ArticleGenome biology2012
Dissecting the regulatory architecture of gene expression QTLs.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers, 2 of them syntheses that pooled it.
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Who cites it
136 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Mechanistic Characterization ofFrontiers in immunology · 2019Pooled it
- Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.PloS one · 2015Pooled it
- Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.Human molecular genetics · 2015Trial
- Single-cell multi-omic integration analysis prioritizes druggable genes and reveals cell-type-specific causal effects in glioblastomagenesis.Journal of translational medicine · 2026Article
- Early and late RNA eQTL are driven by different genetic mechanisms.Nature communications · 2026Article
- Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies.American journal of human genetics · 2026Article
- Genetic variants affecting RNA stability influence complex traits and disease risk.Nature genetics · 2025Article
- Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis.Nature genetics · 2025Article
- Multiome-wide Association Studies: Novel Approaches for Understanding Diseases.Genomics, proteomics & bioinformatics · 2024Review
- Non-coding variants impact cis-regulatory coordination in a cell type-specific manner.Genome biology · 2024Article
- Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles.Nature genetics · 2024Article
- Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster.G3 (Bethesda, Md.) · 2024Article
- Gene expression variation underlying tissue-specific responses to copper stress inbioRxiv : the preprint server for biology · 2023Article
- Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs.Nature communications · 2023Article
- Refined expression quantitative trait locus analysis on adenocarcinoma at the gastroesophageal junction reveals susceptibility and prognostic markers.Frontiers in genetics · 2023Article
- Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.Nature communications · 2022Article
- eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction.BMC genomics · 2022Article
- Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies.Nature communications · 2022Article
- Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms.Nature genetics · 2022Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
76 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundExpression quantitative trait loci (eQTLs) are likely to play an important role in the genetics of complex traits; however, their functional basis remains poorly understood. Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb.
resultsWe use a Bayesian hierarchical model to estimate the enrichment of eQTLs in a wide variety of regulatory annotations. We find that approximately 40% of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions. Analysis of core promoter regions shows that eQTLs also frequently disrupt some known core promoter motifs but, surprisingly, are not enriched in other well-known motifs such as the TATA box. We also show that information from regulatory annotations alone, when weighted by the hierarchical model, can provide a meaningful ranking of the SNPs that are most likely to drive gene expression variation.
conclusionsOur study demonstrates how regulatory annotation and the association signal derived from eQTL-mapping can be combined into a single framework. We used this approach to further our understanding of the biology that drives human gene expression variation, and of the putatively causal SNPs that underlie it.
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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.