Scl58 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Scl58 (Serum cholesterol level QTL 58) Rattus norvegicus

Symbol: Scl58
Name: Serum cholesterol level QTL 58
RGD ID: 2290451
Previously known as: Total cholesterol QTL 10; TC-10
Trait: blood cholesterol amount   (VT:0000180)    
Measurement Type: plasma total cholesterol level   (CMO:0000585)    
LOD Score: 3.48
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21112,831,046 - 25,121,472RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01111,367,306 - 44,444,347RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01115,035,502 - 47,637,447RGDRnor5.0
RGSC_v3.41112,965,570 - 43,157,054RGDRGSC3.4
RGSC_v3.11112,965,570 - 43,214,643RGD
Cross Type: intercross
Strains Crossed: SR/JrHsd SS-Tg(ApoC3-CETP)53Opaz 
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

Clinical Measurement

Experimental Condition

Measurement Method

Vertebrate Trait

Rat Strain

References

References - curated
# Reference Title Reference Citation
1. Genome-wide scan for interacting loci affecting human cholesteryl ester transfer protein-induced hypercholesterolemia in transgenic human cholesteryl ester transfer protein F2-intercross rats. Herrera VL, etal., J Hypertens. 2007 Aug;25(8):1608-12.
Related QTLs

Related QTL Description Reference
SCL37_H maps to syntenic region RGD:2290428


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
620167Robo2roundabout guidance receptor 2111252894914096726Rat
41205137LOC120095537uncharacterized LOC120095537111310651913110886Rat
41303579LOC120095760small nucleolar RNA SNORA17111322574413225871Rat
40981328Trnaa-agc31transfer RNA alanine (anticodon AGC) 31111355288213552953Rat
1589452Tent5b-ps1terminal nucleotidyltransferase 5B, pseudogene 1111372510613728086Rat
1310162Lipilipase I111418932314228992Rat
40969584LOC120095819U6 spliceosomal RNA111419558714195692Rat
1305195Rbm11RNA binding motif protein 11111423485114244092Rat
2319676Snrpe-ps3small nuclear ribonucleoprotein polypeptide E, pseudogene 3111436301514363571Rat
41327136LOC120095809U6 spliceosomal RNA111437012814370234Rat
3775Hspa13heat shock protein family A (Hsp70) member 13111437566914389853Rat
620926Samsn1SAM domain, SH3 domain and nuclear localization signals, 1111448452314534900Rat
41044926LOC120095752small nucleolar RNA SNORA17111475623914756370Rat
40982247LOC120095592uncharacterized LOC120095592111478952014811653Rat
11381419LOC108352292uncharacterized LOC108352292111481178414830208Rat
1311850Nrip1nuclear receptor interacting protein 1111489584314979490Rat
40959210LOC120095593uncharacterized LOC120095593111499880415011347Rat
40937056Rpl7-ps9ribosomal protein L7, pseudogene 9111535176315354240Rat
7613925LOC102556241uncharacterized LOC102556241111537164215380095Rat
7690081LOC102548078uncharacterized LOC102548078111554318415560750Rat
40997737LOC120095594uncharacterized LOC120095594111559600015602092Rat
1309003Usp25ubiquitin specific peptidase 25111560365415711356Rat
9119122LOC103693508uncharacterized LOC103693508111587174916295079Rat
41187853LOC120095539uncharacterized LOC120095539111606394616069167Rat
2325580Mir99amicroRNA 99a111620044316200523Rat
2325435Mirlet7c1microRNA let-7c-1111620116316201256Rat
4888572Mir3588microRNA 3588111624561116245716Rat
2325575Mir125b2microRNA 125b-2111624562016245707Rat
1586139Sord-ps2sorbitol dehydrogenase, pseudogene 2111639227316394420Rat
11369037LOC108352294uncharacterized LOC108352294111641274716425621Rat
41319938LOC120095805U6 spliceosomal RNA111665509016655196Rat
7521170LOC102546782uncharacterized LOC102546782111682631516831065Rat
40966767LOC120095757small nucleolar RNA SNORA17111691977616919914Rat
41087675LOC120095595uncharacterized LOC120095595111693245316939866Rat
619794CxadrCXADR, Ig-like cell adhesion molecule111698286417030078Rat
2226Btg3BTG anti-proliferation factor 3111703015617046069Rat
