Lead cis-eQTL SNPs which located >100kb from the transcription start site (TSS) or transcription end site (TES) of the gene were likely to overlap with capture Hi-C contacts (2.0-fold enrichment compared to when the location of the Hi-C target was flipped relative to the TSS; P<3.3×10−12; two-tailed two-sample test of equal proportions; Methods, Figure 2e, Supplementary Note). This suggests that some long-range cis-eQTLs are caused by physical interactions between the genomic regions of the SNP and the gene. For example, a capture Hi-C contact for IRS1 overlapped the lead eQTL SNP, mapping 630kb downstream from IRS1 (Figure 2f). Similarly, we observed an enriched overlap with Hi-C contacts for short-range cis-eQTL effects (<100kb, 1.3-fold; P<9.1×10−16; two-tailed two-sample test of equal proportions; Figure 2e, Supplementary Note).
