We identified cis-eQTL (defined as variants within 1 Mb of the transcription start site [TSS] of the regulated gene) associated with the fetal brain expression of 1329 genes (eGenes) and 3252 individual transcripts (eTranscripts) at a false discovery rate (FDR) < 0.05 (Additional file 1: Table S2 and Table S3). The majority (86%) of eQTL detected at the whole gene level were also detected at the individual transcript level. Consistent with previous eQTL mapping studies [5, 15, 19], significant eQTL were concentrated in proximity to the TSS of the regulated transcript (Fig. 1a). We further tested for enrichment of high confidence cis-eQTLs (FDR < 0.05) within functional annotations provided by the ENCODE [8] and Roadmap Epigenomics Consortium [9] projects (Additional file 1: Table S4 and Table S5). Fetal brain cis-eQTL were significantly enriched within regions annotated as TSS, flanking promoters, enhancers, weak enhancers, and CTCF binding sites, but significantly depleted in repressed regions (Fig. 1b). Identified cis-eQTL were also notably enriched within regions containing histone modifications indicative of regulatory activity (Additional file 2: Figure S3). We additionally tested for enrichment,
