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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.

rs12069019

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99539921 (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
A=0.143843 (43788/304416, ALFA)
A=0.149756 (39639/264690, TOPMED)
A=0.147570 (20645/139900, GnomAD) (+ 18 more)
A=0.17417 (13705/78688, PAGE_STUDY)
A=0.35758 (5993/16760, 8.3KJPN)
A=0.1989 (996/5008, 1000G)
A=0.1842 (825/4480, Estonian)
A=0.1373 (529/3854, ALSPAC)
A=0.1276 (473/3708, TWINSUK)
A=0.4003 (1173/2930, KOREAN)
A=0.2171 (452/2082, HGDP_Stanford)
A=0.2145 (405/1888, HapMap)
A=0.129 (129/998, GoNL)
A=0.375 (286/762, PRJEB37584)
A=0.180 (108/600, NorthernSweden)
A=0.190 (41/216, Qatari)
A=0.280 (60/214, Vietnamese)
G=0.458 (97/212, SGDP_PRJ)
A=0.23 (9/40, GENOME_DK)
A=0.07 (2/28, Ancient Sardinia)
G=0.46 (11/24, 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.99539921G>A
GRCh38.p13 chr 1 NC_000001.11:g.99539921G>T
GRCh37.p13 chr 1 NC_000001.10:g.100005477G>A
GRCh37.p13 chr 1 NC_000001.10:g.100005477G>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 (New)
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 304416 G=0.856157 A=0.143843
European Sub 269474 G=0.863078 A=0.136922
African Sub 8384 G=0.8746 A=0.1254
African Others Sub 318 G=0.871 A=0.129
African American Sub 8066 G=0.8748 A=0.1252
Asian Sub 3928 G=0.6652 A=0.3348
East Asian Sub 3182 G=0.6191 A=0.3809
Other Asian Sub 746 G=0.862 A=0.138
Latin American 1 Sub 1134 G=0.8598 A=0.1402
Latin American 2 Sub 7224 G=0.7493 A=0.2507
South Asian Sub 5224 G=0.7818 A=0.2182
Other Sub 9048 G=0.8436 A=0.1564


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=0.850244 A=0.149756
gnomAD - Genomes Global Study-wide 139900 G=0.852430 A=0.147570
gnomAD - Genomes European Sub 75800 G=0.85145 A=0.14855
gnomAD - Genomes African Sub 41896 G=0.87297 A=0.12703
gnomAD - Genomes American Sub 13624 G=0.81797 A=0.18203
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.9222 A=0.0778
gnomAD - Genomes East Asian Sub 3116 G=0.6698 A=0.3302
gnomAD - Genomes Other Sub 2148 G=0.8622 A=0.1378
The PAGE Study Global Study-wide 78688 G=0.82583 A=0.17417
The PAGE Study AfricanAmerican Sub 32512 G=0.87454 A=0.12546
The PAGE Study Mexican Sub 10810 G=0.75291 A=0.24709
The PAGE Study Asian Sub 8314 G=0.6641 A=0.3359
The PAGE Study PuertoRican Sub 7916 G=0.8785 A=0.1215
The PAGE Study NativeHawaiian Sub 4534 G=0.8472 A=0.1528
The PAGE Study Cuban Sub 4230 G=0.8716 A=0.1284
The PAGE Study Dominican Sub 3826 G=0.8623 A=0.1377
The PAGE Study CentralAmerican Sub 2448 G=0.7782 A=0.2218
The PAGE Study SouthAmerican Sub 1982 G=0.7593 A=0.2407
The PAGE Study NativeAmerican Sub 1260 G=0.8167 A=0.1833
The PAGE Study SouthAsian Sub 856 G=0.783 A=0.217
8.3KJPN JAPANESE Study-wide 16760 G=0.64242 A=0.35758
1000Genomes Global Study-wide 5008 G=0.8011 A=0.1989
1000Genomes African Sub 1322 G=0.8880 A=0.1120
1000Genomes East Asian Sub 1008 G=0.6776 A=0.3224
1000Genomes Europe Sub 1006 G=0.8410 A=0.1590
1000Genomes South Asian Sub 978 G=0.775 A=0.225
1000Genomes American Sub 694 G=0.794 A=0.206
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8158 A=0.1842
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8627 A=0.1373
