Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs2788089

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:2958655 (GRCh38.p13) 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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.034890 (9235/264690, TOPMED)
G=0.037262 (5227/140278, GnomAD)
G=0.03742 (718/19190, ALFA) (+ 17 more)
G=0.00000 (0/16760, 8.3KJPN)
G=0.0200 (100/5008, 1000G)
G=0.0266 (119/4480, Estonian)
G=0.0558 (215/3854, ALSPAC)
G=0.0615 (228/3708, TWINSUK)
G=0.0000 (0/2930, KOREAN)
C=0.0000 (0/2930, KOREAN)
T=0.0000 (0/2930, KOREAN)
G=0.0000 (0/1832, Korea1K)
G=0.068 (68/998, GoNL)
G=0.053 (32/600, NorthernSweden)
G=0.014 (8/558, SGDP_PRJ)
G=0.016 (5/316, HapMap)
G=0.042 (9/216, Qatari)
G=0.000 (0/216, Vietnamese)
G=0.00 (0/56, Siberian)
G=0.05 (2/40, GENOME_DK)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 19190 G=0.03742 A=0.96258
European Sub 14286 G=0.04438 A=0.95562
African Sub 2970 G=0.0077 A=0.9923
African Others Sub 114 G=0.000 A=1.000
African American Sub 2856 G=0.0081 A=0.9919
Asian Sub 116 G=0.000 A=1.000
East Asian Sub 88 G=0.00 A=1.00
Other Asian Sub 28 G=0.00 A=1.00
Latin American 1 Sub 154 G=0.032 A=0.968
Latin American 2 Sub 616 G=0.028 A=0.972
South Asian Sub 98 G=0.00 A=1.00
Other Sub 950 G=0.041 A=0.959


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=0.034890 A=0.965110
gnomAD - Genomes Global Study-wide 140278 G=0.037262 A=0.962738
gnomAD - Genomes European Sub 75942 G=0.05424 A=0.94576
gnomAD - Genomes African Sub 42068 G=0.00972 A=0.99028
gnomAD - Genomes American Sub 13656 G=0.03676 A=0.96324
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.0328 A=0.9672
gnomAD - Genomes East Asian Sub 3134 G=0.0000 A=1.0000
gnomAD - Genomes Other Sub 2154 G=0.0409 A=0.9591
8.3KJPN JAPANESE Study-wide 16760 G=0.00000 A=1.00000
1000Genomes Global Study-wide 5008 G=0.0200 A=0.9800
1000Genomes African Sub 1322 G=0.0023 A=0.9977
1000Genomes East Asian Sub 1008 G=0.0010 A=0.9990
1000Genomes Europe Sub 1006 G=0.0447 A=0.9553
1000Genomes South Asian Sub 978 G=0.028 A=0.972
1000Genomes American Sub 694 G=0.035 A=0.965
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.0266 A=0.9734
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.0558 A=0.9442
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.0615 A=0.9385
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0000 A=1.0000, C=0.0000, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.0000 A=1.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.068 A=0.932
Northern Sweden ACPOP Study-wide 600 G=0.053 A=0.947
SGDP_PRJ Global Study-wide 558 G=0.014 A=0.986
HapMap Global Study-wide 316 G=0.016 A=0.984
HapMap African Sub 118 G=0.000 A=1.000
HapMap American Sub 118 G=0.042 A=0.958
HapMap Asian Sub 80 G=0.00 A=1.00
Qatari Global Study-wide 216 G=0.042 A=0.958
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.000 A=1.000
Siberian Global Study-wide 56 G=0.00 A=1.00
The Danish reference pan genome Danish Study-wide 40 G=0.05 A=0.95
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.p13 chr 1 NC_000001.11:g.2958655G>A
GRCh38.p13 chr 1 NC_000001.11:g.2958655G>C
GRCh38.p13 chr 1 NC_000001.11:g.2958655G>T
GRCh37.p13 chr 1 NC_000001.10:g.2875220G>A
GRCh37.p13 chr 1 NC_000001.10:g.2875220G>C
GRCh37.p13 chr 1 NC_000001.10:g.2875220G>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= A C T
GRCh38.p13 chr 1 NC_000001.11:g.2958655= NC_000001.11:g.2958655G>A NC_000001.11:g.2958655G>C NC_000001.11:g.2958655G>T
GRCh37.p13 chr 1 NC_000001.10:g.2875220= NC_000001.10:g.2875220G>A NC_000001.10:g.2875220G>C NC_000001.10:g.2875220G>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#.

