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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.

rs213006

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:21352107 (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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.324806 (85973/264690, TOPMED)
G=0.308300 (61298/198826, ALFA)
G=0.08508 (1426/16760, 8.3KJPN) (+ 16 more)
G=0.3171 (1588/5008, 1000G)
G=0.2888 (1294/4480, Estonian)
G=0.3259 (1256/3854, ALSPAC)
G=0.3069 (1138/3708, TWINSUK)
G=0.0732 (214/2922, KOREAN)
G=0.3314 (690/2082, HGDP_Stanford)
G=0.3531 (668/1892, HapMap)
G=0.0857 (157/1832, Korea1K)
G=0.324 (323/998, GoNL)
G=0.335 (201/600, NorthernSweden)
T=0.383 (121/316, SGDP_PRJ)
G=0.412 (89/216, Qatari)
G=0.220 (47/214, Vietnamese)
G=0.35 (14/40, GENOME_DK)
G=0.17 (6/36, Ancient Sardinia)
T=0.44 (8/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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.21352107T>A
GRCh38.p13 chr 1 NC_000001.11:g.21352107T>G
GRCh37.p13 chr 1 NC_000001.10:g.21678600T>A
GRCh37.p13 chr 1 NC_000001.10:g.21678600T>G
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 198826 T=0.691700 A=0.000000, G=0.308300
European Sub 171090 T=0.694658 A=0.000000, G=0.305342
African Sub 8294 T=0.6549 A=0.0000, G=0.3451
African Others Sub 298 T=0.631 A=0.000, G=0.369
African American Sub 7996 T=0.6558 A=0.0000, G=0.3442
Asian Sub 672 T=0.876 A=0.000, G=0.124
East Asian Sub 536 T=0.882 A=0.000, G=0.118
Other Asian Sub 136 T=0.853 A=0.000, G=0.147
Latin American 1 Sub 762 T=0.709 A=0.000, G=0.291
Latin American 2 Sub 6592 T=0.7010 A=0.0000, G=0.2990
South Asian Sub 4982 T=0.6246 A=0.0000, G=0.3754
Other Sub 6434 T=0.6815 A=0.0000, G=0.3185


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 T=0.675194 G=0.324806
8.3KJPN JAPANESE Study-wide 16760 T=0.91492 G=0.08508
1000Genomes Global Study-wide 5008 T=0.6829 G=0.3171
1000Genomes African Sub 1322 T=0.5915 G=0.4085
1000Genomes East Asian Sub 1008 T=0.8730 G=0.1270
1000Genomes Europe Sub 1006 T=0.6879 G=0.3121
1000Genomes South Asian Sub 978 T=0.621 G=0.379
1000Genomes American Sub 694 T=0.661 G=0.339
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7112 G=0.2888
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6741 G=0.3259
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6931 G=0.3069
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9268 G=0.0732
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 T=0.6686 G=0.3314
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.857 G=0.143
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.604 G=0.396
HGDP-CEPH-db Supplement 1 Middle_Est Sub 348 T=0.595 G=0.405
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.634 G=0.366
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.562 G=0.438
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.685 G=0.315
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.62 G=0.38
HapMap Global Study-wide 1892 T=0.6469 G=0.3531
HapMap American Sub 770 T=0.683 G=0.317
HapMap African Sub 692 T=0.509 G=0.491
HapMap Asian Sub 254 T=0.909 G=0.091
HapMap Europe Sub 176 T=0.653 G=0.347
Korean Genome Project KOREAN Study-wide 1832 T=0.9143 G=0.0857
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.676 G=0.324
Northern Sweden ACPOP Study-wide 600 T=0.665 G=0.335
SGDP_PRJ Global Study-wide 316 T=0.383 G=0.617
Qatari Global Study-wide 216 T=0.588 G=0.412
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.780 G=0.220
The Danish reference pan genome Danish Study-wide 40 T=0.65 G=0.35
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 36 T=0.83 G=0.17
Siberian Global Study-wide 18 T=0.44 G=0.56
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 T= A G
GRCh38.p13 chr 1 NC_000001.11:g.21352107= NC_000001.11:g.21352107T>A NC_000001.11:g.21352107T>G
GRCh37.p13 chr 1 NC_000001.10:g.21678600= NC_000001.10:g.21678600T>A NC_000001.10:g.21678600T>G
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#.

