Table 2.
The top 61 associated SNPs from genotyping of Wake Forest non-diabetic nephropathy cases and non-nephropathy controls
| Marker | CHR | Nearest Gene | MAF cases | MAF controls | HWE controls | Lowest p-value | Model | OR (95% CI) | FDR best p-value |
|---|---|---|---|---|---|---|---|---|---|
| rs2239785 | 22q12.3 | APOL1 | 0.209 | 0.376 | 0.753 | 5.91E-24 | Dom | 0.33 (0.27–0.41) | 5.35E-21 |
| rs136148 | 22q12.3 | APOL1 | 0.093 | 0.148 | 0.660 | 1.13E-07 | Add | 0.54 (0.43–0.68) | 5.13E-05 |
| rs1573708 | 22q12.3 | 2.0 kb from RBM9 | 0.052 | 0.106 | 0.437 | 2.64E-06 | Dom | 0.49 (0.36–0.66) | 7.95E-04 |
| rs4820237 | 22q12.3 | FOXRED2 | 0.169 | 0.241 | 0.190 | 6.94E-06 | Add | 0.66 (0.55–0.79) | 0.002 |
| rs6000197 | 22q12.3 | 2.416 kb from APOL4 | 0.370 | 0.430 | 0.598 | 7.98E-05 | Dom | 0.65 (0.53–0.81) | 0.014 |
| rs379489 | 1q31.3 | CFH | 0.243 | 0.295 | 0.790 | 2.05E-04 | Add | 0.73 (0.62–0.86) | 0.031 |
| rs5995255 | 22q12.3 | APOL4 | 0.371 | 0.425 | 0.940 | 2.69E-04 | Dom | 0.67 (0.54–0.83) | 0.035 |
| rs713969 | 22q12.3 | 54.45 kb from HMGXB4 | 0.147 | 0.208 | 0.911 | 3.61E-04 | Add | 0.71 (0.58–0.86) | 0.041 |
| rs12487085 | 3p12.3 | 49.502 kb from ROBO2 | 0.492 | 0.421 | 0.363 | 5.48E-04 | Add | 1.29 (1.12–1.50) | 0.055 |
| rs738518 | 22q12.3 | 20.898 kb from CACNG2 | 0.417 | 0.462 | 0.054 | 7.92E-04 | Rec | 0.64 (0.50–0.83) | 0.072 |
| rs4907110 | 1p22.3 | 12.37 kb from LPAR3 | 0.463 | 0.516 | 0.089 | 0.001 | Rec | 0.68 (0.53–0.86) | 0.093 |
| rs3798696 | 6p24.3 | TFAP2A | 0.068 | 0.100 | 0.148 | 0.001 | Add | 0.65 (0.50–0.84) | 0.090 |
| rs6656763 | 1p31.3 | L1TD1 | 0.265 | 0.314 | 0.732 | 0.001 | Add | 0.77 (0.65–0.90) | 0.091 |
| rs4412 | 22q12.1 | 480.62 kb from MN1 | 0.091 | 0.135 | 0.010 | 0.001 | Add | 0.69 (0.55–0.87) | 0.087 |
| rs5998876 | 22q12.3 | LARGE | 0.271 | 0.329 | 0.132 | 0.002 | Add | 0.78 (0.67–0.91) | 0.107 |
| rs11015914 | 10p12.1 | 50.13 kb from MKX | 0.151 | 0.113 | 0.714 | 0.002 | Dom | 1.46 (1.15–1.85) | 0.102 |
| rs5756069 | 22q12.3 | 24.227 kb from RBM9 | 0.202 | 0.269 | 0.573 | 0.002 | Add | 0.76 (0.65–0.91) | 0.108 |
| rs178139 | 18q23 | 35.195 kb from MBP | 0.171 | 0.138 | 0.877 | 0.002 | Dom | 1.42 (1.13–1.78) | 0.113 |
| rs9505192 | 6p25.3 | 99.875 kb from EXOC2 | 0.191 | 0.242 | 0.763 | 0.002 | Add | 0.76 (0.64–0.91) | 0.111 |
