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LOC111982878 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88785123-88785973 [ Homo sapiens (human) ]

Gene ID: 111982878, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111982878
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88785123-88785973
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (87025366..87026216)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87909001..87909851)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88785349..88785643)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 11 Neighboring gene BMS1 pseudogene 3 Neighboring gene MPRA-validated peak1043 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88779570-88780070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88780071-88780571 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88784270-88785122 Neighboring gene family with sequence similarity 25 member A Neighboring gene RNA, U6 small nuclear 529, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3703 Neighboring gene glutamate dehydrogenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3704 Neighboring gene NANOG hESC enhancer GRCh37_chr10:88852612-88853149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2577 Neighboring gene shieldin complex subunit 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 4381

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_056370.2 

    Range
    101..951
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    87025366..87026216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87909001..87909851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
Molecular Biology Databases