Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) : Downstream (kb, optional, must <= 10 kb) :
Variations Type:

Optional: (The selected data will be displayed in the result page.)
 Show Gene Expression Atlas  Show Chromatin Accessibility Map
 Show Non-coding variation Scores

Search Results:

21 variations found. Os03g0580200/LOC_Os03g38350 (expressed protein), ranging from 21,275,398 bp to 21,276,198 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os03g38350 expressed protein; RAP ID: Os03g0580200; MSU ID: LOC_Os03g38350

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
vg0321275404 (J) chr03 21275404 G A 50.90% 0.00% G -> A
mr1045 (All); LR P-value: 9.23E-08;
mr1669 (All); LR P-value: 1.39E-07;
mr1785 (All); LR P-value: 9.98E-07;
mr1804 (All); LR P-value: 1.21E-07;
mr1588_2 (Ind_All); LR P-value: 9.39E-07;
mr1750_2 (All); LMM P-value: 3.66E-06;
mr1750_2 (Ind_All); LMM P-value: 5.58E-07
LOC_Os03g38350.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 80.377; most accessible tissue: Zhenshan97 flag leaf, score: 91.379
vg0321275479 (J) chr03 21275479 A T 64.30% 0.00% T -> A
mr1670 (All); LR P-value: 1.59E-36;
mr1713 (All); LR P-value: 5.84E-11;
mr1718 (All); LMM P-value: 1.21E-13; LR P-value: 2.80E-95;
mr1750 (All); LMM P-value: 1.96E-20; LR P-value: 2.47E-169;
mr1842 (All); LR P-value: 2.13E-17;
mr1987 (All); LMM P-value: 8.55E-06; LR P-value: 4.76E-116;
mr1004_2 (All); LR P-value: 1.80E-07;
mr1708_2 (All); LR P-value: 5.54E-23;
mr1713_2 (All); LR P-value: 1.16E-12;
mr1718_2 (All); LMM P-value: 8.83E-17; LR P-value: 2.83E-140;
mr1750_2 (All); LMM P-value: 5.13E-33; LR P-value: 1.05E-240;
mr1842_2 (All); LR P-value: 2.36E-16;
mr1893_2 (All); LR P-value: 9.86E-11;
mr1933_2 (All); LR P-value: 5.15E-23;
mr1987_2 (All); LMM P-value: 1.01E-06; LR P-value: 2.69E-158
LOC_Os03g38350.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.588; most accessible tissue: Minghui63 flag leaf, score: 92.071
vg0321275503 (J) chr03 21275503 T TATAGTA 64.30% 0.00% TATAGTA -> T NA
LOC_Os03g38350.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.948; most accessible tissue: Minghui63 flag leaf, score: 92.416
vg0321275523 (J) chr03 21275523 G A 94.90% 0.00% G -> A
mr1757_2 (All); LR P-value: 3.43E-29;
mr1762_2 (All); LR P-value: 3.01E-06
LOC_Os03g38350.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.534; most accessible tissue: Zhenshan97 flag leaf, score: 93.368
vg0321275539 (J) chr03 21275539 GA G 92.80% 0.00% GA -> G NA
LOC_Os03g38350.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.302; most accessible tissue: Zhenshan97 flag leaf, score: 92.719
vg0321275551 (J) chr03 21275551 A ATC 64.30% 0.02% ATC -> A NA
LOC_Os03g38350.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 84.875; most accessible tissue: Zhenshan97 flag leaf, score: 93.632
vg0321275564 (J) chr03 21275564 CTCGA C 64.30% 0.02% C -> CTCGA NA
LOC_Os03g38350.1 Alt: CTCGA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: CTCGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 85.734; most accessible tissue: Zhenshan97 flag leaf, score: 93.992
vg0321275600 (J) chr03 21275600 G C 64.30% 0.02% C -> G
mr1670 (All); LR P-value: 2.98E-37;
