ArticleNature communications2017
The effect of genetic variation on promoter usage and enhancer activity.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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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
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Understanding super enhancers in genome architecture and their roles in livestock breeding.BMC genomics · 2026Review
- Genetic control of non-coding RNAs in the human brain and their implications for complex traits.American journal of human genetics · 2026Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma.Science advances · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Understanding the molecular diversity of synapses.Nature reviews. Neuroscience · 2025Review
- A compendium of genetic variations associated with promoter usage across 49 human tissues.Nature communications · 2024Article
- Fundamentals for predicting transcriptional regulations from DNA sequence patterns.Journal of human genetics · 2024Review
- Deep Resequencing of the 1q22 Locus in Non-Lobar Intracerebral Hemorrhage.Annals of neurology · 2024Article
- Pan-cancer analysis of promoter activity quantitative trait loci.NAR cancer · 2023Article
- eRNA co-expression network uncovers TF dependency and convergent cooperativity.Scientific reports · 2023Article
- Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective.Human genetics · 2023Review
- eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.PLoS genetics · 2023Article
- Characterization of bacteria swarming effect under plasmonic optical fiber illumination.Journal of biomedical optics · 2023Article
- Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning.Nature biomedical engineering · 2023Article
- Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci.bioRxiv : the preprint server for biology · 2023Article
- An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping.Nature communications · 2023Article
- Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of genetic variants affecting gene expression, namely expression quantitative trait loci (eQTLs), has contributed to the understanding of mechanisms underlying human traits and diseases. The majority of these variants map in non-coding regulatory regions of the genome and their identification remains challenging. Here, we use natural genetic variation and CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived from unrelated individuals, to map 5376 and 110 regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively. We characterize five categories of genes associated with puQTLs, distinguishing single from multi-promoter genes. Among multi-promoter genes, we find puQTL effects either specific to a single promoter or to multiple promoters with variable effect orientations. Regulatory variants associated with opposite effects on different mRNA isoforms suggest compensatory mechanisms occurring between alternative promoters. Our analyses identify differential promoter usage and modulation of enhancer activity as molecular mechanisms underlying eQTLs related to regulatory elements.
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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.