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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.

rs4537731

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr11:18047335 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.47874 (60115/125568, TOPMED)
C=0.4677 (14449/30892, GnomAD)
C=0.439 (2197/5008, 1000G) (+ 2 more)
C=0.418 (1610/3854, ALSPAC)
C=0.424 (1574/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
9 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 11 NC_000011.10:g.18047335T>C
GRCh37.p13 chr 11 NC_000011.9:g.18068882T>C
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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
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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
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.52126 C=0.47874
The Genome Aggregation Database Global Study-wide 30892 T=0.5323 C=0.4677
The Genome Aggregation Database European Sub 18458 T=0.5942 C=0.4058
The Genome Aggregation Database African Sub 8700 T=0.337 C=0.663
The Genome Aggregation Database East Asian Sub 1618 T=0.748 C=0.252
The Genome Aggregation Database Other Sub 980 T=0.59 C=0.41
The Genome Aggregation Database American Sub 834 T=0.65 C=0.35
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.68 C=0.32
1000Genomes Global Study-wide 5008 T=0.561 C=0.439
1000Genomes African Sub 1322 T=0.300 C=0.700
1000Genomes East Asian Sub 1008 T=0.773 C=0.227
1000Genomes Europe Sub 1006 T=0.572 C=0.428
1000Genomes South Asian Sub 978 T=0.63 C=0.37
1000Genomes American Sub 694 T=0.64 C=0.36
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.582 C=0.418
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.576 C=0.424
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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 Note
GRCh38.p7 chr 11 NC_000011.10:g.18047335T= NC_000011.10:g.18047335T>C
GRCh37.p13 chr 11 NC_000011.9:g.18068882T= NC_000011.9:g.18068882T>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#.

