Name: rs6704393
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.

rs6704393

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:162182266 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.487370 (129002/264690, TOPMED)
C=0.30291 (8559/28256, 14KJPN)
T=0.30218 (5070/16778, ALFA) (+ 17 more)
C=0.30591 (5127/16760, 8.3KJPN)
C=0.3771 (2415/6404, 1000G_30x)
C=0.3746 (1876/5008, 1000G)
T=0.3393 (1520/4480, Estonian)
T=0.3887 (1498/3854, ALSPAC)
T=0.4016 (1489/3708, TWINSUK)
C=0.2993 (877/2930, KOREAN)
C=0.3046 (558/1832, Korea1K)
T=0.376 (375/998, GoNL)
T=0.407 (244/600, NorthernSweden)
T=0.290 (155/534, MGP)
C=0.262 (116/442, SGDP_PRJ)
C=0.414 (135/326, HapMap)
T=0.449 (97/216, Qatari)
C=0.160 (34/212, Vietnamese)
C=0.45 (18/40, GENOME_DK)
C=0.15 (6/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NOS1AP : 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	16872	C=0.69624	A=0.00000, T=0.30376
European	Sub	15602	C=0.69203	A=0.00000, T=0.30797
African	Sub	458	C=0.828	A=0.000, T=0.172
African Others	Sub	14	C=0.71	A=0.00, T=0.29
African American	Sub	444	C=0.831	A=0.000, T=0.169
Asian	Sub	8	C=0.5	A=0.0, T=0.5
East Asian	Sub	6	C=0.7	A=0.0, T=0.3
Other Asian	Sub	2	C=0.0	A=0.0, T=1.0
Latin American 1	Sub	28	C=1.00	A=0.00, T=0.00
Latin American 2	Sub	156	C=1.000	A=0.000, T=0.000
South Asian	Sub	32	C=0.94	A=0.00, T=0.06
Other	Sub	588	C=0.600	A=0.000, T=0.400

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=0.487370	T=0.512630
14KJPN	JAPANESE	Study-wide	28256	C=0.30291	T=0.69709
Allele Frequency Aggregator	Total	Global	16778	C=0.69782	A=0.00000, T=0.30218
Allele Frequency Aggregator	European	Sub	15526	C=0.69342	A=0.00000, T=0.30658
Allele Frequency Aggregator	Other	Sub	570	C=0.605	A=0.000, T=0.395
Allele Frequency Aggregator	African	Sub	458	C=0.828	A=0.000, T=0.172
Allele Frequency Aggregator	Latin American 2	Sub	156	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	32	C=0.94	A=0.00, T=0.06
Allele Frequency Aggregator	Latin American 1	Sub	28	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	8	C=0.5	A=0.0, T=0.5
8.3KJPN	JAPANESE	Study-wide	16760	C=0.30591	T=0.69409
1000Genomes_30x	Global	Study-wide	6404	C=0.3771	A=0.0002, T=0.6227
1000Genomes_30x	African	Sub	1786	C=0.2788	A=0.0000, T=0.7212
1000Genomes_30x	Europe	Sub	1266	C=0.5853	A=0.0000, T=0.4147
1000Genomes_30x	South Asian	Sub	1202	C=0.3694	A=0.0000, T=0.6306
1000Genomes_30x	East Asian	Sub	1170	C=0.2085	A=0.0009, T=0.7906
1000Genomes_30x	American	Sub	980	C=0.498	A=0.000, T=0.502
1000Genomes	Global	Study-wide	5008	C=0.3746	T=0.6254
1000Genomes	African	Sub	1322	C=0.2753	T=0.7247
1000Genomes	East Asian	Sub	1008	C=0.2212	T=0.7788
1000Genomes	Europe	Sub	1006	C=0.5895	T=0.4105
1000Genomes	South Asian	Sub	978	C=0.359	T=0.641
1000Genomes	American	Sub	694	C=0.497	T=0.503
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6607	T=0.3393
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6113	T=0.3887
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5984	T=0.4016
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2993	A=0.0000, G=0.0000, T=0.7007
Korean Genome Project	KOREAN	Study-wide	1832	C=0.3046	T=0.6954
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.624	T=0.376
Northern Sweden	ACPOP	Study-wide	600	C=0.593	T=0.407
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.710	T=0.290
SGDP_PRJ	Global	Study-wide	442	C=0.262	T=0.738
HapMap	Global	Study-wide	326	C=0.414	T=0.586
HapMap	African	Sub	120	C=0.325	T=0.675
HapMap	American	Sub	118	C=0.619	T=0.381
HapMap	Asian	Sub	88	C=0.26	T=0.74
Qatari	Global	Study-wide	216	C=0.551	T=0.449
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.160	T=0.840
The Danish reference pan genome	Danish	Study-wide	40	C=0.45	T=0.55
Siberian	Global	Study-wide	40	C=0.15	T=0.85