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8724 A=0.1276
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5997 A=0.4003, T=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 G=0.7829 A=0.2171
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.651 A=0.349
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.775 A=0.225
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.817 A=0.183
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.863 A=0.138
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.843 A=0.157
HGDP-CEPH-db Supplement 1 America Sub 214 G=0.785 A=0.215
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.96 A=0.04
HapMap Global Study-wide 1888 G=0.7855 A=0.2145
HapMap American Sub 768 G=0.763 A=0.237
HapMap African Sub 690 G=0.845 A=0.155
HapMap Asian Sub 254 G=0.654 A=0.346
HapMap Europe Sub 176 G=0.841 A=0.159
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.871 A=0.129
CNV burdens in cranial meningiomas Global Study-wide 762 G=0.625 A=0.375
CNV burdens in cranial meningiomas CRM Sub 762 G=0.625 A=0.375
Northern Sweden ACPOP Study-wide 600 G=0.820 A=0.180
Qatari Global Study-wide 216 G=0.810 A=0.190
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.720 A=0.280
SGDP_PRJ Global Study-wide 212 G=0.458 A=0.542
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 28 G=0.93 A=0.07
Siberian Global Study-wide 24 G=0.46 A=0.54
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.99539921= NC_000001.11:g.99539921G>A NC_000001.11:g.99539921G>T
GRCh37.p13 chr 1 NC_000001.10:g.100005477= NC_000001.10:g.100005477G>A NC_000001.10:g.100005477G>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#.

101 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18158066 Feb 28, 2004 (120)
2 PERLEGEN ss23842246 Sep 20, 2004 (123)
3 ILLUMINA ss66604515 Dec 03, 2006 (127)
4 ILLUMINA ss66979913 Dec 03, 2006 (127)
5 ILLUMINA ss67152037 Dec 03, 2006 (127)
6 ILLUMINA ss70404579 May 17, 2007 (127)
7 ILLUMINA ss70554432 May 24, 2008 (130)
8 ILLUMINA ss71090973 May 17, 2007 (127)
9 ILLUMINA ss75482387 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss85179636 Dec 14, 2007 (130)
11 BGI ss102767755 Dec 01, 2009 (131)
12 1000GENOMES ss108453318 Jan 23, 2009 (130)
13 ILLUMINA ss121534025 Dec 01, 2009 (131)
14 ILLUMINA ss153125540 Dec 01, 2009 (131)
15 ILLUMINA ss159202478 Dec 01, 2009 (131)
16 ILLUMINA ss160030857 Dec 01, 2009 (131)
17 ILLUMINA ss170037822 Jul 04, 2010 (132)
18 ILLUMINA ss171831908 Jul 04, 2010 (132)
19 1000GENOMES ss218548446 Jul 14, 2010 (132)
20 1000GENOMES ss230656581 Jul 14, 2010 (132)
21 1000GENOMES ss238323597 Jul 15, 2010 (132)
22 GMI ss275945212 May 04, 2012 (137)
23 ILLUMINA ss479665347 May 04, 2012 (137)
24 ILLUMINA ss479670771 May 04, 2012 (137)
25 ILLUMINA ss480189200 Sep 08, 2015 (146)
26 ILLUMINA ss484631363 May 04, 2012 (137)
27 ILLUMINA ss536751851 Sep 08, 2015 (146)
28 TISHKOFF ss554480208 Apr 25, 2013 (138)
29 SSMP ss648253680 Apr 25, 2013 (138)
30 ILLUMINA ss778399048 Sep 08, 2015 (146)
31 ILLUMINA ss782762493 Sep 08, 2015 (146)
32 ILLUMINA ss783728883 Sep 08, 2015 (146)
33 ILLUMINA ss825373853 Apr 01, 2015 (144)
34 ILLUMINA ss832014776 Sep 08, 2015 (146)
35 ILLUMINA ss832714925 Jul 12, 2019 (153)
36 ILLUMINA ss833854197 Sep 08, 2015 (146)
