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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.

rs7330461

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:46849430 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.401164 (106184/264690, TOPMED)
T=0.09588 (1607/16760, 8.3KJPN)
T=0.14257 (1428/10016, ALFA) (+ 13 more)
T=0.3145 (1575/5008, 1000G)
T=0.2853 (1278/4480, Estonian)
T=0.3638 (1402/3854, ALSPAC)
T=0.3665 (1359/3708, TWINSUK)
T=0.0654 (191/2922, KOREAN)
T=0.369 (368/998, GoNL)
T=0.293 (176/600, NorthernSweden)
T=0.363 (119/328, HapMap)
A=0.362 (81/224, SGDP_PRJ)
T=0.412 (89/216, Qatari)
T=0.084 (18/214, Vietnamese)
T=0.33 (13/40, GENOME_DK)
A=0.39 (7/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HTR2A : Intron Variant
Publications
1 citation
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.46849430A>C
GRCh38.p13 chr 13 NC_000013.11:g.46849430A>G
GRCh38.p13 chr 13 NC_000013.11:g.46849430A>T
GRCh37.p13 chr 13 NC_000013.10:g.47423565A>C
GRCh37.p13 chr 13 NC_000013.10:g.47423565A>G
GRCh37.p13 chr 13 NC_000013.10:g.47423565A>T
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.52605T>G
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.52605T>C
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.52605T>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.614-13791T>G N/A Intron Variant
HTR2A transcript variant 2 NM_001165947.5:c.125-1379…

NM_001165947.5:c.125-13791T>G

N/A Intron Variant
HTR2A transcript variant 3 NM_001378924.1:c.614-1379…

NM_001378924.1:c.614-13791T>G

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 10016 A=0.85743 C=0.00000, G=0.00000, T=0.14257
European Sub 8420 A=0.8417 C=0.0000, G=0.0000, T=0.1583
African Sub 636 A=0.962 C=0.000, G=0.000, T=0.038
African Others Sub 22 A=1.00 C=0.00, G=0.00, T=0.00
African American Sub 614 A=0.961 C=0.000, G=0.000, T=0.039
Asian Sub 90 A=1.00 C=0.00, G=0.00, T=0.00
East Asian Sub 66 A=1.00 C=0.00, G=0.00, T=0.00
Other Asian Sub 24 A=1.00 C=0.00, G=0.00, T=0.00
Latin American 1 Sub 46 A=1.00 C=0.00, G=0.00, T=0.00
Latin American 2 Sub 386 A=1.000 C=0.000, G=0.000, T=0.000
South Asian Sub 58 A=1.00 C=0.00, G=0.00, T=0.00
Other Sub 380 A=0.813 C=0.000, G=0.000, T=0.187


