Table 2.
Variants identified from sequencing the exons and the promoter region of ACTN4. Position is shown relative to the Hg19 assembly of the human genome (column 3) and the first nucleotide of exon 1 (column 4). Samples highlighted in grey were only genotyped on 96 cases and 96 controls from Set 1, whereas the remaining SNPs were identified by sequencing and subsequently genotyped in the entire Set 1 samples, 296 non-DM ESRD cases and 358 non-nephropathy controls. Total alleles shows the number of copies of the minor allele present in cases and controls. MAF = minor allele frequencies
| Total Alleles | MAF | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Variant | Location | Hg19 assembly |
Position (exon 1) |
Alleles | Control | Case | Control | Case | |
| C-2752T | promoter | 39135575 | −2752 | C/T | 2 | 0 | 0.010 | 0.000 | |
| rs12052046 | promoter | 39135874 | −2453 | C/T | 42 | 29 | 0.067 | 0.053 | |
| A-2318T | promoter | 39136009 | −2318 | A/T | 28 | 27 | 0.044 | 0.052 | |
| A-2243G | promoter | 39126084 | −2243 | A/G | 8 | 5 | 0.013 | 0.010 | |
| C-2222T | promoter | 39136105 | −2222 | C/T | 47 | 30 | 0.075 | 0.058 | |
| G-1969A | promoter | 39136358 | −1969 | G/A | 4 | 7 | 0.006 | 0.015 | |
| C-1962T | promoter | 39136365 | −1962 | C/T | 29 | 27 | 0.046 | 0.058 | |
| C-1921T | promoter | 39136406 | −1921 | C/T | 1 | 2 | 0.002 | 0.004 | |
| G-1846A | promoter | 39136481 | −1846 | G/A | 4 | 0 | 0.006 | 0.000 | |
| rs10404257 | promoter | 39136486 | −1841 | G/A | 202 | 125 | 0.320 | 0.264 | |
| C-1547T | promoter | 39136486 | −1547 | C/T | 6 | 4 | 0.009 | 0.008 | |
| C-1291T | promoter | 39136780 | −1291 | C/T | 1 | 2 | 0.002 | 0.004 | |
| G-1201A | promoter | 39137036 | −1201 | G/A | 17 | 5 | 0.027 | 0.014 | |
| C-993T | promoter | 39137126 | −993 | C/T | 3 | 2 | 0.005 | 0.004 | |
| C-850T | promoter | 39137334 | −850 | C/T | 24 | 28 | 0.039 | 0.053 | |
| G-655A | promoter | 39137477 | −655 | G/A | 24 | 28 | 0.039 | 0.053 | |
| G-197C | promoter | 39137672 | −197 | G/C | 3 | 0 | 0.005 | 0.000 | |
| G-181A | promoter | 39138130 | −181 | G/A | 1 | 1 | 0.002 | 0.002 | |
| A-163C | promoter | 39138146 | −163 | A/C | 11 | 11 | 0.019 | 0.026 | |
| A-98C | promoter | 39138164 | −98 | A/C | 3 | 8 | 0.005 | 0.021 | |
| T-85A | promoter | 39138229 | −85 | T/A | 3 | 0 | 0.005 | 0.000 | |
| C52997T | exon 2 | 39191323 | 52997 | C/T | 12 | 14 | 0.019 | 0.026 | Synonymous |
| rs2112649 | intron 2 | 39191383 | 53059 | G/C/A | 265 | 252 | 0.418 | 0.481 | |
| G53218A | intron 2 | 39191544 | 53218 | G/A | 47 | 25 | 0.073 | 0.048 | |
| rs2287728 | intron 3 | 39195558 | 57232 | C/T | 29 | 28 | 0.045 | 0.055 | |
| G57359A | intron 4 | 39195685 | 57359 | G/A | 2 | 0 | 0.003 | 0.000 | |
| rs2368475 | intron 4 | 39195735 | 57409 | C/T | 12 | 14 | 0.019 | 0.026 | |
| C58279T | intron 4 | 39196605 | 58279 | C/T | 0 | 1 | 0.000 | 0.005 | |
| A58329T | intron 4 | 39196655 | 58329 | A/T | 0 | 1 | 0.000 | 0.002 | |
