HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 387

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
granzyme A trans Discovery rs2853928 6:31,257,511 C/A 0.23 994 -0.363 0.051 3.4×10-12 -1.080 2×10-10 2.1×10-6
granzyme A trans Replication rs2853928 6:31,257,511 C/A 0.11 337 -0.230 0.093 0.014 -1.080 0.016 0.036

 

Regional association plots

 

Boxplots and histograms for top associations

Granzyme A (granzyme A)

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

Granzyme A (granzyme A)

Target (abbrv.) granzyme A
Target (full name) Granzyme A
Somalogic ID (Sequence ID) SL004298 (3440-7_2)
Entrez Gene Symbol GZMA
UniProt ID P12544
UniProt Comment
  • Abundant protease in the cytosolic granules of cytotoxic T-cells and NK-cells which activates caspase-independent cell death with morphological features of apoptosis when delivered into the target cell through the immunological synapse. It cleaves after Lys or Arg. Cleaves APEX1 after 'Lys-31' and destroys its oxidative repair activity. Cleaves the nucleosome assembly protein SET after 'Lys-189', which disrupts its nucleosome assembly activity and allows the SET complex to translocate into the nucleus to nick and degrade the DNA.
Pathway Interaction Database
  • IL12-mediated signaling events
Pathway Studio
  • CD8+ T-cell Activation
  • Cell Death Mediated by Cytotoxic Cells
  • Natural Killer Cell Activation

All locus annotations are based on the sentinel SNP (rs2853928) and 16 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


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Genes hit or close-by
eQTL genes
  • PSORS1C3 psoriasis susceptibility 1 candidate 3 (non-protein coding)
  • HLA-C major histocompatibility complex, class I, C
  • XXbac-BPG299F13.17
  • TCF19 transcription factor 19
  • HLA-B major histocompatibility complex, class I, B
  • VARS2 valyl-tRNA synthetase 2, mitochondrial
  • HCG27 HLA complex group 27 (non-protein coding)
  • PSORS1C2 psoriasis susceptibility 1 candidate 2
  • XXbac-BPG181B23.7
  • XXbac-BPG248L24.12
  • CCHCR1 coiled-coil alpha-helical rod protein 1
  • WASF5P WAS protein family, member 5, pseudogene
  • CYP21A1P cytochrome P450, family 21, subfamily A, polypeptide 1 pseudogene
  • DDX39B DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
  • PSORS1C1 psoriasis susceptibility 1 candidate 1
  • LINC00243
  • ATP6V1G2 ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2
  • XXbac-BPG248L24.13
  • MICA MHC class I polypeptide-related sequence A
  • MICB MHC class I polypeptide-related sequence B
  • TSSC4 tumor suppressing subtransferable candidate 4
  • TMEM154 transmembrane protein 154
  • FLOT1 flotillin 1
  • XRCC6 X-ray repair complementing defective repair in Chinese hamster cells 6
  • CD248 CD248 molecule, endosialin
  • CSF3R colony stimulating factor 3 receptor (granulocyte)
  • HCG22 HLA complex group 22
  • BAG6 BCL2-associated athanogene 6
  • C4B complement component 4B (Chido blood group)
  • TNXB tenascin XB

 

