mQTL summary statistics were from five data sets: brain cortical region from ROSMAP study (nind = 468, nprobe = 420,103, nsnp = 5 million)19; fetal brain from Hannon et al. (nind = 166, nprobe = 26,840, nsnp = 0.3 million)36; frontal cortex region from Jaffe et al. (nind = 526, nprobe = 138,917, nsnp = 1.5 million)37; and peripheral blood from McRae et al.38 (Lothian Birth Cohorts54 (LBC): nind = 1366 and Brisbane Systems Genetics Study55 (BSGS): nind = 614). DNAm levels in all these five studies were based on the Illumina HumanMethylation450K array. We performed a meta-analysis of LBC and BSGS, resulting in 397,621 DNAm probes and ~7.7 million SNPs. The DNAm levels of all the five studies were not standardized. We computed the effect size and SE of each mQTL from their z-statistics using the method described in Zhu et al.21
