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Search Results:

24 variations found. Os11g0300600/LOC_Os11g19480 (receptor protein kinase-like protein At4g34220 precursor; putative; expressed), ranging from 11,212,707 bp to 11,214,432 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os11g19480 receptor protein kinase-like protein At4g34220 precursor, putative, expressed; RAP ID: Os11g0300600; MSU ID: LOC_Os11g19480

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
vg1111212718 (J) chr11 11212718 A AT 72.80% 0.00% A -> AT,T
mr1117 (All); LR P-value: 1.07E-18;
mr1119 (All); LR P-value: 1.49E-16;
mr1247 (All); LR P-value: 9.35E-23;
mr1787 (All); LR P-value: 1.23E-06;
mr1119_2 (All); LR P-value: 6.67E-17;
mr1123_2 (All); LR P-value: 8.07E-22;
mr1193_2 (All); LR P-value: 1.90E-10;
mr1247_2 (All); LR P-value: 2.17E-22;
mr1344_2 (All); LR P-value: 2.87E-06;
mr1808_2 (All); LR P-value: 1.33E-07
LOC_Os11g19480.1 Alt: AT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g19470.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g19480.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 94.396; most accessible tissue: Zhenshan97 young leaf, score: 96.764
vg1111212809 (J) chr11 11212809 G A 91.30% 0.00% G -> A NA
LOC_Os11g19480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.335; most accessible tissue: Zhenshan97 young leaf, score: 95.805
vg1111212869 (J) chr11 11212869 C Unkown 99.40% 0.59% C -> G NA
LOC_Os11g19480.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os11g19470.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.736; most accessible tissue: Zhenshan97 young leaf, score: 95.228
vg1111212880 (J) chr11 11212880 C Unkown 99.40% 0.59% C -> T NA
LOC_Os11g19480.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.135; most accessible tissue: Zhenshan97 young leaf, score: 94.955
vg1111212905 (J) chr11 11212905 C Unkown 99.40% 0.59% C -> T NA
LOC_Os11g19480.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 86.486; most accessible tissue: Zhenshan97 young leaf, score: 94.763
vg1111212907 (J) chr11 11212907 A Unkown 99.40% 0.00% A -> C NA
LOC_Os11g19480.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os11g19470.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 86.494; most accessible tissue: Zhenshan97 young leaf, score: 94.848
vg1111212938 (J) chr11 11212938 C T 99.80% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.652; most accessible tissue: Zhenshan97 young leaf, score: 95.320
vg1111212972 (J) chr11 11212972 G A 97.80% 0.53% G -> A NA
LOC_Os11g19480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g19480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.400; most accessible tissue: Zhenshan97 young leaf, score: 95.297
vg1111212981 (J) chr11 11212981 G A 97.80% 0.55% G -> A NA
LOC_Os11g19480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g19480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.190; most accessible tissue: Zhenshan97 young leaf, score: 95.133
vg1111213009 (J) chr11 11213009 T Unkown 97.80% 0.53% T -> TGC NA
The average chromatin accessibility score: 88.001; most accessible tissue: Zhenshan97 young leaf, score: 95.320
vg1111213061 (J) chr11 11213061 C G 97.20% 0.00% C -> G NA
LOC_Os11g19480.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.012; most accessible tissue: Zhenshan97 young leaf, score: 94.820
vg1111213159 (J) chr11 11213159 C T 96.80% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.788; most accessible tissue: Zhenshan97 young leaf, score: 93.636
vg1111213399 (J) chr11 11213399 C T 96.80% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 79.458; most accessible tissue: Zhenshan97 young leaf, score: 89.112
vg1111213411 (J) chr11 11213411 C T 99.90% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.007; most accessible tissue: Zhenshan97 young leaf, score: 89.112
vg1111213479 (J) chr11 11213479 A G 66.30% 0.00% G -> A NA
LOC_Os11g19480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.493; most accessible tissue: Minghui63 panicle, score: 87.605
vg1111213576 (J) chr11 11213576 G C 63.90% 0.00% G -> C
mr1077 (Ind_All); LR P-value: 2.20E-06;
mr1154 (Ind_All); LR P-value: 5.86E-06;
mr1758 (Ind_All); LR P-value: 1.50E-06;
mr1829 (Ind_All); LR P-value: 1.07E-08;
mr1902 (Ind_All); LR P-value: 1.90E-07;
mr1097_2 (All); LR P-value: 2.68E-11;
mr1097_2 (Ind_All); LR P-value: 1.03E-07;
mr1154_2 (Ind_All); LR P-value: 1.36E-09;
mr1758_2 (Ind_All); LR P-value: 2.31E-08
LOC_Os11g19480.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.999; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg1111213649 (J) chr11 11213649 C A 98.30% 0.00% C -> A NA
LOC_Os11g19480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.345; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg1111213736 (J) chr11 11213736 C T 95.00% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.262; most accessible tissue: Zhenshan97 panicle, score: 90.849
vg1111213836 (J) chr11 11213836 G A 66.00% 0.23% A -> G NA
LOC_Os11g19480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g19480.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 74.729; most accessible tissue: Zhenshan97 panicle, score: 90.467
vg1111213870 (J) chr11 11213870 G T 99.90% 0.00% G -> T NA
LOC_Os11g19480.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g19470.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.568; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg1111213982 (J) chr11 11213982 G A 99.80% 0.00% G -> A NA
LOC_Os11g19480.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g19470.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.570; most accessible tissue: Zhenshan97 panicle, score: 88.350
vg1111214025 (J) chr11 11214025 C T 98.30% 0.00% C -> T NA
LOC_Os11g19480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.098; most accessible tissue: Zhenshan97 panicle, score: 87.451
vg1111214162 (J) chr11 11214162 A G 66.30% 0.00% G -> A NA
LOC_Os11g19480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.332; most accessible tissue: Zhenshan97 panicle, score: 88.888
STR1111212806 (J) chr11 11212806 GGCGGC GGCAGC 89.80% 0.00% GGCGGC -> GGCAGC NA