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Search Results:

10 variations found. LOC_Os02g27430 (GRF zinc finger family protein), ranging from 16,160,464 bp to 16,160,890 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
red High impact variants defined by snpEff 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff.
purple 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg0216160596 (J) chr02 16160596 C A 61.80% 0.21% A -> C
mr1082 (All); LR P-value: 3.14E-39;
mr1092 (All); LR P-value: 5.96E-46;
mr1152 (All); LR P-value: 2.28E-43;
mr1504 (All); LR P-value: 2.90E-86;
mr1546 (All); LR P-value: 4.90E-29;
mr1670 (All); LR P-value: 2.88E-35;
mr1711 (All); LR P-value: 4.37E-60;
mr1733 (All); LR P-value: 3.54E-33;
mr1767 (All); LR P-value: 5.24E-19;
mr1922 (All); LR P-value: 3.63E-28;
mr1987 (All); LR P-value: 6.64E-100;
mr1082_2 (All); LR P-value: 4.96E-37;
mr1085_2 (All); LR P-value: 1.43E-32;
mr1103_2 (All); LR P-value: 1.35E-67;
mr1107_2 (All); LR P-value: 1.75E-35;
mr1155_2 (All); LR P-value: 1.16E-36;
mr1226_2 (All); LR P-value: 2.14E-38;
mr1233_2 (All); LR P-value: 2.64E-24;
mr1243_2 (All); LR P-value: 1.45E-40;
mr1246_2 (All); LR P-value: 2.96E-76;
mr1403_2 (All); LR P-value: 6.62E-24;
mr1416_2 (All); LR P-value: 6.64E-17;
mr1541_2 (All); LR P-value: 1.24E-36;
mr1637_2 (All); LR P-value: 1.73E-18;
mr1676_2 (All); LR P-value: 5.33E-21;
mr1733_2 (All); LR P-value: 4.46E-64;
mr1891_2 (All); LR P-value: 3.21E-30
LOC_Os02g27430.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g27430.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 41.873; most accessible tissue: Zhenshan97 young leaf, score: 67.830
vg0216160657 (J) chr02 16160657 A G 61.80% 0.15% G -> A
mr1019 (All); LR P-value: 9.29E-56;
mr1082 (All); LR P-value: 2.27E-39;
mr1092 (All); LR P-value: 9.30E-47;
mr1128 (All); LR P-value: 5.93E-10;
mr1132 (All); LR P-value: 1.18E-67;
mr1135 (All); LR P-value: 5.37E-75;
mr1152 (All); LR P-value: 1.09E-45;
mr1154 (All); LR P-value: 1.39E-50;
mr1504 (All); LR P-value: 8.64E-88;
mr1546 (All); LR P-value: 2.33E-30;
mr1670 (All); LR P-value: 6.27E-37;
mr1711 (All); LR P-value: 8.52E-60;
mr1733 (All); LR P-value: 7.92E-34;
mr1767 (All); LR P-value: 2.40E-19;
mr1922 (All); LR P-value: 1.41E-28;
mr1987 (All); LR P-value: 1.30E-103;
mr1082_2 (All); LR P-value: 1.66E-35;
mr1416_2 (All); LR P-value: 5.23E-16
LOC_Os02g27420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g27430.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 49.061; most accessible tissue: Zhenshan97 young leaf, score: 74.302
vg0216160736 (J) chr02 16160736 A G 65.50% 0.15% G -> A
mr1016 (All); LR P-value: 1.57E-45;
mr1018 (All); LR P-value: 1.59E-73;
mr1082 (All); LR P-value: 5.24E-41;
mr1085 (All); LR P-value: 2.76E-31;
mr1086 (All); LR P-value: 1.12E-30;
mr1089 (All); LMM P-value: 6.01E-08; LR P-value: 9.37E-47;