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 A=0.598836 T=0.401164
8.3KJPN JAPANESE Study-wide 16760 A=0.90412 T=0.09588
Allele Frequency Aggregator Total Global 10016 A=0.85743 C=0.00000, G=0.00000, T=0.14257
Allele Frequency Aggregator European Sub 8420 A=0.8417 C=0.0000, G=0.0000, T=0.1583
Allele Frequency Aggregator African Sub 636 A=0.962 C=0.000, G=0.000, T=0.038
Allele Frequency Aggregator Latin American 2 Sub 386 A=1.000 C=0.000, G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 380 A=0.813 C=0.000, G=0.000, T=0.187
Allele Frequency Aggregator Asian Sub 90 A=1.00 C=0.00, G=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 58 A=1.00 C=0.00, G=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 46 A=1.00 C=0.00, G=0.00, T=0.00
1000Genomes Global Study-wide 5008 A=0.6855 T=0.3145
1000Genomes African Sub 1322 A=0.4092 T=0.5908
1000Genomes East Asian Sub 1008 A=0.9236 T=0.0764
1000Genomes Europe Sub 1006 A=0.6302 T=0.3698
1000Genomes South Asian Sub 978 A=0.848 T=0.152
1000Genomes American Sub 694 A=0.718 T=0.282
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7147 T=0.2853
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6362 T=0.3638
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6335 T=0.3665
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9346 T=0.0654
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.631 T=0.369
Northern Sweden ACPOP Study-wide 600 A=0.707 T=0.293
HapMap Global Study-wide 328 A=0.637 T=0.363
HapMap American Sub 120 A=0.667 T=0.333
HapMap African Sub 118 A=0.432 T=0.568
HapMap Asian Sub 90 A=0.87 T=0.13
SGDP_PRJ Global Study-wide 224 A=0.362 T=0.638
Qatari Global Study-wide 216 A=0.588 T=0.412
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.916 T=0.084
The Danish reference pan genome Danish Study-wide 40 A=0.68 T=0.33
Siberian Global Study-wide 18 A=0.39 T=0.61
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 A= C G T
GRCh38.p13 chr 13 NC_000013.11:g.46849430= NC_000013.11:g.46849430A>C NC_000013.11:g.46849430A>G NC_000013.11:g.46849430A>T
GRCh37.p13 chr 13 NC_000013.10:g.47423565= NC_000013.10:g.47423565A>C NC_000013.10:g.47423565A>G NC_000013.10:g.47423565A>T
HTR2A RefSeqGene (LRG_1008) NG_013011.1:g.52605= NG_013011.1:g.52605T>G NG_013011.1:g.52605T>C NG_013011.1:g.52605T>A
HTR2A transcript variant 1 NM_000621.4:c.614-13791= NM_000621.4:c.614-13791T>G NM_000621.4:c.614-13791T>C NM_000621.4:c.614-13791T>A
HTR2A transcript variant 1 NM_000621.5:c.614-13791= NM_000621.5:c.614-13791T>G NM_000621.5:c.614-13791T>C NM_000621.5:c.614-13791T>A
HTR2A transcript variant 2 NM_001165947.2:c.362-13791= NM_001165947.2:c.362-13791T>G NM_001165947.2:c.362-13791T>C NM_001165947.2:c.362-13791T>A
HTR2A transcript variant 2 NM_001165947.5:c.125-13791= NM_001165947.5:c.125-13791T>G NM_001165947.5:c.125-13791T>C NM_001165947.5:c.125-13791T>A
HTR2A transcript variant 3 NM_001378924.1:c.614-13791= NM_001378924.1:c.614-13791T>G NM_001378924.1:c.614-13791T>C NM_001378924.1:c.614-13791T>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#.

58 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss11082474 Jul 11, 2003 (116)
2 SC_SNP ss13199978 Dec 05, 2003 (119)
3 ABI ss40369000 Mar 14, 2006 (126)
4 HGSV ss78931386 Dec 06, 2007 (129)
5 BCMHGSC_JDW ss89649251 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss97156212 Feb 04, 2009 (130)
7 1000GENOMES ss112759306 Jan 25, 2009 (130)
8 ILLUMINA-UK ss118689791 Feb 14, 2009 (130)
9 ENSEMBL ss133577875 Dec 01, 2009 (131)
10 ENSEMBL ss142771918 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss168059629 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss171131201 Jul 04, 2010 (132)
13 BUSHMAN ss199175746 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss208712584 Jul 04, 2010 (132)
15 1000GENOMES ss211400877 Jul 14, 2010 (132)
16 1000GENOMES ss226173507 Jul 14, 2010 (132)
17 1000GENOMES ss236243394 Jul 15, 2010 (132)
18 1000GENOMES ss242741859 Jul 15, 2010 (132)
19 BL ss254990856 May 09, 2011 (134)
20 GMI ss286700026 Apr 25, 2013 (138)
21 PJP ss291436592 May 09, 2011 (134)
22 TISHKOFF ss563654536 Apr 25, 2013 (138)
23 SSMP ss659257486 Apr 25, 2013 (138)
24 EVA-GONL ss990366374 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1079067674 Aug 21, 2014 (142)
26 1000GENOMES ss1348130188 Aug 21, 2014 (142)
27 DDI ss1427181284 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1576773456 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1630232490 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1673226523 Apr 01, 2015 (144)
31 HAMMER_LAB ss1807600538 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1933734871 Feb 12, 2016 (147)
33 JJLAB ss2027626706 Sep 14, 2016 (149)
34 USC_VALOUEV ss2155992606 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2196137326 Dec 20, 2016 (150)
36 TOPMED ss2360266041 Dec 20, 2016 (150)
37 TOPMED ss2360266042 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2628303641 Nov 08, 2017 (151)
39 GRF ss2700371845 Nov 08, 2017 (151)
40 GNOMAD ss2919381319 Nov 08, 2017 (151)
41 AFFY ss2985638914 Nov 08, 2017 (151)
42 SWEGEN ss3010981650 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3027630574 Nov 08, 2017 (151)
44 TOPMED ss3192072552 Nov 08, 2017 (151)
45 TOPMED ss3192072553 Nov 08, 2017 (151)
46 TOPMED ss3192072554 Nov 08, 2017 (151)
47 CSHL ss3350444430 Nov 08, 2017 (151)
48 URBANLAB ss3650028287 Oct 12, 2018 (152)
49 EGCUT_WGS ss3678245302 Jul 13, 2019 (153)
50 EVA_DECODE ss3695243853 Jul 13, 2019 (153)
51 ACPOP ss3739726223 Jul 13, 2019 (153)
52 EVA ss3751435979 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3816765808 Jul 13, 2019 (153)
54 EVA ss3833534489 Apr 27, 2020 (154)
55 SGDP_PRJ ss3879927653 Apr 27, 2020 (154)
56 KRGDB ss3928776703 Apr 27, 2020 (154)
57 TOPMED ss4945457536 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5209890704 Apr 26, 2021 (155)
59 1000Genomes NC_000013.10 - 47423565 Oct 12, 2018 (152)
60 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 47423565 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000013.10 - 47423565 Oct 12, 2018 (152)
62 The Danish reference pan genome NC_000013.10 - 47423565 Apr 27, 2020 (154)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 430045518 (NC_000013.11:46849429:A:G 1/139928)
Row 430045519 (NC_000013.11:46849429:A:T 55798/139862)

