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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.

rs12021509

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:79119625 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.230273 (60951/264690, TOPMED)
G=0.26777 (20851/77868, ALFA)
G=0.33132 (5553/16760, 8.3KJPN) (+ 17 more)
G=0.2173 (1088/5008, 1000G)
G=0.4121 (1846/4480, Estonian)
G=0.2997 (1155/3854, ALSPAC)
G=0.3058 (1134/3708, TWINSUK)
G=0.2799 (820/2930, KOREAN)
G=0.2164 (451/2084, HGDP_Stanford)
G=0.2011 (380/1890, HapMap)
G=0.3150 (577/1832, Korea1K)
G=0.2262 (257/1136, Daghestan)
G=0.305 (304/998, GoNL)
G=0.387 (232/600, NorthernSweden)
G=0.208 (45/216, Qatari)
G=0.264 (56/212, Vietnamese)
A=0.437 (90/206, SGDP_PRJ)
G=0.28 (11/40, GENOME_DK)
A=0.31 (8/26, Siberian)
G=0.20 (4/20, Ancient Sardinia)
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.79119625A>C
GRCh38.p13 chr 1 NC_000001.11:g.79119625A>G
GRCh37.p13 chr 1 NC_000001.10:g.79585310A>C
GRCh37.p13 chr 1 NC_000001.10:g.79585310A>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 77868 A=0.73223 C=0.00000, G=0.26777
European Sub 62418 A=0.70060 C=0.00000, G=0.29940
African Sub 6888 A=0.9206 C=0.0000, G=0.0794
African Others Sub 258 A=0.973 C=0.000, G=0.027
African American Sub 6630 A=0.9186 C=0.0000, G=0.0814
Asian Sub 152 A=0.789 C=0.000, G=0.211
East Asian Sub 122 A=0.779 C=0.000, G=0.221
Other Asian Sub 30 A=0.83 C=0.00, G=0.17
Latin American 1 Sub 224 A=0.866 C=0.000, G=0.134
Latin American 2 Sub 1056 A=0.8400 C=0.0000, G=0.1600
South Asian Sub 4928 A=0.8113 C=0.0000, G=0.1887
Other Sub 2202 A=0.7934 C=0.0000, G=0.2066


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 A=0.769727 G=0.230273
8.3KJPN JAPANESE Study-wide 16760 A=0.66868 G=0.33132
1000Genomes Global Study-wide 5008 A=0.7827 G=0.2173
1000Genomes African Sub 1322 A=0.9206 G=0.0794
1000Genomes East Asian Sub 1008 A=0.6925 G=0.3075
1000Genomes Europe Sub 1006 A=0.7028 G=0.2972
1000Genomes South Asian Sub 978 A=0.789 G=0.211
1000Genomes American Sub 694 A=0.758 G=0.242
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5879 G=0.4121
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7003 G=0.2997
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6942 G=0.3058
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7201 G=0.2799
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.7836 G=0.2164
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=0.719 G=0.281
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.771 G=0.229
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.837 G=0.163
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.713 G=0.287
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=0.855 G=0.145
HGDP-CEPH-db Supplement 1 America Sub 216 A=0.852 G=0.148
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=0.89 G=0.11
HapMap Global Study-wide 1890 A=0.7989 G=0.2011
HapMap American Sub 770 A=0.729 G=0.271
HapMap African Sub 692 A=0.921 G=0.079
HapMap Asian Sub 252 A=0.706 G=0.294
HapMap Europe Sub 176 A=0.761 G=0.239
Korean Genome Project KOREAN Study-wide 1832 A=0.6850 G=0.3150
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.7738 G=0.2262
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.736 G=0.264
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.861 G=0.139
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.811 G=0.189
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.741 G=0.259
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.84 G=0.16
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.89 G=0.11
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.695 G=0.305
Northern Sweden ACPOP Study-wide 600 A=0.613 G=0.387
Qatari Global Study-wide 216 A=0.792 G=0.208
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.736 G=0.264
SGDP_PRJ Global Study-wide 206 A=0.437 G=0.563
The Danish reference pan genome Danish Study-wide 40 A=0.72 G=0.28
Siberian Global Study-wide 26 A=0.31 G=0.69
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 20 A=0.80 G=0.20
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 A= C G
GRCh38.p13 chr 1 NC_000001.11:g.79119625= NC_000001.11:g.79119625A>C NC_000001.11:g.79119625A>G
GRCh37.p13 chr 1 NC_000001.10:g.79585310= NC_000001.10:g.79585310A>C NC_000001.10:g.79585310A>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#.

