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Search Results:

28 variations found. LOC_Os09g20720 (strictosidine synthase 1 precursor; putative; expressed), ranging from 12,484,351 bp to 12,484,831 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
vg0912484353 (J) chr09 12484353 T C 55.40% 14.79% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 12.428; most accessible tissue: Callus, score: 53.486
vg0912484366 (J) chr09 12484366 A G 55.50% 16.02% A -> G NA
LOC_Os09g20720.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 12.610; most accessible tissue: Callus, score: 53.486
vg0912484379 (J) chr09 12484379 T C 56.40% 22.79% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 12.669; most accessible tissue: Callus, score: 53.486
vg0912484418 (J) chr09 12484418 G T 38.20% 43.23% G -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 13.825; most accessible tissue: Callus, score: 53.486
vg0912484428 (J) chr09 12484428 C T 56.20% 42.00% C -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 15.619; most accessible tissue: Callus, score: 71.216
vg0912484439 (J) chr09 12484439 G T 55.90% 42.47% G -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 15.619; most accessible tissue: Callus, score: 71.216
vg0912484465 (J) chr09 12484465 C T 56.30% 41.98% C -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 16.563; most accessible tissue: Callus, score: 71.216
vg0912484596 (J) chr09 12484596 G A 56.80% 42.42% G -> A NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 15.752; most accessible tissue: Callus, score: 42.290
vg0912484623 (J) chr09 12484623 G T 56.30% 41.83% G -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 15.695; most accessible tissue: Callus, score: 42.290
vg0912484626 (J) chr09 12484626 A G 56.30% 42.04% A -> G NA
LOC_Os09g20720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.695; most accessible tissue: Callus, score: 42.290
vg0912484633 (J) chr09 12484633 C T 56.40% 42.04% C -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.695; most accessible tissue: Callus, score: 42.290
vg0912484636 (J) chr09 12484636 T C 56.50% 42.04% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.695; most accessible tissue: Callus, score: 42.290
vg0912484639 (J) chr09 12484639 T C 56.60% 42.00% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.638; most accessible tissue: Callus, score: 42.290
vg0912484643 (J) chr09 12484643 A G 56.40% 42.07% A -> G NA
LOC_Os09g20720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.638; most accessible tissue: Callus, score: 42.290
vg0912484647 (J) chr09 12484647 C T 56.30% 42.19% C -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 15.638; most accessible tissue: Callus, score: 42.290
vg0912484660 (J) chr09 12484660 T C 56.30% 42.30% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.638; most accessible tissue: Callus, score: 42.290
vg0912484664 (J) chr09 12484664 A C 38.20% 40.94% A -> C
mr1242_2 (Ind_All); LR P-value: 1.04E-06;
mr1422_2 (Ind_All); LR P-value: 3.32E-06;
mr1798_2 (Ind_All); LR P-value: 1.42E-07
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 15.580; most accessible tissue: Callus, score: 42.290
vg0912484670 (J) chr09 12484670 GTGGCGC G 56.20% 42.47% GTGGCGC -> G NA
LOC_Os09g20720.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.580; most accessible tissue: Callus, score: 42.290
vg0912484681 (J) chr09 12484681 C G 56.20% 42.49% C -> G NA
LOC_Os09g20720.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.164; most accessible tissue: Callus, score: 72.002
vg0912484693 (J) chr09 12484693 T C 56.40% 42.36% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 18.045; most accessible tissue: Callus, score: 72.002
vg0912484694 (J) chr09 12484694 A G 56.20% 42.51% A -> G NA
LOC_Os09g20720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.045; most accessible tissue: Callus, score: 72.002
vg0912484702 (J) chr09 12484702 G A 56.20% 42.49% G -> A NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 18.162; most accessible tissue: Callus, score: 72.002
vg0912484726 (J) chr09 12484726 A G 56.30% 41.60% A -> G NA
LOC_Os09g20720.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 17.863; most accessible tissue: Callus, score: 72.002
vg0912484742 (J) chr09 12484742 G A 70.40% 9.99% G -> A NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 17.924; most accessible tissue: Callus, score: 72.002
vg0912484766 (J) chr09 12484766 A G 38.30% 22.15% A -> G
mr1754_2 (All); LR P-value: 6.80E-07;
mr1754_2 (Ind_All); LR P-value: 8.00E-06
LOC_Os09g20720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 17.735; most accessible tissue: Callus, score: 72.002
vg0912484774 (J) chr09 12484774 T C 56.40% 34.62% T -> C NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 17.735; most accessible tissue: Callus, score: 72.002
vg0912484778 (J) chr09 12484778 G A 56.40% 40.92% G -> A NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 17.669; most accessible tissue: Callus, score: 72.002
vg0912484786 (J) chr09 12484786 C T 55.80% 41.98% C -> T NA
LOC_Os09g20720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g20720.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 17.494; most accessible tissue: Callus, score: 72.002