Journal Article
. 2012 Sep; 44(11):1191-8.
doi: 10.1038/ng.2416.

Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

Richard Cowper-Sal lari 1 Xiaoyang Zhang  Jason B Wright  Swneke D Bailey  Michael D Cole  Jerome Eeckhoute  Jason H Moore  Mathieu Lupien  
Affiliations
  • PMID: 23001124
  •     51 References
  •     198 citations

Abstract

Genome-wide association studies (GWAS) have identified thousands of SNPs that are associated with human traits and diseases. But, because the vast majority of these SNPs are located in non-coding regions of the genome, the mechanisms by which they promote disease risk have remained elusive. Employing a new methodology that combines cistromics, epigenomics and genotype imputation, we annotate the non-coding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results show that breast cancer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of histone H3 lysine 4 monomethylation (H3K4me1) in a cancer- and cell type-specific manner. Furthermore, the majority of the risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, thereby resulting in allele-specific gene expression, which is exemplified by the effect of the rs4784227 SNP on the TOX3 gene within the 16q12.1 risk locus.

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Mol Biol Evol, 2015 May 16; 32(8). PMID: 25976354    Free PMC article.
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Swneke D Bailey, Carl Virtanen, Benjamin Haibe-Kains, Mathieu Lupien.
Bioinformatics, 2015 May 23; 31(18). PMID: 25995231    Free PMC article.
Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes.
Kwoneel Kim, Woojin Yang, +7 authors, Jung Kyoon Choi.
Nucleic Acids Res, 2015 May 24; 43(12). PMID: 26001967    Free PMC article.
The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set.
Heloisa Helena Milioli, Renato Vimieiro, +3 authors, Pablo Moscato.
PLoS One, 2015 Jul 02; 10(7). PMID: 26132585    Free PMC article.
Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.
Gosia Trynka, Harm-Jan Westra, +6 authors, Soumya Raychaudhuri.
Am J Hum Genet, 2015 Jul 04; 97(1). PMID: 26140449    Free PMC article.
Highly Cited.
Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk.
Siddhartha P Kar, Jonathan P Tyrer, +152 authors, Paul D P Pharoah.
Cancer Epidemiol Biomarkers Prev, 2015 Jul 26; 24(10). PMID: 26209509    Free PMC article.
Review.
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.
Mufassra Naz, Alpha Tom Kodamullil, Martin Hofmann-Apitius.
Brief Bioinform, 2015 Aug 08; 17(3). PMID: 26249223    Free PMC article.
Predicting effects of noncoding variants with deep learning-based sequence model.
Jian Zhou, Olga G Troyanskaya.
Nat Methods, 2015 Aug 25; 12(10). PMID: 26301843    Free PMC article.
Highly Cited.
The search for cis-regulatory driver mutations in cancer genomes.
Rebecca C Poulos, Mathew A Sloane, Luke B Hesson, Jason W H Wong.
Oncotarget, 2015 Sep 12; 6(32). PMID: 26356674    Free PMC article.
Review.
Transcriptional enhancers: functional insights and role in human disease.
Irene Miguel-Escalada, Lorenzo Pasquali, Jorge Ferrer.
Curr Opin Genet Dev, 2015 Oct 04; 33. PMID: 26433090    Free PMC article.
Review.
Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.
Jennifer L Caswell, Roman Camarda, +6 authors, Elad Ziv.
Hum Mol Genet, 2015 Oct 17; 24(25). PMID: 26472073    Free PMC article.
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.
Haoyang Zeng, Tatsunori Hashimoto, Daniel D Kang, David K Gifford.
Bioinformatics, 2015 Oct 20; 32(4). PMID: 26476779    Free PMC article.
Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.
Derek A Oldridge, Andrew C Wood, +25 authors, John M Maris.
Nature, 2015 Nov 13; 528(7582). PMID: 26560027    Free PMC article.
Highly Cited.
Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.
