Table 3. Association results for the Discovery, Replication and combined Meta-analysis, for SNPs with P<0.05 in the Replication data, by chromosome.
| Discovery | Replication | Meta-analysis* | CCFR only | BCFR only | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | CHR | BP | Coded Allele | Allele Freq |
OR | P | Pfixed | Phet | Pfixed | Phet | P | P | Gene | Variant Type | RegulomeDB |
| rs7429100 | 3 | 79737521 | A | 0.57 | 0.79 (0.70–0.89) | 1.75E-04 | 0.003 | 0.071 | 1.84E-06 | 0.141 | 5.78E-03 | 4.49E-02 | ROBO1 | intronic | 7 |
| rs9631514 | 3 | 79740102 | T | 0.57 | 0.79 (0.70–0.89) | 1.69E-04 | 0.003 | 0.069 | 1.86E-06 | 0.138 | 5.50E-03 | 4.49E-02 | ROBO1 | intronic | 7 |
| rs7635296 | 3 | 79730605 | T | 0.57 | 0.79 (0.70–0.90) | 1.98E-04 | 0.003 | 0.081 | 1.95E-06 | 0.156 | 6.66E-03 | 4.69E-02 | ROBO1 | intronic | 5 |
| rs7613379 | 3 | 79730821 | C | 0.57 | 0.79 (0.70–0.90) | 1.97E-04 | 0.003 | 0.081 | 1.95E-06 | 0.156 | 6.65E-03 | 4.69E-02 | ROBO1 | intronic | 7 |
| rs6762755 | 3 | 79729947 | G | 0.57 | 0.79 (0.70–0.90) | 2.00E-04 | 0.003 | 0.081 | 1.96E-06 | 0.156 | 6.70E-03 | 4.71E-02 | ROBO1 | intronic | 7 |
| rs7635587 | 3 | 79730872 | T | 0.57 | 0.79 (0.70–0.90) | 1.98E-04 | 0.003 | 0.081 | 1.96E-06 | 0.156 | 6.65E-03 | 4.68E-02 | ROBO1 | intronic | 7 |
| rs6548648 | 3 | 79728730 | G | 0.57 | 0.79 (0.70–0.90) | 2.06E-04 | 0.003 | 0.082 | 2.00E-06 | 0.157 | 6.88E-03 | 4.74E-02 | ROBO1 | intronic | 6 |
| rs9862551 | 3 | 79746590 | T | 0.57 | 0.79 (0.70–0.89) | 1.60E-04 | 0.004 | 0.068 | 2.05E-06 | 0.139 | 5.05E-03 | 4.49E-02 | ROBO1 | intronic | 7 |
| rs7431092 | 3 | 79746262 | C | 0.57 | 0.79 (0.70–0.89) | 1.60E-04 | 0.004 | 0.069 | 2.07E-06 | 0.140 | 5.05E-03 | 4.50E-02 | ROBO1 | intronic | 7 |
| rs9812795 | 3 | 79747727 | G | 0.57 | 0.79 (0.70–0.89) | 1.59E-04 | 0.004 | 0.069 | 2.10E-06 | 0.140 | 5.02E-03 | 4.48E-02 | ROBO1 | intronic | 7 |
| rs9873237 | 3 | 79748478 | C | 0.57 | 0.79 (0.70–0.89) | 1.59E-04 | 0.004 | 0.069 | 2.16E-06 | 0.140 | 5.00E-03 | 4.51E-02 | ROBO1 | intronic | 6 |
| rs10212228 | 3 | 79744923 | C | 0.56 | 0.79 (0.70–0.90) | 1.84E-04 | 0.003 | 0.071 | 2.24E-06 | 0.141 | 5.65E-03 | 4.58E-02 | ROBO1 | intronic | 6 |
