rs3748079

A SNP in the ITPR3 gene on chromosome 6. Its most notable genotype is C;C: 1.9x increased risk for SLE (lupus)

Gene
ITPR3
Location
Chr 633,620,370 (GRCh38)
Highest magnitude
0.1Typical
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
18%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TNot ratednormal riskTypical · 0.03% of people
  2. C;TNot ratednormal riskTypical · 0.023% of people
  3. A;GNot ratedNo summary available.Typical · 0.00% of people
  4. C;CMost notableBad1.9x increased risk for SLE (lupus)Typical · 0.174% of people
  5. A;ANot ratedNo summary available.Typical · 0.00% of people

SNPedia records rs3748079 on the minus strand: (A;A), (A;G), (C;T), (G;G), (T;T). 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 3% C;T 23% A;G 0% C;C 74% A;A 0%
  • European ancestry (Utah)T;T 7% C;T 34% A;G 0% C;C 59% A;A 0%
  • Han Chinese (Beijing)T;T 4% C;T 26% A;G 0% C;C 70% A;A 0%
  • Japanese (Tokyo)T;T 4% C;T 20% A;G 0% C;C 76% A;A 0%
  • Yoruba (Nigeria)T;T 0% C;T 0% A;G 0% C;C 100% A;A 0%
  • African ancestry (Southwest US)T;T 0% C;T 11% A;G 0% C;C 90% A;A 0%
  • Chinese (Denver)T;T 3% C;T 26% A;G 0% C;C 72% A;A 0%
  • Gujarati IndianT;T 8% C;T 46% A;G 0% C;C 47% A;A 0%
  • Luhya (Kenya)T;T 0% C;T <1% A;G 0% C;C 99% A;A 0%
  • Mexican ancestry (Los Angeles)T;T 3% C;T 47% A;G 0% C;C 50% A;A 0%
  • Maasai (Kenya)T;T 0% C;T 4% A;G 0% C;C 96% A;A 0%
  • TuscanT;T 3% C;T 39% A;G 0% C;C 58% A;A 0%

Conditions, medicines and genes

Other ITPR3 SNPs

All ITPR3 SNPs

Notes

From SNPedia

Show notes, about 120 words

rs3748079 is a SNP in the promoter region of the ITPR3 gene; it is also known as -1990C>T. rs3748079 has been linked to increased risk for systemic lupus erythematosus (SLE) in two independent Japanese case-control samples (p=0.0000000178 with odds ratio of 1.88, CI:1.51-2.35). Individuals with risk genotypes of both rs3748079 and rs3095870, in the ITPR3 and NKX2.5 genes, respectively, have even high risk for SLE (odds ratio 5.77). This particular SNP also revealed associations with rheumatoid arthritis (RA) (p=0.0084 with odds ratio of 1.23, CI:1.05-1.43) and with Graves' disease (GD) (p=0.00036 with odds ratio of 1.57, CI:1.22-2.02). Note that the orientation of this SNP as published is reversed compared to the dbSNP entry.

Source and license

Adapted from rs3748079 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.