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Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-associated SNPs fall within a distal enhancer that regulates CCND1. Here, we report that, in addition to regulating CCND1, this enhancer regulates two estrogen-regulated long noncoding RNAs, CUPID1 and CUPID2. We provide evidence that the risk-associated SNPs are associated with reduced chromatin looping between the enhancer and the CUPID1 and CUPID2 bidirectional promoter. We further show that CUPID1 and CUPID2 are predominantly expressed in hormone-receptor-positive breast tumors and play a role in modulating pathway choice for the repair of double-strand breaks. These data reveal a mechanism for the involvement of this region in breast cancer.

Original publication




Journal article


Am J Hum Genet

Publication Date





255 - 266


11q13, DNA repair, GWAS, breast cancer, enhancer, long noncoding RNAs, Breast Neoplasms, Cell Line, Tumor, Chromatin, Chromosomes, Human, Pair 11, Cyclin D1, DNA Breaks, Double-Stranded, DNA Damage, DNA Repair, Enhancer Elements, Genetic, Estrogens, Female, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Humans, MCF-7 Cells, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, RNA Interference, RNA, Guide, RNA, Long Noncoding, RNA, Small Interfering