| rs4856257 | 3 | 79720785 | A | 0.57 | 0.80 (0.70–0.90) | 2.78E-04 | 0.003 | 0.086 | 2.88E-06 | 0.163 | 8.56E-03 | 5.11E-02 | ROBO1 | intronic | 6 |
| rs3923148 | 3 | 79727278 | T | 0.56 | 0.80 (0.71–0.90) | 2.87E-04 | 0.003 | 0.094 | 3.01E-06 | 0.175 | 1.29E-02 | 4.04E-02 | ROBO1 | intronic | 7 |
| rs7430339 | 3 | 79766511 | G | 0.58 | 0.80 (0.71–0.89) | 1.20E-04 | 0.008 | 0.066 | 3.06E-06 | 0.141 | 2.11E-03 | 5.99E-02 | ROBO1 | intronic | 7 |
| rs9878764 | 3 | 79719636 | T | 0.57 | 0.80 (0.70–0.90) | 2.89E-04 | 0.003 | 0.085 | 3.12E-06 | 0.162 | 8.80E-03 | 5.16E-02 | ROBO1 | intronic | 5 |
| rs4856253 | 3 | 79719062 | T | 0.57 | 0.80 (0.70–0.90) | 2.95E-04 | 0.003 | 0.085 | 3.26E-06 | 0.162 | 8.97E-03 | 5.18E-02 | ROBO1 | intronic | 7 |
| rs6770961 | 3 | 79716540 | C | 0.57 | 0.80 (0.71–0.90) | 3.23E-04 | 0.003 | 0.084 | 3.78E-06 | 0.161 | 9.59E-03 | 5.29E-02 | ROBO1 | intronic | 6 |
| rs12107379 | 3 | 79738224 | A | 0.56 | 0.79 (0.70–0.90) | 2.07E-04 | 0.007 | 0.066 | 4.55E-06 | 0.140 | 6.07E-03 | 4.63E-02 | ROBO1 | intronic | 6 |
| rs13060599 | 3 | 79738599 | T | 0.56 | 0.79 (0.70–0.90) | 2.09E-04 | 0.009 | 0.052 | 5.73E-06 | 0.115 | 5.80E-03 | 4.89E-02 | ROBO1 | intronic | 6 |
| rs9857798 | 3 | 79715860 | G | 0.57 | 0.80 (0.71–0.91) | 4.91E-04 | 0.005 | 0.128 | 8.68E-06 | 0.236 | 1.29E-02 | 6.20E-02 | ROBO1 | intronic | 7 |
| rs7428022 | 3 | 79709843 | T | 0.54 | 0.79 (0.70–0.89) | 2.05E-04 | 0.014 | 0.109 | 9.02E-06 | 0.218 | 1.24E-02 | 2.48E-02 | ROBO1 | intronic | 6 |
| rs7431260 | 3 | 79708481 | T | 0.54 | 0.79 (0.69–0.89) | 1.80E-04 | 0.017 | 0.113 | 9.23E-06 | 0.224 | 1.05E-02 | 2.70E-02 | ROBO1 | intronic | 6 |
| rs9825870 | 3 | 79715200 | A | 0.56 | 0.80 (0.71–0.91) | 4.27E-04 | 0.007 | 0.088 | 9.33E-06 | 0.176 | 1.59E-02 | 4.75E-02 | ROBO1 | intronic | 6 |
| rs6775448 | 3 | 79705179 | G | 0.54 | 0.79 (0.70–0.90) | 2.83E-04 | 0.011 | 0.103 | 9.50E-06 | 0.208 | 1.45E-02 | 2.75E-02 | ROBO1 | intronic | 5 |
| rs9825204 | 3 | 79714764 | G | 0.56 | 0.80 (0.71–0.91) | 4.34E-04 | 0.007 | 0.087 | 9.55E-06 | 0.174 | 1.61E-02 | 4.78E-02 | ROBO1 | intronic | 7 |
| rs7640127 | 3 | 79707605 | A | 0.54 | 0.79 (0.70–0.90) | 2.50E-04 | 0.013 | 0.102 | 1.02E-05 | 0.206 | 1.49E-02 | 2.52E-02 | ROBO1 | intronic | 6 |
