Name: rs1566141
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.

rs1566141

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99271303 (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: A>C / A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.270369 (71564/264690, TOPMED)
G=0.257433 (36038/139990, GnomAD)
G=0.242167 (28891/119302, ALFA) (+ 16 more)
A=0.17496 (4944/28258, 14KJPN)
A=0.17291 (2898/16760, 8.3KJPN)
G=0.3863 (2474/6404, 1000G_30x)
G=0.4002 (2004/5008, 1000G)
G=0.2326 (1042/4480, Estonian)
G=0.2462 (949/3854, ALSPAC)
G=0.2344 (869/3708, TWINSUK)
A=0.2007 (588/2930, KOREAN)
A=0.1883 (345/1832, Korea1K)
G=0.236 (236/998, GoNL)
G=0.190 (114/600, NorthernSweden)
A=0.345 (96/278, SGDP_PRJ)
G=0.264 (57/216, Qatari)
G=0.480 (98/204, HapMap)
G=0.30 (12/40, GENOME_DK)
A=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	119302	A=0.757833	C=0.000000, G=0.242167	0.58108	0.065414	0.353506	32
European	Sub	106912	A=0.754237	C=0.000000, G=0.245763	0.573425	0.064951	0.361625	18
African	Sub	3824	A=0.8287	C=0.0000, G=0.1713	0.70659	0.049163	0.244247	20
African Others	Sub	158	A=0.848	C=0.000, G=0.152	0.721519	0.025316	0.253165	0
African American	Sub	3666	A=0.8279	C=0.0000, G=0.1721	0.705947	0.050191	0.243863	21
Asian	Sub	228	A=0.224	C=0.000, G=0.776	0.061404	0.614035	0.324561	0
East Asian	Sub	150	A=0.200	C=0.000, G=0.800	0.04	0.64	0.32	32
Other Asian	Sub	78	A=0.27	C=0.00, G=0.73	0.102564	0.564103	0.333333	1
Latin American 1	Sub	576	A=0.776	C=0.000, G=0.224	0.621528	0.069444	0.309028	2
Latin American 2	Sub	1826	A=0.8740	C=0.0000, G=0.1260	0.768894	0.020811	0.210296	1
South Asian	Sub	94	A=0.68	C=0.00, G=0.32	0.489362	0.12766	0.382979	0
Other	Sub	5842	A=0.7612	C=0.0000, G=0.2388	0.598083	0.075659	0.326258	17

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	A=0.729631	G=0.270369
gnomAD - Genomes	Global	Study-wide	139990	A=0.742567	G=0.257433
gnomAD - Genomes	European	Sub	75834	A=0.76842	G=0.23158
gnomAD - Genomes	African	Sub	41916	A=0.71763	G=0.28237
gnomAD - Genomes	American	Sub	13646	A=0.80133	G=0.19867
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.7512	G=0.2488
gnomAD - Genomes	East Asian	Sub	3120	A=0.1971	G=0.8029
gnomAD - Genomes	Other	Sub	2150	A=0.7223	G=0.2777
Allele Frequency Aggregator	Total	Global	119302	A=0.757833	C=0.000000, G=0.242167
Allele Frequency Aggregator	European	Sub	106912	A=0.754237	C=0.000000, G=0.245763
Allele Frequency Aggregator	Other	Sub	5842	A=0.7612	C=0.0000, G=0.2388
Allele Frequency Aggregator	African	Sub	3824	A=0.8287	C=0.0000, G=0.1713
Allele Frequency Aggregator	Latin American 2	Sub	1826	A=0.8740	C=0.0000, G=0.1260
Allele Frequency Aggregator	Latin American 1	Sub	576	A=0.776	C=0.000, G=0.224
Allele Frequency Aggregator	Asian	Sub	228	A=0.224	C=0.000, G=0.776
Allele Frequency Aggregator	South Asian	Sub	94	A=0.68	C=0.00, G=0.32
14KJPN	JAPANESE	Study-wide	28258	A=0.17496	G=0.82504
8.3KJPN	JAPANESE	Study-wide	16760	A=0.17291	G=0.82709
1000Genomes_30x	Global	Study-wide	6404	A=0.6137	G=0.3863
1000Genomes_30x	African	Sub	1786	A=0.7503	G=0.2497
1000Genomes_30x	Europe	Sub	1266	A=0.7370	G=0.2630
1000Genomes_30x	South Asian	Sub	1202	A=0.5000	G=0.5000
1000Genomes_30x	East Asian	Sub	1170	A=0.2068	G=0.7932
1000Genomes_30x	American	Sub	980	A=0.831	G=0.169
