Table 2 Comparison of number of tag SNPs generated by LDselect and Tagger in Haploview using Caucasian datasets (HAPMAP, NHLBI, Seattle SNPs). A "test" in Tagger refers to a combination of one to three tag SNPs used to capture one or more SNPs. The number of tests is the number of tag SNPs combinations required to capture all SNPs with a minimum value of r2 of 80%. HapMap Phase 1 data was all that was available at the time of SNP selection.
From: SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis
No. SNPs | Tagger | LDselect | Difference | Tags/Total Tagger | Tags/Total LDselect | ||
|---|---|---|---|---|---|---|---|
Gene | Data Source | MAF > 3% | Tags/Tests | Tags | |||
ACO1 | HapMap | 27 | 13/15 | 15 | 2 | 0.48 | 0.56 |
CP | HapMap | 11 | 8/8 | 8 | 0 | 0.73 | 0.73 |
CYBRD1 | HapMap | 10 | 5/5 | 5 | 0 | 0.50 | 0.50 |
NHLBI RS&G | 62 | 14/14 | 16 | 2 | 0.23 | 0.26 | |
FLVCR | HapMap | 17 | 6/8 | 8 | 2 | 0.35 | 0.47 |
NHLBI RS&G | 99 | 16/19 | 17 | 1 | 0.16 | 0.17 | |
FTH1 | NHLBI RS&G | 13 | 5/5 | 5 | 0 | 0.38 | 0.38 |
HAMP | NHLBI RS&G | 7 | 4/4 | 4 | 0 | 0.57 | 0.57 |
HCP1 | NHLBI RS&G | 6 | 3/3 | 3 | 0 | 0.50 | 0.50 |
HEPH | HapMap | 40 | 6/6 | 6 | 0 | 0.15 | 0.15 |
IREB2 | HapMap | 12 | 4/5 | 5 | 1 | 0.33 | 0.42 |
SLC11A2 | HapMap | 13 | 4/4 | 4 | 0 | 0.31 | 0.31 |
SLC40A1 | HapMap | 6 | 3/4 | 4 | 1 | 0.50 | 0.67 |
TF | HapMap | 11 | 7/7 | 7 | 0 | 0.64 | 0.64 |
NHLBI RS&G | 43 | 17/20 | 20 | 3 | 0.40 | 0.47 | |
SeattleSNPs | 101 | 29/31 | 31 | 2 | 0.29 | 0.31 | |
TFR2 | NHLBI RS&G | 6 | 4/4 | 4 | 0 | 0.67 | 0.67 |
TFRC | HapMap | 12 | 6/6 | 6 | 0 | 0.50 | 0.50 |
NHLBI RS&G | 117 | 33/38 | 36 | 3 | 0.28 | 0.31 |