LOC116268441 (CRISPRi-validated cis-regulatory element chr12.2135) - Rat Genome Database

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Gene: LOC116268441 (CRISPRi-validated cis-regulatory element chr12.2135) Homo sapiens
Analyze
Symbol: LOC116268441
Name: CRISPRi-validated cis-regulatory element chr12.2135
RGD ID: 38652812
Description: 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 CNPY2 (canopy FGF signaling regulator 2) gene on chromosome 12 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. An overlapping subregion was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2021]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,047,104 - 56,047,499 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371256,440,888 - 56,441,283 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12qNCBI
T2T-CHM13v2.01256,014,171 - 56,014,566 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:27701403   PMID:30612741  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q13.13-13.3(chr12:53420606-56202942)x3 copy number gain See cases [RCV000141435] Chr12:53420606..56202942 [GRCh38]
Chr12:53814390..56596726 [GRCh37]
Chr12:52100657..54882993 [NCBI36]
Chr12:12q13.13-13.3		 pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
NC_000012.10:g.54711095_54731551del deletion Diamond-Blackfan anemia 10 [RCV000074477] Chr12:56031044..56051500 [GRCh38]
Chr12:56424828..56445284 [GRCh37]
Chr12:54711095..54731551 [NCBI36]
Chr12:12q13.2		 pathogenic
Single allele duplication not specified [RCV002286382] Chr12:55986511..56885590 [GRCh38]
Chr12:12q13.2-13.3		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116268441 COSMIC
GTEx LOC116268441 GTEx
Human Proteome Map LOC116268441 Human Proteome Map
NCBI Gene LOC116268441 ENTREZGENE