Name: rs6040427
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.

rs6040427

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:11205318 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.226518 (59957/264690, TOPMED)
T=0.37028 (7379/19928, ALFA)
T=0.1785 (1143/6404, 1000G_30x) (+ 13 more)
T=0.1801 (902/5008, 1000G)
T=0.3924 (1758/4480, Estonian)
T=0.3350 (1291/3854, ALSPAC)
T=0.3412 (1265/3708, TWINSUK)
T=0.1034 (303/2930, KOREAN)
T=0.332 (331/998, GoNL)
T=0.345 (207/600, NorthernSweden)
T=0.109 (58/534, SGDP_PRJ)
T=0.183 (59/322, HapMap)
T=0.157 (34/216, Qatari)
T=0.196 (42/214, Vietnamese)
T=0.17 (8/46, Siberian)
T=0.40 (16/40, 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	19928	T=0.37028	A=0.00000, C=0.62972
European	Sub	17962	T=0.38381	A=0.00000, C=0.61619
African	Sub	372	T=0.151	A=0.000, C=0.849
African Others	Sub	16	T=0.06	A=0.00, C=0.94
African American	Sub	356	T=0.154	A=0.000, C=0.846
Asian	Sub	22	T=0.27	A=0.00, C=0.73
East Asian	Sub	18	T=0.28	A=0.00, C=0.72
Other Asian	Sub	4	T=0.2	A=0.0, C=0.8
Latin American 1	Sub	28	T=0.43	A=0.00, C=0.57
Latin American 2	Sub	114	T=0.368	A=0.000, C=0.632
South Asian	Sub	28	T=0.43	A=0.00, C=0.57
Other	Sub	1402	T=0.2546	A=0.0000, C=0.7454

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	T=0.226518	C=0.773482
Allele Frequency Aggregator	Total	Global	19928	T=0.37028	A=0.00000, C=0.62972
Allele Frequency Aggregator	European	Sub	17962	T=0.38381	A=0.00000, C=0.61619
Allele Frequency Aggregator	Other	Sub	1402	T=0.2546	A=0.0000, C=0.7454
Allele Frequency Aggregator	African	Sub	372	T=0.151	A=0.000, C=0.849
Allele Frequency Aggregator	Latin American 2	Sub	114	T=0.368	A=0.000, C=0.632
Allele Frequency Aggregator	Latin American 1	Sub	28	T=0.43	A=0.00, C=0.57
Allele Frequency Aggregator	South Asian	Sub	28	T=0.43	A=0.00, C=0.57
Allele Frequency Aggregator	Asian	Sub	22	T=0.27	A=0.00, C=0.73
1000Genomes_30x	Global	Study-wide	6404	T=0.1785	C=0.8215
1000Genomes_30x	African	Sub	1786	T=0.0577	C=0.9423
1000Genomes_30x	Europe	Sub	1266	T=0.3428	C=0.6572
1000Genomes_30x	South Asian	Sub	1202	T=0.2080	C=0.7920
1000Genomes_30x	East Asian	Sub	1170	T=0.1453	C=0.8547
1000Genomes_30x	American	Sub	980	T=0.190	C=0.810
1000Genomes	Global	Study-wide	5008	T=0.1801	C=0.8199
1000Genomes	African	Sub	1322	T=0.0613	C=0.9387
1000Genomes	East Asian	Sub	1008	T=0.1429	C=0.8571
1000Genomes	Europe	Sub	1006	T=0.3410	C=0.6590
1000Genomes	South Asian	Sub	978	T=0.211	C=0.789
1000Genomes	American	Sub	694	T=0.184	C=0.816
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3924	C=0.6076
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.3350	C=0.6650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.3412	C=0.6588
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1034	A=0.0017, C=0.8949, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.332	C=0.668
Northern Sweden	ACPOP	Study-wide	600	T=0.345	C=0.655
SGDP_PRJ	Global	Study-wide	534	T=0.109	C=0.891
HapMap	Global	Study-wide	322	T=0.183	C=0.817
HapMap	American	Sub	120	T=0.392	C=0.608
HapMap	African	Sub	114	T=0.053	C=0.947
HapMap	Asian	Sub	88	T=0.07	C=0.93
Qatari	Global	Study-wide	216	T=0.157	C=0.843
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.196	C=0.804
Siberian	Global	Study-wide	46	T=0.17	C=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.40	C=0.60

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.11205318T>A
GRCh38.p14 chr 20	NC_000020.11:g.11205318T>C
GRCh38.p14 chr 20	NC_000020.11:g.11205318T>G
GRCh37.p13 chr 20	NC_000020.10:g.11185966T>A
GRCh37.p13 chr 20	NC_000020.10:g.11185966T>C
GRCh37.p13 chr 20	NC_000020.10:g.11185966T>G

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	T=	A	C	G
GRCh38.p14 chr 20	NC_000020.11:g.11205318=	NC_000020.11:g.11205318T>A	NC_000020.11:g.11205318T>C	NC_000020.11:g.11205318T>G
GRCh37.p13 chr 20	NC_000020.10:g.11185966=	NC_000020.10:g.11185966T>A	NC_000020.10:g.11185966T>C	NC_000020.10:g.11185966T>G

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#.

