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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.

rs2275826

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3830025 (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
C=0.099739 (26400/264690, TOPMED)
C=0.144507 (35552/246022, GnomAD_exome)
C=0.084344 (11813/140058, GnomAD) (+ 18 more)
C=0.141084 (16949/120134, ExAC)
C=0.07041 (1968/27950, ALFA)
C=0.39887 (6685/16760, 8.3KJPN)
C=0.06053 (787/13002, GO-ESP)
C=0.2105 (1054/5008, 1000G)
C=0.0694 (311/4480, Estonian)
C=0.0529 (204/3854, ALSPAC)
C=0.0445 (165/3708, TWINSUK)
G=0.4976 (1458/2930, KOREAN)
G=0.4787 (877/1832, Korea1K)
C=0.045 (45/998, GoNL)
C=0.063 (38/600, NorthernSweden)
C=0.062 (33/534, MGP)
C=0.145 (72/498, SGDP_PRJ)
C=0.111 (24/216, Qatari)
G=0.390 (82/210, Vietnamese)
C=0.27 (14/52, Siberian)
C=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEP104 : 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 1 NC_000001.11:g.3830025C>G
GRCh37.p13 chr 1 NC_000001.10:g.3746589C>G
CEP104 RefSeqGene NG_046726.1:g.32209G>C
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.1837-28G>C N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.1945-28G…

XM_005244815.4:c.1945-28G>C

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.1855-28G…

XM_011542474.3:c.1855-28G>C

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.1663-28G…

XM_017002918.2:c.1663-28G>C

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.1639-28G…

XM_017002919.2:c.1639-28G>C

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.1963-28G…

XM_024451101.1:c.1963-28G>C

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.1789-28G…

XM_024451102.1:c.1789-28G>C

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.1771-28G…

XM_024451103.1:c.1771-28G>C

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.1765-28G…

XM_024451104.1:c.1765-28G>C

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.1591-28G…

XM_024451106.1:c.1591-28G>C

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c.1963-28G…

XM_024451108.1:c.1963-28G>C

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 27950 C=0.07041 G=0.92959
European Sub 20398 C=0.05657 G=0.94343
African Sub 3554 C=0.0867 G=0.9133
African Others Sub 122 C=0.074 G=0.926
African American Sub 3432 C=0.0871 G=0.9129
Asian Sub 168 C=0.494 G=0.506
East Asian Sub 112 C=0.473 G=0.527
Other Asian Sub 56 C=0.54 G=0.46
Latin American 1 Sub 146 C=0.103 G=0.897
Latin American 2 Sub 610 C=0.208 G=0.792
South Asian Sub 98 C=0.35 G=0.65
Other Sub 2976 C=0.0830 G=0.9170


