Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) : Downstream (kb, optional, must <= 10 kb) :
Variations Type:

Optional: (The selected data will be displayed in the result page.)
 Show Gene Expression Atlas  Show Chromatin Accessibility Map
 Show Non-coding variation Scores

Search Results:

25 variations found. LOC_Os05g20480 (retrotransposon protein; putative; Ty3-gypsy subclass; expressed), ranging from 12,019,730 bp to 12,023,462 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
vg0512019746 (J) chr05 12019746 T A 98.50% 0.00% T -> A NA
LOC_Os05g20480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 13.490; most accessible tissue: Zhenshan97 flower, score: 22.370
vg0512019766 (J) chr05 12019766 T A 9.40% 10.24% T -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 13.455; most accessible tissue: Minghui63 young leaf, score: 22.423
vg0512020015 (J) chr05 12020015 C A 77.80% 9.71% C -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.942; most accessible tissue: Minghui63 flag leaf, score: 12.430
vg0512020079 (J) chr05 12020079 G A 88.00% 8.10% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.180; most accessible tissue: Minghui63 young leaf, score: 9.976
vg0512020095 (J) chr05 12020095 C T 88.00% 8.46% C -> T NA
LOC_Os05g20480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.180; most accessible tissue: Minghui63 young leaf, score: 9.976
vg0512020664 (J) chr05 12020664 CA C 86.60% 9.35% CA -> C NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: C/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.295; most accessible tissue: Minghui63 panicle, score: 16.270
vg0512021423 (J) chr05 12021423 C T 87.20% 8.97% C -> T NA
LOC_Os05g20480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.129; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg0512022795 (J) chr05 12022795 T C 87.30% 8.15% T -> C NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 26.185; most accessible tissue: Minghui63 flag leaf, score: 35.832
vg0512022902 (J) chr05 12022902 G A 78.40% 7.58% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 29.205; most accessible tissue: Minghui63 flag leaf, score: 41.254
vg0512023102 (J) chr05 12023102 G A 77.50% 8.32% G -> A
mr1082 (All); LMM P-value: 1.09E-06;
mr1082 (Jap_All); LR P-value: 1.69E-07;
mr1083 (Jap_All); LR P-value: 2.88E-06;
mr1408 (All); LR P-value: 1.63E-06;
mr1422 (Jap_All); LR P-value: 1.09E-06;
mr1551 (Jap_All); LR P-value: 8.41E-09;
mr1554 (All); LR P-value: 1.45E-07;
mr1593 (All); LR P-value: 2.71E-08;
mr1593 (Jap_All); LR P-value: 1.53E-16;
mr1916 (Jap_All); LR P-value: 7.86E-08;
mr1082_2 (Jap_All); LR P-value: 9.50E-06;
mr1277_2 (Jap_All); LR P-value: 1.48E-07;
mr1363_2 (All); LR P-value: 8.72E-08;
mr1408_2 (All); LR P-value: 4.11E-07;
mr1593_2 (All); LR P-value: 1.86E-14;
mr1593_2 (Jap_All); LR P-value: 4.05E-26
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 30.487; most accessible tissue: Zhenshan97 flag leaf, score: 48.165
vg0512023144 (J) chr05 12023144 G A 87.70% 8.19% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 29.174; most accessible tissue: Zhenshan97 flag leaf, score: 47.303
vg0512023190 (J) chr05 12023190 A G 87.30% 5.54% A -> G NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 30.544; most accessible tissue: Zhenshan97 flag leaf, score: 48.165
vg0512023202 (J) chr05 12023202 A G 87.30% 5.73% A -> G NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 29.697; most accessible tissue: Zhenshan97 flag leaf, score: 45.537
vg0512023233 (J) chr05 12023233 T C 87.20% 1.95% T -> C NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 28.586; most accessible tissue: Zhenshan97 flag leaf, score: 47.303
vg0512023244 (J) chr05 12023244 C T 92.70% 4.78% C -> T NA
LOC_Os05g20480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 27.823; most accessible tissue: Zhenshan97 flag leaf, score: 45.537
vg0512023250 (J) chr05 12023250 G A 93.60% 4.78% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 27.227; most accessible tissue: Zhenshan97 flag leaf, score: 44.637
vg0512023267 (J) chr05 12023267 C T 87.80% 1.48% C -> T NA
LOC_Os05g20480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 27.554; most accessible tissue: Zhenshan97 flag leaf, score: 43.728
vg0512023277 (J) chr05 12023277 A C 93.70% 3.26% A -> C NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 28.005; most accessible tissue: Zhenshan97 flag leaf, score: 43.728
vg0512023300 (J) chr05 12023300 G A 91.90% 4.63% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 29.444; most accessible tissue: Zhenshan97 flag leaf, score: 46.427
vg0512023314 (J) chr05 12023314 G A 93.50% 4.74% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 29.634; most accessible tissue: Zhenshan97 flag leaf, score: 47.303
vg0512023323 (J) chr05 12023323 T C 88.60% 2.98% T -> C NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 29.516; most accessible tissue: Zhenshan97 flag leaf, score: 47.303
vg0512023336 (J) chr05 12023336 G A 92.10% 4.68% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 27.624; most accessible tissue: Zhenshan97 flag leaf, score: 47.303
vg0512023367 (J) chr05 12023367 C A 87.30% 6.94% C -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 26.557; most accessible tissue: Zhenshan97 flag leaf, score: 43.728
vg0512023378 (J) chr05 12023378 G A 87.30% 8.46% G -> A NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 26.007; most accessible tissue: Zhenshan97 flag leaf, score: 41.874
vg0512023395 (J) chr05 12023395 A G 85.40% 7.30% A -> G NA
LOC_Os05g20480.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g20480.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 25.717; most accessible tissue: Zhenshan97 flag leaf, score: 36.135