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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:

9 variations found. LOC_Os02g54450 (hypro1; putative; expressed), ranging from 33,353,939 bp to 33,355,216 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
vg0233354124 (J) chr02 33354124 C CT 91.50% 2.41% C -> CT NA
LOC_Os02g54450.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54440.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54460.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 59.006; most accessible tissue: Zhenshan97 flower, score: 67.236
vg0233354125 (J) chr02 33354125 T TA 90.50% 1.69% T -> TA NA
LOC_Os02g54450.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54440.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54460.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 59.006; most accessible tissue: Zhenshan97 flower, score: 67.236
vg0233354314 (J) chr02 33354314 G A 98.10% 0.00% G -> A NA
LOC_Os02g54450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.410; most accessible tissue: Minghui63 root, score: 82.185
vg0233354640 (J) chr02 33354640 C T 99.80% 0.00% C -> T NA
LOC_Os02g54450.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g54430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54460.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624
vg0233354790 (J) chr02 33354790 G T 64.40% 0.00% T -> G NA
LOC_Os02g54450.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.413; most accessible tissue: Zhenshan97 root, score: 80.680
vg0233354792 (J) chr02 33354792 G A 99.50% 0.00% G -> A NA
LOC_Os02g54450.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g54430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g54470.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.374; most accessible tissue: Zhenshan97 root, score: 80.448
vg0233354900 (J) chr02 33354900 G T 99.80% 0.00% G -> T NA
LOC_Os02g54450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 67.361; most accessible tissue: Zhenshan97 root, score: 82.170
vg0233355144 (J) chr02 33355144 A C 94.30% 0.00% A -> C
mr1465 (All); LR P-value: 3.56E-08;
mr1260_2 (All); LR P-value: 1.01E-16
LOC_Os02g54450.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54440.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54460.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 61.436; most accessible tissue: Zhenshan97 root, score: 87.558
STR0233354126 (J) chr02 33354126 AA AAA 93.00% 0.00% AA -> AAA NA