Name: rs28550169
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.

rs28550169

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:2008387 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.167997 (44467/264690, TOPMED)
T=0.158478 (22184/139982, GnomAD)
T=0.33852 (9566/28258, 14KJPN) (+ 17 more)
T=0.16131 (3496/21672, ALFA)
T=0.33825 (5669/16760, 8.3KJPN)
T=0.2308 (1478/6404, 1000G_30x)
T=0.2324 (1164/5008, 1000G)
T=0.1743 (781/4480, Estonian)
T=0.1562 (602/3854, ALSPAC)
T=0.1408 (522/3708, TWINSUK)
T=0.4157 (1218/2930, KOREAN)
T=0.4121 (755/1832, Korea1K)
T=0.1991 (217/1090, Daghestan)
T=0.156 (156/998, GoNL)
T=0.212 (127/600, NorthernSweden)
C=0.379 (107/282, SGDP_PRJ)
T=0.134 (29/216, Qatari)
T=0.430 (92/214, Vietnamese)
T=0.15 (6/40, GENOME_DK)
C=0.33 (12/36, 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	21672	C=0.83869	T=0.16131
European	Sub	14370	C=0.83848	T=0.16152
African	Sub	5574	C=0.8602	T=0.1398
African Others	Sub	198	C=0.884	T=0.116
African American	Sub	5376	C=0.8594	T=0.1406
Asian	Sub	114	C=0.535	T=0.465
East Asian	Sub	88	C=0.53	T=0.47
Other Asian	Sub	26	C=0.54	T=0.46
Latin American 1	Sub	146	C=0.815	T=0.185
Latin American 2	Sub	610	C=0.734	T=0.266
South Asian	Sub	100	C=0.69	T=0.31
Other	Sub	758	C=0.838	T=0.162

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=0.832003	T=0.167997
gnomAD - Genomes	Global	Study-wide	139982	C=0.841522	T=0.158478
gnomAD - Genomes	European	Sub	75856	C=0.84268	T=0.15732
gnomAD - Genomes	African	Sub	41930	C=0.86208	T=0.13792
gnomAD - Genomes	American	Sub	13622	C=0.82550	T=0.17450
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.8634	T=0.1366
gnomAD - Genomes	East Asian	Sub	3108	C=0.5936	T=0.4064
gnomAD - Genomes	Other	Sub	2142	C=0.8259	T=0.1741
14KJPN	JAPANESE	Study-wide	28258	C=0.66148	T=0.33852
Allele Frequency Aggregator	Total	Global	21672	C=0.83869	T=0.16131
Allele Frequency Aggregator	European	Sub	14370	C=0.83848	T=0.16152
Allele Frequency Aggregator	African	Sub	5574	C=0.8602	T=0.1398
Allele Frequency Aggregator	Other	Sub	758	C=0.838	T=0.162
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.734	T=0.266
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.815	T=0.185
Allele Frequency Aggregator	Asian	Sub	114	C=0.535	T=0.465
Allele Frequency Aggregator	South Asian	Sub	100	C=0.69	T=0.31
8.3KJPN	JAPANESE	Study-wide	16760	C=0.66175	T=0.33825
1000Genomes_30x	Global	Study-wide	6404	C=0.7692	T=0.2308
1000Genomes_30x	African	Sub	1786	C=0.8886	T=0.1114
1000Genomes_30x	Europe	Sub	1266	C=0.8689	T=0.1311
1000Genomes_30x	South Asian	Sub	1202	C=0.6905	T=0.3095
1000Genomes_30x	East Asian	Sub	1170	C=0.5726	T=0.4274
1000Genomes_30x	American	Sub	980	C=0.754	T=0.246
1000Genomes	Global	Study-wide	5008	C=0.7676	T=0.2324
1000Genomes	African	Sub	1322	C=0.8888	T=0.1112
1000Genomes	East Asian	Sub	1008	C=0.5883	T=0.4117
1000Genomes	Europe	Sub	1006	C=0.8698	T=0.1302
1000Genomes	South Asian	Sub	978	C=0.690	T=0.310
1000Genomes	American	Sub	694	C=0.758	T=0.242
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8257	T=0.1743
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8438	T=0.1562
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8592	T=0.1408
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5843	T=0.4157
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5879	T=0.4121
Genome-wide autozygosity in Daghestan	Global	Study-wide	1090	C=0.8009	T=0.1991
Genome-wide autozygosity in Daghestan	Daghestan	Sub	604	C=0.820	T=0.180
Genome-wide autozygosity in Daghestan	Near_East	Sub	140	C=0.850	T=0.150
Genome-wide autozygosity in Daghestan	Central Asia	Sub	120	C=0.742	T=0.258
Genome-wide autozygosity in Daghestan	Europe	Sub	100	C=0.80	T=0.20
Genome-wide autozygosity in Daghestan	South Asian	Sub	92	C=0.67	T=0.33
Genome-wide autozygosity in Daghestan	Caucasus	Sub	34	C=0.82	T=0.18
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.844	T=0.156
Northern Sweden	ACPOP	Study-wide	600	C=0.788	T=0.212
SGDP_PRJ	Global	Study-wide	282	C=0.379	T=0.621
Qatari	Global	Study-wide	216	C=0.866	T=0.134
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.570	T=0.430
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	36	C=0.33	T=0.67

