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LOC112163527 OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr12:118557876-118558588 and GRCh37_chr12:118558589-118559300 [ Homo sapiens (human) ]

Gene ID: 112163527, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163527
Gene description
OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr12:118557876-118558588 and GRCh37_chr12:118558589-118559300
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. Two subregions were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac histone modification. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). Another subregion was validated as a functional repressive element by Sharpr-MPRA in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin) and K562 cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (118120071..118121495)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (118107317..118108742)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (118558689..118558983)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903030 Neighboring gene WD repeat and SOCS box containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118523172-118523714 Neighboring gene V-set and immunoglobulin domain containing 10 Neighboring gene uncharacterized LOC124903029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4922 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:118543551-118544266 Neighboring gene Sharpr-MPRA regulatory region 1292 Neighboring gene uncharacterized LOC101928274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118560014-118560725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118560726-118561438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:118564319-118564855 Neighboring gene Sharpr-MPRA regulatory region 10186 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:118573724-118574224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4923 Neighboring gene MPRA-validated peak1994 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7107 Neighboring gene phosphatidylethanolamine binding protein 1 Neighboring gene TAO kinase 3 Neighboring gene Sharpr-MPRA regulatory region 13893 Neighboring gene NANOG hESC enhancer GRCh37_chr12:118666512-118667013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7109 Neighboring gene ribosomal protein S2 pseudogene 5

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

  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:118557876-118558588
  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:118558589-118559300
  • Sharpr-MPRA regulatory region 576
  • Sharpr-MPRA regulatory region 8543

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_056552.2 

    Range
    101..1525
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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
    118120071..118121495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    118107317..118108742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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