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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs13081389

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:12248301 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.041826 (11071/264690, TOPMED)
G=0.056958 (10156/178306, ALFA)
G=0.047983 (6724/140132, GnomAD) (+ 21 more)
G=0.02593 (2037/78560, PAGE_STUDY)
G=0.01883 (532/28258, 14KJPN)
G=0.01879 (315/16760, 8.3KJPN)
G=0.0379 (243/6404, 1000G_30x)
G=0.0389 (195/5008, 1000G)
G=0.0770 (345/4480, Estonian)
G=0.0641 (247/3854, ALSPAC)
G=0.0539 (200/3708, TWINSUK)
G=0.0404 (118/2922, KOREAN)
G=0.0349 (64/1832, Korea1K)
G=0.046 (46/998, GoNL)
G=0.049 (39/790, PRJEB37584)
G=0.097 (58/600, NorthernSweden)
G=0.027 (9/328, HapMap)
G=0.019 (4/216, Qatari)
G=0.024 (5/210, Vietnamese)
G=0.07 (3/40, GENOME_DK)
A=0.46 (12/26, SGDP_PRJ)
G=0.00 (0/14, Ancient Sardinia)
A=0.5 (2/4, Siberian)
G=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
7 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 178522 A=0.943066 G=0.056934 0.889605 0.003473 0.106922 1
European Sub 153164 A=0.940208 G=0.059792 0.884085 0.003669 0.112246 0
African Sub 6974 A=0.9771 G=0.0229 0.954115 0.0 0.045885 1
African Others Sub 252 A=0.980 G=0.020 0.960317 0.0 0.039683 0
African American Sub 6722 A=0.9769 G=0.0231 0.953883 0.0 0.046117 1
Asian Sub 6290 A=0.9577 G=0.0423 0.918601 0.00318 0.078219 2
East Asian Sub 4472 A=0.9611 G=0.0389 0.924866 0.002683 0.072451 1
Other Asian Sub 1818 A=0.9494 G=0.0506 0.90319 0.0044 0.092409 1
Latin American 1 Sub 440 A=0.964 G=0.036 0.931818 0.004545 0.063636 1
Latin American 2 Sub 950 A=0.985 G=0.015 0.972632 0.002105 0.025263 5
South Asian Sub 280 A=0.911 G=0.089 0.835714 0.014286 0.15 1
Other Sub 10424 A=0.94964 G=0.05036 0.902149 0.002878 0.094973 0


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 A=0.958174 G=0.041826
Allele Frequency Aggregator Total Global 178306 A=0.943042 G=0.056958
Allele Frequency Aggregator European Sub 152984 A=0.940190 G=0.059810
Allele Frequency Aggregator Other Sub 10402 A=0.94953 G=0.05047
Allele Frequency Aggregator African Sub 6960 A=0.9770 G=0.0230
Allele Frequency Aggregator Asian Sub 6290 A=0.9577 G=0.0423
Allele Frequency Aggregator Latin American 2 Sub 950 A=0.985 G=0.015
Allele Frequency Aggregator Latin American 1 Sub 440 A=0.964 G=0.036
Allele Frequency Aggregator South Asian Sub 280 A=0.911 G=0.089
gnomAD - Genomes Global Study-wide 140132 A=0.952017 G=0.047983
gnomAD - Genomes European Sub 75896 A=0.93419 G=0.06581
gnomAD - Genomes African Sub 41986 A=0.97471 G=0.02529
gnomAD - Genomes American Sub 13648 A=0.97201 G=0.02799
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9669 G=0.0331
gnomAD - Genomes East Asian Sub 3130 A=0.9668 G=0.0332
gnomAD - Genomes Other Sub 2152 A=0.9670 G=0.0330
The PAGE Study Global Study-wide 78560 A=0.97407 G=0.02593
The PAGE Study AfricanAmerican Sub 32396 A=0.97642 G=0.02358
The PAGE Study Mexican Sub 10810 A=0.98307 G=0.01693
The PAGE Study Asian Sub 8318 A=0.9684 G=0.0316
The PAGE Study PuertoRican Sub 7912 A=0.9626 G=0.0374
The PAGE Study NativeHawaiian Sub 4534 A=0.9782 G=0.0218
The PAGE Study Cuban Sub 4222 A=0.9716 G=0.0284
The PAGE Study Dominican Sub 3822 A=0.9749 G=0.0251
The PAGE Study CentralAmerican Sub 2450 A=0.9824 G=0.0176
The PAGE Study SouthAmerican Sub 1982 A=0.9798 G=0.0202
The PAGE Study NativeAmerican Sub 1258 A=0.9539 G=0.0461
The PAGE Study SouthAsian Sub 856 A=0.912 G=0.088
