Table 21.2. 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 21.1. 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)   
562      A           111    136       286         286            0.700   12063                
562      G           175    150       286         286            1.430   12063                
562      G           183    197       286         286            0.800   12064                
562      A           103    89        286         286            1.250   12064                
562      A           252    214       286         286            2.490   12065                
562      G           34     72        286         286            0.400   12065                
562      T           47     33        286         286            1.510   12067                
562      G           239    253       286         286            0.660   12067                
562      A           123    102       286         286            1.360   12068                
562      G           163    184       286         286            0.730   12068                
563      T           22     56        286         286            0.340   13019                
563      C           264    230       286         286            2.920   13019                
563      C           122    106       286         286            1.260   13020                
563      T           164    180       286         286            0.790   13020                
563      T           123    99        286         286            1.430   13022                
563      C           163    187       286         286            0.700   13022                
564      T           126    102       286         286            1.420   13127                
564      C           160    184       286         286            0.700   13127                
564      T           66     30        286         286            2.560   13129                
564      C           220    256       286         286            0.390   13129                
564      G           228    260       286         286            0.390   13130                
564      A           58     26        286         286            2.540   13130                
564      G           244    269       286         286            0.370   13131                
564      A           42     17        286         286            2.720   13131                
564      G           144    112       286         286            1.580   13134                
564      A           142    174       286         286            0.630   13134                
564      G           141    174       286         286            0.630   13135                
564      A           145    112       286         286            1.600   13135                
564      A           74     53        286         286            1.530   13136                
564      G           212    233       286         286            0.650   13136                
564      T           143    112       286         286            1.550   13137                
564      C           143    174       286         286            0.640   13137                
564      A           175    193       286         286            0.760   13138                
564      G           111    93        286         286            1.320   13138                
564      T           132    156       286         286            0.710   13139                
564      C           154    130       286         286            1.400   13139                
564      A           134    156       286         286            0.730   13141                
564      C           152    130       286         286            1.360   13141                
565      A           44     28        286         286            1.680   13553                
565      G           242    258       286         286            0.600   13553                
565      T           272    236       286         286            4.120   13555                
565      C           14     50        286         286            0.240   13555                
565      G           130    146       286         286            0.800   13557                
565      T           156    140       286         286            1.250   13557                
565      G           257    247       286         286            1.400   13558                
565      A           29     39        286         286            0.710   13558                
566      C           81     60        286         286            1.490   13952                
566      T           205    226       286         286            0.670   13952                
566      C           246    227       286         286            1.600   13954                
566      T           40     59        286         286            0.630   13954                
566      G           90     72        286         286            1.360   13955                
566      A           196    214       286         286            0.730   13955                
566      C           176    209       286         286            0.590   13956                
566      A           110    77        286         286            1.700   13956                
566      A           115    164       286         286            0.500   13957                
566      C           171    122       286         286            2.000   13957                
566      C           130    98        286         286            1.600   13959                
566      T           156    188       286         286            0.630   13959                
566      T           239    253       286         286            0.660   13960                
566      C           47     33        286         286            1.510   13960                
567      C           159    173       286         286            0.820   14091                
567      T           127    113       286         286            1.220   14091                
567      C           35     53        286         286            0.610   14092                
567      T           251    233       286         286            1.630   14092                
567      A           260    230       286         286            2.430   14094                
567      G           26     56        286         286            0.410   14094                
567      A           74     124       286         286            0.460   14095                
567      G           212    162       286         286            2.190   14095                
567      T           106    83        286         286            1.440   14098                
567      C           180    203       286         286            0.690   14098                
568      T           16     24        286         286            0.650   14187                
568      C           270    262       286         286            1.550   14187                
568      T           167    213       286         286            0.480   14188                
568      G           119    73        286         286            2.080   14188                
568      G           117    141       286         286            0.710   14189                
568      A           169    145       286         286            1.400   14189                
568      T           145    165       286         286            0.750   14190                
568      C           141    121       286         286            1.330   14190                
568      T           25     36        286         286            0.670   14191                
568      C           261    250       286         286            1.500   14191                
569      T           208    225       286         286            0.720   14197                
569      C           78     61        286         286            1.380   14197                
569      C           165    186       286         286            0.730   14198                
569      T           121    100       286         286            1.360   14198                
569      C           208    225       286         286            0.720   14199                
569      A           78     61        286         286            1.380   14199                
569      A           91     139       286         286            0.490   14201                
569      G           195    147       286         286            2.030   14201                
569      T           118    88        286         286            1.580   14202                
569      G           168    198       286         286            0.630   14202                
569      A           139    166       286         286            0.680   14203                
569      G           147    120       286         286            1.460   14203                
570      A           248    261       286         286            0.630   14232                
570      G           38     25        286         286            1.600   14232                
570      T           88     68        286         286            1.420   14233                
570      C           198    218       286         286            0.700   14233                
