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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.

rs2279709

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:20178722 (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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.491348 (130055/264690, TOPMED)
T=0.488809 (68398/139928, GnomAD)
G=0.41295 (11669/28258, 14KJPN) (+ 18 more)
T=0.48298 (11577/23970, ALFA)
G=0.41187 (6903/16760, 8.3KJPN)
G=0.4414 (2827/6404, 1000G_30x)
G=0.4361 (2184/5008, 1000G)
T=0.4406 (1974/4480, Estonian)
T=0.4408 (1699/3854, ALSPAC)
T=0.4307 (1597/3708, TWINSUK)
G=0.3666 (1074/2930, KOREAN)
G=0.4556 (861/1890, HapMap)
G=0.3652 (669/1832, Korea1K)
T=0.418 (417/998, GoNL)
G=0.395 (247/626, Chileans)
T=0.420 (252/600, NorthernSweden)
T=0.313 (121/386, SGDP_PRJ)
T=0.449 (97/216, Qatari)
G=0.248 (53/214, Vietnamese)
T=0.29 (12/42, Siberian)
T=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC18A1 : Intron Variant
Publications
4 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 23970 T=0.48298 G=0.51702
European Sub 15670 T=0.43631 G=0.56369
African Sub 3624 T=0.5662 G=0.4338
African Others Sub 126 T=0.540 G=0.460
African American Sub 3498 T=0.5672 G=0.4328
Asian Sub 160 T=0.694 G=0.306
East Asian Sub 102 T=0.696 G=0.304
Other Asian Sub 58 T=0.69 G=0.31
Latin American 1 Sub 292 T=0.521 G=0.479
Latin American 2 Sub 2768 T=0.6012 G=0.3988
South Asian Sub 110 T=0.436 G=0.564
Other Sub 1346 T=0.5297 G=0.4703


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=0.508652 G=0.491348
gnomAD - Genomes Global Study-wide 139928 T=0.488809 G=0.511191
gnomAD - Genomes European Sub 75802 T=0.42701 G=0.57299
gnomAD - Genomes African Sub 41908 T=0.56090 G=0.43910
gnomAD - Genomes American Sub 13628 T=0.57448 G=0.42552
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.4467 G=0.5533
gnomAD - Genomes East Asian Sub 3120 T=0.6875 G=0.3125
gnomAD - Genomes Other Sub 2148 T=0.4963 G=0.5037
14KJPN JAPANESE Study-wide 28258 T=0.58705 G=0.41295
Allele Frequency Aggregator Total Global 23970 T=0.48298 G=0.51702
Allele Frequency Aggregator European Sub 15670 T=0.43631 G=0.56369
Allele Frequency Aggregator African Sub 3624 T=0.5662 G=0.4338
Allele Frequency Aggregator Latin American 2 Sub 2768 T=0.6012 G=0.3988
Allele Frequency Aggregator Other Sub 1346 T=0.5297 G=0.4703
Allele Frequency Aggregator Latin American 1 Sub 292 T=0.521 G=0.479
Allele Frequency Aggregator Asian Sub 160 T=0.694 G=0.306
Allele Frequency Aggregator South Asian Sub 110 T=0.436 G=0.564
8.3KJPN JAPANESE Study-wide 16760 T=0.58813 G=0.41187
1000Genomes_30x Global Study-wide 6404 T=0.5586 G=0.4414
1000Genomes_30x African Sub 1786 T=0.5773 G=0.4227
1000Genomes_30x Europe Sub 1266 T=0.4455 G=0.5545
1000Genomes_30x South Asian Sub 1202 T=0.4892 G=0.5108
1000Genomes_30x East Asian Sub 1170 T=0.6949 G=0.3051
1000Genomes_30x American Sub 980 T=0.593 G=0.407
1000Genomes Global Study-wide 5008 T=0.5639 G=0.4361
1000Genomes African Sub 1322 T=0.5938 G=0.4062
1000Genomes East Asian Sub 1008 T=0.6885 G=0.3115
1000Genomes Europe Sub 1006 T=0.4374 G=0.5626
1000Genomes South Asian Sub 978 T=0.500 G=0.500
1000Genomes American Sub 694 T=0.599 G=0.401
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.4406 G=0.5594
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.4408 G=0.5592
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4307 G=0.5693
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6334 C=0.0000, G=0.3666
HapMap Global Study-wide 1890 T=0.5444 G=0.4556
HapMap American Sub 768 T=0.540 G=0.460
HapMap African Sub 692 T=0.548 G=0.452
HapMap Asian Sub 254 T=0.598 G=0.402
HapMap Europe Sub 176 T=0.472 G=0.528
Korean Genome Project KOREAN Study-wide 1832 T=0.6348 G=0.3652
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.418 G=0.582
Chileans Chilean Study-wide 626 T=0.605 G=0.395
Northern Sweden ACPOP Study-wide 600 T=0.420 G=0.580
SGDP_PRJ Global Study-wide 386 T=0.313 G=0.687
Qatari Global Study-wide 216 T=0.449 G=0.551
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.752 G=0.248
Siberian Global Study-wide 42 T=0.29 G=0.71
The Danish reference pan genome Danish Study-wide 40 T=0.38 G=0.62
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 8 NC_000008.11:g.20178722T>C
GRCh38.p14 chr 8 NC_000008.11:g.20178722T>G
GRCh37.p13 chr 8 NC_000008.10:g.20036233T>C
GRCh37.p13 chr 8 NC_000008.10:g.20036233T>G
Gene: SLC18A1, solute carrier family 18 member A1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC18A1 transcript variant 1 NM_001135691.3:c.489-229A…

