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Search Results:

33 variations found. Os01g0838900/LOC_Os01g62160 (trp repressor%2Freplication initiator; putative; expressed), ranging from 35,983,818 bp to 35,987,592 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os01g62160 trp repressor/replication initiator, putative, expressed; RAP ID: Os01g0838900; MSU ID: LOC_Os01g62160

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
vg0135983852 (J) chr01 35983852 T A 99.70% 0.00% T -> A NA
LOC_Os01g62160.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.226; most accessible tissue: Zhenshan97 flower, score: 84.217
vg0135984016 (J) chr01 35984016 G T 98.20% 0.00% G -> T NA
LOC_Os01g62160.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.332; most accessible tissue: Zhenshan97 flower, score: 85.482
vg0135984043 (J) chr01 35984043 G A 97.90% 0.00% G -> A NA
LOC_Os01g62160.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.260; most accessible tissue: Zhenshan97 flower, score: 85.807
vg0135984153 (J) chr01 35984153 T A 52.10% 0.02% T -> A
mr1078 (Ind_All); LR P-value: 1.45E-09;
mr1096 (Ind_All); LR P-value: 7.16E-07;
mr1133 (Ind_All); LR P-value: 1.66E-08;
mr1887 (Ind_All); LR P-value: 2.60E-08;
mr1133_2 (Ind_All); LR P-value: 1.14E-07;
mr1870_2 (Ind_All); LR P-value: 8.26E-07
LOC_Os01g62160.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 67.233; most accessible tissue: Zhenshan97 flower, score: 83.392
vg0135984170 (J) chr01 35984170 A T 97.90% 0.00% A -> T NA
LOC_Os01g62160.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 67.671; most accessible tissue: Zhenshan97 flower, score: 83.392
vg0135984305 (J) chr01 35984305 A G 87.90% 0.00% A -> G
mr1887 (Ind_All); LR P-value: 5.75E-06;
mr1200_2 (Ind_All); LR P-value: 1.64E-07
LOC_Os01g62160.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.965; most accessible tissue: Zhenshan97 flower, score: 85.963
vg0135984355 (J) chr01 35984355 A G 63.90% 0.02% G -> A
mr1125 (All); LR P-value: 5.78E-48;
mr1251 (All); LR P-value: 5.55E-25;
mr1253 (All); LR P-value: 2.28E-17;
mr1411 (All); LR P-value: 4.93E-25;
mr1435 (All); LR P-value: 3.73E-36;
mr1541 (All); LR P-value: 6.01E-20;
mr1599 (All); LR P-value: 1.63E-49;
mr1125_2 (All); LR P-value: 1.53E-63;
mr1223_2 (All); LR P-value: 3.26E-36;
mr1350_2 (All); LR P-value: 1.79E-24;
mr1968_2 (All); LR P-value: 9.49E-21;
mr1986_2 (All); LR P-value: 3.42E-12
LOC_Os01g62160.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 73.095; most accessible tissue: Zhenshan97 flower, score: 86.268
vg0135984456 (J) chr01 35984456 G A 97.70% 0.00% G -> A NA
LOC_Os01g62160.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.600; most accessible tissue: Zhenshan97 flower, score: 89.944
vg0135984669 (J) chr01 35984669 C G 52.40% 0.08% C -> G
mr1068 (Ind_All); LR P-value: 2.70E-08;
mr1078 (Ind_All); LR P-value: 8.22E-11;
mr1096 (Ind_All); LR P-value: 1.32E-07;
mr1121 (Ind_All); LR P-value: 3.84E-06;
mr1133 (Ind_All); LR P-value: 8.56E-09;
mr1887 (Ind_All); LR P-value: 4.55E-09;
mr1078_2 (Ind_All); LR P-value: 1.58E-08;
mr1133_2 (Ind_All); LR P-value: 9.86E-08;
mr1870_2 (Ind_All); LR P-value: 1.11E-06
LOC_Os01g62160.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g62160.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.606; most accessible tissue: Zhenshan97 flower, score: 92.407
vg0135984741 (J) chr01 35984741 G T 66.50% 0.15% T -> G NA
LOC_Os01g62160.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g62160.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.624; most accessible tissue: Zhenshan97 flower, score: 92.618
vg0135984841 (J) chr01 35984841 T A 97.40% 0.00% T -> A NA
LOC_Os01g62160.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.298; most accessible tissue: Zhenshan97 flower, score: 91.965
vg0135984842 (J) chr01 35984842 C T 87.60% 0.00% C -> T
mr1078 (Ind_All); LR P-value: 3.18E-07;
mr1131 (Ind_All); LR P-value: 9.50E-06;
mr1213 (Ind_All); LR P-value: 3.43E-07;
mr1887 (Ind_All); LR P-value: 2.62E-06;
mr1200_2 (Ind_All); LR P-value: 9.66E-08;
mr1364_2 (Ind_All); LR P-value: 6.64E-06
LOC_Os01g62160.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.295; most accessible tissue: Zhenshan97 flower, score: 91.937
vg0135984885 (J) chr01 35984885 G A 52.40% 0.00% G -> A
mr1068 (Ind_All); LR P-value: 2.32E-08;
mr1078 (Ind_All); LR P-value: 8.02E-11;
mr1096 (Ind_All); LR P-value: 1.05E-07;
mr1121 (Ind_All); LR P-value: 3.25E-06;
mr1133 (Ind_All); LR P-value: 6.66E-09;
mr1887 (Ind_All); LR P-value: 4.56E-09;
mr1078_2 (Ind_All); LR P-value: 1.38E-08;
mr1133_2 (Ind_All); LR P-value: 7.68E-08;
mr1364_2 (Ind_All); LR P-value: 9.55E-06;
mr1870_2 (Ind_All); LR P-value: 1.08E-06
LOC_Os01g62160.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.744; most accessible tissue: Zhenshan97 flower, score: 90.950
vg0135985103 (J) chr01 35985103 C A 66.50% 0.08% A -> C NA
