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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.

rs1836

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3829552 (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
A=0.099758 (26405/264690, TOPMED)
A=0.084218 (11810/140232, GnomAD)
A=0.07275 (1382/18996, ALFA) (+ 16 more)
A=0.39875 (6683/16760, 8.3KJPN)
A=0.2105 (1054/5008, 1000G)
A=0.0681 (305/4480, Estonian)
A=0.0529 (204/3854, ALSPAC)
A=0.0445 (165/3708, TWINSUK)
G=0.4976 (1457/2928, KOREAN)
G=0.4787 (877/1832, Korea1K)
A=0.1101 (124/1126, Daghestan)
A=0.045 (45/998, GoNL)
A=0.063 (38/600, NorthernSweden)
A=0.145 (72/498, SGDP_PRJ)
A=0.111 (24/216, Qatari)
G=0.407 (87/214, Vietnamese)
A=0.00 (0/56, Ancient Sardinia)
A=0.27 (14/52, Siberian)
A=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.3829552A>G
GRCh37.p13 chr 1 NC_000001.10:g.3746116A>G
CEP104 RefSeqGene NG_046726.1:g.32682T>C
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2044-179T>C N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2152-179…

XM_005244815.4:c.2152-179T>C

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2062-179…

XM_011542474.3:c.2062-179T>C

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.1870-179…

XM_017002918.2:c.1870-179T>C

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.1846-179…

XM_017002919.2:c.1846-179T>C

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2170-179…

XM_024451101.1:c.2170-179T>C

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.1996-179…

XM_024451102.1:c.1996-179T>C

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.1978-179…

XM_024451103.1:c.1978-179T>C

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.1972-179…

XM_024451104.1:c.1972-179T>C

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.1798-179…

XM_024451106.1:c.1798-179T>C

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c.2170-179…

XM_024451108.1:c.2170-179T>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 18996 A=0.07275 G=0.92725
European Sub 14370 A=0.05651 G=0.94349
African Sub 2950 A=0.0902 G=0.9098
African Others Sub 114 A=0.070 G=0.930
African American Sub 2836 A=0.0910 G=0.9090
Asian Sub 114 A=0.439 G=0.561
East Asian Sub 88 A=0.45 G=0.55
Other Asian Sub 26 A=0.38 G=0.62
Latin American 1 Sub 146 A=0.103 G=0.897
Latin American 2 Sub 610 A=0.208 G=0.792
South Asian Sub 100 A=0.34 G=0.66
Other Sub 706 A=0.110 G=0.890


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=0.099758 G=0.900242
gnomAD - Genomes Global Study-wide 140232 A=0.084218 G=0.915782
gnomAD - Genomes European Sub 75946 A=0.05604 G=0.94396
gnomAD - Genomes African Sub 42030 A=0.09122 G=0.90878
gnomAD - Genomes American Sub 13656 A=0.12705 G=0.87295
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.0367 G=0.9633
gnomAD - Genomes East Asian Sub 3124 A=0.5294 G=0.4706
gnomAD - Genomes Other Sub 2152 A=0.0971 G=0.9029
8.3KJPN JAPANESE Study-wide 16760 A=0.39875 G=0.60125
1000Genomes Global Study-wide 5008 A=0.2105 G=0.7895
1000Genomes African Sub 1322 A=0.0802 G=0.9198
1000Genomes East Asian Sub 1008 A=0.5208 G=0.4792
1000Genomes Europe Sub 1006 A=0.0557 G=0.9443
1000Genomes South Asian Sub 978 A=0.282 G=0.718
1000Genomes American Sub 694 A=0.131 G=0.869
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.0681 G=0.9319
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0529 G=0.9471
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0445 G=0.9555
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.5024 G=0.4976
Korean Genome Project KOREAN Study-wide 1832 A=0.5213 G=0.4787
Genome-wide autozygosity in Daghestan Global Study-wide 1126 A=0.1101 G=0.8899
Genome-wide autozygosity in Daghestan Daghestan Sub 626 A=0.065 G=0.935
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.146 G=0.854
Genome-wide autozygosity in Daghestan Central Asia Sub 118 A=0.254 G=0.746
Genome-wide autozygosity in Daghestan Europe Sub 106 A=0.047 G=0.953
Genome-wide autozygosity in Daghestan South Asian Sub 96 A=0.28 G=0.72
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.00 G=1.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.045 G=0.955
Northern Sweden ACPOP Study-wide 600 A=0.063 G=0.937
SGDP_PRJ Global Study-wide 498 A=0.145 G=0.855
Qatari Global Study-wide 216 A=0.111 G=0.889
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.593 G=0.407
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 56 A=0.00 G=1.00
Siberian Global Study-wide 52 A=0.27 G=0.73
The Danish reference pan genome Danish Study-wide 40 A=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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.3829552= NC_000001.11:g.3829552A>G
GRCh37.p13 chr 1 NC_000001.10:g.3746116= NC_000001.10:g.3746116A>G
CEP104 RefSeqGene NG_046726.1:g.32682= NG_046726.1:g.32682T>C
CEP104 transcript NM_014704.3:c.2044-179= NM_014704.3:c.2044-179T>C
CEP104 transcript NM_014704.4:c.2044-179= NM_014704.4:c.2044-179T>C
CEP104 transcript variant X1 XM_005244815.1:c.2152-179= XM_005244815.1:c.2152-179T>C
CEP104 transcript variant X2 XM_005244815.4:c.2152-179= XM_005244815.4:c.2152-179T>C
CEP104 transcript variant X3 XM_011542474.3:c.2062-179= XM_011542474.3:c.2062-179T>C
CEP104 transcript variant X7 XM_017002918.2:c.1870-179= XM_017002918.2:c.1870-179T>C
CEP104 transcript variant X8 XM_017002919.2:c.1846-179= XM_017002919.2:c.1846-179T>C
CEP104 transcript variant X1 XM_024451101.1:c.2170-179= XM_024451101.1:c.2170-179T>C
CEP104 transcript variant X4 XM_024451102.1:c.1996-179= XM_024451102.1:c.1996-179T>C
CEP104 transcript variant X5 XM_024451103.1:c.1978-179= XM_024451103.1:c.1978-179T>C
CEP104 transcript variant X6 XM_024451104.1:c.1972-179= XM_024451104.1:c.1972-179T>C
CEP104 transcript variant X9 XM_024451106.1:c.1798-179= XM_024451106.1:c.1798-179T>C
CEP104 transcript variant X10 XM_024451108.1:c.2170-179= XM_024451108.1:c.2170-179T>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#.

