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    LOC122819167 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149855785-149856718 [ Homo sapiens (human) ]

    Gene ID: 122819167, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC122819167
    Gene description
    NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149855785-149856718
    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 associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. 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 non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC122819167 in Genome Data Viewer
    Location:
    2q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (148999271..149000204)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (149449647..149450580)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (149855785..149856718)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149633462-149634040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149634041-149634620 Neighboring gene KIF5C antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:149645774-149646369 Neighboring gene kinesin family member 5C Neighboring gene Sharpr-MPRA regulatory region 1843 Neighboring gene uncharacterized LOC101928553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149683568-149684192 Neighboring gene Sharpr-MPRA regulatory region 9639 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149830455-149831291 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:149856719-149857650 Neighboring gene NANOG hESC enhancer GRCh37_chr2:149883850-149884499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16625 Neighboring gene LY6/PLAUR domain containing 6B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:149937379-149937971 Neighboring gene thioredoxin pseudogene 5 Neighboring gene uncharacterized LOC105373677

    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 variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    General gene information

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    Other Names

    • Sharpr-MPRA regulatory region 317

    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_077027.2 

      Range
      101..1034
      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      148999271..149000204
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003571033.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      71283..72216
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      149449647..149450580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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