We applied the SMR and HEIDI methods to identify genes and DNAm sites associated with brain-related phenotypes through pleiotropy using summary data from GWAS and cis-eQTL/mQTL studies with large sample sizes (nmax = 453,693 for GWAS, nmax = 14,115 for eQTL and nmax = 1980 for mQTL). We identified a number of genes and DNAm sites that showed pleiotropic associations with the phenotypes, consistent with a plausible model that the SNP effects on the phenotypes are mediated by genetic regulation of expression levels of the target genes and/or DNAm levels at the CpG sites. We repeated the analyses using eQTL and mQTL data from brain samples with much smaller sample sizes (nmax = 1194 for eQTL and nmax = 526 for mQTL). Due to the lower power of the data sets, the number of genes or DNAm sites detected in the brain sample was much smaller than that using the blood sample (Fig. 5, Supplementary Figs. 23–25), with at least 50% of genes (DNAm sites) in common between the two sets. These results provide strong justification for the use of
