Name: rs6005401
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.

rs6005401

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:27366738 (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: C=0.489573 (129585/264690, TOPMED)
C=0.464096 (64966/139984, GnomAD)
G=0.36680 (10365/28258, 14KJPN) (+ 17 more)
C=0.39183 (7067/18036, ALFA)
G=0.36695 (6150/16760, 8.3KJPN)
G=0.4247 (2720/6404, 1000G_30x)
G=0.4295 (2151/5008, 1000G)
C=0.3268 (1464/4480, Estonian)
C=0.3275 (1262/3854, ALSPAC)
C=0.3261 (1209/3708, TWINSUK)
G=0.3966 (1162/2930, KOREAN)
G=0.4121 (755/1832, Korea1K)
G=0.3989 (706/1770, HapMap)
C=0.318 (317/998, GoNL)
C=0.273 (164/600, NorthernSweden)
G=0.299 (129/432, SGDP_PRJ)
C=0.454 (98/216, Qatari)
G=0.407 (88/216, Vietnamese)
G=0.43 (18/42, Siberian)
C=0.42 (17/40, 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	18036	G=0.60817	A=0.00000, C=0.39183
European	Sub	13900	G=0.67101	A=0.00000, C=0.32899
African	Sub	2480	G=0.3407	A=0.0000, C=0.6593
African Others	Sub	90	G=0.26	A=0.00, C=0.74
African American	Sub	2390	G=0.3439	A=0.0000, C=0.6561
Asian	Sub	112	G=0.402	A=0.000, C=0.598
East Asian	Sub	86	G=0.38	A=0.00, C=0.62
Other Asian	Sub	26	G=0.46	A=0.00, C=0.54
Latin American 1	Sub	146	G=0.534	A=0.000, C=0.466
Latin American 2	Sub	610	G=0.441	A=0.000, C=0.559
South Asian	Sub	98	G=0.48	A=0.00, C=0.52
Other	Sub	690	G=0.519	A=0.000, C=0.481

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=0.510427	C=0.489573
gnomAD - Genomes	Global	Study-wide	139984	G=0.535904	C=0.464096
gnomAD - Genomes	European	Sub	75810	G=0.66646	C=0.33354
gnomAD - Genomes	African	Sub	41946	G=0.32611	C=0.67389
gnomAD - Genomes	American	Sub	13642	G=0.47163	C=0.52837
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.6028	C=0.3972
gnomAD - Genomes	East Asian	Sub	3124	G=0.3985	C=0.6015
gnomAD - Genomes	Other	Sub	2144	G=0.5299	C=0.4701
14KJPN	JAPANESE	Study-wide	28258	G=0.36680	C=0.63320
Allele Frequency Aggregator	Total	Global	18036	G=0.60817	A=0.00000, C=0.39183
Allele Frequency Aggregator	European	Sub	13900	G=0.67101	A=0.00000, C=0.32899
Allele Frequency Aggregator	African	Sub	2480	G=0.3407	A=0.0000, C=0.6593
Allele Frequency Aggregator	Other	Sub	690	G=0.519	A=0.000, C=0.481
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.441	A=0.000, C=0.559
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.534	A=0.000, C=0.466
Allele Frequency Aggregator	Asian	Sub	112	G=0.402	A=0.000, C=0.598
Allele Frequency Aggregator	South Asian	Sub	98	G=0.48	A=0.00, C=0.52
8.3KJPN	JAPANESE	Study-wide	16760	G=0.36695	C=0.63305
1000Genomes_30x	Global	Study-wide	6404	G=0.4247	C=0.5753
1000Genomes_30x	African	Sub	1786	G=0.2660	C=0.7340
1000Genomes_30x	Europe	Sub	1266	G=0.6517	C=0.3483
1000Genomes_30x	South Asian	Sub	1202	G=0.4551	C=0.5449
1000Genomes_30x	East Asian	Sub	1170	G=0.4009	C=0.5991
1000Genomes_30x	American	Sub	980	G=0.412	C=0.588
1000Genomes	Global	Study-wide	5008	G=0.4295	C=0.5705
1000Genomes	African	Sub	1322	G=0.2663	C=0.7337
1000Genomes	East Asian	Sub	1008	G=0.3998	C=0.6002
1000Genomes	Europe	Sub	1006	G=0.6581	C=0.3419
1000Genomes	South Asian	Sub	978	G=0.453	C=0.547
1000Genomes	American	Sub	694	G=0.419	C=0.581
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6732	C=0.3268
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6725	C=0.3275
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6739	C=0.3261
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3966	C=0.6034, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4121	C=0.5879
HapMap	Global	Study-wide	1770	G=0.3989	C=0.6011
HapMap	African	Sub	692	G=0.264	C=0.736
HapMap	American	Sub	656	G=0.511	C=0.489
HapMap	Asian	Sub	250	G=0.352	C=0.648
HapMap	Europe	Sub	172	G=0.581	C=0.419
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.682	C=0.318
Northern Sweden	ACPOP	Study-wide	600	G=0.727	C=0.273
SGDP_PRJ	Global	Study-wide	432	G=0.299	C=0.701
Qatari	Global	Study-wide	216	G=0.546	C=0.454
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.407	C=0.593
Siberian	Global	Study-wide	42	G=0.43	C=0.57
The Danish reference pan genome	Danish	Study-wide	40	G=0.57	C=0.42

