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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:

17 variations found. LOC_Os12g40460 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 25,035,052 bp to 25,036,501 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
vg1225035211 (J) chr12 25035211 G T 60.00% 5.37% T -> G
Grain_length (All); LR P-value: 2.03E-14;
Grain_length (Jap_All); LR P-value: 2.30E-15;
mr1115 (All); LR P-value: 2.19E-24;
mr1300 (All); LR P-value: 5.00E-22;
mr1486 (All); LR P-value: 8.69E-39;
mr1584 (All); LR P-value: 4.27E-22;
mr1584 (Jap_All); LR P-value: 1.88E-07;
mr1611 (All); LR P-value: 1.90E-22;
mr1778 (All); LR P-value: 5.52E-73;
mr1789 (All); LR P-value: 5.45E-32;
mr1844 (All); LR P-value: 3.52E-13;
mr1844 (Jap_All); LR P-value: 2.72E-06;
mr1853 (All); LR P-value: 1.31E-12;
mr1870 (Jap_All); LR P-value: 1.50E-06;
mr1879 (All); LR P-value: 4.18E-13;
mr1879 (Jap_All); LR P-value: 3.83E-12;
mr1880 (All); LR P-value: 2.25E-06;
mr1880 (Jap_All); LR P-value: 1.90E-10;
mr1013_2 (All); LR P-value: 2.72E-16;
mr1013_2 (Jap_All); LR P-value: 2.37E-07;
mr1031_2 (All); LR P-value: 1.57E-15;
mr1031_2 (Jap_All); LR P-value: 2.50E-09;
mr1047_2 (Jap_All); LR P-value: 3.64E-07;
mr1077_2 (Jap_All); LR P-value: 2.45E-06;
mr1087_2 (Jap_All); LR P-value: 1.26E-12;
mr1090_2 (Jap_All); LR P-value: 1.28E-08;
mr1091_2 (Jap_All); LR P-value: 6.70E-07;
mr1096_2 (Jap_All); LR P-value: 6.48E-08;
mr1115_2 (All); LR P-value: 6.62E-26;
mr1115_2 (Jap_All); LR P-value: 2.39E-14;
mr1156_2 (All); LR P-value: 2.16E-18;
mr1189_2 (Jap_All); LR P-value: 2.64E-09;
mr1235_2 (All); LR P-value: 4.43E-53;
mr1241_2 (All); LR P-value: 3.18E-63;
mr1241_2 (Jap_All); LR P-value: 1.32E-13;
mr1250_2 (All); LR P-value: 1.38E-06;
mr1268_2 (Jap_All); LR P-value: 2.25E-06;
mr1308_2 (All); LR P-value: 1.17E-21;
mr1308_2 (Jap_All); LR P-value: 5.23E-07;
mr1310_2 (All); LR P-value: 1.38E-31;
mr1334_2 (All); LR P-value: 3.79E-95;
mr1350_2 (Jap_All); LR P-value: 1.45E-07;
mr1361_2 (All); LR P-value: 1.19E-23;
mr1361_2 (Jap_All); LR P-value: 1.15E-10;
mr1368_2 (All); LR P-value: 3.62E-35;
mr1368_2 (Jap_All); LR P-value: 1.33E-10;
mr1454_2 (Jap_All); LR P-value: 4.88E-09;
mr1471_2 (Jap_All); LR P-value: 3.08E-10;
mr1486_2 (All); LR P-value: 3.74E-48;
mr1526_2 (Jap_All); LR P-value: 1.74E-08;
mr1539_2 (All); LR P-value: 6.77E-17;
mr1543_2 (Jap_All); LR P-value: 1.87E-09;
mr1584_2 (All); LR P-value: 4.39E-28;
mr1611_2 (All); LR P-value: 4.50E-23;
mr1642_2 (Jap_All); LR P-value: 3.88E-09;
mr1784_2 (All); LR P-value: 5.92E-45;
mr1789_2 (All); LR P-value: 1.34E-32;
mr1789_2 (Jap_All); LR P-value: 1.34E-12;
mr1794_2 (Jap_All); LR P-value: 1.74E-07;
mr1798_2 (Jap_All); LR P-value: 8.82E-07;
mr1805_2 (All); LR P-value: 5.01E-42;
mr1805_2 (Jap_All); LR P-value: 4.95E-08;
mr1844_2 (All); LR P-value: 9.99E-13;
mr1853_2 (All); LR P-value: 4.55E-13;
mr1853_2 (Jap_All); LR P-value: 6.42E-06;
