Name: rs2273502
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.

rs2273502

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:63356470 (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=0.094930 (25127/264690, TOPMED)
T=0.094405 (13208/139908, GnomAD)
T=0.08379 (3177/37914, ALFA) (+ 18 more)
T=0.11173 (3157/28256, 14KJPN)
T=0.11016 (1846/16758, 8.3KJPN)
T=0.1174 (752/6404, 1000G_30x)
T=0.1164 (583/5008, 1000G)
T=0.0946 (432/4566, GO-ESP)
T=0.0717 (321/4480, Estonian)
T=0.0638 (246/3854, ALSPAC)
T=0.0636 (236/3708, TWINSUK)
T=0.1530 (447/2922, KOREAN)
T=0.1564 (284/1816, Korea1K)
T=0.172 (136/792, PRJEB37584)
T=0.097 (58/600, NorthernSweden)
T=0.114 (61/534, MGP)
T=0.208 (45/216, Qatari)
C=0.455 (51/112, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CHRNA4 : Intron Variant
Publications: 4 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	37914	C=0.91621	T=0.08379
European	Sub	30352	C=0.92564	T=0.07436
African	Sub	5580	C=0.8636	T=0.1364
African Others	Sub	198	C=0.838	T=0.162
African American	Sub	5382	C=0.8645	T=0.1355
Asian	Sub	156	C=0.872	T=0.128
East Asian	Sub	130	C=0.862	T=0.138
Other Asian	Sub	26	C=0.92	T=0.08
Latin American 1	Sub	146	C=0.904	T=0.096
Latin American 2	Sub	610	C=0.964	T=0.036
South Asian	Sub	98	C=0.83	T=0.17
Other	Sub	972	C=0.912	T=0.088

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=0.905070	T=0.094930
gnomAD - Genomes	Global	Study-wide	139908	C=0.905595	T=0.094405
gnomAD - Genomes	European	Sub	75806	C=0.92549	T=0.07451
gnomAD - Genomes	African	Sub	41874	C=0.86605	T=0.13395
gnomAD - Genomes	American	Sub	13638	C=0.92382	T=0.07618
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9133	T=0.0867
gnomAD - Genomes	East Asian	Sub	3126	C=0.8666	T=0.1334
gnomAD - Genomes	Other	Sub	2144	C=0.9035	T=0.0965
Allele Frequency Aggregator	Total	Global	37914	C=0.91621	T=0.08379
Allele Frequency Aggregator	European	Sub	30352	C=0.92564	T=0.07436
Allele Frequency Aggregator	African	Sub	5580	C=0.8636	T=0.1364
Allele Frequency Aggregator	Other	Sub	972	C=0.912	T=0.088
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.964	T=0.036
Allele Frequency Aggregator	Asian	Sub	156	C=0.872	T=0.128
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.904	T=0.096
Allele Frequency Aggregator	South Asian	Sub	98	C=0.83	T=0.17
14KJPN	JAPANESE	Study-wide	28256	C=0.88827	T=0.11173
8.3KJPN	JAPANESE	Study-wide	16758	C=0.88984	T=0.11016
1000Genomes_30x	Global	Study-wide	6404	C=0.8826	T=0.1174
1000Genomes_30x	African	Sub	1786	C=0.8589	T=0.1411
1000Genomes_30x	Europe	Sub	1266	C=0.9368	T=0.0632
1000Genomes_30x	South Asian	Sub	1202	C=0.8053	T=0.1947
1000Genomes_30x	East Asian	Sub	1170	C=0.8932	T=0.1068
1000Genomes_30x	American	Sub	980	C=0.938	T=0.062
1000Genomes	Global	Study-wide	5008	C=0.8836	T=0.1164
1000Genomes	African	Sub	1322	C=0.8601	T=0.1399
1000Genomes	East Asian	Sub	1008	C=0.8988	T=0.1012
1000Genomes	Europe	Sub	1006	C=0.9354	T=0.0646
1000Genomes	South Asian	Sub	978	C=0.809	T=0.191
1000Genomes	American	Sub	694	C=0.937	T=0.063
GO Exome Sequencing Project	Global	Study-wide	4566	C=0.9054	T=0.0946
GO Exome Sequencing Project	European American	Sub	3182	C=0.9302	T=0.0698
GO Exome Sequencing Project	African American	Sub	1384	C=0.8483	T=0.1517
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9283	T=0.0717
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9362	T=0.0638
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9364	T=0.0636
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8470	T=0.1530
Korean Genome Project	KOREAN	Study-wide	1816	C=0.8436	T=0.1564
CNV burdens in cranial meningiomas	Global	Study-wide	792	C=0.828	T=0.172
CNV burdens in cranial meningiomas	CRM	Sub	792	C=0.828	T=0.172
Northern Sweden	ACPOP	Study-wide	600	C=0.903	T=0.097
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.886	T=0.114
Qatari	Global	Study-wide	216	C=0.792	T=0.208
SGDP_PRJ	Global	Study-wide	112	C=0.455	T=0.545
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	10	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 20	NC_000020.11:g.63356470C>T
GRCh37.p13 chr 20	NC_000020.10:g.61987822C>T
CHRNA4 RefSeqGene	NG_011931.1:g.9874G>A

Gene: CHRNA4, cholinergic receptor nicotinic alpha 4 subunit (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHRNA4 transcript variant 1	NM_000744.7:c.229-55G>A	N/A	Intron Variant
CHRNA4 transcript variant 2	NM_001256573.2:c.-318-55G… NM_001256573.2:c.-318-55G>A	N/A	Intron Variant
CHRNA4 transcript variant 3	NR_046317.2:n.	N/A	Intron 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.

