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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:

2 variations found. LOC_Os02g07950 (retrotransposon protein; putative; unclassified), ranging from 4,159,540 bp to 4,160,224 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
vg0204160056 (J) chr02 4160056 A G 80.40% 13.73% A -> G NA
LOC_Os02g07950.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g07950.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 48.653; most accessible tissue: Zhenshan97 panicle, score: 71.253
vg0204160066 (J) chr02 4160066 T C 80.60% 15.19% T -> C NA
LOC_Os02g07950.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g07950.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 49.383; most accessible tissue: Zhenshan97 panicle, score: 72.468