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LOC110121446 VISTA enhancer hs1769 [ Homo sapiens (human) ]

Gene ID: 110121446, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121446
Gene description
VISTA enhancer hs1769
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 heart of transgenic mice. Three subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39674694..39678277)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40538259..40541842)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37831124..37834530)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37822021-37822758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37822759-37823496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12101 Neighboring gene titin-cap Neighboring gene phenylethanolamine N-methyltransferase Neighboring gene post-GPI attachment to proteins phospholipase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37835782-37836282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12103 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:37845149-37846109 Neighboring gene erb-b2 receptor tyrosine kinase 2 Neighboring gene Sharpr-MPRA regulatory region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857299-37857800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857801-37858300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37861047-37861919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37882556-37883528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8463 Neighboring gene microRNA 4728 Neighboring gene migration and invasion enhancer 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. 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
  3. 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

  • ATAC-STARR-seq lymphoblastoid silent region 8462
  • H3K4me1 hESC enhancer GRCh37_chr17:37830947-37831494
  • H3K4me1 hESC enhancer GRCh37_chr17:37831495-37832040
  • H3K4me1 hESC enhancer GRCh37_chr17:37832041-37832586

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_054059.2 

    Range
    101..3684
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    39674694..39678277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40538259..40541842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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