Despite concern about epiphenomena (Supplementary Figure 12, Supplementary Text 8), we did find slight but significant enrichment of our 2,104 diagnosis-associated CpGs within the PGC loci – 40/2,104 CpGs (1.9%) compared to only 1.3% of the rest of CpGs on the array (OR=1.6, p=0.004) but none of these 40 were meQTLs to any SNPs, including the risk-associated SNPs identified in the PGC. Overall, among these 2,104 CpGs showing DNAm level differences between patients and controls, only 97 were genome-wide significant meQTLs, a six fold decrease in enrichment than expected by chance (OR=0.165, p=2.32×10−86, see Methods) even though there was strong global correlation among meQTLs identified in adult controls and in the patients with schizophrenia (Supplementary Figure 13).
