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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.

rs12021506

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:188356407 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.389811 (103179/264690, TOPMED)
G=0.46706 (7828/16760, 8.3KJPN)
T=0.22315 (2606/11678, ALFA) (+ 13 more)
T=0.4750 (2379/5008, 1000G)
T=0.3759 (1684/4480, Estonian)
T=0.3560 (1372/3854, ALSPAC)
T=0.3533 (1310/3708, TWINSUK)
G=0.4782 (1401/2930, KOREAN)
T=0.378 (377/998, GoNL)
T=0.412 (247/600, NorthernSweden)
G=0.336 (137/408, SGDP_PRJ)
T=0.443 (124/280, HapMap)
T=0.301 (65/216, Qatari)
G=0.463 (100/216, Vietnamese)
G=0.35 (16/46, Siberian)
T=0.28 (11/40, 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.188356407G>A
GRCh38.p13 chr 1 NC_000001.11:g.188356407G>T
GRCh37.p13 chr 1 NC_000001.10:g.188325538G>A
GRCh37.p13 chr 1 NC_000001.10:g.188325538G>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 11678 G=0.77685 A=0.00000, T=0.22315
European Sub 9888 G=0.7502 A=0.0000, T=0.2498
African Sub 1122 G=0.9492 A=0.0000, T=0.0508
African Others Sub 50 G=0.98 A=0.00, T=0.02
African American Sub 1072 G=0.9478 A=0.0000, T=0.0522
Asian Sub 22 G=0.86 A=0.00, T=0.14
East Asian Sub 18 G=0.94 A=0.00, T=0.06
Other Asian Sub 4 G=0.5 A=0.0, T=0.5
Latin American 1 Sub 58 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 186 G=1.000 A=0.000, T=0.000
South Asian Sub 24 G=0.88 A=0.00, T=0.12
Other Sub 378 G=0.807 A=0.000, T=0.193


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=0.610189 T=0.389811
8.3KJPN JAPANESE Study-wide 16760 G=0.46706 T=0.53294
1000Genomes Global Study-wide 5008 G=0.5250 T=0.4750
1000Genomes African Sub 1322 G=0.6051 T=0.3949
1000Genomes East Asian Sub 1008 G=0.4444 T=0.5556
1000Genomes Europe Sub 1006 G=0.6262 T=0.3738
1000Genomes South Asian Sub 978 G=0.398 T=0.602
1000Genomes American Sub 694 G=0.522 T=0.478
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6241 T=0.3759
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6440 T=0.3560
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6467 T=0.3533
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4782 T=0.5218
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.622 T=0.378
Northern Sweden ACPOP Study-wide 600 G=0.588 T=0.412
SGDP_PRJ Global Study-wide 408 G=0.336 T=0.664
HapMap Global Study-wide 280 G=0.557 T=0.443
HapMap American Sub 104 G=0.596 T=0.404
HapMap African Sub 102 G=0.627 T=0.373
HapMap Asian Sub 74 G=0.41 T=0.59
Qatari Global Study-wide 216 G=0.699 T=0.301
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.463 T=0.537
Siberian Global Study-wide 46 G=0.35 T=0.65
The Danish reference pan genome Danish Study-wide 40 G=0.72 T=0.28
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 T
GRCh38.p13 chr 1 NC_000001.11:g.188356407= NC_000001.11:g.188356407G>A NC_000001.11:g.188356407G>T
GRCh37.p13 chr 1 NC_000001.10:g.188325538= NC_000001.10:g.188325538G>A NC_000001.10:g.188325538G>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#.

