Table 5 Association of SNPs in the HLA region with PBC in the absence of major HLA factors identified in this study.

From: Principal contribution of HLA-DQ alleles, DQB1*06:04 and DQB1*03:01, to disease resistance against primary biliary cholangitis in a Japanese population

Population

Number of individuals

SNPs with p < 5 × 10−8

Odds ratio (95% CI), p

Patients

Controls

rs9268644*

rs9275175†

rs9277509§

All

 

1200

1196

305/4103

0.39 (0.33–0.47), p = 5.64 × 10 −24

0.41 (0.33–0.50), p = 6.06 × 10−18

0.55 (0.46–0.65), p = 1.63 × 10−12

DQB1*06:04 –negative

 

1163

1025

62/4103

0.52 (0.43–0.64), p = 3.69 × 10−10

0.46 (0.36–0.58), p = 8.71 × 10−12

0.63 (0.53–0.75), p = 1.91 × 10−7

DRB1*08:03 –negative

 

917

1017

361/4103

0.42 (0.34–0.51), p = 1.70 × 10−18

0.44 (0.36–0.55), p = 5.76 × 10−14

0.51 (0.42–0.61), p = 5.78 × 10−13

DQB1*03:01 –negative

 

1056

940

333/4103

0.41 (0.33–0.51), p = 3.45 × 10−17

0.43 (0.34–0.56), p = 1.56 × 10−11

0.54 (0.45–0.65), p = 5.45 × 10−11

DQB1*04:01 –negative

 

822

916

251/4103

0.41 (0.33–0.50), p = 1.04 × 10−17

0.43 (0.34–0.53), p = 1.31 × 10−14

0.49 (0.40–0.60), p = 2.05 × 10−12

DQB1*06:04 -negative, DQB1*03:01 –negative

 

1020

790

3/4103

0.65 (0.51–0.83), p = 0.00054

0.54 (0.41–0.71), p = 6.90 × 10−6

0.65 (0.53–0.78), p = 6.87 × 10−6

DRB1*08:03 -negative, DQB1*04:01 –negative

 

594

763

225/4103

0.45 (0.35–0.56), p = 2.13 × 10−12

0.48 (0.38–0.61), p = 5.04 × 10−10

0.45 (0.36–0.57), p = 3.46 × 10−12

DQB1*06:04 -negative, DRB1*08:03 -negative, DQB1*03:01 -negative, DQB1*04:01 -negative

 

476

440

0/4103

0.79 (0.59–1.07), p = 0.13

0.62 (0.46–0.83), p = 0.0013

0.49 (0.37–0.65), p = 2.30 × 10 −7

  1. *A SNP located in the DR locus (the first intron of DRA, chr 6:32408044–32408044), which showed the minimal p value for the dominant model of variant allele in the comparison of all patients and controls (shown in bold).
  2. †A SNP located near the DQ locus (20 kb upstream of DQB1, chr 6: 32654147–32654147), which showed the minimal p value in our previous GWAS (16).
  3. §A SNP located in the DP locus (the fifth intron of DPB1, chr 6: 33054207–33054207), which showed the minimal p value for the dominant model of a variant allele in the absence of four major HLA factors (shown in bold).
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