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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.

rs2661837

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:160369142 (GRCh38.p13) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.005890 (1559/264690, TOPMED)
G=0.004920 (690/140258, GnomAD)
G=0.02947 (494/16760, 8.3KJPN) (+ 10 more)
G=0.00316 (50/15802, ALFA)
G=0.0166 (83/5008, 1000G)
G=0.0260 (76/2922, KOREAN)
G=0.0333 (61/1832, Korea1K)
G=0.003 (1/330, HapMap)
G=0.056 (12/214, Vietnamese)
C=0.5 (4/8, SGDP_PRJ)
G=0.5 (4/8, SGDP_PRJ)
C=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC22A3 : Intron Variant
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.p13 chr 6 NC_000006.12:g.160369142C>G
GRCh37.p13 chr 6 NC_000006.11:g.160790174C>G
Gene: SLC22A3, solute carrier family 22 member 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC22A3 transcript NM_021977.4:c.429+20294C>G N/A Intron Variant
SLC22A3 transcript variant X1 XM_005267106.5:c.36+20084…

XM_005267106.5:c.36+20084C>G

N/A Intron Variant
SLC22A3 transcript variant X6 XM_005267107.3:c.429+2029…

XM_005267107.3:c.429+20294C>G

N/A Intron Variant
SLC22A3 transcript variant X3 XM_011536076.3:c.-28+1995…

XM_011536076.3:c.-28+19957C>G

N/A Intron Variant
SLC22A3 transcript variant X4 XM_017011203.2:c.-28+1847…

XM_017011203.2:c.-28+18472C>G

N/A Intron Variant
SLC22A3 transcript variant X2 XM_011536075.2:c. N/A Genic Upstream Transcript Variant
SLC22A3 transcript variant X5 XR_001743588.1:n. N/A Intron Variant
SLC22A3 transcript variant X7 XR_001743589.1:n. N/A Intron 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 15802 C=0.99684 G=0.00316
European Sub 11108 C=0.99946 G=0.00054
African Sub 2976 C=0.9889 G=0.0111
African Others Sub 114 C=0.991 G=0.009
African American Sub 2862 C=0.9888 G=0.0112
Asian Sub 114 C=0.939 G=0.061
East Asian Sub 88 C=0.95 G=0.05
Other Asian Sub 26 C=0.88 G=0.12
Latin American 1 Sub 150 C=1.000 G=0.000
Latin American 2 Sub 626 C=1.000 G=0.000
South Asian Sub 98 C=1.00 G=0.00
Other Sub 730 C=0.995 G=0.005


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=0.994110 G=0.005890
gnomAD - Genomes Global Study-wide 140258 C=0.995080 G=0.004920
gnomAD - Genomes European Sub 75958 C=0.99982 G=0.00018
gnomAD - Genomes African Sub 42038 C=0.99022 G=0.00978
gnomAD - Genomes American Sub 13662 C=0.99868 G=0.00132
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9976 G=0.0024
gnomAD - Genomes East Asian Sub 3128 C=0.9309 G=0.0691
gnomAD - Genomes Other Sub 2150 C=0.9893 G=0.0107
8.3KJPN JAPANESE Study-wide 16760 C=0.97053 G=0.02947
1000Genomes Global Study-wide 5008 C=0.9834 G=0.0166
1000Genomes African Sub 1322 C=0.9932 G=0.0068
1000Genomes East Asian Sub 1008 C=0.9276 G=0.0724
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.999 G=0.001
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9740 G=0.0260
Korean Genome Project KOREAN Study-wide 1832 C=0.9667 G=0.0333
HapMap Global Study-wide 330 C=0.997 G=0.003
HapMap African Sub 120 C=1.000 G=0.000
HapMap American Sub 120 C=1.000 G=0.000
HapMap Asian Sub 90 C=0.99 G=0.01
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.944 G=0.056
SGDP_PRJ Global Study-wide 8 C=0.5 G=0.5
Siberian Global Study-wide 2 C=0.5 G=0.5
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= G
GRCh38.p13 chr 6 NC_000006.12:g.160369142= NC_000006.12:g.160369142C>G
GRCh37.p13 chr 6 NC_000006.11:g.160790174= NC_000006.11:g.160790174C>G
SLC22A3 transcript NM_021977.3:c.429+20294= NM_021977.3:c.429+20294C>G
SLC22A3 transcript NM_021977.4:c.429+20294= NM_021977.4:c.429+20294C>G
SLC22A3 transcript variant X1 XM_005267106.1:c.36+20084= XM_005267106.1:c.36+20084C>G
SLC22A3 transcript variant X1 XM_005267106.5:c.36+20084= XM_005267106.5:c.36+20084C>G
SLC22A3 transcript variant X2 XM_005267107.1:c.429+20294= XM_005267107.1:c.429+20294C>G
SLC22A3 transcript variant X6 XM_005267107.3:c.429+20294= XM_005267107.3:c.429+20294C>G
SLC22A3 transcript variant X3 XM_011536076.3:c.-28+19957= XM_011536076.3:c.-28+19957C>G
SLC22A3 transcript variant X4 XM_017011203.2:c.-28+18472= XM_017011203.2:c.-28+18472C>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#.

