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Search Results:

25 variations found. LOC_Os03g51580 (helix-loop-helix DNA-binding domain containing protein; expressed), ranging from 29,516,645 bp to 29,519,095 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
vg0329516659 (J) chr03 29516659 A C 14.80% 48.43% C -> A NA
LOC_Os03g51580.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 89.857; most accessible tissue: Zhenshan97 root, score: 97.621
vg0329516713 (J) chr03 29516713 C A 74.50% 0.00% C -> A,T
mr1542 (Ind_All); LR P-value: 4.70E-06;
mr1094_2 (Ind_All); LR P-value: 1.48E-06;
mr1542_2 (Ind_All); LR P-value: 4.75E-08;
mr1931_2 (Ind_All); LR P-value: 1.44E-06
LOC_Os03g51570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51580.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.413; most accessible tissue: Zhenshan97 root, score: 97.752
vg0329516725 (J) chr03 29516725 C T 77.30% 0.00% C -> T
mr1542 (Ind_All); LR P-value: 4.15E-06;
mr1094_2 (Ind_All); LR P-value: 2.33E-06;
mr1542_2 (Ind_All); LR P-value: 4.57E-08;
mr1931_2 (Ind_All); LR P-value: 1.02E-06
LOC_Os03g51570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.561; most accessible tissue: Zhenshan97 root, score: 97.788
vg0329516858 (J) chr03 29516858 AC ACC 99.70% 0.00% AC -> ACC,A NA
LOC_Os03g51580.1 Alt: ACC| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g51570.1 Alt: ACC| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: ACC| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51580.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.411; most accessible tissue: Zhenshan97 flower, score: 95.657
vg0329517075 (J) chr03 29517075 C A 60.90% 0.00% C -> A
mr1193 (All); LR P-value: 8.54E-08;
mr1291 (All); LR P-value: 2.27E-06;
mr1319 (All); LR P-value: 2.19E-06;
mr1322 (All); LR P-value: 7.26E-10;
mr1332 (All); LR P-value: 9.16E-12;
mr1336 (All); LR P-value: 3.84E-09;
mr1542 (Ind_All); LR P-value: 3.00E-06;
mr1557 (All); LR P-value: 5.10E-21;
mr1722 (All); LR P-value: 4.26E-10;
mr1542_2 (Ind_All); LR P-value: 8.92E-09;
mr1557_2 (All); LR P-value: 3.91E-18;
mr1931_2 (Ind_All); LR P-value: 3.75E-06
LOC_Os03g51580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.916; most accessible tissue: Zhenshan97 flower, score: 95.928
vg0329517137 (J) chr03 29517137 C CGCG 96.00% 0.00% C -> CGCG NA
LOC_Os03g51580.1 Alt: CGCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 88.492; most accessible tissue: Zhenshan97 flag leaf, score: 96.063
vg0329517160 (J) chr03 29517160 C T 65.00% 0.00% T -> C NA
LOC_Os03g51580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.088; most accessible tissue: Zhenshan97 flower, score: 96.344
vg0329517182 (J) chr03 29517182 CGCGGCG GCG C 94.80% 1.44% CGCGGCGGCG -> C,CGCGGCGG CGGCG NA
LOC_Os03g51580.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g51580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g51580.1 Alt: CGCGGCGGCGGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 92.131; most accessible tissue: Zhenshan97 flower, score: 96.516
vg0329517220 (J) chr03 29517220 C T 57.80% 6.71% C -> T NA
LOC_Os03g51580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g51580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.355; most accessible tissue: Zhenshan97 flower, score: 96.580
vg0329517272 (J) chr03 29517272 G C 80.10% 7.32% G -> C NA
LOC_Os03g51580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51580.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.729; most accessible tissue: Zhenshan97 flag leaf, score: 96.856
vg0329517510 (J) chr03 29517510 G A 60.90% 0.00% G -> A
mr1193 (All); LR P-value: 9.60E-08;
mr1291 (All); LR P-value: 1.85E-06;
mr1319 (All); LR P-value: 4.81E-06;
mr1322 (All); LR P-value: 7.01E-10;
mr1332 (All); LR P-value: 1.73E-11;
mr1336 (All); LR P-value: 4.11E-09;
mr1542 (All); LR P-value: 6.54E-35;
mr1542 (Ind_All); LR P-value: 6.20E-07;
mr1557 (All); LR P-value: 4.98E-21;
mr1722 (All); LR P-value: 2.20E-10;
mr1815 (All); LR P-value: 2.78E-06;
mr1542_2 (Ind_All); LR P-value: 1.77E-09;
mr1557_2 (All); LR P-value: 2.18E-18;
mr1931_2 (Ind_All); LR P-value: 4.21E-06
LOC_Os03g51580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.276; most accessible tissue: Zhenshan97 flag leaf, score: 97.515
vg0329517642 (J) chr03 29517642 A G 65.00% 0.00% G -> A NA
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51580.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.658; most accessible tissue: Zhenshan97 flag leaf, score: 97.390
vg0329517748 (J) chr03 29517748 G T 74.60% 0.00% G -> T,A
mr1542 (Ind_All); LR P-value: 6.21E-07;
mr1094_2 (Ind_All); LR P-value: 1.03E-06;
mr1542_2 (Ind_All); LR P-value: 2.17E-09
