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LOC127824432 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:62996341-62996862 [ Homo sapiens (human) ]

Gene ID: 127824432, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824432
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:62996341-62996862
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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 LOC127824432 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 (62602561..62603082)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (62581379..62581900)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (62996341..62996862)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MON2 antisense RNA 1 Neighboring gene MON2 homolog, regulator of endosome-to-Golgi trafficking Neighboring gene RNA, U6 small nuclear 399, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:62995817-62996340 Neighboring gene H3K27ac hESC enhancers GRCh37_chr12:62996863-62997384 and GRCh37_chr12:62997385-62997906 Neighboring gene MIRLET7I host gene Neighboring gene long intergenic non-protein coding RNA 1465 Neighboring gene NANOG hESC enhancer GRCh37_chr12:63022918-63023636 Neighboring gene microRNA let-7i Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:63023962-63024586 Neighboring gene MPRA-validated peak1753 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1H

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 6582
  • ATAC-STARR-seq lymphoblastoid active region 6583

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_125949.1 

    Range
    101..622
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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
    62602561..62603082
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    62581379..62581900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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