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:

22 variations found. LOC_Os08g03490 (ATBPM1; putative; expressed), ranging from 1,634,502 bp to 1,635,537 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
vg0801634534 (J) chr08 1634534 C T 70.60% 0.72% C -> T
mr1739 (All); LR P-value: 3.69E-08;
mr1739 (Ind_All); LMM P-value: 8.11E-06; LR P-value: 6.91E-14;
mr1751 (All); LR P-value: 1.28E-11;
mr1734_2 (All); LR P-value: 1.08E-11;
mr1739_2 (Ind_All); LR P-value: 1.27E-11
LOC_Os08g03490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.410; most accessible tissue: Minghui63 root, score: 77.290
vg0801634535 (J) chr08 1634535 C T 93.90% 0.70% C -> T
mr1230 (All); LR P-value: 7.05E-06;
mr1515 (All); LR P-value: 2.44E-18;
mr1633 (All); LR P-value: 7.85E-06;
mr1344_2 (All); LR P-value: 4.66E-06;
mr1510_2 (All); LR P-value: 1.14E-07;
mr1587_2 (All); LR P-value: 1.45E-15;
mr1803_2 (All); LR P-value: 8.76E-13
LOC_Os08g03490.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.410; most accessible tissue: Minghui63 root, score: 77.290
vg0801634584 (J) chr08 1634584 T C 89.50% 0.72% T -> C NA
LOC_Os08g03490.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.703; most accessible tissue: Minghui63 root, score: 79.522
vg0801634656 (J) chr08 1634656 T G 49.90% 0.78% G -> T NA
LOC_Os08g03490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.126; most accessible tissue: Minghui63 flag leaf, score: 83.197
vg0801634692 (J) chr08 1634692 G T 93.90% 0.72% G -> T,GTCAA
mr1344_2 (All); LR P-value: 1.93E-06;
mr1510_2 (All); LR P-value: 1.05E-07;
mr1587_2 (All); LR P-value: 1.32E-15;
mr1803_2 (All); LR P-value: 1.84E-12
LOC_Os08g03490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g03490.1 Alt: GTCAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.459; most accessible tissue: Minghui63 flag leaf, score: 83.197
vg0801634736 (J) chr08 1634736 CAA C 86.00% 0.74% CAA -> C NA
LOC_Os08g03490.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.955; most accessible tissue: Minghui63 flag leaf, score: 82.053
vg0801634797 (J) chr08 1634797 G A 97.20% 0.68% G -> A NA
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.827; most accessible tissue: Minghui63 flag leaf, score: 80.516
vg0801634981 (J) chr08 1634981 T C 70.40% 20.88% T -> C
mr1230 (All); LR P-value: 7.05E-06;
mr1515 (All); LR P-value: 2.44E-18;
mr1633 (All); LR P-value: 7.85E-06;
mr1344_2 (All); LR P-value: 4.66E-06;
mr1510_2 (All); LR P-value: 1.14E-07;
mr1587_2 (All); LR P-value: 1.45E-15;
mr1803_2 (All); LR P-value: 8.76E-13
LOC_Os08g03490.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 75.884; most accessible tissue: Zhenshan97 root, score: 82.361
vg0801634986 (J) chr08 1634986 A AACGGCG GCGACG 56.30% 0.78% AACGGCGGCG ACG -> A NA
LOC_Os08g03490.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 75.910; most accessible tissue: Zhenshan97 root, score: 81.974
vg0801634990 (J) chr08 1634990 G A 38.50% 53.26% G -> A NA
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.082; most accessible tissue: Zhenshan97 root, score: 82.361
vg0801634993 (J) chr08 1634993 G A 94.00% 0.72% G -> A NA
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 76.035; most accessible tissue: Zhenshan97 root, score: 82.361
vg0801635012 (J) chr08 1635012 C G 72.90% 0.78% C -> G
mr1739 (All); LR P-value: 2.92E-11;
mr1739 (Ind_All); LR P-value: 4.21E-09;
