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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:

6 variations found. LOC_Os04g08210 (retrotransposon protein; putative; unclassified; expressed), ranging from 4,362,951 bp to 4,368,402 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
vg0404363080 (J) chr04 4363080 G A 9.80% 66.19% G -> A NA
LOC_Os04g08210.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g08210.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0404363081 (J) chr04 4363081 G T 8.70% 66.65% G -> T NA
LOC_Os04g08210.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g08210.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0404368198 (J) chr04 4368198 C T 17.50% 76.83% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g08210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 7.289; most accessible tissue: Minghui63 flower, score: 11.139
vg0404368253 (J) chr04 4368253 A T 29.10% 49.75% A -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g08210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.391; most accessible tissue: Callus, score: 9.548
vg0404368259 (J) chr04 4368259 T G 18.00% 71.88% T -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g08210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.391; most accessible tissue: Callus, score: 9.548
vg0404368261 (J) chr04 4368261 C G 29.50% 51.12% C -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g08210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.391; most accessible tissue: Callus, score: 9.548