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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:

3 variations found. LOC_Os06g17330 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 10,039,367 bp to 10,041,889 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
vg0610040562 (J) chr06 10040562 T A 2.70% 78.12% T -> A NA
LOC_Os06g17330.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g17330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.807; most accessible tissue: Minghui63 panicle, score: 20.733
vg0610040638 (J) chr06 10040638 C T 11.90% 71.90% C -> T NA
LOC_Os06g17330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g17330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.886; most accessible tissue: Minghui63 panicle, score: 20.733
vg0610041845 (J) chr06 10041845 C T 27.50% 60.16% C -> T NA
LOC_Os06g17330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g17330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.786; most accessible tissue: Minghui63 root, score: 15.664