SNPs in several gene loci, including SEC16B (Padj <  9.48 × 10−7), NEGR1 (Padj < 1.64 × 10−6), FTO (Padj < 2.91 × 10−5), TMEM18 (Padj < 2.27 × 10−5), and WARS2(Padj < 3.25 × 10−5) were similarly associated (albeit not at array-wide signficance (P ≤ 6.7 × 10−7) with various phenotypes including fat mass, PFM, WHR linked to BC in this African cohort, however the associations were driven by different sentinel SNPs. Here, SEC16B is linked to breast cancer.