Significant overlap between human genome-wide association-study nominated breast cancer risk alleles and rat mammary cancer susceptibility loci

Sanders, Jennifer; Samuelson, David J

doi:10.1186/bcr3607

Table 1 Location of rat mammary cancer susceptibility loci and human orthologous regions used in this study

From: Significant overlap between human genome-wide association-study nominated breast cancer risk alleles and rat mammary cancer susceptibility loci

Rat Mcslocus (Overlap)	Boundary markers	Rat chr	Region(UCSC rat assembly 2004)	Reference	Human orthologous region (UCSC human assembly 2009)
DMBA induced mammary carcinogenesis
*Mcs1a*	D2Mit29 to D2Uwm14	RNO2	5,601,528- 10,539,344	Haag et al. [17]	Chr5: 89,216,702-93,113,337
*Mcs1b*	ENSRNOSNP2740854 to g2Ul2-27	RNO2	42,364,155-44,195,382	DenDekker et al. [25]	Chr5: 54,816,178-57,003,049
*Mcs1c*	D2M13Mit286 to D2Uia5	RNO2	13,909,383- 20,666,092	Haag et al. [17]	Chr5: 81,891,633-86,857,442
*Mcs1c*	D2M13Mit286 to D2Uia5	RNO2	13,909,383- 20,666,092	Haag et al. [17]	Chr5: 86,171,198-86,251,067
*Mcs2* (overlaps Mcs6, Emca4)	D7rat39 to D7Uwm12	RNO7	4,936,704-86,028,057	Sanders et al. [18]	Ch12: 57,316,160-108,177,690
					Chr8: 97,242,984-115,650,989
					Chr19: 281,161-2,497,331
					Chr19: 15,059,910-15,808,112
*Mcs3*	D1Rat27 to D1Mit12	RNO1	90,282,174-156,954,117	Shepel et al. [15]	Chr15: 80,282,370-102,265,870
					Chr15: 25,574,935-28,567,541
					Chr11: 17,403,456-22,898,646
					Chr11: 74,958,193-89,350,902
					Chr19: 48,799,986-51,921,957
					Chr19: 28,701,413-30,656,003
*Mcs4*	D8Rat164 to D8Rat108	RNO8	28,414,100-72,403,639	Shepel et al. [15]	Chr11: 107,453,990-132,383,506
					Chr15: 62,105,069-76,028,735
					Chr15: 76,091,658-78,185,872
					Chr15: 78,380,119-78,998,961
					Chr15:51,349,646-51,942,505
*Mcs5a1(overlaps Mcstm1, Emca8*)	SNP-61634906 to SNP- 61666918	RNO5	61,634,727-61,666,739	Samuelson et al. [9]	Chr9: 37,562,516-37,589,491
*Mcs5 a2(overlaps Mcstm1, Emca8*)	SNP-61667232 to gUwm23-29	RNO5	61,667,053-61,751,614	Samuelson et al. [9]	Chr9: 37,590,988-37,654,512
*Mcs5b(overlaps Mcstm1, Emca8*)	gUwm50-20 to D5Got9	RNO5	65,498,190-67,464,050	Samuelson et al. [19]	Chr9: 103,492,712-105,220,552
*Mcs5c(overlaps Mcstm1, Emca8*)	gUwm74-1 to gUwm54-8	RNO5	81,118,457-81,295,367	Veillet et al. [26]	Chr9: 118,231,525-118,416,951
*Mcs5c(overlaps Mcstm1, Emca8*)	gUwm74-1 to gUwm54-8	RNO5	81,118,457-81,295,367	Veillet et al. [26]	Chr12: 72,033,141-72,033,263
*Mcs6(overlaps Mcs2*)	D7Rat171 to gUwm64-3	RNO7	22,382,725-55,384,873	Sanders et al. [18]	Chr12: 71,270,266-105,502,699
*Mcs7(overlaps Mcsta1*)	D10Got124 to gUwm58-136	RNO10	89,575,060-100,335,500	Cotroneo et al. [27]	Chr17: 40,183,547-67,946,104
*Mcs8*	D14Mit1 to D14Rat99	RNO14	12,386,493-26,416,791	Lan et al. [16]	Chr4: 65,556,457-81,559,483
*Mcsm1(overlaps Emca7*)	D6Mit9 to D6Rat12	RNO6	34,039,303-114,032,192	Lan et al. [16]	Chr14: 25,151,530-80,417,386
					Chr2: 334,41-18,603,019
					Chr7: 12,561,599-19,619,365
					Chr7: 107,770,320-111,916,436
