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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.

rs169596

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:31343258 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.440104 (116491/264690, TOPMED)
A=0.459711 (55077/119808, GnomAD)
A=0.44547 (16779/37666, ALFA) (+ 15 more)
A=0.45505 (12848/28234, 14KJPN)
A=0.45917 (7693/16754, 8.3KJPN)
A=0.4472 (2864/6404, 1000G_30x)
A=0.4519 (2263/5008, 1000G)
G=0.4921 (2189/4448, Estonian)
A=0.4813 (1855/3854, ALSPAC)
A=0.4606 (1708/3708, TWINSUK)
A=0.4799 (1406/2930, KOREAN)
A=0.3947 (746/1890, HapMap)
A=0.4737 (865/1826, Korea1K)
G=0.465 (279/600, NorthernSweden)
G=0.339 (135/398, SGDP_PRJ)
A=0.398 (86/216, Qatari)
G=0.28 (14/50, Siberian)
A=0.30 (12/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
XDH : Intron Variant
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 37666 G=0.55453 A=0.44547
European Sub 27228 G=0.53581 A=0.46419
African Sub 5650 G=0.6752 A=0.3248
African Others Sub 200 G=0.740 A=0.260
African American Sub 5450 G=0.6728 A=0.3272
Asian Sub 152 G=0.474 A=0.526
East Asian Sub 120 G=0.467 A=0.533
Other Asian Sub 32 G=0.50 A=0.50
Latin American 1 Sub 496 G=0.589 A=0.411
Latin American 2 Sub 720 G=0.385 A=0.615
South Asian Sub 140 G=0.464 A=0.536
Other Sub 3280 G=0.5418 A=0.4582


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=0.559896 A=0.440104
gnomAD - Genomes Global Study-wide 119808 G=0.540289 A=0.459711
gnomAD - Genomes European Sub 67434 G=0.50810 A=0.49190
gnomAD - Genomes African Sub 33128 G=0.65836 A=0.34164
gnomAD - Genomes American Sub 11438 G=0.41327 A=0.58673
gnomAD - Genomes Ashkenazi Jewish Sub 3152 G=0.5523 A=0.4477
gnomAD - Genomes East Asian Sub 2866 G=0.4456 A=0.5544
gnomAD - Genomes Other Sub 1790 G=0.5101 A=0.4899
Allele Frequency Aggregator Total Global 37666 G=0.55453 A=0.44547
Allele Frequency Aggregator European Sub 27228 G=0.53581 A=0.46419
Allele Frequency Aggregator African Sub 5650 G=0.6752 A=0.3248
Allele Frequency Aggregator Other Sub 3280 G=0.5418 A=0.4582
Allele Frequency Aggregator Latin American 2 Sub 720 G=0.385 A=0.615
Allele Frequency Aggregator Latin American 1 Sub 496 G=0.589 A=0.411
Allele Frequency Aggregator Asian Sub 152 G=0.474 A=0.526
Allele Frequency Aggregator South Asian Sub 140 G=0.464 A=0.536
14KJPN JAPANESE Study-wide 28234 G=0.54495 A=0.45505
8.3KJPN JAPANESE Study-wide 16754 G=0.54083 A=0.45917
1000Genomes_30x Global Study-wide 6404 G=0.5528 A=0.4472
1000Genomes_30x African Sub 1786 G=0.7060 A=0.2940
1000Genomes_30x Europe Sub 1266 G=0.5411 A=0.4589
1000Genomes_30x South Asian Sub 1202 G=0.5441 A=0.4559
1000Genomes_30x East Asian Sub 1170 G=0.4966 A=0.5034
1000Genomes_30x American Sub 980 G=0.366 A=0.634
1000Genomes Global Study-wide 5008 G=0.5481 A=0.4519
1000Genomes African Sub 1322 G=0.7126 A=0.2874
1000Genomes East Asian Sub 1008 G=0.4881 A=0.5119
1000Genomes Europe Sub 1006 G=0.5249 A=0.4751
1000Genomes South Asian Sub 978 G=0.540 A=0.460
1000Genomes American Sub 694 G=0.367 A=0.633
Genetic variation in the Estonian population Estonian Study-wide 4448 G=0.4921 A=0.5079
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5187 A=0.4813
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5394 A=0.4606
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5201 A=0.4799
HapMap Global Study-wide 1890 G=0.6053 A=0.3947
HapMap American Sub 770 G=0.544 A=0.456
HapMap African Sub 690 G=0.741 A=0.259
HapMap Asian Sub 254 G=0.484 A=0.516
HapMap Europe Sub 176 G=0.517 A=0.483
Korean Genome Project KOREAN Study-wide 1826 G=0.5263 A=0.4737
Northern Sweden ACPOP Study-wide 600 G=0.465 A=0.535
SGDP_PRJ Global Study-wide 398 G=0.339 A=0.661
Qatari Global Study-wide 216 G=0.602 A=0.398
Siberian Global Study-wide 50 G=0.28 A=0.72
The Danish reference pan genome Danish Study-wide 40 G=0.70 A=0.30
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 2 NC_000002.12:g.31343258G>A
GRCh37.p13 chr 2 NC_000002.11:g.31566124G>A
XDH RefSeqGene NG_008871.2:g.76488C>T
Gene: XDH, xanthine dehydrogenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
XDH transcript NM_000379.4:c.3405-961C>T N/A Intron Variant
XDH transcript variant X1 XM_011533095.3:c.3402-961…