115 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss278234 Jul 12, 2000 (79)
2 SC_JCM ss672721 Aug 11, 2000 (85)
3 KWOK ss1027629 Oct 13, 2000 (89)
4 KWOK ss1737152 Oct 18, 2000 (89)
5 TSC-CSHL ss2412660 Oct 24, 2000 (92)
6 SC_JCM ss2579257 Nov 09, 2000 (92)
7 ACEVAN ss4257607 Jan 04, 2002 (102)
8 SSAHASNP ss20443345 Apr 05, 2004 (121)
9 ABI ss44074028 Mar 14, 2006 (126)
10 ILLUMINA ss65722683 Oct 16, 2006 (127)
11 ILLUMINA ss66643481 Dec 02, 2006 (127)
12 ILLUMINA ss67226802 Dec 02, 2006 (127)
13 ILLUMINA ss67621811 Dec 02, 2006 (127)
14 PERLEGEN ss68760930 May 18, 2007 (127)
15 ILLUMINA ss70705107 May 25, 2008 (130)
16 ILLUMINA ss71271713 May 18, 2007 (127)
17 ILLUMINA ss75525101 Dec 06, 2007 (129)
18 ILLUMINA ss79115655 Dec 15, 2007 (130)
19 HGSV ss81618239 Dec 15, 2007 (130)
20 KRIBB_YJKIM ss83388168 Dec 15, 2007 (130)
21 BCMHGSC_JDW ss87286640 Mar 23, 2008 (129)
22 HUMANGENOME_JCVI ss97924089 Feb 05, 2009 (130)
23 BGI ss102726067 Dec 01, 2009 (131)
24 1000GENOMES ss110161953 Jan 24, 2009 (130)
25 ILLUMINA-UK ss118552054 Feb 14, 2009 (130)
26 ILLUMINA ss120244565 Dec 01, 2009 (131)
27 ILLUMINA ss121923420 Dec 01, 2009 (131)
28 ENSEMBL ss137836840 Dec 01, 2009 (131)
29 ENSEMBL ss139067944 Dec 01, 2009 (131)
30 ILLUMINA ss153860482 Dec 01, 2009 (131)
31 ILLUMINA ss159360922 Dec 01, 2009 (131)
32 ILLUMINA ss160505105 Dec 01, 2009 (131)
33 COMPLETE_GENOMICS ss163163766 Jul 04, 2010 (132)
34 COMPLETE_GENOMICS ss166213460 Jul 04, 2010 (132)
35 ILLUMINA ss171033650 Jul 04, 2010 (132)
36 ILLUMINA ss173131180 Jul 04, 2010 (132)
37 BUSHMAN ss198142683 Jul 04, 2010 (132)
38 BCM-HGSC-SUB ss205184618 Jul 04, 2010 (132)
39 1000GENOMES ss210448193 Jul 14, 2010 (132)
40 1000GENOMES ss218275681 Jul 14, 2010 (132)
41 1000GENOMES ss230456596 Jul 14, 2010 (132)
42 1000GENOMES ss238165679 Jul 15, 2010 (132)
43 ILLUMINA ss244255251 Jul 04, 2010 (132)
44 GMI ss275747114 May 04, 2012 (137)
45 PJP ss290782966 May 09, 2011 (134)
46 ILLUMINA ss480433462 May 04, 2012 (137)
47 ILLUMINA ss480447057 May 04, 2012 (137)
48 ILLUMINA ss481235028 Sep 08, 2015 (146)
49 ILLUMINA ss485014147 May 04, 2012 (137)
50 ILLUMINA ss537042612 Sep 08, 2015 (146)
51 TISHKOFF ss553875074 Apr 25, 2013 (138)
52 SSMP ss647630003 Apr 25, 2013 (138)
53 ILLUMINA ss778855590 Sep 08, 2015 (146)
54 ILLUMINA ss782953385 Sep 08, 2015 (146)
55 ILLUMINA ss783915595 Sep 08, 2015 (146)
56 ILLUMINA ss825446173 Apr 01, 2015 (144)
57 ILLUMINA ss832209377 Sep 08, 2015 (146)
58 ILLUMINA ss832872812 Jul 12, 2019 (153)
59 ILLUMINA ss834316300 Sep 08, 2015 (146)
60 EVA-GONL ss974931330 Aug 21, 2014 (142)
61 JMKIDD_LAB ss1067724369 Aug 21, 2014 (142)
62 1000GENOMES ss1289978563 Aug 21, 2014 (142)
63 DDI ss1425740561 Apr 01, 2015 (144)
64 EVA_GENOME_DK ss1573931820 Apr 01, 2015 (144)
65 EVA_DECODE ss1584289844 Apr 01, 2015 (144)
66 EVA_UK10K_ALSPAC ss1599697871 Apr 01, 2015 (144)
67 EVA_UK10K_TWINSUK ss1642691904 Apr 01, 2015 (144)
68 EVA_SVP ss1712316874 Apr 01, 2015 (144)
69 ILLUMINA ss1751898488 Sep 08, 2015 (146)
70 HAMMER_LAB ss1794037242 Sep 08, 2015 (146)
71 WEILL_CORNELL_DGM ss1918142852 Feb 12, 2016 (147)
