To assess whether cis-eQTL lead SNPs overlapped with chromosomal contact as measured by Hi-C data, we used promoter capture Hi-C (CHi-C) data71 downloaded from CHiCP72 (https://www.chicp.org/). We took the lead eQTL SNPs, overlapped these with the CHi-C data, and studied the 10,428 cis-eQTL genes for which this data was available. We tested whether the CHi-C target maps within 5kb of the lead SNP. Of the 803 cis-eQTL genes for which the lead SNP mapped more than 100 kb away from the TSS or TES, 223 overlapped with the CHi-C data (27.8%). Of 9,625 cis-eQTL genes for which the lead SNP mapped within 100kb from the TSS or TES, 1,641 overlapped with the CHi-C data (17.0%). To test if these observed overlaps were not happening by chance, we performed the same analysis while flipping the location of the CHi-C target relative to the location of the bait and tested the difference with a two-tailed two-sample test of equal proportions.
