Name: rs250682
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.

rs250682

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:1427688 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.330315 (87431/264690, TOPMED)
C=0.319112 (44670/139982, GnomAD)
G=0.46804 (13226/28258, 14KJPN) (+ 14 more)
C=0.27877 (5266/18890, ALFA)
G=0.47518 (7964/16760, 8.3KJPN)
C=0.4252 (2723/6404, 1000G_30x)
C=0.4299 (2153/5008, 1000G)
C=0.2500 (1120/4480, Estonian)
G=0.4703 (1378/2930, KOREAN)
C=0.4503 (852/1892, HapMap)
C=0.174 (174/998, GoNL)
C=0.270 (162/600, NorthernSweden)
G=0.370 (122/330, SGDP_PRJ)
C=0.343 (74/216, Qatari)
G=0.495 (106/214, Vietnamese)
C=0.25 (10/40, GENOME_DK)
G=0.37 (11/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC6A3 : Intron Variant
Publications: 3 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	G=0.72123	C=0.27877	0.528851	0.086395	0.384754	10
European	Sub	14286	G=0.77369	C=0.22631	0.595968	0.048579	0.355453	1
African	Sub	2946	G=0.5064	C=0.4936	0.262729	0.24983	0.487441	1
African Others	Sub	114	G=0.412	C=0.588	0.157895	0.333333	0.508772	0
African American	Sub	2832	G=0.5102	C=0.4898	0.266949	0.246469	0.486582	1
Asian	Sub	112	G=0.562	C=0.438	0.303571	0.178571	0.517857	0
East Asian	Sub	86	G=0.59	C=0.41	0.348837	0.162791	0.488372	0
Other Asian	Sub	26	G=0.46	C=0.54	0.153846	0.230769	0.615385	0
Latin American 1	Sub	146	G=0.705	C=0.295	0.493151	0.082192	0.424658	0
Latin American 2	Sub	610	G=0.626	C=0.374	0.393443	0.140984	0.465574	0
South Asian	Sub	98	G=0.70	C=0.30	0.489796	0.081633	0.428571	0
Other	Sub	692	G=0.668	C=0.332	0.445087	0.109827	0.445087	0

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.669685	C=0.330315
gnomAD - Genomes	Global	Study-wide	139982	G=0.680888	C=0.319112
gnomAD - Genomes	European	Sub	75860	G=0.77833	C=0.22167
gnomAD - Genomes	African	Sub	41900	G=0.52325	C=0.47675
gnomAD - Genomes	American	Sub	13636	G=0.65554	C=0.34446
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.7163	C=0.2837
gnomAD - Genomes	East Asian	Sub	3114	G=0.4875	C=0.5125
gnomAD - Genomes	Other	Sub	2148	G=0.7011	C=0.2989
14KJPN	JAPANESE	Study-wide	28258	G=0.46804	C=0.53196
Allele Frequency Aggregator	Total	Global	18890	G=0.72123	C=0.27877
Allele Frequency Aggregator	European	Sub	14286	G=0.77369	C=0.22631
Allele Frequency Aggregator	African	Sub	2946	G=0.5064	C=0.4936
Allele Frequency Aggregator	Other	Sub	692	G=0.668	C=0.332
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.626	C=0.374
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.705	C=0.295
Allele Frequency Aggregator	Asian	Sub	112	G=0.562	C=0.438
Allele Frequency Aggregator	South Asian	Sub	98	G=0.70	C=0.30
8.3KJPN	JAPANESE	Study-wide	16760	G=0.47518	C=0.52482
1000Genomes_30x	Global	Study-wide	6404	G=0.5748	C=0.4252
1000Genomes_30x	African	Sub	1786	G=0.4602	C=0.5398
1000Genomes_30x	Europe	Sub	1266	G=0.7599	C=0.2401
1000Genomes_30x	South Asian	Sub	1202	G=0.5291	C=0.4709
1000Genomes_30x	East Asian	Sub	1170	G=0.4974	C=0.5026
1000Genomes_30x	American	Sub	980	G=0.693	C=0.307
1000Genomes	Global	Study-wide	5008	G=0.5701	C=0.4299
1000Genomes	African	Sub	1322	G=0.4599	C=0.5401
1000Genomes	East Asian	Sub	1008	G=0.4891	C=0.5109
1000Genomes	Europe	Sub	1006	G=0.7515	C=0.2485
1000Genomes	South Asian	Sub	978	G=0.530	C=0.470
1000Genomes	American	Sub	694	G=0.692	C=0.308
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7500	C=0.2500
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4703	C=0.5297
HapMap	Global	Study-wide	1892	G=0.5497	C=0.4503
HapMap	American	Sub	770	G=0.587	C=0.413
HapMap	African	Sub	692	G=0.496	C=0.504
HapMap	Asian	Sub	254	G=0.433	C=0.567
HapMap	Europe	Sub	176	G=0.767	C=0.233
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.826	C=0.174
Northern Sweden	ACPOP	Study-wide	600	G=0.730	C=0.270
SGDP_PRJ	Global	Study-wide	330	G=0.370	C=0.630
Qatari	Global	Study-wide	216	G=0.657	C=0.343
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.495	C=0.505
The Danish reference pan genome	Danish	Study-wide	40	G=0.75	C=0.25
Siberian	Global	Study-wide	30	G=0.37	C=0.63

