Table 6.
Estimated Genetic Variance on the Observed and Liability Scale Explained by All SNPs for Type I Diabetes from an Analysis without Chromosome 6 or of Chromosome 6 Only
| Thresholda | No. SNPb | Estimatec(SE) | LR | Adjustedd(SE) | Transformede(SE) |
|---|---|---|---|---|---|
| Analysis without chromosome 6 | |||||
| 200 | 297,028 | 0.23 (0.07) | 11.98 | 0.26 (0.08) | 0.13 (0.04) |
| 20 | 270,332 | 0.22 (0.07) | 10.66 | 0.25 (0.08) | 0.12 (0.04) |
| 7 | 223,039 | 0.20 (0.07) | 9.08 | 0.23 (0.08) | 0.12 (0.04) |
| 4 | 167,099 | 0.20 (0.06) | 10.17 | 0.26 (0.08) | 0.13 (0.04) |
| Analysis of chromosome 6 only | |||||
| 200 | 21,016 | 0.33 (0.02) | 268.55 | 0.37 (0.03) | 0.18 (0.01) |
| 20 | 19,131 | 0.33 (0.02) | 278.09 | 0.37 (0.03) | 0.18 (0.01) |
| 7 | 15,766 | 0.32 (0.02) | 255.65 | 0.36 (0.03) | 0.18 (0.01) |
| 4 | 11,793 | 0.31 (0.02) | 264.63 | 0.38 (0.03) | 0.19 (0.01) |
a
Excluding SNPs with more than the listed number of missing genotypes.
b
After filtering on the basis of SNP missing rate.
c
Estimate of genetic variance proportional to the total phenotypic variance on the observed scale.
d
Estimate adjusted for reduced number of SNPs.
e
Transformed genetic variance proportional to the total phenotypic variance on the liability scale assuming that the population prevalence is 0.5%. SNPs with an MAF > 0.01 were used.