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 |