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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.

rs12143647

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:230672500 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.136896 (36235/264690, TOPMED)
T=0.144570 (20239/139994, GnomAD)
T=0.16032 (13427/83752, ALFA) (+ 16 more)
T=0.15155 (2540/16760, 8.3KJPN)
T=0.1292 (647/5008, 1000G)
T=0.2375 (1064/4480, Estonian)
T=0.1546 (596/3854, ALSPAC)
T=0.1642 (609/3708, TWINSUK)
T=0.1632 (477/2922, KOREAN)
T=0.1521 (317/2084, HGDP_Stanford)
T=0.1062 (201/1892, HapMap)
T=0.1616 (296/1832, Korea1K)
T=0.181 (181/998, GoNL)
T=0.208 (125/600, NorthernSweden)
T=0.106 (23/216, Qatari)
C=0.441 (60/136, SGDP_PRJ)
T=0.10 (8/80, Ancient Sardinia)
T=0.17 (7/40, GENOME_DK)
C=0.44 (7/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COG2 : Intron Variant
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.230672500C>T
GRCh37.p13 chr 1 NC_000001.10:g.230808246C>T
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.899+860C…

NM_001145036.2:c.899+860C>T

N/A Intron Variant
COG2 transcript variant 1 NM_007357.3:c.899+860C>T 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 83752 C=0.83968 T=0.16032
European Sub 69876 C=0.83133 T=0.16867
African Sub 4724 C=0.9545 T=0.0455
African Others Sub 180 C=0.994 T=0.006
African American Sub 4544 C=0.9529 T=0.0471
Asian Sub 202 C=0.856 T=0.144
East Asian Sub 160 C=0.850 T=0.150
Other Asian Sub 42 C=0.88 T=0.12
Latin American 1 Sub 268 C=0.858 T=0.142
Latin American 2 Sub 1316 C=0.7272 T=0.2728
South Asian Sub 4972 C=0.8717 T=0.1283
Other Sub 2394 C=0.8488 T=0.1512


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 C=0.863104 T=0.136896
gnomAD - Genomes Global Study-wide 139994 C=0.855430 T=0.144570
gnomAD - Genomes European Sub 75814 C=0.81176 T=0.18824
gnomAD - Genomes African Sub 41964 C=0.95358 T=0.04642
gnomAD - Genomes American Sub 13614 C=0.79852 T=0.20148
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8561 T=0.1439
gnomAD - Genomes East Asian Sub 3130 C=0.8518 T=0.1482
gnomAD - Genomes Other Sub 2150 C=0.8442 T=0.1558
8.3KJPN JAPANESE Study-wide 16760 C=0.84845 T=0.15155
1000Genomes Global Study-wide 5008 C=0.8708 T=0.1292
1000Genomes African Sub 1322 C=0.9758 T=0.0242
1000Genomes East Asian Sub 1008 C=0.8562 T=0.1438
1000Genomes Europe Sub 1006 C=0.8201 T=0.1799
1000Genomes South Asian Sub 978 C=0.890 T=0.110
1000Genomes American Sub 694 C=0.739 T=0.261
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7625 T=0.2375
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8454 T=0.1546
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8358 T=0.1642
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.8368 T=0.1632
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.8479 T=0.1521
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.857 T=0.143
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.845 T=0.155
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.903 T=0.097
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.872 T=0.128
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.905 T=0.095
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.630 T=0.370
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.89 T=0.11
HapMap Global Study-wide 1892 C=0.8938 T=0.1062
HapMap American Sub 770 C=0.851 T=0.149
HapMap African Sub 692 C=0.967 T=0.033
HapMap Asian Sub 254 C=0.858 T=0.142
HapMap Europe Sub 176 C=0.847 T=0.153
Korean Genome Project KOREAN Study-wide 1832 C=0.8384 T=0.1616
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.819 T=0.181
Northern Sweden ACPOP Study-wide 600 C=0.792 T=0.208
Qatari Global Study-wide 216 C=0.894 T=0.106
SGDP_PRJ Global Study-wide 136 C=0.441 T=0.559
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 80 C=0.90 T=0.10
The Danish reference pan genome Danish Study-wide 40 C=0.82 T=0.17
Siberian Global Study-wide 16 C=0.44 T=0.56
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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.230672500= NC_000001.11:g.230672500C>T
GRCh37.p13 chr 1 NC_000001.10:g.230808246= NC_000001.10:g.230808246C>T
COG2 transcript variant 2 NM_001145036.1:c.899+860= NM_001145036.1:c.899+860C>T
COG2 transcript variant 2 NM_001145036.2:c.899+860= NM_001145036.2:c.899+860C>T
COG2 transcript variant 1 NM_007357.2:c.899+860= NM_007357.2:c.899+860C>T
COG2 transcript variant 1 NM_007357.3:c.899+860= NM_007357.3:c.899+860C>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#.

