To examine whether the GWAS variants associated with both AUD and DPW are mediated by changes in methylation and gene expression patterns, we conducted a summary data-based Mendelian randomization (SMR) analysis59 on a set of mQTLs and eQTLs (Top SNP P < 5 × 10−8) from fetal and adult brains. SMR is a Mendelian randomization-based analysis which integrates GWAS summary statistics with eQTL data in order to test whether the effect size of a SNP on the phenotype of interest is mediated by gene expression. We used this method as it does not require raw eQTL data to build the weights, so we were able to use the meta-analysis of eQTL data for the integration analysis. The gene and SNP positions for the summary statistics of the eQTL and mQTL datasets were standardized and aligned using an in-house summary statistics munging pipeline. The summary statistics were then converted into binary format (BESD) to perform the SMR analysis. The scripts used to create the binary (BESD) files for each dataset have been deposited in GitHub. The European subset of ADGC GWAS
