Are there any good proxy SNPs (r2 ≥ 0.8) for the variants rs7636 and rs13107325?

Introduction

In the practical you will be given two lists, one comprising 23 gene names and the other 21 DNA sequence variants (see table at the end of the document) – the selected genes are part of an ongoing study.

Reporting

Please prepare your report as a word document not exceeding 2000 words excluding Tables and references. Use a 12 font and double spacing throughout the document and list URLs as references.  You will find more detailed guidelines on how to prepare reports on QMplus. Sub-section the report having  a very brief Introduction outlining the objectives  of this practical followed by sections on the  ‘Gene set’, ‘Variation correlated to the gene set’, ‘Assessment of genotype-phenotype correlations ‘, and ‘Conclusions and Discussion’.

Tasks

  1. Establish the correct gene(s) – variant pairs using a genome browser; variants may also be located outside a gene; typically, the nearest gene(s) to this variant will be included in the list. Obtain a reference sequence (rs) id for all variants.
  2. Use database resources to explore what is known about the function of each gene and the protein it encodes (i.e. a few sentences summarising what the gene does) as well as its tissue expression profile. Prepare a table with each gene’s potential implication to disease.
  3. Establish the functional impact of each sequence variant; for example, is a variant located in a coding region of the genome and if yes, does it alter an amino acid? or is it overlapping a regulatory element? Report this element e.g. promoter
  4. Are there any good proxy SNPs (r2 ≥ 0.8) for the variants rs7636 and rs13107325?
  5. Report, where possible, the minor allele frequency of each variant in the population – reference the data source you used (e.g. URL of data base or repository).  Use a database to report MAF in different population groups i.e. HapMap / 1000Genomes panels. Discuss if you observe any frequency differences between populations.
  6. Investigate using both variant identifier and the gene name whether there is a known association to one or more human traits (e.g. blood pressure) including disease.
  7. For those genes you have established an association to a human trait(s) report the number of known rare variants and how many of these rare variants are Loss of Function.
  8. Does rs13107325 have any unusual features in terms of its LD relationship to other nearby common variants in European-descent populations?  In which common diseases this variant may play a role?
  9. Based on all the information assembled, assess whether the genes found in question 1 could be divided in to subgroups underlying a specific trait or combination of traits.
  10. Are there any epigenetic effects known to be associated with the trait(s) of the subgroup(s) you defined (i.e. question 9)
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