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Search Results:

25 variations found. LOC_Os07g36780 (S-domain receptor-like protein kinase; putative; expressed), ranging from 22,036,907 bp to 22,039,724 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
vg0722036907 (J) chr07 22036907 A G 94.30% 0.00% A -> G
Grain_weight (All); LMM P-value: 4.79E-06; LR P-value: 4.62E-15;
Grain_weight (Jap_All); LR P-value: 1.71E-06;
mr1156 (Jap_All); LR P-value: 1.90E-06;
mr1179 (Jap_All); LR P-value: 6.37E-08;
mr1188 (Jap_All); LR P-value: 7.67E-06;
mr1213 (Jap_All); LR P-value: 2.37E-06;
mr1224 (Jap_All); LR P-value: 4.00E-06;
mr1563 (Jap_All); LR P-value: 5.16E-09;
mr1668 (All); LR P-value: 9.39E-08
LOC_Os07g36770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36780.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770-LOC_Os07g36780 Alt: G| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 45.618; most accessible tissue: Zhenshan97 root, score: 62.394
vg0722036933 (J) chr07 22036933 G A 95.80% 0.00% G -> A NA
LOC_Os07g36780.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 49.781; most accessible tissue: Callus, score: 83.434
vg0722037009 (J) chr07 22037009 C G 65.10% 0.00% G -> C
Grain_length (Jap_All); LR P-value: 1.82E-16;
mr1086 (All); LMM P-value: 4.59E-06;
mr1104 (Jap_All); LR P-value: 5.27E-06;
mr1107 (All); LMM P-value: 5.84E-07;
mr1179 (Jap_All); LR P-value: 5.64E-08;
mr1213 (Jap_All); LR P-value: 4.68E-08;
mr1224 (Jap_All); LR P-value: 2.24E-06;
mr1225 (Jap_All); LR P-value: 2.84E-06;
mr1404 (Jap_All); LR P-value: 2.08E-06;
mr1563 (Jap_All); LR P-value: 1.63E-10;
mr1620 (Jap_All); LR P-value: 6.72E-06;
mr1733 (Jap_All); LR P-value: 2.09E-07;
mr1780 (Jap_All); LR P-value: 5.28E-06;
mr1949 (All); LR P-value: 1.52E-11;
mr1082_2 (All); LMM P-value: 1.37E-06;
mr1103_2 (All); LMM P-value: 6.36E-07;
mr1104_2 (All); LMM P-value: 4.27E-07;
mr1107_2 (All); LMM P-value: 1.99E-07;
mr1155_2 (Jap_All); LR P-value: 9.19E-06;
mr1224_2 (All); LMM P-value: 1.61E-06;
mr1224_2 (Jap_All); LR P-value: 2.64E-08;
mr1226_2 (All); LMM P-value: 2.58E-06;
mr1241_2 (All); LMM P-value: 7.62E-06;
mr1246_2 (Jap_All); LR P-value: 1.28E-08;
mr1264_2 (All); LMM P-value: 1.93E-06;
mr1404_2 (All); LMM P-value: 1.74E-06;
mr1404_2 (Jap_All); LR P-value: 9.43E-08;
mr1437_2 (All); LMM P-value: 6.62E-06;
mr1563_2 (Jap_All); LR P-value: 5.60E-08;
mr1620_2 (All); LMM P-value: 2.31E-06;
mr1620_2 (Jap_All); LR P-value: 9.51E-06;
mr1826_2 (All); LR P-value: 9.43E-06
LOC_Os07g36780.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 50.930; most accessible tissue: Callus, score: 83.434
vg0722037032 (J) chr07 22037032 C T 89.20% 0.00% C -> T
mr1188 (Ind_All); LR P-value: 7.21E-08;
mr1188_2 (Ind_All); LR P-value: 5.59E-08
LOC_Os07g36780.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.195; most accessible tissue: Callus, score: 83.434
vg0722037042 (J) chr07 22037042 A G 97.60% 0.00% A -> G NA
LOC_Os07g36780.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 53.694; most accessible tissue: Callus, score: 83.434
vg0722037158 (J) chr07 22037158 A G 95.80% 0.00% A -> G NA
LOC_Os07g36780.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 51.896; most accessible tissue: Callus, score: 67.457