74 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3946471 Sep 28, 2001 (100)
2 WI_SSAHASNP ss6396348 Feb 20, 2003 (113)
3 BCM_SSAHASNP ss9880476 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss17344274 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19845813 Feb 27, 2004 (120)
6 SSAHASNP ss20516194 Apr 05, 2004 (121)
7 PERLEGEN ss24241333 Sep 20, 2004 (123)
8 HGSV ss77300527 Dec 07, 2007 (129)
9 HGSV ss82167654 Dec 15, 2007 (130)
10 HGSV ss82510493 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss87169720 Mar 23, 2008 (129)
12 HUMANGENOME_JCVI ss97915056 Feb 06, 2009 (130)
13 BGI ss105114104 Dec 01, 2009 (131)
14 1000GENOMES ss107943702 Jan 22, 2009 (130)
15 1000GENOMES ss109956334 Jan 24, 2009 (130)
16 ILLUMINA-UK ss118447067 Feb 14, 2009 (130)
17 ENSEMBL ss137760768 Dec 01, 2009 (131)
18 ENSEMBL ss138986620 Dec 01, 2009 (131)
19 GMI ss154550126 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162996429 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss163725732 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss165999482 Jul 04, 2010 (132)
23 BUSHMAN ss197912258 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss205049274 Jul 04, 2010 (132)
25 1000GENOMES ss218198360 Jul 14, 2010 (132)
26 1000GENOMES ss230400899 Jul 14, 2010 (132)
27 1000GENOMES ss238120097 Jul 15, 2010 (132)
28 BL ss252875378 May 09, 2011 (134)
29 GMI ss275688600 May 04, 2012 (137)
30 GMI ss283990013 Apr 25, 2013 (138)
31 PJP ss290496936 May 09, 2011 (134)
32 ILLUMINA ss535858173 Sep 08, 2015 (146)
33 TISHKOFF ss553727065 Apr 25, 2013 (138)
34 SSMP ss647530492 Apr 25, 2013 (138)
35 EVA-GONL ss974787511 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1067621909 Aug 21, 2014 (142)
37 1000GENOMES ss1289418853 Aug 21, 2014 (142)
38 DDI ss1425690353 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1573857140 Apr 01, 2015 (144)
40 EVA_DECODE ss1584147034 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1599410954 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1642404987 Apr 01, 2015 (144)
43 HAMMER_LAB ss1793757084 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1917982466 Feb 12, 2016 (147)
45 GENOMED ss1966669898 Jul 19, 2016 (147)
46 JJLAB ss2019507414 Sep 14, 2016 (149)
47 USC_VALOUEV ss2147497398 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2159507423 Dec 20, 2016 (150)
49 TOPMED ss2321663036 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2624269577 Nov 08, 2017 (151)
51 GRF ss2697390966 Nov 08, 2017 (151)
52 GNOMAD ss2750884604 Nov 08, 2017 (151)
53 SWEGEN ss2986188330 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3023517494 Nov 08, 2017 (151)
55 TOPMED ss3066934697 Nov 08, 2017 (151)
56 CSHL ss3343284646 Nov 08, 2017 (151)
57 ILLUMINA ss3626010000 Oct 11, 2018 (152)
58 URBANLAB ss3646585292 Oct 11, 2018 (152)
59 EGCUT_WGS ss3654289310 Jul 12, 2019 (153)
60 EVA_DECODE ss3686031104 Jul 12, 2019 (153)
61 ACPOP ss3726732649 Jul 12, 2019 (153)
62 EVA ss3745744353 Jul 12, 2019 (153)
63 PACBIO ss3783307024 Jul 12, 2019 (153)
64 PACBIO ss3788984081 Jul 12, 2019 (153)
65 PACBIO ss3793856707 Jul 12, 2019 (153)
66 KHV_HUMAN_GENOMES ss3798766778 Jul 12, 2019 (153)
67 EVA ss3825989915 Apr 25, 2020 (154)
68 EVA ss3836382214 Apr 25, 2020 (154)
69 EVA ss3841786334 Apr 25, 2020 (154)
