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:

23 variations found. LOC_Os11g30552 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 17,776,136 bp to 17,781,092 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
vg1117777843 (J) chr11 17777843 G A 1.00% 93.42% G -> A NA
LOC_Os11g30552.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.298; most accessible tissue: Minghui63 root, score: 15.664
vg1117777874 (J) chr11 17777874 T C 0.30% 96.00% C -> T NA
LOC_Os11g30552.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.062; most accessible tissue: Minghui63 panicle, score: 16.270
vg1117777877 (J) chr11 17777877 A G 0.30% 96.13% G -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.062; most accessible tissue: Minghui63 panicle, score: 16.270
vg1117778239 (J) chr11 17778239 C T 0.30% 95.51% T -> C NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 12.594; most accessible tissue: Minghui63 panicle, score: 20.733
vg1117778359 (J) chr11 17778359 A G 24.00% 73.30% A -> G NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 10.248; most accessible tissue: Minghui63 panicle, score: 16.270
vg1117778384 (J) chr11 17778384 C G 12.40% 75.07% C -> G NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1117778392 (J) chr11 17778392 G A 14.60% 71.67% G -> A NA
LOC_Os11g30552.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1117778415 (J) chr11 17778415 G A 12.30% 74.99% G -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.249; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg1117778472 (J) chr11 17778472 T C 2.00% 90.08% C -> T NA
LOC_Os11g30552.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.208; most accessible tissue: Zhenshan97 root, score: 10.511
vg1117778535 (J) chr11 17778535 A G 0.30% 94.82% G -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.391; most accessible tissue: Zhenshan97 root, score: 10.511
vg1117778679 (J) chr11 17778679 CA C 24.20% 73.87% CA -> C NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.695; most accessible tissue: Zhenshan97 root, score: 12.891
vg1117778689 (J) chr11 17778689 G T 24.30% 73.38% G -> T NA
LOC_Os11g30552.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.695; most accessible tissue: Zhenshan97 root, score: 12.891
vg1117778734 (J) chr11 17778734 G C 28.00% 66.55% G -> C NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 5.217; most accessible tissue: Zhenshan97 root, score: 12.891
vg1117779127 (J) chr11 17779127 C T 12.10% 75.54% C -> T NA
LOC_Os11g30552.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.651; most accessible tissue: Zhenshan97 flag leaf, score: 11.736
vg1117779305 (J) chr11 17779305 C G 1.50% 90.52% C -> G NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 8.629; most accessible tissue: Zhenshan97 flag leaf, score: 15.873
vg1117779418 (J) chr11 17779418 G A 8.70% 78.63% G -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.215; most accessible tissue: Zhenshan97 flag leaf, score: 17.069
vg1117779681 (J) chr11 17779681 C T 17.30% 73.36% T -> C NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.294; most accessible tissue: Zhenshan97 flag leaf, score: 12.605
vg1117779730 (J) chr11 17779730 G A 25.00% 73.17% G -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.602; most accessible tissue: Zhenshan97 flag leaf, score: 7.948
vg1117780036 (J) chr11 17780036 A G 27.00% 68.96% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g30552.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 6.331; most accessible tissue: Minghui63 young leaf, score: 12.713
vg1117780042 (J) chr11 17780042 T A 25.80% 70.61% T -> A NA
LOC_Os11g30552.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.331; most accessible tissue: Minghui63 young leaf, score: 12.713
vg1117780389 (J) chr11 17780389 T A 25.00% 73.57% T -> A NA
LOC_Os11g30552.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.943; most accessible tissue: Minghui63 young leaf, score: 9.976
vg1117780472 (J) chr11 17780472 A C 25.10% 73.80% A -> C NA
LOC_Os11g30552.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g30552.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1117780482 (J) chr11 17780482 C T 24.80% 74.38% C -> T NA
LOC_Os11g30552.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os11g30560.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125