Bmd20 QTL Report (Rattus norvegicus) - Rat Genome Database
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QTL Registration

QTL: Bmd20 (Bone mineral density QTL 20) Rattus norvegicus

Symbol: Bmd20
Name: Bone mineral density QTL 20
RGD ID: 2293706
Trait: femur mineral mass   (VT:0010011)    
Measurement Type: total volumetric bone mineral density   (CMO:0001728)    
LOD Score: 4.3
P Value: 2.0E-4
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0613,122,958 - 21,165,729RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0623,080,221 - 31,059,317RGDRnor5.0
RGSC_v3.4613,286,615 - 19,901,481RGDRGSC3.4
Cross Type: intercross
Strains Crossed: COP/OlaHsd DA/OlaHsd 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Disease Annotations     Click to see Annotation Detail View
osteoporosis  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
Experimental Data Annotations     Click to see Annotation Detail View

Clinical Measurement

Experimental Condition

Vertebrate Trait

Rat Strain
COP/OlaHsd  (IEA)
DA/OlaHsd  (IEA)

References

References - curated
1. Alam I, etal., J Bone Miner Res. 2008 Feb 18;.

Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
620507Crnkl1crooked neck pre-mRNA splicing factor 161834922618351540Rat
628659Nrxn1neurexin 161388675715191660Rat
1304582Mtm1myotubularin 161882182118840449Rat
1304687Alkbh8alkB homolog 8, tRNA methyltransferase61887788518952773Rat
1304612Rasgrp3RAS guanyl releasing protein 362107263421171619Rat
1560460LOC316717protein serine-threonine phosphatase catalytic subunit PP-1c61808894218090200Rat
1310083Cwf19l2CWF19 like cell cycle control factor 261897061619037176Rat
1305486Fam98afamily with sequence similarity 98, member A62105132721065986Rat
1309234Uap1l2UDP-N-acteylglucosamine pyrophosphorylase 1-like 261775424817760364Rat
1564275RGD1564275similar to Zinc finger HIT domain containing protein 161860451518604951Rat
1334223Olr1844-psolfactory receptor pseudogene 184461666977016670518Rat
1583780Hspd1-ps11heat shock protein 1, pseudogene 1162044857920450778Rat
1583779LOC366558similar to suppression of tumorigenicity 1362091378020915080Rat
1583702LOC503015similar to L-lactate dehydrogenase A chain (LDH-A) (LDH muscle subunit) (LDH-M)62094851220949477Rat
1597093LOC366782similar to 60S ribosomal protein L761876852618769385Rat
1598336LOC301686similar to Glycogen [starch] synthase, muscle61547599015478206Rat
1598337LOC301683similar to Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I)61383464313836133Rat
1596478LOC685218similar to RRS1 ribosome biogenesis regulator homolog61878513218787785Rat
1597710LOC685173similar to carbonic anhydrase 1361870877518717266Rat
2319303LOC100361875Egln1 protein-like61877046118771948Rat
2320894LOC100361066ubiquitin-conjugating enzyme E2E 1-like61801357118014309Rat
6502562LOC100909597WW domain-containing adapter protein with coiled-coil-like61747778217542849Rat
6496868LOC100910710NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12-like61929977419301148Rat
6503465LOC100909413alpha-enolase-like61466598614668125Rat
6503641LOC100909448AP-2 complex subunit mu-like61466739214672392Rat
7521850LOC102550058uncharacterized LOC10255005861311253613185314Rat
7537420LOC102550908uncharacterized LOC10255090861459687014599498Rat
7516562LOC102552558xenotropic and polytropic retrovirus receptor 1-like61699915317048644Rat
7242712Crnkl1-ps1crooked neck pre-mRNA splicing factor 1, pseudogene 161834922618351540Rat
7613897LOC102550312uncharacterized LOC10255031261344714513462635Rat
7641963LOC102554832transmembrane protein 126A-like61901654519019635Rat
7676249LOC10254928060S ribosomal protein L32-like62112426821135919Rat
7707848LOC102550556uncharacterized LOC10255055661449677114504794Rat
7723359LOC102553826uncharacterized LOC10255382661880272918821510Rat
7666954LOC102550619polypyrimidine tract-binding protein 1-like61396740414012848Rat
7740587LOC102554743pantothenate kinase 3-like61892203618925972Rat
7670248LOC102553135uncharacterized LOC10255313561796530617970792Rat
7702192LOC102550208uncharacterized LOC10255020861324227013288148Rat
9230730LOC103692559high mobility group protein B3 pseudogene61409786914099320Rat
9290018LOC10369256060S ribosomal protein L10a pseudogene61429965714350180Rat
9255248LOC103692561uncharacterized LOC10369256161476162714783609Rat
11449343LOC108351325proline--tRNA ligase-like61819355518194576Rat
11366009LOC108351354MLV-related proviral Env polyprotein-like61381964613820258Rat
11447028LOC108351355uncharacterized LOC10835135561728393017287813Rat
11385383LOC108351176uncharacterized LOC10835117661575826115778363Rat
11480265LOC108351174uncharacterized LOC10835117461329938313331224Rat
11480659LOC108351175uncharacterized LOC10835117561572614115767729Rat
11495481LOC108351326peptidyl-prolyl cis-trans isomerase D pseudogene61999149819992899Rat
11508425LOC108351177uncharacterized LOC10835117761651460716518933Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
36344D12Mit1012161790460417904724Ratregion
37298D6Rat10521561988810319888321Ratregion
37410D6Rat10717962069621520696387Ratregion
37496D6Rat10815061610012016100257Ratregion
35507D6Rat4317262113329221133468Ratregion
35541D6Rat4716261434914114349286Ratregion
35653D6Rat4214562116559121165729Ratregion
35963D6Rat4614461312295813123101Ratregion
39622D6Rat15114961448552514485679Ratregion
38724D6Rat8622462069916920699402Ratregion
42321D6Rat21224961473831514738548Ratregion
44027D6Got918562116069121160875Ratregion
8693213rs10684487661357229613572296Ratregion
5036845AU04939424962083770520837953Ratregion
5024970AU02287420661834971018349915Ratregion
5025072RH12687218561346206913462267Ratregion
5055129RH14362228761834949218349778Ratregion
5050148RH13388918262107289621073077Ratregion
5054673RH14335914961405520414055352Ratregion
5041606RH12895418561883951418839698Ratregion
5067848AU04749923362050483420505066Ratregion
5068434AU04714715261923881319238964Ratregion
5064428BI30219017961928887219289050Ratregion
5087854AA43797213661775986917760004Ratregion
5088979AU04888221261854887818549089Ratregion
5081162RH14200019061516682715167016Ratregion
5503274UniSTS:23769822562106557221065796Ratregion
5506389UniSTS:47908653961834939918349937Ratregion
Position Markers

