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. 2015 Jan 5;75(5):474–483. doi: 10.1002/pros.22933

Table I.

Association Results in SPC (n = 620) and HPC (n = 312) Patients for 74 Prostate Cancer SNPs

Chromosome SNP Nearest gene(s) Sourced Risk allele Other allele OR original dataf SPC patients (n = 620) HPC patients (n = 312)
OR 95% CI P OR 95% CI P
1 rs1218582 KCNN3 I G A 1.06∼ 1.07 0.94–1.22 0.31 0.92 0.77–1.10 0.34
1 rs4245739e MDM4 I A C 1.10 1.00 0.85–1.18 0.99 1.06 0.87–1.30 0.55
2 rs11902236 GRHL1 I A G 1.07∼ 1.15 0.99–1.32 0.06 0.89 0.72–1.09 0.26
2 rs1465618 THADA II A G 1.08∼ 1.14 0.98–1.33 0.09 1.14 0.92–1.40 0.23
2 rs721048 EHBP1 III A G 1.15 1.14 0.97–1.34 0.11 1.13 0.91–1.40 0.27
2 rs6545977 OTX1 II G A 1.15∼ 1.22 1.07–1.39 <0.01 1.16 0.97–1.39 0.10
2 rs10187424e GGCX, VAMP8 IV A G 1.09 1.10 0.97–1.25.2 0.15 1.17 0.98–1.38 0.09
2 rs12621278 ITGA6 II A G 1.33 1.15 0.87–1.52 0.33 2.16 1.29–3.61 <0.01
2 rs7584330 COL6A3 ‐ MLPH (intergenic) IV C T 1.06 1.16 1.00–1.35237 0.05 1.04 0.84–1.28 0.73
2 rs2292884 MLPH V G A 1.14 1.18 1.02–1.37 0.02 1.10 0.90–1.35 0.36
2 rs3771570 FARP2 I A G 1.12∼ 1.04 0.87–1.26 0.66 1.30 1.03–1.66 0.03
3 rs2660753 PPATP1 ‐ MIR4975 (intergenic) VI T C 1.18 1.26 1.01–1.56 0.04 1.31 0.98–1.75 0.06
3 rs7611694 SIDT1 I A C 1.10 1.13 0.96–1.33 0.13 1.15 0.96–1.37 0.14
3 rs10934853 EEFSEC (intergenic) VII A C 1.12 1.07 0.93–1.23 0.37 1.28 1.06–1.55 0.01
3 rs6763931 ZBTB38 IV T C 1.04 0.97 0.85–1.11 0.68 1.16 0.97–1.38 0.10
3 rs10936632 SKIL, CLDN11 IV A C 1.11 1.07 0.94–1.22 0.31 1.20 1.00–1.44 0.05
4 rs1894292 AFM I G A 1.10 0.99 0.87–1.13 0.91 1.10 0.92–1.31 0.28
4 rs12500426 PDLIM5 II A C 1.08∼ 1.16 1.01–1.32 0.03 1.09 0.91–1.30 0.35
4 rs17021918 PDLIM5 II C T 1.11 1.10 0.96–1.25 0.17 1.10 0.91–1.32 0.32
4 rs7679673 RPL6P14, TET2 II C A 1.10∼ 1.12 0.98–1.28 0.10 1.31 1.09–1.59 <0.01
5 rs2242652 TERT IV G A 1.15 0.92 0.78–1.09 0.33 1.10 0.87–1.40 0.42
5 rs2736098 TERT VIII A G 1.13∼ 1.15 1.00–1.33 0.05 1.18 0.96–1.43 0.11
5 rs401681c CLPTM1 IX C T 1.07∼ 0.95 0.84–1.08 0.44 0.95 0.80–1.14 0.58
5 rs2121875 FGF10 IV G T 1.05 1.09 0.95–1.25 0.21 1.04 0.86–1.26 0.67
5 rs6869841 STC2, BOD1 I A G 1.07∼ 1.07 0.91–1.25 0.43 1.04 0.84–1.29 0.72
6 rs130067 CCHCR1 IV G T 1.05 1.10 0.94–1.29 0.22 1.37 1.13–1.68 <0.01
6 rs3096702 NOTCH4 I A G 1.07∼ 1.10 0.96–1.26 0.16 1.10 0.91–1.32 0.32
6 rs2273669 ARMC2 I G A 1.07∼ 1.23 1.02–1.47 0.03 0.78 0.59–1.03 0.08
6 rs1933488 RGS17 I A G 1.12 1.11 0.97–1.28 0.13 1.21 1.00–1.45 0.05
6 rs651164 SLC22A1, SLC22A2 V G A 1.15 1.16 1.00–1.33 0.04 1.21 0.99–1.47 0.06
6 rs9364554 SLC22A3 VI T C 1.17 1.25 1.08–1.43 <0.01 1.38 1.14–1.66 <0.01
7 rs12155172 RPS26P30, ASS1P11 II A G 1.11 0.94 0.81–1.11 0.47 1.23 1.00–1.51 0.05
7 rs10486567 JAZF1 X G A 1.12 1.16 0.99–1.36 0.07 1.02 0.82–1.26 0.85
7 rs6465657 LMTK2 VI C T 1.12 0.94 0.83–1.07 0.36 1.07 0.90–1.27 0.47
8 rs1512268 FAM6DP, NKX3‐1 II A G 1.18 1.03 0.90–1.17 0.69 1.16 0.97–1.39 0.10
8 rs6984769a EBF2 I A G 1.11∼ 1.17 0.98–1.38 0.08 1.27 1.01–1.59 0.04
8 rs12543663 FAM84B XI C A 1.88∼ 1.11 0.97–1.28 0.14 1.24 1.03–1.49 0.03
