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Search Results:

30 variations found. LOC_Os09g26960 (cytochrome P450; putative; expressed), ranging from 16,387,700 bp to 16,390,415 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
vg0916387730 (J) chr09 16387730 A G 99.90% 0.00% A -> G NA
LOC_Os09g26960.1 Alt: G| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os09g26960.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.537; most accessible tissue: Minghui63 flag leaf, score: 99.690
vg0916387781 (J) chr09 16387781 A G 64.30% 0.00% G -> A NA
LOC_Os09g26960.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.276; most accessible tissue: Minghui63 flag leaf, score: 99.646
vg0916387816 (J) chr09 16387816 A G 99.90% 0.00% A -> G NA
LOC_Os09g26960.1 Alt: G| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os09g26960.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.022; most accessible tissue: Minghui63 flag leaf, score: 99.631
vg0916387949 (J) chr09 16387949 C G 64.40% 0.00% G -> C NA
LOC_Os09g26960.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.620; most accessible tissue: Minghui63 flag leaf, score: 99.562
vg0916387981 (J) chr09 16387981 G A 93.30% 0.00% G -> A
mr1038 (All); LR P-value: 6.30E-08;
mr1038 (Ind_All); LR P-value: 4.76E-08;
mr1389 (All); LR P-value: 9.77E-12;
mr1389 (Ind_All); LR P-value: 2.78E-10;
mr1038_2 (All); LR P-value: 3.45E-12;
mr1038_2 (Ind_All); LR P-value: 3.49E-11;
mr1389_2 (All); LR P-value: 8.09E-12;
mr1389_2 (Ind_All); LR P-value: 1.31E-11
LOC_Os09g26960.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.722; most accessible tissue: Minghui63 flag leaf, score: 99.395
vg0916388154 (J) chr09 16388154 C Unkown 98.20% 0.32% C -> T,G NA
LOC_Os09g26960.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g26960.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 89.180; most accessible tissue: Minghui63 flag leaf, score: 99.114
vg0916388209 (J) chr09 16388209 A Unkown 94.80% 2.79% A -> G NA
LOC_Os09g26960.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.111; most accessible tissue: Minghui63 flag leaf, score: 98.890
vg0916388364 (J) chr09 16388364 T C 99.90% 0.00% T -> C NA
LOC_Os09g26960.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.711; most accessible tissue: Minghui63 flag leaf, score: 98.566
vg0916388464 (J) chr09 16388464 A T 95.10% 2.33% A -> T NA
LOC_Os09g26960.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g26960.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.104; most accessible tissue: Minghui63 flag leaf, score: 98.339
vg0916388547 (J) chr09 16388547 C T 99.80% 0.00% C -> G,T NA
LOC_Os09g26960.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g26960.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 90.260; most accessible tissue: Minghui63 flag leaf, score: 97.719
vg0916388631 (J) chr09 16388631 C Unkown 97.00% 1.76% C -> T NA
LOC_Os09g26960.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.545; most accessible tissue: Minghui63 flag leaf, score: 97.621
vg0916388632 (J) chr09 16388632 A Unkown 97.00% 1.76% A -> C NA
LOC_Os09g26960.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.614; most accessible tissue: Minghui63 flag leaf, score: 97.693
vg0916388633 (J) chr09 16388633 A Unkown 97.00% 1.76% A -> G NA
LOC_Os09g26960.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.612; most accessible tissue: Minghui63 flag leaf, score: 97.684
vg0916388649 (J) chr09 16388649 C Unkown 98.80% 1.02% C -> G NA
LOC_Os09g26960.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.414; most accessible tissue: Minghui63 flag leaf, score: 97.555
vg0916388650 (J) chr09 16388650 G Unkown 98.70% 1.10% G -> A NA
LOC_Os09g26960.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os09g26970.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.414; most accessible tissue: Minghui63 flag leaf, score: 97.555
vg0916388867 (J) chr09 16388867 T C 89.90% 0.00% T -> C
mr1138 (Ind_All); LR P-value: 3.71E-10;
mr1354 (Ind_All); LR P-value: 4.11E-06;
mr1479 (Ind_All); LR P-value: 3.10E-06;
mr1502 (All); LR P-value: 8.64E-06;
mr1502 (Ind_All); LR P-value: 3.77E-06;
mr1707 (All); LMM P-value: 2.10E-07; LR P-value: 4.68E-18;
mr1707 (Ind_All); LR P-value: 1.36E-10;
mr1728 (All); LMM P-value: 1.90E-07; LR P-value: 1.62E-18;
mr1728 (Ind_All); LMM P-value: 7.34E-06; LR P-value: 9.72E-12;
mr1860 (All); LR P-value: 1.69E-15;
mr1860 (Ind_All); LR P-value: 3.50E-10;
mr1138_2 (All); LMM P-value: 3.48E-07;
mr1138_2 (Ind_All); LMM P-value: 5.80E-06; LR P-value: 2.57E-09;
mr1355_2 (All); LR P-value: 6.12E-06;
mr1479_2 (All); LR P-value: 8.29E-07;
mr1479_2 (Ind_All); LR P-value: 5.94E-06;
mr1543_2 (Ind_All); LR P-value: 7.54E-06;
