ArticleGenome biology2017
Systematic identification of regulatory variants associated with cancer risk.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 2 of them syntheses that pooled it.
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Who cites it
64 citing papers in PubMed, 2 syntheses or guidelines pooled it, 125 citations in OpenAlex.
- Linking Iris Cis-Regulatory Variants to Primary Angle-Closure Glaucoma Via Clinical Imaging and Multiomics.Investigative ophthalmology & visual science · 2024Pooled it
- The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.BMC medical genomics · 2022Pooled it
- Systematic analysis of functional genetic and epigenetic variants in colorectal cancer.Science advances · 2026Article
- Association ofInternational journal of medical sciences · 2026Article
- Potential influence of omentin-1 genetic variants on the clinicopathological features of patients with hepatocellular carcinoma.Journal of Cancer · 2026Article
- IP-SNPs-seq links noncoding risk alleles to lineage transcription factor programs in prostate cancer.Cellular and molecular life sciences : CMLS · 2025Article
- Quantifying the impact of genetic mutations on enhancer dynamics.bioRxiv : the preprint server for biology · 2025Article
- Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus.Nature communications · 2025Article
- Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone production.Nature communications · 2025Article
- Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.Cell death discovery · 2025Review
- Functional analysis of cancer-associated germline risk variants.Nature genetics · 2025Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.Genome research · 2024Article
- Review
- An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression.Journal of translational medicine · 2024Article
- Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.Genetics, selection, evolution : GSE · 2024Article
- Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences.BMC bioinformatics · 2024Article
- Analysis ofJournal of Cancer · 2024Article
- Towards functional maps of non-coding variants in cancer.Frontiers in genome editing · 2024Review
- Identification and characterization of colorectal-cancer-associated SNPs on the SMAD7 locus.Journal of cancer research and clinical oncology · 2023Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMost cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically identify the SNPs that affect gene expression by modulating activities of distal regulatory elements, we adapt the self-transcribing active regulatory region sequencing (STARR-seq) strategy, a high-throughput technique to functionally quantify enhancer activities.
resultsFrom 10,673 SNPs linked with 996 cancer risk-associated SNPs identified in previous GWAS studies, we identify 575 SNPs in the fragments that positively regulate gene expression, and 758 SNPs in the fragments with negative regulatory activities. Among them, 70 variants are regulatory variants for which the two alleles confer different regulatory activities. We analyze in depth two regulatory variants-breast cancer risk SNP rs11055880 and leukemia risk-associated SNP rs12142375-and demonstrate their endogenous regulatory activities on expression of ATF7IP and PDE4B genes, respectively, using a CRISPR-Cas9 approach.
conclusionsBy identifying regulatory variants associated with cancer susceptibility and studying their molecular functions, we hope to help the interpretation of GWAS results and provide improved information for cancer risk assessment.
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