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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.

rs10925290

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:237010955 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.098942 (26189/264690, TOPMED)
A=0.040619 (4981/122628, ALFA)
T=0.1052 (527/5008, 1000G) (+ 11 more)
T=0.0429 (192/4480, Estonian)
A=0.3113 (912/2930, KOREAN)
A=0.2280 (363/1592, HapMap)
A=0.0685 (77/1124, Daghestan)
T=0.033 (33/998, GoNL)
T=0.070 (42/600, NorthernSweden)
A=0.014 (3/212, Qatari)
A=0.330 (60/182, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)
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 1 NC_000001.11:g.237010955C>A
GRCh38.p13 chr 1 NC_000001.11:g.237010955C>G
GRCh38.p13 chr 1 NC_000001.11:g.237010955C>T
GRCh37.p13 chr 1 NC_000001.10:g.237174255C>A
GRCh37.p13 chr 1 NC_000001.10:g.237174255C>G
GRCh37.p13 chr 1 NC_000001.10:g.237174255C>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 122628 C=0.957824 A=0.040619, T=0.001558
European Sub 111298 C=0.963701 A=0.034592, T=0.001707
African Sub 4728 C=0.8589 A=0.1411, T=0.0000
African Others Sub 180 C=0.806 A=0.194, T=0.000
African American Sub 4548 C=0.8610 A=0.1390, T=0.0000
Asian Sub 262 C=0.740 A=0.260, T=0.000
East Asian Sub 176 C=0.693 A=0.307, T=0.000
Other Asian Sub 86 C=0.84 A=0.16, T=0.00
Latin American 1 Sub 620 C=0.932 A=0.068, T=0.000
Latin American 2 Sub 1954 C=0.9611 A=0.0389, T=0.0000
South Asian Sub 132 C=0.955 A=0.045, T=0.000
Other Sub 3634 C=0.9249 A=0.0748, T=0.0003


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 C=0.901058 T=0.098942
1000Genomes Global Study-wide 5008 C=0.8093 A=0.0855, T=0.1052
1000Genomes African Sub 1322 C=0.7277 A=0.0015, T=0.2708
1000Genomes East Asian Sub 1008 C=0.6607 A=0.3026, T=0.0367
1000Genomes Europe Sub 1006 C=0.9652 A=0.0000, T=0.0348
1000Genomes South Asian Sub 978 C=0.850 A=0.080, T=0.071
1000Genomes American Sub 694 C=0.898 A=0.062, T=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9571 T=0.0429
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6379 A=0.3113, G=0.0000, T=0.0509
HapMap Global Study-wide 1592 C=0.7720 A=0.2280
HapMap American Sub 766 C=0.825 A=0.175
HapMap African Sub 400 C=0.688 A=0.312
HapMap Asian Sub 254 C=0.606 A=0.394
HapMap Europe Sub 172 C=0.977 A=0.023
Genome-wide autozygosity in Daghestan Global Study-wide 1124 C=0.9315 A=0.0685
Genome-wide autozygosity in Daghestan Daghestan Sub 620 C=0.950 A=0.050
Genome-wide autozygosity in Daghestan Near_East Sub 140 C=0.879 A=0.121
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.893 A=0.107
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.954 A=0.046
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.90 A=0.10
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.97 A=0.03
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.967 T=0.033
Northern Sweden ACPOP Study-wide 600 C=0.930 T=0.070
Qatari Global Study-wide 212 C=0.986 A=0.014
SGDP_PRJ Global Study-wide 182 C=0.385 A=0.330, T=0.286
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
Siberian Global Study-wide 8 C=0.5 T=0.5
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 C= A G T
GRCh38.p13 chr 1 NC_000001.11:g.237010955= NC_000001.11:g.237010955C>A NC_000001.11:g.237010955C>G NC_000001.11:g.237010955C>T
GRCh37.p13 chr 1 NC_000001.10:g.237174255= NC_000001.10:g.237174255C>A NC_000001.10:g.237174255C>G NC_000001.10:g.237174255C>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#.