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 22	NC_000022.11:g.27366738G>A
GRCh38.p14 chr 22	NC_000022.11:g.27366738G>C
GRCh38.p14 chr 22	NC_000022.11:g.27366738G>T
GRCh37.p13 chr 22	NC_000022.10:g.27762699G>A
GRCh37.p13 chr 22	NC_000022.10:g.27762699G>C
GRCh37.p13 chr 22	NC_000022.10:g.27762699G>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	G=	A	C	T
GRCh38.p14 chr 22	NC_000022.11:g.27366738=	NC_000022.11:g.27366738G>A	NC_000022.11:g.27366738G>C	NC_000022.11:g.27366738G>T
GRCh37.p13 chr 22	NC_000022.10:g.27762699=	NC_000022.10:g.27762699G>A	NC_000022.10:g.27762699G>C	NC_000022.10:g.27762699G>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	SC_SNP	ss8302400	Apr 21, 2003 (114)
2	CSHL-HAPMAP	ss16930276	Feb 27, 2004 (120)
3	SSAHASNP	ss21837493	Apr 05, 2004 (121)
4	PERLEGEN	ss24553740	Sep 20, 2004 (123)
5	AFFY	ss76529715	Dec 08, 2007 (130)
6	HGSV	ss86207893	Dec 15, 2007 (130)
7	HUMANGENOME_JCVI	ss96096545	Feb 05, 2009 (130)
8	BGI	ss103850717	Dec 01, 2009 (131)
9	KRIBB_YJKIM	ss104917754	Feb 05, 2009 (130)
10	1000GENOMES	ss112594110	Jan 25, 2009 (130)
11	1000GENOMES	ss114113046	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss117382718	Feb 14, 2009 (130)
13	ENSEMBL	ss142877839	Dec 01, 2009 (131)
14	GMI	ss157104644	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss167804008	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss169051982	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss171896382	Jul 04, 2010 (132)
18	BUSHMAN	ss204068879	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208832873	Jul 04, 2010 (132)
20	1000GENOMES	ss228647739	Jul 14, 2010 (132)
21	1000GENOMES	ss238044186	Jul 15, 2010 (132)
22	1000GENOMES	ss244169215	Jul 15, 2010 (132)
23	GMI	ss283612571	May 04, 2012 (137)
24	GMI	ss287558982	Apr 25, 2013 (138)
25	PJP	ss292748348	May 09, 2011 (134)
26	TISHKOFF	ss566597675	Apr 25, 2013 (138)
27	SSMP	ss662527550	Apr 25, 2013 (138)
28	EVA-GONL	ss995282919	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1082611076	Aug 21, 2014 (142)
30	1000GENOMES	ss1366912775	Aug 21, 2014 (142)
31	DDI	ss1429238841	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1579726751	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1639860120	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1682854153	Apr 01, 2015 (144)
35	EVA_DECODE	ss1699351540	Apr 01, 2015 (144)
36	EVA_SVP	ss1713735968	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1809761290	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1938850316	Feb 12, 2016 (147)
39	GENOMED	ss1969259655	Jul 19, 2016 (147)
40	JJLAB	ss2030196886	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2158811575	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2246811819	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2629597233	Nov 08, 2017 (151)
44	GRF	ss2704561629	Nov 08, 2017 (151)
45	GNOMAD	ss2973660612	Nov 08, 2017 (151)
46	SWEGEN	ss3019197503	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3028936127	Nov 08, 2017 (151)
48	CSHL	ss3352807548	Nov 08, 2017 (151)
49	URBANLAB	ss3651166352	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3685694226	Jul 13, 2019 (153)
51	EVA_DECODE	ss3708068727	Jul 13, 2019 (153)
52	ACPOP	ss3743875726	Jul 13, 2019 (153)
53	EVA	ss3759303233	Jul 13, 2019 (153)
54	PACBIO	ss3788810949	Jul 13, 2019 (153)
55	PACBIO	ss3793679694	Jul 13, 2019 (153)
56	PACBIO	ss3798566115	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3822469703	Jul 13, 2019 (153)
58	EVA	ss3835957761	Apr 27, 2020 (154)
59	EVA	ss3841607768	Apr 27, 2020 (154)
60	EVA	ss3847122465	Apr 27, 2020 (154)
61	SGDP_PRJ	ss3890411000	Apr 27, 2020 (154)
62	KRGDB	ss3940807586	Apr 27, 2020 (154)
63	KOGIC	ss3983507769	Apr 27, 2020 (154)
64	TOPMED	ss5106961381	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5232328705	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5310875744	Oct 16, 2022 (156)