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=0.099739 G=0.900261
gnomAD - Exomes Global Study-wide 246022 C=0.144507 G=0.855493
gnomAD - Exomes European Sub 133196 C=0.056053 G=0.943947
gnomAD - Exomes Asian Sub 47934 C=0.36502 G=0.63498
gnomAD - Exomes American Sub 33448 C=0.24312 G=0.75688
gnomAD - Exomes African Sub 15612 C=0.09179 G=0.90821
gnomAD - Exomes Ashkenazi Jewish Sub 9862 C=0.0430 G=0.9570
gnomAD - Exomes Other Sub 5970 C=0.1005 G=0.8995
gnomAD - Genomes Global Study-wide 140058 C=0.084344 G=0.915656
gnomAD - Genomes European Sub 75866 C=0.05611 G=0.94389
gnomAD - Genomes African Sub 41980 C=0.09142 G=0.90858
gnomAD - Genomes American Sub 13626 C=0.12718 G=0.87282
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.0370 G=0.9630
gnomAD - Genomes East Asian Sub 3114 C=0.5305 G=0.4695
gnomAD - Genomes Other Sub 2150 C=0.0977 G=0.9023
ExAC Global Study-wide 120134 C=0.141084 G=0.858916
ExAC Europe Sub 73026 C=0.05460 G=0.94540
ExAC Asian Sub 24864 C=0.35666 G=0.64334
ExAC American Sub 11402 C=0.26846 G=0.73154
ExAC African Sub 9940 C=0.0924 G=0.9076
ExAC Other Sub 902 C=0.127 G=0.873
8.3KJPN JAPANESE Study-wide 16760 C=0.39887 G=0.60113
GO Exome Sequencing Project Global Study-wide 13002 C=0.06053 G=0.93947
GO Exome Sequencing Project European American Sub 8598 C=0.0463 G=0.9537
GO Exome Sequencing Project African American Sub 4404 C=0.0883 G=0.9117
1000Genomes Global Study-wide 5008 C=0.2105 G=0.7895
1000Genomes African Sub 1322 C=0.0802 G=0.9198
1000Genomes East Asian Sub 1008 C=0.5208 G=0.4792
1000Genomes Europe Sub 1006 C=0.0557 G=0.9443
1000Genomes South Asian Sub 978 C=0.282 G=0.718
1000Genomes American Sub 694 C=0.131 G=0.869
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.0694 G=0.9306
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.0529 G=0.9471
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.0445 G=0.9555
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5024 G=0.4976
Korean Genome Project KOREAN Study-wide 1832 C=0.5213 G=0.4787
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.045 G=0.955
Northern Sweden ACPOP Study-wide 600 C=0.063 G=0.937
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.062 G=0.938
SGDP_PRJ Global Study-wide 498 C=0.145 G=0.855
Qatari Global Study-wide 216 C=0.111 G=0.889
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.610 G=0.390
Siberian Global Study-wide 52 C=0.27 G=0.73
The Danish reference pan genome Danish Study-wide 40 C=0.12 G=0.88
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 1 NC_000001.11:g.3830025= NC_000001.11:g.3830025C>G
GRCh37.p13 chr 1 NC_000001.10:g.3746589= NC_000001.10:g.3746589C>G
CEP104 RefSeqGene NG_046726.1:g.32209= NG_046726.1:g.32209G>C
CEP104 transcript NM_014704.3:c.1837-28= NM_014704.3:c.1837-28G>C
CEP104 transcript NM_014704.4:c.1837-28= NM_014704.4:c.1837-28G>C
CEP104 transcript variant X1 XM_005244815.1:c.1945-28= XM_005244815.1:c.1945-28G>C
CEP104 transcript variant X2 XM_005244815.4:c.1945-28= XM_005244815.4:c.1945-28G>C
CEP104 transcript variant X3 XM_011542474.3:c.1855-28= XM_011542474.3:c.1855-28G>C
CEP104 transcript variant X7 XM_017002918.2:c.1663-28= XM_017002918.2:c.1663-28G>C
CEP104 transcript variant X8 XM_017002919.2:c.1639-28= XM_017002919.2:c.1639-28G>C
CEP104 transcript variant X1 XM_024451101.1:c.1963-28= XM_024451101.1:c.1963-28G>C
CEP104 transcript variant X4 XM_024451102.1:c.1789-28= XM_024451102.1:c.1789-28G>C
CEP104 transcript variant X5 XM_024451103.1:c.1771-28= XM_024451103.1:c.1771-28G>C
CEP104 transcript variant X6 XM_024451104.1:c.1765-28= XM_024451104.1:c.1765-28G>C
CEP104 transcript variant X9 XM_024451106.1:c.1591-28= XM_024451106.1:c.1591-28G>C
CEP104 transcript variant X10 XM_024451108.1:c.1963-28= XM_024451108.1:c.1963-28G>C
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#.

