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. 2013 May 7;14:307. doi: 10.1186/1471-2164-14-307

Table 5.

Details and allele frequencies of SNPs in the nine French cattle breeds, and genotypes in the three other samples

SNP
 SNP ID1
 Chromosome
 Position2
 Gene
 Alleles
 Frequency (allele 1)
 Genotype
          1/2   AUB BLA CHA HOL LIM MAN MON NOR SAL WAT BIS KOU
1
 rs43299525
 2
 29,938,364
 ENSBTAT00000038441
 T/C
  
 0.18
 0
 0.23
 0.28
 0.23
 0.17
 0.45
 0.25
 0.41
 T/T
 T/T
 T/T
2
 rs41255286
 3
 90,246,130
 ENSBTAT00000015460
 C/T
  
 0.23
 0.14
 0.18
 0.36
 0.27
 0.42
 0.45
 0.67
 0.14
 G/G
 G/G
 G/G
3
 rs43360668
 3
 100,666,640
 ENSBTAT00000003878
 T/C
  
 0.09
 1
 1
 0.04
 0.14
 0.17
 0.18
 0.25
 0.04
 G/G
 G/G
 G/G
4
 rs43414903
 4
 115,404,252
 ENSBTAT00000028347
 C/T
  
 0.18
 0.09
 0.27
 0.09
 0.14
 0.08
 0
 0.25
 0.09
 C/C
 C/C
 C/C
5
 rs43484023
 6
 109,946,655
 ENSBTAT00000060963
 G/C
  
 0.18
 0.32
 0.36
 0.14
 0.45
 0.25
 0.68
 0.17
 0.09
 G/C
 C/C
 C/C
6
 rs42722878
 8
 101,639,394
 ENSBTAG00000020243
 T/C
  
 0.18
 0.04
 0.36
 0.04
 0.59
 0.25
 0.41
 0.17
 0.04
 T/C
 C/C
 C/C
7
 rs42722887
 8
 101,642,585
 ENSBTAG00000020244
 G/A
  
 0.27
 0.09
 0.36
 0.04
 0.59
 0.25
 0.41
 0.17
 0.04
 G/A
 G/G
 G/G
8
 rs42722900
 8
 101,645,192
 ENSBTAG00000020245
 C/T
  
 0.04
 0.04
 0.14
 0
 0.41
 0.25
 0.27
 0.08
 0.04
 C/C
 C/C
 C/C
9
 rs42722901
 8
 101,645,255
 ENSBTAG00000020246
 C/T
  
 0.24
 0.09
 0.35
 0.04
 0.59
 0.25
 0.41
 0.17
 0.04
 C/T
 C/C
 C/C
10
 rs42306198
 8
 111,749,876
 ENSBTAT00000008586
 G/A
  
 0
 0.04
 0.09
 0.04
 0.18
 0
 0
 0.08
 0.04
 G/G
 G/G
  
11
 rs17870317
 9
 34,687,597
 ENSBTAT00000038044
 T/G
  
 0.33
 0.32
 0.45
 0.45
 0.41
 0.50
 0.32
 0.67
 0.32
 T/T
 T/T
 T/T
12
 rs17870361
 9
 61,258,934
 ENSBTAT00000015037
 C/T
  
 0.24
 0.14
 0.04
 0.73
 0.14
 0.17
 0.32
 0
 0.04
 C/C
 C/C
  
13
 rs43626955
 10
 51,842,959
 ENSBTAT00000007206
 A/C
  
 0.36
 0.41
 0.23
 0.14
 0.82
 0.92
 0.54
 0.17
 0.68
 A/C
 C/C
 C/C
14
 rs43626956
 10
 51,843,008
 ENSBTAT00000007207
 A/G
  
 0.36
 0.41
 0.23
 0.14
 0.82
 0.92
 0.54
 0.25
 0.68
 A/G
 G/G
 A/G
15
 rs43626957
 10
 51,843,101
 ENSBTAT00000007208
 A/G
  
 0.59
 0.50
 0.32
 0.27
 0.95
 1
 0.54
 0.25
 0.77
 A/G
 G/G
  
16
 rs42748012
 10
 90,111,114
 ENSBTAT00000016066
 C/T
  
 0.64
 0.50
 0.68
 0.77
 0.50
 0.33
 0.86
 0.33
 0.68
 T/T
 C/C
 C/C
17
 rs42738663
 10
 90,126,463
 ENSBTAT00000016067
 A/G
  
 0.36
 0.50
 0.32
 0.23
 0.50
 0.67
 0.14
 0.67
 0.32
 A/A
 G/G
 G/G
18
 rs42311164
 11
 47,748,651
 ENSBTAT00000005725
 G/C
  
