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Background  Mammographic density (MD) is a strong and heritable intermediate phenotype of breast cancer, but much of its genetic variation remains unexplained.    Methods  We conducted a genetic association study of volumetric MD in a Swedish mammography screening cohort ( n  = 9498) to identify novel MD loci. Associations with volumetric MD phenotypes (percent dense volume, absolute dense volume, and absolute nondense volume) were estimated using linear regression adjusting for age, body mass index, menopausal status, and six principal components. We also estimated the proportion of MD variance explained by additive contributions from single-nucleotide polymorphisms (SNP-based heritability [ h  2  SNP ]) in 4948 participants of the cohort.    Results  In total, three novel MD loci were identified (at  P  < 5 × 10 − 8 ): one for percent dense volume ( HABP2 ) and two for the absolute dense volume  (INHBB, LINC01483) .  INHBB  is an established locus for ER-negative breast cancer, and  HABP2  and  LINC01483  represent putative new breast cancer susceptibility loci, because both loci were associated with breast cancer in available meta-analysis data including 122,977 breast cancer cases and 105,974 control subjects ( P  < 0.05).  h  2  SNP  (SE) estimates for percent dense, absolute dense, and nondense volume were 0.29 (0.07), 0.31 (0.07), and 0.25 (0.07), respectively. Corresponding ratios of  h  2  SNP  to previously observed narrow-sense  h  2  estimates in the same cohort were 0.46, 0.72, and 0.41, respectively.    Conclusions  These findings provide new insights into the genetic basis of MD and biological mechanisms linking MD to breast cancer risk. Apart from identifying three novel loci, we demonstrate that at least 25% of the MD variance is explained by common genetic variation with  h  2  SNP / h  2  ratios varying between dense and nondense MD components.    Electronic supplementary material  The online version of this article (10.1186/s13058-018-0954-6) contains supplementary material, which is available to authorized users.

Common genetic variation and novel loci associated with volumetric mammographic density