein_coding|CODING|NM_005438.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0638421 rs637571 -0.693146 0.73302 109 F5 271 ttC/ttT LOW 1 SILENT CODING FOSL1 A protein_coding NM_005438.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65667796 G A 0 89 0 0.0424 0.3618 0.5692 0.4841 0.4374 0.4427 0.0741127 0.213123 0.274379 1 10 175 19 5 0 94 0 47 2 52 318 28 8 0 162 2 66 0.761877 0 . 0 . 10 2,3,1,4 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F5|271|FOSL1|protein_coding|CODING|NM_005438.4|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.952347 0.916482 0 0.523791 rs1058068 -0.590765 0.304345 10 293 75 MODIFIER 2 CODING C11orf68 G protein_coding NM_001135635.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65684855 A G 0 228 0 0.6589 0.8978 0.951 1 0.9821 0.9908 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,27,11 UTR_3_PRIME(MODIFIER||75||293|C11orf68|protein_coding|CODING|NM_001135635.1|2|G),UPSTREAM(MODIFIER||1873||205|DRAP1|protein_coding|CODING|NM_006442.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9326360 -0.693143 0.251933 38 293 1 MODIFIER 2 CODING C11orf68 T protein_coding NM_001135635.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65684929 C T 0 228 0 0.882 0.9661 0.9798 1 1 1 0.890504 0.962521 0.999418 2 9164 117712 11457 8638 6614 65890 875 15074 2 10352 119060 11550 8638 6614 65950 878 15078 0 . 0 . 0 49 0,0,32,15 UTR_3_PRIME(MODIFIER||1||293|C11orf68|protein_coding|CODING|NM_001135635.1|2|T),UPSTREAM(MODIFIER||1799||205|DRAP1|protein_coding|CODING|NM_006442.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9667389 -0.693147 0.00587309 49 Q196R 293 cAg/cGg MODERATE 2 MISSENSE CODING C11orf68 C protein_coding NM_001135635.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65685225 T C 0 228 0 0.6589 0.8978 0.951 1 0.9821 0.9908 0.692413 0.88587 0.984986 2 7005 116016 11212 8616 6552 65405 872 16354 2 10302 120712 11528 8616 6574 66302 898 16492 0 . 0 . 0 120 0,0,67,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q196R|293|C11orf68|protein_coding|CODING|NM_001135635.1|2|C),UPSTREAM(MODIFIER||1503||205|DRAP1|protein_coding|CODING|NM_006442.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7947504 -0.693147 0.0400826 120 *21R 556 Tga/Cga HIGH 1 MISSENSE CODING TSGA10IP C protein_coding NM_152762.2 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65713207 T C 0 228 0 0.9977 0.9994 1 1 1 1 0.998082 0.999283 0.999881 2 9624 120545 11562 8626 6614 66712 895 16512 2 9798 120738 11574 8626 6614 66718 896 16512 0 . 0 . 0 200 0,0,125,59 STOP_LOST(HIGH|MISSENSE|Tga/Cga|*21R|556|TSGA10IP|protein_coding|CODING|NM_152762.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9795469 -0.693147 0.00541751 200 M521V 556 Atg/Gtg MODERATE 8 MISSENSE CODING TSGA10IP G protein_coding NM_152762.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65727301 A G 0 222 0 0.3094 0.4413 0.6066 0.5218 0.4404 0.4202 0.316242 0.401575 0.44147 1 1288 20082 1222 1223 1090 10857 164 4238 2 3310 38812 1726 2024 2060 20052 334 9306 0.937555 0 . 0 . 49 19,8,8,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M521V|556|TSGA10IP|protein_coding|CODING|NM_152762.2|8|G),UPSTREAM(MODIFIER||1859||800|SART1|protein_coding|CODING|NM_005146.4||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965129 rs386596418,rs491973 -0.691153 0.0792407 49 A172 800 gcG/gcA LOW 4 SILENT CODING SART1 A protein_coding NM_005146.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65732651 G A 0 172 0 0.3079 0.4395 0.6023 0.5218 0.4364 0.4202 0.333939 0.411561 0.451339 1 3315 54586 7931 4356 2507 29048 374 7055 2 9780 118062 11456 8542 6432 64554 878 16420 0.779627 0 . 0 . 29 13,4,5,6 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A172|800|SART1|protein_coding|CODING|NM_005146.4|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.739917 rs550435 -0.676189 0.323435 29 T258 800 acC/acT LOW 7 SILENT CODING SART1 T protein_coding NM_005146.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65733393 C T 0 222 0 0.2716 0.3764 0.3228 0.2183 0.5278 0.5634 0.309405 0.448207 0.51932 1 3119 56601 3021 1848 3850 35159 475 9129 2 10390 121186 11564 8640 6610 66568 906 16508 0.981503 0 . 0 COSM429623 80 10,25,11,27 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T258|800|SART1|protein_coding|CODING|NM_005146.4|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.876501 rs688862 -0.693143 0.0932064 80 G485A 800 gGg/gCg MODERATE 12 MISSENSE CODING SART1 C protein_coding NM_005146.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65735174 G C 0 162 0 0.0393 0.3662 0.5793 0.5218 0.4404 0.4202 0.10241 0.309065 0.414519 1 420 16115 707 1498 257 9055 121 4057 2 3148 34144 1042 2558 516 17494 260 9126 0.977114 0 . 0 . 31 8,11,3,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G485A|800|SART1|protein_coding|CODING|NM_005146.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.27191 rs660118 -0.676189 0.582136 31 800 152 MODIFIER 20 CODING SART1 G protein_coding NM_005146.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65746653 A G 0 175 0 0.1929 0.4135 0.5879 0.5198 0.4404 0.4509 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.963419 0 . 0 . 23 0,8,1,13 UTR_3_PRIME(MODIFIER||152||800|SART1|protein_coding|CODING|NM_005146.4|20|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.994773 rs679581 -0.686358 0.214987 23 800 693 MODIFIER 20 CODING SART1 C protein_coding NM_005146.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65747194 T C 0 9.7 0 0.9607 0.9882 0.9971 1 1 0.9949 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||693||800|SART1|protein_coding|CODING|NM_005146.4|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs879509 -0.379885 0 1 165 1940 MODIFIER 6 CODING EIF1AD G protein_coding NM_001242481.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65764130 A G 0 9.7 0 0.8003 0.9205 0.9726 0.8899 1 0.9959 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1940||165|EIF1AD|protein_coding|CODING|NM_001242481.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2847698 -0.379885 0 1 165 519 MODIFIER 6 CODING EIF1AD T protein_coding NM_001242481.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65765551 C T 0 6.3 0 0.4236 0.6729 0.8127 0.6895 0.7863 0.7771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||519||165|EIF1AD|protein_coding|CODING|NM_001242481.1|6|T),UPSTREAM(MODIFIER||3999||89|BANF1|protein_coding|CODING|NM_001143985.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386601560,rs610497 -0.379885 0 1 165 LOW 3 CODING EIF1AD G protein_coding NM_001242481.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65767153 A G 0 228 0 0.5461 0.7482 0.8516 0.8333 0.8161 0.7904 0.583826 0.738956 0.818436 2 6034 98027 10232 7211 5785 54925 739 13101 2 10258 120786 11538 8622 6592 66420 906 16450 1 0 . 0 . 51 0,1,5,43 SPLICE_SITE_REGION+INTRON(LOW||||165|EIF1AD|protein_coding|CODING|NM_001242481.1|3|G),UPSTREAM(MODIFIER||2397||89|BANF1|protein_coding|CODING|NM_001143985.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs507672 -0.693147 0.168168 51 V652I 780 Gta/Ata MODERATE 7 MISSENSE CODING CATSPER1 T protein_coding NM_053054.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65788072 C T 0 228 0 0.8616 0.9365 0.9755 0.8859 1 0.9969 0.890227 0.962438 0.999418 2 9004 115802 11110 7544 6472 64931 849 15892 2 10180 118208 11332 8458 6472 64956 856 15954 0 . 0 . 0 77 0,0,35,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V652I|780|CATSPER1|protein_coding|CODING|NM_053054.3|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3814747 -0.693147 0.240662 77 R408 780 Cgg/Agg LOW 2 SILENT CODING CATSPER1 T protein_coding NM_053054.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65790527 G T 0 228 0 0.1906 0.4319 0.3847 0.377 0.5616 0.7147 0.239891 0.454517 0.564479 2 2416 62691 4327 2947 3545 37359 481 11616 2 10274 120896 11514 8600 6608 66510 904 16486 0 . 0 . 0 75 0,0,21,51 SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R408|780|CATSPER1|protein_coding|CODING|NM_053054.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2845570 -0.693147 0.0398458 75 431 1511 MODIFIER 3 CODING GAL3ST3 T protein_coding NM_033036.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65808467 C T 0 32.6 0 0.1952 0.4341 0.3876 0.379 0.5616 0.7157 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1511||431|GAL3ST3|protein_coding|CODING|NM_033036.2|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2576 -0.379885 0 2 431 103 MODIFIER 3 CODING GAL3ST3 A protein_coding NM_033036.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65809875 C A 0 228 0 0.5401 0.7394 0.8372 0.7639 0.837 0.8139 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 188 0,1,78,88 UTR_3_PRIME(MODIFIER||103||431|GAL3ST3|protein_coding|CODING|NM_033036.2|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs1125078 -0.693147 4.41213e-05 188 P355 431 ccG/ccA LOW 3 SILENT CODING GAL3ST3 T protein_coding NM_033036.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65810209 C T 0 95 0 0.5408 0.7514 0.8746 0.7649 0.8549 0.8282 0.724566 0.859924 0.926339 2 231 9121 78 95 0 2342 98 6277 2 364 10870 94 136 0 2734 120 7422 0 . 0 . 0 5 0,0,1,3 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P355|431|GAL3ST3|protein_coding|CODING|NM_033036.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs61895584 -0.556411 0.249971 5 V175 431 gtA/gtG LOW 3 SILENT CODING GAL3ST3 C protein_coding NM_033036.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 65810749 T C 0 228 0 0.8623 0.9359 0.9769 0.881 1 0.9969 0.893003 0.963268 0.999301 2 8847 115962 11181 7487 6474 64774 873 16326 2 9952 118350 11402 8450 6474 64804 878 16390 0 . 0 . 0 106 0,0,39,61 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V175|431|GAL3ST3|protein_coding|CODING|NM_033036.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7937692 -0.693147 0.742647 106 963 LOW 23 CODING PACS1 C protein_coding NM_018026.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66010633 T C 0 228 0 0.9387 0.983 0.9942 1 1 1 0.950227 0.982987 0.999767 2 9830 120278 11490 8628 6584 66401 903 16442 2 10354 120834 11514 8628 6584 66408 904 16442 0 3 likely-benign 0 . 79 0,0,45,24 SPLICE_SITE_REGION+INTRON(LOW||||963|PACS1|protein_coding|CODING|NM_018026.3|23|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs524268 -0.693147 0.236332 79 D362 622 gaC/gaT LOW 8 SILENT CODING KLC2 T protein_coding NM_001134775.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66031660 C T 0 222 0 0.205 0.3323 0.5086 0.252 0.4841 0.3057 0.247035 0.390106 0.463261 1 1204 19412 1303 742 813 11741 160 3449 2 4440 43476 2316 2326 1462 22968 352 9612 0.133441 0 . 0 . 97 23,17,28,23 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D362|622|KLC2|protein_coding|CODING|NM_001134775.1|8|T),UPSTREAM(MODIFIER||4396||201|RAB1B|protein_coding|CODING|NM_030981.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.787256 rs1151539 -0.693147 0.0107541 97 622 860 MODIFIER 16 CODING KLC2 C protein_coding NM_001134775.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66035286 CA C 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 79 0,0,39,25 UTR_3_PRIME(MODIFIER||860||622|KLC2|protein_coding|CODING|NM_001134775.1|16|C),UPSTREAM(MODIFIER||769||201|RAB1B|protein_coding|CODING|NM_030981.2||C) 0 . 0 74 0.936709 1 1 0 . 0 60 0 0 1 0 . rs5792385 -0.693147 0.0755288 79 201 189 MODIFIER 6 CODING RAB1B A protein_coding NM_030981.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66043898 G A 0 148 0 0.2042 0.3319 0.5086 0.252 0.4831 0.3057 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.370102 0 . 0 . 54 26,1,26,1 UTR_3_PRIME(MODIFIER||189||201|RAB1B|protein_coding|CODING|NM_030981.2|6|A),UPSTREAM(MODIFIER||1774||160|CNIH2|protein_coding|CODING|NM_182553.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.723562 rs2508657 -0.693021 0.74935 54 160 LOW 4 CODING CNIH2 A protein_coding NM_182553.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66050712 G A 0 199 0 0.0507 0.1657 0.1715 0.0516 0.3618 0.2331 0.095 0.262048 0.347614 1 917 32651 1616 388 2314 22993 277 4146 2 10388 121226 11568 8648 6612 66594 906 16510 0.948756 0 . 0 . 46 19,8,14,4 SPLICE_SITE_REGION+INTRON(LOW||||160|CNIH2|protein_coding|CODING|NM_182553.2|4|A),DOWNSTREAM(MODIFIER||1339||293|YIF1A|protein_coding|CODING|NM_020470.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.766206 rs4073582 -0.691153 0.0938959 46 P130R 293 cCc/cGc MODERATE 4 MISSENSE CODING YIF1A C protein_coding NM_020470.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66055107 G C 0 222 0 0 0.0015974 0 0.0079 0 0 0 . 0 1 0 126 0 123 0 1 0 2 2 9784 117622 11250 8506 6456 64356 884 16386 0.225642 0 . 0 COSM147272 78 16,12,21,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cGc|P130R|293|YIF1A|protein_coding|CODING|NM_020470.2|4|C),UPSTREAM(MODIFIER||4266||468|TMEM151A|protein_coding|CODING|NM_153266.3||C),DOWNSTREAM(MODIFIER||3422||160|CNIH2|protein_coding|CODING|NM_182553.2||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0414193 rs139558494 -0.693143 0.0446218 78 468 508 MODIFIER 2 CODING TMEM151A G protein_coding NM_153266.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66063632 A G 0 222 0 0.1278 0.0787 0.0259 0.1835 0.0159 0.0061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.468929 0 . 0 . 109 16,40,9,37 UTR_3_PRIME(MODIFIER||508||468|TMEM151A|protein_coding|CODING|NM_153266.3|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998893 rs79790477 -0.693147 0.257054 109 H457R 757 cAt/cGt MODERATE 1 MISSENSE CODING CD248 C protein_coding NM_020404.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66083129 T C 0 222 0 0.1732 0.2921 0.5476 0.2093 0.4433 0.2014 0.227045 0.375982 0.45227 1 2265 48434 6706 1637 3425 30018 383 4000 2 10400 121250 11556 8634 6608 66640 906 16506 0.924192 0 . 0 . 113 31,27,19,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H457R|757|CD248|protein_coding|CODING|NM_020404.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962308 rs3741367 -0.693143 0.0802873 113 N239 757 aaC/aaT LOW 1 SILENT CODING CD248 A protein_coding NM_020404.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66083782 G A 0 222 0 0.0378 0.2554 0.5303 0.2272 0.4463 0.1871 0.100682 0.329097 0.446179 1 876 45850 6593 1724 3344 29265 355 3693 2 9384 117906 11458 8484 6396 64894 862 16428 0.8747 0 . 0 COSM429643 32 5,6,6,11 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N239|757|CD248|protein_coding|CODING|NM_020404.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.792454 rs3741368 -0.690438 0.825867 32 A704 783 gcG/gcA LOW 10 SILENT CODING RIN1 T protein_coding NM_004292.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66099987 C T 0 222 0 0.2209 0.5607 0.7334 0.5595 0.662 0.7945 0.294318 0.556351 0.69057 1 2948 80896 9399 4520 4736 45532 622 13139 2 10386 121280 11574 8622 6610 66684 904 16500 0.333794 0 . 0 . 96 37,13,31,13 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A704|783|RIN1|protein_coding|CODING|NM_004292.2|10|T),DOWNSTREAM(MODIFIER||4817||290|BRMS1|protein_coding|CODING|NM_001024957.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.392461 rs1784029 -0.693146 0.0910121 96 E649 783 gaA/gaG LOW 10 SILENT CODING RIN1 C protein_coding NM_004292.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66100152 T C 0 228 0 0.8858 0.9675 0.9856 1 0.998 1 0.91242 0.969506 0.998719 2 9289 112371 11473 8622 6614 64504 817 11052 2 10240 113394 11510 8622 6614 64530 822 11056 1 0 . 0 . 152 1,0,41,95 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E649|783|RIN1|protein_coding|CODING|NM_004292.2|10|C),DOWNSTREAM(MODIFIER||4652||290|BRMS1|protein_coding|CODING|NM_001024957.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1784030 -0.693147 0.385875 152 P394 783 ccC/ccT LOW 6 SILENT CODING RIN1 A protein_coding NM_004292.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66102088 G A 0 17.4 0 0.3026 0.1478 0.0836 0.1399 0.0885 0.0532 0.254708 0.136724 0.076472 1 1400 5784 225 611 69 2826 36 617 2 3878 34896 1756 2562 508 17122 234 8836 1 0 . 0 . 17 5,7,0,3 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P394|783|RIN1|protein_coding|CODING|NM_004292.2|6|A),DOWNSTREAM(MODIFIER||2716||290|BRMS1|protein_coding|CODING|NM_001024957.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.687289 rs3814740 -0.511536 0.690245 17 D182 290 gaT/gaC LOW 7 SILENT CODING BRMS1 G protein_coding NM_001024957.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66107674 A G 0 228 0 0.885 0.9669 0.9827 1 0.998 1 0.909318 0.968514 0.998836 2 9391 120219 11526 8654 6608 66647 901 16492 2 10374 121284 11570 8654 6608 66676 906 16496 0 . 0 . 0 35 0,0,9,25 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D182|290|BRMS1|protein_coding|CODING|NM_001024957.1|7|G),UPSTREAM(MODIFIER||3674||783|RIN1|protein_coding|CODING|NM_004292.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1784035 -0.693132 2.00247e-06 35 L67 290 ctA/ctG LOW 3 SILENT CODING BRMS1 C protein_coding NM_001024957.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66109033 T C 0 187 0 0.0234 0.1408 0.17 0.0327 0.329 0.1963 0.0675 0.242571 0.332247 1 636 29613 1469 264 2263 21424 243 3314 2 10400 121376 11570 8650 6614 66726 908 16508 0.524006 0 . 0 . 64 17,25,5,14 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L67|290|BRMS1|protein_coding|CODING|NM_001024957.1|3|C),DOWNSTREAM(MODIFIER||3810||415|B4GAT1|protein_coding|CODING|NM_006876.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994075 rs11537993 -0.69168 0.0921717 64 Q39 415 caG/caA LOW 1 SILENT CODING B4GAT1 T protein_coding NM_006876.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66114900 C T 0 222 0 0.2526 0.1394 0.0749 0.1696 0.0915 0.0501 0.226321 0.126021 0.0746912 1 1799 8762 412 1284 214 4432 60 561 2 5742 50882 3864 4646 1606 29590 340 5094 0.702859 0 . 0 . 132 17,42,20,40 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q39|415|B4GAT1|protein_coding|CODING|NM_006876.2|1|T),UPSTREAM(MODIFIER||2318||290|BRMS1|protein_coding|CODING|NM_001024957.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979282 rs11537930 -0.693147 0.0441021 132 456 359 MODIFIER 14 CODING SLC29A2 T protein_coding NM_001300868.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66130548 C T 0 6.3 0 0.2231 0.5711 0.7349 0.5794 0.66 0.8252 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||359||456|SLC29A2|protein_coding|CODING|NM_001300868.1|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1047029 -0.379885 0 1 456 171 MODIFIER 14 CODING SLC29A2 G protein_coding NM_001300868.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66130736 A G 0 228 0 0.8026 0.9443 0.9769 1 0.998 1 0 . 0 2 842 12722 252 366 24 4628 154 6456 2 1036 12926 258 366 24 4630 154 6458 0 . 0 . 0 48 0,0,45,2 UTR_3_PRIME(MODIFIER||171||456|SLC29A2|protein_coding|CODING|NM_001300868.1|14|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1039593 -0.693147 0.19392 48 L37 802 ctG/ctT LOW 1 SILENT CODING NPAS4 T protein_coding NM_178864.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66188761 G T 0 222 0 0.0204 0.1697 0.3963 0.1696 0.2157 0.1636 0.0511364 0.160046 0.215832 1 479 26670 5576 1117 1994 14406 209 2889 2 10334 120798 11546 8620 6584 66306 900 16508 0.987832 0 . 0 . 168 33,50,25,40 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctT|L37|802|NPAS4|protein_coding|CODING|NM_178864.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.935517 rs77600363 -0.693147 0.337217 168 192 453 MODIFIER 5 CODING MRPL11 C protein_coding NM_016050.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66203025 A C 0 6.3 0 0.3933 0.2696 0.183 0.2867 0.2425 0.1738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||453||192|MRPL11|protein_coding|CODING|NM_016050.4|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2279865 -0.379885 0 1 D209 469 gaT/gaC LOW 6 SILENT CODING PELI3 C protein_coding NM_145065.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66240882 T C 0 228 0 0.3623 0.265 0.1801 0.2877 0.2425 0.1933 0.326136 0.265589 0.234575 2 3472 29084 1614 2198 2538 15795 228 3239 2 10276 119010 11446 8562 6436 65608 880 15802 0 . 0 . 0 50 0,0,19,28 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D209|469|PELI3|protein_coding|CODING|NM_145065.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2277302 -0.693147 0.121409 50 Q145H 737 caG/caT MODERATE 4 MISSENSE CODING DPP3 T protein_coding NM_005700.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66254085 G T 0 228 0 0.1884 0.2163 0.1599 0.2887 0.2416 0.1933 0.168636 0.211624 0.233644 2 1789 27296 1540 2206 2535 15810 225 3191 2 10386 120364 11574 8636 6608 66366 902 15892 0 . 0 . COSM147273 67 0,0,31,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q145H|737|DPP3|protein_coding|CODING|NM_005700.4|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11550299 -0.693147 0.258347 67 T646 737 acA/acG LOW 17 SILENT CODING DPP3 G protein_coding NM_005700.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66272142 A G 0 228 0 0.916 0.615 0.4496 0.5486 0.6113 0.3978 0.848864 0.678214 0.590803 2 8958 69184 3881 4580 4329 40220 539 6677 2 10404 121260 11562 8608 6614 66696 908 16468 0 . 0 . 0 129 0,0,61,60 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T646|737|DPP3|protein_coding|CODING|NM_005700.4|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1671063 -0.693147 0.00132545 129 R678H 737 cGc/cAc MODERATE 17 MISSENSE CODING DPP3 A protein_coding NM_005700.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66272237 G A 0 228 0 0.1475 0.2117 0.1614 0.3036 0.2396 0.2106 0.133409 0.197691 0.230617 2 1392 26986 1510 2292 2510 15623 222 3437 2 10374 119880 11564 8628 6614 66246 890 15564 1 0 . 0 . 106 1,0,33,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R678H|737|DPP3|protein_coding|CODING|NM_005700.4|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2305535 -0.693147 0.136519 106 737 127 MODIFIER 18 CODING DPP3 A protein_coding NM_005700.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66276849 G A 0 228 0 0.1293 0.0665 0.0173 0.1488 0 0 0 . 0 2 110 192 2 63 0 3 2 12 2 922 13536 264 310 10 4116 142 7772 0.0183486 0 . 0 . 121 1,1,74,35 UTR_3_PRIME(MODIFIER||127||737|DPP3|protein_coding|CODING|NM_005700.4|18|A),UPSTREAM(MODIFIER||1270||593|BBS1|protein_coding|CODING|NM_024649.4||A) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 0.389908 rs2290462 -0.693147 0.00222041 121 L126 593 ctG/ctA LOW 4 SILENT CODING BBS1 A protein_coding NM_024649.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66282095 G A 0 228 0 0.1475 0.2117 0.1614 0.3036 0.2396 0.2106 0.133182 0.197614 0.230617 2 1387 27024 1508 2282 2510 15620 222 3495 2 10352 121032 11540 8598 6606 66532 908 16496 1 0 . 0 COSM147274 160 1,0,73,65 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L126|593|BBS1|protein_coding|CODING|NM_024649.4|4|A),DOWNSTREAM(MODIFIER||4965||737|DPP3|protein_coding|CODING|NM_005700.4||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2298806,rs386475528 -0.693147 0.235962 160 593 LOW 8 CODING BBS1 C protein_coding NM_024649.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66288733 G C 0 228 0 0.2587 0.2426 0.1729 0.3036 0.2396 0.2106 0.226591 0.229561 0.231083 2 2405 28119 1555 2282 2507 15649 221 3500 2 10382 121156 11544 8634 6572 66632 908 16484 0 2 benign 0 COSM147275 103 0,0,63,28 SPLICE_SITE_REGION+INTRON(LOW||||593|BBS1|protein_coding|CODING|NM_024649.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10896125 -0.693147 0.059626 103 593 7 MODIFIER 17 CODING BBS1 G protein_coding NM_024649.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66299515 A G 0 228 0 0.9054 0.6128 0.4496 0.5486 0.6133 0.3988 0.842896 0.676616 0.591439 2 6130 47724 2450 3286 1736 28549 346 5227 2 7170 80974 6140 5858 2602 46366 584 12254 1 0 . 0 . 30 0,1,9,16 UTR_3_PRIME(MODIFIER||7||593|BBS1|protein_coding|CODING|NM_024649.4|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs8432 -0.692914 0.32795 30 Q91R 284 cAg/cGg MODERATE 1 MISSENSE CODING ZDHHC24 C protein_coding NM_207340.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66313203 T C 0 228 0 0.1891 0.2278 0.17 0.3165 0.2416 0.2157 0.132861 0.166114 0.182141 2 902 16703 997 1738 963 9600 111 2392 2 3108 50908 4420 4752 2008 28058 360 8202 0 . 0 . 0 12 0,0,7,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q91R|284|ZDHHC24|protein_coding|CODING|NM_207340.1|1|C),UPSTREAM(MODIFIER||663||944|ACTN3|protein_coding|CODING|NM_001258371.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.964642 0 . rs2305534 -0.676189 0.0408454 12 R566Q 944 cGg/cAg MODERATE 14 MISSENSE CODING ACTN3 A protein_coding NM_001258371.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66327673 G A 0 228 0 0.8449 0.5865 0.4193 0.5565 0.5606 0.4131 0.79274 0.633396 0.553387 2 7034 58945 3288 4371 3370 33909 450 6523 2 8644 99596 7980 7304 4574 56328 740 14026 0 . 0 . 0 55 0,0,52,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R566Q|944|ACTN3|protein_coding|CODING|NM_001258371.2|14|A),DOWNSTREAM(MODIFIER||3262||484|CTSF|protein_coding|CODING|NM_003793.3||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs1671064 -0.693147 0.0423312 55 T606 944 acA/acG LOW 15 SILENT CODING ACTN3 G protein_coding NM_001258371.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66328055 A G 0 228 0 0.1732 0.1627 0.1023 0.1815 0.168 0.1667 0.136679 0.15931 0.170763 2 1443 19068 859 1515 1414 10894 136 2807 2 9668 117356 11494 8538 6412 65444 854 14946 1 0 . 0 . 74 0,1,41,31 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T606|944|ACTN3|protein_coding|CODING|NM_001258371.2|15|G),DOWNSTREAM(MODIFIER||2880||484|CTSF|protein_coding|CODING|NM_003793.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2229455 -0.693147 0.366986 74 *620R 944 Tga/Cga HIGH 15 MISSENSE CODING ACTN3 C protein_coding NM_001258371.2 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66328095 T C 0 228 0 0.885 0.5992 0.428 0.5565 0.5656 0.4131 0.82105 0.640918 0.549462 2 8203 66085 3675 4730 4516 37508 518 6935 2 9850 120586 11550 8584 6594 66612 896 16500 1 2|5|255 benign|pathogenic|other 0 . 74 1,0,46,22 STOP_LOST(HIGH|MISSENSE|Tga/Cga|*620R|944|ACTN3|protein_coding|CODING|NM_001258371.2|15|C),DOWNSTREAM(MODIFIER||2840||484|CTSF|protein_coding|CODING|NM_003793.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1815739 -0.693147 0.483246 74 C671R 944 Tgt/Cgt MODERATE 16 MISSENSE CODING ACTN3 C protein_coding NM_001258371.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66328719 T C 0 228 0 0.8956 0.6002 0.4222 0.5546 0.5626 0.4131 0.82325 0.635496 0.545683 2 5396 45001 2319 3162 2446 26524 318 4836 2 6396 74074 5290 5266 3420 43304 538 9860 0 . 0 . 0 85 0,0,55,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C671R|944|ACTN3|protein_coding|CODING|NM_001258371.2|16|C),DOWNSTREAM(MODIFIER||2216||484|CTSF|protein_coding|CODING|NM_003793.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs618838 -0.693147 0.230267 85 E678A 944 gAg/gCg MODERATE 16 MISSENSE CODING ACTN3 C protein_coding NM_001258371.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66328741 A C 0 228 0 0.1702 0.1627 0.1052 0.1815 0.169 0.1677 0.134456 0.156435 0.167142 2 1097 14964 657 1185 889 8766 102 2268 2 6624 81964 6234 5920 3680 47570 576 11360 0 . 0 . 0 102 0,0,69,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E678A|944|ACTN3|protein_coding|CODING|NM_001258371.2|16|C),DOWNSTREAM(MODIFIER||2194||484|CTSF|protein_coding|CODING|NM_003793.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2229456 -0.693147 0.189017 102 Q819R 944 cAg/cGg MODERATE 19 MISSENSE CODING ACTN3 G protein_coding NM_001258371.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66329732 A G 0 228 0 0.8306 0.5831 0.4179 0.5565 0.5636 0.4131 0.785782 0.628211 0.549705 2 7770 65400 3639 4748 4506 37291 517 6929 2 9806 120702 11566 8612 6614 66702 896 16506 0 . 0 . 0 76 0,0,18,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q819R|944|ACTN3|protein_coding|CODING|NM_001258371.2|19|G),DOWNSTREAM(MODIFIER||1203||484|CTSF|protein_coding|CODING|NM_003793.3||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs540874 -0.693147 0.0309945 76 944 104 MODIFIER 21 CODING ACTN3 G protein_coding NM_001258371.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66330768 T G 0 204 0 0.0877 0.0563 0.0115 0.1567 0 0 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,1,15 UTR_3_PRIME(MODIFIER||104||944|ACTN3|protein_coding|CODING|NM_001258371.2|21|G),DOWNSTREAM(MODIFIER||167||484|CTSF|protein_coding|CODING|NM_003793.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11227532 -0.689466 0.0249134 16 484 404 MODIFIER 13 CODING CTSF G protein_coding NM_003793.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66331000 A G 0 64 0 0.2738 0.254 0.1729 0.3075 0.2396 0.2444 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||404||484|CTSF|protein_coding|CODING|NM_003793.3|13|G),DOWNSTREAM(MODIFIER||200||944|ACTN3|protein_coding|CODING|NM_001258371.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4576 -0.511536 0.909987 3 R467 484 cgT/cgC LOW 13 SILENT CODING CTSF G protein_coding NM_003793.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66331458 A G 0 228 0 0.879 0.5891 0.4207 0.5536 0.5497 0.3937 0.8125 0.626559 0.531316 2 8523 63786 3575 4682 4141 35823 497 6545 2 10294 120344 11516 8602 6506 66036 892 16498 0.942605 0 . 0 . 109 2,1,70,24 SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R467|484|CTSF|protein_coding|CODING|NM_003793.3|13|G),DOWNSTREAM(MODIFIER||658||944|ACTN3|protein_coding|CODING|NM_001258371.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.345131 rs572846 -0.693147 0.299739 109 R254 484 agG/agA LOW 6 SILENT CODING CTSF T protein_coding NM_003793.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66333598 C T 0 228 0 0.8775 0.5889 0.4207 0.5536 0.5497 0.3947 0.812727 0.626559 0.531199 2 8609 64417 3605 4722 4196 36233 504 6548 2 10398 121366 11574 8638 6610 66730 906 16510 1 0 . 0 . 50 1,0,36,8 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R254|484|CTSF|protein_coding|CODING|NM_003793.3|6|T),DOWNSTREAM(MODIFIER||2798||944|ACTN3|protein_coding|CODING|NM_001258371.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs545009 -0.693146 0.0230137 50 G73 484 ggT/ggC LOW 2 SILENT CODING CTSF G protein_coding NM_003793.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66335548 A G 0 228 0 0.8767 0.5827 0.415 0.5407 0.5378 0.3937 0 . 0 2 3814 35429 1625 2365 1338 21423 258 4606 2 5000 82244 8480 5532 2868 46200 572 13592 0 . 0 . COSM429664,COSM1605080 46 0,0,4,40 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G73|484|CTSF|protein_coding|CODING|NM_003793.3|2|G),DOWNSTREAM(MODIFIER||4748||944|ACTN3|protein_coding|CODING|NM_001258371.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1127894 -0.693146 0.221543 46 V1034A 2390 gTg/gCg MODERATE 16 MISSENSE CODING SPTBN2 G protein_coding NM_006946.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66468469 A G 0 228 0 0.3268 0.2057 0.1268 0.2827 0.1133 0.1135 0.260692 0.14943 0.0924242 2 2712 15567 1058 2158 1025 6623 127 1864 2 9428 116590 11418 8408 6532 63484 874 16446 1 3 likely-benign 0 . 40 1,0,18,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V1034A|2390|SPTBN2|protein_coding|CODING|NM_006946.2|16|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs506028 -0.693136 0.159547 40 S825G 2390 Agc/Ggc MODERATE 14 MISSENSE CODING SPTBN2 C protein_coding NM_006946.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66472274 T C 0 228 0 0.9607 0.9878 0.9899 1 0.998 1 0.965644 0.988149 0.999649 2 8414 112747 11237 8294 6240 61423 823 16316 2 8732 113100 11254 8294 6240 61438 824 16318 0 . 0 . 0 77 0,0,63,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S825G|2390|SPTBN2|protein_coding|CODING|NM_006946.2|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4930388 -0.693147 0.0224691 77 N170H 421 Aac/Cac MODERATE 4 MISSENSE CODING SYT12 C protein_coding NM_001177880.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66807561 A C 0 228 0 0.2451 0.0777 0.0115 0.0556 0.001 0 0.193409 0.0662048 0.00104773 2 2163 2775 118 417 0 62 9 6 2 10320 120116 11542 8622 6514 65876 884 16358 0.646766 0 . 0 . 102 2,1,53,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Cac|N170H|421|SYT12|protein_coding|CODING|NM_001177880.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.68678 rs11227664 -0.693147 0.0935485 102 421 279 MODIFIER 8 CODING SYT12 C protein_coding NM_001177880.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66816507 T C 0 110 0 0.4939 0.776 0.8501 0.7966 0.9105 0.9448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,0,6 UTR_3_PRIME(MODIFIER||279||421|SYT12|protein_coding|CODING|NM_001177880.1|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3741190 -0.616816 0.0476592 6 C134R 210 Tgc/Cgc MODERATE 4 MISSENSE CODING RHOD C protein_coding NM_014578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66837965 T C 0 228 0 0.9977 0.9994 1 1 1 1 0.999545 0.999846 1 2 10400 121380 11578 8654 6614 66716 906 16512 2 10404 121384 11578 8654 6614 66716 906 16512 0 . 0 . 0 95 0,0,55,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C134R|210|RHOD|protein_coding|CODING|NM_014578.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4930409 -0.693147 0.0428216 95 T351 1162 acT/acC LOW 11 SILENT CODING KDM2A C protein_coding NM_012308.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 66995603 T C 0 228 0 0.8865 0.9449 0.9553 0.9425 0.9811 0.9816 0.901221 0.961865 0.989568 2 8842 117503 11251 8220 6320 65926 868 16076 2 9800 120766 11576 8626 6614 66740 898 16512 0 . 0 . 0 174 0,0,91,66 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T351|1162|KDM2A|protein_coding|CODING|NM_012308.2|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3741189 -0.693147 0.0302968 174 A47 605 gcC/gcT LOW 2 SILENT CODING ANKRD13D T protein_coding NM_207354.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67057599 C T 0 222 0 0.0023 0.0421 0.2522 0.0298 0.003 0 0.00289017 0.00284713 0.00282841 1 5 74 42 9 0 14 0 4 2 1808 17460 302 346 8 6962 168 7866 0.944659 0 . 0 . 171 42,37,37,36 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A47|605|ANKRD13D|protein_coding|CODING|NM_207354.2|2|T),DOWNSTREAM(MODIFIER||3570||689|ADRBK1|protein_coding|CODING|NM_001619.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.555567 rs1574103 -0.693147 0.161959 171 V446 605 gtT/gtC LOW 12 SILENT CODING ANKRD13D C protein_coding NM_207354.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67068859 T C 0 228 0 0.761 0.8948 0.9467 0.8859 0.9642 0.9765 0.794091 0.908006 0.966356 2 8152 113438 10922 7623 6299 63780 850 15812 2 10322 120346 11554 8620 6590 66108 900 16252 0 . 0 . 0 51 0,0,28,21 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V446|605|ANKRD13D|protein_coding|CODING|NM_207354.2|12|C),UPSTREAM(MODIFIER||2060||659|SSH3|protein_coding|CODING|NM_017857.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2298815 -0.693147 0.261329 51 659 LOW 1 CODING SSH3 G protein_coding NM_017857.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67071584 C G 0 228 0 0.82 0.9107 0.9467 0.8879 0.9642 0.9765 0.850607 0.927638 0.966849 2 5545 87951 9191 6527 3895 49221 567 13005 2 6532 92388 9678 7312 4036 50900 594 13336 0 . 0 . 0 19 0,0,12,7 SPLICE_SITE_REGION+INTRON(LOW||||659|SSH3|protein_coding|CODING|NM_017857.3|1|G),DOWNSTREAM(MODIFIER||1629||605|ANKRD13D|protein_coding|CODING|NM_207354.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4244822 -0.69168 0.0265177 19 F81 659 ttC/ttT LOW 3 SILENT CODING SSH3 T protein_coding NM_017857.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67072382 C T 0 222 0 0.0855 0.0661 0.2651 0.0298 0.004 0 0.0641201 0.0245611 0.00430733 1 715 5479 4300 200 3 242 11 8 2 10126 119240 11458 8598 6364 65358 872 16464 0.594626 0 . 0 . 43 9,10,9,13 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F81|659|SSH3|protein_coding|CODING|NM_017857.3|3|T),DOWNSTREAM(MODIFIER||2427||605|ANKRD13D|protein_coding|CODING|NM_207354.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.883931 rs61731786 -0.692562 0.872442 43 S238 659 tcC/tcT LOW 7 SILENT CODING SSH3 T protein_coding NM_017857.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67075131 C T 0 222 0 0.2231 0.1014 0.0634 0.1101 0.0338 0.0245 0.187045 0.0799846 0.0251455 1 1933 6216 494 861 416 1870 51 591 2 10310 120760 11562 8618 6578 66280 902 16510 0.879989 0 . 0 . 71 18,13,16,18 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S238|659|SSH3|protein_coding|CODING|NM_017857.3|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.748151 rs57238619 -0.693132 0.548706 71 R600H 659 cGc/cAc MODERATE 14 MISSENSE CODING SSH3 A protein_coding NM_017857.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67079177 G A 0 222 0 0.0998 0.0699 0.2651 0.0298 0.004 0 0.0775 0.0290993 0.00430733 1 854 5637 4314 200 3 243 12 11 2 10246 120492 11496 8610 6600 66130 902 16508 0.883957 0 . 0 . 130 27,34,31,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R600H|659|SSH3|protein_coding|CODING|NM_017857.3|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.867801 rs1573536 -0.693147 0.177648 130 659 147 MODIFIER 14 CODING SSH3 A protein_coding NM_017857.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67079505 G A 0 79 0 0.3767 0.1464 0.2824 0.0298 0.0089 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.301194 0 . 0 . 14 1,5,0,8 UTR_3_PRIME(MODIFIER||147||659|SSH3|protein_coding|CODING|NM_017857.3|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875173 rs4567468 -0.651104 0.999505 14 391 LOW 3 CODING RAD9A G protein_coding NM_004584.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67160961 A G 0 222 0 0.3328 0.1735 0.1081 0.2292 0.0775 0.046 0.282727 0.141724 0.0694994 1 3014 12735 1098 1877 802 4823 95 1026 2 10350 120358 11498 8602 6594 66196 898 16220 0.78415 0 . 0 . 105 30,20,23,20 SPLICE_SITE_REGION+INTRON(LOW||||391|RAD9A|protein_coding|CODING|NM_004584.2|3|G),DOWNSTREAM(MODIFIER||4691||341|PPP1CA|protein_coding|CODING|NM_001008709.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.421875 rs2066496 -0.693146 0.0756044 105 G338 391 ggT/ggC LOW 10 SILENT CODING RAD9A C protein_coding NM_004584.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67164791 T C 0 116 0 0.8253 0.3514 0.4063 0.2599 0.0805 0.045 0.602975 0.242553 0.0591523 2 3182 11728 3081 1386 322 2913 63 781 2 4908 82576 7138 6536 3690 46092 586 13626 0 . 0 . 0 5 0,0,4,1 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G338|391|RAD9A|protein_coding|CODING|NM_004584.2|10|C),DOWNSTREAM(MODIFIER||861||341|PPP1CA|protein_coding|CODING|NM_001008709.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs872110 -0.590765 0.548401 5 S387 391 agT/agC LOW 11 SILENT CODING RAD9A C protein_coding NM_004584.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67165015 T C 0 222 0 0.0726 0.0635 0.2709 0.0298 0.004 0 0.0527273 0.0207082 0.00430733 1 586 5349 4305 199 3 237 11 8 2 9232 113426 11238 8454 5588 62316 818 15780 0.148573 0 . 0 . 47 11,9,7,12 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S387|391|RAD9A|protein_coding|CODING|NM_004584.2|11|C),DOWNSTREAM(MODIFIER||637||341|PPP1CA|protein_coding|CODING|NM_001008709.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.975053 rs2066494 -0.69168 0.0103866 47 S21 446 tcC/tcT LOW 2 SILENT CODING TBC1D10C T protein_coding NM_198517.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67171736 C T 0 228 0 0.8283 0.3518 0.4049 0.2589 0.0785 0.047 0.670915 0.276226 0.0738623 2 6769 20858 5460 2044 621 4826 108 1030 2 9350 110618 11090 8270 5408 59972 796 15732 1 0 . 0 COSM429704 98 0,1,27,63 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S21|446|TBC1D10C|protein_coding|CODING|NM_198517.3|2|T),UPSTREAM(MODIFIER||2360||341|PPP1CA|protein_coding|CODING|NM_001008709.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2514256 -0.693147 0.101355 98 S338 446 tcA/tcG LOW 10 SILENT CODING TBC1D10C G protein_coding NM_198517.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67176898 A G 0 221 0 0.829 0.3532 0.4063 0.2579 0.0835 0.0481 0.521425 0.210201 0.0595366 2 694 1710 54 117 8 339 16 482 2 942 13616 228 408 26 4310 144 7558 0 . 0 . 0 10 0,0,3,6 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S338|446|TBC1D10C|protein_coding|CODING|NM_198517.3|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.924584 0 . rs11227788 -0.662043 0.211211 10 446 53 MODIFIER 10 CODING TBC1D10C A protein_coding NM_198517.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67177278 G A 0 228 0 1 0.9972 0.9899 1 0.994 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,2,13 UTR_3_PRIME(MODIFIER||53||446|TBC1D10C|protein_coding|CODING|NM_198517.3|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7122299 -0.688148 0.471439 16 950 478 MODIFIER 1 CODING CARNS1 G protein_coding NM_001166222.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67183193 C G 0 9.7 0 0.1815 0.1112 0.0692 0.1875 0.0547 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||478||950|CARNS1|protein_coding|CODING|NM_001166222.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs35899279 -0.379885 0 1 P137T 950 Cca/Aca MODERATE 5 MISSENSE CODING CARNS1 A protein_coding NM_001166222.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67186271 C A 0 222 0 0.4887 0.1771 0.2983 0.0288 0.005 0 0.376875 0.124732 0.00654704 1 2598 5736 2753 131 1 222 15 16 2 5740 56390 6192 3958 1416 29134 410 9540 0.998168 0 . 0 . 137 30,37,30,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P137T|950|CARNS1|protein_coding|CODING|NM_001166222.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.458703 rs868167 -0.693147 0.358022 137 L744 950 Ttg/Ctg LOW 10 SILENT CODING CARNS1 C protein_coding NM_001166222.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67191449 T C 0 228 0 0.8298 0.3598 0.4063 0.2897 0.0835 0.0481 0.669846 0.276803 0.0771685 2 7035 22284 5513 2410 814 5333 121 1058 2 9732 118904 11362 8534 6290 65700 876 16410 0 . 0 . 0 39 0,0,20,18 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L744|950|CARNS1|protein_coding|CODING|NM_001166222.1|10|C),UPSTREAM(MODIFIER||4486||482|RPS6KB2|protein_coding|CODING|NM_003952.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1790747 -0.693143 0.297129 39 950 35 MODIFIER 10 CODING CARNS1 A protein_coding NM_001166222.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67192107 T A 0 228 0 0.8298 0.3596 0.4063 0.2887 0.0835 0.0481 0.619483 0.250247 0.0733042 2 4610 16355 4333 2042 554 4158 82 576 2 6296 77988 8462 6746 3648 45140 526 7170 0 . 0 . 0 61 0,0,12,46 UTR_3_PRIME(MODIFIER||35||950|CARNS1|protein_coding|CODING|NM_001166222.1|10|A),UPSTREAM(MODIFIER||3828||482|RPS6KB2|protein_coding|CODING|NM_003952.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1790748 -0.693147 7.33797e-07 61 950 483 MODIFIER 10 CODING CARNS1 A protein_coding NM_001166222.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67192555 G A 0 76 0 0.8593 0.5086 0.5476 0.4425 0.3559 0.2321 0 . 0 2 144 3175 33 61 0 881 36 2020 2 196 10778 92 134 0 2732 118 7506 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||483||950|CARNS1|protein_coding|CODING|NM_001166222.1|10|A),UPSTREAM(MODIFIER||3380||482|RPS6KB2|protein_coding|CODING|NM_003952.2||A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1626067 -0.511536 0.228191 3 F269 482 ttC/ttT LOW 10 SILENT CODING RPS6KB2 T protein_coding NM_003952.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67200819 C T 0 222 0 0.3283 0.356 0.5389 0.3264 0.4225 0.226 0.309898 0.384628 0.420257 1 3212 46681 6661 2465 2487 27303 324 4229 2 9780 120560 11564 8610 6612 66590 898 16506 0.902294 0 . 0 COSM147279 238 69,50,51,34 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F269|482|RPS6KB2|protein_coding|CODING|NM_003952.2|10|T),DOWNSTREAM(MODIFIER||2162||206|PTPRCAP|protein_coding|CODING|NM_005608.2||T),DOWNSTREAM(MODIFIER||4699||489|CORO1B|protein_coding|CODING|NM_001018070.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.610455 rs4930427 -0.693147 0.103092 238 A420V 482 gCc/gTc MODERATE 14 MISSENSE CODING RPS6KB2 T protein_coding NM_003952.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67202156 C T 0 222 0 0.8079 0.4868 0.5692 0.3264 0.4225 0.226 0.734837 0.526032 0.42784 1 5786 41629 5593 2091 1698 22337 276 3848 2 7822 97016 9446 7040 4434 53266 710 14298 0.984824 0 . 0 COSM1475816,COSM429715 116 16,43,15,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A420V|482|RPS6KB2|protein_coding|CODING|NM_003952.2|14|T),DOWNSTREAM(MODIFIER||825||206|PTPRCAP|protein_coding|CODING|NM_005608.2||T),DOWNSTREAM(MODIFIER||3362||489|CORO1B|protein_coding|CODING|NM_001018070.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997773 rs13859 -0.693147 0.37984 116 482 186 MODIFIER 15 CODING RPS6KB2 A protein_coding NM_003952.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67202826 G A 0 8.1 0 0.326 0.3554 0.5403 0.3264 0.4215 0.226 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.25 0 . 0 . 4 0,2,0,2 UTR_3_PRIME(MODIFIER||186||482|RPS6KB2|protein_coding|CODING|NM_003952.2|15|A),DOWNSTREAM(MODIFIER||155||206|PTPRCAP|protein_coding|CODING|NM_005608.2||A),DOWNSTREAM(MODIFIER||2692||489|CORO1B|protein_coding|CODING|NM_001018070.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs10274 -0.453602 0.6 4 489 LOW 11 CODING CORO1B A protein_coding NM_001018070.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67205978 G A 0 178 0 0.326 0.3544 0.5389 0.3274 0.4165 0.226 0.317334 0.384918 0.41952 1 3068 44323 6518 2430 2248 25679 314 4066 2 9320 113752 11304 8440 6256 62568 840 15024 1 0 . 0 . 16 1,6,4,4 SPLICE_SITE_REGION+INTRON(LOW||||489|CORO1B|protein_coding|CODING|NM_001018070.2|11|A),UPSTREAM(MODIFIER||825||206|PTPRCAP|protein_coding|CODING|NM_005608.2||A),DOWNSTREAM(MODIFIER||3099||482|RPS6KB2|protein_coding|CODING|NM_003952.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.941512 rs872375 -0.651104 0.398764 16 T82 489 acG/acA LOW 4 SILENT CODING CORO1B T protein_coding NM_001018070.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67209515 C T 0 222 0 0.0015 0.0443 0.2622 0.0347 0.003 0 0.00318182 0.00323326 0.0032596 1 29 4776 4334 230 5 161 10 7 2 10112 119004 11498 8572 6482 64972 874 16494 0.768145 0 . 0 . 221 45,49,51,57 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T82|489|CORO1B|protein_coding|CODING|NM_001018070.2|4|T),UPSTREAM(MODIFIER||4362||206|PTPRCAP|protein_coding|CODING|NM_005608.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.367965 rs111451405 -0.693147 0.000610699 221 275 LOW 3 CODING CABP4 G protein_coding NM_145200.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67223920 C G 0 173 0 0.8752 0.5066 0.5692 0.3234 0.4235 0.2382 0.506139 0.273714 0.154715 1 8144 50441 6431 2409 2405 26350 345 4357 2 10056 117562 11184 8448 6378 64252 874 16370 0.774996 0 . 0 . 46 2,21,2,21 SPLICE_SITE_REGION+INTRON(LOW||||275|CABP4|protein_coding|CODING|NM_145200.3|3|G),UPSTREAM(MODIFIER||3720||470|GPR152|protein_coding|CODING|NM_206997.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894445 rs1638564 -0.692717 0.107837 46 275 LOW 3 CODING CABP4 C protein_coding NM_145200.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67223921 A C 0 171 0 0.8752 0.5066 0.5692 0.3234 0.4235 0.2382 0.497271 0.268325 0.151106 1 8136 50405 6431 2408 2401 26326 344 4359 2 10048 117632 11202 8472 6380 64280 874 16376 0.907984 0 . 0 . 46 2,21,2,21 SPLICE_SITE_REGION+INTRON(LOW||||275|CABP4|protein_coding|CODING|NM_145200.3|3|C),UPSTREAM(MODIFIER||3721||470|GPR152|protein_coding|CODING|NM_206997.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894445 rs1638565 -0.692717 0.107837 46 275 876 MODIFIER 6 CODING CABP4 A protein_coding NM_145200.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67227006 G A 0 39.3 0 0.2065 0.2808 0.4986 0.1855 0.3996 0.2025 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||876||275|CABP4|protein_coding|CODING|NM_145200.3|6|A),DOWNSTREAM(MODIFIER||4813||195|TMEM134|protein_coding|CODING|NM_025124.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11601325 -0.453602 0.5 2 Q228K 330 Cag/Aag MODERATE 5 MISSENSE CODING AIP A protein_coding NM_003977.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67257823 C A 0 228 0 0.4365 0.8454 0.9611 1 0.998 1 0.5175 0.834257 0.996508 2 5086 114261 11273 8612 6604 65356 870 16460 2 10102 119650 11502 8612 6604 65474 886 16470 0 . 0 . 0 45 0,0,18,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q228K|330|AIP|protein_coding|CODING|NM_003977.3|5|A),DOWNSTREAM(MODIFIER||1416||1244|PITPNM1|protein_coding|CODING|NM_004910.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs641081 -0.693145 0.426784 45 Q307R 330 cAg/cGg MODERATE 6 MISSENSE CODING AIP G protein_coding NM_003977.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67258391 A G 0 228 0 0.9985 0.9994 1 1 1 0.999 0.999317 0.999769 1 2 9929 117483 11404 8534 6192 64144 838 16442 2 9932 117494 11406 8534 6192 64144 838 16448 0 . 0 . 0 174 0,0,44,120 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q307R|330|AIP|protein_coding|CODING|NM_003977.3|6|G),DOWNSTREAM(MODIFIER||848||1244|PITPNM1|protein_coding|CODING|NM_004910.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4930199 -0.693147 0.00781708 174 P813L 1244 cCg/cTg MODERATE 16 MISSENSE CODING PITPNM1 A protein_coding NM_004910.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67262953 G A 0 222 0 0 0.0023962 0 0.0119 0 0 0 . 0 1 0 31 0 26 0 0 0 5 2 3512 26448 1160 2674 514 13844 194 4550 0.515929 0 . 0 . 216 43,63,28,66 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P813L|1244|PITPNM1|protein_coding|CODING|NM_004910.2|16|A),DOWNSTREAM(MODIFIER||4374||330|AIP|protein_coding|CODING|NM_003977.3||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.122603 rs151074608 -0.693147 0.11045 216 A733 1244 gcT/gcC LOW 15 SILENT CODING PITPNM1 G protein_coding NM_004910.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67263767 A G 0 228 0 0.761 0.9323 0.9841 0.9891 0.999 1 0.786136 0.925932 0.997555 2 8017 117315 11433 8439 6538 65527 874 16487 2 10222 119902 11538 8612 6538 65608 886 16498 0 . 0 . 0 110 0,0,69,27 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A733|1244|PITPNM1|protein_coding|CODING|NM_004910.2|15|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs618633 -0.693147 0.449742 110 R94Q 220 cGg/cAg MODERATE 4 MISSENSE CODING CABP2 T protein_coding NM_016366.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67288594 C T 0 222 0 0.0303 0.4297 0.3775 0.6558 0.5606 0.6391 0.126818 0.418553 0.567986 1 1111 64082 4165 5982 3514 38245 514 10551 2 10362 121162 11546 8628 6582 66638 906 16500 0.855807 0 . 0 . 105 17,25,18,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R94Q|220|CABP2|protein_coding|CODING|NM_016366.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998399 rs2276118 -0.693147 0.190251 105 210 219 MODIFIER 1 CODING GSTP1 G protein_coding NM_000852.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67351096 C G 0 222 0 0.0136 0.0469 0.2651 0.0288 0.004 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.153729 0 . 0 . 40 0,20,3,14 UTR_5_PRIME(MODIFIER||219||210|GSTP1|protein_coding|CODING|NM_000852.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.983421 rs8191438 -0.690438 0.550689 40 210 18 MODIFIER 1 CODING GSTP1 A protein_coding NM_000852.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67351297 G A 0 62 0 0.0136 0.0469 0.2651 0.0288 0.004 0 0.0196078 0.00901907 0.00414053 1 93 2199 1868 114 0 115 3 6 2 1710 24608 3358 1806 184 9546 180 7824 0.428556 0 . 0 . 11 4,1,1,4 UTR_5_PRIME(MODIFIER||18||210|GSTP1|protein_coding|CODING|NM_000852.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.952347 0.952347 0 0.142852 rs8191439 -0.590765 0.378928 11 I105V 210 Atc/Gtc MODERATE 5 MISSENSE CODING GSTP1 G protein_coding NM_000852.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67352689 A G 0 222 0 0.4803 0.3526 0.4755 0.1786 0.331 0.2945 0.419626 0.360837 0.331667 1 4344 39957 6162 1554 1736 21148 263 4750 2 9780 119818 11516 8602 6316 66264 888 16452 0.869129 0 . 0 . 86 9,30,13,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I105V|210|GSTP1|protein_coding|CODING|NM_000852.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913755 rs1695 -0.693144 0.373326 86 S185 210 agT/agC LOW 7 SILENT CODING GSTP1 C protein_coding NM_000852.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67353970 T C 0 222 0 0.5182 0.356 0.4885 0.1736 0.337 0.2505 0.454009 0.378287 0.341335 1 4820 40954 6267 1527 1810 21940 276 4314 2 9766 120310 11532 8602 6520 66508 890 16492 0.94457 0 . 0 . 59 22,10,18,7 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S185|210|GSTP1|protein_coding|CODING|NM_000852.3|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999483 rs4891 -0.692914 0.0696404 59 E138 236 gaG/gaA LOW 4 SILENT CODING NUDT8 T protein_coding NM_001243750.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67395714 C T 0 222 0 0.1815 0.2328 0.4496 0.127 0.332 0.1554 0.194731 0.276067 0.311839 1 2051 33714 5489 1050 2123 19867 264 2870 2 10238 119766 11432 8560 6580 65606 898 16452 0.931447 0 . 0 . 115 19,34,22,35 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E138|236|NUDT8|protein_coding|CODING|NM_001243750.1|4|T),DOWNSTREAM(MODIFIER||3060||385|TBX10|protein_coding|CODING|NM_005995.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.290072 rs7124513 -0.693147 0.0706855 115 385 214 MODIFIER 8 CODING TBX10 T protein_coding NM_005995.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67398862 A T 0 88 0 0.1286 0.4659 0.3818 0.6577 0.5616 0.6851 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,3,1 UTR_3_PRIME(MODIFIER||214||385|TBX10|protein_coding|CODING|NM_005995.4|8|T),UPSTREAM(MODIFIER||1454||236|NUDT8|protein_coding|CODING|NM_001243750.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1531514 -0.556411 0.202231 6 K101T 385 aAg/aCg MODERATE 3 MISSENSE CODING TBX10 G protein_coding NM_005995.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67402362 T G 0 222 0 0.1626 0.2173 0.4236 0.131 0.3042 0.1442 0.173864 0.252926 0.293433 1 1827 30938 5302 1060 1459 18457 225 2608 2 10314 120450 11536 8614 6594 66000 888 16504 0.723378 0 . 0 . 132 39,19,40,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K101T|385|TBX10|protein_coding|CODING|NM_005995.4|3|G),UPSTREAM(MODIFIER||4954||236|NUDT8|protein_coding|CODING|NM_001243750.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.581302 rs3758938 -0.693147 0.768609 132 V281M 319 Gtg/Atg MODERATE 8 MISSENSE CODING ACY3 T protein_coding NM_080658.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67410314 C T 0 222 0 0 0.0065895 0.0014 0.0308 0 0.001 0 0.000384971 0.000582208 1 0 371 3 317 1 30 1 19 2 10372 120846 11552 8636 6606 66270 900 16510 0.796965 0 . 0 . 188 53,36,30,49 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V281M|319|ACY3|protein_coding|CODING|NM_080658.1|8|T),UPSTREAM(MODIFIER||3283||385|TBX10|protein_coding|CODING|NM_005995.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.893278 rs2290959 -0.693147 0.142718 188 R8Q 319 cGg/cAg MODERATE 3 MISSENSE CODING ACY3 T protein_coding NM_080658.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67414492 C T 0 228 0 0.4009 0.7198 0.8473 0.746 0.8121 0.9387 0.488594 0.713567 0.82827 2 1175 19778 725 824 378 9301 176 7199 2 2310 23758 830 1076 424 11098 206 7814 0 . 0 . 0 53 0,0,7,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R8Q|319|ACY3|protein_coding|CODING|NM_080658.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs948445 -0.693147 0.00352902 53 319 540 MODIFIER 2 CODING ACY3 T protein_coding NM_080658.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67415054 C T 0 39.3 0 0.7012 0.8031 0.8689 0.745 0.8131 0.9438 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_5_PRIME(MODIFIER||540||319|ACY3|protein_coding|CODING|NM_080658.1|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2514036 -0.453602 0.26 2 385 422 MODIFIER 10 CODING ALDH3B2 G protein_coding NM_000695.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67430264 A G 0 80 0 0.7852 0.9401 0.9769 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||422||385|ALDH3B2|protein_coding|CODING|NM_000695.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1551885 -0.556411 0.0751808 4 385 290 MODIFIER 10 CODING ALDH3B2 C protein_coding NM_000695.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67430396 T C 0 106 0 0.9932 0.9982 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,3,2 UTR_3_PRIME(MODIFIER||290||385|ALDH3B2|protein_coding|CODING|NM_000695.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2447570 -0.590765 0.244166 5 385 204 MODIFIER 10 CODING ALDH3B2 C protein_coding NM_000695.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67430482 T C 0 61 0 0.5401 0.8083 0.9035 0.8829 0.8857 0.9468 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 6,0,5,0 UTR_3_PRIME(MODIFIER||204||385|ALDH3B2|protein_coding|CODING|NM_000695.3|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.742931 rs866907 -0.590765 0.138089 11 385 97 MODIFIER 10 CODING ALDH3B2 G protein_coding NM_000695.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67430589 A G 0 228 0 0.7292 0.8712 0.9193 0.9107 0.8877 0.9714 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,39,1 UTR_3_PRIME(MODIFIER||97||385|ALDH3B2|protein_coding|CODING|NM_000695.3|10|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs78402723 -0.693145 0.356023 42 H361R 385 cAc/cGc MODERATE 10 MISSENSE CODING ALDH3B2 C protein_coding NM_000695.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67430762 T C 0 228 0 0.7179 0.868 0.9193 0.9097 0.8877 0.9714 0.753182 0.8504 0.90021 2 7787 109727 10983 7906 6343 60113 824 15771 2 10406 121358 11576 8652 6614 66702 906 16502 0 . 0 . 0 125 0,0,76,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H361R|385|ALDH3B2|protein_coding|CODING|NM_000695.3|10|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1551886 -0.693147 0.622448 125 S220G 385 Agc/Ggc MODERATE 7 MISSENSE CODING ALDH3B2 C protein_coding NM_000695.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67432804 T C 0 228 0 0.9985 0.999 1 0.997 1 1 0.999318 0.999769 1 2 10348 121067 11572 8568 6614 66615 905 16445 2 10358 121162 11572 8648 6614 66616 906 16448 1 0 . 0 . 385 1,0,234,123 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S220G|385|ALDH3B2|protein_coding|CODING|NM_000695.3|7|C) 1 0 . 0 . 1 0 1 1 0 58 0 1 0.346986 0 1 rs2447571 -0.693147 0.00260335 385 H203R 385 cAc/cGc MODERATE 7 MISSENSE CODING ALDH3B2 C protein_coding NM_000695.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67432854 T C 0 228 0 0.77 0.9361 0.9769 1 1 1 0.810909 0.93567 0.99965 2 8343 119184 11480 8651 6614 66693 901 16502 2 10400 121382 11576 8652 6614 66726 908 16506 0 . 0 . 0 481 0,0,252,187 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H203R|385|ALDH3B2|protein_coding|CODING|NM_000695.3|7|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.109272 0 . rs41499149,rs6591270 -0.693147 0.265717 481 S52N 385 aGt/aAt MODERATE 5 MISSENSE CODING ALDH3B2 T protein_coding NM_000695.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67433869 C T 0 228 0 0.7201 0.8686 0.9193 0.9097 0.8877 0.9714 0.751591 0.849784 0.900093 2 6691 94232 8854 6405 5037 51962 697 14586 2 8876 104362 9362 7040 5260 57766 772 15286 0 . 0 . 0 25 0,0,12,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S52N|385|ALDH3B2|protein_coding|CODING|NM_000695.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1551888 -0.692717 0.665961 25 385 10 MODIFIER 3 CODING ALDH3B2 A protein_coding NM_000695.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67434416 C A 0 222 0 0.5333 0.8059 0.9035 0.8819 0.8847 0.9458 0.572273 0.787958 0.898463 1 5894 107179 10890 7681 6331 60055 813 15515 2 10404 121384 11576 8652 6604 66728 908 16512 0.109182 0 . 0 . 179 58,44,34,21 UTR_5_PRIME(MODIFIER||10||385|ALDH3B2|protein_coding|CODING|NM_000695.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0268592 rs4646823 -0.693147 0.0114473 179 385 LOW 2 CODING ALDH3B2 T protein_coding NM_000695.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67434936 C T 0 222 0 0.0371 0.4245 0.621 0.6052 0.497 0.5481 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.522182 0 . 0 . 160 67,19,40,24 SPLICE_SITE_REGION+INTRON(LOW||||385|ALDH3B2|protein_coding|CODING|NM_000695.3|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.963267 rs3825021 -0.693147 0.028176 160 385 632 MODIFIER 2 CODING ALDH3B2 C protein_coding NM_000695.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67435038 G C 0 222 0 0.0726 0.0306 0.0072 0.0268 0 0.0256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.840695 0 . 0 . 161 18,38,32,52 UTR_5_PRIME(MODIFIER||632||385|ALDH3B2|protein_coding|CODING|NM_000695.3|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.955422 rs112604855 -0.693147 0.000749742 161 385 7637 MODIFIER 1 CODING ALDH3B2 C protein_coding NM_000695.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67442043 A C 0 26.2 0 0.6006 0.8253 0.9121 0.8829 0.8847 0.9468 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 3,0,1,1 UTR_5_PRIME(MODIFIER||7637||385|ALDH3B2|protein_coding|CODING|NM_000695.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.166667 rs7947978 -0.453602 0.58 5 L415 830 ctG/ctC LOW 11 SILENT CODING TCIRG1 C protein_coding NM_006019.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67814979 G C 0 228 0 0.8933 0.9698 0.9885 1 0.998 1 0.927045 0.974977 0.999534 2 9538 120053 11514 8642 6602 66349 900 16508 2 10338 120930 11556 8642 6602 66380 904 16508 0 . 0 . 0 97 0,0,49,42 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L415|830|TCIRG1|protein_coding|CODING|NM_006019.3|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2471829 -0.693147 0.210252 97 457 1120 MODIFIER 12 CODING CHKA A protein_coding NM_001277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67820335 T A 0 167 0 0.3517 0.6192 0.7709 0.6567 0.672 0.7802 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,20,0 UTR_3_PRIME(MODIFIER||1120||457|CHKA|protein_coding|CODING|NM_001277.2|12|A),DOWNSTREAM(MODIFIER||1969||830|TCIRG1|protein_coding|CODING|NM_006019.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11481 -0.692067 0.102705 20 885 596 MODIFIER 11 CODING KMT5B G protein_coding NM_017635.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67924559 A G 0 225 0 0.7678 0.7608 0.7608 0.87 0.5915 0.8129 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,20,1 UTR_3_PRIME(MODIFIER||596||885|KMT5B|protein_coding|CODING|NM_017635.4|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6591334 -0.692352 0.326186 23 I9N 885 aTc/aAc MODERATE 2 MISSENSE CODING KMT5B T protein_coding NM_017635.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 67957518 A T 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121412 11578 8654 6614 66740 908 16512 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 106 0,0,22,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I9N|885|KMT5B|protein_coding|CODING|NM_017635.4|2|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2512606 -0.693147 0.0400149 106 A150T 449 Gca/Aca MODERATE 4 MISSENSE CODING C11orf24 T protein_coding NM_022338.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68030015 C T 0 222 0 0.3359 0.3504 0.2911 0.4127 0.4473 0.2485 0.345455 0.404373 0.43456 1 3457 46693 2873 3305 3047 28991 358 4662 2 10302 120004 11446 8562 6296 66018 886 16494 0.717819 0 . 0 . 359 112,77,83,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A150T|449|C11orf24|protein_coding|CODING|NM_022338.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.6123 rs901827 -0.693147 0.00158171 359 G97V 449 gGt/gTt MODERATE 4 MISSENSE CODING C11orf24 A protein_coding NM_022338.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68030173 C A 0 222 0 0.1309 0.3834 0.513 0.4752 0.3062 0.6176 0.156818 0.255852 0.306591 1 1647 45180 7056 4283 1945 20639 331 9279 2 10392 121178 11542 8628 6594 66610 904 16508 0.898217 0 . 0 . 234 52,53,39,76 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G97V|449|C11orf24|protein_coding|CODING|NM_022338.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987927 rs3802746 -0.693147 0.444419 234 1615 LOW 4 CODING LRP5 C protein_coding NM_002335.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68133035 T C 0 222 0 0.7496 0.4032 0.4841 0.1161 0.4125 0.1636 0.679545 0.500154 0.408223 1 7230 45617 6216 834 1851 26413 302 2771 2 10384 121148 11572 8628 6614 66536 902 16512 0.764361 0 . 0 . 122 35,23,25,19 SPLICE_SITE_REGION+INTRON(LOW||||1615|LRP5|protein_coding|CODING|NM_002335.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.618833 rs314776 -0.693146 0.0144635 122 1615 LOW 6 CODING LRP5 A protein_coding NM_002335.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68154188 G A 0 213 0 0.1316 0.1154 0.1196 0.1012 0.171 0.0481 0.131099 0.151862 0.1625 1 1289 15485 1396 838 689 10243 109 921 2 8870 113002 11134 8294 6182 62030 834 15658 0.422917 0 . 0 . 42 8,12,5,15 SPLICE_SITE_REGION+INTRON(LOW||||1615|LRP5|protein_coding|CODING|NM_002335.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.198315 rs4988319 -0.692067 0.50062 42 F549 1615 ttT/ttC LOW 8 SILENT CODING LRP5 C protein_coding NM_002335.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68171013 T C 0 228 0 0.5666 0.8415 0.9063 0.9851 0.9215 0.9366 0.636591 0.815368 0.906963 2 6566 109255 10913 8554 6381 60810 824 15207 2 10404 121386 11576 8654 6612 66722 908 16510 0 . 0 . 0 253 0,0,159,75 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F549|1615|LRP5|protein_coding|CODING|NM_002335.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs545382 -0.693147 0.000203922 253 V1119 1615 gtG/gtA LOW 15 SILENT CODING LRP5 A protein_coding NM_002335.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68192690 G A 0 228 0 0.1619 0.5793 0.6758 0.7232 0.6899 0.8129 0.240455 0.526486 0.673032 2 2387 81616 8106 6300 5658 45544 638 12983 2 10324 120826 11510 8612 6542 66432 904 16502 0.845771 0 . 0 . 415 2,0,212,190 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1119|1615|LRP5|protein_coding|CODING|NM_002335.3|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.245025 rs556442 -0.693147 0.00585511 415 123 419 MODIFIER 1 CODING GAL C protein_coding NM_015973.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68451973 T C 0 9.7 0 0.8911 0.8698 0.8372 0.9048 0.833 0.8661 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||419||123|GAL|protein_coding|CODING|NM_015973.4|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11228324 -0.379885 0 1 123 264 MODIFIER 1 CODING GAL T protein_coding NM_015973.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68452128 C T 0 9.7 0 0.3797 0.6625 0.7291 0.8194 0.7376 0.7587 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 START_GAINED(LOW||||123|GAL|protein_coding|CODING|NM_015973.4|1|T),UTR_5_PRIME(MODIFIER||264||123|GAL|protein_coding|CODING|NM_015973.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7101947 -0.379885 0 1 123 15 MODIFIER 6 CODING GAL C protein_coding NM_015973.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68458470 T C 0 228 0 0.3941 0.627 0.6729 0.7867 0.6988 0.6708 0.438182 0.57838 0.65021 2 4422 81764 8370 6721 5809 45248 608 10586 2 10376 121222 11546 8642 6608 66636 908 16506 0 . 0 . 0 45 0,0,22,19 UTR_3_PRIME(MODIFIER||15||123|GAL|protein_coding|CODING|NM_015973.4|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1042577 -0.693145 0.644915 45 773 1202 MODIFIER 19 CODING CPT1A C protein_coding NM_001876.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68523910 T C 0 9.7 0 0.4864 0.6488 0.6686 0.7996 0.6789 0.6677 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1202||773|CPT1A|protein_coding|CODING|NM_001876.3|19|C),UPSTREAM(MODIFIER||4922||508|MTL5|protein_coding|CODING|NM_004923.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2278908 -0.379885 0 1 773 1059 MODIFIER 19 CODING CPT1A A protein_coding NM_001876.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68524053 G A 0 9.7 0 0.323 0.5625 0.5821 0.7778 0.5636 0.6493 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1059||773|CPT1A|protein_coding|CODING|NM_001876.3|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2278907 -0.379885 0 1 F417 773 ttT/ttC LOW 11 SILENT CODING CPT1A G protein_coding NM_001876.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68549340 A G 0 228 0 0.8048 0.8926 0.9265 0.9058 0.9513 0.9131 0.847045 0.911996 0.945272 2 8763 113064 10972 7878 6449 63522 839 14641 2 10406 121404 11578 8646 6614 66740 908 16512 0 2,2 benign,benign 0 . 178 0,0,63,97 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F417|773|CPT1A|protein_coding|CODING|NM_001876.3|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2228502 -0.693147 0.141429 178 L19 993 ctT/ctC LOW 1 SILENT CODING IGHMBP2 C protein_coding NM_002180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68671477 T C 0 222 0 0.5825 0.6751 0.8156 0.4653 0.8509 0.7362 0.657908 0.787609 0.854037 1 1515 14842 348 255 47 6473 157 6047 2 2396 19556 440 578 56 7836 192 8058 0.954405 0 . 0 . 31 3,12,5,9 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L19|993|IGHMBP2|protein_coding|CODING|NM_002180.2|1|C),UPSTREAM(MODIFIER||174||205|MRPL21|protein_coding|CODING|NM_181514.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.734495 rs1249463 -0.686358 0.386171 31 L201S 993 tTa/tCa MODERATE 5 MISSENSE CODING IGHMBP2 C protein_coding NM_002180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68678962 T C 0 222 0 0.6029 0.6805 0.817 0.4633 0.8509 0.7372 0.650455 0.778565 0.844201 1 6647 93626 9109 4274 5111 55453 720 12312 2 10392 121294 11556 8620 6612 66702 904 16508 0.960902 0 . 0 . 78 28,7,21,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L201S|993|IGHMBP2|protein_coding|CODING|NM_002180.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.437054 rs560096 -0.69312 0.727187 78 T879K 993 aCg/aAg MODERATE 14 MISSENSE CODING IGHMBP2 A protein_coding NM_002180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68705674 C A 0 222 0 0.0166 0.1971 0.438 0.2212 0.2654 0.1748 0.0777273 0.210117 0.277946 1 692 30292 5321 2152 1735 17217 221 2954 2 10374 121266 11570 8634 6610 66660 906 16512 0.325951 2 benign 0 . 316 99,26,109,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aAg|T879K|993|IGHMBP2|protein_coding|CODING|NM_002180.2|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.861299 rs17612126 -0.693147 0.00281848 316 E928K 993 Gag/Aag MODERATE 14 MISSENSE CODING IGHMBP2 A protein_coding NM_002180.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68705820 G A 0 222 0 0.0008 0.0236 0.0735 0.0655 0 0 0.00318326 0.00192663 0.00128235 1 20 1760 1026 627 0 36 12 39 2 7124 86508 8408 6422 3932 46848 632 13142 0.810937 0 . 0 . 225 24,67,30,89 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gag/Aag|E928K|993|IGHMBP2|protein_coding|CODING|NM_002180.2|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.924418 rs2275996 -0.693147 0.43768 225 993 255 MODIFIER 15 CODING IGHMBP2 C protein_coding NM_002180.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68707454 T C 0 74 0 0.5749 0.6709 0.8112 0.4623 0.8469 0.7352 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.202566 0 . 0 . 8 0,4,1,2 UTR_3_PRIME(MODIFIER||255||993|IGHMBP2|protein_coding|CODING|NM_002180.2|15|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1 0 0.607698 rs564244 -0.511536 0.354794 8 993 427 MODIFIER 15 CODING IGHMBP2 T protein_coding NM_002180.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68707626 C T 0 73 0 0.0166 0.1967 0.4352 0.2212 0.2654 0.1748 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||427||993|IGHMBP2|protein_coding|CODING|NM_002180.2|15|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3750980 -0.511536 0.0785113 3 T151 321 acA/acG LOW 1 SILENT CODING MRGPRD C protein_coding NM_198923.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68748003 T C 0 222 0 0.8154 0.6292 0.7983 0.4871 0.6412 0.3916 0.809091 0.686788 0.624127 1 8348 73351 9303 4206 3685 40444 532 6833 2 10358 120638 11502 8582 6526 66304 902 16464 0.969625 0 . 0 . 136 44,26,28,21 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T151|321|MRGPRD|protein_coding|CODING|NM_198923.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.405026 rs34847539 -0.693147 0.853731 136 K16R 343 aAg/aGg MODERATE 2 MISSENSE CODING MRGPRF C protein_coding NM_001098515.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68777323 T C 0 222 0 0.3563 0.3063 0.2594 0.2887 0.3012 0.2955 0.327955 0.302972 0.290172 1 3465 34451 3012 2326 1650 18977 261 4760 2 10320 120560 11526 8564 6520 66312 898 16420 0.870047 0 . 0 . 115 39,15,30,17 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|aAg/aGg|K16R|343|MRGPRF|protein_coding|CODING|NM_001098515.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97867 rs11544721 -0.693147 0.106039 115 752 96 MODIFIER 1 CODING TPCN2 G protein_coding NM_139075.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68816370 A G 0 228 0 0.6218 0.8087 0.8184 0.7599 0.9861 0.9223 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,12,3 UTR_5_PRIME(MODIFIER||96||752|TPCN2|protein_coding|CODING|NM_139075.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4930642 -0.688148 0.191012 15 A116 752 gcT/gcC LOW 4 SILENT CODING TPCN2 C protein_coding NM_139075.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68822739 T C 0 228 0 0.9955 0.9988 1 1 1 1 0.9925 0.997459 1 2 10339 121287 11568 8652 6612 66708 906 16502 2 10402 121358 11574 8652 6612 66710 906 16502 0 . 0 . 0 73 0,0,21,46 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A116|752|TPCN2|protein_coding|CODING|NM_139075.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1470892 -0.693147 0.26462 73 752 LOW 7 CODING TPCN2 C protein_coding NM_139075.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68834968 T C 0 228 0 0.8162 0.8984 0.9236 0.8522 0.998 0.9366 0.836364 0.943486 0.99837 2 8638 115788 10540 7385 6570 66313 881 15461 2 10316 120896 11550 8558 6602 66460 906 16504 1 0 . 0 . 88 1,0,40,38 SPLICE_SITE_REGION+INTRON(LOW||||752|TPCN2|protein_coding|CODING|NM_139075.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6591368 -0.693147 0.237025 88 K376R 752 aAa/aGa MODERATE 12 MISSENSE CODING TPCN2 G protein_coding NM_139075.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68840160 A G 0 222 0 0.2322 0.2907 0.1945 0.2063 0.3032 0.5123 0.245 0.291654 0.315557 1 2506 35541 1753 1836 1421 20184 278 7563 2 10368 121124 11560 8624 6602 66558 906 16506 0.999209 0 . 0 COSM1356592 101 26,21,23,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K376R|752|TPCN2|protein_coding|CODING|NM_139075.3|12|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982105 rs3750965 -0.693143 0.234399 101 L564P 752 cTg/cCg MODERATE 19 MISSENSE CODING TPCN2 C protein_coding NM_139075.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68851414 T C 0 222 0 0.7163 0.753 0.6124 0.504 0.9871 0.9182 0.755909 0.911303 0.990918 1 7825 106303 5864 4523 6384 65747 823 15137 2 10370 120840 11520 8606 6534 66410 898 16502 0.798958 0 . 0 . 121 36,18,37,14 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cTg/cCg|L564P|752|TPCN2|protein_coding|CODING|NM_139075.3|19|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.778053 rs2376558 -0.693147 0.158365 121 752 533 MODIFIER 25 CODING TPCN2 G protein_coding NM_139075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68855954 A G 0 9.7 0 0.2337 0.2909 0.1916 0.2073 0.2982 0.5174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||533||752|TPCN2|protein_coding|CODING|NM_139075.3|25|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4930265 -0.379885 0 1 752 1617 MODIFIER 25 CODING TPCN2 T protein_coding NM_139075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68857038 C T 0 9.7 0 0.7141 0.7492 0.6124 0.501 0.9871 0.9049 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1617||752|TPCN2|protein_coding|CODING|NM_139075.3|25|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1551310 -0.379885 0 1 752 1800 MODIFIER 25 CODING TPCN2 A protein_coding NM_139075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 68857221 C A 0 9.7 0 0.003 0.0763 0.2104 0.2282 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1800||752|TPCN2|protein_coding|CODING|NM_139075.3|25|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11228487 -0.379885 0 1 P241 295 ccG/ccA LOW 4 SILENT CODING CCND1 A protein_coding NM_053056.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69462910 G A 0 222 0 0.1876 0.4135 0.3487 0.5714 0.497 0.5164 0.232045 0.386742 0.465999 1 2261 55046 4355 4910 3187 31243 442 8648 2 10340 120946 11546 8622 6598 66448 904 16488 0.902918 255|255|255 other|other|other 0 COSM1179751 91 19,23,9,28 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P241|295|CCND1|protein_coding|CODING|NM_053056.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.805211 rs9344 -0.693141 0.35817 91 295 65 MODIFIER 5 CODING CCND1 A protein_coding NM_053056.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69466115 C A 0 110 0 0.1566 0.491 0.4179 0.8591 0.5626 0.5419 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900862 0 . 0 . 15 0,4,0,11 UTR_3_PRIME(MODIFIER||65||295|CCND1|protein_coding|CODING|NM_053056.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.991513 rs7177 -0.676189 0.480376 15 295 687 MODIFIER 5 CODING CCND1 G protein_coding NM_053056.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69466737 C G 0 46.2 0 0.171 0.5254 0.438 0.8671 0.6581 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,0,3,0 UTR_3_PRIME(MODIFIER||687||295|CCND1|protein_coding|CODING|NM_053056.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.166667 rs678653 -0.511536 0.0618664 5 137 196 MODIFIER 5 CODING ORAOV1 A protein_coding NM_153451.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69482091 C A 0 90 0 0.8737 0.7492 0.5101 0.8948 0.675 0.6769 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.544197 0 . 0 . 25 15,0,9,0 UTR_3_PRIME(MODIFIER||196||137|ORAOV1|protein_coding|CODING|NM_153451.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.491098 rs1789166 -0.662043 0.660946 25 216 692 MODIFIER 3 CODING FGF19 G protein_coding NM_005117.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69513338 A G 0 18.2 0 0.4115 0.4062 0.2867 0.4722 0.2992 0.5256 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 1,0,2,0 UTR_3_PRIME(MODIFIER||692||216|FGF19|protein_coding|CODING|NM_005117.2|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs386622949,rs948992 -0.453602 0.74 3 206 107 MODIFIER 1 CODING FGF4 G protein_coding NM_002007.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 69589959 A G 0 9.7 0 0.4395 0.6044 0.7277 0.751 0.6511 0.5409 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||107||206|FGF4|protein_coding|CODING|NM_002007.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs9666584 -0.379885 0 1 R541 986 agA/agG LOW 17 SILENT CODING ANO1 G protein_coding NM_018043.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 70007311 A G 0 228 0 0.3986 0.6032 0.5807 0.7798 0.6501 0.6656 0.440471 0.586566 0.660185 2 4119 79057 7200 6622 4933 44666 605 10912 2 9784 120512 11524 8596 6606 66600 896 16506 0 . 0 . 0 74 0,0,40,29 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R541|986|ANO1|protein_coding|CODING|NM_018043.5|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276066 -0.693147 0.509231 74 A568 986 gcA/gcG LOW 17 SILENT CODING ANO1 G protein_coding NM_018043.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 70007392 A G 0 228 0 0.5893 0.6581 0.6081 0.7798 0.6561 0.6636 0.588909 0.639104 0.664754 2 5771 81446 7390 6629 4940 45164 618 10934 2 9856 120778 11568 8610 6614 66722 896 16512 0 . 0 . 0 69 0,0,36,29 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A568|986|ANO1|protein_coding|CODING|NM_018043.5|17|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276067 -0.693147 0.344313 69 986 344 MODIFIER 26 CODING ANO1 C protein_coding NM_018043.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 70034454 G C 0 207 0 0.9531 0.9876 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,1,18 UTR_3_PRIME(MODIFIER||344||986|ANO1|protein_coding|CODING|NM_018043.5|26|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs510718 -0.69168 0.325585 19 1785 260 MODIFIER 23 CODING SHANK2 G protein_coding NM_012309.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 70318714 A G 0 228 0 0.888 0.9683 0.9856 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,21,3 UTR_3_PRIME(MODIFIER||260||1785|SHANK2|protein_coding|CODING|NM_012309.4|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs578657 -0.692831 0.269062 25 A335 1785 gcG/gcA LOW 9 SILENT CODING SHANK2 T protein_coding NM_012309.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 70666765 C T 0 95 0 0.0061 0.0931 0.1945 0.0734 0.2097 0.0389 0 . 0 1 26 1158 49 26 2 747 19 289 2 624 7662 180 228 8 2918 80 3624 0.898397 0 . 0 . 15 1,6,1,7 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A335|1785|SHANK2|protein_coding|CODING|NM_012309.4|9|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.0247705 rs11237599 -0.651104 0.49048 15 475 734 MODIFIER 9 CODING DHCR7 C protein_coding NM_001163817.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71145687 T C 0 9.7 0 0.6884 0.7736 0.7939 0.8294 0.9553 0.6299 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||734||475|DHCR7|protein_coding|CODING|NM_001163817.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7690 -0.379885 0 1 475 643 MODIFIER 9 CODING DHCR7 A protein_coding NM_001163817.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71145778 G A 0 9.7 0 0.6399 0.7436 0.7622 0.7688 0.9553 0.6268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||643||475|DHCR7|protein_coding|CODING|NM_001163817.1|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044535 -0.379885 0 1 475 480 MODIFIER 9 CODING DHCR7 A protein_coding NM_001163817.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71145941 G A 0 31.9 0 0.3941 0.3594 0.2363 0.3849 0.2584 0.4775 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||480||475|DHCR7|protein_coding|CODING|NM_001163817.1|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1790345 -0.453602 0.06 3 G424 475 ggC/ggT LOW 9 SILENT CODING DHCR7 A protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71146577 G A 0 222 0 0.2413 0.382 0.513 0.3839 0.6978 0.1524 0.336595 0.602529 0.73875 1 3040 64183 5950 3305 3659 44295 472 3462 2 9500 116716 11342 8404 6322 63848 856 16444 0.979068 2 benign 0 COSM329305 283 66,61,58,79 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G424|475|DHCR7|protein_coding|CODING|NM_001163817.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.382811 rs909217 -0.693147 0.0584617 283 D386 475 gaT/gaC LOW 9 SILENT CODING DHCR7 G protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71146691 A G 0 228 0 0.6861 0.7564 0.7666 0.7688 0.9553 0.6268 0.725227 0.871189 0.945971 2 7193 101648 8267 6690 6164 61386 767 11181 2 10074 119148 11472 8526 6534 65178 878 16486 0 2 benign 0 COSM429787,COSM1475860 226 0,0,98,108 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D386|475|DHCR7|protein_coding|CODING|NM_001163817.1|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs760241 -0.693147 0.00570775 226 N146 475 aaT/aaC LOW 6 SILENT CODING DHCR7 G protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71152461 A G 0 228 0 0.8162 0.8073 0.8055 0.8274 0.9493 0.6299 0.836591 0.909994 0.947601 2 8600 104940 8517 7236 6108 62491 797 11191 2 10292 119966 11262 8512 6474 66236 904 16286 0 2 benign 0 . 140 0,0,52,74 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N146|475|DHCR7|protein_coding|CODING|NM_001163817.1|6|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs949177 -0.693147 0.00126994 140 T77 475 acC/acT LOW 4 SILENT CODING DHCR7 A protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71155129 G A 0 222 0 0.1657 0.1052 0.0447 0.0933 0.0646 0.1207 0.1275 0.0840006 0.061714 1 1373 9687 406 820 493 4417 88 2090 2 9624 114740 10780 8296 5862 63862 854 15462 0.99831 2 benign 0 . 213 56,48,49,40 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T77|475|DHCR7|protein_coding|CODING|NM_001163817.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.967782 rs4316537 -0.693147 0.586798 213 T69 475 acT/acC LOW 4 SILENT CODING DHCR7 G protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71155153 A G 0 228 0 0.8215 0.8101 0.8069 0.8274 0.9553 0.6299 0.845227 0.91292 0.947601 2 8277 102314 8156 7120 5775 61266 771 10949 2 9820 116864 10814 8366 6104 64962 870 15928 0 2 benign 0 . 200 0,0,83,96 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T69|475|DHCR7|protein_coding|CODING|NM_001163817.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1790334 -0.693147 0.0251483 200 Q63 475 caG/caA LOW 4 SILENT CODING DHCR7 T protein_coding NM_001163817.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71155171 C T 0 222 0 0.323 0.401 0.5403 0.3591 0.6978 0.1452 0.415 0.626906 0.7355 1 3743 62638 5541 3045 3188 43432 449 3240 2 9022 109536 10046 7810 5298 61912 778 14670 0.429666 2 benign 0 . 199 37,52,34,52 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q63|475|DHCR7|protein_coding|CODING|NM_001163817.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99813 rs1044482 -0.693147 0.0151838 199 V74L 706 Gtg/Ctg MODERATE 3 MISSENSE CODING NADSYN1 C protein_coding NM_018161.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71169547 G C 0 222 0 0.3472 0.404 0.4697 0.381 0.7018 0.1513 0.425909 0.636511 0.744411 1 4254 67938 5535 3374 3928 46876 502 3469 2 10406 121344 11568 8618 6612 66720 908 16512 0.646053 0 . 0 . 133 50,21,31,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V74L|706|NADSYN1|protein_coding|CODING|NM_018161.4|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.983558 rs2276360 -0.693147 5.0281e-06 133 Q204H 706 caA/caC MODERATE 8 MISSENSE CODING NADSYN1 C protein_coding NM_018161.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71184678 A C 0 228 0 1 1 1 1 1 1 0 . 0 2 10320 120548 11556 8604 6610 66078 902 16478 2 10320 120550 11556 8604 6610 66078 902 16480 0 . 0 . 0 112 0,0,47,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q204H|706|NADSYN1|protein_coding|CODING|NM_018161.4|8|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7950441 -0.693147 0.466888 112 C235 706 tgT/tgC LOW 9 SILENT CODING NADSYN1 C protein_coding NM_018161.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71185479 T C 0 228 0 0.8253 0.8019 0.745 0.8274 0.9563 0.6258 0.839545 0.909763 0.945738 2 8727 105161 8036 7340 6238 62899 798 11123 2 10404 121400 11576 8652 6614 66734 908 16512 0 . 0 . 0 232 0,0,102,102 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C235|706|NADSYN1|protein_coding|CODING|NM_018161.4|9|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.99271 0 . rs2276354 -0.693147 0.0626497 232 I248 706 atT/atC LOW 9 SILENT CODING NADSYN1 C protein_coding NM_018161.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71185518 T C 0 228 0 0.6392 0.7496 0.7248 0.8284 0.9553 0.6237 0.681136 0.855713 0.945156 2 7038 103336 7958 7342 6238 62861 797 11102 2 10404 121408 11576 8654 6614 66740 908 16512 0 . 0 . 0 183 0,0,57,109 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I248|706|NADSYN1|protein_coding|CODING|NM_018161.4|9|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.85677 0 . rs2186778,rs386560131 -0.693147 0.0186317 183 706 LOW 9 CODING NADSYN1 C protein_coding NM_018161.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71189436 T C 0 228 0 0.8275 0.8017 0.7435 0.8284 0.9563 0.6217 0.841913 0.910772 0.945971 2 7017 83650 5850 6166 4150 50846 616 9005 2 8234 94844 7850 7128 4382 53760 690 12800 0 . 0 . 0 77 0,0,49,20 SPLICE_SITE_REGION+INTRON(LOW||||706|NADSYN1|protein_coding|CODING|NM_018161.4|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276353 -0.693147 0.292721 77 P297L 706 cCc/cTc MODERATE 11 MISSENSE CODING NADSYN1 T protein_coding NM_018161.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71191817 C T 0 222 0 0.1762 0.1042 0.0346 0.0863 0.0646 0.1155 0.136591 0.0802279 0.0513507 1 1498 9028 381 695 465 3905 81 2003 2 10392 121288 11572 8644 6604 66660 904 16512 0.940952 0 . 0 . 93 20,29,14,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P297L|706|NADSYN1|protein_coding|CODING|NM_018161.4|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.771896 rs7121106 -0.693141 0.47112 93 R346 706 Cga/Aga LOW 12 SILENT CODING NADSYN1 A protein_coding NM_018161.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71192439 C A 0 222 0 0.1762 0.1042 0.0346 0.0863 0.0646 0.1155 0.136591 0.0802279 0.0513507 1 1500 9035 382 696 465 3908 81 2003 2 10404 121406 11578 8652 6612 66740 908 16512 0.927136 0 . 0 . 80 17,17,17,11 SYNONYMOUS_CODING(LOW|SILENT|Cga/Aga|R346|706|NADSYN1|protein_coding|CODING|NM_018161.4|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992798 rs59379414 -0.693054 0.565472 80 C17 187 tgC/tgT LOW 1 SILENT CODING KRTAP5-8 T protein_coding NM_021046.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71249152 C T 0 143 0 . 0 . 0 . 0 . 0 . 1 36 207 5 22 4 116 0 24 2 9158 117786 11526 8600 6580 64542 890 16490 0.879797 0 . 0 . 65 21,22,9,6 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C17|187|KRTAP5-8|protein_coding|CODING|NM_021046.2|1|T) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.984357 0.915526 0 3.51902e-07 rs112809261 -0.688148 1.47554e-06 65 S19 187 tcT/tcC LOW 1 SILENT CODING KRTAP5-8 C protein_coding NM_021046.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71249158 T C 0 66 0 . 0 . 0 . 0 . 0 . 1 27 134 3 19 3 79 0 3 2 9388 118752 11542 8618 6592 65206 904 16502 0.202059 0 . 0 . 68 26,27,6,5 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S19|187|KRTAP5-8|protein_coding|CODING|NM_021046.2|1|C) 0 0.5 1 0 . 0 . 0 1 0 57 0 0.883263 0.906497 0 5.77995e-06 rs200887508 -0.676189 3.04664e-06 68 C28R 187 Tgc/Cgc MODERATE 1 MISSENSE CODING KRTAP5-8 C protein_coding NM_021046.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71249183 T C 0 228 0 0.27 0.3311 0.4323 0.4772 0.3141 0.2086 0.293864 0.290698 0.289075 2 2875 39333 5560 4298 2639 19713 298 3950 2 9964 120140 11544 8592 6612 66012 906 16510 1 0 . 0 COSM1356753 71 1,0,33,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C28R|187|KRTAP5-8|protein_coding|CODING|NM_021046.2|1|C) 1 0 . 0 . 1 0 1 1 0 58 0 1 0.933034 0 1 rs55921335 -0.693147 0.0121322 71 C95 187 tgT/tgC LOW 1 SILENT CODING KRTAP5-8 C protein_coding NM_021046.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71249386 T C 0 228 0 1 0.9972 0.9798 1 1 1 0.999318 0.999692 0.999883 2 10184 120860 11361 8654 6613 66640 906 16502 2 10196 121120 11578 8654 6614 66660 908 16510 0 . 0 . 0 102 0,0,58,26 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C95|187|KRTAP5-8|protein_coding|CODING|NM_021046.2|1|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.749424 0 . rs7101792 -0.693147 0.145763 102 169 30 MODIFIER 1 CODING KRTAP5-9 C protein_coding NM_005553.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71260243 T C 0 228 0 0.6301 0.5262 0.5908 0.623 0.4692 0.2986 0.601683 0.499538 0.44724 2 6067 59011 7069 5566 3701 30648 438 5522 2 9970 120798 11566 8632 6614 66656 904 16456 1 0 . 0 . 73 0,1,24,45 UTR_3_PRIME(MODIFIER||30||169|KRTAP5-9|protein_coding|CODING|NM_005553.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2664 -0.693147 0.0794996 73 169 83 MODIFIER 1 CODING KRTAP5-9 A protein_coding NM_005553.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71260296 G A 0 228 0 0.2784 0.344 0.451 0.4901 0.333 0.2178 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 68 0,0,34,31 UTR_3_PRIME(MODIFIER||83||169|KRTAP5-9|protein_coding|CODING|NM_005553.3|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2663 -0.693147 0.564144 68 202 2 MODIFIER 1 CODING KRTAP5-10 C protein_coding NM_001012710.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276632 T C 0 228 0 0.8691 0.5905 0.6066 0.6151 0.4751 0.2955 0.800415 0.552162 0.426587 2 7733 60214 7156 5519 3767 30092 437 5510 2 9628 120150 11576 8622 6614 66304 902 16504 0 . 0 . 0 66 0,0,13,50 UTR_5_PRIME(MODIFIER||2||202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|C) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.0389611 0 . rs36164574 -0.693147 1.61686e-06 66 G16 202 ggT/ggC LOW 1 SILENT CODING KRTAP5-10 C protein_coding NM_001012710.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276681 T C 0 220 0 . 0 . 0 . 0 . 0 . 1 114 1013 74 50 59 608 4 104 2 8256 111944 10996 8400 6276 61370 836 15810 0.278037 0 . 0 . 33 4,2,6,19 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G16|202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|C) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.923116 0.191879 0 0.000883826 rs113879786 -0.692914 0.0190551 33 G23 202 ggC/ggT LOW 1 SILENT CODING KRTAP5-10 T protein_coding NM_001012710.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276702 C T 0 105 0 . 0 . 0 . 0 . 0 . 1 35 267 8 10 13 177 0 24 2 8516 113392 11144 8454 6336 62016 860 16066 0.771014 0 . 0 . 36 13,12,2,9 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G23|202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|T) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.999411 0.904023 0 2.15114e-05 rs113977776 -0.676189 0.00272414 36 Y31C 202 tAt/tGt MODERATE 1 MISSENSE CODING KRTAP5-10 G protein_coding NM_001012710.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276725 A G 0 42.2 0 . 0 . 0 . 0 . 0 . 1 30 39 2 1 0 5 0 1 2 9078 117496 11432 8524 6478 64678 888 16418 0.564845 0 . 0 . 43 19,12,3,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y31C|202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.843711 0.748468 0 0.0142839 rs201471375 -0.662043 0.310568 43 S66 202 tcC/tcG LOW 1 SILENT CODING KRTAP5-10 G protein_coding NM_001012710.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276831 C G 0 228 0 0.5008 0.472 0.5735 0.5754 0.4503 0.2771 0 . 0 2 4652 53440 6813 5173 3665 27640 412 5085 2 9258 118406 11536 8560 6564 65100 890 16498 1 0 . 0 . 31 0,1,10,15 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S66|202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|G) 0 . 0 . 0 1 0 . 1 0 56 0 1 0.310971 0 1 rs111211181,rs71473841 -0.692914 0.176752 31 G92 202 ggG/ggA LOW 1 SILENT CODING KRTAP5-10 A protein_coding NM_001012710.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71276909 G A 0 28.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.960789 0 . 0 COSM1561605 15 6,4,4,0 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G92|202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|A) 0 0.5 1 0 . 0 . 0 . 0 51 0 0.738968 0.161621 0 0.18452 rs12289712 -0.556411 0.0846253 15 202 356 MODIFIER 1 CODING KRTAP5-10 C protein_coding NM_001012710.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71277598 A C 0 228 0 0.4909 0.4694 0.572 0.5744 0.4523 0.2771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 145 0,1,64,64 UTR_3_PRIME(MODIFIER||356||202|KRTAP5-10|protein_coding|CODING|NM_001012710.1|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7120471 -0.693147 3.77622e-08 145 327 39 MODIFIER 9 CODING RNF121 G protein_coding NM_018320.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71707400 A G 0 222 0 0 0.0039936 0 0.0188 0 0.001 0.000227273 7.7006e-05 0 1 1 119 0 112 0 3 1 2 2 10174 118200 11362 8606 6410 65544 880 15224 0.92475 0 . 0 . 78 25,14,21,12 UTR_3_PRIME(MODIFIER||39||327|RNF121|protein_coding|CODING|NM_018320.4|9|G),UPSTREAM(MODIFIER||2709||199|IL18BP|protein_coding|CODING|NM_005699.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.852436 rs180980375 -0.693127 0.714797 78 327 104 MODIFIER 9 CODING RNF121 C protein_coding NM_018320.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71707465 T C 0 222 0 0.8306 0.8772 0.8458 0.8651 0.9781 0.8712 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.583826 0 . 0 . 78 19,19,9,22 UTR_3_PRIME(MODIFIER||104||327|RNF121|protein_coding|CODING|NM_018320.4|9|C),UPSTREAM(MODIFIER||2644||199|IL18BP|protein_coding|CODING|NM_005699.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.749166 rs1055452 -0.69311 0.136255 78 327 128 MODIFIER 9 CODING RNF121 C protein_coding NM_018320.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71707489 T C 0 222 0 0.9062 0.8974 0.8473 0.8651 0.9781 0.8712 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.754389 0 . 0 . 76 16,23,7,24 UTR_3_PRIME(MODIFIER||128||327|RNF121|protein_coding|CODING|NM_018320.4|9|C),UPSTREAM(MODIFIER||2620||199|IL18BP|protein_coding|CODING|NM_005699.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.445855 rs3829215 -0.69311 0.878793 76 V23I 199 Gtc/Atc MODERATE 2 MISSENSE CODING IL18BP A protein_coding NM_005699.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71711435 G A 0 222 0 0 0.00059904 0 0.003 0 0 0.000235405 0.000156863 0.000117619 1 1 33 0 27 0 5 0 0 2 9796 120708 11572 8618 6612 66700 900 16510 0.90699 0 . 0 . 90 27,17,20,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V23I|199|IL18BP|protein_coding|CODING|NM_005699.3|2|A),DOWNSTREAM(MODIFIER||2792||327|RNF121|protein_coding|CODING|NM_018320.4||A),DOWNSTREAM(MODIFIER||2475||2115|NUMA1|protein_coding|CODING|NM_006185.3||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.822073 rs189514886 -0.69312 0.0400252 90 2115 495 MODIFIER 27 CODING NUMA1 C protein_coding NM_006185.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71714078 T C 0 222 0 0.9017 0.8964 0.8501 0.8641 0.9781 0.8712 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.455661 0 . 0 . 112 12,51,8,39 UTR_3_PRIME(MODIFIER||495||2115|NUMA1|protein_coding|CODING|NM_006185.3|27|C),DOWNSTREAM(MODIFIER||113||199|IL18BP|protein_coding|CODING|NM_005699.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.998682 rs1541304 -0.693147 0.0190068 112 2115 47 MODIFIER 27 CODING NUMA1 C protein_coding NM_006185.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71714526 G C 0 222 0 0.8162 0.8712 0.8458 0.8611 0.9751 0.8671 0.698182 0.860696 0.943979 1 8686 112696 10225 7237 6280 64781 860 14627 2 10386 121226 11548 8626 6598 66666 906 16496 0.720377 0 . 0 . 80 24,15,22,9 UTR_3_PRIME(MODIFIER||47||2115|NUMA1|protein_coding|CODING|NM_006185.3|27|C),DOWNSTREAM(MODIFIER||561||199|IL18BP|protein_coding|CODING|NM_005699.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.761062 rs949324 -0.69311 0.169827 80 2115 45 MODIFIER 27 CODING NUMA1 G protein_coding NM_006185.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71714528 T G 0 222 0 0.8162 0.871 0.8458 0.8601 0.9751 0.8671 0.691364 0.852148 0.934545 1 8686 112702 10224 7239 6282 64786 860 14625 2 10386 121230 11546 8630 6600 66668 906 16494 0.999177 0 . 0 . 81 24,16,22,9 UTR_3_PRIME(MODIFIER||45||2115|NUMA1|protein_coding|CODING|NM_006185.3|27|G),DOWNSTREAM(MODIFIER||563||199|IL18BP|protein_coding|CODING|NM_005699.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.6644 rs386622975,rs949323 -0.69311 0.169827 81 L23 291 ctG/ctC LOW 4 SILENT CODING LRTOMT C protein_coding NM_001145308.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71816044 G C 0 222 0 0.1505 0.1174 0.1499 0.1359 0.0219 0.1288 0.140173 0.0584757 0.0229415 1 321 1479 51 76 18 218 8 787 2 2142 19938 406 616 276 8452 192 7854 0.878483 2 benign 0 . 103 29,17,29,14 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L23|291|LRTOMT|protein_coding|CODING|NM_001145308.4|4|C),UPSTREAM(MODIFIER||1611||161|LAMTOR1|protein_coding|CODING|NM_017907.2||C),DOWNSTREAM(MODIFIER||4589||125|ANAPC15|protein_coding|CODING|NM_001278485.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.699376 rs12272086 -0.693146 0.138791 103 D72 125 gaT/gaC LOW 5 SILENT CODING ANAPC15 G protein_coding NM_001278485.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71821236 A G 0 222 0 0.208 0.1743 0.1974 0.2242 0.0596 0.1789 0.186136 0.0977976 0.0525274 1 1932 12654 1531 2001 522 3984 82 2602 2 10406 121396 11574 8646 6614 66736 908 16512 0.99959 0 . 0 . 206 58,25,56,35 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D72|125|ANAPC15|protein_coding|CODING|NM_001278485.1|5|G),UTR_3_PRIME(MODIFIER||1265||291|LRTOMT|protein_coding|CODING|NM_001145308.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971718 rs17161980 -0.693147 0.0304792 206 291 1265 MODIFIER 7 CODING LRTOMT G protein_coding NM_001145308.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71821236 A G 0 222 0 0.208 0.1743 0.1974 0.2242 0.0596 0.1789 0.186136 0.0977976 0.0525274 1 1932 12654 1531 2001 522 3984 82 2602 2 10406 121396 11574 8646 6614 66736 908 16512 0.99959 0 . 0 . 206 58,25,56,35 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D72|125|ANAPC15|protein_coding|CODING|NM_001278485.1|5|G),UTR_3_PRIME(MODIFIER||1265||291|LRTOMT|protein_coding|CODING|NM_001145308.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.971718 rs17161980 -0.693147 0.0304792 206 257 2254 MODIFIER 1 CODING FOLR1 A protein_coding NM_000802.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71900964 G A 0 9.7 0 0.0045 0.0984 0.0836 0.1587 0.0636 0.2096 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 0 uncertain 0 . 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2254||257|FOLR1|protein_coding|CODING|NM_000802.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2071010 -0.379885 0 1 K303N 1258 aaG/aaC MODERATE 8 MISSENSE CODING INPPL1 C protein_coding NM_001567.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71941033 G C 0 222 0 0.0242 0.0242 0.0043 0.0823 0.002 0.001 0.0172727 0.00785461 0.00302819 1 233 1184 71 662 4 153 9 52 2 10298 120758 11524 8638 6430 66478 892 16498 0.676874 0 . 0 . 80 37,11,15,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K303N|1258|INPPL1|protein_coding|CODING|NM_001567.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93315 rs17847215 -0.692914 0.375875 80 S329 1258 tcA/tcG LOW 9 SILENT CODING INPPL1 G protein_coding NM_001567.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 71941212 A G 0 222 0 0.5121 0.3622 0.2622 0.3403 0.2087 0.411 0.487955 0.280302 0.173888 1 4977 29848 3000 2803 1368 11698 223 5779 2 10316 119306 11340 8600 6466 65842 880 15862 0.942538 0 . 0 . 69 13,19,9,27 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S329|1258|INPPL1|protein_coding|CODING|NM_001567.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948372 rs2276048 -0.693139 0.0417576 69 941 1078 MODIFIER 31 CODING PDE2A G protein_coding NM_002599.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72287350 A G 0 228 0 0.9652 0.9902 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 36 0,0,7,28 UTR_3_PRIME(MODIFIER||1078||941|PDE2A|protein_coding|CODING|NM_002599.4|31|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1299161 -0.693136 0.235141 36 941 211 MODIFIER 31 CODING PDE2A G protein_coding NM_002599.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72288217 A G 0 228 0 0.9153 0.9766 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,8,4 UTR_3_PRIME(MODIFIER||211||941|PDE2A|protein_coding|CODING|NM_002599.4|31|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs392818 -0.680642 0.730534 12 Y885 941 taC/taT LOW 31 SILENT CODING PDE2A A protein_coding NM_002599.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72288599 G A 0 222 0 0.2526 0.2865 0.245 0.2758 0.3082 0.3507 0.268636 0.292469 0.304682 1 2745 36085 2892 2241 2128 20044 289 5746 2 10338 120618 11540 8580 6566 66198 892 16504 0.774354 0 . 0 COSM1179752 172 24,58,29,44 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y885|941|PDE2A|protein_coding|CODING|NM_002599.4|31|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.473722 rs1980091 -0.693147 0.011234 172 I735 941 atC/atT LOW 26 SILENT CODING PDE2A A protein_coding NM_002599.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72290629 G A 0 222 0 0.2534 0.2855 0.2406 0.2798 0.2942 0.3579 0.269773 0.288002 0.297345 1 2675 34664 2681 2224 2020 19117 259 5688 2 9880 116016 11172 8278 6164 64168 852 15502 0.848849 0 . 0 . 126 51,6,43,5 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I735|941|PDE2A|protein_coding|CODING|NM_002599.4|26|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.109459 rs392565 -0.693147 0.00468322 126 941 LOW 24 CODING PDE2A C protein_coding NM_002599.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72291927 T C 0 228 0 0.9153 0.9766 0.9928 1 1 1 0.930455 0.976128 0.999534 2 9634 120471 11529 8650 6612 66649 902 16495 2 10350 121232 11558 8650 6612 66662 904 16496 0 . 0 . 0 48 0,0,34,14 SPLICE_SITE_REGION+INTRON(LOW||||941|PDE2A|protein_coding|CODING|NM_002599.4|24|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs577536 -0.693147 0.192285 48 D579 941 gaT/gaC LOW 21 SILENT CODING PDE2A G protein_coding NM_002599.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72293602 A G 0 228 0 0.8351 0.9549 0.9885 1 1 1 0.858182 0.951332 0.999068 2 8917 119679 11522 8651 6614 66613 904 16458 2 10400 121252 11576 8654 6614 66640 908 16460 0 . 0 . 0 68 0,0,23,41 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D579|941|PDE2A|protein_coding|CODING|NM_002599.4|21|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4944557 -0.693147 0.0910588 68 619 LOW 3 CODING ATG16L2 T protein_coding NM_033388.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72532708 C T 0 228 0 0.9864 0.9962 0.9986 1 1 1 0.990812 0.996689 0.999841 2 1249 14497 184 262 12 5022 146 7622 2 1262 14510 184 262 12 5022 146 7622 0 . 0 . 0 16 0,0,9,2 SPLICE_SITE_REGION+INTRON(LOW||||619|ATG16L2|protein_coding|CODING|NM_033388.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11235603 -0.676189 0.513951 16 R220W 619 Cgg/Tgg MODERATE 6 MISSENSE CODING ATG16L2 T protein_coding NM_033388.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72533536 C T 0 222 0 0 0.0202 0 0.1002 0 0 0 . 0 1 1 811 3 797 0 5 0 5 2 9928 117656 11364 8532 5878 64774 844 16336 0.60012 0 . 0 . 136 53,12,53,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R220W|619|ATG16L2|protein_coding|CODING|NM_033388.1|6|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.890412 rs11235604 -0.693147 0.079649 136 740 1240 MODIFIER 20 CODING FCHSD2 G protein_coding NM_014824.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72548596 A G 0 125 0 0.9902 0.9972 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,4 UTR_3_PRIME(MODIFIER||1240||740|FCHSD2|protein_coding|CODING|NM_014824.2|20|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6592492 -0.590765 0.0230738 5 377 15758 MODIFIER 1 CODING P2RY2 C protein_coding NM_002564.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72929447 T C 0 46.3 0 0.7171 0.9016 0.9395 1 0.9374 0.9857 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||15758||377|P2RY2|protein_coding|CODING|NM_002564.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7948393 -0.453602 0.22 2 P46L 377 cCt/cTt MODERATE 3 MISSENSE CODING P2RY2 T protein_coding NM_002564.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72945341 C T 0 228 0 0.9017 0.9073 0.9553 0.8839 0.9165 0.8957 0.908409 0.920222 0.926275 2 9443 111903 11219 7660 6056 61863 831 14831 2 10392 121344 11574 8646 6614 66700 908 16510 1 0 . 0 . 158 1,0,70,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P46L|377|P2RY2|protein_coding|CODING|NM_002564.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2511241 -0.693147 0.533119 158 R272 377 cgC/cgT LOW 3 SILENT CODING P2RY2 T protein_coding NM_002564.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72946020 C T 0 228 0 0.5809 0.5767 0.6628 0.619 0.5636 0.4796 0.565455 0.560065 0.557303 2 5875 68047 7612 5567 3751 36800 491 7951 2 10384 121254 11556 8628 6592 66680 906 16508 0.546741 0 . 0 . 290 2,1,149,112 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R272|377|P2RY2|protein_coding|CODING|NM_002564.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.93026 rs1783596 -0.693147 0.00405927 290 R312S 377 agG/agC MODERATE 3 MISSENSE CODING P2RY2 C protein_coding NM_002564.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72946140 G C 0 228 0 0.0121 0.2724 0.4107 0.5397 0.2266 0.2975 0.0593182 0.176883 0.23713 2 513 32774 5588 4764 1726 15650 202 4331 2 10116 119288 11412 8550 6498 65594 878 16240 0.269092 0 . 0 . 257 0,3,108,127 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agC|R312S|377|P2RY2|protein_coding|CODING|NM_002564.3|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.990925 rs3741156 -0.693147 0.0417559 257 377 2640 MODIFIER 3 CODING P2RY2 G protein_coding NM_002564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72948978 A G 0 145 0 0.9902 0.9972 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,4 UTR_3_PRIME(MODIFIER||2640||377|P2RY2|protein_coding|CODING|NM_002564.3|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1791920 -0.590765 0.636041 6 377 4500 MODIFIER 3 CODING P2RY2 T protein_coding NM_002564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72950838 C T 0 32.6 0 0.9478 0.9854 0.9942 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||4500||377|P2RY2|protein_coding|CODING|NM_002564.3|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7944620 -0.453602 0.56 3 377 6062 MODIFIER 3 CODING P2RY2 C protein_coding NM_002564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72952400 A C 0 36.3 0 0.2685 0.4171 0.5432 0.6815 0.3469 0.3282 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||6062||377|P2RY2|protein_coding|CODING|NM_002564.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4382936 -0.453602 0.42 2 377 6158 MODIFIER 3 CODING P2RY2 A protein_coding NM_002564.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 72952496 G A 0 134 0 0.0113 0.2544 0.4107 0.5099 0.2406 0.2229 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,4,2 UTR_3_PRIME(MODIFIER||6158||377|P2RY2|protein_coding|CODING|NM_002564.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10898909 -0.616816 0.368038 6 243 733 MODIFIER 8 CODING PLEKHB1 T protein_coding NM_021200.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73373380 C T 0 39.3 0 0.9788 0.9942 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||733||243|PLEKHB1|protein_coding|CODING|NM_021200.2|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4944853 -0.453602 0.68 2 208 580 MODIFIER 8 CODING RAB6A T protein_coding NM_002869.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73388363 A T 0 228 0 0.0439 0.4085 0.5836 0.626 0.5477 0.41 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 107 0,0,48,47 UTR_3_PRIME(MODIFIER||580||208|RAB6A|protein_coding|CODING|NM_002869.4|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10898931 -0.693147 0.00354638 107 H93 316 caT/caC LOW 3 SILENT CODING DNAJB13 C protein_coding NM_153614.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73670645 T C 0 222 0 0.8971 0.601 0.5663 0.4534 0.4751 0.5072 0.802727 0.576082 0.459935 1 8539 61914 6396 4116 3222 30723 451 8467 2 10404 121350 11572 8624 6608 66724 908 16510 0.999915 0 . 0 . 170 30,44,38,39 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H93|316|DNAJB13|protein_coding|CODING|NM_153614.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0980352 rs653263 -0.693147 0.261424 170 312 980 MODIFIER 7 CODING UCP3 G protein_coding NM_003356.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73711477 A G 0 228 0 0.5658 0.7077 0.6297 0.8423 0.7545 0.7679 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,2,26 UTR_3_PRIME(MODIFIER||980||312|UCP3|protein_coding|CODING|NM_003356.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs15763 -0.693054 3.59147e-06 29 312 437 MODIFIER 7 CODING UCP3 G protein_coding NM_003356.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73712020 A G 0 39.2 0 0.826 0.5765 0.5288 0.4206 0.5209 0.4908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 13 7,1,2,1 UTR_3_PRIME(MODIFIER||437||312|UCP3|protein_coding|CODING|NM_003356.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.829029 rs647126 -0.511536 0.206307 13 Y210 312 taC/taT LOW 5 SILENT CODING UCP3 A protein_coding NM_003356.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73715542 G A 0 222 0 0.8555 0.5907 0.5418 0.4246 0.5378 0.4928 0.8025 0.634299 0.548102 1 8470 68553 6105 3593 4227 37020 493 8645 2 10402 121236 11548 8636 6604 66654 906 16486 0.609551 0 . 0 . 86 32,9,24,9 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y210|312|UCP3|protein_coding|CODING|NM_003356.3|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.583179 rs2075577 -0.693127 0.310933 86 Y99 312 taT/taC LOW 3 SILENT CODING UCP3 G protein_coding NM_003356.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73717254 A G 0 222 0 0.6445 0.3433 0.1556 0.2808 0.2416 0.2382 0.590682 0.361158 0.243536 1 6326 34438 1731 2392 2521 16932 248 4288 2 10346 120224 11466 8584 6468 66046 890 16424 0.354307 0 . 