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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.

rs4292956

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:154576470 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.069791 (18473/264690, TOPMED)
T=0.069849 (9790/140160, GnomAD)
T=0.07365 (5796/78698, PAGE_STUDY) (+ 18 more)
T=0.07075 (1856/26234, ALFA)
T=0.13473 (2258/16760, 8.3KJPN)
T=0.0837 (419/5008, 1000G)
T=0.0734 (329/4480, Estonian)
T=0.0776 (299/3854, ALSPAC)
T=0.0704 (261/3708, TWINSUK)
T=0.1324 (388/2930, KOREAN)
T=0.1441 (264/1832, Korea1K)
T=0.078 (78/998, GoNL)
T=0.146 (115/786, PRJEB37584)
T=0.083 (50/600, NorthernSweden)
T=0.060 (13/216, Qatari)
T=0.192 (41/214, Vietnamese)
C=0.38 (33/86, SGDP_PRJ)
T=0.11 (8/70, Ancient Sardinia)
T=0.07 (3/40, GENOME_DK)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHRNB2 : Non Coding Transcript Variant
Publications
3 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.154576470C>T
GRCh37.p13 chr 1 NC_000001.10:g.154548946C>T
CHRNB2 RefSeqGene NG_008027.1:g.13690C>T
Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB2 transcript NM_000748.3:c.*538= N/A 3 Prime UTR Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.*538= N/A 3 Prime UTR Variant
CHRNB2 transcript variant X1 XR_001736952.2:n.2299C>T N/A Non Coding Transcript 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 26234 C=0.92925 T=0.07075
European Sub 20500 C=0.92820 T=0.07180
African Sub 3402 C=0.9356 T=0.0644
African Others Sub 114 C=0.921 T=0.079
African American Sub 3288 C=0.9361 T=0.0639
Asian Sub 150 C=0.820 T=0.180
East Asian Sub 122 C=0.820 T=0.180
Other Asian Sub 28 C=0.82 T=0.18
Latin American 1 Sub 154 C=0.955 T=0.045
Latin American 2 Sub 616 C=0.953 T=0.047
South Asian Sub 104 C=0.942 T=0.058
Other Sub 1308 C=0.9266 T=0.0734


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=0.930209 T=0.069791
gnomAD - Genomes Global Study-wide 140160 C=0.930151 T=0.069849
gnomAD - Genomes European Sub 75902 C=0.92832 T=0.07168
gnomAD - Genomes African Sub 42004 C=0.93467 T=0.06533
gnomAD - Genomes American Sub 13658 C=0.94882 T=0.05118
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9401 T=0.0599
gnomAD - Genomes East Asian Sub 3120 C=0.8224 T=0.1776
gnomAD - Genomes Other Sub 2152 C=0.9289 T=0.0711
The PAGE Study Global Study-wide 78698 C=0.92635 T=0.07365
The PAGE Study AfricanAmerican Sub 32514 C=0.93461 T=0.06539
The PAGE Study Mexican Sub 10808 C=0.95272 T=0.04728
The PAGE Study Asian Sub 8318 C=0.8710 T=0.1290
The PAGE Study PuertoRican Sub 7918 C=0.9310 T=0.0690
The PAGE Study NativeHawaiian Sub 4534 C=0.8571 T=0.1429
The PAGE Study Cuban Sub 4230 C=0.9303 T=0.0697
The PAGE Study Dominican Sub 3828 C=0.9292 T=0.0708
The PAGE Study CentralAmerican Sub 2450 C=0.9551 T=0.0449
The PAGE Study SouthAmerican Sub 1982 C=0.9612 T=0.0388
The PAGE Study NativeAmerican Sub 1260 C=0.9381 T=0.0619
The PAGE Study SouthAsian Sub 856 C=0.929 T=0.071
Allele Frequency Aggregator Total Global 26234 C=0.92925 T=0.07075
Allele Frequency Aggregator European Sub 20500 C=0.92820 T=0.07180
Allele Frequency Aggregator African Sub 3402 C=0.9356 T=0.0644
Allele Frequency Aggregator Other Sub 1308 C=0.9266 T=0.0734
Allele Frequency Aggregator Latin American 2 Sub 616 C=0.953 T=0.047
Allele Frequency Aggregator Latin American 1 Sub 154 C=0.955 T=0.045
Allele Frequency Aggregator Asian Sub 150 C=0.820 T=0.180
Allele Frequency Aggregator South Asian Sub 104 C=0.942 T=0.058
8.3KJPN JAPANESE Study-wide 16760 C=0.86527 T=0.13473
1000Genomes Global Study-wide 5008 C=0.9163 T=0.0837
1000Genomes African Sub 1322 C=0.9410 T=0.0590
1000Genomes East Asian Sub 1008 C=0.8056 T=0.1944
1000Genomes Europe Sub 1006 C=0.9324 T=0.0676
1000Genomes South Asian Sub 978 C=0.945 T=0.055
1000Genomes American Sub 694 C=0.967 T=0.033
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9266 T=0.0734
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9224 T=0.0776
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9296 T=0.0704
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8676 T=0.1324
Korean Genome Project KOREAN Study-wide 1832 C=0.8559 T=0.1441
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.922 T=0.078
CNV burdens in cranial meningiomas Global Study-wide 786 C=0.854 T=0.146
CNV burdens in cranial meningiomas CRM Sub 786 C=0.854 T=0.146
Northern Sweden ACPOP Study-wide 600 C=0.917 T=0.083
Qatari Global Study-wide 216 C=0.940 T=0.060
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.808 T=0.192
SGDP_PRJ Global Study-wide 86 C=0.38 T=0.62
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 70 C=0.89 T=0.11
The Danish reference pan genome Danish Study-wide 40 C=0.93 T=0.07
Siberian Global Study-wide 4 C=0.5 T=0.5
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= T
GRCh38.p13 chr 1 NC_000001.11:g.154576470= NC_000001.11:g.154576470C>T
GRCh37.p13 chr 1 NC_000001.10:g.154548946= NC_000001.10:g.154548946C>T
CHRNB2 RefSeqGene NG_008027.1:g.13690= NG_008027.1:g.13690C>T
CHRNB2 transcript NM_000748.3:c.*538= NM_000748.3:c.*538C>T
CHRNB2 transcript NM_000748.2:c.*538= NM_000748.2:c.*538C>T
CHRNB2 transcript variant X2 XM_017000180.2:c.*538= XM_017000180.2:c.*538C>T
CHRNB2 transcript variant X1 XR_001736952.2:n.2299= XR_001736952.2:n.2299C>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#.

