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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs3821947

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:4858411 (GRCh38.p7) 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
A=0.40865 (51313/125568, TOPMED)
A=0.3965 (12212/30798, GnomAD)
A=0.368 (1845/5008, 1000G) (+ 2 more)
G=0.468 (1803/3854, ALSPAC)
G=0.464 (1719/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MSX1 : 2KB Upstream Variant
Publications
1 citation
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.p7 chr 4 NC_000004.12:g.4858411A>G
GRCh37.p13 chr 4 NC_000004.11:g.4860138A>G
MSX1 RefSeqGene NG_008121.1:g.3747A>G
Gene: MSX1, msh homeobox 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MSX1 transcript NM_002448.3:c. 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.

Not Reported in ClinVar
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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.40865 G=0.59135
The Genome Aggregation Database Global Study-wide 30798 A=0.3965 G=0.6035
The Genome Aggregation Database European Sub 18386 A=0.4732 G=0.5268
The Genome Aggregation Database African Sub 8698 A=0.221 G=0.779
The Genome Aggregation Database East Asian Sub 1606 A=0.486 G=0.514
The Genome Aggregation Database Other Sub 976 A=0.43 G=0.57
The Genome Aggregation Database American Sub 832 A=0.32 G=0.68
The Genome Aggregation Database Ashkenazi Jewish Sub 300 A=0.41 G=0.59
1000Genomes Global Study-wide 5008 A=0.368 G=0.632
1000Genomes African Sub 1322 A=0.163 G=0.837
1000Genomes East Asian Sub 1008 A=0.448 G=0.552
1000Genomes Europe Sub 1006 A=0.513 G=0.487
1000Genomes South Asian Sub 978 A=0.44 G=0.56
1000Genomes American Sub 694 A=0.33 G=0.67
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.532 G=0.468
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.536 G=0.464
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 Note
GRCh38.p7 chr 4 NC_000004.12:g.4858411A= NC_000004.12:g.4858411A>G
GRCh37.p13 chr 4 NC_000004.11:g.4860138A= NC_000004.11:g.4860138A>G
MSX1 RefSeqGene NG_008121.1:g.3747A= NG_008121.1:g.3747A>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#.

