ArticlePLoS genetics2011
Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 148 papers, 13 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
148 citing papers in PubMed, 13 syntheses or guidelines pooled it, 208 citations in OpenAlex.
- Genome-wide epistasis study highlights genetic interactions influencing severity of COVID-19.European journal of epidemiology · 2023Pooled it
- Genome-wide association study identifies nine novel loci for 2D:4D finger ratio, a putative retrospective biomarker of testosterone exposure in utero.Human molecular genetics · 2018Pooled it
- Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms.Nature genetics · 2017Pooled it
- Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs.Scientific reports · 2016Pooled it
- Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma.Nature genetics · 2015Pooled it
- Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins.Nature communications · 2014Pooled it
- Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci.American journal of human genetics · 2014Pooled it
- Secretory phospholipase A(2)-IIA and cardiovascular disease: a mendelian randomization study.Journal of the American College of Cardiology · 2013Pooled it
- Pooled it
- Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.American journal of human genetics · 2013Pooled it
- Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake.The American journal of clinical nutrition · 2013Pooled it
- Loci influencing blood pressure identified using a cardiovascular gene-centric array.Human molecular genetics · 2013Pooled it
- Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.American journal of human genetics · 2012Pooled it
- Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese.Scientific reports · 2017Trial
- 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
- Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians.PLoS genetics · 2014Trial
- The Lipid Droplet-Associated Hydrolase Is Associated With Obesity and Adipose Tissue Inflammation in Children.Obesity (Silver Spring, Md.) · 2026Article
- Multiomics Investigation of Exhausted T Cells in Glioblastoma Tumor Microenvironment:International journal of molecular sciences · 2025Article
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.Genome research · 2025Article
- Assessing the causal relationship between plasma proteins and osteoporosis: novel insights into pathological mechanisms and therapeutic implications.Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2024Article
88 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
20 authors at 8 institutions in 6 countries.
Funding
Abstract
The discovery of expression quantitative trait loci ("eQTLs") can help to unravel genetic contributions to complex traits. We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent (n = 206) and Illumina (n = 60) expression arrays and Illumina SNP genotyping (550K), and we also incorporated data from a published study (n = 266). We found that ∼30% of SNP-expression correlations in one study failed to replicate in either of the others, even at thresholds yielding high reproducibility in simulations, and we quantified numerous factors affecting reproducibility. Our data suggest that drug exposure, clinical descriptors, and unknown factors associated with tissue ascertainment and analysis have substantial effects on gene expression and that controlling for hidden confounding variables significantly increases replication rate. Furthermore, we found that reproducible eQTL SNPs were heavily enriched near gene starts and ends, and subsequently resequenced the promoters and 3'UTRs for 14 genes and tested the identified haplotypes using luciferase assays. For three genes, significant haplotype-specific in vitro functional differences correlated directly with expression levels, suggesting that many bona fide eQTLs result from functional variants that can be mechanistically isolated in a high-throughput fashion. Finally, given our study design, we were able to discover and validate hundreds of liver eQTLs. Many of these relate directly to complex traits for which liver-specific analyses are likely to be relevant, and we identified dozens of potential connections with disease-associated loci. These included previously characterized eQTL contributors to diabetes, drug response, and lipid levels, and they suggest novel candidates such as a role for NOD2 expression in leprosy risk and C2orf43 in prostate cancer. In general, the work presented here will be valuable for future efforts to precisely identify and functionally characterize genetic contributions to a variety of complex traits.
Indexed as
Identifiers
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.