Name: rs6546090
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.

rs6546090

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:64612850 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.066108 (17498/264690, TOPMED)
T=0.056713 (7946/140108, GnomAD)
T=0.09590 (2710/28258, 14KJPN) (+ 18 more)
T=0.04065 (985/24232, ALFA)
T=0.09582 (1606/16760, 8.3KJPN)
T=0.1259 (806/6404, 1000G_30x)
T=0.1274 (638/5008, 1000G)
T=0.0100 (45/4480, Estonian)
T=0.0109 (42/3854, ALSPAC)
T=0.0113 (42/3708, TWINSUK)
T=0.1373 (245/1784, HapMap)
T=0.006 (6/998, GoNL)
T=0.134 (84/626, Chileans)
T=0.013 (8/600, NorthernSweden)
T=0.088 (19/216, Qatari)
T=0.203 (43/212, Vietnamese)
G=0.460 (57/124, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
T=0.1 (1/8, KOREAN)
G=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02579 : Non Coding Transcript 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	24232	G=0.95935	T=0.04065
European	Sub	15668	G=0.98730	T=0.01270
African	Sub	3634	G=0.8646	T=0.1354
African Others	Sub	126	G=0.841	T=0.159
African American	Sub	3508	G=0.8655	T=0.1345
Asian	Sub	164	G=0.902	T=0.098
East Asian	Sub	104	G=0.913	T=0.087
Other Asian	Sub	60	G=0.88	T=0.12
Latin American 1	Sub	298	G=0.950	T=0.050
Latin American 2	Sub	2770	G=0.9386	T=0.0614
South Asian	Sub	108	G=0.852	T=0.148
Other	Sub	1590	G=0.9516	T=0.0484

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.933892	T=0.066108
gnomAD - Genomes	Global	Study-wide	140108	G=0.943287	T=0.056713
gnomAD - Genomes	European	Sub	75898	G=0.98906	T=0.01094
gnomAD - Genomes	African	Sub	41952	G=0.86904	T=0.13096
gnomAD - Genomes	American	Sub	13654	G=0.94148	T=0.05852
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9542	T=0.0458
gnomAD - Genomes	East Asian	Sub	3132	G=0.8305	T=0.1695
gnomAD - Genomes	Other	Sub	2150	G=0.9349	T=0.0651
14KJPN	JAPANESE	Study-wide	28258	G=0.90410	T=0.09590
Allele Frequency Aggregator	Total	Global	24232	G=0.95935	T=0.04065
Allele Frequency Aggregator	European	Sub	15668	G=0.98730	T=0.01270
Allele Frequency Aggregator	African	Sub	3634	G=0.8646	T=0.1354
Allele Frequency Aggregator	Latin American 2	Sub	2770	G=0.9386	T=0.0614
Allele Frequency Aggregator	Other	Sub	1590	G=0.9516	T=0.0484
Allele Frequency Aggregator	Latin American 1	Sub	298	G=0.950	T=0.050
Allele Frequency Aggregator	Asian	Sub	164	G=0.902	T=0.098
Allele Frequency Aggregator	South Asian	Sub	108	G=0.852	T=0.148
8.3KJPN	JAPANESE	Study-wide	16760	G=0.90418	T=0.09582
1000Genomes_30x	Global	Study-wide	6404	G=0.8741	T=0.1259
1000Genomes_30x	African	Sub	1786	G=0.8264	T=0.1736
1000Genomes_30x	Europe	Sub	1266	G=0.9905	T=0.0095
1000Genomes_30x	South Asian	Sub	1202	G=0.8037	T=0.1963
1000Genomes_30x	East Asian	Sub	1170	G=0.8359	T=0.1641
1000Genomes_30x	American	Sub	980	G=0.943	T=0.057
1000Genomes	Global	Study-wide	5008	G=0.8726	T=0.1274
1000Genomes	African	Sub	1322	G=0.8298	T=0.1702
1000Genomes	East Asian	Sub	1008	G=0.8323	T=0.1677
1000Genomes	Europe	Sub	1006	G=0.9891	T=0.0109
1000Genomes	South Asian	Sub	978	G=0.802	T=0.198
1000Genomes	American	Sub	694	G=0.944	T=0.056
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9900	T=0.0100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9891	T=0.0109
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9887	T=0.0113
HapMap	Global	Study-wide	1784	G=0.8627	T=0.1373
HapMap	African	Sub	692	G=0.829	T=0.171
HapMap	American	Sub	662	G=0.866	T=0.134
HapMap	Asian	Sub	254	G=0.866	T=0.134
HapMap	Europe	Sub	176	G=0.977	T=0.023
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.994	T=0.006
Chileans	Chilean	Study-wide	626	G=0.866	T=0.134
Northern Sweden	ACPOP	Study-wide	600	G=0.987	T=0.013
Qatari	Global	Study-wide	216	G=0.912	T=0.088
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.797	T=0.203
SGDP_PRJ	Global	Study-wide	124	G=0.460	T=0.540
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	T=0.03
KOREAN population from KRGDB	KOREAN	Study-wide	8	G=0.9	T=0.1
Siberian	Global	Study-wide	2	G=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 2	NC_000002.12:g.64612850G>T
GRCh37.p13 chr 2	NC_000002.11:g.64839984G>T

