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Search Results:

36 variations found. LOC_Os01g74230 (retrotransposon protein; putative; unclassified; expressed), ranging from 42,997,433 bp to 43,003,542 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
vg0142998716 (J) chr01 42998716 G A 6.90% 91.49% G -> A NA
LOC_Os01g74230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.687; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0142999117 (J) chr01 42999117 G A 0.90% 94.37% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.478; most accessible tissue: Minghui63 root, score: 13.235
vg0142999150 (J) chr01 42999150 G A 1.10% 87.90% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.478; most accessible tissue: Minghui63 root, score: 13.235
vg0142999351 (J) chr01 42999351 G A 6.90% 90.29% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.742; most accessible tissue: Callus, score: 13.366
vg0142999406 (J) chr01 42999406 T C 7.00% 90.22% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.742; most accessible tissue: Callus, score: 13.366
vg0142999472 (J) chr01 42999472 A G 12.60% 77.78% A -> G NA
LOC_Os01g74230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.978; most accessible tissue: Callus, score: 15.971
vg0142999481 (J) chr01 42999481 G A 15.80% 75.92% G -> A NA
LOC_Os01g74230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.978; most accessible tissue: Callus, score: 15.971
vg0142999498 (J) chr01 42999498 G A 15.00% 76.58% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.978; most accessible tissue: Callus, score: 15.971
vg0142999531 (J) chr01 42999531 C T 0.60% 95.68% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 7.978; most accessible tissue: Callus, score: 15.971
vg0142999780 (J) chr01 42999780 A T 7.20% 89.46% A -> T NA
LOC_Os01g74230.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.120; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0142999785 (J) chr01 42999785 C T 7.50% 88.47% C -> T NA
LOC_Os01g74230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.120; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0142999845 (J) chr01 42999845 C T 12.60% 77.72% C -> T NA
LOC_Os01g74230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.687; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0142999864 (J) chr01 42999864 G A 9.50% 79.20% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.687; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0142999865 (J) chr01 42999865 T C 9.50% 79.09% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.687; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0142999885 (J) chr01 42999885 C T 7.30% 89.00% C -> T NA
LOC_Os01g74230.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.687; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0143000749 (J) chr01 43000749 G A 38.90% 41.87% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.858; most accessible tissue: Zhenshan97 panicle, score: 28.447
vg0143001130 (J) chr01 43001130 G A 11.50% 61.43% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.962; most accessible tissue: Minghui63 young leaf, score: 28.650
vg0143001172 (J) chr01 43001172 G A 7.00% 90.01% G -> A NA
LOC_Os01g74220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g74230.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 12.962; most accessible tissue: Minghui63 young leaf, score: 28.650
vg0143001305 (J) chr01 43001305 C T 10.80% 78.31% C -> T NA
LOC_Os01g74230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308
vg0143001308 (J) chr01 43001308 C T 7.50% 89.19% C -> T NA
LOC_Os01g74230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308
vg0143001310 (J) chr01 43001310 C G 10.60% 79.24% C -> G NA
LOC_Os01g74230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308
vg0143001311 (J) chr01 43001311 T C 10.20% 79.05% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 14.931; most accessible tissue: Zhenshan97 panicle, score: 32.308
vg0143001336 (J) chr01 43001336 G A 9.00% 80.24% G -> A NA
LOC_Os01g74230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.231; most accessible tissue: Zhenshan97 panicle, score: 32.308
vg0143001495 (J) chr01 43001495 G A 12.10% 81.06% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.618; most accessible tissue: Zhenshan97 panicle, score: 46.362
vg0143001519 (J) chr01 43001519 T C 7.70% 85.93% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 17.621; most accessible tissue: Zhenshan97 panicle, score: 46.362
vg0143001530 (J) chr01 43001530 A G 7.00% 87.43% A -> G NA
LOC_Os01g74230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 17.621; most accessible tissue: Zhenshan97 panicle, score: 46.362
vg0143001631 (J) chr01 43001631 G A 7.60% 89.17% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 16.535; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg0143001655 (J) chr01 43001655 G A 8.40% 87.52% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 16.119; most accessible tissue: Zhenshan97 panicle, score: 39.652
vg0143001802 (J) chr01 43001802 G A 7.70% 88.49% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.084; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0143001955 (J) chr01 43001955 T C 12.10% 75.01% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 5.895; most accessible tissue: Callus, score: 12.637
vg0143001958 (J) chr01 43001958 G A 12.20% 74.48% G -> A NA
LOC_Os01g74230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.972; most accessible tissue: Callus, score: 12.637
vg0143001996 (J) chr01 43001996 C T 10.30% 82.31% C -> T NA
LOC_Os01g74230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.048; most accessible tissue: Callus, score: 12.637
vg0143002027 (J) chr01 43002027 A G 9.10% 82.71% A -> G NA
LOC_Os01g74240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g74230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.048; most accessible tissue: Callus, score: 12.637
vg0143002036 (J) chr01 43002036 A G 9.10% 84.87% A -> G NA
LOC_Os01g74240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g74230.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.048; most accessible tissue: Callus, score: 12.637
vg0143002039 (J) chr01 43002039 A T 8.80% 84.93% A -> T NA
LOC_Os01g74240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g74230.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 6.048; most accessible tissue: Callus, score: 12.637
vg0143002415 (J) chr01 43002415 T C 10.40% 81.38% T -> C NA
LOC_Os01g74230.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g74230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 5.247; most accessible tissue: Zhenshan97 young leaf, score: 9.167