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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.

rs2456774

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:60786556 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.256345 (67852/264690, TOPMED)
C=0.251799 (35193/139766, GnomAD)
C=0.25555 (4904/19190, ALFA) (+ 15 more)
C=0.22661 (3798/16760, 8.3KJPN)
C=0.2304 (1154/5008, 1000G)
C=0.2525 (1131/4480, Estonian)
C=0.2657 (1024/3854, ALSPAC)
C=0.2589 (960/3708, TWINSUK)
C=0.1679 (492/2930, KOREAN)
C=0.1632 (299/1832, Korea1K)
C=0.257 (256/998, GoNL)
C=0.175 (105/600, NorthernSweden)
C=0.165 (82/498, SGDP_PRJ)
C=0.273 (90/330, HapMap)
C=0.222 (48/216, Qatari)
C=0.108 (23/212, Vietnamese)
C=0.15 (8/54, Siberian)
C=0.30 (12/40, GENOME_DK)
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.60786556C>G
GRCh38.p13 chr 10 NC_000010.11:g.60786556C>T
GRCh37.p13 chr 10 NC_000010.10:g.62546314C>G
GRCh37.p13 chr 10 NC_000010.10:g.62546314C>T
CDK1 RefSeqGene NG_029877.1:g.13226C>G
CDK1 RefSeqGene NG_029877.1:g.13226C>T
Gene: CDK1, cyclin dependent kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDK1 transcript variant 6 NM_001320918.1:c.318+769C…

NM_001320918.1:c.318+769C>G

N/A Intron Variant
CDK1 transcript variant 1 NM_001786.5:c.318+769C>G N/A Intron Variant
CDK1 transcript variant 2 NM_033379.5:c.318+769C>G N/A Intron Variant
CDK1 transcript variant 4 NM_001170406.1:c.*757= N/A 3 Prime UTR Variant
CDK1 transcript variant 5 NM_001170407.2:c.*757= N/A 3 Prime UTR Variant
CDK1 transcript variant X1 XM_005270303.3:c.318+769C…

XM_005270303.3:c.318+769C>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
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 19190 C=0.25555 T=0.74445
European Sub 14286 C=0.24759 T=0.75241
African Sub 2970 C=0.3108 T=0.6892
African Others Sub 114 C=0.246 T=0.754
African American Sub 2856 C=0.3134 T=0.6866
Asian Sub 116 C=0.147 T=0.853
East Asian Sub 88 C=0.14 T=0.86
Other Asian Sub 28 C=0.18 T=0.82
Latin American 1 Sub 154 C=0.234 T=0.766
Latin American 2 Sub 616 C=0.203 T=0.797
South Asian Sub 98 C=0.19 T=0.81
Other Sub 950 C=0.260 T=0.740


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=0.256345 T=0.743655
gnomAD - Genomes Global Study-wide 139766 C=0.251799 T=0.748201
gnomAD - Genomes European Sub 75686 C=0.23307 T=0.76693
gnomAD - Genomes African Sub 41876 C=0.30378 T=0.69622
gnomAD - Genomes American Sub 13608 C=0.22546 T=0.77454
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.2262 T=0.7738
gnomAD - Genomes East Asian Sub 3126 C=0.1571 T=0.8429
gnomAD - Genomes Other Sub 2150 C=0.2428 T=0.7572
8.3KJPN JAPANESE Study-wide 16760 C=0.22661 T=0.77339
1000Genomes Global Study-wide 5008 C=0.2304 T=0.7696
1000Genomes African Sub 1322 C=0.3298 T=0.6702
1000Genomes East Asian Sub 1008 C=0.1577 T=0.8423
1000Genomes Europe Sub 1006 C=0.2058 T=0.7942
1000Genomes South Asian Sub 978 C=0.208 T=0.792
1000Genomes American Sub 694 C=0.215 T=0.785
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.2525 T=0.7475
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.2657 T=0.7343
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.2589 T=0.7411
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.1679 G=0.0000, T=0.8321
Korean Genome Project KOREAN Study-wide 1832 C=0.1632 T=0.8368
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.257 T=0.743
Northern Sweden ACPOP Study-wide 600 C=0.175 T=0.825
SGDP_PRJ Global Study-wide 498 C=0.165 T=0.835
HapMap Global Study-wide 330 C=0.273 T=0.727
HapMap African Sub 120 C=0.367 T=0.633
HapMap American Sub 120 C=0.225 T=0.775
HapMap Asian Sub 90 C=0.21 T=0.79
Qatari Global Study-wide 216 C=0.222 T=0.778
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.108 T=0.892
Siberian Global Study-wide 54 C=0.15 T=0.85
The Danish reference pan genome Danish Study-wide 40 C=0.30 T=0.70
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 T
GRCh38.p13 chr 10 NC_000010.11:g.60786556= NC_000010.11:g.60786556C>G NC_000010.11:g.60786556C>T
GRCh37.p13 chr 10 NC_000010.10:g.62546314= NC_000010.10:g.62546314C>G NC_000010.10:g.62546314C>T
CDK1 RefSeqGene NG_029877.1:g.13226= NG_029877.1:g.13226C>G NG_029877.1:g.13226C>T
CDK1 transcript variant 5 NM_001170407.2:c.*757= NM_001170407.2:c.*757C>G NM_001170407.2:c.*757C>T
CDK1 transcript variant 5 NM_001170407.1:c.*757= NM_001170407.1:c.*757C>G NM_001170407.1:c.*757C>T
CDK1 transcript variant 4 NM_001170406.1:c.*757= NM_001170406.1:c.*757C>G NM_001170406.1:c.*757C>T
CDK1 transcript variant 6 NM_001320918.1:c.318+769= NM_001320918.1:c.318+769C>G NM_001320918.1:c.318+769C>T
CDK1 transcript variant 1 NM_001786.4:c.318+769= NM_001786.4:c.318+769C>G NM_001786.4:c.318+769C>T
CDK1 transcript variant 1 NM_001786.5:c.318+769= NM_001786.5:c.318+769C>G NM_001786.5:c.318+769C>T
CDK1 transcript variant 2 NM_033379.4:c.318+769= NM_033379.4:c.318+769C>G NM_033379.4:c.318+769C>T
CDK1 transcript variant 2 NM_033379.5:c.318+769= NM_033379.5:c.318+769C>G NM_033379.5:c.318+769C>T
CDK1 transcript variant X1 XM_005270303.1:c.318+769= XM_005270303.1:c.318+769C>G XM_005270303.1:c.318+769C>T
CDK1 transcript variant X1 XM_005270303.3:c.318+769= XM_005270303.3:c.318+769C>G XM_005270303.3:c.318+769C>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#.

