Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs299814

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:79935914 (GRCh38.p14) 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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.037036 (9803/264690, TOPMED)
T=0.00841 (283/33664, ALFA)
T=0.14700 (4154/28258, 14KJPN) (+ 16 more)
T=0.14403 (2414/16760, 8.3KJPN)
T=0.0984 (630/6404, 1000G_30x)
T=0.1008 (505/5008, 1000G)
T=0.0067 (30/4480, Estonian)
T=0.0013 (5/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.1846 (541/2930, KOREAN)
T=0.1812 (332/1832, Korea1K)
T=0.0964 (162/1680, HapMap)
T=0.099 (62/626, Chileans)
T=0.003 (2/600, NorthernSweden)
T=0.009 (2/216, Qatari)
T=0.176 (38/216, Vietnamese)
C=0.400 (48/120, SGDP_PRJ)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 33664 C=0.99159 A=0.00000, T=0.00841
European Sub 26096 C=0.99797 A=0.00000, T=0.00203
African Sub 4688 C=0.9657 A=0.0000, T=0.0343
African Others Sub 158 C=0.930 A=0.000, T=0.070
African American Sub 4530 C=0.9669 A=0.0000, T=0.0331
Asian Sub 130 C=0.808 A=0.000, T=0.192
East Asian Sub 80 C=0.89 A=0.00, T=0.11
Other Asian Sub 50 C=0.68 A=0.00, T=0.32
Latin American 1 Sub 212 C=0.976 A=0.000, T=0.024
Latin American 2 Sub 804 C=0.988 A=0.000, T=0.012
South Asian Sub 106 C=0.981 A=0.000, T=0.019
Other Sub 1628 C=0.9834 A=0.0000, T=0.0166


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=0.962964 T=0.037036
Allele Frequency Aggregator Total Global 33664 C=0.99159 A=0.00000, T=0.00841
Allele Frequency Aggregator European Sub 26096 C=0.99797 A=0.00000, T=0.00203
Allele Frequency Aggregator African Sub 4688 C=0.9657 A=0.0000, T=0.0343
Allele Frequency Aggregator Other Sub 1628 C=0.9834 A=0.0000, T=0.0166
Allele Frequency Aggregator Latin American 2 Sub 804 C=0.988 A=0.000, T=0.012
Allele Frequency Aggregator Latin American 1 Sub 212 C=0.976 A=0.000, T=0.024
Allele Frequency Aggregator Asian Sub 130 C=0.808 A=0.000, T=0.192
Allele Frequency Aggregator South Asian Sub 106 C=0.981 A=0.000, T=0.019
14KJPN JAPANESE Study-wide 28258 C=0.85300 T=0.14700
8.3KJPN JAPANESE Study-wide 16760 C=0.85597 T=0.14403
1000Genomes_30x Global Study-wide 6404 C=0.9016 T=0.0984
1000Genomes_30x African Sub 1786 C=0.9099 T=0.0901
1000Genomes_30x Europe Sub 1266 C=0.9945 T=0.0055
1000Genomes_30x South Asian Sub 1202 C=0.8727 T=0.1273
1000Genomes_30x East Asian Sub 1170 C=0.7735 T=0.2265
1000Genomes_30x American Sub 980 C=0.955 T=0.045
1000Genomes Global Study-wide 5008 C=0.8992 T=0.1008
1000Genomes African Sub 1322 C=0.9100 T=0.0900
1000Genomes East Asian Sub 1008 C=0.7748 T=0.2252
1000Genomes Europe Sub 1006 C=0.9930 T=0.0070
1000Genomes South Asian Sub 978 C=0.877 T=0.123
1000Genomes American Sub 694 C=0.954 T=0.046
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9933 T=0.0067
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9987 T=0.0013
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9992 T=0.0008
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8154 T=0.1846
Korean Genome Project KOREAN Study-wide 1832 C=0.8188 T=0.1812
HapMap Global Study-wide 1680 C=0.9036 T=0.0964
HapMap African Sub 688 C=0.917 T=0.083
HapMap American Sub 564 C=0.895 T=0.105
HapMap Asian Sub 252 C=0.821 T=0.179
HapMap Europe Sub 176 C=0.994 T=0.006
Chileans Chilean Study-wide 626 C=0.901 T=0.099
Northern Sweden ACPOP Study-wide 600 C=0.997 T=0.003
Qatari Global Study-wide 216 C=0.991 T=0.009
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.824 T=0.176
SGDP_PRJ Global Study-wide 120 C=0.400 T=0.600
Siberian Global Study-wide 8 C=0.5 T=0.5
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.p14 chr 1 NC_000001.11:g.79935914C>A
GRCh38.p14 chr 1 NC_000001.11:g.79935914C>T
GRCh37.p13 chr 1 NC_000001.10:g.80401599C>A
GRCh37.p13 chr 1 NC_000001.10:g.80401599C>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
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= A T
GRCh38.p14 chr 1 NC_000001.11:g.79935914= NC_000001.11:g.79935914C>A NC_000001.11:g.79935914C>T
GRCh37.p13 chr 1 NC_000001.10:g.80401599= NC_000001.10:g.80401599C>A NC_000001.10:g.80401599C>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#.

