User:JohnLloydScharf

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Graduate [BS]of School of Community Services and Public Affairs with 242 credit hours and course work in research in sociology, psychology, and math at 400 level [Senior].... John Lloyd Scharf 23:02, 28 August 2011 (UTC)

Contents

[edit] Tested with New FTDNA-Family Finder Change in Platforms And Ordered 23andMe:

[edit] FTDNA

"On February 1st, 2011, Family Tree DNA changed testing platforms for our Family Finder autosomal DNA test. "We changed to the Illumina Omni platform. As part of that change, we retested for FREE all Family Tree DNA customers who previously ordered and paid for a Family Finder test. The new microarray chip for our Family Finder test is the Illumina OmniExpress. It tests about 710,000 unique autosomal DNA SNPs (single nucleotide polymorphisms). "The Omni platform provides better long-term upgrade options than the Affymetrix platform."

http://www.familytreedna.com/faq/answers.aspx?id=39


[edit] Useful Sites

http://genome.ucsc.edu/index.html

[edit] Faulty SNPedia Designations

Note that SNPedia claim of a SNP being tested, "FTDNA2" or "FTDNA" do not necessarily mean it was tested by FTDNA- EXAMPES

  1. rs11276 12 14884706 CC- http://www.snpedia.com/index.php/Rs11276 - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  2. Rs11391-http://www.snpedia.com/index.php/Rs11391 was tested on neither chip used by FTDNA.
  3. rs11701 14 20231893 TG- http://www.snpedia.com/index.php/Rs11701 - is the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  4. "rs1205","1","157948857","TT" - http://www.snpedia.com/index.php/Rs1205 is the newer Illumina test, but this was not tested with the Affy test chip.
  5. rs1835740 8 98236089 CC-http://www.snpedia.com/index.php/Rs1835740 - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  6. Rs11718863 Not tested by FTDNA.
  7. Rs1024161 Not tested by FTDNA.
  8. rs1061170 1 194925860 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  9. rs1473473 12 70690645 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  10. rs1487275 12 70696559 AA - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  11. rs1532701 16 54255528 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  12. rs36029 16 54254257 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  13. rs1566652 16 54289076 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  14. rs5743810 4 38506745 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  15. "rs2232596","20","36422795","AG" & rs2232596 20 36422795 AG Tested by FTDNA on old and new chips.
  16. Rs7900744-Not tested by FTDNA.
  17. rs4986764 17 57118129 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  18. rs1861046 4 15007004 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  19. rs11892031 2 234230022 AA-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  20. rs7586110 2 234255266 TT-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
  21. rs2232165 3 173648838 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.

[edit] Contradictory Results

  1. "rs11574","1","23758085","CC" from "FTDNA2" or Illumina versus rs11574 1 23758085 TC from "FTDNA" or Affy.

[edit] 23andMe Ordered On 09/29/2011

Ordered 09/29/11
Received 10/05/11
Collected 10/06/11
Mailed on 10/06/11
Received 10/20/11
Time will tell. Since I ordered and paid for it online on 09/29/11, it has already been three weeks. When FTDNA processed me, ordered 06/29/08 and received yDNA Results on 09/05/09 and mtDNA Results on 09/11/09 or under eight weeks. I ordered my Family Finder SNPs test on 08/02/10 and received the results on 10/11/10, or ten weeks.

They posted the results on 11/06/11

[edit] FTDNA and 23andMe

[edit] Editing Orientation


If the value is 'plus' you don't need to do anything, 23andMe agrees with dbSNP.
If the value is "minus" you need to change:


[edit] MY Personal SNP Results:


[edit] Disease Risks


[edit] Affective Disorders-General

Affective Disorders-General Page

[edit] Alcoholism


Alcoholism Page

[edit] Alzheimer's Disease


My Alzheimer's Page

[edit] Cancer Risks

Cancer Risks Page

[edit] Coronary Disease


Coronary Disease Page

[edit] Gallbladder Disease


The research indicated gallstone disease was negligible for the group researched. My gallbladder died and I do not know the cause.

