Table 3. Summary of exhaustive haplotype analyses based on sex-adjusted omnibus tests for sliding windows of all possible sizes across 16 SNPs under study for subjects of Group 1.a .
| Sliding window (SW) | SW with omnibus test P emp <0.05 | Most significant result | |||||||
| SNPs/SW | No. of SW | No. of SW | First SW | Last SW | SW | P asym | P emp | ||
| 1 | 16 | 0 | - | - | - | - | - | ||
| 2 | 15 | 2 | S6..S7 | S7..S8 | S6..S7 | 1.12E-08 | 2.00E-05 | ||
| 3 | 14 | 3 | S5..S7 | S7..S9 | S5..S7 | 5.48E-10 | 2.00E-05 | ||
| 4 | 13 | 4 | S4..S7 | S7..S10 | S4..S7 | 3.54E-10 | 2.00E-05 | ||
| 5 | 12 | 5 | S3..S7 | S7..S11 | S3..S7 | 2.24E-08 | 2.00E-05 | ||
| 6 | 11 | 6 | S2..S7 | S7..S12 | S2..S7 | 4.32E-09 | 2.00E-05 | ||
| 7 | 10 | 7 | S1..S7 | S7..S13 | S2..S8 | 6.70E-08 | 2.00E-05 | ||
| 8 | 9 | 7 | S1..S8 | S7..S14 | S2..S9 | 7.48E-08 | 2.00E-05 | ||
| 9 | 8 | 7 | S1..S9 | S7..S15 | S7..S15 | 3.81E-06 | 4.00E-05 | ||
| 10 | 7 | 7 | S1..S10 | S7..S16 | S4..S13 | 5.24E-08 | 2.00E-05 | ||
| 11 | 6 | 6 | S1..S11 | S6..S16 | S4..S14 | 1.40E-06 | 2.00E-05 | ||
| 12 | 5 | 5 | S1..S12 | S5..S16 | S2..S13 | 7.79E-07 | 2.00E-05 | ||
| 13 | 4 | 4 | S1..S13 | S4..S16 | S3..S15 | 1.99E-06 | 2.00E-05 | ||
| 14 | 3 | 3 | S1..S14 | S3..S16 | S3..S16 | 3.87E-06 | 4.00E-05 | ||
| 15 | 2 | 2 | S1..S15 | S2..S16 | S2..S16 | 2.23E-05 | 3.00E-04 | ||
| 16 | 1 | 1 | S1..S16 | S1..S16 | S1..S16 | 1.09E-03 | 2.02E-02 | ||
Exhaustive haplotype analyses were performed using sliding windows (SW) of all possible sizes (i.e. number of SNPs per SW; 1 to 16 SNPs per SW) with PLINK. With logistic regression, a single case-control omnibus test of (H - 1) degrees of freedom was carried out for each sliding window to jointly assess the significance of the haplotype effects for this SW and adjusted for sex (as a covariate), where H is the number of haplotypes for the SW under consideration. Here, a single asymptotic P value (P asym) was produced for each SW. For a given window size, the test was performed for all possible windows of the same size, shifting one SNP at a time. There were a total of 136 windows (the sum of numbers in column 2), and multiple comparisons were corrected by running 50,000 permutations to obtain an empirical P value (P emp). The minimum P value that is achievable with 50,000 permutations is 2.00×10−5. The SW is indicated as Sa..Sb, where a is the first SNP and b the last SNP of the SW. For example, S4..S7 refers to the SW S4-S5-S6-S7. The three rightmost columns show the most significant results for each fixed-size SW. Note that, among all 136 windows tested, S4..S7 ranks the first and S5..S7 the second in providing evidence for association with high myopia.