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LOC110121407 VISTA enhancer hs1602 [ Homo sapiens (human) ]

Gene ID: 110121407, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121407
Gene description
VISTA enhancer hs1602
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. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic branchial arch, dorsal root ganglion and facial mesenchyme of transgenic mice. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are marked by the H3K4me1 histone modification and one is additionally associated with the OCT4 and NANOG transcription factors. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC110121407 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60653083..60655766)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (54859539..54862222)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61120199..61122451)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:61110622-61111184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61113614-61114236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61114237-61114858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61114859-61115480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61115481-61116101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5813 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61119031-61119800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8479 Neighboring gene senescence associated long non-coding RNA 1 Neighboring gene microRNA 9718 Neighboring gene SIX homeobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8481 Neighboring gene SIX homeobox 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8483 Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61246210-61246710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61246711-61247211 Neighboring gene mitotic arrest deficient 2 like 1 pseudogene 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

  • H3K4me1 hESC enhancer GRCh37_chr14:61119801-61120569
  • OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:61121650-61122484

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_054021.2 

    Range
    101..2784
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    60653083..60655766
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    54859539..54862222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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