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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs7566966

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:65955057 (GRCh38.p14) 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=0.404768 (107138/264690, TOPMED)
T=0.394052 (55142/139936, GnomAD)
C=0.46129 (13035/28258, 14KJPN) (+ 17 more)
T=0.38571 (7286/18890, ALFA)
C=0.46462 (7787/16760, 8.3KJPN)
T=0.4327 (2771/6404, 1000G_30x)
T=0.4359 (2183/5008, 1000G)
T=0.3629 (1626/4480, Estonian)
T=0.3762 (1450/3854, ALSPAC)
T=0.3875 (1437/3708, TWINSUK)
C=0.4820 (883/1832, Korea1K)
T=0.398 (397/998, GoNL)
C=0.467 (280/600, NorthernSweden)
C=0.335 (134/400, SGDP_PRJ)
T=0.420 (136/324, HapMap)
T=0.343 (74/216, Qatari)
C=0.463 (99/214, Vietnamese)
T=0.33 (13/40, GENOME_DK)
C=0.34 (11/32, Siberian)
T=0.4 (3/8, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC02934 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.61429 T=0.38571
European Sub 14286 C=0.62460 T=0.37540
African Sub 2946 C=0.5961 T=0.4039
African Others Sub 114 C=0.579 T=0.421
African American Sub 2832 C=0.5968 T=0.4032
Asian Sub 112 C=0.491 T=0.509
East Asian Sub 86 C=0.48 T=0.52
Other Asian Sub 26 C=0.54 T=0.46
Latin American 1 Sub 146 C=0.568 T=0.432
Latin American 2 Sub 610 C=0.487 T=0.513
South Asian Sub 98 C=0.63 T=0.37
Other Sub 692 C=0.618 T=0.382


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 264690 C=0.595232 T=0.404768
gnomAD - Genomes Global Study-wide 139936 C=0.605948 T=0.394052
gnomAD - Genomes European Sub 75794 C=0.62018 T=0.37982
gnomAD - Genomes African Sub 41910 C=0.61331 T=0.38669
gnomAD - Genomes American Sub 13634 C=0.52259 T=0.47741
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.6538 T=0.3462
gnomAD - Genomes East Asian Sub 3126 C=0.4792 T=0.5208
gnomAD - Genomes Other Sub 2150 C=0.5995 T=0.4005
14KJPN JAPANESE Study-wide 28258 C=0.46129 T=0.53871
Allele Frequency Aggregator Total Global 18890 C=0.61429 T=0.38571
Allele Frequency Aggregator European Sub 14286 C=0.62460 T=0.37540
Allele Frequency Aggregator African Sub 2946 C=0.5961 T=0.4039
Allele Frequency Aggregator Other Sub 692 C=0.618 T=0.382
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.487 T=0.513
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.568 T=0.432
Allele Frequency Aggregator Asian Sub 112 C=0.491 T=0.509
Allele Frequency Aggregator South Asian Sub 98 C=0.63 T=0.37
8.3KJPN JAPANESE Study-wide 16760 C=0.46462 T=0.53538
1000Genomes_30x Global Study-wide 6404 C=0.5673 T=0.4327
1000Genomes_30x African Sub 1786 C=0.6081 T=0.3919
1000Genomes_30x Europe Sub 1266 C=0.6414 T=0.3586
1000Genomes_30x South Asian Sub 1202 C=0.6007 T=0.3993
1000Genomes_30x East Asian Sub 1170 C=0.4786 T=0.5214
1000Genomes_30x American Sub 980 C=0.462 T=0.538
1000Genomes Global Study-wide 5008 C=0.5641 T=0.4359
1000Genomes African Sub 1322 C=0.6044 T=0.3956
1000Genomes East Asian Sub 1008 C=0.4772 T=0.5228
1000Genomes Europe Sub 1006 C=0.6362 T=0.3638
1000Genomes South Asian Sub 978 C=0.600 T=0.400
1000Genomes American Sub 694 C=0.458 T=0.542
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6371 T=0.3629
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6238 T=0.3762
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6125 T=0.3875
Korean Genome Project KOREAN Study-wide 1832 C=0.4820 T=0.5180
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.602 T=0.398
Northern Sweden ACPOP Study-wide 600 C=0.467 T=0.533
SGDP_PRJ Global Study-wide 400 C=0.335 T=0.665
HapMap Global Study-wide 324 C=0.580 T=0.420
HapMap African Sub 120 C=0.625 T=0.375
HapMap American Sub 116 C=0.586 T=0.414
HapMap Asian Sub 88 C=0.51 T=0.49
Qatari Global Study-wide 216 C=0.657 T=0.343
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.463 T=0.537
The Danish reference pan genome Danish Study-wide 40 C=0.68 T=0.33
Siberian Global Study-wide 32 C=0.34 T=0.66
KOREAN population from KRGDB KOREAN Study-wide 8 C=0.6 T=0.4
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.p14 chr 2 NC_000002.12:g.65955057C>T
GRCh37.p13 chr 2 NC_000002.11:g.66182191C>T
Gene: LINC02934, uncharacterized LINC02934 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02934 transcript variant X2 XR_007086567.1:n. N/A Intron Variant
LINC02934 transcript variant X3 XR_007086575.1:n. N/A Intron Variant
LINC02934 transcript variant X1 XR_007086560.1:n. N/A Genic Upstream 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