570      T           21     14        286         286            1.540   14234                
570      G           265    272       286         286            0.650   14234                
570      A           62     108       286         286            0.460   14235                
570      G           224    178       286         286            2.190   14235                
570      G           132    96        286         286            1.700   14236                
570      A           154    190       286         286            0.590   14236                
570      T           27     37        286         286            0.700   14237                
570      G           259    249       286         286            1.430   14237                
570      A           186    156       286         286            1.550   14238                
570      C           100    130       286         286            0.650   14238                
570      A           152    129       286         286            1.380   14240                
570      G           134    157       286         286            0.720   14240                
570      A           83     58        286         286            1.610   14241                
570      G           203    228       286         286            0.620   14241                
570      G           205    162       286         286            1.940   14242                
570      A           81     124       286         286            0.520   14242                
570      A           259    269       286         286            0.610   14243                
570      G           27     17        286         286            1.650   14243                
570      A           240    253       286         286            0.680   14245                
570      G           46     33        286         286            1.470   14245                
571      A           112    86        286         286            1.500   14515                
571      G           174    200       286         286            0.670   14515                
571      A           141    117       286         286            1.400   14516                
571      C           145    169       286         286            0.710   14516                
571      G           238    270       286         286            0.290   14517                
571      A           48     16        286         286            3.400   14517                
572      G           33     55        286         286            0.550   14807                
572      A           253    231       286         286            1.830   14807                
572      A           31     45        286         286            0.650   14810                
572      G           255    241       286         286            1.540   14810                
572      A           226    195       286         286            1.760   14811                
572      G           60     91        286         286            0.570   14811                
572      G           162    203       286         286            0.530   14812                
572      A           124    83        286         286            1.870   14812                
572      T           114    165       286         286            0.490   14813                
572      C           172    121       286         286            2.060   14813                
572      A           59     91        286         286            0.560   14814                
572      C           227    195       286         286            1.800   14814                
572      T           255    241       286         286            1.540   14816                
572      C           31     45        286         286            0.650   14816                
573      C           242    252       286         286            0.740   15212                
573      A           44     34        286         286            1.350   15212                
573      A           17     28        286         286            0.580   15213                
573      G           269    258       286         286            1.720   15213                
573      T           189    232       286         286            0.450   15215                
573      G           97     54        286         286            2.200   15215                
573      C           40     30        286         286            1.390   15216                
573      A           246    256       286         286            0.720   15216                
573      T           156    171       286         286            0.810   15217                
573      C           130    115       286         286            1.240   15217                
573      A           22     41        286         286            0.500   15218                
573      G           264    245       286         286            2.010   15218                
574      A           150    181       286         286            0.640   16503                
574      G           136    105       286         286            1.560   16503                
574      C           30     67        286         286            0.380   16506                
574      T           256    219       286         286            2.610   16506                
574      T           112    89        286         286            1.420   16508                
574      C           174    197       286         286            0.700   16508                
575      A           70     32        286         286            2.570   16666                
575      G           216    254       286         286            0.390   16666                
575      T           210    238       286         286            0.560   16668                
575      C           76     48        286         286            1.790   16668                
575      A           72     41        286         286            2.010   16669                
575      G           214    245       286         286            0.500   16669                
576      C           177    161       286         286            1.260   16689                
576      T           109    125       286         286            0.790   16689                
576      C           15     27        286         286            0.530   16692                
576      T           271    259       286         286            1.880   16692                
576      C           15     27        286         286            0.530   16693                
576      T           271    259       286         286            1.880   16693                
576      G           249    235       286         286            1.460   16695                
576      A           37     51        286         286            0.680   16695                
576      G           16     27        286         286            0.570   16696                
576      A           270    259       286         286            1.760   16696                
576      A           171    205       286         286            0.590   16697                
576      G           115    81        286         286            1.700   16697                
576      A           171    205       286         286            0.590   16698                
576      G           115    81        286         286            1.700   16698                
576      T           143    107       286         286            1.670   16699                
576      C           143    179       286         286            0.600   16699                
576      G           165    126       286         286            1.730   16700                
576      A           121    160       286         286            0.580   16700                
576      G           173    134       286         286            1.740   16701                
576      A           113    152       286         286            0.580   16701                
576      A           174    198       286         286            0.690   16702                
576      G           112    88        286         286            1.450   16702                
576      G           153    177       286         286            0.710   16705                
576      A           133    109       286         286            1.410   16705                
576      A           163    202       286         286            0.550   16706                
576      G           123    84        286         286            1.810   16706                
576      C           123    80        286         286            1.940   16707                
576      T           163    206       286         286            0.510   16707                
576      C           138    100       286         286            1.730   16708                
576      T           148    186       286         286            0.580   16708                
576      G           164    207       286         286            0.510   16709                
576      A           122    79        286         286            1.950   16709                
576      C           133    100       286         286            1.620   16711                
