ArticleNature genetics2017
Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues.
Article in Nature genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 2 of them syntheses that pooled it.
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Who cites it
63 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.Nature genetics · 2018Pooled it
- Association of the independent polymorphisms in CDKN2A with susceptibility of acute lymphoblastic leukemia.Bioscience reports · 2018Pooled it
- Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies.Genome biology · 2026Article
- Genetic Determinants of Peanut-Specific IgG4 Levels in the Context of Sustained Oral Peanut Exposure in the LEAP Study.Immunology · 2026Article
- Linked origins but distinct roles for extreme length and sequence variation at a tandem repeat inbioRxiv : the preprint server for biology · 2026Article
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.Cell genomics · 2025Article
- XBP1 expression in pancreatic islet cells is associated with poor glycaemic control especially in young non-obese onset diabetes across ancestries.Communications medicine · 2025Article
- Trans-eQTL hotspots shape complex traits by modulating cellular states.Cell genomics · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.Nature communications · 2025Article
- Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cell type-specific expression of angiotensin receptors in the human lung with implications for health, aging, and chronic disease.bioRxiv : the preprint server for biology · 2024Article
- A statistical approach for identifying single nucleotide variants that affect transcription factor binding.iScience · 2024Article
- Article
- Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.Nucleic acids research · 2024Article
- Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits.Nature communications · 2023Article
- Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population.BMC genomics · 2023Article
- Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation.Communications biology · 2023Article
- Expression profiles of east-west highly differentiated genes in Uyghur genomes.National science review · 2023Article
- Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs. We estimated that 25-70% of causal variants were located in open-chromatin regions, depending on the tissue and experiment. Finally, we identified a set of high-confidence causal variants and showed that these were more enriched in GWAS associations than other eQTLs. Of those, we found 65 associations with GWAS traits and provide examples in which genes implicated by expression are functionally validated as being relevant for complex traits.
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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.