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. 2009 May 7;4(5):e5459. doi: 10.1371/journal.pone.0005459

Table 2. A list of SNP pairs identified by SNP-SNP interaction tests in GWAS.

First SNP in an interactive pair Second SNP in an interactive pair Interaction tests [−log10(p)]
CHR RS PP GI GCR MAF CHR RS PP GI GCR MAF ORT Nominal Ordinal
7 rs1526555 11579529 KIAA0960 99.4 0.140 14 rs765899 68033499 RAD51L1 92.0 0.326 8.9073 2.9786 5.0546
11 rs7950640 58620981 LOC643652 100 0.387 7 rs2214310 25152103 xC7orf9 99.7 0.454 8.7347 3.9040 5.7904
12 rs10506451 61520532 PPM1H 100 0.357 6 rs1115620 113578211 LOC643884 99.4 0.496 8.5318 4.2654 5.8117
11 rs7950640 58620981 LOC643652 100 0.387 7 rs994531 25152938 xC7orf9 99.4 0.441 8.3949 3.7367 5.6075
6 rs1886985 76773462 IMPG1 100 0.491 20 rs2206416 39994257 Intergenic 100 0.486 8.3879 4.7945 6.7676
11 rs10488767 109964045 ARHGAP20 100 0.317 16 rs10500328 5747879 Intergenic 100 0.404 8.2666 3.6095 5.6956
12 rs10506451 61520532 PPM1H 100 0.357 6 rs2502397 113569072 LOC643884 100 0.499 8.1975 4.0066 5.6377
1 rs618171 215537693 LOC643717 100 0.443 7 rs7805441 77766109 MAGI2 100 0.451 8.1824 3.5028 5.3108
6 rs1886985 76773462 IMPG1 100 0.491 20 rs6129969 39967987 Intergenic 99.1 0.419 8.1167 3.7163 6.1904
7 rs1526555 11579529 KIAA0960 99.4 0.140 14 rs2331706 68031318 RAD51L1 100 0.364 8.0217 3.1281 4.9362

Interactive SNP pairs are listed in their order of significance. For each SNP of an interactive pair, chromosome (CHR), RS number (RS), physical position (PP), gene information (GI), genotyping call rate (GCR(%)) and minor allele frequency (MAF) are shown. Finally, the −log10(p) value from three interaction tests is shown: (1) the difference test of odds ratio (ORT), (2) an interaction test of the CLR-NOMINAL analysis [model: logit{Prob(Y = YOH|I11,I12,I21,I22,I11×I21,I11×I22,I12×I21,I12×I22)} = a0+a11×I11+a12×I12+a21×I21+a22×I22+b1×I11×I21+b2×I11×I22+b3×I12×I21+b4×I12×I22] and (3) an interaction test of the CLR-ORDINAL analysis [model: logit{Prob(Y = YOH|X1, X2, X1×X2)} = a0+a1×X1+a2×X2+a3×X1×X2], where Y is YOH status, Iij is an indicator of the three genotypes (j = 1, 2) of SNP i (i = 1, 2) and Xi denotes the number of reference alleles of SNP i (i = 1, 2).