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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.

rs12046196

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:230679451 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.133122 (35236/264690, TOPMED)
A=0.119702 (16765/140056, GnomAD)
A=0.09192 (7885/85784, ALFA) (+ 18 more)
A=0.34266 (5743/16760, 8.3KJPN)
A=0.2063 (1033/5008, 1000G)
A=0.0690 (309/4480, Estonian)
A=0.0737 (284/3854, ALSPAC)
A=0.0833 (309/3708, TWINSUK)
A=0.3768 (1104/2930, KOREAN)
A=0.1799 (375/2084, HGDP_Stanford)
A=0.1940 (367/1892, HapMap)
A=0.3952 (724/1832, Korea1K)
A=0.1250 (139/1112, Daghestan)
A=0.088 (88/998, GoNL)
A=0.082 (49/600, NorthernSweden)
A=0.079 (17/216, Qatari)
A=0.421 (91/216, Vietnamese)
G=0.429 (85/198, SGDP_PRJ)
A=0.08 (6/76, Ancient Sardinia)
A=0.15 (6/40, GENOME_DK)
G=0.45 (9/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COG2 : Intron Variant
Publications
1 citation
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.230679451G>A
GRCh37.p13 chr 1 NC_000001.10:g.230815197G>A
Gene: COG2, component of oligomeric golgi complex 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COG2 transcript variant 2 NM_001145036.2:c.1166+399…

NM_001145036.2:c.1166+399G>A

N/A Intron Variant
COG2 transcript variant 1 NM_007357.3:c.1166+399G>A N/A Intron Variant
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 85784 G=0.90808 A=0.09192
European Sub 69304 G=0.92454 A=0.07546
African Sub 7282 G=0.8248 A=0.1752
African Others Sub 258 G=0.829 A=0.171
African American Sub 7024 G=0.8246 A=0.1754
Asian Sub 204 G=0.593 A=0.407
East Asian Sub 162 G=0.580 A=0.420
Other Asian Sub 42 G=0.64 A=0.36
Latin American 1 Sub 268 G=0.892 A=0.108
Latin American 2 Sub 1316 G=0.8617 A=0.1383
South Asian Sub 4974 G=0.8341 A=0.1659
Other Sub 2436 G=0.8933 A=0.1067


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=0.866878 A=0.133122
gnomAD - Genomes Global Study-wide 140056 G=0.880298 A=0.119702
gnomAD - Genomes European Sub 75858 G=0.92552 A=0.07448
gnomAD - Genomes African Sub 41950 G=0.82849 A=0.17151
gnomAD - Genomes American Sub 13648 G=0.84481 A=0.15519
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9356 A=0.0644
gnomAD - Genomes East Asian Sub 3128 G=0.5700 A=0.4300
gnomAD - Genomes Other Sub 2150 G=0.8870 A=0.1130
8.3KJPN JAPANESE Study-wide 16760 G=0.65734 A=0.34266
1000Genomes Global Study-wide 5008 G=0.7937 A=0.2063
1000Genomes African Sub 1322 G=0.7943 A=0.2057
1000Genomes East Asian Sub 1008 G=0.6131 A=0.3869
1000Genomes Europe Sub 1006 G=0.9304 A=0.0696
1000Genomes South Asian Sub 978 G=0.791 A=0.209
1000Genomes American Sub 694 G=0.860 A=0.140
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9310 A=0.0690
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9263 A=0.0737
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9167 A=0.0833
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6232 A=0.3768
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.8201 A=0.1799
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.634 A=0.366
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.841 A=0.159
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.949 A=0.051
