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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:

16 variations found. LOC_Os06g34360 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 20,000,026 bp to 20,000,815 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
vg0620000034 (J) chr06 20000034 G A 81.50% 4.34% G -> A NA
LOC_Os06g34360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.373; most accessible tissue: Zhenshan97 flower, score: 96.227
vg0620000064 (J) chr06 20000064 C T 82.90% 3.66% C -> T NA
LOC_Os06g34360.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.652; most accessible tissue: Zhenshan97 flower, score: 96.273
vg0620000083 (J) chr06 20000083 C A 89.80% 5.37% C -> A NA
LOC_Os06g34360.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.731; most accessible tissue: Zhenshan97 flower, score: 96.163
vg0620000127 (J) chr06 20000127 G A 91.40% 5.82% G -> A NA
LOC_Os06g34360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.127; most accessible tissue: Zhenshan97 flower, score: 96.097
vg0620000170 (J) chr06 20000170 G A 91.70% 5.44% G -> A NA
LOC_Os06g34360.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.261; most accessible tissue: Zhenshan97 flower, score: 95.508
vg0620000187 (J) chr06 20000187 G GGCA 90.40% 4.66% G -> GGCA NA
LOC_Os06g34360.1 Alt: GGCA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.707; most accessible tissue: Zhenshan97 flower, score: 95.668
vg0620000207 (J) chr06 20000207 G C 44.70% 6.39% C -> G NA
LOC_Os06g34360.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.346; most accessible tissue: Zhenshan97 flower, score: 96.018
vg0620000311 (J) chr06 20000311 G A 96.80% 0.76% G -> A NA
LOC_Os06g34360.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.494; most accessible tissue: Zhenshan97 flower, score: 96.740
vg0620000422 (J) chr06 20000422 C T 72.30% 0.87% T -> C NA
LOC_Os06g34360.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.586; most accessible tissue: Zhenshan97 flower, score: 95.811
vg0620000507 (J) chr06 20000507 C T 99.00% 0.00% C -> T NA
LOC_Os06g34360.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.751; most accessible tissue: Zhenshan97 flower, score: 95.286
vg0620000541 (J) chr06 20000541 C G 99.60% 0.00% C -> G NA
LOC_Os06g34360.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 87.392; most accessible tissue: Zhenshan97 flower, score: 95.779
vg0620000588 (J) chr06 20000588 G A 99.50% 0.34% G -> A NA
LOC_Os06g34360.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 85.957; most accessible tissue: Zhenshan97 root, score: 96.388
vg0620000632 (J) chr06 20000632 C G 92.00% 0.30% C -> G NA
LOC_Os06g34360.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.818; most accessible tissue: Zhenshan97 root, score: 97.282
vg0620000720 (J) chr06 20000720 A C 65.30% 0.32% C -> A
mr1190 (All); LR P-value: 5.45E-07;
mr1245 (All); LR P-value: 6.99E-07;
mr1325 (All); LR P-value: 4.87E-11;
mr1326 (All); LR P-value: 8.46E-13;
mr1532 (All); LR P-value: 3.91E-06;
mr1690 (All); LR P-value: 4.07E-07;
mr1950 (All); LR P-value: 3.51E-15;
mr1846_2 (Ind_All); LR P-value: 4.23E-08
LOC_Os06g34360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.230; most accessible tissue: Zhenshan97 root, score: 97.429
vg0620000738 (J) chr06 20000738 A C 64.40% 0.30% C -> A
mr1245 (All); LR P-value: 7.21E-07;
mr1324 (All); LR P-value: 1.88E-15;
mr1325 (All); LR P-value: 8.94E-11;
mr1326 (All); LR P-value: 1.62E-12;
mr1335 (All); LR P-value: 3.01E-13;
mr1532 (All); LR P-value: 6.34E-06;
mr1646 (All); LR P-value: 2.73E-06;
mr1690 (All); LR P-value: 7.68E-07;
mr1726 (All); LR P-value: 1.80E-13;
mr1950 (All); LR P-value: 3.34E-15;
mr1846_2 (Ind_All); LR P-value: 1.36E-08
LOC_Os06g34360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.846; most accessible tissue: Zhenshan97 root, score: 97.485
vg0620000787 (J) chr06 20000787 T C 64.50% 0.30% C -> T
mr1245 (All); LR P-value: 6.45E-07;
mr1335 (All); LR P-value: 9.26E-13;
mr1726 (All); LR P-value: 1.06E-13;
mr1950 (All); LR P-value: 2.11E-15
LOC_Os06g34360.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 84.888; most accessible tissue: Zhenshan97 root, score: 97.730