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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

16 variations found. LOC_Os06g34560 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 20,098,733 bp to 20,100,496 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
vg0620098763 (J) chr06 20098763 T C 65.30% 7.53% C -> T NA
LOC_Os06g34560.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.755; most accessible tissue: Zhenshan97 flower, score: 98.276
vg0620098852 (J) chr06 20098852 T C 47.40% 7.87% C -> T NA
LOC_Os06g34560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.545; most accessible tissue: Zhenshan97 root, score: 98.164
vg0620098865 (J) chr06 20098865 C CACGT 65.20% 7.62% CACGT -> C NA
LOC_Os06g34560.1 Alt: C| frameshift_variant&splice_donor_variant&splice_region_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.673; most accessible tissue: Zhenshan97 root, score: 98.199
vg0620098962 (J) chr06 20098962 G A 75.10% 7.60% G -> A
mr1006 (All); LR P-value: 6.35E-06;
mr1052 (All); LR P-value: 5.80E-06;
mr1211 (Ind_All); LR P-value: 4.44E-06;
mr1121_2 (Ind_All); LR P-value: 2.33E-07;
mr1211_2 (Ind_All); LR P-value: 1.03E-07;
mr1929_2 (All); LR P-value: 1.13E-07
LOC_Os06g34550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 93.365; most accessible tissue: Zhenshan97 root, score: 97.626
vg0620099096 (J) chr06 20099096 G C 84.20% 7.41% G -> C
mr1121_2 (Ind_All); LR P-value: 1.22E-06;
mr1211_2 (Ind_All); LR P-value: 7.18E-07
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 87.449; most accessible tissue: Zhenshan97 root, score: 96.054
vg0620099120 (J) chr06 20099120 C CGCA 92.60% 6.92% C -> CGCA NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g34550.1 Alt: CGCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: CGCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: CGCA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.446; most accessible tissue: Zhenshan97 root, score: 95.843
vg0620099139 (J) chr06 20099139 C T 91.70% 6.69% C -> T NA
LOC_Os06g34550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 85.547; most accessible tissue: Zhenshan97 root, score: 95.586
vg0620099286 (J) chr06 20099286 C A 47.30% 7.96% A -> C NA
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 81.044; most accessible tissue: Zhenshan97 root, score: 95.778
vg0620099310 (J) chr06 20099310 G C 92.30% 6.86% G -> C NA
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 79.030; most accessible tissue: Zhenshan97 root, score: 95.711
vg0620099347 (J) chr06 20099347 G A 47.40% 7.68% A -> G NA
LOC_Os06g34550.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 76.996; most accessible tissue: Zhenshan97 root, score: 96.111
vg0620099558 (J) chr06 20099558 C T 90.70% 6.77% C -> T NA
LOC_Os06g34550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 66.899; most accessible tissue: Zhenshan97 root, score: 96.248
vg0620099822 (J) chr06 20099822 G A 92.30% 6.98% G -> A NA
LOC_Os06g34550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 55.199; most accessible tissue: Zhenshan97 root, score: 93.745
vg0620100183 (J) chr06 20100183 G A 87.00% 7.36% G -> A NA
LOC_Os06g34560.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.444; most accessible tissue: Minghui63 root, score: 91.102
vg0620100202 (J) chr06 20100202 G A 65.30% 7.58% A -> G NA
LOC_Os06g34560.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.862; most accessible tissue: Minghui63 root, score: 91.062
vg0620100302 (J) chr06 20100302 A T 92.10% 3.51% A -> T NA
LOC_Os06g34560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.742; most accessible tissue: Minghui63 root, score: 92.615
STR0620098866 (J) chr06 20098866 ACGTAC ACGTACG TAC 61.80% 0.00% ACGTACGTAC -> ACGTAC NA