81 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069706 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss19829354 Feb 27, 2004 (120)
3 ABI ss41146457 Mar 13, 2006 (126)
4 ILLUMINA ss75089362 Dec 06, 2007 (129)
5 1000GENOMES ss111988383 Jan 25, 2009 (130)
6 KRIBB_YJKIM ss119651593 Dec 01, 2009 (131)
7 GMI ss156461624 Dec 01, 2009 (131)
8 ILLUMINA ss159939157 Dec 01, 2009 (131)
9 ENSEMBL ss161232636 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss165475885 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss167573296 Jul 04, 2010 (132)
12 ILLUMINA ss170759959 Jul 04, 2010 (132)
13 BUSHMAN ss199795296 Jul 04, 2010 (132)
14 1000GENOMES ss218960243 Jul 14, 2010 (132)
15 1000GENOMES ss230961148 Jul 14, 2010 (132)
16 1000GENOMES ss238563961 Jul 15, 2010 (132)
17 GMI ss276276007 May 04, 2012 (137)
18 ILLUMINA ss479405813 May 04, 2012 (137)
19 ILLUMINA ss479409162 May 04, 2012 (137)
20 ILLUMINA ss479822707 Sep 08, 2015 (146)
21 ILLUMINA ss484502851 May 04, 2012 (137)
22 ILLUMINA ss536653871 Sep 08, 2015 (146)
23 TISHKOFF ss555232093 Apr 25, 2013 (138)
24 ILLUMINA ss778370828 Sep 08, 2015 (146)
25 ILLUMINA ss782697984 Sep 08, 2015 (146)
26 ILLUMINA ss783666071 Sep 08, 2015 (146)
27 ILLUMINA ss831949081 Sep 08, 2015 (146)
28 ILLUMINA ss833825700 Sep 08, 2015 (146)
29 EVA-GONL ss976297131 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1068716844 Aug 21, 2014 (142)
31 1000GENOMES ss1295217937 Aug 21, 2014 (142)
32 1000GENOMES ss1295217938 Aug 21, 2014 (142)
33 HAMMER_LAB ss1397276903 Sep 08, 2015 (146)
34 DDI ss1426156124 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1574777429 Apr 01, 2015 (144)
36 EVA_DECODE ss1585699028 Apr 01, 2015 (144)
37 EVA_DECODE ss1585699029 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1602444645 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1602444646 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1645438678 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1645438679 Apr 01, 2015 (144)
42 EVA_SVP ss1712417118 Apr 01, 2015 (144)
43 ILLUMINA ss1751907340 Sep 08, 2015 (146)
44 HAMMER_LAB ss1795946712 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1919518554 Feb 12, 2016 (147)
46 GENOMED ss1967009256 Jul 19, 2016 (147)
47 USC_VALOUEV ss2148323098 Nov 08, 2017 (151)
48 HUMAN_LONGEVITY ss2171255305 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624656048 Nov 08, 2017 (151)
50 ILLUMINA ss2632648468 Nov 08, 2017 (151)
51 GRF ss2698325717 Nov 08, 2017 (151)
52 GNOMAD ss2767818103 Nov 08, 2017 (151)
53 SWEGEN ss2988686804 Nov 08, 2017 (151)
54 SWEGEN ss2988686805 Nov 08, 2017 (151)
55 TOPMED ss3107059423 Nov 08, 2017 (151)
56 TOPMED ss3107059424 Nov 08, 2017 (151)
57 ILLUMINA ss3626342818 Oct 11, 2018 (152)
58 ILLUMINA ss3630677369 Oct 11, 2018 (152)
59 ILLUMINA ss3632931009 Oct 11, 2018 (152)
60 ILLUMINA ss3633627327 Oct 11, 2018 (152)
61 ILLUMINA ss3634380780 Oct 11, 2018 (152)
62 ILLUMINA ss3635320300 Oct 11, 2018 (152)
63 ILLUMINA ss3636059736 Oct 11, 2018 (152)
64 ILLUMINA ss3637070856 Oct 11, 2018 (152)
65 ILLUMINA ss3637822877 Oct 11, 2018 (152)
66 ILLUMINA ss3640088133 Oct 11, 2018 (152)
67 ILLUMINA ss3642828465 Oct 11, 2018 (152)
68 EGCUT_WGS ss3656645704 Jul 12, 2019 (153)
69 EVA_DECODE ss3688913250 Jul 12, 2019 (153)
70 EVA_DECODE ss3688913251 Jul 12, 2019 (153)
71 ACPOP ss3727989011 Jul 12, 2019 (153)
72 ILLUMINA ss3744681687 Jul 12, 2019 (153)
73 EVA ss3747515717 Jul 12, 2019 (153)
74 ILLUMINA ss3772182461 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3800518068 Jul 12, 2019 (153)
76 KHV_HUMAN_GENOMES ss3800518069 Jul 12, 2019 (153)
77 SGDP_PRJ ss3851196391 Apr 25, 2020 (154)
78 KRGDB ss3896553290 Apr 25, 2020 (154)
79 TOPMED ss4488500617 Apr 25, 2021 (155)
80 TOMMO_GENOMICS ss5149085123 Apr 25, 2021 (155)
81 TOMMO_GENOMICS ss5149085124 Apr 25, 2021 (155)
82 1000Genomes NC_000001.10 - 237174255 Oct 11, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 3374376 (NC_000001.10:237174254:C:C 3726/3854, NC_000001.10:237174254:C:T 128/3854)
Row 3374377 (NC_000001.10:237174254:C:C 3847/3854, NC_000001.10:237174254:C:A 7/3854)

