Name: rs2840186
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.

rs2840186

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:5576786 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.201704 (53389/264690, TOPMED)
G=0.20690 (4598/22223, 14KJPN)
G=0.27266 (5048/18514, ALFA) (+ 9 more)
G=0.20782 (2669/12843, 8.3KJPN)
G=0.2004 (963/4805, 1000G_30x)
G=0.2074 (783/3775, 1000G)
G=0.1952 (572/2930, KOREAN)
G=0.071 (32/450, SGDP_PRJ)
G=0.315 (34/108, Qatari)
G=0.17 (8/48, Vietnamese)
G=0.07 (3/46, Siberian)
G=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	18514	G=0.27266	T=0.72734
European	Sub	14146	G=0.33062	T=0.66938
African	Sub	2898	G=0.0376	T=0.9624
African Others	Sub	114	G=0.000	T=1.000
African American	Sub	2784	G=0.0392	T=0.9608
Asian	Sub	112	G=0.080	T=0.920
East Asian	Sub	86	G=0.09	T=0.91
Other Asian	Sub	26	G=0.04	T=0.96
Latin American 1	Sub	146	G=0.219	T=0.781
Latin American 2	Sub	610	G=0.118	T=0.882
South Asian	Sub	98	G=0.47	T=0.53
Other	Sub	504	G=0.204	T=0.796

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	G=0.201704	T=0.798296
14KJPN	JAPANESE	Study-wide	22223	G=0.20690	T=0.79310
Allele Frequency Aggregator	Total	Global	18514	G=0.27266	T=0.72734
Allele Frequency Aggregator	European	Sub	14146	G=0.33062	T=0.66938
Allele Frequency Aggregator	African	Sub	2898	G=0.0376	T=0.9624
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.118	T=0.882
Allele Frequency Aggregator	Other	Sub	504	G=0.204	T=0.796
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.219	T=0.781
Allele Frequency Aggregator	Asian	Sub	112	G=0.080	T=0.920
Allele Frequency Aggregator	South Asian	Sub	98	G=0.47	T=0.53
8.3KJPN	JAPANESE	Study-wide	12843	G=0.20782	T=0.79218
1000Genomes_30x	Global	Study-wide	4805	G=0.2004	T=0.7996
1000Genomes_30x	African	Sub	1328	G=0.0211	T=0.9789
1000Genomes_30x	Europe	Sub	961	G=0.323	T=0.677
1000Genomes_30x	South Asian	Sub	883	G=0.411	T=0.589
1000Genomes_30x	East Asian	Sub	878	G=0.166	T=0.834
1000Genomes_30x	American	Sub	755	G=0.154	T=0.846
1000Genomes	Global	Study-wide	3775	G=0.2074	T=0.7926
1000Genomes	African	Sub	1003	G=0.0199	T=0.9801
1000Genomes	Europe	Sub	766	G=0.326	T=0.674
1000Genomes	East Asian	Sub	764	G=0.161	T=0.839
1000Genomes	South Asian	Sub	718	G=0.425	T=0.575
1000Genomes	American	Sub	524	G=0.162	T=0.838
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.1952	A=0.0000, T=0.8048
SGDP_PRJ	Global	Study-wide	450	G=0.071	T=0.929
Qatari	Global	Study-wide	108	G=0.315	T=0.685
A Vietnamese Genetic Variation Database	Global	Study-wide	48	G=0.17	T=0.83
Siberian	Global	Study-wide	46	G=0.07	T=0.93
The Danish reference pan genome	Danish	Study-wide	40	G=0.20	T=0.80

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.5576786G>A
GRCh38.p14 chr X	NC_000023.11:g.5576786G>T
GRCh37.p13 chr X	NC_000023.10:g.5494827G>A
GRCh37.p13 chr X	NC_000023.10:g.5494827G>T

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	G=	A	T
GRCh38.p14 chr X	NC_000023.11:g.5576786=	NC_000023.11:g.5576786G>A	NC_000023.11:g.5576786G>T
GRCh37.p13 chr X	NC_000023.10:g.5494827=	NC_000023.10:g.5494827G>A	NC_000023.10:g.5494827G>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#.

