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Search Results:

21 variations found. LOC_Os05g48130 (hypothetical protein), ranging from 27,589,155 bp to 27,589,611 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
vg0527589193 (J) chr05 27589193 T C 74.70% 0.00% C -> T
mr1055 (All); LR P-value: 1.21E-33;
mr1056 (Jap_All); LR P-value: 4.52E-06;
mr1241 (All); LR P-value: 2.38E-51;
mr1301 (Ind_All); LR P-value: 4.64E-10;
mr1364 (Jap_All); LR P-value: 8.09E-06;
mr1410 (Ind_All); LR P-value: 3.58E-08;
mr1471 (All); LR P-value: 2.30E-11;
mr1518 (Jap_All); LR P-value: 3.68E-06;
mr1543 (Jap_All); LR P-value: 9.57E-07;
mr1676 (Jap_All); LR P-value: 1.09E-06;
mr1817 (Jap_All); LR P-value: 9.99E-07;
mr1241_2 (All); LR P-value: 1.44E-62;
mr1422_2 (Jap_All); LR P-value: 1.25E-06;
mr1471_2 (All); LR P-value: 2.76E-09;
mr1629_2 (Jap_All); LR P-value: 1.38E-06;
mr1817_2 (Jap_All); LR P-value: 5.44E-08;
mr1827_2 (All); LR P-value: 1.27E-13
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 29.217; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589247 (J) chr05 27589247 C T 71.60% 0.47% T -> C
mr1055 (All); LR P-value: 1.28E-33;
mr1056 (Jap_All); LR P-value: 2.33E-06;
mr1241 (All); LR P-value: 1.67E-51;
mr1364 (Jap_All); LR P-value: 3.07E-06;
mr1443 (Jap_All); LR P-value: 1.71E-06;
mr1471 (All); LR P-value: 5.00E-11;
mr1676 (Jap_All); LR P-value: 2.95E-06;
mr1817 (Jap_All); LR P-value: 5.00E-07;
mr1241_2 (All); LR P-value: 5.05E-64;
mr1364_2 (Jap_All); LR P-value: 3.55E-09;
mr1422_2 (Jap_All); LR P-value: 2.91E-06
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g48130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 28.405; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589254 (J) chr05 27589254 G A 80.00% 2.18% G -> A NA
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g48130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 28.394; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589256 (J) chr05 27589256 C T 79.80% 2.73% C -> T NA
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 28.471; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589285 (J) chr05 27589285 C T 96.20% 0.13% C -> T NA
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 27.481; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589314 (J) chr05 27589314 A G 51.80% 0.00% G -> A
mr1502 (Jap_All); LR P-value: 2.64E-06;
mr1518 (Jap_All); LR P-value: 1.11E-06;
mr1543 (Jap_All); LR P-value: 5.60E-07;
mr1676 (Jap_All); LR P-value: 3.56E-07;
mr1742 (Jap_All); LR P-value: 2.21E-06;
mr1817 (Jap_All); LR P-value: 5.99E-06;
mr1422_2 (Jap_All); LR P-value: 3.11E-07
LOC_Os05g48130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 27.253; most accessible tissue: Minghui63 panicle, score: 59.629
vg0527589352 (J) chr05 27589352 C A 96.80% 0.00% C -> A NA
LOC_Os05g48130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 24.596; most accessible tissue: Minghui63 panicle, score: 56.842
vg0527589353 (J) chr05 27589353 T A 96.80% 0.00% T -> A NA
LOC_Os05g48130.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 24.596; most accessible tissue: Minghui63 panicle, score: 56.842
vg0527589354 (J) chr05 27589354 C A 96.80% 0.00% C -> A NA