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 5	NC_000005.10:g.1427688G>A
GRCh38.p14 chr 5	NC_000005.10:g.1427688G>C
GRCh37.p13 chr 5	NC_000005.9:g.1427803G>A
GRCh37.p13 chr 5	NC_000005.9:g.1427803G>C
SLC6A3 RefSeqGene	NG_015885.1:g.22741C>T
SLC6A3 RefSeqGene	NG_015885.1:g.22741C>G
GRCh38.p14 chr 5 alt locus HSCHR5_3_CTG1	NT_187547.1:g.82084G>C
GRCh38.p14 chr 5 alt locus HSCHR5_3_CTG1	NT_187547.1:g.82084G>T

Gene: SLC6A3, solute carrier family 6 member 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC6A3 transcript	NM_001044.5:c.653+4776C>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	G=	A	C
GRCh38.p14 chr 5	NC_000005.10:g.1427688=	NC_000005.10:g.1427688G>A	NC_000005.10:g.1427688G>C
GRCh37.p13 chr 5	NC_000005.9:g.1427803=	NC_000005.9:g.1427803G>A	NC_000005.9:g.1427803G>C
SLC6A3 RefSeqGene	NG_015885.1:g.22741=	NG_015885.1:g.22741C>T	NG_015885.1:g.22741C>G
GRCh38.p14 chr 5 alt locus HSCHR5_3_CTG1	NT_187547.1:g.82084G>C	NT_187547.1:g.82084G>T	NT_187547.1:g.82084=
SLC6A3 transcript	NM_001044.4:c.653+4776=	NM_001044.4:c.653+4776C>T	NM_001044.4:c.653+4776C>G
SLC6A3 transcript	NM_001044.5:c.653+4776=	NM_001044.5:c.653+4776C>T	NM_001044.5:c.653+4776C>G

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#.

