Table 2.
GWAS Signals and Related Genes from the MA.27 GWAS
| Top SNPs in Signals | Chr | P Values | Genes | Validation Outcome | |
|---|---|---|---|---|---|
| 1. rs10967942 | Chr 9 | 2.01E-07 | KCNV2 | Not expressed in LCLs | |
| 2. rs10485828 | Chr 20 | 2.56E-07 | TH1L, TUBB1, | CTSZ-SLMO2-ATP5E final validated genes, | |
| CTSZ, SLMO2, | TUBB1 not expressed in LCLs, | ||||
| ATP5E | TH1L failed functional validation | ||||
| 3. rs12248467 | Chr 10 | 2.93E-07 | PRKG1 | Not expressed in LCLs | |
| 4. rs76996285 | Chr 13 | 3.81E-07 | PABPC3 | All SNPs were imputed | |
| 5. rs8092654 | Chr 18 | 4.41E-07 | DLGAP1 | Not expressed in LCLs | |
| 6. rs6842571 | Chr 4 | 8.32E-07 | ANTXR2, PRDM8 | Not expressed in LCLs | |
| 7. rs66520040 | Chr 13 | 8.52E-07 | FLT3 | Not expressed in LCLs | |
| 8. rs6901146 | Chr 6 | 1.15E-06 | TRAM2, TMEM14A | TRAM2-TMEM14A final validated genes | |
| 9. rs6591876 | Chr 11 | 1.47E-06 | Gene desert | ||
| 10. rs112830684 | Chr 3 | 1.57E-06 | ASB14, DNAH12 | Not expressed in LCLs | |
| 11. rs7999876 | Chr 13 | 2.10E-06 | Gene desert | ||
| 12. c13.82322180.B37P0 | Chr 13 | 2.19E-06 | Gene desert | ||
| 13. rs73728712 | Chr 7 | 2.25E-06 | DGKI | Not expressed in LCLs | |
| 14. rs61399156 | Chr 7 | 2.87E-06 | DOCK4 | Not expressed in LCLs | |
| 15. rs4550690 | Chr 2 | 2.89E-06 | MAP4K4 | MAP4K4 final validated gene | |
| 16. rs35112095 | Chr 21 | 4.02E-06 | SLC37A1 | Not expressed in LCLs | |
| 17. rs9878448 | Chr 3 | 4.02E-06 | GADL1 | Not expressed in LCLs | |
| 18. rs17015762 | Chr 3 | 4.11E-06 | Gene desert | ||
| 19. rs73511817 | Chr 9 | 4.54E-06 | Gene desert | ||
| 20. rs117996576 | Chr 8 | 4.64E-06 | TUSC3 | Not expressed in LCLs | |
Abbreviation: Chr, chromosome. The table lists the 20 candidate SNP signals selected from our discovery GWAS analyses for pursuit using the Validation Decision Cascade depicted graphically in Figure 2. For each signal, the top SNP is listed, the chromosomal location of the signal, the P value for the top SNP, genes in or near the signal, and the outcome of functional testing, as described in detail in the text. The 3 signals and 6 genes that were validated functionally have been boxed in red.