Protein Dossier — LY9 (T-lymphocyte surface antigen Ly-9)
MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
1. Published MR estimates (retrieved, not computed)
| Outcome |
beta |
se |
p |
method |
nSNP |
cis/trans |
coloc |
| Inflammatory bowel disease |
0.105 |
0.0256 |
4.04e-05 |
Wald ratio |
1 |
cis |
NA |
| Ulcerative colitis |
0.125 |
0.0321 |
9.83e-05 |
Wald ratio |
1 |
cis |
NA |
| Clear cell ovarian cancer |
-0.392 |
0.107 |
2.57e-04 |
Wald ratio |
1 |
cis |
NA |
| Multiple sclerosis |
0.128 |
0.0411 |
0.00182 |
Wald ratio |
1 |
cis |
NA |
| Crohn’s disease |
0.0906 |
0.031 |
0.00343 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: psoriasis |
0.137 |
0.0501 |
0.00615 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: high cholesterol |
0.0358 |
0.0159 |
0.0244 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
0.0993 |
0.045 |
0.0273 |
Wald ratio |
1 |
cis |
NA |
| Fractured bone site(s): Other bones |
-0.0559 |
0.0281 |
0.0465 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hayfever or allergic rhinitis |
-0.0513 |
0.0264 |
0.0519 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: depression |
0.0464 |
0.024 |
0.0532 |
Wald ratio |
1 |
cis |
NA |
| Putamen volume |
27.4 |
15 |
0.0688 |
Wald ratio |
1 |
cis |
NA |
| …and 64 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3324_51_1 |
LY9 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
70 association rows across 27 traits (68 genome-wide significant rows). Associations are loci, not causal claims; the mapped gene at a locus is not necessarily the effector gene.
| Trait |
best p |
lead SNP |
n assoc |
study |
MR status |
| Circulating LY9 levels |
2e-1425 |
rs12405457 |
5 |
GCST90860013 |
no MR -> candidate analysis |
| ICAM3/LY9 protein level ratio |
4e-781 |
rs535241 |
1 |
GCST90315121 |
no MR -> candidate analysis |
| Circulating SLAMF7 levels |
8e-686 |
rs67841898 |
1 |
GCST90859745 |
no MR -> candidate analysis |
| LY9 protein levels |
9e-214 |
rs35759983 |
10 |
GCST90469824 |
no MR -> candidate analysis |
| T-lymphocyte surface antigen Ly-9 levels |
3e-161 |
rs12128261 |
6 |
GCST90249898 |
no MR -> candidate analysis |
| Hematological traits (multi-trait analysis) |
2e-92 |
rs556753 |
3 |
GCST90838667 |
no MR -> candidate analysis |
| Serum levels of protein LY9 |
4e-51 |
rs6659569 |
1 |
GCST90088316 |
no MR -> candidate analysis |
| SLAMF7 protein levels |
7e-49 |
rs139428867 |
6 |
GCST90470651 |
no MR -> candidate analysis |
| Lymphocyte count |
6e-46 |
rs494091 |
6 |
GCST90002316 |
no MR -> candidate analysis |
| CD48 protein levels |
2e-43 |
rs41266925 |
7 |
GCST90468635 |
no MR -> candidate analysis |
| Lymphocyte count (UKB data field 30120) |
6e-39 |
rs494091 |
1 |
GCST90468082 |
no MR -> candidate analysis |
| Blood protein levels |
5e-34 |
rs540254 |
2 |
GCST006585 |
no MR -> candidate analysis |
| …and 15 more traits (see JSON) |
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4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 147 total). Associations are loci, not causal claims. The causal-status column is a four-state triage per pair: established (curated) = a curated clinical assertion exists (ClinGen/G2P/GEL/Orphanet/ClinVar — any validity level, MR adds little); exploratory rare-variant signal = ExWAS burden evidence without curation — a candidate NEW gene-disease relationship; common-variant locus = GWAS signal, classic pQTL-MR territory; multi-layer = burden+GWAS together, an allelic-series candidate (the strongest causal setup). Burden estimand is carrier-vs-noncarrier, not per-SD MR.
| Disease |
genetic assoc. |
burden (ExWAS) |
causal status |
MR status |
| CINCA syndrome |
0.304 |
— |
established (curated) |
no MR -> candidate analysis |
Of the 1 rows above, 1 have no MR estimate in this resource. Across all retrieved diseases for this gene: 0 exploratory rare-variant signal(s), 0 multi-layer (allelic-series candidate) pair(s). Final triage still belongs to a statistical geneticist.
5. Downstream annotation (druggability & safety preview)
| Layer |
Result |
| ChEMBL druggability |
2 known modulators (SLAM family member 7) |
| gnomAD constraint |
pLI=8.3e-19, LOEUF=1.13 — LoF-tolerant |
| GWAS Catalog |
135 unique SNPs / 320 rows |
| ClinVar |
135 records; 2 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 147 associated diseases by overall score. genetic_association aggregates GWAS common-variant AND rare-variant evidence. These are ASSOCIATIONS (loci), not causal claims.chembl — ChEMBL target matched by text search on ‘LY9’ and resolved to ‘SLAM family member 7’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 135 ClinVar records for this gene; it is a sample, not a rate.pharmgkb — No PharmGKB/ClinPGx clinical annotations (gene may not be a pharmacogene).gwas_traits — Top 20 of 27 traits by best p-value, aggregated from 70 association rows. These are GWAS ASSOCIATIONS (loci), not causal claims; mapped genes at a locus are not necessarily the effector gene.
Sources
uniprot: https://www.uniprot.org/uniprotkb/Q9HBG7 — UniProt release 2026_02 (10-June-2026)mr_outcomes: https://epigraphdb.org/pqtl/ — EpiGraphDB pQTL MR (Zheng et al., Nat Genet 2020) — pre-computed two-sample MR; retrieved, not computed by this agent; EpiGraphDB build 1.0, pQTL dataset v3.0phenome: https://platform.opentargets.org/target/ENSG00000122224/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL3559386/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/LY9 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LY9 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LY9%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LY9 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:39:23 · Tier: A
- Fully mechanical: every cell above is rendered from tool return values. No language model wrote any part of this dossier.
- MR estimates, where present, are retrieved from published work (EpiGraphDB pQTL, Zheng et al. Nat Genet 2020); nothing is computed here.
- Tool errors this run: none