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Search Results:

14 variations found. LOC_Os02g15000 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 8,367,221 bp to 8,368,328 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:

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
vg0208367268 (J) chr02 8367268 G A 83.10% 0.00% G -> A
mr1277 (Jap_All); LR P-value: 8.45E-06;
mr1336 (Ind_All); LR P-value: 9.05E-06;
mr1174_2 (Jap_All); LR P-value: 2.31E-07;
mr1277_2 (Jap_All); LR P-value: 1.02E-06;
mr1347_2 (Jap_All); LR P-value: 8.01E-08
LOC_Os02g15000.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14990.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.081; most accessible tissue: Zhenshan97 flag leaf, score: 92.310
vg0208367282 (J) chr02 8367282 C A 73.60% 0.00% C -> A,T NA
LOC_Os02g15000.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14990.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g15000.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14990.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 83.516; most accessible tissue: Zhenshan97 flag leaf, score: 92.451
vg0208367316 (J) chr02 8367316 C A 82.90% 0.00% C -> A NA
LOC_Os02g15000.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14990.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.949; most accessible tissue: Zhenshan97 flag leaf, score: 92.783
vg0208367386 (J) chr02 8367386 CGTG C 83.50% 0.00% CGTG -> C NA
LOC_Os02g15000.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 85.852; most accessible tissue: Zhenshan97 flag leaf, score: 95.054
vg0208367428 (J) chr02 8367428 G A 99.80% 0.00% G -> A NA
LOC_Os02g15000.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g14990.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g14980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g14980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.258; most accessible tissue: Zhenshan97 flag leaf, score: 95.200
vg0208367452 (J) chr02 8367452 C T 83.10% 0.00% C -> T
mr1277 (Jap_All); LR P-value: 8.45E-06;
mr1319 (All); LR P-value: 9.46E-06;
mr1336 (Ind_All); LR P-value: 7.37E-06;
mr1174_2 (Jap_All); LR P-value: 2.31E-07;
mr1277_2 (Jap_All); LR P-value: 1.02E-06;
mr1347_2 (Jap_All); LR P-value: 8.01E-08
LOC_Os02g15000.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.807; most accessible tissue: Zhenshan97 flag leaf, score: 95.521
vg0208367544 (J) chr02 8367544 CCGCCG C 99.70% 0.00% CCGCCG -> C NA
LOC_Os02g15000.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 90.681; most accessible tissue: Zhenshan97 flag leaf, score: 96.809
vg0208367670 (J) chr02 8367670 C G 75.90% 1.31% G -> C NA
LOC_Os02g15000.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g15000.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.548; most accessible tissue: Zhenshan97 flag leaf, score: 97.647
vg0208367779 (J) chr02 8367779 C T 54.30% 0.00% C -> T,G NA
LOC_Os02g15000.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g15000.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.223; most accessible tissue: Zhenshan97 flag leaf, score: 97.906
vg0208367844 (J) chr02 8367844 C G 90.50% 0.00% C -> G
mr1570 (All); LR P-value: 1.12E-08;
mr1126_2 (All); LR P-value: 1.23E-06
LOC_Os02g15000.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.109; most accessible tissue: Zhenshan97 flag leaf, score: 98.011
vg0208367927 (J) chr02 8367927 G C 69.70% 0.00% G -> C NA
LOC_Os02g15000.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.785; most accessible tissue: Zhenshan97 flag leaf, score: 98.271
vg0208368144 (J) chr02 8368144 G T 99.20% 0.00% G -> T NA
LOC_Os02g15000.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g14990.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.596; most accessible tissue: Zhenshan97 root, score: 98.641
vg0208368157 (J) chr02 8368157 G C 90.40% 0.00% G -> C
mr1570 (All); LR P-value: 2.04E-08;
mr1126_2 (All); LR P-value: 1.25E-06;
mr1612_2 (All); LR P-value: 9.01E-08
LOC_Os02g15000.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g14990.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.451; most accessible tissue: Zhenshan97 root, score: 98.646
STR0208367380 (J) chr02 8367380 CGCCGCC G CGCCG 81.50% 0.00% CGCCGCCG -> CGCCG NA