ArticlePLoS genetics2016
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- Functional characterization of eQTLs and asthma risk loci with scATAC-seq across immune cell types and contexts.American journal of human genetics · 2025Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Characterization of caffeine response regulatory variants in vascular endothelial cells.eLife · 2024Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules.PLoS computational biology · 2022Article
- A signature of Neanderthal introgression on molecular mechanisms of environmental responses.PLoS genetics · 2021Article
- Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators.Bioinformatics (Oxford, England) · 2021Article
- Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.International journal of molecular sciences · 2021Review
- Article
- Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.Cell reports · 2020Article
- Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases.American journal of human genetics · 2020Article
- A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.PLoS computational biology · 2020Article
- Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability.Human molecular genetics · 2020Article
- Allele-Specific QTL Fine Mapping with PLASMA.American journal of human genetics · 2020Article
- Interpreting Coronary Artery Disease Risk Through Gene-Environment Interactions in Gene Regulation.Genetics · 2019Article
- Article
- Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.BMC biology · 2019Article
- Genetic Insights Into Smooth Muscle Cell Contributions to Coronary Artery Disease.Arteriosclerosis, thrombosis, and vascular biology · 2019Review
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6 authors.
Funding
Abstract
Large experimental efforts are characterizing the regulatory genome, yet we are still missing a systematic definition of functional and silent genetic variants in non-coding regions. Here, we integrated DNaseI footprinting data with sequence-based transcription factor (TF) motif models to predict the impact of a genetic variant on TF binding across 153 tissues and 1,372 TF motifs. Each annotation we derived is specific for a cell-type condition or assay and is locally motif-driven. We found 5.8 million genetic variants in footprints, 66% of which are predicted by our model to affect TF binding. Comprehensive examination using allele-specific hypersensitivity (ASH) reveals that only the latter group consistently shows evidence for ASH (3,217 SNPs at 20% FDR), suggesting that most (97%) genetic variants in footprinted regulatory regions are indeed silent. Combining this information with GWAS data reveals that our annotation helps in computationally fine-mapping 86 SNPs in GWAS hit regions with at least a 2-fold increase in the posterior odds of picking the causal SNP. The rich meta information provided by the tissue-specificity and the identity of the putative TF binding site being affected also helps in identifying the underlying mechanism supporting the association. As an example, the enrichment for LDL level-associated SNPs is 9.1-fold higher among SNPs predicted to affect HNF4 binding sites than in a background model already including tissue-specific annotation.
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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.