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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.

rs2260179

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:60780030 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.323246 (85560/264690, TOPMED)
G=0.311765 (43644/139990, GnomAD)
G=0.31810 (6009/18890, ALFA) (+ 16 more)
C=0.47530 (7966/16760, 8.3KJPN)
G=0.3654 (1830/5008, 1000G)
G=0.3321 (1488/4480, Estonian)
G=0.3168 (1221/3854, ALSPAC)
G=0.3376 (1252/3708, TWINSUK)
C=0.3962 (1161/2930, KOREAN)
G=0.3519 (665/1890, HapMap)
C=0.4061 (744/1832, Korea1K)
G=0.355 (354/998, GoNL)
G=0.362 (217/600, NorthernSweden)
G=0.058 (31/534, MGP)
C=0.330 (113/342, SGDP_PRJ)
G=0.375 (81/216, Qatari)
C=0.308 (66/214, Vietnamese)
G=0.40 (16/40, GENOME_DK)
C=0.36 (10/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDK1 : Intron Variant
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 10 NC_000010.11:g.60780030C>G
GRCh37.p13 chr 10 NC_000010.10:g.62539788C>G
CDK1 RefSeqGene NG_029877.1:g.6700C>G
Gene: CDK1, cyclin dependent kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDK1 transcript variant 4 NM_001170406.1:c.-25-111C…

NM_001170406.1:c.-25-111C>G

N/A Intron Variant
CDK1 transcript variant 5 NM_001170407.2:c.-25-111C…

NM_001170407.2:c.-25-111C>G

N/A Intron Variant
CDK1 transcript variant 6 NM_001320918.1:c.-25-111C…

NM_001320918.1:c.-25-111C>G

N/A Intron Variant
CDK1 transcript variant 1 NM_001786.5:c.-25-111C>G N/A Intron Variant
CDK1 transcript variant 2 NM_033379.5:c.-25-111C>G N/A Intron Variant
CDK1 transcript variant X1 XM_005270303.3:c.-25-111C…

XM_005270303.3:c.-25-111C>G

N/A Intron 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

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 18890 C=0.68190 G=0.31810
European Sub 14286 C=0.67857 G=0.32143
African Sub 2946 C=0.7475 G=0.2525
African Others Sub 114 C=0.693 G=0.307
African American Sub 2832 C=0.7496 G=0.2504
Asian Sub 112 C=0.348 G=0.652
East Asian Sub 86 C=0.36 G=0.64
Other Asian Sub 26 C=0.31 G=0.69
Latin American 1 Sub 146 C=0.678 G=0.322
Latin American 2 Sub 610 C=0.541 G=0.459
South Asian Sub 98 C=0.69 G=0.31
Other Sub 692 C=0.649 G=0.351


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=0.676754 G=0.323246
gnomAD - Genomes Global Study-wide 139990 C=0.688235 G=0.311765
gnomAD - Genomes European Sub 75780 C=0.67602 G=0.32398
gnomAD - Genomes African Sub 41978 C=0.74839 G=0.25161
gnomAD - Genomes American Sub 13642 C=0.62879 G=0.37121
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.7746 G=0.2254
gnomAD - Genomes East Asian Sub 3128 C=0.3584 G=0.6416
gnomAD - Genomes Other Sub 2144 C=0.6679 G=0.3321
8.3KJPN JAPANESE Study-wide 16760 C=0.47530 G=0.52470
1000Genomes Global Study-wide 5008 C=0.6346 G=0.3654
1000Genomes African Sub 1322 C=0.7844 G=0.2156
1000Genomes East Asian Sub 1008 C=0.3859 G=0.6141
1000Genomes Europe Sub 1006 C=0.6958 G=0.3042
1000Genomes South Asian Sub 978 C=0.661 G=0.339
1000Genomes American Sub 694 C=0.585 G=0.415
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6679 G=0.3321
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6832 G=0.3168
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6624 G=0.3376
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3962 G=0.6038
HapMap Global Study-wide 1890 C=0.6481 G=0.3519
HapMap American Sub 768 C=0.613 G=0.387
HapMap African Sub 692 C=0.734 G=0.266
HapMap Asian Sub 254 C=0.465 G=0.535
HapMap Europe Sub 176 C=0.727 G=0.273
Korean Genome Project KOREAN Study-wide 1832 C=0.4061 G=0.5939
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.645 G=0.355
Northern Sweden ACPOP Study-wide 600 C=0.638 G=0.362
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.942 G=0.058
SGDP_PRJ Global Study-wide 342 C=0.330 G=0.670
Qatari Global Study-wide 216 C=0.625 G=0.375
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.308 G=0.692
The Danish reference pan genome Danish Study-wide 40 C=0.60 G=0.40
Siberian Global Study-wide 28 C=0.36 G=0.64
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= G
GRCh38.p13 chr 10 NC_000010.11:g.60780030= NC_000010.11:g.60780030C>G
GRCh37.p13 chr 10 NC_000010.10:g.62539788= NC_000010.10:g.62539788C>G
CDK1 RefSeqGene NG_029877.1:g.6700= NG_029877.1:g.6700C>G
CDK1 transcript variant 4 NM_001170406.1:c.-25-111= NM_001170406.1:c.-25-111C>G
CDK1 transcript variant 5 NM_001170407.1:c.-25-111= NM_001170407.1:c.-25-111C>G
CDK1 transcript variant 5 NM_001170407.2:c.-25-111= NM_001170407.2:c.-25-111C>G
CDK1 transcript variant 6 NM_001320918.1:c.-25-111= NM_001320918.1:c.-25-111C>G
CDK1 transcript variant 1 NM_001786.4:c.-25-111= NM_001786.4:c.-25-111C>G
CDK1 transcript variant 1 NM_001786.5:c.-25-111= NM_001786.5:c.-25-111C>G
CDK1 transcript variant 2 NM_033379.4:c.-25-111= NM_033379.4:c.-25-111C>G
CDK1 transcript variant 2 NM_033379.5:c.-25-111= NM_033379.5:c.-25-111C>G
CDK1 transcript variant X1 XM_005270303.1:c.-25-111= XM_005270303.1:c.-25-111C>G
CDK1 transcript variant X1 XM_005270303.3:c.-25-111= XM_005270303.3:c.-25-111C>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#.

