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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.):
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Search Results:

13 variations found. LOC_Os06g10670 (aspartic proteinase nepenthesin-1 precursor; putative; expressed), ranging from 5,569,909 bp to 5,571,471 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
vg0605569922 (J) chr06 5569922 G T 95.50% 0.74% G -> T NA
LOC_Os06g10670.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 86.500; most accessible tissue: Minghui63 root, score: 97.646
vg0605570211 (J) chr06 5570211 A G 40.10% 13.29% A -> G NA
LOC_Os06g10670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 90.371; most accessible tissue: Zhenshan97 flower, score: 95.886
vg0605570558 (J) chr06 5570558 G A 98.10% 0.80% G -> A NA
LOC_Os06g10670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.614; most accessible tissue: Zhenshan97 flower, score: 92.960
vg0605570582 (J) chr06 5570582 A G 98.40% 0.72% A -> G NA
LOC_Os06g10670.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.145; most accessible tissue: Zhenshan97 flower, score: 92.461
vg0605570787 (J) chr06 5570787 A C 98.30% 1.02% A -> C NA
LOC_Os06g10670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.413; most accessible tissue: Minghui63 root, score: 90.598
vg0605570832 (J) chr06 5570832 C T 93.00% 0.74% C -> T NA
LOC_Os06g10670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.089; most accessible tissue: Minghui63 root, score: 90.940
vg0605570858 (J) chr06 5570858 C A 98.90% 0.80% C -> A NA
LOC_Os06g10670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.524; most accessible tissue: Minghui63 root, score: 91.694
vg0605570913 (J) chr06 5570913 G A 98.10% 0.78% G -> A NA
LOC_Os06g10670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.689; most accessible tissue: Minghui63 root, score: 92.303
vg0605571243 (J) chr06 5571243 G T 98.80% 0.83% G -> T NA
LOC_Os06g10670.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.680; most accessible tissue: Minghui63 root, score: 95.353
vg0605571259 (J) chr06 5571259 C T 98.90% 0.80% C -> T NA
LOC_Os06g10670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g10670.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 83.134; most accessible tissue: Minghui63 root, score: 95.288
vg0605571394 (J) chr06 5571394 C T 99.70% 0.00% C -> T NA
LOC_Os06g10670.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.438; most accessible tissue: Minghui63 root, score: 94.097
vg0605571427 (J) chr06 5571427 A T 93.90% 0.00% A -> T NA
LOC_Os06g10670.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 73.665; most accessible tissue: Minghui63 root, score: 93.456
vg0605571453 (J) chr06 5571453 G A 92.60% 0.00% G -> A
mr1852 (All); LR P-value: 6.14E-06;
mr1397_2 (All); LR P-value: 4.59E-06;
mr1923_2 (All); LR P-value: 4.09E-08;
mr1923_2 (Jap_All); LR P-value: 9.92E-06
LOC_Os06g10670.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g10690.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 69.736; most accessible tissue: Minghui63 root, score: 92.642