We therefore concentrated on 737 trans-eQTLs, detected after correcting for 100 PCs, which reflect 526 unique SNPs and 108 unique genes; 127 SNPs had trans-eQTL effects on multiple genes and 461 (88%) of the trans-eQTL SNPs were associated with a significant cis-eQTL in Cortex-EUR. We observed that 150 (33%) of the 461 significant trans-eQTL SNPs overlapping a cis-eQTL SNP were also the cis-eQTL index SNP, which represents an enrichment (Fisher’s exact test, P = 1.2 × 10−28; Supplementary Note); 29 were also cis-eQTL SNPs in tissues other than the cortex (Supplementary Table 17). This indicates that cis-eQTL index SNPs yield trans-eQTL effects more often in the brain in comparison to other cis-eQTL variants.
