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Search Results:

33 variations found. LOC_Os09g07470 (hypothetical protein), ranging from 3,742,149 bp to 3,742,637 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
vg0903742152 (J) chr09 3742152 G A 62.90% 0.02% A -> G NA
LOC_Os09g07470.1 Alt: G| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
LOC_Os09g07470.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 73.803; most accessible tissue: Zhenshan97 young leaf, score: 88.995
vg0903742156 (J) chr09 3742156 G T 65.00% 0.00% T -> G NA
LOC_Os09g07470.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.764; most accessible tissue: Zhenshan97 young leaf, score: 88.995
vg0903742163 (J) chr09 3742163 G A 98.90% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 74.072; most accessible tissue: Zhenshan97 young leaf, score: 88.513
vg0903742174 (J) chr09 3742174 A G 54.60% 0.00% G -> A
mr1208_2 (All); LR P-value: 2.63E-39;
mr1446_2 (All); LR P-value: 3.08E-07;
mr1660_2 (All); LR P-value: 2.61E-08
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.925; most accessible tissue: Zhenshan97 young leaf, score: 87.004
vg0903742183 (J) chr09 3742183 G A 99.20% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.739; most accessible tissue: Zhenshan97 young leaf, score: 87.299
vg0903742186 (J) chr09 3742186 A C 63.00% 0.00% C -> A NA
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.320; most accessible tissue: Zhenshan97 young leaf, score: 87.584
vg0903742195 (J) chr09 3742195 G A 99.70% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.247; most accessible tissue: Zhenshan97 young leaf, score: 87.723
vg0903742207 (J) chr09 3742207 C T 99.10% 0.00% C -> T NA
LOC_Os09g07470.1 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.122; most accessible tissue: Zhenshan97 young leaf, score: 86.852
vg0903742214 (J) chr09 3742214 G A 99.90% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.087; most accessible tissue: Zhenshan97 young leaf, score: 86.542
vg0903742240 (J) chr09 3742240 C A 86.80% 0.00% C -> A
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1206 (All); LR P-value: 1.14E-06;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1554 (All); LR P-value: 6.11E-07;
mr1596 (All); LR P-value: 2.54E-07;
mr1775 (All); LR P-value: 1.60E-10;
mr1880 (All); LR P-value: 1.17E-06;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1184_2 (All); LR P-value: 5.03E-06;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1488_2 (All); LR P-value: 2.38E-06;
mr1502_2 (All); LR P-value: 2.23E-07;
mr1552_2 (All); LR P-value: 1.31E-13;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1554_2 (All); LR P-value: 7.61E-08;
mr1556_2 (All); LR P-value: 5.41E-06;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1593_2 (All); LR P-value: 3.05E-13;
mr1786_2 (All); LR P-value: 9.62E-06;
mr1812_2 (All); LR P-value: 5.92E-06;
mr1864_2 (All); LR P-value: 3.04E-14;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07470.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.037; most accessible tissue: Zhenshan97 young leaf, score: 86.220
vg0903742271 (J) chr09 3742271 A G 54.60% 0.00% G -> A
mr1208_2 (All); LR P-value: 5.21E-38;
mr1446_2 (All); LR P-value: 3.20E-07;
mr1660_2 (All); LR P-value: 2.01E-08
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07470.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.329; most accessible tissue: Zhenshan97 young leaf, score: 84.624
vg0903742274 (J) chr09 3742274 C T 99.20% 0.00% C -> T NA
LOC_Os09g07480.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.516; most accessible tissue: Zhenshan97 young leaf, score: 84.624
vg0903742279 (J) chr09 3742279 C T 92.50% 0.00% C -> T
mr1722 (All); LR P-value: 4.81E-10;
mr1803 (All); LR P-value: 6.40E-07;
mr1808 (All); LR P-value: 2.85E-06;
mr1113_2 (All); LR P-value: 1.80E-17;
mr1114_2 (All); LR P-value: 6.12E-18;
mr1117_2 (All); LR P-value: 6.60E-19;
mr1119_2 (All); LR P-value: 2.05E-17;
mr1582_2 (All); LR P-value: 3.31E-07
LOC_Os09g07480.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.620; most accessible tissue: Zhenshan97 young leaf, score: 84.431
