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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:

15 variations found. LOC_Os06g46960 (nucleic acid binding protein; putative; expressed), ranging from 28,487,833 bp to 28,488,642 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
vg0628487903 (J) chr06 28487903 G A 63.50% 0.00% A -> G
mr1172 (All); LR P-value: 9.67E-11;
mr1350_2 (All); LR P-value: 1.19E-23;
mr1968_2 (All); LR P-value: 1.21E-20
LOC_Os06g46960.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 97.889; most accessible tissue: Minghui63 flower, score: 99.514
vg0628487999 (J) chr06 28487999 T A 91.80% 0.00% T -> A
mr1262 (All); LR P-value: 4.06E-06;
mr1633 (All); LR P-value: 5.67E-06;
mr1158_2 (All); LR P-value: 8.12E-06
LOC_Os06g46950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g46970.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g46960.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.260; most accessible tissue: Minghui63 flower, score: 98.714
vg0628488098 (J) chr06 28488098 G T 91.80% 0.00% G -> T
mr1262 (All); LR P-value: 4.06E-06;
mr1633 (All); LR P-value: 5.67E-06;
mr1158_2 (All); LR P-value: 8.12E-06
LOC_Os06g46960.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.881; most accessible tissue: Minghui63 flower, score: 97.838
vg0628488152 (J) chr06 28488152 T C 91.80% 0.00% T -> C
mr1262 (All); LR P-value: 4.06E-06;
mr1633 (All); LR P-value: 5.67E-06;
mr1158_2 (All); LR P-value: 8.12E-06
LOC_Os06g46960.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.725; most accessible tissue: Zhenshan97 flag leaf, score: 97.754
vg0628488179 (J) chr06 28488179 C T 54.30% 0.00% T -> C NA
LOC_Os06g46960.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.031; most accessible tissue: Zhenshan97 flag leaf, score: 97.448
vg0628488186 (J) chr06 28488186 C A 91.90% 0.00% C -> A
mr1158_2 (All); LR P-value: 8.22E-06;
mr1166_2 (All); LR P-value: 9.90E-09
LOC_Os06g46960.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.951; most accessible tissue: Zhenshan97 flag leaf, score: 97.414
vg0628488255 (J) chr06 28488255 C T 91.80% 0.00% C -> T NA
LOC_Os06g46960.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.743; most accessible tissue: Zhenshan97 flag leaf, score: 97.487
vg0628488420 (J) chr06 28488420 C A 93.40% 0.00% C -> A
mr1158_2 (All); LR P-value: 8.75E-06;
mr1344_2 (All); LR P-value: 5.85E-06;
mr1740_2 (All); LR P-value: 6.66E-06
LOC_Os06g46960.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.892; most accessible tissue: Zhenshan97 flag leaf, score: 97.814
vg0628488430 (J) chr06 28488430 C A 91.80% 0.00% C -> A
mr1633 (All); LR P-value: 6.89E-06;
mr1158_2 (All); LR P-value: 4.26E-06
LOC_Os06g46960.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.109; most accessible tissue: Zhenshan97 flag leaf, score: 97.836
vg0628488468 (J) chr06 28488468 C G 87.60% 0.19% C -> G,T NA
LOC_Os06g46960.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g46960.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g46960.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 94.987; most accessible tissue: Zhenshan97 flag leaf, score: 97.657
vg0628488498 (J) chr06 28488498 C T 62.70% 0.00% T -> C
mr1172 (All); LR P-value: 8.67E-11;
mr1198 (All); LR P-value: 6.22E-09;
mr1480 (All); LR P-value: 1.04E-39;
mr1516 (All); LR P-value: 9.94E-06;
mr1350_2 (All); LR P-value: 2.16E-24;
mr1968_2 (All); LR P-value: 5.55E-21
LOC_Os06g46960.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.936; most accessible tissue: Zhenshan97 flag leaf, score: 97.668
vg0628488565 (J) chr06 28488565 G T 91.80% 0.00% G -> T NA
LOC_Os06g46960.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.474; most accessible tissue: Zhenshan97 flag leaf, score: 97.402
vg0628488567 (J) chr06 28488567 G T 96.00% 0.00% G -> T NA
LOC_Os06g46960.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.491; most accessible tissue: Zhenshan97 flag leaf, score: 97.414
vg0628488640 (J) chr06 28488640 TA T 89.30% 0.00% TA -> T,TAA NA
LOC_Os06g46960.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os06g46960.1 Alt: TAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.768; most accessible tissue: Zhenshan97 flag leaf, score: 96.833
STR0628488641 (J) chr06 28488641 AAA AAAA 88.20% 0.00% AAA -> AA,AAAA NA