Table 5.
The top 46 SNPs from genotyping of Wake Forest non-diabetic nephropathy cases and non-nephropathy controls, adjusted for APOL1 G1/G2 compound risk
| Marker | CHR | Nearest Gene | MAF cases | MAF controls | HWE controls | Lowest p | Model | OR (95% CI) |
|---|---|---|---|---|---|---|---|---|
| rs1355652 | 11q14.1 | None | 0.317 | 0.2631 | 0.022 | 1.35E-04 | Dom | 1.58(1.25–2.00) |
| rs11191727 | 10q24.33 | NEURL | 0.101 | 0.1396 | 0.723 | 3.29E-04 | Dom | 0.59(0.45–0.79) |
| rs379489 | 1q31.3 | CFH | 0.244 | 0.3009 | 0.762 | 4.26E-04 | Add | 0.72(0.60–0.86) |
| rs9318258 | 13q22.1 | 234.83 kb from KLF12 | 0.419 | 0.4703 | 0.799 | 7.02E-04 | Add | 0.75(0.63–0.89) |
| rs10483956 | 14q31.1 | None | 0.138 | 0.1856 | 1 | 7.41E-04 | Add | 0.68(0.54–0.85) |
| rs3798696 | 6p24.3 | TFAP2A | 0.067 | 0.0982 | 0.031 | 7.89E-04 | Add | 0.59(0.44–0.81) |
| rs9540221 | 13q21.31 | None | 0.22 | 0.2829 | 0.676 | 1.10E-03 | Add | 0.72(0.59–0.88) |
| rs4907110 | 1p22.3 | 12.37 kb from LPAR3 | 0.463 | 0.5288 | 0.05 | 1.13E-03 | Rec | 0.64(0.49–0.84) |
| rs852549 | 12p12.2 | 2.237 kb from SLCO1B1 | 0.291 | 0.2369 | 0.557 | 1.54E-03 | Add | 1.36(1.13–1.65) |
| rs335555 | 1q41 | 51.946 kb from CENPF | 0.332 | 0.2919 | 0.081 | 1.63E-03 | Dom | 1.46(1.15–1.85) |
| rs1500474 | 2q37.1 | LOC339766 | 0.4 | 0.4368 | 0.167 | 1.75E-03 | Rec | 0.61(0.45–0.83) |
| rs321601 | 17q12 | LOC100131387 | 0.505 | 0.4649 | 0.006 | 1.92E-03 | Dom | 1.52(1.17–1.97) |
| rs329134 | 3q22.3 | 2.06 kb from CLDN18 | 0.119 | 0.1712 | 0.453 | 1.99E-03 | Add | 0.69(0.55–0.87) |
| rs7021144 | 9q34.13 | FLJ46082 | 0.23 | 0.2613 | 0.227 | 2.14E-03 | Dom | 0.69(0.54–0.87) |
| rs1953232 | 14q23.3 | MAX | 0.184 | 0.2374 | 0.29 | 2.20E-03 | Add | 0.73(0.60–0.89) |
| rs738518 | 22q12.3 | 20.898 kb from CACNG2 | 0.419 | 0.4685 | 0.011 | 2.46E-03 | Rec | 0.64(0.48–0.85) |
| rs4899920 | 14q31.3 | 230.354 kb from GALC | 0.203 | 0.1532 | 0.326 | 2.52E-03 | Dom | 1.48(1.15–1.90) |
| rs2239785 | 22q12.3 | APOL1 | 0.205 | 0.3807 | 0.472 | 3.63E-03 | Add | 0.74(0.60–0.90) |
| rs6118591 | 20p12.2 | PLCB4 | 0.379 | 0.3523 | 0.009 | 3.53E-03 | Dom | 1.43(1.12–1.81) |
| rs17444393 | 9q21.12 | 8.631 kb from MAMDC2 | 0.197 | 0.2283 | 0.629 | 4.02E-03 | Add | 0.74(0.61–0.91) |
| rs1916141 | 2p16.1 | None | 0.258 | 0.2189 | 0.025 | 4.67E-03 | Dom | 1.41(1.11–1.80) |
| rs719676 | 1p34.2 | LOC100129924 | 0.08 | 0.1072 | 0.823 | 4.90E-03 | Add | 0.66(0.49–0.88) |
| rs16854341 | 1q25.2 | NPHS2 | 0.148 | 0.182 | 0.776 | 5.01E-03 | Add | 0.72(0.58–0.91) |
| rs6756739 | 2p16.2 | None | 0.107 | 0.1459 | 0.398 | 5.16E-03 | Dom | 0.67(0.51–0.89) |
