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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.

rs667089

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:16306320 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.403393 (106774/264690, TOPMED)
A=0.409552 (57357/140048, GnomAD)
A=0.42986 (8120/18890, ALFA) (+ 15 more)
A=0.10143 (1700/16760, 8.3KJPN)
A=0.2947 (1476/5008, 1000G)
A=0.4058 (1818/4480, Estonian)
A=0.4593 (1770/3854, ALSPAC)
A=0.4717 (1749/3708, TWINSUK)
A=0.1239 (363/2930, KOREAN)
A=0.1206 (221/1832, Korea1K)
A=0.454 (453/998, GoNL)
A=0.422 (253/600, NorthernSweden)
A=0.209 (104/498, SGDP_PRJ)
A=0.302 (99/328, HapMap)
A=0.324 (70/216, Qatari)
A=0.154 (33/214, Vietnamese)
A=0.13 (7/54, Siberian)
A=0.40 (16/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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 2 NC_000002.12:g.16306320A>T
GRCh37.p13 chr 2 NC_000002.11:g.16487588A>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

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 18890 A=0.42986 T=0.57014
European Sub 14286 A=0.45219 T=0.54781
African Sub 2946 A=0.3500 T=0.6500
African Others Sub 114 A=0.281 T=0.719
African American Sub 2832 A=0.3528 T=0.6472
Asian Sub 112 A=0.170 T=0.830
East Asian Sub 86 A=0.14 T=0.86
Other Asian Sub 26 A=0.27 T=0.73
Latin American 1 Sub 146 A=0.438 T=0.562
Latin American 2 Sub 610 A=0.416 T=0.584
South Asian Sub 98 A=0.16 T=0.84
Other Sub 692 A=0.399 T=0.601