mr1093 (All); LMM P-value: 9.84E-11; LR P-value: 4.09E-52;
mr1103 (All); LR P-value: 1.04E-57;
mr1107 (All); LR P-value: 6.43E-33;
mr1129 (All); LMM P-value: 1.80E-06; LR P-value: 2.39E-33;
mr1132 (All); LR P-value: 4.93E-71;
mr1138 (All); LR P-value: 4.56E-11;
mr1139 (All); LR P-value: 4.64E-39;
mr1141 (All); LR P-value: 2.10E-43;
mr1145 (All); LR P-value: 6.73E-29;
mr1170 (All); LR P-value: 2.03E-12;
mr1178 (All); LR P-value: 3.27E-56;
mr1226 (All); LR P-value: 6.12E-30;
mr1235 (All); LMM P-value: 6.37E-06; LR P-value: 1.19E-45;
mr1243 (All); LR P-value: 2.22E-38;
mr1251 (All); LR P-value: 5.69E-25;
mr1253 (All); LR P-value: 3.29E-18;
mr1257 (All); LR P-value: 3.24E-31;
mr1350 (All); LR P-value: 3.21E-35;
mr1390 (All); LR P-value: 4.19E-54;
mr1411 (All); LR P-value: 9.58E-27;
mr1423 (All); LR P-value: 2.68E-33;
mr1435 (All); LR P-value: 7.29E-39;
mr1448 (All); LR P-value: 2.83E-31;
mr1490 (All); LR P-value: 2.26E-52;
mr1491 (All); LR P-value: 1.74E-61;
mr1518 (All); LR P-value: 1.93E-19;
mr1541 (All); LR P-value: 2.57E-20;
mr1546 (All); LR P-value: 7.46E-33;
mr1599 (All); LMM P-value: 1.46E-06; LR P-value: 1.38E-60;
mr1637 (All); LR P-value: 2.39E-09;
mr1663 (All); LR P-value: 2.99E-09;
mr1676 (All); LR P-value: 1.26E-20;
mr1733 (All); LR P-value: 2.69E-33;
mr1780 (All); LR P-value: 4.47E-37;
mr1932 (All); LR P-value: 7.43E-34;
mr1949 (All); LR P-value: 1.12E-12;
mr1030_2 (All); LR P-value: 5.56E-08;
mr1055_2 (All); LR P-value: 1.08E-47;
mr1070_2 (All); LR P-value: 8.49E-45;
mr1085_2 (All); LR P-value: 1.23E-33;
mr1089_2 (All); LMM P-value: 1.59E-07; LR P-value: 1.80E-59;
mr1093_2 (All); LMM P-value: 1.12E-10; LR P-value: 1.36E-63;
mr1103_2 (All); LR P-value: 3.02E-66;
mr1104_2 (All); LR P-value: 2.77E-38;
mr1107_2 (All); LR P-value: 2.23E-37;
mr1129_2 (All); LR P-value: 1.43E-37;
mr1132_2 (All); LR P-value: 1.10E-81;
mr1138_2 (All); LR P-value: 1.27E-11;
mr1141_2 (All); LR P-value: 4.16E-54;
mr1155_2 (All); LR P-value: 1.64E-37;
mr1178_2 (All); LR P-value: 2.62E-77;
mr1226_2 (All); LR P-value: 3.57E-40;
mr1233_2 (All); LR P-value: 2.75E-24;
mr1235_2 (All); LMM P-value: 1.43E-08; LR P-value: 2.49E-67;
mr1243_2 (All); LR P-value: 7.85E-50;
mr1248_2 (All); LR P-value: 5.10E-13;
mr1251_2 (All); LMM P-value: 2.17E-06; LR P-value: 2.95E-44;
mr1253_2 (All); LR P-value: 1.81E-21;
mr1255_2 (All); LR P-value: 1.24E-19;
mr1257_2 (All); LMM P-value: 3.42E-07; LR P-value: 4.45E-42;
mr1377_2 (All); LR P-value: 2.76E-12;
mr1379_2 (All); LR P-value: 3.79E-09;
mr1390_2 (All); LR P-value: 1.33E-62;
mr1403_2 (All); LR P-value: 4.59E-25;
mr1404_2 (All); LR P-value: 6.65E-50;
mr1416_2 (All); LR P-value: 2.57E-16;
mr1423_2 (All); LR P-value: 4.82E-35;
mr1435_2 (All); LMM P-value: 3.60E-06; LR P-value: 3.85E-44;
mr1437_2 (All); LR P-value: 8.55E-47;
mr1490_2 (All); LR P-value: 2.20E-64;
