Name: rs6047515
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.

rs6047515

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:21620745 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.067872 (17965/264690, TOPMED)
G=0.071850 (10057/139972, GnomAD)
G=0.09183 (2595/28258, 14KJPN) (+ 14 more)
G=0.07750 (1464/18890, ALFA)
G=0.08848 (1483/16760, 8.3KJPN)
G=0.0731 (468/6404, 1000G_30x)
G=0.0745 (373/5008, 1000G)
G=0.0920 (412/4480, Estonian)
G=0.0903 (348/3854, ALSPAC)
G=0.0844 (313/3708, TWINSUK)
G=0.0747 (219/2930, KOREAN)
G=0.116 (116/998, GoNL)
G=0.152 (91/600, NorthernSweden)
G=0.096 (52/542, SGDP_PRJ)
G=0.056 (12/216, Qatari)
G=0.14 (8/56, Siberian)
G=0.07 (3/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01726 : 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	G=0.07750	A=0.92250
European	Sub	14286	G=0.08659	A=0.91341
African	Sub	2946	G=0.0190	A=0.9810
African Others	Sub	114	G=0.000	A=1.000
African American	Sub	2832	G=0.0198	A=0.9802
Asian	Sub	112	G=0.080	A=0.920
East Asian	Sub	86	G=0.08	A=0.92
Other Asian	Sub	26	G=0.08	A=0.92
Latin American 1	Sub	146	G=0.048	A=0.952
Latin American 2	Sub	610	G=0.128	A=0.872
South Asian	Sub	98	G=0.21	A=0.79
Other	Sub	692	G=0.081	A=0.919

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=0.067872	A=0.932128
gnomAD - Genomes	Global	Study-wide	139972	G=0.071850	A=0.928150
gnomAD - Genomes	European	Sub	75816	G=0.09751	A=0.90249
gnomAD - Genomes	African	Sub	41936	G=0.01989	A=0.98011
gnomAD - Genomes	American	Sub	13624	G=0.09828	A=0.90172
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.0367	A=0.9633
gnomAD - Genomes	East Asian	Sub	3130	G=0.0722	A=0.9278
gnomAD - Genomes	Other	Sub	2144	G=0.0667	A=0.9333
14KJPN	JAPANESE	Study-wide	28258	G=0.09183	A=0.90817
Allele Frequency Aggregator	Total	Global	18890	G=0.07750	A=0.92250
Allele Frequency Aggregator	European	Sub	14286	G=0.08659	A=0.91341
Allele Frequency Aggregator	African	Sub	2946	G=0.0190	A=0.9810
Allele Frequency Aggregator	Other	Sub	692	G=0.081	A=0.919
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.128	A=0.872
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.048	A=0.952
Allele Frequency Aggregator	Asian	Sub	112	G=0.080	A=0.920
Allele Frequency Aggregator	South Asian	Sub	98	G=0.21	A=0.79
8.3KJPN	JAPANESE	Study-wide	16760	G=0.08848	A=0.91152
1000Genomes_30x	Global	Study-wide	6404	G=0.0731	A=0.9269
1000Genomes_30x	African	Sub	1786	G=0.0106	A=0.9894
1000Genomes_30x	Europe	Sub	1266	G=0.0790	A=0.9210
1000Genomes_30x	South Asian	Sub	1202	G=0.1622	A=0.8378
1000Genomes_30x	East Asian	Sub	1170	G=0.0632	A=0.9368
1000Genomes_30x	American	Sub	980	G=0.082	A=0.918
1000Genomes	Global	Study-wide	5008	G=0.0745	A=0.9255
1000Genomes	African	Sub	1322	G=0.0113	A=0.9887
1000Genomes	East Asian	Sub	1008	G=0.0625	A=0.9375
1000Genomes	Europe	Sub	1006	G=0.0795	A=0.9205
1000Genomes	South Asian	Sub	978	G=0.161	A=0.839
1000Genomes	American	Sub	694	G=0.084	A=0.916
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.0920	A=0.9080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.0903	A=0.9097
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.0844	A=0.9156
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0747	A=0.9253, C=0.0000, T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.116	A=0.884
Northern Sweden	ACPOP	Study-wide	600	G=0.152	A=0.848
SGDP_PRJ	Global	Study-wide	542	G=0.096	A=0.904
Qatari	Global	Study-wide	216	G=0.056	A=0.944
Siberian	Global	Study-wide	56	G=0.14	A=0.86
The Danish reference pan genome	Danish	Study-wide	40	G=0.07	A=0.93

