PDA

View Full Version : Skin color in Levantines and Jews



jkotl0327
07-13-2020, 03:22 AM
I want to ask about the main two SNPs that affect skin color.

Does anyone know what the genotype frequencies are in modern Levantines and Jewish groups?

I looked at 2 IA Levantines (possibly Israelites) for each SNP: a=I4517_Megiddo_IA, b=I2201_Abel_Beth_Maacah_IA
a) rs1426654 (SLC24A5): AA ("European" genotype), rs16891982 (SLC45A2): CC ("non-European" genotype)
b) rs1426654 (SLC24A5): AA ("European" genotype), rs16891982 (SLC45A2): CG (heterozygous genotype)

I am Ashkenazi Jewish and I've tested five people (including myself) in my family, 4 of whom are relatively fair-skinned (on the order of a typical central or southern European) and 1 of whom is relatively dark-skinned (on the order of a typical Levantine).

All of us get the rs1426654 (SLC24A5): AA ("European" genotype), and the rs16891982 (SLC45A2): GG ("European" genotype).


rs26722 (SLCA45A2) is also mentioned by SNPedia as a SNP that relates to skin color for which Europeans and Africans tend to have the "lighter" (CC) genotype whereas Indians and E. Asians often exhibit the "darker" (TT) or heterozygous (CT) genotype.

My entire family gets the CC genotype, as does the I2201 man, and the I4517 boy has a no-call.

Are there genes that we are not aware of that account for differences in skin color such as between the dark-skinned member of my family and the light-skinned ones, or if not, what do you think causes the variations in skin color between people who have the same genotype for these 2 (or 3) main skin color genes?

1938helerich
02-20-2021, 03:24 AM
To answer your first question, I know some Lebanese people who tested for 23andme. They usually get either AA, CC, CC or AA, CG, CC. I got AA, CC, CC and 23andme predicted a ‘light beige’ skin color. People who get AA, CG, CC are predicted to be ‘moderately fair’. I think there are other snp’s besides the three that predict skin color.

pmokeefe
02-20-2021, 04:30 AM
https://gnomad.broadinstitute.org/variant/rs1426654?dataset=gnomad_r2_1
Ashkenazi Jewish 0.004341
European (non Finnish) 0.003619

https://gnomad.broadinstitute.org/variant/rs26722?dataset=gnomad_r2_1
Ashkenazi Jewish 0.03376
European (non Finnish) 0.01983

Ashkenazi's are not very different from other Europeans for those two variants. I'm not aware of a source comparable to gnomAD for modern Levantines, unfortunately.

jkotl0327
02-20-2021, 04:26 PM
To answer your first question, I know some Lebanese people who tested for 23andme. They usually get either AA, CC, CC or AA, CG, CC. I got AA, CC, CC and 23andme predicted a ‘light beige’ skin color. People who get AA, CG, CC are predicted to be ‘moderately fair’. I think there are other snp’s besides the three that predict skin color.

The one lebanese person I've seen was CG. Do you know any other SNPs that predict skin color?
43431
This is from 23andme, frequency of the G allele. Interesting that people with AA CC like yourself only get light beige, but my point was that Middle East gets ~80% frequency. Presumably this includes some parts of Arabia and N Africa which may be overrepresented in genetic testing and would likely have a pretty low frequency of G alleles. I assumed that Levantines would have a higher frequency of G alleles than that but not as high as the Ashkenazi average. Either way the ratio of CG : GG would be higher in Levantines, I suppose the question is how much higher, and if that really matters considering the number of Ashkenazi Jews, many of them my own relatives, who are at or close to your color and have the AA GG genotype. Would you mind to pm screenshots of the genotype results and ancestry compositions (no identity of course) of any Levantine matches you may have?

drobbah
02-20-2021, 04:59 PM
My father has the same genotype of the first IA Megiddo sample.The IA Megiddo sample must have been brown lol

Thrawn
04-03-2021, 04:31 PM
Ashkenazi Jews are most similar to Southern Europeans and Central Europeans and they represent them in pigmentation (Hair, Eye, Skin Tone) - there is a lot of overlap with Middle Easterners, especially Levantines because Ashkenazis have around Half of this DNA. Interestingly though they do resemble Samaritans which are a very Native Levantine population