SNPs linked to intelligence :lightbul:

[Vessna]

The following SNPs have been connected to intelligence. You can check your genotype in the raw data file by searching the individual SNPs.


rs174575 C-haplotype linked to increased intelligence in breastfed children. Breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ.

rs363039 CC/CT genotypes associated with increased intelligence
(C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype.

rs363043 TT/CT possibly associated with increased intelligence. Studies failed to replicate. The (T;T) genotype averages several PIQ points higher than the (C;T) genotype, which averages several PIQ points higher than the (C;C) genotype.

rs353016 (merged into rs352054 ) TT/CT genotypes possibly associated with increased intelligence. The (T;T) genotype averages almost 3 PIQ points higher than the (C;T) genotype, which averages almost 3 PIQ points higher than the (C;C) genotype.

For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults.

rs363050 AA/AG possibly associated with increased intelligence. Studies failed to replicate. The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ.

rs28379706 C-allele associated with increased intelligence. Using a sample of extremely intelligent adolescents in comparison to a group of more typically intelligent people, it was found that the C allele of this SNP increased IQ and explained 0.16% of the variance in IQ.

rs10784502 CC/CT phenotypes associated with increased intracranial volume and higher IQ. (C;C) has higher cranial capacity (about 2 teaspoons) and over 2% higher IQ. (C;T) is half this positive effect. (T;T) lower intracranial volume.

rs4962322, rs4962520 and rs10794073 linked to extreme intelligence, you can read the study here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987166/. Associated genotypes are rs4962322 (A;C) rs4962520 (C;T) and rs10794073 (C;A).

Feel free to share your results :)

[Sovanz]

How can I know which one I belong Is there a site to upload my data?

[Mortimer]

I use 23andMe raw data

rs174575 C / G

rs363039 A / G

rs363043 C / C

rs353016 no markers found

rs363050 A / G

rs28379706 not genotyped

rs10784502 C / T

rs4962322 A / C, rs4962520 no genes or markers found associated with this snp, rs10794073 A / C

[Sovanz]

I use 23andMe raw data

rs174575 C / G

rs363039 A / G

rs363043 C / C

rs353016 no markers found

rs363050 A / G

rs28379706 not genotyped

rs10784502 C / T

rs4962322 A / C, rs4962520 no genes or markers found associated with this snp, rs10794073 A / C


So the means ur dumb?

[Vessna]

How can I know which one I belong Is there a site to upload my data?

If you have your raw DNA data file in .txt format you can search individual SNPs within the file.
23andMe has an option of searching SNPs directly on their website.

[Mortimer]

So the means ur dumb?

I think it means im intelligent, more intelligent then average going by the snps and the studies about it

[Insuperable]

rs174575 C/G
rs363039 G/G
rs363043 C/T
rs353016 no genotyped
rs363050 A/A
rs28379706 not genotyped
rs10784502 C/C
rs4962322 C/C
rs4962520 not genotyped
rs10794073 C/C

[Sovanz]

If you have your raw DNA data file in .txt format you can search individual SNPs within the file.
23andMe has an option of searching SNPs directly on their website.

I got tested with Ancestry and FTDNA how can I know this genotypes?

[Tie red]

The following SNPs have been connected to intelligence. You can check your genotype in the raw data file by searching the individual SNPs.


rs174575 C-haplotype linked to increased intelligence in breastfed children. Breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ.

rs363039 CC/CT genotypes associated with increased intelligence
(C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype.

rs363043 TT/CT possibly associated with increased intelligence. Studies failed to replicate. The (T;T) genotype averages several PIQ points higher than the (C;T) genotype, which averages several PIQ points higher than the (C;C) genotype.

rs353016 (merged into rs352054 ) TT/CT genotypes possibly associated with increased intelligence. The (T;T) genotype averages almost 3 PIQ points higher than the (C;T) genotype, which averages almost 3 PIQ points higher than the (C;C) genotype.

