Table 1.
The “tag SNPs” were those used to genotype these same genes in our original study [3]; “GWAS SNPs” were obtained by GWAS genotyping of these DNA samples after the tag SNP study was completed; and the “HapMap” imputed and “1000 Genomes” imputed columns list the number of SNPs imputed from those two reference sets after removal of poorly imputed SNPs based on imputation-Rsq values.
| Gene | Tag SNPs | GWAS SNPs | HapMap Imputed |
“1000 Genomes” Imputed |
|---|---|---|---|---|
| GLDC | 76 | 105 | 346 | 1466 |
| AMT | 2 | 17 | 107 | 351 |
| DLD | 12 | 103 | 333 | 765 |
| GCSH | 15 | 117 | 441 | 1802 |
| SHMT1 | 19 | 38 | 167 | 561 |
| SHMT2 | 7 | 38 | 112 | 404 |
| Total | 131 | 418 | 1506 | 5349 |