Table 1 Pairwise SNP interactions with suggestive statistical evidence (p < 10 -8 ) in the meta-analysis of two GWAS datasets gathering 1,953 cases and 2,338 controls
From: A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis
EOVT | MARTHA | Combined | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SNP1 X SNP2 | MAF(2) | Interaction | MAF | Interaction | ||||||||||||||
rsID | Alleles(1) | CHR | rsID | Alleles | CHR | SNP1 | SNP2 | OR(3) | P | SNP1 | SNP2 | OR | P | OR (4) | P | Cochran Q(5) | I2 | P(6) |
rs493014 | T/G | 9 | rs886090 | G/A | 9 | 0.31 | 0.33 | 1.72 | 1.85 × 10-5 | 0.30 | 0.31 | 1.6 | 6.73 × 10-7 | 1.64 | 6.00 × 10-11 | 0.21 | 0% | 0.65 |
rs1336472 | G/A | 1 | rs4715555 | A/G | 6 | 0.41 | 0.39 | 1.64 | 4.10 × 10-5 | 0.40 | 0.38 | 1.49 | 2.00 × 10-6 | 1.54 | 4.24 × 10-10 | 0.42 | 0% | 0.52 |
rs380904 | G/A | 8 | rs8086028 | G/A | 18 | 0.30 | 0.27 | 1.96 | 3.76 × 10-6 | 0.29 | 0.31 | 1.55 | 1.12 × 10-5 | 1.67 | 4.51 × 10-10 | 1.79 | 44% | 0.18 |
rs6815916 | A/G | 4 | rs6092326 | C/T | 20 | 0.09 | 0.48 | 2.37 | 4.32 × 10-5 | 0.09 | 0.47 | 1.98 | 2.95 × 10-6 | 2.10 | 6.84 × 10-10 | 0.51 | 0% | 0.48 |
rs2282015 | T/G | 10 | rs13050454 | G/A | 21 | 0.41 | 0.43 | 1.81 | 3.52 × 10-7 | 0.41 | 0.42 | 1.37 | 7.68 × 10-5 | 1.50 | 8.36 × 10-10 | 3.90 | 74% | 0.05 |
rs7648704 | T/G | 3 | rs4868644 | C/T | 5 | 0.33 | 0.49 | 1.64 | 7.36 × 10-5 | 0.33 | 0.49 | 1.52 | 2.88 × 10-6 | 1.56 | 9.89 × 10-10 | 0.26 | 0% | 0.61 |
rs1985317 | T/C | 9 | rs827637 | G/A | 10 | 0.39 | 0.46 | 0.55 | 7.13 × 10-7 | 0.41 | 0.46 | 0.72 | 7.73 × 10-5 | 0.66 | 1.32 × 10-9 | 3.42 | 71% | 0.06 |
rs2321744 | A/G | 13 | rs6497540 | T/G | 16 | 0.09 | 0.41 | 0.43 | 8.61 × 10-5 | 0.1 | 0.42 | 0.52 | 2.98 × 10-6 | 0.49 | 1.38 × 10-9 | 0.55 | 0% | 0.46 |
rs315122 | T/G | 12 | rs884483 | T/C | 15 | 0.29 | 0.11 | 2.61 | 1.92 × 10-5 | 0.31 | 0.12 | 1.87 | 7.90 × 10-6 | 2.05 | 1.42 × 10-9 | 1.59 | 37% | 0.21 |
rs1423386 | A/G | 5 | rs6491679 | T/G | 13 | 0.2 | 0.29 | 1.92 | 7.24 × 10-5 | 0.2 | 0.29 | 1.66 | 4.17 × 10-6 | 1.73 | 1.63 × 10-9 | 0.56 | 0% | 0.45 |
