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:

3 variations found. LOC_Os09g27910 (aspartic proteinase nepenthesin precursor; putative; expressed), ranging from 16,970,179 bp to 16,971,732 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
vg0916970943 (J) chr09 16970943 T C 65.10% 0.00% C -> T
mr1008 (All); LR P-value: 3.22E-104;
mr1009 (All); LR P-value: 1.83E-101;
mr1019 (All); LR P-value: 9.53E-58;
mr1074 (All); LR P-value: 2.59E-32;
mr1081 (All); LR P-value: 8.08E-37;
mr1092 (All); LR P-value: 1.60E-47;
mr1097 (All); LR P-value: 2.17E-09;
mr1102 (All); LR P-value: 3.93E-21;
mr1103 (All); LR P-value: 1.33E-55;
mr1124 (All); LR P-value: 1.07E-39;
mr1130 (All); LR P-value: 6.69E-26;
mr1135 (All); LR P-value: 4.25E-75;
mr1146 (All); LR P-value: 2.73E-16;
mr1148 (All); LR P-value: 1.21E-27;
mr1150 (All); LR P-value: 5.52E-23;
mr1152 (All); LR P-value: 8.76E-48;
mr1154 (All); LR P-value: 8.46E-55;
mr1172 (All); LR P-value: 3.63E-11;
mr1194 (All); LR P-value: 2.03E-43;
mr1202 (All); LR P-value: 5.48E-29;
mr1222 (All); LR P-value: 6.02E-08;
mr1223 (All); LR P-value: 1.78E-26;
mr1242 (All); LR P-value: 1.84E-18;
mr1254 (All); LR P-value: 2.11E-21;
mr1256 (All); LR P-value: 1.94E-31;
mr1275 (All); LR P-value: 3.70E-09;
mr1276 (All); LR P-value: 6.17E-15;
mr1324 (All); LR P-value: 1.26E-15;
mr1333 (All); LR P-value: 1.70E-32;
mr1335 (All); LR P-value: 6.25E-13;
mr1361 (All); LR P-value: 4.03E-14;
mr1375 (All); LR P-value: 1.29E-23;
mr1442 (All); LR P-value: 2.10E-08;
mr1495 (All); LR P-value: 6.62E-23;
mr1504 (All); LR P-value: 1.47E-88;
mr1517 (All); LR P-value: 1.28E-85;
mr1571 (All); LR P-value: 6.64E-23;
mr1601 (All); LR P-value: 1.16E-41;
mr1623 (All); LR P-value: 6.03E-11;
mr1645 (All); LR P-value: 1.42E-41;
mr1647 (All); LR P-value: 6.94E-33;
mr1660 (All); LR P-value: 3.93E-08;
mr1670 (All); LR P-value: 2.18E-34;
mr1672 (All); LR P-value: 8.62E-82;
mr1681 (All); LR P-value: 3.24E-06;
mr1682 (All); LR P-value: 1.57E-38;
mr1686 (All); LR P-value: 5.79E-28;
mr1695 (All); LR P-value: 3.59E-62;
mr1698 (All); LR P-value: 7.62E-21;
mr1711 (All); LR P-value: 5.54E-62;
mr1723 (All); LR P-value: 4.94E-28;
mr1731 (All); LR P-value: 1.51E-24;
mr1754 (All); LR P-value: 1.79E-20;
mr1758 (All); LR P-value: 1.25E-89;
mr1838 (All); LR P-value: 2.65E-20;
mr1861 (All); LR P-value: 1.17E-54;
mr1865 (All); LR P-value: 4.09E-76;
mr1873 (All); LR P-value: 6.80E-40;
mr1889 (All); LR P-value: 2.07E-55;
mr1896 (All); LR P-value: 7.52E-71;
mr1907 (All); LR P-value: 7.17E-79;
mr1917 (All); LR P-value: 2.81E-26;
mr1922 (All); LR P-value: 4.69E-31;
mr1924 (All); LR P-value: 7.59E-13;
mr1962 (All); LR P-value: 2.17E-61;
mr1987 (All); LR P-value: 4.06E-105;
mr1064_2 (All); LR P-value: 1.27E-57;
mr1072_2 (All); LR P-value: 8.39E-39;
mr1074_2 (All); LR P-value: 4.44E-27;
mr1075_2 (All); LR P-value: 9.53E-38;
mr1081_2 (All); LR P-value: 1.85E-32;
mr1082_2 (All); LR P-value: 3.38E-36;
mr1092_2 (All); LR P-value: 7.82E-41;
mr1103_2 (All); LR P-value: 2.64E-68;
mr1124_2 (All); LR P-value: 1.17E-56;
mr1146_2 (All); LR P-value: 2.15E-17;
mr1149_2 (All); LR P-value: 2.61E-26;
mr1150_2 (All); LR P-value: 1.88E-34;
mr1152_2 (All); LR P-value: 1.11E-39;
mr1154_2 (All); LR P-value: 1.05E-52;
mr1242_2 (All); LR P-value: 8.70E-23;
mr1246_2 (All); LR P-value: 2.11E-76;
mr1256_2 (All); LR P-value: 1.72E-34;
mr1342_2 (All); LR P-value: 7.52E-17;
mr1441_2 (All); LR P-value: 2.56E-26;
mr1486_2 (All); LR P-value: 1.74E-44;
mr1591_2 (All); LR P-value: 2.27E-45;
mr1657_2 (All); LR P-value: 7.95E-19;
mr1861_2 (All); LR P-value: 1.58E-51;
mr1865_2 (All); LR P-value: 4.66E-97;
mr1889_2 (All); LR P-value: 7.65E-66;
mr1890_2 (All); LR P-value: 1.09E-48
LOC_Os09g27910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.677; most accessible tissue: Minghui63 panicle, score: 92.800
vg0916971360 (J) chr09 16971360 G T 99.90% 0.00% G -> T NA
LOC_Os09g27910.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os09g27930.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g27920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.275; most accessible tissue: Zhenshan97 panicle, score: 93.752
vg0916971365 (J) chr09 16971365 C T 88.10% 0.00% C -> T
mr1097 (All); LR P-value: 1.93E-09;
mr1220 (All); LR P-value: 2.13E-07;
mr1405 (All); LR P-value: 6.84E-06;
mr1642 (All); LR P-value: 6.14E-07;
mr1657 (Jap_All); LR P-value: 6.48E-06;
mr1398_2 (All); LR P-value: 2.73E-10;
mr1398_2 (Jap_All); LR P-value: 8.64E-07;
mr1582_2 (Jap_All); LR P-value: 3.26E-06
LOC_Os09g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.332; most accessible tissue: Zhenshan97 panicle, score: 94.026