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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.

rs2020933

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:30234737 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.146209 (38700/264690, TOPMED)
T=0.140434 (19681/140144, GnomAD)
T=0.18271 (14377/78688, PAGE_STUDY) (+ 16 more)
T=0.10561 (1995/18890, ALFA)
T=0.01563 (262/16760, 8.3KJPN)
T=0.1528 (765/5008, 1000G)
T=0.0580 (260/4480, Estonian)
T=0.0555 (214/3854, ALSPAC)
T=0.0510 (189/3708, TWINSUK)
T=0.0394 (115/2922, KOREAN)
T=0.057 (57/998, GoNL)
T=0.060 (36/600, NorthernSweden)
T=0.165 (54/328, HapMap)
T=0.148 (32/216, Qatari)
T=0.079 (17/216, Vietnamese)
A=0.411 (46/112, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
A=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC6A4 : Intron Variant
Publications
20 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 A=0.89439 T=0.10561
European Sub 14286 A=0.94197 T=0.05803
African Sub 2946 A=0.6578 T=0.3422
African Others Sub 114 A=0.623 T=0.377
African American Sub 2832 A=0.6593 T=0.3407
Asian Sub 112 A=0.973 T=0.027
East Asian Sub 86 A=0.98 T=0.02
Other Asian Sub 26 A=0.96 T=0.04
Latin American 1 Sub 146 A=0.897 T=0.103
Latin American 2 Sub 610 A=0.931 T=0.069
South Asian Sub 98 A=0.87 T=0.13
Other Sub 692 A=0.877 T=0.123


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 A=0.853791 T=0.146209
gnomAD - Genomes Global Study-wide 140144 A=0.859566 T=0.140434
gnomAD - Genomes European Sub 75946 A=0.94748 T=0.05252
gnomAD - Genomes African Sub 41938 A=0.67178 T=0.32822
gnomAD - Genomes American Sub 13650 A=0.92278 T=0.07722
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8797 T=0.1203
gnomAD - Genomes East Asian Sub 3134 A=0.9346 T=0.0654
gnomAD - Genomes Other Sub 2152 A=0.8755 T=0.1245
The PAGE Study Global Study-wide 78688 A=0.81729 T=0.18271
The PAGE Study AfricanAmerican Sub 32508 A=0.67789 T=0.32211
The PAGE Study Mexican Sub 10808 A=0.94615 T=0.05385
The PAGE Study Asian Sub 8318 A=0.9716 T=0.0284
The PAGE Study PuertoRican Sub 7914 A=0.8561 T=0.1439
The PAGE Study NativeHawaiian Sub 4534 A=0.9548 T=0.0452
The PAGE Study Cuban Sub 4230 A=0.8875 T=0.1125
The PAGE Study Dominican Sub 3828 A=0.8098 T=0.1902
The PAGE Study CentralAmerican Sub 2450 A=0.9114 T=0.0886
The PAGE Study SouthAmerican Sub 1982 A=0.9379 T=0.0621
The PAGE Study NativeAmerican Sub 1260 A=0.9119 T=0.0881
The PAGE Study SouthAsian Sub 856 A=0.896 T=0.104
Allele Frequency Aggregator Total Global 18890 A=0.89439 T=0.10561
Allele Frequency Aggregator European Sub 14286 A=0.94197 T=0.05803
Allele Frequency Aggregator African Sub 2946 A=0.6578 T=0.3422
Allele Frequency Aggregator Other Sub 692 A=0.877 T=0.123
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.931 T=0.069
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.897 T=0.103
Allele Frequency Aggregator Asian Sub 112 A=0.973 T=0.027
Allele Frequency Aggregator South Asian Sub 98 A=0.87 T=0.13
8.3KJPN JAPANESE Study-wide 16760 A=0.98437 T=0.01563
1000Genomes Global Study-wide 5008 A=0.8472 T=0.1528
1000Genomes African Sub 1322 A=0.6172 T=0.3828
1000Genomes East Asian Sub 1008 A=0.9573 T=0.0427
1000Genomes Europe Sub 1006 A=0.9433 T=0.0567
1000Genomes South Asian Sub 978 A=0.889 T=0.111
1000Genomes American Sub 694 A=0.928 T=0.072
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9420 T=0.0580