0 . 73 17,12,27,10 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y99|312|UCP3|protein_coding|CODING|NM_003356.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.629253 rs1800006 -0.693141 0.548944 73 312 2078 MODIFIER 1 CODING UCP3 A protein_coding NM_003356.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73720165 G A 0 54 0 0.0961 0.1861 0.1052 0.2788 0.2306 0.2239 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,1 START_GAINED(LOW||||312|UCP3|protein_coding|CODING|NM_003356.3|1|A),UTR_5_PRIME(MODIFIER||2078||312|UCP3|protein_coding|CODING|NM_003356.3|1|A),DOWNSTREAM(MODIFIER||3594||2353|C2CD3|protein_coding|CODING|NM_001286577.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1800849 -0.453602 0.28 4 V1641 2353 gtA/gtG LOW 24 SILENT CODING C2CD3 C protein_coding NM_001286577.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73785326 T C 0 222 0 0.4312 0.4511 0.4798 0.4425 0.4692 0.4479 0.416591 0.451717 0.469718 1 4253 57680 5539 3682 3941 32043 433 7789 2 10384 120834 11510 8586 6572 66480 904 16398 0.986337 0 . 0 . 74 22,14,24,8 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1641|2353|C2CD3|protein_coding|CODING|NM_001286577.1|24|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.97584 rs4453265 -0.69312 0.113514 74 R997Q 2353 cGa/cAa MODERATE 17 MISSENSE CODING C2CD3 T protein_coding NM_001286577.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73806443 C T 0 222 0 0.3041 0.2278 0.0994 0.2758 0.175 0.2209 0.297727 0.219313 0.179129 1 3123 25730 1300 2341 2224 12692 200 3850 2 10406 121078 11544 8640 6608 66590 904 16386 0.449661 0 . 0 . 186 22,77,14,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R997Q|2353|C2CD3|protein_coding|CODING|NM_001286577.1|17|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.907936 rs11235995 -0.693147 0.496232 186 S865C 2353 tCt/tGt MODERATE 15 MISSENSE CODING C2CD3 C protein_coding NM_001286577.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73811708 G C 0 222 0 0 0.00059904 0 0.003 0 0 0.000227273 7.7006e-05 0 1 1 14 0 11 0 0 0 2 2 10300 120006 11528 8564 6604 66130 894 15986 0.666766 0 . 0 . 115 13,40,7,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S865C|2353|C2CD3|protein_coding|CODING|NM_001286577.1|15|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.782176 rs148264086 -0.693147 0.0434784 115 P552 2353 ccA/ccG LOW 10 SILENT CODING C2CD3 C protein_coding NM_001286577.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73825503 T C 0 222 0 0.0915 0.1685 0.0879 0.2748 0.17 0.2188 0.116818 0.156168 0.176334 1 1171 23481 1200 2344 2219 12517 191 3839 2 10400 121166 11492 8636 6590 66632 908 16508 0.920308 0 . 0 . 217 80,43,42,30 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P552|2353|C2CD3|protein_coding|CODING|NM_001286577.1|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.396956 rs10898957 -0.693147 0.256765 217 400 207 MODIFIER 1 CODING PPME1 G protein_coding NM_001271593.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73882260 T G 0 149 0 0.941 0.5805 0.4035 0.4415 0.4831 0.4622 0 . 0 1 609 6783 117 119 9 2059 76 3794 2 710 12774 216 268 10 4038 138 7394 0.928358 0 . 0 . 77 39,2,35,0 UTR_5_PRIME(MODIFIER||207||400|PPME1|protein_coding|CODING|NM_001271593.1|1|G),UPSTREAM(MODIFIER||196||2353|C2CD3|protein_coding|CODING|NM_001286577.1||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.8824 rs1726746 -0.693136 0.0684051 77 Q560* 604 Cag/Tag HIGH 13 NONSENSE CODING P4HA3 A protein_coding NM_001288748.1 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73978243 G A 0 144 0 0.2632 0.2266 0.1326 0.2867 0.171 0.2393 0.248636 0.185893 0.153739 1 2717 24047 1663 2379 2194 11048 176 3870 2 9138 104702 9128 7634 5968 57470 784 14580 0.866252 0 . 0 . 32 17,0,13,1 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q560*|604|P4HA3|protein_coding|CODING|NM_001288748.1|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.659183 rs3741132 -0.686358 0.752795 32 D400N 604 Gac/Aac MODERATE 9 MISSENSE CODING P4HA3 T protein_coding NM_001288748.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 73988167 C T 0 222 0 0.0991 0.1771 0.1225 0.2808 0.161 0.2311 0.102955 0.129986 0.143839 1 1095 21854 1630 2389 2101 10575 168 3896 2 10402 121040 11538 8632 6608 66590 906 16364 0.694476 0 . 0 . 126 27,32,16,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D400N|604|P4HA3|protein_coding|CODING|NM_001288748.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.911147 rs2282488,rs386504555 -0.693147 0.077713 126 622 6105 MODIFIER 14 CODING PGM2L1 T protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74041592 A T 0 228 0 0.9947 0.896 0.8213 0.879 0.839 0.8916 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 78 0,0,27,50 UTR_3_PRIME(MODIFIER||6105||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8471 -0.693147 0.350599 78 622 6085 MODIFIER 14 CODING PGM2L1 C protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74041612 A C 0 222 0 0.0008 0.018171 0.0403 0.0556 0.004 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.934225 0 . 0 . 85 21,21,22,19 UTR_3_PRIME(MODIFIER||6085||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.774444 rs78478064 -0.693145 0.849408 85 622 5456 MODIFIER 14 CODING PGM2L1 G protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74042241 A G 0 39.3 0 0.764 0.7402 0.7147 0.7956 0.6819 0.729 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||5456||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs655719 -0.453602 0.5 2 622 4910 MODIFIER 14 CODING PGM2L1 G protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74042787 A G 0 9.7 0 0.503 0.6679 0.6945 0.7956 0.6799 0.728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4910||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3168173 -0.379885 0 1 622 4526 MODIFIER 14 CODING PGM2L1 G protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74043171 A G 0 32.3 0 0.2118 0.5553 0.6254 0.7887 0.6243 0.6585 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||4526||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10793072 -0.453602 0.06 2 622 3989 MODIFIER 14 CODING PGM2L1 A protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74043708 G A 0 228 0 0.7632 0.7406 0.7147 0.7956 0.6849 0.729 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 97 0,0,17,73 UTR_3_PRIME(MODIFIER||3989||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111197555,rs596976 -0.693147 0.0237528 97 622 3558 MODIFIER 14 CODING PGM2L1 A protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74044139 G A 0 127 0 0.2133 0.5559 0.6268 0.7887 0.6243 0.6585 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||3558||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11236061 -0.651104 0.344675 8 622 3140 MODIFIER 14 CODING PGM2L1 T protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74044557 C T 0 9.7 0 0.2133 0.5559 0.6268 0.7887 0.6243 0.6585 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3140||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1053021 -0.379885 0 1 622 2721 MODIFIER 14 CODING PGM2L1 T protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74044976 C T 0 63 0 0.0688 0.3736 0.5058 0.5367 0.4662 0.4284 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||2721||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3193507 -0.453602 0.8 3 622 836 MODIFIER 14 CODING PGM2L1 T protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74046861 C T 0 228 0 0.2118 0.5551 0.6254 0.7877 0.6243 0.6585 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,48,24 UTR_3_PRIME(MODIFIER||836||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7941916 -0.693147 0.692942 81 622 722 MODIFIER 14 CODING PGM2L1 T protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74046975 C T 0 228 0 0.6437 0.7007 0.6916 0.7887 0.67 0.7249 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,12,40 UTR_3_PRIME(MODIFIER||722||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs598869 -0.693147 0.589231 59 622 14 MODIFIER 14 CODING PGM2L1 G protein_coding NM_173582.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74047683 A G 0 228 0 0.3646 0.5972 0.6369 0.7887 0.6243 0.6585 0.404773 0.553596 0.629863 2 4207 76592 7954 6937 4717 41832 587 10358 2 10390 120620 11520 8642 6606 66428 902 16132 0 . 0 . 0 44 0,0,25,15 UTR_3_PRIME(MODIFIER||14||622|PGM2L1|protein_coding|CODING|NM_173582.4|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1044782,rs386513027 -0.693145 0.0413867 44 S570 622 agT/agC LOW 13 SILENT CODING PGM2L1 G protein_coding NM_173582.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74049569 A G 0 228 0 0.2133 0.5547 0.6268 0.7887 0.6243 0.6524 0.287045 0.513553 0.62963 2 2842 75265 7898 6938 4725 41901 582 10379 2 10368 121246 11526 8648 6614 66680 908 16502 0 . 0 . 0 65 0,0,57,5 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S570|622|PGM2L1|protein_coding|CODING|NM_173582.4|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386588387,rs3867270 -0.693147 0.0323046 65 V531I 622 Gtt/Att MODERATE 12 MISSENSE CODING PGM2L1 T protein_coding NM_173582.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74053547 C T 0 228 0 0.7632 0.7404 0.7133 0.7956 0.6849 0.729 0.763864 0.714572 0.689306 2 7970 86537 8463 6972 4984 45869 659 11620 2 10378 120918 11518 8646 6610 66540 906 16320 0 . 0 . 0 92 0,0,78,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V531I|622|PGM2L1|protein_coding|CODING|NM_173582.4|12|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs592644 -0.693147 0.00333476 92 L14P 622 cTc/cCc MODERATE 1 MISSENSE CODING PGM2L1 G protein_coding NM_173582.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74109166 A G 0 222 0 0.112 0.1879 0.1311 0.2669 0.161 0.2771 0.116818 0.138457 0.149546 1 1165 22381 1672 2454 1933 10661 174 4322 2 10278 119652 11496 8578 6414 65828 894 16164 0.952536 0 . 0 COSM429848 474 81,165,54,127 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L14P|622|PGM2L1|protein_coding|CODING|NM_173582.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.60085 rs12049823 -0.693147 0.0429335 474 622 136 MODIFIER 1 CODING PGM2L1 T protein_coding NM_173582.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74109342 C T 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,2,49 UTR_5_PRIME(MODIFIER||136||622|PGM2L1|protein_coding|CODING|NM_173582.4|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs904155 -0.693147 0.00199495 51 103 667 MODIFIER 3 CODING KCNE3 G protein_coding NM_005472.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74167630 A G 0 9.7 0 0.7171 0.5733 0.5288 0.4663 0.5099 0.5859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||667||103|KCNE3|protein_coding|CODING|NM_005472.4|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12271177 -0.379885 0 1 231 176 MODIFIER 2 CODING LIPT2 A protein_coding NM_001144869.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74203004 G A 0 81 0 0.3661 0.5042 0.4928 0.6329 0.6064 0.4611 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8618 0 . 0 . 11 4,1,6,0 UTR_3_PRIME(MODIFIER||176||231|LIPT2|protein_coding|CODING|NM_001144869.1|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.950952 rs3741128 -0.616816 0.503448 11 T190S 231 Aca/Tca MODERATE 2 MISSENSE CODING LIPT2 A protein_coding NM_001144869.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74203308 T A 0 222 0 0.3661 0.5088 0.5014 0.6329 0.6153 0.4693 0 . 0 1 896 12372 215 380 1003 5680 139 4059 2 2186 21928 412 622 1636 8918 240 7914 0.968143 0 . 0 COSM147288 192 55,33,60,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Tca|T190S|231|LIPT2|protein_coding|CODING|NM_001144869.1|2|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.927099 rs586088 -0.693147 0.0183682 192 L8 231 Ttg/Ctg LOW 1 SILENT CODING LIPT2 G protein_coding NM_001144869.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74204727 A G 0 77 0 0.7579 0.9327 0.9769 1 0.999 1 0 . 0 2 66 4365 34 82 0 882 54 3247 2 84 4388 34 82 0 884 54 3250 0 . 0 . 0 3 0,0,1,2 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L8|231|LIPT2|protein_coding|CODING|NM_001144869.1|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4944895 -0.511536 0.845642 3 P142 466 ccT/ccC LOW 6 SILENT CODING POLD3 C protein_coding NM_006591.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74329615 T C 0 228 0 0.5703 0.4491 0.4424 0.3204 0.3221 0.5532 0.568182 0.406053 0.322968 2 5849 44866 4961 2755 1723 20907 322 8349 2 10318 120924 11542 8624 6612 66468 900 16460 0 . 0 . COSM147289 40 0,0,34,4 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P142|466|POLD3|protein_coding|CODING|NM_006591.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4944052 -0.693143 0.957866 40 466 390 MODIFIER 12 CODING POLD3 G protein_coding NM_006591.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74352201 C G 0 164 0 0.3464 0.3409 0.353 0.3204 0.2078 0.4826 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,0,15 UTR_3_PRIME(MODIFIER||390||466|POLD3|protein_coding|CODING|NM_006591.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1051058 -0.688148 0.289748 15 L363 451 Ttg/Ctg LOW 9 SILENT CODING CHRDL2 G protein_coding NM_015424.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74413872 A G 0 228 0 0.3835 0.2925 0.1268 0.3264 0.1332 0.4162 0.323864 0.200601 0.137433 2 3544 24783 1492 2794 1078 9613 195 6067 2 10402 121326 11578 8630 6612 66688 906 16510 1 0 . 0 . 72 1,0,41,20 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L363|451|CHRDL2|protein_coding|CODING|NM_015424.5|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs34528207 -0.693147 0.28118 72 Q172 451 caG/caA LOW 5 SILENT CODING CHRDL2 T protein_coding NM_015424.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74419357 C T 0 228 0 0.7224 0.764 0.8429 0.8006 0.7475 0.7434 0.729347 0.740746 0.746564 2 6399 76502 8173 6139 2957 41801 524 10509 2 8776 100476 9352 7474 4080 56054 706 14034 0 . 0 . COSM1163585 90 0,0,44,33 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q172|451|CHRDL2|protein_coding|CODING|NM_015424.5|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1944937 -0.693147 0.560067 90 P165 451 ccG/ccA LOW 5 SILENT CODING CHRDL2 T protein_coding NM_015424.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74419378 C T 0 222 0 0.1346 0.3339 0.5677 0.5357 0.3807 0.181 0.175774 0.308416 0.376281 1 1514 38531 6132 4143 1806 21685 248 3003 2 7930 97022 9330 7434 3966 54428 688 13246 0.439482 0 . 0 . 97 27,19,18,17 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P165|451|CHRDL2|protein_coding|CODING|NM_015424.5|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.80036 rs7948433 -0.693136 0.200242 97 708 3250 MODIFIER 6 CODING RNF169 A protein_coding NM_001098638.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74551025 C A 0 39.3 0 0.8162 0.6897 0.7435 0.7827 0.5249 0.5542 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||3250||708|RNF169|protein_coding|CODING|NM_001098638.1|6|A),DOWNSTREAM(MODIFIER||930||792|XRRA1|protein_coding|CODING|NM_182969.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2033532 -0.453602 0.18 2 226 39 MODIFIER 1 CODING SPCS2 G protein_coding NM_014752.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74660292 A G 0 228 0 0.1437 0.2806 0.2334 0.2262 0.4264 0.4049 0.182803 0.355234 0.430233 2 386 7420 111 137 23 3631 62 3070 2 2142 18926 396 620 46 8242 184 7296 1 0 . 0 . 107 0,1,85,14 UTR_5_PRIME(MODIFIER||39||226|SPCS2|protein_coding|CODING|NM_014752.2|1|G),UPSTREAM(MODIFIER||60||792|XRRA1|protein_coding|CODING|NM_182969.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs643807 -0.693147 0.288348 107 226 1284 MODIFIER 5 CODING SPCS2 A protein_coding NM_014752.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74689372 G A 0 48.5 0 0.3964 0.3756 0.2853 0.2262 0.4742 0.4642 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1284||226|SPCS2|protein_coding|CODING|NM_014752.2|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs537054 -0.511536 0.142856 3 S79 461 tcT/tcC LOW 2 SILENT CODING NEU3 C protein_coding NM_006656.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74705696 T C 0 228 0 0.615 0.7041 0.8026 0.7748 0.8012 0.5818 0.666748 0.763272 0.810579 2 6303 92689 9595 6694 5357 53773 660 10307 2 9806 120752 11572 8614 6612 66740 898 16510 1 0 . 0 . 58 0,1,23,32 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S79|461|NEU3|protein_coding|CODING|NM_006656.5|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs544115 -0.693147 0.0085059 58 709 71 MODIFIER 1 CODING SLCO2B1 C protein_coding NM_007256.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74862356 T C 0 194 0 0.1445 0.377 0.3718 0.2679 0.6223 0.5552 0.228324 0.49124 0.605594 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.973096 0 . 0 . 27 11,0,12,3 UTR_5_PRIME(MODIFIER||71||709|SLCO2B1|protein_coding|CODING|NM_007256.4|1|C) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.630689 rs2851069 -0.688148 0.331024 27 709 36 MODIFIER 1 CODING SLCO2B1 G protein_coding NM_007256.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74862391 A G 0 222 0 1 0.9758 1 0.8839 1 0.9959 1 0.999461 0.999185 1 9823 115531 11079 7397 6089 64845 857 15441 2 9824 116602 11086 8348 6090 64894 858 15502 0.999538 0 . 0 . 40 15,3,16,3 START_GAINED(LOW||||709|SLCO2B1|protein_coding|CODING|NM_007256.4|1|G),UTR_5_PRIME(MODIFIER||36||709|SLCO2B1|protein_coding|CODING|NM_007256.4|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.807823 rs1944612 -0.69168 0.45747 40 I392T 709 aTc/aCc MODERATE 9 MISSENSE CODING SLCO2B1 C protein_coding NM_007256.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74904362 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 10404 121402 11576 8654 6612 66736 908 16512 2 10404 121402 11576 8654 6612 66736 908 16512 1 0 . 0 . 51 0,1,24,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I392T|709|SLCO2B1|protein_coding|CODING|NM_007256.4|9|C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs1621378 -0.693147 0.924812 51 S486F 709 tCt/tTt MODERATE 10 MISSENSE CODING SLCO2B1 T protein_coding NM_007256.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74907582 C T 0 222 0 0.3737 0.1803 0.098 0.2609 0.0199 0.0593 0.331136 0.128985 0.0253902 1 3546 9715 1122 1984 242 1755 65 1001 2 10334 120156 11542 8598 6600 66008 898 16176 0.861917 0 . 0 . 106 27,30,22,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S486F|709|SLCO2B1|protein_coding|CODING|NM_007256.4|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0157392 rs2306168 -0.693146 0.0586698 106 S532 709 agC/agT LOW 10 SILENT CODING SLCO2B1 T protein_coding NM_007256.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74907721 C T 0 222 0 0.2148 0.0727 0.0245 0.0357 0.0149 0.0123 0.196591 0.0789312 0.018635 1 2043 4173 148 237 208 1260 32 245 2 10102 116198 11328 8498 6300 64406 846 14718 0.879657 0 . 0 . 72 13,25,9,21 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S532|709|SLCO2B1|protein_coding|CODING|NM_007256.4|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.728087 rs61555831 -0.693097 0.325981 72 418 5650 MODIFIER 16 CODING ARRB1 T protein_coding NM_004041.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74971557 G T 0 100 0 0.1604 0.0589 0.0288 0.0079 0.0308 0.0245 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||5650||418|ARRB1|protein_coding|CODING|NM_004041.4|16|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs17133858 -0.511536 0.771809 4 H111 418 caC/caT LOW 5 SILENT CODING ARRB1 A protein_coding NM_004041.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 74994352 G A 0 222 0 0.1891 0.1645 0.2651 0.0982 0.1113 0.183 0.176136 0.133528 0.111693 1 1886 17396 3336 925 803 7609 131 2706 2 10354 117688 11542 8630 6606 65536 860 14160 0.89723 0 . 0 . 63 19,11,17,13 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H111|418|ARRB1|protein_coding|CODING|NM_004041.4|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.492518 rs877711 -0.693097 0.302215 63 605 600 MODIFIER 17 CODING GDPD5 G protein_coding NM_030792.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75145952 A G 0 228 0 0.8933 0.9702 0.9914 1 0.998 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 23 0,0,20,3 UTR_3_PRIME(MODIFIER||600||605|GDPD5|protein_coding|CODING|NM_030792.6|17|G),UPSTREAM(MODIFIER||4278||583|KLHL35|protein_coding|CODING|NM_001039548.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1540214 -0.692717 0.104544 23 605 168 MODIFIER 17 CODING GDPD5 G protein_coding NM_030792.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75146384 A G 0 214 0 0.3079 0.5439 0.7003 0.5625 0.6481 0.6258 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,13,2 UTR_3_PRIME(MODIFIER||168||605|GDPD5|protein_coding|CODING|NM_030792.6|17|G),UPSTREAM(MODIFIER||4710||583|KLHL35|protein_coding|CODING|NM_001039548.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1043638 -0.688148 0.167888 15 A480T 605 Gcc/Acc MODERATE 14 MISSENSE CODING GDPD5 T protein_coding NM_030792.6 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75152243 C T 0 228 0 0.4569 0.6671 0.719 0.9236 0.7147 0.6012 0.510455 0.655629 0.730026 2 5219 84023 8116 7954 3914 47488 632 10700 2 10296 120568 11526 8622 6510 66218 890 16506 0 . 0 . COSM330244 119 0,0,66,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A480T|605|GDPD5|protein_coding|CODING|NM_030792.6|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs571353 -0.693147 0.0415426 119 R185 605 cgC/cgT LOW 8 SILENT CODING GDPD5 A protein_coding NM_030792.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75160575 G A 0 228 0 0.2073 0.5349 0.6282 0.8095 0.6203 0.5409 0.282431 0.517295 0.637883 2 1575 33229 2090 3584 644 19421 238 5677 2 4652 52236 3050 4402 1060 28936 368 9768 0 . 0 . 0 68 0,0,51,8 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R185|605|GDPD5|protein_coding|CODING|NM_030792.6|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs518611 -0.693147 0.170415 68 L78 418 ctA/ctG LOW 3 SILENT CODING SERPINH1 G protein_coding NM_001207014.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75277628 A G 0 222 0 0.9546 0.89 0.9294 0.7282 0.8877 0.9438 0.945177 0.913007 0.896528 1 9293 104422 10482 5775 5625 57290 789 15168 2 9762 116086 11222 8202 6006 63826 852 16216 0.693407 2 benign 0 . 189 46,47,45,34 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L78|418|SERPINH1|protein_coding|CODING|NM_001207014.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.737453 rs584961 -0.693147 0.431123 189 L200 418 Cta/Tta LOW 3 SILENT CODING SERPINH1 T protein_coding NM_001207014.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75277992 C T 0 222 0 0.0847 0.2993 0.3213 0.2976 0.5417 0.3262 0.172437 0.425703 0.55562 1 1493 50859 3389 2263 2834 34945 414 5521 2 9134 115592 11318 8308 6458 63300 854 16220 0.986189 0 . 0 . 100 12,35,11,33 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L200|418|SERPINH1|protein_coding|CODING|NM_001207014.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.875254 rs651581 -0.693146 0.191681 100 418 125 MODIFIER 6 CODING SERPINH1 G protein_coding NM_001207014.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75283253 A G 0 70 0 0.0749 0.2478 0.2939 0.1637 0.5427 0.2321 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.506703 0 . 0 . 12 0,7,0,5 UTR_3_PRIME(MODIFIER||125||418|SERPINH1|protein_coding|CODING|NM_001207014.1|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.95494 0 . 0.838008 rs9175 -0.590765 0.865618 12 I247M 813 atT/atG MODERATE 1 MISSENSE CODING MAP6 C protein_coding NM_033063.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75378674 A C 0 42.3 0 0.556 0.5489 0.5389 0.5655 0.5338 0.545 0 . 0 2 1 12 0 0 0 1 0 10 2 2 18 0 0 0 2 0 14 0 . 0 . COSM1132965 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I247M|813|MAP6|protein_coding|CODING|NM_033063.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs12225010 -0.453602 0.88 2 388 19 MODIFIER 8 CODING DGAT2 C protein_coding NM_032564.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75511572 T C 0 222 0 0.5446 0.2602 0.1354 0.2728 0.0825 0.1339 0.460209 0.217113 0.0925926 1 4709 17209 1298 2251 541 6262 100 2048 2 9732 108426 10140 7932 5452 59386 792 14992 0.969453 0 . 0 . 79 36,16,11,15 UTR_3_PRIME(MODIFIER||19||388|DGAT2|protein_coding|CODING|NM_032564.4|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.299496 rs3060,rs386578956 -0.692976 0.465032 79 S697 699 tcC/tcT LOW 15 SILENT CODING UVRAG T protein_coding NM_003369.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 75852448 C T 0 222 0 0.0038 0.0958 0.0274 0.2698 0.0606 0.1258 0.0177273 0.047366 0.0625582 1 157 10394 294 2649 630 4482 82 2100 2 9938 118660 11502 8540 6596 65558 890 15636 0.994446 0 . 0 . 96 20,24,14,27 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S697|699|UVRAG|protein_coding|CODING|NM_003369.3|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.863921 rs636420 -0.693145 0.136866 96 254 613 MODIFIER 2 CODING LOC100506127 G protein_coding NM_001282456.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76115699 A G 0 31.9 0 0.3033 0.1813 0.1167 0.2153 0.0805 0.1309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||613||254|LOC100506127|protein_coding|CODING|NM_001282456.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs12289955 -0.453602 0.28 3 254 1277 MODIFIER 2 CODING LOC100506127 T protein_coding NM_001282456.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76116363 G T 0 39.3 0 0.2837 0.1787 0.1153 0.2282 0.0805 0.1319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1277||254|LOC100506127|protein_coding|CODING|NM_001282456.2|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs17134828 -0.453602 0.18 2 254 3264 MODIFIER 2 CODING LOC100506127 G protein_coding NM_001282456.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76118350 A G 0 9.7 0 0.882 0.9071 0.9323 0.8988 0.9205 0.9182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3264||254|LOC100506127|protein_coding|CODING|NM_001282456.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10736805,rs386514779 -0.379885 0 1 1337 LOW 11 CODING EMSY A protein_coding NM_001300942.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76227182 G A 0 222 0 0.3828 0.6362 0.755 0.8006 0.6213 0.7403 0.442273 0.549908 0.605079 1 4445 78028 9209 7098 4221 40542 583 11930 2 10398 121190 11520 8646 6604 66634 904 16484 0.986935 0 . 0 . 92 37,10,34,3 SPLICE_SITE_REGION+INTRON(LOW||||1337|EMSY|protein_coding|CODING|NM_001300942.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.189286 rs2508740 -0.693141 0.426187 92 662 2009 MODIFIER 3 CODING LRRC32 C protein_coding NM_001128922.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76368639 A C 0 222 0 0.2852 0.3391 0.4294 0.3452 0.3559 0.3241 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8061 0 . 0 . 189 40,47,35,49 UTR_3_PRIME(MODIFIER||2009||662|LRRC32|protein_coding|CODING|NM_001128922.1|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.442999 rs7685 -0.693147 9.8563e-05 189 662 939 MODIFIER 3 CODING LRRC32 A protein_coding NM_001128922.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76369709 C A 0 222 0 0.2806 0.3357 0.4251 0.3462 0.3469 0.3241 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.442558 0 . 0 . 61 29,5,20,3 UTR_3_PRIME(MODIFIER||939||662|LRRC32|protein_coding|CODING|NM_001128922.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.982657 rs3781700,rs386586171 -0.692717 0.874124 61 662 863 MODIFIER 3 CODING LRRC32 G protein_coding NM_001128922.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76369785 T G 0 222 0 0.2806 0.3363 0.4236 0.3512 0.3479 0.3221 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.992849 0 . 0 . 76 20,18,14,13 UTR_3_PRIME(MODIFIER||863||662|LRRC32|protein_coding|CODING|NM_001128922.1|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.338953 rs3781699,rs386586170 -0.693021 0.113245 76 662 601 MODIFIER 3 CODING LRRC32 C protein_coding NM_001128922.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76370047 T C 0 64 0 0.9168 0.8143 0.7305 0.8829 0.7386 0.7423 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||601||662|LRRC32|protein_coding|CODING|NM_001128922.1|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1320646 -0.511536 0.0681597 3 P615 662 ccT/ccC LOW 3 SILENT CODING LRRC32 G protein_coding NM_001128922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76370792 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10406 121410 11578 8654 6614 66738 908 16512 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 148 0,0,61,73 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P615|662|LRRC32|protein_coding|CODING|NM_001128922.1|3|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs4304809 -0.693147 0.151582 148 G195 662 ggT/ggC LOW 3 SILENT CODING LRRC32 G protein_coding NM_001128922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76372052 A G 0 222 0 0.6316 0.6254 0.5692 0.6349 0.6064 0.6667 0.630227 0.624615 0.621738 1 6658 74153 6225 5498 3430 40963 556 10823 2 10402 121262 11540 8610 6608 66686 906 16510 0.753468 0 . 0 . 153 43,24,48,24 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G195|662|LRRC32|protein_coding|CODING|NM_001128922.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994012 rs3740779 -0.693147 0.487272 153 T73 662 acA/acG LOW 3 SILENT CODING LRRC32 C protein_coding NM_001128922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76372418 T C 0 222 0 0.9924 0.8802 0.7882 0.7976 0.8588 0.9008 0.967955 0.903728 0.870806 1 10122 105146 9123 6783 5312 57898 777 15131 2 10404 121290 11558 8644 6560 66712 902 16510 0.979528 0 . 0 COSM1357053 125 20,33,23,34 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T73|662|LRRC32|protein_coding|CODING|NM_001128922.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.757795 rs3740778,rs386585200 -0.693147 0.0127421 125 D344E 353 gaT/gaA MODERATE 2 MISSENSE CODING TSKU A protein_coding NM_001258210.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76507692 T A 0 222 0 0.9781 0.8251 0.7147 0.8492 0.7535 0.7454 0.94775 0.835785 0.780475 1 1790 8214 350 467 115 4739 62 691 2 1882 10244 484 546 150 6174 84 924 0.622848 0 . 0 . 88 28,14,31,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaA|D344E|353|TSKU|protein_coding|CODING|NM_001258210.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.715103 rs1149621 -0.693143 0.00926275 88 P142 267 ccG/ccA LOW 6 SILENT CODING ACER3 A protein_coding NM_018367.6 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76701606 G A 0 222 0 0.1906 0.5329 0.5072 0.6349 0.7366 0.6994 0.286136 0.599276 0.759786 1 2710 82521 5775 5821 5149 50819 640 11607 2 10398 121388 11574 8650 6614 66734 908 16510 0.980051 0 . 0 . 151 18,45,30,43 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P142|267|ACER3|protein_coding|CODING|NM_018367.6|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.290082 rs3740767 -0.693147 0.479667 151 267 937 MODIFIER 11 CODING ACER3 A protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76732308 G A 0 9.7 0 0.6626 0.6647 0.5461 0.6349 0.7406 0.7045 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||937||267|ACER3|protein_coding|CODING|NM_018367.6|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7925774 -0.379885 0 1 267 1578 MODIFIER 11 CODING ACER3 C protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76732949 T C 0 9.7 0 0.8306 0.7111 0.5605 0.6349 0.7406 0.7045 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1578||267|ACER3|protein_coding|CODING|NM_018367.6|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7123496 -0.379885 0 1 267 1653 MODIFIER 11 CODING ACER3 G protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76733024 A G 0 32.6 0 0.2012 0.5369 0.5086 0.6349 0.7366 0.7045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1653||267|ACER3|protein_coding|CODING|NM_018367.6|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10793231 -0.379885 0 2 267 2476 MODIFIER 11 CODING ACER3 T protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76733847 C T 0 39.3 0 0.6694 0.6665 0.5476 0.6339 0.7406 0.7045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2476||267|ACER3|protein_coding|CODING|NM_018367.6|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2826 -0.453602 0.6 2 267 3474 MODIFIER 11 CODING ACER3 T protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76734845 C T 0 32.6 0 0.4508 0.1306 0.0346 0.0278 0.004 0.002 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3474||267|ACER3|protein_coding|CODING|NM_018367.6|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6592696 -0.379885 0 2 267 4392 MODIFIER 11 CODING ACER3 A protein_coding NM_018367.6 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76735763 T A 0 22.4 0 0.6702 0.6665 0.5476 0.6349 0.7406 0.7025 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,1 UTR_3_PRIME(MODIFIER||4392||267|ACER3|protein_coding|CODING|NM_018367.6|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10899344 -0.453602 0.7 4 A191T 384 Gcg/Acg MODERATE 2 MISSENSE CODING B3GNT6 A protein_coding NM_138706.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76751166 G A 0 222 0 0.3608 0.1905 0.111 0.1825 0.0954 0.1227 0.322096 0.17512 0.0996021 1 3116 14731 1217 1467 560 6274 87 2010 2 9166 114788 11250 8166 6470 62652 836 16248 0.444593 0 . 0 . 176 56,32,56,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A191T|384|B3GNT6|protein_coding|CODING|NM_138706.4|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.793146 rs73493606 -0.693147 0.87956 176 L330 384 ctg/ HIGH 3 CODING B3GNT6 C protein_coding NM_138706.4 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76751584 CT C 0 109 0 1 1 1 1 1 1 0.997964 0.999103 0.999696 2 482 9011 80 140 6 2687 88 5528 2 482 9024 80 140 6 2692 88 5536 0 . 0 . COSM1357066 50 0,0,12,4 FRAME_SHIFT(HIGH||ctg/|L330|384|B3GNT6|protein_coding|CODING|NM_138706.4|3|C) 1 0 . 48 0.96 1 1 1 1 (B3GNT6|B3GNT6|1|1.00) 60 0 0 1 0 . rs11292199 -0.689466 2.14777e-07 50 640 LOW 12 CODING CAPN5 C protein_coding NM_004055.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76833763 G C 0 199 0 0.2829 0.1735 0.0893 0.244 0.0596 0.1299 0.2425 0.126232 0.0666356 1 2700 13144 1322 2118 355 4268 71 2310 2 10346 120958 11552 8612 6612 66464 902 16470 0.978845 0 . 0 . 42 13,11,4,9 SPLICE_SITE_REGION+INTRON(LOW||||640|CAPN5|protein_coding|CODING|NM_004055.4|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799972 rs59430193 -0.683931 0.269079 42 640 1434 MODIFIER 13 CODING CAPN5 C protein_coding NM_004055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76836350 T C 0 222 0 0.5212 0.507 0.4092 0.5694 0.3976 0.6053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.913177 0 . 0 . 122 34,19,24,28 UTR_3_PRIME(MODIFIER||1434||640|CAPN5|protein_coding|CODING|NM_004055.4|13|C),UPSTREAM(MODIFIER||2960||2215|MYO7A|protein_coding|CODING|NM_000260.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.483885 rs1043418 -0.693147 0.0461527 122 640 1948 MODIFIER 13 CODING CAPN5 A protein_coding NM_004055.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76836864 G A 0 222 0 0.7005 0.6036 0.4798 0.5784 0.502 0.6912 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.415554 0 . 0 . 95 15,27,15,26 UTR_3_PRIME(MODIFIER||1948||640|CAPN5|protein_coding|CODING|NM_004055.4|13|A),UPSTREAM(MODIFIER||2446||2215|MYO7A|protein_coding|CODING|NM_000260.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.869759 rs8251 -0.693145 0.0939392 95 G261 2215 ggT/ggC LOW 8 SILENT CODING MYO7A C protein_coding NM_000260.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76868372 T C 0 228 0 0.8351 0.474 0.4971 0.3383 0.3777 0.2086 0.734184 0.47559 0.353282 2 7104 44251 5012 2704 2891 22793 297 3450 2 9186 108852 10284 7778 6008 60598 804 14194 1 2 benign 0 . 103 0,1,59,31 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G261|2215|MYO7A|protein_coding|CODING|NM_000260.3|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs762667 -0.693147 0.0944338 103 S1585 2215 agC/agT LOW 35 SILENT CODING MYO7A T protein_coding NM_000260.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76910766 C T 0 228 0 0.3185 0.4325 0.5937 0.4494 0.5527 0.3313 0.324557 0.457317 0.521548 2 3140 60123 7404 4195 4082 35070 416 5816 2 9300 118284 11350 8510 6508 65684 868 16064 0 2 benign 0 . 30 0,0,18,11 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S1585|2215|MYO7A|protein_coding|CODING|NM_000260.3|35|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7927472 -0.693079 0.164838 30 R1602Q 2215 cGg/cAg MODERATE 35 MISSENSE CODING MYO7A A protein_coding NM_000260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76910816 G A 0 222 0 0 0.011781 0 0.0585 0 0 0.000254842 0.000163961 0.000120861 1 1 391 2 377 0 3 2 6 2 9242 115186 11200 8484 6518 64550 850 14342 0.749117 3|3 likely-benign|likely-benign 0 . 36 10,5,7,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1602Q|2215|MYO7A|protein_coding|CODING|NM_000260.3|35|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.397189 rs139889944 -0.683931 0.270977 36 S1666C 2215 Agt/Tgt MODERATE 36 MISSENSE CODING MYO7A T protein_coding NM_000260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76912636 A T 0 228 0 0.7254 0.5517 0.6455 0.4524 0.5656 0.3384 0.681055 0.589112 0.542543 2 6726 65622 7779 4233 4171 36282 439 5992 2 9832 120630 11558 8586 6600 66654 892 16508 0 2 benign 0 . 114 0,0,57,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S1666C|2215|MYO7A|protein_coding|CODING|NM_000260.3|36|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2276288 -0.693147 0.0501093 114 K1905 2215 aaA/aaG LOW 41 SILENT CODING MYO7A G protein_coding NM_000260.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76917220 A G 0 228 0 0.7708 0.5549 0.5994 0.4683 0.505 0.3722 0.702736 0.553728 0.481731 2 6743 60292 7287 4312 3849 31427 404 6270 2 9486 115234 11068 8246 6302 63828 862 15442 0.574803 2 benign 0 . 151 2,0,75,52 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1905|2215|MYO7A|protein_coding|CODING|NM_000260.3|41|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.0905512 rs2276293 -0.693147 0.0173702 151 2215 LOW 42 CODING MYO7A T protein_coding NM_000260.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76919468 A T 0 228 0 0.5023 0.513 0.6715 0.4653 0.5855 0.3896 0.533943 0.559647 0.572328 2 4879 63966 7420 4196 4121 36309 474 6567 2 9098 112716 10744 8052 6258 62642 828 15094 0 2 benign 0 . 154 0,0,87,45 SPLICE_SITE_REGION+INTRON(LOW||||2215|MYO7A|protein_coding|CODING|NM_000260.3|42|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1320703 -0.693147 0.00155112 154 L1954I 2215 Ctc/Atc MODERATE 43 MISSENSE CODING MYO7A A protein_coding NM_000260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76919478 C A 0 228 0 0.7572 0.499 0.549 0.3343 0.5 0.2832 0.68898 0.549212 0.480523 2 6641 54952 6079 2985 3626 30270 391 4960 2 9476 115066 10962 8190 6376 63818 850 15394 1 2 benign 0 . 152 1,0,84,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Atc|L1954I|2215|MYO7A|protein_coding|CODING|NM_000260.3|43|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs948962 -0.693147 0.00127387 152 K2106 2215 aaG/aaA LOW 46 SILENT CODING MYO7A A protein_coding NM_000260.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76922946 G A 0 222 0 0.3994 0.1957 0.147 0.0635 0.2227 0.0634 0.340027 0.246833 0.199136 1 3602 21676 984 565 1871 13099 163 1392 2 9778 120052 11456 8596 6606 66396 892 16328 0.750786 2 benign 0 . 129 44,24,30,21 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K2106|2215|MYO7A|protein_coding|CODING|NM_000260.3|46|A),DOWNSTREAM(MODIFIER||4657||520|GDPD4|protein_coding|CODING|NM_182833.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.904365 rs11237123 -0.693147 0.267809 129 520 297 MODIFIER 16 CODING GDPD4 G protein_coding NM_182833.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76928025 A G 0 222 0 0.0197 0.1128 0.1628 0.0665 0.2883 0.0706 0 . 0 1 29 2576 35 22 514 1204 40 732 2 612 14186 208 224 1160 4180 178 7624 0.491676 0 . 0 . 136 56,12,44,8 UTR_3_PRIME(MODIFIER||297||520|GDPD4|protein_coding|CODING|NM_182833.1|16|G),DOWNSTREAM(MODIFIER||1739||2215|MYO7A|protein_coding|CODING|NM_000260.3||G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.889223 rs12363944 -0.693147 0.0541365 136 520 173 MODIFIER 16 CODING GDPD4 G protein_coding NM_182833.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76928149 A G 0 228 0 0.5749 0.7939 0.8703 0.7788 0.9642 0.8763 0 . 0 2 1558 23655 636 605 2088 11087 292 7389 2 2374 26342 720 750 2158 11630 316 8394 0 . 0 . 0 198 0,0,97,80 UTR_3_PRIME(MODIFIER||173||520|GDPD4|protein_coding|CODING|NM_182833.1|16|G),DOWNSTREAM(MODIFIER||1863||2215|MYO7A|protein_coding|CODING|NM_000260.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2282576 -0.693147 0.31647 198 520 LOW 11 CODING GDPD4 G protein_coding NM_182833.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 76954898 A G 0 228 0 0.348 0.4087 0.5605 0.38 0.492 0.3272 0.360682 0.440234 0.481011 2 3685 56439 6605 3469 3784 32778 426 5692 2 10322 120418 11512 8538 6594 66350 906 16196 1 0 . 0 . 114 0,1,25,78 SPLICE_SITE_REGION+INTRON(LOW||||520|GDPD4|protein_coding|CODING|NM_182833.1|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7104577 -0.693147 0.0145308 114 1441 50 MODIFIER 1 CODING RSF1 G protein_coding NM_016578.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77531810 T G 0 136 0 1 1 1 1 1 1 0 . 0 2 380 6930 102 240 24 2462 88 3634 2 380 6930 102 240 24 2462 88 3634 0 . 0 . 0 9 0,0,0,9 UTR_5_PRIME(MODIFIER||50||1441|RSF1|protein_coding|CODING|NM_016578.3|1|G),UPSTREAM(MODIFIER||350||147|AAMDC|protein_coding|CODING|NM_001316957.1||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs10751277 -0.662043 0.20008 9 255 260 MODIFIER 2 CODING KCTD14 C protein_coding NM_023930.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77727379 T C 0 105 0 0.0227 0.1004 0.0821 0.122 0.1233 0.1728 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 8 0,1,7,0 UTR_3_PRIME(MODIFIER||260||255|KCTD14|protein_coding|CODING|NM_023930.3|2|C),UTR_3_PRIME(MODIFIER||22331||134|NDUFC2-KCTD14|protein_coding|CODING|NM_001203260.1|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3824865 -0.636426 0.687651 8 134 22331 MODIFIER 4 CODING NDUFC2-KCTD14 C protein_coding NM_001203260.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77727379 T C 0 105 0 0.0227 0.1004 0.0821 0.122 0.1233 0.1728 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 8 0,1,7,0 UTR_3_PRIME(MODIFIER||260||255|KCTD14|protein_coding|CODING|NM_023930.3|2|C),UTR_3_PRIME(MODIFIER||22331||134|NDUFC2-KCTD14|protein_coding|CODING|NM_001203260.1|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs3824865 -0.636426 0.687651 8 526 LOW 13 CODING ALG8 C protein_coding NM_024079.4 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77811990 T C 0 228 0 0.9501 0.8327 0.7161 0.7351 0.8618 0.8272 0.936818 0.880391 0.851468 2 9708 100906 7908 6512 5547 56710 772 13749 2 10392 121294 11554 8634 6612 66690 908 16504 1 2 benign 0 . 58 1,0,45,10 SPLICE_SITE_REGION(LOW||||526|ALG8|protein_coding|CODING|NM_024079.4|13|C),UTR_3_PRIME(MODIFIER||20||526|ALG8|protein_coding|CODING|NM_024079.4|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1263505 -0.693147 0.178548 58 526 20 MODIFIER 13 CODING ALG8 C protein_coding NM_024079.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77811990 T C 0 228 0 0.9501 0.8327 0.7161 0.7351 0.8618 0.8272 0.936818 0.880391 0.851468 2 9708 100906 7908 6512 5547 56710 772 13749 2 10392 121294 11554 8634 6612 66690 908 16504 1 2 benign 0 . 58 1,0,45,10 SPLICE_SITE_REGION(LOW||||526|ALG8|protein_coding|CODING|NM_024079.4|13|C),UTR_3_PRIME(MODIFIER||20||526|ALG8|protein_coding|CODING|NM_024079.4|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1263505 -0.693147 0.178548 58 260 2425 MODIFIER 2 CODING KCTD21 C protein_coding NM_001029859.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77882393 T C 0 222 0 0.7617 0.344 0.1398 0.2262 0.1769 0.2178 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.931215 0 . 0 . 126 45,27,23,26 UTR_3_PRIME(MODIFIER||2425||260|KCTD21|protein_coding|CODING|NM_001029859.2|2|C),INTRAGENIC(MODIFIER|||||KCTD21-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.671568 rs613686 -0.693147 0.514165 126 260 36 MODIFIER 2 CODING KCTD21 T protein_coding NM_001029859.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77884782 C T 0 228 0 0.8601 0.5895 0.6499 0.5 0.5249 0.3395 0.803409 0.616143 0.520154 2 8313 61478 7759 4029 2497 33959 425 4496 2 10172 113054 11486 8542 6602 64398 816 11038 0 . 0 . 0 46 0,0,11,34 UTR_3_PRIME(MODIFIER||36||260|KCTD21|protein_coding|CODING|NM_001029859.2|2|T),INTRAGENIC(MODIFIER|||||KCTD21-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs230661 -0.693147 0.123171 46 P554 1018 ccG/ccT LOW 10 SILENT CODING USP35 T protein_coding NM_020798.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77920563 G T 0 222 0 0.1952 0.2628 0.3156 0.3968 0.1779 0.2658 0.170663 0.161052 0.156485 1 1737 26255 4183 3206 1261 11024 193 4651 2 9692 119704 11498 8580 6560 66076 888 16410 0.880017 0 . 0 . 90 21,22,26,15 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P554|1018|USP35|protein_coding|CODING|NM_020798.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99936 rs2510045 -0.693145 0.133473 90 P654 1018 ccC/ccA LOW 10 SILENT CODING USP35 A protein_coding NM_020798.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77920863 C A 0 222 0 0.0605 0.2177 0.2997 0.4028 0.1551 0.2454 0.0572178 0.106721 0.129688 1 588 22866 4213 3162 917 9612 163 4211 2 8948 112978 10836 8162 5978 62186 822 16046 0.998722 0 . 0 . 90 14,19,19,26 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P654|1018|USP35|protein_coding|CODING|NM_020798.2|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846904 rs2512527 -0.693147 0.0384899 90 I677V 1018 Ata/Gta MODERATE 10 MISSENSE CODING USP35 G protein_coding NM_020798.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77920930 A G 0 222 0 0.4425 0.35 0.3501 0.4087 0.2356 0.2822 0.396448 0.263517 0.199639 1 3573 27969 3554 2656 1437 11986 199 4564 2 8046 95674 8384 6468 5160 52214 702 14700 0.967577 0 . 0 . 58 6,22,6,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I677V|1018|USP35|protein_coding|CODING|NM_020798.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786833 rs2511188 -0.693097 0.148751 58 A876P 1018 Gct/Cct MODERATE 10 MISSENSE CODING USP35 C protein_coding NM_020798.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77921527 G C 0 222 0 0.9985 0.849 0.9207 0.6558 0.9602 0.681 0.988004 0.96959 0.960879 1 9705 107782 10273 5569 5579 63766 783 12107 2 9804 120746 11576 8608 6610 66740 900 16508 0.631826 0 . 0 . 70 25,12,21,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A876P|1018|USP35|protein_coding|CODING|NM_020798.2|10|C),DOWNSTREAM(MODIFIER||4809||676|GAB2|protein_coding|CODING|NM_080491.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.84208 rs2512526 -0.693097 0.80114 70 1018 11 MODIFIER 11 CODING USP35 T protein_coding NM_020798.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77924870 C T 0 222 0 0.1687 0.2616 0.3228 0.3988 0.1899 0.2761 0.139444 0.155217 0.162958 1 1533 26819 4216 3232 1277 11499 203 4859 2 9788 120316 11496 8578 6512 66568 896 16478 0.706656 0 . 0 . 59 14,11,11,16 UTR_3_PRIME(MODIFIER||11||1018|USP35|protein_coding|CODING|NM_020798.2|11|T),DOWNSTREAM(MODIFIER||1466||676|GAB2|protein_coding|CODING|NM_080491.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.804641 rs2450138 -0.693021 0.0950954 59 676 3217 MODIFIER 10 CODING GAB2 G protein_coding NM_080491.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77927101 A G 0 200 0 0.6059 0.3874 0.3573 0.4137 0.1958 0.2832 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.362255 0 . 0 . 51 9,20,3,18 UTR_3_PRIME(MODIFIER||3217||676|GAB2|protein_coding|CODING|NM_080491.2|10|G),DOWNSTREAM(MODIFIER||1344||1018|USP35|protein_coding|CODING|NM_020798.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.188093 rs2511162 -0.692352 0.551044 51 676 2323 MODIFIER 10 CODING GAB2 G protein_coding NM_080491.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77927995 A G 0 55 0 0.9992 0.8466 0.9078 0.6607 0.9632 0.6687 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 1,0,1,1 UTR_3_PRIME(MODIFIER||2323||676|GAB2|protein_coding|CODING|NM_080491.2|10|G),DOWNSTREAM(MODIFIER||2238||1018|USP35|protein_coding|CODING|NM_020798.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2450135 -0.453602 0.52 5 676 2132 MODIFIER 10 CODING GAB2 CATTA protein_coding NM_080491.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77928185 C CATTA 0 18.1 0 0.4614 0.3385 0.3415 0.3859 0.1938 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,2,1,0 UTR_3_PRIME(MODIFIER||2132||676|GAB2|protein_coding|CODING|NM_080491.2|10|CATTA),DOWNSTREAM(MODIFIER||2429||1018|USP35|protein_coding|CODING|NM_020798.2||CATTA) 0 0.5 1 1 0.333333 1 1 0 . 0 60 0 0 1 0 . rs3832723 -0.379885 0.392388 3 676 180 MODIFIER 10 CODING GAB2 C protein_coding NM_080491.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77930138 T C 0 222 0 0.059 0.2216 0.304 0.3938 0.1779 0.2505 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.47643 0 . 0 COSN164009 74 18,25,10,18 UTR_3_PRIME(MODIFIER||180||676|GAB2|protein_coding|CODING|NM_080491.2|10|C),DOWNSTREAM(MODIFIER||4381||1018|USP35|protein_coding|CODING|NM_020798.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.84401 rs1485483,rs386534003 -0.693054 0.359482 74 S668 676 tcA/tcG LOW 10 SILENT CODING GAB2 C protein_coding NM_080491.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77930345 T C 0 222 0 0.1989 0.2646 0.3156 0.3978 0.1779 0.2689 0.180455 0.167976 0.16158 1 1914 26647 4201 3249 1271 11110 199 4703 2 10406 121330 11572 8640 6604 66694 906 16508 0.711849 0 . 0 . 76 28,12,21,6 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S668|676|GAB2|protein_coding|CODING|NM_080491.2|10|C),DOWNSTREAM(MODIFIER||4588||1018|USP35|protein_coding|CODING|NM_020798.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.874584 rs2450122,rs386567428 -0.693021 0.450037 76 V430 676 gtT/gtC LOW 5 SILENT CODING GAB2 G protein_coding NM_080491.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77936166 A G 0 222 0 0.4924 0.3462 0.3357 0.4008 0.1829 0.2679 0.427045 0.253543 0.164609 1 4535 29731 4352 3274 1277 11395 207 4691 2 10396 121296 11568 8644 6614 66678 906 16490 0.976616 0 . 0 . 128 43,21,31,17 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V430|676|GAB2|protein_coding|CODING|NM_080491.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.322148 rs1385600,rs386530136 -0.693147 0.0248364 128 F306 676 ttC/ttT LOW 4 SILENT CODING GAB2 A protein_coding NM_080491.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 77937800 G A 0 222 0 0.3888 0.3159 0.3285 0.3978 0.1789 0.2648 0.338636 0.220887 0.160531 1 3648 28371 4267 3231 1274 11092 202 4657 2 10402 121304 11556 8632 6586 66712 908 16508 0.98219 0 . 0 . 113 27,23,38,12 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F306|676|GAB2|protein_coding|CODING|NM_080491.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720313 rs2248407 -0.693147 0.666631 113 676 9 MODIFIER 1 CODING GAB2 T protein_coding NM_080491.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78128775 C T 0 18.4 0 0.0136 0.1993 0.3055 0.4067 0.1561 0.2055 0.025227 0.0794668 0.106717 1 172 18984 3718 3045 1126 7635 123 3165 2 4852 83512 9470 7354 3586 45456 556 12238 1 0 . 0 . 4 0,2,1,0 UTR_5_PRIME(MODIFIER||9||676|GAB2|protein_coding|CODING|NM_080491.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11237488 -0.379885 0 4 Y138 477 taT/taC LOW 4 SILENT CODING NARS2 G protein_coding NM_024678.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78277277 A G 0 222 0 0.5991 0.6506 0.6023 0.5794 0.7664 0.7086 0.623864 0.73417 0.790725 1 6524 86906 6434 4954 4581 52249 648 11516 2 10400 121336 11564 8630 6612 66718 908 16504 0.995594 0 . 0 . 165 41,28,46,29 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y138|477|NARS2|protein_coding|CODING|NM_024678.5|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.516376 rs10751296 -0.693147 0.00842325 165 N87T 477 aAt/aCt MODERATE 3 MISSENSE CODING NARS2 G protein_coding NM_024678.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78279790 T G 0 222 0 0.7753 0.7101 0.6182 0.6012 0.7694 0.7382 0.779545 0.79071 0.796434 1 8108 89555 6525 5110 4639 52655 665 11853 2 10380 121320 11564 8646 6614 66704 908 16504 0.818246 0 . 0 . 97 20,20,18,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aCt|N87T|477|NARS2|protein_coding|CODING|NM_024678.5|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998962 rs10501429 -0.693146 0.226049 97 477 342 MODIFIER 1 CODING NARS2 T protein_coding NM_024678.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78285875 A T 0 74 0 0.4183 0.6084 0.5893 0.5863 0.7674 0.7382 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.810265 0 . 0 . 9 2,2,1,2 UTR_5_PRIME(MODIFIER||342||477|NARS2|protein_coding|CODING|NM_024678.5|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1.01283 0 0.202566 rs10793337 -0.511536 0.121629 9 2769 4133 MODIFIER 34 CODING TENM4 A protein_coding NM_001098816.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78364970 G A 0 32.6 0 0.8343 0.7544 0.7205 0.5893 0.8857 0.7055 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||4133||2769|TENM4|protein_coding|CODING|NM_001098816.2|34|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1792131 -0.379885 0 2 2769 2517 MODIFIER 34 CODING TENM4 G protein_coding NM_001098816.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78366586 T G 0 31.3 0 0.9992 0.978 0.9049 0.9603 0.998 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2517||2769|TENM4|protein_coding|CODING|NM_001098816.2|34|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1792133 -0.453602 0.32 2 P762 2769 ccG/ccA LOW 16 SILENT CODING TENM4 T protein_coding NM_001098816.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 78498022 C T 0 222 0 0.1679 0.1953 0.1369 0.4107 0.1173 0.1319 0.146383 0.126773 0.117124 1 781 11310 1198 2322 424 4918 97 1570 2 3644 49388 4646 4486 1424 25058 364 9766 0.878161 0 . 0 . 125 30,27,17,46 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P762|2769|TENM4|protein_coding|CODING|NM_001098816.2|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.818318 rs11237621 -0.693147 0.0397485 125 426 74 MODIFIER 1 CODING FAM181B T protein_coding NM_175885.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82443417 C T 0 213 0 0.8949 0.6402 0.5778 0.6319 0.3608 0.636 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,13,0 UTR_3_PRIME(MODIFIER||74||426|FAM181B|protein_coding|CODING|NM_175885.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3780 -0.683931 0.161396 16 R367P 426 cGg/cCg MODERATE 1 MISSENSE CODING FAM181B G protein_coding NM_175885.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82443672 C G 0 146 0 0.8949 0.64 0.5764 0.6319 0.3608 0.636 0.641122 0.420426 0.320927 2 1512 13209 1543 1170 238 5105 102 3539 2 1752 21864 2106 1662 544 10326 178 5296 0 . 0 . 0 8 0,0,1,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R367P|426|FAM181B|protein_coding|CODING|NM_175885.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6592081 -0.651104 0.596623 8 L319 426 Ctg/Ttg LOW 1 SILENT CODING FAM181B A protein_coding NM_175885.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82443817 G A 0 144 0 0.0658 0.2288 0.2262 0.497 0.172 0.2331 0.0381785 0.0826725 0.103538 1 15 514 7 76 1 229 6 180 2 144 1796 28 164 4 1038 22 396 0.5 0 . 0 . 9 2,0,4,2 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L319|426|FAM181B|protein_coding|CODING|NM_175885.3|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.833333 rs2291793 -0.616816 0.236588 9 S251R 426 Agc/Cgc MODERATE 1 MISSENSE CODING FAM181B G protein_coding NM_175885.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82444021 T G 0 71 0 0.0658 0.229 0.2262 0.497 0.172 0.2342 0.0656361 0.115156 0.140087 1 304 12229 1439 2216 297 5504 94 2375 2 2100 42188 4098 3948 988 21658 300 9096 0.562708 0 . 0 . 12 2,5,2,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Cgc|S251R|426|FAM181B|protein_coding|CODING|NM_175885.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.964642 0.964642 0 0.924449 rs66918959 -0.556411 0.598008 12 V186L 426 Gtg/Ctg MODERATE 1 MISSENSE CODING FAM181B G protein_coding NM_175885.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82444216 C G 0 6.3 0 0.2708 0.4453 0.5086 0.627 0.3151 0.5828 0 . 0 1 12 636 9 17 0 47 1 550 2 30 1176 12 24 0 116 4 990 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V186L|426|FAM181B|protein_coding|CODING|NM_175885.3|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs986097 -0.379885 0 1 A513 517 gcG/gcA LOW 10 SILENT CODING PRCP T protein_coding NM_199418.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82535963 C T 0 202 0 0.0272 0.1965 0.1124 0.5496 0.0726 0.2485 0.0329097 0.0648931 0.0812791 1 306 16929 1581 4744 669 5614 139 3876 2 9856 116116 10918 8520 6464 63684 872 15802 0.895471 0 . 0 . 64 31,3,23,3 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A513|517|PRCP|protein_coding|CODING|NM_199418.2|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910669 rs4759 -0.692976 0.473019 64 E133D 517 gaA/gaC MODERATE 4 MISSENSE CODING PRCP G protein_coding NM_199418.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82564294 T G 0 222 0 0.1051 0.1394 0.1297 0.1131 0.1869 0.1708 0.128234 0.162233 0.179651 1 1297 19168 1104 894 966 11841 160 2906 2 10388 121216 11550 8638 6606 66648 902 16484 0.583076 0 . 0 . 73 19,12,22,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E133D|517|PRCP|protein_coding|CODING|NM_199418.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.782884 rs2229437,rs386564200 -0.693097 0.147429 73 R460S 998 agG/agT MODERATE 6 MISSENSE CODING DDIAS T protein_coding NM_145018.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82643760 G T 0 222 0 0.1793 0.3075 0.4049 0.3244 0.3579 0.3425 0.223332 0.308473 0.352093 1 2253 42226 4714 2815 2518 23800 314 5812 2 10378 121220 11554 8628 6606 66646 906 16502 0.991545 0 . 0 . 49 12,13,5,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R460S|998|DDIAS|protein_coding|CODING|NM_145018.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.92208 rs7947780 -0.69168 0.380423 49 V842I 998 Gtt/Att MODERATE 6 MISSENSE CODING DDIAS A protein_coding NM_145018.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82644904 G A 0 222 0 0.7678 0.5535 0.6369 0.3442 0.498 0.4775 0.727417 0.57781 0.501163 1 7630 62622 7329 2904 3202 33279 444 7834 2 10374 121152 11538 8632 6606 66590 902 16510 0.823328 0 . 0 . 85 19,18,22,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V842I|998|DDIAS|protein_coding|CODING|NM_145018.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.13946 rs7130899 -0.693144 0.746464 85 P616 1555 ccT/ccA LOW 6 SILENT CODING PCF11 A protein_coding NM_015885.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82878197 T A 0 222 0 0 0.0228 0 0.0992 0.0109 0.0031 0.00157812 0.00107705 0.000846638 1 8 1641 3 1015 301 261 21 32 2 9776 120584 11566 8624 6612 66602 898 16506 0.527065 0 . 0 . 100 30,12,28,16 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccA|P616|1555|PCF11|protein_coding|CODING|NM_015885.3|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999403 rs76726954 -0.693146 0.0272603 100 254 338 MODIFIER 9 CODING CCDC90B T protein_coding NM_021825.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82972615 C T 0 51 0 0 0.0037939 0 0.0169 0 0.002 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,3,0 UTR_3_PRIME(MODIFIER||338||254|CCDC90B|protein_coding|CODING|NM_021825.4|9|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs150150415 -0.511536 0.107235 4 F10L 254 ttT/ttG MODERATE 1 MISSENSE CODING CCDC90B C protein_coding NM_021825.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 82996986 A C 0 222 0 0.8797 0.6777 0.4813 0.5794 0.673 0.6503 0.840672 0.735158 0.681089 1 8112 75404 4244 4599 4278 43807 533 9831 2 9616 114064 10748 8202 5776 63012 798 15912 0.621953 0 . 0 . 97 21,27,22,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F10L|254|CCDC90B|protein_coding|CODING|NM_021825.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0626918 rs494791 -0.693146 0.55972 97 975 506 MODIFIER 28 CODING DLG2 G protein_coding NM_001142699.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 83170355 A G 0 228 0 0.9992 0.9942 0.9914 1 0.9781 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 103 0,0,31,69 UTR_3_PRIME(MODIFIER||506||975|DLG2|protein_coding|CODING|NM_001142699.1|28|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4533060 -0.693147 0.159515 103 374 331 MODIFIER 1 CODING CCDC89 C protein_coding NM_152723.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85395718 T C 0 9.7 0 0.5424 0.5483 0.487 0.6141 0.5934 0.4857 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||331||374|CCDC89|protein_coding|CODING|NM_152723.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs290185 -0.379885 0 1 S173 935 tcA/tcG LOW 5 SILENT CODING SYTL2 C protein_coding NM_001162953.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85447611 T C 0 228 0 0.823 0.654 0.5677 0.6171 0.6551 0.5235 0.785974 0.701277 0.657864 2 8216 79002 6456 5381 4718 44657 584 8990 2 10396 121014 11544 8616 6604 66476 906 16472 0 . 0 . 0 93 0,0,37,37 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S173|935|SYTL2|protein_coding|CODING|NM_001162953.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs680498 -0.693147 0.823945 93 E122 935 gaA/gaG LOW 3 SILENT CODING SYTL2 C protein_coding NM_001162953.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85456703 T C 0 228 0 0.4788 0.5467 0.5029 0.6141 0.6342 0.5102 0.506809 0.591357 0.634682 2 5151 72891 5600 5379 4419 43209 547 8586 2 10402 121244 11548 8632 6606 66690 906 16460 0 . 0 . 0 53 0,0,31,16 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E122|935|SYTL2|protein_coding|CODING|NM_001162953.2|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs647912 -0.693147 0.313708 53 A590 652 gcT/gcG LOW 17 SILENT CODING PICALM C protein_coding NM_007166.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85692181 A C 0 222 0 0.6097 0.6228 0.585 0.6577 0.5875 0.6677 0.618702 0.603276 0.595371 1 6387 72628 7419 5804 3268 38381 530 10839 2 10402 121372 11574 8650 6612 66716 906 16512 0.862018 0 . 0 COSM1357535,COSM28380,COSM1357534 56 18,4,20,3 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A590|652|PICALM|protein_coding|CODING|NM_007166.3|17|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94365 rs76719109 -0.692717 0.0811719 56 Q174 652 caG/caA LOW 5 SILENT CODING PICALM T protein_coding NM_007166.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85725937 C T 0 222 0 0.916 0.7887 0.7334 0.6815 0.8171 0.7372 0.893409 0.834103 0.803725 1 9185 93204 8237 5841 5328 51856 692 12065 2 10288 118562 11194 8422 6526 64972 890 16270 0.949605 0 . 0 . 46 15,3,15,5 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q174|652|PICALM|protein_coding|CODING|NM_007166.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.619035 rs592297 -0.692067 0.293058 46 652 251 MODIFIER 1 CODING PICALM T protein_coding NM_007166.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85780073 G T 0 228 0 1 0.9864 0.9035 1 1 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 95 0,0,59,25 UTR_5_PRIME(MODIFIER||251||652|PICALM|protein_coding|CODING|NM_007166.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3016326 -0.693147 0.03286 95 L207 466 Ctg/Ttg LOW 6 SILENT CODING EED T protein_coding NM_001308007.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85968623 C T 0 222 0 0.1203 0.2947 0.2565 0.3135 0.4225 0.407 0.178928 0.324412 0.39893 1 1723 44839 3022 3197 2886 27146 352 6513 2 10322 120418 11460 8596 6572 66138 904 16426 0.993626 0 . 0 COSM429983 117 29,33,19,21 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L207|466|EED|protein_coding|CODING|NM_001308007.1|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.807167 rs974144 -0.693145 0.384866 117 466 LOW 7 CODING EED A protein_coding NM_001308007.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 85977117 G A 0 228 0 0.7965 0.765 0.7003 0.7212 0.841 0.7352 0.799727 0.818378 0.827965 2 8305 95370 7658 6441 5047 54818 709 12392 2 10322 121156 11560 8652 6604 66618 904 16496 1 0 . 0 . 118 1,0,75,32 SPLICE_SITE_REGION+INTRON(LOW||||466|EED|protein_coding|CODING|NM_001308007.1|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10898460,rs386515818 -0.693147 0.777527 118 I88 652 atT/atC LOW 3 SILENT CODING CCDC81 C protein_coding NM_001156474.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86098680 T C 0 222 0 0.7632 0.6621 0.4597 0.6875 0.5785 0.729 0.733651 0.616521 0.556525 1 7640 73054 4858 6132 4257 38350 553 11264 2 10386 121326 11562 8634 6614 66720 908 16502 0.736519 0 . 0 . 84 17,18,16,20 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I88|652|CCDC81|protein_coding|CODING|NM_001156474.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988885 rs292109 -0.693139 0.0857276 84 V161 652 gtG/gtA LOW 4 SILENT CODING CCDC81 A protein_coding NM_001156474.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86103767 G A 0 222 0 0 0.0543 0.1023 0.1478 0.001 0.0521 0.00289017 0.00131406 0.000628536 1 3 460 38 94 0 7 4 314 2 2148 19820 410 622 34 8502 190 7914 0.519476 0 . 0 . 146 24,51,26,30 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V161|652|CCDC81|protein_coding|CODING|NM_001156474.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.967792 rs17210546 -0.693147 0.105133 146 A419 652 gcG/gcA LOW 11 SILENT CODING CCDC81 A protein_coding NM_001156474.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86123467 G A 0 222 0 0.2216 0.3221 0.3991 0.2718 0.3897 0.3855 0.245459 0.342947 0.392882 1 2467 43397 4362 2251 1840 25516 336 6625 2 10344 120648 11568 8644 6614 66504 900 16074 0.791724 0 . 0 . 112 40,13,42,6 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A419|652|CCDC81|protein_coding|CODING|NM_001156474.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.490575 rs3741006 -0.693147 0.433331 112 652 27 MODIFIER 15 CODING CCDC81 T protein_coding NM_001156474.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86133784 C T 0 228 0 0.8359 0.8041 0.7089 0.7619 0.7803 0.8967 0.795186 0.780265 0.772622 2 8353 93307 7671 6370 5300 50823 708 14082 2 10350 120124 11412 8498 6560 66078 896 16330 0 . 0 . 0 46 0,0,12,30 UTR_3_PRIME(MODIFIER||27||652|CCDC81|protein_coding|CODING|NM_001156474.1|15|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1056194 -0.693146 0.0790347 46 K324N 604 aaG/aaC MODERATE 8 MISSENSE CODING ME3 G protein_coding NM_001014811.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86161388 C G 0 228 0 0.2201 0.2983 0.3516 0.2728 0.327 0.363 0.233651 0.301184 0.335776 2 2376 38046 4183 2232 1486 21258 297 6214 2 10212 120520 11490 8612 6528 66318 902 16458 0 . 0 . COSM147300 41 0,0,15,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K324N|604|ME3|protein_coding|CODING|NM_001014811.1|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1042780 -0.693141 0.312047 41 L143 604 ctG/ctA LOW 3 SILENT CODING ME3 T protein_coding NM_001014811.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86267633 C T 0 228 0 0.1921 0.2756 0.3487 0.5317 0.1799 0.1708 0.185967 0.174358 0.168411 2 1968 26956 4331 4576 1676 11582 181 2642 2 10380 120850 11512 8572 6574 66484 904 16424 1 0 . 0 . 78 0,1,41,28 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L143|604|ME3|protein_coding|CODING|NM_001014811.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs17211115 -0.693147 0.005895 78 R116 604 cgG/cgT LOW 3 SILENT CODING ME3 A protein_coding NM_001014811.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86267714 C A 0 228 0 0.1921 0.2762 0.3487 0.5327 0.1799 0.1728 0.185967 0.174435 0.168528 2 1973 27093 4350 4630 1688 11607 181 2664 2 10380 121122 11564 8610 6612 66594 904 16458 0 . 0 . 0 73 0,0,24,39 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgT|R116|604|ME3|protein_coding|CODING|NM_001014811.1|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12287767 -0.693147 0.00579462 73 537 4664 MODIFIER 2 CODING FZD4 G protein_coding NM_012193.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86657520 A G 0 122 0 0.4244 0.51 0.5677 0.4554 0.6451 0.502 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,1 UTR_3_PRIME(MODIFIER||4664||537|FZD4|protein_coding|CODING|NM_012193.3|2|G),INTRAGENIC(MODIFIER|||||PRSS23||CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386607718,rs713065 -0.590765 0.944353 5 537 1572 MODIFIER 2 CODING FZD4 G protein_coding NM_012193.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86660612 C G 0 228 0 0.9992 0.9816 0.8718 0.998 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,49,2 UTR_3_PRIME(MODIFIER||1572||537|FZD4|protein_coding|CODING|NM_012193.3|2|G),INTRAGENIC(MODIFIER|||||PRSS23||CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4944641 -0.693147 0.449189 51 537 1298 MODIFIER 2 CODING FZD4 A protein_coding NM_012193.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 86660886 G A 0 222 0 0.8079 0.7037 0.67 0.6349 0.7028 0.6585 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.57771 0 . 0 . 65 13,20,9,18 UTR_3_PRIME(MODIFIER||1298||537|FZD4|protein_coding|CODING|NM_012193.3|2|A),INTRAGENIC(MODIFIER|||||PRSS23||CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.19338 rs3802892 -0.693021 0.0154157 65 G218R 458 Gga/Aga MODERATE 8 MISSENSE CODING TMEM135 A protein_coding NM_022918.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87013438 G A 0 228 0 0.5885 0.5829 0.5086 0.4425 0.6511 0.7025 0.604044 0.663769 0.694348 2 6378 75728 5296 4110 3513 44548 606 11277 2 10402 121382 11576 8648 6614 66724 908 16510 1 0 . 0 . 100 1,0,54,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G218R|458|TMEM135|protein_coding|CODING|NM_022918.3|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2276102 -0.693147 0.103968 100 458 5190 MODIFIER 15 CODING TMEM135 C protein_coding NM_022918.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87037565 T C 0 23.4 0 0.3676 0.4461 0.4395 0.2827 0.6014 0.5654 0 . 0 2 86 6176 41 52 0 1744 65 4188 2 188 10778 92 134 0 2740 118 7506 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||5190||458|TMEM135|protein_coding|CODING|NM_022918.3|15|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7926724 -0.453602 0.1 2 458 7027 MODIFIER 15 CODING TMEM135 A protein_coding NM_022918.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87039402 G A 0 91 0 0.236 0.3411 0.3689 0.2004 0.5099 0.4346 0 . 0 2 66 4968 42 38 0 1497 59 3266 2 188 10754 92 132 0 2720 118 7504 0 . 0 . 0 4 0,0,2,1 UTR_3_PRIME(MODIFIER||7027||458|TMEM135|protein_coding|CODING|NM_022918.3|15|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs386494256,rs4480563 -0.511536 0.0860477 4 458 7092 MODIFIER 15 CODING TMEM135 G protein_coding NM_022918.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87039467 T G 0 39.3 0 0.236 0.3413 0.3689 0.2004 0.5099 0.4356 0 . 0 2 66 4952 42 38 0 1490 59 3257 2 188 10762 92 132 0 2726 118 7506 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||7092||458|TMEM135|protein_coding|CODING|NM_022918.3|15|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs4644661 -0.453602 0.76 2 211 399 MODIFIER 3 CODING RAB38 T protein_coding NM_022337.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87846757 C T 0 228 0 0.8964 0.7169 0.6744 0.6855 0.6123 0.6442 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,4,14 UTR_3_PRIME(MODIFIER||399||211|RAB38|protein_coding|CODING|NM_022337.2|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386620673,rs9144 -0.691153 0.91943 19 211 138 MODIFIER 3 CODING RAB38 T protein_coding NM_022337.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87847018 C T 0 228 0 0.997 0.9215 0.9683 0.8462 0.9076 0.8783 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 87 0,0,58,19 UTR_3_PRIME(MODIFIER||138||211|RAB38|protein_coding|CODING|NM_022337.2|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3740925,rs386585204 -0.693147 0.0590413 87 211 93 MODIFIER 3 CODING RAB38 A protein_coding NM_022337.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87847063 C A 0 222 0 0.4009 0.279 0.3285 0.1438 0.2525 0.2454 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.724088 0 . 0 . 96 26,20,20,21 UTR_3_PRIME(MODIFIER||93||211|RAB38|protein_coding|CODING|NM_022337.2|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.943799 rs1027027 -0.693145 0.0372801 96 211 LOW 1 CODING RAB38 G protein_coding NM_022337.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87908346 C G 0 222 0 0.0968 0.2404 0.281 0.3194 0.337 0.2249 0.139672 0.25177 0.309097 1 994 27781 2941 1925 1673 16449 228 3571 2 5084 69250 6310 4922 3482 38402 530 10520 0.496733 0 . 0 . 108 46,12,32,5 SPLICE_SITE_REGION+INTRON(LOW||||211|RAB38|protein_coding|CODING|NM_022337.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.736399 rs302647 -0.693141 0.0194611 108 S35 211 tcT/tcC LOW 1 SILENT CODING RAB38 G protein_coding NM_022337.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 87908448 A G 0 228 0 0.7965 0.7456 0.7752 0.6012 0.8718 0.6748 0.797365 0.840692 0.862875 2 8237 97253 9030 4816 5032 57261 750 12127 2 10388 121218 11566 8602 6610 66640 906 16506 0.813196 0 . 0 . 169 3,1,69,78 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S35|211|RAB38|protein_coding|CODING|NM_022337.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.993309 rs302646,rs386578762 -0.693147 0.00137907 169 I453V 463 Ata/Gta MODERATE 7 MISSENSE CODING CTSC C protein_coding NM_001814.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 88027209 T C 0 222 0 0.0802 0.0839 0.1023 0.1151 0.0517 0.0767 0.0686052 0.0487692 0.0386136 1 758 7464 1035 837 616 2751 37 1430 2 10400 121240 11506 8638 6606 66672 908 16510 0.214139 2 benign 0 . 60 26,5,16,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I453V|463|CTSC|protein_coding|CODING|NM_001814.4|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.956273 rs386588584,rs3888798 -0.692067 0.30385 60 T391 463 acT/acG LOW 7 SILENT CODING CTSC C protein_coding NM_001814.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 88027393 A C 0 211 0 0.0802 0.0857 0.1023 0.1151 0.0507 0.0869 0.0686052 0.0483077 0.0379158 1 756 7640 1034 836 616 2739 37 1622 2 10394 121270 11498 8638 6614 66710 908 16508 0.435912 0 . 0 . 42 9,13,10,7 SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T391|463|CTSC|protein_coding|CODING|NM_001814.4|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.762523 rs17594,rs386544048 -0.690438 0.158133 42 I153T 463 aTa/aCa MODERATE 3 MISSENSE CODING CTSC G protein_coding NM_001814.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 88045583 A G 0 228 0 0.9251 0.9309 0.9251 0.999 0.8479 0.9581 0.911404 0.864077 0.839846 2 9510 107579 10687 8650 5907 56463 796 15566 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 85 0,0,61,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I153T|463|CTSC|protein_coding|CODING|NM_001814.4|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs217086 -0.693147 0.341252 85 463 57 MODIFIER 1 CODING CTSC A protein_coding NM_001814.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 88070897 C A 0 222 0 0.0015 0.00039936 0 0 0 0 0 . 0 1 0 2 0 0 0 0 0 2 2 786 13876 230 354 14 4676 154 7662 0.726321 0 . 0 . 61 10,18,5,22 UTR_5_PRIME(MODIFIER||57||463|CTSC|protein_coding|CODING|NM_001814.4|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.996463 rs186343021 -0.693021 0.00381907 61 G1125 1212 ggA/ggC LOW 9 SILENT CODING GRM5 G protein_coding NM_001143831.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 88242024 T G 0 183 0 0.9675 0.9694 0.964 0.999 0.9314 0.9847 0.95816 0.939767 0.930432 2 4923 63441 5126 5177 2398 34281 422 11114 2 5134 67028 5320 5180 2528 36946 442 11478 0 . 0 . 0 16 0,0,15,0 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G1125|1212|GRM5|protein_coding|CODING|NM_001143831.2|9|G),INTRAGENIC(MODIFIER|||||GRM5-AS1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs2941563 -0.688148 0.131828 16 599 1823 MODIFIER 18 CODING NOX4 C protein_coding NM_001291927.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89058101 T C 0 46.3 0 0.177 0.1919 0.2277 0.1796 0.2893 0.0992 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1823||599|NOX4|protein_coding|CODING|NM_001291927.1|18|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11018578 -0.453602 0.92 2 M336I 599 atG/atA MODERATE 10 MISSENSE CODING NOX4 T protein_coding NM_001291927.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89133449 C T 0 228 0 1 0.9974 0.9928 1 0.995 0.9969 0.997728 0.993077 0.990696 2 10385 120226 11339 8582 6525 66063 896 16436 2 10404 121130 11454 8582 6608 66668 906 16508 0 . 0 . 0 160 0,0,74,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M336I|599|NOX4|protein_coding|CODING|NM_001291927.1|10|T) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.918891 0 . rs317139,rs386580411 -0.693147 0.302664 160 W148L 452 tGg/tTg MODERATE 4 MISSENSE CODING TRIM49 A protein_coding NM_020358.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89536930 C A 0 41.9 0 . 0 . 0 . 0 . 0 . 1 23 903 34 126 11 341 17 351 2 1468 10442 656 720 428 5314 140 1716 0.534709 0 . 0 . 118 35,63,6,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W148L|452|TRIM49|protein_coding|CODING|NM_020358.2|4|A) 0 0.5 1 0 . 0 . 0 1 0 49 0 0.709516 0.0321137 0 0.957679 rs199962952 -0.692067 0.549521 118 S126 449 agc/ HIGH 1 CODING TRIM64B G protein_coding NM_001164397.1 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89608808 GC G 0 34.9 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 28 8,14,0,6 FRAME_SHIFT(HIGH||agc/|S126|449|TRIM64B|protein_coding|CODING|NM_001164397.1|1|G) 0 0.5 1 6 0.214286 0 1 0 . (TRIM64B|TRIM64B|1|1.00) 36 0 0 0.337058 0 . rs371045630 -0.616816 0.536013 28 V287 452 gtG/gtA LOW 7 SILENT CODING TRIM49D2 T protein_coding NM_001105522.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89645253 C T 0 43.6 0 0.0234 0.1212 0.3184 0.2004 0.0984 0.0552 0 . 0 2 23 746 42 38 16 177 1 449 2 354 10684 142 174 52 2870 116 6976 0 . 0 . 0 4 0,0,1,3 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D2|protein_coding|CODING|NM_001105522.1|7|T),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D1|protein_coding|CODING|NM_001206627.1.2|6|T) 0 . 0 . 0 1 0 . 1 0 21 0 0 1 0 . rs199876662 -0.556411 0.735663 4 V287 452 gtG/gtA LOW 6 SILENT CODING TRIM49D1 T protein_coding NM_001206627.1.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89645253 C T 0 43.6 0 0.0234 0.1212 0.3184 0.2004 0.0984 0.0552 0 . 0 2 23 746 42 38 16 177 1 449 2 354 10684 142 174 52 2870 116 6976 0 . 0 . 0 4 0,0,1,3 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D2|protein_coding|CODING|NM_001105522.1|7|T),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D1|protein_coding|CODING|NM_001206627.1.2|6|T) 0 . 0 . 0 1 0 . 1 0 21 0 0 1 0 . rs199876662 -0.556411 0.735663 4 V287 452 gtG/gtA LOW 7 SILENT CODING TRIM49D2 A protein_coding NM_001105522.1.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89665555 G A 0 11.7 0 0.0045 0.03 0.1009 0.0139 0.0358 0.0245 0 . 0 1 3 101 3 1 1 25 0 68 2 140 4238 38 62 26 1088 46 2838 0.733186 0 . 0 . 13 6,1,2,1 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D2|protein_coding|CODING|NM_001105522.1.2|7|A),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D1|protein_coding|CODING|NM_001206627.1|6|A) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.916482 1 0 0.641538 rs201106937,rs2138054 -0.511536 0.0249187 13 V287 452 gtG/gtA LOW 6 SILENT CODING TRIM49D1 A protein_coding NM_001206627.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89665555 G A 0 11.7 0 0.0045 0.03 0.1009 0.0139 0.0358 0.0245 0 . 0 1 3 101 3 1 1 25 0 68 2 140 4238 38 62 26 1088 46 2838 0.733186 0 . 0 . 13 6,1,2,1 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D2|protein_coding|CODING|NM_001105522.1.2|7|A),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V287|452|TRIM49D1|protein_coding|CODING|NM_001206627.1|6|A) 0 0.5 1 0 . 1 0 . 1 0 28 0 0.916482 1 0 0.641538 rs201106937,rs2138054 -0.511536 0.0249187 13 H293D 452 Cat/Gat MODERATE 8 MISSENSE CODING TRIM49C G protein_coding NM_001195234.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89774236 C G 0 228 0 . 0 . 0 . 0 . 0 . 2 3967 39551 5944 3531 2484 17595 291 5739 2 9452 106206 10410 7846 6132 56710 792 14864 0.745455 0 . 0 . 57 1,1,50,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H293D|452|TRIM49C|protein_coding|CODING|NM_001195234.1|8|G) 0 . 0 . 0 . 0 . 1 0 37 0 0.9 0.346395 0 0.854545 rs74584169 -0.693147 1.09608e-22 57 H346 452 caT/caC LOW 8 SILENT CODING TRIM49C C protein_coding NM_001195234.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89774397 T C 0 220 0 . 0 . 0 . 0 . 0 . 1 3056 33476 5194 3091 2252 14682 255 4946 2 8288 106906 10130 7612 6184 59300 794 14598 0.300787 0 . 0 . 56 3,9,22,20 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H346|452|TRIM49C|protein_coding|CODING|NM_001195234.1|8|C) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.900539 0.405043 0 0.97415 rs150273819 -0.693146 0.165939 56 K363 452 aaG/aaA LOW 8 SILENT CODING TRIM49C A protein_coding NM_001195234.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89774448 G A 0 206 0 0.5265 0.4625 0.5058 0.4603 0.3519 0.4611 0 . 0 2 4363 43049 6640 3893 2647 18608 326 6572 2 9530 115836 11246 8238 6428 63824 854 15716 0.551061 0 . 0 . 79 3,5,49,19 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K363|452|TRIM49C|protein_coding|CODING|NM_001195234.1|8|A) 0 . 0 . 0 1 0 . 1 0 36 0 0.944315 0.603057 0 0.0653599 rs77759231 -0.693147 1.59037e-05 79 G96R 393 Ggt/Cgt MODERATE 1 MISSENSE CODING UBTFL1 C protein_coding NM_001143975.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89819403 G C 0 228 0 0.1074 0.118 0.0692 0.1369 0.0994 0.1667 0 . 0 2 908 9153 251 626 408 4966 66 1928 2 8840 99672 6012 6166 5452 57698 772 14732 0.510204 0 . 0 . 109 1,1,38,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Cgt|G96R|393|UBTFL1|protein_coding|CODING|NM_001143975.1|1|C) 0 . 0 . 0 1 0 . 1 0 32 0 0.0918367 0.296979 0 0.326531 rs200131392 -0.693147 0.105182 109 Y107 393 taC/taT LOW 1 SILENT CODING UBTFL1 T protein_coding NM_001143975.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89819438 C T 0 215 0 . 0 . 0 . 0 . 0 . 2 72 731 17 70 16 308 8 240 2 8304 92390 5436 5608 5050 53706 716 13570 0.469865 0 . 0 . 73 1,2,29,39 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y107|393|UBTFL1|protein_coding|CODING|NM_001143975.1|1|T) 0 . 0 . 0 . 0 . 1 0 29 0 0.0142642 0.979465 0 0.977284 rs79837451 -0.693147 0.00115287 73 R256S 393 agA/agT MODERATE 1 MISSENSE CODING UBTFL1 T protein_coding NM_001143975.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89819885 A T 0 184 0 0.3359 0.2484 0.1599 0.1567 0.2078 0.3292 0 . 0 2 2340 19247 735 680 872 9920 162 4538 2 8186 102180 7146 6900 5704 58530 790 14924 0.496688 0 . 0 . 46 2,1,30,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agT|R256S|393|UBTFL1|protein_coding|CODING|NM_001143975.1|1|T) 0 . 0 . 0 1 0 . 1 0 29 0 0.792218 0.620703 0 0.0436536 rs201853154 -0.693146 2.11353e-11 46 740 55 MODIFIER 1 CODING NAALAD2 T protein_coding NM_005467.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89867872 C T 0 228 0 0.6815 0.5104 0.5389 0.4167 0.3648 0.5051 0.607659 0.437801 0.363922 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . COSN164021 54 0,0,44,7 UTR_5_PRIME(MODIFIER||55||740|NAALAD2|protein_coding|CODING|NM_005467.3|1|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs1892887 -0.693147 0.298289 54 T37 740 acG/acA LOW 2 SILENT CODING NAALAD2 A protein_coding NM_005467.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89868755 G A 0 228 0 0.6815 0.5108 0.5389 0.4177 0.3648 0.5061 0.602453 0.437923 0.353687 2 6358 51634 7171 3677 2593 23263 381 8191 2 10358 121000 11550 8632 6606 66480 906 16468 0 . 0 . COSM147303 75 0,0,55,15 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T37|740|NAALAD2|protein_coding|CODING|NM_005467.3|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10734123 -0.693147 0.0161522 75 740 LOW 17 CODING NAALAD2 C protein_coding NM_005467.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89916080 G C 0 228 0 0.5189 0.4655 0.5187 0.4137 0.3648 0.5123 0.477056 0.394138 0.351675 2 4982 50111 7087 3656 2576 23206 374 8230 2 10376 121204 11544 8624 6606 66652 906 16496 1 0 . 0 COSM147304 97 1,0,86,5 SPLICE_SITE_REGION+INTRON(LOW||||740|NAALAD2|protein_coding|CODING|NM_005467.3|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs9804632 -0.693147 0.00120117 97 740 497 MODIFIER 19 CODING NAALAD2 G protein_coding NM_005467.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89925412 T G 0 9.7 0 0.3964 0.6196 0.6715 0.6756 0.6958 0.7485 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||497||740|NAALAD2|protein_coding|CODING|NM_005467.3|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1138531 -0.379885 0 1 332 1964 MODIFIER 11 CODING CHORDC1 C protein_coding NM_012124.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89933609 T C 0 9.7 0 0.289 0.4583 0.513 0.5615 0.4294 0.5716 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1964||332|CHORDC1|protein_coding|CODING|NM_012124.2|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11018907 -0.379885 0 1 332 1663 MODIFIER 11 CODING CHORDC1 G protein_coding NM_012124.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89933910 T G 0 9.7 0 0.289 0.4583 0.5144 0.5605 0.4304 0.5706 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1663||332|CHORDC1|protein_coding|CODING|NM_012124.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4753261 -0.379885 0 1 A329D 332 gCc/gAc MODERATE 11 MISSENSE CODING CHORDC1 T protein_coding NM_012124.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89935586 G T 0 228 0 0.3714 0.6104 0.6542 0.6756 0.6958 0.7474 0.412955 0.599723 0.695323 2 4261 83541 8699 6188 4757 46412 642 12582 2 10402 121342 11568 8652 6604 66706 908 16502 0 . 0 . 0 101 0,0,64,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A329D|332|CHORDC1|protein_coding|CODING|NM_012124.2|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1045861 -0.693147 0.243935 101 332 LOW 6 CODING CHORDC1 A protein_coding NM_012124.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 89939448 G A 0 228 0 0.3283 0.5986 0.6513 0.6756 0.6958 0.7474 0.368577 0.578842 0.686496 2 3759 82681 8669 6171 4755 46138 638 12551 2 9954 120322 11528 8614 6596 66268 904 16458 0 . 0 . 0 54 0,0,14,35 SPLICE_SITE_REGION+INTRON(LOW||||332|CHORDC1|protein_coding|CODING|NM_012124.2|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1943381,rs386549927 -0.693147 0.384396 54 C356Y 4557 tGt/tAt MODERATE 1 MISSENSE CODING FAT3 A protein_coding NM_001008781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92086345 G A 0 222 0 0 0.0063898 0 0.0317 0 0 0 . 0 1 0 271 1 269 0 0 0 1 2 9726 119744 11332 8562 6580 66282 886 16376 0.767277 0 . 0 . 215 56,49,47,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C356Y|4557|FAT3|protein_coding|CODING|NM_001008781.2|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.999129 rs142950989 -0.693147 0.583393 215 Q1726R 4557 cAg/cGg MODERATE 9 MISSENSE CODING FAT3 G protein_coding NM_001008781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92531356 A G 0 228 0 0.649 0.7698 0.8516 0.755 0.8598 0.7975 0.693557 0.798241 0.847722 2 6672 99334 9897 6409 5708 56396 744 13508 2 9802 120694 11564 8580 6614 66730 898 16506 0 . 0 . 0 96 0,0,32,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1726R|4557|FAT3|protein_coding|CODING|NM_001008781.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7949157 -0.693147 0.674235 96 P2166 4557 ccT/ccC LOW 9 SILENT CODING FAT3 C protein_coding NM_001008781.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92532677 T C 0 228 0 0.7738 0.7993 0.8559 0.755 0.8509 0.7863 0.796012 0.826879 0.841469 2 7656 99113 9836 6293 5447 55768 736 13377 2 9732 119814 11460 8416 6590 66300 888 16428 0 . 0 . 0 99 0,0,55,42 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P2166|4557|FAT3|protein_coding|CODING|NM_001008781.2|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12362722 -0.693147 0.266657 99 I2755V 4557 Ata/Gta MODERATE 9 MISSENSE CODING FAT3 G protein_coding NM_001008781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92534442 A G 0 228 0 0.73 0.8564 0.866 0.9544 0.8708 0.9049 0.753786 0.822877 0.854944 2 7316 104029 9978 8047 6004 57070 785 14829 2 9782 120446 11526 8546 6610 66598 896 16488 0 . 0 . 0 137 0,0,91,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I2755V|4557|FAT3|protein_coding|CODING|NM_001008781.2|9|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3847531 -0.693147 0.00341089 137 R3674W 4557 Cgg/Tgg MODERATE 18 MISSENSE CODING FAT3 T protein_coding NM_001008781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92577553 C T 0 222 0 0 0.0061901 0 0.0308 0 0 0 . 0 1 2 204 1 194 0 4 0 3 2 9796 120458 11536 8618 6604 66510 896 16498 0.869604 0 . 0 . 90 19,32,14,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R3674W|4557|FAT3|protein_coding|CODING|NM_001008781.2|18|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.963861 rs150453320 -0.69312 0.3974 90 S3812G 4557 Agt/Ggt MODERATE 19 MISSENSE CODING FAT3 G protein_coding NM_001008781.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92590448 A G 0 222 0 0.9191 0.8285 0.7968 0.6706 0.8121 0.908 0.912358 0.841788 0.807647 1 8933 98707 9321 5845 5249 53779 748 14832 2 9810 120738 11568 8600 6614 66736 898 16512 0.435923 0 . 0 . 106 25,18,34,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S3812G|4557|FAT3|protein_coding|CODING|NM_001008781.2|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.846992 rs4753069 -0.693147 0.0521161 106 4557 1547 MODIFIER 25 CODING FAT3 T protein_coding NM_001008781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92625826 C T 0 32.6 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1547||4557|FAT3|protein_coding|CODING|NM_001008781.2|25|T) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs61901508 -0.379885 0 2 4557 1665 MODIFIER 25 CODING FAT3 T protein_coding NM_001008781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92625944 G T 0 9.7 0 0.1626 0.1408 0.0893 0.244 0.1183 0.0644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1665||4557|FAT3|protein_coding|CODING|NM_001008781.2|25|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11823754 -0.379885 0 1 4557 2149 MODIFIER 25 CODING FAT3 T protein_coding NM_001008781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92626428 C T 0 9.7 0 0.5847 0.4327 0.3141 0.2996 0.4076 0.4744 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2149||4557|FAT3|protein_coding|CODING|NM_001008781.2|25|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2197678 -0.379885 0 1 4557 3811 MODIFIER 25 CODING FAT3 C protein_coding NM_001008781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92628090 A C 0 9.7 0 0.8328 0.9377 0.9697 0.9812 0.9861 0.9622 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3811||4557|FAT3|protein_coding|CODING|NM_001008781.2|25|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2399586 -0.379885 0 1 362 371 MODIFIER 2 CODING MTNR1B A protein_coding NM_005959.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92715849 G A 0 12.4 0 0.5703 0.6308 0.6888 0.7034 0.5298 0.7004 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666667 0 . 0 . 5 2,1,0,2 UTR_3_PRIME(MODIFIER||371||362|MTNR1B|protein_coding|CODING|NM_005959.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs1562444 -0.453602 0.44 5 504 3037 MODIFIER 11 CODING SLC36A4 C protein_coding NM_152313.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92878666 A C 0 9.7 0 0.1089 0.0915 0.062 0.0595 0.1521 0.0593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3037||504|SLC36A4|protein_coding|CODING|NM_152313.3|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs76935911 -0.379885 0 1 504 2531 MODIFIER 11 CODING SLC36A4 C protein_coding NM_152313.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92879172 T C 0 9.7 0 0.093 0.2454 0.3228 0.4048 0.1113 0.3701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2531||504|SLC36A4|protein_coding|CODING|NM_152313.3|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs67573258 -0.379885 0 1 504 2492 MODIFIER 11 CODING SLC36A4 T protein_coding NM_152313.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92879210 TA T 0 10.1 0 0.2587 0.3071 0.3545 0.4097 0.1322 0.4131 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2492||504|SLC36A4|protein_coding|CODING|NM_152313.3|11|T) 0 . 0 2 1 1 1 0 . 0 60 0 0 . 0 . rs56910072 -0.379885 0 2 504 311 MODIFIER 11 CODING SLC36A4 T protein_coding NM_152313.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92881392 A T 0 23.4 0 0.8517 0.9599 0.9928 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||311||504|SLC36A4|protein_coding|CODING|NM_152313.3|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10741458 -0.453602 0.02 2 504 58 MODIFIER 1 CODING SLC36A4 T protein_coding NM_152313.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92931056 G T 0 99 0 0.1172 0.2648 0.3343 0.4127 0.1183 0.4131 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_5_PRIME(MODIFIER||58||504|SLC36A4|protein_coding|CODING|NM_152313.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11020196 -0.556411 0.106137 4 504 59 MODIFIER 1 CODING SLC36A4 T protein_coding NM_152313.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 92931057 C T 0 91 0 0.1172 0.2648 0.3343 0.4127 0.1183 0.4131 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_5_PRIME(MODIFIER||59||504|SLC36A4|protein_coding|CODING|NM_152313.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11020197 -0.556411 0.106137 4 E440Q 604 Gaa/Caa MODERATE 11 MISSENSE CODING CCDC67 C protein_coding NM_181645.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93129483 G C 0 222 0 0.1929 0.2666 0.1888 0.3363 0.2833 0.3323 0.00163577 0.00261869 0.00305998 1 1271 20372 955 1705 1377 10731 187 4146 2 5068 56590 3156 4002 3616 30392 482 9874 0.990104 0 . 0 . 82 16,26,17,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Caa|E440Q|604|CCDC67|protein_coding|CODING|NM_181645.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999509 rs12288277 -0.693132 0.0165449 82 E440G 604 gAa/gGa MODERATE 11 MISSENSE CODING CCDC67 G protein_coding NM_181645.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93129484 A G 0 222 0 0.1929 0.2668 0.1888 0.3363 0.2843 0.3323 0.00190944 0.00295658 0.00342633 1 1261 19999 924 1675 1352 10497 178 4112 2 5014 55584 3060 3900 3576 29778 464 9792 0.998896 0 . 0 . 83 16,26,17,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E440G|604|CCDC67|protein_coding|CODING|NM_181645.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999509 rs12282288 -0.693132 0.0165449 83 Q504K 604 Caa/Aaa MODERATE 12 MISSENSE CODING CCDC67 A protein_coding NM_181645.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93141580 C A 0 228 0 0.8275 0.8295 0.8602 0.9018 0.7753 0.7914 0.823056 0.794765 0.782234 2 3284 32020 1636 1953 2084 15857 287 6919 2 4048 40162 1836 2204 2618 20512 362 8582 0 . 0 . 0 140 0,0,23,103 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q504K|604|CCDC67|protein_coding|CODING|NM_181645.3|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2259633 -0.693147 1.36352e-06 140 604 40 MODIFIER 14 CODING CCDC67 A protein_coding NM_181645.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93170925 G A 0 33.8 0 0.6271 0.5252 0.3487 0.4405 0.5746 0.5491 0.621212 0.614194 0.611067 1 4889 57493 2838 3434 3647 33970 433 8282 2 8132 109868 11096 7912 6396 59802 818 15712 0.838046 0 . 0 . 12 0,8,0,4 UTR_3_PRIME(MODIFIER||40||604|CCDC67|protein_coding|CODING|NM_181645.3|14|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 0.397295 rs2605584 -0.556411 0.714437 12 604 222 MODIFIER 14 CODING CCDC67 C protein_coding NM_181645.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93171107 T C 0 57 0 0.1846 0.2504 0.1455 0.5367 0.0755 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,2,2,1 UTR_3_PRIME(MODIFIER||222||604|CCDC67|protein_coding|CODING|NM_181645.3|14|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.166667 rs1456244 -0.511536 0.235765 5 59 412 MODIFIER 3 CODING SMCO4 G protein_coding NM_020179.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93211764 A G 0 107 0 0.6172 0.6993 0.7219 0.9435 0.504 0.7434 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,6,0 UTR_3_PRIME(MODIFIER||412||59|SMCO4|protein_coding|CODING|NM_020179.2|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7365 -0.616816 0.969033 6 59 15 MODIFIER 3 CODING SMCO4 G protein_coding NM_020179.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93212161 A G 0 228 0 0.6286 0.7772 0.7983 0.9831 0.663 0.8681 0.663785 0.656558 0.652862 2 6613 87294 9696 8432 4422 43484 662 13985 2 9892 117886 11430 8518 6318 64748 874 16106 0 . 0 . 0 113 0,0,71,30 UTR_3_PRIME(MODIFIER||15||59|SMCO4|protein_coding|CODING|NM_020179.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2605594 -0.693147 0.0498345 113 V34 59 gtG/gtA LOW 3 SILENT CODING SMCO4 T protein_coding NM_020179.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93212254 C T 0 228 0 0.6172 0.6993 0.7219 0.9435 0.504 0.7434 0.628351 0.538698 0.492787 2 6537 73414 8993 8206 3487 33612 536 12043 2 10396 121318 11572 8652 6596 66686 908 16508 0 . 0 . 0 105 0,0,38,58 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V34|59|SMCO4|protein_coding|CODING|NM_020179.2|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2658797 -0.693147 0.0200511 105 I44 2601 atC/atT LOW 3 SILENT CODING CEP295 T protein_coding NM_033395.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93400796 C T 0 222 0 0.1044 0.1368 0.0749 0.2718 0.0974 0.1258 0.108382 0.0926413 0.0857951 1 228 2598 34 162 200 934 32 1008 2 2158 21572 412 618 1642 8848 232 7662 0.850926 0 . 0 COSM147307 214 84,24,62,15 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I44|2601|CEP295|protein_coding|CODING|NM_033395.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94479 rs67112133 -0.693147 0.614023 214 A114 2601 gcA/gcG LOW 4 SILENT CODING CEP295 G protein_coding NM_033395.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93402006 A G 0 222 0 0.0908 0.1332 0.0749 0.2718 0.0974 0.1258 0.0939306 0.0880806 0.0855346 1 203 2588 31 165 202 945 33 1009 2 2180 22024 402 622 1648 9034 244 7894 0.196373 0 . 0 COSM147308 134 45,16,48,15 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A114|2601|CEP295|protein_coding|CODING|NM_033395.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.411855 rs61743303 -0.693147 0.0127228 134 T144 2601 acC/acA LOW 4 SILENT CODING CEP295 A protein_coding NM_033395.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93402096 C A 0 228 0 0.6528 0.8844 0.9452 0.9395 0.9901 0.9888 0 . 0 2 1529 20688 390 598 1624 8541 233 7773 2 2116 21568 402 622 1626 8674 240 7888 0 . 0 . 0 163 0,0,77,69 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T144|2601|CEP295|protein_coding|CODING|NM_033395.1|4|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1944101 -0.693147 0.149695 163 R208Q 2601 cGg/cAg MODERATE 6 MISSENSE CODING CEP295 A protein_coding NM_033395.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93408831 G A 0 228 0 0.6967 0.9087 0.9553 0.995 0.9901 0.9898 0.766618 0.920499 0.987429 2 1605 20897 402 621 1622 8611 236 7800 2 2150 21706 410 622 1624 8744 242 7914 0 . 0 . 0 43 0,0,14,24 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGg/cAg|R208Q|2601|CEP295|protein_coding|CODING|NM_033395.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10831088 -0.693143 0.00292348 43 A499E 2601 gCa/gAa MODERATE 12 MISSENSE CODING CEP295 A protein_coding NM_033395.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93425159 C A 0 228 0 0.6967 0.9083 0.9553 0.9931 0.9901 0.9898 0.765896 0.92028 0.987429 2 1856 22569 442 626 1750 9842 253 7800 2 2482 23468 452 628 1752 9980 260 7914 0 . 0 . 0 68 0,0,12,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gAa|A499E|2601|CEP295|protein_coding|CODING|NM_033395.1|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4753495 -0.693147 4.17472e-05 68 Q1285K 2601 Caa/Aaa MODERATE 15 MISSENSE CODING CEP295 A protein_coding NM_033395.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93431931 C A 0 222 0 0.003 0.0703 0.0231 0.2619 0.007 0.0624 0.00722543 0.00832238 0.0087995 1 10 659 10 161 39 77 15 347 2 2164 21816 410 622 1626 8842 242 7910 0.86469 0 . 0 COSM147310 135 44,31,18,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Aaa|Q1285K|2601|CEP295|protein_coding|CODING|NM_033395.1|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.530299 rs72643380 -0.693147 0.209888 135 E2173A 2601 gAa/gCa MODERATE 24 MISSENSE CODING CEP295 C protein_coding NM_033395.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93460160 A C 0 222 0 0.1566 0.151 0.0778 0.2718 0.0974 0.1258 0.156792 0.107534 0.0861094 1 375 2708 36 166 210 994 33 894 2 2356 18104 392 604 1722 8464 212 4354 0.946915 0 . 0 . 70 18,12,19,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E2173A|2601|CEP295|protein_coding|CODING|NM_033395.1|24|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.104305 rs67879380 -0.693127 0.119222 70 E2437V 2601 gAg/gTg MODERATE 26 MISSENSE CODING CEP295 T protein_coding NM_033395.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93462607 A T 0 222 0 0.2723 0.6522 0.8156 0.6677 0.829 0.8517 0.353324 0.681559 0.824324 1 783 17758 365 435 1383 7944 201 6647 2 2268 22776 438 626 1668 9608 254 7914 0.93363 0 . 0 COSM1135271 83 31,6,26,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gTg|E2437V|2601|CEP295|protein_coding|CODING|NM_033395.1|26|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.21512 rs7131178 -0.693127 0.0942032 83 278 2208 MODIFIER 1 CODING TAF1D C protein_coding NM_024116.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93474678 G C 0 9.7 0 0.6861 0.894 0.9524 0.9385 0.9901 0.9888 0 . 0 1 144 10402 91 131 4 2586 114 7332 2 192 10646 92 138 4 2660 118 7442 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2208||278|TAF1D|protein_coding|CODING|NM_024116.3|1|C),UPSTREAM(MODIFIER||82||315|C11orf54|protein_coding|CODING|NM_001286067.1||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs630648 -0.379885 0 1 315 5769 MODIFIER 1 CODING C11orf54 T protein_coding NM_001286067.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93474791 G T 0 9.7 0 0.6891 0.8948 0.9524 0.9385 0.9901 0.9888 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||5769||315|C11orf54|protein_coding|CODING|NM_001286067.1|1|T),UPSTREAM(MODIFIER||88||278|TAF1D|protein_coding|CODING|NM_024116.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386602019,rs623510 -0.379885 0 1 315 5733 MODIFIER 1 CODING C11orf54 C protein_coding NM_001286067.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93474827 T C 0 46.3 0 0.6831 0.8932 0.9524 0.9385 0.9901 0.9888 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_5_PRIME(MODIFIER||5733||315|C11orf54|protein_coding|CODING|NM_001286067.1|1|C),UPSTREAM(MODIFIER||124||278|TAF1D|protein_coding|CODING|NM_024116.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386602268,rs631116 -0.453602 0.8 2 G65 651 ggC/ggG LOW 1 SILENT CODING MED17 G protein_coding NM_004268.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93517874 C G 0 228 0 0.2821 0.5657 0.7464 0.7411 0.6382 0.5654 0.363636 0.545339 0.636799 2 856 13345 354 921 153 6012 111 4938 2 2248 21614 460 1188 190 9148 184 8196 0 2 benign 0 . 62 0,0,7,54 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G65|651|MED17|protein_coding|CODING|NM_004268.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7116967 -0.693147 0.343371 62 E69D 651 gaG/gaC MODERATE 1 MISSENSE CODING MED17 C protein_coding NM_004268.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93517886 G C 0 228 0 0.2821 0.5657 0.7464 0.7411 0.6382 0.5654 0.368536 0.550581 0.641802 2 812 12569 302 841 107 5481 109 4917 2 2050 20328 398 1084 130 8330 178 8158 0 2 benign 0 . 55 0,0,4,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E69D|651|MED17|protein_coding|CODING|NM_004268.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2848477 -0.693147 0.247341 55 V198 200 gtT/gtA LOW 4 SILENT CODING VSTM5 T protein_coding NM_001144871.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93553744 A T 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.973295 0 . 0 . 139 45,25,38,19 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V198|200|VSTM5|protein_coding|CODING|NM_001144871.1|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.486925 rs190370980 -0.693147 0.144904 139 1159 27 MODIFIER 1 CODING HEPHL1 A protein_coding NM_001098672.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93754508 G A 0 228 0 0.5522 0.7484 0.8285 0.7738 0.8201 0.8569 0.601682 0.752091 0.823458 2 5708 95634 10278 6745 5235 54434 729 12505 2 9752 117558 11518 8586 6610 65780 870 14442 0 . 0 . 0 105 0,0,57,40 UTR_5_PRIME(MODIFIER||27||1159|HEPHL1|protein_coding|CODING|NM_001098672.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2511403,rs386568512 -0.693147 0.110345 105 Y37N 1159 Tac/Aac MODERATE 1 MISSENSE CODING HEPHL1 A protein_coding NM_001098672.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93754643 T A 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 27 0 26 0 0 0 1 2 9796 120392 11552 8626 6614 66590 898 16316 0.999697 0 . 0 . 127 30,34,21,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y37N|1159|HEPHL1|protein_coding|CODING|NM_001098672.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.12321 rs192979315 -0.693147 0.470483 127 N251D 1159 Aac/Gac MODERATE 4 MISSENSE CODING HEPHL1 G protein_coding NM_001098672.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93797619 A G 0 228 0 0.6725 0.9101 0.9784 1 0.998 1 0.747312 0.920527 0.999146 2 7238 117802 11410 8603 6600 66562 887 16502 2 9786 120500 11502 8606 6600 66604 896 16506 0 . 0 . 0 233 0,0,104,95 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N251D|1159|HEPHL1|protein_coding|CODING|NM_001098672.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1945783 -0.693147 0.0175313 233 V759 1159 gtG/gtA LOW 12 SILENT CODING HEPHL1 A protein_coding NM_001098672.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93822117 G A 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 8 0 8 0 0 0 0 2 9766 120552 11566 8616 6614 66602 890 16498 0.576776 0 . 0 . 193 29,60,30,56 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V759|1159|HEPHL1|protein_coding|CODING|NM_001098672.1|12|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.621101 rs142429260 -0.693147 0.00807196 193 1159 2263 MODIFIER 20 CODING HEPHL1 A protein_coding NM_001098672.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93847323 G A 0 46.3 0 0.3956 0.4395 0.5807 0.3482 0.5626 0.3661 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||2263||1159|HEPHL1|protein_coding|CODING|NM_001098672.1|20|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7116300 -0.453602 0.28 2 Q5H 426 caA/caC MODERATE 1 MISSENSE CODING PANX1 C protein_coding NM_015368.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93862493 A C 0 228 0 0.8608 0.6983 0.7723 0.6171 0.6203 0.59 0.8194 0.7008 0.640065 2 8546 80350 9647 5407 4395 41791 578 9986 2 10306 119802 11508 8524 6442 65784 902 16336 1 0 . 0 . 167 1,0,124,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caC|Q5H|426|PANX1|protein_coding|CODING|NM_015368.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1138800 -0.693147 0.014144 167 426 416 MODIFIER 5 CODING PANX1 A protein_coding NM_015368.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93914451 G A 0 42.3 0 0.789 0.7336 0.6037 0.746 0.6481 0.8262 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||416||426|PANX1|protein_coding|CODING|NM_015368.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046805 -0.453602 0.82 2 426 674 MODIFIER 5 CODING PANX1 C protein_coding NM_015368.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93914709 T C 0 9.7 0 0.789 0.7348 0.6052 0.749 0.6501 0.8262 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||674||426|PANX1|protein_coding|CODING|NM_015368.3|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1046812 -0.379885 0 1 426 921 MODIFIER 5 CODING PANX1 G protein_coding NM_015368.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 93914956 A G 0 70 0 0.7897 0.7518 0.6081 0.8036 0.6501 0.8538 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||921||426|PANX1|protein_coding|CODING|NM_015368.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1070 -0.453602 0.56 3 423 2145 MODIFIER 4 CODING GPR83 G protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94111170 T G 0 9.7 0 0.1309 0.1188 0.1614 0.0784 0.0954 0.138 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2145||423|GPR83|protein_coding|CODING|NM_016540.3|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12417810 -0.379885 0 1 423 1688 MODIFIER 4 CODING GPR83 C protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94111627 G C 0 63 0 0.3828 0.5417 0.572 0.6429 0.6064 0.5644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 7 3,0,4,0 UTR_3_PRIME(MODIFIER||1688||423|GPR83|protein_coding|CODING|NM_016540.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 0 . 0.810265 rs7933335 -0.556411 0.325692 7 423 1539 MODIFIER 4 CODING GPR83 G protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94111776 T G 0 228 0 0.8646 0.9621 0.9856 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,43,6 UTR_3_PRIME(MODIFIER||1539||423|GPR83|protein_coding|CODING|NM_016540.3|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7952021 -0.693147 0.029001 54 423 1507 MODIFIER 4 CODING GPR83 A protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94111808 G A 0 222 0 0.3616 0.5337 0.5706 0.6319 0.6064 0.5644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.770507 0 . 0 . 71 24,5,24,8 UTR_3_PRIME(MODIFIER||1507||423|GPR83|protein_coding|CODING|NM_016540.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.968568 rs7933565 -0.69312 0.389803 71 423 1055 MODIFIER 4 CODING GPR83 A protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94112260 G A 0 6.3 0 0.1445 0.1116 0.147 0.0734 0.0746 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1055||423|GPR83|protein_coding|CODING|NM_016540.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs60392353 -0.379885 0 1 423 547 MODIFIER 4 CODING GPR83 G protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94112768 A G 0 9.7 0 0.0552 0.0984 0.1585 0.0784 0.0954 0.138 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||547||423|GPR83|protein_coding|CODING|NM_016540.3|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7924609 -0.379885 0 1 423 511 MODIFIER 4 CODING GPR83 T protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94112804 C T 0 9.7 0 0.0204 0.0779 0.1398 0.0734 0.0746 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||511||423|GPR83|protein_coding|CODING|NM_016540.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs79058928 -0.379885 0 1 423 510 MODIFIER 4 CODING GPR83 G protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94112805 A G 0 9.7 0 0.0408 0.0841 0.1427 0.0734 0.0765 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||510||423|GPR83|protein_coding|CODING|NM_016540.3|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs16920237 -0.379885 0 1 423 362 MODIFIER 4 CODING GPR83 C protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94112953 A C 0 135 0 0.8533 0.9591 0.9856 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,8,0 UTR_3_PRIME(MODIFIER||362||423|GPR83|protein_coding|CODING|NM_016540.3|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs6483333 -0.651104 0.770293 8 423 278 MODIFIER 4 CODING GPR83 T protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94113037 C T 0 121 0 0.0204 0.0779 0.1398 0.0734 0.0746 0.1196 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.921053 0 . 0 . 24 11,0,13,0 UTR_3_PRIME(MODIFIER||278||423|GPR83|protein_coding|CODING|NM_016540.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.545597 rs3740865 -0.683931 0.325636 24 423 244 MODIFIER 4 CODING GPR83 T protein_coding NM_016540.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94113071 C T 0 203 0 0.0552 0.0984 0.1585 0.0784 0.0954 0.138 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.823561 0 . 0 . 34 15,0,15,2 UTR_3_PRIME(MODIFIER||244||423|GPR83|protein_coding|CODING|NM_016540.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.842568 rs3740866 -0.690438 0.29574 34 423 59 MODIFIER 1 CODING GPR83 C protein_coding NM_016540.