HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 374

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
ECM1 cis Discovery rs12724450 1:150,480,571 G/A 0.09 996 0.544 0.076 1.6×10-12 1.070 5.2×10-10 1×10-11
ECM1 cis Replication rs34001546 1:150,459,715 A/G 0.05 337 0.292 0.162 0.072 1.040 0.174 0.178

 

Regional association plots

Extracellular matrix protein 1 (ECM1)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Extracellular matrix protein 1 (ECM1)

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

Extracellular matrix protein 1 (ECM1)

Target (abbrv.) ECM1
Target (full name) Extracellular matrix protein 1
Somalogic ID (Sequence ID) SL006550 (3366-51_2)
Entrez Gene Symbol ECM1
UniProt ID Q16610
UniProt Comment
  • Involved in endochondral bone formation as negative regulator of bone mineralization. Stimulates the proliferation of endothelial cells and promotes angiogenesis. Inhibits MMP9 proteolytic activity.
Biomarker applications (based on IPA annotation)
  • diagnosis

All locus annotations are based on the sentinel SNP (rs12724450) and 69 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
  • AC242988.1
  • MRPS21 mitochondrial ribosomal protein S21
  • PRPF3 pre-mRNA processing factor 3
  • RPRD2 regulation of nuclear pre-mRNA domain containing 2
  • TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative)
  • ECM1 extracellular matrix protein 1
  • FALEC focally amplified long non-coding RNA in epithelial cancer
Potentially regulated genes
  • ADAMTSL4 ADAMTS-like 4
  • PRPF3 pre-mRNA processing factor 3
  • MCL1 myeloid cell leukemia 1
  • RP11-458I7.1
  • TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative)
  • ANP32E acidic (leucine-rich) nuclear phosphoprotein 32 family, member E
  • CTSS cathepsin S
  • VPS45 vacuolar protein sorting 45 homolog (S. cerevisiae)
  • RP11-54A4.2
eQTL genes
  • C1orf54 chromosome 1 open reading frame 54
  • HORMAD1 HORMA domain containing 1
  • FALEC focally amplified long non-coding RNA in epithelial cancer
  • ECM1 extracellular matrix protein 1
  • RPRD2 regulation of nuclear pre-mRNA domain containing 2
  • TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative)
  • CTSS cathepsin S

 

Results from other genome-wide association studies

Trait P Study Source
cg16386293 (chr1:150480832) 7.5×10-109 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg03763518 (chr1:150245020) 6.6×10-22 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg08856268 (chr1:150436971) 2×10-10 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg03851496 (chr1:150488781) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Hip circumfence 6.9×10-7 25673412 (PMID) Supplemental file
Hip circumfence, adjusted for BMI 1.9×10-6 25673412 (PMID) Supplemental file
Waist-to-hip ratio, adjusted for BMI 5.8×10-6 25673412 (PMID) Supplemental file
Serum ratio of (biliverdin)/(pyruvate) 3.1×10-5 21886157 (PMID) GRASP2 metabQTL
Serum concentration of creatine 3.9×10-5 21886157 (PMID) GRASP2 metabQTL
Gene expression of MCL1 in blood 5.2×10-5 21829388 (PMID) GRASP2 eQTL
Serum ratio of (1-eicosadienoylglycerophosphocholine*)/(biliverdin) 1.3×10-4 21886157 (PMID) GRASP2 metabQTL
Gene expression of C1orf54 [probe ILMN_4355] in osteoblasts treated with BMP2 1.5×10-4 21283786 (PMID) GRASP2 eQTL
Heart rate 2.9×10-4 23583979 (PMID) GRASP2 nonQTL
Serum ratio of (eicosapentaenoate (EPA; 20:5n3))/(phenylacetate) 3.3×10-4 21886157 (PMID) GRASP2 metabQTL