| rs4856448 | 3 | 79707387 | A | 0.54 | 0.79 (0.70–0.90) | 2.65E-04 | 0.013 | 0.105 | 1.06E-05 | 0.212 | 1.50E-02 | 2.65E-02 | ROBO1 | intronic | 7 |
| rs7628280 | 3 | 79707453 | G | 0.54 | 0.79 (0.70–0.90) | 2.62E-04 | 0.013 | 0.104 | 1.07E-05 | 0.211 | 1.48E-02 | 2.64E-02 | ROBO1 | intronic | 7 |
| rs9824870 | 3 | 79714522 | C | 0.56 | 0.80 (0.71–0.91) | 4.83E-04 | 0.007 | 0.084 | 1.08E-05 | 0.169 | 1.74E-02 | 4.89E-02 | ROBO1 | intronic | 7 |
| rs4856444 | 3 | 79707182 | A | 0.54 | 0.79 (0.70–0.90) | 2.67E-04 | 0.013 | 0.104 | 1.09E-05 | 0.210 | 1.50E-02 | 2.65E-02 | ROBO1 | intronic | 7 |
| rs9880911 | 3 | 79707817 | G | 0.54 | 0.79 (0.70–0.90) | 2.58E-04 | 0.014 | 0.107 | 1.12E-05 | 0.214 | 1.46E-02 | 2.63E-02 | ROBO1 | intronic | 6 |
| rs4856434 | 3 | 79706132 | C | 0.54 | 0.79 (0.70–0.90) | 2.77E-04 | 0.013 | 0.103 | 1.13E-05 | 0.208 | 1.54E-02 | 2.69E-02 | ROBO1 | intronic | 6 |
| rs9870711 | 3 | 79706168 | C | 0.54 | 0.79 (0.70–0.90) | 2.76E-04 | 0.013 | 0.100 | 1.13E-05 | 0.202 | 1.53E-02 | 2.69E-02 | ROBO1 | intronic | 7 |
| rs4856443 | 3 | 79707150 | G | 0.54 | 0.79 (0.70–0.90) | 2.69E-04 | 0.014 | 0.105 | 1.14E-05 | 0.212 | 1.51E-02 | 2.66E-02 | ROBO1 | intronic | 6 |
| rs4856447 | 3 | 79707357 | T | 0.54 | 0.79 (0.70–0.90) | 2.66E-04 | 0.014 | 0.106 | 1.16E-05 | 0.213 | 1.50E-02 | 2.65E-02 | ROBO1 | intronic | 7 |
| rs4856228 | 3 | 79705541 | G | 0.54 | 0.79 (0.70–0.90) | 2.85E-04 | 0.013 | 0.102 | 1.17E-05 | 0.207 | 1.57E-02 | 2.70E-02 | ROBO1 | intronic | 6 |
| rs4856440 | 3 | 79707004 | G | 0.54 | 0.79 (0.70–0.90) | 2.72E-04 | 0.014 | 0.105 | 1.18E-05 | 0.212 | 1.52E-02 | 2.67E-02 | ROBO1 | intronic | 6 |
| rs4856433 | 3 | 79706059 | A | 0.54 | 0.79 (0.70–0.90) | 2.68E-04 | 0.015 | 0.102 | 1.19E-05 | 0.206 | 1.52E-02 | 2.63E-02 | ROBO1 | intronic | 7 |
| rs6419737 | 3 | 79703548 | G | 0.54 | 0.80 (0.70–0.90) | 3.11E-04 | 0.014 | 0.103 | 1.35E-05 | 0.209 | 1.67E-02 | 2.76E-02 | ROBO1 | intronic | 7 |
| rs9869899 | 3 | 79712822 | T | 0.56 | 0.81 (0.71–0.91) | 6.96E-04 | 0.008 | 0.084 | 1.84E-05 | 0.170 | 2.22E-02 | 5.42E-02 | ROBO1 | intronic | 6 |
| rs7430639 | 3 | 79785085 | A | 0.59 | 0.81 (0.72–0.90) | 2.21E-04 | 0.030 | 0.004 | 1.91E-05 | 0.011 | 4.13E-03 | 5.10E-02 | ROBO1 | intronic | 6 |
