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dbSNP Short Genetic Variations

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.

rs406188

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr18:22723265 (GRCh38.p12) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.39448 (49534/125568, TOPMED)
C=0.4081 (11773/28846, GnomAD)
C=0.413 (2068/5008, 1000G) (+ 3 more)
G=0.472 (1975/4182, Estonian)
C=0.461 (1778/3854, ALSPAC)
C=0.448 (1663/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC101927571 : 500B Downstream 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.p12 chr 18 NC_000018.10:g.22723265C>G
GRCh38.p12 chr 18 NC_000018.10:g.22723265C>T
GRCh37.p13 chr 18 NC_000018.9:g.20303228C>G
GRCh37.p13 chr 18 NC_000018.9:g.20303228C>T
Gene: LOC101927571, uncharacterized LOC101927571 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC101927571 transcript NR_110782.1:n. N/A Downstream 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.39448 G=0.60552
gnomAD - Genomes Global Study-wide 28846 C=0.4081 T=0.0032, G=0.5887
gnomAD - Genomes European Sub 16886 C=0.4767 T=0.0044, G=0.5188
gnomAD - Genomes African Sub 8380 C=0.256 T=0.002, G=0.742
gnomAD - Genomes East Asian Sub 1606 C=0.396 T=0.000, G=0.604
gnomAD - Genomes Other Sub 866 C=0.48 T=0.00, G=0.52
gnomAD - Genomes American Sub 822 C=0.46 T=0.00, G=0.54
gnomAD - Genomes Ashkenazi Jewish Sub 286 C=0.53 T=0.00, G=0.47
1000Genomes Global Study-wide 5008 C=0.413 G=0.587
1000Genomes African Sub 1322 C=0.208 G=0.792
1000Genomes East Asian Sub 1008 C=0.433 G=0.567
1000Genomes Europe Sub 1006 C=0.483 G=0.517
1000Genomes South Asian Sub 978 C=0.54 G=0.46
1000Genomes American Sub 694 C=0.49 G=0.51
Genetic variation in the Estonian population Estonian Study-wide 4182 C=0.528 G=0.472
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.461 G=0.539
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.448 G=0.552
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= G T Note
GRCh38.p12 chr 18 NC_000018.10:g.22...

NC_000018.10:g.22723265C=

NC_000018.10:g.22...

NC_000018.10:g.22723265C>G

NC_000018.10:g.22...

NC_000018.10:g.22723265C>T

GRCh37.p13 chr 18 NC_000018.9:g.203...

NC_000018.9:g.20303228C=

NC_000018.9:g.203...

NC_000018.9:g.20303228C>G

NC_000018.9:g.203...

NC_000018.9:g.20303228C>T

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#.

45 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss5508848 Oct 08, 2002 (108)
2 TSC-CSHL ss5583698 Oct 08, 2002 (108)
3 SC_JCM ss5640778 Sep 28, 2016 (149)
4 WI_SSAHASNP ss12427862 Jul 11, 2003 (116)
5 ABI ss40953330 Mar 14, 2006 (126)
6 HGSV ss77157285 Dec 07, 2007 (129)
7 BCMHGSC_JDW ss90731124 Mar 24, 2008 (129)
8 1000GENOMES ss110220781 Jan 24, 2009 (130)
9 1000GENOMES ss114131274 Jan 25, 2009 (130)
10 ENSEMBL ss137289390 Dec 01, 2009 (131)
11 ENSEMBL ss139782810 Dec 01, 2009 (131)
12 GMI ss154922878 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss169242394 Jul 04, 2010 (132)
14 BUSHMAN ss203039957 Jul 04, 2010 (132)
15 1000GENOMES ss227764743 Jul 14, 2010 (132)
16 1000GENOMES ss237398627 Jul 15, 2010 (132)
17 1000GENOMES ss243663063 Jul 15, 2010 (132)
18 BL ss255530124 May 09, 2011 (134)
19 GMI ss282926822 May 04, 2012 (137)
20 GMI ss287254166 Apr 25, 2013 (138)
21 PJP ss292138420 May 09, 2011 (134)
22 TISHKOFF ss565535591 Apr 25, 2013 (138)
23 EVA-GONL ss993542968 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1081363896 Aug 21, 2014 (142)
25 1000GENOMES ss1360328332 Aug 21, 2014 (142)
26 DDI ss1428164142 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1578330787 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1636498022 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1679492055 Apr 01, 2015 (144)
30 EVA_DECODE ss1697595508 Apr 01, 2015 (144)
31 HAMMER_LAB ss1808977084 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1937019867 Feb 12, 2016 (147)
33 GENOMED ss1968481774 Jul 19, 2016 (147)
34 JJLAB ss2029279060 Sep 14, 2016 (149)
35 USC_VALOUEV ss2157779497 Dec 20, 2016 (150)
36 TOPMED ss2385478036 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2629137318 Nov 08, 2017 (151)
38 GRF ss2702362091 Nov 08, 2017 (151)
39 GNOMAD ss2954705073 Nov 08, 2017 (151)
40 SWEGEN ss3016254058 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3028465617 Nov 08, 2017 (151)
42 TOPMED ss3274734158 Nov 08, 2017 (151)
43 TOPMED ss3274734159 Nov 08, 2017 (151)
44 CSHL ss3351946086 Nov 08, 2017 (151)
45 URBANLAB ss3650755736 Oct 12, 2018 (152)
46 1000Genomes NC_000018.9 - 20303228 Oct 12, 2018 (152)
47 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 20303228 Oct 12, 2018 (152)
48 Genetic variation in the Estonian population NC_000018.9 - 20303228 Oct 12, 2018 (152)
49 gnomAD - Genomes NC_000018.9 - 20303228 Oct 12, 2018 (152)
50 TopMed NC_000018.10 - 22723265 Oct 12, 2018 (152)
51 UK 10K study - Twins NC_000018.9 - 20303228 Oct 12, 2018 (152)
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
ss77157285, ss90731124, ss110220781, ss114131274, ss169242394, ss203039957, ss255530124, ss282926822, ss287254166, ss292138420, ss1697595508 NC_000018.8:18557225:C:G NC_000018.10:22723264:C:G (self)
73633082, 40784997, 28815293, 88406602, 40784997, ss227764743, ss237398627, ss243663063, ss565535591, ss993542968, ss1081363896, ss1360328332, ss1428164142, ss1578330787, ss1636498022, ss1679492055, ss1808977084, ss1937019867, ss1968481774, ss2029279060, ss2157779497, ss2385478036, ss2629137318, ss2702362091, ss2954705073, ss3016254058, ss3351946086 NC_000018.9:20303227:C:G NC_000018.10:22723264:C:G (self)
165956783, ss3028465617, ss3274734158, ss3650755736 NC_000018.10:22723264:C:G NC_000018.10:22723264:C:G (self)
ss12427862 NT_010966.13:1792329:C:G NC_000018.10:22723264:C:G (self)
ss5508848, ss5583698, ss5640778, ss40953330, ss137289390, ss139782810, ss154922878 NT_010966.14:1792329:C:G NC_000018.10:22723264:C:G (self)
88406602, ss2954705073 NC_000018.9:20303227:C:T NC_000018.10:22723264:C:T (self)
ss3274734159 NC_000018.10:22723264:C:T NC_000018.10:22723264:C:T (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 rs406188

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.post104+4a6ee9c