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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.

rs12021511

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:107509235 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.272360 (72091/264690, TOPMED)
G=0.42601 (7140/16760, 8.3KJPN)
A=0.16287 (2162/13274, ALFA) (+ 14 more)
A=0.3219 (1612/5008, 1000G)
A=0.2944 (1319/4480, Estonian)
A=0.3358 (1294/3854, ALSPAC)
A=0.3528 (1308/3708, TWINSUK)
G=0.4113 (1205/2930, KOREAN)
G=0.4023 (737/1832, Korea1K)
A=0.316 (315/998, GoNL)
A=0.268 (161/600, NorthernSweden)
G=0.375 (120/320, SGDP_PRJ)
A=0.321 (97/302, HapMap)
A=0.301 (65/216, Qatari)
G=0.486 (104/214, Vietnamese)
A=0.38 (15/40, GENOME_DK)
G=0.26 (9/34, Siberian)
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.107509235G>A
GRCh38.p13 chr 1 NC_000001.11:g.107509235G>C
GRCh38.p13 chr 1 NC_000001.11:g.107509235G>T
GRCh37.p13 chr 1 NC_000001.10:g.108051857G>A
GRCh37.p13 chr 1 NC_000001.10:g.108051857G>C
GRCh37.p13 chr 1 NC_000001.10:g.108051857G>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 13274 G=0.83713 A=0.16287, C=0.00000, T=0.00000
European Sub 10042 G=0.79337 A=0.20663, C=0.00000, T=0.00000
African Sub 2314 G=0.9914 A=0.0086, C=0.0000, T=0.0000
African Others Sub 94 G=0.99 A=0.01, C=0.00, T=0.00
African American Sub 2220 G=0.9914 A=0.0086, C=0.0000, T=0.0000
Asian Sub 22 G=0.95 A=0.05, C=0.00, T=0.00
East Asian Sub 16 G=0.94 A=0.06, C=0.00, T=0.00
Other Asian Sub 6 G=1.0 A=0.0, C=0.0, T=0.0
Latin American 1 Sub 70 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 306 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 40 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 480 G=0.863 A=0.138, C=0.000, T=0.000


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=0.727640 A=0.272360
8.3KJPN JAPANESE Study-wide 16760 G=0.42601 A=0.57399
1000Genomes Global Study-wide 5008 G=0.6781 A=0.3219
1000Genomes African Sub 1322 G=0.9070 A=0.0930
1000Genomes East Asian Sub 1008 G=0.4306 A=0.5694
1000Genomes Europe Sub 1006 G=0.6233 A=0.3767
1000Genomes South Asian Sub 978 G=0.653 A=0.347
1000Genomes American Sub 694 G=0.716 A=0.284
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7056 A=0.2944
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6642 A=0.3358
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6472 A=0.3528
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4113 A=0.5887
Korean Genome Project KOREAN Study-wide 1832 G=0.4023 A=0.5977
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.684 A=0.316
Northern Sweden ACPOP Study-wide 600 G=0.732 A=0.268
SGDP_PRJ Global Study-wide 320 G=0.375 A=0.625
HapMap Global Study-wide 302 G=0.679 A=0.321
HapMap African Sub 114 G=0.947 A=0.053
HapMap American Sub 108 G=0.556 A=0.444
HapMap Asian Sub 80 G=0.46 A=0.54
Qatari Global Study-wide 216 G=0.699 A=0.301
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.486 A=0.514
The Danish reference pan genome Danish Study-wide 40 G=0.62 A=0.38
Siberian Global Study-wide 34 G=0.26 A=0.74
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 C T
GRCh38.p13 chr 1 NC_000001.11:g.107509235= NC_000001.11:g.107509235G>A NC_000001.11:g.107509235G>C NC_000001.11:g.107509235G>T
GRCh37.p13 chr 1 NC_000001.10:g.108051857= NC_000001.10:g.108051857G>A NC_000001.10:g.108051857G>C NC_000001.10:g.108051857G>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#.

