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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.

rs2368821

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:48561 (GRCh38.p14) 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=0.49805 (14074/28258, 14KJPN)
T=0.49845 (8354/16760, 8.3KJPN)
T=0.49878 (8146/16332, ALFA) (+ 9 more)
T=0.4960 (2484/5008, 1000G)
G=0.5000 (1465/2930, KOREAN)
T=0.5000 (1465/2930, KOREAN)
G=0.500 (277/554, SGDP_PRJ)
T=0.500 (277/554, SGDP_PRJ)
G=0.500 (108/216, Qatari)
T=0.500 (108/216, Qatari)
G=0.50 (27/54, Siberian)
T=0.50 (27/54, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 16332 G=0.50122 T=0.49878
European Sub 12080 G=0.50099 T=0.49901
African Sub 2816 G=0.5018 T=0.4982
African Others Sub 108 G=0.509 T=0.491
African American Sub 2708 G=0.5015 T=0.4985
Asian Sub 108 G=0.509 T=0.491
East Asian Sub 84 G=0.51 T=0.49
Other Asian Sub 24 G=0.50 T=0.50
Latin American 1 Sub 146 G=0.507 T=0.493
Latin American 2 Sub 610 G=0.500 T=0.500
South Asian Sub 94 G=0.50 T=0.50
Other Sub 478 G=0.502 T=0.498


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
14KJPN JAPANESE Study-wide 28258 G=0.50195 T=0.49805
8.3KJPN JAPANESE Study-wide 16760 G=0.50155 T=0.49845
Allele Frequency Aggregator Total Global 16332 G=0.50122 T=0.49878
Allele Frequency Aggregator European Sub 12080 G=0.50099 T=0.49901
Allele Frequency Aggregator African Sub 2816 G=0.5018 T=0.4982
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.500 T=0.500
Allele Frequency Aggregator Other Sub 478 G=0.502 T=0.498
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.507 T=0.493
Allele Frequency Aggregator Asian Sub 108 G=0.509 T=0.491
Allele Frequency Aggregator South Asian Sub 94 G=0.50 T=0.50
1000Genomes Global Study-wide 5008 G=0.5040 T=0.4960
1000Genomes African Sub 1322 G=0.5038 T=0.4962
1000Genomes East Asian Sub 1008 G=0.5099 T=0.4901
1000Genomes Europe Sub 1006 G=0.4970 T=0.5030
1000Genomes South Asian Sub 978 G=0.506 T=0.494
1000Genomes American Sub 694 G=0.503 T=0.497
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5000 T=0.5000
SGDP_PRJ Global Study-wide 554 G=0.500 T=0.500
Qatari Global Study-wide 216 G=0.500 T=0.500
Siberian Global Study-wide 54 G=0.50 T=0.50
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.p14 chr 12 NC_000012.12:g.48561G>T
GRCh37.p13 chr 12 NC_000012.11:g.157727G>T
GRCh38.p14 chr 12 alt locus HSCHR12_1_CTG1 NW_003571049.1:g.36210T>G
GRCh37.p13 chr 12 fix patch HG858_PATCH NW_003571048.1:g.38561G>T
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.

Not Reported in ClinVar
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.p14 chr 12 NC_000012.12:g.48561= NC_000012.12:g.48561G>T
GRCh37.p13 chr 12 NC_000012.11:g.157727= NC_000012.11:g.157727G>T
GRCh38.p14 chr 12 alt locus HSCHR12_1_CTG1 NW_003571049.1:g.36210T>G NW_003571049.1:g.36210=
GRCh37.p13 chr 12 fix patch HG858_PATCH NW_003571048.1:g.38561= NW_003571048.1:g.38561G>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#.

