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LOC110121308 VISTA enhancer hs2384 [ Homo sapiens (human) ]

Gene ID: 110121308, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121308
Gene description
VISTA enhancer hs2384
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 heart, ear and other tissues 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 (MPRA) 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. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (20578534..20580046)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (20611843..20613355)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20778294..20779806)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20687149-20687946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15392 Neighboring gene uncharacterized LOC102724948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20732136-20733133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20734131-20735128 Neighboring gene NDUFAF2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20741509-20742494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20742495-20743479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11211 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20760853-20761375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20763577-20764533 Neighboring gene HCLS1 binding protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20771337-20771837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20774924-20775424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780177-20780738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780739-20781299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784034-20784599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784600-20785164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20785731-20786294 Neighboring gene HS1BP3 intronic transcript 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20798625-20799569 Neighboring gene ribosomal protein S25 pseudogene 3

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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 15394
  • ATAC-STARR-seq lymphoblastoid active region 15395
  • CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:20778593-20779792

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_053923.1 

    Range
    101..1613
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    20578534..20580046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    20611843..20613355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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