81 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069724 Feb 28, 2004 (120)
2 ILLUMINA ss66733982 Nov 29, 2006 (127)
3 ILLUMINA ss66975771 Nov 29, 2006 (127)
4 ILLUMINA ss67146935 Nov 29, 2006 (127)
5 PERLEGEN ss68771278 May 16, 2007 (127)
6 ILLUMINA ss70403760 May 16, 2007 (127)
7 ILLUMINA ss70552315 May 26, 2008 (130)
8 ILLUMINA ss71088398 May 16, 2007 (127)
9 ILLUMINA ss75720959 Dec 05, 2007 (129)
10 KRIBB_YJKIM ss85173075 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss87563678 Mar 23, 2008 (129)
12 ILLUMINA ss121529369 Dec 01, 2009 (131)
13 ENSEMBL ss138014586 Dec 01, 2009 (131)
14 ILLUMINA ss153114133 Dec 01, 2009 (131)
15 GMI ss155228937 Dec 01, 2009 (131)
16 ILLUMINA ss159200214 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164618750 Jul 04, 2010 (132)
18 ILLUMINA ss170024866 Jul 04, 2010 (132)
19 ILLUMINA ss171794644 Jul 04, 2010 (132)
20 BUSHMAN ss198666161 Jul 04, 2010 (132)
21 1000GENOMES ss218475132 Jul 14, 2010 (132)
22 1000GENOMES ss230600396 Jul 14, 2010 (132)
23 1000GENOMES ss238280344 Jul 15, 2010 (132)
24 GMI ss275890534 May 04, 2012 (137)
25 PJP ss290544900 May 09, 2011 (134)
26 ILLUMINA ss480098522 May 04, 2012 (137)
27 ILLUMINA ss482408141 May 04, 2012 (137)
28 ILLUMINA ss533543248 Sep 08, 2015 (146)
29 TISHKOFF ss554293170 Apr 25, 2013 (138)
30 SSMP ss648154228 Apr 25, 2013 (138)
31 ILLUMINA ss779710215 Aug 21, 2014 (142)
32 ILLUMINA ss781146436 Aug 21, 2014 (142)
33 ILLUMINA ss825373068 Apr 01, 2015 (144)
34 ILLUMINA ss832712671 Aug 21, 2014 (142)
35 ILLUMINA ss833303403 Aug 21, 2014 (142)
36 ILLUMINA ss835184535 Aug 21, 2014 (142)
37 EVA-GONL ss975332918 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1068019173 Aug 21, 2014 (142)
39 1000GENOMES ss1291552551 Aug 21, 2014 (142)
40 HAMMER_LAB ss1397250793 Sep 08, 2015 (146)
41 DDI ss1425865482 Apr 01, 2015 (144)
42 EVA_GENOME_DK ss1574172720 Apr 01, 2015 (144)
43 EVA_DECODE ss1584706382 Apr 01, 2015 (144)
44 EVA_UK10K_ALSPAC ss1600521989 Apr 01, 2015 (144)
45 EVA_UK10K_TWINSUK ss1643516022 Apr 01, 2015 (144)
46 EVA_SVP ss1712346137 Apr 01, 2015 (144)
47 HAMMER_LAB ss1794608720 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1918537055 Feb 12, 2016 (147)
49 GENOMED ss1966786842 Jul 19, 2016 (147)
50 JJLAB ss2019788987 Sep 14, 2016 (149)
51 USC_VALOUEV ss2147804793 Dec 20, 2016 (150)
52 HUMAN_LONGEVITY ss2163890040 Dec 20, 2016 (150)
53 TOPMED ss2326174624 Dec 20, 2016 (150)
54 SYSTEMSBIOZJU ss2624405219 Nov 08, 2017 (151)
55 ILLUMINA ss2632536232 Nov 08, 2017 (151)
56 GRF ss2697724980 Nov 08, 2017 (151)
57 GNOMAD ss2757037322 Nov 08, 2017 (151)
58 SWEGEN ss2987077722 Nov 08, 2017 (151)
59 BIOINF_KMB_FNS_UNIBA ss3023656498 Nov 08, 2017 (151)
60 TOPMED ss3080988168 Nov 08, 2017 (151)
61 CSHL ss3343529459 Nov 08, 2017 (151)
62 ILLUMINA ss3626134210 Oct 11, 2018 (152)
63 ILLUMINA ss3630571297 Oct 11, 2018 (152)
64 ILLUMINA ss3637766823 Oct 11, 2018 (152)
65 ILLUMINA ss3638902099 Oct 11, 2018 (152)
66 ILLUMINA ss3639448789 Oct 11, 2018 (152)
67 ILLUMINA ss3641598593 Oct 11, 2018 (152)
68 ILLUMINA ss3642777824 Oct 11, 2018 (152)
69 EGCUT_WGS ss3655156391 Jul 12, 2019 (153)
70 EVA_DECODE ss3687093776 Jul 12, 2019 (153)
71 ACPOP ss3727190462 Jul 12, 2019 (153)
72 EVA ss3746403891 Jul 12, 2019 (153)
73 KHV_HUMAN_GENOMES ss3799409459 Jul 12, 2019 (153)
74 EVA ss3826255475 Apr 25, 2020 (154)
75 HGDP ss3847339113 Apr 25, 2020 (154)
76 SGDP_PRJ ss3849188345 Apr 25, 2020 (154)
77 KRGDB ss3894235559 Apr 25, 2020 (154)
78 KOGIC ss3944827037 Apr 25, 2020 (154)
79 EVA ss3984806801 Apr 25, 2021 (155)
80 TOPMED ss4455673476 Apr 25, 2021 (155)
81 TOMMO_GENOMICS ss5144683615 Apr 25, 2021 (155)
82 1000Genomes NC_000001.10 - 79585310 Oct 11, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 79585310 Oct 11, 2018 (152)
84 Genome-wide autozygosity in Daghestan NC_000001.9 - 79357898 Apr 25, 2020 (154)
85 Genetic variation in the Estonian population NC_000001.10 - 79585310 Oct 11, 2018 (152)
86 The Danish reference pan genome NC_000001.10 - 79585310 Apr 25, 2020 (154)
87 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 16221615 (NC_000001.11:79119624:A:C 1/140128)
Row 16221616 (NC_000001.11:79119624:A:G 35172/140112)