NM_001135691.3:c.489-229A>G

N/A Intron Variant
SLC18A1 transcript variant 3 NM_001142324.2:c.489-229A…

NM_001142324.2:c.489-229A>G

N/A Intron Variant
SLC18A1 transcript variant 4 NM_001142325.2:c.489-229A…

NM_001142325.2:c.489-229A>G

N/A Intron Variant
SLC18A1 transcript variant 2 NM_003053.4:c.489-229A>G N/A Intron Variant
SLC18A1 transcript variant X1 XM_011544625.2:c.489-229A…

XM_011544625.2:c.489-229A>G

N/A Intron Variant
SLC18A1 transcript variant X2 XM_011544626.2:c.489-229A…

XM_011544626.2:c.489-229A>G

N/A Intron Variant
SLC18A1 transcript variant X3 XM_047422119.1:c.489-229A…

XM_047422119.1:c.489-229A>G

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
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 G
GRCh38.p14 chr 8 NC_000008.11:g.20178722= NC_000008.11:g.20178722T>C NC_000008.11:g.20178722T>G
GRCh37.p13 chr 8 NC_000008.10:g.20036233= NC_000008.10:g.20036233T>C NC_000008.10:g.20036233T>G
SLC18A1 transcript variant 1 NM_001135691.2:c.489-229= NM_001135691.2:c.489-229A>G NM_001135691.2:c.489-229A>C
SLC18A1 transcript variant 1 NM_001135691.3:c.489-229= NM_001135691.3:c.489-229A>G NM_001135691.3:c.489-229A>C
SLC18A1 transcript variant 3 NM_001142324.1:c.489-229= NM_001142324.1:c.489-229A>G NM_001142324.1:c.489-229A>C
SLC18A1 transcript variant 3 NM_001142324.2:c.489-229= NM_001142324.2:c.489-229A>G NM_001142324.2:c.489-229A>C
SLC18A1 transcript variant 4 NM_001142325.1:c.489-229= NM_001142325.1:c.489-229A>G NM_001142325.1:c.489-229A>C
SLC18A1 transcript variant 4 NM_001142325.2:c.489-229= NM_001142325.2:c.489-229A>G NM_001142325.2:c.489-229A>C
SLC18A1 transcript variant 2 NM_003053.3:c.489-229= NM_003053.3:c.489-229A>G NM_003053.3:c.489-229A>C
SLC18A1 transcript variant 2 NM_003053.4:c.489-229= NM_003053.4:c.489-229A>G NM_003053.4:c.489-229A>C
SLC18A1 transcript variant X1 XM_011544625.2:c.489-229= XM_011544625.2:c.489-229A>G XM_011544625.2:c.489-229A>C
SLC18A1 transcript variant X2 XM_011544626.2:c.489-229= XM_011544626.2:c.489-229A>G XM_011544626.2:c.489-229A>C
SLC18A1 transcript variant X3 XM_047422119.1:c.489-229= XM_047422119.1:c.489-229A>G XM_047422119.1:c.489-229A>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#.