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.919 A=0.081
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.843 A=0.157
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.819 A=0.181
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.78 A=0.22
HapMap Global Study-wide 1892 G=0.8060 A=0.1940
HapMap American Sub 770 G=0.817 A=0.183
HapMap African Sub 692 G=0.811 A=0.189
HapMap Asian Sub 254 G=0.681 A=0.319
HapMap Europe Sub 176 G=0.920 A=0.080
Korean Genome Project KOREAN Study-wide 1832 G=0.6048 A=0.3952
Genome-wide autozygosity in Daghestan Global Study-wide 1112 G=0.8750 A=0.1250
Genome-wide autozygosity in Daghestan Daghestan Sub 610 G=0.898 A=0.102
Genome-wide autozygosity in Daghestan Near_East Sub 142 G=0.908 A=0.092
Genome-wide autozygosity in Daghestan Central Asia Sub 120 G=0.733 A=0.267
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.944 A=0.056
Genome-wide autozygosity in Daghestan South Asian Sub 96 G=0.77 A=0.23
Genome-wide autozygosity in Daghestan Caucasus Sub 36 G=0.89 A=0.11
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.912 A=0.088
Northern Sweden ACPOP Study-wide 600 G=0.918 A=0.082
Qatari Global Study-wide 216 G=0.921 A=0.079
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.579 A=0.421
SGDP_PRJ Global Study-wide 198 G=0.429 A=0.571
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 76 G=0.92 A=0.08
The Danish reference pan genome Danish Study-wide 40 G=0.85 A=0.15
Siberian Global Study-wide 20 G=0.45 A=0.55
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
GRCh38.p13 chr 1 NC_000001.11:g.230679451= NC_000001.11:g.230679451G>A
GRCh37.p13 chr 1 NC_000001.10:g.230815197= NC_000001.10:g.230815197G>A
COG2 transcript variant 2 NM_001145036.1:c.1166+399= NM_001145036.1:c.1166+399G>A
COG2 transcript variant 2 NM_001145036.2:c.1166+399= NM_001145036.2:c.1166+399G>A
COG2 transcript variant 1 NM_007357.2:c.1166+399= NM_007357.2:c.1166+399G>A
COG2 transcript variant 1 NM_007357.3:c.1166+399= NM_007357.3:c.1166+399G>A
COG2 transcript variant X1 XM_005273087.1:c.233+399= XM_005273087.1:c.233+399G>A
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#.

86 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18116977 Feb 28, 2004 (120)
2 PERLEGEN ss23884570 Sep 20, 2004 (123)
3 ABI ss43963506 Mar 14, 2006 (126)
4 SI_EXO ss61705441 Oct 16, 2006 (127)
5 ILLUMINA ss66978071 Dec 01, 2006 (127)
6 ILLUMINA ss67149608 Dec 01, 2006 (127)
7 ILLUMINA ss68120025 Dec 12, 2006 (127)
8 PERLEGEN ss68795915 May 17, 2007 (127)
9 ILLUMINA ss70553494 May 24, 2008 (130)
10 ILLUMINA ss71089758 May 17, 2007 (127)
11 ILLUMINA ss75568114 Dec 07, 2007 (129)
12 KRIBB_YJKIM ss85176696 Dec 14, 2007 (130)
13 BGI ss102830700 Dec 01, 2009 (131)
14 ILLUMINA-UK ss119240919 Feb 15, 2009 (130)
15 ENSEMBL ss139040886 Dec 01, 2009 (131)
16 ILLUMINA ss153120537 Dec 01, 2009 (131)
17 ILLUMINA ss159201471 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss167558756 Jul 04, 2010 (132)
19 ILLUMINA ss171812348 Jul 04, 2010 (132)
20 1000GENOMES ss218933217 Jul 14, 2010 (132)
21 1000GENOMES ss230940825 Jul 14, 2010 (132)
22 1000GENOMES ss238547402 Jul 15, 2010 (132)
23 GMI ss276256009 May 04, 2012 (137)
24 PJP ss290753127 May 09, 2011 (134)
25 ILLUMINA ss482256244 May 04, 2012 (137)
