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Search Results:

17 variations found. LOC_Os08g40690 (glycosyl hydrolase; putative; expressed), ranging from 25,762,456 bp to 25,763,824 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
vg0825762457 (J) chr08 25762457 AC CC 87.10% 2.52% AC -> CC,ACCCCCC ,ACCCCCCC, A,ACCCCCCC CC NA
LOC_Os08g40690.1 Alt: ACCCCCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: ACCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: ACCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os08g40690.1 Alt: ACCCCCCCCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: ACCCCCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: ACCCCCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40690.1 Alt: CC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: CC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: CC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40690.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40690.1 Alt: ACCCCCCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: ACCCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: ACCCCCCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.556; most accessible tissue: Callus, score: 94.222
vg0825762464 (J) chr08 25762464 A C 94.90% 2.56% A -> C NA
LOC_Os08g40690.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 76.144; most accessible tissue: Callus, score: 94.222
vg0825762465 (J) chr08 25762465 A C 94.90% 2.62% A -> C NA
LOC_Os08g40690.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 76.241; most accessible tissue: Callus, score: 94.222
vg0825762467 (J) chr08 25762467 A C 97.80% 0.95% A -> C NA
LOC_Os08g40690.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 76.097; most accessible tissue: Callus, score: 94.222
vg0825762477 (J) chr08 25762477 T A 69.70% 0.00% T -> A NA
LOC_Os08g40690.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.110; most accessible tissue: Callus, score: 94.222
vg0825762523 (J) chr08 25762523 G C 98.80% 0.00% G -> C NA
LOC_Os08g40690.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.006; most accessible tissue: Callus, score: 94.222
vg0825762827 (J) chr08 25762827 C A 93.80% 0.00% C -> A
mr1073 (All); LR P-value: 5.06E-06;
mr1113 (All); LR P-value: 4.38E-15;
mr1114 (All); LR P-value: 2.98E-18;
mr1117 (All); LR P-value: 2.45E-20;
mr1119 (All); LR P-value: 3.52E-18;
mr1123 (All); LR P-value: 1.41E-23;
mr1126 (All); LR P-value: 2.30E-06;
mr1153 (All); LR P-value: 9.29E-06;
mr1240 (All); LR P-value: 2.78E-17;
mr1262 (All); LR P-value: 2.10E-08;
mr1348 (All); LR P-value: 1.60E-09;
mr1365 (All); LR P-value: 3.80E-07;
mr1409 (All); LR P-value: 1.86E-11;
mr1417 (All); LR P-value: 1.43E-06;
mr1496 (All); LR P-value: 5.97E-15;
mr1522 (All); LR P-value: 4.75E-12;
mr1549 (All); LR P-value: 9.29E-41;
mr1550 (All); LR P-value: 1.20E-53;
mr1757 (All); LR P-value: 4.20E-43;
mr1762 (All); LR P-value: 4.42E-07;
mr1774 (All); LR P-value: 6.21E-06;
mr1931 (All); LR P-value: 4.33E-08;
mr1961 (All); LR P-value: 2.23E-20;
mr1549_2 (All); LR P-value: 4.38E-37;
mr1550_2 (All); LR P-value: 6.01E-56;
mr1757_2 (All); LR P-value: 1.41E-30
LOC_Os08g40690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.874; most accessible tissue: Minghui63 panicle, score: 91.227
vg0825762961 (J) chr08 25762961 T C 98.80% 0.00% T -> C NA
LOC_Os08g40690.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.062; most accessible tissue: Minghui63 panicle, score: 91.586
vg0825762997 (J) chr08 25762997 C G 99.90% 0.00% C -> G NA
LOC_Os08g40690.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os08g40680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40700.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.558; most accessible tissue: Minghui63 panicle, score: 91.227
vg0825763134 (J) chr08 25763134 A C 99.40% 0.00% A -> C NA
LOC_Os08g40690.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os08g40680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.735; most accessible tissue: Minghui63 panicle, score: 89.702
vg0825763345 (J) chr08 25763345 C T 99.70% 0.00% C -> T NA
LOC_Os08g40690.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g40680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40700.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g40710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.382; most accessible tissue: Minghui63 panicle, score: 86.012
vg0825763424 (J) chr08 25763424 G A 78.20% 0.00% G -> A
mr1119 (All); LR P-value: 3.26E-16;
mr1262 (All); LR P-value: 4.03E-06;
mr1417 (All); LR P-value: 9.14E-09;
mr1442 (All); LR P-value: 1.67E-08;
mr1774 (All); LR P-value: 1.98E-06;
mr1817 (All); LR P-value: 1.74E-20
LOC_Os08g40690.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.702; most accessible tissue: Minghui63 panicle, score: 87.238
vg0825763579 (J) chr08 25763579 T C 98.00% 0.00% T -> C NA
LOC_Os08g40690.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 66.716; most accessible tissue: Minghui63 panicle, score: 88.595
vg0825763600 (J) chr08 25763600 GT G 99.10% 0.00% GT -> G,GTT NA
LOC_Os08g40690.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40690.1 Alt: GTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40710.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 67.329; most accessible tissue: Minghui63 panicle, score: 89.949
vg0825763614 (J) chr08 25763614 T G 99.60% 0.00% T -> G NA
LOC_Os08g40690.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 67.046; most accessible tissue: Minghui63 panicle, score: 89.949
vg0825763675 (J) chr08 25763675 C CT 98.80% 0.00% C -> CT NA
LOC_Os08g40690.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40680.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40700.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40710.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 63.417; most accessible tissue: Callus, score: 91.712
STR0825763675 (J) chr08 25763675 C CT 98.40% 0.00% C -> CT NA