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:

15 variations found. LOC_Os04g50188 (retrotransposon protein; putative; unclassified; expressed), ranging from 29,945,953 bp to 29,946,289 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
vg0429945960 (J) chr04 29945960 A G 84.00% 0.00% A -> G
mr1138 (All); LR P-value: 4.40E-14;
mr1138 (Ind_All); LR P-value: 7.90E-09;
mr1169 (All); LMM P-value: 5.10E-06; LR P-value: 7.93E-20;
mr1169 (Ind_All); LMM P-value: 4.78E-06; LR P-value: 1.89E-12;
mr1174 (All); LMM P-value: 2.62E-11; LR P-value: 1.07E-25;
mr1174 (Ind_All); LMM P-value: 5.08E-13; LR P-value: 5.59E-24;
mr1347 (All); LMM P-value: 7.34E-09; LR P-value: 5.64E-14;
mr1347 (Ind_All); LMM P-value: 1.12E-08; LR P-value: 1.13E-14;
mr1354 (All); LR P-value: 1.08E-08;
mr1354 (Ind_All); LR P-value: 7.73E-09;
mr1406 (Ind_All); LR P-value: 7.57E-08;
mr1138_2 (All); LMM P-value: 1.80E-06; LR P-value: 1.12E-15;
mr1138_2 (Ind_All); LMM P-value: 6.86E-06; LR P-value: 1.93E-09;
mr1174_2 (All); LMM P-value: 1.76E-07; LR P-value: 2.34E-24;
mr1174_2 (Ind_All); LMM P-value: 3.91E-09; LR P-value: 1.92E-23;
mr1347_2 (All); LMM P-value: 4.22E-08; LR P-value: 2.20E-19;
mr1347_2 (Ind_All); LMM P-value: 7.49E-07; LR P-value: 3.39E-20;
mr1349_2 (Ind_All); LR P-value: 4.74E-06;
mr1354_2 (All); LR P-value: 1.21E-11;
mr1354_2 (Ind_All); LMM P-value: 2.93E-06; LR P-value: 1.47E-12;
mr1406_2 (Ind_All); LR P-value: 1.75E-06;
mr1540_2 (Ind_All); LR P-value: 4.23E-06;
mr1732_2 (Ind_All); LR P-value: 2.02E-06
LOC_Os04g50188.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 50.943; most accessible tissue: Zhenshan97 panicle, score: 61.671
vg0429945982 (J) chr04 29945982 C T 95.20% 0.00% C -> T
mr1248 (All); LR P-value: 6.35E-08;
mr1248 (Jap_All); LR P-value: 1.21E-09;
mr1518 (Jap_All); LR P-value: 3.83E-06;
mr1676 (Jap_All); LR P-value: 2.51E-06;
mr1769 (All); LR P-value: 8.03E-12;
mr1676_2 (Jap_All); LR P-value: 3.37E-08;
mr1769_2 (All); LR P-value: 3.33E-13;
mr1769_2 (Jap_All); LR P-value: 8.43E-13
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 50.035; most accessible tissue: Zhenshan97 panicle, score: 61.671
vg0429945986 (J) chr04 29945986 T A 94.10% 0.00% T -> A NA
LOC_Os04g50188.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 49.994; most accessible tissue: Zhenshan97 panicle, score: 61.671
vg0429945987 (J) chr04 29945987 C T 89.30% 0.00% C -> T
mr1136 (All); LMM P-value: 5.33E-07;
mr1248 (Jap_All); LR P-value: 2.04E-09;
mr1518 (Jap_All); LR P-value: 3.24E-06;
mr1676 (Jap_All); LR P-value: 2.34E-06;
mr1769 (All); LR P-value: 1.57E-11;
mr1769 (Jap_All); LR P-value: 1.08E-13;
mr1951 (All); LR P-value: 1.47E-07;
mr1951 (Jap_All); LR P-value: 7.69E-07;
mr1082_2 (All); LMM P-value: 5.07E-06;
mr1226_2 (All); LMM P-value: 4.39E-06;
mr1632_2 (Jap_All); LR P-value: 1.07E-06;
mr1676_2 (Jap_All); LR P-value: 4.13E-09;
mr1769_2 (All); LR P-value: 1.05E-11;
mr1769_2 (Jap_All); LR P-value: 6.24E-15