36 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss3326998 Sep 28, 2001 (100)
2 CSHL-HAPMAP ss17463429 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19241801 Feb 27, 2004 (120)
4 HGSV ss83497636 Dec 15, 2007 (129)
5 BCMHGSC_JDW ss88901846 Mar 24, 2008 (129)
6 ILLUMINA-UK ss118502182 Feb 14, 2009 (130)
7 ENSEMBL ss132947462 Dec 01, 2009 (131)
8 ENSEMBL ss137490830 Dec 01, 2009 (131)
9 GMI ss156995342 Dec 01, 2009 (131)
10 BL ss254803728 May 09, 2011 (134)
11 GMI ss281238695 May 04, 2012 (137)
12 GMI ss286488846 Apr 25, 2013 (138)
13 SSMP ss658464412 Apr 25, 2013 (138)
14 1000GENOMES ss1343671531 Aug 21, 2014 (142)
15 DDI ss1426815477 Apr 09, 2015 (144)
16 WEILL_CORNELL_DGM ss1932508715 Feb 17, 2016 (147)
17 USC_VALOUEV ss2155319507 Oct 12, 2018 (152)
18 GRF ss2699636964 Oct 12, 2018 (152)
19 GNOMAD ss2906410439 Oct 12, 2018 (152)
20 SWEGEN ss3009063129 Oct 12, 2018 (152)
21 BIOINF_KMB_FNS_UNIBA ss3027303566 Nov 08, 2017 (151)
22 CSHL ss3349879104 Oct 12, 2018 (152)
23 URBANLAB ss3649743714 Oct 12, 2018 (152)
24 PACBIO ss3787115638 Jul 13, 2019 (153)
25 PACBIO ss3792233042 Jul 13, 2019 (153)
26 PACBIO ss3797115791 Jul 13, 2019 (153)
27 KHV_HUMAN_GENOMES ss3815354172 Jul 13, 2019 (153)
28 SGDP_PRJ ss3877506566 Apr 26, 2020 (154)
29 KRGDB ss3925995817 Apr 26, 2020 (154)
30 VINODS ss4030258561 Apr 26, 2021 (155)
31 TOMMO_GENOMICS ss5204677372 Apr 26, 2021 (155)
32 EVA ss5403388384 Oct 16, 2022 (156)
33 SANFORD_IMAGENETICS ss5652420792 Oct 16, 2022 (156)
34 TOMMO_GENOMICS ss5753352675 Oct 16, 2022 (156)
35 YY_MCH ss5812929123 Oct 16, 2022 (156)
36 EVA ss5837469706 Oct 16, 2022 (156)
37 1000Genomes NC_000012.11 - 157727 Oct 12, 2018 (152)
38 KOREAN population from KRGDB NC_000012.11 - 157727 Apr 26, 2020 (154)
39 Qatari NC_000012.11 - 157727 Apr 26, 2020 (154)
40 SGDP_PRJ NC_000012.11 - 157727 Apr 26, 2020 (154)
41 Siberian NC_000012.11 - 157727 Apr 26, 2020 (154)
42 8.3KJPN NC_000012.11 - 157727 Apr 26, 2021 (155)
43 14KJPN NC_000012.12 - 48561 Oct 16, 2022 (156)
44 ALFA NC_000012.12 - 48561 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83497636 NC_000012.9:27987:G:T NC_000012.12:48560:G:T (self)
ss88901846, ss118502182, ss254803728, ss281238695, ss286488846 NC_000012.10:27987:G:T NC_000012.12:48560:G:T (self)
56277988, 33173211, 14550645, 29523546, 7835861, 62646679, ss658464412, ss1343671531, ss1426815477, ss1932508715, ss2155319507, ss2699636964, ss2906410439, ss3009063129, ss3349879104, ss3787115638, ss3792233042, ss3797115791, ss3877506566, ss3925995817, ss5204677372, ss5403388384, ss5652420792, ss5837469706 NC_000012.11:157726:G:T NC_000012.12:48560:G:T (self)
87189779, 12438985886, ss3027303566, ss3649743714, ss3815354172, ss5753352675, ss5812929123 NC_000012.12:48560:G:T NC_000012.12:48560:G:T (self)
ss17463429, ss19241801 NT_009759.15:11987:G:T NC_000012.12:48560:G:T (self)
ss3326998, ss132947462, ss137490830, ss156995342 NT_009759.16:97726:G:T NC_000012.12:48560:G:T (self)
ss4030258561 NW_003571049.1:36209:T:T NC_000012.12:48560: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.

No publications for rs2368821

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.post761+d5e8e07