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:

18 variations found. LOC_Os01g60860 (spotted leaf 11; putative; expressed), ranging from 35,185,510 bp to 35,188,004 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
vg0135185564 (J) chr01 35185564 AAC A 78.40% 0.00% A -> AAC NA
The average chromatin accessibility score: 98.799; most accessible tissue: Minghui63 flower, score: 99.532
vg0135185703 (J) chr01 35185703 G T 64.30% 0.00% T -> G NA
LOC_Os01g60860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.400; most accessible tissue: Minghui63 flower, score: 99.448
vg0135185709 (J) chr01 35185709 A G 52.90% 0.00% G -> A
mr1003 (All); LR P-value: 4.77E-22;
mr1008 (All); LMM P-value: 4.96E-10;
mr1008 (Ind_All); LMM P-value: 8.94E-12; LR P-value: 2.36E-16;
mr1009 (All); LMM P-value: 1.61E-10;
mr1009 (Ind_All); LMM P-value: 6.70E-13; LR P-value: 2.66E-16;
mr1051 (All); LR P-value: 1.99E-21;
mr1883 (All); LR P-value: 3.24E-11;
mr1914 (All); LR P-value: 2.79E-12;
mr1008_2 (All); LMM P-value: 6.21E-08;
mr1008_2 (Ind_All); LMM P-value: 6.88E-11; LR P-value: 3.49E-15;
mr1051_2 (All); LR P-value: 2.41E-25;
mr1221_2 (All); LR P-value: 4.83E-34;
mr1527_2 (All); LR P-value: 1.23E-07;
mr1782_2 (All); LR P-value: 4.07E-10
LOC_Os01g60860.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.350; most accessible tissue: Minghui63 flower, score: 99.418
vg0135185718 (J) chr01 35185718 A G 97.70% 0.00% A -> G NA
LOC_Os01g60860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.387; most accessible tissue: Minghui63 flower, score: 99.433
vg0135185720 (J) chr01 35185720 ACT A 99.50% 0.00% ACT -> A NA
LOC_Os01g60860.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.378; most accessible tissue: Minghui63 flower, score: 99.421
vg0135185727 (J) chr01 35185727 AC A 99.50% 0.00% AC -> A NA
LOC_Os01g60860.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.416; most accessible tissue: Minghui63 flower, score: 99.437
vg0135185730 (J) chr01 35185730 GCAAGAA GGGGGGA AAAATTA TGT G 99.50% 0.00% GCAAGAAGGG GGGAAAAATT ATGT -> G NA
LOC_Os01g60860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.425; most accessible tissue: Minghui63 flower, score: 99.437
vg0135185736 (J) chr01 35185736 A AGG 42.50% 25.07% A -> AGG NA
LOC_Os01g60860.1 Alt: AGG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 98.410; most accessible tissue: Minghui63 flower, score: 99.427
vg0135185742 (J) chr01 35185742 G GA 74.90% 0.36% GA -> G NA
LOC_Os01g60860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 98.416; most accessible tissue: Minghui63 flower, score: 99.417
vg0135185756 (J) chr01 35185756 C G 99.50% 0.00% C -> G NA
LOC_Os01g60860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.338; most accessible tissue: Minghui63 flower, score: 99.340
vg0135185840 (J) chr01 35185840 A G 64.40% 0.00% G -> A NA
LOC_Os01g60860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.901; most accessible tissue: Minghui63 flower, score: 99.457
vg0135186289 (J) chr01 35186289 A T 64.40% 0.00% T -> A NA
LOC_Os01g60860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.014; most accessible tissue: Minghui63 flower, score: 98.224
vg0135187005 (J) chr01 35187005 T C 98.60% 0.00% T -> C NA
LOC_Os01g60860.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 93.911; most accessible tissue: Zhenshan97 flag leaf, score: 97.862
vg0135187080 (J) chr01 35187080 G A 99.80% 0.00% G -> A NA
LOC_Os01g60860.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 90.766; most accessible tissue: Minghui63 flower, score: 97.650
vg0135187397 (J) chr01 35187397 G A 78.40% 0.00% A -> G
mr1190 (All); LR P-value: 2.83E-07;
mr1532 (All); LR P-value: 7.91E-06;
mr1740 (All); LR P-value: 2.77E-13;
mr1282_2 (All); LR P-value: 3.33E-10;
mr1404_2 (Jap_All); LR P-value: 1.82E-06;
mr1520_2 (All); LR P-value: 1.49E-11
LOC_Os01g60860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.601; most accessible tissue: Minghui63 flower, score: 97.680
vg0135187738 (J) chr01 35187738 A G 77.30% 0.00% G -> A
mr1518 (Jap_All); LR P-value: 1.63E-06;
mr1584 (All); LR P-value: 4.46E-21;
mr1584 (Jap_All); LR P-value: 7.95E-07;
mr1676 (Jap_All); LR P-value: 3.02E-06;
mr1714 (All); LR P-value: 4.84E-10;
mr1740 (All); LR P-value: 1.26E-13;
mr1178_2 (Jap_All); LR P-value: 9.47E-13;
mr1282_2 (All); LR P-value: 4.35E-10;
mr1520_2 (All); LR P-value: 6.00E-12;
mr1568_2 (All); LR P-value: 1.28E-06
LOC_Os01g60860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 97.894; most accessible tissue: Minghui63 flower, score: 99.021
vg0135187866 (J) chr01 35187866 G C 52.90% 0.00% C -> G
mr1003 (All); LR P-value: 4.10E-22;
mr1008 (All); LMM P-value: 5.04E-09;
mr1008 (Ind_All); LMM P-value: 3.37E-10; LR P-value: 3.40E-15;
mr1009 (All); LMM P-value: 1.44E-09;
mr1009 (Ind_All); LMM P-value: 1.17E-11; LR P-value: 1.29E-15;
mr1014 (Ind_All); LR P-value: 6.93E-06;
mr1015 (Ind_All); LR P-value: 4.85E-06;
mr1051 (All); LR P-value: 1.16E-21;
mr1527 (All); LR P-value: 2.47E-06;
mr1580 (All); LR P-value: 1.42E-19;
mr1583 (All); LR P-value: 5.15E-16;
mr1883 (All); LR P-value: 3.62E-11;
mr1914 (All); LR P-value: 1.02E-11;
mr1008_2 (All); LMM P-value: 5.11E-07;
mr1008_2 (Ind_All); LMM P-value: 4.64E-09; LR P-value: 2.25E-14;
mr1015_2 (Ind_All); LR P-value: 2.10E-06;
mr1047_2 (All); LR P-value: 4.17E-10;
mr1051_2 (All); LR P-value: 1.46E-25;
mr1189_2 (All); LR P-value: 2.31E-12;
mr1218_2 (All); LR P-value: 4.76E-19;
mr1221_2 (All); LR P-value: 5.09E-35;
mr1527_2 (All); LR P-value: 4.21E-08;
mr1782_2 (All); LR P-value: 1.21E-10;
mr1825_2 (All); LR P-value: 3.63E-29;
mr1834_2 (All); LR P-value: 6.02E-07;
mr1850_2 (All); LR P-value: 5.66E-11
LOC_Os01g60860.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60870.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.333; most accessible tissue: Zhenshan97 root, score: 99.305
STR0135185743 (J) chr01 35185743 AA AAA 64.50% 0.00% AAA -> AA NA