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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.

rs12021507

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55246212 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.093483 (24744/264690, TOPMED)
C=0.02854 (483/16924, ALFA)
C=0.08353 (1400/16760, 8.3KJPN) (+ 12 more)
C=0.0970 (486/5008, 1000G)
C=0.0683 (306/4480, Estonian)
C=0.1334 (391/2930, KOREAN)
C=0.059 (59/998, GoNL)
C=0.077 (46/600, NorthernSweden)
C=0.097 (32/330, HapMap)
C=0.079 (17/216, Vietnamese)
C=0.131 (28/214, Qatari)
G=0.484 (60/124, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
G=0.5 (5/10, Siberian)
C=0.5 (5/10, 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.55246212G>A
GRCh38.p13 chr 1 NC_000001.11:g.55246212G>C
GRCh37.p13 chr 1 NC_000001.10:g.55711885G>A
GRCh37.p13 chr 1 NC_000001.10:g.55711885G>C
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 16924 G=0.97146 A=0.00000, C=0.02854
European Sub 13178 G=0.96562 A=0.00000, C=0.03438
African Sub 2346 G=0.9949 A=0.0000, C=0.0051
African Others Sub 94 G=1.00 A=0.00, C=0.00
African American Sub 2252 G=0.9947 A=0.0000, C=0.0053
Asian Sub 88 G=1.00 A=0.00, C=0.00
East Asian Sub 66 G=1.00 A=0.00, C=0.00
Other Asian Sub 22 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 130 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 476 G=1.000 A=0.000, C=0.000
South Asian Sub 84 G=1.00 A=0.00, C=0.00
Other Sub 622 G=0.971 A=0.000, C=0.029


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=0.906517 C=0.093483
8.3KJPN JAPANESE Study-wide 16760 G=0.91647 C=0.08353
1000Genomes Global Study-wide 5008 G=0.9030 C=0.0970
1000Genomes African Sub 1322 G=0.8828 C=0.1172
1000Genomes East Asian Sub 1008 G=0.8929 C=0.1071
1000Genomes Europe Sub 1006 G=0.9334 C=0.0666
1000Genomes South Asian Sub 978 G=0.918 C=0.082
1000Genomes American Sub 694 G=0.890 C=0.110
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9317 C=0.0683
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8666 C=0.1334
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.941 C=0.059
Northern Sweden ACPOP Study-wide 600 G=0.923 C=0.077
HapMap Global Study-wide 330 G=0.903 C=0.097
HapMap African Sub 120 G=0.867 C=0.133
HapMap American Sub 120 G=0.925 C=0.075
HapMap Asian Sub 90 G=0.92 C=0.08
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.921 C=0.079
Qatari Global Study-wide 214 G=0.869 C=0.131
SGDP_PRJ Global Study-wide 124 G=0.484 C=0.516
The Danish reference pan genome Danish Study-wide 40 G=0.93 C=0.07
Siberian Global Study-wide 10 G=0.5 C=0.5
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
GRCh38.p13 chr 1 NC_000001.11:g.55246212= NC_000001.11:g.55246212G>A NC_000001.11:g.55246212G>C
GRCh37.p13 chr 1 NC_000001.10:g.55711885= NC_000001.10:g.55711885G>A NC_000001.10:g.55711885G>C
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#.

46 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069714 Feb 28, 2004 (120)
2 PERLEGEN ss23842419 Sep 20, 2004 (123)
3 PERLEGEN ss68766388 May 17, 2007 (127)
4 BUSHMAN ss198460038 Jul 04, 2010 (132)
5 1000GENOMES ss218386045 Jul 14, 2010 (132)
6 1000GENOMES ss230535203 Jul 14, 2010 (132)
7 1000GENOMES ss238229515 Jul 15, 2010 (132)
8 GMI ss275827409 May 04, 2012 (137)
9 TISHKOFF ss554114748 Apr 25, 2013 (138)
10 SSMP ss647946300 Apr 25, 2013 (138)
11 EVA-GONL ss975162307 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1067887718 Aug 21, 2014 (142)
13 1000GENOMES ss1290900952 Aug 21, 2014 (142)
14 DDI ss1425808724 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1574060452 Apr 01, 2015 (144)
16 EVA_DECODE ss1584528808 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1600177575 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1600177576 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1643171608 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1643171609 Apr 01, 2015 (144)
21 WEILL_CORNELL_DGM ss1918371023 Feb 12, 2016 (147)
22 GENOMED ss1966745498 Jul 19, 2016 (147)
23 JJLAB ss2019701095 Sep 14, 2016 (149)
24 USC_VALOUEV ss2147715481 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2162522087 Dec 20, 2016 (150)
26 TOPMED ss2324762577 Dec 20, 2016 (150)
27 GRF ss2697628036 Nov 08, 2017 (151)
28 GNOMAD ss2755175972 Nov 08, 2017 (151)
29 SWEGEN ss2986820941 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3023610598 Nov 08, 2017 (151)
31 TOPMED ss3076708578 Nov 08, 2017 (151)
32 TOPMED ss3076708579 Nov 08, 2017 (151)
33 CSHL ss3343454456 Nov 08, 2017 (151)
34 EGCUT_WGS ss3654884712 Jul 12, 2019 (153)
35 EVA_DECODE ss3686776212 Jul 12, 2019 (153)
36 ACPOP ss3727048819 Jul 12, 2019 (153)
37 EVA ss3746206294 Jul 12, 2019 (153)
38 PACBIO ss3783409363 Jul 12, 2019 (153)
39 PACBIO ss3789067278 Jul 12, 2019 (153)
40 PACBIO ss3793939973 Jul 12, 2019 (153)
41 KHV_HUMAN_GENOMES ss3799215701 Jul 12, 2019 (153)
42 EVA ss3826172710 Apr 25, 2020 (154)
43 SGDP_PRJ ss3848850828 Apr 25, 2020 (154)
44 KRGDB ss3893861883 Apr 25, 2020 (154)
45 TOPMED ss4449814810 Apr 25, 2021 (155)
46 TOMMO_GENOMICS ss5143961173 Apr 25, 2021 (155)
47 1000Genomes NC_000001.10 - 55711885 Oct 11, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 881077 (NC_000001.10:55711884:G:G 3584/3854, NC_000001.10:55711884:G:C 270/3854)
Row 881078 (NC_000001.10:55711884:G:G 3853/3854, NC_000001.10:55711884:G:A 1/3854)

