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LOC110120669 VISTA enhancer hs399 [ Homo sapiens (human) ]

Gene ID: 110120669, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110120669
Gene description
VISTA enhancer hs399
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 includes a conserved genomic element that can function as an enhancer. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic forebrain of transgenic mice. An overlapping 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]
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (60214360..60215539)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (60220049..60221228)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (60441495..60442515)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:59892285-59892785 Neighboring gene RNA, U6 small nuclear 508, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 94 Neighboring gene Sharpr-MPRA regulatory region 2379 Neighboring gene VISTA enhancer hs779 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:60433923-60434131 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:60442675-60443175 Neighboring gene VISTA enhancer hs1535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:60524583-60525113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15797 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:60549375-60549626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15802 Neighboring gene MIR4432 host gene Neighboring gene RNA, U1 small nuclear 32, pseudogene Neighboring gene microRNA 4432

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. 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

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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-H3K4me1 hESC enhancer GRCh37_chr2:60442174-60442674

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_053295.2 

    Range
    101..1280
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    60214360..60215539
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    60220049..60221228
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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