Table 1.
Summary of loci compellingly associated with prostate cancer.
| Locus | Allele Frequency (+) | Association | ||||||
|---|---|---|---|---|---|---|---|---|
| Chr Region | SNP | Allele (- / +) | Controls | Cases | Odds ratio | p value | Nearby Genes / Potential Function | References |
| 2p15 | rs721048 | G/A | 0.19 | 0.21 | 1.15 | 7.7×10-9 | EHBP1: endocytic trafficking | 8 |
| 3p12 | rs2660753 | C/T | 0.10 | 0.12 | 1.30 | 2.7×10-8 | Intergenic | 10 |
| 6q25 | rs9364554 | C/T | 0.29 | 0.33 | 1.21 | 5.5×10-10 | SLC22A3: elimination of drugs and toxins. | 10 |
| 7q21 | rs6465657 | T/C | 0.46 | 0.50 | 1.19 | 1.1×10-9 | LMTK2: endosomal membrane trafficking | 10 |
| 8q24 (region 2) | rs16901979 | C/A | 0.04 | 0.06 | 1.52 | 1.1×10-12 | Intergenic | 3-5,10 |
| 8q24 (region 3) | rs6983267 | T/G | 0.50 | 0.56 | 1.25 | 9.4×10-13 | Intergenic | 4,5,10 |
| 8q24 (region 1) | rs1447295 | C/A | 0.10 | 0.14 | 1.42 | 6.4×10-18 | Intergenic (oncogene MYC 200kb downstream) | 3-5,10 |
| 10q11 | rs10993994 | C/T | 0.38 | 0.46 | 1.38 | 8.7×10-29 | MSMB: tumor suppressor properties | 9,10 |
| 10q26 | rs4962416 | T/C | 0.27 | 0.32 | 1.18 | 2.7×10-8 | CTBP2: antiapoptotic activity | 9 |
| 11q13 | rs7931342 | T/G | 0.51 | 0.56 | 1.21 | 1.7×10-12 | Intergenic | 9,10 |
| 17q12 | rs4430796 | G/A | 0.49 | 0.55 | 1.22 | 1.4×10-11 | HNF1B: suppressor properties, epithelial differentiation | 6,9,10 |
| 17q24 | rs1859962 | T/G | 0.46 | 0.51 | 1.20 | 2.5×10-10 | Intergenic | 6,10 |
| 19q13 | rs2735839 | A/G | 0.83 | 0.87 | 1.37 | 1.5×10-18 | KLK2/KLK3: serine protease impacting PSA concentrations, androgenic | 5,10 |
| Xp11 | rs5945619 | T/C | 0.36 | 0.41 | 1.29 | 1.5×10-9 | NUDT10, NUDT11: apoptosis, DNA repair, stress response | 8,10 |
Results presented for SNPs exhibiting replication within or across studies and with association p-values < 5×10-8. Specific SNPs are those most commonly reported; many other SNPs in linkage disequilibrium with these are also associated with prostate cancer. The second allele (+) is associated with an increased risk of prostate cancer. Allele frequencies are for the risk allele (+) and essentially all results presented here are for European populations. Odds ratios correspond to the effect of carrying one additional copy of the risk allele (+). Allele frequencies, odds ratios, and p-values are from all results in the initial study (listed first in ‘references’ column), except p-values for the 7p15 and 10q26 SNPs are from analyses combining aggressive and non-aggressive prostate cancer cases9, and allele frequencies and odds ratios for the 8q24 loci are from a meta-analysis25. Note that The 3p12 SNP (rs2660753) was only marginally associated with prostate cancer in a recent replication study36. There is also a compelling SNP on 7p15 (rs10486567, JAZF1) that is associated with prostate cancer, though with a slightly larger p value (1.2×10-7)9 and a recently detected second independently associated SNP in HNF1B30.
EHBP1: EH domain binding protein 1; SLC22A3: solute carrier family 22, member 3; LMTK2: lemur tyrosine kinase 2; MSMB: microseminoprotein, beta-; CTBP2: C-terminal binding protein 2; HNF1B: hepatocyte nuclear factor 1 beta, MODY gene; KLK2/KLK3: kallikrein-related peptidase 2/3; NUDT10, NUDT11: nucleoside diphosphate linked moiety X-type motif 10 / 11.