mr1870_2 (Jap_All); LR P-value: 2.91E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40460.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40450.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.699; most accessible tissue: Zhenshan97 panicle, score: 99.948
vg1225035275 (J) chr12 25035275 A G 46.50% 20.19% G -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g40460.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.725; most accessible tissue: Zhenshan97 panicle, score: 99.951
vg1225035374 (J) chr12 25035374 T G 82.40% 0.00% G -> T
Grain_length (All); LR P-value: 6.34E-14;
Grain_length (Jap_All); LR P-value: 1.68E-15;
Grain_thickness (All); LR P-value: 4.08E-34;
mr1115 (All); LR P-value: 1.97E-23;
mr1308 (All); LR P-value: 9.39E-18;
mr1361 (All); LR P-value: 3.70E-14;
mr1368 (All); LR P-value: 1.88E-09;
mr1486 (All); LR P-value: 4.42E-37;
mr1575 (All); LR P-value: 5.46E-09;
mr1584 (All); LR P-value: 5.80E-22;
mr1584 (Jap_All); LR P-value: 8.39E-08;
mr1708 (All); LR P-value: 6.92E-06;
mr1789 (All); LR P-value: 7.78E-31;
mr1844 (All); LR P-value: 1.21E-12;
mr1853 (All); LR P-value: 7.92E-13;
mr1879 (All); LR P-value: 8.49E-13;
mr1880 (Jap_All); LR P-value: 1.47E-10;
mr1013_2 (All); LR P-value: 6.13E-16;
mr1013_2 (Jap_All); LR P-value: 5.89E-07;
mr1031_2 (All); LR P-value: 3.72E-15;
mr1031_2 (Jap_All); LR P-value: 8.96E-09;
mr1072_2 (Jap_All); LR P-value: 8.76E-06;
mr1077_2 (Jap_All); LR P-value: 1.73E-06;
mr1087_2 (Jap_All); LR P-value: 1.49E-12;
mr1090_2 (Jap_All); LR P-value: 1.53E-08;
mr1091_2 (Jap_All); LR P-value: 5.48E-07;
mr1096_2 (Jap_All); LR P-value: 4.21E-08;
mr1115_2 (All); LR P-value: 2.99E-26;
mr1115_2 (Jap_All); LR P-value: 1.76E-15;
mr1129_2 (Jap_All); LR P-value: 5.98E-06;
mr1137_2 (All); LR P-value: 1.00E-32;
mr1156_2 (All); LR P-value: 2.61E-19;
mr1189_2 (Jap_All); LR P-value: 8.16E-09;
mr1235_2 (All); LR P-value: 6.89E-52;
mr1241_2 (All); LR P-value: 8.52E-62;
mr1241_2 (Jap_All); LR P-value: 2.67E-14;
mr1250_2 (All); LR P-value: 7.68E-07;
mr1250_2 (Jap_All); LR P-value: 1.46E-06;
mr1268_2 (Jap_All); LR P-value: 1.99E-06;
mr1308_2 (All); LR P-value: 9.52E-22;
mr1361_2 (All); LR P-value: 1.31E-23;
mr1361_2 (Jap_All); LR P-value: 2.19E-10;
mr1368_2 (All); LR P-value: 1.76E-34;
mr1471_2 (All); LR P-value: 6.65E-09;
mr1486_2 (All); LR P-value: 2.85E-46;
mr1502_2 (Jap_All); LR P-value: 2.02E-07;
mr1526_2 (Jap_All); LR P-value: 4.84E-08;
mr1539_2 (All); LR P-value: 1.07E-17;
mr1543_2 (Jap_All); LR P-value: 2.60E-09;
mr1580_2 (Jap_All); LR P-value: 6.94E-10;
mr1584_2 (All); LR P-value: 1.07E-27;
mr1611_2 (All); LR P-value: 2.54E-23;
mr1611_2 (Jap_All); LR P-value: 2.78E-11;
mr1671_2 (Jap_All); LR P-value: 5.61E-07;
mr1746_2 (All); LR P-value: 2.25E-17;
mr1784_2 (All); LR P-value: 1.22E-44;
mr1789_2 (All); LR P-value: 3.12E-32;
mr1789_2 (Jap_All); LR P-value: 2.86E-13;
mr1794_2 (Jap_All); LR P-value: 1.96E-07;
mr1798_2 (Jap_All); LR P-value: 9.50E-07;
mr1805_2 (All); LR P-value: 8.13E-41;
