Table 4.

Top ranked SNP-epithelial ovarian cancer risk associations

Gene (locus)	SNP (Major/Minor Allele)	Location a	MAF	P HWE	Model b	All subtypes (1815 cases, 1900 controls)
						ORsimple (95% CI)c	Psimpled	EMP1 simple e	ORfull (95% CI) f	Pfull g	EMP1 fullh
MT-CO1 (MT)	MitoT6777C (A/G)	-	0.06	-	AL	0.68 (0.51–0.92)	0.013	0.006	0.57 (0.38–0.83)	0.003	0.007
NRF1 (7q32)	rs10245560 (G/A)	flanking 5’UTR	0.45	0.18	R	0.80 (0.68 –0.95)	0.010	0.016	0.77 (0.62 –0.94)	0.010	0.012
	rs2402976 (A/G) i	intron	0.46	0.46	A	1.12 (1.02 –1.23)	0.016	0.009	1.19 (1.06 –1.33)	0.003	0.004
	rs1882095 (G/A)	flanking 3’UTR	0.34	0.61	A	1.11 (1.00 –1.21)	0.045	0.029	1.13 (1.00 –1.27)	0.044	0.043
MTERF (7q21–q22)	rs2540571 (G/A)	flanking 3’UTR	0.50	0.46	A	0.89 (0.81 –0.97)	0.012	0.015	0.91 (0.81 –1.02)	0.107	0.069
	rs2540592 (G/A) j	flanking 3’UTR	0.38	0.03	D	1.19 (1.03 –1.36)	0.015	0.012	1.13 (0.96 –1.34)	0.139	0.055
	rs12673563 (G/A)	flanking 3’UTR	0.10	0.02	R	2.20 (1.03 –4.79)	0.043	0.038	2.30 (0.97 –5.42)	0.059	0.031
	rs10488506 (G/A) k	flanking 3’UTR	0.07	0.60	A	1.26 (1.06 –1.50)	0.008	0.021	3.12 (1.33 –7.40)	0.009	0.009
	rs6950538 (A/G) l	flanking 3’UTR	0.39	0.73	A	0.90 (0.81 –0.99)	0.031	0.036	0.86 (0.77 –0.97)	0.015	0.041
	rs974508 (G/A)	flanking 3’UTR	0.09	0.16	R	2.90 (1.32 –6.36)	0.008	0.014	3.84 (1.58 –9.36)	0.003	0.001
	rs2269811 (A/G) m	intron	0.10	0.02	R	2.89 (1.31 –6.34)	0.008	0.015	3.30 (1.39 –7.82)	0.007	0.014
PPARGC1A (4p15.1)	rs13151220 (C/A) n	flanking 3’UTR	0.08	1.00	A	1.21 (1.02 –1.42)	0.028	0.025	1.11 (0.91 –1.35)	0.317	0.073
	rs1509241 (A/G)	flanking 3’UTR	0.45	0.71	R	0.84 (0.71 –1.00)	0.048	0.010	0.92 (0.75 –1.13)	0.427	0.110
	rs12498626 (G/A)	flanking 3’UTR	0.12	0.75	D	1.17 (1.01 –1.37)	0.042	0.042	1.26 (1.05 –1.52)	0.014	0.014
	rs6857002 (A/C)	flanking 3’UTR	0.24	0.35	D	1.18 (1.03–1.35)	0.015	0.020	1.26 (1.07 –1.48)	0.005	0.012
	rs4697041 (G/A)	flanking 3’UTR	0.37	0.46	A	1.12 (1.02 –1.24)	0.021	0.026	1.11 (0.98 –1.25)	0.092	0.023
	rs2970882 (A/G)	flanking 3’UTR	0.35	0.76	A	0.90 (0.82 –0.99)	0.044	0.030	0.87 (0.77 –0.98)	0.023	0.026
	rs7682765 (A/G)	intron	0.06	0.34	R	3.84 (1.37 –10.8)	0.011	0.005	5.14 (1.62 –16.3)	0.005	0.009
	rs4550905 (A/G) o	intron	0.32	0.96	A	0.87 (0.78 –0.96)	0.005	0.009	0.87 (0.77 –0.98)	0.025	0.017
	rs4361373 (A/G)	intron	0.18	0.47	A	0.84 (0.74 –0.95)	0.006	0.013	0.85 (0.73 –0.98)	0.029	0.024
	rs10030083 (C/A)	flanking 5’UTR	0.10	1.00	D	1.19 (1.01 –1.41)	0.038	0.034	1.30 (1.06 –1.60)	0.011	0.105
	rs13108219 (C/A)	flanking 5’UTR	0.11	0.49	A	1.22 (1.06 –1.40)	0.007	0.004	1.21 (1.02 –1.44)	0.028	0.038
	rs4697429 (A/G)	flanking 5’UTR	0.20	0.15	A	1.13 (1.01 –1.27)	0.031	0.008	1.17 (0.99 –1.38)	0.066	0.070
	rs9291455 (G/A) p	flanking 5’UTR	0.15	0.59	A	1.15 (1.01 –1.30)	0.039	0.039	1.16 (0.99 –1.36)	0.061	0.073
	rs16874778 (C/A)	flanking 5’UTR	0.29	0.06	D	1.17 (1.03 –1.34)	0.018	0.019	1.28 (1.09 –1.51)	0.003	0.015
	rs640050 (G/A)	flanking 5’UTR	0.38	0.36	A	1.11 (1.01 –1.22)	0.031	0.020	1.25 (1.06 –1.48)	0.009	0.048
	rs614457 (C/A)	flanking 5’UTR	0.34	0.09	D	1.17 (1.02 –1.33)	0.026	0.010	1.22 (1.03 –1.43)	0.018	0.021
	rs7680610 (G/A)	flanking 5’UTR	0.35	3E−3	R	0.78 (0.63 –0.95)	0.015	0.025	0.79 (0.61 –1.01)	0.059	0.005