41011570LOC120095596uncharacterized LOC120095596111710390017113835Rat
1563888C11h21orf91similar to human chromosome 21 open reading frame 91111722912917262307Rat
40952789LOC120095597uncharacterized LOC120095597111742449717510872Rat
1597043Hspa8-ps31heat shock protein family A (Hsp70) member 8, pseudogene 31111746669117468736Rat
1309885Chodlchondrolectin111765413717676450Rat
1311046Tmprss15transmembrane serine protease 15111767774117802255Rat
1585829Rpl27l3ribosomal protein L27 like 3111797005117970433Rat
1333570Or5b129-ps1olfactory receptor family 5 subfamily B member 129, pseudogene 1111801405118014958Rat
41156026LOC12009558440S ribosomal protein S18-like111847231118473770Rat
9135017LOC10369351040S ribosomal protein S6 pseudogene111874827418748918Rat
41256742LOC120095558uncharacterized LOC120095558111876089718767970Rat
41129591LOC120095753small nucleolar RNA SNORA17111887893618879060Rat
41203619LOC120095598uncharacterized LOC120095598111887958818880497Rat
41115113LOC120095718U6 spliceosomal RNA111957838019578477Rat
1597984Pcbp2-ps8poly(rC) binding protein 2, pseudogene 8111969395819697409Rat
1303131Ncam2neural cell adhesion molecule 2112010497420592168Rat
6499722Tmem258-ps5transmembrane protein 258, pseudogene 5112060280420603028Rat
1586138Pes1-ps1pescadillo ribosomal biogenesis factor 1, pseudogene 1112153064721532896Rat
1583562LOC681129triosephosphate isomerase 1 pseudogene112204586522046777Rat
7499203LOC102551587uncharacterized LOC102551587112209068322134713Rat
1583549Rpl32-ps15ribosomal protein L32, pseudogene 15112229514722295534Rat
41054117LOC120095600uncharacterized LOC120095600112246683022530379Rat
1587389Eno1-ps22enolase 1, pseudogene 22112253904522541205Rat
11400799LOC108352387H/ACA ribonucleoprotein complex subunit 3 pseudogene112257400922574422Rat
41257749LOC120095802U4 spliceosomal RNA112287406422874217Rat
40969201LOC120095601uncharacterized LOC120095601112357849723607404Rat
41401168LOC120095602uncharacterized LOC120095602112362682523639139Rat
2324553Tmem126a-ps3transmembrane protein 126A, pseudogene 3112366809823671133Rat
10045371Mir155hgMir155 host gene112377346823775697Rat
7489038Mir155microRNA 155112377465423774718Rat
1591507Mrpl39mitochondrial ribosomal protein L39112377965523795146Rat
41165047LOC120095730small nucleolar RNA SNORA70112379736523797457Rat
1561692Jam2junctional adhesion molecule 2112383082023880071Rat
621376Atp5pfATP synthase peripheral stalk subunit F6112388159423889581Rat
1310802GabpaGA binding protein transcription factor subunit alpha112388858623917612Rat
2139Appamyloid beta precursor protein112401977424236584Rat
1359578Cyyr1cysteine and tyrosine rich 1112455762024664007Rat
41061186LOC120095815U6 spliceosomal RNA112466935824669464Rat
1598007Naca-ps1nascent polypeptide associated complex subunit alpha, pseudogene 1112471836724719061Rat
621241Adamts1ADAM metallopeptidase with thrombospondin type 1 motif, 1112493222724941068Rat
735196Adamts5ADAM metallopeptidase with thrombospondin type 1 motif, 5112500062725047205Rat
7712322LOC102552725uncharacterized LOC102552725112504870325055640Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
33899D11Mit4102112183661521836709Ratregion
34130D11Mgh6100111897620818976310Ratregion
35989D11Rat29145111342715713427302Ratregion
35989D11Rat29145111342715713427540Ratregion
35565D11Rat20143111647204716472185Ratregion
37070D11Rat28246111304993113050172Ratregion
35152D11Rat21180112455591124556101Ratregion
38678D11Rat40240111580806315808309Ratregion
38678D11Rat40240111580806315808402Ratregion
39440D11Rat77116111897199818972110Ratregion
41242D11Rat79156111352863213528786Ratregion
42942D11Rat116126111671706616717194Ratregion
42943D11Rat113248111325183513252084Ratregion
42944D11Rat112143111589081915890978Ratregion
42945D11Rat100214111818514118185343Ratregion
41734D11Rat101245111283104612831293Ratregion
