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Table 2 Significant genome-wide (*) and chromosome-wide associations for serum lipid traits detected with three different mixed-model approaches 1

From: A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants

EMMAX

Trait

CHR

N

SNP

Reg (Mb)

P

q

Bonf.

E

A1

MAF

LDL45

SSC3

3

ASGA0016334

124.6-124.8

2.82x10e-05

0.02

0.05

0.04

A

0.32

LDL190

SSC3

2

ASGA0016334

124.8

6.42x10e-06

0.006

0.02

0.05

A

0.32

CHOL45

SSC16

2

DRGA0015896

17.7

2.64x10e-05

0.01

0.03

-0.05

T

0.12

CHOL190

SSC3

3

ASGA0016334

124.6-124.8

6.82x10e-06*

0.01

0.006

0.03

A

0.32

SSC6

5

ASGA0029689

135.0-135.4

1.32x10e-05*

0.01

0.03

-0.03

G

0.36

TRIG190

SSC6

4

ASGA0101719

10.2-10.7

6.9x10e-05

0.03

0.1

0.06

G

0.36

6

ASGA0089937

135.0-135.4

4.48x10e-06

0.006

0.01

0.06

A

0.34

GEMMA

LDL45

SSC3

3

ALGA0021216

124.6-124.8

1.51x10e-05

0.01

0.03

-0.05

A

0.33

SSC10

5

ASGA0097841

2.5-2.9

1.90x10e-04

0.03

0.25

0.04

G

0.47

5

MARC0064247

18.2-19.3

1.77x10e-05

0.01

0.02

0.06

A

0.34

SSC13

1

ALGA0074022

215.0

1.68x10e-05

0.05

0.05

0.09

G

0.07

LDL190

SSC3

2

ALGA0021216

124.8

4.03x10e-06

0.007

0.01

-0.05

A

0.33

CHOL45

SSC3

3

ALGA0021216

124.8-133.5

4.40x10e-05

0.03

0.08

-0.04

A

0.33

SSC10

2

MARC0064247

19.2

5.73x10e-05

0.04

0.07

0.04

A

0.34

SSC16

2

ASG A0072378

17.7

1.50x10e-05

0.01

0.02

0.05

G

0.12

CHOL190

SSC3

2

ALGA0021216

124.8

4.53x10e-06*

0.004

0.01

-0.04

A

0.33

SSC6

5

INRA0022506

135.0-135.4

6.82x10e-06*

0.01

0.02

0.03

A

0.36

TRIG190

SSC6

4

MARC0042729

10.2-10.7

8.68x10e-05

0.03

0.21

-0.07

A

0.36

1

ASGA0106002

68.1

1.79x10e-04

0.04

0.44

-0.07

A

0.43

6

ASGA0089937

135.0-135.4

3.95x10e-06

0.01

0.01

-0.07

A

0.35

GenABEL 2

LDL45

SSC3

2

ASGA0016334

124.8

1.76x10e-05

0.01

0.03

-0.51

A

0.32

SSC13

1

ALGA0074022

215.0

1.28x10e-05

0.03

0.03

0.94

G

0.06

LDL190

SSC3

2

ASGA0016334

124.8

6.97x10e-06

0.006

0.01

-0.85

A

0.32

CHOL45

SSC16

2

DRGA0015896

17.7

4.06x10e-05

0.02

0.05

0.43

T

0.12

CHOL190

SSC3

2

ASGA0016334

124.8

7.39x10e-06*

0.007

0.01

-0.54

A

0.32

SSC6

5

ASGA0029689

135.0-135.4

1.26x10e-06*

0.001

0.003

0.58

G

0.36

TRIG45

SSC10

1

MARC0003307

38.0

3.12x10e-05

0.04

0.04

-0.95

A

0.32

TRIG190

SSC6

7

ASGA0089937

135.0-136.1

2.30x10e-06

0.003

0.005

-0.88

A

0.34

HLD45

SSC18

5

ALGA0096968

9.8-12.2

6.68x10e-05

0.03

0.06

-1.74

C

0.21

2

MARC0006153

20.8-22.6

6.15x10e-05

0.03

0.05

-1.32

A

0.46

  1. 1N: Number of significant SNPs, CHR: chromosome, SNP: most significant SNP, Reg (Mb): region containing significant SNPs according to Ensembl (S.scrofa 10.2), P: nominal P-value, q: q-value with FDR ≤ 0.05, Bonf: Bonferroni-corrected P-value, E: allelic effect, A1: minority allele, MAF: frequency of the minority allele.
  2. 2In GenABEL, allele effects are corrected dividing by the GRAMMAR-gamma factor, thus, their magnitudes are greater than the effects estimated with GEMMA and EMMAX [23].