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dbSNP Short Genetic Variations

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.

rs7976091

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:47910769 (GRCh38.p12) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.40299 (50603/125568, TOPMED)
T=0.3607 (11307/31346, GnomAD)
T=0.456 (2282/5008, 1000G) (+ 5 more)
T=0.131 (588/4480, Estonian)
T=0.206 (792/3854, ALSPAC)
T=0.201 (744/3708, TWINSUK)
T=0.22 (132/600, NorthernSweden)
T=0.42 (89/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
7 citations
Genomic View
See rs on genome
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.p12 chr 12 NC_000012.12:g.47910769C>T
GRCh37.p13 chr 12 NC_000012.11:g.48304552C>T
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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.

Not Reported in ClinVar
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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.59701 T=0.40299
gnomAD - Genomes Global Study-wide 31346 C=0.6393 T=0.3607
gnomAD - Genomes European Sub 18874 C=0.8265 T=0.1735
gnomAD - Genomes African Sub 8702 C=0.210 T=0.790
gnomAD - Genomes East Asian Sub 1546 C=0.568 T=0.432
gnomAD - Genomes Other Sub 1088 C=0.745 T=0.255
gnomAD - Genomes American Sub 846 C=0.83 T=0.17
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.77 T=0.23
1000Genomes Global Study-wide 5008 C=0.544 T=0.456
1000Genomes African Sub 1322 C=0.109 T=0.891
1000Genomes East Asian Sub 1008 C=0.605 T=0.395
1000Genomes Europe Sub 1006 C=0.772 T=0.228
1000Genomes South Asian Sub 978 C=0.64 T=0.36
1000Genomes American Sub 694 C=0.82 T=0.18
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.869 T=0.131
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.794 T=0.206
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.799 T=0.201
Northern Sweden ACPOP Study-wide 600 C=0.78 T=0.22
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.58 T=0.42
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 C= T Note
GRCh38.p12 chr 12 NC_000012.12:g.47910769= NC_000012.12:g.47910769C>T
GRCh37.p13 chr 12 NC_000012.11:g.48304552= NC_000012.11:g.48304552C>T
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#.

