All Bonferroni-significant mQTLs (P < 3.69×10−13) identified in the fetal brain, for which corresponding mQTL data was available from all three adult brain regions, were tested for heterogeneous relationships between DNA methylation and genetic variation across the datasets (n = 10,663). A null model of no heterogeneity was fitted in line with the linear model fitted to test for mQTL effects between the number of alleles (coded 0,1,2) and DNA methylation (beta value 0–100) with fixed effect covariates for sex, age and the first two genetic principal components. As the adult brain regions were dissected from the same set of individuals, we expect their DNA methylation values to be correlated. In addition, we expect DNA methylation values within a brain region to be correlated, and therefore both of these covariates were included as random effects in addition to an indicator variable discriminating fetal from adult samples to control for absolute differences in DNA methylation level associated with age/development stage. This was compared to a heterogeneity model which included an interaction between genotype and development stage indicator with an ANOVA to calculate the heterogeneity P-value.
