Name: rs6415001
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.

rs6415001

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:82714159 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.145075 (38400/264690, TOPMED)
A=0.141373 (19799/140048, GnomAD)
A=0.10142 (2866/28258, 14KJPN) (+ 17 more)
A=0.10424 (1969/18890, ALFA)
A=0.10095 (1692/16760, 8.3KJPN)
A=0.1596 (1022/6404, 1000G_30x)
A=0.1546 (774/5008, 1000G)
A=0.0618 (277/4480, Estonian)
A=0.0948 (277/2922, KOREAN)
A=0.0999 (183/1832, Korea1K)
A=0.043 (43/998, GoNL)
A=0.082 (49/600, NorthernSweden)
A=0.154 (50/324, HapMap)
A=0.093 (20/216, Qatari)
A=0.150 (32/214, Vietnamese)
C=0.395 (45/114, SGDP_PRJ)
A=0.00 (0/54, Ancient Sardinia)
A=0.10 (4/40, GENOME_DK)
C=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)

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=0.89576	A=0.10424
European	Sub	14286	C=0.94603	A=0.05397
African	Sub	2946	C=0.6507	A=0.3493
African Others	Sub	114	C=0.623	A=0.377
African American	Sub	2832	C=0.6518	A=0.3482
Asian	Sub	112	C=0.893	A=0.107
East Asian	Sub	86	C=0.87	A=0.13
Other Asian	Sub	26	C=0.96	A=0.04
Latin American 1	Sub	146	C=0.884	A=0.116
Latin American 2	Sub	610	C=0.936	A=0.064
South Asian	Sub	98	C=0.92	A=0.08
Other	Sub	692	C=0.866	A=0.134

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=0.854925	A=0.145075
gnomAD - Genomes	Global	Study-wide	140048	C=0.858627	A=0.141373
gnomAD - Genomes	European	Sub	75904	C=0.94633	A=0.05367
gnomAD - Genomes	African	Sub	41906	C=0.66835	A=0.33165
gnomAD - Genomes	American	Sub	13644	C=0.92678	A=0.07322
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9206	A=0.0794
gnomAD - Genomes	East Asian	Sub	3122	C=0.9090	A=0.0910
gnomAD - Genomes	Other	Sub	2148	C=0.8696	A=0.1304
14KJPN	JAPANESE	Study-wide	28258	C=0.89858	A=0.10142
Allele Frequency Aggregator	Total	Global	18890	C=0.89576	A=0.10424
Allele Frequency Aggregator	European	Sub	14286	C=0.94603	A=0.05397
Allele Frequency Aggregator	African	Sub	2946	C=0.6507	A=0.3493
Allele Frequency Aggregator	Other	Sub	692	C=0.866	A=0.134
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.936	A=0.064
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.884	A=0.116
Allele Frequency Aggregator	Asian	Sub	112	C=0.893	A=0.107
Allele Frequency Aggregator	South Asian	Sub	98	C=0.92	A=0.08
8.3KJPN	JAPANESE	Study-wide	16760	C=0.89905	A=0.10095
1000Genomes_30x	Global	Study-wide	6404	C=0.8404	A=0.1596
1000Genomes_30x	African	Sub	1786	C=0.6002	A=0.3998
1000Genomes_30x	Europe	Sub	1266	C=0.9542	A=0.0458
1000Genomes_30x	South Asian	Sub	1202	C=0.9285	A=0.0715
1000Genomes_30x	East Asian	Sub	1170	C=0.9060	A=0.0940
1000Genomes_30x	American	Sub	980	C=0.945	A=0.055
1000Genomes	Global	Study-wide	5008	C=0.8454	A=0.1546
1000Genomes	African	Sub	1322	C=0.6112	A=0.3888
1000Genomes	East Asian	Sub	1008	C=0.9048	A=0.0952
1000Genomes	Europe	Sub	1006	C=0.9523	A=0.0477
1000Genomes	South Asian	Sub	978	C=0.923	A=0.077
1000Genomes	American	Sub	694	C=0.941	A=0.059
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9382	A=0.0618
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9052	A=0.0948
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9001	A=0.0999
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.957	A=0.043
Northern Sweden	ACPOP	Study-wide	600	C=0.918	A=0.082
HapMap	Global	Study-wide	324	C=0.846	A=0.154
HapMap	American	Sub	120	C=0.950	A=0.050
HapMap	African	Sub	114	C=0.693	A=0.307
HapMap	Asian	Sub	90	C=0.90	A=0.10
Qatari	Global	Study-wide	216	C=0.907	A=0.093
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.850	A=0.150
SGDP_PRJ	Global	Study-wide	114	C=0.395	A=0.605
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	54	C=1.00	A=0.00
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	A=0.10
Siberian	Global	Study-wide	6	C=0.5	A=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 6	NC_000006.12:g.82714159C>A
GRCh37.p13 chr 6	NC_000006.11:g.83423876C>A

