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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

33 variations found. LOC_Os12g22540 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 12,722,540 bp to 12,722,987 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
vg1212722547 (J) chr12 12722547 G C 88.20% 0.00% G -> C
mr1425 (Ind_All); LR P-value: 2.02E-06;
mr1425_2 (Ind_All); LR P-value: 3.59E-06
LOC_Os12g22540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.935; most accessible tissue: Minghui63 panicle, score: 66.554
vg1212722591 (J) chr12 12722591 G A 84.90% 0.00% A -> G
mr1489 (All); LR P-value: 8.36E-68;
mr1606 (All); LR P-value: 1.00E-07;
mr1606 (Jap_All); LR P-value: 4.48E-06;
mr1959 (All); LR P-value: 2.72E-09;
mr1013_2 (All); LR P-value: 5.78E-16;
mr1023_2 (All); LR P-value: 3.58E-71;
mr1031_2 (All); LR P-value: 6.17E-15;
mr1338_2 (Jap_All); LR P-value: 1.64E-08;
mr1489_2 (All); LR P-value: 2.85E-77;
mr1606_2 (All); LR P-value: 5.10E-08;
mr1722_2 (All); LR P-value: 2.24E-12;
mr1879_2 (All); LR P-value: 3.71E-13
LOC_Os12g22540.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 47.003; most accessible tissue: Minghui63 panicle, score: 66.554
vg1212722595 (J) chr12 12722595 C A 84.90% 0.00% A -> C
mr1023 (All); LR P-value: 1.88E-60;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1489 (All); LR P-value: 3.06E-69;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.86E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1013_2 (All); LR P-value: 3.65E-16;
mr1023_2 (All); LR P-value: 3.41E-72;
mr1031_2 (All); LR P-value: 5.07E-15;
mr1079_2 (All); LR P-value: 7.63E-54;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 8.89E-09;
mr1489_2 (All); LR P-value: 1.29E-78;
mr1606_2 (All); LR P-value: 9.68E-08;
mr1722_2 (All); LR P-value: 1.51E-12;
mr1879_2 (All); LR P-value: 5.05E-13
LOC_Os12g22540.1 Alt: C| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 48.102; most accessible tissue: Minghui63 panicle, score: 66.554
vg1212722627 (J) chr12 12722627 C T 99.20% 0.00% C -> T NA
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.041; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722628 (J) chr12 12722628 G A 88.20% 0.00% G -> A
mr1425 (Ind_All); LR P-value: 3.70E-06;
mr1425_2 (Ind_All); LR P-value: 4.07E-06
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.831; most accessible tissue: Minghui63 panicle, score: 77.956
vg1212722635 (J) chr12 12722635 C T 99.10% 0.00% C -> T NA
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 52.044; most accessible tissue: Minghui63 panicle, score: 77.956
vg1212722640 (J) chr12 12722640 G A 83.40% 0.02% A -> G
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1308 (All); LR P-value: 5.59E-17;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 9.32E-09;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1013_2 (All); LR P-value: 2.43E-15;
mr1156_2 (All); LR P-value: 3.93E-18;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 5.51E-09;
mr1606_2 (All); LR P-value: 1.23E-07;
mr1722_2 (All); LR P-value: 2.20E-12;
mr1879_2 (All); LR P-value: 4.70E-12
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g22530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.089; most accessible tissue: Minghui63 panicle, score: 76.913
vg1212722663 (J) chr12 12722663 C G 99.70% 0.00% C -> G NA
LOC_Os12g22530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: G| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 52.506; most accessible tissue: Minghui63 panicle, score: 76.913
vg1212722669 (J) chr12 12722669 G A 99.90% 0.00% G -> A NA
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 52.539; most accessible tissue: Minghui63 panicle, score: 76.913
vg1212722683 (J) chr12 12722683 A T 99.60% 0.00% A -> T NA
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.519; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722689 (J) chr12 12722689 G A 88.20% 0.00% G -> A
mr1050 (Ind_All); LR P-value: 4.74E-06;
mr1603 (All); LR P-value: 8.45E-06;
mr1425_2 (Ind_All); LR P-value: 6.22E-06;
