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:

13 variations found. LOC_Os08g25330 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 15,407,810 bp to 15,412,385 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
vg0815409372 (J) chr08 15409372 C G 19.80% 41.96% C -> G NA
LOC_Os08g25330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.719; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410001 (J) chr08 15410001 T C 20.70% 67.01% T -> C NA
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410038 (J) chr08 15410038 A C 16.80% 71.96% A -> C NA
LOC_Os08g25330.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410058 (J) chr08 15410058 G A 20.50% 66.55% G -> A NA
LOC_Os08g25330.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.486; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410076 (J) chr08 15410076 A G 20.50% 68.37% A -> G NA
LOC_Os08g25330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.467; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410091 (J) chr08 15410091 T C 19.90% 68.81% T -> C NA
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.467; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815410433 (J) chr08 15410433 A G 20.60% 67.65% A -> G NA
LOC_Os08g25330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.196; most accessible tissue: Callus, score: 12.491
vg0815410455 (J) chr08 15410455 C T 20.20% 68.41% C -> T NA
LOC_Os08g25330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.196; most accessible tissue: Callus, score: 12.491
vg0815411375 (J) chr08 15411375 A C 30.40% 41.94% A -> C NA
LOC_Os08g25330.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815411661 (J) chr08 15411661 CTAGAGA TCAACTG GT C 19.40% 69.66% CTAGAGATCA ACTGGT -> C NA
LOC_Os08g25330.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815411672 (J) chr08 15411672 C T 18.50% 73.72% C -> T NA
LOC_Os08g25330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125
vg0815412247 (J) chr08 15412247 C T 20.10% 66.10% C -> T NA
LOC_Os08g25330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.667; most accessible tissue: Zhenshan97 root, score: 20.427
vg0815412275 (J) chr08 15412275 G A 26.80% 65.59% G -> A NA
LOC_Os08g25330.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g25330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.012; most accessible tissue: Zhenshan97 root, score: 20.427