LOC116276499 (CRISPRi-validated cis-regulatory element chr19.1096) - Rat Genome Database

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Gene: LOC116276499 (CRISPRi-validated cis-regulatory element chr19.1096) Homo sapiens
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Symbol: LOC116276499
Name: CRISPRi-validated cis-regulatory element chr19.1096
RGD ID: 38617184
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 PLIN3 (perilipin 3) gene on chromosome 19 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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
GRCh38194,870,081 - 4,870,567 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37194,870,093 - 4,870,579 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19pNCBI
T2T-CHM13v2.0194,855,568 - 4,856,054 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:30612741   PMID:32094911   PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.3-13.2(chr19:1972245-9648879)x3 copy number gain See cases [RCV000052879] Chr19:1972245..9648879 [GRCh38]
Chr19:1972244..9759555 [GRCh37]
Chr19:1923244..9620555 [NCBI36]
Chr19:19p13.3-13.2		 pathogenic
GRCh38/hg38 19p13.3(chr19:3947934-5196676)x3 copy number gain See cases [RCV000134164] Chr19:3947934..5196676 [GRCh38]
Chr19:3947932..5196687 [GRCh37]
Chr19:3898932..5147687 [NCBI36]
Chr19:19p13.3		 pathogenic|uncertain significance
GRCh38/hg38 19p13.3(chr19:3080621-4912622)x3 copy number gain See cases [RCV000137713] Chr19:3080621..4912622 [GRCh38]
Chr19:3080619..4912634 [GRCh37]
Chr19:3031619..4863634 [NCBI36]
Chr19:19p13.3		 likely pathogenic
GRCh38/hg38 19p13.3(chr19:3788727-5147354)x1 copy number loss See cases [RCV000143614] Chr19:3788727..5147354 [GRCh38]
Chr19:3788725..5147365 [GRCh37]
Chr19:3739725..5098365 [NCBI36]
Chr19:19p13.3		 likely pathogenic
GRCh38/hg38 19p13.3(chr19:259395-6795611)x3 copy number gain See cases [RCV000142627] Chr19:259395..6795611 [GRCh38]
Chr19:259395..6795622 [GRCh37]
Chr19:210395..6746622 [NCBI36]
Chr19:19p13.3		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298499UAE1_HUrinary albumin excretion QTL 1 (human)2.730.0009Urinary albumin excretionurine albumin:creatinine ratio (ACR)19116075902Human
1643451SLIPL6_HSerum lipid level QTL 6 (human)2.190.0008Lipid level19116075902Human
1581534BP76_HBlood pressure QTL 76 (human)20.001Blood pressurepulse pressure19116075902Human
1581535BP65_HBlood pressure QTL 65 (human)3.10.001Blood pressurepulse pressure19116075902Human
2314591INSUL4_HInsulin level QTL 4 (human)3.80.000038Insulin levelfasting19116075902Human
1298476BP3_HBlood pressure QTL 3 (human)2.4Blood pressuresystolic19116075902Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116276499 COSMIC
GTEx LOC116276499 GTEx
Human Proteome Map LOC116276499 Human Proteome Map
NCBI Gene LOC116276499 ENTREZGENE