11417470
February 2nd, 2018
MBioS 402
Exploration of the Human Genome by Investigation of Personalized SNPs
1. List the 3-5 health-related SNPs
... [Show More] discovered on SNPedia in which you have a personal
interest. For each SNP, write one or two sentences describing why you feel personally
invested in learning more information about it.
1. rs333: This SNP is on the allele CCR5 and is a deletion of 32 nucleotides. The subsequent
deletion renders the individual partially resistant to HIV infection (SNPedia.com). Selective
pressure for this genotype is thought to have resulted from resistance to the plague
(SNPedia.com). I am interested in this SNP because HIV is a prevalent infection in sub-Saharan
Africa. This region has one of the highest rates of HIV infection in the international community.
Given the high rate of carriers in the Caucasian population, I am curious to see what the rate of
carriers are in sub-Saharan Africa.
2. rs4988235: This SNP is on the MCM6 gene and is associated with lactose intolerance. Those
with the T allele are able to digest lactose, while those with the C allele are more likely to be
lactose intolerant. I am interested in this SNP because I am lactose intolerant, but have become
less so in previous years. I believe I have the C allele because of my lactose intolerance and
ethnic heritage.
3. rs148833559: The SNP has been shown to have significance in determining height. Those
with the minor allele (STC2) gene are 2.1 cm taller than those without the allele. I am interested
in this SNP because I knew height was determined by both genetics and environment, and I am
skeptical of the fact that environmental factors were not considered for the statistical
significance.
2. Use the UCSC Genome Browser to uncover the precise chromosomal location for one of
the SNPs listed above. Make sure to write down the chromosome number along with the
base pair position in your answer and confirm that this corresponds to the chromosomal
picture at the top of the page.
The rs4988235 SNP associated with lactose intolerance is located on chromosome 2q21.3. Its
precise base pair location on the chromosome is: 135851076.
3. Using either SNPedia or the UCSF Genome Browser, write out the nucleotide variations
that define the SNP, i.e. the alleles of the SNP. Remember that almost all common SNPs
have only two alleles. Record any known disease risk for individuals that inherit a
particular allele of your SNP.
The nucleotide variations for this SNP are: C/T. (C;C) carriers are more likely to be lactose
intolerant than those who have the (T;C) alleles. Those with lactose non-persistence are more
likely to have an increase in body mass index. However, the lactase persistence genotype is
also involved in protecting the Metabolic Syndrome (Friedrich et al., 2014).
References:
Friedrich DC, de Andrade FM, Fiegenbaum M, de Almeida S, Mattevi VS, Callegari-Jacques
SM, Hutz MH. The lactase persistence genotype is a protective factor for the metabolic
syndrome. Genetics and Molecular Biology. 2014 Jul 15. 37(4):611-615.
4. Write down the name of the gene nearest to your SNP. If your SNP lies within a gene,
record the gene abbreviation and name and determine if the SNP is located within an
exon, an intron, or an untranslated region of that gene.
The SNP is located within an intron of region NM_005915.5, which is the MCM6
(minichromosome maintenance complex component 6) gene.
5. Using NCBI nucleotide search, obtain the RefSeq identification number along with the
amino acid sequence translation of the nearest gene. Copy and paste that information
here.
The Reference Sequence is: NM_008958
Amino Acid Sequence: [Show Less]