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    LOC127403256 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79950324-79951092 [ Homo sapiens (human) ]

    Gene ID: 127403256, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC127403256
    Gene description
    NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79950324-79951092
    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 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 an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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 LOC127403256 in Genome Data Viewer
    Location:
    chromosome: 5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (80654478..80655273)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (81139378..81140182)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79950297..79951092)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1337 Neighboring gene Sharpr-MPRA regulatory region 2279 Neighboring gene Sharpr-MPRA regulatory regions 13584 and 3862 Neighboring gene dihydrofolate reductase Neighboring gene MT-RNR2 like 2 (pseudogene) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79963410-79963977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:79963978-79964546 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:79968379-79969578 Neighboring gene MPRA-validated peak5310 silencer Neighboring gene mutS homolog 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:80040756-80040944 Neighboring gene S-phase kinase-associated protein 1-like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:80043670-80044230 Neighboring gene MPRA-validated peak5311 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:80142431-80142931 Neighboring gene ribosomal protein S26 pseudogene 27

    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 silent region 16140

    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_105205.2 

      Range
      101..896
      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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      80654478..80655273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      81139378..81140182
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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