rs7259278 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

Variant: rs7259278 -  Homo sapiens

RGD ID: 11525213
RS ID: rs7259278
ClinVar ID: CV246290
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: LDLR  
Reference Nucleotide: G
Variant Nucleotide: T
Position
Assembly Chr Position
GRCh37 19 11,227,466
GRCh38 19 11,116,790
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Prevalence Trait Synonyms
LRG_274t1:c.1706-69G>T
NC_000019.10:g.11116790G>T
NC_000019.9:g.11227466G>T
c.1706-69G>T
More... 		06/10/2021 intron variant benign 1-9 / 1 000 000 Fredrickson type IIa hyperlipoproteinemia; Hyper-beta-lipoproteinemia; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; HYPERCHOLESTEROLEMIA, FAMILIAL, MODIFIER OF; HYPERCHOLESTEROLEMIC XANTHOMATOSIS, FAMILIAL; Hyperlipoproteinemia type 2; Hyperlipoproteinemia Type II; Hyperlipoproteinemia Type IIa; LDL RECEPTOR DISORDER
Disease Annotations     Click to see Annotation Detail View

GWAS Catalog Data
GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG SNP Passing QC Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GCST90019496 Apolipoprotein B levels 340,860 European ancestry individuals, 5,962 African ancestry individuals, 7,275 South Asian ancestry individuals T NR 3E-12 11.522878745280337 Affymetrix [9000000] (imputed) 0.0243 apolipoprotein B measurement (EFO:0004615)
 PMID:33462484
GCST90019512 Low density lipoprotein cholesterol levels 341,875 European ancestry individuals, 6,003 African ancestry individuals, 7,319 South Asian ancestry individuals T NR 2E-10 9.698970004336019 Affymetrix [9000000] (imputed) 0.0221 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:33462484

Variant Details
Variant Transcripts
Gene Symbol:LDLR
Accession:NM_001406861
Location:INTRON

Gene Symbol:LDLR
Accession:XM_011528010
Location:INTRON

Gene Symbol:LDLR
Accession:XM_047438831
Location:INTRON

Gene Symbol:LDLR
Accession:NM_001195798
Location:INTRON

Gene Symbol:LDLR
Accession:NM_001195799
Location:INTRON

Gene Symbol:LDLR
Accession:NM_001195803
Location:INTRON

Gene Symbol:LDLR
Accession:NM_001195800
Location:INTRON

Gene Symbol:LDLR
Accession:NM_000527
Location:INTRON

Variant Samples
Additional References at PubMed
PMID:21418584   PMID:25741868  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000238236 CLINVAR
dbSNP (RS) rs7259278 CLINVAR
GWAS Catalog GCST90019496 GWAS Catalog
  GCST90019512 GWAS Catalog
MedGen C0745103 CLINVAR
NCBI Gene LDLR CLINVAR
OMIM 143890 CLINVAR
  144400 CLINVAR
  606945 CLINVAR
SNOMED CT 397915002 CLINVAR