44893D11Got13188111800153518001723Ratregion
44908D11Got16219112380721823807437Ratregion
44909D11Got14127112409693524097059Ratregion
44913D11Got10150111313823913138389Ratregion
66635D11Mco7130111337177013371898Ratregion
1633624D11Got101209111417408814174297Ratregion
1627743D11Got100199111483252614832721Ratregion
1640128D11Got140120111842970218429826Ratregion
1634394D11Got113130111480159814801728Ratregion
5039108RH127517213112499679924997012Ratregion
5037137A005R14123112493214624932269Ratregion
5025986RH130465181111767608617676267Ratregion
5028761RH142228177111437567914375856Ratregion
5031530AU048024204111296558612965787Ratregion
5031928AU046668256112462147424621734Ratregion
5035016Chodl361111766523017665591Ratregion
5035026Nrip1250111490108414901334Ratregion
5032447AI464149123111604709116047214Ratregion
5029797BF387369173112386149523861668Ratregion
5027509AW53635489111723652917236618Ratregion
5033103RH137609237112059165220591889Ratregion
5033205RH137970184111345999313460177Ratregion
5028039MHAa75g1.seq154111655658416556738Ratregion
5030941BE108355178112413337724133555Ratregion
5031075BE109239150111722952117229671Ratregion
5052145RH94865178112423627424236452Ratregion
5054181RH143077114111723374917233863Ratregion
5056795RH144585164111467507014675234Ratregion
5055271RH143705119112387744423877563Ratregion
5055443RH143804248112388569023885938Ratregion
5053547RH142712100111302989513029995Ratregion
5053625RH142757122111372718913727311Ratregion
5049882RH133736211112387871823878928Ratregion
5050950RH134352200111437338014373580Ratregion
5044220RH130478182112388165923882218Ratregion
5044764RH130790205112387970423879909Ratregion
5044338RH130545188112505643725056625Ratregion
5045416RH131165208112383387723834085Ratregion
5049630RH133591195111489594814896143Ratregion
5043654RH130150220112455766624557886Ratregion
5043684RH130167208112049557820495786Ratregion
5072112RH136658210112401765724017867Ratregion
5073898RH137702216111702030917020525Ratregion
5075610RH138693192112464627624646468Ratregion
5076608RH139274162111722922517229373Ratregion
5074890RH138277164111580943615809600Ratregion
5077786RH139959194112377562923775823Ratregion
5076496RH139209233112402007924020312Ratregion
5073272RH137340216111372782613728043Ratregion
5071842RH135316192111726120117261393Ratregion
5066608AU048257130112026089620261026Ratregion
5067574AU047663123111842970318429826Ratregion
5068192AU047293117111683106616831183Ratregion
5068392AU047174219112089351520893734Ratregion
5068652AU047016173111796733917967499Ratregion
5068920AU046841210111748877117488981Ratregion
5070326AF05306279111489923514899314Ratregion
5060102BF388494217112403059224030809Ratregion
5060736BF389056242112410888024109123Ratregion
5061974AW527929176111424386714244043Ratregion
5062654BF403704178112413675324136932Ratregion
5062868BE113128150111597199115972141Ratregion
5064520BI302245216111539530215395518Ratregion
5064528BI302296154111497724014977394Ratregion
5066528AU048303219111747327317473492Ratregion
5066542AU048295228112353362623533854Ratregion
5087193BQ193733203112499857424998777Ratregion
5087227AW530763155111724575517245910Ratregion
5089923AU049444257111588393015884187Ratregion
5083169BF390904205111351359013513795Ratregion
5083583BF391905147112432021124320358Ratregion
5090469AU049769192112281273722812929Ratregion
5090275AU049654151111701481817014969Ratregion
5085040AI23763098112493236524932463Ratregion
5090325AU049684219111609781716098037Ratregion
5081529BE117177199112384132723841526Ratregion
5502605RH1255380112401988524020033Ratregion
5504127Adamts10112493466924935861Ratregion
5500314GDB:185158282112402009224020374Ratregion
5500316GDB:185159326112402035424020680Ratregion
5502813JAM2122112387688823877010Ratregion
5501705NCAM2726112058681920587545Ratregion
5501702APP709112402002224020731Ratregion
10755482rs107338789111945620519456205Ratregion
Position Markers

