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    LOC120961784 Sharpr-MPRA regulatory region 8571 [ Homo sapiens (human) ]

    Gene ID: 120961784, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC120961784
    Gene description
    Sharpr-MPRA regulatory region 8571
    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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion 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. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC120961784 in Genome Data Viewer
    Location:
    2q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (128491759..128492669)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (128927756..128928666)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (129249949..129250243)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129142763-129143262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129146579-129147236 Neighboring gene uncharacterized LOC105373611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129165673-129166670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129166671-129167666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129195850-129196350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129196351-129196851 Neighboring gene Sharpr-MPRA regulatory region 12782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129205981-129206972 Neighboring gene RNA, 5S ribosomal pseudogene 103 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129232933-129233434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129243347-129243848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129243849-129244348 Neighboring gene MPRA-validated peak3859 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129258456-129258956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16513 Neighboring gene iron-sulfur cluster assembly 1 pseudogene 6 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:129294078-129294874 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:129294875-129295671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129310369-129311024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129338761-129339262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129349650-129350150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129350151-129350651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129358354-129358854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129358855-129359355 Neighboring gene uncharacterized LOC124907887

    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

    • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129249333-129250134

    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_074001.2 

      Range
      101..1011
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      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      128491759..128492669
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      128927756..128928666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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