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Search Results:

11 variations found. LOC_Os09g29130 (ZF-HD protein dimerisation region containing protein; expressed), ranging from 17,703,753 bp to 17,705,611 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
vg0917703892 (J) chr09 17703892 C CA 99.90% 0.00% C -> CA NA
The average chromatin accessibility score: 84.587; most accessible tissue: Callus, score: 98.175
vg0917704239 (J) chr09 17704239 G T 54.00% 0.13% G -> T
mr1011 (All); LR P-value: 9.81E-06;
mr1034 (All); LR P-value: 2.28E-12;
mr1058 (All); LR P-value: 2.77E-06;
mr1138 (All); LR P-value: 1.42E-16;
mr1138 (Ind_All); LR P-value: 9.45E-10;
mr1354 (Ind_All); LR P-value: 7.33E-07;
mr1568 (All); LR P-value: 1.71E-06;
mr1637 (All); LR P-value: 1.10E-08;
mr1707 (Ind_All); LR P-value: 2.75E-07;
mr1716 (All); LR P-value: 1.43E-07;
mr1728 (Ind_All); LR P-value: 3.27E-11;
mr1860 (Ind_All); LR P-value: 1.21E-07;
mr1138_2 (All); LR P-value: 2.19E-16;
mr1138_2 (Ind_All); LR P-value: 2.74E-09;
mr1527_2 (All); LR P-value: 1.39E-07;
mr1728_2 (Ind_All); LR P-value: 6.39E-11;
mr1860_2 (Ind_All); LR P-value: 1.76E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.815; most accessible tissue: Minghui63 flag leaf, score: 96.501
vg0917704417 (J) chr09 17704417 G A 65.30% 0.00% A -> G
mr1008 (All); LR P-value: 1.11E-109;
mr1009 (All); LR P-value: 1.06E-107;
mr1014 (All); LR P-value: 5.81E-71;
mr1019 (All); LR P-value: 1.06E-55;
mr1024 (All); LR P-value: 1.99E-25;
mr1027 (All); LR P-value: 2.08E-65;
mr1074 (All); LR P-value: 6.60E-32;
mr1081 (All); LR P-value: 6.10E-37;
mr1082 (All); LR P-value: 5.70E-40;
mr1092 (All); LR P-value: 4.31E-48;
mr1102 (All); LR P-value: 6.23E-20;
mr1103 (All); LR P-value: 4.51E-57;
mr1107 (All); LR P-value: 1.13E-29;
mr1134 (All); LR P-value: 7.06E-86;
mr1135 (All); LR P-value: 7.22E-79;
mr1146 (All); LR P-value: 5.94E-15;
mr1148 (All); LR P-value: 2.23E-28;
mr1152 (All); LR P-value: 2.90E-48;
mr1154 (All); LR P-value: 2.57E-53;
mr1172 (All); LR P-value: 5.61E-11;
mr1194 (All); LR P-value: 9.23E-46;
mr1223 (All); LR P-value: 7.42E-26;
mr1228 (All); LR P-value: 1.86E-15;
mr1254 (All); LR P-value: 8.70E-21;
mr1256 (All); LR P-value: 5.29E-31;
mr1276 (All); LR P-value: 2.67E-15;
mr1298 (All); LR P-value: 1.82E-28;
mr1323 (All); LR P-value: 2.10E-15;
mr1324 (All); LR P-value: 1.44E-16;
mr1333 (All); LR P-value: 4.37E-34;
mr1335 (All); LR P-value: 1.52E-13;
mr1414 (All); LR P-value: 3.71E-27;
mr1504 (All); LR P-value: 3.65E-94;
mr1517 (All); LR P-value: 8.14E-87;
mr1518 (All); LR P-value: 3.95E-20;
mr1542 (All); LR P-value: 3.47E-36;
mr1579 (All); LR P-value: 1.40E-12;
mr1591 (All); LR P-value: 3.36E-42;
mr1594 (All); LR P-value: 1.41E-56;
mr1601 (All); LR P-value: 4.16E-38;
mr1623 (All); LR P-value: 8.04E-11;
mr1645 (All); LR P-value: 5.68E-42;
mr1647 (All); LR P-value: 1.75E-33;
mr1670 (All); LR P-value: 2.80E-35;
mr1672 (All); LR P-value: 1.81E-87;
mr1676 (All); LR P-value: 5.97E-20;
mr1682 (All); LR P-value: 2.46E-39;
mr1686 (All); LR P-value: 1.71E-29;
mr1695 (All); LR P-value: 4.61E-62;
mr1711 (All); LR P-value: 1.51E-65;
mr1723 (All); LR P-value: 4.06E-28;
mr1731 (All); LR P-value: 6.24E-26;
mr1750 (All); LR P-value: 4.30E-116;
mr1754 (All); LR P-value: 8.85E-21;
mr1758 (All); LR P-value: 6.73E-90;
mr1767 (All); LR P-value: 6.92E-18;
mr1839 (All); LR P-value: 2.02E-21;
mr1861 (All); LR P-value: 1.90E-53;
mr1865 (All); LR P-value: 5.61E-78;
mr1873 (All); LR P-value: 3.88E-42;
mr1889 (All); LR P-value: 1.00E-55;
mr1891 (All); LR P-value: 1.22E-38;
