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. Author manuscript; available in PMC: 2013 Aug 2.
Published in final edited form as: Clin Cancer Res. 2010 May 11;16(10):2819–2832. doi: 10.1158/1078-0432.CCR-10-0028

Table 2.

Univariate associations between SNPs and prostate cancer outcomes under codominant model. Boldface represents SNPs with associations at p<0.05 by the “2 degree of freedom test”.

SNP Chromosomal
region		 Number
of
Patients		 MAF Published
AF		 Genotype (%
of patients)		 Biochemical Recurrence
N=351		 Clinical Metastases
N=146		 Prostate Cancer Specific Death
N=91
HR 95% CI P Value1 HR 95% CI P Value1 HR 95% CI P Value1
rs10090154 8q24 759 0.08 NR C/C (85) Ref Ref Ref Ref Ref Ref
C/T (14) 0.97 0.71, 1.32 0.75 0.45, 1.25 0.86 0.47, 1.58
T/T (1) 0.6 0.08, 4.26 0.9 * * 0.5 * * 0.9
Per allele 0.95 0.71, 1.27 0.7 0.72 0.44, 1.19 0.2 0.83 0.46, 1.51 0.5
rs1016343 8q24 749 0.23 NR C/C (60) Ref Ref Ref Ref Ref Ref
T/C (36) 0.96 0.76, 1.21 1.01 0.71, 1.45 0.88 0.55, 1.40
T/T (5) 1.18 0.72, 1.94 0.7 1 0.44, 2.29 1 1.58 0.68, 3.68 0.4
Per allele 1.01 0.84, 1.22 0.9 1.01 0.75, 1.35 1 1.05 0.73, 1.51 0.8
rs10486567 7 762 0.25 0.2 G/G (51) Ref Ref Ref Ref Ref Ref
A/G (42) 1.37 1.09, 1.72 1.36 0.95, 1.95 1.06 0.67, 1.66
A/A (8) 1.89 1.31, 2.74 0.0007 2.11 1.26, 3.55 0.014 1.56 0.80, 3.04 0.4
Per allele 1.37 1.17, 1.62 <0.0005 1.43 1.12, 1.83 0.005 1.18 0.86, 1.62 0.3
rs13254738 8 761 0.45 0.33 A/A (29) Ref Ref Ref Ref Ref Ref
C/A (52) 0.97 0.75, 1.24 0.78 0.54, 1.14 1.06 0.64, 1.73
C/C (19) 0.89 0.64, 1.22 0.7 0.75 0.45, 1.24 0.4 0.94 0.48, 1.83 0.9
Per allele 0.94 0.81, 1.10 0.5 0.85 0.66, 1.09 0.2 0.98 0.71, 1.35 0.9
rs16901979 8q24 792 0.04 0.07 C/C (93) Ref Ref Ref Ref Ref Ref
C/A (7) 1.14 0.77, 1.69 1.6 0.95, 2.69 1.06 0.51, 2.18
A/A (0.1) 5.08 0.71, 36.30 0.2 * * 0.2 * * 1
Per allele 1.2 0.83, 1.76 0.3 1.48 0.89, 2.44 0.13 1.01 0.50, 2.07 1
rs1859962 17q24 765 0.44 0.49 G/G (33) Ref Ref Ref Ref Ref Ref
G/T (47) 1.07 0.84, 1.36 1.15 0.79, 1.68 1.06 0.66, 1.69
T/T (20) 0.95 0.70, 1.30 0.7 1.03 0.63, 1.70 0.7 0.84 0.44, 1.62 0.8
Per allele 0.99 0.85, 1.15 0.9 1.04 0.82, 1.31 0.8 0.94 0.70, 1.28 0.7
rs2659056 19 731 0.27 0.25 A/A (55) Ref Ref Ref Ref Ref Ref
A/G (37) 0.97 0.77, 1.23 0.98 0.68, 1.41 1.05 0.67, 1.66
G/G (8) 0.95 0.61, 1.46 1 0.91 0.45, 1.81 1 1.03 0.44, 2.43 1
Per allele 0.97 0.82, 1.16 0.8 0.97 0.73, 1.27 0.8 1.03 0.74, 1.45 0.8
