Name: rs6686534
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.

rs6686534

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:194335942 (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: C>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.195738 (51810/264690, TOPMED)
C=0.01748 (494/28256, 14KJPN)
C=0.01772 (297/16760, 8.3KJPN) (+ 16 more)
C=0.2380 (1811/7608, ALFA)
C=0.2057 (1317/6404, 1000G_30x)
C=0.2017 (1010/5008, 1000G)
C=0.1946 (872/4480, Estonian)
C=0.1201 (463/3854, ALSPAC)
C=0.1313 (487/3708, TWINSUK)
C=0.0113 (33/2930, KOREAN)
C=0.0087 (16/1832, Korea1K)
C=0.132 (132/998, GoNL)
C=0.122 (73/600, NorthernSweden)
C=0.100 (53/530, SGDP_PRJ)
C=0.220 (72/328, HapMap)
C=0.106 (23/216, Qatari)
C=0.037 (8/216, Vietnamese)
C=0.04 (2/52, Siberian)
C=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107985242 : 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	7608	C=0.2380	A=0.0000, G=0.7620, T=0.0000
European	Sub	6812	C=0.1907	A=0.0000, G=0.8093, T=0.0000
African	Sub	526	C=0.840	A=0.000, G=0.160, T=0.000
African Others	Sub	30	C=0.93	A=0.00, G=0.07, T=0.00
African American	Sub	496	C=0.835	A=0.000, G=0.165, T=0.000
Asian	Sub	4	C=0.0	A=0.0, G=1.0, T=0.0
East Asian	Sub	2	C=0.0	A=0.0, G=1.0, T=0.0
Other Asian	Sub	2	C=0.0	A=0.0, G=1.0, T=0.0
Latin American 1	Sub	6	C=1.0	A=0.0, G=0.0, T=0.0
Latin American 2	Sub	12	C=1.00	A=0.00, G=0.00, T=0.00
South Asian	Sub	10	C=0.7	A=0.0, G=0.3, T=0.0
Other	Sub	238	C=0.189	A=0.000, G=0.811, T=0.000

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	C=0.195738	G=0.804262
14KJPN	JAPANESE	Study-wide	28256	C=0.01748	G=0.98252
8.3KJPN	JAPANESE	Study-wide	16760	C=0.01772	G=0.98228
Allele Frequency Aggregator	Total	Global	7608	C=0.2380	A=0.0000, G=0.7620, T=0.0000
Allele Frequency Aggregator	European	Sub	6812	C=0.1907	A=0.0000, G=0.8093, T=0.0000
Allele Frequency Aggregator	African	Sub	526	C=0.840	A=0.000, G=0.160, T=0.000
Allele Frequency Aggregator	Other	Sub	238	C=0.189	A=0.000, G=0.811, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	12	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	10	C=0.7	A=0.0, G=0.3, T=0.0
Allele Frequency Aggregator	Latin American 1	Sub	6	C=1.0	A=0.0, G=0.0, T=0.0
Allele Frequency Aggregator	Asian	Sub	4	C=0.0	A=0.0, G=1.0, T=0.0
1000Genomes_30x	Global	Study-wide	6404	C=0.2057	G=0.7942, T=0.0002
1000Genomes_30x	African	Sub	1786	C=0.4127	G=0.5873, T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.1532	G=0.8460, T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=0.2055	G=0.7945, T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0359	G=0.9641, T=0.0000
1000Genomes_30x	American	Sub	980	C=0.099	G=0.901, T=0.000
1000Genomes	Global	Study-wide	5008	C=0.2017	G=0.7983
1000Genomes	African	Sub	1322	C=0.4115	G=0.5885
1000Genomes	East Asian	Sub	1008	C=0.0367	G=0.9633
1000Genomes	Europe	Sub	1006	C=0.1451	G=0.8549
1000Genomes	South Asian	Sub	978	C=0.214	G=0.786
1000Genomes	American	Sub	694	C=0.107	G=0.893
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.1946	G=0.8054
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1201	G=0.8799
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1313	G=0.8687
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0113	G=0.9887
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0087	G=0.9913
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.132	G=0.868
Northern Sweden	ACPOP	Study-wide	600	C=0.122	G=0.878
SGDP_PRJ	Global	Study-wide	530	C=0.100	G=0.900
HapMap	Global	Study-wide	328	C=0.220	G=0.780
HapMap	American	Sub	120	C=0.200	G=0.800
HapMap	African	Sub	118	C=0.398	G=0.602
HapMap	Asian	Sub	90	C=0.01	G=0.99
Qatari	Global	Study-wide	216	C=0.106	G=0.894
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.037	G=0.963
Siberian	Global	Study-wide	52	C=0.04	G=0.96
The Danish reference pan genome	Danish	Study-wide	40	C=0.12	G=0.88

