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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.

rs13277254

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr8:42694839 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.351422 (93018/264690, TOPMED)
G=0.344195 (48210/140066, GnomAD)
G=0.28819 (5444/18890, ALFA) (+ 15 more)
G=0.14236 (2386/16760, 8.3KJPN)
G=0.3540 (1773/5008, 1000G)
G=0.2301 (1031/4480, Estonian)
G=0.2234 (861/3854, ALSPAC)
G=0.2317 (859/3708, TWINSUK)
G=0.1754 (514/2930, KOREAN)
G=0.1812 (332/1832, Korea1K)
G=0.200 (200/998, GoNL)
G=0.227 (179/788, PRJEB37584)
G=0.232 (139/600, NorthernSweden)
G=0.224 (109/486, SGDP_PRJ)
G=0.356 (77/216, Qatari)
G=0.139 (30/216, Vietnamese)
G=0.19 (10/52, Siberian)
G=0.25 (10/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
21 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 8 NC_000008.11:g.42694839G>A
GRCh37.p13 chr 8 NC_000008.10:g.42549982G>A
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 18890 G=0.28819 A=0.71181
European Sub 14286 G=0.22526 A=0.77474
African Sub 2946 G=0.5944 A=0.4056
African Others Sub 114 G=0.649 A=0.351
African American Sub 2832 G=0.5922 A=0.4078
Asian Sub 112 G=0.196 A=0.804
East Asian Sub 86 G=0.19 A=0.81
Other Asian Sub 26 G=0.23 A=0.77
Latin American 1 Sub 146 G=0.349 A=0.651
Latin American 2 Sub 610 G=0.233 A=0.767
South Asian Sub 98 G=0.32 A=0.68
Other Sub 692 G=0.331 A=0.669


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 G=0.351422 A=0.648578
gnomAD - Genomes Global Study-wide 140066 G=0.344195 A=0.655805
gnomAD - Genomes European Sub 75890 G=0.22397 A=0.77603
gnomAD - Genomes African Sub 41918 G=0.60010 A=0.39990
gnomAD - Genomes American Sub 13650 G=0.27429 A=0.72571
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.2942 A=0.7058
gnomAD - Genomes East Asian Sub 3134 G=0.2020 A=0.7980
gnomAD - Genomes Other Sub 2150 G=0.3270 A=0.6730
8.3KJPN JAPANESE Study-wide 16760 G=0.14236 A=0.85764
1000Genomes Global Study-wide 5008 G=0.3540 A=0.6460
1000Genomes African Sub 1322 G=0.6566 A=0.3434
1000Genomes East Asian Sub 1008 G=0.2044 A=0.7956
1000Genomes Europe Sub 1006 G=0.2247 A=0.7753
1000Genomes South Asian Sub 978 G=0.273 A=0.727
1000Genomes American Sub 694 G=0.297 A=0.703
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2301 A=0.7699
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2234 A=0.7766
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2317 A=0.7683
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.1754 A=0.8246
Korean Genome Project KOREAN Study-wide 1832 G=0.1812 A=0.8188
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.200 A=0.800
CNV burdens in cranial meningiomas Global Study-wide 788 G=0.227 A=0.773
CNV burdens in cranial meningiomas CRM Sub 788 G=0.227 A=0.773
Northern Sweden ACPOP Study-wide 600 G=0.232 A=0.768
SGDP_PRJ Global Study-wide 486 G=0.224 A=0.776
Qatari Global Study-wide 216 G=0.356 A=0.644
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.139 A=0.861
Siberian Global Study-wide 52 G=0.19 A=0.81
The Danish reference pan genome Danish Study-wide 40 G=0.25 A=0.75
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 G= A
GRCh38.p13 chr 8 NC_000008.11:g.42694839= NC_000008.11:g.42694839G>A
GRCh37.p13 chr 8 NC_000008.10:g.42549982= NC_000008.10:g.42549982G>A
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#.