- Oct 11, 2018 (152)
84 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 3374376 (NC_000001.10:237174254:C:C 3726/3854, NC_000001.10:237174254:C:T 128/3854)
Row 3374377 (NC_000001.10:237174254:C:C 3847/3854, NC_000001.10:237174254:C:A 7/3854)

- Oct 11, 2018 (152)
85 Genome-wide autozygosity in Daghestan NC_000001.9 - 235240878 Apr 25, 2020 (154)
86 Genetic variation in the Estonian population NC_000001.10 - 237174255 Oct 11, 2018 (152)
87 The Danish reference pan genome NC_000001.10 - 237174255 Apr 25, 2020 (154)
88 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 43652368 (NC_000001.11:237010954:C:A 1691/140124)
Row 43652369 (NC_000001.11:237010954:C:T 13396/140104)

- Apr 25, 2021 (155)
89 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 43652368 (NC_000001.11:237010954:C:A 1691/140124)
Row 43652369 (NC_000001.11:237010954:C:T 13396/140104)

- Apr 25, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000001.10 - 237174255 Apr 25, 2020 (154)
91 HapMap NC_000001.11 - 237010955 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000001.10 - 237174255 Apr 25, 2020 (154)
93 Northern Sweden NC_000001.10 - 237174255 Jul 12, 2019 (153)
94 Qatari NC_000001.10 - 237174255 Apr 25, 2020 (154)
95 SGDP_PRJ NC_000001.10 - 237174255 Apr 25, 2020 (154)
96 Siberian NC_000001.10 - 237174255 Apr 25, 2020 (154)
97 8.3KJPN

Submission ignored due to conflicting rows:
Row 7054430 (NC_000001.10:237174254:C:A 6227/16760)
Row 7054431 (NC_000001.10:237174254:C:T 711/16760)

- Apr 25, 2021 (155)
98 8.3KJPN

Submission ignored due to conflicting rows:
Row 7054430 (NC_000001.10:237174254:C:A 6227/16760)
Row 7054431 (NC_000001.10:237174254:C:T 711/16760)

