Original SNPs

Gene

Chromosome

Position

Reference allele

Other allele

African ancestry in Southwest USA (HapMap III) other allele frequency

Yoruba in Ibadan, Nigeria (HapMap III) other allele frequency

Source

Genotyped SNPs

r^2

Genotype platform

Comment/ Alt. snp name

rs1048691

CYP27B1

12

58152948

C

T

0.33

0.394

Haploview Tagger

rs1048691

650Y

rs10488854

GC

4

72624135

C

T

0.198

0.155

Haploview Tagger

rs10488854

Sequenom

rs10735810 /rs2228570

VDR

12

48272895

A

G

0.802

0.808

PharmGKB

rs2228570

Sequenom

FokI

rs10877012

CYP27B1

12

58162085

G

T

0.16

0.088

Haploview Tagger

rs10877012

Sequenom

rs10881578

RXRA

9

137232535

A

G

0.377

0.394

Haploview Tagger

rs10881578

Sequenom

rs10881582

RXRA

9

137256078

G

A

0.623

0.73

Haploview Tagger

rs10881582

650Y

rs11168266

VDR

12

48251533

C

T

0.528

0.673

Haploview Tagger

rs11168266

Sequenom

rs11168268

VDR

12

48251812

G

A

0.566

0.708

Haploview Tagger

rs11168268

Sequenom

rs11172327

CYP27B1

12

58161660

G

A

0.066

0.071

Haploview Tagger

rs8176353

Sequenom

rs11185649

RXRA

9

137228370

T

C

0.585

0.643

Haploview Tagger

rs11185649

Sequenom

rs11185659

RXRA

9

137243383

C

T

0.283

0.319

Haploview Tagger

rs11185659

650Y

rs1155563

GC

4

72643488

T

C

0.057

0.049

Haploview Tagger

rs1155563

650Y

Ahn et al. 2010

rs11568820

VDR

12

48302545

C

T

0.717

0.978

PharmGKB

rs11568820

Sequenom

Cdx2

rs11574114

VDR

12

48238883

C

T

0.151

0.226

Haploview Tagger

rs11574114

Sequenom

rs11574138

VDR

12

48235702

T

C

0.066

0.124

Haploview Tagger

rs11574138

Sequenom

rs11574143

VDR

12

48234917

C

T

0.132

0.08

Haploview Tagger

rs11574143

650Y

rs11829917

CYP27B1

12

58164455

G

A

0.123

0.124

Haploview Tagger

rs11829917

Sequenom

rs12308082

VDR

12

48252139

G

A

0.066

0.054

Haploview Tagger

rs12308082

Sequenom

rs12314197

VDR

12

48242722

A

G

0.245

0.217

Haploview Tagger

rs12314197

Sequenom

rs12339187

RXRA

9

137229327

A

G

0.206

0.221

Haploview Tagger

rs12339187

650Y

rs12348547

RXRA

9

137246262

T

C

0.123

0.168

Haploview Tagger

rs12348547

Sequenom

rs12351315

RXRA

9

137225103

A

T

0.689

0.788

Haploview Tagger

rs11185647

0.965

650Y

LD with SNP on original list

rs12640179

GC

4

72612687

C

G

0.085

0.081

Haploview Tagger

rs12640179

Sequenom