Table 2.
Significant SNPs of the DeepCOMBI method and related association details. For each SNP identifier on a specific chromosome that was found to be significantly associated with a disease by the DeepCOMBI method, we show their χ2 test P-value and indicate whether the RPVT P-value is < 10–5 (i.e. the SNP is a significant finding of RPVT), whether its COMBI P-value is smaller than the corresponding COMBI threshold (i.e. the SNP is a significant finding of the COMBI method) and whether the SNP has been found significant with a P-value < 10–5 in an external study with a corresponding PMID. Please note that the RPVT result in the fifth column corresponds to the χ2P-values we have calculated here, not necessarily to the original WTCCC publication, where they also investigated trend test P-values and potentially applied slightly different preprocessing steps. Similarly, the COMBI result in the sixth column corresponds to the re-calculations of COMBI we performed here, not necessarily to those of the original COMBI publication where slightly different results were produced due to the random nature of the permutation procedure
| Disease | Chromosome | Identifier | χ2P-value | Significant in RPVT | Significant in COMBI | P-value < 10–5 in at least one external GWAS or meta-analysis | References (PMID) |
|---|---|---|---|---|---|---|---|
| Bipolar disorder (BD) | 2 | rs7570682 | 1.77e-05 | YES | YES | 21254220 | |
| 2 | rs1375144 | 1.26e-05 | YES | YES | 21254220 | ||
| 3 | rs514636 | 2.53e-06 | YES | YES | YES | 21254220 | |
| 16 | rs420259 | 5.87e-08 | YES | YES | YES | 21254220 | |
| Coronary artery disease (CAD) | 6 | rs6907487 | 2.92e-05 | YES | 17634449 | ||
| 9 | rs1333049 | 1.12e-13 | YES | YES | YES | 17634449 | |
| 16 | rs8055236 | 5.32e-06 | YES | YES | |||
| 22 | rs688034 | 2.75e-06 | YES | YES | |||
| Crohn’s disease (CD) | 1 | rs11805303 | 6.35e-12 | YES | YES | YES | 17435756 |
| 1 | rs12037606 | 1.02e-05 | YES | 17554261 | |||
| 2 | rs10210302 | 4.52e-14 | YES | YES | YES | 23128233 | |
| 3 | rs11718165 | 2.04e-08 | YES | YES | YES | 21102463 | |
| 5 | rs6596075 | 3.11e-06 | YES | YES | |||
| 5 | rs17234657 | 2.42e-12 | YES | YES | YES | 18587394 | |
| 5 | rs11747270 | 1.05e-06 | YES | YES | YES | 18587394 | |
| 7 | rs7807268 | 5.43e-06 | YES | YES | 26192919 | ||
| 10 | rs10883371 | 5.23e-08 | YES | YES | YES | 21102463 | |
| 10 | rs10761659 | 1.69e-06 | YES | YES | YES | 22936669 | |
| 16 | rs2076756 | 7.55e-15 | YES | YES | YES | 21102463 | |
| Hypertension (HT) | 1 | rs10889923 | 1.38e-05 | ||||
| 15 | rs2398162 | 6.01e-06 | YES | ||||
| Rheumatoid arthritis (RA) | 1 | rs6679677 | <1.0e-15 | YES | YES | YES | 20453842 |
| 4 | rs3816587 | 7.28e-06 | YES | YES | |||
| 6 | rs9272346 | 7.38e-14 | YES | YES | |||
| 22 | rs743777 | 1.01e-06 | YES | YES | 23143596 | ||
| Type 1 diabetes (T1D) | 1 | rs6679677 | <1.0e-15 | YES | YES | YES | 19430480 |
| 2 | rs231726 | 1.43e-05 | YES | 30659077 | |||
| 4 | rs17388568 | 3.07e-06 | YES | YES | YES | 21829393 | |
| 6 | rs9272346 | <1.0e-15 | YES | YES | YES | 18978792 | |
| 12 | rs17696736 | 1.56e-14 | YES | YES | YES | 18978792 | |
| 12 | rs11171739 | 8.36e-11 | YES | YES | 19430480 | ||
| 13 | rs4769283 | 1.20e-05 | |||||
| 16 | rs12924729 | 7.86e-08 | YES | YES | YES | 17554260 | |
| Type 2 diabetes (T2D) | 2 | rs6718526 | 1.00e-05 | YES | YES | 20418489 | |
| 4 | rs1481279 | 9.44e-06 | YES | YES | YES | 28869590 | |
| 6 | rs9465871 | 3.38e-07 | YES | YES | YES | 21490949 | |
| 10 | rs4506565 | 5.01e-12 | YES | YES | YES | 23300278 | |
| 12 | rs1495377 | 7.21e-06 | YES | YES | YES | 22885922 | |
| 16 | rs7193144 | 4.15e-08 | YES | YES | YES | 22693455 |