Table 1.
Thirty-five genes that have not been previously identified in TWAS for AD risk
| Region | Gene name | Typea | Combined P value | Index SNP(s)b | Distance of gene to the index SNP (kb) |
|---|---|---|---|---|---|
| 1q23.3 | NDUFS2 | Protein | 2.81 × 10−10 | rs4575098 | 11.50 |
| FCER1G | Protein | 7.43 × 10−10 | rs4575098 | 29.63 | |
| B4GALT3 | Protein | 1.45 × 10−6 | rs4575098 | 7.63 | |
| NIT1 | Protein | 1.85 × 10−6 | rs4575098 | 60.16 | |
| 4q25 | FAM241A | Protein | 2.88 × 10−6 | rs6448451 | 102,041.93 |
| 6p12.3 | AL355353.1 | lncRNA | 3.16 × 10−8 | rs9381563 | 12.34 |
| CD2AP | Protein | 1.98 × 10−7 | rs10948363 | Within | |
| 6p21.32 | BTNL2 | Protein | 1.95 × 10−11 | rs9271192 | 203.63 |
| 6p21.33 | SAPCD1 | Protein | 3.61 × 10−8 | rs9271192 | 845.90 |
| 7q22.1 | PVRIG | Protein | 4.44 × 10−9 | rs7384878 | 112.94 |
| AZGP1 | Protein | 3.96 × 10−8 | rs7384878 | 358.38 | |
| AC004522.3 | lncRNA | 5.00 × 10−8 | rs7384878 | 385.81 | |
| CNPY4 | Protein | 1.85 × 10−7 | rs7384878 | 208.92 | |
| CASTOR3 | Protein | 2.77 × 10−7 | rs7384878 | 62.19 | |
| LAMTOR4 | Protein | 3.35 × 10−7 | rs7384878 | 178.48 | |
| STAG3 | Protein | 5.62 × 10−7 | rs7384878 | 112.94 | |
| GJC3 | Protein | 8.58 × 10−7 | rs7384878 | 404.81 | |
| GPC2 | Protein | 2.31 × 10−6 | rs7384878 | 157.05 | |
| AP4M1 | Protein | 2.78 × 10−6 | rs7384878 | 224.08 | |
| 11q12.1 | FAM111A | Protein | 9.60 × 10−7 | rs983392 | 1001.00 |
| 15q21.3 | AC090515.2 | lncRNA | 1.13 × 10−6 | rs442495 | 37.66 |
| 15q21.3-q22.1 | MINDY2 | Protein | 1.43 × 10−6 | rs442495 | 40.78 |
| 16p11.2 | KAT8 | Protein | 9.70 × 10−10 | rs59735493 | Within |
| PRSS36 | Protein | 2.96 × 10−9 | rs59735493 | 17.15 | |
| AC135050.6 | lncRNA | 9.24 × 10−8 | rs59735493 | Within | |
| PRSS53 | Protein | 2.25 × 10−7 | rs59735493 | 32.15 | |
| ZNF668 | Protein | 1.81 × 10−6 | rs59735493 | 47.54 | |
| CCDC189 | Protein | 2.16 × 10−6 | rs59735493 | 359.56 | |
| AC135050.1 | lncRNA | 2.66 × 10−6 | rs59735493 | 58.98 | |
| 17p13.2 | AC012146.1 | lncRNA | 8.33 × 10−8 | rs9916042 | 30.32 |
| SCIMP | Protein | 1.47 × 10−6 | rs9916042 | 127.77 | |
| 17q23.3 | ACE | Protein | 8.67 × 10−8 | rs28394864 | 14,103.65 |
| 19q13.31-13.32 | AC243964.3 | lncRNA | 5.89 × 10−25 | rs75627662 | 185.10 |
| 19q13.32 | GEMIN7 | Protein | 5.79 × 10−7 | rs75627662 | 168.88 |
| OPA3 | Protein | 1.12 × 10−6 | rs76320948 | 136.37 |
aProtein: protein coding genes; lncRNA: long noncoding RNAs; bThe risk SNP closest to the gene is presented and a full list of all risk SNPs, and their distances to the genes are presented in Additional file 6: Table S6