42 variations found. Os07g0164000/LOC_Os07g06970 (HEN1; putative; expressed), ranging from 3,429,442 bp to 3,434,747 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g06970 | HEN1, putative, expressed; RAP ID: Os07g0164000; MSU ID: LOC_Os07g06970 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os07g06970 | Os07g0164000 | waf1(waf1-1,waf1-2) | wavy leaf 1-1, wavy leaf 1-2, WAVY LEAF1 | The locus was roughly mapped to the short arm of chromosome 7 between two markers S11633-2 and E12196. AB583903. an Ortholog of Arabidopsis HEN1. | WAF1 | WAVY LEAF 1 |
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.
| 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. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| STR0703433648 (J) | chr07 | 3433648 | GTA | GCG | 52.30% | 0.00% | GTA -> GCG | NA |
|
| STR0703434737 (J) | chr07 | 3434737 | AGGGAAG GGAAG | AGGGAAG GGAAGGG AAGG | 96.50% | 0.00% | AGGGAAGGGA AG -> AGGGAAGGGA AGGGAAGG | NA |
|
| vg0703429473 (J) | chr07 | 3429473 | A | C | 56.00% | 0.02% | A -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g06970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06950.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.671; most accessible tissue: Callus, score: 93.643 |
|
| vg0703429514 (J) | chr07 | 3429514 | GC | G | 56.00% | 0.36% | GC -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g06970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.421; most accessible tissue: Callus, score: 93.643 |
| vg0703429520 (J) | chr07 | 3429520 | G | C | 55.90% | 0.38% | G -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g06970.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.249; most accessible tissue: Callus, score: 93.643 |
|
| vg0703429581 (J) | chr07 | 3429581 | T | G | 55.90% | 0.21% | T -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g06970.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.155; most accessible tissue: Callus, score: 89.304 |
|
| vg0703429870 (J) | chr07 | 3429870 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os07g06970.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.921; most accessible tissue: Zhenshan97 young leaf, score: 87.299 |
| vg0703430062 (J) | chr07 | 3430062 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os07g06970.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g06960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.902; most accessible tissue: Callus, score: 90.727 |
| vg0703430072 (J) | chr07 | 3430072 | C | A | 55.40% | 0.25% | C -> A |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 77.843; most accessible tissue: Callus, score: 90.727 |
|
| vg0703430157 (J) | chr07 | 3430157 | C | T | 63.70% | 0.06% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g06960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.178; most accessible tissue: Minghui63 flower, score: 85.666 |
| vg0703430302 (J) | chr07 | 3430302 | T | C | 97.10% | 0.00% | T -> C | NA |
LOC_Os07g06960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06970.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.762; most accessible tissue: Callus, score: 90.339 |
| vg0703430465 (J) | chr07 | 3430465 | C | T | 55.90% | 0.25% | C -> T,A |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: A| synonymous_variant LOW(snpEff) LOC_Os07g06960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g06970.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 65.603; most accessible tissue: Callus, score: 86.491 |
|
| vg0703430627 (J) | chr07 | 3430627 | G | A | 55.40% | 0.38% | G -> A |
LOC_Os07g06970.1 Alt: DEL/splice_donor_variant(CooVar)
LOC_Os07g06970.1 Alt: A| splice_donor_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar) The average chromatin accessibility score: 57.215; most accessible tissue: Minghui63 flower, score: 73.710 |
|
| vg0703430671 (J) | chr07 | 3430671 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os07g06970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 56.721; most accessible tissue: Minghui63 flower, score: 71.461 |
| vg0703431101 (J) | chr07 | 3431101 | A | C | 56.00% | 0.28% | A -> C |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 52.151; most accessible tissue: Callus, score: 72.299 |
|
| vg0703431182 (J) | chr07 | 3431182 | G | A | 56.00% | 0.36% | G -> A |
mr1130 (Ind_All); LR P-value: 4.88E-06;
mr1291 (All); LR P-value: 4.17E-07; mr1496 (Ind_All); LR P-value: 6.64E-06; mr1531 (Ind_All); LR P-value: 6.15E-06; mr1557 (All); LR P-value: 2.66E-17; mr1679 (Ind_All); LR P-value: 9.32E-06; mr1904 (Ind_All); LR P-value: 6.24E-06; mr1170_2 (All); LR P-value: 8.66E-08 |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 52.148; most accessible tissue: Callus, score: 88.688 |
| vg0703431792 (J) | chr07 | 3431792 | G | A | 85.20% | 0.00% | G -> A,T |
|
LOC_Os07g06960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.185; most accessible tissue: Callus, score: 77.818 |
| vg0703432078 (J) | chr07 | 3432078 | GAA | G | 99.50% | 0.00% | GAA -> G,GAAAA | NA |
LOC_Os07g06960.1 Alt: GAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06980.1 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: GAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.989; most accessible tissue: Zhenshan97 young leaf, score: 65.280 |
| vg0703432101 (J) | chr07 | 3432101 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os07g06960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.877; most accessible tissue: Zhenshan97 young leaf, score: 61.386 |
| vg0703432224 (J) | chr07 | 3432224 | C | T | 92.50% | 0.00% | C -> T | NA |
LOC_Os07g06960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06980.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.166; most accessible tissue: Callus, score: 78.124 |
| vg0703432636 (J) | chr07 | 3432636 | A | G | 55.90% | 0.34% | A -> G |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 59.972; most accessible tissue: Minghui63 flower, score: 70.849 |
|
| vg0703432746 (J) | chr07 | 3432746 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os07g06970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 63.407; most accessible tissue: Callus, score: 82.920 |
| vg0703433029 (J) | chr07 | 3433029 | T | C | 55.50% | 0.06% | T -> C |
LOC_Os07g06970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g06970.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 55.153; most accessible tissue: Callus, score: 77.537 |
|
| vg0703433060 (J) | chr07 | 3433060 | GA | G | 55.10% | 0.00% | GA -> G,GAA | NA |
LOC_Os07g06960.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g06980.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06980.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g06970.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.209; most accessible tissue: Callus, score: 77.537 |
| vg0703433196 (J) | chr07 | 3433196 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os07g06960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os07g06980.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g06980.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g06970.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.395; most accessible tissue: Callus, score: 70.013 |
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