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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:

5 variations found. LOC_Os01g74060 (transposon protein; putative; unclassified), ranging from 42,892,140 bp to 42,892,710 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
vg0142892226 (J) chr01 42892226 G A 55.70% 42.66% G -> A NA
LOC_Os01g74060.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74060.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.383; most accessible tissue: Zhenshan97 flag leaf, score: 21.009
vg0142892283 (J) chr01 42892283 C T 56.10% 42.28% C -> T NA
LOC_Os01g74060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g74060.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.284; most accessible tissue: Zhenshan97 flag leaf, score: 25.809
vg0142892442 (J) chr01 42892442 C T 56.90% 41.03% C -> T NA
LOC_Os01g74060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74060.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 20.638; most accessible tissue: Zhenshan97 flag leaf, score: 44.637
vg0142892524 (J) chr01 42892524 G A 56.20% 41.30% G -> A NA
LOC_Os01g74060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74060.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 27.210; most accessible tissue: Zhenshan97 flag leaf, score: 50.663
vg0142892587 (J) chr01 42892587 C A 51.60% 40.61% C -> A NA
LOC_Os01g74060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74060.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 28.467; most accessible tissue: Zhenshan97 flag leaf, score: 55.285