55 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss12218696 Jul 11, 2003 (116)
2 SC_SNP ss16133240 Feb 27, 2004 (120)
3 SSAHASNP ss20938215 Apr 05, 2004 (121)
4 ABI ss38932412 Mar 15, 2006 (126)
5 HGSV ss82436356 Dec 16, 2007 (130)
6 HGSV ss82634812 Dec 16, 2007 (130)
7 HGSV ss84742406 Dec 16, 2007 (130)
8 HGSV ss84869921 Dec 16, 2007 (130)
9 BCMHGSC_JDW ss89138159 Mar 24, 2008 (129)
10 HUMANGENOME_JCVI ss97227488 Feb 06, 2009 (130)
11 1000GENOMES ss111908738 Jan 25, 2009 (130)
12 1000GENOMES ss113509564 Jan 25, 2009 (130)
13 ILLUMINA-UK ss118787305 Feb 14, 2009 (130)
14 ENSEMBL ss133153660 Dec 01, 2009 (131)
15 ENSEMBL ss137446099 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss168259644 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss169774080 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss175118107 Jul 04, 2010 (132)
19 BUSHMAN ss198141270 Jul 04, 2010 (132)
20 1000GENOMES ss225742103 Jul 14, 2010 (132)
21 1000GENOMES ss235927048 Jul 15, 2010 (132)
22 1000GENOMES ss242488165 Jul 15, 2010 (132)
23 BL ss255097212 May 09, 2011 (134)
24 GMI ss281387859 May 04, 2012 (137)
25 GMI ss286557641 Apr 25, 2013 (138)
26 PJP ss291245816 May 09, 2011 (134)
27 TISHKOFF ss563152069 Apr 25, 2013 (138)
28 SSMP ss658705126 Apr 25, 2013 (138)
29 EVA-GONL ss989508831 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1078444685 Aug 21, 2014 (142)
31 1000GENOMES ss1344916083 Aug 21, 2014 (142)
32 DDI ss1426926879 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1576268803 Apr 01, 2015 (144)
34 EVA_DECODE ss1599179248 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1628541224 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1671535257 Apr 01, 2015 (144)
37 HAMMER_LAB ss1807234427 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1932873430 Feb 12, 2016 (147)
39 JJLAB ss2027188035 Sep 14, 2016 (149)
40 USC_VALOUEV ss2155523615 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2189579747 Dec 20, 2016 (150)
42 TOPMED ss2353512100 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2628073887 Nov 08, 2017 (151)
44 GRF ss2699866470 Nov 08, 2017 (151)
45 GNOMAD ss2910206086 Nov 08, 2017 (151)
46 SWEGEN ss3009644787 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3027402276 Nov 08, 2017 (151)
48 TOPMED ss3170213792 Nov 08, 2017 (151)
49 CSHL ss3350053252 Nov 08, 2017 (151)
50 URBANLAB ss3649833047 Oct 12, 2018 (152)
51 EGCUT_WGS ss3676921222 Jul 13, 2019 (153)
52 EVA_DECODE ss3693620598 Jul 13, 2019 (153)
53 ACPOP ss3739000297 Jul 13, 2019 (153)
54 EVA ss3750450321 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3815780633 Jul 13, 2019 (153)
56 1000Genomes NC_000012.11 - 48304552 Oct 12, 2018 (152)
57 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 48304552 Oct 12, 2018 (152)
58 Genetic variation in the Estonian population NC_000012.11 - 48304552 Oct 12, 2018 (152)
59 gnomAD - Genomes NC_000012.11 - 48304552 Jul 13, 2019 (153)
60 Northern Sweden NC_000012.11 - 48304552 Jul 13, 2019 (153)
61 TopMed NC_000012.12 - 47910769 Oct 12, 2018 (152)
62 UK 10K study - Twins NC_000012.11 - 48304552 Oct 12, 2018 (152)
63 A Vietnamese Genetic Variation Database NC_000012.11 - 48304552 Jul 13, 2019 (153)
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)
rs61232206 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82436356, ss82634812, ss84742406, ss84869921 NC_000012.9:46590818:C:T NC_000012.12:47910768:C:T (self)
ss89138159, ss111908738, ss113509564, ss118787305, ss168259644, ss169774080, ss175118107, ss198141270, ss255097212, ss281387859, ss286557641, ss291245816, ss1599179248 NC_000012.10:46590818:C:T NC_000012.12:47910768:C:T (self)
57661185, 32019635, 22659470, 157362772, 12285162, 32019635, 7109607, ss225742103, ss235927048, ss242488165, ss563152069, ss658705126, ss989508831, ss1078444685, ss1344916083, ss1426926879, ss1576268803, ss1628541224, ss1671535257, ss1807234427, ss1932873430, ss2027188035, ss2155523615, ss2353512100, ss2628073887, ss2699866470, ss2910206086, ss3009644787, ss3350053252, ss3676921222, ss3739000297, ss3750450321 NC_000012.11:48304551:C:T NC_000012.12:47910768:C:T (self)
83247833, ss2189579747, ss3027402276, ss3170213792, ss3649833047, ss3693620598, ss3815780633 NC_000012.12:47910768:C:T NC_000012.12:47910768:C:T (self)
ss12218696, ss16133240, ss20938215 NT_029419.10:10447857:C:T NC_000012.12:47910768:C:T (self)
ss38932412, ss97227488, ss133153660, ss137446099 NT_029419.12:10447857:C:T NC_000012.12:47910768:C:T (self)
Help

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

7 citations for rs7976091
PMID Title Author Year Journal
21309754 Vitamin D receptor gene as a candidate gene for Parkinson disease. Butler MW et al. 2011 Annals of human genetics
22213340 25-hydroxyvitamin D, vitamin D receptor gene polymorphisms, and severity of Parkinson's disease. Suzuki M et al. 2012 Movement disorders
22242137 Prognostic significance of vitamin D receptor polymorphisms in head and neck squamous cell carcinoma. Hama T et al. 2011 PloS one
24595449 Genetic polymorphisms in VDR, ESR1 and ESR2 genes may contribute to susceptibility to Parkinson's disease: a meta-analysis. Gao Z et al. 2014 Molecular biology reports
25266489 Genetic polymorphisms of VIP variants in the Tajik ethnic group of northwest China. Zhang J et al. 2014 BMC genetics
26756741 Systematic Review of the Relationship between Vitamin D and Parkinson's Disease. Rimmelzwaan LM et al. 2016 Journal of Parkinson's disease
27345382 Vitamin D receptor polymorphisms and Parkinson's disease in a Korean population: Revisited. Kang SY et al. 2016 Neuroscience letters

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.post270+ab078da