Table 2 Pairwise and triplet SNP combinations with odds ratios greater than 3

SNP Combinations +RISK ALLELE Freq OReq2 p-value
*rs1412829 (1.58) #rs7530361 (1.89) 11 5.45E-02 3.31 3.58E-07
*rs1412829 (1.58) #rs501700 (1.90) 11 5.51E-02 3.09 1.95E-06
*rs1412829 (1.58) #rs506044 (1.96) 11 5.47E-02 3.23 5.15E-07
*rs1412829 (1.58) #rs640030 (1.95) 11 5.42E-02 3.28 4.30E-07
*rs1412829 (1.58) #rs687513 (1.93) 11 5.52E-02 3.18 7.32E-07
*rs2157719 (1.49) #rs7530361 (1.89) 11 5.51E-02 3.2 6.83E-07
*rs2157719 (1.49) #rs506044 (1.96) 11 5.54E-02 3.12 9.64E-07
*rs2157719 (1.49) #rs640030 (1.95) 11 5.49E-02 3.16 8.12E-07
*rs2157719 (1.49) #rs687513 (1.93) 11 5.59E-02 3.07 1.35E-06
*rs1063192 (1.42) #rs7530361 (1.89) 11 5.60E-02 3.12 1.13E-06
*rs1063192 (1.42) #rs506044 (1.96) 11 5.63E-02 3.05 1.60E-06
*rs1063192 (1.42) #rs640030 (1.95) 11 5.59E-02 3.08 1.35E-06
*rs4977756 (1.60) #rs7530361 (1.89) 11 5.35E-02 4.28 3.14E-10
*rs4977756 (1.60) #rs501700 (1.90) 11 5.44E-02 4.17 5.57E-10
*rs4977756 (1.60) #rs506044 (1.96) 11 5.36E-02 4.18 4.46E-10
*rs4977756 (1.60) #rs640030 (1.95) 11 5.31E-02 4.24 3.66E-10
*rs4977756 (1.60) #rs687513 (1.93) 11 5.41E-02 4.1 6.86E-10
rs2736100 (0.63) #rs7530361 (1.89) rs1920116 (0.68) 212 5.01E-02 4.3 5.02E-10
rs11823971 (1.45) *rs1412829 (1.58) #rs7530361 (1.89) 211 5.21E-02 3.04 5.05E-06
rs11823971 (1.45) *rs1412829 (1.58) #rs506044 (1.96) 211 5.26E-02 3.01 4.67E-06
1. Numbers in parenthesis are single SNP odds ratios. Last column is the Wald test p-value for the odds ratio of the combination. This is an unadjusted p-value, with an 0.05 multiple testing adjusted threshold of p = .05/(50+88) = 3.6 × 10-4. Freq denotes the combined frequency of the given combination in the case and control populations as a whole.
2. + Denotes alleles in which significant shifts occur. 11 denotes significant shift in the minor alleles for both SNPs. 212 denotes significant shifts in major, minor major; 211, significant shifts in major, minor, minor.
3. # denotes SNP on chromosome 1
4. * denotes SNP on chromosome 9 in gene CDKN2A/2B.