81 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss324855	Jul 12, 2000 (79)
2	SC_JCM	ss616813	Jul 16, 2000 (80)
3	KWOK	ss1167628	Oct 04, 2000 (86)
4	KWOK	ss1573139	Oct 18, 2000 (89)
5	TSC-CSHL	ss2187814	Oct 24, 2000 (111)
6	SC_JCM	ss6153531	Feb 20, 2003 (126)
7	WI_SSAHASNP	ss6887153	Feb 20, 2003 (126)
8	CSHL-HAPMAP	ss19619852	Feb 27, 2004 (120)
9	CSHL-HAPMAP	ss20237226	Feb 27, 2004 (120)
10	SSAHASNP	ss22300692	Apr 05, 2004 (121)
11	ABI	ss42583252	Mar 11, 2006 (126)
12	AFFY	ss66445248	Nov 29, 2006 (127)
13	AFFY	ss76229949	Dec 08, 2007 (129)
14	KRIBB_YJKIM	ss81412404	Dec 16, 2007 (130)
15	HUMANGENOME_JCVI	ss98689074	Feb 05, 2009 (130)
16	BGI	ss105900092	Feb 05, 2009 (130)
17	1000GENOMES	ss111294860	Jan 25, 2009 (130)
18	ENSEMBL	ss142926445	Dec 01, 2009 (131)
19	GMI	ss154912388	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss161945622	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss164029977	Jul 04, 2010 (132)
22	AFFY	ss172896079	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss206951159	Jul 04, 2010 (132)
24	1000GENOMES	ss221467389	Jul 14, 2010 (132)
25	1000GENOMES	ss232792686	Jul 14, 2010 (132)
26	1000GENOMES	ss239997332	Jul 15, 2010 (132)
27	GMI	ss278133770	May 04, 2012 (137)
28	GMI	ss285103014	Apr 25, 2013 (138)
29	PJP	ss293340779	May 09, 2011 (134)
30	TISHKOFF	ss558147187	Apr 25, 2013 (138)
31	SSMP	ss651991197	Apr 25, 2013 (138)
32	EVA-GONL	ss981165229	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1072326014	Aug 21, 2014 (142)
34	1000GENOMES	ss1313605106	Aug 21, 2014 (142)
35	DDI	ss1430216849	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1580976354	Apr 01, 2015 (144)
37	EVA_DECODE	ss1590681143	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1612111344	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1612111345	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1655105377	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1655105378	Apr 01, 2015 (144)
42	EVA_SVP	ss1712736961	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1802923475	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1924421537	Feb 12, 2016 (147)
45	GENOMED	ss1969991255	Jul 19, 2016 (147)
46	JJLAB	ss2022803988	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2150954100	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2270768818	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2625900426	Nov 08, 2017 (151)
50	GRF	ss2706475486	Nov 08, 2017 (151)
51	GNOMAD	ss2820334119	Nov 08, 2017 (151)
52	SWEGEN	ss2996316011	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3025184772	Nov 08, 2017 (151)
54	CSHL	ss3346200809	Nov 08, 2017 (151)
55	URBANLAB	ss3647965583	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3664204776	Jul 13, 2019 (153)
57	EVA_DECODE	ss3713954710	Jul 13, 2019 (153)
58	ACPOP	ss3732017705	Jul 13, 2019 (153)
59	EVA	ss3762967479	Jul 13, 2019 (153)
60	PACBIO	ss3784999431	Jul 13, 2019 (153)
61	PACBIO	ss3790419860	Jul 13, 2019 (153)
62	PACBIO	ss3795296328	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3806136387	Jul 13, 2019 (153)
64	EVA	ss3829052496	Apr 26, 2020 (154)
65	SGDP_PRJ	ss3861044817	Apr 26, 2020 (154)
66	KRGDB	ss3907482196	Apr 26, 2020 (154)
67	VINODS	ss4024242866	Apr 26, 2021 (155)
68	TOPMED	ss4647165168	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5170050506	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5262612458	Oct 13, 2022 (156)
71	EVA	ss5355165895	Oct 13, 2022 (156)
72	HUGCELL_USP	ss5460984694	Oct 13, 2022 (156)
73	EVA	ss5507890629	Oct 13, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5545531606	Oct 13, 2022 (156)
75	SANFORD_IMAGENETICS	ss5637027781	Oct 13, 2022 (156)
76	TOMMO_GENOMICS	ss5705632537	Oct 13, 2022 (156)
77	YY_MCH	ss5805952261	Oct 13, 2022 (156)
78	EVA	ss5834410759	Oct 13, 2022 (156)
79	EVA	ss5854645409	Oct 13, 2022 (156)
80	EVA	ss5892686652	Oct 13, 2022 (156)
81	EVA	ss5965435166	Oct 13, 2022 (156)
82	1000Genomes	NC_000005.9 - 1427803	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000005.10 - 1427688	Oct 13, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 13987046 (NC_000005.9:1427802:G:G 3087/3854, NC_000005.9:1427802:G:C 767/3854) Row 13987047 (NC_000005.9:1427802:G:G 3854/3854, NC_000005.9:1427802:G:A 0/3854)	-	Oct 12, 2018 (152)
