U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC116158507 CRISPRi-validated cis-regulatory element chr4.2649 [ Homo sapiens (human) ]

Gene ID: 116158507, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC116158507
Gene description
CRISPRi-validated cis-regulatory element chr4.2649
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 BBS12 (Bardet-Biedl syndrome 12), FGF2 (fibroblast growth factor 2) and AFG2A (AFG2 AAA ATPase homolog A, formerly known as SPATA5) genes on chromosome 4 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Mar 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (122749712..122749853)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (126053812..126053953)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (123670867..123671008)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Bardet-Biedl syndrome 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21875 Neighboring gene centrin 4, pseudogene Neighboring gene DNA damage regulated autophagy modulator 1 pseudogene Neighboring gene Sharpr-MPRA regulatory region 2230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:123705471-123706466 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:123707239-123708438 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:123709565-123710492 Neighboring gene Sharpr-MPRA regulatory region 4773 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:123719262-123720461 Neighboring gene FGF2 promoter region Neighboring gene ribosomal protein L34 pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21877 Neighboring gene Sharpr-MPRA regulatory region 10032 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:123749417-123749942 Neighboring gene fibroblast growth factor 2 Neighboring gene ribosomal protein S26 pseudogene 23

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
  4. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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_066649.1 

    Range
    101..242
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    122749712..122749853
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    126053812..126053953
    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