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How To Analyze Your Single Nucleotide Polymorphism (SNP) Chip Data

Posted in: Genomics and Epigenetics
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So, you’re sitting there with your list of significant SNPs, thinking, “what do I do now”?  Hopefully this article can point you in the right direction!

So far, you will have extracted genomic DNA from your organism of interest, sourced the SNP chips required, and had the DNA run on these chips.  The chips will then have been put through a variety of statistical analyses in order to produce that list of significant SNPs you have lying in front of you.

If you follow the steps below, then it should be quick and easy to determine what genes your SNPs are in or near, and whether they could play a role in the phenotype you’re investigating.

  1. Cluster your SNPs.  First, sort the data by chromosome, and then by chromosome position, in order to cluster your SNPs.  SNPs that are clustered are thought to play a greater role in affecting a trait of interest.
  2. Choose which SNPs to pursue. Your SNP collection will have been assigned a significance value known as a –log10p value, which is determined by performing a statistical test known as a Bonferroni  correction.  Any SNPs with a –log10p value greater than this significance value are worth investigating further.  For example, if your –log10p value is 4.6, then any SNPs with a –log10p value of greater than or equal to 4.6 may play a role in the phenotype you’re looking at.
  3. Find your SNPS on the chromosome. Next you will need to go to a website called Ensembl.  On the homepage there is a dropdown box where you can select your organism of interest and a box next to it where you can type the chromosome number that you are after (make sure you type chromosome as “chr”, otherwise it won’t work).  It will then take to you to an overview of the chromosome. If you click anywhere on that chromosome and then click on “jump to location” view it will bring up that area in greater detail.  Take the chromosome position assigned to each SNP and paste it into the box under the “region in detail” image twice, making sure that the two numbers are separated by a colon (see diagram below).  This will then bring up the location of the SNP along the chromosome (highlighted by the thin red line) and also the genes that it is in or adjacent to.  Make a note of these genes for each SNP.How To Analyze Your Single Nucleotide Polymorphism (SNP) Chip Data
  4. Identify gene functions. Now comes the bit where you can find out what exactly these genes do!  To do this, first go to NCBI.  Type the gene name in the search bar and from the dropdown menu, select GENE.  This will generate a list of all the organisms that the required gene has been reported in.  If you select your organism from the list, this will bring up all the information known about this gene, including its genomic structure and any papers published about it.  If you’re lucky, it will pop up with a summary of the gene’s function; if not, then you’ll need to go on to point six.
  5. Dig deeper.  If NCBI alone doesn’t provide adequate information about the function of your selected gene, then OMIM will be your next point of call.  Here you should find a long summary of things that have been published about your gene. If this still doesn’t have anything informative (in rare cases), then you will have to go with as much info as you can from the name of the gene!

If you have followed all of these steps, then you will hopefully have managed to identify candidate genes associated with your phenotype of interest.  This should go a long way towards helping you understand the role of these genes in complex conditions.

What are your tips for analyzing microarray results?

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Image Credit: jurvetson


  1. Tahir Mujtaba on May 25, 2021 at 12:28 pm

    informative content. keep it up. highly appreciated.

  2. khaled Massoud Hesaien on February 23, 2017 at 9:23 pm

    Hi Emma
    My name is Khaled and I am the plant breeder.
    First of all, I really appreciate your post and I work with different plant genotypes with different levels of resistance. I would do SNP analysis.
    My question is what I need to do it?
    If I need the F1 generation or I need only different genotypes to have results?

  3. Stefany Botero on August 13, 2016 at 4:22 pm

    Hi Emma_hutchinson!!

    My Name is Stefany and I´m Microbiologist from Colombia, but now I´m working as Bioinformatics with mammals data and I´ve had to focusing on in NGS and modern molecular and genomic markers, what have been so difficult to me. I really appreciate your post, although I already had started before ordered my SNPs I didn´t know how to continue.

    Thanks so much!!!
    I hope to continue reading your posts.

    Stefany B

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