Search for validated SNPs based on MarkerID, flavonoid genes and polymorphic alleles. These SNPs have been genotyped using Agena MassARRAY technology
| Marker ID | Chr | snp_name | SNP ID | SNP effect | GeneID | GeneID | Gene name | Pos | Ref/Allele | PH9 | MRQ_100 | MRM_16 | Bali | Belunut | Ceylon_35 | Ceylon_8 | Cho_Ko._To | DNJ_128 | DNJ_131 | DZ_192 | Dewat | DV_1NC7 | Hashikalmi | Ijau | Kataktara | Kedudok | Kyokukei | Lantit | MR27NC | MR_297 | Merjat | Padi_Selasih | Panbira | Pulut_Hitam_Siam | Puya | MRQ_76 | RU_1968_B_22 | Rampangan | Ria | Samambo | Seri_Raja | Siam_48 | Tai_Chung._Yu |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SEQ_gsnp00001 | chr01 | snp_fv1 | chr01_10218069 | missense_variant | Os01g0285300 | Os01g0285300 | MYB | 10218069 | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T |
| SEQ_gsnp00002 | chr01 | snp_fv10 | chr01_39258803 | missense_variant | Os01g0901600 | Os01g0901600 | 4CL | 39258803 | C/CT | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | CT | -- | C | C | CT | C | C | C | C |
| SEQ_gsnp00003 | chr02 | snp_fv14 | chr02_32958590 | missense_variant | Os02g0778500 | Os02g0778500 | CHI | 32958590 | A/G/AG | G | G | G | A | G | G | G | G | G | G | G | G | G | G | AG | G | A | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G |
| SEQ_gsnp00004 | chr04 | snp_fv17 | chr04_259218 | missense_variant | Os04g0103900 | Os04g0103900 | CHS | 259218 | C/G | G | C | C | G | C | G | G | C | G | G | G | G | G | G | G | G | G | C | G | G | G | C | C | G | C | G | G | G | G | G | G | G | G | C |
| SEQ_gsnp00005 | chr04 | snp_fv18 | chr04_27950862 | missense_variant | Os04g0557800 | Os04g0557800 | bHLH | 27950862 | C/T | T | T | T | T | T | C | C | T | T | T | -- | T | C | C | C | T | T | T | T | C | C | T | T | T | -- | C | C | T | T | C | T | C | C | T |
| SEQ_gsnp00006 | chr04 | snp_fv19 | chr04_27951087 | missense_variant | Os04g0557800 | Os04g0557800 | bHLH | 27951087 | C | A | C | C | C | C | C | C | C | C | C | C | C | -- | C | C | C | C | C | -- | C | -- | C | C | C | C | C | -- | -- | C | -- | C | C | C | C |
| SEQ_gsnp00007 | chr01 | snp_fv2 | chr01_11356196 | missense_variant | Os01g0305900 | Os01g0305900 | MYB | 11356196 | A/G/AG | A | G | G | G | A | G | G | A | G | -- | G | G | G | G | AG | G | A | A | A | G | G | A | A | G | A | G | G | G | A | -- | A | -- | G | A |
| SEQ_gsnp00008 | chr05 | snp_fv21 | chr05_1566532 | missense_variant | Os05g0127500 | Os05g0127500 | LDOX | 1566532 | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C |
| SEQ_gsnp00009 | chr05 | snp_fv23 | chr05_26226311 | missense_variant | Os05g0527800 | Os05g0527800 | UGT | 26226311 | C/CT | C | C | C | CT | C | C | C | C | C | C | C | CT | C | C | CT | C | CT | C | C | C | C | C | C | CT | C | CT | C | CT | C | CT | C | CT | CT | C |
| SEQ_gsnp00010 | chr05 | snp_fv24 | chr05_26227130 | missense_variant | Os05g0527800 | Os05g0527800 | UGT | 26227130 | C/T | T | T | C | C | T | C | C | T | C | C | C | C | C | C | C | C | C | T | T | C | C | T | T | C | T | C | C | C | T | C | T | C | C | T |
| SEQ_gsnp00011 | chr06 | snp_fv25 | chr06_26652314 | missense_variant | Os06g0651000 | Os06g0651000 | DFR | 26652314 | C/GC | GC | GC | GC | C | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | GC | -- | GC | -- | GC | GC | GC | GC | GC | GC |
| SEQ_gsnp00012 | chr06 | snp_fv26 | chr06_26943434 | missense_variant | Os06g0656500 | Os06g0656500 | 4CL | 26943434 | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
