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Search Results:

20 variations found. Os02g0527900/LOC_Os02g32620 (PAN domain-containing protein At5g03700 precursor; putative; expressed), ranging from 19,342,026 bp to 19,343,736 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os02g32620 PAN domain-containing protein At5g03700 precursor, putative, expressed; RAP ID: Os02g0527900; MSU ID: LOC_Os02g32620

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg0219342066 (J) chr02 19342066 C CTCT 58.90% 0.38% C -> CTCTTCT,CT CTTCTTCTTC TTCTTCTTCT ,CTCT,CTCT TCTTCTTCTT CTTCTTCTTC T,CTCTTCGT CTTCTTCTTC TTCTTCT,CT CTTCGTCTTC TTCTTCTTCT NA
LOC_Os02g32620.1 Alt: CTCTTCTTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCTTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTCTTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTCTTCGTCTTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCGTCTTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTCTTCGTCTTCTTCTTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCGTCTTCTTCTTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTCTTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTCTTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.370; most accessible tissue: Minghui63 root, score: 98.094
vg0219342069 (J) chr02 19342069 T TTCG 94.20% 0.00% T -> TTCG NA
LOC_Os02g32620.1 Alt: TTCG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: TTCG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.290; most accessible tissue: Minghui63 root, score: 98.050
vg0219342072 (J) chr02 19342072 T G 69.40% 18.83% T -> G NA
LOC_Os02g32620.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 92.260; most accessible tissue: Minghui63 root, score: 98.028
vg0219342098 (J) chr02 19342098 C CTTCTTC TTCTTCT TCTTCTT 96.50% 0.99% C -> CTTCTTCTTC TTCTTCTTCT T,CTTCTTCT TCTTCTTCTT ,CTTCTTCTT CTTCTT,CTT CTTCTT,CTT CTTCTTCTT, CTTCTTCTTC TTCTTCTTCT TCTT NA
LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTTCTTCTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: CTTCTTCTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: CTTCTTCTT| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g32630.1 Alt: CTTCTTCTT| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 90.072; most accessible tissue: Minghui63 root, score: 97.617
vg0219342099 (J) chr02 19342099 C T 85.20% 7.55% C -> T NA
LOC_Os02g32620.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 90.129; most accessible tissue: Minghui63 root, score: 97.617
vg0219342149 (J) chr02 19342149 C G 51.80% 0.59% G -> C
mr1213 (Jap_All); LR P-value: 4.65E-06;
mr1224 (Jap_All); LR P-value: 6.12E-06;
mr1610 (All); LR P-value: 6.54E-08;
mr1180_2 (Ind_All); LR P-value: 1.70E-06;
mr1851_2 (All); LR P-value: 6.45E-09;
mr1885_2 (All); LR P-value: 1.54E-07
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32620.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.218; most accessible tissue: Minghui63 root, score: 96.882
vg0219342248 (J) chr02 19342248 TGCGGCG GCGGCG T 50.40% 0.00% TGCGGCGGCG GCG -> T,TGCGGCGG CGGCGGCG,T GCG NA
LOC_Os02g32620.1 Alt: T| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g32620.1 Alt: TGCGGCGGCGGCGGCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g32620.1 Alt: TGCG| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 90.699; most accessible tissue: Zhenshan97 flag leaf, score: 94.746
vg0219342361 (J) chr02 19342361 C G 65.90% 0.11% C -> G
Plant_height (All); LR P-value: 2.43E-19;
mr1151 (All); LR P-value: 5.25E-10;
mr1180 (All); LR P-value: 4.62E-13;
mr1180 (Ind_All); LR P-value: 4.59E-07;
mr1183 (All); LR P-value: 5.00E-16;
mr1503 (All); LR P-value: 1.27E-16;
mr1627 (Ind_All); LR P-value: 6.46E-07;
mr1881 (All); LR P-value: 3.46E-06;
mr1041_2 (All); LR P-value: 2.86E-06;
mr1084_2 (All); LR P-value: 7.85E-08;
mr1180_2 (All); LR P-value: 2.87E-21;
mr1180_2 (Ind_All); LR P-value: 1.16E-08;
mr1183_2 (All); LR P-value: 6.24E-25;
mr1183_2 (Ind_All); LR P-value: 3.07E-08;
mr1215_2 (All); LR P-value: 6.63E-09;
mr1220_2 (All); LR P-value: 2.67E-11;
mr1294_2 (All); LR P-value: 5.44E-06;
mr1319_2 (All); LR P-value: 3.70E-09;
mr1330_2 (All); LR P-value: 1.90E-13;
mr1360_2 (All); LR P-value: 2.86E-06;
mr1360_2 (Ind_All); LR P-value: 5.74E-06;
