Table 5.2. List of significantly associated haplotypes based on the schizophrenia Disease GWS
results using the Quebec Founder Population (QFP). Individual haplotypes with associated relative
risks are presented in each row of the table; these values were extracted from the associated
marker haplotype window with the most significant p value for each SNP in Table 5.1. The first
column lists the region ID as presented in Table 1. The Haplotype column lists the specific
nucleotides for the individual SNP alleles contributing to the haplotype reported. The Case and
Control columns correspond to the numbers of cases and controls, respectively, containing the
haplotype variant noted in the Haplotype column. The Total Case and Total Control columns list the
total numbers of cases and controls for which genotype data was available for the haplotype in
question. The RR column gives to the relative risk for each particular haplotype. The remainder of
the columns lists the SeqIDs for the SNPs contributing to the haplotype and their relative location
with respect to the central marker. The Central marker (0) column lists the SeqID for the central
marker on which the haplotype is based. Flanking markers are identified by minus (-) or plus (+)
signs to indicate the relative location of flanking SNPs.

Region   Haplotype   Case   Control   TotalCase   TotalControl   RR      Central Marker (0)   
382      G           60     45        812         812            1.360   17052                
382      A           752    767       812         812            0.740   17052                
382      G           741    724       812         812            1.270   17053                
382      A           71     88        812         812            0.790   17053                
382      C           767    716       812         812            2.290   17055                
382      T           45     96        812         812            0.440   17055                
382      G           21     66        812         812            0.300   17056                
382      A           791    746       812         812            3.330   17056                
382      T           340    304       812         812            1.200   17058                
382      C           472    508       812         812            0.830   17058                
382      A           341    305       812         812            1.200   17060                
382      G           471    507       812         812            0.830   17060                
383      A           488    586       812         812            0.580   18060                
383      G           324    226       812         812            1.720   18060                
