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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.

rs3926124

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:154569616 (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
G=0.113061 (29926/264690, TOPMED)
G=0.026461 (6650/251316, GnomAD_exome)
G=0.108293 (15172/140102, GnomAD) (+ 11 more)
G=0.032636 (3956/121214, ExAC)
G=0.03455 (1752/50710, ALFA)
G=0.11895 (1547/13006, GO-ESP)
G=0.1082 (542/5008, 1000G)
G=0.0011 (5/4480, Estonian)
G=0.0005 (2/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.2737 (300/1096, HapMap)
G=0.006 (3/534, MGP)
G=0.088 (19/216, Qatari)
A=0.34 (20/58, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNB2 : Intron Variant
LOC107985206 : 2KB Upstream Variant
Publications
2 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.154569616A>G
GRCh37.p13 chr 1 NC_000001.10:g.154542092A>G
CHRNB2 RefSeqGene NG_008027.1:g.6836A>G
Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB2 transcript NM_000748.3:c.210+9A>G N/A Intron Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.-165+9A>G N/A Intron Variant
CHRNB2 transcript variant X1 XR_001736952.2:n. N/A Intron Variant
Gene: LOC107985206, uncharacterized LOC107985206 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107985206 transcript variant X1 XR_001738237.1:n. N/A Upstream Transcript Variant
LOC107985206 transcript variant X2 XR_001738238.2:n. N/A Upstream 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.

Allele: G (allele ID: 167982 )
ClinVar Accession Disease Names Clinical Significance
RCV000145710.3 not specified Benign
RCV000464092.3 Autosomal dominant nocturnal frontal lobe epilepsy Benign

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 50710 A=0.96545 G=0.03455
European Sub 37248 A=0.99917 G=0.00083
African Sub 4712 A=0.6817 G=0.3183
African Others Sub 152 A=0.553 G=0.447
African American Sub 4560 A=0.6860 G=0.3140
Asian Sub 172 A=1.000 G=0.000
East Asian Sub 114 A=1.000 G=0.000
Other Asian Sub 58 A=1.00 G=0.00
Latin American 1 Sub 504 A=0.877 G=0.123
Latin American 2 Sub 634 A=0.978 G=0.022
South Asian Sub 98 A=1.00 G=0.00
Other Sub 7342 A=0.9803 G=0.0197


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=0.886939 G=0.113061
gnomAD - Exomes Global Study-wide 251316 A=0.973539 G=0.026461
gnomAD - Exomes European Sub 135292 A=0.999394 G=0.000606
gnomAD - Exomes Asian Sub 49006 A=0.99929 G=0.00071
gnomAD - Exomes American Sub 34578 A=0.98395 G=0.01605
gnomAD - Exomes African Sub 16226 A=0.63608 G=0.36392
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=0.99970 G=0.00030
gnomAD - Exomes Other Sub 6134 A=0.9886 G=0.0114
gnomAD - Genomes Global Study-wide 140102 A=0.891707 G=0.108293
gnomAD - Genomes European Sub 75920 A=0.99925 G=0.00075
gnomAD - Genomes African Sub 41918 A=0.65158 G=0.34842
gnomAD - Genomes American Sub 13662 A=0.97431 G=0.02569
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3128 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9260 G=0.0740
ExAC Global Study-wide 121214 A=0.967364 G=0.032636
ExAC Europe Sub 73242 A=0.99934 G=0.00066
ExAC Asian Sub 25136 A=0.99940 G=0.00060
ExAC American Sub 11560 A=0.98599 G=0.01401
ExAC African Sub 10370 A=0.64156 G=0.35844
ExAC Other Sub 906 A=0.985 G=0.015
GO Exome Sequencing Project Global Study-wide 13006 A=0.88105 G=0.11895
GO Exome Sequencing Project European American Sub 8600 A=0.9981 G=0.0019
GO Exome Sequencing Project African American Sub 4406 A=0.6525 G=0.3475
1000Genomes Global Study-wide 5008 A=0.8918 G=0.1082
1000Genomes African Sub 1322 A=0.6014 G=0.3986
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.978 G=0.022
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9989 G=0.0011
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9995 G=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 G=0.0003
HapMap Global Study-wide 1096 A=0.7263 G=0.2737
HapMap African Sub 692 A=0.637 G=0.363
HapMap American Sub 316 A=0.845 G=0.155
HapMap Asian Sub 88 A=1.00 G=0.00
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.994 G=0.006
Qatari Global Study-wide 216 A=0.912 G=0.088
SGDP_PRJ Global Study-wide 58 A=0.34 G=0.66
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.154569616= NC_000001.11:g.154569616A>G
GRCh37.p13 chr 1 NC_000001.10:g.154542092= NC_000001.10:g.154542092A>G
CHRNB2 RefSeqGene NG_008027.1:g.6836= NG_008027.1:g.6836A>G
CHRNB2 transcript NM_000748.2:c.210+9= NM_000748.2:c.210+9A>G
CHRNB2 transcript NM_000748.3:c.210+9= NM_000748.3:c.210+9A>G
CHRNB2 transcript variant X2 XM_017000180.2:c.-165+9= XM_017000180.2:c.-165+9A>G
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#.

