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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs56386996

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:113166696 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.059606 (15777/264690, TOPMED)
C=0.065658 (9204/140182, GnomAD)
C=0.03056 (2405/78696, PAGE_STUDY) (+ 14 more)
C=0.08550 (3646/42642, ALFA)
C=0.0475 (304/6404, 1000G_30x)
C=0.0463 (232/5008, 1000G)
C=0.0839 (376/4480, Estonian)
C=0.0950 (366/3854, ALSPAC)
C=0.0971 (360/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.115 (115/998, GoNL)
C=0.167 (100/600, NorthernSweden)
C=0.083 (18/216, Qatari)
T=0.48 (26/54, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TCF7L2 : 3 Prime UTR 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 42734 T=0.91463 C=0.08537
European Sub 36690 T=0.90687 C=0.09313
African Sub 3408 T=0.9809 C=0.0191
African Others Sub 114 T=0.974 C=0.026
African American Sub 3294 T=0.9812 C=0.0188
Asian Sub 196 T=0.995 C=0.005
East Asian Sub 168 T=1.000 C=0.000
Other Asian Sub 28 T=0.96 C=0.04
Latin American 1 Sub 154 T=0.922 C=0.078
Latin American 2 Sub 616 T=0.966 C=0.034
South Asian Sub 106 T=0.896 C=0.104
Other Sub 1564 T=0.9226 C=0.0774


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 T=0.940394 C=0.059606
gnomAD - Genomes Global Study-wide 140182 T=0.934342 C=0.065658
gnomAD - Genomes European Sub 75890 T=0.90277 C=0.09723
gnomAD - Genomes African Sub 42030 T=0.98349 C=0.01651
gnomAD - Genomes American Sub 13656 T=0.94588 C=0.05412
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9179 C=0.0821
gnomAD - Genomes East Asian Sub 3134 T=0.9990 C=0.0010
gnomAD - Genomes Other Sub 2148 T=0.9460 C=0.0540
The PAGE Study Global Study-wide 78696 T=0.96944 C=0.03056
The PAGE Study AfricanAmerican Sub 32512 T=0.98025 C=0.01975
The PAGE Study Mexican Sub 10810 T=0.95754 C=0.04246
The PAGE Study Asian Sub 8318 T=0.9990 C=0.0010
The PAGE Study PuertoRican Sub 7918 T=0.9481 C=0.0519
The PAGE Study NativeHawaiian Sub 4534 T=0.9746 C=0.0254
The PAGE Study Cuban Sub 4230 T=0.9303 C=0.0697
The PAGE Study Dominican Sub 3826 T=0.9621 C=0.0379
The PAGE Study CentralAmerican Sub 2450 T=0.9624 C=0.0376
The PAGE Study SouthAmerican Sub 1982 T=0.9617 C=0.0383
The PAGE Study NativeAmerican Sub 1260 T=0.9381 C=0.0619
The PAGE Study SouthAsian Sub 856 T=0.902 C=0.098
Allele Frequency Aggregator Total Global 42642 T=0.91450 C=0.08550
Allele Frequency Aggregator European Sub 36616 T=0.90673 C=0.09327
Allele Frequency Aggregator African Sub 3408 T=0.9809 C=0.0191
Allele Frequency Aggregator Other Sub 1546 T=0.9217 C=0.0783
Allele Frequency Aggregator Latin American 2 Sub 616 T=0.966 C=0.034
Allele Frequency Aggregator Asian Sub 196 T=0.995 C=0.005
Allele Frequency Aggregator Latin American 1 Sub 154 T=0.922 C=0.078
Allele Frequency Aggregator South Asian Sub 106 T=0.896 C=0.104
1000Genomes_30x Global Study-wide 6404 T=0.9525 C=0.0475
1000Genomes_30x African Sub 1786 T=0.9950 C=0.0050
1000Genomes_30x Europe Sub 1266 T=0.8823 C=0.1177
1000Genomes_30x South Asian Sub 1202 T=0.9193 C=0.0807
1000Genomes_30x East Asian Sub 1170 T=0.9974 C=0.0026
1000Genomes_30x American Sub 980 T=0.953 C=0.047
1000Genomes Global Study-wide 5008 T=0.9537 C=0.0463
