Name: rs1465107
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.

rs1465107

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:43678769 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.300593 (79564/264690, TOPMED)
G=0.39680 (8818/22223, 14KJPN)
A=0.30475 (5644/18520, ALFA) (+ 12 more)
G=0.39656 (5093/12843, 8.3KJPN)
A=0.4056 (1949/4805, 1000G_30x)
A=0.4167 (1573/3775, 1000G)
A=0.2880 (1068/3708, TWINSUK)
G=0.4282 (1253/2926, KOREAN)
A=0.2876 (831/2889, ALSPAC)
A=0.116 (44/378, SGDP_PRJ)
A=0.437 (90/206, HapMap)
A=0.231 (25/108, Qatari)
G=0.42 (20/48, Vietnamese)
A=0.17 (7/40, GENOME_DK)
A=0.22 (8/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAOA : Intron Variant
Publications: 2 citations
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	18520	A=0.30475	G=0.69525
European	Sub	14152	A=0.30702	G=0.69298
African	Sub	2898	A=0.2660	G=0.7340
African Others	Sub	114	A=0.254	G=0.746
African American	Sub	2784	A=0.2665	G=0.7335
Asian	Sub	112	A=0.518	G=0.482
East Asian	Sub	86	A=0.55	G=0.45
Other Asian	Sub	26	A=0.42	G=0.58
Latin American 1	Sub	146	A=0.233	G=0.767
Latin American 2	Sub	610	A=0.328	G=0.672
South Asian	Sub	98	A=0.68	G=0.32
Other	Sub	504	A=0.335	G=0.665

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	A=0.300593	G=0.699407
14KJPN	JAPANESE	Study-wide	22223	A=0.60320	G=0.39680
Allele Frequency Aggregator	Total	Global	18520	A=0.30475	G=0.69525
Allele Frequency Aggregator	European	Sub	14152	A=0.30702	G=0.69298
Allele Frequency Aggregator	African	Sub	2898	A=0.2660	G=0.7340
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.328	G=0.672
Allele Frequency Aggregator	Other	Sub	504	A=0.335	G=0.665
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.233	G=0.767
Allele Frequency Aggregator	Asian	Sub	112	A=0.518	G=0.482
Allele Frequency Aggregator	South Asian	Sub	98	A=0.68	G=0.32
8.3KJPN	JAPANESE	Study-wide	12843	A=0.60344	G=0.39656
1000Genomes_30x	Global	Study-wide	4805	A=0.4056	G=0.5944
1000Genomes_30x	African	Sub	1328	A=0.2824	G=0.7176
1000Genomes_30x	Europe	Sub	961	A=0.291	G=0.709
1000Genomes_30x	South Asian	Sub	883	A=0.657	G=0.343
1000Genomes_30x	East Asian	Sub	878	A=0.571	G=0.429
1000Genomes_30x	American	Sub	755	A=0.282	G=0.718
1000Genomes	Global	Study-wide	3775	A=0.4167	G=0.5833
1000Genomes	African	Sub	1003	A=0.2832	G=0.7168
1000Genomes	Europe	Sub	766	A=0.296	G=0.704
1000Genomes	East Asian	Sub	764	A=0.572	G=0.428
1000Genomes	South Asian	Sub	718	A=0.659	G=0.341
1000Genomes	American	Sub	524	A=0.290	G=0.710
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.2880	G=0.7120
KOREAN population from KRGDB	KOREAN	Study-wide	2926	A=0.5718	G=0.4282
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	A=0.2876	G=0.7124
SGDP_PRJ	Global	Study-wide	378	A=0.116	G=0.884
HapMap	Global	Study-wide	206	A=0.437	G=0.563
HapMap	African	Sub	120	A=0.250	G=0.750
HapMap	Asian	Sub	86	A=0.70	G=0.30
Qatari	Global	Study-wide	108	A=0.231	G=0.769
A Vietnamese Genetic Variation Database	Global	Study-wide	48	A=0.58	G=0.42
The Danish reference pan genome	Danish	Study-wide	40	A=0.17	G=0.82
Siberian	Global	Study-wide	36	A=0.22	G=0.78

