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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs2242446

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr16:55656513 (GRCh38.p7) 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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.25546 (32078/125568, TOPMED)
C=0.2556 (7880/30824, GnomAD)
C=0.247 (1237/5008, 1000G) (+ 2 more)
C=0.293 (1130/3854, ALSPAC)
C=0.285 (1055/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC6A2 : Intron Variant
Publications
24 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.p7 chr 16 NC_000016.10:g.55656513C>A
GRCh38.p7 chr 16 NC_000016.10:g.55656513C>T
GRCh37.p13 chr 16 NC_000016.9:g.55690425C>A
GRCh37.p13 chr 16 NC_000016.9:g.55690425C>T
SLC6A2 RefSeqGene NG_016969.1:g.5884C>A
SLC6A2 RefSeqGene NG_016969.1:g.5884C>T
Gene: SLC6A2, solute carrier family 6 member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC6A2 transcript variant 2 NM_001172501.1:c. N/A Intron Variant
SLC6A2 transcript variant 3 NM_001043.3:c. N/A 5 Prime UTR Variant
SLC6A2 transcript variant 4 NM_001172502.1:c. N/A Genic Upstream Transcript Variant
SLC6A2 transcript variant 1 NM_001172504.1:c. N/A Genic Upstream Transcript Variant
SLC6A2 transcript variant X2 XM_006721263.2:c. N/A Intron Variant
SLC6A2 transcript variant X1 XM_011523295.1:c. N/A Intron Variant
SLC6A2 transcript variant X3 XM_011523296.1:c. N/A Intron Variant
SLC6A2 transcript variant X4 XM_011523297.2:c. N/A Intron Variant
SLC6A2 transcript variant X6 XM_011523298.1:c. N/A Intron Variant
SLC6A2 transcript variant X7 XM_011523299.2:c. N/A Genic Upstream Transcript Variant
SLC6A2 transcript variant X8 XM_011523300.2:c. N/A Genic Upstream Transcript Variant
SLC6A2 transcript variant X5 XR_933403.2: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.

Allele: T (allele ID: 325781 )
ClinVar Accession Disease Names Clinical Significance
RCV000264953.1 Orthostatic intolerance Likely-Benign
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
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.25546 T=0.74454
The Genome Aggregation Database Global Study-wide 30824 C=0.2556 T=0.7444
The Genome Aggregation Database European Sub 18402 C=0.2847 T=0.7153
The Genome Aggregation Database African Sub 8694 C=0.185 T=0.815
The Genome Aggregation Database East Asian Sub 1616 C=0.308 T=0.692
The Genome Aggregation Database Other Sub 974 C=0.25 T=0.75
The Genome Aggregation Database American Sub 836 C=0.24 T=0.76
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.30 T=0.70
1000Genomes Global Study-wide 5008 C=0.247 T=0.753
1000Genomes African Sub 1322 C=0.179 T=0.821
1000Genomes East Asian Sub 1008 C=0.315 T=0.685
1000Genomes Europe Sub 1006 C=0.257 T=0.743
1000Genomes South Asian Sub 978 C=0.27 T=0.73
1000Genomes American Sub 694 C=0.22 T=0.78
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.293 T=0.707
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.285 T=0.715
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= A T Note
GRCh38.p7 chr 16 NC_000016.10:g.55...

NC_000016.10:g.55656513C=

NC_000016.10:g.55...

NC_000016.10:g.55656513C>A

NC_000016.10:g.55...

NC_000016.10:g.55656513C>T

GRCh37.p13 chr 16 NC_000016.9:g.556...

NC_000016.9:g.55690425C=

NC_000016.9:g.556...

NC_000016.9:g.55690425C>A

NC_000016.9:g.556...

NC_000016.9:g.55690425C>T

SLC6A2 RefSeqGene NG_016969.1:g.5884C= NG_016969.1:g.588...

NG_016969.1:g.5884C>A

NG_016969.1:g.588...