| rs7431063 | 3 | 79785218 | A | 0.59 | 0.81 (0.72–0.90) | 2.40E-04 | 0.031 | 0.004 | 2.15E-05 | 0.011 | 4.37E-03 | 5.25E-02 | ROBO1 | intronic | 7 |
| rs4856298 | 3 | 79783137 | A | 0.58 | 0.81 (0.72–0.90) | 2.00E-04 | 0.040 | 0.007 | 2.25E-05 | 0.018 | 5.28E-03 | 4.19E-02 | ROBO1 | intronic | 7 |
| rs6771093 | 3 | 79709304 | A | 0.56 | 0.81 (0.72–0.92) | 9.21E-04 | 0.008 | 0.078 | 2.28E-05 | 0.156 | 2.68E-02 | 5.86E-02 | ROBO1 | intronic | 5 |
| rs7426439 | 3 | 79789645 | T | 0.57 | 0.80 (0.72–0.91) | 3.06E-04 | 0.026 | 0.003 | 2.30E-05 | 0.009 | 3.72E-03 | 6.23E-02 | ROBO1 | intronic | 7 |
| rs9309831 | 3 | 79789408 | T | 0.59 | 0.81 (0.72–0.91) | 2.64E-04 | 0.031 | 0.004 | 2.34E-05 | 0.011 | 4.67E-03 | 5.41E-02 | ROBO1 | intronic | 7 |
| rs3924599 | 3 | 79789184 | G | 0.59 | 0.81 (0.72–0.91) | 2.60E-04 | 0.032 | 0.004 | 2.36E-05 | 0.011 | 4.62E-03 | 5.38E-02 | ROBO1 | intronic | 6 |
| rs1995402 | 3 | 79790407 | G | 0.59 | 0.81 (0.72–0.91) | 2.70E-04 | 0.031 | 0.004 | 2.42E-05 | 0.011 | 4.75E-03 | 5.45E-02 | ROBO1 | intronic | 6 |
| rs1995401 | 3 | 79790433 | C | 0.59 | 0.81 (0.72–0.91) | 2.72E-04 | 0.031 | 0.004 | 2.43E-05 | 0.011 | 4.77E-03 | 5.46E-02 | ROBO1 | intronic | 6 |
| rs7649774 | 3 | 79791414 | T | 0.59 | 0.81 (0.72–0.91) | 2.79E-04 | 0.033 | 0.004 | 2.58E-05 | 0.010 | 4.85E-03 | 5.50E-02 | ROBO1 | intronic | 7 |
| rs7426689 | 3 | 79785050 | C | 0.55 | 0.81 (0.72–0.91) | 5.21E-04 | 0.031 | 0.004 | 4.50E-05 | 0.011 | 4.17E-03 | 1.02E-01 | ROBO1 | intronic | 6 |
| rs253937 | 5 | 31655104 | A | 0.89 | 1.51 (1.24–1.83) | 2.19E-05 | 0.050 | 0.024 | 4.80E-06 | 0.055 | 1.87E-02 | 1.46E-03 | PDZD2 | 6 | |
| rs1778181 | 9 | 17964230 | T | 0.99 | 0.37 (0.23–0.60) | 3.47E-05 | 0.024 | 0.692 | 3.72E-06 | 0.843 | 2.01E-02 | 7.47E-03 | 167kb 3' of SH3GL2 | 7 | |
| rs113609979 | 9 | 17961146 | T | 0.99 | 0.37 (0.23–0.60) | 3.55E-05 | 0.026 | 0.722 | 3.94E-06 | 0.861 | 9.70E-03 | 1.80E-02 | 164kb 3' of SH3GL2 | 6 | |
| rs145162794 | 9 | 17959449 | A | 0.99 | 0.38 (0.23–0.61) | 4.90E-05 | 0.027 | 0.717 | 5.45E-06 | 0.859 | 1.00E-02 | 2.37E-02 | 162kb 3' of SH3GL2 | 6 | |
| rs2772690 | 9 | 17947742 | G | 0.99 | 0.38 (0.23–0.62) | 8.62E-05 | 0.024 | 0.632 | 8.29E-06 | 0.793 | 3.49E-02 | 1.22E-02 | 151kb 3' of SH3GL2 | 5 | |