Dmitry Svetlichnyy, Hana Imrichova, +2 authors, Stein Aerts.
PLoS Comput Biol, 2015 Nov 13; 11(11). PMID: 26562774    Free PMC article.
Propagation of oestrogen receptor-positive and oestrogen-responsive normal human breast cells in culture.
Agla J Fridriksdottir, Jiyoung Kim, +4 authors, Lone Rønnov-Jessen.
Nat Commun, 2015 Nov 14; 6. PMID: 26564780    Free PMC article.
Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data.
Yi-Juan Hu, Wei Sun, Jung-Ying Tzeng, Charles M Perou.
J Am Stat Assoc, 2015 Nov 17; 110(511). PMID: 26568645    Free PMC article.
Short-Circuiting Gene Regulatory Networks: Origins of B Cell Lymphoma.
Olivia I Koues, Eugene M Oltz, Jacqueline E Payton.
Trends Genet, 2015 Nov 26; 31(12). PMID: 26604030    Free PMC article.
Review.
Regulators of genetic risk of breast cancer identified by integrative network analysis.
Mauro A A Castro, Ines de Santiago, +7 authors, Kerstin B Meyer.
Nat Genet, 2015 Dec 01; 48(1). PMID: 26618344    Free PMC article.
Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.
Xiaoyang Zhang, Peter S Choi, +4 authors, Matthew Meyerson.
Nat Genet, 2015 Dec 15; 48(2). PMID: 26656844    Free PMC article.
Highly Cited.
The Effects of Sequence Variation on Genome-wide NRF2 Binding--New Target Genes and Regulatory SNPs.
Suvi M Kuosmanen, Sari Viitala, +11 authors, Anna-Liisa Levonen.
Nucleic Acids Res, 2016 Jan 31; 44(4). PMID: 26826707    Free PMC article.
GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person.
Youna Hu, Alena Shmygelska, +3 authors, David A Hinds.
Nat Commun, 2016 Feb 03; 7. PMID: 26835600    Free PMC article.
Highly Cited.
Models of human core transcriptional regulatory circuitries.
Violaine Saint-André, Alexander J Federation, +5 authors, Richard A Young.
Genome Res, 2016 Feb 05; 26(3). PMID: 26843070    Free PMC article.
Highly Cited.
A family-based, genome-wide association study of young-onset breast cancer: inherited variants and maternally mediated effects.
Katie M O'Brien, Min Shi, +5 authors, Clarice R Weinberg.
Eur J Hum Genet, 2016 Feb 18; 24(9). PMID: 26883092    Free PMC article.
TOX gene: a novel target for human cancer gene therapy.
Xin Yu, Zheng Li.
Am J Cancer Res, 2016 Feb 18; 5(12). PMID: 26885442    Free PMC article.
Review.
Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170.
Alison M Dunning, Kyriaki Michailidou, +249 authors, Stacey L Edwards.
Nat Genet, 2016 Mar 02; 48(4). PMID: 26928228    Free PMC article.
Highly Cited.
Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.
Marco Cavalli, Gang Pan, +8 authors, Claes Wadelius.
Hum Genet, 2016 Mar 20; 135(5). PMID: 26993500    Free PMC article.
FOXA1 defines cancer cell specificity.
Gaihua Zhang, Yongbing Zhao, +4 authors, Zhaoyu Li.
Sci Adv, 2016 Apr 02; 2(3). PMID: 27034986    Free PMC article.
Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.
Jiajun Shi, Yanfeng Zhang, +126 authors, Jirong Long.
Int J Cancer, 2016 Apr 19; 139(6). PMID: 27087578    Free PMC article.
Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures.
Xinchen Wang, Nathan R Tucker, +16 authors, Laurie A Boyer.
Elife, 2016 May 11; 5. PMID: 27162171    Free PMC article.
Highly Cited.
Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer.
Michael J G Milevskiy, Fares Al-Ejeh, +15 authors, Melissa A Brown.
