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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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Variations Type:

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Search Results:

47 variations found. LOC_Os12g34580 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 20,958,616 bp to 20,962,528 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
vg1220959168 (J) chr12 20959168 C T 9.90% 80.22% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 14.979; most accessible tissue: Minghui63 root, score: 29.362
vg1220960391 (J) chr12 20960391 C A 1.90% 85.23% C -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960393 (J) chr12 20960393 A G 19.20% 49.43% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960398 (J) chr12 20960398 G A 4.70% 71.88% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960402 (J) chr12 20960402 A G 4.50% 70.06% A -> G NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960406 (J) chr12 20960406 T TG 29.00% 44.01% TG -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960417 (J) chr12 20960417 G C 57.80% 40.61% G -> C NA
LOC_Os12g34580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960420 (J) chr12 20960420 C T 59.00% 40.50% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960430 (J) chr12 20960430 C T 59.00% 40.50% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960435 (J) chr12 20960435 C T 55.30% 42.11% T -> C NA
LOC_Os12g34580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960437 (J) chr12 20960437 G A 58.30% 40.50% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960439 (J) chr12 20960439 G A 58.30% 40.52% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960445 (J) chr12 20960445 T C 58.30% 40.52% T -> C NA
LOC_Os12g34580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960449 (J) chr12 20960449 C T 59.10% 40.39% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960450 (J) chr12 20960450 G A 58.10% 40.46% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960451 (J) chr12 20960451 G A 58.40% 40.39% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960452 (J) chr12 20960452 C T 58.60% 40.39% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960456 (J) chr12 20960456 T C 58.50% 40.44% T -> C NA
LOC_Os12g34580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960469 (J) chr12 20960469 GA G 58.90% 40.46% GA -> G NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960479 (J) chr12 20960479 T C 57.80% 40.61% T -> C NA
LOC_Os12g34580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960489 (J) chr12 20960489 C T 56.20% 42.04% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960491 (J) chr12 20960491 A G 34.60% 40.65% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.640; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220960512 (J) chr12 20960512 T C 1.80% 94.01% T -> C NA
LOC_Os12g34580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.161; most accessible tissue: Zhenshan97 root, score: 10.511
vg1220960515 (J) chr12 20960515 T C 0.60% 97.19% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 5.161; most accessible tissue: Zhenshan97 root, score: 10.511
vg1220960632 (J) chr12 20960632 G A 18.70% 80.77% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.534; most accessible tissue: Zhenshan97 root, score: 12.891
vg1220960785 (J) chr12 20960785 A G 37.70% 50.74% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960803 (J) chr12 20960803 G A 57.60% 40.65% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960805 (J) chr12 20960805 A G 23.10% 44.41% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960810 (J) chr12 20960810 A G 32.00% 39.46% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960813 (J) chr12 20960813 G A 58.80% 40.25% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960818 (J) chr12 20960818 G C 56.60% 41.56% G -> C NA
LOC_Os12g34580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960838 (J) chr12 20960838 A C 58.40% 40.27% A -> C NA
LOC_Os12g34580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960847 (J) chr12 20960847 C T 58.90% 40.20% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960849 (J) chr12 20960849 A T 56.60% 41.62% A -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960859 (J) chr12 20960859 A G 56.50% 41.66% A -> G NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960861 (J) chr12 20960861 A G 22.20% 42.30% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960869 (J) chr12 20960869 AC A 55.90% 38.83% AC -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960878 (J) chr12 20960878 G A 22.90% 55.73% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220960884 (J) chr12 20960884 G A 3.20% 72.32% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 8.830; most accessible tissue: Zhenshan97 root, score: 16.934
vg1220961191 (J) chr12 20961191 C T 0.50% 97.84% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220961206 (J) chr12 20961206 C A 1.50% 93.53% C -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220961229 (J) chr12 20961229 C T 2.90% 90.25% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220961247 (J) chr12 20961247 A T 1.00% 95.22% C -> A,T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g34580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220961255 (J) chr12 20961255 A G 3.30% 89.57% A -> G NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1220961621 (J) chr12 20961621 C T 0.60% 97.29% C -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 6.695; most accessible tissue: Zhenshan97 flag leaf, score: 11.736
vg1220961662 (J) chr12 20961662 T G 0.60% 97.33% G -> T NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 6.695; most accessible tissue: Zhenshan97 flag leaf, score: 11.736
vg1220962472 (J) chr12 20962472 G A 0.90% 91.24% G -> A NA
LOC_Os12g34580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g34580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 7.776; most accessible tissue: Minghui63 root, score: 13.235