Name: rs1406946
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.

rs1406946

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:86937873 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.338260 (89534/264690, TOPMED)
T=0.355334 (49778/140088, GnomAD)
T=0.42322 (15218/35958, ALFA) (+ 15 more)
T=0.17797 (5029/28258, 14KJPN)
T=0.17721 (2970/16760, 8.3KJPN)
T=0.2948 (1888/6404, 1000G_30x)
T=0.2991 (1498/5008, 1000G)
C=0.4683 (2098/4480, Estonian)
T=0.2724 (798/2930, KOREAN)
T=0.2167 (410/1892, HapMap)
T=0.2904 (532/1832, Korea1K)
T=0.481 (480/998, GoNL)
T=0.487 (292/600, NorthernSweden)
T=0.275 (147/534, MGP)
C=0.351 (92/262, SGDP_PRJ)
T=0.324 (70/216, Qatari)
C=0.38 (15/40, GENOME_DK)
C=0.45 (17/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HTR1E : Intron Variant
Publications: 1 citation
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	35958	C=0.57678	T=0.42322
European	Sub	28510	C=0.52946	T=0.47054
African	Sub	4312	C=0.8639	T=0.1361
African Others	Sub	158	C=0.930	T=0.070
African American	Sub	4154	C=0.8613	T=0.1387
Asian	Sub	136	C=0.699	T=0.301
East Asian	Sub	108	C=0.667	T=0.333
Other Asian	Sub	28	C=0.82	T=0.18
Latin American 1	Sub	180	C=0.683	T=0.317
Latin American 2	Sub	754	C=0.621	T=0.379
South Asian	Sub	114	C=0.518	T=0.482
Other	Sub	1952	C=0.6019	T=0.3981

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	C=0.661740	T=0.338260
gnomAD - Genomes	Global	Study-wide	140088	C=0.644666	T=0.355334
gnomAD - Genomes	European	Sub	75840	C=0.53070	T=0.46930
gnomAD - Genomes	African	Sub	42008	C=0.85934	T=0.14066
gnomAD - Genomes	American	Sub	13644	C=0.63185	T=0.36815
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.5557	T=0.4443
gnomAD - Genomes	East Asian	Sub	3124	C=0.6767	T=0.3233
gnomAD - Genomes	Other	Sub	2150	C=0.6428	T=0.3572
Allele Frequency Aggregator	Total	Global	35958	C=0.57678	T=0.42322
Allele Frequency Aggregator	European	Sub	28510	C=0.52946	T=0.47054
Allele Frequency Aggregator	African	Sub	4312	C=0.8639	T=0.1361
Allele Frequency Aggregator	Other	Sub	1952	C=0.6019	T=0.3981
Allele Frequency Aggregator	Latin American 2	Sub	754	C=0.621	T=0.379
Allele Frequency Aggregator	Latin American 1	Sub	180	C=0.683	T=0.317
Allele Frequency Aggregator	Asian	Sub	136	C=0.699	T=0.301
Allele Frequency Aggregator	South Asian	Sub	114	C=0.518	T=0.482
14KJPN	JAPANESE	Study-wide	28258	C=0.82203	T=0.17797
8.3KJPN	JAPANESE	Study-wide	16760	C=0.82279	T=0.17721
1000Genomes_30x	Global	Study-wide	6404	C=0.7052	T=0.2948
1000Genomes_30x	African	Sub	1786	C=0.9149	T=0.0851
1000Genomes_30x	Europe	Sub	1266	C=0.5758	T=0.4242
1000Genomes_30x	South Asian	Sub	1202	C=0.5874	T=0.4126
1000Genomes_30x	East Asian	Sub	1170	C=0.6880	T=0.3120
1000Genomes_30x	American	Sub	980	C=0.655	T=0.345
1000Genomes	Global	Study-wide	5008	C=0.7009	T=0.2991
1000Genomes	African	Sub	1322	C=0.9130	T=0.0870
1000Genomes	East Asian	Sub	1008	C=0.6954	T=0.3046
1000Genomes	Europe	Sub	1006	C=0.5706	T=0.4294
1000Genomes	South Asian	Sub	978	C=0.591	T=0.409
1000Genomes	American	Sub	694	C=0.648	T=0.352
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4683	T=0.5317
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7276	T=0.2724
HapMap	Global	Study-wide	1892	C=0.7833	T=0.2167
HapMap	American	Sub	770	C=0.658	T=0.342
HapMap	African	Sub	692	C=0.961	T=0.039
HapMap	Asian	Sub	254	C=0.795	T=0.205
HapMap	Europe	Sub	176	C=0.614	T=0.386
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7096	T=0.2904
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.519	T=0.481
Northern Sweden	ACPOP	Study-wide	600	C=0.513	T=0.487
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.725	T=0.275
SGDP_PRJ	Global	Study-wide	262	C=0.351	T=0.649
Qatari	Global	Study-wide	216	C=0.676	T=0.324
The Danish reference pan genome	Danish	Study-wide	40	C=0.38	T=0.62
Siberian	Global	Study-wide	38	C=0.45	T=0.55

