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LOC127824730 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94070392-94071207 [ Homo sapiens (human) ]

Gene ID: 127824730, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824730
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94070392-94071207
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 region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127824730 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (93676616..93677459)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (93658111..93658954)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (94070392..94071235)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6771 Neighboring gene SOCS2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93975910-93976410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93976411-93976911 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93977698-93978644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93978645-93979590 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93984897-93985456 Neighboring gene suppressor of cytokine signaling 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:94018330-94019529 Neighboring gene phosphoglycerate mutase 1 (brain) pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94071208-94072022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94072839-94073653 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:94092983-94093855 Neighboring gene CASP2 and RIPK1 domain containing adaptor with death domain Neighboring gene CRADD antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:94135094-94136050 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:94136051-94137007 Neighboring gene Sharpr-MPRA regulatory region 12336 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:94178853-94180052 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:94218159-94218894 Neighboring gene RNA, 7SL, cytoplasmic 630, pseudogene

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 6772

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_126246.2 

    Range
    101..944
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    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
    93676616..93677459
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    93658111..93658954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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