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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.

rs146109287

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:68010781 (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=0.028921 (7655/264690, TOPMED)
C=0.025253 (3539/140140, GnomAD)
C=0.12878 (3639/28258, 14KJPN) (+ 16 more)
C=0.02086 (394/18890, ALFA)
C=0.12995 (2178/16760, 8.3KJPN)
C=0.0523 (335/6404, 1000G_30x)
C=0.0547 (274/5008, 1000G)
C=0.0172 (77/4480, Estonian)
C=0.0158 (61/3854, ALSPAC)
C=0.0175 (65/3708, TWINSUK)
C=0.1425 (261/1832, Korea1K)
C=0.011 (11/998, GoNL)
C=0.023 (14/600, NorthernSweden)
C=0.056 (12/216, Qatari)
C=0.189 (40/212, Vietnamese)
T=0.47 (29/62, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 T=0.97914 C=0.02086
European Sub 14286 T=0.98474 C=0.01526
African Sub 2946 T=0.9586 C=0.0414
African Others Sub 114 T=0.974 C=0.026
African American Sub 2832 T=0.9580 C=0.0420
Asian Sub 112 T=0.804 C=0.196
East Asian Sub 86 T=0.79 C=0.21
Other Asian Sub 26 T=0.85 C=0.15
Latin American 1 Sub 146 T=0.979 C=0.021
Latin American 2 Sub 610 T=0.992 C=0.008
South Asian Sub 98 T=1.00 C=0.00
Other Sub 692 T=0.965 C=0.035


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=0.971079 C=0.028921
gnomAD - Genomes Global Study-wide 140140 T=0.974747 C=0.025253
gnomAD - Genomes European Sub 75904 T=0.98551 C=0.01449
gnomAD - Genomes African Sub 42002 T=0.96238 C=0.03762
gnomAD - Genomes American Sub 13644 T=0.98901 C=0.01099
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9657 C=0.0343
gnomAD - Genomes East Asian Sub 3118 T=0.8275 C=0.1725
gnomAD - Genomes Other Sub 2150 T=0.9735 C=0.0265
14KJPN JAPANESE Study-wide 28258 T=0.87122 C=0.12878
Allele Frequency Aggregator Total Global 18890 T=0.97914 C=0.02086
Allele Frequency Aggregator European Sub 14286 T=0.98474 C=0.01526
Allele Frequency Aggregator African Sub 2946 T=0.9586 C=0.0414
Allele Frequency Aggregator Other Sub 692 T=0.965 C=0.035
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.992 C=0.008
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.979 C=0.021
Allele Frequency Aggregator Asian Sub 112 T=0.804 C=0.196
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=0.00
8.3KJPN JAPANESE Study-wide 16760 T=0.87005 C=0.12995
1000Genomes_30x Global Study-wide 6404 T=0.9477 C=0.0523
1000Genomes_30x African Sub 1786 T=0.9664 C=0.0336
1000Genomes_30x Europe Sub 1266 T=0.9834 C=0.0166
1000Genomes_30x South Asian Sub 1202 T=0.9825 C=0.0175
1000Genomes_30x East Asian Sub 1170 T=0.8077 C=0.1923
1000Genomes_30x American Sub 980 T=0.992 C=0.008
1000Genomes Global Study-wide 5008 T=0.9453 C=0.0547
1000Genomes African Sub 1322 T=0.9614 C=0.0386
1000Genomes East Asian Sub 1008 T=0.8175 C=0.1825
1000Genomes Europe Sub 1006 T=0.9861 C=0.0139
1000Genomes South Asian Sub 978 T=0.981 C=0.019
1000Genomes American Sub 694 T=0.991 C=0.009
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9828 C=0.0172
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9842 C=0.0158
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9825 C=0.0175
Korean Genome Project KOREAN Study-wide 1832 T=0.8575 C=0.1425
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.989 C=0.011
Northern Sweden ACPOP Study-wide 600 T=0.977 C=0.023
Qatari Global Study-wide 216 T=0.944 C=0.056
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.811 C=0.189
SGDP_PRJ Global Study-wide 62 T=0.47 C=0.53
The Danish reference pan genome Danish Study-wide 40 T=0.95 C=0.05
Siberian Global Study-wide 6 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 2 NC_000002.12:g.68010781T>C
GRCh37.p13 chr 2 NC_000002.11:g.68237913T>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

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 2 NC_000002.12:g.68010781= NC_000002.12:g.68010781T>C
GRCh37.p13 chr 2 NC_000002.11:g.68237913= NC_000002.11:g.68237913T>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#.

