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LOC110121171 VISTA enhancer hs1640 [ Homo sapiens (human) ]

Gene ID: 110121171, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121171
Gene description
VISTA enhancer hs1640
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 tail of transgenic mice. A subregion was also shown to be an active enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (142550490..142552711)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (143081740..143083961)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141930055..141932276)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:141699157-141699901 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141702584-141703548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141703549-141704511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141711019-141711518 Neighboring gene SPRY4 intronic transcript 1 Neighboring gene SPRY4 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:141721844-141723043 Neighboring gene sprouty RTK signaling antagonist 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141734625-141735426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141735427-141736228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16471 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:141740409-141740647 Neighboring gene Sharpr-MPRA regulatory region 738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141743173-141743894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141768171-141768672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141771555-141772234 Neighboring gene Sharpr-MPRA regulatory region 12170 Neighboring gene Sharpr-MPRA regulatory region 9292 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141854065-141854633 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:141854634-141855201 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141855756-141856266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141902675-141903176 Neighboring gene ribosomal protein S12 pseudogene 10 Neighboring gene FGF1 promoter D Neighboring gene small nucleolar RNA SNORA36 family Neighboring gene fibroblast growth factor 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. 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

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141930613-141931259

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_053789.1 

    Range
    101..2322
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    142550490..142552711
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    143081740..143083961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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