Flank 1: (D11Rat101)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21112,831,046 - 12,831,293 (+)MAPPER
Rnor_6.01111,367,306 - 11,367,552NCBI
Rnor_5.01115,035,502 - 15,035,748UniSTS
RGSC_v3.41112,965,570 - 12,965,817RGD
RGSC_v3.41112,965,571 - 12,965,817UniSTS
RGSC_v3.11112,965,570 - 12,965,817RGD
Celera1112,855,183 - 12,855,429UniSTS
RH 2.0 Map11663.6RGD
SHRSP x BN Map112.5899RGD
Cytogenetic Map11p11UniSTS
Peak: (D11Mgh6)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21118,976,208 - 18,976,310 (+)MAPPER
Rnor_6.01119,016,272 - 19,016,371NCBI
Rnor_5.01122,660,494 - 22,660,593UniSTS
RGSC_v3.41119,445,919 - 19,446,020RGD
RGSC_v3.41119,445,921 - 19,446,020UniSTS
RGSC_v3.11119,445,919 - 19,446,020RGD
Celera1118,900,385 - 18,900,484UniSTS
RH 3.4 Map1170.7UniSTS
RH 3.4 Map1170.7RGD
RH 2.0 Map11359.6RGD
Cytogenetic Map11 RGD
Flank 2: (D11Mgh5)
Rat AssemblyChrPosition (strand)Source
Rnor_6.01144,444,112 - 44,444,347NCBI
Rnor_5.01147,637,212 - 47,637,447UniSTS
RGSC_v3.41143,156,819 - 43,157,054RGD
RGSC_v3.41143,156,820 - 43,157,054UniSTS
RGSC_v3.11143,214,409 - 43,214,643RGD
Celera1142,134,750 - 42,134,984UniSTS
RH 3.4 Map11311.1UniSTS
RH 3.4 Map11311.1RGD
RH 2.0 Map11309.5RGD
SHRSP x BN Map1113.8499RGD
Cytogenetic Map11 RGD


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111945620576331918Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111647204744285911Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111283104625121472Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
1600394Edcs1Endometrial carcinoma susceptibility QTL12.90.04uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)111897620824697116Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat


Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_cross_type intercross  
qtl_general S allele is responsible for the increase in total cholesterol level 2290428
qtl_general this region affects cholesterol metabolism as they house cholesteryl ester transfer protein interacting loci 2290428
qtl_general software used: Map Manager QTXb19 2290428
qtl_general environmental conditions: animals were fasted for 16 hours before the determination of lipid levels 2290428
qtl_general number of animals: 159 male hybrids derived by intercrossing the transgenic animals with SR/JrHsd 2290428
qtl_map spans 19.4 Mbp 2290428