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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.

rs1538925

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:28561157 (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>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.318032 (84180/264690, TOPMED)
A=0.243553 (32792/134640, ALFA)
A=0.06331 (1061/16760, 8.3KJPN) (+ 15 more)
A=0.2939 (1472/5008, 1000G)
A=0.2719 (1218/4480, Estonian)
A=0.2148 (828/3854, ALSPAC)
A=0.2238 (830/3708, TWINSUK)
A=0.1014 (297/2930, KOREAN)
A=0.1059 (194/1832, Korea1K)
A=0.2218 (252/1136, Daghestan)
A=0.224 (224/998, GoNL)
A=0.277 (166/600, NorthernSweden)
A=0.167 (83/498, SGDP_PRJ)
A=0.264 (57/216, Qatari)
A=0.103 (22/214, Vietnamese)
A=0.160 (33/206, HapMap)
A=0.17 (9/54, Siberian)
A=0.33 (13/40, GENOME_DK)
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 13 NC_000013.11:g.28561157A>C
GRCh38.p13 chr 13 NC_000013.11:g.28561157A>T
GRCh37.p13 chr 13 NC_000013.10:g.29135294A>C
GRCh37.p13 chr 13 NC_000013.10:g.29135294A>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 134640 A=0.243553 C=0.756447, T=0.000000
European Sub 115672 A=0.223892 C=0.776108, T=0.000000
African Sub 6452 A=0.5586 C=0.4414, T=0.0000
African Others Sub 240 A=0.696 C=0.304, T=0.000
African American Sub 6212 A=0.5533 C=0.4467, T=0.0000
Asian Sub 514 A=0.111 C=0.889, T=0.000
East Asian Sub 406 A=0.103 C=0.897, T=0.000
Other Asian Sub 108 A=0.139 C=0.861, T=0.000
Latin American 1 Sub 602 A=0.336 C=0.664, T=0.000
Latin American 2 Sub 5600 A=0.2879 C=0.7121, T=0.0000
South Asian Sub 102 A=0.265 C=0.735, T=0.000
Other Sub 5698 A=0.2443 C=0.7557, 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=0.318032 C=0.681968
8.3KJPN JAPANESE Study-wide 16760 A=0.06331 C=0.93669
1000Genomes Global Study-wide 5008 A=0.2939 C=0.7061
1000Genomes African Sub 1322 A=0.5832 C=0.4168
1000Genomes East Asian Sub 1008 A=0.0893 C=0.9107
1000Genomes Europe Sub 1006 A=0.2416 C=0.7584
1000Genomes South Asian Sub 978 A=0.190 C=0.810
1000Genomes American Sub 694 A=0.262 C=0.738
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2719 C=0.7281
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2148 C=0.7852
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2238 C=0.7762
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1014 C=0.8986, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.1059 C=0.8941
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.2218 C=0.7782
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.197 C=0.803
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.264 C=0.736
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.230 C=0.770
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.250 C=0.750
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.30 C=0.70
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.17 C=0.83
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.224 C=0.776
Northern Sweden ACPOP Study-wide 600 A=0.277 C=0.723
SGDP_PRJ Global Study-wide 498 A=0.167 C=0.833
Qatari Global Study-wide 216 A=0.264 C=0.736
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.103 C=0.897
HapMap Global Study-wide 206 A=0.160 C=0.840
HapMap American Sub 116 A=0.250 C=0.750
HapMap Asian Sub 90 A=0.04 C=0.96
Siberian Global Study-wide 54 A=0.17 C=0.83
The Danish reference pan genome Danish Study-wide 40 A=0.33 C=0.68
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= C T
GRCh38.p13 chr 13 NC_000013.11:g.28561157= NC_000013.11:g.28561157A>C NC_000013.11:g.28561157A>T
GRCh37.p13 chr 13 NC_000013.10:g.29135294= NC_000013.10:g.29135294A>C NC_000013.10:g.29135294A>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#.

