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17 variations found. Os03g0825800/LOC_Os03g61060 (protein kinase domain containing protein; expressed), ranging from 34,688,285 bp to 34,690,737 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os03g61060 protein kinase domain containing protein, expressed; RAP ID: Os03g0825800; MSU ID: LOC_Os03g61060

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg0334688295 (J) chr03 34688295 A G 59.90% 0.00% A -> G
mr1850 (All); LR P-value: 1.64E-06;
mr1212_2 (All); LR P-value: 8.42E-08;
mr1649_2 (All); LR P-value: 4.67E-10;
mr1671_2 (All); LMM P-value: 2.47E-07;
mr1671_2 (Ind_All); LMM P-value: 2.30E-07;
mr1798_2 (Ind_All); LR P-value: 1.19E-08
LOC_Os03g61060.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61050.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.841; most accessible tissue: Callus, score: 91.007
vg0334688449 (J) chr03 34688449 CAT C 99.70% 0.00% CAT -> C NA
LOC_Os03g61060.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g61060.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g61050.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g61070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 81.688; most accessible tissue: Callus, score: 95.443
vg0334688532 (J) chr03 34688532 A T 99.70% 0.00% A -> T NA
LOC_Os03g61060.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.035; most accessible tissue: Callus, score: 95.443
vg0334688606 (J) chr03 34688606 T A 94.50% 0.00% T -> A
mr1655 (Ind_All); LMM P-value: 4.00E-06; LR P-value: 4.00E-06;
mr1671_2 (Ind_All); LMM P-value: 3.55E-07
LOC_Os03g61060.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.995; most accessible tissue: Zhenshan97 panicle, score: 93.558
vg0334688632 (J) chr03 34688632 C G 94.50% 0.00% C -> G
mr1655 (Ind_All); LMM P-value: 4.00E-06; LR P-value: 4.00E-06;
mr1671_2 (Ind_All); LMM P-value: 3.55E-07
LOC_Os03g61060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.445; most accessible tissue: Zhenshan97 panicle, score: 94.195
vg0334688701 (J) chr03 34688701 G T 91.00% 0.00% G -> T
mr1096_2 (Ind_All); LR P-value: 5.24E-06;
mr1121_2 (Ind_All); LR P-value: 1.78E-06
LOC_Os03g61060.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.660; most accessible tissue: Zhenshan97 flag leaf, score: 94.015
vg0334688920 (J) chr03 34688920 G A 94.50% 0.00% G -> A
mr1655 (Ind_All); LMM P-value: 4.00E-06; LR P-value: 4.00E-06;
mr1671_2 (Ind_All); LMM P-value: 3.55E-07
LOC_Os03g61050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.030; most accessible tissue: Zhenshan97 flag leaf, score: 94.708
vg0334688937 (J) chr03 34688937 T C 64.10% 0.00% C -> T
Yield (All); LR P-value: 1.26E-18;
mr1024 (All); LR P-value: 4.52E-26;
mr1124 (All); LR P-value: 5.65E-40;
mr1376 (All); LR P-value: 9.24E-15;
mr1431 (All); LR P-value: 9.24E-15;
mr1571 (All); LR P-value: 5.54E-23;
mr1591 (All); LR P-value: 5.86E-43;
mr1629 (All); LR P-value: 8.29E-77;
mr1890 (All); LR P-value: 6.15E-39;
mr1891 (All); LR P-value: 5.30E-40;
mr1933 (All); LR P-value: 5.58E-15;
mr1027_2 (All); LR P-value: 1.75E-80;
mr1205_2 (All); LR P-value: 1.61E-07;
mr1571_2 (All); LR P-value: 5.24E-32;
mr1671_2 (All); LR P-value: 5.43E-78;
mr1723_2 (All); LR P-value: 3.51E-35;
mr1944_2 (All); LR P-value: 3.07E-41
LOC_Os03g61050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.565; most accessible tissue: Zhenshan97 flag leaf, score: 94.853
vg0334689518 (J) chr03 34689518 A T 98.10% 0.00% A -> T NA
LOC_Os03g61050.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.539; most accessible tissue: Callus, score: 90.747
vg0334689631 (J) chr03 34689631 T C 63.50% 0.00% C -> T
Yield (All); LR P-value: 7.14E-19;
mr1024 (All); LR P-value: 9.65E-26;
mr1124 (All); LR P-value: 2.50E-40;
mr1376 (All); LR P-value: 1.38E-14;
mr1431 (All); LR P-value: 1.38E-14;