mr1805_2 (Jap_All); LR P-value: 6.19E-08;
mr1844_2 (All); LR P-value: 3.64E-13;
mr1853_2 (All); LR P-value: 4.52E-13;
mr1862_2 (All); LR P-value: 1.70E-38;
mr1870_2 (Jap_All); LR P-value: 3.77E-06;
mr1952_2 (All); LR P-value: 7.17E-07
LOC_Os12g40460.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.680; most accessible tissue: Zhenshan97 panicle, score: 99.907
vg1225035405 (J) chr12 25035405 C A 82.50% 0.00% A -> C
Grain_length (All); LR P-value: 4.32E-14;
Grain_length (Jap_All); LR P-value: 2.30E-15;
mr1115 (All); LR P-value: 8.56E-24;
mr1308 (All); LR P-value: 3.27E-17;
mr1486 (All); LR P-value: 8.60E-39;
mr1575 (All); LR P-value: 6.81E-09;
mr1584 (All); LR P-value: 7.06E-21;
mr1584 (Jap_All); LR P-value: 1.88E-07;
mr1708 (All); LR P-value: 4.57E-06;
mr1778 (All); LR P-value: 1.34E-72;
mr1789 (All); LR P-value: 6.79E-32;
mr1844 (All); LR P-value: 1.39E-13;
mr1844 (Jap_All); LR P-value: 2.72E-06;
mr1853 (All); LR P-value: 8.23E-13;
mr1870 (Jap_All); LR P-value: 1.50E-06;
mr1879 (All); LR P-value: 2.16E-13;
mr1879 (Jap_All); LR P-value: 3.83E-12;
mr1880 (Jap_All); LR P-value: 1.90E-10;
mr1013_2 (All); LR P-value: 2.14E-16;
mr1013_2 (Jap_All); LR P-value: 2.37E-07;
mr1031_2 (All); LR P-value: 1.79E-15;
mr1031_2 (Jap_All); LR P-value: 2.50E-09;
mr1047_2 (Jap_All); LR P-value: 3.64E-07;
mr1077_2 (Jap_All); LR P-value: 2.45E-06;
mr1087_2 (Jap_All); LR P-value: 1.26E-12;
mr1090_2 (Jap_All); LR P-value: 1.28E-08;
mr1091_2 (Jap_All); LR P-value: 6.70E-07;
mr1096_2 (Jap_All); LR P-value: 6.48E-08;
mr1115_2 (All); LR P-value: 9.80E-26;
mr1115_2 (Jap_All); LR P-value: 2.39E-14;
mr1137_2 (All); LR P-value: 1.23E-32;
mr1156_2 (All); LR P-value: 5.97E-19;
mr1189_2 (Jap_All); LR P-value: 2.64E-09;
mr1235_2 (All); LR P-value: 1.23E-52;
mr1241_2 (All); LR P-value: 7.10E-64;
mr1241_2 (Jap_All); LR P-value: 1.32E-13;
mr1250_2 (All); LR P-value: 1.32E-06;
mr1268_2 (Jap_All); LR P-value: 2.25E-06;
mr1308_2 (All); LR P-value: 8.52E-22;
mr1308_2 (Jap_All); LR P-value: 5.23E-07;
mr1350_2 (Jap_All); LR P-value: 1.45E-07;
mr1361_2 (All); LR P-value: 3.03E-23;
mr1361_2 (Jap_All); LR P-value: 1.15E-10;
mr1368_2 (All); LR P-value: 6.29E-35;
mr1368_2 (Jap_All); LR P-value: 1.33E-10;
mr1454_2 (Jap_All); LR P-value: 4.88E-09;
mr1471_2 (All); LR P-value: 8.43E-09;
mr1471_2 (Jap_All); LR P-value: 3.08E-10;
mr1486_2 (All); LR P-value: 2.92E-48;
mr1526_2 (Jap_All); LR P-value: 1.74E-08;
mr1539_2 (All); LR P-value: 7.72E-17;
mr1543_2 (Jap_All); LR P-value: 1.87E-09;
mr1584_2 (All); LR P-value: 7.00E-28;
mr1611_2 (All); LR P-value: 9.58E-23;
mr1642_2 (Jap_All); LR P-value: 3.88E-09;
mr1746_2 (All); LR P-value: 9.17E-17;
mr1778_2 (All); LR P-value: 1.01E-73;
mr1784_2 (All); LR P-value: 2.32E-45;
mr1789_2 (All); LR P-value: 8.90E-33;
mr1789_2 (Jap_All); LR P-value: 1.34E-12;
mr1794_2 (Jap_All); LR P-value: 1.74E-07;
mr1798_2 (Jap_All); LR P-value: 8.82E-07;
mr1805_2 (All); LR P-value: 1.84E-40;
mr1805_2 (Jap_All); LR P-value: 4.95E-08;