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 20	NC_000020.11:g.21620745G>A
GRCh38.p14 chr 20	NC_000020.11:g.21620745G>C
GRCh38.p14 chr 20	NC_000020.11:g.21620745G>T
GRCh37.p13 chr 20	NC_000020.10:g.21601383G>A
GRCh37.p13 chr 20	NC_000020.10:g.21601383G>C
GRCh37.p13 chr 20	NC_000020.10:g.21601383G>T

Gene: LINC01726, long intergenic non-protein coding RNA 1726 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01726 transcript	NR_109878.1: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	G=	A	C	T
GRCh38.p14 chr 20	NC_000020.11:g.21620745=	NC_000020.11:g.21620745G>A	NC_000020.11:g.21620745G>C	NC_000020.11:g.21620745G>T
GRCh37.p13 chr 20	NC_000020.10:g.21601383=	NC_000020.10:g.21601383G>A	NC_000020.10:g.21601383G>C	NC_000020.10:g.21601383G>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#.

69 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8358709	Apr 21, 2003 (114)
2	SC_SNP	ss11104575	Jul 11, 2003 (117)
3	SSAHASNP	ss21757430	Apr 05, 2004 (121)
4	HGSV	ss86115105	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss91666216	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96190839	Feb 06, 2009 (130)
7	IGMI-SNU	ss115466077	Feb 06, 2009 (130)
8	ENSEMBL	ss135743774	Dec 01, 2009 (131)
9	ENSEMBL	ss138223575	Dec 01, 2009 (131)
10	GMI	ss156266338	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss167979548	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss169328873	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss171997335	Jul 04, 2010 (132)
14	BUSHMAN	ss203856311	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss208696375	Jul 04, 2010 (132)
16	BL	ss255539658	May 09, 2011 (134)
17	GMI	ss283332753	May 04, 2012 (137)
18	GMI	ss287437308	Apr 25, 2013 (138)
19	PJP	ss292630060	May 09, 2011 (134)
20	1000GENOMES	ss340670787	May 09, 2011 (134)
21	TISHKOFF	ss566189193	Apr 25, 2013 (138)
22	SSMP	ss662064455	Apr 25, 2013 (138)
23	EVA-GONL	ss994627427	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1082139044	Aug 21, 2014 (142)
25	1000GENOMES	ss1364386259	Aug 21, 2014 (142)
26	DDI	ss1429022141	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1579473032	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1638588131	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1681582164	Apr 01, 2015 (144)
30	EVA_DECODE	ss1698686415	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1809459612	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1938134308	Feb 12, 2016 (147)
33	JJLAB	ss2029852384	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2158405308	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2241997965	Dec 20, 2016 (150)
36	SYSTEMSBIOZJU	ss2629421437	Nov 08, 2017 (151)
37	GRF	ss2704081320	Nov 08, 2017 (151)
38	GNOMAD	ss2966331928	Nov 08, 2017 (151)
39	SWEGEN	ss3017997436	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3028759448	Nov 08, 2017 (151)
41	CSHL	ss3352458759	Nov 08, 2017 (151)
42	URBANLAB	ss3650989866	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3684722848	Jul 13, 2019 (153)
44	EVA_DECODE	ss3706720057	Jul 13, 2019 (153)
45	ACPOP	ss3743321026	Jul 13, 2019 (153)
46	EVA	ss3758526056	Jul 13, 2019 (153)
47	PACBIO	ss3788621582	Jul 13, 2019 (153)
48	PACBIO	ss3793518643	Jul 13, 2019 (153)
49	PACBIO	ss3798405820	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3821694216	Jul 13, 2019 (153)
51	EVA	ss3835630471	Apr 27, 2020 (154)
52	EVA	ss3841441557	Apr 27, 2020 (154)
53	EVA	ss3846949694	Apr 27, 2020 (154)
54	SGDP_PRJ	ss3888900448	Apr 27, 2020 (154)
55	KRGDB	ss3939106042	Apr 27, 2020 (154)
