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18 variations found. LOC_Os02g14540 (UDP-glucoronosyl and UDP-glucosyl transferase domain containing protein; expressed), ranging from 8,018,191 bp to 8,019,355 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
vg0208018313 (J) chr02 8018313 T C 50.60% 0.00% C -> T NA
LOC_Os02g14540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.766; most accessible tissue: Zhenshan97 root, score: 94.924
vg0208018326 (J) chr02 8018326 TC T 99.20% 0.00% TC -> T NA
LOC_Os02g14540.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.560; most accessible tissue: Zhenshan97 root, score: 95.028
vg0208018476 (J) chr02 8018476 A G 91.60% 2.67% A -> G NA
LOC_Os02g14540.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.726; most accessible tissue: Zhenshan97 young leaf, score: 94.147
vg0208018489 (J) chr02 8018489 G A 90.80% 3.53% G -> A NA
LOC_Os02g14540.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.239; most accessible tissue: Zhenshan97 young leaf, score: 94.848
vg0208018524 (J) chr02 8018524 T C 69.30% 24.14% T -> C NA
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g14540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.081; most accessible tissue: Zhenshan97 young leaf, score: 94.820
vg0208018622 (J) chr02 8018622 C T 81.20% 6.18% C -> T NA
LOC_Os02g14540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.686; most accessible tissue: Minghui63 flag leaf, score: 94.880
vg0208018656 (J) chr02 8018656 C T 50.70% 0.00% T -> C
mr1171 (All); LR P-value: 7.28E-06;
mr1198 (All); LR P-value: 2.15E-09;
mr1232 (All); LR P-value: 4.00E-11;
mr1336 (All); LR P-value: 1.51E-09;
mr1508 (All); LR P-value: 6.01E-06;
mr1516 (All); LR P-value: 9.22E-06;
mr1557 (All); LR P-value: 3.75E-23;
mr1701 (All); LR P-value: 7.31E-13
LOC_Os02g14540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 86.289; most accessible tissue: Minghui63 flag leaf, score: 95.024
vg0208018666 (J) chr02 8018666 T G 50.60% 0.00% G -> T
mr1198 (All); LR P-value: 3.46E-09;
mr1232 (All); LR P-value: 8.37E-11;
mr1336 (All); LR P-value: 4.24E-09;
mr1557 (All); LR P-value: 1.80E-22;
mr1377_2 (All); LR P-value: 1.21E-11;
mr1691_2 (All); LR P-value: 1.48E-06
LOC_Os02g14540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.196; most accessible tissue: Minghui63 flag leaf, score: 95.052
vg0208018717 (J) chr02 8018717 C T 98.30% 0.00% C -> T NA
LOC_Os02g14540.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.517; most accessible tissue: Minghui63 flag leaf, score: 95.242
vg0208018767 (J) chr02 8018767 A C 50.60% 0.00% C -> A
mr1232 (All); LR P-value: 4.53E-11;
mr1336 (All); LR P-value: 5.36E-09;
mr1508 (All); LR P-value: 4.85E-06;
mr1557 (All); LR P-value: 2.72E-22;
mr1377_2 (All); LR P-value: 1.33E-11;
mr1691_2 (All); LR P-value: 1.69E-06
LOC_Os02g14540.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 87.578; most accessible tissue: Minghui63 flag leaf, score: 95.347
vg0208018838 (J) chr02 8018838 C T 50.70% 0.00% T -> C
mr1171 (All); LR P-value: 5.35E-06;
mr1198 (All); LR P-value: 2.15E-09;
mr1232 (All); LR P-value: 7.03E-11;
mr1336 (All); LR P-value: 5.62E-10;
mr1508 (All); LR P-value: 5.86E-06;
mr1557 (All); LR P-value: 1.84E-22;
mr1701 (All); LR P-value: 4.40E-13;
mr1377_2 (All); LR P-value: 1.04E-11
LOC_Os02g14540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.681; most accessible tissue: Minghui63 flag leaf, score: 95.024
vg0208018873 (J) chr02 8018873 G A 56.80% 33.81% G -> A NA
LOC_Os02g14540.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.885; most accessible tissue: Minghui63 flag leaf, score: 95.372
vg0208018934 (J) chr02 8018934 T C 66.50% 30.17% T -> C NA
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g14540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.396; most accessible tissue: Minghui63 flag leaf, score: 95.215
vg0208018957 (J) chr02 8018957 T A 67.70% 27.87% T -> A NA
LOC_Os02g14540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.261; most accessible tissue: Minghui63 flag leaf, score: 95.321
vg0208019029 (J) chr02 8019029 T C 50.40% 0.00% C -> T NA
LOC_Os02g14540.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.862; most accessible tissue: Minghui63 flag leaf, score: 93.917
vg0208019153 (J) chr02 8019153 G A 50.70% 0.00% A -> G
mr1198 (All); LR P-value: 5.73E-09;
mr1232 (All); LR P-value: 2.20E-10;
mr1508 (All); LR P-value: 3.63E-06;
mr1557 (All); LR P-value: 6.26E-22;
mr1570_2 (Ind_All); LR P-value: 8.83E-06
LOC_Os02g14540.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.161; most accessible tissue: Minghui63 flag leaf, score: 93.043
vg0208019252 (J) chr02 8019252 A G 76.80% 7.55% A -> G NA
LOC_Os02g14540.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g14540.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.729; most accessible tissue: Minghui63 flag leaf, score: 91.489
STR0208019028 (J) chr02 8019028 CT CC 46.30% 0.00% CC -> CT NA