We used an extension of MAGMA: “Hi-C coupled MAGMA” or “H-MAGMA” (based on MAGMA version 1.08)28, to assign non-coding (intergenic and intronic) SNPs to cognate genes based on their chromatin interactions. Exonic and promoter SNPs were assigned to genes based on physical position. We used four Hi-C datasets provided with the software89–91. We evaluated Bonferroni-corrected significance, adjusted for the number of tests within each of the four Hi-C datasets (one-sided P < 9.83–9.86×10−7) (Supplementary Tables 17–20).
