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LOC123620069 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24400121-24400856 [ Homo sapiens (human) ]

Gene ID: 123620069, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620069
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24400121-24400856
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. The major subregion was validated as an active enhancer by ChIP-STARR-seq 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. An overlapping subregion was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (24399893..24400635)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (24269928..24270670)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (24400569..24400863)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene doublecortin domain containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24360012-24360600 Neighboring gene RNA, U6 small nuclear 391, pseudogene Neighboring gene kidney associated DCDC2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24400857-24401592 Neighboring gene Sharpr-MPRA regulatory region 326 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24403801-24404535 Neighboring gene magnesium transporter MRS2 Neighboring gene glycosylphosphatidylinositol specific phospholipase D1 Neighboring gene MPRA-validated peak5733 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24153 Neighboring gene aldehyde dehydrogenase 5 family member A1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16992 Neighboring gene uncharacterized LOC124901277

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 571

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_077951.2 

    Range
    101..843
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    24399893..24400635
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    24269928..24270670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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