Exploration of the Human Genome by Investigation of Personalized SNPs
Lani C. Keller
Assignment Answer Key
1.
List the 3-5 health-related SNPs 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.
 rs4402960- risk of type-2 diabetes. My uncle was recently diagnosed with type-2 diabetes
and two other members of my family have it.
 rs2383206- risk of heart disease. My grandfather passed away from a heart attack several
years ago and the doctors told us that he probably had heart disease.
 rs140504- risk of bipolar disorder. I just learned a lot about bipolar disorder in one of my
psychology classes and I’m interested to see if someone can have a genetic
predisposition.
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.
 rs4402960- chr3:185,511,687
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.
 Rs4402960- the common allele is being homozygous G,G. If you are homozygous T,T or
heterozygous G,T you have a 1.5X risk for type-2 diabetes
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 the gene.
 SNP lies within an intron of the IGF2BP2 (insulin-like growth factor 2 binding protein 2)
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.
 Rs4402960 = RefSeq number NM_001007225
 Protein translation
"MMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAI
RAIETLSGKVELHGKIMEVDYSVSKKLRSRKIQIRNIPPHLQWEVLDGLL
AQYGTVENVEQVNTDTETAVVNVTYATREEAKIAMEKLSGHQFENYSFKISYIP
DEEVSSPSPPQRAQRGDHSSREQGHAPGGTSQARQIDFPLRILVPTQFVGAIIGKE
GLTIKNITKQTQSRVDIHRKENSGAAEKPVTIHATPEGTSEACRMILEIMQKEADE
TKLAEEIPLKILAHNGLVGRLIGKEGRNLKKIEHETGTKITISSLQDLSIYNPERTIT
VKGTVEACASAEIEIMKKLREAFENDMLAVNTHSGYFSSLYPHHQFGPFPHHHS
YPEQEIVNLFIPTQAVGAIIGKKGAHIKQLARFAGASIKIAPAEGPDVSERMVIITG
PPEAQFKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNEL
QNLTSAEVIVPRDQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQVKQQEQKYPQ
GVASQRSK”
6.
Based on the nucleotide alignment of your SNP sequence among vertebrates, do you think that
using a mouse model would be beneficial to gain further information about this SNP? Why or why
not? (A mouse model would typically be a pair of mice strains that carry different alleles of your
SNP.)
 No, using a mouse model to further study rs4402960 would be a bad idea because this
region is not conserved between mice and humans!
7.
Using proper Council of Science Editors style referencing, list three published genome-wide
association studies that have identified your SNP.
 Perry JR, Voight BF, Amin N. 2012 Stratifying type 2 diabetes cases by BMI identifies
genetic risk variants in LAMA1 and enrichment for risk variant in lean compared to
obese cases. PLoS Genet 8(5):e1002741.
 Takeuchi F, Serizawa M, Yamamoto K. 2009. Confirmation of multiple risk Loci and
genetic impacts by a genome-wide associate study of type 2 diabetes in the Japanese
population. Diabetes 58(7):1690-9.
 Majajan A, Go MJ, Zhang W. 2014. Genome-wide trans-ancestry meta-analysis provides
insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet
46(3):234-44.
8.
Make screen shots of your SNP’s genomic region including the SNP, the multiple alignments, and
the genome-wide association studies.