Table 2.

Survival results of 18 tag SNPs (r-square >0.6) with FPRP < 0.2 in the MDACC dataset and their replication in the Harvard dataset.

SNP	Gene	Chr	EA	MDACC				Harvard			Meta
				MAF	HR (95%CI)	P*	FPRP	MAF	HR (95%CI)	P**	HR(95%CI)	P	I2	Phet
rs6426914	RXRG	1	G	0.06	2.04 (1.18 – 3.53)	1.10×10−2	0.171	0.06	0.82 (0.32–2.07)	0.669	1.40 (0.58 – 3.30)	0.453	63.60	0.099
rs283695	RXRG	1	A	0.45	1.68 (1.24 – 2.29)	9.00×10−4	0.011	0.44	0.87 (0.57–1.31)	0.492	1.23 (0.65 – 2.34)	0.534	84.18	0.013
rs285480	RXRG	1	G	0.22	1.47 (1.06 – 2.04)	2.05×10−2	0.165	0.22	1.14 (0.72–1.80)	0.581	1.35 (1.03 – 1.76)	0.027	0.00	0.376
rs3767332	RXRG	1	A	0.24	0.59 (0.39 – 0.89)	1.10×10−2	0.120	0.24	0.91 (0.57–1.46)	0.687	0.72 (0.47 – 1.10)	0.127	46.23	0.175
rs157861	RXRG	1	G	0.21	1.51 (1.09 – 2.08)	1.23×10−2	0.099	0.19	0.97 (0.59–1.60)	0.914	1.26 (0.83 – 1.93)	0.285	53.64	0.144
rs115079560	RXRG	1	C	0.16	1.65 (1.18 – 2.30)	3.08×10−3	0.031	0.14	0.87 (0.48–1.58)	0.654	1.26 (0.68 – 2.34)	0.467	70.55	0.066
rs3753896	RXRG	1	G	0.38	1.58 (1.15 – 2.15)	4.35×10−3	0.034	0.35	0.88 (0.57–1.34)	0.541	1.20 (0.68 – 2.13)	0.531	78.92	0.030
rs3820367	RXRG	1	G	0.21	1.51 (1.11 – 2.04)	7.95×10−3	0.063	0.21	0.87 (0.52–1.46)	0.597	1.19 (0.70 – 2.04)	0.514	69.19	0.071
rs2194899	RXRG	1	A	0.37	1.51 (1.13 – 2.01)	5.18×10−3	0.042	0.34	0.72 (0.46–1.14)	0.159	1.07 (0.52 – 2.20)	0.863	86.20	0.007
rs3753898	RXRG	1	G	0.21	1.44 (1.06 – 1.95)	1.84×10−2	0.144	0.20	0.84 (0.49–1.43)	0.515	1.15 (0.69 – 1.94)	0.593	66.11	0.086
rs1529382	CYP27A1	2	T	0.49	1.70 (1.26 – 2.31)	6.00×10−4	0.007	0.50	1.25 (0.83–1.89)	0.282	1.50 (1.12 – 2.02)	0.007	28.86	0.238
rs12512631	VDBP	4	C	0.36	0.70 (0.51 – 0.95)	2.41×10−2	0.168	0.35	0.58 (0.36–0.93)	0.025	0.66 (0.51 – 0.86)	1.88×10−3	0.00	0.516
rs7850212	RXRA	9	A	0.11	0.41 (0.21 – 0.78)	7.15×10−3	0.179	0.09	0.31 (0.10–0.97)	0.043	0.38 (0.22 – 0.68)	9.54×10−4	0.00	0.676
rs67965144	RXRA	9	A	0.12	1.52 (1.07 – 2.16)	2.04×10−2	0.158	0.13	0.79 (0.43–1.48)	0.469	1.15 (0.61 – 2.17)	0.656	68.86	0.071
rs62576319	RXRA	9	T	0.11	1.71 (1.17 – 2.49)	5.12×10−3	0.055	0.12	1.00 (0.55–1.82)	0.992	1.38 (0.82 – 2.31)	0.222	54.59	0.137
rs12895681	SNW1	14	T	0.32	1.42 (1.06 – 1.90)	1.81×10−2	0.142	0.35	0.92 (0.59–1.43)	0.719	1.18 (0.78 – 1.80)	0.439	61.72	0.109
rs12890375	SNW1	14	G	0.26	0.66 (0.45 – 0.95)	2.45×10−2	0.197	0.27	1.10 (0.71–1.72)	0.664	0.84 (0.51 – 1.39)	0.490	66.68	0.084
rs77513685	NCOA3	20	T	0.21	1.50 (1.07 – 2.12)	2.01×10−2	0.170	0.21	1.52 (0.98–2.35)	0.061	1.51 (1.15 – 1.97)	0.003	0.00	0.963

EA = effect allele; MAF=minor allele frequency; HR = hazards ratio; LHR = lower hazards ratio; UHR = upper hazards ratio; FPRP = false positive report probability; Phet = P heterogeniety;

A2 is the effect allele;

^*Adjusted by age, sex, tumor stage, Breslow thickness, Clark level and ulceration of tumor;

^**Adjusted by age, sex.