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Search Results:

20 variations found. Os02g0550900/LOC_Os02g34590 (transposon protein; putative; unclassified; expressed), ranging from 20,737,911 bp to 20,741,031 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os02g34590 transposon protein, putative, unclassified, expressed; RAP ID: Os02g0550900; MSU ID: LOC_Os02g34590

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
vg0220737996 (J) chr02 20737996 C T 87.70% 0.00% C -> T
mr1073 (All); LR P-value: 2.82E-06;
mr1114 (All); LR P-value: 1.43E-18;
mr1114 (Ind_All); LR P-value: 1.00E-06;
mr1153 (All); LR P-value: 6.82E-06;
mr1174 (Ind_All); LR P-value: 7.38E-07;
mr1188 (Ind_All); LR P-value: 9.87E-06;
mr1320 (All); LR P-value: 8.85E-07;
mr1347 (Ind_All); LR P-value: 1.67E-09;
mr1351 (All); LR P-value: 5.99E-06;
mr1523 (All); LR P-value: 7.24E-07;
mr1633 (All); LR P-value: 2.15E-06;
mr1787 (All); LR P-value: 9.41E-06;
mr1917 (Ind_All); LR P-value: 7.64E-06;
mr1921 (All); LR P-value: 2.04E-10
LOC_Os02g34590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34580.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 58.867; most accessible tissue: Callus, score: 82.569
vg0220738046 (J) chr02 20738046 C T 99.10% 0.00% C -> T NA
LOC_Os02g34590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34580.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 56.606; most accessible tissue: Callus, score: 82.569
vg0220738061 (J) chr02 20738061 CA TA 98.40% 0.00% CA -> TA,C NA
LOC_Os02g34590.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34580.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34580.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 56.498; most accessible tissue: Callus, score: 82.569
vg0220738772 (J) chr02 20738772 A C 99.20% 0.00% A -> C NA
LOC_Os02g34590.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 52.182; most accessible tissue: Callus, score: 81.423
vg0220738856 (J) chr02 20738856 T A 90.90% 0.00% T -> A NA
LOC_Os02g34590.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 46.348; most accessible tissue: Minghui63 young leaf, score: 61.007
vg0220738983 (J) chr02 20738983 G A 91.30% 0.00% G -> A
mr1875_2 (Ind_All); LR P-value: 2.73E-06;
mr1908_2 (Ind_All); LR P-value: 1.85E-06
LOC_Os02g34590.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.870; most accessible tissue: Callus, score: 82.114
vg0220739288 (J) chr02 20739288 G A 97.20% 0.00% G -> A
mr1098_2 (Jap_All); LR P-value: 3.83E-06;
mr1851_2 (Jap_All); LR P-value: 3.39E-07
LOC_Os02g34590.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.122; most accessible tissue: Callus, score: 83.375
vg0220739690 (J) chr02 20739690 T C 78.10% 0.00% T -> C NA
LOC_Os02g34590.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.413; most accessible tissue: Callus, score: 80.956
vg0220739821 (J) chr02 20739821 G T 78.10% 0.00% G -> T NA
LOC_Os02g34590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.386; most accessible tissue: Zhenshan97 young leaf, score: 81.353
vg0220740098 (J) chr02 20740098 G A 72.40% 0.00% A -> G NA
LOC_Os02g34590.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.032; most accessible tissue: Zhenshan97 young leaf, score: 88.637
vg0220740277 (J) chr02 20740277 C T 87.70% 0.00% C -> T
mr1073 (All); LR P-value: 5.29E-06;
mr1114 (All); LR P-value: 2.17E-18;
mr1114 (Ind_All); LR P-value: 1.04E-06;
mr1153 (All); LR P-value: 7.83E-06;
mr1174 (Ind_All); LR P-value: 5.42E-06;
mr1188 (Ind_All); LR P-value: 8.12E-06;
mr1320 (All); LR P-value: 5.74E-07;
mr1347 (Ind_All); LMM P-value: 5.84E-06; LR P-value: 6.55E-10;
mr1351 (All); LR P-value: 3.57E-06;
mr1523 (All); LR P-value: 1.15E-06;
mr1633 (All); LR P-value: 1.81E-06;
mr1787 (All); LR P-value: 6.01E-06;
mr1917 (Ind_All); LR P-value: 5.65E-06;
mr1921 (All); LR P-value: 2.70E-10;
mr1939 (All); LR P-value: 8.75E-09
LOC_Os02g34590.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.231; most accessible tissue: Zhenshan97 flower, score: 88.357
vg0220740278 (J) chr02 20740278 G A 88.00% 0.00% G -> A NA
LOC_Os02g34590.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.248; most accessible tissue: Zhenshan97 flower, score: 88.357
vg0220740322 (J) chr02 20740322 C A 98.50% 0.00% C -> A NA
LOC_Os02g34590.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.768; most accessible tissue: Zhenshan97 flower, score: 89.362
vg0220740329 (J) chr02 20740329 C T 98.50% 0.00% C -> T NA
LOC_Os02g34590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.396; most accessible tissue: Zhenshan97 flower, score: 89.362
vg0220740382 (J) chr02 20740382 C T 90.90% 0.00% C -> T NA
LOC_Os02g34590.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.638; most accessible tissue: Zhenshan97 flower, score: 88.465
vg0220740414 (J) chr02 20740414 A G 99.80% 0.00% A -> G NA
LOC_Os02g34590.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os02g34580.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 81.399; most accessible tissue: Zhenshan97 flower, score: 91.124
vg0220740696 (J) chr02 20740696 C A 87.70% 0.00% C -> A
mr1073 (All); LR P-value: 2.61E-06;
mr1114 (All); LR P-value: 1.35E-18;
mr1114 (Ind_All); LR P-value: 6.81E-07;
mr1153 (All); LR P-value: 3.90E-06;
mr1174 (Ind_All); LR P-value: 2.44E-06;
mr1188 (Ind_All); LR P-value: 3.05E-06;
mr1320 (All); LR P-value: 1.47E-06;
mr1347 (Ind_All); LR P-value: 7.60E-09;
mr1351 (All); LR P-value: 8.56E-06;
mr1523 (All); LR P-value: 5.48E-07;
mr1633 (All); LR P-value: 2.96E-06;
mr1917 (Ind_All); LR P-value: 7.80E-06
LOC_Os02g34580.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34590.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.348; most accessible tissue: Minghui63 panicle, score: 93.053
vg0220740800 (J) chr02 20740800 CGCTCGC TG C 78.10% 0.00% CGCTCGCTG -> C NA
LOC_Os02g34580.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.710; most accessible tissue: Zhenshan97 panicle, score: 96.087
vg0220740808 (J) chr02 20740808 C G 50.40% 0.00% G -> C NA
LOC_Os02g34580.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g34590.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.450; most accessible tissue: Zhenshan97 panicle, score: 96.634
STR0220740805 (J) chr02 20740805 GCTGGCT GG G 65.60% 0.00% GCTGGCTGG -> G NA