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Table 3 Haplotype frequencies in six human cohorts (haplotypes with f > 0.001). AD/MCI vs CT:GGATC (last column) represents the association of the haplotype with AD when compared to most common European haplotype (Fisher’s exact test); haplotypes with zero frequencies are excluded from analysis

From: Haplotype analysis of APOE intragenic SNPs

Haplotype # added CG (positions) APOE Allele 1000G ADNI
Afr Asian Eur AD MCI CT AD vs CT:GGATC P value MCI vs CT:GGATC P value
G G G CC 3 (1,4,5) ε4 0.292 0.0035 0.0205 0.0984 0.05 0.0371 1.6e-5 0.1975
C G G T C 1 (5) ε3 0.13 0.628 0.363 0.268 0.354 0.379 1 0.7382
G G A T C 2 (1,5) ε3 0.286 0.191 0.423 0.276 0.346 0.389 NA
G G G T C 2 (1,5) ε3 0.208 0.0175 0.00685 0.0137 0.023 0.0234 0.7979 0.8491
G G G T T 1(1) ε2 0.0811 0.0752 0.0616 0.0219 0.0581 0.0703 0.039 0.8065
G A G C C 3 (1,4,5) ε4 0 0.0839 0.119 0.309 0.165 0.0977 2e-13 0.001
G G A T T 1 (1) ε2 0.0027 0 0 0 0 0   
C G A T C 1 (5) ε3 0 0.00175 0 0 0 0   
C G G T T 0 ε2 0 0 0.00411 0 0 0   
G A G C T 2 (1,4) ε3 0 0 0.00137 0 0 0   
G A G T C 2 (1,5) ε3 0 0 0 0.00273 0.00135 0   
C G G C C 2 (4,5) ε4 0 0 0 0.0082 0 0.00391 0.3419  
C A G C C 2 (4,5) ε4 0 0 0 0.00273 0.00135 0   
G G A C C 3 (1,4,5) ε4 0 0 0 0 0.00135 0   
Total haplotypes    370 572 730 366 740 512   
Sample size    185 286 365 183 370 256   
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