mQTL data were not used for subsequent enrichment analyses, but they enabled us to further refine schizophrenia candidate regions and undertake co-localization analyses in order to identify variants associated with both DNA methylation and schizophrenia. We performed a Bayesian co-localization analysis35 across the 105 autosomal regions associated with schizophrenia12, spanning 19,378 DNA methylation sites included in our analysis. Instead of focusing only on the intersection of significant variants associated with two phenotypes independently, this approach compares the pattern of association results from the schizophrenia GWAS and mQTL analyses across a region, combining the summary statistics into posterior probabilities for five hypotheses (see Online Methods). As this methodology assumes that the causal variant is present, or at least very well tagged, in the dataset, these co-localization analyses were performed using our imputed fetal brain mQTL dataset. The posterior probabilities for 65 regions, involving 296 DNA methylation sites in 306 pairs, were supportive of a co-localized association signal for both schizophrenia and DNA methylation in that region (PP3+PP4 > 0.99; Supplementary Table 17). Twenty-six of these pairs (covering 15 regions associated with schizophrenia) had a higher posterior probability for both schizophrenia and DNA methylation being associated with the same causal variant (PP4/PP3
