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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.

rs9316233

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:46859220 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.262783 (69556/264690, TOPMED)
G=0.33411 (26294/78698, PAGE_STUDY)
G=0.09368 (1296/13834, ALFA) (+ 15 more)
G=0.2977 (1491/5008, 1000G)
G=0.1719 (770/4480, Estonian)
G=0.1829 (705/3854, ALSPAC)
G=0.1912 (709/3708, TWINSUK)
G=0.3099 (908/2930, KOREAN)
G=0.3433 (629/1832, Korea1K)
G=0.194 (194/998, GoNL)
G=0.290 (229/790, PRJEB37584)
G=0.117 (70/600, NorthernSweden)
G=0.322 (103/320, HapMap)
C=0.375 (111/296, SGDP_PRJ)
G=0.245 (53/216, Qatari)
G=0.151 (32/212, Vietnamese)
G=0.35 (14/40, GENOME_DK)
C=0.36 (13/36, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HTR2A : Intron Variant
Publications
8 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.p13 chr 13 NC_000013.11:g.46859220C>A
GRCh38.p13 chr 13 NC_000013.11:g.46859220C>G
GRCh38.p13 chr 13 NC_000013.11:g.46859220C>T
GRCh37.p13 chr 13 NC_000013.10:g.47433355C>A
GRCh37.p13 chr 13 NC_000013.10:g.47433355C>G
GRCh37.p13 chr 13 NC_000013.10:g.47433355C>T
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.42815G>T
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.42815G>C
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.42815G>A
Gene: HTR2A, 5-hydroxytryptamine receptor 2A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HTR2A transcript variant 1 NM_000621.5:c.614-23581G>T N/A Intron Variant
HTR2A transcript variant 2 NM_001165947.5:c.125-2358…

NM_001165947.5:c.125-23581G>T

N/A Intron Variant
HTR2A transcript variant 3 NM_001378924.1:c.614-2358…

NM_001378924.1:c.614-23581G>T

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

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 13834 C=0.90632 G=0.09368, T=0.00000
European Sub 11598 C=0.89757 G=0.10243, T=0.00000
African Sub 1338 C=0.9679 G=0.0321, T=0.0000
African Others Sub 46 C=0.98 G=0.02, T=0.00
African American Sub 1292 C=0.9675 G=0.0325, T=0.0000
Asian Sub 52 C=0.98 G=0.02, T=0.00
East Asian Sub 36 C=1.00 G=0.00, T=0.00
Other Asian Sub 16 C=0.94 G=0.06, T=0.00
Latin American 1 Sub 60 C=1.00 G=0.00, T=0.00
Latin American 2 Sub 254 C=1.000 G=0.000, T=0.000
South Asian Sub 44 C=0.98 G=0.02, T=0.00
Other Sub 488 C=0.871 G=0.129, T=0.000


