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.

rs2894259

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:32465538 (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=0.285594 (39448/138126, GnomAD)
A=0.29857 (8437/28258, 14KJPN)
A=0.29916 (5014/16760, 8.3KJPN) (+ 7 more)
A=0.28711 (4689/16332, ALFA)
A=0.2886 (1848/6404, 1000G_30x)
A=0.2915 (1460/5008, 1000G)
A=0.3147 (1410/4480, Estonian)
A=0.2413 (705/2922, KOREAN)
A=0.322 (193/600, NorthernSweden)
G=0.391 (93/238, SGDP_PRJ)
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=0.71289 A=0.28711
European Sub 12080 G=0.72939 A=0.27061
African Sub 2816 G=0.6456 A=0.3544
African Others Sub 108 G=0.676 A=0.324
African American Sub 2708 G=0.6444 A=0.3556
Asian Sub 108 G=0.750 A=0.250
East Asian Sub 84 G=0.73 A=0.27
Other Asian Sub 24 G=0.83 A=0.17
Latin American 1 Sub 146 G=0.726 A=0.274
Latin American 2 Sub 610 G=0.675 A=0.325
South Asian Sub 94 G=0.72 A=0.28
Other Sub 478 G=0.726 A=0.274


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
gnomAD - Genomes Global Study-wide 138126 G=0.714406 A=0.285594
gnomAD - Genomes European Sub 75038 G=0.73424 A=0.26576
gnomAD - Genomes African Sub 41146 G=0.66427 A=0.33573
gnomAD - Genomes American Sub 13432 G=0.73049 A=0.26951
gnomAD - Genomes Ashkenazi Jewish Sub 3296 G=0.7649 A=0.2351
gnomAD - Genomes East Asian Sub 3094 G=0.7728 A=0.2272
gnomAD - Genomes Other Sub 2120 G=0.7198 A=0.2802
14KJPN JAPANESE Study-wide 28258 G=0.70143 A=0.29857
8.3KJPN JAPANESE Study-wide 16760 G=0.70084 A=0.29916
Allele Frequency Aggregator Total Global 16332 G=0.71289 A=0.28711
Allele Frequency Aggregator European Sub 12080 G=0.72939 A=0.27061
Allele Frequency Aggregator African Sub 2816 G=0.6456 A=0.3544
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.675 A=0.325
Allele Frequency Aggregator Other Sub 478 G=0.726 A=0.274
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.726 A=0.274
Allele Frequency Aggregator Asian Sub 108 G=0.750 A=0.250
Allele Frequency Aggregator South Asian Sub 94 G=0.72 A=0.28
1000Genomes_30x Global Study-wide 6404 G=0.7114 A=0.2886
1000Genomes_30x African Sub 1786 G=0.6221 A=0.3779
1000Genomes_30x Europe Sub 1266 G=0.7662 A=0.2338
1000Genomes_30x South Asian Sub 1202 G=0.7388 A=0.2612
1000Genomes_30x East Asian Sub 1170 G=0.7462 A=0.2538
1000Genomes_30x American Sub 980 G=0.729 A=0.271
1000Genomes Global Study-wide 5008 G=0.7085 A=0.2915
1000Genomes African Sub 1322 G=0.6142 A=0.3858
1000Genomes East Asian Sub 1008 G=0.7391 A=0.2609
1000Genomes Europe Sub 1006 G=0.7555 A=0.2445
1000Genomes South Asian Sub 978 G=0.745 A=0.255
1000Genomes American Sub 694 G=0.723 A=0.277
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6853 A=0.3147
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.7587 A=0.2413
Northern Sweden ACPOP Study-wide 600 G=0.678 A=0.322
SGDP_PRJ Global Study-wide 238 G=0.391 A=0.609
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 6 NC_000006.12:g.32465538G>A
GRCh37.p13 chr 6 NC_000006.11:g.32433315G>A
DR51 genomic region NG_002432.1:g.12806G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3903631A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3903737A>G
DR52 genomic region NG_002392.2:g.29842A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3688630G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3694226G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3705828G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3711413G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3780822G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3780120G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3769791G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3775411G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3806423G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3812008G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.3797783G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.3747699G>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 6 NC_000006.12:g.32465538= NC_000006.12:g.32465538G>A
GRCh37.p13 chr 6 NC_000006.11:g.32433315= NC_000006.11:g.32433315G>A
DR51 genomic region NG_002432.1:g.12806= NG_002432.1:g.12806G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.3903631A>G NT_113891.3:g.3903631=
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.3903737A>G NT_113891.2:g.3903737=
DR52 genomic region NG_002392.2:g.29842A>G NG_002392.2:g.29842=
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.3688630= NT_167248.2:g.3688630G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.3694226= NT_167248.1:g.3694226G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.3705828= NT_167245.2:g.3705828G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.3711413= NT_167245.1:g.3711413G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.3780822= NT_167249.2:g.3780822G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.3780120= NT_167249.1:g.3780120G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.3769791= NT_167246.2:g.3769791G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.3775411= NT_167246.1:g.3775411G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.3806423= NT_167247.2:g.3806423G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.3812008= NT_167247.1:g.3812008G>A
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.3797783= NT_167244.2:g.3797783G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.3747699= NT_167244.1:g.3747699G>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#.

