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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.

rs4625581

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:28627079 (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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.217420 (57549/264690, TOPMED)
A=0.210936 (29556/140118, GnomAD)
A=0.15257 (5429/35584, ALFA) (+ 14 more)
A=0.11259 (1887/16760, 8.3KJPN)
A=0.2027 (1015/5008, 1000G)
A=0.1016 (455/4480, Estonian)
A=0.1399 (539/3854, ALSPAC)
A=0.1421 (527/3708, TWINSUK)
A=0.0952 (279/2930, KOREAN)
A=0.123 (123/998, GoNL)
A=0.125 (75/600, NorthernSweden)
A=0.125 (68/546, SGDP_PRJ)
A=0.134 (29/216, Qatari)
A=0.137 (29/212, Vietnamese)
A=0.11 (6/56, Siberian)
A=0.07 (3/40, GENOME_DK)
A=0.09 (2/22, Ancient Sardinia)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 35584 A=0.15257 G=0.84743, T=0.00000
European Sub 27182 A=0.12387 G=0.87613, T=0.00000
African Sub 3408 A=0.4093 G=0.5907, T=0.0000
African Others Sub 116 A=0.466 G=0.534, T=0.000
African American Sub 3292 A=0.4074 G=0.5926, T=0.0000
Asian Sub 176 A=0.136 G=0.864, T=0.000
East Asian Sub 116 A=0.129 G=0.871, T=0.000
Other Asian Sub 60 A=0.15 G=0.85, T=0.00
Latin American 1 Sub 272 A=0.176 G=0.824, T=0.000
Latin American 2 Sub 1990 A=0.0955 G=0.9045, T=0.0000
South Asian Sub 126 A=0.151 G=0.849, T=0.000
Other Sub 2430 A=0.1588 G=0.8412, T=0.0000


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=0.217420 G=0.782580
gnomAD - Genomes Global Study-wide 140118 A=0.210936 G=0.789064
gnomAD - Genomes European Sub 75914 A=0.12865 G=0.87135
gnomAD - Genomes African Sub 41942 A=0.39876 G=0.60124
gnomAD - Genomes American Sub 13656 A=0.13320 G=0.86680
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.1197 G=0.8803
gnomAD - Genomes East Asian Sub 3128 A=0.1384 G=0.8616
gnomAD - Genomes Other Sub 2154 A=0.1927 G=0.8073
Allele Frequency Aggregator Total Global 35584 A=0.15257 G=0.84743, T=0.00000
Allele Frequency Aggregator European Sub 27182 A=0.12387 G=0.87613, T=0.00000
Allele Frequency Aggregator African Sub 3408 A=0.4093 G=0.5907, T=0.0000
Allele Frequency Aggregator Other Sub 2430 A=0.1588 G=0.8412, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1990 A=0.0955 G=0.9045, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 272 A=0.176 G=0.824, T=0.000
Allele Frequency Aggregator Asian Sub 176 A=0.136 G=0.864, T=0.000
Allele Frequency Aggregator South Asian Sub 126 A=0.151 G=0.849, T=0.000
8.3KJPN JAPANESE Study-wide 16760 A=0.11259 G=0.88741
1000Genomes Global Study-wide 5008 A=0.2027 G=0.7973
1000Genomes African Sub 1322 A=0.4032 G=0.5968
1000Genomes East Asian Sub 1008 A=0.1300 G=0.8700
1000Genomes Europe Sub 1006 A=0.1481 G=0.8519
1000Genomes South Asian Sub 978 A=0.118 G=0.882
1000Genomes American Sub 694 A=0.125 G=0.875
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.1016 G=0.8984
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1399 G=0.8601
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1421 G=0.8579
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0952 G=0.9048
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.123 G=0.877
Northern Sweden ACPOP Study-wide 600 A=0.125 G=0.875
SGDP_PRJ Global Study-wide 546 A=0.125 G=0.875
Qatari Global Study-wide 216 A=0.134 G=0.866
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.137 G=0.863
Siberian Global Study-wide 56 A=0.11 G=0.89
The Danish reference pan genome Danish Study-wide 40 A=0.07 G=0.93
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 22 A=0.09 G=0.91
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 13 NC_000013.11:g.28627079A>G
GRCh38.p13 chr 13 NC_000013.11:g.28627079A>T
GRCh37.p13 chr 13 NC_000013.10:g.29201216A>G
GRCh37.p13 chr 13 NC_000013.10:g.29201216A>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 A= G T
GRCh38.p13 chr 13 NC_000013.11:g.28627079= NC_000013.11:g.28627079A>G NC_000013.11:g.28627079A>T
GRCh37.p13 chr 13 NC_000013.10:g.29201216= NC_000013.10:g.29201216A>G NC_000013.10:g.29201216A>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#.

