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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.

rs6689789

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99614204 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.394137 (104324/264690, TOPMED)
T=0.446061 (104206/233614, ALFA)
T=0.408373 (57111/139850, GnomAD) (+ 20 more)
T=0.31600 (24869/78700, PAGE_STUDY)
T=0.02315 (388/16760, 8.3KJPN)
T=0.2782 (1393/5008, 1000G)
T=0.4674 (2094/4480, Estonian)
T=0.4678 (1803/3854, ALSPAC)
T=0.4741 (1758/3708, TWINSUK)
T=0.0240 (70/2922, KOREAN)
T=0.2898 (604/2084, HGDP_Stanford)
T=0.2744 (518/1888, HapMap)
T=0.0207 (38/1832, Korea1K)
T=0.3574 (406/1136, Daghestan)
T=0.486 (485/998, GoNL)
T=0.046 (36/788, PRJEB37584)
T=0.405 (243/600, NorthernSweden)
C=0.388 (101/260, SGDP_PRJ)
T=0.380 (82/216, Qatari)
T=0.083 (18/216, Vietnamese)
T=0.45 (18/40, GENOME_DK)
C=0.36 (8/22, Siberian)
T=0.43 (6/14, Ancient Sardinia)
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 1 NC_000001.11:g.99614204C>T
GRCh37.p13 chr 1 NC_000001.10:g.100079760C>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 (New)
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 233614 C=0.553939 T=0.446061
European Sub 203976 C=0.536411 T=0.463589
African Sub 9480 C=0.6470 T=0.3530
African Others Sub 350 C=0.691 T=0.309
African American Sub 9130 C=0.6453 T=0.3547
Asian Sub 3828 C=0.9143 T=0.0857
East Asian Sub 3096 C=0.9651 T=0.0349
Other Asian Sub 732 C=0.699 T=0.301
Latin American 1 Sub 1042 C=0.5950 T=0.4050
Latin American 2 Sub 6518 C=0.6915 T=0.3085
South Asian Sub 368 C=0.764 T=0.236
Other Sub 8402 C=0.5893 T=0.4107


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 C=0.605863 T=0.394137
gnomAD - Genomes Global Study-wide 139850 C=0.591627 T=0.408373
gnomAD - Genomes European Sub 75782 C=0.54195 T=0.45805
gnomAD - Genomes African Sub 41844 C=0.65379 T=0.34621
gnomAD - Genomes American Sub 13630 C=0.60345 T=0.39655
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.5470 T=0.4530
gnomAD - Genomes East Asian Sub 3126 C=0.9482 T=0.0518
gnomAD - Genomes Other Sub 2148 C=0.6085 T=0.3915
The PAGE Study Global Study-wide 78700 C=0.68400 T=0.31600
The PAGE Study AfricanAmerican Sub 32514 C=0.64545 T=0.35455
The PAGE Study Mexican Sub 10810 C=0.70435 T=0.29565
The PAGE Study Asian Sub 8318 C=0.9645 T=0.0355
The PAGE Study PuertoRican Sub 7918 C=0.6048 T=0.3952
The PAGE Study NativeHawaiian Sub 4534 C=0.7281 T=0.2719
The PAGE Study Cuban Sub 4230 C=0.5598 T=0.4402
The PAGE Study Dominican Sub 3828 C=0.6142 T=0.3858
The PAGE Study CentralAmerican Sub 2450 C=0.6710 T=0.3290
The PAGE Study SouthAmerican Sub 1982 C=0.6660 T=0.3340
The PAGE Study NativeAmerican Sub 1260 C=0.5944 T=0.4056
The PAGE Study SouthAsian Sub 856 C=0.801 T=0.199
8.3KJPN JAPANESE Study-wide 16760 C=0.97685 T=0.02315
1000Genomes Global Study-wide 5008 C=0.7218 T=0.2782
1000Genomes African Sub 1322 C=0.7103 T=0.2897
1000Genomes East Asian Sub 1008 C=0.9395 T=0.0605
1000Genomes Europe Sub 1006 C=0.5268 T=0.4732
1000Genomes South Asian Sub 978 C=0.790 T=0.210
1000Genomes American Sub 694 C=0.614 T=0.386
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5326 T=0.4674
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5322 T=0.4678
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5259 T=0.4741
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9760 T=0.0240
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.7102 T=0.2898
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.909 T=0.091