| rs10061706 | 5q21.2 | 25.39 kb from RAB9BP1 | 0.4 | 0.4603 | 0.608 | 5.34E-03 | Add | 0.79(0.67–0.93) |
| rs12651295 | 4q13.2 | 22.24 kb from UGT2A3 | 0.268 | 0.2807 | 0.008 | 5.42E-03 | Dom | 0.72(0.56–0.91) |
| rs1046889 | 17q25.3 | FN3KRP | 0.356 | 0.3207 | 0.08 | 5.63E-03 | Dom | 1.4(1.10–1.77) |
| rs1549020 | 2q24.2 | KCNH7 | 0.31 | 0.2739 | 0.595 | 5.63E-03 | Add | 1.3(1.08–1.56) |
| rs12951391 | 17q24.3 | 205.577 kb from SOX9 | 0.221 | 0.2595 | 0.659 | 5.74E-03 | Add | 0.76(0.62–0.92) |
| rs4695355 | 4p12 | TEC | 0.3441 | 0.3396 | 0.002 | 6.43E-03 | Rec | 0.61(0.43–0.87) |
| rs6602318 | 10p14 | 435.907 kb from GATA3 | 0.466 | 0.5324 | 0.865 | 6.48E-03 | Add | 0.79(0.67–0.94) |
| rs930493 | 2p16.1 | FLJ42562 | 0.2128 | 0.2685 | 1 | 6.75E-03 | Add | 0.76(0.63–0.93) |
| rs1532921 | 16p13.3 | A2BP1 | 0.2737 | 0.2297 | 0.904 | 7.24E-03 | Dom | 1.38(1.09–1.75) |
| rs12530731 | 7q11.23 | 78.954 kb from WBSCR28 | 0.4694 | 0.5253 | 0.67 | 7.64E-03 | Add | 0.80(0.68–0.94 |
| rs1638742 | 7q36.3 | PTPRN2 | 0.1641 | 0.136 | 0.475 | 7.76E-03 | Dom | 1.43(1.10–1.86) |
| rs484019 | 6q14.1 | 184.043 kb from BCKDHB | 0.4102 | 0.3649 | 0.647 | 7.88E-03 | Add | 1.26(1.06–1.50) |
| rs168664331 | 2q36.1 | 43.47 kb from KCNE4 | 0.0739 | 0.0892 | 0.11 | 7.95E-03 | Dom | 0.65(0.47–0.89) |
| rs6500291 | 16q12.1 | LOC100130390 | 0.3171 | 0.2955 | 0.032 | 8.08E-03 | Dom | 1.38(1.09–1.75) |
| rs2826366 | 21q21.1 | 203.498 kb from C21orf131 | 0.3664 | 0.3279 | 0.0206 | 8.67E-03 | Dom | 1.37(1.08–1.74) |
| rs17093 | 11p11.2 | 45.614 kb from LOC221122 | 0.2212 | 0.1829 | 0.478 | 8.73E-03 | Dom | 1.39(1.09–1.78) |
| rs6547194 | 2p12 | 275.59 kb from SNAR-H | 0.4297 | 0.4063 | 0.006 | 8.77E-03 | Rec | 1.54(1.11–2.12) |
| rs1547103 | 6p22.3 | 71.756 kb from RBM24 | 0.4103 | 0.4369 | 0.101 | 8.80E-03 | Dom | 0.71(0.55–0.92) |
| rs11071959 | 15q23 | MAP2KS | 0.393 | 0.4179 | 0.931 | 8.82E-03 | Dom | 0.72(0.56–0.92) |
| rs11193608 | 10q25.1 | None | 0.3939 | 1.3538 | 0.853 | 9.17E-03 | Add | 1.26(1.06–1.50) |
| rs7829952 | 8p22 | 155.564 kb from MSR1 | 0.3314 | 0.2812 | 0.092 | 9.76E-03 | Add | 1.26(1.06–1.51) |
| rs2422245 | 2p14 | 9.197 kb from AFTPH | 0.1555 | 0.2054 | 0.152 | 9.92E-03 | Add | 0.75(0.60–0.93) |
The top 46 SNPs (p <0.01) from the Golden Gate 1536 genotyping of Wake Forest non-diabetic nephropathy cases and non-nephropathy controls, adjusted for APOL1 G1/G2 compound risk. (best p-value reported with most significant genetic model,
CHR = chromosomal location, MAF = Minor allele frequency. HWE = Hardy Weinberg Equilibrium, Dom = dominant model, Add = additive model, Rec = recessive model, OR = odds ratio, CI = confidence interval; kb, kilobase; SNP, single-nucleotide polymorphism