NG_016969.1:g.5884C>T

SLC6A2 transcript variant 3 NM_001043.3:c.-182C= NM_001043.3:c.-18...

NM_001043.3:c.-182C>A

NM_001043.3:c.-18...

NM_001043.3:c.-182C>T

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#.

1 ClinVar, 5 Frequency, 93 SubSNP submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3198762 Aug 15, 2001 (98)
2 ILLUMINA ss66644236 Nov 29, 2006 (127)
3 ILLUMINA ss67237112 Nov 29, 2006 (127)
4 ILLUMINA ss67633367 Nov 29, 2006 (127)
5 ILLUMINA ss70715440 May 25, 2008 (130)
6 ILLUMINA ss71283278 May 16, 2007 (127)
7 ILLUMINA ss75543556 Dec 07, 2007 (129)
8 HGSV ss78112646 Dec 07, 2007 (129)
9 ILLUMINA ss79122869 Dec 15, 2007 (130)
10 HGSV ss81249933 Dec 15, 2007 (130)
11 KRIBB_YJKIM ss84006553 Dec 15, 2007 (130)
12 HGSV ss84528918 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss90401906 Mar 24, 2008 (129)
14 BGI ss106473245 Feb 05, 2009 (130)
15 1000GENOMES ss115128225 Jan 25, 2009 (130)
16 ILLUMINA-UK ss118262503 Feb 14, 2009 (130)
17 ILLUMINA ss121963886 Dec 01, 2009 (131)
18 ENSEMBL ss133794167 Dec 01, 2009 (131)
19 ENSEMBL ss136737309 Dec 01, 2009 (131)
20 ILLUMINA ss153892670 Dec 01, 2009 (131)
21 GMI ss157386418 Dec 01, 2009 (131)
22 ILLUMINA ss159371762 Dec 01, 2009 (131)
23 ILLUMINA ss160520574 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss168255953 Jul 04, 2010 (132)
25 ILLUMINA ss171117651 Jul 04, 2010 (132)
26 ILLUMINA ss173208990 Jul 04, 2010 (132)
27 BUSHMAN ss201727157 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss207715222 Jul 04, 2010 (132)
29 1000GENOMES ss210896737 Jul 14, 2010 (132)
30 1000GENOMES ss227256605 Jul 14, 2010 (132)
31 1000GENOMES ss237035557 Jul 15, 2010 (132)
32 1000GENOMES ss243372927 Jul 15, 2010 (132)
33 BL ss255722301 May 09, 2011 (134)
34 GMI ss282542108 May 04, 2012 (137)
35 PHARMGKB_PMT ss290492598 May 09, 2011 (134)
36 PJP ss291848436 May 09, 2011 (134)
37 ILLUMINA ss480481611 May 04, 2012 (137)
38 ILLUMINA ss480495981 May 04, 2012 (137)
39 ILLUMINA ss481296621 Sep 08, 2015 (146)
40 ILLUMINA ss485038294 May 04, 2012 (137)
41 ILLUMINA ss535980610 Sep 08, 2015 (146)
42 SSMP ss660688859 Apr 25, 2013 (138)
43 ILLUMINA ss778487269 Sep 08, 2015 (146)
44 ILLUMINA ss782965386 Sep 08, 2015 (146)
45 ILLUMINA ss783927216 Sep 08, 2015 (146)
46 ILLUMINA ss825453387 Apr 01, 2015 (144)
47 ILLUMINA ss832221655 Sep 08, 2015 (146)
48 ILLUMINA ss833943221 Sep 08, 2015 (146)
49 EVA-GONL ss992515737 Aug 21, 2014 (142)
50 PMT ss1040217376 Aug 21, 2014 (142)
51 JMKIDD_LAB ss1080642998 Aug 21, 2014 (142)
52 1000GENOMES ss1356350628 Aug 21, 2014 (142)
53 DDI ss1427855340 Apr 01, 2015 (144)
54 EVA_GENOME_DK ss1577924552 Apr 01, 2015 (144)
55 EVA_UK10K_ALSPAC ss1634478623 Apr 01, 2015 (144)
