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Search Results:

23 variations found. LOC_Os02g39090 (expressed protein), ranging from 23,609,299 bp to 23,610,643 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
vg0223609340 (J) chr02 23609340 C T 99.20% 0.00% C -> T NA
LOC_Os02g39090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.935; most accessible tissue: Minghui63 panicle, score: 90.408
vg0223609357 (J) chr02 23609357 G GGCCGTC TCTACGG CC 99.70% 0.00% G -> GGCCGTCTCT ACGGCC NA
LOC_Os02g39090.1 Alt: GGCCGTCTCTACGGCC| disruptive_inframe_insertion MODERATE(snpEff)
LOC_Os02g39080.1 Alt: GGCCGTCTCTACGGCC| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g39100.1 Alt: GGCCGTCTCTACGGCC| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.866; most accessible tissue: Minghui63 panicle, score: 90.408
vg0223609382 (J) chr02 23609382 CCGGCGG CGG C 60.80% 0.00% CCGGCGGCGG -> C NA
LOC_Os02g39090.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 78.805; most accessible tissue: Minghui63 panicle, score: 91.410
vg0223609393 (J) chr02 23609393 G A 92.60% 1.27% G -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.246; most accessible tissue: Minghui63 panicle, score: 91.410
vg0223609513 (J) chr02 23609513 G A 84.50% 0.15% G -> A
mr1408 (All); LR P-value: 2.35E-06;
mr1084_2 (All); LR P-value: 5.38E-08;
mr1205_2 (All); LR P-value: 4.39E-08;
mr1369_2 (All); LR P-value: 1.41E-06;
mr1418_2 (All); LR P-value: 8.57E-07;
mr1419_2 (All); LR P-value: 2.39E-06;
mr1420_2 (All); LR P-value: 5.54E-06;
mr1453_2 (All); LR P-value: 2.40E-07;
mr1488_2 (All); LR P-value: 1.27E-06;
mr1492_2 (All); LR P-value: 6.58E-06;
mr1706_2 (All); LR P-value: 3.82E-06;
mr1779_2 (All); LR P-value: 5.22E-06;
mr1863_2 (All); LR P-value: 5.38E-06;
mr1992_2 (All); LR P-value: 3.54E-06
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.517; most accessible tissue: Minghui63 panicle, score: 93.521
vg0223609565 (J) chr02 23609565 C G 84.20% 0.51% C -> G
mr1408 (All); LR P-value: 2.35E-06;
mr1084_2 (All); LR P-value: 5.38E-08;
mr1205_2 (All); LR P-value: 4.39E-08;
mr1369_2 (All); LR P-value: 1.41E-06;
mr1418_2 (All); LR P-value: 8.57E-07;
mr1419_2 (All); LR P-value: 2.39E-06;
mr1420_2 (All); LR P-value: 5.54E-06;
mr1453_2 (All); LR P-value: 2.40E-07;
mr1488_2 (All); LR P-value: 1.27E-06;
mr1492_2 (All); LR P-value: 6.58E-06;
mr1706_2 (All); LR P-value: 3.82E-06;
mr1779_2 (All); LR P-value: 5.22E-06;
mr1863_2 (All); LR P-value: 5.38E-06;
mr1992_2 (All); LR P-value: 3.54E-06
LOC_Os02g39090.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.431; most accessible tissue: Zhenshan97 panicle, score: 93.845
vg0223609600 (J) chr02 23609600 T G 78.60% 0.47% T -> G
mr1408 (All); LR P-value: 8.42E-07;
mr1042_2 (All); LR P-value: 5.04E-22;
mr1084_2 (All); LR P-value: 6.38E-08;
mr1097_2 (All); LR P-value: 1.44E-13;
mr1182_2 (Ind_All); LR P-value: 3.80E-06;
mr1205_2 (All); LR P-value: 7.72E-08;
mr1282_2 (Ind_All); LMM P-value: 6.24E-06; LR P-value: 6.24E-06;
mr1359_2 (Jap_All); LR P-value: 6.63E-06;
mr1369_2 (All); LR P-value: 1.58E-07;
mr1418_2 (All); LR P-value: 1.05E-07;
mr1419_2 (All); LR P-value: 3.97E-07;
mr1420_2 (All); LR P-value: 1.02E-06;
mr1453_2 (All); LR P-value: 2.18E-08;
mr1467_2 (All); LR P-value: 9.80E-06;
mr1479_2 (All); LR P-value: 2.44E-06;
mr1488_2 (All); LR P-value: 5.42E-08;
mr1492_2 (All); LR P-value: 4.11E-06;
mr1502_2 (All); LR P-value: 1.95E-07;
mr1506_2 (All); LR P-value: 2.83E-09;
mr1556_2 (All); LR P-value: 7.31E-06;
mr1604_2 (All); LR P-value: 5.95E-07;
mr1646_2 (All); LR P-value: 9.55E-10;
mr1742_2 (All); LR P-value: 1.02E-12;
mr1779_2 (All); LR P-value: 2.30E-06;
