Table 1. Novel SNPs reaching genome-wide significance and suggestive SNPs approaching genome wide significance.
| SNP/locusI2/Phet | Risk/non-risk allele | Sample | Risk allele frequency cases (%) | Risk allele frequency controls (%) | P value | OR (95% CI) |
|---|---|---|---|---|---|---|
| rs7190997 | C/T | GWAS logistic | 72.0 | 69.2 | 4.00E−05 | 1.207 (1.103–1.320) |
| GWAS gemma | 1.94E−05 | |||||
| chr16: 31368178 | Validation 1 | 73.5 | 66.7 | 3.35E−15 | 1.386 (1.278–1.503) | |
| ITGAX-ITGAM | Validation 2 Southern | 71.9 | 69.3 | 3.91E−02 | 1.129 (1.006–1.267) | |
| Validation 2 Northern | 77.3 | 76.2 | 3.01E−01 | 1.064 (0.946–1.196) | ||
| Validation 3 Southern | 72.9 | 68.4 | 1.16E−03 | 1.239 (1.089–1.411) | ||
| Validation 3 Northern | 77.5 | 74.7 | 7.30E−02 | 1.166 (0.986–1.379) | ||
| All validation | 1.10E−15 | 1.229 (1.168–1.292) | ||||
| Meta-analysis | I2=70.3%, Phet=0.0049 | 2.26E−19 | 1.223 (1.171–1.278) | |||
| rs2074038 | T/G | GWAS logistic | 32.3 | 28.8 | 3.36E−05 | 1.207 (1.104–1.319) |
| GWAS gemma | 4.45E−05 | |||||
| chr11:44087989 | Validation 1 | 31.3 | 28.6 | 1.87E−03 | 1.137 (1.049–1.233) | |
| ACCS | Validation 2 Southern | 32.5 | 28.9 | 4.08E−03 | 1.177 (1.053–1.315) | |
| Validation 2 Northern | 34.8 | 33.6 | 3.24E−01 | 1.054 (0.950–1.170) | ||
| Validation 3 Southern | 30.4 | 29.1 | 3.42E−01 | 1.066 (0.935–1.216) | ||
| Validation 3 Northern | 35.6 | 32.7 | 1.03E−01 | 1.134 (0.975–1.318) | ||
| All validation | 8.76E−06 | 1.116 (1.063–1.171) | ||||
| Meta-analysis | I2=1.26%, Phet=0.408 | 3.93E−09 | 1.136 (1.089–1.185) | |||
| rs2033562 | C/G | GWAS logistic | 51.4 | 47.7 | 7.98E−05 | 1.176 (1.085–1.274) |
| GWAS gemma | 4.14E−04 | |||||
| chr8:103547739 | Validation 1 | 50.5 | 47.7 | 3.45E−03 | 1.116 (1.037–1.201) | |
| KLF10/ODF1 | Validation 2 Southern | 50.6 | 48.8 | 1.77E−01 | 1.074 (0.968–1.192) | |
| Validation 2 Northern | 50.8 | 47.4 | 9.15E−03 | 1.139 (1.033–1.256) | ||
| Validation 3 Southern | 49.8 | 49.0 | 5.90E−01 | 1.033 (0.918–1.163) | ||
| Validation 3 Northern | 50.9 | 45.0 | 1.35E−03 | 1.265 (1.096–1.460) | ||
| All validation | 2.21E−06 | 1.114 (1.065–1.165) | ||||
| Meta-analysis | I2=23.7%, Phet=0.256 | 1.41E−09 | 1.128 (1.085–1.173) | |||
| rs7634389 | C/T | GWAS logistic | 47.4 | 43.5 | 6.80E−04 | 1.151 (1.061–1.248) |
| GWAS gemma | 4.33E−05 | |||||
| chr3:186738421 | Validation 1 | 46.2 | 43.7 | 8.86E−03 | 1.105 (1.026–1.191) | |
| ST6GAL1 | Validation 2 Southern | 46.1 | 44.3 | 1.80E−01 | 1.075 (0.968–1.194) | |
| Validation 2 Northern | 46.6 | 42.6 | 1.48E−03 | 1.176 (1.064–1.300) | ||
| Validation 3 Southern | 47.0 | 42.8 | 5.94E−03 | 1.180 (1.049–1.328) | ||
| Validation 3 Northern | 46.7 | 43.8 | 1.09E−01 | 1.124 (0.974–1.297) | ||
| All validation | 2.48E−07 | 1.126 (1.076–1.178) | ||||
| Meta-analysis | I2=0%, Phet=0.772 | 7.27E−10 | 1.132 (1.088–1.178) | |||
CI, confidence interval; GWAS, genome-wide association study; OR, odds ratio; SNP, single-nucleotide polymorphism.
For the GWAS samples, only the result from logistic regression analyses (GWAS logistic) was used in the fixed-effects meta-analysis with the validation samples. P values shown are from logistic regression analyses unless otherwise stated.