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Challenge questions

The SNP rs601338 controls ’secretor status’ (i.e. whether A/B antigens are secreted into bodily fluids) Individuals with GG or GA genotypes at this SNP are secretors, and individuals with homozygous AA genotypes are non-secretors - as described in this paper based on the ALSPAC cohort.

Can you solve?

Use the UCSC genome browser and Ensembl, and your gene annotation file, to solve:

  • Use the genome browser to find out where rs601338 in the gene. (NB. use GRCh38 assembly coordinates for this.)

  • Does this agree with the gene annotation file? Which exon of FUT2 is the SNP in?

  • Using the genome browser, can you figure out what amino acid change rs601338 makes to the encoded protein?

  • Using the Ensembl site, can you find an individual from the 1000 Genomes Project data with the secretor genotype? And an individual with non-secretor genotype?