mr1794_2 (Jap_All); LR P-value: 1.99E-07;
mr1824_2 (All); LR P-value: 6.40E-07;
mr1851_2 (All); LR P-value: 4.32E-10;
mr1851_2 (Jap_All); LR P-value: 2.36E-06;
mr1864_2 (All); LR P-value: 4.56E-13;
mr1864_2 (Jap_All); LR P-value: 2.66E-09;
mr1871_2 (All); LR P-value: 6.21E-23;
mr1980_2 (Ind_All); LR P-value: 4.71E-06;
mr1992_2 (All); LR P-value: 6.71E-07
LOC_Os02g39090.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.226; most accessible tissue: Minghui63 panicle, score: 94.033
vg0223609660 (J) chr02 23609660 G T 98.10% 0.76% G -> T NA
LOC_Os02g39090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 82.882; most accessible tissue: Minghui63 panicle, score: 94.033
vg0223609693 (J) chr02 23609693 G A 96.50% 0.76% G -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.697; most accessible tissue: Minghui63 panicle, score: 94.794
vg0223609915 (J) chr02 23609915 C G 98.60% 0.55% C -> G NA
LOC_Os02g39090.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.908; most accessible tissue: Minghui63 panicle, score: 95.346
vg0223609951 (J) chr02 23609951 G A 97.80% 0.68% G -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.603; most accessible tissue: Minghui63 panicle, score: 95.218
vg0223609997 (J) chr02 23609997 C T 96.90% 0.49% C -> T NA
LOC_Os02g39090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.699; most accessible tissue: Minghui63 panicle, score: 95.645
vg0223610041 (J) chr02 23610041 G C 91.50% 1.16% G -> C NA
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g39090.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.006; most accessible tissue: Minghui63 panicle, score: 96.113
vg0223610197 (J) chr02 23610197 C G 95.40% 1.46% C -> G NA
LOC_Os02g39090.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.368; most accessible tissue: Minghui63 panicle, score: 95.529
vg0223610237 (J) chr02 23610237 C T 88.20% 2.03% C -> T NA
LOC_Os02g39090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.135; most accessible tissue: Minghui63 panicle, score: 95.083
vg0223610449 (J) chr02 23610449 A G 62.20% 1.18% G -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.331; most accessible tissue: Minghui63 panicle, score: 95.083
vg0223610503 (J) chr02 23610503 C T 95.30% 2.41% C -> T NA
LOC_Os02g39090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.284; most accessible tissue: Minghui63 panicle, score: 95.346
vg0223610506 (J) chr02 23610506 G A 90.30% 1.76% G -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.310; most accessible tissue: Minghui63 panicle, score: 95.408
vg0223610511 (J) chr02 23610511 C T 88.60% 0.72% C -> T NA
LOC_Os02g39090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39090.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.046; most accessible tissue: Minghui63 panicle, score: 95.282
vg0223610526 (J) chr02 23610526 C T 99.70% 0.00% C -> T NA
LOC_Os02g39090.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g39080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g39100.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.634; most accessible tissue: Minghui63 panicle, score: 95.529
vg0223610597 (J) chr02 23610597 TGCGGCG GCAGCGG CA T 97.80% 0.00% TGCGGCGGCA GCGGCA -> T NA
LOC_Os02g39090.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 86.302; most accessible tissue: Minghui63 panicle, score: 94.942
vg0223610623 (J) chr02 23610623 C A 99.20% 0.00% C -> A NA
LOC_Os02g39090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.100; most accessible tissue: Minghui63 panicle, score: 95.151
STR0223609383 (J) chr02 23609383 CGGCGGC GGCGGCG CGGCG 54.00% 0.00% CGGCGGCGGC GGCG -> CGGCG NA