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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.

rs6428189

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:193651686 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.219532 (58108/264690, TOPMED)
C=0.216191 (30249/139918, GnomAD)
C=0.19365 (3658/18890, ALFA) (+ 15 more)
C=0.04224 (708/16760, 8.3KJPN)
C=0.2035 (1019/5008, 1000G)
C=0.1728 (774/4480, Estonian)
C=0.1559 (601/3854, ALSPAC)
C=0.1607 (596/3708, TWINSUK)
C=0.0816 (239/2928, KOREAN)
C=0.2217 (419/1890, HapMap)
C=0.0890 (163/1832, Korea1K)
C=0.134 (134/998, GoNL)
C=0.147 (88/600, NorthernSweden)
C=0.148 (80/540, SGDP_PRJ)
C=0.167 (36/216, Qatari)
C=0.126 (27/214, Vietnamese)
C=0.11 (6/54, Siberian)
C=0.17 (7/40, 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 1 NC_000001.11:g.193651686C>A
GRCh38.p13 chr 1 NC_000001.11:g.193651686C>G
GRCh38.p13 chr 1 NC_000001.11:g.193651686C>T
GRCh37.p13 chr 1 NC_000001.10:g.193620816C>A
GRCh37.p13 chr 1 NC_000001.10:g.193620816C>G
GRCh37.p13 chr 1 NC_000001.10:g.193620816C>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 C=0.19365 G=0.80635
European Sub 14286 C=0.16170 G=0.83830
African Sub 2946 C=0.3500 G=0.6500
African Others Sub 114 C=0.377 G=0.623
African American Sub 2832 C=0.3489 G=0.6511
Asian Sub 112 C=0.107 G=0.893
East Asian Sub 86 C=0.10 G=0.90
Other Asian Sub 26 C=0.12 G=0.88
Latin American 1 Sub 146 C=0.219 G=0.781
Latin American 2 Sub 610 C=0.202 G=0.798
South Asian Sub 98 C=0.08 G=0.92
Other Sub 692 C=0.205 G=0.795


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=0.219532 G=0.780468
gnomAD - Genomes Global Study-wide 139918 C=0.216191 G=0.783809
gnomAD - Genomes European Sub 75856 C=0.15645 G=0.84355
gnomAD - Genomes African Sub 41840 C=0.35091 G=0.64909
gnomAD - Genomes American Sub 13630 C=0.19362 G=0.80638
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.0919 G=0.9081
gnomAD - Genomes East Asian Sub 3126 C=0.1068 G=0.8932
gnomAD - Genomes Other Sub 2146 C=0.1962 G=0.8038
8.3KJPN JAPANESE Study-wide 16760 C=0.04224 G=0.95776
1000Genomes Global Study-wide 5008 C=0.2035 G=0.7965
1000Genomes African Sub 1322 C=0.3729 G=0.6271
1000Genomes East Asian Sub 1008 C=0.1032 G=0.8968
1000Genomes Europe Sub 1006 C=0.1561 G=0.8439
1000Genomes South Asian Sub 978 C=0.102 G=0.898
1000Genomes American Sub 694 C=0.238 G=0.762
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.1728 G=0.8272
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.1559 G=0.8441
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.1607 G=0.8393
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.0816 A=0.0000, G=0.9184, T=0.0000
HapMap Global Study-wide 1890 C=0.2217 G=0.7783
HapMap American Sub 770 C=0.155 G=0.845
HapMap African Sub 690 C=0.375 G=0.625
HapMap Asian Sub 254 C=0.063 G=0.937
HapMap Europe Sub 176 C=0.142 G=0.858
Korean Genome Project KOREAN Study-wide 1832 C=0.0890 G=0.9110
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.134 G=0.866
Northern Sweden ACPOP Study-wide 600 C=0.147 G=0.853
SGDP_PRJ Global Study-wide 540 C=0.148 G=0.852
Qatari Global Study-wide 216 C=0.167 G=0.833
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.126 G=0.874
Siberian Global Study-wide 54 C=0.11 G=0.89
The Danish reference pan genome Danish Study-wide 40 C=0.17 G=0.82
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= A G T
GRCh38.p13 chr 1 NC_000001.11:g.193651686= NC_000001.11:g.193651686C>A NC_000001.11:g.193651686C>G NC_000001.11:g.193651686C>T
GRCh37.p13 chr 1 NC_000001.10:g.193620816= NC_000001.10:g.193620816C>A NC_000001.10:g.193620816C>G NC_000001.10:g.193620816C>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#.