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.2008387C>T
GRCh37.p13 chr 1	NC_000001.10:g.1939826C>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=	T
GRCh38.p14 chr 1	NC_000001.11:g.2008387=	NC_000001.11:g.2008387C>T
GRCh37.p13 chr 1	NC_000001.10:g.1939826=	NC_000001.10:g.1939826C>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#.

72 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35304623	May 24, 2005 (125)
2	ABI	ss41068959	Mar 13, 2006 (126)
3	HGSV	ss81099304	Dec 15, 2007 (130)
4	BGI	ss105112909	Dec 01, 2009 (131)
5	1000GENOMES	ss107940118	Jan 22, 2009 (130)
6	ENSEMBL	ss161202348	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss165989470	Jul 04, 2010 (132)
8	BUSHMAN	ss197899998	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss205380726	Jul 04, 2010 (132)
10	1000GENOMES	ss218194640	Jul 14, 2010 (132)
11	1000GENOMES	ss230398389	Jul 14, 2010 (132)
12	1000GENOMES	ss238117643	Jul 15, 2010 (132)
13	GMI	ss275685187	May 04, 2012 (137)
14	GMI	ss283989045	Apr 25, 2013 (138)
15	PJP	ss290495582	May 09, 2011 (134)
16	TISHKOFF	ss553720974	Apr 25, 2013 (138)
17	SSMP	ss647524239	Apr 25, 2013 (138)
18	EVA-GONL	ss974779833	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1067617680	Aug 21, 2014 (142)
20	1000GENOMES	ss1289384441	Aug 21, 2014 (142)
21	HAMMER_LAB	ss1397238538	Sep 08, 2015 (146)
22	DDI	ss1425687993	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1573854472	Apr 01, 2015 (144)
24	EVA_DECODE	ss1584139330	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1599395825	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1642389858	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1793740972	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1917973318	Feb 12, 2016 (147)
29	GENOMED	ss1966668762	Jul 19, 2016 (147)
30	JJLAB	ss2019503541	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2147491681	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2159442034	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2624267617	Nov 08, 2017 (151)
34	GRF	ss2697383114	Nov 08, 2017 (151)
35	GNOMAD	ss2750775625	Nov 08, 2017 (151)
36	AFFY	ss2985495282	Nov 08, 2017 (151)
37	SWEGEN	ss2986169794	Nov 08, 2017 (151)
38	ILLUMINA	ss3021045297	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3023515738	Nov 08, 2017 (151)
40	CSHL	ss3343278958	Nov 08, 2017 (151)
41	ILLUMINA	ss3640973314	Oct 11, 2018 (152)
42	ILLUMINA	ss3641267125	Oct 11, 2018 (152)
43	ILLUMINA	ss3651367373	Oct 11, 2018 (152)
44	EGCUT_WGS	ss3654276690	Jul 12, 2019 (153)
45	EVA_DECODE	ss3686015003	Jul 12, 2019 (153)
46	ILLUMINA	ss3724989339	Jul 12, 2019 (153)
47	ACPOP	ss3726725696	Jul 12, 2019 (153)
48	EVA	ss3745733859	Jul 12, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3798757353	Jul 12, 2019 (153)
50	EVA	ss3825986374	Apr 25, 2020 (154)
51	EVA	ss3836380615	Apr 25, 2020 (154)
52	EVA	ss3841784706	Apr 25, 2020 (154)
53	SGDP_PRJ	ss3848026733	Apr 25, 2020 (154)
54	KRGDB	ss3892873513	Apr 25, 2020 (154)
55	KOGIC	ss3943658097	Apr 25, 2020 (154)
56	TOPMED	ss4436794903	Apr 25, 2021 (155)
57	TOMMO_GENOMICS	ss5142113343	Apr 25, 2021 (155)
58	EVA	ss5237258424	Apr 25, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5240906665	Oct 12, 2022 (156)
60	EVA	ss5316254807	Oct 12, 2022 (156)
61	HUGCELL_USP	ss5442144997	Oct 12, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5512548626	Oct 12, 2022 (156)
63	SANFORD_IMAGENETICS	ss5624194036	Oct 12, 2022 (156)
64	SANFORD_IMAGENETICS	ss5624773105	Oct 12, 2022 (156)
65	TOMMO_GENOMICS	ss5666275231	Oct 12, 2022 (156)
66	YY_MCH	ss5800254518	Oct 12, 2022 (156)
67	EVA	ss5831435446	Oct 12, 2022 (156)
68	EVA	ss5847150871	Oct 12, 2022 (156)
69	EVA	ss5848752872	Oct 12, 2022 (156)
70	EVA	ss5906746338	Oct 12, 2022 (156)
71	EVA	ss5936602370	Oct 12, 2022 (156)
72	EVA	ss5979260133	Oct 12, 2022 (156)
73	1000Genomes	NC_000001.10 - 1939826	Oct 11, 2018 (152)
74	1000Genomes_30x	NC_000001.11 - 2008387	Oct 12, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 1939826	Oct 11, 2018 (152)
76	Genome-wide autozygosity in Daghestan	NC_000001.9 - 1929686	Apr 25, 2020 (154)
77	Genetic variation in the Estonian population	NC_000001.10 - 1939826	Oct 11, 2018 (152)
78	The Danish reference pan genome	NC_000001.10 - 1939826	Apr 25, 2020 (154)
79	gnomAD - Genomes	NC_000001.11 - 2008387	Apr 25, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000001.10 - 1939826	Apr 25, 2020 (154)
81	KOREAN population from KRGDB	NC_000001.10 - 1939826	Apr 25, 2020 (154)
82	Korean Genome Project	NC_000001.11 - 2008387	Apr 25, 2020 (154)
83	Northern Sweden	NC_000001.10 - 1939826	Jul 12, 2019 (153)
84	Qatari	NC_000001.10 - 1939826	Apr 25, 2020 (154)
85	SGDP_PRJ	NC_000001.10 - 1939826	Apr 25, 2020 (154)
86	Siberian	NC_000001.10 - 1939826	Apr 25, 2020 (154)
87	8.3KJPN	NC_000001.10 - 1939826	Apr 25, 2021 (155)
88	14KJPN	NC_000001.11 - 2008387	Oct 12, 2022 (156)
89	TopMed	NC_000001.11 - 2008387	Apr 25, 2021 (155)
90	UK 10K study - Twins	NC_000001.10 - 1939826	Oct 11, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000001.10 - 1939826	Jul 12, 2019 (153)
92	ALFA	NC_000001.11 - 2008387	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).

