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rms2
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« on: February 20, 2012, 09:36:50 PM »

I am R-L21 and apparently homozygous (homozygotic?) for lactase persistence. How about you?

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.
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rms2
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« Reply #1 on: February 21, 2012, 08:39:03 AM »

If you have done the Family Finder test, see if you can unzip your raw data and find rs4988235. If you wouldn't mind, post what you got and to what R1b subclade you belong here. I am curious.  You might also want to post where your most distant y-dna ancestor came from.

I know this is autosomal stuff and completely separate from y-dna, but it might be interesting to see if there is any sort of pattern.

If you've had the 23andMe test, you should also have a result for rs4988235.

I am tempted to ask Bennett Greenspan if I could start an FTDNA project on this, but, sadly, I am too busy with the projects I already have. In fact, I wouldn't mind letting one or two of them go - like the R-P312 and Subclades Project. Any takers?
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Maliclavelli
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« Reply #2 on: February 21, 2012, 12:19:27 PM »

136325116    rs4988235   A or G   
GG Francesca Guarino
GG Gioiello Tognoni
GG Giorgio Tognarelli
GG Monica De Conti
GG Silvana Vagelli
GG Velthur Tognoni
Reference Links:Entrez GeneGoogle Scholar (Gene)dbSNP LookupGoogle Scholar (SNP)    dbSNP Orientation: Minus


This is my position and of my relatives at 23andMe. We are lactose intolerant, even though we have always drunk infinite “cappuccinos” (“cappuccini” in Italian).

P.S. My daughter is on another account, but being me GG and my wife (Francesca Guarino) GG, it isn't difficult to know that she is GG too. 
If you want to know our Y and mt, these are:
I and my son: R1b1a2/L23/L150+ and also my relative Giorgio Tognarelli, nothing to do with me on the direct line and with a different haplotype
mt: my wife and my son and daughter: K1c1* (FGS)
me  and my mother Silvana Vagelli: K1a1b1 (9932A) (FGS)
my cousin (then my father) H* (the haplotype that Irene Pichler found amongst the Hutterites and searched for it in Central Europe, actually present in Tuscany
Giorgio Tognarelli: H6a1.
« Last Edit: February 21, 2012, 12:31:42 PM by Maliclavelli » Logged

Maliclavelli


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MtDNA: K1a1b1e

rms2
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« Reply #3 on: February 21, 2012, 07:58:15 PM »

Thanks, Gioiello.

I knew a guy I used to ride the train with who was lactose intolerant but who loved to drink lattés. He said he would just have one anyway and put up with the consequences, which for him were abdominal discomfort and gas.
« Last Edit: February 22, 2012, 08:17:27 AM by rms2 » Logged

Jdean
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« Reply #4 on: February 21, 2012, 08:50:38 PM »

I am R-L21 and apparently homozygous (homozygotic?) for lactase persistence. How about you?

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.

Just had a look at mine (had to open it in Notepad as the file was too big for my version of Excel)

I'm AA also, which was no great surprise considering your comments :)
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rms2
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« Reply #5 on: February 21, 2012, 09:03:53 PM »

I am R-L21 and apparently homozygous (homozygotic?) for lactase persistence. How about you?

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.

Just had a look at mine (had to open it in Notepad as the file was too big for my version of Excel)

I'm AA also, which was no great surprise considering your comments :)


Awesome!

That makes two British R-L21s (by descent, in my case) who are homozygous for lactase persistence.
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Maliclavelli
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« Reply #6 on: February 22, 2012, 12:19:38 AM »

Thanks, Gioiello.

I knew a guy I used to ride the train with who was lactose intolerant but who loved to drink latés. He said he would just have one anyway and put up with the consequences, which for him were abdominal discomfort and gas.
These are just the consequences, but for my son, who is a bariton, had also some advantage, giving a greater support. My wife, when was younger, gave also in front, but not due to milk.
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Maliclavelli


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rms2
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« Reply #7 on: February 22, 2012, 08:18:36 AM »

Thanks, Gioiello.

I knew a guy I used to ride the train with who was lactose intolerant but who loved to drink latés. He said he would just have one anyway and put up with the consequences, which for him were abdominal discomfort and gas.

That can happen to me if I drink too much beer. So am I beer intolerant? or perhaps I should call it Ale'ing ;)

Mexican food does it for me sometimes.
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seferhabahir
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« Reply #8 on: February 22, 2012, 01:10:25 PM »

Mexican food does it for me sometimes.

