rs3789604

Chromosome : 1 , Position: 113812320

Most conditions are affected by anywhere from hundreds to millions of genetic variants (SNPs). A single SNP usually has a minor contribution to a person’s overall genetic risk for a certain condition. That is why you shouldn't consider or act on a SNP in isolation. Instead, we use SNPs to determine polygenic risk scores (PRSs), which are the basis of most health reports.

Reference Allele: T

Alternative Alleles: A, C, G

Associated Genes

AP4B1

RSBN1

PTPN22

DCLRE1B

PHTF1

BCL2L15

HIPK1

OLFML3

CSDE1

NRAS

PPM1J

RHOC

BCAS2

CAPZA1

ST7L

MAGI3

SLC16A1

TRIM33

SYT6

SIKE1

TAFA3

Summary

rs3789604 is associated with increased susceptibility to rheumatoid arthritis, based on a study of ~1,000 Caucasian individuals. The odds ratio is 1.55x for (G;T) heterozygotes and 1.73x for (G;G) homozygotes.[PMID 16175503]

However, in a Japanese population, the other allele, rs3789604(T), is associated with increased risk (odds ratio 1.45, p=0.0085) for Graves’ disease (GD).[PMID 18578611]

[PMID 18923449] Further genetic evidence for three psoriasis-risk genes: ADAM33, CDKAL1, and PTPN22

[PMID 19438904] Clinical associations of the genetic variants of CTLA-4, Tg, TSHR, PTPN22, PTPN12 and FCRL3 in patients with Graves’ disease

[PMID 20510318] Association of PTPN22 Haplotypes with Type 1 Diabetes in the Japanese Population

[PMID 20615141] Association of the Protein Tyrosine Phosphatase Nonreceptor 22 Haplotypes with Autoimmune Thyroid Disease in the Japanese Population

[PMID 17135225] The 620W allele is the PTPN22 genetic variant conferring susceptibility to RA in a Dutch population.

[PMID 18341666] Polymorphisms in the PTPN22 region are associated with psoriasis of early onset.

[PMID 18466461] Meta-genetic association of rheumatoid arthritis and PTPN22 using PedGenie 2.1.

[PMID 18466531] Case-control association analysis of rheumatoid arthritis with candidate genes using related cases.

[PMID 18466575] Comparison of the power of haplotype-based versus single- and multilocus association methods for gene x environment (gene x sex) interactions and application to gene x smoking and gene x sex interactions in rheumatoid arthritis.

[PMID 19180477] Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations.

[PMID 19638187] Genetic susceptibility to psoriasis: an emerging picture.

[PMID 22396730] No association of PTPN22 polymorphisms with susceptibility to ocular Behcet’s disease in two Chinese Han populations.

[PMID 25073032] Association Between a Gain-of-Function Variant of PTPN22 and Rejection in Liver Transplantation

More Information

rs3789604 is linked to both the PTPN22 and RSBN1 genes. This SNP has an increased risk of developing Grave's disease and Rheumatoid arthritis (RA).

The TT-genotype and the T-allele frequencies were significantly higher in Graves' disease (GD) patients than in control subjects (T-allele frequency: p = 0.0085, odds ratio = 1.45) [R1, R2].

The minor allele ''G'' is associated with rheumatoid arthritis (RA) susceptibility [R].

Population Alleles Frequency

ethhicity frequency	A	C	G
African/African-American	–	–	0.0809
Latino/Admixed American	–	–	0.1663
Ashkenazi Jewish	–	–	0.1552
East Asian	–	–	0.2471
European	–	–	0.1818
Other (population not assigned)	–	–	0.1961

Frequently Asked Questions

Why Are Alleles for This SNP Different Elsewhere? Major vs. Reference Allele Is My Variant Good or Bad? SNP vs. Mutation

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