74 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss1861 Sep 19, 2000 (36)
2 YUSUKE ss5005425 Aug 28, 2002 (108)
3 SC_SNP ss12992584 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss16427208 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss17353932 Feb 27, 2004 (120)
6 SSAHASNP ss20463184 Apr 05, 2004 (121)
7 PERLEGEN ss23842215 Sep 20, 2004 (123)
8 ABI ss44131842 Mar 14, 2006 (126)
9 HGSV ss81115463 Dec 14, 2007 (130)
10 HGSV ss81617175 Dec 14, 2007 (130)
11 HGSV ss84156712 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss87174544 Mar 23, 2008 (129)
13 HUMANGENOME_JCVI ss97915520 Feb 03, 2009 (130)
14 1000GENOMES ss107949149 Jan 22, 2009 (130)
15 1000GENOMES ss109967826 Jan 24, 2009 (130)
16 ILLUMINA-UK ss118453633 Feb 14, 2009 (130)
17 ENSEMBL ss137763658 Dec 01, 2009 (131)
18 ENSEMBL ss138971175 Dec 01, 2009 (131)
19 GMI ss154559515 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss163005135 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss163738616 Jul 04, 2010 (132)
22 BUSHMAN ss197925350 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss205280462 Jul 04, 2010 (132)
24 1000GENOMES ss218203369 Jul 14, 2010 (132)
25 1000GENOMES ss230404238 Jul 14, 2010 (132)
26 1000GENOMES ss238123112 Jul 15, 2010 (132)
27 BL ss252880611 May 09, 2011 (134)
28 GMI ss275691523 May 04, 2012 (137)
29 GMI ss283991046 Apr 25, 2013 (138)
30 PJP ss290498365 May 09, 2011 (134)
31 TISHKOFF ss553734798 Apr 25, 2013 (138)
32 SSMP ss647536606 Apr 25, 2013 (138)
33 EVA-GONL ss974796656 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067627438 Aug 21, 2014 (142)
35 1000GENOMES ss1289452280 Aug 21, 2014 (142)
36 HAMMER_LAB ss1397238574 Sep 08, 2015 (146)
37 DDI ss1425693093 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1573860226 Apr 01, 2015 (144)
39 EVA_DECODE ss1584155406 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1599427701 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1642421734 Apr 01, 2015 (144)
42 HAMMER_LAB ss1793785259 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1917992176 Feb 12, 2016 (147)
44 GENOMED ss1966671431 Jul 19, 2016 (147)
45 JJLAB ss2019512265 Sep 14, 2016 (149)
46 USC_VALOUEV ss2147502624 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2159575812 Dec 20, 2016 (150)
48 TOPMED ss2321730715 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2624271902 Nov 08, 2017 (151)
50 GRF ss2697396677 Nov 08, 2017 (151)
51 GNOMAD ss2750973858 Nov 08, 2017 (151)
52 SWEGEN ss2986201578 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3023519756 Nov 08, 2017 (151)
54 TOPMED ss3067129860 Nov 08, 2017 (151)
55 CSHL ss3343289057 Nov 08, 2017 (151)
56 OMUKHERJEE_ADBS ss3646220221 Oct 11, 2018 (152)
57 URBANLAB ss3646586813 Oct 11, 2018 (152)
58 EGCUT_WGS ss3654302793 Jul 12, 2019 (153)
59 EVA_DECODE ss3686047515 Jul 12, 2019 (153)
60 ACPOP ss3726740209 Jul 12, 2019 (153)
61 EVA ss3745755571 Jul 12, 2019 (153)
62 PACBIO ss3783308845 Jul 12, 2019 (153)
63 PACBIO ss3788985731 Jul 12, 2019 (153)
64 PACBIO ss3793858358 Jul 12, 2019 (153)
65 KHV_HUMAN_GENOMES ss3798777230 Jul 12, 2019 (153)
66 EVA ss3825994066 Apr 25, 2020 (154)
67 EVA ss3836384219 Apr 25, 2020 (154)
68 EVA ss3841788387 Apr 25, 2020 (154)