ESRRA (11q13)	rs11600990 (G/A)	intron	0.16	0.40	D	0.83 (0.72 –0.97)	0.016	0.042	0.91 (0.76 –1.09)	0.299	0.418
CAMK2D (4q26)	rs3733619 (A/G)	flanking 3’UTR	0.10	0.90	A	1.22 (1.05 –1.42)	0.009	0.014	1.18 (0.98 –1.41)	0.079	0.044
	rs7684418 (G/A)	flanking 3’UTR	0.09	0.05	R	2.57 (1.02 –6.46)	0.045	0.034	5.11 (1.34 –19.5)	0.017	1.000
	rs1525000 (A/G)	intron	0.40	0.08	R	0.80 (0.66 –0.96)	0.017	0.008	0.76 (0.61 –0.96)	0.019	0.124
	rs7697831 (G/A)	intron	0.20	0.14	D	1.17 (1.02 –1.34)	0.028	0.009	1.14 (0.99 –1.31)	0.057	0.023
	rs17630328 (A/C) q	intron	0.07	0.39	A	1.24 (1.04 –1.47)	0.016	0.020	1.30 (1.06 –1.60)	0.014	0.021
	rs10033037 (A/G)	intron	0.15	0.24	A	1.17 (1.03 –1.32)	0.018	0.020	1.13 (0.97 –1.32)	0.114	0.086
	rs13107662 (A/G)	intron	0.35	0.45	A	0.88(0.80 –0.98)	0.018	0.014	0.90 (0.77 –1.06)	0.204	0.036
	rs1029471 (A/G)	intron	0.18	0.88	A	1.13 (1.01–1.28)	0.039	0.039	1.14 (0.97 –1.35)	0.123	0.223
	rs764830 (A/G)	intron	0.37	0.07	R	1.23 (1.02 –1.49)	0.034	0.040	1.19 (0.95 –1.50)	0.133	0.025
	rs6533711 (A/G)	intron	0.38	1.00	R	1.22 (1.02 –1.46)	0.032	0.028	1.21 (0.97 –1.50)	0.093	0.011
	rs2040742 (A/G) r	intron	0.08	1.00	A	0.82 (0.69 –0.98)	0.030	0.045	0.77 (0.62 –0.96)	0.019	0.017
ESR2 (14q23.2)	rs1256062 (A/G)	intron	0.10	0.21	A	1.19 (1.03 –1.38)	0.021	0.025	1.16 (0.97 –1.39)	0.106	0.319
	rs1256061 (C/A) s	intron	0.49	0.71	R	0.82 (0.69 –0.95)	0.010	0.012	0.81 (0.67 –0.98)	0.033	0.017
	rs6573553 (A/C)	intron	0.48	0.68	A	1.11 (1.01 –1.22)	0.032	0.021	1.12 (1.00 –1.26)	0.053	0.019
TUFM (16p11.2)	rs9972768 (A/C)	flanking 5’UTR	0.38	0.63	A	1.11 (1.00 –1.22)	0.043	0.031	1.14 (1.01 –1.28)	0.029	0.055
COX7A1 (19q13.1)	rs753420 (A/C)	5’UTR	0.26	0.63	R	1.37 (1.07 –1.75)	0.013	0.007	1.48 (1.10 –1.99)	0.010	0.001
COX8C (14q32.12)	rs6575325 (G/A) t	flanking 3’UTR	0.29	0.41	A	1.16 (1.04 –1.28)	0.005	0.011	1.14 (1.01 –1.29)	0.038	0.022
NDUFB10 (16p13.3)	rs758335 (G/A) u	intron	0.19	0.05	D	0.80 (0.69 –0.92)	0.002	0.004	0.82 (0.70 –0.98)	0.027	0.021
NDUFA11 (19p13.3)	rs1674159 (G/A)	flanking 3’UTR	0.13	0.10	D	1.21 (1.04 –1.41)	0.017	0.044	1.22 (1.01 –1.46)	0.036	0.062
	rs10421538 (G/A)	intron	0.21	0.83	A	1.17 (1.05 –1.32)	0.006	0.019	1.23 (1.08 –1.41)	0.003	0.010
NDUFA12 (12q22)	rs10777629 (A/G)	flanking 3’UTR	0.22	0.23	D	0.83 (0.73 –0.96)	0.009	0.023	0.85 (0.72 –1.00)	0.050	0.050
	rs10777647 (A/G)	flanking 3’UTR	0.40	0.47	A	1.12 (1.02 –1.24)	0.020	0.021	1.15 (1.03 –1.30)	0.018	0.045
	rs6538566 (C/A)	flanking 3’UTR	0.23	0.56	A	0.87 (0.77 –0.97)	0.015	0.018	0.63 (0.43 –0.92)	0.016	0.034
	rs7965624 (G/A) v	flanking 3’UTR	0.38	0.01	R	0.75 (0.62 –0.90)	0.003	0.005	0.72 (0.57 –0.91)	0.005	0.003
	rs2052741 (A/G)	flanking 3’UTR	0.48	1E−3	R	0.74 (0.63 –0.87)	2E−4	0.001	0.68 (0.56 –0.83)	1E−4	2E−4
	rs2081595 (C/A)	flanking 3’UTR	0.49	0.18	A	1.13 (1.03 –1.24)	0.010	0.017	1.13 (1.01 –1.27)	0.029	0.011
	rs2033092 (G/A)	flanking 3’UTR	0.39	0.25	D	0.83 (0.72 –0.95)	0.008	0.011	0.82 (0.73 –0.92)	0.001	0.001
	rs7133343 (C/A)	flanking 3’UTR	0.33	0.88	A	0.91 (0.81 –1.00)	0.042	0.024	0.86 (0.76 –0.97)	0.014	0.010
	rs11107851 (A/G)	intron	0.21	0.45	R	1.44 (1.06 –1.96)	0.019	0.045	1.45 (1.01 –2.07)	0.042	0.027