54 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069728 Feb 28, 2004 (120)
2 HGSV ss78330063 Dec 06, 2007 (129)
3 BGI ss106593757 Feb 06, 2009 (130)
4 1000GENOMES ss108504620 Jan 23, 2009 (130)
5 GMI ss155498826 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss164972252 Jul 04, 2010 (132)
7 BCM-HGSC-SUB ss205360678 Jul 04, 2010 (132)
8 1000GENOMES ss210612744 Jul 14, 2010 (132)
9 1000GENOMES ss218583820 Jul 14, 2010 (132)
10 1000GENOMES ss230681843 Jul 14, 2010 (132)
11 1000GENOMES ss238342403 Jul 15, 2010 (132)
12 BL ss253361454 May 09, 2011 (134)
13 GMI ss275969028 May 04, 2012 (137)
14 GMI ss284116822 Apr 25, 2013 (138)
15 PJP ss290593372 May 09, 2011 (134)
16 TISHKOFF ss554543229 Apr 25, 2013 (138)
17 SSMP ss648296064 Apr 25, 2013 (138)
18 EVA-GONL ss975544941 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1068174308 Aug 21, 2014 (142)
20 1000GENOMES ss1292335436 Aug 21, 2014 (142)
21 DDI ss1425929558 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1574306579 Apr 01, 2015 (144)
23 EVA_DECODE ss1584923763 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1600937395 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1643931428 Apr 01, 2015 (144)
26 HAMMER_LAB ss1794894762 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1918745230 Feb 12, 2016 (147)
28 JJLAB ss2019896517 Sep 14, 2016 (149)
29 USC_VALOUEV ss2147913733 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2165513016 Dec 20, 2016 (150)
31 TOPMED ss2327869116 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2624457994 Nov 08, 2017 (151)
33 GRF ss2697843162 Nov 08, 2017 (151)
34 GNOMAD ss2759278429 Nov 08, 2017 (151)
35 SWEGEN ss2987397433 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3023712014 Nov 08, 2017 (151)
37 TOPMED ss3086162079 Nov 08, 2017 (151)
38 CSHL ss3343623533 Nov 08, 2017 (151)
39 EGCUT_WGS ss3655486484 Jul 12, 2019 (153)
40 EVA_DECODE ss3687481295 Jul 12, 2019 (153)
41 ACPOP ss3727367053 Jul 12, 2019 (153)
42 EVA ss3746642336 Jul 12, 2019 (153)
43 PACBIO ss3783512446 Jul 12, 2019 (153)
44 PACBIO ss3789155302 Jul 12, 2019 (153)
45 PACBIO ss3794028174 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3799646718 Jul 12, 2019 (153)
47 EVA ss3826356292 Apr 25, 2020 (154)
48 EVA ss3836569512 Apr 25, 2020 (154)
49 EVA ss3841977888 Apr 25, 2020 (154)
50 SGDP_PRJ ss3849598775 Apr 25, 2020 (154)
51 KRGDB ss3894685304 Apr 25, 2020 (154)
52 KOGIC ss3945196663 Apr 25, 2020 (154)
53 TOPMED ss4462744000 Apr 25, 2021 (155)
54 TOMMO_GENOMICS ss5145568256 Apr 25, 2021 (155)
55 1000Genomes NC_000001.10 - 108051857 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 108051857 Oct 11, 2018 (152)
57 Genetic variation in the Estonian population NC_000001.10 - 108051857 Oct 11, 2018 (152)
58 The Danish reference pan genome NC_000001.10 - 108051857 Apr 25, 2020 (154)
59 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 21979846 (NC_000001.11:107509234:G:A 37351/139918)
Row 21979847 (NC_000001.11:107509234:G:C 1/139958)

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

Submission ignored due to conflicting rows:
Row 21979846 (NC_000001.11:107509234:G:A 37351/139918)
Row 21979847 (NC_000001.11:107509234:G:C 1/139958)

- Apr 25, 2021 (155)
61 Genome of the Netherlands Release 5 NC_000001.10 - 108051857 Apr 25, 2020 (154)
62 HapMap NC_000001.11 - 107509235 Apr 25, 2020 (154)
63 KOREAN population from KRGDB NC_000001.10 - 108051857 Apr 25, 2020 (154)
64 Korean Genome Project NC_000001.11 - 107509235 Apr 25, 2020 (154)
65 Northern Sweden NC_000001.10 - 108051857 Jul 12, 2019 (153)
66 Qatari NC_000001.10 - 108051857 Apr 25, 2020 (154)
67 SGDP_PRJ NC_000001.10 - 108051857 Apr 25, 2020 (154)
68 Siberian NC_000001.10 - 108051857 Apr 25, 2020 (154)
69 8.3KJPN NC_000001.10 - 108051857 Apr 25, 2021 (155)
70 TopMed NC_000001.11 - 107509235 Apr 25, 2021 (155)
71 UK 10K study - Twins NC_000001.10 - 108051857 Oct 11, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000001.10 - 108051857 Jul 12, 2019 (153)
73 ALFA NC_000001.11 - 107509235 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
ss78330063 NC_000001.8:107763898:G:A NC_000001.11:107509234:G:A (self)
ss108504620, ss164972252, ss205360678, ss210612744, ss253361454, ss275969028, ss284116822, ss290593372, ss1584923763 NC_000001.9:107853379:G:A NC_000001.11:107509234:G:A (self)
3107814, 1716079, 1224732, 1654253, 747340, 1862698, 651918, 787160, 1615755, 430087, 3537563, 1716079, 372388, ss218583820, ss230681843, ss238342403, ss554543229, ss648296064, ss975544941, ss1068174308, ss1292335436, ss1425929558, ss1574306579, ss1600937395, ss1643931428, ss1794894762, ss1918745230, ss2019896517, ss2147913733, ss2327869116, ss2624457994, ss2697843162, ss2759278429, ss2987397433, ss3343623533, ss3655486484, ss3727367053, ss3746642336, ss3783512446, ss3789155302, ss3794028174, ss3826356292, ss3836569512, ss3849598775, ss3894685304, ss5145568256 NC_000001.10:108051856:G:A NC_000001.11:107509234:G:A (self)
149267, 1574664, 16602185, 26350335, 11555585591, ss2165513016, ss3023712014, ss3086162079, ss3687481295, ss3799646718, ss3841977888, ss3945196663, ss4462744000 NC_000001.11:107509234:G:A NC_000001.11:107509234:G:A (self)
ss18069728 NT_029860.11:4127967:G:A NC_000001.11:107509234:G:A (self)
ss106593757, ss155498826 NT_032977.9:78023774:G:A NC_000001.11:107509234:G:A (self)
11555585591 NC_000001.11:107509234:G:C NC_000001.11:107509234:G:C
11555585591 NC_000001.11:107509234:G:T NC_000001.11:107509234:G:T
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 rs12021511

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