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Search Results:

20 variations found. LOC_Os04g40780 (OsFBX145 - F-box domain containing protein; expressed), ranging from 24,199,123 bp to 24,200,930 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
vg0424199131 (J) chr04 24199131 A G 96.90% 1.21% A -> G NA
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.499; most accessible tissue: Minghui63 root, score: 77.290
vg0424199143 (J) chr04 24199143 G A 98.10% 1.18% G -> A NA
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.341; most accessible tissue: Minghui63 root, score: 78.091
vg0424199421 (J) chr04 24199421 T C 96.80% 1.29% T -> C NA
LOC_Os04g40780.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 40.596; most accessible tissue: Minghui63 root, score: 63.915
vg0424199506 (J) chr04 24199506 G A 57.20% 1.95% G -> A
Grain_length (Ind_All); LR P-value: 2.21E-15;
mr1050 (All); LR P-value: 1.03E-09;
mr1050 (Ind_All); LR P-value: 8.88E-07;
mr1170 (Ind_All); LR P-value: 5.40E-06;
mr1399 (All); LR P-value: 4.39E-10;
mr1399 (Ind_All); LR P-value: 1.95E-06;
mr1458 (Ind_All); LR P-value: 1.55E-07;
mr1598 (Ind_All); LR P-value: 8.62E-06;
mr1835 (All); LR P-value: 3.70E-06;
mr1904 (All); LR P-value: 1.29E-12;
mr1904 (Ind_All); LR P-value: 4.16E-06;
mr1050_2 (All); LR P-value: 4.52E-10;
mr1272_2 (All); LR P-value: 2.20E-06;
mr1355_2 (All); LR P-value: 8.53E-06;
mr1593_2 (Ind_All); LR P-value: 5.40E-08;
mr1598_2 (Ind_All); LR P-value: 6.80E-09;
mr1835_2 (All); LR P-value: 6.22E-10;
mr1895_2 (All); LR P-value: 8.68E-08;
mr1904_2 (All); LR P-value: 6.90E-16;
mr1904_2 (Ind_All); LR P-value: 3.46E-07
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 35.220; most accessible tissue: Callus, score: 76.576
vg0424199521 (J) chr04 24199521 G GCA 57.20% 1.90% G -> GCA NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: GCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: GCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: GCA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.438; most accessible tissue: Callus, score: 76.576
vg0424199537 (J) chr04 24199537 C CAAA 63.10% 18.39% C -> CAAA,CAA,C A NA
LOC_Os04g40770.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.991; most accessible tissue: Callus, score: 76.576
vg0424199539 (J) chr04 24199539 A AG 64.00% 1.90% A -> AG NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: AG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.869; most accessible tissue: Callus, score: 76.576
vg0424199561 (J) chr04 24199561 C T 98.50% 1.16% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 33.320; most accessible tissue: Callus, score: 76.576
vg0424199782 (J) chr04 24199782 G A 57.20% 1.95% G -> A
Grain_length (Ind_All); LR P-value: 8.51E-15;
mr1050 (All); LR P-value: 8.32E-10;
mr1050 (Ind_All); LR P-value: 2.87E-07;
mr1170 (Ind_All); LR P-value: 1.57E-06;
mr1272 (All); LR P-value: 5.39E-11;
mr1399 (All); LR P-value: 5.41E-09;
mr1458 (Ind_All); LR P-value: 3.43E-07;
mr1593 (Ind_All); LR P-value: 6.92E-07;
mr1598 (Ind_All); LR P-value: 4.54E-06;
