Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1425609

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:162964207 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.354675 (93879/264690, TOPMED)
A=0.368982 (51625/139912, GnomAD)
A=0.33495 (26359/78696, PAGE_STUDY) (+ 20 more)
A=0.36628 (28613/78118, ALFA)
A=0.21286 (6015/28258, 14KJPN)
A=0.21187 (3551/16760, 8.3KJPN)
A=0.3506 (2245/6404, 1000G_30x)
A=0.3478 (1742/5008, 1000G)
A=0.3616 (1620/4480, Estonian)
A=0.3747 (1444/3854, ALSPAC)
A=0.3811 (1413/3708, TWINSUK)
A=0.2201 (643/2922, KOREAN)
A=0.2014 (369/1832, Korea1K)
A=0.391 (390/998, GoNL)
A=0.194 (153/790, PRJEB37584)
A=0.473 (284/600, NorthernSweden)
G=0.386 (125/324, SGDP_PRJ)
A=0.375 (81/216, Qatari)
A=0.190 (40/210, Vietnamese)
A=0.292 (59/202, HapMap)
A=0.17 (8/48, Ancient Sardinia)
A=0.42 (17/40, GENOME_DK)
G=0.34 (11/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 83152 G=0.63320 A=0.36680
European Sub 71918 G=0.63116 A=0.36884
African Sub 4152 G=0.6337 A=0.3663
African Others Sub 170 G=0.653 A=0.347
African American Sub 3982 G=0.6328 A=0.3672
Asian Sub 190 G=0.837 A=0.163
East Asian Sub 164 G=0.841 A=0.159
Other Asian Sub 26 G=0.81 A=0.19
Latin American 1 Sub 146 G=0.582 A=0.418
Latin American 2 Sub 610 G=0.618 A=0.382
South Asian Sub 104 G=0.452 A=0.548
Other Sub 6032 G=0.6567 A=0.3433


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=0.645325 A=0.354675
gnomAD - Genomes Global Study-wide 139912 G=0.631018 A=0.368982
gnomAD - Genomes European Sub 75824 G=0.60764 A=0.39236
gnomAD - Genomes African Sub 41876 G=0.64275 A=0.35725
gnomAD - Genomes American Sub 13624 G=0.66133 A=0.33867
gnomAD - Genomes Ashkenazi Jewish Sub 3310 G=0.6761 A=0.3239
gnomAD - Genomes East Asian Sub 3128 G=0.8312 A=0.1688
gnomAD - Genomes Other Sub 2150 G=0.6740 A=0.3260
The PAGE Study Global Study-wide 78696 G=0.66505 A=0.33495
The PAGE Study AfricanAmerican Sub 32514 G=0.63945 A=0.36055
The PAGE Study Mexican Sub 10808 G=0.58161 A=0.41839
The PAGE Study Asian Sub 8316 G=0.7956 A=0.2044
The PAGE Study PuertoRican Sub 7918 G=0.6921 A=0.3079
The PAGE Study NativeHawaiian Sub 4534 G=0.8125 A=0.1875
The PAGE Study Cuban Sub 4230 G=0.6979 A=0.3021
The PAGE Study Dominican Sub 3828 G=0.6727 A=0.3273
The PAGE Study CentralAmerican Sub 2450 G=0.6302 A=0.3698
The PAGE Study SouthAmerican Sub 1982 G=0.6302 A=0.3698
The PAGE Study NativeAmerican Sub 1260 G=0.5952 A=0.4048
The PAGE Study SouthAsian Sub 856 G=0.479 A=0.521
Allele Frequency Aggregator Total Global 78118 G=0.63372 A=0.36628
Allele Frequency Aggregator European Sub 68826 G=0.63187 A=0.36813
Allele Frequency Aggregator Other Sub 5232 G=0.6583 A=0.3417
Allele Frequency Aggregator African Sub 3010 G=0.6326 A=0.3674
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.618 A=0.382
Allele Frequency Aggregator Asian Sub 190 G=0.837 A=0.163
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.582 A=0.418
Allele Frequency Aggregator South Asian Sub 104 G=0.452 A=0.548
14KJPN JAPANESE Study-wide 28258 G=0.78714 A=0.21286
8.3KJPN JAPANESE Study-wide 16760 G=0.78813 A=0.21187
1000Genomes_30x Global Study-wide 6404 G=0.6494 A=0.3506