8 rs10086908 – XII T C 1.31∼ 1.19 1.04–1.38 0.01 1.07 0.88–1.30 0.49
8 rs13252298 PCAT1 ‐ SRRM1P1 (intergenic) V A G 1.12∼ 1.16 1.00–1.34 0.05 1.27 1.03–1.56 0.03
8 rs16901979 SRRM1P1 ‐ POU5F1B (intergenic) XIII A C 1.79 1.71 1.16–2.54 0.01 3.31 2.22–4.94 <0.01
8 rs16902094 SRRM1P1 ‐ POU5F1B (intergenic) VII G A 1.21 1.16 0.97–1.39 0.10 1.29 1.02–1.63 0.03
8 rs445114 SRRM1P1 ‐ POU5F1B (intergenic) VII T C 1.14 1.12 0.97–1.28 0.12 1.01 0.84–1.21 0.95
8 rs6983267 SRRM1P1 ‐ POU5F1B (intergenic) XIV G T 1.26 1.23 1.08–1.40 <0.01 1.69 1.40–2.04 <0.01
8 rs1447295 LOC727677 (intergenic) XV A C 1.60 1.48 1.23–1.78 <0.01 2.18 1.74–2.74 <0.01
9 rs1571801 DAB2IP XVI A C 1.29∼g 0.97 0.84–1.13 0.71 0.84 0.67–1.06 0.14
10 rs10993994 MSMB VI T C 1.16–1.25 1.14 1.00–1.31 0.05 1.52 1.27–1.82 <0.01
10 rs3850699 TRIM8 I A G 1.10∼ 1.07 0.92–1.24 0.36 1.32 1.08–1.63 0.01
10 rs4962416 CTBP2 X C T 1.17 1.10 0.95–1.28 0.21 1.22 0.99–1.49 0.06
11 rs7127900 MIR4686, ASCL2 II A G 1.22 1.22 1.04–1.43 0.02 1.79 1.46–2.19 <0.01
11 rs12418451 TPCN2 ‐ MYEOV (intergenic) XVII G A 1.16∼ 0.82 0.71–0.94 0.01 0.88 0.73–1.06 0.19
11 rs11228565 TPCN2 ‐ MYEOV (intergenic) VII A G 1.23 1.17 1.00–1.36 0.05 1.08 0.87–1.34 0.46
11 rs10896450 TPCN2 ‐ MYEOV (intergenic) X G A 1.10 1.14 1.00–1.30 0.05 1.14 0.95–1.37 0.15
11 rs11568818 MMP7 I A G 1.10 1.07 0.94–1.22 0.29 1.24 1.03–1.48 0.02
12 rs10875943 TUBA1C, PRPH IV C T 1.07 1.05 0.91–1.21 0.51 1.25 1.04–1.52 0.02
12 rs902774 KRT78, RPL7P41 V A G 1.17 1.06 0.89–1.26 0.55 1.07 0.84–1.35 0.59
12 rs1270884 GLULP5, TBX5 I A G 1.07 1.09 0.96–1.24 0.18 1.26 1.05–1.51 0.01
14 rs8008270 FERMT2 I G A 1.12 1.05 0.89–1.24 0.58 0.91 0.73–1.13 0.38
14 rs7141529 PPIAP6, RPL12P7 I G A 1.09∼ 1.07 0.93–1.23 0.34 1.09 0.91–1.30 0.37
17 rs684232 VPS53 I G A 1.10 1.17 1.03–1.34 0.02 1.22 1.02–1.47 0.03
17 rs4054823c HS3ST3A1 (intergenic) XVIII T C 1.13∼ 0.95 0.83–1.08 0.40 1.06 0.89–1.26 0.53
17 rs11649743 HNF1B XIX G A 1.28∼ 1.04 0.89–1.23 0.62 1.70 1.32–2.20 <0.01
17 rs4430796e HNF1B XV A G 1.22 1.23 1.08–1.39 <0.01 1.61 1.35–1.93 <0.01
17 rs11650494 FLJ40194, ZNF652 I A G 1.15∼ 0.97 0.76–1.24 0.79 1.14 0.83–1.56 0.42
17 rs1859962 CALM2P1 ‐ SOX9 (intergenic) XV G T 1.20 1.18 1.03–1.34 0.01 1.44 1.21–1.73 <0.01
18 rs7241993 SALL2, ATP9B I G A 1.09∼ 1.14 0.99–1.32 0.08 0.95 0.78–1.15 0.57
19 rs8102476 DPF1 ‐ PPP1R14A (intergenic) VII C T 1.12 1.10 0.96–1.25 0.17 1.19 0.99–1.43 0.07
19 rs2735839 KLK3, KLK2 VI G A 1.20 1.22 1.01–1.48 0.04 1.19 0.92–1.54 0.19
20 rs2427345 RBBP8NL, GATA5 I C T 1.06 1.12 0.96–1.30 0.15 1.15 0.95–1.39 0.15
20 rs6062509 ZGPAT I A C 1.13∼ 1.12 0.97–1.30 0.11 1.07 0.88–1.29 0.51
22 rs9623117 TNRC6B XX C T 1.18 1.02 0.87–1.20 0.81 0.99 0.79–1.24 0.94
22 rs5759167 RPS25P10, BIK II G T 1.16∼ 1.27 1.11–1.45 <0.01 1.88 1.54–2.28 <0.01
X rs35330386b SHROOM2 I T C 1.14∼ 0.79 0.61–1.03 0.08 0.98 0.71–1.35 0.90
X rs5945572 NUDT10, NUDT11 III A G 1.23 1.34 1.09–1.66 0.01 1.47 1.12–1.93 0.01
X rs5919432 AR, PGK1P1 IV A G 1.06 0.96 0.74–1.25 0.77 1.08 0.76–1.51 0.68