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 C=0.737217 G=0.262783
The PAGE Study Global Study-wide 78698 C=0.66589 G=0.33411
The PAGE Study AfricanAmerican Sub 32516 C=0.65906 G=0.34094
The PAGE Study Mexican Sub 10808 C=0.64184 G=0.35816
The PAGE Study Asian Sub 8318 C=0.6451 G=0.3549
The PAGE Study PuertoRican Sub 7918 C=0.7179 G=0.2821
The PAGE Study NativeHawaiian Sub 4534 C=0.5953 G=0.4047
The PAGE Study Cuban Sub 4228 C=0.7713 G=0.2287
The PAGE Study Dominican Sub 3828 C=0.6915 G=0.3085
The PAGE Study CentralAmerican Sub 2450 C=0.6588 G=0.3412
The PAGE Study SouthAmerican Sub 1982 C=0.6604 G=0.3396
The PAGE Study NativeAmerican Sub 1260 C=0.7325 G=0.2675
The PAGE Study SouthAsian Sub 856 C=0.624 G=0.376
1000Genomes Global Study-wide 5008 C=0.7023 G=0.2977
1000Genomes African Sub 1322 C=0.6369 G=0.3631
1000Genomes East Asian Sub 1008 C=0.7679 G=0.2321
1000Genomes Europe Sub 1006 C=0.8082 G=0.1918
1000Genomes South Asian Sub 978 C=0.633 G=0.367
1000Genomes American Sub 694 C=0.676 G=0.324
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8281 G=0.1719
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8171 G=0.1829
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8088 G=0.1912
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6901 A=0.0000, G=0.3099
Korean Genome Project KOREAN Study-wide 1832 C=0.6567 G=0.3433
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.806 G=0.194
CNV burdens in cranial meningiomas Global Study-wide 790 C=0.710 G=0.290
CNV burdens in cranial meningiomas CRM Sub 790 C=0.710 G=0.290
Northern Sweden ACPOP Study-wide 600 C=0.883 G=0.117
HapMap Global Study-wide 320 C=0.678 G=0.322
HapMap African Sub 116 C=0.578 G=0.422
HapMap American Sub 116 C=0.793 G=0.207
HapMap Asian Sub 88 C=0.66 G=0.34
SGDP_PRJ Global Study-wide 296 C=0.375 G=0.625
Qatari Global Study-wide 216 C=0.755 G=0.245
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.849 G=0.151
The Danish reference pan genome Danish Study-wide 40 C=0.65 G=0.35
Siberian Global Study-wide 36 C=0.36 G=0.64
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 G T
GRCh38.p13 chr 13 NC_000013.11:g.46859220= NC_000013.11:g.46859220C>A NC_000013.11:g.46859220C>G NC_000013.11:g.46859220C>T
GRCh37.p13 chr 13 NC_000013.10:g.47433355= NC_000013.10:g.47433355C>A NC_000013.10:g.47433355C>G NC_000013.10:g.47433355C>T
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.42815= NG_013011.1:g.42815G>T NG_013011.1:g.42815G>C NG_013011.1:g.42815G>A
HTR2A transcript variant 1 NM_000621.4:c.614-23581= NM_000621.4:c.614-23581G>T NM_000621.4:c.614-23581G>C NM_000621.4:c.614-23581G>A
HTR2A transcript variant 1 NM_000621.5:c.614-23581= NM_000621.5:c.614-23581G>T NM_000621.5:c.614-23581G>C NM_000621.5:c.614-23581G>A
HTR2A transcript variant 2 NM_001165947.2:c.362-23581= NM_001165947.2:c.362-23581G>T NM_001165947.2:c.362-23581G>C NM_001165947.2:c.362-23581G>A
HTR2A transcript variant 2 NM_001165947.5:c.125-23581= NM_001165947.5:c.125-23581G>T NM_001165947.5:c.125-23581G>C NM_001165947.5:c.125-23581G>A
HTR2A transcript variant 3 NM_001378924.1:c.614-23581= NM_001378924.1:c.614-23581G>T NM_001378924.1:c.614-23581G>C NM_001378924.1:c.614-23581G>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#.

