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Search Results:

40 variations found. Os02g0627100/LOC_Os02g41680 (phenylalanine ammonia-lyase; putative; expressed), ranging from 25,006,466 bp to 25,009,121 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os02g41680 phenylalanine ammonia-lyase, putative, expressed; RAP ID: Os02g0627100; MSU ID: LOC_Os02g41680
MSU IDRAP IDSymbolNameExplanationRecommended Gene SymbolRecommended Gene Name
LOC_Os02g41680Os02g0627100OsPAL1, PALphenylalanine ammonia-lyase 1, phenylalanine ammonia lyaseQ0DZE0. X87946. A2X7F7.PAL1PHENYLALANINE AMMONIA-LYASE 1

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
vg0225006506 (J) chr02 25006506 T C 97.70% 0.00% T -> C NA
LOC_Os02g41680.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.332; most accessible tissue: Minghui63 root, score: 90.372
vg0225006575 (J) chr02 25006575 G C 55.00% 0.00% C -> G,T
mr1369_2 (All); LR P-value: 1.56E-06;
mr1453_2 (All); LR P-value: 5.00E-07;
mr1806_2 (All); LR P-value: 4.43E-10;
mr1835_2 (All); LR P-value: 4.16E-09
LOC_Os02g41680.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g41680.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 65.799; most accessible tissue: Zhenshan97 root, score: 93.268
vg0225006672 (J) chr02 25006672 C T 94.20% 0.00% C -> T NA
LOC_Os02g41680.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.703; most accessible tissue: Zhenshan97 root, score: 94.941
vg0225006701 (J) chr02 25006701 T C 94.00% 0.00% T -> C NA
LOC_Os02g41680.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.005; most accessible tissue: Zhenshan97 root, score: 95.396
vg0225007028 (J) chr02 25007028 G C 92.60% 0.00% G -> C
mr1389 (All); LR P-value: 3.87E-07;
mr1389 (Ind_All); LR P-value: 2.74E-07;
mr1038_2 (All); LR P-value: 7.32E-07;
mr1038_2 (Ind_All); LR P-value: 2.98E-07;
mr1227_2 (All); LR P-value: 2.20E-06;
mr1389_2 (All); LR P-value: 4.22E-07;
mr1389_2 (Ind_All); LR P-value: 9.36E-08;
mr1416_2 (Ind_All); LMM P-value: 6.91E-06; LR P-value: 6.90E-06;
mr1457_2 (Ind_All); LR P-value: 3.80E-06
LOC_Os02g41680.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.400; most accessible tissue: Zhenshan97 root, score: 97.140
vg0225007295 (J) chr02 25007295 G T 99.00% 0.00% G -> T NA
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.599; most accessible tissue: Zhenshan97 root, score: 95.791
vg0225007371 (J) chr02 25007371 G T 62.90% 0.00% T -> G NA
LOC_Os02g41680.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 78.113; most accessible tissue: Zhenshan97 root, score: 95.366
vg0225007547 (J) chr02 25007547 C A 97.20% 0.00% C -> A NA
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.524; most accessible tissue: Zhenshan97 root, score: 94.685
vg0225007569 (J) chr02 25007569 T C 99.90% 0.00% T -> C NA
LOC_Os02g41680.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 81.044; most accessible tissue: Zhenshan97 root, score: 94.705
vg0225007733 (J) chr02 25007733 C G 75.90% 0.00% C -> G
mr1593 (Ind_All); LR P-value: 7.21E-07;
mr1686 (Ind_All); LR P-value: 5.03E-06;
mr1925 (All); LR P-value: 2.80E-09;
mr1925 (Ind_All); LR P-value: 3.79E-06;
mr1195_2 (Ind_All); LR P-value: 3.42E-09;
mr1593_2 (Ind_All); LR P-value: 4.39E-09;
mr1925_2 (All); LR P-value: 2.94E-06