mr1718 (All); LMM P-value: 2.25E-13; LR P-value: 9.24E-95;
mr1750 (All); LMM P-value: 8.06E-22; LR P-value: 9.29E-171;
mr1842 (All); LR P-value: 4.01E-17;
mr1873 (All); LR P-value: 1.04E-39;
mr1987 (All); LMM P-value: 1.85E-06; LR P-value: 2.58E-117;
mr1342_2 (All); LR P-value: 1.76E-16;
mr1595_2 (All); LR P-value: 3.68E-10;
mr1689_2 (All); LR P-value: 3.86E-36;
mr1713_2 (All); LR P-value: 1.38E-12;
mr1718_2 (All); LMM P-value: 1.10E-17; LR P-value: 1.72E-141;
mr1750_2 (All); LMM P-value: 5.29E-30; LR P-value: 5.60E-240;
mr1842_2 (All); LR P-value: 1.37E-16;
mr1893_2 (All); LR P-value: 7.80E-11;
mr1933_2 (All); LR P-value: 6.12E-23;
mr1987_2 (All); LMM P-value: 6.21E-06; LR P-value: 5.36E-158
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g38350.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.460; most accessible tissue: Zhenshan97 flag leaf, score: 94.613
vg0321275608 (J) chr03 21275608 T G 64.30% 0.00% G -> T
mr1670 (All); LR P-value: 2.98E-37;
mr1718 (All); LMM P-value: 2.25E-13; LR P-value: 9.24E-95;
mr1750 (All); LMM P-value: 8.06E-22; LR P-value: 9.29E-171;
mr1842 (All); LR P-value: 4.01E-17;
mr1873 (All); LR P-value: 1.04E-39;
mr1987 (All); LMM P-value: 1.85E-06; LR P-value: 2.58E-117;
mr1342_2 (All); LR P-value: 1.76E-16;
mr1595_2 (All); LR P-value: 3.68E-10;
mr1689_2 (All); LR P-value: 3.86E-36;
mr1713_2 (All); LR P-value: 1.38E-12;
mr1718_2 (All); LMM P-value: 1.10E-17; LR P-value: 1.72E-141;
mr1750_2 (All); LMM P-value: 5.29E-30; LR P-value: 5.60E-240;
mr1842_2 (All); LR P-value: 1.37E-16;
mr1893_2 (All); LR P-value: 7.80E-11;
mr1933_2 (All); LR P-value: 6.12E-23;
mr1987_2 (All); LMM P-value: 6.21E-06; LR P-value: 5.36E-158
LOC_Os03g38350.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.056; most accessible tissue: Zhenshan97 flag leaf, score: 94.817
vg0321275622 (J) chr03 21275622 G A 64.30% 0.00% A -> G
mr1670 (All); LR P-value: 1.78E-36;
mr1713 (All); LR P-value: 5.88E-11;
mr1718 (All); LMM P-value: 4.52E-15; LR P-value: 2.02E-96;
mr1750 (All); LMM P-value: 3.78E-24; LR P-value: 1.04E-173;
mr1842 (All); LR P-value: 2.73E-17;
mr1873 (All); LR P-value: 3.18E-39;
mr1889 (All); LR P-value: 1.12E-52;
mr1987 (All); LMM P-value: 7.93E-07; LR P-value: 1.08E-118;
mr1342_2 (All); LR P-value: 4.88E-16;
mr1595_2 (All); LR P-value: 5.98E-10;
mr1689_2 (All); LR P-value: 2.40E-36;
mr1713_2 (All); LR P-value: 6.26E-13;
mr1718_2 (All); LMM P-value: 2.34E-20; LR P-value: 2.60E-144;
mr1750_2 (All); LMM P-value: 4.31E-39; LR P-value: 2.81E-247;
mr1842_2 (All); LR P-value: 1.21E-16;
mr1893_2 (All); LR P-value: 8.63E-11;
mr1933_2 (All); LR P-value: 4.76E-23;
mr1987_2 (All); LMM P-value: 1.74E-07; LR P-value: 2.47E-161
LOC_Os03g38350.1 Alt: G| stop_lost HIGH(snpEff)/stop_lost(CooVar)
The average chromatin accessibility score: 86.462; most accessible tissue: Zhenshan97 flag leaf, score: 94.956
vg0321275673 (J) chr03 21275673 G A 92.80% 0.00% G -> A
Spikelet_length (Ind_All); LR P-value: 1.86E-07;
mr1038 (All); LR P-value: 4.18E-06;
mr1038 (Ind_All); LR P-value: 2.34E-06;
mr1389 (All); LR P-value: 6.56E-07;
mr1389 (Ind_All); LR P-value: 1.44E-06;
mr1038_2 (All); LR P-value: 1.21E-06