69 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss22761157 Apr 05, 2004 (121)
2 PERLEGEN ss23481578 Sep 20, 2004 (123)
3 ABI ss43144311 Mar 13, 2006 (126)
4 HGSV ss78531830 Dec 07, 2007 (129)
5 HGSV ss83974495 Dec 15, 2007 (130)
6 HGSV ss84530163 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss93876386 Mar 25, 2008 (129)
8 HUMANGENOME_JCVI ss98069241 Feb 05, 2009 (130)
9 KRIBB_YJKIM ss104806206 Feb 05, 2009 (130)
10 BGI ss105615066 Feb 05, 2009 (130)
11 1000GENOMES ss107989637 Jan 22, 2009 (130)
12 1000GENOMES ss115334195 Jan 25, 2009 (130)
13 ILLUMINA-UK ss115918536 Feb 14, 2009 (130)
14 ENSEMBL ss134403603 Dec 01, 2009 (131)
15 ENSEMBL ss143421082 Dec 01, 2009 (131)
16 GMI ss156307839 Dec 01, 2009 (131)
17 PERLEGEN ss161151698 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss162360709 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss164532496 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss166572582 Jul 04, 2010 (132)
21 BUSHMAN ss199091956 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss206537420 Jul 04, 2010 (132)
23 1000GENOMES ss223674764 Jul 14, 2010 (132)
24 1000GENOMES ss234415981 Jul 15, 2010 (132)
25 1000GENOMES ss241276906 Jul 15, 2010 (132)
26 BL ss254293367 May 09, 2011 (134)
27 GMI ss279785915 May 04, 2012 (137)
28 GMI ss285835219 Apr 25, 2013 (138)
29 PJP ss294264650 May 09, 2011 (134)
30 TISHKOFF ss560711647 Apr 25, 2013 (138)
31 SSMP ss655143624 Apr 25, 2013 (138)
32 EVA-GONL ss985446976 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1075471136 Aug 21, 2014 (142)
34 1000GENOMES ss1329584202 Aug 21, 2014 (142)
35 DDI ss1431493729 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1582660832 Apr 01, 2015 (144)
37 EVA_DECODE ss1595044616 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1620494215 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1663488248 Apr 01, 2015 (144)
40 HAMMER_LAB ss1805508412 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1928736250 Feb 12, 2016 (147)
42 GENOMED ss1970968449 Jul 19, 2016 (147)
43 JJLAB ss2025071094 Sep 14, 2016 (149)
44 USC_VALOUEV ss2153293514 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2302695574 Dec 20, 2016 (150)
46 TOPMED ss2472352506 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2627017645 Nov 08, 2017 (151)
48 GRF ss2709059665 Nov 08, 2017 (151)
49 GNOMAD ss2865985760 Nov 08, 2017 (151)
50 AFFY ss2986081416 Nov 08, 2017 (151)
51 SWEGEN ss3003068352 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3026325464 Nov 08, 2017 (151)
53 CSHL ss3348154802 Nov 08, 2017 (151)
54 TOPMED ss3560225440 Nov 08, 2017 (151)
55 URBANLAB ss3648903288 Oct 12, 2018 (152)
56 EGCUT_WGS ss3670762743 Jul 13, 2019 (153)
57 EVA_DECODE ss3721891204 Jul 13, 2019 (153)
58 ACPOP ss3735610968 Jul 13, 2019 (153)
59 EVA ss3767922408 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3811082824 Jul 13, 2019 (153)
61 EVA ss3831137529 Apr 26, 2020 (154)
62 EVA ss3839078961 Apr 26, 2020 (154)
63 EVA ss3844537809 Apr 26, 2020 (154)
64 SGDP_PRJ ss3869787818 Apr 26, 2020 (154)
65 KRGDB ss3917246157 Apr 26, 2020 (154)
66 KOGIC ss3963730676 Apr 26, 2020 (154)
67 EVA ss3984604743 Apr 26, 2021 (155)
68 TOPMED ss4783789905 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5188402811 Apr 26, 2021 (155)
70 1000Genomes NC_000008.10 - 42549982 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 42549982 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000008.10 - 42549982 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000008.10 - 42549982 Apr 26, 2020 (154)
74 gnomAD - Genomes NC_000008.11 - 42694839 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000008.10 - 42549982 Apr 26, 2020 (154)
76 KOREAN population from KRGDB NC_000008.10 - 42549982 Apr 26, 2020 (154)
77 Korean Genome Project NC_000008.11 - 42694839 Apr 26, 2020 (154)
78 Northern Sweden NC_000008.10 - 42549982 Jul 13, 2019 (153)
79 CNV burdens in cranial meningiomas NC_000008.10 - 42549982 Apr 26, 2021 (155)
80 Qatari NC_000008.10 - 42549982 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000008.10 - 42549982 Apr 26, 2020 (154)
82 Siberian NC_000008.10 - 42549982 Apr 26, 2020 (154)
83 8.3KJPN NC_000008.10 - 42549982 Apr 26, 2021 (155)
84 TopMed NC_000008.11 - 42694839 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000008.10 - 42549982 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000008.10 - 42549982 Jul 13, 2019 (153)
87 ALFA NC_000008.11 - 42694839 Apr 26, 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)
rs58708773 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78531830, ss83974495, ss84530163, ss93876386, ss107989637, ss115334195, ss115918536, ss162360709, ss164532496, ss166572582, ss199091956, ss206537420, ss254293367, ss279785915, ss285835219, ss294264650, ss1595044616 NC_000008.9:42669138:G:A NC_000008.11:42694838:G:A (self)
41701132, 23191825, 16500991, 8825770, 10356809, 24423551, 8895833, 154181, 10778180, 21804798, 5809868, 46372118, 23191825, 5166044, ss223674764, ss234415981, ss241276906, ss560711647, ss655143624, ss985446976, ss1075471136, ss1329584202, ss1431493729, ss1582660832, ss1620494215, ss1663488248, ss1805508412, ss1928736250, ss1970968449, ss2025071094, ss2153293514, ss2472352506, ss2627017645, ss2709059665, ss2865985760, ss2986081416, ss3003068352, ss3348154802, ss3670762743, ss3735610968, ss3767922408, ss3831137529, ss3839078961, ss3869787818, ss3917246157, ss3984604743, ss5188402811 NC_000008.10:42549981:G:A NC_000008.11:42694838:G:A (self)
294036548, 20108677, 388189790, 621167465, 7262562765, ss2302695574, ss3026325464, ss3560225440, ss3648903288, ss3721891204, ss3811082824, ss3844537809, ss3963730676, ss4783789905 NC_000008.11:42694838:G:A NC_000008.11:42694838:G:A (self)
ss22761157 NT_008251.14:4612246:G:A NC_000008.11:42694838:G:A (self)
ss23481578, ss43144311, ss98069241, ss104806206, ss105615066, ss134403603, ss143421082, ss156307839, ss161151698 NT_167187.1:30408127:G:A NC_000008.11:42694838:G:A (self)
Help

