Systemic lupus erythematosus and rheumatoid arthritis

RA, control frequencies P-value* Empirical P-value** 

rs3811021 T 
0.817, 0.780 
0.0197 
0.0737 
+1858 T 
0.176, 0.114 
2.9 E-7 
<1.0 E-5 
-1123 C 
0.300, 0.241 
4.0 E-4 
0.0017 
TTC 
0.175, 0.117 
7.5 E-7 
<1.0 E-5 
CCG 
0.183, 0.215 
0.0175 
0.0667 
TCG 
0.517, 0.548 
0.0642 
0.2230 
TCC 
0.126, 0.121 
0.6398 
0.9838 
* 
χ
2
, ** after 100,000 permutations 
Patients with RA were stratified according to 
HLA-SE
, IgM-RF, and ACPA, and 
the minor allele frequencies of the SNPs compared with those of the control 
population. The 1858T allele was highly associated with 
HLA-SE
, IgM-RF, and 
ACPA positive RA, whereas the -1123C allele was associated regardless of 
stratification (Table 17). 
Although the 1858C/T and -1123G/C polymorphisms were in LD, it was 
possible to identify 144 RA patients carrying the -1123C allele but not the 
1858T allele. However, it was not possible to study the independent effect of 
the 1858T allele since only 2 RA patients were singly positive for the 1858T 
allele. We found that patients singly positive for the -1123C allele had 
significantly lower frequencies 
HLA-SE
and ACPA, compared with patients 
carrying both risk alleles (Table 18). 
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