49 SubSNP, 14 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5160341 Oct 10, 2002 (108)
2 SC_JCM ss5934852 Feb 20, 2003 (111)
3 ABI ss44096232 Mar 13, 2006 (126)
4 ILLUMINA ss75128784 Dec 07, 2007 (129)
5 HGSV ss84886729 Dec 15, 2007 (130)
6 1000GENOMES ss111154420 Jan 25, 2009 (130)
7 ILLUMINA-UK ss119032226 Feb 15, 2009 (130)
8 KRIBB_YJKIM ss119468887 Dec 01, 2009 (131)
9 PERLEGEN ss161151682 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss164119998 Jul 04, 2010 (132)
11 ILLUMINA ss173674758 Jul 04, 2010 (132)
12 BUSHMAN ss199086307 Jul 04, 2010 (132)
13 1000GENOMES ss218651231 Jul 14, 2010 (132)
14 1000GENOMES ss489766911 May 04, 2012 (137)
15 GSK-GENETICS ss491235425 May 04, 2012 (137)
16 CLINSEQ_SNP ss491605071 May 04, 2012 (137)
17 ILLUMINA ss533980700 Sep 08, 2015 (146)
18 TISHKOFF ss554693737 Apr 25, 2013 (138)
19 NHLBI-ESP ss712346809 Apr 25, 2013 (138)
20 JMKIDD_LAB ss974437351 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067426480 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1068269600 Aug 21, 2014 (142)
23 1000GENOMES ss1292925337 Aug 21, 2014 (142)
24 CLINVAR ss1493129976 Dec 05, 2014 (142)
25 EVA_UK10K_ALSPAC ss1601213836 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1644207869 Apr 01, 2015 (144)
27 EVA_EXAC ss1685805540 Apr 01, 2015 (144)
28 EVA_MGP ss1710925481 Apr 01, 2015 (144)
29 HAMMER_LAB ss1795092166 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1918916436 Feb 12, 2016 (147)
31 HUMAN_LONGEVITY ss2166540610 Dec 20, 2016 (150)
32 TOPMED ss2329045507 Dec 20, 2016 (150)
33 GNOMAD ss2731892874 Nov 08, 2017 (151)
34 GNOMAD ss2746450836 Nov 08, 2017 (151)
35 GNOMAD ss2761315160 Nov 08, 2017 (151)
36 TOPMED ss3092141105 Nov 08, 2017 (151)
37 ILLUMINA ss3626208384 Oct 11, 2018 (152)
38 ILLUMINA ss3637787294 Oct 11, 2018 (152)
39 ILLUMINA ss3642796574 Oct 11, 2018 (152)
40 EGCUT_WGS ss3655692210 Jul 12, 2019 (153)
41 KHV_HUMAN_GENOMES ss3799809785 Jul 12, 2019 (153)
42 EVA ss3823663128 Apr 25, 2020 (154)
43 EVA ss3825575793 Apr 25, 2020 (154)
44 EVA ss3826424127 Apr 25, 2020 (154)
45 SGDP_PRJ ss3850006534 Apr 25, 2020 (154)
46 FSA-LAB ss3983947177 Apr 25, 2021 (155)
47 EVA ss3986138970 Apr 25, 2021 (155)
48 EVA ss4016938045 Apr 25, 2021 (155)
49 TOPMED ss4468299644 Apr 25, 2021 (155)
50 1000Genomes NC_000001.10 - 154542092 Oct 11, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 154542092 Oct 11, 2018 (152)