vg0903742294 (J) chr09 3742294 G A 99.90% 0.00% G -> A NA
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g07470.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 72.656; most accessible tissue: Zhenshan97 young leaf, score: 84.235
vg0903742298 (J) chr09 3742298 G A 99.90% 0.00% G -> A NA
LOC_Os09g07480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g07470.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.056; most accessible tissue: Zhenshan97 young leaf, score: 84.624
vg0903742327 (J) chr09 3742327 C CCACG 63.00% 0.00% CCACG -> C NA
LOC_Os09g07470.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 66.864; most accessible tissue: Zhenshan97 young leaf, score: 83.831
vg0903742330 (J) chr09 3742330 C T 99.60% 0.00% C -> T NA
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.093; most accessible tissue: Zhenshan97 young leaf, score: 83.831
vg0903742334 (J) chr09 3742334 C T 82.80% 6.67% C -> T NA
LOC_Os09g07470.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.902; most accessible tissue: Zhenshan97 young leaf, score: 83.831
vg0903742372 (J) chr09 3742372 G A 99.20% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.578; most accessible tissue: Zhenshan97 young leaf, score: 84.035
vg0903742384 (J) chr09 3742384 A G 62.10% 0.00% G -> A
mr1781 (All); LR P-value: 6.90E-07;
mr1756_2 (All); LR P-value: 6.66E-10
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.251; most accessible tissue: Zhenshan97 young leaf, score: 83.199
vg0903742396 (J) chr09 3742396 C A 86.80% 0.00% C -> A
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1206 (All); LR P-value: 1.60E-06;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1554 (All); LR P-value: 2.16E-07;
mr1596 (All); LR P-value: 7.47E-07;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1184_2 (All); LR P-value: 5.19E-06;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1552_2 (All); LR P-value: 8.34E-14;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1554_2 (All); LR P-value: 2.58E-08;
mr1556_2 (All); LR P-value: 6.24E-06;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1593_2 (All); LR P-value: 4.28E-12;
mr1812_2 (All); LR P-value: 7.27E-06;
mr1864_2 (All); LR P-value: 9.46E-14;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.946; most accessible tissue: Zhenshan97 young leaf, score: 83.412
vg0903742399 (J) chr09 3742399 G T 92.60% 0.00% G -> T,A
mr1722 (All); LR P-value: 4.81E-10;
mr1803 (All); LR P-value: 6.40E-07;
mr1808 (All); LR P-value: 2.85E-06;
mr1113_2 (All); LR P-value: 1.80E-17;
mr1114_2 (All); LR P-value: 6.12E-18;
mr1117_2 (All); LR P-value: 6.60E-19;
mr1119_2 (All); LR P-value: 2.05E-17;
mr1582_2 (All); LR P-value: 3.31E-07
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.907; most accessible tissue: Zhenshan97 young leaf, score: 82.982
vg0903742410 (J) chr09 3742410 G A 78.30% 0.00% A -> G
Grain_thickness (All); LR P-value: 9.90E-37;
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1368 (All); LR P-value: 3.19E-09;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1156_2 (All); LR P-value: 2.48E-18;
mr1159_2 (All); LR P-value: 3.82E-06;
mr1277_2 (All); LR P-value: 2.13E-15;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1663_2 (All); LR P-value: 4.98E-06;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (All); LR P-value: 2.84E-19;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07470.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.851; most accessible tissue: Zhenshan97 young leaf, score: 84.035
vg0903742414 (J) chr09 3742414 C T 99.90% 0.00% C -> T NA
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os09g07480.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 66.236; most accessible tissue: Zhenshan97 young leaf, score: 84.431
vg0903742422 (J) chr09 3742422 G A 86.80% 0.00% G -> A
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1206 (All); LR P-value: 7.61E-07;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1554 (All); LR P-value: 4.53E-07;
mr1596 (All); LR P-value: 1.65E-07;
mr1775 (All); LR P-value: 1.14E-10;