For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults.

rs363050 AA/AG possibly associated with increased intelligence. Studies failed to replicate. The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ.

rs28379706 C-allele associated with increased intelligence. Using a sample of extremely intelligent adolescents in comparison to a group of more typically intelligent people, it was found that the C allele of this SNP increased IQ and explained 0.16% of the variance in IQ.

rs10784502 CC/CT phenotypes associated with increased intracranial volume and higher IQ. (C;C) has higher cranial capacity (about 2 teaspoons) and over 2% higher IQ. (C;T) is half this positive effect. (T;T) lower intracranial volume.

rs4962322, rs4962520 and rs10794073 linked to extreme intelligence, you can read the study here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987166/. Associated genotypes are rs4962322 (A;C) rs4962520 (C;T) and rs10794073 (C;A).

Feel free to share your results :)

Most of these snp are from studies from 10-15 years ago with few numbers of case/controls in these studies to be statistically reliable and replicable.
These snp are likely absent from the supplementary materials from the latest and replicable study about IQ/education

https://www.nature.com/articles/s41588-022-01016-z

Thousand of variants, each of very very small effect. Well under 1 point IQ difference per variant.

[Vessna]

Most of these snp are from studies from 10-15 years ago with few numbers of case/controls in these studies to be statistically reliable and replicable.
These snp are likely absent from the supplementary materials from the latest and replicable study about IQ/education

https://www.nature.com/articles/s41588-022-01016-z

Thousand of variants, each of very very small effect. Well under 1 point IQ difference per variant.

This meta-analysis does not address IQ/cognitive abilities (cognitive ability is the mental ability to adapt oneself to the acquired knowledge. Rather than actual knowledge itself, it is concerned with the mechanisms of knowing, remembering, learning, abstract thinking, problem-solving, and reasoning) per se, but rather educational attainments (EA). They analyzed consumer reported years of education (from 23andMe and UKB), not their cognitive test results, that can vary among individuals with the same level of education. There are plenty of examples of high intelligence/high achievement individuals with incomplete degrees or without formal post-secondary education. Authors do acknowledge this difference in the article. "our results concern EA rather than cognitive test scores,." While this analysis is likely important in improving DNA mapping and identifying SNPs involved in human intelligence, the study design does not allow effectively identify potential variants accountable for differences in cognitive abilities based on individual IQs. I think a better study design to address this would be analyzing genome data from high achieving individuals and individuals with known high IQ (eg MENSA members) and comparing it to the general population.

[gixajo]

So the means ur dumb?

Nope.

[MBVC]

rs174575 - C/G
rs363039 - G/G
rs363043 - C/T
rs352054 (rs353016 not found) - A/A
rs363050 - A/A
rs28379706 - C/T
rs10784502 - T/T

rs4962322, rs4962520 and rs10794073 - not found/not genotyped

[Tie red]

This meta-analysis does not address IQ/cognitive abilities per se, but rather educational attainments (EA). They analyzed consumer reported years of education (from 23andMe and UKB), not their cognitive test results, that can vary among individuals with the same level of education. There are plenty of examples of high intelligence/high achievement individuals with incomplete degrees or without formal post-secondary education. Authors do acknowledge this difference in the article. "our results concern EA rather than cognitive test scores,." While this analysis is likely important in improving DNA mapping and identifying SNPs involved in human intelligence, the study design does not allow effectively identify potential variants accountable for differences in cognitive abilities based on individual IQs. I think a better study design to address this would be analyzing genome data from high achieving individuals and individuals with known high IQ (eg MENSA members) and comparing it to the general population.

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411041/

This study also include people with high IQ the HiQ / HRScohort.

"We tested for replication using the proxy phenotype of educational attainment, which is correlated phenotypically (r=~0.40)18 and genetically (r=~0.70)19 with intelligence. We confirmed this high genetic correlation (rg=0.73) and observed sign concordance with educational attainment for 93% of GWS SNPs "

A high numbers of the snp in this study are the same from the EDU genes study https://www.nature.com/articles/s41588-022-01016-z

[Vessna]

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411041/

This study also include people with high IQ the HiQ / HRScohort.

