Table 4.
Additional SNPs independent of the lead SNPs in 7 of 98 established BMI loci associated with BMI in an expanded population-based study of American Indians
| Locus | SNP | Maximum BMI Full-heritage (n=3491) | Maximum BMI Mixed-heritage (n=3298) | Maximum BMI Combined (n=6789) | BMI GIANT (n=339224) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RS# | Allele 1/2 | Freq Allele 1 American Indian | Freq Allele 1European | Beta (Loge) | P after conditional analysis for lead SNP | Beta (Loge) | P after conditional analysis for lead SNP | Beta (Loge) | P after conditional analysis for lead SNP | Beta (SD) | P | |
| ZFP64 | rs6021702 | T/C | 0.17 | 0.36 | 0.024 | 0.01 | 0.020 | 0.009 | 0.021 | 0.0008 | −0.003 | 0.56 |
| PGPEP1 | rs12462812 | A/G | 0.19 | 0.01 | −0.019 | 0.01 | −0.018 | 0.03 | −0.019 | 0.0009 | - | - |
| TCF7L2 | rs146479796 | T/C | 0.80 | 1.00 | −0.020 | 0.01 | −0.016 | 0.05 | −0.018 | 0.001 | - | - |
| CADM1 | rs718484 | A/G | 0.28 | 0.09 | 0.019 | 0.003 | 0.018 | 0.01 | 0.015 | 0.002 | 0.007 | 0.29 |
| CADM1 | rs77550241 | A/G | 0.25 | 0.01 | 0.018 | 0.009 | 0.018 | 0.02 | 0.014 | 0.006 | - | - |
| CADM1 | rs72306674 | -/TCTC | 0.25 | 0.01 | 0.016 | 0.02 | 0.015 | 0.05 | 0.012 | 0.02 | - | - |
| CLIP1 | rs34383196 | T/C | 0.29 | 0.24 | 0.013 | 0.05 | 0.018 | 0.01 | 0.015 | 0.003 | - | - |
| EHBP1 | rs147306320 | T/C | 0.08 | 0.00 | −0.025 | 0.02 | −0.025 | 0.05 | −0.018 | 0.03 | - | - |
Data are given for the analysis of full-heritage Pima Indians, mixed-heritage Pima Indians and combined samples (n as indicated). Allele 1 is defined as the reference allele; allele 2 is as the altered allele. Conditional analyses were conducted in which the European GWAS lead SNP was included as a covariate in the model to determine whether the signal additionally contributed to the BMI association. Beta and p value are also adjusted for age, sex, birth year and the first five genetic principal components. SNPs which were not available in the meta-analysis of GIANT are denoted with “-“.