I think you probably mean "beans" here. Quoting from the web source:

http://www.thenutritiondr.com/beans-legumes-gas-bloatingmonosaccharide-absorption-glucose-fructose-galactose-hormone-response/

People (... pigs and chickens) don’t produce the enzymes (e.g. alpha-galactosidase) necessary to efficiently break down stachyose, raffinose, and verbacose. So, similar to lactose in lactose intolerant people, these carbohydrates remain intact in our small intestine and move into the colon. In the colon, gas producing bacteria breakdown (ferment) these carbohydrates producing gases methane (CH4), CO2 and H2 which lead to bloating, cramping, and flatulence. 
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Jdean
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« Reply #9 on: February 22, 2012, 08:43:15 PM »

I am R-L21 and apparently homozygous (homozygotic?) for lactase persistence. How about you?

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.

Just had a look at mine (had to open it in Notepad as the file was too big for my version of Excel)

I'm AA also, which was no great surprise considering your comments :)


Awesome!

That makes two British R-L21s (by descent, in my case) who are homozygous for lactase persistence.

I wasn't terribly surprised to see I had a lactose tolerant marker, I would imaging most people around here (Wales) would be similar :)

I wonder how many other predictive traits are hidden amongst FF data ?

I sent my results to Gedmatch.com and was presented with an extremely accurate picture of my eyes for my trouble, even down to a brown fleck which I always assumed was some sort of damage (a bit like a spot or mole).
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rms2
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« Reply #10 on: February 22, 2012, 09:23:33 PM »

I did the eye color predictor at Gedmatch, too, and got a pretty accurate picture, as well.

I understand this program allows you to extract all sorts of extra information from your Family Finder raw data, but I haven't had the time to try it yet; it's supposed to take four hours.
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« Reply #11 on: February 23, 2012, 08:49:22 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" indicates probable 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, 09:03:20 PM by rms2 » Logged

Jdean
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« Reply #12 on: February 23, 2012, 09:10:38 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" indicates probable lactose intolerance.

I have a "TT" at rs182549, so I got lactase persistence from both my parents on that one, as well.

And TT here as well :)
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rms2
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« Reply #13 on: February 23, 2012, 09:32:02 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" indicates probable lactose intolerance.

I have a "TT" at rs182549, so I got lactase persistence from both my parents on that one, as well.

And TT here as well :)


Cool!

We should celebrate with a liter of cold milk apiece! :-)
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Mark Jost
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« Reply #14 on: February 24, 2012, 01:23:21 AM »

I am  1/2 tolerent :)

"rs4988235","2","136325116","AG"

"rs182549","2","136333224","TC
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
rms2
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« Reply #15 on: February 24, 2012, 08:06:22 AM »

I am  1/2 tolerent :)

"rs4988235","2","136325116","AG"

"rs182549","2","136333224","TC

Interesting. Now we have all three possible results (at least at rs4988235) represented in this thread.

I think rs182549 may be the same thing as the 13910 from the lactase persistence research literature.
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Maliclavelli
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« Reply #16 on: February 24, 2012, 09:34:28 AM »

136333224   rs182549   C or T   
CC Francesca Guarino
CC Gioiello Tognoni
CC Giorgio Tognarelli
CC Monica De Conti
CC Silvana Vagelli
CC Velthur Tognoni

Of course my daughter will be CC she too.

Perhaps it is interesting to say that I am 100% Tuscan like  Giorgio Tognarelli, my wife 100% Sicilian and my cousin 50% Tuscan and 50% Venetian. Then the whole Italy seems above all lactose intolerant.
« Last Edit: February 24, 2012, 09:38:25 AM by Maliclavelli » Logged

Maliclavelli


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rms2
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« Reply #17 on: February 24, 2012, 04:08:08 PM »

Now we do have all three possible results on both SNPs.

It seems thus far that what one has on one SNP he has on the other, as well.
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« Reply #18 on: February 24, 2012, 07:50:34 PM »

I asked my question about the relationship between 13910 and rs4988235 on Rootsweb, and here is the answer I got from Ann Turner.

Quote
They are the same thing, just different ways of reporting the mutation. The 13910 is usually written with a dash in front of it, -13910. That means the
position of the mutation is 13,910 bases upstream of the LCT gene. It is
involved in gene expression, not in the genetic code for the lactase
enzyme.

Later this mutation was entered into dbSNP and assigned a catalog number,
rs4988235. The mutation was originally reported in the minus orientation,
with the alleles C and T. If you were looking at the other strand of the
double helix (the plus strand), the possible alleles would be the
complementary bases G and A. It is now more common to report all SNPs in
the plus orientation.

Ann Turner

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« Reply #19 on: February 24, 2012, 08:38:45 PM »

I also found out that FTDNA's Family Finder test includes rs1805008, which is one of several SNPs in the MC1R gene associated with red hair color.