56 EVA_UK10K_TWINSUK ss1677472656 Apr 01, 2015 (144)
57 EVA_DECODE ss1696550321 Apr 01, 2015 (144)
58 EVA_SVP ss1713541207 Apr 01, 2015 (144)
59 ILLUMINA ss1752195320 Sep 08, 2015 (146)
60 HAMMER_LAB ss1808524803 Sep 08, 2015 (146)
61 WEILL_CORNELL_DGM ss1935951974 Feb 12, 2016 (147)
62 ILLUMINA ss1946415396 Feb 12, 2016 (147)
63 ILLUMINA ss1959680750 Feb 12, 2016 (147)
64 GENOMED ss1968267687 Jul 19, 2016 (147)
65 JJLAB ss2028759050 Sep 14, 2016 (149)
66 USC_VALOUEV ss2157195371 Dec 20, 2016 (150)
67 HUMAN_LONGEVITY ss2212376426 Dec 20, 2016 (150)
68 SYSTEMSBIOZJU ss2628871139 Nov 08, 2017 (151)
69 ILLUMINA ss2633321364 Nov 08, 2017 (151)
70 GRF ss2701719260 Nov 08, 2017 (151)
71 ILLUMINA ss2710833941 Nov 08, 2017 (151)
72 GNOMAD ss2943307591 Nov 08, 2017 (151)
73 SWEGEN ss3014555086 Nov 08, 2017 (151)
74 ILLUMINA ss3021708421 Nov 08, 2017 (151)
75 BIOINF_KMB_FNS_UNIBA ss3028198174 Nov 08, 2017 (151)
76 TOPMED ss3247207845 Nov 08, 2017 (151)
77 TOPMED ss3247207846 Nov 08, 2017 (151)
78 CSHL ss3351463925 Nov 08, 2017 (151)
79 ILLUMINA ss3625693427 Jul 20, 2018 (151)
80 ILLUMINA ss3627529095 Jul 20, 2018 (151)
81 ILLUMINA ss3631307580 Jul 20, 2018 (151)
82 ILLUMINA ss3633121584 Jul 20, 2018 (151)
83 ILLUMINA ss3633827687 Jul 20, 2018 (151)
84 ILLUMINA ss3634643134 Jul 20, 2018 (151)
85 ILLUMINA ss3635515977 Jul 20, 2018 (151)
86 ILLUMINA ss3636334616 Jul 20, 2018 (151)
87 ILLUMINA ss3637267414 Jul 20, 2018 (151)
88 ILLUMINA ss3638126545 Jul 20, 2018 (151)
89 ILLUMINA ss3639074689 Jul 20, 2018 (151)
90 ILLUMINA ss3639543560 Jul 20, 2018 (151)
91 ILLUMINA ss3640350453 Jul 20, 2018 (151)
92 ILLUMINA ss3643107658 Jul 20, 2018 (151)
93 ILLUMINA ss3644668476 Jul 20, 2018 (151)
94 1000Genomes NC_000016.9 - 55690425 Jul 20, 2018 (151)
95 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 55690425 Jul 20, 2018 (151)
96 The Genome Aggregation Database NC_000016.9 - 55690425 Jul 20, 2018 (151)
97 Trans-Omics for Precision Medicine NC_000016.10 - 55656513 Jul 20, 2018 (151)
98 UK 10K study - Twins NC_000016.9 - 55690425 Jul 20, 2018 (151)
99 ClinVar RCV000264953.1 Jul 20, 2018 (151)
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)
rs59199002 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78112646, ss81249933, ss84528918, ss90401906, ss115128225, ss118262503, ss168255953, ss201727157, ss207715222, ss210896737, ss255722301, ss282542108, ss291848436, ss480481611, ss825453387, ss1696550321, ss1713541207, ss3639074689, ss3639543560, ss3643107658 NC_000016.8:54247925:C= NC_000016.10:55656512:C= (self)