71 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3253821 Sep 28, 2001 (100)
2 SC_JCM ss3432074 Sep 28, 2001 (100)
3 EGP_SNPS ss4473525 Jul 03, 2002 (106)
4 SC_SNP ss12953989 Dec 05, 2003 (130)
5 ABI ss39753014 Mar 13, 2006 (126)
6 ILLUMINA ss65749642 Oct 13, 2006 (127)
7 AFFY ss66483082 Nov 29, 2006 (127)
8 AFFY ss76300902 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss81742428 Dec 15, 2007 (130)
10 HUMANGENOME_JCVI ss97654622 Feb 05, 2009 (130)
11 BGI ss102883660 Dec 01, 2009 (131)
12 1000GENOMES ss109491044 Jan 24, 2009 (130)
13 1000GENOMES ss113347897 Jan 25, 2009 (130)
14 GMI ss155112485 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss170176253 Jul 04, 2010 (132)
16 AFFY ss173181133 Jun 24, 2010 (142)
17 COMPLETE_GENOMICS ss174575057 Jul 04, 2010 (132)
18 BUSHMAN ss201594684 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss207280186 Jul 04, 2010 (132)
20 1000GENOMES ss224758399 Jul 14, 2010 (132)
21 1000GENOMES ss235199373 Jul 15, 2010 (132)
22 1000GENOMES ss241900603 Jul 15, 2010 (132)
23 BL ss254360700 May 09, 2011 (134)
24 GMI ss280640493 May 04, 2012 (137)
25 TISHKOFF ss561993096 Apr 25, 2013 (138)
26 SSMP ss656817958 Apr 25, 2013 (138)
27 EVA-GONL ss987549919 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1077032358 Aug 21, 2014 (142)
29 1000GENOMES ss1337668123 Aug 21, 2014 (142)
30 DDI ss1426339618 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1575154342 Apr 01, 2015 (144)
32 EVA_DECODE ss1597216365 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1624687047 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1667681080 Apr 01, 2015 (144)
35 EVA_MGP ss1711258348 Apr 01, 2015 (144)
36 EVA_SVP ss1713183907 Apr 01, 2015 (144)
37 HAMMER_LAB ss1806416034 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1930913846 Feb 12, 2016 (147)
39 GENOMED ss1967143013 Jul 19, 2016 (147)
40 JJLAB ss2026180176 Sep 14, 2016 (149)
41 USC_VALOUEV ss2154453317 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2175218198 Dec 20, 2016 (150)
43 TOPMED ss2338250498 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2627560463 Nov 08, 2017 (151)
45 GRF ss2698697440 Nov 08, 2017 (151)
46 GNOMAD ss2889431061 Nov 08, 2017 (151)
47 SWEGEN ss3006573006 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3026881259 Nov 08, 2017 (151)
49 TOPMED ss3121338217 Nov 08, 2017 (151)
50 CSHL ss3349150367 Nov 08, 2017 (151)
51 URBANLAB ss3649385553 Oct 12, 2018 (152)
52 EGCUT_WGS ss3673985483 Jul 13, 2019 (153)
53 EVA_DECODE ss3689992819 Jul 13, 2019 (153)
54 ACPOP ss3737373125 Jul 13, 2019 (153)
55 EVA ss3748171946 Jul 13, 2019 (153)
56 PACBIO ss3786689036 Jul 13, 2019 (153)
57 PACBIO ss3791867534 Jul 13, 2019 (153)
58 PACBIO ss3796749552 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3813547603 Jul 13, 2019 (153)
60 EVA ss3825776129 Apr 26, 2020 (154)
61 EVA ss3832155633 Apr 26, 2020 (154)
62 EVA ss3839617323 Apr 26, 2020 (154)
63 EVA ss3845089562 Apr 26, 2020 (154)
64 SGDP_PRJ ss3874329821 Apr 26, 2020 (154)
65 KRGDB ss3922399866 Apr 26, 2020 (154)
66 KOGIC ss3967992436 Apr 26, 2020 (154)
67 FSA-LAB ss3983978376 Apr 27, 2021 (155)