60 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4021583	Sep 28, 2001 (100)
2	TSC-CSHL	ss5211363	Oct 08, 2002 (108)
3	SC_SNP	ss8190426	Apr 21, 2003 (114)
4	SSAHASNP	ss21017303	Apr 05, 2004 (121)
5	ABI	ss43536529	Mar 15, 2006 (126)
6	HGSV	ss78260716	Dec 07, 2007 (129)
7	HGSV	ss78874975	Dec 07, 2007 (129)
8	HGSV	ss82498175	Dec 14, 2007 (130)
9	BGI	ss105711312	Feb 04, 2009 (130)
10	1000GENOMES	ss112768475	Jan 25, 2009 (130)
11	1000GENOMES	ss114404048	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss115589035	Feb 04, 2009 (130)
13	ENSEMBL	ss133874589	Dec 01, 2009 (131)
14	GMI	ss157329986	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss163016300	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss164379967	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss166060345	Jul 04, 2010 (132)
18	BUSHMAN	ss204143810	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208901027	Jul 04, 2010 (132)
20	BL	ss255900710	May 09, 2011 (134)
21	GMI	ss283686012	May 04, 2012 (137)
22	GMI	ss287591492	Apr 25, 2013 (138)
23	PJP	ss294479306	May 09, 2011 (134)
24	1000GENOMES	ss341283159	May 09, 2011 (134)
25	TISHKOFF	ss566750574	Apr 25, 2013 (138)
26	SSMP	ss662681978	Apr 25, 2013 (138)
27	JMKIDD_LAB	ss1082773978	Aug 21, 2014 (142)
28	DDI	ss1431998207	Apr 01, 2015 (144)
29	1000GENOMES	ss1553401568	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1583318101	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1939118054	Feb 12, 2016 (147)
32	GENOMED	ss1971338471	Jul 19, 2016 (147)
33	USC_VALOUEV	ss2158935168	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2315477019	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2629659592	Nov 08, 2017 (151)
36	GRF	ss2710066498	Nov 08, 2017 (151)
37	GNOMAD	ss2976216635	Nov 08, 2017 (151)
38	SWEGEN	ss3019590166	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3029000514	Nov 08, 2017 (151)
40	URBANLAB	ss3651245891	Oct 12, 2018 (152)
41	EVA	ss3769886154	Jul 13, 2019 (153)
42	PACBIO	ss3788870753	Jul 13, 2019 (153)
43	PACBIO	ss3793732902	Jul 13, 2019 (153)
44	PACBIO	ss3798618184	Jul 13, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3822741714	Jul 13, 2019 (153)
46	EVA	ss3836080838	Apr 27, 2020 (154)
47	EVA	ss3841659795	Apr 27, 2020 (154)
48	EVA	ss3847175501	Apr 27, 2020 (154)
49	SGDP_PRJ	ss3890946744	Apr 27, 2020 (154)
50	KRGDB	ss3941268973	Apr 27, 2020 (154)
51	TOPMED	ss5114589317	Apr 26, 2021 (155)
52	TOMMO_GENOMICS	ss5233432425	Apr 26, 2021 (155)
53	1000G_HIGH_COVERAGE	ss5311713416	Oct 16, 2022 (156)
54	HUGCELL_USP	ss5503471714	Oct 16, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5619497634	Oct 16, 2022 (156)
56	SANFORD_IMAGENETICS	ss5664830042	Oct 16, 2022 (156)
57	TOMMO_GENOMICS	ss5794832822	Oct 16, 2022 (156)
58	YY_MCH	ss5818867629	Oct 16, 2022 (156)
59	EVA	ss5857004711	Oct 16, 2022 (156)
60	EVA	ss5977775738	Oct 16, 2022 (156)
61	1000Genomes	NC_000023.10 - 5494827	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000023.11 - 5576786	Oct 16, 2022 (156)
63	The Danish reference pan genome	NC_000023.10 - 5494827	Apr 27, 2020 (154)
64	KOREAN population from KRGDB	NC_000023.10 - 5494827	Apr 27, 2020 (154)
65	Qatari	NC_000023.10 - 5494827	Apr 27, 2020 (154)
66	SGDP_PRJ	NC_000023.10 - 5494827	Apr 27, 2020 (154)
67	Siberian	NC_000023.10 - 5494827	Apr 27, 2020 (154)
68	8.3KJPN	NC_000023.10 - 5494827	Apr 26, 2021 (155)
69	14KJPN	NC_000023.11 - 5576786	Oct 16, 2022 (156)
70	TopMed	NC_000023.11 - 5576786	Apr 26, 2021 (155)
71	A Vietnamese Genetic Variation Database	NC_000023.10 - 5494827	Jul 13, 2019 (153)
72	ALFA	NC_000023.11 - 5576786	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)
rs57699758	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
48446367, ss3941268973	NC_000023.10:5494826:G:A	NC_000023.11:5576785:G:A	(self)
ss78260716, ss78874975, ss82498175	NC_000023.8:5354562:G:T	NC_000023.11:5576785:G:T	(self)
ss112768475, ss114404048, ss115589035, ss163016300, ss164379967, ss166060345, ss204143810, ss208901027, ss255900710, ss283686012, ss287591492, ss294479306	NC_000023.9:5504826:G:T	NC_000023.11:5576785:G:T	(self)
81386982, 9483038, 48446367, 21159976, 42963724, 11451522, 91401732, 9924072, ss341283159, ss566750574, ss662681978, ss1082773978, ss1431998207, ss1553401568, ss1583318101, ss1939118054, ss1971338471, ss2158935168, ss2629659592, ss2710066498, ss2976216635, ss3019590166, ss3769886154, ss3788870753, ss3793732902, ss3798618184, ss3836080838, ss3841659795, ss3890946744, ss3941268973, ss5233432425, ss5664830042, ss5977775738	NC_000023.10:5494826:G:T	NC_000023.11:5576785:G:T	(self)
107023569, 128669926, 678195674, 6194670672, ss2315477019, ss3029000514, ss3651245891, ss3822741714, ss3847175501, ss5114589317, ss5311713416, ss5503471714, ss5619497634, ss5794832822, ss5818867629, ss5857004711	NC_000023.11:5576785:G:T	NC_000023.11:5576785:G:T	(self)
ss21017303	NT_011757.13:1561470:G:T	NC_000023.11:5576785:G:T	(self)
ss4021583, ss5211363, ss8190426, ss43536529, ss105711312, ss133874589, ss157329986	NT_167197.1:3376588:G:T	NC_000023.11:5576785:G: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 rs2840186

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

rs2840186