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94134472 A C 0 108 0 0.6059 0.6829 0.6484 0.7272 0.672 0.7771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.138944 0 . 0 . 18 2,7,0,9 UTR_5_PRIME(MODIFIER||59||423|GPR83|protein_coding|CODING|NM_016540.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.30302 rs3824878 -0.662043 0.122215 18 423 100 MODIFIER 1 CODING GPR83 C protein_coding NM_016540.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94134513 G C 0 56 0 0.5446 0.5743 0.5634 0.6081 0.5785 0.5828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.895781 0 . 0 . 11 2,4,0,4 UTR_5_PRIME(MODIFIER||100||423|GPR83|protein_coding|CODING|NM_016540.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 1 0 0.0559863 rs12791316 -0.556411 0.0169029 11 708 LOW 5 CODING MRE11A T protein_coding NM_005591.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94212048 C T 0 222 0 0.171 0.3131 0.3862 0.3859 0.335 0.3558 0.208087 0.26958 0.30107 1 2089 39196 4903 3479 2350 20287 319 5769 2 10300 120518 11468 8574 6576 66260 900 16440 0.057581 3 likely-benign 0 . 99 15,31,14,27 SPLICE_SITE_REGION+INTRON(LOW||||708|MRE11A|protein_coding|CODING|NM_005591.3|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91523 rs111177591,rs535801 -0.693145 0.482867 99 L93 239 ctC/ctG LOW 3 SILENT CODING ANKRD49 G protein_coding NM_017704.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94231257 C G 0 222 0 0.6604 0.5475 0.5202 0.5208 0.5537 0.4356 0.626533 0.589783 0.570963 1 6521 65250 5297 4437 3570 37799 471 7155 2 10330 120590 11498 8606 6602 66422 904 16228 0.973789 0 . 0 . 63 30,5,19,4 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L93|239|ANKRD49|protein_coding|CODING|NM_017704.2|3|G),UPSTREAM(MODIFIER||4217||708|MRE11A|protein_coding|CODING|NM_005591.3||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.380143 rs2509943 -0.692717 0.864035 63 K16E 126 Aag/Gag MODERATE 1 MISSENSE CODING C11orf97 G protein_coding NM_001190462.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94245740 A G 0 149 0 0.5847 0.531 0.5317 0.5565 0.5875 0.3732 0 . 0 1 128 837 31 38 0 414 7 219 2 204 1368 56 58 0 630 14 406 0.148691 0 . 0 . 19 3,7,4,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K16E|126|C11orf97|protein_coding|CODING|NM_001190462.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.863243 rs2509324 -0.616816 0.250121 19 L86V 126 Ctg/Gtg MODERATE 3 MISSENSE CODING C11orf97 G protein_coding NM_001190462.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94261255 C G 0 222 0 0.8343 0.6759 0.611 0.6617 0.6392 0.5603 0 . 0 1 440 7451 114 125 1 2316 79 4376 2 558 12248 188 198 2 3586 132 7584 0.820484 0 . 0 . 159 59,8,63,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L86V|126|C11orf97|protein_coding|CODING|NM_001190462.1|3|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.513256 rs647484 -0.693147 0.448715 159 L472 530 Ctg/Ttg LOW 1 SILENT CODING FUT4 T protein_coding NM_002033.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94278713 C T 0 222 0 0.034 0.0711 0.1369 0.0536 0.0586 0.1053 0.0258973 0.0450839 0.0549093 1 286 9605 2137 569 412 4326 71 1804 2 10282 120466 11560 8604 6612 66000 896 16512 0.9306 0 . 0 COSM430098 245 47,71,38,55 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L472|530|FUT4|protein_coding|CODING|NM_002033.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997604 rs2230274 -0.693147 0.0546374 245 530 3122 MODIFIER 1 CODING FUT4 A protein_coding NM_002033.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94282014 G A 0 222 0 0.7231 0.4704 0.3948 0.3591 0.3847 0.3855 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.634191 0 . 0 . 143 33,32,40,21 UTR_3_PRIME(MODIFIER||3122||530|FUT4|protein_coding|CODING|NM_002033.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.821397 rs10741490 -0.693147 0.0502758 143 F246 852 ttT/ttC LOW 7 SILENT CODING PIWIL4 C protein_coding NM_152431.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94320237 T C 0 132 0 0.8124 0.5535 0.4524 0.5 0.4016 0.4867 0.746025 0.51631 0.398674 1 7767 54879 5054 4404 2613 26785 406 7850 2 10258 120522 11518 8604 6614 66186 898 16444 0.415949 0 . 0 . 36 19,0,15,1 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F246|852|PIWIL4|protein_coding|CODING|NM_152431.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.540496 rs7110167 -0.689466 0.201006 36 A499 852 gcC/gcT LOW 12 SILENT CODING PIWIL4 T protein_coding NM_152431.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94335077 C T 0 222 0 0.1407 0.1246 0.1686 0.0714 0.0885 0.1636 0.134484 0.109786 0.0971382 1 1340 13972 2339 682 203 6568 82 2758 2 10402 121386 11570 8650 6612 66732 908 16512 0.668532 0 . 0 . 118 34,19,32,18 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A499|852|PIWIL4|protein_coding|CODING|NM_152431.2|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823314 rs624184 -0.693147 0.047967 118 L546 852 Ctg/Ttg LOW 13 SILENT CODING PIWIL4 T protein_coding NM_152431.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94337220 C T 0 222 0 0.9085 0.5857 0.4524 0.502 0.4145 0.5061 0.815742 0.541423 0.401071 1 7827 52569 4733 4295 2409 25395 370 7540 2 9380 111880 10774 8476 6118 60700 804 15628 0.655767 0 . 0 . 125 17,44,15,33 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L546|852|PIWIL4|protein_coding|CODING|NM_152431.2|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0609777 rs593690 -0.693147 0.133348 125 R408Q 523 cGa/cAa MODERATE 3 MISSENSE CODING KDM4D A protein_coding NM_018039.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94731759 G A 0 222 0 0.0976 0.3205 0.3213 0.6468 0.2207 0.3875 0.120854 0.188567 0.223243 1 1178 34744 4676 5887 1933 14825 234 6011 2 10296 120852 11532 8616 6592 66402 906 16508 0.969906 0 . 0 . 91 14,34,12,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R408Q|523|KDM4D|protein_coding|CODING|NM_018039.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.789705 rs3740853 -0.693145 0.155041 91 506 12 MODIFIER 1 CODING KDM4E C protein_coding NM_001161630.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94758710 T C 0 222 0 . 0 . 0 . 0 0.120665 0.184845 0.212759 1 227 3823 86 177 4 1425 41 1863 2 1744 13786 288 336 10 6042 122 5244 0.739395 0 . 0 . 157 65,14,45,11 START_GAINED(LOW||||506|KDM4E|protein_coding|CODING|NM_001161630.1|1|C),UTR_5_PRIME(MODIFIER||12||506|KDM4E|protein_coding|CODING|NM_001161630.1|1|C) 1 0.5 1 0 . 0 . 1 1 0 58 0 0.713464 0.816244 0 0.932832 rs12364644 -0.693147 0.0945249 157 G39 506 ggC/ggT LOW 1 SILENT CODING KDM4E T protein_coding NM_001161630.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94758838 C T 0 222 0 0.0053 0.1194 0.1383 0.3472 0.0557 0.091 0.0144509 0.0381078 0.0483972 1 76 5024 945 1351 226 1527 44 855 2 2142 26378 1880 2174 558 11006 228 8390 0.961853 0 . 0 . 177 57,31,43,28 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G39|506|KDM4E|protein_coding|CODING|NM_001161630.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.941746 0.672169 0 0.95805 rs16921265 -0.693147 0.578462 177 Q113R 506 cAg/cGg MODERATE 1 MISSENSE CODING KDM4E G protein_coding NM_001161630.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94759059 A G 0 228 0 0.8366 0.8764 0.8847 0.9762 0.837 0.862 0 . 0 2 4008 68247 7143 4686 4012 36472 560 11366 2 5002 80642 7772 4728 4602 44622 654 13262 0.287129 0 . 0 . 110 0,2,33,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q113R|506|KDM4E|protein_coding|CODING|NM_001161630.1|1|G) 0 . 0 . 0 1 0 . 1 0 48 0 0.584158 0.0498589 0 0.470297 rs10752685 -0.693147 0.0010327 110 281 247 MODIFIER 1 CODING SRSF8 A protein_coding NM_032102.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94800144 G A 0 108 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,2 UTR_5_PRIME(MODIFIER||247||281|SRSF8|protein_coding|CODING|NM_032102.3|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2922090,rs386577267 -0.556411 0.0949329 4 281 1080 MODIFIER 1 CODING SRSF8 A protein_coding NM_032102.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94802318 G A 0 222 0 0.4697 0.4681 0.5014 0.2758 0.6044 0.5 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.943088 0 . 0 . 58 15,15,10,18 UTR_3_PRIME(MODIFIER||1080||281|SRSF8|protein_coding|CODING|NM_032102.3|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.519949 rs1056986,rs386514426 -0.693054 0.742067 58 281 1382 MODIFIER 1 CODING SRSF8 A protein_coding NM_032102.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94802620 C A 0 222 0 0.3404 0.396 0.4452 0.2758 0.5368 0.4151 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.989001 0 . 0 . 121 23,33,16,34 UTR_3_PRIME(MODIFIER||1382||281|SRSF8|protein_coding|CODING|NM_032102.3|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.483466 rs12627 -0.693147 0.0882393 121 281 1538 MODIFIER 1 CODING SRSF8 C protein_coding NM_032102.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94802776 G C 0 222 0 0.472 0.469 0.5014 0.2778 0.6044 0.5 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.736812 0 . 0 . 117 50,13,30,9 UTR_3_PRIME(MODIFIER||1538||281|SRSF8|protein_coding|CODING|NM_032102.3|1|C|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0264131 rs681695 -0.693144 0.431039 117 281 1714 MODIFIER 1 CODING SRSF8 G protein_coding NM_032102.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94802952 A G 0 222 0 0.472 0.4732 0.5014 0.2976 0.6044 0.501 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.357256 0 . 0 . 122 29,28,33,19 UTR_3_PRIME(MODIFIER||1714||281|SRSF8|protein_coding|CODING|NM_032102.3|1|G|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.707938 rs681134 -0.693147 0.0898082 122 281 1805 MODIFIER 1 CODING SRSF8 T protein_coding NM_032102.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94803043 A T 0 222 0 0.472 0.4696 0.5014 0.2798 0.6054 0.5 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.959378 0 . 0 . 122 34,26,31,27 UTR_3_PRIME(MODIFIER||1805||281|SRSF8|protein_coding|CODING|NM_032102.3|1|T|WARNING_TRANSCRIPT_INCOMPLETE) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999768 rs680673 -0.693147 0.619152 122 500 115 MODIFIER 1 CODING ENDOD1 C protein_coding NM_015036.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94822977 T C 0 9.7 0 0.1558 0.3015 0.2378 0.7004 0.1272 0.3119 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||500|ENDOD1|protein_coding|CODING|NM_015036.2|1|C),UTR_5_PRIME(MODIFIER||115||500|ENDOD1|protein_coding|CODING|NM_015036.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2922091 -0.379885 0 1 G446V 500 gGc/gTc MODERATE 2 MISSENSE CODING ENDOD1 T protein_coding NM_015036.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94862577 G T 0 222 0 0.087 0.2001 0.196 0.122 0.2684 0.3661 0.119608 0.225396 0.276669 1 1093 30874 1908 1084 1838 18976 222 5753 2 9806 120758 11574 8616 6612 66740 900 16510 0.566439 0 . 0 . 113 15,37,13,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gTc|G446V|500|ENDOD1|protein_coding|CODING|NM_015036.2|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913324 rs3740861 -0.693147 0.0870996 113 500 1549 MODIFIER 2 CODING ENDOD1 G protein_coding NM_015036.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94864292 C G 0 39.3 0 0.3608 0.5064 0.5418 0.7817 0.5179 0.3824 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1549||500|ENDOD1|protein_coding|CODING|NM_015036.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs679427 -0.453602 0.06 2 500 2591 MODIFIER 2 CODING ENDOD1 C protein_coding NM_015036.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94865334 T C 0 221 0 0.3638 0.5054 0.5418 0.7817 0.5139 0.3773 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.702821 0 . 0 . 61 31,4,15,5 UTR_3_PRIME(MODIFIER||2591||500|ENDOD1|protein_coding|CODING|NM_015036.2|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.366325 rs586421 -0.692067 0.266887 61 500 2711 MODIFIER 2 CODING ENDOD1 G protein_coding NM_015036.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94865454 T G 0 222 0 0.6808 0.7001 0.6571 0.875 0.672 0.6053 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.666425 0 . 0 . 58 8,29,5,11 UTR_3_PRIME(MODIFIER||2711||500|ENDOD1|protein_coding|CODING|NM_015036.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.619619 rs7729 -0.689466 0.0231221 58 492 308 MODIFIER 10 CODING SESN3 A protein_coding NM_144665.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94906111 G A 0 228 0 0.3169 0.4984 0.4539 0.7371 0.4085 0.6217 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 61 0,0,48,5 UTR_3_PRIME(MODIFIER||308||492|SESN3|protein_coding|CODING|NM_144665.3|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs684856 -0.693147 0.0154846 61 492 133 MODIFIER 10 CODING SESN3 C protein_coding NM_144665.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94906286 A C 0 228 0 0.0545 0.1046 0.1671 0.1339 0.0865 0.1166 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 64 0,0,26,27 UTR_3_PRIME(MODIFIER||133||492|SESN3|protein_coding|CODING|NM_144665.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2155239 -0.693147 0.897786 64 492 LOW 9 CODING SESN3 T protein_coding NM_144665.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 94908658 G T 0 228 0 0.146 0.2572 0.3199 0.2877 0.3201 0.2669 0.186506 0.269811 0.312471 2 1782 36774 4172 2448 1954 21221 303 4894 2 10394 121182 11550 8646 6604 66612 908 16468 0 . 0 . 0 109 0,0,75,16 SPLICE_SITE_REGION+INTRON(LOW||||492|SESN3|protein_coding|CODING|NM_144665.3|9|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11021065 -0.693147 0.652643 109 339 LOW 10 CODING FAM76B C protein_coding NM_144664.4 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95502106 A C 0 186 0 0.0499 0.1985 0.2363 0.252 0.3748 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.436912 0 . 0 . 47 24,2,16,3 SPLICE_SITE_REGION(LOW||||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C),UTR_3_PRIME(MODIFIER||2619||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.894973 rs11021310 -0.69168 0.0169631 47 339 2619 MODIFIER 10 CODING FAM76B C protein_coding NM_144664.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95502106 A C 0 186 0 0.0499 0.1985 0.2363 0.252 0.3748 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.436912 0 . 0 . 47 24,2,16,3 SPLICE_SITE_REGION(LOW||||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C),UTR_3_PRIME(MODIFIER||2619||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.894973 rs11021310 -0.69168 0.0169631 47 339 2597 MODIFIER 10 CODING FAM76B C protein_coding NM_144664.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95502128 G C 0 190 0 0.0499 0.1987 0.2363 0.253 0.3748 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.407313 0 . 0 . 71 31,5,24,3 UTR_3_PRIME(MODIFIER||2597||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.952345 rs3177463 -0.693021 0.452986 71 339 1089 MODIFIER 10 CODING FAM76B C protein_coding NM_144664.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95503636 T C 0 222 0 0.0772 0.2061 0.2363 0.253 0.3757 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991682 0 . 0 . 101 14,40,7,35 UTR_3_PRIME(MODIFIER||1089||339|FAM76B|protein_coding|CODING|NM_144664.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.999448 rs1944080 -0.693146 0.00338787 101 L252 339 Ttg/Ctg LOW 8 SILENT CODING FAM76B G protein_coding NM_144664.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95512060 A G 0 222 0 0.9274 0.5773 0.4942 0.3433 0.5119 0.4714 0.844173 0.616175 0.513325 1 8352 62485 5452 3148 3058 34404 465 7606 2 9762 119880 11348 8568 6570 66298 894 16440 0.757393 0 . 0 . 48 16,7,14,5 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L252|339|FAM76B|protein_coding|CODING|NM_144664.4|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994904 rs1150360,rs386518538 -0.69168 0.0698548 48 339 216 MODIFIER 1 CODING FAM76B C protein_coding NM_144664.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95522858 G C 0 47.2 0 0.0734 0.2049 0.2363 0.253 0.3748 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,0,3 UTR_5_PRIME(MODIFIER||216||339|FAM76B|protein_coding|CODING|NM_144664.4|1|C),UPSTREAM(MODIFIER||767||500|CEP57|protein_coding|CODING|NM_014679.4||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs12786522 -0.511536 0.917785 4 R448G 500 Aga/Gga MODERATE 11 MISSENSE CODING CEP57 G protein_coding NM_014679.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95564259 A G 0 222 0 0.0772 0.2059 0.2363 0.253 0.3738 0.137 0.124035 0.294815 0.382271 1 1190 36004 2222 2324 1605 25689 254 2720 2 10296 120984 11538 8614 6598 66554 906 16478 0.939895 0 . 0 COSM1357997 137 31,32,24,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R448G|500|CEP57|protein_coding|CODING|NM_014679.4|11|G),DOWNSTREAM(MODIFIER||1785||643|MTMR2|protein_coding|CODING|NM_016156.5||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.664637 rs386602809,rs644799 -0.693147 0.428209 137 643 1568 MODIFIER 15 CODING MTMR2 A protein_coding NM_016156.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95566886 G A 0 9.7 0 0.0651 0.2025 0.2349 0.253 0.3738 0.137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1568||643|MTMR2|protein_coding|CODING|NM_016156.5|15|A),DOWNSTREAM(MODIFIER||1029||500|CEP57|protein_coding|CODING|NM_014679.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs596277 -0.379885 0 1 643 1419 MODIFIER 15 CODING MTMR2 T protein_coding NM_016156.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95567035 C T 0 87 0 0.0688 0.2035 0.2363 0.253 0.3738 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.450401 0 . 0 . 8 3,0,4,1 UTR_3_PRIME(MODIFIER||1419||643|MTMR2|protein_coding|CODING|NM_016156.5|15|T),DOWNSTREAM(MODIFIER||1178||500|CEP57|protein_coding|CODING|NM_014679.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.150134 rs496305 -0.590765 0.910445 8 T377 643 acC/acT LOW 10 SILENT CODING MTMR2 A protein_coding NM_016156.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95580926 G A 0 222 0 0.0923 0.2093 0.2378 0.253 0.3708 0.136 0.132894 0.298046 0.38262 1 1325 36146 2233 2325 1601 25681 257 2724 2 10404 121300 11552 8618 6606 66706 906 16508 0.906518 0 . 0 . 275 60,70,51,60 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T377|643|MTMR2|protein_coding|CODING|NM_016156.5|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.864592 rs566204 -0.693147 0.0383031 275 K3T 643 aAg/aCg MODERATE 1 MISSENSE CODING MTMR2 G protein_coding NM_016156.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95657111 T G 0 222 0 0.0681 0.2129 0.2406 0.2688 0.3857 0.1534 0.0894688 0.239819 0.317287 1 195 5649 155 196 37 3503 65 1498 2 1598 19552 600 788 140 8208 188 8030 0.98948 0 . 0 . 126 44,20,28,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K3T|643|MTMR2|protein_coding|CODING|NM_016156.5|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.470996 rs3824874 -0.693147 0.00914825 126 1156 198 MODIFIER 5 CODING MAML2 G protein_coding NM_032427.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95711914 A G 0 66 0 0.5877 0.499 0.5346 0.4633 0.3479 0.546 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.4 0 . 0 . 7 2,0,5,0 UTR_3_PRIME(MODIFIER||198||1156|MAML2|protein_coding|CODING|NM_032427.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.8 rs7104987 -0.590765 0.258586 7 Q596 1156 caG/caA LOW 2 SILENT CODING MAML2 T protein_coding NM_032427.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 95825407 C T 0 9.4 0 . 0 . 0 . 0 . 0 . 1 0 2 0 0 0 2 0 0 2 2224 22514 470 696 1502 9812 240 7570 0.0672016 0 . 0 COSM467609 90 36,23,5,6 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q596|1156|MAML2|protein_coding|CODING|NM_032427.3|2|T) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 1.10987e-06 rs61901862 -0.676189 2.11962e-06 90 524 973 MODIFIER 2 CODING JRKL G protein_coding NM_001261833.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 96126361 A G 0 228 0 0.2829 0.3103 0.3012 0.255 0.3996 0.319 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.745 0 . 0 . 109 2,0,75,25 UTR_3_PRIME(MODIFIER||973||524|JRKL|protein_coding|CODING|NM_001261833.1|2|G),UPSTREAM(MODIFIER||3278||544|CCDC82|protein_coding|CODING|NM_024725.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.435 rs4753751 -0.693147 2.183e-09 109 S1079T 1100 Tct/Act MODERATE 24 MISSENSE CODING CNTN5 A protein_coding NM_001243270.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100226883 T A 0 222 0 0.531 0.3271 0.2896 0.3313 0.1193 0.2873 0.428285 0.210518 0.106311 1 4381 23649 3741 2929 805 7377 156 4260 2 9166 105566 10130 7926 5984 57214 782 14364 0.964852 0 . 0 . 111 24,17,25,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Act|S1079T|1100|CNTN5|protein_coding|CODING|NM_001243270.1|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.969972 rs1216183 -0.693147 0.215638 111 1100 11 MODIFIER 24 CODING CNTN5 T protein_coding NM_001243270.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100226962 C T 0 222 0 0.1967 0.2314 0.2637 0.3224 0.1153 0.2812 0.171915 0.124612 0.102169 1 1498 17458 2926 2497 720 6064 133 3620 2 7168 81054 7482 6274 4818 42262 622 12428 0.458133 0 . 0 . 90 19,27,8,24 UTR_3_PRIME(MODIFIER||11||1100|CNTN5|protein_coding|CODING|NM_001243270.1|24|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987681 rs1216182 -0.69312 0.140143 90 1100 1593 MODIFIER 24 CODING CNTN5 A protein_coding NM_001243270.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100228544 G A 0 9.7 0 0.6604 0.4541 0.3429 0.4613 0.2922 0.4131 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1593||1100|CNTN5|protein_coding|CODING|NM_001243270.1|24|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1230331 -0.379885 0 1 1100 2148 MODIFIER 24 CODING CNTN5 C protein_coding NM_001243270.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100229099 T C 0 39.3 0 0.9372 0.7406 0.6081 0.9256 0.4751 0.6513 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2148||1100|CNTN5|protein_coding|CODING|NM_001243270.1|24|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs485676 -0.453602 0.58 2 R338 874 cgA/cgG LOW 10 SILENT CODING ARHGAP42 G protein_coding NM_152432.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100814570 A G 0 228 0 0.1362 0.4109 0.4308 0.7312 0.2565 0.5971 0.199422 0.259965 0.286298 2 398 8426 184 463 489 2499 83 4310 2 2150 21780 408 620 1626 8828 242 7906 0 . 0 . 0 177 0,0,64,90 SYNONYMOUS_CODING(LOW|SILENT|cgA/cgG|R338|874|ARHGAP42|protein_coding|CODING|NM_152432.2|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs543146 -0.693147 0.000898283 177 P668 874 ccA/ccG LOW 20 SILENT CODING ARHGAP42 G protein_coding NM_152432.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100846936 A G 0 228 0 0.2511 0.5739 0.6081 0.997 0.4344 0.6933 0.340318 0.409987 0.440289 2 735 11765 259 618 870 4101 133 5049 2 2284 22534 422 620 1656 9408 250 7894 0 . 0 . 0 74 0,0,42,26 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P668|874|ARHGAP42|protein_coding|CODING|NM_152432.2|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs654593 -0.693147 0.756226 74 S706 874 tcA/tcG LOW 20 SILENT CODING ARHGAP42 G protein_coding NM_152432.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100847050 A G 0 228 0 0.2027 0.5601 0.6009 0.997 0.4344 0.6933 0.305636 0.399693 0.440603 2 725 12039 280 625 902 4323 133 5051 2 2466 23298 460 628 1706 9880 254 7904 0 . 0 . 0 69 0,0,33,31 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S706|874|ARHGAP42|protein_coding|CODING|NM_152432.2|20|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs569270 -0.693147 0.0258705 69 V713I 874 Gtt/Att MODERATE 20 MISSENSE CODING ARHGAP42 A protein_coding NM_152432.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100847069 G A 0 228 0 0.1505 0.4962 0.5274 0.997 0.2883 0.6391 0.221821 0.283399 0.310182 2 498 9738 245 624 538 3157 109 4567 2 2424 23106 452 626 1688 9770 254 7892 0 . 0 . 0 75 0,0,36,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V713I|874|ARHGAP42|protein_coding|CODING|NM_152432.2|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs569336 -0.693147 0.246597 75 874 LOW 23 CODING ARHGAP42 A protein_coding NM_152432.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100859439 G A 0 222 0 0.0257 0.2107 0.2594 0.3879 0.1213 0.3354 0.0556358 0.11279 0.137649 1 103 4279 107 240 257 1130 41 2401 2 2090 21422 396 608 1622 8580 240 7886 0.980626 0 . 0 . 79 35,7,22,6 SPLICE_SITE_REGION+INTRON(LOW||||874|ARHGAP42|protein_coding|CODING|NM_152432.2|23|A),UPSTREAM(MODIFIER||3372||129|TMEM133|protein_coding|CODING|NM_032021.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.642224 rs111177640,rs524811 -0.693054 0.581767 79 E19 129 gaA/gaG LOW 1 SILENT CODING TMEM133 G protein_coding NM_032021.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100863096 A G 0 228 0 0.1248 0.3882 0.3977 0.7579 0.2028 0.547 0.134362 0.18453 0.210233 2 1391 38251 5922 6423 2019 13892 282 8322 2 10376 120846 11558 8628 6612 66416 902 16354 1 0 . 0 . 148 1,0,72,48 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E19|129|TMEM133|protein_coding|CODING|NM_032021.2|1|G),DOWNSTREAM(MODIFIER||1440||874|ARHGAP42|protein_coding|CODING|NM_152432.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs386506064,rs515552 -0.693147 0.474068 148 V105 129 gtC/gtA LOW 1 SILENT CODING TMEM133 A protein_coding NM_032021.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100863354 C A 0 228 0 0.1225 0.385 0.3934 0.756 0.1988 0.5429 0.132773 0.181608 0.206628 2 1367 37587 5918 6419 1994 13431 276 8182 2 10398 120934 11572 8638 6614 66500 902 16310 0 . 0 . 0 75 0,0,24,44 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtA|V105|129|TMEM133|protein_coding|CODING|NM_032021.2|1|A),DOWNSTREAM(MODIFIER||1698||874|ARHGAP42|protein_coding|CODING|NM_152432.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386594878,rs471933 -0.693147 0.0220945 75 129 938 MODIFIER 1 CODING TMEM133 A protein_coding NM_032021.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100864367 G A 0 228 0 0.8101 0.772 0.7291 0.8125 0.672 0.8119 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,25,24 UTR_3_PRIME(MODIFIER||938||129|TMEM133|protein_coding|CODING|NM_032021.2|1|A),DOWNSTREAM(MODIFIER||2711||874|ARHGAP42|protein_coding|CODING|NM_152432.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386596144,rs488365 -0.693147 0.18433 54 933 9014 MODIFIER 8 CODING PGR C protein_coding NM_000926.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100900833 A C 0 9.7 0 0.3328 0.3766 0.2911 0.7212 0.1252 0.3998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||9014||933|PGR|protein_coding|CODING|NM_000926.4|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7947125 -0.379885 0 1 933 8248 MODIFIER 8 CODING PGR A protein_coding NM_000926.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100901599 G A 0 9.7 0 0.0045 0.1759 0.1931 0.495 0.1074 0.137 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||8248||933|PGR|protein_coding|CODING|NM_000926.4|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3740751 -0.379885 0 1 933 7794 MODIFIER 8 CODING PGR A protein_coding NM_000926.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100902053 C A 0 67 0 0.3018 0.3676 0.2896 0.7232 0.1252 0.3947 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||7794||933|PGR|protein_coding|CODING|NM_000926.4|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1824125 -0.511536 0.833544 3 933 1849 MODIFIER 8 CODING PGR T protein_coding NM_000926.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 100907998 C T 0 70 0 0.7254 0.8021 0.7997 0.997 0.7306 0.7802 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1849||933|PGR|protein_coding|CODING|NM_000926.4|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs502465 -0.453602 0.22 3 933 700 MODIFIER 1 CODING PGR G protein_coding NM_000926.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101000501 A G 0 9.7 0 0.6679 0.8672 0.8934 0.9931 0.9105 0.9438 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||700||933|PGR|protein_coding|CODING|NM_000926.4|1|G),INTRAGENIC(MODIFIER|||||LOC101054525||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs518162 -0.379885 0 1 P15S 931 Ccc/Tcc MODERATE 1 MISSENSE CODING TRPC6 A protein_coding NM_004621.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101454192 G A 0 143 0 0.0038 0.0677 0.0605 0.13 0.1064 0.0552 0.0187284 0.0631685 0.0859671 1 35 1362 32 43 1 635 10 606 2 994 12936 334 336 16 4534 126 6596 0.88059 0 . 0 . 30 1,15,1,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P15S|931|TRPC6|protein_coding|CODING|NM_004621.5|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940317 rs3802829 -0.683931 0.131805 30 R192W 388 Cgg/Tgg MODERATE 7 MISSENSE CODING ANGPTL5 A protein_coding NM_178127.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101771248 G A 0 228 0 0.9992 0.9968 0.9986 1 0.9871 0.999 0.998638 0.995078 0.993254 2 10388 120524 11524 8654 6597 65983 902 16476 2 10402 121396 11576 8654 6614 66732 908 16510 0 . 0 . 0 105 0,0,41,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R192W|388|ANGPTL5|protein_coding|CODING|NM_178127.4|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3858418 -0.693147 0.26533 105 388 70 MODIFIER 2 CODING ANGPTL5 G protein_coding NM_178127.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101778710 A G 0 222 0 0.1566 0.3085 0.2781 0.4464 0.4125 0.2863 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999422 0 . 0 . 91 2,39,5,41 UTR_5_PRIME(MODIFIER||70||388|ANGPTL5|protein_coding|CODING|NM_178127.4|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976767 rs1661410 -0.693147 0.171668 91 G238C 1117 Ggt/Tgt MODERATE 6 MISSENSE CODING CEP126 T protein_coding NM_020802.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101832478 G T 0 228 0 1 1 1 1 1 1 0 . 0 2 9582 114524 11420 8570 6588 64888 848 12628 2 9582 114524 11420 8570 6588 64888 848 12628 0 . 0 . 0 53 0,0,47,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Tgt|G238C|1117|CEP126|protein_coding|CODING|NM_020802.3|6|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7926728 -0.693147 0.00952112 53 T314 1117 acA/acT LOW 6 SILENT CODING CEP126 T protein_coding NM_020802.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101832708 A T 0 222 0 0.0121 0.0998 0.2133 0.122 0.0278 0.1892 0.0177031 0.0207692 0.0223412 1 193 9408 3308 992 422 1849 67 2577 2 10208 120564 11528 8628 6596 66422 904 16278 0.965919 0 . 0 . 113 32,21,31,20 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T314|1117|CEP126|protein_coding|CODING|NM_020802.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.402431 rs3740930 -0.693147 0.667788 113 T626 1117 acC/acT LOW 6 SILENT CODING CEP126 T protein_coding NM_020802.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101833644 C T 0 228 0 0.997 0.9872 0.9755 1 0.9622 0.9949 0.995 0.980373 0.972882 2 9958 118163 11390 8605 6563 64371 887 16389 2 10002 120388 11546 8606 6606 66242 902 16484 0 . 0 . 0 69 0,0,25,38 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T626|1117|CEP126|protein_coding|CODING|NM_020802.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7109233 -0.693147 0.298153 69 S1077N 1117 aGt/aAt MODERATE 9 MISSENSE CODING CEP126 A protein_coding NM_020802.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101857758 G A 0 228 0 0.9977 0.9874 0.9755 1 0.9622 0.9949 0.995007 0.980544 0.973133 2 10324 119087 11407 8648 6571 64833 893 16411 2 10372 121332 11564 8652 6614 66716 908 16506 0 . 0 . 0 105 0,0,30,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S1077N|1117|CEP126|protein_coding|CODING|NM_020802.3|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6590942 -0.693147 9.59972e-05 105 1117 41 MODIFIER 11 CODING CEP126 T protein_coding NM_020802.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101868415 C T 0 222 0 0.6377 0.5777 0.4366 0.7639 0.498 0.4867 0.639582 0.535758 0.482554 1 6631 61046 5012 6891 2946 31231 421 7914 2 10406 121340 11564 8646 6610 66702 908 16504 0.401834 0 . 0 . 137 37,33,25,30 UTR_3_PRIME(MODIFIER||41||1117|CEP126|protein_coding|CODING|NM_020802.3|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995308 rs1783742 -0.693147 0.0013729 137 1117 2581 MODIFIER 11 CODING CEP126 A protein_coding NM_020802.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 101870955 G A 0 9.7 0 0.6014 0.5681 0.4366 0.7639 0.498 0.4867 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2581||1117|CEP126|protein_coding|CODING|NM_020802.3|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2508314 -0.379885 0 1 508 LOW 8 CODING YAP1 T protein_coding NM_001282101.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102100429 C T 0 222 0 0 0.0089856 0 0.0446 0 0 0.00226963 0.000922793 0.000232612 1 14 521 3 467 0 9 2 26 2 10406 120980 11538 8650 6612 66576 902 16296 0.986162 0 . 0 . 98 35,8,38,10 SPLICE_SITE_REGION+INTRON(LOW||||508|YAP1|protein_coding|CODING|NM_001282101.1|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962032 rs116990751 -0.693147 0.20243 98 508 2929 MODIFIER 9 CODING YAP1 A protein_coding NM_001282101.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102103600 G A 0 78 0 0.3699 0.3574 0.3573 0.3938 0.3748 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1.01283 0 . 0 . 7 0,3,1,3 UTR_3_PRIME(MODIFIER||2929||508|YAP1|protein_coding|CODING|NM_001282101.1|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.01283 1 0 0.810265 rs8504 -0.556411 0.803107 7 604 18 MODIFIER 9 CODING BIRC3 A protein_coding NM_001165.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102207851 G A 0 228 0 0.6793 0.6564 0.5937 0.7242 0.6093 0.6483 0.67257 0.636636 0.618222 2 6138 66673 6151 5359 4461 35484 529 8551 2 8938 100490 9704 7630 5950 54880 746 12642 1 0 . 0 . 65 0,1,3,60 UTR_3_PRIME(MODIFIER||18||604|BIRC3|protein_coding|CODING|NM_001165.4|9|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1055088 -0.693147 0.000281263 65 604 1904 MODIFIER 9 CODING BIRC3 C protein_coding NM_001165.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102209737 A C 0 70 0 0.7731 0.6825 0.6066 0.7232 0.6083 0.6483 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1904||604|BIRC3|protein_coding|CODING|NM_001165.4|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13711 -0.453602 0.42 3 267 82 MODIFIER 6 CODING MMP7 A protein_coding NM_002423.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102391425 G A 0 69 0 0.0076 0.1326 0.147 0.248 0.2197 0.0828 0.0419075 0.151555 0.199246 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.972604 0 . 0 . 15 8,1,6,0 UTR_3_PRIME(MODIFIER||82||267|MMP7|protein_coding|CODING|NM_002423.3|6|A) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.465043 rs14983,rs386534532 -0.616816 0.544728 15 R77H 267 cGc/cAc MODERATE 2 MISSENSE CODING MMP7 T protein_coding NM_002423.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102398593 C T 0 222 0 0.0076 0.1336 0.1484 0.248 0.2237 0.0828 0.0460735 0.160489 0.219121 1 453 22491 1827 2171 1488 14875 166 1511 2 10376 121326 11566 8644 6612 66714 908 16506 0.945463 0 . 0 . 126 20,34,35,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R77H|267|MMP7|protein_coding|CODING|NM_002423.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0677949 rs10502001 -0.693147 0.285917 126 T281N 483 aCt/aAt MODERATE 6 MISSENSE CODING MMP20 T protein_coding NM_004771.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102477377 G T 0 222 0 0.2625 0.4199 0.4424 0.4325 0.4364 0.5869 0.30867 0.40649 0.456618 1 3158 54808 5375 3795 2310 30145 414 9611 2 10392 121336 11572 8634 6610 66710 908 16510 0.740004 0 . 0 . 185 32,47,34,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T281N|483|MMP20|protein_coding|CODING|NM_004771.3|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.595299 rs1784424 -0.693147 0.247079 185 V275A 483 gTa/gCa MODERATE 6 MISSENSE CODING MMP20 G protein_coding NM_004771.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102477395 A G 0 222 0 0.2625 0.4199 0.4424 0.4325 0.4364 0.5869 0.308443 0.40649 0.456734 1 3165 54838 5379 3804 2309 30153 414 9614 2 10402 121340 11570 8640 6608 66704 908 16508 0.536552 0 . 0 . 162 23,48,28,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V275A|483|MMP20|protein_coding|CODING|NM_004771.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99541 rs1784423 -0.693147 0.0296675 162 I169L 483 Ata/Cta MODERATE 3 MISSENSE CODING MMP20 G protein_coding NM_004771.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102482504 T G 0 222 0 0.0136 0.0274 0.0043 0.0754 0.005 0.0358 0.0118021 0.00661335 0.00395441 1 107 1598 37 778 0 186 11 479 2 10366 121092 11542 8600 6606 66586 906 16486 0.173654 0 . 0 . 207 42,48,48,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I169L|483|MMP20|protein_coding|CODING|NM_004771.3|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.160498 rs17099008 -0.693147 0.881276 207 K18T 483 aAg/aCg MODERATE 1 MISSENSE CODING MMP20 G protein_coding NM_004771.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102495998 T G 0 228 0 0.6036 0.6765 0.6816 0.8016 0.6262 0.6943 0.624376 0.637419 0.644103 2 6473 80305 7699 7167 4301 42561 587 11517 2 10396 121254 11562 8634 6600 66662 908 16492 0 . 0 . 0 67 0,0,38,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K18T|483|MMP20|protein_coding|CODING|NM_004771.3|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2245803 -0.693147 0.174941 67 G409 513 ggG/ggA LOW 9 SILENT CODING MMP27 T protein_coding NM_022122.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102563739 C T 0 222 0 0.2186 0.4501 0.5072 0.629 0.4453 0.5429 0.273491 0.391879 0.452547 1 2809 56854 6682 5100 3436 29757 427 8643 2 10402 121360 11568 8642 6612 66716 908 16512 0.528547 0 . 0 COSM428286 143 39,29,20,35 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G409|513|MMP27|protein_coding|CODING|NM_022122.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.458516 rs1276289,rs386525960 -0.693147 0.105443 143 E266V 513 gAa/gTa MODERATE 6 MISSENSE CODING MMP27 A protein_coding NM_022122.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102567207 T A 0 222 0 0.1725 0.4375 0.5043 0.629 0.4443 0.544 0.241943 0.38219 0.454059 1 2411 56458 6656 5089 3439 29793 425 8645 2 10406 121194 11496 8610 6604 66668 908 16502 0.836567 0 . 0 COSM428288 103 25,21,17,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gTa|E266V|513|MMP27|protein_coding|CODING|NM_022122.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.622276 rs1276286 -0.693145 0.292894 103 M30V 513 Atg/Gtg MODERATE 1 MISSENSE CODING MMP27 C protein_coding NM_022122.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102576358 T C 0 228 0 0.9213 0.8159 0.7233 0.8839 0.6799 0.8088 0.872901 0.732006 0.659805 2 9073 88064 8435 7841 4415 44859 654 12787 2 10394 121342 11560 8644 6614 66718 908 16504 0 . 0 . 0 77 0,0,67,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M30V|513|MMP27|protein_coding|CODING|NM_022122.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2846707,rs386504020 -0.693147 0.00327848 77 T24M 513 aCg/aTg MODERATE 1 MISSENSE CODING MMP27 A protein_coding NM_022122.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102576375 G A 0 228 0 0.7035 0.7782 0.8184 0.8135 0.834 0.7566 0.736723 0.801676 0.834962 2 7595 99500 9345 6810 5751 56358 754 12887 2 10388 121350 11568 8644 6612 66726 908 16504 0 . 0 . COSM1579495 85 0,0,67,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T24M|513|MMP27|protein_coding|CODING|NM_022122.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1939015 -0.693147 0.00190106 85 R22W 513 Cgg/Tgg MODERATE 1 MISSENSE CODING MMP27 A protein_coding NM_022122.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102576382 G A 0 222 0 0.1687 0.1685 0.1455 0.2996 0.0666 0.1544 0.16818 0.0992771 0.0639684 1 1768 13343 1988 2205 459 4409 83 2431 2 10386 121334 11568 8634 6612 66722 908 16504 0.999913 0 . 0 COSM147312 97 37,7,34,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R22W|513|MMP27|protein_coding|CODING|NM_022122.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.535921 rs12099177 -0.693145 0.0356878 97 467 56 MODIFIER 10 CODING MMP8 A protein_coding NM_002424.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102584023 T A 0 228 0 0.9289 0.9435 0.9424 0.998 0.9076 0.9448 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,47,2 UTR_3_PRIME(MODIFIER||56||467|MMP8|protein_coding|CODING|NM_002424.2|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1939018 -0.693147 0.22479 52 V436A 467 gTc/gCc MODERATE 10 MISSENSE CODING MMP8 G protein_coding NM_002424.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102584176 A G 0 222 0 0 0.0037939 0 0.0179 0 0.001 0 0.000230698 0.000348918 1 0 294 2 276 0 5 2 9 2 10352 120814 11452 8586 6582 66444 904 16494 0.846418 0 . 0 . 75 7,29,9,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V436A|467|MMP8|protein_coding|CODING|NM_002424.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93219 rs34009635 -0.69312 0.19527 75 K87E 467 Aaa/Gaa MODERATE 2 MISSENSE CODING MMP8 C protein_coding NM_002424.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102593248 T C 0 228 0 0.7095 0.6 0.5173 0.5685 0.5467 0.5982 0.646618 0.553445 0.505699 2 6732 65803 5882 5515 3620 34392 479 9183 2 10406 121330 11534 8640 6610 66722 908 16510 1 0 . 0 . 106 0,1,60,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K87E|467|MMP8|protein_coding|CODING|NM_002424.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1940475 -0.693147 0.495271 106 T32I 467 aCt/aTt MODERATE 1 MISSENSE CODING MMP8 A protein_coding NM_002424.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102595492 G A 0 228 0 0.8147 0.6544 0.5605 0.5774 0.5885 0.6513 0.751021 0.622655 0.556874 2 7839 72437 6301 5555 3959 38086 535 10162 2 10396 121304 11578 8652 6612 66688 906 16472 0 . 0 . 0 67 0,0,41,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T32I|467|MMP8|protein_coding|CODING|NM_002424.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3765620 -0.693147 0.798937 67 467 80 MODIFIER 1 CODING MMP8 G protein_coding NM_002424.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102595666 C G 0 228 0 0.9334 0.9459 0.9467 0.998 0.9085 0.9468 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 64 0,0,11,47 UTR_5_PRIME(MODIFIER||80||467|MMP8|protein_coding|CODING|NM_002424.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2155052 -0.693147 0.00700879 64 469 184 MODIFIER 10 CODING MMP1 G protein_coding NM_002421.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102660959 A G 0 72 0 0.3124 0.1985 0.2291 0.2272 0.0596 0.136 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868321 0 . 0 . 8 4,0,3,1 UTR_3_PRIME(MODIFIER||184||469|MMP1|protein_coding|CODING|NM_002421.3|10|G),INTRAGENIC(MODIFIER|||||WTAPP1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.992367 1 0 0.62023 rs2071230 -0.556411 0.211317 8 A216 469 gcA/gcG LOW 5 SILENT CODING MMP1 C protein_coding NM_002421.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102666316 T C 0 222 0 0.9947 0.9313 0.8876 0.8899 0.9483 0.9018 0.987063 0.958628 0.944057 1 10269 112625 9553 7688 6087 63366 822 14840 2 10402 121056 11438 8622 6594 66610 906 16484 0.978366 0 . 0 . 227 54,61,37,45 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A216|469|MMP1|protein_coding|CODING|NM_002421.3|5|C),INTRAGENIC(MODIFIER|||||WTAPP1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.542119 rs386594782,rs470558 -0.693147 0.0961397 227 A362 477 gcT/gcC LOW 8 SILENT CODING MMP3 G protein_coding NM_002422.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102709425 A G 0 222 0 0.5598 0.6224 0.6643 0.6706 0.5298 0.7229 0.542215 0.514226 0.499884 1 5671 68477 8023 5784 3977 33273 545 11204 2 10388 120792 11454 8634 6572 66350 906 16488 0.93489 0 . 0 . 142 20,44,15,49 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A362|477|MMP3|protein_coding|CODING|NM_002422.4|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.333436 rs520540 -0.693147 0.0844206 142 D96 477 gaT/gaC LOW 2 SILENT CODING MMP3 G protein_coding NM_002422.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102713465 A G 0 222 0 0.5499 0.6186 0.6643 0.6667 0.5278 0.7229 0.539038 0.513381 0.500233 1 5631 68319 8035 5760 3890 33275 542 11186 2 10398 120872 11446 8610 6582 66438 906 16492 0.882194 0 . 0 COSM428295 152 44,16,45,21 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D96|477|MMP3|protein_coding|CODING|NM_002422.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.958643 rs602128 -0.693147 0.159899 152 K45E 477 Aaa/Gaa MODERATE 2 MISSENSE CODING MMP3 C protein_coding NM_002422.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102713620 T C 0 222 0 0.671 0.6522 0.6787 0.6657 0.5278 0.7219 0.638901 0.547216 0.500233 1 6512 66832 7748 5466 3779 31788 526 11013 2 9966 113454 10876 8080 6342 61254 864 16072 0.73621 0 . 0 COSM428296 85 13,29,8,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K45E|477|MMP3|protein_coding|CODING|NM_002422.4|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.830891 rs386605145,rs679620 -0.693136 0.158316 85 T210 469 acC/acA LOW 5 SILENT CODING MMP12 T protein_coding NM_002426.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102738795 G T 0 60 0 . 0 . 0 . 0 . 0 . 2 7492 89198 7384 6372 5196 49894 702 12158 2 7492 89198 7384 6372 5196 49894 702 12158 1 0 . 0 . 244 0,1,2,13 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T210|469|MMP12|protein_coding|CODING|NM_002426.4|5|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 . 0 . 1 0 60 0 1 1 0 1 rs68192524,rs5003690 -0.688148 0.0280177 244 237 8573 MODIFIER 8 CODING DCUN1D5 G protein_coding NM_032299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102924515 T G 0 9.7 0 0.882 0.9587 0.9726 1 0.9742 0.9939 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||8573||237|DCUN1D5|protein_coding|CODING|NM_032299.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs540266 -0.379885 0 1 237 1574 MODIFIER 8 CODING DCUN1D5 C protein_coding NM_032299.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 102931514 G C 0 9.7 0 0.0303 0.0942 0.1254 0.1498 0.0646 0.1319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1574||237|DCUN1D5|protein_coding|CODING|NM_032299.3|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs17099877 -0.379885 0 1 D4039 4314 gaT/gaC LOW 84 SILENT CODING DYNC2H1 C protein_coding NM_001080463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 103229027 T C 0 228 0 0.2481 0.495 0.6816 0.4871 0.661 0.5337 0.318431 0.558415 0.665565 2 2235 54021 5915 3391 3433 32151 407 6489 2 5868 81986 7536 5758 4968 45756 618 11482 0 . 0 . 0 27 0,0,14,9 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D4039|4314|DYNC2H1|protein_coding|CODING|NM_001080463.1|84|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2566913 -0.692717 0.310254 27 4314 LOW 85 CODING DYNC2H1 A protein_coding NM_001080463.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 103270607 G A 0 228 0 0.6369 0.5377 0.4957 0.5327 0.4314 0.5481 0.621245 0.504222 0.451834 2 5980 58662 6316 4598 2792 29458 422 9096 2 9744 119428 11378 8502 6582 66014 890 16318 1 0 . 0 . 55 0,1,17,33 SPLICE_SITE_REGION+INTRON(LOW||||4314|DYNC2H1|protein_coding|CODING|NM_001080463.1|85|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10895417 -0.693147 0.387251 55 370 327 MODIFIER 7 CODING PDGFD C protein_coding NM_025208.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 103780095 G C 0 54 0 0.5605 0.4754 0.353 0.4603 0.4523 0.4867 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.726149 0 . 0 . 14 9,0,5,0 UTR_3_PRIME(MODIFIER||327||370|PDGFD|protein_coding|CODING|NM_025208.4|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.726149 rs1056205 -0.590765 0.521429 14 C360 370 tgT/tgC LOW 7 SILENT CODING PDGFD G protein_coding NM_025208.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 103780455 A G 0 222 0 0.5106 0.4615 0.3487 0.4603 0.4523 0.4857 0.481381 0.479695 0.478832 1 5035 54177 3568 3835 2823 30607 412 7897 2 10404 121362 11574 8620 6612 66732 908 16512 0.940424 0 . 0 . 131 40,24,36,21 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C360|370|PDGFD|protein_coding|CODING|NM_025208.4|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.836698 rs10791649 -0.693147 0.245318 131 341 LOW 5 CODING CASP12 A protein_coding NM_001191016.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104758035 G A 0 228 0 0.6248 0.8888 0.9582 0.997 0.994 0.9765 0 . 0 2 378 13909 179 198 1592 3883 183 7496 2 558 14230 188 198 1592 3896 184 7614 0 . 0 . 0 222 0,0,100,94 SPLICE_SITE_REGION+INTRON(LOW||||341|CASP12|protein_coding|CODING|NM_001191016.2|5|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs484438 -0.693147 0.787015 222 H273R 341 cAt/cGt MODERATE 5 MISSENSE CODING CASP12 C protein_coding NM_001191016.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104761100 T C 0 228 0 0.9932 0.9976 0.9971 1 1 0.999 0 . 0 2 677 14709 188 198 1592 4252 186 7616 2 684 14718 188 198 1592 4252 186 7618 0 . 0 . 0 66 0,0,48,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H273R|341|CASP12|protein_coding|CODING|NM_001191016.2|5|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs513131 -0.693147 0.252957 66 G238S 341 Ggt/Agt MODERATE 5 MISSENSE CODING CASP12 T protein_coding NM_001191016.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104761206 C T 0 228 0 0.9955 0.9986 0.9986 1 1 1 0 . 0 2 620 14412 186 198 1594 4010 184 7620 2 626 14418 186 198 1594 4010 184 7620 0 . 0 . 0 87 0,0,37,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G238S|341|CASP12|protein_coding|CODING|NM_001191016.2|5|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs647039 -0.693147 0.271613 87 R125* 341 Cga/Tga HIGH 3 NONSENSE CODING CASP12 A protein_coding NM_001191016.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104763117 G A 0 228 0 0.8351 0.9485 0.9798 0.998 0.999 0.9765 0 . 0 2 518 14187 182 198 1594 4006 184 7505 2 604 14394 188 198 1594 4008 184 7618 0 255 other 0 . 93 0,0,37,51 STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R125*|341|CASP12|protein_coding|CODING|NM_001191016.2|3|A) 0 . 0 . 0 1 0 . 1 (CASP12|CASP12|1|1.00) 60 0 0 1 (CASP12|CASP12|1|1.00) 0 rs497116 -0.693147 0.0191222 93 T68I 341 aCt/aTt MODERATE 2 MISSENSE CODING CASP12 A protein_coding NM_001191016.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104768000 G A 0 228 0 0.8593 0.9553 0.9827 0.998 0.999 0.9765 0 . 0 2 718 15132 202 204 1628 4683 192 7505 2 798 15334 208 204 1628 4686 192 7618 0 . 0 . 0 62 0,0,37,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T68I|341|CASP12|protein_coding|CODING|NM_001191016.2|2|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs693001 -0.693147 0.557614 62 V35 341 gtA/gtG LOW 2 SILENT CODING CASP12 C protein_coding NM_001191016.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104768098 T C 0 228 0 0.9629 0.9898 0.9971 1 1 1 0 . 0 2 777 15301 211 204 1618 4684 190 7617 2 800 15326 212 204 1618 4684 190 7618 0 . 0 . 0 95 0,0,51,36 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V35|341|CASP12|protein_coding|CODING|NM_001191016.2|2|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs555367 -0.693147 0.753669 95 L286 377 ctA/ctG LOW 6 SILENT CODING CASP4 C protein_coding NM_001225.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104819327 T C 0 228 0 0.8169 0.9493 0.9827 1 1 1 0.850817 0.949239 0.999651 2 8818 119508 11371 8644 6608 66652 903 16512 2 10400 121230 11468 8644 6608 66690 908 16512 0 . 0 . 0 124 0,0,59,54 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L286|377|CASP4|protein_coding|CODING|NM_001225.3|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9507 -0.693147 0.055452 124 447 LOW 9 CODING CASP5 T protein_coding NM_001136112.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104866461 A T 0 222 0 0.0552 0.3536 0.3559 0.5952 0.4573 0.3998 0.107856 0.326642 0.438707 1 1067 48103 3320 5216 2518 29440 367 6175 2 10394 120664 11444 8602 6572 66384 902 16366 0.635747 0 . 0 . 179 57,32,41,28 SPLICE_SITE_REGION+INTRON(LOW||||447|CASP5|protein_coding|CODING|NM_001136112.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.751735 rs540819 -0.693147 0.565146 179 L347V 447 Ctc/Gtc MODERATE 7 MISSENSE CODING CASP5 C protein_coding NM_001136112.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104869708 G C 0 222 0 0.4644 0.5292 0.4035 0.7728 0.4732 0.5123 0.443233 0.453699 0.45906 1 4653 56406 3608 6590 2679 30611 425 7840 2 10402 121354 11570 8648 6612 66706 908 16508 0.752798 0 . 0 COSM428310 119 20,39,19,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L347V|447|CASP5|protein_coding|CODING|NM_001136112.1|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.63638 rs523104 -0.693147 0.499249 119 447 LOW 3 CODING CASP5 G protein_coding NM_001136112.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104877803 A G 0 222 0 0.6286 0.3732 0.2478 0.256 0.341 0.271 0.581327 0.418769 0.335543 1 6098 39239 2189 2157 2067 22066 265 4397 2 10396 121032 11532 8642 6612 66576 906 16368 0.373501 0 . 0 . 283 87,54,72,34 SPLICE_SITE_REGION+INTRON(LOW||||447|CASP5|protein_coding|CODING|NM_001136112.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.813114 rs2282657 -0.693147 0.0239345 283 T119A 447 Acc/Gcc MODERATE 3 MISSENSE CODING CASP5 C protein_coding NM_001136112.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104877927 T C 0 222 0 0.646 0.4453 0.4683 0.2341 0.4443 0.3763 0.613987 0.499308 0.440568 1 6416 52748 5828 1883 2998 29247 378 5998 2 10402 121294 11520 8644 6612 66702 906 16508 0.854138 0 . 0 . 132 17,50,10,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T119A|447|CASP5|protein_coding|CODING|NM_001136112.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91896 rs507879 -0.693147 0.548144 132 404 372 MODIFIER 9 CODING CASP1 A protein_coding NM_001257118.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104896613 G A 0 6.3 0 0.3404 0.5447 0.5317 0.7302 0.5567 0.6268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||372||404|CASP1|protein_coding|CODING|NM_001257118.2|9|A),UPSTREAM(MODIFIER||2718||447|CASP5|protein_coding|CODING|NM_001136112.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1790203 -0.379885 0 1 404 141 MODIFIER 9 CODING CASP1 G protein_coding NM_001257118.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 104896844 A G 0 42.1 0 0.2027 0.23 0.1772 0.2639 0.2664 0.2321 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.783809 0 . 0 . 10 6,0,4,0 UTR_3_PRIME(MODIFIER||141||404|CASP1|protein_coding|CODING|NM_001257118.2|9|G),UPSTREAM(MODIFIER||2949||447|CASP5|protein_coding|CODING|NM_001136112.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1.00775 0 . 0.783809 rs1977989 -0.556411 0.66971 10 902 1149 MODIFIER 17 CODING GRIA4 T protein_coding NM_000829.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105851615 C T 0 228 0 0.8903 0.9329 0.9553 0.9752 0.9135 0.9509 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 107 0,0,71,23 UTR_3_PRIME(MODIFIER||1149||902|GRIA4|protein_coding|CODING|NM_000829.3|17|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs594592 -0.693147 0.233019 107 902 2098 MODIFIER 17 CODING GRIA4 A protein_coding NM_000829.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105852564 C A 0 201 0 0.0008 0.011182 0.0086 0.0278 0.0119 0.0092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.598676 0 . 0 . 79 43,2,28,4 UTR_3_PRIME(MODIFIER||2098||902|GRIA4|protein_coding|CODING|NM_000829.3|17|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.517796 rs118004392 -0.69312 0.273116 79 345 1418 MODIFIER 3 CODING MSANTD4 T protein_coding NM_032424.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105878844 C T 0 228 0 0.5242 0.5819 0.6499 0.5754 0.6014 0.5982 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980519 0 . 0 . 178 1,1,76,78 UTR_3_PRIME(MODIFIER||1418||345|MSANTD4|protein_coding|CODING|NM_032424.1|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.75 rs1043144 -0.693147 0.107847 178 612 1378 MODIFIER 3 CODING KBTBD3 A protein_coding NM_152433.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105922199 G A 0 9.7 0 0.8805 0.9277 0.9568 0.9425 0.9294 0.954 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1378||612|KBTBD3|protein_coding|CODING|NM_152433.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6591149 -0.379885 0 1 612 858 MODIFIER 3 CODING KBTBD3 T protein_coding NM_152433.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105922719 C T 0 46.3 0 0.8805 0.9277 0.9568 0.9425 0.9294 0.954 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||858||612|KBTBD3|protein_coding|CODING|NM_152433.3|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1940791 -0.453602 0.02 2 309 1320 MODIFIER 6 CODING AASDHPPT A protein_coding NM_015423.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105968954 G A 0 70 0 0.0015 0.0733 0.0245 0.2966 0.006 0.044 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||1320||309|AASDHPPT|protein_coding|CODING|NM_015423.2|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs80195741 -0.453602 0.06 3 309 1624 MODIFIER 6 CODING AASDHPPT A protein_coding NM_015423.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 105969258 T A 0 6.3 0 0.4516 0.2324 0.1138 0.3294 0.0616 0.0961 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1624||309|AASDHPPT|protein_coding|CODING|NM_015423.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1048683 -0.379885 0 1 763 3427 MODIFIER 9 CODING GUCY1A2 C protein_coding NM_001256424.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 106554848 T C 0 39.3 0 0.1959 0.102 0.1729 0.0843 0.0278 0.0194 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||3427||763|GUCY1A2|protein_coding|CODING|NM_001256424.1|9|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11211862 -0.453602 0.7 2 A593 763 gcC/gcT LOW 6 SILENT CODING GUCY1A2 A protein_coding NM_001256424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 106647222 G A 0 228 0 0.0212 0.0503 0.0389 0.0784 0.0547 0.0644 0.0304407 0.0420834 0.0480456 2 321 5869 383 759 497 3193 35 681 2 10380 120916 11494 8584 6600 66518 906 16434 1 0 . 0 . 135 1,0,52,72 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A593|763|GUCY1A2|protein_coding|CODING|NM_001256424.1|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs34690080 -0.693147 0.356337 135 N144 763 aaC/aaT LOW 3 SILENT CODING GUCY1A2 A protein_coding NM_001256424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 106849400 G A 0 228 0 0.0431 0.0905 0.049 0.1161 0.0885 0.1595 0.053612 0.0763194 0.0879479 2 550 10477 495 1126 550 5612 74 2070 2 10362 121064 11554 8604 6596 66542 900 16506 0 . 0 . 0 42 0,0,20,19 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N144|763|GUCY1A2|protein_coding|CODING|NM_001256424.1|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs35760785 -0.693144 0.0330851 42 A58 763 gcC/gcT LOW 1 SILENT CODING GUCY1A2 A protein_coding NM_001256424.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 106888608 G A 0 9.7 0 0.1142 0.2426 0.2608 0.122 0.3688 0.3978 0 . 0 1 49 1179 28 35 244 615 8 200 2 138 2326 44 106 616 1096 22 304 0 . 0 . 0 1 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A58|763|GUCY1A2|protein_coding|CODING|NM_001256424.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs3107973 -0.379885 0 1 894 401 MODIFIER 18 CODING CWF19L2 T protein_coding NM_152434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107197235 A T 0 39.3 0 0.2095 0.2562 0.2003 0.2927 0.3121 0.2638 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||401||894|CWF19L2|protein_coding|CODING|NM_152434.2|18|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1046095 -0.453602 0.26 2 894 380 MODIFIER 18 CODING CWF19L2 G protein_coding NM_152434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107197256 C G 0 61 0 0.2095 0.2564 0.2003 0.2927 0.3121 0.2648 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||380||894|CWF19L2|protein_coding|CODING|NM_152434.2|18|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1046094 -0.511536 0.519801 3 894 317 MODIFIER 18 CODING CWF19L2 C protein_coding NM_152434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107197319 T C 0 64 0 0.9856 0.7983 0.6484 0.7946 0.8141 0.6391 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||317||894|CWF19L2|protein_coding|CODING|NM_152434.2|18|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs512574 -0.511536 0.354794 3 894 100 MODIFIER 18 CODING CWF19L2 T protein_coding NM_152434.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107197536 C T 0 217 0 0.7269 0.5284 0.4438 0.502 0.501 0.3753 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.51037 0 . 0 . 67 32,3,27,2 UTR_3_PRIME(MODIFIER||100||894|CWF19L2|protein_coding|CODING|NM_152434.2|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.990947 rs630782 -0.693079 0.31677 67 Y894C 894 tAt/tGt MODERATE 18 MISSENSE CODING CWF19L2 C protein_coding NM_152434.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107197640 T C 0 222 0 0.2095 0.2562 0.2003 0.2927 0.3121 0.2638 0.217856 0.294661 0.333993 1 2254 35813 1821 2351 2152 22249 260 4726 2 10342 119458 11384 8582 6588 66098 892 15572 0.885003 0 . 0 . 118 33,23,20,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y894C|894|CWF19L2|protein_coding|CODING|NM_152434.2|18|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.781183 rs3758911 -0.693147 0.10394 118 667 225 MODIFIER 12 CODING ALKBH8 A protein_coding NM_001301010.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107375159 C A 0 142 0 0 0.0051917 0 0.0179 0.005 0.0031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.770381 0 . 0 . 22 10,1,10,1 UTR_3_PRIME(MODIFIER||225||667|ALKBH8|protein_coding|CODING|NM_001301010.1|12|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997846 rs148650310 -0.676189 0.0159422 22 667 LOW 10 CODING ALKBH8 A protein_coding NM_001301010.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107381765 G A 0 222 0 0.2511 0.3446 0.3444 0.1855 0.5537 0.4202 0.28974 0.473281 0.553111 1 714 10998 164 132 935 5543 135 3375 2 2400 22978 446 624 1680 9682 254 7892 0.648487 0 . 0 COSM147320 115 15,46,15,28 SPLICE_SITE_REGION+INTRON(LOW||||667|ALKBH8|protein_coding|CODING|NM_001301010.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.257653 rs386603385,rs654093 -0.693146 0.00305549 115 D243 667 gaT/gaC LOW 7 SILENT CODING ALKBH8 G protein_coding NM_001301010.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107420530 A G 0 222 0 0.5499 0.7115 0.6657 0.6627 0.8499 0.8701 0.600434 0.776172 0.852608 1 1281 17905 290 429 1486 7505 202 6712 2 2148 21712 410 622 1624 8754 242 7912 0.899035 0 . 0 . 173 39,37,40,33 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D243|667|ALKBH8|protein_coding|CODING|NM_001301010.1|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.549905 rs645056 -0.693147 0.000152118 173 31 65 MODIFIER 2 CODING SLN G protein_coding NM_003063.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107578721 C G 0 222 0 0.6989 0.6532 0.6441 0.8234 0.5736 0.5041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.312877 0 . 0 . 64 10,16,5,27 UTR_5_PRIME(MODIFIER||65||31|SLN|protein_coding|CODING|NM_003063.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992208 rs583362 -0.69312 0.658772 64 374 122 MODIFIER 1 CODING SLC35F2 T protein_coding NM_017515.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107729615 G T 0 60 0 0.2632 0.3425 0.3213 0.246 0.3847 0.5204 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,0,4 UTR_5_PRIME(MODIFIER||122||374|SLC35F2|protein_coding|CODING|NM_017515.4|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs2442683 -0.556411 0.176409 5 217 447 MODIFIER 2 CODING RAB39A A protein_coding NM_017516.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107833545 G A 0 135 0 0.1861 0.4681 0.6643 0.7014 0.5179 0.4182 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||447||217|RAB39A|protein_coding|CODING|NM_017516.2|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4754282 -0.651104 0.385012 8 217 927 MODIFIER 2 CODING RAB39A G protein_coding NM_017516.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107834025 C G 0 6.3 0 0.8298 0.9115 0.9438 0.9355 0.9374 0.9479 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||927||217|RAB39A|protein_coding|CODING|NM_017516.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1027733 -0.379885 0 1 217 1009 MODIFIER 2 CODING RAB39A A protein_coding NM_017516.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107834107 C A 0 9.7 0 0.8275 0.9109 0.9438 0.9355 0.9374 0.9479 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1009||217|RAB39A|protein_coding|CODING|NM_017516.2|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1027734 -0.379885 0 1 780 188 MODIFIER 1 CODING CUL5 C protein_coding NM_003478.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107879887 G C 0 198 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 24 0,0,23,1 UTR_5_PRIME(MODIFIER||188||780|CUL5|protein_coding|CODING|NM_003478.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10736442 -0.692831 0.20725 24 Q75 780 caA/caG LOW 3 SILENT CODING CUL5 G protein_coding NM_003478.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107917087 A G 0 228 0 0.3691 0.6621 0.745 0.9038 0.6561 0.7566 0.396184 0.569857 0.658795 2 4139 80994 8747 7769 4228 43775 613 11723 2 10330 121022 11538 8606 6596 66566 908 16478 0 . 0 . 0 65 0,0,16,40 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q75|780|CUL5|protein_coding|CODING|NM_003478.3|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7117111 -0.693147 0.0173829 65 780 2378 MODIFIER 19 CODING CUL5 A protein_coding NM_003478.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107977489 G A 0 164 0 0.5008 0.7586 0.8084 0.9454 0.7684 0.8691 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,0,19 UTR_3_PRIME(MODIFIER||2378||780|CUL5|protein_coding|CODING|NM_003478.3|19|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs15677 -0.69168 0.682472 19 427 9 MODIFIER 1 CODING ACAT1 A protein_coding NM_000019.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107992325 T A 0 228 0 0.0635 0.3137 0.4179 0.3601 0.341 0.502 0.0791768 0.197573 0.25818 2 162 6534 142 162 10 2249 61 3748 2 1590 16836 360 486 26 6320 162 7892 1 2 benign 0 . 70 0,1,28,32 UTR_5_PRIME(MODIFIER||9||427|ACAT1|protein_coding|CODING|NM_000019.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3741055 -0.693147 0.0901248 70 A5P 427 Gcg/Ccg MODERATE 1 MISSENSE CODING ACAT1 C protein_coding NM_000019.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 107992346 G C 0 228 0 0.1293 0.3319 0.4222 0.3601 0.3419 0.502 0.122419 0.209707 0.254406 2 234 6654 172 177 16 2233 62 3760 2 1442 16576 406 518 38 6110 156 7906 0 2 benign 0 . 70 0,0,22,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Ccg|A5P|427|ACAT1|protein_coding|CODING|NM_000019.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3741056 -0.693147 0.259628 70 1427 999 MODIFIER 18 CODING NPAT C protein_coding NM_002519.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108028670 T C 0 222 0 0.0023 0.0443 0.1772 0.0784 0.0169 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.612092 0 . 0 . 85 16,13,24,27 UTR_3_PRIME(MODIFIER||999||1427|NPAT|protein_coding|CODING|NM_002519.2|18|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.268635 rs3758910 -0.693147 0.123176 85 V575I 1427 Gtt/Att MODERATE 13 MISSENSE CODING NPAT T protein_coding NM_002519.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108043988 C T 0 228 0 0.652 0.6156 0.6729 0.4554 0.6302 0.6759 0.63385 0.593223 0.575154 2 6264 71732 7646 3840 4187 38618 526 10651 2 9774 120558 11554 8618 6610 66606 894 16502 0 . 0 . 0 24 0,0,10,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V575I|1427|NPAT|protein_coding|CODING|NM_002519.2|13|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2070661 -0.692352 0.814569 24 3056 4519 MODIFIER 1 CODING ATM A protein_coding NM_000051.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108093833 G A 0 57 0 0.2095 0.476 0.6369 0.4276 0.6213 0.6227 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||4519||3056|ATM|protein_coding|CODING|NM_000051.3|1|A),UPSTREAM(MODIFIER||468||1427|NPAT|protein_coding|CODING|NM_002519.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs189037 -0.511536 0.401962 3 N1983S 3056 aAt/aGt MODERATE 40 MISSENSE CODING ATM G protein_coding NM_000051.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108183167 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 10340 121308 11578 8654 6614 66706 908 16508 2 10340 121308 11578 8654 6614 66706 908 16508 0 2,2 benign,benign 0 . 154 0,0,81,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1983S|3056|ATM|protein_coding|CODING|NM_000051.3|40|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs659243 -0.693147 0.00608919 154 3056 3393 MODIFIER 63 CODING ATM T protein_coding NM_000051.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108239628 G T 0 9.7 0 0.3812 0.5345 0.6513 0.4325 0.6183 0.6779 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3393||3056|ATM|protein_coding|CODING|NM_000051.3|63|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4585 -0.379885 0 1 507 38 MODIFIER 8 CODING KDELC2 GA protein_coding NM_153705.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108345515 G GA 0 228 0 0.3941 0.483 0.5504 0.4563 0.4573 0.6094 0.411008 0.420194 0.424454 2 4010 55826 6701 4056 2630 28565 415 9449 2 9796 120210 11538 8594 6606 66524 896 16256 0 . 0 . 0 46 0,0,37,6 UTR_3_PRIME(MODIFIER||38||507|KDELC2|protein_coding|CODING|NM_153705.4|8|GA) 1 0 . 45 0.978261 1 1 1 1 0 60 0 0 1 0 . rs11374964 -0.693146 0.683573 46 N1967D 1989 Aat/Gat MODERATE 6 MISSENSE CODING EXPH5 C protein_coding NM_015065.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108380335 T C 0 228 0 1 1 1 1 1 1 0.998183 0.999385 1 2 10390 120776 11571 8654 6614 66575 904 16068 2 10402 120794 11576 8654 6614 66576 904 16068 0 . 0 . 0 90 0,0,55,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N1967D|1989|EXPH5|protein_coding|CODING|NM_015065.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1943382 -0.693147 0.0465607 90 G1663R 1989 Gga/Aga MODERATE 6 MISSENSE CODING EXPH5 T protein_coding NM_015065.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108381247 C T 0 228 0 0.028 0.2863 0.3689 0.6419 0.2465 0.2515 0.0626988 0.17795 0.236971 2 596 35451 5831 5768 2083 16419 283 4471 2 10406 121366 11562 8642 6614 66728 908 16506 0.578512 0 . 0 COSM147321 141 1,1,66,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G1663R|1989|EXPH5|protein_coding|CODING|NM_015065.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.826446 rs2640779 -0.693147 0.000831724 141 H1631 1989 caT/caC LOW 6 SILENT CODING EXPH5 G protein_coding NM_015065.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108381341 A G 0 222 0 0 0.0017971 0 0.0089 0 0 0 7.6935e-05 0.000116333 1 0 137 0 136 0 1 0 0 2 10402 121334 11578 8654 6614 66700 908 16478 0.0842159 0 . 0 . 96 19,28,23,23 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H1631|1989|EXPH5|protein_coding|CODING|NM_015065.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.813959 rs3802836 -0.693147 0.282202 96 S676N 1989 aGc/aAc MODERATE 6 MISSENSE CODING EXPH5 T protein_coding NM_015065.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108384207 C T 0 228 0 0.6982 0.6412 0.5533 0.8542 0.4384 0.6155 0.657201 0.501616 0.42194 2 6925 64123 7879 7569 3147 28486 477 9640 2 10402 121300 11578 8644 6610 66690 908 16468 0 . 0 . 0 75 0,0,24,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S676N|1989|EXPH5|protein_coding|CODING|NM_015065.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2846412 -0.693147 0.0900609 75 E137V 1989 gAg/gTg MODERATE 3 MISSENSE CODING EXPH5 A protein_coding NM_015065.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108409784 T A 0 228 0 0.0393 0.2524 0.3501 0.5804 0.17 0.2178 0.0638346 0.134098 0.170079 2 617 28178 5681 5195 1440 11557 217 3471 2 10406 121344 11556 8642 6614 66706 908 16512 0 . 0 . 0 112 0,0,49,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gTg|E137V|1989|EXPH5|protein_coding|CODING|NM_015065.2|3|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2640785 -0.693147 0.291262 112 R19G 1989 Agg/Ggg MODERATE 1 MISSENSE CODING EXPH5 C protein_coding NM_015065.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 108464209 T C 0 222 0 0.2012 0.3882 0.562 0.3839 0.495 0.4121 0.252612 0.400754 0.476617 1 2553 54791 6667 3242 3706 31294 420 6909 2 10406 121374 11578 8632 6608 66732 908 16510 0.409336 0 . 0 COSM147323 116 41,24,22,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R19G|1989|EXPH5|protein_coding|CODING|NM_015065.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.959606 rs2640738 -0.693139 0.186301 116 197 876 MODIFIER 2 CODING C11orf87 A protein_coding NM_207645.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 109295829 G A 0 222 0 0.0008 0.0095847 0 0.0456 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999987 0 . 0 . 129 54,6,51,12 UTR_3_PRIME(MODIFIER||876||197|C11orf87|protein_coding|CODING|NM_207645.3|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.708723 rs144849462 -0.693147 0.0961417 129 883 48 MODIFIER 1 CODING ZC3H12C TG protein_coding NM_033390.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 109964089 T TG 0 45.3 0 1 1 1 1 1 1 0.998435 0.9978 0.997552 2 6 62 2 0 0 38 0 16 2 6 62 2 0 0 38 0 16 0 . 0 . 0 2 0,0,2,0 UTR_5_PRIME(MODIFIER||48||883|ZC3H12C|protein_coding|CODING|NM_033390.1|1|TG) 1 0 . 2 1 1 1 1 1 0 60 0 0 . 0 . rs11395531 -0.453602 0.14 2 Q815 883 caA/caG LOW 6 SILENT CODING ZC3H12C G protein_coding NM_033390.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110036255 A G 0 198 0 0 0.0053914 0 0.0258 0 0.001 0.000258665 8.2481e-05 0 1 1 246 3 238 0 0 2 2 2 9352 115808 10904 8194 6452 64128 870 15908 0.605291 0 . 0 . 65 24,21,10,10 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q815|883|ZC3H12C|protein_coding|CODING|NM_033390.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.695144 rs74548991 -0.692067 0.000313928 65 S510 604 agC/agT LOW 13 SILENT CODING RDX A protein_coding NM_001260492.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110104019 G A 0 222 0 0 0.0011981 0 0.005 0 0.001 0 . 0 1 1 32 3 24 0 3 0 1 2 10406 121408 11576 8654 6614 66738 908 16512 0.289008 0 . 0 . 124 36,22,34,13 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S510|604|RDX|protein_coding|CODING|NM_001260492.1|13|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.426787 rs192239366 -0.693147 0.0151996 124 604 16873 MODIFIER 1 CODING RDX G protein_coding NM_001260492.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110167290 C G 0 9.7 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||16873||604|RDX|protein_coding|CODING|NM_001260492.1|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7107158 -0.379885 0 1 1191 1754 MODIFIER 16 CODING ARHGAP20 G protein_coding NM_020809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110448340 T G 0 222 0 0.1725 0.4123 0.4611 0.4563 0.5586 0.5061 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.990924 0 . 0 . 138 21,47,20,45 UTR_3_PRIME(MODIFIER||1754||1191|ARHGAP20|protein_coding|CODING|NM_020809.3|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0728447 rs3741337 -0.693147 0.431282 138 1191 231 MODIFIER 16 CODING ARHGAP20 A protein_coding NM_020809.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110449863 C A 0 9.2 0 0.0877 0.3868 0.4467 0.4524 0.5577 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 6 4,0,2,0 UTR_3_PRIME(MODIFIER||231||1191|ARHGAP20|protein_coding|CODING|NM_020809.3|16|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs3741338 -0.453602 0.36 6 D595 1191 gaT/gaC LOW 16 SILENT CODING ARHGAP20 G protein_coding NM_020809.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 110451885 A G 0 222 0 0.0454 0.0519 0.0562 0.0397 0.0706 0.0511 0.0497501 0.0647792 0.0724756 1 496 7844 347 287 407 5188 49 1070 2 10392 121318 11570 8648 6614 66686 906 16502 0.654017 0 . 0 . 140 36,38,29,25 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D595|1191|ARHGAP20|protein_coding|CODING|NM_020809.3|16|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.375729 rs10488765 -0.693147 0.907529 140 236 57 MODIFIER 4 CODING C11orf53 C protein_coding NM_198498.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111156836 T C 0 214 0 0.7186 0.733 0.8228 0.6022 0.7316 0.8252 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,1,40 UTR_3_PRIME(MODIFIER||57||236|C11orf53|protein_coding|CODING|NM_198498.2|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3087967 -0.693145 0.466148 41 124 2178 MODIFIER 2 CODING COLCA1 C protein_coding NM_001302644.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111164651 T C 0 222 0 0.1074 0.3045 0.2709 0.4187 0.2992 0.4826 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.251776 0 . 0 . 88 10,37,9,21 UTR_3_PRIME(MODIFIER||2178||124|COLCA1|protein_coding|CODING|NM_001302644.1|2|C),UPSTREAM(MODIFIER||4620||251|COLCA2|protein_coding|CODING|NM_001271458.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.23889 rs11213821 -0.693097 0.202989 88 124 354 MODIFIER 2 CODING COLCA1 C protein_coding NM_001302644.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111167557 A C 0 228 0 0.646 0.7031 0.8012 0.5992 0.7028 0.818 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 126 0,0,48,66 UTR_5_PRIME(MODIFIER||354||124|COLCA1|protein_coding|CODING|NM_001302644.1|2|C),UPSTREAM(MODIFIER||1714||251|COLCA2|protein_coding|CODING|NM_001271458.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6589218 -0.693147 0.123253 126 124 573 MODIFIER 2 CODING COLCA1 G protein_coding NM_001302644.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111167776 C G 0 228 0 0.6467 0.7039 0.8012 0.6002 0.7048 0.818 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 54 1,0,28,23 UTR_5_PRIME(MODIFIER||573||124|COLCA1|protein_coding|CODING|NM_001302644.1|2|G),UPSTREAM(MODIFIER||1495||251|COLCA2|protein_coding|CODING|NM_001271458.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7944895 -0.693147 0.51321 54 124 589 MODIFIER 2 CODING COLCA1 G protein_coding NM_001302644.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111167792 T G 0 222 0 0.1172 0.3069 0.2723 0.4187 0.2982 0.4816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999602 0 . 0 . 60 18,14,10,10 UTR_5_PRIME(MODIFIER||589||124|COLCA1|protein_coding|CODING|NM_001302644.1|2|G),UPSTREAM(MODIFIER||1479||251|COLCA2|protein_coding|CODING|NM_001271458.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.737386 rs10891245 -0.692067 0.297893 60 124 1564 MODIFIER 2 CODING COLCA1 T protein_coding NM_001302644.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111168767 C T 0 222 0 0.1082 0.3047 0.2695 0.4206 0.2982 0.4826 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.964927 0 . 0 . 127 39,28,13,37 UTR_5_PRIME(MODIFIER||1564||124|COLCA1|protein_coding|CODING|NM_001302644.1|2|T),UPSTREAM(MODIFIER||504||251|COLCA2|protein_coding|CODING|NM_001271458.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995623 rs7127721 -0.693147 0.0104017 127 A216 251 gcA/gcG LOW 5 SILENT CODING COLCA2 G protein_coding NM_001271458.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111179054 A G 0 222 0 0.0545 0.3606 0.4841 0.4345 0.5567 0.409 0.139451 0.431888 0.559082 1 272 9816 194 272 732 4712 108 3526 2 2146 21712 410 616 1620 8770 240 7910 0.926444 0 . 0 . 80 13,23,19,23 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A216|251|COLCA2|protein_coding|CODING|NM_001271458.1|5|G),UPSTREAM(MODIFIER||3281||124|COLCA1|protein_coding|CODING|NM_001302644.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987223 rs3087587 -0.693146 0.296068 80 251 265 MODIFIER 5 CODING COLCA2 T protein_coding NM_001271458.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111179427 C T 0 35.3 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 7 1,2,0,3 UTR_3_PRIME(MODIFIER||265||251|COLCA2|protein_coding|CODING|NM_001271458.1|5|T),UPSTREAM(MODIFIER||3654||124|COLCA1|protein_coding|CODING|NM_001302644.1||T) 0 0.5 1 0 . 0 . 0 . 0 60 0 0.861511 1 0 0.861511 rs192226887 -0.511536 0.401962 7 A133 223 gcC/gcA LOW 4 SILENT CODING BTG4 T protein_coding NM_017589.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111368047 G T 0 228 0 0.9244 0.9786 0.9899 1 1 1 0.942753 0.980609 1 2 9756 120172 11539 8652 6614 66560 901 16150 2 10404 120862 11572 8652 6614 66566 904 16150 0 . 0 . 0 124 0,0,51,59 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A133|223|BTG4|protein_coding|CODING|NM_017589.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs489078 -0.693147 0.0778976 124 P143 382 ccA/ccG LOW 4 SILENT CODING LAYN G protein_coding NM_001258390.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111420364 A G 0 228 0 0.8722 0.9639 0.9841 0.999 1 1 0.889368 0.962373 0.999767 2 9190 120058 11521 8652 6614 66688 904 16489 2 10400 121346 11576 8652 6614 66700 908 16496 0 . 0 . 0 90 0,0,37,36 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P143|382|LAYN|protein_coding|CODING|NM_001258390.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs634679 -0.693147 0.177812 90 382 431 MODIFIER 8 CODING LAYN T protein_coding NM_001258390.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111431614 C T 0 228 0 0.2526 0.6208 0.7046 0.9514 0.5924 0.7474 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 0,0,46,7 UTR_3_PRIME(MODIFIER||431||382|LAYN|protein_coding|CODING|NM_001258390.1|8|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs542275 -0.693147 0.098444 59 382 978 MODIFIER 8 CODING LAYN T protein_coding NM_001258390.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111432161 G T 0 6.3 0 0.2625 0.6546 0.7305 0.9514 0.668 0.8108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||978||382|LAYN|protein_coding|CODING|NM_001258390.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs568038 -0.379885 0 1 926 128 MODIFIER 1 CODING SIK2 C protein_coding NM_015191.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111473160 G C 0 23.7 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||128||926|SIK2|protein_coding|CODING|NM_015191.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs59552164 -0.379885 0 2 926 2589 MODIFIER 15 CODING SIK2 G protein_coding NM_015191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111597442 A G 0 228 0 0.8169 0.9439 0.9582 0.999 0.993 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,32,3 UTR_3_PRIME(MODIFIER||2589||926|SIK2|protein_coding|CODING|NM_015191.2|15|G),DOWNSTREAM(MODIFIER||190||667|PPP2R1B|protein_coding|CODING|NM_181699.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs533612 -0.693136 0.159702 38 L22 667 ctA/ctG LOW 1 SILENT CODING PPP2R1B C protein_coding NM_181699.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111637020 T C 0 228 0 0 0.0202 0.0159 0.0764 0.008 0.0051 0 0.000692521 0.00104724 2 5 1523 169 770 285 213 18 63 2 10358 120864 11562 8626 6606 66306 898 16508 0.117303 0 . 0 . 245 1,5,69,141 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L22|667|PPP2R1B|protein_coding|CODING|NM_181699.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.696039 rs76082838 -0.693147 0.000178574 245 H444 618 caC/caT LOW 13 SILENT CODING ALG9 A protein_coding NM_024740.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111708331 G A 0 222 0 0 0.0029952 0 0.0139 0 0.001 0 . 0 1 0 132 0 126 0 1 0 5 2 9728 119780 11396 8530 6590 66284 892 16360 0.858723 0 . 0 . 133 18,26,32,40 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H444|618|ALG9|protein_coding|CODING|NM_024740.2|13|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.30995 rs139516254 -0.693147 0.108389 133 618 HIGH 1 CODING ALG9 C protein_coding NM_024740.2 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111742145 CG C 0 228 0 1 1 1 1 1 1 0.998609 0.999604 1 2 574 12388 188 200 2 3672 134 7618 2 574 12388 188 200 2 3672 134 7618 0 . 0 . 0 110 0,0,97,3 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON(HIGH||||618|ALG9|protein_coding|CODING|NM_024740.2|1|C),DOWNSTREAM(MODIFIER||2634||624|FDXACB1|protein_coding|CODING|NM_138378.2||C) 1 0 . 107 0.972727 1 1 1 1 (ALG9|ALG9|1|1.00) 60 0 0 1 0 . rs10708475 -0.693147 0.0183563 110 I87N 624 aTc/aAc MODERATE 2 MISSENSE CODING FDXACB1 T protein_coding NM_138378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111749349 A T 0 228 0 0.9425 0.9247 0.9049 0.9712 0.832 0.9622 0.9192 0.861241 0.834755 2 7804 93470 8949 7498 5349 49358 692 13820 2 8420 105080 9564 7630 5940 58302 764 14460 0 . 0 . 0 124 0,0,51,63 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I87N|624|FDXACB1|protein_coding|CODING|NM_138378.2|2|T),UPSTREAM(MODIFIER||599||150|C11orf1|protein_coding|CODING|NM_022761.2||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs611010 -0.693147 0.470925 124 293 227 MODIFIER 6 CODING C11orf57 T protein_coding NM_001082969.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111953922 TA T 0 176 0 0.1755 0.4607 0.5562 0.3998 0.667 0.6288 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,3,5 UTR_3_PRIME(MODIFIER||227||293|C11orf57|protein_coding|CODING|NM_001082969.1|6|T),UPSTREAM(MODIFIER||3625||159|SDHD|protein_coding|CODING|NM_003002.3||T),DOWNSTREAM(MODIFIER||1616||98|TIMM8B|protein_coding|CODING|NM_012459.2||T) 0 . 0 9 0.9 1 1 0 . 0 60 0 0 0.900802 0 . rs3839946 -0.651104 0.433664 9 293 1787 MODIFIER 6 CODING C11orf57 A protein_coding NM_001082969.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111955483 G A 0 228 0 0.1762 0.4607 0.5562 0.4018 0.664 0.6288 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,9,9 UTR_3_PRIME(MODIFIER||1787||293|C11orf57|protein_coding|CODING|NM_001082969.1|6|A),UPSTREAM(MODIFIER||2065||159|SDHD|protein_coding|CODING|NM_003002.3||A),DOWNSTREAM(MODIFIER||56||98|TIMM8B|protein_coding|CODING|NM_012459.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs544184 -0.691153 0.524259 18 159 613 MODIFIER 4 CODING SDHD C protein_coding NM_003002.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 111966307 T C 0 9.7 0 0.7738 0.9361 0.9712 1 0.999 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 2 benign 0 . 1 0,0,0,1 UTR_3_PRIME(MODIFIER||613||159|SDHD|protein_coding|CODING|NM_003002.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs386606035,rs693441 -0.379885 0 1 193 230 MODIFIER 6 CODING IL18 C protein_coding NM_001562.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112014089 T C 0 114 0 0.8918 0.9541 0.9827 1 0.9761 0.9479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,5,0 UTR_3_PRIME(MODIFIER||230||193|IL18|protein_coding|CODING|NM_001562.3|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs360727 -0.590765 0.521429 6 193 167 MODIFIER 6 CODING IL18 G protein_coding NM_001562.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112014152 C G 0 142 0 0.8918 0.9541 0.9827 1 0.9761 0.9479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_3_PRIME(MODIFIER||167||193|IL18|protein_coding|CODING|NM_001562.3|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs360728 -0.651104 0.853153 8 S35 193 tcA/tcC LOW 4 SILENT CODING IL18 G protein_coding NM_001562.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112020916 T G 0 222 0 0.1846 0.2198 0.3357 0.1181 0.3082 0.1994 0.203641 0.272245 0.302414 1 1928 33844 3708 1210 2101 20651 249 3997 2 9700 119254 11394 8478 6580 65902 890 16310 0.999678 0 . 0 . 110 27,26,17,27 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S35|193|IL18|protein_coding|CODING|NM_001562.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740387 rs549908 -0.693146 0.705941 110 R12 123 agA/agG LOW 2 SILENT CODING TEX12 G protein_coding NM_031275.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112040027 A G 0 222 0 0.0507 0.1627 0.2637 0.1171 0.2664 0.183 0.0933667 0.198292 0.252036 1 853 28985 3410 1171 1923 17729 223 3676 2 10406 121392 11578 8644 6614 66734 906 16510 0.871774 0 . 0 . 178 29,44,30,53 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R12|123|TEX12|protein_coding|CODING|NM_031275.4|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0021453 rs360712,rs386584402 -0.693147 0.025326 178 L231P 579 cTg/cCg MODERATE 5 MISSENSE CODING BCO2 C protein_coding NM_031938.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112065434 T C 0 228 0 0.947 0.9704 0.9899 1 0.9801 0.9479 0.952522 0.972684 0.983011 2 9890 118529 11457 8650 6489 65484 891 15668 2 10402 121406 11578 8654 6614 66738 908 16512 0 . 0 . 0 102 0,0,53,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L231P|579|BCO2|protein_coding|CODING|NM_031938.5|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10891338 -0.693147 0.013025 102 I548L 579 Atc/Ctc MODERATE 12 MISSENSE CODING BCO2 C protein_coding NM_031938.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112088499 A C 0 228 0 0.9539 0.9866 0.9942 1 0.998 1 0.95343 0.984072 0.999767 2 9912 120831 11522 8654 6614 66711 906 16512 2 10406 121406 11576 8654 6614 66736 908 16512 0 . 0 . 0 86 0,0,57,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I548L|579|BCO2|protein_coding|CODING|NM_031938.5|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2217401 -0.693147 0.708772 86 S142P 207 Tct/Cct MODERATE 3 MISSENSE CODING PLET1 G protein_coding NM_001145024.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112123095 A G 0 222 0 0.3336 0.6458 0.7176 0.7778 0.7217 0.8027 0.399566 0.615418 0.709302 1 854 15130 274 501 1095 6257 167 5982 2 2078 21516 394 620 1622 8664 240 7898 0.925036 0 . 0 . 32 9,2,10,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S142P|207|PLET1|protein_coding|CODING|NM_001145024.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0327108 rs2564872 -0.689466 0.0677706 32 F7L 884 Ttc/Ctc MODERATE 2 MISSENSE CODING NCAM1 C protein_coding NM_001242607.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112832353 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 5710 66778 5088 4574 4154 35909 526 10817 2 5710 66780 5088 4574 4154 35910 526 10818 0 . 0 . 0 48 0,0,12,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F7L|884|NCAM1|protein_coding|CODING|NM_001242607.1|2|C),INTRAGENIC(MODIFIER|||||LOC101928847||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7105734 -0.693147 0.0324401 48 I8 884 atT/atC LOW 2 SILENT CODING NCAM1 C protein_coding NM_001242607.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 112832358 T C 0 228 0 1 1 1 1 1 1 0 . 0 2 5785 68023 5168 4696 4218 36676 532 10948 2 5786 68024 5168 4696 4218 36676 532 10948 1 0 . 0 . 42 0,1,10,30 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I8|884|NCAM1|protein_coding|CODING|NM_001242607.1|2|C),INTRAGENIC(MODIFIER|||||LOC101928847||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 1 1 0 1 rs6589347 -0.693145 0.00202042 42 V576 884 gtT/gtG LOW 15 SILENT CODING NCAM1 G protein_coding NM_001242607.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113103996 T G 0 228 0 0.9077 0.6679 0.5014 0.7312 0.506 0.5634 0.854207 0.639527 0.532977 2 8323 66358 5548 6233 3066 34073 456 8659 2 9694 118290 11176 8512 6478 65484 882 16064 0 . 0 . 0 114 0,0,39,64 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtG|V576|884|NCAM1|protein_coding|CODING|NM_001242607.1|15|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386600109,rs584427 -0.693147 0.00103651 114 705 LOW 7 CODING TTC12 A protein_coding NM_017868.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113200709 G A 0 222 0 0.6815 0.6088 0.5749 0.5347 0.6441 0.5746 0.68219 0.650762 0.63466 1 7059 74397 5041 4551 4488 42820 588 9850 2 10406 121352 11554 8640 6612 66722 908 16510 0.780078 0 . 0 . 229 39,71,40,50 SPLICE_SITE_REGION+INTRON(LOW||||705|TTC12|protein_coding|CODING|NM_017868.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.107243 rs2303380 -0.693147 0.00662469 229 705 LOW 11 CODING TTC12 C protein_coding NM_017868.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113212553 T C 0 222 0 0.292 0.2869 0.2464 0.4752 0.163 0.2423 0.267378 0.188241 0.147696 1 2893 24612 2456 4109 1497 9738 179 3740 2 10406 121366 11572 8634 6614 66722 908 16510 0.966781 0 . 0 . 104 36,24,27,10 SPLICE_SITE_REGION+INTRON(LOW||||705|TTC12|protein_coding|CODING|NM_017868.3|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.200198 rs6589372 -0.693141 0.347197 104 S85 765 tcT/tcC LOW 2 SILENT CODING ANKK1 C protein_coding NM_178510.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113264272 T C 0 222 0 0.3502 0.526 0.5692 0.5536 0.675 0.5511 0.44713 0.600633 0.673653 1 4036 73556 5170 4834 4464 44908 579 9565 2 9798 120628 11536 8600 6596 66690 900 16508 0.898648 0 . 0 . 108 32,25,21,23 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S85|765|ANKK1|protein_coding|CODING|NM_178510.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823472 rs17115439 -0.693146 0.199428 108 I151 765 atA/atC LOW 2 SILENT CODING ANKK1 C protein_coding NM_178510.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113264470 A C 0 222 0 0.8079 0.6605 0.6095 0.5546 0.6799 0.5869 0.791531 0.715799 0.677676 1 7650 77736 5361 4813 4462 44878 593 9979 2 9806 120006 11512 8556 6602 66404 892 16234 0.492174 0 . 0 . 93 16,34,24,15 SYNONYMOUS_CODING(LOW|SILENT|atA/atC|I151|765|ANKK1|protein_coding|CODING|NM_178510.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.365844 rs4938013 -0.693144 0.523504 93 A239T 765 Gcg/Acg MODERATE 5 MISSENSE CODING ANKK1 A protein_coding NM_178510.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113266821 G A 0 222 0 0.3744 0.3205 0.3069 0.4058 0.1819 0.3119 0.307806 0.223047 0.181927 1 3201 29665 5418 3464 1286 11464 169 4663 2 9804 120604 11566 8598 6612 66628 896 16500 0.680276 0 . 0 . 106 32,19,30,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A239T|765|ANKK1|protein_coding|CODING|NM_178510.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.608354 rs7118900 -0.693147 0.535388 106 G442R 765 Ggc/Cgc MODERATE 8 MISSENSE CODING ANKK1 C protein_coding NM_178510.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113270015 G C 0 222 0 0.4259 0.5493 0.6066 0.4663 0.6829 0.6237 0.484543 0.624804 0.695447 1 3287 62362 6117 3270 3332 37336 450 8570 2 6810 94126 8758 6508 4976 53320 688 13066 0.755962 0 . 0 COSM428436 70 22,18,16,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Cgc|G442R|765|ANKK1|protein_coding|CODING|NM_178510.1|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.839987 rs4938016 -0.692976 0.0987409 70 Y561 765 taC/taT LOW 8 SILENT CODING ANKK1 T protein_coding NM_178510.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113270374 C T 0 228 0 0.5242 0.7694 0.8473 0.9514 0.8161 0.8098 0.626072 0.756086 0.820601 2 4570 81567 8350 6897 4537 45180 587 11446 2 7422 99412 9378 7186 5236 55538 712 13940 0 . 0 . 0 47 0,0,22,22 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y561|765|ANKK1|protein_coding|CODING|NM_178510.1|8|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2734848,rs386572907 -0.693146 0.840029 47 E713K 765 Gag/Aag MODERATE 8 MISSENSE CODING ANKK1 A protein_coding NM_178510.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113270828 G A 0 222 0 0.385 0.3257 0.3112 0.4058 0.1879 0.3149 0.326802 0.235393 0.190374 1 3324 30556 5277 3412 1423 12188 172 4760 2 8954 110734 10786 7990 6070 60502 798 15634 0.880577 5 pathogenic 0 . 189 53,34,53,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E713K|765|ANKK1|protein_coding|CODING|NM_178510.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.65726 rs1800497 -0.693147 0.290287 189 765 76 MODIFIER 8 CODING ANKK1 G protein_coding NM_178510.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113271065 T G 0 179 0 0.8192 0.8574 0.866 0.9524 0.8171 0.8466 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,0,53 UTR_3_PRIME(MODIFIER||76||765|ANKK1|protein_coding|CODING|NM_178510.1|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2734847 -0.693147 0.00260449 53 443 376 MODIFIER 8 CODING DRD2 C protein_coding NM_000795.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113281073 G C 0 222 0 0.3404 0.5218 0.6037 0.4673 0.6938 0.5879 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.339254 0 . 0 . 60 16,10,18,12 UTR_3_PRIME(MODIFIER||376||443|DRD2|protein_coding|CODING|NM_000795.3|8|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.992438 rs6279 -0.693097 0.35716 60 443 52 MODIFIER 8 CODING DRD2 T protein_coding NM_000795.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113281397 C T 0 222 0 0.1399 0.4669 0.5951 0.4673 0.6918 0.5859 0.229977 0.556449 0.70005 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.96096 0 . 0 . 113 26,22,20,33 UTR_3_PRIME(MODIFIER||52||443|DRD2|protein_coding|CODING|NM_000795.3|8|T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.350273 rs6276 -0.693147 0.405048 113 H313 443 caT/caC LOW 7 SILENT CODING DRD2 G protein_coding NM_000795.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113283477 A G 0 222 0 0.3434 0.5266 0.6066 0.4712 0.6938 0.6022 0.387778 0.596275 0.703096 1 3888 77776 7939 3980 4418 46542 577 10432 2 10404 121314 11576 8616 6590 66708 908 16512 0.479792 0 . 0 . 156 22,57,23,37 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H313|443|DRD2|protein_coding|CODING|NM_000795.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.144561 rs386602147,rs6275 -0.693147 0.141219 156 443 50445 MODIFIER 1 CODING DRD2 C protein_coding NM_000795.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113345818 G C 0 64 0 0.4297 0.7574 0.8429 0.8631 0.9135 0.8701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.793923 0 . 0 . 12 2,6,1,3 UTR_5_PRIME(MODIFIER||50445||443|DRD2|protein_coding|CODING|NM_000795.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.310905 rs7116768 -0.556411 0.348933 12 F369L 457 Ttc/Ctc MODERATE 11 MISSENSE CODING TMPRSS5 G protein_coding NM_030770.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113561054 A G 0 222 0 0.9637 0.7702 0.7594 0.748 0.6362 0.6769 0.913557 0.73615 0.64751 1 7107 69117 7093 5525 3576 36537 509 8770 2 7762 99320 9276 7618 5538 55874 706 12546 0.899794 0 . 0 . 54 21,5,13,4 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Ctc|F369L|457|TMPRSS5|protein_coding|CODING|NM_030770.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.180444 rs7110736 -0.690438 0.381345 54 L368 457 Ttg/Ctg LOW 11 SILENT CODING TMPRSS5 G protein_coding NM_030770.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113561057 A G 0 222 0 0.9637 0.7702 0.7594 0.748 0.6362 0.6769 0.912683 0.734798 0.646045 1 7208 69993 7218 5594 3656 36936 516 8865 2 7870 100544 9428 7710 5642 56508 716 12670 0.834174 0 . 0 . 52 19,6,13,4 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L368|457|TMPRSS5|protein_coding|CODING|NM_030770.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.337733 rs7110738 -0.690438 0.381345 52 A39 457 gcA/gcG LOW 3 SILENT CODING TMPRSS5 C protein_coding NM_030770.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113570405 T C 0 222 0 0.9675 0.7708 0.7565 0.749 0.6352 0.6769 0.919408 0.742133 0.652909 1 4341 37891 2524 2417 1722 19999 321 6567 2 4686 51794 3122 3132 2488 28652 426 9288 0.946181 0 . 0 . 115 22,43,15,28 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A39|457|TMPRSS5|protein_coding|CODING|NM_030770.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.333905 rs4936280 -0.693146 0.398009 115 T1048 1077 acA/acT LOW 25 SILENT CODING USP28 A protein_coding NM_020886.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113670052 T A 0 228 0 0.8933 0.9702 0.9885 1 1 1 0.899364 0.965676 0.999651 2 9316 120239 11525 8654 6614 66721 902 16507 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 106 0,0,38,62 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T1048|1077|USP28|protein_coding|CODING|NM_020886.3|25|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2459971 -0.693147 0.247059 106 S735 1077 tcG/tcA LOW 18 SILENT CODING USP28 T protein_coding NM_020886.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113679119 C T 0 228 0 0.6339 0.7905 0.853 0.874 0.837 0.8241 0.657428 0.763737 0.818203 2 6806 99324 10472 7732 5478 54598 724 13514 2 10400 121400 11576 8654 6612 66738 908 16512 0 . 0 . 0 13 0,0,2,9 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S735|1077|USP28|protein_coding|CODING|NM_020886.3|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2465647 -0.676189 0.555357 13 516 24 MODIFIER 1 CODING HTR3A C protein_coding NM_213621.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113846006 T C 0 228 0 0.4992 0.7518 0.8314 0.8532 0.7823 0.9008 0.547024 0.706711 0.788524 2 5267 92157 9664 7302 4679 50605 675 13965 2 9400 115722 10978 8370 6040 64086 846 16002 0 . 0 . 0 64 0,0,40,20 UTR_5_PRIME(MODIFIER||24||516|HTR3A|protein_coding|CODING|NM_213621.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1062613 -0.693147 0.22194 64 516 258 MODIFIER 8 CODING HTR3A C protein_coding NM_213621.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 113860743 G C 0 125 0 0.6641 0.906 0.964 1 0.998 1 0 . 0 2 218 11410 125 172 8 3261 124 7502 2 276 11482 126 172 8 3264 124 7512 0 . 0 . 0 5 0,0,1,4 UTR_3_PRIME(MODIFIER||258||516|HTR3A|protein_coding|CODING|NM_213621.3|8|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1150219 -0.590765 0.194159 5 G140 559 ggA/ggG LOW 3 SILENT CODING NXPE2 G protein_coding NM_182495.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 114569054 A G 0 222 0 0.674 0.7626 0.8329 0.8224 0.7773 0.7556 0.715318 0.762155 0.782527 1 6793 95205 10149 7192 5796 52170 710 12395 2 9886 120020 11478 8590 6582 66138 896 16450 0.461461 0 . 0 . 197 44,43,58,36 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G140|559|NXPE2|protein_coding|CODING|NM_182495.5|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.387424 rs1712838 -0.693147 0.283679 197 471 2192 MODIFIER 12 CODING CADM1 G protein_coding NM_001301043.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 115045002 T G 0 85 0 0.2731 0.2087 0.1383 0.2937 0.163 0.1309 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.398871 0 . 0 . 17 6,0,10,0 UTR_3_PRIME(MODIFIER||2192||471|CADM1|protein_coding|CODING|NM_001301043.1|12|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.0844109 rs3210211 -0.670168 0.563606 17 471 1957 MODIFIER 12 CODING CADM1 C protein_coding NM_001301043.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 115045237 T C 0 222 0 0.2995 0.3542 0.3963 0.1954 0.5308 0.3804 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.712697 0 . 0 . 126 29,26,32,28 UTR_3_PRIME(MODIFIER||1957||471|CADM1|protein_coding|CODING|NM_001301043.1|12|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.450667 rs4445669 -0.693147 0.376933 126 P160 619 ccG/ccA LOW 4 SILENT CODING BUD13 T protein_coding NM_032725.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116633825 C T 0 222 0 0.6785 0.5451 0.6023 0.381 0.4821 0.5583 0.621536 0.525627 0.47649 1 6560 62378 6842 3771 3658 32356 494 8697 2 10394 120450 11566 8620 6610 66422 906 15932 0.995403 0 . 0 . 91 30,13,38,7 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P160|619|BUD13|protein_coding|CODING|NM_032725.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973055 rs918144 -0.693147 0.616226 91 459 724 MODIFIER 14 CODING ZPR1 C protein_coding NM_003904.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116648917 G C 0 9.7 0 0.7791 0.7778 0.7233 0.7599 0.838 0.771 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||724||459|ZPR1|protein_coding|CODING|NM_003904.4|14|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs964184 -0.379885 0 1 366 158 MODIFIER 4 CODING APOA5 A protein_coding NM_001166598.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116660686 G A 0 222 0 0.9939 0.8742 0.8674 0.7619 0.9085 0.7975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.646625 255 other 0 . 67 30,6,25,3 UTR_3_PRIME(MODIFIER||158||366|APOA5|protein_coding|CODING|NM_001166598.1|4|A),UPSTREAM(MODIFIER||1932||459|ZPR1|protein_coding|CODING|NM_003904.4||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976829 rs2266788 -0.693054 0.653003 67 366 3 MODIFIER 2 CODING APOA5 T protein_coding NM_001166598.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116662579 C T 0 222 0 0.8396 0.8245 0.8458 0.7123 0.9175 0.8088 0.855066 0.905495 0.931331 1 8749 106079 9389 6173 5993 61573 803 13399 2 10320 120560 11478 8570 6522 66274 900 16496 0.874196 0 . 0 . 103 16,25,25,23 UTR_5_PRIME(MODIFIER||3||366|APOA5|protein_coding|CODING|NM_001166598.1|2|T),UPSTREAM(MODIFIER||3825||459|ZPR1|protein_coding|CODING|NM_003904.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992407 rs651821 -0.693147 0.242394 103 S147N 396 aGc/aAc MODERATE 3 MISSENSE CODING APOA4 T protein_coding NM_000482.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116692334 C T 0 222 0 0.8941 0.7592 0.7565 0.6379 0.826 0.635 0.880736 0.873711 0.870112 1 9051 96729 8645 5703 5016 56701 703 10910 2 10214 119586 11370 8438 6542 65754 898 16370 0.794645 0 . 0 . 128 26,42,23,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S147N|396|APOA4|protein_coding|CODING|NM_000482.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.916874 rs5104 -0.693147 0.261569 128 T29 396 acG/acA LOW 2 SILENT CODING APOA4 T protein_coding NM_000482.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116693464 C T 0 222 0 0.8578 0.7198 0.7233 0.5823 0.7982 0.592 0.847796 0.838541 0.833799 1 8858 93925 8624 5385 4845 55265 666 10282 2 10406 121380 11568 8640 6612 66736 908 16510 0.99958 0 . 0 . 303 41,116,30,93 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T29|396|APOA4|protein_coding|CODING|NM_000482.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.858825 rs5092 -0.693147 0.00414604 303 99 40 MODIFIER 4 CODING APOC3 C protein_coding NM_000040.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 116703640 G C 0 222 0 0.8351 0.7658 0.7709 0.6627 0.8757 0.6616 0.845525 0.885409 0.905843 1 8706 101441 9068 5979 5718 59844 752 11374 2 10310 120922 11534 8616 6602 66442 906 16512 0.894293 0 . 0 . 236 32,63,39,73 UTR_3_PRIME(MODIFIER||40||99|APOC3|protein_coding|CODING|NM_000040.1|4|C),DOWNSTREAM(MODIFIER||2829||267|APOA1|protein_coding|CODING|NM_000039.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.945334 rs5128 -0.693147 0.0505568 236 785 149 MODIFIER 17 CODING PCSK7 G protein_coding NM_004716.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117076564 A G 0 228 0 0.5756 0.4605 0.3156 0.5754 0.2068 0.5501 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 25 0,0,6,19 UTR_3_PRIME(MODIFIER||149||785|PCSK7|protein_coding|CODING|NM_004716.3|17|G),DOWNSTREAM(MODIFIER||1056||201|TAGLN|protein_coding|CODING|NM_001001522.1||G) 0 . 0 . 0 1 0 . 0 . 57 0 0 0.463135 0 . rs1242127,rs55766412 -0.692914 0.471319 25 785 5 MODIFIER 17 CODING PCSK7 C protein_coding NM_004716.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117076708 T C 0 228 0 0.6195 0.5096 0.3617 0.6349 0.2634 0.59 0 . 0 2 932 6403 336 638 287 3000 50 1160 2 1754 17118 900 1128 858 10318 138 2022 0 . 0 . 0 17 0,0,10,7 UTR_3_PRIME(MODIFIER||5||785|PCSK7|protein_coding|CODING|NM_004716.3|17|C),DOWNSTREAM(MODIFIER||1200||201|TAGLN|protein_coding|CODING|NM_001001522.1||C) 0 . 0 . 0 1 0 . 1 0 53 0 0 0.865847 0 . rs35186251 -0.690438 0.427172 17 T679 785 acT/acC LOW 17 SILENT CODING PCSK7 G protein_coding NM_004716.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117077034 A G 0 228 0 0.6989 0.5623 0.4308 0.6538 0.3091 0.637 0 . 0 2 6426 46326 4331 5609 2078 18314 337 9231 2 10080 110482 10716 8406 5776 58808 830 15866 0 . 0 . 0 182 0,0,81,78 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T679|785|PCSK7|protein_coding|CODING|NM_004716.3|17|G),DOWNSTREAM(MODIFIER||1526||201|TAGLN|protein_coding|CODING|NM_001001522.1||G) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.403567 0 . rs28590104 -0.693147 0.114752 182 501 3730 MODIFIER 9 CODING BACE1 C protein_coding NM_012104.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117156552 T C 0 228 0 0.9357 0.8361 0.7421 0.9355 0.5974 0.911 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,19,2 UTR_3_PRIME(MODIFIER||3730||501|BACE1|protein_coding|CODING|NM_012104.4|9|C),DOWNSTREAM(MODIFIER||148||703|RNF214|protein_coding|CODING|NM_001077239.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7083 -0.692352 0.277929 21 501 2904 MODIFIER 9 CODING BACE1 G protein_coding NM_012104.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117157378 A G 0 228 0 0.9955 0.9834 0.9697 1 0.9493 0.9949 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 102 0,0,74,18 UTR_3_PRIME(MODIFIER||2904||501|BACE1|protein_coding|CODING|NM_012104.4|9|G),DOWNSTREAM(MODIFIER||974||703|RNF214|protein_coding|CODING|NM_001077239.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs649555 -0.693147 0.0591385 102 501 1424 MODIFIER 9 CODING BACE1 G protein_coding NM_012104.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117158858 A G 0 120 0 0.0061 0.0677 0.0432 0.1379 0.0666 0.0971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.826565 0 . 0 . 26 0,12,0,14 UTR_3_PRIME(MODIFIER||1424||501|BACE1|protein_coding|CODING|NM_012104.4|9|G),DOWNSTREAM(MODIFIER||2454||703|RNF214|protein_coding|CODING|NM_001077239.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.953497 rs1047857,rs386513192 -0.686358 0.113622 26 C481R 501 Tgc/Cgc MODERATE 9 MISSENSE CODING BACE1 G protein_coding NM_012104.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117160347 A G 0 228 0 1 1 1 1 1 1 1 0.999538 0.999302 2 10404 121368 11578 8654 6614 66699 908 16511 2 10404 121410 11578 8654 6614 66740 908 16512 0 . 0 . 0 98 0,0,68,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C481R|501|BACE1|protein_coding|CODING|NM_012104.4|9|G),DOWNSTREAM(MODIFIER||3943||703|RNF214|protein_coding|CODING|NM_001077239.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs539765 -0.693147 0.487946 98 G391 501 ggC/ggA LOW 8 SILENT CODING BACE1 T protein_coding NM_012104.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117161295 G T 0 222 0 0 0.0025959 0 0.0129 0 0 0.000227169 7.6959e-05 0 1 3 113 0 106 0 0 0 4 2 10404 121364 11560 8654 6610 66722 906 16508 0.0468467 0 . 0 . 184 59,33,39,36 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G391|501|BACE1|protein_coding|CODING|NM_012104.4|8|T),DOWNSTREAM(MODIFIER||4891||703|RNF214|protein_coding|CODING|NM_001077239.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.944532 rs11216349 -0.693147 0.0572859 184 501 LOW 5 CODING BACE1 A protein_coding NM_012104.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117163765 C A 0 228 0 0.9614 0.853 0.7723 0.9315 0.6272 0.9151 0.90527 0.719486 0.624302 2 9494 89505 9840 8181 4792 42029 684 14485 2 10406 121346 11578 8654 6614 66698 906 16490 0 . 0 . 0 182 0,0,75,90 SPLICE_SITE_REGION+INTRON(LOW||||501|BACE1|protein_coding|CODING|NM_012104.4|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs490460 -0.693147 0.130051 182 V262 501 gtG/gtC LOW 5 SILENT CODING BACE1 G protein_coding NM_012104.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117163824 C G 0 222 0 0.5363 0.5535 0.549 0.6498 0.4076 0.6309 0.519991 0.437817 0.395717 1 5465 58513 7492 5692 2918 26655 430 9861 2 10406 121380 11576 8628 6614 66736 908 16512 0.96812 0 . 0 . 139 16,46,21,46 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V262|501|BACE1|protein_coding|CODING|NM_012104.4|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979666 rs638405 -0.693147 0.0409823 139 P494 1460 ccT/ccC LOW 13 SILENT CODING CEP164 C protein_coding NM_014956.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117252489 T C 0 228 0 0.9599 0.9014 0.9092 0.8452 0.9314 0.8436 0.950524 0.935927 0.928455 2 7198 87224 8238 6341 3816 49186 637 11808 2 7506 95600 9446 7418 3994 52952 680 13604 1 0 . 0 . 79 0,1,29,44 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P494|1460|CEP164|protein_coding|CODING|NM_014956.4|13|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs897836 -0.693147 0.523111 79 Q1119R 1460 cAg/cGg MODERATE 27 MISSENSE CODING CEP164 G protein_coding NM_014956.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117267884 A G 0 222 0 0.5318 0.4633 0.3386 0.381 0.5358 0.4693 0.512494 0.533862 0.544809 1 5501 58846 2632 2869 3504 36107 439 7794 2 10398 121284 11566 8622 6598 66682 906 16512 0.986883 0 . 0 . 40 7,12,13,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1119R|1460|CEP164|protein_coding|CODING|NM_014956.4|27|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994149 rs573455 -0.692352 0.492232 40 S1433 1460 tcG/tcT LOW 33 SILENT CODING CEP164 T protein_coding NM_014956.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117282800 G T 0 222 0 0.9599 0.9083 0.9251 0.8284 0.9702 0.8456 0.958428 0.964599 0.967761 1 10033 113906 10201 7297 6483 64611 874 14407 2 10406 121396 11578 8648 6614 66732 908 16510 0.959577 0 . 0 . 