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Search Results:

11 variations found. LOC_Os04g59220 (retrotransposon protein; putative; unclassified; expressed), ranging from 35,226,101 bp to 35,227,499 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
vg0435226116 (J) chr04 35226116 A G 47.10% 27.53% A -> G NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.402; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226127 (J) chr04 35226127 A G 70.10% 19.74% A -> G NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.402; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226140 (J) chr04 35226140 T C 47.10% 27.36% T -> C NA
LOC_Os04g59220.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.402; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226145 (J) chr04 35226145 G A 69.90% 19.83% G -> A NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.402; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226147 (J) chr04 35226147 G A 69.90% 19.74% G -> A NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 7.402; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226174 (J) chr04 35226174 C T 67.40% 20.59% C -> T NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 7.482; most accessible tissue: Zhenshan97 root, score: 10.511
vg0435226336 (J) chr04 35226336 C T 46.00% 51.86% C -> T NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 7.909; most accessible tissue: Minghui63 panicle, score: 16.270
vg0435226685 (J) chr04 35226685 G A 44.90% 52.20% G -> A NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 9.639; most accessible tissue: Minghui63 panicle, score: 25.313
vg0435226987 (J) chr04 35226987 G A 36.40% 49.24% G -> A
mr1057 (All); LR P-value: 3.20E-06;
mr1076 (Jap_All); LR P-value: 1.79E-07;
mr1082 (Jap_All); LR P-value: 9.55E-08;
mr1083 (Jap_All); LR P-value: 7.11E-07;
mr1220 (Jap_All); LR P-value: 4.15E-06;
mr1230 (All); LR P-value: 1.40E-07;
mr1286 (All); LR P-value: 1.10E-06;
mr1345 (All); LR P-value: 2.89E-06;
mr1365 (All); LR P-value: 1.56E-07;
mr1400 (All); LR P-value: 7.13E-06;
mr1408 (Jap_All); LR P-value: 6.66E-06;
mr1417 (All); LR P-value: 7.60E-07;
mr1634 (All); LR P-value: 9.89E-06;
mr1665 (All); LR P-value: 2.33E-07;
mr1047_2 (All); LR P-value: 2.16E-10;
mr1104_2 (All); LMM P-value: 3.29E-06;
mr1220_2 (Jap_All); LR P-value: 2.46E-08;
mr1226_2 (All); LMM P-value: 1.90E-06;
mr1295_2 (All); LR P-value: 9.13E-06;
mr1319_2 (Jap_All); LR P-value: 4.21E-06;
mr1530_2 (All); LR P-value: 1.47E-14;
mr1740_2 (All); LR P-value: 3.61E-06;
mr1936_2 (Jap_All); LR P-value: 8.48E-06
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 10.405; most accessible tissue: Callus, score: 30.589
vg0435227339 (J) chr04 35227339 T C 33.50% 53.26% T -> C NA
LOC_Os04g59220.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.408; most accessible tissue: Callus, score: 14.467
vg0435227422 (J) chr04 35227422 G A 46.00% 52.09% G -> A NA
LOC_Os04g59220.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g59220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 6.408; most accessible tissue: Callus, score: 14.467