Allele: T (allele ID: 1228471 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001637603.3	not provided	Benign

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 20	NC_000020.11:g.63356470=	NC_000020.11:g.63356470C>T
GRCh37.p13 chr 20	NC_000020.10:g.61987822=	NC_000020.10:g.61987822C>T
CHRNA4 RefSeqGene	NG_011931.1:g.9874=	NG_011931.1:g.9874G>A
CHRNA4 transcript variant 1	NM_000744.6:c.229-55=	NM_000744.6:c.229-55G>A
CHRNA4 transcript variant 1	NM_000744.7:c.229-55=	NM_000744.7:c.229-55G>A
CHRNA4 transcript variant 2	NM_001256573.1:c.-318-55=	NM_001256573.1:c.-318-55G>A
CHRNA4 transcript variant 2	NM_001256573.2:c.-318-55=	NM_001256573.2:c.-318-55G>A
CHRNA4 transcript variant X1	XM_005260189.1:c.-85-55=	XM_005260189.1:c.-85-55G>A
CHRNA4 transcript variant X2	XM_005260190.1:c.-145-5443=	XM_005260190.1:c.-145-5443G>A

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#.

66 SubSNP, 20 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss3208990	Sep 28, 2001 (100)
2	SC_SNP	ss8310987	Apr 21, 2003 (114)
3	EGP_SNPS	ss70355360	May 16, 2007 (127)
4	TAPPERS	ss71641166	May 16, 2007 (127)
5	SI_EXO	ss76899924	Dec 07, 2007 (129)
6	UUGC	ss76901626	Dec 07, 2007 (129)
7	BGI	ss103785365	Dec 01, 2009 (131)
8	GMI	ss156620905	Dec 01, 2009 (131)
9	BUSHMAN	ss203945871	Jul 04, 2010 (132)
10	1000GENOMES	ss228451182	Jul 14, 2010 (132)
11	1000GENOMES	ss237901138	Jul 15, 2010 (132)
12	1000GENOMES	ss244056874	Jul 15, 2010 (132)
13	GMI	ss283445451	May 04, 2012 (137)
14	TISHKOFF	ss566367085	Apr 25, 2013 (138)
15	SSMP	ss662247748	Apr 25, 2013 (138)
16	NHLBI-ESP	ss713583246	Apr 25, 2013 (138)
17	EVA-GONL	ss994907227	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1082338408	Aug 21, 2014 (142)
19	1000GENOMES	ss1365485061	Aug 21, 2014 (142)
20	DDI	ss1429106047	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1579577315	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1639162819	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1682156852	Apr 01, 2015 (144)
24	EVA_DECODE	ss1698972121	Apr 01, 2015 (144)
25	EVA_MGP	ss1711547362	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809585120	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1938429908	Feb 12, 2016 (147)
28	JJLAB	ss2029995410	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2158566896	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2244225576	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2629490288	Nov 08, 2017 (151)
32	GRF	ss2704264405	Nov 08, 2017 (151)
33	ILLUMINA	ss2710945009	Nov 08, 2017 (151)
34	GNOMAD	ss2969414763	Nov 08, 2017 (151)
35	AFFY	ss2985839949	Nov 08, 2017 (151)
36	SWEGEN	ss3018473033	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3028831047	Nov 08, 2017 (151)
38	CSHL	ss3352595541	Nov 08, 2017 (151)
39	OMUKHERJEE_ADBS	ss3646552338	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3685158561	Jul 13, 2019 (153)
41	EVA_DECODE	ss3707310931	Jul 13, 2019 (153)
42	ACPOP	ss3743551204	Jul 13, 2019 (153)
43	EVA	ss3758867650	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3822021431	Jul 13, 2019 (153)
45	EVA	ss3825391888	Apr 27, 2020 (154)
46	EVA	ss3835764520	Apr 27, 2020 (154)
47	SGDP_PRJ	ss3889483959	Apr 27, 2020 (154)
48	KRGDB	ss3939809679	Apr 27, 2020 (154)
49	KOGIC	ss3982640674	Apr 27, 2020 (154)
50	FSA-LAB	ss3984221403	Apr 26, 2021 (155)
51	EVA	ss3984753162	Apr 26, 2021 (155)
52	EVA	ss3986839496	Apr 26, 2021 (155)
53	TOPMED	ss5094666112	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5230461461	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5309433118	Oct 16, 2022 (156)
56	EVA	ss5438567052	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5501649653	Oct 16, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5616187868	Oct 16, 2022 (156)
59	SANFORD_IMAGENETICS	ss5663567058	Oct 16, 2022 (156)
60	TOMMO_GENOMICS	ss5790522407	Oct 16, 2022 (156)
61	YY_MCH	ss5818198860	Oct 16, 2022 (156)
62	EVA	ss5845942913	Oct 16, 2022 (156)
63	EVA	ss5848553798	Oct 16, 2022 (156)
64	EVA	ss5853216501	Oct 16, 2022 (156)
65	EVA	ss5924156851	Oct 16, 2022 (156)
66	EVA	ss5958500713	Oct 16, 2022 (156)
67	1000Genomes	NC_000020.10 - 61987822	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000020.11 - 63356470	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 61987822	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000020.10 - 61987822	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000020.10 - 61987822	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000020.11 - 63356470	Apr 26, 2021 (155)
73	GO Exome Sequencing Project	NC_000020.10 - 61987822	Oct 12, 2018 (152)
74	KOREAN population from KRGDB	NC_000020.10 - 61987822	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000020.11 - 63356470	Apr 27, 2020 (154)
76	Medical Genome Project healthy controls from Spanish population	NC_000020.10 - 61987822	Apr 27, 2020 (154)
77	Northern Sweden	NC_000020.10 - 61987822	Jul 13, 2019 (153)
78	CNV burdens in cranial meningiomas	NC_000020.10 - 61987822	Apr 26, 2021 (155)
79	Qatari	NC_000020.10 - 61987822	Apr 27, 2020 (154)
80	SGDP_PRJ	NC_000020.10 - 61987822	Apr 27, 2020 (154)
81	Siberian	NC_000020.10 - 61987822	Apr 27, 2020 (154)
82	8.3KJPN	NC_000020.10 - 61987822	Apr 26, 2021 (155)
83	14KJPN	NC_000020.11 - 63356470	Oct 16, 2022 (156)
84	TopMed	NC_000020.11 - 63356470	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000020.10 - 61987822	Oct 12, 2018 (152)
86	ALFA	NC_000020.11 - 63356470	Apr 26, 2021 (155)
87	ClinVar	RCV001637603.3	Oct 16, 2022 (156)