1000Genomes	Global	Study-wide	5008	A=0.5998	G=0.4002
1000Genomes	African	Sub	1322	A=0.7504	G=0.2496
1000Genomes	East Asian	Sub	1008	A=0.2014	G=0.7986
1000Genomes	Europe	Sub	1006	A=0.7455	G=0.2545
1000Genomes	South Asian	Sub	978	A=0.501	G=0.499
1000Genomes	American	Sub	694	A=0.820	G=0.180
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7674	G=0.2326
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7538	G=0.2462
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7656	G=0.2344
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.2007	G=0.7993, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.1883	G=0.8117
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.764	G=0.236
Northern Sweden	ACPOP	Study-wide	600	A=0.810	G=0.190
SGDP_PRJ	Global	Study-wide	278	A=0.345	G=0.655
Qatari	Global	Study-wide	216	A=0.736	G=0.264
HapMap	Global	Study-wide	204	A=0.520	G=0.480
HapMap	African	Sub	120	A=0.717	G=0.283
HapMap	Asian	Sub	84	A=0.24	G=0.76
The Danish reference pan genome	Danish	Study-wide	40	A=0.70	G=0.30
Siberian	Global	Study-wide	20	A=0.40	G=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 4	NC_000004.12:g.99271303A>C
GRCh38.p14 chr 4	NC_000004.12:g.99271303A>G
GRCh38.p14 chr 4	NC_000004.12:g.99271303A>T
GRCh37.p13 chr 4	NC_000004.11:g.100192460A>C
GRCh37.p13 chr 4	NC_000004.11:g.100192460A>G
GRCh37.p13 chr 4	NC_000004.11:g.100192460A>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	N/A	Intron 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	A=	C	G	T
GRCh38.p14 chr 4	NC_000004.12:g.99271303=	NC_000004.12:g.99271303A>C	NC_000004.12:g.99271303A>G	NC_000004.12:g.99271303A>T
GRCh37.p13 chr 4	NC_000004.11:g.100192460=	NC_000004.11:g.100192460A>C	NC_000004.11:g.100192460A>G	NC_000004.11:g.100192460A>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#.

95 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2410214	Oct 23, 2000 (88)
2	TSC-CSHL	ss5493072	Oct 08, 2002 (108)
3	WI_SSAHASNP	ss11671093	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss17023503	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss17802415	Feb 27, 2004 (120)
6	ABI	ss42285470	Mar 14, 2006 (126)
7	HGSV	ss83074296	Dec 14, 2007 (130)
8	BCMHGSC_JDW	ss92703340	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98986832	Feb 04, 2009 (130)
10	BGI	ss105848316	Feb 04, 2009 (130)
11	1000GENOMES	ss108171082	Jan 23, 2009 (130)
12	1000GENOMES	ss110291839	Jan 24, 2009 (130)
13	ENSEMBL	ss135207833	Dec 01, 2009 (131)
14	ENSEMBL	ss139782236	Dec 01, 2009 (131)
15	GMI	ss157650842	Dec 01, 2009 (131)
16	ILLUMINA	ss160374001	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162380349	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss163917477	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss206398582	Jul 04, 2010 (132)
20	1000GENOMES	ss221098815	Jul 14, 2010 (132)
21	1000GENOMES	ss232515162	Jul 14, 2010 (132)
22	1000GENOMES	ss239780140	Jul 15, 2010 (132)
23	GMI	ss277844465	May 04, 2012 (137)
24	GMI	ss284967900	Apr 25, 2013 (138)
25	PJP	ss293147543	May 09, 2011 (134)
26	ILLUMINA	ss480038392	May 04, 2012 (137)
27	ILLUMINA	ss480047023	May 04, 2012 (137)
28	ILLUMINA	ss480713414	Sep 08, 2015 (146)
29	ILLUMINA	ss484817248	May 04, 2012 (137)
30	ILLUMINA	ss536895815	Sep 08, 2015 (146)
