ArticleNature genetics2016
Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry.
Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 66 citations in OpenAlex.
- 3D genetic architecture of schizophrenia risk across three neuronal subtypes.Molecular psychiatry · 2026Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- An evolving understanding of multiple causal variants underlying genetic association signals.American journal of human genetics · 2025Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Predicting Functional Consequences of Recent Natural Selection in Britain.Molecular biology and evolution · 2024Article
- Predicting functional consequences of recent natural selection in Britain.bioRxiv : the preprint server for biology · 2023Article
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- Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease.Frontiers in immunology · 2023Review
- Intronic enhancers of the humanScience advances · 2022Article
- Nested epistasis enhancer networks for robust genome regulation.Science (New York, N.Y.) · 2022Article
- Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1.Frontiers in genetics · 2022Article
- Global discovery of lupus genetic risk variant allelic enhancer activity.Nature communications · 2021Article
- Diversity and Function of Glial Cell Types in Multiple Sclerosis.Trends in immunology · 2021Review
- Aberrant Non-Coding RNA Expression in Patients with Systemic Lupus Erythematosus: Consequences for Immune Dysfunctions and Tissue Damage.Biomolecules · 2020Review
- Three-dimensional genome: developmental technologies and applications in precision medicine.Journal of human genetics · 2020Article
- Article
- A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons.Genome medicine · 2020Article
- Most chromatin interactions are not in linkage disequilibrium.Genome research · 2019Article
- Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies.eLife · 2019Article
- The Post-GWAS Era: How to Validate the Contribution of Gene Variants in Lupus.Current rheumatology reports · 2019Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
SNPs associated with disease susceptibility often reside in enhancer clusters, or super-enhancers. Constituents of these enhancer clusters cooperate to regulate target genes and often extend beyond the linkage disequilibrium (LD) blocks containing risk SNPs identified in genome-wide association studies (GWAS). We identified 'outside variants', defined as SNPs in weak LD with GWAS risk SNPs that physically interact with risk SNPs as part of a target gene's regulatory circuitry. These outside variants further explain variation in target gene expression beyond that explained by GWAS-associated SNPs. Additionally, the clinical risk associated with GWAS SNPs is considerably modified by the genotype of outside variants. Collectively, these findings suggest a potential model in which outside variants and GWAS SNPs that physically interact in 3D chromatin collude to influence target transcript levels as well as clinical risk. This model offers an additional hypothesis for the source of missing heritability for complex traits.
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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.