Results from other genome-wide association studies

Trait P Study Source
cg23656755 (chr1:230203067) 1.2×10-128 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg01620082 (chr3:125678431) 3.2×10-81 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06606381 (chr12:133084921) 1.8×10-76 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17862947 (chr12:133086950) 2.6×10-74 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in Alzheimer's disease cases and controls 4.8×10-60 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in temporal cortex in Alzheimer's disease cases and controls 5.8×10-56 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-G in liver 1.3×10-44 18462017 (PMID) GRASP2 eQTL
Height 8.3×10-35 25282103 (PMID) Supplemental file
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in non-Alzheimer's disease samples 3.8×10-30 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in cerebellum in Alzheimer's disease cases 5.5×10-29 22685416 (PMID) GRASP2 eQTL
CD4:CD8 lymphocyte ratio 2×10-28 20045101 (PMID) GWAS Catalog via SNiPA
Lymphocyte levels (CD4:CD8) 2.1×10-28 20045101 (PMID) GRASP2 nonQTL
Gene expression of HLA-C (probeID ILMN_2150787) in temporal cortex in Alzheimer's disease cases 3×10-28 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-C (probeID ILMN_2150787) in temporal cortex in non-Alzheimer's disease samples 3.7×10-27 22685416 (PMID) GRASP2 eQTL
cg10154826 (chr6:17601018) 2.2×10-25 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of TMEM154 in blood 1.8×10-24 21829388 (PMID) GRASP2 eQTL
Gene expression of HCG27 in blood 1.5×10-23 21829388 (PMID) GRASP2 eQTL
Total cholesterol 3.9×10-21 24097068 (PMID) Supplemental file
Lymphocyte levels (CD8) 6.2×10-21 20045101 (PMID) GRASP2 nonQTL
Differential exon level expression of HLA-C [probe 2948901] in brain cortex 1.2×10-20 19222302 (PMID) GRASP2 eQTL
cg02753903 (chr19:38943549) 2.2×10-20 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Triglycerides 2.2×10-20 24097068 (PMID) Supplemental file
Gene expression of HLA-C [probe 2948887] in brain cortex 3.9×10-19 19222302 (PMID) GRASP2 eQTL
Gene expression of XRCC6 in blood 2.5×10-18 21829388 (PMID) GRASP2 eQTL
cg07408552 (chr17:40612019) 3×10-18 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17841099 (chr1:153940066) 7.5×10-18 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17169043 (chr6:170863821) 1.7×10-17 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948904] in peripheral blood mononuclear cells 9×10-16 19222302 (PMID) GRASP2 eQTL
cg07408989 (chr17:7116768) 1.3×10-15 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948901] in peripheral blood mononuclear cells 6×10-15 19222302 (PMID) GRASP2 eQTL
cg06419846 (chr11:66083721) 2.5×10-14 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948915] in peripheral blood mononuclear cells 7.4×10-14 19222302 (PMID) GRASP2 eQTL
Idiopathic membranous nephropathy 9.1×10-14 21323541 (PMID) GRASP2 nonQTL
cg01255021 (chr16:1094629) 1.4×10-13 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of hmm31752 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 1.6×10-13 17873874 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948915] in brain cortex 2.4×10-13 19222302 (PMID) GRASP2 eQTL
cg05496363 (chr11:66083790) 3.1×10-13 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of [probeset 2902222] in peripheral blood mononuclear cells 1×10-12 19222302 (PMID) GRASP2 eQTL
HIV-1 control 1.2×10-12 21051598 (PMID) GRASP2 nonQTL
cg10213762 (chr6:169284343) 1.4×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948918] in peripheral blood mononuclear cells 1.5×10-12 19222302 (PMID) GRASP2 eQTL
CCHCR1 gene expression 1.9×10-12 20045101 (PMID) GRASP2 nonQTL
Gene expression of CCHCR1 [probe 209698_at] in lymphoblastoid cell lines 1.9×10-12 17873877 (PMID) GRASP2 eQTL
Height tails (upper and lower 5th percentiles) 3.6×10-12 23563607 (PMID) GRASP2 nonQTL
cg22213242 (chr11:66083549) 6.6×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg03984502 (chr1:151805637) 7.2×10-12 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948897] in peripheral blood mononuclear cells 1.1×10-11 19222302 (PMID) GRASP2 eQTL
Gene expression of HLA-C in CEU-CHB-JPT-YRI lymphoblastoid cell lines 1.9×10-11 17873874 (PMID) GRASP2 eQTL
