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Table 6 Pair-wise interactions among SNPs when GOSemSim threshold=0.27 (P <0.01).

From: Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks

Chromosome1 Chromosome2 Gene1 Gene2 SNP1 SNP2 OR_int Χ 2 P -value
1 17 intergenic KCNH6 rs4658673 rs4968656 0.4873 10.52 0.001183
17 17 intergenic KCNH6 rs11655589 rs4968656 0.5365 10.43 0.001242
11 17 intergenic intergenic rs10501570 rs11655589 0.5096 8.76 0.003083
21 21 ERG ERG rs2836389 rs2836392 0.5642 7.55 0.006017
8 17 intergenic intergenic rs10503868 rs11655589 0.5543 7.49 0.006223
14 21 RAD51L1 ERG rs11626809 rs2836392 2.4410 7.40 0.00652
1 17 intergenic intergenic rs4658673 rs11655589 0.5534 7.37 0.00665
11 17 intergenic KCNH6 rs10501570 rs4968656 0.5551 6.66 0.009844
  1. Pair-wise interactions among SNPs when GOSemSim threshold=0.27 with P <0.01 significance. For each group of the gene network where gene pairs have > 0.27 similarity value, all the pairwise SNP-SNP interactions are checked using PLINK between SNPs involved in the groups of genes and all the other SNPs selected by the shrunken method. SNPs network is constructed based on the P <0.01 value of PLINK epistasis test. This table shows the detailed results of PLINK where the first two columns are the chromosomes the SNPs located in, the third and forth columns are the corresponding gene symbol of the SNPs, the fifth and sixth columns are the SNP ID and the last three columns are the odds ratio for interaction, χ2 test and P value in the PLINK test.