Skip to main content

Table 3 Lead SNP from genome-wide associated regions for milk yield in Nordic Holstein cattle. Base positions are given as position in UMD 3.1.1 [49]

From: RETRACTED ARTICLE: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

BTA

base position

Imputation accuracy

Effect

–log10(p)

Region

Gene

Annotation

2

80753895

0.9454

1.13

9.95

79587952~ 80754103

NABP1 (near)

intergenic

3

56402959

0.9308

−1.36

11.68

56392727~ 56402961

ENSBTAG00000001873 (near)

intergenic

4

101547644

0.7008

−1.66

12.65

100921921~ 101547648

CHRM2 (near)

upstream

5

93953487

0.9726

−2.10

29.52

91953587~ 93953619

MGST1 (near)

upstream

5

23022794a

0.7617

1.38

12.93

21101742~ 23022797

EEA1 (near)

intergenic

5

85080296b

0.7619

−1.28

11.24

84425435~ 85080331

ENSBTAG00000009778 (near)

intergenic

6

88847595

0.9009

−1.78

21.61

88612186~ 88847596

GC (near)

intergenic

6

46901490a

0.7413

−1.28

11.45

46181675~ 46901554

SEL1L3 (near)

intergenic

6

38027010b

0.9950

−4.75

9.47

36909885~ 38027583

ABCG2

missense

7

65370850

0.9848

−1.36

13.58

65256765~ 65370922

GLRA1 (near)

intergenic

8

73877814

0.8453

−1.37

11.14

71877875~ 73877845

ENSBTAG00000010829 (near)

upstream

8

42062591a

0.9595

−1.27

10.07

40245362~ 42062776

KCNV2

intergenic

9

33478527

0.8801

−1.25

9.23

31790030~ 33478670

NUS1 (near)

intergenic

10

1989907

0.9469

−1.15

9.92

448434~ 1990092

ENSBTAG00000047622 (near)

intergenic

13

36822330

0.9933

−1.66

10.74

36663680~ 36822395

MPP7

Intron

14#

1802667

0.7975

5.98

178.35

1702853~ 1797137

DGAT1

Intron

14

67577503a

0.8898

−2.16

11.04

66624772~  67828111

OSR2

intergenic

15

54392611

0.9577

1.57

16.58

52771707~ 54393036

PPME1

Intron

16

28384260

0.9984

1.64

10.50

28012864~ 28384605

CNIH3 (near)

Intergenic

17

66510224

0.9438

1.83

11.63

66119023~ 66510712

CORO1C

Intron

18

46583346

0.9829

1.86

11.97

44583383~ 46583963

UPK1A (near)

upstream

19

27442452

0.7904

−1.26

9.71

26592355~ 27442492

bta-mir-497 (near)

upstream

20

29996719

0.9580

−2.95

31.02

27997007~ 29996870

MRPS30 (near)

intergenic

23

25076472

0.9797

−1.34

9.23

23690289~ 25076491

GCM1

Intron

26

37716420

0.9790

−1.43

12.28

36730021~  37966463

TRPA1

intergenic

28

34972377

0.9991

−1.29

9.81

33464705~ 34972672

ZMIZ1

intergenic

Total number of significant SNPs

57,808

  1. #Eight additional SNPs on chromosome 14 had same highest P value. a indicated this SNP was found on second round, b indicated this SNP was found on third round