84 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6276405 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss11074577 Jul 11, 2003 (116)
3 SC_SNP ss13254274 Dec 05, 2003 (119)
4 SSAHASNP ss21122143 Apr 05, 2004 (121)
5 PERLEGEN ss23468798 Sep 20, 2004 (123)
6 ABI ss43518351 Mar 13, 2006 (126)
7 AFFY ss66485701 Nov 29, 2006 (127)
8 PERLEGEN ss69129441 May 17, 2007 (127)
9 AFFY ss76306038 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss82072462 Dec 14, 2007 (130)
11 HGSV ss83903881 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss89558856 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss96954742 Feb 04, 2009 (130)
14 BGI ss106322399 Feb 04, 2009 (130)
15 1000GENOMES ss112647388 Jan 25, 2009 (130)
16 1000GENOMES ss114467067 Jan 25, 2009 (130)
17 ILLUMINA-UK ss118401667 Feb 14, 2009 (130)
18 ENSEMBL ss133504426 Dec 01, 2009 (131)
19 ENSEMBL ss137273967 Dec 01, 2009 (131)
20 GMI ss154584176 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss167791451 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss169071854 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss170931937 Jul 04, 2010 (132)
24 AFFY ss173199147 Jul 04, 2010 (132)
25 BUSHMAN ss199013248 Jul 04, 2010 (132)
26 BCM-HGSC-SUB ss208635676 Jul 04, 2010 (132)
27 1000GENOMES ss226099281 Jul 14, 2010 (132)
28 1000GENOMES ss236190564 Jul 15, 2010 (132)
29 1000GENOMES ss242698067 Jul 15, 2010 (132)
30 GMI ss281653068 May 04, 2012 (137)
31 GMI ss286675308 Apr 25, 2013 (138)
32 PJP ss291564852 May 09, 2011 (134)
33 ILLUMINA ss483174025 May 04, 2012 (137)
34 ILLUMINA ss483342792 May 04, 2012 (137)
35 ILLUMINA ss535556719 Sep 08, 2015 (146)
36 TISHKOFF ss563571622 Apr 25, 2013 (138)
37 SSMP ss659167403 Apr 25, 2013 (138)
38 ILLUMINA ss779411924 Sep 08, 2015 (146)
39 ILLUMINA ss782114517 Sep 08, 2015 (146)
40 ILLUMINA ss834880989 Sep 08, 2015 (146)
41 EVA-GONL ss990228440 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1078963734 Aug 21, 2014 (142)
43 1000GENOMES ss1347619873 Aug 21, 2014 (142)
44 DDI ss1427140519 Apr 01, 2015 (144)
45 EVA_GENOME_DK ss1576695076 Apr 01, 2015 (144)
46 EVA_UK10K_ALSPAC ss1629957282 Apr 01, 2015 (144)
47 EVA_DECODE ss1642333014 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1672951315 Apr 01, 2015 (144)
49 EVA_SVP ss1713378460 Apr 01, 2015 (144)
50 HAMMER_LAB ss1807541794 Sep 08, 2015 (146)
51 WEILL_CORNELL_DGM ss1933597402 Feb 12, 2016 (147)
52 GENOMED ss1967743384 Jul 19, 2016 (147)
53 JJLAB ss2027554366 Sep 14, 2016 (149)
54 USC_VALOUEV ss2155919107 Dec 20, 2016 (150)
55 HUMAN_LONGEVITY ss2195102885 Dec 20, 2016 (150)
56 TOPMED ss2359203024 Dec 20, 2016 (150)
57 SYSTEMSBIOZJU ss2628265331 Nov 08, 2017 (151)
58 ILLUMINA ss2633043873 Nov 08, 2017 (151)
59 GRF ss2700291256 Nov 08, 2017 (151)
60 GNOMAD ss2917944459 Nov 08, 2017 (151)
61 SWEGEN ss3010774373 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3027592728 Nov 08, 2017 (151)
63 TOPMED ss3188783025 Nov 08, 2017 (151)
64 TOPMED ss3188783026 Nov 08, 2017 (151)
65 CSHL ss3350381978 Nov 08, 2017 (151)
66 ILLUMINA ss3627029681 Oct 12, 2018 (152)
67 ILLUMINA ss3631048117 Oct 12, 2018 (152)
68 URBANLAB ss3649996483 Oct 12, 2018 (152)
69 EGCUT_WGS ss3678035111 Jul 13, 2019 (153)
70 EVA_DECODE ss3694991605 Jul 13, 2019 (153)
71 ACPOP ss3739612525 Jul 13, 2019 (153)
72 EVA ss3751275923 Jul 13, 2019 (153)
73 PACBIO ss3787414316 Jul 13, 2019 (153)
74 PACBIO ss3792486990 Jul 13, 2019 (153)
75 PACBIO ss3797370706 Jul 13, 2019 (153)
76 KHV_HUMAN_GENOMES ss3816606927 Jul 13, 2019 (153)
