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.):
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Search Results:

1 variations found. LOC_Os04g11770 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 6,443,419 bp to 6,447,642 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
vg0406446131 (J) chr04 6446131 C CA 32.50% 42.38% C -> CA NA
LOC_Os04g11770.1 Alt: CA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g11770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.657; most accessible tissue: Minghui63 panicle, score: 7.125