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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.

rs11803785

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:154575739 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.019910 (5270/264690, TOPMED)
A=0.004612 (1159/251284, GnomAD_exome)
A=0.018869 (2645/140178, GnomAD) (+ 11 more)
A=0.005346 (649/121396, ExAC)
A=0.01325 (196/14794, ALFA)
A=0.01861 (242/13006, GO-ESP)
A=0.0188 (94/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.004 (2/534, MGP)
A=0.000 (0/326, HapMap)
A=0.005 (1/216, Qatari)
C=0.50 (6/12, SGDP_PRJ)
A=0.50 (6/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHRNB2 : Intron Variant
Publications
0 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.154575739C>A
GRCh37.p13 chr 1 NC_000001.10:g.154548215C>A
CHRNB2 RefSeqGene NG_008027.1:g.12959C>A
Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB2 transcript NM_000748.3:c.1339-23C>A N/A Intron Variant
CHRNB2 transcript variant X2 XM_017000180.2:c.829-23C>A N/A Intron Variant
CHRNB2 transcript variant X1 XR_001736952.2:n. N/A Intron 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 14794 C=0.98675 A=0.01325
European Sub 9874 C=0.9997 A=0.0003
African Sub 2984 C=0.9393 A=0.0607
African Others Sub 114 C=0.965 A=0.035
African American Sub 2870 C=0.9383 A=0.0617
Asian Sub 116 C=1.000 A=0.000
East Asian Sub 88 C=1.00 A=0.00
Other Asian Sub 28 C=1.00 A=0.00
Latin American 1 Sub 154 C=0.994 A=0.006
Latin American 2 Sub 616 C=0.998 A=0.002
South Asian Sub 98 C=1.00 A=0.00
Other Sub 952 C=0.989 A=0.011


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=0.980090 A=0.019910
gnomAD - Exomes Global Study-wide 251284 C=0.995388 A=0.004612
gnomAD - Exomes European Sub 135224 C=0.999830 A=0.000170
gnomAD - Exomes Asian Sub 49010 C=0.99988 A=0.00012
gnomAD - Exomes American Sub 34584 C=0.99667 A=0.00333
gnomAD - Exomes African Sub 16256 C=0.93855 A=0.06145
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=0.99980 A=0.00020
gnomAD - Exomes Other Sub 6134 C=0.9977 A=0.0023
gnomAD - Genomes Global Study-wide 140178 C=0.981131 A=0.018869
gnomAD - Genomes European Sub 75950 C=0.99983 A=0.00017
gnomAD - Genomes African Sub 41982 C=0.93959 A=0.06041
gnomAD - Genomes American Sub 13650 C=0.99473 A=0.00527
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3124 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9888 A=0.0112
ExAC Global Study-wide 121396 C=0.994654 A=0.005346
ExAC Europe Sub 73344 C=0.99981 A=0.00019
ExAC Asian Sub 25166 C=0.99992 A=0.00008
ExAC American Sub 11576 C=0.99698 A=0.00302
ExAC African Sub 10404 C=0.94262 A=0.05738
ExAC Other Sub 906 C=0.999 A=0.001
GO Exome Sequencing Project Global Study-wide 13006 C=0.98139 A=0.01861
GO Exome Sequencing Project European American Sub 8600 C=0.9997 A=0.0003
GO Exome Sequencing Project African American Sub 4406 C=0.9458 A=0.0542
1000Genomes Global Study-wide 5008 C=0.9812 A=0.0188
1000Genomes African Sub 1322 C=0.9312 A=0.0688
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=0.996 A=0.004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 A=0.0000
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 A=0.004
HapMap Global Study-wide 326 C=1.000 A=0.000
HapMap American Sub 120 C=1.000 A=0.000
HapMap African Sub 116 C=1.000 A=0.000
HapMap Asian Sub 90 C=1.00 A=0.00
Qatari Global Study-wide 216 C=0.995 A=0.005
SGDP_PRJ Global Study-wide 12 C=0.50 A=0.50
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= A
GRCh38.p13 chr 1 NC_000001.11:g.154575739= NC_000001.11:g.154575739C>A
GRCh37.p13 chr 1 NC_000001.10:g.154548215= NC_000001.10:g.154548215C>A
CHRNB2 RefSeqGene NG_008027.1:g.12959= NG_008027.1:g.12959C>A
CHRNB2 transcript NM_000748.2:c.1339-23= NM_000748.2:c.1339-23C>A
CHRNB2 transcript NM_000748.3:c.1339-23= NM_000748.3:c.1339-23C>A
CHRNB2 transcript variant X2 XM_017000180.2:c.829-23= XM_017000180.2:c.829-23C>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#.

