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Table 3 Predicted haplotypes from the tagging SNPs for each gene and their association with breast cancer

From: Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk

  Set 1 Sets 1 and 2
Gene Haplotype Frequency P value OR 95 percent CI Haplotype Frequency P value OR 95 percent CI
ATM
04,05,06,07,08,09,10,11,12 h010100100 0.30 0.2        
  h000001000 0.28 0.7        
  h000010000 0.14 0.05 0.9 0.78–0.99      
  h100000000 0.09 0.6        
  h010100101 0.07 0.9        
  h010100110 0.05 0.2        
  Combined rare   0.4        
BRCA1
02,01,05,07,06 h00000 0.60 0.7        
  h01101 0.14 0.3        
  h01000 0.09 0.2        
  h01011 0.09 0.2        
  h10000 0.06 0.08 0.9 0.71–1.02      
  Combined rare   0.5        
BRCA2
Block 1: 01,02,03,04,05 h10000 0.42 0.6    h_0_00 0.42 0.5   
  h01000 0.17 0.007 1.2 0.78–0.98 h_1_00 0.17 0.2   
  h01010 0.17 0.02 0.9 0.78–0.98 h_1_10 0.17 0.3   
  h00101 0.15 0.8    h_0_01 0.18 0.3   
  Combined rare   0.4        
Block 2: 07,09,10,22,11 h01010 0.27 0.8    h_1_10 0.27 0.9   
  h01000 0.19 0.05 0.9 0.80–1.00 h_1_00 0.20 0.4   
  h00100 0.18 0.9        
  h10000 0.17 0.8    h_0_00 0.40 0.6   
  h10001 0.07 0.07 1.2 0.99–1.37 h_0_01 0.11 0.2   
  h00000 0.05 0.7        
  Combined rare   0.4        
Block 3: 13,14,16,18,19,21 h000010 0.27 0.6    h0____0 0.57 0.9   
  h000001 0.21 0.1 0.9 0.83–1.02 h0____1 0.22 0.5   
  h100000 0.15 0.04 1.1 1.01–1.27 h1____0 0.21 0.5   
  h010000 0.15 0.2        
  h011000 0.12 0.4        
  h100100 0.06 0.1 1.2 0.98–1.35      
  Combined rare   0.8        
CHEK2
10,11,6,7,5,8,12,13,14,9 h0000000000 0.23 0.3    h_0______00 0.54 0.02 0.9 0.88–0.99
  h1000111000 0.20 0.5        
  h0000000011 0.13 0.2    h_0______11 0.13 0.07 1.1 0.99–1.18
  h0111000010 0.07 0.08 0.9 0.74–1.02 h_1______10 0.07 0.1 0.9 0.81–1.02
  h0000111000 0.07 0.8        
  h0011000010 0.06 0.6    h_0______10 0.25 0.06 1.1 0.99–1.15
  h0010000110 0.06 0.2        
  h0000100010 0.04 0.05 1.3 1.00–1.56      
  Combined rare   0.5    h_0______10 delC 0.004 0.003 2.7 1.40–5.05
TP53
03,01,02,06,07,08 h000000 0.42 0.8        
  h000001 0.28 0.9        
  h011000 0.11 0.3        
  h001001 0.05 0.2        
  Combined rare   0.4        
  1. All haplotypes with predicted frequencies of >0.05 in controls are shown individually. Rarer ones are combined. The single nucleotide polymorphism (SNP) IDs and their order are shown in the first column. CI, confidence interval; OR, odds ratio.