# AD Fine-mapping and MPRA 
Chia-Yi Lee*, Ashvin Ravi*, Tzu-Chieh Huang, Briana Wyman, Ziyu Liu, Ariana Chriss, Jack
Humphrey, David A. Knowles, Chris Cotsapas, Laura M. Huckins, Towfique Raj, Kristen
J. Brennand

Pre-print: https://www.medrxiv.org/content/10.1101/2025.10.13.25337902v1.full.pdf

<img width="2125" height="2746" alt="fig1_mpra (1)" src="https://github.com/user-attachments/assets/8b018537-3a2d-4f31-b850-5530be1e5f5c" />

This repository contains all analyses regarding this manuscript, "Regulatory landscape of Alzheimer’s Disease Variants in Human Microglia." 

### Fine-mapping Tables 
**Full AD fine-mapping results and variants split by method are included within the finemapping_full_results folder within this repository.** 

All Supplementary Tables can be found in the Supplementary_Tables_AD_MPRA.xlsx file. Variants within each supplementary table can also be queried via the R Markdown files provided in this README.md file. 


### Fine-mapping Analyses:
Figure 2a-b: [Credible Set Summary](https://ashvinravi.github.io/AD_MPRA/credible_set_summary/credible_set_summary.html)

Figure 2c-e: [Epigenomic Overlap Analysis](https://ashvinravi.github.io/AD_MPRA/epigenomic_overlaps/epigenomic_overlaps.html) 

Figure 2f-g: [ABC Enrichment Analysis](https://ashvinravi.github.io/AD_MPRA/ABC_enrichment_results/ABC_enrichment.html)

### MPRA Analyses:

**emVars full results prioritized in the MPRA are included within the emVars_results folder within this repository**

[All Variants Tested for Microglia MPRA](https://ashvinravi.github.io/AD_MPRA/MPRA_library_design/MPRA_library.html)