U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116216100 CRISPRi-validated cis-regulatory element chr9.2942 [ Homo sapiens (human) ]

Gene ID: 116216100, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116216100
Gene description
CRISPRi-validated cis-regulatory element chr9.2942
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a cis-regulatory element for the PTGES2 (prostaglandin E synthase 2) gene on chromosome 9 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128142126..128142299)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140349220..140349393)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130904405..130904578)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene prostaglandin E synthase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20326 Neighboring gene PTGES2 antisense RNA 1 (head to head) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130900289-130900788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130908453-130908952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130916023-130916694 Neighboring gene lipocalin 2 Neighboring gene MPRA-validated peak7335 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130920069-130920264 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:130921445-130922398 and GRCh37_chr9:130922399-130923352 Neighboring gene bublin coiled coil protein

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_066867.1 

    Range
    101..274
    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
    128142126..128142299
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    140349220..140349393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases