Table 7.1. Genome wide association study results in the Quebec Founder Population (QFP). SNP
markers found to be associated with Endometriosis from the analysis of genome wide scan (GWS) data:
NOT INFERTILE. Columns include: Region ID; Chromosome; Build 36 location in base pairs (bp); rs#,
dbSNP data base (NCBI) reference number; Sequence ID, unique numerical identifier for this patent
application; Sequence, 21 bp of sequence covering 10 base pair of unique sequence flanking either
side of central polymorphic SNP; - log10 P values for GWS, - log10 of the P value for statistical
significance from the GWS for single SNP markers (both T test and Permutation test p-values are
displayed; see Example section) and for the most highly associated multi-marker haplotypes centered
at the reference marker and defined by the sliding windows of specified sizes.

                                                                             ldstatv2        ldstatv2   ldstatv2   ldstatv2   ldstatv2   ldstatv4        ldstatv4   ldstatv4   ldstatv4   ldstatv4   singletype                         singletype                       
Region ID   Chr   B36 Position   RS#        Seq ID   Flanking Sequence       Single Marker   W03        W05        W07        W09        Single Marker   W03        W05        W07        W09        Single Genotype Likelihood Ratio   Single Allele Likelihood Ratio   
98          1     220087702      10495181   4428     GAAAAACAATKTATTATCAGA   0.069           -          -          -          -          0.039           -          -          -          -          0.077                              0.069                            
98          1     220092935      11118874   4429     TCTGCTCCACYGCCTATCTCA   1.278           0.574      -          -          -          1.210           0.556      -          -          -          0.896                              1.255                            
98          1     220112069      6691170    4430     TAAAGATCCTKGCAGTTCTTT   0.698           1.590      0.609      -          -          0.631           1.605      0.611      -          -          0.504                              0.701                            
98          1     220145183      2378494    4431     GCAGTGTTCTYTCATCACTCA   2.536           0.985      2.506      2.550      -          2.459           1.086      2.302      2.342      -          2.085                              2.536                            
98          1     220157567      10863668   4432     ATGAGAGTCARAACCAAACTC   0.468           3.601      4.320      2.166      -          0.429           4.000      3.635      2.006      -          0.363                              0.491                            
98          1     220169205      7554115    4433     GTTGCGCTGAYTTCAGGTTTG   4.847           3.990      3.540      -          -          4.772           4.246      3.100      -          -          4.719                              4.908                            
98          1     220192151      12137323   4434     TACGGGGCCARTTCCACATAT   0.232           3.352      -          -          -          0.165           3.422      -          -          -          0.112                              0.280                            
98          1     220249849      2800860    4435     TTGTTTAATAYGGATAGAACA   0.049           -          -          -          -          0.018           -          -          -          -          0.519                              0.049                            
99          2     122755725      1344759    4566     TACAGACGGARGAGTTGATTA   0.032           -          -          -          -          0.000           -          -          -          -          0.054                              0.059                            
99          2     122764499      13396216   4567     ACACATCTTARAAACAAATAC   0.030           1.710      -          -          -          0.000           1.738      -          -          -          0.478                              0.030                            
99          2     122770055      12612483   4568     TATAGTCATAYAGATGAAGCA   1.707           0.973      0.969      -          -          1.647           0.973      0.947      -          -          2.617                              1.707                            
99          2     122792918      11122897   4569     ACAAAACTGTRTCATTTTACA   0.100           1.386      3.158      2.546      -          0.075           1.508      2.745      2.323      -          0.060                              0.100                            
99          2     122809398      1881893    4570     CTCTAGGACAYTACATTTGGT   1.457           2.694      3.506      2.926      2.551      1.346           3.102      2.909      2.553      2.309      1.151                              1.457                            
99          2     122815563      10496579   4571     AGCAAACTGARGAACAGCAAA   2.554           3.120      4.093      3.566      3.466      2.473           3.350      3.153      2.853      3.018      1.943                              2.554                            
99          2     122816017      10496581   4572     TCGGGTAACTRGTGAGTTGCT   4.765           3.153      4.285      3.734      2.530      4.684           3.431      3.392      3.231      2.347      4.141                              4.765                            
99          2     122818658      12469494   4573     TATCATTTTCRTCTGCTTCCT   1.485           3.214      5.380      3.664      -          1.413           3.880      3.975      3.009      -          1.163                              1.485                            
99          2     122832476      1453690    4574     CTACTCTGCCYGACTCCCATG   1.251           0.765      3.739      -          -          1.176           0.792      3.129      -          -          1.015                              1.251                            
99          2     122850882      1320869    4575     GCTCCAGTTTRACCCTAGCCA   0.163           0.387      -          -          -          0.128           0.380      -          -          -          0.083                              0.157                            
99          2     122853360      1919922    4576     TCATATCCTAYGCACTAGACC   0.178           -          -          -          -          0.134           -          -          -          -          0.036                              0.149                            
100         3     12583045       2442802    4672     AAACTCATCTMATGTAATTCT   1.148           -          -          -          -          1.092           -          -          -          -          0.990                              1.148                            
100         3     12591533       3773341    4673     TCTTAGCTGTRGGAGCTAGGA   0.469           0.479      -          -          -          0.402           0.455      -          -          -          0.830                              0.469                            
100         3     12599070       15997      4674     CTGGCTCTTAYCTTTGATCTT   0.667           1.228      2.221      -          -          0.615           1.266      2.065      -          -          0.359                              0.667                            
100         3     12610706       1532533    4675     AGGGATGAAGRTAAGAAATCC   1.150           3.662      3.543      1.993      -          1.116           3.719      3.198      1.825      -          0.792                              1.150                            
100         3     12611255       1532534    4676     TTCTAAATCCKCACTACTATG   4.871           3.846      3.550      3.290      1.993      4.775           3.882      3.025      2.954      1.845      4.178                              4.871                            
100         3     12630689       9809501    4677     CCAAGACTTTKGGCTCATATG   1.228           3.894      4.138      3.550      3.006      1.141           3.942      3.452      3.030      2.776      0.781                              1.228                            
100         3     12643726       6792773    4678     CTAAACCATAYAAATTATTTC   1.507           1.067      4.855      3.541      3.936      1.462           1.095      3.946      3.084      3.211      1.231                              1.507                            
100         3     12648275       11128607   4679     CCATGTGTCTRGTATACAGAC   1.507           1.507      2.003      4.390      -          1.409           1.409      1.819      3.413      -          1.231                              1.507                            
100         3     12651113       9817675    4680     CAAGAATCCAYAATTATGTGA   1.507           2.202      2.036      -          -          1.427           2.195      1.852      -          -          1.231                              1.507                            
100         3     12664858       6442322    4681     AAACACTAACRATTTCCACAC   0.751           1.838      -          -          -          0.699           1.835      -          -          -          0.425                              0.752                            
100         3     12671288       11710163   4682     ACAACATTATRCACAAGTTTA   0.423           -          -          -          -          0.347           -          -          -          -          0.450                              0.547                            
101         6     168687447      2180346    5136     CAACGGCAGAYGCTGTTAGGA   0.000           -          -          -          -          0.000           -          -          -          -          0.020                              0.007                            
101         6     168695540      2144749    5137     CTATAATTTGRTTTAAGTCAG   2.008           2.342      -          -          -          1.918           2.443      -          -          -          1.572                              2.018                            
101         6     168703401      10945513   5138     TTTCTCTGTARTCACCCTTAT   1.552           3.760      2.908      -          -          1.487           3.826      2.699      -          -          1.111                              1.552                            
101         6     168706442      6455529    5139     AATCTTTCTCYTAAAAGCTCC   0.616           1.361      2.687      2.419      -          0.606           1.380      2.525      2.305      -          0.518                              0.655                            
101         6     168710540      2342630    5140     CTAACCTCGCRTTTTTATAGC   2.678           1.768      2.710      2.054      1.385      2.588           1.791      2.553      1.975      1.364      2.466                              2.666                            
101         6     168727218      4708751    5141     GCTCCCCAACYTCCTGCTGGC   0.239           4.020      2.184      1.474      1.380      0.195           4.190      2.051      1.435      1.357      1.108                              0.239                            
101         6     168728405      11964985   5142     AGCACATCCAYCCCGGGACAG   5.077           4.123      2.900      1.694      0.825      4.987           4.476      2.705      1.679      0.838      4.494                              5.077                            
101         6     168745262      9456232    5143     GTGGCTAAGAMAGTCTTGGTT   3.766           3.133      3.938      1.800      1.481      3.696           3.358      3.547      1.770      1.450      3.586                              3.766                            
101         6     168760104      7761264    5144     GTTTCTCCCAYGACCTTTCAA   1.766           1.940      3.921      3.370      2.032      1.698           2.219      3.486      3.107      1.918      1.494                              1.766                            
101         6     168762605      2342638    5145     TCTGTGCTCCYTGAGGTTGGC   3.080           1.885      3.796      3.621      1.811      3.017           2.164      3.406      3.270      1.707      2.775                              3.080                            
101         6     168763978      12197584   5146     ATTTTAAAAAYGTCTCCTAAG   2.873           3.167      3.162      2.195      2.701      2.775           3.335      2.731      2.042      2.579      2.790                              2.873                            
101         6     168765063      9283862    5147     TCCTGGTGCCYGGCAAGTCTC   0.915           2.943      2.227      2.937      2.898      0.835           2.949      2.084      2.726      2.659      0.679                              0.915                            
101         6     168765804      16886236   5148     GATTGAGTCARCAAACCAAGG   1.748           0.905      4.473      3.292      2.597      1.658           0.932      4.003      3.077      2.349      2.210                              1.748                            
101         6     168771092      9455679    5149     CCAGGTCTCCRGACACTCTGT   0.199           2.546      1.637      3.788      2.856      0.181           2.598      1.563      3.473      2.645      0.163                              0.199                            
101         6     168775007      2342646    5150     ACCAGAAACCRTGTATGAAAA   0.735           1.404      3.135      2.864      3.082      0.714           1.406      2.834      2.718      2.917      1.166                              0.735                            
101         6     168776885      2342647    5151     AGAATGATACKAAGTCCTGAG   1.245           2.298      2.619      2.052      -          1.190           2.382      2.457      1.973      -          1.274                              1.245                            
101         6     168781519      4708481    5152     AAATCTCCAGYGCCCAGCTGC   0.823           4.915      2.606      -          -          0.782           4.900      2.449      -          -          0.455                              0.823                            
101         6     168785425      911946     5153     TAAACTGCATRGAAAGTTAAA   0.030           0.484      -          -          -          0.000           0.502      -          -          -          0.108                              0.030                            
101         6     168789015      6931082    5154     TCCAGGTTACRGGAAGGAAGC   0.169           -          -          -          -          0.143           -          -          -          -          0.111                              0.169                            
97          7     4429121        13232858   5155     TAATGTGGGARAAAGAATTCA   0.237           -          -          -          -          0.192           -          -          -          -          0.109                              0.237                            
97          7     4431724        13238627   5156     GTGATTACTGYCTGAAAGTTT   0.119           0.348      -          -          -          0.062           0.350      -          -          -          0.457                              0.119                            
97          7     4436371        2158628    5157     TAAAATATCTRTACTACCCAT   0.607           0.936      0.556      -          -          0.582           0.960      0.545      -          -          0.649                              0.607                            
97          7     4441231        314587     5158     TTTATTAAACYTAAGACTCTC   1.822           1.074      0.756      0.521      -          1.677           1.146      0.788      0.546      -          1.579                              1.822                            
97          7     4443207        4723748    5159     TCTCCTGCACKGGCTTGGGCT   0.890           1.282      0.563      2.523      1.824      0.826           1.585      0.595      2.251      1.741      0.769                              0.843                            
97          7     4443538        314583     5160     AGTCACTTTGYCTGCAAGGAC   1.736           1.282      2.708      2.522      2.714      1.617           1.404      2.333      2.212      2.398      1.492                              1.736                            
97          7     4443550        314582     5161     TGCAAGGACAMCTTTGTATGT   0.290           1.243      3.442      3.376      4.031      0.249           1.297      2.785      2.736      3.365      0.257                              0.290                            
97          7     4445114        7783362    5162     TAGATGATATRTAGATTAGAT   0.019           0.536      1.174      5.321      4.253      0.000           0.587      1.161      4.211      3.600      0.031                              0.019                            
97          7     4445666        423854     5163     AAGAAGTTTCYGTCAATAGAA   0.324           1.098      1.990      3.057      7.885      0.294           1.099      1.779      2.520      6.301      0.343                              0.309                            
97          7     4449442        6951056    5164     CTACTGTACTRTAAAATCTAA   1.822           1.116      2.890      7.907      6.349      1.657           1.211      2.446      6.155      5.301      1.593                              1.838                            
97          7     4450383        172707     5165     CAAAGTGGAARCCTGCCTGGT   1.428           2.568      4.719      6.019      5.354      1.368           2.623      3.944      5.149      4.578      1.374                              1.428                            
97          7     4461527        6958864    5166     ATGTAGGGGARTGCCTCCAAC   2.241           2.923      3.322      4.163      3.977      2.133           3.153      3.009      3.668      3.524      1.578                              2.218                            
97          7     4464214        895710     5167     ACCTGAGATAYTCGCCCCTCT   2.145           1.914      4.540      4.176      -          2.112           2.086      4.122      3.752      -          1.496                              2.077                            
97          7     4469915        1470539    5168     TATTCTCTCCMCAGCTCCATA   0.670           1.815      2.127      -          -          0.653           1.852      1.958      -          -          0.539                              0.625                            
97          7     4474567        1466065    5169     TCATTCAATCKGATCCAAAGC   0.230           0.738      -          -          -          0.216           0.785      -          -          -          0.110                              0.230                            
97          7     4480332        4720301    5170     TGGTGGCTCAYGCCTGTAATC   0.280           -          -          -          -          0.232           -          -          -          -          0.206                              0.280                            
102         9     109236018      12342660   5425     CCTGAGTGCCYTAAACAACAG   0.000           -          -          -          -          0.000           -          -          -          -          0.081                              0.000                            
102         9     109236689      10978854   5426     AAGAAGGTCAMATTCTCAGGT   0.634           0.245      -          -          -          0.535           0.224      -          -          -          0.466                              0.634                            
102         9     109236850      2417791    5427     ACAGAAGGCTYTCATACATCT   0.314           3.018      2.399      -          -          0.277           3.222      2.237      -          -          0.291                              0.299                            
102         9     109243828      7874117    5428     TGTTAGGCAGRGAGATTTCAT   4.894           2.821      2.354      1.679      -          4.742           3.011      2.231      1.627      -          4.250                              4.894                            
102         9     109250069      1972384    5429     GAATAATCAGRACAATGAGCC   1.485           3.254      1.812      1.249      0.624      1.418           3.342      1.733      1.201      0.615      1.002                              1.485                            
102         9     109250183      10978861   5430     TTGAGCATCTRCTGTGTACAT   2.870           3.073      2.233      1.160      0.982      2.777           3.389      2.079      1.144      0.937      2.207                              2.870                            
102         9     109254168      10759237   5431     AACAAGTTTGRCCATGAGGAC   0.336           2.160      1.510      1.581      1.837      0.314           2.376      1.444      1.506      1.752      0.112                              0.325                            
102         9     109257563      882942     5432     CTTTTAACTGMAGATACAGTC   1.940           1.464      0.727      1.343      1.330      1.854           1.496      0.706      1.295      1.308      1.607                              1.940                            
102         9     109261165      1342321    5433     CTAGGAACTTYACTCCAACAA   0.998           1.252      1.684      1.043      -          0.934           1.224      1.568      1.054      -          0.541                              0.998                            
102         9     109270991      10759238   5434     GGTCTGAGTARAATCAGGTTT   0.507           0.952      0.827      -          -          0.447           0.995      0.882      -          -          0.208                              0.507                            
102         9     109271684      1819730    5435     TAAACAAAATRAACAAAACCC   1.029           0.595      -          -          -          0.980           0.595      -          -          -          1.412                              1.010                            
102         9     109278182      17725250   5436     GGTCAATTCCRCGCACTGTCA   0.335           -          -          -          -          0.277           -          -          -          -          0.347                              0.335                            
103         10    63500292       7090871    5508     ATAACTGGCAYTTCCCTTTGG   0.548           -          -          -          -          0.500           -          -          -          -          0.320                              0.548                            
103         10    63510068       4948503    5509     AGATCTTCTGYGGCTCACATC   0.165           0.739      -          -          -          0.147           0.771      -          -          -          0.216                              0.165                            
103         10    63513118       2278305    5510     ATGGTGCCCTRCTTTGTGAAC   0.373           2.771      2.712      -          -          0.350           3.167      2.369      -          -          0.150                              0.373                            
103         10    63518662       9414761    5511     TGGTGGGAAGYTAACATTTAA   4.797           3.139      4.697      3.165      -          4.660           3.342      3.985      2.875      -          4.093                              4.797                            
103         10    63526862       7916978    5512     TTGGCAAATAYCTCTTATCTT   2.280           2.739      3.656      3.111      -          2.191           3.004      3.321      2.842      -          1.583                              2.280                            
103         10    63532640       10821956   5513     AGGCTGCATARTAATAGAACT   0.139           1.186      2.310      -          -          0.109           1.196      2.176      -          -          0.605                              0.139                            
103         10    63552022       9415646    5514     TTGTGGTCTAKCTCTTCTTTT   0.824           0.666      -          -          -          0.750           0.669      -          -          -          0.838                              0.824                            
103         10    63557721       750412     5515     TTTTCTTCCARTCTGGTTTGT   0.090           -          -          -          -          0.068           -          -          -          -          0.085                              0.090                            
104         11    20626547       1617769    5594     TGCGTTGACAYGAACATCATA   0.265           -          -          -          -          0.242           -          -          -          -          0.081                              0.265                            
104         11    20630443       2276433    5595     ACCAGTGGGARCCCATGACCT   1.265           0.972      -          -          -          1.199           1.028      -          -          -          0.851                              1.265                            
