|  | beta (p-value) of SNP | |||
---|---|---|---|---|---|
 |  | sSNP* | nSNP** | Positive Control SNPs | |
Method for selecting PCs | Selected PCs | rs2322659 | rs2290305 | rs1042725 | rs6060369 |
No PC Adjustment | NA | -0.406 (< 0.001) | -0.086 (0.338) | -0.251 (0.002) | 0.221 (0.007) |
Top 2 PCs | PC1, PC2 | -0.043 (0.646) | -0.064 (0.491) | -0.149 (0.073) | 0.336 (< 0.001) |
Top 10 PCs | PC1 - PC10 | -0.057 (0.563) | -0.054 (0.571) | -0.132 (0.121) | 0.322 (< 0.001) |
Tracy-Widom statistic | PC1 - PC81 | -0.062 (0.566) | -0.057 (0.581) | -0.174 (0.061) | 0.318 (0.001) |
Associated with the outcome at α = 0.05 | PC1, PC2, PC4, PC8, PC21, PC25, PC28, PC39, PC47, PC49, PC56, PC64, PC77 | -0.03 (0.762) | -0.049 (0.617) | -0.164 (0.059) | 0.313 (0.001) |
Associated with the outcome at α = 0.01 | PC1, PC4, PC21, PC25, PC28, PC49, PC77 | -0.015 (0.875) | -0.053 (0.578) | -0.162 (0.059) | 0.322 (< 0.001) |
Associated with the outcome at α = 0.001 | PC1, PC4, PC28 | 0.014 (0.884) | -0.047 (0.619) | -0.163 (0.055) | 0.322 (< 0.001) |
Associated with the SNP at α = 0.05 | varied by SNP | -0.041 (0.677) | -0.092 (0.312) | -0.148 (0.075) | 0.333 (< 0.001) |
Associated with the SNP at α = 0.01 | varied by SNP | -.038 (0.703) | -0.086 (0.338) | -0.164 (0.170) | 0.313 (< 0.001) |
10% Rule | PC1# | -0.037 (0.692) | -0.086 (0.338) | -0.148 (0.075) | 0.333 (< 0.001) |
PC-Finder [21] | NA | -0.406 (< 0.001) | -0.086 (0.338) | -0.251 (0.002) | 0.221 (0.007) |