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
GRCh38.p14 chr 2 NC_000002.12:g.65955057= NC_000002.12:g.65955057C>T
GRCh37.p13 chr 2 NC_000002.11:g.66182191= NC_000002.11:g.66182191C>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#.

70 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11451111 Jul 11, 2003 (116)
2 AFFY ss66037623 Nov 29, 2006 (127)
3 CSHL-HAPMAP ss68386347 Jan 12, 2007 (127)
4 KRIBB_YJKIM ss82448255 Dec 15, 2007 (130)
5 HGSV ss83824909 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss91192609 Mar 24, 2008 (129)
7 BGI ss106095587 Feb 04, 2009 (130)
8 1000GENOMES ss110399571 Jan 24, 2009 (130)
9 ILLUMINA-UK ss117739826 Feb 14, 2009 (130)
10 ENSEMBL ss138459106 Dec 01, 2009 (131)
11 GMI ss157167134 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss163537968 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss164564657 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss166712093 Jul 04, 2010 (132)
15 BUSHMAN ss200556594 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss205808906 Jul 04, 2010 (132)
17 1000GENOMES ss210495349 Jul 14, 2010 (132)
18 1000GENOMES ss219297699 Jul 14, 2010 (132)
19 1000GENOMES ss231206701 Jul 14, 2010 (132)
20 1000GENOMES ss238752229 Jul 15, 2010 (132)
21 GMI ss276505449 May 04, 2012 (137)
22 GMI ss284361466 Apr 25, 2013 (138)
23 TISHKOFF ss555626703 Apr 25, 2013 (138)
24 SSMP ss649214890 Apr 25, 2013 (138)
25 EVA-GONL ss976937673 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1069192600 Aug 21, 2014 (142)
27 1000GENOMES ss1297630695 Aug 21, 2014 (142)
28 DDI ss1428606611 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1578920239 Apr 01, 2015 (144)
30 EVA_DECODE ss1586351763 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1603728002 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1646722035 Apr 01, 2015 (144)
33 HAMMER_LAB ss1796875903 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1920165002 Feb 12, 2016 (147)
35 GENOMED ss1968793167 Jul 19, 2016 (147)
36 JJLAB ss2020616601 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148661513 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2231129799 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2624818391 Nov 08, 2017 (151)
40 GRF ss2703233304 Nov 08, 2017 (151)
41 GNOMAD ss2774603402 Nov 08, 2017 (151)
42 SWEGEN ss2989659601 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3024075247 Nov 08, 2017 (151)
44 CSHL ss3344271697 Nov 08, 2017 (151)
45 EGCUT_WGS ss3657637042 Jul 13, 2019 (153)
46 EVA_DECODE ss3704080183 Jul 13, 2019 (153)
47 ACPOP ss3728514710 Jul 13, 2019 (153)
48 EVA ss3756876995 Jul 13, 2019 (153)
49 PACBIO ss3783886780 Jul 13, 2019 (153)
50 PACBIO ss3789469803 Jul 13, 2019 (153)
51 PACBIO ss3794342723 Jul 13, 2019 (153)
52 KHV_HUMAN_GENOMES ss3801243808 Jul 13, 2019 (153)
53 EVA ss3827028219 Apr 25, 2020 (154)
54 SGDP_PRJ ss3852464207 Apr 25, 2020 (154)
55 KRGDB ss3897930290 Apr 25, 2020 (154)
56 KOGIC ss3947940344 Apr 25, 2020 (154)
57 TOPMED ss4509211630 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5151802716 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5248393506 Oct 12, 2022 (156)
60 EVA ss5329548698 Oct 12, 2022 (156)
61 HUGCELL_USP ss5448566872 Oct 12, 2022 (156)
62 EVA ss5506440659 Oct 12, 2022 (156)
63 1000G_HIGH_COVERAGE ss5523792752 Oct 12, 2022 (156)
