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Search Results:

23 variations found. LOC_Os04g41599 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 24,675,323 bp to 24,685,375 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
vg0424676929 (J) chr04 24676929 G C 0.30% 85.34% G -> C NA
LOC_Os04g41599.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.526; most accessible tissue: Minghui63 root, score: 13.235
vg0424676968 (J) chr04 24676968 G A 16.10% 82.92% G -> A NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.526; most accessible tissue: Minghui63 root, score: 13.235
vg0424677282 (J) chr04 24677282 G A 16.20% 71.24% G -> A NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 10.241; most accessible tissue: Minghui63 young leaf, score: 18.030
vg0424677314 (J) chr04 24677314 C G 18.40% 67.27% C -> G NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 11.846; most accessible tissue: Minghui63 young leaf, score: 22.423
vg0424677667 (J) chr04 24677667 G A 14.60% 81.63% G -> A NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 9.515; most accessible tissue: Minghui63 panicle, score: 16.270
vg0424677684 (J) chr04 24677684 C T 14.60% 81.61% C -> T NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.515; most accessible tissue: Minghui63 panicle, score: 16.270
vg0424677770 (J) chr04 24677770 C T 12.30% 76.77% C -> T NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424679374 (J) chr04 24679374 G T 43.50% 54.25% G -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 5.808; most accessible tissue: Zhenshan97 root, score: 10.511
vg0424679705 (J) chr04 24679705 T C 40.20% 54.57% T -> C NA
LOC_Os04g41599.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.201; most accessible tissue: Callus, score: 22.426
vg0424679714 (J) chr04 24679714 T C 40.20% 55.76% T -> C NA
LOC_Os04g41599.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 7.201; most accessible tissue: Callus, score: 22.426
vg0424680896 (J) chr04 24680896 G A 24.10% 64.33% G -> A,T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424680902 (J) chr04 24680902 G C 21.70% 68.13% G -> T,C NA
LOC_Os04g41599.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424680903 (J) chr04 24680903 A T 22.00% 68.13% A -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424680904 (J) chr04 24680904 G C 22.00% 68.13% G -> C NA
LOC_Os04g41599.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424680914 (J) chr04 24680914 G A 26.70% 59.65% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424682148 (J) chr04 24682148 C T 71.80% 8.89% C -> T NA
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.359; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424682364 (J) chr04 24682364 G A 99.70% 0.00% G -> A NA
LOC_Os04g41599.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 4.589; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424682646 (J) chr04 24682646 C T 69.00% 8.82% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.505; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424682732 (J) chr04 24682732 G A 85.80% 6.39% A -> G,T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41620.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41620.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.505; most accessible tissue: Minghui63 panicle, score: 7.125
vg0424682788 (J) chr04 24682788 G T 85.30% 8.40% T -> G,A NA
LOC_Os04g41599.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os04g41599.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41599.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 5.330; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg0424682869 (J) chr04 24682869 G Unkown 81.80% 3.62% G -> A NA
LOC_Os04g41620.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g41599.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0424682891 (J) chr04 24682891 G A 17.60% 49.15% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41620.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0424682893 (J) chr04 24682893 T A 29.70% 47.06% T -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41620.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41599.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.182; most accessible tissue: Zhenshan97 panicle, score: 20.424