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Search Results:

29 variations found. LOC_Os06g48010 (peroxidase precursor; putative; expressed), ranging from 29,027,002 bp to 29,028,481 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
vg0629027041 (J) chr06 29027041 AT A 89.90% 0.00% AT -> A NA
LOC_Os06g48010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 65.181; most accessible tissue: Callus, score: 80.658
vg0629027065 (J) chr06 29027065 T G 90.10% 1.69% T -> G NA
LOC_Os06g48010.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 65.176; most accessible tissue: Callus, score: 80.658
vg0629027073 (J) chr06 29027073 GT G 53.20% 2.24% G -> GT NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g48010.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 63.730; most accessible tissue: Callus, score: 80.658
vg0629027109 (J) chr06 29027109 T C 90.00% 0.00% T -> C NA
LOC_Os06g48010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 62.160; most accessible tissue: Minghui63 root, score: 77.565
vg0629027111 (J) chr06 29027111 T G 99.80% 0.00% T -> G NA
LOC_Os06g48010.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os06g48000.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.160; most accessible tissue: Minghui63 root, score: 77.565
vg0629027139 (J) chr06 29027139 A C 89.90% 0.00% A -> C NA
LOC_Os06g48010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 62.474; most accessible tissue: Minghui63 root, score: 77.290
vg0629027143 (J) chr06 29027143 A G 53.00% 0.00% G -> A NA
LOC_Os06g48010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 63.395; most accessible tissue: Minghui63 root, score: 77.832
vg0629027181 (J) chr06 29027181 CACGTCA CG C 90.20% 0.99% CACGTCACG -> C NA
LOC_Os06g48010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 66.630; most accessible tissue: Zhenshan97 panicle, score: 80.486
vg0629027203 (J) chr06 29027203 T A 52.60% 0.00% A -> T NA
LOC_Os06g48010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.894; most accessible tissue: Zhenshan97 panicle, score: 82.888
vg0629027213 (J) chr06 29027213 C T 50.70% 0.53% T -> C NA
LOC_Os06g48010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48000.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 70.502; most accessible tissue: Zhenshan97 panicle, score: 82.888
vg0629027309 (J) chr06 29027309 C A 51.70% 1.90% C -> A NA
LOC_Os06g48010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g48010.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 70.633; most accessible tissue: Minghui63 panicle, score: 82.797
vg0629027538 (J) chr06 29027538 C T 53.00% 0.21% C -> T NA
LOC_Os06g48010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g48010.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 75.633; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg0629027833 (J) chr06 29027833 C T 97.60% 0.00% C -> T NA
LOC_Os06g48010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.096; most accessible tissue: Zhenshan97 panicle, score: 83.904
vg0629027841 (J) chr06 29027841 T C 63.30% 0.00% C -> T
mr1251 (All); LR P-value: 2.54E-25;
mr1253 (All); LR P-value: 8.19E-18;
mr1968 (All); LR P-value: 4.18E-16;
mr1253_2 (All); LR P-value: 2.20E-22;
mr1349_2 (All); LR P-value: 8.14E-10
LOC_Os06g48010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.941; most accessible tissue: Zhenshan97 panicle, score: 82.888
vg0629027845 (J) chr06 29027845 C T 63.30% 0.00% T -> C
mr1251 (All); LR P-value: 3.72E-25;
mr1253 (All); LR P-value: 2.65E-17;
mr1638 (All); LR P-value: 4.34E-29;
mr1968 (All); LR P-value: 5.84E-16;
mr1129_2 (All); LR P-value: 8.83E-36;
mr1253_2 (All); LR P-value: 1.76E-22;
mr1349_2 (All); LR P-value: 8.94E-10
LOC_Os06g48010.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.380; most accessible tissue: Zhenshan97 panicle, score: 83.410
vg0629027947 (J) chr06 29027947 T C 99.00% 0.00% T -> C NA