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 1	NC_000001.11:g.162182266C>A
GRCh38.p14 chr 1	NC_000001.11:g.162182266C>G
GRCh38.p14 chr 1	NC_000001.11:g.162182266C>T
GRCh37.p13 chr 1	NC_000001.10:g.162152056C>A
GRCh37.p13 chr 1	NC_000001.10:g.162152056C>G
GRCh37.p13 chr 1	NC_000001.10:g.162152056C>T
NOS1AP RefSeqGene	NG_015979.2:g.117476C>A
NOS1AP RefSeqGene	NG_015979.2:g.117476C>G
NOS1AP RefSeqGene	NG_015979.2:g.117476C>T

Gene: NOS1AP, nitric oxide synthase 1 adaptor protein (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NOS1AP transcript variant 3	NM_001164757.2:c.177+2779… NM_001164757.2:c.177+27790C>A	N/A	Intron Variant
NOS1AP transcript variant 1	NM_014697.3:c.177+27790C>A	N/A	Intron Variant
NOS1AP transcript variant 2	NM_001126060.2:c.	N/A	Genic Upstream Transcript 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=	A	G	T
GRCh38.p14 chr 1	NC_000001.11:g.162182266=	NC_000001.11:g.162182266C>A	NC_000001.11:g.162182266C>G	NC_000001.11:g.162182266C>T
GRCh37.p13 chr 1	NC_000001.10:g.162152056=	NC_000001.10:g.162152056C>A	NC_000001.10:g.162152056C>G	NC_000001.10:g.162152056C>T
NOS1AP RefSeqGene	NG_015979.2:g.117476=	NG_015979.2:g.117476C>A	NG_015979.2:g.117476C>G	NG_015979.2:g.117476C>T
NOS1AP transcript variant 3	NM_001164757.1:c.177+27790=	NM_001164757.1:c.177+27790C>A	NM_001164757.1:c.177+27790C>G	NM_001164757.1:c.177+27790C>T
NOS1AP transcript variant 3	NM_001164757.2:c.177+27790=	NM_001164757.2:c.177+27790C>A	NM_001164757.2:c.177+27790C>G	NM_001164757.2:c.177+27790C>T
NOS1AP transcript variant 1	NM_014697.2:c.177+27790=	NM_014697.2:c.177+27790C>A	NM_014697.2:c.177+27790C>G	NM_014697.2:c.177+27790C>T
NOS1AP transcript variant 1	NM_014697.3:c.177+27790=	NM_014697.3:c.177+27790C>A	NM_014697.3:c.177+27790C>G	NM_014697.3:c.177+27790C>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#.

