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LOC127816395 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134405807-134406720 [ Homo sapiens (human) ]

Gene ID: 127816395, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127816395
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134405807-134406720
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 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 OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to repress 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 LOC127816395 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 (131530420..131531358)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (143743382..143744315)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene proline rich coiled-coil 2B Neighboring gene uncharacterized LOC124902290 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:134375403-134376602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134378091-134378958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134378959-134379824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134388206-134388706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134388707-134389207 Neighboring gene uncharacterized LOC105376301 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:134403902-134405101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20421 Neighboring gene protein O-mannosyltransferase 1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:134426802-134427303 Neighboring gene uridine-cytidine kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134443475-134443974 Neighboring gene proline rich transmembrane protein 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134464737-134465236 Neighboring gene Rap guanine nucleotide exchange factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134481176-134481676 Neighboring gene Sharpr-MPRA regulatory region 10461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134493979-134494945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134499860-134500360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134504170-134504919 Neighboring gene Sharpr-MPRA regulatory region 12258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134530670-134531170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134534752-134535285 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134535286-134535818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29207 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:134558729-134559329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134584807-134585588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587455-134587956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587957-134588456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134598083-134598582 Neighboring gene RNA, 7SL, cytoplasmic 328, pseudogene

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 20419
  • ATAC-STARR-seq lymphoblastoid silent region 20420

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_117888.2 

    Range
    101..1039
    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
    131530420..131531358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    143743382..143744315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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