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Author Topic: Family Finder and Lactase Persistence (rs4988235)  (Read 2780 times)
rms2
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« on: February 20, 2012, 09:41:35 PM »

I just found out that FTDNA's Family Finder test includes rs4988235, which is the most common European SNP associated with lactase persistence. Once I downloaded 7-zip (which is free, btw) and figured out how to unzip my raw autosomal data, I discovered rs4988235 is there.

23andMe on rs4988235 and Lactose Intolerance

I have "AA" there, which means I am lactase persistent and can drink milk and consume other dairy products without discomfort or ill effect.

I knew that from experience already, but I was always curious what dna testing would show in that regard.

It's a bit confusing to me, since I have only heard the lactase persistence allele referred to as 13910 and lactase persistence as either a CT or a TT there. Maybe someone with more genetics expertise than I have can explain the distinction.

Anyway, according to 23andMe, an "AG" or "AA" at rs4988235 makes one likely to be lactase persistent.

This is pretty cool. I just "milked" Family Finder for more information than I thought it would provide. :-)
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rms2
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« Reply #1 on: February 21, 2012, 08:46:07 AM »

If you have had the Family Finder test, see if you can unzip your raw data and have a look. Use the Excel "Find" utility to locate rs4988235 and see what you have there. If you wouldn't mind, post that here in this thread and let us know how it corresponds to your own personal experience with milk and other dairy products.

Are you able to drink milk without discomfort (gas, bloating, diarrhea, etc.)? Or are you lactose intolerant?

In my case, the dna finding matches my experience. I have never experienced any problems with milk or other dairy products, and my result at rs4988235 is right in line with that.

How about you?
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rms2
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« Reply #2 on: February 23, 2012, 08:50:24 PM »

Hey! I just discovered a second indicator of lactase persistence, rs182549. It is also included in FTDNA Family Finder results.

In this case  a "CT" or "TT" result indicates lactase persistence. A "CC" would be indicative of lactose intolerance.

I have a "TT" at rs182549, so I got lactase persistence from both my parents on that one, as well.
« Last Edit: February 23, 2012, 08:50:46 PM by rms2 » Logged

rms2
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« Reply #3 on: February 25, 2012, 05:38:31 PM »

I also found out I have a "TC" at rs1805008, which is one of several SNPs in the MC1R gene associated with red hair color. A "T" contributes red hair, but it is recessive, so, although I carry the trait for red hair, I don't have it myself. I did pass it on to my youngest daughter, however, since she does have red hair, but she had to get the other "T" from her mother.

I have an "AA" at rs1426654, which, according to my Promethease report means the following:

Quote
probably light-skinned, European ancestry[.] This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.

(I'll keep talking about my Family Finder results here until I run out of things to say or someone else chimes in to discuss his or her results.)
« Last Edit: February 25, 2012, 05:58:51 PM by rms2 » Logged

Mike Forsythe
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« Reply #4 on: April 10, 2012, 08:37:09 PM »

rs4988235=cc
rs1805008=cc
rs1426654=aa
rs182549=cc
I have no problems with milk,have green eyes and light skin. My hair had a reddish tinge to it when I was younger.
Is there a site  where one might find other such indications for autosomal results
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Jim Rohrer
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« Reply #5 on: April 11, 2012, 12:18:26 PM »

Now I am confused.  The autosomal dna tests that I ordered from FTDNA involve STR alleles such as those shown below. Can the rs codes mentioned in other postings be cross-walked over or are they not the same as the forensic STRs?


D8S1179
D21S11
D7S820
CSFIPO
D3S1358
THO1
D13S317
D16S539
D2S1338
D19S433
VWA
TPOX
D18S51
D5S818
FGA
Penta D
Penta E
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Jim R
rms2
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« Reply #6 on: April 11, 2012, 07:58:10 PM »

Now I am confused.  The autosomal dna tests that I ordered from FTDNA involve STR alleles such as those shown below. Can the rs codes mentioned in other postings be cross-walked over or are they not the same as the forensic STRs?


D8S1179
D21S11
D7S820
CSFIPO
D3S1358
THO1
D13S317
D16S539
D2S1338
D19S433
VWA
TPOX
D18S51
D5S818
FGA
Penta D
Penta E


Honestly, I don't know. You will have to ask FTDNA.
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rms2
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« Reply #7 on: April 11, 2012, 08:07:15 PM »

rs4988235=cc
rs1805008=cc
rs1426654=aa
rs182549=cc
I have no problems with milk,have green eyes and light skin. My hair had a reddish tinge to it when I was younger.
Is there a site  where one might find other such indications for autosomal results

Well, your results at rs4988235 and rs182549 would tend to indicate that you should be lactose intolerant, but I guess there are varying degrees of that. Can you drink a lot of milk without discomfort?

