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LOC110121262 VISTA enhancer hs2129 [ Homo sapiens (human) ]

Gene ID: 110121262, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110121262
Gene description
VISTA enhancer hs2129
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. The major subregion can activate a Hsp68 promoter coupled to a LacZ reporter gene in embryonic heart of transgenic mice. Three overlapping 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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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See LOC110121262 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156102512..156107245)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155240978..155245691)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156072303..156076849)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RAB25, member RAS oncogene family Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:156045982-156046889 and GRCh37_chr1:156046890-156047796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156051244-156052056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156052057-156052870 Neighboring gene mex-3 RNA binding family member A Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156056191-156057025 Neighboring gene Sharpr-MPRA regulatory region 15377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1838 Neighboring gene lamin A/C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156067261-156068134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156077037-156077778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156087275-156087774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156090429-156091415 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156093390-156094377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1843 Neighboring gene Sharpr-MPRA regulatory region 4592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156096352-156097337 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:156099693-156100892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1849 Neighboring gene semaphorin 4A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1850 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:156131887-156132038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156146693-156147195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156149713-156150215 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156151223-156151726 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156151727-156152229 Neighboring gene uncharacterized LOC124900449

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 active region 1840
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156073317-156074060
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156074805-156075548
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156076293-156077036

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_053877.2 

    Range
    101..4834
    Download
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156102512..156107245
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155240978..155245691
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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