ArticlePLoS genetics2022
Transcription factor regulation of eQTL activity across individuals and tissues.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 47 citations in OpenAlex.
- Robust cis-by-trans epistasis in the human plasma proteome highlights an ABO-centered interaction network.American journal of human genetics · 2026Article
- Genome-wide pQTL mapping in human skin identifies specific genetic regulators and mechanistic links to skin disorders.Nature communications · 2026Article
- Genomic, Transcriptomic, and Regulomic Analyses Do Not Support Profound Autism as a Distinct Biological Category.bioRxiv : the preprint server for biology · 2026Article
- A novel machine learning-based algorithm for eQTL identification reveals complex pleiotropic effects in the MHC region.Briefings in bioinformatics · 2026Article
- ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation.Briefings in bioinformatics · 2026Article
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- LIPA, a risk locus for coronary artery disease: decoding the variant-to-function relationship.European heart journal · 2025Article
- Effects of aging on gene expression networks in the Drosophila genetic reference panel.Cell reports · 2025Article
- Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis.Nature genetics · 2025Article
- Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals.Communications biology · 2025Article
- reg-eQTL: Integrating transcription factor effects to unveil regulatory variants.American journal of human genetics · 2025Article
- Implications of gene × environment interactions in post-traumatic stress disorder risk and treatment.The Journal of clinical investigation · 2025Review
- MAAT: a new nonparametric Bayesian framework for incorporating multiple functional annotations in transcriptome-wide association studies.Genome biology · 2025Article
- Genetic variation and pesticide exposure influence blood DNA methylation signatures in females with early-stage Parkinson's disease.NPJ Parkinson's disease · 2024Article
- Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues.Briefings in bioinformatics · 2024Article
- The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease.Human genetics · 2024Article
- Article
- PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs.Genome biology · 2024Article
- Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective.Human genetics · 2023Review
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
Abstract
Tens of thousands of genetic variants associated with gene expression (cis-eQTLs) have been discovered in the human population. These eQTLs are active in various tissues and contexts, but the molecular mechanisms of eQTL variability are poorly understood, hindering our understanding of genetic regulation across biological contexts. Since many eQTLs are believed to act by altering transcription factor (TF) binding affinity, we hypothesized that analyzing eQTL effect size as a function of TF level may allow discovery of mechanisms of eQTL variability. Using GTEx Consortium eQTL data from 49 tissues, we analyzed the interaction between eQTL effect size and TF level across tissues and across individuals within specific tissues and generated a list of 10,098 TF-eQTL interactions across 2,136 genes that are supported by at least two lines of evidence. These TF-eQTLs were enriched for various TF binding measures, supporting with orthogonal evidence that these eQTLs are regulated by the implicated TFs. We also found that our TF-eQTLs tend to overlap genes with gene-by-environment regulatory effects and to colocalize with GWAS loci, implying that our approach can help to elucidate mechanisms of context-specificity and trait associations. Finally, we highlight an interesting example of IKZF1 TF regulation of an APBB1IP gene eQTL that colocalizes with a GWAS signal for blood cell traits. Together, our findings provide candidate TF mechanisms for a large number of eQTLs and offer a generalizable approach for researchers to discover TF regulators of genetic variant effects in additional QTL datasets.
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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.