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Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

12 variations found. LOC_Os03g08930 (helix-loop-helix DNA-binding protein; putative; expressed), ranging from 4,628,934 bp to 4,630,514 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
vg0304629001 (J) chr03 4629001 GA G 64.60% 0.00% G -> GA,C NA
LOC_Os03g08930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08930.1 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.744; most accessible tissue: Minghui63 root, score: 95.988
vg0304629012 (J) chr03 4629012 G C 64.90% 0.00% C -> G
mr1008 (All); LR P-value: 8.53E-102;
mr1009 (All); LR P-value: 3.13E-99;
mr1072 (All); LR P-value: 1.37E-26;
mr1075 (All); LR P-value: 3.64E-29;
mr1081 (All); LR P-value: 3.44E-33;
mr1092 (All); LR P-value: 5.48E-44;
mr1103 (All); LR P-value: 1.48E-55;
mr1124 (All); LR P-value: 1.36E-39;
mr1152 (All); LR P-value: 2.47E-44;
mr1154 (All); LR P-value: 1.44E-49;
mr1202 (All); LR P-value: 6.49E-29;
mr1256 (All); LR P-value: 1.51E-30;
mr1325 (All); LR P-value: 7.90E-11;
mr1326 (All); LR P-value: 7.64E-13;
mr1690 (All); LR P-value: 7.81E-07;
mr1695 (All); LR P-value: 1.74E-60;
mr1698 (All); LR P-value: 1.43E-21;
mr1711 (All); LR P-value: 4.47E-61;
mr1758 (All); LR P-value: 2.22E-94;
mr1861 (All); LR P-value: 2.69E-56;
mr1865 (All); LR P-value: 5.27E-72;
mr1874 (All); LR P-value: 2.02E-13;
mr1987 (All); LR P-value: 1.11E-98;
mr1072_2 (All); LR P-value: 2.74E-38;
mr1075_2 (All); LR P-value: 2.04E-37;
mr1082_2 (All); LR P-value: 4.87E-37;
mr1085_2 (All); LR P-value: 7.09E-33;
mr1103_2 (All); LR P-value: 5.77E-69;
mr1104_2 (All); LR P-value: 8.48E-37;
mr1107_2 (All); LR P-value: 9.71E-36;
mr1145_2 (All); LR P-value: 5.72E-43;
mr1155_2 (All); LR P-value: 2.46E-37;
mr1264_2 (All); LR P-value: 1.93E-40;
mr1324_2 (All); LR P-value: 3.82E-15;
mr1326_2 (All); LR P-value: 6.32E-14;
mr1333_2 (All); LR P-value: 5.74E-15;
mr1342_2 (All); LR P-value: 1.74E-16;
mr1403_2 (All); LR P-value: 3.64E-26;
mr1404_2 (All); LR P-value: 4.96E-50;
mr1486_2 (All); LR P-value: 7.02E-48;
mr1592_2 (All); LR P-value: 2.97E-16;
mr1623_2 (All); LR P-value: 4.06E-07;
mr1637_2 (All); LR P-value: 1.44E-18;
mr1671_2 (All); LR P-value: 4.26E-79;
mr1695_2 (All); LR P-value: 1.02E-59;
mr1713_2 (All); LR P-value: 1.73E-12;
mr1721_2 (All); LR P-value: 1.33E-48;
mr1733_2 (All); LR P-value: 1.68E-62;
mr1783_2 (All); LR P-value: 1.30E-07;
mr1795_2 (All); LR P-value: 7.98E-90;
mr1804_2 (All); LR P-value: 1.66E-07;
mr1861_2 (All); LR P-value: 6.42E-49;
mr1878_2 (All); LR P-value: 4.26E-36
LOC_Os03g08930.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.099; most accessible tissue: Minghui63 root, score: 95.527
vg0304629026 (J) chr03 4629026 T C 64.80% 0.00% C -> T
mr1072 (All); LR P-value: 1.90E-26;
mr1075 (All); LR P-value: 1.09E-28;
mr1092 (All); LR P-value: 1.04E-43;
mr1103 (All); LR P-value: 9.34E-56;
mr1124 (All); LR P-value: 8.15E-40;
mr1152 (All); LR P-value: 2.01E-43;
mr1256 (All); LR P-value: 2.01E-29;
mr1325 (All); LR P-value: 6.38E-11;
