meQTL analysis in the adult control samples (age > 13, N=258) allowing for up to 20kb between SNPs and CpGs, controlling for factors related to ancestry and global epigenetic variation (see Methods), and identified 4,107,214 significant SNP-CpG methylation associations (meQTLs) at FDR < 1% (corresponding to p < 8.6×10−4, Online Table 2, Online Table 3, Supplementary Text 6). We note that many of these meQTLs identified in the adult samples appear largely consistent in directionality (κ = 0.741) and magnitude (ρ = 0.707) with meQTLs in the smaller set of fetal samples (Supplementary Figure 8). While many may not be cell type-specific, as the composition of the fetal brains differs dramatically from the adult samples (see Figure 2), a subset may impart fetal-specific effects not present in adult subjects29.
