Table 1.
The unreported significant loci for prostate cancer in the multi-ancestry meta-analysis
| rsID | Chr | Position | Gene | Location | Ref | Alt | META | BBJ | EUR | AFR | HIS | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Beta | BF | Fixed P | Freq | Beta | P value | Freq | Beta | P value | Freq | Beta | P value | Freq | Beta | P value | |||||||
| rs2235558 | 1 | 24783311 | NIPAL3 | Intronic | A | G | 0.039 | 6.408 | 1.71E−08 | 0.747 | 0.064 | 8.63E−04 | 0.618 | 0.032 | 5.01E−05 | 0.747 | 0.062 | 1.04E−02 | 0.690 | 0.048 | 2.67E−01 |
| rs4893909 | 2 | 1.81E+08 | CWC22/SCHLAP1 | Intergenic | T | G | 0.043 | 7.110 | 3.10E−09 | 0.672 | 0.061 | 5.91E−04 | 0.729 | 0.043 | 1.43E−06 | 0.550 | 0.034 | 9.76E−02 | 0.698 | −0.007 | 8.67E−01 |
| rs4704108 | 5 | 73392666 | ARHGEF28/LINC01335 | Intergenic | G | A | −0.045 | 7.172 | 2.41E−09 | 0.214 | −0.086 | 1.69E−05 | 0.267 | −0.038 | 2.05E−05 | 0.383 | −0.028 | 1.83E−01 | 0.324 | −0.074 | 6.86E−02 |
| rs35055448 | 8 | 81135961 | TPD52/MIR5708 | Intergenic | G | A | −0.041 | 6.072 | 4.87E−08 | 0.543 | −0.064 | 1.74E−04 | 0.252 | −0.034 | 1.16E−04 | 0.153 | −0.045 | 1.32E−01 | 0.343 | −0.042 | 3.23E−01 |
| rs11259192 | 10 | 5726821 | FAM208B | 5′ UTR | G | A | 0.062 | 7.217 | 3.24E−09 | 0.069 | 0.086 | 8.13E−03 | 0.119 | 0.054 | 2.38E−06 | 0.025 | 0.107 | 1.20E−01 | 0.163 | 0.135 | 8.72E−03 |
| rs11857866 | 15 | 33349563 | FMN1 | intronic | T | C | 0.043 | 7.282 | 2.47E−09 | 0.201 | 0.065 | 1.66E−03 | 0.310 | 0.039 | 2.33E−06 | 0.262 | 0.042 | 6.49E−02 | 0.208 | 0.056 | 2.55E−01 |
| rs8052683* | 16 | 73002421 | ZFHX3 | Intronic | G | A | −0.038 | 7.086 | 1.85E−07 | 0.253 | −0.113 | 4.46E−09 | 0.296 | −0.026 | 3.05E−03 | 0.185 | −0.033 | 2.31E−01 | 0.254 | −0.012 | 8.04E−01 |
| rs11087515 | 20 | 25399979 | GINS1 | Intronic | G | GA | 0.039 | 6.056 | 3.83E−08 | 0.105 | 0.054 | 6.09E−02 | 0.477 | 0.034 | 1.68E−05 | 0.470 | 0.062 | 4.45E−03 | 0.573 | 0.067 | 1.27E−01 |
| rs10154043 | 21 | 35535103 | MRPS6/LINC00310 | Intergenic | C | T | −0.038 | 6.558 | 1.27E−08 | 0.229 | −0.047 | 1.66E−02 | 0.441 | −0.037 | 1.56E−06 | 0.536 | −0.060 | 3.23E−03 | 0.333 | 0.061 | 1.45E−01 |
Prioritized variants based on BF are indicated.Beta and BF of meta-analysis was calculated based on MANTRA algorithm. BBJ sample were analyzed with SAIGE software which contains a generalized linear mixed model (two-tailed).
Chr chromosome, Ref reference allele, Alt alternative allele, META meta-analysis, BBJ Biobank Japan, EUR Europeans, AFR Africans, HIS Hispanic, Beta beta of alternative allele, BF bayse factor, Fixed P P value of fixed-effect meta-analysis using METAL software (two-tailed), Freq alternative allele frequency, UTR untranslated region.
* ; Other variants in this gene region showed significant associations with p values smaller than 5E−08 in the fixed-effect model (Supplementary Fig. 3).