rs7714670 | T/C | 5 | rs12880735 | G/A | 14 | 0.44 | 0.34 | 1.75 | 4.59 × 10-6 | 0.44 | 0.36 | 1.42 | 3.32 × 10-5 | 1.52 | 1.75 × 10-9 | 1.99 | 50% | 0.16 |
rs9392653 | C/T | 6 | rs7780976 | A/C | 7 | 0.27 | 0.18 | 2.14 | 2.28 × 10-6 | 0.29 | 0.19 | 1.57 | 5.49 × 10-5 | 1.74 | 1.83 × 10-9 | 2.47 | 60% | 0.12 |
rs9804128 | A/G | 1 | rs4784379 | G/A | 16 | 0.27 | 0.25 | 1.97 | 2.73 × 10-5 | 0.26 | 0.24 | 1.60 | 9.45 × 10-6 | 1.71 | 1.90 × 10-9 | 1.14 | 13% | 0.28 |
rs1364505 | G/A | 7 | rs1204660 | G/A | 20 | 0.30 | 0.16 | 2.14 | 2.32 × 10-5 | 0.33 | 0.16 | 1.67 | 1.11 × 10-5 | 1.80 | 2.10 × 10-9 | 1.35 | 26% | 0.25 |
rs2288073 | A/G | 2 | rs10771022 | G/T | 12 | 0.30 | 0.34 | 1.71 | 7.94 × 10-5 | 0.29 | 0.34 | 1.55 | 5.51 × 10-6 | 1.60 | 2.11 × 10-9 | 0.35 | 0% | 0.55 |
rs1367228 | C/A | 2 | rs3905075 | C/T | 13 | 0.43 | 0.41 | 1.61 | 9.44 × 10-5 | 0.45 | 0.4 | 1.44 | 4.22 × 10-6 | 1.49 | 2.20 × 10-9 | 0.62 | 0% | 0.43 |
rs536477 | G/A | 1 | rs1937920 | A/G | 10 | 0.43 | 0.26 | 0.57 | 3.27 × 10-5 | 0.43 | 0.27 | 0.67 | 1.40 × 10-5 | 0.63 | 2.93 × 10-9 | 0.90 | 0% | 0.34 |
rs2710201 | A/G | 7 | rs3780293 | G/A | 9 | 0.06 | 0.34 | 0.35 | 6.84 × 10-5 | 0.06 | 0.36 | 0.43 | 9.92 × 10-6 | 0.40 | 3.30 × 10-9 | 0.38 | 0% | 0.54 |
rs12541254 | G/A | 8 | rs305009 | G/A | 15 | 0.35 | 0.23 | 1.99 | 3.15 × 10-6 | 0.34 | 0.23 | 1.50 | 7.63 × 10-5 | 1.65 | 3.33 × 10-9 | 2.39 | 58% | 0.12 |
rs4507975 | A/G | 1 | rs9914518 | G/A | 17 | 0.29 | 0.46 | 0.61 | 9.59 × 10-5 | 0.29 | 0.47 | 0.67 | 7.95 × 10-6 | 0.65 | 3.58 × 10-9 | 0.32 | 0% | 0.57 |
rs2771051 | T/G | 9 | rs827637 | G/A | 10 | 0.37 | 0.46 | 0.52 | 9.27 × 10-8 | 0.37 | 0.46 | 0.75 | 4.59 × 10-4 | 0.67 | 3.82 × 10-9 | 6.08 | 84% | 0.01 |
rs10516089 | T/C | 5 | rs11072930 | T/C | 15 | 0.32 | 0.28 | 0.51 | 2.66 × 10-6 | 0.31 | 0.3 | 0.69 | 7.19 × 10-5 | 0.63 | 3.86 × 10-9 | 3.12 | 68% | 0.08 |
rs10504130 | G/A | 8 | rs2847351 | A/G | 18 | 0.15 | 0.3 | 2.46 | 1.04 × 10-5 | 0.14 | 0.32 | 1.69 | 3.07 × 10-5 | 1.88 | 4.46 × 10-9 | 2.40 | 58% | 0.12 |
rs318497 | G/A | 6 | rs7019259 | A/G | 9 | 0.49 | 0.07 | 0.29 | 2.56 × 10-6 | 0.49 | 0.07 | 0.51 | 8.40 × 10-5 | 0.43 | 4.54 × 10-9 | 3.21 | 69% | 0.07 |
