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LOC110120696 VISTA enhancer hs541 [ Homo sapiens (human) ]

Gene ID: 110120696, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110120696
Gene description
VISTA enhancer hs541
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. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic forebrain of transgenic mice. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the NANOG transcription factor, one is additionally associated with OCT4, and the other is marked by the H3K27ac histone modification. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC110120696 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44802780..44805600)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44808100..44810914)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45030569..45032739)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene calmodulin-lysine N-methyltransferase Neighboring gene uncharacterized LOC124905999 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:44689999-44690600 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:44690601-44691200 Neighboring gene uncharacterized LOC124907758 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:44771195-44771973 Neighboring gene Sharpr-MPRA regulatory region 6726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:44816361-44817060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11432 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:44907608-44908156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45014758-45015258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45015259-45015759 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45017091-45017794 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:45028054-45028854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45028855-45029655 Neighboring gene uncharacterized LOC105374573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15686 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45089860-45089961 Neighboring gene VISTA enhancer hs149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:45153974-45154534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164020-45164553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164554-45165086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11434 Neighboring gene long intergenic non-protein coding RNA 1833

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-H3K27ac hESC enhancer GRCh37_chr2:45031773-45032292
  • OCT4-NANOG hESC enhancer GRCh37_chr2:45029919-45030751

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_053322.2 

    Range
    101..2921
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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
    44802780..44805600
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    44808100..44810914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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