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LOC110121314 VISTA enhancer hs1020 [ Homo sapiens (human) ]

Gene ID: 110121314, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121314
Gene description
VISTA enhancer hs1020
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. A subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic hindbrain and neural tube of transgenic mice. An overlapping 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: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (77784243..77786551)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (78015780..78018088)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (75496338..75498507)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C8 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75370231-75371192 Neighboring gene uncharacterized LOC107985129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75465232-75465784 Neighboring gene NANOG hESC enhancer GRCh37_chr18:75474392-75475106 Neighboring gene MPRA-validated peak3188 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:75535169-75536368 Neighboring gene VISTA enhancer hs1186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75577351-75577852 Neighboring gene RNA, 5S ribosomal pseudogene 461 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:75609611-75610121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:75611971-75612487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:75617943-75618714 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:75629975-75630209 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50500 Neighboring gene NANOG hESC enhancer GRCh37_chr18:75682747-75683315 Neighboring gene long intergenic non-protein coding RNA 1029

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_chr18:75496199-75497398

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_053929.2 

    Range
    101..2409
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    77784243..77786551
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    78015780..78018088
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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