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

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Locus annotations

Locus 210

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
NXPH1 trans Discovery rs626457 1:57,407,484 C/T 0.32 994 0.414 0.045 3.3×10-19 1.120 1.7×10-17 1.9×10-16
NXPH1 trans Replication rs607268 1:57,379,672 A/G 0.50 337 0.380 0.066 1.7×10-8 1.150 7.6×10-9 7.4×10-8
I-309 trans Discovery rs626457 1:57,407,484 C/T 0.32 994 0.278 0.046 2.7×10-9 1.040 1.3×10-5 0.002
I-309 trans Replication rs607268 1:57,379,672 A/G 0.50 337 0.064 0.062 0.306 1.010 0.514 0.768

 

Regional association plots

 

Boxplots and histograms for top associations

Neurexophilin-1 (NXPH1)

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

C-C motif chemokine 1 (I-309)

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

Neurexophilin-1 (NXPH1)

Target (abbrv.) NXPH1
Target (full name) Neurexophilin-1
Somalogic ID (Sequence ID) SL012457 (4562-1_2)
Entrez Gene Symbol NXPH1
UniProt ID P58417
UniProt Comment
  • May be signaling molecules that resemble neuropeptides and that act by binding to alpha-neurexins and possibly other receptors.

C-C motif chemokine 1 (I-309)

Target (abbrv.) I-309
Target (full name) C-C motif chemokine 1
Somalogic ID (Sequence ID) SL003176 (2770-51_2)
Entrez Gene Symbol CCL1
UniProt ID P22362
UniProt Comment
  • Cytokine that is chemotactic for monocytes but not for neutrophils. Binds to CCR8.

All locus annotations are based on the sentinel SNP (rs626457) and 33 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
  • C8A complement component 8, alpha polypeptide
  • C8B complement component 8, beta polypeptide
Potentially regulated genes
  • DAB1 Dab, reelin signal transducer, homolog 1 (Drosophila)
  • C1orf168 chromosome 1 open reading frame 168
eQTL genes
  • C1orf168 chromosome 1 open reading frame 168

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of P2RY11 in liver 8.7×10-44 18462017 (PMID) GRASP2 eQTL
cg11738198 (chr1:57390596) 9.7×10-24 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum ratio of (margarate (17:0))/(sebacate (decanedioate)) 3.6×10-4 21886157 (PMID) GRASP2 metabQTL

Possible link between cis-variants and protein levels of NXPH1.

This locus harbours a replicated trans-pQTL to Neurexophilin-1 (NXPH1).

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.