Genome
2022-10-12: https://genealogical-musings.blogspot.com/2017/04/finally-gedmatch-admixture-guide.html https://dna.jameslick.com/mthap/
- SelfDecode = $200 one-time cost, $10/month billed anually, $79/month for ancestry report
Genome
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Gonna analyze random stuff about my genome here.
- When sequencing is done, individual strands are mearused.
- Unfortunately, there doesn’t really seem to be a way to know whether an SNP means an increase or decrease in function of the gene.
- GEDMatch:
- UJ8680733 = Ancestry.
- CN7324912 = 23andme “combinedkit”. The 23andme V5 thing is too small
- They differ by less than like .5% so seems legit.
- Mosquito Bite Frequency: GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci
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- rs309403_T (T/C): IL21-AS1 (IL-21 antisense RNA 1)
- rs1858074_G (G/G): IL-3
- rs9268659_T (T/C): ?
- Genome-wide association analysis of self-reported daytime sleepiness identifies 42 loci that suggest biological subtypes 0th percentile low daytime sleepiness
- rs2069837 (A/A): IL-6.
- FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease 97th percentile autoimmune thyroid disease - but idk any of these genes.
- Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income 95th percentile higher income
- 87th percentile Addison’s disease - these are immune/T-Cell genes mostly.
- 83rd percentile risk tolerance
- rs121912617_G (
G/GCC) of BHLHE41 shorter need for sleep (~6-6.5 instead of 8-9. Presumaply one less cycle maybe?)- https://www.snpedia.com/index.php/Ambiguous_flip
- SNPedia is annoying man. It’s an ambiguous flip: most companies use the forward strand, and this one uses reverse. How many other fucking SNPs are out there.
- For example: rs96067 (G/G) has two alleles C and T. Because its “Orientation” is “minus”, the alleles on the GRCh38 strand is G and A, consistent with the dbSNP information.
- I don’t think this is related to when there are 2 different base pairs being used, no?
- Eye color:
- rs1800407 (T>CC) actually associated with brown eyes!
- OCA2 (associated with melanin producing cells) is the main important one regarding inheritance of blue/brown.
- rs12913832 (GG): Blue Eye color. Lowers promotion of OCA2.
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A Three–Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation
- rs7495174 (T>AG). The other 2 I don’t have in my data
- HERC2 (ultimately determines OCA2 function—even if OCA2 contains alleles for brown eyes). A specific mutation is strongly linked to blue eyes.
- Tyrosinase: associated with difference between blue and green.
- SLC24A4: associated with difference between blue and green.
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Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci
- LYST, 17q25.3, TTC3/DSCR9.
- SLC2A4, TRYP1, SLC45A2, IRF4 contribute to eye color ariation.
- GPR143 mutations cause ocular albinism.
Metabolism #
- Genomic analysis of diet composition finds novel loci and associations with health and lifestyle 1st percentile fat consumption
- Genomic analysis of diet composition finds novel loci and associations with health and lifestyle 85th percentile sugar consumption. Veeeerry strange how this is negatively correlated to obesity, BMI, fasting glucose, and diabetes.
- CYP1A2: High activity. Part of caffeine metabolism.
- rs762551: (A/A)
- rs2472297 (C/T)
- CYP2D6
- There exists *1-6, 9, 10, 17. 5 is total deletion!
- rs3892097 (CYP2D6*4) (G>A/A), a nonsense mutation.
- According to some sources, the whole CYP2D6*4 genotype consists of multiple mutations.
- CYP2D6*4 Allele Polymorphism Increases the Risk of Parkinson’s Disease: Evidence from Meta-Analysi
- rs1135840 (G>C/C)
- CYP2C9 rs7089580 (A>TT) associated with higher warfarin dose requirement. More expression pretty sure R
- Aromatase: rs4646 (A>CC) = lower activity, I think?
- COMT: rs4680 (A>A/G) lower activity with A/Met (due to thermoinstability) (thus higher dopaminergic signaling. This leads to a U-shape dopamine level in models of schizophrenia.)
