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Table 1 Overview of the nine autoimmune diseases (AIDs) included in this study

From: Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity

Autoimmune disease Number of Immunochip top SNPs 1000 genomes pilot project HapMap 3 SNP 500 kb Number of genes (Gencode version 14)  
SNPs found Proxy SNPs (r2= 1) Average locus size (bp) SNPs found Average locus size (bp) SNPs found Locus size (bp) Protein-coding lncRNA Reference
CD 29 29 338 123,953 - - - - 50 14 [45]
CeD 32 30 246 125,799 - - 2 1,000,000 127 37 [44]
IBD (shared) 97 95 984 139,174 2 172,626 2 1,000,000 254 107 [45]
JIA 16 15 112 152,964 - - 1 1,000,000 73 20 [46]
PBC 18 16 143 176,717 1 859,903 2 1,000,000 90 38 [47]
PS 33a 32 287 111,617 - - 1 1,000,000 131 48 [48]
PsCh 12 12 81 227,273 - - - - 50 17 [49]
RA 26 23 132 96,343 - - 3 1,000,000 127 36 [50]
UC 22 22 198 127,674 - - - - 48 24 [45]
Total 285 274 2,521 142,390 3 516,265 11 1,000,000 950 341  
  1. CD, Crohn's disease-specific; CeD, celiac disease; IBD (shared), inflammatory bowel disease shared by Crohn's disease and ulcerative colitis; JIA, juvenile idiopathic arthritis; PBC, primary biliary cirrhosis; PS, psoriasis; PsCh, primary sclerosing cholangitis; RA, rheumatoid arthritis; UC, ulcerative colitis-specific. Each disease is characterized by the number of genome-wide significant SNPs associated with the disease phenotype, the number of disease loci, and the genes located inside them. We subdivided inflammatory bowel disease loci into Crohn's disease-specific loci (CD), ulcerative colitis-specific loci (UC), and CD-UC shared loci (IBD shared) to reveal phenotype-specific features. aPsoriasis (PS) was associated with 33 genome-wide significant SNPs. After defining the PS disease loci, we discovered that one locus (chr.19: 10,745,764-10,894,728) is located within a bigger 1 Mb locus (chr.19: 9,963,118-10,963,118), resulting in 32 PS loci and making the total number of AID loci 284. In summary, the total number of AID-associated SNPs was 285 and these led to 284 AID loci. After all the disease loci annotation with genes from the reference dataset (Gencode version 14), we discovered 950 protein-coding genes in total but 186 of them were shared between at least two disease phenotypes (AID-shared coding genes) and 626 were unique across all diseases (AID-coding genes). For lncRNAs, the total number of genes was 341, with 61 shared (AID-shared lncRNAs) and 240 unique genes (AID-lncRNAs).
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