Name: rs6586477
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.

rs6586477

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:104313431 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.285519 (75574/264690, TOPMED)
C=0.268544 (37557/139854, GnomAD)
T=0.42469 (12000/28256, 14KJPN) (+ 17 more)
C=0.21186 (4002/18890, ALFA)
T=0.42709 (7158/16760, 8.3KJPN)
C=0.3560 (2280/6404, 1000G_30x)
C=0.3538 (1772/5008, 1000G)
C=0.1551 (695/4480, Estonian)
C=0.1798 (693/3854, ALSPAC)
C=0.1799 (667/3708, TWINSUK)
T=0.4454 (1305/2930, KOREAN)
T=0.4547 (833/1832, Korea1K)
C=0.171 (171/998, GoNL)
C=0.140 (84/600, NorthernSweden)
C=0.224 (105/468, SGDP_PRJ)
C=0.390 (128/328, HapMap)
C=0.241 (52/216, Qatari)
T=0.477 (102/214, Vietnamese)
C=0.23 (10/44, Siberian)
C=0.10 (4/40, 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	C=0.21186	T=0.78814
European	Sub	14286	C=0.15715	T=0.84285
African	Sub	2946	C=0.4138	T=0.5862
African Others	Sub	114	C=0.474	T=0.526
African American	Sub	2832	C=0.4114	T=0.5886
Asian	Sub	112	C=0.527	T=0.473
East Asian	Sub	86	C=0.56	T=0.44
Other Asian	Sub	26	C=0.42	T=0.58
Latin American 1	Sub	146	C=0.192	T=0.808
Latin American 2	Sub	610	C=0.374	T=0.626
South Asian	Sub	98	C=0.21	T=0.79
Other	Sub	692	C=0.292	T=0.708

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=0.285519	T=0.714481
gnomAD - Genomes	Global	Study-wide	139854	C=0.268544	T=0.731456
gnomAD - Genomes	European	Sub	75816	C=0.17437	T=0.82563
gnomAD - Genomes	African	Sub	41860	C=0.41037	T=0.58963
gnomAD - Genomes	American	Sub	13588	C=0.33868	T=0.66132
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.1165	T=0.8835
gnomAD - Genomes	East Asian	Sub	3116	C=0.5112	T=0.4888
gnomAD - Genomes	Other	Sub	2152	C=0.2681	T=0.7319
14KJPN	JAPANESE	Study-wide	28256	C=0.57531	T=0.42469
Allele Frequency Aggregator	Total	Global	18890	C=0.21186	T=0.78814
Allele Frequency Aggregator	European	Sub	14286	C=0.15715	T=0.84285
Allele Frequency Aggregator	African	Sub	2946	C=0.4138	T=0.5862
Allele Frequency Aggregator	Other	Sub	692	C=0.292	T=0.708
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.374	T=0.626
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.192	T=0.808
Allele Frequency Aggregator	Asian	Sub	112	C=0.527	T=0.473
Allele Frequency Aggregator	South Asian	Sub	98	C=0.21	T=0.79
8.3KJPN	JAPANESE	Study-wide	16760	C=0.57291	T=0.42709
1000Genomes_30x	Global	Study-wide	6404	C=0.3560	T=0.6440
1000Genomes_30x	African	Sub	1786	C=0.4401	T=0.5599
1000Genomes_30x	Europe	Sub	1266	C=0.1746	T=0.8254
1000Genomes_30x	South Asian	Sub	1202	C=0.2612	T=0.7388
1000Genomes_30x	East Asian	Sub	1170	C=0.5103	T=0.4897
1000Genomes_30x	American	Sub	980	C=0.369	T=0.631
1000Genomes	Global	Study-wide	5008	C=0.3538	T=0.6462
1000Genomes	African	Sub	1322	C=0.4365	T=0.5635
1000Genomes	East Asian	Sub	1008	C=0.5040	T=0.4960
1000Genomes	Europe	Sub	1006	C=0.1759	T=0.8241
1000Genomes	South Asian	Sub	978	C=0.263	T=0.737
1000Genomes	American	Sub	694	C=0.365	T=0.635
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.1551	T=0.8449
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1798	T=0.8202
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1799	T=0.8201
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5546	G=0.0000, T=0.4454
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5453	T=0.4547
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.171	T=0.829
Northern Sweden	ACPOP	Study-wide	600	C=0.140	T=0.860
SGDP_PRJ	Global	Study-wide	468	C=0.224	T=0.776
HapMap	Global	Study-wide	328	C=0.390	T=0.610
HapMap	African	Sub	120	C=0.442	T=0.558
HapMap	American	Sub	120	C=0.183	T=0.817
HapMap	Asian	Sub	88	C=0.60	T=0.40
Qatari	Global	Study-wide	216	C=0.241	T=0.759
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.523	T=0.477
Siberian	Global	Study-wide	44	C=0.23	T=0.77
The Danish reference pan genome	Danish	Study-wide	40	C=0.10	T=0.90