Hum Mol Genet, 2016 Jul 06; 25(15). PMID: 27378691    Free PMC article.
Integrative Functional Genomics Implicates EPB41 Dysregulation in Hepatocellular Carcinoma Risk.
Xinyu Yang, Dianke Yu, +6 authors, Ming Yang.
Am J Hum Genet, 2016 Jul 28; 99(2). PMID: 27453575    Free PMC article.
The breast cancer susceptibility-related polymorphisms at the TOX3/LOC643714 locus associated with lung cancer risk in a Han Chinese population.
Chaowen Jiang, Shilong Yu, +12 authors, Fuyun Ji.
Oncotarget, 2016 Aug 04; 7(37). PMID: 27486757    Free PMC article.
The Estrogen Receptor α-Cistrome Beyond Breast Cancer.
Marjolein Droog, Mark Mensink, Wilbert Zwart.
Mol Endocrinol, 2016 Aug 05; 30(10). PMID: 27489947    Free PMC article.
Review.
Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer.
Haiyang Guo, Musaddeque Ahmed, +25 authors, Housheng Hansen He.
Nat Genet, 2016 Aug 16; 48(10). PMID: 27526323
Highly Cited.
Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.
Swneke D Bailey, Kinjal Desai, +16 authors, Mathieu Lupien.
Nat Genet, 2016 Aug 30; 48(10). PMID: 27571262    Free PMC article.
Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus.
Kate Lawrenson, Siddhartha Kar, +284 authors, Simon A Gayther.
Nat Commun, 2016 Sep 08; 7. PMID: 27601076    Free PMC article.
Identification of novel susceptibility markers for the risk of overall breast cancer as well as subtypes defined by hormone receptor status in the Chinese population.
Zhiping Deng, Hua Yang, +5 authors, Hong Ren.
J Hum Genet, 2016 Sep 09; 61(12). PMID: 27604554
Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation.
Maya Ghoussaini, Juliet D French, +122 authors, Stacey L Edwards.
Am J Hum Genet, 2016 Sep 20; 99(4). PMID: 27640304    Free PMC article.
Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry.
Olivia Corradin, Andrea J Cohen, +3 authors, Peter C Scacheri.
Nat Genet, 2016 Oct 28; 48(11). PMID: 27643537    Free PMC article.
Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity.
Wen Fong Ooi, Manjie Xing, +32 authors, Patrick Tan.
Nat Commun, 2016 Sep 30; 7. PMID: 27677335    Free PMC article.
FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer.
Xiaoyong Fu, Rinath Jeselsohn, +24 authors, Rachel Schiff.
Proc Natl Acad Sci U S A, 2016 Oct 30; 113(43). PMID: 27791031    Free PMC article.
Genetic and Epigenetic Regulation of TOX3 Expression in Breast Cancer.
Yoo-Jeong Han, Jing Zhang, +2 authors, Olufunmilayo I Olopade.
PLoS One, 2016 Nov 03; 11(11). PMID: 27806084    Free PMC article.
Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations.
Stanley Zhou, Aislinn E Treloar, Mathieu Lupien.
Cancer Discov, 2016 Nov 04; 6(11). PMID: 27807102    Free PMC article.
Review.
A functional variant rs4442975 modulating FOXA1-binding affinity does not influence the risk or progression of breast cancer in Chinese Han population.
Yi Zhang, Yan Li, +14 authors, Rong Zhong.
Oncotarget, 2016 Nov 12; 7(49). PMID: 27835577    Free PMC article.
Previous GWAS hits in relation to young-onset breast cancer.
Min Shi, Katie M O'Brien, +3 authors, Clarice R Weinberg.
Breast Cancer Res Treat, 2016 Nov 17; 161(2). PMID: 27848153    Free PMC article.
A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a.
Jiangchuan Ye, Nathan R Tucker, +3 authors, Patrick T Ellinor.
Am J Hum Genet, 2016 Nov 22; 99(6). PMID: 27866707    Free PMC article.
