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. 2016 Apr 12;114(10):1165–1174. doi: 10.1038/bjc.2016.94

Table 2. SNPs associated with prostate cancer.

        RAPPER
 RADIOGEN
 GenePARE
 CCI
SNP Chromosome Position Alleles major/minor MAF R2 a MAF R2 a MAF R2 a MAF R2 a
rs1218582 1 154834183 A/G 0.45 0.94 0.50 0.87 0.43 0.96 0.48 0.96
rs4245739 1 204518842 A/C 0.24 0.99 0.30 0.99 0.28 1 0.23 1
rs11902236 2 10117868 G/A 0.27 0.93 0.29 1 0.27 0.91 0.28 1
rs13385191 2 20888265 G/Ab 0.25 0.99 0.24 1 0.27 1 0.26 1
rs1465618 2 43553949 G/A 0.22 0.98 0.26 0.98 0.23 0.98 0.22 1
rs721048 2 63131731 G/A 0.22 1 0.22 1 0.18 0.94 0.17 0.93
rs10187424 2 85794297 A/G 0.37 1 0.44 0.99 0.42 0.99 0.42 1
rs12621278 2 173311553 A/G 0.04 0.97 0.04 1 — — — —
rs2292884 2 238443226 A/G 0.28 1 0.23 0.97 0.24 0.99 0.22 0.99
rs3771570 2 242382864 G/A 0.18 0.99 0.16 0.96 0.14 1 0.15 1
rs2660753 3 87110674 C/T 0.11 1 0.16 1 0.19 0.96 0.08 0.98
rs2055109 3 87467332 C/Tb 0.26 1 0.28 0.99 0.24 0.86 0.22 0.99
rs7611694 3 113275624 A/C 0.41 1 0.37 0.98 0.36 1 0.39 1
rs10934853 3 128038373 C/A 0.29 0.98 0.29 0.94 0.32 1 0.34 1
rs6763931 3 141102833 C/T 0.45 0.98 0.39 1 0.40 0.96 0.39 1
rs10936632 3 170130102 A/C 0.49 0.94 0.45 0.95 0.46 0.94 0.47 0.95
rs1894292 4 74349158 G/A 0.47 0.86 0.47 1 0.40 0.91 0.44 1
rs12500426 4 95514609 C/A 0.48 0.96 0.48 0.98 0.49 0.98 0.49 0.99
rs17021918 4 95562877 C/T 0.31 0.99 0.31 0.99 0.35 1 0.37 1
rs7679673 4 106061534 C/A 0.34 1 0.38 0.99 0.49 0.99 0.38 1
rs2242652 5 1280028 G/A 0.19 0.91 0.15 0.45 0.22 0.62 0.19 0.62
rs12653946 5 1895829 C/T 0.45 1 0.46 0.58 0.48 0.90 0.44 0.90
rs2121875 5 44365545 T/G 0.35 1 0.37 1 0.41 0.99 0.34 1
rs6869841 5 172939426 G/A 0.23 0.98 0.21 0.99 0.24 0.99 0.23 0.99
rs130067c 6 31118511 T/G 0.21 1 0.19 1 NA NA NA NA
rs3096702d 6 32192331 G/A 0.42 0.97 0.28 1 NA NA NA NA
rs1983891 6 41536427 C/T 0.29 0.95 0.35 0.98 0.31 1 0.31 1
rs2273669 6 109285189 A/G 0.15 0.99 0.16 0.97 0.12 0.97 0.14 0.99
rs339331 6 117210052 T/Cb 0.27 0.97 0.25 1 0.19 1 0.32 1
rs1933488 6 153441079 A/G 0.38 0.99 0.41 1 0.44 1 0.41 1
rs9364554 6 160833664 C/T 0.33 0.99 0.25 1 0.25 1 0.29 1
rs12155172 7 20994491 G/A 0.22 0.82 0.21 1 0.21 0.97 0.22 0.97
rs10486567 7 27976563 G/Ab 0.19 0.97 0.20 1 0.25 0.99 0.21 0.98
rs6465657 7 97816327 T/C 0.49 1 0.47 1 0.41 1 0.49 1
rs2928679 8 23438975 C/T 0.48 1 0.45 0.99 0.49 0.97 0.46 1
rs1512268 8 23526463 G/A 0.45 0.99 0.50 0.98 0.49 0.99 0.42 1
rs11135910 8 25892142 G/A 0.2 0.93 0.15 1 0.16 0.97 0.18 0.99
rs12543663 8 127924659 A/C 0.35 0.94 0.26 0.97 0.31 0.94 0.33 0.94
rs10086908 8 128011937 T/C 0.27 1 0.31 1 0.26 1 0.26 0.99
rs16901979 8 128124916 C/A 0.05 0.99 0.05 1 0.05 1 0.05 1
rs620861 8 128335673 C/T 0.34 1 0.36 0.99 0.36 0.99 0.31 0.99
