Table 1.
Genome-wide Significant Associations at Newly Identified Loci
| SNP | Trait | Chr:position | Nearest Gene | Effect/Other Allele |
Stage 1 |
Stage 2 |
Stage 1 + Stage 2 |
Variance Explained (%) | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Frequency (Effect Allele) | Beta (SE) | p Value | n | I2 | Phet | Frequency (Effect Allele) | Beta (SE) | p Value | n | I2 | Phet | Frequency (Effect Allele) | Beta (SE) | p Value | n | I2 | Phet | ||||||
| Low-Frequency or Rare | |||||||||||||||||||||||
| rs202238847 | height | 3: 49,263,637 | CCDC36 | C/CT | 0.021 | 0.1091 (0.0233) | 2.83 × 10−6 | 51,309 | 26.8 | 0.132 | 0.023 | 0.0908 (0.0129) | 2.04 × 10−12 | 134,797 | 0.0 | 1.000 | 0.022 | 0.0951 (0.0113) | 3.76 × 10−17 | 186,106 | 24.3 | 0.153 | 0.0787 |
| Common | |||||||||||||||||||||||
| rs1264622 | height | 6: 30,256,936 | HLA-L/HCG17/HCG18 | T/C | 0.190 | 0.0455 (0.0087) | 1.76 × 10−7 | 50,372 | 13.0 | 0.296 | 0.202 | 0.0257 (0.0047) | 4.61 × 10−8 | 134,797 | 0.0 | 1.000 | 0.199 | 0.0302 (0.0041) | 3.05 × 10−13 | 185,169 | 22.9 | 0.172 | 0.0291 |
| rs11042397 | hip | 11: 9,524,255 | ZNF143 | T/C | 0.056 | 0.0763 (0.0150) | 3.56 × 10−7 | 45,588 | 2.3 | 0.429 | 0.057 | 0.0386 (0.0082) | 2.68 × 10−6 | 134,797 | 0.0 | 1.000 | 0.056 | 0.0473 (0.0072) | 5.20 × 10−11 | 180,385 | 18.3 | 0.226 | 0.0238 |
| rs13213884 | height | 6: 141,665,522 | RP11-63E9.1 | T/C | 0.247 | 0.0419 (0.0074) | 1.57 × 10−8 | 51,309 | 49.5 | 0.007 | 0.257 | 0.0176 (0.0043) | 4.68 × 10−5 | 134,797 | 0.0 | 1.000 | 0.254 | 0.0238 (0.0037) | 1.94 × 10−10 | 186,106 | 56.2 | 0.001 | 0.0215 |
| rs12424892 | height | 12: 132,623,389 | DDX51 | C/G | 0.153 | 0.0457 (0.0095) | 1.60 × 10−6 | 44,180 | 0.0 | 0.907 | 0.148 | 0.0241 (0.0053) | 5.80 × 10−6 | 134,797 | 0.0 | 1.000 | 0.149 | 0.0292 (0.0046) | 3.06 × 10−10 | 178,977 | 0.0 | 0.731 | 0.0216 |
| rs35863206 | height | 11: 101,055,183 | RP11-788M5.4 | C/CAG | 0.222 | −0.0384 (0.0082) | 2.77 × 10−6 | 45,588 | 21.8 | 0.190 | 0.224 | −0.0185 (0.0046) | 5.17 × 10−5 | 134,797 | 0.0 | 1.000 | 0.224 | −0.0232 (0.004) | 5.91 × 10−9 | 180,385 | 31.0 | 0.093 | 0.0187 |
SNP positions are reported according to build 37 and their alleles are coded based on the positive strand. The reported gene is the closest in physical distance. Association p values are based on the inverse-variance weighted meta-analysis model (fixed effects). Effect sizes are measured in standard deviation units. Abbreviations are as follows: BMI, body mass index; SNP, single-nucleotide polymorphism; Beta, effect size; SE, standard error; n, sample size; I2, measure of heterogeneity (based on Cochran’s Q-test for heterogeneity) that indicates the percentage of variance in a meta-analysis that is attributable to study heterogeneity; Phet, p value assessing evidence of heterogeneity as reported by METAL.