1000Genomes_30x African Sub 1786 G=0.6450 A=0.3550
1000Genomes_30x Europe Sub 1266 G=0.5948 A=0.4052
1000Genomes_30x South Asian Sub 1202 G=0.5191 A=0.4809
1000Genomes_30x East Asian Sub 1170 G=0.8479 A=0.1521
1000Genomes_30x American Sub 980 G=0.651 A=0.349
1000Genomes Global Study-wide 5008 G=0.6522 A=0.3478
1000Genomes African Sub 1322 G=0.6437 A=0.3563
1000Genomes East Asian Sub 1008 G=0.8482 A=0.1518
1000Genomes Europe Sub 1006 G=0.5994 A=0.4006
1000Genomes South Asian Sub 978 G=0.518 A=0.482
1000Genomes American Sub 694 G=0.648 A=0.352
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6384 A=0.3616
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6253 A=0.3747
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6189 A=0.3811
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.7799 A=0.2201
Korean Genome Project KOREAN Study-wide 1832 G=0.7986 A=0.2014
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.609 A=0.391
CNV burdens in cranial meningiomas Global Study-wide 790 G=0.806 A=0.194
CNV burdens in cranial meningiomas CRM Sub 790 G=0.806 A=0.194
Northern Sweden ACPOP Study-wide 600 G=0.527 A=0.473
SGDP_PRJ Global Study-wide 324 G=0.386 A=0.614
Qatari Global Study-wide 216 G=0.625 A=0.375
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.810 A=0.190
HapMap Global Study-wide 202 G=0.708 A=0.292
HapMap African Sub 114 G=0.649 A=0.351
HapMap Asian Sub 88 G=0.78 A=0.22
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 48 G=0.83 A=0.17
The Danish reference pan genome Danish Study-wide 40 G=0.57 A=0.42
Siberian Global Study-wide 32 G=0.34 A=0.66
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.162964207G>A
GRCh37.p13 chr 3 NC_000003.11:g.162681995G>A
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= A
GRCh38.p14 chr 3 NC_000003.12:g.162964207= NC_000003.12:g.162964207G>A
GRCh37.p13 chr 3 NC_000003.11:g.162681995= NC_000003.11:g.162681995G>A
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 TSC-CSHL ss2232235 Oct 23, 2000 (88)
2 BCM_SSAHASNP ss14204947 Dec 05, 2003 (119)
3 ABI ss44418921 Mar 14, 2006 (126)
4 BCMHGSC_JDW ss92355512 Mar 24, 2008 (129)
5 HUMANGENOME_JCVI ss96070000 Feb 06, 2009 (130)
6 1000GENOMES ss112643198 Jan 25, 2009 (130)
7 ILLUMINA-UK ss117355185 Feb 14, 2009 (130)
8 ENSEMBL ss139268933 Dec 01, 2009 (131)
9 ENSEMBL ss143926891 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss167394614 Jul 04, 2010 (132)
11 BUSHMAN ss203454791 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss206184625 Jul 04, 2010 (132)
13 1000GENOMES ss220546014 Jul 14, 2010 (132)
14 1000GENOMES ss232118993 Jul 14, 2010 (132)
15 1000GENOMES ss239471806 Jul 15, 2010 (132)
16 BL ss253651863 May 09, 2011 (134)
17 GMI ss277433473 May 04, 2012 (137)
18 PJP ss292963126 May 09, 2011 (134)
19 TISHKOFF ss557079757 Apr 25, 2013 (138)
20 SSMP ss650820040 Apr 25, 2013 (138)
21 EVA-GONL ss979391036 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1071005592 Aug 21, 2014 (142)
23 1000GENOMES ss1307032318 Aug 21, 2014 (142)
24 DDI ss1429653901 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1580271773 Apr 01, 2015 (144)
