Table 3.

Associations of newly identified mammographic density loci with breast cancer risk, overall and stratified by estrogen receptor status

						Karma		BCAC
						Pooled MD analysis		MAF	Breast cancer overall		Breast cancer ER−		Breast cancer ER+
Locus	Base pair	Lead SNP	Gene	A1	A2	β (SE)	P overall		OR (95% CI)	P value	OR (95% CI)	P value	OR (95% CI)	P value
Percent dense volume
10q25.3	115,248,851	rs2089176	HABP2	A	G	− 0.07 (0.01)	4.1 × 10− 9	0.36	0.98 (0.97–0.99)	0.01	1.00 (0.98–1.03)	0.70	0.97 (0.96–0.99)	5.3 × 10− 4
Absolute dense volume
2q14.2	121,092,388	rs12468790	INHBB	A	G	0.08 (0.01)	2.1 × 10− 8	0.40	0.97 (0.96–0.98)	4.8 × 10− 6	0.93 (0.91–0.95)	1.5 × 10− 9	0.98 (0.96–0.99)	3.8 × 10− 3
17q24.3	67,836,371	rs9302903	LINC01483	T	C	− 0.14 (0.02)	5.9 × 10− 9	0.09	0.96 (0.94–0.99)	1.1 × 10− 3	0.98 (0.94–1.02)	0.26	0.95 (0.93–0.98)	1.5 × 10− 4

Abbreviations: BCAC Breast Cancer Association Consortium, SNP Single-nucleotide polymorphism, A1 Major allele, A2 Minor allele, MAF Minor allele frequency, ER− Estrogen receptor-negative, ER+ Estrogen receptor-positive

MAF in BCAC as observed in genotyped control subjects (Europeans only). Gene refers to nearest gene