U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116216120 CRISPRi-validated cis-regulatory element chr10.3946 [ Homo sapiens (human) ]

Gene ID: 116216120, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116216120
Gene description
CRISPRi-validated cis-regulatory element chr10.3946
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 NT5C2 (5'-nucleotidase, cytosolic II) gene on chromosome 10 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:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (103197122..103197603)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104083371..104083852)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104956879..104957360)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene 5'-nucleotidase, cytosolic II Neighboring gene ribosomal protein S15a pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3953 Neighboring gene MARCKS like 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104946165-104946666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104946667-104947166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104951770-104952458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104952459-104953145 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:104962099-104962305 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104964236-104964895 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:104964896-104965554 Neighboring gene ST13, Hsp70 interacting protein pseudogene 13 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104990595-104991592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104991593-104992590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3955 Neighboring gene ribulose-5-phosphate-3-epimerase like 1

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_066887.1 

    Range
    101..582
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    103197122..103197603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    104083371..104083852
    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.

Other Literature Sources
Molecular Biology Databases