mr1608 (Ind_All); LR P-value: 3.92E-06;
mr1731 (Ind_All); LR P-value: 9.85E-06;
mr1835 (All); LR P-value: 2.57E-06;
mr1860 (All); LR P-value: 3.13E-08;
mr1904 (All); LR P-value: 2.19E-12;
mr1904 (Ind_All); LR P-value: 3.59E-06;
mr1050_2 (All); LR P-value: 6.26E-11;
mr1272_2 (All); LR P-value: 7.38E-07;
mr1593_2 (Ind_All); LR P-value: 2.64E-08;
mr1835_2 (All); LR P-value: 3.82E-10;
mr1895_2 (All); LR P-value: 4.96E-07;
mr1904_2 (All); LR P-value: 1.03E-16;
mr1904_2 (Ind_All); LR P-value: 5.56E-08;
mr1931_2 (Ind_All); LR P-value: 6.09E-06;
mr1942_2 (Ind_All); LR P-value: 3.53E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 38.038; most accessible tissue: Callus, score: 79.457
vg0424199800 (J) chr04 24199800 A G 97.50% 1.38% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g40770.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40790.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g40780.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 37.226; most accessible tissue: Callus, score: 79.457
vg0424199828 (J) chr04 24199828 T A 96.80% 1.40% T -> A NA
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 37.674; most accessible tissue: Callus, score: 66.196
vg0424199886 (J) chr04 24199886 G A 59.00% 1.76% G -> A
Grain_length (Ind_All); LR P-value: 5.59E-14;
mr1050 (All); LR P-value: 3.09E-10;
mr1050 (Ind_All); LR P-value: 2.39E-07;
mr1272 (All); LR P-value: 4.66E-11;
mr1333 (Ind_All); LR P-value: 7.57E-06;
mr1399 (All); LR P-value: 6.36E-09;
mr1458 (Ind_All); LR P-value: 6.05E-07;
mr1731 (Ind_All); LR P-value: 6.32E-06;
mr1904 (All); LR P-value: 5.86E-12;
mr1050_2 (All); LR P-value: 1.03E-10;
mr1272_2 (All); LR P-value: 1.11E-06;
mr1355_2 (All); LR P-value: 7.08E-06;
mr1593_2 (Ind_All); LR P-value: 4.21E-08;
mr1835_2 (All); LR P-value: 2.31E-09;
mr1895_2 (All); LR P-value: 1.04E-07;
mr1902_2 (Ind_All); LR P-value: 1.15E-09;
mr1904_2 (All); LR P-value: 4.04E-15;
mr1942_2 (Ind_All); LR P-value: 5.88E-06
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 41.801; most accessible tissue: Callus, score: 66.196
vg0424199959 (J) chr04 24199959 A G 57.30% 1.57% A -> G
Grain_length (Ind_All); LR P-value: 1.33E-13;
mr1050 (All); LR P-value: 4.61E-10;
mr1050 (Ind_All); LR P-value: 2.14E-07;
mr1170 (Ind_All); LR P-value: 1.71E-06;
mr1272 (All); LR P-value: 5.91E-11;
mr1399 (All); LR P-value: 1.91E-09;
mr1458 (Ind_All); LR P-value: 3.62E-07;
mr1593 (Ind_All); LR P-value: 1.29E-07;
mr1608 (Ind_All); LR P-value: 8.89E-07;
mr1835 (All); LR P-value: 6.29E-07;
mr1860 (All); LR P-value: 2.27E-08;
mr1904 (All); LR P-value: 9.02E-13;
mr1904 (Ind_All); LR P-value: 2.85E-06;
mr1050_2 (All); LR P-value: 3.28E-10;
mr1272_2 (All); LR P-value: 8.08E-07;
mr1593_2 (Ind_All); LR P-value: 4.11E-09;
mr1835_2 (All); LR P-value: 1.80E-10;
mr1895_2 (All); LR P-value: 2.96E-07;
mr1904_2 (All); LR P-value: 5.08E-17;
mr1904_2 (Ind_All); LR P-value: 5.06E-08;
mr1931_2 (Ind_All); LR P-value: 6.47E-06;
mr1942_2 (Ind_All); LR P-value: 7.78E-06
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 46.759; most accessible tissue: Callus, score: 86.818
