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Search Results:

23 variations found. LOC_Os08g28790 (dirigent; putative; expressed), ranging from 17,613,570 bp to 17,614,373 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
vg0817613577 (J) chr08 17613577 G A 99.20% 0.00% G -> A NA
LOC_Os08g28790.1 Alt: A| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.916; most accessible tissue: Minghui63 young leaf, score: 91.500
vg0817613578 (J) chr08 17613578 C G 92.00% 0.00% C -> G,A NA
LOC_Os08g28790.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g28790.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.916; most accessible tissue: Minghui63 young leaf, score: 91.500
vg0817613580 (J) chr08 17613580 A G 99.20% 0.00% A -> G NA
LOC_Os08g28790.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g28790.1 Alt: G| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.613; most accessible tissue: Minghui63 young leaf, score: 92.035
vg0817613622 (J) chr08 17613622 A T 94.20% 0.00% A -> T NA
LOC_Os08g28790.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.869; most accessible tissue: Zhenshan97 young leaf, score: 93.129
vg0817613678 (J) chr08 17613678 C G 96.10% 0.00% C -> G NA
LOC_Os08g28790.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.147; most accessible tissue: Zhenshan97 young leaf, score: 93.963
vg0817613700 (J) chr08 17613700 G A 78.20% 7.28% G -> A NA
LOC_Os08g28790.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g28790.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.194; most accessible tissue: Zhenshan97 young leaf, score: 94.000
vg0817613736 (J) chr08 17613736 C G 88.30% 6.37% C -> G NA
LOC_Os08g28790.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g28790.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.295; most accessible tissue: Zhenshan97 young leaf, score: 94.820
vg0817613747 (J) chr08 17613747 G A 55.70% 5.37% A -> G NA
LOC_Os08g28790.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g28790.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.478; most accessible tissue: Zhenshan97 young leaf, score: 94.220
vg0817613750 (J) chr08 17613750 G A 88.30% 6.31% G -> A NA
LOC_Os08g28790.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g28790.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.417; most accessible tissue: Zhenshan97 young leaf, score: 94.290
vg0817613832 (J) chr08 17613832 G A 99.70% 0.00% G -> A NA
LOC_Os08g28790.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os08g28800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.995; most accessible tissue: Zhenshan97 young leaf, score: 92.924
vg0817613838 (J) chr08 17613838 C T 99.30% 0.00% C -> T NA
LOC_Os08g28790.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.012; most accessible tissue: Zhenshan97 young leaf, score: 93.276
vg0817613924 (J) chr08 17613924 G T 99.10% 0.00% G -> T NA
LOC_Os08g28790.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.067; most accessible tissue: Zhenshan97 young leaf, score: 93.636
vg0817613971 (J) chr08 17613971 G A 99.10% 0.00% G -> A NA
LOC_Os08g28790.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 84.638; most accessible tissue: Zhenshan97 flag leaf, score: 93.061
vg0817613978 (J) chr08 17613978 C T 94.70% 0.00% C -> T
mr1040 (Jap_All); LR P-value: 1.23E-07;
mr1410 (Jap_All); LR P-value: 1.44E-12;
mr1533 (Jap_All); LR P-value: 2.78E-09;
mr1836 (Jap_All); LR P-value: 6.73E-07;
mr1980 (Jap_All); LR P-value: 2.30E-12;
mr1040_2 (Jap_All); LMM P-value: 4.11E-06; LR P-value: 1.99E-06;
mr1277_2 (Jap_All); LR P-value: 1.96E-06;
mr1362_2 (Jap_All); LMM P-value: 3.12E-06; LR P-value: 3.72E-08;
mr1410_2 (Jap_All); LR P-value: 1.93E-12;
mr1533_2 (Jap_All); LR P-value: 2.32E-11;
mr1578_2 (Jap_All); LR P-value: 7.61E-08;
mr1836_2 (Jap_All); LMM P-value: 3.97E-06; LR P-value: 4.23E-07;
mr1860_2 (Jap_All); LR P-value: 5.23E-06
LOC_Os08g28790.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.756; most accessible tissue: Zhenshan97 flag leaf, score: 93.147
vg0817614054 (J) chr08 17614054 C T 99.70% 0.00% C -> T NA
LOC_Os08g28790.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os08g28800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.323; most accessible tissue: Zhenshan97 flag leaf, score: 92.089
vg0817614141 (J) chr08 17614141 C G 92.90% 0.00% C -> G NA
LOC_Os08g28790.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.526; most accessible tissue: Zhenshan97 flag leaf, score: 90.631
vg0817614177 (J) chr08 17614177 C T 97.20% 0.00% C -> T NA
LOC_Os08g28790.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.927; most accessible tissue: Zhenshan97 flag leaf, score: 89.066
vg0817614184 (J) chr08 17614184 G C 99.60% 0.00% G -> C NA
LOC_Os08g28790.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.776; most accessible tissue: Zhenshan97 flag leaf, score: 88.843
vg0817614193 (J) chr08 17614193 G A 96.10% 0.00% G -> A NA
LOC_Os08g28790.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.414; most accessible tissue: Zhenshan97 flag leaf, score: 88.606
vg0817614254 (J) chr08 17614254 G A 98.50% 0.00% G -> A NA
LOC_Os08g28790.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g28800.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.903; most accessible tissue: Zhenshan97 flag leaf, score: 86.673
vg0817614363 (J) chr08 17614363 A G 92.80% 0.00% A -> G NA
LOC_Os08g28790.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g28800.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 65.162; most accessible tissue: Minghui63 young leaf, score: 79.191
vg0817614367 (J) chr08 17614367 C T 93.40% 0.00% C -> T NA
LOC_Os08g28790.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g28800.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.858; most accessible tissue: Minghui63 young leaf, score: 78.821
STR0817614252 (J) chr08 17614252 CCGGCCG GGA CCAGCCG GGA 96.10% 0.00% CCGGCCGGGA -> CCAGCCGGGA NA