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 6	NC_000006.12:g.86937873C>T
GRCh37.p13 chr 6	NC_000006.11:g.87647591C>T

Gene: HTR1E, 5-hydroxytryptamine receptor 1E (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HTR1E transcript	NM_000865.3:c.-186+50C>T	N/A	Intron Variant
HTR1E transcript variant X1	XM_011535789.3:c.-197=	N/A	5 Prime UTR 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	C=	T
GRCh38.p14 chr 6	NC_000006.12:g.86937873=	NC_000006.12:g.86937873C>T
GRCh37.p13 chr 6	NC_000006.11:g.87647591=	NC_000006.11:g.87647591C>T
HTR1E transcript variant X1	XM_011535789.3:c.-197=	XM_011535789.3:c.-197C>T
HTR1E transcript variant X1	XM_011535789.2:c.-197=	XM_011535789.2:c.-197C>T
HTR1E transcript variant X1	XM_011535789.1:c.-197=	XM_011535789.1:c.-197C>T
HTR1E transcript	NM_000865.2:c.-186+50=	NM_000865.2:c.-186+50C>T
HTR1E transcript	NM_000865.3:c.-186+50=	NM_000865.3:c.-186+50C>T

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, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2206588	Oct 23, 2000 (88)
2	YUSUKE	ss3220569	Sep 28, 2001 (100)
3	SC_JCM	ss6166977	Feb 20, 2003 (111)
4	CSHL-HAPMAP	ss20274973	Feb 27, 2004 (120)
5	SSAHASNP	ss22483987	Apr 05, 2004 (121)
6	ABI	ss44729379	Mar 15, 2006 (126)
7	ILLUMINA	ss75049903	Dec 07, 2007 (129)
8	BCMHGSC_JDW	ss93510986	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98517644	Feb 03, 2009 (130)
10	BGI	ss104334468	Dec 01, 2009 (131)
11	KRIBB_YJKIM	ss119391294	Dec 01, 2009 (131)
12	ENSEMBL	ss142763780	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162582722	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss166980417	Jul 04, 2010 (132)
15	ILLUMINA	ss172478284	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207524527	Jul 04, 2010 (132)
17	1000GENOMES	ss222522042	Jul 14, 2010 (132)
18	1000GENOMES	ss233572230	Jul 15, 2010 (132)
19	1000GENOMES	ss240608961	Jul 15, 2010 (132)
20	BL	ss254528813	May 09, 2011 (134)
21	GMI	ss278908870	May 04, 2012 (137)
22	GMI	ss285456080	Apr 25, 2013 (138)
23	PJP	ss293657123	May 09, 2011 (134)
24	ILLUMINA	ss483347804	May 04, 2012 (137)
25	ILLUMINA	ss485297846	May 04, 2012 (137)
26	ILLUMINA	ss535561544	Sep 08, 2015 (146)
27	SSMP	ss653336189	Apr 25, 2013 (138)
28	ILLUMINA	ss780243377	Sep 08, 2015 (146)
29	ILLUMINA	ss782117027	Sep 08, 2015 (146)
30	ILLUMINA	ss835728868	Sep 08, 2015 (146)
31	EVA-GONL	ss983198290	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1073807207	Aug 21, 2014 (142)
33	1000GENOMES	ss1321134327	Aug 21, 2014 (142)
34	DDI	ss1430810558	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1581779074	Apr 01, 2015 (144)
36	EVA_DECODE	ss1592749551	Apr 01, 2015 (144)
37	EVA_MGP	ss1711137232	Apr 01, 2015 (144)
38	EVA_SVP	ss1712879367	Apr 01, 2015 (144)
39	WEILL_CORNELL_DGM	ss1926456224	Feb 12, 2016 (147)
40	GENOMED	ss1970458534	Jul 19, 2016 (147)
41	JJLAB	ss2023871120	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2152063266	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2285947498	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2626430798	Nov 08, 2017 (151)
45	ILLUMINA	ss2634478284	Nov 08, 2017 (151)
46	GRF	ss2707681533	Nov 08, 2017 (151)
47	GNOMAD	ss2841828845	Nov 08, 2017 (151)
48	AFFY	ss2986005259	Nov 08, 2017 (151)
49	SWEGEN	ss2999491267	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3025729327	Nov 08, 2017 (151)
51	CSHL	ss3347097408	Nov 08, 2017 (151)
52	ILLUMINA	ss3629595342	Oct 12, 2018 (152)
53	ILLUMINA	ss3632393280	Oct 12, 2018 (152)
54	ILLUMINA	ss3638642283	Oct 12, 2018 (152)
55	ILLUMINA	ss3642501972	Oct 12, 2018 (152)
56	ILLUMINA	ss3643582482	Oct 12, 2018 (152)
57	URBANLAB	ss3648409624	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3667370877	Jul 13, 2019 (153)
59	EVA_DECODE	ss3717706956	Jul 13, 2019 (153)
60	ACPOP	ss3733730611	Jul 13, 2019 (153)
61	EVA	ss3765322501	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3808472900	Jul 13, 2019 (153)
63	EVA	ss3830054053	Apr 26, 2020 (154)
