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LOC110121220 VISTA enhancer hs1887 [ Homo sapiens (human) ]

Gene ID: 110121220, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121220
Gene description
VISTA enhancer hs1887
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 of transgenic mice. Five subregions marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (35488868..35492897)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35311945..35315974)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35457129..35460603)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17092 Neighboring gene FA complementation group E Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24405 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35435944-35436500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24408 Neighboring gene ribosomal protein L10a Neighboring gene microRNA 7111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35447729-35448229 Neighboring gene TEA domain transcription factor 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35453191-35453766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35454343-35454918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35456069-35456644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35463100-35463885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35464832-35465762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35465763-35466692 Neighboring gene uncharacterized LOC124901309 Neighboring gene TUB like protein 1 Neighboring gene MPRA-validated peak5766 silencer Neighboring gene uncharacterized LOC101929309

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_chr6:35456645-35457220
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35457221-35457796
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35457797-35458372
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35459525-35460100
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35460101-35460674

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_053835.2 

    Range
    101..4130
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    35488868..35492897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    35311945..35315974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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