Name: rs4292956
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154576470 (GRCh38.p14) 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) (+ 20 more)
T=0.13427 (3794/28256, 14KJPN)
T=0.07075 (1856/26234, ALFA)
T=0.13473 (2258/16760, 8.3KJPN)
T=0.0820 (525/6404, 1000G_30x)
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

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	26328	C=0.92924	T=0.07076
European	Sub	20576	C=0.92812	T=0.07188
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	1326	C=0.9276	T=0.0724

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").

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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
14KJPN	JAPANESE	Study-wide	28256	C=0.86573	T=0.13427
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_30x	Global	Study-wide	6404	C=0.9180	T=0.0820
1000Genomes_30x	African	Sub	1786	C=0.9384	T=0.0616
1000Genomes_30x	Europe	Sub	1266	C=0.9336	T=0.0664
1000Genomes_30x	South Asian	Sub	1202	C=0.9409	T=0.0591
1000Genomes_30x	East Asian	Sub	1170	C=0.8026	T=0.1974
1000Genomes_30x	American	Sub	980	C=0.970	T=0.030
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

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.p14 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_017000180.3:c.*538=	N/A	3 Prime UTR Variant
CHRNB2 transcript variant X1	XR_001736952.3:n.2314C>T	N/A	Non Coding Transcript Variant

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

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.p14 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_017000180.3:c.*538=	XM_017000180.3:c.*538C>T
CHRNB2 transcript variant X2	XM_017000180.2:c.*538=	XM_017000180.2:c.*538C>T
CHRNB2 transcript variant X2	XM_017000180.1:c.*538=	XM_017000180.1:c.*538C>T
CHRNB2 transcript variant X1	XR_001736952.3:n.2314=	XR_001736952.3:n.2314C>T
CHRNB2 transcript variant X1	XR_001736952.2:n.2299=	XR_001736952.2:n.2299C>T
CHRNB2 transcript variant X1	XR_001736952.1:n.2299=	XR_001736952.1:n.2299C>T

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#.

