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
SNPChromosomePosition (Mb)Nearest gene(s)Risk allele (non–risk allele)Control subjectsCase subjectsPControl subjectsCase subjectsPPOR (95% CI)
n413379472441
rs390597p29.2CPVL/CHN2A(G)0.610.698.8 × 10−40.600.671.7 × 10−35.0 × 10−61.39 (1.20–1.61)
rs390757p29.2CPVL/CHN2G(A)0.570.662.0 × 10−40.570.648.2 × 10−46.5 × 10−71.43 (1.23–1.64)
rs18887479q85.3FRMD3G(C)0.680.733.6 × 10−30.660.744.4 × 10−56.3 × 10−71.45 (1.25–1.67)
rs108680259q85.4FRMD3A(G)0.590.661.9 × 10−30.560.667.2 × 10−55.0 × 10−71.45 (1.25–1.67)
rs73940111p3.0CARSC(T)0.460.544.7 × 10−40.490.553.6 × 10−36.4 × 10−61.36 (1.19–1.56)
rs45104111p3.0CARSA(G)0.460.546.9 × 10−40.480.561.3 × 10−33.1 × 10−61.36 (1.19–1.56)
rs104146613q109.0No geneG(A)0.390.473.6 × 10−30.430.512.7 × 10−43.2 × 10−61.38 (1.20–1.58)
rs1411766/rs1741285813q109.1No geneA(G)/G(A)0.310.398.5 × 10−40.320.406.4 × 10−41.8 × 10−61.41 (1.23–1.63)
rs6492208/rs2391777§13q109.1No geneT(C)/G(A)0.550.628.7 × 10−30.560.651.9 × 10−46.1 × 10−61.37 (1.20–1.59)
rs798984813q109.1No geneA(G)0.490.562.0 × 10−30.500.571.1 × 10−37.0 × 10−61.37 (1.19–1.56)
rs952144513q109.1No geneA(C)0.470.542.1 × 10−30.470.554.2 × 10−42.9 × 10−61.38 (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).