HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 201

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Cathepsin S cis Discovery rs1336900 1:150,679,033 G/A 0.38 995 0.401 0.043 1.4×10-19 1.070 6.4×10-18 4.1×10-11
Cathepsin S cis Replication rs12402939 1:150,615,094 A/C 0.47 337 0.227 0.057 8.2×10-5 1.050 9.5×10-5 0.001

 

Regional association plots

 

Boxplots and histograms for top associations

Cathepsin S

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

Cathepsin S

Target (abbrv.) Cathepsin S
Target (full name) Cathepsin S
Somalogic ID (Sequence ID) SL004673 (3181-50_2)
Entrez Gene Symbol CTSS
UniProt ID P25774
UniProt Comment
  • Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L and cathepsin N.
Reactome
  • Assembly of collagen fibrils and other multimeric structures
  • Degradation of the extracellular matrix
  • Endosomal/Vacuolar pathway
  • MHC class II antigen presentation
  • Trafficking and processing of endosomal TLR
Pathway Studio
  • MHC2-Mediated Antigen Presentation

All locus annotations are based on the sentinel SNP (rs1336900) and 181 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
  • BNIPL BCL2/adenovirus E1B 19kD interacting protein like
  • SEMA6C sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C
  • RP11-316M1.3
  • ARNT aryl hydrocarbon receptor nuclear translocator
  • SETDB1 SET domain, bifurcated 1
  • CTSS cathepsin S
  • PRPF3 pre-mRNA processing factor 3
  • ADAMTSL4 ADAMTS-like 4
  • PIP5K1A phosphatidylinositol-4-phosphate 5-kinase, type I, alpha
  • MCL1 myeloid cell leukemia 1
  • RP11-54A4.2
  • TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative)
  • CTSK cathepsin K
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg04414720 (chr1:150670172) 3.3×10-310 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg26891210 (chr1:150703117) 3.3×10-310 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg09365446 (chr1:150670398) 8.5×10-304 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg22823121 (chr1:150693506) 1.3×10-159 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg14037218 (chr1:150522391) 1.1×10-106 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CTSS in blood 3.2×10-37 21829388 (PMID) GRASP2 eQTL
Gene expression of CTSS in peripheral blood monocytes 3.6×10-33 20502693 (PMID) GRASP2 eQTL
Gene expression of CTSS [probe 232617_at] in lymphoblastoid cell lines 5.8×10-24 17873877 (PMID) GRASP2 eQTL
Gene expression of ARNT probe [GI_30795239-A] in brain cortex with no Alzheimer's interaction 5.2×10-22 19361613 (PMID) GRASP2 eQTL
Gene expression of HORMAD1 in normal prepouch ileum 6.6×10-16 23474282 (PMID) GRASP2 eQTL
Gene expression of POMZP3 in liver 1.3×10-15 18462017 (PMID) GRASP2 eQTL
Gene expression of ARNT in blood 3.6×10-15 21829388 (PMID) GRASP2 eQTL
Gene expression of CTSS in CEU-CHB-JPT-YRI lymphoblastoid cell lines 8.1×10-15 17873874 (PMID) GRASP2 eQTL
Gene expression of ARNT [probe 230619_at] in lymphoblastoid cell lines 3.9×10-14 17873877 (PMID) GRASP2 eQTL
Differential exon level expression of [probeset 2434570] in peripheral blood mononuclear cells 1.6×10-13 19222302 (PMID) GRASP2 eQTL
Gene expression of CTSS [probe 202902_s_at] in lymphoblastoid cell lines 1.8×10-13 17873877 (PMID) GRASP2 eQTL
Gene expression of ARNT in liver 1.2×10-12 22006096 (PMID) GRASP2 eQTL
Gene expression of CTSK in peripheral blood monocytes 3.9×10-12 20502693 (PMID) GRASP2 eQTL
Gene expression of CTSK in blood 1.9×10-11 21829388 (PMID) GRASP2 eQTL
HORMAD1 gene expression in normal skin 1.4×10-10 21129726 (PMID) GRASP2 eQTL
HORMAD1 gene expression in psoriatic lesional skin 3.7×10-10 21129726 (PMID) GRASP2 eQTL
Gene expression of ARNT (probeID ILMN_1697519) in whole blood 4.8×10-10 22692066 (PMID) GRASP2 eQTL
Gene expression of GOLPH3L in peripheral blood monocytes 5.4×10-10 20502693 (PMID) GRASP2 eQTL
Gene expression of CTSS in CEU-CHB-JPT lymphoblastoid cell lines 9.8×10-10 17873874 (PMID) GRASP2 eQTL
Gene expression of HORMAD1 in peripheral blood monocytes 1.3×10-8 20502693 (PMID) GRASP2 eQTL
Fat body mass 4×10-8 24064335 (PMID) GWAS Catalog via SNiPA
Gene expression of CTSK in CEU-CHB-JPT-YRI lymphoblastoid cell lines 3×10-7 17873874 (PMID) GRASP2 eQTL
Gene expression of CTSS (probeID ILMN_1743032) in cerebellum in Alzheimer's disease cases and controls 3.5×10-7 22685416 (PMID) GRASP2 eQTL
cg12912293 (chr1:150849781) 3.5×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CTSS in JPT lymphoblastoid cell lines 1.4×10-6 17873874 (PMID) GRASP2 eQTL
cg09059988 (chr1:150693275) 2×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CTSS (probeID ILMN_1743032) in temporal cortex in Alzheimer's disease cases and controls 2.8×10-6 22685416 (PMID) GRASP2 eQTL
Serum concentration of glutamate 4×10-6 21886157 (PMID) GRASP2 metabQTL
Differential exon level expression of CTSS [probe 2434577] in peripheral blood mononuclear cells 6×10-6 19222302 (PMID) GRASP2 eQTL
Coronary artery disease (CAD) 1×10-5 23202125 (PMID) GRASP2 nonQTL
Inflammatory bowel disease 1.8×10-5 Supplemental file
Coronary artery disease and myocardial infarction 3.4×10-5 23202125 (PMID) Supplemental file
Serum ratio of (2-hydroxybutyrate (AHB))/(octadecanedioate) 3.4×10-5 21886157 (PMID) GRASP2 metabQTL
Serum ratio of (tetradecanedioate)/(thromboxane B2) 3.7×10-5 21886157 (PMID) GRASP2 metabQTL
Gene expression of CTSS in normal prepouch ileum 4.6×10-5 23474282 (PMID) GRASP2 eQTL
cg11175032 (chr1:150529915) 5×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Ulcerative collitis 1.6×10-4 Supplemental file