576      A           153    186       286         286            0.620   16711                
576      G           164    139       286         286            1.420   16713                
576      A           122    147       286         286            0.700   16713                
576      T           137    185       286         286            0.500   16714                
576      C           149    101       286         286            1.990   16714                
576      C           120    86        286         286            1.680   16715                
576      T           166    200       286         286            0.590   16715                
576      A           150    101       286         286            2.020   16716                
576      G           136    185       286         286            0.490   16716                
576      C           12     20        286         286            0.580   16717                
576      T           274    266       286         286            1.720   16717                
576      T           222    236       286         286            0.730   16718                
576      C           64     50        286         286            1.360   16718                
576      A           202    218       286         286            0.750   16719                
576      G           84     68        286         286            1.330   16719                
576      G           132    107       286         286            1.430   16720                
576      A           154    179       286         286            0.700   16720                
577      A           156    139       286         286            1.270   17261                
577      G           130    147       286         286            0.790   17261                
577      A           111    125       286         286            0.820   17262                
577      G           175    161       286         286            1.220   17262                
577      C           103    118       286         286            0.800   17263                
577      T           183    168       286         286            1.250   17263                
577      T           80     40        286         286            2.390   17264                
577      G           206    246       286         286            0.420   17264                
577      T           84     105       286         286            0.720   17265                
577      C           202    181       286         286            1.400   17265                
578      T           228    201       286         286            1.660   17551                
578      C           58     85        286         286            0.600   17551                
578      T           262    242       286         286            1.980   17552                
578      G           24     44        286         286            0.500   17552                
578      A           242    219       286         286            1.680   17553                
578      G           44     67        286         286            0.590   17553                
578      A           34     49        286         286            0.650   17554                
578      G           252    237       286         286            1.530   17554                
578      C           278    269       286         286            2.200   17555                
578      T           8      17        286         286            0.460   17555                
578      T           262    251       286         286            1.520   17556                
578      C           24     35        286         286            0.660   17556                
578      T           61     95        286         286            0.550   17557                
578      C           225    191       286         286            1.830   17557                
578      T           147    93        286         286            2.190   17559                
578      C           139    193       286         286            0.460   17559                
578      C           97     56        286         286            2.110   17560                
578      T           189    230       286         286            0.470   17560                
578      G           71     94        286         286            0.670   17561                
578      A           215    192       286         286            1.480   17561                
578      G           164    149       286         286            1.240   17562                
578      A           122    137       286         286            0.810   17562                
578      A           171    188       286         286            0.780   17564                
578      G           115    98        286         286            1.290   17564                
578      C           15     36        286         286            0.380   17566                
578      T           271    250       286         286            2.600   17566                
579      A           239    263       286         286            0.440   18406                
579      G           47     23        286         286            2.250   18406                
579      A           22     40        286         286            0.510   18407                
579      G           264    246       286         286            1.950   18407                
579      A           76     114       286         286            0.550   18409                
579      G           210    172       286         286            1.830   18409                
579      T           255    235       286         286            1.790   18410                
579      C           31     51        286         286            0.560   18410                
579      T           241    223       286         286            1.510   18411                
579      G           45     63        286         286            0.660   18411                
579      A           54     74        286         286            0.670   18412                
579      C           232    212       286         286            1.500   18412                
579      T           237    218       286         286            1.510   18413                
579      C           49     68        286         286            0.660   18413                
579      T           67     103       286         286            0.540   18414                
579      C           219    183       286         286            1.840   18414                
579      C           40     52        286         286            0.730   18415                
579      T           246    234       286         286            1.370   18415                
579      A           33     60        286         286            0.490   18417                
579      G           253    226       286         286            2.040   18417                
579      G           49     62        286         286            0.750   18420                
579      A           237    224       286         286            1.340   18420                
579      A           237    224       286         286            1.340   18421                
579      G           49     62        286         286            0.750   18421                
579      A           75     121       286         286            0.480   18422                
579      G           211    165       286         286            2.060   18422                
579      A           211    165       286         286            2.060   18423                
579      G           75     121       286         286            0.480   18423                
579      A           246    225       286         286            1.670   18424                
579      C           40     61        286         286            0.600   18424                
579      T           31     51        286         286            0.560   18425                
579      C           255    235       286         286            1.790   18425                
579      A           251    228       286         286            1.820   18426                
579      G           35     58        286         286            0.550   18426                
579      A           200    160       286         286            1.830   18427                
579      G           86     126       286         286            0.550   18427                
579      A           31     54        286         286            0.520   18428                
579      G           255    232       286         286            1.910   18428                
579      G           233    188       286         286            2.290   18430                
579      A           53     98        286         286            0.440   18430                
579      A           230    247       286         286            0.650   18431                
579      G           56     39        286         286            1.540   18431                
579      C           36     47        286         286            0.730   18433                
579      T           250    239       286         286            1.370   18433                