56 16,14,15,4 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcT|S1433|1460|CEP164|protein_coding|CODING|NM_014956.4|33|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979167 rs522885 -0.69168 0.478545 56 1460 207 MODIFIER 33 CODING CEP164 T protein_coding NM_014956.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117283091 C T 0 225 0 0.4864 0.5323 0.5591 0.5 0.6849 0.4519 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 10 0,0,5,5 UTR_3_PRIME(MODIFIER||207||1460|CEP164|protein_coding|CODING|NM_014956.4|33|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.952347 0 . rs2279013 -0.670168 0.356497 10 1460 792 MODIFIER 33 CODING CEP164 C protein_coding NM_014956.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117283676 T C 0 25.9 0 0.6536 0.53 0.4049 0.3968 0.6312 0.4847 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,0,2 UTR_3_PRIME(MODIFIER||792||1460|CEP164|protein_coding|CODING|NM_014956.4|33|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs8258 -0.453602 0.02 3 L1439 2113 ctG/ctA LOW 23 SILENT CODING DSCAML1 T protein_coding NM_020693.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117309989 C T 0 222 0 0.1997 0.2522 0.1758 0.5565 0.1064 0.2137 0.187188 0.127751 0.0972998 1 2013 20246 2148 5127 588 6649 151 3570 2 10396 120834 11574 8622 6614 66536 896 16196 0.992359 0 . 0 . 163 35,32,39,35 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L1439|2113|DSCAML1|protein_coding|CODING|NM_020693.3|23|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974091 rs11216386 -0.693147 0.606578 163 T1428 2113 acT/acC LOW 23 SILENT CODING DSCAML1 G protein_coding NM_020693.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117310022 A G 0 222 0 0.3116 0.3041 0.3012 0.5605 0.1233 0.2178 0.282144 0.166077 0.106611 1 2966 24708 4701 5170 643 7363 167 3698 2 10394 121236 11564 8624 6612 66646 906 16490 0.979497 0 . 0 COSM147329 129 21,48,19,37 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1428|2113|DSCAML1|protein_coding|CODING|NM_020693.3|23|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99975 rs11216387 -0.693147 0.0275382 129 Q1127 2113 caA/caG LOW 17 SILENT CODING DSCAML1 C protein_coding NM_020693.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117335722 T C 0 228 0 0.8585 0.7358 0.6787 0.8958 0.501 0.6871 0.791004 0.615053 0.524907 2 8290 74562 8756 7798 3667 34505 541 11005 2 10400 121366 11572 8650 6610 66716 906 16512 0 . 0 . 0 112 0,0,76,19 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1127|2113|DSCAML1|protein_coding|CODING|NM_020693.3|17|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs538847 -0.693147 0.200533 112 P666 2113 ccC/ccT LOW 9 SILENT CODING DSCAML1 A protein_coding NM_020693.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117376413 G A 0 222 0 0.143 0.0877 0.0764 0.0833 0.0507 0.0634 0.126079 0.0797291 0.0559823 1 1312 8354 740 755 290 3655 76 1526 2 10346 120524 11512 8612 6368 66346 892 16448 0.322742 0 . 0 . 257 51,59,57,61 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P666|2113|DSCAML1|protein_coding|CODING|NM_020693.3|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.925019 rs34138305 -0.693147 0.192977 257 H232N 2113 Cac/Aac MODERATE 4 MISSENSE CODING DSCAML1 T protein_coding NM_020693.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117403235 G T 0 222 0 0.4796 0.4527 0.3732 0.5417 0.2654 0.5736 0.437983 0.322687 0.263617 1 4704 44234 4606 4604 2435 18270 349 9266 2 10396 120638 11552 8634 6610 66398 906 16142 0.953749 0 . 0 COSM147330 124 26,28,25,26 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Cac/Aac|H232N|2113|DSCAML1|protein_coding|CODING|NM_020693.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.878182 rs3741280 -0.693147 0.0466025 124 95 2580 MODIFIER 8 CODING FXYD6 C protein_coding NM_001164831.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117707937 T C 0 20.4 0 0.6339 0.6198 0.6254 0.7381 0.4602 0.6391 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.333333 0 . 0 . 5 1,2,2,0 UTR_3_PRIME(MODIFIER||2580||95|FXYD6|protein_coding|CODING|NM_001164831.2|8|C),INTRON(MODIFIER||||144|FXYD6-FXYD2|protein_coding|CODING|NM_001204268.1|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.666667 rs3087563 -0.453602 0.32 5 567 1557 MODIFIER 13 CODING TMPRSS13 G protein_coding NM_001077263.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117771397 C G 0 105 0 0.9758 0.9934 0.9986 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,2 UTR_3_PRIME(MODIFIER||1557||567|TMPRSS13|protein_coding|CODING|NM_001077263.2|13|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs568060 -0.556411 0.0949329 4 567 1066 MODIFIER 13 CODING TMPRSS13 C protein_coding NM_001077263.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117771888 A C 0 125 0 0.8245 0.9046 0.9337 0.8869 0.9652 0.9479 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||1066||567|TMPRSS13|protein_coding|CODING|NM_001077263.2|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs572675 -0.636426 0.366715 7 567 725 MODIFIER 13 CODING TMPRSS13 C protein_coding NM_001077263.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117772229 G C 0 125 0 0.4024 0.4607 0.4395 0.5952 0.3807 0.498 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,0,8 UTR_3_PRIME(MODIFIER||725||567|TMPRSS13|protein_coding|CODING|NM_001077263.2|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs575535 -0.651104 0.314454 8 567 106 MODIFIER 13 CODING TMPRSS13 T protein_coding NM_001077263.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117772848 C T 0 228 0 0.3434 0.4449 0.438 0.6141 0.3688 0.4908 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,24,2 UTR_3_PRIME(MODIFIER||106||567|TMPRSS13|protein_coding|CODING|NM_001077263.2|13|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs491822 -0.692976 0.125863 27 S311 567 tcT/tcC LOW 7 SILENT CODING TMPRSS13 G protein_coding NM_001077263.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117781435 A G 0 228 0 0.9259 0.9167 0.9524 0.875 0.9682 0.8691 0.94352 0.962718 0.971901 2 8372 106706 10149 7314 5693 60782 771 13625 2 8912 113098 10838 8300 6006 62738 822 15482 0 . 0 . 0 166 0,0,95,52 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S311|567|TMPRSS13|protein_coding|CODING|NM_001077263.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2155194 -0.693147 0.315257 166 Q78R 567 cAg/cGg MODERATE 2 MISSENSE CODING TMPRSS13 C protein_coding NM_001077263.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117789342 T C 0 5.9 0 . 0 . 0 . 0 . 0 . 1 0 34 0 14 13 7 0 0 2 9626 119130 11534 8590 6528 65472 884 16496 0.827706 0 . 0 . 232 63,100,12,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q78R|567|TMPRSS13|protein_coding|CODING|NM_001077263.2|2|C) 0 0.5 1 0 . 0 . 0 1 0 60 0 1 1 0 1.76192e-06 rs75037497 -0.69312 4.2983e-12 232 567 61 MODIFIER 1 CODING TMPRSS13 C protein_coding NM_001077263.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117800083 T C 0 228 0 0.6694 0.6216 0.611 0.6716 0.5398 0.5971 0.684249 0.589356 0.548083 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,3,21 UTR_5_PRIME(MODIFIER||61||567|TMPRSS13|protein_coding|CODING|NM_001077263.2|1|C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs10892196 -0.692831 0.225917 26 A60 578 gcG/gcA LOW 2 SILENT CODING IL10RA A protein_coding NM_001558.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117859209 G A 0 222 0 0.1694 0.1256 0.1859 0.0625 0.1123 0.1022 0.157428 0.123519 0.106145 1 1647 13703 2177 447 805 6812 112 1703 2 10402 121366 11566 8648 6608 66722 908 16512 0.139673 0 . 0 . 186 46,45,35,40 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A60|578|IL10RA|protein_coding|CODING|NM_001558.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.284732 rs4252249 -0.693147 0.109337 186 A153 578 gcA/gcG LOW 4 SILENT CODING IL10RA G protein_coding NM_001558.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117864047 A G 0 222 0 0.4569 0.5168 0.5663 0.5536 0.506 0.5358 0.467955 0.501385 0.518506 1 4785 63996 7144 5300 2938 34680 463 8686 2 10404 121356 11568 8626 6612 66734 906 16506 0.953983 0 . 0 . 101 25,22,19,24 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A153|578|IL10RA|protein_coding|CODING|NM_001558.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.94914 rs2256111 -0.693146 0.80172 101 R351G 578 Agg/Ggg MODERATE 7 MISSENSE CODING IL10RA G protein_coding NM_001558.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117869670 A G 0 228 0 0.8177 0.8111 0.8141 0.9931 0.6829 0.7444 0.808182 0.728448 0.687616 2 8358 89427 10077 8606 4135 45440 650 12161 2 10386 121152 11570 8644 6594 66602 902 16454 0 . 0 . 0 62 0,0,22,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R351G|578|IL10RA|protein_coding|CODING|NM_001558.3|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2229113 -0.693147 0.00639958 62 437 HIGH 1 CODING TMPRSS4 G protein_coding NM_019894.3 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117965530 A G 0 228 0 0.0408 0.3067 0.402 0.3502 0.3499 0.5092 0.110227 0.280095 0.367086 2 931 42781 5261 3129 2245 23374 308 7533 2 8896 106882 9900 7802 5548 59116 796 14824 0 . 0 . 0 152 0,0,104,35 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||437|TMPRSS4|protein_coding|CODING|NM_019894.3|1|G) 1 0 . 0 . 1 0 1 1 (TMPRSS4|TMPRSS4|1|1.00) 60 0 0 1 0 . rs2276122 -0.693147 0.0760643 152 V208G 437 gTg/gGg MODERATE 8 MISSENSE CODING TMPRSS4 G protein_coding NM_019894.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117982495 T G 0 228 0 0.9932 0.9792 0.9669 0.995 0.9672 0.9652 0.986136 0.969674 0.961243 2 10246 117062 11324 8576 6328 63804 869 15915 2 10400 121342 11570 8648 6608 66700 906 16510 0 . 0 . 0 55 0,0,34,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V208G|437|TMPRSS4|protein_coding|CODING|NM_019894.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1941635 -0.693147 0.91141 55 I222 437 atC/atA LOW 8 SILENT CODING TMPRSS4 A protein_coding NM_019894.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117982538 C A 0 222 0 0 0.0077875 0 0.0387 0 0 0.000454545 0.000153941 0 1 8 249 2 238 0 0 0 1 2 10398 121340 11574 8642 6614 66696 904 16512 0.441432 0 . 0 . 70 24,6,15,15 SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I222|437|TMPRSS4|protein_coding|CODING|NM_019894.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993871 rs144341799 -0.693097 0.131131 70 S405 437 agT/agC LOW 12 SILENT CODING TMPRSS4 C protein_coding NM_019894.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117988082 T C 0 222 0 0.8994 0.7833 0.9207 0.5734 0.9095 0.6155 0.904318 0.909483 0.912128 1 9275 103067 10259 4961 6114 60888 782 10788 2 10404 121384 11576 8630 6614 66740 908 16512 0.638838 0 . 0 . 136 52,10,52,12 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S405|437|TMPRSS4|protein_coding|CODING|NM_019894.3|12|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.600392 rs642215 -0.693147 0.105162 136 437 156 MODIFIER 13 CODING TMPRSS4 G protein_coding NM_019894.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117988784 A G 0 163 0 0.6596 0.6739 0.6326 0.7113 0.5964 0.7638 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.167501 0 . 0 . 17 0,8,2,6 UTR_3_PRIME(MODIFIER||156||437|TMPRSS4|protein_coding|CODING|NM_019894.3|13|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.422455 rs8924 -0.651104 0.325119 17 437 169 MODIFIER 13 CODING TMPRSS4 A protein_coding NM_019894.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117988797 G A 0 87 0 0.0068 0.1462 0.0447 0.2788 0.0467 0.3722 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8618 0 . 0 . 11 0,6,1,4 UTR_3_PRIME(MODIFIER||169||437|TMPRSS4|protein_coding|CODING|NM_019894.3|13|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.297172 rs17121760 -0.590765 0.345017 11 437 1207 MODIFIER 13 CODING TMPRSS4 T protein_coding NM_019894.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117989835 A T 0 32.6 0 0.3828 0.5593 0.5303 0.625 0.5895 0.7198 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1207||437|TMPRSS4|protein_coding|CODING|NM_019894.3|13|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10892220 -0.379885 0 2 437 1375 MODIFIER 13 CODING TMPRSS4 C protein_coding NM_019894.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 117990003 G C 0 18.4 0 0.0499 0.1905 0.0519 0.4147 0.0527 0.3896 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,1,0 UTR_3_PRIME(MODIFIER||1375||437|TMPRSS4|protein_coding|CODING|NM_019894.3|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs12576605 -0.379885 0 4 228 3054 MODIFIER 5 CODING SCN4B G protein_coding NM_174934.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118004688 A G 0 112 0 0.6399 0.6408 0.5634 0.6528 0.5954 0.7311 0 . 0 1 297 7850 72 142 5 2035 92 5207 2 450 11748 110 212 8 3324 136 7508 0.148586 0 . 0 COSN407468 12 1,5,1,4 UTR_3_PRIME(MODIFIER||3054||228|SCN4B|protein_coding|CODING|NM_174934.3|5|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.950952 1 0 0.8618 rs3741315 -0.590765 0.781662 12 228 986 MODIFIER 5 CODING SCN4B C protein_coding NM_174934.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118006756 G C 0 222 0 0.0189 0.1807 0.0576 0.4048 0.0537 0.3865 0 . 0 1 8 1883 18 66 0 111 15 1665 2 300 7342 98 154 0 1994 84 4712 0.765017 0 . 0 . 52 3,13,4,24 UTR_3_PRIME(MODIFIER||986||228|SCN4B|protein_coding|CODING|NM_174934.3|5|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.96772 rs28675746 -0.693054 0.28279 52 228 812 MODIFIER 5 CODING SCN4B C protein_coding NM_174934.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118006930 T C 0 64 0 0.0098 0.1789 0.0504 0.4087 0.0537 0.3906 0 . 0 2 7 2610 18 49 0 149 21 2366 2 190 10766 92 132 0 2728 118 7506 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||812||228|SCN4B|protein_coding|CODING|NM_174934.3|5|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs1317544 -0.511536 0.0860477 3 215 4057 MODIFIER 4 CODING SCN2B C protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118033545 T C 0 129 0 0.9841 0.7406 0.6282 0.8552 0.5467 0.5726 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,6,0 UTR_3_PRIME(MODIFIER||4057||215|SCN2B|protein_coding|CODING|NM_004588.4|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs625464 -0.616816 0.287141 7 215 3379 MODIFIER 4 CODING SCN2B A protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118034223 G A 0 228 0 0.4818 0.1821 0.0994 0.0139 0.1103 0.0828 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 76 0,0,51,15 UTR_3_PRIME(MODIFIER||3379||215|SCN2B|protein_coding|CODING|NM_004588.4|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs611979 -0.693147 0.110855 76 215 3374 MODIFIER 4 CODING SCN2B G protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118034228 T G 0 228 0 0.4818 0.1823 0.0994 0.0139 0.1113 0.0828 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 81 0,0,54,17 UTR_3_PRIME(MODIFIER||3374||215|SCN2B|protein_coding|CODING|NM_004588.4|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs611960 -0.693147 0.187209 81 215 1064 MODIFIER 4 CODING SCN2B C protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118036538 T C 0 9.7 0 0.6513 0.6154 0.5562 0.7996 0.5 0.5378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1064||215|SCN2B|protein_coding|CODING|NM_004588.4|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs653598 -0.379885 0 1 215 660 MODIFIER 4 CODING SCN2B A protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118036942 G A 0 31.3 0 0.5983 0.5845 0.549 0.7569 0.4901 0.5102 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||660||215|SCN2B|protein_coding|CODING|NM_004588.4|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs676685 -0.453602 0.22 2 215 38 MODIFIER 4 CODING SCN2B A protein_coding NM_004588.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118037564 G A 0 228 0 0.112 0.0781 0.0605 0.0139 0.1054 0.0828 0.102955 0.0962131 0.0927607 2 1097 11001 462 176 856 6947 94 1369 2 10388 121150 11544 8640 6586 66576 906 16510 0.167131 0 . 0 . 74 2,1,48,14 UTR_3_PRIME(MODIFIER||38||215|SCN2B|protein_coding|CODING|NM_004588.4|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.234164 rs8192614 -0.693147 0.414662 74 V193A 394 gTg/gCg MODERATE 6 MISSENSE CODING JAML G protein_coding NM_001098526.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118074337 A G 0 222 0 0.9251 0.8025 0.7954 0.6736 0.7356 0.8436 0.902727 0.807343 0.758496 1 9401 93745 9023 5866 4953 50172 669 13661 2 10406 121380 11566 8640 6612 66736 908 16512 0.857434 0 . 0 COSM147331 58 14,7,11,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V193A|394|JAML|protein_coding|CODING|NM_001098526.1|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.34708 rs1793174 -0.69312 0.584687 58 I94N 394 aTc/aAc MODERATE 4 MISSENSE CODING JAML T protein_coding NM_001098526.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118081345 A T 0 222 0 0.1346 0.4675 0.487 0.5387 0.5298 0.7658 0.205 0.447352 0.571462 1 2034 65177 5244 4593 3537 37366 469 11934 2 10406 121382 11560 8644 6614 66738 908 16512 0.897457 0 . 0 COSM147332 131 38,28,27,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I94N|394|JAML|protein_coding|CODING|NM_001098526.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.89857 rs17121881 -0.693147 0.0332353 131 D69 215 gaC/gaT LOW 2 SILENT CODING MPZL2 A protein_coding NM_005797.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118133664 G A 0 222 0 0 0.0057907 0.0375 0.001 0.001 0.001 0 0.000384852 0.000581937 1 3 414 336 21 0 37 2 15 2 10396 121258 11576 8648 6614 66648 902 16474 0.906655 0 . 0 . 98 30,20,22,19 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D69|215|MPZL2|protein_coding|CODING|NM_005797.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.579292 rs140274135 -0.693145 0.0118875 98 1073 1629 MODIFIER 20 CODING UBE4A A protein_coding NM_004788.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118268784 C A 0 222 0 0 0.00019968 0 0.001 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996022 0 . 0 . 86 31,11,22,9 UTR_3_PRIME(MODIFIER||1629||1073|UBE4A|protein_coding|CODING|NM_004788.3|20|A),UPSTREAM(MODIFIER||3320||103|ATP5L|protein_coding|CODING|NM_006476.4||A),INTRAGENIC(MODIFIER|||||LOC100131626||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.711049 rs186445215 -0.69311 0.255852 86 3972 509 MODIFIER 36 CODING KMT2A G protein_coding NM_001197104.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118393396 A G 0 222 0 0.5333 0.6042 0.8559 0.4276 0.7982 0.5041 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.946276 0 . 0 . 150 62,21,37,15 UTR_3_PRIME(MODIFIER||509||3972|KMT2A|protein_coding|CODING|NM_001197104.1|36|G),UPSTREAM(MODIFIER||4814||189|TTC36|protein_coding|CODING|NM_001080441.1||G),INTRAGENIC(MODIFIER|||||LOC101929089||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.641229 rs573971 -0.693147 0.0353507 150 P299 366 ccG/ccA LOW 7 SILENT CODING TMEM25 A protein_coding NM_032780.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118404804 G A 0 222 0 0.1921 0.24 0.4337 0.2302 0.2932 0.1227 0.195909 0.262972 0.297322 1 1970 35117 6453 2340 2042 19610 254 2448 2 10404 121322 11568 8642 6608 66694 906 16500 0.956843 0 . 0 COSM147336 100 24,12,22,30 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P299|366|TMEM25|protein_coding|CODING|NM_032780.3|7|A),DOWNSTREAM(MODIFIER||3064||189|TTC36|protein_coding|CODING|NM_001080441.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.140367 rs6589664 -0.693147 3.85458e-05 100 366 48 MODIFIER 9 CODING TMEM25 A protein_coding NM_032780.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118405343 G A 0 228 0 0.9985 0.9834 0.9784 1 0.9414 0.9928 0.989318 0.958199 0.942258 2 10126 115259 11257 8622 5991 62252 862 16149 2 10228 120120 11436 8622 6512 66160 894 16268 0 . 0 . 0 53 0,0,16,29 UTR_3_PRIME(MODIFIER||48||366|TMEM25|protein_coding|CODING|NM_032780.3|9|A),DOWNSTREAM(MODIFIER||3603||189|TTC36|protein_coding|CODING|NM_001080441.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs512849 -0.693147 0.0817368 53 E865 1377 gaA/gaG LOW 11 SILENT CODING PHLDB1 G protein_coding NM_001144758.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118509668 A G 0 228 0 0.4773 0.5727 0.7089 0.6558 0.5368 0.5562 0.474534 0.525793 0.552037 2 4741 69096 8843 6047 3514 36557 492 8902 2 9966 117884 11330 8480 6182 64942 858 16126 0.316009 0 . 0 . 169 2,1,96,43 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E865|1377|PHLDB1|protein_coding|CODING|NM_001144758.2|11|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.0864094 rs483598 -0.693147 0.348606 169 S995 1377 agC/agT LOW 14 SILENT CODING PHLDB1 T protein_coding NM_001144758.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118514625 C T 0 228 0 0.1082 0.2204 0.2118 0.2302 0.2157 0.3732 0.121136 0.183554 0.215533 2 1223 27272 2447 2071 1463 14537 209 5322 2 9876 116440 11498 8566 6434 64652 854 14560 1 0 . 0 COSM1561066 70 0,1,52,13 SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S995|1377|PHLDB1|protein_coding|CODING|NM_001144758.2|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11216938 -0.693147 0.0478601 70 1377 891 MODIFIER 23 CODING PHLDB1 T protein_coding NM_001144758.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118528424 C T 0 228 0 0.0514 0.2039 0.2046 0.2272 0.2137 0.3753 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 52 1,0,24,25 UTR_3_PRIME(MODIFIER||891||1377|PHLDB1|protein_coding|CODING|NM_001144758.2|23|T),DOWNSTREAM(MODIFIER||518||582|TREH|protein_coding|CODING|NM_007180.2||T|WARNING_TRANSCRIPT_INCOMPLETE) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs17748 -0.693147 0.135933 52 *578S 582 tAa/tCa HIGH 15 MISSENSE CODING TREH G protein_coding NM_007180.2 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118529017 T G 0 228 0 1 1 1 1 1 1 0 . 0 2 6108 76395 5620 5427 2678 44003 528 12031 2 6108 76398 5620 5428 2678 44004 528 12032 0 . 0 . 0 109 0,0,54,47 STOP_LOST(HIGH|MISSENSE|tAa/tCa|*578S|582|TREH|protein_coding|CODING|NM_007180.2|15|G|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||269||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6589669 -0.693147 1.25888e-06 109 G569A? 582 ggg/gCgg HIGH 15 CODING TREH CG protein_coding NM_007180.2 FRAME_SHIFT outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118529044 C CG 0 225 0 0.9992 0.9998 1 1 1 1 0 . 0 2 6530 84359 7254 6047 3094 48405 602 12427 2 6532 84372 7254 6050 3094 48410 602 12430 0 . 0 . 0 103 0,0,35,43 FRAME_SHIFT(HIGH||ggg/gCgg|G569A?|582|TREH|protein_coding|CODING|NM_007180.2|15|CG|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||297||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||CG) 0 . 0 93 0.902913 1 1 0 1 0 60 0 0 1 0 . rs11448549 -0.693147 0.645043 103 P561A 582 Cct/Gct MODERATE 15 MISSENSE CODING TREH C protein_coding NM_007180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118529069 G C 0 228 0 1 1 1 1 1 1 0 . 0 2 8184 105381 10036 7757 4680 59626 738 14360 2 8184 105382 10036 7758 4680 59626 738 14360 0 . 0 . 0 83 0,0,16,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P561A|582|TREH|protein_coding|CODING|NM_007180.2|15|C|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||321||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6589670 -0.693147 0.120956 83 P558A 582 Ccc/Gcc MODERATE 15 MISSENSE CODING TREH C protein_coding NM_007180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118529078 G C 0 228 0 1 1 1 1 1 1 0 . 0 2 8513 109581 10539 8135 5060 61738 764 14832 2 8514 109586 10540 8136 5060 61740 764 14832 0 . 0 . 0 83 0,0,16,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P558A|582|TREH|protein_coding|CODING|NM_007180.2|15|C|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||330||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6589671 -0.693147 0.112653 83 G541 582 ggC/ggT LOW 15 SILENT CODING TREH A protein_coding NM_007180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118529127 G A 0 228 0 0.1082 0.22 0.2118 0.2282 0.2147 0.3742 0.118624 0.183472 0.215632 2 1145 26935 2384 2049 1295 14377 202 5483 2 8488 110782 10660 8212 5116 62216 776 15314 0.96615 0 . 0 . 66 2,1,14,45 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G541|582|TREH|protein_coding|CODING|NM_007180.2|15|A|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||379||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.566468 rs7928371 -0.693147 0.00411413 66 T389A 582 Aca/Gca MODERATE 11 MISSENSE CODING TREH C protein_coding NM_007180.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118530611 T C 0 228 0 0.0946 0.2169 0.2118 0.2272 0.2167 0.3753 0.102654 0.163939 0.192969 2 262 5640 105 157 359 2043 54 2660 2 2214 22000 414 628 1430 9166 234 7914 1 0 . 0 . 113 0,1,61,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T389A|582|TREH|protein_coding|CODING|NM_007180.2|11|C|WARNING_TRANSCRIPT_INCOMPLETE),DOWNSTREAM(MODIFIER||1863||1377|PHLDB1|protein_coding|CODING|NM_001144758.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2276065 -0.693147 0.0813435 113 K52 582 aaG/aaA LOW 2 SILENT CODING TREH T protein_coding NM_007180.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118534082 C T 0 228 0 0.0318 0.1971 0.196 0.2262 0.2137 0.3742 0.0582865 0.160235 0.211607 2 381 19385 1599 1606 1049 10562 144 4044 2 4528 62990 4662 4696 3508 34470 500 10626 1 0 . 0 . 89 0,1,42,37 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K52|582|TREH|protein_coding|CODING|NM_007180.2|2|T|WARNING_TRANSCRIPT_INCOMPLETE) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10790256 -0.693147 0.256655 89 483 6374 MODIFIER 14 CODING DDX6 G protein_coding NM_001257191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118619047 T G 0 9.7 0 0.0492 0.1587 0.1614 0.125 0.2018 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||6374||483|DDX6|protein_coding|CODING|NM_001257191.2|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2077579 -0.379885 0 1 483 5461 MODIFIER 14 CODING DDX6 T protein_coding NM_001257191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118619960 C T 0 9.7 0 0.0401 0.1559 0.1599 0.125 0.2008 0.2955 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5461||483|DDX6|protein_coding|CODING|NM_001257191.2|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3889239 -0.379885 0 1 483 3176 MODIFIER 14 CODING DDX6 A protein_coding NM_001257191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118622245 G A 0 200 0 0.7799 0.8868 0.9078 0.999 0.8728 0.9151 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,25,1 UTR_3_PRIME(MODIFIER||3176||483|DDX6|protein_coding|CODING|NM_001257191.2|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs485901 -0.692976 0.748054 26 483 2677 MODIFIER 14 CODING DDX6 A protein_coding NM_001257191.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118622744 G A 0 228 0 1 0.9942 0.9914 1 0.9841 0.9928 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 48 0,0,21,21 UTR_3_PRIME(MODIFIER||2677||483|DDX6|protein_coding|CODING|NM_001257191.2|14|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6589689 -0.693146 0.000355286 48 T338 372 acG/acC LOW 2 SILENT CODING CXCR5 C protein_coding NM_001716.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118765267 G C 0 228 0 0.4992 0.3217 0.4366 0.2212 0.2714 0.1554 0.450455 0.3301 0.268452 2 4640 33498 5824 1866 2095 17246 214 1613 2 10172 110592 11456 8472 6608 63806 794 9284 1 0 . 0 . 34 1,0,20,12 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T338|372|CXCR5|protein_coding|CODING|NM_001716.4|2|C),DOWNSTREAM(MODIFIER||1584||1499|BCL9L|protein_coding|CODING|NM_182557.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs598207 -0.69312 0.230299 34 372 228 MODIFIER 2 CODING CXCR5 G protein_coding NM_001716.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118765600 A G 0 228 0 0.6868 0.4433 0.5476 0.2907 0.4165 0.2249 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,25,28 UTR_3_PRIME(MODIFIER||228||372|CXCR5|protein_coding|CODING|NM_001716.4|2|G),DOWNSTREAM(MODIFIER||1251||1499|BCL9L|protein_coding|CODING|NM_182557.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386589386,rs3922 -0.693147 0.484206 54 372 316 MODIFIER 2 CODING CXCR5 G protein_coding NM_001716.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118765688 C G 0 228 0 0.0212 0.1542 0.389 0.0843 0.2475 0.1431 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,26,22 UTR_3_PRIME(MODIFIER||316||372|CXCR5|protein_coding|CODING|NM_001716.4|2|G),DOWNSTREAM(MODIFIER||1163||1499|BCL9L|protein_coding|CODING|NM_182557.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs676925 -0.693147 0.607068 52 1499 2047 MODIFIER 8 CODING BCL9L C protein_coding NM_182557.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118767077 T C 0 64 0 0.8548 0.5222 0.6023 0.2887 0.4592 0.3211 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||2047||1499|BCL9L|protein_coding|CODING|NM_182557.2|8|C),DOWNSTREAM(MODIFIER||97||372|CXCR5|protein_coding|CODING|NM_001716.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs581063 -0.511536 0.309755 3 P1394 1499 ccT/ccC LOW 8 SILENT CODING BCL9L G protein_coding NM_182557.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118769442 A G 0 228 0 0.6906 0.4441 0.5476 0.2927 0.4135 0.2249 0.627843 0.485901 0.413211 2 6210 49489 6574 2637 2677 26507 368 4516 2 9712 116550 11256 8460 6164 63842 856 16260 0 . 0 . 0 32 0,0,19,10 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1394|1499|BCL9L|protein_coding|CODING|NM_182557.2|8|G),DOWNSTREAM(MODIFIER||2462||372|CXCR5|protein_coding|CODING|NM_001716.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7104819 -0.693079 0.318209 32 *185 184 tAa/tGa LOW 5 SILENT CODING UPK2 G protein_coding NM_006760.3 SYNONYMOUS_STOP outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118828942 A G 0 120 0 0.3782 0.2408 0.1383 0.0952 0.172 0.3487 0.375 0.234642 0.162747 1 3824 22760 1252 816 1481 10198 171 5018 2 10186 116938 11134 8444 6200 64354 852 15768 0.935917 0 . 0 . 28 3,11,0,13 SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*185|184|UPK2|protein_coding|CODING|NM_006760.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.50754 rs623500 -0.683931 0.367989 28 R302 332 cgC/cgT LOW 10 SILENT CODING CCDC84 T protein_coding NM_198489.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118886117 C T 0 222 0 0.3517 0.2518 0.2334 0.0685 0.2286 0.3425 0.337727 0.26332 0.225198 1 3446 27019 1811 535 1609 14236 211 5171 2 10326 120838 11554 8640 6606 66312 906 16494 0.999959 0 . 0 . 88 23,13,34,14 SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R302|332|CCDC84|protein_coding|CODING|NM_198489.2|10|T),UPSTREAM(MODIFIER||3124||219|TRAPPC4|protein_coding|CODING|NM_016146.4||T),DOWNSTREAM(MODIFIER||305||125|RPS25|protein_coding|CODING|NM_001028.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.712998 rs10111 -0.693147 0.485209 88 125 LOW 3 CODING RPS25 A protein_coding NM_001028.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118886656 G A 0 222 0 0.4622 0.2825 0.2406 0.0704 0.2296 0.3425 0.425682 0.29361 0.22596 1 4483 28315 1870 581 1610 14373 213 5185 2 10402 121314 11570 8648 6614 66690 908 16482 0.964579 0 . 0 . 140 13,50,14,52 SPLICE_SITE_REGION+INTRON(LOW||||125|RPS25|protein_coding|CODING|NM_001028.2|3|A),UPSTREAM(MODIFIER||2585||219|TRAPPC4|protein_coding|CODING|NM_016146.4||A),DOWNSTREAM(MODIFIER||154||332|CCDC84|protein_coding|CODING|NM_198489.2||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0327425 rs7131534 -0.693147 0.001101 140 219 258 MODIFIER 1 CODING TRAPPC4 AG protein_coding NM_016146.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118889247 A AG 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 38 0,0,12,22 UTR_5_PRIME(MODIFIER||258||219|TRAPPC4|protein_coding|CODING|NM_016146.4|1|AG),UPSTREAM(MODIFIER||191||125|RPS25|protein_coding|CODING|NM_001028.2||AG),DOWNSTREAM(MODIFIER||2746||332|CCDC84|protein_coding|CODING|NM_198489.2||AG) 0 . 0 35 0.921053 1 1 0 . 0 60 0 0 1 0 . rs11440855 -0.693132 0.594108 38 219 128 MODIFIER 1 CODING TRAPPC4 A protein_coding NM_016146.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118889378 G A 0 174 0 0.7769 0.403 0.2752 0.1429 0.2734 0.3896 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.704665 0 . 0 . 38 15,6,14,3 UTR_5_PRIME(MODIFIER||128||219|TRAPPC4|protein_coding|CODING|NM_016146.4|1|A),UPSTREAM(MODIFIER||321||125|RPS25|protein_coding|CODING|NM_001028.2||A),DOWNSTREAM(MODIFIER||2876||332|CCDC84|protein_coding|CODING|NM_198489.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.755618 rs7113753 -0.690438 0.475603 38 F115 219 ttC/ttT LOW 2 SILENT CODING TRAPPC4 T protein_coding NM_016146.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118890022 C T 0 222 0 0.059 0.1092 0.0663 0.0685 0.0944 0.2648 0.0645455 0.0786759 0.0859139 1 737 12299 727 677 911 5508 87 3652 2 10400 121054 11574 8648 6612 66554 904 16362 0.080712 0 . 0 . 145 32,41,21,32 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F115|219|TRAPPC4|protein_coding|CODING|NM_016146.4|2|T),UPSTREAM(MODIFIER||965||125|RPS25|protein_coding|CODING|NM_001028.2||T),DOWNSTREAM(MODIFIER||3520||332|CCDC84|protein_coding|CODING|NM_198489.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.101326 rs3802881 -0.693147 0.00491169 145 219 178 MODIFIER 5 CODING TRAPPC4 G protein_coding NM_016146.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118894287 A G 0 96 0 0.087 0.1785 0.2032 0.0843 0.2276 0.3313 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.67032 0 . 0 . 24 0,15,0,9 UTR_3_PRIME(MODIFIER||178||219|TRAPPC4|protein_coding|CODING|NM_016146.4|5|G),DOWNSTREAM(MODIFIER||774||451|SLC37A4|protein_coding|CODING|NM_001164278.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.978458 rs569 -0.662043 0.928022 24 451 418 MODIFIER 12 CODING SLC37A4 G protein_coding NM_001164278.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118895202 A G 0 18.4 0 0.09 0.1819 0.2032 0.0843 0.2296 0.3425 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 2,0,1,0 UTR_3_PRIME(MODIFIER||418||451|SLC37A4|protein_coding|CODING|NM_001164278.1|12|G),DOWNSTREAM(MODIFIER||817||219|TRAPPC4|protein_coding|CODING|NM_016146.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs11006 -0.379885 0 4 451 125 MODIFIER 12 CODING SLC37A4 G protein_coding NM_001164278.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118895495 C G 0 119 0 0.3177 0.2835 0.2709 0.1438 0.2893 0.3845 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.870278 0 . 0 . 25 13,0,9,1 UTR_3_PRIME(MODIFIER||125||451|SLC37A4|protein_coding|CODING|NM_001164278.1|12|G),DOWNSTREAM(MODIFIER||1110||219|TRAPPC4|protein_coding|CODING|NM_016146.4||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.976718 rs8301 -0.670168 0.534485 25 T430 451 acG/acA LOW 12 SILENT CODING SLC37A4 T protein_coding NM_001164278.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118895686 C T 0 222 0 0.3638 0.2478 0.2161 0.0823 0.2157 0.317 0.337209 0.255724 0.216336 1 3463 26296 1626 785 1479 13884 200 4859 2 9762 120212 11494 8592 6584 66396 894 16490 0.587246 2 benign 0 . 105 33,19,30,13 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T430|451|SLC37A4|protein_coding|CODING|NM_001164278.1|12|T),DOWNSTREAM(MODIFIER||1301||219|TRAPPC4|protein_coding|CODING|NM_016146.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999825 rs8192696 -0.693146 0.53956 105 451 1183 MODIFIER 2 CODING SLC37A4 T protein_coding NM_001164278.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118901262 C T 0 9.7 0 0.5136 0.5262 0.3228 0.7431 0.4264 0.5665 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 2 benign 0 . 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1183||451|SLC37A4|protein_coding|CODING|NM_001164278.1|2|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3759012 -0.379885 0 1 999 1307 MODIFIER 26 CODING HYOU1 G protein_coding NM_001130991.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118914998 A G 0 222 0 0.0091 0.1346 0.0504 0.2599 0.1093 0.2607 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.920006 0 . 0 . 67 17,18,9,17 UTR_3_PRIME(MODIFIER||1307||999|HYOU1|protein_coding|CODING|NM_001130991.2|26|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.774657 rs35588561 -0.692976 3.80796e-07 67 999 550 MODIFIER 26 CODING HYOU1 C protein_coding NM_001130991.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118915755 G C 0 25.6 0 0.3238 0.3694 0.5648 0.2599 0.3996 0.3742 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||550||999|HYOU1|protein_coding|CODING|NM_001130991.2|26|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs13929 -0.453602 0.96 3 999 361 MODIFIER 26 CODING HYOU1 G protein_coding NM_001130991.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118915944 A G 0 70 0 0.4221 0.519 0.3386 0.7391 0.493 0.5777 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,3,0 UTR_3_PRIME(MODIFIER||361||999|HYOU1|protein_coding|CODING|NM_001130991.2|26|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1043314 -0.511536 0.121629 6 A745 999 gcA/gcG LOW 19 SILENT CODING HYOU1 C protein_coding NM_001130991.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118919206 T C 0 228 0 0.6694 0.8039 0.6196 0.9454 0.841 0.9325 0.6775 0.794611 0.854598 2 6928 99186 6120 8246 5441 56365 770 15316 2 10396 121376 11572 8652 6614 66728 908 16506 0 . 0 . 0 41 0,0,27,12 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A745|999|HYOU1|protein_coding|CODING|NM_001130991.2|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs568922 -0.693144 0.469891 41 N492 999 aaC/aaT LOW 13 SILENT CODING HYOU1 A protein_coding NM_001130991.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118922200 G A 0 222 0 0.0787 0.1617 0.0562 0.2986 0.1133 0.2577 0.0613636 0.0861432 0.0988359 1 645 16467 754 2889 823 7376 148 3832 2 10404 121398 11576 8648 6614 66736 908 16512 0.541692 0 . 0 . 151 57,17,45,9 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N492|999|HYOU1|protein_coding|CODING|NM_001130991.2|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.774953 rs1804690 -0.693147 0.111023 151 N181 999 aaC/aaT LOW 7 SILENT CODING HYOU1 A protein_coding NM_001130991.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118925341 G A 0 222 0 0.1868 0.4323 0.2954 0.7192 0.4821 0.5143 0.233636 0.372825 0.444121 1 2368 53960 2983 6571 3488 29937 452 8161 2 10392 121216 11550 8636 6594 66634 902 16508 0.976051 0 . 0 . 44 7,14,4,13 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N181|999|HYOU1|protein_coding|CODING|NM_001130991.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0612612 rs386598526,rs538478 -0.690438 0.0851372 44 G161 940 ggC/ggG LOW 4 SILENT CODING VPS11 G protein_coding NM_021729.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118940957 C G 0 222 0 0.5408 0.3832 0.3487 0.2143 0.3598 0.3926 0.493896 0.436165 0.409688 1 4745 42210 2847 1464 1830 24638 291 6395 2 8954 106210 9268 7292 5894 59222 802 14778 0.913654 0 . 0 . 105 38,6,38,16 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G161|940|VPS11|protein_coding|CODING|NM_021729.5|4|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.142258 rs1784302 -0.693147 0.28708 105 Y421 940 taC/taT LOW 8 SILENT CODING VPS11 T protein_coding NM_021729.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118947634 C T 0 222 0 0.202 0.4319 0.2954 0.7192 0.4811 0.4928 0.238669 0.369185 0.434644 1 2360 53195 2950 6518 3463 29585 452 7867 2 9584 119584 11368 8586 6550 66238 886 16372 0.98262 0 . 0 . 87 27,9,26,14 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y421|940|VPS11|protein_coding|CODING|NM_021729.5|8|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955511 rs540261 -0.693145 0.178865 87 361 65 MODIFIER 1 CODING HMBS T protein_coding NM_000190.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118955679 C T 0 228 0 0.112 0.4042 0.2795 0.7063 0.4712 0.5072 0.160116 0.340718 0.419745 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 66 0,0,50,11 UTR_5_PRIME(MODIFIER||65||361|HMBS|protein_coding|CODING|NM_000190.3|1|T),DOWNSTREAM(MODIFIER||2991||940|VPS11|protein_coding|CODING|NM_021729.5||T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs589925 -0.693147 0.576931 66 143 625 MODIFIER 1 CODING H2AFX A protein_coding NM_002105.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118965048 G A 0 9.8 0 0.1467 0.2835 0.2536 0.4623 0.3936 0.1922 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||625||143|H2AFX|protein_coding|CODING|NM_002105.2|1|A),DOWNSTREAM(MODIFIER||789||361|HMBS|protein_coding|CODING|NM_000190.3||A),DOWNSTREAM(MODIFIER||2165||408|DPAGT1|protein_coding|CODING|NM_001382.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7350 -0.453602 0.84 3 143 335 MODIFIER 1 CODING H2AFX A protein_coding NM_002105.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118965338 T A 0 42.3 0 0.1157 0.2624 0.2334 0.4673 0.3708 0.1585 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||335||143|H2AFX|protein_coding|CODING|NM_002105.2|1|A),DOWNSTREAM(MODIFIER||1079||361|HMBS|protein_coding|CODING|NM_000190.3||A),DOWNSTREAM(MODIFIER||1875||408|DPAGT1|protein_coding|CODING|NM_001382.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1064193 -0.453602 0.14 2 408 184 MODIFIER 9 CODING DPAGT1 T protein_coding NM_001382.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118967524 C T 0 6.4 0 0.2769 0.4367 0.2983 0.6329 0.4553 0.5297 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.4 0 . 0 . 7 4,1,1,1 UTR_3_PRIME(MODIFIER||184||408|DPAGT1|protein_coding|CODING|NM_001382.3|9|T),UPSTREAM(MODIFIER||1347||143|H2AFX|protein_coding|CODING|NM_002105.2||T),DOWNSTREAM(MODIFIER||3265||361|HMBS|protein_coding|CODING|NM_000190.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.4 rs8551 -0.453602 0.06 7 I393V 408 Atc/Gtc MODERATE 9 MISSENSE CODING DPAGT1 C protein_coding NM_001382.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 118967758 T C 0 222 0 0.2844 0.4333 0.2983 0.631 0.4563 0.5031 0.297045 0.387221 0.433411 1 3024 51106 2833 5584 2507 28820 389 7949 2 10384 121256 11544 8636 6606 66670 908 16508 0.196611 2 benign 0 . 119 44,24,30,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I393V|408|DPAGT1|protein_coding|CODING|NM_001382.3|9|C),UPSTREAM(MODIFIER||1581||143|H2AFX|protein_coding|CODING|NM_002105.2||C),DOWNSTREAM(MODIFIER||3499||361|HMBS|protein_coding|CODING|NM_000190.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.02541 rs643788 -0.693145 0.0473364 119 I478 517 atC/atT LOW 11 SILENT CODING HINFP T protein_coding NM_015517.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119005088 C T 0 228 0 0.9977 0.9872 0.9856 1 0.9622 0.9867 0.993409 0.97244 0.9617 2 10342 118198 11462 8654 6394 64157 883 16306 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 136 0,0,57,55 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I478|517|HINFP|protein_coding|CODING|NM_015517.4|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs512703 -0.693147 0.169399 136 A493V 517 gCc/gTc MODERATE 11 MISSENSE CODING HINFP T protein_coding NM_015517.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119005132 C T 0 228 0 0.1687 0.4018 0.2839 0.7183 0.4433 0.4315 0.191591 0.342802 0.420256 2 1987 50303 3028 6502 3130 28170 432 7054 2 10308 120958 11550 8640 6594 66478 906 16482 0 . 0 . 0 109 0,0,34,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A493V|517|HINFP|protein_coding|CODING|NM_015517.4|11|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs100803 -0.693147 0.148171 109 517 277 MODIFIER 11 CODING HINFP T protein_coding NM_015517.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119005485 C T 0 197 0 0.1694 0.4014 0.2824 0.7163 0.4433 0.4315 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,21,1 UTR_3_PRIME(MODIFIER||277||517|HINFP|protein_coding|CODING|NM_015517.4|11|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7234 -0.692562 0.226269 22 P63S 975 Ccc/Tcc MODERATE 4 MISSENSE CODING NLRX1 T protein_coding NM_001282143.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119043656 C T 0 228 0 0.6936 0.6823 0.402 0.8829 0.5497 0.7955 0.650682 0.56582 0.522352 2 6974 69661 3906 7647 3465 34660 537 12472 2 10386 121308 11566 8640 6610 66690 904 16512 0 . 0 . 0 77 0,0,34,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P63S|975|NLRX1|protein_coding|CODING|NM_001282143.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs643423 -0.693147 0.00329309 77 A793E 975 gCg/gAg MODERATE 9 MISSENSE CODING NLRX1 A protein_coding NM_001282143.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119052826 C A 0 228 0 0.708 0.6883 0.4179 0.8839 0.5477 0.7965 0.675227 0.573364 0.521187 2 7097 69446 3897 7657 3444 34357 538 12456 2 10264 120686 11566 8648 6612 66194 900 16502 1 0 . 0 . 184 1,0,110,59 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A793E|975|NLRX1|protein_coding|CODING|NM_001282143.1|9|A),UPSTREAM(MODIFIER||3340||505|PDZD3|protein_coding|CODING|NM_001168468.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4245191 -0.693147 0.146946 184 975 340 MODIFIER 10 CODING NLRX1 T protein_coding NM_001282143.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119054488 C T 0 228 0 0.5703 0.5118 0.366 0.6518 0.4642 0.4407 0.525407 0.4673 0.438638 2 5469 55267 3312 5782 3288 29632 442 7342 2 9724 118898 11218 8538 6554 65746 886 16232 0.985714 0 . 0 . 159 2,0,72,68 UTR_3_PRIME(MODIFIER||340||975|NLRX1|protein_coding|CODING|NM_001282143.1|10|T),UPSTREAM(MODIFIER||1678||505|PDZD3|protein_coding|CODING|NM_001168468.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.7 rs10790286 -0.693147 0.143282 159 R372Q 505 cGg/cAg MODERATE 9 MISSENSE CODING PDZD3 A protein_coding NM_001168468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119059404 G A 0 228 0 0.6014 0.6649 0.4251 0.879 0.5716 0.7965 0.588636 0.559045 0.543888 2 6259 70468 3907 7624 3463 36059 543 12613 2 10372 121278 11566 8654 6594 66676 906 16510 0 . 0 . 0 53 0,0,43,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R372Q|505|PDZD3|protein_coding|CODING|NM_001168468.1|9|A),DOWNSTREAM(MODIFIER||4678||975|NLRX1|protein_coding|CODING|NM_001282143.1||A),DOWNSTREAM(MODIFIER||1559||210|CCDC153|protein_coding|CODING|NM_001145018.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1815811 -0.693147 0.268517 53 210 LOW 7 CODING CCDC153 C protein_coding NM_001145018.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119060963 T C 0 222 0 0.2421 0.3844 0.1916 0.5169 0.3241 0.6391 0.240909 0.269438 0.284051 1 2374 39843 2094 4163 2001 19208 309 9694 2 9984 119804 11530 8542 6600 65782 896 16470 0.77073 0 . 0 . 73 30,3,26,6 SPLICE_SITE_REGION(LOW||||210|CCDC153|protein_coding|CODING|NM_001145018.1|7|C),UTR_3_PRIME(MODIFIER||46||210|CCDC153|protein_coding|CODING|NM_001145018.1|7|C),DOWNSTREAM(MODIFIER||31||505|PDZD3|protein_coding|CODING|NM_001168468.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7634 rs45535039 -0.69312 5.72791e-05 73 210 46 MODIFIER 7 CODING CCDC153 C protein_coding NM_001145018.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119060963 T C 0 222 0 0.2421 0.3844 0.1916 0.5169 0.3241 0.6391 0.240909 0.269438 0.284051 1 2374 39843 2094 4163 2001 19208 309 9694 2 9984 119804 11530 8542 6600 65782 896 16470 0.77073 0 . 0 . 73 30,3,26,6 SPLICE_SITE_REGION(LOW||||210|CCDC153|protein_coding|CODING|NM_001145018.1|7|C),UTR_3_PRIME(MODIFIER||46||210|CCDC153|protein_coding|CODING|NM_001145018.1|7|C),DOWNSTREAM(MODIFIER||31||505|PDZD3|protein_coding|CODING|NM_001168468.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7634 rs45535039 -0.69312 5.72791e-05 73 R101H 210 cGc/cAc MODERATE 5 MISSENSE CODING CCDC153 T protein_coding NM_001145018.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119063908 C T 0 222 0 0.2595 0.245 0.2089 0.3542 0.2455 0.138 0.260573 0.25231 0.248079 1 2773 28185 1731 3339 1509 16100 223 2510 2 10394 121336 11560 8632 6610 66722 908 16510 0.976248 0 . 0 COSM147337 43 8,12,10,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R101H|210|CCDC153|protein_coding|CODING|NM_001145018.1|5|T),DOWNSTREAM(MODIFIER||2976||505|PDZD3|protein_coding|CODING|NM_001168468.1||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.437206 rs2301574 -0.691153 0.021209 43 210 LOW 2 CODING CCDC153 C protein_coding NM_001145018.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119065709 G C 0 228 0 0.8351 0.7308 0.4409 0.8859 0.5716 0.7996 0.782514 0.617389 0.545569 2 1782 13255 198 544 22 4718 113 5878 2 2214 19850 404 620 36 8480 190 7906 0 . 0 . 0 56 0,0,7,48 SPLICE_SITE_REGION+INTRON(LOW||||210|CCDC153|protein_coding|CODING|NM_001145018.1|2|C),DOWNSTREAM(MODIFIER||4777||505|PDZD3|protein_coding|CODING|NM_001168468.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10750139 -0.693147 0.187504 56 906 125 MODIFIER 1 CODING CBL T protein_coding NM_005188.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119077003 C T 0 6.3 0 0.236 0.3448 0.1916 0.4196 0.3211 0.5481 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||125||906|CBL|protein_coding|CODING|NM_005188.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7108857 -0.379885 0 1 906 560 MODIFIER 16 CODING CBL TCAA protein_coding NM_005188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119171050 T TCAA 0 222 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 63 15,18,15,8 UTR_3_PRIME(MODIFIER||560||906|CBL|protein_coding|CODING|NM_005188.3|16|TCAA) 0 0.5 1 23 0.365079 0 1 0 . 0 60 0 0 1 0 . rs3833768 -0.692717 0.290825 63 906 2045 MODIFIER 16 CODING CBL G protein_coding NM_005188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119172536 A G 0 9.7 0 0.1823 0.2192 0.2161 0.3155 0.2505 0.1401 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2045||906|CBL|protein_coding|CODING|NM_005188.3|16|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1047417 -0.379885 0 1 906 4931 MODIFIER 16 CODING CBL C protein_coding NM_005188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119175422 T C 0 9.7 0 1 0.9994 1 1 0.997 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4931||906|CBL|protein_coding|CODING|NM_005188.3|16|C),DOWNSTREAM(MODIFIER||3812||646|MCAM|protein_coding|CODING|NM_006500.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2510145 -0.379885 0 1 906 7447 MODIFIER 16 CODING CBL G protein_coding NM_005188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119177938 A G 0 172 0 0.1868 0.2324 0.219 0.3542 0.2624 0.1472 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.968931 0 . 0 . 54 24,6,21,2 UTR_3_PRIME(MODIFIER||7447||906|CBL|protein_coding|CODING|NM_005188.3|16|G),DOWNSTREAM(MODIFIER||1296||646|MCAM|protein_coding|CODING|NM_006500.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.877396 rs11217234 -0.692717 0.0977337 54 906 7559 MODIFIER 16 CODING CBL G protein_coding NM_005188.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119178050 C G 0 222 0 0.7322 0.4121 0.3141 0.3571 0.3121 0.2086 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.954041 0 . 0 . 181 57,26,48,24 UTR_3_PRIME(MODIFIER||7559||906|CBL|protein_coding|CODING|NM_005188.3|16|G),DOWNSTREAM(MODIFIER||1184||646|MCAM|protein_coding|CODING|NM_006500.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0388146 rs1052121 -0.693147 0.0187887 181 646 918 MODIFIER 16 CODING MCAM C protein_coding NM_006500.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119179678 T C 0 9.7 0 0.6944 0.6366 0.7133 0.5149 0.7475 0.5153 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||918||646|MCAM|protein_coding|CODING|NM_006500.2|16|C),DOWNSTREAM(MODIFIER||819||906|CBL|protein_coding|CODING|NM_005188.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1131467 -0.379885 0 1 646 280 MODIFIER 16 CODING MCAM A protein_coding NM_006500.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119180316 G A 0 45.8 0 0.3835 0.4075 0.2911 0.497 0.2455 0.5971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 2,0,3,0 UTR_3_PRIME(MODIFIER||280||646|MCAM|protein_coding|CODING|NM_006500.2|16|A),DOWNSTREAM(MODIFIER||1457||906|CBL|protein_coding|CODING|NM_005188.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.666667 rs7914 -0.511536 0.185719 5 L600 646 ctA/ctG LOW 15 SILENT CODING MCAM C protein_coding NM_006500.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119181170 T C 0 222 0 0.767 0.7482 0.7695 0.6577 0.7107 0.8395 0.752615 0.72567 0.711874 1 7734 89849 9930 5557 4681 47677 654 13616 2 10396 121344 11578 8626 6614 66712 908 16510 0.986741 0 . 0 COSM1162429 68 17,13,14,14 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L600|646|MCAM|protein_coding|CODING|NM_006500.2|15|C),DOWNSTREAM(MODIFIER||2311||906|CBL|protein_coding|CODING|NM_005188.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.862168 rs2249466 -0.693054 0.022577 68 H180 579 caT/caC LOW 5 SILENT CODING MFRP G protein_coding NM_031433.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119216231 A G 0 228 0 0.8449 0.902 0.8732 0.875 0.9493 0.9785 0.873124 0.927702 0.955646 2 9121 113461 9922 7535 6210 63802 847 16024 2 10388 121170 11564 8646 6614 66542 904 16512 0 2 benign 0 . 45 0,0,14,27 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H180|579|MFRP|protein_coding|CODING|NM_031433.3|5|G),UPSTREAM(MODIFIER||4638||243|C1QTNF5|protein_coding|CODING|NM_001278431.1||G),INTRAGENIC(MODIFIER|||||C1QTNF5||CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2510143 -0.693145 0.0126064 45 Y164 579 taC/taT LOW 5 SILENT CODING MFRP A protein_coding NM_031433.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119216279 G A 0 222 0 0.2489 0.2015 0.1657 0.2024 0.2028 0.1605 0.236016 0.225054 0.219441 1 2354 25775 1268 1932 1885 15468 189 2679 2 10338 120690 11540 8620 6590 66196 900 16506 0.749312 3|2 likely-benign|benign 0 . 37 3,11,7,11 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y164|579|MFRP|protein_coding|CODING|NM_031433.3|5|A),UPSTREAM(MODIFIER||4686||243|C1QTNF5|protein_coding|CODING|NM_001278431.1||A),INTRAGENIC(MODIFIER|||||C1QTNF5||CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.83135 rs36015759 -0.691153 0.192221 37 579 31 MODIFIER 1 CODING MFRP T protein_coding NM_031433.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119217254 C T 0 228 0 0.5514 0.6356 0.5562 0.7748 0.5865 0.7127 0.5407 0.567293 0.580908 2 5553 71707 6685 6216 3511 38298 548 10896 2 10350 120498 11476 8598 6550 66122 902 16500 0 . 0 . 0 42 0,0,7,32 UTR_5_PRIME(MODIFIER||31||579|MFRP|protein_coding|CODING|NM_031433.3|1|T),INTRAGENIC(MODIFIER|||||C1QTNF5||CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386619272,rs883247 -0.693144 0.0153882 42 579 88 MODIFIER 1 CODING MFRP A protein_coding NM_031433.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119217311 G A 0 228 0 0.4395 0.5839 0.5115 0.7708 0.5249 0.6984 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 20 0,0,3,15 START_GAINED(LOW||||579|MFRP|protein_coding|CODING|NM_031433.3|1|A),UTR_5_PRIME(MODIFIER||88||579|MFRP|protein_coding|CODING|NM_031433.3|1|A),INTRAGENIC(MODIFIER|||||C1QTNF5||CODING|||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs883245 -0.691153 0.471467 20 Y346 605 taC/taT LOW 5 SILENT CODING USP2 A protein_coding NM_004205.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119229964 G A 0 228 0 0.5598 0.7077 0.6383 0.8611 0.7247 0.7812 0.570941 0.66061 0.706519 2 5807 86518 7332 7233 5066 47942 657 12481 2 10386 121110 11526 8636 6608 66560 904 16490 0.966292 0 . 0 . 99 2,0,39,50 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y346|605|USP2|protein_coding|CODING|NM_004205.4|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.955056 rs2241646 -0.693147 0.0112589 99 P32 605 ccG/ccA LOW 2 SILENT CODING USP2 T protein_coding NM_004205.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119244095 C T 0 228 0 0.5174 0.651 0.6095 0.8353 0.6252 0.6973 0.540473 0.583154 0.605006 2 5458 75294 7654 6863 3784 39897 565 11073 2 10196 120078 11484 8524 6504 65988 892 16490 0.992308 0 . 0 . 154 2,0,78,52 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P32|605|USP2|protein_coding|CODING|NM_004205.4|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.784615 rs587985 -0.693147 0.103883 154 605 8009 MODIFIER 1 CODING USP2 G protein_coding NM_004205.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119252199 T G 0 228 0 0.9788 0.9315 0.9294 0.9603 0.8728 0.8998 0 . 0 2 551 10969 171 191 3 3141 118 6794 2 564 12334 188 198 4 3632 132 7616 0 . 0 . 0 310 0,0,108,174 UTR_5_PRIME(MODIFIER||8009||605|USP2|protein_coding|CODING|NM_004205.4|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs386506847,rs670906 -0.693147 0.0214622 310 161 84 MODIFIER 4 CODING THY1 C protein_coding NM_001311160.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119290034 G C 0 228 0 0.3548 0.629 0.5692 0.88 0.6133 0.7996 0 . 0 2 1178 20448 666 1360 601 9644 174 6825 2 2598 29802 990 1574 902 14650 264 8824 0 . 0 . 0 108 0,0,36,64 UTR_3_PRIME(MODIFIER||84||161|THY1|protein_coding|CODING|NM_001311160.1|4|C),INTRAGENIC(MODIFIER|||||USP2-AS1||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1054735 -0.693147 0.887241 108 161 1097 MODIFIER 1 CODING THY1 C protein_coding NM_001311160.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119292712 T C 0 6.3 0 0.3684 0.6324 0.5692 0.879 0.6133 0.7996 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1097||161|THY1|protein_coding|CODING|NM_001311160.1|1|C),INTRAGENIC(MODIFIER|||||USP2-AS1||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1001205,rs386508787 -0.379885 0 1 517 3301 MODIFIER 6 CODING PVRL1 G protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119532156 A G 0 222 0 0.4962 0.1641 0.0461 0.1111 0.005 0.0174 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.90677 0 . 0 . 95 33,12,33,10 UTR_3_PRIME(MODIFIER||3301||517|PVRL1|protein_coding|CODING|NM_002855.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.361042 rs11217380 -0.693146 0.120811 95 517 3136 MODIFIER 6 CODING PVRL1 T protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119532321 C T 0 222 0 0.0008 0.0087859 0 0.0427 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.844604 0 . 0 . 93 16,22,16,28 UTR_3_PRIME(MODIFIER||3136||517|PVRL1|protein_coding|CODING|NM_002855.4|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.654589 rs76084281 -0.693146 0.36388 93 517 1139 MODIFIER 6 CODING PVRL1 T protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119534318 C T 0 9.7 0 0.0265 0.019369 0.0029 0.0437 0.004 0.0123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1139||517|PVRL1|protein_coding|CODING|NM_002855.4|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs60405761 -0.379885 0 1 517 532 MODIFIER 6 CODING PVRL1 G protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119534925 A G 0 165 0 0.0242 0.017971 0 0.0446 0 0.0133 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.897415 0 . 0 . 39 15,6,13,2 UTR_3_PRIME(MODIFIER||532||517|PVRL1|protein_coding|CODING|NM_002855.4|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.648595 rs138678304 -0.688148 0.163725 39 517 352 MODIFIER 6 CODING PVRL1 A protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119535105 G A 0 222 0 0.0008 0.011182 0 0.0427 0 0.0123 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.594699 0 . 0 . 89 25,10,28,12 UTR_3_PRIME(MODIFIER||352||517|PVRL1|protein_coding|CODING|NM_002855.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0644579 rs59681945 -0.693145 0.172376 89 517 72 MODIFIER 6 CODING PVRL1 C protein_coding NM_002855.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119535385 G C 0 117 0 0.0242 0.017572 0 0.0427 0 0.0133 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,1 UTR_3_PRIME(MODIFIER||72||517|PVRL1|protein_coding|CODING|NM_002855.4|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs59612995 -0.616816 0.23129 7 L273 588 Ttg/Ctg LOW 2 SILENT CODING TRIM29 G protein_coding NM_012101.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 119999191 A G 0 228 0 0.9917 0.9257 0.8761 0.9583 0.8569 0.909 0.976353 0.921081 0.892782 2 10150 110090 10591 8350 5985 59011 787 15216 2 10364 120994 11540 8630 6606 66476 904 16474 0 . 0 . 0 16 0,0,4,10 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L273|588|TRIM29|protein_coding|CODING|NM_012101.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs569044 -0.686358 0.738512 16 H154R 438 cAc/cGc MODERATE 7 MISSENSE CODING POU2F3 G protein_coding NM_001244682.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120175749 A G 0 228 0 0.9682 0.8303 0.7104 0.9405 0.5567 0.8967 0.891512 0.682636 0.575599 2 9461 83444 9311 8155 3429 38002 613 14473 2 10402 121328 11576 8654 6614 66678 906 16498 0 . 0 . 0 141 0,0,103,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H154R|438|POU2F3|protein_coding|CODING|NM_001244682.1|7|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.998274 0 . rs7110845 -0.693147 1.12758e-10 141 956 LOW 1 CODING GRIK4 T protein_coding NM_001282470.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120530973 C T 0 228 0 0.1687 0.5128 0.5418 0.7351 0.6352 0.6022 0.24422 0.49781 0.608108 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 51 0,0,39,7 SPLICE_SITE_REGION+INTRON(LOW||||956|GRIK4|protein_coding|CODING|NM_001282470.2|1|T) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs6589829 -0.693147 0.602205 51 E425 956 gaG/gaA LOW 12 SILENT CODING GRIK4 A protein_coding NM_001282470.2 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120776001 G A 0 228 0 0.9508 0.878 0.8084 0.9157 0.8638 0.8047 0.937131 0.880729 0.851826 2 9826 103846 8796 7856 5834 57516 789 13229 2 10402 121384 11574 8648 6614 66728 906 16512 1 0 . 0 . 103 1,0,63,28 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E425|956|GRIK4|protein_coding|CODING|NM_001282470.2|12|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2156634,rs386559038 -0.693147 0.408488 103 P545 956 ccG/ccA LOW 14 SILENT CODING GRIK4 A protein_coding NM_001282470.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120823608 G A 0 222 0 0.0772 0.2578 0.3674 0.3264 0.334 0.2751 0.115978 0.246693 0.313678 1 1163 38305 5046 2766 2680 21334 293 5023 2 10406 121406 11576 8652 6614 66738 908 16512 0.943417 0 . 0 . 107 15,22,27,25 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P545|956|GRIK4|protein_coding|CODING|NM_001282470.2|14|A),INTRAGENIC(MODIFIER|||||LOC101929208||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0830175 rs2298725 -0.693147 0.00825789 107 Q607 956 caA/caG LOW 15 SILENT CODING GRIK4 G protein_coding NM_001282470.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120827609 A G 0 228 0 0.416 0.7147 0.7709 0.9911 0.6779 0.8313 0.435996 0.605814 0.692836 2 4470 88389 9879 8617 4947 46285 634 13557 2 10340 121010 11560 8640 6594 66490 900 16486 0 . 0 . 0 93 0,0,27,60 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q607|956|GRIK4|protein_coding|CODING|NM_001282470.2|15|G),INTRAGENIC(MODIFIER|||||LOC101929208||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs644057 -0.693147 0.259683 93 424 1995 MODIFIER 8 CODING TBCEL A protein_coding NM_001130047.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 120959800 G A 0 54 0 0.1679 0.2151 0.1787 0.3244 0.1829 0.2249 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,1,1 UTR_3_PRIME(MODIFIER||1995||424|TBCEL|protein_coding|CODING|NM_001130047.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs2298491 -0.453602 0.56 4 S1724N 2155 aGc/aAc MODERATE 15 MISSENSE CODING TECTA A protein_coding NM_005422.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121032978 G A 0 228 0 0.9985 0.9968 0.9986 1 0.9881 0.999 0.997503 0.992079 0.9893 2 10374 120476 11524 8654 6561 65978 899 16486 2 10396 121366 11578 8654 6614 66706 906 16512 0 2 benign 0 . 98 0,0,45,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S1724N|2155|TECTA|protein_coding|CODING|NM_005422.2|15|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs526433 -0.693147 0.230974 98 299 81 MODIFIER 5 CODING SC5D C protein_coding NM_001024956.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121178302 A C 0 97 0 0.7625 0.7246 0.781 0.7103 0.6938 0.68 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.891517 0 . 0 . 11 0,5,1,5 UTR_3_PRIME(MODIFIER||81||299|SC5D|protein_coding|CODING|NM_001024956.2|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.0891517 rs1061332 -0.616816 0.441597 11 A551 2214 gcT/gcC LOW 12 SILENT CODING SORL1 C protein_coding NM_003105.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121403229 T C 0 228 0 0.9455 0.9852 0.9971 1 1 1 0.948706 0.982621 1 2 9860 120791 11526 8646 6614 66732 907 16506 2 10402 121356 11546 8646 6614 66732 908 16508 0 . 0 . 0 78 0,0,30,40 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A551|2214|SORL1|protein_coding|CODING|NM_003105.5|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs636588 -0.693147 0.0199747 78 Q1074E 2214 Caa/Gaa MODERATE 22 MISSENSE CODING SORL1 G protein_coding NM_003105.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121437819 C G 0 228 0 0.9448 0.9848 0.9957 1 1 1 0.940309 0.979699 0.999884 2 9813 120710 11549 8644 6612 66682 907 16503 2 10404 121328 11572 8644 6612 66684 908 16504 0 . 0 . 0 101 0,0,33,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1074E|2214|SORL1|protein_coding|CODING|NM_003105.5|22|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1699107 -0.693147 0.155395 101 S1187 2214 tcT/tcG LOW 25 SILENT CODING SORL1 G protein_coding NM_003105.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121448090 T G 0 222 0 0.0787 0.3409 0.438 0.5685 0.2406 0.4949 0.10168 0.187558 0.231565 1 1059 37401 6363 4994 1653 15752 296 7284 2 10372 119598 11570 8626 6612 66092 884 15442 0.580071 0 . 0 COSM147339 164 40,39,28,31 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S1187|2214|SORL1|protein_coding|CODING|NM_003105.5|25|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981828 rs2070045 -0.693147 0.0649659 164 A1584 2214 gcT/gcA LOW 34 SILENT CODING SORL1 A protein_coding NM_003105.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121475922 T A 0 222 0 0.1324 0.3962 0.4899 0.5883 0.3032 0.5838 0.146164 0.254922 0.310654 1 1534 46146 6636 5250 2506 20866 373 8981 2 10404 121080 11576 8644 6610 66598 904 16344 0.582071 0 . 0 . 139 29,28,36,31 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A1584|2214|SORL1|protein_coding|CODING|NM_003105.5|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.932618 rs3824968 -0.693147 0.553835 139 V1967I 2214 Gtt/Att MODERATE 44 MISSENSE CODING SORL1 A protein_coding NM_003105.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121491782 G A 0 228 0 0.9259 0.9794 0.9928 1 1 1 0.950954 0.98331 0.999884 2 9867 120733 11551 8654 6614 66656 902 16489 2 10402 121304 11576 8654 6614 66664 904 16490 0 . 0 . 0 65 0,0,50,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1967I|2214|SORL1|protein_coding|CODING|NM_003105.5|44|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1792120,rs386482492 -0.693147 0.235761 65 2214 1134 MODIFIER 48 CODING SORL1 C protein_coding NM_003105.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121501406 T C 0 9.7 0 0.056 0.3826 0.4078 0.5556 0.4742 0.5337 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1134||2214|SORL1|protein_coding|CODING|NM_003105.5|48|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10790449 -0.379885 0 1 2214 1483 MODIFIER 48 CODING SORL1 A protein_coding NM_003105.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121501755 G A 0 9.7 0 0.8033 0.6358 0.5476 0.7401 0.4423 0.5634 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1483||2214|SORL1|protein_coding|CODING|NM_003105.5|48|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1133174 -0.379885 0 1 2214 3909 MODIFIER 48 CODING SORL1 C protein_coding NM_003105.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 121504181 A C 0 9.7 0 0.0023 0.0545 0.0908 0.2014 0.002 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3909||2214|SORL1|protein_coding|CODING|NM_003105.5|48|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs77931594 -0.379885 0 1 A68T 649 Gca/Aca MODERATE 2 MISSENSE CODING UBASH3B A protein_coding NM_032873.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122646967 G A 0 222 0 0.0325 0.1957 0.3069 0.1726 0.3111 0.2423 0.0853769 0.240886 0.32054 1 765 33034 3205 1687 1562 21122 280 4413 2 10372 121152 11546 8642 6600 66610 908 16474 0.819313 0 . 0 COSM147340 70 21,10,19,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A68T|649|UBASH3B|protein_coding|CODING|NM_032873.4|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.282499 rs12790613 -0.693021 0.0720262 70 S336 649 tcA/tcG LOW 7 SILENT CODING UBASH3B G protein_coding NM_032873.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122665437 A G 0 228 0 0.7602 0.5623 0.5317 0.5615 0.3917 0.4928 0.698683 0.501692 0.400791 2 7363 55077 5936 4908 1934 26186 394 8356 2 10406 121392 11578 8642 6614 66732 908 16512 0 . 0 . 0 47 0,0,24,22 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S336|649|UBASH3B|protein_coding|CODING|NM_032873.4|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs872414 -0.693147 0.726734 47 649 LOW 7 CODING UBASH3B T protein_coding NM_032873.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122665549 C T 0 222 0 0.2209 0.1759 0.1614 0.0119 0.2247 0.2444 0.229337 0.246193 0.254827 1 2361 25481 1512 121 795 16256 205 4231 2 10400 121384 11576 8654 6614 66722 906 16512 0.995275 0 . 0 . 55 14,9,17,10 SPLICE_SITE_REGION+INTRON(LOW||||649|UBASH3B|protein_coding|CODING|NM_032873.4|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984772 rs11218816 -0.693021 0.171618 55 649 940 MODIFIER 14 CODING UBASH3B G protein_coding NM_032873.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122681534 A G 0 39.3 0 0.1021 0.1152 0.1023 0.2629 0.0239 0.0838 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||940||649|UBASH3B|protein_coding|CODING|NM_032873.4|14|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1557455 -0.453602 0.38 2 K321R 393 aAa/aGa MODERATE 8 MISSENSE CODING CRTAM G protein_coding NM_019604.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122738261 A G 0 228 0 0.3646 0.5503 0.7478 0.4325 0.7316 0.5961 0.421208 0.62152 0.724122 2 4291 80721 8574 3826 4513 48440 610 10467 2 10382 121120 11542 8628 6584 66578 904 16502 0 . 0 . 0 98 0,0,53,37 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|aAa/aGa|K321R|393|CRTAM|protein_coding|CODING|NM_019604.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2272094 -0.693147 0.00358262 98 393 321 MODIFIER 10 CODING CRTAM G protein_coding NM_019604.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122742428 T G 0 197 0 0.3956 0.2746 0.366 0.2629 0.166 0.1697 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.453089 0 . 0 . 37 1,18,2,14 UTR_3_PRIME(MODIFIER||321||393|CRTAM|protein_coding|CODING|NM_019604.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.930061 rs7126620 -0.689466 0.0534108 37 393 353 MODIFIER 10 CODING CRTAM T protein_coding NM_019604.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122742460 A T 0 171 0 0.5371 0.7254 0.7579 0.8323 0.7744 0.7965 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,1,14 UTR_3_PRIME(MODIFIER||353||393|CRTAM|protein_coding|CODING|NM_019604.3|10|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3134421 -0.688148 0.0509106 17 393 700 MODIFIER 10 CODING CRTAM A protein_coding NM_019604.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122742807 C A 0 9.7 0 0.0787 0.3057 0.3991 0.1577 0.5666 0.4305 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||700||393|CRTAM|protein_coding|CODING|NM_019604.3|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs67366392 -0.379885 0 1 393 715 MODIFIER 10 CODING CRTAM G protein_coding NM_019604.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122742822 A G 0 9.7 0 0.8464 0.9311 0.928 0.9722 0.9592 0.9765 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||715||393|CRTAM|protein_coding|CODING|NM_019604.3|10|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3107607 -0.379885 0 1 393 1097 MODIFIER 10 CODING CRTAM C protein_coding NM_019604.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122743204 T C 0 185 0 0.0787 0.3059 0.3991 0.1587 0.5666 0.4305 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.625535 0 . 0 . 55 29,3,18,2 UTR_3_PRIME(MODIFIER||1097||393|CRTAM|protein_coding|CODING|NM_019604.3|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.764109 rs55783424 -0.692067 0.114584 55 D316 778 gaT/gaC LOW 4 SILENT CODING C11orf63 C protein_coding NM_024806.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122795688 T C 0 222 0 0.0764 0.1803 0.2104 0.2024 0.2903 0.1636 0.112398 0.240732 0.306467 1 1105 29565 1580 1725 2003 20025 250 2877 2 10400 121300 11560 8624 6612 66696 908 16500 0.950869 0 . 0 . 139 35,36,21,31 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D316|778|C11orf63|protein_coding|CODING|NM_024806.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.910666 rs11218891 -0.693147 0.467298 139 778 61 MODIFIER 9 CODING C11orf63 A protein_coding NM_024806.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122830214 G A 0 144 0 0.5348 0.4577 0.3718 0.3571 0.5706 0.4018 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.497203 0 . 0 . 42 1,22,1,17 UTR_3_PRIME(MODIFIER||61||778|C11orf63|protein_coding|CODING|NM_024806.3|9|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997846 rs7107502 -0.691153 0.492861 42 778 98 MODIFIER 9 CODING C11orf63 G protein_coding NM_024806.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122830251 T G 0 114 0 0.3018 0.221 0.1153 0.3145 0.1402 0.1738 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.990797 0 . 0 . 25 0,13,0,12 UTR_3_PRIME(MODIFIER||98||778|C11orf63|protein_coding|CODING|NM_024806.3|9|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.822311 rs1057703 -0.680642 0.913441 25 778 121 MODIFIER 9 CODING C11orf63 C protein_coding NM_024806.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122830274 T C 0 91 0 0.5242 0.4547 0.3703 0.3571 0.5706 0.4018 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.759945 0 . 0 . 16 0,9,0,7 UTR_3_PRIME(MODIFIER||121||778|C11orf63|protein_coding|CODING|NM_024806.3|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.0664381 rs1057704 -0.636426 0.219617 16 A587 646 gcT/gcC LOW 9 SILENT CODING HSPA8 G protein_coding NM_006597.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 122928622 A G 0 222 0 0.5703 0.4323 0.3631 0.5506 0.2227 0.3885 0.513397 0.331872 0.238893 1 5459 38954 5146 5002 1604 15577 243 5923 2 10284 119612 11558 8620 6610 66152 890 15498 0.737649 0 . 0 . 59 15,13,10,14 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A587|646|HSPA8|protein_coding|CODING|NM_006597.5|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.259387 rs4802 -0.692831 0.697385 59 373 35 MODIFIER 1 CODING CLMP T protein_coding NM_024769.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123065683 C T 0 228 0 0.1029 0.4822 0.6571 0.5933 0.5924 0.6431 0.194432 0.431048 0.55164 2 1738 62104 7604 4800 3485 34087 458 9932 2 9138 111878 10896 8162 5600 61260 812 16010 1 0 . 0 . 99 0,1,12,77 UTR_5_PRIME(MODIFIER||35||373|CLMP|protein_coding|CODING|NM_024769.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2302605 -0.693147 0.0970973 99 E317 745 gaG/gaA LOW 11 SILENT CODING GRAMD1B A protein_coding NM_001286563.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123477352 G A 0 222 0 0.1944 0.2694 0.2493 0.1736 0.3012 0.4509 0.2257 0.288512 0.318347 1 2111 35492 3172 1456 1774 20216 273 6490 2 8502 108176 9864 7532 5940 60692 794 14852 0.999433 0 . 0 . 91 34,18,16,14 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E317|745|GRAMD1B|protein_coding|CODING|NM_001286563.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.666904 rs2279519 -0.693097 0.939336 91 H482 745 caT/caC LOW 14 SILENT CODING GRAMD1B C protein_coding NM_001286563.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123480981 T C 0 222 0 0.0719 0.2418 0.2392 0.1746 0.3141 0.4683 0.100924 0.252078 0.326071 1 992 36387 3254 1474 1898 21438 284 7047 2 9816 120734 11568 8602 6612 66728 900 16508 0.992554 0 . 0 . 164 45,37,36,28 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H482|745|GRAMD1B|protein_coding|CODING|NM_001286563.1|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.500077 rs10893053 -0.693147 0.157029 164 745 550 MODIFIER 21 CODING GRAMD1B G protein_coding NM_001286563.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123493853 A G 0 63 0 0.5825 0.8009 0.8069 0.9921 0.8181 0.8773 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||550||745|GRAMD1B|protein_coding|CODING|NM_001286563.1|21|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1148116,rs386518427 -0.453602 0.56 3 745 1702 MODIFIER 21 CODING GRAMD1B C protein_coding NM_001286563.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123495005 T C 0 64 0 0.6362 0.7326 0.611 0.9385 0.6998 0.771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||1702||745|GRAMD1B|protein_coding|CODING|NM_001286563.1|21|C),DOWNSTREAM(MODIFIER||4890||215|SCN3B|protein_coding|CODING|NM_001040151.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11219210 -0.511536 0.21346 3 V244 648 gtA/gtG LOW 6 SILENT CODING ZNF202 C protein_coding NM_001301779.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123598941 T C 0 222 0 0.0159 0.2292 0.2968 0.3552 0.2694 0.2986 0.0599455 0.205738 0.280414 1 539 31715 3563 3111 1940 17954 224 4384 2 10406 121366 11576 8618 6612 66736 908 16510 0.897453 0 . 0 . 194 48,26,52,32 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V244|648|ZNF202|protein_coding|CODING|NM_001301779.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.786307 rs2282644 -0.693147 0.12669 194 T276K 313 aCa/aAa MODERATE 1 MISSENSE CODING OR6M1 T protein_coding NM_001005325.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123676231 G T 0 222 0 0.1029 0.2434 0.317 0.2946 0.2853 0.2853 0.122616 0.23904 0.298674 1 1256 33601 3763 2731 2059 19096 249 4447 2 10406 121300 11520 8628 6612 66716 908 16510 0.835543 0 . 0 COSM1352200 122 34,26,30,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T276K|313|OR6M1|protein_coding|CODING|NM_001005325.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414265 rs4936845 -0.693147 0.0499108 122 225 159 MODIFIER 4 CODING TMEM225 A protein_coding NM_001013743.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123753686 G A 0 81 0 0.3608 0.4533 0.5447 0.5327 0.4364 0.4489 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.927743 0 . 0 . 14 8,0,6,0 UTR_3_PRIME(MODIFIER||159||225|TMEM225|protein_coding|CODING|NM_001013743.2|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs1054041 -0.616816 0.189016 14 C196R 225 Tgc/Cgc MODERATE 4 MISSENSE CODING TMEM225 G protein_coding NM_001013743.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123753937 A G 0 222 0 0.9962 0.9153 0.9193 0.8353 0.8847 0.9172 0.977066 0.909706 0.875204 1 10206 108492 10923 7145 5813 58730 803 14872 2 10406 121200 11486 8590 6610 66690 906 16512 0.841634 0 . 0 . 147 19,35,40,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C196R|225|TMEM225|protein_coding|CODING|NM_001013743.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999271 rs1939927 -0.693147 0.0607532 147 N134S 225 aAt/aGt MODERATE 3 MISSENSE CODING TMEM225 C protein_coding NM_001013743.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123754844 T C 0 228 0 1 1 1 1 1 1 1 0.999385 0.99907 2 10402 121209 11502 8606 6612 66669 908 16510 2 10404 121254 11506 8606 6612 66708 908 16510 0 . 0 . 0 87 0,0,19,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N134S|225|TMEM225|protein_coding|CODING|NM_001013743.2|3|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.944294 0 . rs10893099 -0.693147 0.457562 87 C120Y 314 tGc/tAc MODERATE 1 MISSENSE CODING OR8D4 A protein_coding NM_001005197.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123777497 G A 0 228 0 0.8986 0.8077 0.8718 0.7688 0.8032 0.684 0.875341 0.819335 0.790649 2 9096 97268 10339 6889 5476 53274 721 11473 2 10406 121364 11576 8626 6610 66728 908 16510 0 . 0 . 0 91 0,0,44,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C120Y|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10750250 -0.693147 0.242153 91 C120 314 tgC/tgT LOW 1 SILENT CODING OR8D4 T protein_coding NM_001005197.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123777498 C T 0 228 0 0.0794 0.2666 0.3271 0.378 0.3151 0.3119 0.12693 0.261114 0.329844 2 1249 37538 4488 3343 2320 21026 260 4852 2 10404 121350 11574 8612 6612 66730 908 16510 0 . 0 . 0 91 0,0,44,42 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C120|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10893102 -0.693147 0.244442 91 R133K 314 aGg/aAg MODERATE 1 MISSENSE CODING OR8D4 A protein_coding NM_001005197.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123777536 G A 0 228 0 0.6475 0.6873 0.7911 0.7262 0.6809 0.6339 0.646004 0.675742 0.690975 2 6754 84772 9868 6409 4695 46035 635 10376 2 10406 121344 11578 8618 6608 66718 908 16508 0 . 0 . 0 83 0,0,35,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R133K|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7926767 -0.693147 0.053363 83 F200L 314 Ttt/Ctt MODERATE 1 MISSENSE CODING OR8D4 C protein_coding NM_001005197.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123777736 T C 0 228 0 0.0794 0.2678 0.3271 0.378 0.3141 0.319 0.127384 0.262498 0.331705 2 1248 37626 4490 3353 2319 21026 260 4930 2 10386 121298 11574 8614 6612 66698 908 16506 0 . 0 . 0 45 0,0,23,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F200L|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10790610 -0.693146 0.790024 45 L283P 314 cTc/cCc MODERATE 1 MISSENSE CODING OR8D4 C protein_coding NM_001005197.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123777986 T C 0 228 0 0.8986 0.8079 0.8718 0.7688 0.8042 0.684 0.874432 0.819182 0.790882 2 9036 97091 10329 6837 5470 53232 721 11466 2 10356 121140 11564 8564 6606 66654 908 16488 0 . 0 . 0 80 0,0,45,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L283P|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7942047 -0.693147 0.0992267 80 R298K 314 aGa/aAa MODERATE 1 MISSENSE CODING OR8D4 A protein_coding NM_001005197.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123778031 G A 0 228 0 0.6467 0.6877 0.7911 0.7262 0.6809 0.637 0.646912 0.67505 0.689463 2 6441 83729 9844 6316 4683 45601 630 10214 2 9912 119432 11550 8506 6592 66022 890 15960 0 . 0 . 0 83 0,0,42,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R298K|314|OR8D4|protein_coding|CODING|NM_001005197.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7927385 -0.693147 0.395705 83 C241 323 tgC/tgT LOW 1 SILENT CODING OR6T1 A protein_coding NM_001005187.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123813823 G A 0 228 0 0.0552 0.2628 0.3228 0.3839 0.3181 0.319 0.108084 0.257268 0.333682 2 1018 37602 4491 3447 2322 21133 265 4926 2 10404 121346 11572 8618 6612 66722 908 16510 0.547491 0 . 0 . 175 2,1,64,98 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C241|323|OR6T1|protein_coding|CODING|NM_001005187.1|1|A),DOWNSTREAM(MODIFIER||2543||318|OR4D5|protein_coding|CODING|NM_001001965.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.98751 rs7129884 -0.693147 0.283381 175 L202 323 ctC/ctG LOW 1 SILENT CODING OR6T1 C protein_coding NM_001005187.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123813940 G C 0 228 0 0.0582 0.2632 0.3199 0.3839 0.3181 0.319 0.109219 0.257345 0.333217 2 1036 37550 4482 3443 2316 21083 265 4925 2 10400 121260 11560 8596 6604 66682 906 16512 0 . 0 . 0 112 0,0,37,67 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L202|323|OR6T1|protein_coding|CODING|NM_001005187.1|1|C),DOWNSTREAM(MODIFIER||2660||318|OR4D5|protein_coding|CODING|NM_001001965.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7130003 -0.693147 0.291201 112 S19 323 agT/agC LOW 1 SILENT CODING OR6T1 G protein_coding NM_001005187.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123814489 A G 0 228 0 0.056 0.263 0.3228 0.3839 0.3181 0.319 0.108084 0.257422 0.333915 2 1019 37610 4491 3458 2322 21131 265 4924 2 10394 121166 11562 8616 6614 66636 908 16436 0 . 0 . 0 110 0,0,45,54 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S19|323|OR6T1|protein_coding|CODING|NM_001005187.1|1|G),DOWNSTREAM(MODIFIER||3209||318|OR4D5|protein_coding|CODING|NM_001001965.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4936859 -0.693147 0.304591 110 A9 311 gcA/gcG LOW 1 SILENT CODING OR10G4 G protein_coding NM_001004462.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123886308 A G 0 228 0 0.5219 0.6629 0.804 0.7173 0.7276 0.6309 0.563579 0.684664 0.746685 2 5877 86266 9750 6036 5029 49813 634 9127 2 10376 118796 11438 8466 6556 65820 878 15262 0 . 0 . 0 75 0,0,24,49 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A9|311|OR10G4|protein_coding|CODING|NM_001004462.1|1|G) 1 0 . 0 . 1 0 1 1 0 53 0 0 0.000300072 0 . rs11219407 -0.693147 0.0322101 75 T13 311 acA/acG LOW 1 SILENT CODING OR10G4 G protein_coding NM_001004462.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123886320 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 406 17039 1913 1724 1318 10230 107 1341 2 10212 112208 10178 7890 6062 61822 822 15222 0.957353 0 . 0 . 63 3,0,17,42 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T13|311|OR10G4|protein_coding|CODING|NM_001004462.1|1|G) 0 . 0 . 0 . 0 . 1 0 51 0 0.957353 2.76077e-06 0 0.168809 rs12224056 -0.693147 0.0324795 63 L24P 311 cTc/cCc MODERATE 1 MISSENSE CODING OR10G4 C protein_coding NM_001004462.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123886352 T C 0 169 0 . 0 . 0 . 0 . 0 . 2 549 17939 2040 1752 1423 10422 129 1624 2 10142 110964 9914 7780 6030 60922 830 15346 0.998124 0 . 0 . 52 3,0,4,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L24P|311|OR10G4|protein_coding|CODING|NM_001004462.1|1|C) 0 . 0 . 0 . 0 . 1 0 54 0 0.919948 0.0379181 0 0.839098 rs547068 -0.693147 0.827254 52 V195E 311 gTg/gAg MODERATE 1 MISSENSE CODING OR10G4 A protein_coding NM_001004462.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123886865 T A 0 228 0 0.5083 0.6605 0.7997 0.7232 0.7276 0.6339 0.562699 0.695308 0.763201 2 5788 88851 9896 6319 5090 50753 663 10342 2 10406 121404 11578 8652 6614 66734 908 16512 0 . 0 . 0 270 0,0,128,123 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V195E|311|OR10G4|protein_coding|CODING|NM_001004462.1|1|A) 1 0 . 0 . 1 0 1 1 0 58 0 0 0.982993 0 . rs4084209,rs55884373 -0.693147 0.02688 270 L301 311 ctT/ctG LOW 1 SILENT CODING OR10G4 G protein_coding NM_001004462.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123887184 T G 0 228 0 0.5166 0.6617 0.804 0.7173 0.7266 0.6329 0.571104 0.698 0.762968 2 5862 88510 9896 6231 5088 50608 661 10164 2 10390 120526 11566 8620 6612 66508 902 15928 0 . 0 . COSM147353 197 0,0,39,144 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L301|311|OR10G4|protein_coding|CODING|NM_001004462.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 1 0 . rs4936882 -0.693147 0.0183442 197 R89 311 Agg/Cgg LOW 1 SILENT CODING OR10G9 C protein_coding NM_001001953.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123893984 A C 0 228 0 0.0333 0.2302 0.2983 0.3591 0.2843 0.2597 0 . 0 2 578 25717 3225 2245 1623 14482 194 3370 2 8300 99876 9364 7166 5496 53964 754 14832 0.325862 0 . 0 . 56 0,10,14,32 SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R89|311|OR10G9|protein_coding|CODING|NM_001001953.1|1|C) 0 . 0 . 0 1 0 . 1 0 50 0 0.000247424 0.474846 0 0.890612 rs148015773 -0.693147 0.053309 56 A90V 311 gCt/gTt MODERATE 1 MISSENSE CODING OR10G9 T protein_coding NM_001001953.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123893988 C T 0 228 0 0.0333 0.2294 0.2983 0.3591 0.2843 0.2556 0 . 0 2 576 25435 3175 2219 1590 14363 193 3319 2 8160 98076 9062 7086 5376 52918 748 14726 0.856786 0 . 0 . 57 0,10,15,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A90V|311|OR10G9|protein_coding|CODING|NM_001001953.1|1|T) 0 . 0 . 0 1 0 . 1 0 50 0 0.000231853 0.401973 0 0.856786 rs145930558 -0.693147 0.112557 57 R139 311 agA/agG LOW 1 SILENT CODING OR10G9 G protein_coding NM_001001953.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123894136 A G 0 228 0 0.9077 0.8233 0.8876 0.7837 0.8469 0.68 0 . 0 2 9355 102026 10381 6793 5843 57596 755 11303 2 10324 120588 11488 8480 6594 66370 902 16430 0 . 0 . 0 87 0,0,79,6 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R139|311|OR10G9|protein_coding|CODING|NM_001001953.1|1|G) 0 . 0 . 0 1 0 . 1 0 55 0 0 0.0524944 0 . rs28499345 -0.693147 0.15711 87 Q172R 311 cAg/cGg MODERATE 1 MISSENSE CODING OR10G9 G protein_coding NM_001001953.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123894234 A G 0 228 0 0.1407 0.3129 0.4553 0.503 0.2922 0.2699 0.163789 0.259077 0.307862 2 1752 39784 6736 4502 2469 19929 289 4107 2 10406 121398 11578 8642 6614 66738 908 16512 1 0 . 0 COSM147358 256 1,0,161,77 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q172R|311|OR10G9|protein_coding|CODING|NM_001001953.1|1|G) 1 0 . 0 . 1 0 1 1 0 58 0 1 0.584658 0 1 rs11219413 -0.693147 0.0084912 256 H228R 311 cAc/cGc MODERATE 1 MISSENSE CODING OR10G9 G protein_coding NM_001001953.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123894402 A G 0 228 0 0.1664 0.3255 0.4568 0.505 0.2922 0.2965 0.194684 0.271308 0.310537 2 1962 40495 6767 4528 2471 19945 292 4530 2 10406 121354 11574 8626 6612 66726 908 16502 1 0 . 0 COSM147361 232 1,0,93,127 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H228R|311|OR10G9|protein_coding|CODING|NM_001001953.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.923101 0 1 rs12221656 -0.693147 0.19207 232 L212 311 ctG/ctC LOW 1 SILENT CODING OR10G7 G protein_coding NM_001004463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909073 C G 0 228 0 0.0356 0.2398 0.3026 0.3363 0.2873 0.3231 0.0863636 0.233267 0.308444 2 781 34865 4430 2997 2050 19501 256 4850 2 10404 121366 11572 8624 6610 66736 908 16512 1 0 . 0 . 257 1,0,125,115 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L212|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.970186 0 1 rs11219419 -0.693147 0.180379 257 D179 311 gaC/gaT LOW 1 SILENT CODING OR10G7 A protein_coding NM_001004463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909172 G A 0 228 0 0.0356 0.2254 0.2867 0.3135 0.2823 0.2894 0.0856429 0.229378 0.303002 2 753 30018 3653 2499 1781 17019 223 4090 2 10400 121118 11552 8634 6588 66602 906 16436 0.995149 0 . 0 . 267 6,1,124,111 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D179|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|A) 1 0 . 0 . 1 0 1 1 0 56 0 0.0324021 0.0043145 0 0.981261 rs28414940 -0.693147 0.0494379 267 L123 311 Ctg/Ttg LOW 1 SILENT CODING OR10G7 A protein_coding NM_001004463.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909342 G A 0 228 0 0.0363 0.2372 0.2983 0.3264 0.2853 0.3241 0.0822727 0.218264 0.287858 2 802 34752 4393 2903 2079 19442 255 4878 2 10402 121374 11576 8638 6614 66724 908 16512 0.857143 0 . 0 . 177 0,2,65,103 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L123|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|A) 1 0 . 0 . 1 0 1 1 0 56 0 0.875 0.157114 0 0.723214 rs470242 -0.693147 4.69697e-10 177 G20A 311 gGg/gCg MODERATE 1 MISSENSE CODING OR10G7 G protein_coding NM_001004463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909650 C G 0 221 0 0.1997 0.2564 0.268 0.3016 0.2495 0.2853 0 . 0 1 2134 31239 3643 2744 1739 16591 217 4171 2 10374 121046 11576 8626 6614 66570 904 16382 0.980788 0 . 0 . 220 10,37,55,92 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G20A|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|G) 0 0.5 1 0 . 1 0 . 1 0 47 0 5.86679e-09 0.00179745 0 6.98128e-11 rs3894199 -0.693147 8.24919e-09 220 P19Q 311 cCa/cAa MODERATE 1 MISSENSE CODING OR10G7 T protein_coding NM_001004463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909653 G T 0 221 0 0.1997 0.2564 0.268 0.3016 0.2495 0.2853 0 . 0 1 2136 31240 3643 2742 1739 16591 217 4172 2 10374 121046 11576 8624 6614 66566 904 16388 0.947616 0 . 0 . 215 7,38,55,92 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cAa|P19Q|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|T) 0 0.5 1 0 . 1 0 . 1 0 47 0 2.58901e-08 0.000375464 0 2.96514e-08 rs4998340 -0.693147 7.76654e-09 215 A18V 311 gCc/gTc MODERATE 1 MISSENSE CODING OR10G7 A protein_coding NM_001004463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909656 G A 0 220 0 0.1997 0.2564 0.268 0.3016 0.2495 0.2853 0 . 0 1 2135 31237 3643 2740 1739 16591 217 4172 2 10374 121026 11576 8622 6614 66568 904 16368 0.852037 0 . 0 . 211 5,38,55,92 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A18V|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 47 0 6.30397e-08 0.000263525 0 2.64711e-06 rs3894198 -0.693147 8.24919e-09 211 T5S 311 aCc/aGc MODERATE 1 MISSENSE CODING OR10G7 C protein_coding NM_001004463.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 123909695 G C 0 228 0 0.3828 0.6182 0.781 0.6964 0.7237 0.6319 0.4675 0.659101 0.757153 2 4646 86771 9668 6387 5073 50430 652 9915 2 10388 121012 11570 8648 6612 66602 906 16286 1 0 . 0 . 140 0,1,32,95 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aGc|T5S|311|OR10G7|protein_coding|CODING|NM_001004463.1|1|C) 1 0 . 0 . 1 0 1 1 0 55 0 1 0.326229 0 1 rs3894197 -0.693147 0.529288 140 H735 786 caC/caT LOW 18 SILENT CODING VWA5A T protein_coding NM_001130142.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124015994 C T 0 228 0 0.7821 0.6046 0.5403 0.7093 0.5229 0.3865 0.708542 0.586077 0.523378 2 7545 66307 6010 6492 3718 34626 491 7425 2 10398 121292 11550 8644 6604 66690 908 16498 0 . 0 . 0 101 0,0,44,52 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H735|786|VWA5A|protein_coding|CODING|NM_001130142.1|18|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1056615 -0.693147 0.152004 101 786 88 MODIFIER 19 CODING VWA5A T protein_coding NM_001130142.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124016740 A T 0 180 0 0.9017 0.7025 0.6124 0.7788 0.6074 0.5164 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 54 0,0,0,54 UTR_3_PRIME(MODIFIER||88||786|VWA5A|protein_coding|CODING|NM_001130142.1|19|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9326269 -0.693147 0.293006 54 786 168 MODIFIER 19 CODING VWA5A G protein_coding NM_001130142.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124016820 A G 0 208 0 0.3578 0.4046 0.4207 0.6429 0.3986 0.2168 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,1,14 UTR_3_PRIME(MODIFIER||168||786|VWA5A|protein_coding|CODING|NM_001130142.1|19|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3824997 -0.688148 0.599011 15 786 439 MODIFIER 19 CODING VWA5A T protein_coding NM_001130142.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124017091 C T 0 103 0 0.8661 0.6869 0.6037 0.7788 0.5905 0.5082 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||439||786|VWA5A|protein_coding|CODING|NM_001130142.1|19|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1939861,rs386549792 -0.556411 0.10325 4 786 506 MODIFIER 19 CODING VWA5A G protein_coding NM_001130142.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124017158 C G 0 9.7 0 0.8517 0.6827 0.5994 0.7798 0.5905 0.5082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||506||786|VWA5A|protein_coding|CODING|NM_001130142.1|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1939860 -0.379885 0 1 786 841 MODIFIER 19 CODING VWA5A A protein_coding NM_001130142.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124017493 G A 0 20.4 0 0.0401 0.1969 0.255 0.4306 0.2107 0.1125 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||841||786|VWA5A|protein_coding|CODING|NM_001130142.1|19|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4936894 -0.453602 0.44 2 *259Y 308 taG/taC HIGH 1 MISSENSE CODING OR8G1 C protein_coding NM_001002905.1 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124121199 G C 0 222 0 0.3154 0.4447 0.5591 0.5833 0.5527 0.2843 0.352161 0.483789 0.547219 1 3508 60226 6389 5038 3819 36032 444 4996 2 9804 120548 11460 8600 6612 66660 900 16512 0.753659 0 . 0 . 86 9,21,13,34 STOP_LOST(HIGH|MISSENSE|taG/taC|*259Y|308|OR8G1|protein_coding|CODING|NM_001002905.1|1|C|WARNING_TRANSCRIPT_INCOMPLETE) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.747721 rs4268525 -0.693147 0.0887878 86 G7 346 ggG/ggA LOW 1 SILENT CODING OR8G5 A protein_coding NM_001005198.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124134743 G A 0 222 0 0.292 0.4383 0.5591 0.5823 0.5527 0.2843 0.338816 0.482125 0.546224 1 2929 52269 5352 4339 3459 31306 390 4494 2 7786 96662 8888 7156 5754 54140 732 12206 0.544694 0 . 0 . 61 15,22,13,10 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G7|346|OR8G5|protein_coding|CODING|NM_001005198.1|1|A),INTRON(MODIFIER||||308|OR8G1|protein_coding|CODING|NM_001002905.1|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.744707 rs2466637 -0.692717 0.530252 61 C96Y 346 tGt/tAt MODERATE 1 MISSENSE CODING OR8G5 A protein_coding NM_001005198.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124135009 G A 0 222 0 0.292 0.4385 0.5591 0.5833 0.5527 0.2843 0.31789 0.46517 0.540187 1 3324 59940 6397 4995 3814 35972 445 4993 2 9884 120704 11532 8592 6610 66672 904 16510 0.760459 0 . 0 . 337 106,53,91,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C96Y|346|OR8G5|protein_coding|CODING|NM_001005198.1|1|A),INTRON(MODIFIER||||308|OR8G1|protein_coding|CODING|NM_001002905.1|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.745642 0.462097 0 0.265596 rs2512168 -0.693147 0.992139 337 G239E 346 gGa/gAa MODERATE 1 MISSENSE CODING OR8G5 A protein_coding NM_001005198.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124135438 G A 0 222 0 0.292 0.4385 0.5591 0.5833 0.5527 0.2843 0.331081 0.47519 0.54568 1 3313 60101 6436 5051 3820 36043 444 4994 2 9836 120806 11568 8642 6614 66732 902 16512 0.866429 0 . 0 . 178 56,33,48,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G239E|346|OR8G5|protein_coding|CODING|NM_001005198.1|1|A),INTRON(MODIFIER||||308|OR8G1|protein_coding|CODING|NM_001002905.1|1|A|WARNING_TRANSCRIPT_INCOMPLETE) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903507 rs2512167 -0.693147 0.0399055 178 Y253 346 taC/taT LOW 1 SILENT CODING OR8G5 T protein_coding NM_001005198.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124135481 C T 0 222 0 0.292 0.4385 0.5591 0.5833 0.5527 0.2843 0.335028 0.476035 0.54728 1 3318 60112 6436 5054 3820 36046 444 4994 2 9852 120824 11568 8646 6612 66734 902 16510 0.947535 0 . 0 . 208 56,39,61,30 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y253|346|OR8G5|protein_coding|CODING|NM_001005198.1|1|T),INTRON(MODIFIER||||308|OR8G1|protein_coding|CODING|NM_001002905.1|1|T|WARNING_TRANSCRIPT_INCOMPLETE) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.942779 rs2466701 -0.693147 0.174288 208 V276 308 gtG/gtA LOW 1 SILENT CODING OR8D1 T protein_coding NM_001002917.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124179835 C T 0 222 0 0.1626 0.2875 0.3429 0.4167 0.4066 0.1616 0.213766 0.332692 0.39358 1 2048 39353 3807 3661 2851 24926 304 1756 2 10224 110726 11412 8440 6604 64098 792 9156 0.327962 0 . 0 . 166 51,32,35,34 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V276|308|OR8D1|protein_coding|CODING|NM_001002917.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.162081 rs4936918 -0.693147 0.00216948 166 L194P 308 cTc/cCc MODERATE 1 MISSENSE CODING OR8D1 G protein_coding NM_001002917.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124180082 A G 0 222 0 0.1543 0.2865 0.3458 0.4206 0.4066 0.1616 0.199091 0.326127 0.391137 1 1925 41160 3803 3669 2832 25458 324 3149 2 9954 119224 11394 8440 6558 65498 894 16486 0.509784 0 . 0 . 171 57,32,47,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L194P|308|OR8D1|protein_coding|CODING|NM_001002917.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.825186 rs4936919 -0.693147 0.423903 171 C127W 308 tgT/tgG MODERATE 1 MISSENSE CODING OR8D1 C protein_coding NM_001002917.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124180282 A C 0 222 0 0.0893 0.2676 0.3372 0.4177 0.4066 0.1616 0.140618 0.307692 0.393231 1 1368 40398 3706 3578 2807 25479 325 3135 2 10306 119290 11172 8260 6524 65742 898 16388 0.99983 0 . 0 . 204 58,47,52,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgT/tgG|C127W|308|OR8D1|protein_coding|CODING|NM_001002917.1|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.918733 rs7107539 -0.693147 0.309064 204 P263L 311 cCt/cTt MODERATE 1 MISSENSE CODING OR8D2 A protein_coding NM_001002918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124189306 G A 0 222 0 0.4531 0.2776 0.2003 0.1895 0.1292 0.3384 0.423217 0.241615 0.148639 1 4508 24852 2036 1634 1011 10408 164 5091 2 10384 119144 11516 8614 6610 66134 880 15006 0.265537 0 . 0 . 138 40,28,16,36 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P263L|311|OR8D2|protein_coding|CODING|NM_001002918.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989066 rs2466620 -0.693147 0.00258986 138 R122H 311 cGt/cAt MODERATE 1 MISSENSE CODING OR8D2 T protein_coding NM_001002918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124189729 C T 0 222 0 0.4531 0.2776 0.2003 0.1895 0.1292 0.3384 0.423217 0.241385 0.14829 1 4507 24990 2017 1594 1008 10430 166 5268 2 10394 120818 11438 8450 6590 66550 904 16492 0.996315 0 . 0 . 102 26,34,17,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R122H|311|OR8D2|protein_coding|CODING|NM_001002918.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.737388 rs2512219 -0.693144 0.0260005 102 A50 311 gcT/gcC LOW 1 SILENT CODING OR8D2 G protein_coding NM_001002918.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124189944 A G 0 222 0 0 0.004992 0 0.0248 0 0 0.000227169 0.000153846 0.000116306 1 0 193 2 177 1 5 2 6 2 10254 120834 11484 8516 6608 66560 906 16506 0.96723 0 . 0 . 129 31,21,40,24 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A50|311|OR8D2|protein_coding|CODING|NM_001002918.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.988414 rs149661949 -0.693147 0.745062 129 S273F 313 tCt/tTt MODERATE 1 MISSENSE CODING OR8B2 A protein_coding NM_001005468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124252422 G A 0 222 0 0.4402 0.3566 0.3026 0.2788 0.3072 0.4131 0 . 0 1 4095 38710 3984 2404 1656 19806 305 6460 2 10286 120948 11460 8638 6608 66542 908 16506 0.699832 0 . 0 . 73 28,12,15,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S273F|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 48 0 0.300833 0.00389626 0 0.204767 rs503220,rs80334894 -0.693079 0.103453 73 I174 313 atC/atT LOW 1 SILENT CODING OR8B2 A protein_coding NM_001005468.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124252718 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 3946 37118 3717 2316 1610 19044 292 6193 2 9832 113346 10342 7914 6306 62312 854 15786 0.946875 0 . 0 . 149 21,63,9,52 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I174|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 52 0 0.914601 0.0126861 0 0.43987 rs886201 -0.693147 0.255423 149 L164F 313 Ctt/Ttt MODERATE 1 MISSENSE CODING OR8B2 A protein_coding NM_001005468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124252750 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 3547 34131 3272 2060 1489 17491 276 5996 2 9008 105574 9304 7124 5974 58002 796 15366 0.583594 0 . 0 . 115 26,40,6,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L164F|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 52 0 0.946736 0.0360901 0 0.996165 rs886202 -0.693147 0.27979 115 T116 313 acT/acC LOW 1 SILENT CODING OR8B2 G protein_coding NM_001005468.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124252892 A G 0 211 0 . 0 . 0 . 0 0.298501 0.252078 0.228299 1 4092 38667 3958 2392 1649 19790 305 6481 2 10346 120954 11412 8604 6602 66586 908 16496 0.309703 0 . 0 . 166 66,35,33,19 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T116|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|G) 1 0.5 1 0 . 0 . 1 1 0 53 0 0.0241422 0.00664044 0 0.841539 rs644147 -0.693147 0.202319 166 F31 313 ttT/ttC LOW 1 SILENT CODING OR8B2 G protein_coding NM_001005468.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124253147 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 3314 32393 3280 2063 1442 16890 247 5157 2 10400 121352 11546 8642 6612 66732 908 16512 0.67894 0 . 0 . 340 70,117,26,93 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F31|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|G) 0 0.5 1 0 . 0 . 0 1 0 56 0 0.0462136 0.438626 0 0.994603 rs530704 -0.693147 0.012455 340 L27F 313 Ctc/Ttc MODERATE 1 MISSENSE CODING OR8B2 A protein_coding NM_001005468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124253161 G A 0 222 0 0.3525 0.2957 0.2622 0.244 0.2684 0.3241 0 . 0 1 3313 32356 3275 2039 1441 16884 247 5157 2 10402 121330 11542 8622 6612 66732 908 16512 0.857505 0 . 0 . 326 57,131,22,89 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L27F|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|A) 0 0.5 1 0 . 1 0 . 1 0 55 0 0.0222184 0.700208 0 0.434575 rs530740 -0.693147 0.0110228 326 R24W 313 Cgg/Tgg MODERATE 1 MISSENSE CODING OR8B2 A protein_coding NM_001005468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124253170 G A 0 222 0 . 0 . 0 . 0 . 0 . 1 3305 32346 3276 2039 1441 16882 247 5156 2 10396 121316 11546 8616 6612 66728 908 16510 0.329185 0 . 0 . 311 51,127,19,84 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R24W|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|A) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.00756564 0.910917 0 0.999993 rs530765 -0.693147 0.00141257 311 H20R 313 cAt/cGt MODERATE 1 MISSENSE CODING OR8B2 C protein_coding NM_001005468.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124253181 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 7111 63237 6442 4511 3255 32870 486 8562 2 10314 117136 11296 8436 6394 64294 876 15526 0.4847 0 . 0 . 270 16,70,44,116 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|313|OR8B2|protein_coding|CODING|NM_001005468.1|1|C) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.326748 0.429633 0 0.47269 rs28373946 -0.693147 6.59139e-05 270 M114I 313 atG/atA MODERATE 1 MISSENSE CODING OR8B3 T protein_coding NM_001005467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124266906 C T 0 222 0 . 0 . 0 . 0 0.353021 0.297385 0.2689 1 3421 33124 3462 2080 1447 17243 244 5227 2 10236 119714 11262 8512 6544 65948 888 16324 0.83047 0 . 0 . 169 37,51,48,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M114I|313|OR8B3|protein_coding|CODING|NM_001005467.1|1|T) 1 0.5 1 0 . 0 . 1 1 0 53 0 0.308728 0.000588511 0 0.00862251 rs530992 -0.693147 0.357138 169 C112 313 tgT/tgC LOW 1 SILENT CODING OR8B3 G protein_coding NM_001005467.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124266912 A G 0 228 0 0.9009 0.8734 0.8256 0.8641 0.8419 0.9121 0 . 0 2 8163 97653 9143 7278 5474 53420 742 13433 2 10074 118764 11222 8474 6516 65486 884 16108 0.490884 0 . 0 . 164 0,8,90,57 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C112|313|OR8B3|protein_coding|CODING|NM_001005467.1|1|G) 0 . 0 . 0 1 0 . 1 0 55 0 6.60301e-05 0.0189835 0 0.000144311 rs28398895 -0.693147 0.238121 164 Q24R 313 cAg/cGg MODERATE 1 MISSENSE CODING OR8B3 C protein_coding NM_001005467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124267177 T C 0 228 0 0.8797 0.8568 0.7983 0.8581 0.83 0.8937 0.777971 0.756956 0.746995 2 4366 80379 6625 6293 4929 46267 634 11265 2 6106 102152 9102 7654 6120 59110 772 13288 0 . 0 . 0 89 0,0,7,75 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q24R|313|OR8B3|protein_coding|CODING|NM_001005467.1|1|C) 1 0 . 0 . 1 0 1 1 0 46 0 0 0.063486 0 . rs507360,rs61910862 -0.693147 0.192009 89 H20R 313 cAt/cGt MODERATE 1 MISSENSE CODING OR8B3 C protein_coding NM_001005467.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124267189 T C 0 228 0 0.882 0.8588 0.8012 0.8571 0.832 0.8978 0 . 0 2 4386 78074 6491 6109 4912 45155 612 10409 2 6032 99270 8932 7480 6068 57768 746 12244 0 . 0 . 0 70 0,0,4,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H20R|313|OR8B3|protein_coding|CODING|NM_001005467.1|1|C) 0 . 0 . 0 1 0 . 1 0 45 0 0 0.376662 0 . rs507335 -0.693147 0.165944 70 E22G 309 gAg/gGg MODERATE 1 MISSENSE CODING OR8B4 C protein_coding NM_001005196.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124294703 T C 0 228 0 0.2874 0.3464 0.3242 0.5952 0.3121 0.2209 0.274648 0.298769 0.311119 2 2892 39205 4144 5245 2181 20753 305 3685 2 10064 119792 11440 8594 6604 65786 900 16404 0 . 0 . 0 72 0,0,15,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E22G|309|OR8B4|protein_coding|CODING|NM_001005196.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10750270 -0.693147 5.57077e-05 72 Y120 311 taT/taC LOW 1 SILENT CODING OR8B8 G protein_coding NM_012378.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124310622 A G 0 228 0 0.0303 0.2484 0.33 0.5317 0.2644 0.1769 0.0681508 0.215308 0.290649 2 662 34870 4706 4632 2039 19586 258 2987 2 10402 121282 11556 8626 6612 66672 904 16510 0.834532 0 . 0 . 148 0,2,66,73 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y120|311|OR8B8|protein_coding|CODING|NM_012378.1|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.507194 rs4296049 -0.693147 0.0311779 148 S218L 326 tCg/tTg MODERATE 1 MISSENSE CODING OR8A1 T protein_coding NM_001005194.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124440617 C T 0 228 0 0.7375 0.7726 0.7651 0.8929 0.7316 0.7434 0.760336 0.750692 0.745755 2 7846 92270 8788 7749 5053 49701 715 12418 2 10406 121316 11526 8640 6604 66724 908 16508 0 . 0 . 0 131 0,0,60,53 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S218L|326|OR8A1|protein_coding|CODING|NM_001005194.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12792184 -0.693147 0.585719 131 R416H 1386 cGt/cAt MODERATE 8 MISSENSE CODING ROBO3 A protein_coding NM_022370.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124742365 G A 0 222 0 0.0053 0.1288 0.1023 0.2698 0.1252 0.1728 0.0219443 0.0804932 0.109699 1 225 15318 1527 2210 530 7688 134 3004 2 9800 120676 11558 8590 6612 66706 898 16512 0.999961 0 . 0 . 97 36,17,18,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R416H|1386|ROBO3|protein_coding|CODING|NM_022370.3|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.497827 rs3862618,rs386588292 -0.693127 0.158404 97 A997 1386 gcG/gcA LOW 21 SILENT CODING ROBO3 A protein_coding NM_022370.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124747837 G A 0 218 0 0.8623 0.632 0.4957 0.4276 0.6918 0.5665 0.830275 0.728802 0.68284 1 6017 61126 3535 2927 3694 36252 447 8254 2 7060 90086 6910 5800 5278 50724 688 13626 0.982155 0 . 0 . 37 14,4,10,6 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A997|1386|ROBO3|protein_coding|CODING|NM_022370.3|21|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.797448 rs7933204 -0.689466 0.378167 37 H215 1007 caT/caC LOW 4 SILENT CODING ROBO4 G protein_coding NM_019055.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124766128 A G 0 222 0 0.8162 0.4958 0.2853 0.4534 0.334 0.4223 0.718083 0.449615 0.312166 1 7777 46678 3012 3655 2687 22141 363 7043 2 10404 121286 11560 8614 6608 66684 908 16508 0.0885184 0 . 0 . 153 28,45,15,45 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H215|1007|ROBO4|protein_coding|CODING|NM_019055.5|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997702 rs4078313 -0.693147 0.0728551 153 Q54R 1007 cAa/cGa MODERATE 2 MISSENSE CODING ROBO4 C protein_coding NM_019055.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124767067 T C 0 222 0 0.646 0.3846 0.2176 0.378 0.2555 0.2894 0.56179 0.343514 0.231736 1 5329 28087 2130 2828 1093 14206 199 2302 2 8710 81006 7594 6830 3664 47320 546 6342 0.260609 0 . 0 . 153 27,48,24,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q54R|1007|ROBO4|protein_coding|CODING|NM_019055.5|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.50936 rs59648931 -0.693147 0.000680197 153 L35 1007 Cta/Tta LOW 2 SILENT CODING ROBO4 A protein_coding NM_019055.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124767125 G A 0 222 0 0.003 0.0994 0.0735 0.2054 0.0974 0.1411 0.020862 0.0688265 0.0933255 1 66 3224 180 507 101 2005 31 334 2 2484 19278 1034 1776 658 11742 132 1452 0.612848 0 . 0 . 83 12,29,9,24 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L35|1007|ROBO4|protein_coding|CODING|NM_019055.5|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.993502 rs73016370 -0.693127 0.208875 83 W37R 88 Tgg/Cgg MODERATE 1 MISSENSE CODING HEPN1 C protein_coding NM_001037558.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124789755 T C 0 228 0 0.8775 0.7989 0.6455 0.9236 0.7276 0.7464 0.869499 0.754809 0.700265 2 8548 88983 6960 7865 5125 47418 658 12409 2 9808 120718 11558 8622 6614 66706 898 16512 0 . 0 . 