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4 variations found. LOC_Os01g61310 (DUF640 domain containing protein; putative; expressed), ranging from 35,473,694 bp to 35,474,333 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
vg0135473772 (J) chr01 35473772 T C 57.00% 0.00% C -> T
mr1003 (All); LR P-value: 7.57E-22;
mr1008 (All); LMM P-value: 8.48E-09;
mr1008 (Ind_All); LMM P-value: 9.51E-09; LR P-value: 5.77E-13;
mr1009 (All); LMM P-value: 4.60E-09;
mr1009 (Ind_All); LMM P-value: 6.07E-10; LR P-value: 9.19E-14;
mr1527 (All); LR P-value: 2.15E-06;
mr1008_2 (All); LMM P-value: 4.83E-08;
mr1008_2 (Ind_All); LMM P-value: 5.13E-09; LR P-value: 9.03E-14;
mr1015_2 (Ind_All); LR P-value: 2.40E-06;
mr1051_2 (All); LR P-value: 2.45E-25;
mr1335_2 (All); LR P-value: 3.77E-08;
mr1517_2 (All); LMM P-value: 3.55E-07;
mr1527_2 (All); LR P-value: 4.91E-08
LOC_Os01g61310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.438; most accessible tissue: Minghui63 flower, score: 87.534
vg0135473791 (J) chr01 35473791 TGCAGCT GCAGCAG AA T 93.00% 0.00% TGCAGCTGCA GCAGAA -> T NA
LOC_Os01g61310.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 80.129; most accessible tissue: Minghui63 flower, score: 88.293
vg0135474260 (J) chr01 35474260 G A 99.20% 0.00% G -> A NA
LOC_Os01g61310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 85.151; most accessible tissue: Minghui63 root, score: 90.510
STR0135473786 (J) chr01 35473786 GCAGCTG CAGCTGC AG G 86.80% 0.00% GCAGCTGCAG CTGCAG -> G NA