ArticlePLoS genetics2014
Cis and trans effects of human genomic variants on gene expression.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers, 2 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.
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
80 citing papers in PubMed, 2 syntheses or guidelines pooled it, 139 citations in OpenAlex.
- Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus.Nature communications · 2025Pooled it
- Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders.Molecular psychiatry · 2017Pooled it
- Co-expression-based models improve eQTL predictions for transcriptome-wide association studies and highlight new schizophrenia-associated genes.Nature genetics · 2026Article
- Transcripts with high distal heritability mediate genetic effects on complex metabolic traits.Nature communications · 2025Article
- Sequence and parent-of-origin dependent mThe EMBO journal · 2025Article
- Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues.Genetics · 2025Article
- Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA.Molecular biology reports · 2024Article
- Air pollution exposure is associated with gene expression in children.Environmental epigenetics · 2024Article
- Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen.BMC biology · 2023Article
- Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2023Article
- Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits.Nature communications · 2023Article
- Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response.Nature communications · 2023Article
- Molecular mechanisms underpinning quantitative resistance toFrontiers in plant science · 2023Article
- Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.Nature communications · 2022Article
- Association of genetic ancestry with HER2, GRB7 AND estrogen receptor expression among Colombian women with breast cancer.Frontiers in oncology · 2022Article
- BACH1 Binding Links the Genetic Risk for Severe Periodontitis withJournal of dental research · 2022Article
- Sclerostin Downregulation Globally by Naturally Occurring Genetic Variants, or Locally in Atherosclerotic Plaques, Does Not Associate With Cardiovascular Events in Humans.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2021Article
- Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses.Bioinformatics (Oxford, England) · 2021Article
- Molecular and evolutionary processes generating variation in gene expression.Nature reviews. Genetics · 2021Review
- A Novel Evaluation System of Psoriasis Curative Effect Based on Bayesian Maximum Entropy Weight Self-Learning and Extended Set Pair Analysis.Evidence-based complementary and alternative medicine : eCAM · 2021Article
20 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
12 authors at 5 institutions in 5 countries.
Funding
Abstract
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
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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.