Table 2.
List of key variants or risk allele associated with Vitamin D level as reported by the GWAS catalog.
| Number | SNP | Reported gene | Region | Location | Functional class | Reported trait | References |
|---|---|---|---|---|---|---|---|
| 1 | rs3755967-T | *GC (Group Specific Component) | 4q13.3 | 4:71743681 | Intron variant | Vitamin D levels | (96) |
| 2 | rs4588-T | GC (Group Specific Component) | 4q13.3 | 4:71752606 | Missense_variant | Vitamin D levels | (97) |
| 3 | rs2282679-T | GC (Group Specific Component) | 4q13.3 | 4:71742666 | Intron_variant | Vitamin D levels (dietary vitamin D intake interaction) | (96) |
| 4 | rs705117-G | GC (Group Specific Component) | 4q13.3 | 4:71742398 | Intron_variant | Serum vitamin D-binding protein levels | (98) |
| 5 | rs7041-T | GC (Group Specific Component) | 4q13.3 | 4:71752617 | Missense_variant | Serum vitamin D binding protein levels | (98) |
| 6 | rs2282679 | GC (Group Specific Component) | 4q13.3 | 4:71742666 | Intron_variant | Vitamin D insufficiency | (92) |
| 7 | rs1607741-C | GC (Group Specific Component) | 4q13.3 | 4:71853316 | Intergenic_variant | Vitamin D levels | (97) |
| 8 | rs2282679-C | GC (Group Specific Component) | 4q13.3 | 4:71742666 | Intron_variant | Vitamin D levels | (99) |
| 9 | rs79761689-C | GC (Group Specific Component) | 4q13.3 | 4:72005565 | Intergenic_variant | Vitamin D levels | (97) |
| 10 | rs2282679-? | GC (Group Specific Component) | 4q13.3 | 4:71742666 | Intron_variant | Vitamin D levels | (100) |
| 11 | rs17467825-A | GC (Group Specific Component) | 4q13.3 | 4:71739800 | Downstream_gene_variant | Vitamin D levels | (101) |
| 12 | rs1155563-C | GC (Group Specific Component) | 4q13.3 | 4:71777771 | Intron_variant | Vitamin D levels | (101) |
| 13 | rs4588-A | GC (Group Specific Component) | 4q13.3 | 4:71752606 | Missense_variant | Serum 25-Hydroxyvitamin D levels | (102) |
| 14 | rs116970203-A | CYP2R1 (Vitamin D 25-hydroxylase) | 11p15.2 | 11:14855172 | Intron_variant | Vitamin D levels | (97) |
| 15 | rs10741657-A | CYP2R1 (Vitamin D 25-hydroxylase) | 11p15.2 | 11:14893332 | Upstream_gene_variant | Vitamin D levels | (96) |
| 16 | rs10741657-? | CYP2R1 (Vitamin D 25-hydroxylase) | 11p15.2 | 11:14893332 | Upstream_gene_variant | Vitamin D insufficiency | (92) |
| 17 | rs2060793-A | CYP2R1(Vitamin D 25-hydroxylase) | 11p15.2 | 11:14893764 | Upstream_gene_variant | Vitamin D levels | (99) |
| 18 | rs117913124-A | CYP2R1 (Vitamin D 25-hydroxylase) | 11p15.2 | 11:14879385 | Synonymous_variant | Serum 25-Hydroxyvitamin D levels | (102) |
| 19 | rs17216707-T | CYP24A1 (1,25-dihydroxyvitamin D(3) 24-hydroxylase) | 20q13.2 | 20:54115823 | Regulatory_region_variant | Vitamin D levels | (96) |
| 20 | rs6127099-T | CYP24A1 (1,25-dihydroxyvitamin D(3) 24-hydroxylase) | 20q13.2 | 20:54114863 | Intergenic_variant | Vitamin D levels | (97) |
| 21 | rs12785878-T | NADSYN1/DHCR7 (7-dehydrocholestrol reductase) | 11q13.4 | 11:71456403 | Intron_variant | Vitamin D levels | (96) |
| 22 | rs12785878-? | NADSYN1 (7-dehydrocholestrol reductase) | 11q13.4 | 11:71456403 | Intron_variant | Vitamin D insufficiency | (92) |
| 23 | rs4423214-T | NADSYN1(7-dehydrocholestrol reductase) | 11q13.4 | 11:71462208 | Intron_variant | Vitamin D levels | (97) |
| 24 | rs4944062-T | NADSYN1(7-dehydrocholestrol reductase) | 11q13.4 | 11:71476248 | 3_prime_UTR_variant | Vitamin D levels (dietary vitamin D intake interaction) | (96) |
