Name: rs1181201
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.

rs1181201

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:53838107 (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=0.131452 (34794/264690, TOPMED)
T=0.124633 (17480/140252, GnomAD)
T=0.00099 (28/28258, 14KJPN) (+ 15 more)
T=0.09132 (1725/18890, ALFA)
T=0.00089 (15/16760, 8.3KJPN)
T=0.1259 (806/6404, 1000G_30x)
T=0.1190 (596/5008, 1000G)
T=0.0317 (142/4480, Estonian)
T=0.0457 (176/3854, ALSPAC)
T=0.0494 (183/3708, TWINSUK)
T=0.0010 (3/2916, KOREAN)
T=0.033 (33/998, GoNL)
T=0.012 (7/600, NorthernSweden)
T=0.111 (24/216, Qatari)
C=0.396 (42/106, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: NDC1 : 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	18890	C=0.90868	T=0.09132
European	Sub	14286	C=0.95037	T=0.04963
African	Sub	2946	C=0.7003	T=0.2997
African Others	Sub	114	C=0.640	T=0.360
African American	Sub	2832	C=0.7027	T=0.2973
Asian	Sub	112	C=0.982	T=0.018
East Asian	Sub	86	C=0.98	T=0.02
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.842	T=0.158
Latin American 2	Sub	610	C=0.956	T=0.044
South Asian	Sub	98	C=0.99	T=0.01
Other	Sub	692	C=0.884	T=0.116

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=0.868548	T=0.131452
gnomAD - Genomes	Global	Study-wide	140252	C=0.875367	T=0.124633
gnomAD - Genomes	European	Sub	75958	C=0.95653	T=0.04347
gnomAD - Genomes	African	Sub	42024	C=0.69981	T=0.30019
gnomAD - Genomes	American	Sub	13660	C=0.92042	T=0.07958
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9332	T=0.0668
gnomAD - Genomes	East Asian	Sub	3132	C=0.9869	T=0.0131
gnomAD - Genomes	Other	Sub	2154	C=0.9011	T=0.0989
14KJPN	JAPANESE	Study-wide	28258	C=0.99901	T=0.00099
Allele Frequency Aggregator	Total	Global	18890	C=0.90868	T=0.09132
Allele Frequency Aggregator	European	Sub	14286	C=0.95037	T=0.04963
Allele Frequency Aggregator	African	Sub	2946	C=0.7003	T=0.2997
Allele Frequency Aggregator	Other	Sub	692	C=0.884	T=0.116
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.956	T=0.044
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.842	T=0.158
Allele Frequency Aggregator	Asian	Sub	112	C=0.982	T=0.018
Allele Frequency Aggregator	South Asian	Sub	98	C=0.99	T=0.01
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99911	T=0.00089
1000Genomes_30x	Global	Study-wide	6404	C=0.8741	T=0.1259
1000Genomes_30x	African	Sub	1786	C=0.6316	T=0.3684
1000Genomes_30x	Europe	Sub	1266	C=0.9494	T=0.0506
1000Genomes_30x	South Asian	Sub	1202	C=0.9917	T=0.0083
1000Genomes_30x	East Asian	Sub	1170	C=0.9966	T=0.0034
1000Genomes_30x	American	Sub	980	C=0.929	T=0.071
1000Genomes	Global	Study-wide	5008	C=0.8810	T=0.1190
1000Genomes	African	Sub	1322	C=0.6354	T=0.3646
1000Genomes	East Asian	Sub	1008	C=0.9950	T=0.0050
1000Genomes	Europe	Sub	1006	C=0.9503	T=0.0497
1000Genomes	South Asian	Sub	978	C=0.992	T=0.008
1000Genomes	American	Sub	694	C=0.927	T=0.073
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9683	T=0.0317
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9543	T=0.0457
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9506	T=0.0494
KOREAN population from KRGDB	KOREAN	Study-wide	2916	C=0.9990	T=0.0010
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.967	T=0.033
Northern Sweden	ACPOP	Study-wide	600	C=0.988	T=0.012
Qatari	Global	Study-wide	216	C=0.889	T=0.111
SGDP_PRJ	Global	Study-wide	106	C=0.396	T=0.604
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	4	C=0.5	T=0.5