66 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9906409	Jul 11, 2003 (116)
2	SC_SNP	ss15415627	Feb 27, 2004 (120)
3	PERLEGEN	ss24247543	Sep 20, 2004 (123)
4	BGI	ss106605414	Feb 04, 2009 (130)
5	1000GENOMES	ss111235248	Jan 25, 2009 (130)
6	COMPLETE_GENOMICS	ss164238824	Jul 04, 2010 (132)
7	BUSHMAN	ss199154037	Jul 04, 2010 (132)
8	1000GENOMES	ss218678059	Jul 14, 2010 (132)
9	1000GENOMES	ss230751507	Jul 14, 2010 (132)
10	1000GENOMES	ss238395432	Jul 15, 2010 (132)
11	BL	ss253550360	May 09, 2011 (134)
12	GMI	ss276072123	May 04, 2012 (137)
13	PJP	ss290648030	May 09, 2011 (134)
14	ILLUMINA	ss410768330	Sep 17, 2011 (135)
15	TISHKOFF	ss554765598	Apr 25, 2013 (138)
16	EVA-GONL	ss975738059	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1068308468	Aug 21, 2014 (142)
18	1000GENOMES	ss1293137015	Aug 21, 2014 (142)
19	DDI	ss1425995067	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1574427698	Apr 01, 2015 (144)
21	EVA_DECODE	ss1585121114	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1601325365	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1644319398	Apr 01, 2015 (144)
24	EVA_MGP	ss1710930427	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1795164012	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918974562	Feb 12, 2016 (147)
27	GENOMED	ss1966879294	Jul 19, 2016 (147)
28	JJLAB	ss2020001165	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2148028052	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2166960840	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2624509543	Nov 08, 2017 (151)
32	GRF	ss2698003588	Nov 08, 2017 (151)
33	GNOMAD	ss2761924097	Nov 08, 2017 (151)
34	AFFY	ss2985527494	Nov 08, 2017 (151)
35	SWEGEN	ss2987840121	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3023757785	Nov 08, 2017 (151)
37	CSHL	ss3343734786	Nov 08, 2017 (151)
38	ILLUMINA	ss3653652373	Oct 11, 2018 (152)
39	EGCUT_WGS	ss3655779251	Jul 12, 2019 (153)
40	EVA_DECODE	ss3687886794	Jul 12, 2019 (153)
41	ACPOP	ss3727531173	Jul 12, 2019 (153)
42	EVA	ss3746872118	Jul 12, 2019 (153)
43	PACBIO	ss3783581886	Jul 12, 2019 (153)
44	PACBIO	ss3789210820	Jul 12, 2019 (153)
45	PACBIO	ss3794082846	Jul 12, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3799872481	Jul 12, 2019 (153)
47	EVA	ss3826451810	Apr 25, 2020 (154)
48	EVA	ss3836620882	Apr 25, 2020 (154)
49	EVA	ss3842030444	Apr 25, 2020 (154)
50	SGDP_PRJ	ss3850115377	Apr 25, 2020 (154)
51	KRGDB	ss3895341669	Apr 25, 2020 (154)
52	KOGIC	ss3945763007	Apr 25, 2020 (154)
53	TOPMED	ss4470167145	Apr 25, 2021 (155)
54	TOMMO_GENOMICS	ss5146730163	Apr 25, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5244476429	Oct 12, 2022 (156)
56	EVA	ss5322383133	Oct 12, 2022 (156)
57	HUGCELL_USP	ss5445044085	Oct 12, 2022 (156)
58	EVA	ss5506046505	Oct 12, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5517896117	Oct 12, 2022 (156)
60	SANFORD_IMAGENETICS	ss5626695378	Oct 12, 2022 (156)
61	TOMMO_GENOMICS	ss5674001464	Oct 12, 2022 (156)
62	YY_MCH	ss5801306123	Oct 12, 2022 (156)
63	EVA	ss5832738437	Oct 12, 2022 (156)
64	EVA	ss5849129276	Oct 12, 2022 (156)
65	EVA	ss5910452847	Oct 12, 2022 (156)
66	EVA	ss5938492201	Oct 12, 2022 (156)
67	1000Genomes	NC_000001.10 - 162152056	Oct 11, 2018 (152)
68	1000Genomes_30x	NC_000001.11 - 162182266	Oct 12, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 162152056	Oct 11, 2018 (152)
70	Genetic variation in the Estonian population	NC_000001.10 - 162152056	Oct 11, 2018 (152)
71	The Danish reference pan genome	NC_000001.10 - 162152056	Apr 25, 2020 (154)