cg17329534 (chr1:154980719) 3.7×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HIV-1 control (viral load at set point) 4.4×10-11 20041166 (PMID) GRASP2 nonQTL
cg22379212 (chr19:38944024) 4.4×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Schizophrenia 4.4×10-11 25056061 (PMID) Supplemental file
cg18224038 (chr2:87042695) 8.5×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg21578195 (chr20:62168703) 9×10-11 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Immune control of HIV-1 viremia 9.1×10-11 20045101 (PMID) GRASP2 nonQTL
cg25652859 (chr20:57427388) 1×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg03407631 (chr6:52998845) 1.1×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-C [probe 2948887] in peripheral blood mononuclear cells 1.2×10-10 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-B [probe 2948952] in peripheral blood mononuclear cells 1.2×10-10 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948907] in peripheral blood mononuclear cells 1.5×10-10 19222302 (PMID) GRASP2 eQTL
cg19589727 (chr20:57427786) 1.6×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg15128876 (chr1:161146049) 1.8×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HLA-B gene expression in HIV-infected CD4+ T cells 2×10-10 20195503 (PMID) GRASP2 eQTL
cg11067179 (chr11:66083565) 2.4×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg12550496 (chr6:169284320) 2.5×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg15007120 (chr3:109128526) 3.2×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg24137511 (chr19:18260306) 3.3×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Methylation levels at chr6:31347249-31347299 [hg18 coord, probe cg10409680] in Temporal cortex 4×10-10 20485568 (PMID) GRASP2 meQTL
cg06065549 (chr20:57427419) 4.4×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Lupus erythematosus, systemic 5.2×10-10 pha002848 (dbGaP) dbGaP via SNiPA
Differential exon level expression of [probeset 2902222] in brain cortex 5.4×10-10 19222302 (PMID) GRASP2 eQTL
cg08127462 (chr1:153514240) 8.2×10-10 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19473529 (chr20:48726807) 1.2×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-C in Lymphoblastoid cell lines 1.3×10-9 19644074 (PMID) GRASP2 eQTL
Type 1 diabetes 1.8×10-9 17632545 (PMID) GRASP2 nonQTL
cg01949403 (chr22:36562378) 2.3×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg06099246 (chr16:1094837) 2.4×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg14564778 (chr20:57427532) 2.5×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HLA-B gene expression 2.5×10-9 20045101 (PMID) GRASP2 nonQTL
cg19808620 (chr1:153514466) 3.1×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Gene expression of HLA-C [probe ILMN_23822] in osteoblasts 3.5×10-9 19654370 (PMID) GRASP2 eQTL
Methylation levels at chr6:31347249-31347299 [hg18 coord, probe cg10409680] in Frontal cortex 3.6×10-9 20485568 (PMID) GRASP2 meQTL
Methylation levels at chr6:31538845-31538895 [hg18 coord, probe cg13784557] in Temporal cortex 7.3×10-9 20485568 (PMID) GRASP2 meQTL
cg06706159 (chr19:18260326) 7.9×10-9 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg25598890 (chr12:117501471) 1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg13210595 (chr1:167471288) 1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg12321149 (chr20:57427402) 1.1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
LDL cholesterol 1.4×10-8 24097068 (PMID) Supplemental file
cg27661264 (chr20:57427762) 1.8×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Methylation levels at chr6:31954925-31954975 [hg18 coord, probe cg07363637] in Temporal cortex 2×10-8 20485568 (PMID) GRASP2 meQTL
cg00236729 (chr10:62409841) 2×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17372758 (chr10:73976774) 2.5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22354132 (chr1:55273613) 3.1×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17414107 (chr20:57427854) 3.3×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg19640589 (chr20:57427997) 3.5×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg04232128 (chr5:138861217) 3.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22787191 (chr1:245524793) 3.8×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg20528838 (chr20:57427754) 3.9×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
