Table 3 True positive rates (TPR) by causal SNP pairs based on bootstrap results.

From: Cluster effect for SNP–SNP interaction pairs for predicting complex traits

Causal pair

SNP1

p-value (p-main)1

SNP2

p-value (p-main)1

SNP–SNP interaction

p-value (p-pair)1

Bootstrap2

1pRule

TPR%3

3pRule

TPR%3

rs17632542–rs4783709

2.2 × 10–15

0.027

5.7 × 10–18

95.0

91.8

rs2569735–rs7613553

5.5 × 10–9

0.551

4.4 × 10–13

98.2

98.0

rs1058205–rs2274545

9.5 × 10–8

0.065

2.0 × 10–9

83.6

81.0

rs4802755–rs4473378

1.8 × 10–7

0.728

2.3 × 10–9

86.6

86.0

rs174776–rs1250240

7.9 × 10–7

0.279

2.4 × 10–9

94.0

93.8

rs2271095–rs7446

2.0 × 10–6

2.0 × 10–5

1.7 × 10–12

95.4

94.4

rs266876–rs9521694

3.2 × 10–6

0.001

3.4 × 10–9

77.0

75.6

  1. 1Bold for significant results based on the Bonferroni criteria. p-main < 8.1 × 10–5 (= 0.05/614), and p-pair < 2.7 × 10–7 (= 0.05/614C2).
  2. 2Based on 500 bootstrap datasets with a sample size of 20,000 and 614 SNPs (7 causal pairs + 600 null SNPs).
  3. 3Significance rules: 1pRule: p-pair < 2.7 × 10–7; 3pRule: p-pair < 2.7 × 10–7, p-pair < p-main for SNP1, and p-pair < p-main for SNP2.
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