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Exploring a SNP in zebrafish

The missense variant rs180018766 is found in the zebrafish ift88 gene.

(a) Find the page with information for rs180018766.

(b) Is rs180018766 a missense variation in all transcripts of the ift88 gene?

(c) Does the rs180018766 variant affect any other genes? If so, which genes?

(d) What is the major allele in rs180018766?

(a) Please note there is more than one way to get this answer. Either go to the Variant Table for the zebrafish ift88 gene, and filter variants to the missense variants, or search Ensembl for rs180018766 directly.

(b) Once you’re in the Variation tab, click on the Genes and regulation link or icon.

This SNP is found in six transcripts from two genes. It is a missense variant in three of these transcripts, an intron variant in two of the transcripts and an upstream variant of the last transcript.

(c) From the Genes and Transcript consequences table, you can see that rs180018766 is an upstream variant of transcript ENSDART00000018251 from the ENSDARG00000010700 (interleukin 17d) gene.

(d) Select Population genetics from the side menu.

From the Frequency data table, the Sanger Stemple submission shows that C is the major allele (50.6% of the population) compared to T (49.4% of the population). Note that T is the reference allele, irrespective of population prevalence.