93 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2380521 Oct 23, 2000 (88)
2 BCM_SSAHASNP ss11066577 Jul 11, 2003 (116)
3 SC_SNP ss13254266 Dec 05, 2003 (119)
4 BCM_SSAHASNP ss14156936 Dec 05, 2003 (119)
5 SSAHASNP ss21104337 Apr 05, 2004 (121)
6 ABI ss43462710 Mar 15, 2006 (126)
7 HGSV ss78440054 Dec 07, 2007 (129)
8 HGSV ss83692181 Dec 15, 2007 (130)
9 HGSV ss84169955 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss89558292 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96954651 Feb 05, 2009 (130)
12 BGI ss106322346 Feb 05, 2009 (130)
13 1000GENOMES ss112646732 Jan 25, 2009 (130)
14 1000GENOMES ss114465914 Jan 25, 2009 (130)
15 ENSEMBL ss133503973 Dec 01, 2009 (131)
16 ENSEMBL ss137274237 Dec 01, 2009 (131)
17 GMI ss154582926 Dec 01, 2009 (131)
18 ILLUMINA ss160369073 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167789779 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss169069735 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss208609355 Jul 04, 2010 (132)
22 1000GENOMES ss226098905 Jul 14, 2010 (132)
23 1000GENOMES ss236190300 Jul 15, 2010 (132)
24 1000GENOMES ss242697830 Jul 15, 2010 (132)
25 BL ss254884622 May 09, 2011 (134)
26 GMI ss281652796 May 04, 2012 (137)
27 GMI ss286675157 Apr 25, 2013 (138)
28 PJP ss291564681 May 09, 2011 (134)
29 ILLUMINA ss480022599 May 04, 2012 (137)
30 ILLUMINA ss480031390 May 04, 2012 (137)
31 ILLUMINA ss480693709 Sep 08, 2015 (146)
32 ILLUMINA ss484809474 May 04, 2012 (137)
33 ILLUMINA ss536889996 Sep 08, 2015 (146)
34 TISHKOFF ss563571217 Apr 25, 2013 (138)
35 SSMP ss659167024 Apr 25, 2013 (138)
36 ILLUMINA ss778437502 Sep 08, 2015 (146)
37 ILLUMINA ss782851303 Sep 08, 2015 (146)
38 ILLUMINA ss783815836 Sep 08, 2015 (146)
39 ILLUMINA ss832105188 Sep 08, 2015 (146)
40 ILLUMINA ss833893015 Sep 08, 2015 (146)
41 EVA-GONL ss990227882 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1078963276 Aug 21, 2014 (142)
43 1000GENOMES ss1347617820 Aug 21, 2014 (142)
44 HAMMER_LAB ss1397653060 Sep 08, 2015 (146)
45 DDI ss1427140274 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1576694586 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1629956114 Apr 01, 2015 (144)
48 EVA_DECODE ss1642332485 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1672950147 Apr 01, 2015 (144)
50 ILLUMINA ss1752099375 Sep 08, 2015 (146)
51 HAMMER_LAB ss1807541464 Sep 08, 2015 (146)
52 WEILL_CORNELL_DGM ss1933596812 Feb 12, 2016 (147)
53 GENOMED ss1967743204 Jul 19, 2016 (147)
54 JJLAB ss2027554019 Sep 14, 2016 (149)
55 USC_VALOUEV ss2155918732 Dec 20, 2016 (150)
56 HUMAN_LONGEVITY ss2195098920 Dec 20, 2016 (150)
57 TOPMED ss2359199071 Dec 20, 2016 (150)
58 SYSTEMSBIOZJU ss2628265111 Nov 08, 2017 (151)
59 ILLUMINA ss2633043764 Nov 08, 2017 (151)
60 GRF ss2700290855 Nov 08, 2017 (151)
61 GNOMAD ss2917939075 Nov 08, 2017 (151)
62 SWEGEN ss3010773547 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3027592510 Nov 08, 2017 (151)
64 TOPMED ss3188770701 Nov 08, 2017 (151)
65 CSHL ss3350381680 Nov 08, 2017 (151)
66 ILLUMINA ss3627029531 Oct 12, 2018 (152)
67 ILLUMINA ss3631048009 Oct 12, 2018 (152)
68 ILLUMINA ss3633044109 Oct 12, 2018 (152)
69 ILLUMINA ss3633746225 Oct 12, 2018 (152)
70 ILLUMINA ss3634537335 Oct 12, 2018 (152)
71 ILLUMINA ss3635436447 Oct 12, 2018 (152)
72 ILLUMINA ss3636223905 Oct 12, 2018 (152)
73 ILLUMINA ss3637187502 Oct 12, 2018 (152)
74 ILLUMINA ss3640244666 Oct 12, 2018 (152)
75 URBANLAB ss3649996292 Oct 12, 2018 (152)
76 EGCUT_WGS ss3678034315 Jul 13, 2019 (153)
77 EVA_DECODE ss3694990676 Jul 13, 2019 (153)
78 ACPOP ss3739611959 Jul 13, 2019 (153)
79 ILLUMINA ss3744838069 Jul 13, 2019 (153)
80 EVA ss3751275215 Jul 13, 2019 (153)
81 ILLUMINA ss3772337184 Jul 13, 2019 (153)
82 PACBIO ss3787414110 Jul 13, 2019 (153)
83 PACBIO ss3792486792 Jul 13, 2019 (153)
84 PACBIO ss3797370509 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3816606229 Jul 13, 2019 (153)
86 EVA ss3833466611 Apr 27, 2020 (154)
87 EVA ss3840310446 Apr 27, 2020 (154)
88 EVA ss3845795183 Apr 27, 2020 (154)
89 SGDP_PRJ ss3879659824 Apr 27, 2020 (154)
90 KRGDB ss3928481116 Apr 27, 2020 (154)
91 KOGIC ss3973267206 Apr 27, 2020 (154)
92 TOPMED ss4940982373 Apr 26, 2021 (155)
93 TOMMO_GENOMICS ss5209314502 Apr 26, 2021 (155)
94 1000Genomes NC_000013.10 - 29135294 Oct 12, 2018 (152)
95 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 29135294 Oct 12, 2018 (152)
96 Genome-wide autozygosity in Daghestan NC_000013.9 - 28033294 Apr 27, 2020 (154)
97 Genetic variation in the Estonian population NC_000013.10 - 29135294 Oct 12, 2018 (152)
98 The Danish reference pan genome NC_000013.10 - 29135294 Apr 27, 2020 (154)
99 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 426371393 (NC_000013.11:28561156:A:C 95176/139906)
Row 426371394 (NC_000013.11:28561156:A:T 8/139962)