62 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5683070 Feb 20, 2003 (111)
2 TAPPERS ss69809239 May 17, 2007 (127)
3 SI_EXO ss71647844 May 17, 2007 (127)
4 UUGC ss76901693 Dec 07, 2007 (129)
5 SHGC ss99307548 Feb 06, 2009 (130)
6 1000GENOMES ss111154455 Jan 25, 2009 (130)
7 GMI ss155752769 Dec 01, 2009 (131)
8 PERLEGEN ss161151672 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss164120054 Jul 04, 2010 (132)
10 BUSHMAN ss199086371 Jul 04, 2010 (132)
11 1000GENOMES ss218651250 Jul 14, 2010 (132)
12 1000GENOMES ss230731932 Jul 14, 2010 (132)
13 1000GENOMES ss238379844 Jul 15, 2010 (132)
14 GMI ss276051215 May 04, 2012 (137)
15 GMI ss284152644 Apr 25, 2013 (138)
16 GSK-GENETICS ss491235567 May 04, 2012 (137)
17 ILLUMINA ss536119915 Sep 08, 2015 (146)
18 TISHKOFF ss554693769 Apr 25, 2013 (138)
19 SSMP ss648413997 Apr 25, 2013 (138)
20 EVA-GONL ss975682561 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1068269624 Aug 21, 2014 (142)
22 1000GENOMES ss1292925504 Aug 21, 2014 (142)
23 EVA_GENOME_DK ss1574392087 Apr 01, 2015 (144)
24 EVA_DECODE ss1585063979 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1601213930 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1644207963 Apr 01, 2015 (144)
27 WEILL_CORNELL_DGM ss1918916466 Feb 12, 2016 (147)
28 ILLUMINA ss1958317579 Feb 12, 2016 (147)
29 JJLAB ss2019973771 Sep 14, 2016 (149)
30 USC_VALOUEV ss2147998285 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2166540963 Dec 20, 2016 (150)
32 TOPMED ss2329045885 Dec 20, 2016 (150)
33 GRF ss2697971177 Nov 08, 2017 (151)
34 GNOMAD ss2761315622 Nov 08, 2017 (151)
35 AFFY ss2984879306 Nov 08, 2017 (151)
36 AFFY ss2985525067 Nov 08, 2017 (151)
37 SWEGEN ss2987752073 Nov 08, 2017 (151)
38 ILLUMINA ss3021136274 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023744054 Nov 08, 2017 (151)
40 TOPMED ss3092142283 Nov 08, 2017 (151)
41 CSHL ss3343710533 Nov 08, 2017 (151)
42 ILLUMINA ss3626208407 Oct 11, 2018 (152)
43 OMUKHERJEE_ADBS ss3646246102 Oct 11, 2018 (152)
44 ILLUMINA ss3651470518 Oct 11, 2018 (152)
45 ILLUMINA ss3653648501 Oct 11, 2018 (152)
46 EGCUT_WGS ss3655692288 Jul 12, 2019 (153)
47 EVA_DECODE ss3687782307 Jul 12, 2019 (153)
48 ILLUMINA ss3725065374 Jul 12, 2019 (153)
49 ACPOP ss3727485707 Jul 12, 2019 (153)
50 EVA ss3746808076 Jul 12, 2019 (153)
51 PAGE_CC ss3770840932 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3799809813 Jul 12, 2019 (153)
53 EVA ss3825575808 Apr 25, 2020 (154)
54 EVA ss3826424137 Apr 25, 2020 (154)
55 SGDP_PRJ ss3850006604 Apr 25, 2020 (154)
56 KRGDB ss3895212944 Apr 25, 2020 (154)
57 KOGIC ss3945651177 Apr 25, 2020 (154)
58 EVA ss3984464756 Apr 25, 2021 (155)
59 EVA ss3984825421 Apr 25, 2021 (155)
60 TOPMED ss4468301390 Apr 25, 2021 (155)
61 TOMMO_GENOMICS ss5146483016 Apr 25, 2021 (155)
62 EVA ss5237274014 Apr 25, 2021 (155)
63 1000Genomes NC_000001.10 - 154548946 Oct 11, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 154548946 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 154548946 Oct 11, 2018 (152)