XM_011533095.3:c.3402-961C>T

N/A Intron Variant
XDH transcript variant X2 XM_011533096.3:c. N/A Genic Downstream Transcript Variant
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
GRCh38.p14 chr 2 NC_000002.12:g.31343258= NC_000002.12:g.31343258G>A
GRCh37.p13 chr 2 NC_000002.11:g.31566124= NC_000002.11:g.31566124G>A
XDH RefSeqGene NG_008871.2:g.76488= NG_008871.2:g.76488C>T
XDH transcript NM_000379.3:c.3405-961= NM_000379.3:c.3405-961C>T
XDH transcript NM_000379.4:c.3405-961= NM_000379.4:c.3405-961C>T
XDH transcript variant X1 XM_011533095.3:c.3402-961= XM_011533095.3:c.3402-961C>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#.

73 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss226090 Jul 12, 2000 (79)
2 SC_JCM ss831397 Aug 11, 2000 (87)
3 KWOK ss1050108 Oct 04, 2000 (86)
4 KWOK ss1969386 Oct 18, 2000 (87)
5 BCM_SSAHASNP ss9916201 Jul 11, 2003 (116)
6 CSHL-HAPMAP ss20086122 Feb 27, 2004 (120)
7 ILLUMINA ss75248658 Dec 07, 2007 (129)
8 BCMHGSC_JDW ss91106100 Mar 24, 2008 (129)
9 1000GENOMES ss109375077 Jan 24, 2009 (130)
10 KRIBB_YJKIM ss119342611 Dec 01, 2009 (131)
11 GMI ss156866126 Dec 01, 2009 (131)
12 ILLUMINA ss160402875 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss164105116 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss166363259 Jul 04, 2010 (132)
15 ILLUMINA ss172680001 Jul 04, 2010 (132)
16 BUSHMAN ss200228476 Jul 04, 2010 (132)
17 1000GENOMES ss219150969 Jul 14, 2010 (132)
18 1000GENOMES ss231097832 Jul 14, 2010 (132)
19 1000GENOMES ss238668929 Jul 15, 2010 (132)
20 GMI ss276404830 May 04, 2012 (137)
21 GMI ss284317516 Apr 25, 2013 (138)
22 ILLUMINA ss480828504 Sep 08, 2015 (146)
23 TISHKOFF ss555451708 Apr 25, 2013 (138)
24 SSMP ss649032308 Apr 25, 2013 (138)
25 EVA-GONL ss976644129 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1068975208 Aug 21, 2014 (142)
27 1000GENOMES ss1296511082 Aug 21, 2014 (142)
28 DDI ss1428523471 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1578803012 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1603130804 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1646124837 Apr 01, 2015 (144)
32 EVA_SVP ss1712442622 Apr 01, 2015 (144)
33 HAMMER_LAB ss1796499102 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1919877238 Feb 12, 2016 (147)
35 GENOMED ss1968728711 Jul 19, 2016 (147)
36 JJLAB ss2020468020 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148512014 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2228767594 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624748326 Nov 08, 2017 (151)
40 GRF ss2703073625 Nov 08, 2017 (151)
41 GNOMAD ss2771419786 Nov 08, 2017 (151)
42 SWEGEN ss2989217919 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3024000571 Nov 08, 2017 (151)
44 CSHL ss3344143597 Nov 08, 2017 (151)
45 ILLUMINA ss3636444401 Oct 11, 2018 (152)
46 ILLUMINA ss3638250763 Oct 11, 2018 (152)
47 ILLUMINA ss3643221625 Oct 11, 2018 (152)
48 EGCUT_WGS ss3657174645 Jul 13, 2019 (153)
49 EVA_DECODE ss3703545058 Jul 13, 2019 (153)
50 ACPOP ss3728281270 Jul 13, 2019 (153)
51 EVA ss3756540149 Jul 13, 2019 (153)
52 PACBIO ss3783819019 Jul 13, 2019 (153)
53 PACBIO ss3789413811 Jul 13, 2019 (153)
54 PACBIO ss3794286586 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3800918407 Jul 13, 2019 (153)
56 EVA ss3826895277 Apr 25, 2020 (154)
57 EVA ss3836855443 Apr 25, 2020 (154)
58 EVA ss3842270163 Apr 25, 2020 (154)
59 SGDP_PRJ ss3851901695 Apr 25, 2020 (154)
60 KRGDB ss3897321048 Apr 25, 2020 (154)
