LOC113939967 (Sharpr-MPRA regulatory region 3609) - 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   new 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
Gene: LOC113939967 (Sharpr-MPRA regulatory region 3609) Homo sapiens
Analyze
Symbol: LOC113939967
Name: Sharpr-MPRA regulatory region 3609
RGD ID: 38605013
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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2019]
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
GRCh381910,113,673 - 10,113,967 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371910,224,349 - 10,224,643 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19pNCBI
T2T-CHM13v2.01910,239,882 - 10,240,176 (+)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:27701403  


Genomics

Variants

.
Variants in LOC113939967
10 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_002566.5(P2RY11):c.258C>T (p.Ala86=) single nucleotide variant not provided [RCV000926470] Chr19:10113871 [GRCh38]
Chr19:10224547 [GRCh37]
Chr19:19p13.2		 likely benign
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13		 likely pathogenic
NM_002566.5(P2RY11):c.340C>T (p.Leu114=) single nucleotide variant not provided [RCV000923458] Chr19:10113953 [GRCh38]
Chr19:10224629 [GRCh37]
Chr19:19p13.2		 likely benign
NM_002566.5(P2RY11):c.198C>A (p.Val66=) single nucleotide variant not provided [RCV000880704] Chr19:10113811 [GRCh38]
Chr19:10224487 [GRCh37]
Chr19:19p13.2		 likely benign
NM_002566.5(P2RY11):c.330C>T (p.Thr110=) single nucleotide variant not provided [RCV000899894] Chr19:10113943 [GRCh38]
Chr19:10224619 [GRCh37]
Chr19:19p13.2		 benign
NM_002566.5(P2RY11):c.141C>A (p.Gly47=) single nucleotide variant PPAN-P2RY11-related condition [RCV003915955]|not provided [RCV000957880] Chr19:10113754 [GRCh38]
Chr19:10224430 [GRCh37]
Chr19:19p13.2		 benign|likely benign
GRCh38/hg38 19p13.2(chr19:9735443-11228001)x1 copy number loss See cases [RCV000135403] Chr19:9735443..11228001 [GRCh38]
Chr19:9846119..11338677 [GRCh37]
Chr19:9707119..11199677 [NCBI36]
Chr19:19p13.2		 pathogenic
NM_002566.5(P2RY11):c.348C>T (p.Ser116=) single nucleotide variant not provided [RCV000959779] Chr19:10113961 [GRCh38]
Chr19:10224637 [GRCh37]
Chr19:19p13.2		 benign
NM_002566.5(P2RY11):c.234C>T (p.Cys78=) single nucleotide variant not provided [RCV000953385] Chr19:10113847 [GRCh38]
Chr19:10224523 [GRCh37]
Chr19:19p13.2		 benign|likely benign
NM_002566.5(P2RY11):c.250C>T (p.Pro84Ser) single nucleotide variant Inborn genetic diseases [RCV003185526] Chr19:10113863 [GRCh38]
Chr19:10224539 [GRCh37]
Chr19:19p13.2		 uncertain significance
NM_002566.5(P2RY11):c.192C>T (p.Ala64=) single nucleotide variant Inborn genetic diseases [RCV003370097] Chr19:10113805 [GRCh38]
Chr19:10224481 [GRCh37]
Chr19:19p13.2		 likely benign
NM_002566.5(P2RY11):c.180A>G (p.Pro60=) single nucleotide variant not provided [RCV003406842] Chr19:10113793 [GRCh38]
Chr19:10224469 [GRCh37]
Chr19:19p13.2		 likely benign
NM_002566.5(P2RY11):c.207C>A (p.Val69=) single nucleotide variant P2RY11-related condition [RCV003901826] Chr19:10113820 [GRCh38]
Chr19:10224496 [GRCh37]
Chr19:19p13.2		 likely benign
NM_002566.5(P2RY11):c.259G>A (p.Ala87Thr) single nucleotide variant P2RY11-related condition [RCV003981999] Chr19:10113872 [GRCh38]
Chr19:10224548 [GRCh37]
Chr19:19p13.2		 benign
NM_002566.5(P2RY11):c.198C>T (p.Val66=) single nucleotide variant PPAN-P2RY11-related condition [RCV003932280] Chr19:10113811 [GRCh38]
Chr19:10224487 [GRCh37]
Chr19:19p13.2		 likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC113939967 COSMIC
GTEx LOC113939967 GTEx
Human Proteome Map LOC113939967 Human Proteome Map
NCBI Gene LOC113939967 ENTREZGENE