- aka Val108/158 Met. A = Met; G = Val.
- Apparently those with highest COMT respond best to Modafinil.
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COMT Val158Met polymorphism, cognitive stability and cognitive flexibility: an experimental examination
- A/A had faster reaction time.
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The Functional Val158Met Polymorphism of COMT Predicts Interindividual Differences in Brain α Oscillations in Young Men #
- PPAR-δ: rs2267668
- Fatty Acid Desaturase (FADS)
- FADS1 rs174537 (GG) = FADS-D instead of FADS-A. Higher activity. Highest prevalence in african, and 2:1 in asian and oceanic population.
- FADS1 rs174570 (CC)
- TT is associated with decreased cholesterol and higher triglycerides.
- I’m not sure which, but one of them is associated with decreased concentrations of LC-PUFAs in favor of SC-PUFAs - compensating for a diet high in fatty fish in areas like Greenland.
- FADS1 rs174550 (TT): higher activity.
- FADS2 rs174575 (CC) higher LCPUFA levels in serum/plasma like DHA (see graph below) (R
Common genetic variants of the FADS1 FADS2 gene cluster and their reconstructed haplotypes are associated with the fatty acid composition in phospholipids)
- FADS2 polymorphisms modify the effect of breastfeeding on child IQ (2010): an interaction with this polymorphism was observed such that breastfed GG children performed better than their formula fed counterparts by an additional 5.8 points.
- SCD1: rs1535 (AA): Higher activity; associated with higher mead acid (i.e. more oleic acid Δ6 desaturation).
- Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism (Caspi 2007) +4 IQ points? from higher DHA/LCPUFA from breastfeeding. I.e., smallest decrease in average IQ if formula-fed.
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Polyunsaturated fatty acid levels in blood during pregnancy, at birth and at 7 years: Their associations with two common FADS2 polymorphisms
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- Deiodinase:
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Common genetic variations of deiodinase genes and prognosis of brain tumor patients
- DIO1: rs2235544 (CC): greater T4->T3 Conversion (YESSS)
- DIO1: rs11206244 (CC): normal; no risk of reduced thyroid hormone metabolism
- DIO2: rs12885300 (CC): Higher risk of osteoarthiritis and bipolar.
- TT associated with greater mortality risk and has weaker negative feedback of fT4 on TSH.
- DIO2: rs225014 (TT) - normal. CC = higher risk of osteoarthiritis
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Common genetic variations of deiodinase genes and prognosis of brain tumor patients
- PEMT: rs7946 (TT) associated with fatty liver; common in caucasians.
Longevity #
- 83rd percentile ulcerative colitis
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A meta-analysis of genome-wide association studies of epigenetic age acceleration 5th percentile accelerated aging
- rs76244256_T: Thiopurine S-methyltransferase (NA)
- rs388649_A-: (T/A) Glyceraldehyde 3-Phosphate dehydrogenase psuedogene 39
- rs4712953_A+ (A/A): Secretagogin
- Related to CRH release
- 98th percentile later puberty timing
Alzheimer’s #
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Genome-wide association study of habitual physical activity in over 377,000 UK Biobank participants identifies multiple variants including CADM2 and APOE 97th percentile increased physical activity
- rs429358_T (T/C): ApoE
- APOE4 status is indicated by this and rs7412 (I have C/C). This comes out to the 3/4 phenotype.
- ClinicalTrials.gov - Gene Therapy for APOE4 Homozygote of Alzheimer’s Disease AAV vector. But of course, they went the cautious (pussy) route merely to make them heterozygous with ε2/ε4.
- APOE4 status is indicated by this and rs7412 (I have C/C). This comes out to the 3/4 phenotype.
- rs2764261: FOXO3
- rs12212067 G;G: FOXO3A. Downregulation of proinflammatory cytokines.
- rs13243553: EXOC4 (also in Sniekers)
- rs429358_T (T/C): ApoE
- 100th percentile Apolipoprotein B level
- Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture 89th percentile lewy body dementia. Realistically I only have 1 variant though just with a higher effect size: rs769449_A (G/A): ApoE associated with LDL, HDL, and triglyceride levels.
