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Assume the effect of homozygous mutant genotype (AA) is 2e. Meanwhile the effect of homozygous wild type genotype (TT) is 2b. The slope of the regression line (beta) will be e-b. Figure S2. Relationship between r2 and beta estimate of the possible dependent SNP for a given major allele frequency of the top hit and observed beta for the top SNP. Different colors refer to different intervals of major allele frequency of the possible dependent SNP (called q1): red for 0.5 http://www.selleckchem.com/products/PD-0332991.html for 0.7 http://www.selleckchem.com/products/Everolimus(RAD001).html with a HDL variant; (E) CETP loci most likely to be tightly associated with a HDL variant. For all the methods, cross (��) denotes inclusion in the best model. Figure S4. Comparison between SSS-RAP and conditional analysis using meta-analysis data in ECG traits. Linkage disequilibrium and haplotype block structure were linked to related SNPs in A and B, SCN5A loci associated with PR interval and QTC interval, respectively. For both methods, cross (��) denotes inclusion in the best model. Figure S5. The influence of MAF on the standard error of beta. (A) Relationship between the observed standard errors and the MAF. (B) Relationship between the simulated standard errors and the MAFs. Figure S6. Comparison of the observed standard error to the simulated standard errors and the transformed standard errors in different r2 region. Figure S7. The three SNPs model for the admixed population simulations. We assume rs328 was the top hit, rs327 was an independent effect SNP and rs263 was a bystander SNP. Alleles in red means they were the effect/minor alleles. Figure S8. A special case of the three SNPs model. (A) We used the same three SNPs model as showed in Figure http://www.selleck.cn/products/Bortezomib.html S7. In this model, we assumed that rs327 (MAF = 0.4) and rs328 (MAF = 0.3) were two significant SNPs associated with a trail and there is no LD between them. In (B) we calculated the haplotype frequencies between rs327 and rs328. Then in (C and D), we introduced a previous hidden SNP, rs263 (unknown MAF = X/X-bar). Since we know the haplotypes of rs263, we can calculate the haplotype frequencies between rs327/rs328 and rs263 (values at the bottom of each grids). We then assumed there were some LD between rs263 and rs327/rs328 (D and D-bar were the LD measures).