From the eQTL discovery results, we selected the 1,108 SNP-transcript pairs (755 eQTL SNPs) in cis with discovery pGWAS <0.05 (Figure 1). To confirm the hypothesis that disease-associated SNPs are more likely to be cis eQTLs [20], we searched for enrichment for eQTLs in our list of SNPs with pGWAS <0.05. We first determined the number of cis eQTLs in the set of SNPs with pGWAS <0.05 (n = 755). Then, we randomly selected a subset of 14,167 SNPs with pGWAS >0.05, matched for minor allele frequency to the set of SNPs with pGWAS <0.05 (in 5% frequency bins). Subsequently, we determined the number of eQTLs present in each of these sets of SNPs, using 100,000 permutations. By determining how often more than the initial number of eQTLs were observed, we showed that there was evidence for enrichment for eQTLs in the set of disease-associated SNPs (empirical p = 0.003).
