Zoom views of the association results in the loci associated with IL-6 and ESR.

<p>Each panel shows the association curve around the strongest SNP, which is highlighted with a purple dot. The SNPs are coloured according to their linkage disequilibrium (r²) with the top variant in the 1000 Genomes European data set, with symbols that reflect genomic annotation as indicated in the legend. Arrows highlight independent signals, if any, described in the manuscript; while light blue lines indicate the recombination rate, according to the right-hand Y axis. Genomic positions are as in build 37. Gene transcripts are annotated in the lower box. Plots were drawn using the standalone LocusZoom version <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002480#pgen.1002480-Pruim1" target="_blank">[65]</a>.</p

Manhattan plot and QQ plot of association findings.

<p>The figure summarizes the association results obtained on the ImmunoChip and MetaboChip markers (Step 3). The blue dotted line marks the Bonferroni threshold significance levels (1.7×10⁻⁷), and SNPs in loci exceeding this threshold are highlighted in green. The bottom panel represents the QQ plot, where the red line corresponds to all test statistics, and the blue line to results after excluding statistics at top markers (highlighted in green in the Manhattan Plot). The gray area corresponds to the 90% confidence region from a null distribution of P values (generated from 100 simulations).</p

Top genome-wide association results for IL-6, ESR, MCP-1, and hsCRP.

<p>The table summarizes top genome-wide association signals for IL-6, ESR, MCP-1 and hsCRP phenotypes in the HapMap based GWAS (Step 1), as well as results in the replication independent cohort (Step 2) and in the combined data-sets. For each marker, frequency and effect estimates are given with respect to the minor allele. Imputation quality scores (RSQ) are reported for imputed SNPs. Novel signals are indicated in bold.</p>a<p>The effect size is measured in standard deviation units, being estimated as the β coefficient of the regression model when using the normalized trait (e.g. an effect size of 1.0 implies each additional copy of the allele being evaluated increases trait values by 1.0 standard deviations).</p>b<p>Independent signals.</p

Zoom views of the association results in the loci associated with MCP-1 and hsCRP.

<p>Each panel shows the association curve around the strongest SNP, which is highlighted with a purple dot. The SNPs are coloured according to their linkage disequilibrium (r²) with the top variant in the 1000 Genomes European data set, with symbols that reflect genomic annotation as indicated in the legend. Arrows highlight independent signals, if any, described in the manuscript; while light blue lines indicate the recombination rate, according to the right-hand Y axis. Genomic positions are as in build 37. Gene transcripts are annotated in the lower box. Plots were drawn using the standalone LocusZoom version <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002480#pgen.1002480-Pruim1" target="_blank">[65]</a>.</p

Top association signals for IL-6, ESR, MCP-1, and hsCRP in the ImmunoChip and MetaboChip data-sets.

<p>The table summarizes top association signals for IL-6, ESR, MCP-1 and hsCRP phenotypes in the ImmunoChip and MetaboChip data-sets (Step 3). For each marker, frequency and effect estimates are given with respect to the minor allele. We also reported the r² with the SNP detected in the GWAS scan (Step 1). Novel signals are indicated in bold.</p>a<p>The effect size is measured in standard deviation units, being estimated as the β coefficient of the regression model when using the normalized trait (e.g. an effect size of 1.0 implies each additional copy of the allele being evaluated increases trait values by 1.0 standard deviations).</p>b<p>I =  ImmunoChip, M =  MetaboChip.</p>c<p>The table reports the pvalue on the primary analysis. On the conditional analysis, the pvalue for the independent SNPs were: rs12378220, 9.43×10⁻⁰⁸; rs3093077, 9.02×10⁻¹¹; rs2259816, 7.58×10⁻¹⁰.</p>d<p>Independent signals.</p

Regional plot of 6p21.3, a non-overlapping locus that was more significantly associated with fibrinogen in the HapMap GWA study, including variants from both the HapMap (red) and 1000G (green) GWA studies.

<p>Regional plot of 6p21.3, a non-overlapping locus that was more significantly associated with fibrinogen in the HapMap GWA study, including variants from both the HapMap (red) and 1000G (green) GWA studies.</p

Summary of the differences between HapMap and 1000G imputation for the seven non-overlapping loci.

<p>Summary of the differences between HapMap and 1000G imputation for the seven non-overlapping loci.</p

Regional plots of non-overlapping loci that were more significantly associated with fibrinogen in the 1000G GWA study, including variants from both the HapMap (red) and 1000G (green) GWA studies.

<p>Regional plots of non-overlapping loci that were more significantly associated with fibrinogen in the 1000G GWA study, including variants from both the HapMap (red) and 1000G (green) GWA studies.</p

Summary of the differences between HapMap and 1000G imputation for the 29 overlapping loci.

<p>Summary of the differences between HapMap and 1000G imputation for the 29 overlapping loci.</p

Overlapping loci that were significant in both the HapMap and 1000G GWA studies.

<p>Overlapping loci that were significant in both the HapMap and 1000G GWA studies.</p