Table 2.

Novel loci associated with volumetric mammographic density

						Karma-OncoArray (n = 5827)			Karma-iCOGS (n = 4021)			Karma pooled MD analysis (N = 9848)
Locus	Base pair	Lead SNP	Gene	A1	A2	MAF	β (SE)	P value	MAF	β (SE)	P value	β (SE)	P overall	P value for heterogeneity
Percent dense volume
10q25.3	115,248,851	rs2089176	HABP2	A	G	0.41	− 0.05 (0.01)	3.2 × 10− 4	0.41	− 0.08 (0.02)	1.4 × 10− 6	− 0.07 (0.01)	4.1 × 10− 9	0.20
Absolute dense volume
2q14.2	121,092,388	rs12468790	INHBB	A	G	0.39	0.08 (0.02)	2.4 × 10− 5	0.36	0.08 (0.02)	2.3 × 10− 4	0.08 (0.01)	2.1 × 10− 8	0.84
17q24.3	67,836,371	rs9302903	LINC01483	T	C	0.08	− 0.12 (0.03)	7.5 × 10− 5	0.08	− 0.17 (0.04)	1.3 × 10− 5	− 0.14 (0.02)	5.9 × 10− 9	0.36

Abbreviations: iCOGS Illumina iSelect genotyping array of the Collaborative Oncological Gene-environment Study, Karma Karolinska Mammography Project for Risk Prediction of. Breast Cancer, SNP Single-nucleotide polymorphism, A1 Major allele, A2 Minor allele, MAF Minor allele frequency

Gene refers to nearest gene. All lead SNPs were imputed: INFO scores Karma-OncoArray: rs2089176 (0.99), rs12468790 (0.96), rs9302903 (0.99)