mr1880 (All); LR P-value: 9.17E-07;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1184_2 (All); LR P-value: 7.27E-06;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1552_2 (All); LR P-value: 1.22E-13;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1554_2 (All); LR P-value: 6.76E-08;
mr1556_2 (All); LR P-value: 7.88E-06;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1593_2 (All); LR P-value: 2.24E-12;
mr1812_2 (All); LR P-value: 9.90E-06;
mr1864_2 (All); LR P-value: 1.00E-13;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.859; most accessible tissue: Zhenshan97 young leaf, score: 84.035
vg0903742431 (J) chr09 3742431 G A 86.80% 0.00% G -> A
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1554 (All); LR P-value: 2.63E-07;
mr1596 (All); LR P-value: 8.01E-07;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1184_2 (All); LR P-value: 5.03E-06;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1552_2 (All); LR P-value: 1.20E-13;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1554_2 (All); LR P-value: 3.63E-08;
mr1556_2 (All); LR P-value: 6.80E-06;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1593_2 (All); LR P-value: 8.44E-13;
mr1812_2 (All); LR P-value: 6.29E-06;
mr1864_2 (All); LR P-value: 6.98E-15;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.491; most accessible tissue: Zhenshan97 young leaf, score: 84.814
vg0903742445 (J) chr09 3742445 C T 92.50% 0.00% C -> T
mr1722 (All); LR P-value: 4.81E-10;
mr1803 (All); LR P-value: 6.40E-07;
mr1808 (All); LR P-value: 2.85E-06;
mr1113_2 (All); LR P-value: 1.80E-17;
mr1114_2 (All); LR P-value: 6.12E-18;
mr1117_2 (All); LR P-value: 6.60E-19;
mr1119_2 (All); LR P-value: 2.05E-17;
mr1582_2 (All); LR P-value: 3.31E-07
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.820; most accessible tissue: Zhenshan97 young leaf, score: 84.431
vg0903742469 (J) chr09 3742469 C A 99.00% 0.00% C -> A,T NA
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g07470.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 67.340; most accessible tissue: Zhenshan97 young leaf, score: 82.982
vg0903742520 (J) chr09 3742520 C T 86.80% 0.00% C -> T
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1301 (Jap_All); LR P-value: 5.80E-14;
mr1554 (All); LR P-value: 3.34E-07;
mr1593 (All); LR P-value: 2.94E-08;
mr1596 (All); LR P-value: 1.12E-06;
mr1916 (Jap_All); LR P-value: 2.84E-08;
mr1993 (Jap_All); LR P-value: 6.56E-08;
mr1184_2 (All); LR P-value: 3.56E-06;
mr1277_2 (Jap_All); LR P-value: 1.19E-06;
mr1278_2 (All); LR P-value: 9.52E-06;
mr1363_2 (Jap_All); LR P-value: 4.48E-06;
mr1398_2 (All); LR P-value: 2.09E-09;
mr1488_2 (All); LR P-value: 2.33E-06;
mr1552_2 (All); LR P-value: 1.21E-13;
mr1552_2 (Jap_All); LR P-value: 1.10E-10;
mr1554_2 (All); LR P-value: 3.91E-08;
mr1556_2 (All); LR P-value: 4.80E-06;
mr1578_2 (Jap_All); LR P-value: 2.73E-09;
mr1593_2 (All); LR P-value: 1.37E-13;
mr1812_2 (All); LR P-value: 3.90E-06;
mr1864_2 (All); LR P-value: 2.18E-15;
mr1864_2 (Jap_All); LR P-value: 2.37E-09;
mr1980_2 (Jap_All); LR P-value: 5.39E-06
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.470; most accessible tissue: Zhenshan97 young leaf, score: 80.589
vg0903742544 (J) chr09 3742544 C T 99.20% 0.00% C -> T NA
LOC_Os09g07470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.223; most accessible tissue: Zhenshan97 young leaf, score: 81.841
vg0903742550 (J) chr09 3742550 G A 99.20% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.604; most accessible tissue: Zhenshan97 young leaf, score: 82.310
vg0903742584 (J) chr09 3742584 C T 92.70% 0.00% C -> T
mr1722 (All); LR P-value: 4.81E-10;
mr1803 (All); LR P-value: 6.40E-07;
mr1808 (All); LR P-value: 2.85E-06;
mr1113_2 (All); LR P-value: 1.80E-17;
mr1114_2 (All); LR P-value: 6.12E-18;
mr1117_2 (All); LR P-value: 6.60E-19;
mr1119_2 (All); LR P-value: 2.05E-17;
mr1582_2 (All); LR P-value: 3.31E-07
LOC_Os09g07470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.395; most accessible tissue: Zhenshan97 young leaf, score: 81.102
vg0903742586 (J) chr09 3742586 G A 98.80% 0.00% G -> A NA
LOC_Os09g07470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 61.906; most accessible tissue: Zhenshan97 young leaf, score: 81.353