mr1326 (All); LR P-value: 5.14E-13;
mr1350 (All); LR P-value: 6.72E-34;
mr1690 (All); LR P-value: 1.05E-06;
mr1695 (All); LR P-value: 1.81E-59;
mr1698 (All); LR P-value: 5.98E-21;
mr1711 (All); LR P-value: 7.53E-61;
mr1733 (All); LR P-value: 2.96E-33;
mr1758 (All); LR P-value: 4.06E-95;
mr1795 (All); LR P-value: 1.04E-51;
mr1861 (All); LR P-value: 2.99E-56;
mr1865 (All); LR P-value: 1.10E-72;
mr1987 (All); LR P-value: 1.02E-98;
mr1064_2 (All); LR P-value: 5.87E-58;
mr1070_2 (All); LR P-value: 6.66E-45;
mr1072_2 (All); LR P-value: 5.85E-38;
mr1075_2 (All); LR P-value: 4.88E-37;
mr1082_2 (All); LR P-value: 9.75E-37;
mr1085_2 (All); LR P-value: 2.94E-33;
mr1103_2 (All); LR P-value: 1.99E-69;
mr1107_2 (All); LR P-value: 1.85E-35;
mr1145_2 (All); LR P-value: 2.41E-43;
mr1155_2 (All); LR P-value: 3.26E-38;
mr1216_2 (All); LR P-value: 3.98E-11;
mr1246_2 (All); LR P-value: 2.41E-75;
mr1264_2 (All); LR P-value: 8.48E-41;
mr1299_2 (All); LR P-value: 5.74E-08;
mr1324_2 (All); LR P-value: 2.37E-15;
mr1326_2 (All); LR P-value: 4.40E-14;
mr1333_2 (All); LR P-value: 3.57E-15;
mr1342_2 (All); LR P-value: 1.28E-16;
mr1402_2 (All); LR P-value: 7.65E-61;
mr1403_2 (All); LR P-value: 4.56E-26;
mr1437_2 (All); LR P-value: 2.05E-44;
mr1486_2 (All); LR P-value: 2.54E-47;
mr1536_2 (All); LR P-value: 7.98E-94;
mr1592_2 (All); LR P-value: 9.30E-17;
mr1623_2 (All); LR P-value: 2.01E-07;
mr1637_2 (All); LR P-value: 4.93E-19;
mr1671_2 (All); LR P-value: 4.60E-81;
mr1689_2 (All); LR P-value: 3.91E-36;
mr1695_2 (All); LR P-value: 2.63E-59;
mr1713_2 (All); LR P-value: 7.71E-13;
mr1721_2 (All); LR P-value: 1.96E-47;
mr1733_2 (All); LR P-value: 9.84E-65;
mr1783_2 (All); LR P-value: 8.88E-08;
mr1795_2 (All); LR P-value: 6.49E-91;
mr1804_2 (All); LR P-value: 1.25E-07;
mr1861_2 (All); LR P-value: 1.82E-48;
mr1865_2 (All); LR P-value: 4.46E-89;
mr1878_2 (All); LR P-value: 1.11E-35
LOC_Os03g08930.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g08930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.692; most accessible tissue: Minghui63 root, score: 95.016
vg0304629209 (J) chr03 4629209 C T 89.70% 0.00% C -> T
mr1554 (All); LR P-value: 1.34E-08;
mr1602 (All); LR P-value: 7.94E-07;
mr1097_2 (All); LR P-value: 3.60E-13;
mr1295_2 (All); LR P-value: 2.23E-07;
mr1668_2 (All); LR P-value: 1.39E-08
LOC_Os03g08930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.642; most accessible tissue: Minghui63 panicle, score: 91.410
vg0304629293 (J) chr03 4629293 C A 64.90% 0.00% A -> C NA
LOC_Os03g08930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.104; most accessible tissue: Zhenshan97 panicle, score: 91.374
vg0304629336 (J) chr03 4629336 C T 83.90% 0.00% C -> T NA
LOC_Os03g08930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.762; most accessible tissue: Minghui63 panicle, score: 90.408
vg0304629908 (J) chr03 4629908 G A 82.10% 0.00% A -> G
Heading_date (Jap_All); LR P-value: 4.55E-11;
Plant_height (Jap_All); LR P-value: 2.19E-14;
Spikelet_length (Jap_All); LR P-value: 4.91E-13;
mr1010 (Jap_All); LR P-value: 1.36E-06;
