using linkage disequilibrium pruning (R2 > 0.5, plink parameters – indep 50 5 2), removing approximately 90% of variants. Second, from the original VCF file, we performed association mapping using only the most significant GTEx cis-eQTL per eGene per tissue. Third, from the original VCF file, we performed association mapping using only variants that had been found to have a trait association in a genome-wide association study47 (P ≤2.0×10−5). The three association mapping analyses and FDR estimation were performed in each tissue separately. For all trans association tests, we applied stringent quality control to account for potential false positives due to RNA-seq read mapping errors, repeat elements, and population stratification (Supplementary Information 7).
