Table 2.
Summary of TWAS with the susceptibility genes for CD in Japanese patients (non-HLA genes).
| Tissue | Gene | Chr | GWAS | eQTL | TWAS | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Best SNP | Z-Score | SNP | R2 | Z-Score | Z-Score | P-Value | FDR | |||
| Significantly associated genes (FDR < 0.05) | ||||||||||
| Whole blood | TNFSF15 | 9 | rs4979462 | 9.81 | rs7866342 | 6.47E-02 | 5.12 | −8.48 | 2.28E-17 | 1.35E-13 |
| Blood - EBV-transformed lymphocytes | ERV3-1 | 7 | rs4718244 | −3.67 | rs4718244 | 8.28E-02 | 3.90 | −4.07 | 4.79E-05 | 2.18E-02 |
| Colon – Sigmoid | ZNF713 | 7 | rs6971250 | −3.88 | rs6593287 | 1.06E-01 | 5.31 | 4.08 | 4.41E-05 | 3.04E-02 |
| Candidate genes (FDR < 0.10) | ||||||||||
| Whole blood | APOBEC3A | 22 | rs5750616 | −3.02 | rs4821843 | 2.14E-02 | −4.71 | 3.90 | 9.66E-05 | 6.79E-02 |
| Colon - Transverse | NPIPB9 | 16 | rs4788076 | 4.16 | rs17640009 | 5.35E-02 | −4.60 | −3.92 | 8.74E-05 | 7.66E-02 |
| Colon - Sigmoid | WDR31 | 9 | rs10981725 | −4.38 | rs10817477 | 1.70E-01 | −5.96 | 3.82 | 1.34E-04 | 8.07E-02 |
| Blood - EBV-transformed lymphocytes | RAP1A | 1 | rs2786991 | −4.30 | rs530801 | 9.98E-04 | 3.48 | 3.67 | 2.42E-04 | 9.45E-02 |
| Colon - Transverse | IGLV3-29 | 22 | rs9623882 | 4.80 | rs8140385 | 3.58E-02 | 4.31 | 3.83 | 1.29E-04 | 9.70E-02 |
Chr: Chromosome, GWAS: genome-wide association study, TWAS: transcriptome-wide association study, FDR: false discovery rate