HelmholtzZentrum munich
WCMC

Connecting genetic risk to disease endpoints through the human blood plasma proteome

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 223

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Siglec-3 cis Discovery rs10421385 19:51,701,891 A/G 0.31 996 0.412 0.046 2.9×10-18 1.180 2×10-17 4.7×10-18
Siglec-3 cis Replication rs10421385 19:51,701,891 A/G 0.26 337 0.150 0.072 0.039 1.060 0.048 0.035

 

Regional association plots

Myeloid cell surface antigen CD33 (Siglec-3)

 

Boxplots and histograms for top associations

Myeloid cell surface antigen CD33 (Siglec-3)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Myeloid cell surface antigen CD33 (Siglec-3)

Target (abbrv.) Siglec-3
Target (full name) Myeloid cell surface antigen CD33
Somalogic ID (Sequence ID) SL005215 (3166-92_1)
Entrez Gene Symbol CD33
UniProt ID P20138
UniProt Comment
  • Putative adhesion molecule of myelomonocytic-derived cells that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,6-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, may act as an inhibitory receptor upon ligand induced tyrosine phosphorylation by recruiting cytoplasmic phosphatase(s) via their SH2 domain(s) that block signal transduction through dephosphorylation of signaling molecules. Induces apoptosis in acute myeloid leukemia (in vitro).
Targeted by drugs (based on IPA annotation)
  • arsenic trioxide/gemtuzumab ozogamicin/tretinoin
  • gemtuzumab ozogamicin
Biomarker applications (based on IPA annotation)
  • efficacy

All locus annotations are based on the sentinel SNP (rs10421385) and 27 proxy variant(s) that is/are in linkage disequilibrium r2 ≥ 0.8. Linkage disequilibrium is based on data from the 1000 Genomes Project, phase 3 version 5, European population and was retrieved using SNiPA's Block Annotation feature.
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes

Genes hit or close-by
eQTL genes
  • SIGLEC20P sialic acid binding Ig-like lectin 20, pseudogene

 

Results from other genome-wide association studies

Trait P Study Source
cg19545560 (chr19:51688963) 2.7×10-41 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CD33 in blood 7.7×10-11 21829388 (PMID) GRASP2 eQTL
cg18568930 (chr19:51815634) 8.8×10-8 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg19230715 (chr19:51684963) 1.4×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of GRHL1 in peripheral blood monocytes 7.7×10-6 20502693 (PMID) GRASP2 eQTL
cg02018326 (chr19:51670275) 9.2×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg17923401 (chr19:51644144) 4.5×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs