ArticleNature genetics2015
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 149 papers, 1 of them a synthesis 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
149 citing papers in PubMed, 1 synthesis or guideline pooled it, 249 citations in OpenAlex.
- PATJ Low Frequency Variants Are Associated With Worse Ischemic Stroke Functional Outcome.Circulation research · 2019Pooled it
- The G→C rs590352 in the Protein-Coding Region of ATXN7L3B Gene Upregulates Its Expression In Vivo.Biochemical genetics · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- The genetic basis for DNA methylation variation across tissues and development.Nature communications · 2026Article
- Silencer variants are key drivers of gene up-regulation in Alzheimer's disease.Science advances · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- Evolving computational paradigms for noncoding variant pathogenicity prediction.Frontiers in molecular biosciences · 2026Review
- MAZ regulates fetal hemoglobin repression by activating MYB transcription.Scientific reports · 2025Article
- Iterative improvement of deep learning models using synthetic regulatory genomics.Genome research · 2025Article
- Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings.Nature cancer · 2025Article
- G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing.Nature genetics · 2025Article
- Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data.Briefings in bioinformatics · 2025Article
- The Single Nucleotide Substitution T → A rs2072580 Damages the CREB1 Binding Site in the BidirectionalGenes · 2025Article
- Coronary Artery Disease Risk Variant rs6903956 Links to Endothelial Dysfunction viabioRxiv : the preprint server for biology · 2025Article
- Whole genome sequencing analysis of body mass index identifies novel African ancestry-specific risk allele.Nature communications · 2025Article
- Identifying deleterious noncoding variation through gain and loss of CTCF binding activity.American journal of human genetics · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Viral cis-regulatory elements as sensors of cellular states and environmental cues.Trends in genetics : TIG · 2024Review
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
89 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The function of human regulatory regions depends exquisitely on their local genomic environment and on cellular context, complicating experimental analysis of common disease- and trait-associated variants that localize within regulatory DNA. We use allelically resolved genomic DNase I footprinting data encompassing 166 individuals and 114 cell types to identify >60,000 common variants that directly influence transcription factor occupancy and regulatory DNA accessibility in vivo. The unprecedented scale of these data enables systematic analysis of the impact of sequence variation on transcription factor occupancy in vivo. We leverage this analysis to develop accurate models of variation affecting the recognition sites for diverse transcription factors and apply these models to discriminate nearly 500,000 common regulatory variants likely to affect transcription factor occupancy across the human genome. The approach and results provide a new foundation for the analysis and interpretation of noncoding variation in complete human genomes and for systems-level investigation of disease-associated variants.
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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.