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LOC110121486 VISTA enhancer hs2143 [ Homo sapiens (human) ]

Gene ID: 110121486, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121486
Gene description
VISTA enhancer hs2143
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 and somite of transgenic mice. A subregion marked by the H3K27ac and H3K4me1 histone modifications was also shown to be an active enhancer by ChIP-STARR-seq in naive human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86684072..86689569)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87568226..87573724)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88443829..88449326)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3694 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88409215-88409901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88409902-88410587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88411272-88412121 Neighboring gene ribosomal protein L7a pseudogene 8 Neighboring gene uncharacterized LOC105378409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3695 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:88433149-88433337 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88441665-88442166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88442167-88442666 Neighboring gene opsin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88459642-88460142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88460143-88460643 Neighboring gene LIM domain binding 3 Neighboring gene hESC enhancers GRCh37_chr10:88470545-88471164 and GRCh37_chr10:88471165-88471784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2573 Neighboring gene bone morphogenetic protein receptor type 1A Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:88552774-88553500 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:88597221-88597813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88615649-88616230 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624164-88624816 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624817-88625468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88627361-88627948 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88631460-88632021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3697 Neighboring gene RNA polymerase II associated protein 2 pseudogene 1 Neighboring gene RNA, U1 small nuclear 19, pseudogene

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88446913-88447450

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_054099.1 

    Range
    101..5598
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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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    86684072..86689569
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87568226..87573724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
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