| rs551927 | 20p12.2 | LOC100131208 | 0.405 | 0.460 | 0.603 | 0.002 | Add | 0.80 (0.69–0.92) | 0.108 |
| rs1549020 | 2q24.2 | KCNH7 | 0.314 | 0.280 | 0.119 | 0.002 | Dom | 1.38 (1.12–1.69) | 0.104 |
| rs6007220 | 22q13.31 | 38.087 kb from PRRS | 0.207 | 0.263 | 0.046 | 0.002 | Add | 0.77 (0.65–0.91) | 0.102 |
| rs7079133 | 10q21.1 | PCDH15 | 0.294 | 0.339 | 0.680 | 0.003 | Add | 0.79 (0.68–0.92) | 0.101 |
| rs9626698 | 22q13.31 | 23.69 kb from TBC1D22A | 0.359 | 0.400 | 0.000 | 0.003 | Rec | 0.66 (0.50–0.86) | 0.101 |
| rs1355652 | 10q21.1 | None within 500 kb | 0.312 | 0.278 | 0.043 | 0.003 | Dom | 1.36 (1.11–1.67) | 0.102 |
| rs9540221 | 10q21.1 | None within 500 kb | 0.222 | 0.275 | 0.711 | 0.003 | Add | 0.77 (0.65–0.91) | 0.100 |
| rs238973 | 21q21.1 | C21orf34 | 0.275 | 0.326 | 0.401 | 0.003 | Dom | 0.73 (0.60–0.90) | 0.098 |
| rs6118591 | 20p12.2 | PLCB4 | 0.383 | 0.358 | 0.054 | 0.003 | Dom | 1.37 (1.11–1.69) | 0.097 |
| rs727852 | 10q24.1 | BLNK | 0.181 | 0.235 | 0.918 | 0.003 | Add | 0.76 (0.64–0.91) | 0.102 |
| rs2826366 | 21q21.1 | 78.329 kb from NCAM2 | 0.368 | 0.329 | 0.209 | 0.003 | Dom | 1.36 (1.11–1.67) | 0.100 |
| rs17093 | 11p11.2 | 45.614 kb from LOC221122 | 0.227 | 0.185 | 1 | 0.004 | Add | 1.30 (1.09–1.56) | 0.102 |
| rs5998705 | 22q12.3 | 37.33 kb from SYN3 | 0.466 | 0.408 | 0.702 | 0.004 | Add | 1.24 (1.07–1.44) | 0.099 |
| rs930493 | 2p16.1 | FLJ42562 | 0.215 | 0.267 | 0.706 | 0.004 | Add | 0.78 (0.65–0.92) | 0.113 |
| rs12651295 | 4q13.2 | 22.24 kb from UGT2A3 | 0.268 | 0.286 | 0.005 | 0.004 | Dom | 0.74 (0.60–0.91) | 0.111 |
| rs329134 | 3q22.3 | 2.06 kb from CLDN18 | 0.123 | 0.166 | 0.79 | 0.004 | Add | 0.74 (0.60–0.91) | 0.108 |
| rs16854341 | 1q25.2 | NPHS2 | 0.149 | 0.172 | 0.603 | 0.004 | Dom | 0.72(0.58–0.90) | 0.105 |
| rs1532921 | 16p13.3 | A2BP1 | 0.275 | 0.233 | 0.68 | 0.004 | Dom | 1.35(1.10–1.65) | 0.108 |
| rs852549 | 12p12.2 | 2.237 kb from SLCO1B1 | 0.287 | 0.238 | 0.308 | 0.005 | Add | 1.27(1.08–1.50) | 0.111 |
| rs10515944 | 2q33.2 | CD28 | 0.152 | 0.118 | 0.724 | 0.005 | Add | 1.36(1.10–1.68) | 0.110 |
| rs1046889 | 17q25.3 | FN3KRP | 0.358 | 0.315 | 0.231 | 0.005 | Dom | 1.34(1.09–1.64) | 0.119 |
| rs11071959 | 15q23 | MAP2K5 | 0.391 | 0.416 | 0.698 | 0.005 | Dom | 0.74(0.60–0.91) | 0.119 |
