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. 2013 Sep 17;11(9):e1001661. doi: 10.1371/journal.pbio.1001661

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(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 (Figure S2) 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 p<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.