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 X	NC_000023.11:g.43678769A>G
GRCh37.p13 chr X	NC_000023.10:g.43538017A>G
MAOA RefSeqGene	NG_008957.2:g.27609A>G

Gene: MAOA, monoamine oxidase A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAOA transcript variant 1	NM_000240.4:c.74-4744A>G	N/A	Intron Variant
MAOA transcript variant 2	NM_001270458.2:c.-326-474… NM_001270458.2:c.-326-4744A>G	N/A	Intron 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	A=	G
GRCh38.p14 chr X	NC_000023.11:g.43678769=	NC_000023.11:g.43678769A>G
GRCh37.p13 chr X	NC_000023.10:g.43538017=	NC_000023.10:g.43538017A>G
MAOA RefSeqGene	NG_008957.2:g.27609=	NG_008957.2:g.27609A>G
MAOA transcript variant 1	NM_000240.3:c.74-4744=	NM_000240.3:c.74-4744A>G
MAOA transcript variant 1	NM_000240.4:c.74-4744=	NM_000240.4:c.74-4744A>G
MAOA transcript variant 2	NM_001270458.1:c.-326-4744=	NM_001270458.1:c.-326-4744A>G
MAOA transcript variant 2	NM_001270458.2:c.-326-4744=	NM_001270458.2:c.-326-4744A>G

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#.

60 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2285351	Oct 23, 2000 (88)
2	SC_SNP	ss8178589	Apr 21, 2003 (114)
3	SC_SNP	ss8491244	Jul 11, 2003 (116)
4	SC_SNP	ss15865997	Feb 27, 2004 (120)
5	PERLEGEN	ss24227249	Sep 20, 2004 (123)
6	ABI	ss43550655	Mar 13, 2006 (126)
7	HGSV	ss78332425	Dec 06, 2007 (129)
8	KRIBB_YJKIM	ss102650280	Feb 05, 2009 (130)
9	1000GENOMES	ss112871196	Jan 25, 2009 (130)
10	1000GENOMES	ss114662731	Jan 25, 2009 (130)
11	ILLUMINA-UK	ss115611344	Feb 05, 2009 (130)
12	ENSEMBL	ss133970633	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss164831497	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss166213570	Jul 04, 2010 (132)
15	BUSHMAN	ss204225252	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss208888257	Jul 04, 2010 (132)
17	BL	ss255982828	May 09, 2011 (134)
18	GMI	ss283741916	May 04, 2012 (137)
19	GMI	ss287608576	Apr 25, 2013 (138)
20	PJP	ss294548228	May 09, 2011 (134)
21	1000GENOMES	ss341453155	May 09, 2011 (134)
22	TISHKOFF	ss566850758	Apr 25, 2013 (138)
23	SSMP	ss662784950	Apr 25, 2013 (138)
24	JMKIDD_LAB	ss1082896572	Aug 21, 2014 (142)
25	DDI	ss1432035279	Apr 01, 2015 (144)
26	1000GENOMES	ss1554247437	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1583381578	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1640681076	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1683675109	Apr 01, 2015 (144)
30	WEILL_CORNELL_DGM	ss1939305858	Feb 12, 2016 (147)
31	GENOMED	ss1971372761	Jul 19, 2016 (147)
32	USC_VALOUEV	ss2159034984	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2317048240	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2629696724	Nov 08, 2017 (151)
35	GRF	ss2710156714	Nov 08, 2017 (151)
36	GNOMAD	ss2978331123	Nov 08, 2017 (151)
37	SWEGEN	ss3019897002	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3029042068	Nov 08, 2017 (151)
39	URBANLAB	ss3651269045	Oct 12, 2018 (152)
40	EVA	ss3770116458	Jul 13, 2019 (153)
41	PACBIO	ss3788894457	Jul 13, 2019 (153)
42	PACBIO	ss3793758514	Jul 13, 2019 (153)
43	PACBIO	ss3798643589	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3822948241	Jul 13, 2019 (153)
45	EVA	ss3836157877	Apr 27, 2020 (154)
46	EVA	ss3841692059	Apr 27, 2020 (154)
47	EVA	ss3847211180	Apr 27, 2020 (154)
48	SGDP_PRJ	ss3891343199	Apr 27, 2020 (154)
49	KRGDB	ss3941745929	Apr 27, 2020 (154)
50	EVA	ss3984765374	Apr 26, 2021 (155)
51	TOPMED	ss5121338590	Apr 26, 2021 (155)
52	TOMMO_GENOMICS	ss5234265953	Apr 26, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5312392617	Oct 16, 2022 (156)
54	HUGCELL_USP	ss5504079492	Oct 16, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5620546171	Oct 16, 2022 (156)
56	SANFORD_IMAGENETICS	ss5665161078	Oct 16, 2022 (156)
57	TOMMO_GENOMICS	ss5795911756	Oct 16, 2022 (156)
58	YY_MCH	ss5819013781	Oct 16, 2022 (156)
59	EVA	ss5857070868	Oct 16, 2022 (156)
60	EVA	ss5978162031	Oct 16, 2022 (156)
61	1000Genomes	NC_000023.10 - 43538017	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000023.11 - 43678769	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 43538017	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000023.10 - 43538017	Apr 27, 2020 (154)
65	HapMap	NC_000023.11 - 43678769	Apr 27, 2020 (154)
66	KOREAN population from KRGDB	NC_000023.10 - 43538017	Apr 27, 2020 (154)
67	Qatari	NC_000023.10 - 43538017	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000023.10 - 43538017	Apr 27, 2020 (154)
69	Siberian	NC_000023.10 - 43538017	Apr 27, 2020 (154)
70	8.3KJPN	NC_000023.10 - 43538017	Apr 26, 2021 (155)
71	14KJPN	NC_000023.11 - 43678769	Oct 16, 2022 (156)
72	TopMed	NC_000023.11 - 43678769	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000023.10 - 43538017	Oct 12, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000023.10 - 43538017	Jul 13, 2019 (153)
75	ALFA	NC_000023.11 - 43678769	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).

