Table 5.
SNP allele and genotype frequency association analysis for the three Sample sets.
| Gene | Function | SNP | Alleles | Sample set | MAF A/U | OR (95% CI)* |
P-values allele | P-values genotype | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| * | Empirical | Cochran- Armitage trend* | Dominant model* | Recessive model* | |||||||
| CLOCK | Intron | rs11240 | G/C | 1. | 0.44/0.33 | 1.65 (1.14-2.38) |
0.0077 | 0.0072 | 0.0077 | 0.055 | 0.013 |
| 2. | 0.33/0.33 | 1.02 (0.85-1.24) |
Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.44/0.33 | 1.59 (1.13-2.26) |
0.0084 | 0.0068 | 0.0082 | 0.048 | 0.016 | ||||
| ARNTL2 | Intron | rs2306074 | C/T | 1. | 0.30/0.35 | 0.77 (0.53-1.12) |
Ns | Ns | Ns | 0.043 | Ns |
| 2. | 0.33/0.35 | 0.90 (0.74-1.09) |
Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.30/0.34 | 0.80 (0.55-1.15) |
Ns | Ns | Ns | 0.056 | Ns | ||||
| ACADS | Mis-sense mutation | rs1799958 | A/G | 1. | 0.34/0.26 | 1.47 (1.01-2.15) |
0.045 | 0.044 | 0.045 | 0.097 | Ns |
| 2. | 0.28/0.26 | 1.11 (0.91-1.37) |
Ns | Ns | Ns | Ns | Ns | ||||
| 3. | 0.34/0.27 | 1.44 (1.01-2.07) |
0.046 | 0.040 | 0.046 | 0.097 | Ns | ||||
SNPs which showed nominal association (allelic or genotypic) P < 0.05 for Sample set 1 are displayed as are the p-values P < 0.1. Ns = non significant. Analysis in Sample set 2 and 3 were then performed for these SNPs. Alleles: the minor allele first. Odds ratio (OR): the proportion of minor versus major allele in the affected (A) divided by the proportion of minor versus major allele in the non-affected (U) individuals. Empirical P is the point-wise P-value after 10,000 permutations.* gender was used as covariate.