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    LOC127271955 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231004239-231004830 [ Homo sapiens (human) ]

    Gene ID: 127271955, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC127271955
    Gene description
    NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231004239-231004830
    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 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 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 LOC127271955 in Genome Data Viewer
    Location:
    chromosome: 1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230868450..230869084)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230248911..230249545)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (231004196..231004830)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 79 Neighboring gene uncharacterized LOC124904548 Neighboring gene chromosome 1 open reading frame 198 Neighboring gene VISTA enhancer hs1766 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:230990988-230992187 Neighboring gene uncharacterized LOC101927604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231012485-231012986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231012987-231013486 Neighboring gene uncharacterized LOC124904547 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:231024325-231024499 Neighboring gene uncharacterized LOC105373167 Neighboring gene RNA, 7SL, cytoplasmic 837, pseudogene

    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 1943

    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_093806.2 

      Range
      101..735
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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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      230868450..230869084
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      230248911..230249545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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