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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.

rs16941940

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr18:287648 (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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.06571 (8251/125568, TOPMED)
G=0.0652 (2047/31388, GnomAD)
G=0.118 (593/5008, 1000G) (+ 5 more)
G=0.071 (320/4480, Estonian)
G=0.053 (204/3854, ALSPAC)
G=0.059 (219/3708, TWINSUK)
G=0.08 (48/600, NorthernSweden)
G=0.41 (89/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.287648T>A
GRCh38.p12 chr 18 NC_000018.10:g.287648T>G
GRCh37.p13 chr 18 NC_000018.9:g.287648T>A
GRCh37.p13 chr 18 NC_000018.9:g.287648T>G
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 T=0.93428 G=0.06571, A=0.00001
gnomAD - Genomes Global Study-wide 31388 T=0.9348 G=0.0652
gnomAD - Genomes European Sub 18898 T=0.9379 G=0.0621
gnomAD - Genomes African Sub 8716 T=0.988 G=0.012
gnomAD - Genomes East Asian Sub 1550 T=0.601 G=0.399
gnomAD - Genomes Other Sub 1088 T=0.929 G=0.071
gnomAD - Genomes American Sub 846 T=0.93 G=0.07
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.95 G=0.05
1000Genomes Global Study-wide 5008 T=0.882 G=0.118
1000Genomes African Sub 1322 T=0.995 G=0.005
1000Genomes East Asian Sub 1008 T=0.585 G=0.415
1000Genomes Europe Sub 1006 T=0.940 G=0.060
1000Genomes South Asian Sub 978 T=0.95 G=0.05
1000Genomes American Sub 694 T=0.92 G=0.08
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.929 G=0.071
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.947 G=0.053
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.941 G=0.059
Northern Sweden ACPOP Study-wide 600 T=0.92 G=0.08
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.59 G=0.41
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 T= A G Note
GRCh38.p12 chr 18 NC_000018.10:g.28...

NC_000018.10:g.287648=

NC_000018.10:g.28...

NC_000018.10:g.287648T>A

NC_000018.10:g.28...

NC_000018.10:g.287648T>G

GRCh37.p13 chr 18 NC_000018.9:g.287...

NC_000018.9:g.287648=

NC_000018.9:g.287...

NC_000018.9:g.287648T>A

NC_000018.9:g.287...

NC_000018.9:g.287648T>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#.