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 1	NC_000001.11:g.194335942C>A
GRCh38.p14 chr 1	NC_000001.11:g.194335942C>G
GRCh38.p14 chr 1	NC_000001.11:g.194335942C>T
GRCh37.p13 chr 1	NC_000001.10:g.194305072C>A
GRCh37.p13 chr 1	NC_000001.10:g.194305072C>G
GRCh37.p13 chr 1	NC_000001.10:g.194305072C>T

Gene: LOC107985242, uncharacterized LOC107985242 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985242 transcript variant X3	XR_001738356.2:n.	N/A	Intron Variant
LOC107985242 transcript variant X2	XR_001738351.2:n.	N/A	Genic Upstream Transcript Variant
LOC107985242 transcript variant X1	XR_001738352.2:n.	N/A	Genic Upstream Transcript Variant
LOC107985242 transcript variant X4	XR_001738353.2:n.	N/A	Genic Upstream 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	C=	A	G	T
GRCh38.p14 chr 1	NC_000001.11:g.194335942=	NC_000001.11:g.194335942C>A	NC_000001.11:g.194335942C>G	NC_000001.11:g.194335942C>T
GRCh37.p13 chr 1	NC_000001.10:g.194305072=	NC_000001.10:g.194305072C>A	NC_000001.10:g.194305072C>G	NC_000001.10:g.194305072C>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#.