14KJPN JAPANESE Study-wide 28258 A=0.98117 G=0.01883
8.3KJPN JAPANESE Study-wide 16760 A=0.98121 G=0.01879
1000Genomes_30x Global Study-wide 6404 A=0.9621 G=0.0379
1000Genomes_30x African Sub 1786 A=0.9759 G=0.0241
1000Genomes_30x Europe Sub 1266 A=0.9510 G=0.0490
1000Genomes_30x South Asian Sub 1202 A=0.9210 G=0.0790
1000Genomes_30x East Asian Sub 1170 A=0.9769 G=0.0231
1000Genomes_30x American Sub 980 A=0.984 G=0.016
1000Genomes Global Study-wide 5008 A=0.9611 G=0.0389
1000Genomes African Sub 1322 A=0.9743 G=0.0257
1000Genomes East Asian Sub 1008 A=0.9772 G=0.0228
1000Genomes Europe Sub 1006 A=0.9533 G=0.0467
1000Genomes South Asian Sub 978 A=0.918 G=0.082
1000Genomes American Sub 694 A=0.984 G=0.016
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9230 G=0.0770
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9359 G=0.0641
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9461 G=0.0539
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9596 G=0.0404
Korean Genome Project KOREAN Study-wide 1832 A=0.9651 G=0.0349
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.954 G=0.046
CNV burdens in cranial meningiomas Global Study-wide 790 A=0.951 G=0.049
CNV burdens in cranial meningiomas CRM Sub 790 A=0.951 G=0.049
Northern Sweden ACPOP Study-wide 600 A=0.903 G=0.097
HapMap Global Study-wide 328 A=0.973 G=0.027
HapMap American Sub 120 A=0.958 G=0.042
HapMap African Sub 118 A=1.000 G=0.000
HapMap Asian Sub 90 A=0.96 G=0.04
Qatari Global Study-wide 216 A=0.981 G=0.019
A Vietnamese Genetic Variation Database Global Study-wide 210 A=0.976 G=0.024
The Danish reference pan genome Danish Study-wide 40 A=0.93 G=0.07
SGDP_PRJ Global Study-wide 26 A=0.46 G=0.54
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 14 A=1.00 G=0.00
Siberian Global Study-wide 4 A=0.5 G=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.p14 chr 3 NC_000003.12:g.12248301A>G
GRCh37.p13 chr 3 NC_000003.11:g.12289800A>G
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 A= G
GRCh38.p14 chr 3 NC_000003.12:g.12248301= NC_000003.12:g.12248301A>G
GRCh37.p13 chr 3 NC_000003.11:g.12289800= NC_000003.11:g.12289800A>G
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#.

83 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21957488 Apr 05, 2004 (121)
2 PERLEGEN ss23870753 Sep 20, 2004 (123)
3 ABI ss44394225 Mar 14, 2006 (126)
4 HUMANGENOME_JCVI ss95985654 Feb 05, 2009 (130)
5 BGI ss103901762 Dec 01, 2009 (131)
6 ENSEMBL ss135529583 Dec 01, 2009 (131)
7 BUSHMAN ss202146228 Jul 04, 2010 (132)
8 1000GENOMES ss231710759 Jul 14, 2010 (132)
9 1000GENOMES ss239144394 Jul 15, 2010 (132)
10 BL ss252937589 May 09, 2011 (134)
11 GMI ss277016927 May 04, 2012 (137)
12 PJP ss292933870 May 09, 2011 (134)
13 ILLUMINA ss410840991 Sep 17, 2011 (135)
14 EXOME_CHIP ss491335704 May 04, 2012 (137)
15 TISHKOFF ss556430537 Apr 25, 2013 (138)
16 SSMP ss650096952 Apr 25, 2013 (138)
17 ILLUMINA ss780681694 Aug 21, 2014 (142)
18 ILLUMINA ss783355023 Aug 21, 2014 (142)
19 EVA-GONL ss978279327 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1070180538 Aug 21, 2014 (142)
21 1000GENOMES ss1302830831 Aug 21, 2014 (142)
22 EVA_GENOME_DK ss1579848176 Apr 01, 2015 (144)
23 EVA_DECODE ss1587740741 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1606429531 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1649423564 Apr 01, 2015 (144)
26 ILLUMINA ss1752436231 Sep 08, 2015 (146)