64 SANFORD_IMAGENETICS ss5628927183 Oct 12, 2022 (156)
65 TOMMO_GENOMICS ss5680552918 Oct 12, 2022 (156)
66 YY_MCH ss5802284083 Oct 12, 2022 (156)
67 EVA ss5820226401 Oct 12, 2022 (156)
68 EVA ss5852558434 Oct 12, 2022 (156)
69 EVA ss5930754145 Oct 12, 2022 (156)
70 EVA ss5955170908 Oct 12, 2022 (156)
71 1000Genomes NC_000002.11 - 66182191 Oct 11, 2018 (152)
72 1000Genomes_30x NC_000002.12 - 65955057 Oct 12, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 66182191 Oct 11, 2018 (152)
74 Genetic variation in the Estonian population NC_000002.11 - 66182191 Oct 11, 2018 (152)
75 The Danish reference pan genome NC_000002.11 - 66182191 Apr 25, 2020 (154)
76 gnomAD - Genomes NC_000002.12 - 65955057 Apr 26, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000002.11 - 66182191 Apr 25, 2020 (154)
78 HapMap NC_000002.12 - 65955057 Apr 25, 2020 (154)
79 KOREAN population from KRGDB NC_000002.11 - 66182191 Apr 25, 2020 (154)
80 Korean Genome Project NC_000002.12 - 65955057 Apr 25, 2020 (154)
81 Northern Sweden NC_000002.11 - 66182191 Jul 13, 2019 (153)
82 Qatari NC_000002.11 - 66182191 Apr 25, 2020 (154)
83 SGDP_PRJ NC_000002.11 - 66182191 Apr 25, 2020 (154)
84 Siberian NC_000002.11 - 66182191 Apr 25, 2020 (154)
85 8.3KJPN NC_000002.11 - 66182191 Apr 26, 2021 (155)
86 14KJPN NC_000002.12 - 65955057 Oct 12, 2022 (156)
87 TopMed NC_000002.12 - 65955057 Apr 26, 2021 (155)
88 UK 10K study - Twins NC_000002.11 - 66182191 Oct 11, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000002.11 - 66182191 Jul 13, 2019 (153)
90 ALFA NC_000002.12 - 65955057 Apr 26, 2021 (155)
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)
rs57884815 May 24, 2008 (130)
rs60570551 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83824909 NC_000002.9:66093841:C:T NC_000002.12:65955056:C:T (self)
ss91192609, ss110399571, ss117739826, ss163537968, ss164564657, ss166712093, ss200556594, ss205808906, ss210495349, ss276505449, ss284361466, ss1586351763 NC_000002.10:66035694:C:T NC_000002.12:65955056:C:T (self)
8587800, 4777296, 3375290, 5090884, 2099062, 5107684, 1799575, 2206932, 4481187, 1177867, 9772023, 4777296, 1035545, ss219297699, ss231206701, ss238752229, ss555626703, ss649214890, ss976937673, ss1069192600, ss1297630695, ss1428606611, ss1578920239, ss1603728002, ss1646722035, ss1796875903, ss1920165002, ss1968793167, ss2020616601, ss2148661513, ss2624818391, ss2703233304, ss2774603402, ss2989659601, ss3344271697, ss3657637042, ss3728514710, ss3756876995, ss3783886780, ss3789469803, ss3794342723, ss3827028219, ss3852464207, ss3897930290, ss5151802716, ss5329548698, ss5506440659, ss5628927183, ss5820226401, ss5955170908 NC_000002.11:66182190:C:T NC_000002.12:65955056:C:T (self)
11318687, 61007454, 1817413, 4318345, 14390022, 313034509, 9705270528, ss2231129799, ss3024075247, ss3704080183, ss3801243808, ss3947940344, ss4509211630, ss5248393506, ss5448566872, ss5523792752, ss5680552918, ss5802284083, ss5852558434, ss5930754145 NC_000002.12:65955056:C:T NC_000002.12:65955056:C:T (self)
ss11451111 NT_022184.12:44998122:C:T NC_000002.12:65955056:C:T (self)
ss66037623, ss68386347, ss82448255, ss106095587, ss138459106, ss157167134 NT_022184.15:45004077:C:T NC_000002.12:65955056: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 rs7566966

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07