Examples of secondary alleles in the AA population.

<p>(a) At rs28927680 (APOA1/C3/A4/A5 gene cluster, logTG) the index tagSNP fine maps (red point in upper right of a). Panel (b) shows residual signal in the same region after adjustment for genotype at this variant, and significant secondary signals are observed. (c) At FTO, the SNPs tagged by rs9939069 in EA are all null in the subsample, but a secondary association is observed at very low frequency SNP (rs75569526, MAF 1% in AA_mchip). In this example the secondary SNP is the only significant association in the region from our subsample analysis. Panels (d–f) illustrate multiple, independent associations at CETP. At CETP, the significant residual signal after adjusting for the best signal in each EA-tagged bin (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001661#pbio.1001661.s002" target="_blank">Figure S2</a>) is consistent multiple factors that might contribute to differential signal in the region. The number of independent statistical associations observed within the locus is a rough proxy for the number of functional alleles. Here we show a series of LocusZoom plots sequentially adjusting results for the SNP with the strongest observed association in the previous cycle. LD in EA samples is color coded relative to rs3764261 in all panels, and the region-wide threshold for significance after Bonferroni adjustment for the 84 SNPs genotyped in the 25 kb region (residual <i>p</i><1.1 * 10⁻⁴) is shown as a horizontal red line. (d) CETP/HDL regional data adjusted only for ancestry. The strongest observed association at rs17231520 is indicated with an arrowhead. (e) After adjustment for genotype at rs17231520, the strongest residual association at rs4783961 is indicated with an arrowhead. (f) After adjustment for genotype at rs17231520 and rs4783961, the strongest residual association is still significant. These results suggest the presence of at least three statistically independent associations with HDL in the CETP region, in the AA population. Assuming that the functional variation has been directly genotyped, rather than tagged by LD, this would indicate the presence of at least three functional alleles, clustered within a 5 kb window spanning the putative CETP promoter region.</p

Summary of direction and strength of β relative to EA.

a<p><i>p</i> values were computed from the binomial sign test against null expectation of 50% in same direction, not adjusted for multiple tests.</p>b<p>Maximum number of samples per population. Not all SNPs were genotyped in all PAGE substudies; detailed numbers genotyped per variant are available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001661#pbio.1001661.s004" target="_blank">Table S2</a>.</p>c<p>Although some effects were observed where the sign of the coefficient differed between EA and AA, in none of these cases were both coefficients significantly different from zero, so no significantly opposite effects were observed in any non-EA population.</p>d<p>Strength was evaluated only for index SNPs that replicated in EA, <i>and</i> showed differential effects in the non-EA population (ß_pop≠ß_EA). <i>p</i> values computed from the binomial sign test against null expectation of 50% stronger, not adjusted for multiple tests.</p>*<p><i>p</i><0.05,</p>**<p><i>p</i><0.01,</p>***<p><i>p</i><0.001.</p

Examples of loci without evidence of association in AA_mchip or fine mapping EA signal.

<p>(a) At rs16996148 (CILP2/LDL) we are reasonably well powered, and no significant associations were observed in AA, suggesting that either the associated variant, or the synthetic allele that tags it is EA-restricted. Similar null results at (b) rs5219 (KCNJ11/T2D) and (c) rs17145738 (MLXIPL/logTG) were underpowered to draw strong conclusions. (d) At rs780094 (GCKR/logTG) and (e) rs599839 (PSRC1/LDL) the index tagSNP from EA showed significantly diluted signal in AA (purple dot). However, in each region a tagged SNP showed an effect size consistent with the EA index tagSNP, and after adjustment for this variant no residual evidence for association was observed at any additional variants in the region. (f) At rs2954029 (TRIB1/logTG) a similar effect was observed, save for the fact that the strongest AA association was imperfectly tagged in EA (r² = 0.33).</p

Dilution of effect size at PSRC1 for LDL.

<p>In panel (a), we show a locuszoom plot for the tagSNP rs599839 and LDL, using imputed data in a meta-analysis of more than 100,000 European individuals (image from the GLGC consortium locuszoom website <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001661#pbio.1001661-Teslovich1" target="_blank">[31]</a>). The <i>y</i>-axis plots −log10(<i>p</i> value), which is a proxy for effect size, assuming similar allele frequencies. In panel (a) the size of the dot for each tagSNP represents the effective number of samples for which imputed data were available. The cluster of overlapping red dots at the top represents a bin of SNPs that are in very strong LD with the tagSNP, and have indistinguishable effect sizes in the EA study. Panel (b) shows data from our metabochip analysis in African Americans, but with dots color-coded using LD from the EA population. The scale of the <i>y</i>-axis has changed due to dramatically different sample sizes, but <i>p</i> value is still a useful proxy for effect size. Note how the tagSNP and several strongly associated SNPs (red data points) have effect sizes indistinguishable from background, while several other EA strongly associated SNPs remain significant, including rs12740374, the strongest signal in our data. Panel (c) shows our metabochip data again, but now color coding LD with the tagSNP rs599839 in our AA samples, rather than using EA LD. Rs599839 continues to tag several SNPs strongly in AA, and these are all among the SNPs with nonsignificant effect sizes in AA, while the SNPs with strongest residual signal are weakly tagged in AA. These data suggest that rs12740374 is the functional SNP; if so, then differential LD between rs12740374 and rs599839 in EA (r²>0.8) and AA (r²<0.2) would explain the diluted effect observed at rs599839 in AA.</p

Summary of generalization results.

a<p>See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001661#pbio-1001661-box001" target="_blank">Box 1</a> for definitions.</p>b<p>Totals differ between populations because not all SNPs were genotyped in all populations.</p>c<p>Not visible in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001661#pbio-1001661-g001" target="_blank">Figure 1</a> because of very small ß_EA.</p