Table 5.
Estimates (D′, r2 and p values) of linkage disequilibrium (LD) between pairs of SLC2A1 variants.
| Variant | LD | rs2297976 | rs710221 | rs2086856 | rs12130264 | rs841847 | rs841853 | rs3729548 | rs841855 | rs3768029 | rs12071418 | rs3820549 | rs3820546 | rs11537641 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs12407920 | D′ | 0.99 (0.99) | 1.00 (0.99) | 1.00 (1.00) | 0.04 (0.59) | 0.31 (0.49) | 0.89 (0.83) | 0.85 (0.89) | 0.99 (0.99) | 0.04 (0.22) | 0.04 (1.00) | 0.19 (0.65) | 0.41 (0.57) | 0.69 (0.99) |
| r2 | 0.03 (0.02) | 0.09 (0.05) | 0.21 (0.15) | 0.00 (0.00) | 0.02 (0.06) | 0.16 (0.12) | 0.05 (0.05) | 0.03 (0.01) | 0.00 (0.00) | 0.00 (0.00) | 0.00 (0.01) | 0.02 (0.02) | 0.01 (0.02) | |
| p | .03 (.09) | <.01 | <.01 | .18 (.29) | .1 (<.01) | <.01 | .12 (<.01) | .45 (.15) | .26 (.29) | 1.00 (.18) | .40 (.14) | .20 (.01) | .28 (.06) | |
| rs2297976 | D′ | – | 1.00 (1.00) | 0.99 (0.99) | 1.00 (0.99) | 0.76 (0.63) | 0.77 (0.64) | 0.87 (0.97) | 0.99 (0.53) | 0.90 (0.84) | 0.58 (0.80) | 0.65 (0.10) | 0.04 (0.24) | 0.17 (0.04) |
| r2 | – | 0.35 (0.33) | 0.13 (0.11) | 0.01 (0.02) | 0.30 (0.32) | 0.24 (0.25) | 0.12 (0.19) | 0.05 (0.01) | 0.17 (0.18) | 0.01 (0.04) | 0.04 (0.01) | 0.00 (0.01) | 0.00 (0.00) | |
| p | – | <.01 | <.01 | <.01 (.09) | <.01 | <.01 | <.01 | .26 (.80 | <.01 | .38 (.02) | .19 (.61) | .45 (.30) | .97 (.21) | |
| rs710221 | D′ | – | – | 0.38 (0.51) | 1.00 (0.99) | 0.18 (0.26) | 0.09 (0.21) | 0.88 (0.88) | 0.85 (0.93) | 0.76 (0.66) | 0.26 (0.99) | 0.31 (0.59) | 0.42 (0.43) | 0.89 (0.87) |
| r2 | – | – | 0.10 (0.16) | 0.04 (0.05) | 0.02 (0.03) | 0.00 (0.02) | 0.37 (0.49) | 0.21 (0.21) | 0.35 (0.32) | 0.00 (0.02) | 0.05 (0.19) | 0.11 (0.12) | 0.21 (0.25) | |
| p | – | – | <.01 | <.01 | .38 (.04) | .68 (.13) | <.01 | <.01 | <.01 | .73 (.09) | .02 (<.01) | <.01 | <.01 | |
| rs2086856 | D′ | – | – | – | 0.99 (0.99) | 0.47 (0.29) | 0.13 (0.05) | 0.81 (0.79) | 0.85 (0.85) | 0.43 (0.46) | 0.04 (0.63) | 0.40 (0.37) | 0.58 (0.65) | 0.70 (0.54) |
| r2 | – | – | – | 0.03 (0.03) | 0.05 (0.01) | 0.00 (0.00) | 0.21 (0.24) | 0.30 (0.31) | 0.08 (0.10) | 0.00 (0.00) | 0.12 (0.12) | 0.15 (0.18) | 0.19 (0.16) | |
| p | – | – | – | .04 (.28) | .02 (.03) | .48 (.47) | <.01 | <.01 | .01 (<.01) | .57 (.89) | <.01 | <.01 | <.01 | |
| rs12130264 | D′ | – | – | – | – | 0.16 (0.99) | 0.32 (0.81) | 0.72 (0.91) | 0.97 (0.99) | 0.47 (0.45) | 1.00 (0.99) | 0.99 (0.84) | 0.26 (0.72) | 0.96 (0.99) |
| r2 | – | – | – | – | 0.00 (0.02) | 0.00 (0.02) | 0.04 (0.07) | 0.01 (0.01) | 0.01 (0.01) | 0.00 (0.00) | 0.02 (0.02) | 0.01 (0.04) | 0.01 (0.02) | |
| p | – | – | – | – | .10 (.13) | .06 (.07) | <.01 | .28 (.65) | .12 (.09) | .17 (.86) | .10 (.03) | .01 (.02) | .22 (.23) | |
