Figure 2.

Quantile-Quantile Plots after Positional Binning and LD-Based Binning Using the 1,868 WTCCC BP Individuals and 2,938 Common Controls Randomly Assigned to Case-Control Status

(A) Positional binning with no extension.

(B) Positional binning with 1 kb extension upstream and downstream of a gene.

(C) Positional binning with 10 kb extension upstream and downstream of a gene.

(D) LD-based binning with no extension (r² = 0.5).

(E) LD-based binning with 1 kb extension upstream and downstream of a gene (r² = 0.5).

(F) LD-based binning with 10 kb extension upstream and downstream of a gene (r² = 0.5).

(G) LD-based binning with no extension (r² = 0.8).

(H) LD-based binning with 1 kb extension upstream and downstream of a gene (r² = 0.8).

(I) LD-based binning with 10 kb extension upstream and downstream of a gene (r² = 0.8).

The small λ values in (D–I) are caused by substantially more observed p values close to 1.