75 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13218674 Dec 05, 2003 (119)
2 SC_SNP ss14804421 Dec 05, 2003 (119)
3 PERLEGEN ss23991028 Sep 20, 2004 (123)
4 PERLEGEN ss69133968 May 16, 2007 (127)
5 KRIBB_YJKIM ss80739769 Dec 14, 2007 (130)
6 HGSV ss83960777 Dec 14, 2007 (130)
7 1000GENOMES ss114664424 Jan 25, 2009 (130)
8 ILLUMINA-UK ss118692356 Feb 14, 2009 (130)
9 GMI ss154766385 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss169493297 Jul 04, 2010 (132)
11 BUSHMAN ss199175888 Jul 04, 2010 (132)
12 1000GENOMES ss226173573 Jul 14, 2010 (132)
13 1000GENOMES ss236243440 Jul 15, 2010 (132)
14 1000GENOMES ss242741898 Jul 15, 2010 (132)
15 GMI ss281705386 May 04, 2012 (137)
16 GMI ss286700054 Apr 25, 2013 (138)
17 PJP ss291436627 May 09, 2011 (134)
18 ILLUMINA ss483197919 May 04, 2012 (137)
19 ILLUMINA ss483568644 May 04, 2012 (137)
20 ILLUMINA ss535774817 Sep 08, 2015 (146)
21 TISHKOFF ss563654595 Apr 25, 2013 (138)
22 SSMP ss659257549 Apr 25, 2013 (138)
23 ILLUMINA ss780326552 Aug 21, 2014 (142)
24 ILLUMINA ss782227780 Aug 21, 2014 (142)
25 ILLUMINA ss835813801 Aug 21, 2014 (142)
26 EVA-GONL ss990366473 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1079067752 Aug 21, 2014 (142)
28 1000GENOMES ss1348130524 Aug 21, 2014 (142)
29 DDI ss1427181327 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1576773506 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1630232686 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1673226719 Apr 01, 2015 (144)
33 EVA_DECODE ss1684889333 Apr 01, 2015 (144)
34 HAMMER_LAB ss1807600590 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1933734962 Feb 12, 2016 (147)
36 ILLUMINA ss1959500125 Feb 12, 2016 (147)
37 GENOMED ss1967777451 Jul 19, 2016 (147)
38 JJLAB ss2027626764 Sep 14, 2016 (149)
39 USC_VALOUEV ss2155992657 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2196137967 Dec 20, 2016 (150)
41 TOPMED ss2360266651 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2628303675 Nov 08, 2017 (151)
43 ILLUMINA ss2633061764 Nov 08, 2017 (151)
44 ILLUMINA ss2635045251 Nov 08, 2017 (151)
45 GRF ss2700371896 Nov 08, 2017 (151)
46 GNOMAD ss2919382100 Nov 08, 2017 (151)
47 AFFY ss2985003429 Nov 08, 2017 (151)
48 AFFY ss2985638949 Nov 08, 2017 (151)
49 SWEGEN ss3010981767 Nov 08, 2017 (151)
50 ILLUMINA ss3021506789 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3027630612 Nov 08, 2017 (151)
52 TOPMED ss3192074284 Nov 08, 2017 (151)
53 TOPMED ss3192074285 Nov 08, 2017 (151)
54 CSHL ss3350444479 Nov 08, 2017 (151)
55 ILLUMINA ss3627061089 Oct 12, 2018 (152)
56 ILLUMINA ss3631065213 Oct 12, 2018 (152)
57 ILLUMINA ss3641837583 Oct 12, 2018 (152)
58 ILLUMINA ss3651894344 Oct 12, 2018 (152)
59 ILLUMINA ss3653774259 Oct 12, 2018 (152)
60 EGCUT_WGS ss3678245442 Jul 13, 2019 (153)
61 EVA_DECODE ss3695244005 Jul 13, 2019 (153)
62 ILLUMINA ss3725392848 Jul 13, 2019 (153)
63 ACPOP ss3739726289 Jul 13, 2019 (153)
64 EVA ss3751436090 Jul 13, 2019 (153)
65 PAGE_CC ss3771745464 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3816765918 Jul 13, 2019 (153)
67 EVA ss3833534542 Apr 27, 2020 (154)
68 SGDP_PRJ ss3879927812 Apr 27, 2020 (154)
69 KRGDB ss3928776854 Apr 27, 2020 (154)
70 KOGIC ss3973518639 Apr 27, 2020 (154)
71 EVA ss3984680092 Apr 26, 2021 (155)
72 TOPMED ss4945460033 Apr 26, 2021 (155)
73 TOMMO_GENOMICS ss5209890985 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5209890986 Apr 26, 2021 (155)
75 EVA ss5237526335 Apr 26, 2021 (155)
76 1000Genomes NC_000013.10 - 47433355 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 47433355 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000013.10 - 47433355 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000013.10 - 47433355 Apr 27, 2020 (154)
80 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 430047430 (NC_000013.11:46859219:C:G 34652/139894)
Row 430047431 (NC_000013.11:46859219:C:T 1/139960)

- Apr 26, 2021 (155)
81 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 430047430 (NC_000013.11:46859219:C:G 34652/139894)
Row 430047431 (NC_000013.11:46859219:C:T 1/139960)

- Apr 26, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000013.10 - 47433355 Apr 27, 2020 (154)
83 HapMap NC_000013.11 - 46859220 Apr 27, 2020 (154)
84 KOREAN population from KRGDB NC_000013.10 - 47433355 Apr 27, 2020 (154)
85 Korean Genome Project NC_000013.11 - 46859220 Apr 27, 2020 (154)
86 Northern Sweden NC_000013.10 - 47433355 Jul 13, 2019 (153)
87 The PAGE Study NC_000013.11 - 46859220 Jul 13, 2019 (153)
88 CNV burdens in cranial meningiomas NC_000013.10 - 47433355 Apr 26, 2021 (155)
89 Qatari NC_000013.10 - 47433355 Apr 27, 2020 (154)
90 SGDP_PRJ NC_000013.10 - 47433355 Apr 27, 2020 (154)
91 Siberian NC_000013.10 - 47433355 Apr 27, 2020 (154)
92 8.3KJPN