76 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9869699	Jul 11, 2003 (116)
2	CSHL-HAPMAP	ss16447919	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss19143563	Feb 27, 2004 (120)
4	SSAHASNP	ss20475892	Apr 05, 2004 (121)
5	PERLEGEN	ss23196727	Sep 20, 2004 (123)
6	ABI	ss44034100	Mar 13, 2006 (126)
7	PERLEGEN	ss68788155	May 18, 2007 (127)
8	HGSV	ss80725854	Dec 15, 2007 (130)
9	HGSV	ss85814212	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss87919388	Mar 23, 2008 (129)
11	HUMANGENOME_JCVI	ss97994221	Feb 05, 2009 (130)
12	BGI	ss106620619	Feb 05, 2009 (130)
13	1000GENOMES	ss108822356	Jan 23, 2009 (130)
14	1000GENOMES	ss111564452	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss119157563	Feb 15, 2009 (130)
16	ENSEMBL	ss138128605	Dec 01, 2009 (131)
17	ENSEMBL	ss139115765	Dec 01, 2009 (131)
18	GMI	ss156097808	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss164796879	Jul 04, 2010 (132)
20	BUSHMAN	ss199426081	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205067312	Jul 04, 2010 (132)
22	1000GENOMES	ss218800482	Jul 14, 2010 (132)
23	1000GENOMES	ss230840645	Jul 14, 2010 (132)
24	1000GENOMES	ss238464926	Jul 15, 2010 (132)
25	BL	ss253715162	May 09, 2011 (134)
26	GMI	ss276156689	May 04, 2012 (137)
27	GMI	ss284201219	Apr 25, 2013 (138)
28	PJP	ss290693770	May 09, 2011 (134)
29	SSMP	ss648595701	Apr 25, 2013 (138)
30	EVA-GONL	ss975976656	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1068482958	Aug 21, 2014 (142)
32	1000GENOMES	ss1294029698	Aug 21, 2014 (142)
33	DDI	ss1426063985	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1574577689	Apr 01, 2015 (144)
35	EVA_DECODE	ss1585371111	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1601804470	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1644798503	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1795501188	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1919209657	Feb 12, 2016 (147)
40	GENOMED	ss1966934101	Jul 19, 2016 (147)
41	JJLAB	ss2020122649	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2148149499	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2168821876	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2624569095	Nov 08, 2017 (151)
45	GRF	ss2698137122	Nov 08, 2017 (151)
46	GNOMAD	ss2764456573	Nov 08, 2017 (151)
47	SWEGEN	ss2988195898	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3023820527	Nov 08, 2017 (151)
49	CSHL	ss3343839432	Nov 08, 2017 (151)
50	URBANLAB	ss3646852698	Oct 11, 2018 (152)
51	EGCUT_WGS	ss3656153636	Jul 12, 2019 (153)
52	EVA_DECODE	ss3688321679	Jul 12, 2019 (153)
53	ACPOP	ss3727725030	Jul 12, 2019 (153)
54	EVA	ss3747144406	Jul 12, 2019 (153)
55	PACBIO	ss3783645009	Jul 12, 2019 (153)
56	PACBIO	ss3789263891	Jul 12, 2019 (153)
57	PACBIO	ss3794136049	Jul 12, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3800150071	Jul 12, 2019 (153)
59	EVA	ss3826565425	Apr 25, 2020 (154)
60	EVA	ss3836680758	Apr 25, 2020 (154)
61	EVA	ss3842091600	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3850576575	Apr 25, 2020 (154)
63	KRGDB	ss3895852915	Apr 25, 2020 (154)
64	KOGIC	ss3946184619	Apr 25, 2020 (154)
65	TOPMED	ss4478101224	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5147727465	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5245254140	Oct 12, 2022 (156)
68	HUGCELL_USP	ss5445744905	Oct 12, 2022 (156)
69	EVA	ss5506132786	Oct 12, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5519076074	Oct 12, 2022 (156)
71	SANFORD_IMAGENETICS	ss5627139077	Oct 12, 2022 (156)
72	TOMMO_GENOMICS	ss5675282192	Oct 12, 2022 (156)
73	YY_MCH	ss5801501373	Oct 12, 2022 (156)
74	EVA	ss5833043617	Oct 12, 2022 (156)
75	EVA	ss5849219408	Oct 12, 2022 (156)
76	EVA	ss5938961959	Oct 12, 2022 (156)
77	1000Genomes	NC_000001.10 - 194305072	Oct 11, 2018 (152)
78	1000Genomes_30x	NC_000001.11 - 194335942	Oct 12, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 194305072	Oct 11, 2018 (152)