High-throughput allele-specific expression across 250 environmental conditions.
Gregory A Moyerbrailean, Allison L Richards, +11 authors, Francesca Luca.
Genome Res, 2016 Dec 10; 26(12). PMID: 27934696    Free PMC article.
Non-coding single nucleotide variants affecting estrogen receptor binding and activity.
Amir Bahreini, Kevin Levine, +5 authors, Adrian V Lee.
Genome Med, 2016 Dec 15; 8(1). PMID: 27964748    Free PMC article.
Association between the HOTAIR polymorphisms and cancer risk: an updated meta-analysis.
Zhao-Xiong Zhang, Xue Tong, Wan-Ni Zhang, Wei-Neng Fu.
Oncotarget, 2016 Dec 15; 8(3). PMID: 27965458    Free PMC article.
Quantifying deleterious effects of regulatory variants.
Shan Li, Roberto Vera Alvarez, +2 authors, Ivan Ovcharenko.
Nucleic Acids Res, 2016 Dec 17; 45(5). PMID: 27980060    Free PMC article.
GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps.
Miloš Nikolic, Argyris Papantonis, Alvaro Rada-Iglesias.
Hum Mol Genet, 2016 Dec 23; 26(4). PMID: 28007912    Free PMC article.
Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci.
Siddhartha P Kar, Emily Adler, +83 authors, Kate Lawrenson.
Br J Cancer, 2017 Jan 20; 116(4). PMID: 28103614    Free PMC article.
Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci.
Julio E Molineros, Wanling Yang, +17 authors, Swapan K Nath.
Hum Mol Genet, 2017 Jan 22; 26(6). PMID: 28108556    Free PMC article.
Genome-wide association analysis of chronic lymphocytic leukaemia, Hodgkin lymphoma and multiple myeloma identifies pleiotropic risk loci.
Philip J Law, Amit Sud, +38 authors, Richard S Houlston.
Sci Rep, 2017 Jan 24; 7. PMID: 28112199    Free PMC article.
Keap1/Nrf2 impairing revised: are we missing the single nucleotide polymorphisms?
Lucia Anna Muscarella, Vito Michele Fazio.
J Thorac Dis, 2017 Feb 06; 8(12). PMID: 28149633    Free PMC article.
Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia.
Philip J Law, Sonja I Berndt, +94 authors, Susan Slager.
Nat Commun, 2017 Feb 07; 8. PMID: 28165464    Free PMC article.
Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome.
Andrea J Cohen, Alina Saiakhova, +16 authors, Peter C Scacheri.
Nat Commun, 2017 Feb 09; 8. PMID: 28169291    Free PMC article.
Genetic polymorphisms (rs10636 and rs28366003) in metallothionein 2A increase breast cancer risk in Chinese Han population.
Di Liu, Meng Wang, +11 authors, Zhi-Jun Dai.
Aging (Albany NY), 2017 Feb 24; 9(2). PMID: 28228606    Free PMC article.
Imputation for transcription factor binding predictions based on deep learning.
Qian Qin, Jianxing Feng.
PLoS Comput Biol, 2017 Feb 25; 13(2). PMID: 28234893    Free PMC article.
Variant Set Enrichment: an R package to identify disease-associated functional genomic regions.
Musaddeque Ahmed, Richard C Sallari, +3 authors, Mathieu Lupien.
BioData Min, 2017 Feb 28; 10. PMID: 28239419    Free PMC article.
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer.
Rebecca F Lowdon, Ting Wang.
PLoS One, 2017 Mar 24; 12(3). PMID: 28333948    Free PMC article.
A sequence-based method to predict the impact of regulatory variants using random forest.
Qiao Liu, Mingxin Gan, Rui Jiang.
BMC Syst Biol, 2017 Apr 01; 11(Suppl 2). PMID: 28361702    Free PMC article.
Role of steroid receptor and coregulator mutations in hormone-dependent cancers.
Anna C Groner, Myles Brown.
