Table 2.
Results From the JAG Test in EAs
| Gene | No. of SNPs | No. of effective SNPsa | COPDGene Pemp | SAGE Pemp | MESA Pemp | CADD-GADD Pemp | Combined Pemp | FDR corrected P |
|---|---|---|---|---|---|---|---|---|
| CPD | ||||||||
| CHRNA3 | 102 | 2 | .0001 | .128 | .209 | .434 | .0001 | .013 |
| CHRNA5 | 29 | 1 | .0001 | .304 | .348 | .620 | .0001 | .013 |
| CHRNB4 | 17 | 3b | .0001 | .639 | .742 | .212 | .0001 | .013 |
| NCAM1 | 402 | 5c | .006 | .154 | .721 | .337 | .004 | .193 |
| CHRNE | 79 | 3 | .004 | .182 | .924 | .800 | .005 | .193 |
| DNAJA3 | 111 | 2 | .004 | .527 | .900 | .472 | .007 | .258 |
| IQGAP1 | 246 | 2 | .010 | .898 | .268 | .813 | .022 | .556 |
| MAPRE1 | 148 | 5 | .015 | .829 | .784 | .196 | .025 | .601 |
| UNC50 | 53 | 1 | .043 | .181 | .514 | .249 | .029 | .644 |
| CHRNB1 | 63 | 3 | .038 | .216 | .878 | .531 | .039 | .729 |
| EPHA4 | 212 | 5 | .133 | .073 | .238 | .105 | .064 | .782 |
| NRXN1 | 2433 | 22d | .022 | .992 | .516 | .493 | .064 | .782 |
| LRP4 | 106 | 3e | .089 | .178 | .599 | .441 | .070 | .782 |
| CRELD2 | 127 | 1f | .097 | .009 | .638 | .991 | .071 | .782 |
| CAMK2A | 89 | 5 | .178 | .059 | .034 | .174 | .075 | .782 |
| ITGA7 | 41 | 1 | .075 | .451 | .725 | .304 | .078 | .782 |
| APC | 231 | 2 | .061 | .245 | .876 | .920 | .079 | .782 |
| FTND | ||||||||
| CHRNA3 | 102 | 2 | .003 | .028 | NA | NA | .00042 | .042 |
| CHRNA5 | 29 | 1 | .012 | .060 | NA | NA | .003 | .193 |
| CHRNB4 | 17 | 2 | .012 | .080 | NA | NA | .004 | .193 |
| CHRNA9 | 239 | 4 | .009 | .221 | NA | NA | .008 | .280 |
| DNAJA3 | 111 | 2 | .008 | .338 | NA | NA | .012 | .381 |
| CHRNE | 79 | 3 | .218 | .004 | NA | NA | .017 | .482 |
| EPHA4 | 212 | 5 | .116 | .112 | NA | NA | .048 | .782 |
| CAMK2G | 61 | 2 | .008 | .794 | NA | NA | .056 | .782 |
| SVEP1 | 598 | 13 | .263 | .035 | NA | NA | .064 | .782 |
| CAMK2A | 89 | 5 | .368 | .013 | NA | NA | .067 | .782 |
| ERBB2 | 64 | 1 | .049 | .458 | NA | NA | .075 | .782 |
| RAPSN | 65 | 2 | .253 | .056 | NA | NA | .077 | .782 |
| CRELD2 | 127 | 1 | .237 | .073 | NA | NA | .081 | .782 |
| LRP4 | 106 | 3g | .106 | .269 | NA | NA | .084 | .782 |
The P-value is shown for each study as well as the combined P-value for genes associated with CPD or FTND at P < .1.
aThe number of signals tested in the gene in each study (unless otherwise noted) as calculated by JAG.
bOnly two signals calculated in the COPDGene sample.
cSix signals calculated in the COPDGene sample.
dTwenty-three signals calculated in the CADD-GADD and MESA samples.
eTwo signals calculated in the SAGE sample.
fTwo signals calculated in the MESA sample.
gTwo signals calculated in SAGE.