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Search Results:

20 variations found. LOC_Os06g35950 (expressed protein), ranging from 20,982,673 bp to 20,983,248 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
vg0620982675 (J) chr06 20982675 TAA T 46.70% 9.23% TAA -> T,TA,AAA NA
LOC_Os06g35950.1 Alt: AAA| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os06g35950.1 Alt: T| frameshift_variant&stop_lost&splice_region_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: TA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 96.630; most accessible tissue: Zhenshan97 panicle, score: 98.592
vg0620982676 (J) chr06 20982676 A T 58.40% 9.33% A -> T NA
LOC_Os06g35950.1 Alt: T| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 96.629; most accessible tissue: Zhenshan97 panicle, score: 98.592
vg0620982691 (J) chr06 20982691 G A 47.40% 9.20% G -> A
mr1574_2 (All); LR P-value: 7.99E-06;
mr1806_2 (All); LR P-value: 4.21E-10;
mr1904_2 (All); LR P-value: 2.15E-12
LOC_Os06g35950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.225; most accessible tissue: Zhenshan97 panicle, score: 97.761
vg0620982693 (J) chr06 20982693 G A 75.50% 8.82% G -> A NA
LOC_Os06g35950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.247; most accessible tissue: Zhenshan97 panicle, score: 97.761
vg0620982706 (J) chr06 20982706 G A 58.80% 9.33% A -> G NA
LOC_Os06g35950.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.824; most accessible tissue: Zhenshan97 panicle, score: 97.512
vg0620982712 (J) chr06 20982712 C CA 47.40% 9.33% C -> CA NA
LOC_Os06g35950.1 Alt: CA/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.694; most accessible tissue: Zhenshan97 panicle, score: 97.468
vg0620982730 (J) chr06 20982730 TTCTTCT CCTTC T 75.30% 9.08% TTCTTCTCCT TC -> T NA
LOC_Os06g35950.1 Alt: T/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.433; most accessible tissue: Zhenshan97 panicle, score: 97.422
vg0620982737 (J) chr06 20982737 C CCTTCT 90.50% 9.12% C -> CCTTCT NA
LOC_Os06g35950.1 Alt: CCTTCT/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.194; most accessible tissue: Zhenshan97 panicle, score: 96.668
vg0620982748 (J) chr06 20982748 CTT C 90.90% 8.72% CTT -> C NA
LOC_Os06g35950.1 Alt: C/frameshift_variant(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.267; most accessible tissue: Zhenshan97 panicle, score: 96.668
vg0620982754 (J) chr06 20982754 T A 75.30% 9.01% T -> A NA
LOC_Os06g35950.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.375; most accessible tissue: Zhenshan97 panicle, score: 96.769
vg0620982755 (J) chr06 20982755 C A 58.80% 9.29% A -> C NA
LOC_Os06g35950.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.385; most accessible tissue: Zhenshan97 panicle, score: 96.801
vg0620982808 (J) chr06 20982808 T G 91.00% 8.57% T -> G NA
LOC_Os06g35950.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.046; most accessible tissue: Zhenshan97 panicle, score: 96.414
vg0620982835 (J) chr06 20982835 C T 47.40% 9.18% C -> T
mr1860 (All); LR P-value: 8.69E-09;
mr1734_2 (All); LR P-value: 7.73E-12;
mr1782_2 (All); LR P-value: 9.77E-10;
mr1860_2 (All); LR P-value: 1.06E-09
LOC_Os06g35950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.361; most accessible tissue: Zhenshan97 flower, score: 96.067
vg0620982847 (J) chr06 20982847 G A 88.80% 8.91% G -> A NA
LOC_Os06g35950.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.533; most accessible tissue: Zhenshan97 flower, score: 96.172
vg0620982877 (J) chr06 20982877 C T 75.40% 8.74% C -> T NA
LOC_Os06g35950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.456; most accessible tissue: Zhenshan97 flower, score: 96.246
vg0620982929 (J) chr06 20982929 G A 75.60% 9.08% G -> A NA
LOC_Os06g35950.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.825; most accessible tissue: Zhenshan97 flower, score: 95.844
vg0620982989 (J) chr06 20982989 G A 47.40% 9.27% G -> A
mr1806 (All); LR P-value: 4.08E-08;
mr1574_2 (All); LR P-value: 1.64E-06;
mr1806_2 (All); LR P-value: 3.61E-10
LOC_Os06g35950.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 92.186; most accessible tissue: Zhenshan97 panicle, score: 95.143
vg0620983050 (J) chr06 20983050 C G 75.30% 9.06% C -> G,T NA
LOC_Os06g35950.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g35950.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.670; most accessible tissue: Zhenshan97 flag leaf, score: 94.727
vg0620983079 (J) chr06 20983079 T C 75.30% 9.01% T -> C NA
LOC_Os06g35950.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.496; most accessible tissue: Zhenshan97 flag leaf, score: 94.708
vg0620983150 (J) chr06 20983150 G A 58.70% 9.25% A -> G NA
LOC_Os06g35950.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g35950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.650; most accessible tissue: Zhenshan97 panicle, score: 93.845