Table 19.3. 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 19.2. 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)   
534      C           62     80        360         360            0.730   12057                
534      T           298    280       360         360            1.370   12057                
534      A           137    155       360         360            0.810   12058                
534      G           223    205       360         360            1.230   12058                
534      C           238    259       360         360            0.760   12059                
534      T           122    101       360         360            1.310   12059                
534      G           94     138       360         360            0.570   12060                
534      A           266    222       360         360            1.760   12060                
534      A           58     93        360         360            0.550   12061                
534      G           302    267       360         360            1.810   12061                
534      G           216    190       360         360            1.340   12063                
534      A           144    170       360         360            0.750   12063                
534      A           131    109       360         360            1.320   12064                
534      G           229    251       360         360            0.760   12064                
534      A           313    266       360         360            2.350   12065                
534      G           47     94        360         360            0.420   12065                
535      T           336    300       360         360            2.800   13555                
535      C           24     60        360         360            0.360   13555                
536      C           203    221       360         360            0.810   14091                
536      T           157    139       360         360            1.230   14091                
536      C           49     64        360         360            0.730   14092                
536      T           311    296       360         360            1.370   14092                
536      G           39     65        360         360            0.550   14094                
536      A           321    295       360         360            1.810   14094                
536      A           100    152       360         360            0.530   14095                
536      G           260    208       360         360            1.900   14095                
537      G           241    186       360         360            1.890   14201                
537      A           119    174       360         360            0.530   14201                
537      G           180    153       360         360            1.350   14203                
537      A           180    207       360         360            0.740   14203                
538      C           290    322       360         360            0.490   14685                
538      T           70     38        360         360            2.050   14685                
538      G           29     19        360         360            1.570   14695                
538      T           331    341       360         360            0.640   14695                
539      C           214    158       360         360            1.870   14813                
539      T           146    202       360         360            0.530   14813                
540      A           305    340       360         360            0.330   14953                
540      G           55     20        360         360            3.070   14953                
540      T           223    262       360         360            0.610   14954                
540      C           137    98        360         360            1.640   14954                
541      G           115    67        360         360            2.050   15215                
541      T           245    293       360         360            0.490   15215                
542      C           272    248       360         360            1.400   15916                
542      T           88     112       360         360            0.720   15916                
542      A           202    159       360         360            1.620   15920                
542      A           202    159       360         360            1.620   15920                
542      G           158    201       360         360            0.620   15920                
542      G           158    201       360         360            0.620   15920                
542      C           152    208       360         360            0.530   15922                
542      C           152    208       360         360            0.530   15922                
542      T           208    152       360         360            1.870   15922                
542      T           208    152       360         360            1.870   15922                
542      G           276    238       360         360            1.680   15923                
542      A           84     122       360         360            0.590   15923                
542      G           269    227       360         360            1.730   15924                
542      T           91     133       360         360            0.580   15924                
542      G           92     133       360         360            0.590   15925                
542      T           268    227       360         360            1.710   15925                
542      T           193    137       360         360            1.880   15926                
542      T           193    137       360         360            1.880   15926                
542      C           167    223       360         360            0.530   15926                
542      C           167    223       360         360            0.530   15926                
543      A           79     99        360         360            0.740   16672                
543      C           281    261       360         360            1.350   16672                
543      T           159    216       360         360            0.530   16676                
543      G           201    144       360         360            1.900   16676                
544      T           178    124       360         360            1.860   17559                
544      C           182    236       360         360            0.540   17559                
545      A           201    183       360         360            1.220   17866                
545      A           201    183       360         360            1.220   17866                
545      G           159    177       360         360            0.820   17866                
545      G           159    177       360         360            0.820   17866                
545      C           118    79        360         360            1.730   17867                
545      T           242    281       360         360            0.580   17867                
545      C           118    79        360         360            1.730   17867                
545      T           242    281       360         360            0.580   17867                
545      A           318    339       360         360            0.470   17868                
545      C           42     21        360         360            2.130   17868                
545      G           236    258       360         360            0.750   17869                
545      A           124    102       360         360            1.330   17869                
545      T           111    165       360         360            0.530   17870                
545      C           249    195       360         360            1.900   17870                
545      G           194    166       360         360            1.370   17872                
545      A           166    194       360         360            0.730   17872                
546      T           104    80        360         360            1.420   18266                
546      C           256    280       360         360            0.700   18266                
546      G           250    197       360         360            1.880   18268                
546      A           110    163       360         360            0.530   18268                
547      T           82     40        360         360            2.360   18853                
547      C           278    320       360         360            0.420   18853                
547      C           37     15        360         360            2.630   18856                
547      T           323    345       360         360            0.380   18856                
