Name: rs9303628
Published: September 21, 2022
License: Open Access

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.

rs9303628

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:30200210 (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>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.423492 (112094/264690, TOPMED)
T=0.441973 (61923/140106, GnomAD)
T=0.17719 (5007/28258, 14KJPN) (+ 17 more)
T=0.48258 (11278/23370, ALFA)
T=0.17434 (2922/16760, 8.3KJPN)
T=0.3649 (2337/6404, 1000G_30x)
T=0.3630 (1818/5008, 1000G)
C=0.4833 (2165/4480, Estonian)
C=0.4925 (1898/3854, ALSPAC)
C=0.4746 (1760/3708, TWINSUK)
T=0.1976 (579/2930, KOREAN)
T=0.3116 (587/1884, HapMap)
T=0.2020 (370/1832, Korea1K)
C=0.478 (477/998, GoNL)
T=0.475 (285/600, NorthernSweden)
T=0.246 (114/464, SGDP_PRJ)
T=0.477 (103/216, Qatari)
T=0.238 (50/210, Vietnamese)
T=0.26 (12/46, Siberian)
C=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC6A4 : 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	23370	T=0.48258	A=0.00000, C=0.51742
European	Sub	17620	T=0.51748	A=0.00000, C=0.48252
African	Sub	3644	T=0.3455	A=0.0000, C=0.6545
African Others	Sub	126	T=0.317	A=0.000, C=0.683
African American	Sub	3518	T=0.3465	A=0.0000, C=0.6535
Asian	Sub	124	T=0.218	A=0.000, C=0.782
East Asian	Sub	96	T=0.22	A=0.00, C=0.78
Other Asian	Sub	28	T=0.21	A=0.00, C=0.79
Latin American 1	Sub	168	T=0.464	A=0.000, C=0.536
Latin American 2	Sub	670	T=0.401	A=0.000, C=0.599
South Asian	Sub	98	T=0.46	A=0.00, C=0.54
Other	Sub	1046	T=0.4608	A=0.0000, C=0.5392

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=0.423492	C=0.576508
gnomAD - Genomes	Global	Study-wide	140106	T=0.441973	C=0.558027
gnomAD - Genomes	European	Sub	75880	T=0.51986	C=0.48014
gnomAD - Genomes	African	Sub	41974	T=0.32928	C=0.67072
gnomAD - Genomes	American	Sub	13648	T=0.42219	C=0.57781
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.4145	C=0.5855
gnomAD - Genomes	East Asian	Sub	3130	T=0.1859	C=0.8141
gnomAD - Genomes	Other	Sub	2152	T=0.4340	C=0.5660
14KJPN	JAPANESE	Study-wide	28258	T=0.17719	C=0.82281
Allele Frequency Aggregator	Total	Global	23370	T=0.48258	A=0.00000, C=0.51742
Allele Frequency Aggregator	European	Sub	17620	T=0.51748	A=0.00000, C=0.48252
Allele Frequency Aggregator	African	Sub	3644	T=0.3455	A=0.0000, C=0.6545
Allele Frequency Aggregator	Other	Sub	1046	T=0.4608	A=0.0000, C=0.5392
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.401	A=0.000, C=0.599
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.464	A=0.000, C=0.536
Allele Frequency Aggregator	Asian	Sub	124	T=0.218	A=0.000, C=0.782
Allele Frequency Aggregator	South Asian	Sub	98	T=0.46	A=0.00, C=0.54
8.3KJPN	JAPANESE	Study-wide	16760	T=0.17434	C=0.82566
1000Genomes_30x	Global	Study-wide	6404	T=0.3649	C=0.6351
1000Genomes_30x	African	Sub	1786	T=0.2934	C=0.7066
1000Genomes_30x	Europe	Sub	1266	T=0.5450	C=0.4550
1000Genomes_30x	South Asian	Sub	1202	T=0.4293	C=0.5707
1000Genomes_30x	East Asian	Sub	1170	T=0.1761	C=0.8239
1000Genomes_30x	American	Sub	980	T=0.409	C=0.591
1000Genomes	Global	Study-wide	5008	T=0.3630	C=0.6370
1000Genomes	African	Sub	1322	T=0.2965	C=0.7035
1000Genomes	East Asian	Sub	1008	T=0.1746	C=0.8254
1000Genomes	Europe	Sub	1006	T=0.5348	C=0.4652
1000Genomes	South Asian	Sub	978	T=0.435	C=0.565
1000Genomes	American	Sub	694	T=0.414	C=0.586
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5167	C=0.4833
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5075	C=0.4925
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5254	C=0.4746
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1976	A=0.0000, C=0.8024, G=0.0000
HapMap	Global	Study-wide	1884	T=0.3116	C=0.6884
HapMap	American	Sub	768	T=0.388	C=0.612
HapMap	African	Sub	686	T=0.257	C=0.743
HapMap	Asian	Sub	254	T=0.161	C=0.839
HapMap	Europe	Sub	176	T=0.409	C=0.591
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2020	C=0.7980
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.522	C=0.478
Northern Sweden	ACPOP	Study-wide	600	T=0.475	C=0.525
SGDP_PRJ	Global	Study-wide	464	T=0.246	C=0.754
Qatari	Global	Study-wide	216	T=0.477	C=0.523
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.238	C=0.762
Siberian	Global	Study-wide	46	T=0.26	C=0.74
The Danish reference pan genome	Danish	Study-wide	40	T=0.62	C=0.38