- Apr 25, 2021 (155)
99 TopMed NC_000001.11 - 237010955 Apr 25, 2021 (155)
100 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 3374376 (NC_000001.10:237174254:C:C 3579/3708, NC_000001.10:237174254:C:T 129/3708)
Row 3374377 (NC_000001.10:237174254:C:C 3704/3708, NC_000001.10:237174254:C:A 4/3708)

- Oct 11, 2018 (152)
101 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 3374376 (NC_000001.10:237174254:C:C 3579/3708, NC_000001.10:237174254:C:T 129/3708)
Row 3374377 (NC_000001.10:237174254:C:C 3704/3708, NC_000001.10:237174254:C:A 4/3708)

- Oct 11, 2018 (152)
102 A Vietnamese Genetic Variation Database

Submission ignored due to conflicting rows:
Row 734432 (NC_000001.10:237174254:C:C 154/163, NC_000001.10:237174254:C:T 9/163)
Row 734433 (NC_000001.10:237174254:C:C 154/207, NC_000001.10:237174254:C:A 53/207)

- Jul 12, 2019 (153)
103 A Vietnamese Genetic Variation Database

Submission ignored due to conflicting rows:
Row 734432 (NC_000001.10:237174254:C:C 154/163, NC_000001.10:237174254:C:T 9/163)
Row 734433 (NC_000001.10:237174254:C:C 154/207, NC_000001.10:237174254:C:A 53/207)

- Jul 12, 2019 (153)
104 ALFA NC_000001.11 - 237010955 Apr 25, 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)
rs117019876 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
37989, ss276276007, ss479405813, ss1397276903, ss1585699028, ss1712417118, ss3642828465 NC_000001.9:235240877:C:A NC_000001.11:237010954:C:A (self)
6093468, 3730684, 1560484, 3213371, ss218960243, ss230961148, ss238563961, ss479409162, ss479822707, ss484502851, ss536653871, ss778370828, ss782697984, ss783666071, ss831949081, ss833825700, ss1068716844, ss1295217937, ss1602444646, ss1645438679, ss1751907340, ss1919518554, ss2632648468, ss2698325717, ss2767818103, ss2988686805, ss3626342818, ss3630677369, ss3632931009, ss3633627327, ss3634380780, ss3635320300, ss3636059736, ss3637070856, ss3637822877, ss3640088133, ss3744681687, ss3747515717, ss3772182461, ss3851196391, ss3896553290, ss5149085123 NC_000001.10:237174254:C:A NC_000001.11:237010954:C:A (self)
298442, 6024230634, ss2171255305, ss3107059423, ss3688913250, ss3800518069 NC_000001.11:237010954:C:A NC_000001.11:237010954:C:A (self)
ss18069706, ss19829354 NT_004836.15:1932043:C:A NC_000001.11:237010954:C:A (self)
ss41146457, ss75089362, ss119651593, ss159939157, ss161232636, ss170759959 NT_167186.1:30692033:C:A NC_000001.11:237010954:C:A (self)
3730684, ss3896553290 NC_000001.10:237174254:C:G NC_000001.11:237010954:C:G (self)
ss111988383, ss165475885, ss167573296, ss199795296, ss276276007, ss1585699029 NC_000001.9:235240877:C:T NC_000001.11:237010954:C:T (self)
6093468, 2383952, 1946280, 1476132, 3730684, 1273876, 3213371, 839452, ss218960243, ss230961148, ss238563961, ss555232093, ss976297131, ss1295217938, ss1426156124, ss1574777429, ss1602444645, ss1645438678, ss1795946712, ss1967009256, ss2148323098, ss2624656048, ss2767818103, ss2988686804, ss3656645704, ss3727989011, ss3851196391, ss3896553290, ss5149085124 NC_000001.10:237174254:C:T NC_000001.11:237010954:C:T (self)
52106952, 6024230634, ss2171255305, ss3107059424, ss3688913251, ss3800518068, ss4488500617 NC_000001.11:237010954:C:T NC_000001.11:237010954:C:T (self)
ss156461624 NT_167186.1:30692033:C:T NC_000001.11:237010954:C: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 rs10925290

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