The 304 SNPs among the 348 eQTLs were examined using the Ensembl Variant Effect Predictor54 (Supplementary Table 6), with each SNP assigned based on the most severe predicted consequence. Most of the SNPs were intronic, followed by intergenic, up- or downstream of protein coding sequence, and exonic (Figure 5b). The 53 intergenic SNPs had the lowest rate of overlapping regulatory features, or replication in NESDA (Supplementary Figure 8). SNPs in up/downstream sequences were more likely to overlap with regulatory elements, and SNPs in intronic/exonic regions were more likely to replicate in NESDA. Only 6 of the 348 distant eQTLs were exonic, suggesting they influence expression rather than modify proteins, consistent with our finding that these distant eQTL SNPs are more likely to be local eQTLs (Supplementary Figure 9).