69516414, 38560122, 77009118, 38560122, ss227256605, ss237035557, ss243372927, ss480495981, ss481296621, ss485038294, ss535980610, ss660688859, ss778487269, ss782965386, ss783927216, ss832221655, ss833943221, ss992515737, ss1040217376, ss1080642998, ss1356350628, ss1427855340, ss1577924552, ss1634478623, ss1677472656, ss1752195320, ss1808524803, ss1935951974, ss1946415396, ss1959680750, ss1968267687, ss2028759050, ss2157195371, ss2628871139, ss2633321364, ss2701719260, ss2710833941, ss2943307591, ss3014555086, ss3021708421, ss3351463925, ss3625693427, ss3627529095, ss3631307580, ss3633121584, ss3633827687, ss3634643134, ss3635515977, ss3636334616, ss3637267414, ss3638126545, ss3640350453, ss3644668476 NC_000016.9:55690424:C= NC_000016.10:55656512:C= (self)
144763625, ss2212376426, ss3028198174, ss3247207845, ss3247207846 NC_000016.10:55656512:C= NC_000016.10:55656512:C= (self)
ss3198762, ss66644236, ss67237112, ss67633367, ss70715440, ss71283278, ss75543556, ss79122869, ss84006553, ss106473245, ss121963886, ss133794167, ss136737309, ss153892670, ss157386418, ss159371762, ss160520574, ss171117651, ss173208990, ss290492598 NT_010498.15:9304623:C= NC_000016.10:55656512:C= (self)
ss3247207845 NC_000016.10:55656512:C>A NC_000016.10:55656512:C>A (self)
ss78112646, ss81249933, ss84528918, ss90401906, ss115128225, ss118262503, ss168255953, ss201727157, ss207715222, ss210896737, ss255722301, ss282542108, ss291848436, ss480481611, ss825453387, ss1696550321, ss1713541207, ss3639074689, ss3639543560, ss3643107658 NC_000016.8:54247925:C>T NC_000016.10:55656512:C>T (self)
69516414, 38560122, 77009118, 38560122, ss227256605, ss237035557, ss243372927, ss480495981, ss481296621, ss485038294, ss535980610, ss660688859, ss778487269, ss782965386, ss783927216, ss832221655, ss833943221, ss992515737, ss1040217376, ss1080642998, ss1356350628, ss1427855340, ss1577924552, ss1634478623, ss1677472656, ss1752195320, ss1808524803, ss1935951974, ss1946415396, ss1959680750, ss1968267687, ss2028759050, ss2157195371, ss2628871139, ss2633321364, ss2701719260, ss2710833941, ss2943307591, ss3014555086, ss3021708421, ss3351463925, ss3625693427, ss3627529095, ss3631307580, ss3633121584, ss3633827687, ss3634643134, ss3635515977, ss3636334616, ss3637267414, ss3638126545, ss3640350453, ss3644668476 NC_000016.9:55690424:C>T NC_000016.10:55656512:C>T (self)
RCV000264953.1, 144763625, ss2212376426, ss3028198174, ss3247207846 NC_000016.10:55656512:C>T NC_000016.10:55656512:C>T (self)
ss3198762, ss66644236, ss67237112, ss67633367, ss70715440, ss71283278, ss75543556, ss79122869, ss84006553, ss106473245, ss121963886, ss133794167, ss136737309, ss153892670, ss157386418, ss159371762, ss160520574, ss171117651, ss173208990, ss290492598 NT_010498.15:9304623:C>T NC_000016.10:55656512:C>T (self)
Help

