Trans-eQTL mapping was performed using a previously described pipeline5 while testing a subset of 10,317 SNPs associated with complex traits. We required the distance between the SNP and the center of the gene to be >5 Mb. To maximize the power to identify trans-eQTL effects, the expression matrices were corrected for the results of summary-statistics-based or iterative conditional cis-eQTL mapping analyses (Supplementary Note) before trans-eQTL mapping. For that, lead SNPs for significant (FDR<0.05) conditional cis-eQTLs were regressed out from the expression matrix. Finally, we removed potential false positive trans-eQTLs caused by reads cross-mapping with cis regions (Supplementary Note).
