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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.

rs12025301

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99604245 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.096267 (25481/264690, TOPMED)
G=0.121811 (17330/142270, ALFA)
G=0.095690 (13409/140130, GnomAD) (+ 15 more)
G=0.19911 (3337/16760, 8.3KJPN)
G=0.1294 (648/5008, 1000G)
G=0.0699 (313/4480, Estonian)
G=0.1331 (513/3854, ALSPAC)
G=0.1284 (476/3708, TWINSUK)
G=0.1276 (374/2930, KOREAN)
G=0.1376 (252/1832, Korea1K)
G=0.121 (121/998, GoNL)
G=0.088 (53/600, NorthernSweden)
G=0.098 (32/328, HapMap)
G=0.088 (19/216, Qatari)
G=0.229 (49/214, Vietnamese)
A=0.434 (46/106, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
A=0.4 (4/10, 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.99604245A>G
GRCh37.p13 chr 1 NC_000001.10:g.100069801A>G
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 (New)
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 142270 A=0.878189 G=0.121811
European Sub 122798 A=0.872311 G=0.127689
African Sub 5532 A=0.9588 G=0.0412
African Others Sub 208 A=0.966 G=0.034
African American Sub 5324 A=0.9585 G=0.0415
Asian Sub 622 A=0.772 G=0.228
East Asian Sub 490 A=0.773 G=0.227
Other Asian Sub 132 A=0.765 G=0.235
Latin American 1 Sub 738 A=0.901 G=0.099
Latin American 2 Sub 6266 A=0.9250 G=0.0750
South Asian Sub 184 A=0.788 G=0.212
Other Sub 6130 A=0.8861 G=0.1139


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=0.903733 G=0.096267
gnomAD - Genomes Global Study-wide 140130 A=0.904310 G=0.095690
gnomAD - Genomes European Sub 75894 A=0.87923 G=0.12077
gnomAD - Genomes African Sub 42004 A=0.95565 G=0.04435
gnomAD - Genomes American Sub 13642 A=0.91321 G=0.08679
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.8981 G=0.1019
gnomAD - Genomes East Asian Sub 3130 A=0.8013 G=0.1987
gnomAD - Genomes Other Sub 2144 A=0.8899 G=0.1101
8.3KJPN JAPANESE Study-wide 16760 A=0.80089 G=0.19911
1000Genomes Global Study-wide 5008 A=0.8706 G=0.1294
1000Genomes African Sub 1322 A=0.9713 G=0.0287
1000Genomes East Asian Sub 1008 A=0.7817 G=0.2183
1000Genomes Europe Sub 1006 A=0.8648 G=0.1352
1000Genomes South Asian Sub 978 A=0.789 G=0.211
1000Genomes American Sub 694 A=0.931 G=0.069
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9301 G=0.0699
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8669 G=0.1331
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8716 G=0.1284
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.8724 G=0.1276
Korean Genome Project KOREAN Study-wide 1832 A=0.8624 G=0.1376
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.879 G=0.121
Northern Sweden ACPOP Study-wide 600 A=0.912 G=0.088
HapMap Global Study-wide 328 A=0.902 G=0.098
HapMap American Sub 120 A=0.900 G=0.100
HapMap African Sub 118 A=0.975 G=0.025
HapMap Asian Sub 90 A=0.81 G=0.19
Qatari Global Study-wide 216 A=0.912 G=0.088
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.771 G=0.229
SGDP_PRJ Global Study-wide 106 A=0.434 G=0.566
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
Siberian Global Study-wide 10 A=0.4 G=0.6