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.970; most accessible tissue: Zhenshan97 root, score: 93.988
vg0225007748 (J) chr02 25007748 A G 75.90% 0.00% A -> G
mr1593 (Ind_All); LR P-value: 7.70E-07;
mr1686 (Ind_All); LR P-value: 2.83E-06;
mr1925 (All); LR P-value: 8.71E-10;
mr1925 (Ind_All); LR P-value: 1.13E-06;
mr1498_2 (All); LR P-value: 7.92E-07;
mr1593_2 (Ind_All); LR P-value: 6.80E-09;
mr1925_2 (All); LR P-value: 1.36E-06
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.455; most accessible tissue: Zhenshan97 root, score: 94.124
vg0225007757 (J) chr02 25007757 G C 76.00% 0.00% G -> C
mr1593 (Ind_All); LR P-value: 1.29E-06;
mr1686 (Ind_All); LR P-value: 2.93E-06;
mr1925 (All); LR P-value: 4.56E-10;
mr1925 (Ind_All); LR P-value: 5.79E-07;
mr1498_2 (All); LR P-value: 4.74E-07;
mr1593_2 (Ind_All); LR P-value: 2.29E-08;
mr1677_2 (All); LR P-value: 8.55E-06;
mr1925_2 (All); LR P-value: 9.98E-07
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.229; most accessible tissue: Zhenshan97 root, score: 93.844
vg0225007770 (J) chr02 25007770 G A 76.40% 5.76% G -> A NA
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.388; most accessible tissue: Zhenshan97 root, score: 94.011
vg0225007771 (J) chr02 25007771 C A 76.40% 5.71% C -> A NA
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.224; most accessible tissue: Zhenshan97 root, score: 93.988
vg0225007772 (J) chr02 25007772 G A 68.90% 22.22% G -> A
mr1389 (All); LR P-value: 3.82E-07;
mr1389 (Ind_All); LR P-value: 3.42E-07;
mr1038_2 (All); LR P-value: 3.01E-07;
mr1038_2 (Ind_All); LR P-value: 2.83E-07;
mr1389_2 (All); LR P-value: 3.27E-07;
mr1389_2 (Ind_All); LR P-value: 7.45E-08;
mr1457_2 (Ind_All); LR P-value: 2.76E-06
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.224; most accessible tissue: Zhenshan97 root, score: 93.988
vg0225007778 (J) chr02 25007778 A G 77.10% 21.69% A -> G NA
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.846; most accessible tissue: Zhenshan97 root, score: 94.124
vg0225007805 (J) chr02 25007805 T C 76.90% 22.41% T -> C
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06;
mr1686 (Ind_All); LR P-value: 5.22E-06;
mr1925 (All); LR P-value: 1.51E-09;
mr1925 (Ind_All); LR P-value: 2.03E-06;
mr1498_2 (All); LR P-value: 9.44E-07;
mr1593_2 (Ind_All); LR P-value: 1.51E-08;
mr1925_2 (All); LR P-value: 2.20E-06
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.752; most accessible tissue: Zhenshan97 root, score: 94.168
vg0225007808 (J) chr02 25007808 G C 76.80% 22.37% G -> C
mr1195 (All); LR P-value: 4.72E-10;
mr1593 (Ind_All); LR P-value: 6.62E-07;
mr1686 (Ind_All); LR P-value: 6.51E-06;
mr1925 (All); LR P-value: 5.18E-09;
mr1925 (Ind_All); LR P-value: 5.54E-06;
mr1593_2 (Ind_All); LR P-value: 4.56E-09
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.734; most accessible tissue: Zhenshan97 root, score: 94.168
vg0225007811 (J) chr02 25007811 T C 76.50% 22.60% T -> C
mr1195 (All); LR P-value: 4.72E-10;
mr1593 (Ind_All); LR P-value: 6.62E-07;
mr1686 (Ind_All); LR P-value: 6.51E-06;
mr1925 (All); LR P-value: 5.18E-09;
mr1925 (Ind_All); LR P-value: 5.54E-06;
mr1593_2 (Ind_All); LR P-value: 4.56E-09
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.479; most accessible tissue: Zhenshan97 root, score: 94.146
