Skip to main content

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