Supplementary Table 1. Evaluation of 14 PRSs calculated with two methods
	OR	pval	OR_L	OR_U	
LDpred.inf	1.1730944	5.34E-05	1.0857074	1.267619	
LDpred_p1.0000e.00	1.2254876	2.87E-07	1.1339923	1.324563	
LDpred_p1.0000e.01	1.2392402	6.31E-08	1.1466684	1.339505	
LDpred_p1.0000e.02	1.3601543	2.24E-14	1.257133	1.4722	
LDpred_p1.0000e.03	1.2782548	8.43E-10	1.1820023	1.382694	
LDpred_p1.0000e.04	1.1646223	9.15E-05	1.0788544	1.256867	
LDpred_p3.0000e.01	1.2287311	2.02E-07	1.1369856	1.328082	
LDpred_p3.0000e.02	1.2766903	8.13E-10	1.1810819	1.380347	
LDpred_p3.0000e.03	1.4431112	1.59E-19	1.3330451	1.562923	
LDpred_p3.0000e.04	1.1060843	1.07E-02	1.0237226	1.195185	
bWICD10	1.3991755	1.40E-16	1.2923015	1.515521	
bRICD10	1.4445315	1.54E-19	1.3341299	1.564776	
marginalEst	0.9499823	2.00E-01	0.877938	1.027192	
marginalEst_UK_Kaiser	1.2345218	1.26E-07	1.1417615	1.334899	

Supplementary Table 2. Predictors of HPV status using Score 2
Variable (baseline)		OR	95% CI	p value	
Genetic risk from Score 2		1.28	(1.1,1.48)	0.0015	
Financial condition (Poor)		1			
	Average	1.1	(0.7,1.75)	0.6744	
	Good	1.17	(0.68,2.01)	0.576	
Marital status (Married)		1			
	Widow	1.56	(0.84,2.92)	0.1621	
	Partnered	1.71	(1.14,2.57)	0.0093	
	Divorced	2.39	(1.46,3.92)	0.0006	
	Single	2.71	(1.68,4.38)	<0.0001	
Nationality (Estonian)		1			
	Not Estonian	1.42	(0.97,2.1)	0.0749	
Parity class (0)		1			
	3+	0.8	(0.43,1.47)	0.4773	
	1-2	0.71	(0.49,1.04)	0.0788	
Age group (30-33)		1			
	57-60	0.92	(0.57,1.47)	0.7211	
	67-70	1.36	(0.71,2.59)	0.3553	
First intercourse age		0.99	(0.94,1.05)	0.864	
Used hormonal contraceptives (No)		1			
	Yes	1.62	(1.02,2.56)	0.0459	
Education (Higher)		1			
	Lower	1.44	(1.05,1.98)	0.0226	
Number of abortions		1.01	(0.87,1.17)	0.8972	
Total partners		1.04	(1.01,1.06)	0.0022	

Supplementary Table 3. Predictors of HPV status using Score 1
Variable (baseline)		OR	95% CI	p value	
Genetic risk from Score 1 		1.28	(1.11,1.47)	0.0008	
Financial condition (Poor)		1			
	Average	1.07	(0.68,1.7)	0.7652	
	Good	1.1	(0.65,1.87)	0.7228	
Marital status (Married)		1			
	Widow	1.62	(0.87,3.02)	0.1291	
	Partnered	1.77	(1.17,2.68)	0.0073	
	Divorced	2.39	(1.45,3.94)	0.0006	
	Single	2.65	(1.64,4.3)	0.0001	
Nationality (Estonian)		1			
	Not Estonian	1.34	(0.91,1.97)	0.1389	
Parity class (0)		1			
	3+	0.84	(0.46,1.54)	0.5784	
	1-2	0.7	(0.46,1.07)	0.1077	
Age group (30-33)		1			
	57-60	0.86	(0.54,1.39)	0.5434	
	67-70	1.24	(0.65,2.39)	0.5157	
First intercourse age		0.99	(0.94,1.05)	0.848	
Used hormonal contraceptives (No)		1			
	Yes	1.41	(0.92,2.14)	0.1152	
Education (Higher)		1			
	Lower	1.42	(1.01,1.98)	0.0417	
Number of abortions		1.01	(0.85,1.21)	0.8781	
Total partners		1.04	(1.02,1.07)	0.0004	

Supplementary Table 4. Summary statistics for the traits that potentially had an effect on HPV status. 

		hrHPV positive		hrHPV negative		hrHPV total		
	n		n		n		p	
Birth year, median (IQR)	207	1988 (1961-1989)	1140	1963 (1960-1989)	1347	1963 (1960-1989)	0.02	
Age at first intercourse, median (IQR)	202	18 (16-20)	1062	18 (17-20)	1264	18 (17-20)	0.009	
Number of pregnancies, median (IQR)	140	3 (2-4)	888	3 (2-4)	1028	3 (2-4)	0.922	
Age at pregnancy, median (IQR)	134	22 (20-27)	861	23 (20-26)	995	22 (20-26)	0.748	
Number of partners, median (IQR)	193	6 (4-10)	1038	4 (2-6)	1231	4 (2-7)	< 0.001	
Marital status, n (%)	207		1138		1345		< 0.001	
    Divorced		24(12%)		115 (10%)		139 (10%)		
    Married		56 (27%)		507 (45%)		563 (42%)		
    Partnered		71 (34%)		304 (27%)		375 (28%)		
    Single		42 (20%)		125 (11%)		167 (12%)		
    Widowed		14 (7%)		87 (8%)		101 (8%)		
Education, n (%)	205		1133		1338		0.153	
    Primary school		7 (3%)		17 (2%)		24 (2%)		
    Secondary school		82 (40%)		446 (39%)		528 (39%)		
    University		116 (57%)		670 (59%)		786 (59%)		
Contraceptives at first intercourse, n (%)	199		1055		1254		0.087	
    Condom		98 (49%)		426 (40%)		524 (42%)		
    Hormonal/Intrauterine/Emergency pill		11 (6%)		50 (5%)		61 (5%)		
    Nothing		69 (35%)		459 (44%)		528 (42%)		
    Other		21 (11%)		120 (11%)		141 (11%)		
Pregnancy end code 1, n (%)	16		104		120		0.001	
    No		5 (31%)		3 (3%)		8 (7%)		
    Yes		11 (69%)		101 (97%)		112 (93%)		
Venereal diseases, n (%)	199		1062		1261		0.204	
    No		173 (87%)		957 (90%)		1130 (90%)		
    Yes		26 (13%)		105 (10%)		131 (10%)		
Last reproductive health exam, n (%)	203		1125		1328		0.068	
    < 1 year ago		110 (54%)		486 (43%)		596 (45%)		
    1-2 years ago		36 (18%)		261 (23%)		297 (22%)		
    2-3 years ago		20 (10%)		128 (11%)		148 (11%)		
    3+ years ago		27 (13%)		173 (15%)		200 (15%)		
    Never or did not know		10 (5%)		77 (7%)		87 (7%)		
Pap test awareness, n (%)	204		1121		1325		0.898	
    Did not know		45 (22%)		262 (23%)		307 (23%)		
    No		9 (4%)		45 (4%)		54 (4%)		
    Yes		150 (74%)		814 (73%)		964 (73%)		
Pap test interval awareness, n (%)	206		1120		1326		0.511	
    No		59 (29%)		350 (31%)		409 (31%)		
    Yes		147 (71%)		770 (69%)		917 (69%)