Name: rs11143166
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.

rs11143166

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:68618862 (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>C / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.216846 (57397/264690, TOPMED)
T=0.209424 (29337/140084, GnomAD)
T=0.20182 (15873/78650, PAGE_STUDY) (+ 18 more)
T=0.12892 (3643/28258, 14KJPN)
T=0.21445 (4051/18890, ALFA)
T=0.12959 (2172/16760, 8.3KJPN)
T=0.2133 (1366/6404, 1000G_30x)
T=0.2169 (1086/5008, 1000G)
T=0.2062 (924/4480, Estonian)
T=0.2540 (979/3854, ALSPAC)
T=0.2424 (899/3708, TWINSUK)
T=0.2003 (587/2930, KOREAN)
T=0.2005 (379/1890, HapMap)
T=0.1818 (333/1832, Korea1K)
T=0.261 (260/998, GoNL)
T=0.298 (179/600, NorthernSweden)
T=0.176 (38/216, Qatari)
A=0.439 (93/212, SGDP_PRJ)
T=0.198 (42/212, Vietnamese)
T=0.25 (10/40, GENOME_DK)
A=0.42 (5/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMEM252-DT : 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	A=0.78555	T=0.21445
European	Sub	14286	A=0.76914	T=0.23086
African	Sub	2946	A=0.8819	T=0.1181
African Others	Sub	114	A=0.904	T=0.096
African American	Sub	2832	A=0.8810	T=0.1190
Asian	Sub	112	A=0.839	T=0.161
East Asian	Sub	86	A=0.84	T=0.16
Other Asian	Sub	26	A=0.85	T=0.15
Latin American 1	Sub	146	A=0.808	T=0.192
Latin American 2	Sub	610	A=0.689	T=0.311
South Asian	Sub	98	A=0.65	T=0.35
Other	Sub	692	A=0.805	T=0.195

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=0.783154	T=0.216846
gnomAD - Genomes	Global	Study-wide	140084	A=0.790576	T=0.209424
gnomAD - Genomes	European	Sub	75862	A=0.76207	T=0.23793
gnomAD - Genomes	African	Sub	41988	A=0.87997	T=0.12003
gnomAD - Genomes	American	Sub	13638	A=0.69724	T=0.30276
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.6866	T=0.3134
gnomAD - Genomes	East Asian	Sub	3128	A=0.8037	T=0.1963
gnomAD - Genomes	Other	Sub	2146	A=0.7842	T=0.2158
The PAGE Study	Global	Study-wide	78650	A=0.79818	T=0.20182
The PAGE Study	AfricanAmerican	Sub	32494	A=0.87653	T=0.12347
The PAGE Study	Mexican	Sub	10798	A=0.65679	T=0.34321
The PAGE Study	Asian	Sub	8318	A=0.8423	T=0.1577
The PAGE Study	PuertoRican	Sub	7912	A=0.7556	T=0.2444
The PAGE Study	NativeHawaiian	Sub	4530	A=0.7179	T=0.2821
The PAGE Study	Cuban	Sub	4228	A=0.7580	T=0.2420
The PAGE Study	Dominican	Sub	3826	A=0.8048	T=0.1952
The PAGE Study	CentralAmerican	Sub	2450	A=0.6980	T=0.3020
The PAGE Study	SouthAmerican	Sub	1980	A=0.6949	T=0.3051
The PAGE Study	NativeAmerican	Sub	1258	A=0.7838	T=0.2162
The PAGE Study	SouthAsian	Sub	856	A=0.714	T=0.286
14KJPN	JAPANESE	Study-wide	28258	A=0.87108	T=0.12892
Allele Frequency Aggregator	Total	Global	18890	A=0.78555	T=0.21445
Allele Frequency Aggregator	European	Sub	14286	A=0.76914	T=0.23086
Allele Frequency Aggregator	African	Sub	2946	A=0.8819	T=0.1181
Allele Frequency Aggregator	Other	Sub	692	A=0.805	T=0.195
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.689	T=0.311
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.808	T=0.192
Allele Frequency Aggregator	Asian	Sub	112	A=0.839	T=0.161
Allele Frequency Aggregator	South Asian	Sub	98	A=0.65	T=0.35
8.3KJPN	JAPANESE	Study-wide	16760	A=0.87041	T=0.12959
1000Genomes_30x	Global	Study-wide	6404	A=0.7867	T=0.2133
1000Genomes_30x	African	Sub	1786	A=0.8903	T=0.1097
1000Genomes_30x	Europe	Sub	1266	A=0.7425	T=0.2575
1000Genomes_30x	South Asian	Sub	1202	A=0.6972	T=0.3028
1000Genomes_30x	East Asian	Sub	1170	A=0.8231	T=0.1769
1000Genomes_30x	American	Sub	980	A=0.721	T=0.279
1000Genomes	Global	Study-wide	5008	A=0.7831	T=0.2169
1000Genomes	African	Sub	1322	A=0.8911	T=0.1089
1000Genomes	East Asian	Sub	1008	A=0.8214	T=0.1786
1000Genomes	Europe	Sub	1006	A=0.7435	T=0.2565
1000Genomes	South Asian	Sub	978	A=0.685	T=0.315
1000Genomes	American	Sub	694	A=0.718	T=0.282
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7937	T=0.2062
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7460	T=0.2540
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7576	T=0.2424
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.7997	C=0.0000, T=0.2003
HapMap	Global	Study-wide	1890	A=0.7995	T=0.2005
HapMap	American	Sub	768	A=0.733	T=0.267
HapMap	African	Sub	692	A=0.870	T=0.130
HapMap	Asian	Sub	254	A=0.827	T=0.173
HapMap	Europe	Sub	176	A=0.773	T=0.227
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8182	T=0.1818
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.739	T=0.261
Northern Sweden	ACPOP	Study-wide	600	A=0.702	T=0.298
Qatari	Global	Study-wide	216	A=0.824	T=0.176
SGDP_PRJ	Global	Study-wide	212	A=0.439	T=0.561
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.802	T=0.198
The Danish reference pan genome	Danish	Study-wide	40	A=0.75	T=0.25
Siberian	Global	Study-wide	12	A=0.42	T=0.58

