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chromhmm model  (Epigenomics ag)

 
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    Structured Review

    Epigenomics ag chromhmm model
    rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). <t>Roadmap</t> Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).
    Chromhmm Model, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/spatial+transcriptomic+model-based+clustering+method/pmc09391468-92-0-1?v=Epigenomics+ag
    Average 90 stars, based on 1 article reviews
    chromhmm model - by Bioz Stars, 2026-07
    90/100 stars

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    1) Product Images from "Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants"

    Article Title: Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants

    Journal: Scientific Reports

    doi: 10.1038/s41598-022-18296-4

    rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). Roadmap Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).
    Figure Legend Snippet: rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). Roadmap Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).

    Techniques Used: Binding Assay, Expressing



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