52 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24012691 Sep 20, 2004 (123)
2 ILLUMINA ss67159464 Nov 29, 2006 (127)
3 ILLUMINA ss67508165 Nov 29, 2006 (127)
4 ILLUMINA ss68166478 Dec 12, 2006 (127)
5 ILLUMINA ss70645767 May 24, 2008 (130)
6 ILLUMINA ss71200195 May 16, 2007 (127)
7 ILLUMINA ss75601168 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss85339580 Dec 14, 2007 (130)
9 ILLUMINA ss153581513 Dec 01, 2009 (131)
10 GMI ss154732636 Dec 01, 2009 (131)
11 ILLUMINA ss159298849 Dec 01, 2009 (131)
12 ILLUMINA ss172671588 Jul 04, 2010 (132)
13 1000GENOMES ss237348229 Jul 15, 2010 (132)
14 1000GENOMES ss243622378 Jul 15, 2010 (132)
15 GMI ss282868907 May 04, 2012 (137)
16 ILLUMINA ss536922684 Sep 08, 2015 (146)
17 TISHKOFF ss565451568 Apr 25, 2013 (138)
18 SSMP ss661270312 Apr 25, 2013 (138)
19 ILLUMINA ss832810938 Jul 13, 2019 (153)
20 EVA-GONL ss993406424 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1081263965 Aug 21, 2014 (142)
22 1000GENOMES ss1359820076 Aug 21, 2014 (142)
23 HAMMER_LAB ss1397736186 Sep 08, 2015 (146)
24 EVA_UK10K_ALSPAC ss1636243809 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1679237842 Apr 01, 2015 (144)
26 EVA_DECODE ss1697457732 Apr 01, 2015 (144)
27 EVA_SVP ss1713602856 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1936876296 Feb 12, 2016 (147)
29 JJLAB ss2029208626 Sep 14, 2016 (149)
30 USC_VALOUEV ss2157703028 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2219197391 Dec 20, 2016 (150)
32 TOPMED ss2384441741 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2629099984 Nov 08, 2017 (151)
34 ILLUMINA ss2635075661 Nov 08, 2017 (151)
35 GRF ss2702270709 Nov 08, 2017 (151)
36 GNOMAD ss2953257608 Nov 08, 2017 (151)
37 SWEGEN ss3016027931 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3028428466 Nov 08, 2017 (151)
39 TOPMED ss3270599002 Nov 08, 2017 (151)
40 TOPMED ss3270599003 Nov 08, 2017 (151)
41 CSHL ss3351877373 Nov 08, 2017 (151)
42 ILLUMINA ss3627740999 Oct 12, 2018 (152)
43 ILLUMINA ss3638179044 Oct 12, 2018 (152)
44 ILLUMINA ss3639097351 Oct 12, 2018 (152)
45 ILLUMINA ss3639856717 Oct 12, 2018 (152)
46 ILLUMINA ss3643156063 Oct 12, 2018 (152)
47 ILLUMINA ss3643906006 Oct 12, 2018 (152)
48 EGCUT_WGS ss3682882393 Jul 13, 2019 (153)
49 EVA_DECODE ss3701062752 Jul 13, 2019 (153)
50 ACPOP ss3742280147 Jul 13, 2019 (153)
51 EVA ss3755022193 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3820284187 Jul 13, 2019 (153)
53 1000Genomes NC_000018.9 - 287648 Oct 12, 2018 (152)
54 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 287648 Oct 12, 2018 (152)
55 Genetic variation in the Estonian population NC_000018.9 - 287648 Oct 12, 2018 (152)
56 gnomAD - Genomes NC_000018.9 - 287648 Jul 13, 2019 (153)
57 Northern Sweden NC_000018.9 - 287648 Jul 13, 2019 (153)
58 TopMed NC_000018.10 - 287648 Oct 12, 2018 (152)
59 UK 10K study - Twins NC_000018.9 - 287648 Oct 12, 2018 (152)
60 A Vietnamese Genetic Variation Database NC_000018.9 - 287648 Jul 13, 2019 (153)
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)
rs57749538 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
163271285, ss3270599002 NC_000018.10:287647:T:A NC_000018.10:287647:T:A (self)
ss282868907, ss1397736186, ss1697457732, ss1713602856, ss2635075661, ss3639097351, ss3639856717, ss3643156063, ss3643906006 NC_000018.8:277647:T:G NC_000018.10:287647:T:G (self)
73106109, 40504357, 28620641, 199546010, 15565012, 40504357, 8951454, ss237348229, ss243622378, ss536922684, ss565451568, ss661270312, ss832810938, ss993406424, ss1081263965, ss1359820076, ss1636243809, ss1679237842, ss1936876296, ss2029208626, ss2157703028, ss2384441741, ss2629099984, ss2702270709, ss2953257608, ss3016027931, ss3351877373, ss3627740999, ss3638179044, ss3682882393, ss3742280147, ss3755022193 NC_000018.9:287647:T:G NC_000018.10:287647:T:G (self)
163271285, ss2219197391, ss3028428466, ss3270599003, ss3701062752, ss3820284187 NC_000018.10:287647:T:G NC_000018.10:287647:T:G (self)
ss24012691, ss67159464, ss67508165, ss68166478, ss70645767, ss71200195, ss75601168, ss85339580, ss153581513, ss154732636, ss159298849, ss172671588 NT_010859.14:277647:T:G NC_000018.10:287647:T:G (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 rs16941940

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.post270+ab078da