HLA-C gene expression 4.4×10-8 17641165 (PMID) GRASP2 nonQTL
cg02042585 (chr6:160783761) 5.4×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17768600 (chr6:160783969) 6.7×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg18651192 (chr3:125677598) 7.4×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-C [probe 2948914] in brain cortex 7.9×10-8 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948904] in brain cortex 8.5×10-8 19222302 (PMID) GRASP2 eQTL
Gene expression of MICA in normal prepouch ileum 9.3×10-8 23474282 (PMID) GRASP2 eQTL
cg01817393 (chr20:57427618) 10×10-8 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg02976539 (chr17:72757278) 1.1×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg22900360 (chr10:72360348) 1.5×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg17051543 (chr10:135092265) 1.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Hip circumfence, adjusted for BMI 1.7×10-7 25673412 (PMID) Supplemental file
cg04257105 (chr20:57427689) 1.8×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg11011533 (chr17:3674625) 1.9×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg00262061 (chr3:39322751) 2×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg07105596 (chr20:57427496) 2×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-B [probe 2948958] in peripheral blood mononuclear cells 2.1×10-7 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948906] in brain cortex 2.5×10-7 19222302 (PMID) GRASP2 eQTL
cg02135077 (chr8:103820794) 2.5×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
cg10302550 (chr20:57427845) 2.5×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Differential exon level expression of HLA-B [probe 2948946] in peripheral blood mononuclear cells 3×10-7 19222302 (PMID) GRASP2 eQTL
Rheumatoid arthritis 3×10-7 17804836 (PMID) GRASP2 nonQTL
Gene expression of hmm31752 in CHB-JPT lymphoblastoid cell lines 3.2×10-7 17873874 (PMID) GRASP2 eQTL
Gene expression of HCG27 (probeID ILMN_1746436) in temporal cortex in Alzheimer's disease cases and controls 3.2×10-7 22685416 (PMID) GRASP2 eQTL
Waist-to-hip ratio, adjusted for BMI 3.3×10-7 25673412 (PMID) Supplemental file
Sarcoidosis 4.5×10-7 22952805 (PMID) GRASP2 nonQTL
Gene expression of HLA-B [probeset 211911_x_at] in sputum 6.3×10-7 21949713 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948893] in peripheral blood mononuclear cells 7.3×10-7 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948909] in peripheral blood mononuclear cells 1.2×10-6 19222302 (PMID) GRASP2 eQTL
Crohn's disease 1.3×10-6 Supplemental file
Bipolar disorder vs. Schizophrenia 2.5×10-6 24280982 (PMID) Supplemental file
HIV-1 seropositive nonprogression 2.9×10-6 19115949 (PMID) GRASP2 nonQTL
Hip circumfence 3×10-6 25673412 (PMID) Supplemental file
Gene expression of HCG27 (probeID ILMN_1746436) in cerebellum in Alzheimer's disease cases and controls 7.2×10-6 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948893] in brain cortex 7.4×10-6 19222302 (PMID) GRASP2 eQTL
Lung cancer 7.8×10-6 19836008 (PMID) GRASP2 nonQTL
HIV-1 control (viral load) 8.6×10-6 21490045 (PMID) GRASP2 nonQTL
Gene expression of ATP6V1G2///BAT1 in blood 9.9×10-6 21829388 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probe 2948918] in brain cortex 2.1×10-5 19222302 (PMID) GRASP2 eQTL
Multiple sclerosis 2.8×10-5 20598377 (PMID) GRASP2 nonQTL
Irritible bowel syndrome 3×10-5 18587394 (PMID) GRASP2 nonQTL
Differential exon level expression of HLA-C [probe 2948897] in brain cortex 3.8×10-5 19222302 (PMID) GRASP2 eQTL
Gene expression of HLA-C [probeset 214459_x_at] in sputum 4×10-5 21949713 (PMID) GRASP2 eQTL
Blood pressure 7.1×10-5 pha003050 (dbGaP) dbGaP via SNiPA
Gene expression of HCG27 (probeID ILMN_1746436) in cerebellum in Alzheimer's disease cases 9.7×10-5 22685416 (PMID) GRASP2 eQTL
Gene expression of HLA-C [probeset 208812_x_at] in sputum 1.3×10-4 21949713 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probeset 2948907] in brain cortex 2.1×10-4 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of HLA-C [probeset 2948897] in brain cortex 2.3×10-4 19222302 (PMID) GRASP2 eQTL
Waist-to-hip ratio 3.3×10-4 25673412 (PMID) Supplemental file