mr1844_2 (All); LR P-value: 5.75E-13;
mr1853_2 (All); LR P-value: 2.36E-13;
mr1853_2 (Jap_All); LR P-value: 6.42E-06;
mr1870_2 (Jap_All); LR P-value: 2.91E-06
LOC_Os12g40460.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40450.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g40470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.498; most accessible tissue: Zhenshan97 panicle, score: 99.840
vg1225035494 (J) chr12 25035494 G A 79.40% 1.84% A -> G NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.954; most accessible tissue: Zhenshan97 panicle, score: 99.563
vg1225035684 (J) chr12 25035684 G GCGCCGC 31.80% 41.66% G -> GCGCCGC NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: GCGCCGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 93.361; most accessible tissue: Minghui63 panicle, score: 98.670
vg1225035686 (J) chr12 25035686 GCCGCCT G 44.30% 28.42% G -> GCCGCCT NA
LOC_Os12g40460.1 Alt: GCCGCCT| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 93.289; most accessible tissue: Minghui63 panicle, score: 98.608
vg1225035800 (J) chr12 25035800 T C 52.70% 19.45% C -> T NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.013; most accessible tissue: Minghui63 panicle, score: 98.135
vg1225036027 (J) chr12 25036027 C G 51.90% 14.41% G -> C NA
LOC_Os12g40460.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.482; most accessible tissue: Zhenshan97 flag leaf, score: 98.182
vg1225036175 (J) chr12 25036175 G A 61.80% 10.33% G -> A NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.209; most accessible tissue: Zhenshan97 flag leaf, score: 98.121
vg1225036188 (J) chr12 25036188 G A 63.10% 12.76% G -> A NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.107; most accessible tissue: Zhenshan97 flag leaf, score: 98.047
vg1225036192 (J) chr12 25036192 A G 64.10% 13.48% A -> G NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.119; most accessible tissue: Zhenshan97 flag leaf, score: 98.047
vg1225036195 (J) chr12 25036195 C G 64.50% 13.25% C -> G NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.113; most accessible tissue: Zhenshan97 flag leaf, score: 98.047
vg1225036199 (J) chr12 25036199 C T 66.10% 12.12% C -> T NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.117; most accessible tissue: Zhenshan97 flag leaf, score: 98.027
vg1225036212 (J) chr12 25036212 G GCTC 88.20% 7.43% G -> GCTC NA
LOC_Os12g40460.1 Alt: GCTC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.112; most accessible tissue: Zhenshan97 flag leaf, score: 98.019
vg1225036217 (J) chr12 25036217 G T 88.20% 7.30% G -> T NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.106; most accessible tissue: Zhenshan97 flag leaf, score: 98.043
vg1225036224 (J) chr12 25036224 C A 90.00% 6.41% C -> A NA
LOC_Os12g40460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g40460.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.105; most accessible tissue: Zhenshan97 flag leaf, score: 98.027