vg0225007814 (J) chr02 25007814 C G 76.40% 22.18% C -> G
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06;
mr1686 (Ind_All); LR P-value: 5.22E-06;
mr1925 (All); LR P-value: 1.51E-09;
mr1925 (Ind_All); LR P-value: 2.03E-06;
mr1498_2 (All); LR P-value: 9.44E-07;
mr1593_2 (Ind_All); LR P-value: 1.51E-08;
mr1925_2 (All); LR P-value: 2.20E-06
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.500; most accessible tissue: Zhenshan97 root, score: 94.146
vg0225007828 (J) chr02 25007828 G T 76.00% 0.00% G -> T
mr1195 (All); LR P-value: 4.40E-10;
mr1593 (Ind_All); LR P-value: 5.25E-07;
mr1686 (Ind_All); LR P-value: 4.70E-06;
mr1925 (All); LR P-value: 2.99E-09;
mr1925 (Ind_All); LR P-value: 3.84E-06;
mr1195_2 (Ind_All); LR P-value: 1.60E-09;
mr1498_2 (All); LR P-value: 5.25E-07;
mr1593_2 (Ind_All); LR P-value: 3.73E-09;
mr1925_2 (All); LR P-value: 1.45E-06
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.507; most accessible tissue: Zhenshan97 root, score: 94.343
vg0225007832 (J) chr02 25007832 T C 76.00% 0.00% T -> C
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06;
mr1686 (Ind_All); LR P-value: 5.22E-06;
mr1925 (All); LR P-value: 1.51E-09;
mr1925 (Ind_All); LR P-value: 2.03E-06;
mr1498_2 (All); LR P-value: 9.44E-07;
mr1593_2 (Ind_All); LR P-value: 1.51E-08;
mr1925_2 (All); LR P-value: 2.20E-06
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.503; most accessible tissue: Zhenshan97 root, score: 94.343
vg0225007849 (J) chr02 25007849 G A 75.90% 0.00% G -> A
mr1195 (All); LR P-value: 6.33E-10;
mr1593 (Ind_All); LR P-value: 9.10E-07;
mr1686 (Ind_All); LR P-value: 8.73E-06;
mr1925 (All); LR P-value: 7.64E-09;
mr1925 (Ind_All); LR P-value: 7.35E-06;
mr1593_2 (Ind_All); LR P-value: 7.04E-09;
mr1677_2 (All); LR P-value: 8.01E-06
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.998; most accessible tissue: Zhenshan97 root, score: 94.102
vg0225007850 (J) chr02 25007850 T C 75.90% 0.00% T -> C
mr1925 (All); LR P-value: 3.01E-09;
mr1925 (Ind_All); LR P-value: 3.56E-06;
mr1593_2 (Ind_All); LR P-value: 9.11E-09
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.988; most accessible tissue: Zhenshan97 root, score: 94.102
vg0225007858 (J) chr02 25007858 G T 99.20% 0.00% G -> T NA
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 80.713; most accessible tissue: Zhenshan97 root, score: 94.168
vg0225007867 (J) chr02 25007867 G C 98.50% 0.00% G -> C NA
LOC_Os02g41680.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.939; most accessible tissue: Zhenshan97 root, score: 94.212
vg0225008143 (J) chr02 25008143 C T 99.70% 0.00% C -> T NA
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 78.637; most accessible tissue: Zhenshan97 root, score: 93.720
vg0225008205 (J) chr02 25008205 G A 99.60% 0.00% G -> A NA
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 82.243; most accessible tissue: Zhenshan97 root, score: 93.618
vg0225008207 (J) chr02 25008207 C T 98.40% 0.00% C -> T NA
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.152; most accessible tissue: Zhenshan97 root, score: 93.538
vg0225008447 (J) chr02 25008447 G C 77.70% 0.00% G -> C NA
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.499; most accessible tissue: Zhenshan97 root, score: 92.181