mr1896 (All); LR P-value: 2.26E-73;
mr1907 (All); LR P-value: 2.84E-76;
mr1917 (All); LR P-value: 1.41E-26;
mr1922 (All); LR P-value: 1.35E-30;
mr1924 (All); LR P-value: 6.51E-13;
mr1987 (All); LR P-value: 1.50E-111;
mr1074_2 (All); LR P-value: 1.31E-26;
mr1081_2 (All); LR P-value: 3.48E-33;
mr1082_2 (All); LR P-value: 1.49E-36;
mr1085_2 (All); LR P-value: 1.97E-32;
mr1092_2 (All); LR P-value: 3.03E-41;
mr1103_2 (All); LR P-value: 1.18E-70;
mr1104_2 (All); LR P-value: 1.57E-36;
mr1107_2 (All); LR P-value: 1.03E-37;
mr1145_2 (All); LR P-value: 2.60E-41;
mr1150_2 (All); LR P-value: 7.63E-31;
mr1152_2 (All); LR P-value: 2.38E-40;
mr1154_2 (All); LR P-value: 4.79E-52;
mr1233_2 (All); LR P-value: 1.40E-25;
mr1242_2 (All); LR P-value: 2.72E-23;
mr1246_2 (All); LR P-value: 3.51E-78;
mr1256_2 (All); LR P-value: 6.29E-35;
mr1264_2 (All); LR P-value: 9.72E-39;
mr1281_2 (All); LR P-value: 2.30E-17;
mr1324_2 (All); LR P-value: 1.76E-15;
mr1342_2 (All); LR P-value: 4.67E-19;
mr1403_2 (All); LR P-value: 5.92E-24;
mr1404_2 (All); LR P-value: 6.55E-50;
mr1416_2 (All); LR P-value: 2.55E-16;
mr1486_2 (All); LR P-value: 7.20E-46;
mr1591_2 (All); LR P-value: 8.31E-47;
mr1657_2 (All); LR P-value: 1.08E-18;
mr1672_2 (All); LR P-value: 1.91E-118;
mr1676_2 (All); LR P-value: 1.21E-21;
mr1686_2 (All); LR P-value: 6.38E-15;
mr1733_2 (All); LR P-value: 2.04E-61;
mr1795_2 (All); LR P-value: 2.73E-86;
mr1861_2 (All); LR P-value: 6.38E-49;
mr1865_2 (All); LR P-value: 5.87E-99;
mr1878_2 (All); LR P-value: 1.24E-35;
mr1889_2 (All); LR P-value: 2.30E-67;
mr1890_2 (All); LR P-value: 2.34E-50;
mr1891_2 (All); LR P-value: 1.88E-31;
mr1949_2 (All); LR P-value: 4.97E-23;
mr1962_2 (All); LR P-value: 1.56E-120
LOC_Os09g29130.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.467; most accessible tissue: Minghui63 flag leaf, score: 97.346
vg0917704683 (J) chr09 17704683 G A 69.10% 0.42% A -> G NA
LOC_Os09g29130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g29130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.120; most accessible tissue: Minghui63 flag leaf, score: 97.994
vg0917704696 (J) chr09 17704696 G A 47.90% 1.88% G -> A NA
LOC_Os09g29130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.955; most accessible tissue: Minghui63 flag leaf, score: 97.979
vg0917704846 (J) chr09 17704846 G A 65.30% 0.00% A -> G
mr1008 (All); LR P-value: 5.35E-106;
mr1009 (All); LR P-value: 2.51E-104;
mr1014 (All); LR P-value: 3.27E-69;
mr1074 (All); LR P-value: 1.32E-31;
mr1081 (All); LR P-value: 1.01E-36;
mr1082 (All); LR P-value: 1.02E-39;
mr1092 (All); LR P-value: 1.74E-47;
mr1102 (All); LR P-value: 6.47E-20;
mr1103 (All); LR P-value: 8.19E-57;
mr1116 (All); LR P-value: 2.36E-16;
mr1134 (All); LR P-value: 1.59E-83;
mr1135 (All); LR P-value: 2.77E-77;
mr1146 (All); LR P-value: 2.08E-14;
mr1148 (All); LR P-value: 1.30E-27;
mr1152 (All); LR P-value: 6.45E-47;
mr1154 (All); LR P-value: 2.42E-52;
mr1194 (All); LR P-value: 2.39E-45;
mr1228 (All); LR P-value: 2.59E-15;
mr1256 (All); LR P-value: 5.96E-31;
mr1275 (All); LR P-value: 1.23E-08;
mr1276 (All); LR P-value: 1.06E-14;
mr1298 (All); LR P-value: 3.42E-28;
mr1323 (All); LR P-value: 2.16E-15;
mr1324 (All); LR P-value: 2.88E-16;
mr1333 (All); LR P-value: 5.24E-34;
mr1335 (All); LR P-value: 2.31E-13;
mr1414 (All); LR P-value: 1.06E-27;
mr1504 (All); LR P-value: 1.56E-92;
mr1518 (All); LR P-value: 1.07E-19;
mr1579 (All); LR P-value: 2.62E-12;
mr1601 (All); LR P-value: 3.92E-39;
mr1623 (All); LR P-value: 1.12E-10;
mr1645 (All); LR P-value: 3.50E-41;
mr1647 (All); LR P-value: 5.79E-33;
