SNPWatch: Genetic Variation is in the Eye of the Beholder


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Editor’s note: Pending an FDA decision, 23andMe no longer offers new customers access to health reports referred to in this post. Customers who purchased prior to November 22, 2013 will still be able to see their health reports, but those who purchased after that time will not. Those customers will have access to ancestry information as well as access to their uninterpreted raw data.

Your iris (the colored part of the eye) can tell a lot about you. Like your fingerprint, the patterns on your iris are complex and unique. Because of this, iris recognition is used in some countries for national identification systems and to automate border crossings.

Although we know that no two irises are the same, very little is understood about the genetics underlying these differences. Investigators are studying this topic to learn more about iris-related diseases and to provide clues about the brain, since iris and brain development appear to be connected. This is true on a genetic level, for instance, a mutation linked to iris loss is also associated with defects in a portion of the brain called the frontal lobe. In addition, some iris characteristics correlate with neurological diseases like Down syndrome.

A recently published genome-wide association study (GWAS) sought to elucidate the genetic factors involved in normal iris variation between people. Scientists from Australia scanned the genomes of nearly 2,700 individuals, all of European descent, and measured iris characteristics such as crypts, pigmented rings, furrow contractions, and pigmented spots on the iris.

The authors found one SNP—*—that associated with the presence of crypts, oval-shaped areas that represent openings in the iris. This SNP is located near the SEMA3A gene, which codes for a protein that acts in both the iris and brain and directs cell movement. Interestingly, mutations in the SEMA3A gene have been previously linked to neurological disorders including schizophrenia and Alzheimer’s disease.

(23andMe customers can view their data for these SNPs in the Iris Patterns Preliminary Research report in their account or by using the table at the end of this post.)

The arrows mark examples of crypts. A. No crypts. E. Many large crypts. The American Journal of Human Genetics 89, 334–343, August 12, 2011.

The arrow marks a pigmented ring around the pupil. A. Absence of pigmented ring. B. Yellow/green ring on a blue iris. The American Journal of Human Genetics 89, 334–343, August 12, 2011.

Another SNP——was associated with more pronounced furrow contractions, which are circular and radial bands that result from the iris folding in exactly the same location each time it adapts to different light conditions. A third SNP (**), located near the SLC24A4 gene, was linked to pigmented rings that are visible around the pupil and distinguish different shades of green and hazel eyes. Interestingly, previous studies have also linked SLC24A4 to differences in eye color (blue versus green eyes). Since pigmented rings on blue irises can cause the eye to appear green or hazel, the authors of this study suggest that the presence or absence of pigmented rings may drive the association between and eye color.

The authors noted that older participants tended to have more furrow contractions and pigmented spots on the iris. Males had more crypts than females, but fewer pigmented spots on the iris, furrow contractions, or pigmentation rings.

It is interesting to wonder why no two irises are the same and this study suggests that some of the differences are due to our genes. These findings also add evidence to the idea that the iris and brain are tightly linked starting very early in human development. Thus, while iris patterns can be used to tell people apart, they may also truly be a window into our minds.

SNP Version Effect
* A More crypts
A More pronounced furrows
** G Pigmented rings

* is equivalent to described in the paper.

** is equivalent to described in the paper.

SNPwatch gives you the latest news about research linking various traits and conditions to individual genetic variations. These studies are exciting because they offer a glimpse into how genetics may affect our bodies and health; but in most cases, more work is needed before this research can provide information of value to individuals. For that reason it is important to remember that like all information we provide, the studies we describe in SNPwatch are for research and educational purposes only. SNPwatch is not intended to be a substitute for professional medical advice; you should always seek the advice of your physician or other appropriate healthcare professional with any questions you may have regarding diagnosis, cure, treatment or prevention of any disease or other medical condition.






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  • Mike

    Not easy to photograph one’s eye to look at close up, but with

    SNP Version Effect
    rs1533995* A More crypts
    rs3739070 A More pronounced furrows

    it sort of looks like I have mild versions of those above effects for my AA’s.

    and having green-hazel eyes and TT and being of European decent any effect like that below was barely there

    rs12896399** G Pigmented rings

  • http://www.simplerna.com twri

    Similar to Iris Recognition, will Genome Recognition be used to identify people in real-time?

    It will be more accurate than other methods.

    Of course this is still many years in the future but with genome sequencing getting faster and cheaper day by day, this may become practical.

  • Kyrie Smith

    Amazing, I now have an answer to a question I had. My husband and I have brown eyes and our son has hazel with a ring. I have AA and my husband has GG so our son has AG. Our son’s outer ring is greyish, middle ring yellow, and inner brown. I looked at my daughter’s eyes and she has more crypts but not as many as me and my son has none. My daughter is AA.

  • Kyrie Smith

    More Specifically

    rs1533995
    AA Ethan Marvick – daughter’s father
    GG John Smith – son’s father
    AA Kyrie Smith – me

    rs3739070
    AA Ethan Marvick
    AA John Smith
    AA Kyrie Smith

    rs12896399
    GG Ethan Marvick
    GT John Smith
    GG Kyrie Smith

    So it’s still a bit odd, we don’t have colored rings except my son. Also, we don’t have big crypts or furrows, just little ones here and there.

  • ScattyShirley

    interesting as I had already been given information that I have a high risk( 46%) of contracting( is that the right term) alzheimers, ( scary but 54% chance of not getting it)
    now the crypt pattern also suggests that I am at risk.

    Not sure how I feel about this but refuse to worry. Having cancer and being out of remission after 3 years clear is enough to think about.

    • http://23andme.com Shwu

      Hi Scatty,

      Thanks for reading! Note that there is no known association between crypt patterns and Alzheimer’s disease. There may be genetic factors that influence Alzheimer’s risk that are close to genetic factors that influence iris patterns, but whether one actually interacts with the other is not known. Future research may shed more light on these topics.

  • Mary

    I have a daughter, she is now 36, that has blue eyes and blond hair. But within the iris of her left eye she has a large (about 1/4 of the total iris) spot that is light brown. This showed up at about 4-6 months of age. It has never bothered her. I want to mention that my older brother had the same thing in his right eye, he had brown hair. What is it called, and is it rare? I have never seen any other people with it. I might mention that I have hazel eyes and blond hair, and her father has blue eyes and blond hair. Her father was adopted and we know nothing of his ancestry. Thank you for your help, and such a great and facinating site.

  • Kaela

    Mary, my family develops something like that as well. It’s not only in one eye. It’s in both eyes. There is a brown center surrounded by a yellow ring. It appears to grow with age. We start out with bright blue eyes and as we age, the ring grows bigger and bigger until our eyes appear hazel to brown or yellow. My grandma literally has almost yellow eyes, but I look at photos of her in college, and they’re blue! My eyes are half brown-yellow, half blue at the moment. I love my eyes. I don’t want them to change. What’s interesting to note is that both schizophrenia and dementia run in the family. I didn’t know that until recently because my dad is adopted as well. Mary, there’s an interesting fable about that that is represented in the “Unborn” movie where someone with that eye coloring that you’re describing is in fact a Jewish twin or something, but it’s just a fable.

  • Loquacious Caveman

    Is it possible to have a colored ring around the iris, that matches the iris and is undetectable?

  • Mary C-Edwards

    Interesting – sounds like trouble??? Mine are mainly full of large crypts and rings. This is so fascinating can’t wait to get my test back!!

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