| rs1755276 | 9 | 17942032 | A | 0.99 | 0.38 (0.23–0.62) | 7.99E-05 | 0.026 | 0.634 | 8.63E-06 | 0.795 | 3.63E-02 | 1.13E-02 | 145kb 3' of SH3GL2 | 6 | |
| rs2383057 | 9 | 17946622 | T | 0.99 | 0.38 (0.23–0.62) | 8.62E-05 | 0.028 | 0.584 | 9.82E-06 | 0.742 | 3.49E-02 | 1.23E-02 | 149kb 3' of SH3GL2 | 6 | |
| rs2840779 | 9 | 17950343 | G | 0.99 | 0.38 (0.23–0.62) | 8.69E-05 | 0.029 | 0.578 | 1.02E-05 | 0.734 | 3.49E-02 | 1.21E-02 | 153kb 3' of SH3GL2 | 6 | |
| rs2840782 | 9 | 17947425 | A | 0.99 | 0.38 (0.23–0.62) | 8.63E-05 | 0.030 | 0.577 | 1.03E-05 | 0.733 | 3.49E-02 | 1.23E-02 | 150kb 3' of SH3GL2 | 7 | |
| rs2772692 | 9 | 17949040 | G | 0.99 | 0.38 (0.23–0.62) | 8.67E-05 | 0.030 | 0.578 | 1.04E-05 | 0.733 | 3.49E-02 | 1.22E-02 | 152kb 3' of SH3GL2 | 7 | |
| rs2811824 | 9 | 17948254 | C | 0.99 | 0.38 (0.23–0.62) | 8.63E-05 | 0.030 | 0.575 | 1.05E-05 | 0.730 | 3.49E-02 | 1.22E-02 | 151kb 3' of SH3GL2 | 5 | |
| rs10217546 | 9 | 35986887 | C | 0.54 | 0.82 (0.73–0.92) | 8.89E-04 | 0.040 | 0.830 | 8.24E-02 | 0.006 | 2.59E-02 | 3.21E-02 | 29kb 5' of OR2S2 | 6 | |
| rs72886417 | 18 | 36602286 | G | 0.71 | 0.75 (0.66–0.85) | 1.31E-05 | 0.029 | 0.168 | 1.13E-06 | 0.298 | 8.17E-06 | 4.31E-02 | 6kb 5' of 7SK | 6 | |
| rs17659787 | 18 | 36600043 | T | 0.71 | 0.75 (0.65–0.85) | 1.31E-05 | 0.028 | 0.167 | 1.14E-06 | 0.296 | 8.28E-06 | 4.29E-02 | 3.7kb 5' of 7SK | 5 | |
| rs72904570 | 18 | 36585235 | G | 0.72 | 0.75 (0.65–0.85) | 1.62E-05 | 0.028 | 0.164 | 1.37E-06 | 0.293 | 1.28E-05 | 3.73E-02 | 11kb 3' of 7SK | 6 | |
| rs72886457 | 18 | 36643966 | C | 0.70 | 0.76 (0.67–0.86) | 1.99E-05 | 0.036 | 0.250 | 2.09E-06 | 0.412 | 2.86E-05 | 3.69E-02 | 30kb 3' of U6 | 7 | |
| rs113118767 | 20 | 19499434 | T | 0.99 | 4.02 (1./99-8.13) | 8.97E-06 | 0.026 | 0.290 | 1.29E-01 | 0.000 | 4.94E-03 | 3.72E-03 | SLC24A3 | intronic | 5 |
*Meta-analysis of BCFR, CCFR, WHI1, WHI2 and VITAL GWAS data; CCFR, Colon Cancer Family Registry; BCFR, Breast Cancer Family Registry; SNP, single nucleotide polymorphism; CHR, chromosome number; BP, location in base-pairs; Freq, frequency; OR, odds ratio; CI, confidence interval; Pfixed, P value for fixed-effects meta-analysis; Phet, P value for heterogeneity.