RiceVarMap2

Search for Variation by Gene:

Search Results:

13 variations found. LOC_Os07g19040 (glycosyl hydrolase; putative; expressed), ranging from 11,273,993 bp to 11,274,887 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:

Color	Explain	Details
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:

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Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
vg0711274039 (J)	chr07	11274039	G	A	99.40%	0.00%	G -> A	NA	LOC_Os07g19040.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 66.124; most accessible tissue: Zhenshan97 young leaf, score: 85.184
vg0711274294 (J)	chr07	11274294	C	G	73.60%	0.25%	G -> C	mr1578 (All); LR P-value: 9.27E-10; mr1900 (All); LR P-value: 6.32E-14; mr1042_2 (All); LR P-value: 8.15E-23; mr1062_2 (All); LR P-value: 3.72E-19; mr1227_2 (All); LR P-value: 1.20E-06; mr1289_2 (All); LR P-value: 4.58E-06; mr1405_2 (All); LR P-value: 2.42E-06; mr1418_2 (All); LR P-value: 5.69E-07; mr1479_2 (All); LR P-value: 1.32E-06; mr1488_2 (All); LR P-value: 1.77E-06; mr1624_2 (Jap_All); LR P-value: 1.78E-07; mr1636_2 (All); LR P-value: 1.61E-12; mr1641_2 (All); LR P-value: 1.70E-12; mr1646_2 (All); LR P-value: 7.87E-11; mr1680_2 (All); LR P-value: 1.93E-10; mr1681_2 (All); LR P-value: 9.53E-08; mr1726_2 (All); LR P-value: 3.25E-16; mr1726_2 (Jap_All); LR P-value: 5.85E-06; mr1741_2 (Jap_All); LR P-value: 2.32E-06; mr1751_2 (All); LR P-value: 1.28E-09; mr1765_2 (All); LR P-value: 3.71E-08; mr1838_2 (All); LR P-value: 1.18E-13; mr1871_2 (All); LR P-value: 7.18E-20; mr1986_2 (All); LR P-value: 2.39E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.931; most accessible tissue: Zhenshan97 young leaf, score: 91.616
vg0711274303 (J)	chr07	11274303	G	T	73.60%	0.25%	T -> G	mr1578 (All); LR P-value: 9.27E-10; mr1900 (All); LR P-value: 6.32E-14; mr1042_2 (All); LR P-value: 8.15E-23; mr1062_2 (All); LR P-value: 3.72E-19; mr1227_2 (All); LR P-value: 1.20E-06; mr1289_2 (All); LR P-value: 4.58E-06; mr1405_2 (All); LR P-value: 2.42E-06; mr1418_2 (All); LR P-value: 5.69E-07; mr1479_2 (All); LR P-value: 1.32E-06; mr1488_2 (All); LR P-value: 1.77E-06; mr1624_2 (Jap_All); LR P-value: 1.78E-07; mr1636_2 (All); LR P-value: 1.61E-12; mr1641_2 (All); LR P-value: 1.70E-12; mr1646_2 (All); LR P-value: 7.87E-11; mr1680_2 (All); LR P-value: 1.93E-10; mr1681_2 (All); LR P-value: 9.53E-08; mr1726_2 (All); LR P-value: 3.25E-16; mr1726_2 (Jap_All); LR P-value: 5.85E-06; mr1741_2 (Jap_All); LR P-value: 2.32E-06; mr1751_2 (All); LR P-value: 1.28E-09; mr1765_2 (All); LR P-value: 3.71E-08; mr1838_2 (All); LR P-value: 1.18E-13; mr1871_2 (All); LR P-value: 7.18E-20; mr1986_2 (All); LR P-value: 2.39E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: G\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.957; most accessible tissue: Zhenshan97 young leaf, score: 91.389
vg0711274318 (J)	chr07	11274318	C	G	73.70%	0.23%	G -> C	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 1.85E-09; mr1900 (All); LR P-value: 7.34E-14; mr1042_2 (All); LR P-value: 1.56E-22; mr1062_2 (All); LR P-value: 4.69E-19; mr1167_2 (All); LR P-value: 1.19E-18; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.19E-06; mr1289_2 (All); LR P-value: 6.44E-06; mr1405_2 (All); LR P-value: 3.55E-06; mr1418_2 (All); LR P-value: 1.22E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 3.60E-12; mr1641_2 (All); LR P-value: 9.73E-12; mr1646_2 (All); LR P-value: 2.34E-10; mr1680_2 (All); LR P-value: 3.88E-10; mr1681_2 (All); LR P-value: 1.38E-07; mr1726_2 (All); LR P-value: 3.90E-16; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1751_2 (All); LR P-value: 1.91E-09; mr1765_2 (All); LR P-value: 4.77E-08; mr1838_2 (All); LR P-value: 9.42E-14; mr1986_2 (All); LR P-value: 9.95E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 81.892; most accessible tissue: Zhenshan97 young leaf, score: 91.466
