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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Variations Type:

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Search Results:

31 variations found. LOC_Os02g46080 (protein phosphatase 2C; putative; expressed), ranging from 28,078,821 bp to 28,081,773 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
vg0228078827 (J) chr02 28078827 G A 99.90% 0.00% G -> A NA
LOC_Os02g46080.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g46070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g46080.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.046; most accessible tissue: Minghui63 root, score: 72.134
vg0228078837 (J) chr02 28078837 G A 59.90% 0.15% A -> G NA
LOC_Os02g46080.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 57.085; most accessible tissue: Minghui63 root, score: 72.134
vg0228078870 (J) chr02 28078870 A G 57.90% 0.13% G -> A NA
LOC_Os02g46080.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 55.989; most accessible tissue: Zhenshan97 flower, score: 70.106
vg0228078907 (J) chr02 28078907 T C 99.50% 0.00% T -> C NA
LOC_Os02g46080.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 56.495; most accessible tissue: Zhenshan97 flower, score: 71.071
vg0228078910 (J) chr02 28078910 A AT 99.40% 0.00% A -> AT NA
LOC_Os02g46080.2 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46070.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.335; most accessible tissue: Zhenshan97 flower, score: 71.071
vg0228078985 (J) chr02 28078985 A T 99.40% 0.00% A -> T NA
LOC_Os02g46080.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g46070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g46080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 60.759; most accessible tissue: Callus, score: 81.712
vg0228079118 (J) chr02 28079118 C T 99.90% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g46070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.997; most accessible tissue: Minghui63 flower, score: 71.756
vg0228079438 (J) chr02 28079438 G A 58.50% 0.34% A -> G
mr1342 (All); LR P-value: 1.74E-08;
mr1629 (All); LR P-value: 1.99E-76;
mr1322_2 (All); LR P-value: 2.22E-08
LOC_Os02g46070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 52.018; most accessible tissue: Callus, score: 82.378
vg0228079496 (J) chr02 28079496 C T 59.90% 0.06% T -> C
mr1629 (All); LMM P-value: 4.28E-06; LR P-value: 1.82E-81;
mr1905 (All); LR P-value: 1.02E-09;
mr1629_2 (All); LMM P-value: 7.45E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g46070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.230; most accessible tissue: Callus, score: 82.378
vg0228079723 (J) chr02 28079723 C T 98.90% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46080.2 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 54.991; most accessible tissue: Callus, score: 79.824
vg0228079799 (J) chr02 28079799 TA T 60.00% 0.00% T -> TA NA
LOC_Os02g46070.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.087; most accessible tissue: Callus, score: 79.824
vg0228079862 (J) chr02 28079862 A G 92.60% 0.23% A -> G NA
LOC_Os02g46070.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 50.182; most accessible tissue: Callus, score: 58.395
vg0228079966 (J) chr02 28079966 C T 58.80% 0.00% T -> C NA
LOC_Os02g46070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 46.333; most accessible tissue: Callus, score: 81.178
vg0228079970 (J) chr02 28079970 C T 99.00% 0.00% C -> T NA
LOC_Os02g46070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g46080.1 Alt: T| intron_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 47.179; most accessible tissue: Callus, score: 81.178
vg0228080027 (J) chr02 28080027 A G 50.50% 0.00% G -> A
mr1063 (All); LR P-value: 9.26E-52;
mr1078 (All); LR P-value: 5.36E-50;
mr1090 (All); LR P-value: 3.44E-54;
mr1121 (All); LR P-value: 1.07E-48;
mr1125 (All); LR P-value: 4.60E-48;
mr1164 (All); LR P-value: 6.56E-16;
mr1200 (All); LR P-value: 1.45E-41;
mr1208 (All); LR P-value: 1.53E-31;
mr1221 (All); LR P-value: 7.28E-28;
mr1237 (All); LR P-value: 4.39E-29;
mr1244 (All); LR P-value: 2.87E-20;
mr1426 (All); LR P-value: 9.60E-28;
mr1717 (All); LR P-value: 8.31E-07;
mr1721 (All); LR P-value: 1.06E-41;
mr1916 (All); LR P-value: 4.45E-15;
mr1063_2 (All); LR P-value: 4.83E-53;
mr1068_2 (All); LR P-value: 7.78E-63;
mr1078_2 (All); LR P-value: 1.50E-62;
mr1110_2 (All); LR P-value: 8.40E-38;
mr1125_2 (All); LR P-value: 4.41E-62;
mr1144_2 (All); LR P-value: 2.03E-50;
mr1164_2 (All); LR P-value: 6.70E-23;
mr1228_2 (All); LR P-value: 2.66E-10;
mr1244_2 (All); LR P-value: 9.22E-26;
mr1260_2 (All); LR P-value: 1.77E-17;
mr1514_2 (All); LR P-value: 9.57E-13;
mr1580_2 (All); LR P-value: 4.23E-31;
mr1666_2 (All); LR P-value: 8.80E-12;
mr1734_2 (All); LR P-value: 1.49E-10;
mr1825_2 (All); LR P-value: 1.42E-29;
mr1943_2 (All); LR P-value: 1.23E-24
LOC_Os02g46070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 45.891; most accessible tissue: Callus, score: 81.178
vg0228080043 (J) chr02 28080043 C T 98.90% 0.00% C -> T NA
LOC_Os02g46070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g46080.1 Alt: T| intron_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 44.852; most accessible tissue: Callus, score: 81.178
vg0228080390 (J) chr02 28080390 C T 99.40% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46080.2 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 51.954; most accessible tissue: Minghui63 flower, score: 67.065
vg0228080520 (J) chr02 28080520 C T 92.60% 0.23% C -> T NA