mr1751 (Ind_All); LR P-value: 8.35E-06;
mr1277_2 (Ind_All); LR P-value: 7.94E-06
LOC_Os08g03490.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 75.028; most accessible tissue: Zhenshan97 root, score: 81.772
vg0801635017 (J) chr08 1635017 C A 97.80% 0.72% C -> A NA
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.791; most accessible tissue: Zhenshan97 root, score: 81.772
vg0801635046 (J) chr08 1635046 G A 79.30% 0.78% G -> A
mr1739 (All); LR P-value: 4.07E-10;
mr1739 (Ind_All); LR P-value: 7.74E-08
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.821; most accessible tissue: Zhenshan97 root, score: 83.590
vg0801635056 (J) chr08 1635056 G A 93.90% 0.72% G -> A
mr1230 (All); LR P-value: 7.05E-06;
mr1515 (All); LR P-value: 2.44E-18;
mr1633 (All); LR P-value: 7.85E-06;
mr1344_2 (All); LR P-value: 4.66E-06;
mr1510_2 (All); LR P-value: 1.14E-07;
mr1587_2 (All); LR P-value: 1.45E-15;
mr1803_2 (All); LR P-value: 8.76E-13
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 74.279; most accessible tissue: Zhenshan97 root, score: 83.259
vg0801635116 (J) chr08 1635116 T TC 94.00% 0.70% T -> TC NA
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os08g03490.1 Alt: TC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.996; most accessible tissue: Zhenshan97 root, score: 83.259
vg0801635118 (J) chr08 1635118 A C 94.00% 0.70% A -> C NA
LOC_Os08g03490.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 72.254; most accessible tissue: Zhenshan97 root, score: 83.259
vg0801635160 (J) chr08 1635160 C T 97.80% 0.44% C -> T NA
LOC_Os08g03490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 72.887; most accessible tissue: Zhenshan97 root, score: 82.733
vg0801635240 (J) chr08 1635240 G A 99.20% 0.00% G -> A NA
LOC_Os08g03490.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os08g03500.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os08g03470.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g03480.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 76.438; most accessible tissue: Zhenshan97 root, score: 83.590
vg0801635294 (J) chr08 1635294 T C 58.00% 0.76% C -> T
mr1003 (All); LR P-value: 4.72E-21;
mr1109 (All); LR P-value: 1.10E-47;
mr1224 (All); LR P-value: 1.18E-30;
mr1745 (All); LR P-value: 1.00E-30;
mr1793 (All); LR P-value: 6.02E-29;
mr1828 (All); LR P-value: 1.28E-34;
mr1862 (All); LR P-value: 2.37E-23;
mr1088_2 (All); LR P-value: 1.77E-74;
mr1109_2 (All); LR P-value: 2.20E-56;
mr1131_2 (All); LR P-value: 3.73E-18;
mr1208_2 (All); LR P-value: 1.13E-38;
mr1224_2 (All); LR P-value: 1.70E-36;
mr1246_2 (All); LR P-value: 4.46E-75;
mr1270_2 (All); LR P-value: 7.33E-28;
mr1316_2 (All); LR P-value: 3.78E-23;
mr1745_2 (All); LR P-value: 9.88E-45;
mr1793_2 (All); LR P-value: 1.63E-45;
mr1932_2 (All); LR P-value: 3.26E-31;
mr1973_2 (All); LR P-value: 2.17E-98
LOC_Os08g03490.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.635; most accessible tissue: Zhenshan97 root, score: 83.751
vg0801635304 (J) chr08 1635304 C T 97.70% 0.70% C -> T NA
LOC_Os08g03490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.551; most accessible tissue: Zhenshan97 root, score: 84.358
vg0801635532 (J) chr08 1635532 G A 97.50% 0.40% G -> A NA
LOC_Os08g03490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g03490.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 73.072; most accessible tissue: Minghui63 root, score: 81.505