26 ILLUMINA ss484211874 May 04, 2012 (137)
27 ILLUMINA ss536398931 Sep 08, 2015 (146)
28 TISHKOFF ss555199545 Apr 25, 2013 (138)
29 SSMP ss648772760 Apr 25, 2013 (138)
30 ILLUMINA ss780568791 Sep 08, 2015 (146)
31 ILLUMINA ss782551925 Sep 08, 2015 (146)
32 ILLUMINA ss832713923 Jul 12, 2019 (153)
33 ILLUMINA ss836061228 Sep 08, 2015 (146)
34 EVA-GONL ss976245715 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1068678097 Aug 21, 2014 (142)
36 1000GENOMES ss1295033980 Aug 21, 2014 (142)
37 HAMMER_LAB ss1397275117 Sep 08, 2015 (146)
38 DDI ss1426140601 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1574742007 Apr 01, 2015 (144)
40 EVA_DECODE ss1585645653 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1602344167 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1645338200 Apr 01, 2015 (144)
43 EVA_SVP ss1712412831 Apr 01, 2015 (144)
44 HAMMER_LAB ss1795861803 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1919467442 Feb 12, 2016 (147)
46 GENOMED ss1966996722 Jul 19, 2016 (147)
47 JJLAB ss2020258927 Sep 14, 2016 (149)
48 ILLUMINA ss2095002553 Dec 20, 2016 (150)
49 USC_VALOUEV ss2148294675 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2170878585 Dec 20, 2016 (150)
51 TOPMED ss2333527297 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2624641380 Nov 08, 2017 (151)
53 ILLUMINA ss2632641500 Nov 08, 2017 (151)
54 GRF ss2698294510 Nov 08, 2017 (151)
55 GNOMAD ss2767309107 Nov 08, 2017 (151)
56 SWEGEN ss2988609209 Nov 08, 2017 (151)
57 TOPMED ss3105895953 Nov 08, 2017 (151)
58 CSHL ss3343956590 Nov 08, 2017 (151)
59 ILLUMINA ss3626330521 Oct 11, 2018 (152)
60 ILLUMINA ss3630670679 Oct 11, 2018 (152)
61 ILLUMINA ss3637819692 Oct 11, 2018 (152)
62 ILLUMINA ss3638924871 Oct 11, 2018 (152)
63 ILLUMINA ss3639774127 Oct 11, 2018 (152)
64 ILLUMINA ss3641645443 Oct 11, 2018 (152)
65 ILLUMINA ss3642825643 Oct 11, 2018 (152)
66 ILLUMINA ss3643827229 Oct 11, 2018 (152)
67 BIOINF_KMB_FNS_UNIBA ss3645103167 Oct 11, 2018 (152)
68 URBANLAB ss3646907405 Oct 11, 2018 (152)
69 ILLUMINA ss3651535753 Oct 11, 2018 (152)
70 EGCUT_WGS ss3656567575 Jul 12, 2019 (153)
71 EVA_DECODE ss3688818786 Jul 12, 2019 (153)
72 ACPOP ss3727945912 Jul 12, 2019 (153)
73 EVA ss3747457335 Jul 12, 2019 (153)
74 PACBIO ss3783713052 Jul 12, 2019 (153)
75 PACBIO ss3789321045 Jul 12, 2019 (153)
76 PACBIO ss3794193458 Jul 12, 2019 (153)
77 KHV_HUMAN_GENOMES ss3800459024 Jul 12, 2019 (153)
78 EVA ss3826693573 Apr 25, 2020 (154)
79 HGDP ss3847366506 Apr 25, 2020 (154)
80 SGDP_PRJ ss3851098266 Apr 25, 2020 (154)
81 KRGDB ss3896444570 Apr 25, 2020 (154)
82 KOGIC ss3946692763 Apr 25, 2020 (154)
83 EVA ss3984857943 Apr 25, 2021 (155)
84 EVA ss4016967369 Apr 25, 2021 (155)
85 TOPMED ss4486949816 Apr 25, 2021 (155)
86 TOMMO_GENOMICS ss5148874885 Apr 25, 2021 (155)
87 1000Genomes NC_000001.10 - 230815197 Oct 11, 2018 (152)
88 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 230815197 Oct 11, 2018 (152)
89 Genome-wide autozygosity in Daghestan NC_000001.9 - 228881820 Apr 25, 2020 (154)
90 Genetic variation in the Estonian population NC_000001.10 - 230815197 Oct 11, 2018 (152)
91 The Danish reference pan genome NC_000001.10 - 230815197 Apr 25, 2020 (154)
