Chromatin marks identify critical cell types for fine mapping complex trait variants
Open accessAbstract
If trait-associated variants alter regulatory regions, then they should fall within chromatin marks in relevant cell types. However, it is unclear which of the many marks are most useful in defining cell types associated with disease and fine mapping variants. We hypothesized that informative marks are phenotypically cell type specific; that is, SNPs associated with the same trait likely overlap marks in the same cell type. We examined 15 chromatin marks and found that those highlighting active gene regulation were phenotypically cell type specific. Trimethylation of histone H3 at lysine 4 (H3K4me3) was the most phenotypically cell type specific (P < 1 × 10(-6)), driven by colocalization of variants and marks rather than gene proximity (P < 0.001). H3K4me3 peaks overlapped with 37 SNPs for plasma low-density lipoprotein concentration in the liver (P < 7 × 10(-5)), 31 SNPs for rheumatoid arthritis within CD4(+) regulatory T cells (P = 1 × 10(-4)), 67 SNPs for type 2 diabetes in pancreatic islet cells (P = 0.003) and the liver (P = 0.003), and 14 SNPs for neuropsychiatric disease in neuronal tissues (P = 0.007). We show how cell type-specific H3K4me3 peaks can inform the fine mapping of associated SNPs to identify causal variation.
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Schizophrenia GWAS SNPs occur more often than chance in cis-regulatory functional genomic elements such as enhancers or eQTL SNPs.
“Indeed, GWAS SNPs associated with SCZ risk occur more often than expected by chance in cis-regulatory functional genomic elements, such as enhancers or eQTL SNPs3,21–24.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [23]
GWAS SNPs associated with schizophrenia risk occur more often than expected by chance in cis-regulatory functional genomic elements, such as enhancers or eQTL SNPs.
“Indeed, GWAS SNPs associated with SCZ risk occur more often than expected by chance in cis-regulatory functional genomic elements, such as enhancers or eQTL SNPs3,21–24.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [23]
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- Authors
- Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B. E., Liu, X. S., & Raychaudhuri, S.
- Affiliations
- Brigham and Women's Hospital (US)
- Broad Institute (US)
- Harvard University (US)
- Corresponding author
- Raychaudhuri, Soumya
- ORCID
- Venue
- Nature Genetics
- Published
- 2012-12-23
- Volume
- 45
- Issue
- 2
- Pages
- 124-130
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3826950
- OpenAlex
- W2133009026
- Cited by
- 580
- References
- 56
- Citations by year
- 2026: 15 · 2025: 24 · 2024: 40 · 2023: 30 · 2022: 38 · 2021: 55 · 2020: 40 · 2019: 46 · 2018: 49 · 2017: 62 · 2016: 56 · 2015: 52 · 2014: 51 · 2013: 22
- FWCI
- 24.09
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG004069, U01HG007033, U01 HG0070033)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (UH2AR067677, K08AR055688)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- chromatin marks, H3K4me3, cell type specificity, fine mapping, complex traits, regulatory variants, causal variants, low-density lipoprotein, rheumatoid arthritis, CD4+ regulatory T cells, type 2 diabetes, pancreatic islets, neuropsychiatric disorders, neurons
- MeSH terms
- Arthritis, Rheumatoid, Chromatin, Diabetes Mellitus, Type 2, Genetic Markers, Histones, Humans, Nervous System Diseases, Phenotype, Software, Polymorphism, Single Nucleotide, Databases, Genetic
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