Name: rs9442371
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.

rs9442371

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:1083182 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.498587 (131971/264690, TOPMED)
T=0.488474 (68361/139948, GnomAD)
C=0.18665 (5273/28250, 14KJPN) (+ 17 more)
C=0.49303 (8913/18078, ALFA)
C=0.18702 (3133/16752, 8.3KJPN)
C=0.4780 (3061/6404, 1000G_30x)
C=0.4698 (2353/5008, 1000G)
C=0.4911 (2200/4480, Estonian)
C=0.4154 (1601/3854, ALSPAC)
C=0.4215 (1563/3708, TWINSUK)
C=0.2068 (606/2930, KOREAN)
C=0.439 (438/998, GoNL)
C=0.473 (284/600, NorthernSweden)
C=0.252 (114/452, SGDP_PRJ)
T=0.485 (159/328, HapMap)
T=0.384 (83/216, Qatari)
C=0.159 (34/214, Vietnamese)
C=0.40 (17/42, Siberian)
C=0.50 (20/40, GENOME_DK)
T=0.50 (20/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C1orf159 : Intron Variant
Publications: 0 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	18078	C=0.49303	A=0.00000, T=0.50697
European	Sub	13750	C=0.45593	A=0.00000, T=0.54407
African	Sub	2674	C=0.7364	A=0.0000, T=0.2636
African Others	Sub	100	C=0.80	A=0.00, T=0.20
African American	Sub	2574	C=0.7339	A=0.0000, T=0.2661
Asian	Sub	112	C=0.223	A=0.000, T=0.777
East Asian	Sub	86	C=0.19	A=0.00, T=0.81
Other Asian	Sub	26	C=0.35	A=0.00, T=0.65
Latin American 1	Sub	146	C=0.459	A=0.000, T=0.541
Latin American 2	Sub	610	C=0.330	A=0.000, T=0.670
South Asian	Sub	98	C=0.38	A=0.00, T=0.62
Other	Sub	688	C=0.501	A=0.000, T=0.499

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=0.498587	T=0.501413
gnomAD - Genomes	Global	Study-wide	139948	C=0.511526	T=0.488474
gnomAD - Genomes	European	Sub	75790	C=0.45092	T=0.54908
gnomAD - Genomes	African	Sub	41922	C=0.70464	T=0.29536
gnomAD - Genomes	American	Sub	13642	C=0.35229	T=0.64771
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.4061	T=0.5939
gnomAD - Genomes	East Asian	Sub	3124	C=0.2270	T=0.7730
gnomAD - Genomes	Other	Sub	2146	C=0.4692	T=0.5308
14KJPN	JAPANESE	Study-wide	28250	C=0.18665	T=0.81335
Allele Frequency Aggregator	Total	Global	18078	C=0.49303	A=0.00000, T=0.50697
Allele Frequency Aggregator	European	Sub	13750	C=0.45593	A=0.00000, T=0.54407
Allele Frequency Aggregator	African	Sub	2674	C=0.7364	A=0.0000, T=0.2636
Allele Frequency Aggregator	Other	Sub	688	C=0.501	A=0.000, T=0.499
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.330	A=0.000, T=0.670
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.459	A=0.000, T=0.541
Allele Frequency Aggregator	Asian	Sub	112	C=0.223	A=0.000, T=0.777
Allele Frequency Aggregator	South Asian	Sub	98	C=0.38	A=0.00, T=0.62
8.3KJPN	JAPANESE	Study-wide	16752	C=0.18702	T=0.81298
1000Genomes_30x	Global	Study-wide	6404	C=0.4780	T=0.5220
1000Genomes_30x	African	Sub	1786	C=0.7676	T=0.2324
1000Genomes_30x	Europe	Sub	1266	C=0.4400	T=0.5600
1000Genomes_30x	South Asian	Sub	1202	C=0.4609	T=0.5391
1000Genomes_30x	East Asian	Sub	1170	C=0.2137	T=0.7863
1000Genomes_30x	American	Sub	980	C=0.336	T=0.664
1000Genomes	Global	Study-wide	5008	C=0.4698	T=0.5302
1000Genomes	African	Sub	1322	C=0.7648	T=0.2352
1000Genomes	East Asian	Sub	1008	C=0.2103	T=0.7897
1000Genomes	Europe	Sub	1006	C=0.4414	T=0.5586
1000Genomes	South Asian	Sub	978	C=0.457	T=0.543
1000Genomes	American	Sub	694	C=0.344	T=0.656
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4911	T=0.5089
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4154	T=0.5846
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4215	T=0.5785
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2068	T=0.7932
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.439	T=0.561
Northern Sweden	ACPOP	Study-wide	600	C=0.473	T=0.527
SGDP_PRJ	Global	Study-wide	452	C=0.252	T=0.748
HapMap	Global	Study-wide	328	C=0.515	T=0.485
HapMap	American	Sub	120	C=0.408	T=0.592
HapMap	African	Sub	118	C=0.847	T=0.153
HapMap	Asian	Sub	90	C=0.22	T=0.78
Qatari	Global	Study-wide	216	C=0.616	T=0.384
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.159	T=0.841
Siberian	Global	Study-wide	42	C=0.40	T=0.60
The Danish reference pan genome	Danish	Study-wide	40	C=0.50	T=0.50

