Table 9.2. List of significantly associated haplotypes based on the Endometriosis Disease 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 9.1. 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)   
126      G           135    156       246         246            0.700   4531                 
126      A           111    90        246         246            1.430   4531                 
126      A           109    88        246         246            1.430   4532                 
126      G           137    158       246         246            0.700   4532                 
126      C           102    74        246         246            1.650   4533                 
126      T           144    172       246         246            0.610   4533                 
126      T           59     31        246         246            2.190   4534                 
126      C           187    215       246         246            0.460   4534                 
126      T           46     14        246         246            3.810   4535                 
126      C           200    232       246         246            0.260   4535                 
126      G           40     25        246         246            1.720   4537                 
126      A           206    221       246         246            0.580   4537                 
127      T           186    168       248         248            1.430   5102                 
127      C           62     80        248         248            0.700   5102                 
127      A           29     38        248         248            0.730   5103                 
127      G           219    210       248         248            1.370   5103                 
127      C           95     121       248         248            0.650   5104                 
127      T           153    127       248         248            1.530   5104                 
127      T           73     32        248         248            2.820   5106                 
127      C           175    216       248         248            0.360   5106                 
127      C           195    175       248         248            1.530   5107                 
127      T           53     73        248         248            0.650   5107                 
