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Search Results:

18 variations found. LOC_Os03g57920 (AN1-like zinc finger domain containing protein; expressed), ranging from 32,987,042 bp to 32,988,118 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
vg0332987087 (J) chr03 32987087 C A 99.80% 0.00% C -> A NA
LOC_Os03g57920.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g57900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 75.961; most accessible tissue: Minghui63 flower, score: 87.888
vg0332987119 (J) chr03 32987119 T TGA 61.10% 0.00% TGA -> T NA
LOC_Os03g57920.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g57930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.291; most accessible tissue: Minghui63 flower, score: 85.758
vg0332987338 (J) chr03 32987338 C G 98.80% 0.00% C -> G NA
LOC_Os03g57920.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 76.631; most accessible tissue: Minghui63 panicle, score: 90.184
vg0332987496 (J) chr03 32987496 C T 98.10% 0.00% C -> T NA
LOC_Os03g57920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 83.744; most accessible tissue: Minghui63 panicle, score: 94.394
vg0332987543 (J) chr03 32987543 C A 99.80% 0.00% C -> A NA
LOC_Os03g57920.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g57900.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.820; most accessible tissue: Minghui63 panicle, score: 94.477
vg0332987560 (J) chr03 32987560 C T 99.80% 0.00% C -> T NA
LOC_Os03g57920.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g57900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.897; most accessible tissue: Minghui63 panicle, score: 94.218
vg0332987640 (J) chr03 32987640 A C 61.10% 0.00% C -> A
mr1630 (All); LR P-value: 3.42E-10;
mr1723 (All); LMM P-value: 1.04E-06; LR P-value: 6.45E-39;
mr1723 (Ind_All); LR P-value: 1.29E-08;
mr1891 (All); LR P-value: 4.91E-40;
mr1723_2 (All); LMM P-value: 1.36E-06; LR P-value: 1.76E-44;
mr1723_2 (Ind_All); LR P-value: 8.69E-10
LOC_Os03g57920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.285; most accessible tissue: Minghui63 panicle, score: 94.307
vg0332987644 (J) chr03 32987644 T C 98.00% 0.00% T -> C NA
LOC_Os03g57920.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.468; most accessible tissue: Minghui63 panicle, score: 94.394
vg0332987681 (J) chr03 32987681 AGAG A 61.60% 0.02% A -> AGAG NA
LOC_Os03g57920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g57920.1 Alt: AGAG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 85.104; most accessible tissue: Minghui63 panicle, score: 93.630
vg0332987697 (J) chr03 32987697 C T 94.00% 0.00% C -> T NA
LOC_Os03g57920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.184; most accessible tissue: Minghui63 panicle, score: 93.630
vg0332987751 (J) chr03 32987751 A G 59.10% 0.02% G -> A
mr1566 (All); LR P-value: 3.43E-17;
mr1630 (All); LR P-value: 1.90E-10;
mr1723 (All); LMM P-value: 8.45E-06; LR P-value: 4.92E-38;
mr1723 (Ind_All); LR P-value: 1.31E-07;
mr1891 (All); LR P-value: 1.91E-39;
mr1723_2 (All); LR P-value: 3.05E-43;
mr1723_2 (Ind_All); LR P-value: 1.38E-08
LOC_Os03g57920.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g57920.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.867; most accessible tissue: Minghui63 panicle, score: 92.666
vg0332987820 (J) chr03 32987820 T G 99.40% 0.00% T -> G NA
LOC_Os03g57920.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.676; most accessible tissue: Minghui63 panicle, score: 91.034
vg0332987824 (J) chr03 32987824 C A 98.00% 0.00% C -> A NA
LOC_Os03g57920.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 85.587; most accessible tissue: Minghui63 panicle, score: 90.833
vg0332987882 (J) chr03 32987882 CGCGACG GCGACG C 97.80% 0.00% CGCGACGGCG ACG -> C,CGCGACG NA
LOC_Os03g57920.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g57920.1 Alt: CGCGACG| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 83.404; most accessible tissue: Zhenshan97 young leaf, score: 90.175
vg0332987934 (J) chr03 32987934 C G 59.00% 0.00% G -> C
mr1723 (All); LMM P-value: 3.55E-06; LR P-value: 1.71E-38;
mr1723 (Ind_All); LR P-value: 7.06E-08;
mr1891 (All); LR P-value: 3.96E-39;
mr1723_2 (All); LMM P-value: 3.36E-07; LR P-value: 6.06E-45;
mr1723_2 (Ind_All); LR P-value: 4.10E-10
LOC_Os03g57920.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 85.893; most accessible tissue: Zhenshan97 young leaf, score: 90.547
vg0332987963 (J) chr03 32987963 C T 99.40% 0.00% C -> T NA
LOC_Os03g57920.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g57900.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g57930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 86.137; most accessible tissue: Zhenshan97 young leaf, score: 90.456
STR0332987335 (J) chr03 32987335 CGAC CGAG 98.60% 0.00% CGAC -> CGAG NA
STR0332987682 (J) chr03 32987682 GAGG G 62.30% 0.00% G -> GAGG NA