1000Genomes African Sub 1322 T=0.9939 C=0.0061
1000Genomes East Asian Sub 1008 T=0.9980 C=0.0020
1000Genomes Europe Sub 1006 T=0.8837 C=0.1163
1000Genomes South Asian Sub 978 T=0.921 C=0.079
1000Genomes American Sub 694 T=0.960 C=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9161 C=0.0839
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9050 C=0.0950
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9029 C=0.0971
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9997 C=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.885 C=0.115
Northern Sweden ACPOP Study-wide 600 T=0.833 C=0.167
Qatari Global Study-wide 216 T=0.917 C=0.083
SGDP_PRJ Global Study-wide 54 T=0.48 C=0.52
The Danish reference pan genome Danish Study-wide 40 T=0.97 C=0.03
Siberian Global Study-wide 4 T=0.5 C=0.5
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 10 NC_000010.11:g.113166696T>C
GRCh37.p13 chr 10 NC_000010.10:g.114926455T>C
TCF7L2 RefSeqGene NG_012631.1:g.221447T>C
Gene: TCF7L2, transcription factor 7 like 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TCF7L2 transcript variant 15 NM_001349871.1:c.*1160= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 1 NM_001146274.2:c.*724= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 17 NM_001367943.1:c.*724= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 2 NM_030756.5:c.*724= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 11 NM_001198529.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 7 NM_001198525.2:c.*1172= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 4 NM_001146284.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 8 NM_001198526.2:c.*724= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 9 NM_001198527.2:c.*1160= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 6 NM_001146286.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 13 NM_001198531.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 10 NM_001198528.2:c.*1160= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 14 NM_001349870.2:c.*1160= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 3 NM_001146283.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 16 NM_001363501.2:c.*1062= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 5 NM_001146285.2:c.*724= N/A 3 Prime UTR Variant
TCF7L2 transcript variant 12 NM_001198530.2:c.*1062= N/A 3 Prime UTR 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 T= C
GRCh38.p14 chr 10 NC_000010.11:g.113166696= NC_000010.11:g.113166696T>C
GRCh37.p13 chr 10 NC_000010.10:g.114926455= NC_000010.10:g.114926455T>C
TCF7L2 RefSeqGene NG_012631.1:g.221447= NG_012631.1:g.221447T>C
TCF7L2 transcript variant 2 NM_030756.5:c.*724= NM_030756.5:c.*724T>C
TCF7L2 transcript variant 2 NM_030756.4:c.*724= NM_030756.4:c.*724T>C
TCF7L2 transcript variant 7 NM_001198525.2:c.*1172= NM_001198525.2:c.*1172T>C
TCF7L2 transcript variant 7 NM_001198525.1:c.*1172= NM_001198525.1:c.*1172T>C
TCF7L2 transcript variant 10 NM_001198528.2:c.*1160= NM_001198528.2:c.*1160T>C
TCF7L2 transcript variant 10 NM_001198528.1:c.*1160= NM_001198528.1:c.*1160T>C
TCF7L2 transcript variant 1 NM_001146274.2:c.*724= NM_001146274.2:c.*724T>C
TCF7L2 transcript variant 1 NM_001146274.1:c.*724= NM_001146274.1:c.*724T>C