J Clin Invest, 2017 Apr 04; 127(4). PMID: 28368289    Free PMC article.
Review.
The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions.
Julie Dubois-Chevalier, Vanessa Dubois, +15 authors, Jérôme Eeckhoute.
Genome Res, 2017 Apr 13; 27(6). PMID: 28400425    Free PMC article.
Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor.
Kevin Litchfield, Max Levy, +30 authors, Clare Turnbull.
Nat Genet, 2017 Jun 13; 49(7). PMID: 28604728    Free PMC article.
Highly Cited.
Recurrent and functional regulatory mutations in breast cancer.
Esther Rheinbay, Prasanna Parasuraman, +30 authors, Gad Getz.
Nature, 2017 Jun 29; 547(7661). PMID: 28658208    Free PMC article.
Highly Cited.
FOXO3 longevity interactome on chromosome 6.
Timothy A Donlon, Brian J Morris, +5 authors, Bradley J Willcox.
Aging Cell, 2017 Jul 20; 16(5). PMID: 28722347    Free PMC article.
FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?
Allyson C Espinal, Matthew F Buas, +17 authors, Michael J Higgins.
Breast Cancer Res Treat, 2017 Aug 02; 166(2). PMID: 28756535    Free PMC article.
Genetic variability and functional implication of the long control region in HPV-16 variants in Southwest China.
Juemin Xi, Junying Chen, +7 authors, Qiangming Sun.
PLoS One, 2017 Aug 03; 12(8). PMID: 28767682    Free PMC article.
Characterization of noncoding regulatory DNA in the human genome.
Ran Elkon, Reuven Agami.
Nat Biotechnol, 2017 Aug 09; 35(8). PMID: 28787426
Review.
Identification of breast cancer associated variants that modulate transcription factor binding.
Yunxian Liu, Ninad M Walavalkar, +3 authors, Michael J Guertin.
PLoS Genet, 2017 Sep 29; 13(9). PMID: 28957321    Free PMC article.
Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.
Xiaoyang Zhang, Peter S Choi, +16 authors, Matthew Meyerson.
Cancer Discov, 2017 Oct 01; 8(1). PMID: 28963353    Free PMC article.
A STATISTICAL MODEL TO ASSESS (ALLELE-SPECIFIC) ASSOCIATIONS BETWEEN GENE EXPRESSION AND EPIGENETIC FEATURES USING SEQUENCING DATA.
Naim U Rashid, Wei Sun, Joseph G Ibrahim.
Ann Appl Stat, 2016 Jan 01; 10(4). PMID: 29034055    Free PMC article.
Finding the Sources of Missing Heritability within Rare Variants Through Simulation.
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang.
Bioinform Biol Insights, 2017 Oct 21; 11. PMID: 29051702    Free PMC article.
Chromatin accessibility prediction via a hybrid deep convolutional neural network.
Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang.
Bioinformatics, 2017 Oct 27; 34(5). PMID: 29069282    Free PMC article.
Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders.
Mang Ching Lai, Anne-Laure Bechy, +6 authors, Tara M Caffrey.
Mol Neurodegener, 2017 Nov 01; 12(1). PMID: 29084565    Free PMC article.
Organizing combinatorial transcription factor recruitment at cis-regulatory modules.
Julie Dubois-Chevalier, Parisa Mazrooei, +3 authors, Jérôme Eeckhoute.
Transcription, 2017 Nov 07; 9(4). PMID: 29105538    Free PMC article.
Review.
Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility.
Amit Sud, Hauke Thomsen, +33 authors, Richard S Houlston.
Nat Commun, 2017 Dec 03; 8(1). PMID: 29196614    Free PMC article.
Breast cancer: The translation of big genomic data to cancer precision medicine.
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura.
Cancer Sci, 2017 Dec 08; 109(3). PMID: 29215763    Free PMC article.
Review.
Intergenic disease-associated regions are abundant in novel transcripts.