LOC_Os05g48130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 24.596; most accessible tissue: Minghui63 panicle, score: 56.842
vg0527589358 (J) chr05 27589358 G T 96.80% 0.00% G -> T NA
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 24.057; most accessible tissue: Minghui63 panicle, score: 53.770
vg0527589440 (J) chr05 27589440 C T 98.90% 0.00% C -> T NA
LOC_Os05g48130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 24.379; most accessible tissue: Minghui63 panicle, score: 42.799
vg0527589449 (J) chr05 27589449 G A 93.30% 0.00% G -> A NA
LOC_Os05g48130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 24.267; most accessible tissue: Minghui63 panicle, score: 42.799
vg0527589451 (J) chr05 27589451 C A 97.60% 0.00% C -> A NA
LOC_Os05g48130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.170; most accessible tissue: Minghui63 panicle, score: 42.799
vg0527589454 (J) chr05 27589454 C T 99.70% 0.00% C -> T NA
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.170; most accessible tissue: Minghui63 panicle, score: 42.799
vg0527589456 (J) chr05 27589456 G A 80.00% 0.00% A -> G
mr1115 (Jap_All); LR P-value: 6.97E-17;
mr1241 (Jap_All); LR P-value: 2.74E-11;
mr1448 (Jap_All); LR P-value: 5.29E-06;
mr1575 (All); LR P-value: 9.17E-09;
mr1611 (All); LR P-value: 3.97E-22;
mr1611 (Jap_All); LR P-value: 9.62E-14;
mr1742 (Jap_All); LR P-value: 2.81E-07;
mr1879 (All); LR P-value: 9.16E-12;
mr1879 (Jap_All); LR P-value: 4.36E-12;
mr1920 (All); LR P-value: 6.12E-22;
mr1920 (Jap_All); LR P-value: 4.15E-12;
mr1047_2 (Jap_All); LR P-value: 2.21E-07;
mr1189_2 (Jap_All); LR P-value: 6.10E-09;
mr1241_2 (All); LR P-value: 1.21E-61;
mr1241_2 (Jap_All); LR P-value: 9.10E-13;
mr1268_2 (Jap_All); LR P-value: 1.90E-06;
mr1304_2 (All); LR P-value: 2.23E-22;
mr1446_2 (All); LR P-value: 2.86E-07;
mr1454_2 (Jap_All); LR P-value: 1.15E-08;
mr1471_2 (All); LR P-value: 4.32E-10;
mr1471_2 (Jap_All); LR P-value: 6.50E-12;
mr1530_2 (Jap_All); LR P-value: 4.88E-10;
mr1539_2 (All); LR P-value: 1.29E-16;
mr1540_2 (All); LR P-value: 8.58E-17;
mr1543_2 (Jap_All); LR P-value: 2.83E-09;
mr1642_2 (Jap_All); LR P-value: 2.56E-10;
mr1722_2 (All); LR P-value: 5.72E-12;
mr1732_2 (All); LR P-value: 3.28E-16;
mr1789_2 (Jap_All); LR P-value: 3.04E-11;
mr1808_2 (Jap_All); LR P-value: 5.34E-08;
mr1827_2 (All); LR P-value: 4.93E-14;
mr1842_2 (All); LR P-value: 1.18E-15;
mr1879_2 (Jap_All); LR P-value: 3.43E-08;
mr1902_2 (All); LR P-value: 9.81E-15
LOC_Os05g48130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.170; most accessible tissue: Minghui63 panicle, score: 42.799
vg0527589502 (J) chr05 27589502 T C 20.30% 69.61% T -> C
mr1115 (All); LR P-value: 5.60E-22;
mr1115 (Jap_All); LR P-value: 6.97E-17;
mr1241 (All); LR P-value: 2.89E-52;
mr1241 (Jap_All); LR P-value: 2.74E-11;
mr1448 (Jap_All); LR P-value: 5.29E-06;
mr1611 (All); LR P-value: 1.28E-22;
mr1611 (Jap_All); LR P-value: 9.62E-14;
mr1742 (Jap_All); LR P-value: 2.81E-07;
mr1879 (Jap_All); LR P-value: 4.36E-12;
mr1920 (All); LR P-value: 1.83E-22;
mr1920 (Jap_All); LR P-value: 4.15E-12;
mr1047_2 (Jap_All); LR P-value: 2.21E-07;
mr1189_2 (Jap_All); LR P-value: 6.10E-09;
mr1241_2 (All); LR P-value: 9.35E-62;
mr1241_2 (Jap_All); LR P-value: 9.10E-13;
mr1268_2 (Jap_All); LR P-value: 1.90E-06;