66 The Danish reference pan genome NC_000001.10 - 154548946 Apr 25, 2020 (154)
67 gnomAD - Genomes NC_000001.11 - 154576470 Apr 25, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000001.10 - 154548946 Apr 25, 2020 (154)
69 KOREAN population from KRGDB NC_000001.10 - 154548946 Apr 25, 2020 (154)
70 Korean Genome Project NC_000001.11 - 154576470 Apr 25, 2020 (154)
71 Northern Sweden NC_000001.10 - 154548946 Jul 12, 2019 (153)
72 The PAGE Study NC_000001.11 - 154576470 Jul 12, 2019 (153)
73 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 154548946 Apr 25, 2021 (155)
74 CNV burdens in cranial meningiomas NC_000001.10 - 154548946 Apr 25, 2021 (155)
75 Qatari NC_000001.10 - 154548946 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000001.10 - 154548946 Apr 25, 2020 (154)
77 Siberian NC_000001.10 - 154548946 Apr 25, 2020 (154)
78 8.3KJPN NC_000001.10 - 154548946 Apr 25, 2021 (155)
79 TopMed NC_000001.11 - 154576470 Apr 25, 2021 (155)
80 UK 10K study - Twins NC_000001.10 - 154548946 Oct 11, 2018 (152)
81 A Vietnamese Genetic Variation Database NC_000001.10 - 154548946 Jul 12, 2019 (153)
82 ALFA NC_000001.11 - 154576470 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
ss111154455, ss164120054, ss199086371, ss276051215, ss284152644, ss491235567, ss1585063979 NC_000001.9:152815569:C:T NC_000001.11:154576469:C:T (self)
3717557, 2021159, 1430536, 1708643, 878202, 2390338, 770572, 51348, 14070, 958396, 2023584, 514639, 4452323, 2021159, 434387, ss218651250, ss230731932, ss238379844, ss536119915, ss554693769, ss648413997, ss975682561, ss1068269624, ss1292925504, ss1574392087, ss1601213930, ss1644207963, ss1918916466, ss1958317579, ss2019973771, ss2147998285, ss2329045885, ss2697971177, ss2761315622, ss2984879306, ss2985525067, ss2987752073, ss3021136274, ss3343710533, ss3626208407, ss3646246102, ss3651470518, ss3653648501, ss3655692288, ss3727485707, ss3746808076, ss3825575808, ss3826424137, ss3850006604, ss3895212944, ss3984464756, ss3984825421, ss5146483016, ss5237274014 NC_000001.10:154548945:C:T NC_000001.11:154576469:C:T (self)
27050470, 2029178, 62401, 20031779, 31907725, 579561163, ss2166540963, ss3023744054, ss3092142283, ss3687782307, ss3725065374, ss3770840932, ss3799809813, ss3945651177, ss4468301390 NC_000001.11:154576469:C:T NC_000001.11:154576469:C:T (self)
ss5683070, ss69809239, ss71647844, ss76901693, ss99307548, ss155752769, ss161151672 NT_004487.19:6037587:C:T NC_000001.11:154576469: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.

3 citations for rs4292956
PMID Title Author Year Journal
20736995 Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerström test for nicotine dependence. Wessel J et al. 2010 Neuropsychopharmacology
21606948 Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes. Swan GE et al. 2012 The pharmacogenomics journal
22048466 Smoking cessation pharmacogenetics: analysis of varenicline and bupropion in placebo-controlled clinical trials. King DP et al. 2012 Neuropsychopharmacology
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