30 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17343205 Feb 28, 2004 (120)
2 ABI ss43907718 Mar 13, 2006 (126)
3 PERLEGEN ss161151678 Dec 01, 2009 (131)
4 ENSEMBL ss161175986 Dec 01, 2009 (131)
5 1000GENOMES ss218651244 Jul 14, 2010 (132)
6 1000GENOMES ss489766929 May 04, 2012 (137)
7 GSK-GENETICS ss491235506 May 04, 2012 (137)
8 ILLUMINA ss533979986 Sep 08, 2015 (146)
9 NHLBI-ESP ss712346838 Apr 25, 2013 (138)
10 JMKIDD_LAB ss1067426486 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1068269618 Aug 21, 2014 (142)
12 1000GENOMES ss1292925473 Aug 21, 2014 (142)
13 EVA_UK10K_ALSPAC ss1601213917 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1644207950 Apr 01, 2015 (144)
15 EVA_EXAC ss1685805752 Apr 01, 2015 (144)
16 EVA_MGP ss1710925492 Apr 01, 2015 (144)
17 WEILL_CORNELL_DGM ss1918916455 Feb 12, 2016 (147)
18 HUMAN_LONGEVITY ss2166540911 Dec 20, 2016 (150)
19 TOPMED ss2329045825 Dec 20, 2016 (150)
20 GNOMAD ss2731893300 Nov 08, 2017 (151)
21 GNOMAD ss2746450925 Nov 08, 2017 (151)
22 GNOMAD ss2761315552 Nov 08, 2017 (151)
23 AFFY ss2985525059 Nov 08, 2017 (151)
24 TOPMED ss3092142132 Nov 08, 2017 (151)
25 ILLUMINA ss3626208398 Oct 11, 2018 (152)
26 KHV_HUMAN_GENOMES ss3799809805 Jul 12, 2019 (153)
27 EVA ss3823663173 Apr 25, 2020 (154)
28 SGDP_PRJ ss3850006592 Apr 25, 2020 (154)
29 EVA ss3986138980 Apr 25, 2021 (155)
30 TOPMED ss4468301161 Apr 25, 2021 (155)
31 1000Genomes NC_000001.10 - 154548215 Oct 11, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 154548215 Oct 11, 2018 (152)
33 ExAC NC_000001.10 - 154548215 Oct 11, 2018 (152)
34 gnomAD - Genomes NC_000001.11 - 154575739 Apr 25, 2021 (155)
35 gnomAD - Exomes NC_000001.10 - 154548215 Jul 12, 2019 (153)
36 GO Exome Sequencing Project NC_000001.10 - 154548215 Oct 11, 2018 (152)
37 HapMap NC_000001.11 - 154575739 Apr 25, 2020 (154)
38 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 154548215 Apr 25, 2020 (154)
39 Qatari NC_000001.10 - 154548215 Apr 25, 2020 (154)
40 SGDP_PRJ NC_000001.10 - 154548215 Apr 25, 2020 (154)
41 TopMed NC_000001.11 - 154575739 Apr 25, 2021 (155)
42 UK 10K study - Twins NC_000001.10 - 154548215 Oct 11, 2018 (152)
43 ALFA NC_000001.11 - 154575739 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
ss491235506 NC_000001.9:152814838:C:A NC_000001.11:154575738:C:A (self)
3717526, 2021146, 5024445, 915682, 121771, 42244, 958385, 2023572, 2021146, ss218651244, ss489766929, ss533979986, ss712346838, ss1067426486, ss1068269618, ss1292925473, ss1601213917, ss1644207950, ss1685805752, ss1710925492, ss1918916455, ss2329045825, ss2731893300, ss2746450925, ss2761315552, ss2985525059, ss3626208398, ss3823663173, ss3850006592, ss3986138980 NC_000001.10:154548214:C:A NC_000001.11:154575738:C:A (self)
27050304, 176439, 20031640, 31907496, 13118306095, ss2166540911, ss3092142132, ss3799809805, ss4468301161 NC_000001.11:154575738:C:A NC_000001.11:154575738:C:A (self)
ss43907718, ss161151678, ss161175986 NT_004487.19:6036856:C:A NC_000001.11:154575738:C:A (self)
ss17343205 NT_079484.1:998046:C:A NC_000001.11:154575738:C:A (self)
Help

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

No publications for rs11803785

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