vg0722037209 (J) chr07 22037209 G A 95.80% 0.00% G -> A NA
LOC_Os07g36780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 56.366; most accessible tissue: Callus, score: 85.836
vg0722037297 (J) chr07 22037297 T C 56.70% 0.02% C -> T
mr1212_2 (All); LR P-value: 2.28E-07;
mr1241_2 (All); LMM P-value: 9.03E-06;
mr1949_2 (All); LR P-value: 8.49E-24
LOC_Os07g36780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 60.888; most accessible tissue: Callus, score: 85.836
vg0722037442 (J) chr07 22037442 G A 68.90% 0.00% A -> G
Grain_length (Jap_All); LR P-value: 9.97E-16;
mr1104 (All); LMM P-value: 9.96E-06;
mr1104 (Jap_All); LR P-value: 5.06E-06;
mr1107 (All); LMM P-value: 2.13E-06;
mr1179 (Jap_All); LR P-value: 2.95E-07;
mr1213 (All); LR P-value: 9.51E-32;
mr1213 (Jap_All); LR P-value: 9.42E-08;
mr1224 (Jap_All); LR P-value: 4.92E-06;
mr1225 (Jap_All); LR P-value: 8.59E-06;
mr1404 (Jap_All); LR P-value: 3.82E-07;
mr1563 (Jap_All); LR P-value: 1.54E-09;
mr1620 (Jap_All); LR P-value: 8.76E-06;
mr1780 (Jap_All); LR P-value: 4.53E-06;
mr1949 (All); LR P-value: 1.01E-14;
mr1082_2 (All); LMM P-value: 1.39E-06;
mr1103_2 (All); LMM P-value: 1.53E-06;
mr1104_2 (All); LMM P-value: 7.75E-07;
mr1107_2 (All); LMM P-value: 3.11E-07;
mr1224_2 (Jap_All); LR P-value: 3.38E-08;
mr1226_2 (All); LMM P-value: 9.68E-07;
mr1246_2 (Jap_All); LR P-value: 4.66E-08;
mr1404_2 (Jap_All); LR P-value: 7.51E-08;
mr1620_2 (All); LMM P-value: 6.12E-06;
mr1949_2 (All); LR P-value: 5.77E-23
LOC_Os07g36780.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.515; most accessible tissue: Callus, score: 88.307
vg0722037460 (J) chr07 22037460 C A 99.80% 0.00% C -> A NA
LOC_Os07g36780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.166; most accessible tissue: Callus, score: 88.307
vg0722037535 (J) chr07 22037535 TCCC ACCC 98.90% 0.00% TCCC -> ACCC,T NA
LOC_Os07g36780.1 Alt: ACCC| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g36780.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os07g36770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.680; most accessible tissue: Callus, score: 88.307
vg0722037631 (J) chr07 22037631 A G 89.20% 0.00% A -> G
mr1188 (Ind_All); LR P-value: 7.21E-08;
mr1188_2 (Ind_All); LR P-value: 5.59E-08
LOC_Os07g36780.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.317; most accessible tissue: Zhenshan97 flower, score: 76.539
vg0722037727 (J) chr07 22037727 G A 59.70% 0.00% G -> A NA
LOC_Os07g36780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.174; most accessible tissue: Callus, score: 87.696
vg0722038000 (J) chr07 22038000 G A 99.00% 0.00% G -> A NA
LOC_Os07g36780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.263; most accessible tissue: Minghui63 flag leaf, score: 84.973
vg0722038252 (J) chr07 22038252 A G 52.60% 0.02% G -> A NA
LOC_Os07g36780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.710; most accessible tissue: Callus, score: 85.123
vg0722038448 (J) chr07 22038448 T C 52.60% 0.00% C -> T NA
LOC_Os07g36780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.219; most accessible tissue: Callus, score: 86.462
vg0722038682 (J) chr07 22038682 C T 59.70% 0.00% C -> T,G
mr1717 (All); LR P-value: 8.05E-09;
