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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.

rs9594109

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:86045011 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.197922 (52388/264690, TOPMED)
C=0.189220 (25609/135340, GnomAD)
C=0.03766 (1064/28250, 14KJPN) (+ 19 more)
C=0.12066 (3046/25244, ALFA)
C=0.03854 (646/16760, 8.3KJPN)
C=0.1993 (1276/6404, 1000G_30x)
C=0.1927 (965/5008, 1000G)
C=0.0522 (234/4480, Estonian)
C=0.0664 (256/3854, ALSPAC)
C=0.0661 (245/3708, TWINSUK)
C=0.0270 (79/2928, KOREAN)
C=0.0246 (45/1832, Korea1K)
C=0.2515 (430/1710, HapMap)
C=0.067 (67/998, GoNL)
C=0.094 (59/626, Chileans)
C=0.058 (35/600, NorthernSweden)
C=0.130 (28/216, Qatari)
C=0.033 (7/210, Vietnamese)
T=0.381 (48/126, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
T=0.5 (4/8, Siberian)
C=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 25244 T=0.87934 A=0.00000, C=0.12066
European Sub 17322 T=0.93465 A=0.00000, C=0.06535
African Sub 3256 T=0.5590 A=0.0000, C=0.4410
African Others Sub 110 T=0.455 A=0.000, C=0.545
African American Sub 3146 T=0.5626 A=0.0000, C=0.4374
Asian Sub 160 T=0.988 A=0.000, C=0.013
East Asian Sub 102 T=1.000 A=0.000, C=0.000
Other Asian Sub 58 T=0.97 A=0.00, C=0.03
Latin American 1 Sub 292 T=0.884 A=0.000, C=0.116
Latin American 2 Sub 2764 T=0.9128 A=0.0000, C=0.0872
South Asian Sub 110 T=0.873 A=0.000, C=0.127
Other Sub 1340 T=0.8604 A=0.0000, C=0.1396


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 T=0.802078 C=0.197922
gnomAD - Genomes Global Study-wide 135340 T=0.810780 C=0.189220
gnomAD - Genomes European Sub 73500 T=0.93144 C=0.06856
gnomAD - Genomes African Sub 40252 T=0.54730 C=0.45270
gnomAD - Genomes American Sub 13110 T=0.88124 C=0.11876
gnomAD - Genomes Ashkenazi Jewish Sub 3282 T=0.8943 C=0.1057
gnomAD - Genomes East Asian Sub 3106 T=0.9736 C=0.0264
gnomAD - Genomes Other Sub 2090 T=0.8268 C=0.1732
14KJPN JAPANESE Study-wide 28250 T=0.96234 C=0.03766
Allele Frequency Aggregator Total Global 25244 T=0.87934 A=0.00000, C=0.12066
Allele Frequency Aggregator European Sub 17322 T=0.93465 A=0.00000, C=0.06535
Allele Frequency Aggregator African Sub 3256 T=0.5590 A=0.0000, C=0.4410
Allele Frequency Aggregator Latin American 2 Sub 2764 T=0.9128 A=0.0000, C=0.0872
Allele Frequency Aggregator Other Sub 1340 T=0.8604 A=0.0000, C=0.1396
Allele Frequency Aggregator Latin American 1 Sub 292 T=0.884 A=0.000, C=0.116
Allele Frequency Aggregator Asian Sub 160 T=0.988 A=0.000, C=0.013
Allele Frequency Aggregator South Asian Sub 110 T=0.873 A=0.000, C=0.127
8.3KJPN JAPANESE Study-wide 16760 T=0.96146 C=0.03854
1000Genomes_30x Global Study-wide 6404 T=0.8007 C=0.1993
1000Genomes_30x African Sub 1786 T=0.4849 C=0.5151
1000Genomes_30x Europe Sub 1266 T=0.9297 C=0.0703
1000Genomes_30x South Asian Sub 1202 T=0.8935 C=0.1065
1000Genomes_30x East Asian Sub 1170 T=0.9735 C=0.0265
1000Genomes_30x American Sub 980 T=0.890 C=0.110
1000Genomes Global Study-wide 5008 T=0.8073 C=0.1927
1000Genomes African Sub 1322 T=0.4924 C=0.5076
1000Genomes East Asian Sub 1008 T=0.9732 C=0.0268
1000Genomes Europe Sub 1006 T=0.9235 C=0.0765
1000Genomes South Asian Sub 978 T=0.883 C=0.117
1000Genomes American Sub 694 T=0.890 C=0.110
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9478 C=0.0522
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9336 C=0.0664
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9339 C=0.0661
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.9730 C=0.0270
Korean Genome Project KOREAN Study-wide 1832 T=0.9754 C=0.0246
HapMap Global Study-wide 1710 T=0.7485 C=0.2515
HapMap African Sub 692 T=0.527 C=0.473
HapMap American Sub 594 T=0.867 C=0.133
HapMap Asian Sub 250 T=0.980 C=0.020
HapMap Europe Sub 174 T=0.891 C=0.109
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.933 C=0.067
Chileans Chilean Study-wide 626 T=0.906 C=0.094
Northern Sweden ACPOP Study-wide 600 T=0.942 C=0.058
Qatari Global Study-wide 216 T=0.870 C=0.130
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.967 C=0.033
SGDP_PRJ Global Study-wide 126 T=0.381 C=0.619
The Danish reference pan genome Danish Study-wide 40 T=0.93 C=0.07
Siberian Global Study-wide 8 T=0.5 C=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 13 NC_000013.11:g.86045011T>A
GRCh38.p14 chr 13 NC_000013.11:g.86045011T>C
GRCh37.p13 chr 13 NC_000013.10:g.86619146T>A
GRCh37.p13 chr 13 NC_000013.10:g.86619146T>C
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 T= A C
GRCh38.p14 chr 13 NC_000013.11:g.86045011= NC_000013.11:g.86045011T>A NC_000013.11:g.86045011T>C
GRCh37.p13 chr 13 NC_000013.10:g.86619146= NC_000013.10:g.86619146T>A NC_000013.10:g.86619146T>C
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#.

