Table 3.
Tests of Association: Principal Component and Bvariate Principal Component Analyses
| SNP | Trait |
Genotypic means [mean ± SD (median)] |
Model-based p values |
|||||
| 1/1 | 1/2 | 2/2 | 2DF | Add | Dom | Rec | ||
| rs2182435* | BMDPC2 | 0.10 ± 0.80 (0.06) | −0.03 ± 0.81 (0.11) | 0.04 ± 1.30 (−0.08) | 0.091 | 0.095 | 0.046 | 0.745 |
| VCPC | 5.22 ± 2.07 (5.42) | 5.20 ± 1.93 (5.48) | 4.84 ± 2.25 (4.49) | 0.802 | 0.512 | 0.544 | 0.675 | |
| BMDPC2 VCPC | 0.093 | 0.069 | 0.038 | 0.912 | ||||
| rs3787380* | BMDPC2 | 0.09 ± 0.81 (0.10) | 0.13 ± 0.83 (0.12) | −0.07 ± 0.73 (−0.11) | 0.007 | 0.330 | 0.406 | 0.007 |
| VCPC | 5.11 ± 2.11 (5.09) | 5.28 ± 2.02 (5.62) | 5.19 ± 2.03 (5.48) | 0.832 | 0.560 | 0.688 | 0.586 | |
| BMDPC2 VCPC | 0.002 | 0.105 | 0.312 | 0.001 | ||||
| rs13037653* | BMDPC2 | 0.09 ± 0.81 (0.06) | 0.05 ± 0.76 (0.12) | 1.06 ± 1.62 (1.06) | 0.044 | 0.680 | 0.424 | 0.024 |
| VCPC | 5.23 ± 2.06 (5.46) | 5.11 ± 1.96 (5.06) | 5.70 ± 4.29 (5.70) | 0.717 | 0.439 | 0.422 | 0.968 | |
| BMDPC2 VCPC | 0.016 | 0.746 | 0.521 | 0.006 | ||||
| rs6070015† | BMDPC2 | 0.09 ± 0.81 (0.09) | 0.02 ± 0.76 (0.03) | NA | 0.977 | 0.831 | 0.831 | 1.000 |
| VCPC | 5.17 ± 2.04 (5.38) | 5.40 ± 2.15 (5.97) | NA | 0.130 | 0.045 | 0.043 | 0.846 | |
| BMDPC2 VCPC | 0.133 | 0.047 | 0.045 | 0.854 | ||||
| rs6064508 | BMDPC2 | 0.12 ± 0.75 (0.07) | 0.05 ± 0.85 (0.07) | 0.10 ± 0.79 (0.06) | 0.897 | 0.680 | 0.805 | 0.653 |
| VCPC | 5.03 ± 2.05 (5.04) | 5.28 ± 2.03 (5.62) | 5.45 ± 2.08 (5.84) | 0.285 | 0.135 | 0.119 | 0.478 | |
| BMDPC2 VCPC | 0.163 | 0.077 | 0.059 | 0.438 | ||||
| rs6123674† | BMDPC2 | 0.14 ± 0.76 (0.08) | 0.06 ± 0.84 (0.10) | 0.05 ± 0.79 (−0.04) | 0.881 | 0.979 | 0.802 | 0.729 |
| VCPC | 5.03 ± 2.02 (5.04) | 5.20 ± 2.05 (5.50) | 5.50 ± 2.06 (5.86) | 0.083 | 0.026 | 0.065 | 0.084 | |
| BMDPC2 VCPC | 0.029 | 0.010 | 0.035 | 0.035 | ||||
| rs6123678† | BMDPC2 | 0.10 ± 0.74 (0.06) | 0.08 ± 0.84 (0.11) | 0.06 ± 0.80 (−0.001) | 0.331 | 0.956 | 0.341 | 0.402 |
| VCPC | 5.00 ± 1.95 (4.96) | 5.15 ± 2.11 (5.40) | 5.47 ± 2.00 (5.91) | 0.031 | 0.009 | 0.061 | 0.021 | |
| BMDPC2 VCPC | 0.014 | 0.018 | 0.135 | 0.008 | ||||
| rs6123679 | BMDPC2 | 0.08 ± 0.81 (0.06) | 0.10 ± 0.72 (0.26) | NA | 0.592 | 0.306 | 0.306 | 1.000 |
| VCPC | 5.21 ± 2.04 (5.40) | 5.07 ± 2.31 (5.69) | NA | 0.940 | 0.724 | 0.724 | 1.000 | |
| BMDPC2 VCPC | 0.805 | 0.511 | 0.511 | 1.000 | ||||
| rs172983* | BMDPC2 | 0.06 ± 0.81 (0.05) | 0.21 ± 0.76 (0.27) | −0.62 ± 0.44 (−0.51) | 0.013 | 0.041 | 0.014 | 0.227 |