mr1770 (All); LR P-value: 4.25E-08;
mr1783 (All); LR P-value: 6.76E-06
LOC_Os07g36780.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g36770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g36790.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g36780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 82.626; most accessible tissue: Minghui63 flag leaf, score: 88.223
vg0722038849 (J) chr07 22038849 A T 95.80% 0.00% A -> T,C NA
LOC_Os07g36780.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os07g36780.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os07g36770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g36790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 80.024; most accessible tissue: Minghui63 flag leaf, score: 87.189
vg0722038942 (J) chr07 22038942 A G 65.20% 0.00% G -> A
Grain_length (Jap_All); LR P-value: 1.82E-16;
mr1104 (Jap_All); LR P-value: 5.27E-06;
mr1107 (All); LMM P-value: 3.15E-06;
mr1179 (Jap_All); LR P-value: 5.64E-08;
mr1213 (Jap_All); LR P-value: 4.68E-08;
mr1224 (Jap_All); LR P-value: 2.24E-06;
mr1225 (Jap_All); LR P-value: 2.84E-06;
mr1404 (Jap_All); LR P-value: 2.08E-06;
mr1563 (Jap_All); LR P-value: 1.63E-10;
mr1620 (Jap_All); LR P-value: 6.72E-06;
mr1733 (Jap_All); LR P-value: 2.09E-07;
mr1780 (Jap_All); LR P-value: 5.28E-06;
mr1082_2 (All); LMM P-value: 1.64E-06;
mr1103_2 (All); LMM P-value: 1.83E-06;
mr1104_2 (All); LMM P-value: 2.31E-06;
mr1107_2 (All); LMM P-value: 1.33E-06;
mr1155_2 (Jap_All); LR P-value: 9.19E-06;
mr1224_2 (All); LMM P-value: 7.13E-06;
mr1224_2 (Jap_All); LR P-value: 2.64E-08;
mr1226_2 (All); LMM P-value: 8.06E-06;
mr1246_2 (Jap_All); LR P-value: 1.28E-08;
mr1264_2 (All); LMM P-value: 6.78E-06;
mr1404_2 (All); LMM P-value: 8.10E-06;
mr1404_2 (Jap_All); LR P-value: 9.43E-08;
mr1563_2 (Jap_All); LR P-value: 5.60E-08;
mr1620_2 (Jap_All); LR P-value: 9.51E-06;
mr1826_2 (All); LR P-value: 6.33E-06
LOC_Os07g36780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.341; most accessible tissue: Zhenshan97 flag leaf, score: 91.974
vg0722039204 (J) chr07 22039204 A T 59.40% 0.00% A -> T NA
LOC_Os07g36780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.815; most accessible tissue: Minghui63 flag leaf, score: 93.673
vg0722039270 (J) chr07 22039270 T C 89.10% 0.00% T -> C
mr1188 (Ind_All); LR P-value: 7.21E-08;
mr1188_2 (Ind_All); LR P-value: 5.59E-08
LOC_Os07g36780.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.652; most accessible tissue: Minghui63 flag leaf, score: 94.110
vg0722039543 (J) chr07 22039543 A G 52.50% 0.00% G -> A NA
LOC_Os07g36780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.194; most accessible tissue: Zhenshan97 root, score: 95.177
vg0722039607 (J) chr07 22039607 AGAG A 97.90% 0.00% AGAG -> A NA
LOC_Os07g36780.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 91.619; most accessible tissue: Zhenshan97 root, score: 96.388
vg0722039667 (J) chr07 22039667 G A 52.50% 0.00% A -> G NA
LOC_Os07g36780.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g36790.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.791; most accessible tissue: Zhenshan97 root, score: 97.768
STR0722039608 (J) chr07 22039608 GAGGAGG AGGA GAGGAGG A 99.20% 0.00% GAGGAGGAGG A -> GAGGAGGA NA