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 17	NC_000017.11:g.30200210T>A
GRCh38.p14 chr 17	NC_000017.11:g.30200210T>C
GRCh38.p14 chr 17	NC_000017.11:g.30200210T>G
GRCh37.p13 chr 17	NC_000017.10:g.28527228T>A
GRCh37.p13 chr 17	NC_000017.10:g.28527228T>C
GRCh37.p13 chr 17	NC_000017.10:g.28527228T>G
SLC6A4 RefSeqGene	NG_011747.2:g.40727A>T
SLC6A4 RefSeqGene	NG_011747.2:g.40727A>G
SLC6A4 RefSeqGene	NG_011747.2:g.40727A>C

Gene: SLC6A4, solute carrier family 6 member 4 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC6A4 transcript	NM_001045.6:c.1819-1680A>T	N/A	Intron Variant

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

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=	A	C	G
GRCh38.p14 chr 17	NC_000017.11:g.30200210=	NC_000017.11:g.30200210T>A	NC_000017.11:g.30200210T>C	NC_000017.11:g.30200210T>G
GRCh37.p13 chr 17	NC_000017.10:g.28527228=	NC_000017.10:g.28527228T>A	NC_000017.10:g.28527228T>C	NC_000017.10:g.28527228T>G
SLC6A4 RefSeqGene	NG_011747.2:g.40727=	NG_011747.2:g.40727A>T	NG_011747.2:g.40727A>G	NG_011747.2:g.40727A>C
SLC6A4 transcript	NM_001045.5:c.1819-1680=	NM_001045.5:c.1819-1680A>T	NM_001045.5:c.1819-1680A>G	NM_001045.5:c.1819-1680A>C
SLC6A4 transcript	NM_001045.6:c.1819-1680=	NM_001045.6:c.1819-1680A>T	NM_001045.6:c.1819-1680A>G	NM_001045.6:c.1819-1680A>C
SLC6A4 transcript variant X1	XM_005258025.1:c.1945-1680=	XM_005258025.1:c.1945-1680A>T	XM_005258025.1:c.1945-1680A>G	XM_005258025.1:c.1945-1680A>C

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#.