| rs3935962 | 15 | 302.8 kb from RORA | 0.349 | 0.368 | 0.002 | 0.006 | Rec | 0.66(0.49–0.88) | 0.119 |
| rs715541 | 22q12.3 | 17.196 kb from CACNG2 | 0.33 | 0.383 | 0.389 | 0.006 | Add | 0.81(0.70–0.94) | 0.117 |
| rs11649200 | 15q22.2 | MLYCD | 0.373 | 0.413 | 0.939 | 0.006 | Add | 0.81(0.70–0.94) | 0.115 |
| rs401681 | 5p15.33 | CLPTM1L | 0.379 | 0.424 | 0.13 | 0.006 | Dom | 0.74(0.60–0.92) | 0.113 |
| rs10483956 | 14q31.1 | None within 500 kb | 0.144 | 0.179 | 1 | 0.006 | Add | 0.76(0.62–0.92) | 0.111 |
| rs6085252 | 20p12.3 | 35.988 kb from C20orf196 | 0.22 | 0.257 | 0.847 | 0.006 | Add | 0.79(0.66–0.93) | 0.113 |
| rs5003374 | 10q21.1 | PCDH15 | 0.321 | 0.374 | 0.049 | 0.006 | Add | 0.81(0.70–0.94) | 0.118 |
| rs6602318 | 10p14 | 435.907 kb from GATA3 | 0.469 | 0.526 | 0.657 | 0.007 | Add | 0.82(0.71–0.95) | 0.123 |
| rs9318258 | 13q22.1 | 234.83 kb from KLF12 | 0.421 | 0.459 | 0.824 | 0.007 | Add | 0.82(0.71–0.95) | 0.126 |
| rs10062080 | 5q32 | AFAP1L1 | 0.396 | 0.38 | 0.034 | 0.007 | Rec | 1.5(1.12–2.00) | 0.125 |
| rs9533534 | 13q14.11 | ENOX1 | 0.429 | 0.375 | 0.813 | 0.007 | Add | 1.22(1.06–1.42) | 0.123 |
| rs335555 | 1q41 | 51.946 kb from CENPF | 0.328 | 0.288 | 0.279 | 0.007 | Dom | 1.32(1.08–1.62) | 0.127 |
| rs268529 | 5p15.31 | SEMA5A | 0.416 | 0.45 | 0.03 | 0.008 | Dom | 0.74(0.60–0.92) | 0.128 |
| rs1517320 | 2q24.3 | STK39 | 0.234 | 0.203 | 0.209 | 0.008 | Dom | 1.33(1.08–1.64) | 0.133 |
| rs243034 | 2p16.1 | 75.408 kb from BCL11A | 0.41 | 0.451 | 0.823 | 0.008 | Add | 0.82(0.71–0.95) | 0.136 |
| rs10491542 | 9q21.32 | 130.013 kb from RASEF | 0.315 | 0.278 | 0.168 | 0.009 | Dom | 1.31(1.07–1.61) | 0.147 |
| rs10121793 | 9q21.32 | 129.508 kb from RASEF | 0.315 | 0.278 | 0.168 | 0.009 | Dom | 1.31(1.07–1.61) | 0.144 |
| rs7710366 | 5q22.3 | KCNN2 | 0.168 | 0.205 | 1 | 0.009 | Add | 0.78(0.65–0.94) | 0.144 |
| rs2029099 | 2p24.3 | 375.892 kb from FAM84A | 0.374 | 0.394 | 0.025 | 0.009 | Dom | 0.76(0.61–0.93) | 0.142 |
| rs7021144 | 9q34.13 | FLJ46082 | 0.233 | 0.257 | 0.081 | 0.01 | Dom | 0.76(0.62–0.94) | 0.148 |
Note: Associated SNPs are those with p <0.01; genotyping is by GoldenGate 1536-plex chip. The lowest p-value is reported with the 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, FDR = false discovery rate; kb, kilobase