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.1083182C>A
GRCh38.p14 chr 1	NC_000001.11:g.1083182C>T
GRCh37.p13 chr 1	NC_000001.10:g.1018562C>A
GRCh37.p13 chr 1	NC_000001.10:g.1018562C>T

Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C1orf159 transcript variant 1	NM_001330306.2:c.1049-195… NM_001330306.2:c.1049-195G>T	N/A	Intron Variant
C1orf159 transcript variant 3	NM_001363525.2:c.941-195G… NM_001363525.2:c.941-195G>T	N/A	Intron Variant
C1orf159 transcript variant 2	NM_017891.5:c.503-195G>T	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	C=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.1083182=	NC_000001.11:g.1083182C>A	NC_000001.11:g.1083182C>T
GRCh37.p13 chr 1	NC_000001.10:g.1018562=	NC_000001.10:g.1018562C>A	NC_000001.10:g.1018562C>T
C1orf159 transcript variant 1	NM_001330306.2:c.1049-195=	NM_001330306.2:c.1049-195G>T	NM_001330306.2:c.1049-195G>A
C1orf159 transcript variant 3	NM_001363525.2:c.941-195=	NM_001363525.2:c.941-195G>T	NM_001363525.2:c.941-195G>A
C1orf159 transcript variant 2	NM_017891.4:c.503-195=	NM_017891.4:c.503-195G>T	NM_017891.4:c.503-195G>A
C1orf159 transcript variant 2	NM_017891.5:c.503-195=	NM_017891.5:c.503-195G>T	NM_017891.5:c.503-195G>A
C1orf159 transcript variant X1	XM_005244764.1:c.1049-195=	XM_005244764.1:c.1049-195G>T	XM_005244764.1:c.1049-195G>A
C1orf159 transcript variant X16	XM_005244765.1:c.941-195=	XM_005244765.1:c.941-195G>T	XM_005244765.1:c.941-195G>A
C1orf159 transcript variant X3	XM_005244766.1:c.611-195=	XM_005244766.1:c.611-195G>T	XM_005244766.1:c.611-195G>A

