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LOC112163629 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:63052702-63053227 [ Homo sapiens (human) ]

Gene ID: 112163629, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163629
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:63052702-63053227
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 and H3K4me1 histone modifications. 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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 15:Elon, transcriptional elongation, stronger H3K36me3, more exonic) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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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 (62658922..62659447)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (62637700..62638231)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (63052729..63053023)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr12:62996863-62997384 and GRCh37_chr12:62997385-62997906 Neighboring gene MIRLET7I host gene Neighboring gene microRNA let-7i Neighboring gene NANOG hESC enhancer GRCh37_chr12:63022918-63023636 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:63023962-63024586 Neighboring gene MPRA-validated peak1753 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:63047149-63047770 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:63047771-63048392 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:63049635-63050255 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:63053228-63053754 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1H Neighboring gene ribosomal protein L32 pseudogene 26 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:63095785-63096388 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:63097597-63098198 Neighboring gene NANOG hESC enhancer GRCh37_chr12:63111348-63111860 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:63118179-63119378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6584 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 44 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4610 Neighboring gene uncharacterized LOC105369795 Neighboring gene RNA, U1 small nuclear 83, pseudogene

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 14116

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_056606.2 

    Range
    101..626
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    62658922..62659447
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    62637700..62638231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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