26 EVA_DECODE ss1588883869 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1608678815 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1651672848 Apr 01, 2015 (144)
29 HAMMER_LAB ss1800347111 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1922614442 Feb 12, 2016 (147)
31 ILLUMINA ss1946101177 Feb 12, 2016 (147)
32 ILLUMINA ss1958623496 Feb 12, 2016 (147)
33 GENOMED ss1969575143 Jul 19, 2016 (147)
34 JJLAB ss2021881317 Sep 14, 2016 (149)
35 USC_VALOUEV ss2149976992 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2257651037 Dec 20, 2016 (150)
37 ILLUMINA ss2634037654 Nov 08, 2017 (151)
38 GRF ss2705395701 Nov 08, 2017 (151)
39 ILLUMINA ss2710990505 Nov 08, 2017 (151)
40 GNOMAD ss2801634507 Nov 08, 2017 (151)
41 SWEGEN ss2993546370 Nov 08, 2017 (151)
42 ILLUMINA ss3022307597 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3024708194 Nov 08, 2017 (151)
44 CSHL ss3345367878 Nov 08, 2017 (151)
45 ILLUMINA ss3625830481 Oct 12, 2018 (152)
46 ILLUMINA ss3644833833 Oct 12, 2018 (152)
47 URBANLAB ss3647573063 Oct 12, 2018 (152)
48 ILLUMINA ss3652788304 Oct 12, 2018 (152)
49 EGCUT_WGS ss3661488117 Jul 13, 2019 (153)
50 EVA_DECODE ss3710711096 Jul 13, 2019 (153)
51 ILLUMINA ss3726076108 Jul 13, 2019 (153)
52 ACPOP ss3730540743 Jul 13, 2019 (153)
53 ILLUMINA ss3744225427 Jul 13, 2019 (153)
54 ILLUMINA ss3744518245 Jul 13, 2019 (153)
55 EVA ss3760962662 Jul 13, 2019 (153)
56 PAGE_CC ss3771078809 Jul 13, 2019 (153)
57 PACBIO ss3784523289 Jul 13, 2019 (153)
58 PACBIO ss3790007652 Jul 13, 2019 (153)
59 PACBIO ss3794882297 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3804097063 Jul 13, 2019 (153)
61 EVA ss3828185657 Apr 25, 2020 (154)
62 EVA ss3837526188 Apr 25, 2020 (154)
63 EVA ss3842957957 Apr 25, 2020 (154)
64 SGDP_PRJ ss3857431120 Apr 25, 2020 (154)
65 KRGDB ss3903490139 Apr 25, 2020 (154)
66 KOGIC ss3952831164 Apr 25, 2020 (154)
67 EVA ss3984518405 Apr 26, 2021 (155)
68 EVA ss3985033888 Apr 26, 2021 (155)
69 TOPMED ss4591254409 Apr 26, 2021 (155)
70 TOMMO_GENOMICS ss5162567896 Apr 26, 2021 (155)
71 1000G_HIGH_COVERAGE ss5256788380 Oct 12, 2022 (156)
72 EVA ss5344661458 Oct 12, 2022 (156)
73 HUGCELL_USP ss5455852849 Oct 12, 2022 (156)
74 EVA ss5507286428 Oct 12, 2022 (156)
75 1000G_HIGH_COVERAGE ss5536627280 Oct 12, 2022 (156)
76 SANFORD_IMAGENETICS ss5624536746 Oct 12, 2022 (156)
77 SANFORD_IMAGENETICS ss5633625783 Oct 12, 2022 (156)
78 TOMMO_GENOMICS ss5695728676 Oct 12, 2022 (156)
79 YY_MCH ss5804438470 Oct 12, 2022 (156)
80 EVA ss5826775037 Oct 12, 2022 (156)
81 EVA ss5853932811 Oct 12, 2022 (156)
82 EVA ss5871880692 Oct 12, 2022 (156)
83 EVA ss5961996844 Oct 12, 2022 (156)
84 1000Genomes NC_000003.11 - 162681995 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000003.12 - 162964207 Oct 12, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 162681995 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000003.11 - 162681995 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000003.11 - 162681995 Apr 25, 2020 (154)
89 gnomAD - Genomes NC_000003.12 - 162964207 Apr 26, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000003.11 - 162681995 Apr 25, 2020 (154)
