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Search Results:

20 variations found. Os07g0594400/LOC_Os07g40380 (expressed protein), ranging from 24,210,968 bp to 24,212,734 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os07g40380 expressed protein; RAP ID: Os07g0594400; MSU ID: LOC_Os07g40380

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg0724211173 (J) chr07 24211173 G GTGT 82.00% 3.81% G -> GTGT NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: GTGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: GTGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: GTGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 63.756; most accessible tissue: Callus, score: 88.369
vg0724211175 (J) chr07 24211175 GT G 75.30% 0.00% GT -> G NA
LOC_Os07g40370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.237; most accessible tissue: Callus, score: 93.754
vg0724211176 (J) chr07 24211176 TTG T 56.20% 0.00% T -> TTG NA
LOC_Os07g40370.1 Alt: TTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: TTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: TTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.002; most accessible tissue: Callus, score: 93.754
vg0724211178 (J) chr07 24211178 T G 77.30% 10.11% T -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 64.002; most accessible tissue: Callus, score: 93.754
vg0724211269 (J) chr07 24211269 T A 87.20% 0.00% T -> A NA
LOC_Os07g40370.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 52.693; most accessible tissue: Callus, score: 93.754
vg0724211584 (J) chr07 24211584 A C 58.00% 0.34% C -> A
mr1181 (All); LR P-value: 2.04E-26;
mr1408 (All); LR P-value: 1.55E-06;
mr1761 (All); LR P-value: 4.16E-07;
mr1878 (All); LR P-value: 2.20E-31;
mr1181_2 (Ind_All); LR P-value: 6.70E-06
LOC_Os07g40380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g40380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.847; most accessible tissue: Callus, score: 67.615
vg0724211615 (J) chr07 24211615 A G 97.10% 0.00% A -> G NA
LOC_Os07g40370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 47.051; most accessible tissue: Callus, score: 67.615
vg0724211720 (J) chr07 24211720 T G 85.10% 0.00% G -> T
mr1182 (All); LMM P-value: 1.79E-06; LR P-value: 7.35E-17;
mr1182 (Jap_All); LR P-value: 2.51E-08;
mr1282 (All); LR P-value: 1.71E-13;
mr1282 (Jap_All); LR P-value: 3.13E-07;
mr1650 (All); LR P-value: 4.81E-15;
mr1650 (Jap_All); LR P-value: 3.66E-06;
mr1658 (All); LR P-value: 1.15E-11;
mr1658 (Jap_All); LR P-value: 2.27E-06;
mr1853 (All); LR P-value: 3.62E-13;
mr1959 (All); LR P-value: 2.83E-09;
mr1182_2 (All); LMM P-value: 1.52E-06; LR P-value: 1.68E-18;
mr1182_2 (Jap_All); LR P-value: 1.29E-09;
mr1282_2 (All); LR P-value: 6.51E-13;
mr1282_2 (Jap_All); LR P-value: 4.47E-07;
mr1310_2 (All); LR P-value: 8.99E-33;
mr1399_2 (All); LR P-value: 1.25E-07;
mr1607_2 (All); LR P-value: 8.44E-08;
mr1667_2 (All); LR P-value: 7.49E-12;
mr1681_2 (All); LR P-value: 1.32E-07;
mr1691_2 (All); LMM P-value: 3.13E-06;
mr1866_2 (Jap_All); LR P-value: 7.99E-07;
mr1942_2 (All); LR P-value: 1.15E-09;
mr1959_2 (All); LR P-value: 9.32E-17;
mr1959_2 (Jap_All); LR P-value: 5.43E-06
LOC_Os07g40380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 54.984; most accessible tissue: Callus, score: 93.197
vg0724211846 (J) chr07 24211846 C CGCCACG TTCAT 58.00% 0.04% CGCCACGTTC AT -> C NA
LOC_Os07g40380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g40380.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 64.393; most accessible tissue: Callus, score: 87.580
vg0724211934 (J) chr07 24211934 G A 78.40% 0.19% G -> A
