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Search Results:

6 variations found. Os01g0245532/LOC_Os01g14320 (expressed protein), ranging from 8,023,786 bp to 8,024,935 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os01g14320 hypothetical protein; RAP ID: Os01g0245532; MSU ID: LOC_Os01g14320

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
vg0108024311 (J) chr01 8024311 T C 92.20% 0.00% T -> C
mr1098 (All); LR P-value: 1.57E-28;
mr1099 (All); LR P-value: 5.99E-27;
mr1113 (All); LR P-value: 2.20E-17;
mr1114 (All); LR P-value: 2.77E-18;
mr1120 (All); LR P-value: 6.79E-22;
mr1166 (All); LR P-value: 2.04E-13;
mr1247 (All); LR P-value: 3.20E-22;
mr1286 (All); LR P-value: 3.88E-07;
mr1409 (All); LR P-value: 1.65E-11;
mr1420 (All); LR P-value: 1.85E-06;
mr1465 (All); LR P-value: 4.06E-09;
mr1515 (All); LR P-value: 2.57E-18;
mr1589 (All); LR P-value: 6.45E-22;
mr1777 (All); LR P-value: 6.59E-06;
mr1868 (All); LR P-value: 7.75E-25;
mr1961 (All); LR P-value: 2.87E-19;
mr1120_2 (All); LR P-value: 9.11E-22;
mr1240_2 (All); LR P-value: 2.57E-17;
mr1247_2 (All); LR P-value: 2.03E-22;
mr1388_2 (All); LR P-value: 3.69E-10;
mr1510_2 (All); LR P-value: 1.09E-07;
mr1583_2 (All); LR P-value: 7.38E-14;
mr1740_2 (All); LR P-value: 1.20E-06;
mr1741_2 (All); LR P-value: 5.88E-09;
mr1817_2 (All); LR P-value: 1.50E-17;
mr1961_2 (All); LR P-value: 5.64E-15
LOC_Os01g14320.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.461; most accessible tissue: Minghui63 panicle, score: 90.833
vg0108024503 (J) chr01 8024503 A G 89.90% 0.00% A -> G
mr1113 (All); LR P-value: 9.35E-15;
mr1166 (All); LR P-value: 7.38E-14;
mr1409 (All); LR P-value: 1.08E-13;
mr1465 (All); LR P-value: 1.42E-08;
mr1480 (Jap_All); LMM P-value: 7.60E-06; LR P-value: 7.60E-06;
mr1549 (All); LR P-value: 3.42E-37;
mr1621 (All); LR P-value: 2.63E-06;
mr1649 (All); LR P-value: 3.06E-11;
mr1583_2 (All); LR P-value: 1.70E-14
LOC_Os01g14320.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.523; most accessible tissue: Minghui63 panicle, score: 90.184
vg0108024522 (J) chr01 8024522 G A 97.70% 0.00% G -> A NA
LOC_Os01g14320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.053; most accessible tissue: Minghui63 panicle, score: 88.893
vg0108024528 (J) chr01 8024528 G A 99.80% 0.00% G -> A NA
LOC_Os01g14320.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 80.571; most accessible tissue: Zhenshan97 panicle, score: 88.625
vg0108024531 (J) chr01 8024531 A G 92.10% 0.00% A -> G
mr1095 (All); LR P-value: 8.84E-22;
mr1098 (All); LR P-value: 7.22E-30;
mr1099 (All); LR P-value: 3.05E-27;
mr1101 (All); LR P-value: 5.76E-26;
mr1113 (All); LR P-value: 5.66E-19;
mr1114 (All); LR P-value: 1.45E-19;
mr1117 (All); LR P-value: 4.47E-20;
mr1119 (All); LR P-value: 1.28E-17;
mr1120 (All); LR P-value: 1.42E-23;
mr1123 (All); LR P-value: 2.42E-23;
mr1166 (All); LR P-value: 1.23E-14;
mr1210 (All); LR P-value: 1.25E-21;
mr1247 (All); LR P-value: 1.84E-23;
mr1286 (All); LR P-value: 4.32E-07;
mr1305 (All); LR P-value: 1.54E-23;
mr1409 (All); LR P-value: 2.37E-12;
mr1465 (All); LR P-value: 7.19E-09;
mr1496 (All); LR P-value: 3.76E-14;
mr1515 (All); LR P-value: 6.79E-19;
mr1549 (All); LR P-value: 1.67E-38;
mr1589 (All); LR P-value: 1.06E-22;
mr1649 (All); LR P-value: 1.14E-11;
mr1777 (All); LR P-value: 4.51E-06;
mr1868 (All); LR P-value: 8.16E-27;
mr1918 (All); LR P-value: 1.19E-12;
mr1936 (All); LR P-value: 2.17E-18;
mr1961 (All); LR P-value: 3.51E-20;
mr1098_2 (All); LR P-value: 7.29E-30;
mr1099_2 (All); LR P-value: 1.75E-23;
mr1113_2 (All); LR P-value: 5.43E-18;
mr1114_2 (All); LR P-value: 1.50E-17;
mr1117_2 (All); LR P-value: 6.32E-20;
mr1119_2 (All); LR P-value: 1.37E-17;
mr1120_2 (All); LR P-value: 3.55E-24;
mr1240_2 (All); LR P-value: 2.37E-19;
mr1247_2 (All); LR P-value: 3.21E-24;
mr1388_2 (All); LR P-value: 3.32E-11;
mr1530_2 (All); LR P-value: 3.29E-15;
mr1583_2 (All); LR P-value: 1.57E-14;
mr1740_2 (All); LR P-value: 1.83E-06;
mr1817_2 (All); LR P-value: 3.75E-18;
mr1911_2 (All); LR P-value: 2.41E-14;
mr1961_2 (All); LR P-value: 2.03E-16
LOC_Os01g14320.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.704; most accessible tissue: Zhenshan97 panicle, score: 88.625
vg0108024813 (J) chr01 8024813 C T 97.70% 0.00% C -> T NA
LOC_Os01g14320.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.519; most accessible tissue: Zhenshan97 young leaf, score: 86.852