Skip to main content

Table 2 SNPs within candidate genes used for association analysis

From: Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14

Gene Name

SNP name

Location

Allelesa

MAFb

Pc

%vard

Versican

VCAN_1

Exon 8

A/G

0.45

n.s.

0.2

Versican

VCAN_2

Exon 8

G/A

0.45

n.s.

0.4

Versican

VCAN_3

Exon 8

T/G

0.45

n.s.

0.4

Versican

VCAN_4

Exon 8

C/T

0.45

n.s.

0.2

Versican

VCAN_5

Exon 8

C/A

0.38

n.s.

0.4

Versican

VCAN_6

Exon 8

C/T

0.38

n.s.

0.4

Leukemia inhibitory factor

LIF_1

Intron 1

A/G

0.47

0.001

8.6

Matrix metallopeptidase 13

MMP13_1

Intron 7

G/A

0.33

n.s.

0.08

Matrix metallopeptidase 13

MMP13_2

Intron 7

T/G

0.33

n.s.

0.05

Matrix metallopeptidase 13

MMP13_3

Exon 8

A/G

0.33

n.s.

0.1

Matrix metallopeptidase 13

MMP13_4

Intron 8

C/T

0.33

n.s.

0.03

Matrix metallopeptidase 13

MMP13_5

Intron 8

T/C

0.32

n.s.

0.01

Matrix metallopeptidase 13

MMP13_6

Intron 8

G/T

0.33

n.s.

0.3

Oncostatin M

OSM_1

Exon 3

C/T

0.47

0.001

7.7

Oncostatin M

OSM_2

Exon 3

T/C

0.47

0.001

8.6

Oncostatin M

OSM_3

Exon 3

T/C

0.47

0.001

8.6

Oncostatin M

OSM_4

Exon 3

G/T

0.47

0.0008

8.6

Oncostatin M

OSM_5

Exon 3

A/G

0.47

0.001

8.6

Oncostatin M

OSM_6

Intron 3

C/T

0.47

0.001

7.7

Oncostatin M

OSM_7

Intron 3

T/C

0.47

0.001

7.7

Oncostatin M

OSM_8

Intron 3

A/G

0.47

0.001

7.7

Pyrroline-5-carboxylate reductase 1

PYCR1_1

5’ UTR

A/T

0.11

n.s.

2.5

Pyrroline-5-carboxylate reductase 1

PYCR1_2

5’ UTR

C/T

0.13

n.s.

1.0

Pyrroline-5-carboxylate reductase 1

PYCR1_3

Intron 1

C/T

0.03

n.s.

1.0

Vimentin

VIM_1

Intron 5

C/T

0.21

n.s.

0.2

Vimentin

VIM_2

Intron 5

A/G

0.36

n.s.

0.3

Vimentin

VIM_3

Intron 5

C/T

0.17

n.s.

0.01

Vimentin

VIM_4

Intron 5

A/G

0.19

n.s.

0.6

Vimentin

VIM_5

Intron 5

C/T

0.15

n.s.

0.00

Vimentin

VIM_6

Intron 5

C/A

0.34

n.s.

0.3

Vimentin

VIM_7

Intron 5

C/A

0.11

n.s.

0.7

  1. amajor/minor allele, where risk allele is indicated in bold
  2. bminor allele frequency (MAF)
  3. cp-value (p > 0.001 is n.s)
  4. dthe percentage of explained phenotypic variance (%var)