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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:

23 variations found. LOC_Os11g43670 (retrotransposon protein; putative; unclassified; expressed), ranging from 26,361,419 bp to 26,367,575 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
vg1126361470 (J) chr11 26361470 C T 12.70% 67.88% C -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.558; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1126361491 (J) chr11 26361491 C T 9.40% 69.85% C -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.435; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1126361847 (J) chr11 26361847 G A 30.80% 53.64% G -> A NA
LOC_Os11g43670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126361876 (J) chr11 26361876 G T 15.10% 61.96% G -> T NA
LOC_Os11g43670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126362703 (J) chr11 26362703 A G 6.50% 64.58% A -> G NA
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 11.376; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg1126362807 (J) chr11 26362807 G A 7.70% 80.96% G -> A NA
LOC_Os11g43670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.875; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126362815 (J) chr11 26362815 A G 12.40% 60.85% A -> G NA
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 13.016; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126362833 (J) chr11 26362833 A G 6.50% 82.97% A -> G NA
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 12.965; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126362910 (J) chr11 26362910 A G 6.70% 77.00% A -> G NA
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 13.073; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126362959 (J) chr11 26362959 T A 12.20% 60.83% T -> A NA
LOC_Os11g43670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.360; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126363002 (J) chr11 26363002 A T 30.10% 53.11% A -> T NA
LOC_Os11g43670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.881; most accessible tissue: Minghui63 panicle, score: 25.313
vg1126363031 (J) chr11 26363031 G A 29.30% 48.92% G -> A NA
LOC_Os11g43670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.881; most accessible tissue: Minghui63 panicle, score: 25.313
vg1126363195 (J) chr11 26363195 G T 6.50% 69.42% G -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.299; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126363321 (J) chr11 26363321 T C 6.60% 80.15% T -> C NA
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.050; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126363345 (J) chr11 26363345 C T 20.70% 57.60% C -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.564; most accessible tissue: Minghui63 panicle, score: 20.733
vg1126363430 (J) chr11 26363430 G T 24.10% 56.09% G -> T NA
LOC_Os11g43670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.158; most accessible tissue: Minghui63 panicle, score: 16.270
vg1126363963 (J) chr11 26363963 T C 0.30% 77.78% C -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126364023 (J) chr11 26364023 C T 0.90% 84.17% C -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126364035 (J) chr11 26364035 G A 3.40% 73.70% G -> A NA
LOC_Os11g43670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126364368 (J) chr11 26364368 T A 15.90% 60.73% T -> A NA
LOC_Os11g43670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126364375 (J) chr11 26364375 C CA 19.60% 56.86% C -> CA NA
LOC_Os11g43670.1 Alt: CA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126364380 (J) chr11 26364380 A T 7.90% 77.53% A -> T NA
LOC_Os11g43670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1126365360 (J) chr11 26365360 C T 13.40% 60.92% C -> T NA
LOC_Os11g43670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g43670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.645; most accessible tissue: Zhenshan97 young leaf, score: 10.848