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= G
GRCh38.p13 chr 1 NC_000001.11:g.99604245= NC_000001.11:g.99604245A>G
GRCh37.p13 chr 1 NC_000001.10:g.100069801= NC_000001.10:g.100069801A>G
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 SC_SNP ss18076956 Feb 28, 2004 (120)
2 ABI ss44096708 Mar 13, 2006 (126)
3 PERLEGEN ss68775409 May 17, 2007 (127)
4 HUMANGENOME_JCVI ss99232665 Feb 06, 2009 (130)
5 1000GENOMES ss108453827 Jan 23, 2009 (130)
6 ENSEMBL ss143245561 Dec 01, 2009 (131)
7 ILLUMINA ss160026899 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss164869440 Jul 04, 2010 (132)
9 1000GENOMES ss230656796 Jul 14, 2010 (132)
10 1000GENOMES ss238323760 Jul 15, 2010 (132)
11 GMI ss275945371 May 04, 2012 (137)
12 PJP ss290580530 May 09, 2011 (134)
13 ILLUMINA ss479654248 May 04, 2012 (137)
14 ILLUMINA ss479659559 May 04, 2012 (137)
15 ILLUMINA ss480173433 Sep 08, 2015 (146)
16 ILLUMINA ss484625773 May 04, 2012 (137)
17 ILLUMINA ss536747487 Sep 08, 2015 (146)
18 TISHKOFF ss554480782 Apr 25, 2013 (138)
19 SSMP ss648254038 Apr 25, 2013 (138)
20 ILLUMINA ss778772444 Aug 21, 2014 (142)
21 ILLUMINA ss782759700 Aug 21, 2014 (142)
22 ILLUMINA ss783726164 Aug 21, 2014 (142)
23 ILLUMINA ss832011940 Apr 01, 2015 (144)
24 ILLUMINA ss834232309 Aug 21, 2014 (142)
25 EVA-GONL ss975483146 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1068127813 Aug 21, 2014 (142)
27 1000GENOMES ss1292108270 Aug 21, 2014 (142)
28 EVA_GENOME_DK ss1574271730 Apr 01, 2015 (144)
29 EVA_DECODE ss1584861454 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1600817285 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1643811318 Apr 01, 2015 (144)
32 ILLUMINA ss1751859122 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1918682734 Feb 12, 2016 (147)
34 JJLAB ss2019862884 Sep 14, 2016 (149)
35 USC_VALOUEV ss2147881582 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2165032407 Dec 20, 2016 (150)
37 TOPMED ss2327383183 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624442853 Nov 08, 2017 (151)
39 ILLUMINA ss2632553641 Nov 08, 2017 (151)
40 GRF ss2697808921 Nov 08, 2017 (151)
41 GNOMAD ss2758639420 Nov 08, 2017 (151)
42 SWEGEN ss2987305895 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023695033 Nov 08, 2017 (151)
44 TOPMED ss3084653824 Nov 08, 2017 (151)
45 CSHL ss3343596003 Nov 08, 2017 (151)
46 ILLUMINA ss3626165317 Oct 11, 2018 (152)
47 ILLUMINA ss3630587817 Oct 11, 2018 (152)
48 ILLUMINA ss3632903292 Oct 11, 2018 (152)
49 ILLUMINA ss3633598290 Oct 11, 2018 (152)
50 ILLUMINA ss3634339264 Oct 11, 2018 (152)
51 ILLUMINA ss3635291900 Oct 11, 2018 (152)
52 ILLUMINA ss3636016819 Oct 11, 2018 (152)
53 ILLUMINA ss3637042356 Oct 11, 2018 (152)
54 ILLUMINA ss3640046624 Oct 11, 2018 (152)
55 ILLUMINA ss3640984525 Oct 11, 2018 (152)
56 ILLUMINA ss3641278513 Oct 11, 2018 (152)
57 URBANLAB ss3646731489 Oct 11, 2018 (152)
58 EGCUT_WGS ss3655391011 Jul 12, 2019 (153)
59 EVA_DECODE ss3687367416 Jul 12, 2019 (153)
60 ACPOP ss3727314207 Jul 12, 2019 (153)
61 ILLUMINA ss3744640233 Jul 12, 2019 (153)
62 EVA ss3746574307 Jul 12, 2019 (153)
63 ILLUMINA ss3772141470 Jul 12, 2019 (153)
64 KHV_HUMAN_GENOMES ss3799575071 Jul 12, 2019 (153)