TCF7L2 transcript variant 3 NM_001146283.2:c.*1062= NM_001146283.2:c.*1062T>C
TCF7L2 transcript variant 3 NM_001146283.1:c.*1062= NM_001146283.1:c.*1062T>C
TCF7L2 transcript variant 9 NM_001198527.2:c.*1160= NM_001198527.2:c.*1160T>C
TCF7L2 transcript variant 9 NM_001198527.1:c.*1160= NM_001198527.1:c.*1160T>C
TCF7L2 transcript variant 16 NM_001363501.2:c.*1062= NM_001363501.2:c.*1062T>C
TCF7L2 transcript variant 16 NM_001363501.1:c.*1062= NM_001363501.1:c.*1062T>C
TCF7L2 transcript variant 8 NM_001198526.2:c.*724= NM_001198526.2:c.*724T>C
TCF7L2 transcript variant 8 NM_001198526.1:c.*724= NM_001198526.1:c.*724T>C
TCF7L2 transcript variant 5 NM_001146285.2:c.*724= NM_001146285.2:c.*724T>C
TCF7L2 transcript variant 5 NM_001146285.1:c.*724= NM_001146285.1:c.*724T>C
TCF7L2 transcript variant 13 NM_001198531.2:c.*1062= NM_001198531.2:c.*1062T>C
TCF7L2 transcript variant 13 NM_001198531.1:c.*1062= NM_001198531.1:c.*1062T>C
TCF7L2 transcript variant 11 NM_001198529.2:c.*1062= NM_001198529.2:c.*1062T>C
TCF7L2 transcript variant 11 NM_001198529.1:c.*1062= NM_001198529.1:c.*1062T>C
TCF7L2 transcript variant 4 NM_001146284.2:c.*1062= NM_001146284.2:c.*1062T>C
TCF7L2 transcript variant 4 NM_001146284.1:c.*1062= NM_001146284.1:c.*1062T>C
TCF7L2 transcript variant 6 NM_001146286.2:c.*1062= NM_001146286.2:c.*1062T>C
TCF7L2 transcript variant 6 NM_001146286.1:c.*1062= NM_001146286.1:c.*1062T>C
TCF7L2 transcript variant 12 NM_001198530.2:c.*1062= NM_001198530.2:c.*1062T>C
TCF7L2 transcript variant 12 NM_001198530.1:c.*1062= NM_001198530.1:c.*1062T>C
TCF7L2 transcript variant 14 NM_001349870.2:c.*1160= NM_001349870.2:c.*1160T>C
TCF7L2 transcript variant 14 NM_001349870.1:c.*1160= NM_001349870.1:c.*1160T>C
TCF7L2 transcript variant 17 NM_001367943.1:c.*724= NM_001367943.1:c.*724T>C
TCF7L2 transcript variant 15 NM_001349871.1:c.*1160= NM_001349871.1:c.*1160T>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#.

48 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss77394890 Dec 07, 2007 (129)
2 1000GENOMES ss235340228 Jul 15, 2010 (132)
3 ILLUMINA ss535134717 Sep 08, 2015 (146)
4 EVA-GONL ss987940444 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1077310642 Aug 21, 2014 (142)
6 1000GENOMES ss1339138269 Aug 21, 2014 (142)
7 DDI ss1426449063 Apr 01, 2015 (144)
8 EVA_GENOME_DK ss1575364080 Apr 01, 2015 (144)
9 EVA_DECODE ss1597618487 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1625477290 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1668471323 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1931300581 Feb 12, 2016 (147)
13 ILLUMINA ss1959295761 Feb 12, 2016 (147)
14 JJLAB ss2026383283 Sep 14, 2016 (149)
15 USC_VALOUEV ss2154661057 Dec 20, 2016 (150)
16 HUMAN_LONGEVITY ss2178228958 Dec 20, 2016 (150)
17 ILLUMINA ss2710720760 Nov 08, 2017 (151)
18 GNOMAD ss2893604566 Nov 08, 2017 (151)
19 AFFY ss2984923812 Nov 08, 2017 (151)
20 AFFY ss2985571363 Nov 08, 2017 (151)
21 SWEGEN ss3007178571 Nov 08, 2017 (151)
22 ILLUMINA ss3021276734 Nov 08, 2017 (151)
23 BIOINF_KMB_FNS_UNIBA ss3026980526 Nov 08, 2017 (151)
24 CSHL ss3349319094 Nov 08, 2017 (151)
25 ILLUMINA ss3626537939 Oct 12, 2018 (152)
26 OMUKHERJEE_ADBS ss3646415536 Oct 12, 2018 (152)
27 ILLUMINA ss3651636108 Oct 12, 2018 (152)