mr1655_2 (All); LR P-value: 6.88E-06;
mr1707_2 (All); LMM P-value: 5.37E-06; LR P-value: 1.13E-12;
mr1707_2 (Ind_All); LR P-value: 5.95E-07;
mr1728_2 (All); LMM P-value: 1.02E-08; LR P-value: 7.19E-24;
mr1728_2 (Ind_All); LMM P-value: 1.29E-06; LR P-value: 7.63E-13;
mr1860_2 (All); LMM P-value: 5.71E-06; LR P-value: 5.32E-18;
mr1860_2 (Ind_All); LR P-value: 6.55E-12;
mr1895_2 (All); LR P-value: 2.82E-07;
mr1895_2 (Ind_All); LR P-value: 6.61E-06;
mr1899_2 (All); LR P-value: 6.50E-06
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.914; most accessible tissue: Zhenshan97 young leaf, score: 95.617
vg0916388883 (J) chr09 16388883 T TCAA 99.90% 0.00% T -> TCAA NA
LOC_Os09g26970.1 Alt: TCAA| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g26960.1 Alt: TCAA| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.248; most accessible tissue: Zhenshan97 young leaf, score: 95.617
vg0916388891 (J) chr09 16388891 A C 64.30% 0.00% C -> A NA
LOC_Os09g26970.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.496; most accessible tissue: Minghui63 flag leaf, score: 95.707
vg0916388935 (J) chr09 16388935 A G 72.60% 0.06% A -> G
mr1174 (All); LR P-value: 2.45E-10;
mr1502 (Ind_All); LR P-value: 6.74E-06;
mr1695 (Ind_All); LR P-value: 1.29E-06;
mr1974 (All); LR P-value: 8.23E-08;
mr1974 (Ind_All); LR P-value: 4.42E-07;
mr1527_2 (All); LR P-value: 2.34E-07;
mr1598_2 (Ind_All); LR P-value: 4.57E-09;
mr1659_2 (All); LR P-value: 4.75E-08;
mr1904_2 (Ind_All); LR P-value: 2.68E-07
LOC_Os09g26970.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 88.485; most accessible tissue: Minghui63 flag leaf, score: 95.569
vg0916389242 (J) chr09 16389242 T A 99.90% 0.00% T -> A NA
LOC_Os09g26970.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g26960.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.109; most accessible tissue: Minghui63 flag leaf, score: 94.790
vg0916389457 (J) chr09 16389457 T A 64.30% 0.00% A -> T NA
LOC_Os09g26970.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.251; most accessible tissue: Zhenshan97 young leaf, score: 96.524
vg0916389643 (J) chr09 16389643 C T 99.20% 0.00% C -> T NA
LOC_Os09g26960.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.213; most accessible tissue: Zhenshan97 young leaf, score: 97.760
vg0916389645 (J) chr09 16389645 C A 92.60% 0.00% C -> A NA
LOC_Os09g26960.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.210; most accessible tissue: Zhenshan97 young leaf, score: 97.760
vg0916390030 (J) chr09 16390030 T C 99.90% 0.00% T -> C NA
LOC_Os09g26960.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 92.510; most accessible tissue: Zhenshan97 young leaf, score: 98.329
vg0916390185 (J) chr09 16390185 C G 64.50% 0.06% G -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.117; most accessible tissue: Zhenshan97 young leaf, score: 98.245
vg0916390219 (J) chr09 16390219 CTG C 72.40% 0.13% CTG -> C NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.788; most accessible tissue: Zhenshan97 young leaf, score: 97.927
vg0916390331 (J) chr09 16390331 C T 93.30% 0.00% C -> T
mr1038 (All); LR P-value: 2.11E-07;
mr1038 (Ind_All); LR P-value: 1.48E-07;
mr1389 (All); LR P-value: 2.93E-11;
mr1389 (Ind_All); LR P-value: 7.22E-10;
mr1038_2 (All); LR P-value: 1.29E-11;
mr1038_2 (Ind_All); LR P-value: 1.03E-10;
mr1389_2 (All); LR P-value: 1.11E-11;
mr1389_2 (Ind_All); LR P-value: 1.65E-11
LOC_Os09g26960.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.957; most accessible tissue: Zhenshan97 young leaf, score: 97.505
vg0916390365 (J) chr09 16390365 T C 61.90% 0.06% T -> C
mr1174 (All); LR P-value: 6.96E-09;
mr1707 (All); LR P-value: 8.76E-10;
mr1728 (All); LR P-value: 3.47E-09;
mr1389_2 (All); LR P-value: 8.58E-08;
mr1389_2 (Ind_All); LR P-value: 1.65E-06;
mr1728_2 (All); LR P-value: 7.41E-14
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.569; most accessible tissue: Zhenshan97 young leaf, score: 97.295
vg0916390383 (J) chr09 16390383 T C 61.90% 0.06% T -> C
mr1174 (All); LR P-value: 1.32E-08;
mr1707 (All); LR P-value: 1.09E-09;
mr1728 (All); LR P-value: 4.79E-09;
mr1744 (All); LR P-value: 5.33E-12;
mr1389_2 (All); LR P-value: 1.00E-06;
mr1728_2 (All); LR P-value: 1.39E-13
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g26960.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.103; most accessible tissue: Zhenshan97 young leaf, score: 96.911
vg0916390388 (J) chr09 16390388 A G 87.60% 0.00% G -> A
mr1082_2 (All); LMM P-value: 7.54E-06;
mr1164_2 (Jap_All); LR P-value: 8.76E-07
LOC_Os09g26960.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g26970.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.907; most accessible tissue: Zhenshan97 young leaf, score: 96.787