Replication results of nine signals in 7,000 African Americans.

<p>RAF risk allele frequency, SE standard error.</p

Loci with significant evidence of independent lipid association signals.

<p>Chr chromosome, BP base pair, RAF risk allele frequency, SE standard error.</p

Regional plots for novel lipid loci with array-wide significant regions in IBC meta-analysis of African ancestry.

<p><b>A.. </b><i>CD36</i> region, <b>B.. </b><i>ICAM1</i> region. Loci are shown as the lead SNP with a flanking region depicting the candidate gene and nearby genes included on the array. The purple diamond represents the lead SNP in the IBC meta-analysis and the dots represent the surrounding SNPs, with the different colors showing the LD relationship with the lead SNP based on YRI HapMap II information. −log10 p-values for association with HDL-C (for <i>CD36</i>) and TC (for <i>ICAM1</i>) are shown for each SNP (left-hand axis). Recombination rates in YRI HapMap II is shown in blue traces (right-hand axis).</p

Schematic design of study for the multi-ethnic IBC-Lipid association meta-analysis.

<p>The workflow includes primary analyses and secondary analyses. Details can be found in the text.</p

Interrogation of best SNPs with the smallest p-value within known EA loci in AA for trait WHR ratio adjusted for BMI.

<p>The index SNPs are from Heid et al, Nature Genetics 2010 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen.1003681-Heid1" target="_blank">[17]</a>. Note that <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t003" target="_blank"><b>Tables 3</b></a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>4</b></a> show different information for the same loci (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t003" target="_blank"><b>Table 3</b></a> for index SNP and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>Table 4</b></a> for best SNPs with the smallest p-value).</p>1<p>effect allele/other allele.</p>2<p>effect allele frequency.</p>3<p>number of independent (typed) SNPs interrogated in AA sample.</p>4<p>Bonferroni p-value threshold (0.05/N³).</p>5<p>HapMAP LD information.</p>6<p>one-side test p-value.</p>7<p>P_2GC: double GC-corrected p-value.</p

Regional association plots for <i>LHX2</i> and <i>RREB1</i> in GIANT consortium with participants of European ancestry.

<p>The blue arrow points to the index SNPs identified from the samples of African ancestry and red arrow points to the best SNPs in GIANT consortium samples of European ancestry.</p

Cross-trait associations for novel loci from Stage1 + Stage 2 in participants of African ancestry.

1<p>effect allele/other allele.</p>2<p>effect size based on Stage 1 and Stage 2 combined sample.</p

SNPs associated with waist-related trait at p<5.0E-6 in Stage 1.

1<p>effect allele/other allele.</p>2<p>effect allele frequency.</p>3<p>one-side test p-value.</p>4<p>P_2GC: double GC-corrected p-value.</p

Examination of index SNPs within known loci in EA in AA for trait WHR ratio adjusted for BMI.

<p>The index SNPs is from Heid et al, Nature Genetics 2010 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen.1003681-Heid1" target="_blank">[17]</a>.</p>1<p>effect allele/other allele.</p>2<p>effect allele frequency.</p>3<p>Significance classification refers to the interrogation results of best SNP in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>Table 4</b></a>.</p>4<p>p-value of heterogeneity test of beta between EA and AA samples.</p

Regional association plots for all confirmed loci from the GIANT locus interrogation.

<p>Each figure is centered by the index SNP (big red) with rs-number and p-value information (stage 1 only); another big rectangle is the best SNP in African Americans, with information including MAF = minor allele frequency; linkage disequilibrium information in HapMap YRI and CEU<i>; P_D, P_F, and P_J</i> are the single GC-corrected p-value obtained from discovery cohorts only, follow-up cohorts and joint discovery and follow-up data, respectively. Double GC-corrected p-value can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003681#pgen-1003681-t004" target="_blank"><b>Table 4</b></a>.</p