76 SubSNP, 22 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	GRF	ss2697971177	Nov 08, 2017 (151)
33	GNOMAD	ss2761315622	Nov 08, 2017 (151)
34	AFFY	ss2984879306	Nov 08, 2017 (151)
35	AFFY	ss2985525067	Nov 08, 2017 (151)
36	SWEGEN	ss2987752073	Nov 08, 2017 (151)
37	ILLUMINA	ss3021136274	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3023744054	Nov 08, 2017 (151)
39	CSHL	ss3343710533	Nov 08, 2017 (151)
40	ILLUMINA	ss3626208407	Oct 11, 2018 (152)
41	OMUKHERJEE_ADBS	ss3646246102	Oct 11, 2018 (152)
42	ILLUMINA	ss3651470518	Oct 11, 2018 (152)
43	ILLUMINA	ss3653648501	Oct 11, 2018 (152)
44	EGCUT_WGS	ss3655692288	Jul 12, 2019 (153)
45	EVA_DECODE	ss3687782307	Jul 12, 2019 (153)
46	ILLUMINA	ss3725065374	Jul 12, 2019 (153)
47	ACPOP	ss3727485707	Jul 12, 2019 (153)
48	EVA	ss3746808076	Jul 12, 2019 (153)
49	PAGE_CC	ss3770840932	Jul 12, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3799809813	Jul 12, 2019 (153)
51	EVA	ss3825575808	Apr 25, 2020 (154)
52	EVA	ss3826424137	Apr 25, 2020 (154)
53	SGDP_PRJ	ss3850006604	Apr 25, 2020 (154)
54	KRGDB	ss3895212944	Apr 25, 2020 (154)
55	KOGIC	ss3945651177	Apr 25, 2020 (154)
56	EVA	ss3984464756	Apr 25, 2021 (155)
57	EVA	ss3984825421	Apr 25, 2021 (155)
58	TOPMED	ss4468301390	Apr 25, 2021 (155)
59	TOMMO_GENOMICS	ss5146483016	Apr 25, 2021 (155)
60	EVA	ss5237274014	Apr 25, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5244292964	Oct 12, 2022 (156)
62	EVA	ss5322049728	Oct 12, 2022 (156)
63	HUGCELL_USP	ss5444886427	Oct 12, 2022 (156)
64	EVA	ss5506029233	Oct 12, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5517621044	Oct 12, 2022 (156)
66	SANFORD_IMAGENETICS	ss5624218048	Oct 12, 2022 (156)
67	SANFORD_IMAGENETICS	ss5626591410	Oct 12, 2022 (156)
68	TOMMO_GENOMICS	ss5673678640	Oct 12, 2022 (156)
69	YY_MCH	ss5801260115	Oct 12, 2022 (156)
70	EVA	ss5832665535	Oct 12, 2022 (156)
71	EVA	ss5847166837	Oct 12, 2022 (156)
72	EVA	ss5847556364	Oct 12, 2022 (156)
73	EVA	ss5849108926	Oct 12, 2022 (156)
74	EVA	ss5910245619	Oct 12, 2022 (156)
75	EVA	ss5938385258	Oct 12, 2022 (156)
76	EVA	ss5979290075	Oct 12, 2022 (156)
77	1000Genomes	NC_000001.10 - 154548946	Oct 11, 2018 (152)
78	1000Genomes_30x	NC_000001.11 - 154576470	Oct 12, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154548946	Oct 11, 2018 (152)
80	Genetic variation in the Estonian population	NC_000001.10 - 154548946	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 154548946	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000001.11 - 154576470	Apr 25, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000001.10 - 154548946	Apr 25, 2020 (154)
84	KOREAN population from KRGDB	NC_000001.10 - 154548946	Apr 25, 2020 (154)
85	Korean Genome Project	NC_000001.11 - 154576470	Apr 25, 2020 (154)
86	Northern Sweden	NC_000001.10 - 154548946	Jul 12, 2019 (153)
87	The PAGE Study	NC_000001.11 - 154576470	Jul 12, 2019 (153)
88	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 154548946	Apr 25, 2021 (155)
89	CNV burdens in cranial meningiomas	NC_000001.10 - 154548946	Apr 25, 2021 (155)
90	Qatari	NC_000001.10 - 154548946	Apr 25, 2020 (154)
91	SGDP_PRJ	NC_000001.10 - 154548946	Apr 25, 2020 (154)
92	Siberian	NC_000001.10 - 154548946	Apr 25, 2020 (154)
93	8.3KJPN	NC_000001.10 - 154548946	Apr 25, 2021 (155)
94	14KJPN	NC_000001.11 - 154576470	Oct 12, 2022 (156)
95	TopMed	NC_000001.11 - 154576470	Apr 25, 2021 (155)
96	UK 10K study - Twins	NC_000001.10 - 154548946	Oct 11, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000001.10 - 154548946	Jul 12, 2019 (153)
98	ALFA	NC_000001.11 - 154576470	Apr 25, 2021 (155)

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, ss2697971177, ss2761315622, ss2984879306, ss2985525067, ss2987752073, ss3021136274, ss3343710533, ss3626208407, ss3646246102, ss3651470518, ss3653648501, ss3655692288, ss3727485707, ss3746808076, ss3825575808, ss3826424137, ss3850006604, ss3895212944, ss3984464756, ss3984825421, ss5146483016, ss5237274014, ss5322049728, ss5506029233, ss5624218048, ss5626591410, ss5832665535, ss5847166837, ss5847556364, ss5938385258, ss5979290075	NC_000001.10:154548945:C:T	NC_000001.11:154576469:C:T	(self)
5146979, 27050470, 2029178, 62401, 7515744, 31907725, 579561163, ss2166540963, ss3023744054, ss3687782307, ss3725065374, ss3770840932, ss3799809813, ss3945651177, ss4468301390, ss5244292964, ss5444886427, ss5517621044, ss5673678640, ss5801260115, ss5849108926, ss5910245619	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)

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

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4292956