Name: rs6490542
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.

rs6490542

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:18630531 (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: T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.211508 (55984/264690, TOPMED)
G=0.213941 (29950/139992, GnomAD)
G=0.12365 (3494/28258, 14KJPN) (+ 13 more)
G=0.21371 (4037/18890, ALFA)
G=0.12202 (2045/16760, 8.3KJPN)
G=0.1724 (1104/6404, 1000G_30x)
G=0.1683 (843/5008, 1000G)
G=0.2167 (835/3854, ALSPAC)
G=0.2230 (827/3708, TWINSUK)
G=0.0982 (287/2922, KOREAN)
G=0.0890 (163/1832, Korea1K)
G=0.213 (213/998, GoNL)
G=0.177 (106/600, NorthernSweden)
G=0.185 (40/216, Qatari)
T=0.477 (62/130, SGDP_PRJ)
G=0.15 (6/40, 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	18890	T=0.78629	G=0.21371
European	Sub	14286	T=0.78167	G=0.21833
African	Sub	2946	T=0.7963	G=0.2037
African Others	Sub	114	T=0.851	G=0.149
African American	Sub	2832	T=0.7941	G=0.2059
Asian	Sub	112	T=0.938	G=0.062
East Asian	Sub	86	T=0.97	G=0.03
Other Asian	Sub	26	T=0.85	G=0.15
Latin American 1	Sub	146	T=0.788	G=0.212
Latin American 2	Sub	610	T=0.772	G=0.228
South Asian	Sub	98	T=0.96	G=0.04
Other	Sub	692	T=0.802	G=0.198

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	T=0.788492	G=0.211508
gnomAD - Genomes	Global	Study-wide	139992	T=0.786059	G=0.213941
gnomAD - Genomes	European	Sub	75836	T=0.78012	G=0.21988
gnomAD - Genomes	African	Sub	41932	T=0.79610	G=0.20390
gnomAD - Genomes	American	Sub	13634	T=0.76104	G=0.23896
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.7908	G=0.2092
gnomAD - Genomes	East Asian	Sub	3126	T=0.9024	G=0.0976
gnomAD - Genomes	Other	Sub	2146	T=0.7819	G=0.2181
14KJPN	JAPANESE	Study-wide	28258	T=0.87635	G=0.12365
Allele Frequency Aggregator	Total	Global	18890	T=0.78629	G=0.21371
Allele Frequency Aggregator	European	Sub	14286	T=0.78167	G=0.21833
Allele Frequency Aggregator	African	Sub	2946	T=0.7963	G=0.2037
Allele Frequency Aggregator	Other	Sub	692	T=0.802	G=0.198
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.772	G=0.228
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.788	G=0.212
Allele Frequency Aggregator	Asian	Sub	112	T=0.938	G=0.062
Allele Frequency Aggregator	South Asian	Sub	98	T=0.96	G=0.04
8.3KJPN	JAPANESE	Study-wide	16760	T=0.87798	G=0.12202
1000Genomes_30x	Global	Study-wide	6404	T=0.8276	G=0.1724
1000Genomes_30x	African	Sub	1786	T=0.7721	G=0.2279
1000Genomes_30x	Europe	Sub	1266	T=0.7749	G=0.2251
1000Genomes_30x	South Asian	Sub	1202	T=0.9418	G=0.0582
1000Genomes_30x	East Asian	Sub	1170	T=0.8974	G=0.1026
1000Genomes_30x	American	Sub	980	T=0.773	G=0.227
1000Genomes	Global	Study-wide	5008	T=0.8317	G=0.1683
1000Genomes	African	Sub	1322	T=0.7693	G=0.2307
1000Genomes	East Asian	Sub	1008	T=0.9028	G=0.0972
1000Genomes	Europe	Sub	1006	T=0.7803	G=0.2197
1000Genomes	South Asian	Sub	978	T=0.942	G=0.058
1000Genomes	American	Sub	694	T=0.767	G=0.233
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7833	G=0.2167
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7770	G=0.2230
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9018	G=0.0982
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9110	G=0.0890
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.787	G=0.213
Northern Sweden	ACPOP	Study-wide	600	T=0.823	G=0.177
Qatari	Global	Study-wide	216	T=0.815	G=0.185
SGDP_PRJ	Global	Study-wide	130	T=0.477	G=0.523
The Danish reference pan genome	Danish	Study-wide	40	T=0.85	G=0.15

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 13	NC_000013.11:g.18630531T>G
GRCh37.p13 chr 13	NC_000013.10:g.19204671T>G

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	T=	G
GRCh38.p14 chr 13	NC_000013.11:g.18630531=	NC_000013.11:g.18630531T>G
GRCh37.p13 chr 13	NC_000013.10:g.19204671=	NC_000013.10:g.19204671T>G

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#.

