Table 2 Top associated variants (P < 5E−04) from the age-adjusted logistic regression with high-risk prostate cancer cases (ISUP grade group 3-5; HRPCa; N = 203) against low-risk or no PCa (LR/No PCa; N = 461)
From: Prostate cancer genetic risk and associated aggressive disease in men of African ancestry
CHR | SNP | BP | A1/A2 alleles | OR (95% CI) | P-value | MAF HRPCa | MAF LR/No PCa | MAF African ancestry | Overlapped/Closest genes (distance away) | SIFT | PolyPhen | ClinVar |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | rs78726268 | 183037313 | T/C | 4.78 (2.39–9.57) | 9.74E–06 | 0.062 | 0.014 | 0.026 | MCCC1 | T | B | B/LB |
10 | rs11009235 | 33132620 | A/G | 1.73 (1.34–2.22) | 2.23E–05 | 0.436 | 0.321 | 0.412 | IATPR (15.8 kb), NRP1 (44.9 kb) | |||
6 | rs34644326 | 63712963 | C/G | 3.15 (1.82–5.44) | 4.02E–05 | 0.079 | 0.029 | 0.048 | PHF3 | T | B | |
X | rs2897495 | 10808235 | A/G | 2.04 (1.45–2.86) | 4.37E–05 | 0.463 | 0.3 | 0.437 | MID1 | |||
11 | rs1194099 | 65582378 | A/T | 1.82 (1.36–2.43) | 5.23E–05 | 0.264 | 0.168 | 0.158 | EHBP1L1 | Ta | ||
14 | rs28670114 | 93622023 | C/T | 1.91 (1.39–2.61) | 5.87E–05 | 0.224 | 0.137 | 0.164 | UNC79 | Ta | B | |
11 | rs75062275 | 65581112 | A/G | 1.79 (1.34–2.39) | 7.75E−05 | 0.261 | 0.168 | 0.154 | EHBP1L1 | Ta | ||
12 | rs11068997 | 109945336 | A/G | 2.05 (1.44–2.94) | 8.25E−05 | 0.16 | 0.089 | 0.094 | TCHP, GIT2 | Da | B | |
5 | rs12658464 | 122153427 | T/C | 0.61 (0.47–0.78) | 1.06E−04 | 0.291 | 0.403 | 0.543 | ZNF474 | |||
16 | rs61734425 | 81207531 | G/T | 2.55 (1.59–4.11) | 1.13E−04 | 0.096 | 0.045 | 0.036 | PKD1L2 | |||
5 | rs10074434 | 135153492 | G/T | 0.62 (0.49–0.79) | 1.39E−04 | 0.35 | 0.457 | 0.548 | PITX1-AS1 | |||
16 | rs75279347 | 88532007 | A/G | 2.37 (1.5–3.74) | 2.24E−04 | 0.099 | 0.044 | 0.038 | ZFPM1 | T | ||
6 | rs11970638 | 27867099 | C/T | 1.91 (1.35–2.71) | 2.72E−04 | 0.158 | 0.09 | 0.088 | H1-5 | T | ||
16 | rs1135045 | 23478390 | C/G | 0.64 (0.5–0.81) | 3.04E−04 | 0.399 | 0.505 | 0.416 | GGA2 | T | B | |
15 | rs80278342 | 101313285 | A/G | 3.1 (1.68–5.74) | 3.07E−04 | 0.062 | 0.021 | 0.012 | PCSK6 | |||
10 | rs8473 | 128101314 | T/C | 0.64 (0.5–0.82) | 3.09E−04 | 0.416 | 0.521 | 0.534 | MKI67 | T | ||
2 | rs60322991 | 219216123 | T/C | 0.57 (0.42–0.78) | 3.42E−04 | 0.153 | 0.241 | 0.153 | ABCB6 | D | PD | B |
12 | rs7963300 | 53864157 | A/G | 2 (1.37–2 .92) | 3.43E−04 | 0.144 | 0.082 | 0.092 | ENSG00000286069 | |||
7 | rs877834 | 25228315 | C/T | 1.71 (1.28–2.3) | 3.54E−04 | 0.239 | 0.154 | 0.117 | NPVF | D | PD | |
10 | rs35299879 | 122841282 | A/C | 2.63 (1.54–4.49) | 3.75E−04 | 0.074 | 0.028 | 0.014 | CUZD1 | T | B | |
10 | rs34246902 | 122841318 | C/G | 2.63 (1.54–4.49) | 3.75E−04 | 0.074 | 0.028 | 0.014 | CUZD1 | T | B | |
9 | rs2075662 | 98985952 | A/G | 0.59 (0.44–0.79) | 3.78E−04 | 0.182 | 0.274 | 0.312 | COL15A1 | D | P | |
3 | rs7648947 | 43132737 | A/G | 0.62 (0.47–0.81) | 3.98E−04 | 0.251 | 0.347 | 0.361 | POMGNT2 (26.7 kb) | |||
17 | rs77944357 | 69215844 | T/G | 2.83 (1.59–5.03) | 4.01E−04 | 0.067 | 0.023 | 0.018 | ABCA10 | D | PrD | |
16 | rs9937453 | 22144308 | A/G | 1.55 (1.21–1.99) | 4.80E−04 | 0.51 | 0.413 | 0.53 | VWA3A | T | B |