LOC_Os03g51580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g51580.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 93.895; most accessible tissue: Zhenshan97 flag leaf, score: 97.225
vg0329517871 (J) chr03 29517871 C A 89.30% 0.00% C -> A
mr1241 (Jap_All); LR P-value: 1.16E-11;
mr1301 (All); LR P-value: 2.60E-18;
mr1382 (Jap_All); LR P-value: 3.29E-06;
mr1518 (Jap_All); LR P-value: 1.67E-06;
mr1552 (Jap_All); LR P-value: 2.29E-09;
mr1554 (All); LR P-value: 4.78E-08;
mr1600 (Jap_All); LR P-value: 4.34E-06;
mr1602 (All); LR P-value: 1.96E-08;
mr1676 (Jap_All); LR P-value: 1.01E-06;
mr1696 (All); LMM P-value: 3.80E-07; LR P-value: 8.89E-11;
mr1696 (Jap_All); LR P-value: 2.79E-09;
mr1697 (All); LR P-value: 4.74E-06;
mr1916 (Jap_All); LR P-value: 3.21E-08;
mr1042_2 (All); LR P-value: 8.30E-20;
mr1083_2 (All); LMM P-value: 4.34E-06;
mr1096_2 (Jap_All); LR P-value: 2.51E-06;
mr1103_2 (All); LMM P-value: 2.50E-06;
mr1104_2 (All); LMM P-value: 1.16E-07;
mr1107_2 (All); LMM P-value: 5.05E-07;
mr1226_2 (All); LMM P-value: 3.70E-07;
mr1241_2 (All); LMM P-value: 7.23E-06;
mr1241_2 (Jap_All); LR P-value: 1.12E-12;
mr1388_2 (All); LR P-value: 5.40E-09;
mr1502_2 (All); LR P-value: 2.32E-07;
mr1554_2 (All); LR P-value: 1.05E-06;
mr1578_2 (Jap_All); LR P-value: 1.09E-07;
mr1680_2 (All); LR P-value: 6.31E-11;
mr1696_2 (All); LR P-value: 1.95E-07;
mr1742_2 (All); LR P-value: 2.17E-14;
mr1786_2 (All); LR P-value: 6.64E-07;
mr1860_2 (Jap_All); LR P-value: 1.28E-06;
mr1864_2 (All); LR P-value: 1.98E-13;
mr1871_2 (All); LR P-value: 9.92E-22;
mr1952_2 (Jap_All); LR P-value: 1.22E-08
LOC_Os03g51580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.723; most accessible tissue: Zhenshan97 flag leaf, score: 96.245
vg0329518121 (J) chr03 29518121 C T 74.50% 0.00% C -> T
mr1542 (Ind_All); LR P-value: 2.94E-06;
mr1094_2 (Ind_All); LR P-value: 4.43E-07;
mr1542_2 (Ind_All); LR P-value: 2.50E-08;
mr1931_2 (Ind_All); LR P-value: 3.56E-06
LOC_Os03g51570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.531; most accessible tissue: Zhenshan97 flower, score: 95.635
vg0329518282 (J) chr03 29518282 G A 99.90% 0.00% G -> A NA
LOC_Os03g51580.1 Alt: A| stop_retained_variant LOW(snpEff)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.878; most accessible tissue: Zhenshan97 flower, score: 94.459
vg0329518322 (J) chr03 29518322 T A 99.40% 0.00% T -> A NA
LOC_Os03g51580.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g51570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 86.794; most accessible tissue: Zhenshan97 flower, score: 93.594
vg0329518348 (J) chr03 29518348 C A 65.10% 0.00% A -> C NA
LOC_Os03g51580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.580; most accessible tissue: Zhenshan97 flower, score: 93.715
vg0329518565 (J) chr03 29518565 A AT 74.60% 0.00% A -> AT NA
LOC_Os03g51580.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.860; most accessible tissue: Zhenshan97 root, score: 95.113
vg0329518619 (J) chr03 29518619 T C 65.10% 0.00% C -> T NA
LOC_Os03g51580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.248; most accessible tissue: Zhenshan97 root, score: 95.817
vg0329518665 (J) chr03 29518665 A G 74.50% 0.00% A -> G
mr1542 (Ind_All); LR P-value: 1.44E-06;
mr1094_2 (Ind_All); LR P-value: 1.56E-06;
mr1542_2 (Ind_All); LR P-value: 1.52E-08;
mr1931_2 (Ind_All); LR P-value: 1.44E-06
LOC_Os03g51580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.906; most accessible tissue: Zhenshan97 root, score: 95.656
vg0329518676 (J) chr03 29518676 T A 65.00% 0.00% A -> T NA
LOC_Os03g51580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.587; most accessible tissue: Callus, score: 96.429
vg0329518859 (J) chr03 29518859 GC G 99.40% 0.00% GC -> G NA
LOC_Os03g51580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g51570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g51590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.550; most accessible tissue: Zhenshan97 root, score: 97.082
vg0329518993 (J) chr03 29518993 C G 60.90% 0.00% C -> G
mr1319 (All); LR P-value: 2.49E-06;
mr1322 (All); LR P-value: 1.01E-09;
mr1332 (All); LR P-value: 1.90E-11;
mr1542 (Ind_All); LR P-value: 2.07E-06;
mr1557 (All); LR P-value: 4.73E-21;
mr1722 (All); LR P-value: 7.26E-10;
mr1542_2 (Ind_All); LR P-value: 5.00E-09;
mr1557_2 (All); LR P-value: 5.23E-18;
mr1931_2 (Ind_All); LR P-value: 9.00E-06
LOC_Os03g51580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g51590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.332; most accessible tissue: Callus, score: 97.591
STR0329518566 (J) chr03 29518566 TT TTT 80.90% 0.00% TT -> TTT NA