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LOC110121068 VISTA enhancer hs1340 [ Homo sapiens (human) ]

Gene ID: 110121068, updated on 17-Sep-2024

Summary

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Gene symbol
LOC110121068
Gene description
VISTA enhancer hs1340
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 includes a conserved genomic element that can function as an enhancer. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic forebrain, hindbrain, midbrain and neural tube of transgenic mice. An overlapping subregion associated with the NANOG transcription factor was also shown to be an active enhancer by ChIP-STARR-seq in primed human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC110121068 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (20866869..20870298)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (20738706..20742129)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (20867100..20870529)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CDK5 regulatory subunit associated protein 1 like 1 Neighboring gene uncharacterized LOC105374968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20629440-20630213 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20630214-20630986 Neighboring gene NANOG hESC enhancer GRCh37_chr6:20686272-20686773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16981 Neighboring gene MPRA-validated peak5720 silencer Neighboring gene ribosomal protein L36a pseudogene 25 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:20798064-20798254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:20810592-20811186 Neighboring gene MPRA-validated peak5721 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:20834311-20834850 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:20877312-20878511 Neighboring gene Sharpr-MPRA regulatory region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24134 Neighboring gene MPRA-validated peak5723 silencer Neighboring gene RNA, U6 small nuclear 150, pseudogene Neighboring gene uncharacterized LOC105374966

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • NANOG hESC enhancer GRCh37_chr6:20867100-20867621

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_053688.2 

    Range
    101..3530
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    20866869..20870298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    20738706..20742129
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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