Given the hypothesized neurodevelopmental component to schizophrenia, we examined the extent to which the mQTLs overlapping with schizophrenia-associated variants are characterized by fetal-specific effects (Supplementary Table 16). Across the 78 mQTLs also tested in adult brain samples, overall effect sizes were significantly larger in fetal brain than all adult brain regions tested (Wilcoxon rank-sum test: PFC P = 0.0420, STR P = 0.00226, CER P = 0.00998) (Fig. 4). Our heterogeneity analysis highlighted 16 (20.5%) instances where significantly different relationships between genotype and DNA methylation are found across the adult and fetal datasets, with eight classed as fetal-specific variants (i.e. those not reaching our replication threshold (P < 1.00×10−5) in any adult brain region) and the remaining eight demonstrating smaller effects across the adult brain.