rs6695223 | T/C | 1 | rs1763510 | C/T | 6 | 0.12 | 0.39 | 2.49 | 6.00 × 10-6 | 0.13 | 0.39 | 1.66 | 4.31 × 10-5 | 1.86 | 4.70 × 10-9 | 2.91 | 66% | 0.09 |
rs1336708 | A/G | 13 | rs1423386 | A/G | 5 | 0.26 | 0.2 | 0.51 | 6.77 × 10-5 | 0.25 | 0.2 | 0.61 | 1.20 × 10-5 | 0.58 | 4.85 × 10-9 | 0.79 | 0% | 0.37 |
rs6771316 | G/A | 3 | rs10986432 | T/C | 9 | 0.14 | 0.18 | 2.41 | 4.64 × 10-5 | 0.13 | 0.17 | 1.99 | 2.20 × 10-5 | 2.13 | 5.26 × 10-9 | 0.50 | 0% | 0.48 |
rs664910 | A/G | 3 | rs877228 | G/A | 15 | 0.30 | 0.47 | 1.63 | 6.05 × 10-5 | 0.30 | 0.44 | 1.44 | 1.92 × 10-5 | 1.50 | 6.63 × 10-9 | 0.71 | 0% | 0.40 |
rs9945428 | C/A | 18 | rs4823535 | G/A | 22 | 0.30 | 0.28 | 0.58 | 7.47 × 10-5 | 0.30 | 0.26 | 0.65 | 1.85 × 10-5 | 0.62 | 6.88 × 10-9 | 0.46 | 0% | 0.50 |
rs1910358 | T/C | 5 | rs9981595(7) | T/G | 21 | 0.23 | 0.12 | 2.21 | 9.60 × 10-5 | 0.23 | 0.11 | 1.93 | 1.63 × 10-5 | 2.03 | 7.14 × 10-9 | 0.30 | 0% | 0.59 |
rs6771725 | G/T | 3 | rs10507246 | G/T | 12 | 0.26 | 0.08 | 2.6 | 4.02 × 10-5 | 0.28 | 0.09 | 2.04 | 3.77 × 10-5 | 2.22 | 8.60 × 10-9 | 0.71 | 0% | 0.40 |
rs16865717 | C/T | 2 | rs2009579 | C/T | 20 | 0.27 | 0.36 | 1.9 | 5.22 × 10-6 | 0.29 | 0.36 | 1.43 | 9.59 × 10-5 | 1.56 | 8.82 × 10-9 | 2.88 | 65% | 0.09 |
rs2028385 | A/G | 12 | rs2038227 | A/C | 16 | 0.16 | 0.39 | 2.19 | 3.36 × 10-7 | 0.16 | 0.37 | 1.47 | 7.11 × 10-4 | 1.69 | 8.82 × 10-9 | 4.40 | 77% | 0.04 |
rs10476160 | A/G | 5 | rs1707420 | C/T | 8 | 0.21 | 0.48 | 0.56 | 6.35 × 10-5 | 0.20 | 0.48 | 0.65 | 2.48 × 10-5 | 0.62 | 9.09 × 10-9 | 0.75 | 0% | 0.39 |
rs971572 | C/A | 1 | rs10828151 | A/C | 10 | 0.32 | 0.07 | 0.35 | 3.43 × 10-5 | 0.32 | 0.07 | 0.47 | 4.38 × 10-5 | 0.42 | 9.30 × 10-9 | 0.88 | 0% | 0.35 |
rs6858430 | C/T | 4 | rs4800250 | A/G | 18 | 0.20 | 0.40 | 1.86 | 2.44 × 10-5 | 0.21 | 0.40 | 1.52 | 5.16 × 10-5 | 1.62 | 9.67 × 10-9 | 1.30 | 23% | 0.25 |
rs467650 | T/C | 5 | rs7153749 | T/C | 14 | 0.36 | 0.44 | 0.59 | 1.69 × 10-5 | 0.37 | 0.44 | 0.71 | 6.00 × 10-5 | 0.67 | 9.91 × 10-9 | 1.75 | 43% | 0.19 |