"We tested for replication using the proxy phenotype of educational attainment, which is correlated phenotypically (r=~0.40)18 and genetically (r=~0.70)19 with intelligence. We confirmed this high genetic correlation (rg=0.73) and observed sign concordance with educational attainment for 93% of GWS SNPs "

A high numbers of the snp in this study are the same from the EDU genes study https://www.nature.com/articles/s41588-022-01016-z

Great article, thank you.
One of the limitations is that all subjects are of European ancestry. They did not analyze non-Europeans. "We performed a genome-wide association (GWAS) meta-analysis of 14 independent epidemiological cohorts of European ancestry and 9,295,118 genetic variants passing quality control"

Basically they expanded on gene mapping (190 novel loci/ 939 novel associated genes) and replicated some prior ones replicating previous associations with 15 loci and 77 genes. I did not go through all the supplemental tables.

Highest observed probability of a deleterious protein effect (CADD23 score=34) was found for rs13107325. This missense mutation (MAF=0.065, P=2.23×10−21) in SLC39A8 was the lead SNP in locus 71 and the ancestral allele C was associated with higher scores on intelligence measures. --> Any studies to replicate/confirm this?


A high numbers of the snp in this study are the same from the EDU genes study [url]https://www.nature.com/articles/s41588-022-01016-z
They used the same database for analysis. Although, the EDU genes study expanded their data with 23andMe.

[Luke35]

rs174575 - C / C (increased intelligence)
rs363039 - A / G (nope)
rs363043 - C / C (dumb / dumb)
rs353016 - No matching markers
rs363050 - A / G (possibly increased intelligence)
rs28379706 - C / T (increased intelligence)
rs10784502 - C / T (big brain)

[Live The Magic]

rs174575 CC
rs363039 AG
rs363043 CT
rs353016 N/A
rs363050 AG
rs28379706 TT
rs10784502 CT
rs4962322 CC
rs4962520 CC
rs10794073 CC

[Vessna]

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence


I do agree that all these should be taken with a grain of salt until more research is available.

[Brás Garcia de Mascarenhas]

Me:

rs174575 - C/C
rs363039 - G/G
rs363043 - C/C
rs353016 - Not genotyped
rs363050 - A/A
rs28379706 - Not genotyped
rs10784502 - C/C
rs4962322 - C/C
rs4962520 - Not genotyped
rs10794073 - C/C

Wife:

rs174575 - C/C
rs363039 - G/G
rs363043 - C/T
rs353016 - Not genotyped
rs363050 - A/A
rs28379706 - T/T
rs10784502 - T/T
rs4962322 - Not genotyped
rs4962520 - Not genotyped
rs10794073 - Not genotyped

Father:

rs174575 - C/G
rs363039 - A/G
rs363043 - C/C
rs353016 - Not genotyped
rs363050 - A/G
rs28379706 - T/T
rs10784502 - C/T
rs4962322 - Not genotyped
rs4962520 - Not genotyped
rs10794073 - Not genotyped

[Vessna]

rs174575 C/G
rs363039 C/T
rs363043 C/C
rs352054 T/T
rs363039 - rs363043 - rs353016 haplotype C-C-T
rs363050 A/G
rs28379706 C/T
rs10784502 C/T
rs4962322, rs4962520, not genotyped
rs10794073 C/C

[Petalpusher]

rs174575 C/G
rs363039 C/T
rs363043 C/C
rs353016 no genotyped
rs363050 A/G
rs28379706 not genotyped
rs10784502 C/T
rs4962322 A/C
rs4962520 not genotyped
rs10794073 A/C

Bonus
rs17070145 C/T
rs1006737 A/A


The T allele of rs17070145 has been associated with better memory performance and possibly higher cognitive abilities. Individuals with the TT genotype might exhibit enhanced memory function, which can contribute to overall intelligence.

The A allele of rs1006737 has been associated with better cognitive performance. Individuals with the AA genotype have shown better performance in tasks involving executive function and processing speed, which are components of intelligence.

[Anatolya]

rs174575 - no data
rs363039 AA
rs363043 - no data
rs353016 (merged into rs352054) - no data
rs363050 - no data
rs28379706 TT
rs10784502 CT
rs4962322- no data
rs4962520 - no data
rs10794073 - no data

Is it normal that I have several no results? Would that deficit make my DNA results incorrect due to lack of data?

[Petalpusher]

rs174575 - no data
rs363039 AA
rs363043 - no data
rs353016 (merged into rs352054) - no data
rs363050 - no data
rs28379706 TT
rs10784502 CT
rs4962322- no data
rs4962520 - no data
rs10794073 - no data

Is it normal that I have several no results? Would that deficit make my DNA results incorrect due to lack of data?

