Table 5.
Prostate Cancer SNP Associations Common to Both CGEMS Top 500 Ranked SNPs and FHS 100K SNPs
| CGEMS Phase 1a | FHS 100K | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| DBSNP_ID | Chr | Physical Position | CGEMS p-value | CGEMS Rank | 100K SNP | Physical Position | GEE p-value | FBAT p-value | MAF | Nearest Gene |
| Minor Allele Frequency ≥10% | ||||||||||
| rs3017183 | 18 | 51,319,241 | 0.00024100 | 85 | rs3794889 | 51,212,935 | 0.017 | 0.799 | 0.224 | TCF4 |
| rs3017183 | 18 | 51,319,241 | 0.00024100 | 85 | rs4801149 | 51,214,227 | 0.044 | 0.983 | 0.221 | TCF4 |
| rs2253319 | 21 | 35,109,916 | 0.00041100 | 137 | rs2834645 | 35,109,556 | 0.009 | 0.293 | 0.206 | RUNX1 |
| rs392715 | 16 | 24,023,323 | 0.00041800 | 141 | rs10492797 | 24,122,453 | 0.036 | 0.407 | 0.175 | PRKCB1 |
| rs10256504 | 7 | 3,516,796 | 0.00092200 | 295 | rs4418248 | 3,194,181 | 1.8 × 10-4 | 0.056 | 0.109 | SDK1 |
| rs6102912 | 20 | 40,636,349 | 0.00111000 | 350 | rs986831 | 40,594,892 | 0.009 | 0.094 | 0.407 | PTPRT |
| rs4782742 | 16 | 81,573,151 | 0.00127400 | 395 | rs254315 | 82,313,913 | 7.1 × 10-4 | 0.011 | 0.141 | CDH13 |
| rs2371438 | 2 | 212,791,037 | 0.00128500 | 401 | rs10497958 | 212,771,465 | 0.055 | 0.047 | 0.164 | ERBB4 |
| rs6577648 | 8 | 135,555,688 | 0.00144900 | 445 | rs10505624 | 135,607,862 | 4.9 × 10-4 | 0.007 | 0.147 | ZFAT1 |
| rs9327886 | 5 | 102,931,646 | 0.00154600 | 468 | rs10515347 | 102,950,833 | 0.006 | 0.062 | 0.354 | NUDT12 |
| rs6555491 | 5 | 7,799,792 | 0.00158700 | 478 | rs10512920 | 7,455,561 | 0.009 | 0.647 | 0.244 | ADCY2 |
| Minor Allele Frequency <10% | ||||||||||
| rs38276 | 7 | 14,078,240 | 0.00055700 | 181 | rs10486031 | 14,258,703 | 1.7 × 10-5 | 0.759 | 0.032 | DGKB |
| rs216666 | 2 | 80,745,015 | 0.00057000 | 184 | rs10520247 | 79,693,452 | 2.8 × 10-5 | 0.240 | 0.065 | CTNNA2 |
| rs216666 | 2 | 80,745,015 | 0.00057000 | 184 | rs10520246 | 79,693,324 | 1.5 × 10-4 | 0.198 | 0.050 | CTNNA2 |
| rs1261256 | 5 | 22,490,853 | 0.00060200 | 193 | rs10520880 | 22,634,003 | 8.5 × 10-5 | 0.356 | 0.065 | CDH12 |
| rs7610584 | 3 | 171,635,885 | 0.00061900 | 196 | rs10513681 | 171,624,010 | 7.8 × 10-7 | 0.402 | 0.025 | CLDN11 |
| rs7329659 | 13 | 97,872,564 | 0.00064700 | 209 | rs7989050 | 97,680,299 | 6.0 × 10-6 | 0.258 | 0.014 | FARP1 |
| rs208354 | 7 | 2,554,104 | 0.00065000 | 211 | rs10487577 | 2,583,719 | 2.0 × 10-7 | N/A | 0.012 | GNA12 |
| rs3751832 | 16 | 77,771,773 | 0.00079900 | 257 | rs10514443 | 77,353,386 | 9.3 × 10-4 | N/A | 0.008 | WWOX |
CGEMS = Cancer Genetics Markers of Susceptibility; MAF = minor allele frequency; N/A= not available, less than 10 informative families for FBAT