68 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss387084 Jul 12, 2000 (79)
2 KWOK ss1134686 Oct 04, 2000 (86)
3 KWOK ss1135361 Oct 04, 2000 (86)
4 KWOK ss1136546 Oct 04, 2000 (86)
5 KWOK ss1884261 Oct 18, 2000 (87)
6 KWOK ss1884364 Oct 18, 2000 (87)
7 KWOK ss1884947 Oct 18, 2000 (87)
8 SC_JCM ss2618514 Nov 08, 2000 (89)
9 CSHL-HAPMAP ss19137911 Feb 27, 2004 (120)
10 ABI ss44131832 Mar 13, 2006 (126)
11 PERLEGEN ss46534272 Mar 13, 2006 (126)
12 AFFY ss66265844 Dec 03, 2006 (127)
13 AFFY ss76410878 Dec 06, 2007 (129)
14 KRIBB_YJKIM ss81415322 Dec 15, 2007 (130)
15 GMI ss155236907 Dec 01, 2009 (131)
16 ENSEMBL ss161276976 Dec 01, 2009 (131)
17 AFFY ss173502953 Jul 04, 2010 (132)
18 ILLUMINA ss173549301 Jul 04, 2010 (132)
19 1000GENOMES ss218478768 Jul 14, 2010 (132)
20 1000GENOMES ss238282587 Jul 15, 2010 (132)
21 GMI ss275893098 May 04, 2012 (137)
22 ILLUMINA ss480777254 May 04, 2012 (137)
23 ILLUMINA ss482409624 May 04, 2012 (137)
24 ILLUMINA ss533939160 Sep 08, 2015 (146)
25 TISHKOFF ss554300636 Apr 25, 2013 (138)
26 SSMP ss648158719 Apr 25, 2013 (138)
27 ILLUMINA ss779088837 Sep 08, 2015 (146)
28 ILLUMINA ss781315605 Sep 08, 2015 (146)
29 ILLUMINA ss834552693 Sep 08, 2015 (146)
30 JMKIDD_LAB ss1068023930 Aug 21, 2014 (142)
31 1000GENOMES ss1291576670 Aug 21, 2014 (142)
32 DDI ss1425868042 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1600534355 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1643528388 Apr 01, 2015 (144)
35 EVA_SVP ss1712346548 Apr 01, 2015 (144)
36 WEILL_CORNELL_DGM ss1918543783 Feb 12, 2016 (147)
37 GENOMED ss1966788381 Jul 19, 2016 (147)
38 USC_VALOUEV ss2147808457 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2163940053 Dec 20, 2016 (150)
40 ILLUMINA ss2632536929 Nov 08, 2017 (151)
41 GRF ss2697728906 Nov 08, 2017 (151)
42 GNOMAD ss2757104867 Nov 08, 2017 (151)
43 SWEGEN ss2987087278 Nov 08, 2017 (151)
44 ILLUMINA ss3626135312 Oct 11, 2018 (152)
45 ILLUMINA ss3630571921 Oct 11, 2018 (152)
46 ILLUMINA ss3637767095 Oct 11, 2018 (152)
47 EGCUT_WGS ss3655166483 Jul 12, 2019 (153)
48 EVA_DECODE ss3687105750 Jul 12, 2019 (153)
49 ACPOP ss3727196011 Jul 12, 2019 (153)
50 EVA ss3746411342 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3799417085 Jul 12, 2019 (153)
52 SGDP_PRJ ss3849200825 Apr 25, 2020 (154)
53 KRGDB ss3894248951 Apr 25, 2020 (154)
54 KOGIC ss3944838221 Apr 25, 2020 (154)
55 TOPMED ss4455883157 Apr 25, 2021 (155)
56 TOMMO_GENOMICS ss5144709825 Apr 25, 2021 (155)
57 1000G_HIGH_COVERAGE ss5242859433 Oct 12, 2022 (156)
58 EVA ss5314628114 Oct 12, 2022 (156)
59 EVA ss5319825031 Oct 12, 2022 (156)
60 HUGCELL_USP ss5443864468 Oct 12, 2022 (156)
61 1000G_HIGH_COVERAGE ss5515454633 Oct 12, 2022 (156)
62 SANFORD_IMAGENETICS ss5625868189 Oct 12, 2022 (156)
63 TOMMO_GENOMICS ss5669698777 Oct 12, 2022 (156)
64 YY_MCH ss5800743252 Oct 12, 2022 (156)
65 EVA ss5832187080 Oct 12, 2022 (156)
66 EVA ss5848977979 Oct 12, 2022 (156)
67 EVA ss5908945155 Oct 12, 2022 (156)
68 EVA ss5937715531 Oct 12, 2022 (156)
69 1000Genomes NC_000001.10 - 80401599 Oct 11, 2018 (152)
70 1000Genomes_30x NC_000001.11 - 79935914 Oct 12, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 80401599 Oct 11, 2018 (152)
72 Chileans NC_000001.10 - 80401599 Apr 25, 2020 (154)
73 Genetic variation in the Estonian population NC_000001.10 - 80401599 Oct 11, 2018 (152)
74 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 16392854 (NC_000001.11:79935913:C:A 1/140220)
Row 16392855 (NC_000001.11:79935913:C:T 4122/140208)

