| SNPs Id | Position | Function |
| Scaffold_2646 | 49774 | Histone-lysine N-methyltransferase ATXR3 (EC 2.1.1.43) (Protein SET DOMAIN GROUP 2) (Trithorax-related protein 3) (TRX-related protein 3) |
| Scaffold_2646 | 51483 | Chorismate mutase 2 (AtCM2) (EC 5.4.99.5) (CM-2) |
| Scaffold_2646 | 55773 | Unannotated |
| Scaffold_2646 | 80059 | Unannotated |
| Scaffold_2651 | 30105 | Calcium-dependent protein kinase 25 (OsCDPK25) (OsCPK25) (EC 2.7.11.1) |
| Scaffold_2659 | 713 | Unannotated |
| Scaffold_2660 | 29172 | Unannotated |
| Scaffold_2660 | 78880 | Probable splicing factor 3A subunit 1 |
| Scaffold_2677 | 5044 | Probable splicing factor 3A subunit 1 |
| Scaffold_2677 | 111488 | Probable splicing factor 3A subunit 1 |
| Scaffold_2677 | 138623 | Unannotated |
| Scaffold_2679 | 15835 | BTB/POZ domain-containing protein At3g09030 |
| Scaffold_2679 | 43559 | Unannotated |
| Scaffold_2679 | 50684 | Unannotated |
| Scaffold_2681 | 54019 | Unannotated |
| Scaffold_2683 | 65760 | Unannotated |
| Scaffold_2683 | 80938 | Unannotated |
| Scaffold_2683 | 100582 | PAP-specific phosphatase HAL2-like (3'(2'),5'-bisphosphate nucleotidase) (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrolase) (DPNPase) (Halotolerance protein) |
| Scaffold_2684 | 103964 | Unannotated |
| Scaffold_2685 | 99882 | Unannotated |