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12 variations found. LOC_Os03g57900 (zinc finger A20 and AN1 domain-containing stress-associated protein; putative; expressed), ranging from 32,982,031 bp to 32,982,969 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
vg0332982053 (J) chr03 32982053 G A 62.20% 0.00% A -> G NA
LOC_Os03g57900.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.893; most accessible tissue: Minghui63 panicle, score: 75.788
vg0332982231 (J) chr03 32982231 G T 99.70% 0.00% G -> T NA
LOC_Os03g57900.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.106; most accessible tissue: Minghui63 flower, score: 86.285
vg0332982323 (J) chr03 32982323 T A 62.20% 0.00% A -> T NA
LOC_Os03g57900.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.657; most accessible tissue: Zhenshan97 flag leaf, score: 90.842
vg0332982357 (J) chr03 32982357 T C 62.20% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.979; most accessible tissue: Zhenshan97 flag leaf, score: 91.894
vg0332982494 (J) chr03 32982494 C T 99.90% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.763; most accessible tissue: Zhenshan97 flag leaf, score: 94.459
vg0332982537 (J) chr03 32982537 C T 99.40% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 89.414; most accessible tissue: Zhenshan97 flag leaf, score: 94.613
vg0332982585 (J) chr03 32982585 A C 59.10% 0.00% C -> A
mr1723 (All); LMM P-value: 1.15E-06; LR P-value: 1.83E-39;
mr1723 (Ind_All); LR P-value: 7.08E-09;
mr1891 (All); LR P-value: 3.20E-39;
mr1723_2 (All); LMM P-value: 6.99E-08; LR P-value: 2.46E-46;
mr1723_2 (Ind_All); LMM P-value: 3.49E-06; LR P-value: 1.24E-11
LOC_Os03g57900.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.372; most accessible tissue: Zhenshan97 flag leaf, score: 96.478
vg0332982718 (J) chr03 32982718 C T 99.40% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.653; most accessible tissue: Zhenshan97 flag leaf, score: 96.286
vg0332982746 (J) chr03 32982746 C T 99.70% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.808; most accessible tissue: Zhenshan97 flag leaf, score: 96.523
vg0332982824 (J) chr03 32982824 C T 99.40% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 96.101; most accessible tissue: Minghui63 panicle, score: 97.817
vg0332982897 (J) chr03 32982897 C T 99.60% 0.00% C -> T NA
LOC_Os03g57900.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g57910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.543; most accessible tissue: Minghui63 panicle, score: 98.608
vg0332982928 (J) chr03 32982928 C G 99.40% 0.00% C -> G NA
LOC_Os03g57900.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.440; most accessible tissue: Minghui63 panicle, score: 98.566