Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) : Downstream (kb, optional, must <= 10 kb) :
Variations Type:

Optional: (The selected data will be displayed in the result page.)
 Show Gene Expression Atlas  Show Chromatin Accessibility Map
 Show Non-coding variation Scores

Search Results:

21 variations found. LOC_Os09g17160 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 10,529,066 bp to 10,530,379 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
vg0910529405 (J) chr09 10529405 G A 9.20% 86.52% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17152.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 8.184; most accessible tissue: Callus, score: 29.427
vg0910529759 (J) chr09 10529759 C T 75.80% 22.62% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529766 (J) chr09 10529766 C T 75.20% 22.60% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529769 (J) chr09 10529769 C T 74.90% 22.58% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529770 (J) chr09 10529770 C Unkown 75.90% 22.56% C -> T NA
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529774 (J) chr09 10529774 C T 75.80% 22.20% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529777 (J) chr09 10529777 G A 75.80% 22.26% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.858; most accessible tissue: Callus, score: 36.782
vg0910529798 (J) chr09 10529798 A C 75.80% 22.26% A -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.365; most accessible tissue: Callus, score: 36.782
vg0910529805 (J) chr09 10529805 C T 75.70% 22.15% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.897; most accessible tissue: Callus, score: 36.782
vg0910529817 (J) chr09 10529817 C T 74.90% 22.18% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.820; most accessible tissue: Callus, score: 36.782
vg0910529819 (J) chr09 10529819 TC T 76.00% 21.79% TC -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.820; most accessible tissue: Callus, score: 36.782
vg0910529820 (J) chr09 10529820 C T 75.20% 21.82% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.820; most accessible tissue: Callus, score: 36.782
vg0910529823 (J) chr09 10529823 C A 75.90% 21.79% C -> A,T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 10.820; most accessible tissue: Callus, score: 36.782
vg0910529825 (J) chr09 10529825 A G 76.20% 21.79% A -> G NA
LOC_Os09g17160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 10.820; most accessible tissue: Callus, score: 36.782
vg0910529826 (J) chr09 10529826 C T 76.20% 21.73% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 8.810; most accessible tissue: Callus, score: 14.669
vg0910529827 (J) chr09 10529827 A C 75.20% 21.77% A -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 8.810; most accessible tissue: Callus, score: 14.669
vg0910529953 (J) chr09 10529953 C T 10.40% 78.35% C -> T NA
LOC_Os09g17160.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17160.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.931; most accessible tissue: Callus, score: 14.755
vg0910530234 (J) chr09 10530234 C T 53.40% 24.65% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.719; most accessible tissue: Minghui63 root, score: 15.664
vg0910530241 (J) chr09 10530241 C T 22.80% 49.41% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.669; most accessible tissue: Minghui63 root, score: 15.664
vg0910530299 (J) chr09 10530299 C T 11.30% 64.68% C -> T NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g17160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 9.393; most accessible tissue: Minghui63 root, score: 13.235
vg0910530353 (J) chr09 10530353 C CG 12.00% 62.67% C -> CG NA
LOC_Os09g17160.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g17160.1 Alt: CG/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.382; most accessible tissue: Minghui63 root, score: 13.235