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WCMC

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

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Locus annotations

Locus 4

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
MSP cis Discovery rs9858542 3:49,701,983 G/A 0.28 994 -1.299 0.029 1.4×10-242 -2.350 1.7×10-238 0
MSP cis Replication rs1131095 3:49,714,225 A/G 0.25 337 -1.134 0.054 5.1×10-62 -2.330 1.4×10-72 1.9×10-82

 

Regional association plots

Hepatocyte growth factor-like protein (MSP)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Hepatocyte growth factor-like protein (MSP)

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

Hepatocyte growth factor-like protein (MSP)

Target (abbrv.) MSP
Target (full name) Hepatocyte growth factor-like protein
Somalogic ID (Sequence ID) SL005202 (4407-10_1)
Entrez Gene Symbol MST1
UniProt ID P26927
UniProt Comment
  • Dimer of an alpha chain and a beta chain linked by a disulfide bond. Interacts (via beta chain) with MST1R (via SEMA domain).
Pathway Interaction Database
  • FoxO family signaling
  • a6b1 and a6b4 Integrin signaling
  • amb2 Integrin signaling

All locus annotations are based on the sentinel SNP (rs9858542) and 108 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
  • GPX1 glutathione peroxidase 1
  • RHOA ras homolog family member A
  • RHOA-IT1 RHOA intronic transcript 1
  • TCTA T-cell leukemia translocation altered
  • AMT aminomethyltransferase
  • NICN1 nicolin 1
  • DAG1 dystroglycan 1 (dystrophin-associated glycoprotein 1)
  • RNA5SP130 RNA, 5S ribosomal pseudogene 130
  • BSN bassoon presynaptic cytomatrix protein
  • BSN-AS2 BSN antisense RNA 2 (head to head)
  • BSN-AS1 BSN antisense RNA 1
  • AC099668.1
  • APEH acylaminoacyl-peptide hydrolase
  • MST1 macrophage stimulating 1
  • AC099668.5
  • RNF123 ring finger protein 123
Potentially regulated genes
  • ARIH2 ariadne RBR E3 ubiquitin protein ligase 2
  • MST1 macrophage stimulating 1
  • LAMB2 laminin, beta 2 (laminin S)
  • UBA7 ubiquitin-like modifier activating enzyme 7
  • USP4 ubiquitin specific peptidase 4 (proto-oncogene)
  • RP11-3B7.1
  • IMPDH2 IMP (inosine 5'-monophosphate) dehydrogenase 2
  • QRICH1 glutamine-rich 1
  • DALRD3 DALR anticodon binding domain containing 3
  • NDUFAF3 NADH dehydrogenase (ubiquinone) complex I, assembly factor 3
  • SLC25A20 solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
  • KLHDC8B kelch domain containing 8B
  • APEH acylaminoacyl-peptide hydrolase
  • IP6K1 inositol hexakisphosphate kinase 1
  • CAMKV CaM kinase-like vesicle-associated
  • QARS glutaminyl-tRNA synthetase
  • CDHR4 cadherin-related family member 4
  • BSN bassoon presynaptic cytomatrix protein
  • AMT
  • AMT aminomethyltransferase
  • MON1A MON1 secretory trafficking family member A
  • TRAIP TRAF interacting protein
  • DAG1 dystroglycan 1 (dystrophin-associated glycoprotein 1)
eQTL genes
  • GPX1 glutathione peroxidase 1
  • RBM6 RNA binding motif protein 6
  • UBA7 ubiquitin-like modifier activating enzyme 7
  • AMT aminomethyltransferase
  • RNF123 ring finger protein 123
  • QRICH1 glutamine-rich 1
  • WDR6 WD repeat domain 6
  • MIR5193 microRNA 5193
  • NICN1 nicolin 1
  • MST1R macrophage stimulating 1 receptor
  • IP6K2 inositol hexakisphosphate kinase 2
  • FAM212A family with sequence similarity 212, member A
  • APEH acylaminoacyl-peptide hydrolase
  • KLHDC8B kelch domain containing 8B
  • MST1 macrophage stimulating 1
  • C3orf62 chromosome 3 open reading frame 62
  • USP4 ubiquitin specific peptidase 4 (proto-oncogene)
  • CDHR4 cadherin-related family member 4
  • ACTBP13 actin, beta pseudogene 13
  • RN7SL217P RNA, 7SL, cytoplasmic 217, pseudogene
  • RP11-3B7.1
  • CISH cytokine inducible SH2-containing protein
  • DOCK3 dedicator of cytokinesis 3

 

