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Table 3 Independent SNPs in conditional analysis of RA susceptibility

From: Conditional analysis of the major histocompatibility complex in rheumatoid arthritis

Locus (sequence #)a

Unadjusted single-marker

p-value from

haploviewb

Single-marker EIGENSTRAT

p-value (rank)

p-value conditional on loci abovec

p-value conditional on other 3 locic

Location (kb)

Closest gene(s)

Shared epitope (#129)

1.9 × 10-188

N/A

N/A

8.6 × 10-74

32,655-32,666

In DRB1

rs261946 (#1)

7.2 × 10-17

1.9 × 10-9 (185)

0.00019

0.0027

30,379

TRIM39

rs2074488 (#5)

2.3 × 10-24

5.0 × 10-12 (151)

6.6 × 10-5

0.0011

31,348

HLA-C

rs2395175 (#119)

1.4 × 10-117

1.9 × 10-80 (2)

0.00031

0.00031

32,513

Between BTNL2 and HLA-DRA

  1. a# indicates marker position in Figure 1. Loci are in order added by conditional algorithm (see Methods).
  2. bFor shared epitope, multi-allelic SNP test in Whap using No-Low-High risk.
  3. cWhap log ratio test using all loci as alternate model versus null model without this locus.
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BMC Proceedings

ISSN: 1753-6561

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