64	SGDP_PRJ	ss3865110445	Apr 26, 2020 (154)
65	KRGDB	ss3912001184	Apr 26, 2020 (154)
66	KOGIC	ss3959525899	Apr 26, 2020 (154)
67	EVA	ss4017286013	Apr 26, 2021 (155)
68	TOPMED	ss4711729625	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5178634631	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5269337815	Oct 14, 2022 (156)
71	EVA	ss5315171226	Oct 14, 2022 (156)
72	EVA	ss5367192140	Oct 14, 2022 (156)
73	HUGCELL_USP	ss5466878084	Oct 14, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5555737294	Oct 14, 2022 (156)
75	SANFORD_IMAGENETICS	ss5640915796	Oct 14, 2022 (156)
76	TOMMO_GENOMICS	ss5717139658	Oct 14, 2022 (156)
77	YY_MCH	ss5807704922	Oct 14, 2022 (156)
78	EVA	ss5842600770	Oct 14, 2022 (156)
79	EVA	ss5855460146	Oct 14, 2022 (156)
80	EVA	ss5884798671	Oct 14, 2022 (156)
81	EVA	ss5969418125	Oct 14, 2022 (156)
82	1000Genomes	NC_000006.11 - 87647591	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000006.12 - 86937873	Oct 14, 2022 (156)
84	Genetic variation in the Estonian population	NC_000006.11 - 87647591	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000006.11 - 87647591	Apr 26, 2020 (154)
86	gnomAD - Genomes	NC_000006.12 - 86937873	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000006.11 - 87647591	Apr 26, 2020 (154)
88	HapMap	NC_000006.12 - 86937873	Apr 26, 2020 (154)
89	KOREAN population from KRGDB	NC_000006.11 - 87647591	Apr 26, 2020 (154)
90	Korean Genome Project	NC_000006.12 - 86937873	Apr 26, 2020 (154)
91	Medical Genome Project healthy controls from Spanish population	NC_000006.11 - 87647591	Apr 26, 2020 (154)
92	Northern Sweden	NC_000006.11 - 87647591	Jul 13, 2019 (153)
93	Qatari	NC_000006.11 - 87647591	Apr 26, 2020 (154)
94	SGDP_PRJ	NC_000006.11 - 87647591	Apr 26, 2020 (154)
95	Siberian	NC_000006.11 - 87647591	Apr 26, 2020 (154)
96	8.3KJPN	NC_000006.11 - 87647591	Apr 26, 2021 (155)
97	14KJPN	NC_000006.12 - 86937873	Oct 14, 2022 (156)
98	TopMed	NC_000006.12 - 86937873	Apr 26, 2021 (155)
99	ALFA	NC_000006.12 - 86937873	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93510986, ss162582722, ss166980417, ss207524527, ss254528813, ss278908870, ss285456080, ss293657123, ss485297846, ss1592749551, ss1712879367, ss3643582482	NC_000006.10:87704309:C:T	NC_000006.12:86937872:C:T	(self)
32959266, 13109125, 7944013, 8180331, 19178578, 252992, 7015476, 8498154, 17127425, 4579620, 36603938, ss222522042, ss233572230, ss240608961, ss483347804, ss535561544, ss653336189, ss780243377, ss782117027, ss835728868, ss983198290, ss1073807207, ss1321134327, ss1430810558, ss1581779074, ss1711137232, ss1926456224, ss1970458534, ss2023871120, ss2152063266, ss2626430798, ss2634478284, ss2707681533, ss2841828845, ss2986005259, ss2999491267, ss3347097408, ss3629595342, ss3632393280, ss3638642283, ss3642501972, ss3667370877, ss3733730611, ss3765322501, ss3830054053, ss3865110445, ss3912001184, ss4017286013, ss5178634631, ss5315171226, ss5367192140, ss5640915796, ss5842600770, ss5969418125	NC_000006.11:87647590:C:T	NC_000006.12:86937872:C:T	(self)
43263229, 232591587, 3184581, 15903900, 50976762, 549107183, 4663673997, ss2285947498, ss3025729327, ss3648409624, ss3717706956, ss3808472900, ss3959525899, ss4711729625, ss5269337815, ss5466878084, ss5555737294, ss5717139658, ss5807704922, ss5855460146, ss5884798671	NC_000006.12:86937872:C:T	NC_000006.12:86937872:C:T	(self)
ss20274973, ss22483987	NT_007299.12:25467761:C:T	NC_000006.12:86937872:C:T	(self)
ss2206588, ss3220569, ss6166977, ss44729379, ss75049903, ss98517644, ss104334468, ss119391294, ss142763780, ss172478284	NT_007299.13:25767424:C:T	NC_000006.12:86937872:C:T	(self)

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

1 citation for rs1406946

PMID	Title	Author	Year	Journal
18937842	The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis.	Oades RD et al.	2008	Behavioral and brain functions

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1406946