CTCF and breast cancer: Following identification of cell-type specific cis-regulatory elements (CRE), defined as the intersection between cell-type agnostic cCREs from ENCODE and the cell type-specific open chromatin regions analyzed using ATAC-seq (in HMEC, NHM, HepG2, and the breast cancer cell line MCF-7), with the incorporation of H3K4me1 peaks and exclusion of a blacklist of ambiguous genomic regions32, k-means clustering (k = 5) was performed using the ChIP-seq signal from H3K4me1, H3K4me3, H3K27ac, H3K27me3, mH2A1, mH2A2 and when available, H2A.Z and CTCF.