We also asked whether the specific SNP-gene links (“genetic links”) predicted by our eQTL analysis were supported by enhancer-gene links based on functional correlation (“functional links”) (14). We found that open chromatin regions containing an eQTL SNP show higher correlation to the corresponding gene, relative to open chromatin regions without an eQTL at similar distances and linked to genes also containing an independent eQTL (r = 0.037 versus 0.030, paired Mann-Whitney two-sided P = 4.3 × 10−11, SE = 0.00114, n = 32,168 eQTL-SNP pairs).
