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Search Results:

18 variations found. LOC_Os09g23730 (HMG-Y-related protein A; putative; expressed), ranging from 14,106,176 bp to 14,107,337 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
vg0914106177 (J) chr09 14106177 T G 96.10% 0.00% T -> G NA
LOC_Os09g23730.1 Alt: G| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os09g23730.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23725.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 85.578; most accessible tissue: Zhenshan97 flower, score: 93.594
vg0914106197 (J) chr09 14106197 T A 99.90% 0.00% T -> A NA
LOC_Os09g23730.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os09g23725.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g23740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.215; most accessible tissue: Zhenshan97 flower, score: 93.075
vg0914106320 (J) chr09 14106320 G A 99.90% 0.00% G -> A NA
LOC_Os09g23730.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os09g23725.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g23740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.172; most accessible tissue: Zhenshan97 root, score: 92.461
vg0914106520 (J) chr09 14106520 AT GT 91.90% 0.00% AT -> GT,A NA
LOC_Os09g23730.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23725.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23740.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23730.1 Alt: A| frameshift_variant&stop_lost HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.952; most accessible tissue: Minghui63 flag leaf, score: 96.124
vg0914106542 (J) chr09 14106542 G A 99.80% 0.00% G -> A NA
LOC_Os09g23730.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os09g23725.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g23740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 92.189; most accessible tissue: Minghui63 flag leaf, score: 96.221
vg0914106626 (J) chr09 14106626 C T 91.20% 2.12% C -> T NA
LOC_Os09g23730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g23730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.195; most accessible tissue: Minghui63 flag leaf, score: 97.011
vg0914106781 (J) chr09 14106781 A T 38.70% 22.37% A -> T NA
LOC_Os09g23730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g23730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.435; most accessible tissue: Minghui63 flag leaf, score: 97.820
vg0914106818 (J) chr09 14106818 G A 71.60% 5.76% G -> A NA
LOC_Os09g23730.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g23730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.766; most accessible tissue: Minghui63 flag leaf, score: 98.184
vg0914106884 (J) chr09 14106884 C T 97.00% 0.00% C -> T NA
LOC_Os09g23730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.969; most accessible tissue: Minghui63 flag leaf, score: 98.282
vg0914106896 (J) chr09 14106896 G A 82.10% 0.00% G -> A
mr1084 (All); LR P-value: 4.94E-11;
mr1205 (All); LR P-value: 1.23E-12;
mr1338 (All); LR P-value: 1.73E-06;
mr1642 (All); LR P-value: 8.73E-07;
mr1063_2 (Jap_All); LR P-value: 5.42E-06;
mr1084_2 (All); LR P-value: 1.35E-08;
mr1161_2 (Jap_All); LR P-value: 2.61E-06;
mr1205_2 (All); LR P-value: 9.48E-08;
mr1206_2 (All); LR P-value: 4.38E-06;
mr1229_2 (Jap_All); LR P-value: 6.35E-07;
mr1509_2 (Jap_All); LR P-value: 5.00E-06;
mr1543_2 (All); LR P-value: 6.31E-09;
mr1543_2 (Jap_All); LR P-value: 5.06E-09;
mr1611_2 (Jap_All); LR P-value: 3.42E-11;
mr1646_2 (All); LR P-value: 6.08E-11;
mr1880_2 (Jap_All); LR P-value: 2.24E-07;
mr1966_2 (All); LR P-value: 2.31E-06
LOC_Os09g23730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.997; most accessible tissue: Minghui63 flag leaf, score: 98.299
vg0914107070 (J) chr09 14107070 C G 61.40% 0.00% C -> G
mr1446_2 (All); LR P-value: 2.79E-08;
mr1511_2 (Ind_All); LR P-value: 6.37E-06;
mr1622_2 (Ind_All); LR P-value: 3.22E-07;
mr1870_2 (Ind_All); LR P-value: 2.48E-06
LOC_Os09g23730.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 98.007; most accessible tissue: Minghui63 flag leaf, score: 99.275
vg0914107141 (J) chr09 14107141 A G 82.10% 0.00% A -> G
mr1050 (All); LR P-value: 4.05E-09;
mr1063 (Jap_All); LR P-value: 4.46E-06;
mr1084 (All); LR P-value: 1.81E-11;
mr1205 (All); LR P-value: 1.17E-12;
mr1330 (All); LR P-value: 2.58E-12;
mr1338 (All); LR P-value: 3.69E-07;
mr1063_2 (Jap_All); LR P-value: 3.10E-06;
mr1084_2 (All); LR P-value: 3.10E-08;
mr1115_2 (Jap_All); LR P-value: 7.09E-15;
mr1161_2 (Jap_All); LR P-value: 1.02E-06;
mr1205_2 (All); LR P-value: 7.80E-08;
mr1206_2 (All); LR P-value: 7.18E-06;
mr1229_2 (Jap_All); LR P-value: 7.48E-07;
mr1449_2 (All); LR P-value: 2.42E-08;
mr1509_2 (Jap_All); LR P-value: 8.83E-06;
mr1543_2 (All); LR P-value: 7.27E-09;
mr1543_2 (Jap_All); LR P-value: 2.42E-09;
mr1611_2 (Jap_All); LR P-value: 7.51E-12;
mr1646_2 (All); LR P-value: 4.99E-11;
mr1880_2 (Jap_All); LR P-value: 3.34E-07;
mr1966_2 (All); LR P-value: 1.63E-06
LOC_Os09g23725.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23730.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 98.102; most accessible tissue: Minghui63 flag leaf, score: 99.531
vg0914107175 (J) chr09 14107175 G A 61.40% 0.00% G -> A
mr1446_2 (All); LR P-value: 2.28E-09;
mr1446_2 (Ind_All); LR P-value: 9.39E-06;
mr1622_2 (Ind_All); LR P-value: 1.81E-07
LOC_Os09g23730.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 99.582; most accessible tissue: Callus, score: 99.777
vg0914107176 (J) chr09 14107176 G A 97.10% 0.00% G -> A NA
LOC_Os09g23730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 99.583; most accessible tissue: Callus, score: 99.777
vg0914107209 (J) chr09 14107209 G A 97.10% 0.00% G -> A NA
LOC_Os09g23730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 99.692; most accessible tissue: Callus, score: 99.777
vg0914107268 (J) chr09 14107268 G A 96.10% 0.00% G -> A NA
LOC_Os09g23730.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23725.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.859; most accessible tissue: Zhenshan97 young leaf, score: 99.913
vg0914107313 (J) chr09 14107313 TCTC T 96.10% 0.00% TCTC -> T NA
LOC_Os09g23730.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23725.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g23740.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.866; most accessible tissue: Zhenshan97 young leaf, score: 99.924
STR0914107314 (J) chr09 14107314 CTCCTCC TCCTC CTCCTCC TC 99.00% 0.00% CTCCTCCTCC TC -> CTCCTCCTC NA