In the meQTL analyses of the 719 genome-wide significant SNPs and 158 CpG sites within the target region, methylation values of 16 CpG sites showed statistically significant association with 173 of the SNPs (FDR corrected p<0.05) (S6 Table). Among the highlighted genes were EGLN2, CYP2A7, CYP2F1 (Cytochrome P450, Family 2, Subfamily F, Polypeptide 1) (ENSG00000197446), and DLL3 (Delta-like 3 (Drosophila)) (ENSG00000090932) (S7 Table). To distinguish between our hypotheses B (‘SNPs affect NMR via methylation’) and C (‘SNPs affect methylation via NMR’) we performed CIT, and confirmed that methylation at the CpG site tagged by cg08551532 (in DLL3) mediates the effect of SNPs on NMR (S8 Table). We detected no evidence supporting hypothesis C.