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 50.544; most accessible tissue: Minghui63 panicle, score: 62.157
vg0429945988 (J) chr04 29945988 G A 90.30% 0.00% G -> A
mr1248 (All); LMM P-value: 8.96E-06; LR P-value: 2.11E-10;
mr1248 (Jap_All); LR P-value: 4.07E-10;
mr1518 (Jap_All); LR P-value: 3.28E-06;
mr1676 (Jap_All); LR P-value: 1.28E-06;
mr1769 (Jap_All); LR P-value: 6.22E-14;
mr1951 (Jap_All); LR P-value: 1.57E-07;
mr1510_2 (Jap_All); LR P-value: 2.88E-06;
mr1632_2 (Jap_All); LR P-value: 3.91E-07;
mr1676_2 (Jap_All); LR P-value: 1.12E-09;
mr1696_2 (All); LR P-value: 6.58E-07;
mr1769_2 (Jap_All); LR P-value: 7.03E-14
LOC_Os04g50188.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 50.026; most accessible tissue: Minghui63 panicle, score: 62.157
vg0429946010 (J) chr04 29946010 T G 94.10% 0.00% T -> G NA
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 49.644; most accessible tissue: Minghui63 panicle, score: 62.157
vg0429946012 (J) chr04 29946012 G C 94.10% 0.00% G -> C NA
LOC_Os04g50188.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 50.423; most accessible tissue: Zhenshan97 panicle, score: 63.607
vg0429946042 (J) chr04 29946042 A G 74.90% 0.25% A -> G
mr1169 (Ind_All); LR P-value: 1.37E-11;
mr1174 (All); LMM P-value: 4.07E-07; LR P-value: 4.06E-17;
mr1174 (Ind_All); LMM P-value: 3.14E-10; LR P-value: 3.74E-21;
mr1347 (All); LMM P-value: 7.25E-06; LR P-value: 7.74E-09;
mr1347 (Ind_All); LMM P-value: 7.75E-08; LR P-value: 6.42E-14;
mr1354 (Ind_All); LR P-value: 2.93E-07;
mr1406 (Ind_All); LMM P-value: 8.05E-06; LR P-value: 5.21E-09;
mr1174_2 (All); LMM P-value: 1.36E-06; LR P-value: 8.92E-15;
mr1174_2 (Ind_All); LMM P-value: 2.79E-11; LR P-value: 4.18E-25;
mr1347_2 (All); LMM P-value: 7.54E-08; LR P-value: 6.68E-11;
mr1347_2 (Ind_All); LMM P-value: 2.66E-11; LR P-value: 1.18E-23;
mr1354_2 (Ind_All); LR P-value: 8.32E-09;
mr1406_2 (Ind_All); LMM P-value: 8.12E-06; LR P-value: 3.37E-09;
mr1540_2 (Ind_All); LR P-value: 1.58E-06;
mr1732_2 (Ind_All); LR P-value: 2.04E-06
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 51.023; most accessible tissue: Zhenshan97 panicle, score: 63.607
vg0429946046 (J) chr04 29946046 C T 94.10% 0.00% C -> T
mr1117 (Jap_All); LR P-value: 4.95E-06;
mr1745 (Jap_All); LR P-value: 2.79E-07;
mr1117_2 (Jap_All); LR P-value: 3.21E-07;
mr1119_2 (Jap_All); LR P-value: 9.54E-07;
mr1240_2 (Jap_All); LR P-value: 2.15E-06;
mr1496_2 (Jap_All); LR P-value: 6.27E-06;
mr1519_2 (Jap_All); LR P-value: 9.91E-06;
mr1745_2 (Jap_All); LR P-value: 5.47E-06
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 51.288; most accessible tissue: Zhenshan97 panicle, score: 63.607
vg0429946080 (J) chr04 29946080 C T 74.90% 0.53% C -> T
mr1138 (Ind_All); LR P-value: 8.37E-06;
mr1169 (Ind_All); LMM P-value: 1.33E-06; LR P-value: 1.82E-13;
mr1174 (All); LMM P-value: 1.04E-06; LR P-value: 2.81E-16;
mr1174 (Ind_All); LMM P-value: 2.58E-10; LR P-value: 1.67E-20;
mr1347 (All); LR P-value: 1.16E-07;
mr1347 (Ind_All); LMM P-value: 2.85E-06; LR P-value: 6.38E-12;