85	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 13987046 (NC_000005.9:1427802:G:G 3087/3854, NC_000005.9:1427802:G:C 767/3854) Row 13987047 (NC_000005.9:1427802:G:G 3854/3854, NC_000005.9:1427802:G:A 0/3854)	-	Oct 12, 2018 (152)
86	Genetic variation in the Estonian population	NC_000005.9 - 1427803	Oct 12, 2018 (152)
87	The Danish reference pan genome	NC_000005.9 - 1427803	Apr 26, 2020 (154)
88	gnomAD - Genomes	NC_000005.10 - 1427688	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000005.9 - 1427803	Apr 26, 2020 (154)
90	HapMap	NC_000005.10 - 1427688	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000005.9 - 1427803	Apr 26, 2020 (154)
92	Northern Sweden	NC_000005.9 - 1427803	Jul 13, 2019 (153)
93	Qatari	NC_000005.9 - 1427803	Apr 26, 2020 (154)
94	SGDP_PRJ	NC_000005.9 - 1427803	Apr 26, 2020 (154)
95	Siberian	NC_000005.9 - 1427803	Apr 26, 2020 (154)
96	8.3KJPN	NC_000005.9 - 1427803	Apr 26, 2021 (155)
97	14KJPN	NC_000005.10 - 1427688	Oct 13, 2022 (156)
98	TopMed	NC_000005.10 - 1427688	Apr 26, 2021 (155)
99	UK 10K study - Twins Submission ignored due to conflicting rows: Row 13987046 (NC_000005.9:1427802:G:G 2916/3708, NC_000005.9:1427802:G:C 792/3708) Row 13987047 (NC_000005.9:1427802:G:G 3707/3708, NC_000005.9:1427802:G:A 1/3708)	-	Oct 12, 2018 (152)
100	UK 10K study - Twins Submission ignored due to conflicting rows: Row 13987046 (NC_000005.9:1427802:G:G 2916/3708, NC_000005.9:1427802:G:C 792/3708) Row 13987047 (NC_000005.9:1427802:G:G 3707/3708, NC_000005.9:1427802:G:A 1/3708)	-	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000005.9 - 1427803	Jul 13, 2019 (153)
102	ALFA	NC_000005.10 - 1427688	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)
rs1162711	Nov 09, 2000 (89)
rs1587615	Feb 20, 2003 (111)
rs4554270	Mar 11, 2006 (126)
rs4975545	Mar 11, 2006 (126)
rs61342177	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1612111345, ss1655105378	NC_000005.9:1427802:G:A	NC_000005.10:1427687:G:A	(self)
ss2270768818	NC_000005.10:1427687:G:A	NC_000005.10:1427687:G:A	(self)
ss66445248, ss76229949, ss111294860, ss161945622, ss164029977, ss172896079, ss206951159, ss278133770, ss285103014, ss293340779, ss1590681143, ss1712736961	NC_000005.8:1480802:G:C	NC_000005.10:1427687:G:C	(self)
25149579, 9943024, 7141293, 6208679, 14659590, 5302570, 6463467, 13061797, 3470454, 28019813, 3100951, ss221467389, ss232792686, ss239997332, ss558147187, ss651991197, ss981165229, ss1072326014, ss1313605106, ss1430216849, ss1580976354, ss1612111344, ss1655105377, ss1802923475, ss1924421537, ss1969991255, ss2022803988, ss2150954100, ss2625900426, ss2706475486, ss2820334119, ss2996316011, ss3346200809, ss3664204776, ss3732017705, ss3762967479, ss3784999431, ss3790419860, ss3795296328, ss3829052496, ss3861044817, ss3907482196, ss5170050506, ss5355165895, ss5507890629, ss5637027781, ss5834410759, ss5965435166	NC_000005.9:1427802:G:C	NC_000005.10:1427687:G:C	(self)
33057541, 177864041, 2790135, 39469641, 484542725, 13817765442, ss2270768818, ss3025184772, ss3647965583, ss3713954710, ss3806136387, ss4647165168, ss5262612458, ss5460984694, ss5545531606, ss5705632537, ss5805952261, ss5854645409, ss5892686652	NC_000005.10:1427687:G:C	NC_000005.10:1427687:G:C	(self)
ss324855, ss616813, ss1167628, ss1573139, ss2187814, ss6153531, ss6887153, ss42583252, ss81412404, ss98689074, ss105900092, ss142926445, ss154912388	NT_006576.16:1417802:G:C	NC_000005.10:1427687:G:C	(self)
ss19619852, ss20237226, ss22300692	NT_023089.13:1410540:G:C	NC_000005.10:1427687:G:C	(self)
ss4024242866	NT_187547.1:82083:G:G	NC_000005.10:1427687:G:C	(self)

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

3 citations for rs250682

PMID	Title	Author	Year	Journal
19901083	Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis.	Cobat A et al.	2009	The Journal of experimental medicine
22290120	The evolutionary significance of depression in Pathogen Host Defense (PATHOS-D).	Raison CL et al.	2013	Molecular psychiatry
22832519	A two-locus genetic interaction between LPHN3 and 11q predicts ADHD severity and long-term outcome.	Acosta MT et al.	2011	Translational psychiatry

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

rs250682