78 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3212054 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss9896209 Jul 11, 2003 (116)
3 SC_SNP ss12992586 Dec 05, 2003 (119)
4 SSAHASNP ss20574397 Apr 05, 2004 (121)
5 HGSV ss83175289 Dec 15, 2007 (130)
6 HGSV ss83944047 Dec 15, 2007 (130)
7 HGSV ss85480124 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss87174557 Mar 23, 2008 (129)
9 HUMANGENOME_JCVI ss97915522 Feb 05, 2009 (130)
10 1000GENOMES ss109967842 Jan 24, 2009 (130)
11 ILLUMINA-UK ss118453647 Feb 14, 2009 (130)
12 ENSEMBL ss137763667 Dec 01, 2009 (131)
13 ENSEMBL ss138971163 Dec 01, 2009 (131)
14 GMI ss154559542 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss163005150 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss163738649 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss166008884 Jul 04, 2010 (132)
18 BUSHMAN ss197925365 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss205151558 Jul 04, 2010 (132)
20 1000GENOMES ss218203374 Jul 14, 2010 (132)
21 1000GENOMES ss230404242 Jul 14, 2010 (132)
22 1000GENOMES ss238123117 Jul 15, 2010 (132)
23 BL ss252880623 May 09, 2011 (134)
24 GMI ss275691528 May 04, 2012 (137)
25 GMI ss283991049 Apr 25, 2013 (138)
26 PJP ss290498367 May 09, 2011 (134)
27 1000GENOMES ss489716765 May 04, 2012 (137)
28 TISHKOFF ss553734803 Apr 25, 2013 (138)
29 SSMP ss647536610 Apr 25, 2013 (138)
30 NHLBI-ESP ss712268036 Apr 25, 2013 (138)
31 EVA-GONL ss974796663 Aug 21, 2014 (142)
32 1000GENOMES ss1289452302 Aug 21, 2014 (142)
33 DDI ss1425693097 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1573860231 Apr 01, 2015 (144)
35 EVA_DECODE ss1584155414 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1599427716 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1642421749 Apr 01, 2015 (144)
38 EVA_EXAC ss1685263130 Apr 01, 2015 (144)
39 EVA_MGP ss1710885696 Apr 01, 2015 (144)
40 HAMMER_LAB ss1793785266 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1917992181 Feb 12, 2016 (147)
42 GENOMED ss1966671435 Jul 19, 2016 (147)
43 JJLAB ss2019512271 Sep 14, 2016 (149)
44 USC_VALOUEV ss2147502629 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2159575844 Dec 20, 2016 (150)
46 TOPMED ss2321730744 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2624271906 Nov 08, 2017 (151)
48 GRF ss2697396682 Nov 08, 2017 (151)
49 GNOMAD ss2731058819 Nov 08, 2017 (151)
50 GNOMAD ss2746195798 Nov 08, 2017 (151)
51 GNOMAD ss2750973901 Nov 08, 2017 (151)
52 SWEGEN ss2986201592 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3023519760 Nov 08, 2017 (151)
54 TOPMED ss3067129951 Nov 08, 2017 (151)
55 CSHL ss3343289061 Nov 08, 2017 (151)
56 OMUKHERJEE_ADBS ss3646220225 Oct 11, 2018 (152)
57 URBANLAB ss3646586815 Oct 11, 2018 (152)
58 EGCUT_WGS ss3654302803 Jul 12, 2019 (153)
59 EVA_DECODE ss3686047525 Jul 12, 2019 (153)
60 ACPOP ss3726740217 Jul 12, 2019 (153)
61 EVA ss3745755579 Jul 12, 2019 (153)
62 PACBIO ss3783308847 Jul 12, 2019 (153)
63 PACBIO ss3788985733 Jul 12, 2019 (153)
64 PACBIO ss3793858360 Jul 12, 2019 (153)
65 KHV_HUMAN_GENOMES ss3798777238 Jul 12, 2019 (153)
66 EVA ss3823550955 Apr 25, 2020 (154)
67 EVA ss3825994070 Apr 25, 2020 (154)
68 EVA ss3836384222 Apr 25, 2020 (154)
69 EVA ss3841788390 Apr 25, 2020 (154)
70 SGDP_PRJ ss3848069855 Apr 25, 2020 (154)
71 KRGDB ss3892931504 Apr 25, 2020 (154)
72 KOGIC ss3943693190 Apr 25, 2020 (154)
