Published 450K array probe annotations23 were used to identify probes located in transcription factor binding sites (TFBSs) or DNase1 hypersensitivity sites (DHSs) based on data made publically available as part of the ENCODE project10,26. In addition, brain specific DHSs were downloaded from the UCSC (University of California, Santa Cruz) Genome Browser for ‘Frontal_cortex_OC’, ‘Cerebellum_OC’ and ‘Cerebrum_frontal_OC’ and used to annotate DNA methylation sites in the same manner. Peaks associated with 5 histone modifications identified separately in two fetal brain samples (17 weeks gestation; 1 male, 1 female; sample IDs E081 and E082) were downloaded from the Epigenomics Roadmap project24. Due to the heterogeneity in the Chip-seq profiles, presumed due to experimental differences rather than biological differences47, DNA methylation sites had to be located within peaks generated from both brain samples to be classed as overlapping any of the histone marks. The overlap between regulatory features and the DNA methylation sites identified from the set of Bonferroni significant mQTLs in the fetal brain dataset was tested for enrichment using a two sided Fisher’s 2×2 exact test. The significance level for enrichment