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.104313431C>G
GRCh38.p14 chr 1	NC_000001.11:g.104313431C>T
GRCh37.p13 chr 1	NC_000001.10:g.104856053C>G
GRCh37.p13 chr 1	NC_000001.10:g.104856053C>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	C=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.104313431=	NC_000001.11:g.104313431C>G	NC_000001.11:g.104313431C>T
GRCh37.p13 chr 1	NC_000001.10:g.104856053=	NC_000001.10:g.104856053C>G	NC_000001.10:g.104856053C>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, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9807265	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss11340433	Jul 11, 2003 (116)
3	SSAHASNP	ss20527442	Apr 05, 2004 (121)
4	PERLEGEN	ss23853709	Sep 20, 2004 (123)
5	ABI	ss43998090	Mar 14, 2006 (126)
6	HUMANGENOME_JCVI	ss97964242	Feb 05, 2009 (130)
7	BGI	ss102770543	Dec 01, 2009 (131)
8	1000GENOMES	ss108482663	Jan 23, 2009 (130)
9	1000GENOMES	ss110941254	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118941143	Feb 15, 2009 (130)
11	ENSEMBL	ss138051056	Dec 01, 2009 (131)
12	ENSEMBL	ss139292681	Dec 01, 2009 (131)
13	GMI	ss155460425	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163804436	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss164926745	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss166939615	Jul 04, 2010 (132)
17	BUSHMAN	ss198874034	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205174456	Jul 04, 2010 (132)
19	1000GENOMES	ss218568568	Jul 14, 2010 (132)
20	1000GENOMES	ss230670896	Jul 14, 2010 (132)
21	1000GENOMES	ss238333897	Jul 15, 2010 (132)
22	BL	ss253342286	May 09, 2011 (134)
23	GMI	ss275958355	May 04, 2012 (137)
24	GMI	ss284112346	Apr 25, 2013 (138)
25	PJP	ss290587749	May 09, 2011 (134)
26	TISHKOFF	ss554513634	Apr 25, 2013 (138)
27	SSMP	ss648277699	Apr 25, 2013 (138)
28	EVA-GONL	ss975518407	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1068153734	Aug 21, 2014 (142)
30	1000GENOMES	ss1292236253	Aug 21, 2014 (142)
31	DDI	ss1425921771	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1574290691	Apr 01, 2015 (144)
33	EVA_DECODE	ss1584896703	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1600886409	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1643880442	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1794859962	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1918717859	Feb 12, 2016 (147)
38	GENOMED	ss1966828662	Jul 19, 2016 (147)
39	JJLAB	ss2019882581	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2147899561	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2165304913	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624450427	Nov 08, 2017 (151)
43	GRF	ss2697828110	Nov 08, 2017 (151)
44	GNOMAD	ss2759001586	Nov 08, 2017 (151)
45	SWEGEN	ss2987358328	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023704282	Nov 08, 2017 (151)
47	CSHL	ss3343611720	Nov 08, 2017 (151)
48	URBANLAB	ss3646740031	Oct 11, 2018 (152)
49	EGCUT_WGS	ss3655445202	Jul 12, 2019 (153)
50	EVA_DECODE	ss3687433165	Jul 12, 2019 (153)
51	ACPOP	ss3727344611	Jul 12, 2019 (153)
52	EVA	ss3746612815	Jul 12, 2019 (153)
53	PACBIO	ss3783506294	Jul 12, 2019 (153)
54	PACBIO	ss3789149959	Jul 12, 2019 (153)
55	PACBIO	ss3794022814	Jul 12, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3799614440	Jul 12, 2019 (153)
57	EVA	ss3826342931	Apr 25, 2020 (154)
58	EVA	ss3836562280	Apr 25, 2020 (154)
59	EVA	ss3841970501	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3849546115	Apr 25, 2020 (154)
61	KRGDB	ss3894629841	Apr 25, 2020 (154)
62	KOGIC	ss3945151921	Apr 25, 2020 (154)
63	TOPMED	ss4461875061	Apr 25, 2021 (155)
64	TOMMO_GENOMICS	ss5145458715	Apr 25, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5243437216	Oct 12, 2022 (156)
