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LOC110121361 VISTA enhancer hs1397 [ Homo sapiens (human) ]

Gene ID: 110121361, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121361
Gene description
VISTA enhancer hs1397
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 ear and nose of transgenic mice. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (58804415..58807634)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (59005527..59008746)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (56471647..56474866)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9487 Neighboring gene uncharacterized LOC105372146 Neighboring gene MALT1 antisense RNA 1 Neighboring gene MALT1 paracaspase Neighboring gene mitochondrial ribosomal protein L37 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13403 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56442191-56442692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56449282-56450044 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56450045-56450806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56456348-56457153 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56475059-56476049 Neighboring gene RNA, U6 small nuclear 219, pseudogene Neighboring gene U8 small nucleolar RNA Neighboring gene long intergenic non-protein coding RNA 1926 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56513039-56513851 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56513852-56514664 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56514665-56515477 Neighboring gene Sharpr-MPRA regulatory region 466 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:56529025-56529566 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56529567-56530106 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56537205-56538186 Neighboring gene zinc finger protein 532 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56556548-56557048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56557049-56557549 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:56559638-56560464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56582766-56583276 Neighboring gene RNA, U2 small nuclear 69, 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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 13404
  • ATAC-STARR-seq lymphoblastoid active region 13405

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_053975.1 

    Range
    101..3320
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    58804415..58807634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    59005527..59008746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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