U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116268458 CRISPRi-validated cis-regulatory element chr14.550 [ Homo sapiens (human) ]

Gene ID: 116268458, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116268458
Gene description
CRISPRi-validated cis-regulatory element chr14.550
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 high-confidence cis-regulatory element for the NFKBIA (NFKB inhibitor alpha) gene on chromosome 14 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:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (35369737..35370007)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (29557371..29557641)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (35838943..35839213)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene PRORP-PSMA6 readthrough Neighboring gene protein only RNase P catalytic subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8266 Neighboring gene ribosomal protein L9 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35761289-35761875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8272 Neighboring gene proteasome 20S subunit alpha 6 Neighboring gene Sharpr-MPRA regulatory region 8744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35801329-35802250 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:35802261-35802870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35805755-35806276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:35811147-35812003 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35816286-35816830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35836533-35837122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:35837123-35837710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35837711-35838299 Neighboring gene Sharpr-MPRA regulatory region 4470 Neighboring gene PSMA6-RPLP0P3 intergenic CAGE-defined low expression enhancer Neighboring gene Sharpr-MPRA regulatory region 12595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:35871323-35872196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8277 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5676 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35873941-35874812 Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 3 Neighboring gene NFKB inhibitor alpha

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_066973.1 

    Range
    101..371
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    35369737..35370007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    29557371..29557641
    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