regress out (Supplementary Fig. 7). We assessed those combinations of SNPs and genes where the SNP–TSS distance was >5 Mb or where the gene and SNP were on different chromosomes as trans-eQTLs. To determine significance, we employed a previously used FDR estimation method91 using ten genome-wide permutations (Supplementary Note) and deemed trans-eQTLs with an FDR < 0.05 significant. We finally used an alignment-based approach to detect potential crossmapping artifacts, after which the FDR estimates were recalculated (Supplementary Note).