| rs841847 | D′ | – | – | – | – | – | 1.00 (1.00) | 1.00 (1.00) | 0.99 (0.99) | 0.93 (0.95) | 1.00 (0.96) | 0.33 (0.35) | 0.24 (0.40) | 0.81 (0.81) |
| r2 | – | – | – | – | – | 0.78 (0.74) | 0.30 (0.26) | 0.10 (0.06) | 0.34 (0.28) | 0.01 (0.01) | 0.02 (0.02) | 0.02 (0.04) | 0.06 (0.05) | |
| p | – | – | – | – | – | <.01 | <.01 | <.01 (.01) | <.01 | .25 (.37) | .23 (.18) | .21 (.00) | .02 (.00) | |
| rs841853 | D′ | – | – | – | – | – | – | 1.00 (1.00) | 0.99 (0.99) | 0.69 (0.63) | 0.99 (0.99) | 0.19 (0.13) | 0.29 (0.39) | 0.85 (0.80) |
| r2 | – | – | – | – | – | – | 0.39 (0.35) | 0.13 ((0.08) | 0.24 (0.16) | 0.01 (0.01) | 0.01 (0.00) | 0.04 (0.05) | 0.09 (0.06) | |
| p | – | – | – | – | – | – | <.01 | <.01 | <.01 | .36 (.38) | .29 (.46) | .06 (<.01) | <.01 | |
| rs3729548 | D′ | – | – | – | – | – | – | – | 1.00 (1.00) | 0.94 (0.84) | 0.04 (0.99) | 0.71 (0.75) | 0.63 (0.56) | 0.79 (0.89) |
| r2 | – | – | – | – | – | – | – | 0.13 (0.16) | 0.66 (0.61) | 0.00 (0.01) | 0.12 (0.19) | 0.29 (0.29 | 0.08 (0.17 | |
| p | – | – | – | – | – | – | – | <.01 | <.01 | .65 (.29) | <.01 | <.01 | <.01 | |
| rs841855 | D′ | – | – | – | – | – | – | – | – | 1.00 (1.00) | 0.59 (0.08) | 0.78 (0.94) | 0.72 (0.91) | 0.80 (0.85) |
| r2 | – | – | – | – | – | – | – | – | 0.17 (0.19) | 0.00 (0.00) | 0.34 (0.42) | 0.09 (0.14) | 0.60 (0.59) | |
| p | – | – | – | – | – | – | – | – | <.01 | 1.00 (.84) | <.01 | <.01 | <.01 | |
| rs3768029 | D′ | – | – | – | – | – | – | – | – | – | 0.91 (0.99) | 0.52 (0.57) | 0.57 (0.59) | 0.84 (0.88) |
| r2 | – | – | – | – | – | – | – | – | – | 0.01 (0.02) | 0.09 (0.13) | 0.30 (0.32) | 0.12 (0.18) | |
| p | – | – | – | – | – | – | – | – | – | .84 (.13) | <.01 | <.01 | <.01 | |
| rs12071418 | D′ | – | – | – | – | – | – | – | – | – | – | 0.99 (1.00) | 0.96 (0.99) | 0.23 (0.81) |
| r2 | – | – | – | – | – | – | – | – | – | – | 0.02 (0.04) | 0.01 (0.02) | <0.01 (0.05) | |
| p | – | – | – | – | – | – | – | – | – | – | .13 (.01) | .17 (.19) | .59 (.01) | |
| rs3820549 | D′ | – | – | – | – | – | – | – | – | – | – | – | 1.00 (1.00) | 0.93 (0.95) |
| r2 | – | – | – | – | – | – | – | – | – | – | – | 0.33 (0.37) | 0.45 (0.54) | |
| p | – | – | – | – | – | – | – | – | – | – | – | <.01 | <.01 | |
| rs3820546 | D′ | – | – | – | – | – | – | – | – | – | – | – | – | 1.00 (1.00) |
| r2 | – | – | – | – | – | – | – | – | – | – | – | – | 0.17 (0.22) | |
| p | – | – | – | – | – | – | – | – | – | – | – | – | <.01 |
Estimates (D, r2 and p values) of linkage disequilibrium (LD) between pairs of SLC2A1 variants (SNPs) in patients with type 2 diabetes leading to nephropathy (cases, DN) and in healthy controls (HC). LD estimates of HC are shown in brackets.