73 FSA-LAB ss3983913167 Apr 25, 2021 (155)
74 FSA-LAB ss3983913168 Apr 25, 2021 (155)
75 EVA ss3986095401 Apr 25, 2021 (155)
76 TOPMED ss4437310019 Apr 25, 2021 (155)
77 TOMMO_GENOMICS ss5142202348 Apr 25, 2021 (155)
78 EVA ss5237158809 Apr 25, 2021 (155)
79 1000Genomes NC_000001.10 - 3746589 Oct 11, 2018 (152)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3746589 Oct 11, 2018 (152)
81 Genetic variation in the Estonian population NC_000001.10 - 3746589 Oct 11, 2018 (152)
82 ExAC NC_000001.10 - 3746589 Oct 11, 2018 (152)
83 The Danish reference pan genome NC_000001.10 - 3746589 Apr 25, 2020 (154)
84 gnomAD - Genomes NC_000001.11 - 3830025 Apr 25, 2021 (155)
85 gnomAD - Exomes NC_000001.10 - 3746589 Jul 12, 2019 (153)
86 GO Exome Sequencing Project NC_000001.10 - 3746589 Oct 11, 2018 (152)
87 Genome of the Netherlands Release 5 NC_000001.10 - 3746589 Apr 25, 2020 (154)
88 KOREAN population from KRGDB NC_000001.10 - 3746589 Apr 25, 2020 (154)
89 Korean Genome Project NC_000001.11 - 3830025 Apr 25, 2020 (154)
90 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3746589 Apr 25, 2020 (154)
91 Northern Sweden NC_000001.10 - 3746589 Jul 12, 2019 (153)
92 Qatari NC_000001.10 - 3746589 Apr 25, 2020 (154)
93 SGDP_PRJ NC_000001.10 - 3746589 Apr 25, 2020 (154)
94 Siberian NC_000001.10 - 3746589 Apr 25, 2020 (154)
95 8.3KJPN NC_000001.10 - 3746589 Apr 25, 2021 (155)
96 TopMed NC_000001.11 - 3830025 Apr 25, 2021 (155)
97 UK 10K study - Twins NC_000001.10 - 3746589 Oct 11, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000001.10 - 3746589 Jul 12, 2019 (153)
99 ALFA NC_000001.11 - 3830025 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)
rs59720757 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83175289, ss83944047, ss85480124 NC_000001.8:3769745:C:G NC_000001.11:3830024:C:G (self)
ss87174557, ss109967842, ss118453647, ss163005150, ss163738649, ss166008884, ss197925365, ss205151558, ss252880623, ss275691528, ss283991049, ss290498367, ss1584155414 NC_000001.9:3736448:C:G NC_000001.11:3830024:C:G (self)
120343, 53980, 41051, 4439531, 1367465, 73841, 9688, 23266, 108898, 2448, 25082, 34111, 86835, 18983, 171655, 53980, 11439, ss218203374, ss230404242, ss238123117, ss489716765, ss553734803, ss647536610, ss712268036, ss974796663, ss1289452302, ss1425693097, ss1573860231, ss1599427716, ss1642421749, ss1685263130, ss1710885696, ss1793785266, ss1917992181, ss1966671435, ss2019512271, ss2147502629, ss2321730744, ss2624271906, ss2697396682, ss2731058819, ss2746195798, ss2750973901, ss2986201592, ss3343289061, ss3646220225, ss3654302803, ss3726740217, ss3745755579, ss3783308847, ss3788985733, ss3793858360, ss3823550955, ss3825994070, ss3836384222, ss3848069855, ss3892931504, ss3983913167, ss3983913168, ss3986095401, ss5142202348 NC_000001.10:3746588:C:G NC_000001.11:3830024:C:G (self)
867281, 71191, 570566, 916354, 4854039454, ss2159575844, ss3023519760, ss3067129951, ss3646586815, ss3686047525, ss3798777238, ss3841788390, ss3943693190, ss4437310019, ss5237158809 NC_000001.11:3830024:C:G NC_000001.11:3830024:C:G (self)
ss9896209, ss12992586, ss20574397 NT_004321.15:1053362:C:G NC_000001.11:3830024:C:G (self)
ss3212054, ss97915522, ss137763667, ss138971163, ss154559542 NT_004350.19:3225220:C:G NC_000001.11:3830024: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 rs2275826

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