RiceVarMap2

Search for Variation by Gene:

Search Results:

19 variations found. LOC_Os10g42320 (nonsense-mediated mRNA decay protein 3; putative; expressed), ranging from 22,781,928 bp to 22,784,426 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:

Color	Explain	Details
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:

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Search:

Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
STR1022781981 (J)	chr10	22781981	AA	AAAA	37.10%	0.00%	AAA -> AA,AAAA	NA
vg1022781936 (J)	chr10	22781936	T	C	98.70%	0.00%	T -> C	NA	LOC_Os10g42320.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022781980 (J)	chr10	22781980	G	GA	46.70%	0.00%	GA -> G,GAA	NA	LOC_Os10g42320.1 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42320.1 Alt: GAA\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: GAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: GAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: GAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: GAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: GAA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782009 (J)	chr10	22782009	T	A	84.10%	0.00%	T -> A	NA	LOC_Os10g42320.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782106 (J)	chr10	22782106	T	G	53.10%	0.11%	T -> G	mr1369 (All); LR P-value: 2.66E-07; mr1866 (All); LR P-value: 1.31E-08	LOC_Os10g42320.1 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782151 (J)	chr10	22782151	T	A	64.40%	0.11%	A -> T	mr1322 (All); LR P-value: 1.68E-09; mr1325 (All); LR P-value: 5.67E-11; mr1326 (All); LR P-value: 8.68E-14; mr1532 (All); LR P-value: 2.31E-06; mr1623 (All); LR P-value: 2.28E-10	LOC_Os10g42320.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782269 (J)	chr10	22782269	G	A	54.40%	0.00%	G -> A	mr1275 (All); LR P-value: 9.29E-09; mr1307 (All); LR P-value: 4.37E-10; mr1369 (All); LR P-value: 6.78E-08; mr1425 (All); LR P-value: 6.85E-06; mr1866 (All); LR P-value: 8.47E-09	LOC_Os10g42320.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782347 (J)	chr10	22782347	A	G	82.70%	0.00%	A -> G	NA	LOC_Os10g42320.1 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782411 (J)	chr10	22782411	G	A	99.80%	0.00%	G -> A	NA	LOC_Os10g42320.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os10g42299.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.4 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.5 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.3 Alt: A\| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782417 (J)	chr10	22782417	T	C	99.90%	0.00%	T -> C	NA	LOC_Os10g42320.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os10g42299.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.4 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.5 Alt: C\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.3 Alt: C\| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782558 (J)	chr10	22782558	C	T	53.30%	0.02%	C -> T	mr1275 (All); LR P-value: 1.05E-08; mr1307 (All); LR P-value: 2.84E-10; mr1369 (All); LR P-value: 1.69E-07; mr1425 (All); LR P-value: 4.50E-06; mr1866 (All); LR P-value: 1.25E-08	LOC_Os10g42320.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782587 (J)	chr10	22782587	C	T	64.30%	0.02%	T -> C	mr1322 (All); LR P-value: 1.68E-09; mr1325 (All); LR P-value: 5.67E-11; mr1326 (All); LR P-value: 8.68E-14; mr1532 (All); LR P-value: 2.31E-06; mr1623 (All); LR P-value: 2.28E-10	LOC_Os10g42320.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782650 (J)	chr10	22782650	G	T	98.80%	0.00%	G -> T	NA	LOC_Os10g42320.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.4 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.5 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g42299.3 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022782753 (J)	chr10	22782753	T	A	64.30%	0.04%	A -> T	mr1322 (All); LR P-value: 1.86E-09; mr1325 (All); LR P-value: 9.99E-11; mr1326 (All); LR P-value: 2.35E-13; mr1532 (All); LR P-value: 4.73E-06; mr1548 (All); LR P-value: 4.89E-22; mr1781 (All); LR P-value: 1.43E-06	LOC_Os10g42320.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os10g42320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022783061 (J)	chr10	22783061	G	A	53.30%	0.02%	G -> A	mr1369 (All); LR P-value: 3.39E-07; mr1425 (All); LR P-value: 7.93E-06	LOC_Os10g42320.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os10g42320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022783203 (J)	chr10	22783203	C	T	99.00%	0.00%	C -> T	NA	LOC_Os10g42320.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022783865 (J)	chr10	22783865	G	A	64.30%	0.00%	A -> G	mr1322 (All); LR P-value: 7.28E-10; mr1325 (All); LR P-value: 1.68E-11; mr1326 (All); LR P-value: 2.92E-14; mr1532 (All); LR P-value: 1.20E-06; mr1623 (All); LR P-value: 3.47E-10; mr1624 (Ind_All); LR P-value: 4.83E-06; mr1781 (All); LR P-value: 8.76E-07; mr1324_2 (All); LR P-value: 1.16E-14; mr1623_2 (All); LR P-value: 6.79E-07; mr1682_2 (Ind_All); LR P-value: 6.68E-06	LOC_Os10g42320.1 Alt: G\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022784261 (J)	chr10	22784261	C	T	64.30%	0.00%	T -> C	mr1322 (All); LR P-value: 1.82E-09; mr1325 (All); LR P-value: 8.86E-11; mr1326 (All); LR P-value: 1.18E-13; mr1532 (All); LR P-value: 3.61E-06; mr1548 (All); LR P-value: 1.98E-22; mr1623 (All); LR P-value: 3.81E-10; mr1781 (All); LR P-value: 1.17E-06	LOC_Os10g42320.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg1022784351 (J)	chr10	22784351	G	A	99.80%	0.00%	G -> A	NA	LOC_Os10g42320.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os10g42299.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.4 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.5 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42299.3 Alt: A\| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g42340.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125

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