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LOC127459356 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:42698061-42698851 [ Homo sapiens (human) ]

Gene ID: 127459356, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127459356
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:42698061-42698851
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 genomic region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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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See LOC127459356 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42842918..42843708)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (43111031..43111821)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42698061..42698851)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cholinergic receptor nicotinic beta 3 subunit Neighboring gene RPL7L1 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27315 Neighboring gene cholinergic receptor nicotinic alpha 6 subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42649154-42649988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27317 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:42671563-42671730 Neighboring gene uncharacterized LOC124901940 Neighboring gene THAP domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27319 Neighboring gene ring finger protein 170 Neighboring gene RNA, 7SL, cytoplasmic 806, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42750865-42751426 Neighboring gene microRNA 4469

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 27318
  • ATAC-STARR-seq lymphoblastoid silent region 19158

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_114125.1 

    Range
    101..891
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    42842918..42843708
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    43111031..43111821
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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