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LOC116186909 CRISPRi-validated cis-regulatory element chr7.4048 [ Homo sapiens (human) ]

Gene ID: 116186909, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116186909
Gene description
CRISPRi-validated cis-regulatory element chr7.4048
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 PRKAR2B (protein kinase cAMP-dependent type II regulatory subunit beta1) gene on chromosome 7 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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See LOC116186909 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (107025631..107025827)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (108341734..108341930)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (106666076..106666272)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2577 Neighboring gene RNA, 5S ribosomal pseudogene 236 Neighboring gene Sharpr-MPRA regulatory region 12136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26490 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chr7.4040 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4041 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4042 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4045 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4046 Neighboring gene CRISPRi-validated cis-regulatory element chr7.4050 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106681203-106681414 Neighboring gene Sharpr-MPRA regulatory region 8060 Neighboring gene PRKAR2B antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12069 Neighboring gene protein kinase cAMP-dependent type II regulatory subunit beta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:106792322-106793521 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:106808976-106809549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18538 Neighboring gene HMG-box transcription factor 1 Neighboring gene component of oligomeric golgi complex 5

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. The DNA sequence of human chromosome 7. Hillier LW, et al. Nature, 2003 Jul 10. PMID 12853948
  2. 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
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. 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

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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)

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_066830.1 

    Range
    101..297
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    107025631..107025827
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    108341734..108341930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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