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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).