69 SGDP_PRJ ss3848069843 Apr 25, 2020 (154)
70 KRGDB ss3892931494 Apr 25, 2020 (154)
71 KOGIC ss3943693185 Apr 25, 2020 (154)
72 EVA ss3984774957 Apr 25, 2021 (155)
73 TOPMED ss4437309896 Apr 25, 2021 (155)
74 TOMMO_GENOMICS ss5142202327 Apr 25, 2021 (155)
75 1000Genomes NC_000001.10 - 3746116 Oct 11, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3746116 Oct 11, 2018 (152)
77 Genome-wide autozygosity in Daghestan NC_000001.9 - 3735976 Apr 25, 2020 (154)
78 Genetic variation in the Estonian population NC_000001.10 - 3746116 Oct 11, 2018 (152)
79 The Danish reference pan genome NC_000001.10 - 3746116 Apr 25, 2020 (154)
80 gnomAD - Genomes NC_000001.11 - 3829552 Apr 25, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000001.10 - 3746116 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000001.10 - 3746116 Apr 25, 2020 (154)
83 Korean Genome Project NC_000001.11 - 3829552 Apr 25, 2020 (154)
84 Northern Sweden NC_000001.10 - 3746116 Jul 12, 2019 (153)
85 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 3746116 Apr 25, 2021 (155)
86 Qatari NC_000001.10 - 3746116 Apr 25, 2020 (154)
87 SGDP_PRJ NC_000001.10 - 3746116 Apr 25, 2020 (154)
88 Siberian NC_000001.10 - 3746116 Apr 25, 2020 (154)
89 8.3KJPN NC_000001.10 - 3746116 Apr 25, 2021 (155)
90 TopMed NC_000001.11 - 3829552 Apr 25, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 3746116 Oct 11, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000001.10 - 3746116 Jul 12, 2019 (153)
93 ALFA NC_000001.11 - 3829552 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)
rs3819010 Oct 08, 2002 (108)
rs56926330 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81115463, ss81617175, ss84156712 NC_000001.8:3769272:A:G NC_000001.11:3829551:A:G (self)
61, ss87174544, ss107949149, ss109967826, ss118453633, ss163005135, ss163738616, ss197925350, ss205280462, ss252880611, ss275691523, ss283991046, ss290498365, ss1397238574, ss1584155406 NC_000001.9:3735975:A:G NC_000001.11:3829551:A:G (self)
120321, 53964, 41041, 1367460, 23259, 108888, 25074, 884, 34106, 86823, 18978, 171634, 53964, 11436, ss218203369, ss230404238, ss238123112, ss553734798, ss647536606, ss974796656, ss1067627438, ss1289452280, ss1425693093, ss1573860226, ss1599427701, ss1642421734, ss1793785259, ss1917992176, ss1966671431, ss2019512265, ss2147502624, ss2321730715, ss2624271902, ss2697396677, ss2750973858, ss2986201578, ss3343289057, ss3646220221, ss3654302793, ss3726740209, ss3745755571, ss3783308845, ss3788985731, ss3793858358, ss3825994066, ss3836384219, ss3848069843, ss3892931494, ss3984774957, ss5142202327 NC_000001.10:3746115:A:G NC_000001.11:3829551:A:G (self)
867188, 71186, 570482, 916231, 10947058125, ss2159575812, ss3023519756, ss3067129860, ss3646586813, ss3686047515, ss3798777230, ss3841788387, ss3943693185, ss4437309896 NC_000001.11:3829551:A:G NC_000001.11:3829551:A:G (self)
ss12992584, ss16427208, ss17353932, ss20463184 NT_004321.15:1052889:A:G NC_000001.11:3829551:A:G (self)
ss1861, ss5005425, ss23842215, ss44131842, ss97915520, ss137763658, ss138971175, ss154559515 NT_004350.19:3224747:A:G NC_000001.11:3829551: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 rs1836

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