Chromatin interactions with CTCF sites upstream of the KCNK9 promoter, the PEG13 -DMR and a novel brain-specific enhancer. (A) A schematic map of the TRAPPC9 and KCNK9 genes and annotated ChIA-PET data showing CTCF interactions. The red star represents the location of the brain-specific enhancer. (B) The 3C looping profile in brain using a constant primer 5′ to the KCNK9 promoter (upper graph) or within the enhancer located within intron 17 of TRAPPC9 (lower graph). (C) Sequence track for H3K4me1 and H3K27ac for a 30 kb region containing the TRAPPC9 intron 17 ChIA-PET site. Tracks are shown in expressing in brain and non-neuronal lymphocyte samples. The two shades of grey peaks in the meDIP and ChIP-seq panels represent two independent biological replicates compared to input (black peaks) with the y-axis showing the number of ChIP-seq reads. The red star depicts the location of the proposed enhancer region. (D) A proposed model of higher-order chromatin looping within the 8q24 domain, showing the special organisation of the allele-specific PEG13 enhancer-blocker in relation to the gene promoters, CTCF binding sites and H3K4me1/H3K27ac enhancer region. (●) methylated cytosine, (O) unmethylated cytosines and green block representing the H3K4me1/H3K27ac region associated with the brain-specific enhancer (e).