Capture Hi-C identifies putative target genes of breast cancer risk loci

Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. We generated CHi-C libraries in two ER+ breast cancer cell lines (T-47D, ZR-75-1), two ER- breast cancer cell lines (BT-20, MDA-MB-231), one "normal" breast epithelial cell line (Bre80-Q-TERT (Bre80)) and a control, non-breast lymphoblastoid cell line (GM06990). We used these data to annotate 63 loci, identifying 110 putative target genes at 33 loci. All CHi-C interaction peaks can be viewed at bit.ly/CHiC-BC.