We used eQTL data from ten adult brain regions30 to test whether identified fetal brain mQTLs overlap with genetic variants associated with RNA transcript abundance in cis. We compared the distribution of the minimum brain eQTL P-value of all interrogated SNPs split into the subsets of those identified as fetal brain mQTLs and those not (Supplementary Fig. 7), finding that variants associated with DNA methylation are indeed more likely to be associated with gene expression in cis (Wilcoxon rank sum test P < 2.2×10−16). Of the 414,172 SNPs tested in both the mQTL and eQTL datasets, 9,869 were identified as being Bonferroni-significant cis mQTLs and 2,674 as Bonferroni-significant (P < 5.99×10−9) eQTLs, with an overlap of 750 variants associated with 227 DNA methylation probes and 127 transcript probes (Supplementary Table 12). At a more relaxed eQTL threshold (P < 1.00×10−7), there is an overlap of 1,042 variants associated with 315 DNA methylation probes and 183 transcript probes. A list of all variants associated with both DNA methylation and gene expression in cis is given in Supplementary Table 13. This overlapping