31	TISHKOFF	ss557721273	Apr 25, 2013 (138)
32	SSMP	ss651525794	Apr 25, 2013 (138)
33	ILLUMINA	ss778813670	Sep 08, 2015 (146)
34	ILLUMINA	ss782855184	Sep 08, 2015 (146)
35	ILLUMINA	ss783819644	Sep 08, 2015 (146)
36	ILLUMINA	ss832109114	Sep 08, 2015 (146)
37	ILLUMINA	ss834273956	Sep 08, 2015 (146)
38	EVA-GONL	ss980450346	Aug 21, 2014 (142)
39	JMKIDD_LAB	ss1071787275	Aug 21, 2014 (142)
40	1000GENOMES	ss1310980600	Aug 21, 2014 (142)
41	EVA_GENOME_DK	ss1580687528	Apr 01, 2015 (144)
42	EVA_DECODE	ss1589954382	Apr 01, 2015 (144)
43	EVA_UK10K_ALSPAC	ss1610736712	Apr 01, 2015 (144)
44	EVA_UK10K_TWINSUK	ss1653730745	Apr 01, 2015 (144)
45	ILLUMINA	ss1752489163	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1923690384	Feb 12, 2016 (147)
47	GENOMED	ss1969816859	Jul 19, 2016 (147)
48	JJLAB	ss2022431165	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2150560336	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2265426888	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2625714516	Nov 08, 2017 (151)
52	ILLUMINA	ss2634154528	Nov 08, 2017 (151)
53	GRF	ss2706037159	Nov 08, 2017 (151)
54	GNOMAD	ss2812856757	Nov 08, 2017 (151)
55	SWEGEN	ss2995210837	Nov 08, 2017 (151)
56	BIOINF_KMB_FNS_UNIBA	ss3024990848	Nov 08, 2017 (151)
57	CSHL	ss3345861916	Nov 08, 2017 (151)
58	ILLUMINA	ss3629025526	Oct 12, 2018 (152)
59	ILLUMINA	ss3632088886	Oct 12, 2018 (152)
60	ILLUMINA	ss3633343316	Oct 12, 2018 (152)
61	ILLUMINA	ss3634062619	Oct 12, 2018 (152)
62	ILLUMINA	ss3634963418	Oct 12, 2018 (152)
63	ILLUMINA	ss3635745347	Oct 12, 2018 (152)
64	ILLUMINA	ss3636667727	Oct 12, 2018 (152)
65	ILLUMINA	ss3637497884	Oct 12, 2018 (152)
66	ILLUMINA	ss3640670712	Oct 12, 2018 (152)
67	URBANLAB	ss3647802693	Oct 12, 2018 (152)
68	EGCUT_WGS	ss3663106691	Jul 13, 2019 (153)
69	EVA_DECODE	ss3712657225	Jul 13, 2019 (153)
70	ACPOP	ss3731422001	Jul 13, 2019 (153)
71	ILLUMINA	ss3745263678	Jul 13, 2019 (153)
72	EVA	ss3762167277	Jul 13, 2019 (153)
73	ILLUMINA	ss3772758216	Jul 13, 2019 (153)
74	KHV_HUMAN_GENOMES	ss3805315708	Jul 13, 2019 (153)
75	EVA	ss3828703663	Apr 26, 2020 (154)
76	SGDP_PRJ	ss3859611036	Apr 26, 2020 (154)
77	KRGDB	ss3905888575	Apr 26, 2020 (154)
78	KOGIC	ss3954742628	Apr 26, 2020 (154)
79	EVA	ss4017159543	Apr 26, 2021 (155)
80	TOPMED	ss4624647580	Apr 26, 2021 (155)
81	TOMMO_GENOMICS	ss5167079273	Apr 26, 2021 (155)
82	1000G_HIGH_COVERAGE	ss5260289159	Oct 13, 2022 (156)
83	EVA	ss5314977539	Oct 13, 2022 (156)
84	EVA	ss5350977573	Oct 13, 2022 (156)
85	HUGCELL_USP	ss5458931532	Oct 13, 2022 (156)
86	EVA	ss5507641591	Oct 13, 2022 (156)
87	1000G_HIGH_COVERAGE	ss5541957415	Oct 13, 2022 (156)
88	SANFORD_IMAGENETICS	ss5635665999	Oct 13, 2022 (156)
89	TOMMO_GENOMICS	ss5701810764	Oct 13, 2022 (156)
90	EVA	ss5799622234	Oct 13, 2022 (156)
91	YY_MCH	ss5805354148	Oct 13, 2022 (156)
92	EVA	ss5844424521	Oct 13, 2022 (156)
93	EVA	ss5854356059	Oct 13, 2022 (156)
94	EVA	ss5864677843	Oct 13, 2022 (156)
95	EVA	ss5964056715	Oct 13, 2022 (156)
96	1000Genomes	NC_000004.11 - 100192460	Oct 12, 2018 (152)
97	1000Genomes_30x	NC_000004.12 - 99271303	Oct 13, 2022 (156)
98	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100192460	Oct 12, 2018 (152)
99	Genetic variation in the Estonian population	NC_000004.11 - 100192460	Oct 12, 2018 (152)