N Bartonicek, M B Clark, +11 authors, M E Dinger.
Genome Biol, 2017 Dec 30; 18(1). PMID: 29284497    Free PMC article.
Single nucleotide polymorphisms and cancer susceptibility.
Na Deng, Heng Zhou, Hua Fan, Yuan Yuan.
Oncotarget, 2018 Jan 05; 8(66). PMID: 29299175    Free PMC article.
Highly Cited. Review.
Break Breast Cancer Addiction by CRISPR/Cas9 Genome Editing.
Haitao Yang, MariaLynn Jaeger, +3 authors, Tao Weitao.
J Cancer, 2018 Jan 19; 9(2). PMID: 29344267    Free PMC article.
Review.
Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.
Henrik Hornshøj, Morten Muhlig Nielsen, +8 authors, Jakob Skou Pedersen.
NPJ Genom Med, 2018 Jan 23; 3. PMID: 29354286    Free PMC article.
Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
Sílvia Bonàs-Guarch, Marta Guindo-Martínez, +40 authors, David Torrents.
Nat Commun, 2018 Jan 24; 9(1). PMID: 29358691    Free PMC article.
Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia.
Jayaram Vijayakrishnan, James Studd, +37 authors, Richard S Houlston.
Nat Commun, 2018 Apr 11; 9(1). PMID: 29632299    Free PMC article.
DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.
Xuecong Wang, Yogesh Srivastava, +6 authors, Ralf Jauch.
Nucleic Acids Res, 2018 Apr 19; 46(11). PMID: 29669022    Free PMC article.
Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension.
Daiane Hemerich, Jessica van Setten, Vinicius Tragante, Folkert W Asselbergs.
Front Cardiovasc Med, 2018 Apr 20; 5. PMID: 29670885    Free PMC article.
Bayesian nonparametric discovery of isoforms and individual specific quantification.
Derek Aguiar, Li-Fang Cheng, +3 authors, Barbara E Engelhardt.
Nat Commun, 2018 Apr 29; 9(1). PMID: 29703885    Free PMC article.
Meta-analysis of GWAS on both Chinese and European populations identifies GPR173 as a novel X chromosome susceptibility gene for SLE.
Huoru Zhang, Yan Zhang, +13 authors, Wanling Yang.
Arthritis Res Ther, 2018 May 05; 20(1). PMID: 29724251    Free PMC article.
High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing.
Peng Zhang, Ji-Han Xia, +14 authors, Liang Wang.
Nat Commun, 2018 May 24; 9(1). PMID: 29789573    Free PMC article.
Intronic variant of EGFR is associated with GBAS expression and survival outcome of early-stage non-small cell lung cancer.
Mi Jeong Hong, Shin Yup Lee, +12 authors, Jae Yong Park.
Thorac Cancer, 2018 May 29; 9(8). PMID: 29806744    Free PMC article.
A promoter interaction map for cardiovascular disease genetics.
Lindsey E Montefiori, Debora R Sobreira, +7 authors, Marcelo A Nóbrega.
Elife, 2018 Jul 11; 7. PMID: 29988018    Free PMC article.
Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer.
Darren K Patten, Giacomo Corleone, +17 authors, Luca Magnani.
Nat Med, 2018 Jul 25; 24(9). PMID: 30038216    Free PMC article.
Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses.
Mahdi Rivandi, John W M Martens, Antoinette Hollestelle.
Front Genet, 2018 Aug 18; 9. PMID: 30116257    Free PMC article.
Review.
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk.
Yakir A Reshef, Hilary K Finucane, +16 authors, Alkes L Price.
Nat Genet, 2018 Sep 05; 50(10). PMID: 30177862    Free PMC article.
Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma.
Molly Went, Amit Sud, +67 authors, PRACTICAL consortium.
Nat Commun, 2018 Sep 15; 9(1). PMID: 30213928    Free PMC article.
Highly Cited.