[edit] Lactose Intolerance

"rs4988235","2","136325116","AA"=TT
rs4988235Orientation minus
rs4988235 2 136325116 AA=TT
"rs182549","2","136333224","TT"
http://en.wikipedia.org/wiki/Lactose_intolerance


[edit] Longevity

[edit] Medications


Medications Page

[edit] New SNPs
"rs37973","7","7974401","AA"
FTDNA Illumina; Not FTDNA Affy
Normal/Most Common
http://www.snpedia.com/index.php/Rs37973

[edit] Nicotine Dependence

http://www.snpedia.com/index.php/Rs3750344
[PMID 15759211] Associated with Nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. Interestingly, the risk allele varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 [TC-(--)-AA] had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype[AA-NN-CC-AA] was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated.[PMID 15759211]


rs16969968 increases susceptibility to Substance dependence, Nicotine 1.10 times for heterozygotes (AG) and 1.90 times for homozygotes (AA) [PMID 17135278]
http://www.snpedia.com/index.php/Rs16969968


[edit] Pain



Rs6269-Not FTDNA Tested. rs6269
Rs4818-Not FTDNA Tested. rs4818

I am an rs4633(C;T) (chr22 19,950,235 plus) higher risk for endometrial cancer



[edit] Rheumatoid Arthritis

"rs805297","6","31730585","--" The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA.

[edit] Schizophrenia

I have relatives with schizophrenia.

[edit] Tasting


I hated coke and coffee when I was young and chocolate had to have a great deal of sugar with it.


[edit] Triglycerides

[edit] Type II Diabetes


Type II Diabetes Page

[edit] Physical Features


Note: I have straight black hair[now white], brown eyes, and dark or olive brown skin and tan easily.

[edit] Physical Features In General

Physical Features In General


[edit] Hair Coloring

My Hair Color is Black
Hair Coloring Page

[edit] Skin Coloring

My Skin Color is Olive
Skin Coloring Page

[edit] Eye Color

My Eyes Are Brown
Eye Color Page

[edit] Baldness

NOTE: I have a full head of hair and was born in 1951.
Baldness Page

[edit] Neanderthal Similarities

Neanderthal Similarities

[edit] Haplogroups of mtDNA and yDNA

[edit] I am H3 Haplogroup mtDNA

[edit] HVR2 differences from CRS

[edit] CR differences from CRS

[edit] HVR1 differences from CRS

[edit] Migration Route

[edit] I am J1c3d Subclade yDNA

M267+=J1
P58+=J1c3
L147.1+=J1c3d
M367-=Not J1c3a
M368-=Not J1c3a
M369-=Not J1c3b
L174-=Not J1c3d1
L222.2-=Not J1c3d2
L65.2-=Not J1c3d2a

[edit] I am not

[edit] To Be Sorted





[edit] HMOX1




[edit] FGA Alleles 21-23

[PMID 20167083] Fibrinogen beta variants confer protection against coronary artery disease in a Greek case-control study


[edit] LPL Alleles 10-12

rs264 8 19857460 GG
rs270 8 19857956 CC
rs276 8 19858569 TT
rs283 8 19859378 CC
rs285 8 19859469 CC
rs291 8 19860132 TT
rs297 8 19860651 TT
rs316 8 19862716 CC
rs327 8 19863816 TT


[edit] HSD11B1

[PMID 18611262] Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II


[PMID 19130090] rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development.




http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs11755393
http://www.snpedia.com/index.php/Rs11755393


http://www.snpedia.com/index.php/Rs2232165


rs27048(T;T) normal
http://www.snpedia.com/index.php/Rs27048
rs27072(T;T) normal
http://www.snpedia.com/index.php/Rs27072


rs1042173(G;G) normal
rs1042173(G;T) normal
rs1042173(T;T) among alcoholics, likely to be heavier drinkers
rs1042173 is a SNP in the solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 SLC6A4 gene.A study of 275 patients seeking treatment for alcoholism concluded that Caucasians of with the rs1042173(T;T) genotype consumed an average of 11.17 drinks per drinking day, compared with an average of 8.58 for carriers of a rs1042173(G) allele (p = 0.0034). While this held true for both men and women, this association was not seen in Hispanics. [PMID 19032574] [PMID 21247998] Pharmacogenetic Approach at the Serotonin Transporter Gene as a Method of Reducing the Severity of Alcohol Drinking
In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. [PMID 17196743]
The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism.


[PMID 18043716] (T;T) under-represented in elite strength athletes, consistent with previous reports of impaired muscle performance.


rs1004819(C;T)1.5x risk for Crohn's disease in both Jewish and non-Jewish populations. [PMID 17068223]
http://www.snpedia.com/index.php/Rs1004819


rs1061170(C;C) 5.9x risk for AMD; higher mortality among nonagenarians
http://www.snpedia.com/index.php/Rs1061170


"rs7566605","2","118552495","CG" Weak, if any, association with obesity. http://www.snpedia.com/index.php/Rs7566605

http://www.snpedia.com/index.php/Rs4986791


rs1143634 increases susceptibility to Myasthenia gravis 1.29 times for heterozygotes (CT) and 4.63 times for homozygotes (TT) [PMID 9521608]
http://www.snpedia.com/index.php/Rs1143634


http://www.snpedia.com/index.php/Rs4986790


http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1801275
http://www.snpedia.com/index.php/Rs1801275


