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LOC121740663 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:111576355-111577001 [ Homo sapiens (human) ]

Gene ID: 121740663, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740663
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:111576355-111577001
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 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 an 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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (111255152..111255798)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112438270..112438916)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111576369..111576663)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 16 member 10 Neighboring gene small nucleolar RNA, C/D box 166 Neighboring gene uncharacterized LOC124901377 Neighboring gene MFSD4B divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111573581-111573781 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:111575060-111575706 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:111575707-111576354 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:111577002-111577648 Neighboring gene uncharacterized LOC124901378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24942 Neighboring gene Sharpr-MPRA regulatory region 12211 Neighboring gene major facilitator superfamily domain containing 4B Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_87657

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 9088

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_075725.2 

    Range
    101..747
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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
    111255152..111255798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    112438270..112438916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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