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Table 2 PTPN22 analysis with LR and the Mantel statistic (adjusted p-values)

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 4f Model 5g Mantelh
Marker MAFa D'b r 2b Model 1c Model 2d Model 3e Main Int. Main Int. I II III
rs3789604 0.20 1.00 0.04 0.97 0.96 0.96 0.95 0.95 0.97 0.94 0.40 0.03 i <0.001
rs3811021 0.20 0.95 0.04 0.97 0.96 0.97 0.95 0.95 0.97 0.95 0.40 0.03 <0.001
rs1217413 0.21 0.99 0.46 0.05 0.026 0.15 0.94 0.62 0.37 0.86 0.35 0.02 <0.001
ss38346942 0.01 0.60 0.00 0.95 0.96 0.97 1.00 1.00 0.97 0.97 0.35 0.02 <0.001
rs1217388 0.25 0.99 0.40 0.21 0.10 0.41 0.68 0.39 0.60 0.90 0.35 0.02 <0.001
ss38346943 0.03 0.05 0.00 0.81 0.88 0.97 0.95 0.96 0.28 0.49 0.40 0.02 <0.001
rs1310182 0.45 0.99 0.17 0.40 0.21 0.78 0.43 0.20 0.49 0.81 0.40 0.03 <0.001
ss38346944 0.02 0.19 0.00 0.97 0.96 0.91 0.94 0.94 1.00 1.00 0.40 0.03 <0.001
R620W 0.10 1.00 1.00 0.004 0.001 0.02 0.18 0.01 0.28 0.86 0.40 0.02 <0.001
rs12730735 0.30 0.94 0.05 0.81 0.74 0.78 0.95 0.94 0.97 0.94 0.40 0.03 <0.001
rs11102685 0.08 0.99 0.02 0.97 0.96 0.94 1.00 1.00 0.86 0.78 0.32 0.03 <0.001
rs12760457 0.29 0.97 0.06 0.90 0.88 0.87 0.93 0.81 0.97 0.92 0.38 0.03 <0.001
rs2488458 0.25 0.99 0.40 0.15 0.08 0.31 0.85 0.56 0.65 0.94 0.23 0.03 <0.001
rs1217414 0.26 1.00 0.05 0.69 0.47 0.97 0.74 0.54 0.09 0.21 0.23 0.03 <0.001
  1. aMinor allele frequency among controls
  2. bLD values calculated using the control population. All LR models consider one SNP at a time and include main effects of sex and smoking.
  3. cModel 1, main effect
  4. dModel 2, interaction term with sex
  5. eModel 3, interaction term with smoking
  6. fModel 4, main and interaction with sex
  7. gModel 5, main and interaction with smoking
  8. hMantel statistics: I, main effect (M0); II, joint effect (M1) with sex; III, joint effect (M1) with smoking
  9. ip-Values ≤ 0.05 are given in bold.