Flank 1: (D6Rat46)
Rat AssemblyChrPosition (strand)Source
Rnor_6.0613,122,958 - 13,123,101NCBI
Rnor_5.0623,080,221 - 23,080,364UniSTS
RGSC_v3.4613,286,616 - 13,286,759UniSTS
RGSC_v3.4613,286,615 - 13,286,759RGD
RGSC_v3.1613,286,615 - 13,286,759RGD
Celera64,866,677 - 4,866,820UniSTS
SHRSP x BN Map61.1499UniSTS
SHRSP x BN Map61.1499RGD
Peak: (D6Rat46)
Rat AssemblyChrPosition (strand)Source
Rnor_6.0613,122,958 - 13,123,101NCBI
Rnor_5.0623,080,221 - 23,080,364UniSTS
RGSC_v3.4613,286,616 - 13,286,759UniSTS
RGSC_v3.4613,286,615 - 13,286,759RGD
RGSC_v3.1613,286,615 - 13,286,759RGD
Celera64,866,677 - 4,866,820UniSTS
SHRSP x BN Map61.1499UniSTS
SHRSP x BN Map61.1499RGD
Flank 2: (D6Rat42)
Rat AssemblyChrPosition (strand)Source
Rnor_6.0621,165,591 - 21,165,729NCBI
Rnor_5.0631,059,179 - 31,059,317UniSTS
RGSC_v3.4619,901,342 - 19,901,481RGD
RGSC_v3.4619,901,343 - 19,901,481UniSTS
RGSC_v3.1619,904,295 - 19,904,434RGD
Celera619,556,115 - 19,556,253UniSTS
SHRSP x BN Map619.5099UniSTS
SHRSP x BN Map619.5099RGD


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6123620518Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6125048718Rat
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)613505323600274Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61312295821165729Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat


Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_cross_type intercross  
qtl_general allele: COP alleles affect the hip structure 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 volumetric BMD (mg/mm3 ) measurements taken from pQCT slices 2293456
qtl_general software package: MAPMAKER/EXP 2293456
qtl_general number of animals used: 405 males and 423 females from F2 progeny 2293456