Table 4 Candidate allele-specific regulatory variants identified

From: Gene regulatory activity associated with polycystic ovary syndrome revealed DENND1A-dependent testosterone production

Variant position

rsID

Effect size

MAF

Posterior probability

Overlap with orthogonal genomic data

eQTL gene

chr9:123399942

rs4466467

0.56

0.096

0.97

DNase-seq

CRB2

chr9:123356770

rs10985986

1.32

0.226

0.96

pELS

CRB2

chr9:123930320

rs10117455

0.71

0.312

0.99

ATAC-seq

DENND1A

chr9:123930321

rs10120705

0.73

0.311

0.98

ATAC-seq

DENND1A

chr9:123922454

rs28441318

1.66

0.102

0.96

ATAC-seq

DENND1A

chr9:123708987

rs73665345

1.24

0.183

0.95

dELS

DENND1A

chr9:123679118

rs10760295

0.77

0.454

0.91

dELS

DENND1A

chr9:123281731

rs10760271

0.81

0.237

0.91

dELS

RABGAP1

chr9:123338729

rs10114139

0.73

0.435

0.91

dELS

STRBP

chr9:123358280

rs62579936

1.30

0.104

0.91

dELS

STRBP, CRB2

chr9:123359685

rs10156609

1.57

0.104

0.99

pELS

STRBP, CRB2

chr9:123391031

rs2491351

0.79

0.471

0.97

dELS

STRBP,CRB2, DENND1A

  1. The effect size is measured using the BIRD model (see methods). MAF = minor allele frequency. Posterior probability is the probability of that variant being a regulatory element. Overlap with orthogonal genomic data indicates whether that variant is present in open chromatin as measured by ATAC-seq or DNase-seq, in proximal enhancer like elements (pELS) or distal enhancer like elements (dELS) from ENCODE. The eQTL gene are the gene(s) that variant is associated with as an eQTL from GTEx data.
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