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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

21 variations found. Os11g0631100/LOC_Os11g41300 (MBTB65 - Bric-a-Brac; Tramtrack; Broad Complex BTB domain with Meprin and TRAF Homology MATH domain; expressed), ranging from 24,756,165 bp to 24,757,242 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os11g41300 MBTB65 - Bric-a-Brac, Tramtrack, Broad Complex BTB domain with Meprin and TRAF Homology MATH domain; RAP ID: Os11g0631100; MSU ID: LOC_Os11g41300

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg1124756282 (J) chr11 24756282 G A 99.50% 0.00% G -> A NA
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.536; most accessible tissue: Zhenshan97 young leaf, score: 82.982
vg1124756461 (J) chr11 24756461 C T 99.50% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.672; most accessible tissue: Minghui63 flag leaf, score: 85.670
vg1124756478 (J) chr11 24756478 G A 96.50% 0.00% G -> A
mr1238 (Jap_All); LMM P-value: 5.64E-06; LR P-value: 3.70E-07;
mr1900 (Jap_All); LR P-value: 6.68E-06;
mr1238_2 (Jap_All); LMM P-value: 4.81E-08; LR P-value: 7.40E-10;
mr1484_2 (Jap_All); LMM P-value: 2.07E-07; LR P-value: 2.07E-07;
mr1841_2 (Jap_All); LR P-value: 2.64E-07;
mr1900_2 (Jap_All); LR P-value: 4.96E-07;
mr1945_2 (Jap_All); LMM P-value: 4.88E-09; LR P-value: 4.88E-09
LOC_Os11g41300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.193; most accessible tissue: Minghui63 flag leaf, score: 85.151
vg1124756486 (J) chr11 24756486 C T 97.30% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.941; most accessible tissue: Minghui63 flag leaf, score: 85.151
vg1124756573 (J) chr11 24756573 C A 99.40% 0.00% C -> A NA
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.247; most accessible tissue: Minghui63 flag leaf, score: 84.608
vg1124756610 (J) chr11 24756610 G A 95.80% 0.00% G -> A
mr1238 (Jap_All); LMM P-value: 5.02E-06; LR P-value: 3.72E-07;
mr1484 (Jap_All); LR P-value: 6.45E-06;
mr1900 (Jap_All); LR P-value: 9.38E-07;
mr1238_2 (Jap_All); LMM P-value: 1.29E-08; LR P-value: 3.27E-10;
mr1484_2 (Jap_All); LMM P-value: 4.40E-08; LR P-value: 4.40E-08;
mr1841_2 (Jap_All); LMM P-value: 4.51E-06; LR P-value: 8.36E-08;
mr1866_2 (Jap_All); LR P-value: 1.01E-06;
mr1900_2 (Jap_All); LMM P-value: 7.51E-06; LR P-value: 3.70E-07;
mr1945_2 (Jap_All); LMM P-value: 3.02E-09; LR P-value: 3.02E-09
LOC_Os11g41300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 73.623; most accessible tissue: Minghui63 flag leaf, score: 86.315
vg1124756687 (J) chr11 24756687 G T 96.70% 0.00% G -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.356; most accessible tissue: Minghui63 flag leaf, score: 88.459
vg1124756717 (J) chr11 24756717 G A 95.50% 0.00% G -> A NA
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.861; most accessible tissue: Minghui63 flag leaf, score: 87.725
vg1124756762 (J) chr11 24756762 C T 99.80% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g41310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.642; most accessible tissue: Minghui63 flag leaf, score: 88.103
vg1124756775 (J) chr11 24756775 C T 96.70% 0.00% C -> T,A NA
LOC_Os11g41300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g41300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.946; most accessible tissue: Minghui63 flag leaf, score: 87.980
vg1124756834 (J) chr11 24756834 C A 98.90% 0.00% C -> A NA
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g41310.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 76.064; most accessible tissue: Minghui63 flag leaf, score: 87.326
vg1124756852 (J) chr11 24756852 C T 97.90% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.891; most accessible tissue: Minghui63 flag leaf, score: 85.836
vg1124756886 (J) chr11 24756886 G T 69.50% 0.38% T -> G
mr1543 (Jap_All); LR P-value: 1.73E-06;
mr1871 (Jap_All); LR P-value: 5.67E-08
LOC_Os11g41300.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g41300.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.205; most accessible tissue: Minghui63 flag leaf, score: 84.791
vg1124756897 (J) chr11 24756897 C A 99.70% 0.00% C -> A NA
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.808; most accessible tissue: Minghui63 flag leaf, score: 84.420
vg1124756905 (J) chr11 24756905 T C 97.40% 0.00% T -> C NA
LOC_Os11g41300.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 73.673; most accessible tissue: Minghui63 flag leaf, score: 84.028
vg1124757031 (J) chr11 24757031 A G 69.50% 0.40% G -> A
mr1543 (Jap_All); LR P-value: 5.79E-07;
mr1871 (Jap_All); LR P-value: 2.46E-08;
mr1871_2 (Jap_All); LR P-value: 1.57E-08
LOC_Os11g41300.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g41300.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.558; most accessible tissue: Zhenshan97 young leaf, score: 84.624
vg1124757050 (J) chr11 24757050 C T 95.50% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.013; most accessible tissue: Zhenshan97 young leaf, score: 83.199
vg1124757052 (J) chr11 24757052 T C 95.60% 0.00% T -> C NA
LOC_Os11g41300.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.037; most accessible tissue: Zhenshan97 young leaf, score: 83.199
vg1124757078 (J) chr11 24757078 T C 97.50% 0.00% T -> C NA
LOC_Os11g41300.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.070; most accessible tissue: Zhenshan97 young leaf, score: 82.077
vg1124757134 (J) chr11 24757134 G A 96.50% 0.00% G -> A
mr1238 (Jap_All); LMM P-value: 1.31E-06; LR P-value: 1.53E-07;
mr1484 (Jap_All); LR P-value: 4.49E-06;
mr1763 (Jap_All); LR P-value: 8.00E-06;
mr1900 (Jap_All); LR P-value: 1.25E-06;
mr1951 (Jap_All); LR P-value: 6.03E-07;
mr1238_2 (Jap_All); LMM P-value: 6.62E-09; LR P-value: 2.25E-10;
mr1484_2 (Jap_All); LMM P-value: 3.94E-08; LR P-value: 3.94E-08;
mr1609_2 (Jap_All); LMM P-value: 7.89E-06; LR P-value: 7.89E-06;
mr1841_2 (Jap_All); LMM P-value: 3.45E-06; LR P-value: 9.21E-08;
mr1900_2 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 2.17E-07;
mr1945_2 (Jap_All); LMM P-value: 3.43E-09; LR P-value: 3.43E-09
LOC_Os11g41300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.634; most accessible tissue: Zhenshan97 young leaf, score: 81.353
vg1124757182 (J) chr11 24757182 C T 95.50% 0.00% C -> T NA
LOC_Os11g41300.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.443; most accessible tissue: Callus, score: 82.604