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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:

5 variations found. LOC_Os02g54420 (hypro1; putative; expressed), ranging from 33,346,333 bp to 33,347,257 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
vg0233346565 (J) chr02 33346565 C A 64.50% 0.00% A -> C NA
LOC_Os02g54420.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.870; most accessible tissue: Zhenshan97 root, score: 83.907
vg0233347033 (J) chr02 33347033 C A 94.10% 0.00% C -> A NA
LOC_Os02g54420.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.496; most accessible tissue: Zhenshan97 young leaf, score: 81.353
vg0233347130 (J) chr02 33347130 G A 99.90% 0.00% G -> A NA
LOC_Os02g54420.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g54410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54440.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.322; most accessible tissue: Minghui63 root, score: 77.290
vg0233347207 (J) chr02 33347207 G A 98.10% 0.00% G -> A NA
LOC_Os02g54420.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.654; most accessible tissue: Callus, score: 78.078
STR0233347032 (J) chr02 33347032 GC GA 96.90% 0.00% GC -> GA NA