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LOC116186941 hESC enhancers GRCh37_chr9:90024569-90025224 and GRCh37_chr9:90025225-90025878 [ Homo sapiens (human) ]

Gene ID: 116186941, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116186941
Gene description
hESC enhancers GRCh37_chr9:90024569-90025224 and GRCh37_chr9:90025225-90025878
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. Two subregions were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac histone modification, and one is additionally marked by H3K4me1. An overlapping subregion was also validated as a high-confidence cis-regulatory element for the DAPK1 (death associated protein kinase 1) gene on chromosome 9 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (87409654..87410963)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (99563136..99564445)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (90025122..90025695)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376126 Neighboring gene uncharacterized LOC124900285 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:89891312-89892511 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:89951383-89951552 Neighboring gene uncharacterized LOC105376127 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:90001899-90002782 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90017019-90017636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90017637-90018252 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:90020422-90020972 Neighboring gene cytochrome c oxidase subunit NDUFA4-like Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90025879-90026532 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:90031115-90031768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20001 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:90113131-90113888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28520 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:90145230-90146212 Neighboring gene death associated protein kinase 1 Neighboring gene ribosomal protein S29 pseudogene 18 Neighboring gene DAPK1 intronic transcript 1

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CRISPRi-validated cis-regulatory element chr9.1038
  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:90024569-90025224
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90025225-90025878

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_066860.2 

    Range
    101..1410
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    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
    87409654..87410963
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    99563136..99564445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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