Table 2. Summary statistics of PAX6 SNPs in the initial study and the replication study: Genotype counts, Hardy-Weinberg equilibrium testing, minor allele frequencies and single-marker association analysis.a .
| Allele | Genotype counts (11/12/22) | HWE (P value) | Minor allele freq | Association (best result) | ||||||
| SNP | 1 | 2 | Cases | Controls | Cases | Controls | Cases | Controls | P value | Model |
| Initial study – Group 1 subjects | ||||||||||
| rs3026354(S1) | T | C | 144/129/27 | 159/115/26 | 0.8919 | 0.4718 | 0.3050 | 0.2783 | 0.2206 | Dom |
| rs667773(S2) | C | T | 191/102/7 | 181/110/9 | 0.1407 | 0.1242 | 0.1933 | 0.2133 | 0.3668 | Add |
| rs3026390(S3) | A | G | 103/146/51 | 96/146/58 | 1.0000 | 0.9065 | 0.4133 | 0.4367 | 0.4136 | Allelic |
| rs2071754(S4) | G | A | 101/141/58 | 89/144/67 | 0.4811 | 0.5621 | 0.4283 | 0.4633 | 0.2226 | Allelic |
| rs3026393(S5) | T | G | 89/163/48 | 81/161/58 | 0.0775 | 0.2013 | 0.4317 | 0.4617 | 0.2726 | Add |
| rs1506(S6) | A | T | 69/167/64 | 78/154/68 | 0.0643 | 0.7286 | 0.4917 | 0.4833 | 0.3929 | Dom |
| rs12421026(S7) | G | A | 95/162/43 | 85/158/57 | 0.0573 | 0.2970 | 0.4133 | 0.4533 | 0.1251 | Rec |
| rs662702(S8) | G | A | 195/94/11 | 181/107/21 | 1.0000 | 0.5019 | 0.1933 | 0.2183 | 0.2373 | Dom |
| rs3026401(S9) | G | A | 62/176/62 | 71/171/58 | 0.0038 | 0.0155 | 0.5000 | 0.4783 | 0.3764 | Dom |
| rs7125966(S10) | G | C | 96/166/49 | 89/147/55 | 0.3443 | 0.4129 | 0.4217 | 0.4433 | 0.4356 | Add |
| rs2863231(S11) | T | C | 109/142/48 | 107/147/46 | 0.9047 | 0.8095 | 0.3983 | 0.3983 | 0.8223 | Rec |
| rs964112(S12) | G | T | 80/159/61 | 90/144/66 | 0.2977 | 0.5623 | 0.4683 | 0.4600 | 0.3649 | Dom |
| rs7947424(S13) | C | T | 133/140/27 | 133/133/34 | 0.2918 | 1.0000 | 0.3233 | 0.3350 | 0.3443 | Rec |
| rs11031423(S14) | T | C | 192/99/9 | 188/97/15 | 0.4635 | 0.6037 | 0.1950 | 0.2117 | 0.2113 | Rec |
| rs11031419(S15) | A | T | 208/86/6 | 195/101/4 | 0.5266 | 0.0304 | 0.1633 | 0.1817 | 0.2584 | Dom |
| rs509628(S16) | C | T | 119/148/33 | 125/138/37 | 0.2109 | 1.0000 | 0.3567 | 0.3533 | 0.6110 | Rec |
| Replication study – Group 2 subjects | ||||||||||
| rs3026390(S3) | A | G | 107/141/51 | 111/133/55 | 0.719 | 0.1875 | 0.4064 | 0.4064 | 0.6684 | Rec |
| rs2071754(S4) | G | A | 98/145/55 | 99/135/65 | 0.906 | 0.1593 | 0.4279 | 0.4431 | 0.317 | Rec |
| rs3026393(S5) | T | G | 106/143/50 | 99/138/62 | 0.905 | 0.2909 | 0.4064 | 0.4381 | 0.2085 | Rec |
| rs1506(S6) | A | T | 80/159/60 | 85/141/73 | 0.295 | 0.3544 | 0.4666 | 0.4799 | 0.2011 | Rec |
| rs12421026(S7) | G | A | 98/151/50 | 110/131/58 | 0.555 | 0.0959 | 0.4197 | 0.4130 | 0.2588 | Geno |
The SNPs are arranged in sequential order from the 5′ end to the 3′ end of the sense strand of the PAX6 gene, and are also designated as S1 to S16 for the sake of easy reference and discussion. The major allele is designated as “1” and minor allele as “2”; and the genotype counts are indicated as the counts of the genotypes 11, 12 and 22, respectively. HWE stands Hardy-Weinberg equilibrium. Single-marker association analysis is performed under five models for each SNP: genotypic (Geno), additive (Add; tested by Armitage trend test), dominant (Dom), recessive (Rec) and allelic models. However, only the best result and the corresponding model are shown for each SNP. Note that single-marker analysis did not show significant results for any of the 16 SNPs tested.