vg0711274342 (J)	chr07	11274342	T	C	73.60%	0.23%	C -> T	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 1.85E-09; mr1900 (All); LR P-value: 7.34E-14; mr1042_2 (All); LR P-value: 1.56E-22; mr1062_2 (All); LR P-value: 4.69E-19; mr1167_2 (All); LR P-value: 1.19E-18; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.19E-06; mr1289_2 (All); LR P-value: 6.44E-06; mr1405_2 (All); LR P-value: 3.55E-06; mr1418_2 (All); LR P-value: 1.22E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 3.60E-12; mr1641_2 (All); LR P-value: 9.73E-12; mr1646_2 (All); LR P-value: 2.34E-10; mr1680_2 (All); LR P-value: 3.88E-10; mr1681_2 (All); LR P-value: 1.38E-07; mr1726_2 (All); LR P-value: 3.90E-16; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1751_2 (All); LR P-value: 1.91E-09; mr1765_2 (All); LR P-value: 4.77E-08; mr1838_2 (All); LR P-value: 9.42E-14; mr1986_2 (All); LR P-value: 9.95E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: T\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 80.132; most accessible tissue: Zhenshan97 young leaf, score: 91.069
vg0711274428 (J)	chr07	11274428	C	T	99.60%	0.00%	C -> T	NA	LOC_Os07g19040.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 84.822; most accessible tissue: Zhenshan97 young leaf, score: 92.294
vg0711274486 (J)	chr07	11274486	C	T	74.90%	0.13%	T -> C,G	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 3.07E-09; mr1677 (All); LR P-value: 2.94E-06; mr1900 (All); LR P-value: 2.88E-15; mr1905 (All); LR P-value: 4.89E-10; mr1042_2 (All); LR P-value: 1.56E-23; mr1062_2 (All); LR P-value: 7.21E-19; mr1167_2 (All); LR P-value: 1.62E-20; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.58E-06; mr1405_2 (All); LR P-value: 2.11E-06; mr1479_2 (All); LR P-value: 6.17E-07; mr1574_2 (All); LR P-value: 8.67E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 1.88E-12; mr1641_2 (All); LR P-value: 4.62E-12; mr1646_2 (All); LR P-value: 4.24E-10; mr1681_2 (All); LR P-value: 1.16E-07; mr1717_2 (All); LR P-value: 4.60E-13; mr1726_2 (All); LR P-value: 1.20E-17; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1765_2 (All); LR P-value: 3.09E-09; mr1838_2 (All); LR P-value: 3.59E-13	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: G\| synonymous_variant LOW(snpEff) LOC_Os07g19050.1 Alt: G\| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g19030.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g19040.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.697; most accessible tissue: Zhenshan97 young leaf, score: 92.535
vg0711274593 (J)	chr07	11274593	C	T	73.70%	0.17%	T -> C	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 1.85E-09; mr1900 (All); LR P-value: 7.34E-14; mr1042_2 (All); LR P-value: 1.56E-22; mr1062_2 (All); LR P-value: 4.69E-19; mr1167_2 (All); LR P-value: 1.19E-18; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.19E-06; mr1289_2 (All); LR P-value: 6.44E-06; mr1405_2 (All); LR P-value: 3.55E-06; mr1418_2 (All); LR P-value: 1.22E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 3.60E-12; mr1641_2 (All); LR P-value: 9.73E-12; mr1646_2 (All); LR P-value: 2.34E-10; mr1680_2 (All); LR P-value: 3.88E-10; mr1681_2 (All); LR P-value: 1.38E-07; mr1726_2 (All); LR P-value: 3.90E-16; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1751_2 (All); LR P-value: 1.91E-09; mr1765_2 (All); LR P-value: 4.77E-08; mr1838_2 (All); LR P-value: 9.42E-14; mr1986_2 (All); LR P-value: 9.95E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 83.003; most accessible tissue: Zhenshan97 young leaf, score: 91.069