rs2660753 3p12 755 0.24 0.13 C/C (57) Ref Ref Ref Ref Ref Ref
T/C (36) 0.98 0.78, 1.23 0.75 0.52, 1.07 0.73 0.46, 1.16
T/T (6) 0.88 0.56, 1.38 0.8 0.59 0.27, 1.28 0.16 0.81 0.35, 1.90 0.4
Per allele 0.96 0.80, 1.14 0.6 0.76 0.57, 1.01 0.055 0.82 0.57, 1.16 0.3
rs266849 19 764 0.24 0.19 A/A (59) Ref Ref Ref Ref Ref Ref
A/G (34) 1.09 0.87, 1.37 1.31 0.93, 1.86 1.34 0.86, 2.09
G/G (7) 0.88 0.56, 1.40 0.6 1.14 0.57, 2.27 0.3 1.8 0.85, 3.83 0.2
Per allele 1.01 0.85, 1.20 0.9 1.17 0.90, 1.52 0.2 1.34 0.97, 1.85 0.075
rs4242382 8q24 759 0.8 0.14 G/G (85) Ref Ref Ref Ref Ref Ref
A/G (14) 1.05 0.78, 1.41 0.77 0.47, 1.27 1 0.57, 1.78
A/A (1) 1.13 0.36, 3.52 0.9 * * 0.6 * * 1
Per allele 1.05 0.80, 1.37 0.7 0.71 0.44, 1.14 0.16 0.91 0.53, 1.57 0.7
rs4430796 17q12 751 0.47 0.56 G/G (29) Ref Ref Ref Ref Ref Ref
A/G (49) 0.82 0.64, 1.05 0.88 0.60, 1.29 1.22 0.73, 2.03
A/A (22) 0.87 0.64, 1.18 0.3 0.87 0.54, 1.40 0.8 1.28 0.70, 2.33 0.7
Per allele 0.92 0.79, 1.07 0.3 0.93 0.73, 1.17 0.5 1.13 0.85, 1.52 0.4
rs4962416 10q26 756 0.33 0.28 T/T (46) Ref Ref Ref Ref Ref Ref
T/C (42) 0.94 0.75, 1.18 0.71 0.50, 1.01 0.8 0.51, 1.26
C/C (12) 0.74 0.51, 1.08 0.3 0.47 0.23, 0.93 0.031 0.64 0.29, 1.42 0.4
Per allele 0.89 0.76, 1.04 0.15 0.69 0.53, 0.91 0.008 0.8 0.58, 1.11 0.19
rs5945572 Xp11 766 0.3 0.35 G/G (71) Ref Ref Ref Ref Ref Ref
A/G (0.3) 1.23 0.17, 8.80 * * * *
A/A (29) 0.89 0.69, 1.13 0.6 1.42 1.00, 2.03 0.15 1.17 0.73, 1.85 0.8
Per allele 0.94 0.83, 1.06 0.3 1.19 1.00, 1.42 0.051 1.08 0.86, 1.36 0.5
rs721048 2p15 772 0.15 0.19 G/G (71) Ref Ref Ref Ref Ref Ref
A/G (26) 1.12 0.88, 1.42 1.02 0.70, 1.49 1.07 0.67, 1.73
A/A (3) 1.31 0.73, 2.33 0.5 0.99 0.37, 2.71 1 2.28 0.91, 5.72 0.2
Per allele 1.13 0.93, 1.37 0.2 1.01 0.74, 1.39 0.9 1.26 0.86, 1.83 0.2
rs7501939 17q12 759 0.41 0.62 C/C (35) Ref Ref Ref Ref Ref Ref
C/T (48) 0.94 0.74, 1.19 1.12 0.77, 1.63 0.87 0.55, 1.38
T/T (17) 0.97 0.71, 1.32 0.9 1.14 0.68, 1.90 0.8 0.84 0.43, 1.63 0.8
Per allele 0.98 0.84, 1.14 0.8 1.08 0.84, 1.38 0.5 0.91 0.66, 1.24 0.5
rs7920517 10 758 0.43 0.53 G/G (34) Ref Ref Ref Ref Ref Ref
A/G (47) 1.26 0.98, 1.61 0.94 0.64, 1.38 0.92 0.57, 1.48
A/A (19) 1.42 1.05, 1.92 0.056 1.01 0.64, 1.61 0.9 0.83 0.45, 1.53 0.8
Per allele 1.2 1.03, 1.39 0.017 1 0.79, 1.26 1 0.91 0.68, 1.23 0.5
rs7931342 11q13 760 0.29 0.44 G/G (51) Ref Ref Ref Ref Ref Ref
