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LOC124625894 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:6324019-6324520 and GRCh37_chr12:6324521-6325024 [ Homo sapiens (human) ]

Gene ID: 124625894, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124625894
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:6324019-6324520 and GRCh37_chr12:6324521-6325024
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 and are 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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC124625894 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6214853..6215858)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6222468..6223473)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6324019..6325024)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6268183-6268756 Neighboring gene Sharpr-MPRA regulatory region 14257 Neighboring gene uncharacterized LOC105369623 Neighboring gene uncharacterized LOC105369622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6289294-6289864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6299563-6300248 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6300249-6300934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6308438-6309050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6309051-6309662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6310889-6311501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6311502-6312113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6319522-6320145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6320176-6320677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6323515-6324018 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:6327115-6328314 Neighboring gene Sharpr-MPRA regulatory region 3368 Neighboring gene CD9 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332057-6332610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332611-6333162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6333163-6333716 Neighboring gene uncharacterized LOC105369625 Neighboring gene Sharpr-MPRA regulatory region 10655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350388-6350888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350889-6351389 Neighboring gene CRISPRi-validated cis-regulatory element chr12.283 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6378001-6378746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4158 Neighboring gene ATP synthase membrane subunit f pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 10601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6390295-6390794 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:6402555-6402765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6404819-6405319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6418662-6419382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6427837-6428456 Neighboring gene pleckstrin homology and RhoGEF domain containing G6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6432098-6432639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433181-6433722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433723-6434262

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6324019-6324520
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6324521-6325024
  • Sharpr-MPRA regulatory region 8477

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_079576.2 

    Range
    101..1106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6214853..6215858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6222468..6223473
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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