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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:

16 variations found. LOC_Os08g42090 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 26,581,257 bp to 26,585,480 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
vg0826581362 (J) chr08 26581362 C T 30.70% 60.66% C -> T NA
LOC_Os08g42090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.326; most accessible tissue: Zhenshan97 flower, score: 11.396
vg0826581373 (J) chr08 26581373 C T 31.00% 60.33% C -> T NA
LOC_Os08g42090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.326; most accessible tissue: Zhenshan97 flower, score: 11.396
vg0826581428 (J) chr08 26581428 T C 16.60% 48.75% T -> C NA
LOC_Os08g42090.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.550; most accessible tissue: Zhenshan97 flower, score: 11.396
vg0826581833 (J) chr08 26581833 C T 18.50% 60.94% C -> T NA
LOC_Os08g42090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.638; most accessible tissue: Minghui63 panicle, score: 7.125
vg0826583961 (J) chr08 26583961 G A 30.40% 44.92% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0826583973 (J) chr08 26583973 G A 30.30% 42.74% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0826584209 (J) chr08 26584209 G A 1.80% 77.49% G -> A NA
LOC_Os08g42090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188
vg0826584274 (J) chr08 26584274 C T 12.50% 67.37% C -> T NA
LOC_Os08g42090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.690; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0826584279 (J) chr08 26584279 T C 18.10% 45.13% T -> C NA
LOC_Os08g42090.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.690; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0826584358 (J) chr08 26584358 G A 78.40% 7.83% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.979; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0826584564 (J) chr08 26584564 G A 0.60% 74.19% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.359; most accessible tissue: Minghui63 panicle, score: 20.733
vg0826584603 (J) chr08 26584603 G A 17.50% 57.24% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.359; most accessible tissue: Minghui63 panicle, score: 20.733
vg0826584621 (J) chr08 26584621 G A 17.90% 55.59% G -> A NA
LOC_Os08g42090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.454; most accessible tissue: Minghui63 panicle, score: 20.733
vg0826584838 (J) chr08 26584838 C T 2.60% 68.96% T -> C NA
LOC_Os08g42090.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.425; most accessible tissue: Minghui63 panicle, score: 16.270
vg0826584839 (J) chr08 26584839 G A 3.20% 73.13% A -> G NA
LOC_Os08g42090.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: G| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g42090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.425; most accessible tissue: Minghui63 panicle, score: 16.270
vg0826585260 (J) chr08 26585260 C T 29.70% 48.94% C -> T NA
LOC_Os08g42090.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.945; most accessible tissue: Minghui63 young leaf, score: 11.521