91 HapMap NC_000003.12 - 162964207 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000003.11 - 162681995 Apr 25, 2020 (154)
93 Korean Genome Project NC_000003.12 - 162964207 Apr 25, 2020 (154)
94 Northern Sweden NC_000003.11 - 162681995 Jul 13, 2019 (153)
95 The PAGE Study NC_000003.12 - 162964207 Jul 13, 2019 (153)
96 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000003.11 - 162681995 Apr 26, 2021 (155)
97 CNV burdens in cranial meningiomas NC_000003.11 - 162681995 Apr 26, 2021 (155)
98 Qatari NC_000003.11 - 162681995 Apr 25, 2020 (154)
99 SGDP_PRJ NC_000003.11 - 162681995 Apr 25, 2020 (154)
100 Siberian NC_000003.11 - 162681995 Apr 25, 2020 (154)
101 8.3KJPN NC_000003.11 - 162681995 Apr 26, 2021 (155)
102 14KJPN NC_000003.12 - 162964207 Oct 12, 2022 (156)
103 TopMed NC_000003.12 - 162964207 Apr 26, 2021 (155)
104 UK 10K study - Twins NC_000003.11 - 162681995 Oct 12, 2018 (152)
105 A Vietnamese Genetic Variation Database NC_000003.11 - 162681995 Jul 13, 2019 (153)
106 ALFA NC_000003.12 - 162964207 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
ss92355512, ss112643198, ss117355185, ss167394614, ss203454791, ss206184625, ss253651863, ss277433473, ss292963126, ss1588883869 NC_000003.10:164164688:G:A NC_000003.12:162964206:G:A (self)
18328658, 10213246, 7226365, 6436712, 4487164, 10667533, 3825608, 259815, 67757, 4656372, 9448100, 2493346, 20537203, 10213246, 2231490, ss220546014, ss232118993, ss239471806, ss557079757, ss650820040, ss979391036, ss1071005592, ss1307032318, ss1429653901, ss1580271773, ss1608678815, ss1651672848, ss1800347111, ss1922614442, ss1946101177, ss1958623496, ss1969575143, ss2021881317, ss2149976992, ss2634037654, ss2705395701, ss2710990505, ss2801634507, ss2993546370, ss3022307597, ss3345367878, ss3625830481, ss3644833833, ss3652788304, ss3661488117, ss3730540743, ss3744225427, ss3744518245, ss3760962662, ss3784523289, ss3790007652, ss3794882297, ss3828185657, ss3837526188, ss3857431120, ss3903490139, ss3984518405, ss3985033888, ss5162567896, ss5344661458, ss5507286428, ss5624536746, ss5633625783, ss5826775037, ss5961996844 NC_000003.11:162681994:G:A NC_000003.12:162964206:G:A (self)
24153215, 130186179, 2499056, 9209165, 300278, 29565780, 428631964, 4380951190, ss2257651037, ss3024708194, ss3647573063, ss3710711096, ss3726076108, ss3771078809, ss3804097063, ss3842957957, ss3952831164, ss4591254409, ss5256788380, ss5455852849, ss5536627280, ss5695728676, ss5804438470, ss5853932811, ss5871880692 NC_000003.12:162964206:G:A NC_000003.12:162964206:G:A (self)
ss14204947 NT_005612.14:69177152:G:A NC_000003.12:162964206:G:A (self)
ss2232235, ss44418921, ss96070000, ss139268933, ss143926891 NT_005612.16:69177140:G:A NC_000003.12:162964206:G:A (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 rs1425609
PMID Title Author Year Journal
21782286 A genome-wide association study of aging. Walter S et al. 2011 Neurobiology of aging
22499766 The search for longevity and healthy aging genes: insights from epidemiological studies and samples of long-lived individuals. Murabito JM et al. 2012 The journals of gerontology. Series A, Biological sciences and medical sciences
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