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Search Results:

12 variations found. LOC_Os02g41980 (expressed protein), ranging from 25,229,202 bp to 25,229,673 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
vg0225229239 (J) chr02 25229239 CCA C 99.90% 0.00% CCA -> C NA
LOC_Os02g41980.1 Alt: C| frameshift_variant HIGH(snpEff)
LOC_Os02g41990.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.313; most accessible tissue: Callus, score: 93.471
vg0225229241 (J) chr02 25229241 G A 90.80% 0.00% A -> G
mr1183 (Jap_All); LR P-value: 3.79E-06;
mr1617 (Jap_All); LR P-value: 2.00E-08;
mr1712 (All); LR P-value: 6.11E-14;
mr1748 (All); LR P-value: 4.52E-07;
mr1826 (All); LR P-value: 1.45E-06;
mr1910 (All); LR P-value: 1.23E-06;
mr1946 (All); LR P-value: 1.25E-07;
mr1977 (All); LR P-value: 7.84E-09;
mr1164_2 (Jap_All); LR P-value: 9.32E-07;
mr1229_2 (All); LR P-value: 3.15E-08;
mr1596_2 (All); LR P-value: 3.86E-06;
mr1617_2 (Jap_All); LR P-value: 1.34E-06;
mr1627_2 (Jap_All); LR P-value: 2.42E-06;
mr1693_2 (All); LR P-value: 4.09E-06;
mr1748_2 (All); LR P-value: 1.78E-07;
mr1763_2 (All); LR P-value: 4.64E-06;
mr1880_2 (All); LR P-value: 1.03E-09;
mr1880_2 (Jap_All); LR P-value: 1.75E-07;
mr1977_2 (All); LR P-value: 7.80E-07
LOC_Os02g41980.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.227; most accessible tissue: Callus, score: 93.471
vg0225229400 (J) chr02 25229400 C A 99.70% 0.00% C -> A NA
LOC_Os02g41980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.729; most accessible tissue: Minghui63 panicle, score: 91.227
vg0225229436 (J) chr02 25229436 C T 96.30% 0.00% C -> T
mr1047_2 (Jap_All); LR P-value: 5.01E-07;
mr1815_2 (Jap_All); LR P-value: 4.48E-06
LOC_Os02g41980.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.493; most accessible tissue: Callus, score: 96.577
vg0225229459 (J) chr02 25229459 G A 99.70% 0.00% G -> A NA
LOC_Os02g41980.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.778; most accessible tissue: Callus, score: 96.577
vg0225229467 (J) chr02 25229467 C A 78.90% 0.00% A -> C NA
LOC_Os02g41980.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.589; most accessible tissue: Callus, score: 96.577
vg0225229502 (J) chr02 25229502 C G 50.80% 0.30% G -> C NA
LOC_Os02g41980.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41980.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.921; most accessible tissue: Callus, score: 96.577
vg0225229523 (J) chr02 25229523 C T 79.00% 0.00% T -> C NA
LOC_Os02g41980.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.632; most accessible tissue: Callus, score: 96.577
vg0225229656 (J) chr02 25229656 G A 87.90% 0.00% A -> G
mr1193 (Jap_All); LMM P-value: 4.69E-06; LR P-value: 4.69E-06;
mr1240 (All); LMM P-value: 3.17E-07;
mr1555 (All); LR P-value: 9.27E-06;
mr1617 (Jap_All); LR P-value: 1.18E-07;
mr1712 (All); LR P-value: 6.23E-13;
mr1748 (All); LR P-value: 2.89E-09;
mr1910 (All); LR P-value: 2.86E-06;
mr1977 (All); LR P-value: 1.10E-06
LOC_Os02g41980.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.936; most accessible tissue: Minghui63 panicle, score: 93.735
vg0225229663 (J) chr02 25229663 T TG 72.20% 0.00% T -> TG,TGG NA
LOC_Os02g41980.1 Alt: TGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g41980.1 Alt: TG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.869; most accessible tissue: Minghui63 panicle, score: 93.630
vg0225229667 (J) chr02 25229667 G A 96.30% 0.00% G -> A
mr1047_2 (Jap_All); LR P-value: 5.01E-07;
mr1815_2 (Jap_All); LR P-value: 4.48E-06
LOC_Os02g41980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.780; most accessible tissue: Minghui63 panicle, score: 93.630
vg0225229670 (J) chr02 25229670 C A 97.70% 0.00% C -> A NA
LOC_Os02g41980.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.720; most accessible tissue: Minghui63 panicle, score: 93.630