mr1660 (All); LR P-value: 7.15E-08;
mr1670 (All); LR P-value: 1.25E-34;
mr1672 (All); LR P-value: 7.77E-85;
mr1682 (All); LR P-value: 8.00E-39;
mr1686 (All); LR P-value: 1.48E-28;
mr1695 (All); LR P-value: 3.84E-62;
mr1711 (All); LR P-value: 6.73E-66;
mr1731 (All); LR P-value: 8.35E-26;
mr1754 (All); LR P-value: 1.52E-20;
mr1758 (All); LR P-value: 3.34E-86;
mr1767 (All); LR P-value: 1.03E-17;
mr1865 (All); LR P-value: 7.73E-76;
mr1873 (All); LR P-value: 1.33E-40;
mr1889 (All); LR P-value: 1.91E-55;
mr1896 (All); LR P-value: 1.20E-71;
mr1917 (All); LR P-value: 1.99E-26;
mr1922 (All); LR P-value: 1.54E-30;
mr1924 (All); LR P-value: 4.00E-13;
mr1987 (All); LR P-value: 9.72E-109;
mr1072_2 (All); LR P-value: 8.27E-38;
mr1075_2 (All); LR P-value: 9.30E-37;
mr1081_2 (All); LR P-value: 6.68E-32;
mr1082_2 (All); LR P-value: 4.09E-37;
mr1085_2 (All); LR P-value: 1.85E-33;
mr1092_2 (All); LR P-value: 3.86E-39;
mr1103_2 (All); LR P-value: 7.70E-71;
mr1104_2 (All); LR P-value: 4.26E-37;
mr1107_2 (All); LR P-value: 3.08E-38;
mr1145_2 (All); LR P-value: 1.41E-42;
mr1149_2 (All); LR P-value: 3.79E-26;
mr1154_2 (All); LR P-value: 4.82E-50;
mr1155_2 (All); LR P-value: 1.43E-36;
mr1233_2 (All); LR P-value: 2.95E-26;
mr1242_2 (All); LR P-value: 1.07E-22;
mr1246_2 (All); LR P-value: 1.38E-78;
mr1256_2 (All); LR P-value: 1.66E-33;
mr1264_2 (All); LR P-value: 9.16E-40;
mr1324_2 (All); LR P-value: 2.09E-15;
mr1333_2 (All); LR P-value: 3.93E-14;
mr1342_2 (All); LR P-value: 6.37E-19;
mr1403_2 (All); LR P-value: 1.91E-24;
mr1404_2 (All); LR P-value: 9.97E-51;
mr1416_2 (All); LR P-value: 7.85E-17;
mr1486_2 (All); LR P-value: 3.56E-46;
mr1591_2 (All); LR P-value: 6.88E-47;
mr1620_2 (All); LR P-value: 4.18E-47;
mr1637_2 (All); LR P-value: 3.42E-19;
mr1676_2 (All); LR P-value: 8.72E-22;
mr1733_2 (All); LR P-value: 1.59E-62;
mr1770_2 (All); LR P-value: 1.47E-12;
mr1861_2 (All); LR P-value: 2.27E-48;
mr1865_2 (All); LR P-value: 8.79E-97;
mr1878_2 (All); LR P-value: 1.25E-36;
mr1890_2 (All); LR P-value: 3.80E-50;
mr1891_2 (All); LR P-value: 5.28E-31;
mr1949_2 (All); LR P-value: 9.93E-24
LOC_Os09g29130.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.996; most accessible tissue: Minghui63 flag leaf, score: 98.688
vg0917705039 (J) chr09 17705039 T C 65.30% 0.00% C -> T NA
LOC_Os09g29130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.906; most accessible tissue: Minghui63 flag leaf, score: 98.767
vg0917705490 (J) chr09 17705490 GCTCTCT GCTCTCT CT 60.80% 1.76% GCTCTCT -> GCTCTATCTC TCT,GCTCTC TCT,GCTCTC TCTCTCTCT, GCTCTCTCTC T,GCTCTCTC TCTCT,G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: GCTCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: GCTCTATCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: GCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: GCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: GCTCTCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.995; most accessible tissue: Minghui63 flag leaf, score: 99.526
vg0917705491 (J) chr09 17705491 C CTCTA 78.60% 9.65% C -> CTCTA NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: CTCTA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.999; most accessible tissue: Minghui63 flag leaf, score: 99.526
vg0917705493 (J) chr09 17705493 CTA C 57.00% 0.00% C -> CTA NA
The average chromatin accessibility score: 96.071; most accessible tissue: Minghui63 flag leaf, score: 99.529
vg0917705495 (J) chr09 17705495 C A 63.20% 25.22% C -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 96.036; most accessible tissue: Minghui63 flag leaf, score: 99.524