Identify a specific SNP or haplotype that is associated with a nutrition-related disease of your interest.

This assignment addresses the learning objective:

Describe the difference between an SNP and a haplotype.

Write a 300-400 word paper in which you do the following:

Identify a specific SNP or haplotype that is associated with a nutrition-related disease of your interest. I suggest that you start with PubMed then, use


Links to an external site.  and/or other databases to learn more about that SNP or haplotype (see more details below in “What is an rs#?”).

Note the exact variant (SNP ID# format is rsXXXXXX) or haplotype group of variants associated with a single gene.

Specify the nucleotide variant, i.e., SNP rs602662 is G to A.

Describe the downstream effect of the SNP, if known, e.g., it creates an amino acid change (missense) in the resulting protein (e.g., glycine to serine), creates a stop codon (non-sense) and early termination of protein translation, or alters mRNA levels/splicing.

You may use a short “nickname” for the variant but you must first define it in each write-up.  For example, “I am writing about SNP rs602662 (FUT2 Gly258Ser).” In this example, it is clear which SNP you are interested in, which gene it is located in (FUT2), and how the protein encoded by this gene is impacted by the SNP (e.g., amino acid change from glycine to serine).

Share some general information about this SNP.  What gene is it located in or near? What protein does that gene code for? What biological or metabolic function does this SNP variant influence? How might this SNP variant impact human health, etc.?

Explain why you want to explore this SNP and associated gene further.

What is an rs#? An rs# is a unique DNA variant identifier (ID). It refers to the specific variations at a specific DNA locus. The dbSNP database has all DNA sequence variant types, including single nucleotide polymorphisms (SNPs), deletions, insertions, etc. Not all variants are associated with disease. You can use

PubMed (Links to an external site.).

to look for SNPs related to your area of interest and publications. Refer to dbSNP and to examine these more closely with respect to overall peer-reviewed research [publications] support and what nucleotide and amino acid changes, if any, occur for this SNP. Use the rs# to search dbSNP and PubMed.

Note about all the different IDs that you’ll come across: SNP variants have associated IDs related to the mRNA, cDNA, or protein sequences generated from them (remember the Central Dogma). For clarity in this class, we will primarily use the rs# SNP ID. Variant IDs for mRNAs are NM or XM #s, for cDNAs are NC or XC #s, for protein are NP or XP #s. A single SNP could have many NM, XM, NP, XP, etc. IDs associated with it, as well as other names, like “MTHFR C667T”. You may note the other IDs in your write ups if you want to, but this is not necessary.

  • Remember: Not all DNA variants that impact health result in a single amino acid change in a protein. Some health-impacting variants might be located in a regulatory region of a gene and could change that gene’s mRNA transcription or affect the stability or splicing of the resulting mRNA. Some variants are not “causal” at all, i.e., they don’t directly impact health, but are genetically linked (close by on the same chromosome) to another variant that does. Such variants may be associated with a disease in genome-wide association studies and are a marker of disease risk.
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