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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.

rs10495298

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:230677568 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.112834 (29866/264690, TOPMED)
T=0.116639 (16356/140228, GnomAD)
T=0.13563 (2562/18890, ALFA) (+ 16 more)
T=0.13771 (2308/16760, 8.3KJPN)
T=0.1162 (582/5008, 1000G)
T=0.1888 (846/4480, Estonian)
T=0.1232 (475/3854, ALSPAC)
T=0.1284 (476/3708, TWINSUK)
T=0.1564 (457/2922, KOREAN)
T=0.1578 (289/1832, Korea1K)
T=0.141 (141/998, GoNL)
T=0.177 (106/600, NorthernSweden)
T=0.082 (27/328, HapMap)
T=0.102 (22/216, Qatari)
T=0.112 (24/214, Vietnamese)
A=0.437 (55/126, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
T=0.12 (2/16, Ancient Sardinia)
A=0.43 (6/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COG2 : Intron Variant
LOC107985358 : 2KB Upstream 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.230677568A>T
GRCh37.p13 chr 1 NC_000001.10:g.230813314A>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.1027-134…

NM_001145036.2:c.1027-1345A>T

N/A Intron Variant
COG2 transcript variant 1 NM_007357.3:c.1027-1345A>T N/A Intron Variant
Gene: LOC107985358, uncharacterized LOC107985358 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107985358 transcript XR_001738517.1:n. N/A Upstream Transcript 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 18890 A=0.86437 T=0.13563
European Sub 14286 A=0.84887 T=0.15113
African Sub 2946 A=0.9684 T=0.0316
African Others Sub 114 A=1.000 T=0.000
African American Sub 2832 A=0.9672 T=0.0328
Asian Sub 112 A=0.866 T=0.134
East Asian Sub 86 A=0.86 T=0.14
Other Asian Sub 26 A=0.88 T=0.12
Latin American 1 Sub 146 A=0.897 T=0.103
Latin American 2 Sub 610 A=0.713 T=0.287
South Asian Sub 98 A=0.89 T=0.11
Other Sub 692 A=0.864 T=0.136


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=0.887166 T=0.112834
gnomAD - Genomes Global Study-wide 140228 A=0.883361 T=0.116639
gnomAD - Genomes European Sub 75926 A=0.85008 T=0.14992
gnomAD - Genomes African Sub 42062 A=0.97147 T=0.02853
gnomAD - Genomes American Sub 13642 A=0.81095 T=0.18905
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.8605 T=0.1395
gnomAD - Genomes East Asian Sub 3130 A=0.8562 T=0.1438
gnomAD - Genomes Other Sub 2148 A=0.8692 T=0.1308
8.3KJPN JAPANESE Study-wide 16760 A=0.86229 T=0.13771
1000Genomes Global Study-wide 5008 A=0.8838 T=0.1162
1000Genomes African Sub 1322 A=0.9917 T=0.0083
1000Genomes East Asian Sub 1008 A=0.8621 T=0.1379
1000Genomes Europe Sub 1006 A=0.8499 T=0.1501
1000Genomes South Asian Sub 978 A=0.890 T=0.110
1000Genomes American Sub 694 A=0.751 T=0.249
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8112 T=0.1888
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8768 T=0.1232
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8716 T=0.1284
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.8436 T=0.1564
Korean Genome Project KOREAN Study-wide 1832 A=0.8422 T=0.1578
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.859 T=0.141
Northern Sweden ACPOP Study-wide 600 A=0.823 T=0.177
HapMap Global Study-wide 328 A=0.918 T=0.082
HapMap African Sub 120 A=1.000 T=0.000
HapMap American Sub 120 A=0.867 T=0.133
HapMap Asian Sub 88 A=0.88 T=0.12
Qatari Global Study-wide 216 A=0.898 T=0.102
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.888 T=0.112
SGDP_PRJ Global Study-wide 126 A=0.437 T=0.563
The Danish reference pan genome Danish Study-wide 40 A=0.85 T=0.15
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 16 A=0.88 T=0.12
Siberian Global Study-wide 14 A=0.43 T=0.57
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= T
GRCh38.p13 chr 1 NC_000001.11:g.230677568= NC_000001.11:g.230677568A>T
GRCh37.p13 chr 1 NC_000001.10:g.230813314= NC_000001.10:g.230813314A>T
COG2 transcript variant 2 NM_001145036.1:c.1027-1345= NM_001145036.1:c.1027-1345A>T
COG2 transcript variant 2 NM_001145036.2:c.1027-1345= NM_001145036.2:c.1027-1345A>T
COG2 transcript variant 1 NM_007357.2:c.1027-1345= NM_007357.2:c.1027-1345A>T
COG2 transcript variant 1 NM_007357.3:c.1027-1345= NM_007357.3:c.1027-1345A>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#.

