ArticleHuman mutation2019
Predicting functional variants in enhancer and promoter elements using RegulomeDB.
Article in Human mutation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 3 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
65 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Trans-ethnic GWAS meta-analysis of idiopathic spermatogenic failure highlights the immune-mediated nature of Sertoli cell-only syndrome.Communications biology · 2025Pooled it
- Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia.Human molecular genetics · 2024Pooled it
- Cross-cancer pleiotropic analysis identifies three novel genetic risk loci for colorectal cancer.Human molecular genetics · 2023Pooled it
- Genetic Factors Contributing to Interindividual Variability of α-Tocopherol Levels in Subcutaneous Adipose Tissue among Healthy Adult Males.Nutrients · 2024Trial
- Genome-wide association study of aromatase inhibitor discontinuation due to musculoskeletal symptoms.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2022Trial
- AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants.Molecular and cellular endocrinology · 2021Trial
- Genetic Determinants of Interindividual Differences in Provitamin A Carotenoid Concentrations in Human Adipose Tissue.Molecular nutrition & food research · 2026Observational
- Genome-wide association of pica within a cohort of volunteer blood donors potentially implicates the gene encoding neuropeptide VF.Transfusion · 2026Article
- Can classical statistics and deep learning converge on explainable, causally driven target discovery?DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Review
- "SERBP1 (Hero45) is a Novel Link with Ischemic Heart Disease Risk: Associations with Coronary Arteries Occlusion, Blood Coagulation and Lipid Profile".Cell biochemistry and biophysics · 2025Article
- Comprehensive molecular impact mapping of common and rare variants at GWAS loci.bioRxiv : the preprint server for biology · 2025Article
- Bioinformatic analysis of the regulatory potential of tagging SNPs provides evidence of the involvement of genes encoding the heat-resistant obscure (Hero) proteins in the pathogenesis of cardiovascular diseases.Journal of integrative bioinformatics · 2025Article
- Cutting-edge AI tools revolutionizing scientific research in life sciences.Biotechnologia · 2025Review
- Low-frequency variants in genes involved in glutamic acid metabolism and γ-glutamyl cycle and risk of coronary artery disease in type 2 diabetes.Cardiovascular diabetology · 2024Article
- Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration.PLoS genetics · 2024Article
- MTF1 genetic variants are associated with lung cancer risk in the Chinese Han population.BMC cancer · 2024Article
- Genetic variants for head size share genes and pathways with cancer.Cell reports. Medicine · 2024Article
- Dissecting the genetic overlap between severe mental disorders and markers of cellular aging: Identification of pleiotropic genes and druggable targets.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024Article
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- Genetic and environmental factors driving congenital solitary functioning kidney.Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association · 2024Article
5 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
2 authors.
Funding
Abstract
Here we present a computational model, Score of Unified Regulatory Features (SURF), that predicts functional variants in enhancer and promoter elements. SURF is trained on data from massively parallel reporter assays and predicts the effect of variants on reporter expression levels. It achieved the top performance in the Fifth Critical Assessment of Genome Interpretation "Regulation Saturation" challenge. We also show that features queried through RegulomeDB, which are direct annotations from functional genomics data, help improve prediction accuracy beyond transfer learning features from DNA sequence-based deep learning models. Some of the most important features include DNase footprints, especially when coupled with complementary ChIP-seq data. Furthermore, we found our model achieved good performance in predicting allele-specific transcription factor binding events. As an extension to the current scoring system in RegulomeDB, we expect our computational model to prioritize variants in regulatory regions, thus help the understanding of functional variants in noncoding regions that lead to disease.
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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 Socratic graph.