Table 1.
Loci with most significant concordant and discordant heterogeneity and loci with cross-ancestry associations driven by the UKB AFR ancestry sample
| Heterogeneity | rsID | REF | ALT | Phenotype description | Ancestry | Effect allele frequency | Beta | SE | P | P heterogeneity |
|---|---|---|---|---|---|---|---|---|---|---|
| Concordant | rs35390 | C | A | Hair color (natural, before graying): black | AFR | 0.572/0.620 | -0.111 | 0.056 | 4.64E-02 | 6.49E-192 |
| AMR | 0.622/0.804 | -0.629 | 0.143 | 1.03E-05 | ||||||
| CSA | 0.3885/0.410 | -0.058 | 0.037 | 1.19E-01 | ||||||
| EAS | 0.417/0.456 | 0.013 | 0.075 | 8.62E-01 | ||||||
| EUR | 0.959/0.985 | -1.928 | 0.055 | 5.12E-265 | ||||||
| MID | 0.6306/0.784 | -0.380 | 0.101 | 1.54E-04 | ||||||
| Meta-analysis | 0.9372/0.964 | -0.456 | 0.024 | 1.95E-78 | ||||||
| Discordant | rs7189975 | G | A | Mean corpuscular hemoglobin | AFR | 0.479 | -0.336 | 0.021 | 1.81E-58 | 6.03E-104 |
| AMR | 0.096 | -0.134 | 0.084 | 1.12E-01 | ||||||
| CSA | 0.043 | 0.059 | 0.039 | 1.30E-01 | ||||||
| EAS | 0.006 | 0.197 | 0.210 | 3.47E-01 | ||||||
| EUR | 0.068 | 0.134 | 0.005 | 2.26E-151 | ||||||
| MID | 0.131 | 0.002 | 0.061 | 9.79E-01 | ||||||
| Meta-analysis | 0.074 | 0.105 | 0.005 | 2.82E-102 | ||||||
| AFR-concordant | rs12466997 | T | C | Total bilirubin | AFR | 0.284 | -0.554 | 0.022 | 5.18E-142 | 1.50E-109 |
| AMR | 0.106 | -0.097 | 0.085 | 2.56E-01 | ||||||
| CSA | 0.176 | -0.214 | 0.020 | 6.11E-26 | ||||||
| EAS | 0.202 | 0.081 | 0.033 | 1.53E-02 | ||||||
| EUR | 0.054 | -0.072 | 0.006 | 8.42E-36 | ||||||
| MID | 0.132 | -0.173 | 0.056 | 2.07E-03 | ||||||
| Meta-analysis | 0.061 | -0.107 | 0.005 | 3.54E-91 | ||||||
| rs9411476 | G | A | Alkaline phosphatase | AFR | 0.125 | -0.228 | 0.028 | 3.21E-16 | 5.00E-24 | |
| AMR | 0.017 | -0.203 | 0.181 | 2.63E-01 | ||||||
| CSA | 0.056 | -0.208 | 0.034 | 1.63E-09 | ||||||
| EAS | 0.158 | -0.292 | 0.036 | 6.39E-16 | ||||||
| EUR | 0.007 | 0.026 | 0.016 | 1.14E-01 | ||||||
| MID | 0.031 | -0.045 | 0.115 | 6.97E-01 | ||||||
| Meta-analysis | 0.011 | -0.088 | 0.012 | 2.99E-13 | ||||||
| rs782604098 | A | ATG | Glycated hemoglobin | AFR | 0.251 | -0.544 | 0.024 | 1.45E-109 | 5.59E-103 | |
| AMR | 0.042 | -0.475 | 0.106 | 6.84E-06 | ||||||
| CSA | 0.011 | -0.022 | 0.083 | 7.95E-01 | ||||||
| EAS | 0.015 | 0.155 | 0.133 | 2.44E-01 | ||||||
| EUR | 0.019 | -0.007 | 0.005 | 1.01E-01 | ||||||
| MID | 0.075 | -0.117 | 0.064 | 6.98E-02 | ||||||
| Meta-analysis | 0.022 | -0.027 | 0.004 | 2.71E-09 |
The alternate allele (ALT) is the effect allele. For binary outcomes, we report the effect allele frequency for both cases and controls. REF, reference allele; SE, standard error; P: P-value.