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Search Results:

26 variations found. LOC_Os04g51730 (retrotransposon protein; putative; unclassified; expressed), ranging from 30,653,188 bp to 30,655,189 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
vg0430653203 (J) chr04 30653203 A G 13.60% 58.63% A -> G NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.608; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653642 (J) chr04 30653642 A G 0.10% 89.00% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653672 (J) chr04 30653672 A G 74.60% 17.05% A -> G NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653703 (J) chr04 30653703 C T 84.30% 15.26% C -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653708 (J) chr04 30653708 A T 84.20% 15.26% A -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653732 (J) chr04 30653732 G A 84.00% 15.43% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653739 (J) chr04 30653739 A C 82.70% 15.36% A -> C NA
LOC_Os04g51730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653744 (J) chr04 30653744 T Unkown 84.40% 15.38% T -> C NA
LOC_Os04g51730.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os04g51720.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g51740.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653750 (J) chr04 30653750 T A 41.60% 19.53% T -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.428; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653768 (J) chr04 30653768 C T 65.70% 18.45% C -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653771 (J) chr04 30653771 G A 51.10% 34.98% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430653774 (J) chr04 30653774 G A 47.00% 37.96% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.246; most accessible tissue: Minghui63 panicle, score: 20.733
vg0430654071 (J) chr04 30654071 G A 84.10% 15.09% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654076 (J) chr04 30654076 C T 64.00% 15.07% C -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654080 (J) chr04 30654080 G T 47.40% 16.76% G -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654095 (J) chr04 30654095 C T 84.50% 14.92% C -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654098 (J) chr04 30654098 A G 84.30% 15.09% A -> G NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654100 (J) chr04 30654100 C T 84.60% 14.92% C -> T NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654111 (J) chr04 30654111 T C 84.10% 15.02% T -> C NA
LOC_Os04g51730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654119 (J) chr04 30654119 G A 84.70% 14.90% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654148 (J) chr04 30654148 G A 76.00% 16.80% G -> A NA
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g51730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654182 (J) chr04 30654182 T C 14.00% 51.40% T -> C NA
LOC_Os04g51730.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g51730.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661
vg0430654505 (J) chr04 30654505 A G 13.20% 63.39% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 5.261; most accessible tissue: Minghui63 flower, score: 7.958
vg0430654546 (J) chr04 30654546 A G 13.30% 58.29% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 5.654; most accessible tissue: Minghui63 flower, score: 7.958
vg0430654714 (J) chr04 30654714 TA T 4.20% 57.24% TA -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51740.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51730.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122
vg0430654813 (J) chr04 30654813 A G 13.80% 56.94% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g51720.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g51730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491