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)

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

African ancestry minor allele frequency (of allele A1) was retrieved from gnomAD v3.1.2.

CHR chromosome, SNP single nucleotide polymorphism, BP base pair (GRCh38), A1 minor allele, A2 major allele, OR odds ratio, CI confidence interval, MAF minor allele frequency, T tolerated, B benign, LB likely benign, D deleterious, PD possibly damaging, PrD probably damaging.

^aLow confidence.