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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:

7 variations found. LOC_Os12g04680 (expressed protein), ranging from 1,983,961 bp to 1,984,386 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
vg1201983970 (J) chr12 1983970 G A 74.80% 11.32% G -> A NA
LOC_Os12g04680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04680.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 85.945; most accessible tissue: Minghui63 root, score: 94.716
vg1201984044 (J) chr12 1984044 A G 99.60% 0.00% A -> G NA
LOC_Os12g04680.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g04670.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04690.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.703; most accessible tissue: Minghui63 root, score: 94.870
vg1201984083 (J) chr12 1984083 G T 99.60% 0.00% G -> T NA
LOC_Os12g04680.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g04670.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04690.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.120; most accessible tissue: Minghui63 root, score: 93.695
vg1201984088 (J) chr12 1984088 AG A 99.60% 0.00% AG -> A NA
LOC_Os12g04680.1 Alt: A| frameshift_variant HIGH(snpEff)
LOC_Os12g04670.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.637; most accessible tissue: Minghui63 root, score: 93.365
vg1201984209 (J) chr12 1984209 G T 99.60% 0.00% G -> T NA
LOC_Os12g04670.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04690.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04680.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.767; most accessible tissue: Zhenshan97 root, score: 85.305
vg1201984307 (J) chr12 1984307 A G 99.70% 0.00% A -> G NA
LOC_Os12g04680.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g04670.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g04690.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 62.863; most accessible tissue: Zhenshan97 root, score: 76.397
vg1201984316 (J) chr12 1984316 A G 56.40% 30.39% A -> G NA
LOC_Os12g04680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g04680.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 62.813; most accessible tissue: Zhenshan97 root, score: 76.397