mr1520_2 (All); LR P-value: 3.00E-11;
mr1546_2 (All); LR P-value: 3.25E-50;
mr1599_2 (All); LMM P-value: 6.91E-08; LR P-value: 4.75E-76;
mr1620_2 (All); LR P-value: 1.32E-47;
mr1637_2 (All); LR P-value: 1.69E-20;
mr1683_2 (All); LR P-value: 2.94E-07;
mr1691_2 (All); LR P-value: 1.16E-06;
mr1749_2 (All); LR P-value: 5.57E-08;
mr1780_2 (All); LR P-value: 6.97E-37;
mr1821_2 (All); LR P-value: 9.64E-08;
mr1828_2 (All); LR P-value: 3.14E-66;
mr1838_2 (All); LR P-value: 4.39E-13;
mr1949_2 (All); LR P-value: 2.29E-24
LOC_Os02g27430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g27430.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 56.499; most accessible tissue: Zhenshan97 young leaf, score: 79.507
vg0216160760 (J) chr02 16160760 C T 94.90% 0.00% C -> T NA
LOC_Os02g27430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 57.837; most accessible tissue: Zhenshan97 young leaf, score: 82.982
vg0216160804 (J) chr02 16160804 C T 65.70% 0.00% T -> C
mr1016 (All); LR P-value: 5.33E-45;
mr1018 (All); LR P-value: 6.32E-75;
mr1082 (All); LR P-value: 1.27E-41;
mr1085 (All); LR P-value: 8.91E-31;
mr1086 (All); LR P-value: 1.86E-31;
mr1089 (All); LMM P-value: 2.77E-08; LR P-value: 2.47E-46;
mr1093 (All); LMM P-value: 1.29E-10; LR P-value: 4.61E-51;
mr1103 (All); LR P-value: 7.40E-58;
mr1107 (All); LR P-value: 2.01E-33;
mr1132 (All); LR P-value: 1.61E-71;
mr1134 (All); LR P-value: 1.99E-80;
mr1136 (All); LR P-value: 2.30E-42;
mr1138 (All); LR P-value: 2.00E-11;
mr1145 (All); LR P-value: 3.03E-28;
mr1170 (All); LR P-value: 2.67E-12;
mr1178 (All); LR P-value: 1.02E-56;
mr1226 (All); LR P-value: 1.54E-29;
mr1235 (All); LR P-value: 1.80E-44;
mr1243 (All); LR P-value: 5.99E-37;
mr1253 (All); LR P-value: 1.20E-17;
mr1257 (All); LR P-value: 4.91E-30;
mr1350 (All); LR P-value: 2.06E-34;
mr1390 (All); LR P-value: 8.21E-54;
mr1411 (All); LR P-value: 6.32E-26;
mr1423 (All); LR P-value: 4.86E-32;
mr1435 (All); LR P-value: 9.45E-38;
mr1448 (All); LR P-value: 1.40E-31;
mr1480 (All); LR P-value: 2.05E-39;
mr1490 (All); LR P-value: 2.64E-52;
mr1491 (All); LR P-value: 1.28E-61;
mr1518 (All); LR P-value: 7.12E-20;
mr1541 (All); LR P-value: 2.19E-20;
mr1546 (All); LR P-value: 3.24E-31;
mr1599 (All); LR P-value: 9.99E-59;
mr1629 (All); LR P-value: 1.04E-74;
mr1637 (All); LR P-value: 7.69E-09;
mr1676 (All); LR P-value: 3.26E-21;
mr1692 (All); LR P-value: 3.59E-49;
mr1733 (All); LR P-value: 6.28E-33;
mr1767 (All); LR P-value: 7.45E-18;
mr1780 (All); LR P-value: 2.90E-37;
mr1909 (All); LR P-value: 7.78E-14;
mr1932 (All); LR P-value: 6.00E-35;
mr1949 (All); LR P-value: 7.21E-13;
mr1030_2 (All); LR P-value: 1.09E-07;
mr1055_2 (All); LR P-value: 6.15E-47;
mr1082_2 (All); LR P-value: 7.20E-35;
mr1085_2 (All); LR P-value: 1.60E-33;
mr1089_2 (All); LMM P-value: 2.31E-06; LR P-value: 3.52E-57;
