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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:

4 variations found. LOC_Os02g54390 (hypro1; putative; expressed), ranging from 33,330,508 bp to 33,331,432 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
vg0233330713 (J) chr02 33330713 C A 64.40% 0.00% A -> C NA
LOC_Os02g54390.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.804; most accessible tissue: Minghui63 root, score: 90.139
vg0233330944 (J) chr02 33330944 G T 99.90% 0.00% G -> T NA
LOC_Os02g54390.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g54400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.852; most accessible tissue: Minghui63 root, score: 84.686
vg0233330973 (J) chr02 33330973 C T 99.90% 0.00% C -> T NA
LOC_Os02g54390.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g54400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 76.783; most accessible tissue: Minghui63 root, score: 83.939
vg0233331348 (J) chr02 33331348 C A 64.50% 0.00% A -> C NA
LOC_Os02g54390.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.256; most accessible tissue: Zhenshan97 young leaf, score: 79.783