Gene: LINC02579, long intergenic non-protein coding RNA 2579 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02579 transcript	NR_034023.1:n.194G>T	N/A	Non Coding Transcript 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	G=	T
GRCh38.p14 chr 2	NC_000002.12:g.64612850=	NC_000002.12:g.64612850G>T
GRCh37.p13 chr 2	NC_000002.11:g.64839984=	NC_000002.11:g.64839984G>T
LINC02579 transcript	NR_034023.1:n.194=	NR_034023.1:n.194G>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#.

53 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9957763	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss11479228	Jul 11, 2003 (116)
3	AFFY	ss66256495	Nov 30, 2006 (127)
4	PERLEGEN	ss68817061	May 17, 2007 (127)
5	AFFY	ss76401864	Dec 07, 2007 (129)
6	KRIBB_YJKIM	ss82259413	Dec 15, 2007 (130)
7	GMI	ss157156161	Dec 01, 2009 (131)
8	AFFY	ss173480851	Jul 04, 2010 (132)
9	BUSHMAN	ss200544078	Jul 04, 2010 (132)
10	1000GENOMES	ss219292347	Jul 14, 2010 (132)
11	1000GENOMES	ss238749307	Jul 15, 2010 (132)
12	GMI	ss276501737	May 04, 2012 (137)
13	ILLUMINA	ss535807295	Sep 08, 2015 (146)
14	TISHKOFF	ss555619953	Apr 25, 2013 (138)
15	SSMP	ss649208837	Apr 25, 2013 (138)
16	EVA-GONL	ss976927040	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1069185058	Aug 21, 2014 (142)
18	1000GENOMES	ss1297591585	Aug 21, 2014 (142)
19	DDI	ss1428603400	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1578915919	Apr 01, 2015 (144)
21	EVA_DECODE	ss1586340919	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1603706665	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1646700698	Apr 01, 2015 (144)
24	EVA_SVP	ss1712462069	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1920154620	Feb 12, 2016 (147)
26	GENOMED	ss1968790773	Jul 19, 2016 (147)
27	JJLAB	ss2020611400	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2148656020	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2231048460	Dec 20, 2016 (150)
30	GRF	ss2703227755	Nov 08, 2017 (151)
31	GNOMAD	ss2774493559	Nov 08, 2017 (151)
32	SWEGEN	ss2989643489	Nov 08, 2017 (151)
33	ILLUMINA	ss3628082084	Oct 11, 2018 (152)
34	EGCUT_WGS	ss3657620790	Jul 13, 2019 (153)
35	EVA_DECODE	ss3704060018	Jul 13, 2019 (153)
36	ACPOP	ss3728506219	Jul 13, 2019 (153)
37	EVA	ss3756865175	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3801231811	Jul 13, 2019 (153)
39	SGDP_PRJ	ss3852444156	Apr 25, 2020 (154)
40	KRGDB	ss3897927229	Apr 25, 2020 (154)
41	TOPMED	ss4508881038	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5151758919	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5248358954	Oct 12, 2022 (156)
44	EVA	ss5329486926	Oct 12, 2022 (156)
45	HUGCELL_USP	ss5448534753	Oct 12, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5523742031	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5628907516	Oct 12, 2022 (156)
48	TOMMO_GENOMICS	ss5680495887	Oct 12, 2022 (156)
49	YY_MCH	ss5802275851	Oct 12, 2022 (156)