51 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14884931 Dec 05, 2003 (119)
2 SSAHASNP ss20580791 Apr 05, 2004 (121)
3 PERLEGEN ss24296493 Sep 20, 2004 (123)
4 ABI ss44041465 Mar 14, 2006 (126)
5 AFFY ss65924111 Nov 30, 2006 (127)
6 PERLEGEN ss68795914 May 17, 2007 (127)
7 HGSV ss83822997 Dec 14, 2007 (130)
8 HUMANGENOME_JCVI ss99294587 Feb 04, 2009 (130)
9 ENSEMBL ss139040889 Dec 01, 2009 (131)
10 GMI ss276256001 May 04, 2012 (137)
11 PJP ss290753124 May 09, 2011 (134)
12 1000GENOMES ss454729470 Sep 17, 2011 (135)
13 TISHKOFF ss555199534 Apr 25, 2013 (138)
14 SSMP ss648772747 Apr 25, 2013 (138)
15 EVA-GONL ss976245696 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1068678084 Aug 21, 2014 (142)
17 1000GENOMES ss1295033918 Aug 21, 2014 (142)
18 DDI ss1426140597 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1574741993 Apr 01, 2015 (144)
20 EVA_DECODE ss1585645631 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1602344133 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1645338166 Apr 01, 2015 (144)
23 WEILL_CORNELL_DGM ss1919467429 Feb 12, 2016 (147)
24 GENOMED ss1966996717 Jul 19, 2016 (147)
25 JJLAB ss2020258918 Sep 14, 2016 (149)
26 USC_VALOUEV ss2148294665 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2170878471 Dec 20, 2016 (150)
28 TOPMED ss2333527193 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2624641377 Nov 08, 2017 (151)
30 GRF ss2698294501 Nov 08, 2017 (151)
31 GNOMAD ss2767308952 Nov 08, 2017 (151)
32 SWEGEN ss2988609188 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023890035 Nov 08, 2017 (151)
34 TOPMED ss3105895660 Nov 08, 2017 (151)
35 CSHL ss3343956585 Nov 08, 2017 (151)
36 URBANLAB ss3646907402 Oct 11, 2018 (152)
37 EGCUT_WGS ss3656567548 Jul 12, 2019 (153)
38 EVA_DECODE ss3688818755 Jul 12, 2019 (153)
39 ACPOP ss3727945896 Jul 12, 2019 (153)
40 EVA ss3747457316 Jul 12, 2019 (153)
41 PACBIO ss3783713050 Jul 12, 2019 (153)
42 PACBIO ss3789321043 Jul 12, 2019 (153)
43 PACBIO ss3794193456 Jul 12, 2019 (153)
44 KHV_HUMAN_GENOMES ss3800459005 Jul 12, 2019 (153)
45 EVA ss3826693567 Apr 25, 2020 (154)
46 SGDP_PRJ ss3851098234 Apr 25, 2020 (154)
47 KRGDB ss3896444544 Apr 25, 2020 (154)
48 KOGIC ss3946692743 Apr 25, 2020 (154)
49 EVA ss3984857941 Apr 25, 2021 (155)
50 TOPMED ss4486949363 Apr 25, 2021 (155)
51 TOMMO_GENOMICS ss5148874831 Apr 25, 2021 (155)
52 1000Genomes NC_000001.10 - 230813314 Oct 11, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 230813314 Oct 11, 2018 (152)
54 Genetic variation in the Estonian population NC_000001.10 - 230813314 Oct 11, 2018 (152)
55 The Danish reference pan genome NC_000001.10 - 230813314 Apr 25, 2020 (154)
56 gnomAD - Genomes NC_000001.11 - 230677568 Apr 25, 2021 (155)
57 Genome of the Netherlands Release 5 NC_000001.10 - 230813314 Apr 25, 2020 (154)
58 HapMap NC_000001.11 - 230677568 Apr 25, 2020 (154)
59 KOREAN population from KRGDB NC_000001.10 - 230813314 Apr 25, 2020 (154)
60 Korean Genome Project NC_000001.11 - 230677568 Apr 25, 2020 (154)
61 Northern Sweden NC_000001.10 - 230813314 Jul 12, 2019 (153)
62 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 230813314 Apr 25, 2021 (155)
63 Qatari NC_000001.10 - 230813314 Apr 25, 2020 (154)
64 SGDP_PRJ NC_000001.10 - 230813314 Apr 25, 2020 (154)
65 Siberian NC_000001.10 - 230813314 Apr 25, 2020 (154)
66 8.3KJPN NC_000001.10 - 230813314 Apr 25, 2021 (155)
67 TopMed NC_000001.11 - 230677568 Apr 25, 2021 (155)
68 UK 10K study - Twins NC_000001.10 - 230813314 Oct 11, 2018 (152)
69 A Vietnamese Genetic Variation Database NC_000001.10 - 230813314 Jul 12, 2019 (153)
70 ALFA NC_000001.11 - 230677568 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)
rs17716832 Oct 07, 2004 (123)
rs57349420 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83822997 NC_000001.8:227120048:A:T NC_000001.11:230677567:A:T (self)
ss276256001, ss290753124, ss1585645631 NC_000001.9:228879936:A:T NC_000001.11:230677567:A:T (self)
5902360, 3263428, 2305796, 1925347, 1426071, 3621938, 1230761, 83868, 1509359, 3115214, 811019, 6844138, 3263428, 709821, ss454729470, ss555199534, ss648772747, ss976245696, ss1068678084, ss1295033918, ss1426140597, ss1574741993, ss1602344133, ss1645338166, ss1919467429, ss1966996717, ss2020258918, ss2148294665, ss2333527193, ss2624641377, ss2698294501, ss2767308952, ss2988609188, ss3343956585, ss3656567548, ss3727945896, ss3747457316, ss3783713050, ss3789321043, ss3794193456, ss3826693567, ss3851098234, ss3896444544, ss3984857941, ss5148874831 NC_000001.10:230813313:A:T NC_000001.11:230677567:A:T (self)
42354770, 287958, 3070744, 31773377, 50555698, 6590055133, ss2170878471, ss3023890035, ss3105895660, ss3646907402, ss3688818755, ss3800459005, ss3946692743, ss4486949363 NC_000001.11:230677567:A:T NC_000001.11:230677567:A:T (self)
ss20580791 NT_021973.16:744302:A:T NC_000001.11:230677567:A:T (self)
ss14884931, ss24296493, ss44041465, ss65924111, ss68795914, ss99294587, ss139040889 NT_167186.1:24331092:A:T NC_000001.11:230677567:A:T (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 rs10495298
PMID Title Author Year Journal
17903301 Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. Vasan RS et al. 2007 BMC medical genetics
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