To explore the functional consequences of genetic variation in the developing human brain, we characterized mQTLs in human fetal brain samples (spanning 56–166 days post-conception), identifying over 16,000 associated pairs of SNPs and DNA methylation sites. We find that fetal brain mQTLs are significantly enriched in functional regulatory domains including DHSs, regions of repressive histone modifications, and specific transcription factor binding sites across the genome, and show significant overlap with genetic variants influencing gene expression in the brain. Although the majority of fetal brain mQTLs appear to be conserved across adult brain regions, we find evidence for fetal-specific genetic effects at certain loci. Our data concur with findings from an independent study of cortical mQTLs across development [Jaffe et al, Nat Neuro, in press]; mQTL effects are highly consistent across both analyses (Supplementary Fig. 13) and largely conserved between fetal and adult brain.
