Supplementary Materials

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Towfique Raj, Katie Rothamel, Sara Mostafavi, Chun Ye, Mark N. Lee, Joseph M. Replogle, Ting Feng, Michelle Lee, Natasha Asinovski, Irene Frohlich, Selina Imboywa, Alina Von Korff, Yukinori Okada, Nikolaos A. Patsopoulos, Scott Davis, Cristin McCabe, Hyun-il Paik, Gyan P. Srivastava, Soumya Raychaudhuri, David A. Hafler, Daphne Koller, Aviv Regev, Nir Hacohen, Diane Mathis, Christophe Benoist, Barbara E. Stranger, Philip L. De Jager

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S25
  • Tables S1 to S3, S10, S15, and S18
  • Full Reference List
Table S4
Significant cis-eQTLs at FDR 0.05 in CD4+T-cells of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman's rho, -log10 (P-value) and P-value are reported.
Table S5
Significant cis-eQTLs at FDR 0.05 in CD4+T-cells of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman's rho, -log10 (P-value) and P-value are reported.
Table S6
Significant cis-eQTLs at FDR 0.05 in CD4+T-cells of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman's rho, -log10 (P-value) and P-value are reported.
Table S7
Significant cis-eQTLs at FDR 0.05 in monocytes of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman’s rho, -log10 (P-value) and P-value are reported.
Table S8
Significant cis-eQTLs at FDR 0.05 in monocytes of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman’s rho, -log10 (P-value) and P-value are reported.
Table S9
Significant cis-eQTLs at FDR 0.05 in monocytes of European-American, East Asian and African-American subjects. All significant SNPs (within 1MB of TSS of a gene), SNP chromosome, gene chromosome, physical position of each SNP, TSS of each gene (largest transcript), distance from SNP to TSS, Spearman’s rho, -log10 (P-value) and P-value are reported.
Table S11
Meta-analysis cis-eQTLs at FDR 0.05 in Monocytes. The best cis-SNP associated with each gene expression is reported, including effect size estimates, standard error of the effect size and P-values.
Table S12
Meta-analysis cis-eQTLs at FDR 0.05 in CD4+ T-cells. The best cis-SNP associated with each gene expression is reported, including effect size estimates, standard error of the effect size and P-values.
Table S13
Significant trans-eQTLs in monocytes from meta-analysis. All SNP-gene pairs at Bonferroni corrected P-value is reported, including effect size estimates, standard error of the effect size and P-values.
Table S14
Significant trans-eQTLs in CD4+T from meta-analysis. All SNP-gene pairs at Bonferroni corrected P-value is reported, including effect size estimates, standard error of the effect size and P-values.
Table S16
GWAS SNPs with significant cis-regulatory effects in monocytes. GWAS index SNP, effect size estimates (β), standard error of the effect size, meta-analysis P-value and disease/trait.
Table S17
GWAS SNPs with significant cis-regulatory effects in CD4+ T-cells. GWAS index SNP, effect size estimates (β), standard error of the effect size, meta-analysis P-value and disease/trait.
Table S19
Autoimmune disease-associated SNPs with significant cis-regulatory effects. GWAS index SNP, best proxy SNP (LD: r2 > 0.8), effect size estimates (β), standard error of the effect size, meta-analysis P-value, disease, and cell type.