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LOC112163545 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:13679281-13680273 [ Homo sapiens (human) ]

Gene ID: 112163545, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163545
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:13679281-13680273
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 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 an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating 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 LOC112163545 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (13526347..13527339)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (13400768..13401760)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (13679529..13679823)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6036 Neighboring gene RNA, U6 small nuclear 590, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:13651563-13652064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:13652065-13652564 Neighboring gene MPRA-validated peak1577 silencer Neighboring gene Sharpr-MPRA regulatory region 1907 Neighboring gene glutamate ionotropic receptor NMDA type subunit 2B Neighboring gene uncharacterized LOC105369668 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:13748291-13749049 Neighboring gene RN7SK pseudogene 162

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 1480

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_056569.2 

    Range
    101..1093
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    13526347..13527339
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    13400768..13401760
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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