92 gnomAD - Genomes NC_000001.11 - 230679451 Apr 25, 2021 (155)
93 Genome of the Netherlands Release 5 NC_000001.10 - 230815197 Apr 25, 2020 (154)
94 HGDP-CEPH-db Supplement 1 NC_000001.9 - 228881820 Apr 25, 2020 (154)
95 HapMap NC_000001.11 - 230679451 Apr 25, 2020 (154)
96 KOREAN population from KRGDB NC_000001.10 - 230815197 Apr 25, 2020 (154)
97 Korean Genome Project NC_000001.11 - 230679451 Apr 25, 2020 (154)
98 Northern Sweden NC_000001.10 - 230815197 Jul 12, 2019 (153)
99 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 230815197 Apr 25, 2021 (155)
100 Qatari NC_000001.10 - 230815197 Apr 25, 2020 (154)
101 SGDP_PRJ NC_000001.10 - 230815197 Apr 25, 2020 (154)
102 Siberian NC_000001.10 - 230815197 Apr 25, 2020 (154)
103 8.3KJPN NC_000001.10 - 230815197 Apr 25, 2021 (155)
104 TopMed NC_000001.11 - 230679451 Apr 25, 2021 (155)
105 UK 10K study - Twins NC_000001.10 - 230815197 Oct 11, 2018 (152)
106 A Vietnamese Genetic Variation Database NC_000001.10 - 230815197 Jul 12, 2019 (153)
107 ALFA NC_000001.11 - 230679451 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)
rs57819723 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638924871, ss3639774127, ss3643827229 NC_000001.8:227121931:G:A NC_000001.11:230679450:G:A (self)
36220, 44398, ss119240919, ss167558756, ss276256009, ss290753127, ss482256244, ss1397275117, ss1585645653, ss1712412831, ss3642825643, ss3847366506 NC_000001.9:228881819:G:A NC_000001.11:230679450:G:A (self)
5902423, 3263464, 2305823, 1925352, 1426090, 3621964, 1230777, 83870, 1509372, 3115246, 811029, 6844192, 3263464, 709833, ss218933217, ss230940825, ss238547402, ss484211874, ss536398931, ss555199545, ss648772760, ss780568791, ss782551925, ss832713923, ss836061228, ss976245715, ss1068678097, ss1295033980, ss1426140601, ss1574742007, ss1602344167, ss1645338200, ss1795861803, ss1919467442, ss1966996722, ss2020258927, ss2095002553, ss2148294675, ss2333527297, ss2624641380, ss2632641500, ss2698294510, ss2767309107, ss2988609209, ss3343956590, ss3626330521, ss3630670679, ss3637819692, ss3641645443, ss3651535753, ss3656567575, ss3727945912, ss3747457335, ss3783713052, ss3789321045, ss3794193458, ss3826693573, ss3851098266, ss3896444570, ss3984857943, ss4016967369, ss5148874885 NC_000001.10:230815196:G:A NC_000001.11:230679450:G:A (self)
42355129, 287961, 3070764, 31773656, 50556151, 4727881481, ss2170878585, ss3105895953, ss3645103167, ss3646907405, ss3688818786, ss3800459024, ss3946692763, ss4486949816 NC_000001.11:230679450:G:A NC_000001.11:230679450:G:A (self)
ss61705441 NT_004559.12:6991390:G:A NC_000001.11:230679450:G:A (self)
ss18116977 NT_021973.16:746185:G:A NC_000001.11:230679450:G:A (self)
ss23884570, ss43963506, ss66978071, ss67149608, ss68120025, ss68795915, ss70553494, ss71089758, ss75568114, ss85176696, ss102830700, ss139040886, ss153120537, ss159201471, ss171812348 NT_167186.1:24332975:G:A NC_000001.11:230679450:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs12046196
PMID Title Author Year Journal
21444836 Association of hypertension drug target genes with blood pressure and hypertension in 86,588 individuals. Johnson AD et al. 2011 Hypertension (Dallas, Tex.
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