Table 5.
SNPs significantly associated with CMT high and low risk breed groups after Bonferroni correction
|
SNP |
NCBI SNP ID |
Minor allele |
Frequency minor allele |
Major allele |
OR |
PRawa |
PBonfb |
PPermc |
PBPermd |
|
|---|---|---|---|---|---|---|---|---|---|---|
| High risk breeds | Low risk breeds | |||||||||
|
CHEK2 INT 8-9 |
ss244244336 |
G |
0.269 |
0.040 |
T |
8.8 |
8.6E-19 |
7.8E-18 |
<1.0E-07 |
0.076 |
|
ESR1 EX 2 |
rs21960513 |
T |
0.629 |
0.305 |
C |
3.9 |
5.0E-21 |
4.5E-20 |
<1.0E-07 |
0.107 |
|
ERBB2 EX 14 |
rs24537331 |
A |
0.253 |
0.511 |
G |
0.3 |
8.4E-15 |
7.6E-14 |
<1.0E-07 |
0.110 |
|
BRCA2 INT 18-19 |
ss244244323 |
G |
0.000 |
0.133 |
A |
_ e |
1.8E-16 |
1.6E-15 |
<1.0E-07 |
0.110 |
|
ERBB2 INT 3-4 |
ss244244348 |
G |
0.330 |
0.681 |
A |
0.2 |
2.4E-24 |
2.2E-23 |
<1.0E-07 |
0.112 |
|
BRCA2 EX 11 |
rs23244160 |
G |
0.174 |
0.346 |
T |
0.4 |
8.4E-09 |
7.6E-08 |
4.2E-05 |
0.151 |
|
CHEK2 INT 5-6 |
ss244244335 |
G |
0.051 |
0.000 |
A |
_ e |
9.6E-06 |
8.6E-05 |
0.005 |
0.182 |
|
ESR1 EX 4 |
ss244244343 |
G |
0.061 |
0.394 |
A |
0.1 |
9.8E-33 |
8.8E-32 |
<1.0E-07 |
0.204 |
|
PTEN EX 9 |
ss244244369 |
T |
0.112 |
0.346 |
C |
0.3 |
1.3E-16 |
1.2E-15 |
<1.0E-07 |
0.209 |
|
BRCA2 EX 5 |
rs23250374 |
C |
0.429 |
0.23 |
T |
2.5 |
1.1E-09 |
1.0E-08 |
1.0E-05 |
0.321 |
|
ERBB2 INT 12-13b |
rs24537327 |
A |
0.485 |
0.283 |
G |
2.4 |
2.2E-09 |
1.9E-08 |
2.0E-05 |
0.362 |
|
ERBB2 EX 13b |
rs24537329 |
T |
0.486 |
0.285 |
C |
2.4 |
2.4E-09 |
2.2E-08 |
2.1E-05 |
0.368 |
|
PTEN INT 7-8 |
ss244244368 |
A |
0.183 |
0.356 |
G |
0.5 |
8.0E-09 |
7.2E-08 |
4.0E-05 |
0.385 |
|
BRCA2 5UTR |
ss244244322 |
T |
0.343 |
0.506 |
C |
0.5 |
2.7E-06 |
2.4E-05 |
0.002 |
0.407 |
|
PTEN INT 3-4 |
ss244244367 |
G |
0.191 |
0.346 |
A |
0.6 |
2.8E-07 |
2.5E-06 |
5.0E-04 |
0.416 |
|
STK11 INT 1-2 |
rs22928814 |
T |
0.241 |
0.362 |
C |
0.6 |
1.1E-04 |
1.0E-03 |
0.031 |
0.476 |
|
BRIP1 EX 19b |
ss244244329 |
T |
0.538 |
0.386 |
T |
1.9 |
9.9E-06 |
8.9E-05 |
0.006 |
0.521 |
|
ERBB2 INT 8-9 |
ss244244349 |
G |
0.089 |
0.027 |
A |
3.2 |
0.001 |
5.8E-03 |
0.101 |
0.566 |
|
ESR1 INT 7-8a |
ss244244344 |
A |
0.124 |
0.223 |
G |
0.5 |
2.3E-04 |
2.2E-03 |
0.051 |
0.708 |
|
BRIP1 INT 8-9a |
ss244244325 |
G |
0.135 |
0.011 |
A |
14.5 |
3.2E-11 |
2.9E-10 |
<1.0E-07 |
0.817 |
|
ERBB2 INT 1-2 |
ss244244347 |
T |
0.021 |
0.000 |
C |
_ e |
0.005 |
0.045 |
0.340 |
0.845 |
|
BRIP1 INT 15-16 |
ss244244327 |
T |
0.131 |
0.011 |
A |
14.0 |
8.0E-11 |
7.2E-10 |
<1.0E-07 |
0.874 |
| ERBB2 EX13a | rs24616607 | G | 0.044 | 0.005 | C | 8.5 | 0.001 | 5.2E-03 | 0.095 | 0.983 |
(n = 237 and n = 191, respectively, after QC).
aP-value from chi-square test.
b Corrected for the number of across-breed LD blocks (9).
c EMP1 value after 107 permutations.
d EMP1 value after 10,000 breed permutations.
e OR could not be calculated as the minor allele was absent in either cases or controls.