100	The Danish reference pan genome	NC_000004.11 - 100192460	Apr 26, 2020 (154)
101	gnomAD - Genomes	NC_000004.12 - 99271303	Apr 26, 2021 (155)
102	Genome of the Netherlands Release 5	NC_000004.11 - 100192460	Apr 26, 2020 (154)
103	HapMap	NC_000004.12 - 99271303	Apr 26, 2020 (154)
104	KOREAN population from KRGDB	NC_000004.11 - 100192460	Apr 26, 2020 (154)
105	Korean Genome Project	NC_000004.12 - 99271303	Apr 26, 2020 (154)
106	Northern Sweden	NC_000004.11 - 100192460	Jul 13, 2019 (153)
107	Qatari	NC_000004.11 - 100192460	Apr 26, 2020 (154)
108	SGDP_PRJ	NC_000004.11 - 100192460	Apr 26, 2020 (154)
109	Siberian	NC_000004.11 - 100192460	Apr 26, 2020 (154)
110	8.3KJPN	NC_000004.11 - 100192460	Apr 26, 2021 (155)
111	14KJPN	NC_000004.12 - 99271303	Oct 13, 2022 (156)
112	TopMed	NC_000004.12 - 99271303	Apr 26, 2021 (155)
113	UK 10K study - Twins	NC_000004.11 - 100192460	Oct 12, 2018 (152)
114	ALFA	NC_000004.12 - 99271303	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)
rs57305161	May 23, 2008 (130)
rs386538447	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
12397347904	NC_000004.12:99271302:A:C	NC_000004.12:99271302:A:C	(self)
ss83074296	NC_000004.9:100549637:A:G	NC_000004.12:99271302:A:G	(self)
ss92703340, ss108171082, ss110291839, ss160374001, ss162380349, ss163917477, ss206398582, ss277844465, ss284967900, ss293147543, ss480038392, ss1589954382	NC_000004.10:100411482:A:G	NC_000004.12:99271302:A:G	(self)
22422822, 12472969, 8844939, 6852467, 5513828, 13065969, 4706866, 5732314, 11628016, 3076690, 25048580, 12472969, ss221098815, ss232515162, ss239780140, ss480047023, ss480713414, ss484817248, ss536895815, ss557721273, ss651525794, ss778813670, ss782855184, ss783819644, ss832109114, ss834273956, ss980450346, ss1071787275, ss1310980600, ss1580687528, ss1610736712, ss1653730745, ss1752489163, ss1923690384, ss1969816859, ss2022431165, ss2150560336, ss2625714516, ss2634154528, ss2706037159, ss2812856757, ss2995210837, ss3345861916, ss3629025526, ss3632088886, ss3633343316, ss3634062619, ss3634963418, ss3635745347, ss3636667727, ss3637497884, ss3640670712, ss3663106691, ss3731422001, ss3745263678, ss3762167277, ss3772758216, ss3828703663, ss3859611036, ss3905888575, ss4017159543, ss5167079273, ss5314977539, ss5350977573, ss5507641591, ss5635665999, ss5799622234, ss5844424521, ss5964056715	NC_000004.11:100192459:A:G	NC_000004.12:99271302:A:G	(self)
29483350, 158839555, 2670292, 11120629, 35647868, 462025136, 12397347904, ss2265426888, ss3024990848, ss3647802693, ss3712657225, ss3805315708, ss3954742628, ss4624647580, ss5260289159, ss5458931532, ss5541957415, ss5701810764, ss5805354148, ss5854356059, ss5864677843	NC_000004.12:99271302:A:G	NC_000004.12:99271302:A:G	(self)
ss11671093	NT_016354.15:24687163:A:G	NC_000004.12:99271302:A:G	(self)
ss17023503, ss17802415	NT_016354.16:24687163:A:G	NC_000004.12:99271302:A:G	(self)
ss2410214, ss5493072, ss42285470, ss98986832, ss105848316, ss135207833, ss139782236, ss157650842	NT_016354.19:24740180:A:G	NC_000004.12:99271302:A:G	(self)
13065969, ss3905888575	NC_000004.11:100192459:A:T	NC_000004.12:99271302:A: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 rs1566141

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1566141