0 242 0,0,86,140 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W37R|88|HEPN1|protein_coding|CODING|NM_001037558.2|1|C),UTR_3_PRIME(MODIFIER||1279||416|HEPACAM|protein_coding|CODING|NM_152722.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3802904 -0.693147 0.145018 242 416 1279 MODIFIER 7 CODING HEPACAM C protein_coding NM_152722.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124789755 T C 0 228 0 0.8775 0.7989 0.6455 0.9236 0.7276 0.7464 0.869499 0.754809 0.700265 2 8548 88983 6960 7865 5125 47418 658 12409 2 9808 120718 11558 8622 6614 66706 898 16512 0 . 0 . 0 242 0,0,86,140 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W37R|88|HEPN1|protein_coding|CODING|NM_001037558.2|1|C),UTR_3_PRIME(MODIFIER||1279||416|HEPACAM|protein_coding|CODING|NM_152722.4|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3802904 -0.693147 0.145018 242 M218V 416 Atg/Gtg MODERATE 3 MISSENSE CODING HEPACAM C protein_coding NM_152722.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124793682 T C 0 228 0 0.8858 0.7939 0.6398 0.9107 0.7177 0.7372 0.877783 0.751923 0.687485 2 9189 88422 6815 7722 5051 46651 656 12338 2 10404 121358 11570 8654 6604 66708 908 16510 0 . 0 . 0 224 0,0,108,95 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M218V|416|HEPACAM|protein_coding|CODING|NM_152722.4|3|C),DOWNSTREAM(MODIFIER||3109||88|HEPN1|protein_coding|CODING|NM_001037558.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10790715 -0.693147 0.0467892 224 951 103 MODIFIER 16 CODING CCDC15 A protein_coding NM_025004.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124910710 G A 0 228 0 0.7814 0.8003 0.6282 0.9306 0.7187 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 52 0,0,9,41 UTR_3_PRIME(MODIFIER||103||951|CCDC15|protein_coding|CODING|NM_025004.2|16|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10750293 -0.693147 0.251871 52 505 LOW 7 CODING SLC37A2 C protein_coding NM_198277.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124951311 T C 0 222 0 0.2118 0.2526 0.2421 0.2837 0.2137 0.3231 0.21672 0.210615 0.20749 1 2308 29043 2873 2211 1412 14513 226 5500 2 10392 120006 11574 8626 6606 66254 896 15658 0.940856 0 . 0 . 65 26,7,17,10 SPLICE_SITE_REGION+INTRON(LOW||||505|SLC37A2|protein_coding|CODING|NM_198277.2|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952482 rs75801851 -0.693021 0.916799 65 D415 505 gaT/gaC LOW 14 SILENT CODING SLC37A2 C protein_coding NM_198277.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124955032 T C 0 167 0 0.9478 0.6651 0.513 0.4643 0.6213 0.6431 0.889368 0.708846 0.616422 1 9370 74045 5117 3964 3846 40595 533 10620 2 10380 121126 11542 8604 6594 66604 908 16494 0.488445 0 . 0 . 25 7,4,3,7 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D415|505|SLC37A2|protein_coding|CODING|NM_198277.2|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.869825 rs386622897,rs948268 -0.670168 0.913584 25 505 1995 MODIFIER 19 CODING SLC37A2 G protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958122 A G 0 162 0 0.9039 0.8145 0.67 0.7966 0.7485 0.8824 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.668718 0 . 0 . 37 3,19,2,13 UTR_3_PRIME(MODIFIER||1995||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.856395 rs3802808 -0.688148 0.349404 37 505 2199 MODIFIER 19 CODING SLC37A2 C protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958326 G C 0 222 0 0.8979 0.8123 0.67 0.7937 0.7495 0.8814 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.979748 0 . 0 . 64 27,3,20,8 UTR_3_PRIME(MODIFIER||2199||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.729868 rs7110840 -0.693054 0.205234 64 505 2270 MODIFIER 19 CODING SLC37A2 C protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958397 T C 0 222 0 0.9017 0.8075 0.67 0.7669 0.7485 0.8804 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.966761 0 . 0 . 83 19,20,14,18 UTR_3_PRIME(MODIFIER||2270||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.516296 rs3802809 -0.69312 0.54132 83 505 2332 MODIFIER 19 CODING SLC37A2 T protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958459 C T 0 222 0 0.8986 0.7899 0.6542 0.7669 0.7316 0.8231 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.919831 0 . 0 . 51 5,15,7,20 UTR_3_PRIME(MODIFIER||2332||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875173 rs3824926 -0.693021 0.203139 51 505 2449 MODIFIER 19 CODING SLC37A2 A protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958576 G A 0 42.8 0 0.8986 0.7899 0.6542 0.7659 0.7326 0.8231 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.916482 0 . 0 . 10 0,7,1,2 UTR_3_PRIME(MODIFIER||2449||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.916482 1 0 0.916482 rs10750295 -0.511536 0.635923 10 505 2582 MODIFIER 19 CODING SLC37A2 C protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958709 T C 0 103 0 0.9841 0.8139 0.6628 0.7669 0.7326 0.8231 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||2582||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4936977 -0.556411 0.160409 4 505 2583 MODIFIER 19 CODING SLC37A2 A protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958710 G A 0 99 0 0.2965 0.2798 0.1715 0.5655 0.1163 0.2076 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,3 UTR_3_PRIME(MODIFIER||2583||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs73024339 -0.556411 0.160409 4 505 2612 MODIFIER 19 CODING SLC37A2 AC protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958738 A AC 0 86 0 0.9002 0.7903 0.6542 0.7669 0.7316 0.8231 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,1,2 UTR_3_PRIME(MODIFIER||2612||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|AC) 0 . 0 3 0.75 1 1 0 . 0 60 0 0 1 0 . rs3842257 -0.511536 0.0860477 4 505 2717 MODIFIER 19 CODING SLC37A2 G protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124958844 A G 0 9.7 0 0.8986 0.7901 0.6542 0.7669 0.7326 0.8231 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2717||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7111168 -0.379885 0 1 505 3295 MODIFIER 19 CODING SLC37A2 G protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124959422 A G 0 15.5 0 0.8979 0.7901 0.6542 0.7688 0.7326 0.8221 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 4 1,1,2,0 UTR_3_PRIME(MODIFIER||3295||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|G),DOWNSTREAM(MODIFIER||4844||150|TMEM218|protein_coding|CODING|NM_001258239.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs111803860,rs7936882 -0.453602 0.36 4 505 4157 MODIFIER 19 CODING SLC37A2 C protein_coding NM_198277.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124960284 A C 0 46.3 0 0.8979 0.7923 0.6542 0.7778 0.7336 0.8231 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||4157||505|SLC37A2|protein_coding|CODING|NM_198277.2|19|C),DOWNSTREAM(MODIFIER||3982||150|TMEM218|protein_coding|CODING|NM_001258239.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111799548,rs112596336,rs1142924 -0.453602 0.22 2 150 2745 MODIFIER 5 CODING TMEM218 G protein_coding NM_001258239.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124964757 C G 0 9.7 0 0.7065 0.5613 0.3818 0.6687 0.4642 0.4816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2745||150|TMEM218|protein_coding|CODING|NM_001258239.1|5|G),DOWNSTREAM(MODIFIER||4345||505|SLC37A2|protein_coding|CODING|NM_198277.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1048592 -0.379885 0 1 150 2369 MODIFIER 5 CODING TMEM218 T protein_coding NM_001258239.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124965133 A T 0 63 0 0.0356 0.2123 0.1398 0.5754 0.1083 0.2352 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||2369||150|TMEM218|protein_coding|CODING|NM_001258239.1|5|T),DOWNSTREAM(MODIFIER||4721||505|SLC37A2|protein_coding|CODING|NM_198277.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4935904 -0.453602 0.76 3 150 15 MODIFIER 5 CODING TMEM218 A protein_coding NM_001258239.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124967487 T A 0 222 0 0.6929 0.5585 0.3804 0.6687 0.4652 0.4857 0.660154 0.537923 0.475343 1 6949 61098 4181 6170 3223 32232 467 7876 2 10404 121244 11572 8640 6606 66658 908 16456 0.91258 0 . 0 . 169 59,17,61,18 UTR_3_PRIME(MODIFIER||15||150|TMEM218|protein_coding|CODING|NM_001258239.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.799306 rs1043821 -0.693147 0.0709676 169 L12S 150 tTg/tCg MODERATE 3 MISSENSE CODING TMEM218 G protein_coding NM_001258239.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124972208 A G 0 133 0 0.8979 0.7919 0.6513 0.7817 0.7247 0.8282 0 . 0 1 4136 39812 1632 2726 1296 20243 297 9482 2 4724 51060 2372 3284 1714 26954 382 11630 0.887122 0 . 0 . 82 3,31,0,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L12S|150|TMEM218|protein_coding|CODING|NM_001258239.1|3|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.952908 rs14065 -0.693147 0.025623 82 150 130 MODIFIER 2 CODING TMEM218 C protein_coding NM_001258239.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 124972691 T C 0 118 0 0.9879 0.8417 0.6801 0.8363 0.7674 0.8405 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.640197 0 . 0 . 14 0,7,1,6 UTR_5_PRIME(MODIFIER||130||150|TMEM218|protein_coding|CODING|NM_001258239.1|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.966012 1 0 0.966012 rs2155666 -0.636426 0.850265 14 472 LOW 8 CODING PKNOX2 A protein_coding NM_022062.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125280225 G A 0 228 0 0 0.0509 0.0216 0.2341 0 0.0041 0.001998 0.00178253 0.00167906 2 18 2682 617 1794 12 152 9 80 2 9654 119900 11518 8530 6598 66228 900 16472 1 0 . 0 . 71 0,1,33,28 SPLICE_SITE_REGION+INTRON(LOW||||472|PKNOX2|protein_coding|CODING|NM_022062.2|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3824918 -0.693147 0.000366859 71 472 299 MODIFIER 13 CODING PKNOX2 C protein_coding NM_022062.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125301587 T C 0 9.7 0 0.6536 0.8367 0.8746 0.9931 0.8221 0.911 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||299||472|PKNOX2|protein_coding|CODING|NM_022062.2|13|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1630030 -0.379885 0 1 472 1434 MODIFIER 13 CODING PKNOX2 A protein_coding NM_022062.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125302722 G A 0 228 0 0.6498 0.8347 0.8703 0.9931 0.8201 0.911 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 62 0,0,48,13 UTR_3_PRIME(MODIFIER||1434||472|PKNOX2|protein_coding|CODING|NM_022062.2|13|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386602830,rs645172 -0.693147 0.635527 62 S332 705 tcG/tcA LOW 11 SILENT CODING STT3A A protein_coding NM_001278503.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125479363 G A 0 222 0 0.5227 0.4193 0.2752 0.4335 0.3787 0.409 0.50159 0.412692 0.367178 1 5298 44779 2639 3730 2198 24319 342 6253 2 10406 121220 11572 8636 6614 66650 906 16436 0.960343 0 . 0 . 147 43,22,45,22 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S332|705|STT3A|protein_coding|CODING|NM_001278503.1|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998251 rs2241502 -0.693147 0.324514 147 705 239 MODIFIER 19 CODING STT3A G protein_coding NM_001278503.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125490944 A G 0 222 0 0 0.0077875 0 0.0387 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.797729 0 . 0 . 64 11,18,13,14 UTR_3_PRIME(MODIFIER||239||705|STT3A|protein_coding|CODING|NM_001278503.1|19|G),UPSTREAM(MODIFIER||4087||476|CHEK1|protein_coding|CODING|NM_001114121.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.863812 rs141474800 -0.693021 0.00156136 64 705 880 MODIFIER 19 CODING STT3A A protein_coding NM_001278503.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125491585 G A 0 9.7 0 0.5227 0.4193 0.2752 0.4335 0.3787 0.409 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||880||705|STT3A|protein_coding|CODING|NM_001278503.1|19|A),UPSTREAM(MODIFIER||3446||476|CHEK1|protein_coding|CODING|NM_001114121.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs473468 -0.379885 0 1 I471V 476 Att/Gtt MODERATE 13 MISSENSE CODING CHEK1 G protein_coding NM_001114121.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125525195 A G 0 228 0 0.997 0.9858 0.9726 1 0.9672 0.9847 0.993639 0.973846 0.963713 2 10343 117863 11356 8651 6357 64099 868 16189 2 10394 121184 11530 8654 6590 66608 908 16500 0 . 0 . 0 118 0,0,72,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I471V|476|CHEK1|protein_coding|CODING|NM_001114121.2|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs506504 -0.693147 0.025247 118 V46I 126 Gtt/Att MODERATE 4 MISSENSE CODING PATE1 A protein_coding NM_138294.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125617606 G A 0 222 0 0.2073 0.2742 0.2925 0.2282 0.334 0.3374 0.229441 0.311769 0.35392 1 2328 40316 3502 1912 2114 23563 305 6592 2 10370 121168 11526 8604 6610 66650 908 16500 0.941321 0 . 0 . 154 54,26,43,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V46I|126|PATE1|protein_coding|CODING|NM_138294.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992263 rs537916 -0.693147 0.358138 154 Q47R 126 cAg/cGg MODERATE 4 MISSENSE CODING PATE1 G protein_coding NM_138294.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125617610 A G 0 222 0 0.3797 0.3375 0.2219 0.4375 0.2893 0.3088 0.377328 0.318538 0.288439 1 3947 35973 2080 3683 1847 18974 284 5158 2 10394 121228 11522 8620 6610 66672 908 16502 0.517417 0 . 0 . 162 49,26,51,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q47R|126|PATE1|protein_coding|CODING|NM_138294.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.636348 rs2114084,rs386557634 -0.693147 0.338134 162 126 103 MODIFIER 5 CODING PATE1 C protein_coding NM_138294.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125618731 T C 0 222 0 0.3971 0.3017 0.1484 0.3968 0.2127 0.2751 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.945358 0 . 0 . 41 1,16,4,16 UTR_3_PRIME(MODIFIER||103||126|PATE1|protein_coding|CODING|NM_138294.2|5|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.997102 rs7939499 -0.692067 0.30385 41 113 156 MODIFIER 4 CODING PATE2 G protein_coding NM_212555.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125647121 A G 0 228 0 0.8359 0.8994 0.9236 0.997 0.8678 0.8998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 42 0,0,39,1 UTR_3_PRIME(MODIFIER||156||113|PATE2|protein_coding|CODING|NM_212555.2|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs548597 -0.693145 0.306972 42 98 505 MODIFIER 3 CODING PATE3 C protein_coding NM_001129883.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125661002 T C 0 39.3 0 0.7761 0.8818 0.9164 0.997 0.8668 0.8967 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||505||98|PATE3|protein_coding|CODING|NM_001129883.3|3|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs493486 -0.453602 0.26 2 98 HIGH 1 CODING PATE4 C protein_coding NM_001144874.1 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125707761 A C 0 228 0 0.4017 0.4928 0.4553 0.5308 0.5775 0.5164 0 . 0 2 881 11294 211 351 16 5098 118 4619 2 2102 19548 396 614 32 8378 192 7834 1 0 . 0 . 60 1,0,43,9 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||98|PATE4|protein_coding|CODING|NM_001144874.1|1|C) 0 . 0 . 0 1 0 . 1 (PATE4|PATE4|1|1.00) 60 0 1 1 0 1 rs11220236 -0.693147 0.273522 60 98 LOW 2 CODING PATE4 T protein_coding NM_001144874.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125708198 C T 0 228 0 0.7769 0.8822 0.9164 0.997 0.8668 0.8978 0.810694 0.865309 0.889063 2 1662 16805 341 580 24 7320 160 6718 2 2118 18992 374 580 26 8242 186 7466 0 . 0 . 0 37 0,0,24,10 SPLICE_SITE_REGION+INTRON(LOW||||98|PATE4|protein_coding|CODING|NM_001144874.1|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10160391 -0.693132 0.250071 37 98 688 MODIFIER 3 CODING PATE4 T protein_coding NM_001144874.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125709010 C T 0 32.6 0 0.7769 0.8822 0.9164 0.997 0.8668 0.8978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||688||98|PATE4|protein_coding|CODING|NM_001144874.1|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7110718 -0.379885 0 2 98 1102 MODIFIER 3 CODING PATE4 C protein_coding NM_001144874.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125709424 T C 0 9.7 0 0.7769 0.8822 0.9164 0.997 0.8668 0.8978 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1102||98|PATE4|protein_coding|CODING|NM_001144874.1|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3851106 -0.379885 0 1 481 113 MODIFIER 4 CODING PUS3 T protein_coding NM_031307.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125763566 TC T 0 40.2 0 0.5257 0.5583 0.5908 0.5734 0.5358 0.5869 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 1,0,5,0 UTR_3_PRIME(MODIFIER||113||481|PUS3|protein_coding|CODING|NM_031307.3|4|T),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|T) 0 . 0 5 0.714286 1 1 0 . 0 60 0 0 . 0 . rs141738016 -0.590765 0.741566 7 E460D 481 gaG/gaC MODERATE 4 MISSENSE CODING PUS3 G protein_coding NM_031307.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125763746 C G 0 228 0 0.3933 0.4587 0.4236 0.5327 0.501 0.4519 0.404134 0.466769 0.498837 2 4161 59848 5300 4666 3383 33466 429 8443 2 10404 121372 11568 8644 6608 66730 906 16512 1 0 . 0 . 121 1,0,80,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E460D|481|PUS3|protein_coding|CODING|NM_031307.3|4|G),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3088241 -0.693147 0.327292 121 A46S 481 Gca/Tca MODERATE 2 MISSENSE CODING PUS3 A protein_coding NM_031307.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125766044 C A 0 228 0 0.6074 0.6374 0.6023 0.6964 0.673 0.6053 0.625852 0.662462 0.681205 2 6451 81140 6855 6335 4696 45234 617 10952 2 10402 121394 11576 8654 6614 66730 908 16510 0 . 0 . COSM1127862 91 0,0,34,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A46S|481|PUS3|protein_coding|CODING|NM_031307.3|2|A),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs549990 -0.693147 0.0319367 91 Y3D 481 Tat/Gat MODERATE 2 MISSENSE CODING PUS3 C protein_coding NM_031307.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125766173 A C 0 228 0 0.6339 0.8027 0.889 0.8542 0.8569 0.8609 0.677647 0.804769 0.869853 2 6912 104005 10691 7718 5637 58048 764 14235 2 10352 121218 11574 8648 6614 66662 904 16464 0 . 0 . 0 45 0,0,10,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y3D|481|PUS3|protein_coding|CODING|NM_031307.3|2|C),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs622756 -0.693143 0.0772796 45 481 25 MODIFIER 2 CODING PUS3 C protein_coding NM_031307.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125766204 G C 0 228 0 0.612 0.7953 0.8818 0.8542 0.8559 0.8589 0.652885 0.795615 0.86869 2 6531 101973 10622 7678 5626 57414 753 13349 2 10166 119392 11532 8620 6608 66072 892 15502 0 . 0 . 0 22 0,0,2,19 START_GAINED(LOW||||481|PUS3|protein_coding|CODING|NM_031307.3|2|C),UTR_5_PRIME(MODIFIER||25||481|PUS3|protein_coding|CODING|NM_031307.3|2|C),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs600761 -0.692352 0.00529103 22 481 28 MODIFIER 2 CODING PUS3 T protein_coding NM_031307.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125766207 C T 0 228 0 0.612 0.7953 0.8818 0.8542 0.8559 0.8589 0.652885 0.795769 0.868923 2 6519 101702 10618 7680 5630 57359 747 13149 2 10156 119102 11528 8624 6612 66012 884 15286 0 . 0 . 0 22 0,0,2,19 UTR_5_PRIME(MODIFIER||28||481|PUS3|protein_coding|CODING|NM_031307.3|2|T),INTRON(MODIFIER||||299|HYLS1|protein_coding|CODING|NM_001134793.1|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs471980 -0.692352 0.00550547 22 C31R 299 Tgt/Cgt MODERATE 3 MISSENSE CODING HYLS1 C protein_coding NM_001134793.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125769354 T C 0 228 0 0.3177 0.2993 0.2291 0.3542 0.2416 0.3272 0.301 0.259308 0.237962 2 3151 34342 3047 3058 1782 16921 235 6148 2 10390 121320 11560 8628 6610 66714 908 16510 0 . 0 . 0 103 0,0,35,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C31R|299|HYLS1|protein_coding|CODING|NM_001134793.1|3|C),UPSTREAM(MODIFIER||4907||483|DDX25|protein_coding|CODING|NM_013264.4||C),INTRON(MODIFIER||||481|PUS3|protein_coding|CODING|NM_031307.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs667782 -0.693147 0.343682 103 C398 483 tgT/tgC LOW 10 SILENT CODING DDX25 C protein_coding NM_013264.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125788678 T C 0 222 0 0.7103 0.6899 0.7507 0.6627 0.675 0.6626 0.714472 0.688937 0.677048 1 3665 40513 2378 2086 2633 22153 329 7269 2 5082 56670 2942 3104 3680 31114 470 10278 0.994831 0 . 0 . 212 40,56,44,53 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C398|483|DDX25|protein_coding|CODING|NM_013264.4|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.578413 rs683155 -0.693147 0.013095 212 1287 4052 MODIFIER 20 CODING CDON A protein_coding NM_001243597.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125826785 G A 0 9.7 0 0.1104 0.2402 0.255 0.2837 0.3082 0.2904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4052||1287|CDON|protein_coding|CODING|NM_001243597.1|20|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3039 -0.379885 0 1 1287 1933 MODIFIER 20 CODING CDON C protein_coding NM_001243597.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125828904 T C 0 17 0 0.5272 0.495 0.5893 0.4385 0.4891 0.4489 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 0,4,0,2 UTR_3_PRIME(MODIFIER||1933||1287|CDON|protein_coding|CODING|NM_001243597.1|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.75 rs2509616 -0.453602 0.48 6 1287 140 MODIFIER 20 CODING CDON C protein_coding NM_001243597.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125830697 T C 0 222 0 0.0998 0.2424 0.2565 0.2857 0.3101 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.526356 0 . 0 . 100 22,28,25,20 UTR_3_PRIME(MODIFIER||140||1287|CDON|protein_coding|CODING|NM_001243597.1|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.95863 rs3737336 -0.693147 0.0812649 100 I1244N 1287 aTc/aAc MODERATE 20 MISSENSE CODING CDON T protein_coding NM_001243597.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125830970 A T 0 228 0 . 0 . 0 . 0 0.825761 0.73 0.680972 2 8757 88675 9160 7954 4576 45710 664 11854 2 10396 121308 11568 8654 6604 66668 908 16510 0 . 0 . 0 100 0,0,43,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I1244N|1287|CDON|protein_coding|CODING|NM_001243597.1|20|T) 1 0 . 0 . 0 . 1 1 0 60 0 0 1 0 . rs684535 -0.693147 0.0259614 100 V1183 1287 gtC/gtT LOW 19 SILENT CODING CDON A protein_coding NM_001243597.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125831701 G A 0 222 0 0.1014 0.2422 0.2565 0.2837 0.3091 0.3108 0.13244 0.253077 0.314841 1 1286 35178 3278 2364 2117 20655 269 5209 2 10394 121066 11512 8624 6594 66552 906 16484 0.752587 0 . 0 . 81 20,14,25,18 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V1183|1287|CDON|protein_coding|CODING|NM_001243597.1|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.492635 rs2276061 -0.693146 0.00510727 81 T1098 1287 acG/acA LOW 18 SILENT CODING CDON T protein_coding NM_001243597.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 125848261 C T 0 222 0 0.382 0.3996 0.4337 0.4127 0.3797 0.4059 0.348478 0.356462 0.360549 1 3464 42995 4753 3190 2589 22774 307 5918 2 9064 103780 9758 7896 5512 57048 776 13726 0.939703 0 . 0 COSM147373 88 23,21,16,18 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1098|1287|CDON|protein_coding|CODING|NM_001243597.1|18|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99079 rs3740904 -0.693132 0.0150794 88 377 625 MODIFIER 7 CODING RPUSD4 T protein_coding NM_032795.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126072688 C T 0 63 0 0.5212 0.7861 0.8256 0.996 0.7664 0.9202 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||625||377|RPUSD4|protein_coding|CODING|NM_032795.2|7|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs627911 -0.453602 0.48 3 S276 377 tcT/tcC LOW 6 SILENT CODING RPUSD4 G protein_coding NM_032795.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126074192 A G 0 222 0 0.0408 0.2592 0.3242 0.623 0.1143 0.2822 0.0715584 0.101308 0.116539 1 699 24652 4662 5574 819 8447 170 4281 2 10126 120224 11496 8594 6606 66082 898 16422 0.724406 0 . 0 . 59 5,27,5,19 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S276|377|RPUSD4|protein_coding|CODING|NM_032795.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.580424 rs2276312 -0.692831 0.52706 59 Q44R 377 cAg/cGg MODERATE 1 MISSENSE CODING RPUSD4 C protein_coding NM_032795.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126081403 T C 0 222 0 0.2534 0.4792 0.5576 0.8175 0.338 0.5256 0.267606 0.296308 0.311003 1 2771 49674 7892 7168 2103 21372 344 8024 2 10406 121350 11578 8644 6614 66690 908 16510 0.641076 0 . 0 . 197 52,38,57,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q44R|377|RPUSD4|protein_coding|CODING|NM_032795.2|1|C),UPSTREAM(MODIFIER||216||351|FAM118B|protein_coding|CODING|NM_024556.3||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937463 rs2282580 -0.693147 0.449582 197 638 603 MODIFIER 14 CODING SRPRA A protein_coding NM_003139.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126133208 C A 0 143 0 0.0809 0.3125 0.3934 0.6161 0.2058 0.365 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.958011 0 . 0 . 47 28,3,13,2 UTR_3_PRIME(MODIFIER||603||638|SRPRA|protein_coding|CODING|NM_003139.3|14|A),DOWNSTREAM(MODIFIER||329||351|FAM118B|protein_coding|CODING|NM_024556.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.734843 rs9106 -0.688148 0.136474 47 638 235 MODIFIER 14 CODING SRPRA G protein_coding NM_003139.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126133576 A G 0 222 0 0.1316 0.1214 0.062 0.1399 0.1103 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.980192 0 . 0 . 65 24,8,24,4 UTR_3_PRIME(MODIFIER||235||638|SRPRA|protein_coding|CODING|NM_003139.3|14|G),DOWNSTREAM(MODIFIER||697||351|FAM118B|protein_coding|CODING|NM_024556.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.995373 rs1049666 -0.693054 0.54632 65 638 224 MODIFIER 14 CODING SRPRA A protein_coding NM_003139.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126133587 C A 0 222 0 0.1218 0.1186 0.0605 0.1399 0.1103 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.554698 0 . 0 . 72 26,9,27,4 UTR_3_PRIME(MODIFIER||224||638|SRPRA|protein_coding|CODING|NM_003139.3|14|A),DOWNSTREAM(MODIFIER||708||351|FAM118B|protein_coding|CODING|NM_024556.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.979092 rs3189850 -0.69311 0.384538 72 638 179 MODIFIER 14 CODING SRPRA C protein_coding NM_003139.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126133632 T C 0 222 0 0.1369 0.1228 0.062 0.1399 0.1103 0.1421 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.534519 0 . 0 . 116 47,12,30,17 UTR_3_PRIME(MODIFIER||179||638|SRPRA|protein_coding|CODING|NM_003139.3|14|C),DOWNSTREAM(MODIFIER||753||351|FAM118B|protein_coding|CODING|NM_024556.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.813604 rs1049665 -0.693147 0.349217 116 A312 638 gcG/gcA LOW 8 SILENT CODING SRPRA T protein_coding NM_003139.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126135973 C T 0 222 0 0.0083 0.0747 0.0187 0.3393 0.001 0.0072 0.00885961 0.00376923 0.00116306 1 81 3839 397 3172 0 75 23 91 2 10400 121356 11578 8628 6614 66716 908 16512 0.774243 0 . 0 . 65 10,19,10,19 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A312|638|SRPRA|protein_coding|CODING|NM_003139.3|8|T),UPSTREAM(MODIFIER||2962||486|FOXRED1|protein_coding|CODING|NM_017547.3||T),DOWNSTREAM(MODIFIER||3094||351|FAM118B|protein_coding|CODING|NM_024556.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.501936 rs2962118,rs386577854 -0.693079 0.411651 65 486 2 MODIFIER 1 CODING FOXRED1 C protein_coding NM_017547.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126139100 T C 0 228 0 0.5204 0.7861 0.8256 0.996 0.7674 0.9202 0.567924 0.694876 0.759888 2 5793 94963 10055 8630 5137 50116 675 14557 2 10282 120348 11542 8640 6540 65946 890 16508 0 . 0 . 0 93 0,0,54,33 UTR_5_PRIME(MODIFIER||2||486|FOXRED1|protein_coding|CODING|NM_017547.3|1|C),UPSTREAM(MODIFIER||223||638|SRPRA|protein_coding|CODING|NM_003139.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1786702 -0.693147 0.18317 93 235 52 MODIFIER 5 CODING TIRAP G protein_coding NM_148910.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126163064 A G 0 116 0 0.1331 0.1218 0.0634 0.1359 0.1143 0.1411 0.125965 0.121498 0.119337 1 1096 12137 611 955 853 6706 96 1820 2 7676 97516 9296 7002 5826 54878 762 12076 0.998622 0 . 0 . 16 4,4,1,7 UTR_3_PRIME(MODIFIER||52||235|TIRAP|protein_coding|CODING|NM_148910.2|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.733299 rs8177375 -0.651104 0.603537 16 F63 337 ttC/ttT LOW 1 SILENT CODING DCPS T protein_coding NM_014026.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126174164 C T 0 222 0 0.0749 0.3057 0.3905 0.624 0.2008 0.3374 0.105861 0.168411 0.200442 1 1035 32772 5063 5540 1601 14030 243 5260 2 10396 121292 11560 8634 6608 66682 904 16508 0.682099 0 . 0 . 126 20,47,18,31 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F63|337|DCPS|protein_coding|CODING|NM_014026.4|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998736 rs695029 -0.693147 0.480489 126 Q105 337 caG/caA LOW 2 SILENT CODING DCPS A protein_coding NM_014026.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126176578 G A 0 228 0 0.9917 0.9329 0.9035 1 0.7972 0.9448 0.966152 0.864056 0.811773 2 10090 104186 10613 8652 5280 53648 741 15162 2 10400 121270 11570 8654 6588 66648 906 16504 0 . 0 . 0 127 0,0,70,47 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q105|337|DCPS|protein_coding|CODING|NM_014026.4|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs637462 -0.693147 0.288988 127 L147 333 Ttg/Ctg LOW 8 SILENT CODING ST3GAL4 C protein_coding NM_001254757.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126278203 T C 0 222 0 0.0129 0.0859 0.0706 0.2222 0.0815 0.0593 0.0222626 0.057932 0.0761982 1 224 10248 1092 1795 736 5408 80 913 2 10404 121274 11572 8626 6614 66668 906 16484 0.988876 0 . 0 COSM147378 157 31,51,31,32 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L147|333|ST3GAL4|protein_coding|CODING|NM_001254757.1|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.990846 rs2298475 -0.693147 0.700267 157 778 395 MODIFIER 17 CODING KIRREL3 G protein_coding NM_032531.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126294080 C G 0 9.7 0 0.8215 0.7179 0.5548 0.8919 0.6113 0.6237 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||395||778|KIRREL3|protein_coding|CODING|NM_032531.3|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7113456 -0.379885 0 1 G665 778 ggC/ggT LOW 17 SILENT CODING KIRREL3 A protein_coding NM_032531.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126294817 G A 0 228 0 0.7201 0.7037 0.5677 0.9067 0.6491 0.6247 0.726995 0.664833 0.633538 2 6873 79092 6569 7735 4186 42612 598 10519 2 9566 117822 11174 8574 6410 65250 858 15990 0 3 likely-benign 0 . 53 0,0,9,39 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G665|778|KIRREL3|protein_coding|CODING|NM_032531.3|17|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs948052 -0.693147 0.0881391 53 778 13 MODIFIER 1 CODING KIRREL3 T protein_coding NM_032531.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 126870418 C T 0 228 0 0.1664 0.1607 0.0677 0.4196 0.0358 0.0808 0.138402 0.0644709 0.0296332 2 1110 6488 387 2480 116 1615 46 734 2 5800 65580 4874 5288 2494 36280 478 10366 0 . 0 . COSN164092 71 0,0,33,28 UTR_5_PRIME(MODIFIER||13||778|KIRREL3|protein_coding|CODING|NM_032531.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3802824 -0.693147 0.0733082 71 485 1736 MODIFIER 10 CODING ETS1 C protein_coding NM_001143820.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128330520 T C 0 67 0 0.2315 0.4411 0.3689 0.5397 0.5169 0.5961 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||1736||485|ETS1|protein_coding|CODING|NM_001143820.1|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4937333 -0.511536 0.833544 3 Q210 452 caA/caG LOW 5 SILENT CODING FLI1 G protein_coding NM_002017.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128651893 A G 0 228 0 0.4576 0.2141 0.1585 0.1766 0.0805 0.1002 0.380304 0.180742 0.0884988 2 4169 15792 2046 1671 725 5624 83 1474 2 9802 120758 11576 8614 6614 66740 900 16512 0.910891 0 . 0 . 118 1,1,56,45 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q210|452|FLI1|protein_coding|CODING|NM_002017.4|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.584158 rs35195224 -0.693147 0.0330973 118 A229 452 gcT/gcA LOW 6 SILENT CODING FLI1 A protein_coding NM_002017.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128675292 T A 0 222 0 0.2579 0.1751 0.1254 0.1706 0.1093 0.1708 0.24797 0.152148 0.108855 1 2015 11703 940 1125 515 5041 73 1994 2 6092 53444 3042 4424 3118 26228 444 10096 0.978296 0 . 0 . 95 26,15,27,15 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A229|452|FLI1|protein_coding|CODING|NM_002017.4|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.995437 rs7113191 -0.693146 0.0471364 95 391 1045 MODIFIER 2 CODING KCNJ1 C protein_coding NM_000220.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128707975 G C 0 174 0 0.1641 0.1643 0.085 0.1062 0.1481 0.2975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.797261 0 . 0 . 100 45,1,48,0 UTR_3_PRIME(MODIFIER||1045||391|KCNJ1|protein_coding|CODING|NM_000220.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.842145 rs675759 -0.693147 0.154339 100 391 1011 MODIFIER 2 CODING KCNJ1 A protein_coding NM_000220.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128708009 G A 0 222 0 0.1339 0.1573 0.0821 0.1062 0.1481 0.3047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974203 0 . 0 . 140 60,7,56,6 UTR_3_PRIME(MODIFIER||1011||391|KCNJ1|protein_coding|CODING|NM_000220.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.670999 rs386604882,rs675388 -0.693147 0.646573 140 391 676 MODIFIER 2 CODING KCNJ1 C protein_coding NM_000220.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128708344 T C 0 203 0 0.1664 0.1665 0.0865 0.1062 0.1481 0.3047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.679237 0 . 0 . 20 0,5,2,12 UTR_3_PRIME(MODIFIER||676||391|KCNJ1|protein_coding|CODING|NM_000220.4|2|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.97357 rs673992 -0.686358 0.433274 20 391 73 MODIFIER 2 CODING KCNJ1 A protein_coding NM_000220.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128708947 T A 0 222 0 0.1664 0.1665 0.0865 0.1062 0.1481 0.3047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.695022 0 . 0 . 144 62,8,58,6 UTR_3_PRIME(MODIFIER||73||391|KCNJ1|protein_coding|CODING|NM_000220.4|2|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.574139 rs1231254 -0.693147 0.0102887 144 145 2094 MODIFIER 4 CODING C11orf45 T protein_coding NM_001256088.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128770358 G T 0 9.7 0 0.177 0.1765 0.1499 0.247 0.0129 0.2904 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2094||145|C11orf45|protein_coding|CODING|NM_001256088.1|4|T),INTRON(MODIFIER||||419|KCNJ5|protein_coding|CODING|NM_000890.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3740835 -0.379885 0 1 145 1979 MODIFIER 4 CODING C11orf45 T protein_coding NM_001256088.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128770473 C T 0 9.7 0 0.8495 0.653 0.5403 0.6171 0.5149 0.6462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1979||145|C11orf45|protein_coding|CODING|NM_001256088.1|4|T),INTRON(MODIFIER||||419|KCNJ5|protein_coding|CODING|NM_000890.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2846699 -0.379885 0 1 145 1978 MODIFIER 4 CODING C11orf45 G protein_coding NM_001256088.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128770474 A G 0 9.7 0 0.8979 0.7806 0.7017 0.7173 0.7406 0.7843 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1978||145|C11orf45|protein_coding|CODING|NM_001256088.1|4|G),INTRON(MODIFIER||||419|KCNJ5|protein_coding|CODING|NM_000890.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2846698 -0.379885 0 1 S57 419 agT/agC LOW 2 SILENT CODING KCNJ5 C protein_coding NM_000890.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128781339 T C 0 228 0 0.8918 0.8698 0.8026 0.877 0.8499 0.9008 0.893685 0.848261 0.824994 2 9347 102410 9334 7605 5225 55367 748 14784 2 10406 121402 11574 8652 6614 66738 906 16512 1 2 benign 0 . 154 1,0,92,55 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S57|419|KCNJ5|protein_coding|CODING|NM_000890.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs6590357 -0.693147 0.699645 154 L270 419 ctT/ctG LOW 2 SILENT CODING KCNJ5 G protein_coding NM_000890.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128781978 T G 0 228 0 0.8805 0.8662 0.7997 0.876 0.8479 0.9029 0.883916 0.842721 0.82162 2 9148 101780 9303 7588 5219 55047 746 14729 2 10282 120960 11548 8632 6612 66504 906 16476 1 2 benign 0 . 26 0,1,4,21 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L270|419|KCNJ5|protein_coding|CODING|NM_000890.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7118824 -0.692914 0.286389 26 H278 419 caT/caC LOW 2 SILENT CODING KCNJ5 C protein_coding NM_000890.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128782002 T C 0 228 0 0.882 0.867 0.8026 0.876 0.8479 0.9029 0.887551 0.843952 0.82162 2 9127 101603 9285 7584 5222 54933 747 14705 2 10226 120728 11528 8628 6614 66378 908 16446 1 2 benign 0 . 24 0,1,7,16 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H278|419|KCNJ5|protein_coding|CODING|NM_000890.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7118833 -0.692717 0.732789 24 Q282E 419 Cag/Gag MODERATE 2 MISSENSE CODING KCNJ5 G protein_coding NM_000890.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128782012 C G 0 228 0 0.9977 0.995 0.9942 1 0.9841 0.998 0.997047 0.987073 0.981964 2 10178 118999 11499 8628 6456 64929 898 16411 2 10202 120630 11528 8628 6614 66318 906 16434 0 2 benign 0 . 21 0,0,6,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q282E|419|KCNJ5|protein_coding|CODING|NM_000890.3|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7102584 -0.692352 0.632184 21 419 LOW 2 CODING KCNJ5 T protein_coding NM_000890.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128782112 C T 0 142 0 0.1891 0.0763 0.0432 0.0863 0.0089 0.0061 0.158026 0.0590503 0.00828085 1 1742 3599 237 737 51 709 25 98 2 9732 117602 11398 8386 6588 64264 884 16350 0.950952 2 benign 0 . 13 4,1,2,4 SPLICE_SITE_REGION+INTRON(LOW||||419|KCNJ5|protein_coding|CODING|NM_000890.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 0.950952 0.950952 0 0.950952 rs45516097 -0.616816 0.317275 13 419 410 MODIFIER 3 CODING KCNJ5 T protein_coding NM_000890.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128787036 C T 0 9.7 0 0.8926 0.8752 0.804 0.9028 0.8499 0.8998 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||410||419|KCNJ5|protein_coding|CODING|NM_000890.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2846675 -0.379885 0 1 419 928 MODIFIER 3 CODING KCNJ5 T protein_coding NM_000890.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128787554 C T 0 39.3 0 0.8192 0.8542 0.7939 0.9028 0.8489 0.8998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||928||419|KCNJ5|protein_coding|CODING|NM_000890.3|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7925056 -0.453602 0.76 2 419 1063 MODIFIER 3 CODING KCNJ5 A protein_coding NM_000890.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128787689 G A 0 9.7 0 0.5825 0.6823 0.6758 0.6637 0.7525 0.7689 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1063||419|KCNJ5|protein_coding|CODING|NM_000890.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2846696 -0.379885 0 1 124 107 MODIFIER 4 CODING TP53AIP1 T protein_coding NM_022112.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128805379 C T 0 97 0 0.0144 0.0559 0.0504 0.1488 0.0308 0.046 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.761877 0 . 0 . 10 5,0,3,2 UTR_3_PRIME(MODIFIER||107||124|TP53AIP1|protein_coding|CODING|NM_022112.2|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.952347 1 0 0.666643 rs74463293 -0.590765 0.391905 10 E376 2087 gaA/gaG LOW 11 SILENT CODING ARHGAP32 C protein_coding NM_001142685.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 128868239 T C 0 222 0 0.5855 0.5711 0.5951 0.5813 0.6769 0.4151 0.594275 0.660742 0.694787 1 6055 75996 6432 5145 4291 45613 609 7851 2 10406 120788 11562 8644 6614 66606 902 16054 0.992215 0 . 0 COSM147379 112 38,16,39,12 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E376|2087|ARHGAP32|protein_coding|CODING|NM_001142685.1|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.508103 rs386604511,rs670440 -0.693147 0.132153 112 1324 178 MODIFIER 25 CODING NFRKB A protein_coding NM_006165.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 129734442 G A 0 86 0 0 0.0017971 0 0.0069 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.475476 0 . 0 . 11 4,1,6,0 UTR_3_PRIME(MODIFIER||178||1324|NFRKB|protein_coding|CODING|NM_006165.3|25|A),DOWNSTREAM(MODIFIER||4544||275|TMEM45B|protein_coding|CODING|NM_138788.3||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 1 0 0.683497 rs370754101 -0.616816 0.0930359 11 1160 1101 MODIFIER 22 CODING PRDM10 T protein_coding NM_020228.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 129771107 C T 0 228 0 0.9977 0.994 0.987 1 0.9841 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 166 0,0,124,30 UTR_3_PRIME(MODIFIER||1101||1160|PRDM10|protein_coding|CODING|NM_020228.2|22|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1617778 -0.693147 0.18988 166 N405 855 aaC/aaT LOW 10 SILENT CODING ST14 T protein_coding NM_021978.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130066335 C T 0 222 0 0.3684 0.639 0.7752 0.7103 0.6869 0.7853 0.42299 0.568647 0.643273 1 3746 71517 8213 5407 3703 38851 507 11090 2 8366 103580 9836 7610 4742 57344 744 14938 0.999958 0 . 0 . 54 4,25,6,17 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N405|855|ST14|protein_coding|CODING|NM_021978.3|10|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.875408 rs476106 -0.692717 0.0153575 54 G553 855 ggG/ggC LOW 14 SILENT CODING ST14 C protein_coding NM_021978.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130068491 G C 0 222 0 0.1029 0.1176 0.0749 0.1974 0.1133 0.09 0.109041 0.129732 0.14033 1 1136 15146 730 1671 832 8916 101 1760 2 10192 119530 11466 8580 6330 65662 878 16422 0.978784 0 . 0 . 67 12,19,10,19 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G553|855|ST14|protein_coding|CODING|NM_021978.3|14|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.607438 rs11827924,rs386489415 -0.693079 0.0364036 67 A525V 889 gCa/gTa MODERATE 6 MISSENSE CODING ADAMTS8 A protein_coding NM_007037.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130281488 G A 0 228 0 0.705 0.744 0.8012 0.8304 0.7694 0.6411 0.711205 0.740081 0.754004 2 6938 89437 9568 6907 4926 50070 657 10371 2 9806 120612 11568 8620 6598 66658 900 16462 0 . 0 . 0 111 0,0,41,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A525V|889|ADAMTS8|protein_coding|CODING|NM_007037.4|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2131535 -0.693147 0.184118 111 E78D 889 gaG/gaC MODERATE 1 MISSENSE CODING ADAMTS8 G protein_coding NM_007037.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130297948 C G 0 131 0 0.1732 0.4692 0.6916 0.6319 0.5825 0.4274 0.191153 0.39489 0.479763 2 180 10489 927 517 142 5212 83 3428 2 460 18356 1140 744 216 7882 152 7762 0 . 0 . 0 6 0,0,1,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E78D|889|ADAMTS8|protein_coding|CODING|NM_007037.4|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7927048 -0.616816 0.52412 6 L75 889 ctA/ctG LOW 1 SILENT CODING ADAMTS8 C protein_coding NM_007037.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130297957 T C 0 135 0 0.9834 0.9137 0.9424 0.9692 0.839 0.819 0.957891 0.887302 0.857212 2 1002 20560 1709 1211 289 9708 151 6490 2 1052 24578 1810 1254 372 11652 176 8262 0 . 0 . 0 6 0,0,1,5 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L75|889|ADAMTS8|protein_coding|CODING|NM_007037.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7942034 -0.616816 0.856113 6 992 1086 MODIFIER 11 CODING SNX19 G protein_coding NM_014758.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130747231 C G 0 51 0 0.3464 0.473 0.5576 0.4802 0.4414 0.6094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 2,1,2,1 UTR_3_PRIME(MODIFIER||1086||992|SNX19|protein_coding|CODING|NM_014758.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.861511 rs1050071 -0.511536 0.588406 6 992 931 MODIFIER 11 CODING SNX19 G protein_coding NM_014758.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130747386 C G 0 21.8 0 0.3472 0.4732 0.5576 0.4802 0.4414 0.6094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.750668 0 . 0 . 8 5,0,3,0 UTR_3_PRIME(MODIFIER||931||992|SNX19|protein_coding|CODING|NM_014758.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 0 . 0.900802 rs6590520 -0.511536 0.220755 8 992 186 MODIFIER 11 CODING SNX19 G protein_coding NM_014758.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130748131 A G 0 131 0 0.3744 0.4812 0.562 0.4812 0.4414 0.6094 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.616426 0 . 0 . 17 6,1,8,0 UTR_3_PRIME(MODIFIER||186||992|SNX19|protein_coding|CODING|NM_014758.2|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.941512 rs3190331 -0.651104 0.5 17 L878R 992 cTg/cGg MODERATE 9 MISSENSE CODING SNX19 C protein_coding NM_014758.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130750642 A C 0 222 0 0.944 0.8127 0.7767 0.6974 0.7356 0.8589 0.919355 0.807095 0.749593 1 9556 94687 8794 6085 5368 50321 683 13880 2 10400 121360 11568 8642 6612 66720 906 16512 0.92649 0 . 0 . 103 21,31,22,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L878R|992|SNX19|protein_coding|CODING|NM_014758.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.267053 rs2298566 -0.693145 0.247937 103 N753S 992 aAt/aGt MODERATE 6 MISSENSE CODING SNX19 C protein_coding NM_014758.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130776524 T C 0 222 0 0.5537 0.6631 0.6916 0.6468 0.6372 0.8344 0.569741 0.631271 0.662788 1 5856 82460 8192 5590 4535 44360 593 13334 2 10406 121362 11578 8632 6606 66722 908 16510 0.988773 0 . 0 . 167 54,19,63,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N753S|992|SNX19|protein_coding|CODING|NM_014758.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.523993 rs4414223 -0.693147 0.0148684 167 S723 992 tcT/tcC LOW 6 SILENT CODING SNX19 G protein_coding NM_014758.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130776613 A G 0 222 0 0.5537 0.6631 0.6916 0.6468 0.6372 0.8344 0.569968 0.631425 0.662904 1 5851 82440 8189 5586 4535 44354 593 13332 2 10398 121328 11574 8634 6598 66708 908 16508 0.984906 0 . 0 . 187 29,49,33,52 SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S723|992|SNX19|protein_coding|CODING|NM_014758.2|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.246178 rs4373936 -0.693147 0.0881917 187 P644 992 ccG/ccA LOW 4 SILENT CODING SNX19 T protein_coding NM_014758.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130780015 C T 0 222 0 0.2436 0.5769 0.6686 0.6448 0.6342 0.8333 0.324171 0.546938 0.661043 1 3169 79530 8048 5582 4547 44284 579 13321 2 10404 121368 11576 8636 6606 66728 908 16510 0.992768 0 . 0 . 149 36,26,44,28 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P644|992|SNX19|protein_coding|CODING|NM_014758.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.527394 rs1781 -0.693147 0.356644 149 L618F 992 ttG/ttT MODERATE 3 MISSENSE CODING SNX19 A protein_coding NM_014758.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130780225 C A 0 228 0 . 0 . 0 . 0 . 0 . 2 10388 121304 11570 8628 6610 66696 908 16504 2 10388 121304 11570 8628 6610 66696 908 16504 0 . 0 . 0 96 0,0,28,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L618F|992|SNX19|protein_coding|CODING|NM_014758.2|3|A) 0 . 0 . 0 . 0 . 1 0 60 0 0 1 0 . rs681982 -0.693147 1.14036e-05 96 992 LOW 2 CODING SNX19 A protein_coding NM_014758.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130780270 C A 0 228 0 0.7829 0.8405 0.8703 0.8512 0.8917 0.8333 0 . 0 2 3910 48571 4678 3272 2779 26841 387 6704 2 6940 91368 8180 6328 5146 51384 718 12672 0 . 0 . 0 40 0,0,5,14 SPLICE_SITE_REGION+INTRON(LOW||||992|SNX19|protein_coding|CODING|NM_014758.2|2|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1237478,rs57880168 -0.69168 0.0365919 40 V361L 992 Gtt/Ctt MODERATE 1 MISSENSE CODING SNX19 G protein_coding NM_014758.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130784754 C G 0 221 0 0.6831 0.7304 0.7421 0.6796 0.7167 0.8528 0.684462 0.711604 0.725506 1 7093 90283 8562 5972 5322 48895 655 13784 2 10398 121306 11570 8634 6608 66676 908 16512 0.972554 0 . 0 . 89 8,12,34,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V361L|992|SNX19|protein_coding|CODING|NM_014758.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997898 rs3751037 -0.693147 0.0985228 89 P288 992 ccG/ccC LOW 1 SILENT CODING SNX19 G protein_coding NM_014758.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130784971 C G 0 217 0 0.9145 0.7969 0.7723 0.6806 0.7207 0.8538 0.882553 0.783934 0.733419 1 9208 93055 8726 5984 5324 49332 668 13813 2 10368 121212 11568 8616 6612 66640 906 16502 0.896504 0 . 0 . 23 4,5,6,7 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P288|992|SNX19|protein_coding|CODING|NM_014758.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.705828 rs3751036 -0.683931 0.225613 23 992 511 MODIFIER 1 CODING SNX19 A protein_coding NM_014758.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 130786345 C A 0 32.6 0 0.6626 0.5946 0.6254 0.5357 0.4463 0.6943 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_5_PRIME(MODIFIER||511||992|SNX19|protein_coding|CODING|NM_014758.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs3751033 -0.379885 0 2 R193 355 Agg/Cgg LOW 4 SILENT CODING NTM C protein_coding NM_001144058.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 132177633 A C 0 228 0 0.9123 0.8806 0.8991 0.9266 0.8211 0.8384 0.907088 0.853878 0.826623 2 9384 102721 10826 8004 5520 55035 758 13194 2 10404 121374 11576 8648 6610 66718 908 16510 1 0 . 0 . 155 1,0,68,71 SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R193|355|NTM|protein_coding|CODING|NM_001144058.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2305271 -0.693147 0.00227785 155 355 354 MODIFIER 8 CODING NTM T protein_coding NM_001144058.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 132205394 C T 0 26.4 0 0.2307 0.1947 0.1239 0.1677 0.0944 0.3272 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,2,0 UTR_3_PRIME(MODIFIER||354||355|NTM|protein_coding|CODING|NM_001144058.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs11634 -0.453602 0.1 4 355 466 MODIFIER 8 CODING NTM A protein_coding NM_001144058.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 132205506 C A 0 40.2 0 0.2315 0.1977 0.1239 0.1796 0.0944 0.3292 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.900802 0 . 0 . 8 5,0,1,2 UTR_3_PRIME(MODIFIER||466||355|NTM|protein_coding|CODING|NM_001144058.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.900802 1 0 0.900802 rs2706 -0.511536 0.588406 8 A50V 167 gCt/gTt MODERATE 3 MISSENSE CODING SPATA19 A protein_coding NM_001291992.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 133714522 G A 0 222 0 0.1044 0.3395 0.317 0.6022 0.3926 0.3476 0.168333 0.304478 0.374215 1 1569 45328 3807 5185 3119 25935 344 5369 2 10320 118510 11554 8634 6612 65948 886 14556 0.849119 0 . 0 . 114 9,45,15,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A50V|167|SPATA19|protein_coding|CODING|NM_001291992.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.372089 rs2282602 -0.693147 0.0108392 114 167 LOW 2 CODING SPATA19 A protein_coding NM_001291992.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 133714543 G A 0 222 0 0.0635 0.0929 0.0706 0.1339 0.0388 0.1616 0.0506588 0.0414743 0.0367698 1 542 7032 978 1018 108 2518 42 1826 2 10216 114174 11506 8600 6614 64698 824 11716 0.90166 0 . 0 . 88 10,37,4,33 SPLICE_SITE_REGION+INTRON(LOW||||167|SPATA19|protein_coding|CODING|NM_001291992.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940128 rs2282603 -0.693141 0.0144484 88 Y111 1437 taT/taC LOW 3 SILENT CODING IGSF9B G protein_coding NM_001277285.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 133814191 A G 0 222 0 0.2602 0.488 0.5389 0.4028 0.7117 0.6176 0.360726 0.597768 0.71525 1 3074 74801 5543 3223 4601 47669 581 10110 2 9740 120026 11450 8532 6548 66460 890 16406 0.834036 0 . 0 . 115 31,19,23,29 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y111|1437|IGSF9B|protein_coding|CODING|NM_001277285.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.871043 rs595986 -0.693147 0.208897 115 1437 LOW 2 CODING IGSF9B G protein_coding NM_001277285.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 133815951 C G 0 222 0 0.0378 0.1186 0.1037 0.0804 0.1421 0.2536 0.0496078 0.102895 0.130021 1 281 8087 615 277 248 5178 38 1450 2 3602 35714 2490 1828 1244 22682 224 3644 0.774363 0 . 0 . 175 44,38,43,31 SPLICE_SITE_REGION+INTRON(LOW||||1437|IGSF9B|protein_coding|CODING|NM_001277285.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0414281 rs12291005 -0.693147 0.708189 175 P79 1437 ccG/ccC LOW 2 SILENT CODING IGSF9B G protein_coding NM_001277285.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 133815981 C G 0 222 0 0.3011 0.3546 0.438 0.5208 0.2992 0.2536 0.272427 0.288959 0.297252 1 2188 31319 4333 3702 1088 16351 205 3452 2 6356 80374 8054 6360 3246 46046 556 9756 0.924958 0 . 0 . 163 54,31,27,37 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P79|1437|IGSF9B|protein_coding|CODING|NM_001277285.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.825487 rs10894768 -0.693147 0.470009 163 310 LOW 7 CODING JAM3 C protein_coding NM_032801.4 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134018656 T C 0 222 0 0.8192 0.5381 0.4697 0.6429 0.329 0.3139 0.736938 0.458987 0.316616 1 7850 48675 5619 5283 2688 21941 347 4947 2 10404 121288 11552 8642 6608 66676 904 16502 0.918684 0 . 0 . 66 7,16,11,25 SPLICE_SITE_REGION+INTRON(LOW||||310|JAM3|protein_coding|CODING|NM_032801.4|7|C),DOWNSTREAM(MODIFIER||3681||1498|NCAPD3|protein_coding|CODING|NM_015261.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0789255 rs610382 -0.693139 0.00293344 66 V964 1498 gtA/gtG LOW 23 SILENT CODING NCAPD3 C protein_coding NM_015261.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134047243 T C 0 222 0 0.8245 0.473 0.33 0.4137 0.329 0.3088 0.734439 0.457218 0.31522 1 7863 44324 3180 3456 2686 21951 324 4864 2 10400 121290 11564 8610 6612 66690 908 16506 0.972776 0 . 0 . 97 15,26,13,36 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V964|1498|NCAPD3|protein_coding|CODING|NM_015261.2|23|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.979697 rs2276265,rs386563296 -0.693147 0.270356 97 R622Q 1498 cGg/cAg MODERATE 16 MISSENSE CODING NCAPD3 T protein_coding NM_015261.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134062764 C T 0 222 0 0.0008 0.026 0.0231 0.0149 0.0537 0.045 0.00885961 0.0420899 0.059111 1 76 6088 285 143 486 4456 41 601 2 10384 121282 11570 8650 6614 66644 908 16512 0.836642 0 . 0 . 61 9,17,9,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R622Q|1498|NCAPD3|protein_coding|CODING|NM_015261.2|16|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.913979 rs12292394 -0.693054 0.0647915 61 336 1531 MODIFIER 6 CODING VPS26B C protein_coding NM_052875.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134117015 T C 0 48.5 0 0.9864 0.9253 0.987 0.8343 0.9742 0.8425 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||1531||336|VPS26B|protein_coding|CODING|NM_052875.4|6|C),DOWNSTREAM(MODIFIER||1158||225|THYN1|protein_coding|CODING|NM_001037305.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs492761 -0.511536 0.617121 3 R163P 653 cGc/cCc MODERATE 5 MISSENSE CODING GLB1L3 C protein_coding NM_001080407.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134151975 G C 0 228 0 0.9766 0.9077 0.8559 0.8135 0.9871 0.8671 0 . 0 2 9660 106027 8204 6710 5656 62398 767 12632 2 9886 113358 10830 8348 5740 63376 812 14366 1 0 . 0 . 53 0,1,31,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R163P|653|GLB1L3|protein_coding|CODING|NM_001080407.2|5|C) 0 . 0 . 0 1 0 . 1 0 57 0 1 0.932131 0 1 rs472287 -0.693147 0.572052 53 S230 653 tcA/tcG LOW 7 SILENT CODING GLB1L3 G protein_coding NM_001080407.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134158745 A G 0 228 0 0.1589 0.2336 0.1311 0.3502 0.1759 0.3466 0.169277 0.179247 0.183995 2 1693 25748 1758 2675 1355 12880 201 5186 2 9590 118878 11388 8524 6558 65948 884 15986 0 . 0 . COSM1127835 119 0,0,61,43 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S230|653|GLB1L3|protein_coding|CODING|NM_001080407.2|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3824995 -0.693147 0.0112656 119 V474M 653 Gtg/Atg MODERATE 14 MISSENSE CODING GLB1L3 A protein_coding NM_001080407.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134182375 G A 0 228 0 1 0.9984 0.9986 0.996 0.997 1 1 0.999764 0.999646 2 9772 120137 11553 8577 6557 66298 893 16487 2 9772 120354 11554 8610 6612 66414 894 16498 0 . 0 . 0 61 0,0,17,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V474M|653|GLB1L3|protein_coding|CODING|NM_001080407.2|14|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2509062 -0.693147 0.491834 61 636 LOW 6 CODING GLB1L2 G protein_coding NM_138342.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134226291 A G 0 222 0 0.0408 0.1178 0.0346 0.3105 0.0089 0.1943 0.0299864 0.0135426 0.00511985 1 357 7037 398 2915 261 419 44 2643 2 10332 120954 11550 8618 6612 66470 906 16466 0.106226 0 . 0 . 60 4,19,6,24 SPLICE_SITE_REGION+INTRON(LOW||||636|GLB1L2|protein_coding|CODING|NM_138342.3|6|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.130283 rs3802929 -0.693097 0.389951 60 636 332 MODIFIER 19 CODING GLB1L2 C protein_coding NM_138342.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134245284 T C 0 46.3 0 0.6694 0.7865 0.7968 0.9266 0.7594 0.8211 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||332||636|GLB1L2|protein_coding|CODING|NM_138342.3|19|C),DOWNSTREAM(MODIFIER||3114||334|B3GAT1|protein_coding|CODING|NM_018644.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9783402 -0.453602 0.38 2 334 2511 MODIFIER 7 CODING B3GAT1 C protein_coding NM_018644.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134249321 T C 0 228 0 0.7254 0.7989 0.7882 0.9365 0.7505 0.8139 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 133 0,0,26,99 UTR_3_PRIME(MODIFIER||2511||334|B3GAT1|protein_coding|CODING|NM_018644.3|7|C),DOWNSTREAM(MODIFIER||3103||636|GLB1L2|protein_coding|CODING|NM_138342.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs893953 -0.693147 0.00370246 133 334 2483 MODIFIER 7 CODING B3GAT1 C protein_coding NM_018644.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 11 134249349 T C 0 228 0 0.7254 0.7893 0.7795 0.9365 0.7416 0.7802 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 106 0,0,15,88 UTR_3_PRIME(MODIFIER||2483||334|B3GAT1|protein_coding|CODING|NM_018644.3|7|C),DOWNSTREAM(MODIFIER||3131||636|GLB1L2|protein_coding|CODING|NM_138342.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs893952 -0.693147 0.0649514 106 P283S 1182 Ccc/Tcc MODERATE 3 MISSENSE CODING IQSEC3 T protein_coding NM_001170738.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 235022 C T 0 228 0 0.8593 0.9583 0.9741 1 0.995 1 0.904762 0.968579 0.995273 2 348 11745 136 186 20 3393 116 7546 2 398 11862 138 186 20 3448 120 7552 0 . 0 . 0 28 0,0,15,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P283S|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12822449 -0.692831 0.834718 28 E457 1182 gaG/gaA LOW 4 SILENT CODING IQSEC3 A protein_coding NM_001170738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 247900 G A 0 95 0 0.149 0.2592 0.1427 0.371 0.2445 0.3906 0 . 0 1 268 6325 163 516 175 2651 41 2511 2 1050 16566 720 1092 682 7096 130 5796 0.428674 0 . 0 COSM430910,COSM430909 16 6,4,5,1 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E457|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|4|A),INTRAGENIC(MODIFIER|||||LOC574538||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.65377 rs7313003 -0.616816 0.329692 16 A558G 1182 gCg/gGg MODERATE 4 MISSENSE CODING IQSEC3 G protein_coding NM_001170738.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 248202 C G 0 228 0 0.6127 0.6561 0.6412 0.7093 0.6054 0.7229 0.65672 0.650283 0.647081 2 871 9778 575 697 308 4891 76 2360 2 1282 13528 756 930 444 6924 114 3078 1 0 . 0 . 17 0,1,7,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gGg|A558G|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|4|G),INTRAGENIC(MODIFIER|||||LOC574538||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs56204927 -0.689466 0.118542 17 R743H 1182 cGt/cAt MODERATE 6 MISSENSE CODING IQSEC3 A protein_coding NM_001170738.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 266265 G A 0 222 0 0.0008 0.0017971 0 0.0079 0 0 0.00113533 0.000384615 0 1 19 86 2 63 0 1 0 1 2 6414 63040 5174 4708 2158 34460 466 9660 0.907956 0 . 0 COSM1254920,COSM1254919 140 34,22,46,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R743H|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0816337 rs145520553 -0.693147 0.0750645 140 F919 1182 ttT/ttC LOW 10 SILENT CODING IQSEC3 C protein_coding NM_001170738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 274647 T C 0 222 0 0.087 0.2608 0.3199 0.3393 0.326 0.3057 0.134589 0.255421 0.317326 1 1321 37813 4364 3111 2174 21972 269 4602 2 10406 121300 11564 8628 6614 66676 904 16508 0.918057 0 . 0 . 184 49,28,34,53 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F919|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.124107 rs4980859 -0.693147 0.270348 184 G1136 1182 ggT/ggC LOW 14 SILENT CODING IQSEC3 C protein_coding NM_001170738.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 284058 T C 0 228 0 0.9455 0.9237 0.9481 0.8502 0.9543 0.9213 0.955959 0.955001 0.954584 2 3798 57750 6098 3584 2451 31744 397 9678 2 4014 61210 6272 4176 2610 33128 432 10578 0 . 0 . 0 53 0,0,2,50 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1136|1182|IQSEC3|protein_coding|CODING|NM_001170738.1|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs216230 -0.693147 9.38229e-09 53 1182 2282 MODIFIER 14 CODING IQSEC3 G protein_coding NM_001170738.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 286481 A G 0 69 0 0.2141 0.2933 0.2997 0.381 0.3101 0.2883 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 UTR_3_PRIME(MODIFIER||2282||1182|IQSEC3|protein_coding|CODING|NM_001170738.1|14|G) 0 . 0 . 0 1 0 . 0 . 59 0 0 1 0 . rs113879277 -0.453602 0.78 3 1182 2313 MODIFIER 14 CODING IQSEC3 G protein_coding NM_001170738.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 286512 C G 0 21.4 0 0.1293 0.268 0.2867 0.38 0.3052 0.2883 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2313||1182|IQSEC3|protein_coding|CODING|NM_001170738.1|14|G) 0 . 0 . 0 1 0 . 0 . 59 0 0 . 0 . rs367731117 -0.453602 0.02 2 1182 2315 MODIFIER 14 CODING IQSEC3 G protein_coding NM_001170738.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 286514 C G 0 34.3 0 0.1293 0.268 0.2867 0.38 0.3052 0.2883 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||2315||1182|IQSEC3|protein_coding|CODING|NM_001170738.1|14|G) 0 . 0 . 0 1 0 . 0 . 59 0 0 . 0 . rs60912613 -0.453602 0.02 2 614 347 MODIFIER 16 CODING SLC6A12 T protein_coding NM_001122847.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 299887 C T 0 157 0 0.5265 0.4381 0.3415 0.4048 0.3559 0.5061 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 10 0,1,7,1 UTR_3_PRIME(MODIFIER||347||614|SLC6A12|protein_coding|CODING|NM_001122847.2|16|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2075228 -0.651104 0.55693 10 T149 614 acT/acC LOW 5 SILENT CODING SLC6A12 G protein_coding NM_001122847.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 311949 A G 0 228 0 0.767 0.616 0.5908 0.6339 0.4632 0.5685 0.695642 0.528679 0.44314 2 7453 61405 6733 5550 2923 29362 448 8936 2 10404 121332 11560 8636 6610 66706 906 16510 1 0 . 0 . 181 0,1,96,64 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T149|614|SLC6A12|protein_coding|CODING|NM_001122847.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs216250 -0.693147 0.00535107 181 A14 614 gcA/gcG LOW 3 SILENT CODING SLC6A12 C protein_coding NM_001122847.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 319111 T C 0 222 0 0.7284 0.5292 0.4366 0.3075 0.5268 0.5562 0.710395 0.594187 0.534651 1 7374 63965 4842 2951 3488 35607 460 9243 2 10406 121324 11558 8638 6606 66700 906 16510 0.789547 0 . 0 . 102 16,32,16,26 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A14|614|SLC6A12|protein_coding|CODING|NM_001122847.2|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999183 rs526690 -0.693146 0.271904 102 C10R 614 Tgt/Cgt MODERATE 3 MISSENSE CODING SLC6A12 G protein_coding NM_001122847.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 319125 A G 0 222 0 0.7126 0.525 0.4308 0.3145 0.5229 0.5573 0.702224 0.587729 0.52907 1 7277 63491 4821 2988 3461 35252 458 9234 2 10404 121206 11540 8624 6580 66650 906 16502 0.0772965 0 . 0 . 92 13,31,13,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C10R|614|SLC6A12|protein_coding|CODING|NM_001122847.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.903037 rs557881 -0.693144 0.809245 92 S1383 1690 tcC/tcT LOW 25 SILENT CODING KDM5A A protein_coding NM_001042603.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 406292 G A 0 222 0 0.3306 0.3526 0.3199 0.5109 0.2326 0.3661 0.315189 0.273243 0.254017 1 3165 37255 4243 4275 2267 17278 275 5752 2 9760 120040 11464 8490 6586 66386 896 16458 0.97232 0 . 0 . 64 16,19,9,12 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1383|1690|KDM5A|protein_coding|CODING|NM_001042603.2|25|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.432518 rs2229351 -0.692352 0.0321801 64 M865T 1690 aTg/aCg MODERATE 19 MISSENSE CODING KDM5A G protein_coding NM_001042603.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 427575 A G 0 220 0 0.3321 0.353 0.3199 0.5109 0.2326 0.3661 0.316694 0.273405 0.253773 1 3173 37455 4268 4341 2276 17355 275 5767 2 9802 120744 11576 8616 6614 66724 900 16512 0.212803 0 . 0 . 50 3,21,2,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M865T|1690|KDM5A|protein_coding|CODING|NM_001042603.2|19|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.939981 rs11062385,rs386516556 -0.692562 0.0737738 50 1690 23 MODIFIER 1 CODING KDM5A G protein_coding NM_001042603.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 498279 GGGGT G 0 67 0 . 0 . 0 . 0 . 0 . 1 32 479 22 16 13 163 2 231 2 5940 92266 8640 6666 5176 50200 676 14968 0 . 0 . 0 184 12,44,18,6 UTR_5_PRIME(MODIFIER||23||1690|KDM5A|protein_coding|CODING|NM_001042603.2|1|G) 0 0.5 1 2 0.0108696 0 1 0 1 0 60 0 0 1 0 . rs374055994 -0.692831 0.0558391 184 1690 24 MODIFIER 1 CODING KDM5A G protein_coding NM_001042603.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 498280 GGGT G 0 9.1 0 . 0 . 0 . 0 . 0 . 1 33 1331 62 43 91 557 12 533 2 4688 76720 6784 5532 4316 42266 582 12552 0 . 0 . 0 172 14,45,21,5 UTR_5_PRIME(MODIFIER||24||1690|KDM5A|protein_coding|CODING|NM_001042603.2|1|G) 0 0.5 1 2 0.0114943 0 1 0 1 0 60 0 0 1 0 . rs376841529 -0.692976 0.00851604 172 S25R 488 Agt/Cgt MODERATE 4 MISSENSE CODING CCDC77 C protein_coding NM_032358.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 520947 A C 0 222 0 0.3563 0.223 0.1455 0.2996 0.0825 0.1636 0.331139 0.171921 0.0903488 1 3414 16969 1538 2403 723 6134 122 2635 2 10402 121234 11544 8620 6612 66648 906 16502 0.492152 0 . 0 . 178 62,30,39,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S25R|488|CCDC77|protein_coding|CODING|NM_032358.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.183022 rs4980895 -0.693147 0.0157725 178 M335T 488 aTg/aCg MODERATE 10 MISSENSE CODING CCDC77 C protein_coding NM_032358.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 547683 T C 0 222 0 0.2943 0.3229 0.4107 0.3433 0.2594 0.3436 0.289378 0.271951 0.263023 1 2936 34963 5212 3144 988 16930 274 5479 2 10350 121268 11564 8644 6614 66692 908 16496 0.819751 0 . 0 . 181 28,39,35,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M335T|488|CCDC77|protein_coding|CODING|NM_032358.3|10|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.762636 rs735295 -0.693147 0.0359029 181 488 209 MODIFIER 13 CODING CCDC77 T protein_coding NM_032358.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 551295 C T 0 164 0 0.9455 0.983 0.9899 0.994 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,1,11 UTR_3_PRIME(MODIFIER||209||488|CCDC77|protein_coding|CODING|NM_032358.3|13|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4980907 -0.680642 0.179238 12 L453 998 ctT/ctC LOW 14 SILENT CODING B4GALNT3 C protein_coding NM_173593.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 662448 T C 0 228 0 0.944 0.8472 0.7968 0.8958 0.659 0.8957 0.905583 0.734276 0.646512 2 9341 88244 9516 7837 3997 42868 651 14034 2 10328 120898 11564 8642 6614 66338 904 16508 0 . 0 . 0 172 0,0,84,68 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L453|998|B4GALNT3|protein_coding|CODING|NM_173593.3|14|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs758790 -0.693147 0.058395 172 188 886 MODIFIER 4 CODING NINJ2 C protein_coding NM_016533.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 673515 T C 0 57 0 0.3654 0.2294 0.2666 0.2361 0.0924 0.1534 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_3_PRIME(MODIFIER||886||188|NINJ2|protein_coding|CODING|NM_016533.5|4|C),DOWNSTREAM(MODIFIER||2457||998|B4GALNT3|protein_coding|CODING|NM_173593.3||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2245918 -0.511536 0.707536 3 188 613 MODIFIER 4 CODING NINJ2 G protein_coding NM_016533.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 673788 A G 0 46.3 0 0.3654 0.2296 0.2666 0.2371 0.0924 0.1534 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||613||188|NINJ2|protein_coding|CODING|NM_016533.5|4|G),DOWNSTREAM(MODIFIER||2730||998|B4GALNT3|protein_coding|CODING|NM_173593.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2245906 -0.453602 0.92 2 188 LOW 3 CODING NINJ2 G protein_coding NM_016533.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 673854 A G 0 9.7 0 0.8101 0.8446 0.8228 0.9375 0.8211 0.8354 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 SPLICE_SITE_REGION+INTRON(LOW||||188|NINJ2|protein_coding|CODING|NM_016533.5|3|G),DOWNSTREAM(MODIFIER||2796||998|B4GALNT3|protein_coding|CODING|NM_173593.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1468624 -0.379885 0 1 2642 91 MODIFIER 1 CODING WNK1 G protein_coding NM_001184985.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 862641 T G 0 161 0 0.261 0.3399 0.4424 0.3165 0.4334 0.3016 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_5_PRIME(MODIFIER||91||2642|WNK1|protein_coding|CODING|NM_001184985.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3088353 -0.651104 0.405689 8 C86 2642 tgT/tgC LOW 1 SILENT CODING WNK1 C protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 862989 T C 0 217 0 0.9123 0.9756 0.9914 1 1 1 0.918747 0.972397 0.999884 2 9023 117922 11427 8545 6596 65039 885 16407 2 9888 118826 11458 8546 6596 65044 886 16408 0 . 0 . 0 10 0,0,3,7 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C86|2642|WNK1|protein_coding|CODING|NM_001184985.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 0.916482 0 . rs3168640 -0.670168 0.855481 10 A429 2642 gcA/gcG LOW 4 SILENT CODING WNK1 G protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 939302 A G 0 228 0 0.5076 0.6935 0.7594 0.871 0.7406 0.6667 0.561734 0.68553 0.748953 2 5713 90424 8933 7483 5276 50721 675 11623 2 10398 121360 11562 8648 6608 66726 908 16510 0 . 0 . 0 131 0,0,50,70 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A429|2642|WNK1|protein_coding|CODING|NM_001184985.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10774466 -0.693147 0.0643686 131 D493 2642 gaT/gaC LOW 6 SILENT CODING WNK1 C protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 968489 T C 0 193 0 0.0378 0.0935 0.0692 0.0675 0.171 0.1329 0.0474353 0.115426 0.150267 1 471 17964 813 580 1742 11266 181 2911 2 10112 120760 11524 8628 6610 66506 902 16478 0.892062 2 benign 0 . 38 10,12,10,3 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D493|2642|WNK1|protein_coding|CODING|NM_001184985.1|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.948766 rs2286006 -0.683931 0.877199 38 Q1189 2642 caG/caA LOW 11 SILENT CODING WNK1 A protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 987482 G A 0 228 0 0.5113 0.6795 0.7493 0.8284 0.7336 0.6483 0.560372 0.679533 0.740581 2 5786 89045 8874 6912 5278 50245 668 11282 2 10404 121322 11568 8636 6612 66684 908 16510 0 . 0 . 0 58 0,0,16,39 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1189|2642|WNK1|protein_coding|CODING|NM_001184985.1|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1012729 -0.693147 2.8638e-10 58 T1608 2642 acC/acT LOW 19 SILENT CODING WNK1 T protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 994014 C T 0 228 0 0.0363 0.1158 0.1052 0.1825 0.1531 0.1237 0.0526555 0.111795 0.142093 2 485 18858 1475 1745 1681 10610 193 2669 2 10400 121336 11570 8640 6608 66698 908 16512 1 2 benign 0 . 77 1,0,28,43 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1608|2642|WNK1|protein_coding|CODING|NM_001184985.1|19|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10849577 -0.693147 0.202988 77 C1766S 2642 tGc/tCc MODERATE 19 MISSENSE CODING WNK1 C protein_coding NM_001184985.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 994487 G C 0 228 0 0.9516 0.9868 0.9971 1 1 1 0.95892 0.986083 1 2 10001 120962 11552 8654 6614 66726 907 16508 2 10404 121406 11578 8654 6614 66736 908 16512 0 . 0 . 0 46 0,0,33,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tCc|C1766S|2642|WNK1|protein_coding|CODING|NM_001184985.1|19|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7955371 -0.693146 0.216165 46 Y2536 2642 taC/taT LOW 27 SILENT CODING WNK1 T protein_coding NM_001184985.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1017197 C T 0 228 0 0.9523 0.987 0.9971 1 1 1 0.959147 0.98616 1 2 9805 120221 11496 8616 6612 66321 903 16468 2 10198 120652 11520 8616 6612 66330 904 16472 0 . 0 . 0 20 0,0,2,17 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y2536|2642|WNK1|protein_coding|CODING|NM_001184985.1|27|T),DOWNSTREAM(MODIFIER||3705||418|RAD52|protein_coding|CODING|NM_001297419.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386595250,rs4766334 -0.69168 0.954225 20 2642 1986 MODIFIER 28 CODING WNK1 A protein_coding NM_001184985.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1019944 G A 0 36.3 0 0.9546 0.9872 0.9971 1 0.999 0.999 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1986||2642|WNK1|protein_coding|CODING|NM_001184985.1|28|A),DOWNSTREAM(MODIFIER||958||418|RAD52|protein_coding|CODING|NM_001297419.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2023944 -0.453602 0.22 2 1116 2326 MODIFIER 19 CODING ERC1 G protein_coding NM_178040.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1601722 C G 0 125 0 0.9508 0.9117 0.8977 0.9226 0.8449 0.9264 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,1,3 UTR_3_PRIME(MODIFIER||2326||1116|ERC1|protein_coding|CODING|NM_178040.3|19|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs10773946 -0.556411 0.535497 5 1116 5255 MODIFIER 19 CODING ERC1 A protein_coding NM_178040.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1604651 G A 0 9.7 0 0.2655 0.378 0.4063 0.1746 0.6382 0.4519 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5255||1116|ERC1|protein_coding|CODING|NM_178040.3|19|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs739971 -0.379885 0 1 418 285 MODIFIER 2 CODING FBXL14 G protein_coding NM_152441.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1675629 A G 0 23.4 0 0.0575 0.0829 0.0274 0.2698 0.0089 0.0399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 2,0,2,0 UTR_3_PRIME(MODIFIER||285||418|FBXL14|protein_coding|CODING|NM_152441.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs11061858 -0.453602 0.36 5 G338 418 ggA/ggG LOW 1 SILENT CODING FBXL14 C protein_coding NM_152441.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1702219 T C 0 222 0 0.0008 0.005591 0 0.0169 0.002 0.0082 0.000453926 0.0012302 0.00162791 1 2 405 11 158 14 80 5 135 2 10384 121236 11574 8636 6614 66622 908 16498 0.35742 0 . 0 . 165 37,40,25,48 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G338|418|FBXL14|protein_coding|CODING|NM_152441.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.90398 rs2302029 -0.693147 0.645962 165 Q265 386 caG/caA LOW 6 SILENT CODING ADIPOR2 A protein_coding NM_024551.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1890199 G A 0 222 0 0.208 0.1062 0.0663 0.0258 0.1252 0.0603 0.203132 0.149393 0.12186 1 2128 13336 577 222 631 8471 84 1223 2 10404 121278 11572 8654 6612 66678 906 16452 0.982048 0 . 0 . 98 23,20,27,12 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q265|386|ADIPOR2|protein_coding|CODING|NM_024551.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931737 rs16928751 -0.693144 0.30316 98 I290 386 atC/atA LOW 7 SILENT CODING ADIPOR2 A protein_coding NM_024551.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1893077 C A 0 222 0 0.1952 0.1024 0.0663 0.0258 0.1252 0.0583 0.194734 0.146471 0.121744 1 2048 13207 573 222 631 8442 84 1207 2 10388 119366 11568 8648 6610 66182 888 15082 0.903632 0 . 0 . 50 18,7,16,3 SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I290|386|ADIPOR2|protein_coding|CODING|NM_024551.2|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.00724046 rs35854772 -0.69168 0.0410456 50 Y321 386 taC/taT LOW 7 SILENT CODING ADIPOR2 T protein_coding NM_024551.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1893170 C T 0 222 0 0.5416 0.2374 0.111 0.1111 0.1302 0.1564 0.460962 0.240504 0.127558 1 5009 18623 809 788 650 8873 109 2385 2 10402 121180 11562 8652 6604 66652 906 16402 0.527831 0 . 0 COSM147390 67 20,14,9,14 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y321|386|ADIPOR2|protein_coding|CODING|NM_024551.2|7|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.447163 rs9805042 -0.692717 0.128361 67 386 134 MODIFIER 8 CODING ADIPOR2 A protein_coding NM_024551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1895372 G A 0 222 0 0.0121 0.131 0.1556 0.119 0.2505 0.1636 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.780409 0 . 0 . 42 9,12,10,9 UTR_3_PRIME(MODIFIER||134||386|ADIPOR2|protein_coding|CODING|NM_024551.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.893755 rs730032 -0.69168 0.667443 42 386 135 MODIFIER 8 CODING ADIPOR2 G protein_coding NM_024551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1895373 T G 0 228 0 0.8903 0.9689 0.9856 1 0.999 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 41 0,0,19,20 UTR_3_PRIME(MODIFIER||135||386|ADIPOR2|protein_coding|CODING|NM_024551.2|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs758169 -0.693144 0.343536 41 386 1718 MODIFIER 8 CODING ADIPOR2 T protein_coding NM_024551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1896956 C T 0 76 0 0.1725 0.3466 0.3372 0.3889 0.4702 0.4182 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.950952 0 . 0 . 11 5,0,6,0 UTR_3_PRIME(MODIFIER||1718||386|ADIPOR2|protein_coding|CODING|NM_024551.2|8|T),DOWNSTREAM(MODIFIER||4167||1137|CACNA2D4|protein_coding|CODING|NM_172364.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.950952 0 . 0.950952 rs1044471 -0.616816 0.00552884 11 386 2046 MODIFIER 8 CODING ADIPOR2 T protein_coding NM_024551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1897284 A T 0 222 0 0.202 0.1042 0.0663 0.0258 0.1252 0.0583 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.939256 0 . 0 . 121 17,44,17,31 UTR_3_PRIME(MODIFIER||2046||386|ADIPOR2|protein_coding|CODING|NM_024551.2|8|T),DOWNSTREAM(MODIFIER||3839||1137|CACNA2D4|protein_coding|CODING|NM_172364.4||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.250746 rs2286380 -0.693147 0.100961 121 1137 55 MODIFIER 38 CODING CACNA2D4 G protein_coding NM_172364.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1902766 T G 0 222 0 0.1596 0.384 0.3703 0.4653 0.5447 0.4479 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.737649 0 . 0 . 54 20,8,19,5 UTR_3_PRIME(MODIFIER||55||1137|CACNA2D4|protein_coding|CODING|NM_172364.4|38|G),DOWNSTREAM(MODIFIER||4921||386|ADIPOR2|protein_coding|CODING|NM_024551.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.943974 rs2058111 -0.692831 0.0380206 54 G1110 1137 ggC/ggT LOW 38 SILENT CODING CACNA2D4 A protein_coding NM_172364.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1902905 G A 0 222 0 0.1218 0.1224 0.2478 0.0774 0.1044 0.0992 0.120879 0.0971188 0.085728 1 1219 13033 2789 446 737 5642 81 2119 2 9190 116878 11368 8476 6542 64032 854 16416 0.911749 2 benign 0 . 71 8,11,34,16 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1110|1137|CACNA2D4|protein_coding|CODING|NM_172364.4|38|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.197881 rs33912216 -0.693147 0.0175669 71 370 1612 MODIFIER 5 CODING LRTM2 A protein_coding NM_001039029.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1945499 G A 0 77 0 0.1755 0.5419 0.5173 0.9484 0.5239 0.6544 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||1612||370|LRTM2|protein_coding|CODING|NM_001039029.2|5|A),INTRON(MODIFIER||||1137|CACNA2D4|protein_coding|CODING|NM_172364.4|26|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11061996 -0.511536 0.336489 3 I327V 1137 Att/Gtt MODERATE 8 MISSENSE CODING CACNA2D4 C protein_coding NM_172364.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 1995403 T C 0 228 0 0.9947 0.9371 0.8847 0.999 0.8509 0.9213 0.977436 0.916468 0.886288 2 9616 109457 10281 8621 5890 59188 794 15067 2 9804 120758 11572 8626 6614 66734 898 16510 0 . 0 . 0 100 0,0,47,47 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I327V|1137|CACNA2D4|protein_coding|CODING|NM_172364.4|8|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10735005 -0.693147 0.22024 100 617 106 MODIFIER 9 CODING DCP1B C protein_coding NM_152640.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2055266 T C 0 181 0 0.5371 0.514 0.4063 0.7292 0.5149 0.3364 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.247977 0 . 0 . 56 24,0,25,1 UTR_3_PRIME(MODIFIER||106||617|DCP1B|protein_coding|CODING|NM_152640.3|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.756193 rs7222 -0.692976 0.0520644 56 617 LOW 8 CODING DCP1B C protein_coding NM_152640.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2058245 T C 0 222 0 0.5257 0.5244 0.4366 0.7292 0.5477 0.3497 0.54108 0.526757 0.519419 1 5583 62311 4331 6408 3371 35889 453 6276 2 10398 120766 11526 8624 6518 66474 892 16334 0.976989 0 . 0 . 70 21,17,14,9 SPLICE_SITE_REGION+INTRON(LOW||||617|DCP1B|protein_coding|CODING|NM_152640.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.603811 rs2240612 -0.692717 0.618089 70 T1835 2221 acG/acA LOW 44 SILENT CODING CACNA1C A protein_coding NM_199460.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2788879 G A 0 222 0 0.1717 0.5264 0.6542 0.6062 0.7038 0.6503 0.275234 0.581122 0.729465 1 1924 73807 7532 4986 4549 43881 565 10370 2 6890 106154 10150 7564 5790 59712 794 15254 0.581653 2 benign 0 . 93 11,31,11,33 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T1835|2221|CACNA1C|protein_coding|CODING|NM_199460.3|44|A),INTRAGENIC(MODIFIER|||||CACNA1C-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.734152 rs1051375 -0.693146 0.407478 93 P1868L 2221 cCg/cTg MODERATE 45 MISSENSE CODING CACNA1C T protein_coding NM_199460.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2791130 C T 0 222 0 0.4622 0.6691 0.7248 0.5744 0.8191 0.8528 0.504145 0.724757 0.821329 1 4765 92814 8969 5084 5614 53748 732 13902 2 9758 120198 11564 8580 6610 66278 900 16508 0.89932 2 benign 0 COSM1582946,COSM1582947 93 25,26,17,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1868L|2221|CACNA1C|protein_coding|CODING|NM_199460.3|45|T),INTRAGENIC(MODIFIER|||||CACNA1C-AS1||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.817944 rs10848683 -0.693141 0.0817434 93 M1869V 2221 Atg/Gtg MODERATE 45 MISSENSE CODING CACNA1C G protein_coding NM_199460.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2791132 A G 0 222 0 0.7844 0.7706 0.7651 0.6081 0.83 0.862 0.793686 0.819612 0.83096 1 7665 96981 9184 5342 5624 54329 756 14081 2 9758 120198 11560 8594 6608 66270 900 16508 0.528385 2 benign 0 . 91 25,24,17,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M1869V|2221|CACNA1C|protein_coding|CODING|NM_199460.3|45|G),INTRAGENIC(MODIFIER|||||CACNA1C-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.946552 rs10774053 -0.693141 0.0817434 91 K1893R 2221 aAa/aGa MODERATE 45 MISSENSE CODING CACNA1C G protein_coding NM_199460.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2791205 A G 0 228 0 1 1 1 1 1 1 0.999362 0.999806 1 2 9744 120256 11576 8626 6614 66296 898 16502 2 9756 120268 11576 8626 6614 66296 898 16502 0 2 benign 0 . 102 0,0,42,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K1893R|2221|CACNA1C|protein_coding|CODING|NM_199460.3|45|G),INTRAGENIC(MODIFIER|||||CACNA1C-AS1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10774054 -0.693147 0.144533 102 2221 284 MODIFIER 50 CODING CACNA1C T protein_coding NM_199460.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2800649 C T 0 228 0 0.7663 0.8834 0.8501 0.9821 0.8708 0.9765 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 98 1,0,66,16 UTR_3_PRIME(MODIFIER||284||2221|CACNA1C|protein_coding|CODING|NM_199460.3|50|T) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs11062319 -0.693147 0.215685 98 2221 5970 MODIFIER 50 CODING CACNA1C C protein_coding NM_199460.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2806335 A C 0 76 0 0.879 0.9669 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||5970||2221|CACNA1C|protein_coding|CODING|NM_199460.3|50|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4765976 -0.511536 0.868052 3 459 805 MODIFIER 10 CODING FKBP4 GC protein_coding NM_002014.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2913228 G GC 0 219 0 0.736 0.5258 0.4078 0.5188 0.3579 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,24,2,27 UTR_3_PRIME(MODIFIER||805||459|FKBP4|protein_coding|CODING|NM_002014.3|10|GC) 0 0.5 1 29 0.508772 1 1 0 . 0 60 0 0 1 0 . rs35667665 -0.693079 0.0141387 57 V214 281 gtG/gtA LOW 4 SILENT CODING NRIP2 T protein_coding NM_031474.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2937150 C T 0 222 0 0.0015 0.0383 0.0922 0.12 0 0.0051 0.00204267 0.00146086 0.00116279 1 21 2065 983 940 26 51 16 28 2 10244 120424 11532 8572 6588 66178 904 16406 0.991379 0 . 0 . 71 16,19,10,20 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V214|281|NRIP2|protein_coding|CODING|NM_031474.2|4|T),DOWNSTREAM(MODIFIER||2913||447|ITFG2|protein_coding|CODING|NM_018463.3||T),INTRAGENIC(MODIFIER|||||ITFG2||CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.973833 rs77620161 -0.693097 0.40793 71 P42 281 ccC/ccG LOW 1 SILENT CODING NRIP2 C protein_coding NM_031474.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2944024 G C 0 222 0 0.0537 0.1092 0.1326 0.2917 0.0368 0.0542 0.0610531 0.0486698 0.0423256 1 623 8554 1345 2590 219 2871 50 856 2 10374 121202 11572 8618 6612 66618 908 16500 0.336538 0 . 0 . 96 13,22,25,27 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P42|281|NRIP2|protein_coding|CODING|NM_031474.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.430457 rs35645225 -0.693147 0.0184029 96 R584 801 agA/agG LOW 10 SILENT CODING FOXM1 C protein_coding NM_202002.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2968458 T C 0 228 0 1 0.9972 0.9928 1 0.992 0.999 0.996142 0.986314 0.981279 2 10337 120017 11513 8646 6589 65625 899 16408 2 10368 121240 11568 8646 6612 66636 904 16506 0 . 0 . 0 65 0,0,24,39 SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R584|801|FOXM1|protein_coding|CODING|NM_202002.2|10|C),INTRAGENIC(MODIFIER|||||LOC100507424||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2215292 -0.693147 0.357796 65 S163 238 tcG/tcA LOW 3 SILENT CODING RHNO1 A protein_coding NM_001252499.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 2997397 G A 0 222 0 0.5976 0.526 0.5706 0.6458 0.3489 0.456 0.550613 0.414501 0.344767 1 5865 52460 6925 5456 2370 24063 367 7414 2 10406 121374 11578 8636 6612 66724 906 16512 0.92169 0 . 0 . 129 44,31,26,19 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S163|238|RHNO1|protein_coding|CODING|NM_001252499.2|3|A),UPSTREAM(MODIFIER||2636||501|TULP3|protein_coding|CODING|NM_001160408.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977901 rs2907608,rs386577024 -0.693147 0.529094 129 239 LOW 1 CODING TSPAN9 T protein_coding NM_001168320.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3310335 C T 0 222 0 0.2806 0.2997 0.3977 0.2847 0.3201 0.2505 0.299138 0.307704 0.312093 1 3045 39770 4911 2690 2188 21909 314 4713 2 10404 121318 11578 8646 6612 66682 908 16488 0.942292 0 . 0 . 95 19,21,18,23 SPLICE_SITE_REGION+INTRON(LOW||||239|TSPAN9|protein_coding|CODING|NM_001168320.1|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.748919 rs386609888,rs740777 -0.693145 0.0198068 95 239 69 MODIFIER 8 CODING TSPAN9 G protein_coding NM_001168320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3392351 A G 0 222 0 0.5038 0.3826 0.428 0.2014 0.4394 0.3149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.792454 0 . 0 . 29 4,7,7,10 UTR_3_PRIME(MODIFIER||69||239|TSPAN9|protein_coding|CODING|NM_001168320.1|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.75334 rs632887 -0.690438 0.0752835 29 239 276 MODIFIER 8 CODING TSPAN9 T protein_coding NM_001168320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3392558 C T 0 222 0 0.0862 0.2025 0.3084 0.0933 0.335 0.2607 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.620251 0 . 0 . 80 14,12,20,18 UTR_3_PRIME(MODIFIER||276||239|TSPAN9|protein_coding|CODING|NM_001168320.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.144087 rs634076 -0.693143 0.325291 80 239 1137 MODIFIER 8 CODING TSPAN9 T protein_coding NM_001168320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3393419 C T 0 222 0 0.326 0.4962 0.4942 0.4464 0.6083 0.6636 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.301992 0 . 0 . 95 18,23,21,26 UTR_3_PRIME(MODIFIER||1137||239|TSPAN9|protein_coding|CODING|NM_001168320.1|8|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.245024 rs12827449 -0.693147 0.00383851 95 239 1221 MODIFIER 8 CODING TSPAN9 A protein_coding NM_001168320.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3393503 G A 0 167 0 0.4539 0.5755 0.5504 0.5456 0.665 0.6963 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999597 0 . 0 . 52 1,22,1,27 UTR_3_PRIME(MODIFIER||1221||239|TSPAN9|protein_coding|CODING|NM_001168320.1|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.841827 rs6489451 -0.693054 0.0870684 52 R349 394 cgG/cgA LOW 9 SILENT CODING PRMT8 A protein_coding NM_019854.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3701464 G A 0 222 0 0.1218 0.103 0.0836 0.1052 0.1332 0.0583 0.131639 0.132631 0.13314 1 1324 13509 794 821 570 8953 100 947 2 10396 121372 11574 8646 6614 66722 908 16512 0.0579007 0 . 0 . 159 32,38,40,32 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R349|394|PRMT8|protein_coding|CODING|NM_019854.4|9|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.890549 rs34000611 -0.693147 0.0200028 159 394 441 MODIFIER 10 CODING PRMT8 A protein_coding NM_019854.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 3702789 C A 0 222 0 0.1914 0.125 0.0965 0.1071 0.1402 0.0583 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.996455 0 . 0 . 179 49,28,43,37 UTR_3_PRIME(MODIFIER||441||394|PRMT8|protein_coding|CODING|NM_019854.4|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.914376 rs7298428 -0.693147 0.485016 179 289 171 MODIFIER 1 CODING CCND2 T protein_coding NM_001759.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4383036 C T 0 222 0 0.5545 0.5861 0.6916 0.7202 0.5716 0.4305 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.436619 0 . 0 . 132 55,13,33,12 UTR_5_PRIME(MODIFIER||171||289|CCND2|protein_coding|CODING|NM_001759.3|1|T),INTRAGENIC(MODIFIER|||||CCND2-AS1||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.391498 rs1049606 -0.693147 0.00231751 132 289 49 MODIFIER 1 CODING CCND2 C protein_coding NM_001759.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4383158 T C 0 228 0 0.8933 0.9706 0.9914 1 1 1 0.930216 0.976109 0.99953 2 5713 80658 7004 5878 3606 45027 576 12854 2 6284 81264 7034 5878 3606 45030 578 12854 0 . 0 . 0 103 0,0,45,51 UTR_5_PRIME(MODIFIER||49||289|CCND2|protein_coding|CODING|NM_001759.3|1|C),INTRAGENIC(MODIFIER|||||CCND2-AS1||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3217786 -0.693147 0.206082 103 289 2464 MODIFIER 5 CODING CCND2 T protein_coding NM_001759.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4411639 C T 0 78 0 0.2731 0.2788 0.1715 0.3601 0.2535 0.3047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||2464||289|CCND2|protein_coding|CODING|NM_001759.3|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3217925 -0.556411 0.281254 4 289 2629 MODIFIER 5 CODING CCND2 A protein_coding NM_001759.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4411804 G A 0 57 0 0.8116 0.8942 0.9597 0.7837 0.999 0.9652 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||2629||289|CCND2|protein_coding|CODING|NM_001759.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3217927 -0.511536 0.62656 3 289 4951 MODIFIER 5 CODING CCND2 A protein_coding NM_001759.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4414126 G A 0 228 0 0.9395 0.9828 0.9957 1 1 0.9969 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 0,0,12,25 UTR_3_PRIME(MODIFIER||4951||289|CCND2|protein_coding|CODING|NM_001759.3|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4765775 -0.693141 0.00197207 40 T80 270 acG/acA LOW 4 SILENT CODING TIGAR A protein_coding NM_020375.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4459032 G A 0 222 0 0.3109 0.2734 0.2435 0.5109 0.0984 0.1789 0.292329 0.149085 0.0756977 1 3138 20831 4461 4530 607 5287 113 2695 2 10394 121342 11568 8646 6614 66704 908 16508 0.974262 0 . 0 . 92 27,14,25,8 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T80|270|TIGAR|protein_coding|CODING|NM_020375.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.984031 rs7309402 -0.693127 0.053667 92 270 183 MODIFIER 6 CODING TIGAR T protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4462040 C T 0 143 0 0.3888 0.4575 0.4092 0.5833 0.3787 0.5358 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 12 0,3,1,8 UTR_3_PRIME(MODIFIER||183||270|TIGAR|protein_coding|CODING|NM_020375.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.811069 rs1046161 -0.662043 0.815679 12 270 289 MODIFIER 6 CODING TIGAR A protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4462146 G A 0 52 0 0.2088 0.2332 0.1744 0.2401 0.2296 0.3047 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 5 0,2,1,1 UTR_3_PRIME(MODIFIER||289||270|TIGAR|protein_coding|CODING|NM_020375.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1046164 -0.453602 0.8 5 270 304 MODIFIER 6 CODING TIGAR T protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4462161 C T 0 18.4 0 0.1936 0.2857 0.2695 0.5188 0.1789 0.2914 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,2,1,0 UTR_3_PRIME(MODIFIER||304||270|TIGAR|protein_coding|CODING|NM_020375.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1046165 -0.379885 0 4 270 648 MODIFIER 6 CODING TIGAR A protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4462505 G A 0 9.7 0 0.8275 0.8866 0.9092 0.9732 0.8658 0.8824 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||648||270|TIGAR|protein_coding|CODING|NM_020375.2|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11063099 -0.379885 0 1 270 916 MODIFIER 6 CODING TIGAR T protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4462773 C T 0 39.3 0 0 0.00079872 0.0014 0.002 0 0.001 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||916||270|TIGAR|protein_coding|CODING|NM_020375.2|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs183115585 -0.453602 0.72 2 270 1163 MODIFIER 6 CODING TIGAR G protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4463020 C G 0 152 0 0.5091 0.4922 0.3862 0.6419 0.3479 0.5389 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.882821 0 . 0 . 58 32,3,19,2 UTR_3_PRIME(MODIFIER||1163||270|TIGAR|protein_coding|CODING|NM_020375.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0137559 rs7297048 -0.692352 0.0177042 58 270 1175 MODIFIER 6 CODING TIGAR T protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4463032 G T 0 173 0 0.4697 0.4692 0.3804 0.5933 0.3419 0.5348 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0757718 0 . 0 . 72 35,7,23,3 UTR_3_PRIME(MODIFIER||1175||270|TIGAR|protein_coding|CODING|NM_020375.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.955169 rs7296130 -0.692976 0.020137 72 270 1347 MODIFIER 6 CODING TIGAR T protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4463204 C T 0 222 0 0.4584 0.4936 0.5821 0.3889 0.6133 0.4632 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.957039 0 . 0 . 57 3,19,6,24 UTR_3_PRIME(MODIFIER||1347||270|TIGAR|protein_coding|CODING|NM_020375.2|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.447157 rs7962818 -0.693097 0.500652 57 270 4044 MODIFIER 6 CODING TIGAR C protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4465901 T C 0 9.7 0 0.8729 0.9643 0.9928 1 0.999 0.9949 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4044||270|TIGAR|protein_coding|CODING|NM_020375.2|6|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10735033 -0.379885 0 1 270 5462 MODIFIER 6 CODING TIGAR G protein_coding NM_020375.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4467319 A G 0 9.7 0 0.8729 0.9639 0.9899 1 0.999 0.9949 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||5462||270|TIGAR|protein_coding|CODING|NM_020375.2|6|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2358726 -0.379885 0 1 208 20 MODIFIER 3 CODING FGF6 A protein_coding NM_020996.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4543361 G A 0 222 0 0.0008 0.0439 0 0.2073 0.005 0.0051 0.00158874 0.00146086 0.00139535 1 13 2576 118 2003 118 200 18 106 2 10346 120454 11478 8576 6574 66308 898 16274 0.727731 0 . 0 . 139 43,20,55,14 UTR_3_PRIME(MODIFIER||20||208|FGF6|protein_coding|CODING|NM_020996.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998507 rs2241286 -0.693147 0.0621515 139 V139 208 gtT/gtC LOW 2 SILENT CODING FGF6 G protein_coding NM_020996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4553332 A G 0 222 0 0.5749 0.4722 0.3487 0.4177 0.3857 0.5665 0.559237 0.453329 0.39907 1 5866 51371 4099 3620 2710 26196 357 8523 2 10374 121014 11524 8626 6576 66560 904 16450 0.957084 0 . 0 . 77 14,16,18,18 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V139|208|FGF6|protein_coding|CODING|NM_020996.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.518508 rs2241280,rs386562266 -0.693139 0.000601294 77 T122 208 acT/acC LOW 2 SILENT CODING FGF6 G protein_coding NM_020996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4553383 A G 0 222 0 0.6021 0.4796 0.3473 0.4206 0.3857 0.5654 0.582388 0.461249 0.399186 1 6091 51439 4096 3598 2704 26116 357 8477 2 10328 120596 11496 8602 6552 66336 904 16378 0.58123 0 . 0 . 54 8,18,5,18 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T122|208|FGF6|protein_coding|CODING|NM_020996.2|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966656 rs2241279,rs386562265 -0.692717 0.0645254 54 A63 208 gcC/gcG LOW 1 SILENT CODING FGF6 C protein_coding NM_020996.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4554548 G C 0 228 0 0.652 0.9032 0.9669 1 0.998 1 0.726963 0.905582 0.997093 2 7303 117974 11381 8645 6612 66636 898 16499 2 10394 121354 11570 8646 6612 66714 906 16512 0 . 0 . 0 63 0,0,28,27 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcG|A63|208|FGF6|protein_coding|CODING|NM_020996.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7358740 -0.693147 0.890674 63 L42 520 Cta/Tta LOW 4 SILENT CODING DYRK4 T protein_coding NM_003845.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4702173 C T 0 228 0 0.1657 0.1394 0.0303 0.2639 0.0239 0.1718 0.150704 0.071813 0.0313953 2 1601 9388 288 2468 302 2173 54 2502 2 10392 121234 11576 8646 6614 66654 908 16444 0 . 0 . 0 61 0,0,32,24 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L42|520|DYRK4|protein_coding|CODING|NM_003845.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2240763,rs386562242 -0.693147 0.000327396 61 K43Q 520 Aag/Cag MODERATE 4 MISSENSE CODING DYRK4 C protein_coding NM_003845.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4702176 A C 0 228 0 . 0 . 0 . 0 . 0 . 2 0 32 0 32 0 0 0 0 2 10394 121278 11576 8654 6614 66664 908 16468 0 . 0 . 0 61 0,0,32,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K43Q|520|DYRK4|protein_coding|CODING|NM_003845.2|4|C) 0 . 0 . 0 . 0 . 1 0 60 0 0 1 0 . rs370590188 -0.693147 0.000327396 61 A325 520 gcC/gcT LOW 10 SILENT CODING DYRK4 T protein_coding NM_003845.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4716513 C T 0 228 0 0.2322 0.1561 0.0461 0.2649 0.0209 0.1585 0.218793 0.0943411 0.0305814 2 2203 9893 291 2502 300 2123 52 2422 2 10406 121388 11576 8642 6614 66730 908 16512 0 . 0 . 0 68 0,0,39,21 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A325|520|DYRK4|protein_coding|CODING|NM_003845.2|10|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2255588 -0.693147 0.0727624 68 Q778 853 caA/caG LOW 5 SILENT CODING AKAP3 C protein_coding NM_001278309.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4735734 T C 0 228 0 0.1989 0.1482 0.0432 0.2679 0.0219 0.1605 0.178393 0.080732 0.0306977 2 1853 9499 274 2471 300 2134 52 2415 2 10404 121312 11544 8606 6614 66726 908 16510 0.717492 0 . 0 . 90 2,2,31,42 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q778|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.236319 rs2072359 -0.693147 0.396004 90 S725L 853 tCa/tTa MODERATE 5 MISSENSE CODING AKAP3 A protein_coding NM_001278309.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4735894 G A 0 228 0 0.2247 0.1548 0.0519 0.2688 0.0239 0.1503 0.193827 0.0871905 0.0325581 2 2052 9737 341 2467 300 2306 58 2213 2 10382 121066 11502 8592 6600 66592 904 16494 1 0 . 0 . 29 0,1,6,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S725L|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2072357 -0.693021 0.0974795 29 I661T 853 aTa/aCa MODERATE 5 MISSENSE CODING AKAP3 G protein_coding NM_001278309.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4736086 A G 0 210 0 0.1997 0.1787 0.0879 0.378 0.0219 0.1708 0.180436 0.0821159 0.0317442 2 1873 11684 1193 3467 319 2230 62 2540 2 10296 120618 11490 8578 6608 66280 898 16468 0 . 0 . 0 20 0,0,18,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I661T|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1990313 -0.69168 0.863858 20 E525K 853 Gag/Aag MODERATE 5 MISSENSE CODING AKAP3 T protein_coding NM_001278309.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4736495 C T 0 228 0 0.938 0.9828 0.9942 1 1 1 0.932365 0.977011 0.999884 2 9742 120607 11488 8646 6612 66707 907 16505 2 10396 121310 11526 8646 6612 66712 908 16510 0 . 0 . 0 33 0,0,6,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E525K|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1990312 -0.69311 0.422125 33 F479 853 ttT/ttC LOW 5 SILENT CODING AKAP3 G protein_coding NM_001278309.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4736631 A G 0 228 0 0.938 0.9828 0.9942 1 1 1 0.931911 0.976857 0.999884 2 9734 120405 11458 8592 6612 66598 907 16504 2 10392 121112 11496 8592 6612 66604 908 16508 0 . 0 . 0 32 0,0,19,10 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F479|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11063265 -0.693079 0.128443 32 T464S 853 aCt/aGt MODERATE 5 MISSENSE CODING AKAP3 C protein_coding NM_001278309.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4736677 G C 0 228 0 0.8472 0.9115 0.9769 0.9147 0.996 0.862 0.856105 0.9491 0.996744 2 8938 116802 11392 8063 6610 66406 882 14511 2 10394 121340 11554 8652 6614 66708 908 16510 0 . 0 . 0 30 0,0,15,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T464S|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11063266 -0.693079 0.755031 30 L460 853 Ttg/Ctg LOW 5 SILENT CODING AKAP3 G protein_coding NM_001278309.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4736690 A G 0 228 0 0.9054 0.9726 0.9856 1 0.998 1 0.907172 0.967169 0.997907 2 9446 120099 11458 8652 6614 66525 900 16504 2 10388 121352 11570 8652 6614 66710 908 16510 0 . 0 . 0 28 0,0,15,9 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L460|853|AKAP3|protein_coding|CODING|NM_001278309.1|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10774251 -0.692831 0.71803 28 Y53D 637 Tac/Gac MODERATE 1 MISSENSE CODING GALNT8 G protein_coding NM_017417.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4830000 T G 0 222 0 0.4977 0.382 0.415 0.3611 0.3777 0.228 0.465275 0.410118 0.38186 1 4928 43623 4976 3192 2368 24240 317 3602 2 10406 121384 11572 8644 6614 66728 908 16512 0.516506 0 . 0 COSM1128586 79 20,22,15,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Gac|Y53D|637|GALNT8|protein_coding|CODING|NM_017417.1|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.861121 rs10849133 -0.69311 0.0722695 79 L132 637 ctT/ctG LOW 2 SILENT CODING GALNT8 G protein_coding NM_017417.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4835882 T G 0 222 0 0.1838 0.3131 0.4179 0.3601 0.4274 0.2474 0.238084 0.355221 0.415233 1 2380 44858 5001 3185 2585 27202 332 4173 2 10376 120908 11494 8550 6580 66512 906 16490 0.991413 0 . 0 . 159 30,42,30,38 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L132|637|GALNT8|protein_coding|CODING|NM_017417.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.43728 rs2286578 -0.693147 0.149952 159 V515F 637 Gtt/Ttt MODERATE 9 MISSENSE CODING GALNT8 T protein_coding NM_017417.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4873163 G T 0 222 0 0.2466 0.3297 0.4251 0.3611 0.4225 0.2464 0.296187 0.377826 0.419651 1 2981 46052 5127 3215 2605 27621 341 4162 2 10404 121370 11576 8636 6606 66730 908 16510 0.801469 0 . 0 COSM1179986 214 59,28,58,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V515F|637|GALNT8|protein_coding|CODING|NM_017417.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.930217 rs1468556 -0.693147 0.00647887 214 637 3 MODIFIER 11 CODING GALNT8 T protein_coding NM_017417.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4881766 C T 0 222 0 0.3896 0.4281 0.5245 0.3552 0.6213 0.2883 0.460281 0.542673 0.584884 1 4639 61025 5901 3116 3534 38203 456 5176 2 10376 120654 11496 8578 6586 66394 904 16320 0.993731 0 . 0 . 81 8,32,4,33 UTR_3_PRIME(MODIFIER||3||637|GALNT8|protein_coding|CODING|NM_017417.1|11|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940011 rs2286581 -0.693141 0.857078 81 637 12 MODIFIER 11 CODING GALNT8 C protein_coding NM_017417.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4881775 T C 0 204 0 0.3896 0.4281 0.5245 0.3552 0.6213 0.2883 0.460508 0.54298 0.585233 1 4636 61018 5896 3121 3534 38196 456 5179 2 10366 120468 11480 8566 6580 66340 904 16232 0.38564 0 . 0 . 73 8,27,2,31 UTR_3_PRIME(MODIFIER||12||637|GALNT8|protein_coding|CODING|NM_017417.1|11|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.911898 rs2286582 -0.693127 0.644162 73 G20 529 ggA/ggG LOW 1 SILENT CODING KCNA6 G protein_coding NM_002235.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4919267 A G 0 215 0 0.4576 0.4471 0.4121 0.4395 0.4433 0.4693 0.423953 0.414008 0.408922 1 4171 46812 4969 3521 2151 26747 326 4927 2 9062 107162 11298 8290 6364 61316 778 10054 0.202776 0 . 0 . 58 16,15,21,5 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G20|529|KCNA6|protein_coding|CODING|NM_002235.3|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.547584 rs758534 -0.692976 0.449101 58 529 431 MODIFIER 1 CODING KCNA6 C protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4921228 T C 0 222 0 0.438 0.4305 0.3357 0.4395 0.3052 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.863248 0 . 0 . 75 24,8,28,10 UTR_3_PRIME(MODIFIER||431||529|KCNA6|protein_coding|CODING|NM_002235.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.927112 rs2239503 -0.693143 0.0506552 75 529 504 MODIFIER 1 CODING KCNA6 C protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4921301 T C 0 222 0 0.4365 0.4295 0.3329 0.4385 0.3052 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.565022 0 . 0 . 113 26,24,29,21 UTR_3_PRIME(MODIFIER||504||529|KCNA6|protein_coding|CODING|NM_002235.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.993935 rs2239504 -0.693147 0.783201 113 529 892 MODIFIER 1 CODING KCNA6 T protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4921689 C T 0 222 0 0.1808 0.2696 0.3934 0.3323 0.2555 0.2515 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.0383229 0 . 0 . 109 29,18,40,12 UTR_3_PRIME(MODIFIER||892||529|KCNA6|protein_coding|CODING|NM_002235.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.970374 rs2239505 -0.693147 0.107463 109 529 985 MODIFIER 1 CODING KCNA6 G protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4921782 C G 0 222 0 0.2496 0.1713 0.1513 0.1617 0.0626 0.2014 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.758927 0 . 0 . 123 41,29,21,18 UTR_3_PRIME(MODIFIER||985||529|KCNA6|protein_coding|CODING|NM_002235.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.529084 rs2239506 -0.693144 0.208413 123 529 1233 MODIFIER 1 CODING KCNA6 G protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4922030 C G 0 222 0 0.444 0.4291 0.33 0.4315 0.3022 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.786298 0 . 0 . 86 28,21,30,7 UTR_3_PRIME(MODIFIER||1233||529|KCNA6|protein_coding|CODING|NM_002235.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.99885 rs3319 -0.693141 0.161355 86 529 1937 MODIFIER 1 CODING KCNA6 G protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4922734 A G 0 222 0 0.4365 0.4285 0.3314 0.4375 0.3022 0.6074 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.242953 0 . 0 . 39 13,6,5,10 UTR_3_PRIME(MODIFIER||1937||529|KCNA6|protein_coding|CODING|NM_002235.3|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.655468 rs7303721 -0.688148 0.0961009 39 529 2252 MODIFIER 1 CODING KCNA6 C protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4923049 T C 0 222 0 0.4455 0.4301 0.3314 0.4365 0.3022 0.6043 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.688179 0 . 0 . 48 9,12,12,12 UTR_3_PRIME(MODIFIER||2252||529|KCNA6|protein_coding|CODING|NM_002235.3|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.974452 rs7310372 -0.692831 0.673544 48 529 2900 MODIFIER 1 CODING KCNA6 T protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4923697 G T 0 222 0 0.1906 0.3081 0.4049 0.5179 0.2575 0.2342 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99869 0 . 0 . 57 17,16,11,6 UTR_3_PRIME(MODIFIER||2900||529|KCNA6|protein_coding|CODING|NM_002235.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.458255 rs2058205 -0.690438 0.00973614 57 529 39292 MODIFIER 2 CODING KCNA6 C protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4960089 T C 0 9.7 0 0.5023 0.49 0.6225 0.2708 0.6153 0.4765 0 . 0 1 68 2506 30 40 1 724 29 1614 2 132 6066 60 122 2 1540 64 4146 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||39292||529|KCNA6|protein_coding|CODING|NM_002235.3|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs700480 -0.379885 0 1 529 39320 MODIFIER 2 CODING KCNA6 C protein_coding NM_002235.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 4960117 T C 0 9.7 0 0.5023 0.49 0.6225 0.2708 0.6153 0.4765 0 . 0 1 24 788 11 27 3 245 10 468 2 58 2814 30 96 4 714 32 1880 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||39320||529|KCNA6|protein_coding|CODING|NM_002235.3|2|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs12336 -0.379885 0 1 T268 495 acG/acC LOW 2 SILENT CODING KCNA1 C protein_coding NM_000217.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5021348 G C 0 228 0 0.4796 0.5333 0.5764 0.6627 0.5159 0.4601 0.465729 0.50346 0.522791 2 4769 63775 7340 5699 3266 34420 465 7816 2 10394 121330 11566 8636 6604 66712 908 16510 1 2|3 benign|likely-benign 0 . 