5 Frequency, 52 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6124788 Feb 20, 2003 (111)
2 SUNLAB ss8487100 Aug 26, 2003 (117)
3 SC_SNP ss15794326 Feb 27, 2004 (120)
4 HGBASE ss16383790 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss19195930 Feb 27, 2004 (120)
6 SSAHASNP ss20817596 Apr 05, 2004 (121)
7 ABI ss39958460 Mar 15, 2006 (126)
8 HGSV ss82074324 Dec 14, 2007 (130)
9 BCMHGSC_JDW ss88484697 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97455437 Feb 03, 2009 (130)
11 1000GENOMES ss110095314 Jan 24, 2009 (130)
12 1000GENOMES ss114272604 Jan 25, 2009 (130)
13 ILLUMINA-UK ss119706064 Dec 01, 2009 (131)
14 ENSEMBL ss132328670 Dec 01, 2009 (131)
15 ENSEMBL ss137791674 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss167927946 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss169219470 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss170574238 Jul 04, 2010 (132)
19 BUSHMAN ss202445746 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss207530765 Jul 04, 2010 (132)
21 1000GENOMES ss225117823 Jul 14, 2010 (132)
22 1000GENOMES ss235465994 Jul 15, 2010 (132)
23 1000GENOMES ss242115616 Jul 15, 2010 (132)
24 BL ss254931527 May 09, 2011 (134)
25 GMI ss280903487 May 04, 2012 (137)
26 PJP ss291189330 May 09, 2011 (134)
27 TISHKOFF ss562416831 Apr 25, 2013 (138)
28 SSMP ss657839210 Apr 25, 2013 (138)
29 EVA-GONL ss988260755 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1077539803 Aug 21, 2014 (142)
31 1000GENOMES ss1340314664 Aug 21, 2014 (142)
32 DDI ss1426552699 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1575555823 Apr 01, 2015 (144)
34 EVA_DECODE ss1597939005 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1626096636 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1669090669 Apr 01, 2015 (144)
37 HAMMER_LAB ss1806715082 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1931621668 Feb 12, 2016 (147)
39 GENOMED ss1967305063 Jul 19, 2016 (147)
40 JJLAB ss2026555090 Sep 14, 2016 (149)
41 USC_VALOUEV ss2154843211 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2180596559 Dec 20, 2016 (150)
43 TOPMED ss2343760459 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2627747470 Nov 08, 2017 (151)
45 GRF ss2699116551 Nov 08, 2017 (151)
46 GNOMAD ss2896887847 Nov 08, 2017 (151)
47 AFFY ss2984936134 Nov 08, 2017 (151)
48 AFFY ss2985581506 Nov 08, 2017 (151)
49 SWEGEN ss3007677486 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3027073771 Nov 08, 2017 (151)
51 TOPMED ss3138347856 Nov 08, 2017 (151)
52 CSHL ss3349477025 Nov 08, 2017 (151)
53 1000Genomes NC_000011.9 - 18068882 Jul 20, 2018 (151)
54 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 18068882 Jul 20, 2018 (151)
55 The Genome Aggregation Database NC_000011.9 - 18068882 Jul 20, 2018 (151)
56 Trans-Omics for Precision Medicine NC_000011.10 - 18047335 Jul 20, 2018 (151)
57 UK 10K study - Twins NC_000011.9 - 18068882 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)
rs56817437 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss82074324, ss88484697, ss110095314, ss114272604, ss119706064, ss167927946, ss169219470, ss170574238, ss202445746, ss207530765, ss254931527, ss280903487, ss291189330, ss1597939005 NC_000011.8:18025457:T= NC_000011.10:18047334:T= (self)
52804324, 29333353, 30589369, 29333353, ss225117823, ss235465994, ss242115616, ss562416831, ss657839210, ss988260755, ss1077539803, ss1340314664, ss1426552699, ss1575555823, ss1626096636, ss1669090669, ss1806715082, ss1931621668, ss1967305063, ss2026555090, ss2154843211, ss2343760459, ss2627747470, ss2699116551, ss2896887847, ss2984936134, ss2985581506, ss3007677486, ss3349477025 NC_000011.9:18068881:T= NC_000011.10:18047334:T= (self)
58059163, ss2180596559, ss3027073771, ss3138347856 NC_000011.10:18047334:T= NC_000011.10:18047334:T= (self)
ss15794326, ss19195930, ss20817596 NT_009237.16:16832821:T= NC_000011.10:18047334:T= (self)
ss6124788, ss8487100, ss16383790, ss39958460, ss97455437, ss132328670, ss137791674 NT_009237.18:18008881:T= NC_000011.10:18047334:T= (self)
ss82074324, ss88484697, ss110095314, ss114272604, ss119706064, ss167927946, ss169219470, ss170574238, ss202445746, ss207530765, ss254931527, ss280903487, ss291189330, ss1597939005 NC_000011.8:18025457:T>C NC_000011.10:18047334:T>C (self)
52804324, 29333353, 30589369, 29333353, ss225117823, ss235465994, ss242115616, ss562416831, ss657839210, ss988260755, ss1077539803, ss1340314664, ss1426552699, ss1575555823, ss1626096636, ss1669090669, ss1806715082, ss1931621668, ss1967305063, ss2026555090, ss2154843211, ss2343760459, ss2627747470, ss2699116551, ss2896887847, ss2984936134, ss2985581506, ss3007677486, ss3349477025 NC_000011.9:18068881:T>C NC_000011.10:18047334:T>C (self)
58059163, ss2180596559, ss3027073771, ss3138347856 NC_000011.10:18047334:T>C NC_000011.10:18047334:T>C (self)
ss15794326, ss19195930, ss20817596 NT_009237.16:16832821:T>C NC_000011.10:18047334:T>C (self)
ss6124788, ss8487100, ss16383790, ss39958460, ss97455437, ss132328670, ss137791674 NT_009237.18:18008881:T>C NC_000011.10:18047334:T>C (self)
Help

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

9 citations for rs4537731
PMID Title Author Year Journal
17203304 Evidence for epistasis between SLC6A4 and ITGB3 in autism etiology and in the determination of platelet serotonin levels. Coutinho AM et al. 2007 Human genetics
20580984 Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers. Andreou D et al. 2010 Psychiatry research
21073637 Associations of tryptophan hydroxylase gene polymorphisms with irritable bowel syndrome. Jun S et al. 2011 Neurogastroenterology and motility
21989108 Interaction between tryptophan hydroxylase I polymorphisms and childhood abuse is associated with increased risk for borderline personality disorder in adulthood. Wilson ST et al. 2012 Psychiatric genetics
23172723 TPH gene polymorphisms are associated with disease perception and quality of life in women with irritable bowel syndrome. Jun SE et al. 2014 Biological research for nursing
25073638 Polymorphisms in genes implicated in dopamine, serotonin and noradrenalin metabolism suggest association with cerebrospinal fluid monoamine metabolite concentrations in psychosis. Andreou D et al. 2014 Behavioral and brain functions
25428414 Pilot study of Biomarkers for predicting effectiveness of ramosetron in diarrhea-predominant irritable bowel syndrome: expression of S100A10 and polymorphisms of TPH1. Shiotani A et al. 2015 Neurogastroenterology and motility
25548468 Genetic polymorphism in pathogenesis of irritable bowel syndrome. Cheung CK et al. 2014 World journal of gastroenterology
26710093 Tryptophan hydroxylase 1 gene polymorphisms alter prefrontal cortex activation during response inhibition. Ruocco AC et al. 2016 Neuropsychology

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