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LOC110121124 VISTA enhancer hs1484 [ Homo sapiens (human) ]

Gene ID: 110121124, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121124
Gene description
VISTA enhancer hs1484
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 forebrain and limb 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. The subregion was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. [provided by RefSeq, Mar 2023]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (61579788..61582487)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (61458652..61461351)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (62045460..62048159)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear factor I A Neighboring gene NANOG hESC enhancer GRCh37_chr1:61715889-61716390 Neighboring gene NFIA antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:61766471-61767069 Neighboring gene MPRA-validated peak260 silencer Neighboring gene Sharpr-MPRA regulatory region 1245 Neighboring gene MPRA-validated peak261 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:61902263-61902764 Neighboring gene VISTA enhancer hs1309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:61942976-61943490 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:61946773-61947972 Neighboring gene uncharacterized LOC105378766 Neighboring gene VISTA enhancer hs1450 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:62071813-62073012 Neighboring gene uncharacterized LOC107984964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1113 Neighboring gene sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene

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

  • BRD4-independent group 4 enhancer GRCh37_chr1:62046463-62047662

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_053743.1 

    Range
    101..2800
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    61579788..61582487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    61458652..61461351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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