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Nat Genet DOI:10.1038/ng.2504

Chromatin marks identify critical cell types for fine mapping complex trait variants.

Publication TypeJournal Article
Year of Publication2013
AuthorsTrynka, G, Sandor, C, Han, B, Xu, H, Stranger, BE, X Liu, S, Raychaudhuri, S
JournalNat Genet
Date Published2013 Feb
KeywordsArthritis, Rheumatoid, Chromatin, Databases, Genetic, Diabetes Mellitus, Type 2, Genetic Markers, Histones, Humans, Nervous System Diseases, Phenotype, Polymorphism, Single Nucleotide, Software

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


Alternate JournalNat. Genet.
PubMed ID23263488
PubMed Central IDPMC3826950
Grant ListU01 HG007033 / HG / NHGRI NIH HHS / United States
K08AR055688 / AR / NIAMS NIH HHS / United States
U19 AI111224 / AI / NIAID NIH HHS / United States
UH2 AR067677 / AR / NIAMS NIH HHS / United States
R01 HG004069 / HG / NHGRI NIH HHS / United States
U01HG0070033 / HG / NHGRI NIH HHS / United States
K08 AR055688 / AR / NIAMS NIH HHS / United States