27 HAMMER_LAB ss1798869644 Sep 08, 2015 (146)
28 ILLUMINA ss1917763392 Feb 12, 2016 (147)
29 WEILL_CORNELL_DGM ss1921531902 Feb 12, 2016 (147)
30 ILLUMINA ss1946074788 Feb 12, 2016 (147)
31 ILLUMINA ss1958537877 Feb 12, 2016 (147)
32 JJLAB ss2021319096 Sep 14, 2016 (149)
33 USC_VALOUEV ss2149386802 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2249131292 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2625159789 Nov 08, 2017 (151)
36 ILLUMINA ss2633912478 Nov 08, 2017 (151)
37 ILLUMINA ss2633912479 Nov 08, 2017 (151)
38 GRF ss2704747524 Nov 08, 2017 (151)
39 GNOMAD ss2789610319 Nov 08, 2017 (151)
40 AFFY ss2985247261 Nov 08, 2017 (151)
41 AFFY ss2985868324 Nov 08, 2017 (151)
42 SWEGEN ss2991840853 Nov 08, 2017 (151)
43 ILLUMINA ss3022212364 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3024422477 Nov 08, 2017 (151)
45 CSHL ss3344888739 Nov 08, 2017 (151)
46 ILLUMINA ss3628591886 Oct 11, 2018 (152)
47 ILLUMINA ss3634880637 Oct 11, 2018 (152)
48 ILLUMINA ss3640587940 Oct 11, 2018 (152)
49 ILLUMINA ss3644807339 Oct 11, 2018 (152)
50 URBANLAB ss3647342358 Oct 11, 2018 (152)
51 ILLUMINA ss3652678484 Oct 11, 2018 (152)
52 ILLUMINA ss3654015783 Oct 11, 2018 (152)
53 EGCUT_WGS ss3659740860 Jul 13, 2019 (153)
54 EVA_DECODE ss3708650663 Jul 13, 2019 (153)
55 ILLUMINA ss3725990797 Jul 13, 2019 (153)
56 ACPOP ss3729638182 Jul 13, 2019 (153)
57 ILLUMINA ss3744506234 Jul 13, 2019 (153)
58 ILLUMINA ss3745180441 Jul 13, 2019 (153)
59 EVA ss3759670136 Jul 13, 2019 (153)
60 PAGE_CC ss3771011259 Jul 13, 2019 (153)
61 ILLUMINA ss3772676227 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3802819443 Jul 13, 2019 (153)
63 SGDP_PRJ ss3855241521 Apr 25, 2020 (154)
64 KRGDB ss3901015516 Apr 25, 2020 (154)
65 KOGIC ss3950676968 Apr 25, 2020 (154)
66 EVA ss3984503106 Apr 26, 2021 (155)
67 EVA ss3984973471 Apr 26, 2021 (155)
68 TOPMED ss4554441766 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5157830266 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5253072772 Oct 13, 2022 (156)
71 EVA ss5314834366 Oct 13, 2022 (156)
72 EVA ss5337937006 Oct 13, 2022 (156)
73 HUGCELL_USP ss5452571320 Oct 13, 2022 (156)
74 EVA ss5506887155 Oct 13, 2022 (156)
75 1000G_HIGH_COVERAGE ss5530916743 Oct 13, 2022 (156)
76 SANFORD_IMAGENETICS ss5631556119 Oct 13, 2022 (156)
77 TOMMO_GENOMICS ss5689107379 Oct 13, 2022 (156)
78 YY_MCH ss5803487494 Oct 13, 2022 (156)
79 EVA ss5825355411 Oct 13, 2022 (156)
80 EVA ss5847953941 Oct 13, 2022 (156)
81 EVA ss5853493492 Oct 13, 2022 (156)
82 EVA ss5867657941 Oct 13, 2022 (156)
83 EVA ss5959816021 Oct 13, 2022 (156)
84 1000Genomes NC_000003.11 - 12289800 Oct 11, 2018 (152)
85 1000Genomes_30x NC_000003.12 - 12248301 Oct 13, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 12289800 Oct 11, 2018 (152)
87 Genetic variation in the Estonian population NC_000003.11 - 12289800 Oct 11, 2018 (152)
88 The Danish reference pan genome NC_000003.11 - 12289800 Apr 25, 2020 (154)
89 gnomAD - Genomes NC_000003.12 - 12248301 Apr 26, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000003.11 - 12289800 Apr 25, 2020 (154)
91 HapMap NC_000003.12 - 12248301 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000003.11 - 12289800 Apr 25, 2020 (154)
93 Korean Genome Project NC_000003.12 - 12248301 Apr 25, 2020 (154)
94 Northern Sweden NC_000003.11 - 12289800 Jul 13, 2019 (153)
95 The PAGE Study NC_000003.12 - 12248301 Jul 13, 2019 (153)