Associated ID	History Updated (Build)
rs58660130	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss35304623, ss81099304	NC_000001.8:1971987:C:T	NC_000001.11:2008386:C:T	(self)
25, ss107940118, ss165989470, ss197899998, ss205380726, ss275685187, ss283989045, ss290495582, ss1397238538, ss1584139330	NC_000001.9:1929685:C:T	NC_000001.11:2008386:C:T	(self)
50714, 19701, 14938, 1361706, 8524, 50907, 10561, 15248, 43713, 8035, 82650, 19701, 3942, ss218194640, ss230398389, ss238117643, ss553720974, ss647524239, ss974779833, ss1067617680, ss1289384441, ss1425687993, ss1573854472, ss1599395825, ss1642389858, ss1793740972, ss1917973318, ss1966668762, ss2019503541, ss2147491681, ss2624267617, ss2697383114, ss2750775625, ss2985495282, ss2986169794, ss3021045297, ss3343278958, ss3640973314, ss3641267125, ss3651367373, ss3654276690, ss3726725696, ss3745733859, ss3825986374, ss3836380615, ss3848026733, ss3892873513, ss5142113343, ss5237258424, ss5316254807, ss5624194036, ss5624773105, ss5831435446, ss5847150871, ss5936602370, ss5979260133	NC_000001.10:1939825:C:T	NC_000001.11:2008386:C:T	(self)
74561, 389218, 36098, 112335, 401238, 8238620284, ss2159442034, ss3023515738, ss3686015003, ss3724989339, ss3798757353, ss3841784706, ss3943658097, ss4436794903, ss5240906665, ss5442144997, ss5512548626, ss5666275231, ss5800254518, ss5848752872, ss5906746338	NC_000001.11:2008386:C:T	NC_000001.11:2008386:C:T	(self)
ss41068959, ss105112909, ss161202348	NT_004350.19:1418457:C:T	NC_000001.11:2008386: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 rs28550169

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

rs28550169