72 GENOMED ss1966701790 Jul 19, 2016 (147)
73 AMU ss1971465194 Jul 19, 2016 (147)
74 JJLAB ss2019583224 Sep 14, 2016 (149)
75 USC_VALOUEV ss2147587289 Dec 20, 2016 (150)
76 HUMAN_LONGEVITY ss2160610767 Dec 20, 2016 (150)
77 TOPMED ss2322793481 Dec 20, 2016 (150)
78 ILLUMINA ss2632487881 Nov 08, 2017 (151)
79 GRF ss2697491997 Nov 08, 2017 (151)
80 GNOMAD ss2752501818 Nov 08, 2017 (151)
81 AFFY ss2984848768 Nov 08, 2017 (151)
82 SWEGEN ss2986441514 Nov 08, 2017 (151)
83 BIOINF_KMB_FNS_UNIBA ss3023556805 Nov 08, 2017 (151)
84 TOPMED ss3070550744 Nov 08, 2017 (151)
85 CSHL ss3343360094 Nov 08, 2017 (151)
86 ILLUMINA ss3626044756 Oct 11, 2018 (152)
87 ILLUMINA ss3630525639 Oct 11, 2018 (152)
88 ILLUMINA ss3632883759 Oct 11, 2018 (152)
89 ILLUMINA ss3633577789 Oct 11, 2018 (152)
90 ILLUMINA ss3634311653 Oct 11, 2018 (152)
91 ILLUMINA ss3635271836 Oct 11, 2018 (152)
92 ILLUMINA ss3635987840 Oct 11, 2018 (152)
93 ILLUMINA ss3637022216 Oct 11, 2018 (152)
94 ILLUMINA ss3637742096 Oct 11, 2018 (152)
95 ILLUMINA ss3638891995 Oct 11, 2018 (152)
96 ILLUMINA ss3639443043 Oct 11, 2018 (152)
97 ILLUMINA ss3640019017 Oct 11, 2018 (152)
98 ILLUMINA ss3642755489 Oct 11, 2018 (152)
99 URBANLAB ss3646618767 Oct 11, 2018 (152)
100 EGCUT_WGS ss3654512204 Jul 12, 2019 (153)
101 EVA_DECODE ss3686316201 Jul 12, 2019 (153)
102 ACPOP ss3726856609 Jul 12, 2019 (153)
103 ILLUMINA ss3744612613 Jul 12, 2019 (153)
104 EVA ss3745923071 Jul 12, 2019 (153)
105 ILLUMINA ss3772114178 Jul 12, 2019 (153)
106 KHV_HUMAN_GENOMES ss3798942477 Jul 12, 2019 (153)
107 EVA ss3826063112 Apr 25, 2020 (154)
108 HGDP ss3847326884 Apr 25, 2020 (154)
109 SGDP_PRJ ss3848375077 Apr 25, 2020 (154)
110 KRGDB ss3893286562 Apr 25, 2020 (154)
111 KOGIC ss3944001153 Apr 25, 2020 (154)
112 EVA ss3984783238 Apr 25, 2021 (155)
113 EVA ss4016897487 Apr 25, 2021 (155)
114 TOPMED ss4441646013 Apr 25, 2021 (155)
115 TOMMO_GENOMICS ss5142859901 Apr 25, 2021 (155)
116 1000Genomes NC_000001.10 - 21678600 Oct 11, 2018 (152)
117 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 21678600 Oct 11, 2018 (152)
118 Genetic variation in the Estonian population NC_000001.10 - 21678600 Oct 11, 2018 (152)
119 The Danish reference pan genome NC_000001.10 - 21678600 Apr 25, 2020 (154)
120 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4625090 (NC_000001.11:21352106:T:A 0/140002)
Row 4625091 (NC_000001.11:21352106:T:G 46647/139942)

- Apr 25, 2021 (155)
121 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4625090 (NC_000001.11:21352106:T:A 0/140002)
Row 4625091 (NC_000001.11:21352106:T:G 46647/139942)

- Apr 25, 2021 (155)
122 Genome of the Netherlands Release 5 NC_000001.10 - 21678600 Apr 25, 2020 (154)
123 HGDP-CEPH-db Supplement 1 NC_000001.9 - 21551187 Apr 25, 2020 (154)
124 HapMap NC_000001.11 - 21352107 Apr 25, 2020 (154)
125 KOREAN population from KRGDB NC_000001.10 - 21678600 Apr 25, 2020 (154)
126 Korean Genome Project NC_000001.11 - 21352107 Apr 25, 2020 (154)
127 Northern Sweden NC_000001.10 - 21678600 Jul 12, 2019 (153)
128 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 21678600 Apr 25, 2021 (155)
129 Qatari NC_000001.10 - 21678600 Apr 25, 2020 (154)