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.795 T=0.205
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.534 T=0.466
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.578 T=0.422
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.657 T=0.343
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.750 T=0.250
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.43 T=0.57
HapMap Global Study-wide 1888 C=0.7256 T=0.2744
HapMap American Sub 768 C=0.708 T=0.292
HapMap African Sub 690 C=0.703 T=0.297
HapMap Asian Sub 254 C=0.965 T=0.035
HapMap Europe Sub 176 C=0.545 T=0.455
Korean Genome Project KOREAN Study-wide 1832 C=0.9793 T=0.0207
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.6426 T=0.3574
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.616 T=0.384
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.646 T=0.354
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.779 T=0.221
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.528 T=0.472
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.78 T=0.22
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.61 T=0.39
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.514 T=0.486
CNV burdens in cranial meningiomas Global Study-wide 788 C=0.954 T=0.046
CNV burdens in cranial meningiomas CRM Sub 788 C=0.954 T=0.046
Northern Sweden ACPOP Study-wide 600 C=0.595 T=0.405
SGDP_PRJ Global Study-wide 260 C=0.388 T=0.612
Qatari Global Study-wide 216 C=0.620 T=0.380
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.917 T=0.083
The Danish reference pan genome Danish Study-wide 40 C=0.55 T=0.45
Siberian Global Study-wide 22 C=0.36 T=0.64
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 14 C=0.57 T=0.43
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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.99614204= NC_000001.11:g.99614204C>T
GRCh37.p13 chr 1 NC_000001.10:g.100079760= NC_000001.10:g.100079760C>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#.

103 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9876391 Jul 11, 2003 (116)
2 PERLEGEN ss24244158 Sep 20, 2004 (123)
3 ILLUMINA ss67842983 Nov 29, 2006 (127)
4 ILLUMINA ss71470256 May 16, 2007 (127)
5 ILLUMINA ss75404933 Dec 07, 2007 (129)
6 HGSV ss77552736 Dec 07, 2007 (129)
7 BCMHGSC_JDW ss87656669 Mar 23, 2008 (129)
8 1000GENOMES ss108453905 Jan 23, 2009 (130)
9 KRIBB_YJKIM ss119521057 Dec 01, 2009 (131)
10 ENSEMBL ss138045137 Dec 01, 2009 (131)
11 ILLUMINA ss160798380 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss164869687 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss166904994 Jul 04, 2010 (132)
14 ILLUMINA ss174070386 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205301637 Jul 04, 2010 (132)
16 1000GENOMES ss210597692 Jul 14, 2010 (132)
17 1000GENOMES ss218548768 Jul 14, 2010 (132)
18 1000GENOMES ss230656828 Jul 14, 2010 (132)
19 BL ss253316085 May 09, 2011 (134)
20 GMI ss275945399 May 04, 2012 (137)
21 GMI ss284105720 Apr 25, 2013 (138)
22 PJP ss290580550 May 09, 2011 (134)
23 ILLUMINA ss481318466 May 04, 2012 (137)
24 ILLUMINA ss481343618 May 04, 2012 (137)
25 ILLUMINA ss482325348 Sep 08, 2015 (146)
26 ILLUMINA ss485454387 May 04, 2012 (137)
27 ILLUMINA ss537378905 Sep 08, 2015 (146)
28 TISHKOFF ss554480861 Apr 25, 2013 (138)
29 SSMP ss648254098 Apr 25, 2013 (138)
30 ILLUMINA ss778947915 Sep 08, 2015 (146)
31 ILLUMINA ss783172657 Sep 08, 2015 (146)
32 ILLUMINA ss784128152 Sep 08, 2015 (146)
33 ILLUMINA ss832432214 Sep 08, 2015 (146)
