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Search Results:

18 variations found. LOC_Os02g13200 (expressed protein), ranging from 7,032,297 bp to 7,034,871 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
vg0207032313 (J) chr02 7032313 C T 99.90% 0.00% C -> T NA
LOC_Os02g13200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g13190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.046; most accessible tissue: Callus, score: 72.774
vg0207032362 (J) chr02 7032362 C T 68.40% 0.13% C -> T
mr1091 (Jap_All); LR P-value: 5.52E-07;
mr1229 (All); LR P-value: 8.28E-07;
mr1486 (Jap_All); LR P-value: 1.34E-09;
mr1161_2 (Jap_All); LR P-value: 5.50E-06;
mr1383_2 (Jap_All); LR P-value: 8.73E-08;
mr1530_2 (Jap_All); LR P-value: 6.87E-11
LOC_Os02g13200.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 58.660; most accessible tissue: Zhenshan97 root, score: 69.506
vg0207032875 (J) chr02 7032875 T G 55.20% 0.30% G -> T
mr1557 (All); LR P-value: 3.28E-17;
mr1383_2 (All); LR P-value: 2.40E-18
LOC_Os02g13190.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13200.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 63.738; most accessible tissue: Minghui63 flower, score: 75.217
vg0207033058 (J) chr02 7033058 A AC 95.80% 0.00% A -> AC NA
LOC_Os02g13190.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13200.1 Alt: AC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.147; most accessible tissue: Callus, score: 85.843
vg0207033079 (J) chr02 7033079 G A 91.20% 0.00% G -> A
mr1570 (All); LR P-value: 2.92E-10;
mr1629 (Ind_All); LR P-value: 2.23E-06;
mr1126_2 (All); LR P-value: 1.51E-06;
mr1612_2 (All); LR P-value: 4.04E-10
LOC_Os02g13200.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g13190.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.817; most accessible tissue: Zhenshan97 flower, score: 80.463
vg0207033231 (J) chr02 7033231 G C 95.80% 0.00% G -> C
mr1053_2 (Ind_All); LR P-value: 2.94E-07;
mr1128_2 (Ind_All); LMM P-value: 5.82E-06; LR P-value: 1.24E-06;
mr1147_2 (Ind_All); LR P-value: 5.58E-07
LOC_Os02g13190.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13200.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.289; most accessible tissue: Callus, score: 86.236
vg0207033740 (J) chr02 7033740 T A 65.80% 0.00% T -> A NA
LOC_Os02g13200.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 55.654; most accessible tissue: Callus, score: 75.191
vg0207033828 (J) chr02 7033828 A G 91.20% 0.00% A -> G
mr1570 (All); LR P-value: 9.88E-11;
mr1126_2 (All); LR P-value: 3.77E-07;
mr1612_2 (All); LR P-value: 5.52E-10
LOC_Os02g13200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.289; most accessible tissue: Minghui63 flower, score: 72.895
vg0207033859 (J) chr02 7033859 C A 87.20% 0.00% A -> C
Grain_length (All); LR P-value: 3.50E-13;
mr1137 (All); LR P-value: 1.33E-29;
mr1383_2 (Jap_All); LR P-value: 8.53E-06;
mr1530_2 (Jap_All); LR P-value: 2.80E-11
LOC_Os02g13200.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 61.249; most accessible tissue: Minghui63 flag leaf, score: 77.153
vg0207033923 (J) chr02 7033923 T C 55.20% 0.06% C -> T
mr1557 (All); LR P-value: 2.37E-17;
mr1383_2 (All); LR P-value: 1.13E-18
LOC_Os02g13200.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 61.599; most accessible tissue: Zhenshan97 flower, score: 77.755
vg0207034046 (J) chr02 7034046 C T 99.50% 0.00% C -> T NA
LOC_Os02g13200.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.057; most accessible tissue: Minghui63 flag leaf, score: 87.052
vg0207034217 (J) chr02 7034217 T G 55.30% 0.00% G -> T NA
LOC_Os02g13200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.873; most accessible tissue: Zhenshan97 flower, score: 90.623
vg0207034474 (J) chr02 7034474 G A 95.80% 0.00% G -> A
mr1053_2 (Ind_All); LR P-value: 2.68E-07;
mr1128_2 (Ind_All); LMM P-value: 5.42E-06; LR P-value: 1.14E-06;
mr1147_2 (Ind_All); LR P-value: 5.51E-07
LOC_Os02g13200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.133; most accessible tissue: Zhenshan97 flower, score: 94.106
vg0207034717 (J) chr02 7034717 G C 99.60% 0.00% G -> C NA
LOC_Os02g13200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.607; most accessible tissue: Zhenshan97 flower, score: 94.492
vg0207034728 (J) chr02 7034728 AG A 55.40% 0.00% A -> AG NA
LOC_Os02g13200.1 Alt: AG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.534; most accessible tissue: Zhenshan97 flower, score: 93.832
vg0207034752 (J) chr02 7034752 C G 91.30% 0.00% C -> G
mr1570 (All); LR P-value: 1.04E-09;
mr1126_2 (All); LR P-value: 4.76E-07;
mr1612_2 (All); LR P-value: 5.44E-10
LOC_Os02g13200.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.101; most accessible tissue: Zhenshan97 flower, score: 93.634
vg0207034758 (J) chr02 7034758 G C 95.80% 0.00% G -> C
mr1053_2 (Ind_All); LR P-value: 2.80E-06;
mr1147_2 (Ind_All); LR P-value: 1.52E-06
LOC_Os02g13200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.055; most accessible tissue: Zhenshan97 flower, score: 93.614
vg0207034842 (J) chr02 7034842 G C 91.20% 0.00% G -> C
mr1570 (All); LR P-value: 9.88E-11;
mr1126_2 (All); LR P-value: 3.77E-07;
mr1612_2 (All); LR P-value: 5.52E-10
LOC_Os02g13200.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.588; most accessible tissue: Zhenshan97 flower, score: 92.487