Bss49 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Bss49 (Bone structure and strength QTL 49) Rattus norvegicus

Symbol: Bss49
Name: Bone structure and strength QTL 49
RGD ID: 2293699
Trait: lumbar vertebra size trait   (VT:0010518)    
Measurement Type: lumbar vertebra trabecular cross-sectional area   (CMO:0001692)    
LOD Score: 5.61
P Value: 1.0E-4
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81216,135,029 - 52,308,831RGD_MAPPER_PIPELINE
mRatBN7.21210,474,137 - 46,669,029RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01215,908,900 - 52,716,770RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01217,789,999 - 54,450,796RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.41211,612,769 - 46,782,294RGD_MAPPER_PIPELINERGSC3.4
Cross Type: intercross
Strains Crossed: COP/OlaHsd DA/OlaHsd 
JBrowse: View Region in Genome Browser (JBrowse)
Model




  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratosteoporosis susceptibilityIAGP 2293455 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratabnormal bone strength susceptibilityIDA 2293455 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratlumbar vertebra trabecular cross-sectional area  IDA 2293455 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratcontrol condition  IDA 2293455 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratex vivo peripheral quantitative computed tomography  IDA 2293455 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49RatCOP/OlaHsd  IEA 2293455 RGD 
Bss49RatDA/OlaHsd  IEA 2293455 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bss49Ratlumbar vertebra size trait  IDA 2293455 RGD 


#
Reference Title
Reference Citation
1. Genetic loci affecting bone structure and strength in inbred COP and DA rats. Sun Q, etal., Bone. 2008 Mar;42(3):547-53. Epub 2007 Nov 28.


1 to 20 of 780 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
1598332Lmtk2lemur tyrosine kinase 2121042677210508750Rat
3222Ocmoncomodulin121053561910596705Rat
1306410Ccz1CCZ1 homolog, vacuolar protein trafficking and biogenesis associated121060106610624608Rat
1311893Rsph10bradial spoke head 10 homolog B121062743410675227Rat
1305483Pms2PMS1 homolog 2, mismatch repair system component121067681810701161Rat
40982078LOC120096114small nucleolar RNA SNORA51121068966410689796Rat
1560787Aimp2aminoacyl tRNA synthetase complex-interacting multifunctional protein 2121070119410710772Rat
70883Eif2ak1eukaryotic translation initiation factor 2 alpha kinase 1121071077110744597Rat
1586393Ankrd61ankyrin repeat domain 61121071890810723267Rat
1585013Aldoa-ps3aldolase, fructose-bisphosphate A, pseudogene 3121077795210779290Rat
1305231Usp42ubiquitin specific peptidase 42121080086410840785Rat
41127121LOC120095931collagen alpha-1(I) chain-like121080481010821511Rat
620399Cyth3cytohesin 3121084013710933792Rat
1561923Fam220afamily with sequence similarity 220, member A121099796911013962Rat
619755Rac1Rac family small GTPase 1121103702811057251Rat
1310193Daglbdiacylglycerol lipase, beta121105973211102170Rat
1304618Kdelr2KDEL endoplasmic reticulum protein retention receptor 2121113882011157117Rat
1310492Grid2ipGrid2 interacting protein121116656711203765Rat
1308389Zdhhc4zinc finger DHHC-type palmitoyltransferase 4121123086411244898Rat
1584479Ints15integrator complex subunit 15121124504511260170Rat

1 to 20 of 780 rows
1 to 20 of 1200 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
5060552BE110334150121061401910614169Ratregion
5026192RH131271200121062439410624594Ratregion
5082263BE119075158121064556110645719Ratregion
5080736RH141752202121067691910677121Ratregion
5502357RH124577138121071048010710618Ratregion
5078992RH140671197121071091510711112Ratregion
5063916BE120231163121072308110723244Ratregion
5053799RH142857119121073845810738577Ratregion
5059402BG377917131121078216310782294Ratregion
5083067BF390734209121079363910793848Ratregion
44940D12Got15270121080911110809378Ratregion
5084104AI01303399121081005310810152Ratregion
5073576RH137516922121083586110836783Ratregion
5032497D5Ertd591e213121083945210839665Ratregion
44948D12Got20234121091241010912644Ratregion
44941D12Got21274121095792810958202Ratregion
44944D12Got17131121098458710984718Ratregion
5051182RH134487189121099790710998097Ratregion
5079246RH140831220121105733911057559Ratregion
5025384RH128108211121105809911058310Ratregion
1 to 20 of 1200 rows

Peak: (D12Rat30)
Rat AssemblyChrPosition (strand)Source
GRCr81238,634,928 - 38,635,130 (+)Marker Load Pipeline
mRatBN7.21232,974,036 - 32,974,238 (+)MAPPER
Rnor_6.01238,408,800 - 38,409,001NCBI
Rnor_5.01240,289,899 - 40,290,100UniSTS
RGSC_v3.41234,112,682 - 34,112,883UniSTS
RGSC_v3.41234,112,589 - 34,112,949RGD
RGSC_v3.11233,976,070 - 33,976,271RGD
Celera1234,659,399 - 34,659,602UniSTS
RH 3.4 Map12585.8UniSTS
RH 3.4 Map12585.8RGD
SHRSP x BN Map1242.1099RGD
SHRSP x BN Map1242.1099UniSTS
Cytogenetic Map12q15UniSTS


1 to 10 of 70 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
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122308134044726024Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12931821612829686Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat

1 to 10 of 70 rows


Note Type Note Reference
qtl_cross_type intercross  
qtl_general allele: DA alleles cause stronger skeletal structure and strength 2293455
qtl_general number of animals used: 405 males and 423 females from F2 progeny 2293455
qtl_general software package: MAPMAKER/EXP 2293455
qtl_general measurement method: at 26 weeks of age lumbar 5 vertebrae was removed and frozen at -20oC, later slices were cut from lumbar spine and neural arch and measurements taken from pQCT images 2293455