68 EVA ss3986485166 Apr 27, 2021 (155)
69 TOPMED ss4854407833 Apr 27, 2021 (155)
70 TOMMO_GENOMICS ss5197891625 Apr 27, 2021 (155)
71 EVA ss5237209010 Apr 27, 2021 (155)
72 1000Genomes NC_000010.10 - 62539788 Oct 12, 2018 (152)
73 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 62539788 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000010.10 - 62539788 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000010.10 - 62539788 Apr 26, 2020 (154)
76 gnomAD - Genomes NC_000010.11 - 60780030 Apr 27, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000010.10 - 62539788 Apr 26, 2020 (154)
78 HapMap NC_000010.11 - 60780030 Apr 26, 2020 (154)
79 KOREAN population from KRGDB NC_000010.10 - 62539788 Apr 26, 2020 (154)
80 Korean Genome Project NC_000010.11 - 60780030 Apr 26, 2020 (154)
81 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 62539788 Apr 26, 2020 (154)
82 Northern Sweden NC_000010.10 - 62539788 Jul 13, 2019 (153)
83 Qatari NC_000010.10 - 62539788 Apr 26, 2020 (154)
84 SGDP_PRJ NC_000010.10 - 62539788 Apr 26, 2020 (154)
85 Siberian NC_000010.10 - 62539788 Apr 26, 2020 (154)
86 8.3KJPN NC_000010.10 - 62539788 Apr 27, 2021 (155)
87 TopMed NC_000010.11 - 60780030 Apr 27, 2021 (155)
88 UK 10K study - Twins NC_000010.10 - 62539788 Oct 12, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000010.10 - 62539788 Jul 13, 2019 (153)
90 ALFA NC_000010.11 - 60780030 Apr 27, 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)
rs9414750 May 24, 2008 (130)
rs59866867 Feb 26, 2009 (130)
rs111191376 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66483082, ss76300902, ss109491044, ss113347897, ss170176253, ss173181133, ss174575057, ss201594684, ss207280186, ss254360700, ss280640493, ss1597216365, ss1713183907 NC_000010.9:62209793:C:G NC_000010.11:60780029:C:G (self)
50064489, 27786340, 19723731, 2181682, 12392326, 29577260, 374108, 10657990, 12955776, 26346801, 6969671, 55860932, 27786340, 6171236, ss224758399, ss235199373, ss241900603, ss561993096, ss656817958, ss987549919, ss1077032358, ss1337668123, ss1426339618, ss1575154342, ss1624687047, ss1667681080, ss1711258348, ss1806416034, ss1930913846, ss1967143013, ss2026180176, ss2154453317, ss2338250498, ss2627560463, ss2698697440, ss2889431061, ss3006573006, ss3349150367, ss3673985483, ss3737373125, ss3748171946, ss3786689036, ss3791867534, ss3796749552, ss3825776129, ss3832155633, ss3839617323, ss3874329821, ss3922399866, ss3983978376, ss3986485166, ss5197891625 NC_000010.10:62539787:C:G NC_000010.11:60780029:C:G (self)
353873587, 415729, 24370437, 43953235, 69953488, 13001377617, ss2175218198, ss3026881259, ss3121338217, ss3649385553, ss3689992819, ss3813547603, ss3845089562, ss3967992436, ss4854407833, ss5237209010 NC_000010.11:60780029:C:G NC_000010.11:60780029:C:G (self)
ss12953989 NT_008583.15:11090935:C:G NC_000010.11:60780029:C:G (self)
ss3253821, ss3432074, ss4473525, ss39753014, ss65749642, ss81742428, ss97654622, ss102883660, ss155112485 NT_030059.13:13344251:C:G NC_000010.11:60780029:C: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 rs2260179

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