80	Genetic variation in the Estonian population	NC_000001.10 - 194305072	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 194305072	Apr 25, 2020 (154)
82	gnomAD - Genomes Submission ignored due to conflicting rows: Row 35069065 (NC_000001.11:194335941:C:A 1/139848) Row 35069066 (NC_000001.11:194335941:C:G 111566/139794) Row 35069067 (NC_000001.11:194335941:C:T 5/139848)	-	Apr 25, 2021 (155)
83	gnomAD - Genomes Submission ignored due to conflicting rows: Row 35069065 (NC_000001.11:194335941:C:A 1/139848) Row 35069066 (NC_000001.11:194335941:C:G 111566/139794) Row 35069067 (NC_000001.11:194335941:C:T 5/139848)	-	Apr 25, 2021 (155)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 35069065 (NC_000001.11:194335941:C:A 1/139848) Row 35069066 (NC_000001.11:194335941:C:G 111566/139794) Row 35069067 (NC_000001.11:194335941:C:T 5/139848)	-	Apr 25, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000001.10 - 194305072	Apr 25, 2020 (154)
86	HapMap	NC_000001.11 - 194335942	Apr 25, 2020 (154)
87	KOREAN population from KRGDB	NC_000001.10 - 194305072	Apr 25, 2020 (154)
88	Korean Genome Project	NC_000001.11 - 194335942	Apr 25, 2020 (154)
89	Northern Sweden	NC_000001.10 - 194305072	Jul 12, 2019 (153)
90	Qatari	NC_000001.10 - 194305072	Apr 25, 2020 (154)
91	SGDP_PRJ	NC_000001.10 - 194305072	Apr 25, 2020 (154)
92	Siberian	NC_000001.10 - 194305072	Apr 25, 2020 (154)
93	8.3KJPN	NC_000001.10 - 194305072	Apr 25, 2021 (155)
94	14KJPN	NC_000001.11 - 194335942	Oct 12, 2022 (156)
95	TopMed	NC_000001.11 - 194335942	Apr 25, 2021 (155)
96	UK 10K study - Twins	NC_000001.10 - 194305072	Oct 11, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000001.10 - 194305072	Jul 12, 2019 (153)
98	ALFA	NC_000001.11 - 194335942	Apr 25, 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)
rs59746703	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2764456573	NC_000001.10:194305071:C:A	NC_000001.11:194335941:C:A	(self)
3021553660	NC_000001.11:194335941:C:A	NC_000001.11:194335941:C:A	(self)
ss80725854, ss85814212	NC_000001.8:191036728:C:G	NC_000001.11:194335941:C:G	(self)
ss87919388, ss108822356, ss111564452, ss119157563, ss164796879, ss199426081, ss205067312, ss253715162, ss276156689, ss284201219, ss290693770, ss1585371111	NC_000001.9:192571694:C:G	NC_000001.11:194335941:C:G	(self)
4861702, 2669859, 1891884, 1821405, 1164593, 3030309, 1009895, 1251587, 2593555, 665853, 5696772, 2669859, 575982, ss218800482, ss230840645, ss238464926, ss648595701, ss975976656, ss1068482958, ss1294029698, ss1426063985, ss1574577689, ss1601804470, ss1644798503, ss1795501188, ss1919209657, ss1966934101, ss2020122649, ss2148149499, ss2624569095, ss2698137122, ss2764456573, ss2988195898, ss3343839432, ss3656153636, ss3727725030, ss3747144406, ss3783645009, ss3789263891, ss3794136049, ss3826565425, ss3836680758, ss3850576575, ss3895852915, ss5147727465, ss5506132786, ss5627139077, ss5833043617, ss5938961959	NC_000001.10:194305071:C:G	NC_000001.11:194335941:C:G	(self)
6602009, 234194, 2562620, 9119296, 41707559, 3021553660, ss2168821876, ss3023820527, ss3646852698, ss3688321679, ss3800150071, ss3842091600, ss3946184619, ss4478101224, ss5245254140, ss5445744905, ss5519076074, ss5675282192, ss5801501373, ss5849219408	NC_000001.11:194335941:C:G	NC_000001.11:194335941:C:G	(self)
ss23196727, ss44034100, ss68788155, ss97994221, ss106620619, ss138128605, ss139115765, ss156097808	NT_004487.19:45793713:C:G	NC_000001.11:194335941:C:G	(self)
ss9869699, ss16447919, ss19143563, ss20475892	NT_004671.15:5660057:C:G	NC_000001.11:194335941:C:G	(self)
ss276156689	NC_000001.9:192571694:C:T	NC_000001.11:194335941:C:T	(self)
6602009, 3021553660, ss5519076074	NC_000001.11:194335941:C:T	NC_000001.11:194335941:C: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 rs6686534

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

rs6686534