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

21 citations for rs13277254
PMID Title Author Year Journal
17135278 Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Saccone SF et al. 2007 Human molecular genetics
17158188 Novel genes identified in a high-density genome wide association study for nicotine dependence. Bierut LJ et al. 2007 Human molecular genetics
18571741 Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Portugal GS et al. 2008 Behavioural brain research
19029397 Nicotinic receptor gene variants influence susceptibility to heavy smoking. Stevens VL et al. 2008 Cancer epidemiology, biomarkers & prevention
19259974 Multiple distinct risk loci for nicotine dependence identified by dense coverage of the complete family of nicotinic receptor subunit (CHRN) genes. Saccone NL et al. 2009 American journal of medical genetics. Part B, Neuropsychiatric genetics
19492010 The genetic components of alcohol and nicotine co-addiction: from genes to behavior. Schlaepfer IR et al. 2008 Current drug abuse reviews
19760673 Association of CHRN genes with "dizziness" to tobacco. Ehringer MA et al. 2010 American journal of medical genetics. Part B, Neuropsychiatric genetics
20418888 Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Thorgeirsson TE et al. 2010 Nature genetics
20584212 Multiple cholinergic nicotinic receptor genes affect nicotine dependence risk in African and European Americans. Saccone NL et al. 2010 Genes, brain, and behavior
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
20840187 Peer smoking and the nicotinic receptor genes: an examination of genetic and environmental risks for nicotine dependence. Johnson EO et al. 2010 Addiction (Abingdon, England)
21079997 Uncovering hidden variance: pair-wise SNP analysis accounts for additional variance in nicotine dependence. Culverhouse RC et al. 2011 Human genetics
21191315 Genetic association of bipolar disorder with the β(3) nicotinic receptor subunit gene. Hartz SM et al. 2011 Psychiatric genetics
21606948 Varenicline for smoking cessation: nausea severity and variation in nicotinic receptor genes. Swan GE et al. 2012 The pharmacogenomics journal
23691092 Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language. Eicher JD et al. 2013 PloS one
25036316 Joint association of nicotinic acetylcholine receptor variants with abdominal obesity in American Indians: the Strong Heart Family Study. Zhu Y et al. 2014 PloS one
25778907 The DYX2 locus and neurochemical signaling genes contribute to speech sound disorder and related neurocognitive domains. Eicher JD et al. 2015 Genes, brain, and behavior
26318101 The β3 subunit of the nicotinic acetylcholine receptor: Modulation of gene expression and nicotine consumption. Kamens HM et al. 2015 Neuropharmacology
27166759 Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions. Yang J et al. 2016 Molecular psychiatry
27327258 Crucial roles of the CHRNB3-CHRNA6 gene cluster on chromosome 8 in nicotine dependence: update and subjects for future research. Wen L et al. 2016 Translational psychiatry
27827986 Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence. Zuo L et al. 2016 Genes
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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