| SEQ_gsnp00013 | chr06 | snp_fv27 | chr06_26949256 | missense_variant | Os06g0656500 | Os06g0656500 | 4CL | 26949256 | G/T/GT | T | G | G | T | GT | T | G | GT | G | G | G | T | T | T | T | G | T | GT | GT | T | G | GT | GT | T | GT | T | G | T | GT | T | G | T | T | GT |
| SEQ_gsnp00014 | chr06 | snp_fv29 | chr06_6240098 | missense_variant | Os06g0221000 | Os06g0221000 | MYB | 6240098 | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T |
| SEQ_gsnp00015 | chr06 | snp_fv30 | chr06_6240837 | missense_variant | Os06g0221000 | Os06g0221000 | MYB | 6240837 | C/T/CT | T | C | C | C | C | C | C | C | C | C | C | C | T | C | C | C | C | C | C | C | C | C | C | C | C | C | C | T | C | T | C | C | C | C |
| SEQ_gsnp00016 | chr07 | snp_fv31 | chr07_10018833 | missense_variant | Os07g0271500 | Os07g0271500 | CHS | 10018833 | A/G/AG | G | A | G | G | G | G | A | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G |
| SEQ_gsnp00017 | chr07 | snp_fv38 | chr07_2490069 | missense_variant | Os07g0148200 | Os07g0148200 | LDOX | 2490069 | A/G/AG | G | G | G | A | G | A | A | G | A | A | A | A | A | A | A | A | A | G | G | A | A | G | G | A | G | A | A | G | G | A | G | A | A | G |
| SEQ_gsnp00018 | chr08 | snp_fv44 | chr08_25592457 | missense_variant | Os08g0515900 | Os08g0515900 | DFR | 25592457 | G/T/GT | G | G | G | G | G | T | T | G | T | T | T | T | T | T | T | T | G | G | G | G | T | G | G | G | G | T | G | G | G | GT | G | GT | T | G |
| SEQ_gsnp00019 | chr08 | snp_fv52 | chr08_8877857 | missense_variant | Os08g0245200 | Os08g0245200 | 4CL | 8877857 | C/T | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | T | C | C | C | C | C | C | C | C | C | T | C | C | C | C | C | C | C |
| SEQ_gsnp00020 | chr08 | snp_fv53 | chr08_8878252 | missense_variant | Os08g0245200 | Os08g0245200 | 4CL | 8878252 | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
| SEQ_gsnp00021 | chr09 | snp_fv54 | chr09_11288999 | missense_variant | Os09g0353400 | Os09g0353400 | LDOX | 11288999 | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G |
| SEQ_gsnp00022 | chr09 | snp_fv55 | chr09_11290674 | missense_variant | Os09g0353400 | Os09g0353400 | LDOX | 11290674 | C/G/CG | C | CG | CG | CG | -- | CG | CG | CG | CG | CG | CG | C | C | CG | CG | CG | CG | -- | -- | CG | CG | CG | C | CG | CG | CG | CG | C | CG | CG | -- | C | CG | G |
| SEQ_gsnp00023 | chr09 | snp_fv57 | chr09_11322729 | missense_variant | Os09g0354100 | Os09g0354100 | LDOX | 11322729 | A/G | A | A | A | A | A | A | A | G | A | A | A | A | A | A | A | A | A | A | A | A | G | A | A | G | A | A | G | A | A | A | A | A | A | A |
| SEQ_gsnp00024 | chr09 | snp_fv59 | chr09_11322916 | missense_variant | Os09g0354100 | Os09g0354100 | LDOX | 11322916 | C/T | C | C | C | T | C | C | C | C | T | T | T | T | C | T | T | C | T | C | C | T | C | C | C | C | C | T | C | C | C | T | C | T | T | C |
| SEQ_gsnp00025 | chr01 | snp_fv6 | chr01_25384314 | missense_variant | Os01g0633500 | Os01g0633500 | DFR | 25384314 | C/CA | C | C | C | CA | C | C | -- | C | C | C | C | CA | -- | C | CA | C | CA | C | C | CA | CA | C | C | C | C | C | -- | CA | C | CA | C | CA | CA | C |
| SEQ_gsnp00026 | chr09 | snp_fv60 | chr09_19012056 | missense_variant | Os09g0491820 | Os09g0491820 | DFR | 19012056 | A/G | A | A | G | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | G | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
| SEQ_gsnp00027 | chr10 | snp_fv61 | chr10_23085559 | missense_variant | Os10g0578950 | Os10g0578950 | 4CL | 23085559 | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G | G |
