Given this enrichment for eQTLs, we asked whether the enrichment for cis mQTLs could be explained by our observation on the excess of cis eQTLs relative to expectation in cerebellum. Of the 132 cis mQTLs among the top Bipolar Disorder associated SNPs, 55 were found to be mQTLs that are not cis eQTLs. The remaining 77 SNPs are cis eQTLs. However, when we required that cis mQTLs and cis eQTLs have the same target genes in the SNP-gene pair, of 169 identified mQTL-gene pairs (resulting from several of the 132 cis mQTLs having multiple methylation gene targets), we identified only 8 pairs with the same SNP-gene combination as cis eQTL. A cis mQTL SNP for a given gene may be a cis eQTL of a different gene target. Of these 8 pairs, 5 are for one gene, DLG5 (for cis joint eQTLs-mQTLs: rs10762763, rs11002306, rs1866437, rs2579177, and rs2579178, the first two of which are intronic to the gene). The overlap of the target genes of the cis mQTL and of the cis eQTL is not greater than expected (hypergeometric distribution, p = 0.25).
