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000169291 0247_ $$2doi$$a10.1016/j.ajhg.2021.05.013
000169291 0247_ $$2pmid$$apmid:34146516
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000169291 037__ $$aDKFZ-2021-01388
000169291 041__ $$aEnglish
000169291 082__ $$a570
000169291 1001_ $$aBaxter, Joseph S$$b0
000169291 245__ $$aFunctional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element.
000169291 260__ $$aNew York, NY$$bElsevier$$c2021
000169291 3367_ $$2DRIVER$$aarticle
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000169291 500__ $$a2021 Jul 1;108(7):1190-1203
000169291 520__ $$aA combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31).
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000169291 650_7 $$2Other$$abreast cancer risk
000169291 650_7 $$2Other$$afunctional annotation
000169291 650_7 $$2Other$$arisk locus
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