DOI: 10.6084/m9.figshare.25959295
title: Accounting for genetic effect heterogeneity in fine-mapping and improving power to detect gene-environment interactions with SharePro

description: Summary statistics, fine-mapping, and GxE analysis results for smoking-status stratified GWAS in FFR and sex stratified GWAS in WHRadjBMI.WHR_statistics.txt contains the following columns: (1) SNP (rsID of variants); (2) CHR (chromosome); (3) POS (position in hg19); (4) A1 (effect allele); (5) A2 (other allele) (6) Index (CHR.POS.A1.A2) (7) BETA0 (effect size in female); (8) SE0 (standard error in female); (9) N0 (sample size in female); (10) AF10 (allele frequency in female); (11) bhat0 (standardized effect size in female); (12) BETA1 (effect size in male); (13) SE1 (standard error in male); (14) N1 (sample size in male); (15) AF11 (allele frequency in male); (16) bhat1 (standardized effect size in male); (17) PIP (posterior inclusion probability obtained using SharePro); (18) block (LD blocks); (19) cs (95% credible sets index); (20) cs_variants (variants included in the 95% credible set); (21) cs_purity (purity of credible sets); (22) nlog10pGxE_0_1(variant-level negative log10 of GxSex p-value); (23) nlog10pdiff_0_1 (negative log10 of GxSex p-value in SharePro); (24) nlog10p0 (negative log10 of p-value in female); (25) nlog10p1 (negative log10 of p-value in male); (26) SharePro (identified by SharePro as top variant in 95% credible set); (27) Clump (identified by LD clumping); (28) COJO (identified by COJO)FFR_statistics.txt contains the following columns: (1) SNP (rsID of variants); (2) CHR (chromosome); (3) POS (position in hg19); (4) A1 (effect allele); (5) A2 (other allele) (6) Index (CHR.POS.A1.A2) (7) BETA0 (effect size in current smokers); (8) SE0 (standard error in current smokers); (9) N0 (sample size in current smokers); (10) AF10 (allele frequency in current smokers); (11) bhat0 (standardized effect size in current smokers); (12) BETA1 (effect size in past smokers); (13) SE1 (standard error in past smokers); (14) N1 (sample size in past smokers); (15) AF11 (allele frequency in past smokers); (16) bhat1 (standardized effect size in past smokers); (17) BETA2 (effect size in never smokers); (18) SE2 (standard error in never smokers); (19) N2 (sample size in never smokers); (20) AF12 (allele frequency in never smokers); (21) bhat2 (standardized effect size in never smokers); (22) PIP (posterior inclusion probability obtained using SharePro); (23) block (LD blocks); (24) cs (95% credible sets index); (25) cs_variants (variants included in the 95% credible set); (26) cs_purity (purity of credible sets); (27) nlog10pGxE_0_1(variant-level negative log10 of GxSmoking p-value in current smokers vs past smokers); (28) nlog10pdiff_0_1(negative log10 of GxSex p-value in SharePro in current smokers vs past smokers); (29) nlog10pGxE_0_2(variant-level negative log10 of GxSmoking p-value in current smokers vs never smokers); (30) nlog10pdiff_0_2(negative log10 of GxSex p-value in SharePro in current smokers vs never smokers); (31) nlog10pGxE_0_2(variant-level negative log10 of GxSmoking p-value in past smokers vs never smokers); (32) nlog10pdiff_0_2(negative log10 of GxSex p-value in SharePro in past smokers vs never smokers); (33) nlog10p0 (negative log10 of p-value in current smokers); (34) nlog10p1 (negative log10 of p-value in past smokers); (35) nlog10p2 (negative log10 of p-value in never smokers); (36) SharePro (identified by SharePro as top variant in 95% credible set); (37) Clump (identified by LD clumping); (38) COJO (identified by COJO)Source code of SharePro is included.