To provide insights into possible shared aetiologies or mechanisms of disease, we assessed association of our five unreported novel HR-SNVs (and their proxies, r2 ≥ 0.8) with other traits. Genome-wide significant phenotype–genotype associations were observed for three novel loci (Supplementary Material, Table S7). The SNV at the DLRD3 locus was associated with age of menarche. The SNV at the JAZF1 locus was highly pleiotropic, as shown by associations with several autoimmune disorders (systemic lupus erythematosus, Crohn’s disease and selective immunoglobulin A deficiency), height, type 2 diabetes and JAZF1 transcript levels in adipose tissue. The SNV at the SEC31B locus was associated with plasma palmitoleic acid levels and differential exon expression of SEC31B.
