ArticleNature communications2018
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 94 citations in OpenAlex.
- Selective control of HLA-DRB1 and HLA-DQA1 transcription through DR/DQ super enhancer microelements.Cell reports · 2026Article
- Genome-wide pQTL mapping in human skin identifies specific genetic regulators and mechanistic links to skin disorders.Nature communications · 2026Article
- Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.Nature communications · 2026Article
- Functional and computational interrogation of juvenile idiopathic arthritis risk loci in CD4+ T cells.HGG advances · 2026Article
- Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.bioRxiv : the preprint server for biology · 2026Article
- Predicting disease-specific histone modifications and functional effects of non-coding variants by leveraging DNA language models.Genome biology · 2026Article
- Functional and Computational Interrogation of the Juvenile Idiopathic Arthritis Risk Loci Identifies Candidate Causal SNPs and Target Genes in CD4+ T cells.medRxiv : the preprint server for health sciences · 2025Article
- Haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines.Genes & diseases · 2025Article
- Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals.Communications biology · 2025Article
- Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma.Science advances · 2025Article
- Defining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes.BMC medical genomics · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 2025Article
- Polygenic modelling and machine learning approaches in pharmacogenomics: Importance in downstream analysis of genome-wide association study data.British journal of clinical pharmacology · 2025Review
- Fundamentals for predicting transcriptional regulations from DNA sequence patterns.Journal of human genetics · 2024Review
- Systemic lupus erythematosus genetics: insights into pathogenesis and implications for therapy.Nature reviews. Rheumatology · 2024Review
- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits.Communications biology · 2024Article
- Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis.American journal of human genetics · 2024Article
- Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective.Human genetics · 2023Review
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
Genetic variants can confer risk to complex genetic diseases by modulating gene expression through changes to the epigenome. To assess the degree to which genetic variants influence epigenome activity, we integrate epigenetic and genotypic data from lupus patient lymphoblastoid cell lines to identify variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs). We demonstrate that enhancer hQTLs are enriched on autoimmune disease risk haplotypes and disproportionately influence gene expression variability compared with non-hQTL variants in strong linkage disequilibrium. We show that the epigenome regulates HLA class II genes differently in individuals who carry HLA-DR3 or HLA-DR15 haplotypes, resulting in differential 3D chromatin conformation and gene expression. Finally, we identify significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.
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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.