LOC_Os06g48000.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48010.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 68.586; most accessible tissue: Zhenshan97 panicle, score: 79.071
vg0629027952 (J) chr06 29027952 C T 99.00% 0.00% C -> T NA
LOC_Os06g48000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g48010.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 67.840; most accessible tissue: Zhenshan97 panicle, score: 79.071
vg0629027972 (J) chr06 29027972 G A 99.90% 0.00% G -> A NA
LOC_Os06g48000.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g48010.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 67.343; most accessible tissue: Minghui63 root, score: 77.832
vg0629027974 (J) chr06 29027974 TACAGAT A T 99.20% 0.00% TACAGATA -> T NA
LOC_Os06g48000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g48010.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 67.405; most accessible tissue: Minghui63 root, score: 77.832
vg0629028001 (J) chr06 29028001 G A 99.80% 0.00% G -> A NA
LOC_Os06g48010.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os06g48000.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 65.840; most accessible tissue: Minghui63 root, score: 78.594
vg0629028006 (J) chr06 29028006 C T 99.80% 0.00% C -> T NA
LOC_Os06g48010.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g48000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 64.955; most accessible tissue: Minghui63 root, score: 78.091
vg0629028016 (J) chr06 29028016 A G 99.80% 0.00% A -> G NA
LOC_Os06g48010.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os06g48000.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 64.917; most accessible tissue: Minghui63 root, score: 78.833
vg0629028061 (J) chr06 29028061 C T 63.40% 0.00% T -> C
mr1251 (All); LR P-value: 1.10E-25;
mr1253 (All); LR P-value: 1.00E-17;
mr1638 (All); LR P-value: 3.86E-29;
mr1968 (All); LR P-value: 4.76E-16;
mr1129_2 (All); LR P-value: 2.25E-36;
mr1253_2 (All); LR P-value: 8.53E-23
LOC_Os06g48010.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.862; most accessible tissue: Minghui63 root, score: 77.565
vg0629028180 (J) chr06 29028180 C T 99.80% 0.00% C -> T NA
LOC_Os06g48010.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g48000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.540; most accessible tissue: Minghui63 root, score: 80.760
vg0629028229 (J) chr06 29028229 C A 85.30% 0.00% C -> A NA
LOC_Os06g48010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.998; most accessible tissue: Minghui63 root, score: 80.951
vg0629028329 (J) chr06 29028329 C T 63.00% 0.21% T -> C
mr1251 (All); LR P-value: 3.72E-25;
mr1253 (All); LR P-value: 2.65E-17;
mr1638 (All); LR P-value: 4.34E-29;
mr1968 (All); LR P-value: 5.84E-16;
mr1129_2 (All); LR P-value: 8.83E-36;
mr1253_2 (All); LR P-value: 1.76E-22;
mr1349_2 (All); LR P-value: 8.94E-10
LOC_Os06g48010.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g48010.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 66.895; most accessible tissue: Minghui63 root, score: 84.918
vg0629028341 (J) chr06 29028341 G A 63.30% 0.00% A -> G
mr1251 (All); LR P-value: 3.17E-26;
mr1253 (All); LR P-value: 2.44E-18;
mr1257 (All); LR P-value: 6.50E-30;
mr1435 (All); LR P-value: 2.20E-36;
mr1638 (All); LR P-value: 1.01E-28;
mr1968 (All); LR P-value: 7.55E-16;
mr1064_2 (All); LR P-value: 1.46E-57;
mr1129_2 (All); LR P-value: 6.23E-38;
mr1253_2 (All); LR P-value: 2.01E-23
LOC_Os06g48010.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.250; most accessible tissue: Minghui63 root, score: 85.770
vg0629028362 (J) chr06 29028362 G A 99.80% 0.00% G -> A NA
LOC_Os06g48010.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g48000.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 67.598; most accessible tissue: Minghui63 root, score: 86.346
STR0629027180 (J) chr06 29027180 TCACGTC ACGTC TCAC 79.50% 0.00% TCACGTCACG TC -> TCAC NA