49 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss11087050	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss12256994	Jul 11, 2003 (116)
3	HGSV	ss80403063	Dec 15, 2007 (130)
4	ILLUMINA-UK	ss118370083	Feb 14, 2009 (130)
5	ENSEMBL	ss137303291	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss168824183	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss208750043	Jul 04, 2010 (132)
8	GMI	ss286657303	Apr 25, 2013 (138)
9	1000GENOMES	ss337729055	May 09, 2011 (134)
10	SSMP	ss659107484	Apr 25, 2013 (138)
11	EVA-GONL	ss990138650	Aug 21, 2014 (142)
12	1000GENOMES	ss1347311597	Aug 21, 2014 (142)
13	DDI	ss1427109311	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1576632974	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1629797057	Apr 01, 2015 (144)
16	EVA_DECODE	ss1642246804	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1672791090	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1807501907	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1933503859	Feb 12, 2016 (147)
20	GENOMED	ss1967720793	Jul 19, 2016 (147)
21	JJLAB	ss2027505705	Sep 14, 2016 (149)
22	SYSTEMSBIOZJU	ss2628239412	Nov 08, 2017 (151)
23	GRF	ss2700235559	Nov 08, 2017 (151)
24	GNOMAD	ss2917082091	Nov 08, 2017 (151)
25	SWEGEN	ss3010634598	Nov 08, 2017 (151)
26	CSHL	ss3350336346	Nov 08, 2017 (151)
27	URBANLAB	ss3649972905	Oct 12, 2018 (152)
28	EVA_DECODE	ss3694827954	Jul 13, 2019 (153)
29	ACPOP	ss3739535904	Jul 13, 2019 (153)
30	EVA	ss3751177900	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3816505171	Jul 13, 2019 (153)
32	EVA	ss3833419858	Apr 27, 2020 (154)
33	EVA	ss3840283404	Apr 27, 2020 (154)
34	EVA	ss3845767356	Apr 27, 2020 (154)
35	SGDP_PRJ	ss3879489039	Apr 27, 2020 (154)
36	KRGDB	ss3928294185	Apr 27, 2020 (154)
37	KOGIC	ss3973115772	Apr 27, 2020 (154)
38	TOPMED	ss4938440081	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5208966497	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5292928007	Oct 16, 2022 (156)
41	EVA	ss5409325885	Oct 16, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5591488362	Oct 16, 2022 (156)
43	SANFORD_IMAGENETICS	ss5654300799	Oct 16, 2022 (156)
44	TOMMO_GENOMICS	ss5760545874	Oct 16, 2022 (156)
45	YY_MCH	ss5813903245	Oct 16, 2022 (156)
46	EVA	ss5839150691	Oct 16, 2022 (156)
47	EVA	ss5850624909	Oct 16, 2022 (156)
48	EVA	ss5924193035	Oct 16, 2022 (156)
49	EVA	ss5945710556	Oct 16, 2022 (156)
50	1000Genomes	NC_000013.10 - 19204671	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000013.11 - 18630531	Oct 16, 2022 (156)
52	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 19204671	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000013.10 - 19204671	Apr 27, 2020 (154)
54	gnomAD - Genomes	NC_000013.11 - 18630531	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000013.10 - 19204671	Apr 27, 2020 (154)
56	KOREAN population from KRGDB	NC_000013.10 - 19204671	Apr 27, 2020 (154)
57	Korean Genome Project	NC_000013.11 - 18630531	Apr 27, 2020 (154)
58	Northern Sweden	NC_000013.10 - 19204671	Jul 13, 2019 (153)
59	Qatari	NC_000013.10 - 19204671	Apr 27, 2020 (154)
60	SGDP_PRJ	NC_000013.10 - 19204671	Apr 27, 2020 (154)
61	8.3KJPN	NC_000013.10 - 19204671	Apr 26, 2021 (155)
62	14KJPN	NC_000013.11 - 18630531	Oct 16, 2022 (156)
63	TopMed	NC_000013.11 - 18630531	Apr 26, 2021 (155)
64	UK 10K study - Twins	NC_000013.10 - 19204671	Oct 12, 2018 (152)
65	ALFA	NC_000013.11 - 18630531	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)
rs59875753	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80403063, ss118370083, ss168824183, ss208750043, ss286657303, ss1642246804	NC_000013.9:18102670:T:G	NC_000013.11:18630530:T:G	(self)
60147435, 33405434, 3197431, 14898493, 35471579, 12820769, 15545789, 31506019, 66935804, 33405434, ss337729055, ss659107484, ss990138650, ss1347311597, ss1427109311, ss1576632974, ss1629797057, ss1672791090, ss1807501907, ss1933503859, ss1967720793, ss2027505705, ss2628239412, ss2700235559, ss2917082091, ss3010634598, ss3350336346, ss3739535904, ss3751177900, ss3833419858, ss3840283404, ss3879489039, ss3928294185, ss5208966497, ss5409325885, ss5654300799, ss5839150691, ss5945710556	NC_000013.10:19204670:T:G	NC_000013.11:18630530:T:G	(self)
79014297, 424234803, 29493773, 94382978, 153985739, 2998040760, ss3649972905, ss3694827954, ss3816505171, ss3845767356, ss3973115772, ss4938440081, ss5292928007, ss5591488362, ss5760545874, ss5813903245, ss5850624909, ss5924193035	NC_000013.11:18630530:T:G	NC_000013.11:18630530:T:G	(self)
ss11087050, ss12256994	NT_009799.12:184670:T:G	NC_000013.11:18630530:T:G	(self)
ss137303291	NT_024524.14:184670:T:G	NC_000013.11:18630530:T:G	(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 rs6490542

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

rs6490542