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

Submission ignored due to conflicting rows:
Row 16221615 (NC_000001.11:79119624:A:C 1/140128)
Row 16221616 (NC_000001.11:79119624:A:G 35172/140112)

- Apr 25, 2021 (155)
89 Genome of the Netherlands Release 5 NC_000001.10 - 79585310 Apr 25, 2020 (154)
90 HGDP-CEPH-db Supplement 1 NC_000001.9 - 79357898 Apr 25, 2020 (154)
91 HapMap NC_000001.11 - 79119625 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000001.10 - 79585310 Apr 25, 2020 (154)
93 Korean Genome Project NC_000001.11 - 79119625 Apr 25, 2020 (154)
94 Northern Sweden NC_000001.10 - 79585310 Jul 12, 2019 (153)
95 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 79585310 Apr 25, 2021 (155)
96 Qatari NC_000001.10 - 79585310 Apr 25, 2020 (154)
97 SGDP_PRJ NC_000001.10 - 79585310 Apr 25, 2020 (154)
98 Siberian NC_000001.10 - 79585310 Apr 25, 2020 (154)
99 8.3KJPN NC_000001.10 - 79585310 Apr 25, 2021 (155)
100 TopMed NC_000001.11 - 79119625 Apr 25, 2021 (155)
101 UK 10K study - Twins NC_000001.10 - 79585310 Oct 11, 2018 (152)
102 A Vietnamese Genetic Variation Database NC_000001.10 - 79585310 Jul 12, 2019 (153)
103 ALFA NC_000001.11 - 79119625 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)
rs60623978 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2757037322 NC_000001.10:79585309:A:C NC_000001.11:79119624:A:C (self)
4248616460, ss2163890040 NC_000001.11:79119624:A:C NC_000001.11:79119624:A:C (self)
ss3638902099, ss3639448789 NC_000001.8:79297330:A:G NC_000001.11:79119624:A:G (self)
12142, 17005, ss87563678, ss164618750, ss198666161, ss275890534, ss290544900, ss482408141, ss825373068, ss1397250793, ss1584706382, ss1712346137, ss3642777824, ss3847339113 NC_000001.9:79357897:A:G NC_000001.11:79119624:A:G (self)
2295098, 1259009, 894639, 1570183, 540549, 1412953, 475327, 32728, 578985, 1205325, 321147, 2652922, 1259009, 266915, ss218475132, ss230600396, ss238280344, ss480098522, ss533543248, ss554293170, ss648154228, ss779710215, ss781146436, ss832712671, ss833303403, ss835184535, ss975332918, ss1068019173, ss1291552551, ss1425865482, ss1574172720, ss1600521989, ss1643516022, ss1794608720, ss1918537055, ss1966786842, ss2019788987, ss2147804793, ss2326174624, ss2624405219, ss2632536232, ss2697724980, ss2757037322, ss2987077722, ss3343529459, ss3626134210, ss3630571297, ss3637766823, ss3641598593, ss3655156391, ss3727190462, ss3746403891, ss3826255475, ss3849188345, ss3894235559, ss3984806801, ss5144683615 NC_000001.10:79585309:A:G NC_000001.11:79119624:A:G (self)
105954, 1205038, 12142398, 19279811, 4248616460, ss2163890040, ss3023656498, ss3080988168, ss3687093776, ss3799409459, ss3944827037, ss4455673476 NC_000001.11:79119624:A:G NC_000001.11:79119624:A:G (self)
ss18069724 NT_026943.13:4405483:A:G NC_000001.11:79119624:A:G (self)
ss66733982, ss66975771, ss67146935, ss68771278, ss70403760, ss70552315, ss71088398, ss75720959, ss85173075, ss121529369, ss138014586, ss153114133, ss155228937, ss159200214, ss170024866, ss171794644 NT_032977.9:49557227:A:G NC_000001.11:79119624:A:G (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 rs12021509

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