- Oct 11, 2018 (152)
49 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 881077 (NC_000001.10:55711884:G:G 3584/3854, NC_000001.10:55711884:G:C 270/3854)
Row 881078 (NC_000001.10:55711884:G:G 3853/3854, NC_000001.10:55711884:G:A 1/3854)

- Oct 11, 2018 (152)
50 Genetic variation in the Estonian population NC_000001.10 - 55711885 Oct 11, 2018 (152)
51 The Danish reference pan genome NC_000001.10 - 55711885 Apr 25, 2020 (154)
52 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 11460143 (NC_000001.11:55246211:G:A 24/140118)
Row 11460144 (NC_000001.11:55246211:G:C 12053/140104)

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

Submission ignored due to conflicting rows:
Row 11460143 (NC_000001.11:55246211:G:A 24/140118)
Row 11460144 (NC_000001.11:55246211:G:C 12053/140104)

- Apr 25, 2021 (155)
54 Genome of the Netherlands Release 5 NC_000001.10 - 55711885 Apr 25, 2020 (154)
55 HapMap NC_000001.11 - 55246212 Apr 25, 2020 (154)
56 KOREAN population from KRGDB NC_000001.10 - 55711885 Apr 25, 2020 (154)
57 Northern Sweden NC_000001.10 - 55711885 Jul 12, 2019 (153)
58 Qatari NC_000001.10 - 55711885 Apr 25, 2020 (154)
59 SGDP_PRJ NC_000001.10 - 55711885 Apr 25, 2020 (154)
60 Siberian NC_000001.10 - 55711885 Apr 25, 2020 (154)
61 8.3KJPN NC_000001.10 - 55711885 Apr 25, 2021 (155)
62 TopMed NC_000001.11 - 55246212 Apr 25, 2021 (155)
63 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 881077 (NC_000001.10:55711884:G:G 3451/3708, NC_000001.10:55711884:G:C 257/3708)
Row 881078 (NC_000001.10:55711884:G:G 3708/3708, NC_000001.10:55711884:G:A 0/3708)

- Oct 11, 2018 (152)
64 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 881077 (NC_000001.10:55711884:G:G 3451/3708, NC_000001.10:55711884:G:C 257/3708)
Row 881078 (NC_000001.10:55711884:G:G 3708/3708, NC_000001.10:55711884:G:A 0/3708)

- Oct 11, 2018 (152)
65 A Vietnamese Genetic Variation Database NC_000001.10 - 55711885 Jul 12, 2019 (153)
66 ALFA NC_000001.11 - 55246212 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
ss1600177576, ss1643171609, ss2755175972 NC_000001.10:55711884:G:A NC_000001.11:55246211:G:A (self)
2645865973, ss2162522087, ss3076708578 NC_000001.11:55246211:G:A NC_000001.11:55246211:G:A (self)
ss198460038, ss275827409, ss1584528808 NC_000001.9:55484472:G:C NC_000001.11:55246211:G:C (self)
1619705, 622960, 1502270, 373671, 1039277, 333684, 412953, 867808, 231835, 1930480, 180802, ss218386045, ss230535203, ss238229515, ss554114748, ss647946300, ss975162307, ss1067887718, ss1290900952, ss1425808724, ss1574060452, ss1600177575, ss1643171608, ss1918371023, ss1966745498, ss2019701095, ss2147715481, ss2324762577, ss2697628036, ss2755175972, ss2986820941, ss3343454456, ss3654884712, ss3727048819, ss3746206294, ss3783409363, ss3789067278, ss3793939973, ss3826172710, ss3848850828, ss3893861883, ss5143961173 NC_000001.10:55711884:G:C NC_000001.11:55246211:G:C (self)
68411, 8447161, 13421145, 2645865973, ss2162522087, ss3023610598, ss3076708579, ss3686776212, ss3799215701, ss4449814810 NC_000001.11:55246211:G:C NC_000001.11:55246211:G:C (self)
ss18069714 NT_032977.6:17274955:G:C NC_000001.11:55246211:G:C (self)
ss23842419, ss68766388 NT_032977.9:25683802:G:C NC_000001.11:55246211:G:C (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 rs12021507

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