mr1446_2 (All); LR P-value: 2.65E-07
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.141; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722691 (J) chr12 12722691 G A 92.30% 0.00% G -> A NA
LOC_Os12g22540.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.420; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722693 (J) chr12 12722693 G A 93.70% 0.42% G -> A
mr1063 (Ind_All); LR P-value: 2.90E-06;
mr1088 (Ind_All); LR P-value: 4.15E-06;
mr1180 (Ind_All); LR P-value: 1.61E-06;
mr1246 (Ind_All); LR P-value: 2.82E-06;
mr1063_2 (Ind_All); LR P-value: 4.38E-07;
mr1246_2 (Ind_All); LR P-value: 4.51E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.903; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722699 (J) chr12 12722699 C Unkown 99.40% 0.38% C -> T NA
LOC_Os12g22540.1 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 52.242; most accessible tissue: Minghui63 panicle, score: 74.563
vg1212722703 (J) chr12 12722703 G T 83.90% 0.36% T -> G
mr1023 (All); LR P-value: 1.88E-60;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1489 (All); LR P-value: 3.06E-69;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.86E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1013_2 (All); LR P-value: 3.65E-16;
mr1023_2 (All); LR P-value: 3.41E-72;
mr1031_2 (All); LR P-value: 5.07E-15;
mr1079_2 (All); LR P-value: 7.63E-54;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 8.89E-09;
mr1489_2 (All); LR P-value: 1.29E-78;
mr1606_2 (All); LR P-value: 9.68E-08;
mr1722_2 (All); LR P-value: 1.51E-12;
mr1879_2 (All); LR P-value: 5.05E-13
LOC_Os12g22540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g22540.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 52.856; most accessible tissue: Minghui63 young leaf, score: 75.006
vg1212722710 (J) chr12 12722710 T Unkown 99.60% 0.36% T -> C NA
LOC_Os12g22540.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os12g22530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 53.937; most accessible tissue: Minghui63 young leaf, score: 75.937
vg1212722721 (J) chr12 12722721 TG Unkown 99.50% 0.49% TG -> T NA
LOC_Os12g22540.1 Alt: T| frameshift_variant HIGH(snpEff)
The average chromatin accessibility score: 55.863; most accessible tissue: Minghui63 young leaf, score: 78.054
vg1212722741 (J) chr12 12722741 A G 99.80% 0.00% A -> G NA
LOC_Os12g22540.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os12g22530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 56.778; most accessible tissue: Minghui63 young leaf, score: 78.443
vg1212722795 (J) chr12 12722795 A G 99.80% 0.00% A -> G NA
LOC_Os12g22540.1 Alt: G| missense_variant&splice_region_variant MODERATE(snpEff)
LOC_Os12g22530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 59.086; most accessible tissue: Minghui63 young leaf, score: 79.896
vg1212722797 (J) chr12 12722797 G A 89.80% 0.00% G -> A,T
mr1164_2 (Ind_All); LR P-value: 5.41E-06;
mr1308_2 (Ind_All); LR P-value: 1.26E-06;
mr1361_2 (Ind_All); LR P-value: 1.02E-06;
mr1745_2 (Ind_All); LR P-value: 7.84E-06
LOC_Os12g22540.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g22540.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 59.045; most accessible tissue: Minghui63 young leaf, score: 79.896
vg1212722807 (J) chr12 12722807 G A 99.80% 0.00% G -> A NA
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 58.691; most accessible tissue: Minghui63 young leaf, score: 78.054
vg1212722819 (J) chr12 12722819 G T 99.80% 0.00% G -> T NA
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 58.447; most accessible tissue: Minghui63 young leaf, score: 78.054
vg1212722824 (J) chr12 12722824 G A 99.00% 0.00% G -> A NA
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 57.820; most accessible tissue: Minghui63 young leaf, score: 78.054
vg1212722844 (J) chr12 12722844 AC A 99.70% 0.00% AC -> A NA
LOC_Os12g22530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 55.301; most accessible tissue: Zhenshan97 flag leaf, score: 76.642
vg1212722845 (J) chr12 12722845 T C 71.40% 0.02% C -> T
