HelmholtzZentrum munich

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


Proteome annotation
Locus annotations

Locus 293

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Cystatin C cis Discovery rs6036478 20:23,611,359 C/A 0.20 992 -0.391 0.050 9.6×10-15 -1.060 5.3×10-11 9.2×10-7
Cystatin C cis Replication rs6036478 20:23,611,359 C/A 0.23 337 -0.097 0.067 0.148 -1.020 0.186 0.295


Regional association plots


Boxplots and histograms for top associations

Cystatin-C (Cystatin C)

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

Cystatin-C (Cystatin C)

Target (abbrv.) Cystatin C
Target (full name) Cystatin-C
Somalogic ID (Sequence ID) SL001777 (2609-59_2)
Entrez Gene Symbol CST3
UniProt ID P01034
UniProt Comment
  • As an inhibitor of cysteine proteinases, this protein is thought to serve an important physiological role as a local regulator of this enzyme activity.
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • prognosis
  • safety
  • unspecified application
  • Amyloids

All locus annotations are based on the sentinel SNP (rs6036478) and 117 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
Potentially regulated genes
  • RP11-218C14.2
  • CST5 cystatin D
  • CSTL1 cystatin-like 1
  • CST8 cystatin 8 (cystatin-related epididymal specific)
  • CST11 cystatin 11
  • CSTP1 cystatin pseudogene 1
  • GGTLC1 gamma-glutamyltransferase light chain 1
  • POM121L3P POM121 transmembrane nucleoporin-like 3, pseudogene
  • CST3 cystatin C
  • GZF1 GDNF-inducible zinc finger protein 1
eQTL genes


Results from other genome-wide association studies

Trait P Study Source
Cystatin C in serum 0×100 20383146 (PMID) GRASP2 nonQTL
Chronic kidney disease 2×10-138 20383146 (PMID) GWAS Catalog via SNiPA
Serum cystatin c estimated glomerular filtration rate (eGFR) 2.3×10-138 20383146 (PMID) GRASP2 nonQTL
Gene expression of CST3 in blood 4.3×10-71 21829388 (PMID) GRASP2 eQTL
cg03669268 (chr20:23549082) 1.9×10-27 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Plasma cystastin c levels in acute coronary syndrome 1×10-26 24952865 (PMID) GWAS Catalog via SNiPA
Gene expression of CST3 in peripheral blood monocytes 2.8×10-26 20502693 (PMID) GRASP2 eQTL
cg01886570 (chr8:123966081) 1.1×10-18 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Cystatin C 8×10-9 17903292 (PMID) GRASP2 nonQTL
Cystatins 8.5×10-9 pha001330 (dbGaP) dbGaP via SNiPA
Gene expression of IL15 in peripheral blood monocytes 2.3×10-7 20502693 (PMID) GRASP2 eQTL
Crohn's disease, combined control dataset, gender differentiated 1.8×10-5 17554300 (PMID) GRASP2 nonQTL
cg16320910 (chr20:23614565) 5×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
chiro-inositol 6.5×10-5 24816252 (PMID) gwas.eu via SNiPA
Blood pressure 7.5×10-5 pha002898 (dbGaP) dbGaP via SNiPA
Hypertension, combined control dataset, gender differentiated 1.2×10-4 17554300 (PMID) GRASP2 nonQTL
Schizophrenia 1.6×10-4 19571809 (PMID) GRASP2 nonQTL