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Search Results:

28 variations found. LOC_Os06g15880 (retrotransposon protein; putative; unclassified), ranging from 9,017,522 bp to 9,018,636 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
vg0609017552 (J) chr06 9017552 G A 52.10% 32.88% G -> A NA
LOC_Os06g15880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.447; most accessible tissue: Zhenshan97 flower, score: 52.192
vg0609017612 (J) chr06 9017612 G A 32.40% 50.80% G -> A NA
LOC_Os06g15880.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 23.747; most accessible tissue: Zhenshan97 flag leaf, score: 58.772
vg0609017794 (J) chr06 9017794 C G 48.60% 40.58% C -> G NA
LOC_Os06g15870.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 29.745; most accessible tissue: Zhenshan97 flower, score: 69.089
vg0609017853 (J) chr06 9017853 T A 50.90% 38.47% T -> A NA
LOC_Os06g15870.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582
vg0609017854 (J) chr06 9017854 G T 50.90% 38.49% G -> T NA
LOC_Os06g15870.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582
vg0609017893 (J) chr06 9017893 G A 50.00% 41.77% G -> A NA
LOC_Os06g15870.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825
vg0609017914 (J) chr06 9017914 G A 49.60% 42.26% G -> A NA
LOC_Os06g15870.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 31.333; most accessible tissue: Zhenshan97 flag leaf, score: 76.356
vg0609017960 (J) chr06 9017960 G A 29.40% 43.17% A -> G NA
LOC_Os06g15870.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 32.130; most accessible tissue: Zhenshan97 flag leaf, score: 76.356
vg0609017968 (J) chr06 9017968 A T 50.80% 39.65% A -> T NA
LOC_Os06g15870.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 32.188; most accessible tissue: Zhenshan97 flag leaf, score: 76.642
vg0609017977 (J) chr06 9017977 T C 48.20% 48.62% T -> C NA
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 30.975; most accessible tissue: Zhenshan97 flag leaf, score: 75.143
vg0609017980 (J) chr06 9017980 T A 48.10% 48.73% T -> A NA
LOC_Os06g15870.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 30.859; most accessible tissue: Zhenshan97 flag leaf, score: 75.143
vg0609017986 (J) chr06 9017986 T C 48.50% 48.33% T -> C NA
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 29.930; most accessible tissue: Zhenshan97 flag leaf, score: 74.162
vg0609018001 (J) chr06 9018001 C T 50.90% 40.52% C -> T NA
LOC_Os06g15870.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761
vg0609018014 (J) chr06 9018014 A G 48.90% 48.20% A -> G NA
LOC_Os06g15870.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 30.662; most accessible tissue: Zhenshan97 flag leaf, score: 77.473
vg0609018033 (J) chr06 9018033 T C 49.70% 47.42% T -> C NA
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 31.574; most accessible tissue: Zhenshan97 flag leaf, score: 79.006
vg0609018048 (J) chr06 9018048 T C 49.80% 46.47% T -> C NA
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 32.241; most accessible tissue: Zhenshan97 flag leaf, score: 80.799
vg0609018155 (J) chr06 9018155 T C 48.50% 40.56% T -> C NA
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 26.350; most accessible tissue: Zhenshan97 flag leaf, score: 79.006
vg0609018352 (J) chr06 9018352 G A 49.00% 40.82% G -> A NA
LOC_Os06g15870.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15880.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 31.820; most accessible tissue: Zhenshan97 flag leaf, score: 80.373
vg0609018460 (J) chr06 9018460 T C 47.70% 4.36% T -> C
