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LOC123956174 OCT4-NANOG hESC enhancers GRCh37_chr7:83857426-83857944 and GRCh37_chr7:83857945-83858461 [ Homo sapiens (human) ]

Gene ID: 123956174, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956174
Gene description
OCT4-NANOG hESC enhancers GRCh37_chr7:83857426-83857944 and GRCh37_chr7:83857945-83858461
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 and primed human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors. 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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (84228110..84229145)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (85478075..85479110)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (83857909..83858203)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83314287-83314786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83315470-83315977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:83320326-83320837 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83322516-83323158 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:83337804-83339003 Neighboring gene RAD23B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83463173-83463673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18337 Neighboring gene uncharacterized LOC107986745 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83623841-83624402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83624403-83624963 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:83631626-83632189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26218 Neighboring gene semaphorin 3A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83684723-83685314 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83684131-83684722 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:83720483-83720983 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:83779267-83779791 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83779792-83780315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:83795422-83795922 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:83824219-83825026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:83835322-83836064 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:83880131-83881330 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:83906806-83907406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26219 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:84001008-84002207 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100327 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100336 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100364 Neighboring gene long intergenic non-protein coding RNA 3017 Neighboring gene ribosomal protein L7 pseudogene 30

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 hESC enhancer GRCh37_chr7:83857426-83857944
  • OCT4-NANOG hESC enhancer GRCh37_chr7:83857945-83858461
  • Sharpr-MPRA regulatory region 9013

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_078368.2 

    Range
    101..1136
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    84228110..84229145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    85478075..85479110
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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