Skip to main page content
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.

rs13303179

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:890030 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.435491 (115270/264690, TOPMED)
G=0.40056 (7045/17588, ALFA)
G=0.37249 (6243/16760, 8.3KJPN) (+ 8 more)
G=0.4227 (2117/5008, 1000G)
G=0.4863 (1425/2930, KOREAN)
G=0.2817 (516/1832, Korea1K)
G=0.295 (177/600, NorthernSweden)
G=0.284 (124/436, SGDP_PRJ)
G=0.444 (96/216, Qatari)
G=0.30 (12/40, GENOME_DK)
G=0.28 (11/40, 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.890030G>A
GRCh38.p13 chr 1 NC_000001.11:g.890030G>C
GRCh38.p13 chr 1 NC_000001.11:g.890030G>T
GRCh37.p13 chr 1 NC_000001.10:g.825410G>A
GRCh37.p13 chr 1 NC_000001.10:g.825410G>C
GRCh37.p13 chr 1 NC_000001.10:g.825410G>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
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 17588 G=0.40056 A=0.59939, C=0.00006
European Sub 13580 G=0.35891 A=0.64102, C=0.00007
African Sub 2542 G=0.6050 A=0.3950, C=0.0000
African Others Sub 92 G=0.65 A=0.35, C=0.00
African American Sub 2450 G=0.6033 A=0.3967, C=0.0000
Asian Sub 112 G=0.205 A=0.795, C=0.000
East Asian Sub 86 G=0.20 A=0.80, C=0.00
Other Asian Sub 26 G=0.23 A=0.77, C=0.00
Latin American 1 Sub 146 G=0.493 A=0.507, C=0.000
Latin American 2 Sub 610 G=0.462 A=0.538, C=0.000
South Asian Sub 98 G=0.33 A=0.67, C=0.00
Other Sub 500 G=0.448 A=0.552, C=0.000


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=0.435491 A=0.564509
8.3KJPN JAPANESE Study-wide 16760 G=0.37249 A=0.62751
1000Genomes Global Study-wide 5008 G=0.4227 A=0.5773
1000Genomes African Sub 1322 G=0.6172 A=0.3828
1000Genomes East Asian Sub 1008 G=0.2599 A=0.7401
1000Genomes Europe Sub 1006 G=0.3579 A=0.6421
1000Genomes South Asian Sub 978 G=0.344 A=0.656
1000Genomes American Sub 694 G=0.494 A=0.506
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4863 A=0.5137, C=0.0000, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.2817 A=0.7183
Northern Sweden ACPOP Study-wide 600 G=0.295 A=0.705
SGDP_PRJ Global Study-wide 436 G=0.284 A=0.716
Qatari Global Study-wide 216 G=0.444 A=0.556
The Danish reference pan genome Danish Study-wide 40 G=0.30 A=0.70
Siberian Global Study-wide 40 G=0.28 A=0.72
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 C T
GRCh38.p13 chr 1 NC_000001.11:g.890030= NC_000001.11:g.890030G>A NC_000001.11:g.890030G>C NC_000001.11:g.890030G>T
GRCh37.p13 chr 1 NC_000001.10:g.825410= NC_000001.10:g.825410G>A NC_000001.10:g.825410G>C NC_000001.10:g.825410G>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#.