34 ILLUMINA ss834409730 Sep 08, 2015 (146)
35 EVA-GONL ss975483218 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1068127870 Aug 21, 2014 (142)
37 1000GENOMES ss1292108525 Aug 21, 2014 (142)
38 HAMMER_LAB ss1397255160 Sep 08, 2015 (146)
39 DDI ss1425911058 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1574271779 Apr 01, 2015 (144)
41 EVA_DECODE ss1584861535 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1600817429 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1643811462 Apr 01, 2015 (144)
44 EVA_SVP ss1712357164 Apr 01, 2015 (144)
45 ILLUMINA ss1751859125 Sep 08, 2015 (146)
46 HAMMER_LAB ss1794807934 Sep 08, 2015 (146)
47 WEILL_CORNELL_DGM ss1918682799 Feb 12, 2016 (147)
48 ILLUMINA ss1946002826 Feb 12, 2016 (147)
49 ILLUMINA ss1958296802 Feb 12, 2016 (147)
50 GENOMED ss1966820832 Jul 19, 2016 (147)
51 JJLAB ss2019862926 Sep 14, 2016 (149)
52 USC_VALOUEV ss2147881616 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2165032967 Dec 20, 2016 (150)
54 TOPMED ss2327383768 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2624442877 Nov 08, 2017 (151)
56 ILLUMINA ss2632553651 Nov 08, 2017 (151)
57 GRF ss2697808965 Nov 08, 2017 (151)
58 GNOMAD ss2758640177 Nov 08, 2017 (151)
59 SWEGEN ss2987305995 Nov 08, 2017 (151)
60 ILLUMINA ss3021113810 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3023695060 Nov 08, 2017 (151)
62 TOPMED ss3084655561 Nov 08, 2017 (151)
63 CSHL ss3343596036 Nov 08, 2017 (151)
64 ILLUMINA ss3625546138 Oct 11, 2018 (152)
65 ILLUMINA ss3626165329 Oct 11, 2018 (152)
66 ILLUMINA ss3630587827 Oct 11, 2018 (152)
67 ILLUMINA ss3632903294 Oct 11, 2018 (152)
68 ILLUMINA ss3633598293 Oct 11, 2018 (152)
69 ILLUMINA ss3634339267 Oct 11, 2018 (152)
70 ILLUMINA ss3635291902 Oct 11, 2018 (152)
71 ILLUMINA ss3636016822 Oct 11, 2018 (152)
72 ILLUMINA ss3637042359 Oct 11, 2018 (152)
73 ILLUMINA ss3637775464 Oct 11, 2018 (152)
74 ILLUMINA ss3640046627 Oct 11, 2018 (152)
75 ILLUMINA ss3642785649 Oct 11, 2018 (152)
76 ILLUMINA ss3644498788 Oct 11, 2018 (152)
77 ILLUMINA ss3651444593 Oct 11, 2018 (152)
78 EGCUT_WGS ss3655391109 Jul 12, 2019 (153)
79 EVA_DECODE ss3687367533 Jul 12, 2019 (153)
80 ILLUMINA ss3725048151 Jul 12, 2019 (153)
81 ACPOP ss3727314263 Jul 12, 2019 (153)
82 ILLUMINA ss3744050998 Jul 12, 2019 (153)
83 ILLUMINA ss3744640236 Jul 12, 2019 (153)
84 EVA ss3746574398 Jul 12, 2019 (153)
85 PAGE_CC ss3770828009 Jul 12, 2019 (153)
86 ILLUMINA ss3772141473 Jul 12, 2019 (153)
87 PACBIO ss3783495955 Jul 12, 2019 (153)
88 PACBIO ss3789140983 Jul 12, 2019 (153)
89 PACBIO ss3794013827 Jul 12, 2019 (153)
90 KHV_HUMAN_GENOMES ss3799575158 Jul 12, 2019 (153)
91 EVA ss3826326701 Apr 25, 2020 (154)
92 EVA ss3836553630 Apr 25, 2020 (154)
93 EVA ss3841961626 Apr 25, 2020 (154)
94 HGDP ss3847343751 Apr 25, 2020 (154)
95 SGDP_PRJ ss3849478012 Apr 25, 2020 (154)
96 KRGDB ss3894556062 Apr 25, 2020 (154)
97 KOGIC ss3945091728 Apr 25, 2020 (154)
98 EVA ss3984461732 Apr 25, 2021 (155)
99 EVA ss3984814989 Apr 25, 2021 (155)
100 EVA ss4016927705 Apr 25, 2021 (155)
101 TOPMED ss4460705585 Apr 25, 2021 (155)
102 TOMMO_GENOMICS ss5145314148 Apr 25, 2021 (155)
103 EVA ss5237270834 Apr 25, 2021 (155)
104 1000Genomes NC_000001.10 - 100079760 Oct 11, 2018 (152)
105 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100079760 Oct 11, 2018 (152)
106 Genome-wide autozygosity in Daghestan NC_000001.9 - 99852348 Apr 25, 2020 (154)
107 Genetic variation in the Estonian population NC_000001.10 - 100079760 Oct 11, 2018 (152)
