ArticleGenome biology2019
Common DNA sequence variation influences 3-dimensional conformation of the human genome.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Hi-C informed kernel association test for integrating 3D genome structure into variant-set analysis.Briefings in bioinformatics · 2026Article
- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Article
- DiffHiChIP: Identifying differential chromatin contacts from HiChIP data.Cell reports methods · 2025Article
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.bioRxiv : the preprint server for biology · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
- Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci.Genome biology · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Genetic coupling of enhancer activity and connectivity in gene expression control.Nature communications · 2025Article
- An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Genome research · 2024Article
- Identifying genetic variants associated with chromatin looping and genome function.Nature communications · 2024Article
- In silico generation and augmentation of regulatory variants from massively parallel reporter assay using conditional variational autoencoder.bioRxiv : the preprint server for biology · 2024Article
- Removing unwanted variation between samples in Hi-C experiments.Briefings in bioinformatics · 2024Article
- Transcriptomics and chromatin accessibility in multiple African population samples.bioRxiv : the preprint server for biology · 2023Article
- Article
- Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA.Briefings in bioinformatics · 2023Article
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13 authors.
Funding
Abstract
backgroundThe 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation.
resultsTo address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk.
conclusionOur results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized.
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