69 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3443682 Sep 28, 2001 (100)
2 EGP_SNPS ss4473561 Jul 03, 2002 (106)
3 SC_SNP ss12953994 Dec 05, 2003 (119)
4 SC_SNP ss16021729 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss16503593 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss17406920 Feb 27, 2004 (120)
7 CSHL-HAPMAP ss19897438 Feb 27, 2004 (120)
8 SSAHASNP ss20663781 Apr 05, 2004 (121)
9 HGSV ss80465870 Dec 14, 2007 (130)
10 HGSV ss85984325 Dec 14, 2007 (130)
11 BCMHGSC_JDW ss88235998 Mar 23, 2008 (129)
12 HUMANGENOME_JCVI ss97560259 Feb 04, 2009 (130)
13 BGI ss102883672 Dec 01, 2009 (131)
14 1000GENOMES ss109491096 Jan 24, 2009 (130)
15 ILLUMINA-UK ss119190247 Feb 15, 2009 (130)
16 ENSEMBL ss137964343 Dec 01, 2009 (131)
17 GMI ss155112585 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss170176385 Jul 04, 2010 (132)
19 BUSHMAN ss201594764 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss207207097 Jul 04, 2010 (132)
21 1000GENOMES ss210987019 Jul 14, 2010 (132)
22 1000GENOMES ss224758423 Jul 14, 2010 (132)
23 1000GENOMES ss235199393 Jul 15, 2010 (132)
24 1000GENOMES ss241900621 Jul 15, 2010 (132)
25 GMI ss280640513 May 04, 2012 (137)
26 PJP ss290850732 May 09, 2011 (134)
27 ILLUMINA ss536357325 Sep 08, 2015 (146)
28 TISHKOFF ss561993124 Apr 25, 2013 (138)
29 SSMP ss656818046 Apr 25, 2013 (138)
30 EVA-GONL ss987549979 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1077032390 Aug 21, 2014 (142)
32 1000GENOMES ss1337668287 Aug 21, 2014 (142)
33 DDI ss1426339635 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1575154381 Apr 01, 2015 (144)
35 EVA_DECODE ss1597216417 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1624687132 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1667681165 Apr 01, 2015 (144)
38 HAMMER_LAB ss1806416053 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1930913889 Feb 12, 2016 (147)
40 GENOMED ss1967143028 Jul 19, 2016 (147)
41 JJLAB ss2026180202 Sep 14, 2016 (149)
42 USC_VALOUEV ss2154453344 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2175218518 Dec 20, 2016 (150)
44 TOPMED ss2338250820 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2627560478 Nov 08, 2017 (151)
46 GRF ss2698697463 Nov 08, 2017 (151)
47 GNOMAD ss2889431457 Nov 08, 2017 (151)
48 SWEGEN ss3006573076 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3026881275 Nov 08, 2017 (151)
50 TOPMED ss3121339214 Nov 08, 2017 (151)
51 CSHL ss3349150385 Nov 08, 2017 (151)
52 ILLUMINA ss3626458035 Oct 12, 2018 (152)
53 URBANLAB ss3649385572 Oct 12, 2018 (152)
54 EGCUT_WGS ss3673985552 Jul 13, 2019 (153)
55 EVA_DECODE ss3689992887 Jul 13, 2019 (153)
56 ACPOP ss3737373171 Jul 13, 2019 (153)
57 EVA ss3748171988 Jul 13, 2019 (153)
58 PACBIO ss3786689052 Jul 13, 2019 (153)
59 PACBIO ss3791867548 Jul 13, 2019 (153)
60 PACBIO ss3796749566 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3813547653 Jul 13, 2019 (153)
62 EVA ss3832155657 Apr 26, 2020 (154)
63 EVA ss3839617339 Apr 26, 2020 (154)
64 EVA ss3845089578 Apr 26, 2020 (154)
65 SGDP_PRJ ss3874329896 Apr 26, 2020 (154)
66 KRGDB ss3922399938 Apr 26, 2020 (154)
