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LOC110121051 VISTA enhancer hs1310 [ Homo sapiens (human) ]

Gene ID: 110121051, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121051
Gene description
VISTA enhancer hs1310
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 brain, neural tube and somite 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, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (170438007..170439776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (171809357..171811126)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170747095..170748864)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 120 member B Neighboring gene uncharacterized LOC124901474 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:170695897-170697096 Neighboring gene uncharacterized LOC124901475 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:170712439-170713033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170742555-170743054 Neighboring gene Sharpr-MPRA regulatory region 11687 Neighboring gene uncharacterized LOC107986676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170749082-170749660 Neighboring gene uncharacterized LOC124901477 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:170752981-170753211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170757529-170758036 Neighboring gene uncharacterized LOC124901235

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

  • CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:170747174-170748373

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_053671.1 

    Range
    101..1870
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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
    170438007..170439776
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187553.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    174568..176337
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    171809357..171811126
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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