Table 2.
CaP aggressiveness associated SNPs at P-value threshold of 0.05 in either of AA and EA for SNPs in GWAS reported regions
| SNP | Chr | Position | Type* | Nearest Gene# | Reference genotype | AA
|
EA
|
||
|---|---|---|---|---|---|---|---|---|---|
| P | OR | P | OR | ||||||
| rs2660753 | 3p12.1 | 87193364 | replication | LOC285232||CHMP2B | CC | 0.173 | 1.1(0.9–1.3) | 0.007 | 1.5(1.1–1.9) |
| rs2293850 | 8q24.21 | 127450879 | flanking | LOC100130158||FAM84B | CC | 0.017 | 0.8(0.7–0.9) | 0.078 | 0.8(0.7–1.0) |
| rs6993569 | 8q24.21 | 128153279 | flanking | FAM84B||POU5F1P1 | GG | 0.404 | 0.9(0.8–1.1) | 0.031 | 1.5(1.0–2.1) |
| rs13254738 | 8q24.21 | 128173525 | replication | FAM84B||POU5F1P1 | AA | 0.032 | 1.2(1.0–1.4) | 0.306 | 1.1(0.9–1.3) |
| rs1456305 | 8q24.21 | 128196434 | flanking | FAM84B||POU5F1P1 | AA | 0.048 | 1.3(1.0–1.7) | 0.370 | 1.1(0.9–1.5) |
| rs10505476 | 8q24.21 | 128477298 | flanking | FAM84B||POU5F1P1 | CC | 0.766 | 0.9(0.8–1.2) | 0.045 | 1.2(1.0–1.5) |
| rs6999921 | 8q24.21 | 128510110 | flanking | POU5F1P1||MYC | AA | 0.005 | 0.7(0.5–0.9) | 0.051 | 1.3(0.9–1.8) |
| rs10090154 | 8q24.21 | 128601319 | replication | POU5F1P1||MYC | CC | 0.043 | 1.2(1.0–1.5) | 0.601 | 0.9(0.7–1.2) |
| rs266870 | 19q13.33 | 56043746 | flanking | KLK15||KLK3 | TT | 0.049 | 0.8(0.7–1.0) | 0.015 | 1.2(1.0–1.5) |
| rs1058205 | 19q13.33 | 56055210 | flanking | KLK3 | TT | 0.004 | 0.8(0.6–0.9) | 0.485 | 0.9(0.7–1.2) |
| rs2735839 | 19q13.33 | 56056435 | replication | KLK3||KLK2 | GG | 0.005 | 0.8(0.6–0.9) | 0.248 | 0.9(0.7–1.1) |
*
: “flanking” indicates SNPs located at nearby of GWAS reported replication SNP.
#
: symbol “||” indicates a intergenic SNP located between 2 specified genes.
“replicated SNPs”, i.e. SNPs that were the primary findings of GWAS and replication studies, represented 21 different chromosomal regions (see Supplementary Table 1). Not all of these SNPs had been established as replicated SNPs at the time of selection.