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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:

2 variations found. LOC_Os12g02220 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 691,572 bp to 691,998 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
vg1200691669 (J) chr12 691669 A G 99.90% 0.00% A -> G NA
LOC_Os12g02220.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.258; most accessible tissue: Zhenshan97 young leaf, score: 98.300
vg1200691824 (J) chr12 691824 C T 94.50% 0.00% C -> T
mr1073 (All); LR P-value: 9.03E-07;
mr1119 (All); LR P-value: 9.56E-18;
mr1153 (All); LR P-value: 4.90E-06;
mr1262 (All); LR P-value: 4.53E-08;
mr1320 (All); LR P-value: 3.45E-06;
mr1348 (All); LR P-value: 1.89E-08;
mr1442 (All); LR P-value: 1.92E-08;
mr1496 (All); LR P-value: 1.18E-15;
mr1545 (All); LR P-value: 9.45E-07;
mr1762 (All); LR P-value: 1.21E-06
LOC_Os12g02220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.433; most accessible tissue: Zhenshan97 young leaf, score: 98.932