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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.

rs626629

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:203802 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.244467 (64708/264690, TOPMED)
A=0.13328 (1864/13986, ALFA)
A=0.2244 (1437/6404, 1000G_30x) (+ 11 more)
A=0.2256 (1130/5008, 1000G)
A=0.2607 (1168/4480, Estonian)
A=0.2802 (1080/3854, ALSPAC)
A=0.2613 (969/3708, TWINSUK)
A=0.3392 (994/2930, KOREAN)
A=0.282 (281/998, GoNL)
A=0.307 (184/600, NorthernSweden)
G=0.378 (93/246, SGDP_PRJ)
A=0.185 (40/216, Qatari)
A=0.23 (9/40, GENOME_DK)
G=0.42 (15/36, 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 13986 G=0.86672 A=0.13328, C=0.00000, T=0.00000
European Sub 10934 G=0.83812 A=0.16188, C=0.00000, T=0.00000
African Sub 1988 G=0.9829 A=0.0171, C=0.0000, T=0.0000
African Others Sub 78 G=0.97 A=0.03, C=0.00, T=0.00
African American Sub 1910 G=0.9832 A=0.0168, C=0.0000, T=0.0000
Asian Sub 62 G=0.95 A=0.05, C=0.00, T=0.00
East Asian Sub 46 G=0.96 A=0.04, C=0.00, T=0.00
Other Asian Sub 16 G=0.94 A=0.06, C=0.00, T=0.00
Latin American 1 Sub 88 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 328 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 68 G=0.99 A=0.01, C=0.00, T=0.00
Other Sub 518 G=0.892 A=0.108, C=0.000, T=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=0.755533 A=0.244467
Allele Frequency Aggregator Total Global 13986 G=0.86672 A=0.13328, C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 10934 G=0.83812 A=0.16188, C=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 1988 G=0.9829 A=0.0171, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 518 G=0.892 A=0.108, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 328 G=1.000 A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 88 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 68 G=0.99 A=0.01, C=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 62 G=0.95 A=0.05, C=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.7751 A=0.2244, C=0.0005
1000Genomes_30x African Sub 1786 G=0.8163 A=0.1837, C=0.0000
1000Genomes_30x Europe Sub 1266 G=0.7464 A=0.2536, C=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.8245 A=0.1747, C=0.0008
1000Genomes_30x East Asian Sub 1170 G=0.6991 A=0.2991, C=0.0017
1000Genomes_30x American Sub 980 G=0.767 A=0.233, C=0.000
1000Genomes Global Study-wide 5008 G=0.7744 A=0.2256
1000Genomes African Sub 1322 G=0.8230 A=0.1770
1000Genomes East Asian Sub 1008 G=0.6974 A=0.3026
1000Genomes Europe Sub 1006 G=0.7386 A=0.2614
1000Genomes South Asian Sub 978 G=0.830 A=0.170
1000Genomes American Sub 694 G=0.767 A=0.233
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7393 A=0.2607
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7198 A=0.2802
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7387 A=0.2613
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6597 A=0.3392, C=0.0010
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.718 A=0.282
Northern Sweden ACPOP Study-wide 600 G=0.693 A=0.307
SGDP_PRJ Global Study-wide 246 G=0.378 A=0.622
Qatari Global Study-wide 216 G=0.815 A=0.185
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 36 G=0.42 A=0.58
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 9 NC_000009.12:g.203802G>A
GRCh38.p14 chr 9 NC_000009.12:g.203802G>C
GRCh38.p14 chr 9 NC_000009.12:g.203802G>T
GRCh37.p13 chr 9 NC_000009.11:g.203802G>A
GRCh37.p13 chr 9 NC_000009.11:g.203802G>C
GRCh37.p13 chr 9 NC_000009.11:g.203802G>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 G= A C T
GRCh38.p14 chr 9 NC_000009.12:g.203802= NC_000009.12:g.203802G>A NC_000009.12:g.203802G>C NC_000009.12:g.203802G>T
GRCh37.p13 chr 9 NC_000009.11:g.203802= NC_000009.11:g.203802G>A NC_000009.11:g.203802G>C NC_000009.11:g.203802G>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#.