mr1425 (Ind_All); LR P-value: 1.19E-06;
mr1942 (All); LR P-value: 5.32E-08;
mr1338_2 (Jap_All); LR P-value: 4.56E-08;
mr1425_2 (Ind_All); LR P-value: 4.51E-07;
mr1942_2 (All); LR P-value: 4.67E-13
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.280; most accessible tissue: Zhenshan97 flag leaf, score: 76.642
vg1212722858 (J) chr12 12722858 T C 83.60% 0.00% C -> T
mr1606 (Jap_All); LR P-value: 2.98E-06;
mr1657 (Jap_All); LR P-value: 8.56E-06;
mr1031_2 (Jap_All); LR P-value: 1.16E-07;
mr1189_2 (Jap_All); LR P-value: 1.73E-08;
mr1338_2 (Jap_All); LR P-value: 8.31E-09;
mr1471_2 (All); LR P-value: 1.29E-08;
mr1606_2 (All); LR P-value: 1.16E-07;
mr1879_2 (All); LR P-value: 8.18E-12
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.413; most accessible tissue: Minghui63 young leaf, score: 75.479
vg1212722861 (J) chr12 12722861 C T 99.90% 0.00% C -> T NA
LOC_Os12g22530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os12g22540.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 53.390; most accessible tissue: Minghui63 young leaf, score: 75.479
vg1212722887 (J) chr12 12722887 G C 77.00% 21.31% G -> C NA
LOC_Os12g22530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 54.620; most accessible tissue: Minghui63 young leaf, score: 76.820
vg1212722891 (J) chr12 12722891 CTT C 75.50% 0.00% CTT -> C NA
LOC_Os12g22530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g22540.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 54.620; most accessible tissue: Minghui63 young leaf, score: 77.243
vg1212722921 (J) chr12 12722921 G A 75.60% 0.00% G -> A,T
mr1677 (All); LR P-value: 1.57E-06;
mr1363_2 (All); LR P-value: 1.78E-06;
mr1925_2 (All); LR P-value: 1.82E-06
LOC_Os12g22540.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g22540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 56.689; most accessible tissue: Minghui63 young leaf, score: 78.821
vg1212722943 (J) chr12 12722943 G A 89.70% 0.00% G -> A
mr1164_2 (Ind_All); LR P-value: 5.67E-06;
mr1170_2 (Ind_All); LR P-value: 5.38E-07;
mr1308_2 (Ind_All); LMM P-value: 8.62E-06; LR P-value: 5.10E-08;
mr1361_2 (Ind_All); LR P-value: 8.57E-08;
mr1745_2 (Ind_All); LR P-value: 3.19E-06
LOC_Os12g22540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 57.710; most accessible tissue: Zhenshan97 flag leaf, score: 77.203
vg1212722969 (J) chr12 12722969 T C 99.70% 0.00% T -> C NA
LOC_Os12g22540.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.292; most accessible tissue: Zhenshan97 flag leaf, score: 77.473
vg1212722982 (J) chr12 12722982 G T 82.90% 0.00% G -> T
mr1016 (Ind_All); LR P-value: 6.29E-16;
mr1017 (Ind_All); LR P-value: 3.67E-14;
mr1022 (Ind_All); LR P-value: 5.50E-17;
mr1023 (Ind_All); LR P-value: 9.53E-12;
mr1055 (Ind_All); LR P-value: 1.51E-15;
mr1079 (Ind_All); LR P-value: 1.73E-15;
mr1132 (Ind_All); LR P-value: 1.40E-11;
mr1142 (Ind_All); LR P-value: 1.48E-12;
mr1178 (Ind_All); LR P-value: 4.82E-15;
mr1390 (Ind_All); LR P-value: 4.16E-14;
mr1408 (All); LR P-value: 1.73E-08;
mr1489 (Ind_All); LR P-value: 6.02E-07;
mr1490 (Ind_All); LR P-value: 3.64E-13;
mr1491 (Ind_All); LR P-value: 9.72E-12;
mr1546 (Ind_All); LR P-value: 1.22E-10;
mr1554 (All); LR P-value: 7.55E-07;
mr1805 (Ind_All); LR P-value: 3.99E-08;
mr1022_2 (Ind_All); LR P-value: 2.28E-17;
mr1023_2 (Ind_All); LR P-value: 1.20E-11;
mr1055_2 (Ind_All); LR P-value: 5.18E-16;
mr1079_2 (Ind_All); LR P-value: 1.01E-14;
mr1132_2 (Ind_All); LR P-value: 2.08E-12;
mr1178_2 (Ind_All); LR P-value: 1.90E-16;
mr1269_2 (All); LR P-value: 2.87E-06;
mr1390_2 (Ind_All); LR P-value: 1.43E-15;
mr1490_2 (Ind_All); LR P-value: 3.16E-14;
mr1546_2 (Ind_All); LMM P-value: 1.52E-06; LR P-value: 2.92E-13;
mr1587_2 (Ind_All); LR P-value: 3.56E-06;
mr1677_2 (All); LR P-value: 8.23E-06;
mr1792_2 (Ind_All); LR P-value: 3.34E-07;
mr1803_2 (Ind_All); LR P-value: 8.57E-06;
mr1805_2 (Ind_All); LR P-value: 1.21E-09
LOC_Os12g22540.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 57.126; most accessible tissue: Zhenshan97 flag leaf, score: 76.925