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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss13052165	Dec 05, 2003 (119)
2	ABI	ss44052656	Mar 13, 2006 (126)
3	PERLEGEN	ss68756310	May 17, 2007 (127)
4	HGSV	ss82183208	Dec 16, 2007 (130)
5	HGSV	ss82523184	Dec 16, 2007 (130)
6	BCMHGSC_JDW	ss87158094	Mar 23, 2008 (129)
7	HUMANGENOME_JCVI	ss99179683	Feb 06, 2009 (130)
8	ENSEMBL	ss131630212	Dec 01, 2009 (131)
9	ENSEMBL	ss137754346	Dec 01, 2009 (131)
10	GMI	ss154527275	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss163706936	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss165982076	Jul 04, 2010 (132)
13	BUSHMAN	ss197888366	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss205287801	Jul 04, 2010 (132)
15	1000GENOMES	ss210446518	Jul 14, 2010 (132)
16	1000GENOMES	ss218191727	Jul 14, 2010 (132)
17	1000GENOMES	ss230396317	Jul 14, 2010 (132)
18	1000GENOMES	ss238115881	Jul 15, 2010 (132)
19	BL	ss252866233	May 09, 2011 (134)
20	GMI	ss275682300	May 04, 2012 (137)
21	GMI	ss283987993	Apr 25, 2013 (138)
22	PJP	ss290494291	May 09, 2011 (134)
23	TISHKOFF	ss553713105	Apr 25, 2013 (138)
24	SSMP	ss647518188	Apr 25, 2013 (138)
25	EVA-GONL	ss974771683	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1067613474	Aug 21, 2014 (142)
27	1000GENOMES	ss1289348961	Aug 21, 2014 (142)
28	DDI	ss1425685719	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1573851883	Apr 01, 2015 (144)
30	EVA_DECODE	ss1584131578	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1599381895	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1642375928	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1793716478	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1917963551	Feb 12, 2016 (147)
35	GENOMED	ss1966667709	Jul 19, 2016 (147)
36	JJLAB	ss2019499654	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2147486326	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2159383408	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2624265439	Nov 08, 2017 (151)
40	GRF	ss2697377273	Nov 08, 2017 (151)
41	GNOMAD	ss2750668045	Nov 08, 2017 (151)
42	SWEGEN	ss2986153818	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3023514215	Nov 08, 2017 (151)
44	CSHL	ss3343274057	Nov 08, 2017 (151)
45	URBANLAB	ss3646581832	Oct 11, 2018 (152)
46	EGCUT_WGS	ss3654264919	Jul 12, 2019 (153)
47	EVA_DECODE	ss3685997298	Jul 12, 2019 (153)
48	ACPOP	ss3726718422	Jul 12, 2019 (153)
49	EVA	ss3745723891	Jul 12, 2019 (153)
50	PACBIO	ss3783303001	Jul 12, 2019 (153)
51	PACBIO	ss3788980789	Jul 12, 2019 (153)
52	PACBIO	ss3793853338	Jul 12, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3798746534	Jul 12, 2019 (153)
54	EVA	ss3825982472	Apr 25, 2020 (154)
55	EVA	ss3836378995	Apr 25, 2020 (154)
56	EVA	ss3841783022	Apr 25, 2020 (154)
57	SGDP_PRJ	ss3848003069	Apr 25, 2020 (154)
58	KRGDB	ss3892845608	Apr 25, 2020 (154)
59	TOPMED	ss4436510328	Apr 25, 2021 (155)
60	TOMMO_GENOMICS	ss5142065325	Apr 25, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5240872343	Oct 12, 2022 (156)
62	EVA	ss5316198114	Oct 12, 2022 (156)
63	HUGCELL_USP	ss5442119266	Oct 12, 2022 (156)
64	EVA	ss5505748336	Oct 12, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5512500606	Oct 12, 2022 (156)
66	SANFORD_IMAGENETICS	ss5624754661	Oct 12, 2022 (156)
67	TOMMO_GENOMICS	ss5666209210	Oct 12, 2022 (156)
