LOC115995519 (CRISPRi-validated cis-regulatory element chr3.3677) - Rat Genome Database

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Gene: LOC115995519 (CRISPRi-validated cis-regulatory element chr3.3677) Homo sapiens
Analyze
Symbol: LOC115995519
Name: CRISPRi-validated cis-regulatory element chr3.3677
RGD ID: 38603848
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 high-confidence cis-regulatory element for the GATA2 (GATA binding protein 2) gene on chromosome 3 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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
GRCh383128,412,521 - 128,413,816 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373128,131,364 - 128,132,659 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3qNCBI
T2T-CHM13v2.03131,154,128 - 131,155,423 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:30033119   PMID:30612741  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q21.3-23(chr3:126106779-140918089)x3 copy number gain See cases [RCV000142010] Chr3:126106779..140918089 [GRCh38]
Chr3:125825622..140636931 [GRCh37]
Chr3:127308312..142119621 [NCBI36]
Chr3:3q21.3-23		 uncertain significance
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q21.3(chr3:126797420-128946623)x1 copy number loss See cases [RCV000137444] Chr3:126797420..128946623 [GRCh38]
Chr3:126516263..128665466 [GRCh37]
Chr3:127998953..130148156 [NCBI36]
Chr3:3q21.3		 pathogenic|uncertain significance
GRCh38/hg38 3q21.3-22.1(chr3:127607945-133566661)x1 copy number loss See cases [RCV000142787] Chr3:127607945..133566661 [GRCh38]
Chr3:127326788..133285505 [GRCh37]
Chr3:128809478..134768195 [NCBI36]
Chr3:3q21.3-22.1		 likely pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q21.3(chr3:127818502-128451950)x3 copy number gain See cases [RCV000140881] Chr3:127818502..128451950 [GRCh38]
Chr3:127537345..128170793 [GRCh37]
Chr3:129020035..129653483 [NCBI36]
Chr3:3q21.3		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC115995519 COSMIC
GTEx LOC115995519 GTEx
Human Proteome Map LOC115995519 Human Proteome Map
NCBI Gene LOC115995519 ENTREZGENE