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9445 T=0.0555
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9490 T=0.0510
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9606 T=0.0394
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.943 T=0.057
Northern Sweden ACPOP Study-wide 600 A=0.940 T=0.060
HapMap Global Study-wide 328 A=0.835 T=0.165
HapMap African Sub 120 A=0.608 T=0.392
HapMap American Sub 120 A=0.950 T=0.050
HapMap Asian Sub 88 A=0.99 T=0.01
Qatari Global Study-wide 216 A=0.852 T=0.148
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.921 T=0.079
SGDP_PRJ Global Study-wide 112 A=0.411 T=0.589
The Danish reference pan genome Danish Study-wide 40 A=0.97 T=0.03
Siberian Global Study-wide 8 A=0.5 T=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.p13 chr 17 NC_000017.11:g.30234737A>T
GRCh37.p13 chr 17 NC_000017.10:g.28561755A>T
SLC6A4 RefSeqGene NG_011747.2:g.6200T>A
Gene: SLC6A4, solute carrier family 6 member 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC6A4 transcript NM_001045.6:c.-221+876T>A 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 A= T
GRCh38.p13 chr 17 NC_000017.11:g.30234737= NC_000017.11:g.30234737A>T
GRCh37.p13 chr 17 NC_000017.10:g.28561755= NC_000017.10:g.28561755A>T
SLC6A4 RefSeqGene NG_011747.2:g.6200= NG_011747.2:g.6200T>A
SLC6A4 transcript NM_001045.5:c.-221+876= NM_001045.5:c.-221+876T>A
SLC6A4 transcript NM_001045.6:c.-221+876= NM_001045.6:c.-221+876T>A
SLC6A4 transcript variant X1 XM_005258025.1:c.-95+876= XM_005258025.1:c.-95+876T>A
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, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 LDN ss2924051 Apr 12, 2001 (94)
2 BCM_SSAHASNP ss14286613 Dec 05, 2003 (119)
3 PERLEGEN ss69194176 May 17, 2007 (127)
4 KRIBB_YJKIM ss80745146 Dec 14, 2007 (130)
5 HGSV ss81860083 Dec 14, 2007 (130)
6 1000GENOMES ss113433215 Jan 25, 2009 (130)
7 ILLUMINA-UK ss118031524 Feb 14, 2009 (130)
8 COMPLETE_GENOMICS ss169387076 Jul 04, 2010 (132)
9 BUSHMAN ss202371021 Jul 04, 2010 (132)
10 1000GENOMES ss227511316 Jul 14, 2010 (132)
11 1000GENOMES ss237217519 Jul 15, 2010 (132)
12 GMI ss282738754 May 04, 2012 (137)
13 PJP ss292036352 May 09, 2011 (134)
14 TISHKOFF ss565225882 Apr 25, 2013 (138)
15 SSMP ss661025233 Apr 25, 2013 (138)
16 EVA-GONL ss993025990 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1081003649 Aug 21, 2014 (142)
18 1000GENOMES ss1358325841 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1578127037 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1635487911 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1678481944 Apr 01, 2015 (144)
22 EVA_DECODE ss1697067222 Apr 01, 2015 (144)
23 HAMMER_LAB ss1808748311 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1936483398 Feb 12, 2016 (147)
25 ILLUMINA ss1959738174 Feb 12, 2016 (147)
26 GENOMED ss1968374796 Jul 19, 2016 (147)
27 JJLAB ss2029022404 Sep 14, 2016 (149)
28 USC_VALOUEV ss2157486346 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2216218493 Dec 20, 2016 (150)
30 TOPMED ss2381254645 Dec 20, 2016 (150)
31 GRF ss2702045897 Nov 08, 2017 (151)
32 GNOMAD ss2948900551 Nov 08, 2017 (151)
33 AFFY ss2985091616 Nov 08, 2017 (151)
34 AFFY ss2985728216 Nov 08, 2017 (151)
35 SWEGEN ss3015396652 Nov 08, 2017 (151)
36 ILLUMINA ss3021769821 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3028331642 Nov 08, 2017 (151)
38 TOPMED ss3260589844 Nov 08, 2017 (151)
39 CSHL ss3351709780 Nov 08, 2017 (151)
