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Table 2 SNPs with statistical significance in the genome-wide association study for hyperpigmentation of visceral peritoneum (HVP)

From: Genetic parameters and genome-wide association study of hyperpigmentation of the visceral peritoneum in chickens

SNP

GGAa

Position (bp)

Nearest geneb

Alleles

RAc

FAW

P-value

AE

r2

rs14822943

1

52,576,468

0.5 Kb U MAP3K7IP1

C/T

T

0.21

2.65 × 10-14

0.05

0.13

GGaluGA017356

1

52,358,970

CACNA1I

T/C

T

0.24

2.95 × 10-12

0.06

0.10

GGaluGA017598

1

52,940,122

PLA2G6

T/C

C

0.43

9.03 × 10-12

0.08

0.09

GGaluGA018011

1

53,833,467

70.8 Kb U MYH9

G/A

G

0.24

1.03 × 10-11

0.05

0.10

rs13865536

1

52,554,283

13.3 Kb D MAP3K7IP1

C/T

C

0.24

5.07 × 10-11

0.05

0.10

GGaluGA017030

1

51,619,588

0.8 Kb U RANGAP1

G/A

A

0.49

5.80 × 10-11

0.08

0.08

rs13652125

1

50,923,554

TTC26

A/G

A

0.15

1.97 × 10-10

0.04

0.06

GGaluGA016761

1

51,087,457

SERHL2

T/C

C

0.48

4.62 × 10-9

0.07

0.06

GGaluGA016965

1

51,488,752

2.5 Kb D ACO2

T/C

C

0.25

5.75 × 10-9

0.05

0.07

GGaluGA017484

1

52,642,092

PDGFB

G/A

G

0.26

1.52 × 10-8

0.05

0.09

GGaluGA017730

1

53,094,788

5.6 Kb U TRIOBP

T/C

T

0.64

4.74 × 10-8

0.11

0.09

GGaluGA019336

1

58,058,352

55.3 Kb U HIPK2

G/A

G

0.70

1.55 × 10-7

0.10

0.04

rs13873173

1

60,462,801

SLC13A4

G/T

T

0.75

2.37 × 10-7

0.10

0.05

rs13865344

1

52,399,455

CACNA1I

T/C

T

0.27

4.85 × 10-7

0.04

0.03

rs13865892

1

53,177,756

LGALS2

G/A

G

0.61

5.79 × 10-7

0.08

0.06

rs16174305

20

11,707,312

30.0 Kb D BMP7

C/T

C

0.42

2.44 × 10-8

0.06

0.05

GGaluGA180727

20

11,075,280

36.9 Kb U STX16

G/A

A

0.36

9.25 × 10-8

0.06

0.05

rs14278900

20

10,911,015

GNAS

G/A

A

0.37

1.24 × 10-7

0.05

0.05

GGaluGA180980

20

11,591,655

3.5 Kb U RBM38

G/A

A

0.44

2.59 × 10-7

0.06

0.03

GGaluGA181122

20

11,874,967

27.0 Kb D TFAP2C

T/C

C

0.48

3.98 × 10-7

0.06

0.05

  1. a GGA = chicken (Gallus gallus) chromosome;
  2. b Gene information from NCBI, 06 July 2011;
  3. c RA = risk allele related to HVP; FAW = frequency of the allele related to HVP in F2 population; AE = additive effect of SNP markers; r2 = contribution of each SNP to HVP.