Submission ignored due to conflicting rows:
Row 67860292 (NC_000013.10:47433354:C:G 6314/16760)
Row 67860293 (NC_000013.10:47433354:C:A 1/16760)

- Apr 26, 2021 (155)
93 8.3KJPN

Submission ignored due to conflicting rows:
Row 67860292 (NC_000013.10:47433354:C:G 6314/16760)
Row 67860293 (NC_000013.10:47433354:C:A 1/16760)

- Apr 26, 2021 (155)
94 TopMed NC_000013.11 - 46859220 Apr 26, 2021 (155)
95 UK 10K study - Twins NC_000013.10 - 47433355 Oct 12, 2018 (152)
96 A Vietnamese Genetic Variation Database NC_000013.10 - 47433355 Jul 13, 2019 (153)
97 ALFA NC_000013.11 - 46859220 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)
rs57868858 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
35954248, ss3928776854, ss5209890986 NC_000013.10:47433354:C:A NC_000013.11:46859219:C:A (self)
ss83960777, ss114664424, ss118692356, ss169493297, ss199175888, ss281705386, ss286700054, ss291436627, ss483197919, ss1684889333, ss2635045251 NC_000013.9:46331355:C:G NC_000013.11:46859219:C:G (self)
60998325, 33887303, 23983690, 3289556, 15119610, 35954248, 13011154, 229597, 15776892, 31944792, 8509011, 33887303, 7518949, ss226173573, ss236243440, ss242741898, ss483568644, ss535774817, ss563654595, ss659257549, ss780326552, ss782227780, ss835813801, ss990366473, ss1079067752, ss1348130524, ss1427181327, ss1576773506, ss1630232686, ss1673226719, ss1807600590, ss1933734962, ss1959500125, ss1967777451, ss2027626764, ss2155992657, ss2360266651, ss2628303675, ss2633061764, ss2700371896, ss2919382100, ss2985003429, ss2985638949, ss3010981767, ss3021506789, ss3350444479, ss3627061089, ss3631065213, ss3641837583, ss3651894344, ss3653774259, ss3678245442, ss3739726289, ss3751436090, ss3833534542, ss3879927812, ss3928776854, ss3984680092, ss5209890985, ss5237526335 NC_000013.10:47433354:C:G NC_000013.11:46859219:C:G (self)
986057, 29896640, 966933, 100697707, 161005691, 6430961184, ss2196137967, ss3027630612, ss3192074284, ss3695244005, ss3725392848, ss3771745464, ss3816765918, ss3973518639, ss4945460033 NC_000013.11:46859219:C:G NC_000013.11:46859219:C:G (self)
ss13218674 NT_024524.12:16007846:C:G NC_000013.11:46859219:C:G (self)
ss14804421, ss23991028, ss69133968, ss80739769, ss154766385 NT_024524.14:28413354:C:G NC_000013.11:46859219:C:G (self)
6430961184, ss2196137967, ss3192074285 NC_000013.11:46859219:C:T NC_000013.11:46859219: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.

8 citations for rs9316233
PMID Title Author Year Journal
19365399 Genetic predictors of response to antidepressants in the GENDEP project. Uher R et al. 2009 The pharmacogenomics journal
20848240 Overview of the genetics of major depressive disorder. Lohoff FW et al. 2010 Current psychiatry reports
21172166 Pharmacogenetics of antidepressant response. Porcelli S et al. 2011 Journal of psychiatry & neuroscience
22074755 Potential genetic risk factors for chronic TMD: genetic associations from the OPPERA case control study. Smith SB et al. 2011 The journal of pain
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
24944790 Screening for 392 polymorphisms in 141 pharmacogenes. Kim JY et al. 2014 Biomedical reports
27521242 TPH-2 Polymorphisms Interact with Early Life Stress to Influence Response to Treatment with Antidepressant Drugs. Xu Z et al. 2016 The international journal of neuropsychopharmacology
30093869 Biological Predictors of Clozapine Response: A Systematic Review. Samanaite R et al. 2018 Frontiers in psychiatry
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.post596+ae089ad