61 KOGIC ss3947411610 Apr 25, 2020 (154)
62 EVA ss4016987475 Apr 26, 2021 (155)
63 TOPMED ss4499356680 Apr 26, 2021 (155)
64 TOMMO_GENOMICS ss5150545221 Apr 26, 2021 (155)
65 1000G_HIGH_COVERAGE ss5247437574 Oct 17, 2022 (156)
66 1000G_HIGH_COVERAGE ss5522325440 Oct 17, 2022 (156)
67 SANFORD_IMAGENETICS ss5628389004 Oct 17, 2022 (156)
68 TOMMO_GENOMICS ss5678933289 Oct 17, 2022 (156)
69 YY_MCH ss5802052205 Oct 17, 2022 (156)
70 EVA ss5819857219 Oct 17, 2022 (156)
71 EVA ss5852451502 Oct 17, 2022 (156)
72 EVA ss5929636332 Oct 17, 2022 (156)
73 EVA ss5954595799 Oct 17, 2022 (156)
74 1000Genomes NC_000002.11 - 31566124 Oct 11, 2018 (152)
75 1000Genomes_30x NC_000002.12 - 31343258 Oct 17, 2022 (156)
76 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 31566124 Oct 11, 2018 (152)
77 Genetic variation in the Estonian population NC_000002.11 - 31566124 Oct 11, 2018 (152)
78 The Danish reference pan genome NC_000002.11 - 31566124 Apr 25, 2020 (154)
79 gnomAD - Genomes NC_000002.12 - 31343258 Apr 26, 2021 (155)
80 HapMap NC_000002.12 - 31343258 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000002.11 - 31566124 Apr 25, 2020 (154)
82 Korean Genome Project NC_000002.12 - 31343258 Apr 25, 2020 (154)
83 Northern Sweden NC_000002.11 - 31566124 Jul 13, 2019 (153)
84 Qatari NC_000002.11 - 31566124 Apr 25, 2020 (154)
85 SGDP_PRJ NC_000002.11 - 31566124 Apr 25, 2020 (154)
86 Siberian NC_000002.11 - 31566124 Apr 25, 2020 (154)
87 8.3KJPN NC_000002.11 - 31566124 Apr 26, 2021 (155)
88 14KJPN NC_000002.12 - 31343258 Oct 17, 2022 (156)
89 TopMed NC_000002.12 - 31343258 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000002.11 - 31566124 Oct 11, 2018 (152)
91 ALFA NC_000002.12 - 31343258 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)
rs658280 Oct 23, 2000 (87)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91106100, ss109375077, ss164105116, ss166363259, ss200228476, ss276404830, ss284317516, ss1712442622, ss3643221625 NC_000002.10:31419627:G:A NC_000002.12:31343257:G:A (self)
7433203, 4128597, 2912893, 4978513, 4498442, 1566135, 1919168, 3918675, 1028368, 8514528, 4128597, ss219150969, ss231097832, ss238668929, ss480828504, ss555451708, ss649032308, ss976644129, ss1068975208, ss1296511082, ss1428523471, ss1578803012, ss1603130804, ss1646124837, ss1796499102, ss1919877238, ss1968728711, ss2020468020, ss2148512014, ss2624748326, ss2703073625, ss2771419786, ss2989217919, ss3344143597, ss3636444401, ss3638250763, ss3657174645, ss3728281270, ss3756540149, ss3783819019, ss3789413811, ss3794286586, ss3826895277, ss3836855443, ss3851901695, ss3897321048, ss4016987475, ss5150545221, ss5628389004, ss5819857219, ss5954595799 NC_000002.11:31566123:G:A NC_000002.12:31343257:G:A (self)
9851375, 52789072, 1764384, 3789611, 12770393, 303179559, 14182623225, ss2228767594, ss3024000571, ss3703545058, ss3800918407, ss3842270163, ss3947411610, ss4499356680, ss5247437574, ss5522325440, ss5678933289, ss5802052205, ss5852451502, ss5929636332 NC_000002.12:31343257:G:A NC_000002.12:31343257:G:A (self)
ss9916201 NT_022184.12:10382056:G:A NC_000002.12:31343257:G:A (self)
ss20086122 NT_022184.13:10382056:G:A NC_000002.12:31343257:G:A (self)
ss226090, ss831397, ss1050108, ss1969386, ss75248658, ss119342611, ss156866126, ss160402875, ss172680001 NT_022184.15:10388010:G:A NC_000002.12:31343257:G:A (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 rs169596

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