Table 3. Clinico-pathologic analysis of IGAP loci.
| IGAP Paper* | Primary Analysis | Complete Analysis | ||||||||||||
| Type | SNP | GENE | CHR | POS | Major/Minor | MAF | OR | p-value | MAF | OR | p-value | MAF | OR | p-value |
| Known | rs6656401 | CR1 | 1 | 207,692,049 | G/A | 0.197 | 1.18 | 5.7E-24 | 0.197 | 1.16 | 4.00E-02 | 0.197 | 1.00 | 9.80E-01 |
| Known | rs6733839 | BIN1 | 2 | 127,892,810 | C/T | 0.409 | 1.22 | 6.9E-44 | 0.430 | 1.39 | 3.40E-06 | 0.431 | 1.36 | 2.50E-04 |
| Known | rs10948363 | CD2AP | 6 | 47,487,762 | A/G | 0.266 | 1.10 | 5.2E-11 | 0.278 | 1.10 | 1.60E-01 | 0.274 | 1.08 | 3.80E-01 |
| Known | rs11771145 | EPHA1 | 7 | 143,110,762 | G/A | 0.338 | 0.90 | 1.1E-13 | 0.334 | 0.89 | 7.30E-02 | 0.338 | 0.88 | 9.10E-02 |
| Known | rs9331896 | CLU | 8 | 27,467,686 | T/C | 0.379 | 0.86 | 2.8E-25 | 0.376 | 0.84 | 4.70E-03 | 0.370 | 0.85 | 4.20E-02 |
| Known | rs983392 | MS4A6A | 11 | 59,923,508 | A/G | 0.403 | 0.90 | 6.1E-16 | 0.398 | 0.80 | 1.30E-04 | 0.396 | 0.85 | 3.60E-02 |
| Known | rs10792832 | PICALM | 11 | 85,867,875 | G/A | 0.358 | 0.87 | 9.3E-26 | 0.351 | 0.80 | 1.30E-04 | 0.351 | 0.79 | 1.70E-03 |
| Known | rs4147929 | ABCA7 | 19 | 1,063,443 | G/A | 0.190 | 1.15 | 1.1E-15 | 0.188 | 1.24 | 1.40E-02 | 0.186 | 1.32 | 1.00E-02 |
| Known | rs3865444 | CD33 | 19 | 51,727,962 | C/A | 0.307 | 0.94 | 3.0E-06 | 0.297 | 0.86 | 1.60E-02 | 0.296 | 0.84 | 2.60E-02 |
| New D | rs9271192 | HLA-DRB5/HLA-DRB | 6 | 32,578,530 | A/C | 0.276 | 1.11 | 2.9E-12 | 0.286 | 1.04 | 5.90E-01 | 0.283 | 1.08 | 3.40E-01 |
| New D | rs28834970 | PTK2B | 8 | 27,195,121 | T/C | 0.366 | 1.10 | 7.4E-14 | 0.383 | 1.13 | 4.60E-02 | 0.381 | 1.09 | 2.30E-01 |
| New D | rs11218343 | SORL1 | 11 | 121,435,587 | T/C | 0.039 | 0.77 | 9.7E-15 | 0.040 | 0.68 | 4.30E-03 | 0.039 | 0.74 | 1.00E-01 |
| New D | rs10498633 | SLC24A4/RIN3 | 14 | 92,926,952 | G/T | 0.217 | 0.91 | 5.5E-09 | 0.216 | 0.93 | 3.10E-01 | 0.218 | 1.03 | 7.20E-01 |
| New D | rs8093731 | DSG2 | 18 | 29,088,958 | C/T | 0.017 | 0.73 | 1.0E-04 | . | . | . | 0.014 | 0.81 | 8.40E-01 |
| New D&R | rs35349669 | INPP5D | 2 | 234,068,476 | C/T | 0.488 | 1.08 | 3.2E-08 | 0.485 | 1.01 | 8.40E-01 | 0.490 | 0.98 | 8.40E-01 |
| New D&R | rs190982 | MEF2C | 5 | 88,223,420 | A/G | 0.408 | 0.93 | 3.2E-08 | 0.412 | 0.81 | 1.10E-03 | 0.406 | 0.81 | 6.60E-03 |
| New D&R | rs2718058 | NME8 | 7 | 37,841,534 | A/G | 0.373 | 0.93 | 4.8E-09 | 0.359 | 0.96 | 5.50E-01 | 0.354 | 0.95 | 4.70E-01 |
| New D&R | rs1476679 | ZCWPW1 | 7 | 100,004,446 | T/C | 0.287 | 0.91 | 5.6E-10 | 0.291 | 0.86 | 1.80E-02 | 0.285 | 0.86 | 6.10E-02 |
| New D&R | rs10838725 | CELF1 | 11 | 47,557,871 | T/C | 0.316 | 1.08 | 1.1E-08 | 0.308 | 0.97 | 6.20E-01 | 0.308 | 0.99 | 8.80E-01 |
| New D&R | rs17125944 | FERMT2 | 14 | 53,400,629 | T/C | 0.092 | 1.14 | 7.9E-09 | 0.093 | 1.20 | 8.50E-02 | 0.092 | 1.27 | 6.90E-02 |
| New D&R | rs7274581 | CASS4 | 20 | 55,018,260 | T/C | 0.083 | 0.88 | 2.5E-08 | 0.073 | 0.73 | 3.30E-03 | 0.076 | 0.72 | 1.10E-02 |