Table 2.
IBC array-wide significant SNPs associated with WHR among females
| Nearest gene | Chr | IBC |
GIANT, female (26) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | N | CA | CAF | Effect (SE) | P-value | I2 | SNPa | R2b | CA | CAF | Effect (SE) | P-value | ||
| RSPO3 | 6 | rs11154383 | 28 916 | G | 0.30 | 0.064 (0.009) | 1.5E−12 | 0.0 | rs9491696 | 0.28 | G | 0.48 | 0.050 (0.004) | 1.9E−32 |
| ADAMTS9 | 3 | rs4607103 | 28 927 | C | 0.75 | 0.055 (0.010) | 8.5E−09 | 0.0 | rs6795735 | 0.27 | C | 0.59 | 0.038 (0.005) | 1.9E−16 |
| TMCC1 | 3 | rs2811337 | 32 165 | G | 0.82 | 0.055 (0.010) | 1.7E−07 | 3.3 | rs2811337 | N/A | G | 0.82 | 0.038 (0.009) | 1.1E−05 |
| ITPR2 | 12 | rs1049376 | 31 254 | C | 0.26 | 0.046 (0.009) | 3.8E−07 | 0.0 | rs718314 | 0.64 | G | 0.26 | 0.042 (0.005) | 2.4E−17 |
| SHC1 | 1 | rs12076073 | 30 191 | A | 0.96 | 0.101 (0.021) | 1.9E−06 | 0.0 | rs12076073 | N/A | A | 0.96 | 0.087 (0.025) | 5.6E−04 |
| ATPBD4 | 15 | rs1037575 | 31 255 | A | 0.79 | 0.046 (0.010) | 2.2E−06 | 0.0 | rs1037575 | N/A | A | 0.79 | 0.017 (0.008) | 0.042 |
| SNPs that were significant in sex combined analysis (Table 1) but did not reach significance in female-specific analysis | ||||||||||||||
| HOXC10 | 12 | rs7302703 | 32 166 | G | 0.83 | 0.040 (0.010) | 1.3E−04 | 3.9 | rs7302703 | N/A | G | 0.84 | 0.007 (0.011) | 0.52 |
| PEMT | 17 | rs936108 | 24 807 | C | 0.46 | 0.037 (0.009) | 4.4E−05 | 38.9 | rs936108 | N/A | C | 0.47 | 0.020 (0.007) | 3.2E−03 |
Chr, chromosome; Pos, position; CA, coded allele; CAF, coded allele frequency; WHR, waist-to-hip ratio (adjusted for BMI, age, age2, center site and ancestry), SE, standard error.
aSame SNP used where available; otherwise closest proxy SNP was used (highest R2 in 1000 Genomes Pilot 1 CEU).
bR2 with IBC SNP in 1000 Genomes Pilot 1 CEU. The coding allele was selected based on consistency of MAF with the IBC SNP.