ArticleNature genetics2019
High-resolution genetic mapping of putative causal interactions between regions of open chromatin.
Article in Nature genetics, 2019. 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.
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Who cites it
80 citing papers in PubMed, 2 syntheses or guidelines pooled it, 120 citations in OpenAlex.
- Pooled it
- Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis.Nature genetics · 2022Pooled it
- xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction.Molecular systems biology · 2026Article
- Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.Nature communications · 2026Article
- Integrating Multi-Omics Summary Data Identifies Candidate Molecular Mechanisms for Major Depression.Biological psychiatry · 2026Article
- Multiple instance fine-mapping: Predicting causal regulatory variants with a deep sequence model.PLoS genetics · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Chromatin Accessibility in Cancer: Biological Functions, Mechanisms, Therapeutic Potential, and Future Directions.MedComm · 2026Review
- Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts.Cell genomics · 2026Article
- Article
- Hybrids reveal accessible chromatinbioRxiv : the preprint server for biology · 2025Article
- GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids.HGG advances · 2025Article
- Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.Nature communications · 2025Article
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.Genome research · 2025Article
- The genetic architecture of cell type-specific cis regulation in maize.Science (New York, N.Y.) · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 2025Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.Nature communications · 2025Article
- Genome-wide association studies and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating polyunsaturated, monounsaturated, and saturated fatty acids.medRxiv : the preprint server for health sciences · 2024Article
- The STAT3/SETDB2 axis dictates NF-κB-mediated inflammation in macrophages during wound repair.JCI insight · 2024Article
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
3 authors at 1 institution in 1 country.
Funding
Abstract
Physical interaction of regulatory elements in three-dimensional space poses a challenge for studies of disease because non-coding risk variants may be great distances from the genes they regulate. Experimental methods to capture these interactions, such as chromosome conformation capture, usually cannot assign causal direction of effect between regulatory elements, an important component of fine-mapping studies. We developed a Bayesian hierarchical approach that uses two-stage least squares and applied it to an ATAC-seq (assay for transposase-accessible chromatin using sequencing) data set from 100 individuals, to identify over 15,000 high-confidence causal interactions. Most (60%) interactions occurred over <20 kb, where chromosome conformation capture-based methods perform poorly. For a fraction of loci, we identified a single variant that alters accessibility across multiple regions, and experimentally validated the BLK locus, which is associated with multiple autoimmune diseases, using CRISPR genome editing. Our study highlights how association genetics of chromatin state is a powerful approach for identifying interactions between regulatory elements.
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What OpenQuestion holds
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.