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Search Results:

32 variations found. LOC_Os01g54660 (retrotransposon protein; putative; unclassified; expressed), ranging from 31,444,255 bp to 31,450,372 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
vg0131444744 (J) chr01 31444744 G A 8.20% 70.82% A -> G NA
LOC_Os01g54660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.133; most accessible tissue: Zhenshan97 flag leaf, score: 23.298
vg0131445223 (J) chr01 31445223 G A 10.60% 72.20% G -> A NA
LOC_Os01g54660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 16.438; most accessible tissue: Zhenshan97 flag leaf, score: 35.167
vg0131445777 (J) chr01 31445777 C T 31.50% 66.02% C -> T NA
LOC_Os01g54660.1 Alt: T| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
LOC_Os01g54660.1 Alt: DEL/splice_acceptor_variant(CooVar)
The average chromatin accessibility score: 16.090; most accessible tissue: Zhenshan97 flag leaf, score: 42.807
vg0131446075 (J) chr01 31446075 G T 28.90% 67.63% G -> T NA
LOC_Os01g54660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.857; most accessible tissue: Zhenshan97 flag leaf, score: 42.807
vg0131446155 (J) chr01 31446155 G A 22.40% 63.27% G -> A NA
LOC_Os01g54660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.796; most accessible tissue: Zhenshan97 flag leaf, score: 38.066
vg0131446411 (J) chr01 31446411 C T 31.20% 66.67% C -> T NA
LOC_Os01g54660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.176; most accessible tissue: Zhenshan97 flag leaf, score: 24.112
vg0131446501 (J) chr01 31446501 G A 10.10% 71.27% G -> A NA
LOC_Os01g54660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.984; most accessible tissue: Zhenshan97 flag leaf, score: 24.112
vg0131447782 (J) chr01 31447782 T C 31.10% 68.30% T -> C NA
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g54660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 18.469; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg0131447795 (J) chr01 31447795 G A 44.50% 40.92% G -> A NA
LOC_Os01g54660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 21.937; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131447818 (J) chr01 31447818 T C 54.50% 40.16% T -> C NA
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g54660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 23.371; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131447836 (J) chr01 31447836 C T 52.30% 41.85% C -> T NA
LOC_Os01g54660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 23.721; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131447850 (J) chr01 31447850 G A 51.60% 44.16% G -> A NA
LOC_Os01g54660.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 24.244; most accessible tissue: Zhenshan97 panicle, score: 54.901
vg0131447854 (J) chr01 31447854 G A 40.30% 37.96% G -> A NA
LOC_Os01g54660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 25.293; most accessible tissue: Zhenshan97 panicle, score: 59.590
vg0131447860 (J) chr01 31447860 C T 51.20% 44.37% C -> T NA
LOC_Os01g54660.1 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 25.886; most accessible tissue: Zhenshan97 panicle, score: 59.590
vg0131447867 (J) chr01 31447867 C A 52.80% 44.27% C -> A NA
LOC_Os01g54660.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g54650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 26.973; most accessible tissue: Zhenshan97 panicle, score: 59.590
vg0131447871 (J) chr01 31447871 G A 51.80% 44.46% G -> A NA
LOC_Os01g54650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g54660.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 26.912; most accessible tissue: Zhenshan97 panicle, score: 59.590
vg0131447880 (J) chr01 31447880 C T 47.90% 44.54% C -> T NA
LOC_Os01g54650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g54660.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 27.392; most accessible tissue: Zhenshan97 panicle, score: 61.671
vg0131448227 (J) chr01 31448227 C T 59.10% 37.30% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 38.542; most accessible tissue: Zhenshan97 panicle, score: 71.253
vg0131448228 (J) chr01 31448228 C T 53.40% 37.58% C -> T NA
LOC_Os01g54660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 38.542; most accessible tissue: Zhenshan97 panicle, score: 71.253
vg0131448296 (J) chr01 31448296 C T 27.60% 61.45% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 36.082; most accessible tissue: Zhenshan97 root, score: 65.566
vg0131448525 (J) chr01 31448525 A G 31.70% 64.90% A -> G NA
LOC_Os01g54660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 21.325; most accessible tissue: Zhenshan97 panicle, score: 49.416
vg0131448546 (J) chr01 31448546 C T 33.70% 44.94% C -> T NA
LOC_Os01g54660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 21.067; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131448560 (J) chr01 31448560 C T 47.50% 44.03% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 21.390; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131448594 (J) chr01 31448594 G A 47.00% 43.91% G -> A NA
LOC_Os01g54660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 21.181; most accessible tissue: Zhenshan97 panicle, score: 52.263
vg0131448967 (J) chr01 31448967 C T 31.80% 64.60% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.284; most accessible tissue: Zhenshan97 flag leaf, score: 49.013
vg0131448983 (J) chr01 31448983 C T 31.80% 63.86% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.879; most accessible tissue: Zhenshan97 flag leaf, score: 48.165
vg0131449053 (J) chr01 31449053 G A 31.30% 66.04% G -> A NA
LOC_Os01g54660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 17.923; most accessible tissue: Zhenshan97 flag leaf, score: 48.165
vg0131449516 (J) chr01 31449516 C T 30.60% 67.67% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.396; most accessible tissue: Zhenshan97 root, score: 46.166
vg0131449624 (J) chr01 31449624 T G 31.00% 68.64% T -> G NA
LOC_Os01g54660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 23.122; most accessible tissue: Zhenshan97 root, score: 57.640
vg0131449933 (J) chr01 31449933 C T 30.30% 64.92% C -> T NA
LOC_Os01g54660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 32.373; most accessible tissue: Zhenshan97 root, score: 73.143
vg0131450153 (J) chr01 31450153 C T 16.20% 64.96% T -> C NA
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g54660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 34.543; most accessible tissue: Zhenshan97 panicle, score: 75.670
vg0131450301 (J) chr01 31450301 A G 16.00% 64.62% A -> G NA
LOC_Os01g54660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g54660.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 34.292; most accessible tissue: Zhenshan97 panicle, score: 75.670