Table 16.2. 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 16.1. 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)   
232      G           110    177       594         594            0.540   6497                 
232      T           484    417       594         594            1.870   6497                 
232      C           421    495       594         594            0.490   6499                 
232      T           173    99        594         594            2.050   6499                 
232      G           169    103       594         594            1.900   6501                 
232      A           425    491       594         594            0.530   6501                 
232      T           126    185       594         594            0.600   6502                 
232      C           468    409       594         594            1.680   6502                 
232      G           441    477       594         594            0.710   6503                 
232      A           153    117       594         594            1.410   6503                 
232      A           107    78        594         594            1.450   6504                 
232      G           487    516       594         594            0.690   6504                 
232      A           186    228       594         594            0.730   6506                 
232      G           408    366       594         594            1.370   6506                 
232      T           186    228       594         594            0.730   6507                 
232      C           408    366       594         594            1.370   6507                 
232      T           487    515       594         594            0.700   6508                 
232      C           107    79        594         594            1.430   6508                 
232      T           443    424       594         594            1.180   6510                 
232      C           151    170       594         594            0.850   6510                 
232      T           560    547       594         594            1.420   6511                 
232      C           34     47        594         594            0.710   6511                 
232      G           295    238       594         594            1.480   6512                 
232      A           299    356       594         594            0.680   6512                 
232      C           259    186       594         594            1.700   6513                 
232      T           335    408       594         594            0.590   6513                 
232      G           24     34        594         594            0.690   6514                 
232      A           570    560       594         594            1.440   6514                 
232      G           451    413       594         594            1.380   6515                 
232      A           143    181       594         594            0.720   6515                 
232      C           382    357       594         594            1.200   6519                 
232      T           212    237       594         594            0.840   6519                 
232      T           82     56        594         594            1.540   6522                 
232      C           512    538       594         594            0.650   6522                 
232      G           50     39        594         594            1.310   6523                 
232      T           544    555       594         594            0.760   6523                 
