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    LOC127815045 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:86595393-86595900 [ Homo sapiens (human) ]

    Gene ID: 127815045, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC127815045
    Gene description
    NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:86595393-86595900
    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 primed 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 four 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 LOC127815045 in Genome Data Viewer
    Location:
    chromosome: 9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (83980469..83980985)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (96130750..96131266)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (86595384..86595900)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19981 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:86595901-86596409 Neighboring gene HNRNPK antisense RNA 1 Neighboring gene heterogeneous nuclear ribonucleoprotein K Neighboring gene microRNA 7-1 Neighboring gene RecQ mediated genome instability 1 Neighboring gene uncharacterized LOC101927575 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 33 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:86766071-86767007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:86787894-86788403 Neighboring gene Sharpr-MPRA regulatory region 11289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19983 Neighboring gene NANOG hESC enhancer GRCh37_chr9:86891619-86892170 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:86892303-86893502 Neighboring gene SLC28A3 regulatory antisense RNA 1 Neighboring gene solute carrier family 28 member 3

    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 28498
    • ATAC-STARR-seq lymphoblastoid active region 28499
    • ATAC-STARR-seq lymphoblastoid active region 28500
    • ATAC-STARR-seq lymphoblastoid active region 28501

    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_116563.2 

      Range
      101..617
      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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      83980469..83980985
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      96130750..96131266
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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