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LOC127815690 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117349328-117350146 [ Homo sapiens (human) ]

Gene ID: 127815690, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127815690
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117349328-117350146
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 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 LOC127815690 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114587048..114588204)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126779466..126780622)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene whirlin Neighboring gene uncharacterized LOC124902254 Neighboring gene small EDRK-rich factor 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117266242-117267132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117267133-117268023 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:117276161-117276362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28868 Neighboring gene uncharacterized LOC105376229 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:117345492-117345996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117348508-117349327 Neighboring gene ATPase H+ transporting V1 subunit G1 Neighboring gene MPRA-validated peak7324 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28873 Neighboring gene transmembrane protein 268 Neighboring gene NANOG hESC enhancer GRCh37_chr9:117415620-117416126 Neighboring gene testis expressed 53

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 28869
  • ATAC-STARR-seq lymphoblastoid active region 28870

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_117196.2 

    Range
    101..1257
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    114587048..114588204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    126779466..126780622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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