I had a question about the CFS dataset and I wondered if you could help. I am interested to look at the CRP and IL6 genotype data included with the study for a recall x genotype type design, but I am somewhat confused about what the variable names mean in terms of genetic data.
For example, there are variables called snp_crp01919 and snp_il6_07592. I am trying to cross-reference these with published GWAS for CRP/IL6 but the variable names don’t seem to correspond to standard rs – type names that are given to snps e.g. supplementary table 5 in https://www.nature.com/articles/s41467-022-29650-5
Is there information available about how the snp variables in CFS are named? Thanks!
These are old SNP labels- you may need to match to OmniExpress / Affy 6 data in dbGaP.
The IL6 variables are as follows:
phv00124108.v1.p1 snp_crp05237 5237A/G rs2808630 PMID: 17164456
phv00124111.v1.p1 snp_crp03872 3872G/A rs1205 PMID: 17164456
phv00124114.v1.p1 snp_crp02667 2667G/C rs1800947 PMID: 17164456
phv00124117.v1.p1 snp_crp01919 1919A/T rs1417938 PMID: 17164456
phv00124120.v1.p1 snp_il6_07592 IL6–7592 rs1818879 PMC3078635
phv00124123.v1.p1 snp_il6_1111 IL6–1111 rs1800796 PMC3078635
phv00124126.v1.p1 snp_il6_1510 IL‐6–1510 rs1800795 PMC3078635
phv00124129.v1.p1 snp_il6_2892 IL6–2892 rs2069837 PMC3078635
phv00124132.v1.p1 snp_il6_3572 IL6–3572 rs1554606 PMC3078635
phv00124135.v1.p1 snp_il6_6021 IL6–6021 rs2069849 PMC3078635
Thanks! This is exactly the information I was looking for