| C58409T | exon 5 | 39196735 | 58409 | C/T | 6 | 3 | 0.009 | 0.006 | Non-synonymous pro-leu |
| rs11553600 | exon 5 | 39196736 | 58410 | G/A | 51 | 33 | 0.082 | 0.063 | synonymous |
| rs3745859 | exon 5 | 39196745 | 58419 | C/T | 177 | 118 | 0.276 | 0.227 | synonymous |
| G61654T | intron 6 | 39199980 | 61654 | G/T | 64 | 58 | 0.099 | 0.112 | |
| C61663G | intron 6 | 39199989 | 61663 | C/G | 0 | 1 | 0.000 | 0.005 | |
| G61672A | intron 6 | 39199998 | 61672 | G/A | 20 | 21 | 0.111 | 0.112 | |
| G61675T | intron 6 | 39200001 | 61675 | G/T | 20 | 21 | 0.111 | 0.112 | |
| G62427A | intron 7 | 39200753 | 62427 | G/A | 3 | 3 | 0.005 | 0.006 | |
| C62517T | intron 7 | 39200843 | 62517 | C/T | 89 | 41 | 0.138 | 0.075 | |
| T62682G | intron 8 | 39201008 | 62682 | T/G | 0 | 1 | 0.000 | 0.002 | |
| G62719A | intron 8 | 39201045 | 62719 | G/A | 1 | 3 | 0.002 | 0.006 | |
| G62777A | intron 8 | 39201103 | 62777 | G/A | 3 | 3 | 0.005 | 0.006 | |
| T66655A | intron 8 | 39204981 | 66655 | T/A | 2 | 0 | 0.003 | 0.000 | |
| rs2306196 | intron 8 | 39205015 | 66689 | C/T | 9 | 7 | 0.014 | 0.014 | |
| G69271A | intron 9 | 39207597 | 69271 | G/A | 1 | 0 | 0.002 | 0.000 | |
| C70315A | exon 11 | 39208641 | 70315 | C/A | 4 | 5 | 0.006 | 0.009 | synonymous |
| C70387T | exon 11 | 39208713 | 70387 | C/T | 1 | 2 | 0.002 | 0.004 | synonymous |
| rs7248577 | intron 11 | 39208795 | 70469 | C/T | 39 | 27 | 0.064 | 0.052 | |
| C73985T | exon 12 | 39212311 | 73985 | C/T | 1 | 0 | 0.002 | 0.000 | synonymous |
| C74066T | intron 12 | 39212392 | 74066 | C/T | 53 | 29 | 0.083 | 0.057 | |
| rs2306197 | intron 12 | 39212400 | 74074 | C/T | 14 | 11 | 0.024 | 0.021 | |
| C76085T | intron 13 | 39214411 | 76085 | C/T | 28 | 30 | 0.048 | 0.056 | |
| G76310A | exon 14 | 39214636 | 76310 | G/A | 1 | 1 | 0.005 | 0.005 | synonymous |
| C76548T | exon 15 | 39214874 | 76548 | C/T | 4 | 6 | 0.006 | 0.011 | synonymous |
| rs12986337 | exon 16 | 39215172 | 76846 | T/C | 27 | 29 | 0.043 | 0.055 | synonymous |
| G76867A | exon 16 | 39215193 | 76867 | G/A | 1 | 2 | 0.002 | 0.004 | synonymous |
| rs3786851 | intron 16 | 39215333 | 77007 | C/T | 156 | 108 | 0.244 | 0.213 | |
| G77865A | intron 16 | 39216191 | 77865 | G/A | 31 | 31 | 0.050 | 0.057 | |
| rs12979947 | intron 16 | 39216203 | 77877 | T/C | 30 | 28 | 0.047 | 0.055 | |
| G77942A | intron 16 | 39216268 | 77942 | G/A | 3 | 2 | 0.005 | 0.004 | |
| C78043T | exon 17 | 39216369 | 78043 | C/T | 3 | 3 | 0.005 | 0.006 | synonymous |
| rs1105759 | intron 17 | 39217507 | 79181 | G/A | 37 | 31 | 0.060 | 0.061 | |
| G79206A | intron 17 | 39217532 | 79206 | G/A | 0 | 1 | 0.000 | 0.002 | |
| C79225T | intron 17 | 39217551 | 79225 | C/T | 6 | 4 | 0.010 | 0.008 | |
| C80196T | intron 18 | 39218522 | 80196 | C/T | 2 | 0 | 0.003 | 0.000 | |
| rs12981131 | intron 19 | 39218694 | 80368 | A/G | 48 | 35 | 0.076 | 0.067 | |
| rs12974733 | intron 19 | 39219560 | 81234 | G/T | 30 | 30 | 0.046 | 0.055 | |
| T82862A | 3' UTR | 39221188 | 82862 | T/A | 5 | 9 | 0.008 | 0.017 | |