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Search Results:

18 variations found. LOC_Os04g17520 (retrotransposon; putative; centromere-specific), ranging from 9,586,151 bp to 9,586,864 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
vg0409586287 (J) chr04 9586287 G A 24.70% 53.05% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 5.266; most accessible tissue: Minghui63 young leaf, score: 8.301
vg0409586309 (J) chr04 9586309 TA T 26.80% 49.85% TA -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.859; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586319 (J) chr04 9586319 C T 27.00% 49.09% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.859; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586345 (J) chr04 9586345 C T 34.10% 46.42% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586364 (J) chr04 9586364 C T 4.10% 74.78% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586368 (J) chr04 9586368 AG A 2.50% 82.46% AG -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586370 (J) chr04 9586370 A T 2.50% 82.16% A -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 4.551; most accessible tissue: Minghui63 panicle, score: 7.125
vg0409586432 (J) chr04 9586432 T Unkown 42.60% 46.09% T -> C NA
LOC_Os04g17510.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g17530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g17540.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g17520.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 6.646; most accessible tissue: Minghui63 root, score: 10.708
vg0409586482 (J) chr04 9586482 G A 46.90% 41.13% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.709; most accessible tissue: Minghui63 panicle, score: 16.270
vg0409586493 (J) chr04 9586493 C T 38.00% 42.04% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.856; most accessible tissue: Minghui63 panicle, score: 16.270
vg0409586505 (J) chr04 9586505 G A 28.80% 44.58% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.262; most accessible tissue: Minghui63 root, score: 17.665
vg0409586681 (J) chr04 9586681 G C 54.60% 41.39% G -> C NA
LOC_Os04g17510.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362
vg0409586690 (J) chr04 9586690 A G 35.80% 30.91% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362
vg0409586691 (J) chr04 9586691 G A 47.40% 42.66% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362
vg0409586692 (J) chr04 9586692 C A 54.50% 42.15% C -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g17510.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g17520.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 16.091; most accessible tissue: Minghui63 root, score: 29.362
vg0409586716 (J) chr04 9586716 A G 54.50% 42.00% A -> G NA
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 16.014; most accessible tissue: Minghui63 root, score: 29.362
vg0409586728 (J) chr04 9586728 C T 51.80% 42.62% C -> T NA
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 16.014; most accessible tissue: Minghui63 root, score: 29.362
vg0409586830 (J) chr04 9586830 A T 23.10% 68.85% A -> T NA
LOC_Os04g17520.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17520.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 15.542; most accessible tissue: Minghui63 root, score: 27.443