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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:

24 variations found. LOC_Os01g49990 (retrotransposon protein; putative; unclassified), ranging from 28,724,107 bp to 28,724,440 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
vg0128724151 (J) chr01 28724151 C T 36.30% 51.65% C -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.320; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0128724161 (J) chr01 28724161 G A 31.80% 48.73% G -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.320; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0128724165 (J) chr01 28724165 G A 33.80% 52.26% G -> A NA
LOC_Os01g49990.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 9.320; most accessible tissue: Zhenshan97 panicle, score: 20.424
vg0128724176 (J) chr01 28724176 T C 33.50% 49.83% T -> C NA
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49990.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 10.888; most accessible tissue: Callus, score: 22.262
vg0128724188 (J) chr01 28724188 C Unkown 70.00% 26.81% C -> T NA
LOC_Os01g49990.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g49980.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g50010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g50000.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 10.888; most accessible tissue: Callus, score: 22.262
vg0128724191 (J) chr01 28724191 C A 66.70% 27.00% C -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.888; most accessible tissue: Callus, score: 22.262
vg0128724198 (J) chr01 28724198 C T 46.70% 16.25% C -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.888; most accessible tissue: Callus, score: 22.262
vg0128724214 (J) chr01 28724214 C T 69.60% 26.51% C -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.968; most accessible tissue: Callus, score: 22.262
vg0128724226 (J) chr01 28724226 C G 69.10% 26.72% C -> G NA
LOC_Os01g49990.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.799; most accessible tissue: Callus, score: 22.262
vg0128724229 (J) chr01 28724229 C T 69.10% 26.89% C -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.720; most accessible tissue: Callus, score: 22.262
vg0128724230 (J) chr01 28724230 G A 70.00% 26.87% G -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.720; most accessible tissue: Callus, score: 22.262
vg0128724232 (J) chr01 28724232 G T 70.10% 26.79% G -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.720; most accessible tissue: Callus, score: 22.262
vg0128724237 (J) chr01 28724237 T C 68.40% 26.56% T -> C NA
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 11.799; most accessible tissue: Callus, score: 22.262
vg0128724247 (J) chr01 28724247 C T 70.00% 26.77% C -> T NA
LOC_Os01g49990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.799; most accessible tissue: Callus, score: 22.262
vg0128724248 (J) chr01 28724248 G A 66.30% 28.40% G -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 11.799; most accessible tissue: Callus, score: 22.262
vg0128724263 (J) chr01 28724263 T C 67.00% 27.08% T -> C NA
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49990.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 13.416; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724266 (J) chr01 28724266 A G 69.00% 28.86% A -> G NA
LOC_Os01g49990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.840; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724268 (J) chr01 28724268 A G 32.90% 35.21% A -> G
mr1277 (Jap_All); LR P-value: 9.46E-06;
mr1837 (All); LR P-value: 2.50E-06
LOC_Os01g49990.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.840; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724279 (J) chr01 28724279 T C 31.60% 41.24% T -> C NA
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 14.372; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724293 (J) chr01 28724293 G A 32.50% 47.25% G -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 14.853; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724305 (J) chr01 28724305 A G 30.80% 57.85% A -> G NA
LOC_Os01g49990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.596; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724307 (J) chr01 28724307 T C 30.50% 59.69% T -> C NA
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49990.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 15.596; most accessible tissue: Zhenshan97 panicle, score: 24.575
vg0128724314 (J) chr01 28724314 A G 30.40% 58.23% A -> G NA
LOC_Os01g49990.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 16.599; most accessible tissue: Zhenshan97 panicle, score: 28.447
vg0128724425 (J) chr01 28724425 G A 27.30% 58.65% G -> A NA
LOC_Os01g49990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49990.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 17.918; most accessible tissue: Minghui63 panicle, score: 25.313