You have the light skin allele but not the one for red hair, but I think there is more than one component to the gene for red hair.
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Mike Forsythe
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« Reply #8 on: April 11, 2012, 11:05:24 PM »

I can drink a quart of milk  and have no problems...My maternal grandmother Kennedy had red hair and a lot of my cousins have red or blond hair. I have a brother with blond hair....I uploaded my Gedmatch, all I can find are my ancestral matches. Where did you locate your 11% Eastern European in Gedmatch...Family Finder is a little difficult at first, since I didn't have a lot of names to work with, however I now see a pattern developing, with the various surnames locating in the same locations, all within the same timeframe.
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rms2
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« Reply #9 on: April 12, 2012, 07:15:01 AM »

I can drink a quart of milk  and have no problems...My maternal grandmother Kennedy had red hair and a lot of my cousins have red or blond hair. I have a brother with blond hair....I uploaded my Gedmatch, all I can find are my ancestral matches. Where did you locate your 11% Eastern European in Gedmatch...Family Finder is a little difficult at first, since I didn't have a lot of names to work with, however I now see a pattern developing, with the various surnames locating in the same locations, all within the same timeframe.

I'll have to look when I get home, but there is a Gedmatch version of the Dodecad thing. It's there on the web site, but I forget what it's called.

I understand there are or may be other adaptions that allow one to keep producing lactase other than the most common ones. Perhaps you have one of those that has enabled you to drink milk without discomfort.
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BSLeonard
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« Reply #10 on: April 20, 2012, 05:03:47 PM »

What does CC mean for rs1805008?

I have the lactose intolerant indicator and I am lactose intolerant.

Very new to this so trying to figure things out!
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BSLeonard
rms2
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« Reply #11 on: April 20, 2012, 05:47:32 PM »

What does CC mean for rs1805008?

I have the lactose intolerant indicator and I am lactose intolerant.

Very new to this so trying to figure things out!

That is one of the alleles for red hair. A "CC" there means you don't carry the mutation for red hair, at least not at that position.
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seferhabahir
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« Reply #12 on: May 25, 2012, 04:03:30 PM »

rs4988235=cc
rs1805008=cc
rs1426654=aa
rs182549=cc
I have no problems with milk,have green eyes and light skin. My hair had a reddish tinge to it when I was younger.
Is there a site  where one might find other such indications for autosomal results

OK, here are my results:

rs4988235=gg
rs1805008=cc
rs1426654=aa
rs182549=cc

I am lactose intolerant. When I was in college I had thought I was "bologna sandwich" intolerant, until I figured out that I was always drinking a large glass of 4% milk with my bologna sandwich. I don't have red hair, but I have light skin and tan with difficulty.
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Y-DNA: R-L21 (Z251+ L583+)

mtDNA: J1c7a

rms2
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« Reply #13 on: July 20, 2012, 08:26:38 AM »

I also found out I have a "TC" at rs1805008, which is one of several SNPs in the MC1R gene associated with red hair color. A "T" contributes red hair, but it is recessive, so, although I carry the trait for red hair, I don't have it myself. I did pass it on to my youngest daughter, however, since she does have red hair, but she had to get the other "T" from her mother.

I have an "AA" at rs1426654, which, according to my Promethease report means the following:


Quote
probably light-skinned, European ancestry[.] This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.

(I'll keep talking about my Family Finder results here until I run out of things to say or someone else chimes in to discuss his or her results.)

Rs1805008 is apparently the same thing as R160W or Arg160Trp, which is one of the "RHC" (Red Hair Color) variants on the MC1R gene.

One of the two others is rs1805007, also known as R151C or Arg151Cys, but I could not find that one in my FF data, so apparently it wasn't part of the FF test.

The third (and, I believe, final) RHC variant is rs1805009 aka D294H or Asp294His. Apparently it is also not part of the Family Finder test, because I could not find a result for it in my FF data either.

« Last Edit: July 20, 2012, 08:40:32 AM by rms2 » Logged

rms2
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« Reply #14 on: July 20, 2012, 02:30:30 PM »

I also found out I have a "TC" at rs1805008, which is one of several SNPs in the MC1R gene associated with red hair color. A "T" contributes red hair, but it is recessive, so, although I carry the trait for red hair, I don't have it myself. I did pass it on to my youngest daughter, however, since she does have red hair, but she had to get the other "T" from her mother.

I have an "AA" at rs1426654, which, according to my Promethease report means the following:


Quote
probably light-skinned, European ancestry[.] This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.

(I'll keep talking about my Family Finder results here until I run out of things to say or someone else chimes in to discuss his or her results.)

Rs1805008 is apparently the same thing as R160W or Arg160Trp, which is one of the "RHC" (Red Hair Color) variants on the MC1R gene.

One of the two others is rs1805007, also known as R151C or Arg151Cys, but I could not find that one in my FF data, so apparently it wasn't part of the FF test.

The third (and, I believe, final) RHC variant is rs1805009 aka D294H or Asp294His. Apparently it is also not part of the Family Finder test, because I could not find a result for it in my FF data either.




The Wikipedia article on red hair says there is yet a fourth RHC variant: Arg142His.

I couldn't find anything on it in SNPedia.
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