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Table 5 Genome-wide eQTL for 497 candidate genes expressed in the gluteus medius (GM) muscle of Duroc pigs

From: Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

Ensembl ID

SSC

N

SNP

Region (Mb)

q-value

B

δ ± SE

A1

MAF

ENSSSCG00000004064

1

27

rs81289665

5.69–10.57

4.34E−03

1.30E−02

− 0.45 ± 0.09

G

0.42

ENSSSCG00000004071

1

6

rs81278169

12.26–13.05

8.75E−04

8.75E−04

0.51 ± 0.09

A

0.40

ENSSSCG00000014432

2

1

rs80929229

149.45–149.45

3.71E−03

2.97E−02

− 0.47 ± 0.10

A

0.10

ENSSSCG00000014432

2

9

rs81290831

150.27–151.35

2.72E−03

1.91E−02

− 0.46 ± 0.09

A

0.11

ENSSSCG00000005976

4

6

rs80965603

14.33–15.13

1.55E−02

3.10E−02

0.24 ± 0.05

C

0.28

ENSSSCG00000005976

4

1

rs81261174

29.68–29.68

4.40E−02

3.08E−01

0.23 ± 0.05

C

0.29

ENSSSCG00000032907

4

3

rs80955389

89.79–89.95

4.01E−02

1.00E+00

− 0.24 ± 0.06

C

0.48

ENSSSCG00000032907

4

32

rs80977488

90.00–99.43

4.25E−04

4.25E−04

0.35 ± 0.06

G

0.36

ENSSSCG00000032907

4

4

rs80889119

103.32–103.47

4.01E−02

1.00E+00

0.31 ± 0.08

G

0.45

ENSSSCG00000033497

6

4

rs81388022

68.99–69.13

1.85E−02

7.41E−02

0.34 ± 0.07

C

0.23

ENSSSCG00000027659

6

25

rs81389074

80.81–82.56

8.02E−04

1.36E−02

− 0.30 ± 0.06

A

0.15

ENSSSCG00000038994

6

19

rs81389074

80.81–82.15

6.32E−03

1.14E−01

0.85 ± 0.18

A

0.15

ENSSSCG00000027659

6

2

rs81309503

111.39–111.40

3.98E−02

1.00E+00

− 0.26 ± 0.06

G

0.15

ENSSSCG00000025087

6

2

rs81393449

156.12–156.13

4.27E−02

8.55E−02

− 0.42 ± 0.09

A

0.09

ENSSSCG00000003844

6

3

rs81345502

157.59–158.65

1.13E−06

1.13E−06

0.30 ± 0.05

G

0.43

ENSSSCG00000003844

6

1

rs81333128

162.74–162.74

2.37E−02

7.10E−02

0.21 ± 0.04

A

0.34

ENSSSCG00000001455

7

12

rs339209635

23.40–26.06

9.64E−03

1.98E−02

0.60 ± 0.12

A

0.49

ENSSSCG00000024596

8

1

rs81237638

37.96–37.96

1.60E−02

6.55E−01

− 0.33 ± 0.08

G

0.33

ENSSSCG00000024596

8

22

rs81402024

83.19–89.67

1.58E−02

1.23E−01

− 0.37 ± 0.08

C

0.37

ENSSSCG00000024596

8

39

rs81402439

90.31–99.95

1.58E−02

2.99E−01

0.34 ± 0.08

G

0.33

ENSSSCG00000024596

8

11

rs81310686

100.02–101.17

1.58E−02

4.81E−01

0.34 ± 0.08

A

0.31

ENSSSCG00000024596

9

1

rs81420190

14.32–14.32

4.59E−02

1.00E+00

− 0.30 ± 0.08

C

0.24

ENSSSCG00000015129

9

4

rs81408352

24.50–28.89

6.62E−03

1.28E−01

− 0.27 ± 0.06

G

0.10

ENSSSCG00000015129

9

28

rs81318704

35.15–39.98

6.62E−03

1.39E−01

− 0.25 ± 0.06

A

0.12

ENSSSCG00000015129

9

10

rs81410722

45.90–47.65

2.64E−05

5.28E−05

− 0.25 ± 0.04

G

0.17

ENSSSCG00000015129

9

3

rs81226448

54.24–54.49

2.97E−02

7.72E−01

− 0.15 ± 0.03

C

0.28

ENSSSCG00000015129

9

1

rs81412811

65.10–65.10

4.49E−02

1.00E+00

− 0.19 ± 0.05

C

0.12

ENSSSCG00000017895

12

9

rs81436670

50.91–53.86

4.50E−07

1.36E−06

0.40 ± 0.06

G

0.33

ENSSSCG00000023829

14

1

rs80875259

31.27–31.27

1.24E−06

3.74E−02

− 0.36 ± 0.07

G

0.42

ENSSSCG00000014791

17

1

rs81466737

47.44–47.44

9.17E−07

2.76E−02

0.33 ± 0.07

A

0.22

  1. SSC, Sus scrofa chromosome; N, number of SNPs significantly associated with the gene under study; SNP, corresponds to the most significant associated SNP; Region (Mb), region containing the SNPs significantly associated with the gene under study; P-value, nominal P-value of association between gene expression and SNP; q-value, q-value calculated with a false discovery rate approach; B, Bonferroni corrected P-values; δ, effect size of the marker and its standard error (SE); A1, minor allele; MAF, minor allele frequency
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Genetics Selection Evolution

ISSN: 1297-9686