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Table 1 The results of the PC score based and haplotype-based tests using Replicate 48

From: Association tests based on the principal-component analysis

      Association test via logistic regressionc H0: Global β = 0 AIC
  LD block (SNP) No. SNPs No. PC scorea No. haplotypeb PC score Haplotype PC score Haplotype
Blocks not associated with RA 1 (47~51) 5 1 3 (3) 0.4602 0.9947 2252.880 d 2254.346
  2 (79~82) 4 1 3 (8) 1.4472 3.3423 2251.893 2254.004
  3 (356~361) 6 3 5 (16) 0.8239 3.3700 2256.517 2257.973
  4 (387~390) 4 2 4 (9) 2.7136 3.3676 2252.627 2256.012
Blocks associated with RA 5 (128~130) 3 1 3 (6) 15.0769 18.1052 2238.264 2239.058
  6 (140~144) 5 3 4 (14) 17.4702 5.5822 2239.870 2253.928
  7 (149~151) 3 2 3 (5) 10.1205 11.6309 2245.220 2245.644
  8 (162~163) 2 2 2 (4) 40.4704 40.3278 2214.870 2215.014
  1. aWe consider the haplotypes that have frequencies greater than 0.05, and PC score whose sum of variations explains more than 70% of the total variations.
  2. bNumber in parentheses is the number of estimated haplotypes. Haplotypes with frequencies less than 0.05 were pooled together and included in the model as one group.
  3. cWe test all β = 0 using the likelihood ratio test.
  4. dBold indicates the smallest AIC value.