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LOC110121134 VISTA enhancer hs1533 [ Homo sapiens (human) ]

Gene ID: 110121134, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121134
Gene description
VISTA enhancer hs1533
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 eye, forebrain and midbrain of transgenic mice. A subregion was also validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC110121134 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (19718991..19722679)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (19590621..19594309)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (19719222..19722910)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 pseudogene 3 Neighboring gene RNA, U6 small nuclear 801, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:19691659-19692162 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:19715338-19715863 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:19730720-19731919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:19734675-19735175 Neighboring gene lncRNA bladder and prostate cancer suppressor, hnRNPK interacting Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:19749583-19750782 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:19764761-19765373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:19765374-19765985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16976 Neighboring gene uncharacterized LOC105374963 Neighboring gene NANOG hESC enhancer GRCh37_chr6:19811543-19812108

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:19719350-19720549

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_053753.1 

    Range
    101..3789
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    19718991..19722679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    19590621..19594309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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