mr1063 (Jap_All); LR P-value: 8.51E-06;
mr1115 (Jap_All); LR P-value: 1.98E-15;
mr1163 (All); LR P-value: 9.15E-22;
mr1163 (Jap_All); LR P-value: 2.19E-08;
mr1183 (Jap_All); LR P-value: 8.47E-07;
mr1503 (Jap_All); LR P-value: 1.24E-06;
mr1531 (Jap_All); LR P-value: 5.45E-07;
mr1570 (Jap_All); LR P-value: 2.43E-06;
mr1611 (Jap_All); LR P-value: 2.77E-13;
mr1657 (Jap_All); LR P-value: 9.70E-06;
mr1723 (Jap_All); LR P-value: 4.20E-07;
mr1729 (Jap_All); LR P-value: 8.37E-08;
mr1740 (All); LR P-value: 3.43E-13;
mr1920 (All); LR P-value: 3.66E-22;
mr1920 (Jap_All); LR P-value: 1.19E-12;
mr1977 (All); LR P-value: 4.93E-06;
mr1002_2 (All); LR P-value: 2.45E-09;
mr1010_2 (All); LR P-value: 1.17E-23;
mr1010_2 (Jap_All); LR P-value: 5.19E-08;
mr1011_2 (All); LR P-value: 1.12E-10;
mr1011_2 (Jap_All); LR P-value: 4.08E-06;
mr1013_2 (All); LR P-value: 6.17E-19;
mr1013_2 (Jap_All); LR P-value: 1.93E-07;
mr1031_2 (All); LR P-value: 7.65E-17;
mr1031_2 (Jap_All); LR P-value: 1.05E-07;
mr1115_2 (All); LR P-value: 1.59E-28;
mr1115_2 (Jap_All); LR P-value: 2.23E-17;
mr1137_2 (All); LR P-value: 9.77E-32;
mr1156_2 (All); LR P-value: 4.63E-19;
mr1180_2 (Jap_All); LR P-value: 1.70E-08;
mr1183_2 (Jap_All); LR P-value: 4.55E-08;
mr1229_2 (All); LR P-value: 6.37E-07;
mr1241_2 (All); LR P-value: 3.33E-61;
mr1252_2 (All); LR P-value: 8.71E-07;
mr1277_2 (All); LR P-value: 1.25E-14;
mr1359_2 (Jap_All); LR P-value: 2.65E-06;
mr1482_2 (All); LR P-value: 2.89E-08;
mr1486_2 (All); LR P-value: 6.63E-48;
mr1486_2 (Jap_All); LR P-value: 7.52E-11;
mr1521_2 (Jap_All); LR P-value: 2.18E-07;
mr1570_2 (Jap_All); LR P-value: 3.31E-07;
mr1580_2 (Jap_All); LR P-value: 1.45E-10;
mr1588_2 (Jap_All); LR P-value: 9.38E-06;
mr1611_2 (All); LR P-value: 1.84E-24;
mr1611_2 (Jap_All); LR P-value: 1.16E-12;
mr1671_2 (Jap_All); LR P-value: 1.48E-08;
mr1741_2 (All); LR P-value: 6.62E-10;
mr1789_2 (All); LR P-value: 1.46E-29;
mr1794_2 (Jap_All); LR P-value: 4.07E-08;
mr1825_2 (Jap_All); LR P-value: 5.39E-10;
mr1865_2 (Jap_All); LR P-value: 8.23E-06;
mr1879_2 (Jap_All); LR P-value: 6.47E-08
LOC_Os03g08930.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.060; most accessible tissue: Zhenshan97 panicle, score: 89.143
vg0304630073 (J) chr03 4630073 G C 51.40% 0.00% G -> C
mr1739 (All); LMM P-value: 2.03E-06;
mr1739 (Ind_All); LMM P-value: 4.39E-07;
mr1045_2 (All); LR P-value: 1.00E-06;
mr1053_2 (All); LR P-value: 1.67E-07;
mr1144_2 (Ind_All); LR P-value: 1.74E-06;
mr1147_2 (All); LR P-value: 2.12E-12;
mr1212_2 (All); LR P-value: 9.83E-07;
mr1299_2 (All); LR P-value: 5.89E-09;
mr1624_2 (All); LR P-value: 2.01E-09;
mr1700_2 (All); LR P-value: 7.48E-09;
mr1713_2 (All); LR P-value: 8.09E-13;
mr1727_2 (All); LR P-value: 1.41E-07;
mr1756_2 (All); LR P-value: 2.04E-10;
mr1785_2 (All); LR P-value: 5.81E-07;
mr1804_2 (All); LR P-value: 1.11E-07;
mr1837_2 (All); LR P-value: 2.28E-07;
mr1842_2 (Ind_All); LR P-value: 3.14E-07;
mr1915_2 (All); LR P-value: 1.56E-06;
mr1938_2 (All); LR P-value: 7.27E-14
LOC_Os03g08930.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 79.037; most accessible tissue: Minghui63 young leaf, score: 84.814
