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

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Locus annotations

Locus 157

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Alkaline phosphatase, bone trans Discovery rs1126478 3:46,501,213 T/C 0.30 995 0.498 0.046 5.1×10-26 1.140 2.2×10-24 3.1×10-21
Alkaline phosphatase, bone trans Replication rs1126478 3:46,501,213 G/A 0.46 337 -0.511 0.068 4.1×10-13 -1.230 2.4×10-11 7.2×10-12

 

Regional association plots

Alkaline phosphatase, tissue-nonspecific isozyme (Alkaline phosphatase, bone)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Alkaline phosphatase, tissue-nonspecific isozyme (Alkaline phosphatase, bone)

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

Alkaline phosphatase, tissue-nonspecific isozyme (Alkaline phosphatase, bone)

Target (abbrv.) Alkaline phosphatase, bone
Target (full name) Alkaline phosphatase, tissue-nonspecific isozyme
Somalogic ID (Sequence ID) SL002077 (2795-23_3)
Entrez Gene Symbol ALPL
UniProt ID P05186
UniProt Comment
  • This isozyme may play a role in skeletal mineralization.
Biomarker applications (based on IPA annotation)
  • efficacy
  • safety
Wiki Pathways
  • Endochondral Ossification

All locus annotations are based on the sentinel SNP (rs1126478) and 23 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
  • LTF lactotransferrin
Potentially regulated genes
  • CCR5 chemokine (C-C motif) receptor 5 (gene/pseudogene)
  • LTF lactotransferrin
eQTL genes
  • CCR3 chemokine (C-C motif) receptor 3

 

Results from other genome-wide association studies

Trait P Study Source
cg16975587 (chr3:46506230) 1.4×10-91 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg04910591 (chr3:46506080) 3.7×10-91 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg15261665 (chr3:46506398) 1.8×10-62 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25930780 (chr3:46506316) 5.7×10-51 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Allele-specific methylation of LTF in blood 2.7×10-29 20159110 (PMID) GRASP2 meQTL
cg23009419 (chr3:46618573) 6.6×10-25 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg20941258 (chr3:46618692) 2.2×10-12 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg10365562 (chr3:46615525) 4.3×10-11 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg07225641 (chr3:46618349) 9.2×10-10 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg18599081 (chr3:46448060) 5.5×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25821245 (chr3:46608080) 4.2×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Juvenile idiopathic arthritis 1.7×10-4 22354554 (PMID) GRASP2 nonQTL
Serum concentration of 4-ethylphenylsulfate 3.2×10-4 21886157 (PMID) GRASP2 metabQTL
Pulse pressure 3.4×10-4 20877124 (PMID) GRASP2 nonQTL

Possible link between cis-variants in CCR3, CCR5 or LTF and protein levels of ALPL.

This locus harbours a replicated trans-pQTL to Alkaline phosphatase, tissue-nonspecific isozyme (ALPL).

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.

SOMAscan assay update regarding Alkaline phosphatase

According to a SOMAscan assay change log issued on 12/22/2016, the SOMAmer reagent 2795-23 (targeting Alkaline phosphatase, tissue-nonspecific isozyme) was removed from the SOMAscan panel for the following reason: "Mass spectrometry identifies Lactotransferrin as the protein captured from the commercial protein preparation using SOMAmer reagent 2795-23. The original, and subsequent, protein preparations purchased as 'Alkaline phosphatase, bone' primarily consisted of Lactotransferrin, not Alkaline phosphatase."