55 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069711 Feb 28, 2004 (120)
2 SSAHASNP ss20429351 Apr 05, 2004 (121)
3 ABI ss41164748 Mar 15, 2006 (126)
4 HUMANGENOME_JCVI ss97990344 Feb 05, 2009 (130)
5 1000GENOMES ss108784392 Jan 23, 2009 (130)
6 1000GENOMES ss111501645 Jan 25, 2009 (130)
7 ILLUMINA-UK ss119138876 Feb 15, 2009 (130)
8 ENSEMBL ss139131844 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss164690182 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss165572460 Jul 04, 2010 (132)
11 BUSHMAN ss199372907 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss205077082 Jul 04, 2010 (132)
13 1000GENOMES ss218776477 Jul 14, 2010 (132)
14 1000GENOMES ss230823795 Jul 14, 2010 (132)
15 1000GENOMES ss238451447 Jul 15, 2010 (132)
16 BL ss253685130 May 09, 2011 (134)
17 GMI ss276140064 May 04, 2012 (137)
18 PJP ss290684508 May 09, 2011 (134)
19 TISHKOFF ss554963887 Apr 25, 2013 (138)
20 SSMP ss648568388 Apr 25, 2013 (138)
21 EVA-GONL ss975928089 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1068448605 Aug 21, 2014 (142)
23 1000GENOMES ss1293858959 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1574545555 Apr 01, 2015 (144)
25 EVA_DECODE ss1585320940 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1601713770 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1644707803 Apr 01, 2015 (144)
28 HAMMER_LAB ss1795437219 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1919162588 Feb 12, 2016 (147)
30 GENOMED ss1966923557 Jul 19, 2016 (147)
31 JJLAB ss2020098071 Sep 14, 2016 (149)
32 USC_VALOUEV ss2148126416 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2168454902 Dec 20, 2016 (150)
34 TOPMED ss2331017540 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624557268 Nov 08, 2017 (151)
36 GRF ss2698111271 Nov 08, 2017 (151)
37 GNOMAD ss2763959727 Nov 08, 2017 (151)
38 SWEGEN ss2988126801 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023808760 Nov 08, 2017 (151)
40 TOPMED ss3098198406 Nov 08, 2017 (151)
41 TOPMED ss3098198407 Nov 08, 2017 (151)
42 CSHL ss3343819255 Nov 08, 2017 (151)
43 URBANLAB ss3646841743 Oct 11, 2018 (152)
44 EGCUT_WGS ss3656079578 Jul 12, 2019 (153)
45 EVA_DECODE ss3688235071 Jul 12, 2019 (153)
46 ACPOP ss3727686416 Jul 12, 2019 (153)
47 EVA ss3747093146 Jul 12, 2019 (153)
48 KHV_HUMAN_GENOMES ss3800095353 Jul 12, 2019 (153)
49 EVA ss3826543999 Apr 25, 2020 (154)
50 EVA ss3836668968 Apr 25, 2020 (154)
51 EVA ss3842079496 Apr 25, 2020 (154)
52 SGDP_PRJ ss3850486576 Apr 25, 2020 (154)
53 KRGDB ss3895754816 Apr 25, 2020 (154)
54 TOPMED ss4476540523 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5147531854 Apr 25, 2021 (155)
56 1000Genomes NC_000001.10 - 188325538 Oct 11, 2018 (152)
57 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 188325538 Oct 11, 2018 (152)
58 Genetic variation in the Estonian population NC_000001.10 - 188325538 Oct 11, 2018 (152)
59 The Danish reference pan genome NC_000001.10 - 188325538 Apr 25, 2020 (154)
60 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 33780652 (NC_000001.11:188356406:G:A 2/140038)
Row 33780653 (NC_000001.11:188356406:G:T 54170/139986)

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

Submission ignored due to conflicting rows:
Row 33780652 (NC_000001.11:188356406:G:A 2/140038)
Row 33780653 (NC_000001.11:188356406:G:T 54170/139986)

- Apr 25, 2021 (155)
62 Genome of the Netherlands Release 5 NC_000001.10 - 188325538 Apr 25, 2020 (154)
63 HapMap NC_000001.11 - 188356407 Apr 25, 2020 (154)
64 KOREAN population from KRGDB NC_000001.10 - 188325538 Apr 25, 2020 (154)
65 Northern Sweden NC_000001.10 - 188325538 Jul 12, 2019 (153)
66 Qatari NC_000001.10 - 188325538 Apr 25, 2020 (154)
67 SGDP_PRJ NC_000001.10 - 188325538 Apr 25, 2020 (154)
68 Siberian NC_000001.10 - 188325538 Apr 25, 2020 (154)
69 8.3KJPN NC_000001.10 - 188325538 Apr 25, 2021 (155)
70 TopMed NC_000001.11 - 188356407 Apr 25, 2021 (155)
71 UK 10K study - Twins NC_000001.10 - 188325538 Oct 11, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000001.10 - 188325538 Jul 12, 2019 (153)
73 ALFA NC_000001.11 - 188356407 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
4349536459, ss2168454902, ss3098198406 NC_000001.11:188356406:G:A NC_000001.11:188356406:G:A (self)
ss108784392, ss111501645, ss119138876, ss164690182, ss165572460, ss199372907, ss205077082, ss253685130, ss276140064, ss290684508, ss1585320940 NC_000001.9:186592160:G:T NC_000001.11:188356406:G:T (self)
4684076, 2569846, 1817826, 1803017, 1117396, 2932210, 971281, 1204518, 2503556, 642770, 5501161, 2569846, 552203, ss218776477, ss230823795, ss238451447, ss554963887, ss648568388, ss975928089, ss1068448605, ss1293858959, ss1574545555, ss1601713770, ss1644707803, ss1795437219, ss1919162588, ss1966923557, ss2020098071, ss2148126416, ss2331017540, ss2624557268, ss2698111271, ss2763959727, ss2988126801, ss3343819255, ss3656079578, ss3727686416, ss3747093146, ss3826543999, ss3836668968, ss3850486576, ss3895754816, ss5147531854 NC_000001.10:188325537:G:T NC_000001.11:188356406:G:T (self)
225352, 25208525, 40146858, 4349536459, ss2168454902, ss3023808760, ss3098198407, ss3646841743, ss3688235071, ss3800095353, ss3842079496, ss4476540523 NC_000001.11:188356406:G:T NC_000001.11:188356406:G:T (self)
ss18069711, ss20429351 NT_004487.16:17373645:G:T NC_000001.11:188356406:G:T (self)
ss41164748, ss97990344, ss139131844 NT_004487.19:39814179:G:T NC_000001.11:188356406: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 rs12021506

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