72	gnomAD - Genomes Submission ignored due to conflicting rows: Row 28594082 (NC_000001.11:162182265:C:A 2/140012) Row 28594083 (NC_000001.11:162182265:C:T 69298/139950)	-	Apr 25, 2021 (155)
73	gnomAD - Genomes Submission ignored due to conflicting rows: Row 28594082 (NC_000001.11:162182265:C:A 2/140012) Row 28594083 (NC_000001.11:162182265:C:T 69298/139950)	-	Apr 25, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000001.10 - 162152056	Apr 25, 2020 (154)
75	HapMap	NC_000001.11 - 162182266	Apr 25, 2020 (154)
76	KOREAN population from KRGDB	NC_000001.10 - 162152056	Apr 25, 2020 (154)
77	Korean Genome Project	NC_000001.11 - 162182266	Apr 25, 2020 (154)
78	Medical Genome Project healthy controls from Spanish population	NC_000001.10 - 162152056	Apr 25, 2020 (154)
79	Northern Sweden	NC_000001.10 - 162152056	Jul 12, 2019 (153)
80	Qatari	NC_000001.10 - 162152056	Apr 25, 2020 (154)
81	SGDP_PRJ	NC_000001.10 - 162152056	Apr 25, 2020 (154)
82	Siberian	NC_000001.10 - 162152056	Apr 25, 2020 (154)
83	8.3KJPN	NC_000001.10 - 162152056	Apr 25, 2021 (155)
84	14KJPN	NC_000001.11 - 162182266	Oct 12, 2022 (156)
85	TopMed	NC_000001.11 - 162182266	Apr 25, 2021 (155)
86	UK 10K study - Twins	NC_000001.10 - 162152056	Oct 11, 2018 (152)
87	A Vietnamese Genetic Variation Database	NC_000001.10 - 162152056	Jul 12, 2019 (153)
88	ALFA	NC_000001.11 - 162182266	Apr 25, 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)
rs17423438	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2519063, ss2761924097, ss3895341669	NC_000001.10:162152055:C:A	NC_000001.11:162182265:C:A	(self)
5422052, 2807397362, ss2166960840, ss5517896117	NC_000001.11:162182265:C:A	NC_000001.11:162182265:C:A	(self)
2519063, ss3895341669	NC_000001.10:162152055:C:G	NC_000001.11:162182265:C:G	(self)
ss111235248, ss164238824, ss199154037, ss253550360, ss276072123, ss290648030, ss1585121114	NC_000001.9:160418679:C:T	NC_000001.11:162182265:C:T	(self)
3935892, 2143261, 1517499, 1729296, 931494, 2519063, 47179, 816038, 1016492, 2132357, 544406, 4699470, 2143261, 459068, ss218678059, ss230751507, ss238395432, ss554765598, ss975738059, ss1068308468, ss1293137015, ss1425995067, ss1574427698, ss1601325365, ss1644319398, ss1710930427, ss1795164012, ss1918974562, ss1966879294, ss2020001165, ss2148028052, ss2624509543, ss2698003588, ss2761924097, ss2985527494, ss2987840121, ss3343734786, ss3653652373, ss3655779251, ss3727531173, ss3746872118, ss3783581886, ss3789210820, ss3794082846, ss3826451810, ss3836620882, ss3850115377, ss3895341669, ss5146730163, ss5322383133, ss5506046505, ss5626695378, ss5832738437, ss5938492201	NC_000001.10:162152055:C:T	NC_000001.11:162182265:C:T	(self)
5422052, 187331, 2141008, 7838568, 33773480, 2807397362, ss2166960840, ss3023757785, ss3687886794, ss3799872481, ss3842030444, ss3945763007, ss4470167145, ss5244476429, ss5445044085, ss5517896117, ss5674001464, ss5801306123, ss5849129276, ss5910452847	NC_000001.11:162182265:C:T	NC_000001.11:162182265:C:T	(self)
ss24247543, ss106605414, ss410768330	NT_004487.19:13640697:C:T	NC_000001.11:162182265:C:T	(self)
ss9906409	NT_004668.15:8522614:C:T	NC_000001.11:162182265:C:T	(self)
ss15415627	NT_004668.16:657527:C:T	NC_000001.11:162182265:C:T	(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 rs6704393

PMID	Title	Author	Year	Journal
26384012	Association of NOS1AP variants and depression phenotypes in schizophrenia.	Cheah SY et al.	2015	Journal of affective disorders
35494330	Association of nitric oxide synthase 1 adaptor protein gene polymorphisms with schizophrenia in a Chinese Han population.	Yang X et al.	2022	Indian journal of psychiatry

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

rs6704393