ArticleGenome research2019
Most chromatin interactions are not in linkage disequilibrium.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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Who cites it
25 citing papers in PubMed, 42 citations in OpenAlex.
- Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci.Cell genomics · 2025Article
- An evolving understanding of multiple causal variants underlying genetic association signals.American journal of human genetics · 2025Review
- CTCF-anchored chromatin loop dynamics during human meiosis.BMC biology · 2025Article
- Roles for the 3D genome in the cell cycle, DNA replication, and double strand break repair.Frontiers in cell and developmental biology · 2025Review
- Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns.Molecular biology and evolution · 2024Article
- Long-Term Maintenance of Complex Chromosomal Inversion Polymorphism inEcology and evolution · 2024Article
- Machine learning reveals the diversity of human 3D chromatin contact patterns.bioRxiv : the preprint server for biology · 2023Article
- cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions.PLoS genetics · 2023Article
- Article
- The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong!Biology open · 2022Review
- Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study.Human genomics · 2022Article
- Integrating Multimorbidity into a Whole-Body Understanding of Disease Using Spatial Genomics.Results and problems in cell differentiation · 2022Article
- Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits.International journal of molecular sciences · 2021Review
- Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.American journal of human genetics · 2021Article
- From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries.Frontiers in genetics · 2021Review
- Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease.Current opinion in genetics & development · 2020Review
- Rare variant association testing in the non-coding genome.Human genetics · 2020Review
- Genomic Chaos Begets Psychiatric Disorder.Complex psychiatry · 2020Review
- Generalizability of "GWAS Hits" in Clinical Populations: Lessons from Childhood Cancer Survivors.American journal of human genetics · 2020Article
- The three-dimensional landscape of the genome in human brain tissue unveils regulatory mechanisms leading to schizophrenia risk.Schizophrenia research · 2020Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Chromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along mammalian chromosomes. Their values are generally high for sites that are nearby in the linear genome but abruptly drop across block boundaries. One function of chromatin boundaries is to insulate regulatory domains from one another. Since recombination is depressed within genes and between distal regulatory elements and their promoters, we hypothesized that LD and chromatin contact frequency might be correlated genome-wide with the boundaries of LD blocks and chromatin domains frequently coinciding. To comprehensively address this question, we compared chromatin contacts in 22 cell types to LD across billions of pairs of loci in the human genome. These computationally intensive analyses revealed that there is no concordance between LD and chromatin interactions, even at genomic distances below 25 kilobases (kb) where both tend to be high. At genomic distances where LD is approximately zero, chromatin interactions are frequent. While LD is somewhat elevated between distal regulatory elements and their promoters, LD block boundaries are depleted-not enriched-at chromatin boundaries. Finally, gene expression and ontology data suggest that chromatin contacts identify regulatory variants more reliably than do LD and genomic proximity. We conclude that the genomic architectures of genetic and physical interactions are independent, with important implications for gene regulatory evolution, interpretation of genetic association studies, and precision medicine.
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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.