mr1354 (Ind_All); LR P-value: 1.26E-08;
mr1406 (Ind_All); LR P-value: 5.20E-07;
mr1531 (Ind_All); LR P-value: 4.68E-06;
mr1138_2 (Ind_All); LR P-value: 7.82E-06;
mr1174_2 (All); LMM P-value: 7.39E-07; LR P-value: 1.37E-14;
mr1174_2 (Ind_All); LMM P-value: 2.22E-11; LR P-value: 1.01E-23;
mr1347_2 (All); LMM P-value: 3.60E-07; LR P-value: 2.91E-10;
mr1347_2 (Ind_All); LMM P-value: 8.79E-10; LR P-value: 9.08E-21;
mr1354_2 (Ind_All); LR P-value: 1.01E-09;
mr1406_2 (Ind_All); LR P-value: 1.73E-08;
mr1540_2 (Ind_All); LR P-value: 1.85E-07;
mr1732_2 (Ind_All); LR P-value: 2.30E-07
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.974; most accessible tissue: Zhenshan97 panicle, score: 67.020
vg0429946087 (J) chr04 29946087 C T 74.80% 0.53% C -> T
mr1138 (Ind_All); LR P-value: 6.81E-06;
mr1169 (Ind_All); LMM P-value: 3.52E-06; LR P-value: 6.08E-13;
mr1174 (All); LMM P-value: 5.78E-08; LR P-value: 6.75E-18;
mr1174 (Ind_All); LMM P-value: 7.60E-12; LR P-value: 8.76E-23;
mr1347 (All); LR P-value: 6.84E-08;
mr1347 (Ind_All); LMM P-value: 2.11E-06; LR P-value: 2.38E-12;
mr1354 (Ind_All); LR P-value: 6.65E-09;
mr1406 (Ind_All); LR P-value: 2.50E-07;
mr1531 (Ind_All); LR P-value: 4.59E-06;
mr1138_2 (Ind_All); LR P-value: 3.80E-06;
mr1174_2 (All); LMM P-value: 1.68E-06; LR P-value: 3.42E-14;
mr1174_2 (Ind_All); LMM P-value: 1.49E-11; LR P-value: 2.61E-24;
mr1347_2 (All); LMM P-value: 1.51E-06; LR P-value: 1.23E-09;
mr1347_2 (Ind_All); LMM P-value: 9.92E-10; LR P-value: 6.72E-21;
mr1354_2 (Ind_All); LR P-value: 2.33E-10;
mr1406_2 (Ind_All); LR P-value: 1.51E-08;
mr1540_2 (Ind_All); LR P-value: 7.24E-07;
mr1732_2 (Ind_All); LR P-value: 8.17E-07
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 51.941; most accessible tissue: Zhenshan97 panicle, score: 67.020
vg0429946123 (J) chr04 29946123 C T 89.40% 0.00% C -> T
mr1082 (Ind_All); LR P-value: 1.32E-06;
mr1890 (Jap_All); LR P-value: 8.87E-06
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 52.612; most accessible tissue: Zhenshan97 flag leaf, score: 66.327
vg0429946139 (J) chr04 29946139 A G 99.70% 0.00% A -> G NA
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 51.909; most accessible tissue: Zhenshan97 flag leaf, score: 67.310
vg0429946193 (J) chr04 29946193 G A 94.10% 0.00% G -> A
mr1117 (Jap_All); LR P-value: 4.95E-06;
mr1745 (Jap_All); LR P-value: 2.79E-07;
mr1117_2 (Jap_All); LR P-value: 3.21E-07;
mr1119_2 (Jap_All); LR P-value: 9.54E-07;
mr1240_2 (Jap_All); LR P-value: 2.15E-06;
mr1496_2 (Jap_All); LR P-value: 6.27E-06;
mr1519_2 (Jap_All); LR P-value: 9.91E-06;
mr1745_2 (Jap_All); LR P-value: 5.47E-06
LOC_Os04g50188.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 53.763; most accessible tissue: Minghui63 root, score: 67.730
vg0429946245 (J) chr04 29946245 C T 89.40% 0.00% C -> T
mr1082 (Ind_All); LR P-value: 9.49E-07;
mr1890 (Jap_All); LR P-value: 8.87E-06
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 59.717; most accessible tissue: Minghui63 root, score: 73.351