62 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13327069 Dec 05, 2003 (119)
2 SSAHASNP ss21143109 Apr 05, 2004 (121)
3 ABI ss40324161 Mar 14, 2006 (126)
4 AFFY ss66036200 Jul 04, 2010 (132)
5 AFFY ss75924971 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss82601162 Dec 15, 2007 (130)
7 HUMANGENOME_JCVI ss97179311 Feb 06, 2009 (130)
8 1000GENOMES ss115044622 Jan 25, 2009 (130)
9 ILLUMINA-UK ss118898256 Dec 01, 2009 (131)
10 ENSEMBL ss132263700 Dec 01, 2009 (131)
11 AFFY ss169197164 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss170305917 Jul 04, 2010 (132)
13 BUSHMAN ss199502926 Jul 04, 2010 (132)
14 1000GENOMES ss226320533 Jul 14, 2010 (132)
15 1000GENOMES ss236359153 Jul 15, 2010 (132)
16 GMI ss281816728 May 04, 2012 (137)
17 PJP ss291497475 May 09, 2011 (134)
18 TISHKOFF ss563814424 Apr 25, 2013 (138)
19 SSMP ss659449393 Apr 25, 2013 (138)
20 EVA-GONL ss990667099 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1079293483 Aug 21, 2014 (142)
22 1000GENOMES ss1349214315 Aug 21, 2014 (142)
23 DDI ss1427271797 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1576951510 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1630806657 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1673800690 Apr 01, 2015 (144)
27 EVA_DECODE ss1685198912 Apr 01, 2015 (144)
28 EVA_SVP ss1713409591 Apr 01, 2015 (144)
29 HAMMER_LAB ss1807717780 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1934026531 Feb 12, 2016 (147)
31 JJLAB ss2027786096 Sep 14, 2016 (149)
32 USC_VALOUEV ss2156151467 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2198427633 Dec 20, 2016 (150)
34 GRF ss2700542836 Nov 08, 2017 (151)
35 GNOMAD ss2922502506 Nov 08, 2017 (151)
36 SWEGEN ss3011433503 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3027712309 Nov 08, 2017 (151)
38 CSHL ss3350580143 Nov 08, 2017 (151)
39 URBANLAB ss3650095110 Oct 12, 2018 (152)
40 EGCUT_WGS ss3678714003 Jul 13, 2019 (153)
41 EVA_DECODE ss3695787108 Jul 13, 2019 (153)
42 ACPOP ss3739974610 Jul 13, 2019 (153)
43 EVA ss3751772118 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3817102143 Jul 13, 2019 (153)
45 EVA ss3833679427 Apr 27, 2020 (154)
46 SGDP_PRJ ss3880499499 Apr 27, 2020 (154)
47 KRGDB ss3929410323 Apr 27, 2020 (154)
48 KOGIC ss3974032515 Apr 27, 2020 (154)
49 TOPMED ss4955308864 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5211125401 Apr 26, 2021 (155)
51 1000G_HIGH_COVERAGE ss5294603700 Oct 16, 2022 (156)
52 EVA ss5412360194 Oct 16, 2022 (156)
53 HUGCELL_USP ss5488880346 Oct 16, 2022 (156)
54 EVA ss5511082360 Oct 16, 2022 (156)
55 1000G_HIGH_COVERAGE ss5594060494 Oct 16, 2022 (156)
56 SANFORD_IMAGENETICS ss5655281955 Oct 16, 2022 (156)
57 TOMMO_GENOMICS ss5763310252 Oct 16, 2022 (156)
58 YY_MCH ss5814336162 Oct 16, 2022 (156)
59 EVA ss5839824982 Oct 16, 2022 (156)
60 EVA ss5850838230 Oct 16, 2022 (156)
61 EVA ss5926101460 Oct 16, 2022 (156)
62 EVA ss5946716789 Oct 16, 2022 (156)