5 Frequency, 68 SubSNP submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss5008393 Aug 28, 2002 (107)
2 BCM_SSAHASNP ss10118516 Jul 11, 2003 (116)
3 CSHL-HAPMAP ss17805226 Feb 27, 2004 (120)
4 ABI ss44540070 Mar 15, 2006 (126)
5 ILLUMINA ss75257014 Dec 07, 2007 (129)
6 HGSV ss77526212 Dec 07, 2007 (129)
7 HGSV ss79986920 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss92449726 Mar 24, 2008 (129)
9 BGI ss104035457 Dec 01, 2009 (131)
10 ILLUMINA-UK ss116849264 Feb 14, 2009 (130)
11 KRIBB_YJKIM ss119465930 Dec 01, 2009 (131)
12 ENSEMBL ss139413462 Dec 01, 2009 (131)
13 ILLUMINA ss160647862 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss161899090 Jul 04, 2010 (132)
15 ILLUMINA ss173655081 Jul 04, 2010 (132)
16 BUSHMAN ss197947128 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss206655773 Jul 04, 2010 (132)
18 1000GENOMES ss220709500 Jul 14, 2010 (132)
19 1000GENOMES ss232236335 Jul 14, 2010 (132)
20 1000GENOMES ss239563014 Jul 15, 2010 (132)
21 GMI ss277552621 May 04, 2012 (137)
22 GMI ss284835050 Apr 25, 2013 (138)
23 PJP ss293059801 May 09, 2011 (134)
24 ILLUMINA ss480852403 May 04, 2012 (137)
25 ILLUMINA ss480870230 May 04, 2012 (137)
26 ILLUMINA ss481806130 Sep 08, 2015 (146)
27 ILLUMINA ss485221170 May 04, 2012 (137)
28 ILLUMINA ss537200831 Sep 08, 2015 (146)
29 SSMP ss651028124 Apr 25, 2013 (138)
30 ILLUMINA ss778704306 Sep 08, 2015 (146)
31 ILLUMINA ss783056532 Sep 08, 2015 (146)
32 ILLUMINA ss784014776 Sep 08, 2015 (146)
33 ILLUMINA ss832314438 Sep 08, 2015 (146)
34 ILLUMINA ss834163353 Sep 08, 2015 (146)
35 EVA-GONL ss979702086 Aug 21, 2014 (142)
36 1000GENOMES ss1308203939 Aug 21, 2014 (142)
37 DDI ss1429751236 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1580390232 Apr 01, 2015 (144)
39 EVA_DECODE ss1589196702 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1609290509 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1652284542 Apr 01, 2015 (144)
42 EVA_SVP ss1712647160 Apr 01, 2015 (144)
43 ILLUMINA ss1752524330 Sep 08, 2015 (146)
44 HAMMER_LAB ss1800897418 Sep 08, 2015 (146)
45 WEILL_CORNELL_DGM ss1922936479 Feb 12, 2016 (147)
46 JJLAB ss2022040321 Sep 14, 2016 (149)
47 USC_VALOUEV ss2150150225 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2260020566 Dec 20, 2016 (150)
49 TOPMED ss2427451161 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2625522297 Nov 08, 2017 (151)
51 ILLUMINA ss2634074222 Nov 08, 2017 (151)
52 GRF ss2705587099 Nov 08, 2017 (151)
53 GNOMAD ss2805016256 Nov 08, 2017 (151)
54 SWEGEN ss2994043161 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3024789385 Nov 08, 2017 (151)
56 CSHL ss3345514090 Nov 08, 2017 (151)
57 TOPMED ss3418947697 Nov 08, 2017 (151)
58 ILLUMINA ss3628889237 Jul 20, 2018 (151)
59 ILLUMINA ss3632013425 Jul 20, 2018 (151)
60 ILLUMINA ss3633323896 Jul 20, 2018 (151)
61 ILLUMINA ss3634042415 Jul 20, 2018 (151)
62 ILLUMINA ss3634938428 Jul 20, 2018 (151)
63 ILLUMINA ss3635725612 Jul 20, 2018 (151)
64 ILLUMINA ss3636637073 Jul 20, 2018 (151)
65 ILLUMINA ss3637478082 Jul 20, 2018 (151)
66 ILLUMINA ss3638468867 Jul 20, 2018 (151)
67 ILLUMINA ss3640645724 Jul 20, 2018 (151)
68 ILLUMINA ss3643421687 Jul 20, 2018 (151)
69 1000Genomes NC_000004.11 - 4860138 Jul 20, 2018 (151)
70 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 4860138 Jul 20, 2018 (151)
71 The Genome Aggregation Database NC_000004.11 - 4860138 Jul 20, 2018 (151)
72 Trans-Omics for Precision Medicine NC_000004.12 - 4858411 Jul 20, 2018 (151)
73 UK 10K study - Twins NC_000004.11 - 4860138 Jul 20, 2018 (151)
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)
rs57260804 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77526212, ss79986920 NC_000004.9:4978209:A= NC_000004.12:4858410:A= (self)
ss92449726, ss116849264, ss161899090, ss197947128, ss206655773, ss277552621, ss284835050, ss293059801, ss480852403, ss1589196702, ss1712647160, ss3643421687 NC_000004.10:4911038:A= NC_000004.12:4858410:A= (self)
19545367, 10887796, 145644011, 10887796, ss220709500, ss232236335, ss239563014, ss480870230, ss481806130, ss485221170, ss537200831, ss651028124, ss778704306, ss783056532, ss784014776, ss832314438, ss834163353, ss979702086, ss1308203939, ss1429751236, ss1580390232, ss1609290509, ss1652284542, ss1752524330, ss1800897418, ss1922936479, ss2022040321, ss2150150225, ss2427451161, ss2625522297, ss2634074222, ss2705587099, ss2805016256, ss2994043161, ss3345514090, ss3628889237, ss3632013425, ss3633323896, ss3634042415, ss3634938428, ss3635725612, ss3636637073, ss3637478082, ss3638468867, ss3640645724 NC_000004.11:4860137:A= NC_000004.12:4858410:A= (self)
274086492, ss2260020566, ss3024789385, ss3418947697 NC_000004.12:4858410:A= NC_000004.12:4858410:A= (self)
ss10118516 NT_006051.15:908491:A= NC_000004.12:4858410:A= (self)
ss17805226 NT_006051.16:947582:A= NC_000004.12:4858410:A= (self)
ss5008393, ss44540070, ss75257014, ss104035457, ss119465930, ss139413462, ss160647862, ss173655081 NT_006051.18:3381491:A= NC_000004.12:4858410:A= (self)
ss77526212, ss79986920 NC_000004.9:4978209:A>G NC_000004.12:4858410:A>G (self)
ss92449726, ss116849264, ss161899090, ss197947128, ss206655773, ss277552621, ss284835050, ss293059801, ss480852403, ss1589196702, ss1712647160, ss3643421687 NC_000004.10:4911038:A>G NC_000004.12:4858410:A>G (self)
19545367, 10887796, 145644011, 10887796, ss220709500, ss232236335, ss239563014, ss480870230, ss481806130, ss485221170, ss537200831, ss651028124, ss778704306, ss783056532, ss784014776, ss832314438, ss834163353, ss979702086, ss1308203939, ss1429751236, ss1580390232, ss1609290509, ss1652284542, ss1752524330, ss1800897418, ss1922936479, ss2022040321, ss2150150225, ss2427451161, ss2625522297, ss2634074222, ss2705587099, ss2805016256, ss2994043161, ss3345514090, ss3628889237, ss3632013425, ss3633323896, ss3634042415, ss3634938428, ss3635725612, ss3636637073, ss3637478082, ss3638468867, ss3640645724 NC_000004.11:4860137:A>G NC_000004.12:4858410:A>G (self)
274086492, ss2260020566, ss3024789385, ss3418947697 NC_000004.12:4858410:A>G NC_000004.12:4858410:A>G (self)
ss10118516 NT_006051.15:908491:A>G NC_000004.12:4858410:A>G (self)
ss17805226 NT_006051.16:947582:A>G NC_000004.12:4858410:A>G (self)
ss5008393, ss44540070, ss75257014, ss104035457, ss119465930, ss139413462, ss160647862, ss173655081 NT_006051.18:3381491:A>G NC_000004.12:4858410: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.

1 citation for rs3821947
PMID Title Author Year Journal
24123566 A novel multidisciplinary approach toward a better understanding of cranial suture closure: the first evidence of genetic effects in adulthood. Wolff K et al. 2013 American journal of human biology

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: 0.1.4.post833+d3ba21e