68	EVA	ss5800076458	Oct 12, 2022 (156)
69	YY_MCH	ss5800246045	Oct 12, 2022 (156)
70	EVA	ss5831422341	Oct 12, 2022 (156)
71	EVA	ss5848749654	Oct 12, 2022 (156)
72	EVA	ss5906713645	Oct 12, 2022 (156)
73	EVA	ss5936587005	Oct 12, 2022 (156)
74	EVA	ss5979926428	Oct 12, 2022 (156)
75	1000Genomes	NC_000001.10 - 1018562	Oct 11, 2018 (152)
76	1000Genomes_30x	NC_000001.11 - 1083182	Oct 12, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 1018562	Oct 11, 2018 (152)
78	Genetic variation in the Estonian population	NC_000001.10 - 1018562	Oct 11, 2018 (152)
79	The Danish reference pan genome	NC_000001.10 - 1018562	Apr 25, 2020 (154)
80	gnomAD - Genomes	NC_000001.11 - 1083182	Apr 25, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000001.10 - 1018562	Apr 25, 2020 (154)
82	HapMap	NC_000001.11 - 1083182	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000001.10 - 1018562	Apr 25, 2020 (154)
84	Northern Sweden	NC_000001.10 - 1018562	Jul 12, 2019 (153)
85	Qatari	NC_000001.10 - 1018562	Apr 25, 2020 (154)
86	SGDP_PRJ	NC_000001.10 - 1018562	Apr 25, 2020 (154)
87	Siberian	NC_000001.10 - 1018562	Apr 25, 2020 (154)
88	8.3KJPN	NC_000001.10 - 1018562	Apr 25, 2021 (155)
89	14KJPN	NC_000001.11 - 1083182	Oct 12, 2022 (156)
90	TopMed	NC_000001.11 - 1083182	Apr 25, 2021 (155)
91	UK 10K study - Twins	NC_000001.10 - 1018562	Oct 11, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000001.10 - 1018562	Jul 12, 2019 (153)
93	ALFA	NC_000001.11 - 1083182	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)
rs61276853	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
14533873258	NC_000001.11:1083181:C:A	NC_000001.11:1083181:C:A	(self)
ss82183208, ss82523184	NC_000001.8:1058484:C:T	NC_000001.11:1083181:C:T	(self)
ss87158094, ss163706936, ss165982076, ss197888366, ss205287801, ss210446518, ss252866233, ss275682300, ss283987993, ss290494291, ss1584131578	NC_000001.9:1008424:C:T	NC_000001.11:1083181:C:T	(self)
14050, 4240, 3167, 1359117, 2054, 23002, 3287, 5481, 20049, 2680, 34632, 4240, 975, ss218191727, ss230396317, ss238115881, ss553713105, ss647518188, ss974771683, ss1067613474, ss1289348961, ss1425685719, ss1573851883, ss1599381895, ss1642375928, ss1793716478, ss1917963551, ss1966667709, ss2019499654, ss2147486326, ss2624265439, ss2697377273, ss2750668045, ss2986153818, ss3343274057, ss3654264919, ss3726718422, ss3745723891, ss3783303001, ss3788980789, ss3793853338, ss3825982472, ss3836378995, ss3848003069, ss3892845608, ss5142065325, ss5316198114, ss5505748336, ss5624754661, ss5800076458, ss5831422341, ss5936587005, ss5979926428	NC_000001.10:1018561:C:T	NC_000001.11:1083181:C:T	(self)
26541, 132899, 181, 46314, 116663, 14533873258, ss2159383408, ss3023514215, ss3646581832, ss3685997298, ss3798746534, ss3841783022, ss4436510328, ss5240872343, ss5442119266, ss5512500606, ss5666209210, ss5800246045, ss5848749654, ss5906713645	NC_000001.11:1083181:C:T	NC_000001.11:1083181:C:T	(self)
ss44052656, ss68756310, ss99179683, ss131630212, ss137754346, ss154527275	NT_004350.19:497193:C:T	NC_000001.11:1083181:C:T	(self)
ss13052165	NT_077960.1:90047:C:T	NC_000001.11:1083181:C:T	(self)

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

No publications for rs9442371

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs9442371