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

Submission ignored due to conflicting rows:
Row 430045518 (NC_000013.11:46849429:A:G 1/139928)
Row 430045519 (NC_000013.11:46849429:A:T 55798/139862)

- Apr 26, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000013.10 - 47423565 Apr 27, 2020 (154)
66 HapMap NC_000013.11 - 46849430 Apr 27, 2020 (154)
67 KOREAN population from KRGDB NC_000013.10 - 47423565 Apr 27, 2020 (154)
68 Northern Sweden NC_000013.10 - 47423565 Jul 13, 2019 (153)
69 Qatari NC_000013.10 - 47423565 Apr 27, 2020 (154)
70 SGDP_PRJ NC_000013.10 - 47423565 Apr 27, 2020 (154)
71 Siberian NC_000013.10 - 47423565 Apr 27, 2020 (154)
72 8.3KJPN NC_000013.10 - 47423565 Apr 26, 2021 (155)
73 TopMed NC_000013.11 - 46849430 Apr 26, 2021 (155)
74 UK 10K study - Twins NC_000013.10 - 47423565 Oct 12, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000013.10 - 47423565 Jul 13, 2019 (153)
76 ALFA NC_000013.11 - 46849430 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1957988638, ss3192072552 NC_000013.11:46849429:A:C NC_000013.11:46849429:A:C (self)
ss2360266041 NC_000013.10:47423564:A:G NC_000013.11:46849429:A:G (self)
100696148, 1957988638, ss3192072553 NC_000013.11:46849429:A:G NC_000013.11:46849429:A:G (self)
ss78931386, ss89649251, ss112759306, ss118689791, ss168059629, ss171131201, ss199175746, ss208712584, ss211400877, ss254990856, ss286700026, ss291436592 NC_000013.9:46321565:A:T NC_000013.11:46849429:A:T (self)
60997976, 33887092, 23983550, 3289507, 15119511, 35954097, 13011088, 15776801, 31944633, 8508960, 67860011, 33887092, 7518898, ss226173507, ss236243394, ss242741859, ss563654536, ss659257486, ss990366374, ss1079067674, ss1348130188, ss1427181284, ss1576773456, ss1630232490, ss1673226523, ss1807600538, ss1933734871, ss2027626706, ss2155992606, ss2360266042, ss2628303641, ss2700371845, ss2919381319, ss2985638914, ss3010981650, ss3350444430, ss3678245302, ss3739726223, ss3751435979, ss3833534489, ss3879927653, ss3928776703, ss5209890704 NC_000013.10:47423564:A:T NC_000013.11:46849429:A:T (self)
986017, 100696148, 161003194, 1957988638, ss2196137326, ss3027630574, ss3192072554, ss3650028287, ss3695243853, ss3816765808, ss4945457536 NC_000013.11:46849429:A:T NC_000013.11:46849429:A:T (self)
ss11082474, ss13199978 NT_024524.12:15998056:A:T NC_000013.11:46849429:A:T (self)
ss40369000, ss97156212, ss133577875, ss142771918 NT_024524.14:28403564:A:T NC_000013.11:46849429:A:T (self)
Help

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

1 citation for rs7330461
PMID Title Author Year Journal
26861400 Serotonin 2A Receptor SNP rs7330461 Association with Treatment Response to Pomaglumetad Methionil in Patients with Schizophrenia. Nisenbaum LK et al. 2016 Journal of personalized medicine
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