Sorted by nDNA pathway-level significance and gene-level significance (Supplementary Table 1) and then by SNP position (base pair). Only SNPs in genes with gene-level P < 0.05 are listed, and only SNPs with P<0.05 and EMP1<0.05 are listed. All P-values are two-sided.

Abbreviations: MT=Mitochondrial DNA; MAF=minor allele frequency among controls; P_HWE =P-value for deviation from Hardy Weinberg Equilibrium among controls (P_HWE <0.05); OR (CI) = Odds ratio (confidence interval);

^aSNP location was derived from the Illumina Infinium 610K Array annotation file that obtains this information from GenBank, a genetic sequence database, along with dbSNP;

^bBest-fitting genetic model (A = Log-additive; D = Dominant; R = Recessive; AL=Allelic);

^cOR and 95% CI adjusted for the simple model (age at diagnosis/interview (continuous)and study site (indicator variable for NCO, TOR, and TBO);

^dAsymptotic P-value for testing the genetic effects related to overall ovarian cancer risk before permutation testing using the simple model. P-value under an additive model represents P-trend;

^eEmpirical point-wise P-value for testing the genetic effects related to overall ovarian cancer risk using the simple model;

^fOR and 95% CI adjusted for the full model (age at diagnosis/interview (continuous), study site (indicator variable for NCO, TOR, and TBO), LOC category (low, medium, high), duration of hormone replacement therapy (HRT) use (continuous), and pack-years of cigarettes smoked (continuous));

^gAsymptotic P-value for testing the genetic effects related to ovarian cancer risk before permutation testing using the full model;

^hEmpirical point-wise P-value for testing the genetic effects related to ovarian cancer risk using the full model;

ⁱrs2402976 is in linkage disequilibrium (LD) (r²=1.0) with imputed SNP rs10954252;

^jrs2540592 is in LD (r²=1.0) with rs2540552;

^krs10488506 is in LD (0.76≤r²≤0.87) rs12668203 and rs12667992;

^lrs6950538 is in LD (0.97≤r²≤0.99) with rs6949881, rs13229505, rs2049314, and rs9656002;

^mrs2269811 is in LD (r²=0.97) with rs7781767;

ⁿrs13151220 is in LD (r²=1.0) with rs13143346;

^ors4550905 is in LD (0.95≤r²≤1.0) with imputed SNPs rs13106578, rs13131226, and rs6838600;

^prs9291455 is in LD (0.86≤r²≤1.0) with rs16874486 and rs16874509;

^qrs17630328 is in LD (r²=1.0) with imputed SNP rs7657655;

^rrs2040742 is in LD (r²=1.0) with rs6842343;

^srs1256061 is in LD (r²=0.86) with rs12435857;

^trs6575325 is in LD(r²=1.0) with rs1503959;

^urs758335 is in LD (r²=0.96) with imputed SNP rs397435;

^vrs7965624 is in LD (r²=1.0) with rs7306940.