ReviewBriefings in bioinformatics2019
Regulatory variants: from detection to predicting impact.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 2 of them syntheses that pooled it.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
60 citing papers in PubMed, 2 syntheses or guidelines pooled it, 121 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
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Rare germline variants in canonical and candidate genes in apparently sporadic bilateral primary aldosteronism.Journal of the Endocrine Society · 2026Article
- From GWAS Signals to Molecular Mechanisms: Explainable AI for Causal Gene Prioritization and Biomolecular Target Interpretation.Biomolecules · 2026Review
- Genotype-Dependent Transcriptome Divergence Associated With Variation at vgll3 in Juvenile Gilthead Seabream (Sparus aurata).Molecular ecology · 2026Article
- eQTL in diseased colon tissue identifies potential target genes associated with IBD.Nature communications · 2026Article
- DisCP-Atlas: a comprehensive resource mapping cellular processes to complex diseases.Nucleic acids research · 2026Article
- Beyond the Exome: The Role of Noncoding and Regulatory Variants in Monogenic Diseases.Current issues in molecular biology · 2025Review
- Super-silencers are crucial for development and carcinogenesis in B cells.Nature communications · 2025Article
- Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension.Science (New York, N.Y.) · 2025Article
- DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations.GigaScience · 2025Article
- Genomic insights into mRNA COVID-19 vaccines efficacy: Linking genetic polymorphisms to waning immunity.Human vaccines & immunotherapeutics · 2024Article
- Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease.American journal of human genetics · 2024Article
- Integrative annotation scores of variants for impact on RNA binding protein activities.Bioinformatics (Oxford, England) · 2024Article
- Genetic Variants of Adrenoceptors.Handbook of experimental pharmacology · 2024Review
- LDLR and PCSK9 3´UTR variants and their putative effects on microRNA molecular interactions in familial hypercholesterolemia: a computational approach.Molecular biology reports · 2023Article
- Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants.Genomics, proteomics & bioinformatics · 2023Article
- A Comprehensive Investigation of Genomic Variants in Prostate Cancer Reveals 30 Putative Regulatory Variants.International journal of molecular sciences · 2023Article
- Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy.Handbook of experimental pharmacology · 2023Article
- Resources and tools for rare disease variant interpretation.Frontiers in molecular biosciences · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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What OpenQuestion holds
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.