P values for all cis eQTLs (within 1Mb) were supplied by the authors of a recent manuscript documenting eQTLs in the human brain30 to enable a more thorough examination of the overlap of eQTL and mQTL. To identify all variants associated with DNA methylation and gene expression in cis, our definition of cis mQTL was relaxed to match that used in the eQTL study. Chromosome and base position of the SNPs were used to map between the two datasets. A Bonferroni significance threshold was established for the eQTL results (P from aveALL analysis < 5.99×10−9), based on the number of cis eQTLs tested across all SNPs overlapping with those tested in the mQTL dataset (414,172), in addition to two more relaxed exploratory thresholds (P < 10−9; 10−7).