Grain_length (Jap_All); LR P-value: 2.71E-14;
mr1057 (All); LR P-value: 9.38E-07;
mr1087 (Jap_All); LR P-value: 8.12E-06;
mr1096 (Jap_All); LR P-value: 3.99E-06;
mr1570 (Jap_All); LR P-value: 1.14E-07;
mr1057_2 (All); LR P-value: 4.35E-09;
mr1087_2 (Jap_All); LMM P-value: 2.44E-06; LR P-value: 2.42E-14;
mr1091_2 (Jap_All); LR P-value: 6.17E-06;
mr1096_2 (Jap_All); LR P-value: 2.10E-07;
mr1341_2 (All); LR P-value: 1.47E-06;
mr1530_2 (Jap_All); LR P-value: 5.43E-10;
mr1570_2 (Jap_All); LMM P-value: 1.91E-06; LR P-value: 5.59E-14;
mr1578_2 (Ind_All); LR P-value: 2.83E-06
LOC_Os06g15880.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os06g15870.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15900.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g15890.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 34.750; most accessible tissue: Zhenshan97 flag leaf, score: 80.799
vg0609018487 (J) chr06 9018487 A G 94.30% 1.25% A -> G NA
LOC_Os06g15880.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 34.868; most accessible tissue: Zhenshan97 flag leaf, score: 81.008
vg0609018524 (J) chr06 9018524 A T 94.30% 3.39% A -> T NA
LOC_Os06g15880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 35.172; most accessible tissue: Zhenshan97 flag leaf, score: 81.008
vg0609018542 (J) chr06 9018542 C A 68.90% 1.84% C -> A,G
mr1122 (Ind_All); LR P-value: 9.60E-06;
mr1242 (Ind_All); LR P-value: 4.63E-06;
mr1570_2 (Jap_All); LR P-value: 1.89E-10
LOC_Os06g15880.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 37.419; most accessible tissue: Zhenshan97 flag leaf, score: 83.366
vg0609018547 (J) chr06 9018547 T A 77.20% 3.68% T -> A
mr1570 (All); LMM P-value: 6.72E-06; LR P-value: 1.63E-08;
mr1570 (Ind_All); LMM P-value: 3.76E-06; LR P-value: 5.19E-09;
mr1570_2 (Ind_All); LR P-value: 4.27E-07;
mr1668_2 (All); LR P-value: 4.00E-07;
mr1668_2 (Ind_All); LR P-value: 2.24E-06
LOC_Os06g15880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 37.717; most accessible tissue: Zhenshan97 flag leaf, score: 83.840
vg0609018551 (J) chr06 9018551 A T 93.70% 4.36% A -> T NA
LOC_Os06g15880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 37.722; most accessible tissue: Zhenshan97 flag leaf, score: 83.994
vg0609018595 (J) chr06 9018595 G C 62.50% 25.33% G -> C,A NA
LOC_Os06g15880.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 38.469; most accessible tissue: Zhenshan97 flag leaf, score: 83.684
vg0609018598 (J) chr06 9018598 A G 48.60% 43.02% A -> G
mr1057 (All); LR P-value: 1.07E-06;
mr1096 (Jap_All); LR P-value: 3.99E-06;
mr1570 (Jap_All); LR P-value: 1.61E-08;
mr1606 (Jap_All); LR P-value: 6.14E-06;
mr1057_2 (All); LR P-value: 1.16E-07;
mr1087_2 (Jap_All); LR P-value: 3.61E-13;
mr1096_2 (Jap_All); LR P-value: 1.45E-07;
mr1338_2 (Jap_All); LR P-value: 8.04E-08;
mr1341_2 (All); LR P-value: 5.51E-06;
mr1530_2 (Jap_All); LR P-value: 5.50E-10;
mr1570_2 (Jap_All); LMM P-value: 1.42E-08; LR P-value: 4.90E-16;
mr1642_2 (All); LR P-value: 1.36E-07
LOC_Os06g15880.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 39.322; most accessible tissue: Zhenshan97 flag leaf, score: 83.994
vg0609018604 (J) chr06 9018604 G A 50.00% 42.02% G -> A NA
LOC_Os06g15880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 39.475; most accessible tissue: Zhenshan97 flag leaf, score: 83.840
vg0609018613 (J) chr06 9018613 A C 47.80% 49.41% A -> C NA
LOC_Os06g15880.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g15880.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 40.181; most accessible tissue: Zhenshan97 flag leaf, score: 83.840