77 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3217469 Sep 28, 2001 (100)
2 ABI ss44914384 Mar 14, 2006 (126)
3 AFFY ss76643655 Dec 06, 2007 (129)
4 HGSV ss82522859 Dec 15, 2007 (130)
5 BCMHGSC_JDW ss93851830 Mar 25, 2008 (129)
6 HUMANGENOME_JCVI ss98056609 Feb 05, 2009 (130)
7 KRIBB_YJKIM ss104868316 Feb 05, 2009 (130)
8 1000GENOMES ss112895889 Jan 25, 2009 (130)
9 1000GENOMES ss115102369 Jan 25, 2009 (130)
10 ILLUMINA-UK ss115864612 Feb 14, 2009 (130)
11 ENSEMBL ss134460167 Dec 01, 2009 (131)
12 ENSEMBL ss143322011 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162225377 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss164135261 Jul 04, 2010 (132)
15 BUSHMAN ss198890555 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss206539063 Jul 04, 2010 (132)
17 1000GENOMES ss223586992 Jul 14, 2010 (132)
18 1000GENOMES ss234353355 Jul 15, 2010 (132)
19 1000GENOMES ss241228016 Jul 15, 2010 (132)
20 BL ss254173462 May 09, 2011 (134)
21 GMI ss279724822 May 04, 2012 (137)
22 GMI ss285808262 Apr 25, 2013 (138)
23 PJP ss294234695 May 09, 2011 (134)
24 TISHKOFF ss560601686 Apr 25, 2013 (138)
25 SSMP ss655036941 Apr 25, 2013 (138)
26 EVA-GONL ss985274814 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1075341953 Aug 21, 2014 (142)
28 1000GENOMES ss1328923570 Aug 21, 2014 (142)
29 DDI ss1431442233 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1582594647 Apr 01, 2015 (144)
31 EVA_DECODE ss1594864525 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1620138356 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1663132389 Apr 01, 2015 (144)
34 EVA_SVP ss1713021275 Apr 01, 2015 (144)
35 HAMMER_LAB ss1805433806 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1928564692 Feb 12, 2016 (147)
37 JJLAB ss2024981804 Sep 14, 2016 (149)
38 USC_VALOUEV ss2153203138 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2301305633 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2626975748 Nov 08, 2017 (151)
41 GRF ss2708963717 Nov 08, 2017 (151)
42 GNOMAD ss2864115176 Nov 08, 2017 (151)
43 AFFY ss2986076530 Nov 08, 2017 (151)
44 SWEGEN ss3002807507 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3026281774 Nov 08, 2017 (151)
46 CSHL ss3348082958 Nov 08, 2017 (151)
47 OMUKHERJEE_ADBS ss3646373060 Oct 12, 2018 (152)
48 URBANLAB ss3648868916 Oct 12, 2018 (152)
49 EGCUT_WGS ss3670487793 Jul 13, 2019 (153)
50 EVA_DECODE ss3721559431 Jul 13, 2019 (153)
51 ACPOP ss3735468835 Jul 13, 2019 (153)
52 EVA ss3767720402 Jul 13, 2019 (153)
53 PACBIO ss3786087898 Jul 13, 2019 (153)
54 PACBIO ss3791354254 Jul 13, 2019 (153)
55 PACBIO ss3796235424 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3810883922 Jul 13, 2019 (153)
57 EVA ss3831056083 Apr 26, 2020 (154)
58 EVA ss3839038182 Apr 26, 2020 (154)
59 EVA ss3844496212 Apr 26, 2020 (154)
60 SGDP_PRJ ss3869440934 Apr 26, 2020 (154)
61 KRGDB ss3916866877 Apr 26, 2020 (154)
62 KOGIC ss3963405922 Apr 26, 2020 (154)
63 TOPMED ss4778161586 Apr 27, 2021 (155)
64 TOMMO_GENOMICS ss5187662944 Apr 27, 2021 (155)
65 1000G_HIGH_COVERAGE ss5276337249 Oct 14, 2022 (156)
66 EVA ss5379655258 Oct 14, 2022 (156)
67 HUGCELL_USP ss5472987522 Oct 14, 2022 (156)
68 EVA ss5509275893 Oct 14, 2022 (156)
69 1000G_HIGH_COVERAGE ss5566264731 Oct 14, 2022 (156)
70 SANFORD_IMAGENETICS ss5644928079 Oct 14, 2022 (156)
71 TOMMO_GENOMICS ss5729281940 Oct 14, 2022 (156)
72 YY_MCH ss5809518360 Oct 14, 2022 (156)
73 EVA ss5830227228 Oct 14, 2022 (156)
74 EVA ss5856287936 Oct 14, 2022 (156)
75 EVA ss5888029880 Oct 14, 2022 (156)
76 EVA ss5974108852 Oct 14, 2022 (156)
77 EVA ss5980492759 Oct 14, 2022 (156)
78 1000Genomes NC_000008.10 - 20036233 Oct 12, 2018 (152)
