Table 2.
Proportion of Interactions Consistent with Confounding Factors
| Confounder |
All Interactions (n = 1,119) |
Bonferroni Replicating Interactions (n = 90) |
||
|---|---|---|---|---|
| Total | (%) | Total | (%) | |
| Ceiling/floor Effect | 48 | (4.30) | 11 | (12.22) |
| Variants in probe | 308 | (27.52) | 15 | (16.68) |
| cis-eQTL | 980 | (87.58) | 78 | (86.68) |
| D′ haplotype | 313 | (27.97) | 43 | (47.78) |
| Population-specific effects | 430 | (38.43) | 58 | (64.44) |
| Missing genotypes | 457 | (40.84) | 37 | (41.11) |
We counted the number of interactions consistent with each alternative explanation; interactions can be consistent with multiple confounders. We considered two categories of interactions: all interactions identified (n = 1,119) and the subset of those that replicated with p values exceeding the Bonferroni multiple testing correction threshold for the entire replication analysis (n = 90).