FOXO3 on the Road to Longevity: Lessons From SNPs and Chromatin Hubs.
Paola Sanese, Giovanna Forte, +2 authors, Cristiano Simone.
Comput Struct Biotechnol J, 2019 Jul 16; 17. PMID: 31303978    Free PMC article.
Review.
Identification of atrial fibrillation associated genes and functional non-coding variants.
Antoinette F van Ouwerkerk, Fernanda M Bosada, +13 authors, Vincent M Christoffels.
Nat Commun, 2019 Oct 20; 10(1). PMID: 31628324    Free PMC article.
Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk.
Jayaram Vijayakrishnan, Maoxiang Qian, +23 authors, Jun J Yang.
Nat Commun, 2019 Nov 27; 10(1). PMID: 31767839    Free PMC article.
Chromatin interactome mapping at 139 independent breast cancer risk signals.
Jonathan Beesley, Haran Sivakumaran, +21 authors, Stacey L Edwards.
Genome Biol, 2020 Jan 09; 21(1). PMID: 31910858    Free PMC article.
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes.
Laura Fachal, Hugues Aschard, +343 authors, Alison M Dunning.
Nat Genet, 2020 Jan 09; 52(1). PMID: 31911677    Free PMC article.
Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer.
Stanley Zhou, James R Hawley, +25 authors, Mathieu Lupien.
Nat Commun, 2020 Jan 25; 11(1). PMID: 31974375    Free PMC article.
Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors.
Yunlong Ma, Jingjing Li, +20 authors, Ming D Li.
Aging (Albany NY), 2020 Feb 06; 12(3). PMID: 32012119    Free PMC article.
Genetic correlation between multiple myeloma and chronic lymphocytic leukaemia provides evidence for shared aetiology.
Molly Went, Amit Sud, +52 authors, Richard S Houlston.
Blood Cancer J, 2019 Jan 04; 9(1). PMID: 30602759    Free PMC article.
Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia.
Hui-Min Niu, Ping Yang, +10 authors, Yan Guo.
Transl Psychiatry, 2019 Feb 02; 9(1). PMID: 30705251    Free PMC article.
Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control.
Yosr Hamdi, Martin Leclerc, +9 authors, Jacques Simard.
Genes (Basel), 2019 Mar 03; 10(3). PMID: 30823486    Free PMC article.
Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts.
Anastasis Oulas, George Minadakis, Margarita Zachariou, George M Spyrou.
Sci Rep, 2019 Mar 03; 9(1). PMID: 30824863    Free PMC article.
BRCA1-associated R-loop affects transcription and differentiation in breast luminal epithelial cells.
Huai-Chin Chiang, Xiaowen Zhang, +7 authors, Rong Li.
Nucleic Acids Res, 2019 Apr 16; 47(10). PMID: 30982901    Free PMC article.
Association analyses identify 31 new risk loci for colorectal cancer susceptibility.
Philip J Law, Maria Timofeeva, +96 authors, Malcolm G Dunlop.
Nat Commun, 2019 May 16; 10(1). PMID: 31089142    Free PMC article.
Highly Cited.
Transcriptional regulation of normal human mammary cell heterogeneity and its perturbation in breast cancer.
Davide Pellacani, Susanna Tan, Sylvain Lefort, Connie J Eaves.
EMBO J, 2019 Jul 16; 38(14). PMID: 31304632    Free PMC article.
Review.
Relationships between SNPs and prognosis of breast cancer and pathogenic mechanism.
Yaning He, Hui Liu, +2 authors, Suxia Luo.
Mol Genet Genomic Med, 2019 Jul 19; 7(9). PMID: 31317673    Free PMC article.
Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer.
Soyeon Kim, Hyun Jung Park, Xiangqin Cui, Degui Zhi.
Sci Rep, 2020 Mar 05; 10(1). PMID: 32127627    Free PMC article.
A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation.
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Hum Mol Genet, 2019 Nov 07; 29(4). PMID: 31691800    Free PMC article.
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