ArticlePLoS genetics2011
Rare and common regulatory variation in population-scale sequenced human genomes.
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 70 papers, 1 of them a synthesis that pooled it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Molecular genetic evidence for overlap between general cognitive ability and risk for schizophrenia: a report from the Cognitive Genomics consorTium (COGENT).Molecular psychiatry · 2014Pooled it
- Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation.Science advances · 2026Article
- Harnessing iPSC technology for population-level human disease/traits modeling -where are we?Frontiers in cell and developmental biology · 2026Review
- Transcriptome-wide outlier approach identifies individuals with minor spliceopathies.American journal of human genetics · 2025Article
- The functional impact of rare variation across the regulatory cascade.Cell genomics · 2023Article
- Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression.Molecular biology and evolution · 2022Article
- Nonsense-mediated RNA decay: an emerging modulator of malignancy.Nature reviews. Cancer · 2022Review
- Integration of rare expression outlier-associated variants improves polygenic risk prediction.American journal of human genetics · 2022Article
- Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma.Genome biology · 2022Article
- Toward transcriptomics as a primary tool for rare disease investigation.Cold Spring Harbor molecular case studies · 2022Article
- Article
- Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles.PLoS genetics · 2020Article
- Unsupervised Clustering of Missense Variants in HNF1A Using Multidimensional Functional Data Aids Clinical Interpretation.American journal of human genetics · 2020Article
- Transcriptomic signatures across human tissues identify functional rare genetic variation.Science (New York, N.Y.) · 2020Article
- Predicting target genes of non-coding regulatory variants with IRT.Bioinformatics (Oxford, England) · 2020Article
- ORE identifies extreme expression effects enriched for rare variants.Bioinformatics (Oxford, England) · 2019Article
- Ultrarare variants drive substantial cis heritability of human gene expression.Nature genetics · 2019Article
- A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.Molecular cell · 2019Article
- Local ancestry transitions modify snp-trait associations.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Human gene essentiality.Nature reviews. Genetics · 2018Review
10 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.
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4 authors.
Funding
Abstract
Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs) when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs) discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.
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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.