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Table 3 Power for the CLR and Mantel statistic using 500 case-control pairs

From: Comparison of the power of haplotype-based versus single- and multilocus association methods for gene × environment (gene × sex) interactions and application to gene × smoking and gene × sex interactions in rheumatoid arthritis

       Model 3e Model 4f Mantel
  MAFa D'b r 2b Model 1c Model 2d Main Interaction Main Interaction M(0) (main effect) M(1) (joint effect)
SNP1 0.32 1 0.16 1 1 0.28 0 0.02 0.01 1.00 1.00
SNP2 0.12 1 0.04 0.99 0.99 0.06 0 0.01 0.01 1.00 1.00
SNP3 0.37 0.95 0.17 1 1 0.48 0.01 0.02 0.01 1.00 1.00
SNP4 0.49 1 0.34 1 1 0.37 0 0.02 0.01 1.00 1.00
SNP5 0.05 0.21 0 0.01 0.01 0 0.01 0.01 0.01 1.00 1.00
SNP6 0.13 1 0.05 1 1 0.08 0 0.01 0.01 1.00 1.00
SNP7 0.13 1 0.05 1 1 0.08 0 0.01 0 1.00 1.00
SNP8 0.23 1 0.1 1 1 0.36 0 0.02 0.02 1.00 1.00
SNP9 0.23 1 0.1 1 1 0.36 0 0 0 1.00 1.00
SNP10 0.41 0.94 0.41 1 1 0.51 0.01 0.05 0.01 1.00 1.00
DR locus 0.25 1 1 1 1 0.44 0.01 0.14 0.01 1.00 1.00
Locus C 0.42 1 0.45 1 1 0.2 0.01 0.04 0.01 1.00 1.00
SNP13 0.4 1 0.22 1 1 0.42 0.01 0.09 0.02 1.00 1.00
SNP14 0.33 0.99 0.65 1 1 0.4 0.03 0.03 0.01 1.00 1.00
SNP15 0.48 0.93 0.3 0.15 0.07 0 0 0.01 0.01 1.00 1.00
SNP16 0 0.92 0 1 1 0.56 0 0.02 0.01 1.00 1.00
SNP17 0.24 0.98 0.92 1 0.99 0.03 0 0.01 0.01 1.00 1.00
SNP18 0.1 1 0.04 1 0.99 0.07 0 0.01 0.01 1.00 1.00
SNP19 0.12 1 0.05 1 1 0.12 0 0.01 0.01 1.00 1.00
SNP20 0.39 0.56 0.07 1 1 0.52 0 0.01 0.01 1.00 1.00
SNP21 0.47 0.94 0.26 1 1 0 0.02 0.01 0.01 1.00 1.00
SNP22 0.1 0.71 0.02 1 1 0.33 0 0.07 0.01 1.00 1.00
  1. Power is the percentage of replicates in which the main or interaction effect of the respective marker had an adjusted p-value ≤ 0.05.
  2. aMinor allele frequency among controls
  3. bLD values calculated using the control population in Replicate 1
  4. cModel 1, main effect of one SNP at a time
  5. dModel 2, interaction term with sex of one SNP at a time
  6. eModel 3, main and interaction with sex of one SNP at a time
  7. fModel 4, stepwise model with main and interaction effects of all SNPs