Results from other genome-wide association studies

Trait P Study Source
cg06313718 (chr3:49714175) 3.3×10-310 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg08510456 (chr3:49591032) 1.2×10-218 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg21659725 (chr3:3221552) 1.4×10-200 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg21665057 (chr3:196295740) 2.2×10-159 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg21582582 (chr3:182698629) 1.2×10-111 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg21574349 (chr3:185080975) 1.6×10-50 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Inflammatory bowel disease 1×10-47 23128233 (PMID) GWAS Catalog via SNiPA
Gene expression of C3orf54///UBA7 in blood 4.2×10-43 21829388 (PMID) GRASP2 eQTL
Primary sclerosing cholangitis 2.5×10-26 23603763 (PMID) GRASP2 nonQTL
cg10075733 (chr9:94495770) 3.9×10-25 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of APEH [probe 2622214] in peripheral blood mononuclear cells 3.8×10-20 19222302 (PMID) GRASP2 eQTL
cg16503057 (chr3:49711275) 1.1×10-18 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Ulcerative colitis 1.6×10-17 21297633 (PMID) GRASP2 nonQTL
Crohn's disease (time to surgery) 6×10-17 21102463 (PMID) GWAS Catalog via SNiPA
Crohn's disease 6.2×10-17 21297633 (PMID) GRASP2 nonQTL
Ulcerative collitis 2.3×10-15 Supplemental file
cg03555424 (chr3:49711281) 4.8×10-15 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Differential exon level expression of APEH [probe 2622214] in brain cortex 6.7×10-15 19222302 (PMID) GRASP2 eQTL
cg16323843 (chr3:49711287) 6.9×10-14 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Selective immunoglobulin A deficiency (IgAD) 1.2×10-12 20694011 (PMID) GRASP2 nonQTL
Gene expression of AMT///NICN1 in blood 2.7×10-12 21829388 (PMID) GRASP2 eQTL
cg08415592 (chr22:36648949) 2.8×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Irritable bowel disorder 2.4×10-11 19915574 (PMID) GRASP2 nonQTL
Gene expression of USP4 in peripheral blood monocytes 2.9×10-11 20502693 (PMID) GRASP2 eQTL
Gene expression of C3orf62///USP4 in blood 2.4×10-10 21829388 (PMID) GRASP2 eQTL
Gene expression of APEH in peripheral blood monocytes 2.5×10-10 20502693 (PMID) GRASP2 eQTL
Gene expression of NICN1 in peripheral blood monocytes 1.2×10-9 20502693 (PMID) GRASP2 eQTL
Crohn's disease, combined control dataset 2.1×10-9 17554300 (PMID) GRASP2 nonQTL
Gene expression of MST1 in liver 2.2×10-9 18462017 (PMID) GRASP2 eQTL
cg10708588 (chr1:23810840) 2.4×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22111074 (chr3:49690677) 3.1×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Educational attainment 5×10-9 25201988 (PMID) GWAS Catalog via SNiPA
Gene expression of MST1///APEH in blood 5.1×10-9 21829388 (PMID) GRASP2 eQTL
cg14021345 (chr14:42076781) 5.5×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
MST1 gene expression in subcutaneous adipose tissue 4×10-8 21602305 (PMID) GRASP2 eQTL
Gene expression of ATRIP in peripheral blood monocytes 4.5×10-8 20502693 (PMID) GRASP2 eQTL
Fasting blood glucose 4.9×10-8 22885924 (PMID) GRASP2 nonQTL
Fasting glucose 4.9×10-8 22885924 (PMID) Supplemental file
Gene expression of GPX1 in peripheral blood monocytes 4.9×10-8 20502693 (PMID) GRASP2 eQTL
cg03540175 (chr3:49236922) 8.3×10-8 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Irritible bowel syndrome 1.9×10-7 18587394 (PMID) GRASP2 nonQTL
Educational attainment, Education years 2.4×10-7 23722424 (PMID) Supplemental file
Years of education 2.4×10-7 23722424 (PMID) GRASP2 nonQTL
cg03688818 (chr3:49711123) 2.4×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg00782925 (chr19:38398365) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of UBA7 in peripheral blood monocytes 8.2×10-7 20502693 (PMID) GRASP2 eQTL
PC aa C40:2 / Tyr-PTC 9×10-7 20037589 (PMID) GRASP2 metabQTL
Differential exon level expression of BSN [probe 2622187] in brain cortex 9.6×10-7 19222302 (PMID) GRASP2 eQTL
Gene expression of RBM6 in peripheral blood monocytes 2.8×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of CAMSAP1 in peripheral blood monocytes 3.5×10-6 20502693 (PMID) GRASP2 eQTL
Coronary artery disease (CAD) 6.3×10-6 23202125 (PMID) GRASP2 nonQTL
Coronary artery disease and myocardial infarction 6.3×10-6 23202125 (PMID) Supplemental file
Schizophrenia (in multiplex schizophrenia pedigrees) 1.1×10-5 22885689 (PMID) GRASP2 nonQTL
cg00174179 (chr3:49450269) 2.2×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
College completion 5.2×10-5 23722424 (PMID) GRASP2 nonQTL
Educational attainment, College 5.2×10-5 23722424 (PMID) Supplemental file
Neuroticism 5.6×10-5 18957941 (PMID) GRASP2 nonQTL
benzoate 6.7×10-5 24816252 (PMID) gwas.eu via SNiPA
Serum concentration of inosine 9.4×10-5 21886157 (PMID) GRASP2 metabQTL
cg20786367 (chr3:49395949) 1×10-4 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of C14orf21 in normal prepouch ileum 1.1×10-4 23474282 (PMID) GRASP2 eQTL
Gene expression of FLJ32154 in normal prepouch ileum 1.3×10-4 23474282 (PMID) GRASP2 eQTL
Biploar disorder (bipolar schizoaffective disorder) 1.3×10-4 19567891 (PMID) GRASP2 nonQTL
PC aa C42:2 1.4×10-4 20037589 (PMID) GRASP2 metabQTL
Fasting glucose, main effect 1.9×10-4 22581228 (PMID) Supplemental file
Gene expression of GPX1 [probe 200736_s_at] in prefrontal cortex 2.2×10-4 20351726 (PMID) GRASP2 eQTL
Gene expression of TMEM90A in normal prepouch ileum 2.8×10-4 23474282 (PMID) GRASP2 eQTL
Asthma 4.8×10-4 20159242 (PMID) GRASP2 nonQTL

Possible link to diabetes.

This locus harbours a cis-association with MSP/MST1/HGFL (Hepatocyte growth factor-like protein); rs9858542 tags a borderline significant association with fasting glucose (p=4.9×10-8) in Magic and with CVD (p=6.3×10-6) in CardioGram; HGFL is a paralogue of HGF; HGF levels are associated with the presence of type 2 diabetes in postmenopausal women.

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.