Associated ID	History Updated (Build)
rs17310595	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78332425	NC_000023.8:43294270:A:G	NC_000023.11:43678768:A:G	(self)
ss112871196, ss114662731, ss115611344, ss164831497, ss166213570, ss204225252, ss208888257, ss255982828, ss283741916, ss287608576, ss294548228	NC_000023.9:43422960:A:G	NC_000023.11:43678768:A:G	(self)
82224211, 45404181, 9546515, 48923323, 21347780, 43360179, 11551338, 92235260, 45404181, 10008291, ss341453155, ss566850758, ss662784950, ss1082896572, ss1432035279, ss1554247437, ss1583381578, ss1640681076, ss1683675109, ss1939305858, ss1971372761, ss2159034984, ss2629696724, ss2710156714, ss2978331123, ss3019897002, ss3770116458, ss3788894457, ss3793758514, ss3798643589, ss3836157877, ss3841692059, ss3891343199, ss3941745929, ss3984765374, ss5234265953, ss5665161078, ss5978162031	NC_000023.10:43538016:A:G	NC_000023.11:43678768:A:G	(self)
108072106, 3978157, 129748860, 684944947, 12635369844, ss2317048240, ss3029042068, ss3651269045, ss3822948241, ss3847211180, ss5121338590, ss5312392617, ss5504079492, ss5620546171, ss5795911756, ss5819013781, ss5857070868	NC_000023.11:43678768:A:G	NC_000023.11:43678768:A:G	(self)
ss8491244	NT_011568.12:6376154:A:G	NC_000023.11:43678768:A:G	(self)
ss15865997	NT_079573.1:6387825:A:G	NC_000023.11:43678768:A:G	(self)
ss2285351, ss8178589, ss24227249, ss43550655, ss102650280, ss133970633	NT_079573.4:6389760:A:G	NC_000023.11:43678768:A:G	(self)

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

2 citations for rs1465107

PMID	Title	Author	Year	Journal
20691428	A cis-phase interaction study of genetic variants within the MAOA gene in major depressive disorder.	Zhang J et al.	2010	Biological psychiatry
28982350	Pilot study indicate role of preferentially transmitted monoamine oxidase gene variants in behavioral problems of male ADHD probands.	Karmakar A et al.	2017	BMC medical genetics

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
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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

rs1465107