LOC_Os01g62160.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g62160.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.512; most accessible tissue: Zhenshan97 flower, score: 86.194
vg0135985338 (J) chr01 35985338 T A 97.40% 0.00% T -> A NA
LOC_Os01g62160.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 54.986; most accessible tissue: Zhenshan97 flower, score: 70.434
vg0135985469 (J) chr01 35985469 G A 87.60% 0.00% G -> A
mr1078 (Ind_All); LR P-value: 3.18E-07;
mr1131 (Ind_All); LR P-value: 9.50E-06;
mr1213 (Ind_All); LR P-value: 3.43E-07;
mr1887 (Ind_All); LR P-value: 2.62E-06;
mr1200_2 (Ind_All); LR P-value: 9.66E-08;
mr1364_2 (Ind_All); LR P-value: 6.64E-06
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 44.229; most accessible tissue: Callus, score: 65.033
vg0135985488 (J) chr01 35985488 G A 87.70% 0.00% G -> A
mr1078 (Ind_All); LR P-value: 3.18E-07;
mr1131 (Ind_All); LR P-value: 9.50E-06;
mr1213 (Ind_All); LR P-value: 3.43E-07;
mr1887 (Ind_All); LR P-value: 2.62E-06;
mr1200_2 (Ind_All); LR P-value: 9.66E-08;
mr1364_2 (Ind_All); LR P-value: 6.64E-06
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 42.652; most accessible tissue: Callus, score: 65.033
vg0135985532 (J) chr01 35985532 G A 99.30% 0.00% G -> A NA
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 40.876; most accessible tissue: Callus, score: 65.033
vg0135985571 (J) chr01 35985571 T C 61.70% 0.00% C -> T
mr1260 (All); LR P-value: 4.06E-08;
mr1714 (All); LR P-value: 3.66E-10;
mr1746_2 (Ind_All); LR P-value: 4.89E-06
LOC_Os01g62160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 38.163; most accessible tissue: Callus, score: 65.033
vg0135985611 (J) chr01 35985611 C T 52.30% 0.00% C -> T
mr1078 (Ind_All); LR P-value: 2.48E-10;
mr1096 (Ind_All); LR P-value: 2.78E-07;
mr1133 (Ind_All); LR P-value: 3.17E-09;
mr1155 (All); LR P-value: 3.17E-21;
mr1887 (Ind_All); LR P-value: 2.04E-09;
mr1078_2 (Ind_All); LR P-value: 1.00E-07;
mr1133_2 (Ind_All); LR P-value: 6.06E-08;
mr1428_2 (Ind_All); LR P-value: 7.29E-06;
mr1870_2 (Ind_All); LR P-value: 7.89E-07
LOC_Os01g62160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 33.260; most accessible tissue: Minghui63 root, score: 41.911
vg0135985648 (J) chr01 35985648 G A 66.50% 0.11% A -> G NA
LOC_Os01g62160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 34.441; most accessible tissue: Zhenshan97 flag leaf, score: 44.637
vg0135985694 (J) chr01 35985694 A T 66.70% 0.00% T -> A NA
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 34.247; most accessible tissue: Callus, score: 57.796
vg0135986031 (J) chr01 35986031 G C 98.20% 0.00% G -> C NA
LOC_Os01g62160.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.036; most accessible tissue: Callus, score: 69.060
vg0135986131 (J) chr01 35986131 G A 66.70% 0.00% A -> G NA
LOC_Os01g62160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 35.956; most accessible tissue: Callus, score: 51.778
vg0135986294 (J) chr01 35986294 A G 66.50% 0.28% G -> A NA
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 43.497; most accessible tissue: Callus, score: 76.692
vg0135986444 (J) chr01 35986444 TA T 52.80% 0.00% TA -> T,TAA NA
LOC_Os01g62160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g62160.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 45.112; most accessible tissue: Callus, score: 74.913
vg0135986454 (J) chr01 35986454 T A 97.40% 0.00% T -> A NA
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 44.513; most accessible tissue: Callus, score: 74.913
vg0135986518 (J) chr01 35986518 A T 99.80% 0.00% A -> T NA
LOC_Os01g62160.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 47.906; most accessible tissue: Callus, score: 74.913
vg0135987209 (J) chr01 35987209 A G 87.60% 0.00% A -> G
mr1078 (Ind_All); LR P-value: 6.04E-07;
mr1133 (Ind_All); LR P-value: 3.54E-07;
mr1213 (Ind_All); LR P-value: 3.70E-07;
mr1887 (Ind_All); LR P-value: 4.06E-06;
mr1200_2 (Ind_All); LR P-value: 7.42E-08
LOC_Os01g62160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.478; most accessible tissue: Zhenshan97 panicle, score: 91.845
vg0135987281 (J) chr01 35987281 A G 66.70% 0.00% G -> A NA
LOC_Os01g62160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.925; most accessible tissue: Zhenshan97 flag leaf, score: 90.522
vg0135987302 (J) chr01 35987302 T G 97.40% 0.00% T -> G NA
LOC_Os01g62160.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.543; most accessible tissue: Zhenshan97 flower, score: 91.257
vg0135987413 (J) chr01 35987413 G T 97.40% 0.00% G -> T NA
LOC_Os01g62160.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.291; most accessible tissue: Zhenshan97 flower, score: 93.734
vg0135987564 (J) chr01 35987564 GA G 60.50% 0.00% G -> GA,GAA NA
LOC_Os01g62160.1 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g62160.1 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.017; most accessible tissue: Callus, score: 95.262