mr1401 (Jap_All); LR P-value: 6.92E-08;
mr1408 (All); LR P-value: 2.99E-08;
mr1632 (Jap_All); LR P-value: 8.21E-06;
mr1682 (Jap_All); LR P-value: 7.19E-06;
mr1942 (Jap_All); LR P-value: 3.19E-06;
mr1182_2 (Jap_All); LR P-value: 5.80E-06
LOC_Os07g40380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g40380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.045; most accessible tissue: Callus, score: 97.192
vg0724211942 (J) chr07 24211942 A G 98.10% 0.00% A -> G NA
LOC_Os07g40380.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 67.089; most accessible tissue: Callus, score: 97.192
vg0724212140 (J) chr07 24212140 A G 99.90% 0.00% A -> G NA
LOC_Os07g40380.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g40370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g40390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 60.945; most accessible tissue: Callus, score: 92.713
vg0724212377 (J) chr07 24212377 A AGAG 58.70% 0.34% AGAG -> A NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.296; most accessible tissue: Callus, score: 98.341
vg0724212519 (J) chr07 24212519 A T 58.10% 0.34% T -> A
mr1082 (Ind_All); LR P-value: 9.69E-07;
mr1181 (All); LR P-value: 2.91E-27;
mr1213 (All); LR P-value: 1.13E-31;
mr1408 (All); LR P-value: 8.88E-07;
mr1761 (All); LR P-value: 2.55E-07;
mr1878 (All); LR P-value: 8.13E-33;
mr1181_2 (Ind_All); LR P-value: 2.24E-06;
mr1319_2 (All); LR P-value: 1.66E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.868; most accessible tissue: Callus, score: 99.911
vg0724212535 (J) chr07 24212535 G A 58.10% 0.34% A -> G
mr1082 (Ind_All); LR P-value: 9.69E-07;
mr1181 (All); LR P-value: 2.91E-27;
mr1213 (All); LR P-value: 1.13E-31;
mr1408 (All); LR P-value: 8.88E-07;
mr1761 (All); LR P-value: 2.55E-07;
mr1878 (All); LR P-value: 8.13E-33;
mr1181_2 (Ind_All); LR P-value: 2.24E-06;
mr1319_2 (All); LR P-value: 1.66E-08
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.604; most accessible tissue: Callus, score: 99.911
vg0724212549 (J) chr07 24212549 G GT 78.80% 0.21% G -> GT NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.948; most accessible tissue: Callus, score: 99.911
vg0724212644 (J) chr07 24212644 C A 95.80% 0.00% C -> A NA
LOC_Os07g40380.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.482; most accessible tissue: Callus, score: 98.501
vg0724212704 (J) chr07 24212704 C A 58.10% 0.32% A -> C
mr1082 (Ind_All); LR P-value: 6.78E-07;
mr1181 (All); LR P-value: 8.36E-27;
mr1408 (All); LR P-value: 6.36E-07;
mr1666 (All); LR P-value: 1.25E-07;
mr1761 (All); LR P-value: 1.73E-07;
mr1878 (All); LR P-value: 1.63E-32;
mr1915 (All); LR P-value: 5.55E-07;
mr1181_2 (Ind_All); LR P-value: 6.58E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.927; most accessible tissue: Callus, score: 99.593
vg0724212725 (J) chr07 24212725 C T 58.80% 0.28% T -> C
mr1011 (All); LR P-value: 9.18E-06;
mr1082 (Ind_All); LR P-value: 9.69E-07;
mr1181 (All); LR P-value: 8.09E-27;
mr1408 (All); LR P-value: 5.63E-07;
mr1666 (All); LR P-value: 5.62E-08;
mr1761 (All); LR P-value: 3.25E-08;
mr1949 (All); LR P-value: 2.30E-11;
mr1181_2 (Ind_All); LR P-value: 2.24E-06;
mr1579_2 (All); LR P-value: 3.52E-15;
mr1646_2 (All); LR P-value: 4.77E-10;
mr1761_2 (All); LR P-value: 7.27E-10
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g40380.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40370.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g40390.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 73.192; most accessible tissue: Callus, score: 99.593
STR0724212378 (J) chr07 24212378 GAGGAG GAGGAGG AG 57.00% 0.00% GAGGAGGAG -> GAGGAG NA