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

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Locus annotations

Locus 159

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
C34 gp41 HIV Fragment trans Discovery rs387608 6:31,941,557 G/A 0.12 996 0.670 0.063 2.5×10-25 1.170 2.4×10-21 4.5×10-12
C34 gp41 HIV Fragment trans Replication rs387608 6:31,941,557 G/A 0.20 337 0.426 0.075 2.4×10-8 1.150 6.1×10-7 0.001

 

Regional association plots

gp41 C34 peptide, HIV (C34 gp41 HIV Fragment)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

gp41 C34 peptide, HIV (C34 gp41 HIV Fragment)

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

gp41 C34 peptide, HIV (C34 gp41 HIV Fragment)

Target (abbrv.) C34 gp41 HIV Fragment
Target (full name) gp41 C34 peptide, HIV
Somalogic ID (Sequence ID) SL016148 (4792-51_2)
Entrez Gene Symbol Human-virus
UniProt ID Q70626
UniProt Comment
  • Envelope glycoprotein gp160: Oligomerizes in the host endoplasmic reticulum into predominantly trimers. In a second time, gp160 transits in the host Golgi, where glycosylation is completed. The precursor is then proteolytically cleaved in the trans-Golgi and thereby activated by cellular furin or furin-like proteases to produce gp120 and gp41.

All locus annotations are based on the sentinel SNP (rs387608) and 17 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.

Linked genes

Genes hit or close-by
  • SKIV2L superkiller viralicidic activity 2-like (S. cerevisiae)
  • DXO decapping exoribonuclease
  • STK19 serine/threonine kinase 19
  • C4A complement component 4A (Rodgers blood group)
  • C4A-AS1 C4A antisense RNA 1
  • CYP21A1P cytochrome P450, family 21, subfamily A, polypeptide 1 pseudogene
  • TNXA tenascin XA (pseudogene)
  • AL645922.1
  • STK19B serine/threonine kinase 19B, pseudogene
  • C4B complement component 4B (Chido blood group)
  • TNXB tenascin XB
  • CYP21A2 cytochrome P450, family 21, subfamily A, polypeptide 2
  • C4B-AS1 C4B antisense RNA 1
Potentially regulated genes
eQTL genes
  • SKIV2L superkiller viralicidic activity 2-like (S. cerevisiae)
  • C4B complement component 4B (Chido blood group)
  • NELFE negative elongation factor complex member E
  • LSM2 LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)
  • HSPA1L heat shock 70kDa protein 1-like

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of SKIV2L///DOM3Z in blood 1.9×10-42 21829388 (PMID) GRASP2 eQTL
Rheumatoid arthritis 4×10-33 20453842 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration 2.1×10-29 23455636 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD 1.4×10-21 23455636 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (geographic atrophy) 2.1×10-11 23455636 (PMID) GRASP2 nonQTL
Type 1 diabetes 5.1×10-11 17632545 (PMID) GRASP2 nonQTL
Rheumatoid arthritis (ACPA-positive) 1.6×10-10 21156761 (PMID) GRASP2 nonQTL
Gene expression of CFB///RDBP in blood 2.8×10-9 21829388 (PMID) GRASP2 eQTL
Macular degeneration 5.5×10-9 pha002869 (dbGaP) dbGaP via SNiPA
Gene expression of SKIV2L in normal prepouch ileum 3.8×10-7 23474282 (PMID) GRASP2 eQTL
Lung cancer (squamous cell carcinoma) 3.6×10-6 19836008 (PMID) GRASP2 nonQTL
Age-related macular degeneration 3.4×10-5 22694956 (PMID) GRASP2 nonQTL
Neuroblastoma 3.8×10-5 pha002895 (dbGaP) dbGaP via SNiPA
Neuroblastoma (brain cancer) 3.8×10-5 21124317 (PMID) GRASP2 nonQTL
Multiple sclerosis, age of onset 5.4×10-5 19010793 (PMID) GRASP2 nonQTL
Gene expression of SKIV2L [probe 2902884] in peripheral blood mononuclear cells 4.5×10-4 19222302 (PMID) GRASP2 eQTL