mr1446_2 (All); LR P-value: 2.74E-07;
mr1454_2 (Jap_All); LR P-value: 1.15E-08;
mr1471_2 (All); LR P-value: 3.34E-09;
mr1471_2 (Jap_All); LR P-value: 6.50E-12;
mr1530_2 (Jap_All); LR P-value: 4.88E-10;
mr1543_2 (Jap_All); LR P-value: 2.83E-09;
mr1611_2 (All); LR P-value: 1.75E-22;
mr1642_2 (Jap_All); LR P-value: 2.56E-10;
mr1789_2 (Jap_All); LR P-value: 3.04E-11;
mr1808_2 (Jap_All); LR P-value: 5.34E-08;
mr1879_2 (Jap_All); LR P-value: 3.43E-08;
mr1902_2 (All); LR P-value: 1.75E-14
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g48130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.525; most accessible tissue: Minghui63 panicle, score: 38.588
vg0527589532 (J) chr05 27589532 T C 20.20% 68.24% T -> C
mr1115 (All); LR P-value: 5.60E-22;
mr1115 (Jap_All); LR P-value: 6.97E-17;
mr1241 (All); LR P-value: 2.89E-52;
mr1241 (Jap_All); LR P-value: 2.74E-11;
mr1448 (Jap_All); LR P-value: 5.29E-06;
mr1611 (All); LR P-value: 1.28E-22;
mr1611 (Jap_All); LR P-value: 9.62E-14;
mr1742 (Jap_All); LR P-value: 2.81E-07;
mr1879 (Jap_All); LR P-value: 4.36E-12;
mr1920 (All); LR P-value: 1.83E-22;
mr1920 (Jap_All); LR P-value: 4.15E-12;
mr1047_2 (Jap_All); LR P-value: 2.21E-07;
mr1189_2 (Jap_All); LR P-value: 6.10E-09;
mr1241_2 (All); LR P-value: 9.35E-62;
mr1241_2 (Jap_All); LR P-value: 9.10E-13;
mr1268_2 (Jap_All); LR P-value: 1.90E-06;
mr1446_2 (All); LR P-value: 2.74E-07;
mr1454_2 (Jap_All); LR P-value: 1.15E-08;
mr1471_2 (All); LR P-value: 3.34E-09;
mr1471_2 (Jap_All); LR P-value: 6.50E-12;
mr1530_2 (Jap_All); LR P-value: 4.88E-10;
mr1543_2 (Jap_All); LR P-value: 2.83E-09;
mr1611_2 (All); LR P-value: 1.75E-22;
mr1642_2 (Jap_All); LR P-value: 2.56E-10;
mr1789_2 (Jap_All); LR P-value: 3.04E-11;
mr1808_2 (Jap_All); LR P-value: 5.34E-08;
mr1879_2 (Jap_All); LR P-value: 3.43E-08;
mr1902_2 (All); LR P-value: 1.75E-14
LOC_Os05g48130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g48130.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 22.721; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg0527589547 (J) chr05 27589547 G T 97.20% 0.00% G -> T NA
LOC_Os05g48130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 25.040; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg0527589584 (J) chr05 27589584 G A 80.10% 0.00% A -> G
mr1115 (All); LR P-value: 7.94E-22;
mr1115 (Jap_All); LR P-value: 6.97E-17;
mr1241 (All); LR P-value: 3.49E-52;
mr1241 (Jap_All); LR P-value: 2.74E-11;
mr1448 (Jap_All); LR P-value: 5.29E-06;
mr1575 (All); LR P-value: 5.05E-09;
mr1611 (All); LR P-value: 3.96E-22;
mr1611 (Jap_All); LR P-value: 9.62E-14;
mr1742 (Jap_All); LR P-value: 2.81E-07;
mr1879 (All); LR P-value: 3.80E-12;
mr1879 (Jap_All); LR P-value: 4.36E-12;
mr1920 (All); LR P-value: 2.13E-22;
mr1920 (Jap_All); LR P-value: 4.15E-12;
mr1047_2 (Jap_All); LR P-value: 2.21E-07;
mr1189_2 (Jap_All); LR P-value: 6.10E-09;
mr1241_2 (All); LR P-value: 3.78E-62;
mr1241_2 (Jap_All); LR P-value: 9.10E-13;
mr1268_2 (Jap_All); LR P-value: 1.90E-06;
mr1304_2 (All); LR P-value: 5.78E-23;
mr1446_2 (All); LR P-value: 2.36E-07;
mr1454_2 (Jap_All); LR P-value: 1.15E-08;
mr1471_2 (All); LR P-value: 7.61E-10;
mr1471_2 (Jap_All); LR P-value: 6.50E-12;
mr1530_2 (Jap_All); LR P-value: 4.88E-10;
