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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs2229829

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:47844824 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000366 (97/264690, TOPMED)
T=0.000756 (190/251442, GnomAD_exome)
T=0.000135 (19/140280, GnomAD) (+ 8 more)
T=0.000634 (77/121382, ExAC)
T=0.00013 (3/23408, ALFA)
T=0.00268 (45/16760, 8.3KJPN)
T=0.0018 (9/5008, 1000G)
T=0.0082 (24/2920, KOREAN)
T=0.0044 (8/1832, Korea1K)
G=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
VDR : Synonymous Variant
Publications
2 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 23408 G=0.99987 T=0.00013
European Sub 15886 G=1.00000 T=0.00000
African Sub 3540 G=1.0000 T=0.0000
African Others Sub 122 G=1.000 T=0.000
African American Sub 3418 G=1.0000 T=0.0000
Asian Sub 168 G=0.982 T=0.018
East Asian Sub 112 G=0.991 T=0.009
Other Asian Sub 56 G=0.96 T=0.04
Latin American 1 Sub 146 G=1.000 T=0.000
Latin American 2 Sub 610 G=1.000 T=0.000
South Asian Sub 98 G=1.00 T=0.00
Other Sub 2960 G=1.0000 T=0.0000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999634 T=0.000366
gnomAD - Exomes Global Study-wide 251442 G=0.999244 T=0.000756
gnomAD - Exomes European Sub 135386 G=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 49010 G=0.99616 T=0.00384
gnomAD - Exomes American Sub 34574 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6140 G=0.9997 T=0.0003
gnomAD - Genomes Global Study-wide 140280 G=0.999865 T=0.000135
gnomAD - Genomes European Sub 75944 G=1.00000 T=0.00000
gnomAD - Genomes African Sub 42062 G=1.00000 T=0.00000
gnomAD - Genomes American Sub 13664 G=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9943 T=0.0057
gnomAD - Genomes Other Sub 2152 G=0.9995 T=0.0005
ExAC Global Study-wide 121382 G=0.999366 T=0.000634
ExAC Europe Sub 73328 G=1.00000 T=0.00000
ExAC Asian Sub 25166 G=0.99694 T=0.00306
ExAC American Sub 11576 G=1.00000 T=0.00000
ExAC African Sub 10406 G=1.00000 T=0.00000
ExAC Other Sub 906 G=1.000 T=0.000
Allele Frequency Aggregator Total Global 23408 G=0.99987 T=0.00013
Allele Frequency Aggregator European Sub 15886 G=1.00000 T=0.00000
Allele Frequency Aggregator African Sub 3540 G=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 2960 G=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 G=0.982 T=0.018
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.99732 T=0.00268
1000Genomes Global Study-wide 5008 G=0.9982 T=0.0018
1000Genomes African Sub 1322 G=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 G=0.9911 T=0.0089
1000Genomes Europe Sub 1006 G=1.0000 T=0.0000
1000Genomes South Asian Sub 978 G=1.000 T=0.000
1000Genomes American Sub 694 G=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9918 T=0.0082
Korean Genome Project KOREAN Study-wide 1832 G=0.9956 T=0.0044
SGDP_PRJ Global Study-wide 2 G=0.5 T=0.5
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 12 NC_000012.12:g.47844824G>T
GRCh37.p13 chr 12 NC_000012.11:g.48238607G>T
VDR RefSeqGene NG_008731.1:g.65208C>A
Gene: VDR, vitamin D receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
VDR transcript variant 1 NM_000376.3:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRA NP_000367.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant 3 NM_001017536.2:c.1356C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRB1 NP_001017536.1:p.Arg452= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant 4 NM_001374661.1:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRA NP_001361590.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant 5 NM_001374662.1:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRA NP_001361591.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant 2 NM_001017535.2:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRA NP_001017535.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant 1 NM_001364085.2:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform VDRAx NP_001351014.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant X2 XM_011538720.2:c.1206C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform X2 XP_011537022.1:p.Arg402= R (Arg) > R (Arg) Synonymous Variant
VDR transcript variant X1 XM_024449178.1:c.1275C>A R [CGC] > R [CGA] Coding Sequence Variant
vitamin D3 receptor isoform X1 XP_024304946.1:p.Arg425= R (Arg) > R (Arg) Synonymous Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 784390 )
ClinVar Accession Disease Names Clinical Significance
RCV000980271.1 not provided Benign
RCV001111881.1 Vitamin D-dependent rickets type II with alopecia Likely-Benign
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement G= T