LOC_Os02g46080.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g46080.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g46080.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g46080.2 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 62.471; most accessible tissue: Callus, score: 89.557
vg0228080556 (J) chr02 28080556 T G 58.60% 0.00% G -> T
mr1342 (All); LR P-value: 9.08E-09;
mr1629 (All); LR P-value: 1.88E-77
LOC_Os02g46080.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 65.346; most accessible tissue: Callus, score: 89.557
vg0228080650 (J) chr02 28080650 A G 50.40% 0.38% G -> A
mr1063 (All); LR P-value: 1.58E-51;
mr1078 (All); LR P-value: 4.59E-50;
mr1090 (All); LR P-value: 6.05E-54;
mr1121 (All); LR P-value: 5.94E-49;
mr1125 (All); LR P-value: 3.13E-48;
mr1164 (All); LR P-value: 1.43E-15;
mr1200 (All); LR P-value: 4.35E-42;
mr1208 (All); LR P-value: 1.55E-31;
mr1221 (All); LR P-value: 6.75E-28;
mr1237 (All); LR P-value: 1.09E-29;
mr1244 (All); LR P-value: 4.00E-20;
mr1426 (All); LR P-value: 8.29E-28;
mr1717 (All); LR P-value: 7.42E-07;
mr1721 (All); LR P-value: 1.55E-42;
mr1883 (All); LR P-value: 4.99E-11;
mr1916 (All); LR P-value: 2.32E-15;
mr1063_2 (All); LR P-value: 5.91E-53;
mr1078_2 (All); LR P-value: 3.50E-62;
mr1110_2 (All); LR P-value: 1.56E-37;
mr1125_2 (All); LR P-value: 8.12E-62;
mr1164_2 (All); LR P-value: 4.10E-23;
mr1244_2 (All); LR P-value: 7.43E-26;
mr1260_2 (All); LR P-value: 1.73E-17;
mr1514_2 (All); LR P-value: 7.91E-13;
mr1580_2 (All); LR P-value: 7.11E-31;
mr1734_2 (All); LR P-value: 7.33E-11;
mr1825_2 (All); LR P-value: 2.13E-29
LOC_Os02g46080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 67.773; most accessible tissue: Callus, score: 83.710
vg0228080817 (J) chr02 28080817 C T 99.80% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| intron_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.031; most accessible tissue: Callus, score: 93.090
vg0228080951 (J) chr02 28080951 T C 99.10% 0.00% T -> C NA
LOC_Os02g46080.1 Alt: C| intron_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.453; most accessible tissue: Callus, score: 89.578
vg0228081078 (J) chr02 28081078 T A 99.40% 0.00% T -> A NA
LOC_Os02g46080.1 Alt: A| intron_variant MODIFIER(snpEff)
LOC_Os02g46080.2 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 82.004; most accessible tissue: Minghui63 flower, score: 90.712
vg0228081102 (J) chr02 28081102 G A 92.60% 0.23% G -> A NA
LOC_Os02g46080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 82.428; most accessible tissue: Minghui63 flower, score: 91.539
vg0228081106 (J) chr02 28081106 A C 58.70% 0.00% C -> A NA
LOC_Os02g46080.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.561; most accessible tissue: Minghui63 flower, score: 91.539
vg0228081260 (J) chr02 28081260 C T 99.20% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46080.2 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 89.306; most accessible tissue: Minghui63 flower, score: 94.203
vg0228081428 (J) chr02 28081428 C T 99.00% 0.00% C -> T NA
LOC_Os02g46080.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46080.2 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g46090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.963; most accessible tissue: Minghui63 flower, score: 95.545
vg0228081529 (J) chr02 28081529 T C 58.40% 0.00% C -> T
mr1342 (All); LR P-value: 1.38E-08;
mr1629 (All); LR P-value: 3.27E-75
LOC_Os02g46080.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 92.094; most accessible tissue: Minghui63 flower, score: 95.773
vg0228081584 (J) chr02 28081584 C T 50.40% 0.08% T -> C
mr1063 (All); LR P-value: 8.60E-51;
mr1090 (All); LR P-value: 1.70E-52;
mr1121 (All); LR P-value: 2.45E-47;
mr1151 (All); LR P-value: 2.84E-09;
mr1164 (All); LR P-value: 5.77E-16;
mr1208 (All); LR P-value: 1.14E-30;
mr1717 (All); LR P-value: 1.03E-06;
mr1721 (All); LR P-value: 1.75E-41;
mr1914 (All); LR P-value: 3.55E-12;
mr1916 (All); LR P-value: 3.94E-15;
mr1063_2 (All); LR P-value: 9.43E-52;
mr1164_2 (All); LR P-value: 6.48E-23;
mr1244_2 (All); LR P-value: 2.69E-25;
mr1260_2 (All); LR P-value: 3.80E-17;
mr1580_2 (All); LR P-value: 3.67E-30;
mr1666_2 (All); LR P-value: 4.30E-12;
mr1825_2 (All); LR P-value: 9.94E-29
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 93.989; most accessible tissue: Zhenshan97 flower, score: 96.948
vg0228081723 (J) chr02 28081723 TGG TGGGG 19.40% 38.87% TGG -> TG,TGGGG,T GGG,TGGGGG ,TGGGGGG,T NA
LOC_Os02g46080.1 Alt: TGGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TGGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: TGGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: TGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: TGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: TG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: TG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: TGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: TGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.1 Alt: TGGGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: TGGGGGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: TGGGGGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.686; most accessible tissue: Zhenshan97 flower, score: 98.894
vg0228081725 (J) chr02 28081725 G A 59.30% 13.39% G -> A NA
LOC_Os02g46080.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46080.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g46090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 97.842; most accessible tissue: Zhenshan97 flower, score: 98.963