Table 2: SNPs within the PTPRN2 gene associated with risk and age
at onset of cancer using PLINK (p < 0.05)
SNP |
Positiona |
Alleleb |
MAFc |
HWEd |
OR-Cancere |
p-Cancerf |
EMPg |
β-AAOh |
p-AAOi |
EMPj |
rs7783909 |
157287177 |
A |
0.15 |
0.413 |
1.42(1.1-1.83) |
6.52E-03 |
4.0E-03 |
-0.017 |
0.0713 |
0.0739 |
rs4909140 |
157721662 |
G |
0.46 |
0.727 |
1.16(1.03-1.31) |
1.57E-02 |
1.1E-02 |
-0.017 |
6.18E-04 |
4.0E-03 |
rs10244830 |
157674626 |
T |
0.35 |
0.318 |
0.84(0.73-0.97) |
1.81E-02 |
1.4E-02 |
0.002 |
0.7115 |
0.699 |
rs7795387 |
157764272 |
G |
0.22 |
0.409 |
0.74(0.57-0.96) |
2.23E-02 |
2.2E-02 |
0.002 |
0.844 |
0.856 |
rs6970487 |
157712908 |
G |
0.42 |
0.561 |
0.86(0.76-0.98) |
2.55E-02 |
2.8E-02 |
0.01 |
0.0653 |
0.0579 |
rs4595081 |
157700684 |
T |
0.42 |
0.475 |
0.86(0.76-0.98) |
2.69E-02 |
2.9E-02 |
0.01 |
0.065 |
0.058 |
rs6944416 |
157708321 |
G |
0.42 |
0.623 |
0.86(0.76-0.98) |
2.78E-02 |
3.0E-02 |
0.01 |
0.064 |
0.06 |
rs17837789 |
157128182 |
G |
0.15 |
0.186 |
0.63(0.41-0.96) |
3.29E-02 |
2.8E-02 |
-0.027 |
0.159 |
0.155 |
rs920023 |
157427075 |
G |
0.24 |
0.768 |
0.8(0.65-0.99) |
4.03E-02 |
3.9E-02 |
0.016 |
0.0751 |
0.0739 |
rs4909289 |
157647665 |
A |
0.26 |
0.82 |
0.82(0.68-0.99) |
4.85E-02 |
4.3E-02 |
0.003 |
0.699 |
0.687 |
rs1670340 |
157963783 |
C |
0.49 |
0.385 |
0.97(0.86-1.1) |
0.654 |
0.687 |
-0.016 |
1.69E-03 |
2.0E-03 |
rs1630862 |
157961357 |
G |
0.45 |
0.965 |
0.97(0.86-1.09) |
0.588 |
0.598 |
-0.013 |
1.17E-02 |
0.012 |
rs11760246 |
157523437 |
T |
0.37 |
0.016 |
1.04(0.91-1.19) |
0.529 |
0.54 |
0.013 |
1.81E-02 |
0.025 |
rs1268391 |
157111665 |
C |
0.32 |
0.841 |
0.96(0.83-1.12) |
0.606 |
0.62 |
-0.015 |
2.16E-02 |
0.023 |
rs7777448 |
157724510 |
A |
0.39 |
0.99 |
0.98(0.86-1.12) |
0.736 |
0.712 |
-0.013 |
2.38E-02 |
0.034 |
rs3752374 |
157581981 |
G |
0.05 |
0.662 |
1.73(0.73-4.11) |
0.239 |
0.155 |
-0.07 |
3.29E-02 |
0.04 |
rs10949670 |
157388704 |
T |
0.39 |
0.142 |
1.0(0.88-1.14) |
0.956 |
0.95 |
0.011 |
3.95E-02 |
0.043 |
rs12698149 |
rs12698149 |
T |
0.39 |
0.238 |
1.05(0.92-1.19) |
0.494 |
0.504 |
0.011 |
3.95E-02 |
0.045 |
a Physical position(bp); b
Minor allele; c Minor allele frequency; d Hardy-Weinberg
equilibrium test p-value;
e Odds ratio for the risk of cancer based on logistic
regression using PLINK; f p-value for the risk of cancer based on logistic regression;
g empirical
p-value for the risk of cancer generated by 100,000 permutation tests using Max
(T) permutation procedure implemented in PLINK;
h Regression coefficient for AAO of cancer based on linear
regression using PLINK; i p-value
for AAO of cancer based on linear regression ;
j empirical p-value for AAO of cancer generated by 100,000
permutation tests using Max (T) permutation procedure implemented in PLINK.