Scl78 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Scl78 (Serum cholesterol level QTL 78) Rattus norvegicus

Symbol: Scl78
Name: Serum cholesterol level QTL 78
RGD ID: 10450825
Previously known as: f6-C (med. VLDL)
Trait: blood VLDL cholesterol amount   (VT:0005144)    
Measurement Type: blood low density lipoprotein cholesterol level   (CMO:0000053)    
LOD Score: 3.7
P Value: 0.01
Variance: 64.0
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2449,178,116 - 57,114,705RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0447,685,694 - 55,791,834RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0447,489,708 - 55,539,285RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.4446,657,899 - 55,370,202RGD_MAPPER_PIPELINERGSC3.4
Cross Type: Not Available
Strains Crossed: SHR.BN-(D8Mit5-D8Mgh6)/Ipcv BXH2/Cub 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
Experimental Data Annotations     Click to see Annotation Detail View

Experimental Condition

Measurement Method

Vertebrate Trait

Rat Strain

References

References - curated
# Reference Title Reference Citation
1. Genomic determinants of triglyceride and cholesterol distribution into lipoprotein fractions in the rat. Hodulova M, etal., PLoS One. 2014 Oct 8;9(10):e109983. doi: 10.1371/journal.pone.0109983. eCollection 2014.

Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
41283447LOC120102623small nucleolar RNA SNORA7244956519549565318Rat
2321181Nid2-ps1nidogen 2, pseudogene 144963262849633166Rat
7531073Kcnd2l1potassium voltage-gated channel subfamily D member 2 like 144977514649777251Rat
68393Kcnd2potassium voltage-gated channel subfamily D member 244977581250277746Rat
9383752LOC10369208160S ribosomal protein L3 pseudogene44999112250003764Rat
9374544Sdad1-ps1SDA1 domain containing 1, pseudogene 145000501450017758Rat
1311102Tspan12tetraspanin 1245031376850389246Rat
1310556Ing3inhibitor of growth family, member 345047795450505168Rat
1563491Cped1cadherin-like and PC-esterase domain containing 145051671250789651Rat
1562253Wnt16Wnt family member 1645082096850831380Rat
735193Fam3cFAM3 metabolism regulating signaling molecule C45083992950887276Rat
40966555Rps2-ps30ribosomal protein S2, pseudogene 3045118082051181483Rat
2323280Ddx50-ps1DExD-box helicase 50, pseudogene 145122310151296237Rat
3455Ptprz1protein tyrosine phosphatase, receptor type Z145139731651595220Rat
1310811Aassaminoadipate-semialdehyde synthase45160646151663136Rat
1593790Rps3-ps7ribosomal protein S3, pseudogene 745168221851683038Rat
9348766LOC10369208460S ribosomal protein L27 pseudogene45174224651742683Rat
1560480Fezf1Fez family zinc finger 145176275151766078Rat
1559440Cadps2calcium dependent secretion activator 245178041552309641Rat
1596695Rnf133ring finger protein 13345214058452143357Rat
1595417Rnf148ring finger protein 14845214579852152508Rat
11494192LOC108350675uncharacterized LOC10835067545230586952306706Rat
620735Tas2r118taste receptor, type 2, member 11845244920852450107Rat
61919Slc13a1solute carrier family 13 member 145256917952647126Rat
41390060Thrap3-ps3thyroid hormone receptor associated protein 3, pseudogene 345261899952623801Rat
1591364Impdh2-ps1inosine monophosphate dehydrogenase 2, pseudogene 145273881252740348Rat
4145674IqubIQ motif and ubiquitin domain containing45293176852993795Rat
3155Ndufa5NADH:ubiquinone oxidoreductase subunit A545299732753005685Rat
11519975LOC108350676uncharacterized LOC10835067645301133153070210Rat
727860Asb15ankyrin repeat and SOCS box containing 1545302155353050846Rat
1592092Lmod2leiomodin 245306742853075124Rat
735144WaslWASP like actin nucleation promoting factor45308353653132061Rat
41046683LOC120102245thymosin beta-10-like45316672153167501Rat
1564219Hyal6hyaluronoglucosaminidase 645323811853250783Rat
1303194Hyal4hyaluronidase 445325617953274819Rat
620547Spam1sperm adhesion molecule 145330274553312913Rat
1566275Hyal5hyaluronoglucosaminidase 545334110553412280Rat
41007128LOC120102673small nucleolar RNA SNORA1745338598353386111Rat
1590212Tmem229atransmembrane protein 229A45344028753445286Rat
40982331LOC120102560U4 spliceosomal RNA45344725653447395Rat
41116076LOC120102770small nucleolar RNA U345347260253472711Rat
41340465LOC120102695small nucleolar RNA SNORA1745369658653696709Rat
1590185Suv39h2-ps1SUV39H2 histone lysine methyltransferase, pseudogene 145377885553779842Rat
619848Gpr37G protein-coupled receptor 3745413886054160927Rat
1562696Pot1protection of telomeres 145420533054263137Rat
41278566LOC120102621U7 small nuclear RNA45424986854249928Rat
41203940LOC120102612U7 small nuclear RNA45424994254250003Rat
40965413LOC120102246uncharacterized LOC12010224645426329454267934Rat
41126584Rnu6-321RNA, U6 small nuclear 32145430365054303756Rat
11449079LOC108350678uncharacterized LOC10835067845431932854357983Rat
41236019LOC120102247uncharacterized LOC12010224745443222054444023Rat
1588991Tk1-ps1thymidine kinase 1, pseudogene 145476723154775827Rat
41096447LOC120102705small nucleolar RNA SNORA1745488282354882955Rat
2320107Snx11-ps1sorting nexin 11, pseudogene 145491521154915991Rat