40 ILLUMINA ss3652183819 Oct 12, 2018 (152)
41 ILLUMINA ss3653863200 Oct 12, 2018 (152)
42 EGCUT_WGS ss3682301466 Jul 13, 2019 (153)
43 EVA_DECODE ss3700303762 Jul 13, 2019 (153)
44 ILLUMINA ss3725612888 Jul 13, 2019 (153)
45 ACPOP ss3741958555 Jul 13, 2019 (153)
46 EVA ss3754571965 Jul 13, 2019 (153)
47 PAGE_CC ss3771920896 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3819848677 Jul 13, 2019 (153)
49 EVA ss3834828234 Apr 27, 2020 (154)
50 SGDP_PRJ ss3885574035 Apr 27, 2020 (154)
51 KRGDB ss3935227241 Apr 27, 2020 (154)
52 TOPMED ss5033118595 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss5222016764 Apr 26, 2021 (155)
54 1000Genomes NC_000017.10 - 28561755 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 28561755 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000017.10 - 28561755 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000017.10 - 28561755 Apr 27, 2020 (154)
58 gnomAD - Genomes NC_000017.11 - 30234737 Apr 26, 2021 (155)
59 Genome of the Netherlands Release 5 NC_000017.10 - 28561755 Apr 27, 2020 (154)
60 HapMap NC_000017.11 - 30234737 Apr 27, 2020 (154)
61 KOREAN population from KRGDB NC_000017.10 - 28561755 Apr 27, 2020 (154)
62 Northern Sweden NC_000017.10 - 28561755 Jul 13, 2019 (153)
63 The PAGE Study NC_000017.11 - 30234737 Jul 13, 2019 (153)
64 Qatari NC_000017.10 - 28561755 Apr 27, 2020 (154)
65 SGDP_PRJ NC_000017.10 - 28561755 Apr 27, 2020 (154)
66 Siberian NC_000017.10 - 28561755 Apr 27, 2020 (154)
67 8.3KJPN NC_000017.10 - 28561755 Apr 26, 2021 (155)
68 TopMed NC_000017.11 - 30234737 Apr 26, 2021 (155)
69 UK 10K study - Twins NC_000017.10 - 28561755 Oct 12, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000017.10 - 28561755 Jul 13, 2019 (153)
71 ALFA NC_000017.11 - 30234737 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)
rs58019660 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81860083, ss113433215, ss118031524, ss169387076, ss202371021, ss282738754, ss292036352, ss1697067222 NC_000017.9:25585880:A:T NC_000017.11:30234736:A:T (self)
71555527, 39665890, 28039714, 4330520, 17681963, 42404635, 15243420, 18525320, 37591015, 10002700, 79986071, 39665890, 8782647, ss227511316, ss237217519, ss565225882, ss661025233, ss993025990, ss1081003649, ss1358325841, ss1578127037, ss1635487911, ss1678481944, ss1808748311, ss1936483398, ss1959738174, ss1968374796, ss2029022404, ss2157486346, ss2381254645, ss2702045897, ss2948900551, ss2985091616, ss2985728216, ss3015396652, ss3021769821, ss3351709780, ss3652183819, ss3653863200, ss3682301466, ss3741958555, ss3754571965, ss3834828234, ss3885574035, ss3935227241, ss5222016764 NC_000017.10:28561754:A:T NC_000017.11:30234736:A:T (self)
504801180, 1474686, 1142365, 155177612, 248664257, 5482116811, ss2216218493, ss3028331642, ss3260589844, ss3700303762, ss3725612888, ss3771920896, ss3819848677, ss5033118595 NC_000017.11:30234736:A:T NC_000017.11:30234736:A:T (self)
ss14286613 NT_010799.14:3298747:A:T NC_000017.11:30234736:A:T (self)
ss2924051, ss69194176, ss80745146 NT_010799.15:3298748:A:T NC_000017.11:30234736:A:T (self)
Help

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

20 citations for rs2020933
PMID Title Author Year Journal
15995945 Allelic heterogeneity at the serotonin transporter locus (SLC6A4) confers susceptibility to autism and rigid-compulsive behaviors. Sutcliffe JS et al. 2005 American journal of human genetics
