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WCMC

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

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Locus annotations

Locus 427

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
LAG-1 trans Discovery rs6808835 3:46,449,864 G/T 0.14 997 0.430 0.064 3.5×10-11 1.130 1.4×10-8 0.018

 

Regional association plots

 

Boxplots and histograms for top associations

C-C motif chemokine 4-like (LAG-1)

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

C-C motif chemokine 4-like (LAG-1)

Target (abbrv.) LAG-1
Target (full name) C-C motif chemokine 4-like
Somalogic ID (Sequence ID) SL004356 (2781-63_2)
Entrez Gene Symbol CCL4L1
UniProt ID Q8NHW4
UniProt Comment
  • Chemokine that induces chemotaxis of cells expressing CCR5 or CCR1. Inhibits HIV replication in peripheral blood monocytes that express CCR5.

All locus annotations are based on the sentinel SNP (rs6808835) and 89 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
  • CCR3 chemokine (C-C motif) receptor 3
  • UQCRC2P1 ubiquinol-cytochrome c reductase core protein II pseudogene 1
  • CCR2 chemokine (C-C motif) receptor 2
  • RP11-24F11.2
  • CCR5 chemokine (C-C motif) receptor 5 (gene/pseudogene)
  • CCRL2 chemokine (C-C motif) receptor-like 2
  • LTF lactotransferrin
Potentially regulated genes
  • ALS2CL ALS2 C-terminal like
  • RP11-24F11.2
  • CCRL2 chemokine (C-C motif) receptor-like 2
  • XCR1 chemokine (C motif) receptor 1
  • CCR1 chemokine (C-C motif) receptor 1
  • CCR3 chemokine (C-C motif) receptor 3
  • CCR9 chemokine (C-C motif) receptor 9
  • CXCR6 chemokine (C-X-C motif) receptor 6
  • LZTFL1 leucine zipper transcription factor-like 1
  • CCR5 chemokine (C-C motif) receptor 5 (gene/pseudogene)
  • LTF lactotransferrin
  • PRSS44 protease, serine, 44
  • PRSS50 protease, serine, 50
  • CCR2 chemokine (C-C motif) receptor 2
  • LRRC2 leucine rich repeat containing 2
  • AC104304.1
eQTL genes
  • LIMD1-AS1 LIMD1 antisense RNA 1
  • LIMD1 LIM domains containing 1
  • LRRC2 leucine rich repeat containing 2
  • CCR3 chemokine (C-C motif) receptor 3

 

Results from other genome-wide association studies

Trait P Study Source
Cerebrospinal fluid levels of Alzheimer's disease-related proteins 2×10-13 25340798 (PMID) GWAS Catalog via SNiPA
Gene expression of CCR1 in peripheral blood monocytes 5.8×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of CCRL2 in normal prepouch ileum 6.1×10-8 23474282 (PMID) GRASP2 eQTL
Serum ratio of (1-palmitoleoylglycerophosphocholine*)/(5-dodecenoate (12:1n7)) 6.8×10-6 21886157 (PMID) GRASP2 metabQTL
Serum ratio of (1-oleoylglycerophosphocholine)/(5-dodecenoate (12:1n7)) 1×10-5 21886157 (PMID) GRASP2 metabQTL
"Gene expression of CCR1 [transcript NM_001295, probe A_24_P148717] in liver" 1.3×10-5 21637794 (PMID) GRASP2 eQTL
Serum ratio of (1-palmitoylglycerophosphocholine)/(5-dodecenoate (12:1n7)) 1.7×10-5 21886157 (PMID) GRASP2 metabQTL
HIV-1 control (viral load at set point) 2.1×10-5 20041166 (PMID) GRASP2 nonQTL
Ulcerative collitis 2.8×10-5 Supplemental file
Alanine/N,N-dimethylglycine ratio 5.7×10-5 21572414 (PMID) GRASP2 metabQTL
cg13672136 (chr3:46477705) 7.8×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum ratio of (pyroglutamine*)/(pyroglutamylglycine) 8.7×10-5 21886157 (PMID) GRASP2 metabQTL
Salmonella-induced pyroptosis 2.6×10-4 22837397 (PMID) GRASP2 nonQTL