RiceVarMap2

Search for Variation by Gene:

Search Results:

204 variations found. LOC_Os01g57540 (protein kinase; putative; expressed), ranging from 33,240,485 bp to 33,243,618 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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Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
vg0133240523 (J)	chr01	33240523	C	T	39.80%	58.78%	C -> T	NA	LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.645; most accessible tissue: Zhenshan97 panicle, score: 94.360
vg0133240524 (J)	chr01	33240524	C	T	39.90%	58.76%	C -> T	NA	LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.676; most accessible tissue: Zhenshan97 panicle, score: 94.440
vg0133240536 (J)	chr01	33240536	C	T	40.10%	58.87%	C -> T	NA	LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.757; most accessible tissue: Zhenshan97 panicle, score: 94.360
vg0133240537 (J)	chr01	33240537	G	A	37.00%	58.59%	G -> A	mr1545 (All); LR P-value: 9.58E-06; mr1510_2 (All); LR P-value: 2.68E-08; mr1702_2 (All); LR P-value: 8.15E-06	LOC_Os01g57540.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 51.727; most accessible tissue: Zhenshan97 panicle, score: 94.278
vg0133240555 (J)	chr01	33240555	T	C	34.70%	58.80%	T -> C	mr1545 (All); LR P-value: 9.75E-06; mr1510_2 (All); LR P-value: 1.07E-07	N Alt: DEL/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.945; most accessible tissue: Zhenshan97 panicle, score: 94.440
vg0133240670 (J)	chr01	33240670	G	T	37.30%	58.23%	G -> T	NA	LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 47.311; most accessible tissue: Zhenshan97 root, score: 91.389
vg0133240801 (J)	chr01	33240801	TGCGTCT TGG	T	37.00%	58.68%	TGCGTCTTGG -> T	NA	LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.288; most accessible tissue: Callus, score: 89.688
vg0133240937 (J)	chr01	33240937	AT	A	34.10%	58.93%	AT -> A,ATT	NA	LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: ATT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: ATT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: ATT\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: ATT\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 34.073; most accessible tissue: Callus, score: 91.770
vg0133240994 (J)	chr01	33240994	T	C	36.90%	58.78%	T -> C	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.980; most accessible tissue: Callus, score: 91.770
vg0133241416 (J)	chr01	33241416	G	T	37.00%	58.21%	G -> T	NA	LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 44.812; most accessible tissue: Zhenshan97 root, score: 94.797
vg0133241438 (J)	chr01	33241438	G	A	34.80%	58.42%	G -> A	NA	LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 44.981; most accessible tissue: Callus, score: 94.799
vg0133241501 (J)	chr01	33241501	T	TCA	35.80%	58.68%	T -> TCA,TCG	NA	LOC_Os01g57530.1 Alt: TCA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: TCA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: TCA\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: TCA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: TCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: TCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: TCG\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: TCG\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.876; most accessible tissue: Callus, score: 94.799
vg0133241518 (J)	chr01	33241518	C	T	40.10%	58.40%	C -> T	NA	LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.854; most accessible tissue: Callus, score: 94.799
vg0133241530 (J)	chr01	33241530	C	T	40.90%	58.89%	C -> T	NA	LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.955; most accessible tissue: Callus, score: 94.799
vg0133241534 (J)	chr01	33241534	C	T	40.80%	58.46%	C -> T	NA	LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.168; most accessible tissue: Callus, score: 94.799
vg0133241538 (J)	chr01	33241538	C	A	41.00%	58.80%	C -> A	NA	LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.206; most accessible tissue: Callus, score: 94.799
vg0133241542 (J)	chr01	33241542	G	A	41.20%	58.70%	G -> A	NA	LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.048; most accessible tissue: Callus, score: 94.799
vg0133241566 (J)	chr01	33241566	G	A	38.10%	58.25%	G -> A	NA	LOC_Os01g57530.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: A\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 45.666; most accessible tissue: Callus, score: 94.799
vg0133241649 (J)	chr01	33241649	A	G	34.90%	57.70%	A -> G	NA	LOC_Os01g57530.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.630; most accessible tissue: Zhenshan97 root, score: 90.472
vg0133241712 (J)	chr01	33241712	A	G	41.30%	55.18%	A -> G	NA	LOC_Os01g57530.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 46.597; most accessible tissue: Zhenshan97 root, score: 88.158
vg0133241761 (J)	chr01	33241761	T	G	57.30%	0.34%	G -> T	NA	LOC_Os01g57540.1 Alt: T\| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 48.425; most accessible tissue: Zhenshan97 root, score: 86.991
vg0133241766 (J)	chr01	33241766	T	A	52.90%	0.80%	A -> T	NA	LOC_Os01g57540.1 Alt: T\| splice_region_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 48.991; most accessible tissue: Zhenshan97 root, score: 86.991
vg0133241779 (J)	chr01	33241779	C	T	60.10%	0.00%	T -> C	NA	LOC_Os01g57540.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: C\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.715; most accessible tissue: Zhenshan97 root, score: 86.472
vg0133241791 (J)	chr01	33241791	A	T	40.00%	0.00%	A -> G,T	NA	LOC_Os01g57540.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: G\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.353; most accessible tissue: Zhenshan97 root, score: 86.472
vg0133241792 (J)	chr01	33241792	T	C	60.10%	0.00%	C -> T	NA	LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g57540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57530.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g57550.2 Alt: T\| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.353; most accessible tissue: Zhenshan97 root, score: 86.472

Showing 1 to 25 of 204 entries

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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: All SNP Only INDEL Only STR Only
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Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

Detailed Variation Information:

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