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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_Os12g41280 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 25,599,453 bp to 25,603,362 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
vg1225599490 (J) chr12 25599490 G A 53.40% 35.87% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 20.806; most accessible tissue: Zhenshan97 flag leaf, score: 33.231
vg1225599558 (J) chr12 25599558 C T 55.60% 31.63% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 19.867; most accessible tissue: Zhenshan97 flag leaf, score: 29.417
vg1225599699 (J) chr12 25599699 A G 58.70% 36.23% A -> G NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 13.073; most accessible tissue: Zhenshan97 flag leaf, score: 27.583
vg1225600169 (J) chr12 25600169 C T 55.70% 31.49% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 10.529; most accessible tissue: Zhenshan97 panicle, score: 28.447
vg1225600237 (J) chr12 25600237 A G 60.40% 30.94% A -> G NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 14.493; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg1225600262 (J) chr12 25600262 C T 60.00% 32.12% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 14.409; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg1225600745 (J) chr12 25600745 T C 54.30% 31.78% T -> C NA
LOC_Os12g41280.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.040; most accessible tissue: Zhenshan97 root, score: 25.639
vg1225600858 (J) chr12 25600858 C A 14.50% 43.91% C -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.886; most accessible tissue: Zhenshan97 root, score: 22.162
vg1225600884 (J) chr12 25600884 C T 53.10% 41.77% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 8.674; most accessible tissue: Zhenshan97 root, score: 20.427
vg1225601251 (J) chr12 25601251 C A 53.40% 41.30% C -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 12.951; most accessible tissue: Zhenshan97 flower, score: 23.247
vg1225601283 (J) chr12 25601283 A G 53.50% 40.67% A -> G NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 12.867; most accessible tissue: Zhenshan97 flower, score: 23.247
vg1225601599 (J) chr12 25601599 G A 55.00% 31.91% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 10.309; most accessible tissue: Zhenshan97 flower, score: 19.853
vg1225601711 (J) chr12 25601711 C T 55.20% 32.92% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 9.765; most accessible tissue: Zhenshan97 flag leaf, score: 18.943
vg1225601767 (J) chr12 25601767 G A 54.10% 33.09% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.568; most accessible tissue: Zhenshan97 flower, score: 15.748
vg1225602644 (J) chr12 25602644 C T 68.70% 27.82% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 7.660; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1225603245 (J) chr12 25603245 C T 80.60% 13.42% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 15.867; most accessible tissue: Zhenshan97 flag leaf, score: 27.583
vg1225603252 (J) chr12 25603252 C T 77.00% 14.33% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.509; most accessible tissue: Zhenshan97 flag leaf, score: 27.583
vg1225603256 (J) chr12 25603256 C T 74.90% 14.90% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 15.427; most accessible tissue: Zhenshan97 flag leaf, score: 26.688
vg1225603315 (J) chr12 25603315 C G 70.10% 27.42% C -> G NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 17.756; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg1225603321 (J) chr12 25603321 G A 57.60% 30.13% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg1225603322 (J) chr12 25603322 G A 70.80% 27.42% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 17.845; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg1225603337 (J) chr12 25603337 C T 69.70% 27.68% C -> T NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 17.652; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg1225603349 (J) chr12 25603349 G A 68.60% 28.08% G -> A NA
LOC_Os12g41280.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g41280.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 17.317; most accessible tissue: Zhenshan97 panicle, score: 36.038