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Search Results:

10 variations found. Os04g0488700/LOC_Os04g41160 (protein kinase; putative; expressed), ranging from 24,416,320 bp to 24,418,474 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os04g41160 protein kinase, putative, expressed; RAP ID: Os04g0488700; MSU ID: LOC_Os04g41160

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:

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
vg0424416336 (J) chr04 24416336 C T 97.80% 0.00% C -> T NA
LOC_Os04g41160.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.902; most accessible tissue: Zhenshan97 flower, score: 97.735
vg0424416872 (J) chr04 24416872 C T 99.70% 0.00% C -> T NA
LOC_Os04g41160.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os04g41170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.323; most accessible tissue: Minghui63 flower, score: 97.148
vg0424417295 (J) chr04 24417295 C T 98.60% 0.00% C -> T NA
LOC_Os04g41160.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.455; most accessible tissue: Minghui63 flag leaf, score: 97.221
vg0424417397 (J) chr04 24417397 G A 99.80% 0.00% G -> A NA
LOC_Os04g41160.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os04g41170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.705; most accessible tissue: Minghui63 flag leaf, score: 97.535
vg0424417521 (J) chr04 24417521 A G 55.20% 0.38% G -> A
mr1609 (All); LR P-value: 8.54E-12;
mr1825 (All); LR P-value: 1.22E-16;
mr1609_2 (All); LR P-value: 2.89E-23;
mr1666_2 (All); LR P-value: 7.13E-12
LOC_Os04g41160.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41160.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.861; most accessible tissue: Minghui63 flag leaf, score: 97.621
vg0424417775 (J) chr04 24417775 C G 51.90% 0.32% G -> C
mr1609 (All); LR P-value: 5.44E-11;
mr1754_2 (All); LR P-value: 2.74E-06
LOC_Os04g41160.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g41160.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 90.315; most accessible tissue: Minghui63 flag leaf, score: 98.458
vg0424417800 (J) chr04 24417800 A T 99.90% 0.00% A -> T NA
LOC_Os04g41170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g41160.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 90.237; most accessible tissue: Minghui63 flag leaf, score: 98.426
vg0424417804 (J) chr04 24417804 T A 98.60% 0.00% T -> A NA
LOC_Os04g41170.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41160.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.256; most accessible tissue: Minghui63 flag leaf, score: 98.426
vg0424418008 (J) chr04 24418008 A G 55.00% 0.38% G -> A
mr1609 (All); LR P-value: 1.05E-11;
mr1609_2 (All); LR P-value: 6.06E-23
LOC_Os04g41160.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41160.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.136; most accessible tissue: Minghui63 flag leaf, score: 99.085
vg0424418449 (J) chr04 24418449 G T 99.00% 0.00% G -> T NA
LOC_Os04g41160.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g41170.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 99.267; most accessible tissue: Minghui63 flag leaf, score: 99.725