Search for SNPs Within Gene:

Search SNPs with MSU Gene Locus:

Please Input a Gene ID:

Search for SNPs in Larger Region:

Upstream: kb

Downstream: kb

You can search for SNPs using only a gene ID (MSU gene locus identifier, e.g., LOC_Os01g39670) or using upstream and downstream distance together with the gene ID (e.g., LOC_Os01g39670 + Upstream: 1kb, Downstream: 0kb) for a larger region.


8 results found. Your gene id is LOC_Os01g39670, from 22374530 to 22376515. Upstream: 0 kb, downstream: 0 kb.

Haplotype Network Analysis:

This plot is generated using functions in R package pegas with some modifications. Only haplotypes found in ≥10 rice accessions were used to construct the haplotype network. The detailed haplotype information could be downloaded from here. The PDF format of the plot could be downloaded from here. You may go to Haplotype Network Analysis page to do more analysis.

Detailed SNP Information:

Note: SNPs are highligted when they have 'big' effect.

SNP ID Chromosome Position Major Allele Minor Allele Frequency of Major Allele Var Effect
sf0122374902(G,I) chr01 22374902 C T 95.91% C->T

LOC_Os01g39670.1 SNPs that introduce stop codons

sf0122375383(G,I) chr01 22375383 G A 99.58% G->A

LOC_Os01g39670.1 Non-Synonymous SNP

sf0122375389(G,I) chr01 22375389 T C 57.55% C->T

LOC_Os01g39670.1 Non-Synonymous SNP

sf0122375600(G,I) chr01 22375600 G A 99.22% G->A

LOC_Os01g39670.1 Non-Synonymous SNP

sf0122376228(G,I) chr01 22376228 A G 55.23% A->G

LOC_Os01g39670.1 Non-Synonymous SNP

sf0122376317(G,I) chr01 22376317 A C 55.27% A->C

LOC_Os01g39670.1 UTR_3_PRIME

sf0122376334(G,I) chr01 22376334 A C 55.19% A->C

LOC_Os01g39670.1 UTR_3_PRIME

sf0122376442(G,I) chr01 22376442 T C 57.87% C->T

LOC_Os01g39670.1 UTR_3_PRIME

Search SNPs with Gene Function or Gene Symbol:

Please Input a Keyword:

You can retrieve gene IDs using a specific functional keyword (e.g., Cellulose synthase, cellulose or glycosyltransferase), a gene symbol (e.g., Ghd7, Ghd8, or GS3), a RAP ID (e.g., Os01g0100500), or a MSU ID (e.g., LOC_Os01g01040), and then click the listed gene IDs to get detailed information.

Note: wildcard character '%' can be accepted, e.g., cellulos%thase matches Cellulose synthase.