Table 1.
Top 36 path associations found by NETAM in the AD data (Zhang et al., 2013) related to VAMP1, RHOBTB3, and ZNF720 genes
| SNP | SNP location | Genes nearby SNP within 1 Mbp | Gene | Gene Location | Path Score | Related Biology | SNP-pheno P-val |
|---|---|---|---|---|---|---|---|
| rs1892695 | chr21:31366451 | GRIK1 | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 0.01 |
| rs9565180 | chr13:75129470 | LINC00347 | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 0.01 |
| rs12415404 | chr10:61035110 | PHYHIPL,FAM13C | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 0.11 |
| rs873590 | chr11:122175599 | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 0.01 | |
| rs1542282 | chr2:52915337 | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 0.84 | |
| rs675804 | chr6:150761402 | IYD | ZNF720 | chr16:31724565-31766243 | 0.95 | Beta-amyloid | 4.9e-3 |
| rs3816096 | chr2:11670369 | MIR4429,GREB1,E2F6 | ZNF720 | chr16:31724565-31766243 | 0.94 | Beta-amyloid | 0.67 |
| rs10507833 | chr13:75124139 | LINC00347 | ZNF720 | chr16:31724565-31766243 | 0.93 | Beta-amyloid | 0.01 |
| rs12501944 | chr4:112716904 | ZNF720 | chr16:31724565-31766243 | 0.93 | Beta-amyloid | 0.07 | |
| rs4833235 | chr4:122914585 | TRPC3 | ZNF720 | chr16:31724565-31766243 | 0.92 | Beta-amyloid | 2.1e-3 |
| rs1010546 | chr17:62115026 | ICAM2,DQ572107,ERN1,SCN4A,C17orf72 | ZNF720 | chr16:31724565-31766243 | 0.91 | Beta-amyloid | 0.28 |
| rs674026 | chr6:150743619 | IYD | ZNF720 | chr16:31724565-31766243 | 0.90 | Beta-amyloid | 0.67 |
| rs722861 | chr22:44046385 | EFCAB6 | ZNF720 | chr16:31724565-31766243 | 0.89 | Beta-amyloid | 0.35 |
| rs3105290 | chr4:112593771 | ZNF720 | chr16:31724565-31766243 | 0.89 | Beta-amyloid | 0.05 | |
| rs640927 | chr11:75022553 | SNORD15B,SNORD15A,ARRB1,TPBGL,RPS3,MIR326 | ZNF720 | chr16:31724565-31766243 | 0.89 | Beta-amyloid | 0.04 |
| rs12734338 | chr1:200736345 | DDX59,CAMSAP2 | ZNF720 | chr16:31724565-31766243 | 0.88 | Beta-amyloid | 7.7e-5 |
| rs2282714 | chr1:21460435 | ECE1 | ZNF720 | chr16:31724565-31766243 | 0.88 | Beta-amyloid | 0.69 |
| rs2833249 | chr21:31358680 | GRIK1 | ZNF720 | chr16:31724565-31766243 | 0.77 | Beta-amyloid | 4.6e-3 |
| rs2156801 | chr11:122159265 | ZNF720 | chr16:31724565-31766243 | 0.75 | Beta-amyloid | 0.11 | |
| rs1478652 | chr13:54155871 | ZNF720 | chr16:31724565-31766243 | 0.67 | Beta-amyloid | 0.2 | |
| rs1361643 | chr11:29594339 | ZNF720 | chr16:31724565-31766243 | 0.67 | Beta-amyloid | 2.1e-3 | |
| rs9527255 | chr13:54150358 | ZNF720 | chr16:31724565-31766243 | 0.56 | Beta-amyloid | 0.25 | |
| rs1947305 | chr11:29567353 | ZNF720 | chr16:31724565-31766243 | 0.55 | Beta-amyloid | 3.4e-3 | |
| rs2974135 | chr2:80028801 | CTNNA2 | RHOBTB3 | chr5:95053336-95091797 | 0.64 | Estrogen | 0.03 |
| rs16838621 | chr2:207275786 | ADAM23,ZDBF2 | RHOBTB3 | chr5:95053336-95091797 | 0.60 | Estrogen | 0.02 |
| rs11057512 | chr12:123254323 | HCAR3,HCAR1,VPS37B,DENR,CCDC62,HCAR2,HIP1R | RHOBTB3 | chr5:95053336-95091797 | 0.58 | Estrogen | 0.26 |
| rs4676431 | chr2:241105073 | MYEOV2,OTOS | RHOBTB3 | chr5:95053336-95091797 | 0.55 | Estrogen | 0.17 |
| rs6686515 | chr1:198326330 | NEK7 | RHOBTB3 | chr5:95053336-95091797 | 0.55 | Estrogen | 0.02 |
| rs9804184 | chr10:63908170 | ARID5B,RTKN2 | RHOBTB3 | chr5:95053336-95091797 | 0.55 | Estrogen | 0.91 |
| rs10514262 | chr5:83062888 | HAPLN1 | VAMP1 | chr12:6571403-6579843 | 0.58 | Nicotine | 1 |
| rs4656888 | chr1:158395294 | AK057554,OR10R2,CD1E,OR10T2,CD1B,OR10K2,OR10K1 | VAMP1 | chr12:6571403-6579843 | 0.58 | Nicotine | 0.67 |
| rs729657 | chr7:21750561 | DNAH11 | VAMP1 | chr12:6571403-6579843 | 0.58 | Nicotine | 0.34 |
| rs7298053 | chr12:6489314 | CD27,SCNN1A,TAPBPL,CD27-AS1,LTBR,VAMP1,PLEKHG6,TNFRSF1A | VAMP1 | chr12:6571403-6579843 | 0.58 | Nicotine | 0.06 |
| rs740851 | chr12:6508610 | CD27,SCNN1A,TAPBPL,CD27-AS1,LTBR,VAMP1 | VAMP1 | chr12:6571403-6579843 | 0.58 | Nicotine | 0.04 |
| MRPL51,PLEKHG6,TNFRSF1A,NCAPD2 | |||||||
| rs17154957 | chr7:80705911 | VAMP1 | chr12:6571403-6579843 | 0.57 | Nicotine | 0.19 | |
| rs1326419 | chr13:88080652 | MIR4500HG | VAMP1 | chr12:6571403-6579843 | 0.57 | Nicotine | 3.9e-3 |
Note: In this table, we omit the AD case/control phenotype because it is identical for all paths. For reference, in the column of ‘SNP-pheno P-val’, we show P-value for the association between SNP and the phenotype, computed by PLINK software (Purcell et al., 2007).