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

24 citations for rs2242446
PMID Title Author Year Journal
15722184 Norepinephrine transporter (NET) promoter and 5'-UTR polymorphisms: association analysis in panic disorder. Lee YJ et al. 2005 Neuroscience letters
17630229 Norepinephrine transporter polymorphisms T-182C and G1287A are not associated with alcohol dependence and its clinical subgroups. Huang SY et al. 2008 Drug and alcohol dependence
18081710 Multivariate permutation analysis associates multiple polymorphisms with subphenotypes of major depression. Hahn MK et al. 2008 Genes, brain, and behavior
18779921 The combined effect of norepinephrine transporter gene and negative life events in major depression of Chinese Han population. Sun N et al. 2008 Journal of neural transmission (Vienna, Austria
18821566 SNPs in dopamine D2 receptor gene (DRD2) and norepinephrine transporter gene (NET) are associated with continuous performance task (CPT) phenotypes in ADHD children and their families. Kollins SH et al. 2008 American journal of medical genetics. Part B, Neuropsychiatric genetics
19693267 Financial and psychological risk attitudes associated with two single nucleotide polymorphisms in the nicotine receptor (CHRNA4) gene. Roe BE et al. 2009 PloS one
20863575 Lack of association between response of OROS-methylphenidate and norepinephrine transporter (SLC6A2) polymorphism in Korean ADHD. Lee SH et al. 2011 Psychiatry research
21412203 Genetic variation in the presynaptic norepinephrine transporter is associated with blood pressure responses to exercise in healthy humans. Kohli U et al. 2011 Pharmacogenetics and genomics
21687501 Pharmacogenetics of antidepressants. Crisafulli C et al. 2011 Frontiers in pharmacology
23185385 Comprehensive phenotype/genotype analyses of the norepinephrine transporter gene (SLC6A2) in ADHD: relation to maternal smoking during pregnancy. Thakur GA et al. 2012 PloS one
23442739 Psychomotor depressive symptoms may differentially respond to venlafaxine. Singh AB et al. 2013 International clinical psychopharmacology
23648227 Association between major depressive disorder and the norepinephrine transporter polymorphisms T-182C and G1287A: a meta-analysis. Zhao X et al. 2013 Journal of affective disorders
24655776 Association between norepinephrine transporter gene (SLC6A2) polymorphisms and suicide in patients with major depressive disorder. Kim YK et al. 2014 Journal of affective disorders
24881125 From pharmacogenetics to pharmacogenomics: the way toward the personalization of antidepressant treatment. Fabbri C et al. 2014 Canadian journal of psychiatry. Revue canadienne de psychiatrie
25912538 Effects of persisting emotional impact from child abuse and norepinephrine transporter genetic variation on antidepressant efficacy in major depression: a pilot study. Singh AB et al. 2015 Clinical psychopharmacology and neuroscience
25990886 Impact of monoamine-related gene polymorphisms on hippocampal volume in treatment-resistant depression. Phillips JL et al. 2015 Acta neuropsychiatrica
26508020 Potential involvement of NET polymorphism in serotonin/norepinephrine reuptake inhibitor response in panic disorder. Park HJ et al. 2016 Nordic journal of psychiatry
26678348 Effects of norepinephrine transporter gene variants on NET binding in ADHD and healthy controls investigated by PET. Sigurdardottir HL et al. 2016 Human brain mapping
27147943 Neuroendorine and Epigentic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome. Lemche E et al. 2016 Frontiers in neuroscience
27541794 Investigating the genetic basis of attention to facial expressions: the role of the norepinephrine transporter gene. Yang X et al. 2016 Psychiatric genetics
28068779 Norepinephrine Transporter Gene Variants and Remission From Depression With Venlafaxine Treatment in Older Adults. Marshe VS et al. 2017 The American journal of psychiatry
28454051 No association between SLC6A2, SLC6A3, DRD2 polymorphisms and schizophrenia in the Han Chinese population. Bi Y et al. 2017 Psychiatry research
29198060 No major role of norepinephrine transporter gene variations in the cardiostimulant effects of MDMA. Vizeli P et al. 2018 European journal of clinical pharmacology
29374517 Association analysis of norepinephrine transporter polymorphisms and methylphenidate response in ADHD patients. Angyal N et al. 2018 Progress in neuro-psychopharmacology & biological psychiatry

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: 0.1.4.post833+d3ba21e