| 25 | rs3829251-A | NADSYN1 (7-dehydrocholestrol reductase) | 11q13.4 | 11:71483513 | Intron_variant | Vitamin D levels | (99) |
| 26 | rs182244780-A | RRAS2 (RAS related 2) | 11p15.2 | 11:14363985 | Intron_variant | Vitamin D levels | (97) |
| 27 | rs12287212-A | RRAS2 (RAS related 2) | 11p15.2 | 11:14428315 | Intergenic_variant | Vitamin D levels | (101) |
| 28 | rs11023332-C | PDE3B (phosphodiesterase 3B) | 11p15.2 | 11:14762564 | Intron_variant | Vitamin D levels | (101) |
| 29 | rs1007392-A | PDE3B (Phosphodiesterase 3B) | 11p15.2 | 11:14753045 | Intron_variant | Vitamin D levels | (101) |
| 30 | rs117300835-A | CALCB/INSC (Calcitonin Related Polypeptide Beta) | 11p15.2 | 11:15097429 | Intergenic_variant | Vitamin D levels | (97) |
| 31 | rs55665837-T | COPB1(Coatomer Protein Complex Subunit Beta 1) | 11p15.2 | 11:14473503 | Intron_variant | Vitamin D levels | (97) |
| 32 | rs148189294-A | SLC4A4(Sodium bicarbonate cotransporter 1) | 4q13.3 | 4:71575200 | Downstream_gene_variant | Vitamin D levels | (97) |
| 33 | rs117865811-G | SPON1(Spondin 1) | 11p15.2 | 11:14180763 | Intron_variant | Vitamin D levels | (97) |
| 34 | rs138485827-T | NPFFR2/ADAMTS3 (Neuropeptide FF Receptor2)/(A disintegrin and metalloproteinase with thrombospondin motifs 3) | 4q13.3 | 4:72166226 | Intergenic_variant | Vitamin D levels | (97) |
| 35 | rs78862524-A | ADAMTS3 (A disintegrin and metalloproteinase with thrombospondin motifs 3) | 4q13.3 | 4:72305473 | Intron_variant | Vitamin D levels | (97) |
| 36 | rs8018720-C | SEC23A | 14q21.1 | 14:39086981 | Missense_variant | Vitamin D levels | (96) |
| 37 | rs3819817-T | HAL (Histidine ammonia-lyase) | 12q23.1 | 12:95984993 | Intron_variant | Vitamin D levels | (97) |
| 38 | rs185378533-G | FLJ42102 (Uncharacterized LOC399923) | 11q13.4 | 11:71422087 | Intron_variant | Vitamin D levels | (97) |
| 39 | rs2207173-G | CYB5AP4(Cytochrome B5 Type A Pseudogene 4) | 20p11.21 | 20:22824423 | Intergenic_variant | Vitamin D levels | (103) |
| 40 | rs2277458-G | GEMIN2 (Gem Nuclear Organelle Associated Protein 2) | 14q21.1 | 14:39114277 | 5_prime_UTR_variant | Vitamin D levels | (97) |
| 41 | rs10745742-T | AMDHD1(Amidohydrolase Domain Containing 1) | 12q23.1 | 12:95964751 | Intron_variant | Vitamin D levels (dietary vitamin D intake interaction) | (96) |
| 42 | rs12868495-A | VDAC1P12(Voltage dependent anion channel 1 pseudogene 12) | 13q13.2 | 13:34067425 | Intergenic_variant | Vitamin D levels | (101) |
| 43 | rs12144344-T | ST6GALNAC3(ST6 N-Acetylgalactosaminide Alpha-2,6-Sialyltransferase 3) | 1p31.1 | 1:76373851 | Intron_variant | Serum Vitamin D-binding protein levels | (98) |
| 44 | rs11586313-G | IVL (Involucrin) | 1q21.3 | 1:152917994 | TF_binding_site_variant | Vitamin D levels | (103) |
| 45 | rs6730714-A | PAX3 (Paired box gene 3) | 2q36.1 | 2:222184302 | Intergenic_variant | Vitamin D levels | (101) |
| 46 | rs156299-G | NPY (Neuropeptide Y) | 7p15.3 | 7:24185113 | Intergenic_variant | Vitamin D levels | (101) |
| 47 | rs2302190-C | MTMR4(Myotubularin Related Protein 4) | 17q22 | 17:58507147 | Missense_variant | Vitamin D levels | (101) |
| 48 | rs10508196-A | FAM155A (Family with sequence similarity 155 member A) | 13q33.3 | 13:107827618 | Intron_variant | Vitamin D levels | (101) |
| 49 | rs4751058-A | MKLN1 (Muskelin 1) | 10q26.3 | 10:129075861 | Intergenic_variant | Vitamin D levels | (101) |
*
GC gene codes for the Vitamin D binding protein (VDBP).