As many of the risk variants for schizophrenia in the NHGRI GWAS Catalog only reached genome-wide suggestive but not significant evidence for association, we last sought to determine the proportion of PGC2 risk genotypes that associated with nearby DNAm levels, which would suggest a possible mechanism of risk. Using all marginally (at p < 1×10−4, N=1302/2107 in our data, see Methods) and genome-wide (at p<5×10−8, 104/111 in our data, see Methods) significant “index” SNPs and their highly correlated proxies (R2 > 0.6) within the PGC2 52 study discovery dataset, we identified that 579/1302 (44.4%) of all marginally significant loci, and 62/104 (59.6%) genome-wide significant loci interrogated, had a risk or proxy SNP that was also a meQTL in our cortex DNAm data (Supplementary Table 9). We hypothesize that these epigenetic signals highlight the particular risk gene in a locus with wide linkage disequilibrium, and we highlight 12 loci that feature meQTL p-values < 1.0×10−20 in Figure 4. These CpGs associated with risk variants map to TOM1L2, ITIH1, MAD1L1, NT5C2, OGFOD2, MMP16, BCL11B, PLCH2, SLC12A4, CACNA1C, WBP2NL, and C2orf82. DNAm levels