56	TOPMED	ss5085079938	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5229199339	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5308363096	Oct 13, 2022 (156)
59	EVA	ss5436780038	Oct 13, 2022 (156)
60	HUGCELL_USP	ss5500740597	Oct 13, 2022 (156)
61	EVA	ss5512183395	Oct 13, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5614587115	Oct 13, 2022 (156)
63	SANFORD_IMAGENETICS	ss5663025043	Oct 13, 2022 (156)
64	TOMMO_GENOMICS	ss5788287696	Oct 13, 2022 (156)
65	YY_MCH	ss5817887830	Oct 13, 2022 (156)
66	EVA	ss5845557424	Oct 13, 2022 (156)
67	EVA	ss5853104650	Oct 13, 2022 (156)
68	EVA	ss5923000843	Oct 13, 2022 (156)
69	EVA	ss5957939270	Oct 13, 2022 (156)
70	1000Genomes	NC_000020.10 - 21601383	Oct 12, 2018 (152)
71	1000Genomes_30x	NC_000020.11 - 21620745	Oct 13, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 21601383	Oct 12, 2018 (152)
73	Genetic variation in the Estonian population	NC_000020.10 - 21601383	Oct 12, 2018 (152)
74	The Danish reference pan genome	NC_000020.10 - 21601383	Apr 27, 2020 (154)
75	gnomAD - Genomes	NC_000020.11 - 21620745	Apr 26, 2021 (155)
76	Genome of the Netherlands Release 5	NC_000020.10 - 21601383	Apr 27, 2020 (154)
77	KOREAN population from KRGDB	NC_000020.10 - 21601383	Apr 27, 2020 (154)
78	Northern Sweden	NC_000020.10 - 21601383	Jul 13, 2019 (153)
79	Qatari	NC_000020.10 - 21601383	Apr 27, 2020 (154)
80	SGDP_PRJ	NC_000020.10 - 21601383	Apr 27, 2020 (154)
81	Siberian	NC_000020.10 - 21601383	Apr 27, 2020 (154)
82	8.3KJPN	NC_000020.10 - 21601383	Apr 26, 2021 (155)
83	14KJPN	NC_000020.11 - 21620745	Oct 13, 2022 (156)
84	TopMed	NC_000020.11 - 21620745	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000020.10 - 21601383	Oct 12, 2018 (152)
86	ALFA	NC_000020.11 - 21620745	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)
rs7343274	Aug 26, 2003 (117)
rs60606002	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss86115105, ss91666216, ss167979548, ss169328873, ss171997335, ss203856311, ss208696375, ss255539658, ss283332753, ss287437308, ss292630060, ss1698686415	NC_000020.9:21549382:G:A	NC_000020.11:21620744:G:A	(self)
77837112, 43097413, 30461096, 5637971, 19203877, 46283436, 16605891, 20176230, 40917428, 10921662, 87168646, 43097413, ss340670787, ss566189193, ss662064455, ss994627427, ss1082139044, ss1364386259, ss1429022141, ss1579473032, ss1638588131, ss1681582164, ss1809459612, ss1938134308, ss2029852384, ss2158405308, ss2629421437, ss2704081320, ss2966331928, ss3017997436, ss3352458759, ss3684722848, ss3743321026, ss3758526056, ss3788621582, ss3793518643, ss3798405820, ss3835630471, ss3841441557, ss3888900448, ss3939106042, ss5229199339, ss5436780038, ss5512183395, ss5663025043, ss5845557424, ss5957939270	NC_000020.10:21601382:G:A	NC_000020.11:21620744:G:A	(self)
102113050, 548776810, 122124800, 360188883, 9477691383, ss2241997965, ss3028759448, ss3650989866, ss3706720057, ss3821694216, ss3846949694, ss5085079938, ss5308363096, ss5500740597, ss5614587115, ss5788287696, ss5817887830, ss5853104650, ss5923000843	NC_000020.11:21620744:G:A	NC_000020.11:21620744:G:A	(self)
ss8358709, ss11104575, ss21757430, ss96190839, ss115466077, ss135743774, ss138223575, ss156266338	NT_011387.8:21541382:G:A	NC_000020.11:21620744:G:A	(self)
46283436, ss3939106042	NC_000020.10:21601382:G:C	NC_000020.11:21620744:G:C	(self)
46283436, ss3939106042	NC_000020.10:21601382:G:T	NC_000020.11:21620744: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 rs6047515

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

rs6047515