ArticleAmerican journal of human genetics2013
Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1.
Article in American journal of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 2 of them syntheses that pooled it.
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Who cites it
76 citing papers in PubMed, 2 syntheses or guidelines pooled it, 114 citations in OpenAlex.
- The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.BMC medical genomics · 2022Pooled it
- Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.International journal of cancer · 2016Pooled it
- Massively parallel functional profiling prioritizes breast cancer risk variants and implicates CCDC88C in ER-positive breast cancer.HGG advances · 2026Article
- Prioritizing context-specific genetic risk mechanisms in 11 solid cancers.Journal of the National Cancer Institute · 2026Article
- WDCN: a comprehensive neural network based approach for estimating breast cancer risk.Briefings in bioinformatics · 2026Article
- Prioritizing context-specific genetic risk mechanisms in 11 solid cancers.medRxiv : the preprint server for health sciences · 2025Article
- Illuminating the Noncoding Genome in Cancer Using Artificial Intelligence.Cancer research · 2025Review
- Article
- FGFR2 genetic variants in women with breast cancer.Molecular medicine reports · 2023Article
- Identification of non-coding silencer elements and their regulation of gene expression.Nature reviews. Molecular cell biology · 2023Review
- CRISPR screens identify gene targets at breast cancer risk loci.Genome biology · 2023Article
- Identification of loci associated with water use efficiency and symbiotic nitrogen fixation in soybean.Frontiers in plant science · 2023Article
- Efficient and accurate frailty model approach for genome-wide survival association analysis in large-scale biobanks.Nature communications · 2022Article
- Functional annotation of breast cancer risk loci: current progress and future directions.British journal of cancer · 2022Review
- Article
- Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.BMC genomic data · 2022Article
- Rare germline copy number variants (CNVs) and breast cancer risk.Communications biology · 2022Article
- Transcription factor regulation of eQTL activity across individuals and tissues.PLoS genetics · 2022Article
- Review
- Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element.American journal of human genetics · 2021Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
203 authors at 20 institutions in 24 countries.
Funding
Abstract
The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ERα to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.