RiceVarMap2

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10 variations found. Os02g0832150/LOC_Os02g58540 (RING-H2 finger protein; putative; expressed), ranging from 35,783,283 bp to 35,784,146 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene ID	Annotation
LOC_Os02g58540	RING-H2 finger protein, putative, expressed; RAP ID: Os02g0832150; MSU ID: LOC_Os02g58540

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
STR0235783515 (J)	chr02	35783515	GGCGGTG G	GGCGGTG GCGGTGG CGGTGG	67.10%	0.00%	GGCGGTGGCG GTGGCGGTGG -> GGCGGTGG	NA
STR0235783761 (J)	chr02	35783761	CTGC	CTGCTGC	85.30%	0.00%	CTGCTGC -> CTGC	NA
vg0235783402 (J)	chr02	35783402	G	A	98.80%	0.00%	G -> A	NA	LOC_Os02g58540.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.868; most accessible tissue: Minghui63 flower, score: 85.758
vg0235783514 (J)	chr02	35783514	G	GGGCGGT GGCGGT	57.90%	0.00%	GGGCGGTGGC GGT -> G	NA	LOC_Os02g58540.1 Alt: G\| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 87.426; most accessible tissue: Callus, score: 93.514
vg0235783638 (J)	chr02	35783638	GCAGGTG GCGTGGG TCCCCAG C	G	99.90%	0.00%	GCAGGTGGCG TGGGTCCCCA GC -> G	NA	LOC_Os02g58540.1 Alt: G\| disruptive_inframe_deletion MODERATE(snpEff) LOC_Os02g58530.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.303; most accessible tissue: Zhenshan97 panicle, score: 93.133
vg0235783760 (J)	chr02	35783760	C	CCTG	88.30%	0.00%	CCTG -> C	NA	LOC_Os02g58540.1 Alt: C\| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 93.227; most accessible tissue: Zhenshan97 panicle, score: 95.654
vg0235783884 (J)	chr02	35783884	A	G	99.90%	0.00%	A -> G	NA	LOC_Os02g58540.1 Alt: G\| synonymous_variant LOW(snpEff) LOC_Os02g58530.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.961; most accessible tissue: Zhenshan97 panicle, score: 96.528
vg0235783924 (J)	chr02	35783924	A	G	59.30%	0.00%	G -> A	mr1021 (All); LR P-value: 1.35E-19; mr1029 (All); LR P-value: 2.57E-06; mr1047 (All); LR P-value: 3.79E-10; mr1189 (All); LR P-value: 1.85E-06; mr1325 (All); LR P-value: 4.36E-11; mr1326 (All); LR P-value: 2.70E-13; mr1580 (All); LR P-value: 1.13E-19; mr1625 (All); LR P-value: 5.25E-06; mr1657 (All); LR P-value: 1.01E-11; mr1744 (All); LR P-value: 1.55E-12; mr1782 (All); LR P-value: 7.88E-06; mr1796 (All); LR P-value: 1.19E-07; mr1990 (All); LR P-value: 2.92E-06; mr1064_2 (All); LR P-value: 3.51E-60; mr1270_2 (All); LR P-value: 2.00E-27; mr1316_2 (All); LR P-value: 6.52E-22; mr1323_2 (All); LR P-value: 1.72E-27; mr1326_2 (All); LR P-value: 2.04E-13; mr1744_2 (All); LR P-value: 1.44E-16; mr1745_2 (All); LR P-value: 1.01E-40; mr1782_2 (All); LR P-value: 1.55E-10; mr1932_2 (All); LR P-value: 4.57E-30; mr1970_2 (All); LR P-value: 1.37E-62; mr1973_2 (All); LR P-value: 8.78E-99	LOC_Os02g58540.1 Alt: A\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 91.799; most accessible tissue: Zhenshan97 panicle, score: 96.702
vg0235784118 (J)	chr02	35784118	A	G	98.80%	0.00%	A -> G	NA	LOC_Os02g58540.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58530.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.171; most accessible tissue: Zhenshan97 panicle, score: 98.187
vg0235784137 (J)	chr02	35784137	G	T	99.90%	0.00%	G -> T	NA	LOC_Os02g58540.1 Alt: T\| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g58530.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: T\| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.076; most accessible tissue: Zhenshan97 panicle, score: 98.145

Showing 1 to 10 of 10 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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Show Gene Expression Atlas	Show Chromatin Accessibility Map
Show Non-coding variation Scores

Search for Variation by Gene:

Optional: (The selected data will be displayed in the result page.)

Search Results:

Gene Expression Atlas:

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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