mr1093_2 (All); LMM P-value: 1.86E-09; LR P-value: 2.09E-61;
mr1103_2 (All); LR P-value: 9.00E-67;
mr1104_2 (All); LR P-value: 5.43E-39;
mr1107_2 (All); LR P-value: 5.99E-38;
mr1129_2 (All); LR P-value: 1.26E-35;
mr1132_2 (All); LR P-value: 1.95E-82;
mr1134_2 (All); LR P-value: 3.46E-97;
mr1138_2 (All); LR P-value: 1.09E-11;
mr1141_2 (All); LR P-value: 1.83E-53;
mr1155_2 (All); LR P-value: 8.16E-37;
mr1175_2 (All); LR P-value: 5.81E-21;
mr1178_2 (All); LR P-value: 1.74E-77;
mr1226_2 (All); LR P-value: 1.47E-39;
mr1233_2 (All); LR P-value: 8.53E-25;
mr1235_2 (All); LMM P-value: 1.74E-07; LR P-value: 1.56E-65;
mr1243_2 (All); LR P-value: 8.75E-49;
mr1248_2 (All); LR P-value: 2.36E-12;
mr1251_2 (All); LMM P-value: 9.78E-06; LR P-value: 4.52E-43;
mr1253_2 (All); LR P-value: 9.02E-21;
mr1255_2 (All); LR P-value: 2.06E-19;
mr1257_2 (All); LMM P-value: 2.93E-06; LR P-value: 6.45E-41;
mr1377_2 (All); LR P-value: 6.76E-12;
mr1379_2 (All); LR P-value: 2.33E-09;
mr1390_2 (All); LR P-value: 4.26E-62;
mr1403_2 (All); LR P-value: 7.04E-25;
mr1404_2 (All); LR P-value: 8.47E-51;
mr1416_2 (All); LR P-value: 2.24E-17;
mr1423_2 (All); LR P-value: 8.91E-34;
mr1435_2 (All); LR P-value: 5.89E-43;
mr1437_2 (All); LR P-value: 5.58E-46;
mr1490_2 (All); LR P-value: 5.52E-64;
mr1546_2 (All); LR P-value: 7.35E-49;
mr1599_2 (All); LMM P-value: 2.12E-07; LR P-value: 7.90E-75;
mr1620_2 (All); LR P-value: 6.48E-48;
mr1629_2 (All); LR P-value: 7.55E-101;
mr1637_2 (All); LR P-value: 1.46E-19;
mr1676_2 (All); LR P-value: 7.27E-21;
mr1749_2 (All); LR P-value: 2.42E-08;
mr1780_2 (All); LR P-value: 8.57E-37;
mr1821_2 (All); LR P-value: 4.01E-08;
mr1828_2 (All); LR P-value: 1.70E-66;
mr1944_2 (All); LR P-value: 8.62E-42;
mr1949_2 (All); LR P-value: 7.95E-25
LOC_Os02g27430.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.577; most accessible tissue: Zhenshan97 young leaf, score: 86.852
vg0216160840 (J) chr02 16160840 G T 93.80% 0.00% G -> T NA
LOC_Os02g27430.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 60.186; most accessible tissue: Zhenshan97 young leaf, score: 86.383
vg0216160858 (J) chr02 16160858 G A 96.40% 0.00% G -> A NA
LOC_Os02g27430.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.480; most accessible tissue: Zhenshan97 young leaf, score: 86.698
vg0216160886 (J) chr02 16160886 G A 96.40% 0.00% G -> A NA
LOC_Os02g27430.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.184; most accessible tissue: Zhenshan97 young leaf, score: 87.153
vg0216160889 (J) chr02 16160889 G A 65.50% 0.00% A -> G
mr1016 (All); LR P-value: 4.46E-45;
mr1018 (All); LR P-value: 4.67E-73;
mr1082 (All); LR P-value: 9.18E-41;
mr1085 (All); LR P-value: 1.34E-31;
mr1086 (All); LR P-value: 2.71E-31;
mr1089 (All); LMM P-value: 4.74E-07; LR P-value: 2.33E-45;
mr1093 (All); LMM P-value: 1.87E-09; LR P-value: 1.28E-50;
mr1103 (All); LR P-value: 4.40E-57;