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=0.403393 T=0.596607
gnomAD - Genomes Global Study-wide 140048 A=0.409552 T=0.590448
gnomAD - Genomes European Sub 75826 A=0.45763 T=0.54237
gnomAD - Genomes African Sub 41990 A=0.34723 T=0.65277
gnomAD - Genomes American Sub 13640 A=0.40015 T=0.59985
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.3779 T=0.6221
gnomAD - Genomes East Asian Sub 3128 A=0.1579 T=0.8421
gnomAD - Genomes Other Sub 2146 A=0.4059 T=0.5941
8.3KJPN JAPANESE Study-wide 16760 A=0.10143 T=0.89857
1000Genomes Global Study-wide 5008 A=0.2947 T=0.7053
1000Genomes African Sub 1322 A=0.3230 T=0.6770
1000Genomes East Asian Sub 1008 A=0.1508 T=0.8492
1000Genomes Europe Sub 1006 A=0.4712 T=0.5288
1000Genomes South Asian Sub 978 A=0.143 T=0.857
1000Genomes American Sub 694 A=0.408 T=0.592
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4058 T=0.5942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4593 T=0.5407
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4717 T=0.5283
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1239 T=0.8761
Korean Genome Project KOREAN Study-wide 1832 A=0.1206 T=0.8794
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.454 T=0.546
Northern Sweden ACPOP Study-wide 600 A=0.422 T=0.578
SGDP_PRJ Global Study-wide 498 A=0.209 T=0.791
HapMap Global Study-wide 328 A=0.302 T=0.698
HapMap African Sub 120 A=0.275 T=0.725
HapMap American Sub 120 A=0.450 T=0.550
HapMap Asian Sub 88 A=0.14 T=0.86
Qatari Global Study-wide 216 A=0.324 T=0.676
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.154 T=0.846
Siberian Global Study-wide 54 A=0.13 T=0.87
The Danish reference pan genome Danish Study-wide 40 A=0.40 T=0.60
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= T
GRCh38.p13 chr 2 NC_000002.12:g.16306320= NC_000002.12:g.16306320A>T
GRCh37.p13 chr 2 NC_000002.11:g.16487588= NC_000002.11:g.16487588A>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 ss840387 Aug 11, 2000 (83)
2 KWOK ss1266653 Oct 04, 2000 (86)
3 TSC-CSHL ss2233768 Oct 23, 2000 (88)
4 SC_JCM ss5656918 Feb 20, 2003 (111)
5 BCM_SSAHASNP ss9922030 Jul 11, 2003 (116)
6 WI_SSAHASNP ss11446051 Jul 11, 2003 (116)
7 PERLEGEN ss24646667 Sep 20, 2004 (123)
8 ABI ss44322609 Mar 15, 2006 (126)
9 ILLUMINA ss65719295 Oct 16, 2006 (127)
10 PERLEGEN ss68805273 May 17, 2007 (127)
11 KRIBB_YJKIM ss80755435 Dec 15, 2007 (130)
12 HGSV ss84955845 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss91070162 Mar 24, 2008 (129)
14 HUMANGENOME_JCVI ss97016256 Feb 05, 2009 (130)
15 BGI ss106072165 Feb 05, 2009 (130)
16 1000GENOMES ss109261451 Jan 23, 2009 (130)
17 1000GENOMES ss112330628 Jan 25, 2009 (130)
18 ILLUMINA-UK ss117606835 Feb 14, 2009 (130)
19 ILLUMINA ss120244573 Dec 01, 2009 (131)
20 ENSEMBL ss136083026 Dec 01, 2009 (131)
21 ENSEMBL ss138396645 Dec 01, 2009 (131)
22 GMI ss156747813 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss163138923 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss163931519 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss166201737 Jul 04, 2010 (132)
26 BUSHMAN ss200095291 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss205896429 Jul 04, 2010 (132)
28 1000GENOMES ss219092656 Jul 14, 2010 (132)
29 1000GENOMES ss231056116 Jul 14, 2010 (132)
30 1000GENOMES ss238637193 Jul 15, 2010 (132)
31 GMI ss276367795 May 04, 2012 (137)
32 GMI ss284299224 Apr 25, 2013 (138)
33 PJP ss292455588 May 09, 2011 (134)
34 TISHKOFF ss555385306 Apr 25, 2013 (138)
35 SSMP ss648962699 Apr 25, 2013 (138)
36 EVA-GONL ss976533857 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1068895046 Aug 21, 2014 (142)
38 1000GENOMES ss1296081978 Aug 21, 2014 (142)
39 DDI ss1428492789 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1578758692 Apr 01, 2015 (144)
41 EVA_DECODE ss1585934636 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1602901144 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1645895177 Apr 01, 2015 (144)
44 HAMMER_LAB ss1796348390 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1919768234 Feb 12, 2016 (147)
46 GENOMED ss1968704968 Jul 19, 2016 (147)
47 JJLAB ss2020409849 Sep 14, 2016 (149)