| VCPC | 5.21 ± 2.07 (5.39) | 5.20 ± 1.95 (5.48) | 4.26 ± 2.52 (5.04) | 0.576 | 0.954 | 0.757 | 0.352 | |
| BMDPC2 VCPC | 0.008 | 0.069 | 0.021 | 0.086 | ||||
| rs17404303† | BMDPC2 | 0.08 ± 0.79 (0.12) | 0.11 ± 0.82 (0.11) | 0.03 ± 0.79 (−0.08) | 0.356 | 0.220 | 0.538 | 0.156 |
| VCPC | 4.99 ± 2.06 (4.98) | 5.19 ± 2.03 (5.41) | 5.55 ± 2.04 (5.95) | 0.085 | 0.029 | 0.104 | 0.056 | |
| BMDPC2 VCPC | 0.040 | 0.019 | 0.148 | 0.016 | ||||
| rs193044† | BMDPC2 | 0.03 ± 0.76 (−0.06) | 0.12 ± 0.84 (0.13) | 0.09 ± 0.77 (0.13) | 0.962 | 0.899 | 0.809 | 0.945 |
| VCPC | 5.40 ± 2.02 (5.74) | 5.14 ± 2.08 (5.41) | 5.07 ± 1.98 (4.98) | 0.018 | 0.006 | 0.007 | 0.106 | |
| BMDPC2 VCPC | 0.016 | 0.014 | 0.004 | 0.362 | ||||
| rs7273197† | BMDPC2 | 0.09 ± 0.82 (0.12) | 0.11 ± 0.80 (0.09) | −0.11 ± 0.71 (−0.15) | 0.118 | 0.112 | 0.406 | 0.041 |
| VCPC | 5.04 ± 2.05 (4.98) | 5.28 ± 2.02 (5.60) | 5.54 ± 2.11 (6.05) | 0.278 | 0.117 | 0.211 | 0.197 | |
| BMDPC2 VCPC | 0.018 | 0.013 | 0.114 | 0.008 | ||||
| rs6127978 | BMDPC2 | 0.09 ± 0.81 (0.07) | 0.05 ± 0.79 (0.06) | 0.02 ± 0.58 (−0.21) | 0.179 | 0.091 | 0.154 | 0.156 |
| VCPC | 5.25 ± 2.05 (5.42) | 5.08 ± 2.01 (5.29) | 4.57 ± 2.43 (4.33) | 0.620 | 0.513 | 0.407 | 0.726 | |
| BMDPC2 VCPC | 0.132 | 0.080 | 0.098 | 0.202 | ||||
| rs6064517 | BMDPC2 | 0.07 ± 0.80 (0.08) | 0.11 ± 0.79 (0.05) | 0.19 ± 1.28 (−0.18) | 0.786 | 0.559 | 0.638 | 0.558 |
| VCPC | 5.18 ± 2.06 (5.40) | 5.24 ± 2.02 (5.73) | 5.63 ± 1.98 (5.61) | 0.546 | 0.373 | 0.472 | 0.346 | |
| BMDPC2 VCPC | 0.564 | 0.479 | 0.594 | 0.323 | ||||
| rs6127984* | BMDPC2 | 0.13 ± 0.83 (0.12) | 0.06 ± 0.80 (0.06) | −0.06 ± 0.75 (−0.18) | 0.551 | 0.629 | 0.973 | 0.292 |
| VCPC | 5.12 ± 2.01 (5.06) | 5.27 ± 2.10 (5.64) | 5.18 ± 2.02 (5.43) | 0.029 | 0.057 | 0.011 | 0.994 | |
| BMDPC2 VCPC | 0.015 | 0.053 | 0.014 | 0.201 | ||||
| rs6014967 | BMDPC2 | 0.10 ± 0.82 (0.07) | 0.07 ± 0.78 (0.10) | −0.06 ± 0.74 (−0.27) | 0.987 | 0.873 | 0.873 | 0.954 |
| VCPC | 5.25 ± 2.09 (5.52) | 5.15 ± 2.00 (5.24) | 4.62 ± 1.89 (4.68) | 0.638 | 0.893 | 0.839 | 0.390 | |
| BMDPC2 VCPC | 0.765 | 0.635 | 0.800 | 0.471 | ||||
Pearson correlation of BMDPC2 with VCPC = 0.359.
Genetic correlation of BMDPC2 with VCPC = −0.222 ± 0.145; environmental correlation of BMDPC2 with VCPC = 0.387 ± 0.148.
* Significant bivariate PCA lacking graded effect for median result across genotypes.
† Statistically significant opposing result for bivariate PCA across genotypes.
NA, not applicable.