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LOC123575676 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14639937-14640920 [ Homo sapiens (human) ]

Gene ID: 123575676, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575676
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14639937-14640920
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 naive 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 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2023]
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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 (14639706..14640689)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (14512105..14513088)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14640429..14640723)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374943 Neighboring gene uncharacterized LOC105374942 Neighboring gene uncharacterized LOC101928331 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:14441647-14442345 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14450188-14450778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14472912-14473412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14473413-14473913 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14474901-14475125 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:14508670-14509869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14540385-14540955 Neighboring gene uncharacterized LOC101928354 Neighboring gene Sharpr-MPRA regulatory region 399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24051 Neighboring gene uncharacterized LOC102724463 Neighboring gene RNA, U6 small nuclear 793, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24053

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 8489

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_077935.2 

    Range
    101..1084
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    14639706..14640689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    14512105..14513088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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