83 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13472292	Dec 05, 2003 (119)
2	BCM_SSAHASNP	ss13737769	Dec 05, 2003 (119)
3	ABI	ss40820498	Mar 14, 2006 (126)
4	ILLUMINA	ss65798192	Oct 16, 2006 (127)
5	ILLUMINA	ss74989074	Dec 06, 2007 (129)
6	EGP_SNPS	ss76882953	Dec 06, 2007 (129)
7	HGSV	ss78365982	Dec 06, 2007 (129)
8	HGSV	ss79930281	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss90566897	Mar 24, 2008 (129)
10	BGI	ss106503200	Feb 05, 2009 (130)
11	1000GENOMES	ss109713111	Jan 24, 2009 (130)
12	ILLUMINA-UK	ss118031457	Feb 14, 2009 (130)
13	KRIBB_YJKIM	ss119588213	Dec 01, 2009 (131)
14	ENSEMBL	ss137036546	Dec 01, 2009 (131)
15	GMI	ss157961561	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss168003764	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss169386441	Jul 04, 2010 (132)
18	ILLUMINA	ss174801155	Jul 04, 2010 (132)
19	BUSHMAN	ss202370773	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss207982691	Jul 04, 2010 (132)
21	1000GENOMES	ss211788716	Jul 14, 2010 (132)
22	1000GENOMES	ss227511207	Jul 14, 2010 (132)
23	1000GENOMES	ss237217461	Jul 15, 2010 (132)
24	1000GENOMES	ss243521689	Jul 15, 2010 (132)
25	GMI	ss282738691	May 04, 2012 (137)
26	GMI	ss287168614	Apr 25, 2013 (138)
27	PJP	ss292036321	May 09, 2011 (134)
28	ILLUMINA	ss537583633	Sep 08, 2015 (146)
29	TISHKOFF	ss565225756	Apr 25, 2013 (138)
30	SSMP	ss661025126	Apr 25, 2013 (138)
31	EVA-GONL	ss993025774	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1081003502	Aug 21, 2014 (142)
33	1000GENOMES	ss1358324872	Aug 21, 2014 (142)
34	DDI	ss1428013004	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1578126976	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1635487407	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1678481440	Apr 01, 2015 (144)
38	EVA_DECODE	ss1697066997	Apr 01, 2015 (144)
39	EVA_SVP	ss1713576792	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1808748237	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1936483157	Feb 12, 2016 (147)
42	GENOMED	ss1968374760	Jul 19, 2016 (147)
43	JJLAB	ss2029022327	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2157486231	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2216216571	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2629006940	Nov 08, 2017 (151)
47	GRF	ss2702045794	Nov 08, 2017 (151)
48	GNOMAD	ss2948898018	Nov 08, 2017 (151)
49	AFFY	ss2985728136	Nov 08, 2017 (151)
50	SWEGEN	ss3015396330	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3028331603	Nov 08, 2017 (151)
52	CSHL	ss3351709691	Nov 08, 2017 (151)
53	ILLUMINA	ss3627649542	Oct 12, 2018 (152)
54	ILLUMINA	ss3638155800	Oct 12, 2018 (152)
55	ILLUMINA	ss3643134728	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3682301126	Jul 13, 2019 (153)
57	EVA_DECODE	ss3700303318	Jul 13, 2019 (153)
58	ACPOP	ss3741958366	Jul 13, 2019 (153)
59	EVA	ss3754571719	Jul 13, 2019 (153)
60	PACBIO	ss3788180833	Jul 13, 2019 (153)
61	PACBIO	ss3793143027	Jul 13, 2019 (153)
62	PACBIO	ss3798028944	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3819848429	Jul 13, 2019 (153)
64	EVA	ss3834828135	Apr 27, 2020 (154)
65	EVA	ss3841024092	Apr 27, 2020 (154)
66	EVA	ss3846520944	Apr 27, 2020 (154)
67	SGDP_PRJ	ss3885573616	Apr 27, 2020 (154)
68	KRGDB	ss3935226702	Apr 27, 2020 (154)
69	KOGIC	ss3978706667	Apr 27, 2020 (154)
70	TOPMED	ss5033110675	Apr 26, 2021 (155)
71	TOMMO_GENOMICS	ss5222015666	Apr 26, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5302835809	Oct 16, 2022 (156)
73	EVA	ss5427067617	Oct 16, 2022 (156)
74	HUGCELL_USP	ss5495933875	Oct 16, 2022 (156)
75	EVA	ss5511747236	Oct 16, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5606414318	Oct 16, 2022 (156)
77	SANFORD_IMAGENETICS	ss5659938333	Oct 16, 2022 (156)
78	TOMMO_GENOMICS	ss5778096912	Oct 16, 2022 (156)
79	YY_MCH	ss5816474764	Oct 16, 2022 (156)
80	EVA	ss5833871172	Oct 16, 2022 (156)
81	EVA	ss5851778487	Oct 16, 2022 (156)
82	EVA	ss5913637324	Oct 16, 2022 (156)
83	EVA	ss5951335321	Oct 16, 2022 (156)
84	1000Genomes	NC_000017.10 - 28527228	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000017.11 - 30200210	Oct 16, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 28527228	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000017.10 - 28527228	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000017.10 - 28527228	Apr 27, 2020 (154)
89	gnomAD - Genomes	NC_000017.11 - 30200210	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000017.10 - 28527228	Apr 27, 2020 (154)
91	HapMap	NC_000017.11 - 30200210	Apr 27, 2020 (154)
92	KOREAN population from KRGDB	NC_000017.10 - 28527228	Apr 27, 2020 (154)
93	Korean Genome Project	NC_000017.11 - 30200210	Apr 27, 2020 (154)
94	Northern Sweden	NC_000017.10 - 28527228	Jul 13, 2019 (153)
95	Qatari	NC_000017.10 - 28527228	Apr 27, 2020 (154)
96	SGDP_PRJ	NC_000017.10 - 28527228	Apr 27, 2020 (154)
97	Siberian	NC_000017.10 - 28527228	Apr 27, 2020 (154)
98	8.3KJPN	NC_000017.10 - 28527228	Apr 26, 2021 (155)
99	14KJPN	NC_000017.11 - 30200210	Oct 16, 2022 (156)
100	TopMed	NC_000017.11 - 30200210	Apr 26, 2021 (155)
101	UK 10K study - Twins	NC_000017.10 - 28527228	Oct 12, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000017.10 - 28527228	Jul 13, 2019 (153)
103	ALFA	NC_000017.11 - 30200210	Apr 26, 2021 (155)