G/T (39) 0.96 0.76, 1.20 1.55 1.09, 2.20 1.41 0.91, 2.20
T/T (9) 0.95 0.65, 1.40 0.9 1.3 0.71, 2.37 0.053 1.06 0.47, 2.37 0.3
Per allele 0.97 0.82, 1.14 0.7 1.26 0.99, 1.61 0.06 1.16 0.85, 1.59 0.3
rs902774 12 749 0.14 0.15 G/G (74) Ref Ref Ref Ref Ref Ref
A/G (24) 1.05 0.82, 1.35 0.84 0.56, 1.25 1.01 0.62, 1.63
A/A (2) 1.09 0.51, 2.31 0.9 0.62 0.15, 2.50 0.6 1.02 0.25, 4.19 1
Per allele 1.05 0.85, 1.30 0.7 0.82 0.58, 1.18 0.3 1.01 0.67, 1.53 1
rs9364554 6p25 767 0.21 0.32 C/C (62) Ref Ref Ref Ref Ref Ref
T/C (34) 1.06 0.84, 1.32 1.11 0.78, 1.58 1.32 0.85, 2.05
T/T (4) 0.74 0.39, 1.40 0.6 0.73 0.23, 2.30 0.7 0.87 0.21, 3.57 0.4
Per allele 0.98 0.81, 1.19 0.9 1.03 0.76, 1.39 0.9 1.18 0.82, 1.72 0.4
rs10896449 11q13 778 0.3 0.45 G/G (50) Ref Ref Ref Ref Ref Ref
G/A (40) 0.96 0.76, 1.20 1.52 1.07, 2.15 1.43 0.93, 2.22
A/A (10) 0.89 0.61, 1.29 0.8 1.33 0.76, 2.34 0.062 1.22 0.59, 2.52 0.3
Per allele 0.95 0.81, 1.11 0.5 1.26 0.99, 1.59 0.058 1.2 0.89, 1.62 0.2
rs109939944 10q11 772 0.47 0.44 T/T (29) Ref Ref Ref Ref Ref Ref
T/C (48) 1.07 0.82, 1.38 1.11 0.75, 1.66 1.03 0.64, 1.67
C/C (23) 1.34 1.00, 1.78 0.11 0.93 0.58, 1.48 0.7 0.78 0.43, 1.41 0.6
Per allele 1.16 1.00, 1.34 0.052 0.97 0.77, 1.21 0.8 0.89 0.68, 1.19 0.4
rs1447295 8q24 764 0.08 0.16 C/C (86) Ref Ref Ref Ref Ref Ref Ref
C/A (13) 0.99 0.72, 1.35 0.82 0.50, 1.35 0.95 0.53, 1.71
A/A (1) 1.07 0.27, 4.29 1 * * * * 1
Per allele 0.99 0.74, 1.32 1 0.78 0.48, 1.25 0.3 0.9 0.51, 1.59 0.7
rs2735839 19q13 774 0.17 0.13 G/G (70) Ref Ref Ref Ref Ref Ref
G/A (26) 1 0.79, 1.28 1.39 0.97, 1.98 1.96 1.28, 3.02
A/A (4) 0.76 0.40, 1.43 0.7 1.11 0.45, 2.75 0.2 1.83 0.66, 5.07 0.007
Per allele 0.95 0.78, 1.16 0.6 1.24 0.93, 1.64 0.14 1.65 1.18, 2.30 0.003
rs4242384 8q24 768 0.08 NR A/A (86) Ref Ref Ref Ref Ref Ref
C/A (14) 1.03 0.76, 1.39 0.78 0.47, 1.27 0.98 0.55, 1.74
C/C (1) 0.61 0.09, 4.33 0.9 * * 0.6 * * 1
Per allele 1 0.75, 1.33 1 0.75 0.46, 1.22 0.2 0.94 0.54, 1.66 0.8
rs6465657 7q21 766 0.44 0.49 T/T (33) Ref Ref Ref Ref Ref Ref
T/C (47) 1.11 0.87, 1.42 1.12 0.75, 1.67 0.87 0.53, 1.43
C/C (20) 0.99 0.73, 1.35 0.6 1.82 1.17, 2.84 0.017 1.61 0.94, 2.75 0.052
Per allele 1.01 0.87, 1.17 0.9 1.35 1.07, 1.70 0.011 1.26 0.94, 1.68 0.12
rs6983267 8q24 773 0.45 0.56 G/G (32) Ref Ref Ref Ref Ref Ref
G/T (47) 1.16 0.90, 1.48 1.03 0.71, 1.51 1.59 0.95, 2.64