SNP, single nucleotide polymorphism; SPC, sporadic prostate cancer; HPC, hereditary prostate cancer; OR, odds ratios; CI, confidence interval; HWE, Hardy–Weinberg equilibrium.

a

rs6984769 is a correlate (r2 = 1) for rs11135910.

b

rs35330386 is a correlate (r2 = 0.987) for rs2405942.

c

rs401681 has been associated with prostate‐specific antigen (PSA) levels, rs4054823 has been associated with prostate cancer aggressiveness.

d

Literature source: I Eeles, Nat Gen 2013; II Eeles, Nat Gen 2009; III Gudmundsson, Nat Gen 2008; IV Kote‐Jarai, Nat Gen 2011; V Schumacher, HMG 2011; VI Eeles, Nat Gen 2008; VII Gudmundsson, Nat Gen 2009; VIII Rafnar, Nat Gen 2009; IX Gudmundsson, Sci Tr Med 2011; X Thomas, Nat Gen 2008; XI Wang, Zhonghua Zhong Liu Za Zhi. 2013; XII Xu, CEBP 2009; XIII Gudmundsson, Nat Gen 2007; XIV Yeager, Nat Gen 2007; XV Gudmundsson, Nat Gen 2007 (2); XVI Duggan, JNCI 2007; XVII Zheng, CEBP 2009; XVIII Xu, PNAS 2010; XIX Sun, Nat Gen 2008; XX Sun, Cancer Res 2009.

e

Quality control indicated that the referents were not in HWE (P  = 0.007 for rs4245739; P = 0.0007 for rs10187424; P = 0.002 for rs4430796); a manual check of the allele frequencies showed no deviations from the frequencies in the literature.

f

ORs were extracted from www.genome.gov (accessed on 16 April 2014; SNPs that were not present in this database were individually extracted from the original article (indicated with∼).

g

The OR for rs1571801 was calculated by combining the numbers for aggressive and non‐aggressive PC in the European populations (CAPS + CGEMS) in the original article.