Table 3.
Proportion of p-values falling below nominal levels for selected traits
| SNPs with MAF ≥ 10%, HWE p ≥ 0.001 and Genotyping Call Rate ≥ 80% | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Nominal alpha level | |||||||||
| # SNPs | 0.05 | 0.01 | 0.001 | 1 × 10-4 | 1 × 10-5 | 1 × 10-6 | 1 × 10-7 | 1 × 10-8 | |
| Metabolic Traits* | |||||||||
| Mean† FBAT | 70987 | 0.050 | 0.010 | 8.5 × 10-4 | 7.3 × 10-5 | 5.1 × 10-6 | 6.1 × 10-7 | 1.4 × 10-7 | 0 |
| Min† FBAT | 0.046 | 0.008 | 4.4 × 10-4 | 0 | 0 | 0 | 0 | 0 | |
| Max† FBAT | 0.056 | 0.012 | 1.5 × 10-3 | 2.7 × 10-4 | 5.6 × 10-5 | 4.2 × 10-5 | 2.8 × 10-5 | 0 | |
| Mean GEE | 70987 | 0.058 | 0.013 | 1.6 × 10-3 | 2.3 × 10-4 | 3.7 × 10-5 | 7.9 × 10-6 | 1.9 × 10-6 | 1.0 × 10-7 |
| Min GEE | 0.051 | 0.010 | 9.2 × 10-4 | 5.6 × 10-5 | 0 | 0 | 0 | 0 | |
| Max GEE | 0.081 | 0.022 | 3.3 × 10-3 | 6.6 × 10-4 | 1.4 × 10-4 | 8.5 × 10-5 | 5.6 × 10-5 | 1.4 × 10-5 | |
| CVD Events* | |||||||||
| Mean FBAT | 70987 | 0.050 | 0.009 | 6.6 × 10-4 | 4.4 × 10-5 | 4.0 × 10-6 | 0 | 0 | 0 |
| Min FBAT | 0.047 | 0.006 | 1.7 × 10-4 | 0 | 0 | 0 | 0 | 0 | |
| Max FBAT | 0.053 | 0.010 | 9.4 × 10-4 | 8.5 × 10-5 | 1.4 × 10-5 | 0 | 0 | 0 | |
| Mean GEE | 70987 | 0.054 | 0.012 | 1.4 × 10-3 | 1.8 × 10-4 | 2.4 × 10-5 | 6.7 × 10-6 | 2.7 × 10-6 | 6.7 × 10-7 |
| Min GEE | 0.046 | 0.009 | 7.9 × 10-4 | 4.2 × 10-5 | 0 | 0 | 0 | 0 | |
| Max GEE | 0.062 | 0.015 | 2.5 × 10-3 | 5.9 × 10-4 | 1.3 × 10-4 | 5.6 × 10-5 | 2.8 × 10-5 | 1.4 × 10-5 | |
| All SNPs posted on website http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 | |||||||||
| Metabolic Traits* | |||||||||
| Mean FBAT | 100584 | 0.050 | 0.009 | 7.7 × 10-4 | 6.3 × 10-5 | 4.3 × 10-6 | 5.7 × 10-7 | 1.2 × 10-7 | 0 |
| Min FBAT | 0.046 | 0.008 | 4.4 × 10-4 | 0 | 0 | 0 | 0 | 0 | |
| Max FBAT | 0.054 | 0.011 | 1.3 × 10-3 | 2.2 × 10-4 | 5.0 × 10-5 | 3.0 × 10-5 | 2.0 × 10-5 | 0 | |
| Mean GEE | 101944 | 0.061 | 0.015 | 2.4 × 10-3 | 5.5 × 10-4 | 1.9 × 10-4 | 8.4 × 10-5 | 4.3 × 10-5 | 2.5 × 10-5 |
| Min GEE | 0.052 | 0.012 | 1.5 × 10-3 | 1.9 × 10-4 | 3.0 × 10-5 | 0 | 0 | 0 | |
| Max GEE | 0.082 | 0.025 | 1.1 × 10-2 | 6.8 × 10-3 | 4.3 × 10-3 | 2.6 × 10-3 | 1.7 × 10-3 | 9.4 × 10-4 | |
| CVD Events* | |||||||||
| Mean FBAT | 101060 | 0.048 | 0.008 | 5.9 × 10-4 | 3.5 × 10-5 | 3.3 × 10-6 | 0 | 0 | 0 |
| Min FBAT | 0.043 | 0.005 | 1.2 × 10-4 | 0 | 0 | 0 | 0 | 0 | |
| Max FBAT | 0.052 | 0.010 | 9.1 × 10-4 | 9.9 × 10-5 | 1.0 × 10-5 | 0 | 0 | 0 | |
| Mean GEE | 103194 | 0.059 | 0.016 | 3.4 × 10-3 | 1.1 × 10-3 | 4.7 × 10-4 | 2.0 × 10-4 | 9.5 × 10-5 | 4.4 × 10-5 |
| Min GEE | 0.050 | 0.011 | 1.1 × 10-3 | 1.3 × 10-4 | 2.9 × 10-5 | 0 | 0 | 0 | |
| Max GEE | 0.078 | 0.033 | 1.4 × 10-2 | 7.1 × 10-3 | 3.6 × 10-3 | 1.6 × 10-3 | 7.8 × 10-4 | 3.3 × 10-4 | |
* There were 415 Metabolic Traits and 14 CVD Events from which these descriptive statistics were calculated using the # SNPs indicated. # SNPs = average number of SNPs across all traits in the Trait Group; †Mean = average proportion of SNPs below nominal level across phenotypes in the trait group; Min = minimum proportion below nominal level across phenotypes in the trait group; Max = maximum proportion below nominal level across phenotypes in the trait group.