Table 2.

New cross-cancer loci identified at P < 10⁻⁸ that were over 1 Mb away from known index SNPs

Region, positiona	Index SNP, (n), nearest gene	Alleles (E/R), EAF	Cancer Type	OR (95% CI)	P	ASSET model, Phetb	r2c
A: From the three-cancer meta-analysis
Associations with breast, ovarian and prostate cancer risk with the same direction of effect
2q13	rs17041869	A/G	Breast cancer	0.97 (0.94–0.99)	7.1×10−3	3-cancer	1d
111896243	(3)	0.88	Ovarian cancer	0.93 (0.88–0.97)	5.3×10−4	0.07	1d
	BCL2L11		Prostate cancer	0.92 (0.89–0.95)	2.6×10−6		1d
			Meta-analysis	0.94 (0.93–0.96)	5.1×10−9
11q12	rs7937840	T/C	Breast cancer	1.04 (1.02–1.06)	3.6×10−5	3-cancer	0.89
61893972	(1)	0.26	Ovarian cancer	1.05 (1.01–1.09)	5.8×10−3	0.95	0.90
	INCENP		Prostate cancer	1.05 (1.02–1.08)	8.9×10−4		0.89
			Meta-analysis	1.05 (1.03–1.06)	5.0×10−9
19p13	rs1469713	A/G	Breast cancer	0.95 (0.94–0.97)	9.9×10−8	3-cancer	0.98
19528806	(89)	0.64	Ovarian cancer	0.96 (0.93–0.99)	6.3×10−3	0.64	0.98
	GATAD2A		Prostate cancer	0.97 (0.94–0.99)	1.0×10−2		0.95
			Meta-analysis	0.96 (0.95–0.97)	3.4×10−10
B: From the pairwise meta-analyses
Associations with breast and ovarian cancer risk with the same direction of effect
9q31	rs200182588	G/GGC	Breast cancer	0.96 (0.94–0.98)	1.9×10−5	2-cancer	0.81
106856690	(15)	0.56	Ovarian cancer	0.93 (0.89–0.96)	2.8×10−6	0.08	0.82
	SMC2		Meta-analysis	0.95 (0.94–0.97)	8.9×10−9
15q26	rs8037137	T/C	Breast cancer	1.07 (1.04–1.10)	1.8×10−7	2-cancer	0.98
91506637	(33)	0.86	Ovarian cancer	1.09 (1.04–1.14)	2.1×10−4	0.58	0.98
	RCCD1		Meta-analysis	1.07 (1.05–1.10)	9.1×10−10
Associations with breast and prostate cancer risk with the same direction of effect
1p34	rs5013329	T/C	Breast cancer	1.04 (1.02–1.06)	7.8×10−6	2-cancer	0.98
46815091	(218)	0.31	Prostate cancer	1.07 (1.04–1.10)	1.4×10−7	0.09	0.98
	NSUN4		Meta-analysis	1.05 (1.04–1.07)	1.8×10−11
6q23	rs9375701	T/C	Breast cancer	1.04 (1.02–1.06)	3.6×10−6	2-cancer	0.99
130384057	(53)	0.67	Prostate cancer	1.06 (1.03–1.08)	1.5×10−5	0.41	0.99
	L3MBTL3		Meta-analysis	1.05 (1.03–1.06)	3.4×10−10

Abbreviations: n, Number of SNPs with P < 10⁻⁸ within 1 Mb of the index SNP; (E/R), (effect/reference) alleles; EAF: effect allele frequency.

^aBuild 37 coordinates.

^bCochran’s Q-test for heterogeneity P-value.

^cImputation accuracy, r², in iCOGS European samples.

^dGenotyped SNP.