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.53838107C>T
GRCh37.p13 chr 1	NC_000001.10:g.54303780C>T

Gene: NDC1, NDC1 transmembrane nucleoporin (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NDC1 transcript variant 2	NM_001168551.2:c.57+98G>A	N/A	Intron Variant
NDC1 transcript variant 1	NM_018087.5:c.57+98G>A	N/A	Intron Variant
NDC1 transcript variant 3	NR_033142.2:n.	N/A	Intron Variant
NDC1 transcript variant X1	XM_011541766.3:c.-147=	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 1	NC_000001.11:g.53838107=	NC_000001.11:g.53838107C>T
GRCh37.p13 chr 1	NC_000001.10:g.54303780=	NC_000001.10:g.54303780C>T
NDC1 transcript variant X1	XM_011541766.3:c.-147=	XM_011541766.3:c.-147G>A
NDC1 transcript variant 2	NM_001168551.1:c.57+98=	NM_001168551.1:c.57+98G>A
NDC1 transcript variant 2	NM_001168551.2:c.57+98=	NM_001168551.2:c.57+98G>A
NDC1 transcript variant 1	NM_018087.4:c.57+98=	NM_018087.4:c.57+98G>A
NDC1 transcript variant 1	NM_018087.5:c.57+98=	NM_018087.5:c.57+98G>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#.