65 EVA ss3826326665 Apr 25, 2020 (154)
66 EVA ss3836553609 Apr 25, 2020 (154)
67 EVA ss3841961605 Apr 25, 2020 (154)
68 SGDP_PRJ ss3849477871 Apr 25, 2020 (154)
69 KRGDB ss3894555943 Apr 25, 2020 (154)
70 KOGIC ss3945091609 Apr 25, 2020 (154)
71 EVA ss4016927701 Apr 25, 2021 (155)
72 TOPMED ss4460703112 Apr 25, 2021 (155)
73 TOMMO_GENOMICS ss5145313895 Apr 25, 2021 (155)
74 1000Genomes NC_000001.10 - 100069801 Oct 11, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100069801 Oct 11, 2018 (152)
76 Genetic variation in the Estonian population NC_000001.10 - 100069801 Oct 11, 2018 (152)
77 The Danish reference pan genome NC_000001.10 - 100069801 Apr 25, 2020 (154)
78 gnomAD - Genomes NC_000001.11 - 99604245 Apr 25, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000001.10 - 100069801 Apr 25, 2020 (154)
80 HapMap NC_000001.11 - 99604245 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000001.10 - 100069801 Apr 25, 2020 (154)
82 Korean Genome Project NC_000001.11 - 99604245 Apr 25, 2020 (154)
83 Northern Sweden NC_000001.10 - 100069801 Jul 12, 2019 (153)
84 Qatari NC_000001.10 - 100069801 Apr 25, 2020 (154)
85 SGDP_PRJ NC_000001.10 - 100069801 Apr 25, 2020 (154)
86 Siberian NC_000001.10 - 100069801 Apr 25, 2020 (154)
87 8.3KJPN NC_000001.10 - 100069801 Apr 25, 2021 (155)
88 TopMed NC_000001.11 - 99604245 Apr 25, 2021 (155)
89 UK 10K study - Twins NC_000001.10 - 100069801 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000001.10 - 100069801 Jul 12, 2019 (153)
91 ALFA NC_000001.11 - 99604245 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108453827, ss160026899, ss164869440, ss275945371, ss290580530, ss479654248, ss1584861454 NC_000001.9:99842388:A:G NC_000001.11:99604244:A:G (self)
2871857, 1584240, 1129259, 1629014, 687240, 1733337, 599072, 724664, 1494851, 397936, 3283202, 1584240, 341270, ss230656796, ss238323760, ss479659559, ss480173433, ss484625773, ss536747487, ss554480782, ss648254038, ss778772444, ss782759700, ss783726164, ss832011940, ss834232309, ss975483146, ss1068127813, ss1292108270, ss1574271730, ss1600817285, ss1643811318, ss1751859122, ss1918682734, ss2019862884, ss2147881582, ss2327383183, ss2624442853, ss2632553641, ss2697808921, ss2758639420, ss2987305895, ss3343596003, ss3626165317, ss3630587817, ss3632903292, ss3633598290, ss3634339264, ss3635291900, ss3636016819, ss3637042356, ss3640046624, ss3640984525, ss3641278513, ss3655391011, ss3727314207, ss3744640233, ss3746574307, ss3772141470, ss3826326665, ss3836553609, ss3849477871, ss3894555943, ss4016927701, ss5145313895 NC_000001.10:100069800:A:G NC_000001.11:99604244:A:G (self)
20301181, 136605, 1469610, 15310780, 24309447, 12544884619, ss2165032407, ss3023695033, ss3084653824, ss3646731489, ss3687367416, ss3799575071, ss3841961605, ss3945091609, ss4460703112 NC_000001.11:99604244:A:G NC_000001.11:99604244:A:G (self)
ss18076956 NT_028050.13:8258744:A:G NC_000001.11:99604244:A:G (self)
ss44096708, ss68775409, ss99232665, ss143245561 NT_032977.9:70041718:A:G NC_000001.11:99604244:A:G (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 rs12025301

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