67	EVA	ss5440895430	Oct 16, 2022 (156)
68	HUGCELL_USP	ss5502738191	Oct 16, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5618327246	Oct 16, 2022 (156)
70	SANFORD_IMAGENETICS	ss5664370660	Oct 16, 2022 (156)
71	TOMMO_GENOMICS	ss5793353974	Oct 16, 2022 (156)
72	YY_MCH	ss5818655934	Oct 16, 2022 (156)
73	EVA	ss5821983152	Oct 16, 2022 (156)
74	EVA	ss5853369998	Oct 16, 2022 (156)
75	EVA	ss5881566901	Oct 16, 2022 (156)
76	EVA	ss5959220438	Oct 16, 2022 (156)
77	1000Genomes	NC_000022.10 - 27762699	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000022.11 - 27366738	Oct 16, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 27762699	Oct 12, 2018 (152)
80	Genetic variation in the Estonian population	NC_000022.10 - 27762699	Oct 12, 2018 (152)
81	The Danish reference pan genome	NC_000022.10 - 27762699	Apr 27, 2020 (154)
82	gnomAD - Genomes	NC_000022.11 - 27366738	Apr 26, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000022.10 - 27762699	Apr 27, 2020 (154)
84	HapMap	NC_000022.11 - 27366738	Apr 27, 2020 (154)
85	KOREAN population from KRGDB	NC_000022.10 - 27762699	Apr 27, 2020 (154)
86	Korean Genome Project	NC_000022.11 - 27366738	Apr 27, 2020 (154)
87	Northern Sweden	NC_000022.10 - 27762699	Jul 13, 2019 (153)
88	Qatari	NC_000022.10 - 27762699	Apr 27, 2020 (154)
89	SGDP_PRJ	NC_000022.10 - 27762699	Apr 27, 2020 (154)
90	Siberian	NC_000022.10 - 27762699	Apr 27, 2020 (154)
91	8.3KJPN	NC_000022.10 - 27762699	Apr 26, 2021 (155)
92	14KJPN	NC_000022.11 - 27366738	Oct 16, 2022 (156)
93	TopMed	NC_000022.11 - 27366738	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000022.10 - 27762699	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000022.10 - 27762699	Jul 13, 2019 (153)
96	ALFA	NC_000022.11 - 27366738	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)
rs17440375	Oct 07, 2004 (123)
rs56613527	May 25, 2008 (130)
rs59201884	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
12470108692	NC_000022.11:27366737:G:A	NC_000022.11:27366737:G:A	(self)
ss86207893	NC_000022.8:26087252:G:C	NC_000022.11:27366737:G:C	(self)
ss76529715, ss112594110, ss114113046, ss117382718, ss167804008, ss169051982, ss171896382, ss204068879, ss208832873, ss283612571, ss287558982, ss292748348, ss1699351540, ss1713735968	NC_000022.9:26092698:G:C	NC_000022.11:27366737:G:C	(self)
80455454, 44500194, 31432474, 5891690, 19830050, 47984980, 17160591, 20892238, 42427980, 11327929, 90298012, 44500194, 9819533, ss228647739, ss238044186, ss244169215, ss566597675, ss662527550, ss995282919, ss1082611076, ss1366912775, ss1429238841, ss1579726751, ss1639860120, ss1682854153, ss1809761290, ss1938850316, ss1969259655, ss2030196886, ss2158811575, ss2629597233, ss2704561629, ss2973660612, ss3019197503, ss3352807548, ss3685694226, ss3743875726, ss3759303233, ss3788810949, ss3793679694, ss3798566115, ss3835957761, ss3841607768, ss3890411000, ss3940807586, ss5232328705, ss5440895430, ss5664370660, ss5821983152, ss5959220438	NC_000022.10:27762698:G:C	NC_000022.11:27366737:G:C	(self)
105853181, 568121912, 2240269, 39885770, 127191078, 382070328, 12470108692, ss2246811819, ss3028936127, ss3651166352, ss3708068727, ss3822469703, ss3847122465, ss3983507769, ss5106961381, ss5310875744, ss5502738191, ss5618327246, ss5793353974, ss5818655934, ss5853369998, ss5881566901	NC_000022.11:27366737:G:C	NC_000022.11:27366737:G:C	(self)
ss16930276, ss21837493	NT_011520.9:7153267:G:C	NC_000022.11:27366737:G:C	(self)
ss8302400, ss24553740, ss96096545, ss103850717, ss104917754, ss142877839, ss157104644	NT_011520.12:7153267:G:C	NC_000022.11:27366737:G:C	(self)
47984980, ss3940807586	NC_000022.10:27762698:G:T	NC_000022.11:27366737: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 rs6005401

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

rs6005401