We systematically profiled histone modification patterns and gene expression programs in a set of well characterized cell lines that represent 5 major breast cancer subtypes, including two ER positive subtypes, Luminal-A and Luminal-B, the HER2 positive subtype, and two triple-negative subtypes, TNBC-Claudin Low, and TNBC-Basal, as well as two normal immortalized breast cell lines as controls (Fig. 1a; color codes indicated for each cell line will be used throughout the paper). Here, ESR1 is linked to breast cancer.