108 The Danish reference pan genome NC_000001.10 - 100079760 Apr 25, 2020 (154)
109 gnomAD - Genomes NC_000001.11 - 99614204 Apr 25, 2021 (155)
110 Genome of the Netherlands Release 5 NC_000001.10 - 100079760 Apr 25, 2020 (154)
111 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99852348 Apr 25, 2020 (154)
112 HapMap NC_000001.11 - 99614204 Apr 25, 2020 (154)
113 KOREAN population from KRGDB NC_000001.10 - 100079760 Apr 25, 2020 (154)
114 Korean Genome Project NC_000001.11 - 99614204 Apr 25, 2020 (154)
115 Northern Sweden NC_000001.10 - 100079760 Jul 12, 2019 (153)
116 The PAGE Study NC_000001.11 - 99614204 Jul 12, 2019 (153)
117 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100079760 Apr 25, 2021 (155)
118 CNV burdens in cranial meningiomas NC_000001.10 - 100079760 Apr 25, 2021 (155)
119 Qatari NC_000001.10 - 100079760 Apr 25, 2020 (154)
120 SGDP_PRJ NC_000001.10 - 100079760 Apr 25, 2020 (154)
121 Siberian NC_000001.10 - 100079760 Apr 25, 2020 (154)
122 8.3KJPN NC_000001.10 - 100079760 Apr 25, 2021 (155)
123 TopMed NC_000001.11 - 99614204 Apr 25, 2021 (155)
124 UK 10K study - Twins NC_000001.10 - 100079760 Oct 11, 2018 (152)
125 A Vietnamese Genetic Variation Database NC_000001.10 - 100079760 Jul 12, 2019 (153)
126 ALFA NC_000001.11 - 99614204 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)
rs17405296 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77552736 NC_000001.8:99791780:C:T NC_000001.11:99614203:C:T (self)
16462, 21643, ss87656669, ss108453905, ss164869687, ss166904994, ss205301637, ss210597692, ss253316085, ss275945399, ss284105720, ss290580550, ss481318466, ss1397255160, ss1584861535, ss1712357164, ss3642785649, ss3847343751 NC_000001.9:99852347:C:T NC_000001.11:99614203:C:T (self)
2872119, 1584392, 1129357, 1629050, 687312, 1733456, 599128, 40916, 11044, 724729, 1494992, 397970, 3283455, 1584392, 341316, ss218548768, ss230656828, ss481343618, ss482325348, ss485454387, ss537378905, ss554480861, ss648254098, ss778947915, ss783172657, ss784128152, ss832432214, ss834409730, ss975483218, ss1068127870, ss1292108525, ss1425911058, ss1574271779, ss1600817429, ss1643811462, ss1751859125, ss1794807934, ss1918682799, ss1946002826, ss1958296802, ss1966820832, ss2019862926, ss2147881616, ss2327383768, ss2624442877, ss2632553651, ss2697808965, ss2758640177, ss2987305995, ss3021113810, ss3343596036, ss3625546138, ss3626165329, ss3630587827, ss3632903294, ss3633598293, ss3634339267, ss3635291902, ss3636016822, ss3637042359, ss3637775464, ss3640046627, ss3644498788, ss3651444593, ss3655391109, ss3727314263, ss3744050998, ss3744640236, ss3746574398, ss3772141473, ss3783495955, ss3789140983, ss3794013827, ss3826326701, ss3836553630, ss3849478012, ss3894556062, ss3984461732, ss3984814989, ss4016927705, ss5145314148, ss5237270834 NC_000001.10:100079759:C:T NC_000001.11:99614203:C:T (self)
20303129, 136623, 1469729, 49478, 15312371, 24311920, 10660122811, ss2165032967, ss3023695060, ss3084655561, ss3687367533, ss3725048151, ss3770828009, ss3799575158, ss3841961626, ss3945091728, ss4460705585 NC_000001.11:99614203:C:T NC_000001.11:99614203:C:T (self)
ss9876391 NT_028050.12:953430:C:T NC_000001.11:99614203:C:T (self)
ss24244158, ss67842983, ss71470256, ss75404933, ss119521057, ss138045137, ss160798380, ss174070386 NT_032977.9:70051677:C:T NC_000001.11:99614203:C: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 rs6689789

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