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Table 1 Conditional tests of association between RA and classical HLA alleles through SNP surrogates

From: On the association between rheumatoid arthritis and classical HLA class I and class II alleles predicted from single-nucleotide polymorphism data

     

SE-e

SE+f

HLA allele

Frequencya

Surrogate (allele/haplotype)b

r 2c

p-valued

OR

CI-low

CI-high

OR

CI-low

CI-high

DQA*0301

0.27

rs660895 (G)

0.96

2.13 × 10-12

2.11

1.38

3.24

2.11

1.65

2.71

DQB*0501

0.11

rs17533090, rs9275406, rs9275439 (AAG)

1.00

4.30 × 10-11

0.33

0.04

2.61

0.43

0.33

0.55

DQA*0101

0.13

rs9268832, rs2395185, rs7774434 (GCG)

0.80

5.12 × 10-08

0.58

0.20

1.68

0.48

0.37

0.62

B*0801

0.16

rs3134792 (C)

1.00

1.86 × 10-4

1.54

1.03

2.30

3.03

1.27

7.23

DQB*0302

0.19

rs9275312 (G)

0.94

1.96 × 10-4

2.23

1.28

3.89

1.38

1.07

1.79

C*0401

0.08

rs9264904 (A)

1.00

1.99 × 10-4

0.85

0.56

1.30

0.59

0.44

0.79

  1. aFrequency estimated from the data of de Bakker et al. [8]
  2. bAlleles or haplotypes used as surrogate for the HLA alleles, with corresponding SNPs
  3. cr2 measure of linkage disequilibrium between the HLA allele and the surrogate
  4. dp-value for the two degrees of freedom conditional test of association
  5. eOdds ratio and 95% confidence interval for HLA alleles on non-SE allele bearing haplotypes
  6. fOdds ratio and 95% confidence interval for HLA alleles on SE allele bearing haplotypes