38 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss329695481 May 09, 2011 (134)
2 TISHKOFF ss555636130 Apr 25, 2013 (138)
3 SSMP ss649225231 Apr 25, 2013 (138)
4 EVA-GONL ss976954046 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1069204418 Aug 21, 2014 (142)
6 1000GENOMES ss1297691573 Aug 21, 2014 (142)
7 EVA_GENOME_DK ss1578927013 Apr 01, 2015 (144)
8 EVA_DECODE ss1586368893 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1603760347 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1646754380 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1920180686 Feb 12, 2016 (147)
12 JJLAB ss2020624956 Sep 14, 2016 (149)
13 USC_VALOUEV ss2148669960 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2231255531 Dec 20, 2016 (150)
15 GRF ss2703242295 Nov 08, 2017 (151)
16 GNOMAD ss2774776330 Nov 08, 2017 (151)
17 SWEGEN ss2989684344 Nov 08, 2017 (151)
18 CSHL ss3344278952 Nov 08, 2017 (151)
19 EGCUT_WGS ss3657663316 Jul 13, 2019 (153)
20 EVA_DECODE ss3704110425 Jul 13, 2019 (153)
21 ACPOP ss3728528131 Jul 13, 2019 (153)
22 EVA ss3756895769 Jul 13, 2019 (153)
23 KHV_HUMAN_GENOMES ss3801262648 Jul 13, 2019 (153)
24 SGDP_PRJ ss3852495315 Apr 25, 2020 (154)
25 KOGIC ss3947968201 Apr 25, 2020 (154)
26 TOPMED ss4509747188 Apr 26, 2021 (155)
27 TOMMO_GENOMICS ss5151869502 Apr 26, 2021 (155)
28 1000G_HIGH_COVERAGE ss5248446146 Oct 12, 2022 (156)
29 EVA ss5329645163 Oct 12, 2022 (156)
30 HUGCELL_USP ss5448613910 Oct 12, 2022 (156)
31 1000G_HIGH_COVERAGE ss5523873326 Oct 12, 2022 (156)
32 SANFORD_IMAGENETICS ss5628957051 Oct 12, 2022 (156)
33 TOMMO_GENOMICS ss5680638568 Oct 12, 2022 (156)
34 YY_MCH ss5802296944 Oct 12, 2022 (156)
35 EVA ss5820247392 Oct 12, 2022 (156)
36 EVA ss5852564720 Oct 12, 2022 (156)
37 EVA ss5930814669 Oct 12, 2022 (156)
38 EVA ss5955202034 Oct 12, 2022 (156)
39 1000Genomes NC_000002.11 - 68237913 Oct 11, 2018 (152)
40 1000Genomes_30x NC_000002.12 - 68010781 Oct 12, 2022 (156)
41 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 68237913 Oct 11, 2018 (152)
42 Genetic variation in the Estonian population NC_000002.11 - 68237913 Oct 11, 2018 (152)
43 The Danish reference pan genome NC_000002.11 - 68237913 Apr 25, 2020 (154)
44 gnomAD - Genomes NC_000002.12 - 68010781 Apr 26, 2021 (155)
45 Genome of the Netherlands Release 5 NC_000002.11 - 68237913 Apr 25, 2020 (154)
46 Korean Genome Project NC_000002.12 - 68010781 Apr 25, 2020 (154)
47 Northern Sweden NC_000002.11 - 68237913 Jul 13, 2019 (153)
48 Qatari NC_000002.11 - 68237913 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000002.11 - 68237913 Apr 25, 2020 (154)
50 Siberian NC_000002.11 - 68237913 Apr 25, 2020 (154)
51 8.3KJPN NC_000002.11 - 68237913 Apr 26, 2021 (155)
52 14KJPN NC_000002.12 - 68010781 Oct 12, 2022 (156)
53 TopMed NC_000002.12 - 68010781 Apr 26, 2021 (155)
54 UK 10K study - Twins NC_000002.11 - 68237913 Oct 11, 2018 (152)
55 A Vietnamese Genetic Variation Database NC_000002.11 - 68237913 Jul 13, 2019 (153)
56 ALFA NC_000002.12 - 68010781 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
ss1586368893 NC_000002.10:68091416:T:C NC_000002.12:68010780:T:C (self)
8650961, 4813036, 3401564, 5097346, 2115123, 1812996, 2222616, 4512295, 1186314, 9838809, 4813036, 1043358, ss329695481, ss555636130, ss649225231, ss976954046, ss1069204418, ss1297691573, ss1578927013, ss1603760347, ss1646754380, ss1920180686, ss2020624956, ss2148669960, ss2703242295, ss2774776330, ss2989684344, ss3344278952, ss3657663316, ss3728528131, ss3756895769, ss3852495315, ss5151869502, ss5329645163, ss5628957051, ss5820247392, ss5955202034 NC_000002.11:68237912:T:C NC_000002.12:68010780:T:C (self)
11399261, 61448580, 4346202, 14475672, 313570067, 13176285988, ss2231255531, ss3704110425, ss3801262648, ss3947968201, ss4509747188, ss5248446146, ss5448613910, ss5523873326, ss5680638568, ss5802296944, ss5852564720, ss5930814669 NC_000002.12:68010780:T:C NC_000002.12:68010780: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 rs146109287

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