48 USC_VALOUEV ss2148454357 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2227868137 Dec 20, 2016 (150)
50 TOPMED ss2393777997 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624722434 Nov 08, 2017 (151)
52 GRF ss2703013710 Nov 08, 2017 (151)
53 GNOMAD ss2770215227 Nov 08, 2017 (151)
54 SWEGEN ss2989048351 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3023972161 Nov 08, 2017 (151)
56 TOPMED ss3300403381 Nov 08, 2017 (151)
57 CSHL ss3344095858 Nov 08, 2017 (151)
58 URBANLAB ss3646975312 Oct 11, 2018 (152)
59 EGCUT_WGS ss3656997706 Jul 12, 2019 (153)
60 EVA_DECODE ss3703338458 Jul 12, 2019 (153)
61 ACPOP ss3728191240 Jul 12, 2019 (153)
62 EVA ss3756408165 Jul 12, 2019 (153)
63 PACBIO ss3783791076 Jul 12, 2019 (153)
64 PACBIO ss3789390555 Jul 12, 2019 (153)
65 PACBIO ss3794263283 Jul 12, 2019 (153)
66 KHV_HUMAN_GENOMES ss3800793249 Jul 12, 2019 (153)
67 EVA ss3826842611 Apr 25, 2020 (154)
68 EVA ss3836827358 Apr 25, 2020 (154)
69 EVA ss3842241555 Apr 25, 2020 (154)
70 SGDP_PRJ ss3851687400 Apr 25, 2020 (154)
71 KRGDB ss3897077852 Apr 25, 2020 (154)
72 KOGIC ss3947195673 Apr 25, 2020 (154)
73 TOPMED ss4495631084 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5150068500 Apr 26, 2021 (155)
75 1000Genomes NC_000002.11 - 16487588 Oct 11, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 16487588 Oct 11, 2018 (152)
77 Genetic variation in the Estonian population NC_000002.11 - 16487588 Oct 11, 2018 (152)
78 The Danish reference pan genome NC_000002.11 - 16487588 Apr 25, 2020 (154)
79 gnomAD - Genomes NC_000002.12 - 16306320 Apr 26, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000002.11 - 16487588 Apr 25, 2020 (154)
81 HapMap NC_000002.12 - 16306320 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000002.11 - 16487588 Apr 25, 2020 (154)
83 Korean Genome Project NC_000002.12 - 16306320 Apr 25, 2020 (154)
84 Northern Sweden NC_000002.11 - 16487588 Jul 12, 2019 (153)
85 Qatari NC_000002.11 - 16487588 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000002.11 - 16487588 Apr 25, 2020 (154)
87 Siberian NC_000002.11 - 16487588 Apr 25, 2020 (154)
88 8.3KJPN NC_000002.11 - 16487588 Apr 26, 2021 (155)
89 TopMed NC_000002.12 - 16306320 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000002.11 - 16487588 Oct 11, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000002.11 - 16487588 Jul 12, 2019 (153)
92 ALFA NC_000002.12 - 16306320 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)
rs17468423 Oct 07, 2004 (123)
rs59389330 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84955845 NC_000002.9:16409215:A:T NC_000002.12:16306319:A:T (self)
ss91070162, ss109261451, ss112330628, ss117606835, ss163138923, ss163931519, ss166201737, ss200095291, ss205896429, ss276367795, ss284299224, ss292455588, ss1585934636 NC_000002.10:16351068:A:T NC_000002.12:16306319:A:T (self)
6989390, 3876978, 2735954, 4936166, 1705131, 4255246, 1476105, 1810164, 3704380, 970711, 8037807, 3876978, 846171, ss219092656, ss231056116, ss238637193, ss555385306, ss648962699, ss976533857, ss1068895046, ss1296081978, ss1428492789, ss1578758692, ss1602901144, ss1645895177, ss1796348390, ss1919768234, ss1968704968, ss2020409849, ss2148454357, ss2393777997, ss2624722434, ss2703013710, ss2770215227, ss2989048351, ss3344095858, ss3656997706, ss3728191240, ss3756408165, ss3783791076, ss3789390555, ss3794263283, ss3826842611, ss3836827358, ss3851687400, ss3897077852, ss5150068500 NC_000002.11:16487587:A:T NC_000002.12:16306319:A:T (self)
49699169, 1743661, 3573674, 186812218, 299453963, 2387520020, ss2227868137, ss3023972161, ss3300403381, ss3646975312, ss3703338458, ss3800793249, ss3842241555, ss3947195673, ss4495631084 NC_000002.12:16306319:A:T NC_000002.12:16306319:A:T (self)
ss9922030, ss11446051 NT_015926.13:129665:A:T NC_000002.12:16306319:A:T (self)
ss840387, ss1266653, ss2233768, ss5656918, ss24646667, ss44322609, ss65719295, ss68805273, ss80755435, ss97016256, ss106072165, ss120244573, ss136083026, ss138396645, ss156747813 NT_015926.15:157863:A:T NC_000002.12:16306319:A: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 rs667089

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.post596+ae089ad