T/T (21) 1.16 0.86, 1.57 0.5 1.11 0.70, 1.77 0.9 1.66 0.91, 3.03 0.15
Per allele 1.08 0.94, 1.25 0.3 1.05 0.84, 1.32 0.7 1.29 0.97, 1.72 0.077
rs6983561 8q24 769 0.04 NR A/A (92) Ref Ref Ref Ref Ref Ref
C/A (7) 1.16 0.78, 1.72 1.62 0.96, 2.74 1.07 0.52, 2.22
C/C (0.1) 5.21 0.73, 37.28 0.2 * * 0.19 * * 1
Per allele 1.23 0.84, 1.79 0.3 1.5 0.91, 2.49 0.11 1.03 0.50, 2.10 0.9
rs7000448 8q24 772 0.48 NR T/T (29) Ref Ref Ref Ref Ref Ref
T/C (47) 0.94 0.73, 1.20 1.1 0.74, 1.65 1.15 0.68, 1.93
C/C (24) 0.95 0.71, 1.27 0.9 1.53 0.99, 2.39 0.13 1.78 1.02, 3.09 0.087
Per allele 0.97 0.84, 1.13 0.7 1.24 0.99, 1.56 0.063 1.34 1.01, 1.79 0.042
rs7008482 8q24 742 0.36 NR T/T (43) Ref Ref Ref Ref Ref Ref
G/T (43) 0.78 0.62, 0.98 0.96 0.67, 1.37 1.15 0.73, 1.79
G/G (14) 0.68 0.48, 0.98 0.036 0.65 0.36, 1.19 0.4 0.79 0.38, 1.64 0.6
Per allele 0.81 0.69, 0.95 0.012 0.86 0.67, 1.10 0.2 0.96 0.71, 1.31 0.8
rs11670728 19 506 0.26 0.36 G (56) Ref Ref Ref Ref Ref Ref
GA (36) 1.1 0.83, 1.47 0.73 0.46, 1.16 0.67 0.38, 1.21
A (8) 1.25 0.77, 2.04 0.6 0.42 0.15, 1.15 0.13 0.98 0.41, 2.34 0.4
Per allele 1.11 0.90, 1.37 0.3 0.69 0.48, 0.99 0.042 0.86 0.57, 1.29 0.5
1541int 19 499 0.05 NR G (91) Ref Ref Ref Ref Ref Ref
GT (9) 0.69 0.40, 1.19 1.31 0.63, 2.72 1.21 0.48, 3.05
T (0.4) 21.26 5.02, 90.04 <0.0005 17.35 4.11, 73.26 <0.0005 0 * 0.9
Per allele 0.89 0.55, 1.44 0.6 1.87 1.04, 3.38 0.037 1.12 0.46, 2.70 0.8
rs1654553 19 494 0.45 0.49 G (32) Ref Ref Ref Ref Ref Ref
GA (46) 1.13 0.83, 1.54 1.25 0.76, 2.06 1.19 0.65, 2.19
A (22) 1.01 0.68, 1.49 0.7 1.15 0.62, 2.14 0.7 1.1 0.51, 2.35 0.9
Per allele 1.02 0.84, 1.23 0.9 1.09 0.81, 1.46 0.6 1.06 0.74, 1.53 0.8
rs17526278 19 509 0.1 0.1 G (83) Ref Ref Ref Ref Ref Ref
AG (15) 1.34 0.93, 1.91 1.56 0.89, 2.73 1.31 0.64, 2.67
A (2) 1.05 0.39, 2.82 0.3 3.16 0.76, 13.15 0.1 3.19 0.43, 23.70 0.4
Per allele 1.21 0.90, 1.61 0.2 1.63 1.03, 2.59 0.039 1.42 0.77, 2.64 0.3
rs198972 19 495 0.37 0.3 C (42) Ref Ref Ref Ref Ref Ref
CT (43) 1.15 0.86, 1.53 0.93 0.59, 1.49 0.94 0.55, 1.62
T (15) 0.74 0.47, 1.15 0.14 1.07 0.58, 1.98 0.9 0.56 0.21, 1.46 0.5
Per allele 0.93 0.77, 1.12 0.4 1.01 0.75, 1.37 0.9 0.81 0.55, 1.20 0.3
rs198977 19 500 0.25 0.26 C (57) Ref Ref Ref Ref Ref Ref
CT (37) 1.07 0.81, 1.42 1.08 0.69, 1.69 0.7 0.39, 1.24
T (6) 0.71 0.35, 1.46 0.5 1.42 0.56, 3.57 0.7 1.15 0.35, 3.74 0.4
Per allele 0.97 0.77, 1.22 0.8 1.13 0.79, 1.62 0.5 0.83 0.52, 1.33 0.4
