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. 2014 Apr 23;23(17):4738–4744. doi: 10.1093/hmg/ddu183

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Published by Oxford University Press 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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Figure 1. — Regional plot of loci LYPLAL1 and ADAMTS9. The top panel is obtained from the trans-ethnic meta-analysis result with HapMAP II YRI LD information. The middle panel classifies variants based on whether they are included in the none, either or both of CSs. The red points represent variants retained in both credible regions constructed using EA and trans-ethnic samples; yellow and green points represent variants retained in CSs constructed using EA and trans-ethnic samples, separately; the gray points represents variants which do not fall in any CS.The bottom panel is from EA sample only analysis with HapMap II CEU linkage disequilbrium information. (A) Regional plot of loci LYPLAL1 (Chr1:217 413 815–217 452 830). There are eight SNPs commonly shared by the CSs obtained from EA-only and EA + AA. Fifteen additional SNPs are included in the EA-only derived CS while no additional SNP is included in the EA + AA-derived CS. The length change from 148 141 to 27 409 bp for EA-only and EA + AA derived CSs, respectively. The LD surrounding the original index SNP is much stronger in CEU compared with that in YRI. In addition, few SNPs with high LD with the index SNP in both populations have enhanced association signals and the LD block with the index SNP is much narrower in YRI samples, leading to a much narrower CS in trans-ethnic analysis and dropping 15 variants from EA-derived CS. (B). Regional plot of loci ADAMTS9 (Chr3:64 575 591–64 648 405). There are 7 SNPs commonly shared by the CSs obtained from EA-only and EA + AA. Six additional SNPs are included in the EA-only derived CS while no additional SNP is included in the EA + AA-derived CS. The length change from 30 676 to 8669 bp for EA-only and EA + AA derived CSs, respectively. Neither CEU nor YRI have strong LD for many variants surrounding the original index SNPs; however, the variants with strong LD with index SNP are within a narrow region in both samples of ancestries (narrower in YRI than in CEU). The association signals are highly enhanced and association signals for those top variants are more distinguishable in trans-ethnic analysis compared with EA sample only analysis. These lead to the dropping of six variants from EA-derived CS to form a more compact and narrower trans-ethnic analysis derived CS.