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GWAS

Analyses

I ran S-LDSC on annotations from ENCODE, Roadmap, TCGA, and other papers.

• Enrichment Analyses (03/09/2020)

Annotations were merged into broad categories (immune histones, immune open chromatin, etc.). Torus was ran to estimate prior probabilities per SNP. SuSiE was ran with L = 1. SuSiE was also ran with no prior probability, and the resulting PIPs were compared below.

• Effect of Torus Prior on Finemapping (03/20/2020)

Torus + SuSiE finemapping results for immune SNPs with PIP > 0.05

• Spreadsheets of finemapping results (03/24/2020)

HiC data for GM12878 (LCLs) from Bing Ren et al. were obtained ( only the significant links were kept). These were merged with HiC data with CHiCAGO score > 5 for 17 immune primary cell types from Ulirsch, J.C., Lareau, C.A., Bao, E.L. et al. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet 51, 683–693 (2019).

Immune fine-mapped SNPs were matched to genes via the HiC data. A gene-level PIP is constructed at:

• HiC Gene PIPs (03/24/2020)

The ones with obvious immune function are highlighted in red.