Fig. 1

Integrated haplotype score analysis of the SNP sets corresponding to two AMD candidate protective nsSNPs in C2 and CFB genes and one nsSNP protective against hypertension in LPL. High LD SNP sets, represented as genetic trees, for (a) CFB R32Q, (b) C2 E318D and (d) LPL S447X, where SNPs are numbered on the branches. The numbers at the bottom of each branch represent the number of haplotypes it is comprised of. SNPs on genetic trees are aligned against UCSC genome browser (c) and (e), displaying RefSeq genes in the respective regions (nsSNPs are designated with an asterisk *). The integrated haplotype score (iHS) for each of these SNPs is calculated, represented by the distributions shown in (f) for each nsSNP. Mean iHS is represented by a black circle (●), median by a thick black line and the box represents the central 50% of the data. An outlier is represented by white circle (∘)