89 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18293899 Feb 28, 2004 (120)
2 SSAHASNP ss20551333 Apr 05, 2004 (121)
3 PERLEGEN ss24296402 Sep 20, 2004 (123)
4 ILLUMINA ss66766806 Nov 30, 2006 (127)
5 ILLUMINA ss66985541 Nov 30, 2006 (127)
6 ILLUMINA ss67159569 Nov 30, 2006 (127)
7 PERLEGEN ss68795909 May 17, 2007 (127)
8 ILLUMINA ss70405575 May 17, 2007 (127)
9 ILLUMINA ss70557307 May 23, 2008 (130)
10 ILLUMINA ss71094791 May 17, 2007 (127)
11 ILLUMINA ss75778768 Dec 06, 2007 (129)
12 HGSV ss82016021 Dec 14, 2007 (130)
13 KRIBB_YJKIM ss85189121 Dec 14, 2007 (130)
14 HUMANGENOME_JCVI ss99294582 Feb 02, 2009 (130)
15 ILLUMINA-UK ss119240905 Feb 15, 2009 (130)
16 ILLUMINA ss121539943 Dec 01, 2009 (131)
17 ILLUMINA ss153141144 Dec 01, 2009 (131)
18 ILLUMINA ss159205594 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167558736 Jul 04, 2010 (132)
20 ILLUMINA ss170055351 Jul 04, 2010 (132)
21 ILLUMINA ss171891969 Jul 04, 2010 (132)
22 BUSHMAN ss199728851 Jul 04, 2010 (132)
23 1000GENOMES ss218933192 Jul 14, 2010 (132)
24 1000GENOMES ss230940795 Jul 14, 2010 (132)
25 1000GENOMES ss238547377 Jul 15, 2010 (132)
26 GMI ss276255984 May 04, 2012 (137)
27 PJP ss290753113 May 09, 2011 (134)
28 ILLUMINA ss479304276 May 04, 2012 (137)
29 ILLUMINA ss482256205 May 04, 2012 (137)
30 ILLUMINA ss532877353 Sep 08, 2015 (146)
31 TISHKOFF ss555199506 Apr 25, 2013 (138)
32 SSMP ss648772718 Apr 25, 2013 (138)
33 ILLUMINA ss779561734 Sep 08, 2015 (146)
34 ILLUMINA ss780948151 Sep 08, 2015 (146)
35 ILLUMINA ss825374849 Apr 01, 2015 (144)
36 ILLUMINA ss832718029 Jul 12, 2019 (153)
37 ILLUMINA ss835032880 Sep 08, 2015 (146)
38 EVA-GONL ss976245664 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1068678050 Aug 21, 2014 (142)
40 1000GENOMES ss1295033773 Aug 21, 2014 (142)
41 DDI ss1426140581 Apr 01, 2015 (144)
42 EVA_GENOME_DK ss1574741964 Apr 01, 2015 (144)
43 EVA_DECODE ss1585645587 Apr 01, 2015 (144)
44 EVA_UK10K_ALSPAC ss1602344052 Apr 01, 2015 (144)
45 EVA_UK10K_TWINSUK ss1645338085 Apr 01, 2015 (144)
46 EVA_SVP ss1712412825 Apr 01, 2015 (144)
47 HAMMER_LAB ss1795861722 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1919467396 Feb 12, 2016 (147)
49 GENOMED ss1966996704 Jul 19, 2016 (147)
50 JJLAB ss2020258897 Sep 14, 2016 (149)
51 USC_VALOUEV ss2148294643 Dec 20, 2016 (150)
52 HUMAN_LONGEVITY ss2170878186 Dec 20, 2016 (150)
53 TOPMED ss2333526919 Dec 20, 2016 (150)
54 SYSTEMSBIOZJU ss2624641365 Nov 08, 2017 (151)
55 ILLUMINA ss2632641484 Nov 08, 2017 (151)
56 ILLUMINA ss2635008206 Nov 08, 2017 (151)
57 GRF ss2698294478 Nov 08, 2017 (151)
58 GNOMAD ss2767308583 Nov 08, 2017 (151)
59 SWEGEN ss2988609141 Nov 08, 2017 (151)
60 BIOINF_KMB_FNS_UNIBA ss3023890023 Nov 08, 2017 (151)
61 TOPMED ss3105894829 Nov 08, 2017 (151)
62 CSHL ss3343956571 Nov 08, 2017 (151)
63 ILLUMINA ss3626330492 Oct 11, 2018 (152)
64 ILLUMINA ss3630670664 Oct 11, 2018 (152)
65 ILLUMINA ss3637819687 Oct 11, 2018 (152)
66 ILLUMINA ss3638924867 Oct 11, 2018 (152)
67 ILLUMINA ss3639461419 Oct 11, 2018 (152)
68 ILLUMINA ss3641645432 Oct 11, 2018 (152)
69 ILLUMINA ss3642825638 Oct 11, 2018 (152)
70 URBANLAB ss3646907393 Oct 11, 2018 (152)
71 EGCUT_WGS ss3656567502 Jul 12, 2019 (153)
72 EVA_DECODE ss3688818696 Jul 12, 2019 (153)
73 ACPOP ss3727945869 Jul 12, 2019 (153)
74 EVA ss3747457268 Jul 12, 2019 (153)
75 PACBIO ss3783713040 Jul 12, 2019 (153)
76 PACBIO ss3789321035 Jul 12, 2019 (153)
77 PACBIO ss3794193448 Jul 12, 2019 (153)
78 KHV_HUMAN_GENOMES ss3800458958 Jul 12, 2019 (153)
79 EVA ss3826693551 Apr 25, 2020 (154)
80 EVA ss3836748513 Apr 25, 2020 (154)
81 EVA ss3842160922 Apr 25, 2020 (154)