GRCh38.p13 chr 12 NC_000012.12:g.47844824= NC_000012.12:g.47844824G>T
GRCh37.p13 chr 12 NC_000012.11:g.48238607= NC_000012.11:g.48238607G>T
VDR RefSeqGene NG_008731.1:g.65208= NG_008731.1:g.65208C>A
VDR transcript variant 1 NM_000376.3:c.1206= NM_000376.3:c.1206C>A
VDR transcript variant 1 NM_000376.2:c.1206= NM_000376.2:c.1206C>A
VDR transcript variant 3 NM_001017536.2:c.1356= NM_001017536.2:c.1356C>A
VDR transcript variant 3 NM_001017536.1:c.1356= NM_001017536.1:c.1356C>A
VDR transcript variant 2 NM_001017535.2:c.1206= NM_001017535.2:c.1206C>A
VDR transcript variant 2 NM_001017535.1:c.1206= NM_001017535.1:c.1206C>A
VDR transcript variant 1 NM_001364085.2:c.1206= NM_001364085.2:c.1206C>A
VDR transcript variant 1 NM_001364085.1:c.1206= NM_001364085.1:c.1206C>A
VDR transcript variant 4 NM_001374661.1:c.1206= NM_001374661.1:c.1206C>A
VDR transcript variant 5 NM_001374662.1:c.1206= NM_001374662.1:c.1206C>A
VDR transcript variant X2 XM_011538720.2:c.1206= XM_011538720.2:c.1206C>A
VDR transcript variant X1 XM_024449178.1:c.1275= XM_024449178.1:c.1275C>A
vitamin D3 receptor isoform VDRA NP_000367.1:p.Arg402= NP_000367.1:p.Arg402=
vitamin D3 receptor isoform VDRB1 NP_001017536.1:p.Arg452= NP_001017536.1:p.Arg452=
vitamin D3 receptor isoform VDRA NP_001017535.1:p.Arg402= NP_001017535.1:p.Arg402=
vitamin D3 receptor isoform VDRAx NP_001351014.1:p.Arg402= NP_001351014.1:p.Arg402=
vitamin D3 receptor isoform VDRA NP_001361590.1:p.Arg402= NP_001361590.1:p.Arg402=
vitamin D3 receptor isoform VDRA NP_001361591.1:p.Arg402= NP_001361591.1:p.Arg402=
vitamin D3 receptor isoform X2 XP_011537022.1:p.Arg402= XP_011537022.1:p.Arg402=
vitamin D3 receptor isoform X1 XP_024304946.1:p.Arg425= XP_024304946.1:p.Arg425=
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

22 SubSNP, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 WICVAR ss3176884 Aug 15, 2001 (98)
2 SNP500CANCER ss5586955 Mar 31, 2003 (113)
3 SC_SNP ss14739712 Dec 05, 2003 (119)
4 KRIBB_YJKIM ss80762904 Dec 15, 2007 (130)
5 1000GENOMES ss462851609 Sep 17, 2011 (135)
6 1000GENOMES ss491040670 May 04, 2012 (137)
7 1000GENOMES ss1344913968 Aug 21, 2014 (142)
8 EVA_EXAC ss1690872895 Apr 01, 2015 (144)
9 HUMAN_LONGEVITY ss2189575451 Dec 20, 2016 (150)
10 TOPMED ss2353507919 Dec 20, 2016 (150)
11 GNOMAD ss2739762358 Nov 08, 2017 (151)
12 GNOMAD ss2748852313 Nov 08, 2017 (151)
13 GNOMAD ss2910200501 Nov 08, 2017 (151)
14 TOPMED ss3170201299 Nov 08, 2017 (151)
15 EVA ss3750449659 Jul 13, 2019 (153)
16 KHV_HUMAN_GENOMES ss3815780031 Jul 13, 2019 (153)
17 SGDP_PRJ ss3878222209 Apr 27, 2020 (154)
18 KRGDB ss3926839662 Apr 27, 2020 (154)
19 KOGIC ss3971873719 Apr 27, 2020 (154)
20 TOPMED ss4917393073 Apr 26, 2021 (155)
21 TOMMO_GENOMICS ss5206195003 Apr 26, 2021 (155)
22 EVA ss5236904858 Apr 26, 2021 (155)
23 1000Genomes NC_000012.11 - 48238607 Oct 12, 2018 (152)
24 ExAC NC_000012.11 - 48238607 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000012.12 - 47844824 Apr 26, 2021 (155)
26 gnomAD - Exomes NC_000012.11 - 48238607 Jul 13, 2019 (153)
27 KOREAN population from KRGDB NC_000012.11 - 48238607 Apr 27, 2020 (154)
28 Korean Genome Project NC_000012.12 - 47844824 Apr 27, 2020 (154)
29 SGDP_PRJ NC_000012.11 - 48238607 Apr 27, 2020 (154)
30 8.3KJPN NC_000012.11 - 48238607 Apr 26, 2021 (155)
31 TopMed NC_000012.12 - 47844824 Apr 26, 2021 (155)
32 ALFA NC_000012.12 - 47844824 Apr 26, 2021 (155)
33 ClinVar RCV000980271.1 Apr 27, 2020 (154)
34 ClinVar RCV001111881.1 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs60970661 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
57659007, 1167766, 8991403, 34017056, 30239189, 64164310, ss462851609, ss491040670, ss1344913968, ss1690872895, ss2353507919, ss2739762358, ss2748852313, ss2910200501, ss3750449659, ss3878222209, ss3926839662, ss5206195003 NC_000012.11:48238606:G:T NC_000012.12:47844823:G:T (self)
RCV000980271.1, RCV001111881.1, 406569173, 28251720, 83237477, 132938730, 13354921669, ss2189575451, ss3170201299, ss3815780031, ss3971873719, ss4917393073, ss5236904858 NC_000012.12:47844823:G:T NC_000012.12:47844823:G:T (self)
ss14739712 NT_029419.10:10381912:G:T NC_000012.12:47844823:G:T (self)
ss3176884, ss5586955, ss80762904 NT_029419.12:10381912:G:T NC_000012.12:47844823:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs2229829
PMID Title Author Year Journal
21168462 Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism. Andraos C et al. 2011 Human immunology
28219207 [Mutations of vitamin D receptor gene found in patients with multiple myeloma]. Liu Y et al. 2017 Zhonghua zhong liu za zhi [Chinese journal of oncology]
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post676+237644a