Eighty-four BMI/obesity-associated CNVs were catalogued from the literature and tested for association with BMI and obesity in the SAGE sample (Additional file 2: Table S2). Of the common CNVs, only a 21-kb deletion on 16p12.3 showed evidence for association with BMI (β = −0.057, p = 0.003, frequency = 16.9%). This CNV was also nominally associated with obese class I (OR = 0.743, p = 0.022) and II (OR = 0.630, p = 0.020). We would like to note that this CNV is correlated with SNP rs12444979, which was included in the GRSS (r = 0.798). However, since they were not in perfect LD and diagnostics between them did not suggest multicolinearity (variance inflation factor < 2.8) we chose to include both in subsequent analyses because it is possible that the SNP is capturing variation beyond the effect of the CNV. Additionally, rs2815752 near NEGR1 has been previously shown to tag a common deletion [9, 48, 49]. Although the SNP (included in the SNP-GRSS) was nominally associated (p =0.007) with BMI the CNV was not, which could be due in