70 SGDP_PRJ ss3848050399 Apr 25, 2020 (154)
71 KRGDB ss3892909967 Apr 25, 2020 (154)
72 KOGIC ss3943673587 Apr 25, 2020 (154)
73 TOPMED ss4437054783 Apr 25, 2021 (155)
74 TOMMO_GENOMICS ss5142163911 Apr 25, 2021 (155)
75 1000Genomes NC_000001.10 - 2875220 Oct 11, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2875220 Oct 11, 2018 (152)
77 Genetic variation in the Estonian population NC_000001.10 - 2875220 Oct 11, 2018 (152)
78 The Danish reference pan genome NC_000001.10 - 2875220 Apr 25, 2020 (154)
79 gnomAD - Genomes NC_000001.11 - 2958655 Apr 25, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000001.10 - 2875220 Apr 25, 2020 (154)
81 HapMap NC_000001.11 - 2958655 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000001.10 - 2875220 Apr 25, 2020 (154)
83 Korean Genome Project NC_000001.11 - 2958655 Apr 25, 2020 (154)
84 Northern Sweden NC_000001.10 - 2875220 Jul 12, 2019 (153)
85 Qatari NC_000001.10 - 2875220 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 2875220 Apr 25, 2020 (154)
87 Siberian NC_000001.10 - 2875220 Apr 25, 2020 (154)
88 8.3KJPN NC_000001.10 - 2875220 Apr 25, 2021 (155)
89 TopMed NC_000001.11 - 2958655 Apr 25, 2021 (155)
90 UK 10K study - Twins NC_000001.10 - 2875220 Oct 11, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000001.10 - 2875220 Jul 12, 2019 (153)
92 ALFA NC_000001.11 - 2958655 Apr 25, 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)
rs4648357 Mar 31, 2003 (113)
rs17389126 Oct 07, 2004 (123)
rs60183294 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77300527, ss82167654, ss82510493 NC_000001.8:2898376:G:A NC_000001.11:2958654:G:A (self)
ss87169720, ss107943702, ss109956334, ss118447067, ss162996429, ss163725732, ss165999482, ss197912258, ss205049274, ss252875378, ss275688600, ss283990013, ss290496936, ss1584147034 NC_000001.9:2865079:G:A NC_000001.11:2958654:G:A (self)
85932, 35916, 27558, 1364374, 15038, 87361, 17514, 24396, 67379, 13752, 133218, 35916, 7365, ss218198360, ss230400899, ss238120097, ss535858173, ss553727065, ss647530492, ss974787511, ss1067621909, ss1289418853, ss1425690353, ss1573857140, ss1599410954, ss1642404987, ss1793757084, ss1917982466, ss1966669898, ss2019507414, ss2147497398, ss2321663036, ss2624269577, ss2697390966, ss2750884604, ss2986188330, ss3343284646, ss3626010000, ss3654289310, ss3726732649, ss3745744353, ss3783307024, ss3788984081, ss3793856707, ss3825989915, ss3836382214, ss3848050399, ss3892909967, ss5142163911 NC_000001.10:2875219:G:A NC_000001.11:2958654:G:A (self)
649798, 1614, 51588, 407629, 661118, 5432243909, ss2159507423, ss3023517494, ss3066934697, ss3646585292, ss3686031104, ss3798766778, ss3841786334, ss3943673587, ss4437054783 NC_000001.11:2958654:G:A NC_000001.11:2958654:G:A (self)
ss9880476, ss17344274, ss19845813, ss20516194 NT_004321.15:181994:G:A NC_000001.11:2958654:G:A (self)
ss3946471, ss6396348, ss24241333, ss97915056, ss105114104, ss137760768, ss138986620, ss154550126 NT_004350.19:2353851:G:A NC_000001.11:2958654:G:A (self)
87361, ss3892909967 NC_000001.10:2875219:G:C NC_000001.11:2958654:G:C (self)
87361, ss3892909967 NC_000001.10:2875219:G:T NC_000001.11:2958654: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 rs2788089

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.post629+eb05767