mr1543_2 (Jap_All); LR P-value: 2.83E-09;
mr1642_2 (Jap_All); LR P-value: 2.56E-10;
mr1722_2 (All); LR P-value: 1.36E-11;
mr1789_2 (All); LR P-value: 2.17E-28;
mr1789_2 (Jap_All); LR P-value: 3.04E-11;
mr1808_2 (Jap_All); LR P-value: 5.34E-08;
mr1827_2 (All); LR P-value: 4.80E-14;
mr1842_2 (All); LR P-value: 1.46E-15;
mr1879_2 (Jap_All); LR P-value: 3.43E-08;
mr1902_2 (All); LR P-value: 1.09E-14;
mr1952_2 (All); LR P-value: 6.93E-07
LOC_Os05g48130.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 23.543; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg0527589588 (J) chr05 27589588 G A 80.20% 0.00% A -> G
mr1115 (All); LR P-value: 7.94E-22;
mr1115 (Jap_All); LR P-value: 6.97E-17;
mr1241 (All); LR P-value: 3.49E-52;
mr1241 (Jap_All); LR P-value: 2.74E-11;
mr1448 (Jap_All); LR P-value: 5.29E-06;
mr1575 (All); LR P-value: 5.05E-09;
mr1611 (All); LR P-value: 3.96E-22;
mr1611 (Jap_All); LR P-value: 9.62E-14;
mr1742 (Jap_All); LR P-value: 2.81E-07;
mr1879 (All); LR P-value: 3.80E-12;
mr1879 (Jap_All); LR P-value: 4.36E-12;
mr1920 (All); LR P-value: 2.13E-22;
mr1920 (Jap_All); LR P-value: 4.15E-12;
mr1047_2 (Jap_All); LR P-value: 2.21E-07;
mr1189_2 (Jap_All); LR P-value: 6.10E-09;
mr1241_2 (All); LR P-value: 3.78E-62;
mr1241_2 (Jap_All); LR P-value: 9.10E-13;
mr1268_2 (Jap_All); LR P-value: 1.90E-06;
mr1304_2 (All); LR P-value: 5.78E-23;
mr1446_2 (All); LR P-value: 2.36E-07;
mr1454_2 (Jap_All); LR P-value: 1.15E-08;
mr1471_2 (All); LR P-value: 7.61E-10;
mr1471_2 (Jap_All); LR P-value: 6.50E-12;
mr1530_2 (Jap_All); LR P-value: 4.88E-10;
mr1543_2 (Jap_All); LR P-value: 2.83E-09;
mr1642_2 (Jap_All); LR P-value: 2.56E-10;
mr1722_2 (All); LR P-value: 1.36E-11;
mr1789_2 (All); LR P-value: 2.17E-28;
mr1789_2 (Jap_All); LR P-value: 3.04E-11;
mr1808_2 (Jap_All); LR P-value: 5.34E-08;
mr1827_2 (All); LR P-value: 4.80E-14;
mr1842_2 (All); LR P-value: 1.46E-15;
mr1879_2 (Jap_All); LR P-value: 3.43E-08;
mr1902_2 (All); LR P-value: 1.09E-14;
mr1952_2 (All); LR P-value: 6.93E-07
LOC_Os05g48130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 23.585; most accessible tissue: Zhenshan97 panicle, score: 36.038
vg0527589602 (J) chr05 27589602 T C 80.10% 0.00% C -> T
mr1115 (All); LR P-value: 4.32E-22;
mr1115 (Jap_All); LR P-value: 5.75E-17;
mr1241 (All); LR P-value: 1.45E-52;
mr1241 (Jap_All); LR P-value: 8.96E-12;
mr1611 (All); LR P-value: 6.52E-23;
mr1611 (Jap_All); LR P-value: 4.44E-14;
mr1742 (Jap_All); LR P-value: 7.79E-07;
mr1879 (All); LR P-value: 1.24E-11;
mr1879 (Jap_All); LR P-value: 1.95E-12;
mr1920 (All); LR P-value: 5.25E-22;
mr1920 (Jap_All); LR P-value: 9.03E-12;
mr1047_2 (Jap_All); LR P-value: 2.88E-07;
mr1189_2 (Jap_All); LR P-value: 1.91E-08;
mr1241_2 (All); LR P-value: 3.42E-61;
mr1241_2 (Jap_All); LR P-value: 4.50E-13;
mr1268_2 (Jap_All); LR P-value: 7.70E-07;
mr1454_2 (Jap_All); LR P-value: 1.09E-08;
mr1471_2 (All); LR P-value: 1.44E-08;
mr1471_2 (Jap_All); LR P-value: 5.28E-11;
mr1611_2 (All); LR P-value: 6.50E-22;
mr1642_2 (Jap_All); LR P-value: 8.66E-10;
mr1808_2 (Jap_All); LR P-value: 1.05E-07;
mr1952_2 (All); LR P-value: 4.67E-07
LOC_Os05g48130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 22.914; most accessible tissue: Zhenshan97 panicle, score: 36.038