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Search Results:

19 variations found. LOC_Os11g26350 (expressed protein), ranging from 15,079,149 bp to 15,081,594 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
vg1115079160 (J) chr11 15079160 G A 97.80% 0.06% G -> A NA
LOC_Os11g26350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.514; most accessible tissue: Minghui63 panicle, score: 42.799
vg1115079183 (J) chr11 15079183 G A 47.30% 28.44% G -> A NA
LOC_Os11g26350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.034; most accessible tissue: Minghui63 panicle, score: 38.588
vg1115079187 (J) chr11 15079187 G A 41.30% 30.66% G -> A NA
LOC_Os11g26350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.034; most accessible tissue: Minghui63 panicle, score: 38.588
vg1115079352 (J) chr11 15079352 C G 29.30% 38.55% C -> G
mr1382 (Jap_All); LR P-value: 5.38E-07;
mr1445 (Jap_All); LMM P-value: 4.95E-06; LR P-value: 4.95E-06;
mr1676 (Jap_All); LR P-value: 1.10E-06;
mr1830 (Jap_All); LR P-value: 5.51E-06;
mr1905 (All); LR P-value: 6.12E-10
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g26340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.681; most accessible tissue: Minghui63 panicle, score: 16.270
vg1115079389 (J) chr11 15079389 TTG T 98.80% 0.15% TTG -> T NA
LOC_Os11g26340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 10.248; most accessible tissue: Minghui63 panicle, score: 16.270
vg1115079390 (J) chr11 15079390 TG T 88.20% 1.54% TG -> T NA
LOC_Os11g26340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 10.248; most accessible tissue: Minghui63 panicle, score: 16.270
vg1115079407 (J) chr11 15079407 G T 98.80% 0.00% G -> T NA
LOC_Os11g26340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.366; most accessible tissue: Minghui63 panicle, score: 16.270
vg1115079430 (J) chr11 15079430 G A 86.10% 1.78% G -> A NA
LOC_Os11g26340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 9.889; most accessible tissue: Minghui63 panicle, score: 16.270
vg1115079449 (J) chr11 15079449 C G 88.70% 2.73% C -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g26340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 8.066; most accessible tissue: Callus, score: 10.872
vg1115079454 (J) chr11 15079454 CCGTATC CCTG C 58.10% 3.62% CCGTATCCCT G -> C,CTATCCCT G NA
LOC_Os11g26340.1 Alt: CTATCCCTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: CTATCCCTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: CTATCCCTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g26340.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 8.066; most accessible tissue: Callus, score: 10.872
vg1115079678 (J) chr11 15079678 G A 83.00% 0.00% G -> A NA
LOC_Os11g26340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474
vg1115079712 (J) chr11 15079712 G T 98.90% 0.00% G -> T,A NA
LOC_Os11g26340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26340.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g26360.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g26350.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 6.536; most accessible tissue: Zhenshan97 flag leaf, score: 9.474
vg1115079735 (J) chr11 15079735 A G 99.40% 0.00% A -> G NA
LOC_Os11g26340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g26360.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g26350.1 Alt: G| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 6.160; most accessible tissue: Minghui63 flower, score: 7.958
vg1115080008 (J) chr11 15080008 G GT 47.70% 24.23% G -> GT NA
LOC_Os11g26340.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 15.593; most accessible tissue: Minghui63 root, score: 25.504
vg1115080066 (J) chr11 15080066 C T 98.90% 0.00% C -> T NA
LOC_Os11g26340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 16.436; most accessible tissue: Minghui63 root, score: 25.504
vg1115080358 (J) chr11 15080358 A G 57.50% 20.48% A -> G NA
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g26350.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 10.971; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1115080661 (J) chr11 15080661 C A 53.60% 21.63% C -> A NA
LOC_Os11g26350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.664; most accessible tissue: Minghui63 panicle, score: 7.125
vg1115080722 (J) chr11 15080722 A G 69.60% 19.81% A -> G NA
LOC_Os11g26350.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g26350.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.876; most accessible tissue: Callus, score: 8.966
vg1115080773 (J) chr11 15080773 C CA 63.50% 19.49% C -> CA NA
LOC_Os11g26340.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26360.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g26350.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 4.876; most accessible tissue: Callus, score: 8.966