U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC110120812 VISTA enhancer hs965 [ Homo sapiens (human) ]

    Gene ID: 110120812, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC110120812
    Gene description
    VISTA enhancer hs965
    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 locus represents a conserved genomic element that can function as an enhancer. It can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic limb and other tissues of transgenic mice. A subregion was also shown to be an active enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. [provided by RefSeq, Nov 2022]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    chromosome: 3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (71050006..71051700)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (71086504..71088198)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (71099157..71100851)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:70838694-70838912 Neighboring gene high mobility group box 1 pseudogene 36 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:70882268-70882846 Neighboring gene RNA, U6 small nuclear 281, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:70902705-70903904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:70903859-70904359 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:70926235-70926734 Neighboring gene OCT4 hESC enhancer GRCh37_chr3:70976354-70976889 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:70998543-70998739 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:71012492-71013094 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:71025197-71026396 Neighboring gene VISTA enhancer hs864 Neighboring gene forkhead box P1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:71114251-71114751 Neighboring gene uncharacterized LOC124906247 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:71128185-71128767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20059 Neighboring gene VISTA enhancer hs1092 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:71178876-71179618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:71193639-71194138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:71205831-71206536 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:71214878-71215027 Neighboring gene NANOG hESC enhancer GRCh37_chr3:71259322-71259867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:71275618-71276118 Neighboring gene VISTA enhancer hs630 Neighboring gene VISTA enhancer hs187 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:71354949-71355604 Neighboring gene FOXP1 antisense RNA 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, 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

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    General gene information

    Go to the top of the page Help

    Other Names

    • NANOG-H3K4me1 hESC enhancer GRCh37_chr3:71100029-71100592

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_053437.1 

      Range
      101..1795
      Download
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      71050006..71051700
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      71086504..71088198
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases