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    LOC127821110 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:58345528-58346220 [ Homo sapiens (human) ]

    Gene ID: 127821110, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC127821110
    Gene description
    NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:58345528-58346220
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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    Genomic context

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    See LOC127821110 in Genome Data Viewer
    Location:
    chromosome: 11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (58577917..58578747)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (58527422..58528252)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (58345390..58346220)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 5 subfamily B member 12 Neighboring gene uncharacterized LOC105369313 Neighboring gene olfactory receptor family 5 subfamily B member 21 Neighboring gene Sharpr-MPRA regulatory region 15251 Neighboring gene leupaxin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:58346914-58347605 Neighboring gene ZFP91-CNTF readthrough (NMD candidate) Neighboring gene ZFP91 zinc finger protein, atypical E3 ubiquitin ligase Neighboring gene ciliary neurotrophic factor

    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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

    • ATAC-STARR-seq lymphoblastoid active region 4738
    • ATAC-STARR-seq lymphoblastoid active region 4739

    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_122567.2 

      Range
      101..931
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      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      58577917..58578747
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      58527422..58528252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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