[PMID 20122735] Screening of DNA-variants in the properdin gene (CFP) in age-related macular degeneration (AMD)
http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1048118
http://www.snpedia.com/index.php/Rs1048118


I am an rs6609257(G;G) (chrX 43,612,708 plus) and lefthanded from lefthanded parents with a lefthanded son.
[PMID 19028548] mentioned as potentially affecting white matter volume, sample size tiny, GG higher among Africans than Europeans and Mexicans.
16 healthy participants (14 males) took part. All participants were right-handed, Caucasian, and psychiatrically, medically andneurologically healthy. Ages ranged from 18 to 36 years (mean = 23.69, S.D. = 4.33) and participants had spent an average (S.D.) of 16.81 (2.64) years in full-time education.
http://www.snpedia.com/index.php/Rs6609257


[PMID 19260141] gwas among adults residing on Korcula Island in Croatia, fibrinogen, the G allele associated with decreased fibrinogen levels.


Gene variants associated with deep vein thrombosis.[PMID 18349091]
Updated analysis of gene variants associated with deep vein thrombosis.[PMID 20124536]


rs2297480 is a SNP in the FDPS gene, which encodes an enzyme in the mevalonate pathway and therefore might alter the response to amino-bisphonate (drug) treatment of postmenopausal osteoporosis.
A study of 234 Danish postmenopausal women treated for at least 2 years with amino-bisphonates concluded that rs2297480(C;C) homozygotes do not respond as successfully as (A;A) or (A;C) genotypes.[PMID 18687167]
http://www.snpedia.com/index.php/Rs2297480


Kaplan-Meier analysis showed that the combination of the T variant allele (CT+TT) of HDAC1 SNP rs1741981 and the homozygous TT variant allele of HDAC3 SNP rs2547547 was the most favorable prognostic factor.
http://www.snpedia.com/index.php/Rs1741981
http://www.snpedia.com/index.php/Rs2547547


[PMID 20731616] Combination of polymorphisms within the HDAC1 and HDAC3 gene predict tumor recurrence in hepatocellular carcinoma patients that have undergone transplant therapy
http://www.snpedia.com/index.php/Rs11391(T;T)


Orientation-minus
Genotype Effect
rs320995(C;C)* ?
rs320995(C;T)* ?
rs320995(T;T)* ?
http://www.snpedia.com/index.php/Rs320995

[PMID 18829683] subjects without T-allele in SNP rs320995 had 3.1 times higher risk of asthma (Pobserved=0.00004)

rs3764880(A;A)Magnitude: 1.6
References:2
1.2 - 1.8x increased tuberculosis risk rs3764880 is a SNP in the TLR8 gene, located on the X chromosome. rs3764880 is also known as Met1Val. A study of both Indonesian and Russian tuberculosis patients (and controls) concluded that the minor (A) allele of rs3764880 was associated with increased risk for tuberculosis. In the Indonesian population of 375 patients, the odds ratio was 1.8 (CI: 1.22.7); in the Russian population of 1,837 patients, the odds ratio was 1.2 (CI: 1.021.48); the combined evidence for association was p = 1.210e?3 610e?4. Note that the association was found primarily in males (although also to a lesser extent in homozygous females), presumably due to the presence of only one X chromosome in males.

http://www.snpedia.com/index.php/Rs3764880

Those individuals carrying the variant TNFRSF1B rs3397 C allele showed a statistically significant reduction in the probability of developing Crohn disease with penetrating behavior, as compared with those carrying the T allele (OR = 0.62, 95% CI = 0.40–0.95, P = .03).

http://www.snpedia.com/index.php/Rs3397

rs6684865 has been reported in a large study to be associated with rheumatoid arthritis.
Rs6684865(A;A) 0 1.5x risk
Rs6684865(A;G) 1.2x risk
Rs6684865(G;G) normal
http://www.snpedia.com/index.php/Rs6684865


The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. [PMID 16501576] rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function. The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. [PMID 16501576] rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function.

http://www.snpedia.com/index.php/Rs10239794


"rs9897526","17","39782466","GG" G is most common allele. Common variants (rs9897526, rs34424835, and rs850713) and haplotypes were significantly associated with a reduction in age at onset and a shorter survival after onset of ALS in both the Belgian and the Dutch studies.



Genotype Effect
rs6718526(C;C) 1.9x risk
rs6718526(C;T) 1.5x risk
rs6718526(T;T) normal
http://www.snpedia.com/index.php/Rs6718526


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