Where did you test? Commercial ones don't extract much and have a lot of bad call but it's more than enough for ancestry purposes.

[Nurzat]

in blue the ones matching:

rs174575 - CC (but I was not breastfed at all, zero)
rs363043 - TT
rs363050 - AA
rs10784502 - CT
rs4962322 - CC
rs10794073 - CC

not genotyped:
rs363039
rs353016 / rs352054
rs28379706
rs4962520


ps. tested the maximum on the online Mensa testing (126 points out of 126 - they limit it to this as their entry test requires 132) but then failed the in-person Mensa test so I didn't enter it. anyway, knowing some people who succeeded and they're not extraordinary people, nothing special - when IQ doesn't meet culture, general knowledge, common sense and kindness, it's really nothing special, and it's not uncommon that such high IQ people just waste it, I know high IQ people (close friends) who are very dictatorial with their opinions and hard to interact with (both from the extreme left and the extreme right and centrists), and while they all read a lot and are naturally curious, none of them are really interested in let's say high culture, literature, art etc, and taste is something probably at least partly acquired, since one of them is especially attracted to kitsch, and not in a hipster way. so while high IQ is preferable, it's a pity when it's not put to work or it's used for stupid things. what all of these friends have in common is that they think of themselves being superior and overly smart and outsmarting everyone around them, though they do not - especially because a lack of experience, them being childish on many levels, two of them being lifelong singles, maybe that's why, and with limited work experience in a group at work, so they're not great with crowds and in public. and while I'm around two standard deviations from average IQ myself (even more compared to average IQ where I am from, in Romania), I share little with these friends in terms of attitude, maybe because of the different social path I've got (poor background taught me humbleness, working from early age taught me interact with all sorts of people, having gfs taught me share space and all with someone else at a deeper level, also overcome various situations that arise when two people share the same space or a relationship, then having kids puts you on another level vs your pre-kids period, it's instantly growing up almost, plus my love for reading and high culture/literature/art etc and my humanist/anarchist take on relationships, not feeling that I need to impose my views on others and not favouring the centres of power of any kind etc - and sorry it sounds like bragging or like virtue signaling, but I wanted to share this since it is a subject I know well, having around such high IQ specimens that cannot get over it and are so self-aware of their superior nature and all xD )

[Vessna]

in blue the ones matching:

rs174575 - CC (but I was not breastfed at all, zero)
rs363043 - TT
rs363050 - AA
rs10784502 - CT
rs4962322 - CC
rs10794073 - CC

not genotyped:
rs363039
rs353016 / rs352054
rs28379706
rs4962520


ps. tested the maximum on the online Mensa testing (126 points out of 126 - they limit it to this as their entry test requires 132) but then failed the in-person Mensa test so I didn't enter it. anyway, knowing some people who succeeded and they're not extraordinary people, nothing special - when IQ doesn't meet culture, general knowledge, common sense and kindness, it's really nothing special, and it's not uncommon that such high IQ people just waste it, I know high IQ people (close friends) who are very dictatorial with their opinions and hard to interact with (both from the extreme left and the extreme right and centrists), and while they all read a lot and are naturally curious, none of them are really interested in let's say high culture, literature, art etc, and taste is something probably at least partly acquired, since one of them is especially attracted to kitsch, and not in a hipster way. so while high IQ is preferable, it's a pity when it's not put to work or it's used for stupid things. what all of these friends have in common is that they think of themselves being superior and overly smart and outsmarting everyone around them, though they do not - especially because a lack of experience, them being childish on many levels, two of them being lifelong singles, maybe that's why, and with limited work experience in a group at work, so they're not great with crowds and in public. and while I'm around two standard deviations from average IQ myself (even more compared to average IQ where I am from, in Romania), I share little with these friends in terms of attitude, maybe because of the different social path I've got (poor background taught me humbleness, working from early age taught me interact with all sorts of people, having gfs taught me share space and all with someone else at a deeper level, also overcome various situations that arise when two people share the same space or a relationship, then having kids puts you on another level vs your pre-kids period, it's instantly growing up almost, plus my love for reading and high culture/literature/art etc and my humanist/anarchist take on relationships, not feeling that I need to impose my views on others and not favouring the centres of power of any kind etc - and sorry it sounds like bragging or like virtue signaling, but I wanted to share this since it is a subject I know well, having around such high IQ specimens that cannot get over it and are so self-aware of their superior nature and all xD )