120 0,1,32,82 SYNONYMOUS_CODING(LOW|SILENT|acG/acC|T268|495|KCNA1|protein_coding|CODING|NM_000217.2|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2227910 -0.693147 0.000219351 120 T480 495 acT/acA LOW 2 SILENT CODING KCNA1 A protein_coding NM_000217.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5021984 T A 0 228 0 0.8903 0.8205 0.7493 0.9623 0.6928 0.7618 0.856105 0.742503 0.684302 2 8903 89600 8756 8327 5011 45896 668 12039 2 10394 121324 11572 8650 6612 66680 908 16508 1 255 other 0 . 98 1,0,44,43 SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T480|495|KCNA1|protein_coding|CODING|NM_000217.2|2|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs4766309 -0.693147 0.000140889 98 495 1524 MODIFIER 2 CODING KCNA1 G protein_coding NM_000217.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5023556 A G 0 228 0 0.0681 0.0495 0.0648 0.0496 0.0189 0.045 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 35 0,0,28,7 UTR_3_PRIME(MODIFIER||1524||495|KCNA1|protein_coding|CODING|NM_000217.2|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs79357862 -0.693136 0.422693 35 495 2163 MODIFIER 2 CODING KCNA1 G protein_coding NM_000217.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5024195 C G 0 222 0 0 0.00079872 0 0.004 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.977008 0 . 0 . 106 28,32,20,16 UTR_3_PRIME(MODIFIER||2163||495|KCNA1|protein_coding|CODING|NM_000217.2|2|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.843844 rs180733846 -0.693139 0.581641 106 495 2333 MODIFIER 2 CODING KCNA1 A protein_coding NM_000217.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5024365 G A 0 228 0 0.1051 0.0723 0.0648 0.0923 0.0189 0.0675 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 54 0,1,17,30 UTR_3_PRIME(MODIFIER||2333||495|KCNA1|protein_coding|CODING|NM_000217.2|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs2109420 -0.693147 0.0353051 54 495 4439 MODIFIER 2 CODING KCNA1 T protein_coding NM_000217.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5026471 C T 0 228 0 0.2262 0.2438 0.2003 0.2619 0.1938 0.3313 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 72 0,0,28,41 UTR_3_PRIME(MODIFIER||4439||495|KCNA1|protein_coding|CODING|NM_000217.2|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12424292 -0.693147 0.675953 72 495 5141 MODIFIER 2 CODING KCNA1 A protein_coding NM_000217.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5027173 G A 0 228 0 0.0779 0.0605 0.0706 0.0645 0.0219 0.0654 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.964912 0 . 0 . 123 1,1,67,47 UTR_3_PRIME(MODIFIER||5141||495|KCNA1|protein_coding|CODING|NM_000217.2|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.640351 rs41482147 -0.693147 0.975327 123 613 167 MODIFIER 1 CODING KCNA5 T protein_coding NM_002234.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5153147 C T 0 57 0 0.6051 0.5317 0.4207 0.6498 0.3678 0.5583 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_5_PRIME(MODIFIER||167||613|KCNA5|protein_coding|CODING|NM_002234.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3741930 -0.511536 0.851467 3 G383 613 ggT/ggC LOW 1 SILENT CODING KCNA5 C protein_coding NM_002234.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5154462 T C 0 228 0 0.9372 0.981 0.9885 0.996 1 1 0.955061 0.984699 0.999884 2 9913 120812 11558 8607 6614 66708 902 16510 2 10402 121376 11576 8654 6614 66712 906 16512 0 . 0 . 0 54 0,0,21,26 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G383|613|KCNA5|protein_coding|CODING|NM_002234.3|1|C) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.705948 0 . rs2359641 -0.693147 0.372685 54 P97 270 ccG/ccA LOW 2 SILENT CODING NTF3 A protein_coding NM_001102654.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 5603632 G A 0 222 0 0.5325 0.4882 0.438 0.4583 0.503 0.4796 0.52837 0.516838 0.51093 1 5448 59321 4394 4011 2861 34105 430 8072 2 10294 120902 11542 8574 6606 66488 900 16498 0.732867 0 . 0 . 103 16,30,29,21 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P97|270|NTF3|protein_coding|CODING|NM_001102654.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.455481 rs6332 -0.693147 0.111192 103 1003 12 MODIFIER 1 CODING ANO2 G protein_coding NM_001278596.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6054395 A G 0 228 0 0.59 0.8115 0.9063 0.8383 0.9493 0.8742 0 . 0 2 391 10946 168 165 2 3413 118 6689 2 560 12226 184 198 2 3582 132 7568 0 . 0 . 0 91 0,0,16,66 UTR_5_PRIME(MODIFIER||12||1003|ANO2|protein_coding|CODING|NM_001278596.1|1|G),DOWNSTREAM(MODIFIER||3645||2813|VWF|protein_coding|CODING|NM_000552.3||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs6489680 -0.693147 0.686906 91 T2413 2813 acT/acC LOW 42 SILENT CODING VWF G protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6091000 A G 0 228 0 0.708 0.8251 0.8991 0.9028 0.8817 0.7924 0.74512 0.843918 0.894535 2 7666 105456 10874 8063 5918 58989 779 13167 2 10406 121394 11572 8648 6614 66736 908 16510 0 . 0 . 0 48 0,0,27,16 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T2413|2813|VWF|protein_coding|CODING|NM_000552.3|42|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs216867 -0.693146 0.0212517 48 2813 LOW 41 CODING VWF A protein_coding NM_000552.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6091164 G A 0 222 0 0.1029 0.3033 0.3559 0.4831 0.2535 0.4029 0.152065 0.249731 0.299767 1 1517 39674 5553 4247 1993 19379 283 6702 2 9994 118284 11328 8472 6294 64984 882 16330 0.879417 0 . 0 . 25 3,5,8,5 SPLICE_SITE_REGION+INTRON(LOW||||2813|VWF|protein_coding|CODING|NM_000552.3|41|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994117 rs216868 -0.683931 0.245026 25 C1948 2813 tgC/tgT LOW 35 SILENT CODING VWF A protein_coding NM_000552.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6105387 G A 0 228 0 0.2784 0.4561 0.4179 0.7252 0.3648 0.5399 0.309805 0.356066 0.379767 2 2963 49001 5703 6089 2510 23179 348 8209 2 8944 107068 10026 8162 5702 58282 792 15160 1 0 . 0 . 86 0,1,25,54 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1948|2813|VWF|protein_coding|CODING|NM_000552.3|35|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs216902 -0.693147 0.000197631 86 V1565L 2813 Gtg/Ttg MODERATE 28 MISSENSE CODING VWF A protein_coding NM_000552.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6127891 C A 0 222 0 0.0061 0.1757 0.2795 0.37 0.0755 0.2342 0.0233772 0.0610487 0.0803488 1 219 17328 4426 3279 298 5597 122 3387 2 10332 120810 11532 8576 6596 66370 904 16500 0.948695 0 . 0 . 121 43,23,22,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V1565L|2813|VWF|protein_coding|CODING|NM_000552.3|28|A) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.997813 0.558423 0 0.998884 rs1800385,rs56286209 -0.693146 0.030721 121 A1555 2813 gcA/gcC LOW 28 SILENT CODING VWF G protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6127919 T G 0 222 0 0.0061 0.1759 0.2795 0.372 0.0755 0.2331 0.0226963 0.0591266 0.0777907 1 217 17234 4356 3265 298 5590 123 3385 2 10312 120606 11454 8550 6586 66316 904 16484 0.847553 0 . 0 . 141 53,32,26,23 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A1555|2813|VWF|protein_coding|CODING|NM_000552.3|28|G) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.999997 0.0612651 0 0.465999 rs1800384,rs41456147 -0.693147 0.810651 141 T1547 2813 acT/acC LOW 28 SILENT CODING VWF G protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6127943 A G 0 222 0 0.9221 0.7766 0.7752 0.746 0.6014 0.7924 0 . 0 1 9138 81959 9225 6402 3508 40608 613 12465 2 10252 119610 11324 8444 6524 65710 902 16454 0.998756 0 . 0 . 144 59,34,17,25 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1547|2813|VWF|protein_coding|CODING|NM_000552.3|28|G) 0 0.5 1 0 . 1 0 . 1 0 56 0 0.978854 0.0884418 0 0.977882 rs216310 -0.693146 0.131323 144 T1381A 2813 Acc/Gcc MODERATE 28 MISSENSE CODING VWF C protein_coding NM_000552.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6128443 T C 0 222 0 0.9228 0.7756 0.7752 0.746 0.6014 0.7863 0.881979 0.708673 0.619884 1 8699 80797 9231 6520 3541 39942 611 12253 2 9804 118862 11356 8562 6564 65302 902 16372 0.990512 0 . 0 . 187 54,33,50,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T1381A|2813|VWF|protein_coding|CODING|NM_000552.3|28|C) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.385459 0.97347 0 0.311735 rs216311 -0.693147 0.192986 187 Q852R 2813 cAg/cGg MODERATE 20 MISSENSE CODING VWF C protein_coding NM_000552.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6143984 T C 0 222 0 0.9584 0.897 0.9265 0.7907 0.9135 0.8855 0.949614 0.923881 0.910698 1 9881 109129 10597 6901 5885 60574 830 14461 2 10404 121368 11572 8646 6610 66718 908 16510 0.897262 0 . 0 . 129 16,44,8,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q852R|2813|VWF|protein_coding|CODING|NM_000552.3|20|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.440128 rs216321 -0.693147 0.760009 129 A542 2813 gcG/gcA LOW 14 SILENT CODING VWF T protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6167118 C T 0 228 0 0.0386 0.0823 0.0461 0.1687 0.0696 0.091 0.0385837 0.0698908 0.0859302 2 446 9791 336 1254 495 5680 67 1513 2 9936 119304 11554 8582 6614 65232 892 16494 0.999781 0 . 0 COSM1363508 193 2,2,102,61 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A542|2813|VWF|protein_coding|CODING|NM_000552.3|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.363075 rs35365059 -0.693147 0.0264698 193 Y516 2813 taT/taC LOW 14 SILENT CODING VWF G protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6167196 A G 0 228 0 0.6422 0.377 0.2709 0.2103 0.3628 0.2802 0.587392 0.430883 0.350769 2 5848 40614 1829 1510 2382 23533 297 5215 2 9698 117818 11526 8526 6608 64092 882 16486 0.999834 0 . 0 COSM1162475 168 1,3,44,96 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y516|2813|VWF|protein_coding|CODING|NM_000552.3|14|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.262706 rs1800379 -0.693147 0.0533647 168 H484R 2813 cAt/cGt MODERATE 13 MISSENSE CODING VWF C protein_coding NM_000552.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6172202 T C 0 222 0 0.1437 0.5188 0.5101 0.6667 0.6541 0.7403 0.219246 0.508611 0.65686 1 2134 74480 5969 6087 4243 43699 604 11744 2 10086 119902 11426 8596 6354 66110 882 16448 0.766877 0 . 0 COSM431631 60 10,19,8,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H484R|2813|VWF|protein_coding|CODING|NM_000552.3|13|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974891 rs1800378 -0.692914 0.337421 60 V471I 2813 Gtc/Atc MODERATE 12 MISSENSE CODING VWF T protein_coding NM_000552.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6173433 C T 0 222 0 0.1346 0.136 0.0749 0.1885 0.0934 0.1708 0.138675 0.119868 0.110233 1 1372 14323 581 1459 635 7250 107 2919 2 10362 120818 11554 8604 6516 66378 896 16508 0.950789 0 . 0 . 85 22,24,20,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V471I|2813|VWF|protein_coding|CODING|NM_000552.3|12|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.929247 rs1800377 -0.693139 0.437384 85 S394 2813 tcA/tcC LOW 11 SILENT CODING VWF G protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6174414 T G 0 222 0 0.5386 0.2798 0.134 0.247 0.1213 0.2301 0.494326 0.251422 0.126977 1 5042 21084 969 1916 695 8319 152 3991 2 10256 120220 11450 8574 6454 66238 896 16352 0.963718 0 . 0 . 103 30,21,18,22 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S394|2813|VWF|protein_coding|CODING|NM_000552.3|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.785075 rs1800376 -0.693145 0.289904 103 T391 2813 acA/acT LOW 11 SILENT CODING VWF A protein_coding NM_000552.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6174423 T A 0 222 0 0.5076 0.271 0.1297 0.247 0.1213 0.2301 0.466409 0.241965 0.126977 1 4762 20745 950 1915 692 8282 150 3994 2 10252 120168 11430 8580 6448 66212 890 16356 0.935421 0 . 0 COSM147397 102 30,20,17,23 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T391|2813|VWF|protein_coding|CODING|NM_000552.3|11|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.982712 rs1800375 -0.693145 0.293423 102 228 68 MODIFIER 1 CODING CD9 T protein_coding NM_001769.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6309598 C T 0 174 0 0.3449 0.1426 0.0937 0.0536 0.1044 0.0348 0.304191 0.153307 0.0876807 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.974778 0 . 0 . 64 26,1,31,0 START_GAINED(LOW||||228|CD9|protein_coding|CODING|NM_001769.3|1|T),UTR_5_PRIME(MODIFIER||68||228|CD9|protein_coding|CODING|NM_001769.3|1|T) 1 0.5 1 0 . 1 0 1 0 . 60 0 1 1 0 0.551371 rs11539945 -0.69311 0.00732583 64 A393T 728 Gca/Aca MODERATE 5 MISSENSE CODING SCNN1A T protein_coding NM_001159576.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6464581 C T 0 185 0 0.5053 0.1923 0.0663 0.1379 0.0507 0.0603 0.448252 0.176303 0.0369767 1 4597 10385 316 1202 640 2748 67 815 2 10012 115552 10894 8480 5770 63740 842 15814 0.573631 2 benign 0 . 24 2,11,3,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A393T|728|SCNN1A|protein_coding|CODING|NM_001159576.1|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.897472 rs11542844 -0.670168 0.251186 24 435 174 MODIFIER 1 CODING LTBR G protein_coding NM_002342.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6493351 A G 0 9.7 0 0.9879 0.854 0.8012 0.8661 0.7376 0.818 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||174||435|LTBR|protein_coding|CODING|NM_002342.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10849448 -0.379885 0 1 A172 435 gcC/gcA LOW 5 SILENT CODING LTBR A protein_coding NM_002342.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6495275 C A 0 228 0 0.9713 0.8482 0.7954 0.873 0.7346 0.8108 0.933727 0.804167 0.737791 2 9774 94374 8998 7489 4965 49071 664 13413 2 10406 121402 11576 8654 6614 66732 908 16512 0 . 0 . 0 82 0,0,50,19 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A172|435|LTBR|protein_coding|CODING|NM_002342.2|5|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2364480 -0.693147 0.329634 82 435 2 MODIFIER 10 CODING LTBR G protein_coding NM_002342.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6500105 T G 0 228 0 0.9856 0.8431 0.7839 0.8681 0.7117 0.8016 0.943486 0.787867 0.70814 2 9751 89319 8882 7402 4940 46598 623 11123 2 10282 116976 11512 8580 6610 65348 862 13782 0.722034 0 . 0 . 194 2,1,76,93 UTR_3_PRIME(MODIFIER||2||435|LTBR|protein_coding|CODING|NM_002342.2|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.398329 rs12354 -0.693147 0.00205754 194 H233R 260 cAt/cGt MODERATE 6 MISSENSE CODING CD27 G protein_coding NM_001242.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6560473 A G 0 228 0 1 0.9974 0.9986 1 0.9901 0.998 0.996369 0.991696 0.989302 2 10375 120410 11546 8650 6600 65921 893 16425 2 10394 121306 11574 8650 6612 66670 900 16506 0 . 0 . 0 220 0,0,125,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H233R|260|CD27|protein_coding|CODING|NM_001242.4|6|G),UPSTREAM(MODIFIER||704||468|TAPBPL|protein_coding|CODING|NM_018009.4||G),INTRAGENIC(MODIFIER|||||CD27-AS1||NON_CODING|||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2532502,rs386569058 -0.693147 0.168711 220 260 15 MODIFIER 6 CODING CD27 T protein_coding NM_001242.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6560573 G T 0 228 0 0.0234 0.36 0.3386 0.4315 0.5467 0.5644 0.109446 0.409643 0.563372 2 1004 58326 4127 3718 3656 36270 437 9114 2 9942 118198 11430 8516 6450 64996 872 15992 1 0 . 0 . 201 1,0,75,109 UTR_3_PRIME(MODIFIER||15||260|CD27|protein_coding|CODING|NM_001242.4|6|T),UPSTREAM(MODIFIER||604||468|TAPBPL|protein_coding|CODING|NM_018009.4||T),INTRAGENIC(MODIFIER|||||CD27-AS1||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1059501 -0.693147 0.00532941 201 C39 468 tgC/tgT LOW 2 SILENT CODING TAPBPL T protein_coding NM_018009.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562285 C T 0 221 0 0.1074 0.228 0.1628 0.3224 0.2932 0.273 0.121308 0.230651 0.286645 1 848 19166 571 1877 733 11462 158 3517 2 5624 55830 1928 4692 1682 30804 404 10696 0.894421 0 . 0 . 128 58,26,24,10 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C39|468|TAPBPL|protein_coding|CODING|NM_018009.4|2|T),DOWNSTREAM(MODIFIER||1401||260|CD27|protein_coding|CODING|NM_001242.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.981526 rs2041384,rs386423571 -0.693132 0.104629 128 A42V 468 gCg/gTg MODERATE 2 MISSENSE CODING TAPBPL T protein_coding NM_018009.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562293 C T 0 221 0 0.1074 0.2276 0.1628 0.3204 0.2932 0.273 0.12148 0.231544 0.287907 1 896 20270 640 1927 854 12200 173 3580 2 5888 59142 2232 4866 1972 32830 444 10910 0.349636 0 . 0 . 133 58,25,24,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A42V|468|TAPBPL|protein_coding|CODING|NM_018009.4|2|T),DOWNSTREAM(MODIFIER||1409||260|CD27|protein_coding|CODING|NM_001242.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.976281 rs2041385 -0.693132 0.152406 133 M146V 468 Atg/Gtg MODERATE 3 MISSENSE CODING TAPBPL G protein_coding NM_018009.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562753 A G 0 228 0 0.6225 0.6877 0.5591 0.7887 0.675 0.7761 0.586473 0.656466 0.692326 2 6209 82821 6611 6630 4599 45672 588 12512 2 10394 121224 11550 8638 6598 66636 904 16504 0 . 0 . 0 74 0,0,22,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M146V|468|TAPBPL|protein_coding|CODING|NM_018009.4|3|G),DOWNSTREAM(MODIFIER||1869||260|CD27|protein_coding|CODING|NM_001242.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2532501 -0.693147 0.738028 74 G151R 468 Ggg/Cgg MODERATE 3 MISSENSE CODING TAPBPL C protein_coding NM_018009.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562768 G C 0 222 0 0.0386 0.0589 0.0432 0.124 0.0119 0.0787 0.0299591 0.017761 0.0115116 1 335 3868 503 922 144 915 30 1019 2 10384 121178 11556 8630 6594 66604 904 16506 0.997729 0 . 0 . 60 12,17,9,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Cgg|G151R|468|TAPBPL|protein_coding|CODING|NM_018009.4|3|C),DOWNSTREAM(MODIFIER||1884||260|CD27|protein_coding|CODING|NM_001242.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.901595 rs7295376 -0.692976 0.428518 60 T165A 468 Acc/Gcc MODERATE 3 MISSENSE CODING TAPBPL G protein_coding NM_018009.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562810 A G 0 228 0 0.6225 0.6873 0.5591 0.7887 0.675 0.774 0.5867 0.656543 0.692326 2 6181 82415 6570 6587 4572 45418 584 12503 2 10332 120672 11478 8584 6556 66324 900 16498 1 0 . 0 . 68 0,1,17,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T165A|468|TAPBPL|protein_coding|CODING|NM_018009.4|3|G),DOWNSTREAM(MODIFIER||1926||260|CD27|protein_coding|CODING|NM_001242.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2532500 -0.693147 0.934301 68 A169V 468 gCg/gTg MODERATE 3 MISSENSE CODING TAPBPL T protein_coding NM_018009.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562823 C T 0 222 0 0.1846 0.2582 0.1744 0.3224 0.3042 0.3037 0.187245 0.265032 0.304884 1 1919 33600 1487 2875 1945 19605 282 5487 2 10192 119726 11408 8544 6482 65836 896 16368 0.952166 0 . 0 . 66 14,21,5,16 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A169V|468|TAPBPL|protein_coding|CODING|NM_018009.4|3|T),DOWNSTREAM(MODIFIER||1939||260|CD27|protein_coding|CODING|NM_001242.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0957095 rs2041387 -0.692352 0.687944 66 P173 468 ccG/ccA LOW 3 SILENT CODING TAPBPL A protein_coding NM_018009.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6562836 G A 0 161 0 0.0136 0.2029 0.1599 0.3224 0.2932 0.273 0.0565138 0.211287 0.290581 1 508 30417 1353 2870 1931 18657 263 4835 2 9910 118672 11368 8530 6438 65400 888 16138 0.847647 0 . 0 . 60 16,20,2,14 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P173|468|TAPBPL|protein_coding|CODING|NM_018009.4|3|A),DOWNSTREAM(MODIFIER||1952||260|CD27|protein_coding|CODING|NM_001242.4||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.842788 rs2041388 -0.689466 0.00149215 60 118 1937 MODIFIER 5 CODING VAMP1 A protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6571699 G A 0 207 0 0.618 0.6889 0.5576 0.7857 0.675 0.7924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,9,3 UTR_3_PRIME(MODIFIER||1937||118|VAMP1|protein_coding|CODING|NM_014231.4|5|A),DOWNSTREAM(MODIFIER||211||468|TAPBPL|protein_coding|CODING|NM_018009.4||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7390 -0.680642 0.136363 12 118 1588 MODIFIER 5 CODING VAMP1 G protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6572048 A G 0 228 0 0.7474 0.73 0.572 0.7877 0.6779 0.8129 0.722877 0.706095 0.697919 2 5269 62087 4290 4909 2793 34393 439 9994 2 7408 89054 7476 6438 4006 50338 666 12722 0 . 0 . 0 190 0,0,94,77 UTR_3_PRIME(MODIFIER||1588||118|VAMP1|protein_coding|CODING|NM_014231.4|5|G),DOWNSTREAM(MODIFIER||560||468|TAPBPL|protein_coding|CODING|NM_018009.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1045452 -0.693147 0.104143 190 118 1445 MODIFIER 5 CODING VAMP1 C protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6572191 T C 0 228 0 0.3737 0.5252 0.428 0.7788 0.496 0.5675 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 37 0,0,2,34 UTR_3_PRIME(MODIFIER||1445||118|VAMP1|protein_coding|CODING|NM_014231.4|5|C),DOWNSTREAM(MODIFIER||703||468|TAPBPL|protein_coding|CODING|NM_018009.4||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12964 -0.693139 0.31267 37 118 1087 MODIFIER 5 CODING VAMP1 T protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6572549 C T 0 101 0 0.6218 0.6929 0.5591 0.7966 0.6779 0.7924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,2,2 UTR_3_PRIME(MODIFIER||1087||118|VAMP1|protein_coding|CODING|NM_014231.4|5|T),DOWNSTREAM(MODIFIER||1061||468|TAPBPL|protein_coding|CODING|NM_018009.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2534712 -0.556411 0.939765 4 118 1075 MODIFIER 5 CODING VAMP1 T protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6572561 A T 0 134 0 0.6218 0.6911 0.5591 0.7877 0.6779 0.7924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,2,3 UTR_3_PRIME(MODIFIER||1075||118|VAMP1|protein_coding|CODING|NM_014231.4|5|T),DOWNSTREAM(MODIFIER||1073||468|TAPBPL|protein_coding|CODING|NM_018009.4||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13842 -0.590765 0.216674 5 118 490 MODIFIER 5 CODING VAMP1 C protein_coding NM_014231.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6573146 T C 0 38 0 0.2141 0.2728 0.1844 0.3294 0.3231 0.3047 0 . 0 1 49 3629 23 45 1 866 38 2607 2 190 10776 92 136 2 2736 118 7502 0.900802 0 . 0 . 9 5,0,3,0 UTR_3_PRIME(MODIFIER||490||118|VAMP1|protein_coding|CODING|NM_014231.4|5|C),DOWNSTREAM(MODIFIER||1658||468|TAPBPL|protein_coding|CODING|NM_018009.4||C) 0 0.5 1 0 . 1 0 . 1 0 60 0 0.900802 0 . 0.900802 rs2534715 -0.511536 0.301053 9 A84 118 gcC/gcA LOW 3 SILENT CODING VAMP1 T protein_coding NM_014231.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6575044 G T 0 222 0 0.2095 0.2724 0.1859 0.3284 0.3241 0.3078 0.201089 0.280255 0.320814 1 2091 35626 1544 2963 2212 20923 295 5598 2 10402 121338 11574 8638 6608 66704 904 16508 0.752533 0 . 0 . 181 62,45,33,20 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcA|A84|118|VAMP1|protein_coding|CODING|NM_014231.4|3|T),DOWNSTREAM(MODIFIER||3556||468|TAPBPL|protein_coding|CODING|NM_018009.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.392977 rs2072375,rs386556399 -0.693147 0.104206 181 118 60 MODIFIER 1 CODING VAMP1 C protein_coding NM_014231.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6579757 T C 0 228 0 1 0.9968 0.9986 1 0.9881 0.9969 0.998555 0.994087 0.992143 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 157 0,0,46,92 UTR_5_PRIME(MODIFIER||60||118|VAMP1|protein_coding|CODING|NM_014231.4|1|C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2532489 -0.693147 0.602326 157 118 115 MODIFIER 1 CODING VAMP1 C protein_coding NM_014231.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6579812 T C 0 222 0 0.5507 0.4613 0.3862 0.4603 0.3688 0.4898 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8457 0 . 0 . 109 3,36,9,53 UTR_5_PRIME(MODIFIER||115||118|VAMP1|protein_coding|CODING|NM_014231.4|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.772527 rs2072376 -0.693147 0.156129 109 Q83E 1401 Caa/Gaa MODERATE 4 MISSENSE CODING NCAPD2 G protein_coding NM_014865.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6619284 C G 0 222 0 0.9826 0.7955 0.8285 0.6706 0.7256 0.7198 0.942805 0.792942 0.716163 1 9864 91410 10206 5661 5050 48403 649 11577 2 10402 121298 11570 8642 6610 66660 906 16508 0.997154 0 . 0 . 141 42,43,20,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q83E|1401|NCAPD2|protein_coding|CODING|NM_014865.3|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.270637 rs714774 -0.693145 0.621201 141 R1100 1401 cgT/cgC LOW 26 SILENT CODING NCAPD2 C protein_coding NM_014865.3 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6637845 T C 0 222 0 0.9811 0.7971 0.8271 0.6925 0.7137 0.7209 0.93872 0.785407 0.70686 1 9824 90330 10181 5775 4975 47518 649 11408 2 10398 121154 11574 8618 6606 66622 902 16434 0.437935 0 . 0 . 109 33,22,33,10 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R1100|1401|NCAPD2|protein_coding|CODING|NM_014865.3|26|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.834587 rs2072374 -0.693146 0.103917 109 V1267 1401 gtA/gtG LOW 29 SILENT CODING NCAPD2 G protein_coding NM_014865.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6639088 A G 0 222 0 0.9115 0.7815 0.8228 0.7063 0.7137 0.7239 0.893554 0.770183 0.706977 1 9343 90172 10153 5993 5007 47583 647 11446 2 10406 121314 11574 8624 6610 66710 908 16482 0.960472 0 . 0 . 93 23,23,15,22 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1267|1401|NCAPD2|protein_coding|CODING|NM_014865.3|29|G),UPSTREAM(MODIFIER||4483||335|GAPDH|protein_coding|CODING|NM_001289745.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.751532 rs1043262 -0.693141 0.609751 93 D127 335 gaT/gaC LOW 6 SILENT CODING GAPDH C protein_coding NM_001289745.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6646320 T C 0 222 0 0.5651 0.405 0.3112 0.5188 0.2217 0.3262 0.47163 0.29471 0.20407 1 5106 33537 3588 4266 1830 13895 212 4640 2 10372 120892 11432 8588 6608 66526 904 16462 0.249875 0 . 0 . 126 59,11,39,9 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D127|335|GAPDH|protein_coding|CODING|NM_001289745.1|6|C),DOWNSTREAM(MODIFIER||2374||571|IFFO1|protein_coding|CODING|NM_001193457.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.987885 rs1065691 -0.693147 0.322556 126 F295 335 ttT/ttC LOW 8 SILENT CODING GAPDH C protein_coding NM_001289745.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6647109 T C 0 222 0 0.5666 0.4147 0.3228 0.5486 0.2217 0.3354 0.465666 0.292873 0.204445 1 4892 33789 3655 4557 1835 13939 212 4699 2 9882 120626 11548 8622 6610 66572 904 16488 0.982076 0 . 0 . 103 31,20,19,18 SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F295|335|GAPDH|protein_coding|CODING|NM_001289745.1|8|C),DOWNSTREAM(MODIFIER||1585||571|IFFO1|protein_coding|CODING|NM_001193457.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.454823 rs1803621 -0.693141 0.175939 103 335 117 MODIFIER 9 CODING GAPDH T protein_coding NM_001289745.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6647453 G T 0 75 0 0.5174 0.3926 0.3026 0.5298 0.2197 0.3241 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.935229 0 . 0 . 13 0,8,1,4 UTR_3_PRIME(MODIFIER||117||335|GAPDH|protein_coding|CODING|NM_001289745.1|9|T),DOWNSTREAM(MODIFIER||1241||571|IFFO1|protein_coding|CODING|NM_001193457.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.84246 rs1803622 -0.590765 0.273436 13 571 545 MODIFIER 10 CODING IFFO1 T protein_coding NM_001193457.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6649104 C T 0 168 0 1 0.9788 0.9942 1 0.9841 0.9121 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 22 0,0,22,0 UTR_3_PRIME(MODIFIER||545||571|IFFO1|protein_coding|CODING|NM_001193457.1|10|T),DOWNSTREAM(MODIFIER||1563||335|GAPDH|protein_coding|CODING|NM_001289745.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs758740 -0.692562 0.101272 22 571 109 MODIFIER 10 CODING IFFO1 G protein_coding NM_001193457.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6649540 A G 0 127 0 0.5908 0.4056 0.2896 0.5218 0.2217 0.3067 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.925537 0 . 0 . 38 22,2,13,1 UTR_3_PRIME(MODIFIER||109||571|IFFO1|protein_coding|CODING|NM_001193457.1|10|G),DOWNSTREAM(MODIFIER||1999||335|GAPDH|protein_coding|CODING|NM_001289745.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.930956 rs2240875 -0.686358 0.262455 38 E357 1912 gaG/gaA LOW 9 SILENT CODING CHD4 T protein_coding NM_001273.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6709554 C T 0 222 0 0 0.00039936 0 0.002 0 0 0 . 0 1 0 3 0 3 0 0 0 0 2 10406 121220 11576 8652 6614 66654 906 16412 0.994738 0 . 0 . 123 22,41,13,34 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E357|1912|CHD4|protein_coding|CODING|NM_001273.3|9|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.990801 rs373676246 -0.693147 0.0252631 123 E139D 1912 gaG/gaT MODERATE 4 MISSENSE CODING CHD4 A protein_coding NM_001273.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6711147 C A 0 222 0 0.9009 0.5531 0.3617 0.4821 0.4066 0.4427 0.825571 0.548741 0.407191 1 5729 44922 3843 3176 3036 22942 298 5898 2 7440 109092 10786 8004 6332 60250 830 15450 0.46997 0 . 0 COSM1363775,COSM1363776,COSM1363777 118 12,42,12,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E139D|1912|CHD4|protein_coding|CODING|NM_001273.3|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977782 rs1639122 -0.693147 0.00356921 118 543 153 MODIFIER 10 CODING ACRBP A protein_coding NM_032489.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6747295 G A 0 222 0 0.4062 0.6368 0.7911 0.626 0.7893 0.6933 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.587237 0 . 0 . 221 47,58,38,49 UTR_3_PRIME(MODIFIER||153||543|ACRBP|protein_coding|CODING|NM_032489.2|10|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875688 rs1045553 -0.693147 0.0176476 221 543 LOW 9 CODING ACRBP C protein_coding NM_032489.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6747578 G C 0 222 0 0.5408 0.6793 0.7968 0.6448 0.7913 0.7035 0.581707 0.721359 0.792907 1 5938 91462 8787 5600 5276 53143 688 12030 2 10260 120860 11532 8616 6604 66468 906 16474 0.984808 0 . 0 . 41 6,7,14,10 SPLICE_SITE_REGION+INTRON(LOW||||543|ACRBP|protein_coding|CODING|NM_032489.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.51899 rs1882553 -0.692831 0.182582 41 577 913 MODIFIER 11 CODING ZNF384 G protein_coding NM_001135734.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6775967 A G 0 191 0 0.9463 0.5493 0.4712 0.1409 0.5477 0.4908 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.556527 0 . 0 . 33 0,14,2,16 UTR_3_PRIME(MODIFIER||913||577|ZNF384|protein_coding|CODING|NM_001135734.2|11|G),UPSTREAM(MODIFIER||3659||249|ING4|protein_coding|CODING|NM_001127582.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.965264 rs6786 -0.691153 9.46748e-08 33 L239 275 Ctg/Ttg LOW 6 SILENT CODING COPS7A T protein_coding NM_001164093.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6839913 C T 0 222 0 0.2632 0.1098 0.0591 0.0694 0.0656 0.0256 0.232864 0.13909 0.0910465 1 2416 9849 387 568 444 5520 52 462 2 10350 120892 11534 8638 6532 66446 898 16494 0.826566 0 . 0 . 55 16,13,16,7 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L239|275|COPS7A|protein_coding|CODING|NM_001164093.1|6|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.787669 rs2286730 -0.692717 0.00143182 55 275 4 MODIFIER 7 CODING COPS7A A protein_coding NM_001164093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6840209 G A 0 222 0 0.5446 0.6683 0.5922 0.749 0.661 0.8139 0.55833 0.618407 0.649186 1 5827 81131 7269 6688 4361 43092 641 13253 2 10394 121296 11560 8636 6606 66680 908 16512 0.991272 0 . 0 . 66 25,15,14,8 UTR_3_PRIME(MODIFIER||4||275|COPS7A|protein_coding|CODING|NM_001164093.1|7|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0755198 rs3168600 -0.692562 0.0242596 66 275 166 MODIFIER 7 CODING COPS7A T protein_coding NM_001164093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6840371 G T 0 167 0 0.5446 0.6685 0.5922 0.75 0.661 0.8139 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 29 1,11,1,15 UTR_3_PRIME(MODIFIER||166||275|COPS7A|protein_coding|CODING|NM_001164093.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.96195 rs11227 -0.689466 0.280252 29 275 483 MODIFIER 7 CODING COPS7A T protein_coding NM_001164093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6840688 C T 0 205 0 0.2595 0.1082 0.0576 0.0694 0.0656 0.0235 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.973504 0 . 0 . 26 8,3,9,4 UTR_3_PRIME(MODIFIER||483||275|COPS7A|protein_coding|CODING|NM_001164093.1|7|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.135657 rs9478 -0.683931 0.684685 26 248 297 MODIFIER 9 CODING MLF2 CA protein_coding NM_005439.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6857663 C CA 0 222 0 0.2224 0.1362 0.1571 0.121 0.1034 0.0542 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 124 13,53,4,38 UTR_3_PRIME(MODIFIER||297||248|MLF2|protein_coding|CODING|NM_005439.2|9|CA) 0 0.5 1 43 0.346774 1 1 0 . 0 60 0 0 1 0 . rs61179059 -0.693146 0.416717 124 D194 248 gaC/gaT LOW 8 SILENT CODING MLF2 A protein_coding NM_005439.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6858126 G A 0 222 0 0.0393 0.0851 0.1427 0.119 0.1044 0.0511 0.0544419 0.100988 0.124854 1 456 11181 1346 877 472 7194 83 753 2 7120 89412 8290 6440 3632 49344 650 13936 0.689277 0 . 0 COSM431733 271 78,40,74,47 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D194|248|MLF2|protein_coding|CODING|NM_005439.2|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.964586 rs2302371,rs386564363 -0.693147 0.217234 271 I455T 525 aTc/aCc MODERATE 7 MISSENSE CODING LAG3 C protein_coding NM_002286.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6887020 T C 0 222 0 0.5787 0.6693 0.6816 0.8224 0.6093 0.6871 0.555152 0.598416 0.620581 1 5733 77602 8395 7313 4077 40895 542 10647 2 10406 121406 11576 8654 6612 66738 908 16512 0.999247 0 . 0 . 56 15,10,10,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I455T|525|LAG3|protein_coding|CODING|NM_002286.5|7|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.351779 rs870849 -0.692914 0.659598 56 S341 458 agT/agC LOW 7 SILENT CODING CD4 C protein_coding NM_000616.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6926363 T C 0 228 0 0.792 0.7468 0.6686 0.9137 0.5696 0.7515 0.743305 0.610795 0.542907 2 7772 77620 8156 8005 4350 37021 521 11795 2 10382 120552 11440 8650 6580 66144 904 16452 0 . 0 . 0 178 0,0,82,79 SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S341|458|CD4|protein_coding|CODING|NM_000616.4|7|C),UPSTREAM(MODIFIER||4600||588|GPR162|protein_coding|CODING|NM_019858.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1055141 -0.693147 0.0281031 178 C447 458 tgT/tgC LOW 9 SILENT CODING CD4 C protein_coding NM_000616.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6928075 T C 0 199 0 0.8245 0.7562 0.6758 0.9117 0.5686 0.7536 0.7725 0.620191 0.542229 2 7791 76949 8148 7956 4308 36415 517 11814 2 9956 119026 11462 8598 6514 65160 888 16448 0 . 0 . 0 12 0,0,1,10 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C447|458|CD4|protein_coding|CODING|NM_000616.4|9|C),UPSTREAM(MODIFIER||2888||588|GPR162|protein_coding|CODING|NM_019858.1||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs12821756 -0.676189 0.249966 12 458 91 MODIFIER 10 CODING CD4 A protein_coding NM_000616.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6928586 C A 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 75 1,0,17,52 UTR_3_PRIME(MODIFIER||91||458|CD4|protein_coding|CODING|NM_000616.4|10|A),UPSTREAM(MODIFIER||2377||588|GPR162|protein_coding|CODING|NM_019858.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs7136817 -0.693147 0.000253714 75 458 92 MODIFIER 10 CODING CD4 G protein_coding NM_000616.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6928587 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 75 0,0,18,52 UTR_3_PRIME(MODIFIER||92||458|CD4|protein_coding|CODING|NM_000616.4|10|G),UPSTREAM(MODIFIER||2376||588|GPR162|protein_coding|CODING|NM_019858.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7307451 -0.693147 0.000465123 75 458 1142 MODIFIER 10 CODING CD4 C protein_coding NM_000616.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6929637 T C 0 31.9 0 0.2693 0.2967 0.2075 0.4732 0.1541 0.362 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,1 UTR_3_PRIME(MODIFIER||1142||458|CD4|protein_coding|CODING|NM_000616.4|10|C),UPSTREAM(MODIFIER||1326||588|GPR162|protein_coding|CODING|NM_019858.1||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1045261 -0.453602 0.68 3 588 98 MODIFIER 2 CODING GPR162 C protein_coding NM_019858.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6932967 G C 0 222 0 0.2103 0.1482 0.0807 0.2391 0.0825 0.0859 0.192907 0.121777 0.0879397 1 2066 12982 476 2068 1048 5878 93 1353 2 9754 119256 11550 8566 6468 66230 876 15812 0.969375 0 . 0 . 64 8,23,6,21 UTR_5_PRIME(MODIFIER||98||588|GPR162|protein_coding|CODING|NM_019858.1|2|C),UPSTREAM(MODIFIER||4571||735|P3H3|protein_coding|CODING|NM_014262.4||C),DOWNSTREAM(MODIFIER||2991||458|CD4|protein_coding|CODING|NM_000616.4||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0404236 rs2040353 -0.693021 0.280024 64 C53 588 tgC/tgT LOW 2 SILENT CODING GPR162 T protein_coding NM_019858.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6933223 C T 0 222 0 0.2057 0.1464 0.0807 0.2381 0.0815 0.0849 0.199047 0.125942 0.0884884 1 2129 12915 468 2072 971 5826 89 1360 2 10320 120496 11516 8578 6594 66112 898 16478 0.999818 0 . 0 . 71 25,14,20,8 SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C53|588|GPR162|protein_coding|CODING|NM_019858.1|2|T),UPSTREAM(MODIFIER||4315||735|P3H3|protein_coding|CODING|NM_014262.4||T),DOWNSTREAM(MODIFIER||3247||458|CD4|protein_coding|CODING|NM_000616.4||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.438561 rs11575110 -0.693054 0.271768 71 V241 588 gtA/gtG LOW 2 SILENT CODING GPR162 G protein_coding NM_019858.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6933787 A G 0 228 0 0.5734 0.4894 0.5144 0.5675 0.4563 0.3119 0.55084 0.489005 0.457326 2 5727 56576 6081 4730 3805 30515 367 5351 2 10342 119830 11544 8582 6604 66174 886 15698 0 . 0 . 0 101 0,0,88,6 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V241|588|GPR162|protein_coding|CODING|NM_019858.1|2|G),UPSTREAM(MODIFIER||3751||735|P3H3|protein_coding|CODING|NM_014262.4||G),DOWNSTREAM(MODIFIER||3811||458|CD4|protein_coding|CODING|NM_000616.4||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1051409 -0.693147 2.69782e-05 101 T300A 735 Aca/Gca MODERATE 4 MISSENSE CODING P3H3 G protein_coding NM_014262.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6939850 A G 0 228 0 0.8154 0.6416 0.6628 0.7073 0.4761 0.4939 0.750981 0.563826 0.472621 2 7295 63543 8128 5928 3035 30622 458 8077 2 9578 118218 11320 8512 6458 65182 878 16290 1 0 . 0 . 78 1,0,58,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T300A|735|P3H3|protein_coding|CODING|NM_014262.4|4|G),DOWNSTREAM(MODIFIER||3267||588|GPR162|protein_coding|CODING|NM_019858.1||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10744716 -0.693147 0.115892 78 G384 735 ggG/ggA LOW 6 SILENT CODING P3H3 A protein_coding NM_014262.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6941021 G A 0 228 0 0.2995 0.3049 0.2896 0.3472 0.2793 0.3057 0.252955 0.260006 0.263531 2 2489 31671 3129 2696 1616 16655 255 4831 2 7760 96646 8878 7318 4870 53600 706 13514 0.59322 0 . 0 . 71 0,2,36,23 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G384|735|P3H3|protein_coding|CODING|NM_014262.4|6|A),DOWNSTREAM(MODIFIER||4438||588|GPR162|protein_coding|CODING|NM_019858.1||A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.508475 rs1047771 -0.693147 0.463361 71 A518 735 gcG/gcT LOW 10 SILENT CODING P3H3 T protein_coding NM_014262.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6946247 G T 0 228 0 0.4743 0.3914 0.3804 0.3542 0.3469 0.3712 0.421923 0.363525 0.3359 2 4270 41627 4049 2866 1867 21856 318 6401 2 9458 117982 11396 8418 6460 65020 874 16356 0 . 0 . COSM431757,COSM431758 191 0,0,96,78 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcT|A518|735|P3H3|protein_coding|CODING|NM_014262.4|10|T),UPSTREAM(MODIFIER||3771||340|GNB3|protein_coding|CODING|NM_002075.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1129646 -0.693147 0.0183836 191 I684T 735 aTa/aCa MODERATE 15 MISSENSE CODING P3H3 C protein_coding NM_014262.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6948468 T C 0 228 0 0.4017 0.3788 0.3501 0.4216 0.3588 0.3446 0.358118 0.345877 0.33989 2 994 9363 214 342 332 4266 90 3125 2 2482 23746 528 806 760 10886 228 8056 0 . 0 . 0 81 0,0,23,52 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I684T|735|P3H3|protein_coding|CODING|NM_014262.4|15|C),UPSTREAM(MODIFIER||1550||340|GNB3|protein_coding|CODING|NM_002075.3||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1129649 -0.693147 0.175958 81 735 67 MODIFIER 15 CODING P3H3 G protein_coding NM_014262.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6948692 A G 0 228 0 0.7171 0.7804 0.7651 0.9772 0.6451 0.8129 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,4,14 UTR_3_PRIME(MODIFIER||67||735|P3H3|protein_coding|CODING|NM_014262.4|15|G),UPSTREAM(MODIFIER||1326||340|GNB3|protein_coding|CODING|NM_002075.3||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047776 -0.691153 0.123095 19 735 274 MODIFIER 15 CODING P3H3 G protein_coding NM_014262.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6948899 A G 0 9.7 0 0.7156 0.6192 0.5 0.6438 0.5199 0.6503 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||274||735|P3H3|protein_coding|CODING|NM_014262.4|15|G),UPSTREAM(MODIFIER||1119||340|GNB3|protein_coding|CODING|NM_002075.3||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs5440 -0.379885 0 1 S275 340 tcC/tcT LOW 9 SILENT CODING GNB3 T protein_coding NM_002075.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6954875 C T 0 228 0 0.8192 0.4922 0.379 0.503 0.3072 0.3098 0.722424 0.449792 0.310116 2 7724 43631 3968 4523 1665 20218 287 5246 2 10400 121276 11570 8606 6614 66668 906 16512 1 0 . 0 COSM147403 108 1,0,39,58 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S275|340|GNB3|protein_coding|CODING|NM_002075.3|9|T),DOWNSTREAM(MODIFIER||3097||268|CDCA3|protein_coding|CODING|NM_031299.5||T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs5443 -0.693147 0.0112212 108 340 400 MODIFIER 10 CODING GNB3 T protein_coding NM_002075.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6956462 C T 0 228 0 0.4622 0.3169 0.268 0.2024 0.3032 0.2873 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 50 0,0,37,9 UTR_3_PRIME(MODIFIER||400||340|GNB3|protein_coding|CODING|NM_002075.3|10|T),UPSTREAM(MODIFIER||4823||858|USP5|protein_coding|CODING|NM_001098536.1||T),DOWNSTREAM(MODIFIER||1510||268|CDCA3|protein_coding|CODING|NM_031299.5||T),INTRAGENIC(MODIFIER|||||CDCA3||CODING|||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs5446 -0.693147 0.021474 50 268 777 MODIFIER 1 CODING CDCA3 T protein_coding NM_031299.5 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6960893 A T 0 9.7 0 0.848 0.5038 0.3847 0.5069 0.3181 0.3108 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||777||268|CDCA3|protein_coding|CODING|NM_031299.5|1|T),UPSTREAM(MODIFIER||392||858|USP5|protein_coding|CODING|NM_001098536.1||T),DOWNSTREAM(MODIFIER||4334||340|GNB3|protein_coding|CODING|NM_002075.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2071058 -0.379885 0 1 G106 858 ggA/ggG LOW 4 SILENT CODING USP5 G protein_coding NM_001098536.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6965194 A G 0 228 0 0.8517 0.5034 0.3847 0.505 0.3181 0.3057 0.748298 0.456174 0.306512 2 8011 44265 4130 4564 1671 20370 303 5216 2 10406 121356 11574 8624 6612 66724 908 16508 0 . 0 . 0 219 0,0,122,79 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G106|858|USP5|protein_coding|CODING|NM_001098536.1|4|G),UPSTREAM(MODIFIER||3964||268|CDCA3|protein_coding|CODING|NM_031299.5||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2226955 -0.693147 0.0602169 219 858 265 MODIFIER 20 CODING USP5 T protein_coding NM_001098536.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 6975506 C T 0 76 0 0.0862 0.1192 0.0519 0.3095 0.0427 0.0941 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,3,1 UTR_3_PRIME(MODIFIER||265||858|USP5|protein_coding|CODING|NM_001098536.1|20|T),UPSTREAM(MODIFIER||1078||286|TPI1|protein_coding|CODING|NM_001159287.1||T),DOWNSTREAM(MODIFIER||4594||263|SPSB2|protein_coding|CODING|NM_001146316.1||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2071064 -0.556411 0.497461 4 343 722 MODIFIER 1 CODING LRRC23 G protein_coding NM_001135217.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7014076 C G 0 155 0 0.6029 0.3706 0.2767 0.2569 0.2972 0.316 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,3,3 UTR_5_PRIME(MODIFIER||722||343|LRRC23|protein_coding|CODING|NM_001135217.1|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.861511 0 . rs2239163 -0.616816 0.544728 6 343 691 MODIFIER 1 CODING LRRC23 A protein_coding NM_001135217.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7014107 T A 0 170 0 0.885 0.5136 0.366 0.5159 0.2962 0.3374 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,3,3 UTR_5_PRIME(MODIFIER||691||343|LRRC23|protein_coding|CODING|NM_001135217.1|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.861511 0 . rs1007923 -0.616816 0.080746 7 V317E 343 gTg/gAg MODERATE 7 MISSENSE CODING LRRC23 A protein_coding NM_001135217.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7022085 T A 0 228 0 0.7141 0.4014 0.2752 0.2579 0.2952 0.3252 0.616886 0.39428 0.280233 2 6559 36966 2376 2054 1569 18732 290 5386 2 10404 121388 11574 8650 6614 66730 906 16510 0 . 0 . 0 432 0,0,200,199 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gAg|V317E|343|LRRC23|protein_coding|CODING|NM_001135217.1|7|A),UPSTREAM(MODIFIER||1529||434|ENO2|protein_coding|CODING|NM_001975.2||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1057077 -0.693147 0.205422 432 343 956 MODIFIER 8 CODING LRRC23 G protein_coding NM_001135217.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7023123 A G 0 228 0 0.8169 0.4778 0.2896 0.4732 0.2972 0.3436 0.70699 0.427187 0.283837 2 7548 40398 2473 3919 1579 18993 302 5584 2 10406 121054 11576 8626 6612 66592 908 16334 0.695906 0 . 0 . 183 1,1,126,45 UTR_3_PRIME(MODIFIER||956||343|LRRC23|protein_coding|CODING|NM_001135217.1|8|G),UPSTREAM(MODIFIER||491||434|ENO2|protein_coding|CODING|NM_001975.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.997076 rs386607453,rs710415 -0.693147 0.628778 183 343 1133 MODIFIER 8 CODING LRRC23 C protein_coding NM_001135217.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7023300 A C 0 228 0 0.8185 0.4778 0.2867 0.4732 0.2972 0.3436 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 111 0,0,23,79 UTR_3_PRIME(MODIFIER||1133||343|LRRC23|protein_coding|CODING|NM_001135217.1|8|C),UPSTREAM(MODIFIER||314||434|ENO2|protein_coding|CODING|NM_001975.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs710416 -0.693147 9.10079e-05 111 434 1193 MODIFIER 1 CODING ENO2 G protein_coding NM_001975.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7023804 T G 0 109 0 0.8177 0.4778 0.2882 0.4732 0.2972 0.3436 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 5 0,0,4,0 UTR_5_PRIME(MODIFIER||1193||434|ENO2|protein_coding|CODING|NM_001975.2|1|G),DOWNSTREAM(MODIFIER||398||343|LRRC23|protein_coding|CODING|NM_001135217.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2239164 -0.556411 0.281254 5 624 LOW 8 CODING PTPN6 A protein_coding NM_080549.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7065576 G A 0 228 0 0.4077 0.8161 0.9207 0.9812 0.9394 0.9969 0.514727 0.797759 0.940476 2 4684 110377 11003 8599 6121 62829 832 16309 2 9818 120750 11576 8626 6614 66706 898 16512 0 . 0 . 0 121 0,0,82,29 SPLICE_SITE_REGION+INTRON(LOW||||624|PTPN6|protein_coding|CODING|NM_080549.3|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2110071 -0.693147 0.357922 121 G326 624 ggT/ggC LOW 9 SILENT CODING PTPN6 C protein_coding NM_080549.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7065635 T C 0 228 0 0.8782 0.9487 0.951 0.998 0.9433 0.9969 0.878211 0.921578 0.94323 2 8586 114697 11233 8620 6121 62965 846 16326 2 9816 120752 11576 8622 6614 66714 898 16512 0 . 0 . 0 158 0,0,72,64 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G326|624|PTPN6|protein_coding|CODING|NM_080549.3|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2110072 -0.693147 0.35095 158 243 HIGH 1 CODING EMG1 C protein_coding NM_006331.7 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7080212 T C 0 74 0 1 1 1 1 1 1 0 . 0 2 9306 116593 11082 8366 6414 64699 864 15862 2 9306 116596 11082 8366 6414 64702 864 15862 0 . 0 . 0 203 0,0,6,4 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON(HIGH||||243|EMG1|protein_coding|CODING|NM_006331.7|1|C),UPSTREAM(MODIFIER||296||299|PHB2|protein_coding|CODING|NM_001144831.1||C) 0 . 0 . 0 1 0 . 1 (EMG1|EMG1|1|1.00) 60 0 0 1.00775 0 . rs17857448 -0.670168 0.913584 203 243 HIGH 1 CODING EMG1 TC protein_coding NM_006331.7 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7080212 T TC 0 228 0 . 0 . 0 . 0 0.999467 0.999657 0.999747 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 203 0,0,104,90 SPLICE_SITE_ACCEPTOR+SPLICE_SITE_DONOR+INTRON(HIGH||||243|EMG1|protein_coding|CODING|NM_006331.7|1|TC),UPSTREAM(MODIFIER||297||299|PHB2|protein_coding|CODING|NM_001144831.1||TC) 1 0 . 1 0.00492611 0 1 1 0 (EMG1|EMG1|1|1.00) 60 0 0 1 0 . rs11428482 -0.693147 0.000804783 203 E184K 627 Gaa/Aaa MODERATE 4 MISSENSE CODING C1R T protein_coding NM_001733.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7242204 C T 0 228 0 0.1513 0.1749 0.062 0.3512 0.1014 0.181 0.140244 0.102003 0.0832936 2 1441 14157 628 3160 500 5727 108 2593 2 9782 120596 11562 8596 6614 66636 898 16508 0 . 0 . 0 38 0,0,21,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E184K|627|C1R|protein_coding|CODING|NM_001733.4|4|T),DOWNSTREAM(MODIFIER||4942||487|C1RL|protein_coding|CODING|NM_016546.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1126605 -0.69311 0.534274 38 M115L 135 Atg/Ttg MODERATE 3 MISSENSE CODING RBP5 A protein_coding NM_031491.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7277236 T A 0 222 0 0.1702 0.2945 0.4827 0.1736 0.3738 0.3722 0.195869 0.323235 0.388488 1 1978 43813 5677 1265 2201 26103 305 6284 2 10394 121050 11570 8630 6614 66664 908 16270 0.903254 0 . 0 . 107 26,16,37,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M115L|135|RBP5|protein_coding|CODING|NM_031491.2|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999294 rs2290237 -0.693147 0.0540557 107 D19N 135 Gac/Aac MODERATE 1 MISSENSE CODING RBP5 T protein_coding NM_031491.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7281317 C T 0 222 0 0.2095 0.2025 0.1686 0.3938 0.1103 0.1145 0.219927 0.140935 0.100465 1 1835 14339 1766 3034 676 5435 99 1494 2 6682 67440 5168 6094 2428 35892 476 10700 0.902712 0 . 0 . 125 40,26,24,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D19N|135|RBP5|protein_coding|CODING|NM_031491.2|1|T),UPSTREAM(MODIFIER||1650||956|CLSTN3|protein_coding|CODING|NM_014718.3||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.523046 rs10963 -0.693147 0.28699 125 N847 1463 aaC/aaT LOW 10 SILENT CODING CD163L1 A protein_coding NM_001297650.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7528471 G A 0 222 0 0.6331 0.4639 0.4841 0.4752 0.2714 0.407 0.561507 0.355067 0.249302 1 5983 44565 6732 4103 2475 18313 330 6629 2 10402 121340 11564 8630 6614 66718 908 16504 0.790965 0 . 0 COSM1364236 115 22,36,8,45 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N847|1463|CD163L1|protein_coding|CODING|NM_001297650.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.771524 rs7306824 -0.693147 0.0430954 115 G592A 1463 gGc/gCc MODERATE 8 MISSENSE CODING CD163L1 G protein_coding NM_001297650.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7548996 C G 0 175 0 0.2829 0.1651 0.0836 0.2073 0.0328 0.1564 0.213572 0.0919576 0.0296512 1 2274 9620 890 1492 180 2597 71 2116 2 9154 99264 8986 7186 4916 54846 736 13440 0.737991 0 . 0 . 78 9,30,1,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G592A|1463|CD163L1|protein_coding|CODING|NM_001297650.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.445233 rs4072796 -0.693136 0.189396 78 D588N 1463 Gat/Aat MODERATE 8 MISSENSE CODING CD163L1 T protein_coding NM_001297650.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7549009 C T 0 128 0 0.3351 0.1803 0.0937 0.2073 0.0328 0.1564 0.278257 0.115562 0.0322093 1 2652 9729 876 1424 178 2511 74 2014 2 8582 89716 7888 6530 4406 49536 684 12090 0.925966 0 . 0 COSM1562469 65 4,29,0,30 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Gat/Aat|D588N|1463|CD163L1|protein_coding|CODING|NM_001297650.1|8|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.484313 rs4072797 -0.693097 0.0961008 65 L533M 1463 Ttg/Atg MODERATE 7 MISSENSE CODING CD163L1 T protein_coding NM_001297650.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7551022 A T 0 228 0 0.9773 0.9938 0.9986 1 1 1 0.97458 0.991312 0.999884 2 10143 121122 11564 8650 6614 66734 907 16510 2 10406 121400 11576 8650 6614 66736 908 16510 0 . 0 . 0 266 0,0,125,111 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L533M|1463|CD163L1|protein_coding|CODING|NM_001297650.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6488268 -0.693147 0.107306 266 V523 1463 gtT/gtG LOW 7 SILENT CODING CD163L1 C protein_coding NM_001297650.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7551050 A C 0 228 0 0.9773 0.9938 0.9986 1 1 1 0.974807 0.991389 0.999884 2 10135 121105 11557 8652 6614 66732 907 16508 2 10406 121392 11570 8652 6614 66734 908 16508 0 . 0 . 0 227 0,0,95,112 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtG|V523|1463|CD163L1|protein_coding|CODING|NM_001297650.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6488269 -0.693147 0.00173418 227 G187 1463 ggA/ggG LOW 4 SILENT CODING CD163L1 C protein_coding NM_001297650.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7585247 T C 0 228 0 0.8843 0.6058 0.5706 0.6409 0.3221 0.5102 0.784158 0.464709 0.301047 2 8316 54353 7764 5390 2592 21725 388 8178 2 10352 120916 11542 8628 6610 66400 908 16476 0 . 0 . 0 91 0,0,19,61 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G187|1463|CD163L1|protein_coding|CODING|NM_001297650.1|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs58195891 -0.693147 0.189543 91 1156 LOW 10 CODING CD163 A protein_coding NM_004244.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7638020 G A 0 201 0 0.1241 0.4782 0.7075 0.38 0.7704 0.5951 0.222424 0.578425 0.760814 1 2128 80676 7950 3209 5463 50769 647 10510 2 9980 120166 11542 8568 6610 66358 900 16208 0.990132 0 . 0 . 23 2,8,3,8 SPLICE_SITE_REGION+INTRON(LOW||||1156|CD163|protein_coding|CODING|NM_004244.5|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.740818 rs10743939 -0.676189 0.44694 23 I342V 1156 Atc/Gtc MODERATE 5 MISSENSE CODING CD163 C protein_coding NM_004244.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7649484 T C 0 228 0 0.5628 0.7626 0.8487 0.6905 0.9662 0.8364 0.626192 0.852145 0.967907 2 6344 107596 9255 5994 6434 64630 847 14092 2 10400 121300 11562 8610 6610 66702 908 16508 0.601266 0 . 0 . 94 1,1,62,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I342V|1156|CD163|protein_coding|CODING|NM_004244.5|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.601266 rs4883263 -0.693147 0.73251 94 G285 1156 ggA/ggG LOW 5 SILENT CODING CD163 C protein_coding NM_004244.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7649653 T C 0 222 0 0.1241 0.4812 0.7233 0.3839 0.7694 0.5961 0.22424 0.579348 0.761279 1 2170 81370 8214 3291 5424 51034 651 10586 2 10406 121358 11564 8624 6612 66732 908 16512 0.936108 0 . 0 . 119 26,28,22,30 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G285|1156|CD163|protein_coding|CODING|NM_004244.5|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.677996 rs4883264 -0.693147 0.397477 119 L24 1156 Ttg/Ctg LOW 2 SILENT CODING CD163 G protein_coding NM_004244.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7655137 A G 0 222 0 0.1452 0.4621 0.6931 0.3829 0.7346 0.5276 0.226942 0.553 0.719935 1 1842 61719 6316 2417 4856 37702 518 8068 2 6970 92452 8762 5488 6002 50706 754 13770 0.967995 0 . 0 . 127 24,34,22,29 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L24|1156|CD163|protein_coding|CODING|NM_004244.5|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.596094 rs3210140,rs386580824 -0.693147 0.2023 127 Y178 236 taC/taT LOW 5 SILENT CODING APOBEC1 A protein_coding NM_001304566.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7803646 G A 0 222 0 0.1483 0.242 0.1916 0.2312 0.2594 0.3978 0.14276 0.208442 0.242093 1 1537 28906 1934 1797 1328 15648 236 6426 2 10404 121392 11578 8650 6612 66728 908 16512 0.741266 0 . 0 COSM147408 104 28,20,26,18 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y178|236|APOBEC1|protein_coding|CODING|NM_001304566.1|5|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.763443 rs10431309,rs386512934 -0.693146 0.123848 104 M80I 236 atG/atC MODERATE 4 MISSENSE CODING APOBEC1 G protein_coding NM_001304566.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7805236 C G 0 222 0 0.4962 0.6591 0.6225 0.5565 0.8946 0.7689 0.560599 0.778718 0.890465 1 5658 95225 6185 4888 5623 59082 786 13003 2 10388 121256 11528 8620 6610 66706 904 16500 0.71818 0 . 0 . 50 13,16,8,12 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atC|M80I|236|APOBEC1|protein_coding|CODING|NM_001304566.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.928031 rs2302515 -0.692067 0.036809 50 V328L 364 Gtg/Ctg MODERATE 2 MISSENSE CODING GDF3 G protein_coding NM_020634.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7842587 C G 0 222 0 0.0015 0.0377 0.0173 0.0585 0.0229 0.0951 0.00726282 0.0216823 0.0290698 1 48 4073 78 328 253 2211 22 1133 2 10406 121394 11574 8650 6614 66730 908 16512 0.940984 0 . 0 . 72 17,22,21,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V328L|364|GDF3|protein_coding|CODING|NM_020634.1|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.989985 rs2302516 -0.69311 0.187359 72 159 28 MODIFIER 4 CODING DPPA3 C protein_coding NM_199286.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7869701 G C 0 209 0 . 0 . 0 . 0 . 0 . 2 7302 116123 11345 8393 6602 65143 881 16457 2 9592 118578 11456 8394 6602 65180 892 16462 0 . 0 . 0 47 0,0,1,46 UTR_3_PRIME(MODIFIER||28||159|DPPA3|protein_coding|CODING|NM_199286.3|4|C) 0 . 0 . 0 . 0 . 1 0 54 0 0 1 0 . rs11055388 -0.693147 0.00315617 47 159 144 MODIFIER 4 CODING DPPA3 T protein_coding NM_199286.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7869817 A T 0 4.5 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.896649 0 . 0 . 14 4,7,0,3 UTR_3_PRIME(MODIFIER||144||159|DPPA3|protein_coding|CODING|NM_199286.3|4|T) 0 0.5 1 0 . 0 . 0 . 0 35 0 0.973096 0.367879 0 0.973096 rs200786984 -0.511536 0.0349627 14 159 217 MODIFIER 4 CODING DPPA3 A protein_coding NM_199286.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7869890 T A 0 134 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,1,6 UTR_3_PRIME(MODIFIER||217||159|DPPA3|protein_coding|CODING|NM_199286.3|4|A) 0 . 0 . 0 . 0 . 0 . 42 0 0 1 0 . rs1055423 -0.636426 0.634913 7 159 236 MODIFIER 4 CODING DPPA3 C protein_coding NM_199286.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7869909 T C 0 65 0 0.3381 0.3878 0.2767 0.373 0.4324 0.5031 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,0,4 UTR_3_PRIME(MODIFIER||236||159|DPPA3|protein_coding|CODING|NM_199286.3|4|C) 0 . 0 . 0 1 0 . 0 . 40 0 0 . 0 . rs117431141,rs61938676 -0.556411 0.548121 4 L177 305 ctT/ctC LOW 4 SILENT CODING NANOG C protein_coding NM_024865.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7947304 T C 0 222 0 . 0 . 0 . 0 0.327735 0.445154 0.505353 1 4027 61291 6020 1114 3769 37611 481 8269 2 9796 116474 11334 8622 6548 64588 880 14706 0.795935 0 . 0 . 175 59,55,17,36 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L177|305|NANOG|protein_coding|CODING|NM_024865.3|4|C) 1 0.5 1 0 . 0 . 1 1 0 51 0 0.00266181 0.0249322 0 0.138319 rs4012939,rs61937160 -0.693147 2.63262e-06 175 A266 305 gcC/gcT LOW 4 SILENT CODING NANOG T protein_coding NM_024865.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7947571 C T 0 128 0 . 0 . 0 . 0 . 0 . 1 1234 17357 1546 478 1279 10424 134 2262 2 3042 38796 3278 2322 2734 22140 286 4994 0.860268 0 . 0 . 116 63,12,38,3 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A266|305|NANOG|protein_coding|CODING|NM_024865.3|4|T) 0 0.5 1 0 . 0 . 0 1 0 37 0 0.862984 0.18297 0 0.0263289 rs4012937,rs61937161 -0.693145 0.000905685 116 535 1155 MODIFIER 10 CODING SLC2A14 A protein_coding NM_001286237.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7965757 G A 0 202 0 0.9909 0.9976 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,10,2 UTR_3_PRIME(MODIFIER||1155||535|SLC2A14|protein_coding|CODING|NM_001286237.1|10|A) 0 . 0 . 0 1 0 . 0 . 48 0 0 0.3 0 . rs7132811 -0.680642 0.217648 12 535 1110 MODIFIER 10 CODING SLC2A14 C protein_coding NM_001286237.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7965802 A C 0 38.1 0 0.0809 0.2438 0.2291 0.4196 0.2525 0.2843 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.197899 0 . 0 . 17 4,5,3,2 UTR_3_PRIME(MODIFIER||1110||535|SLC2A14|protein_coding|CODING|NM_001286237.1|10|C) 0 0.5 1 0 . 1 0 . 0 . 50 0 0.526122 0.497296 0 0.83527 rs11055935 -0.590765 0.80114 17 G521E 535 gGg/gAg MODERATE 10 MISSENSE CODING SLC2A14 T protein_coding NM_001286237.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7966958 C T 0 222 0 0.0961 0.2554 0.2421 0.4216 0.2674 0.2965 0.110758 0.217515 0.272209 1 1395 31633 2562 3764 1790 17804 218 4100 2 10358 120352 11382 8588 6580 66088 900 16456 0.959538 0 . 0 COSM431882 185 47,41,35,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G521E|535|SLC2A14|protein_coding|CODING|NM_001286237.1|10|T) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.00492291 0.429889 0 0.139466 rs10845981 -0.693147 0.161954 185 535 LOW 9 CODING SLC2A14 A protein_coding NM_001286237.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7967135 T A 0 222 0 0.1551 0.2885 0.2421 0.4831 0.2555 0.3354 0.177808 0.222376 0.245173 1 1898 31491 2415 3840 1728 16623 217 4770 2 9286 110632 10068 7668 6364 60780 838 15628 0.95987 0 . 0 COSM147411 93 11,33,9,26 SPLICE_SITE_REGION+INTRON(LOW||||535|SLC2A14|protein_coding|CODING|NM_001286237.1|9|A) 1 0.5 1 0 . 1 0 1 1 0 56 0 0.0577205 0.732391 0 0.617451 rs11055945 -0.693136 0.0288093 93 L297 535 ctG/ctA LOW 6 SILENT CODING SLC2A14 T protein_coding NM_001286237.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 7980178 C T 0 53 0 0.351 0.1607 0.098 0.1558 0.007 0.1115 0 . 0 1 1693 4039 704 659 20 138 16 809 2 9026 117630 10556 7980 6586 66598 890 15994 0.33919 0 . 0 . 124 43,37,3,16 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L297|535|SLC2A14|protein_coding|CODING|NM_001286237.1|6|T) 0 0.5 1 0 . 1 0 . 1 0 47 0 0.304755 0.200575 0 0.315294 rs1043712,rs59958086 -0.69168 0.406363 124 L12 535 ctC/ctG LOW 1 SILENT CODING SLC2A14 C protein_coding NM_001286237.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8043688 G C 0 32.6 0 0.913 0.8201 0.7651 0.8313 0.7763 0.7669 0 . 0 2 166 7879 65 104 2 1903 78 5561 2 194 10798 92 132 2 2754 118 7506 0 . 0 . 0 3 0,0,2,0 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L12|535|SLC2A14|protein_coding|CODING|NM_001286237.1|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs7297809 -0.453602 0.38 3 496 2001 MODIFIER 10 CODING SLC2A3 C protein_coding NM_006931.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8072008 T C 0 150 0 0.9032 0.9056 0.8833 0.9712 0.8767 0.8865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 14 0,0,0,14 UTR_3_PRIME(MODIFIER||2001||496|SLC2A3|protein_coding|CODING|NM_006931.2|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs12842 -0.686358 0.588227 14 496 LOW 8 CODING SLC2A3 T protein_coding NM_006931.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8077002 C T 0 11.1 0 . 0 . 0 . 0 . 0 . 1 133 368 28 107 0 6 3 91 2 9994 120248 11398 8282 6614 66700 898 16362 0.958844 0 . 0 . 67 37,12,0,9 SPLICE_SITE_REGION+INTRON(LOW||||496|SLC2A3|protein_coding|CODING|NM_006931.2|8|T) 0 0.5 1 0 . 0 . 0 1 0 43 0 0.0540125 0.000170247 0 0.491493 rs17847972,rs3931701 -0.662043 0.517352 67 496 136 MODIFIER 1 CODING SLC2A3 C protein_coding NM_006931.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8088766 T C 0 228 0 0.9697 0.9914 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 57 0,0,2,54 UTR_5_PRIME(MODIFIER||136||496|SLC2A3|protein_coding|CODING|NM_006931.2|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2541281 -0.693147 0.0200637 57 574 6576 MODIFIER 1 CODING FOXJ2 C protein_coding NM_018416.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8185853 A C 0 100 0 0.1611 0.2692 0.4813 0.0585 0.4751 0.2699 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.846482 0 . 0 . 17 9,0,7,1 UTR_5_PRIME(MODIFIER||6576||574|FOXJ2|protein_coding|CODING|NM_018416.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.055381 rs35297839 -0.651104 0.114068 17 237 43 MODIFIER 1 CODING CLEC4A T protein_coding NM_016184.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8276432 C T 0 228 0 0.4569 0.8121 0.9395 0.9752 0.9791 0.862 0.553563 0.840228 0.987093 2 5344 111279 11212 8159 6401 65053 859 14251 2 10208 119762 11458 8342 6588 65910 898 16358 0 . 0 . 0 73 0,0,53,7 START_GAINED(LOW||||237|CLEC4A|protein_coding|CODING|NM_016184.3|1|T),UTR_5_PRIME(MODIFIER||43||237|CLEC4A|protein_coding|CODING|NM_016184.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7295783 -0.693147 0.0100353 73 H36L 237 cAc/cTc MODERATE 2 MISSENSE CODING CLEC4A T protein_coding NM_016184.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8278181 A T 0 228 0 0.351 0.5096 0.5216 0.5208 0.6789 0.5297 0.403541 0.582424 0.67407 2 4052 72452 5148 4641 4173 45248 587 8603 2 10406 121358 11572 8638 6614 66712 908 16508 0 . 0 . 0 165 0,0,96,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cTc|H36L|237|CLEC4A|protein_coding|CODING|NM_016184.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2024301 -0.693147 0.00917553 165 R67W 300 Cgg/Tgg MODERATE 3 MISSENSE CODING ZNF705A T protein_coding NM_001004328.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8327883 C T 0 48.4 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.435975 0 . 0 . 974 265,293,149,86 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R67W|300|ZNF705A|protein_coding|CODING|NM_001004328.2|3|T) 0 0.5 1 0 . 0 . 0 . 0 32 0 0.000155725 8.64806e-11 0 0.948434 rs201454011 -0.693147 0.420535 974 464 180 MODIFIER 7 CODING FAM90A1 G protein_coding NM_018088.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8374238 T G 0 228 0 0.239 0.2919 0.2017 0.4276 0.2286 0.3528 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,5,5 UTR_3_PRIME(MODIFIER||180||464|FAM90A1|protein_coding|CODING|NM_018088.3|7|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 0.952347 0 . rs3825299 -0.670168 0.364597 11 T348I 464 aCa/aTa MODERATE 7 MISSENSE CODING FAM90A1 A protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8374770 G A 0 228 0 0.9523 0.9868 0.9971 1 0.999 1 0.963232 0.987381 0.999767 2 9820 119903 11553 8638 6612 65868 901 16511 2 10218 120336 11568 8638 6612 65886 902 16512 0 . 0 . 0 130 0,0,41,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T348I|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs9668474 -0.693147 0.000158147 130 T344TV 464 acg/acCGTg MODERATE 7 CODING FAM90A1 CACG protein_coding NM_018088.3 CODON_CHANGE_PLUS_CODON_INSERTION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8374781 C CACG 0 222 0 0.0802 0.4327 0.5101 0.5764 0.6968 0.4346 0.178153 0.525304 0.705424 1 1599 68584 4525 4338 4212 45779 537 7594 2 10000 118884 11480 8540 6518 64962 886 16498 0 . 0 . COSM943980 121 23,49,13,28 CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||acg/acCGTg|T344TV|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|CACG) 1 0.5 1 41 0.338843 1 1 1 1 0 59 0 0 0.972249 0 . rs71265055 -0.693145 0.0136583 121 P334L 464 cCg/cTg MODERATE 7 MISSENSE CODING FAM90A1 A protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8374812 G A 0 222 0 0.0983 0.226 0.1801 0.4087 0.1829 0.2873 0.086877 0.128227 0.149346 1 831 23159 2049 4039 1291 10044 184 4721 2 8978 115878 11394 8462 6482 63254 870 16438 0.334363 0 . 0 COSM1364570 84 8,25,13,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P334L|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|A) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.999711 0.961504 0 0.0544623 rs17855656 -0.693147 0.15434 84 S255R 464 agC/agA MODERATE 7 MISSENSE CODING FAM90A1 T protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8375048 G T 0 88 0 0.056 0.2121 0.1715 0.4107 0.175 0.2853 0 . 0 1 513 19980 1750 3318 1189 8467 161 4582 2 9188 116494 11374 8170 6532 63984 868 16378 6.17507e-05 0 . 0 . 271 131,46,36,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S255R|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|T) 0 0.5 1 0 . 1 0 . 1 0 52 0 3.42491e-25 0.0235408 0 0.266338 rs17857270 -0.693147 0.00113407 271 V254A 464 gTc/gCc MODERATE 7 MISSENSE CODING FAM90A1 G protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8375052 A G 0 132 0 0.0567 0.2125 0.1715 0.4117 0.175 0.2853 0.0254717 0.0489822 0.0609405 1 512 19984 1753 3328 1187 8461 160 4583 2 9180 115876 11336 8092 6514 63584 856 16314 0.99992 0 . 0 . 277 128,48,40,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V254A|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|G) 1 0.5 1 0 . 1 0 1 1 0 52 0 1.59712e-24 0.0253105 0 0.0433939 rs17857269 -0.693147 0.00174359 277 A234E 464 gCg/gAg MODERATE 7 MISSENSE CODING FAM90A1 T protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8375112 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 1635 23802 1925 3691 1264 10133 192 4962 2 9456 117712 11364 8350 6552 64684 888 16418 0.642712 0 . 0 . 384 112,110,83,42 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A234E|464|FAM90A1|protein_coding|CODING|NM_018088.3|7|T) 0 0.5 1 0 . 0 . 0 1 0 56 0 2.02055e-10 0.851603 0 4.92737e-06 rs9668582 -0.693147 2.02095e-07 384 R123G 464 Agg/Ggg MODERATE 6 MISSENSE CODING FAM90A1 C protein_coding NM_018088.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8376110 T C 0 228 0 0.2829 0.6829 0.6758 0.9802 0.8757 0.7239 0.345612 0.682805 0.855364 2 3385 94290 6575 8527 5599 57230 734 12240 2 9946 120688 11562 8652 6612 66510 900 16506 0 . 0 . 0 264 0,0,113,124 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R123G|464|FAM90A1|protein_coding|CODING|NM_018088.3|6|C) 1 0 . 0 . 1 0 1 1 0 57 0 0 0.186577 0 . rs9738115 -0.693147 0.312685 264 464 1095 MODIFIER 3 CODING FAM90A1 C protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8378523 A C 0 9.7 0 0.1233 0.2919 0.3213 0.5526 0.2505 0.273 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1095||464|FAM90A1|protein_coding|CODING|NM_018088.3|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2965685 -0.379885 0 1 464 1111 MODIFIER 3 CODING FAM90A1 G protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8378539 A G 0 9.7 0 0.8654 0.9487 0.964 0.9901 0.992 0.9632 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||1111||464|FAM90A1|protein_coding|CODING|NM_018088.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2953223 -0.379885 0 1 464 1507 MODIFIER 2 CODING FAM90A1 T protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8378935 A T 0 48.5 0 0.2322 0.5206 0.4928 0.8631 0.5755 0.5204 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,3,0 UTR_5_PRIME(MODIFIER||1507||464|FAM90A1|protein_coding|CODING|NM_018088.3|2|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2077467 -0.511536 0.228191 3 464 1539 MODIFIER 2 CODING FAM90A1 A protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8378967 G A 0 121 0 0.5469 0.7418 0.7378 0.9127 0.8042 0.7679 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_5_PRIME(MODIFIER||1539||464|FAM90A1|protein_coding|CODING|NM_018088.3|2|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2970173 -0.636426 0.291224 7 464 1570 MODIFIER 2 CODING FAM90A1 G protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8378998 A G 0 143 0 0.6074 0.7622 0.7522 0.9127 0.8131 0.771 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,11,0 UTR_5_PRIME(MODIFIER||1570||464|FAM90A1|protein_coding|CODING|NM_018088.3|2|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2953222 -0.676189 0.401428 11 464 2691 MODIFIER 1 CODING FAM90A1 T protein_coding NM_018088.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8380119 G T 0 107 0 0.2837 0.344 0.4164 0.4792 0.2425 0.3395 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.887766 0 . 0 . 17 10,0,6,1 START_GAINED(LOW||||464|FAM90A1|protein_coding|CODING|NM_018088.3|1|T),UTR_5_PRIME(MODIFIER||2691||464|FAM90A1|protein_coding|CODING|NM_018088.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.708895 rs2970176 -0.636426 0.656385 17 H155 198 caC/caT LOW 4 SILENT CODING AICDA A protein_coding NM_020661.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8757481 G A 0 177 0 0.2776 0.4842 0.6484 0.4812 0.6203 0.5102 0.336313 0.549351 0.643138 1 3166 70902 7640 4311 4020 42284 545 8936 2 9672 120086 11542 8586 6608 66332 896 16450 0.969596 0 . 0 . 39 3,17,2,16 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H155|198|AICDA|protein_coding|CODING|NM_020661.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0820061 rs2028373 -0.691153 0.00375154 39 386 15816 MODIFIER 1 CODING RIMKLB A protein_coding NM_001297776.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8850647 G A 0 9.7 0 0.0439 0.011781 0.0014 0 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 START_GAINED(LOW||||386|RIMKLB|protein_coding|CODING|NM_001297776.1|1|A),UTR_5_PRIME(MODIFIER||15816||386|RIMKLB|protein_coding|CODING|NM_001297776.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs74766418 -0.379885 0 1 D264 386 gaT/gaC LOW 6 SILENT CODING RIMKLB C protein_coding NM_001297776.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8926011 T C 0 228 0 0.9939 0.9984 1 1 1 1 0.995663 0.998412 0.999763 2 9766 120734 11576 8626 6614 66740 900 16512 2 9820 120788 11576 8626 6614 66740 900 16512 0 . 0 . 0 124 0,0,54,53 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D264|386|RIMKLB|protein_coding|CODING|NM_001297776.1|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2969089 -0.693147 0.000664772 124 386 426 MODIFIER 6 CODING RIMKLB T protein_coding NM_001297776.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 8926806 A T 0 148 0 0.9085 0.8504 0.8516 0.8998 0.7843 0.7883 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,3,4 UTR_3_PRIME(MODIFIER||426||386|RIMKLB|protein_coding|CODING|NM_001297776.1|6|T) 0 . 0 . 0 1 0 . 0 . 53 0 0 0.810265 0 . rs2969088 -0.636426 0.901494 7 P789 1454 ccG/ccA LOW 19 SILENT CODING A2ML1 A protein_coding NM_144670.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9004512 G A 0 228 0 0.6952 0.8682 0.9006 1 0.838 0.9744 0.738228 0.807824 0.840865 2 7128 105077 10825 8625 5432 56353 801 15913 2 9808 120774 11576 8626 6612 66740 900 16512 0 . 0 . COSM1364786 85 0,0,50,28 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P789|1454|A2ML1|protein_coding|CODING|NM_144670.5|19|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1860927 -0.693147 0.484763 85 D850E 1454 gaC/gaA MODERATE 20 MISSENSE CODING A2ML1 A protein_coding NM_144670.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9004892 C A 0 228 0 0.879 0.9661 0.9856 1 1 1 0.890411 0.964704 0.999761 2 8655 119537 11518 8626 6614 66719 898 16507 2 9804 120772 11576 8626 6614 66740 900 16512 0 . 0 . 0 60 0,0,22,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D850E|1454|A2ML1|protein_coding|CODING|NM_144670.5|20|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1860926 -0.693147 0.0211406 60 R1122W 1454 Cgg/Tgg MODERATE 28 MISSENSE CODING A2ML1 T protein_coding NM_144670.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9013755 C T 0 228 0 0.1067 0.4323 0.5231 0.7857 0.3867 0.4908 0.151854 0.30165 0.372653 2 1457 52176 7606 6767 2837 25077 385 8047 2 9802 120748 11572 8622 6612 66730 900 16510 0 . 0 . 0 117 0,0,48,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R1122W|1454|A2ML1|protein_coding|CODING|NM_144670.5|28|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1860967,rs386546824 -0.693147 0.421423 117 H1229R 1454 cAc/cGc MODERATE 29 MISSENSE CODING A2ML1 G protein_coding NM_144670.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9016573 A G 0 228 0 0.8843 0.9679 0.9885 1 1 1 0.900882 0.968115 0.999515 2 8801 119645 11516 8626 6614 66689 893 16506 2 9800 120720 11568 8626 6614 66706 896 16510 0 . 0 . 0 54 0,0,14,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H1229R|1454|A2ML1|protein_coding|CODING|NM_144670.5|29|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10219561 -0.693147 0.510534 54 M1257V 1454 Atg/Gtg MODERATE 30 MISSENSE CODING A2ML1 G protein_coding NM_144670.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9020489 A G 0 228 0 0.6316 0.8526 0.9035 1 0.8429 0.9734 0.645726 0.777458 0.839251 2 6239 103755 10756 8624 5473 55946 806 15911 2 9802 120770 11576 8626 6614 66740 900 16512 0 . 0 . 0 95 0,0,49,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M1257V|1454|A2ML1|protein_coding|CODING|NM_144670.5|30|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7308811 -0.693147 0.28838 95 Q1340 1454 caA/caG LOW 31 SILENT CODING A2ML1 G protein_coding NM_144670.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9020912 A G 0 222 0 0.6301 0.6777 0.6758 0.5427 0.7734 0.7843 0.644972 0.746482 0.794366 1 6193 88771 7112 4286 4464 52786 690 13240 2 9804 120742 11570 8616 6612 66734 898 16508 0.73885 0 . 0 COSM1364799 73 22,18,10,19 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1340|1454|A2ML1|protein_coding|CODING|NM_144670.5|31|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992638 rs1476910 -0.693079 0.128274 73 L31 1004 ctT/ctA LOW 2 SILENT CODING PHC1 A protein_coding NM_004426.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9070366 T A 0 222 0 0.5469 0.6877 0.5908 0.749 0.7167 0.8538 0.597367 0.681993 0.725349 1 5949 85178 6943 6442 4463 47222 652 13507 2 10048 118506 11058 8514 6460 65434 882 16110 0.966651 0 . 0 . 71 15,16,14,17 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L31|1004|PHC1|protein_coding|CODING|NM_004426.2|2|A) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.976472 0.979294 0 0.957237 rs4883198 -0.69311 0.693603 71 P123 1004 ccC/ccT LOW 5 SILENT CODING PHC1 T protein_coding NM_004426.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9074259 C T 0 222 0 0.3782 0.6334 0.5764 0.7202 0.7078 0.8528 0 . 0 1 4504 84197 7091 6267 4366 47505 662 13802 2 10390 121230 11534 8616 6596 66674 908 16512 0.166476 0 . 0 . 89 35,13,21,15 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P123|1004|PHC1|protein_coding|CODING|NM_004426.2|5|T) 0 0.5 1 0 . 1 0 . 1 0 59 0 0.948436 0.965321 0 0.995506 rs1805741 -0.693139 0.378947 89 Q389* 1004 Cag/Tag HIGH 8 NONSENSE CODING PHC1 T protein_coding NM_004426.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9085218 C T 0 18.6 0 . 0 . 0 . 0 . 0 . 1 7 477 126 293 0 12 7 32 2 10400 120330 11228 7998 6612 66704 904 16484 0.988483 0 . 0 COSM1606741 114 67,12,22,0 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q389*|1004|PHC1|protein_coding|CODING|NM_004426.2|8|T) 0 0.5 1 0 . 0 . 0 1 (PHC1|PHC1|1|1.00) 43 0 0.00338151 0.000794231 (PHC1|PHC1|1|1.00) 0.515111 rs201644380 -0.692562 0.0100782 114 T693A 1004 Act/Gct MODERATE 10 MISSENSE CODING PHC1 G protein_coding NM_004426.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9086898 A G 0 222 0 0.1551 0.3534 0.3818 0.4107 0.4274 0.4663 0.197004 0.359373 0.442558 1 1893 48203 4867 3426 2781 28134 372 6730 2 10376 120128 11442 8560 6538 66056 896 16260 0.346388 0 . 0 . 102 31,15,29,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T693A|1004|PHC1|protein_coding|CODING|NM_004426.2|10|G) 1 0.5 1 0 . 1 0 1 1 0 55 0 0.98826 0.402579 0 0.60717 rs1049925 -0.693147 0.515755 102 1004 946 MODIFIER 15 CODING PHC1 A protein_coding NM_004426.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9093001 G A 0 222 0 0.5416 0.4677 0.428 0.4077 0.4443 0.4816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.936869 0 . 0 . 97 43,6,27,7 UTR_3_PRIME(MODIFIER||946||1004|PHC1|protein_coding|CODING|NM_004426.2|15|A),UTR_3_PRIME(MODIFIER||1413||277|M6PR|protein_coding|CODING|NM_002355.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 53 0 9.23023e-05 0.993662 0 0.219731 rs56130437,rs6832 -0.693132 0.20469 97 277 1413 MODIFIER 7 CODING M6PR A protein_coding NM_002355.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9093001 G A 0 222 0 0.5416 0.4677 0.428 0.4077 0.4443 0.4816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.936869 0 . 0 . 97 43,6,27,7 UTR_3_PRIME(MODIFIER||946||1004|PHC1|protein_coding|CODING|NM_004426.2|15|A),UTR_3_PRIME(MODIFIER||1413||277|M6PR|protein_coding|CODING|NM_002355.3|7|A) 0 0.5 1 0 . 1 0 . 0 . 53 0 9.23023e-05 0.993662 0 0.219731 rs56130437,rs6832 -0.693132 0.20469 97 Y22 189 taT/taC LOW 1 SILENT CODING KLRG1 C protein_coding NM_005810.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9142297 T C 0 222 0 0.1377 0.3456 0.3775 0.3998 0.4334 0.4581 0.172719 0.353452 0.446047 1 1756 51219 5325 3465 3124 29973 395 7181 2 10334 121012 11524 8606 6608 66562 906 16472 0.577138 0 . 0 . 39 8,10,12,3 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y22|189|KLRG1|protein_coding|CODING|NM_005810.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980423 rs1805723 -0.688148 0.891107 39 D145 189 gaT/gaC LOW 4 SILENT CODING KLRG1 C protein_coding NM_005810.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9161648 T C 0 222 0 0.0545 0.2534 0.2997 0.379 0.2634 0.3497 0.0764866 0.223666 0.29907 1 776 35158 4525 3187 1744 19452 271 5203 2 10388 120856 11440 8576 6598 66520 906 16428 0.981834 0 . 0 . 64 10,14,7,23 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D145|189|KLRG1|protein_coding|CODING|NM_005810.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.770322 rs3026251 -0.693097 0.628724 64 189 763 MODIFIER 5 CODING KLRG1 T protein_coding NM_005810.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9162896 C T 0 55 0 0.0514 0.2522 0.2968 0.379 0.2634 0.3497 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,1,2 UTR_3_PRIME(MODIFIER||763||189|KLRG1|protein_coding|CODING|NM_005810.3|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs1805716 -0.511536 0.951887 4 I1000V 1474 Atc/Gtc MODERATE 24 MISSENSE CODING A2M C protein_coding NM_000014.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9232268 T C 0 222 0 0.329 0.2544 0.3919 0.0823 0.3191 0.1667 0.301956 0.319653 0.32821 1 3079 37096 4568 799 2685 22423 285 3257 2 9748 119582 11304 8582 6558 66200 882 16308 0.226787 2|255 benign|other 0 . 167 51,27,54,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I1000V|1474|A2M|protein_coding|CODING|NM_000014.4|24|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.977466 rs669 -0.693147 0.119542 167 N639D 1474 Aat/Gat MODERATE 16 MISSENSE CODING A2M C protein_coding NM_000014.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9248233 T C 0 228 0 0.9917 0.9978 1 1 1 1 0.992485 0.997653 1 2 9742 120708 11576 8626 6614 66738 900 16512 2 9802 120768 11576 8626 6614 66738 900 16512 0 . 0 . 0 161 0,0,61,74 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N639D|1474|A2M|protein_coding|CODING|NM_000014.4|16|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs226405 -0.693147 0.109976 161 1474 28 MODIFIER 1 CODING A2M C protein_coding NM_000014.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9268473 A C 0 222 0 0.8018 0.4732 0.5115 0.124 0.497 0.3374 0.759907 0.586266 0.504714 1 7438 57171 5559 1129 3399 33262 422 5962 2 9798 120288 11450 8566 6598 66504 896 16476 0.828818 0 . 0 . 105 24,31,15,21 UTR_5_PRIME(MODIFIER||28||1474|A2M|protein_coding|CODING|NM_000014.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.994015 rs226380 -0.693139 0.0371583 105 I1443N 1482 aTc/aAc MODERATE 34 MISSENSE CODING PZP T protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9303296 A T 0 222 0 0.1172 0.1905 0.3458 0.0655 0.2823 0.2137 0.141852 0.24481 0.297558 1 1456 32522 4081 619 2348 20412 242 3364 2 10398 121240 11524 8644 6598 66670 908 16498 0.764174 0 . 0 COSM147424,COSM147423 137 42,15,47,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I1443N|1482|PZP|protein_coding|CODING|NM_002864.2|34|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999465 rs10842971 -0.693147 0.159449 137 Q1356 1482 caA/caG LOW 31 SILENT CODING PZP C protein_coding NM_002864.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9305473 T C 0 222 0 0.5318 0.6552 0.5937 0.8899 0.6322 0.6472 0.554925 0.601569 0.625465 1 5676 77193 6967 7688 3973 41309 577 11003 2 10402 121366 11556 8648 6614 66726 908 16512 0.943617 0 . 0 . 89 17,26,17,21 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1356|1482|PZP|protein_coding|CODING|NM_002864.2|31|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.894089 rs10771357,rs386515060 -0.693143 0.0492673 89 T1205P 1482 Acc/Ccc MODERATE 29 MISSENSE CODING PZP G protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9307373 T G 0 228 0 0.9395 0.9834 0.9957 1 1 1 0.934635 0.977703 0.999767 2 9754 120694 11524 8654 6614 66734 906 16508 2 10404 121392 11562 8654 6614 66740 908 16510 0 . 0 . 0 160 0,0,67,67 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T1205P|1482|PZP|protein_coding|CODING|NM_002864.2|29|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2377741 -0.693147 0.00138097 160 G1200A 1482 gGg/gCg MODERATE 29 MISSENSE CODING PZP G protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9307387 C G 0 222 0 0 0.00059904 0 0.003 0 0 0 . 0 1 0 14 0 14 0 0 0 0 2 10378 121020 11494 8642 6588 66596 902 16420 0.697477 0 . 0 . 163 32,45,29,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G1200A|1482|PZP|protein_coding|CODING|NM_002864.2|29|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.866239 rs181999391 -0.693147 0.0148429 163 T1003M 1482 aCg/aTg MODERATE 24 MISSENSE CODING PZP A protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9312951 G A 0 222 0 0.1619 0.2708 0.2695 0.4762 0.1909 0.2894 0.161144 0.166539 0.169302 1 1692 25503 2806 4070 922 10957 200 4856 2 10406 121388 11578 8650 6612 66724 908 16510 0.999979 0 . 0 . 115 46,10,38,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1003M|1482|PZP|protein_coding|CODING|NM_002864.2|24|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.133098 rs57006764 -0.693147 0.0574421 115 V813A 1482 gTc/gCc MODERATE 19 MISSENSE CODING PZP G protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9317784 A G 0 222 0 0.3411 0.3862 0.2421 0.5357 0.3419 0.4407 0.332274 0.307627 0.295 1 3449 40000 2084 4798 1674 20050 316 7629 2 10406 121378 11576 8640 6614 66726 908 16508 0.435461 0 . 0 . 305 85,73,42,58 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V813A|1482|PZP|protein_coding|CODING|NM_002864.2|19|G) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.941648 0.616383 0 0.0411756 rs200958196,rs2277413 -0.693147 0.00935457 305 Q598* 1482 Caa/Taa HIGH 15 NONSENSE CODING PZP A protein_coding NM_002864.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9333626 G A 0 222 0 0.0008 0.015176 0 0.0704 0 0.0041 0 . 0 1 2 759 1 716 0 14 5 21 2 10374 121138 11514 8624 6608 66612 908 16498 0.989157 0 . 0 COSM249340,COSM249339 116 47,15,33,15 STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q598*|1482|PZP|protein_coding|CODING|NM_002864.2|15|A) 0 0.5 1 0 . 1 0 . 1 (PZP|PZP|1|1.00) 60 0 1 1 (PZP|PZP|1|1.00) 0.995646 rs117889746 -0.693147 0.0611981 116 G439 1482 ggT/ggC LOW 12 SILENT CODING PZP G protein_coding NM_002864.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9345273 A G 0 228 0 0.6868 0.8744 0.9395 0.9762 0.9274 0.9223 0.722197 0.852453 0.919186 2 7457 110519 11127 8441 6301 61036 847 15310 2 10402 121404 11576 8654 6614 66738 908 16512 0 . 0 . 0 160 0,0,50,92 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G439|1482|PZP|protein_coding|CODING|NM_002864.2|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10771407 -0.693147 0.193942 160 L379V 1482 Ctc/Gtc MODERATE 11 MISSENSE CODING PZP C protein_coding NM_002864.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9346792 G C 0 228 0 0.1876 0.2778 0.232 0.3819 0.3072 0.2945 0.181344 0.245963 0.27907 2 1889 32109 1960 3648 1560 17719 278 5055 2 10406 121370 11576 8638 6614 66718 908 16510 1 0 . 0 . 242 1,0,122,93 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L379V|1482|PZP|protein_coding|CODING|NM_002864.2|11|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs12230214 -0.693147 0.548386 242 I168T 225 aTa/aCa MODERATE 5 MISSENSE CODING KLRB1 G protein_coding NM_002258.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9750669 A G 0 228 0 0.1475 0.404 0.5029 0.5317 0.4205 0.5317 0.170527 0.340647 0.427906 2 1788 50308 5894 4441 3165 26391 392 8237 2 9622 112804 10858 8106 6364 61228 860 15766 0.466851 0 . 0 . 173 1,3,62,99 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I168T|225|KLRB1|protein_coding|CODING|NM_002258.2|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.609009 rs1135816 -0.693147 0.107211 173 194 1057 MODIFIER 6 CODING CLEC2D C protein_coding NM_001004419.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9848454 A C 0 55 0 0.7935 0.6861 0.7104 0.6349 0.6491 0.6145 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,1,6 UTR_3_PRIME(MODIFIER||1057||194|CLEC2D|protein_coding|CODING|NM_001004419.4|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11052488,rs78879891 -0.636426 0.936771 31 194 1060 MODIFIER 6 CODING CLEC2D C protein_coding NM_001004419.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9848457 A C 0 82 0 0.1339 0.4209 0.5245 0.5982 0.4781 0.4939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,2,6 UTR_3_PRIME(MODIFIER||1060||194|CLEC2D|protein_coding|CODING|NM_001004419.4|6|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs77724586 -0.651104 0.865149 31 194 1486 MODIFIER 6 CODING CLEC2D G protein_coding NM_001004419.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9848883 A G 0 228 0 0.0923 0.395 0.4769 0.5992 0.4404 0.4888 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 60 1,0,36,20 UTR_3_PRIME(MODIFIER||1486||194|CLEC2D|protein_coding|CODING|NM_001004419.4|6|G) 0 . 0 . 0 1 0 . 0 . 58 0 1 0.896193 0 1 rs2894 -0.693147 0.311512 60 194 1878 MODIFIER 6 CODING CLEC2D T protein_coding NM_001004419.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9849275 C T 0 140 0 0.0545 0.3846 0.4755 0.5992 0.4404 0.4877 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,0,11 UTR_3_PRIME(MODIFIER||1878||194|CLEC2D|protein_coding|CODING|NM_001004419.4|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs11052497 -0.676189 0.424842 11 194 4532 MODIFIER 6 CODING CLEC2D A protein_coding NM_001004419.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9851929 C A 0 9.7 0 0.0545 0.3672 0.4741 0.5972 0.4404 0.4018 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4532||194|CLEC2D|protein_coding|CODING|NM_001004419.4|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1044771 -0.379885 0 1 199 601 MODIFIER 5 CODING CD69 C protein_coding NM_001781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9905476 T C 0 228 0 0.4909 0.8598 0.9582 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 21 0,0,10,10 UTR_3_PRIME(MODIFIER||601||199|CD69|protein_coding|CODING|NM_001781.2|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7484445 -0.692067 0.123556 21 199 519 MODIFIER 5 CODING CD69 A protein_coding NM_001781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9905558 G A 0 228 0 0.3132 0.6965 0.7464 0.9643 0.7376 0.8609 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 43 0,0,40,3 UTR_3_PRIME(MODIFIER||519||199|CD69|protein_coding|CODING|NM_001781.2|5|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs386430755,rs704223 -0.693146 0.167798 43 199 226 MODIFIER 5 CODING CD69 C protein_coding NM_001781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9905851 A C 0 228 0 0.0552 0.3409 0.415 0.5923 0.3579 0.3978 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 50 0,0,16,33 UTR_3_PRIME(MODIFIER||226||199|CD69|protein_coding|CODING|NM_001781.2|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs917911 -0.693147 0.0393018 50 199 10 MODIFIER 5 CODING CD69 C protein_coding NM_001781.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 9906067 T C 0 228 0 0.3124 0.6937 0.7421 0.9643 0.7276 0.8609 0.394008 0.616503 0.730519 2 3829 85991 8714 8106 4797 46877 651 13017 2 9730 115146 10984 8482 6400 62892 882 15776 0 . 0 . 0 67 0,0,32,25 UTR_3_PRIME(MODIFIER||10||199|CD69|protein_coding|CODING|NM_001781.2|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1051065 -0.693147 0.146852 67 149 121 MODIFIER 5 CODING CLEC2B G protein_coding NM_005127.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10005778 A G 0 98 0 0.6316 0.5501 0.4625 0.4861 0.5726 0.545 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 7 2,0,4,1 UTR_3_PRIME(MODIFIER||121||149|CLEC2B|protein_coding|CODING|NM_005127.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs2594072 -0.590765 0.485334 7 149 119 MODIFIER 5 CODING CLEC2B A protein_coding NM_005127.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10005780 G A 0 92 0 0.8185 0.614 0.4957 0.4841 0.6103 0.5593 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.8 0 . 0 . 7 2,0,4,1 UTR_3_PRIME(MODIFIER||119||149|CLEC2B|protein_coding|CODING|NM_005127.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0 rs2539933 -0.590765 0.485334 7 149 LOW 1 CODING CLEC2B G protein_coding NM_005127.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10015177 A G 0 222 0 0.6626 0.5703 0.4856 0.4871 0.6064 0.5542 0.649515 0.601483 0.576923 1 4734 50192 4114 3250 2708 27083 379 7924 2 7130 85658 8688 6444 4856 44034 662 13844 0.999407 0 . 0 . 82 12,31,8,21 SPLICE_SITE_REGION+INTRON(LOW||||149|CLEC2B|protein_coding|CODING|NM_005127.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.486864 rs253146 -0.693079 0.184785 82 149 6978 MODIFIER 1 CODING CLEC2B G protein_coding NM_005127.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10022148 T G 0 9.7 0 0.3207 0.3876 0.2205 0.6587 0.166 0.545 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_5_PRIME(MODIFIER||6978||149|CLEC2B|protein_coding|CODING|NM_005127.2|1|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7313141 -0.379885 0 1 V68I 207 Gtc/Atc MODERATE 3 MISSENSE CODING KLRF2 A protein_coding NM_001190765.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10041364 G A 0 228 0 0.6218 0.7286 0.7478 0.7302 0.7724 0.8129 0 . 0 2 362 9610 142 147 2 2785 100 6072 2 560 12318 188 198 2 3624 132 7614 0 . 0 . 0 136 0,0,83,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V68I|207|KLRF2|protein_coding|CODING|NM_001190765.1|3|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1797517,rs386545506 -0.693147 0.263428 136 P131T 207 Cct/Act MODERATE 5 MISSENSE CODING KLRF2 A protein_coding NM_001190765.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10046052 C A 0 222 0 0.2995 0.5417 0.6556 0.4544 0.7018 0.7137 0 . 0 1 220 8196 123 83 3 2446 87 5234 2 554 12300 186 196 4 3614 132 7614 0.893594 0 . 0 . 55 22,7,12,7 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P131T|207|KLRF2|protein_coding|CODING|NM_001190765.1|5|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.948009 rs576601 -0.69168 0.36825 55 G136D 174 gGt/gAt MODERATE 4 MISSENSE CODING CLEC2A T protein_coding NM_001130711.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10069302 C T 0 222 0 0.5106 0.5258 0.5403 0.3085 0.675 0.6063 0.569364 0.634034 0.662162 1 1568 14474 238 227 1058 6250 172 4961 2 2822 22832 412 650 1632 9154 254 7908 0.752325 0 . 0 COSM467639 154 50,18,43,17 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G136D|174|CLEC2A|protein_coding|CODING|NM_001130711.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720707 rs526680 -0.693147 0.475241 154 H75 275 caC/caT LOW 4 SILENT CODING CLEC12A T protein_coding NM_001207010.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10131939 C T 0 219 0 0.0998 0.1933 0.1167 0.2222 0.1829 0.3548 0.0913221 0.139462 0.164108 1 673 14997 892 1186 724 7031 140 4351 2 4864 55592 4232 3892 3656 26516 516 11916 0.942454 0 . 0 . 36 15,4,8,3 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H75|275|CLEC12A|protein_coding|CODING|NM_001207010.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.967211 rs536947 -0.676189 0.237402 36 K254Q 275 Aaa/Caa MODERATE 7 MISSENSE CODING CLEC12A C protein_coding NM_001207010.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10137557 A C 0 228 0 0.6687 0.7374 0.6686 0.8998 0.5994 0.8538 0.644658 0.638064 0.63471 2 4036 40419 3651 4028 1890 17428 340 9046 2 5902 55884 5056 4460 2992 25884 474 11116 0 . 0 . 0 70 0,0,28,31 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K254Q|275|CLEC12A|protein_coding|CODING|NM_001207010.1|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs111169197,rs479499 -0.693147 0.0546446 70 275 20 MODIFIER 7 CODING CLEC12A G protein_coding NM_001207010.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10137645 T G 0 228 0 0.7292 0.7538 0.6744 0.8988 0.5994 0.8528 0.715128 0.677052 0.657584 2 2067 12961 310 642 107 5803 138 3894 2 2832 18436 450 718 154 9020 196 5066 0 . 0 . 0 28 0,0,3,24 UTR_3_PRIME(MODIFIER||20||275|CLEC12A|protein_coding|CODING|NM_001207010.1|7|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs588272 -0.693021 0.128979 28 229 LOW 4 CODING CLEC1B C protein_coding NM_016509.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10147850 T C 0 222 0 0.4085 0.3197 0.1888 0.2411 0.2594 0.4356 0.390296 0.298317 0.256548 1 3905 34311 1832 2027 1594 17991 275 6687 2 9692 120012 11500 8536 6596 66314 898 16476 0.485767 0 . 0 . 53 4,15,5,24 SPLICE_SITE_REGION+INTRON(LOW||||229|CLEC1B|protein_coding|CODING|NM_016509.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.87032 rs521040 -0.693079 0.227 53 G64D 229 gGt/gAt MODERATE 3 MISSENSE CODING CLEC1B T protein_coding NM_016509.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10149851 C T 0 228 0 0.9448 0.9848 0.9957 1 1 1 0.953501 0.985391 0.999634 2 9343 120180 11496 8624 6610 66708 896 16503 2 9800 120680 11526 8624 6610 66714 900 16506 0 . 0 . 0 79 0,0,22,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G64D|229|CLEC1B|protein_coding|CODING|NM_016509.3|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs583903 -0.693147 6.33941e-05 79 I20V 229 Atc/Gtc MODERATE 1 MISSENSE CODING CLEC1B C protein_coding NM_016509.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10151642 T C 0 228 0 0.9531 0.9874 0.9986 1 1 1 0.959217 0.987153 0.999755 2 9403 120324 11549 8626 6614 66728 898 16506 2 9800 120762 11576 8626 6614 66734 900 16512 0 . 0 . 0 54 0,0,39,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I20V|229|CLEC1B|protein_coding|CODING|NM_016509.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs612593 -0.693147 0.185788 54 229 64 MODIFIER 1 CODING CLEC1B TC protein_coding NM_016509.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10151762 T TC 0 124 0 0.5174 0.656 0.8084 0.751 0.7435 0.547 0.535348 0.677256 0.743742 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 40 5,18,2,12 UTR_5_PRIME(MODIFIER||64||229|CLEC1B|protein_coding|CODING|NM_016509.3|1|TC) 1 0.5 1 14 0.35 1 1 1 0 . 60 0 0 1 0 . rs11379994,rs72524065 -0.686358 0.521177 40 T59 276 acA/acG LOW 2 SILENT CODING CLEC12B G protein_coding NM_001129998.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10165469 A G 0 228 0 0.9191 0.9395 0.9582 0.9792 0.9225 0.9305 0.894235 0.908273 0.915465 2 9415 111787 11211 8418 5961 60612 832 15338 2 10406 121396 11576 8652 6614 66730 908 16510 0 . 0 . 0 130 0,0,68,46 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T59|276|CLEC12B|protein_coding|CODING|NM_001129998.1|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs476474 -0.693147 0.756641 130 V116L 276 Gta/Cta MODERATE 3 MISSENSE CODING CLEC12B C protein_coding NM_001129998.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10167277 G C 0 228 0 0.9191 0.9391 0.9582 0.9782 0.9225 0.9294 0.894235 0.907889 0.914884 2 9415 111682 11166 8417 5952 60564 832 15336 2 10402 121326 11534 8652 6612 66710 908 16508 0 . 0 . 0 115 0,0,61,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V116L|276|CLEC12B|protein_coding|CODING|NM_001129998.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs637790 -0.693147 0.0215346 115 241 LOW 7 CODING CLEC9A CTT protein_coding NM_207345.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10217326 C CTT 0 228 0 0.8298 0.9529 0.9841 1 1 1 0.872011 0.95607 0.999515 2 8997 119848 11513 8652 6614 66659 903 16510 2 10406 121344 11556 8652 6614 66696 908 16512 0 . 0 . 0 101 0,0,70,23 SPLICE_SITE_REGION+INTRON(LOW||||241|CLEC9A|protein_coding|CODING|NM_207345.3|7|CTT),DOWNSTREAM(MODIFIER||4826||280|CLEC1A|protein_coding|CODING|NM_016511.3||CTT) 1 0 . 95 0.940594 1 1 1 1 0 60 0 0 1 0 . rs10622534 -0.693147 0.00211749 101 280 1222 MODIFIER 6 CODING CLEC1A A protein_coding NM_016511.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10222710 G A 0 36.3 0 0.8109 0.9479 0.9841 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||1222||280|CLEC1A|protein_coding|CODING|NM_016511.3|6|A),DOWNSTREAM(MODIFIER||4081||241|CLEC9A|protein_coding|CODING|NM_207345.3||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4764228 -0.453602 0.84 2 280 1027 MODIFIER 6 CODING CLEC1A T protein_coding NM_016511.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10222905 C T 0 9.7 0 0.8079 0.9471 0.9841 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1027||280|CLEC1A|protein_coding|CODING|NM_016511.3|6|T),DOWNSTREAM(MODIFIER||4276||241|CLEC9A|protein_coding|CODING|NM_207345.3||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4764229 -0.379885 0 1 273 550 MODIFIER 6 CODING OLR1 T protein_coding NM_002543.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10311929 C T 0 15.2 0 0.1747 0.3191 0.5403 0.2381 0.5109 0.2434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 6 1,0,0,3 UTR_3_PRIME(MODIFIER||550||273|OLR1|protein_coding|CODING|NM_002543.3|6|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs17808009 -0.511536 0.93184 6 273 190 MODIFIER 6 CODING OLR1 A protein_coding NM_002543.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10312289 G A 0 179 0 0.1732 0.3187 0.5403 0.2381 0.5109 0.2434 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999781 0 . 0 . 30 6,11,3,10 UTR_3_PRIME(MODIFIER||190||273|OLR1|protein_coding|CODING|NM_002543.3|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.431008 rs1050283 -0.683931 0.676481 30 273 151 MODIFIER 6 CODING OLR1 A protein_coding NM_002543.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10312328 T A 0 228 0 0.9909 0.9972 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,15,13 UTR_3_PRIME(MODIFIER||151||273|OLR1|protein_coding|CODING|NM_002543.3|6|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4237962 -0.693054 0.580415 29 183 68 MODIFIER 6 CODING TMEM52B A protein_coding NM_001079815.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10342806 AC A 0 222 0 0.0053 0.2037 0.2205 0.4871 0.0765 0.2986 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 59 6,23,8,14 UTR_3_PRIME(MODIFIER||68||183|TMEM52B|protein_coding|CODING|NM_001079815.1|6|A) 0 0.5 1 23 0.38983 1 1 0 . 0 60 0 0 1 0 . rs11307497 -0.692562 0.0205537 59 183 272 MODIFIER 6 CODING TMEM52B A protein_coding NM_001079815.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10343011 G A 0 47 0 0.1309 0.3351 0.2925 0.6915 0.1928 0.4202 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,0,3 UTR_3_PRIME(MODIFIER||272||183|TMEM52B|protein_coding|CODING|NM_001079815.1|6|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs10431295 -0.511536 0.78654 4 183 354 MODIFIER 6 CODING TMEM52B T protein_coding NM_001079815.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10343093 G T 0 39.3 0 0.8283 0.9451 0.9712 1 0.9742 0.998 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||354||183|TMEM52B|protein_coding|CODING|NM_001079815.1|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4523782 -0.453602 0.32 2 117 155 MODIFIER 1 CODING GABARAPL1 G protein_coding NM_031412.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10365574 C G 0 153 0 0.3026 0.4177 0.3934 0.623 0.2753 0.5256 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 13 1,0,11,0 UTR_5_PRIME(MODIFIER||155||117|GABARAPL1|protein_coding|CODING|NM_031412.2|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 1 0 . 1 rs2302486 -0.676189 0.0888151 13 117 268 MODIFIER 4 CODING GABARAPL1 C protein_coding NM_031412.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10374719 T C 0 195 0 0.292 0.1428 0.062 0.1389 0.0209 0.1278 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999748 0 . 0 . 32 15,3,7,4 UTR_3_PRIME(MODIFIER||268||117|GABARAPL1|protein_coding|CODING|NM_031412.2|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.944766 rs11539 -0.676189 0.967041 32 S25A 179 Tct/Gct MODERATE 3 MISSENSE CODING KLRD1 G protein_coding NM_001114396.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10462052 T G 0 228 0 0.7655 0.9355 0.9813 1 1 1 0.77054 0.921959 0.999535 2 8021 118844 11451 8654 6614 66702 898 16504 2 10406 121404 11578 8654 6614 66734 908 16510 0 . 0 . 0 85 0,0,34,43 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S25A|179|KLRD1|protein_coding|CODING|NM_001114396.1|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10772256 -0.693147 0.370479 85 179 141 MODIFIER 7 CODING KLRD1 A protein_coding NM_001114396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10467533 T A 0 90 0 0.2489 0.4756 0.4697 0.4385 0.6163 0.68 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.333524 0 . 0 . 16 0,7,0,9 UTR_3_PRIME(MODIFIER||141||179|KLRD1|protein_coding|CODING|NM_001114396.1|7|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.914264 rs2537752 -0.662043 0.26398 16 179 862 MODIFIER 7 CODING KLRD1 G protein_coding NM_001114396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10468254 A G 0 9.7 0 0.1778 0.4563 0.4654 0.4395 0.6143 0.681 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||862||179|KLRD1|protein_coding|CODING|NM_001114396.1|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs12829155 -0.379885 0 1 179 1256 MODIFIER 7 CODING KLRD1 C protein_coding NM_001114396.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10468648 T C 0 9.7 0 0.9818 0.9946 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1256||179|KLRD1|protein_coding|CODING|NM_001114396.1|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7966660 -0.379885 0 1 216 69 MODIFIER 8 CODING KLRK1 G protein_coding NM_007360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10525644 A G 0 223 0 0.469 0.7157 0.7738 0.87 0.7068 0.8579 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,27,1 UTR_3_PRIME(MODIFIER||69||216|KLRK1|protein_coding|CODING|NM_007360.3|8|G),UTR_3_PRIME(MODIFIER||69||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|13|G),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1351113 -0.693054 0.533949 29 216 69 MODIFIER 13 CODING KLRC4-KLRK1 G protein_coding NM_001199805.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10525644 A G 0 223 0 0.469 0.7157 0.7738 0.87 0.7068 0.8579 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 29 0,0,27,1 UTR_3_PRIME(MODIFIER||69||216|KLRK1|protein_coding|CODING|NM_007360.3|8|G),UTR_3_PRIME(MODIFIER||69||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|13|G),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1351113 -0.693054 0.533949 29 T208 216 acG/acA LOW 8 SILENT CODING KLRK1 T protein_coding NM_007360.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10525740 C T 0 228 0 0.4652 0.7145 0.7723 0.872 0.7048 0.8579 0.503404 0.633631 0.700349 2 5197 88646 9928 7517 4744 47093 624 13543 2 10400 121386 11578 8654 6612 66726 908 16508 0 . 0 . 0 68 0,0,46,17 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T208|216|KLRK1|protein_coding|CODING|NM_007360.3|8|T),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T208|216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|13|T),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1049172 -0.693147 0.0474874 68 T208 216 acG/acA LOW 13 SILENT CODING KLRC4-KLRK1 T protein_coding NM_001199805.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10525740 C T 0 228 0 0.4652 0.7145 0.7723 0.872 0.7048 0.8579 0.503404 0.633631 0.700349 2 5197 88646 9928 7517 4744 47093 624 13543 2 10400 121386 11578 8654 6612 66726 908 16508 0 . 0 . 0 68 0,0,46,17 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T208|216|KLRK1|protein_coding|CODING|NM_007360.3|8|T),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T208|216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|13|T),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1049172 -0.693147 0.0474874 68 T72A 216 Aca/Gca MODERATE 4 MISSENSE CODING KLRK1 C protein_coding NM_007360.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10532326 T C 0 228 0 0.553 0.7624 0.8401 0.7857 0.8171 0.91 0.57921 0.724973 0.799651 2 6026 97349 10326 6543 5336 53776 723 14619 2 10342 121148 11566 8636 6608 66598 904 16494 0 . 0 . COSM430206 51 0,0,22,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T72A|216|KLRK1|protein_coding|CODING|NM_007360.3|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T72A|216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|9|C),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2255336 -0.693147 0.497941 51 T72A 216 Aca/Gca MODERATE 9 MISSENSE CODING KLRC4-KLRK1 C protein_coding NM_001199805.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10532326 T C 0 228 0 0.553 0.7624 0.8401 0.7857 0.8171 0.91 0.57921 0.724973 0.799651 2 6026 97349 10326 6543 5336 53776 723 14619 2 10342 121148 11566 8636 6608 66598 904 16494 0 . 0 . COSM430206 51 0,0,22,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T72A|216|KLRK1|protein_coding|CODING|NM_007360.3|4|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T72A|216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|9|C),INTRAGENIC(MODIFIER|||||LOC101928100||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2255336 -0.693147 0.497941 51 N104S 158 aAt/aGt MODERATE 3 MISSENSE CODING KLRC4 C protein_coding NM_013431.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10560957 T C 0 228 0 0.4327 0.5567 0.6671 0.5496 0.663 0.544 0.477727 0.610512 0.678638 2 4812 75468 7352 4611 4262 44738 541 9152 2 10170 119674 11414 8578 6542 65738 894 16338 1 0 . 0 COSM1358386 106 1,0,49,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N104S|158|KLRC4|protein_coding|CODING|NM_013431.2|3|C),UTR_5_PRIME(MODIFIER||19548||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2617170 -0.693147 0.000866861 106 216 19548 MODIFIER 3 CODING KLRC4-KLRK1 C protein_coding NM_001199805.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10560957 T C 0 228 0 0.4327 0.5567 0.6671 0.5496 0.663 0.544 0.477727 0.610512 0.678638 2 4812 75468 7352 4611 4262 44738 541 9152 2 10170 119674 11414 8578 6542 65738 894 16338 1 0 . 0 COSM1358386 106 1,0,49,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N104S|158|KLRC4|protein_coding|CODING|NM_013431.2|3|C),UTR_5_PRIME(MODIFIER||19548||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|3|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2617170 -0.693147 0.000866861 106 S50 158 tcG/tcA LOW 1 SILENT CODING KLRC4 T protein_coding NM_013431.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10562025 C T 0 228 0 0.208 0.494 0.6311 0.5605 0.663 0.5409 0.289055 0.546293 0.678023 2 2861 74133 7337 4727 4306 45254 546 9102 2 10400 121386 11574 8654 6614 66726 908 16510 1 0 . 0 . 195 1,0,99,69 SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S50|158|KLRC4|protein_coding|CODING|NM_013431.2|1|T),INTRON(MODIFIER||||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1841957,rs386546399 -0.693147 0.0205713 195 I29S 158 aTc/aGc MODERATE 1 MISSENSE CODING KLRC4 C protein_coding NM_013431.