Conditional logistic regression analysis of the MS associated variants.

<p>F_A, Frequency of affected; F_U, Frequency of unaffected; NA, not applicable; <i>P</i> cond, <i>P</i>-value of logistic regression analysis conditioned on the respective SNP; <i>OR</i>, odds ratio; <i>SNP</i>, single-nucleotide polymorphism. The data from African American are from McElroy et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-McElroy2" target="_blank">[7]</a>.</p

Association of the MS-risk variant rs9271100 with <i>DRB1</i> gene expression levels.

<p>In all plots, expression levels are represented for the three genotype groups. (<b>A</b>) Box plots of expression data from normalized results of ILMN_1715169 (<i>DRB1</i>) probe generated by Illumina Human-6 v2 Expression BeadChip (EMBL-EBI database (<a href="http://www.ebi.ac.uk/arrayexpress/" target="_blank">http://www.ebi.ac.uk/arrayexpress/</a>) ID projects E-MTAB-198). (<b>B</b>) Box plot of expression data from the NM_002124 (<i>DRB1</i>) transcript of 41 CEU individuals obtained from RNA-Seq <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-Cheung1" target="_blank">[19]</a>. P-values are calculated by Kruskal Wallis Test.</p

LD plots of the GWAS- SNPs associated with different immune related disease.

<p>Data are from HapMap III CEU population. (<b>A</b>) Linkage disequilibrium by r². (<b>B</b>) Linkage disequilibrium by D′. Disease abbreviations: Type 1 diabetes (T1D), inflammatory bowel disease (IBD), ulcerative colitis (UC), systemic lupus erythematosus (SLE), asthma and IgA deficiency.</p

Association of HapMap III SNPs from the HLA region with expression levels of the HLA <i>DRB1</i> gene.

<p>The figure shows the strength of association between SNPs and gene expression levels, plotted as −log <i>P</i>-values. Coordinates are in NCBI Build 36. Shown are the CEU, YRI, LWK, MEX, GHI, CHB and JPT HapMap populations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-International1" target="_blank">[26]</a>.</p

Association of risk-variants for different immune-related diseases with expression levels of HLA genes.

<p>Expression data are from CEU individuals obtained from RNA-Seq <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029819#pone.0029819-Caballero1" target="_blank">[9]</a>. The data are from the transcripts <i>DQB1</i> NM_002123, <i>DQA1</i> NM_002122, <i>DRB1</i> NM_002124, <i>DQA2</i> NM_020056 and <i>DRB5</i> NM_002125. Underlined are marked the risk alleles.</p