ArticleNucleic acids research2019
HACER: an atlas of human active enhancers to interpret regulatory variants.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed, 132 citations in OpenAlex.
- A systematic single-cell analysis of enhancer RNAs across human and mouse.Nucleic acids research · 2026Article
- EnhancerDB 2.0: a comprehensive cross-species enhancer atlas.Molecular biology and evolution · 2026Article
- Enhancer-mediated Etv4 activation stimulates osteogenic differentiation.Nature communications · 2026Article
- Hypoxia-inducible factors drive miRNA-mediated downregulation ofbioRxiv : the preprint server for biology · 2025Article
- scAED: a framework for mapping the enhancer state at single-cell resolution.Briefings in bioinformatics · 2025Article
- Intra-tumoral epigenetic heterogeneity and aberrant molecular clocks in hepatocellular carcinoma.medRxiv : the preprint server for health sciences · 2025Article
- CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.Nature communications · 2025Article
- Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy.Genome medicine · 2025Article
- Prioritizing effector genes at trait-associated loci using multimodal evidence.Nature genetics · 2025Article
- TFTG: A comprehensive database for human transcription factors and their targets.Computational and structural biotechnology journal · 2024Article
- VCAT: an integrated variant function annotation tools.Human genetics · 2024Article
- Genetic association with autoimmune diseases identifies molecular mechanisms of coronary artery disease.iScience · 2024Article
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- Single-Cell Chromatin Accessibility Analysis Reveals Subgroup-Specific TF-NTR Regulatory Circuits in Medulloblastoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes.Nature communications · 2024Article
- Examination of the shared genetic architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel lupus risk loci.Human genetics · 2024Article
- DNA methylation differences between the female and male X chromosomes in human brain.bioRxiv : the preprint server for biology · 2024Article
- eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse.Nucleic acids research · 2024Article
- Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA.International journal of molecular sciences · 2023Article
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
15 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Recent studies have shown that disease-susceptibility variants frequently lie in cell-type-specific enhancer elements. To identify, interpret, and prioritize such risk variants, we must identify the enhancers active in disease-relevant cell types, their upstream transcription factor (TF) binding, and their downstream target genes. To address this need, we built HACER (http://bioinfo.vanderbilt.edu/AE/HACER/), an atlas of Human ACtive Enhancers to interpret Regulatory variants. The HACER atlas catalogues and annotates in-vivo transcribed cell-type-specific enhancers, as well as placing enhancers within transcriptional regulatory networks by integrating ENCODE TF ChIP-Seq and predicted/validated chromatin interaction data. We demonstrate the utility of HACER in (i) offering a mechanistic hypothesis to explain the association of SNP rs614367 with ER-positive breast cancer risk, (ii) exploring tumor-specific enhancers in selective MYC dysregulation and (iii) prioritizing/annotating non-coding regulatory regions targeting CCND1. HACER provides a valuable resource for studies of GWAS, non-coding variants, and enhancer-mediated regulation.
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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.