72 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9807773 Jul 11, 2003 (116)
2 WI_SSAHASNP ss11340903 Jul 11, 2003 (116)
3 SC_SNP ss18096806 Feb 27, 2004 (126)
4 SC_SNP ss18175105 Feb 27, 2004 (126)
5 SC_SNP ss18270957 Feb 27, 2004 (126)
6 CSHL-HAPMAP ss19851784 Feb 27, 2004 (126)
7 AFFY ss66135955 Nov 30, 2006 (127)
8 AFFY ss76147722 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss82226186 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss87916961 Mar 23, 2008 (129)
11 HUMANGENOME_JCVI ss97993694 Feb 06, 2009 (130)
12 BGI ss106619796 Feb 06, 2009 (130)
13 1000GENOMES ss108817167 Jan 23, 2009 (130)
14 1000GENOMES ss111555223 Jan 25, 2009 (130)
15 ILLUMINA-UK ss119155441 Feb 15, 2009 (130)
16 ENSEMBL ss138127478 Dec 01, 2009 (131)
17 ENSEMBL ss139118155 Dec 01, 2009 (131)
18 GMI ss156090442 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss164781245 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss165618300 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss167393883 Jul 04, 2010 (132)
22 BUSHMAN ss199419092 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss205158567 Jul 04, 2010 (132)
24 1000GENOMES ss218797384 Jul 14, 2010 (132)
25 1000GENOMES ss230838321 Jul 14, 2010 (132)
26 1000GENOMES ss238463234 Jul 15, 2010 (132)
27 BL ss253711394 May 09, 2011 (134)
28 GMI ss276154437 May 04, 2012 (137)
29 GMI ss284199930 Apr 25, 2013 (138)
30 PJP ss290692395 May 09, 2011 (134)
31 TISHKOFF ss554996243 Apr 25, 2013 (138)
32 SSMP ss648592024 Apr 25, 2013 (138)
33 EVA-GONL ss975970488 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1068478459 Aug 21, 2014 (142)
35 1000GENOMES ss1294009671 Aug 21, 2014 (142)
36 DDI ss1426062002 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1574573424 Apr 01, 2015 (144)
38 EVA_DECODE ss1585364838 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1601793404 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1644787437 Apr 01, 2015 (144)
41 EVA_SVP ss1712392195 Apr 01, 2015 (144)
42 HAMMER_LAB ss1795492879 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1919203762 Feb 12, 2016 (147)
44 GENOMED ss1966932596 Jul 19, 2016 (147)
45 JJLAB ss2020119306 Sep 14, 2016 (149)
46 USC_VALOUEV ss2148146572 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2168779573 Dec 20, 2016 (150)
48 TOPMED ss2331350301 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624567538 Nov 08, 2017 (151)
50 GRF ss2698133852 Nov 08, 2017 (151)
51 GNOMAD ss2764397746 Nov 08, 2017 (151)
52 SWEGEN ss2988186999 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3023818944 Nov 08, 2017 (151)
54 TOPMED ss3099211816 Nov 08, 2017 (151)
55 CSHL ss3343836488 Nov 08, 2017 (151)
56 URBANLAB ss3646850848 Oct 11, 2018 (152)
57 EGCUT_WGS ss3656144499 Jul 12, 2019 (153)
58 EVA_DECODE ss3688310564 Jul 12, 2019 (153)
59 ACPOP ss3727719870 Jul 12, 2019 (153)
60 EVA ss3747137974 Jul 12, 2019 (153)
61 PACBIO ss3783642977 Jul 12, 2019 (153)
62 PACBIO ss3789262048 Jul 12, 2019 (153)
63 PACBIO ss3794134212 Jul 12, 2019 (153)
64 KHV_HUMAN_GENOMES ss3800142554 Jul 12, 2019 (153)
65 EVA ss3826562464 Apr 25, 2020 (154)
66 EVA ss3836679264 Apr 25, 2020 (154)
67 EVA ss3842090036 Apr 25, 2020 (154)
68 SGDP_PRJ ss3850565126 Apr 25, 2020 (154)
