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Table 3 Study design. Lengths of re-sequenced genomic regions, and number of tag SNPs or single SNPs genotyped in a pragmatic two-step genotyping design for NRAMP1, 4-1BB, FRAP1, CD101, B2M, and VAV3.

From: Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

Locus

Re-sequenced region (kb)

n common SNPs*

n tag SNPs

Genotyping strategy (step 1 → step 2)

NRAMP1

12.13

12

4

Case-control → Family set 1+2

4-1BB

13.66

8

DIL4279/ss23142250

Family set 1

   

DIL4277/rs226476

 
   

DIL4569/rs226478

 
   

DIL4274/ss23142263

 
   

DIL4570/ss23142264

 
   

DIL4571/rs679563

 
   

DIL4273/ss23142265

 
   

DIL4272/ss23142270

 

FRAP1

30.88

21

6

Family set 1

CD101

15.9

18

8

Family set 1

B2M

9.33

10

8

Case-control → Family set 1

VAV3

27.69

19 (block 1)

18 (block 2)

15 (block 3)

7 (block 1)

11 (block 2)

10 (block 3)

Family set 1

  1. *For the selection of tag SNPs, minor allele frequencies of 0.03 were used for 4-1BB, CD101 and FRAP1, and 0.05 for NRAMP1, B2M and VAV3. Note that the numbers of attempted and actual genotypes are given in Additional file 8. n, number.