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
GRCh38.p14 chr 6	NC_000006.12:g.82714159=	NC_000006.12:g.82714159C>A
GRCh37.p13 chr 6	NC_000006.11:g.83423876=	NC_000006.11:g.83423876C>A

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#.

56 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10271498	Jul 11, 2003 (116)
2	SC_SNP	ss11121489	Jul 11, 2003 (116)
3	WI_SSAHASNP	ss11771665	Jul 11, 2003 (116)
4	SC_SNP	ss12818872	Dec 05, 2003 (119)
5	BGI	ss104331795	Dec 01, 2009 (131)
6	ILLUMINA-UK	ss116578093	Feb 14, 2009 (130)
7	BUSHMAN	ss202101555	Jul 04, 2010 (132)
8	1000GENOMES	ss211874953	Jul 14, 2010 (132)
9	1000GENOMES	ss222507031	Jul 14, 2010 (132)
10	1000GENOMES	ss233561462	Jul 15, 2010 (132)
11	1000GENOMES	ss240600387	Jul 15, 2010 (132)
12	PJP	ss293650786	May 09, 2011 (134)
13	TISHKOFF	ss559333223	Apr 25, 2013 (138)
14	SSMP	ss653299514	Apr 25, 2013 (138)
15	EVA-GONL	ss983165480	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1073784778	Aug 21, 2014 (142)
17	1000GENOMES	ss1321006584	Aug 21, 2014 (142)
18	DDI	ss1430801840	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1581767266	Apr 01, 2015 (144)
20	EVA_DECODE	ss1592713992	Apr 01, 2015 (144)
21	HAMMER_LAB	ss1804532707	Sep 08, 2015 (146)
22	WEILL_CORNELL_DGM	ss1926424881	Feb 12, 2016 (147)
23	JJLAB	ss2023855460	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2152047794	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2285683087	Dec 20, 2016 (150)
26	SYSTEMSBIOZJU	ss2626423202	Nov 08, 2017 (151)
27	GRF	ss2707663708	Nov 08, 2017 (151)
28	GNOMAD	ss2841462888	Nov 08, 2017 (151)
29	SWEGEN	ss2999440753	Nov 08, 2017 (151)
30	CSHL	ss3347083288	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3645967925	Oct 12, 2018 (152)
32	EGCUT_WGS	ss3667317377	Jul 13, 2019 (153)
33	EVA_DECODE	ss3717647802	Jul 13, 2019 (153)
34	ACPOP	ss3733704778	Jul 13, 2019 (153)
35	EVA	ss3765285176	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3808436003	Jul 13, 2019 (153)
37	EVA	ss3830039631	Apr 26, 2020 (154)
38	SGDP_PRJ	ss3865045674	Apr 26, 2020 (154)
39	KRGDB	ss3911928728	Apr 26, 2020 (154)
40	KOGIC	ss3959466722	Apr 26, 2020 (154)
41	EVA	ss3985233899	Apr 26, 2021 (155)
42	TOPMED	ss4710601902	Apr 26, 2021 (155)
43	TOMMO_GENOMICS	ss5178493795	Apr 26, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5269228225	Oct 13, 2022 (156)
45	EVA	ss5366992733	Oct 13, 2022 (156)
46	HUGCELL_USP	ss5466784027	Oct 13, 2022 (156)
47	EVA	ss5508591629	Oct 13, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5555567242	Oct 13, 2022 (156)
49	SANFORD_IMAGENETICS	ss5640852966	Oct 13, 2022 (156)
50	TOMMO_GENOMICS	ss5716960078	Oct 13, 2022 (156)
51	YY_MCH	ss5807678675	Oct 13, 2022 (156)
52	EVA	ss5842558630	Oct 13, 2022 (156)
53	EVA	ss5855447898	Oct 13, 2022 (156)