37 EVA-GONL ss975482659 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1068127428 Aug 21, 2014 (142)
39 1000GENOMES ss1292106454 Aug 21, 2014 (142)
40 EVA_GENOME_DK ss1574271271 Apr 01, 2015 (144)
41 EVA_DECODE ss1584860932 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1600816231 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1643810264 Apr 01, 2015 (144)
44 EVA_SVP ss1712357116 Apr 01, 2015 (144)
45 ILLUMINA ss1751859098 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1918682283 Feb 12, 2016 (147)
47 ILLUMINA ss1946002819 Feb 12, 2016 (147)
48 ILLUMINA ss1958296779 Feb 12, 2016 (147)
49 GENOMED ss1966820702 Jul 19, 2016 (147)
50 JJLAB ss2019862584 Sep 14, 2016 (149)
51 USC_VALOUEV ss2147881309 Dec 20, 2016 (150)
52 HUMAN_LONGEVITY ss2165028627 Dec 20, 2016 (150)
53 TOPMED ss2327379425 Dec 20, 2016 (150)
54 SYSTEMSBIOZJU ss2624442785 Nov 08, 2017 (151)
55 ILLUMINA ss2632553593 Nov 08, 2017 (151)
56 GRF ss2697808663 Nov 08, 2017 (151)
57 ILLUMINA ss2710678268 Nov 08, 2017 (151)
58 GNOMAD ss2758634538 Nov 08, 2017 (151)
59 SWEGEN ss2987305247 Nov 08, 2017 (151)
60 ILLUMINA ss3021113779 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3023694890 Nov 08, 2017 (151)
62 TOPMED ss3084642524 Nov 08, 2017 (151)
63 CSHL ss3343595764 Nov 08, 2017 (151)
64 ILLUMINA ss3625546131 Oct 11, 2018 (152)
65 ILLUMINA ss3626165232 Oct 11, 2018 (152)
66 ILLUMINA ss3630587767 Oct 11, 2018 (152)
67 ILLUMINA ss3632903270 Oct 11, 2018 (152)
68 ILLUMINA ss3633598268 Oct 11, 2018 (152)
69 ILLUMINA ss3634339242 Oct 11, 2018 (152)
70 ILLUMINA ss3635291880 Oct 11, 2018 (152)
71 ILLUMINA ss3636016796 Oct 11, 2018 (152)
72 ILLUMINA ss3637042335 Oct 11, 2018 (152)
73 ILLUMINA ss3637775436 Oct 11, 2018 (152)
74 ILLUMINA ss3638905821 Oct 11, 2018 (152)
75 ILLUMINA ss3639450866 Oct 11, 2018 (152)
76 ILLUMINA ss3640046602 Oct 11, 2018 (152)
77 ILLUMINA ss3640984519 Oct 11, 2018 (152)
78 ILLUMINA ss3641278507 Oct 11, 2018 (152)
79 ILLUMINA ss3642785622 Oct 11, 2018 (152)
80 ILLUMINA ss3644498781 Oct 11, 2018 (152)
81 ILLUMINA ss3651444559 Oct 11, 2018 (152)
82 EGCUT_WGS ss3655390259 Jul 12, 2019 (153)
83 EVA_DECODE ss3687366534 Jul 12, 2019 (153)
84 ILLUMINA ss3725048120 Jul 12, 2019 (153)
85 ACPOP ss3727313800 Jul 12, 2019 (153)
86 ILLUMINA ss3744050992 Jul 12, 2019 (153)
87 ILLUMINA ss3744640211 Jul 12, 2019 (153)
88 EVA ss3746573748 Jul 12, 2019 (153)
89 PAGE_CC ss3770827990 Jul 12, 2019 (153)
90 ILLUMINA ss3772141448 Jul 12, 2019 (153)
91 KHV_HUMAN_GENOMES ss3799574499 Jul 12, 2019 (153)
92 EVA ss3826326388 Apr 25, 2020 (154)
93 HGDP ss3847343728 Apr 25, 2020 (154)
94 SGDP_PRJ ss3849476958 Apr 25, 2020 (154)
95 KRGDB ss3894554943 Apr 25, 2020 (154)
96 EVA ss3984461727 Apr 25, 2021 (155)
97 EVA ss3984814945 Apr 25, 2021 (155)
98 EVA ss4016927678 Apr 25, 2021 (155)
99 TOPMED ss4460687436 Apr 25, 2021 (155)
100 TOMMO_GENOMICS ss5145312060 Apr 25, 2021 (155)
101 EVA ss5237270822 Apr 25, 2021 (155)
102 1000Genomes NC_000001.10 - 100005477 Oct 11, 2018 (152)
103 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100005477 Oct 11, 2018 (152)
104 Genetic variation in the Estonian population NC_000001.10 - 100005477 Oct 11, 2018 (152)
105 The Danish reference pan genome NC_000001.10 - 100005477 Apr 25, 2020 (154)
106 gnomAD - Genomes NC_000001.11 - 99539921 Apr 25, 2021 (155)