59 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss799124 Aug 11, 2000 (83)
2 SC_JCM ss3475625 Sep 28, 2001 (100)
3 SC_SNP ss16020027 Feb 27, 2004 (120)
4 BCMHGSC_JDW ss93991373 Mar 25, 2008 (129)
5 BGI ss105654555 Feb 06, 2009 (130)
6 GMI ss157053528 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss164231822 Jul 04, 2010 (132)
8 1000GENOMES ss224061516 Jul 14, 2010 (132)
9 1000GENOMES ss234684394 Jul 15, 2010 (132)
10 1000GENOMES ss241486573 Jul 15, 2010 (132)
11 BL ss253971436 May 09, 2011 (134)
12 GMI ss280061014 May 04, 2012 (137)
13 PJP ss294265693 May 09, 2011 (134)
14 TISHKOFF ss561165055 Apr 25, 2013 (138)
15 SSMP ss655597375 Apr 25, 2013 (138)
16 EVA-GONL ss986200931 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1076024727 Aug 21, 2014 (142)
18 1000GENOMES ss1332474359 Aug 21, 2014 (142)
19 DDI ss1431715738 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1582942597 Apr 01, 2015 (144)
21 EVA_DECODE ss1595823691 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1622029536 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1665023569 Apr 01, 2015 (144)
24 HAMMER_LAB ss1805828845 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1929479183 Feb 12, 2016 (147)
26 JJLAB ss2025445401 Sep 14, 2016 (149)
27 USC_VALOUEV ss2153676944 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2308528903 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2627198746 Nov 08, 2017 (151)
30 GRF ss2709470369 Nov 08, 2017 (151)
31 GNOMAD ss2874259025 Nov 08, 2017 (151)
32 SWEGEN ss3004223346 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3026510472 Nov 08, 2017 (151)
34 CSHL ss3348473758 Nov 08, 2017 (151)
35 EGCUT_WGS ss3671949888 Jul 13, 2019 (153)
36 EVA_DECODE ss3723280527 Jul 13, 2019 (153)
37 ACPOP ss3736220856 Jul 13, 2019 (153)
38 EVA ss3768785739 Jul 13, 2019 (153)
39 KHV_HUMAN_GENOMES ss3811944007 Jul 13, 2019 (153)
40 EVA ss3831483883 Apr 26, 2020 (154)
41 SGDP_PRJ ss3871303857 Apr 26, 2020 (154)
42 KRGDB ss3918929704 Apr 26, 2020 (154)
43 KOGIC ss3965114635 Apr 26, 2020 (154)
44 KOGIC ss3965114636 Apr 26, 2020 (154)
45 TOPMED ss4808866141 Apr 26, 2021 (155)
46 TOMMO_GENOMICS ss5191626546 Apr 26, 2021 (155)
47 TOMMO_GENOMICS ss5191626547 Apr 26, 2021 (155)
48 1000G_HIGH_COVERAGE ss5279434368 Oct 16, 2022 (156)
49 1000G_HIGH_COVERAGE ss5279434369 Oct 16, 2022 (156)
50 EVA ss5385375865 Oct 16, 2022 (156)
51 HUGCELL_USP ss5475756553 Oct 16, 2022 (156)
52 1000G_HIGH_COVERAGE ss5571010185 Oct 16, 2022 (156)
53 SANFORD_IMAGENETICS ss5646696502 Oct 16, 2022 (156)
54 TOMMO_GENOMICS ss5734548746 Oct 16, 2022 (156)
55 TOMMO_GENOMICS ss5734548747 Oct 16, 2022 (156)
56 YY_MCH ss5810254796 Oct 16, 2022 (156)
57 EVA ss5828711185 Oct 16, 2022 (156)
58 EVA ss5856627971 Oct 16, 2022 (156)
59 EVA ss5975957009 Oct 16, 2022 (156)
60 1000Genomes NC_000009.11 - 203802 Oct 12, 2018 (152)
61 1000Genomes_30x NC_000009.12 - 203802 Oct 16, 2022 (156)
62 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 203802 Oct 12, 2018 (152)
63 Genetic variation in the Estonian population NC_000009.11 - 203802 Oct 12, 2018 (152)
64 The Danish reference pan genome NC_000009.11 - 203802 Apr 26, 2020 (154)
65 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 315109438 (NC_000009.12:203801:G:A 34281/139530)
Row 315109439 (NC_000009.12:203801:G:C 1/139662)
Row 315109440 (NC_000009.12:203801:G:T 1/139662)

- Apr 26, 2021 (155)
66 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 315109438 (NC_000009.12:203801:G:A 34281/139530)
Row 315109439 (NC_000009.12:203801:G:C 1/139662)
Row 315109440 (NC_000009.12:203801:G:T 1/139662)

