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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.

rs2820443

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:219580167 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.22823 (28658/125568, TOPMED)
C=0.2268 (7013/30926, GnomAD)
C=0.223 (1118/5008, 1000G) (+ 3 more)
C=0.262 (1172/4480, Estonian)
C=0.287 (1107/3854, ALSPAC)
C=0.289 (1071/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p12 chr 1 NC_000001.11:g.219580167T>C
GRCh37.p13 chr 1 NC_000001.10:g.219753509T>C
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
TopMed Global Study-wide 125568 T=0.77177 C=0.22823
gnomAD - Genomes Global Study-wide 30926 T=0.7732 C=0.2268
gnomAD - Genomes European Sub 18474 T=0.7157 C=0.2843
gnomAD - Genomes African Sub 8718 T=0.928 C=0.072
gnomAD - Genomes East Asian Sub 1616 T=0.751 C=0.249
gnomAD - Genomes Other Sub 980 T=0.72 C=0.28
gnomAD - Genomes American Sub 836 T=0.53 C=0.47
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.77 C=0.23
1000Genomes Global Study-wide 5008 T=0.777 C=0.223
1000Genomes African Sub 1322 T=0.958 C=0.042
1000Genomes East Asian Sub 1008 T=0.759 C=0.241
1000Genomes Europe Sub 1006 T=0.714 C=0.286
1000Genomes South Asian Sub 978 T=0.80 C=0.20
1000Genomes American Sub 694 T=0.52 C=0.48
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.738 C=0.262
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.713 C=0.287
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.711 C=0.289
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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= C Note
GRCh38.p12 chr 1 NC_000001.11:g.219580167T= NC_000001.11:g.21958016...

NC_000001.11:g.219580167T>C

GRCh37.p13 chr 1 NC_000001.10:g.219753509T= NC_000001.10:g.21975350...

NC_000001.10:g.219753509T>C

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#.

54 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3994210 Sep 28, 2001 (100)
2 SC_SNP ss13026703 Dec 05, 2003 (123)
3 PERLEGEN ss24268151 Sep 20, 2004 (123)
4 ILLUMINA ss74982553 Dec 06, 2007 (129)
5 HGSV ss77272725 Dec 06, 2007 (129)
6 BCMHGSC_JDW ss87976762 Mar 23, 2008 (129)
7 BGI ss102823227 Dec 01, 2009 (131)
8 1000GENOMES ss108964198 Jan 23, 2009 (130)
9 KRIBB_YJKIM ss119446694 Dec 01, 2009 (131)
10 ENSEMBL ss138157352 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss167518109 Jul 04, 2010 (132)
12 ILLUMINA ss173474357 Jul 04, 2010 (132)
13 BUSHMAN ss199633326 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss205322206 Jul 04, 2010 (132)
15 1000GENOMES ss218892902 Jul 14, 2010 (132)
16 1000GENOMES ss230910901 Jul 14, 2010 (132)
17 1000GENOMES ss238520913 Jul 15, 2010 (132)
18 GMI ss276224384 May 04, 2012 (137)
19 PJP ss290738235 May 09, 2011 (134)
20 ILLUMINA ss410926070 Sep 17, 2011 (135)
21 ILLUMINA ss537130155 Sep 08, 2015 (146)
22 TISHKOFF ss555151461 Apr 25, 2013 (138)
23 SSMP ss648715086 Apr 25, 2013 (138)
24 EVA-GONL ss976166265 Aug 21, 2014 (142)
25 1000GENOMES ss1294729295 Aug 21, 2014 (142)
26 DDI ss1426118268 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1574693668 Apr 01, 2015 (144)
28 EVA_DECODE ss1585562824 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1602183215 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1645177248 Apr 01, 2015 (144)
31 EVA_SVP ss1712407061 Apr 01, 2015 (144)
32 WEILL_CORNELL_DGM ss1919389028 Feb 12, 2016 (147)
33 ILLUMINA ss1958358986 Feb 12, 2016 (147)
34 GENOMED ss1966978472 Jul 19, 2016 (147)
35 JJLAB ss2020218126 Sep 14, 2016 (149)
36 USC_VALOUEV ss2148249089 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2170255214 Dec 20, 2016 (150)
38 TOPMED ss2332875684 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624618248 Nov 08, 2017 (151)
40 ILLUMINA ss2632632155 Nov 08, 2017 (151)
41 GRF ss2698243169 Nov 08, 2017 (151)
42 ILLUMINA ss2710694609 Nov 08, 2017 (151)
43 GNOMAD ss2766432146 Nov 08, 2017 (151)
44 SWEGEN ss2988482338 Nov 08, 2017 (151)
45 ILLUMINA ss3021182254 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023869327 Nov 08, 2017 (151)
47 TOPMED ss3103899278 Nov 08, 2017 (151)
48 CSHL ss3343920929 Nov 08, 2017 (151)
49 ILLUMINA ss3626313585 Oct 11, 2018 (152)
50 ILLUMINA ss3637815398 Oct 11, 2018 (152)
51 ILLUMINA ss3640992713 Oct 11, 2018 (152)
52 ILLUMINA ss3641286836 Oct 11, 2018 (152)
53 ILLUMINA ss3642821659 Oct 11, 2018 (152)
54 ILLUMINA ss3651527598 Oct 11, 2018 (152)
55 1000Genomes NC_000001.10 - 219753509 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 219753509 Oct 11, 2018 (152)
57 Genetic variation in the Estonian population NC_000001.10 - 219753509 Oct 11, 2018 (152)
58 gnomAD - Genomes NC_000001.10 - 219753509 Oct 11, 2018 (152)
59 TopMed NC_000001.11 - 219580167 Oct 11, 2018 (152)
60 UK 10K study - Twins NC_000001.10 - 219753509 Oct 11, 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).

Associated ID History Updated (Build)
rs9431590 Sep 24, 2004 (123)
rs17545718 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77272725 NC_000001.8:216141903:T:C NC_000001.11:219580166:T:C (self)
ss87976762, ss108964198, ss167518109, ss199633326, ss205322206, ss276224384, ss290738235, ss1585562824, ss1712407061, ss3642821659 NC_000001.9:217820131:T:C NC_000001.11:219580166:T:C (self)
5586657, 3086338, 2182465, 15831345, 3086338, ss218892902, ss230910901, ss238520913, ss537130155, ss555151461, ss648715086, ss976166265, ss1294729295, ss1426118268, ss1574693668, ss1602183215, ss1645177248, ss1919389028, ss1958358986, ss1966978472, ss2020218126, ss2148249089, ss2332875684, ss2624618248, ss2632632155, ss2698243169, ss2710694609, ss2766432146, ss2988482338, ss3021182254, ss3343920929, ss3626313585, ss3637815398, ss3640992713, ss3641286836, ss3651527598 NC_000001.10:219753508:T:C NC_000001.11:219580166:T:C (self)
30082255, ss2170255214, ss3023869327, ss3103899278 NC_000001.11:219580166:T:C NC_000001.11:219580166:T:C (self)
ss13026703 NT_021953.15:846806:T:C NC_000001.11:219580166:T:C (self)
ss3994210, ss24268151, ss74982553, ss102823227, ss119446694, ss138157352, ss173474357, ss410926070 NT_167186.1:13271287:T:C NC_000001.11:219580166:T:C (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 rs2820443
PMID Title Author Year Journal
26977168 Association Between LYPLAL1 rs12137855 Polymorphism With Ultrasound-Defined Non-Alcoholic Fatty Liver Disease in a Chinese Han Population. Yuan C et al. 2015 Hepatitis monthly

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