54	EVA	ss5884674510	Oct 13, 2022 (156)
55	EVA	ss5969352274	Oct 13, 2022 (156)
56	EVA	ss5980379210	Oct 13, 2022 (156)
57	1000Genomes	NC_000006.11 - 83423876	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000006.12 - 82714159	Oct 13, 2022 (156)
59	Genetic variation in the Estonian population	NC_000006.11 - 83423876	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000006.11 - 83423876	Apr 26, 2020 (154)
61	gnomAD - Genomes	NC_000006.12 - 82714159	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000006.11 - 83423876	Apr 26, 2020 (154)
63	HapMap	NC_000006.12 - 82714159	Apr 26, 2020 (154)
64	KOREAN population from KRGDB	NC_000006.11 - 83423876	Apr 26, 2020 (154)
65	Korean Genome Project	NC_000006.12 - 82714159	Apr 26, 2020 (154)
66	Northern Sweden	NC_000006.11 - 83423876	Jul 13, 2019 (153)
67	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 83423876	Apr 26, 2021 (155)
68	Qatari	NC_000006.11 - 83423876	Apr 26, 2020 (154)
69	SGDP_PRJ	NC_000006.11 - 83423876	Apr 26, 2020 (154)
70	Siberian	NC_000006.11 - 83423876	Apr 26, 2020 (154)
71	8.3KJPN	NC_000006.11 - 83423876	Apr 26, 2021 (155)
72	14KJPN	NC_000006.12 - 82714159	Oct 13, 2022 (156)
73	TopMed	NC_000006.12 - 82714159	Apr 26, 2021 (155)
74	A Vietnamese Genetic Variation Database	NC_000006.11 - 83423876	Jul 13, 2019 (153)
75	ALFA	NC_000006.12 - 82714159	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss116578093, ss202101555, ss211874953, ss293650786, ss1592713992	NC_000006.10:83480594:C:A	NC_000006.12:82714158:C:A	(self)
32827175, 13055625, 7932205, 8148296, 19106122, 6989643, 459826, 8466811, 17062654, 4564148, 36463102, 4065420, ss222507031, ss233561462, ss240600387, ss559333223, ss653299514, ss983165480, ss1073784778, ss1321006584, ss1430801840, ss1581767266, ss1804532707, ss1926424881, ss2023855460, ss2152047794, ss2626423202, ss2707663708, ss2841462888, ss2999440753, ss3347083288, ss3667317377, ss3733704778, ss3765285176, ss3830039631, ss3865045674, ss3911928728, ss3985233899, ss5178493795, ss5366992733, ss5508591629, ss5640852966, ss5842558630, ss5969352274, ss5980379210	NC_000006.11:83423875:C:A	NC_000006.12:82714158:C:A	(self)
43093177, 231660194, 3178802, 15844723, 50797182, 547979460, 13745399636, ss2285683087, ss3645967925, ss3717647802, ss3808436003, ss3959466722, ss4710601902, ss5269228225, ss5466784027, ss5555567242, ss5716960078, ss5807678675, ss5855447898, ss5884674510	NC_000006.12:82714158:C:A	NC_000006.12:82714158:C:A	(self)
ss10271498, ss11121489, ss11771665	NT_007299.12:21244046:C:A	NC_000006.12:82714158:C:A	(self)
ss12818872, ss104331795	NT_007299.13:21543709:C:A	NC_000006.12:82714158:C:A	(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 rs6415001

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

rs6415001