HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 130

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 rs13063312 3:48,661,985 G/A 0.10 997 -0.790 0.067 4.4×10-30 -1.680 1.1×10-29 4.1×10-39
MSP cis Replication rs34566463 3:49,245,077 A/G 0.06 337 -0.604 0.144 3.5×10-5 -1.380 0.002 5×10-6

 

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 (rs13063312) and 74 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
  • ARIH2 ariadne RBR E3 ubiquitin protein ligase 2
  • ZNF589 zinc finger protein 589
  • WDR6 WD repeat domain 6
  • CDC25A cell division cycle 25A
  • SHISA5
  • DALRD3 DALR anticodon binding domain containing 3
  • QARS glutaminyl-tRNA synthetase
  • CCDC51 coiled-coil domain containing 51
  • QRICH1 glutamine-rich 1
  • PLXNB1 plexin B1
  • NCKIPSD NCK interacting protein with SH3 domain
  • COL7A1
  • COL7A1 collagen, type VII, alpha 1
  • SLC25A20 solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
  • SLC26A6 solute carrier family 26 (anion exchanger), member 6
  • ATRIP ATR interacting protein
  • IP6K2 inositol hexakisphosphate kinase 2
  • SPINK8 serine peptidase inhibitor, Kazal type 8 (putative)
  • PRKAR2A protein kinase, cAMP-dependent, regulatory, type II, alpha
eQTL genes
  • PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4
  • C3orf62 chromosome 3 open reading frame 62
  • NCKIPSD NCK interacting protein with SH3 domain
  • UBA7 ubiquitin-like modifier activating enzyme 7
  • RP11-3B7.1
  • USP4 ubiquitin specific peptidase 4 (proto-oncogene)
  • WDR6 WD repeat domain 6
  • MIR5193 microRNA 5193
  • TMEM89 transmembrane protein 89
  • CCDC36 coiled-coil domain containing 36
  • SLC26A6 solute carrier family 26 (anion exchanger), member 6
  • IP6K2 inositol hexakisphosphate kinase 2
  • KLHDC8B kelch domain containing 8B
  • ATRIP ATR interacting protein
  • TREX1 three prime repair exonuclease 1
  • TREX1 three prime repair exonuclease 1
  • NICN1 nicolin 1
  • CELSR3 cadherin, EGF LAG seven-pass G-type receptor 3
  • RBM6 RNA binding motif protein 6
  • CCDC71 coiled-coil domain containing 71

 

Results from other genome-wide association studies

Trait P Study Source
cg24608717 (chr3:48678307) 6.1×10-50 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of WDR6 in peripheral blood monocytes 1.8×10-33 20502693 (PMID) GRASP2 eQTL
cg09397359 (chr3:48694697) 10×10-22 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of USP4 in peripheral blood monocytes 4.7×10-21 20502693 (PMID) GRASP2 eQTL
cg15142694 (chr3:48694558) 1.4×10-19 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg14012610 (chr3:48673427) 1.2×10-15 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Inflammatory bowel disease 2×10-11 Supplemental file
cg18656024 (chr3:48633168) 2.1×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Ulcerative collitis 2.9×10-9 Supplemental file
cg07466493 (chr3:48670386) 3.3×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Differential exon level expression of CELSR3 [probe 2673630] in brain cortex 1.6×10-8 19222302 (PMID) GRASP2 eQTL
Gene expression of NCKIPSD in blood 4.2×10-8 21829388 (PMID) GRASP2 eQTL
Gene expression of CELSR3 in blood 8.8×10-8 21829388 (PMID) GRASP2 eQTL
Gene expression of SLC26A6 in liver 9.6×10-8 21637794 (PMID) GRASP2 eQTL
Gene expression of [probe 150692 centered at chr3:48638191] in blood 1.3×10-7 21829388 (PMID) GRASP2 eQTL
cg21950072 (chr3:48755000) 3.1×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of NCKIPSD in peripheral blood monocytes 3.2×10-7 20502693 (PMID) GRASP2 eQTL
cg04890406 (chr3:48647346) 3.4×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Differential exon level expression of CELSR3 [probe 2673639] in brain cortex 1.1×10-6 19222302 (PMID) GRASP2 eQTL
Gene expression of WDR6 in normal prepouch ileum 1.9×10-6 23474282 (PMID) GRASP2 eQTL
cg08105844 (chr3:48659264) 2.9×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of NCKIPSD (ENSG00000213672) in dendritic cells 3.1×10-6 22233810 (PMID) GRASP2 eQTL
Crohn's disease 3.7×10-6 Supplemental file
Gene expression of ZFAT in peripheral blood monocytes 4.8×10-6 20502693 (PMID) GRASP2 eQTL
Blood pressure 9.4×10-6 pha003047 (dbGaP) dbGaP via SNiPA
Serum ratio of (heptanoate (7:0))/(phenylacetate) 2.6×10-5 21886157 (PMID) GRASP2 metabQTL
Psoriasis 5×10-5 20953190 (PMID) GRASP2 nonQTL
Gene expression of USP4 [probe 202681_at] in prefrontal cortex 5.9×10-5 20351726 (PMID) GRASP2 eQTL
Serum ratio of (1-oleoylglycerophosphoethanolamine)/(glycerol 2-phosphate) 1.3×10-4 21886157 (PMID) GRASP2 metabQTL
Serum ratio of (deoxycholate)/(taurochenodeoxycholate) 1.6×10-4 21886157 (PMID) GRASP2 metabQTL
Gene expression of IHPK2 in blood 1.9×10-4 21829388 (PMID) GRASP2 eQTL
Serum creatinine 1.9×10-4 20383146 (PMID) GRASP2 nonQTL
Anorexia nervosa 4.2×10-4 24514567 (PMID) Supplemental file