Results were entered into our custom installation of the Generic Genome Browser (Stein et al., 2002). Panels A, B and C of Figure 2 display plots of the negative logarithm of the primary (log-additive model) p-values for the three gene clusters that contained SNPs significant after multiple test correction (α5-α3-β4 and β3-α6, δ-γ). Figure 3A, 3B and 3C display the pairwise LD patterns (signed D’ and r2) for these gene clusters in cases and controls, labeled by rs number and primary p-value. Supplementary figure S2 extends the CHRNA5-CHRNA3-CHRNB4 LD plot to include the neighboring genes PSMA4, LOC123688 and IREB2.
