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18 variations found. LOC_Os08g01250 (retrotransposon protein; putative; unclassified), ranging from 164,156 bp to 164,483 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
vg0800164184 (J) chr08 164184 C T 31.60% 62.63% C -> T NA
LOC_Os08g01250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164252 (J) chr08 164252 G T 32.30% 63.84% G -> T NA
LOC_Os08g01250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164267 (J) chr08 164267 G A 33.00% 62.61% G -> A NA
LOC_Os08g01250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164289 (J) chr08 164289 C A 31.30% 56.41% C -> A
mr1118 (Jap_All); LR P-value: 2.25E-07;
mr1123 (Jap_All); LR P-value: 2.63E-08;
mr1150 (Jap_All); LR P-value: 3.89E-06;
mr1240 (Jap_All); LR P-value: 2.40E-07;
mr1242 (Jap_All); LR P-value: 7.48E-06;
mr1495 (Jap_All); LR P-value: 5.71E-07;
mr1496 (Jap_All); LR P-value: 6.99E-07;
mr1693 (Jap_All); LR P-value: 2.73E-08;
mr1936 (Jap_All); LR P-value: 4.12E-06;
mr1961 (Jap_All); LR P-value: 1.49E-07;
mr1113_2 (Jap_All); LR P-value: 1.86E-06;
mr1118_2 (Jap_All); LR P-value: 3.63E-07;
mr1240_2 (Jap_All); LR P-value: 5.72E-06
LOC_Os08g01250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164306 (J) chr08 164306 T C 29.20% 65.34% T -> C
mr1746 (All); LR P-value: 1.17E-10;
mr1020_2 (All); LR P-value: 4.61E-06;
mr1529_2 (All); LR P-value: 1.78E-14;
mr1746_2 (All); LR P-value: 2.04E-19;
mr1746_2 (Jap_All); LR P-value: 1.52E-09;
mr1805_2 (Jap_All); LR P-value: 9.13E-08;
mr1866_2 (All); LR P-value: 3.86E-15
LOC_Os08g01250.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164325 (J) chr08 164325 A G 73.70% 19.64% A -> G NA
LOC_Os08g01250.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164332 (J) chr08 164332 G A 38.50% 18.58% G -> A NA
LOC_Os08g01250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164338 (J) chr08 164338 G A 74.60% 18.83% G -> A NA
LOC_Os08g01250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164349 (J) chr08 164349 T C 32.20% 19.30% T -> C
mr1653 (All); LR P-value: 1.23E-14;
mr1746 (All); LR P-value: 2.12E-10;
mr1746_2 (All); LR P-value: 3.23E-18
LOC_Os08g01250.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01250.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164350 (J) chr08 164350 A G 32.00% 18.56% A -> G
mr1746 (All); LR P-value: 9.02E-10;
mr1746_2 (All); LR P-value: 2.79E-18
LOC_Os08g01250.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164360 (J) chr08 164360 A G 74.40% 18.39% A -> G NA
LOC_Os08g01250.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164366 (J) chr08 164366 A G 76.20% 19.53% A -> G NA
LOC_Os08g01250.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164367 (J) chr08 164367 C A 38.30% 18.01% C -> A NA
LOC_Os08g01250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164390 (J) chr08 164390 C T 70.50% 19.89% C -> T NA
LOC_Os08g01250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164396 (J) chr08 164396 C T 74.30% 18.66% C -> T NA
LOC_Os08g01250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164413 (J) chr08 164413 G A 32.30% 48.12% G -> A
mr1653 (All); LR P-value: 6.56E-14;
mr1746 (All); LR P-value: 5.26E-09
LOC_Os08g01250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164418 (J) chr08 164418 A G 40.10% 49.45% A -> G NA
LOC_Os08g01250.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0800164423 (J) chr08 164423 C T 38.40% 51.54% C -> T NA
LOC_Os08g01250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g01250.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125