47 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss22882847 Apr 05, 2004 (121)
2 ABI ss41201945 Mar 15, 2006 (126)
3 HGSV ss77712638 Dec 07, 2007 (129)
4 HGSV ss78624114 Dec 07, 2007 (129)
5 HGSV ss80869507 Dec 14, 2007 (130)
6 HGSV ss85982848 Dec 14, 2007 (130)
7 BGI ss105111802 Dec 01, 2009 (131)
8 1000GENOMES ss107938311 Jan 22, 2009 (130)
9 ENSEMBL ss133804975 Dec 01, 2009 (131)
10 GMI ss154524004 Dec 01, 2009 (131)
11 BCM-HGSC-SUB ss205443398 Jul 04, 2010 (132)
12 1000GENOMES ss210449132 Jul 14, 2010 (132)
13 BL ss252865038 May 09, 2011 (134)
14 GMI ss275681484 May 04, 2012 (137)
15 GMI ss283987670 Apr 25, 2013 (138)
16 PJP ss290493936 May 09, 2011 (134)
17 1000GENOMES ss1289341015 Aug 21, 2014 (142)
18 DDI ss1425685091 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1573851269 Apr 01, 2015 (144)
20 WEILL_CORNELL_DGM ss1917961108 Feb 12, 2016 (147)
21 GENOMED ss1966667420 Jul 19, 2016 (147)
22 JJLAB ss2019498574 Sep 14, 2016 (149)
23 USC_VALOUEV ss2147485029 Dec 20, 2016 (150)
24 TOPMED ss2321506481 Dec 20, 2016 (150)
25 SYSTEMSBIOZJU ss2624264873 Nov 08, 2017 (151)
26 GRF ss2697375901 Nov 08, 2017 (151)
27 GNOMAD ss2750644762 Nov 08, 2017 (151)
28 SWEGEN ss2986150310 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3023513753 Nov 08, 2017 (151)
30 TOPMED ss3066411489 Nov 08, 2017 (151)
31 TOPMED ss3066411490 Nov 08, 2017 (151)
32 CSHL ss3343272991 Nov 08, 2017 (151)
33 EVA_DECODE ss3685992830 Jul 12, 2019 (153)
34 ACPOP ss3726716646 Jul 12, 2019 (153)
35 EVA ss3745721392 Jul 12, 2019 (153)
36 PACBIO ss3783302452 Jul 12, 2019 (153)
37 PACBIO ss3788980118 Jul 12, 2019 (153)
38 PACBIO ss3793852679 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3798744105 Jul 12, 2019 (153)
40 EVA ss3825981575 Apr 25, 2020 (154)
41 EVA ss3836378506 Apr 25, 2020 (154)
42 EVA ss3841782518 Apr 25, 2020 (154)
43 SGDP_PRJ ss3847997052 Apr 25, 2020 (154)
44 KRGDB ss3892838717 Apr 25, 2020 (154)
45 KOGIC ss3943630648 Apr 25, 2020 (154)
46 TOPMED ss4436445740 Apr 25, 2021 (155)
47 TOMMO_GENOMICS ss5142054846 Apr 25, 2021 (155)
48 1000Genomes NC_000001.10 - 825410 Oct 11, 2018 (152)
49 The Danish reference pan genome NC_000001.10 - 825410 Apr 25, 2020 (154)
50 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 76405 (NC_000001.11:890029:G:A 79474/139718)
Row 76406 (NC_000001.11:890029:G:C 1/139778)

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

Submission ignored due to conflicting rows:
Row 76405 (NC_000001.11:890029:G:A 79474/139718)
Row 76406 (NC_000001.11:890029:G:C 1/139778)

- Apr 25, 2021 (155)
52 KOREAN population from KRGDB NC_000001.10 - 825410 Apr 25, 2020 (154)
53 Korean Genome Project NC_000001.11 - 890030 Apr 25, 2020 (154)
54 Northern Sweden NC_000001.10 - 825410 Jul 12, 2019 (153)
55 Qatari NC_000001.10 - 825410 Apr 25, 2020 (154)
56 SGDP_PRJ NC_000001.10 - 825410 Apr 25, 2020 (154)
57 Siberian NC_000001.10 - 825410 Apr 25, 2020 (154)
58 8.3KJPN NC_000001.10 - 825410 Apr 25, 2021 (155)
59 TopMed NC_000001.11 - 890030 Apr 25, 2021 (155)
60 ALFA NC_000001.11 - 890030 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)
rs57255438 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77712638, ss78624114, ss80869507, ss85982848 NC_000001.8:865272:G:A NC_000001.11:890029:G:A (self)
ss107938311, ss205443398, ss210449132, ss252865038, ss275681484, ss283987670, ss290493936 NC_000001.9:815272:G:A NC_000001.11:890029:G:A (self)
5814, 1358503, 16111, 1511, 3038, 14032, 1383, 24153, ss1289341015, ss1425685091, ss1573851269, ss1917961108, ss1966667420, ss2019498574, ss2147485029, ss2321506481, ss2624264873, ss2697375901, ss2750644762, ss2986150310, ss3343272991, ss3726716646, ss3745721392, ss3783302452, ss3788980118, ss3793852679, ss3825981575, ss3836378506, ss3847997052, ss3892838717, ss5142054846 NC_000001.10:825409:G:A NC_000001.11:890029:G:A (self)
8649, 24766, 52075, 8661392751, ss3023513753, ss3066411489, ss3685992830, ss3798744105, ss3841782518, ss3943630648, ss4436445740 NC_000001.11:890029:G:A NC_000001.11:890029:G:A (self)
ss22882847, ss41201945, ss105111802, ss133804975, ss154524004 NT_004350.19:304041:G:A NC_000001.11:890029:G:A (self)
16111, ss2750644762, ss3892838717 NC_000001.10:825409:G:C NC_000001.11:890029:G:C (self)
8661392751, ss3066411490 NC_000001.11:890029:G:C NC_000001.11:890029:G:C (self)
16111, ss3892838717 NC_000001.10:825409:G:T NC_000001.11:890029: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 rs13303179

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