vg0225008770 (J) chr02 25008770 C T 85.10% 0.00% C -> T
mr1069 (Ind_All); LR P-value: 2.62E-06;
mr1072 (Ind_All); LR P-value: 9.45E-06;
mr1074 (Ind_All); LR P-value: 1.04E-06;
mr1077 (Ind_All); LR P-value: 1.48E-06;
mr1791 (All); LR P-value: 2.31E-06;
mr1074_2 (Ind_All); LR P-value: 6.25E-06;
mr1095_2 (Ind_All); LMM P-value: 8.15E-06;
mr1098_2 (Ind_All); LMM P-value: 2.02E-06;
mr1099_2 (All); LMM P-value: 6.62E-06;
mr1099_2 (Ind_All); LMM P-value: 7.29E-08;
mr1124_2 (Ind_All); LMM P-value: 5.13E-06;
mr1150_2 (Ind_All); LMM P-value: 3.81E-08; LR P-value: 1.36E-07;
mr1222_2 (Ind_All); LMM P-value: 4.84E-06; LR P-value: 3.70E-06;
mr1247_2 (Ind_All); LMM P-value: 2.93E-06;
mr1861_2 (Ind_All); LR P-value: 2.01E-09
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.829; most accessible tissue: Zhenshan97 root, score: 96.480
vg0225008865 (J) chr02 25008865 C T 99.70% 0.00% C -> T NA
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.515; most accessible tissue: Zhenshan97 root, score: 97.162
vg0225008878 (J) chr02 25008878 C T 99.10% 0.00% C -> T NA
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 85.936; most accessible tissue: Zhenshan97 root, score: 97.184
vg0225008896 (J) chr02 25008896 C T 85.00% 0.00% C -> T
mr1069 (Ind_All); LR P-value: 1.68E-06;
mr1072 (Ind_All); LR P-value: 3.85E-06;
mr1074 (Ind_All); LR P-value: 4.79E-07;
mr1077 (Ind_All); LR P-value: 9.88E-07;
mr1592 (Ind_All); LR P-value: 7.98E-06;
mr1791 (All); LR P-value: 6.88E-06;
mr1072_2 (Ind_All); LR P-value: 8.27E-08;
mr1074_2 (Ind_All); LR P-value: 6.70E-06;
mr1075_2 (Ind_All); LR P-value: 2.14E-07;
mr1095_2 (Ind_All); LMM P-value: 9.72E-06;
mr1099_2 (Ind_All); LMM P-value: 4.13E-06;
mr1124_2 (Ind_All); LMM P-value: 2.61E-06; LR P-value: 3.01E-08;
mr1150_2 (Ind_All); LMM P-value: 6.48E-07; LR P-value: 1.70E-07;
mr1222_2 (Ind_All); LR P-value: 3.72E-06;
mr1861_2 (Ind_All); LR P-value: 7.30E-10
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.758; most accessible tissue: Zhenshan97 root, score: 97.867
vg0225008901 (J) chr02 25008901 C G 99.70% 0.00% C -> G NA
LOC_Os02g41680.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 86.817; most accessible tissue: Zhenshan97 root, score: 98.021
vg0225008927 (J) chr02 25008927 G A 77.70% 0.00% G -> A NA
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.973; most accessible tissue: Zhenshan97 root, score: 98.633
vg0225009017 (J) chr02 25009017 G T 88.80% 0.00% G -> T NA
LOC_Os02g41680.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.799; most accessible tissue: Zhenshan97 root, score: 99.541
vg0225009022 (J) chr02 25009022 A G 58.00% 0.00% G -> A NA
LOC_Os02g41680.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g41680.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.780; most accessible tissue: Minghui63 root, score: 99.554
vg0225009038 (J) chr02 25009038 GAGTATA T G 99.80% 0.00% GAGTATAT -> G NA
LOC_Os02g41680.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.191; most accessible tissue: Zhenshan97 root, score: 99.626
vg0225009077 (J) chr02 25009077 A G 99.70% 0.00% A -> G NA
LOC_Os02g41680.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.945; most accessible tissue: Minghui63 root, score: 99.703