130 SGDP_PRJ NC_000001.10 - 21678600 Apr 25, 2020 (154)
131 Siberian NC_000001.10 - 21678600 Apr 25, 2020 (154)
132 8.3KJPN NC_000001.10 - 21678600 Apr 25, 2021 (155)
133 TopMed NC_000001.11 - 21352107 Apr 25, 2021 (155)
134 UK 10K study - Twins NC_000001.10 - 21678600 Oct 11, 2018 (152)
135 A Vietnamese Genetic Variation Database NC_000001.10 - 21678600 Jul 12, 2019 (153)
136 ALFA NC_000001.11 - 21352107 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)
rs502730 Sep 19, 2000 (85)
rs1090368 Nov 09, 2000 (89)
rs1308904 Nov 09, 2000 (89)
rs1610252 Jan 18, 2001 (92)
rs1737461 Jan 18, 2001 (92)
rs59315274 May 25, 2008 (130)
rs386558180 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5019023330 NC_000001.11:21352106:T:A NC_000001.11:21352106:T:A
ss81618239, ss3638891995, ss3639443043 NC_000001.8:21423905:T:G NC_000001.11:21352106:T:G (self)
4776, ss87286640, ss110161953, ss118552054, ss163163766, ss166213460, ss198142683, ss205184618, ss210448193, ss275747114, ss290782966, ss480433462, ss825446173, ss1584289844, ss1712316874, ss3642755489, ss3847326884 NC_000001.9:21551186:T:G NC_000001.11:21352106:T:G (self)
664641, 351533, 250452, 1419965, 152268, 463956, 141474, 9165, 184782, 392057, 103643, 829208, 351533, 74981, ss218275681, ss230456596, ss238165679, ss480447057, ss481235028, ss485014147, ss537042612, ss553875074, ss647630003, ss778855590, ss782953385, ss783915595, ss832209377, ss832872812, ss834316300, ss974931330, ss1067724369, ss1289978563, ss1425740561, ss1573931820, ss1599697871, ss1642691904, ss1751898488, ss1794037242, ss1918142852, ss1966701790, ss1971465194, ss2019583224, ss2147587289, ss2322793481, ss2632487881, ss2697491997, ss2752501818, ss2984848768, ss2986441514, ss3343360094, ss3626044756, ss3630525639, ss3632883759, ss3633577789, ss3634311653, ss3635271836, ss3635987840, ss3637022216, ss3637742096, ss3640019017, ss3654512204, ss3726856609, ss3744612613, ss3745923071, ss3772114178, ss3826063112, ss3848375077, ss3893286562, ss3984783238, ss4016897487, ss5142859901 NC_000001.10:21678599:T:G NC_000001.11:21352106:T:G (self)
27550, 379154, 3301257, 5252348, 5019023330, ss2160610767, ss3023556805, ss3070550744, ss3646618767, ss3686316201, ss3798942477, ss3944001153, ss4441646013 NC_000001.11:21352106:T:G NC_000001.11:21352106:T:G (self)
ss20443345 NT_004610.16:2481849:T:G NC_000001.11:21352106:T:G (self)
ss278234, ss672721, ss1027629, ss1737152, ss2412660, ss2579257, ss4257607, ss44074028, ss65722683, ss66643481, ss67226802, ss67621811, ss68760930, ss70705107, ss71271713, ss75525101, ss79115655, ss83388168, ss97924089, ss102726067, ss120244565, ss121923420, ss137836840, ss139067944, ss153860482, ss159360922, ss160505105, ss171033650, ss173131180, ss244255251 NT_004610.19:8358687:T:G NC_000001.11:21352106:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs213006
PMID Title Author Year Journal
21242547 Autosomal dominant progressive sensorineural hearing loss due to a novel mutation in the KCNQ4 gene. Arnett J et al. 2011 Archives of otolaryngology--head & neck surgery
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