Associations for proteinuria and eGFR meta-analysis lead SNPs controlling for the additive effects of either APOL1 G1/G2, APOL1 G1, APOL1 G2, or MYH9 rs16996672
| Gene . | Lead SNP . | Allele . | Phenotype . | P value . | OR/beta . | MYH9/APOL1 covariate∗ . | Covariate P value† . | Covariate OR/beta† . |
|---|---|---|---|---|---|---|---|---|
| CRYL1 | rs9315599 | G | Proteinuria | 2.01E-06 | 3.54 | G1/G2 | 1.17E-04 | 3.13 |
| Proteinuria | 3.36E-06 | 3.40 | G1 | 5.22E-04 | 1.79 | |||
| Proteinuria | 2.38E-06 | 3.47 | G2 | .64 | 0.90 | |||
| Proteinuria | 9.07E-07 | 3.54 | MYH9 | 3.73E-05 | 1.98 | |||
| VWF | rs2238104 | T | Proteinuria | 1.11E-03 | 2.11 | G1/G2 | 9.23E-05 | 3.16 |
| Proteinuria | 4.48E-04 | 2.21 | G1 | 3.75E-04 | 1.80 | |||
| Proteinuria | 8.13E-04 | 2.10 | G2 | .6 | 0.89 | |||
| Proteinuria | 1.81E-03 | 1.99 | MYH9 | 4.44E-05 | 1.95 | |||
| ADAMTS7 | rs3743057 | T | Proteinuria | 6.49E-06 | 0.40 | G1/G2 | 2.68E-04 | 2.95 |
| Proteinuria | 2.64E-06 | 0.38 | G1 | 6.58E-04 | 1.77 | |||
| Proteinuria | 1.95E-06 | 0.38 | G2 | .62 | 0.90 | |||
| Proteinuria | 2.22E-07 | 0.35 | MYH9 | 3.75E-06 | 2.20 | |||
| LRP1B | rs1968911 | G | eGFR | 1.68E-04 | −25.18 | G1/G2 | .24 | −10.94 |
| eGFR | 1.98E-04 | −24.45 | G1 | 2.90E-03 | −14.58 | |||
| eGFR | 1.33E-04 | −24.54 | G2 | .73 | 2.23 | |||
| eGFR | 7.40E-05 | −25.96 | MYH9 | .86 | −0.83 | |||
| linc02288 | rs4903539 | G | eGFR | 9.69E-05 | −19.27 | G1/G2 | .3 | −9.56 |
| eGFR | 4.79E-05 | −19.72 | G1 | 1.67E-03 | −15.35 | |||
| eGFR | 9.32E-05 | −19.32 | G2 | .75 | 2.03 | |||
| eGFR | 2.67E-05 | −20.25 | MYH9 | .93 | −0.42 | |||
| TNNI3K; FPGT-TNNI3K | rs7526762 | G | eGFR | 3.81E-02 | 11.65 | G1/G2 | .3 | −9.79 |
| eGFR | 4.75E-02 | 10.90 | G1 | 2.19E-03 | −15.34 | |||
| eGFR | 3.59E-02 | 11.79 | G2 | .68 | 2.72 | |||
| eGFR | 2.45E-02 | 12.17 | MYH9 | .88 | −0.76 |
| Gene . | Lead SNP . | Allele . | Phenotype . | P value . | OR/beta . | MYH9/APOL1 covariate∗ . | Covariate P value† . | Covariate OR/beta† . |
|---|---|---|---|---|---|---|---|---|
| CRYL1 | rs9315599 | G | Proteinuria | 2.01E-06 | 3.54 | G1/G2 | 1.17E-04 | 3.13 |
| Proteinuria | 3.36E-06 | 3.40 | G1 | 5.22E-04 | 1.79 | |||
| Proteinuria | 2.38E-06 | 3.47 | G2 | .64 | 0.90 | |||
| Proteinuria | 9.07E-07 | 3.54 | MYH9 | 3.73E-05 | 1.98 | |||
| VWF | rs2238104 | T | Proteinuria | 1.11E-03 | 2.11 | G1/G2 | 9.23E-05 | 3.16 |
| Proteinuria | 4.48E-04 | 2.21 | G1 | 3.75E-04 | 1.80 | |||
| Proteinuria | 8.13E-04 | 2.10 | G2 | .6 | 0.89 | |||
| Proteinuria | 1.81E-03 | 1.99 | MYH9 | 4.44E-05 | 1.95 | |||
| ADAMTS7 | rs3743057 | T | Proteinuria | 6.49E-06 | 0.40 | G1/G2 | 2.68E-04 | 2.95 |
| Proteinuria | 2.64E-06 | 0.38 | G1 | 6.58E-04 | 1.77 | |||
| Proteinuria | 1.95E-06 | 0.38 | G2 | .62 | 0.90 | |||
| Proteinuria | 2.22E-07 | 0.35 | MYH9 | 3.75E-06 | 2.20 | |||
| LRP1B | rs1968911 | G | eGFR | 1.68E-04 | −25.18 | G1/G2 | .24 | −10.94 |
| eGFR | 1.98E-04 | −24.45 | G1 | 2.90E-03 | −14.58 | |||
| eGFR | 1.33E-04 | −24.54 | G2 | .73 | 2.23 | |||
| eGFR | 7.40E-05 | −25.96 | MYH9 | .86 | −0.83 | |||
| linc02288 | rs4903539 | G | eGFR | 9.69E-05 | −19.27 | G1/G2 | .3 | −9.56 |
| eGFR | 4.79E-05 | −19.72 | G1 | 1.67E-03 | −15.35 | |||
| eGFR | 9.32E-05 | −19.32 | G2 | .75 | 2.03 | |||
| eGFR | 2.67E-05 | −20.25 | MYH9 | .93 | −0.42 | |||
| TNNI3K; FPGT-TNNI3K | rs7526762 | G | eGFR | 3.81E-02 | 11.65 | G1/G2 | .3 | −9.79 |
| eGFR | 4.75E-02 | 10.90 | G1 | 2.19E-03 | −15.34 | |||
| eGFR | 3.59E-02 | 11.79 | G2 | .68 | 2.72 | |||
| eGFR | 2.45E-02 | 12.17 | MYH9 | .88 | −0.76 |
All models included PCs and hemoglobin genotype as covariates; the proteinuria models also included age and Duffy.
ORs are provided for proteinuria models; betas are provided for eGFR models.
OR, odds ratio.
MYH9/APOL1 covariate specifies which covariate was included separately in each regression model to control for the effect of APOL1.
Covariate P value and effect size (OR/beta) is the marginal effect of the specified APOL1 covariate in each regression model.