69 KRGDB ss3895841032 Apr 25, 2020 (154)
70 KOGIC ss3946174854 Apr 25, 2020 (154)
71 TOPMED ss4477919487 Apr 25, 2021 (155)
72 TOMMO_GENOMICS ss5147703661 Apr 25, 2021 (155)
73 1000Genomes NC_000001.10 - 193620816 Oct 11, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 193620816 Oct 11, 2018 (152)
75 Genetic variation in the Estonian population NC_000001.10 - 193620816 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000001.10 - 193620816 Apr 25, 2020 (154)
77 gnomAD - Genomes NC_000001.11 - 193651686 Apr 25, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000001.10 - 193620816 Apr 25, 2020 (154)
79 HapMap NC_000001.11 - 193651686 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 193620816 Apr 25, 2020 (154)
81 Korean Genome Project NC_000001.11 - 193651686 Apr 25, 2020 (154)
82 Northern Sweden NC_000001.10 - 193620816 Jul 12, 2019 (153)
83 Qatari NC_000001.10 - 193620816 Apr 25, 2020 (154)
84 SGDP_PRJ NC_000001.10 - 193620816 Apr 25, 2020 (154)
85 Siberian NC_000001.10 - 193620816 Apr 25, 2020 (154)
86 8.3KJPN NC_000001.10 - 193620816 Apr 25, 2021 (155)
87 TopMed NC_000001.11 - 193651686 Apr 25, 2021 (155)
88 UK 10K study - Twins NC_000001.10 - 193620816 Oct 11, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000001.10 - 193620816 Jul 12, 2019 (153)
90 ALFA NC_000001.11 - 193651686 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)
rs10754068 Mar 10, 2006 (126)
rs56901897 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3018426, ss3895841032 NC_000001.10:193620815:C:A NC_000001.11:193651685:C:A (self)
ss66135955, ss76147722, ss87916961, ss108817167, ss111555223, ss119155441, ss164781245, ss165618300, ss167393883, ss199419092, ss205158567, ss253711394, ss276154437, ss284199930, ss290692395, ss1585364838, ss1712392195 NC_000001.9:191887438:C:G NC_000001.11:193651685:C:G (self)
4840778, 2657483, 1882747, 1818828, 1158658, 3018426, 1004735, 1245692, 2582106, 662926, 5672968, 2657483, 572816, ss218797384, ss230838321, ss238463234, ss554996243, ss648592024, ss975970488, ss1068478459, ss1294009671, ss1426062002, ss1574573424, ss1601793404, ss1644787437, ss1795492879, ss1919203762, ss1966932596, ss2020119306, ss2148146572, ss2331350301, ss2624567538, ss2698133852, ss2764397746, ss2988186999, ss3343836488, ss3656144499, ss3727719870, ss3747137974, ss3783642977, ss3789262048, ss3794134212, ss3826562464, ss3836679264, ss3850565126, ss3895841032, ss5147703661 NC_000001.10:193620815:C:G NC_000001.11:193651685:C:G (self)
34918714, 233051, 2552855, 26084354, 41525822, 3138618642, ss2168779573, ss3023818944, ss3099211816, ss3646850848, ss3688310564, ss3800142554, ss3842090036, ss3946174854, ss4477919487 NC_000001.11:193651685:C:G NC_000001.11:193651685:C:G (self)
ss82226186, ss97993694, ss106619796, ss138127478, ss139118155, ss156090442 NT_004487.19:45109457:C:G NC_000001.11:193651685:C:G (self)
ss9807773, ss11340903, ss18096806, ss18175105, ss18270957, ss19851784 NT_004671.15:4975801:C:G NC_000001.11:193651685:C:G (self)
3018426, ss3895841032 NC_000001.10:193620815:C:T NC_000001.11:193651685: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 rs6428189

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