rs2280714

A SNP in the TNPO3 gene on chromosome 7. Its most notable genotype is T;T: 1.4x increased risk of SLE

Gene
TNPO3
Location
Chr 7128,954,671 (GRCh38)
Highest magnitude
1.5Minor
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
41%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TMost notableBad1.4x increased risk of SLEMinor · 1.536% of people
  2. C;TBad1.4x increased risk of SLEMinor · 1.548% of people
  3. C;CGoodNormal risk of SLEMinor · 1.016% of people

SNPedia records rs2280714 on the minus strand: (A;A), (A;G), (G;G). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Frequency

Share of each genotype in 11 HapMap populations.

  • AverageT;T 36% C;T 48% C;C 16%
  • European ancestry (Utah)T;T 35% C;T 52% C;C 12%
  • Han Chinese (Beijing)T;T 26% C;T 58% C;C 15%
  • Japanese (Tokyo)T;T 29% C;T 44% C;C 27%
  • Yoruba (Nigeria)T;T 36% C;T 46% C;C 18%
  • African ancestry (Southwest US)T;T 35% C;T 58% C;C 7%
  • Chinese (Denver)T;T 38% C;T 44% C;C 18%
  • Gujarati IndianT;T 46% C;T 41% C;C 13%
  • Luhya (Kenya)T;T 35% C;T 46% C;C 19%
  • Mexican ancestry (Los Angeles)T;T 33% C;T 52% C;C 16%
  • Maasai (Kenya)T;T 33% C;T 51% C;C 17%
  • TuscanT;T 51% C;T 39% C;C 10%

Conditions, medicines and genes

Other TNPO3 SNPs

All TNPO3 SNPs

Notes

From SNPedia

Show notes, about 210 words

The rs2004640(A) allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640(A) allele with SLE were observed. The estimate of risk was OR = 1.44 (CI: 1.34-1.55), with an overall P = 1.85 x 10(-23) for the rs2004640(A) allele. The haplotype (rs2004640T-rs2280714A) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 x 10(-16)). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations. A meta-analysis comprising 5 case-control studies, totaling 6,582 rheumatoid arthritis cases and 5,375 controls, concluded that several IRF5 gene SNPs were indeed (still) significantly associated with the disease. The rs2280714(A) allele was associated with a slight protective effect (odds ratio 0.9, CI: 0.87-0.99, p = 0.029). Of 3 IRF5 SNPs studied, the rs2280714(A) allele had the strongest association (odds ratio 1.42, CI: 1.15-1.75) in Japanese SLE patients.

Source and license

Adapted from rs2280714 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.