80 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8349288	Apr 21, 2003 (114)
2	PERLEGEN	ss24711297	Sep 20, 2004 (123)
3	HGSV	ss77627593	Dec 07, 2007 (129)
4	HGSV	ss80706765	Dec 15, 2007 (130)
5	HGSV	ss83844951	Dec 15, 2007 (130)
6	BGI	ss106179257	Feb 05, 2009 (130)
7	1000GENOMES	ss111729839	Jan 25, 2009 (130)
8	1000GENOMES	ss113091139	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss117486468	Feb 14, 2009 (130)
10	GMI	ss156170248	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss167818272	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss169097710	Jul 04, 2010 (132)
13	BUSHMAN	ss203832572	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss208583298	Jul 04, 2010 (132)
15	1000GENOMES	ss228259932	Jul 14, 2010 (132)
16	1000GENOMES	ss237765187	Jul 15, 2010 (132)
17	1000GENOMES	ss243951212	Jul 15, 2010 (132)
18	BL	ss255484847	May 09, 2011 (134)
19	GMI	ss283302289	May 04, 2012 (137)
20	GMI	ss287423611	Apr 25, 2013 (138)
21	PJP	ss292611774	May 09, 2011 (134)
22	ILLUMINA	ss484158011	May 04, 2012 (137)
23	ILLUMINA	ss484376210	May 04, 2012 (137)
24	ILLUMINA	ss536558360	Sep 08, 2015 (146)
25	TISHKOFF	ss566139582	Apr 25, 2013 (138)
26	SSMP	ss662011006	Apr 25, 2013 (138)
27	ILLUMINA	ss780630318	Aug 21, 2014 (142)
28	ILLUMINA	ss782634411	Aug 21, 2014 (142)
29	ILLUMINA	ss836124116	Aug 21, 2014 (142)
30	EVA-GONL	ss994545589	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1082078186	Aug 21, 2014 (142)
32	1000GENOMES	ss1364088910	Aug 21, 2014 (142)
33	DDI	ss1428997565	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579439659	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1638425857	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1681419890	Apr 01, 2015 (144)
37	EVA_DECODE	ss1698601573	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1809425186	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1938055648	Feb 12, 2016 (147)
40	GENOMED	ss1969092363	Jul 19, 2016 (147)
41	JJLAB	ss2029807436	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2158360943	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2241377289	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2629400501	Nov 08, 2017 (151)
45	ILLUMINA	ss2633778065	Nov 08, 2017 (151)
46	GRF	ss2704034552	Nov 08, 2017 (151)
47	GNOMAD	ss2965498508	Nov 08, 2017 (151)
48	SWEGEN	ss3017877153	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3028736682	Nov 08, 2017 (151)
50	CSHL	ss3352422023	Nov 08, 2017 (151)
51	ILLUMINA	ss3628352655	Oct 12, 2018 (152)
52	ILLUMINA	ss3631735787	Oct 12, 2018 (152)
53	ILLUMINA	ss3642173779	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3684594881	Jul 13, 2019 (153)
55	EVA_DECODE	ss3706571293	Jul 13, 2019 (153)
56	ACPOP	ss3743254117	Jul 13, 2019 (153)
57	EVA	ss3758429376	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3821602757	Jul 13, 2019 (153)
59	EVA	ss3835590894	Apr 27, 2020 (154)
60	EVA	ss3841420395	Apr 27, 2020 (154)
61	EVA	ss3846928132	Apr 27, 2020 (154)
62	SGDP_PRJ	ss3888744338	Apr 27, 2020 (154)
63	KRGDB	ss3938934616	Apr 27, 2020 (154)
64	KOGIC	ss3981833525	Apr 27, 2020 (154)
65	KOGIC	ss3981833526	Apr 27, 2020 (154)
66	TOPMED	ss5082475799	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5228866704	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5228866705	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5308106213	Oct 13, 2022 (156)
70	EVA	ss5315995331	Oct 13, 2022 (156)
71	HUGCELL_USP	ss5500504814	Oct 13, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5614198445	Oct 13, 2022 (156)
73	SANFORD_IMAGENETICS	ss5662876951	Oct 13, 2022 (156)
74	TOMMO_GENOMICS	ss5787861844	Oct 13, 2022 (156)
75	TOMMO_GENOMICS	ss5787861845	Oct 13, 2022 (156)
76	YY_MCH	ss5817821391	Oct 13, 2022 (156)
77	EVA	ss5845452664	Oct 13, 2022 (156)
78	EVA	ss5853071563	Oct 13, 2022 (156)
79	EVA	ss5922699360	Oct 13, 2022 (156)
80	EVA	ss5957779233	Oct 13, 2022 (156)
81	1000Genomes	NC_000020.10 - 11185966	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000020.11 - 11205318	Oct 13, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 11185966	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000020.10 - 11185966	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000020.10 - 11185966	Apr 27, 2020 (154)
