Results of single point analysis for JIA subtypes and 5723 WTCCC2 controls, showing tSNPs associated at p<0.05. MAF = minor allele frequency.

<p>Significant evidence of association was detected at rs1400986 for sJIA.</p>*<p>Allele frequencies of the first allele (minor allele) is indicated.</p>∧<p>rs2981572 is from PGA.</p>†<p>tSNPs examined for correlation between lymphoblastoid mRNA expression and HapMap genotypes.</p

Imputation analysis for sJIA, pOJIA, and eOJIA, showing nominal (p = 0.05) and region-wide significance at p = 00016.

<p>For imputed SNPs a cut-off of Rsq >0.3 was used (see text).</p

Conditional analysis, conditioning on the SNP with the strongest evidence of association, and adding additional SNPs into the model.

<p>For each JIA subtype, the most significant SNP from single point analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047673#pone-0047673-t001" target="_blank">Table 1</a>) was used to start the conditional analysis, and then the most significant SNP achieving at least suggestive significance (p<0.0189) was added into the conditional model until no further SNPs were identified. In parentheses are reported the empirical p-values obtained by running 100,000 permutations.</p

Linear regression analysis between tSNPs and HapMap lymphoblastoid cell line expression levels <i>of MAPKAPK2, IL-10, IL-20, FCAMR</i> and <i>C1orf116</i>.

*<p>Allele with increased frequency in children with JIA compared with controls. This corresponds to the minor alleles for all except rs4129024 where the frequency of major allele G is higher in cases than controls.</p>†<p>Two transcript encoding two different isoforms have been found for this gene. They code for the same number of exons but differ at the 3′UTR region.</p>‡<p>The linear regression model was used to evaluate the association between log2-transformed expression values and genotypes of tSNPs. Associations reaching nominal significance (p<0.05) are shown in bold. One SNP reached the Bonferroni corrected threshold for 12 tests of 0.0042 = 0.05/12.</p

Odds ratios for each haplotype in the best-fitting model for each JIA subtypes, with 95% CI (grey band, with width proportional to haplotype frequency in controls).

<p>Odds ratios for each haplotype in the best-fitting model for each JIA subtypes, with 95% CI (grey band, with width proportional to haplotype frequency in controls).</p

Conditional analysis on the most significant SNPs for each JIA subtype.

<p>For each SNP, the square represents the p-value after adjusting for the effect of the conditioned SNP, while the other end of the line shows the p-value of a single-locus analysis, prior to conditioning. Colours show the range of r² between the conditioned SNP and the tested SNP as indicated in the insert. Location of the conditioned SNPs is indicated by a black square. Thresholds are indicated for nominal (p = 0.05), suggestive (p = 0.0189) thresholds, with tSNPs above suggestive threshold indicated in bold.</p

Single point results for sJIA, pOJIA, and eOJIA.

<p>Point colours indicate the different JIA subtypes. Thresholds are indicated for nominal (p = 0.05) and region-wide significance (p = 0.00166).</p