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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.

rs17280262

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr14:96587587 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.04716 (5922/125568, TOPMED)
T=0.0551 (1728/31366, GnomAD)
T=0.038 (189/5008, 1000G) (+ 5 more)
T=0.085 (379/4480, Estonian)
T=0.054 (207/3854, ALSPAC)
T=0.059 (217/3708, TWINSUK)
T=0.10 (59/600, NorthernSweden)
T=0.02 (4/212, 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 14 NC_000014.9:g.96587587C>T
GRCh37.p13 chr 14 NC_000014.8:g.97053924C>T
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 C=0.95284 T=0.04716
gnomAD - Genomes Global Study-wide 31366 C=0.9449 T=0.0551
gnomAD - Genomes European Sub 18880 C=0.9278 T=0.0722
gnomAD - Genomes African Sub 8700 C=0.979 T=0.021
gnomAD - Genomes East Asian Sub 1560 C=0.967 T=0.033
gnomAD - Genomes Other Sub 1088 C=0.929 T=0.071
gnomAD - Genomes American Sub 848 C=0.96 T=0.04
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.93 T=0.07
1000Genomes Global Study-wide 5008 C=0.962 T=0.038
1000Genomes African Sub 1322 C=0.982 T=0.018
1000Genomes East Asian Sub 1008 C=0.955 T=0.045
1000Genomes Europe Sub 1006 C=0.927 T=0.073
1000Genomes South Asian Sub 978 C=0.98 T=0.02
1000Genomes American Sub 694 C=0.95 T=0.05
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.915 T=0.085
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.946 T=0.054
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.941 T=0.059
Northern Sweden ACPOP Study-wide 600 C=0.90 T=0.10
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.98 T=0.02
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= T Note
GRCh38.p12 chr 14 NC_000014.9:g.96587587= NC_000014.9:g.96587587C>T
GRCh37.p13 chr 14 NC_000014.8:g.97053924= NC_000014.8:g.97053924C>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#.

