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Search Results:

41 variations found. LOC_Os03g48120 (BTB%2FPOZ domain containing protein; putative), ranging from 27,370,118 bp to 27,370,836 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
vg0327370190 (J) chr03 27370190 C T 94.90% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.232; most accessible tissue: Zhenshan97 panicle, score: 87.126
vg0327370193 (J) chr03 27370193 C T 65.30% 0.15% T -> C NA
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.494; most accessible tissue: Zhenshan97 panicle, score: 87.126
vg0327370221 (J) chr03 27370221 T C 64.40% 0.23% C -> T NA
LOC_Os03g48120.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.274; most accessible tissue: Zhenshan97 panicle, score: 86.788
vg0327370239 (J) chr03 27370239 G C 66.00% 0.00% C -> G NA
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 78.061; most accessible tissue: Zhenshan97 panicle, score: 86.788
vg0327370258 (J) chr03 27370258 G T 99.80% 0.00% G -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.529; most accessible tissue: Zhenshan97 panicle, score: 87.764
vg0327370277 (J) chr03 27370277 C T 99.20% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.359; most accessible tissue: Zhenshan97 panicle, score: 88.350
vg0327370301 (J) chr03 27370301 C T 99.90% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.861; most accessible tissue: Zhenshan97 panicle, score: 89.389
vg0327370317 (J) chr03 27370317 G A 99.80% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 81.162; most accessible tissue: Zhenshan97 panicle, score: 89.846
vg0327370322 (J) chr03 27370322 G A 65.80% 0.21% A -> G NA
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 81.793; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg0327370337 (J) chr03 27370337 A C 50.80% 0.19% C -> A
mr1524 (All); LR P-value: 3.36E-11;
mr1609 (All); LR P-value: 6.28E-11;
mr1916 (All); LR P-value: 2.25E-15;
mr1449_2 (All); LR P-value: 6.25E-09;
mr1514_2 (All); LR P-value: 3.72E-13
LOC_Os03g48120.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.878; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0327370363 (J) chr03 27370363 C T 99.30% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.125; most accessible tissue: Zhenshan97 panicle, score: 90.661
vg0327370369 (J) chr03 27370369 T C 64.50% 0.25% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.300; most accessible tissue: Zhenshan97 panicle, score: 90.661
vg0327370424 (J) chr03 27370424 C T 65.90% 0.00% T -> C NA
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g48120.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.264; most accessible tissue: Zhenshan97 panicle, score: 90.661
vg0327370425 (J) chr03 27370425 G A 99.80% 0.00% G -> A NA
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g48120.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 84.911; most accessible tissue: Zhenshan97 panicle, score: 90.661
vg0327370471 (J) chr03 27370471 G A 99.90% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 84.515; most accessible tissue: Zhenshan97 panicle, score: 91.030
vg0327370496 (J) chr03 27370496 G A 99.80% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.442; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg0327370525 (J) chr03 27370525 C G 98.70% 0.00% C -> G NA
LOC_Os03g48120.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.166; most accessible tissue: Zhenshan97 panicle, score: 91.374
vg0327370526 (J) chr03 27370526 A G 64.50% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 84.124; most accessible tissue: Zhenshan97 panicle, score: 91.374
vg0327370540 (J) chr03 27370540 C T 99.80% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.207; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370551 (J) chr03 27370551 C CAA 99.80% 0.00% C -> CAA NA
The average chromatin accessibility score: 82.765; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370552 (J) chr03 27370552 G GGAGCTC CATGGTG GACTCCG CCATGGA CCCA 99.80% 0.00% G -> GGAGCTCCAT GGTGGACTCC GCCATGGACC CA NA
The average chromatin accessibility score: 82.765; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370572 (J) chr03 27370572 C A 99.10% 0.00% C -> A NA
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.969; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0327370583 (J) chr03 27370583 A G 65.30% 0.23% G -> A NA
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.160; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370585 (J) chr03 27370585 A G 64.40% 0.23% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.295; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370609 (J) chr03 27370609 G A 65.50% 0.23% A -> G NA
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.641; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0327370621 (J) chr03 27370621 G A 99.80% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.049; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg0327370626 (J) chr03 27370626 C T 91.60% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.967; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0327370634 (J) chr03 27370634 G A 65.80% 0.23% A -> G NA
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g48120.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.520; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg0327370639 (J) chr03 27370639 G A 99.90% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.938; most accessible tissue: Zhenshan97 panicle, score: 89.389
vg0327370647 (J) chr03 27370647 T C 64.50% 0.25% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.076; most accessible tissue: Zhenshan97 panicle, score: 88.625
vg0327370655 (J) chr03 27370655 C T 99.80% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.058; most accessible tissue: Zhenshan97 panicle, score: 88.350
vg0327370661 (J) chr03 27370661 A G 65.80% 0.06% G -> A NA
LOC_Os03g48120.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.914; most accessible tissue: Zhenshan97 panicle, score: 88.350
vg0327370669 (J) chr03 27370669 G A 96.60% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.451; most accessible tissue: Zhenshan97 panicle, score: 87.764
vg0327370671 (J) chr03 27370671 T C 65.30% 0.06% C -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g48120.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.369; most accessible tissue: Zhenshan97 panicle, score: 87.764
vg0327370685 (J) chr03 27370685 A T 99.90% 0.00% A -> T NA
LOC_Os03g48120.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.159; most accessible tissue: Zhenshan97 panicle, score: 86.788
vg0327370717 (J) chr03 27370717 A G 64.50% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.225; most accessible tissue: Zhenshan97 panicle, score: 85.665
vg0327370726 (J) chr03 27370726 G A 99.80% 0.00% G -> A NA
LOC_Os03g48120.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g48140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.232; most accessible tissue: Zhenshan97 panicle, score: 85.665
vg0327370737 (J) chr03 27370737 T C 99.30% 0.00% T -> C NA
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 72.076; most accessible tissue: Zhenshan97 panicle, score: 84.374
vg0327370785 (J) chr03 27370785 T C 99.60% 0.00% T -> C NA
LOC_Os03g48120.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g48140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 67.611; most accessible tissue: Zhenshan97 panicle, score: 81.752
vg0327370818 (J) chr03 27370818 C T 99.80% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 65.026; most accessible tissue: Zhenshan97 panicle, score: 78.302
vg0327370831 (J) chr03 27370831 C T 99.80% 0.00% C -> T NA
LOC_Os03g48120.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g48140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 61.739; most accessible tissue: Zhenshan97 panicle, score: 77.482