52 Genetic variation in the Estonian population NC_000001.10 - 154542092 Oct 11, 2018 (152)
53 ExAC NC_000001.10 - 154542092 Oct 11, 2018 (152)
54 gnomAD - Genomes NC_000001.11 - 154569616 Apr 25, 2021 (155)
55 gnomAD - Exomes NC_000001.10 - 154542092 Jul 12, 2019 (153)
56 GO Exome Sequencing Project NC_000001.10 - 154542092 Oct 11, 2018 (152)
57 HapMap NC_000001.11 - 154569616 Apr 25, 2020 (154)
58 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 154542092 Apr 25, 2020 (154)
59 Qatari NC_000001.10 - 154542092 Apr 25, 2020 (154)
60 SGDP_PRJ NC_000001.10 - 154542092 Apr 25, 2020 (154)
61 TopMed NC_000001.11 - 154569616 Apr 25, 2021 (155)
62 UK 10K study - Twins NC_000001.10 - 154542092 Oct 11, 2018 (152)
63 ALFA NC_000001.11 - 154569616 Apr 25, 2021 (155)
64 ClinVar RCV000145710.3 Oct 11, 2018 (152)
65 ClinVar RCV000464092.3 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)
rs58773401 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84886729 NC_000001.8:151355164:A:G NC_000001.11:154569615:A:G (self)
ss111154420, ss119032226, ss164119998, ss199086307, ss491235425, ss491605071, ss3642796574 NC_000001.9:152808715:A:G NC_000001.11:154569615:A:G (self)
3717385, 2021060, 1430458, 5024222, 915291, 121726, 42233, 958366, 2023514, 2021060, ss218651231, ss489766911, ss533980700, ss554693737, ss712346809, ss974437351, ss1067426480, ss1068269600, ss1292925337, ss1601213836, ss1644207869, ss1685805540, ss1710925481, ss1795092166, ss1918916436, ss2329045507, ss2731892874, ss2746450836, ss2761315160, ss3626208384, ss3637787294, ss3655692210, ss3823663128, ss3825575793, ss3826424127, ss3850006534, ss3983947177, ss3986138970, ss4016938045 NC_000001.10:154542091:A:G NC_000001.11:154569615:A:G (self)
RCV000145710.3, RCV000464092.3, 27049142, 176435, 20030695, 31905979, 3225182267, ss1493129976, ss2166540610, ss3092141105, ss3799809785, ss4468299644 NC_000001.11:154569615:A:G NC_000001.11:154569615:A:G (self)
ss5160341, ss5934852, ss44096232, ss75128784, ss119468887, ss161151682, ss173674758 NT_004487.19:6030733:A:G NC_000001.11:154569615: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.

2 citations for rs3926124
PMID Title Author Year Journal
18043764 Association of alpha4beta2 nicotinic receptor and heavy smoking in schizophrenia. Voineskos S et al. 2007 Journal of psychiatry & neuroscience
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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