Bmd38 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Bmd38 (Bone mineral density QTL 38) Rattus norvegicus

Symbol: Bmd38
Name: Bone mineral density QTL 38
RGD ID: 2293666
Trait: femur size trait   (VT:1000369)    
Measurement Type: femoral neck cortical cross-sectional area   (CMO:0001702)    
LOD Score: 4.4
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8513,731,153 - 43,590,997RGD_MAPPER_PIPELINE
mRatBN7.258,948,228 - 53,948,228RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.058,632,285 - 53,632,285RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0513,440,622 - 58,440,622RGDRnor5.0
RGSC_v3.458,464,827 - 40,137,122RGDRGSC3.4
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)
Bmd38Ratosteoporosis susceptibilityIAGP 2293456 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38Ratincreased bone mineral density susceptibilityIDA 2293456 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38Ratfemoral neck cortical cross-sectional area  IDA 2293456 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38Ratcontrol condition  IDA 2293456 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38Ratex vivo peripheral quantitative computed tomography  IDA 2293456 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38RatCOP/OlaHsd  IEA 2293456 RGD 
Bmd38RatDA/OlaHsd  IEA 2293456 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Bmd38Ratfemur 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 345 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
1560793Arfgef1ARF guanine nucleotide exchange factor 1589820619076326Rat
1307055Cspp1centrosome and spindle pole associated protein 1590771619192402Rat
1310301Cops5COP9 signalosome subunit 5591922339210498Rat
40943670Rnu6-1297RNA, U6 small nuclear 1297592263019226401Rat
1585679Ppp1r42protein phosphatase 1, regulatory subunit 42592271099274461Rat
1589398Tcf24transcription factor 24592746599282876Rat
1561068Mcmdc2minichromosome maintenance domain containing 2592919679337526Rat
7721328LOC102556004uncharacterized LOC102556004592960849316974Rat
41182145Snord87small nucleolar RNA, C/D box 87592974899297573Rat
620242Sgk3serum/glucocorticoid regulated kinase family, member 3593457619472243Rat
1586147Eef1g-ps4eukaryotic translation elongation factor 1 gamma, pseudogene 4594987619503171Rat
708520Vcpip1valosin containing protein interacting protein 1595342479560889Rat
1306940Mybl1MYB proto-oncogene like 1595829059618179Rat
1561849Vxnvexin596592139684684Rat
1308863Adhfe1alcohol dehydrogenase, iron containing, 1597059669732580Rat
1311403Rrs1ribosome biogenesis regulator 1 homolog597334869735119Rat
1560290Sntg1syntrophin, gamma 15998055010794666Rat
1585836Tra2a-ps3transformer 2 alpha, pseudogene 351010664210108431Rat
40974341LOC120103228U6 spliceosomal RNA51026308710263191Rat
1584848Hnrnpa1-ps5heterogeneous nuclear ribonucleoprotein A1, pseudogene 551085591210856695Rat

1 to 20 of 345 rows
1 to 20 of 456 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
40562D5Rat187176589482288948404Ratregion
42312D5Rat248239589591978959394Ratregion
5028037MHAa74a4.seq195589621528962347Ratregion
5086801BE114642152590453679045519Ratregion
5030849BE120681209591300579130266Ratregion
5044558RH130672201593459819346182Ratregion
42731D5Rat21598593596939359791Ratregion
43871D16Got27149594531439453292Ratregion
5036673AU048828256595295209529776Ratregion
5028208D1Mit296158595326129532770Ratregion
5053179RH142499109595407549540863Ratregion
5044696RH130751181596178119617992Ratregion
5043950RH130324207596592639659470Ratregion
5038908RH127402207597060739706280Ratregion
5054341RH143168202597156829715884Ratregion
5033849RH140347136597282889728424Ratregion
5089781AU049360167597725989772767Ratregion
41076D5Rat121194598232669823460Ratregion
5067124AU047949263598356469835906Ratregion
44552D9Wox21136598842169884268Ratregion
1 to 20 of 456 rows

Flank 1: (D5Rat187)
Rat AssemblyChrPosition (strand)Source
GRCr8513,731,153 - 13,731,329 (+)Marker Load Pipeline
mRatBN7.258,948,228 - 8,948,404 (+)MAPPER
Rnor_6.058,632,285 - 8,632,460NCBI
Rnor_5.0513,440,622 - 13,440,797UniSTS
RGSC_v3.458,464,827 - 8,465,004RGD
RGSC_v3.458,464,828 - 8,465,003UniSTS
RGSC_v3.158,464,562 - 8,465,043RGD
Celera58,460,750 - 8,460,925UniSTS
SHRSP x BN Map53.55RGD
SHRSP x BN Map53.55UniSTS
FHH x ACI Map50.0RGD
Flank 2: (D5Rat3)
Rat AssemblyChrPosition (strand)Source
GRCr8543,590,825 - 43,590,997 (+)Marker Load Pipeline
RGSC_v3.4540,136,821 - 40,136,992UniSTS
RGSC_v3.4540,136,669 - 40,137,122RGD
RGSC_v3.1540,137,000 - 40,137,171RGD
Celera537,727,967 - 37,728,130UniSTS
RH 3.4 Map5191.1UniSTS
RH 3.4 Map5191.1RGD
RH 2.0 Map5227.9RGD
SHRSP x BN Map520.3999RGD
FHH x ACI Map521.34RGD


1 to 10 of 40 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
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat

1 to 10 of 40 rows


Note Type Note Reference
qtl_cross_type intercross  
qtl_general number of animals used: 405 males and 423 females from F2 progeny 2293456
qtl_general measurement method: at 26 weeks of age femur was removed and frozen at -20oC, later slices were cut from the femoral neck and cortical area (mm2) measurements taken from pQCT slices 2293456
qtl_general allele: COP alleles affect the hip structure 2293456
qtl_general software package: MAPMAKER/EXP 2293456