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LOC110121417 VISTA enhancer hs1636 [ Homo sapiens (human) ]

Gene ID: 110121417, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121417
Gene description
VISTA enhancer hs1636
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 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 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, Aug 2022]
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Genomic context

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Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (27920941..27924250)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (28115821..28119130)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (25500905..25504214)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:25090256-25090883 Neighboring gene NANOG hESC enhancer GRCh37_chr18:25136675-25137176 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:25141435-25141968 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:25149311-25150510 Neighboring gene Sharpr-MPRA regulatory region 9527 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:25241352-25242317 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:25292902-25293680 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:25322897-25324096 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:25329836-25330411 Neighboring gene NANOG hESC enhancer GRCh37_chr18:25358819-25359514 Neighboring gene uncharacterized LOC105372042 Neighboring gene cadherin 2 Neighboring gene VISTA enhancer hs1634 Neighboring gene Sharpr-MPRA regulatory region 6705 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:25734930-25735628 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:25820685-25821299 Neighboring gene OCT4 hESC enhancer GRCh37_chr18:25828556-25829185 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:25867001-25867592 Neighboring gene NANOG hESC enhancer GRCh37_chr18:25930929-25931430 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:26001477-26002172 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:26002173-26002868 Neighboring gene NANOG hESC enhancer GRCh37_chr18:26102096-26102597 Neighboring gene ariadne RBR E3 ubiquitin protein ligase 2 pseudogene 1

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_chr18:25501241-25502440

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_054031.1 

    Range
    101..3410
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    27920941..27924250
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    28115821..28119130
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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