Table 3.

Functional annotation of candidate SNPs from significant regions

SNP	ID	case-only	CADD	RegulomeDB
POS	SNP	P	PHREDa	Function annotation	Probabilityb
17:49639139:G:A	rs17662871	4.29×10−8	2.534	TF binding or DNase peak	0.49
20:15642704:G:A	rs76314075	1.33×10−7	1.445	Other	0.18
20:15644218:T:C	rs79942605	2.81×10−8	8.228	TF binding or DNase peak	0.04
21:18776825:C:T	rs208900	5.87×10−6	0.668	TF binding or DNase peak	0.13
21:18779654:G:A	rs184089	5.79×10−6	1.066	Motif hit	0.48
21:18783833:G:A	rs11088636	4.24×10−6	0.039	Other	0.18
21:18784296:T:C	rs423598	4.78×10−6	2.243	TF binding or DNase peak	0.13
21:18785818:G:A	rs208908	4.54×10 −8	5.773	TF binding or DNase peak	0.92
21:18787462:T:C	rs208914	5.01×10−6	2.944	TF binding + DNase peak	0.61
21:18787572:T:C	rs9637031	1.34×10−7	4.018	TF binding + DNase peak	0.61
21:18787948:A:G	rs6517771	1.76×10−6	5.095	Motif hit	0.34
21:18788445:A:C	rs1389157	1.30×10−6	6.257	TF binding or DNase peak	0.03

SNPs with case-only joint P-value <1×10⁻⁵ were selected for annotation analysis. eQTL displayed the information from GTEx Portal. The annotation information for rs208908 was bolded.

^aScaled CADD score by expressing the rank in order of magnitude terms.

^bRegulomeDB probability score is ranging from 0 to 1, with 1 being most likely to be a regulatory variant.