LOC_Os03g38350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.780; most accessible tissue: Zhenshan97 flag leaf, score: 95.681
vg0321275737 (J) chr03 21275737 G A 92.80% 0.00% G -> A
Spikelet_length (Ind_All); LR P-value: 8.56E-07;
mr1038 (All); LR P-value: 4.17E-06;
mr1038 (Ind_All); LR P-value: 2.14E-06;
mr1389 (All); LR P-value: 1.04E-06;
mr1389 (Ind_All); LR P-value: 2.06E-06;
mr1038_2 (All); LR P-value: 2.15E-06
LOC_Os03g38350.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.894; most accessible tissue: Zhenshan97 flag leaf, score: 95.949
vg0321275790 (J) chr03 21275790 G A 98.90% 0.00% G -> A,C NA
LOC_Os03g38350.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g38350.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.176; most accessible tissue: Zhenshan97 flag leaf, score: 96.336
vg0321275807 (J) chr03 21275807 T G 64.30% 0.00% G -> T
mr1014 (All); LR P-value: 1.55E-68;
mr1670 (All); LR P-value: 1.48E-34;
mr1713 (All); LR P-value: 3.30E-11;
mr1718 (All); LMM P-value: 8.59E-14; LR P-value: 4.33E-96;
mr1750 (All); LMM P-value: 8.64E-21; LR P-value: 3.39E-168;
mr1842 (All); LR P-value: 3.49E-17;
mr1987 (All); LMM P-value: 3.04E-06; LR P-value: 6.64E-116;
mr1040_2 (All); LR P-value: 1.66E-15;
mr1362_2 (All); LR P-value: 4.92E-20;
mr1537_2 (All); LR P-value: 9.35E-11;
mr1541_2 (All); LR P-value: 3.27E-36;
mr1689_2 (All); LR P-value: 1.36E-36;
mr1708_2 (All); LR P-value: 6.14E-23;
mr1713_2 (All); LR P-value: 1.57E-13;
mr1718_2 (All); LMM P-value: 1.31E-17; LR P-value: 7.49E-143;
mr1750_2 (All); LMM P-value: 1.53E-27; LR P-value: 3.18E-233;
mr1842_2 (All); LR P-value: 1.32E-16;
mr1933_2 (All); LR P-value: 4.37E-22;
mr1987_2 (All); LMM P-value: 4.35E-07; LR P-value: 5.73E-157
LOC_Os03g38350.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.941; most accessible tissue: Zhenshan97 flag leaf, score: 96.286
vg0321275827 (J) chr03 21275827 T G 64.20% 0.00% G -> T
mr1014 (All); LR P-value: 8.23E-70;
mr1670 (All); LR P-value: 4.28E-35;
mr1713 (All); LR P-value: 3.01E-11;
mr1718 (All); LMM P-value: 5.11E-15; LR P-value: 1.39E-97;
mr1750 (All); LMM P-value: 2.14E-23; LR P-value: 1.57E-171;
mr1842 (All); LR P-value: 1.83E-17;
mr1987 (All); LMM P-value: 1.65E-06; LR P-value: 1.91E-117;
mr1040_2 (All); LR P-value: 1.59E-15;
mr1362_2 (All); LR P-value: 4.39E-20;
mr1689_2 (All); LR P-value: 5.54E-37;
mr1713_2 (All); LR P-value: 1.87E-13;
mr1718_2 (All); LMM P-value: 9.76E-19; LR P-value: 1.67E-144;
mr1750_2 (All); LMM P-value: 5.41E-35; LR P-value: 6.97E-241;
mr1842_2 (All); LR P-value: 1.86E-16;
mr1933_2 (All); LR P-value: 1.14E-22;
mr1987_2 (All); LMM P-value: 1.45E-08; LR P-value: 3.39E-162
LOC_Os03g38350.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.867; most accessible tissue: Zhenshan97 flag leaf, score: 96.578
vg0321276123 (J) chr03 21276123 A AT 64.30% 0.00% AT -> A NA
LOC_Os03g38350.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.729; most accessible tissue: Zhenshan97 flag leaf, score: 94.939
vg0321276130 (J) chr03 21276130 G A 94.90% 0.00% G -> A NA
LOC_Os03g38350.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.141; most accessible tissue: Zhenshan97 flag leaf, score: 95.038
vg0321276131 (J) chr03 21276131 G A 64.30% 0.00% A -> G
mr1014 (All); LR P-value: 3.21E-68;