vg0711274604 (J)	chr07	11274604	C	T	99.40%	0.00%	C -> T	NA	LOC_Os07g19040.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 83.708; most accessible tissue: Zhenshan97 young leaf, score: 91.760
vg0711274627 (J)	chr07	11274627	G	A	93.20%	0.00%	G -> A	NA	LOC_Os07g19040.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.010; most accessible tissue: Zhenshan97 young leaf, score: 91.899
vg0711274645 (J)	chr07	11274645	G	A	73.60%	0.15%	A -> G	mr1666 (All); LR P-value: 8.69E-08; mr1900 (All); LR P-value: 3.14E-13; mr1042_2 (All); LR P-value: 6.21E-23; mr1062_2 (All); LR P-value: 3.56E-18; mr1167_2 (All); LR P-value: 5.67E-19; mr1167_2 (Jap_All); LR P-value: 7.94E-06; mr1227_2 (All); LR P-value: 8.74E-07; mr1289_2 (All); LR P-value: 7.34E-06; mr1418_2 (All); LR P-value: 1.33E-06; mr1479_2 (All); LR P-value: 1.42E-06; mr1636_2 (All); LR P-value: 4.59E-12; mr1641_2 (All); LR P-value: 1.22E-11; mr1646_2 (All); LR P-value: 4.05E-10; mr1681_2 (All); LR P-value: 1.34E-07; mr1726_2 (All); LR P-value: 2.34E-16; mr1751_2 (All); LR P-value: 8.55E-09; mr1765_2 (All); LR P-value: 1.50E-08; mr1838_2 (All); LR P-value: 1.51E-13; mr1871_2 (All); LR P-value: 8.84E-20	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: G\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 82.800; most accessible tissue: Zhenshan97 young leaf, score: 91.616
vg0711274661 (J)	chr07	11274661	C	T	73.70%	0.11%	T -> C	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 1.85E-09; mr1900 (All); LR P-value: 7.34E-14; mr1042_2 (All); LR P-value: 1.56E-22; mr1062_2 (All); LR P-value: 4.69E-19; mr1167_2 (All); LR P-value: 1.19E-18; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.19E-06; mr1289_2 (All); LR P-value: 6.44E-06; mr1405_2 (All); LR P-value: 3.55E-06; mr1418_2 (All); LR P-value: 1.22E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 3.60E-12; mr1641_2 (All); LR P-value: 9.73E-12; mr1646_2 (All); LR P-value: 2.34E-10; mr1680_2 (All); LR P-value: 3.88E-10; mr1681_2 (All); LR P-value: 1.38E-07; mr1726_2 (All); LR P-value: 3.90E-16; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1751_2 (All); LR P-value: 1.91E-09; mr1765_2 (All); LR P-value: 4.77E-08; mr1838_2 (All); LR P-value: 9.42E-14; mr1986_2 (All); LR P-value: 9.95E-11	LOC_Os07g19040.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g19040.1 Alt: C\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 82.743; most accessible tissue: Zhenshan97 young leaf, score: 91.232
vg0711274866 (J)	chr07	11274866	T	G	73.70%	0.00%	G -> T	Awn_length (Jap_All); LR P-value: 1.53E-07; mr1578 (All); LR P-value: 1.85E-09; mr1900 (All); LR P-value: 7.34E-14; mr1042_2 (All); LR P-value: 1.56E-22; mr1062_2 (All); LR P-value: 4.69E-19; mr1167_2 (All); LR P-value: 1.19E-18; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.19E-06; mr1289_2 (All); LR P-value: 6.44E-06; mr1405_2 (All); LR P-value: 3.55E-06; mr1418_2 (All); LR P-value: 1.22E-06; mr1479_2 (All); LR P-value: 1.79E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 3.60E-12; mr1641_2 (All); LR P-value: 9.73E-12; mr1646_2 (All); LR P-value: 2.34E-10; mr1680_2 (All); LR P-value: 3.88E-10; mr1681_2 (All); LR P-value: 1.38E-07; mr1726_2 (All); LR P-value: 3.90E-16; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1751_2 (All); LR P-value: 1.91E-09; mr1765_2 (All); LR P-value: 4.77E-08; mr1838_2 (All); LR P-value: 9.42E-14; mr1986_2 (All); LR P-value: 9.95E-11	LOC_Os07g19040.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 78.079; most accessible tissue: Zhenshan97 flower, score: 86.118

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