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
ss203945871, ss283445451, ss1698972121	NC_000020.9:61458265:C:T	NC_000020.11:63356469:C:T	(self)
78973076, 43727850, 30896809, 5742254, 1848782, 46987073, 663122, 16836069, 302738, 20471830, 41500939, 11083250, 88430768, 43727850, ss228451182, ss237901138, ss244056874, ss566367085, ss662247748, ss713583246, ss994907227, ss1082338408, ss1365485061, ss1429106047, ss1579577315, ss1639162819, ss1682156852, ss1711547362, ss1809585120, ss1938429908, ss2029995410, ss2158566896, ss2629490288, ss2704264405, ss2710945009, ss2969414763, ss2985839949, ss3018473033, ss3352595541, ss3646552338, ss3685158561, ss3743551204, ss3758867650, ss3825391888, ss3835764520, ss3889483959, ss3939809679, ss3984221403, ss3984753162, ss3986839496, ss5230461461, ss5438567052, ss5663567058, ss5845942913, ss5848553798, ss5958500713	NC_000020.10:61987821:C:T	NC_000020.11:63356469:C:T	(self)
RCV001637603.3, 103713803, 556929692, 39018675, 124359511, 369775057, 366999894, ss2244225576, ss3028831047, ss3707310931, ss3822021431, ss3982640674, ss5094666112, ss5309433118, ss5501649653, ss5616187868, ss5790522407, ss5818198860, ss5853216501, ss5924156851	NC_000020.11:63356469:C:T	NC_000020.11:63356469:C:T	(self)
ss8310987, ss76899924	NT_011333.5:724451:C:T	NC_000020.11:63356469:C:T	(self)
ss3208990, ss70355360, ss71641166, ss76901626, ss103785365, ss156620905	NT_011333.6:724452:C:T	NC_000020.11:63356469:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs2273502

PMID	Title	Author	Year	Journal
15154117	A common haplotype of the nicotine acetylcholine receptor alpha 4 subunit gene is associated with vulnerability to nicotine addiction in men.	Feng Y et al.	2004	American journal of human genetics
17373692	No evidence for association between 19 cholinergic genes and bipolar disorder.	Shi J et al.	2007	American journal of medical genetics. Part B, Neuropsychiatric genetics
19693267	Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene.	Roe BE et al.	2009	PloS one
22180580	Association between nicotinic acetylcholine receptor single nucleotide polymorphisms and smoking cessation.	Spruell T et al.	2012	Nicotine & tobacco research

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
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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

rs2273502