mr1670 (All); LR P-value: 4.02E-36;
mr1718 (All); LMM P-value: 3.10E-13; LR P-value: 8.87E-95;
mr1750 (All); LMM P-value: 8.31E-18; LR P-value: 2.11E-166;
mr1842 (All); LR P-value: 1.72E-16;
mr1987 (All); LMM P-value: 1.15E-06; LR P-value: 3.16E-118;
mr1594_2 (All); LR P-value: 2.08E-67;
mr1595_2 (All); LR P-value: 5.09E-10;
mr1645_2 (All); LR P-value: 7.00E-08;
mr1657_2 (All); LR P-value: 5.18E-19;
mr1689_2 (All); LR P-value: 1.15E-37;
mr1713_2 (All); LR P-value: 2.89E-13;
mr1718_2 (All); LMM P-value: 7.76E-19; LR P-value: 5.31E-143;
mr1750_2 (All); LMM P-value: 6.72E-27; LR P-value: 1.30E-232;
mr1842_2 (All); LR P-value: 5.09E-16;
mr1893_2 (All); LR P-value: 4.67E-11;
mr1933_2 (All); LR P-value: 2.85E-22;
mr1987_2 (All); LMM P-value: 3.39E-06; LR P-value: 7.34E-157
LOC_Os03g38350.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.226; most accessible tissue: Zhenshan97 flag leaf, score: 95.087
vg0321276138 (J) chr03 21276138 C T 64.20% 0.00% T -> C
mr1376 (All); LR P-value: 5.83E-14;
mr1431 (All); LR P-value: 5.83E-14;
mr1670 (All); LR P-value: 3.37E-36;
mr1713 (All); LR P-value: 6.29E-11;
mr1718 (All); LMM P-value: 2.20E-13; LR P-value: 1.61E-94;
mr1750 (All); LMM P-value: 7.19E-18; LR P-value: 1.18E-165;
mr1842 (All); LR P-value: 9.41E-17;
mr1987 (All); LMM P-value: 5.87E-07; LR P-value: 2.44E-118;
mr1595_2 (All); LR P-value: 3.28E-10;
mr1645_2 (All); LR P-value: 6.17E-08;
mr1657_2 (All); LR P-value: 5.43E-19;
mr1689_2 (All); LR P-value: 5.23E-38;
mr1713_2 (All); LR P-value: 6.58E-13;
mr1718_2 (All); LMM P-value: 2.21E-19; LR P-value: 4.65E-142;
mr1750_2 (All); LMM P-value: 1.89E-25; LR P-value: 1.54E-231;
mr1842_2 (All); LR P-value: 3.71E-16;
mr1893_2 (All); LR P-value: 6.91E-11;
mr1933_2 (All); LR P-value: 2.98E-22;
mr1987_2 (All); LMM P-value: 6.15E-07; LR P-value: 5.12E-159
LOC_Os03g38350.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g38350.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.453; most accessible tissue: Zhenshan97 flag leaf, score: 95.262
vg0321276146 (J) chr03 21276146 G T 64.20% 0.00% T -> G
mr1670 (All); LR P-value: 1.39E-36;
mr1713 (All); LR P-value: 4.44E-11;
mr1718 (All); LMM P-value: 2.58E-14; LR P-value: 1.34E-95;
mr1750 (All); LMM P-value: 7.04E-22; LR P-value: 1.00E-170;
mr1842 (All); LR P-value: 5.91E-17;
mr1987 (All); LMM P-value: 1.36E-06; LR P-value: 1.23E-117;
mr1537_2 (All); LR P-value: 1.67E-10;
mr1594_2 (All); LR P-value: 3.77E-68;
mr1595_2 (All); LR P-value: 3.69E-10;
mr1657_2 (All); LR P-value: 1.52E-18;
mr1689_2 (All); LR P-value: 1.28E-37;
mr1713_2 (All); LR P-value: 1.89E-13;
mr1718_2 (All); LMM P-value: 9.53E-21; LR P-value: 6.19E-145;
mr1750_2 (All); LMM P-value: 3.35E-32; LR P-value: 4.18E-238;
mr1842_2 (All); LR P-value: 1.49E-16;
mr1893_2 (All); LR P-value: 2.74E-11;
mr1933_2 (All); LR P-value: 6.41E-23;
mr1987_2 (All); LMM P-value: 2.78E-06; LR P-value: 4.99E-157
LOC_Os03g38350.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g38330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.948; most accessible tissue: Zhenshan97 flag leaf, score: 95.136
STR0321275565 (J) chr03 21275565 TCGATCG ATCGATC TCGATCG ATC 48.70% 0.00% TCGATCGATC -> TCGATCGATC GATC NA