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Search Results:

10 variations found. LOC_Os11g17580 (enoyl-CoA hydratase%2Fisomerase family protein; expressed), ranging from 9,788,006 bp to 9,788,714 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
vg1109788022 (J) chr11 9788022 T A 96.40% 0.00% T -> A
mr1100 (Ind_All); LR P-value: 8.98E-07;
mr1723_2 (Ind_All); LR P-value: 7.65E-07
LOC_Os11g17580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 68.856; most accessible tissue: Callus, score: 85.410
vg1109788044 (J) chr11 9788044 G C 89.30% 0.00% G -> C
mr1154 (Ind_All); LR P-value: 6.74E-06;
mr1050_2 (Ind_All); LR P-value: 3.59E-06;
mr1097_2 (Ind_All); LR P-value: 1.89E-06;
mr1154_2 (Ind_All); LR P-value: 2.37E-09
LOC_Os11g17580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.889; most accessible tissue: Callus, score: 85.410
vg1109788068 (J) chr11 9788068 C T 99.20% 0.00% C -> T NA
LOC_Os11g17580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.424; most accessible tissue: Callus, score: 85.410
vg1109788196 (J) chr11 9788196 G C 67.20% 0.00% C -> G
mr1005 (All); LR P-value: 1.64E-09;
mr1449 (All); LR P-value: 2.71E-12;
mr1566 (All); LR P-value: 3.22E-17;
mr1758 (All); LR P-value: 2.12E-89;
mr1767 (All); LR P-value: 1.06E-17;
mr1484_2 (All); LR P-value: 5.48E-25;
mr1900_2 (All); LR P-value: 2.91E-20
LOC_Os11g17580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 72.807; most accessible tissue: Zhenshan97 young leaf, score: 87.584
vg1109788305 (J) chr11 9788305 C T 98.80% 0.00% C -> T NA
LOC_Os11g17580.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g17570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542
vg1109788337 (J) chr11 9788337 T G 94.00% 0.00% T -> G
mr1100 (Ind_All); LR P-value: 4.11E-06;
mr1723_2 (Ind_All); LR P-value: 6.84E-07
LOC_Os11g17580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.041; most accessible tissue: Zhenshan97 young leaf, score: 88.127
vg1109788343 (J) chr11 9788343 C T 62.50% 0.00% T -> C NA
LOC_Os11g17580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.873; most accessible tissue: Zhenshan97 young leaf, score: 87.859
vg1109788437 (J) chr11 9788437 C A 95.90% 0.00% C -> A NA
LOC_Os11g17580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.645; most accessible tissue: Zhenshan97 young leaf, score: 87.443
vg1109788492 (J) chr11 9788492 G C 96.50% 0.00% G -> C NA
LOC_Os11g17580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.223; most accessible tissue: Zhenshan97 young leaf, score: 88.259
vg1109788700 (J) chr11 9788700 A G 94.10% 0.00% A -> G
mr1100 (Ind_All); LR P-value: 4.11E-06;
mr1723_2 (Ind_All); LR P-value: 6.84E-07
LOC_Os11g17580.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.308; most accessible tissue: Callus, score: 89.320