- Apr 26, 2021 (155)
67 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 315109438 (NC_000009.12:203801:G:A 34281/139530)
Row 315109439 (NC_000009.12:203801:G:C 1/139662)
Row 315109440 (NC_000009.12:203801:G:T 1/139662)

- Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000009.11 - 203802 Apr 26, 2020 (154)
69 KOREAN population from KRGDB NC_000009.11 - 203802 Apr 26, 2020 (154)
70 Korean Genome Project

Submission ignored due to conflicting rows:
Row 21492636 (NC_000009.12:203801:G:A 632/1832)
Row 21492637 (NC_000009.12:203801:G:C 1/1832)

- Apr 26, 2020 (154)
71 Korean Genome Project

Submission ignored due to conflicting rows:
Row 21492636 (NC_000009.12:203801:G:A 632/1832)
Row 21492637 (NC_000009.12:203801:G:C 1/1832)

- Apr 26, 2020 (154)
72 Northern Sweden NC_000009.11 - 203802 Jul 13, 2019 (153)
73 Qatari NC_000009.11 - 203802 Apr 26, 2020 (154)
74 SGDP_PRJ NC_000009.11 - 203802 Apr 26, 2020 (154)
75 Siberian NC_000009.11 - 203802 Apr 26, 2020 (154)
76 8.3KJPN

Submission ignored due to conflicting rows:
Row 49595853 (NC_000009.11:203801:G:A 5616/16760)
Row 49595854 (NC_000009.11:203801:G:C 3/16760)

- Apr 26, 2021 (155)
77 8.3KJPN

Submission ignored due to conflicting rows:
Row 49595853 (NC_000009.11:203801:G:A 5616/16760)
Row 49595854 (NC_000009.11:203801:G:C 3/16760)

- Apr 26, 2021 (155)
78 14KJPN

Submission ignored due to conflicting rows:
Row 68385850 (NC_000009.12:203801:G:A 9574/28256)
Row 68385851 (NC_000009.12:203801:G:C 6/28256)

- Oct 16, 2022 (156)
79 14KJPN

Submission ignored due to conflicting rows:
Row 68385850 (NC_000009.12:203801:G:A 9574/28256)
Row 68385851 (NC_000009.12:203801:G:C 6/28256)

- Oct 16, 2022 (156)
80 TopMed NC_000009.12 - 203802 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000009.11 - 203802 Oct 12, 2018 (152)
82 ALFA NC_000009.12 - 203802 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93991373, ss164231822, ss253971436, ss280061014, ss294265693, ss1595823691 NC_000009.10:193801:G:A NC_000009.12:203801:G:A (self)
44691263, 24870377, 17688136, 9107534, 11091208, 26107098, 9505721, 11521113, 23320837, 6193298, 24870377, ss224061516, ss234684394, ss241486573, ss561165055, ss655597375, ss986200931, ss1076024727, ss1332474359, ss1431715738, ss1582942597, ss1622029536, ss1665023569, ss1805828845, ss1929479183, ss2025445401, ss2153676944, ss2627198746, ss2709470369, ss2874259025, ss3004223346, ss3348473758, ss3671949888, ss3736220856, ss3768785739, ss3831483883, ss3871303857, ss3918929704, ss5191626546, ss5385375865, ss5646696502, ss5828711185, ss5975957009 NC_000009.11:203801:G:A NC_000009.12:203801:G:A (self)
58536120, 646243702, 5257120121, ss2308528903, ss3026510472, ss3723280527, ss3811944007, ss3965114635, ss4808866141, ss5279434368, ss5475756553, ss5571010185, ss5734548746, ss5810254796, ss5856627971 NC_000009.12:203801:G:A NC_000009.12:203801:G:A (self)
ss16020027 NT_008413.16:193801:G:A NC_000009.12:203801:G:A (self)
ss799124, ss3475625, ss105654555, ss157053528 NT_008413.18:193801:G:A NC_000009.12:203801:G:A (self)
26107098, ss2874259025, ss3918929704, ss5191626547 NC_000009.11:203801:G:C NC_000009.12:203801:G:C (self)
58536120, 5257120121, ss3965114636, ss5279434369, ss5571010185, ss5734548747 NC_000009.12:203801:G:C NC_000009.12:203801:G:C (self)
5257120121 NC_000009.12:203801:G:T NC_000009.12:203801: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 rs626629

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