mr1376_2 (All); LR P-value: 1.27E-07;
mr1378_2 (Ind_All); LR P-value: 7.88E-07;
mr1386_2 (Ind_All); LR P-value: 7.34E-06;
mr1431_2 (All); LR P-value: 1.21E-07;
mr1604_2 (All); LR P-value: 5.93E-07;
mr1627_2 (All); LR P-value: 1.46E-25;
mr1627_2 (Ind_All); LR P-value: 6.60E-13;
mr1794_2 (All); LR P-value: 3.27E-15;
mr1885_2 (All); LR P-value: 1.56E-07
LOC_Os02g32620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.217; most accessible tissue: Zhenshan97 flag leaf, score: 95.693
vg0219342438 (J) chr02 19342438 C A 56.60% 0.32% A -> C
mr1543_2 (Ind_All); LR P-value: 5.52E-06;
mr1885_2 (All); LR P-value: 2.45E-07
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.489; most accessible tissue: Zhenshan97 flag leaf, score: 95.494
vg0219342441 (J) chr02 19342441 G T 56.60% 0.32% T -> G
mr1180_2 (Ind_All); LR P-value: 9.30E-07;
mr1885_2 (All); LR P-value: 2.03E-07
LOC_Os02g32620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 90.449; most accessible tissue: Zhenshan97 flag leaf, score: 95.494
vg0219342492 (J) chr02 19342492 G A 82.00% 0.00% G -> A
mr1063 (Ind_All); LR P-value: 9.13E-06;
mr1213 (Jap_All); LR P-value: 8.02E-06;
mr1215 (Ind_All); LR P-value: 6.78E-06;
mr1460 (Ind_All); LMM P-value: 2.52E-06; LR P-value: 2.52E-06;
mr1215_2 (Ind_All); LR P-value: 7.46E-06;
mr1220_2 (Ind_All); LR P-value: 6.05E-06;
mr1381_2 (Ind_All); LR P-value: 8.64E-06;
mr1661_2 (Ind_All); LR P-value: 5.10E-07;
mr1696_2 (Ind_All); LR P-value: 3.65E-06
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.056; most accessible tissue: Zhenshan97 flag leaf, score: 95.925
vg0219342827 (J) chr02 19342827 G A 51.90% 0.00% A -> G
mr1213 (Jap_All); LR P-value: 4.65E-06;
mr1224 (Jap_All); LR P-value: 6.12E-06;
mr1610 (All); LR P-value: 8.85E-08;
mr1180_2 (All); LR P-value: 1.42E-15;
mr1180_2 (Ind_All); LR P-value: 1.08E-06;
mr1543_2 (Ind_All); LR P-value: 8.14E-06;
mr1627_2 (Ind_All); LR P-value: 1.81E-08;
mr1851_2 (All); LR P-value: 3.31E-09;
mr1885_2 (All); LR P-value: 1.39E-07
LOC_Os02g32620.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.789; most accessible tissue: Zhenshan97 young leaf, score: 96.130
vg0219342947 (J) chr02 19342947 A C 99.80% 0.00% A -> C,G NA
LOC_Os02g32620.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g32630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32620.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os02g32630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 93.381; most accessible tissue: Zhenshan97 young leaf, score: 96.065
vg0219342956 (J) chr02 19342956 C A 51.80% 0.00% A -> C NA
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.412; most accessible tissue: Zhenshan97 flag leaf, score: 96.074
vg0219342957 (J) chr02 19342957 A G 51.70% 0.00% G -> A NA
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.410; most accessible tissue: Zhenshan97 flag leaf, score: 96.074
vg0219342960 (J) chr02 19342960 C A 82.00% 0.00% C -> A
mr1063 (Ind_All); LR P-value: 9.13E-06;
mr1213 (Jap_All); LR P-value: 8.02E-06;
mr1215 (Ind_All); LR P-value: 6.78E-06;
mr1460 (Ind_All); LMM P-value: 2.52E-06; LR P-value: 2.52E-06;
mr1215_2 (Ind_All); LR P-value: 7.46E-06;
mr1220_2 (Ind_All); LR P-value: 6.05E-06;
mr1381_2 (Ind_All); LR P-value: 8.64E-06;
mr1661_2 (Ind_All); LR P-value: 5.10E-07;
mr1696_2 (Ind_All); LR P-value: 3.65E-06
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.463; most accessible tissue: Zhenshan97 flag leaf, score: 96.129
vg0219343200 (J) chr02 19343200 G C 65.30% 0.38% G -> C NA
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g32620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 93.616; most accessible tissue: Zhenshan97 flag leaf, score: 96.171
vg0219343219 (J) chr02 19343219 G A 81.50% 1.23% G -> A NA
LOC_Os02g32620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 93.900; most accessible tissue: Zhenshan97 root, score: 96.529
vg0219343316 (J) chr02 19343316 C T 97.50% 0.59% C -> T NA
LOC_Os02g32620.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g32620.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.719; most accessible tissue: Zhenshan97 root, score: 97.104
STR0219343193 (J) chr02 19343193 CGCCGCC G CGCCGCC C 47.80% 0.00% CGCCGCCG -> CGCCGCCC NA