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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

23 variations found. LOC_Os07g05910 (expressed protein), ranging from 2,848,446 bp to 2,848,931 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
vg0702848455 (J) chr07 2848455 T Unkown 92.30% 5.08% T -> G NA
LOC_Os07g05910.1 Alt: G| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 78.312; most accessible tissue: Zhenshan97 young leaf, score: 92.168
vg0702848470 (J) chr07 2848470 G Unkown 91.40% 7.51% G -> A NA
LOC_Os07g05910.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 78.730; most accessible tissue: Zhenshan97 young leaf, score: 92.976
vg0702848474 (J) chr07 2848474 C Unkown 91.40% 7.32% C -> T NA
LOC_Os07g05910.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 78.328; most accessible tissue: Zhenshan97 young leaf, score: 92.594
vg0702848482 (J) chr07 2848482 G T 91.30% 7.64% G -> T NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.276; most accessible tissue: Zhenshan97 young leaf, score: 92.477
vg0702848486 (J) chr07 2848486 C T 77.30% 21.54% C -> T NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: T/stop_gained(CooVar)
The average chromatin accessibility score: 78.285; most accessible tissue: Zhenshan97 young leaf, score: 92.356
vg0702848506 (J) chr07 2848506 A G 72.50% 25.35% A -> G NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.112; most accessible tissue: Zhenshan97 young leaf, score: 91.389
vg0702848507 (J) chr07 2848507 A Unkown 99.70% 0.00% A -> G NA
LOC_Os07g05910.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 77.112; most accessible tissue: Zhenshan97 young leaf, score: 91.389
vg0702848511 (J) chr07 2848511 G A 77.50% 21.54% G -> A NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 76.939; most accessible tissue: Zhenshan97 young leaf, score: 91.232
vg0702848581 (J) chr07 2848581 T C 77.70% 21.52% T -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05910.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.349; most accessible tissue: Minghui63 flag leaf, score: 90.986
vg0702848603 (J) chr07 2848603 G A 76.90% 21.54% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05910.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.508; most accessible tissue: Minghui63 flag leaf, score: 91.207
vg0702848633 (J) chr07 2848633 C T 77.60% 21.54% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g05910.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.192; most accessible tissue: Minghui63 flag leaf, score: 91.758
vg0702848648 (J) chr07 2848648 G A 99.80% 0.00% G -> A NA
LOC_Os07g05910.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.422; most accessible tissue: Minghui63 flag leaf, score: 91.886
vg0702848687 (J) chr07 2848687 G A 99.90% 0.00% G -> A NA
LOC_Os07g05910.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.129; most accessible tissue: Minghui63 flag leaf, score: 93.233
vg0702848719 (J) chr07 2848719 A G 77.80% 21.31% A -> G NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.125; most accessible tissue: Minghui63 flag leaf, score: 93.957
vg0702848749 (J) chr07 2848749 C CA 78.30% 20.14% C -> CA NA
LOC_Os07g05910.1 Alt: CA/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.391; most accessible tissue: Minghui63 flag leaf, score: 93.838
vg0702848785 (J) chr07 2848785 G A 80.60% 0.00% A -> G NA
LOC_Os07g05910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.194; most accessible tissue: Minghui63 flag leaf, score: 92.994
vg0702848802 (J) chr07 2848802 G A 77.70% 21.10% G -> A NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.867; most accessible tissue: Minghui63 flag leaf, score: 93.091
vg0702848816 (J) chr07 2848816 G A 77.80% 21.10% G -> A NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.641; most accessible tissue: Minghui63 flag leaf, score: 92.994
vg0702848858 (J) chr07 2848858 G C 78.00% 21.39% G -> C NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.794; most accessible tissue: Minghui63 flag leaf, score: 94.034
vg0702848865 (J) chr07 2848865 G A 78.00% 21.33% G -> A,T NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g05910.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 77.288; most accessible tissue: Minghui63 flag leaf, score: 93.917
vg0702848877 (J) chr07 2848877 C A 77.80% 21.35% C -> A NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.514; most accessible tissue: Minghui63 flag leaf, score: 93.996
vg0702848918 (J) chr07 2848918 CG C 77.50% 21.48% CG -> C NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.562; most accessible tissue: Minghui63 flag leaf, score: 94.399
vg0702848923 (J) chr07 2848923 G A 77.50% 21.56% G -> A NA
LOC_Os07g05910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g05910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.659; most accessible tissue: Minghui63 flag leaf, score: 94.399