Table 2.
SNPs with statistical significance in the genome-wide association study for hyperpigmentation of visceral peritoneum (HVP)
| 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 |
a GGA = chicken (Gallus gallus) chromosome;
b Gene information from NCBI, 06 July 2011;
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.