104         11    20632221       17298481   5596     AGACATTCCTRTTATTTTTAG   0.730           3.301      2.629      -          -          0.660           3.319      2.230      -          -          0.615                              0.730                            
104         11    20632829       2276432    5597     TTTGGCTTCTYTGCAGAGGCT   4.412           2.885      2.877      -          -          4.293           3.124      2.459      -          -          3.717                              4.412                            
104         11    20636859       7127159    5598     AGCAAGCAGTRGTTTGACTTG   0.081           2.522      -          -          -          0.040           3.027      -          -          -          0.184                              0.081                            
104         11    20638015       10466424   5599     CTGATCAGGTYAACCCAGAGG   0.370           -          -          -          -          0.334           -          -          -          -          0.144                              0.371                            
105         12    22872528       2466889    5677     GTTTGGGTAARTACACTCTAT   0.549           -          -          -          -          0.500           -          -          -          -          1.096                              0.549                            
105         12    22876418       17175003   5678     TATTAATCATYGGACTTCATG   0.436           2.103      -          -          -          0.372           2.383      -          -          -          1.639                              0.436                            
105         12    22878730       2433644    5679     TCAGGAGAAGMACATGGGTAA   0.513           3.184      3.710      -          -          0.502           3.460      3.353      -          -          0.472                              0.558                            
105         12    22879373       17175038   5680     GATTATTGTTKTCCAGGCAGT   4.588           2.530      2.638      2.508      -          4.448           2.722      2.454      2.350      -          3.745                              4.588                            
105         12    22880649       2466887    5681     TGTGCTTATTYGGAGGAGGGT   0.608           2.381      1.719      -          -          0.550           2.811      1.611      -          -          0.395                              0.608                            
105         12    22884532       7137690    5682     CCTTAAGGCTRCTCTGGTCAA   0.143           0.327      -          -          -          0.132           0.319      -          -          -          0.227                              0.143                            
105         12    22886997       2433633    5683     CATGACACTCRTCATCTTCTA   0.254           -          -          -          -          0.226           -          -          -          -          0.509                              0.254                            
106         20    55613281       8118279    6327     TGGCCTGGGCRTTTCCACAGG   0.250           -          -          -          -          0.199           -          -          -          -          0.079                              0.250                            
106         20    55617366       6070180    6328     TTTCTACCCAYTGGTGGGACT   0.464           2.682      -          -          -          0.449           2.835      -          -          -          0.248                              0.464                            
106         20    55618538       742724     6329     ATCGATGAGARTGAATGAATG   4.214           2.437      1.599      -          -          4.098           2.512      1.521      -          -          3.184                              4.214                            
106         20    55624040       2073145    6330     TGGGGCCTCTYGGCTGCAGAA   0.366           2.412      -          -          -          0.302           2.750      -          -          -          0.177                              0.366                            
106         20    55633032       2026763    6331     CCAAGTCTCCYTTCTACCAGG   0.236           -          -          -          -          0.190           -          -          -          -          0.464                              0.236                            
107         21    46705737       2078203    6411     ACTGTACTGCRTTTGTTAAGG   0.288           -          -          -          -          0.268           -          -          -          -          0.088                              0.288                            
107         21    46717234       1023355    6412     AGAACTTTCTKCTACGATGGG   1.351           0.862      -          -          -          1.249           0.893      -          -          -          0.755                              1.259                            
107         21    46728784       2032110    6413     GCAACCACTAKCTGTATCTGA   0.310           3.801      4.257      -          -          0.253           3.964      3.659      -          -          0.450                              0.310                            
107         21    46729013       718496     6414     CAGTGTTTCCMGTTTTTCAAT   4.278           3.498      4.524      4.257      -          4.182           3.734      3.903      3.732      -          3.782                              4.681                            
107         21    46729924       7279991    6415     GAAAATCTTAYAGGAAGATTG   1.495           2.900      4.200      -          -          1.396           3.182      3.611      -          -          0.940                              1.495                            
107         21    46746267       2839297    6416     TCAAGGGTTGYGAAAAATCTT   1.564           1.023      -          -          -          1.517           1.043      -          -          -          1.072                              1.638                            
107         21    46755673       1029262    6417     TTAAAAAACARTATTATAAAC   1.933           -          -          -          -          1.863           -          -          -          -          1.308                              1.933                            
