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Table 5 SNPs significantly associated with CMT high and low risk breed groups after Bonferroni correction

From: The ESR1 gene is associated with risk for canine mammary tumours

SNP NCBI SNP ID Minor allele Frequency minor allele Major allele OR P Raw a P Bonf b P Perm c P BPerm d
    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
  1. (n = 237 and n = 191, respectively, after QC).
  2. aP-value from chi-square test.
  3. b Corrected for the number of across-breed LD blocks (9).
  4. c EMP1 value after 107 permutations.
  5. d EMP1 value after 10,000 breed permutations.
  6. e OR could not be calculated as the minor allele was absent in either cases or controls.
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