vg0424200160 (J) chr04 24200160 T C 59.00% 1.99% T -> C
Grain_length (Ind_All); LR P-value: 2.73E-14;
mr1050 (All); LR P-value: 1.74E-10;
mr1050 (Ind_All); LR P-value: 2.08E-07;
mr1170 (Ind_All); LR P-value: 9.56E-06;
mr1272 (All); LR P-value: 2.60E-11;
mr1333 (Ind_All); LR P-value: 7.91E-06;
mr1593 (Ind_All); LR P-value: 9.98E-07;
mr1598 (Ind_All); LR P-value: 9.48E-06;
mr1608 (Ind_All); LR P-value: 8.82E-06;
mr1731 (Ind_All); LR P-value: 6.82E-06;
mr1835 (All); LR P-value: 3.77E-06;
mr1902 (All); LR P-value: 2.27E-11;
mr1902 (Ind_All); LR P-value: 3.02E-07;
mr1904 (All); LR P-value: 6.83E-12;
mr1050_2 (All); LR P-value: 9.68E-11;
mr1272_2 (All); LR P-value: 8.65E-07;
mr1355_2 (All); LR P-value: 7.89E-06;
mr1593_2 (Ind_All); LR P-value: 2.86E-08;
mr1835_2 (All); LR P-value: 1.28E-09;
mr1895_2 (All); LR P-value: 2.21E-07;
mr1902_2 (Ind_All); LR P-value: 7.35E-10;
mr1904_2 (All); LR P-value: 1.33E-15;
mr1904_2 (Ind_All); LR P-value: 5.69E-07;
mr1942_2 (Ind_All); LR P-value: 3.72E-06
LOC_Os04g40780.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 63.669; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0424200248 (J) chr04 24200248 C T 97.60% 1.38% C -> T
Grain_weight (Jap_All); LR P-value: 1.03E-06;
mr1191_2 (Jap_All); LMM P-value: 5.76E-06; LR P-value: 5.76E-06;
mr1827_2 (Jap_All); LR P-value: 8.23E-06
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 71.556; most accessible tissue: Zhenshan97 panicle, score: 90.849
vg0424200268 (J) chr04 24200268 A T 98.00% 1.40% A -> T NA
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 73.290; most accessible tissue: Zhenshan97 panicle, score: 92.403
vg0424200644 (J) chr04 24200644 G GAGA 57.20% 0.17% G -> GAGA NA
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: GAGA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 78.665; most accessible tissue: Zhenshan97 panicle, score: 96.863
vg0424200736 (J) chr04 24200736 G A 63.40% 0.53% G -> A
Grain_length (Ind_All); LR P-value: 2.12E-14;
mr1050 (All); LR P-value: 1.34E-08;
mr1050 (Ind_All); LR P-value: 3.51E-07;
mr1170 (Ind_All); LR P-value: 9.06E-06;
mr1324 (Ind_All); LR P-value: 2.89E-06;
mr1333 (Ind_All); LR P-value: 1.12E-06;
mr1707 (All); LR P-value: 4.50E-08;
mr1728 (All); LR P-value: 2.39E-08;
mr1860 (All); LR P-value: 2.90E-09;
mr1974 (Ind_All); LR P-value: 7.09E-06;
mr1355_2 (All); LR P-value: 5.60E-06;
mr1655_2 (All); LR P-value: 6.19E-06;
mr1728_2 (All); LR P-value: 6.00E-12;
mr1860_2 (All); LR P-value: 1.12E-08;
mr1895_2 (All); LR P-value: 1.39E-07;
mr1904_2 (Ind_All); LR P-value: 6.20E-07;
mr1910_2 (All); LR P-value: 1.49E-06;
mr1942_2 (Ind_All); LR P-value: 2.20E-06
LOC_Os04g40780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g40780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.471; most accessible tissue: Zhenshan97 panicle, score: 96.130
vg0424200777 (J) chr04 24200777 CGAA C 98.20% 0.00% CGAA -> C NA
LOC_Os04g40780.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 78.359; most accessible tissue: Zhenshan97 panicle, score: 95.903
STR0424200780 (J) chr04 24200780 AGGA A 99.60% 0.00% AGGA -> A NA