Table 2.

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

Region, positionaIndex SNP, (n), nearest geneAlleles (E/R), EAFCancer typeOR (95% CI)PASSET model, Phetbr2c
A: From the three-cancer meta-analysis
Associations with breast, ovarian, and prostate cancer risk with the same direction of effect
2q13rs17041869A/GBreast cancer0.97 (0.94–0.99)7.1 × 10−33-cancer1d
111896243(3)0.88Ovarian cancer0.93 (0.88–0.97)5.3 × 10−40.071d
BCL2L11Prostate cancer0.92 (0.89–0.95)2.6 × 10−61d
Meta-analysis0.94 (0.93–0.96)5.1 × 10−9
11q12rs7937840T/CBreast cancer1.04 (1.02–1.06)3.6 × 10−53-cancer0.89
61893972(1)0.26Ovarian cancer1.05 (1.01–1.09)5.8 × 10−30.950.90
INCENPProstate cancer1.05 (1.02–1.08)8.9 × 10−40.89
Meta-analysis1.05 (1.03–1.06)5.0 × 10−9
19p13rs1469713A/GBreast cancer0.95 (0.94–0.97)9.9 × 10−83-cancer0.98
19528806(89)0.64Ovarian cancer0.96 (0.93–0.99)6.3 × 10−30.640.98
GATAD2AProstate cancer0.97 (0.94–0.99)1.0 × 10−20.95
Meta-analysis0.96 (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
9q31rs200182588G/GGCBreast cancer0.96 (0.94–0.98)1.9 × 10−52-cancer0.81
106856690(15)0.56Ovarian cancer0.93 (0.89–0.96)2.8 × 10−60.080.82
SMC2Meta-analysis0.95 (0.94–0.97)8.9 × 10−9
15q26rs8037137T/CBreast cancer1.07 (1.04–1.10)1.8 × 10−72-cancer0.98
91506637(33)0.86Ovarian cancer1.09 (1.04–1.14)2.1 × 10−40.580.98
RCCD1Meta-analysis1.07 (1.05–1.10)9.1 × 1010
Associations with breast and prostate cancer risk with the same direction of effect
1p34rs5013329T/CBreast cancer1.04 (1.02–1.06)7.8 × 10−62-cancer0.98
46815091(218)0.31Prostate cancer1.07 (1.04–1.10)1.4 × 10−70.090.98
NSUN4Meta-analysis1.05 (1.04–1.07)1.8 × 10−11
6q23rs9375701T/CBreast cancer1.04 (1.02–1.06)3.6 × 10−62-cancer0.99
130384057(53)0.67Prostate cancer1.06 (1.03–1.08)1.5 × 10−50.410.99
L3MBTL3Meta-analysis1.05 (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 Q-test for heterogeneity P value.

  • cImputation accuracy, r2, in iCOGS European samples.

  • dGenotyped SNP.