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)
rs59585822	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
42404096, ss3935226702	NC_000017.10:28527227:T:A	NC_000017.11:30200209:T:A	(self)
1319270788	NC_000017.11:30200209:T:A	NC_000017.11:30200209:T:A	(self)
ss78365982, ss79930281, ss90566897, ss109713111, ss118031457, ss168003764, ss169386441, ss202370773, ss207982691, ss211788716, ss282738691, ss287168614, ss292036321, ss1697066997, ss1713576792, ss3643134728	NC_000017.9:25551353:T:C	NC_000017.11:30200209:T:C	(self)
71554540, 39665345, 28039374, 4330461, 17681756, 42404096, 15243231, 18525079, 37590596, 10002585, 79984973, 39665345, 8782558, ss227511207, ss237217461, ss243521689, ss537583633, ss565225756, ss661025126, ss993025774, ss1081003502, ss1358324872, ss1428013004, ss1578126976, ss1635487407, ss1678481440, ss1808748237, ss1936483157, ss1968374760, ss2029022327, ss2157486231, ss2629006940, ss2702045794, ss2948898018, ss2985728136, ss3015396330, ss3351709691, ss3627649542, ss3638155800, ss3682301126, ss3741958366, ss3754571719, ss3788180833, ss3793143027, ss3798028944, ss3834828135, ss3841024092, ss3885573616, ss3935226702, ss5222015666, ss5427067617, ss5511747236, ss5659938333, ss5833871172, ss5951335321	NC_000017.10:28527227:T:C	NC_000017.11:30200209:T:C	(self)
93940253, 504794350, 1474640, 35084668, 111934016, 248656337, 1319270788, ss2216216571, ss3028331603, ss3700303318, ss3819848429, ss3846520944, ss3978706667, ss5033110675, ss5302835809, ss5495933875, ss5606414318, ss5778096912, ss5816474764, ss5851778487, ss5913637324	NC_000017.11:30200209:T:C	NC_000017.11:30200209:T:C	(self)
ss13472292, ss13737769	NT_010799.14:3264220:T:C	NC_000017.11:30200209:T:C	(self)
ss40820498, ss65798192, ss74989074, ss76882953, ss106503200, ss119588213, ss137036546, ss157961561, ss174801155	NT_010799.15:3264221:T:C	NC_000017.11:30200209:T:C	(self)
42404096, ss3935226702	NC_000017.10:28527227:T:G	NC_000017.11:30200209:T:G	(self)

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

4 citations for rs9303628

PMID	Title	Author	Year	Journal
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
26556226	A pharmacogenomic study revealed an association between SLC6A4 and risperidone-induced weight gain in Chinese Han population.	Wang F et al.	2015	Pharmacogenomics
30607769	Pharmacogenetic Correlates of Antipsychotic-Induced Weight Gain in the Chinese Population.	Luo C et al.	2019	Neuroscience bulletin
32964515	Rs9303628 and rs2054847 of SLC6A4 are protective factors for the onset of lifelong premature ejaculation among the Chinese population.	Wang F et al.	2021	Andrologia

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs9303628