31 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss4087461 Nov 05, 2001 (101)
2 SI_MHC_SNP ss12693885 Oct 31, 2003 (119)
3 1000GENOMES ss1319581085 Aug 21, 2014 (142)
4 HAMMER_LAB ss1804361794 Sep 08, 2015 (146)
5 SYSTEMSBIOZJU ss2626311819 Nov 08, 2017 (151)
6 GRF ss2707409464 Nov 08, 2017 (151)
7 GNOMAD ss2837491387 Nov 08, 2017 (151)
8 SWEGEN ss2998809516 Nov 08, 2017 (151)
9 BIOINF_KMB_FNS_UNIBA ss3645944855 Oct 12, 2018 (152)
10 EGCUT_WGS ss3666722842 Jul 13, 2019 (153)
11 ACPOP ss3733369789 Jul 13, 2019 (153)
12 KHV_HUMAN_GENOMES ss3807987232 Jul 13, 2019 (153)
13 EVA ss3829837748 Apr 26, 2020 (154)
14 EVA ss3838397747 Apr 26, 2020 (154)
15 EVA ss3843840022 Apr 26, 2020 (154)
16 SGDP_PRJ ss3864269656 Apr 26, 2020 (154)
17 KRGDB ss3911047140 Apr 26, 2020 (154)
18 VINODS ss4025172575 Apr 26, 2021 (155)
19 VINODS ss4025211143 Apr 26, 2021 (155)
20 VINODS ss4025231170 Apr 26, 2021 (155)
21 VINODS ss4025249960 Apr 26, 2021 (155)
22 VINODS ss4025268750 Apr 26, 2021 (155)
23 VINODS ss4025289590 Apr 26, 2021 (155)
24 TOMMO_GENOMICS ss5176866675 Apr 26, 2021 (155)
25 1000G_HIGH_COVERAGE ss5267958375 Oct 17, 2022 (156)
26 EVA ss5364758283 Oct 17, 2022 (156)
27 EVA ss5508433929 Oct 17, 2022 (156)
28 1000G_HIGH_COVERAGE ss5553622250 Oct 17, 2022 (156)
29 SANFORD_IMAGENETICS ss5640103228 Oct 17, 2022 (156)
30 TOMMO_GENOMICS ss5714731107 Oct 17, 2022 (156)
31 YY_MCH ss5807316500 Oct 17, 2022 (156)
32 1000Genomes NC_000006.11 - 32433315 Oct 12, 2018 (152)
33 1000Genomes_30x NC_000006.12 - 32465538 Oct 17, 2022 (156)
34 Genetic variation in the Estonian population NC_000006.11 - 32433315 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000006.12 - 32465538 Apr 26, 2021 (155)
36 KOREAN population from KRGDB NC_000006.11 - 32433315 Apr 26, 2020 (154)
37 Northern Sweden NC_000006.11 - 32433315 Jul 13, 2019 (153)
38 SGDP_PRJ NC_000006.11 - 32433315 Apr 26, 2020 (154)
39 8.3KJPN NC_000006.11 - 32433315 Apr 26, 2021 (155)
40 14KJPN NC_000006.12 - 32465538 Oct 17, 2022 (156)
41 ALFA NC_000006.12 - 32465538 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)
rs9268935 Dec 04, 2003 (119)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
31349563, 12461090, 18224534, 6654654, 16286636, 34835982, ss1319581085, ss1804361794, ss2626311819, ss2707409464, ss2837491387, ss2998809516, ss3666722842, ss3733369789, ss3829837748, ss3838397747, ss3864269656, ss3911047140, ss5176866675, ss5364758283, ss5508433929, ss5640103228 NC_000006.11:32433314:G:A NC_000006.12:32465537:G:A (self)
41148185, 221376980, 48568211, 11323822360, ss3645944855, ss3807987232, ss3843840022, ss5267958375, ss5553622250, ss5714731107, ss5807316500 NC_000006.12:32465537:G:A NC_000006.12:32465537:G:A (self)
ss4087461, ss12693885 NT_007592.15:32373314:G:A NC_000006.12:32465537:G:A (self)
ss4025172575 NT_167244.2:3797782:G:A NC_000006.12:32465537:G:A (self)
ss4025211143 NT_167245.2:3705827:G:A NC_000006.12:32465537:G:A (self)
ss4025231170 NT_167246.2:3769790:G:A NC_000006.12:32465537:G:A (self)
ss4025249960 NT_167247.2:3806422:G:A NC_000006.12:32465537:G:A (self)
ss4025268750 NT_167248.2:3688629:G:A NC_000006.12:32465537:G:A (self)
ss4025289590 NT_167249.2:3780821:G:A NC_000006.12:32465537: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.

No publications for rs2894259

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