66	EVA	ss5320876552	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5444378878	Oct 12, 2022 (156)
68	EVA	ss5505979776	Oct 12, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5516341752	Oct 12, 2022 (156)
70	SANFORD_IMAGENETICS	ss5626198423	Oct 12, 2022 (156)
71	TOMMO_GENOMICS	ss5670664171	Oct 12, 2022 (156)
72	YY_MCH	ss5800889323	Oct 12, 2022 (156)
73	EVA	ss5832416547	Oct 12, 2022 (156)
74	EVA	ss5849046894	Oct 12, 2022 (156)
75	EVA	ss5909605343	Oct 12, 2022 (156)
76	EVA	ss5938061542	Oct 12, 2022 (156)
77	1000Genomes	NC_000001.10 - 104856053	Oct 11, 2018 (152)
78	1000Genomes_30x	NC_000001.11 - 104313431	Oct 12, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 104856053	Oct 11, 2018 (152)
80	Genetic variation in the Estonian population	NC_000001.10 - 104856053	Oct 11, 2018 (152)
81	The Danish reference pan genome	NC_000001.10 - 104856053	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000001.11 - 104313431	Apr 25, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000001.10 - 104856053	Apr 25, 2020 (154)
84	HapMap	NC_000001.11 - 104313431	Apr 25, 2020 (154)
85	KOREAN population from KRGDB	NC_000001.10 - 104856053	Apr 25, 2020 (154)
86	Korean Genome Project	NC_000001.11 - 104313431	Apr 25, 2020 (154)
87	Northern Sweden	NC_000001.10 - 104856053	Jul 12, 2019 (153)
88	Qatari	NC_000001.10 - 104856053	Apr 25, 2020 (154)
89	SGDP_PRJ	NC_000001.10 - 104856053	Apr 25, 2020 (154)
90	Siberian	NC_000001.10 - 104856053	Apr 25, 2020 (154)
91	8.3KJPN	NC_000001.10 - 104856053	Apr 25, 2021 (155)
92	14KJPN	NC_000001.11 - 104313431	Oct 12, 2022 (156)
93	TopMed	NC_000001.11 - 104313431	Apr 25, 2021 (155)
94	UK 10K study - Twins	NC_000001.10 - 104856053	Oct 11, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000001.10 - 104856053	Jul 12, 2019 (153)
96	ALFA	NC_000001.11 - 104313431	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1807235, ss3894629841	NC_000001.10:104856052:C:G	NC_000001.11:104313430:C:G	(self)
ss108482663, ss110941254, ss118941143, ss163804436, ss164926745, ss166939615, ss198874034, ss205174456, ss253342286, ss275958355, ss284112346, ss290587749, ss1584896703	NC_000001.9:104657575:C:T	NC_000001.11:104313430:C:T	(self)
3004828, 1660285, 1183450, 1643325, 721532, 1807235, 629476, 759789, 1563095, 415915, 3428022, 1660285, 358673, ss218568568, ss230670896, ss238333897, ss554513634, ss648277699, ss975518407, ss1068153734, ss1292236253, ss1425921771, ss1574290691, ss1600886409, ss1643880442, ss1794859962, ss1918717859, ss1966828662, ss2019882581, ss2147899561, ss2624450427, ss2697828110, ss2759001586, ss2987358328, ss3343611720, ss3655445202, ss3727344611, ss3746612815, ss3783506294, ss3789149959, ss3794022814, ss3826342931, ss3836562280, ss3849546115, ss3894629841, ss5145458715, ss5320876552, ss5505979776, ss5626198423, ss5832416547, ss5938061542	NC_000001.10:104856052:C:T	NC_000001.11:104313430:C:T	(self)
3867687, 21266241, 143945, 1529922, 4501275, 25481396, 7759653973, ss2165304913, ss3023704282, ss3646740031, ss3687433165, ss3799614440, ss3841970501, ss3945151921, ss4461875061, ss5243437216, ss5444378878, ss5516341752, ss5670664171, ss5800889323, ss5849046894, ss5909605343	NC_000001.11:104313430:C:T	NC_000001.11:104313430:C:T	(self)
ss20527442	NT_029860.11:932142:C:T	NC_000001.11:104313430:C:T	(self)
ss9807265, ss11340433	NT_030567.5:932143:C:T	NC_000001.11:104313430:C:T	(self)
ss23853709, ss43998090, ss97964242, ss102770543, ss138051056, ss139292681, ss155460425	NT_032977.9:74827970:C:T	NC_000001.11:104313430: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 rs6586477

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

rs6586477