Table 34.2. List of significantly associated haplotypes based on the schizohrenia 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 34.1. 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)   
654      G           137    88        310         310            2.000   11704                
654      A           173    222       310         310            0.500   11704                
655      T           67     42        310         310            1.760   11784                
655      C           243    268       310         310            0.570   11784                
655      G           246    201       310         310            2.080   11785                
655      T           64     109       310         310            0.480   11785                
655      A           156    187       310         310            0.670   11786                
655      C           154    123       310         310            1.500   11786                
655      T           92     62        310         310            1.690   11787                
655      C           218    248       310         310            0.590   11787                
655      T           182    144       310         310            1.640   11790                
655      C           128    166       310         310            0.610   11790                
656      T           230    245       310         310            0.760   13774                
656      C           80     65        310         310            1.310   13774                
656      T           78     59        310         310            1.430   13775                
656      C           232    251       310         310            0.700   13775                
656      C           264    235       310         310            1.830   13777                
656      T           46     75        310         310            0.550   13777                
656      T           10     20        310         310            0.480   13778                
656      C           300    290       310         310            2.070   13778                
656      G           284    268       310         310            1.710   13779                
656      A           26     42        310         310            0.580   13779                
656      A           237    190       310         310            2.050   13780                
656      G           73     120       310         310            0.490   13780                
656      C           49     82        310         310            0.520   13781                
656      A           261    228       310         310            1.920   13781                
656      C           245    211       310         310            1.770   13782                
656      A           65     99        310         310            0.570   13782                
656      C           74     120       310         310            0.500   13783                
656      T           236    190       310         310            2.010   13783                
656      T           27     37        310         310            0.700   13784                
656      C           283    273       310         310            1.420   13784                
656      G           60     92        310         310            0.570   13785                
656      A           250    218       310         310            1.760   13785                
656      T           86     120       310         310            0.610   13786                
656      C           224    190       310         310            1.650   13786                
656      C           167    187       310         310            0.770   13788                
656      T           143    123       310         310            1.300   13788                
656      T           210    247       310         310            0.540   13791                
656      C           100    63        310         310            1.870   13791                
656      C           33     45        310         310            0.700   13794                
656      A           277    265       310         310            1.430   13794                
657      A           95     123       310         310            0.670   14521                
657      G           215    187       310         310            1.490   14521                
657      T           216    190       310         310            1.450   14522                
657      G           94     120       310         310            0.690   14522                
657      G           94     117       310         310            0.720   14523                
657      A           216    193       310         310            1.390   14523                
657      T           28     4         310         310            7.600   14524                
657      C           282    306       310         310            0.130   14524                
657      A           28     4         310         310            7.600   14525                
657      G           282    306       310         310            0.130   14525                
658      A           196    227       310         310            0.630   17979                
658      G           114    83        310         310            1.590   17979                
658      A           86     61        310         310            1.570   17980                
658      G           224    249       310         310            0.640   17980                
658      G           201    246       310         310            0.480   17981                
658      A           109    64        310         310            2.080   17981                
658      C           233    251       310         310            0.710   17982                
658      T           77     59        310         310            1.410   17982                
658      T           291    298       310         310            0.620   17983                
658      C           19     12        310         310            1.620   17983                
659      T           243    209       310         310            1.750   18992                
659      C           67     101       310         310            0.570   18992                
659      T           130    185       310         310            0.490   18993                
659      C           180    125       310         310            2.050   18993                
659      C           284    295       310         310            0.560   18994                
659      T           26     15        310         310            1.800   18994                
660      T           50     33        204         204            1.680   19253                
660      C           154    171       204         204            0.590   19253                
660      A           27     16        204         204            1.790   19254                
660      C           177    188       204         204            0.560   19254                
660      A           173    184       204         204            0.610   19255                
660      G           31     20        204         204            1.650   19255                
660      T           168    194       204         204            0.240   19256                
660      C           36     10        204         204            4.160   19256                
660      T           57     35        204         204            1.870   19258                
660      C           147    169       204         204            0.530   19258                
660      A           40     30        204         204            1.410   19259                
660      G           164    174       204         204            0.710   19259                
