Only SNPs genotyped in this study are listed by name.

<p>SNPs in linkage disequilibrium with SNPs genotyped in this study are shown in brown. SNPs in gray were not genotyped or haplotype tagged due to low minor allele frequency (MAF). SNP - Single Nucleotide Polymorphism. 5251* is not yet registered in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p

Odds ratios for the protective effect of the rs231778 G allele in African Americans with RA.

<p>Analysis compares number of patients and controls for genotype AA vs those with either AG or GG in a 2×2 Fisher's exact test. OR – odds ratio; CI – confidence interval.</p

This plot, generated from HaploView v3.31 (Broad Institute), shows the r² values between SNPs genotyped in <i>CTLA4</i>.

<p>Darker boxes represent stronger r² values. 5251* is not yet registered in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p

Association with rheumatoid arthritis at rs231778 in African Americans.

<p>Values indicate number of samples with allele frequency in parentheses. Analysis compares number of patients and controls for each genotype (AA vs AG vs GG) in a 3×2 Fisher's exact test.</p

Minor allele frequencies of CTLA4 SNPs for African American RA patients and controls.

<p>This table represents combined data from CLEAR I and CLEAR II. rs3087243 (+60C/T) has been associated with RA in Caucasians, and rs231775 (+49A/G) has been associated with other autoimmune conditions. Position is the physical location of each polymorphism relative to the start codon (position = 0) in dbSNP build 129. CCP refers to anti-cyclic citrullinated antibody status. SE refers to presence of HLA-DRB1 shared epitope. Public databases include allele frequencies from HapMap or SeattleSNP. rs231776 was not in Hardy-Weinberg Equilibrium. *5251 is not currently listed in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p

Mean percentage of European ancestry segregated by genotype of rs231778.

<p>This table provides data for the 347 samples with complete admixture and rs231778 genotyping data. Standard error is provided in parenthesis. Brackets indicate frequency counts used in determining association of the rs231778 G allele with rheumatoid arthritis among 366 samples, as described in the text.</p

Minor allele frequency (MAF) of rs231778 segregated by HLA-DRB1 shared epitope status.

<p>This table combines samples from both CLEAR I and CLEAR II and only incorporates data where HLA-DRB1 shared epitope (SE) status has been determined. The ‘N’ listed below each MAF represents the number of ‘G’ alleles over the total number of alleles for each number of SE alleles present. SE – <i>HLA-DRB1</i> shared epitope.</p