41167571LOC120102158uncharacterized LOC12010215845547681655492390Rat
41153446LOC120102756U2 spliceosomal RNA45579655355796713Rat
619858Grm8glutamate metabotropic receptor 845580576256731690Rat
41002790LOC120102608small nucleolar RNA SNORA73 family45625815156258354Rat
40972881LOC120102759U2 spliceosomal RNA45645195256452095Rat
2314878Mir592microRNA 59245650528056505375Rat
1560157Zfp800zinc finger protein 80045679832656849766Rat
41034677LOC120102248uncharacterized LOC12010224845680319656805686Rat
1587791H3f3cl2H3 histone, family 3C like 245684980056862528Rat
40930852LOC120102657U1 spliceosomal RNA45695629256956455Rat
2319954Gcc1GRIP and coiled-coil domain containing 145703081757042682Rat
621278Arf5ARF GTPase 545703852157041447Rat
1303047Fscn3fascin actin-bundling protein 345704279757052224Rat
620433Pax4paired box 445705845357065995Rat
631340Snd1staphylococcal nuclease and tudor domain containing 145709520557494501Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
34282D4Mgh1513945669879056698927Ratregion
33656D4Mit99945664777656647873Ratregion
33757D4Mit224945711443257114705Ratregion
34967D4Rat1516245011984850119996Ratregion
39748D4Rat15715045406901054069154Ratregion
39918D4Rat15521944952467449524880Ratregion
38434D4Rat13413945275413852754255Ratregion
39980D4Rat15622144917811649178333Ratregion
40008D4Rat22422345136763751367850Ratregion
41846D4Rat25423345316451053164745Ratregion
43789D4Got3218945079114750791338Ratregion
43791D4Got2927544994382349944098Ratregion
43793D4Got3112645326282153262949Ratregion
60429D4Got14714645499159154991735Ratregion
60438D4Got3026345114149051141755Ratregion
60439D4Got3316245614286156143023Ratregion
1639418D4Got3616645700072657000890Ratregion
1639433D4Got30314845581475255814897Ratregion
1636528D2Got33213144970212349702153Ratregion
5039044RH12748019445299579452995988Ratregion
5036573AU04847316344995639549956437Ratregion
5036875AU04948417944968424349684422Ratregion
5033869RH14042318245413895154139133Ratregion
5026456RH13228420345344058153440784Ratregion
5027111GDB:131795414645195579551955941Ratregion
5027139A005W0915345050310950503262Ratregion
5025012AW55010813645178069051780826Ratregion
5033123RH13768112145194339751943518Ratregion
5030467BF39786514345177263651772779Ratregion
5030681BI30178415445287830552878465Ratregion
5028358RH6611815345344395853444111Ratregion
5055919RH14407823345015838950158622Ratregion
5055903RH14406910045139779651397896Ratregion
5058084AI07045121045685115456851364Ratregion
5059912BF40010516445308287653083040Ratregion
5052289MDB107115845027845150278609Ratregion
5057712BF38606316245154219951542361Ratregion
5047484RH13235420645299441152994617Ratregion
5047688RH13247121845256925852569476Ratregion
5047340RH13227119445027815550278349Ratregion
5040010RH12803821745308558053085797Ratregion
5042606RH12953621845293187652932094Ratregion
5042828RH12966915745704128957041446Ratregion
5075504RH13863215845176845251768610Ratregion
5074640RH13813318545027754550277730Ratregion
5076990RH13949619945083878050838979Ratregion
5079366RH14095521445704972457050283Ratregion
5079018RH14068620845498337654983584Ratregion
5078762RH14053724745679898756799234Ratregion
5072080RH13663918645083280550832991Ratregion
5074358RH13797117545154607551546250Ratregion
5074506RH13805615645692463756924731Ratregion
5067204AU04789812745038832050388447Ratregion
5068072AU04736515145328295553283106Ratregion
5068494AU04711217945694585856946037Ratregion
5069084AU04673520345700068757000890Ratregion
5065392BE11532117545412715054127325Ratregion
5065872AA96407821145704121057041421Ratregion
5066252PMC126259P312345178047751780600Ratregion
5082089BF40941910345415292354153026Ratregion
5082621BE11986419345179831551798508Ratregion
5083349AW52123318545159489951595084Ratregion
5088481AU04859519044995639549956437Ratregion
5084056AI17605314045709649357096633Ratregion
5084236AI23292019145680453856804729Ratregion
5084546AI41102322145256744052567660Ratregion
5085503AI23127617145308509753085268Ratregion
5090117AU04956028645226287852263163Ratregion
5082773BF39006719245002019450020385Ratregion
5503065Wnt1622845083098150831209Ratregion
5503067Wnt1618345083102650831209Ratregion
5507525REN11424324445673122156731465Ratregion
5507527REN11424024645673067156730917Ratregion
5507529REN11477525245682902256829274Ratregion
5507531REN11485919745684917056849367Ratregion
5507533REN11485826545684892256849187Ratregion
5507535REN11543925645701091357011169Ratregion
5503212ha2063161945686498456866603Ratregion
5504520PMC263877P1045261511352616079Ratregion
5506082UniSTS:498320116045027490850276068Ratregion
5506278G2054715345050310950503262Ratregion
5506135UniSTS:4984417145159430951594380Ratregion
5503003Fezf16545176573751765802Ratregion
5503097ARF59545703864657039263Ratregion
5503124ING3-179045049585550496645Ratregion
5500773stSG61372671745704143457042151Ratregion
5500452AI72259962545176366951764294Ratregion
5501325ECD1705139445684944256849836Ratregion
5505855UniSTS:4959549145416034554160436Ratregion
5506757G4521321245574503355745245Ratregion
Position Markers