107 Genome of the Netherlands Release 5 NC_000001.10 - 100005477 Apr 25, 2020 (154)
108 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99778065 Apr 25, 2020 (154)
109 HapMap NC_000001.11 - 99539921 Apr 25, 2020 (154)
110 KOREAN population from KRGDB NC_000001.10 - 100005477 Apr 25, 2020 (154)
111 Northern Sweden NC_000001.10 - 100005477 Jul 12, 2019 (153)
112 The PAGE Study NC_000001.11 - 99539921 Jul 12, 2019 (153)
113 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100005477 Apr 25, 2021 (155)
114 CNV burdens in cranial meningiomas NC_000001.10 - 100005477 Apr 25, 2021 (155)
115 Qatari NC_000001.10 - 100005477 Apr 25, 2020 (154)
116 SGDP_PRJ NC_000001.10 - 100005477 Apr 25, 2020 (154)
117 Siberian NC_000001.10 - 100005477 Apr 25, 2020 (154)
118 8.3KJPN NC_000001.10 - 100005477 Apr 25, 2021 (155)
119 TopMed NC_000001.11 - 99539921 Apr 25, 2021 (155)
120 UK 10K study - Twins NC_000001.10 - 100005477 Oct 11, 2018 (152)
121 A Vietnamese Genetic Variation Database NC_000001.10 - 100005477 Jul 12, 2019 (153)
122 ALFA NC_000001.11 - 99539921 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)
rs57798314 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638905821, ss3639450866 NC_000001.8:99717497:G:A NC_000001.11:99539920:G:A (self)
21620, ss108453318, ss275945212, ss479665347, ss825373853, ss1584860932, ss1712357116, ss3642785622, ss3847343728 NC_000001.9:99778064:G:A NC_000001.11:99539920:G:A (self)
2869981, 1583103, 1128507, 1628813, 686759, 1732337, 598665, 40872, 11039, 724213, 1493938, 397663, 3281367, 1583103, 341027, ss218548446, ss230656581, ss238323597, ss479670771, ss480189200, ss484631363, ss536751851, ss554480208, ss648253680, ss778399048, ss782762493, ss783728883, ss832014776, ss832714925, ss833854197, ss975482659, ss1068127428, ss1292106454, ss1574271271, ss1600816231, ss1643810264, ss1751859098, ss1918682283, ss1946002819, ss1958296779, ss1966820702, ss2019862584, ss2147881309, ss2327379425, ss2624442785, ss2632553593, ss2697808663, ss2710678268, ss2758634538, ss2987305247, ss3021113779, ss3343595764, ss3625546131, ss3626165232, ss3630587767, ss3632903270, ss3633598268, ss3634339242, ss3635291880, ss3636016796, ss3637042335, ss3637775436, ss3640046602, ss3640984519, ss3641278507, ss3644498781, ss3651444559, ss3655390259, ss3727313800, ss3744050992, ss3744640211, ss3746573748, ss3772141448, ss3826326388, ss3849476958, ss3894554943, ss3984461727, ss3984814945, ss4016927678, ss5145312060, ss5237270822 NC_000001.10:100005476:G:A NC_000001.11:99539920:G:A (self)
20288756, 136461, 49459, 15300796, 24293771, 11186630935, ss2165028627, ss3023694890, ss3084642524, ss3687366534, ss3725048120, ss3770827990, ss3799574499, ss4460687436 NC_000001.11:99539920:G:A NC_000001.11:99539920:G:A (self)
ss18158066 NT_028050.13:8194420:G:A NC_000001.11:99539920:G:A (self)
ss23842246, ss66604515, ss66979913, ss67152037, ss70404579, ss70554432, ss71090973, ss75482387, ss85179636, ss102767755, ss121534025, ss153125540, ss159202478, ss160030857, ss170037822, ss171831908 NT_032977.9:69977394:G:A NC_000001.11:99539920:G:A (self)
1732337, ss3894554943 NC_000001.10:100005476:G:T NC_000001.11:99539920: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 rs12069019

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