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LOC110121107 VISTA enhancer hs1449 [ Homo sapiens (human) ]

Gene ID: 110121107, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121107
Gene description
VISTA enhancer hs1449
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 transgenic mice embryos. An overlapping subregion marked by the H3K4me1 histone modification 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: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132265137..132266418)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132785017..132786298)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131600830..131602104)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:131520231-131520732 Neighboring gene Sharpr-MPRA regulatory region 7421 Neighboring gene P4HA2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543137-131543638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543639-131544138 Neighboring gene prolyl 4-hydroxylase subunit alpha 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16313 Neighboring gene microRNA 6830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131586685-131587186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131587187-131587686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131593943-131594732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131603965-131604508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131605973-131606861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131607809-131608310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131608311-131608810 Neighboring gene PDZ and LIM domain 4 Neighboring gene Sharpr-MPRA regulatory region 4855 Neighboring gene uncharacterized LOC124901063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131613864-131614676 Neighboring gene CAGE-defined mid-level expression enhancer upstream of SLC22A4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16316 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131656893-131657393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131657550-131658068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131658069-131658587

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_chr5:131601611-131602111

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_053726.2 

    Range
    101..1382
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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
    132265137..132266418
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132785017..132786298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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