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LOC122817722 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:109191556-109192512 [ Homo sapiens (human) ]

Gene ID: 122817722, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122817722
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:109191556-109192512
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122817722 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (108575100..108576056)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (109035717..109036674)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (109191556..109192512)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small integral membrane protein 12 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:109064602-109065584 and GRCh37_chr2:109065585-109066566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109066652-109067152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109067153-109067653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16343 Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene 2q12.3 distal recombination region Neighboring gene GCC2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 7983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11849 Neighboring gene LIM zinc finger domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16345 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:109210352-109211551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16348 Neighboring gene NANOG hESC enhancer GRCh37_chr2:109225689-109226190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109252737-109253311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:109271409-109272023 Neighboring gene Sharpr-MPRA regulatory region 6630 Neighboring gene LIMS1 antisense RNA 1 Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial-like

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 1013

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_076994.2 

    Range
    101..1057
    Download
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    108575100..108576056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    109035717..109036674
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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