| SEQ_gsnp00028 | chr11 | snp_fv62 | chr11_14673251 | missense_variant | Os11g0444000 | Os11g0444000 | UGT | 14673251 | G/T | G | G | G | G | G | T | T | G | T | T | T | G | T | T | T | T | T | G | G | T | T | G | G | T | G | T | G | G | G | T | G | GT | T | G |
| SEQ_gsnp00029 | chr11 | snp_fv63 | chr11_19280813 | missense_variant | Os11g0530600 | Os11g0530600 | CHS | 19280813 | C/T | C | C | C | T | C | C | C | C | C | C | C | T | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C |
| SEQ_gsnp00030 | chr11 | snp_fv64 | chr11_22927285 | missense_variant | Os11g0599200 | Os11g0599200 | UGT | 22927285 | C/T/CT | C | C | C | C | C | C | C | C | C | C | C | T | C | C | T | C | T | C | C | C | C | C | C | C | C | C | T | T | C | T | C | CT | T | C |
| SEQ_gsnp00031 | chr12 | snp_fv66 | chr12_1201292 | missense_variant | Os12g0125000 | Os12g0125000 | MYB | 1201292 | A/G/AG | A | A | A | G | A | A | G | A | G | G | G | G | A | G | G | G | G | A | A | A | A | A | A | G | A | A | A | A | A | A | A | A | A | A |
| SEQ_gsnp00032 | chr12 | snp_fv67 | chr12_767050 | missense_variant | Os12g0115700 | Os12g0115700 | CHI | 767050 | C/CT | T | C | C | C | C | C | C | C | C | C | C | C | C | C | CT | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C |
| SEQ_gsnp00033 | chr01 | snp_fv68 | chr01_10219510 | 5_prime_UTR_variant | Os01g0285300 | Os01g0285300 | MYB | 10219510 | C/T/CT | C | C | C | C | C | C | T | C | T | T | T | C | T | T | C | T | C | C | C | C | C | C | C | C | C | C | T | C | C | C | C | C | C | C |
| SEQ_gsnp00034 | chr01 | snp_fv69 | chr01_17975912 | 3_prime_UTR_variant | Os01g0511000 | Os01g0511000 | LBD | 17975912 | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T | T |
| SEQ_gsnp00035 | chr01 | snp_fv7 | chr01_34963117 | missense_variant | Os01g0820000 | Os01g0820000 | C4H | 34963117 | C/T | -- | C | C | T | C | T | T | C | C | C | T | T | C | C | T | T | T | C | C | T | -- | C | C | T | C | T | T | C | C | T | C | T | T | C |
| SEQ_gsnp00036 | chr08 | snp_fv70 | chr08_27486521 | 3_prime_UTR_variant | Os08g0548000 | Os08g0548000 | MYB | 27486521 | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C | C |
| SEQ_gsnp00037 | chr01 | snp_fv74 | chr01_23451253 | upstream_gene_variant | Os01g0597800 | Os01g0597800 | UGT | 23451253 | C/CG | -- | C | C | C | C | C | C | CA | C | C | C | C | C | C | C | C | C | C | C | C | C | C | CA | C | C | C | C | CA | C | C | C | C | C | C |
| SEQ_gsnp00038 | chr01 | snp_fv9 | chr01_3920111 | missense_variant | Os01g0176000 | Os01g0176000 | UGT | 3920111 | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
| SEQ_gsnp00039 | chr03 | snp_OXC3_1240727 | chr03_1240727 | intron_variant | Os03g0122300 | Os03g0122300 | F3H | 1240727 | A/T | T | A | T | T | A | A | A | T | T | T | T | A | T | T | AT | T | T | A | T | T | A | A | T | A | T | A | T | A | A | A | A | T | T | T |
| SEQ_gsnp00040 | chr03 | snp_OXC3_1240727_1 | chr03_1240727 | intron_variant | Os03g0122300 | Os03g0122300 | F3H | 1240727 | C/T | T | C | T | T | C | C | C | T | T | T | T | C | T | T | CT | T | T | C | T | T | C | C | T | C | T | C | T | C | C | C | C | T | T | T |
| SEQ_gsnp00041 | chr04 | snp_OXC4_27953839 | chr04_27953839 | intron_variant | Os04g0557800 | Os04g0557800 | bHLH | 27953839 | G/A | G | A | A | A | A | G | G | G | A | A | A | A | G | GA | G | A | G | A | G | A | A | G | G | G | G | G | G | G | G | G | G | G | G | A |
| SEQ_gsnp00042 | chr04 | snp_OXC4_27953839_1 | chr04_27953839 | intron_variant | Os04g0557800 | Os04g0557800 | bHLH | 27953839 | G/T | G | T | T | T | T | G | G | G | T | T | T | T | G | GT | G | T | G | T | G | T | T | G | G | G | G | G | G | G | G | G | G | G | G | T |
| Marker ID | Chr | SNP effect | GeneID |