HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 24

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 rs13294 1:150,484,987 G/A 0.40 996 -0.849 0.035 7.7×10-102 -1.130 6.8×10-87 5.5×10-96
ECM1 cis Replication rs13294 1:150,484,987 G/A 0.38 337 -0.818 0.058 1×10-35 -1.140 9.4×10-28 1.3×10-30

 

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 (rs13294) and 138 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
  • MRPS21 mitochondrial ribosomal protein S21
  • AC242988.1
  • 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
eQTL genes
  • RP11-54A4.2
  • CDC42SE1 CDC42 small effector 1
  • ADAMTSL4 ADAMTS-like 4
  • RPRD2 regulation of nuclear pre-mRNA domain containing 2
  • TARS2 threonyl-tRNA synthetase 2, mitochondrial (putative)
  • ECM1 extracellular matrix protein 1
  • MRPS21 mitochondrial ribosomal protein S21
  • ENSA endosulfine alpha

 

Results from other genome-wide association studies

Trait P Study Source
cg15654264 (chr1:150339987) 3.3×10-124 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of [probe 3890500 centered at chr1:148533237] in blood 1.5×10-33 21829388 (PMID) GRASP2 eQTL
cg09563216 (chr1:150255217) 2.1×10-16 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg03960066 (chr1:150255527) 2.2×10-16 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of KIAA0460 probe [GI_45433544-S] in brain cortex with no Alzheimer's interaction 1.6×10-14 19361613 (PMID) GRASP2 eQTL
cg04560832 (chr1:150267020) 1.5×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum IgG 1.8×10-8 22673310 (PMID) GRASP2 nonQTL
Gene expression of MRPS21 (probeID ILMN_1660292) in cerebellum in Alzheimer's disease cases and controls 3.1×10-8 22685416 (PMID) GRASP2 eQTL
Gene expression of MRPS21 (probeID ILMN_1660292) in temporal cortex in Alzheimer's disease cases and controls 1.4×10-7 22685416 (PMID) GRASP2 eQTL
cg15720675 (chr1:150293280) 6.1×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Lesion load (multiple sclerosis) 5×10-5 19010793 (PMID) GRASP2 nonQTL
Serum concentration of 1-palmitoylglycerol (1-monopalmitin) 7.3×10-5 21886157 (PMID) GRASP2 metabQTL
"Gene expression of RPRD2 [transcript NM_015203, probe A_23_P60657] in liver" 2.1×10-4 21637794 (PMID) GRASP2 eQTL
Neuroblastoma (brain cancer) 2.6×10-4 21124317 (PMID) GRASP2 nonQTL
Serum ratio of (3-methoxytyrosine)/(paraxanthine) 2.9×10-4 21886157 (PMID) GRASP2 metabQTL
Serum concentration of pipecolate 4×10-4 21886157 (PMID) GRASP2 metabQTL
Ulcerative collitis 4.5×10-4 Supplemental file