Table 29.2. 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 29.1. 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)   
411      T           468    436       684         684            1.230   11698                
411      C           216    248       684         684            0.810   11698                
411      T           184    209       684         684            0.840   11699                
411      G           500    475       684         684            1.200   11699                
411      T           414    495       684         684            0.590   11700                
411      C           270    189       684         684            1.710   11700                
411      A           88     113       684         684            0.750   11701                
411      G           596    571       684         684            1.340   11701                
411      C           102    131       684         684            0.740   11702                
411      T           582    553       684         684            1.350   11702                
412      G           241    212       684         684            1.210   11778                
412      A           443    472       684         684            0.830   11778                
412      C           454    419       684         684            1.250   11779                
412      T           230    265       684         684            0.800   11779                
412      C           357    442       684         684            0.600   11781                
412      T           327    242       684         684            1.670   11781                
412      C           509    539       684         684            0.780   11782                
412      T           175    145       684         684            1.280   11782                
412      C           511    540       684         684            0.790   11783                
412      A           173    144       684         684            1.270   11783                
412      C           521    567       684         684            0.660   11784                
412      T           163    117       684         684            1.520   11784                
412      T           152    213       684         684            0.630   11785                
412      G           532    471       684         684            1.580   11785                
412      C           361    276       684         684            1.650   11786                
412      A           323    408       684         684            0.610   11786                
412      C           463    529       684         684            0.610   11787                
412      T           221    155       684         684            1.630   11787                
412      A           173    197       684         684            0.840   11788                
412      G           511    487       684         684            1.190   11788                
412      T           394    356       684         684            1.250   11790                
412      C           290    328       684         684            0.800   11790                
412      T           174    207       684         684            0.790   11791                
412      C           510    477       684         684            1.270   11791                
413      T           320    377       684         684            0.720   13348                
413      C           364    307       684         684            1.400   13348                
413      T           260    213       684         684            1.360   13349                
413      C           424    471       684         684            0.740   13349                
413      C           172    107       684         684            1.810   13350                
413      A           512    577       684         684            0.550   13350                
413      C           262    214       684         684            1.360   13351                
413      T           422    470       684         684            0.730   13351                
413      G           301    261       684         684            1.270   13353                
413      A           383    423       684         684            0.790   13353                
414      A           113    130       684         684            0.840   13359                
414      G           571    554       684         684            1.190   13359                
414      G           289    245       684         684            1.310   13360                
414      A           395    439       684         684            0.760   13360                
414      G           508    569       684         684            0.580   13361                
414      A           176    115       684         684            1.710   13361                
414      G           176    115       684         684            1.710   13362                
414      A           508    569       684         684            0.580   13362                
414      A           395    439       684         684            0.760   13364                
414      G           289    245       684         684            1.310   13364                
414      T           301    255       684         684            1.320   13365                
414      C           383    429       684         684            0.760   13365                
414      T           485    558       684         684            0.550   13366                
414      C           199    126       684         684            1.820   13366                
414      A           584    563       684         684            1.260   13367                
414      G           100    121       684         684            0.800   13367                
414      T           584    563       684         684            1.260   13368                
414      C           100    121       684         684            0.800   13368                
414      A           592    576       684         684            1.210   13369                
414      G           92     108       684         684            0.830   13369                
414      A           523    488       684         684            1.300   13370                
414      C           161    196       684         684            0.770   13370                
415      T           79     96        684         684            0.800   16464                
415      G           605    588       684         684            1.250   16464                
415      A           416    334       684         684            1.630   16466                
415      G           268    350       684         684            0.610   16466                
415      T           125    79        684         684            1.710   16467                
415      C           559    605       684         684            0.580   16467                
415      A           80     42        684         684            2.020   16469                
415      C           604    642       684         684            0.490   16469                
415      T           351    379       684         684            0.850   16470                
415      C           333    305       684         684            1.180   16470                
416      A           634    649       684         684            0.680   17052                
416      G           50     35        684         684            1.460   17052                
416      A           55     75        684         684            0.710   17053                
416      G           629    609       684         684            1.410   17053                
416      T           34     84        684         684            0.370   17055                
416      C           650    600       684         684            2.680   17055                
416      A           669    625       684         684            4.210   17056                
416      G           15     59        684         684            0.240   17056                
416      T           287    255       684         684            1.220   17058                
416      C           397    429       684         684            0.820   17058                
416      A           288    256       684         684            1.220   17060                
416      G           396    428       684         684            0.820   17060                
417      C           365    338       684         684            1.170   17850                
417      T           319    346       684         684            0.850   17850                
417      A           623    663       684         684            0.320   17851                
417      C           61     21        684         684            3.090   17851                
417      C           350    387       684         684            0.800   17853                
417      T           334    297       684         684            1.240   17853                
418      T           414    390       684         684            1.160   18058                
418      C           270    294       684         684            0.870   18058                
418      G           270    185       684         684            1.760   18060                
418      A           414    499       684         684            0.570   18060                
418      A           50     37        684         684            1.380   18062                
418      G           634    647       684         684            0.730   18062                
419      T           501    531       684         684            0.790   19006                
419      C           183    153       684         684            1.270   19006                
419      T           555    591       684         684            0.680   19008                
419      C           129    93        684         684            1.480   19008                
419      T           253    312       684         684            0.700   19010                
419      C           431    372       684         684            1.430   19010                
419      T           485    555       684         684            0.570   19011                
419      C           199    129       684         684            1.770   19011                
419      G           472    423       684         684            1.370   19012                
419      A           212    261       684         684            0.730   19012                
420      G           51     40        448         448            1.310   19255                
420      A           396    408       448         448            0.760   19255                
420      C           63     24        448         448            2.900   19256                
420      T           384    424       448         448            0.350   19256                
420      T           43     57        448         448            0.730   19257                
420      C           404    391       448         448            1.370   19257                
