Table 2 Significant intragenic SNPs above the Bonferroni genome-wide threshold of 0.05

BovineHD0100007623

rs137585939

4.43E-08

1

26254309

ROBO1

BovineHD0100040084

rs43273786

5.41E-08

1

141228619

NEK11

BovineHD0200004154

rs110997154

3.76E-08

2

15142189

SSFA2

BovineHD0300000560

rs110459674

inf

3

2612333

TADA1

BovineHD0300002104

rs110093914

1.87E-08

3

7276675

DDR2

BovineHD0300018913

rs42371455

1.87E-09

3

66866123

LPHN2

BovineHD0300023699

rs135870054

8.96E-10

3

87296944

ALG6

BovineHD0400026934

rs109307332

4.69E-08

4

98543003

PLXNA4

BovineHD0500003126

rs134685896

3.26E-10

5

12834395

ACSS3

BovineHD0700010213

rs133885406

4.73E-08

7

33526558

HSD17B4

BovineHD0900019961

rs136413030

3.70E-08

9

73355572

VNN1

BovineHD1000004333

rs43612234

5.32E-10

10

12722576

MEGF11

BovineHD1000009424

rs43623003

6.65E-08

10

28079552

MIR2284Z-1

BovineHD1000009428

rs110034517

5.56E-09

10

28102288

MIR2284Z-1

BovineHD1000017503

rs42486408

1.16E-09

10

60793897

TRPM7

BovineHD1100003814

rs109489659

5.53E-12

11

11771322

CCT7

BovineHD1300006368

rs109943824

1.12E-08

13

20845530

PLXDC2

BovineHD1300022672

rs41710487

4.53E-10

13

78416778

KCNB1

BovineHD1500008135

rs134980659

6.49E-08

15

28399876

THY1

Hapmap40064-BTA-36665

rs41631137

4.65E-12

15

33953859

PIK3C2A

BovineHD1500015036

rs41769292

5.15E-09

15

50730325

NUP98

BovineHD1500015037

rs134338365

2.50E-10

15

50733648

NUP98

BTB-00604170

rs41769258

5.84E-10

15

50753778

NUP98

BovineHD1500015042

rs41769237

3.41E-10

15

50765770

NUP98

BovineHD1500015044

rs109649273

6.55E-08

15

50769861

NUP98

BovineHD1500015047

rs41768429

7.66E-12

15

50774198

NUP98

BovineHD1500015049

rs41768423

1.42E-08

15

50780537

NUP98

BovineHD1500015051

rs41768414

6.94E-11

15

50784307

NUP98

BovineHD1500015054

rs41768364

7.12E-08

15

50792403

NUP98

BovineHD1500015055

rs109966062

1.99E-08

15

50795681

NUP98

BovineHD1500015056

rs41768379

9.17E-13

15

50799229

NUP98

BovineHD4100012071

rs136525289

7.93E-09

15

51638163

PDE2A

BTA-18105-no-rs

rs109715014

4.33E-09

15

62952170

CCDC73

BovineHD1600009946

rs41798963

4.62E-08

16

31290905

CEP170

BovineHD1600021693

rs41819133

7.33E-08

16

71743691

CAMK1G

BovineHD1700002750

rs110828704

1.11E-09

17

10472292

NR3C2

BovineHD1700018352

rs135157738

2.29E-09

17

64466089

RPH3A

BovineHD1700019237

rs110644998

2.43E-10

17

67344705

CORO1C

BovineHD1700019238

rs134453171

1.90E-09

17

67347843

CORO1C

BovineHD1700020721

rs109085689

4.61E-08

17

72364594

MTMR3

BovineHD1700021131

rs135044766

4.88E-08

17

73638738

DEPDC5

BovineHD1700021132

rs135814317

7.10E-08

17

73640453

DEPDC5

BovineHD1900006167

rs134967563

7.01E-10

19

20731168

SSH2

BovineHD4100014346

rs29017164

2.41E-13

19

57590345

ATP5H

BovineHD2100001405

rs133992914

6.47E-08

21

6826694

IGF1R

ARS-BFGL-NGS-10830

rs109014211

1.74E-09

21

14303664

SLCO3A1

BovineHD2200009526

rs110064285

8.84E-09

22

33753508

FAM19A1

BovineHD2200009645

rs135018045

3.20E-08

22

34006051

FAM19A1

BovineHD2200009658

rs133223316

5.38E-09

22

34051778

FAM19A1

BovineHD2300014695

rs110724706

4.60E-09

23

50469508

TUBB2B

BovineHD2500003334

rs42064606

1.77E-08

25

13011549

SHISA9

BovineHD2500003336

rs109087355

2.45E-09

25

13017281

SHISA9