Additional file 1 of Functional characterisation of the amyotrophic lateral sclerosis risk locus GPX3/TNIP1

Additional file 1: Supplementary Tables. Table S1: Significant risk loci detected from ALS case-control GWAS. Table S2: Lead SNPs identified from independent significant SNPs of ALS GWAS. Table S3: Independent significant SNPs at r2 < 0:6 identified from ALS GWAS. Table S4: FUMA identifies 92 genes (ALS GWAS). Table S5: Prioritized genes from ALS GWAS by functional mapping. Table S6: FUMA annotation pathway categories. Table S7: S-LDSC annotation categories enriched in ALS GWAS. Table S8: S-LDSC cell-type categories enriched in ALS GWAS. Table S9: GCTA-COJO analyses. Table S10: GCTA-COJO analysis conditioned based on lead SNP (rs10463311) and different co-linearity thresholds. Table S11: FUMA chromatin interactions. Table S12: SMR results for GPX3, TNIP1 and C9orf72. Table S13: SMR significant genes. Table S14: Brain eQTL SMR results to follow-up significant genes in blood eQTL data. Table S15: The top GWAS and SMR chromosome 5 SNPs in brain expression datasets. Table S16: Significantly associated genes using TWAS models elastic net and CONTENT models. Table S17: Significantly associated genes using TWAS models elastic net and CONTENT models for each identified tissue. Table S18: TWAS CONTENT full model with significantly expressed GPX3 or TNIP1 in relevant tissue types. Table S19: Gene correlation in 48 GTEx tissues. Table S20: Gene correlation of 16 ALS genes in 45 GTEx tissues. Table S21: Top two prioritized candidates per chromosome in ALS GWAS using PoPS. Table S22: Platforms used for microarray ALS and control samples and genotype counts. Table S23: Morpholino (MO) abnormalities after injection of GPX3-knock-down mRNA were no different from controls or non-injected MO. Table S24: No severe motor abnormalities in zebrafish morpholinos (MO) with increasing GPX3 mRNA.