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Table 2 QTL regions for each of the trait. Top SNP for each QTL are shown including position, -log10(p)-values, minor allele frequency (MAF), gene information, annotation of the top SNP, allele substitution effect (b.value) and standard error for b.value (SE)

From: Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

CHR

Start (bp)

End (bp)

Length of the QTL region (bp)

Significant SNPs in region

No of genes with significant SNPs within the QTL region

Top SNP

Position of the top SNP (bp)

- log10(p)

MAF

Gene

Annotation of the top SNP

b.value

SE

Fat yield

             

 5

92,372,732

94,425,668

2,052,936

330

3

rs209818856

93,945,694

27.49

0.38

MGST1

intron variant

−2.807

0.253

 14

1,448,510

2271832

823,322

509

49

rs136783505

1,807,140

42.01

0.07

DGAT1/HSF1

downstream variant/intron variant

−6.709

0.484

 23

28,567,796

28,591,530

23,734

5

1

rs381390819

28,567,796

9.36

0.45

TRIM26

intron variant

1.148

0.184

 25

8,222,347

11,507,986

3,285,639

883

16

rs379546164

9,870,005

14.40

0.24

CLEC16A

intron variant

−1.769

0.224

 25

36,226,978

36,227,132

154

2

 

rs109480808

36,226,978

8.72

0.16

 

intergenic variant

1.635

0.272

 26

22,144,777

24,793,744

2,648,967

595

32

rs438420348

24,379,571

14.28

0.16

NEURL1

intron variant

−2.273

0.290

 26

44,802,991

44,802,991

0

1

 

rs135624939

44,802,991

9.72

0.28

 

intergenic variant

−1.474

0.231

Milk yield

             

 5

112,343,204

11,2450,860

107,656

2

1

rs383553819

112,343,204

8.70

0.36

MKL1

intron variant

1.437

0.239

 14

1,448,510

2,271,832

823,322

455

48

rs133033480

1,743,939

33.01

0.09

CPSF1/ADCK5

downstream variant/splice region variant, intron variant

6.266

0.513

 16

1,322,611

1,322,611

0

1

1

rs108979795

1,322,611

8.58

0.28

LAX1

upstream variant

−1.451

0.243

 19

61,447,138

61,449,096

1958

5

 

rs210324693

61,449,096

8.93

0.32

 

intergenic variant

1.490

0.244

 20

30,531,217

32,952,019

2,420,802

74

5

rs385640152

31,909,478

15.56

0.11

GHR

missense variant

−3.877

0.472

 20

37,766,226

39,183,141

1,416,915

34

3

NA

38,828,254

9.54

0.16

 

intergenic variant

−2.250

0.356

 25

2,669,704

2,669,704

0

1

 

rs209691835

2,669,704

9.21

0.13

 

intergenic variant

−2.855

0.460

 25

3,494,706

3,516,671

21,965

13

4

rs110749311

3,498,960

9.32

0.41

PAM16/GLIS2

downstream variant

1.225

0.196

Protein yield

             

 5

112,450,860

112,450,860

0

1

 

rs109041054

112,450,860

8.88

0.48

 

intergenic variant

−1.473

0.242

 14

1,802,667

1,802,667

0

1

2

NA

1,802,667

8.52

0.06

DGAT1/HSF1

intron variant/downstream variant

3.354

0.564

 25

1,094,996

1,257,612

162,616

12

3

rs136085792

1,103,856

10.83

0.22

UNKL

intron variant

1.694

0.250

 25

3,306,363

3,516,671

210,308

40

8

rs110749311

3,498,960

11.70

0.41

PAM16/GLIS2

downstream variant

1.427

0.202