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

Submission ignored due to conflicting rows:
Row 16392854 (NC_000001.11:79935913:C:A 1/140220)
Row 16392855 (NC_000001.11:79935913:C:T 4122/140208)

- Apr 25, 2021 (155)
76 HapMap NC_000001.11 - 79935914 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 80401599 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 79935914 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 80401599 Jul 12, 2019 (153)
80 Qatari NC_000001.10 - 80401599 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 80401599 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 80401599 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 80401599 Apr 25, 2021 (155)
84 14KJPN NC_000001.11 - 79935914 Oct 12, 2022 (156)
85 TopMed NC_000001.11 - 79935914 Apr 25, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 80401599 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 80401599 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 79935914 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)
rs59336387 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2757104867 NC_000001.10:80401598:C:A NC_000001.11:79935913:C:A (self)
4857880242 NC_000001.11:79935913:C:A NC_000001.11:79935913:C:A (self)
ss66265844, ss76410878, ss173502953, ss275893098, ss482409624, ss1712346548 NC_000001.9:80174186:C:T NC_000001.11:79935913:C:T (self)
2320111, 1272588, 13141, 904731, 1426345, 480876, 585713, 1217805, 324811, 2679132, 1272588, 270425, ss218478768, ss238282587, ss480777254, ss533939160, ss554300636, ss648158719, ss779088837, ss781315605, ss834552693, ss1068023930, ss1291576670, ss1425868042, ss1600534355, ss1643528388, ss1918543783, ss1966788381, ss2147808457, ss2632536929, ss2697728906, ss2757104867, ss2987087278, ss3626135312, ss3630571921, ss3637767095, ss3655166483, ss3727196011, ss3746411342, ss3849200825, ss3894248951, ss5144709825, ss5314628114, ss5319825031, ss5625868189, ss5832187080, ss5937715531 NC_000001.10:80401598:C:T NC_000001.11:79935913:C:T (self)
2980568, 107252, 1216222, 3535881, 19489492, 4857880242, ss2163940053, ss3687105750, ss3799417085, ss3944838221, ss4455883157, ss5242859433, ss5443864468, ss5515454633, ss5669698777, ss5800743252, ss5848977979, ss5908945155 NC_000001.11:79935913:C:T NC_000001.11:79935913:C:T (self)
ss19137911 NT_026943.13:5221772:C:T NC_000001.11:79935913:C:T (self)
ss387084, ss1134686, ss1135361, ss1136546, ss1884261, ss1884364, ss1884947, ss2618514, ss44131832, ss46534272, ss81415322, ss155236907, ss161276976, ss173549301 NT_032977.9:50373516:C:T NC_000001.11:79935913: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 rs299814

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.post761+d5e8e07