96 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000003.11 - 12289800 Apr 26, 2021 (155)
97 CNV burdens in cranial meningiomas NC_000003.11 - 12289800 Apr 26, 2021 (155)
98 Qatari NC_000003.11 - 12289800 Apr 25, 2020 (154)
99 SGDP_PRJ NC_000003.11 - 12289800 Apr 25, 2020 (154)
100 Siberian NC_000003.11 - 12289800 Apr 25, 2020 (154)
101 8.3KJPN NC_000003.11 - 12289800 Apr 26, 2021 (155)
102 14KJPN NC_000003.12 - 12248301 Oct 13, 2022 (156)
103 TopMed NC_000003.12 - 12248301 Apr 26, 2021 (155)
104 UK 10K study - Twins NC_000003.11 - 12289800 Oct 11, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000003.11 - 12289800 Jul 13, 2019 (153)
106 ALFA NC_000003.12 - 12248301 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
ss202146228, ss252937589, ss277016927, ss292933870, ss410840991, ss1587740741 NC_000003.10:12264799:A:G NC_000003.12:12248300:A:G (self)
13976697, 7748056, 5479108, 6013115, 3401879, 8192910, 2923047, 199398, 52449, 3573832, 7258501, 1903156, 15799573, 7748056, 1687097, ss231710759, ss239144394, ss491335704, ss556430537, ss650096952, ss780681694, ss783355023, ss978279327, ss1070180538, ss1302830831, ss1579848176, ss1606429531, ss1649423564, ss1752436231, ss1798869644, ss1917763392, ss1921531902, ss1946074788, ss1958537877, ss2021319096, ss2149386802, ss2625159789, ss2633912478, ss2633912479, ss2704747524, ss2789610319, ss2985247261, ss2985868324, ss2991840853, ss3022212364, ss3344888739, ss3628591886, ss3634880637, ss3640587940, ss3644807339, ss3652678484, ss3654015783, ss3659740860, ss3729638182, ss3744506234, ss3745180441, ss3759670136, ss3772676227, ss3855241521, ss3901015516, ss3984503106, ss3984973471, ss5157830266, ss5314834366, ss5337937006, ss5506887155, ss5631556119, ss5825355411, ss5847953941, ss5959816021 NC_000003.11:12289799:A:G NC_000003.12:12248300:A:G (self)
18442678, 99231790, 2304220, 7054969, 232728, 22944483, 391819321, 8184575239, ss2249131292, ss3024422477, ss3647342358, ss3708650663, ss3725990797, ss3771011259, ss3802819443, ss3950676968, ss4554441766, ss5253072772, ss5452571320, ss5530916743, ss5689107379, ss5803487494, ss5853493492, ss5867657941 NC_000003.12:12248300:A:G NC_000003.12:12248300:A:G (self)
ss21957488 NT_022517.16:12229799:A:G NC_000003.12:12248300:A:G (self)
ss23870753, ss44394225, ss95985654, ss103901762, ss135529583 NT_022517.18:12229799:A:G NC_000003.12:12248300:A:G (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 rs13081389
PMID Title Author Year Journal
20581827 Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Voight BF et al. 2010 Nature genetics
22770979 Presence of multiple independent effects in risk loci of common complex human diseases. Ke X et al. 2012 American journal of human genetics
24748924 Expression quantitative trait analyses to identify causal genetic variants for type 2 diabetes susceptibility. Das SK et al. 2014 World journal of diabetes
24843659 Insights into the genetic basis of type 2 diabetes. Kato N et al. 2013 Journal of diabetes investigation
25774817 Genetics of type 2 diabetes-pitfalls and possibilities. Prasad RB et al. 2015 Genes
27312935 Genetics of Insulin Resistance and the Metabolic Syndrome. Brown AE et al. 2016 Current cardiology reports
27551309 Several type 2 diabetes-associated variants in genes annotated to WNT signaling interact with dietary fiber in relation to incidence of type 2 diabetes. Hindy G et al. 2016 Genes & nutrition
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.post820+afb47a3d