RiceVarMap2

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18 variations found. Os02g0624300/LOC_Os02g41510 (MYB family transcription factor; putative; expressed), ranging from 24,878,774 bp to 24,879,934 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene ID	Annotation
LOC_Os02g41510	MYB family transcription factor, putative, expressed; RAP ID: Os02g0624300; MSU ID: LOC_Os02g41510

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
STR0224878997 (J)	chr02	24878997	CGACG	CGACA	98.20%	0.00%	CGACG -> CGACA	NA
vg0224878894 (J)	chr02	24878894	A	G	99.00%	0.00%	A -> G	NA	LOC_Os02g41510.1 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g41500.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.425; most accessible tissue: Minghui63 young leaf, score: 94.199
vg0224878973 (J)	chr02	24878973	G	A	98.30%	0.00%	G -> A	NA	LOC_Os02g41510.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.940; most accessible tissue: Minghui63 young leaf, score: 93.956
vg0224878975 (J)	chr02	24878975	C	T	99.70%	0.00%	C -> T	NA	LOC_Os02g41510.1 Alt: T\| missense_variant MODERATE(snpEff) LOC_Os02g41500.1 Alt: T\| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.921; most accessible tissue: Zhenshan97 root, score: 93.893
vg0224879001 (J)	chr02	24879001	G	A	99.10%	0.00%	G -> A	NA	LOC_Os02g41510.1 Alt: A\| missense_variant MODERATE(snpEff) LOC_Os02g41500.1 Alt: A\| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.139; most accessible tissue: Zhenshan97 root, score: 94.386
vg0224879221 (J)	chr02	24879221	G	T	99.90%	0.00%	G -> T	NA	LOC_Os02g41510.1 Alt: T\| missense_variant MODERATE(snpEff) The average chromatin accessibility score: 88.440; most accessible tissue: Zhenshan97 root, score: 95.161
vg0224879222 (J)	chr02	24879222	C	A	99.90%	0.00%	C -> A	NA	LOC_Os02g41510.1 Alt: A\| synonymous_variant LOW(snpEff) The average chromatin accessibility score: 88.701; most accessible tissue: Zhenshan97 root, score: 95.209
vg0224879276 (J)	chr02	24879276	C	T	98.60%	0.00%	C -> T	NA	LOC_Os02g41510.1 Alt: T\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.909; most accessible tissue: Zhenshan97 young leaf, score: 94.791
vg0224879495 (J)	chr02	24879495	TATCCAA GGCAAAA G	T	98.70%	0.00%	TATCCAAGGC AAAAG -> T	NA	LOC_Os02g41510.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.988; most accessible tissue: Zhenshan97 root, score: 96.030
vg0224879522 (J)	chr02	24879522	G	T	99.50%	0.00%	G -> T	NA	LOC_Os02g41510.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.871; most accessible tissue: Zhenshan97 root, score: 96.146
vg0224879645 (J)	chr02	24879645	G	T	99.60%	0.00%	G -> T	NA	LOC_Os02g41510.1 Alt: T\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.271; most accessible tissue: Zhenshan97 root, score: 97.730
vg0224879664 (J)	chr02	24879664	G	A	87.00%	0.00%	G -> A	mr1158_2 (All); LR P-value: 4.12E-09; mr1167_2 (Ind_All); LR P-value: 8.41E-08	LOC_Os02g41510.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.560; most accessible tissue: Zhenshan97 root, score: 97.896
vg0224879731 (J)	chr02	24879731	G	C	99.50%	0.00%	G -> C	NA	LOC_Os02g41510.1 Alt: C\| missense_variant MODERATE(snpEff) The average chromatin accessibility score: 93.591; most accessible tissue: Zhenshan97 root, score: 98.886
vg0224879757 (J)	chr02	24879757	C	T	99.50%	0.00%	C -> T	NA	LOC_Os02g41510.1 Alt: T\| synonymous_variant LOW(snpEff) The average chromatin accessibility score: 94.272; most accessible tissue: Zhenshan97 root, score: 99.185
vg0224879763 (J)	chr02	24879763	C	T	99.50%	0.00%	C -> T	NA	LOC_Os02g41510.1 Alt: T\| synonymous_variant LOW(snpEff) The average chromatin accessibility score: 94.289; most accessible tissue: Zhenshan97 root, score: 99.190
vg0224879882 (J)	chr02	24879882	G	A	98.30%	0.00%	G -> A	NA	LOC_Os02g41510.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.072; most accessible tissue: Zhenshan97 root, score: 99.602
vg0224879887 (J)	chr02	24879887	CTCGGTG TGTGTGT GTGTTGC TGATGCT GCGTCG	C	86.80%	0.00%	CTCGGTGTGT GTGTGTGTTG CTGATGCTGC GTCG -> C	NA	LOC_Os02g41510.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.062; most accessible tissue: Zhenshan97 root, score: 99.610
vg0224879890 (J)	chr02	24879890	GGT	G	79.40%	11.55%	GGT -> G,GGTGT	NA	LOC_Os02g41510.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g41510.1 Alt: GGTGT\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.041; most accessible tissue: Zhenshan97 root, score: 99.602

Showing 1 to 18 of 18 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 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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