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10562089 A C 0 228 0 0.6558 0.737 0.8012 0.7431 0.6789 0.8548 0.651384 0.672766 0.683721 2 6814 87246 9953 6224 4536 45702 609 13408 2 10402 121382 11572 8646 6614 66730 908 16510 1 0 . 0 . 178 0,1,68,90 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aGc|I29S|158|KLRC4|protein_coding|CODING|NM_013431.2|1|C),INTRON(MODIFIER||||216|KLRC4-KLRK1|protein_coding|CODING|NM_001199805.1|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1841958 -0.693147 0.0157923 178 C155S 257 tGt/tCt MODERATE 4 MISSENSE CODING KLRC3 G protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10570965 C G 0 228 0 0.9539 0.9868 0.9928 1 1 1 0.955969 0.985084 1 2 9886 120824 11553 8654 6614 66705 906 16506 2 10396 121364 11578 8654 6614 66708 908 16506 0 . 0 . 0 236 0,0,142,68 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C155S|257|KLRC3|protein_coding|CODING|NM_007333.2|4|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.972949 0 . rs2682495 -0.693147 0.184316 236 Y129 257 taT/taC LOW 4 SILENT CODING KLRC3 G protein_coding NM_007333.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10571042 A G 0 228 0 0.9539 0.9866 0.9928 1 0.999 1 0 . 0 2 9875 120796 11553 8654 6614 66685 905 16510 2 10386 121366 11578 8654 6614 66716 908 16510 0 . 0 . 0 260 0,0,132,92 SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y129|257|KLRC3|protein_coding|CODING|NM_007333.2|4|G) 0 . 0 . 0 1 0 . 1 0 57 0 0 0.798069 0 . rs2741882 -0.693147 0.00640544 260 H113P 257 cAt/cCt MODERATE 4 MISSENSE CODING KLRC3 G protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10571091 T G 0 228 0 0.9539 0.9862 0.9914 1 0.998 1 0 . 0 2 9804 120471 11532 8641 6603 66538 899 16454 2 10320 121150 11572 8644 6612 66634 902 16466 0 . 0 . 0 217 0,0,76,127 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H113P|257|KLRC3|protein_coding|CODING|NM_007333.2|4|G) 0 . 0 . 0 1 0 . 1 0 56 0 0 0.112644 0 . rs2682494 -0.693147 0.0470391 217 T108 257 acC/acG LOW 3 SILENT CODING KLRC3 C protein_coding NM_007333.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10571650 G C 0 122 0 0.9062 0.973 0.987 0.999 0.999 1 0 . 0 2 74 533 33 48 8 354 4 12 2 1036 1554 82 48 8 360 8 12 0 . 0 . 0 8 0,0,1,7 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T108|257|KLRC3|protein_coding|CODING|NM_007333.2|3|C) 0 . 0 . 0 1 0 . 1 0 42 0 0 1 0 . rs28521176 -0.651104 0.0576189 8 A106T 257 Gca/Aca MODERATE 3 MISSENSE CODING KLRC3 T protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10571658 C T 0 141 0 0.9054 0.9722 0.987 0.998 0.999 0.998 0 . 0 2 131 846 43 70 36 522 10 34 2 1080 1854 92 70 36 528 14 34 0 . 0 . 0 9 0,0,1,8 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A106T|257|KLRC3|protein_coding|CODING|NM_007333.2|3|T) 0 . 0 . 0 1 0 . 1 0 41 0 0 1 0 . rs28626640 -0.662043 0.115419 9 E69 257 gaA/gaG LOW 2 SILENT CODING KLRC3 C protein_coding NM_007333.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10572544 T C 0 125 0 . 0 . 0 . 0 . 0 . 2 436 2449 155 170 14 1418 28 228 2 1406 3474 200 170 14 1424 32 228 0 . 0 . 0 7 0,0,7,0 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E69|257|KLRC3|protein_coding|CODING|NM_007333.2|2|C) 0 . 0 . 0 . 0 . 1 0 59 0 0 . 0 . rs143188402 -0.636426 0.166446 7 D56 257 gaT/gaC LOW 1 SILENT CODING KLRC3 G protein_coding NM_007333.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10572982 A G 0 228 0 0.9539 0.9868 0.9928 1 1 1 0.955742 0.984853 0.999767 2 9891 120826 11551 8650 6614 66709 906 16505 2 10402 121370 11576 8650 6614 66714 908 16506 0 . 0 . 0 145 0,0,98,36 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D56|257|KLRC3|protein_coding|CODING|NM_007333.2|1|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.634591 0 . rs2741881 -0.693147 0.655702 145 W19S 257 tGg/tCg MODERATE 1 MISSENSE CODING KLRC3 G protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10573094 C G 0 118 0 0.2012 0.4435 0.5576 0.5159 0.5785 0.4765 0 . 0 2 2643 61857 5830 3788 3797 36979 460 8360 2 10248 114592 10768 8154 6274 62236 864 16048 0.997235 0 . 0 . 74 8,1,1,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W19S|257|KLRC3|protein_coding|CODING|NM_007333.2|1|G) 0 . 0 . 0 1 0 . 1 0 44 0 0.218256 0.116033 0 0.0542036 rs2682491 -0.693147 0.0135736 74 W19R 257 Tgg/Cgg MODERATE 1 MISSENSE CODING KLRC3 G protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10573095 A G 0 228 0 0.9508 0.9856 0.9928 0.999 0.999 1 0 . 0 2 9766 120449 11520 8627 6598 66569 900 16469 2 10282 121004 11544 8628 6598 66580 902 16470 0 . 0 . 0 73 0,0,9,64 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W19R|257|KLRC3|protein_coding|CODING|NM_007333.2|1|G) 0 . 0 . 0 1 0 . 1 0 44 0 0 0.127333 0 . rs2682490,rs77715293 -0.693147 0.0717543 73 S2N 257 aGt/aAt MODERATE 1 MISSENSE CODING KLRC3 T protein_coding NM_007333.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10573145 C T 0 115 0 . 0 . 0 . 0 . 0 . 1 6695 65406 6308 4829 3674 35249 483 8168 2 9502 114396 11258 8190 6548 64310 848 13740 0.049215 0 . 0 . 59 11,1,1,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S2N|257|KLRC3|protein_coding|CODING|NM_007333.2|1|T) 0 0.5 1 0 . 0 . 0 1 0 33 0 0.996234 0.896711 0 0.976691 rs2682489 -0.693145 0.188953 59 231 105 MODIFIER 6 CODING KLRC2 T protein_coding NM_002260.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10583611 C T 0 200 0 0.3275 0.6122 0.7219 0.7252 0.7903 0.6196 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 27 0,0,26,1 UTR_3_PRIME(MODIFIER||105||231|KLRC2|protein_coding|CODING|NM_002260.3|6|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3003 -0.693021 0.0826751 27 231 20 MODIFIER 6 CODING KLRC2 T protein_coding NM_002260.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10583696 C T 0 228 0 0.2489 0.483 0.5922 0.7113 0.5298 0.4387 0.259395 0.451558 0.546573 2 2478 60206 6824 5552 3687 34236 431 6998 2 9466 114416 11290 7898 6258 62804 850 15850 0 . 0 . 0 129 0,0,111,9 UTR_3_PRIME(MODIFIER||20||231|KLRC2|protein_coding|CODING|NM_002260.3|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2981593 -0.693147 0.000466147 129 F102S 231 tTt/tCt MODERATE 3 MISSENSE CODING KLRC2 G protein_coding NM_002260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10587111 A G 0 228 0 . 0 . 0 . 0 . 0 . 2 6600 99107 8862 7012 5630 58132 741 12130 2 10324 121160 11568 8644 6608 66616 906 16494 0 . 0 . 0 375 0,0,161,158 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F102S|231|KLRC2|protein_coding|CODING|NM_002260.3|3|G) 0 . 0 . 0 . 0 . 1 0 56 0 0 0.99735 0 . rs1141715,rs61917677 -0.693147 0.000243435 375 231 LOW 1 CODING KLRC2 T protein_coding NM_002260.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10588012 G T 0 89 0 . 0 . 0 . 0 . 0 . 1 0 102 2 45 3 41 0 11 2 10404 121384 11576 8652 6614 66722 908 16508 0.940001 0 . 0 . 286 60,143,19,32 SPLICE_SITE_REGION+INTRON(LOW||||231|KLRC2|protein_coding|CODING|NM_002260.3|1|T) 0 0.5 1 0 . 0 . 0 1 0 38 0 0.700194 1.85563e-09 0 0.887183 rs368882379 -0.693147 4.24149e-06 286 R19P 231 cGg/cCg MODERATE 1 MISSENSE CODING KLRC2 G protein_coding NM_002260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10588530 C G 0 47.3 0 . 0 . 0 . 0 . 0 . 1 2422 49824 4959 3367 2885 29593 371 6227 2 10380 120988 11560 8638 6608 66634 900 16268 0.44566 0 . 0 COSM1628343 156 36,76,25,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R19P|231|KLRC2|protein_coding|CODING|NM_002260.3|1|G) 0 0.5 1 0 . 0 . 0 1 0 55 0 0.6907 0.0161571 0 0.86095 rs75545535 -0.692976 0.0856421 156 N2S 231 aAt/aGt MODERATE 1 MISSENSE CODING KLRC2 C protein_coding NM_002260.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10588581 T C 0 222 0 . 0 . 0 . 0 . 0 . 1 2153 47401 4520 3070 2832 27995 368 6463 2 10120 118626 11142 8330 6552 65266 896 16320 0.175224 0 . 0 . 113 23,9,11,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N2S|231|KLRC2|protein_coding|CODING|NM_002260.3|1|C) 0 0.5 1 0 . 0 . 0 1 0 52 0 0.159626 0.801498 0 0.997003 rs28403159 -0.693147 0.00111763 113 N29S 233 aAc/aGc MODERATE 2 MISSENSE CODING KLRC1 C protein_coding NM_002259.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10603670 T C 0 228 0 0.9546 0.987 0.9928 1 1 1 0.957104 0.985468 1 2 9906 120867 11556 8648 6614 66727 906 16510 2 10402 121390 11578 8648 6614 66730 908 16510 0 . 0 . 0 115 0,0,49,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N29S|233|KLRC1|protein_coding|CODING|NM_002259.4|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2253849 -0.693147 0.215762 115 148 2262 MODIFIER 5 CODING MAGOHB C protein_coding NM_018048.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10756612 T C 0 32.6 0 0.5492 0.7776 0.8228 0.9901 0.7724 0.8405 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2262||148|MAGOHB|protein_coding|CODING|NM_018048.3|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs10772332 -0.379885 0 2 148 1166 MODIFIER 5 CODING MAGOHB T protein_coding NM_018048.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10757708 A T 0 9.7 0 0.5348 0.757 0.7882 0.9931 0.7117 0.8384 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1166||148|MAGOHB|protein_coding|CODING|NM_018048.3|5|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4763563 -0.379885 0 1 148 346 MODIFIER 5 CODING MAGOHB G protein_coding NM_018048.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10758528 A G 0 5.7 0 0.264 0.358 0.4107 0.1974 0.5258 0.4407 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 11 7,1,2,0 UTR_3_PRIME(MODIFIER||346||148|MAGOHB|protein_coding|CODING|NM_018048.3|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.3125 rs9988929 -0.453602 0.36 11 148 171 MODIFIER 5 CODING MAGOHB G protein_coding NM_018048.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10758703 A G 0 228 0 0.7995 0.8498 0.853 0.9931 0.7753 0.8446 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 121 0,0,90,12 UTR_3_PRIME(MODIFIER||171||148|MAGOHB|protein_coding|CODING|NM_018048.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1052871 -0.693147 0.00139272 121 V46 148 gtC/gtG LOW 2 SILENT CODING MAGOHB C protein_coding NM_018048.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10763236 G C 0 228 0 0.413 0.7408 0.8184 0.9901 0.7724 0.8395 0.496142 0.69606 0.798603 2 4866 92489 10183 8394 5311 49989 675 13071 2 10072 117120 11340 8468 6478 63702 892 16168 0 . 0 . 0 25 0,0,17,2 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtG|V46|148|MAGOHB|protein_coding|CODING|NM_018048.3|2|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10845182 -0.69168 0.000443728 25 S204G 422 Agc/Ggc MODERATE 6 MISSENSE CODING STYK1 C protein_coding NM_018423.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10782115 T C 0 228 0 0.3457 0.5986 0.7032 0.7917 0.6431 0.6217 0.379936 0.518145 0.588953 2 3841 75401 8915 6919 4532 40283 579 10332 2 10372 120988 11534 8616 6584 66498 898 16486 0.297297 0 . 0 . 83 2,0,40,34 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S204G|422|STYK1|protein_coding|CODING|NM_018423.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.77027 rs3759259 -0.693147 0.122808 83 372 2115 MODIFIER 10 CODING YBX3 T protein_coding NM_003651.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10851772 A T 0 222 0 0.1135 0.2642 0.2565 0.4881 0.1899 0.319 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.521386 0 . 0 . 192 36,52,36,53 UTR_3_PRIME(MODIFIER||2115||372|YBX3|protein_coding|CODING|NM_003651.4|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.939419 rs7270 -0.693147 0.0282522 192 372 1781 MODIFIER 10 CODING YBX3 C protein_coding NM_003651.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10852106 T C 0 222 0 0.1634 0.273 0.281 0.2599 0.2863 0.4151 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.845023 0 . 0 . 139 50,23,42,12 UTR_3_PRIME(MODIFIER||1781||372|YBX3|protein_coding|CODING|NM_003651.4|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.562405 rs17629 -0.693147 0.471384 139 T75A 372 Acc/Gcc MODERATE 1 MISSENSE CODING YBX3 C protein_coding NM_003651.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10875488 T C 0 51 0 0.1445 0.2833 0.2824 0.5069 0.1779 0.3497 0.119527 0.123999 0.126289 1 784 17379 3008 2613 393 6922 103 3556 2 3376 55594 6476 4948 1906 29410 378 9100 1 0 . 0 . 5 1,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Gcc|T75A|372|YBX3|protein_coding|CODING|NM_003651.4|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1126501 -0.453602 0.1 5 M308V 309 Atg/Gtg MODERATE 1 MISSENSE CODING TAS2R8 C protein_coding NM_023918.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10958658 T C 0 228 0 0.5635 0.8734 0.951 1 0.997 0.9796 0.636239 0.873066 0.9945 2 5790 113558 11206 8626 6562 64758 862 15754 2 9326 118078 11436 8626 6562 65086 888 16154 0 . 0 . 0 87 0,0,58,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M308V|309|TAS2R8|protein_coding|CODING|NM_023918.1|1|C),UPSTREAM(MODIFIER||3432||318|TAS2R7|protein_coding|CODING|NM_023919.2||C),DOWNSTREAM(MODIFIER||3035||312|TAS2R9|protein_coding|CODING|NM_023917.2||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2537817 -0.693147 0.136078 87 L183 309 ttG/ttA LOW 1 SILENT CODING TAS2R8 T protein_coding NM_023918.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10959031 C T 0 222 0 0.1641 0.504 0.5692 0.6448 0.6789 0.592 0.232864 0.477933 0.603488 1 2336 70584 6502 5725 4550 41065 580 9826 2 10364 120992 11458 8624 6600 66546 908 16492 0.501924 0 . 0 . 169 66,20,47,17 SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L183|309|TAS2R8|protein_coding|CODING|NM_023918.1|1|T),UPSTREAM(MODIFIER||3805||318|TAS2R7|protein_coding|CODING|NM_023919.2||T),DOWNSTREAM(MODIFIER||2662||312|TAS2R9|protein_coding|CODING|NM_023917.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940725 rs1548803 -0.693147 0.00198095 169 V187A 312 gTg/gCg MODERATE 1 MISSENSE CODING TAS2R9 G protein_coding NM_023917.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10962115 A G 0 222 0 0.1982 0.531 0.5749 0.7183 0.6839 0.5992 0.260554 0.493311 0.612558 1 2641 72169 6548 6228 4573 41661 596 9922 2 10338 121010 11416 8626 6612 66616 906 16496 0.996986 0 . 0 . 155 35,44,30,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V187A|312|TAS2R9|protein_coding|CODING|NM_023917.2|1|G),UPSTREAM(MODIFIER||2536||309|TAS2R8|protein_coding|CODING|NM_023918.1||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955685 rs3741845 -0.693147 0.0891934 155 T156M 307 aCg/aTg MODERATE 1 MISSENSE CODING TAS2R10 A protein_coding NM_023921.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10978402 G A 0 228 0 0.8101 0.9429 0.9841 1 0.997 0.9785 0.83144 0.939781 0.99534 2 8571 118158 11288 8638 6598 66121 889 16053 2 10282 120744 11408 8638 6598 66422 904 16492 0 . 0 . 0 114 0,0,35,74 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T156M|307|TAS2R10|protein_coding|CODING|NM_023921.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs597468 -0.693147 0.000821217 114 Q120R 134 cAg/cGg MODERATE 3 MISSENSE CODING PRR4 C protein_coding NM_007244.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10999708 T C 0 228 0 0.3684 0.7374 0.8501 0.9196 0.8429 0.8599 0.465352 0.71157 0.828106 2 4225 98848 10315 8070 5914 55654 764 13906 2 9796 120236 11570 8624 6614 66594 896 16142 0 . 0 . 0 111 0,0,76,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q120R|134|PRR4|protein_coding|CODING|NM_007244.2|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1047699 -0.693147 0.133047 111 R96Q 134 cGa/cAa MODERATE 3 MISSENSE CODING PRR4 T protein_coding NM_007244.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 10999780 C T 0 222 0 0.1354 0.5218 0.621 0.7093 0.6252 0.6738 0.209669 0.458387 0.5792 1 1984 71174 7594 6194 4186 39447 570 11199 2 9802 120694 11576 8606 6614 66716 900 16480 0.291519 0 . 0 . 149 38,34,40,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R96Q|134|PRR4|protein_coding|CODING|NM_007244.2|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.82305 rs1063193 -0.693147 0.0777809 149 R153C 200 Cgt/Tgt MODERATE 5 MISSENSE CODING PRH1 A protein_coding NM_001291315.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11034980 G A 0 222 0 . 0 . 0 . 0 0.115949 0.147937 0.164492 1 1622 21918 2382 1578 1477 12342 147 2370 2 9350 110302 10904 7900 6258 61012 818 14060 0.841948 0 . 0 . 91 35,22,19,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R153C|200|PRH1|protein_coding|CODING|NM_001291315.1|5|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 0 . 1 1 0 40 0 0.304406 5.32147e-13 0 0.825452 rs61914782 -0.693132 0.66022 91 Q110 200 caA/caG LOW 5 SILENT CODING PRH1 C protein_coding NM_001291315.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11035107 T C 0 30.3 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.997325 0 . 0 . 13 7,1,5,0 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q110|200|PRH1|protein_coding|CODING|NM_001291315.1|5|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 0 0.5 1 0 . 0 . 0 . 0 30 0 0.765017 1 0 0.0137638 rs2946841 -0.590765 0.00328272 13 L55I 200 Cta/Ata MODERATE 5 MISSENSE CODING PRH1 T protein_coding NM_001291315.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11035274 G T 0 180 0 0.1256 0.4704 0.5432 0.6806 0.5716 0.5644 0 . 0 1 633 24630 2304 2478 1711 14229 214 3061 2 9282 81944 7136 5360 4290 45672 598 9606 0.521317 0 . 0 . 118 33,38,17,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L55I|200|PRH1|protein_coding|CODING|NM_001291315.1|5|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 0 0.5 1 0 . 1 0 . 1 0 47 0 8.12859e-11 0.0168326 0 0.767168 rs28607516 -0.693143 0.991453 118 N259S 303 aAc/aGc MODERATE 1 MISSENSE CODING TAS2R13 C protein_coding NM_023920.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11061122 T C 0 222 0 0.1528 0.5204 0.5908 0.7242 0.6243 0.6503 0.219473 0.459173 0.581977 1 2170 70717 7235 6287 4282 39302 574 10867 2 10312 120820 11436 8614 6590 66470 902 16496 0.469306 0 . 0 . 109 37,11,27,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N259S|303|TAS2R13|protein_coding|CODING|NM_023920.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0318638 rs1015443 -0.693147 0.00446678 109 N66D 166 Aat/Gat MODERATE 3 MISSENSE CODING PRH2 G protein_coding NM_001110213.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11083356 A G 0 222 0 . 0 . 0 . 0 . 0 . 1 345 2894 229 135 72 1844 17 252 2 9692 112106 10582 8194 5964 61544 816 15314 0.788834 0 . 0 . 125 43,30,27,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N66D|166|PRH2|protein_coding|CODING|NM_001110213.1|3|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 0 0.5 1 0 . 0 . 0 1 0 50 0 0.117623 0.685691 0 0.927934 rs116998526 -0.693147 0.976332 125 166 LOW 3 CODING PRH2 C protein_coding NM_001110213.1 SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11083677 T C 0 228 0 0.5106 0.7825 0.8501 0.9226 0.8668 0.8712 0.482452 0.696799 0.806882 2 4594 91060 10018 7911 5994 52060 713 9770 2 9064 108910 11234 8450 6536 61522 804 11300 1 0 . 0 . 57 1,0,35,16 SPLICE_SITE_REGION(LOW||||166|PRH2|protein_coding|CODING|NM_001110213.1|3|C),UTR_3_PRIME(MODIFIER||16||166|PRH2|protein_coding|CODING|NM_001110213.1|3|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 55 0 1 0.101018 0 1 rs10772391,rs56288219 -0.693147 0.117343 57 166 16 MODIFIER 3 CODING PRH2 C protein_coding NM_001110213.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11083677 T C 0 228 0 0.5106 0.7825 0.8501 0.9226 0.8668 0.8712 0.482452 0.696799 0.806882 2 4594 91060 10018 7911 5994 52060 713 9770 2 9064 108910 11234 8450 6536 61522 804 11300 1 0 . 0 . 57 1,0,35,16 SPLICE_SITE_REGION(LOW||||166|PRH2|protein_coding|CODING|NM_001110213.1|3|C),UTR_3_PRIME(MODIFIER||16||166|PRH2|protein_coding|CODING|NM_001110213.1|3|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0 . 0 . 1 0 1 1 0 55 0 1 0.101018 0 1 rs10772391,rs56288219 -0.693147 0.117343 57 R125 317 agG/agA LOW 1 SILENT CODING TAS2R14 T protein_coding NM_023922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11091432 C T 0 228 0 0.5015 0.7758 0.8444 0.9226 0.8638 0.8558 0.55379 0.742347 0.838995 2 5479 101926 10327 8111 6071 56736 803 14399 2 10250 120910 11500 8624 6604 66542 906 16484 0 . 0 . 0 106 0,0,47,49 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R125|317|TAS2R14|protein_coding|CODING|NM_023922.1|1|T),DOWNSTREAM(MODIFIER||3988||166|PRH2|protein_coding|CODING|NM_001110213.1||T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|4|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3741843 -0.693147 0.0301874 106 G38 317 ggA/ggT LOW 1 SILENT CODING TAS2R14 A protein_coding NM_023922.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11091693 T A 0 222 0 0.2337 0.223 0.2911 0.2073 0.2147 0.1851 0.223332 0.234968 0.24093 1 2296 29155 3588 1904 1770 16334 209 3054 2 10360 120724 11438 8642 6590 66364 904 16426 0.961516 0 . 0 . 100 18,26,16,27 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G38|317|TAS2R14|protein_coding|CODING|NM_023922.1|1|A),DOWNSTREAM(MODIFIER||4249||166|PRH2|protein_coding|CODING|NM_001110213.1||A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|3|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|4|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997696 rs7138535 -0.693146 0.385973 100 P259 299 ccG/ccA LOW 1 SILENT CODING TAS2R50 T protein_coding NM_176890.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11138683 C T 0 222 0 0.1755 0.5471 0.6009 0.755 0.6571 0.684 0.244212 0.485314 0.608837 1 2472 73946 7476 6499 4328 41234 588 11349 2 10374 121298 11560 8638 6610 66698 908 16510 0.727849 0 . 0 . 148 38,26,44,25 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P259|299|TAS2R50|protein_coding|CODING|NM_176890.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.702805 rs10772397 -0.693147 0.00502774 148 C203Y 299 tGt/tAt MODERATE 1 MISSENSE CODING TAS2R50 T protein_coding NM_176890.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11138852 C T 0 222 0 0.056 0.4103 0.3775 0.755 0.3579 0.6115 0.0953246 0.253575 0.334651 1 969 48155 5188 6505 2191 23030 378 9894 2 10404 121366 11568 8646 6610 66724 906 16508 0.757048 0 . 0 . 146 33,33,32,37 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C203Y|299|TAS2R50|protein_coding|CODING|NM_176890.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.698382 rs1376251,rs386529788 -0.693147 0.273501 146 309 155 MODIFIER 1 CODING TAS2R20 G protein_coding NM_176889.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11149390 T G 0 5.7 0 0.0635 0.1655 0.2305 0.1964 0.2058 0.184 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.75 0 . 0 . 4 2,0,2,0 UTR_3_PRIME(MODIFIER||155||309|TAS2R20|protein_coding|CODING|NM_176889.2|1|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|G),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.5 rs61912291 -0.453602 0.68 4 309 13 MODIFIER 1 CODING TAS2R20 G protein_coding NM_176889.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11149532 A G 0 222 0 0.0651 0.4233 0.3847 0.755 0.3827 0.635 0.100318 0.2658 0.350581 1 1037 48859 5253 6475 2203 23893 381 9617 2 10320 118534 11454 8614 6604 65898 886 14758 0.987279 0 . 0 . 96 36,8,43,2 UTR_3_PRIME(MODIFIER||13||309|TAS2R20|protein_coding|CODING|NM_176889.2|1|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|G),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.91927 rs1450839 -0.693147 0.111899 96 R255L 309 cGa/cTa MODERATE 1 MISSENSE CODING TAS2R20 A protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11149711 C A 0 222 0 0.0651 0.4231 0.3847 0.755 0.3827 0.6339 0.100318 0.265877 0.350698 1 1038 49849 5252 6489 2206 24091 390 10383 2 10400 121244 11494 8638 6608 66694 904 16506 0.404821 0 . 0 . 189 65,30,36,44 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cTa|R255L|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.139627 rs10845279 -0.693147 0.568964 189 F252S 309 tTt/tCt MODERATE 1 MISSENSE CODING TAS2R20 G protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11149720 A G 0 222 0 0.0651 0.4229 0.3847 0.755 0.3817 0.6339 0.100318 0.265877 0.350698 1 1038 49849 5252 6489 2206 24090 390 10384 2 10404 121238 11494 8636 6608 66688 906 16502 0.471949 0 . 0 . 184 66,31,34,45 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F252S|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|G),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.401001 rs10845280 -0.693147 0.0840566 184 I236V 309 Ata/Gta MODERATE 1 MISSENSE CODING TAS2R20 C protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11149769 T C 0 222 0 0.0651 0.4229 0.3847 0.755 0.3817 0.6339 0.100318 0.265877 0.350698 1 1040 49930 5287 6504 2206 24120 391 10382 2 10406 121336 11542 8648 6612 66718 908 16502 0.888453 0 . 0 . 228 73,30,59,40 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I236V|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0394669 rs10845281 -0.693147 0.154129 228 H148N 309 Cac/Aac MODERATE 1 MISSENSE CODING TAS2R20 T protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11150033 G T 0 222 0 0.0847 0.4283 0.3847 0.755 0.3827 0.6339 0.118929 0.272028 0.350465 1 1232 50070 5271 6479 2206 24108 391 10383 2 10404 121244 11500 8626 6610 66690 906 16508 0.536215 0 . 0 . 123 27,38,19,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H148N|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.884947 rs12226919 -0.693146 0.0218453 123 H143Q 309 caC/caA MODERATE 1 MISSENSE CODING TAS2R20 T protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11150046 G T 0 222 0 0.0651 0.4231 0.3847 0.755 0.3827 0.6339 0.100091 0.26557 0.350349 1 1040 49866 5266 6481 2206 24098 391 10384 2 10400 121254 11504 8632 6612 66690 906 16510 0.992908 0 . 0 . 119 23,39,24,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caA|H143Q|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.303184 rs12226920 -0.693147 0.454237 119 A87 309 gcC/gcT LOW 1 SILENT CODING TAS2R20 A protein_coding NM_176889.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11150214 G A 0 222 0 0.0651 0.4229 0.3847 0.755 0.3817 0.6339 0.0979545 0.26266 0.346986 1 987 49760 5261 6480 2206 24058 389 10379 2 9778 120416 11492 8628 6602 66514 902 16500 0.960499 0 . 0 . 87 22,21,17,21 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A87|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.355368 rs11054142 -0.693143 0.0338048 87 K79E 309 Aaa/Gaa MODERATE 1 MISSENSE CODING TAS2R20 C protein_coding NM_176889.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11150240 T C 0 222 0 0.2171 0.2075 0.2392 0.1964 0.2068 0.184 0.20636 0.220728 0.227964 1 1997 27152 2818 1848 1753 15448 208 3080 2 9720 119948 11466 8596 6602 66176 900 16488 0.899619 0 . 0 . 91 24,17,23,19 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Gaa|K79E|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998964 rs7135018 -0.693146 0.757647 91 A52 309 gcA/gcG LOW 1 SILENT CODING TAS2R20 C protein_coding NM_176889.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11150319 T C 0 222 0 0.0651 0.4229 0.3847 0.755 0.3817 0.6339 0.0983197 0.264113 0.349035 1 1004 49811 5261 6483 2205 24084 391 10383 2 9832 120360 11466 8632 6594 66440 900 16496 0.395704 0 . 0 . 107 24,17,21,21 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A52|309|TAS2R20|protein_coding|CODING|NM_176889.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.418066 rs11054143 -0.693146 0.0598197 107 R299C 299 Cgc/Tgc MODERATE 1 MISSENSE CODING TAS2R19 A protein_coding NM_176888.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11174276 G A 0 222 0 0.3593 0.3498 0.464 0.1944 0.505 0.2566 0.379029 0.459865 0.501279 1 3851 54850 5288 2198 3987 34310 431 4785 2 10354 117852 11308 8214 6528 65600 878 14970 0.579716 0 . 0 . 115 52,8,32,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R299C|299|TAS2R19|protein_coding|CODING|NM_176888.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.851476 rs10772420 -0.693145 0.780963 115 L140 299 Ctg/Ttg LOW 1 SILENT CODING TAS2R19 A protein_coding NM_176888.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11174753 G A 0 222 0 0.4062 0.7009 0.8026 0.8611 0.8141 0.7454 0.45892 0.681916 0.796163 1 4660 94716 9974 7668 5594 53676 732 12412 2 10382 121352 11572 8648 6614 66724 908 16504 0.880446 0 . 0 . 202 51,58,36,41 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L140|299|TAS2R19|protein_coding|CODING|NM_176888.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.728268 rs1868769 -0.693147 0.533162 202 A28 299 gcC/gcT LOW 1 SILENT CODING TAS2R19 A protein_coding NM_176888.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11175087 G A 0 222 0 0.3601 0.3518 0.4669 0.1944 0.5109 0.2577 0.379029 0.462556 0.505349 1 3847 53971 5150 1844 4031 34104 420 4575 2 10366 121126 11526 8622 6598 66622 908 16484 0.695669 0 . 0 . 131 21,41,14,41 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A28|299|TAS2R19|protein_coding|CODING|NM_176888.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.823833 rs12313469 -0.693147 0.0364735 131 V240I 309 Gtt/Att MODERATE 1 MISSENSE CODING TAS2R31 T protein_coding NM_176885.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11183217 C T 0 222 0 0.3427 0.3353 0.4568 0.1944 0.4801 0.2352 0.360191 0.441335 0.482907 1 3564 51458 5027 1847 3880 32656 404 4080 2 10070 121050 11576 8650 6614 66734 904 16502 0.875023 0 . 0 . 281 59,86,48,60 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V240I|309|TAS2R31|protein_coding|CODING|NM_176885.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.155119 0.999395 0 0.578879 rs10772423 -0.693147 0.679014 281 A227V 309 gCt/gTt MODERATE 1 MISSENSE CODING TAS2R31 A protein_coding NM_176885.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11183255 G A 0 222 0 0.3593 0.3498 0.464 0.1944 0.505 0.2566 0.374943 0.457558 0.499884 1 3799 53392 5147 1848 3894 33739 420 4545 2 10308 121298 11574 8652 6614 66734 908 16508 0.73762 0 . 0 . 228 52,61,43,54 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A227V|309|TAS2R31|protein_coding|CODING|NM_176885.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 58 0 0.303445 0.5641 0 0.854162 rs10845293 -0.693147 0.202281 228 L162M 309 Ttg/Atg MODERATE 1 MISSENSE CODING TAS2R31 T protein_coding NM_176885.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11183451 A T 0 222 0 0.4039 0.6943 0.7954 0.8611 0.7982 0.7362 0.471225 0.687597 0.797042 1 4412 93111 9871 7662 5582 52563 718 12303 2 9900 120630 11554 8628 6602 66612 902 16432 0.705183 0 . 0 . 157 40,30,42,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L162M|309|TAS2R31|protein_coding|CODING|NM_176885.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.275506 rs10743938 -0.693147 0.180656 157 A141 309 gcT/gcC LOW 1 SILENT CODING TAS2R31 G protein_coding NM_176885.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11183512 A G 0 222 0 0.2375 0.2127 0.2406 0.1944 0.2068 0.184 0.212531 0.215724 0.217263 1 2008 25011 2576 1681 1576 14081 190 2899 2 9836 120518 11536 8620 6598 66556 898 16474 0.803184 0 . 0 . 166 49,28,45,33 SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A141|309|TAS2R31|protein_coding|CODING|NM_176885.2|1|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|G),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.426069 rs12370363 -0.693147 0.951483 166 R35W 309 Cgg/Tgg MODERATE 1 MISSENSE CODING TAS2R31 A protein_coding NM_176885.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11183832 G A 0 222 0 0.3434 0.3355 0.4568 0.1944 0.4801 0.2352 0.353721 0.440861 0.481636 1 3509 54536 5357 2451 4007 33887 433 4892 2 9724 119182 11380 8394 6558 65976 892 16258 0.748715 0 . 0 . 135 37,20,34,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R35W|309|TAS2R31|protein_coding|CODING|NM_176885.2|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|2|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|3|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 59 0 1 1 0 0.898965 rs10845295 -0.693147 0.450897 135 200 80 MODIFIER 2 CODING PRH1 C protein_coding NM_001291315.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11199734 T C 0 228 0 0.4085 0.761 0.8473 0.9514 0.8678 0.8701 0.449422 0.718887 0.836164 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,5,36 UTR_5_PRIME(MODIFIER||80||200|PRH1|protein_coding|CODING|NM_001291315.1|2|C),UTR_5_PRIME(MODIFIER||80||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|2|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2597984 -0.693145 0.332 44 176 80 MODIFIER 2 CODING PRH1-TAS2R14 C protein_coding NM_001316893.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11199734 T C 0 228 0 0.4085 0.761 0.8473 0.9514 0.8678 0.8701 0.449422 0.718887 0.836164 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 44 0,0,5,36 UTR_5_PRIME(MODIFIER||80||200|PRH1|protein_coding|CODING|NM_001291315.1|2|C),UTR_5_PRIME(MODIFIER||80||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|2|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0 . 0 . 1 0 1 0 . 60 0 0 1 0 . rs2597984 -0.693145 0.332 44 W250* 309 tGg/tAg HIGH 1 NONSENSE CODING TAS2R46 T protein_coding NM_176887.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11214145 C T 0 222 0 0.2375 0.2119 0.2378 0.1925 0.2068 0.184 0.228552 0.227587 0.227093 1 2269 27383 2821 1837 1740 15444 206 3066 2 10074 121016 11550 8646 6610 66724 906 16506 0.734189 0 . 0 . 321 60,96,49,92 STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W250*|309|TAS2R46|protein_coding|CODING|NM_176887.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.440416 rs2708381 -0.693147 0.82998 321 L228M 309 Ttg/Atg MODERATE 1 MISSENSE CODING TAS2R46 T protein_coding NM_176887.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11214212 A T 0 222 0 0.3404 0.3359 0.4625 0.1925 0.4841 0.2352 0.366546 0.447016 0.488253 1 3691 51630 5022 1851 3879 32724 404 4059 2 10384 121324 11550 8648 6614 66716 908 16504 0.942964 0 . 0 . 254 39,72,43,83 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L228M|309|TAS2R46|protein_coding|CODING|NM_176887.2|1|T),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|T),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|T),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.937641 rs2708380 -0.693147 0.598156 254 T221 309 acC/acG LOW 1 SILENT CODING TAS2R43 C protein_coding NM_176884.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11244166 G C 0 228 0 0.1218 0.6388 0.7205 0.9405 0.7793 0.8241 0 . 0 2 1004 40328 4246 4170 1905 20603 327 8073 2 10020 117044 11266 8562 6378 64336 870 15612 0 . 0 . COSM1127568 131 0,0,42,77 SYNONYMOUS_CODING(LOW|SILENT|acC/acG|T221|309|TAS2R43|protein_coding|CODING|NM_176884.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.973096 0 . rs35720106 -0.693147 0.0141128 131 H212R 309 cAt/cGt MODERATE 1 MISSENSE CODING TAS2R43 C protein_coding NM_176884.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11244194 T C 0 228 0 0.0998 0.6218 0.7104 0.9425 0.7525 0.7996 0 . 0 2 914 45345 4730 4658 2349 22644 370 9680 2 9366 104562 10160 8246 4948 55850 750 15242 0 . 0 . COSM430341 115 0,0,37,71 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H212R|309|TAS2R43|protein_coding|CODING|NM_176884.2|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 0 . 0 . 0 1 0 . 1 0 59 0 0 0.971722 0 . rs71443637 -0.693147 0.230653 115 W35S 309 tGg/tCg MODERATE 1 MISSENSE CODING TAS2R43 G protein_coding NM_176884.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11244725 C G 0 228 0 0.0976 0.6216 0.7118 0.9425 0.7525 0.8006 0 . 0 2 1079 63632 7095 7485 3334 32126 506 12007 2 8458 95896 9278 8156 4302 49626 710 15366 0 . 0 . COSM430344,COSM430345 155 0,0,62,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tCg|W35S|309|TAS2R43|protein_coding|CODING|NM_176884.2|1|G),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|G),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|G),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs68157013 -0.693147 9.38915e-05 155 F252L 319 ttT/ttG MODERATE 1 MISSENSE CODING TAS2R30 C protein_coding NM_001097643.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11286088 A C 0 222 0 0.357 0.3512 0.4697 0.1944 0.5109 0.2566 0.377384 0.461006 0.503838 1 3658 53073 5142 1849 3877 33603 416 4528 2 9968 120868 11556 8646 6606 66686 902 16504 0.999756 0 . 0 . 278 55,70,56,74 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F252L|319|TAS2R30|protein_coding|CODING|NM_001097643.1|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456842 rs2599404 -0.693147 0.0578546 278 V18 319 gtT/gtG LOW 1 SILENT CODING TAS2R30 C protein_coding NM_001097643.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11286790 A C 0 222 0 0.357 0.3516 0.4712 0.1944 0.5109 0.2577 0 . 0 1 3538 52030 4981 1812 3836 32932 415 4516 2 9658 119184 11336 8568 6564 65718 898 16442 0.943245 0 . 0 . 124 16,45,7,47 SYNONYMOUS_CODING(LOW|SILENT|gtT/gtG|V18|319|TAS2R30|protein_coding|CODING|NM_001097643.1|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 1 0 58 0 0.791586 0.437103 0 0.258554 rs2600355 -0.693147 0.00797637 124 68 17 MODIFIER 1 CODING SMIM10L1 C protein_coding NM_001271592.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11323939 G C 0 117 0 0.1717 0.5391 0.6037 0.7569 0.6372 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.966813 0 . 0 . 25 12,0,12,0 UTR_5_PRIME(MODIFIER||17||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|C),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|C),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|C),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.635242 rs7488095 -0.680642 0.637461 25 R13 68 agG/agA LOW 1 SILENT CODING SMIM10L1 A protein_coding NM_001271592.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11323994 G A 0 222 0 0.1717 0.5391 0.6037 0.7569 0.6372 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.45424 0 . 0 . 47 18,2,22,3 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R13|68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),INTRON(MODIFIER||||200|PRH1|protein_coding|CODING|NM_001291315.1|1|A),INTRON(MODIFIER||||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.910124 rs7488102 -0.692914 0.22152 47 200 124522 MODIFIER 1 CODING PRH1 A protein_coding NM_001291315.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324176 C A 0 222 0 0.1732 0.5429 0.6066 0.7569 0.6521 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98394 0 . 0 . 120 16,38,16,41 UTR_5_PRIME(MODIFIER||124522||200|PRH1|protein_coding|CODING|NM_001291315.1|1|A),UTR_5_PRIME(MODIFIER||124522||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|A),UTR_3_PRIME(MODIFIER||14||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996092 rs2416548 -0.693147 0.00268648 120 176 124522 MODIFIER 1 CODING PRH1-TAS2R14 A protein_coding NM_001316893.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324176 C A 0 222 0 0.1732 0.5429 0.6066 0.7569 0.6521 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98394 0 . 0 . 120 16,38,16,41 UTR_5_PRIME(MODIFIER||124522||200|PRH1|protein_coding|CODING|NM_001291315.1|1|A),UTR_5_PRIME(MODIFIER||124522||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|A),UTR_3_PRIME(MODIFIER||14||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996092 rs2416548 -0.693147 0.00268648 120 68 14 MODIFIER 1 CODING SMIM10L1 A protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324176 C A 0 222 0 0.1732 0.5429 0.6066 0.7569 0.6521 0.6646 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.98394 0 . 0 . 120 16,38,16,41 UTR_5_PRIME(MODIFIER||124522||200|PRH1|protein_coding|CODING|NM_001291315.1|1|A),UTR_5_PRIME(MODIFIER||124522||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1|1|A),UTR_3_PRIME(MODIFIER||14||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),INTRAGENIC(MODIFIER|||||PRH1-PRR4||NON_CODING|||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.996092 rs2416548 -0.693147 0.00268648 120 68 182 MODIFIER 1 CODING SMIM10L1 T protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324344 C T 0 44 0 0.174 0.5433 0.6066 0.7569 0.6521 0.6656 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.763675 0 . 0 . 11 1,6,0,4 UTR_3_PRIME(MODIFIER||182||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|T),UPSTREAM(MODIFIER||122||200|PRH1|protein_coding|CODING|NM_001291315.1||T),UPSTREAM(MODIFIER||122||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 1 0 0.200967 rs1047709 -0.556411 0.0665622 11 68 193 MODIFIER 1 CODING SMIM10L1 A protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324355 G A 0 173 0 0.4077 0.7622 0.8473 0.9514 0.8718 0.8732 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,1,10 UTR_3_PRIME(MODIFIER||193||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),UPSTREAM(MODIFIER||133||200|PRH1|protein_coding|CODING|NM_001291315.1||A),UPSTREAM(MODIFIER||133||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047710 -0.676189 0.181116 11 68 201 MODIFIER 1 CODING SMIM10L1 C protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324363 T C 0 158 0 0.4077 0.7622 0.8473 0.9514 0.8718 0.8732 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,1,8 UTR_3_PRIME(MODIFIER||201||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|C),UPSTREAM(MODIFIER||141||200|PRH1|protein_coding|CODING|NM_001291315.1||C),UPSTREAM(MODIFIER||141||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047711 -0.662043 0.0517194 9 68 202 MODIFIER 1 CODING SMIM10L1 A protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324364 G A 0 42.3 0 0.1762 0.5447 0.6066 0.7569 0.6531 0.6687 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.730948 0 . 0 . 9 1,4,0,4 UTR_3_PRIME(MODIFIER||202||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),UPSTREAM(MODIFIER||142||200|PRH1|protein_coding|CODING|NM_001291315.1||A),UPSTREAM(MODIFIER||142||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.974597 1 0 0.406082 rs1047712 -0.556411 0.0665622 9 68 239 MODIFIER 1 CODING SMIM10L1 G protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324401 C G 0 118 0 0.4062 0.7608 0.8473 0.9514 0.8698 0.8701 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 6 0,0,1,5 UTR_3_PRIME(MODIFIER||239||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|G),UPSTREAM(MODIFIER||179||200|PRH1|protein_coding|CODING|NM_001291315.1||G),UPSTREAM(MODIFIER||179||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1047713 -0.616816 0.839859 6 68 397 MODIFIER 1 CODING SMIM10L1 G protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324559 C G 0 10.8 0 0.4054 0.7606 0.8473 0.9514 0.8698 0.8701 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||397||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|G),UPSTREAM(MODIFIER||337||200|PRH1|protein_coding|CODING|NM_001291315.1||G),UPSTREAM(MODIFIER||337||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8181 -0.453602 0.26 2 68 588 MODIFIER 1 CODING SMIM10L1 A protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11324750 G A 0 6.3 0 0.2315 0.2165 0.232 0.1944 0.2177 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||588||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),UPSTREAM(MODIFIER||528||200|PRH1|protein_coding|CODING|NM_001291315.1||A),UPSTREAM(MODIFIER||528||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs8300 -0.379885 0 1 68 1642 MODIFIER 1 CODING SMIM10L1 A protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11325804 G A 0 9.7 0 0.1732 0.5437 0.6153 0.756 0.6521 0.6636 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1642||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|A),UPSTREAM(MODIFIER||1582||200|PRH1|protein_coding|CODING|NM_001291315.1||A),UPSTREAM(MODIFIER||1582||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2416549 -0.379885 0 1 68 2153 MODIFIER 1 CODING SMIM10L1 C protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11326315 T C 0 39.3 0 0.4047 0.7602 0.8473 0.9514 0.8688 0.8701 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2153||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|C),UPSTREAM(MODIFIER||2093||200|PRH1|protein_coding|CODING|NM_001291315.1||C),UPSTREAM(MODIFIER||2093||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4763637 -0.453602 0.96 2 68 2186 MODIFIER 1 CODING SMIM10L1 T protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11326348 C T 0 9.7 0 0.2511 0.2218 0.2334 0.1944 0.2177 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2186||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|T),UPSTREAM(MODIFIER||2126||200|PRH1|protein_coding|CODING|NM_001291315.1||T),UPSTREAM(MODIFIER||2126||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4763638 -0.379885 0 1 68 3151 MODIFIER 1 CODING SMIM10L1 T protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11327313 C T 0 222 0 0.2496 0.221 0.2291 0.1954 0.2177 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.499253 0 . 0 . 175 71,26,52,11 UTR_3_PRIME(MODIFIER||3151||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|T),UPSTREAM(MODIFIER||3091||200|PRH1|protein_coding|CODING|NM_001291315.1||T),UPSTREAM(MODIFIER||3091||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0984883 rs61928645 -0.693147 0.0838128 175 68 3152 MODIFIER 1 CODING SMIM10L1 G protein_coding NM_001271592.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11327314 A G 0 222 0 0.2519 0.2214 0.2291 0.1944 0.2177 0.2065 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.285162 0 . 0 . 176 72,27,51,11 UTR_3_PRIME(MODIFIER||3152||68|SMIM10L1|protein_coding|CODING|NM_001271592.1|1|G),UPSTREAM(MODIFIER||3092||200|PRH1|protein_coding|CODING|NM_001291315.1||G),UPSTREAM(MODIFIER||3092||176|PRH1-TAS2R14|protein_coding|CODING|NM_001316893.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.109853 rs61928646 -0.693147 0.0901063 176 A311P 314 Gct/Cct MODERATE 1 MISSENSE CODING TAS2R42 G protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338613 C G 0 228 0 0.407 0.7608 0.8473 0.9514 0.8688 0.8701 0.394235 0.66254 0.8 2 4670 100257 10243 8332 6029 56151 786 14046 2 10262 119748 11478 8632 6560 65956 896 15964 0 . 0 . 0 81 0,0,57,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A311P|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1650017 -0.693147 0.00440354 81 N310 314 aaT/aaC LOW 1 SILENT CODING TAS2R42 G protein_coding NM_181429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338614 A G 0 228 0 0.407 0.7608 0.8473 0.9514 0.8688 0.8701 0.393781 0.66231 0.799884 2 4672 100301 10246 8332 6031 56168 786 14066 2 10264 119818 11482 8632 6562 65982 896 16000 0 . 0 . 0 81 0,0,57,14 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N310|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1669411 -0.693147 0.00450618 81 R292Q 314 cGa/cAa MODERATE 1 MISSENSE CODING TAS2R42 T protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338669 C T 0 222 0 0.2474 0.22 0.2305 0.1944 0.2167 0.2055 0.24217 0.238967 0.237326 1 2496 28793 2931 1836 1642 16170 214 3504 2 10396 121130 11514 8634 6598 66610 902 16476 0.987021 0 . 0 . 127 39,28,34,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R292Q|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.968653 rs1669412 -0.693147 0.0969254 127 Y265C 314 tAc/tGc MODERATE 1 MISSENSE CODING TAS2R42 C protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338750 T C 0 222 0 0.2474 0.22 0.2305 0.1944 0.2167 0.2055 0.24217 0.23889 0.237209 1 2496 28788 2927 1839 1643 16166 214 3503 2 10398 121202 11502 8640 6606 66642 906 16508 0.709245 0 . 0 . 150 35,31,39,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tGc|Y265C|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.597315 rs1451772 -0.693147 0.390491 150 G255W 314 Ggg/Tgg MODERATE 1 MISSENSE CODING TAS2R42 A protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338781 C A 0 228 0 0.407 0.7608 0.8473 0.9514 0.8688 0.8701 0.467771 0.713671 0.839651 2 4748 101610 10295 8355 6079 56868 796 14469 2 10386 121260 11520 8648 6608 66678 908 16512 0 . 0 . 0 127 0,0,59,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Tgg|G255W|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1669413 -0.693147 0.170254 127 F196S 314 tTc/tCc MODERATE 1 MISSENSE CODING TAS2R42 G protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338957 A G 0 222 0 0.1596 0.5407 0.6167 0.7569 0.6521 0.6646 0.219035 0.469737 0.597859 1 2113 72393 7349 6495 4438 40471 579 10948 2 9782 120214 11502 8622 6610 66300 904 16494 0.575354 0 . 0 . 154 39,36,28,28 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F196S|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.98109 rs5020531 -0.693147 0.263991 154 L187 314 ttA/ttG LOW 1 SILENT CODING TAS2R42 C protein_coding NM_181429.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11338983 T C 0 228 0 0.407 0.7608 0.8473 0.9514 0.8688 0.8701 0.469891 0.714297 0.839119 2 4484 101051 10284 8337 6083 56605 794 14464 2 9844 120372 11508 8630 6612 66366 906 16506 0 . 0 . 0 138 0,0,52,67 SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L187|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1650019 -0.693147 0.000138231 138 Y175F 314 tAt/tTt MODERATE 1 MISSENSE CODING TAS2R42 A protein_coding NM_181429.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11339020 T A 0 222 0 0.1596 0.5407 0.6167 0.7569 0.6521 0.6646 0.214451 0.46717 0.595009 1 2109 72213 7331 6469 4435 40365 580 10924 2 9718 119878 11480 8590 6606 66136 904 16444 0.697479 0 . 0 . 100 27,29,12,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tTt|Y175F|314|TAS2R42|protein_coding|CODING|NM_181429.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.72193 rs35969491 -0.693132 0.476366 100 309 1172 MODIFIER 5 CODING PRB3 G protein_coding NM_006249.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11418954 A G 0 228 0 0.6543 0.8037 0.9496 0.6984 0.9553 0.8548 0 . 0 2 401 10944 176 147 2 3464 121 6633 2 568 12360 188 200 2 3650 134 7618 0 . 0 . 0 201 0,0,112,59 UTR_3_PRIME(MODIFIER||1172||309|PRB3|protein_coding|CODING|NM_006249.5|5|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1896551 -0.693147 1.27692e-05 201 309 LOW 3 CODING PRB3 C protein_coding NM_006249.5 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11420454 T C 0 228 0 0.2829 0.5098 0.5274 0.6349 0.5398 0.6442 0 . 0 2 91 615 29 42 9 432 4 8 2 4286 6916 366 96 196 1722 32 218 1 0 . 0 . 21 1,0,2,16 SPLICE_SITE_REGION+INTRON(LOW||||309|PRB3|protein_coding|CODING|NM_006249.5|3|C) 0 . 0 . 0 1 0 . 1 0 46 0 1 0.437551 0 1 rs11054202 -0.691153 9.10897e-08 21 P230S 309 Cca/Tca MODERATE 3 MISSENSE CODING PRB3 A protein_coding NM_006249.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11420495 G A 0 47.4 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868321 0 . 0 . 12 1,3,4,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P230S|309|PRB3|protein_coding|CODING|NM_006249.5|3|A) 0 0.5 1 0 . 0 . 0 . 0 47 0 0.868321 0.750668 0 0.124046 rs12811806 -0.556411 0.0138351 12 P228S 309 Cca/Tca MODERATE 3 MISSENSE CODING PRB3 A protein_coding NM_006249.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11420501 G A 0 64 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.679965 0 . 0 COSN496248 22 6,4,7,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P228S|309|PRB3|protein_coding|CODING|NM_006249.5|3|A) 0 0.5 1 0 . 0 . 0 . 0 36 0 0.79189 0.960728 0 0.591555 rs12811811 -0.636426 0.00238139 22 P222 309 ccG/ccA LOW 3 SILENT CODING PRB3 T protein_coding NM_006249.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11420517 C T 0 103 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.252539 0 . 0 COSM1359020,COSN231964 38 8,4,12,3 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P222|309|PRB3|protein_coding|CODING|NM_006249.5|3|T) 0 0.5 1 0 . 0 . 0 . 0 37 0 0.295511 0.895309 0 0.92664 rs12368171 -0.688148 5.51138e-05 38 P156 309 ccG/ccA LOW 3 SILENT CODING PRB3 T protein_coding NM_006249.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11420715 C T 0 11.4 0 . 0 . 0 . 0 . 0 . 1 22 25 1 1 0 1 0 0 2 3502 30124 1336 5320 1868 14236 182 3680 1 0 . 0 . 3 0,1,0,2 SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P156|309|PRB3|protein_coding|CODING|NM_006249.5|3|T) 0 0.5 1 0 . 0 . 0 1 0 36 0 1 0 . 1 rs11054207 -0.453602 0.02 3 247 1110 MODIFIER 4 CODING PRB4 A protein_coding NM_002723.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11460063 C A 0 228 0 0.6218 0.7552 0.8429 0.8075 0.8509 0.7209 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,39,11 UTR_3_PRIME(MODIFIER||1110||247|PRB4|protein_coding|CODING|NM_002723.5|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1863842 -0.693147 0.00416716 56 A209P 247 Gca/Cca MODERATE 3 MISSENSE CODING PRB4 G protein_coding NM_002723.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461292 C G 0 228 0 0.6218 0.755 0.8429 0.8075 0.8499 0.7209 0.679074 0.776565 0.826512 2 6891 96981 9316 6930 5668 55609 730 11837 2 10286 120724 11576 8628 6614 66558 904 16158 1 0 . 0 . 72 1,0,38,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Cca|A209P|247|PRB4|protein_coding|CODING|NM_002723.5|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 1 0.983051 0 1 rs1052808 -0.693147 0.56781 72 G149 247 ggT/ggC LOW 3 SILENT CODING PRB4 G protein_coding NM_002723.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461470 A G 0 228 0 0.6218 0.7554 0.8429 0.8095 0.8499 0.7209 0.684294 0.779471 0.828289 2 5106 82967 8761 6355 5011 48734 614 8386 2 7366 102700 10782 7814 5834 58004 764 12136 0 . 0 . 0 53 0,0,10,39 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G149|247|PRB4|protein_coding|CODING|NM_002723.5|3|G) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.941475 0 . rs1052807 -0.693147 0.185941 53 R122G 247 Aga/Gga MODERATE 3 MISSENSE CODING PRB4 C protein_coding NM_002723.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461553 T C 0 72 0 0.0061 0.0045927 0.0058 0.001 0 0.0102 0 . 0 1 1 2 0 0 0 1 0 0 2 1318 15090 1422 1482 816 7832 90 2130 0.688179 0 . 0 . 41 9,11,3,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R122G|247|PRB4|protein_coding|CODING|NM_002723.5|3|C) 0 0.5 1 0 . 1 0 . 1 0 54 0 0.946832 0.21973 0 0.0246942 rs11054244 -0.651104 0.0618676 41 P116H 247 cCt/cAt MODERATE 3 MISSENSE CODING PRB4 T protein_coding NM_002723.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461570 G T 0 96 0 . 0 . 0 . 0 . 0 . 1 1629 9324 807 781 484 4714 53 856 2 4074 32980 2312 2098 1194 15566 238 7498 0.89586 0 . 0 . 40 8,14,2,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P116H|247|PRB4|protein_coding|CODING|NM_002723.5|3|T) 0 0.5 1 0 . 0 . 0 1 0 49 0 0.700259 0.0847556 0 0.000735341 rs59189129 -0.651104 0.00266632 40 T113P 247 Acc/Ccc MODERATE 3 MISSENSE CODING PRB4 G protein_coding NM_002723.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461580 T G 0 209 0 0.0045 0.0021965 0.0029 0.003 0 0 0 . 0 1 1173 4389 328 288 186 2002 25 387 2 3302 21974 1382 1124 624 10324 186 5032 0.602496 0 . 0 . 44 7,7,9,9 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T113P|247|PRB4|protein_coding|CODING|NM_002723.5|3|G) 0 0.5 1 0 . 1 0 . 1 0 50 0 0.716402 0.0520931 0 0.026329 rs12303607 -0.691153 0.86563 44 G107 247 ggA/ggC LOW 3 SILENT CODING PRB4 G protein_coding NM_002723.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461596 T G 0 142 0 . 0 . 0 . 0 . 0 . 1 31 467 34 38 11 321 1 31 2 3746 24616 1298 1136 548 10408 208 7272 0.940151 0 . 0 . 48 11,14,10,4 SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G107|247|PRB4|protein_coding|CODING|NM_002723.5|3|G) 0 0.5 1 0 . 0 . 0 1 0 54 0 0.993166 0.288101 0 0.154609 rs59021567 -0.686358 0.123939 48 P71T 247 Ccc/Acc MODERATE 3 MISSENSE CODING PRB4 T protein_coding NM_002723.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11461706 G T 0 40.3 0 . 0 . 0 . 0 . 0 . 1 1125 10377 1700 781 851 5152 78 690 2 4200 48434 5162 2908 2158 23026 430 10550 0.478308 0 . 0 . 78 35,13,4,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P71T|247|PRB4|protein_coding|CODING|NM_002723.5|3|T) 0 0.5 1 0 . 0 . 0 1 0 59 0 0.959325 0.625209 0 0.29889 rs12308381 -0.670168 0.149496 78 P303L 331 cCc/cTc MODERATE 3 MISSENSE CODING PRB1 A protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506129 G A 0 143 0 0 0.0021965 0 0.0109 0 0 0 . 0 1 0 174 0 138 0 18 1 17 2 8490 113640 11384 8572 6360 63670 868 14296 0.798444 0 . 0 . 70 31,2,33,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P303L|331|PRB1|protein_coding|CODING|NM_005039.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 44 0 0.998409 0.444564 0 0.33454 rs201872688 -0.693132 0.0861875 70 S276A 331 Tct/Gct MODERATE 3 MISSENSE CODING PRB1 C protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506211 A C 0 222 0 0.2746 0.4553 0.5706 0.4355 0.668 0.4192 0.344186 0.55751 0.664795 1 3218 71114 6450 3767 4575 44443 575 8086 2 9732 119608 11520 8600 6496 65910 902 16448 0.995315 0 . 0 COSM1127550 194 38,43,44,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S276A|331|PRB1|protein_coding|CODING|NM_005039.3|3|C) 1 0.5 1 0 . 1 0 1 1 0 51 0 0.826654 0.0128108 0 0.849179 rs76504934 -0.693147 0.0427609 194 P230 331 ccC/ccT LOW 3 SILENT CODING PRB1 A protein_coding NM_005039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506347 G A 0 66 0 0.3094 0.4391 0.5216 0.4464 0.5944 0.3885 0 . 0 1 1978 51128 4363 2425 3574 32060 424 6304 2 6304 92770 8630 5538 5658 52794 698 13148 0.0778517 0 . 0 COSN392241 88 31,25,5,17 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P230|331|PRB1|protein_coding|CODING|NM_005039.3|3|A) 0 0.5 1 0 . 1 0 . 1 0 43 0 0.126881 0.318123 0 0.770697 rs371841290 -0.692562 0.409804 88 S212P 331 Tcc/Ccc MODERATE 3 MISSENSE CODING PRB1 G protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506403 A G 0 222 0 0.1762 0.2356 0.1801 0.3363 0.174 0.3149 0 . 0 1 1867 46748 3673 1886 3471 30015 379 5457 2 4774 70564 5812 3420 4720 42086 534 9218 0.608291 0 . 0 COSN160927 82 16,21,17,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S212P|331|PRB1|protein_coding|CODING|NM_005039.3|3|G) 0 0.5 1 0 . 1 0 . 1 0 46 0 0.00156695 0.268452 0 0.948022 rs113897264 -0.693136 0.412282 82 K188N 331 aaG/aaC MODERATE 3 MISSENSE CODING PRB1 G protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506473 C G 0 7.9 0 0.4743 0.5697 0.5922 0.753 0.6292 0.4325 0 . 0 1 890 6661 617 1466 158 2823 41 666 2 4582 40704 4742 3570 1994 20132 268 5416 0.99778 0 . 0 . 24 14,4,3,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K188N|331|PRB1|protein_coding|CODING|NM_005039.3|3|G) 0 0.5 1 0 . 1 0 . 1 0 50 0 0.164474 0.987474 0 0.135335 rs61930109 -0.616816 0.168702 24 Q168 331 caA/caG LOW 3 SILENT CODING PRB1 C protein_coding NM_005039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506533 T C 0 9.3 0 . 0 . 0 . 0 . 0 . 1 2 23 1 0 0 10 0 10 2 6828 63824 6792 6820 2812 31564 438 8570 0.33285 0 . 0 . 54 25,11,9,4 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q168|331|PRB1|protein_coding|CODING|NM_005039.3|3|C) 0 0.5 1 0 . 0 . 0 1 0 47 0 0.000406569 0.785888 0 0.762744 rs113485215 -0.683931 0.167798 54 *152R 331 Tga/Cga HIGH 3 MISSENSE CODING PRB1 G protein_coding NM_005039.3 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506583 A G 0 150 0 0.4569 0.65 0.7176 0.8036 0.7724 0.5787 0 . 0 1 2074 27583 2799 4553 1200 13528 202 3227 2 5670 47876 4894 6074 2114 22814 338 5972 0.42516 0 . 0 COSN164173 70 21,17,19,5 STOP_LOST(HIGH|MISSENSE|Tga/Cga|*152R|331|PRB1|protein_coding|CODING|NM_005039.3|3|G) 0 0.5 1 0 . 1 0 . 1 0 49 0 1.91897e-05 0.998675 0 0.351946 rs111877208 -0.692831 0.0214258 70 P123Q 331 cCa/cAa MODERATE 3 MISSENSE CODING PRB1 T protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506669 G T 0 222 0 . 0 . 0 . 0 . 0 . 1 3515 53814 5576 3747 3197 31149 394 6236 2 8700 111664 11424 8510 6406 62848 818 12958 0.638148 0 . 0 COSN405349 137 34,23,38,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cAa|P123Q|331|PRB1|protein_coding|CODING|NM_005039.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 46 0 0.372385 0.897 0 0.999909 rs74903687 -0.693147 0.00159266 137 R88Q 331 cGa/cAa MODERATE 3 MISSENSE CODING PRB1 T protein_coding NM_005039.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506774 C T 0 87 0 . 0 . 0 . 0 . 0 . 1 213 2378 162 123 101 1539 16 224 2 9028 114630 11436 8554 6452 63522 868 14770 0.413689 0 . 0 COSM226277 86 28,27,2,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R88Q|331|PRB1|protein_coding|CODING|NM_005039.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 48 0 4.1755e-06 0.100928 0 0.195728 rs202083397 -0.692914 0.0465364 86 G84 331 ggG/ggA LOW 3 SILENT CODING PRB1 T protein_coding NM_005039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506785 C T 0 66 0 . 0 . 0 . 0 . 0 . 1 169 1924 121 98 74 1297 13 152 2 9044 115536 11466 8572 6494 63868 864 15228 0.499102 0 . 0 . 82 27,25,1,23 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G84|331|PRB1|protein_coding|CODING|NM_005039.3|3|T) 0 0.5 1 0 . 0 . 0 1 0 50 0 2.81486e-07 0.00580721 0 0.502392 rs201935302 -0.692831 0.665001 82 Q48 331 caG/caA LOW 3 SILENT CODING PRB1 T protein_coding NM_005039.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11506893 C T 0 210 0 0.5772 0.6883 0.7334 0.8224 0.7684 0.5859 0.625926 0.727287 0.778585 1 5955 89074 8230 6881 5029 51495 694 10790 2 9522 119500 11524 8634 6530 65936 896 16458 0.984411 0 . 0 . 50 8,18,10,10 SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q48|331|PRB1|protein_coding|CODING|NM_005039.3|3|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.759184 0.948138 0 0.469447 rs10845341 -0.692067 0.706407 50 416 1236 MODIFIER 4 CODING PRB2 TA protein_coding NM_006248.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11544524 T TA 0 95 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 178 59,27,53,30 UTR_3_PRIME(MODIFIER||1236||416|PRB2|protein_coding|CODING|NM_006248.3|4|TA) 0 0.5 1 84 0.47191 0 1 0 . 0 59 0 0 1 0 . rs75653436 -0.693147 0.00191133 178 P274S 416 Cct/Tct MODERATE 3 MISSENSE CODING PRB2 A protein_coding NM_006248.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11546192 G A 0 67 0 0.0439 0.3127 0.3588 0.376 0.5477 0.3364 0.141278 0.454959 0.610085 1 1084 58748 3623 3505 4334 40057 488 5657 2 8850 114604 11350 8508 6576 64032 864 14424 0.131191 0 . 0 COSM1600287,COSM1600286 61 19,24,5,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P274S|416|PRB2|protein_coding|CODING|NM_006248.3|3|A) 1 0.5 1 0 . 1 0 1 1 0 36 0 0.824365 0.519408 0 0.690133 rs10845349 -0.688148 0.425169 61 K77 416 aaG/aaA LOW 3 SILENT CODING PRB2 T protein_coding NM_006248.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 11546781 C T 0 195 0 . 0 . 0 . 0 0.0433071 0.12641 0.168876 1 363 20673 2736 998 1209 10799 154 4414 2 8748 114680 11294 8472 6546 63254 870 15496 0.330051 0 . 0 . 72 17,27,14,12 SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K77|416|PRB2|protein_coding|CODING|NM_006248.3|3|T) 1 0.5 1 0 . 0 . 1 1 0 42 0 0.728389 0.0610579 0 0.079803 rs71443675 -0.692976 0.648467 72 452 781 MODIFIER 8 CODING ETV6 G protein_coding NM_001987.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12044761 C G 0 83 0 0 0.010583 0 0.0506 0 0.002 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,2,2 UTR_3_PRIME(MODIFIER||781||452|ETV6|protein_coding|CODING|NM_001987.4|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs72552353 -0.556411 0.168287 5 Y162 327 taC/taT LOW 3 SILENT CODING BCL2L14 T protein_coding NM_138722.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12240199 C T 0 222 0 0.4009 0.4649 0.4582 0.4712 0.5775 0.4335 0.408761 0.519683 0.576512 1 4269 64771 5087 3960 3921 39198 529 7807 2 10406 121376 11578 8634 6612 66730 906 16510 0.765645 0 . 0 . 84 12,19,18,31 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y162|327|BCL2L14|protein_coding|CODING|NM_138722.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.853476 rs879732 -0.693147 0.226716 84 327 156 MODIFIER 6 CODING BCL2L14 G protein_coding NM_138722.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12252078 T G 0 208 0 0.1021 0.251 0.2536 0.3641 0.2823 0.3016 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 19 0,0,1,18 UTR_3_PRIME(MODIFIER||156||327|BCL2L14|protein_coding|CODING|NM_138722.1|6|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1797647 -0.69168 0.244135 19 1613 3077 MODIFIER 23 CODING LRP6 G protein_coding NM_002336.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12270983 A G 0 9.7 0 0.1014 0.0325 0.013 0.0149 0.004 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3077||1613|LRP6|protein_coding|CODING|NM_002336.2|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs75937324 -0.379885 0 1 V1062I 1613 Gtt/Att MODERATE 14 MISSENSE CODING LRP6 T protein_coding NM_002336.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12301898 C T 0 228 0 0.8691 0.8856 0.9121 0.9196 0.83 0.911 0.874489 0.839997 0.822326 2 9053 102882 10818 8043 5373 54154 770 14671 2 10406 121410 11578 8652 6614 66740 908 16512 0 . 0 . 0 175 0,0,103,57 PROTEIN_INTERACTION_LOCUS(HIGH||||1613|LRP6|protein_coding|CODING||14|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1062I|1613|LRP6|protein_coding|CODING|NM_002336.2|14|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2302685 -0.693147 0.857125 175 431 158 MODIFIER 4 CODING MANSC1 G protein_coding NM_018050.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12482803 A G 0 143 0 0.6475 0.7953 0.8689 0.6726 0.993 0.8661 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.220998 0 . 0 . 48 24,1,21,1 UTR_3_PRIME(MODIFIER||158||431|MANSC1|protein_coding|CODING|NM_018050.2|4|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.929009 rs4328285 -0.692562 0.312946 48 L328 431 Cta/Tta LOW 4 SILENT CODING MANSC1 A protein_coding NM_018050.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12483275 G A 0 222 0 0.5454 0.5972 0.6628 0.38 0.7266 0.7117 0.581026 0.695525 0.754186 1 5919 83322 7308 3223 4748 49244 646 12234 2 10384 121336 11566 8636 6614 66718 908 16510 0.690981 0 . 0 COSM147444 70 24,16,17,11 SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L328|431|MANSC1|protein_coding|CODING|NM_018050.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961457 rs1861676 -0.693054 0.453612 70 L182 431 Ttg/Ctg LOW 4 SILENT CODING MANSC1 G protein_coding NM_018050.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12483713 A G 0 222 0 0.4894 0.5819 0.6614 0.375 0.7306 0.7106 0.524966 0.677072 0.755 1 5397 82921 7281 3202 4786 49392 647 12216 2 10398 121348 11564 8636 6610 66720 908 16512 0.717202 0 . 0 COSM147446 104 29,27,23,20 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L182|431|MANSC1|protein_coding|CODING|NM_018050.2|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.367267 rs4763282 -0.693146 0.262897 104 196 289 MODIFIER 1 CODING BORCS5 T protein_coding NM_058169.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12510097 C T 0 106 0 0.0575 0.3644 0.5086 0.2748 0.5288 0.6002 0 . 0 1 31 5956 47 39 0 1441 64 4334 2 210 10484 96 132 0 2686 118 7242 0.50373 0 . 0 . 14 4,4,1,4 UTR_5_PRIME(MODIFIER||289||196|BORCS5|protein_coding|CODING|NM_058169.4|1|T) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.989343 rs10772552 -0.590765 0.345017 14 196 5 MODIFIER 4 CODING BORCS5 C protein_coding NM_058169.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12618715 T C 0 228 0 0.7995 0.9429 0.9784 1 0.999 0.9949 0.843253 0.946456 0.999417 2 7207 110605 10974 8204 6159 61140 801 16120 2 8514 112186 11096 8204 6160 61204 810 16198 0 . 0 . 0 28 0,0,2,25 UTR_3_PRIME(MODIFIER||5||196|BORCS5|protein_coding|CODING|NM_058169.4|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs967648 -0.693021 0.307591 28 196 187 MODIFIER 4 CODING BORCS5 A protein_coding NM_058169.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12618897 G A 0 39.3 0 0.1589 0.4742 0.464 0.7153 0.4165 0.7188 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||187||196|BORCS5|protein_coding|CODING|NM_058169.4|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs9412 -0.453602 0.06 2 120 1940 MODIFIER 4 CODING CREBL2 C protein_coding NM_001310.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12796872 T C 0 222 0 0.1505 0.3594 0.3184 0.4226 0.5497 0.41 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.626401 0 . 0 . 72 18,13,29,4 UTR_3_PRIME(MODIFIER||1940||120|CREBL2|protein_coding|CODING|NM_001310.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.783497 rs386593733,rs4555 -0.693127 0.509537 72 120 2671 MODIFIER 4 CODING CREBL2 T protein_coding NM_001310.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12797603 C T 0 222 0 0.7254 0.88 0.9409 0.9385 0.9423 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.99774 0 . 0 . 65 9,25,5,25 UTR_3_PRIME(MODIFIER||2671||120|CREBL2|protein_coding|CODING|NM_001310.3|4|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.975663 rs15597 -0.693097 0.077786 65 120 2838 MODIFIER 4 CODING CREBL2 C protein_coding NM_001310.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12797770 G C 0 83 0 0.7239 0.8796 0.9409 0.9385 0.9423 0.9213 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.991996 0 . 0 . 19 0,12,0,7 UTR_3_PRIME(MODIFIER||2838||120|CREBL2|protein_coding|CODING|NM_001310.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.724465 rs1802173 -0.636426 0.0490878 19 V189I 415 Gtc/Atc MODERATE 4 MISSENSE CODING GPR19 T protein_coding NM_006143.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12814818 C T 0 228 0 0.7088 0.8878 0.9222 0.997 0.9304 0.9489 0.746482 0.869676 0.932791 2 7794 112656 10929 8568 6509 62686 826 15344 2 10404 121406 11576 8654 6614 66738 908 16512 0 . 0 . 0 72 0,0,31,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V189I|415|GPR19|protein_coding|CODING|NM_006143.2|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4763862 -0.693147 0.151717 72 198 79 MODIFIER 1 CODING CDKN1B C protein_coding NM_004064.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12870695 T C 0 222 0 0.5265 0.6617 0.7824 0.5317 0.7545 0.7975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.969103 0 . 0 . 72 31,4,27,4 UTR_5_PRIME(MODIFIER||79||198|CDKN1B|protein_coding|CODING|NM_004064.4|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.957278 rs34330 -0.69311 0.659606 72 198 2582 MODIFIER 3 CODING CDKN1B A protein_coding NM_004064.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12874462 G A 0 169 0 0.0015 0.0302 0.0202 0.125 0.001 0.0082 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.83527 0 . 0 . 37 3,17,2,13 UTR_3_PRIME(MODIFIER||2582||198|CDKN1B|protein_coding|CODING|NM_004064.4|3|A),UPSTREAM(MODIFIER||4389||279|APOLD1|protein_coding|CODING|NM_001130415.1||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.192023 rs4251697 -0.688148 0.111591 37 198 3037 MODIFIER 3 CODING CDKN1B A protein_coding NM_004064.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12874917 C A 0 80 0 0.3926 0.6256 0.5418 0.8671 0.6431 0.7331 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 4 0,0,4,0 UTR_3_PRIME(MODIFIER||3037||198|CDKN1B|protein_coding|CODING|NM_004064.4|3|A),UPSTREAM(MODIFIER||3934||279|APOLD1|protein_coding|CODING|NM_001130415.1||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7330 -0.556411 0.118267 4 I50 455 atC/atT LOW 2 SILENT CODING DDX47 T protein_coding NM_016355.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 12967127 C T 0 228 0 0.2511 0.3868 0.4121 0.5992 0.2734 0.4499 0.264639 0.273028 0.277326 2 2690 40840 5087 4888 1921 18979 295 6980 2 10406 121396 11578 8640 6614 66738 908 16512 1 0 . 0 . 122 1,0,33,73 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I50|455|DDX47|protein_coding|CODING|NM_016355.3|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs1051374 -0.693147 1.58038e-08 122 A37 357 gcC/gcT LOW 2 SILENT CODING GPRC5A T protein_coding NM_003979.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13061294 C T 0 222 0 0.0401 0.3616 0.4481 0.7173 0.331 0.3998 0.0733091 0.209826 0.279767 1 726 42173 5766 6471 2675 19645 360 6530 2 10402 121222 11572 8634 6606 66666 906 16436 0.97721 0 . 0 . 160 39,31,41,39 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A37|357|GPRC5A|protein_coding|CODING|NM_003979.3|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.119666 rs2075288 -0.693147 0.00710211 160 357 231 MODIFIER 4 CODING GPRC5A A protein_coding NM_003979.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13065704 T A 0 44.4 0 0.7405 0.6593 0.6427 0.874 0.4513 0.5542 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.861511 0 . 0 . 6 2,1,0,3 UTR_3_PRIME(MODIFIER||231||357|GPRC5A|protein_coding|CODING|NM_003979.3|4|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.861511 1 0 0.861511 rs1061036 -0.511536 0.318564 6 357 747 MODIFIER 4 CODING GPRC5A C protein_coding NM_003979.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13066220 T C 0 222 0 0.2731 0.353 0.3026 0.7133 0.2087 0.274 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.824223 0 . 0 . 56 5,21,3,22 UTR_3_PRIME(MODIFIER||747||357|GPRC5A|protein_coding|CODING|NM_003979.3|4|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.960846 rs1061047 -0.692914 0.0516094 56 D238 345 gaC/gaT LOW 1 SILENT CODING GPRC5D A protein_coding NM_018654.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13102605 G A 0 222 0 0.0204 0.2067 0.2046 0.1865 0.3817 0.3006 0.0794371 0.287944 0.394767 1 720 40299 1837 1480 3164 27264 301 5533 2 10404 121360 11568 8622 6612 66734 908 16512 0.975108 0 . 0 . 69 17,17,14,18 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D238|345|GPRC5D|protein_coding|CODING|NM_018654.1|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.93533 rs4630382 -0.69312 0.0949978 69 189 184 MODIFIER 4 CODING HEBP1 C protein_coding NM_015987.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13128058 T C 0 161 0 0.6808 0.877 0.9553 0.9772 0.9384 0.9202 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,16,0 UTR_3_PRIME(MODIFIER||184||189|HEBP1|protein_coding|CODING|NM_015987.4|4|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13479 -0.689466 0.235684 16 D35 622 gaC/gaT LOW 2 SILENT CODING FAM234B T protein_coding NM_020853.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13208552 C T 0 222 0 0.3903 0.3279 0.2752 0.4901 0.17 0.2761 0.353382 0.213748 0.142209 1 3747 28996 4648 4494 1471 9919 188 4529 2 10404 121302 11568 8644 6608 66680 904 16494 0.986723 0 . 0 . 126 28,35,25,28 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D35|622|FAM234B|protein_coding|CODING|NM_020853.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.992594 rs4763924 -0.693147 0.0662348 126 V187 622 gtA/gtG LOW 4 SILENT CODING FAM234B G protein_coding NM_020853.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13214537 A G 0 222 0 0.4735 0.6314 0.7061 0.502 0.827 0.7239 0.526328 0.744964 0.856977 1 5327 90601 6780 4114 5127 56587 714 11952 2 10370 120748 11410 8570 6584 66472 906 16436 0.952408 0 . 0 . 116 35,19,31,19 SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V187|622|FAM234B|protein_coding|CODING|NM_020853.1|4|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.524951 rs3741818 -0.693147 0.285007 116 D443 622 gaT/gaC LOW 9 SILENT CODING FAM234B C protein_coding NM_020853.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13221606 T C 0 228 0 0.9463 0.9844 0.9928 0.999 0.999 1 0.945529 0.981086 0.999302 2 9839 120767 11542 8650 6614 66705 906 16511 2 10406 121402 11578 8650 6614 66734 908 16512 0 . 0 . 0 187 0,0,79,83 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D443|622|FAM234B|protein_coding|CODING|NM_020853.1|9|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1386005 -0.693147 0.107519 187 157 1571 MODIFIER 5 CODING EMP1 T protein_coding NM_001423.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13369196 C T 0 46.3 0 0.2451 0.4333 0.4467 0.5327 0.5278 0.4785 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1571||157|EMP1|protein_coding|CODING|NM_001423.2|5|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8885 -0.453602 0.8 2 1484 988 MODIFIER 13 CODING GRIN2B C protein_coding NM_000834.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13714729 T C 0 228 0 0.6082 0.8914 0.9683 1 0.996 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 83 0,0,47,35 UTR_3_PRIME(MODIFIER||988||1484|GRIN2B|protein_coding|CODING|NM_000834.3|13|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1805477 -0.693147 0.191228 83 T888 1484 acC/acT LOW 13 SILENT CODING GRIN2B A protein_coding NM_000834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 13717508 G A 0 222 0 0.0703 0.3033 0.3213 0.5208 0.2783 0.407 0.108034 0.217823 0.27407 1 1032 37445 4038 4459 2438 18371 320 6787 2 10190 120702 11552 8610 6612 66334 908 16496 0.921994 1|3 not-provided|likely-benign 0 COSM430806 111 34,21,35,19 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T888|1484|GRIN2B|protein_coding|CODING|NM_000834.3|13|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.463917 rs1806201 -0.693147 0.102971 111 P122 1484 ccC/ccG LOW 2 SILENT CODING GRIN2B C protein_coding NM_000834.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14018777 G C 0 222 0 0.4955 0.4415 0.3112 0.4931 0.3618 0.4898 0.492737 0.431032 0.399419 1 5249 50644 3331 4171 2676 26497 396 8324 2 10406 121392 11574 8646 6614 66736 908 16508 0.728844 255 other 0 . 81 22,17,22,14 SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P122|1484|GRIN2B|protein_coding|CODING|NM_000834.3|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.962702 rs7301328 -0.693139 0.346986 81 N356I 1278 aAt/aTt MODERATE 2 MISSENSE CODING ATF7IP T protein_coding NM_181352.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14577892 A T 0 222 0 0.0953 0.3213 0.4928 0.3284 0.3867 0.4305 0.131866 0.307781 0.397907 1 1350 46196 5889 2926 2158 26458 367 7048 2 9864 120326 11538 8620 6606 66352 908 16438 0.499223 0 . 0 . 85 19,19,16,18 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aTt|N356I|1278|ATF7IP|protein_coding|CODING|NM_181352.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.479428 rs2231909 -0.693132 0.00405963 85 K538R 1278 aAa/aGa MODERATE 3 MISSENSE CODING ATF7IP G protein_coding NM_181352.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14587301 A G 0 222 0 0.2852 0.4395 0.3674 0.6181 0.496 0.4571 0.297322 0.42242 0.486512 1 2895 56981 4574 5206 3957 32509 451 7389 2 10280 120886 11528 8628 6612 66456 904 16478 0.925923 0 . 0 COSM1128636 99 25,14,31,13 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K538R|1278|ATF7IP|protein_coding|CODING|NM_181352.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.79125 rs3213764 -0.693146 0.0334077 99 1278 791 MODIFIER 15 CODING ATF7IP T protein_coding NM_181352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14651798 A T 0 8.7 0 0.6611 0.5294 0.5951 0.3869 0.4891 0.4928 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.857143 0 . 0 . 11 0,7,0,2 UTR_3_PRIME(MODIFIER||791||1278|ATF7IP|protein_coding|CODING|NM_181352.1|15|T),DOWNSTREAM(MODIFIER||4799||553|PLBD1|protein_coding|CODING|NM_024829.5||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.714286 rs34712916 -0.453602 0.44 11 1278 2660 MODIFIER 15 CODING ATF7IP A protein_coding NM_181352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14653667 T A 0 9.7 0 0.7413 0.6384 0.5101 0.6627 0.6392 0.5644 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2660||1278|ATF7IP|protein_coding|CODING|NM_181352.1|15|A),DOWNSTREAM(MODIFIER||2930||553|PLBD1|protein_coding|CODING|NM_024829.5||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7955289 -0.379885 0 1 1278 2860 MODIFIER 15 CODING ATF7IP T protein_coding NM_181352.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14653867 C T 0 20.4 0 0.0174 0.267 0.4683 0.2579 0.3489 0.3865 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||2860||1278|ATF7IP|protein_coding|CODING|NM_181352.1|15|T),DOWNSTREAM(MODIFIER||2730||553|PLBD1|protein_coding|CODING|NM_024829.5||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2900333 -0.453602 0.02 2 P534A 553 Cca/Gca MODERATE 11 MISSENSE CODING PLBD1 C protein_coding NM_024829.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14656768 G C 0 222 0 0.6437 0.5136 0.5778 0.38 0.4573 0.4877 0.626646 0.521452 0.467558 1 6704 59205 6684 3446 2594 31163 424 8190 2 10406 121350 11558 8630 6608 66730 908 16510 0.821889 0 . 0 . 257 79,23,90,38 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Gca|P534A|553|PLBD1|protein_coding|CODING|NM_024829.5|11|C),DOWNSTREAM(MODIFIER||899||1278|ATF7IP|protein_coding|CODING|NM_181352.1||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.676173 rs1600 -0.693147 0.561474 257 V377A 553 gTg/gCg MODERATE 8 MISSENSE CODING PLBD1 G protein_coding NM_024829.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14664250 A G 0 222 0 0.0061 0.0725 0.2478 0.0159 0.0537 0.1155 0.0149796 0.0521298 0.0711628 1 162 10328 3587 86 329 4491 58 1615 2 10398 120386 11568 8636 6614 66434 898 15838 0.908252 0 . 0 . 192 77,16,64,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V377A|553|PLBD1|protein_coding|CODING|NM_024829.5|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.868396 rs2287541 -0.693147 0.633802 192 L299 553 Ttg/Ctg LOW 7 SILENT CODING PLBD1 G protein_coding NM_024829.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14664595 A G 0 222 0 0.1876 0.2835 0.3919 0.1925 0.2555 0.4591 0.194961 0.267415 0.304535 1 2058 38405 4802 1725 1301 20594 287 7638 2 10354 121266 11566 8628 6610 66692 908 16508 0.726477 0 . 0 . 106 22,30,17,23 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L299|553|PLBD1|protein_coding|CODING|NM_024829.5|7|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.368105 rs10846013 -0.693145 0.72551 106 V265I 553 Gtc/Atc MODERATE 6 MISSENSE CODING PLBD1 T protein_coding NM_024829.5 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14688644 C T 0 228 0 0.6346 0.8852 0.9553 0.9861 0.9841 0.9683 0.695642 0.881978 0.977442 2 7102 115892 11314 8550 6532 65486 873 16035 2 10406 121410 11578 8654 6614 66738 908 16512 0 . 0 . 0 205 0,0,115,70 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V265I|553|PLBD1|protein_coding|CODING|NM_024829.5|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7957558 -0.693147 0.381805 205 P16 553 ccA/ccG LOW 1 SILENT CODING PLBD1 C protein_coding NM_024829.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14720583 T C 0 127 0 0.7663 0.9239 0.9741 0.9861 0.9871 0.9724 0 . 0 2 144 9675 88 127 6 2278 110 6922 2 178 9888 90 130 6 2294 112 7078 0 . 0 . 0 5 0,0,2,3 SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P16|553|PLBD1|protein_coding|CODING|NM_024829.5|1|C) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs7954623 -0.590765 0.0886428 5 R888Q 1073 cGg/cAg MODERATE 23 MISSENSE CODING GUCY2C T protein_coding NM_004963.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14774089 C T 0 222 0 0 0.0009984 0 0.005 0 0 0.000226963 7.6888e-05 0 1 2 25 0 21 0 0 0 2 2 10404 121328 11542 8646 6614 66706 906 16510 0.942293 0 . 0 . 138 34,41,22,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R888Q|1073|GUCY2C|protein_coding|CODING|NM_004963.3|23|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.778463 rs373549158 -0.693147 0.82987 138 I674 1073 atC/atT LOW 18 SILENT CODING GUCY2C A protein_coding NM_004963.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14794062 G A 0 228 0 0.3896 0.8235 0.951 0.9911 0.992 0.9734 0.494553 0.819622 0.986163 2 4958 114214 11271 8547 6535 65847 872 16184 2 10398 121364 11564 8634 6614 66734 908 16512 0 . 0 . 0 132 0,0,62,60 SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I674|1073|GUCY2C|protein_coding|CODING|NM_004963.3|18|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10772800 -0.693147 0.0382528 132 F281L 1073 ttT/ttG MODERATE 7 MISSENSE CODING GUCY2C C protein_coding NM_004963.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14829893 A C 0 228 0 0.9486 0.9862 0.9986 1 1 1 0.962097 0.98716 1 2 9992 120850 11498 8636 6610 66703 908 16503 2 10406 121306 11532 8636 6610 66708 908 16506 0 . 0 . 0 157 0,0,67,78 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F281L|1073|GUCY2C|protein_coding|CODING|NM_004963.3|7|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1420635 -0.693147 0.368173 157 129 200 MODIFIER 1 CODING H2AFJ C protein_coding NM_177925.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14927994 T C 0 117 0 0.5915 0.5463 0.6484 0.3383 0.5865 0.5859 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.449818 0 . 0 . 32 13,10,4,4 UTR_3_PRIME(MODIFIER||200||129|H2AFJ|protein_coding|CODING|NM_177925.3|1|C),UPSTREAM(MODIFIER||3929||103|HIST4H4|protein_coding|CODING|NM_175054.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.770381 rs2195199 -0.651104 0.806508 32 129 2078 MODIFIER 1 CODING H2AFJ G protein_coding NM_177925.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14929872 A G 0 228 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 85 0,0,39,42 UTR_3_PRIME(MODIFIER||2078||129|H2AFJ|protein_coding|CODING|NM_177925.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6488710 -0.693147 0.0976385 85 129 2261 MODIFIER 1 CODING H2AFJ T protein_coding NM_177925.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14930055 G T 0 222 0 0.5923 0.5461 0.6484 0.3393 0.5895 0.5798 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.252823 0 . 0 . 28 5,8,10,5 UTR_3_PRIME(MODIFIER||2261||129|H2AFJ|protein_coding|CODING|NM_177925.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0668145 rs3789999 -0.688148 0.303795 28 641 2014 MODIFIER 1 CODING WBP11 T protein_coding NM_016312.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14956331 C T 0 21.2 0 0.6445 0.4812 0.5764 0.2252 0.4523 0.4867 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,1,0 UTR_5_PRIME(MODIFIER||2014||641|WBP11|protein_coding|CODING|NM_016312.2|1|T),UPSTREAM(MODIFIER||175||245|C12orf60|protein_coding|CODING|NM_175874.3||T),DOWNSTREAM(MODIFIER||1253||225|SMCO3|protein_coding|CODING|NM_001013698.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3177269 -0.379885 0 3 K75R 225 aAa/aGa MODERATE 2 MISSENSE CODING SMCO3 C protein_coding NM_001013698.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14959391 T C 0 222 0 0.3215 0.1899 0.0893 0.0823 0.1431 0.2423 0.253871 0.183749 0.151777 1 2599 18947 983 646 645 9807 122 4145 2 9802 120762 11572 8626 6614 66736 900 16512 0.924712 0 . 0 . 109 24,29,20,25 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K75R|225|SMCO3|protein_coding|CODING|NM_001013698.2|2|C),UPSTREAM(MODIFIER||2990||641|WBP11|protein_coding|CODING|NM_016312.2||C),INTRON(MODIFIER||||245|C12orf60|protein_coding|CODING|NM_175874.3|1|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.922084 rs2241221 -0.693147 0.735623 109 K65R 245 aAa/aGa MODERATE 2 MISSENSE CODING C12orf60 G protein_coding NM_175874.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14976063 A G 0 222 0 0.3238 0.1903 0.0893 0.0823 0.1431 0.2413 0.260327 0.189143 0.152674 1 2743 19064 981 647 645 9797 122 4129 2 10284 121216 11576 8636 6612 66692 906 16510 0.719877 0 . 0 . 63 26,11,20,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K65R|245|C12orf60|protein_coding|CODING|NM_175874.3|2|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.210623 rs7304054 -0.692914 0.147484 63 N103K 245 aaT/aaA MODERATE 2 MISSENSE CODING C12orf60 A protein_coding NM_175874.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 14976178 T A 0 222 0 0.3238 0.1903 0.0893 0.0823 0.1431 0.2413 0.260327 0.189067 0.152558 1 2758 19082 982 647 645 9799 122 4129 2 10406 121380 11570 8650 6614 66724 908 16508 0.945711 0 . 0 . 136 49,21,29,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N103K|245|C12orf60|protein_coding|CODING|NM_175874.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999471 rs7307438 -0.693146 0.105516 136 128 77 MODIFIER 5 CODING MGP A protein_coding NM_001190839.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15034996 T A 0 228 0 0.9871 0.9966 1 1 1 1 0 . 0 2 9894 119225 11471 8260 6556 65662 896 16486 2 10042 119382 11476 8260 6556 65666 896 16486 0 . 0 . 0 43 0,0,35,6 UTR_3_PRIME(MODIFIER||77||128|MGP|protein_coding|CODING|NM_001190839.1|5|A) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2430735 -0.693145 0.00950646 43 201 128 MODIFIER 6 CODING ARHGDIB C protein_coding NM_001175.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15095328 T C 0 63 0 0 0.0037939 0 0.0179 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.923116 0 . 0 . 14 9,0,5,0 UTR_3_PRIME(MODIFIER||128||201|ARHGDIB|protein_coding|CODING|NM_001175.5|6|C),UPSTREAM(MODIFIER||3845||273|ERP27|protein_coding|CODING|NM_152321.3||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.965069 rs11056249 -0.590765 0.41821 14 D14 201 gaT/gaC LOW 2 SILENT CODING ARHGDIB G protein_coding NM_001175.5 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15103605 A G 0 228 0 1 1 1 1 1 1 0.999773 0.999923 1 2 10404 121348 11558 8652 6614 66704 908 16508 2 10404 121348 11558 8652 6614 66704 908 16508 0 . 0 . 0 38 0,0,10,25 SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D14|201|ARHGDIB|protein_coding|CODING|NM_001175.5|2|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2430711 -0.693136 0.781077 38 G542 1216 ggT/ggC LOW 9 SILENT CODING PTPRO C protein_coding NM_030667.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15669737 T C 0 222 0 0.0605 0.1196 0.134 0.0843 0.1869 0.1564 0.0719473 0.144318 0.181395 1 785 18924 1295 732 1103 12639 135 2235 2 10406 121390 11574 8646 6614 66732 908 16510 0.525628 0 . 0 . 101 34,8,39,8 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G542|1216|PTPRO|protein_coding|CODING|NM_030667.2|9|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.56014 rs1050646 -0.693147 0.10732 101 G1012 1216 ggG/ggA LOW 22 SILENT CODING PTPRO A protein_coding NM_030667.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15733669 G A 0 222 0 0.0681 0.1326 0.049 0.2986 0.0706 0.1718 0.0701316 0.0810395 0.0866279 1 714 11988 604 2767 239 5027 92 2545 2 10404 121278 11568 8578 6604 66704 908 16512 0.607818 0 . 0 . 100 30,20,23,20 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1012|1216|PTPRO|protein_coding|CODING|NM_030667.2|22|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997857 rs3748299 -0.693146 0.522039 100 1216 2416 MODIFIER 27 CODING PTPRO A protein_coding NM_030667.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15750391 G A 0 73 0 0.2526 0.78 0.9236 0.9524 0.993 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2416||1216|PTPRO|protein_coding|CODING|NM_030667.2|27|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs984303 -0.511536 0.878371 3 1216 2788 MODIFIER 27 CODING PTPRO A protein_coding NM_030667.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15750763 G A 0 9.7 0 0.8313 0.9529 0.9813 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2788||1216|PTPRO|protein_coding|CODING|NM_030667.2|27|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs111170663,rs1981754 -0.379885 0 1 822 600 MODIFIER 21 CODING EPS8 G protein_coding NM_004447.5 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 15773651 C G 0 228 0 0.966 0.9904 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 17 0,0,2,15 UTR_3_PRIME(MODIFIER||600||822|EPS8|protein_coding|CODING|NM_004447.5|21|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4304842 -0.690438 0.0245801 17 350 LOW 6 CODING STRAP A protein_coding NM_007178.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16050808 T A 0 228 0 0.2663 0.6701 0.634 0.8552 0.833 0.8834 0.365166 0.673726 0.831742 2 3488 94928 7187 7572 5456 56169 746 14310 2 9930 120254 11554 8610 6602 66464 900 16194 1 0 . 0 . 210 1,0,83,91 SPLICE_SITE_REGION+INTRON(LOW||||350|STRAP|protein_coding|CODING|NM_007178.3|6|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs10772879 -0.693147 0.370652 210 579 390 MODIFIER 9 CODING SLC15A5 C protein_coding NM_001170798.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16342212 T C 0 23.4 0 0.4372 0.5697 0.5288 0.7024 0.4652 0.7485 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,1,2,0 UTR_3_PRIME(MODIFIER||390||579|SLC15A5|protein_coding|CODING|NM_001170798.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs3852572 -0.453602 0.42 4 579 302 MODIFIER 9 CODING SLC15A5 C protein_coding NM_001170798.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16342300 A C 0 9.7 0 0.4365 0.5625 0.5202 0.7024 0.4563 0.728 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||302||579|SLC15A5|protein_coding|CODING|NM_001170798.1|9|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3864919 -0.379885 0 1 N521 579 aaC/aaT LOW 8 SILENT CODING SLC15A5 A protein_coding NM_001170798.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16347308 G A 0 222 0 0.4372 0.5697 0.5288 0.7024 0.4652 0.7485 0.443642 0.469339 0.480515 1 910 11522 172 225 648 3954 109 5504 2 2008 20438 328 338 1622 8050 228 7864 0.973415 0 . 0 . 139 37,24,40,24 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N521|579|SLC15A5|protein_coding|CODING|NM_001170798.1|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.999753 rs3942536 -0.693147 0.204913 139 D494E 579 gaT/gaA MODERATE 7 MISSENSE CODING SLC15A5 T protein_coding NM_001170798.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16369828 A T 0 228 0 0.9856 0.9958 0.9971 1 1 1 0.984827 0.995401 1 2 1947 20185 314 336 1634 7934 226 7794 2 1982 20222 316 336 1634 7934 226 7794 0 . 0 . 0 131 0,0,69,44 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gaT/gaA|D494E|579|SLC15A5|protein_coding|CODING|NM_001170798.1|7|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1671511 -0.693147 0.370465 131 P271L 579 cCg/cTg MODERATE 4 MISSENSE CODING SLC15A5 A protein_coding NM_001170798.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16397677 G A 0 228 0 0.8631 0.9437 0.9438 0.9921 0.9642 0.9816 0.880058 0.939991 0.966059 2 1911 20398 338 334 1614 8299 225 7677 2 2184 21290 354 340 1720 8586 238 7868 0 . 0 . 0 214 0,0,87,111 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P271L|579|SLC15A5|protein_coding|CODING|NM_001170798.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1527014 -0.693147 0.0240635 214 R252L 579 cGt/cTt MODERATE 4 MISSENSE CODING SLC15A5 A protein_coding NM_001170798.1 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16397734 C A 0 222 0 0.4758 0.502 0.4597 0.5069 0.4235 0.6431 0.472543 0.450285 0.440603 1 1065 10878 170 147 705 3855 99 4837 2 2212 21406 380 340 1728 8644 238 7864 0.695995 0 . 0 . 172 25,45,33,47 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGt/cTt|R252L|579|SLC15A5|protein_coding|CODING|NM_001170798.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.119202 rs1852450 -0.693147 0.928954 172 H141Q 579 caT/caA MODERATE 2 MISSENSE CODING SLC15A5 T protein_coding NM_001170798.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16425656 A T 0 222 0 0.5295 0.2788 0.3242 0.1329 0.2097 0.1288 0.475434 0.280333 0.195475 1 1046 4264 114 52 206 1627 43 1176 2 2114 20644 332 336 1636 8128 230 7868 0.998798 0 . 0 . 133 23,39,18,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H141Q|579|SLC15A5|protein_coding|CODING|NM_001170798.1|2|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.677298 rs1799516 -0.693147 0.181737 133 Y112 579 taC/taT LOW 1 SILENT CODING SLC15A5 A protein_coding NM_001170798.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 16430284 G A 0 228 0 0.9766 0.9934 0.9971 1 1 1 0.972543 0.991678 1 2 1751 17021 301 334 6 6860 166 7603 2 1800 17072 302 334 6 6860 166 7604 0 . 0 . 0 113 0,0,96,9 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y112|579|SLC15A5|protein_coding|CODING|NM_001170798.1|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1671487 -0.693147 0.000249368 113 P146L 1486 cCa/cTa MODERATE 2 MISSENSE CODING PIK3C2G T protein_coding NM_001288772.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 18435452 C T 0 228 0 0.3616 0.3532 0.4078 0.3046 0.3917 0.3139 0.355764 0.385896 0.399312 2 3497 46105 4337 2289 2956 27093 330 5603 2 9724 119284 11284 8424 6562 65926 892 16472 1 0 . 0 . 88 0,1,23,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P146L|1486|PIK3C2G|protein_coding|CODING|NM_001288772.1|2|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs11044004 -0.693147 0.321702 88 1486 LOW 11 CODING PIK3C2G G protein_coding NM_001288772.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 18499777 C G 0 228 0 1 1 1 1 1 1 0 . 0 2 9632 118123 11170 8416 6560 65127 884 16334 2 9632 118124 11170 8416 6560 65128 884 16334 0 . 0 . 0 51 0,0,8,42 SPLICE_SITE_REGION+INTRON(LOW||||1486|PIK3C2G|protein_coding|CODING|NM_001288772.1|11|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs10770357 -0.693147 0.3136 51 P952L 1486 cCg/cTg MODERATE 21 MISSENSE CODING PIK3C2G T protein_coding NM_001288772.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 18649057 C T 0 222 0 0.5008 0.3744 0.366 0.3046 0.2425 0.4172 0.444353 0.293299 0.22562 1 1881 11360 517 782 394 4315 90 3381 2 3698 31914 1156 1860 1848 14488 314 8550 0.795378 0 . 0 . 73 18,18,13,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P952L|1486|PIK3C2G|protein_coding|CODING|NM_001288772.1|21|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.113973 rs12312266 -0.693054 0.839548 73 1486 55 MODIFIER 33 CODING PIK3C2G C protein_coding NM_001288772.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 18801017 T C 0 228 0 0.9962 0.999 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 65 0,0,8,53 UTR_3_PRIME(MODIFIER||55||1486|PIK3C2G|protein_coding|CODING|NM_001288772.1|33|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs501379 -0.693147 0.350048 65 1282 64 MODIFIER 1 CODING PLEKHA5 T protein_coding NM_001256470.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 19282670 C T 0 87 0 0.1452 0.4325 0.5447 0.3522 0.7425 0.5051 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.759945 0 . 0 . 16 9,0,7,0 UTR_5_PRIME(MODIFIER||64||1282|PLEKHA5|protein_coding|CODING|NM_001256470.1|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.844114 rs28512290 -0.636426 0.419382 16 G301 517 ggT/ggC LOW 3 SILENT CODING AEBP2 C protein_coding NM_001114176.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 19626205 T C 0 222 0 0.177 0.0929 0.0303 0.1835 0.0089 0.0164 0.12716 0.040919 0.00206762 1 1158 3738 331 1428 358 309 29 125 2 6372 59790 3986 5508 3810 30048 486 9580 0.892476 0 . 0 . 95 18,34,8,18 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G301|517|AEBP2|protein_coding|CODING|NM_001114176.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961319 rs56666201 -0.692976 0.115384 95 V398 1141 gtC/gtT LOW 3 SILENT CODING PDE3A T protein_coding NM_000921.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 20766559 C T 0 228 0 0.7882 0.9105 0.9424 1 0.9364 0.9346 0.805719 0.890358 0.933721 2 8356 112867 10997 8612 6383 62478 847 15194 2 10404 121388 11576 8636 6614 66738 908 16512 0 . 0 . 0 171 0,0,69,86 SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V398|1141|PDE3A|protein_coding|CODING|NM_000921.4|3|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10743380 -0.693147 0.0529423 171 C707R 1141 Tgt/Cgt MODERATE 9 MISSENSE CODING PDE3A C protein_coding NM_000921.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 20790151 T C 0 222 0 0 0.0017971 0 0.0089 0 0 0 . 0 1 0 81 0 78 0 0 1 2 2 10226 117908 11320 8406 6532 64800 882 15742 0.86478 0 . 0 . 133 38,34,27,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C707R|1141|PDE3A|protein_coding|CODING|NM_000921.4|9|C) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.980157 rs141574563 -0.693147 0.0284681 133 A425 730 gcA/gcG LOW 11 SILENT CODING SLCO1C1 G protein_coding NM_001145946.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 20885931 A G 0 222 0 0.0522 0.0787 0.0288 0.1855 0.0865 0.0317 0.0542442 0.0705059 0.0788372 1 578 10107 351 1491 1017 6085 81 504 2 10406 121228 11572 8644 6614 66640 908 16444 0.729669 0 . 0 COSM147455 219 69,37,55,31 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A425|730|SLCO1C1|protein_coding|CODING|NM_001145946.1|11|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.954008 rs16923154 -0.693147 0.710949 219 730 759 MODIFIER 16 CODING SLCO1C1 T protein_coding NM_001145946.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 20906172 C T 0 48.5 0 0.4667 0.6092 0.6614 0.7044 0.6233 0.6524 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 0,1,2,0 UTR_3_PRIME(MODIFIER||759||730|SLCO1C1|protein_coding|CODING|NM_001145946.1|16|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7295794 -0.453602 0.42 4 S112A 702 Tct/Gct MODERATE 5 MISSENSE CODING SLCO1B3 G protein_coding NM_019844.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21011480 T G 0 228 0 0.3563 0.7025 0.8372 0.6974 0.8648 0.9131 0.448025 0.722931 0.863806 2 4558 97627 9174 6272 4995 56908 738 14982 2 10400 121358 11578 8654 6610 66700 908 16508 0.728805 0 . 0 . 310 3,2,114,144 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S112A|702|SLCO1B3|protein_coding|CODING|NM_019844.3|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.0337884 rs4149117 -0.693147 0.211275 310 702 LOW 5 CODING SLCO1B3 T protein_coding NM_019844.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21013948 C T 0 228 0 0.3555 0.7023 0.8372 0.6984 0.8638 0.9131 0.448064 0.722239 0.863147 2 4246 95861 9009 6231 4930 55864 709 14872 2 9534 118852 11384 8592 6528 65542 872 16400 0 . 0 . 0 120 0,0,65,47 SPLICE_SITE_REGION+INTRON(LOW||||702|SLCO1B3|protein_coding|CODING|NM_019844.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3764009 -0.693147 0.944157 120 M233I 702 atG/atA MODERATE 8 MISSENSE CODING SLCO1B3 A protein_coding NM_019844.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21015760 G A 0 228 0 0.3555 0.7025 0.8372 0.6984 0.8648 0.9131 0.447571 0.72282 0.863837 2 4557 97617 9169 6270 4997 56909 738 14977 2 10402 121360 11576 8650 6614 66704 908 16506 1 0 . 0 . 152 1,0,51,80 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M233I|702|SLCO1B3|protein_coding|CODING|NM_019844.3|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs7311358 -0.693147 0.00462891 152 A519 702 gcA/gcG LOW 13 SILENT CODING SLCO1B3 G protein_coding NM_019844.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21036411 A G 0 228 0 0.3578 0.7029 0.8357 0.6974 0.8648 0.9141 0.448706 0.723051 0.863605 2 4558 97604 9145 6274 4995 56897 738 14997 2 10386 121296 11546 8644 6608 66700 908 16504 1 0 . 0 . 138 1,0,78,46 SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A519|702|SLCO1B3|protein_coding|CODING|NM_019844.3|13|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2053098 -0.693147 0.000910642 138 G611 702 ggG/ggA LOW 15 SILENT CODING SLCO1B3 A protein_coding NM_019844.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21054369 G A 0 222 0 0.2375 0.6787 0.7882 0.7312 0.8757 0.9407 0.362914 0.712364 0.891395 1 3480 99311 8953 6510 5114 58978 750 15526 2 10406 121376 11558 8652 6614 66726 908 16512 0.951889 0 . 0 . 111 27,25,15,28 SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G611|702|SLCO1B3|protein_coding|CODING|NM_019844.3|15|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0122107 rs3764006 -0.693146 0.00756065 111 V167A 640 gTa/gCa MODERATE 5 MISSENSE CODING SLCO1B7 C protein_coding NM_001009562.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21176135 T C 0 228 0 0.9599 0.9597 0.9078 0.998 0.9443 0.9724 0.964986 0.948233 0.939851 2 9447 113543 10181 8553 6280 62272 851 15959 2 9828 119570 11218 8582 6576 66058 898 16410 0 . 0 . 0 242 0,0,160,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V167A|640|SLCO1B7|protein_coding|CODING|NM_001009562.4|5|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1546308 -0.693147 0.0361967 242 A338T 640 Gct/Act MODERATE 8 MISSENSE CODING SLCO1B7 A protein_coding NM_001009562.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21201663 G A 0 204 0 0.0885 0.4738 0.634 0.3829 0.6402 0.8037 0.206633 0.514713 0.658793 1 929 34979 2905 1472 2458 18681 304 8230 2 3862 52086 3850 2780 3708 27018 480 10388 0.989747 0 . 0 . 59 20,3,28,2 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A338T|640|SLCO1B7|protein_coding|CODING|NM_001009562.4|8|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.673973 rs11045689 -0.693097 0.193659 59 N628 640 aaC/aaT LOW 13 SILENT CODING SLCO1B7 T protein_coding NM_001009562.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21243001 C T 0 222 0 0.0688 0.1406 0.0476 0.4663 0.0606 0.0501 0.0631604 0.0465814 0.0384615 1 638 10007 573 3889 1136 2853 100 818 2 9310 112488 10446 8252 6426 61710 858 15486 0.855931 0 . 0 . 149 32,30,38,34 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|640|SLCO1B7|protein_coding|CODING|NM_001009562.4|13|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.974436 rs73241801 -0.693147 0.524629 149 N130D 691 Aat/Gat MODERATE 5 MISSENSE CODING SLCO1B1 G protein_coding NM_006446.4 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21329738 A G 0 228 0 0.8177 0.6224 0.4726 0.7619 0.4026 0.547 0.765121 0.526295 0.403734 2 7933 58012 4955 6487 2968 27306 452 7911 2 10330 120988 11516 8650 6604 66488 900 16500 0 . 0 . 0 71 0,0,32,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N130D|691|SLCO1B1|protein_coding|CODING|NM_006446.4|5|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2306283 -0.693147 0.139216 71 F199 691 ttC/ttT LOW 6 SILENT CODING SLCO1B1 T protein_coding NM_006446.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21331625 C T 0 228 0 0.5598 0.4155 0.3314 0.5109 0.3966 0.2014 0.544939 0.448947 0.399767 2 5725 46708 2874 4419 3029 27014 386 3261 2 10402 121276 11530 8650 6606 66674 908 16506 1 0 . 0 . 158 1,0,59,77 SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F199|691|SLCO1B1|protein_coding|CODING|NM_006446.4|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2291075 -0.693147 0.0535944 158 691 167 MODIFIER 15 CODING SLCO1B1 C protein_coding NM_006446.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21392290 T C 0 161 0 0 0.0819 0.0144 0.3373 0.0199 0.0409 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 18 0,0,0,18 UTR_3_PRIME(MODIFIER||167||691|SLCO1B1|protein_coding|CODING|NM_006446.4|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4149085 -0.691153 0.873966 18 691 439 MODIFIER 15 CODING SLCO1B1 G protein_coding NM_006446.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21392562 T G 0 9.7 0 0.2935 0.4477 0.3919 0.745 0.4125 0.4254 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||439||691|SLCO1B1|protein_coding|CODING|NM_006446.4|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4149087 -0.379885 0 1 691 463 MODIFIER 15 CODING SLCO1B1 G protein_coding NM_006446.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21392586 A G 0 9.7 0 0.2935 0.4485 0.3963 0.745 0.4135 0.4254 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||463||691|SLCO1B1|protein_coding|CODING|NM_006446.4|15|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4149088 -0.379885 0 1 670 4583 MODIFIER 14 CODING SLCO1A2 G protein_coding NM_021094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21417899 T G 0 26.4 0 0.1248 0.1388 0.0288 0.3651 0.0209 0.1237 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,0,2 UTR_3_PRIME(MODIFIER||4583||670|SLCO1A2|protein_coding|CODING|NM_021094.3|14|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs10841778 -0.453602 0.74 4 670 4357 MODIFIER 14 CODING SLCO1A2 A protein_coding NM_021094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21418125 G A 0 9.7 0 1 1 1 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4357||670|SLCO1A2|protein_coding|CODING|NM_021094.3|14|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2219790,rs386561347 -0.379885 0 1 670 4339 MODIFIER 14 CODING SLCO1A2 T protein_coding NM_021094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21418143 C T 0 9.7 0 0.1543 0.149 0.036 0.3651 0.0249 0.1268 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4339||670|SLCO1A2|protein_coding|CODING|NM_021094.3|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs10841780 -0.379885 0 1 670 2011 MODIFIER 14 CODING SLCO1A2 T protein_coding NM_021094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21420471 C T 0 77 0 0.5756 0.3812 0.2406 0.37 0.2962 0.317 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2011||670|SLCO1A2|protein_coding|CODING|NM_021094.3|14|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4149009 -0.511536 0.267404 3 670 117 MODIFIER 14 CODING SLCO1A2 T protein_coding NM_021094.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21422365 G T 0 51 0 0.4569 0.2861 0.1513 0.3651 0.17 0.1892 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.110265 0 . 0 . 20 12,1,7,0 UTR_3_PRIME(MODIFIER||117||670|SLCO1A2|protein_coding|CODING|NM_021094.3|14|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.838107 rs386591284,rs4140389 -0.636426 0.15244 20 500 108 MODIFIER 1 CODING PYROXD1 C protein_coding NM_024854.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21590557 A C 0 145 0 0.4955 0.4972 0.4971 0.5486 0.4801 0.4642 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.90879 0 . 0 . 57 4,0,52,1 UTR_5_PRIME(MODIFIER||108||500|PYROXD1|protein_coding|CODING|NM_024854.3|1|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.998903 rs2058463 -0.693147 0.981548 57 500 44 MODIFIER 1 CODING PYROXD1 C protein_coding NM_024854.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21590621 T C 0 228 0 0.4932 0.4866 0.4841 0.5476 0.4483 0.456 0.467108 0.477931 0.483482 2 2485 30040 1703 2564 731 17237 230 5090 2 5042 61202 3392 4504 1616 35186 440 11022 0.960154 0 . 0 . 131 4,0,102,17 START_GAINED(LOW||||500|PYROXD1|protein_coding|CODING|NM_024854.3|1|C),UTR_5_PRIME(MODIFIER||44||500|PYROXD1|protein_coding|CODING|NM_024854.3|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.201681 rs2058464 -0.693147 0.096308 131 500 363 MODIFIER 12 CODING PYROXD1 C protein_coding NM_024854.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21622051 A C 0 77 0 0.0212 0.0895 0.0807 0.2669 0.0487 0.047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||363||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|C),UTR_3_PRIME(MODIFIER||1077||649|RECQL|protein_coding|CODING|NM_002907.3|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13266 -0.511536 0.036923 3 649 1077 MODIFIER 15 CODING RECQL C protein_coding NM_002907.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21622051 A C 0 77 0 0.0212 0.0895 0.0807 0.2669 0.0487 0.047 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||363||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|C),UTR_3_PRIME(MODIFIER||1077||649|RECQL|protein_coding|CODING|NM_002907.3|15|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs13266 -0.511536 0.036923 3 Q633 649 caA/caG LOW 15 SILENT CODING RECQL C protein_coding NM_002907.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21623179 T C 0 228 0 0.1483 0.1508 0.1066 0.2917 0.0895 0.1033 0.0829169 0.0746303 0.0703799 2 1272 13339 1122 2805 659 5807 105 1569 2 10112 119516 11292 8576 6550 65746 894 16346 0.255102 0 . 0 . 101 1,4,39,41 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q633|649|RECQL|protein_coding|CODING|NM_002907.3|15|C),UTR_3_PRIME(MODIFIER||1491||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|C) 1 0 . 0 . 1 0 1 1 0 44 0 0.430639 2.08418e-07 0 0.908171 rs17849408,rs61754415 -0.693147 4.79478e-05 101 500 1491 MODIFIER 12 CODING PYROXD1 C protein_coding NM_024854.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21623179 T C 0 228 0 0.1483 0.1508 0.1066 0.2917 0.0895 0.1033 0.0829169 0.0746303 0.0703799 2 1272 13339 1122 2805 659 5807 105 1569 2 10112 119516 11292 8576 6550 65746 894 16346 0.255102 0 . 0 . 101 1,4,39,41 SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q633|649|RECQL|protein_coding|CODING|NM_002907.3|15|C),UTR_3_PRIME(MODIFIER||1491||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|C) 1 0 . 0 . 1 0 1 1 0 44 0 0.430639 2.08418e-07 0 0.908171 rs17849408,rs61754415 -0.693147 4.79478e-05 101 N577 649 aaT/aaC LOW 14 SILENT CODING RECQL G protein_coding NM_002907.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21623969 A G 0 228 0 0.1483 0.1514 0.1066 0.2946 0.0895 0.1033 0.113028 0.0989695 0.0917655 2 1292 13431 1127 2826 659 5841 105 1581 2 10272 119970 11288 8604 6518 65998 900 16390 0.0818182 0 . 0 . 133 2,0,71,39 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N577|649|RECQL|protein_coding|CODING|NM_002907.3|14|G),UTR_3_PRIME(MODIFIER||2281||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.345455 rs6500 -0.693147 0.715801 133 500 2281 MODIFIER 12 CODING PYROXD1 G protein_coding NM_024854.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21623969 A G 0 228 0 0.1483 0.1514 0.1066 0.2946 0.0895 0.1033 0.113028 0.0989695 0.0917655 2 1292 13431 1127 2826 659 5841 105 1581 2 10272 119970 11288 8604 6518 65998 900 16390 0.0818182 0 . 0 . 133 2,0,71,39 SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N577|649|RECQL|protein_coding|CODING|NM_002907.3|14|G),UTR_3_PRIME(MODIFIER||2281||500|PYROXD1|protein_coding|CODING|NM_024854.3|12|G) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.345455 rs6500 -0.693147 0.715801 133 138 27 MODIFIER 1 CODING GOLT1B T protein_coding NM_016072.