53 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3754555 Sep 28, 2001 (100)
2 ILLUMINA ss75242062 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119441897 Dec 01, 2009 (131)
4 ILLUMINA ss160567648 Dec 01, 2009 (131)
5 ILLUMINA ss173422075 Jul 04, 2010 (132)
6 1000GENOMES ss240765759 Jul 15, 2010 (132)
7 GMI ss279105363 May 04, 2012 (137)
8 ILLUMINA ss410859471 Sep 17, 2011 (135)
9 ILLUMINA ss480629065 May 04, 2012 (137)
10 ILLUMINA ss480644152 May 04, 2012 (137)
11 ILLUMINA ss481484791 Sep 08, 2015 (146)
12 ILLUMINA ss485109696 May 04, 2012 (137)
13 ILLUMINA ss537113644 Sep 08, 2015 (146)
14 TISHKOFF ss559669011 Apr 25, 2013 (138)
15 SSMP ss654012387 Apr 25, 2013 (138)
16 ILLUMINA ss778342316 Aug 21, 2014 (142)
17 ILLUMINA ss783001128 Aug 21, 2014 (142)
18 ILLUMINA ss783961611 Aug 21, 2014 (142)
19 ILLUMINA ss832258263 Apr 01, 2015 (144)
20 ILLUMINA ss833796926 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1074207831 Aug 21, 2014 (142)
22 1000GENOMES ss1323149017 Aug 21, 2014 (142)
23 EVA_SVP ss1712916976 Apr 01, 2015 (144)
24 ILLUMINA ss1752613038 Sep 08, 2015 (146)
25 USC_VALOUEV ss2152345846 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2290210366 Dec 20, 2016 (150)
27 TOPMED ss2458899987 Dec 20, 2016 (150)
28 ILLUMINA ss2634539673 Nov 08, 2017 (151)
29 GRF ss2707984799 Nov 08, 2017 (151)
30 GNOMAD ss2847592380 Nov 08, 2017 (151)
31 TOPMED ss3517549282 Nov 08, 2017 (151)
32 ILLUMINA ss3629706413 Oct 12, 2018 (152)
33 ILLUMINA ss3632451303 Oct 12, 2018 (152)
34 ILLUMINA ss3633445444 Oct 12, 2018 (152)
35 ILLUMINA ss3634169392 Oct 12, 2018 (152)
36 ILLUMINA ss3635098886 Oct 12, 2018 (152)
37 ILLUMINA ss3635849650 Oct 12, 2018 (152)
38 ILLUMINA ss3636827888 Oct 12, 2018 (152)
39 ILLUMINA ss3637602556 Oct 12, 2018 (152)
40 ILLUMINA ss3638669657 Oct 12, 2018 (152)
41 ILLUMINA ss3640806187 Oct 12, 2018 (152)
42 ILLUMINA ss3643607858 Oct 12, 2018 (152)
43 EVA_DECODE ss3718709027 Jul 13, 2019 (153)
44 ILLUMINA ss3745398801 Jul 13, 2019 (153)
45 EVA ss3765940175 Jul 13, 2019 (153)
46 ILLUMINA ss3772892102 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3809102990 Jul 13, 2019 (153)
48 SGDP_PRJ ss3866172855 Apr 26, 2020 (154)
49 KRGDB ss3913163680 Apr 26, 2020 (154)
50 KOGIC ss3960496517 Apr 26, 2020 (154)
51 EVA ss4017311073 Apr 26, 2021 (155)
52 TOPMED ss4729307038 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss5180909509 Apr 26, 2021 (155)
54 1000Genomes NC_000006.11 - 160790174 Oct 12, 2018 (152)
55 gnomAD - Genomes NC_000006.12 - 160369142 Apr 26, 2021 (155)
56 HapMap NC_000006.12 - 160369142 Apr 26, 2020 (154)
57 KOREAN population from KRGDB NC_000006.11 - 160790174 Apr 26, 2020 (154)
58 Korean Genome Project NC_000006.12 - 160369142 Apr 26, 2020 (154)
59 SGDP_PRJ NC_000006.11 - 160790174 Apr 26, 2020 (154)
60 Siberian NC_000006.11 - 160790174 Apr 26, 2020 (154)
61 8.3KJPN NC_000006.11 - 160790174 Apr 26, 2021 (155)
62 TopMed NC_000006.12 - 160369142 Apr 26, 2021 (155)
63 A Vietnamese Genetic Variation Database NC_000006.11 - 160790174 Jul 13, 2019 (153)
64 ALFA NC_000006.12 - 160369142 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
ss279105363, ss410859471, ss480629065, ss1712916976, ss3643607858 NC_000006.10:160710163:C:G NC_000006.12:160369141:C:G (self)
35051370, 20341074, 18189835, 4862200, 38878816, 4350336, ss240765759, ss480644152, ss481484791, ss485109696, ss537113644, ss559669011, ss654012387, ss778342316, ss783001128, ss783961611, ss832258263, ss833796926, ss1074207831, ss1323149017, ss1752613038, ss2152345846, ss2458899987, ss2634539673, ss2707984799, ss2847592380, ss3629706413, ss3632451303, ss3633445444, ss3634169392, ss3635098886, ss3635849650, ss3636827888, ss3637602556, ss3638669657, ss3640806187, ss3745398801, ss3765940175, ss3772892102, ss3866172855, ss3913163680, ss4017311073, ss5180909509 NC_000006.11:160790173:C:G NC_000006.12:160369141:C:G (self)
247422117, 3297682, 16874518, 354477448, 566684596, 12277585711, ss2290210366, ss3517549282, ss3718709027, ss3809102990, ss3960496517, ss4729307038 NC_000006.12:160369141:C:G NC_000006.12:160369141:C:G (self)
ss3754555, ss75242062, ss119441897, ss160567648, ss173422075 NT_025741.15:64959630:C:G NC_000006.12:160369141:C:G (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 rs2661837

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.post596+ae089ad