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 9	NC_000009.12:g.68618862A>C
GRCh38.p14 chr 9	NC_000009.12:g.68618862A>T
GRCh37.p13 chr 9	NC_000009.11:g.71233778A>C
GRCh37.p13 chr 9	NC_000009.11:g.71233778A>T

Gene: TMEM252-DT, uncharacterized TMEM252-DT (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM252-DT transcript variant X2	XR_001746701.3:n.	N/A	Intron Variant
TMEM252-DT transcript variant X1	XR_007061564.1:n.	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=	C	T
GRCh38.p14 chr 9	NC_000009.12:g.68618862=	NC_000009.12:g.68618862A>C	NC_000009.12:g.68618862A>T
GRCh37.p13 chr 9	NC_000009.11:g.71233778=	NC_000009.11:g.71233778A>C	NC_000009.11:g.71233778A>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, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss16160344	Feb 27, 2004 (120)
2	SC_SNP	ss18580925	Feb 27, 2004 (120)
3	AFFY	ss66291755	Dec 02, 2006 (127)
4	AFFY	ss75957022	Dec 07, 2007 (129)
5	KRIBB_YJKIM	ss82859962	Dec 15, 2007 (130)
6	COMPLETE_GENOMICS	ss165088612	Jul 04, 2010 (132)
7	COMPLETE_GENOMICS	ss166467233	Jul 04, 2010 (132)
8	BUSHMAN	ss200400106	Jul 04, 2010 (132)
9	1000GENOMES	ss210768164	Jul 14, 2010 (132)
10	1000GENOMES	ss224246507	Jul 14, 2010 (132)
11	1000GENOMES	ss234817219	Jul 15, 2010 (132)
12	1000GENOMES	ss241593167	Jul 15, 2010 (132)
13	GMI	ss280246924	May 04, 2012 (137)
14	GMI	ss286026577	Apr 25, 2013 (138)
15	TISHKOFF	ss561383773	Apr 25, 2013 (138)
16	SSMP	ss655868858	Apr 25, 2013 (138)
17	EVA-GONL	ss986567186	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1076300700	Aug 21, 2014 (142)
19	1000GENOMES	ss1333909157	Aug 21, 2014 (142)
20	DDI	ss1431840648	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1583098411	Apr 01, 2015 (144)
22	EVA_DECODE	ss1596195702	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1622731411	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1665725444	Apr 01, 2015 (144)
25	EVA_SVP	ss1713108889	Apr 01, 2015 (144)
26	WEILL_CORNELL_DGM	ss1929884662	Feb 12, 2016 (147)
27	ILLUMINA	ss1959184938	Feb 12, 2016 (147)
28	GENOMED	ss1971214467	Jul 19, 2016 (147)
29	JJLAB	ss2025654858	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2153879174	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2311265731	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2627295263	Nov 08, 2017 (151)
33	GRF	ss2709741608	Nov 08, 2017 (151)
34	GNOMAD	ss2878817577	Nov 08, 2017 (151)
35	SWEGEN	ss3004959993	Nov 08, 2017 (151)
36	ILLUMINA	ss3022929959	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3026608191	Nov 08, 2017 (151)
38	CSHL	ss3348673991	Nov 08, 2017 (151)
39	URBANLAB	ss3649157309	Oct 12, 2018 (152)
40	ILLUMINA	ss3653482242	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3672495158	Jul 13, 2019 (153)
42	EVA_DECODE	ss3723984613	Jul 13, 2019 (153)
43	ILLUMINA	ss3726611946	Jul 13, 2019 (153)
44	ACPOP	ss3736533742	Jul 13, 2019 (153)
45	EVA	ss3769208697	Jul 13, 2019 (153)
46	PAGE_CC	ss3771500300	Jul 13, 2019 (153)
47	PACBIO	ss3786418363	Jul 13, 2019 (153)
48	PACBIO	ss3791634773	Jul 13, 2019 (153)
49	PACBIO	ss3796516058	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3812379016	Jul 13, 2019 (153)
51	EVA	ss3831660419	Apr 26, 2020 (154)
52	SGDP_PRJ	ss3872261954	Apr 26, 2020 (154)
53	KRGDB	ss3920044120	Apr 26, 2020 (154)
54	KOGIC	ss3965974881	Apr 26, 2020 (154)