*Mcstm1(overlaps Mcs5,Emca1, Emca8)*	D5rat124 to Pla2g2a	RNO5	19,206,257-157,657,360	Piessevaux et al. [21]	Chr1: 20,301,931-59,012,763
					Chr1: 59,119,520-67,602,141
					Chr9: 27,325,071-123,488,955
					Chr6: 87,792,854-100,245,025
					Chr8: 87,055,841-97,247,307
					Chr8: 58,994,818-62,700,945
*Mcstm2(overlaps Emca2*)	D18Wox8 to D18Rat44	RNO18	32,458,819-86,863,412	Piessevaux et al. [21]	Chr18: 10,202,644-13,129,349
					Chr18: 41,356,963-54,158,113
					Chr18: 54,267,924-58,201,561
					Chr18: 66,912,039-78,010,606
					Chr5: 112,300,500-130,363,372
					Chr5: 142,780,151-147,624,793
					Chr5:147,647,196-150,176,352
*Mcsta1(overlaps Mcs7*)	D10Rat91 to D10Rat97	RNO10	9,762,188-108,776,963	Piessevaux et al. [21]	Chr5: 130,482,861-173,663,969
					Chr5: 177,530,539-180,675,650
					Chr17: 690,639-15,624,409
					Chr17: 16,916,926-20,222,700
					Chr17: 25,525,650-78,247,249
					Chr16: 78,402-6,094,950
β -estradiol induced mammary carcinogenesis
*Emca1(overlaps Mcstm1, Emca8*)	D5Rat53 to D5Rat57	RNO5	103,677,474-155,121,024	Gould et al. [22]	Chr1: 23,607,020-59,012,763
					Chr1: 59,119,520-67,602,141
					Chr9: 17,037,252-27,300,264
*Emca2(overlaps Mcstm2*)	D18Rat27 to D18Rat43	RNO18	18,562,643-66,652,947	Gould et al. [22]	Chr5: 110,259,180-130,363,372
					Chr5: 137,224,929-147,624,793
					Chr5: 147,647,196-150,176,352
					Chr18: 10,202,644-13,129,349
					Chr18: 35,982,130-41,016,602
					Chr18: 52,597,120-54,158,113
					Chr18: 54,267,924-58,201,561
					Chr2: 127,805,417-128,786,719
*Emca4(overlaps Mcs2*)	D7Rat44 to D7Rat15	RNO7	66,201,980-107,428,439	Schaffer et al. [23]	Chr8: 97,242,984-137,409,536
*Emca4(overlaps Mcs2*)	D7Rat44 to D7Rat15	RNO7	66,201,980-107,428,439	Schaffer et al. [23]	Chr12: 57,316,160-59,093,375
*Emca5*	D3Rat227 to D3Rat210	RNO3	41,054,012-171,063,335	Schaffer et al. [23]	Chr20: 1,746,912-62,907,504
					Chr2: 110,841,402-113,650,057
					Chr2: 159,530,076-188,395,371
					Chr11: 26,296,319-57,753,858
					Chr15: 32,905,485-34,664,466
					Chr15: 34,933,152-51,298,144
*Emca6*	D4Rat14 to D4Rat202	RNO4	41,729,583-159,115,617	Schaffer et al. [23]	Chr7: 23,252,368-33,103,107
					Chr7: 115,026,301-150,558,396
					Chr3: 88,756-12,883,445
					Chr3: 13,004,609-15,163,132
					Chr3: 64,018,604-75,322,612
					Chr3: 125,977,400-128,219,297
					Chr2: 68,713,643-89,165,869
					Chr4: 89,504,626-95,273,083
					Chr4: 120,978,632-122,320,931
					Chr12: 156,786-2,821,588
					Chr10: 43,277,230-46,218,580
*Emca7(overlaps Mcsm1*)	D6Rat68 to D6Rat81	RNO6	2,802,670-111,967,837	Schaffer et al. [23]	Chr14: 25,151,530-78,362,253
					Chr2: 33,441-35,642,893
					Chr2: 38,644,737-51,698,454
					Chr7: 12,561,599-19,619,365
					Chr7: 105,197,211-111,916,436
*Emca8(overlaps Mcs5, Mcstm1, Emca1*)	D5Rat134 to D5Rat37	RNO5	52,434,178-148,460,381	Schaffer et al. [23]	Chr9: 6,756,013-27,300,264
					Chr9: 27,925,947-123,488,955
					Chr1: 33,159,021-59,012,763
					Chr1: 59,119,520-67,602,141

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