Figure 2

Linkage disequilibrium plots of SNPs located in KIAA0319. (A) Inter-SNP linkage disequilibrium was generated for studied markers covering KIAA0319 using Haploview 4.0 [13]. Color scheme represents the r² value (stronger linkage disequilibrium is shown using progressively darker shading). Schematic diagram of KIAA0319 and TDP2 genes obtained from Ensembl (http://www.ensembl.org). Right bottom: Linkage disequilibrium plots of the significant haplotype rs2760157-rs807507 (Red box) found in this study (Hong Kong sample) and the haplotype rs4504469-2038137-2143340 (Blue box) studied in Paracchini et al. (UK sample) [16]. Linkage disequilibrium plot represent D’ measure was also generated. The cells are color in red gradually representing strength of LD between the two markers: Bright red (LOD ≥ 2 D’ = 1), pink red (LOD ≥ 2 D’ < 1) and white color for no or weak LD (LOD < 2, D’ < 1). (B) Regional LD plots in KIAA0319 5′ and TTRAP (TDP2) genomic region (plots were generated using SNAP web-based software at the Broad Institute [17] and data from 1000 Genomes Project Pilot 1). r² value relative to rs2038137 and rs2143340 (indicated by blue arrows) in CEU and CHBJPT populations for SNP in a 100Kb window around it plotted against their genomic location. Dotted vertical lines delimit regions including SNPs with r² > 0.5. Size and color intensity of markers are proportional to r² values.