86	gnomAD - Genomes Submission ignored due to conflicting rows: Row 546654824 (NC_000020.11:11205317:T:A 1/140052) Row 546654825 (NC_000020.11:11205317:T:C 105457/140004)	-	Apr 26, 2021 (155)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 546654824 (NC_000020.11:11205317:T:A 1/140052) Row 546654825 (NC_000020.11:11205317:T:C 105457/140004)	-	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000020.10 - 11185966	Apr 27, 2020 (154)
89	HapMap	NC_000020.11 - 11205318	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000020.10 - 11185966	Apr 27, 2020 (154)
91	Korean Genome Project Submission ignored due to conflicting rows: Row 38211526 (NC_000020.11:11205317:T:C 1600/1832) Row 38211527 (NC_000020.11:11205317:T:A 1/1832)	-	Apr 27, 2020 (154)
92	Korean Genome Project Submission ignored due to conflicting rows: Row 38211526 (NC_000020.11:11205317:T:C 1600/1832) Row 38211527 (NC_000020.11:11205317:T:A 1/1832)	-	Apr 27, 2020 (154)
93	Northern Sweden	NC_000020.10 - 11185966	Jul 13, 2019 (153)
94	Qatari	NC_000020.10 - 11185966	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000020.10 - 11185966	Apr 27, 2020 (154)
96	Siberian	NC_000020.10 - 11185966	Apr 27, 2020 (154)
97	8.3KJPN Submission ignored due to conflicting rows: Row 86836011 (NC_000020.10:11185965:T:C 15168/16760) Row 86836012 (NC_000020.10:11185965:T:A 4/16760)	-	Apr 26, 2021 (155)
98	8.3KJPN Submission ignored due to conflicting rows: Row 86836011 (NC_000020.10:11185965:T:C 15168/16760) Row 86836012 (NC_000020.10:11185965:T:A 4/16760)	-	Apr 26, 2021 (155)
99	14KJPN Submission ignored due to conflicting rows: Row 121698948 (NC_000020.11:11205317:T:C 25538/28256) Row 121698949 (NC_000020.11:11205317:T:A 8/28256)	-	Oct 13, 2022 (156)
100	14KJPN Submission ignored due to conflicting rows: Row 121698948 (NC_000020.11:11205317:T:C 25538/28256) Row 121698949 (NC_000020.11:11205317:T:A 8/28256)	-	Oct 13, 2022 (156)
101	TopMed	NC_000020.11 - 11205318	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000020.10 - 11185966	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000020.10 - 11185966	Jul 13, 2019 (153)
104	ALFA	NC_000020.11 - 11205318	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)
rs17800130	Oct 07, 2004 (123)
rs60018082	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
46112010, ss3938934616, ss5228866705	NC_000020.10:11185965:T:A	NC_000020.11:11205317:T:A	(self)
11768741250, ss3981833526, ss5787861845	NC_000020.11:11205317:T:A	NC_000020.11:11205317:T:A	(self)
ss77627593, ss80706765, ss83844951, ss111729839, ss113091139, ss117486468, ss167818272, ss169097710, ss203832572, ss208583298, ss255484847, ss283302289, ss287423611, ss292611774, ss484158011, ss1698601573	NC_000020.9:11133965:T:C	NC_000020.11:11205317:T:C	(self)
77529236, 42919627, 30333129, 5604598, 19123594, 46112010, 16538982, 20097570, 40761318, 10877297, 42919627, 9475345, ss228259932, ss237765187, ss243951212, ss484376210, ss536558360, ss566139582, ss662011006, ss780630318, ss782634411, ss836124116, ss994545589, ss1082078186, ss1364088910, ss1428997565, ss1579439659, ss1638425857, ss1681419890, ss1809425186, ss1938055648, ss1969092363, ss2029807436, ss2158360943, ss2629400501, ss2633778065, ss2704034552, ss2965498508, ss3017877153, ss3352422023, ss3628352655, ss3631735787, ss3642173779, ss3684594881, ss3743254117, ss3758429376, ss3835590894, ss3841420395, ss3888744338, ss3938934616, ss5228866704, ss5315995331, ss5662876951, ss5845452664, ss5957779233	NC_000020.10:11185965:T:C	NC_000020.11:11205317:T:C	(self)
101724380, 2072640, 357584744, 11768741250, ss2241377289, ss3028736682, ss3706571293, ss3821602757, ss3846928132, ss3981833525, ss5082475799, ss5308106213, ss5500504814, ss5614198445, ss5787861844, ss5817821391, ss5853071563, ss5922699360	NC_000020.11:11205317:T:C	NC_000020.11:11205317:T:C	(self)
ss8349288, ss24711297, ss106179257, ss156170248	NT_011387.8:11125965:T:C	NC_000020.11:11205317:T:C	(self)
46112010, ss3938934616	NC_000020.10:11185965:T:G	NC_000020.11:11205317:T:G	(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 rs6040427

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

rs6040427