mr1107 (All); LR P-value: 4.49E-33;
mr1132 (All); LR P-value: 4.28E-71;
mr1136 (All); LR P-value: 1.34E-42;
mr1138 (All); LR P-value: 6.50E-12;
mr1145 (All); LR P-value: 6.19E-29;
mr1170 (All); LR P-value: 2.34E-12;
mr1178 (All); LR P-value: 1.05E-56;
mr1226 (All); LR P-value: 1.12E-29;
mr1235 (All); LR P-value: 1.67E-44;
mr1243 (All); LR P-value: 1.46E-36;
mr1251 (All); LR P-value: 1.23E-24;
mr1257 (All); LR P-value: 6.63E-30;
mr1390 (All); LR P-value: 6.54E-54;
mr1411 (All); LR P-value: 3.97E-26;
mr1423 (All); LR P-value: 2.00E-32;
mr1435 (All); LR P-value: 5.41E-38;
mr1448 (All); LR P-value: 1.01E-31;
mr1490 (All); LR P-value: 1.41E-52;
mr1518 (All); LR P-value: 6.26E-20;
mr1541 (All); LR P-value: 3.84E-21;
mr1546 (All); LR P-value: 8.66E-32;
mr1599 (All); LR P-value: 1.91E-58;
mr1629 (All); LR P-value: 6.86E-74;
mr1637 (All); LR P-value: 1.97E-09;
mr1663 (All); LR P-value: 2.56E-09;
mr1676 (All); LR P-value: 3.95E-21;
mr1767 (All); LR P-value: 1.11E-17;
mr1780 (All); LR P-value: 2.46E-37;
mr1905 (All); LR P-value: 9.94E-10;
mr1932 (All); LR P-value: 2.16E-33;
mr1949 (All); LR P-value: 1.63E-13;
mr1030_2 (All); LR P-value: 1.03E-07;
mr1055_2 (All); LR P-value: 1.44E-47;
mr1085_2 (All); LR P-value: 3.93E-32;
mr1089_2 (All); LR P-value: 3.28E-55;
mr1093_2 (All); LMM P-value: 4.17E-07; LR P-value: 1.46E-59;
mr1104_2 (All); LR P-value: 1.28E-37;
mr1107_2 (All); LR P-value: 1.18E-36;
mr1132_2 (All); LR P-value: 2.20E-82;
mr1138_2 (All); LR P-value: 3.59E-12;
mr1155_2 (All); LR P-value: 1.63E-35;
mr1175_2 (All); LR P-value: 3.45E-21;
mr1178_2 (All); LR P-value: 5.72E-78;
mr1226_2 (All); LR P-value: 1.22E-38;
mr1233_2 (All); LR P-value: 1.70E-24;
mr1235_2 (All); LMM P-value: 6.31E-06; LR P-value: 8.54E-64;
mr1243_2 (All); LR P-value: 2.15E-47;
mr1251_2 (All); LR P-value: 1.75E-41;
mr1257_2 (All); LR P-value: 1.38E-39;
mr1377_2 (All); LR P-value: 2.20E-11;
mr1379_2 (All); LR P-value: 1.83E-09;
mr1390_2 (All); LR P-value: 7.61E-63;
mr1403_2 (All); LR P-value: 2.57E-24;
mr1416_2 (All); LR P-value: 1.94E-17;
mr1423_2 (All); LR P-value: 1.07E-32;
mr1435_2 (All); LR P-value: 2.26E-41;
mr1437_2 (All); LR P-value: 1.32E-44;
mr1490_2 (All); LR P-value: 1.38E-64;
mr1546_2 (All); LR P-value: 2.40E-49;
mr1599_2 (All); LR P-value: 3.52E-72;
mr1637_2 (All); LR P-value: 1.31E-19;
mr1683_2 (All); LR P-value: 2.35E-07;
mr1749_2 (All); LR P-value: 3.97E-08;
mr1780_2 (All); LR P-value: 3.62E-36;
mr1806_2 (All); LR P-value: 5.23E-10;
mr1821_2 (All); LR P-value: 6.74E-08;
mr1838_2 (All); LR P-value: 3.88E-13;
mr1944_2 (All); LR P-value: 1.01E-40;
mr1949_2 (All); LR P-value: 1.52E-24
LOC_Os02g27430.1 Alt: G| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.092; most accessible tissue: Zhenshan97 young leaf, score: 87.153
STR0216160591 (J) chr02 16160591 CCAAAC CCAAAA 56.60% 0.00% CCAAAA -> CCAAAC NA