ArticleNucleic acids research2013
GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 3 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
63 citing papers in PubMed, 3 syntheses or guidelines pooled it, 112 citations in OpenAlex.
- Integrative functional analysis of super enhancer SNPs for coronary artery disease.Journal of human genetics · 2018Pooled it
- Pooled it
- Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.Circulation research · 2017Pooled it
- Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs.BMC bioinformatics · 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
- Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.Nucleic acids research · 2022Article
- VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases.Nucleic acids research · 2022Article
- Review
- DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.Nucleic acids research · 2021Article
- Article
- Variant to Gene Mapping to Discover New Targets for Immune Tolerance.Frontiers in immunology · 2021Article
- Rare variant association testing in the non-coding genome.Human genetics · 2020Review
- Turning genome-wide association study findings into opportunities for drug repositioning.Computational and structural biotechnology journal · 2020Review
- CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- Predicting functional variants in enhancer and promoter elements using RegulomeDB.Human mutation · 2019Article
- CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC bioinformatics · 2019Article
- OncoBase: a platform for decoding regulatory somatic mutations in human cancers.Nucleic acids research · 2019Article
- Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits.American journal of human genetics · 2019Article
- GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits.Nucleic acids research · 2018Article
3 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 at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interpreting the genetic variants located in the regulatory regions, such as enhancers and promoters, is an indispensable step to understand molecular mechanism of complex traits. Recent studies show that genetic variants detected by genome-wide association study (GWAS) are significantly enriched in the regulatory regions. Therefore, detecting, annotating and prioritizing of genetic variants affecting gene regulation are critical to our understanding of genotype-phenotype relationships. Here, we developed a web server GWAS3D to systematically analyze the genetic variants that could affect regulatory elements, by integrating annotations from cell type-specific chromatin states, epigenetic modifications, sequence motifs and cross-species conservation. The regulatory elements are inferred from the genome-wide chromosome interaction data, chromatin marks in 16 different cell types and 73 regulatory factors motifs from the Encyclopedia of DNA Element project. Furthermore, we used these function elements, as well as risk haplotype, binding affinity, conservation and P-values reported from the original GWAS to reprioritize the genetic variants. Using studies from low-density lipoprotein cholesterol, we demonstrated that our reprioritizing approach was effective and cell type specific. In conclusion, GWAS3D provides a comprehensive annotation and visualization tool to help users interpreting their results. The web server is freely available at http://jjwanglab.org/gwas3d.
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Registered trials
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.