rs198978 19 496 0.35 0.34 G (44) Ref Ref Ref Ref Ref Ref
GT (43) 1.05 0.79, 1.40 1.12 0.71, 1.78 0.87 0.50, 1.51
T (13) 0.86 0.55, 1.34 0.7 0.92 0.45, 1.86 0.8 0.51 0.18, 1.45 0.4
Per allele 0.96 0.79, 1.17 0.7 1 0.74, 1.37 1 0.77 0.51, 1.17 0.2
rs2271094 19 455 0.38 0.43 A (40) Ref Ref Ref Ref Ref Ref
GA (45) 0.89 0.65, 1.21 0.78 0.48, 1.27 0.95 0.52, 1.74
G (15) 1.06 0.69, 1.62 0.6 0.7 0.32, 1.51 0.5 1.05 0.44, 2.49 1
Per allele 0.99 0.81, 1.22 1 0.82 0.58, 1.16 0.3 1.01 0.67, 1.52 1
rs3760728 19 505 0.25 0.42 C (56) Ref Ref Ref Ref Ref Ref
GC (36) 1.14 0.86, 1.52 0.79 0.50, 1.23 0.73 0.41, 1.29
G (7) 1.4 0.86, 2.28 0.3 0.44 0.16, 1.21 0.2 1.03 0.43, 2.46 0.5
Per allele 1.17 0.95, 1.44 0.15 0.73 0.51, 1.03 0.075 0.89 0.59, 1.35 0.6
rs6998 19 488 0.22 0.29 G (63) Ref Ref Ref Ref Ref Ref
GA (31) 1.13 0.84, 1.52 0.64 0.39, 1.02 0.62 0.34, 1.13
A (6) 1.01 0.57, 1.79 0.7 0.35 0.11, 1.12 0.051 0.77 0.27, 2.15 0.3
Per allele 1.06 0.85, 1.32 0.6 0.62 0.42, 0.91 0.014 0.74 0.48, 1.16 0.2
rs61752561 19 440 0.03 0.04 G (95) Ref Ref Ref Ref Ref Ref
GA (4) 0.71 0.32, 1.61 1.85 0.75, 4.60 4.49 2.00, 10.07
A (1) 0.77 0.11, 5.52 0.7 5.79 1.41, 23.79 0.025 6.49 1.56, 27.05 <0.0005
Per allele 0.77 0.40, 1.47 0.4 2.16 1.20, 3.90 0.011 3.1 1.84, 5.20 <0.0005
rs10993994swe 19 505 0.48 0.44 T (30) Ref Ref Ref Ref Ref Ref
TC (45) 1.1 0.79 1.52 1.16 0.70, 1.91 0.97 0.54, 1.77
C (25) 1.21 0.84 1.74 0.6 0.81 0.44, 1.48 0.4 0.62 0.29, 1.32 0.4
Per allele 1.1 0.92 1.32 0.3 0.91 0.69, 1.21 0.5 0.81 0.57, 1.15 0.2
rs2735839swe 19 490 0.19 0.13 G (68) Ref Ref Ref Ref Ref Ref
GA (27) 1.09 0.81 1.48 1.78 1.13, 2.82 2.11 1.21, 3.67
A (5) 0.93 0.47 1.82 0.8 2.21 0.94, 5.22 0.02 3.1 1.19, 8.09 0.008
Per allele 1.03 0.81 1.30 0.8 1.61 1.15, 2.24 0.005 1.88 1.27, 2.79 0.002
1

The first p-value shown for each SNP was determined by a “2 degree of freedom test” for a global difference across genotypes; the second p-value shown was determined by a log-additive (linear trend) model

*

Hazard ratios were not estimated due to the low number of events and the low number of patients with genotype frequency.

Abbreviations: SNP, single nucleotide polymorphism; MAF, minor allele frequency; published AF, published allele frequency; HR, hazard ratio; swe, represents genotyping from second analysis performed in Malmo, Sweden; NR, not reported; Ref, reference.