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Search Results:

34 variations found. LOC_Os10g14130 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 7,670,410 bp to 7,672,240 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
vg1007670429 (J) chr10 7670429 G A 80.80% 17.29% G -> A NA
LOC_Os10g14130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670442 (J) chr10 7670442 C T 80.90% 17.33% C -> T NA
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670457 (J) chr10 7670457 G A 81.50% 17.41% G -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670461 (J) chr10 7670461 C A 80.00% 17.69% C -> A NA
LOC_Os10g14130.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670474 (J) chr10 7670474 G A 81.50% 17.60% G -> A NA
LOC_Os10g14130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670475 (J) chr10 7670475 T A 75.80% 17.60% T -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670486 (J) chr10 7670486 G C 81.50% 17.63% G -> C NA
LOC_Os10g14130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670489 (J) chr10 7670489 A T 79.90% 17.50% A -> T,C NA
LOC_Os10g14130.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os10g14120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g14140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os10g14150.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os10g14130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670505 (J) chr10 7670505 T A 76.60% 17.71% T -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Callus, score: 17.483
vg1007670593 (J) chr10 7670593 A C 25.10% 53.94% A -> C NA
LOC_Os10g14130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.584; most accessible tissue: Callus, score: 15.821
vg1007670732 (J) chr10 7670732 A G 49.80% 8.40% G -> A NA
LOC_Os10g14130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.147; most accessible tissue: Callus, score: 26.336
vg1007670741 (J) chr10 7670741 C T 83.00% 8.44% C -> T NA
LOC_Os10g14130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.113; most accessible tissue: Callus, score: 26.336
vg1007670790 (J) chr10 7670790 C A 80.60% 13.97% C -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.755; most accessible tissue: Callus, score: 26.336
vg1007670843 (J) chr10 7670843 G T 14.70% 66.67% G -> T NA
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.875; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007670937 (J) chr10 7670937 G C 55.40% 17.22% G -> C NA
LOC_Os10g14130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.339; most accessible tissue: Callus, score: 18.912
vg1007670943 (J) chr10 7670943 C T 30.60% 43.69% C -> T NA
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.339; most accessible tissue: Callus, score: 18.912
vg1007670968 (J) chr10 7670968 C T 33.00% 43.29% C -> T NA
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1007670982 (J) chr10 7670982 A G 46.00% 38.85% A -> G NA
LOC_Os10g14130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1007671145 (J) chr10 7671145 C A 86.90% 8.27% C -> A NA
LOC_Os10g14120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 10.496; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671163 (J) chr10 7671163 G A 63.10% 13.22% G -> A NA
LOC_Os10g14120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 9.987; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671320 (J) chr10 7671320 G A 48.60% 18.71% G -> A NA
LOC_Os10g14120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.760; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671330 (J) chr10 7671330 C T 26.10% 44.67% C -> T NA
LOC_Os10g14120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671341 (J) chr10 7671341 G A 49.50% 35.74% G -> A NA
LOC_Os10g14120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671345 (J) chr10 7671345 A G 45.50% 38.76% A -> G NA
LOC_Os10g14120.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14130.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.481; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1007671362 (J) chr10 7671362 G A 39.00% 40.94% G -> A NA
LOC_Os10g14130.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g14120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g14150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605
vg1007671399 (J) chr10 7671399 G A 16.00% 69.26% G -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605
vg1007671423 (J) chr10 7671423 A G 13.80% 75.18% A -> G NA
LOC_Os10g14130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.735; most accessible tissue: Zhenshan97 flag leaf, score: 12.605
vg1007671514 (J) chr10 7671514 G A 80.60% 13.86% G -> A NA
LOC_Os10g14130.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.761; most accessible tissue: Zhenshan97 flag leaf, score: 12.605
vg1007671530 (J) chr10 7671530 T C 14.90% 64.75% T -> C NA
LOC_Os10g14130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.521; most accessible tissue: Zhenshan97 flag leaf, score: 10.769
vg1007671788 (J) chr10 7671788 C A 13.40% 78.82% C -> A NA
LOC_Os10g14130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.753; most accessible tissue: Minghui63 panicle, score: 16.270
vg1007671802 (J) chr10 7671802 C T 13.40% 79.28% C -> T NA
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.753; most accessible tissue: Minghui63 panicle, score: 16.270
vg1007671811 (J) chr10 7671811 C A 13.50% 78.67% C -> A NA
LOC_Os10g14130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.753; most accessible tissue: Minghui63 panicle, score: 16.270
vg1007671817 (J) chr10 7671817 C T 14.40% 73.78% C -> T
Spikelet_length (Ind_All); LR P-value: 1.19E-06;
mr1026 (All); LR P-value: 1.17E-38;
mr1026 (Ind_All); LR P-value: 4.51E-13;
mr1113 (Ind_All); LR P-value: 2.62E-07;
mr1114 (Ind_All); LR P-value: 5.46E-07;
mr1116 (Ind_All); LMM P-value: 1.23E-07; LR P-value: 8.81E-09;
mr1118 (All); LR P-value: 2.50E-15;
mr1118 (Ind_All); LMM P-value: 5.74E-06; LR P-value: 8.93E-19;
mr1120 (Ind_All); LR P-value: 3.55E-06;
mr1161 (All); LR P-value: 3.29E-36;
mr1161 (Ind_All); LR P-value: 1.44E-11;
mr1247 (Ind_All); LMM P-value: 2.69E-06; LR P-value: 4.49E-08;
mr1261 (Ind_All); LR P-value: 6.07E-06;
mr1495 (Ind_All); LR P-value: 6.31E-18;
mr1496 (Ind_All); LR P-value: 5.86E-06;
mr1794 (Ind_All); LMM P-value: 6.85E-07; LR P-value: 7.67E-10;
mr1113_2 (Ind_All); LR P-value: 8.26E-06;
mr1114_2 (Ind_All); LR P-value: 7.58E-06;
mr1118_2 (All); LR P-value: 1.00E-18;
mr1118_2 (Ind_All); LMM P-value: 6.68E-08; LR P-value: 2.45E-23;
mr1120_2 (Ind_All); LR P-value: 8.16E-08;
mr1123_2 (Ind_All); LR P-value: 7.32E-06;
mr1161_2 (All); LR P-value: 1.39E-40;
mr1161_2 (Ind_All); LR P-value: 2.69E-14;
mr1247_2 (Ind_All); LR P-value: 2.99E-07;
mr1495_2 (All); LMM P-value: 9.64E-07; LR P-value: 2.92E-26;
mr1495_2 (Ind_All); LMM P-value: 8.85E-09; LR P-value: 1.67E-23;
mr1496_2 (Ind_All); LR P-value: 1.03E-07;
mr1936_2 (Ind_All); LR P-value: 2.14E-07
LOC_Os10g14130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.753; most accessible tissue: Minghui63 panicle, score: 16.270
vg1007672199 (J) chr10 7672199 G A 15.10% 49.98% G -> A NA
LOC_Os10g14130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g14130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.500; most accessible tissue: Zhenshan97 root, score: 22.162