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Search Results:

18 variations found. LOC_Os02g06280 (receptor-like protein kinase 2 precursor; putative; expressed), ranging from 3,136,182 bp to 3,137,965 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
vg0203136261 (J) chr02 3136261 AC A 55.10% 2.33% AC -> A NA
LOC_Os02g06270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 53.021; most accessible tissue: Callus, score: 82.944
vg0203136530 (J) chr02 3136530 C T 97.80% 1.80% C -> T NA
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 54.504; most accessible tissue: Callus, score: 86.347
vg0203136531 (J) chr02 3136531 G A 94.00% 2.09% G -> A NA
LOC_Os02g06270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 54.465; most accessible tissue: Callus, score: 86.347
vg0203136771 (J) chr02 3136771 A T 51.20% 2.29% A -> T
mr1527 (All); LR P-value: 1.72E-06;
mr1582_2 (All); LR P-value: 1.71E-11;
mr1582_2 (Ind_All); LR P-value: 3.22E-07
LOC_Os02g06280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 55.479; most accessible tissue: Callus, score: 83.936
vg0203137069 (J) chr02 3137069 A T 54.90% 2.26% A -> T
mr1517_2 (Ind_All); LR P-value: 1.09E-06;
mr1582_2 (All); LR P-value: 5.89E-09;
mr1582_2 (Ind_All); LR P-value: 1.19E-06
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 52.960; most accessible tissue: Callus, score: 82.405
vg0203137179 (J) chr02 3137179 A T 55.10% 2.33% A -> T
mr1517_2 (Ind_All); LR P-value: 1.85E-06;
mr1582_2 (All); LR P-value: 5.52E-09;
mr1582_2 (Ind_All); LR P-value: 1.53E-06
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 47.338; most accessible tissue: Callus, score: 84.278
vg0203137192 (J) chr02 3137192 C T 54.90% 2.33% C -> T
mr1517_2 (Ind_All); LR P-value: 1.85E-06;
mr1582_2 (All); LR P-value: 6.83E-09;
mr1582_2 (Ind_All); LR P-value: 1.53E-06
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 49.409; most accessible tissue: Callus, score: 84.278
vg0203137419 (J) chr02 3137419 T A 90.60% 2.14% T -> A NA
LOC_Os02g06270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 58.869; most accessible tissue: Zhenshan97 flower, score: 79.196
vg0203137432 (J) chr02 3137432 G T 54.90% 2.33% G -> T
mr1511_2 (All); LR P-value: 7.78E-06;
mr1517_2 (Ind_All); LR P-value: 6.99E-07;
mr1582_2 (All); LR P-value: 3.40E-09;
mr1582_2 (Ind_All); LR P-value: 5.80E-07
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 62.077; most accessible tissue: Callus, score: 83.704
vg0203137445 (J) chr02 3137445 C T 97.20% 1.76% C -> T NA
LOC_Os02g06270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 63.052; most accessible tissue: Callus, score: 83.704
vg0203137495 (J) chr02 3137495 GT G 83.30% 1.95% GT -> G,GTT NA
LOC_Os02g06270.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06270.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06290.2 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g06280.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 63.366; most accessible tissue: Callus, score: 83.704
vg0203137684 (J) chr02 3137684 C G 98.00% 1.69% C -> G NA
LOC_Os02g06280.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 72.473; most accessible tissue: Zhenshan97 flower, score: 88.571
vg0203137768 (J) chr02 3137768 G A 98.00% 1.78% G -> A NA
LOC_Os02g06280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.272; most accessible tissue: Zhenshan97 flower, score: 92.592
vg0203137792 (J) chr02 3137792 G T 83.30% 2.18% G -> T NA
LOC_Os02g06280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.985; most accessible tissue: Zhenshan97 flower, score: 93.144
vg0203137848 (J) chr02 3137848 C A 92.10% 1.88% C -> A
mr1028 (All); LR P-value: 3.14E-07;
mr1120 (All); LR P-value: 1.03E-21;
mr1157 (All); LR P-value: 7.47E-08;
mr1158 (All); LR P-value: 3.36E-16;
mr1230 (All); LR P-value: 1.66E-06;
mr1328 (All); LR P-value: 5.20E-07;
mr1348 (All); LR P-value: 1.42E-08;
mr1349 (All); LR P-value: 3.73E-06;
mr1365 (All); LR P-value: 1.70E-06;
mr1369 (All); LR P-value: 6.39E-07;
mr1445 (All); LR P-value: 3.50E-06;
mr1446 (All); LR P-value: 7.56E-09;
mr1453 (All); LR P-value: 4.53E-08;
mr1522 (All); LR P-value: 5.85E-12;
mr1621 (All); LR P-value: 3.41E-07;
mr1652 (All); LR P-value: 2.59E-08;
mr1706 (All); LR P-value: 1.28E-07;
mr1730 (All); LR P-value: 1.16E-09;
mr1120_2 (All); LR P-value: 1.74E-21;
mr1610_2 (All); LR P-value: 2.19E-11;
mr1818_2 (All); LR P-value: 8.49E-10;
mr1927_2 (All); LR P-value: 1.63E-18
LOC_Os02g06280.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.199; most accessible tissue: Zhenshan97 flower, score: 95.064
vg0203137855 (J) chr02 3137855 A C 54.80% 2.24% A -> C
mr1517_2 (Ind_All); LR P-value: 1.09E-06;
mr1582_2 (All); LR P-value: 5.89E-09;
mr1582_2 (Ind_All); LR P-value: 1.19E-06
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g06280.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.052; most accessible tissue: Zhenshan97 flower, score: 95.064
vg0203137930 (J) chr02 3137930 A G 94.40% 1.59% A -> G NA
LOC_Os02g06280.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g06280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.630; most accessible tissue: Zhenshan97 flower, score: 96.996
STR0203137843 (J) chr02 3137843 CTCCTC CTCCTA 97.50% 0.00% CTCCTC -> CTCCTA NA