TABLE 2.
Summary of SNPs associated with diabetic nephropathy in the GoKinD collection
| Locus |
Risk allele frequencies and P values for control and case subjects by panel |
P values and ORs for combined analysis |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GWU GoKinD |
JDC GoKinD |
|||||||||||
| SNP | Chromosome | Position (Mb) | Nearest gene(s) | Risk allele (non–risk allele) | Control subjects | Case subjects | P | Control subjects | Case subjects | P | P | OR (95% CI) |
| n | — | — | — | — | 413 | 379 | — | 472 | 441 | — | — | — |
| rs39059 | 7p | 29.2 | CPVL/CHN2 | A(G) | 0.61 | 0.69 | 8.8 × 10−4 | 0.60 | 0.67 | 1.7 × 10−3 | 5.0 × 10−6 | 1.39 (1.20–1.61) |
| rs39075† | 7p | 29.2 | CPVL/CHN2 | G(A) | 0.57 | 0.66 | 2.0 × 10−4 | 0.57 | 0.64 | 8.2 × 10−4 | 6.5 × 10−7 | 1.43 (1.23–1.64) |
| rs1888747† | 9q | 85.3 | FRMD3 | G(C) | 0.68 | 0.73 | 3.6 × 10−3 | 0.66 | 0.74 | 4.4 × 10−5 | 6.3 × 10−7 | 1.45 (1.25–1.67) |
| rs10868025 | 9q | 85.4 | FRMD3 | A(G) | 0.59 | 0.66 | 1.9 × 10−3 | 0.56 | 0.66 | 7.2 × 10−5 | 5.0 × 10−7 | 1.45 (1.25–1.67) |
| rs739401 | 11p | 3.0 | CARS | C(T) | 0.46 | 0.54 | 4.7 × 10−4 | 0.49 | 0.55 | 3.6 × 10−3 | 6.4 × 10−6 | 1.36 (1.19–1.56) |
| rs451041 | 11p | 3.0 | CARS | A(G) | 0.46 | 0.54 | 6.9 × 10−4 | 0.48 | 0.56 | 1.3 × 10−3 | 3.1 × 10−6 | 1.36 (1.19–1.56) |
| rs1041466 | 13q | 109.0 | No gene | G(A) | 0.39 | 0.47 | 3.6 × 10−3 | 0.43 | 0.51 | 2.7 × 10−4 | 3.2 × 10−6 | 1.38 (1.20–1.58) |
| rs1411766/rs17412858‡ | 13q | 109.1 | No gene | A(G)/G(A) | 0.31 | 0.39 | 8.5 × 10−4 | 0.32 | 0.40 | 6.4 × 10−4 | 1.8 × 10−6 | 1.41 (1.23–1.63) |
| rs6492208/rs2391777§ | 13q | 109.1 | No gene | T(C)/G(A) | 0.55 | 0.62 | 8.7 × 10−3 | 0.56 | 0.65 | 1.9 × 10−4 | 6.1 × 10−6 | 1.37 (1.20–1.59) |
| rs7989848 | 13q | 109.1 | No gene | A(G) | 0.49 | 0.56 | 2.0 × 10−3 | 0.50 | 0.57 | 1.1 × 10−3 | 7.0 × 10−6 | 1.37 (1.19–1.56) |
| rs9521445 | 13q | 109.1 | No gene | A(C) | 0.47 | 0.54 | 2.1 × 10−3 | 0.47 | 0.55 | 4.2 × 10−4 | 2.9 × 10−6 | 1.38 (1.20–1.58) |
The most strongly associated SNPs from the combined analysis of the GWU and JDC GoKinD panels are presented along with the risk allele frequencies and P values (calculated using the Cochran-Mantel-Haenszel method, adjusting for sex, between case and control subjects within each collection) for each separate collection. Combined P values and ORs were calculated using the Cochran-Mantel-Haenszel method. Chromosomal locations, SNP positions, and gene annotations are in reference to NCBI Build 36.1. A summary of the genotype frequencies for the most strongly associated SNPs in the GoKinD collection are presented in supplementary Table 3.
†rs39075 and rs1888747 were identified through imputation and genotyped using Taqman assays in the GoKinD collection;
‡rs1411766 and rs17412858 were both genotyped on the Affymetrix array and are in complete linkage disequilibrium (r2 = 1.0);
§rs6492208 and rs2391777 were both genotyped on the Affymetrix array and are in complete linkage disequilibrium (r2 = 1.0).