79 1000Genomes_30x NC_000008.11 - 20178722 Oct 14, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 20036233 Oct 12, 2018 (152)
81 Chileans NC_000008.10 - 20036233 Apr 26, 2020 (154)
82 Genetic variation in the Estonian population NC_000008.10 - 20036233 Oct 12, 2018 (152)
83 The Danish reference pan genome NC_000008.10 - 20036233 Apr 26, 2020 (154)
84 gnomAD - Genomes NC_000008.11 - 20178722 Apr 27, 2021 (155)
85 Genome of the Netherlands Release 5 NC_000008.10 - 20036233 Apr 26, 2020 (154)
86 HapMap NC_000008.11 - 20178722 Apr 26, 2020 (154)
87 KOREAN population from KRGDB NC_000008.10 - 20036233 Apr 26, 2020 (154)
88 Korean Genome Project NC_000008.11 - 20178722 Apr 26, 2020 (154)
89 Northern Sweden NC_000008.10 - 20036233 Jul 13, 2019 (153)
90 Qatari NC_000008.10 - 20036233 Apr 26, 2020 (154)
91 SGDP_PRJ NC_000008.10 - 20036233 Apr 26, 2020 (154)
92 Siberian NC_000008.10 - 20036233 Apr 26, 2020 (154)
93 8.3KJPN NC_000008.10 - 20036233 Apr 27, 2021 (155)
94 14KJPN NC_000008.11 - 20178722 Oct 14, 2022 (156)
95 TopMed NC_000008.11 - 20178722 Apr 27, 2021 (155)
96 UK 10K study - Twins NC_000008.10 - 20036233 Oct 12, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000008.10 - 20036233 Jul 13, 2019 (153)
98 ALFA NC_000008.11 - 20178722 Apr 27, 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)
rs58571733 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
24044271, ss3916866877 NC_000008.10:20036232:T:C NC_000008.11:20178721:T:C (self)
ss76643655, ss82522859, ss93851830, ss112895889, ss115102369, ss115864612, ss162225377, ss164135261, ss198890555, ss206539063, ss254173462, ss279724822, ss285808262, ss294234695, ss1594864525, ss1713021275 NC_000008.9:20080512:T:G NC_000008.11:20178721:T:G (self)
41018502, 22802046, 429708, 16226041, 8759585, 10189105, 24044271, 8753700, 10606622, 21457914, 5719492, 45632251, 22802046, 5084551, ss223586992, ss234353355, ss241228016, ss560601686, ss655036941, ss985274814, ss1075341953, ss1328923570, ss1431442233, ss1582594647, ss1620138356, ss1663132389, ss1805433806, ss1928564692, ss2024981804, ss2153203138, ss2626975748, ss2708963717, ss2864115176, ss2986076530, ss3002807507, ss3348082958, ss3646373060, ss3670487793, ss3735468835, ss3767720402, ss3786087898, ss3791354254, ss3796235424, ss3831056083, ss3839038182, ss3869440934, ss3916866877, ss5187662944, ss5379655258, ss5509275893, ss5644928079, ss5830227228, ss5974108852, ss5980492759 NC_000008.10:20036232:T:G NC_000008.11:20178721:T:G (self)
53790666, 289251941, 3581444, 19783923, 63119044, 615539146, 2671643886, ss2301305633, ss3026281774, ss3648868916, ss3721559431, ss3810883922, ss3844496212, ss3963405922, ss4778161586, ss5276337249, ss5472987522, ss5566264731, ss5729281940, ss5809518360, ss5856287936, ss5888029880 NC_000008.11:20178721:T:G NC_000008.11:20178721:T:G (self)
ss3217469, ss44914384, ss98056609, ss104868316, ss134460167, ss143322011 NT_167187.1:7894378:T:G NC_000008.11:20178721:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs2279709
PMID Title Author Year Journal
16936705 Variations in the vesicular monoamine transporter 1 gene (VMAT1/SLC18A1) are associated with bipolar i disorder. Lohoff FW et al. 2006 Neuropsychopharmacology
18451639 Association between polymorphisms in the vesicular monoamine transporter 1 gene (VMAT1/SLC18A1) on chromosome 8p and schizophrenia. Lohoff FW et al. 2008 Neuropsychobiology
28476685 Association study of the vesicular monoamine transporter 1 (VMAT1) gene with autism in an Iranian population. Noroozi R et al. 2017 Gene
29536333 Association Study of VMAT1 Polymorphisms and Suicide Behavior. Sayad A et al. 2018 Journal of molecular neuroscience
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