63 1000Genomes NC_000013.10 - 86619146 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000013.11 - 86045011 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 86619146 Oct 12, 2018 (152)
66 Chileans NC_000013.10 - 86619146 Apr 27, 2020 (154)
67 Genetic variation in the Estonian population NC_000013.10 - 86619146 Oct 12, 2018 (152)
68 The Danish reference pan genome NC_000013.10 - 86619146 Apr 27, 2020 (154)
69 gnomAD - Genomes NC_000013.11 - 86045011 Apr 26, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000013.10 - 86619146 Apr 27, 2020 (154)
71 HapMap NC_000013.11 - 86045011 Apr 27, 2020 (154)
72 KOREAN population from KRGDB NC_000013.10 - 86619146 Apr 27, 2020 (154)
73 Korean Genome Project NC_000013.11 - 86045011 Apr 27, 2020 (154)
74 Northern Sweden NC_000013.10 - 86619146 Jul 13, 2019 (153)
75 Qatari NC_000013.10 - 86619146 Apr 27, 2020 (154)
76 SGDP_PRJ NC_000013.10 - 86619146 Apr 27, 2020 (154)
77 Siberian NC_000013.10 - 86619146 Apr 27, 2020 (154)
78 8.3KJPN NC_000013.10 - 86619146 Apr 26, 2021 (155)
79 14KJPN NC_000013.11 - 86045011 Oct 16, 2022 (156)
80 TopMed NC_000013.11 - 86045011 Apr 26, 2021 (155)
81 UK 10K study - Twins NC_000013.10 - 86619146 Oct 12, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000013.10 - 86619146 Jul 13, 2019 (153)
83 ALFA NC_000013.11 - 86045011 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)
rs60877208 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6739292571 NC_000013.11:86045010:T:A NC_000013.11:86045010:T:A (self)
ss75924971, ss115044622, ss118898256, ss169197164, ss170305917, ss199502926, ss281816728, ss291497475, ss1685198912, ss1713409591 NC_000013.9:85517146:T:C NC_000013.11:86045010:T:C (self)
62125998, 34520475, 126370, 24452251, 3408448, 15412967, 36587717, 13259475, 16068461, 32516479, 8667821, 69094708, 34520475, 7671048, ss226320533, ss236359153, ss563814424, ss659449393, ss990667099, ss1079293483, ss1349214315, ss1427271797, ss1576951510, ss1630806657, ss1673800690, ss1807717780, ss1934026531, ss2027786096, ss2156151467, ss2700542836, ss2922502506, ss3011433503, ss3350580143, ss3678714003, ss3739974610, ss3751772118, ss3833679427, ss3880499499, ss3929410323, ss5211125401, ss5412360194, ss5511082360, ss5655281955, ss5839824982, ss5946716789 NC_000013.10:86619145:T:C NC_000013.11:86045010:T:C (self)
81586429, 438111637, 1048302, 30410516, 97147356, 170854522, 6739292571, ss2198427633, ss3027712309, ss3650095110, ss3695787108, ss3817102143, ss3974032515, ss4955308864, ss5294603700, ss5488880346, ss5594060494, ss5763310252, ss5814336162, ss5850838230, ss5926101460 NC_000013.11:86045010:T:C NC_000013.11:86045010:T:C (self)
ss13327069 NT_024524.12:55193638:T:C NC_000013.11:86045010:T:C (self)
ss21143109 NT_024524.13:67599146:T:C NC_000013.11:86045010:T:C (self)
ss40324161, ss82601162, ss97179311, ss132263700 NT_024524.14:67599145:T:C NC_000013.11:86045010:T:C (self)
ss66036200 NT_024524.15:67636904:T:C NC_000013.11:86045010:T:C (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 rs9594109

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