28 ILLUMINA ss3653694903 Oct 12, 2018 (152)
29 EGCUT_WGS ss3674594567 Jul 13, 2019 (153)
30 EVA_DECODE ss3690718528 Jul 13, 2019 (153)
31 ILLUMINA ss3725190216 Jul 13, 2019 (153)
32 ACPOP ss3737695223 Jul 13, 2019 (153)
33 EVA ss3748626727 Jul 13, 2019 (153)
34 PAGE_CC ss3771584152 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3813985856 Jul 13, 2019 (153)
36 EVA ss3825784127 Apr 26, 2020 (154)
37 EVA ss3832341896 Apr 26, 2020 (154)
38 SGDP_PRJ ss3875094088 Apr 26, 2020 (154)
39 KRGDB ss3923261954 Apr 26, 2020 (154)
40 FSA-LAB ss3983986660 Apr 26, 2021 (155)
41 TOPMED ss4867169275 Apr 26, 2021 (155)
42 1000G_HIGH_COVERAGE ss5285533515 Oct 16, 2022 (156)
43 HUGCELL_USP ss5480950519 Oct 16, 2022 (156)
44 1000G_HIGH_COVERAGE ss5580245658 Oct 16, 2022 (156)
45 SANFORD_IMAGENETICS ss5650134343 Oct 16, 2022 (156)
46 EVA ss5824984486 Oct 16, 2022 (156)
47 EVA ss5880604504 Oct 16, 2022 (156)
48 EVA ss5941436213 Oct 16, 2022 (156)
49 1000Genomes NC_000010.10 - 114926455 Oct 12, 2018 (152)
50 1000Genomes_30x NC_000010.11 - 113166696 Oct 16, 2022 (156)
51 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 114926455 Oct 12, 2018 (152)
52 Genetic variation in the Estonian population NC_000010.10 - 114926455 Oct 12, 2018 (152)
53 The Danish reference pan genome NC_000010.10 - 114926455 Apr 26, 2020 (154)
54 gnomAD - Genomes NC_000010.11 - 113166696 Apr 26, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000010.10 - 114926455 Apr 26, 2020 (154)
56 KOREAN population from KRGDB NC_000010.10 - 114926455 Apr 26, 2020 (154)
57 Northern Sweden NC_000010.10 - 114926455 Jul 13, 2019 (153)
58 The PAGE Study NC_000010.11 - 113166696 Jul 13, 2019 (153)
59 Qatari NC_000010.10 - 114926455 Apr 26, 2020 (154)
60 SGDP_PRJ NC_000010.10 - 114926455 Apr 26, 2020 (154)
61 Siberian NC_000010.10 - 114926455 Apr 26, 2020 (154)
62 TopMed NC_000010.11 - 113166696 Apr 26, 2021 (155)
63 UK 10K study - Twins NC_000010.10 - 114926455 Oct 12, 2018 (152)
64 ALFA NC_000010.11 - 113166696 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77394890 NC_000010.8:114916444:T:C NC_000010.11:113166695:T:C (self)
ss1597618487 NC_000010.9:114916444:T:C NC_000010.11:113166695:T:C (self)
51587871, 28654727, 20332815, 2334046, 12771623, 30439348, 10980088, 13342511, 27111068, 7177411, 28654727, ss235340228, ss535134717, ss987940444, ss1077310642, ss1339138269, ss1426449063, ss1575364080, ss1625477290, ss1668471323, ss1931300581, ss1959295761, ss2026383283, ss2154661057, ss2710720760, ss2893604566, ss2984923812, ss2985571363, ss3007178571, ss3021276734, ss3349319094, ss3626537939, ss3646415536, ss3651636108, ss3653694903, ss3674594567, ss3737695223, ss3748626727, ss3825784127, ss3832341896, ss3875094088, ss3923261954, ss3983986660, ss5650134343, ss5824984486, ss5941436213 NC_000010.10:114926454:T:C NC_000010.11:113166695:T:C (self)
67771593, 364531363, 805621, 82714930, 1598831236, ss2178228958, ss3026980526, ss3690718528, ss3725190216, ss3771584152, ss3813985856, ss4867169275, ss5285533515, ss5480950519, ss5580245658, ss5880604504 NC_000010.11:113166695:T:C NC_000010.11:113166695: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.

No publications for rs56386996

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