A key aim of epidemiological neuroscience studies is the identification of novel markers to assess brain health and evaluate the efficacy of therapeutic interventions. A broad range of tissue constituents associated with healthy brain functions and diseases (e.g., iron, myelin and calcium) are characterised by unique magnetic properties, motivating the development of measurements sensitive to these effects. Quantitative susceptibility mapping (QSM) is an emerging MRI technique which enables in vivo quantification of tissue magnetic susceptibility, providing the opportunity to identify such markers. In this study, we developed a robust QSM modelling pipeline and evaluated the potential of QSM in a cohort of 35,885 subjects (ages 45-82), alongside extensive genetic and phenotypic associations as part of UK Biobank. Our analysis identified a rich set of distinctive phenotypic and genetic associations with QSM. This included phenotypic associations with body iron, diet, alcohol and diseases, and genetic associations related to a broad range of biological functions including iron, calcium homeostasis, myelination, extracellular matrix. Importantly, we found that QSM and T2* have unique patterns of associations, demonstrating the added value in including QSM IDPs in the UK Biobank brain imaging resource, with considerable promise to identify novel in vivo brain health markers.