mr1449 (All); LR P-value: 1.99E-12;
mr1591 (All); LR P-value: 1.02E-42;
mr1629 (All); LR P-value: 9.70E-73;
mr1671 (All); LR P-value: 2.55E-58;
mr1723 (All); LR P-value: 1.79E-27;
mr1890 (All); LR P-value: 5.28E-40;
mr1891 (All); LR P-value: 3.30E-40;
mr1933 (All); LR P-value: 2.03E-15;
mr1125_2 (All); LR P-value: 5.00E-63;
mr1386_2 (All); LR P-value: 1.21E-22;
mr1671_2 (All); LR P-value: 1.65E-82;
mr1723_2 (All); LR P-value: 1.28E-36
LOC_Os03g61060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g61060.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.635; most accessible tissue: Zhenshan97 flag leaf, score: 88.765
vg0334689987 (J) chr03 34689987 A T 64.10% 0.00% T -> A
mr1024 (All); LR P-value: 1.24E-25;
mr1124 (All); LR P-value: 5.92E-40;
mr1376 (All); LR P-value: 3.43E-14;
mr1431 (All); LR P-value: 3.43E-14;
mr1566 (All); LR P-value: 1.61E-17;
mr1591 (All); LR P-value: 2.80E-43;
mr1629 (All); LR P-value: 2.02E-76;
mr1671 (All); LR P-value: 1.60E-57;
mr1890 (All); LR P-value: 1.11E-39;
mr1891 (All); LR P-value: 4.01E-40;
mr1933 (All); LR P-value: 9.06E-16;
mr1945 (All); LR P-value: 1.48E-09;
mr1027_2 (All); LR P-value: 2.51E-81;
mr1386_2 (All); LR P-value: 2.24E-23;
mr1484_2 (All); LR P-value: 1.34E-24;
mr1571_2 (All); LR P-value: 7.89E-32;
mr1671_2 (All); LR P-value: 7.16E-81;
mr1723_2 (All); LR P-value: 3.23E-35;
mr1841_2 (All); LR P-value: 4.48E-32
LOC_Os03g61060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.567; most accessible tissue: Callus, score: 91.005
vg0334690067 (J) chr03 34690067 G C 98.10% 0.00% G -> C NA
LOC_Os03g61050.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.921; most accessible tissue: Callus, score: 91.005
vg0334690120 (J) chr03 34690120 G T 64.10% 0.00% T -> G
mr1024 (All); LR P-value: 4.28E-26;
mr1124 (All); LR P-value: 5.28E-40;
mr1376 (All); LR P-value: 2.16E-14;
mr1431 (All); LR P-value: 2.16E-14;
mr1566 (All); LR P-value: 2.59E-17;
mr1591 (All); LR P-value: 5.12E-44;
mr1629 (All); LR P-value: 2.21E-77;
mr1890 (All); LR P-value: 1.41E-40;
mr1891 (All); LR P-value: 3.07E-41;
mr1933 (All); LR P-value: 2.40E-15;
mr1027_2 (All); LR P-value: 1.81E-81;
mr1205_2 (All); LR P-value: 2.54E-07;
mr1323_2 (All); LR P-value: 1.97E-25;
mr1386_2 (All); LR P-value: 2.31E-23;
mr1671_2 (All); LR P-value: 3.99E-80;
mr1723_2 (All); LR P-value: 9.43E-36;
mr1944_2 (All); LR P-value: 5.73E-41
LOC_Os03g61050.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.396; most accessible tissue: Zhenshan97 flag leaf, score: 89.557
vg0334690194 (J) chr03 34690194 T C 94.50% 0.00% T -> C
mr1655 (Ind_All); LMM P-value: 4.00E-06; LR P-value: 4.00E-06;
mr1671_2 (Ind_All); LMM P-value: 3.55E-07
LOC_Os03g61050.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g61060.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.626; most accessible tissue: Zhenshan97 flag leaf, score: 90.181
vg0334690327 (J) chr03 34690327 C A 59.80% 0.00% C -> A
mr1850 (All); LR P-value: 7.06E-07;
mr1212_2 (All); LR P-value: 1.38E-07;
mr1649_2 (All); LR P-value: 5.20E-10;
mr1671_2 (All); LMM P-value: 4.91E-07;
mr1671_2 (Ind_All); LMM P-value: 2.93E-07;
mr1798_2 (Ind_All); LR P-value: 1.26E-08
LOC_Os03g61060.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.813; most accessible tissue: Zhenshan97 flag leaf, score: 93.422
vg0334690605 (J) chr03 34690605 C T 59.90% 0.00% C -> T
mr1850 (All); LR P-value: 1.78E-06;
mr1212_2 (All); LR P-value: 1.16E-07;
mr1649_2 (All); LR P-value: 4.35E-10;
mr1671_2 (All); LMM P-value: 3.53E-07;
mr1671_2 (Ind_All); LMM P-value: 2.93E-07;
mr1798_2 (Ind_All); LR P-value: 1.26E-08
LOC_Os03g61060.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g61060.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.925; most accessible tissue: Minghui63 root, score: 97.339
STR0334690194 (J) chr03 34690194 T C 97.00% 0.00% T -> C NA