ArticleNature genetics2009
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis.
Article in Nature genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers, 6 of them syntheses that pooled it.
What it found
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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.
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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.
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Who cites it
140 citing papers in PubMed, 6 syntheses or guidelines pooled it, 216 citations in OpenAlex.
- Genome-wide association study of age at menarche in African-American women.Human molecular genetics · 2013Pooled it
- Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.Nature genetics · 2012Pooled it
- Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.PLoS genetics · 2011Pooled it
- Association of BLK (rs13277113, rs2248932) polymorphism with systemic lupus erythematosus: a meta-analysis.Molecular biology reports · 2011Pooled it
- Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.Nature genetics · 2011Pooled it
- Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sjögren's syndrome.Genes and immunity · 2011Pooled it
- Allele-specific expression of mutated in colorectal cancer (MCC) gene and alternative susceptibility to colorectal cancer in schizophrenia.Scientific reports · 2016Trial
- Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells.bioRxiv : the preprint server for biology · 2026Article
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Allele specific expression in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.Genome research · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis.Scientific reports · 2024Article
- Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq.Cell discovery · 2024Article
- Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses.G3 (Bethesda, Md.) · 2023Article
- Allele-specific RNAGenome research · 2023Article
- Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing.BMC bioinformatics · 2022Article
- Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant.NPJ breast cancer · 2022Article
- Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression.Genome research · 2022Article
80 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
27 authors at 7 institutions in 2 countries.
Funding
Abstract
Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.
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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.