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Search Results:

18 variations found. LOC_Os06g45920 (ZmEBE-1 protein; putative; expressed), ranging from 27,800,907 bp to 27,802,149 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
vg0627801112 (J) chr06 27801112 G GAT 99.10% 0.00% G -> GAT NA
LOC_Os06g45910.1 Alt: GAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g45920.1 Alt: GAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 47.297; most accessible tissue: Callus, score: 67.738
vg0627801117 (J) chr06 27801117 A ACTCCCT CCG 99.70% 0.00% A -> ACTCCCTCCG ,ACTCCCTCC GT,ACTCCCT CCGTTTCGAA ATGTTTGACG CCGT,ACTCC CTCCGTTTCG AAATGTTTGA CGCCG NA
LOC_Os06g45910.1 Alt: ACTCCCTCCG| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g45920.1 Alt: ACTCCCTCCG| intron_variant MODIFIER(snpEff)
LOC_Os06g45910.1 Alt: ACTCCCTCCGT| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g45920.1 Alt: ACTCCCTCCGT| intron_variant MODIFIER(snpEff)
LOC_Os06g45910.1 Alt: ACTCCCTCCGTTTCGAAATGTTTGACGCCGT| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g45920.1 Alt: ACTCCCTCCGTTTCGAAATGTTTGACGCCGT| intron_variant MODIFIER(snpEff)
LOC_Os06g45910.1 Alt: ACTCCCTCCGTTTCGAAATGTTTGACGCCG| downstream_gene_variant MODIFIER(snpEff)
LOC_Os06g45920.1 Alt: ACTCCCTCCGTTTCGAAATGTTTGACGCCG| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 48.546; most accessible tissue: Callus, score: 67.738
vg0627801195 (J) chr06 27801195 C A 94.10% 0.00% C -> A
mr1184 (All); LR P-value: 7.56E-06;
mr1348 (All); LR P-value: 4.00E-09
LOC_Os06g45920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 54.864; most accessible tissue: Callus, score: 84.596
vg0627801213 (J) chr06 27801213 A G 94.40% 0.00% A -> G
mr1442_2 (Ind_All); LR P-value: 7.56E-06;
mr1533_2 (Ind_All); LR P-value: 3.10E-07;
mr1980_2 (Ind_All); LR P-value: 9.11E-07
LOC_Os06g45920.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os06g45910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 56.084; most accessible tissue: Callus, score: 84.596
vg0627801354 (J) chr06 27801354 A G 94.30% 0.00% A -> G
mr1533_2 (Ind_All); LR P-value: 2.29E-07;
mr1980_2 (Ind_All); LR P-value: 7.16E-07
LOC_Os06g45920.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 49.775; most accessible tissue: Minghui63 panicle, score: 64.459
vg0627801383 (J) chr06 27801383 G T 98.90% 0.00% G -> T NA
LOC_Os06g45920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 47.077; most accessible tissue: Minghui63 panicle, score: 59.629
vg0627801502 (J) chr06 27801502 C T 99.00% 0.00% C -> T NA
LOC_Os06g45910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g45920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.345; most accessible tissue: Callus, score: 72.628
vg0627801527 (J) chr06 27801527 T A 94.10% 0.00% T -> A
mr1184 (All); LR P-value: 7.56E-06;
mr1348 (All); LR P-value: 4.00E-09
LOC_Os06g45910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g45920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.191; most accessible tissue: Callus, score: 72.628
vg0627801667 (J) chr06 27801667 G A 99.00% 0.00% G -> A NA
LOC_Os06g45910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g45920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.469; most accessible tissue: Minghui63 flower, score: 62.973
vg0627801768 (J) chr06 27801768 C A 87.00% 0.00% C -> A
mr1184 (All); LR P-value: 3.96E-06;
mr1388_2 (All); LR P-value: 6.53E-10;
mr1511_2 (All); LR P-value: 6.31E-06;
mr1587_2 (All); LR P-value: 6.47E-16
LOC_Os06g45910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g45920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.235; most accessible tissue: Callus, score: 80.193
vg0627801785 (J) chr06 27801785 A G 98.90% 0.00% A -> G NA
LOC_Os06g45920.1 Alt: G| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 57.078; most accessible tissue: Callus, score: 80.193
vg0627801883 (J) chr06 27801883 G T 93.90% 0.00% G -> T
mr1184 (All); LR P-value: 7.56E-06;
mr1348 (All); LR P-value: 4.00E-09
LOC_Os06g45920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 63.875; most accessible tissue: Zhenshan97 flower, score: 78.853
vg0627801917 (J) chr06 27801917 C G 99.80% 0.00% C -> G NA
LOC_Os06g45920.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os06g45910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.326; most accessible tissue: Zhenshan97 flower, score: 77.945
vg0627801947 (J) chr06 27801947 C A 94.40% 0.00% C -> A
mr1533_2 (Ind_All); LR P-value: 2.29E-07;
mr1980_2 (Ind_All); LR P-value: 7.16E-07
LOC_Os06g45920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 65.653; most accessible tissue: Callus, score: 87.029
vg0627802059 (J) chr06 27802059 A G 94.30% 0.00% A -> G
mr1442_2 (Ind_All); LR P-value: 7.56E-06;
mr1533_2 (Ind_All); LR P-value: 3.10E-07;
mr1980_2 (Ind_All); LR P-value: 9.11E-07
LOC_Os06g45920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.204; most accessible tissue: Callus, score: 87.029
vg0627802083 (J) chr06 27802083 C A 99.80% 0.00% C -> A NA
LOC_Os06g45920.1 Alt: A| stop_gained HIGH(snpEff)
LOC_Os06g45910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.997; most accessible tissue: Zhenshan97 panicle, score: 82.336
vg0627802128 (J) chr06 27802128 G GCCAGGT 98.90% 0.00% G -> GCCAGGT NA
LOC_Os06g45920.1 Alt: GCCAGGT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 70.990; most accessible tissue: Zhenshan97 panicle, score: 83.904
STR0627801667 (J) chr06 27801667 G A 99.50% 0.00% G -> A NA