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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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Variations Type:

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Search Results:

32 variations found. LOC_Os01g02710 (LRk-type protein; putative; expressed), ranging from 924,450 bp to 925,175 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
vg0100924471 (J) chr01 924471 T A 59.80% 13.56% T -> A NA
LOC_Os01g02710.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.561; most accessible tissue: Zhenshan97 flag leaf, score: 97.978
vg0100924519 (J) chr01 924519 C T 61.80% 35.25% C -> T NA
LOC_Os01g02710.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 81.080; most accessible tissue: Zhenshan97 flag leaf, score: 97.716
vg0100924523 (J) chr01 924523 A G 61.70% 35.12% A -> G NA
LOC_Os01g02710.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.885; most accessible tissue: Zhenshan97 flag leaf, score: 97.568
vg0100924553 (J) chr01 924553 A C 63.00% 32.50% A -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.778; most accessible tissue: Zhenshan97 flag leaf, score: 97.373
vg0100924560 (J) chr01 924560 G A 86.00% 8.32% G -> A NA
LOC_Os01g02710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 81.197; most accessible tissue: Zhenshan97 flag leaf, score: 97.318
vg0100924595 (J) chr01 924595 C A 99.00% 0.97% C -> A,T NA
LOC_Os01g02710.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g02700.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02710.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g02700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.860; most accessible tissue: Zhenshan97 flag leaf, score: 96.933
vg0100924602 (J) chr01 924602 C T 65.00% 30.94% C -> T NA
LOC_Os01g02710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.883; most accessible tissue: Zhenshan97 flag leaf, score: 96.856
vg0100924603 (J) chr01 924603 A G 62.50% 33.22% A -> G,C NA
LOC_Os01g02710.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: G| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os01g02700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.928; most accessible tissue: Zhenshan97 flag leaf, score: 96.856
vg0100924607 (J) chr01 924607 C Unkown 98.00% 2.01% C -> T NA
LOC_Os01g02710.1 Alt: T| stop_gained HIGH(snpEff)
LOC_Os01g02700.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.056; most accessible tissue: Zhenshan97 flag leaf, score: 96.864
vg0100924618 (J) chr01 924618 G A 60.00% 12.93% G -> A NA
LOC_Os01g02710.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.001; most accessible tissue: Zhenshan97 flag leaf, score: 96.777
vg0100924621 (J) chr01 924621 C T 65.10% 31.70% C -> T NA
LOC_Os01g02710.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.904; most accessible tissue: Zhenshan97 flag leaf, score: 96.692
vg0100924666 (J) chr01 924666 C T 98.90% 0.97% C -> T NA
LOC_Os01g02710.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g02700.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.565; most accessible tissue: Zhenshan97 flag leaf, score: 96.346
vg0100924667 (J) chr01 924667 CTGTA C 99.80% 0.00% CTGTA -> C NA
LOC_Os01g02710.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.558; most accessible tissue: Zhenshan97 flag leaf, score: 96.346
vg0100924673 (J) chr01 924673 C T 98.20% 1.59% C -> T NA
LOC_Os01g02710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.759; most accessible tissue: Zhenshan97 flag leaf, score: 96.394
vg0100924730 (J) chr01 924730 T A 62.20% 34.43% T -> A NA
LOC_Os01g02710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 80.489; most accessible tissue: Zhenshan97 flag leaf, score: 95.913
vg0100924740 (J) chr01 924740 T C 62.00% 34.53% T -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.331; most accessible tissue: Zhenshan97 flag leaf, score: 95.842
vg0100924771 (J) chr01 924771 T C 64.40% 33.16% T -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.028; most accessible tissue: Zhenshan97 flag leaf, score: 95.308
vg0100924786 (J) chr01 924786 G T 62.10% 35.67% G -> T NA
LOC_Os01g02710.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.035; most accessible tissue: Zhenshan97 flag leaf, score: 95.337
vg0100924821 (J) chr01 924821 A C 61.70% 35.44% A -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 78.437; most accessible tissue: Zhenshan97 flag leaf, score: 94.800
vg0100924877 (J) chr01 924877 G Unkown 98.00% 1.69% G -> A NA
LOC_Os01g02700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g02710.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.219; most accessible tissue: Zhenshan97 flag leaf, score: 93.341
vg0100924913 (J) chr01 924913 G A 86.40% 11.34% G -> A NA
LOC_Os01g02700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 68.523; most accessible tissue: Zhenshan97 flag leaf, score: 92.274
vg0100924925 (J) chr01 924925 T C 98.50% 1.35% T -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.754; most accessible tissue: Zhenshan97 flag leaf, score: 92.520
vg0100924944 (J) chr01 924944 CAT TAT 95.20% 0.00% CAT -> TAT,C NA
LOC_Os01g02700.1 Alt: TAT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: TAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: TAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: TAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02700.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.343; most accessible tissue: Zhenshan97 flag leaf, score: 91.729
vg0100924946 (J) chr01 924946 T TCC 65.20% 31.63% T -> TCC NA
LOC_Os01g02700.1 Alt: TCC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: TCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: TCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: TCC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 69.147; most accessible tissue: Zhenshan97 flag leaf, score: 91.771
vg0100924947 (J) chr01 924947 AT A 64.90% 31.95% AT -> A NA
LOC_Os01g02700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02720.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02710.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 69.159; most accessible tissue: Zhenshan97 flag leaf, score: 91.771
vg0100924963 (J) chr01 924963 C T 65.50% 31.15% C -> T NA
LOC_Os01g02710.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.733; most accessible tissue: Zhenshan97 flag leaf, score: 91.644
vg0100924967 (J) chr01 924967 A G 91.50% 8.13% A -> G NA
LOC_Os01g02710.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.461; most accessible tissue: Zhenshan97 flag leaf, score: 91.644
vg0100924986 (J) chr01 924986 A T 70.10% 0.00% T -> A NA
LOC_Os01g02710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 65.435; most accessible tissue: Zhenshan97 flag leaf, score: 90.685
vg0100925037 (J) chr01 925037 T C 90.80% 8.46% T -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.430; most accessible tissue: Zhenshan97 flag leaf, score: 90.240
vg0100925107 (J) chr01 925107 G C 76.20% 19.09% G -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 59.445; most accessible tissue: Zhenshan97 flag leaf, score: 88.196
vg0100925146 (J) chr01 925146 T C 98.20% 1.35% T -> C NA
LOC_Os01g02710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 58.622; most accessible tissue: Zhenshan97 flag leaf, score: 87.846
vg0100925152 (J) chr01 925152 T A 84.70% 0.00% A -> T
Heading_date (All); LMM P-value: 9.88E-06;
mr1354_2 (All); LMM P-value: 8.22E-06
LOC_Os01g02710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 59.144; most accessible tissue: Zhenshan97 flag leaf, score: 87.846