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Search Results:

29 variations found. LOC_Os07g08940 (expressed protein), ranging from 4,649,673 bp to 4,650,555 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
vg0704649717 (J) chr07 4649717 A G 59.30% 0.23% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 41.440; most accessible tissue: Zhenshan97 young leaf, score: 67.830
vg0704649735 (J) chr07 4649735 G A 59.30% 0.23% A -> G NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.079; most accessible tissue: Zhenshan97 young leaf, score: 70.177
vg0704649789 (J) chr07 4649789 C G 99.60% 0.00% C -> G NA
LOC_Os07g08940.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08930.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 41.795; most accessible tissue: Zhenshan97 young leaf, score: 71.065
vg0704649873 (J) chr07 4649873 A G 58.70% 0.25% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.595; most accessible tissue: Zhenshan97 young leaf, score: 73.923
vg0704649875 (J) chr07 4649875 C T 99.90% 0.00% C -> T NA
LOC_Os07g08940.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g08934.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 42.595; most accessible tissue: Zhenshan97 young leaf, score: 73.923
vg0704649876 (J) chr07 4649876 G A 88.80% 0.00% G -> A NA
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 42.460; most accessible tissue: Zhenshan97 young leaf, score: 73.923
vg0704649894 (J) chr07 4649894 G A 99.90% 0.00% G -> A NA
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 43.317; most accessible tissue: Zhenshan97 young leaf, score: 73.147
vg0704649898 (J) chr07 4649898 G A 99.90% 0.00% G -> A NA
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 42.558; most accessible tissue: Zhenshan97 young leaf, score: 72.340
vg0704649907 (J) chr07 4649907 A C 58.70% 0.23% C -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.577; most accessible tissue: Zhenshan97 young leaf, score: 70.625
vg0704649960 (J) chr07 4649960 T A 99.90% 0.00% T -> A NA
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 46.843; most accessible tissue: Zhenshan97 young leaf, score: 75.751
vg0704649961 (J) chr07 4649961 C T 99.90% 0.00% C -> T NA
LOC_Os07g08940.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 46.843; most accessible tissue: Zhenshan97 young leaf, score: 75.751
vg0704650004 (J) chr07 4650004 A G 59.30% 0.23% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 48.585; most accessible tissue: Zhenshan97 young leaf, score: 73.923
vg0704650011 (J) chr07 4650011 G A 99.90% 0.00% G -> A NA
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.700; most accessible tissue: Zhenshan97 young leaf, score: 73.147
vg0704650033 (J) chr07 4650033 C T 88.90% 0.00% C -> T NA
LOC_Os07g08940.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 48.445; most accessible tissue: Zhenshan97 young leaf, score: 69.723
vg0704650105 (J) chr07 4650105 C T 96.70% 0.00% C -> T NA
LOC_Os07g08940.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.279; most accessible tissue: Zhenshan97 young leaf, score: 67.830
vg0704650141 (J) chr07 4650141 T A 99.90% 0.00% T -> A NA
LOC_Os07g08940.1 Alt: A| stop_gained HIGH(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.667; most accessible tissue: Zhenshan97 young leaf, score: 70.177
vg0704650193 (J) chr07 4650193 G A 70.50% 0.21% A -> G
mr1057 (All); LR P-value: 2.61E-06;
mr1552_2 (All); LR P-value: 2.87E-13
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.325; most accessible tissue: Zhenshan97 young leaf, score: 67.830
vg0704650217 (J) chr07 4650217 A T 99.90% 0.00% A -> T NA
LOC_Os07g08940.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g08934.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 56.289; most accessible tissue: Zhenshan97 young leaf, score: 70.625
vg0704650249 (J) chr07 4650249 C T 59.30% 0.23% T -> C NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 56.111; most accessible tissue: Zhenshan97 young leaf, score: 68.315
vg0704650310 (J) chr07 4650310 T C 58.70% 0.17% C -> T NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 54.211; most accessible tissue: Zhenshan97 flag leaf, score: 66.327
vg0704650313 (J) chr07 4650313 T C 99.90% 0.00% T -> C NA
LOC_Os07g08940.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os07g08934.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 54.816; most accessible tissue: Zhenshan97 flag leaf, score: 66.327
vg0704650378 (J) chr07 4650378 T C 59.30% 0.17% C -> T NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 56.036; most accessible tissue: Zhenshan97 young leaf, score: 73.540
vg0704650412 (J) chr07 4650412 G A 59.30% 0.28% A -> G NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 56.150; most accessible tissue: Zhenshan97 young leaf, score: 76.440
vg0704650424 (J) chr07 4650424 A G 59.30% 0.28% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.713; most accessible tissue: Zhenshan97 young leaf, score: 76.099
vg0704650437 (J) chr07 4650437 A G 59.30% 0.21% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 61.401; most accessible tissue: Callus, score: 77.921
vg0704650445 (J) chr07 4650445 C T 89.30% 0.00% C -> T
mr1057 (All); LR P-value: 1.74E-07;
mr1100 (Jap_All); LR P-value: 5.15E-06;
mr1613 (Jap_All); LR P-value: 2.47E-07;
mr1962 (Jap_All); LR P-value: 5.92E-07;
mr1057_2 (All); LR P-value: 1.28E-07;
mr1522_2 (All); LR P-value: 5.62E-06
LOC_Os07g08940.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.520; most accessible tissue: Zhenshan97 young leaf, score: 78.044
vg0704650451 (J) chr07 4650451 G A 99.90% 0.00% G -> A NA
LOC_Os07g08940.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g08934.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08950.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.805; most accessible tissue: Zhenshan97 young leaf, score: 78.044
vg0704650490 (J) chr07 4650490 A G 59.30% 0.19% G -> A NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.368; most accessible tissue: Zhenshan97 young leaf, score: 79.507
vg0704650509 (J) chr07 4650509 C T 59.30% 0.25% T -> C NA
LOC_Os07g08940.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08940.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 63.350; most accessible tissue: Zhenshan97 young leaf, score: 79.783