I see your point. IQ is not really about being interested in high culture or being a decent human being (this has more to do with individual environment, upbringing, personality traits eg sociopathic and narcissistic tendencies etc.). It's an ability to solve problems, remembering, learning, abstract thinking, reasoning, and it's up to an individual how they would apply themselves. A lot of high IQ adults were gifted or "smart" as children and their self-worth is frequency tied to their academic achievements i.e the gifted child syndrome.

[Tie red]

Great article, thank you.
One of the limitations is that all subjects are of European ancestry. They did not analyze non-Europeans. "We performed a genome-wide association (GWAS) meta-analysis of 14 independent epidemiological cohorts of European ancestry and 9,295,118 genetic variants passing quality control"

Basically they expanded on gene mapping (190 novel loci/ 939 novel associated genes) and replicated some prior ones replicating previous associations with 15 loci and 77 genes. I did not go through all the supplemental tables.

Highest observed probability of a deleterious protein effect (CADD23 score=34) was found for rs13107325. This missense mutation (MAF=0.065, P=2.23×10−21) in SLC39A8 was the lead SNP in locus 71 and the ancestral allele C was associated with higher scores on intelligence measures. --> Any studies to replicate/confirm this?


They used the same database for analysis. Although, the EDU genes study expanded their data with 23andMe.

Of course. The rarer T allele has been associated with various traits from decreasing intelligence to crohn’s disease and brain volume measurement in many studies...

https://www.ebi.ac.uk/gwas/variants/rs13107325

[Tie red]

Genetic architecture of cognitive performance is far too complex.
This snp list is not really meaningfull

rs174575
rs363039
rs363043
rs353016
rs363050
rs28379706
rs10784502
rs4962322
rs4962520
rs10794073

It looks like there are many many more snp with interesting effects.

Thirty novel sequence variants impacting human intracranial volume
https://academic.oup.com/braincomms/article/4/6/fcac271/6772836?login=false
64 associating sequence variants explaining 5.0% of its variance


The genetic architecture of the human cerebral cortex
https://www.science.org/doi/10.1126/science.aay6690
"Of the 360 loci for which the SNP or a proxy was available, 307 (SA: 241, TH: 66) remained genome-wide significant when the replication data were included in the meta-analysis, with 237 passing multiple testing correction (P ≤ 8.3 × 10−10; SA: 187, TH: 50). "

"The 6q21 locus influencing total SA is intronic to FOXO3 (which also showed a significant gene-based association with total SA) (table S6). The major allele of the lead variant rs2802295 is associated with larger total SA (z-score PMA = 2.5 × 10−10; Prep = 2.5 × 10−13) and is in complete LD with rs2490272, a SNP previously associated with higher general cognitive function (33)."

"The strongest regional association was observed on chromosome 15q14 with the precentral SA (rs1080066, z-score PMA = 1.8 × 10−137; Prep = 4.6 × 10−189; variance explained = 1.03%) (Fig. 4A). Across 12 traits, we observed 48 independent significant associations from 21 LD blocks (r2 threshold ≤ 0.02) (Fig. 4B and table S5). As we observed strong association with the SA of both pre- and post-central gyri (Fig. 4C), we localized the association within the central sulcus in 5993 unrelated individuals from the UK Biobank. The most significant association between rs1080066 and sulcal depth was observed around the pli de passage fronto-pariétal moyen "

[Demirkazık]

Me
rs363039 (G;G)
rs28379706 (T;T)
rs10784502 (?;?)

Father
rs363039 (G;G)
rs28379706 (T;T)
rs10784502 (C;T)

Mother
rs363039 (G;G)
rs28379706 (C;T)
rs10784502 (T;T)

[Anatolya]

Where did you test? Commercial ones don't extract much and have a lot of bad call but it's more than enough for ancestry purposes.

MyHeritage. It's a complete disappointment tbh.