rs6983267 8 128413305 G/Tb 0.43 0.95 0.40 1 0.48 0.98 0.45 1
rs1447295 8 128485038 C/A 0.14 0.97 0.07 1 0.09 0.99 0.10 0.99
rs817826 9 110156300 T/C 0.17 0.64 0.17 0.94 0.21 1 0.12 1
rs1571801 9 124427373 C/A 0.28 0.76 0.23 1 0.22 1 0.32 1
rs10993994 10 51549496 C/T 0.46 0.79 0.43 1 0.47 0.92 0.43 0.92
rs3850699 10 104414221 A/G 0.28 0.99 0.28 0.96 0.29 0.97 0.26 0.97
rs2252004 10 122844709 G/Tb 0.09 0.99 0.09 0.99 0.11 1 0.09 1
rs4962416 10 126696872 T/C 0.28 0.93 0.31 1 0.31 0.98 0.24 0.98
rs7127900 11 2233574 G/A 0.22 0.98 0.23 0.91 0.27 0.59 0.22 0.96
rs1938781 11 58915110 T/C 0.21 1 0.21 1 0.20 0.99 0.19 1
rs7931342 11 68994497 G/T 0.46 1 0.41 1 0.36 1 0.41 1
rs11568818 11 102401661 A/G 0.44 0.89 0.46 0.99 0.42 0.91 0.42 0.93
rs902774 12 53273904 G/A 0.16 0.98 0.14 1 0.17 0.99 0.18 1
rs1270884 12 114685571 G/A 0.48 0.93 0.49 0.98 0.48 0.98 0.48 1
rs10875943 12 49676010 T/C 0.32 0.86 0.28 1 0.32 0.93 0.29 0.95
rs9600079 13 73728139 G/T 0.46 0.86 0.47 1 0.43 0.89 0.46 0.95
rs8008270 14 53372330 G/A 0.15 1 0.19 0.99 0.19 1 0.16 1
rs7141529 14 69126744 G/Ab 0.47 1 0.45 1 0.46 0.99 0.49 0.99
rs4430796 17 36098040 G/A 0.47 0.94 0.49 0.88 0.49 0.90 0.45 0.93
rs7210100e 17 47436749 A/G — — — — — — — —
rs11649743 17 36074979 G/Ab 0.2 1 0.19 1 0.15 1 0.16 1
rs11650494 17 47345186 G/A 0.09 0.99 0.08 0.93 0.13 0.99 0.09 0.99
rs684232 17 618965 A/G 0.35 0.99 0.33 0.98 0.34 0.98 0.39 0.99
rs1859962 17 69108753 T/G 0.5 0.99 0.45 1 0.43 1 0.47 1
rs7241993 18 76773973 G/A 0.28 0.94 0.28 0.91 0.32 0.51 0.32 0.56
rs8102476 19 38735613 C/Tb 0.42 0.99 0.34 0.96 0.38 0.97 0.43 0.97
rs11672691 19 41985587 A/Gb 0.24 0.87 0.21 0.93 0.23 0.93 0.27 0.93
rs103294f 19 54797848 T/C 0.23 1 0.20 1 0.22 0.30 — —
rs2735839 19 51364623 G/A 0.12 1 0.15 1 0.17 0.93 0.16 0.97
rs2427345 20 61015611 G/A 0.35 0.99 0.35 0.37 0.39 0.91 0.40 0.96
rs6062509 20 62362563 A/C 0.32 1 0.26 0.99 0.27 0.98 0.28 0.98
rs5759167 22 43500212 G/T 0.47 1 0.45 0.90 0.46 0.80 0.47 1
rs2405942 23 9814135 A/G 0.17 1 0.20 0.95 0.21 0.94 0.23 0.93
rs5919432 23 67021550 A/G 0.14 0.98 0.18 1 0.21 1 0.18 1
rs5945619 23 51241672 T/C 0.41 0.92 0.44 1 0.38 1 0.33 1

Abbreviations: MAF=minor allele frequency; NA=not available; SNP=single-nucleotide polymorphism.

a

R2 refers to the ‘imputation info' metric produced by IMPUTE2 that represents the certainty with which the SNP has been imputed and lies between 0 (no certainty) and 1 (high certainty; R2=1 for genotyped SNPs).

b

Major allele is associated with increased risk of prostate cancer.

c

Merged SNP rs115664826.

d

Merged SNP rs114376585.

e

The rs7210100 MAF=0, R2=0, excluded from RAPPER analyses; RADIOGEN R2=0.005; not imputed in GenePARE or CCI data sets.

f

rs103294 poorly imputed in CCI.