vg0304630176 (J) chr03 4630176 T C 99.60% 0.00% T -> C NA
LOC_Os03g08940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g08930.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.235; most accessible tissue: Callus, score: 88.143
vg0304630358 (J) chr03 4630358 G T 90.10% 0.00% G -> T
mr1248 (All); LR P-value: 2.95E-07;
mr1248 (Jap_All); LR P-value: 1.73E-08;
mr1252 (Jap_All); LR P-value: 1.60E-06;
mr1449_2 (All); LR P-value: 1.98E-08;
mr1449_2 (Jap_All); LR P-value: 9.35E-06;
mr1696_2 (All); LR P-value: 2.05E-07;
mr1905_2 (All); LR P-value: 1.07E-09
LOC_Os03g08930.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08940.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.627; most accessible tissue: Zhenshan97 panicle, score: 86.788
vg0304630399 (J) chr03 4630399 T C 96.20% 0.00% T -> C NA
LOC_Os03g08930.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08940.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.273; most accessible tissue: Zhenshan97 panicle, score: 88.062
vg0304630468 (J) chr03 4630468 G T 83.20% 0.00% G -> T
Heading_date (Jap_All); LR P-value: 6.92E-10;
Plant_height (Jap_All); LR P-value: 4.45E-13;
Spikelet_length (Jap_All); LR P-value: 2.12E-11;
mr1010 (Jap_All); LR P-value: 8.86E-06;
mr1163 (Jap_All); LR P-value: 1.71E-07;
mr1183 (Jap_All); LR P-value: 3.78E-06;
mr1338 (All); LR P-value: 1.79E-06;
mr1503 (Jap_All); LR P-value: 5.18E-06;
mr1531 (Jap_All); LR P-value: 1.96E-06;
mr1729 (All); LR P-value: 2.74E-06;
mr1729 (Jap_All); LR P-value: 1.08E-06;
mr1871 (All); LR P-value: 7.19E-13;
mr1920 (Jap_All); LR P-value: 3.90E-11;
mr1010_2 (Jap_All); LR P-value: 1.27E-07;
mr1011_2 (Jap_All); LR P-value: 3.53E-06;
mr1013_2 (Jap_All); LR P-value: 3.67E-07;
mr1031_2 (Jap_All); LR P-value: 1.00E-07;
mr1115_2 (Jap_All); LR P-value: 6.28E-16;
mr1180_2 (Jap_All); LR P-value: 2.13E-08;
mr1183_2 (Jap_All); LR P-value: 6.92E-08;
mr1338_2 (All); LR P-value: 6.63E-10;
mr1338_2 (Jap_All); LR P-value: 2.01E-07;
mr1359_2 (Jap_All); LR P-value: 6.60E-06;
mr1388_2 (All); LR P-value: 1.03E-08;
mr1449_2 (All); LR P-value: 1.12E-11;
mr1449_2 (Jap_All); LR P-value: 3.65E-06;
mr1454_2 (All); LR P-value: 8.65E-16;
mr1454_2 (Jap_All); LR P-value: 1.25E-08;
mr1486_2 (Jap_All); LR P-value: 1.44E-09;
mr1521_2 (Jap_All); LR P-value: 5.26E-07;
mr1543_2 (All); LR P-value: 1.87E-08;
mr1554_2 (All); LR P-value: 7.50E-09;
mr1580_2 (Jap_All); LR P-value: 2.02E-10;
mr1611_2 (Jap_All); LR P-value: 2.14E-11;
mr1671_2 (Jap_All); LR P-value: 5.62E-08;
mr1680_2 (All); LR P-value: 4.28E-10;
mr1742_2 (All); LR P-value: 5.35E-14;
mr1794_2 (Jap_All); LR P-value: 8.30E-08;
mr1825_2 (Jap_All); LR P-value: 6.92E-10;
mr1851_2 (All); LR P-value: 1.26E-10;
mr1864_2 (All); LR P-value: 5.75E-15;
mr1865_2 (Jap_All); LR P-value: 4.50E-06;
mr1966_2 (All); LR P-value: 1.30E-08
LOC_Os03g08930.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g08940.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.222; most accessible tissue: Zhenshan97 panicle, score: 86.788