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Table 3 Haplotype association resultsa

From: Comparison of tagging single-nucleotide polymorphism methods in association analyses

  LRAP HLA-DRB2 CPNE1 AA827892 CSTB
  p-set/dfb min(p)c p-set/df min(p) p-set/df min(p) p-set/df min(p) p-set/df min(p)
All SNPs 1.8 × 10 -3 /5 d 1.3 × 10 -5 1.6 × 10-2/3 5.1 × 10 -5 3.4 × 10 -3 /2 7.1 × 10 -5 2.1 × 10-1/2 1.8 × 10 -4 2.1 × 10 -4 /2 3.3 × 10 -4
ldSelect 7.5 × 10 -4 /4 1.7 × 10 -4 8.5 × 10 -3 /4 5.1 × 10 -5 7.1 × 10 -5 /2 7.1 × 10 -5 5.2 × 10-2/2 5.2 × 10-2 1.8 × 10 -4 /2 2.3 × 10 -3
TagSNPs-Rspair 1.4 × 10 -3 /5 3.9 × 10 -5 2.1 × 10-2/3 5.6 × 10 -5 7.1 × 10 -5 /2 7.1 × 10 -5 2.1 × 10-1/2 5.2 × 10-2 1.8 × 10 -4 /2 3.1 × 10 -3
TagSNPs-Rspair-trios 1.4 × 10 -3 /5 3.9 × 10 -5 2.1 × 10-2/3 2.3 × 10 -4 7.1 × 10 -5 /2 7.1 × 10 -5 2.1 × 10-1/2 5.2 × 10-2 2.1 × 10 -4 /2 1.1 × 10 -3
Tagger-pairwise 3.3 × 10 -4 /4 1.7 × 10 -5 9.5 × 10-3/4 5.1 × 10 -5 7.1 × 10 -5 /2 7.1 × 10 -5 5.2 × 10-2/2 5.2 × 10-2 1.8 × 10 -4 /2 3.0 × 10 -3
TagSNPs-Rs 4.0 × 10 -4 /3 1.7 × 10 -4 4.1 × 10-2/3 1.5 × 10-5 1.1 × 10-4/2 1.1 × 10-4 1.7 × 10-1/2 1.7 × 10-1 5.0 × 10-1/4 2.7 × 10-2
TagSNPs-Rs-trios 1.2 × 10 -3 /4 1.6 × 10 -4 1.3 × 10-3/4 5.7 × 10-4 7.1 × 10-5/2 7.1 × 10-5 1.7 × 10-1/2 1.7 × 10-1 5.0 × 10-1/4 2.7 × 10-2
Tagger-multimarker 3.3 × 10 -4 /4 5.7 × 10 -5 1.7 × 10-2/3 5.7 × 10-5 7.1 × 10-5/2 7.1 × 10-5 5.2 × 10-2/2 5.2 × 10-2 1.8 × 10-4/2 1.3 × 10-3
TagSNPs-Rh 8.7 × 10 -4 /4 2.0 × 10 -4 2.4 × 10-3/2 5.1 × 10-4 1.3 × 10-2/1 1.3 × 10-2 5.2 × 10-2/2 5.2 × 10-2 5.5 × 10-4/3 3.2 × 10-3
TagSNPs-Rh-trios 6.4 × 10 -4 /3 1.4 × 10 -4 2.8 × 10-2/4 4.1 × 10-4 1.3 × 10-2/1 1.3 × 10-2 5.2 × 10-2/2 5.2 × 10-2 1.2 × 10-4/2 8.4 × 10-3
  1. aSubset methods are sorted into pairwise, multimarker, and haplotype-based methods.
  2. bp-set/df, global score test considering entire set.
  3. cmin(p), smallest p-value considering three-SNP haplotypes across set.
  4. dBold, <0.01.