Mcs12 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL: Mcs12 (Mammary carcinoma susceptibility QTL 12) Rattus norvegicus

Symbol: Mcs12
Name: Mammary carcinoma susceptibility QTL 12
RGD ID: 1598868
Previously known as: Mcs5a
Trait: mammary gland integrity trait   (VT:0010552)    
Measurement Type: mammary tumor number   (CMO:0000343)    
LOD Score: Not Available
P Value: 1.0E-4
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2558,973,449 - 60,051,321RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0560,225,095 - 61,370,302RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0564,739,245 - 65,886,550RGDRnor5.0
RGSC_v3.4561,238,737 - 62,299,211RGDRGSC3.4
Cross Type: Not Available
Strains Crossed: WF.WKY-(D5Wox8-D5Uwm62)/Uwm WF.WKY-(D5Uwm63-D5Uwm64)/Uwm 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Experimental Data Annotations    Click to see Annotation Detail View

Clinical Measurement
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
mammary tumor number  IDA 1559294 RGD 

Experimental Condition
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
7,12-dimethyltetraphene (DMBA)  IDA 1559294 RGD 

Measurement Method
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
in vivo visual assessment  IDA 1559294 RGD 

Rat Strain
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
WF.WKY-(D5Uwm63-D5Uwm64)/Uwm  IEA 1559294 RGD 
WF.WKY-(D5Wox8-D5Uwm62)/Uwm  IEA 1559294 RGD 

Vertebrate Trait
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
mammary gland integrity trait  IDA 1559294 RGD 

Disease Annotations     Click to see Annotation Detail View

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. Rat Mcs5a is a compound quantitative trait locus with orthologous human loci that associate with breast cancer risk. Samuelson DJ, et al., Proc Natl Acad Sci U S A. 2007 Apr 2; 104(15):6299-304.
2. Fine mapping reveals multiple loci and a possible epistatic interaction within the mammary carcinoma susceptibility quantitative trait locus, Mcs5. Samuelson DJ, etal., Cancer Res. 2005 Nov 1;65(21):9637-42.
3. The non-protein coding breast cancer susceptibility locus Mcs5a acts in a non-mammary cell-autonomous fashion through the immune system and modulates T-cell homeostasis and functions. Smits BM, etal., Breast Cancer Res. 2011 Aug 16;13(4):R81.
4. Hormone replacement therapy: risks and benefits. Whitcroft SI and Stevenson JC, Clin Endocrinol (Oxf). 1992 Jan;36(1):15-20.
Related QTLs

Related QTL Description Reference
Mcs23 sub_region RGD:1601189
Mcs24 sub_region RGD:1601189


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
1304730Dcaf10DDB1 and CUL4 associated factor 1055960779559647209Rat
1304739Exosc3exosome component 355957384959579065Rat
1305190Slc25a51solute carrier family 25, member 5155965022759663454Rat
1307367Zbtb5zinc finger and BTB domain containing 555924413259265461Rat
1310467Zcchc7zinc finger CCHC-type containing 755899255859173308Rat
1305229Frmpd1FERM and PDZ domain containing 155944307659545125Rat
1305465Fbxo10F-box protein 1055929701659343429Rat
1308851Grhprglyoxylate and hydroxypyruvate reductase55923417959243614Rat
1565773Polr1eRNA polymerase I subunit E55927945659295346Rat
1310735Trmt10btRNA methyltransferase 10B55954884559572529Rat
1565350ShbSH2 domain containing adaptor protein B55967806659785443Rat
1586079LOC366365hypothetical LOC36636555960217759607812Rat
1596808Tomm5translocase of outer mitochondrial membrane 555936236059365217Rat
9246609LOC103692348uncharacterized LOC10369234855991124059915448Rat
9330186LOC10369234660S ribosomal protein L24 pseudogene55937347759374019Rat
9455316Pgam1-ps8phosphoglycerate mutase 1, pseudogene 855959321759593995Rat
41380328LOC120103148uncharacterized LOC12010314855939229559395154Rat
41206741LOC120102863uncharacterized LOC12010286355921362759226603Rat
41200968LOC120102864uncharacterized LOC12010286455947188159475003Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
34322D5Mgh1014155979339959793528Ratregion
66639D5Mco1526755939345159393701Ratregion
1581988D5Uwm6224555897344958973694Ratregion
1582038D5Uwm6427456005104760051321Ratregion
1640185D5Got31523255944884359449075Ratregion
5032359AI59350110755957397459574081Ratregion
5054185RH14307911155964445259644563Ratregion
5055731RH14397012255916050259160624Ratregion
5046862RH13199719555990586959906064Ratregion
5047210RH13219721155924420359244414Ratregion
5072540RH13690819655917295459173150Ratregion
5072780RH13704916055917257559172735Ratregion
5074606RH13811413155926419259264323Ratregion
5078086RH14013520655962895659629162Ratregion
5076524RH13922518355964461259644795Ratregion
5071174RH13493020655915753359157739Ratregion
5071174RH13493020655915753359157739Ratregion
5061094AW53223218255953275559532937Ratregion
5089451AU04916421855937693559377153Ratregion
5085728BQ20195021455964340359643617Ratregion
5081290RH14207520655957228159572487Ratregion
Position Markers

Flank 1: (D5Uwm62)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2558,973,449 - 58,973,694 (+)MAPPER
Rnor_6.0560,225,095 - 60,225,339NCBI
Rnor_5.0564,739,245 - 64,739,489UniSTS
RGSC_v3.4561,238,737 - 61,238,981UniSTS
Celera557,548,225 - 57,548,469UniSTS
Cytogenetic Map5 RGD
Flank 2: (D5Uwm64)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2560,051,047 - 60,051,321 (+)MAPPER
Rnor_6.0561,370,029 - 61,370,302NCBI
Rnor_5.0565,886,277 - 65,886,550UniSTS
RGSC_v3.4562,298,938 - 62,299,211UniSTS
Celera558,615,727 - 58,616,000UniSTS
Cytogenetic Map5 RGD


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
1598868Mcs12Mammary carcinoma susceptibility QTL 120.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)55897344960051321Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat


Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_general WF alleles associated with increased mammary tumor susceptibility in this region 1559294
qtl_statistics_details Kruskal-Wallis nonparametric test and ANOVA were used to analyze multiplicity data 1559294