LOC112272587 (Sharpr-MPRA regulatory region 5929) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: LOC112272587 (Sharpr-MPRA regulatory region 5929) Homo sapiens
Analyze
Symbol: LOC112272587
Name: Sharpr-MPRA regulatory region 5929
RGD ID: 38634833
Description: This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by Sharpr-MPRA (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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 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
GRCh381541,827,951 - 41,828,245 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371542,120,149 - 42,120,443 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map15qNCBI
T2T-CHM13v2.01539,633,864 - 39,634,158 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27701403   PMID:35858748  


Genomics

Variants

.
Variants in LOC112272587
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 15q15.1(chr15:41697762-42489559)x3 copy number gain See cases [RCV000140056] Chr15:41697762..42489559 [GRCh38]
Chr15:41989960..42781757 [GRCh37]
Chr15:39777252..40569049 [NCBI36]
Chr15:15q15.1		 uncertain significance
NM_001114632.2(JMJD7):c.50C>T (p.Pro17Leu) single nucleotide variant not provided [RCV000906616] Chr15:41828174 [GRCh38]
Chr15:42120372 [GRCh37]
Chr15:15q15.1		 benign
NM_005090.4(JMJD7-PLA2G4B):c.20A>G (p.Glu7Gly) single nucleotide variant JMJD7-PLA2G4B-related disorder [RCV003978927] Chr15:41828144 [GRCh38]
Chr15:42120342 [GRCh37]
Chr15:15q15.1		 benign
NM_001114632.2(JMJD7):c.-5C>A single nucleotide variant JMJD7-related disorder [RCV003944624] Chr15:41828120 [GRCh38]
Chr15:42120318 [GRCh37]
Chr15:15q15.1		 likely benign
NM_005090.4(JMJD7-PLA2G4B):c.34G>C (p.Glu12Gln) single nucleotide variant not specified [RCV004401332] Chr15:41828158 [GRCh38]
Chr15:42120356 [GRCh37]
Chr15:15q15.1		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2289410BW327_HBody weight QTL 327 (human)3.320.0001Body fat amount151998012945980129Human
1643273BW330_HBody Weight QTL 330 (human)1.050.014Body weightbody mass index152686671952866719Human
2289430BMD7_HBone mineral density QTL 7 (human)3.320.0001Bone mineral density151998012945980129Human
1559411SCL107_HSerum cholesterol level QTL 107 (human)3.88Lipid leveltriglyceride152654355252543552Human
2299958PRSTS330_HProstate tumor susceptibility QTL 330 (human)1.020.0151Prostate tumor susceptibility153479023060790230Human
1643523BW284_HBody Weight QTL 284 (human)1.950.0013Body weight152179288947792889Human
407151038GWAS800014_HBMI-adjusted waist circumference QTL GWAS800014 (human)3e-09BMI-adjusted waist circumference154182823941828240Human
407160287GWAS809263_HBMI-adjusted waist-hip ratio QTL GWAS809263 (human)1e-09BMI-adjusted waist-hip ratio154182823941828240Human
1559354LDLPS4_HLow density lipoprotein particle size QTL 4 (human)2.20.019LDL particle size153479023060790230Human
2289420BW314_HBody weight QTL 314 (human)2.720.0003Body weightlean mass151998012945980129Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC112272587 COSMIC
GTEx LOC112272587 GTEx
Human Proteome Map LOC112272587 Human Proteome Map
NCBI Gene LOC112272587 ENTREZGENE