82 HGDP ss3847366502 Apr 25, 2020 (154)
83 SGDP_PRJ ss3851098168 Apr 25, 2020 (154)
84 KRGDB ss3896444477 Apr 25, 2020 (154)
85 KOGIC ss3946692696 Apr 25, 2020 (154)
86 EVA ss3984857936 Apr 25, 2021 (155)
87 EVA ss4016967364 Apr 25, 2021 (155)
88 TOPMED ss4486948181 Apr 25, 2021 (155)
89 TOMMO_GENOMICS ss5148874694 Apr 25, 2021 (155)
90 1000Genomes NC_000001.10 - 230808246 Oct 11, 2018 (152)
91 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 230808246 Oct 11, 2018 (152)
92 Genetic variation in the Estonian population NC_000001.10 - 230808246 Oct 11, 2018 (152)
93 The Danish reference pan genome NC_000001.10 - 230808246 Apr 25, 2020 (154)
94 gnomAD - Genomes NC_000001.11 - 230672500 Apr 25, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000001.10 - 230808246 Apr 25, 2020 (154)
96 HGDP-CEPH-db Supplement 1 NC_000001.9 - 228874869 Apr 25, 2020 (154)
97 HapMap NC_000001.11 - 230672500 Apr 25, 2020 (154)
98 KOREAN population from KRGDB NC_000001.10 - 230808246 Apr 25, 2020 (154)
99 Korean Genome Project NC_000001.11 - 230672500 Apr 25, 2020 (154)
100 Northern Sweden NC_000001.10 - 230808246 Jul 12, 2019 (153)
101 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 230808246 Apr 25, 2021 (155)
102 Qatari NC_000001.10 - 230808246 Apr 25, 2020 (154)
103 SGDP_PRJ NC_000001.10 - 230808246 Apr 25, 2020 (154)
104 Siberian NC_000001.10 - 230808246 Apr 25, 2020 (154)
105 8.3KJPN NC_000001.10 - 230808246 Apr 25, 2021 (155)
106 TopMed NC_000001.11 - 230672500 Apr 25, 2021 (155)
107 UK 10K study - Twins NC_000001.10 - 230808246 Oct 11, 2018 (152)
108 ALFA NC_000001.11 - 230672500 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)
rs17716561 Oct 07, 2004 (123)
rs56684952 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82016021, ss3638924867, ss3639461419 NC_000001.8:227114980:C:T NC_000001.11:230672499:C:T (self)
44394, ss119240905, ss167558736, ss199728851, ss276255984, ss290753113, ss482256205, ss825374849, ss1585645587, ss1712412825, ss2635008206, ss3642825638, ss3847366502 NC_000001.9:228874868:C:T NC_000001.11:230672499:C:T (self)
5902211, 3263341, 2305750, 1925334, 1426039, 3621871, 1230734, 83863, 1509326, 3115148, 810997, 6844001, 3263341, ss218933192, ss230940795, ss238547377, ss479304276, ss532877353, ss555199506, ss648772718, ss779561734, ss780948151, ss832718029, ss835032880, ss976245664, ss1068678050, ss1295033773, ss1426140581, ss1574741964, ss1602344052, ss1645338085, ss1795861722, ss1919467396, ss1966996704, ss2020258897, ss2148294643, ss2333526919, ss2624641365, ss2632641484, ss2698294478, ss2767308583, ss2988609141, ss3343956571, ss3626330492, ss3630670664, ss3637819687, ss3641645432, ss3656567502, ss3727945869, ss3747457268, ss3783713040, ss3789321035, ss3794193448, ss3826693551, ss3836748513, ss3851098168, ss3896444477, ss3984857936, ss4016967364, ss5148874694 NC_000001.10:230808245:C:T NC_000001.11:230672499:C:T (self)
42353863, 287942, 3070697, 31772625, 50554516, 4499503687, ss2170878186, ss3023890023, ss3105894829, ss3646907393, ss3688818696, ss3800458958, ss3842160922, ss3946692696, ss4486948181 NC_000001.11:230672499:C:T NC_000001.11:230672499:C:T (self)
ss18293899, ss20551333 NT_021973.16:739234:C:T NC_000001.11:230672499:C:T (self)
ss24296402, ss66766806, ss66985541, ss67159569, ss68795909, ss70405575, ss70557307, ss71094791, ss75778768, ss85189121, ss99294582, ss121539943, ss153141144, ss159205594, ss170055351, ss171891969 NT_167186.1:24326024:C:T NC_000001.11:230672499:C: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 rs12143647

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