Table 5 Comprehensive annotation of SNPs in strong LD (r2 > 0.8) with rs10499194.

From: TNFAIP3 genetic polymorphisms reduce ankylosing spondylitis risk in Eastern Chinese Han population

CHR

BP

SNP

r 2

A1

A2

Gene

Position

H3K4ME3a

H3K4ME1a

H3K27ACa

Regulome DBb

Weighted _PINESc

6

138002061

rs77027760

0.86

A

G

TNFAIP3

intergenic

T

T

T

3a

0.030

6

138002637

rs10499194

1

T

C

TNFAIP3

intergenic

T

T

T

4

0.184

6

138004508

rs142761146

0.86

A

T

TNFAIP3

intergenic

   

5

0.851

6

138004568

rs80351603

1

A

G

TNFAIP3

intergenic

   

6

0.851

6

138005428

rs13205649

1

G

C

TNFAIP3

intergenic

   

6

0.503

6

138008679

rs66499821

1

C

T

TNFAIP3

intergenic

 

T

 

6

0.564

6

138009900

rs34654849

0.91

T

C

TNFAIP3

intergenic

 

T

T

No Data

0.364

6

138011151

rs12525643

1

G

A

TNFAIP3

intergenic

   

No Data

0.150

  1. BP: base position; A1: effective allele; A2: reference allele; T: True, own the specific histone modification.
  2. ahistone modifications were derived from Primary mononuclear and T cells from peripheral blood (Roadmap Epigenomics Consortium, http://www.roadmapepigenomics.org/);
  3. bRegulome DB (http://www.regulomedb.org/) annotated SNPs with known and predicted regulatory elements in the intergenic region. The scores refer to the possible regulatory function of a SNP, 3a:TF binding, any motif and DNase peak; 4:TF binding and DNase peak; 5:TF binding or DNase; 6:other function;
  4. cPINES (http://genetics.bwh.harvard.edu/pines) provided a powerful in silico method to prioritize and fine map functional noncoding variants. SNPs with lower P values indicated more abundant function.
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