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Search Results:

13 variations found. LOC_Os02g41930 (OsFBX57 - F-box domain containing protein; expressed), ranging from 25,195,758 bp to 25,196,955 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
vg0225195824 (J) chr02 25195824 C T 91.70% 0.00% C -> T
mr1077 (Ind_All); LR P-value: 2.83E-06;
mr1619 (Ind_All); LR P-value: 3.96E-06;
mr1042_2 (Ind_All); LR P-value: 3.45E-07;
mr1150_2 (Ind_All); LR P-value: 4.81E-06;
mr1479_2 (Ind_All); LR P-value: 3.16E-06;
mr1502_2 (Ind_All); LR P-value: 8.89E-06;
mr1543_2 (Ind_All); LR P-value: 2.51E-06;
mr1680_2 (Ind_All); LMM P-value: 4.74E-06; LR P-value: 4.74E-06;
mr1871_2 (Ind_All); LMM P-value: 3.19E-06; LR P-value: 2.27E-08;
mr1892_2 (All); LR P-value: 7.55E-06;
mr1892_2 (Ind_All); LR P-value: 3.69E-06
LOC_Os02g41930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.501; most accessible tissue: Minghui63 panicle, score: 92.078
vg0225196029 (J) chr02 25196029 G T 93.00% 0.00% G -> T NA
LOC_Os02g41930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.077; most accessible tissue: Minghui63 panicle, score: 92.928
vg0225196162 (J) chr02 25196162 T A 98.10% 0.00% T -> A NA
LOC_Os02g41930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.305; most accessible tissue: Minghui63 panicle, score: 94.394
vg0225196341 (J) chr02 25196341 C T 91.70% 0.00% C -> T
mr1077 (Ind_All); LR P-value: 4.68E-06;
mr1042_2 (Ind_All); LR P-value: 7.05E-07;
mr1150_2 (Ind_All); LR P-value: 4.95E-06;
mr1479_2 (Ind_All); LR P-value: 4.17E-06;
mr1502_2 (Ind_All); LR P-value: 9.24E-06;
mr1543_2 (Ind_All); LR P-value: 3.10E-06;
mr1871_2 (Ind_All); LMM P-value: 2.49E-06; LR P-value: 2.83E-08;
mr1892_2 (All); LR P-value: 5.39E-06;
mr1892_2 (Ind_All); LR P-value: 2.42E-06
LOC_Os02g41930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.726; most accessible tissue: Minghui63 panicle, score: 95.408
vg0225196472 (J) chr02 25196472 G A 98.60% 0.00% G -> A NA
LOC_Os02g41930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.425; most accessible tissue: Minghui63 panicle, score: 95.862
vg0225196741 (J) chr02 25196741 G A 99.00% 0.00% G -> A NA
LOC_Os02g41930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.341; most accessible tissue: Minghui63 panicle, score: 96.016
vg0225196747 (J) chr02 25196747 C T 83.40% 0.00% C -> T NA
LOC_Os02g41930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.356; most accessible tissue: Minghui63 panicle, score: 96.016
vg0225196797 (J) chr02 25196797 T C 94.50% 0.00% T -> C
mr1029 (All); LR P-value: 1.47E-07;
mr1189 (All); LR P-value: 1.25E-07;
mr1570 (All); LR P-value: 2.09E-08;
mr1625 (All); LR P-value: 2.20E-06;
mr1734 (All); LR P-value: 2.43E-06
LOC_Os02g41930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.142; most accessible tissue: Minghui63 panicle, score: 96.016
vg0225196842 (J) chr02 25196842 CG C 98.80% 0.00% CG -> C NA
LOC_Os02g41930.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.523; most accessible tissue: Minghui63 panicle, score: 95.346
vg0225196844 (J) chr02 25196844 G A 68.20% 1.23% G -> A
mr1088 (Ind_All); LR P-value: 5.69E-06;
mr1479_2 (All); LR P-value: 6.95E-07;
mr1677_2 (All); LR P-value: 4.90E-06;
mr1835_2 (All); LR P-value: 3.63E-09
LOC_Os02g41930.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41930.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.587; most accessible tissue: Minghui63 panicle, score: 95.346
vg0225196895 (J) chr02 25196895 A C 52.60% 0.00% C -> A NA
LOC_Os02g41930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.607; most accessible tissue: Minghui63 panicle, score: 94.127
vg0225196940 (J) chr02 25196940 C T 97.90% 0.00% C -> T NA
LOC_Os02g41930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.898; most accessible tissue: Minghui63 panicle, score: 93.630
STR0225196462 (J) chr02 25196462 TGCCGCT GCCG TGCCGCT GCCA 98.70% 0.00% TGCCGCTGCC G -> TGCCGCTGCC A NA