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21654831 G T 0 228 0 0.2753 0.7057 0.7723 0.9732 0.7714 0.8967 0.376078 0.641627 0.777674 2 3406 91346 9592 8277 4960 50379 640 14092 2 9734 116852 11160 8510 5854 64526 840 16228 0 . 0 . 0 222 0,0,105,94 UTR_5_PRIME(MODIFIER||27||138|GOLT1B|protein_coding|CODING|NM_016072.4|1|T),UPSTREAM(MODIFIER||228||649|RECQL|protein_coding|CODING|NM_002907.3||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1060126 -0.693147 0.00555159 222 138 1611 MODIFIER 5 CODING GOLT1B C protein_coding NM_016072.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21670252 G C 0 228 0 0.0038 0.0605 0.0591 0.1954 0.0199 0.0409 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.987422 0 . 0 . 147 2,1,53,77 UTR_3_PRIME(MODIFIER||1611||138|GOLT1B|protein_coding|CODING|NM_016072.4|5|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 0.984931 rs71539413 -0.693147 0.0330208 147 138 2466 MODIFIER 5 CODING GOLT1B G protein_coding NM_016072.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21671107 A G 0 67 0 0.0431 0.0881 0.0692 0.2044 0.0676 0.0634 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||2466||138|GOLT1B|protein_coding|CODING|NM_016072.4|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs80115468 -0.511536 0.421281 3 T87 341 acT/acC LOW 4 SILENT CODING LDHB G protein_coding NM_001315537.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 21797029 A G 0 228 0 0.8328 0.9523 0.9942 1 0.996 0.9898 0.870404 0.954175 0.997093 2 9072 119530 11464 8642 6606 66473 900 16373 2 10398 121304 11538 8646 6610 66702 908 16502 0 . 0 . 0 67 0,0,14,47 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T87|341|LDHB|protein_coding|CODING|NM_001315537.1|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1650294 -0.693147 0.00138769 67 P432 1549 ccT/ccC LOW 8 SILENT CODING ABCC9 G protein_coding NM_005691.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22063115 A G 0 228 0 0.9902 0.9972 0.9986 1 1 1 0.98956 0.996463 1 2 10297 121175 11517 8642 6612 66696 907 16504 2 10402 121300 11534 8642 6612 66698 908 16504 0 3,2 likely-benign,benign 0 . 49 0,0,27,19 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P432|1549|ABCC9|protein_coding|CODING|NM_005691.3|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs10770865 -0.693147 0.105805 49 1549 LOW 4 CODING ABCC9 T protein_coding NM_005691.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22068849 G T 0 228 0 0.5893 0.6448 0.549 0.8026 0.6402 0.6299 0.579055 0.587937 0.592485 2 5749 72760 6082 6681 3895 39284 581 10488 2 9730 118540 11276 8496 6554 65200 890 16394 1 2,2 benign,benign 0 . 61 0,1,5,52 SPLICE_SITE_REGION+INTRON(LOW||||1549|ABCC9|protein_coding|CODING|NM_005691.3|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3759236 -0.693147 0.233603 61 Y238 434 taC/taT LOW 5 SILENT CODING CMAS T protein_coding NM_018686.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22213786 C T 0 222 0 0.1452 0.2532 0.1902 0.4524 0.0885 0.408 0.154562 0.118905 0.100628 1 1571 22649 2902 4154 872 7005 145 6000 2 10402 121348 11574 8642 6614 66698 908 16510 0.983179 0 . 0 . 199 76,14,63,17 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y238|434|CMAS|protein_coding|CODING|NM_018686.4|5|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.99103 rs10841930 -0.693147 0.0101904 199 356 3947 MODIFIER 5 CODING ST8SIA1 G protein_coding NM_003034.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22350539 A G 0 32.6 0 0.0651 0.0457 0.0216 0.1062 0.008 0.0133 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||3947||356|ST8SIA1|protein_coding|CODING|NM_003034.3|5|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs16924743 -0.379885 0 2 356 1303 MODIFIER 5 CODING ST8SIA1 A protein_coding NM_003034.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22353183 G A 0 9.7 0 0.6876 0.8101 0.8689 0.8462 0.7654 0.9427 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1303||356|ST8SIA1|protein_coding|CODING|NM_003034.3|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4762737 -0.379885 0 1 I212 356 atT/atC LOW 5 SILENT CODING ST8SIA1 G protein_coding NM_003034.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22354921 A G 0 222 0 0.6876 0.8101 0.8689 0.8462 0.7654 0.9427 0.72719 0.761725 0.779419 1 7608 97751 9924 7256 4700 52139 740 15384 2 10392 121176 11520 8638 6606 66610 906 16504 0.988989 0 . 0 . 72 11,12,15,23 SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I212|356|ST8SIA1|protein_coding|CODING|NM_003034.3|5|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.416005 rs386606889,rs704219 -0.693143 0.177671 72 E288 452 gaA/gaG LOW 4 SILENT CODING ETNK1 G protein_coding NM_018638.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22814036 A G 0 228 0 0.0794 0.256 0.196 0.6925 0.1292 0.2178 0.0891965 0.106874 0.11593 2 874 22994 3486 6051 1415 7704 204 3260 2 10392 121292 11538 8650 6612 66684 908 16508 0 . 0 . 0 99 0,0,56,38 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E288|452|ETNK1|protein_coding|CODING|NM_018638.4|4|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs386486630,rs4963793 -0.693147 0.0784725 99 452 5319 MODIFIER 8 CODING ETNK1 C protein_coding NM_018638.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 22843207 A C 0 228 0 0.0605 0.2776 0.1916 0.7589 0.1412 0.2761 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 91 0,1,33,52 UTR_3_PRIME(MODIFIER||5319||452|ETNK1|protein_coding|CODING|NM_018638.4|8|C) 0 . 0 . 0 1 0 . 0 . 60 0 1 1 0 1 rs9435 -0.693147 0.29619 91 398 7372 MODIFIER 11 CODING BCAT1 A protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24963570 G A 0 9.7 0 0.5976 0.5228 0.5648 0.3274 0.6292 0.4836 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||7372||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2353484 -0.379885 0 1 398 2193 MODIFIER 11 CODING BCAT1 G protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24968749 A G 0 32.6 0 0.7421 0.7796 0.8069 0.8442 0.7097 0.816 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||2193||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4453321 -0.379885 0 2 398 1888 MODIFIER 11 CODING BCAT1 C protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24969054 T C 0 9.7 0 0.761 0.7851 0.8098 0.8442 0.7097 0.817 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1888||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2046524 -0.379885 0 1 398 1579 MODIFIER 11 CODING BCAT1 G protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24969363 C G 0 6.3 0 0.7413 0.7794 0.8069 0.8442 0.7097 0.816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1579||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3198082 -0.379885 0 1 398 1133 MODIFIER 11 CODING BCAT1 T protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24969809 C T 0 18.2 0 0.7413 0.7794 0.8069 0.8442 0.7097 0.816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 3 0,1,2,0 UTR_3_PRIME(MODIFIER||1133||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs7134871 -0.453602 0.36 3 398 707 MODIFIER 11 CODING BCAT1 G protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24970235 A G 0 136 0 0.7405 0.779 0.8055 0.8442 0.7097 0.816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.922496 0 . 0 . 31 13,4,10,0 UTR_3_PRIME(MODIFIER||707||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.679751 rs6487421 -0.670168 0.717543 31 398 234 MODIFIER 11 CODING BCAT1 A protein_coding NM_001178093.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 24970708 G A 0 113 0 0.7368 0.778 0.8055 0.8442 0.7097 0.816 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.958048 0 . 0 . 17 7,0,10,0 UTR_3_PRIME(MODIFIER||234||398|BCAT1|protein_coding|CODING|NM_001178093.1|11|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.989343 rs2220269 -0.670168 0.874265 17 145 361 MODIFIER 4 CODING C12orf77 G protein_coding NM_001101339.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25146870 A G 0 46.3 0 0.8434 0.9575 0.9914 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||361||145|C12orf77|protein_coding|CODING|NM_001101339.2|4|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs699029 -0.453602 0.82 2 145 39 MODIFIER 4 CODING C12orf77 T protein_coding NM_001101339.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25147192 A T 0 174 0 0.0038 0.1579 0.0533 0.3264 0.0596 0.3681 0.0223881 0.0590685 0.0753559 1 141 11670 667 2094 519 3978 95 4176 2 7208 83468 6520 6048 4678 45876 642 12496 0.980625 0 . 0 . 27 9,3,9,1 UTR_3_PRIME(MODIFIER||39||145|C12orf77|protein_coding|CODING|NM_001101339.2|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.533519 rs16928315 -0.670168 0.86321 27 L131F 145 ttG/ttC MODERATE 3 MISSENSE CODING C12orf77 G protein_coding NM_001101339.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25148755 C G 0 228 0 0.8616 0.9493 0.9726 1 0.9553 0.9928 0.883224 0.963844 0.999877 2 8421 115961 11262 8620 6374 64090 860 16334 2 9654 120344 11568 8620 6614 66484 892 16512 0 . 0 . 0 80 0,0,45,29 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L131F|145|C12orf77|protein_coding|CODING|NM_001101339.2|3|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs864161 -0.693147 0.00363409 80 499 17101 MODIFIER 1 CODING LRMP C protein_coding NM_001204126.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25205241 G C 0 148 0 0.2224 0.2218 0.1902 0.2708 0.2127 0.2025 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.938005 0 . 0 . 29 13,2,8,1 UTR_5_PRIME(MODIFIER||17101||499|LRMP|protein_coding|CODING|NM_001204126.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.978458 rs2086939 -0.662043 0.871535 29 L141V 499 Ctt/Gtt MODERATE 10 MISSENSE CODING LRMP G protein_coding NM_001204126.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25242595 C G 0 228 0 0.5832 0.7354 0.7594 0.8968 0.7416 0.7515 0.609623 0.711364 0.763488 2 6344 90354 7998 7599 4329 51456 671 11957 2 10400 121204 11538 8638 6588 66630 908 16502 0 . 0 . 0 172 0,0,105,48 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Gtt|L141V|499|LRMP|protein_coding|CODING|NM_001204126.1|10|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7969931 -0.693147 8.31875e-05 172 C197S 499 tGt/tCt MODERATE 12 MISSENSE CODING LRMP C protein_coding NM_001204126.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25243115 G C 0 228 0 0.1657 0.4994 0.5231 0.8095 0.5189 0.5941 0.229687 0.429494 0.53186 2 2271 65115 5978 6705 3724 36217 530 9690 2 10220 120886 11534 8620 6610 66600 908 16394 0 . 0 . 0 172 0,0,42,111 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C197S|499|LRMP|protein_coding|CODING|NM_001204126.1|12|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs1908946 -0.693147 2.51427e-06 172 A639E 722 gCa/gAa MODERATE 16 MISSENSE CODING CASC1 T protein_coding NM_018272.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25261735 G T 0 197 0 0.9894 0.9968 0.9971 1 1 1 0.995915 0.998616 1 2 10252 120758 11502 8628 6606 66406 900 16464 2 10308 120818 11506 8628 6606 66406 900 16464 0 . 0 . 0 47 0,0,0,46 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gAa|A639E|722|CASC1|protein_coding|CODING|NM_018272.3|16|T),DOWNSTREAM(MODIFIER||466||499|LRMP|protein_coding|CODING|NM_001204126.1||T) 1 0 . 0 . 1 0 1 1 0 60 0 0 . 0 . rs859146 -0.693147 5.70086e-15 47 90 329 MODIFIER 3 CODING LYRM5 C protein_coding NM_001001660.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25357574 CAA C 0 228 0 0.2617 0.5435 0.5086 0.8175 0.5229 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,8,1 UTR_3_PRIME(MODIFIER||329||90|LYRM5|protein_coding|CODING|NM_001001660.2|3|C),DOWNSTREAM(MODIFIER||148||189|KRAS|protein_coding|CODING|NM_033360.3||C) 0 . 0 9 1 1 1 0 . 0 60 0 0 1 0 . rs34624917 -0.662043 0.195999 9 90 383 MODIFIER 3 CODING LYRM5 T protein_coding NM_001001660.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25357628 TA T 0 152 0 0.2784 0.5485 0.5115 0.8175 0.5239 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 12 0,0,11,0 UTR_3_PRIME(MODIFIER||383||90|LYRM5|protein_coding|CODING|NM_001001660.2|3|T),DOWNSTREAM(MODIFIER||94||189|KRAS|protein_coding|CODING|NM_033360.3||T) 0 . 0 12 1 1 1 0 . 0 60 0 0 . 0 . rs61501128 -0.676189 0.409198 12 189 9725 MODIFIER 6 CODING KRAS T protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25358650 A T 0 228 0 0.2791 0.5483 0.5101 0.8175 0.5229 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 31 0,0,7,23 UTR_3_PRIME(MODIFIER||9725||189|KRAS|protein_coding|CODING|NM_033360.3|6|T),DOWNSTREAM(MODIFIER||701||90|LYRM5|protein_coding|CODING|NM_001001660.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12245 -0.693097 0.00586877 31 189 9547 MODIFIER 6 CODING KRAS G protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25358828 T G 0 45.5 0 0.2791 0.5483 0.5101 0.8175 0.5229 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||9547||189|KRAS|protein_coding|CODING|NM_033360.3|6|G),DOWNSTREAM(MODIFIER||879||90|LYRM5|protein_coding|CODING|NM_001001660.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs12587 -0.511536 0.392388 3 189 9432 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25358943 T C 0 176 0 0.2791 0.5485 0.5115 0.8175 0.5229 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,10,1 UTR_3_PRIME(MODIFIER||9432||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||994||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs8720 -0.676189 0.44694 11 189 9406 MODIFIER 6 CODING KRAS G protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25358969 T G 0 186 0 0.087 0.4333 0.4741 0.8095 0.4354 0.4826 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 11 0,0,9,2 UTR_3_PRIME(MODIFIER||9406||189|KRAS|protein_coding|CODING|NM_033360.3|6|G),DOWNSTREAM(MODIFIER||1020||90|LYRM5|protein_coding|CODING|NM_001001660.2||G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1137196 -0.676189 0.594614 11 189 9197 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25359178 G C 0 222 0 0 0.0019968 0 0.0089 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.999836 0 . 0 . 122 44,19,34,13 UTR_3_PRIME(MODIFIER||9197||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||1229||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.950929 rs188922523 -0.693147 0.244897 122 189 9047 MODIFIER 6 CODING KRAS T protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25359328 A T 0 228 0 0.2791 0.5481 0.5115 0.8165 0.5229 0.6871 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 77 0,0,17,49 UTR_3_PRIME(MODIFIER||9047||189|KRAS|protein_coding|CODING|NM_033360.3|6|T),DOWNSTREAM(MODIFIER||1379||90|LYRM5|protein_coding|CODING|NM_001001660.2||T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1137189 -0.693147 0.00100744 77 189 9023 MODIFIER 6 CODING KRAS A protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25359352 G A 0 228 0 0.2791 0.5485 0.5115 0.8175 0.5229 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 56 0,0,10,40 UTR_3_PRIME(MODIFIER||9023||189|KRAS|protein_coding|CODING|NM_033360.3|6|A),DOWNSTREAM(MODIFIER||1403||90|LYRM5|protein_coding|CODING|NM_001001660.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1137188 -0.693147 0.0272353 56 189 8534 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25359841 T C 0 39.3 0 0.1944 0.5256 0.5072 0.8185 0.5219 0.6881 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,2,0 UTR_3_PRIME(MODIFIER||8534||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||1892||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs13096 -0.453602 0.32 2 189 8237 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25360138 T C 0 39.3 0 0.9592 0.9886 0.9957 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||8237||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||2189||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4963858 -0.453602 0.76 2 189 7284 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25361091 T C 0 228 0 0.9917 0.9974 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 254 0,0,199,42 UTR_3_PRIME(MODIFIER||7284||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||3142||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4597149 -0.693147 0.184887 254 189 6158 MODIFIER 6 CODING KRAS G protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25362217 A G 0 228 0 0.2806 0.5491 0.5115 0.8185 0.5229 0.6881 0 . 0 2 97 6953 62 109 0 1725 82 4878 2 260 10934 102 142 0 2826 120 7484 0 . 0 . 0 20 0,0,7,13 UTR_3_PRIME(MODIFIER||6158||189|KRAS|protein_coding|CODING|NM_033360.3|6|G),DOWNSTREAM(MODIFIER||4268||90|LYRM5|protein_coding|CODING|NM_001001660.2||G) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs386621250,rs9266 -0.692067 0.799558 20 189 5910 MODIFIER 6 CODING KRAS A protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25362465 G A 0 228 0 0.9909 0.9972 0.9971 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 121 0,0,83,22 UTR_3_PRIME(MODIFIER||5910||189|KRAS|protein_coding|CODING|NM_033360.3|6|A),DOWNSTREAM(MODIFIER||4516||90|LYRM5|protein_coding|CODING|NM_001001660.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4285970 -0.693147 0.0425742 121 189 5823 MODIFIER 6 CODING KRAS C protein_coding NM_033360.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25362552 A C 0 228 0 0.177 0.5206 0.5058 0.8185 0.5219 0.6871 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 132 0,0,50,72 UTR_3_PRIME(MODIFIER||5823||189|KRAS|protein_coding|CODING|NM_033360.3|6|C),DOWNSTREAM(MODIFIER||4603||90|LYRM5|protein_coding|CODING|NM_001001660.2||C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs111193901,rs712 -0.693147 0.572451 132 R161 189 agG/agA LOW 5 SILENT CODING KRAS T protein_coding NM_033360.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25368462 C T 0 228 0 0.9924 0.9976 0.9971 1 1 1 0.995688 0.998539 1 2 10347 121320 11571 8654 6614 66718 906 16510 2 10400 121376 11574 8654 6614 66718 906 16510 0 2,2|2 benign,benign|benign 0 . 95 0,0,45,39 SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R161|189|KRAS|protein_coding|CODING|NM_033360.3|5|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs4362222 -0.693147 0.0715042 95 T387S 409 Act/Tct MODERATE 8 MISSENSE CODING LMNTD1 A protein_coding NM_001145728.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25671759 T A 0 228 0 0.5287 0.7149 0.7248 0.876 0.7942 0.7117 0.575579 0.744041 0.830349 2 5938 95354 8799 7461 4510 55194 709 12743 2 10406 121392 11574 8644 6614 66734 908 16512 0.941667 0 . 0 . 133 1,1,81,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Tct|T387S|409|LMNTD1|protein_coding|CODING|NM_001145728.2|8|A) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.308333 rs1479500 -0.693147 0.0144457 133 409 241 MODIFIER 1 CODING LMNTD1 A protein_coding NM_001145728.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 25706134 G A 0 169 0 0.531 0.6188 0.6844 0.6786 0.7177 0.5276 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 26 0,0,0,26 START_GAINED(LOW||||409|LMNTD1|protein_coding|CODING|NM_001145728.2|1|A),UTR_5_PRIME(MODIFIER||241||409|LMNTD1|protein_coding|CODING|NM_001145728.2|1|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs829047 -0.692976 0.0230382 26 419 2736 MODIFIER 1 CODING RASSF8 A protein_coding NM_001164746.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26205541 T A 0 9.7 0 0.8048 0.8876 0.9092 0.9851 0.8439 0.9284 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2736||419|RASSF8|protein_coding|CODING|NM_001164746.1|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1513125 -0.379885 0 1 419 2719 MODIFIER 1 CODING RASSF8 C protein_coding NM_001164746.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26205558 T C 0 9.7 0 0.2663 0.3502 0.2954 0.2817 0.503 0.4162 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_5_PRIME(MODIFIER||2719||419|RASSF8|protein_coding|CODING|NM_001164746.1|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1513124 -0.379885 0 1 T80 419 acT/acC LOW 3 SILENT CODING RASSF8 C protein_coding NM_001164746.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26217567 T C 0 222 0 0.0121 0.1298 0.1988 0.3105 0.001 0.1861 0.0201997 0.0113794 0.00686046 1 193 9039 3152 2442 6 446 49 2751 2 10402 121230 11560 8644 6612 66656 908 16448 0.993267 0 . 0 . 90 22,22,21,17 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T80|419|RASSF8|protein_coding|CODING|NM_001164746.1|3|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.946971 rs1495660 -0.693143 0.985979 90 419 408 MODIFIER 5 CODING RASSF8 C protein_coding NM_001164746.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26222158 CTT C 0 30.4 0 0.2617 0.3153 0.2291 0.2907 0.4374 0.3487 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 1,0,1,1 UTR_3_PRIME(MODIFIER||408||419|RASSF8|protein_coding|CODING|NM_001164746.1|5|C) 0 0.5 1 2 0.666667 1 1 0 . 0 60 0 0 1 0 . rs3832809 -0.453602 0.036923 3 419 2282 MODIFIER 5 CODING RASSF8 A protein_coding NM_001164746.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26224033 T A 0 9.7 0 0.9281 0.8333 0.7493 0.8165 0.8012 0.8149 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2282||419|RASSF8|protein_coding|CODING|NM_001164746.1|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs7961722 -0.379885 0 1 419 3308 MODIFIER 5 CODING RASSF8 G protein_coding NM_001164746.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26225059 T G 0 9.7 0 0.9607 0.989 0.9957 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3308||419|RASSF8|protein_coding|CODING|NM_001164746.1|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1513130 -0.379885 0 1 482 1911 MODIFIER 5 CODING BHLHE41 G protein_coding NM_030762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26273088 C G 0 119 0 0.1392 0.5016 0.6427 0.7659 0.6143 0.5031 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.557713 0 . 0 . 33 17,0,16,0 UTR_3_PRIME(MODIFIER||1911||482|BHLHE41|protein_coding|CODING|NM_030762.2|5|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.948805 rs1048155 -0.689466 0.162806 33 482 271 MODIFIER 5 CODING BHLHE41 A protein_coding NM_030762.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26274728 G A 0 69 0 0 0.014177 0 0.0704 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 5 0,1,2,1 UTR_3_PRIME(MODIFIER||271||482|BHLHE41|protein_coding|CODING|NM_030762.2|5|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs76060407 -0.511536 0.267404 5 482 157 MODIFIER 1 CODING BHLHE41 C protein_coding NM_030762.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26277869 G C 0 110 0 0 0.0047923 0 0.0228 0 0.001 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.838046 0 . 0 . 12 1,3,1,7 UTR_5_PRIME(MODIFIER||157||482|BHLHE41|protein_coding|CODING|NM_030762.2|1|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.594978 rs183634927 -0.651104 0.452509 12 Y178 243 taC/taT LOW 3 SILENT CODING SSPN T protein_coding NM_005086.4 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26383811 C T 0 222 0 0 0.017572 0 0.0863 0 0.001 0.00158874 0.000615101 0.000116279 1 12 823 3 786 0 6 1 15 2 10406 121398 11578 8644 6614 66736 908 16512 0.949568 0 . 0 . 114 39,24,25,18 SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y178|243|SSPN|protein_coding|CODING|NM_005086.4|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.940369 rs117506538 -0.693146 0.763188 114 2701 855 MODIFIER 57 CODING ITPR2 C protein_coding NM_002223.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26491475 T C 0 228 0 0.1679 0.2965 0.4294 0.5218 0.2704 0.1708 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 16 0,0,2,14 UTR_3_PRIME(MODIFIER||855||2701|ITPR2|protein_coding|CODING|NM_002223.3|57|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1049376 -0.689466 0.257102 16 H786 2701 caC/caT LOW 19 SILENT CODING ITPR2 A protein_coding NM_002223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26809316 G A 0 222 0 0.1422 0.2949 0.3804 0.5635 0.1809 0.2812 0.147218 0.157164 0.161979 1 1527 28861 5870 4776 1465 11001 181 4041 2 9794 120652 11560 8600 6610 66682 896 16510 0.904595 0 . 0 . 106 30,21,31,13 SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H786|2701|ITPR2|protein_coding|CODING|NM_002223.3|19|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.941554 rs2230379 -0.693146 0.705779 106 S685 2701 tcA/tcG LOW 18 SILENT CODING ITPR2 C protein_coding NM_002223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26810777 T C 0 222 0 0.1921 0.3974 0.4524 0.6518 0.3628 0.409 0.218421 0.309943 0.352212 1 2215 47229 6770 5611 2477 23439 339 6378 2 9796 120712 11570 8612 6612 66712 898 16512 0.993931 0 . 0 . 83 16,20,20,17 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S685|2701|ITPR2|protein_coding|CODING|NM_002223.3|18|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.507876 rs2291264 -0.693141 0.0716118 83 S672 2701 tcA/tcC LOW 18 SILENT CODING ITPR2 G protein_coding NM_002223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26810816 T G 0 222 0 0.09 0.2806 0.3775 0.5635 0.1799 0.2812 0.103123 0.145221 0.164307 1 1047 28314 5844 4754 1467 10974 180 4048 2 9796 120598 11554 8582 6608 66662 896 16500 0.979399 0 . 0 . 73 17,18,18,16 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S672|2701|ITPR2|protein_coding|CODING|NM_002223.3|18|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.747936 rs2291263 -0.693132 0.375374 73 E255 2701 gaA/gaG LOW 8 SILENT CODING ITPR2 C protein_coding NM_002223.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26868322 T C 0 222 0 0.0295 0.2169 0.2435 0.1944 0.492 0.1912 0.0824907 0.348682 0.470231 1 759 42924 2410 1639 2848 31175 344 3749 2 9800 120606 11506 8584 6606 66710 900 16500 0.948261 0 . 0 . 129 23,47,22,26 SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E255|2701|ITPR2|protein_coding|CODING|NM_002223.3|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.278184 rs1900941 -0.693147 0.140844 129 2701 384 MODIFIER 1 CODING ITPR2 A protein_coding NM_002223.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 26986098 G A 0 5.4 0 0.0083 0.0629 0.1412 0.0605 0.1054 0.0399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.25 0 . 0 . 5 1,1,2,0 UTR_5_PRIME(MODIFIER||384||2701|ITPR2|protein_coding|CODING|NM_002223.3|1|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 1 rs61751917 -0.453602 0.38 5 E608 706 gaG/gaA LOW 15 SILENT CODING ASUN T protein_coding NM_018164.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27064232 C T 0 222 0 0.5514 0.5793 0.4366 0.7609 0.492 0.6207 0.514526 0.487312 0.473366 1 5462 62693 4808 6792 3397 31813 497 9924 2 10354 120942 11512 8614 6598 66464 908 16492 0.887955 0 . 0 . 45 9,12,8,11 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E608|706|ASUN|protein_coding|CODING|NM_018164.2|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.249769 rs3210635 -0.69168 0.463847 45 253 947 MODIFIER 7 CODING FGFR1OP2 A protein_coding NM_015633.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27118613 C A 0 214 0 0.8101 0.8367 0.8199 0.8403 0.8419 0.8753 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,1,13 UTR_3_PRIME(MODIFIER||947||253|FGFR1OP2|protein_coding|CODING|NM_015633.2|7|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs900743 -0.686358 0.474446 15 570 222 MODIFIER 12 CODING TM7SF3 G protein_coding NM_016551.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27126676 A G 0 137 0 0.0038 0.0607 0.0865 0.129 0.0785 0.0307 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 9 0,0,9,0 UTR_3_PRIME(MODIFIER||222||570|TM7SF3|protein_coding|CODING|NM_016551.2|12|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs4856 -0.662043 0.0273202 9 P248L 570 cCg/cTg MODERATE 6 MISSENSE CODING TM7SF3 A protein_coding NM_016551.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27143508 G A 0 222 0 0.0144 0.0487 0.0807 0.0595 0.0775 0.0317 0.0283704 0.0771951 0.102209 1 245 10037 1230 581 730 6371 76 804 2 10404 121374 11576 8654 6614 66712 906 16508 0.531072 0 . 0 . 73 25,14,14,14 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P248L|570|TM7SF3|protein_coding|CODING|NM_016551.2|6|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.531072 rs10771314 -0.693054 0.174063 73 144 19 MODIFIER 1 CODING MED21 C protein_coding NM_004264.4 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27175494 T C 0 228 0 0.8578 0.9323 0.9553 0.999 0.9404 0.9397 0.857921 0.90735 0.932674 2 8758 106042 11058 8563 6444 60604 761 9854 2 10268 112954 11498 8566 6614 64640 818 10550 0 . 0 . 0 59 0,0,35,17 UTR_5_PRIME(MODIFIER||19||144|MED21|protein_coding|CODING|NM_004264.4|1|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs3963548 -0.693147 0.0319282 59 144 405 MODIFIER 4 CODING MED21 A protein_coding NM_004264.4 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27181799 G A 0 39.3 0 0.8525 0.9297 0.9553 0.999 0.9404 0.9335 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 UTR_3_PRIME(MODIFIER||405||144|MED21|protein_coding|CODING|NM_004264.4|4|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1872193 -0.453602 0.28 2 T331 464 acG/acA LOW 11 SILENT CODING STK38L A protein_coding NM_015000.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27470866 G A 0 228 0 0.9841 0.9848 0.9914 1 0.9652 0.9857 0.985701 0.97678 0.972209 2 10255 118509 11375 8654 6425 64733 881 16186 2 10404 121368 11572 8654 6610 66712 906 16510 0 . 0 . 0 149 0,0,96,41 SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T331|464|STK38L|protein_coding|CODING|NM_015000.3|11|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs6487601 -0.693147 0.00672305 149 A107 343 gcG/gcA LOW 4 SILENT CODING SMCO2 A protein_coding NM_001145010.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27627805 G A 0 228 0 0.6921 0.7488 0.8098 0.7321 0.7793 0.7679 0.705925 0.772887 0.802011 2 1593 17563 341 449 1232 7506 196 6246 2 2246 22224 414 622 1630 9156 242 7914 0 . 0 . 0 132 0,0,34,86 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A107|343|SMCO2|protein_coding|CODING|NM_001145010.1|4|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs411816 -0.693147 0.256152 132 T292 343 acC/acT LOW 9 SILENT CODING SMCO2 T protein_coding NM_001145010.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27654898 C T 0 222 0 0.0318 0.1172 0.1282 0.0327 0.2336 0.1922 0.0578331 0.194677 0.253459 1 132 4735 51 13 464 2589 60 1426 2 2138 20874 408 620 1630 8890 234 6954 0.95961 0 . 0 . 109 35,21,28,14 SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T292|343|SMCO2|protein_coding|CODING|NM_001145010.1|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.912813 rs61731840 -0.693146 0.732116 109 V148L 1011 Gtg/Ttg MODERATE 6 MISSENSE CODING PPFIBP1 T protein_coding NM_177444.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27800746 G T 0 228 0 0.9811 0.9944 0.9957 1 1 1 0.984567 0.993541 0.99814 2 10260 121051 11549 8644 6614 66601 905 16478 2 10406 121396 11578 8650 6614 66732 908 16508 0 . 0 . 0 116 0,0,46,56 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V148L|1011|PPFIBP1|protein_coding|CODING|NM_177444.2|6|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2194816 -0.693147 0.00767593 116 R949H 1011 cGc/cAc MODERATE 27 MISSENSE CODING PPFIBP1 A protein_coding NM_177444.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27844824 G A 0 222 0 0 0.018171 0 0.0833 0 0.0072 0.000907853 0.00030755 0 1 10 863 2 767 0 5 6 73 2 10400 121188 11574 8654 6614 66642 906 16398 0.988375 0 . 0 . 121 33,25,30,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R949H|1011|PPFIBP1|protein_coding|CODING|NM_177444.2|27|A),UPSTREAM(MODIFIER||4604||236|REP15|protein_coding|CODING|NM_001029874.1||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.829368 rs61757741 -0.693147 0.132419 121 1011 109 MODIFIER 29 CODING PPFIBP1 T protein_coding NM_177444.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27845924 C T 0 188 0 0.4062 0.5903 0.7334 0.6706 0.6948 0.547 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.571777 0 . 0 . 22 0,7,2,13 UTR_3_PRIME(MODIFIER||109||1011|PPFIBP1|protein_coding|CODING|NM_177444.2|29|T),UPSTREAM(MODIFIER||3504||236|REP15|protein_coding|CODING|NM_001029874.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.970024 rs3764010 -0.688148 0.204966 22 1011 2257 MODIFIER 29 CODING PPFIBP1 T protein_coding NM_177444.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27848072 C T 0 9.7 0 0.3442 0.095 0.0288 0 0.001 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2257||1011|PPFIBP1|protein_coding|CODING|NM_177444.2|29|T),UPSTREAM(MODIFIER||1356||236|REP15|protein_coding|CODING|NM_001029874.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs145772097 -0.379885 0 1 S100 236 tcC/tcT LOW 1 SILENT CODING REP15 T protein_coding NM_001029874.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27849795 C T 0 222 0 0.6399 0.596 0.6888 0.5268 0.6262 0.5112 0.629823 0.621252 0.61686 1 6547 74449 8149 4839 4032 41312 568 9002 2 10380 121306 11566 8634 6608 66708 908 16502 0.323162 0 . 0 . 47 9,13,14,11 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S100|236|REP15|protein_coding|CODING|NM_001029874.1|1|T),DOWNSTREAM(MODIFIER||1298||1011|PPFIBP1|protein_coding|CODING|NM_177444.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0607962 rs929948 -0.692914 0.130421 47 N101D 236 Aac/Gac MODERATE 1 MISSENSE CODING REP15 G protein_coding NM_001029874.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27849796 A G 0 228 0 0.91 0.9748 0.9899 1 1 1 0.919655 0.972397 0.999419 2 9525 120367 11471 8654 6614 66698 900 16505 2 10386 121370 11574 8654 6614 66726 908 16508 0 . 0 . 0 44 0,0,23,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N101D|236|REP15|protein_coding|CODING|NM_001029874.1|1|G),DOWNSTREAM(MODIFIER||1299||1011|PPFIBP1|protein_coding|CODING|NM_177444.2||G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs929949 -0.693146 0.228553 44 323 LOW 1 CODING MRPS35 T protein_coding NM_021821.3 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27867706 C T 0 228 0 0.885 0.7346 0.7565 0.6657 0.7008 0.6217 0.839991 0.736506 0.683488 2 8858 84312 8803 5866 4212 45410 630 10533 2 10394 120850 11532 8616 6606 66356 906 16440 0 . 0 . 0 143 0,0,79,40 SPLICE_SITE_REGION+INTRON(LOW||||323|MRPS35|protein_coding|CODING|NM_021821.3|1|T) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs11049106 -0.693147 0.272651 143 G43R 323 Gga/Aga MODERATE 2 MISSENSE CODING MRPS35 A protein_coding NM_021821.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27867727 G A 0 222 0 0.0068 0.1194 0.1009 0.1944 0.173 0.1524 0.0335906 0.116869 0.159535 1 287 16724 931 1488 953 10583 118 2364 2 10348 120792 11518 8634 6602 66392 904 16394 0.554723 0 . 0 . 140 36,27,28,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Aga|G43R|323|MRPS35|protein_coding|CODING|NM_021821.3|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.998142 rs1127787 -0.693147 0.446152 140 323 220 MODIFIER 8 CODING MRPS35 G protein_coding NM_021821.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27908603 A G 0 5.8 0 0.0083 0.122 0.1009 0.1935 0.175 0.1626 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 10 2,6,0,2 UTR_3_PRIME(MODIFIER||220||323|MRPS35|protein_coding|CODING|NM_021821.3|8|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.875 rs3751233 -0.453602 0.96 10 S326T 340 Tcc/Acc MODERATE 3 MISSENSE CODING MANSC4 T protein_coding NM_001146221.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27915718 A T 0 94 0 0.4939 0.4922 0.572 0.4692 0.508 0.4407 0.497832 0.499124 0.499686 1 1048 10538 210 289 767 4309 137 3778 2 2056 21084 348 594 1624 8444 236 7782 0.902783 0 . 0 . 19 11,0,6,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Acc|S326T|340|MANSC4|protein_coding|CODING|NM_001146221.1|3|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 0 . 1 rs10842975 -0.616816 0.951477 19 P250 340 ccT/ccC LOW 3 SILENT CODING MANSC4 G protein_coding NM_001146221.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27915944 A G 0 222 0 0.0234 0.1248 0.1023 0.2044 0.173 0.1462 0.0455202 0.120018 0.15242 1 92 3086 38 131 270 1365 29 1161 2 2162 21842 412 622 1630 8856 246 7914 0.852872 0 . 0 . 95 36,18,26,10 SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P250|340|MANSC4|protein_coding|CODING|NM_001146221.1|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.834651 rs11049124 -0.693139 0.153996 95 T163M 340 aCg/aTg MODERATE 3 MISSENSE CODING MANSC4 A protein_coding NM_001146221.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27916206 G A 0 222 0 0.0234 0.1248 0.1023 0.2044 0.173 0.1462 0.0455202 0.120018 0.15242 1 94 3079 38 132 268 1357 29 1161 2 2166 21800 412 624 1626 8816 242 7914 0.853198 0 . 0 . 104 25,26,22,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T163M|340|MANSC4|protein_coding|CODING|NM_001146221.1|3|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.299695 rs11049125 -0.693146 0.250614 104 L157S 340 tTa/tCa MODERATE 3 MISSENSE CODING MANSC4 G protein_coding NM_001146221.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27916224 A G 0 222 0 0.0234 0.1248 0.1023 0.2044 0.173 0.1462 0 . 0 1 98 3114 38 131 270 1387 29 1161 2 2178 21898 412 622 1632 8898 242 7914 0.816176 0 . 0 . 91 17,22,20,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L157S|340|MANSC4|protein_coding|CODING|NM_001146221.1|3|G) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.424502 rs11049126 -0.693145 0.313486 91 505 2363 MODIFIER 3 CODING KLHL42 C protein_coding NM_020782.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27953462 T C 0 9.7 0 0 0.0041933 0 0.0208 0 0 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2363||505|KLHL42|protein_coding|CODING|NM_020782.1|3|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs75407915 -0.379885 0 1 505 3873 MODIFIER 3 CODING KLHL42 A protein_coding NM_020782.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27954972 G A 0 9.7 0 0.9796 0.9944 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3873||505|KLHL42|protein_coding|CODING|NM_020782.1|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4930976 -0.379885 0 1 505 3876 MODIFIER 3 CODING KLHL42 T protein_coding NM_020782.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27954975 C T 0 9.7 0 0.9796 0.9944 0.9986 1 1 1 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||3876||505|KLHL42|protein_coding|CODING|NM_020782.1|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4931486 -0.379885 0 1 505 4197 MODIFIER 3 CODING KLHL42 T protein_coding NM_020782.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 27955296 C T 0 127 0 0.2867 0.4271 0.5231 0.6379 0.337 0.4243 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,7,0 UTR_3_PRIME(MODIFIER||4197||505|KLHL42|protein_coding|CODING|NM_020782.1|3|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs1050288 -0.636426 0.781662 7 V314M 441 Gtg/Atg MODERATE 10 MISSENSE CODING CCDC91 A protein_coding NM_018318.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 28605426 G A 0 222 0 0.8268 0.6691 0.6398 0.4702 0.7475 0.6012 0.825216 0.783755 0.762526 1 8301 85688 7106 4081 4881 50535 638 10146 2 9984 120638 11514 8622 6606 66520 902 16490 0.860512 0 . 0 . 54 19,10,14,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V314M|441|CCDC91|protein_coding|CODING|NM_018318.3|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.529364 rs10771427 -0.69168 0.212125 54 L26 515 ctG/ctA LOW 2 SILENT CODING FAR2 A protein_coding NM_001271783.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29423460 G A 0 222 0 0.6399 0.4279 0.2781 0.4058 0.3459 0.3548 0.59714 0.453022 0.379186 1 6233 44165 2739 3247 2320 24233 323 5070 2 10404 121242 11536 8630 6606 66668 908 16490 0.908775 0 . 0 COSM147460 105 39,13,36,7 SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L26|515|FAR2|protein_coding|CODING|NM_001271783.1|2|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966339 rs2216854 -0.693146 0.269 105 A881P 1134 Gca/Cca MODERATE 22 MISSENSE CODING OVCH1 G protein_coding NM_183378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29604392 C G 0 222 0 0.621 0.5106 0.3934 0.4008 0.5726 0.4939 0.653192 0.591956 0.563959 1 6204 62819 3686 3558 3766 37306 494 7805 2 9752 119732 11262 8532 6574 66284 894 16434 0.207733 0 . 0 . 82 19,24,12,20 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Cca|A881P|1134|OVCH1|protein_coding|CODING|NM_183378.2|22|G),INTRAGENIC(MODIFIER|||||OVCH1-AS1||NON_CODING|||G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.679916 rs1347570 -0.69312 0.0773665 82 A526 1134 gcC/gcT LOW 14 SILENT CODING OVCH1 A protein_coding NM_183378.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29628016 G A 0 222 0 0.6687 0.51 0.3934 0.3948 0.5517 0.454 0.679286 0.584119 0.541086 1 4763 39651 2030 2427 2475 22588 332 5036 2 6798 68890 4270 4898 4062 37474 558 10830 0.958835 0 . 0 COSM147462 161 37,44,30,33 SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A526|1134|OVCH1|protein_coding|CODING|NM_183378.2|14|A),INTRAGENIC(MODIFIER|||||OVCH1-AS1||NON_CODING|||A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.554912 rs2043623,rs386554447 -0.693147 0.0040851 161 T444I 1134 aCa/aTa MODERATE 12 MISSENSE CODING OVCH1 A protein_coding NM_183378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29630081 G A 0 228 0 0.6445 0.8209 0.8977 0.9147 0.8638 0.864 0.649658 0.791784 0.85749 2 6247 101620 10496 7850 5328 56524 763 14412 2 9626 119154 11272 8512 6530 65956 880 16378 0 . 0 . 0 112 0,0,80,23 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T444I|1134|OVCH1|protein_coding|CODING|NM_183378.2|12|A),INTRAGENIC(MODIFIER|||||OVCH1-AS1||NON_CODING|||A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs7975356 -0.693147 1.54894e-08 112 K330E 1134 Aag/Gag MODERATE 8 MISSENSE CODING OVCH1 C protein_coding NM_183378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29639186 T C 0 222 0 0.6778 0.6154 0.4813 0.7331 0.6044 0.5164 0.659326 0.607582 0.584351 1 6442 68631 4860 6619 3382 38601 521 8206 2 9798 120726 11568 8616 6610 66726 898 16510 0.858566 0 . 0 . 131 50,12,44,15 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K330E|1134|OVCH1|protein_coding|CODING|NM_183378.2|8|C),INTRAGENIC(MODIFIER|||||OVCH1-AS1||NON_CODING|||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0577828 rs3847680 -0.693147 0.732173 131 W228G 1134 Tgg/Ggg MODERATE 6 MISSENSE CODING OVCH1 C protein_coding NM_183378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29642573 A C 0 222 0 0.3585 0.4225 0.3012 0.5685 0.4692 0.3967 0.350592 0.407172 0.433802 1 3243 43562 2507 4301 2325 25400 354 5432 2 8180 98276 8058 7398 5526 54856 776 13482 0.934604 0 . 0 COSM1361161 45 8,10,18,5 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W228G|1134|OVCH1|protein_coding|CODING|NM_183378.2|6|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.955391 rs967181 -0.692717 0.843465 45 R133C 1134 Cgt/Tgt MODERATE 4 MISSENSE CODING OVCH1 A protein_coding NM_183378.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29648275 G A 0 222 0 0.3185 0.4475 0.3689 0.5347 0.5716 0.4601 0.31791 0.467742 0.535137 1 3229 58264 3587 4383 3310 35949 462 7344 2 9796 120736 11574 8618 6614 66730 896 16508 0.485801 0 . 0 . 65 16,15,15,11 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R133C|1134|OVCH1|protein_coding|CODING|NM_183378.2|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.720854 rs10843438 -0.692976 0.194624 65 882 5891 MODIFIER 18 CODING TMTC1 AAT protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29653887 A AAT 0 44.8 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 194 63,49,36,18 UTR_3_PRIME(MODIFIER||5891||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|AAT),UPSTREAM(MODIFIER||3269||1134|OVCH1|protein_coding|CODING|NM_183378.2||AAT) 0 0.5 1 4 0.0206186 0 1 0 . 0 60 0 0 1 0 . rs146445675 -0.693147 0.0641353 194 882 5607 MODIFIER 18 CODING TMTC1 A protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29654172 G A 0 77 0 0.6959 0.6474 0.5303 0.6895 0.5775 0.6933 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,2 UTR_3_PRIME(MODIFIER||5607||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|A),UPSTREAM(MODIFIER||3553||1134|OVCH1|protein_coding|CODING|NM_183378.2||A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7503 -0.511536 0.519801 3 882 4835 MODIFIER 18 CODING TMTC1 T protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29654944 G T 0 9.7 0 0.7776 0.6869 0.5447 0.7679 0.5755 0.6963 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4835||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|T),UPSTREAM(MODIFIER||4325||1134|OVCH1|protein_coding|CODING|NM_183378.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs822875 -0.379885 0 1 882 4745 MODIFIER 18 CODING TMTC1 A protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29655034 T A 0 9.7 0 0.8646 0.7774 0.6196 0.7708 0.7366 0.82 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||4745||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|A),UPSTREAM(MODIFIER||4415||1134|OVCH1|protein_coding|CODING|NM_183378.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs822874 -0.379885 0 1 882 2892 MODIFIER 18 CODING TMTC1 C protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29656887 T C 0 9.7 0 0.8018 0.7278 0.572 0.8601 0.6362 0.6963 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||2892||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs822873 -0.379885 0 1 882 2646 MODIFIER 18 CODING TMTC1 T protein_coding NM_001193451.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29657133 A T 0 9.7 0 0.2958 0.3253 0.281 0.5288 0.2028 0.3129 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2646||882|TMTC1|protein_coding|CODING|NM_001193451.1|18|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs6487834 -0.379885 0 1 H426 882 caT/caC LOW 8 SILENT CODING TMTC1 G protein_coding NM_001193451.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29736480 A G 0 222 0 0.5182 0.3702 0.3112 0.4623 0.2376 0.2536 0.455742 0.312779 0.239535 1 4927 34227 3013 3858 1811 16552 236 3830 2 10282 118544 11168 8378 6444 65258 896 16118 0.875521 0 . 0 . 79 17,23,13,19 SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H426|882|TMTC1|protein_coding|CODING|NM_001193451.1|8|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.456554 rs2113879,rs386557632 -0.69312 0.420414 79 L24 882 ctA/ctC LOW 1 SILENT CODING TMTC1 G protein_coding NM_001193451.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 29936613 T G 0 168 0 0.6974 0.9071 0.9669 0.999 0.9692 0.9898 0 . 0 2 49 1818 23 12 0 230 21 1483 2 66 1882 24 12 0 238 22 1520 0 . 0 . 0 20 0,0,0,20 SYNONYMOUS_CODING(LOW|SILENT|ctA/ctC|L24|882|TMTC1|protein_coding|CODING|NM_001193451.1|1|G) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs184221 -0.692067 2.69052e-05 20 1037 1718 MODIFIER 25 CODING IPO8 C protein_coding NM_006390.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30782076 T C 0 32.6 0 0.8533 0.5359 0.304 0.4484 0.5099 0.3885 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||1718||1037|IPO8|protein_coding|CODING|NM_006390.3|25|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7327 -0.379885 0 2 1037 51 MODIFIER 25 CODING IPO8 T protein_coding NM_006390.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30783743 C T 0 222 0 0.2882 0.2574 0.1383 0.373 0.2515 0.1871 0.286201 0.271183 0.263488 1 2993 30513 1553 3351 1937 17186 223 3270 2 10392 120198 11536 8588 6600 66274 894 15914 0.924239 0 . 0 . 52 20,5,16,5 UTR_3_PRIME(MODIFIER||51||1037|IPO8|protein_coding|CODING|NM_006390.3|25|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.103895 rs2278558,rs386563408 -0.692352 0.841231 52 L323 1037 ctT/ctC LOW 9 SILENT CODING IPO8 G protein_coding NM_006390.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30823971 A G 0 222 0 0.702 0.494 0.2911 0.4484 0.5089 0.3885 0.658647 0.565201 0.517326 1 7018 60382 3015 3851 3883 35224 470 6921 2 10406 121400 11576 8652 6614 66732 908 16512 0.66634 0 . 0 . 127 31,17,30,32 SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L323|1037|IPO8|protein_coding|CODING|NM_006390.3|9|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.965447 rs1054426 -0.693147 0.451546 127 1037 94 MODIFIER 1 CODING IPO8 T protein_coding NM_006390.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30848675 C T 0 124 0 0.034 0.1617 0.1196 0.2827 0.2336 0.1656 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.375311 0 . 0 . 49 1,23,0,25 UTR_5_PRIME(MODIFIER||94||1037|IPO8|protein_coding|CODING|NM_006390.3|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.310227 rs12809335,rs386526102 -0.692914 0.515054 49 V847 1127 gtG/gtA LOW 15 SILENT CODING CAPRIN2 T protein_coding NM_001002259.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30868002 C T 0 222 0 0.8729 0.596 0.3818 0.4633 0.5905 0.5164 0.825465 0.676534 0.600233 1 8726 70394 3678 4018 4163 40572 576 8661 2 10406 121378 11558 8648 6610 66736 908 16512 0.646658 0 . 0 . 167 61,31,23,29 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V847|1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|15|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.344511 rs13656 -0.693147 0.0458951 167 1127 LOW 9 CODING CAPRIN2 T protein_coding NM_001002259.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30877391 G T 0 222 0 0.1831 0.257 0.2075 0.2937 0.3161 0.2935 0.219473 0.297863 0.338023 1 2255 36074 2044 2648 1987 21958 307 4875 2 10348 120638 11476 8578 6570 66288 906 16472 0.979978 0 . 0 . 98 13,35,11,29 SPLICE_SITE_REGION+INTRON(LOW||||1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|9|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.0061154 rs7299800 -0.693145 0.00272989 98 M519V 1127 Atg/Gtg MODERATE 8 MISSENSE CODING CAPRIN2 C protein_coding NM_001002259.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30881809 T C 0 222 0 0.8192 0.5553 0.3732 0.369 0.5736 0.501 0.786201 0.660003 0.595349 1 8271 68063 3602 3180 3928 40093 561 8428 2 10406 121358 11556 8636 6614 66726 908 16512 0.886708 0 . 0 . 197 49,39,44,41 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M519V|1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|8|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.727852 rs2304630,rs386564459 -0.693147 0.0281626 197 K237R 1127 aAa/aGa MODERATE 4 MISSENSE CODING CAPRIN2 C protein_coding NM_001002259.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30888001 T C 0 222 0 0.0348 0.1617 0.121 0.2788 0.2376 0.1636 0.0671811 0.193219 0.257791 1 622 26343 1426 2604 1726 16768 205 2992 2 10404 121398 11578 8648 6612 66738 908 16510 0.680178 0 . 0 . 154 50,31,31,24 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K237R|1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.991481 rs12146709 -0.693147 0.0577201 154 1127 178 MODIFIER 1 CODING CAPRIN2 T protein_coding NM_001002259.2 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 30906875 C T 0 39.3 0 1 1 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,0,2 START_GAINED(LOW||||1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|1|T),UTR_5_PRIME(MODIFIER||178||1127|CAPRIN2|protein_coding|CODING|NM_001002259.2|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs33255 -0.453602 0.78 2 C156 253 tgT/tgC LOW 6 SILENT CODING TSPAN11 C protein_coding NM_001080509.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31135478 T C 0 228 0 0.9425 0.9515 0.9481 0.9673 0.9523 0.9489 0.944369 0.952916 0.957296 2 9687 115284 11252 8277 6566 63241 853 15408 2 10256 120426 11564 8626 6614 66084 902 16380 0 . 0 . COSM431013 123 0,0,39,80 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C156|253|TSPAN11|protein_coding|CODING|NM_001080509.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs35089 -0.693147 0.0713746 123 V190A 253 gTg/gCg MODERATE 6 MISSENSE CODING TSPAN11 C protein_coding NM_001080509.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31135579 T C 0 228 0 0.6415 0.7077 0.7478 0.7242 0.6998 0.7597 0.632848 0.664767 0.681109 2 6040 78632 8802 5619 4215 41337 595 12024 2 9046 109510 10832 7918 5828 59300 814 15772 1 0 . 0 COSM431014 87 1,0,37,39 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V190A|253|TSPAN11|protein_coding|CODING|NM_001080509.2|6|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs2075333 -0.693147 0.84739 87 253 34 MODIFIER 8 CODING TSPAN11 G protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31144884 A G 0 228 0 0.4236 0.5693 0.4539 0.9425 0.3748 0.6636 0.402406 0.377518 0.364767 2 4210 55005 4949 8096 2523 24434 450 10343 2 10350 121042 11538 8646 6586 66532 904 16486 0 . 0 . 0 31 0,0,8,21 UTR_3_PRIME(MODIFIER||34||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|G) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs35076 -0.693079 0.0859317 31 253 179 MODIFIER 8 CODING TSPAN11 G protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31145029 A G 0 124 0 0.3253 0.5419 0.4467 0.9425 0.3738 0.6626 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,0,7 UTR_3_PRIME(MODIFIER||179||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs35075 -0.636426 0.940274 7 253 234 MODIFIER 8 CODING TSPAN11 A protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31145084 G A 0 19.4 0 0.053 0.0723 0.0634 0.124 0.0686 0.0552 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.5 0 . 0 . 4 0,2,1,1 UTR_3_PRIME(MODIFIER||234||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.5 rs3741868 -0.453602 0.5 4 253 1210 MODIFIER 8 CODING TSPAN11 A protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31146060 G A 0 9.7 0 0.2481 0.4369 0.3285 0.8313 0.2644 0.5399 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1210||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs35073 -0.379885 0 1 253 1785 MODIFIER 8 CODING TSPAN11 G protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31146635 A G 0 42.3 0 0.3048 0.4557 0.3343 0.8323 0.2654 0.5532 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||1785||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs35072 -0.453602 0.22 2 253 2024 MODIFIER 8 CODING TSPAN11 A protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31146874 G A 0 63 0 0.2595 0.4405 0.3314 0.8323 0.2674 0.5368 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,0 UTR_3_PRIME(MODIFIER||2024||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs35071 -0.453602 0.42 3 253 3812 MODIFIER 8 CODING TSPAN11 A protein_coding NM_001080509.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31148662 G A 0 9.7 0 0.5787 0.6136 0.4496 0.9544 0.3618 0.6851 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3812||253|TSPAN11|protein_coding|CODING|NM_001080509.2|8|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs35068 -0.379885 0 1 970 LOW 6 CODING DDX11 G protein_coding NM_001257144.1 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31240925 A G 0 228 0 0.7088 0.633 0.6066 0.8095 0.4314 0.5746 0.682705 0.527603 0.44814 2 6267 57027 6717 6425 2556 26294 415 8353 2 9386 112344 10216 8010 6262 62726 856 14888 0.651646 0 . 0 . 157 2,1,80,52 SPLICE_SITE_REGION+INTRON(LOW||||970|DDX11|protein_coding|CODING|NM_001257144.1|6|G) 1 0 . 0 . 1 0 1 1 0 53 0 0.798036 0.00113152 0 0.937845 rs7308773 -0.693147 9.58517e-08 157 C285 970 tgT/tgC LOW 8 SILENT CODING DDX11 C protein_coding NM_001257144.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31242399 T C 0 228 0 0.7179 0.6456 0.6311 0.7748 0.4682 0.6074 0.669315 0.519529 0.442791 2 7013 62272 7706 6510 2724 28512 432 9375 2 10270 119440 11376 8540 6498 65530 892 16334 0 . 0 . 0 151 0,0,56,79 SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C285|970|DDX11|protein_coding|CODING|NM_001257144.1|8|C) 1 0 . 0 . 1 0 1 1 0 54 0 0 0.00922253 0 . rs3881298 -0.693147 0.198131 151 A395 970 gcG/gcA LOW 10 SILENT CODING DDX11 A protein_coding NM_001257144.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31244748 G A 0 222 0 . 0 . 0 . 0 0.00385837 0.00353955 0.00337602 1 44 6080 1680 1759 356 402 35 1804 2 9976 120016 11544 8600 6602 65896 902 16496 0.9922 0 . 0 . 278 79,72,50,45 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A395|970|DDX11|protein_coding|CODING|NM_001257144.1|10|A) 1 0.5 1 0 . 0 . 1 1 0 56 0 0.504651 0.00256157 0 0.983042 rs150466604 -0.693147 0.31171 278 Q567E 970 Caa/Gaa MODERATE 17 MISSENSE CODING DDX11 G protein_coding NM_001257144.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31249861 C G 0 228 0 0.708 0.6412 0.6066 0.8294 0.4284 0.6002 0.684294 0.529832 0.450698 2 7051 63592 7788 7214 2731 28609 437 9762 2 10338 120588 11472 8602 6562 66268 902 16444 1 0 . 0 . 154 1,0,86,51 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q567E|970|DDX11|protein_coding|CODING|NM_001257144.1|17|G) 1 0 . 0 . 1 0 1 1 0 57 0 1 0.83088 0 1 rs2075322 -0.693147 0.0443955 154 L661 970 ctC/ctT LOW 20 SILENT CODING DDX11 T protein_coding NM_001257144.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31253995 C T 0 228 0 0.6861 0.6284 0.6124 0.8065 0.4394 0.5726 0.667726 0.527295 0.455349 2 6906 63814 7904 7031 2832 29307 440 9394 2 10406 121346 11570 8648 6612 66692 908 16510 0 . 0 . 0 90 0,0,46,33 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L661|970|DDX11|protein_coding|CODING|NM_001257144.1|20|T) 1 0 . 0 . 1 0 1 1 0 59 0 0 0.997582 0 . rs1046456 -0.693147 0.113409 90 L772 970 ctC/ctT LOW 23 SILENT CODING DDX11 T protein_coding NM_001257144.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31255405 C T 0 222 0 0.1029 0.0793 0.0245 0.1508 0.0239 0.0695 0.0853382 0.0482854 0.0293023 1 918 5369 184 1328 64 1525 47 1303 2 10364 121050 11578 8648 6614 66426 908 16512 0.437527 0 . 0 . 215 39,59,43,50 SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L772|970|DDX11|protein_coding|CODING|NM_001257144.1|23|T) 1 0.5 1 0 . 1 0 1 1 0 57 0 0.982864 0.990043 0 0.986906 rs77340729 -0.693147 0.120542 215 R856H 970 cGt/cAt MODERATE 26 MISSENSE CODING DDX11 A protein_coding NM_001257144.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31256546 G A 0 228 0 0.708 0.6342 0.611 0.8075 0.4384 0.5736 0.646297 0.49823 0.422406 2 6363 59372 7189 6594 2569 27091 423 9143 2 9562 116532 10896 8260 6340 64354 890 16230 0 . 0 . 0 141 0,0,69,61 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R856H|970|DDX11|protein_coding|CODING|NM_001257144.1|26|A) 1 0 . 0 . 1 0 1 1 0 50 0 0 4.50476e-05 0 . rs1046457 -0.693147 0.500203 141 C951R 970 Tgc/Cgc MODERATE 27 MISSENSE CODING DDX11 C protein_coding NM_001257144.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31256905 T C 0 228 0 0.708 0.6384 0.6153 0.8105 0.4553 0.5716 0 . 0 2 2012 18153 871 1008 619 8381 167 5095 2 3498 44474 1932 1548 2218 24986 388 9904 0 . 0 . 0 77 0,0,21,55 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C951R|970|DDX11|protein_coding|CODING|NM_001257144.1|27|C) 0 . 0 . 0 1 0 . 1 0 50 0 0 0.15757 0 . rs1046458 -0.693147 0.016674 77 970 27 MODIFIER 27 CODING DDX11 T protein_coding NM_001257144.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31256994 C T 0 222 0 0.0015 0.0931 0.1023 0.2302 0.0089 0.1554 0.00176367 0.00272232 0.00322284 1 6 1055 42 139 1 63 3 801 2 1424 16650 428 658 46 7266 166 6662 0.897415 0 . 0 . 37 4,11,4,17 UTR_3_PRIME(MODIFIER||27||970|DDX11|protein_coding|CODING|NM_001257144.1|27|T) 1 0.5 1 0 . 1 0 1 1 0 52 0 0.995378 0.391322 0 0.31301 rs12578575 -0.692352 0.247821 37 970 360 MODIFIER 27 CODING DDX11 C protein_coding NM_001257144.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31257327 T C 0 73 0 0.7073 0.6304 0.6009 0.8056 0.4294 0.5736 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 UTR_3_PRIME(MODIFIER||360||970|DDX11|protein_coding|CODING|NM_001257144.1|27|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs1046467 -0.511536 0.917785 3 970 497 MODIFIER 27 CODING DDX11 A protein_coding NM_001257144.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31257464 G A 0 138 0 0.708 0.6348 0.6095 0.8075 0.4423 0.5736 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,6,1 UTR_3_PRIME(MODIFIER||497||970|DDX11|protein_coding|CODING|NM_001257144.1|27|A) 0 . 0 . 0 1 0 . 0 . 54 0 0 1 0 . rs9750 -0.636426 0.846879 7 970 728 MODIFIER 27 CODING DDX11 C protein_coding NM_001257144.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31257695 T C 0 201 0 0.708 0.6346 0.6124 0.8075 0.4394 0.5736 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,3,4 UTR_3_PRIME(MODIFIER||728||970|DDX11|protein_coding|CODING|NM_001257144.1|27|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1.01283 0 . rs11219 -0.636426 0.93404 8 221 1031 MODIFIER 7 CODING FAM60A C protein_coding NM_001135811.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31434615 T C 0 6.3 0 0.0015 0.0657 0.0014 0.2381 0.005 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||1031||221|FAM60A|protein_coding|CODING|NM_001135811.1|7|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3741872 -0.379885 0 1 221 974 MODIFIER 7 CODING FAM60A G protein_coding NM_001135811.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31434672 A G 0 9.7 0 0.0015 0.0655 0.0014 0.2371 0.005 0.0828 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||974||221|FAM60A|protein_coding|CODING|NM_001135811.1|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs3741873 -0.379885 0 1 1309 2619 MODIFIER 23 CODING DENND5B T protein_coding NM_001308339.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31537918 C T 0 9.7 0 0.6142 0.6573 0.7349 0.8244 0.5408 0.6084 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2619||1309|DENND5B|protein_coding|CODING|NM_001308339.1|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2888762 -0.379885 0 1 1309 2600 MODIFIER 23 CODING DENND5B T protein_coding NM_001308339.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31537937 C T 0 9.7 0 0.7731 0.9211 0.9683 0.994 0.9742 0.9581 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2600||1309|DENND5B|protein_coding|CODING|NM_001308339.1|23|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs708202 -0.379885 0 1 1309 2471 MODIFIER 23 CODING DENND5B G protein_coding NM_001308339.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31538066 T G 0 9.7 0 0.3835 0.4798 0.6354 0.5764 0.4165 0.4652 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||2471||1309|DENND5B|protein_coding|CODING|NM_001308339.1|23|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2892638 -0.379885 0 1 1309 1415 MODIFIER 23 CODING DENND5B G protein_coding NM_001308339.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31539122 A G 0 228 0 0.3116 0.4609 0.6326 0.5774 0.4175 0.4652 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 49 0,0,37,7 UTR_3_PRIME(MODIFIER||1415||1309|DENND5B|protein_coding|CODING|NM_001308339.1|23|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs3741877 -0.693146 0.14075 49 R87K 1309 aGa/aAa MODERATE 4 MISSENSE CODING DENND5B T protein_coding NM_001308339.1 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31648826 C T 0 228 0 0.084 0.3966 0.6095 0.5734 0.4165 0.4652 0.125824 0.316534 0.401543 2 1151 50369 7586 4801 2705 26500 405 7221 2 8838 110622 10798 8158 6216 60564 852 15196 0.952 0 . 0 . 283 1,1,120,130 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R87K|1309|DENND5B|protein_coding|CODING|NM_001308339.1|4|T) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 0.018 rs4930979 -0.693147 0.196003 283 1309 40 MODIFIER 2 CODING DENND5B T protein_coding NM_001308339.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31653532 G T 0 98 0 0.9009 0.8628 0.9222 0.8929 0.7823 0.8211 0 . 0 2 0 6 0 0 0 6 0 0 2 0 8 0 0 0 8 0 0 0 . 0 . 0 5 0,0,0,5 UTR_5_PRIME(MODIFIER||40||1309|DENND5B|protein_coding|CODING|NM_001308339.1|2|T) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs1259354 -0.590765 0.345017 5 1309 89852 MODIFIER 1 CODING DENND5B G protein_coding NM_001308339.1 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31743344 A G 0 6.3 0 0.9017 0.8421 0.9092 0.871 0.7525 0.7761 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 START_GAINED(LOW||||1309|DENND5B|protein_coding|CODING|NM_001308339.1|1|G),UTR_5_PRIME(MODIFIER||89852||1309|DENND5B|protein_coding|CODING|NM_001308339.1|1|G),INTRAGENIC(MODIFIER|||||DENND5B-AS1||NON_CODING|||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1259423 -0.379885 0 1 135 218 MODIFIER 1 CODING H3F3C T protein_coding NM_001013699.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31944475 C T 0 222 0 0.1384 0.1108 0.0418 0.122 0.0875 0.135 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.442432 0 . 0 . 105 37,17,23,17 UTR_3_PRIME(MODIFIER||218||135|H3F3C|protein_coding|CODING|NM_001013699.2|1|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.970502 rs11051595 -0.693145 0.354497 105 H39P 135 cAt/cCt MODERATE 1 MISSENSE CODING H3F3C G protein_coding NM_001013699.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 31944985 T G 0 222 0 0.0628 0.0837 0.0865 0.125 0.0457 0.1063 0.0540172 0.0582808 0.0604651 1 577 9105 1160 1215 211 3789 62 2091 2 10348 121162 11572 8632 6612 66586 904 16508 0.924419 0 . 0 . 155 47,33,30,33 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cCt|H39P|135|H3F3C|protein_coding|CODING|NM_001013699.2|1|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.95277 rs3759295 -0.693147 0.0860262 155 N117 1747 aaC/aaT LOW 4 SILENT CODING KIAA1551 T protein_coding NM_018169.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32134240 C T 0 222 0 0.7118 0.7258 0.7608 0.7827 0.6928 0.6953 0.705629 0.697601 0.693488 1 7328 87039 8531 6922 5056 46851 671 11680 2 10404 121328 11568 8650 6606 66690 906 16504 0.882262 0 . 0 . 121 43,14,32,23 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N117|1747|KIAA1551|protein_coding|CODING|NM_018169.3|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.961729 rs2388982 -0.693147 0.00383558 121 L250P 1747 cTa/cCa MODERATE 4 MISSENSE CODING KIAA1551 C protein_coding NM_018169.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32134638 T C 0 222 0 0.9062 0.8403 0.8184 0.8244 0.7893 0.8354 0.881071 0.817161 0.784419 1 9115 98419 9062 7180 5435 52967 750 13910 2 10338 121160 11562 8630 6612 66618 908 16492 0.279997 0 . 0 . 94 10,32,14,32 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L250P|1747|KIAA1551|protein_coding|CODING|NM_018169.3|4|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.155363 rs2166807 -0.693147 0.499429 94 S518P 1747 Tca/Cca MODERATE 4 MISSENSE CODING KIAA1551 C protein_coding NM_018169.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32135441 T C 0 228 0 0.9977 0.9451 0.9597 0.8839 0.9404 0.9315 0.989106 0.958019 0.942093 2 10251 114387 11277 7711 6334 62611 855 15348 2 10344 121152 11570 8644 6610 66590 906 16488 1 0 . 0 . 44 0,1,16,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S518P|1747|KIAA1551|protein_coding|CODING|NM_018169.3|4|C) 1 0 . 0 . 1 0 1 1 0 60 0 1 1 0 1 rs3759301 -0.693146 0.497052 44 R1332H 1747 cGt/cAt MODERATE 4 MISSENSE CODING KIAA1551 A protein_coding NM_018169.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32137884 G A 0 222 0 0 0.0025959 0 0.0129 0 0 0 . 0 1 0 145 0 141 0 3 0 1 2 10328 121062 11550 8644 6614 66534 902 16490 0.957311 0 . 0 . 113 26,21,28,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1332H|1747|KIAA1551|protein_coding|CODING|NM_018169.3|4|A) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.715046 rs147866721 -0.693147 0.149789 113 V568 975 gtG/gtC LOW 5 SILENT CODING BICD1 C protein_coding NM_001714.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32481093 G C 0 222 0 0.1377 0.2646 0.2118 0.5764 0.2296 0.1881 0.147753 0.188605 0.209535 1 1531 28378 2257 5162 2039 14460 198 2731 2 10370 121232 11564 8622 6608 66662 908 16498 0.969673 0 . 0 COSM1562146 115 43,17,28,14 SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V568|975|BICD1|protein_coding|CODING|NM_001714.2|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.516739 rs3748275 -0.693146 0.12861 115 D257 878 gaC/gaT LOW 4 SILENT CODING FGD4 T protein_coding NM_001304480.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32735236 C T 0 222 0 0.7247 0.4671 0.4928 0.2401 0.4036 0.3998 0.687926 0.498924 0.402093 1 7115 49840 5882 1970 2192 25328 384 6969 2 10404 121350 11572 8646 6614 66696 908 16510 0.964568 0 . 0 . 102 26,28,26,13 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D257|878|FGD4|protein_coding|CODING|NM_001304480.1|4|T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.952663 rs904582 -0.693144 0.134477 102 R547 878 cgG/cgA LOW 10 SILENT CODING FGD4 A protein_coding NM_001304480.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32764184 G A 0 222 0 0.2027 0.2652 0.2781 0.1657 0.3161 0.3906 0.238084 0.28756 0.312907 1 2349 35860 2860 1398 1547 20570 275 6861 2 10384 121334 11576 8652 6614 66694 906 16508 0.249283 2 benign 0 . 102 20,26,23,16 SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R547|878|FGD4|protein_coding|CODING|NM_001304480.1|10|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.7221 rs10844253 -0.693144 0.0845694 102 A618 878 gcG/gcA LOW 12 SILENT CODING FGD4 A protein_coding NM_001304480.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32777362 G A 0 222 0 0.1536 0.2516 0.268 0.1667 0.3191 0.3906 0.194961 0.272259 0.31186 1 1785 33130 2643 1352 1467 19026 251 6606 2 9234 107694 10340 7758 5978 58048 824 15512 0.993974 2 benign 0 . 52 8,14,10,14 SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A618|878|FGD4|protein_coding|CODING|NM_001304480.1|12|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.997826 rs11052110 -0.692831 0.455708 52 878 1954 MODIFIER 17 CODING FGD4 G protein_coding NM_001304480.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32795421 A G 0 9.7 0 0.9622 0.7418 0.6326 0.7798 0.4682 0.7638 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1954||878|FGD4|protein_coding|CODING|NM_001304480.1|17|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1239829,rs386524030 -0.379885 0 1 878 3770 MODIFIER 17 CODING FGD4 T protein_coding NM_001304480.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32797237 G T 0 9.7 0 0.5045 0.4337 0.4697 0.2113 0.4523 0.5225 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||3770||878|FGD4|protein_coding|CODING|NM_001304480.1|17|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11052123 -0.379885 0 1 878 5198 MODIFIER 17 CODING FGD4 A protein_coding NM_001304480.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32798665 G A 0 9.7 0 0.6225 0.4677 0.487 0.2123 0.4533 0.5225 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||5198||878|FGD4|protein_coding|CODING|NM_001304480.1|17|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1133509 -0.379885 0 1 S40 749 tcA/tcC LOW 2 SILENT CODING DNM1L C protein_coding NM_001278464.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32854366 A C 0 222 0 0.177 0.1266 0.0937 0.0813 0.161 0.093 0.16364 0.151392 0.145116 1 1776 15206 798 671 656 9357 118 1830 2 10386 121088 11540 8628 6602 66538 906 16488 0.981601 0 . 0 . 173 49,31,58,23 SYNONYMOUS_CODING(LOW|SILENT|tcA/tcC|S40|749|DNM1L|protein_coding|CODING|NM_001278464.1|2|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.202006 rs10844308 -0.693147 0.00225307 173 G97 749 ggG/ggA LOW 4 SILENT CODING DNM1L A protein_coding NM_001278464.1 SPLICE_SITE_REGION+SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32860302 G A 0 222 0 0.2103 0.144 0.1037 0.0833 0.164 0.1247 0.195504 0.162737 0.145906 1 2111 16093 830 672 663 9557 119 2141 2 10300 121190 11576 8652 6614 66630 908 16510 0.916115 0 . 0 . 407 110,60,96,72 SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G97|749|DNM1L|protein_coding|CODING|NM_001278464.1|4|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.701741 rs2272238 -0.693147 0.340071 407 T319 749 acA/acG LOW 10 SILENT CODING DNM1L G protein_coding NM_001278464.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32875406 A G 0 222 0 0.177 0.1266 0.0937 0.0813 0.161 0.093 0.16364 0.151392 0.145116 1 1768 15204 796 670 656 9369 116 1829 2 10100 119958 11452 8604 6558 65984 894 16366 0.917784 0 . 0 . 236 83,40,64,27 SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T319|749|DNM1L|protein_coding|CODING|NM_001278464.1|10|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.414289 rs10844318 -0.693147 0.118152 236 749 21 MODIFIER 21 CODING DNM1L C protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32896365 G C 0 222 0 0.2103 0.1436 0.1037 0.0833 0.165 0.1217 0.055833 0.0389051 0.0302326 1 2104 15938 822 663 656 9454 115 2124 2 10352 120154 11492 8596 6582 65902 898 16332 0.701128 0 . 0 . 135 47,18,34,17 UTR_3_PRIME(MODIFIER||21||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|C),DOWNSTREAM(MODIFIER||3113||477|YARS2|protein_coding|CODING|NM_001040436.2||C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738447 rs1059422,rs386422400 -0.693147 0.305539 135 749 22 MODIFIER 21 CODING DNM1L T protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32896366 A T 0 222 0 0.2103 0.1436 0.1037 0.0833 0.165 0.1217 0.0497049 0.0343688 0.0265116 1 2104 15938 822 663 656 9454 115 2124 2 10354 120184 11498 8598 6582 65924 898 16330 0.849992 0 . 0 . 136 47,18,34,17 UTR_3_PRIME(MODIFIER||22||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|T),DOWNSTREAM(MODIFIER||3112||477|YARS2|protein_coding|CODING|NM_001040436.2||T) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.738447 rs3200103 -0.693147 0.305539 136 749 271 MODIFIER 21 CODING DNM1L G protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32896615 C G 0 120 0 0.2103 0.1438 0.1037 0.0833 0.166 0.1217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.868815 0 . 0 . 16 0,9,1,5 UTR_3_PRIME(MODIFIER||271||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|G),DOWNSTREAM(MODIFIER||2863||477|YARS2|protein_coding|CODING|NM_001040436.2||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.972604 rs1020670 -0.616816 0.631962 16 749 744 MODIFIER 21 CODING DNM1L T protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32897088 A T 0 9.7 0 0.208 0.1422 0.1037 0.0813 0.162 0.1227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||744||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|T),DOWNSTREAM(MODIFIER||2390||477|YARS2|protein_coding|CODING|NM_001040436.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1971911,rs41516953 -0.379885 0 1 749 1093 MODIFIER 21 CODING DNM1L C protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32897437 T C 0 39.2 0 0.4266 0.2055 0.121 0.0853 0.172 0.1247 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.833333 0 . 0 . 5 2,0,3,0 UTR_3_PRIME(MODIFIER||1093||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|C),DOWNSTREAM(MODIFIER||2041||477|YARS2|protein_coding|CODING|NM_001040436.2||C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.333333 rs1971910 -0.511536 0.833544 5 749 1213 MODIFIER 21 CODING DNM1L T protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32897557 G T 0 139 0 0.2103 0.144 0.1037 0.0853 0.165 0.1217 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.915014 0 . 0 . 19 6,0,12,0 UTR_3_PRIME(MODIFIER||1213||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|T),DOWNSTREAM(MODIFIER||1921||477|YARS2|protein_coding|CODING|NM_001040436.2||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.372752 rs11052213 -0.680642 0.068433 19 749 1242 MODIFIER 21 CODING DNM1L A protein_coding NM_001278464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32897586 G A 0 140 0 0.177 0.127 0.0937 0.0833 0.162 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.95891 0 . 0 . 25 11,0,13,0 UTR_3_PRIME(MODIFIER||1242||749|DNM1L|protein_coding|CODING|NM_001278464.1|21|A),DOWNSTREAM(MODIFIER||1892||477|YARS2|protein_coding|CODING|NM_001040436.2||A) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.769328 rs10844336 -0.683931 0.195805 25 477 643 MODIFIER 5 CODING YARS2 T protein_coding NM_001040436.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32899495 C T 0 9.7 0 0.177 0.1266 0.0937 0.0813 0.162 0.092 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||643||477|YARS2|protein_coding|CODING|NM_001040436.2|5|T),DOWNSTREAM(MODIFIER||911||749|DNM1L|protein_coding|CODING|NM_001278464.1||T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11052214,rs111190403 -0.379885 0 1 477 209 MODIFIER 5 CODING YARS2 G protein_coding NM_001040436.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32899929 C G 0 115 0 0.2103 0.1438 0.1037 0.0833 0.165 0.1227 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.911373 0 . 0 . 23 11,0,12,0 UTR_3_PRIME(MODIFIER||209||477|YARS2|protein_coding|CODING|NM_001040436.2|5|G),DOWNSTREAM(MODIFIER||1345||749|DNM1L|protein_coding|CODING|NM_001278464.1||G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.970151 rs10844337 -0.680642 0.919643 23 G191V 477 gGt/gTt MODERATE 1 MISSENSE CODING YARS2 A protein_coding NM_001040436.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32908237 C A 0 222 0 0.177 0.1266 0.0937 0.0833 0.162 0.09 0.162052 0.149546 0.14314 1 1772 15214 798 675 658 9370 118 1823 2 10336 120880 11568 8628 6614 66318 904 16512 0.469931 0 . 0 . 91 28,23,24,10 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G191V|477|YARS2|protein_coding|CODING|NM_001040436.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.630873 rs11539445 -0.693132 0.0125675 91 G97 477 ggC/ggT LOW 1 SILENT CODING YARS2 A protein_coding NM_001040436.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 32908518 G A 0 222 0 0.177 0.127 0.0937 0.0833 0.162 0.092 0.164321 0.151699 0.145233 1 1779 15246 796 677 658 9392 118 1826 2 10288 120600 11552 8604 6610 66134 904 16508 0.998121 2 benign 0 . 105 35,13,34,15 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G97|477|YARS2|protein_coding|CODING|NM_001040436.2|1|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.381134 rs11539444 -0.693147 0.197668 105 523 477 MODIFIER 7 CODING SYT10 C protein_coding NM_198992.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 33529288 T C 0 153 0 0.9546 0.8257 0.7421 0.9375 0.6262 0.8006 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 8 0,0,7,1 UTR_3_PRIME(MODIFIER||477||523|SYT10|protein_coding|CODING|NM_198992.3|7|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs9888363 -0.651104 0.385012 8 523 414 MODIFIER 7 CODING SYT10 G protein_coding NM_198992.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 33529351 C G 0 34.5 0 0.8132 0.5727 0.5231 0.6151 0.3241 0.4949 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.651439 0 . 0 . 13 9,0,4,0 UTR_3_PRIME(MODIFIER||414||523|SYT10|protein_coding|CODING|NM_198992.3|7|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs9888320 -0.556411 0.794163 13 523 224 MODIFIER 1 CODING SYT10 G protein_coding NM_198992.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 33592681 C G 0 157 0 0.7632 0.6773 0.5058 0.874 0.4891 0.6738 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 15 0,0,0,15 UTR_5_PRIME(MODIFIER||224||523|SYT10|protein_coding|CODING|NM_198992.3|1|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7309229 -0.688148 0.626441 15 473 113 MODIFIER 1 CODING ALG10B T protein_coding NM_001013620.3 UTR_5_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38710583 C T 0 228 0 0.5787 0.6615 0.6599 0.8581 0.5249 0.7127 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 53 0,0,39,11 START_GAINED(LOW||||473|ALG10B|protein_coding|CODING|NM_001013620.3|1|T),UTR_5_PRIME(MODIFIER||113||473|ALG10B|protein_coding|CODING|NM_001013620.3|1|T) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs7296576 -0.693147 0.00528438 53 L42 473 Ctg/Ttg LOW 1 SILENT CODING ALG10B T protein_coding NM_001013620.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38710819 C T 0 222 0 0.0658 0.1492 0.0548 0.4524 0.0229 0.1462 0.0574217 0.0362141 0.0253488 1 606 8680 351 3843 110 1534 54 2182 2 10404 121380 11574 8636 6614 66732 908 16512 0.994966 0 . 0 . 87 14,21,25,18 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L42|473|ALG10B|protein_coding|CODING|NM_001013620.3|1|T) 1 0.5 1 0 . 1 0 1 1 0 59 0 0.984664 0.981192 0 0.805328 rs74618076 -0.693146 0.0924815 87 A84G 473 gCa/gGa MODERATE 2 MISSENSE CODING ALG10B G protein_coding NM_001013620.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38712142 C G 0 228 0 0.9039 0.9667 0.9726 1 0.9851 0.9939 0.919882 0.966169 0.989884 2 9546 119264 11437 8654 6437 65873 898 16419 2 10406 121412 11578 8654 6614 66740 908 16512 0 . 0 . 0 326 0,0,133,175 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gGa|A84G|473|ALG10B|protein_coding|CODING|NM_001013620.3|2|G) 1 0 . 0 . 1 0 1 1 0 53 0 0 0.11706 0 . rs6582584 -0.693147 0.00121985 326 473 154 MODIFIER 3 CODING ALG10B G protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38715168 GT G 0 204 0 0.0643 0.149 0.0548 0.4534 0.0229 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 64 35,7,16,5 UTR_3_PRIME(MODIFIER||154||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|G) 0 0.5 1 21 0.328125 1 1 0 . 0 60 0 0 1 0 . rs3841370 -0.692352 0.759333 64 473 452 MODIFIER 3 CODING ALG10B A protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38715467 G A 0 228 0 0.7466 0.7117 0.6816 0.8571 0.5388 0.7137 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 111 0,0,61,45 UTR_3_PRIME(MODIFIER||452||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|A) 0 . 0 . 0 1 0 . 0 . 59 0 0 0.989712 0 . rs7306030 -0.693147 0.0619556 111 473 950 MODIFIER 3 CODING ALG10B G protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38715965 T G 0 36.3 0 0.7466 0.7119 0.6816 0.8571 0.5388 0.7147 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 UTR_3_PRIME(MODIFIER||950||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|G) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs6582599 -0.453602 0.02 2 473 4228 MODIFIER 3 CODING ALG10B A protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38719243 C A 0 64 0 0.9024 0.9663 0.9712 1 0.9861 0.9939 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,0,3 UTR_3_PRIME(MODIFIER||4228||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7312123 -0.511536 0.764235 3 473 6255 MODIFIER 3 CODING ALG10B G protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38721270 A G 0 6.3 0 0.5794 0.6659 0.6686 0.8571 0.5388 0.7147 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||6255||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4882354 -0.379885 0 1 473 6447 MODIFIER 3 CODING ALG10B T protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38721462 A T 0 9.7 0 0.7466 0.7117 0.6816 0.8562 0.5388 0.7147 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||6447||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs4882355 -0.379885 0 1 473 7445 MODIFIER 3 CODING ALG10B A protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38722460 G A 0 23.7 0 0.5794 0.6657 0.6686 0.8562 0.5388 0.7147 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 UTR_3_PRIME(MODIFIER||7445||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs7977738 -0.379885 0 2 473 8366 MODIFIER 3 CODING ALG10B G protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38723381 A G 0 9.7 0 0.7466 0.7071 0.6758 0.8562 0.5229 0.7117 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||8366||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|G) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs1046071 -0.379885 0 1 473 8453 MODIFIER 3 CODING ALG10B A protein_coding NM_001013620.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 38723468 T A 0 9.7 0 0.0666 0.1474 0.0548 0.4425 0.0229 0.1462 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 UTR_3_PRIME(MODIFIER||8453||473|ALG10B|protein_coding|CODING|NM_001013620.3|3|A) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs59621452 -0.379885 0 1 564 1620 MODIFIER 20 CODING CPNE8 C protein_coding NM_153634.2 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 39046064 T C 0 100 0 0.0741 0.4413 0.5231 0.2867 0.8708 0.5971 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.605479 0 . 0 . 15 6,0,9,0 UTR_3_PRIME(MODIFIER||1620||564|CPNE8|protein_coding|CODING|NM_153634.2|20|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 0.778801 rs7970273 -0.662043 0.0698567 15 1674 472 MODIFIER 38 CODING KIF21A C protein_coding NM_001173464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 39687754 T C 0 101 0 0.5825 0.382 0.2061 0.379 0.1938 0.4325 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.952672 0 . 0 . 32 1,19,0,12 UTR_3_PRIME(MODIFIER||472||1674|KIF21A|protein_coding|CODING|NM_001173464.1|38|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.611027 rs11171674 -0.680642 0.338575 32 1674 237 MODIFIER 38 CODING KIF21A C protein_coding NM_001173464.1 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 39687989 T C 0 151 0 0.5825 0.3822 0.2061 0.379 0.1948 0.4325 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.905336 0 . 0 . 45 20,2,22,0 UTR_3_PRIME(MODIFIER||237||1674|KIF21A|protein_coding|CODING|NM_001173464.1|38|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 1 0 0.0508124 rs11171675 -0.692562 0.0227803 45 L1590 1674 Ctg/Ttg LOW 37 SILENT CODING KIF21A A protein_coding NM_001173464.1 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 39695445 G A 0 222 0 0.0219 0.0811 0.121 0.128 0.0696 0.0961 0.0265547 0.0426726 0.0509302 1 251 7873 1111 1068 235 3753 62 1393 2 10384 121356 11574 8648 6614 66716 908 16512 0.649604 0 . 0 . 92 26,15,19,20 SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1590|1674|KIF21A|protein_coding|CODING|NM_001173464.1|37|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.807181 rs2271477 -0.693144 0.0571073 92 740 389 MODIFIER 10 CODING ABCD2 C protein_coding NM_005164.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 39947325 T C 0 37.5 0 0.0038 0.1374 0.1023 0.247 0.0716 0.2975 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 1 0 . 0 . 4 1,0,3,0 UTR_3_PRIME(MODIFIER||389||740|ABCD2|protein_coding|CODING|NM_005164.3|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 1 0 . 1 rs11172566 -0.511536 0.690245 4 652 LOW 3 CODING C12orf40 G protein_coding NM_001031748.2 SPLICE_SITE_REGION+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40037727 A G 0 222 0 0.649 0.7175 0.8069 0.6022 0.8718 0.7065 0.675028 0.807496 0.866741 1 6506 97347 9360 5262 5890 57278 777 12274 2 9760 120294 11380 8612 6596 66546 898 16502 0.960712 0 . 0 . 78 13,26,12,20 SPLICE_SITE_REGION+INTRON(LOW||||652|C12orf40|protein_coding|CODING|NM_001031748.2|3|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.776814 rs10735878,rs386430397 -0.69312 0.0770367 78 648 4446 MODIFIER 10 CODING SLC2A13 T protein_coding NM_052885.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40149382 G T 0 6.3 0 0.0703 0.2123 0.1758 0.4296 0.1282 0.2924 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||4446||648|SLC2A13|protein_coding|CODING|NM_052885.3|10|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs11173440 -0.379885 0 1 648 1458 MODIFIER 10 CODING SLC2A13 C protein_coding NM_052885.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40152370 T C 0 9.7 0 0.0703 0.2127 0.1758 0.4306 0.1292 0.2924 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 UTR_3_PRIME(MODIFIER||1458||648|SLC2A13|protein_coding|CODING|NM_052885.3|10|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs79519820 -0.379885 0 1 648 928 MODIFIER 10 CODING SLC2A13 A protein_coding NM_052885.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40152900 G A 0 228 0 0.9992 0.9894 0.9928 0.999 0.9742 0.9796 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 122 0,0,58,45 UTR_3_PRIME(MODIFIER||928||648|SLC2A13|protein_coding|CODING|NM_052885.3|10|A) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs4447240 -0.693147 0.0126681 122 648 288 MODIFIER 10 CODING SLC2A13 C protein_coding NM_052885.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40153540 T C 0 161 0 0.0703 0.2125 0.1758 0.4306 0.1282 0.2924 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 7 0,0,5,1 UTR_3_PRIME(MODIFIER||288||648|SLC2A13|protein_coding|CODING|NM_052885.3|10|C) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs11173459,rs386481149 -0.616816 0.915302 7 R50H 2527 cGc/cAc MODERATE 1 MISSENSE CODING LRRK2 A protein_coding NM_198578.3 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40619082 G A 0 228 0 0.8865 0.9692 0.9942 1 1 1 0.898547 0.965477 0.999767 2 9334 120159 11527 8652 6604 66649 903 16490 2 10372 121236 11552 8652 6604 66656 906 16494 0 0 uncertain 0 . 180 0,0,45,124 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cGc/cAc|R50H|2527|LRRK2|protein_coding|CODING|NM_198578.3|1|A) 1 0 . 0 . 1 0 1 1 0 60 0 0 1 0 . rs2256408 -0.693147 0.0136246 180 L153 2527 Ttg/Ctg LOW 5 SILENT CODING LRRK2 C protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40631791 T C 0 222 0 0.3608 0.4529 0.3905 0.3552 0.5656 0.6063 0.384476 0.529064 0.60314 1 3999 63784 3583 2995 3398 39326 467 10016 2 10396 121202 11528 8642 6604 66624 904 16504 0.925181 0 uncertain 0 COSM1128598,COSM1128599 166 44,50,27,29 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L153|2527|LRRK2|protein_coding|CODING|NM_198578.3|5|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.711158 rs10878245 -0.693147 0.00937026 166 N551K 2527 aaC/aaG MODERATE 14 MISSENSE CODING LRRK2 G protein_coding NM_198578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40657700 C G 0 222 0 0.1278 0.0994 0.1614 0.1042 0.0636 0.0491 0.138221 0.0946008 0.0722429 1 1458 10413 1827 933 394 5073 64 664 2 10348 120988 11516 8644 6596 66486 906 16492 0.999577 0 uncertain 0 . 202 35,66,28,50 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaG|N551K|2527|LRRK2|protein_coding|CODING|NM_198578.3|14|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.775709 rs7308720 -0.693147 0.0384133 202 L953 2527 Tta/Cta LOW 22 SILENT CODING LRRK2 C protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40688695 T C 0 222 0 0.0159 0.0901 0.1282 0.1458 0.1292 0.0654 0.0236042 0.0948821 0.131536 1 233 12684 957 1610 540 8224 93 1027 2 9998 119636 11350 8604 6536 65820 894 16434 0.605739 0 uncertain 0 COSM147475,COSM147474 163 45,17,50,21 SYNONYMOUS_CODING(LOW|SILENT|Tta/Cta|L953|2527|LRRK2|protein_coding|CODING|NM_198578.3|22|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.731036 rs7966550 -0.693147 1.83e-05 163 G1624 2527 ggC/ggA LOW 34 SILENT CODING LRRK2 A protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40713834 C A 0 222 0 0.7844 0.6829 0.6902 0.5218 0.668 0.7219 0.759318 0.685903 0.648325 1 7806 82093 8456 4326 5145 43798 638 11924 2 10200 121066 11554 8644 6608 66650 908 16502 0.964203 0 uncertain 0 . 144 44,20,28,29 SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G1624|2527|LRRK2|protein_coding|CODING|NM_198578.3|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.966858 rs1427263 -0.693147 0.0835568 144 R1628P 2527 cGt/cCt MODERATE 34 MISSENSE CODING LRRK2 C protein_coding NM_198578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40713845 G C 0 222 0 0 0.0063898 0 0.0317 0 0 0.00181818 0.000923503 0.000465441 1 8 211 0 163 0 39 0 1 2 10132 120950 11540 8652 6610 66606 906 16504 0.771392 5 pathogenic 0 . 140 43,20,27,26 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R1628P|2527|LRRK2|protein_coding|CODING|NM_198578.3|34|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.931445 rs33949390 -0.693147 0.0817193 140 K1637 2527 aaA/aaG LOW 34 SILENT CODING LRRK2 G protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40713873 A G 0 222 0 0.587 0.5857 0.6052 0.501 0.5427 0.7014 0.575034 0.551732 0.539804 1 5973 69303 7638 4100 3554 36122 516 11400 2 10158 120870 11524 8640 6604 66546 906 16492 0.969702 0 uncertain 0 COSM289939,COSM289938 116 31,23,16,32 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K1637|2527|LRRK2|protein_coding|CODING|NM_198578.3|34|G) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.760019 rs11176013 -0.693147 0.422695 116 S1647T 2527 Tca/Aca MODERATE 34 MISSENSE CODING LRRK2 A protein_coding NM_198578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40713901 T A 0 222 0 0.174 0.2859 0.2349 0.3373 0.3171 0.3885 0.178945 0.257737 0.298068 1 1782 35862 2258 2880 2418 20204 290 6030 2 9900 120232 11488 8620 6600 66238 902 16484 0.959061 0 uncertain 0 . 82 15,27,5,27 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Aca|S1647T|2527|LRRK2|protein_coding|CODING|NM_198578.3|34|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.980899 rs11564148 -0.69312 0.0366137 82 G1819 2527 ggT/ggC LOW 37 SILENT CODING LRRK2 C protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40716260 T C 0 222 0 0.5862 0.5853 0.6037 0.501 0.5427 0.7014 0.576714 0.553437 0.541512 1 6084 69555 7675 4107 3555 36200 517 11417 2 10392 121322 11566 8636 6610 66700 908 16510 0.999622 0 uncertain 0 . 142 28,32,28,36 SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1819|2527|LRRK2|protein_coding|CODING|NM_198578.3|37|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.453548 rs10878371 -0.693147 0.148171 142 E2108 2527 gaG/gaA LOW 43 SILENT CODING LRRK2 A protein_coding NM_198578.3 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40742254 G A 0 222 0 0.1241 0.2738 0.2349 0.3383 0.3231 0.3865 0.146618 0.256075 0.312166 1 1468 36217 2264 2875 2520 20896 288 5906 2 10354 120672 11486 8608 6586 66286 908 16444 0.495192 0 uncertain 0 . 125 31,24,31,20 SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E2108|2527|LRRK2|protein_coding|CODING|NM_198578.3|43|A) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.506364 rs10878405 -0.693147 0.00210276 125 M2397T 2527 aTg/aCg MODERATE 49 MISSENSE CODING LRRK2 C protein_coding NM_198578.3 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40758652 T C 0 222 0 0.4917 0.5517 0.5288 0.4603 0.67 0.6217 0.52861 0.612273 0.655116 1 5356 73865 5314 3942 4876 43434 580 10363 2 10058 118378 11150 8332 6506 65166 892 16274 0.936482 0 uncertain 0 . 79 35,0,33,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M2397T|2527|LRRK2|protein_coding|CODING|NM_198578.3|49|C) 1 0.5 1 0 . 1 0 1 1 0 60 0 1 1 0 0.37972 rs3761863 -0.693139 0.146021 79 2527 364 MODIFIER 51 CODING LRRK2 C protein_coding NM_198578.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40761931 A C 0 53 0 0.4939 0.5513 0.5288 0.4603 0.67 0.6166 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924449 0 . 0 . 11 0,7,0,4 UTR_3_PRIME(MODIFIER||364||2527|LRRK2|protein_coding|CODING|NM_198578.3|51|C) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.964642 0 . 0.924449 rs10878441 -0.556411 0.43429 11 2527 384 MODIFIER 51 CODING LRRK2 T protein_coding NM_198578.3 UTR_3_PRIME outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40761951 C T 0 35.9 0 0.4947 0.5515 0.5288 0.4603 0.67 0.6166 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0.924584 0 . 0 . 9 0,6,0,3 UTR_3_PRIME(MODIFIER||384||2527|LRRK2|protein_coding|CODING|NM_198578.3|51|T) 0 0.5 1 0 . 1 0 . 0 . 60 0 0.924584 0 . 0.924584 rs3886747 -0.511536 0.267404 9 G88R 8221 Ggt/Cgt MODERATE 4 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40799975 G C 0 23.4 0 0.3949 0.4085 0.3674 0.4772 0.3698 0.4254 0 . 0 1 76 3984 28 58 2 1041 31 2748 2 190 10512 92 134 4 2646 108 7338 1 0 . 0 . 4 0,2,0,2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|Ggt/Cgt|G88R|8221|MUC19|protein_coding|CODING|NM_173600.2|4|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 0 . 1 rs10784596 -0.453602 0.92 4 G129S 8221 Ggt/Agt MODERATE 5 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40802150 G A 0 49.3 0 0.5681 0.6006 0.621 0.5397 0.5656 0.729 0 . 0 1 127 7441 55 61 47 1639 69 5443 2 202 10784 94 132 74 2696 124 7462 0.666667 0 . 0 . 7 2,1,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G129S|8221|MUC19|protein_coding|CODING|NM_173600.2|5|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.666667 rs1019709 -0.453602 0.06 7 D176H 8221 Gat/Cat MODERATE 6 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40805948 G C 0 222 0 0.0068 0.112 0.1066 0.2262 0.164 0.0869 0 . 0 1 20 2257 24 104 345 925 31 808 2 876 16304 268 464 1610 5312 204 7570 0.796435 0 . 0 COSM1606056 30 9,6,5,6 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D176H|8221|MUC19|protein_coding|CODING|NM_173600.2|6|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.662021 rs10878538 -0.676189 0.427987 30 8221 HIGH 17 CODING MUC19 A protein_coding NM_173600.2 SPLICE_SITE_ACCEPTOR+INTRON outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40820208 G A 0 228 0 0.4274 0.4311 0.3977 0.4722 0.4026 0.4468 0 . 0 2 447 7079 97 212 702 2441 78 3102 2 978 17144 296 486 1636 5874 216 7658 1 0 . 0 . 54 1,0,44,5 SPLICE_SITE_ACCEPTOR+INTRON(HIGH||||8221|MUC19|protein_coding|CODING|NM_173600.2|17|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 (MUC19|MUC19|1|1.00) 60 0 1 1 0 1 rs11176575 -0.693147 0.224677 54 G717E 8221 gGa/gAa MODERATE 19 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40821176 G A 0 228 0 0.7852 0.8325 0.8761 0.7183 0.9264 0.8865 0 . 0 2 793 15257 245 333 1525 5297 190 6874 2 974 17006 292 488 1640 5758 208 7646 1 0 . 0 . 119 1,0,87,20 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|gGa/gAa|G717E|8221|MUC19|protein_coding|CODING|NM_173600.2|19|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 52 0 1 0.113999 0 1 rs7955308 -0.693147 0.148915 119 S780 8221 tcC/tcT LOW 20 SILENT CODING MUC19 T protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40821839 C T 0 222 0 0.0817 0.1142 0.134 0.1577 0.1362 0.0767 0 . 0 1 101 1872 33 82 179 852 26 599 2 1104 17732 318 490 1696 6244 218 7662 0.993877 0 . 0 . 234 46,54,46,50 SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S780|8221|MUC19|protein_coding|CODING|NM_173600.2|20|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.806971 rs11176584 -0.693147 0.151269 234 V790I 8221 Gtc/Atc MODERATE 20 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40821867 G A 0 222 0 0.236 0.3131 0.2608 0.3462 0.328 0.4049 0 . 0 1 270 5803 71 157 607 1940 63 2695 2 1026 17324 310 488 1660 5972 210 7658 0.968003 0 . 0 . 245 34,82,26,62 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V790I|8221|MUC19|protein_coding|CODING|NM_173600.2|20|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.955501 rs7958987 -0.693147 0.0167999 245 N1139 8221 aaC/aaT LOW 28 SILENT CODING MUC19 T protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40832126 C T 0 222 0 0.3601 0.5182 0.5648 0.4742 0.5447 0.7168 0 . 0 1 441 10616 165 213 971 3509 123 5194 2 1070 17414 308 486 1662 6018 212 7658 0.547492 0 . 0 . 210 46,46,44,48 SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N1139|8221|MUC19|protein_coding|CODING|NM_173600.2|28|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.700155 rs10878584 -0.693147 0.308336 210 I1151T 8221 aTt/aCt MODERATE 28 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40832161 T C 0 222 0 0.3601 0.5184 0.5663 0.4742 0.5447 0.7168 0 . 0 1 379 10287 154 213 957 3286 122 5176 2 954 16748 292 484 1636 5612 208 7562 0.863934 0 . 0 . 195 35,56,26,57 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aCt|I1151T|8221|MUC19|protein_coding|CODING|NM_173600.2|28|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.991447 rs11176635,rs386517380 -0.693147 0.335426 195 C1156W 8221 tgC/tgG MODERATE 29 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40834376 C G 0 199 0 0.3601 0.518 0.5648 0.4742 0.5447 0.7157 0 . 0 1 356 10121 142 200 948 3187 123 5165 2 866 16486 258 458 1624 5444 212 7624 0.957116 0 . 0 . 30 12,4,7,4 NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|tgC/tgG|C1156W|8221|MUC19|protein_coding|CODING|NM_173600.2|29|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.197492 rs10878592 -0.676189 0.836722 30 C1238* 8221 tgC/tgA HIGH 31 NONSENSE CODING MUC19 A protein_coding NM_173600.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40834955 C A 0 222 0 0.3601 0.5184 0.5663 0.4742 0.5447 0.7168 0 . 0 1 435 10649 167 214 963 3550 127 5193 2 1058 17458 312 488 1646 6076 216 7662 0.398266 0 . 0 . 79 19,23,8,21 STOP_GAINED(HIGH|NONSENSE|tgC/tgA|C1238*|8221|MUC19|protein_coding|CODING|NM_173600.2|31|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 (MUC19|MUC19|1|1.00) 60 0 1 1 (MUC19|MUC19|1|1.00) 0.197384 rs10784618 -0.693079 0.205248 79 I1278M 8221 atC/atG MODERATE 32 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40835734 C G 0 222 0 0.3601 0.5184 0.5663 0.4742 0.5447 0.7168 0 . 0 1 365 10206 153 213 948 3274 119 5134 2 930 16714 294 486 1614 5610 206 7574 0.586426 0 . 0 . 188 50,39,40,35 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I1278M|8221|MUC19|protein_coding|CODING|NM_173600.2|32|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.858264 rs7966110 -0.693147 0.541197 188 A1367T 8221 Gca/Aca MODERATE 34 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40837149 G A 0 222 0 0.0008 0.0262 0.072 0.0774 0 0.002 0 . 0 1 1 113 17 38 15 23 1 18 2 926 16628 292 486 1622 5494 206 7602 0.501774 0 . 0 . 124 41,11,35,21 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1367T|8221|MUC19|protein_coding|CODING|NM_173600.2|34|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.970937 rs11564141 -0.693147 0.00960445 124 V1493A 8221 gTg/gCg MODERATE 36 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40838216 T C 0 222 0 0.3601 0.5184 0.5663 0.4752 0.5437 0.7168 0 . 0 1 430 10507 159 216 964 3424 125 5189 2 1032 17224 302 490 1642 5884 214 7660 0.988084 0 . 0 . 92 14,27,12,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V1493A|8221|MUC19|protein_coding|CODING|NM_173600.2|36|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.946237 rs10784621 -0.693146 0.289188 92 L1591 8221 Ttg/Ctg LOW 38 SILENT CODING MUC19 C protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40840325 T C 0 222 0 0.3601 0.5184 0.5663 0.4742 0.5447 0.7168 0 . 0 1 467 10678 169 213 971 3555 121 5182 2 1124 17504 320 486 1652 6076 208 7638 0.61952 0 . 0 . 114 45,11,27,14 SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L1591|8221|MUC19|protein_coding|CODING|NM_173600.2|38|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.839496 rs10878597 -0.693145 0.113191 114 T1651I 8221 aCa/aTa MODERATE 41 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40843503 C T 0 222 0 0 0.0057907 0 0.0288 0 0 0 . 0 1 0 16 0 15 0 0 1 0 2 906 16464 284 482 1620 5314 206 7652 0.701331 0 . 0 . 155 51,17,42,22 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T1651I|8221|MUC19|protein_coding|CODING|NM_173600.2|41|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 1 1 0 0.49221 rs142090558 -0.693147 0.0123866 155 E1762A 8221 gAa/gCa MODERATE 47 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40857943 A C 0 228 0 0.5219 0.6921 0.7622 0.6607 0.7475 0.8476 0 . 0 2 523 12811 202 306 1238 4102 154 6286 2 900 16484 290 484 1606 5332 206 7666 0 . 0 . 0 106 0,0,60,30 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E1762A|8221|MUC19|protein_coding|CODING|NM_173600.2|47|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2933353 -0.693147 0.712857 106 A2301T 8221 Gca/Aca MODERATE 56 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40873655 G A 0 9.7 0 0.3646 0.5198 0.5591 0.5397 0.5586 0.6411 0 . 0 1 8 26 1 0 0 15 2 0 2 18 38 2 0 0 16 2 0 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2301T|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2588401 -0.379885 0 1 T2445I 8221 aCa/aTa MODERATE 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40874088 C T 0 46.3 0 0.3646 0.5198 0.5591 0.5397 0.5586 0.6411 0 . 0 2 5 24 0 2 0 17 0 0 2 6 28 0 2 0 20 0 0 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T2445I|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2638864 -0.453602 0.36 2 A2529T 8221 Gct/Act MODERATE 56 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40874339 G A 0 9.7 0 0.3646 0.5198 0.5591 0.5397 0.5586 0.6411 0 . 0 1 2 10 0 3 0 5 0 0 2 8 18 0 4 0 6 0 0 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2529T|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2638865 -0.379885 0 1 K2866T 8221 aAa/aCa MODERATE 56 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40875351 A C 0 9.7 0 0.4917 0.656 0.7219 0.6121 0.7068 0.8241 0 . 0 1 2 19 0 0 0 17 0 0 2 4 24 0 0 0 20 0 0 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K2866T|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2251431 -0.379885 0 1 T3000S 8221 Aca/Tca MODERATE 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40875752 A T 0 39.3 0 0.4939 0.6518 0.7075 0.6121 0.6988 0.818 0 . 0 2 1 9 0 0 0 8 0 0 2 4 14 0 0 0 10 0 0 0 . 0 . 0 2 0,0,2,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Tca|T3000S|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 . 0 . rs1492320 -0.453602 0.86 2 T3077P 8221 Act/Cct MODERATE 56 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40875983 A C 0 46.3 0 0.3646 0.5208 0.5634 0.5407 0.5596 0.6411 0 . 0 2 4 13 0 0 0 9 0 0 2 4 16 0 0 0 12 0 0 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Cct|T3077P|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs1492322 -0.453602 0.9 2 T3436 8221 acA/acT LOW 56 SILENT CODING MUC19 T protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40877062 A T 0 9.7 0 0.3646 0.5204 0.5605 0.5407 0.5586 0.6421 0 . 0 1 1 9 0 0 0 8 0 0 2 6 20 0 0 0 14 0 0 0 . 0 . 0 1 0,0,0,1 SYNONYMOUS_CODING(LOW|SILENT|acA/acT|T3436|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 1 0 60 0 0 . 0 . rs2933356 -0.379885 0 1 A4031V 8221 gCg/gTg MODERATE 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40878846 C T 0 118 0 0.5371 0.5681 0.572 0.5397 0.5636 0.6411 0 . 0 2 5 16 0 1 0 10 0 0 2 10 28 0 2 0 16 0 0 0 . 0 . 0 5 0,0,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A4031V|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2638867 -0.556411 0.100421 5 P4039A 8221 Cct/Gct MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40878869 C G 0 122 0 0.525 0.6929 0.7622 0.6617 0.7475 0.8466 0 . 0 2 10 56 0 2 0 44 0 0 2 18 70 0 4 0 48 0 0 0 . 0 . 0 5 0,0,1,3 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Gct|P4039A|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 1 0 60 0 0 1 0 . rs2588413 -0.556411 0.100421 5 G4436S 8221 Ggt/Agt MODERATE 56 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880060 G A 0 46.3 0 0.525 0.6945 0.7723 0.6627 0.7475 0.8466 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4436S|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2638868 -0.453602 0.1 2 Q4443* 8221 Cag/Tag HIGH 56 NONSENSE CODING MUC19 T protein_coding NM_173600.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880081 C T 0 46.3 0 0.3646 0.5218 0.572 0.5407 0.5586 0.6411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q4443*|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 (MUC19|MUC19|1|1.00) 60 0 0 1 (MUC19|MUC19|1|1.00) 0 rs2638869 -0.453602 0.1 2 S4558T 8221 aGt/aCt MODERATE 56 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880427 G C 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S4558T|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs370171939 -0.379885 0 1 K4562 8221 aaA/aaG LOW 56 SILENT CODING MUC19 G protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880440 A G 0 9.7 0 0.3865 0.4692 0.5303 0.4226 0.508 0.546 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K4562|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs374475412 -0.379885 0 1 T4564 8221 acT/acC LOW 56 SILENT CODING MUC19 C protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880446 T C 0 9.7 0 0.3865 0.4692 0.5303 0.4226 0.508 0.546 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T4564|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs377712357 -0.379885 0 1 S4566R 8221 agC/agG MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880452 C G 0 9.7 0 0.3835 0.4653 0.5288 0.4206 0.503 0.5378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agG|S4566R|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs371181116 -0.379885 0 1 *4567C 8221 tgA/tgT HIGH 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 STOP_LOST outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880455 A T 0 9.7 0 0.3835 0.4653 0.5288 0.4206 0.503 0.5378 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 STOP_LOST(HIGH|MISSENSE|tgA/tgT|*4567C|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs376190866 -0.379885 0 1 N4571D 8221 Aac/Gac MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880465 A G 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N4571D|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs112864659 -0.379885 0 1 R4693W 8221 Agg/Tgg MODERATE 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880831 A T 0 46.3 0 0.525 0.6941 0.7709 0.6617 0.7475 0.8466 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Tgg|R4693W|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2933364 -0.453602 0.26 2 T4724A 8221 Act/Gct MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40880924 A G 0 70 0 0.3638 0.5208 0.5692 0.5397 0.5586 0.6401 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T4724A|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2933365 -0.453602 0.42 3 R5232S 8221 agG/agC MODERATE 56 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40882450 G C 0 9.7 0 0.4123 0.5733 0.6902 0.5139 0.6083 0.7331 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agC|R5232S|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2920823 -0.379885 0 1 S5246G 8221 Agc/Ggc MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40882490 A G 0 32.6 0 0.2231 0.3183 0.4438 0.3423 0.3221 0.3292 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S5246G|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2588390,rs76949892 -0.379885 0 2 D5539 8221 gaC/gaT LOW 56 SILENT CODING MUC19 T protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40883371 C T 0 67 0 0.2231 0.3183 0.4424 0.3433 0.3191 0.3323 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 3 0,0,2,1 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D5539|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2638873 -0.511536 0.873285 3 N5611D 8221 Aac/Gac MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40883585 A G 0 9.7 0 0.4123 0.5753 0.6902 0.5228 0.6074 0.7352 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N5611D|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2588391 -0.379885 0 1 W5613* 8221 tGg/tAg HIGH 56 NONSENSE CODING MUC19 A protein_coding NM_173600.2 STOP_GAINED outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40883592 G A 0 9.7 0 0.211 0.2642 0.268 0.2639 0.3111 0.2853 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W5613*|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 (MUC19|MUC19|1|1.00) 60 0 0 . (MUC19|MUC19|1|1.00) 0 rs2638874 -0.379885 0 1 N5642K 8221 aaC/aaG MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40883680 C G 0 32.6 0 . 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaG|N5642K|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 . 0 . 0 . 60 0 0 . 0 . rs78081795 -0.379885 0 2 D5769 8221 gaC/gaT LOW 56 SILENT CODING MUC19 T protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884061 C T 0 46.3 0 0.3646 0.5198 0.5591 0.5397 0.5586 0.6411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D5769|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2588393 -0.453602 0.28 2 E5781D 8221 gaA/gaC MODERATE 56 MISSENSE CODING MUC19 C protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884097 A C 0 19.4 0 0.9924 0.998 1 1 1 1 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E5781D|8221|MUC19|protein_coding|CODING|NM_173600.2|56|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 1 0 . rs2638878 -0.453602 0.28 2 T5883 8221 acC/acA LOW 56 SILENT CODING MUC19 A protein_coding NM_173600.2 SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884403 C A 0 32.6 0 0.3646 0.5198 0.5591 0.5397 0.5586 0.6411 0 . 0 2 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 2 0,0,1,0 SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T5883|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 . 0 . 0 1 0 . 0 . 60 0 0 . 0 . rs2588394 -0.379885 0 2 T5971N 8221 aCc/aAc MODERATE 56 MISSENSE CODING MUC19 A protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884666 C A 0 9.7 0 0.4327 0.611 0.6888 0.5744 0.7406 0.7014 0 . 0 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T5971N|8221|MUC19|protein_coding|CODING|NM_173600.2|56|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 1 0 . 0 . 60 0 0 . 0 . rs2638879 -0.379885 0 1 N6001K 8221 aaC/aaG MODERATE 56 MISSENSE CODING MUC19 G protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884757 C G 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaG|N6001K|8221|MUC19|protein_coding|CODING|NM_173600.2|56|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs200694240 -0.379885 0 1 R6002W 8221 Agg/Tgg MODERATE 56 MISSENSE CODING MUC19 T protein_coding NM_173600.2 NON_SYNONYMOUS_CODING outputs/D025211_combined_R1.anno.vcf.gz D025211_combined_R1 12 40884758 A T 0 9.7 0 . 0 . 0 . 0 . 0 . 1 0 . 0 . 0 . 0 . 2 0 . 0 . 0 . 0 . 0 . 0 . 0 1 0,0,0,1 NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Tgg|R6002W|8221|MUC19|protein_coding|CODING|NM_173600.2|56|T|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS) 0 0.5 1 0 . 0 . 0 . 0 60 0 0 . 0 . rs78354426 -0.379885 0 1