Flank 1: (D4Rat156)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2449,178,116 - 49,178,333 (+)MAPPER
Rnor_6.0447,685,694 - 47,685,910NCBI
Rnor_5.0447,489,708 - 47,489,924UniSTS
RGSC_v3.4446,657,899 - 46,658,116RGD
RGSC_v3.4446,657,900 - 46,658,116UniSTS
RGSC_v3.1446,888,473 - 46,888,690RGD
Celera444,407,763 - 44,407,979UniSTS
RH 2.0 Map4360.6RGD
SHRSP x BN Map429.45RGD
Flank 2: (D4Mit2)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2457,114,432 - 57,114,705 (+)MAPPER
Rnor_6.0455,791,564 - 55,791,834NCBI
Rnor_5.0455,539,015 - 55,539,285UniSTS
RGSC_v3.4455,369,931 - 55,370,202RGD
RGSC_v3.4455,369,932 - 55,370,202UniSTS
RGSC_v3.1455,620,765 - 55,621,035RGD
RH 3.4 Map4304.7RGD
RH 3.4 Map4304.7UniSTS
Cytogenetic Map4q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)426775591168368347Rat
10450825Scl78Serum cholesterol level QTL 783.70.01blood VLDL cholesterol amount (VT:0005144)blood low density lipoprotein cholesterol level (CMO:0000053)44917811657114705Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
10450821Scl77Serum cholesterol level QTL 774.10.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450818Scl76Serum cholesterol level QTL 763.60.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41794699962946999Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45711443281266970Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat


Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_general number of animals used: 8-13 males, 4 month old from 15 PXO recombinant inbred strains 10402111
qtl_general software used: STATISTICA 10 CZ; ANOVA 10402111
qtl_general measurement method: 4 month old male rats were fed high-sucrose diet for 1 week; blood samples were taken from the tail vein after overnight fasting, lipoprotein fractions were determined by HPLC 10402111
qtl_general confidence interval: 48,953-50,153 Kbp 10402111
qtl_general 5 genes are present in this region 10402111
qtl_general 6th fraction of medium VLDL 10402111