ArticleNucleic acids research2012
FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 6 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
76 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Genome-wide meta-analysis of SNP-by9-ACEI/ARB and SNP-by-thiazide diuretic and effect on serum potassium in cohorts of European and African ancestry.The pharmacogenomics journal · 2019Pooled it
- A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2016Pooled it
- Genome-wide association study identifies variants at 16p13 associated with survival in multiple myeloma patients.Nature communications · 2015Pooled it
- A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.Nature genetics · 2014Pooled it
- A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.Nature communications · 2014Pooled it
- A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11.Human molecular genetics · 2012Pooled it
- Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms.Bioinformatics (Oxford, England) · 2025Article
- Genome-wide association studies are enriched for interacting genes.BioData mining · 2025Article
- Genome wide association studies are enriched for interacting genes.Research square · 2024Article
- Implications of SNP-triggered miRNA dysregulation in Schizophrenia development.Frontiers in genetics · 2024Review
- Contribution of common and rare variants to Asian neovascular age-related macular degeneration subtypes.Nature communications · 2023Article
- Predicting functional consequences of SNPs on mRNA translation via machine learning.Nucleic acids research · 2023Article
- Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis.Clinical epigenetics · 2022Review
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- Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck.Biology · 2022Article
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- Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci.Human molecular genetics · 2020Article
- Functional annotation of melanoma risk loci identifies novel susceptibility genes.Carcinogenesis · 2020Article
- Replication of GWAS identifies RTEL1, CDKN2A/B, and PHLDB1 SNPs as risk factors in Portuguese gliomas patients.Molecular biology reports · 2020Article
- Systematic analyses of genetic variants in chromatin interaction regions identified four novel lung cancer susceptibility loci.Journal of Cancer · 2020Article
16 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
5 authors.
Funding
Abstract
unlabelledSingle nucleotide polymorphisms (SNPs) are increasingly used to tag genetic loci associated with phenotypes such as risk of complex diseases. Technically, this is done genome-wide without prior restriction or knowledge of biological feasibility in scans referred to as genome-wide association studies (GWAS). Depending on the linkage disequilibrium (LD) structure at a particular locus, such tagSNPs may be surrogates for many thousands of other SNPs, and it is difficult to distinguish those that may play a functional role in the phenotype from those simply genetically linked. Because a large proportion of tagSNPs have been identified within non-coding regions of the genome, distinguishing functional from non-functional SNPs has been an even greater challenge. A strategy was recently proposed that prioritizes surrogate SNPs based on non-coding chromatin and epigenomic mapping techniques that have become feasible with the advent of massively parallel sequencing. Here, we introduce an R/Bioconductor software package that enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which may have functional significance. AVAILABILITY: FunciSNP is available from Bioconductor (bioconductor.org).
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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.