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    LOC125371454 H3K27ac hESC enhancer GRCh37_chr19:3969519-3970148 [ Homo sapiens (human) ]

    Gene ID: 125371454, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC125371454
    Gene description
    H3K27ac hESC enhancer GRCh37_chr19:3969519-3970148
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer, silencer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC125371454 in Genome Data Viewer
    Location:
    19p
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3969521..3970150)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3948777..3949406)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3969519..3970148)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3938329-3939088 Neighboring gene nicotinamide riboside kinase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3951361-3952130 Neighboring gene death associated protein kinase 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3970149-3970780 Neighboring gene microRNA 637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3981471-3982322 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3984027-3984878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13748 Neighboring gene eukaryotic translation elongation factor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3987713-3988214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3988215-3988714 Neighboring gene small nucleolar RNA, C/D box 37 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3998837-3999482 Neighboring gene H3K27ac hESC enhancers GRCh37_chr19:4006760-4007651 and GRCh37_chr19:4007652-4008542 Neighboring gene protein inhibitor of activated STAT 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
    2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    General gene information

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    Other Names

    • Sharpr-MPRA regulatory region 11828

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_080724.2 

      Range
      101..730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      3969521..3970150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      3948777..3949406
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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