We first grouped non-coding SNPs into intronic and intergenic SNPs. Proximal genes were defined by positional mapping: for intronic SNPs, genes in which SNPs are located were defined as proximal genes; for intergenic SNPs, nearest genes were defined as proximal genes. Intronic and intergenic SNPs were then overlapped with the SNPs annotated by Hi-C (Hi-C non-coding SNPs: SNPs that interact with gene promoters and exons) and eQTLs (eQTL non-coding SNPs: SNPs that have associations with gene expression). For Hi-C non-coding SNPs, we compared proximal genes with genes that physically interact with the SNPs. For eQTL non-coding SNPs, we compared proximal genes with e-genes (genes that show eQTL associations). We assessed how often (1) physically interacting genes and/or e-genes for a given SNP contain proximal (nearest) genes (Extended Data Fig. 1a), and (2) SNPs show any interactions/associations with distal (non-nearest) genes (Fig. 1b).
