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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.

rs1280

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr3:170995501 (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=0.19196 (24104/125568, TOPMED)
C=0.1923 (5936/30872, GnomAD)
C=0.184 (922/5008, 1000G) (+ 3 more)
C=0.132 (593/4480, Estonian)
C=0.127 (490/3854, ALSPAC)
C=0.129 (478/3708, 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 3 NC_000003.12:g.170995501T>C
GRCh37.p13 chr 3 NC_000003.11:g.170713290T>C
SLC2A2 RefSeqGene NG_008108.1:g.36479A>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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.80804 C=0.19196
gnomAD - Genomes Global Study-wide 30872 T=0.8077 C=0.1923
gnomAD - Genomes European Sub 18460 T=0.8654 C=0.1346
gnomAD - Genomes African Sub 8696 T=0.641 C=0.359
gnomAD - Genomes East Asian Sub 1596 T=0.996 C=0.004
gnomAD - Genomes Other Sub 980 T=0.83 C=0.17
gnomAD - Genomes American Sub 838 T=0.85 C=0.15
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.88 C=0.12
1000Genomes Global Study-wide 5008 T=0.816 C=0.184
1000Genomes African Sub 1322 T=0.626 C=0.374
1000Genomes East Asian Sub 1008 T=0.983 C=0.017
1000Genomes Europe Sub 1006 T=0.865 C=0.135
1000Genomes South Asian Sub 978 T=0.84 C=0.16
1000Genomes American Sub 694 T=0.83 C=0.17
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.868 C=0.132
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.873 C=0.127
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.871 C=0.129
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= C Note
GRCh38.p12 chr 3 NC_000003.12:g.170995501T= NC_000003.12:g.17099550...

NC_000003.12:g.170995501T>C

GRCh37.p13 chr 3 NC_000003.11:g.170713290T= NC_000003.11:g.17071329...

NC_000003.11:g.170713290T>C

SLC2A2 RefSeqGene NG_008108.1:g.36479A= NG_008108.1:g.36479A>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#.

40 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss1305 Sep 19, 2000 (36)
2 ILLUMINA ss75004855 Dec 06, 2007 (129)
3 BCMHGSC_JDW ss92370033 Mar 23, 2008 (129)
4 1000GENOMES ss111341684 Jan 25, 2009 (130)
5 1000GENOMES ss112688609 Jan 25, 2009 (130)
6 ILLUMINA-UK ss117376025 Feb 14, 2009 (130)
7 KRIBB_YJKIM ss119336967 Dec 01, 2009 (131)
8 ENSEMBL ss139291698 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss164959831 Jul 04, 2010 (132)
10 ILLUMINA ss172247783 Jul 04, 2010 (132)
11 BUSHMAN ss203518837 Jul 04, 2010 (132)
12 1000GENOMES ss220576282 Jul 14, 2010 (132)
13 1000GENOMES ss232140931 Jul 14, 2010 (132)
14 1000GENOMES ss239489060 Jul 15, 2010 (132)
15 ILLUMINA ss410902209 Sep 17, 2011 (135)
16 TISHKOFF ss557112445 Apr 25, 2013 (138)
17 SSMP ss650858511 Apr 25, 2013 (138)
18 EVA-GONL ss979450612 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1071050200 Aug 21, 2014 (142)
20 1000GENOMES ss1307254370 Aug 21, 2014 (142)
21 DDI ss1429670262 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1580294562 Apr 01, 2015 (144)
23 EVA_DECODE ss1588945075 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1608794664 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1651788697 Apr 01, 2015 (144)
26 EVA_SVP ss1712631192 Apr 01, 2015 (144)
27 HAMMER_LAB ss1800428236 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1922671276 Feb 12, 2016 (147)
29 GENOMED ss1969588532 Jul 19, 2016 (147)
30 JJLAB ss2021910929 Sep 14, 2016 (149)
31 USC_VALOUEV ss2150008439 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2258124347 Dec 20, 2016 (150)
33 TOPMED ss2425520028 Dec 20, 2016 (150)
34 GNOMAD ss2802282762 Nov 08, 2017 (151)
35 SWEGEN ss2993635656 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3024723668 Nov 08, 2017 (151)
37 CSHL ss3345393443 Nov 08, 2017 (151)
38 TOPMED ss3412763737 Nov 08, 2017 (151)
39 ILLUMINA ss3638456070 Oct 12, 2018 (152)
40 ILLUMINA ss3643409816 Oct 12, 2018 (152)
41 1000Genomes NC_000003.11 - 170713290 Oct 12, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 170713290 Oct 12, 2018 (152)
43 Genetic variation in the Estonian population NC_000003.11 - 170713290 Oct 12, 2018 (152)
44 gnomAD - Genomes NC_000003.11 - 170713290 Oct 12, 2018 (152)
45 TopMed NC_000003.12 - 170995501 Oct 12, 2018 (152)
46 UK 10K study - Twins NC_000003.11 - 170713290 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
ss92370033, ss111341684, ss112688609, ss117376025, ss164959831, ss203518837, ss1588945075, ss1712631192, ss3643409816 NC_000003.10:172195983:T:C NC_000003.12:170995500:T:C (self)
18559789, 10340828, 7322124, 142910516, 10340828, ss220576282, ss232140931, ss239489060, ss557112445, ss650858511, ss979450612, ss1071050200, ss1307254370, ss1429670262, ss1580294562, ss1608794664, ss1651788697, ss1800428236, ss1922671276, ss1969588532, ss2021910929, ss2150008439, ss2425520028, ss2802282762, ss2993635656, ss3345393443, ss3638456070 NC_000003.11:170713289:T:C NC_000003.12:170995500:T:C (self)
269156639, ss2258124347, ss3024723668, ss3412763737 NC_000003.12:170995500:T:C NC_000003.12:170995500:T:C (self)
ss1305, ss75004855, ss119336967, ss139291698, ss172247783, ss410902209 NT_005612.16:77208435:T:C NC_000003.12:170995500: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 rs1280
PMID Title Author Year Journal
26785747 Polymorphisms in genes involved in the absorption, distribution, metabolism, and excretion of drugs in the Kazakhs of Kazakhstan. Iskakova AN et al. 2016 BMC genetics

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