18330705 Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Windemuth A et al. 2008 Annals of biomedical engineering
18444253 Additional functional variation at the SLC6A4 gene. Lipsky RH et al. 2009 American journal of medical genetics. Part B, Neuropsychiatric genetics
18663369 Panic disorder is associated with the serotonin transporter gene (SLC6A4) but not the promoter region (5-HTTLPR). Strug LJ et al. 2010 Molecular psychiatry
18824000 How the serotonin story is being rewritten by new gene-based discoveries principally related to SLC6A4, the serotonin transporter gene, which functions to influence all cellular serotonin systems. Murphy DL et al. 2008 Neuropharmacology
19141529 Serotonin transporter polymorphisms in patients with portopulmonary hypertension. Roberts KE et al. 2009 Chest
19541292 Accurate, Large-Scale Genotyping of 5HTTLPR and Flanking Single Nucleotide Polymorphisms in an Association Study of Depression, Anxiety, and Personality Measures. Wray NR et al. 2009 Biological psychiatry
19567893 Moderation of antidepressant response by the serotonin transporter gene. Huezo-Diaz P et al. 2009 The British journal of psychiatry
19860858 Combinatorial interaction between two human serotonin transporter gene variable number tandem repeats and their regulation by CTCF. Ali FR et al. 2010 Journal of neurochemistry
20602615 Physiogenomic analysis of statin-treated patients: domain-specific counter effects within the ACACB gene on low-density lipoprotein cholesterol? Ruaño G et al. 2010 Pharmacogenomics
20691427 Genetic associations of brain structural networks in schizophrenia: a preliminary study. Jagannathan K et al. 2010 Biological psychiatry
21119772 A Hybrid Machine Learning Method for Fusing fMRI and Genetic Data: Combining both Improves Classification of Schizophrenia. Yang H et al. 2010 Frontiers in human neuroscience
21453464 The influence of psychiatric screening in healthy populations selection: a new study and meta-analysis of functional 5-HTTLPR and rs25531 polymorphisms and anxiety-related personality traits. Minelli A et al. 2011 BMC psychiatry
21545724 Serotonin transporter gene polymorphisms and brain function during emotional distraction from cognitive processing in posttraumatic stress disorder. Morey RA et al. 2011 BMC psychiatry
21906503 Different phenotypic and genotypic presentations in alcohol dependence: age at onset matters. Chen YC et al. 2011 Journal of studies on alcohol and drugs
22384070 AVPR1A and SLC6A4 polymorphisms in choral singers and non-musicians: a gene association study. Morley AP et al. 2012 PloS one
22738351 Genome-wide approaches to antidepressant treatment: working towards understanding and predicting response. Hodgson K et al. 2012 Genome medicine
23226060 Association of the 5-HTT gene-linked promoter region (5-HTTLPR) polymorphism with psychiatric disorders: review of psychopathology and pharmacotherapy. Kenna GA et al. 2012 Pharmacogenomics and personalized medicine
26227246 Susceptibility loci for heroin and cocaine addiction in the serotonergic and adrenergic pathways in populations of different ancestry. Levran O et al. 2015 Pharmacogenomics
28314127 Suicide attempt in mental disorders (MeDi): Association with 5-HTT, IL-10 and TNF-alpha polymorphisms. de Medeiros Alves V et al. 2017 Journal of psychiatric research
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.post676+237644a