Chr:position (hg38) SNP ID Risk allele Odds Ratio GWAS
Chr:position (hg38) SNP ID Risk allele Odds Ratio GWAS
p-value Nearest gene
19:50374423 rs35463555 A 1.1 1.9 x 10-13 NR1H2
INCLUDEPICTURE "https://lh7-us.googleusercontent.com/docsz/AD_4nXeQ0dBM9nVU71NdPl3sAoKzUoNBfA7Hel0TR0ja4ukdmZndt2vRa_hc-YBWNzThu6ol6ZPO0oP-DboD0Acz0nzectQiqHCg8VtPkrBxGkmR4ohQZ3HolrAwARMZmZmIy3LAizGgz5JTrIXgNJ35ZywMmpE0?key=sSLC-oKaynUKHEd_PfT3mw" * MERGEFORMATINET
hg38 Human: Gene Expression in 54 tissues from GTEx RNA-seq of 17382 samples, 948 donors (V8, Aug 2019) (NR1H2)
Highest median expression: 143.90 TPM in Artery - Tibial
Description: Homo sapiens nuclear receptor subfamily 1 group H member 2 (NR1H2), transcript variant 1, mRNA.
INCLUDEPICTURE "https://lh7-us.googleusercontent.com/docsz/AD_4nXeBeA0ML--Ck-Q1tW2lg0iR5zEoqDjC68e66SKXb4tIqhO8ufvZTAiTcp9bBeIctdM2RFEEnARMqkeRrJTQR3M3khCGhdKJQgFNtmuZh3sE6T95L-qndjvsUHJkg34fu38CQAF7i8dswHADTi9hHei14Fxe?key=sSLC-oKaynUKHEd_PfT3mw" * MERGEFORMATINET
Non coding region inbetween genes
dbSNP: rs35463555Position: chr19:50374423-50374423Band: 19q13.33
Genomic Size: 1
View DNA for this feature (hg38/Human)
Reported region: 19q13.33
Publication: Pairo-Castineira E et al. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature. 2023-05-17
Disease or trait: COVID-19 (critical illness vs population)
Initial sample size: 682 African ancestry cases, 2,540 African ancestry controls, 401 East Asian ancestry cases, 759 East Asian ancestry controls, 13,199 European ancestry cases, 745,011 European ancestry controls, 1,141 South Asian ancestry cases, 5,384 South Asian ancestry controls, 8,779 cases, 1,001,875 controls
Replication sample size: NA
Reported gene(s): Not reportedStrongest SNP-Risk allele: rs35463555-A
dbSNP build 144 observed alleles for rs35463555: A/G
Risk Allele Frequency: 0.32
p-Value: 2E-13
Odds Ratio or beta: 1.1
95% confidence interval: [1.07-1.13]
Platform: Illumina [Not reported] (imputed)
Copy Number Variant (CNV)?: No
Part 2a Forming the Argument
You will use the outcome of a GWAS and the UCSC Genome Browser to consider how genetic variability in the human genome is linked to the immune disease you are reporting on. In forming your argument, you will be expected to consider linkage disequilibrium (LD), chromatin structure (ENCODE annotation), single-cell RNA sequencing (scRNAseq), and eQTLs.
Using data from an appropriate GWAS study, one or more figures generated from the UCSC Genome Browser clearly and concisely use information on LD, ENCODE annotation, scRNAseq, and eQTL to identify a gene that contributes to some aspect of innate or adaptive
Data used to backup claim will be GWAS, Eqtl, linkage equilibrium, chromatin structure, scRNAseq graphs/data
Use UCSC genome browser to find themUsing data from an appropriate GWAS study, one or more figures generated from the UCSC Genome Browser clearly and concisely use information on LD, ENCODE annotation, scRNAseq, and eQTL to identify a gene that contributes to some aspect of innate or adaptive immune cell activation.
Use Vancouver style referencing
Word limit: 500
