Scl14 QTL Report (Rattus norvegicus) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
QTL Registration

QTL: Scl14 (Serum cholesterol level QTL 14) Rattus norvegicus

Symbol: Scl14
Name: Serum cholesterol level QTL 14
RGD ID: 1298089
Previously known as: Total cholesterol 1; Tc1
Trait: blood cholesterol amount   (VT:0000180)    
Measurement Type: plasma total cholesterol level   (CMO:0000585)    
LOD Score: 5.8
P Value: 4.0E-4
Variance: 12.0
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85114,131,300 - 159,131,300RGD_MAPPER_PIPELINE
mRatBN7.25108,845,856 - 153,845,856RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.05114,140,832 - 159,140,832RGD_MAPPER_PIPELINERnor6.0
Rnor_5.05117,929,881 - 162,929,881RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.45115,772,027 - 160,772,027RGD_MAPPER_PIPELINERGSC3.4
RGSC_v3.15115,777,253 - 160,777,253RGD
Cross Type: Not Available
Strains Crossed: SS/Hsd SR/Hsd 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Cyp4a2 is a candidate Gene for Scl14
Scp2 is a candidate Gene for Scl14


  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14RatHypercholesterolemia  IDA 737694 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14Ratincreased circulating cholesterol level  QTM 737694 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14Ratplasma total cholesterol level  IDA 737694 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14Ratfasting  IDA 737694 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14Ratplasma total cholesterol measurement test  IDA 737694 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14RatSR/Hsd  IEA 737694 RGD 
Scl14RatSS/Hsd  IEA 737694 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Scl14Ratblood cholesterol amount  IDA 737694 RGD 


#
Reference Title
Reference Citation
1. Genome-wide scan identifies novel QTLs for cholesterol and LDL levels in F2-intercross rats. Herrera VL, etal., Circ Res 2004 Mar 5;94(4):446-52. Epub 2004 Jan 22.


1 to 20 of 919 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
41215040LOC120102919uncharacterized LOC1201029195108831467108907138Rat
1560251Caap1caspase activity and apoptosis inhibitor 15109313253109414323Rat
40937684LOC120102920uncharacterized LOC1201029205109330329109338769Rat
621245Plaaphospholipase A2, activating protein5109428600109460373Rat
1359704Ift74intraflagellar transport 745109460372109563839Rat
1591722Lrrc19leucine rich repeat containing 195109494891109507948Rat
2325363Mir872microRNA 8725109539086109539166Rat
620980TekTEK receptor tyrosine kinase5109607077109733805Rat
1563332Eqtnequatorin5109734495109762048Rat
1311787Mysm1myb-like, SWIRM and MPN domains 15109761345109826652Rat
40989424LOC120103252small nucleolar RNA SNORA705109807447109807582Rat
41394229LOC120102921uncharacterized LOC1201029215109883550109887133Rat
2943JunJun proto-oncogene, AP-1 transcription factor subunit5109894175109897268Rat
6494360LOC100911221uncharacterized LOC1009112215109897523109949196Rat
7593337LOC102550339uncharacterized LOC1025503395110107244110110709Rat
40929618LOC120102923uncharacterized LOC1201029235110179996110186201Rat
41402458LOC120102924uncharacterized LOC1201029245110208856110225659Rat
41145702LOC120103235U1 spliceosomal RNA5110355813110355974Rat
1359429FggyFGGY carbohydrate kinase domain containing5110398866110786019Rat
9417869LOC103692418uncharacterized LOC1036924185110605125110712729Rat

1 to 20 of 919 rows
1 to 20 of 1309 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
2315222D16Nkg703195108885691108885972Ratregion
42319D5Rat2562405108938288108938528Ratregion
502793135.MMHAP28FLD5.seq1825109001682109001863Ratregion
60808D5Wox251475109050865109051012Ratregion
5028029MHAa43g3.seq1055109077085109077190Ratregion
43943D5Got361265109141749109141875Ratregion
5060104AI0723721835109346692109346875Ratregion
5084616AA8507361905109428866109429056Ratregion
5084018AI2324231105109497180109497290Ratregion
44552D9Wox211365109552936109552993Ratregion
5041180RH1287081995109563602109563801Ratregion
5075366RH1385531205109666343109666463Ratregion
69527D5Uwm292635109719127109719390Ratregion
5057098D5Lev121055109721675109721780Ratregion
5075302RH1385162185109732963109733181Ratregion
5072908RH1371231805109733610109733790Ratregion
5079796RH1412082095109783368109783577Ratregion
5081246RH1420509785109787740109788718Ratregion
7206270Mysm16175109793011109793628Ratregion
5084024AI4075721155109894371109894486Ratregion
1 to 20 of 1309 rows

Peak: (D5Mit13)
Rat AssemblyChrPosition (strand)Source
GRCr85136,631,198 - 136,631,402 (+)Marker Load Pipeline
mRatBN7.25131,345,754 - 131,345,958 (+)MAPPER
Rnor_6.05136,640,731 - 136,640,934NCBI
Rnor_5.05140,429,780 - 140,429,983UniSTS
RGSC_v3.45138,271,925 - 138,272,129RGD
RGSC_v3.45138,271,926 - 138,272,129UniSTS
RGSC_v3.15138,277,152 - 138,277,355RGD
Celera5129,894,089 - 129,894,292UniSTS
RH 3.4 Map5854.4UniSTS
RH 3.4 Map5854.4RGD
RH 2.0 Map5847.4RGD
Cytogenetic Map5 RGD


1 to 10 of 84 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
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat

1 to 10 of 84 rows


Database
Acc Id
Source(s)
NCBI Gene Scl14

Note Type Note Reference
qtl_gene candidate genes are syntenic in human homologues 737694
qtl_general QTL linkage was determined from brother, sister crosses of F2[SR/HsdxSS/Hsd] 737694