Bmd90 QTL Report (Rattus norvegicus) - 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)
QTL Registration

QTL: Bmd90 (Bone mineral density QTL 90) Rattus norvegicus

Symbol: Bmd90
Name: Bone mineral density QTL 90
RGD ID: 7207811
Trait: femur size trait   (VT:1000369)    
Measurement Type: femoral neck cross-sectional area   (CMO:0001697)    
LOD Score: 5.2
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81049,943,710 - 94,943,710RGD_MAPPER_PIPELINE
mRatBN7.21049,444,551 - 81,709,989RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01051,289,203 - 84,596,393RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01051,047,525 - 84,389,655RGDRnor5.0
RGSC_v3.41051,099,067 - 85,484,602RGDRGSC3.4
Cross Type: Not Available
Strains Crossed: COP/OlaHsd DA/OlaHsd 
JBrowse: View Region in Genome Browser (JBrowse)
Model




Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd90Ratfemoral neck cross-sectional area  IDA 2293456 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd90Ratcontrol condition  IDA 2293456 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd90Ratex vivo peripheral quantitative computed tomography  IDA 2293456 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd90RatCOP/OlaHsd  IEA 2293456 RGD 
Bmd90RatDA/OlaHsd  IEA 2293456 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd90Ratfemur size trait  IDA 2293456 RGD 


#
Reference Title
Reference Citation
1. Sex-specific Genetic Loci for Femoral Neck Bone Mass and Strength Identified in Inbred COP and DA Rats. Alam I, etal., J Bone Miner Res. 2008 Feb 18;.


1 to 20 of 842 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
628882Elac2elaC ribonuclease Z 2104963230849655614Rat
1305664Arhgap44Rho GTPase activating protein 44104965558349822876Rat
631347Myocdmyocardin104983321949928806Rat
40945377LOC120095121uncharacterized LOC120095121104990525749908359Rat
7523178LOC102554159uncharacterized LOC102554159105004628650199221Rat
1307040Map2k4mitogen activated protein kinase kinase 4105034322750447956Rat
1305130Zfp18zinc finger protein 18105047342850495707Rat
621799Dnah9dynein, axonemal, heavy chain 9105049617450864909Rat
40931177LOC120095122uncharacterized LOC120095122105086476351013804Rat
1564618Shisa6shisa family member 6105089774051192111Rat
7554930LOC102554448glyceraldehyde-3-phosphate dehydrogenase-like105123287851233686Rat
1587327Rps2-ps29ribosomal protein S2, pseudogene 29105126154451262251Rat
1561050Eno1-ps14enolase 1, pseudogene 14105129963251300633Rat
6499408Rpl15-ps7ribosomal protein L15, pseudogene 7105144754451448165Rat
1563963Pgam1-ps11phosphoglycerate mutase 1, pseudogene 11105144914151480570Rat
41236741LOC120095342histidine triad nucleotide-binding protein 1-like105158249551582818Rat
41127486LOC120095442small nucleolar RNA SNORA48105159446451594601Rat
7616564LOC102554726uncharacterized LOC102554726105160857151614414Rat
1565284Pirtphosphoinositide-interacting regulator of transient receptor potential channels105161320251628108Rat
40983152LOC120095123uncharacterized LOC120095123105162571051701636Rat

1 to 20 of 842 rows
1 to 20 of 1120 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
40302D10Rat162155104944455149444706Ratregion
5072988RH137170181104965497449655155Ratregion
5045512RH131220156104965560749655763Ratregion
5501592RH1133983104972087249720955Ratregion
5074876RH138269128104981194749812075Ratregion
5084066AI011711106104983347849833584Ratregion
5501153PMC150745P1108104984955449849663Ratregion
5504582PMC309615P1294104984991949850213Ratregion
34803D10Rat62126104990028749900435Ratregion
5049626RH133589193104990792049908113Ratregion
44747D10Got76223104994457549944798Ratregion
5505402Map2k4964105034345050344414Ratregion
5052319U18310177105034533550345513Ratregion
5085437BM383035196105047967050479866Ratregion
5506056UniSTS:498260427105049454150494968Ratregion
5033717RH139858189105049546250495651Ratregion
5077794RH139963210105049879150499001Ratregion
38102D10Rat102233105050909650509331Ratregion
5033115RH137651132105089933950899471Ratregion
5068928AU046836104105100079051000894Ratregion
1 to 20 of 1120 rows

Flank 1: (D10Rat162)
Rat AssemblyChrPosition (strand)Source
GRCr81049,943,710 - 49,943,865 (+)Marker Load Pipeline
mRatBN7.21049,444,551 - 49,444,706 (+)MAPPER
Rnor_6.01051,289,203 - 51,289,357NCBI
Rnor_5.01051,047,525 - 51,047,679UniSTS
RGSC_v3.41051,099,067 - 51,099,471RGD
RGSC_v3.41051,099,309 - 51,099,463UniSTS
RGSC_v3.11051,112,932 - 51,113,086RGD
Celera1048,660,568 - 48,660,722UniSTS
RH 3.4 Map10578.0UniSTS
RH 3.4 Map10578.0RGD
RH 2.0 Map10567.0RGD
SHRSP x BN Map1043.0299RGD
Flank 2: (D10Rat124)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21081,709,788 - 81,709,989 (+)MAPPER
Rnor_6.01084,596,193 - 84,596,393NCBI
Rnor_5.01084,389,455 - 84,389,655UniSTS
RGSC_v3.41085,484,402 - 85,484,602UniSTS
RGSC_v3.41085,484,401 - 85,484,602RGD
RGSC_v3.11085,498,771 - 85,498,972RGD
Celera1080,471,819 - 80,472,019UniSTS
RH 3.4 Map10744.2RGD
RH 3.4 Map10744.2UniSTS
RH 2.0 Map10906.5RGD
SHRSP x BN Map1058.54RGD
FHH x ACI Map1066.97RGD
Cytogenetic Map10q31UniSTS


1 to 10 of 163 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
631565Hcuc4Hepatic copper content QTL 44.15liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)106694181373452992Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat

1 to 10 of 163 rows


Note Type Note Reference