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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:

11 variations found. LOC_Os01g60730 (RING-H2 finger protein; putative; expressed), ranging from 35,121,624 bp to 35,122,989 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
vg0135121841 (J) chr01 35121841 T A 99.40% 0.00% T -> A NA
LOC_Os01g60730.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.300; most accessible tissue: Zhenshan97 panicle, score: 99.774
vg0135121938 (J) chr01 35121938 GC G 64.60% 0.00% G -> GC NA
LOC_Os01g60730.1 Alt: GC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: GC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: GC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.435; most accessible tissue: Zhenshan97 panicle, score: 99.798
vg0135121971 (J) chr01 35121971 G A 99.70% 0.00% G -> A NA
LOC_Os01g60730.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.468; most accessible tissue: Zhenshan97 panicle, score: 99.809
vg0135122590 (J) chr01 35122590 T C 64.50% 0.00% C -> T NA
LOC_Os01g60730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g60730.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 97.510; most accessible tissue: Minghui63 flower, score: 99.493
vg0135122756 (J) chr01 35122756 G A 61.60% 0.00% A -> G
mr1003 (All); LR P-value: 9.79E-22;
mr1010 (All); LR P-value: 2.77E-13;
mr1517 (All); LR P-value: 2.56E-85;
mr1538 (All); LR P-value: 6.72E-68;
mr1776 (All); LR P-value: 2.50E-08;
mr1386_2 (All); LR P-value: 3.59E-23;
mr1781_2 (All); LR P-value: 4.57E-13;
mr1835_2 (All); LR P-value: 6.61E-09
LOC_Os01g60730.1 Alt: G| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: G| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.771; most accessible tissue: Minghui63 flower, score: 99.629
vg0135122839 (J) chr01 35122839 G C 99.50% 0.00% G -> C NA
LOC_Os01g60730.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os01g60730.2 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os01g60730.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g60730.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g60720.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.961; most accessible tissue: Minghui63 flower, score: 99.715
vg0135122869 (J) chr01 35122869 T C 64.50% 0.13% C -> T NA
LOC_Os01g60730.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 99.136; most accessible tissue: Minghui63 flower, score: 99.771
vg0135122922 (J) chr01 35122922 TGAG T 99.70% 0.00% TGAG -> TGAGGAG,T NA
LOC_Os01g60730.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.1 Alt: TGAGGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: TGAGGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: TGAGGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.297; most accessible tissue: Minghui63 flower, score: 99.809
vg0135122946 (J) chr01 35122946 A ACAG 64.00% 0.00% ACAG -> A NA
LOC_Os01g60730.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.639; most accessible tissue: Callus, score: 99.900
vg0135122962 (J) chr01 35122962 A T 90.90% 0.00% A -> T NA
LOC_Os01g60730.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60730.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.637; most accessible tissue: Callus, score: 99.900
STR0135122941 (J) chr01 35122941 CAAC CAACAAC 60.70% 0.00% CAACAAC -> CAAC NA