- ApoE: 3/4: I am rs429358 T/C and rs7412 C/C:
- Note how 2/4 is possible but not 3/2 or 4/2…
- rs3818361(T;T): CR1 (complement receptor 1)
- ApoA5 rs662799 (G>AA) normal. GG is associated with 2x higher early heart attack and less weight gain on HFD
Brain #
- 98th percentile predisposition to brain aneurysms
- Autism:
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Identification of common genetic risk variants for autism spectrum disorder 81st percentile
- rs1620977_A (A/G)+: NEGR1
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Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism
- rs1000177_T (T/C): ZNF877P/KIZ
- rs112436750_A (AT/A):
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Identification of common genetic risk variants for autism spectrum disorder 81st percentile
- Big brain:
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The genetic architecture of the human cerebral cortex 4th percentile high cerebral cortex surface area (it’s over)
- A lot of disorders like PTSD were taken into account which I seem to be susceptible to.
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The genetic architecture of the human cerebral cortex 4th percentile high cerebral cortex surface area (it’s over)
- 5-HT1A: rs6295_G (G/C) - heterozygous. Associated with higher neuroticism, relationship status, and spirituality.
- MAO-A: I have dozens of SNPs. ‘Warrior gene’ is not an SNP but all of them.
- rs6323_G (T/T) higher activity.
- α-Synuclein: rs3756059_A A/A - associated with REM sleep behavior disorder, which is when you enact dreams and is an early symptom of alpha synucleinopathies.
- CNP/CNPase (2’,3’-Cyclic-nucleotide 3’-phosphodiesterase) rs2070106_A A/A: associated with catatonia and Schizophrenia. Expressed exclusively by CNS Oligodendrocytes. Undergoes significant age-related changes.
- DARPP-32 rs907094 (AA) (so probably TT)
- D2: rs1800497 (GG) (so probably CC (normal)) aka Taq1A. TT is associated with ADHD and poor avoidance of errors.
- D4: rs1800443 TT (common). Overall I don’t seem to have anything interesting
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- Novelty-seeking DRD4 polymorphisms are associated with human migration distance out-of-Africa after controlling for neutral population gene structure
- 7R VNTR: gotta find what sequence it is, and then open IGV and go to DRD4 and ‘Find motif’ for whatever it is. It repeats anywhere between 2 and 11 times. The 7R allele has lower affinity for dopamine, thus less inhibition on postsynaptic neurons, leading to increased sensitivity to both aversive and rewarding cues. Associated with sugar intake (aka, according to researchers, non-healthy food). Associated with creativity.
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- 5-HT2A: rs6314 (GG) (CC = higher risk for rheumatoid arthritis. TT=average). I think it’s TT that has reduced ligand binding.
- BDNF: rs6265 (TC) aka Val66Met
- Adenosine Deaminase: rs73598374 (AA) reduced function.
- Functional ADA polymorphism increases sleep depth and reduces vigilant attention in humans
- Deep sleep and EEG 0.75- to 1.5-Hz oscillations in non-REM sleep were significantly higher in G/A than in G/G genotype. Moreover, attention and vigor were reduced, whereas waking EEG alpha activity (8.5-12 Hz), sleepiness, fatigue, and α-amylase in saliva were enhanced.
- A2A: rs2236624 (CC)
Diabetes #
- rs1889018(T;T): SREBPF1. 1.12x increased risk for T2D.
- CCR5: rs1799987 (A>GG) associated with diabetic kidney disease in T2D. Susceptibility to and severity of HIV. individuals with one or two copies of the A allele have 58% lower risk of developing AIDS during the first 4 years after testing positive for HIV, 19% lower risk during the subsequent 4 years, and no significant protection thereafter.
- Other things for HIV:
- Delta 32 rs333 (GG). But it’s something different than an SNP
- rs9264942 (T>CC) 90% reduction in HIV viral load
- rs4418214 (TC)
- rs2395029 (TT) the GG is rarer and increases viral load from various things including HIV
- rs3131018 (AC)