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

Submission ignored due to conflicting rows:
Row 426371393 (NC_000013.11:28561156:A:C 95176/139906)
Row 426371394 (NC_000013.11:28561156:A:T 8/139962)

- Apr 26, 2021 (155)
101 Genome of the Netherlands Release 5 NC_000013.10 - 29135294 Apr 27, 2020 (154)
102 HapMap NC_000013.11 - 28561157 Apr 27, 2020 (154)
103 KOREAN population from KRGDB NC_000013.10 - 29135294 Apr 27, 2020 (154)
104 Korean Genome Project NC_000013.11 - 28561157 Apr 27, 2020 (154)
105 Northern Sweden NC_000013.10 - 29135294 Jul 13, 2019 (153)
106 Qatari NC_000013.10 - 29135294 Apr 27, 2020 (154)
107 SGDP_PRJ NC_000013.10 - 29135294 Apr 27, 2020 (154)
108 Siberian NC_000013.10 - 29135294 Apr 27, 2020 (154)
109 8.3KJPN NC_000013.10 - 29135294 Apr 26, 2021 (155)
110 TopMed NC_000013.11 - 28561157 Apr 26, 2021 (155)
111 UK 10K study - Twins NC_000013.10 - 29135294 Oct 12, 2018 (152)
112 A Vietnamese Genetic Variation Database NC_000013.10 - 29135294 Jul 13, 2019 (153)
113 ALFA NC_000013.11 - 28561157 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)
rs59187452 May 25, 2008 (130)
rs386536414 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
123740, ss78440054, ss83692181, ss84169955, ss89558292, ss112646732, ss114465914, ss167789779, ss169069735, ss208609355, ss254884622, ss281652796, ss286675157, ss291564681, ss480022599, ss1397653060, ss1642332485 NC_000013.9:28033293:A:C NC_000013.11:28561156:A:C (self)
60466170, 33582834, 23772563, 3234191, 14984368, 35658510, 12896824, 15638742, 31676804, 8435086, 67283809, 33582834, 7449304, ss226098905, ss236190300, ss242697830, ss480031390, ss480693709, ss484809474, ss536889996, ss563571217, ss659167024, ss778437502, ss782851303, ss783815836, ss832105188, ss833893015, ss990227882, ss1078963276, ss1347617820, ss1427140274, ss1576694586, ss1629956114, ss1672950147, ss1752099375, ss1807541464, ss1933596812, ss1967743204, ss2027554019, ss2155918732, ss2359199071, ss2628265111, ss2633043764, ss2700290855, ss2917939075, ss3010773547, ss3350381680, ss3627029531, ss3631048009, ss3633044109, ss3633746225, ss3634537335, ss3635436447, ss3636223905, ss3637187502, ss3640244666, ss3678034315, ss3739611959, ss3744838069, ss3751275215, ss3772337184, ss3787414110, ss3792486792, ss3797370509, ss3833466611, ss3840310446, ss3879659824, ss3928481116, ss5209314502 NC_000013.10:29135293:A:C NC_000013.11:28561156:A:C (self)
954993, 29645207, 97882139, 156528031, 5611480182, ss2195098920, ss3027592510, ss3188770701, ss3649996292, ss3694990676, ss3816606229, ss3845795183, ss3973267206, ss4940982373 NC_000013.11:28561156:A:C NC_000013.11:28561156:A:C (self)
ss11066577, ss13254266 NT_009799.12:10115293:A:C NC_000013.11:28561156:A:C (self)
ss14156936, ss21104337 NT_024524.13:10115293:A:C NC_000013.11:28561156:A:C (self)
ss2380521, ss43462710, ss96954651, ss106322346, ss133503973, ss137274237, ss154582926, ss160369073 NT_024524.14:10115293:A:C NC_000013.11:28561156:A:C (self)
35658510, ss2917939075, ss3928481116 NC_000013.10:29135293:A:T NC_000013.11:28561156:A:T (self)
5611480182 NC_000013.11:28561156:A:T NC_000013.11:28561156:A:T
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 rs1538925

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