If you have "TT" at rs1805008, you are likely to have red hair. I have a "TC" there, which means I carry the red hair trait but in recessive form.

I ran the Promethease thingy and paid $2 for the expedited and expanded version. Mostly it's pretty scary stuff (disease risks, etc.), but the red hair result was interesting.

It's a good thing I never took up smoking. I have an increased risk both for nicotine addiction and lung cancer! Yikes!
« Last Edit: February 24, 2012, 08:43:41 PM by rms2 » Logged

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« Reply #20 on: February 24, 2012, 09:01:25 PM »

I also found out that FTDNA's Family Finder test includes rs1805008, which is one of several SNPs in the MC1R gene associated with red hair color.

If you have "TT" at rs1805008, you are likely to have red hair. I have a "TC" there, which means I carry the red hair trait but in recessive form.

I ran the Promethease thingy and paid $2 for the expedited and expanded version. Mostly it's pretty scary stuff (disease risks, etc.), but the red hair result was interesting.

It's a good thing I never took up smoking. I have an increased risk both for nicotine addiction and lung cancer! Yikes!


FTDNA's Family Finder also includes rs1426654.

I have an "AA" there, and here is what my Promethease report said on that score:

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.
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OConnor
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« Reply #21 on: February 26, 2012, 10:16:56 AM »

I guess you have a little extra milk in your coffee. :)

I'm wondering if I should have done the 23andme thing?

I have updated my snp's below in my signature. Do I get the R-L21* ?
Or is there something else I should test for?
« Last Edit: February 26, 2012, 10:24:02 AM by OConnor » Logged

R1b1a2a1a1b4


R-DF13**(L21>DF13)
M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, M173+, M269+, M343+, P312+, L21+, DF13+, M207+, P25+, L11+, L138+, L141+, L15+, L150+, L16+, L23+, L51+, L52+, M168+, M173+, M207+, M213+, M269+, M294+, M299+, M306+, M343+, P69+, P9.1+, P97+, PK1+, SRY10831.1+, L21+, L226-, M37-, M222-, L96-, L193-, L144-, P66-, SRY2627-, M222-, DF49-, L371-, DF41-, L513-, L555-, L1335-, L1406-, Z251-, L526-, L130-, L144-, L159.2-, L192.1-, L193-, L195-, L96-, DF21-, Z255-, DF23-, DF1-, Z253-, M37-, M65-, M73-, M18-, M126-, M153-, M160-, P66-

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rms2
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« Reply #22 on: February 26, 2012, 11:09:34 AM »

I guess you have a little extra milk in your coffee. :)

I'm wondering if I should have done the 23andme thing?

I have updated my snp's below in my signature. Do I get the R-L21* ?
Or is there something else I should test for?

Go with Family Finder instead. 23andMe charges a monthly subscription fee, although the initial testing is cheaper. I am very happy with my Family Finder results and the tools FTDNA provides to use them.

Yeah, I guess you qualify for that asterisk - more than I do, because I haven't ordered all the SNPs yet - nor am I likely to. I can't afford all that. I have to pick and choose and go with what I think is most likely to produce a positive result.
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« Reply #23 on: February 26, 2012, 11:12:02 AM »

I just finished emailing all of my closest y-dna 67-marker matches, asking them to consider ordering the Family Finder test. It might give us some additional clues as to just how closely and recently related we are.

I should add that I did not send that email to my known Stevens relatives. Although it would be nice to get Family Finder results in their cases, it isn't necessary. We already know how we are related.
« Last Edit: February 26, 2012, 11:13:54 AM by rms2 » Logged

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« Reply #24 on: February 27, 2012, 08:44:50 AM »

I just finished emailing all of my closest y-dna 67-marker matches, asking them to consider ordering the Family Finder test. It might give us some additional clues as to just how closely and recently related we are.

I should add that I did not send that email to my known Stevens relatives. Although it would be nice to get Family Finder results in their cases, it isn't necessary. We already know how we are related.

I already heard back from a 64/67 match with a variant spelling of my surname. The lady in charge of her dad's sample said she will consider the Family Finder test.

I know an autosomal match is a long shot, but I have already confirmed a match with a 5th cousin (on the line coming from my dad's paternal grandmother). Our most recent common ancestors are a set of our 4th great grandparents, both of whom were born in the 1770s. That's reaching pretty far back and still sharing some fairly substantial segments of autosomal dna.

So, who knows? A Family Finder match with a close y-dna match is not impossible and might be informative.
« Last Edit: February 27, 2012, 08:45:51 AM by rms2 » Logged

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