62 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24721612 Sep 20, 2004 (123)
2 ABI ss43600977 Mar 14, 2006 (126)
3 ILLUMINA ss75048456 Dec 06, 2007 (129)
4 HUMANGENOME_JCVI ss96939399 Feb 05, 2009 (130)
5 KRIBB_YJKIM ss119883811 Dec 01, 2009 (131)
6 ILLUMINA ss160437850 Dec 01, 2009 (131)
7 ILLUMINA ss172800659 Jul 04, 2010 (132)
8 BUSHMAN ss200465820 Jul 04, 2010 (132)
9 1000GENOMES ss243078119 Jul 15, 2010 (132)
10 ILLUMINA ss480222674 May 04, 2012 (137)
11 ILLUMINA ss480233312 May 04, 2012 (137)
12 ILLUMINA ss480967586 Sep 08, 2015 (146)
13 ILLUMINA ss484909347 May 04, 2012 (137)
14 ILLUMINA ss536962086 Sep 08, 2015 (146)
15 TISHKOFF ss564295102 Apr 25, 2013 (138)
16 SSMP ss659991941 Apr 25, 2013 (138)
17 ILLUMINA ss778459211 Sep 08, 2015 (146)
18 ILLUMINA ss782900983 Sep 08, 2015 (146)
19 ILLUMINA ss783864335 Sep 08, 2015 (146)
20 ILLUMINA ss832155782 Sep 08, 2015 (146)
21 ILLUMINA ss833914897 Sep 08, 2015 (146)
22 EVA-GONL ss991483897 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1079910377 Aug 21, 2014 (142)
24 1000GENOMES ss1352278316 Aug 21, 2014 (142)
25 HAMMER_LAB ss1397689710 Sep 08, 2015 (146)
26 EVA_GENOME_DK ss1577452104 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1632423111 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1675417144 Apr 01, 2015 (144)
29 EVA_DECODE ss1695500068 Apr 01, 2015 (144)
30 EVA_SVP ss1713469582 Apr 01, 2015 (144)
31 ILLUMINA ss1752150252 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1934854977 Feb 12, 2016 (147)
33 JJLAB ss2028212521 Sep 14, 2016 (149)
34 USC_VALOUEV ss2156597356 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2204616876 Dec 20, 2016 (150)
36 TOPMED ss2369023242 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2628596097 Nov 08, 2017 (151)
38 ILLUMINA ss2633194224 Nov 08, 2017 (151)
39 GRF ss2701033553 Nov 08, 2017 (151)
40 GNOMAD ss2931284561 Nov 08, 2017 (151)
41 SWEGEN ss3012720331 Nov 08, 2017 (151)
42 TOPMED ss3219410595 Nov 08, 2017 (151)
43 ILLUMINA ss3627296468 Oct 12, 2018 (152)
44 ILLUMINA ss3631189792 Oct 12, 2018 (152)
45 ILLUMINA ss3633087861 Oct 12, 2018 (152)
46 ILLUMINA ss3633791839 Oct 12, 2018 (152)
47 ILLUMINA ss3634592695 Oct 12, 2018 (152)
48 ILLUMINA ss3635481051 Oct 12, 2018 (152)
49 ILLUMINA ss3636282024 Oct 12, 2018 (152)
50 ILLUMINA ss3637232244 Oct 12, 2018 (152)
51 ILLUMINA ss3638069316 Oct 12, 2018 (152)
52 ILLUMINA ss3640300022 Oct 12, 2018 (152)
53 ILLUMINA ss3643054610 Oct 12, 2018 (152)
54 BIOINF_KMB_FNS_UNIBA ss3645365716 Oct 12, 2018 (152)
55 URBANLAB ss3650272428 Oct 12, 2018 (152)
56 EGCUT_WGS ss3679987366 Jul 13, 2019 (153)
57 EVA_DECODE ss3697313827 Jul 13, 2019 (153)
58 ACPOP ss3740666719 Jul 13, 2019 (153)
59 ILLUMINA ss3744893283 Jul 13, 2019 (153)
60 EVA ss3752721625 Jul 13, 2019 (153)
61 ILLUMINA ss3772392041 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3818044793 Jul 13, 2019 (153)
63 1000Genomes NC_000014.8 - 97053924 Oct 12, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 97053924 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000014.8 - 97053924 Oct 12, 2018 (152)
66 gnomAD - Genomes NC_000014.8 - 97053924 Jul 13, 2019 (153)
67 Northern Sweden NC_000014.8 - 97053924 Jul 13, 2019 (153)
68 TopMed NC_000014.9 - 96587587 Oct 12, 2018 (152)
69 UK 10K study - Twins NC_000014.8 - 97053924 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000014.8 - 97053924 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss200465820, ss480222674, ss1397689710, ss1695500068, ss1713469582, ss3643054610 NC_000014.7:96123676:C:T NC_000014.9:96587586:C:T (self)
65307020, 36301365, 25725614, 178243910, 13951584, 36301365, 8076194, ss243078119, ss480233312, ss480967586, ss484909347, ss536962086, ss564295102, ss659991941, ss778459211, ss782900983, ss783864335, ss832155782, ss833914897, ss991483897, ss1079910377, ss1352278316, ss1577452104, ss1632423111, ss1675417144, ss1752150252, ss1934854977, ss2028212521, ss2156597356, ss2369023242, ss2628596097, ss2633194224, ss2701033553, ss2931284561, ss3012720331, ss3627296468, ss3631189792, ss3633087861, ss3633791839, ss3634592695, ss3635481051, ss3636282024, ss3637232244, ss3638069316, ss3640300022, ss3679987366, ss3740666719, ss3744893283, ss3752721625, ss3772392041 NC_000014.8:97053923:C:T NC_000014.9:96587586:C:T (self)
123355468, ss2204616876, ss3219410595, ss3645365716, ss3650272428, ss3697313827, ss3818044793 NC_000014.9:96587586:C:T NC_000014.9:96587586:C:T (self)
ss24721612, ss43600977, ss75048456, ss96939399, ss119883811, ss160437850, ss172800659 NT_026437.12:78053923:C:T NC_000014.9:96587586: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 rs17280262

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.post246+3cda961