77 EVA ss3833466945 Apr 27, 2020 (154)
78 EVA ss3840310671 Apr 27, 2020 (154)
79 EVA ss3845795413 Apr 27, 2020 (154)
80 SGDP_PRJ ss3879660906 Apr 27, 2020 (154)
81 KRGDB ss3928482360 Apr 27, 2020 (154)
82 EVA ss3985630924 Apr 26, 2021 (155)
83 TOPMED ss4940998753 Apr 26, 2021 (155)
84 TOMMO_GENOMICS ss5209316912 Apr 26, 2021 (155)
85 1000Genomes NC_000013.10 - 29201216 Oct 12, 2018 (152)
86 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 29201216 Oct 12, 2018 (152)
87 Genetic variation in the Estonian population NC_000013.10 - 29201216 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000013.10 - 29201216 Apr 27, 2020 (154)
89 gnomAD - Genomes NC_000013.11 - 28627079 Apr 26, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000013.10 - 29201216 Apr 27, 2020 (154)
91 KOREAN population from KRGDB NC_000013.10 - 29201216 Apr 27, 2020 (154)
92 Northern Sweden NC_000013.10 - 29201216 Jul 13, 2019 (153)
93 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000013.10 - 29201216 Apr 26, 2021 (155)
94 Qatari NC_000013.10 - 29201216 Apr 27, 2020 (154)
95 SGDP_PRJ NC_000013.10 - 29201216 Apr 27, 2020 (154)
96 Siberian NC_000013.10 - 29201216 Apr 27, 2020 (154)
97 8.3KJPN NC_000013.10 - 29201216 Apr 26, 2021 (155)
98 TopMed NC_000013.11 - 28627079 Apr 26, 2021 (155)
99 UK 10K study - Twins NC_000013.10 - 29201216 Oct 12, 2018 (152)
100 A Vietnamese Genetic Variation Database NC_000013.10 - 29201216 Jul 13, 2019 (153)
101 ALFA NC_000013.11 - 28627079 Apr 26, 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)
rs56713168 Feb 26, 2009 (130)
rs57338479 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83903881, ss89558856, ss112647388, ss114467067, ss118401667, ss167791451, ss169071854, ss170931937, ss199013248, ss208635676, ss281653068, ss286675308, ss291564852, ss483174025, ss1642333014, ss1713378460 NC_000013.9:28099215:A:G NC_000013.11:28627078:A:G (self)
60468292, 33584131, 23773359, 3234474, 14984920, 35659754, 12897390, 856851, 15639332, 31677886, 8435461, 67286219, 33584131, 7449615, ss226099281, ss236190564, ss242698067, ss483342792, ss535556719, ss563571622, ss659167403, ss779411924, ss782114517, ss834880989, ss990228440, ss1078963734, ss1347619873, ss1427140519, ss1576695076, ss1629957282, ss1672951315, ss1807541794, ss1933597402, ss1967743384, ss2027554366, ss2155919107, ss2359203024, ss2628265331, ss2633043873, ss2700291256, ss2917944459, ss3010774373, ss3350381978, ss3627029681, ss3631048117, ss3678035111, ss3739612525, ss3751275923, ss3787414316, ss3792486990, ss3797370706, ss3833466945, ss3840310671, ss3879660906, ss3928482360, ss3985630924, ss5209316912 NC_000013.10:29201215:A:G NC_000013.11:28627078:A:G (self)
426387090, 97892475, 156544411, 1067106092, ss2195102885, ss3027592728, ss3188783025, ss3649996483, ss3694991605, ss3816606927, ss3845795413, ss4940998753 NC_000013.11:28627078:A:G NC_000013.11:28627078:A:G (self)
ss11074577, ss13254274 NT_009799.12:10181215:A:G NC_000013.11:28627078:A:G (self)
ss21122143 NT_024524.13:10181215:A:G NC_000013.11:28627078:A:G (self)
ss6276405, ss23468798, ss43518351, ss66485701, ss69129441, ss76306038, ss82072462, ss96954742, ss106322399, ss133504426, ss137273967, ss154584176, ss173199147 NT_024524.14:10181215:A:G NC_000013.11:28627078:A:G (self)
1067106092, ss3188783026 NC_000013.11:28627078:A:T NC_000013.11:28627078: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.

No publications for rs4625581

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.post629+eb05767