53 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1642923	Oct 18, 2000 (87)
2	SC_JCM	ss2581408	Nov 08, 2000 (89)
3	SC_SNP	ss13040206	Dec 05, 2003 (119)
4	ABI	ss44037428	Mar 15, 2006 (126)
5	BCMHGSC_JDW	ss87430438	Mar 23, 2008 (129)
6	HUMANGENOME_JCVI	ss99207867	Feb 03, 2009 (130)
7	ENSEMBL	ss131797062	Dec 01, 2009 (131)
8	1000GENOMES	ss218380182	Jul 14, 2010 (132)
9	1000GENOMES	ss230530916	Jul 14, 2010 (132)
10	PJP	ss290509569	May 09, 2011 (134)
11	TISHKOFF	ss554103079	Apr 25, 2013 (138)
12	SSMP	ss647928569	Apr 25, 2013 (138)
13	EVA-GONL	ss975151342	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1067879288	Aug 21, 2014 (142)
15	1000GENOMES	ss1290859489	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1574052765	Apr 01, 2015 (144)
17	EVA_DECODE	ss1584517383	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1600155764	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1643149797	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1794345797	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1918360186	Feb 12, 2016 (147)
22	JJLAB	ss2019695073	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2147709116	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2162437336	Dec 20, 2016 (150)
25	GNOMAD	ss2755060899	Nov 08, 2017 (151)
26	SWEGEN	ss2986803595	Nov 08, 2017 (151)
27	CSHL	ss3343449569	Nov 08, 2017 (151)
28	OMUKHERJEE_ADBS	ss3646230777	Oct 11, 2018 (152)
29	URBANLAB	ss3646660860	Oct 11, 2018 (152)
30	EGCUT_WGS	ss3654867190	Jul 12, 2019 (153)
31	EVA_DECODE	ss3686754571	Jul 12, 2019 (153)
32	ACPOP	ss3727039257	Jul 12, 2019 (153)
33	EVA	ss3746192713	Jul 12, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3799202182	Jul 12, 2019 (153)
35	EVA	ss3826166761	Apr 25, 2020 (154)
36	SGDP_PRJ	ss3848828735	Apr 25, 2020 (154)
37	KRGDB	ss3893836760	Apr 25, 2020 (154)
38	FSA-LAB	ss3983931792	Apr 25, 2021 (155)
39	EVA	ss3986120523	Apr 25, 2021 (155)
40	TOPMED	ss4449467006	Apr 25, 2021 (155)
41	TOMMO_GENOMICS	ss5143913016	Apr 25, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5242240361	Oct 12, 2022 (156)
43	EVA	ss5318671505	Oct 12, 2022 (156)
44	HUGCELL_USP	ss5443304707	Oct 12, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5514503213	Oct 12, 2022 (156)
46	EVA	ss5623992707	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5625512163	Oct 12, 2022 (156)
48	TOMMO_GENOMICS	ss5668675176	Oct 12, 2022 (156)
49	EVA	ss5800081814	Oct 12, 2022 (156)
50	EVA	ss5831947423	Oct 12, 2022 (156)
51	EVA	ss5848260861	Oct 12, 2022 (156)
52	EVA	ss5908225861	Oct 12, 2022 (156)
53	EVA	ss5937343128	Oct 12, 2022 (156)
54	1000Genomes	NC_000001.10 - 54303780	Oct 11, 2018 (152)
55	1000Genomes_30x	NC_000001.11 - 53838107	Oct 12, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 54303780	Oct 11, 2018 (152)
57	Genetic variation in the Estonian population	NC_000001.10 - 54303780	Oct 11, 2018 (152)
58	The Danish reference pan genome	NC_000001.10 - 54303780	Apr 25, 2020 (154)
59	gnomAD - Genomes	NC_000001.11 - 53838107	Apr 25, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000001.10 - 54303780	Apr 25, 2020 (154)
61	KOREAN population from KRGDB	NC_000001.10 - 54303780	Apr 25, 2020 (154)
62	Northern Sweden	NC_000001.10 - 54303780	Jul 12, 2019 (153)
63	Qatari	NC_000001.10 - 54303780	Apr 25, 2020 (154)
64	SGDP_PRJ	NC_000001.10 - 54303780	Apr 25, 2020 (154)
65	Siberian	NC_000001.10 - 54303780	Apr 25, 2020 (154)
66	8.3KJPN	NC_000001.10 - 54303780	Apr 25, 2021 (155)
67	14KJPN	NC_000001.11 - 53838107	Oct 12, 2022 (156)
68	TopMed	NC_000001.11 - 53838107	Apr 25, 2021 (155)
69	UK 10K study - Twins	NC_000001.10 - 54303780	Oct 11, 2018 (152)
70	ALFA	NC_000001.11 - 53838107	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87430438, ss290509569, ss1584517383	NC_000001.9:54076367:C:T	NC_000001.11:53838106:C:T	(self)
1576652, 856923, 605438, 1497931, 363083, 1014154, 324122, 402116, 845715, 225470, 1882323, 856923, ss218380182, ss230530916, ss554103079, ss647928569, ss975151342, ss1067879288, ss1290859489, ss1574052765, ss1600155764, ss1643149797, ss1794345797, ss1918360186, ss2019695073, ss2147709116, ss2755060899, ss2986803595, ss3343449569, ss3646230777, ss3654867190, ss3727039257, ss3746192713, ss3826166761, ss3848828735, ss3893836760, ss3983931792, ss3986120523, ss5143913016, ss5318671505, ss5623992707, ss5625512163, ss5800081814, ss5831947423, ss5848260861, ss5937343128	NC_000001.10:54303779:C:T	NC_000001.11:53838106:C:T	(self)
2029148, 11169659, 2512280, 13073341, 1699680941, ss2162437336, ss3646660860, ss3686754571, ss3799202182, ss4449467006, ss5242240361, ss5443304707, ss5514503213, ss5668675176, ss5908225861	NC_000001.11:53838106:C:T	NC_000001.11:53838106:C:T	(self)
ss13040206	NT_032977.5:6752691:C:T	NC_000001.11:53838106:C:T	(self)
ss1642923, ss2581408, ss44037428, ss99207867, ss131797062	NT_032977.9:24275697:C:T	NC_000001.11:53838106: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 rs1181201

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

rs1181201