 0.27
 0.36
 0.23
 0.14
 0.32
 0.67
 0.27
 0.42
 0.50
 G/G
 C/C
 C/C
19
 rs42613762
 13
 51,391,698
 ENSBTAT00000025981
 G/A
  
 0.73
 0.95
 0.70
 0.23
 0.68
 0.92
 0.54
 0.58
 0.86
  
 G/A
 G/A
20
 rs41255356
 13
 67,838,559
 ENSBTAT00000018669
 T/C
  
 0.36
 0.32
 0.73
 0.23
 0.54
 0.08
 0.27
 0.83
 0
 T/T
 T/C
  
21
 rs41774805
 15
 57,309,934
 ENSBTAT00000006638
 G/A
  
 0.27
 0.45
 0.27
 0.27
 0.64
 0.33
 0.36
 0.50
 0.50
 G/G
 G/G
 G/G
22
 rs41720009
 17
 68,389,438
 ENSBTAT00000053508
 A/G
  
 0.41
 0.41
 0.54
 0.27
 0.23
 0.08
 0.23
 0.25
 0.23
 G/G
 A/A
  
23
 rs41905209
 19
 25,255,424
 ENSBTAT00000061398
 C/T
  
 0.14
 0
 0.14
 0.59
 0.09
 0.17
 0
 0.08
 0
 C/C
 C/C
 C/C
24
 rs42803062
 19
 28,474,511
 ENSBTAT00000044661
 C/T
  
 0.36
 0.68
 0.59
 0.23
 0.59
 0.08
 0.73
 0.58
 0.54
 C/C
  
  
25
 rs41969933
 21
 19,283,173
 ENSBTAT00000014089
 C/T
  
 0.77
 0.68
 0.86
 0.36
 0.77
 0.67
 0.82
 0.58
 0.86
 C/C
 C/C
 T/T
26
 rs42013154
 22
 48,725,986
 ENSBTAT00000019339
 G/T
  
 0.27
 0.04
 0.14
 0.09
 0.36
 0.25
 0.23
 0
 0.14
 G/G
 G/G
  
27
 rs42016156
 22
 49,203,698
 ENSBTAT00000045850
 C/T
  
 0.56
 0.50
 0.65
 0.32
 0.82
 1
 0.86
 0.58
 0.68
 C/C
 C/C
  
28
 rs42015934
 22
 51,561,550
 ENSBTAT00000007217
 C/T
  
 0.23
 0.04
 0.14
 0.04
 0.04
 0.17
 0.18
 0.33
 0.09
 C/C
 C/C
 C/C
29
 rs42451508
 25
 21,535,844
 ENSBTAT00000008398
 G/A
  
 0.14
 0.09
 0.27
 0.04
 0.31
 0.83
 0.41
 0.33
 0.27
 G/G
 G/G
 G/G
30
 rs42174698
 29
 26,367,840
 ENSBTAG00000001660
 T/C
  
 0.36
 0.50
 0.91
 0.54
 0
 0.50
 0.04
 0
 0.41
  
 C/C
 C/C
31
 rs17871172
 29
 26,368,230
 ENSBTAG00000001661
 C/T
  
 0
 0.04
 0
 0
 0.04
 0
 0
 0.08
 0
 C/T
 C/C
 C/C
32
 rs42188070
 29
 45,033,799
 ENSBTAT00000023514
 C/T
  
 0.14
 0.09
 0.54
 0.14
 0.18
 0.25
 0.18
 0.25
 0.27
 C/C
 C/C
 C/C
33
 rs29024659
 X
 81,605,181
 ENSBTAG00000002585
 C/T
  
  
  
  
  
  
  
  
  
  
  
 C/C
 C/C
34
 rs55617351
 X
 141,005,664
 ENSBTAT00000029896
 G/A
  
  
  
  
  
  
  
  
  
  
 G/G
 A/A
 A/A
35
 rs55617145
 X
 141,005,870
 ENSBTAT00000029897
 C/A
  
  
  
  
  
  
  
  
  
  
 C/C
 A/A
 C/C
36
 rs55617174
 X
 141,005,964
 ENSBTAT00000029898
 A/T
  
  
  
  
  
  
  
  
  
  
 T/T
 T/T
  
Mean MAF (autosomes)             0.25 0.22 0.25 0.19 0.27 0.20 0.26 0.24 0.20      

1 rs number from dbSNP.

2 Position on the UMD3.1 cattle genome assembly.

AUB, Aubrac, BLA, Blonde d’Aquitaine, CHA, Charolais, HOL, Holstein, LIM, Limousin, MAN, Maine Anjou, MON, Montbéliarde, NOR, Normande, SAL, Salers, WAT, Watusi, BIS, European bison, KOU, Greater Koudou.