Having shown that cis-eQTL effects are highly correlated between brain and blood, we then turned to estimate the correlation of genetic effects on DNAm between the two tissues by applying the rb method to mQTL data. We analyzed summary-level mQTL data from five studies based on the Illumina HumanMethylation450K array: fetal brain from Hannon et al. (n = 166)36, brain cortical region from ROSMAP (n = 468)19, frontal cortex region from Jaffe et al. (n = 526)37, and peripheral blood from McRae et al. (LBC: n = 1366 and BSGS: n = 614)38 (Supplementary Table 3). All the mQTL effects are in SD units. We matched the SNPs in common across data sets, selected the top-associated cis-mQTL at PmQTL < 1 × 10−10 for 26,840 DNAm probes in the data from Hannon et al. (because only SNPs with PmQTL < 1 × 10−10 are available in this data set) and matched the selected probes with those in the other data sets (the number of matched probes ranged from 4892 to 6561) (Supplementary Table 4). The correlation of cis-mQTL effects between