55	TOPMED	ss4821942378	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5193541243	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5280816187	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5476823304	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5573194225	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5647492686	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5737552573	Oct 16, 2022 (156)
62	YY_MCH	ss5810662851	Oct 16, 2022 (156)
63	EVA	ss5829211985	Oct 16, 2022 (156)
64	EVA	ss5856770957	Oct 16, 2022 (156)
65	EVA	ss5916468368	Oct 16, 2022 (156)
66	EVA	ss5976667477	Oct 16, 2022 (156)
67	1000Genomes	NC_000009.11 - 71233778	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000009.12 - 68618862	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 71233778	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000009.11 - 71233778	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000009.11 - 71233778	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000009.12 - 68618862	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000009.11 - 71233778	Apr 26, 2020 (154)
74	HapMap	NC_000009.12 - 68618862	Apr 26, 2020 (154)
75	KOREAN population from KRGDB	NC_000009.11 - 71233778	Apr 26, 2020 (154)
76	Korean Genome Project	NC_000009.12 - 68618862	Apr 26, 2020 (154)
77	Northern Sweden	NC_000009.11 - 71233778	Jul 13, 2019 (153)
78	The PAGE Study	NC_000009.12 - 68618862	Jul 13, 2019 (153)
79	Qatari	NC_000009.11 - 71233778	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000009.11 - 71233778	Apr 26, 2020 (154)
81	Siberian	NC_000009.11 - 71233778	Apr 26, 2020 (154)
82	8.3KJPN	NC_000009.11 - 71233778	Apr 26, 2021 (155)
83	14KJPN	NC_000009.12 - 68618862	Oct 16, 2022 (156)
84	TopMed	NC_000009.12 - 68618862	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000009.11 - 71233778	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000009.11 - 71233778	Jul 13, 2019 (153)
87	ALFA	NC_000009.12 - 68618862	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)
rs59593125	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
27221514, ss3920044120	NC_000009.11:71233777:A:C	NC_000009.12:68618861:A:C	(self)
ss66291755, ss75957022, ss165088612, ss166467233, ss200400106, ss210768164, ss280246924, ss286026577, ss1596195702, ss1713108889	NC_000009.10:70423597:A:T	NC_000009.12:68618861:A:T	(self)
46169994, 25634086, 18233406, 9263348, 11443416, 27221514, 9818607, 11926592, 24278934, 6395528, 51510550, 25634086, 5696831, ss224246507, ss234817219, ss241593167, ss561383773, ss655868858, ss986567186, ss1076300700, ss1333909157, ss1431840648, ss1583098411, ss1622731411, ss1665725444, ss1929884662, ss1959184938, ss1971214467, ss2025654858, ss2153879174, ss2627295263, ss2709741608, ss2878817577, ss3004959993, ss3022929959, ss3348673991, ss3653482242, ss3672495158, ss3736533742, ss3769208697, ss3786418363, ss3791634773, ss3796516058, ss3831660419, ss3872261954, ss3920044120, ss5193541243, ss5647492686, ss5829211985, ss5976667477	NC_000009.11:71233777:A:T	NC_000009.12:68618861:A:T	(self)
60720160, 326437630, 3831116, 22352882, 721769, 71389677, 659319939, 13590518898, ss2311265731, ss3026608191, ss3649157309, ss3723984613, ss3726611946, ss3771500300, ss3812379016, ss3965974881, ss4821942378, ss5280816187, ss5476823304, ss5573194225, ss5737552573, ss5810662851, ss5856770957, ss5916468368	NC_000009.12:68618861:A:T	NC_000009.12:68618861:A:T	(self)
ss82859962	NT_008470.19:398309:A:T	NC_000009.12:68618861:A:T	(self)
ss16160344, ss18580925	NT_023935.16:398309:A:T	NC_000009.12:68618861:A: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 rs11143166

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

rs11143166