67 KOGIC ss3967992509 Apr 26, 2020 (154)
68 TOPMED ss4854409252 Apr 27, 2021 (155)
69 TOMMO_GENOMICS ss5197891783 Apr 27, 2021 (155)
70 1000Genomes NC_000010.10 - 62546314 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 62546314 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000010.10 - 62546314 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000010.10 - 62546314 Apr 26, 2020 (154)
74 gnomAD - Genomes NC_000010.11 - 60786556 Apr 27, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000010.10 - 62546314 Apr 26, 2020 (154)
76 HapMap NC_000010.11 - 60786556 Apr 26, 2020 (154)
77 KOREAN population from KRGDB NC_000010.10 - 62546314 Apr 26, 2020 (154)
78 Korean Genome Project NC_000010.11 - 60786556 Apr 26, 2020 (154)
79 Northern Sweden NC_000010.10 - 62546314 Jul 13, 2019 (153)
80 Qatari NC_000010.10 - 62546314 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000010.10 - 62546314 Apr 26, 2020 (154)
82 Siberian NC_000010.10 - 62546314 Apr 26, 2020 (154)
83 8.3KJPN NC_000010.10 - 62546314 Apr 27, 2021 (155)
84 TopMed NC_000010.11 - 60786556 Apr 27, 2021 (155)
85 UK 10K study - Twins NC_000010.10 - 62546314 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000010.10 - 62546314 Jul 13, 2019 (153)
87 ALFA NC_000010.11 - 60786556 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)
rs57066318 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
29577332, ss3922399938 NC_000010.10:62546313:C:G NC_000010.11:60786555:C:G (self)
ss80465870, ss85984325 NC_000010.8:62216319:C:T NC_000010.11:60786555:C:T (self)
ss88235998, ss109491096, ss119190247, ss170176385, ss201594764, ss207207097, ss210987019, ss280640513, ss290850732, ss1597216417 NC_000010.9:62216319:C:T NC_000010.11:60786555:C:T (self)
50064662, 27786433, 19723800, 2181700, 12392386, 29577332, 10658036, 12955819, 26346876, 6969698, 55861090, 27786433, 6171262, ss224758423, ss235199393, ss241900621, ss536357325, ss561993124, ss656818046, ss987549979, ss1077032390, ss1337668287, ss1426339635, ss1575154381, ss1624687132, ss1667681165, ss1806416053, ss1930913889, ss1967143028, ss2026180202, ss2154453344, ss2338250820, ss2627560478, ss2698697463, ss2889431457, ss3006573076, ss3349150385, ss3626458035, ss3673985552, ss3737373171, ss3748171988, ss3786689052, ss3791867548, ss3796749566, ss3832155657, ss3839617339, ss3874329896, ss3922399938, ss5197891783 NC_000010.10:62546313:C:T NC_000010.11:60786555:C:T (self)
353874702, 415757, 24370510, 43954149, 69954907, 5528420774, ss2175218518, ss3026881275, ss3121339214, ss3649385572, ss3689992887, ss3813547653, ss3845089578, ss3967992509, ss4854409252 NC_000010.11:60786555:C:T NC_000010.11:60786555:C:T (self)
ss12953994 NT_008583.15:11097461:C:T NC_000010.11:60786555:C:T (self)
ss16021729, ss16503593, ss17406920, ss19897438, ss20663781 NT_008583.16:11097468:C:T NC_000010.11:60786555:C:T (self)
ss3443682, ss4473561, ss97560259, ss102883672, ss137964343, ss155112585 NT_030059.13:13350777:C:T NC_000010.11:60786555: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 rs2456774

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