Schizophrenia associated genomic loci were taken as the 105 autosomal regions published as part of the PGC mega-analysis12. Given our definition of cis mQTLs (i.e. associations between SNPs and DNA methylation probes within 500kb), all DNA methylation sites located within 500kb of these regions were identified and cis mQTL analysis was repeated using the imputed genotypes using MatrixEQTL46 and recording all mQTL results. Colocalization analysis was performed as previously described35 using the R coloc package (http://cran.r-project.org/web/packages/coloc) for each DNA methylation site within each region. In total 19,607 possible mQTLs were tested. From both the PGC schizophrenia GWAS data and our mQTL results we inputted the regression coefficients, their variances and SNP minor allele frequencies, and the prior probabilities were left as their default values. This methodology quantifies the support across the results of each GWAS for 5 hypotheses by calculating the posterior probabilities, denoted as PPi for hypothesis Hi.
