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LOC110121093 VISTA enhancer hs1417 [ Homo sapiens (human) ]

Gene ID: 110121093, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121093
Gene description
VISTA enhancer hs1417
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 includes a conserved genomic element that can function as an enhancer. A subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic forebrain of transgenic mice. An overlapping subregion marked by the H3K27ac histone modification was also shown to be an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (95511433..95513032)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (107681072..107682671)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (98274342..98275314)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98196113-98196685 Neighboring gene metallothionein 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98196686-98197257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98209829-98210813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98224469-98225332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98225569-98226070 Neighboring gene uncharacterized LOC100507346 Neighboring gene patched 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98255961-98256702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:98256703-98257442 Neighboring gene VISTA enhancer hs1258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:98269229-98269862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20071 Neighboring gene NANOG hESC enhancer GRCh37_chr9:98271448-98271997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:98272951-98273714 Neighboring gene uncharacterized LOC105376157 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110687 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:98314166-98315130 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:98315131-98316095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98326699-98327200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98327201-98327700 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110694 Neighboring gene uncharacterized LOC105376158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98362911-98363412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:98363413-98363912

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 20073
  • H3K27ac hESC enhancer GRCh37_chr9:98273715-98274476

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_053713.2 

    Range
    101..1700
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    95511433..95513032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    107681072..107682671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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