50	EVA	ss5820212729	Oct 12, 2022 (156)
51	EVA	ss5852554445	Oct 12, 2022 (156)
52	EVA	ss5930714370	Oct 12, 2022 (156)
53	EVA	ss5955150348	Oct 12, 2022 (156)
54	1000Genomes	NC_000002.11 - 64839984	Oct 11, 2018 (152)
55	1000Genomes_30x	NC_000002.12 - 64612850	Oct 12, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 64839984	Oct 11, 2018 (152)
57	Chileans	NC_000002.11 - 64839984	Apr 25, 2020 (154)
58	Genetic variation in the Estonian population	NC_000002.11 - 64839984	Oct 11, 2018 (152)
59	The Danish reference pan genome	NC_000002.11 - 64839984	Apr 25, 2020 (154)
60	gnomAD - Genomes	NC_000002.12 - 64612850	Apr 26, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000002.11 - 64839984	Apr 25, 2020 (154)
62	HapMap	NC_000002.12 - 64612850	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000002.11 - 64839984	Apr 25, 2020 (154)
64	Northern Sweden	NC_000002.11 - 64839984	Jul 13, 2019 (153)
65	Qatari	NC_000002.11 - 64839984	Apr 25, 2020 (154)
66	SGDP_PRJ	NC_000002.11 - 64839984	Apr 25, 2020 (154)
67	Siberian	NC_000002.11 - 64839984	Apr 25, 2020 (154)
68	8.3KJPN	NC_000002.11 - 64839984	Apr 26, 2021 (155)
69	14KJPN	NC_000002.12 - 64612850	Oct 12, 2022 (156)
70	TopMed	NC_000002.12 - 64612850	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000002.11 - 64839984	Oct 11, 2018 (152)
72	A Vietnamese Genetic Variation Database	NC_000002.11 - 64839984	Jul 13, 2019 (153)
73	ALFA	NC_000002.12 - 64612850	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)
rs59885336	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66256495, ss76401864, ss173480851, ss200544078, ss276501737, ss1586340919, ss1712462069	NC_000002.10:64693487:G:T	NC_000002.12:64612849:G:T	(self)
8547252, 4753699, 220120, 3359038, 5086775, 2088740, 5104623, 1791084, 2196550, 4461136, 1172374, 9728226, 4753699, 1030788, ss219292347, ss238749307, ss535807295, ss555619953, ss649208837, ss976927040, ss1069185058, ss1297591585, ss1428603400, ss1578915919, ss1603706665, ss1646700698, ss1920154620, ss1968790773, ss2020611400, ss2148656020, ss2703227755, ss2774493559, ss2989643489, ss3628082084, ss3657620790, ss3728506219, ss3756865175, ss3852444156, ss3897927229, ss5151758919, ss5329486926, ss5628907516, ss5820212729, ss5955150348	NC_000002.11:64839983:G:T	NC_000002.12:64612849:G:T	(self)
11267966, 60726919, 1815385, 14332991, 312703917, 4762168187, ss2231048460, ss3704060018, ss3801231811, ss4508881038, ss5248358954, ss5448534753, ss5523742031, ss5680495887, ss5802275851, ss5852554445, ss5930714370	NC_000002.12:64612849:G:T	NC_000002.12:64612849:G:T	(self)
ss9957763, ss11479228	NT_022184.12:43655915:G:T	NC_000002.12:64612849:G:T	(self)
ss68817061, ss82259413, ss157156161	NT_022184.15:43661870:G:T	NC_000002.12:64612849: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 rs6546090

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

rs6546090