Name: rs2535228
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.

rs2535228

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:17531157 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.305214 (80787/264690, TOPMED)
A=0.269435 (41548/154204, ALFA)
A=0.308536 (43184/139964, GnomAD) (+ 20 more)
A=0.29897 (23529/78700, PAGE_STUDY)
A=0.02382 (673/28258, 14KJPN)
A=0.02237 (375/16760, 8.3KJPN)
A=0.2700 (1729/6404, 1000G_30x)
A=0.2632 (1318/5008, 1000G)
A=0.2473 (1108/4480, Estonian)
A=0.2735 (1054/3854, ALSPAC)
A=0.2629 (975/3708, TWINSUK)
A=0.0127 (37/2922, KOREAN)
A=0.0109 (20/1832, Korea1K)
A=0.3612 (510/1412, HapMap)
A=0.279 (278/998, GoNL)
A=0.176 (110/626, Chileans)
A=0.282 (169/600, NorthernSweden)
A=0.366 (79/216, Qatari)
A=0.019 (4/210, Vietnamese)
G=0.437 (76/174, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
G=0.50 (8/16, Siberian)
A=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 1 citation
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	154204	G=0.730565	A=0.269435	0.537159	0.076029	0.386812	13
European	Sub	130148	G=0.733596	A=0.266404	0.538817	0.071626	0.389557	0
African	Sub	7758	G=0.5416	A=0.4584	0.294406	0.211137	0.494457	0
African Others	Sub	250	G=0.456	A=0.544	0.208	0.296	0.496	0
African American	Sub	7508	G=0.5445	A=0.4555	0.297283	0.208311	0.494406	0
Asian	Sub	702	G=0.981	A=0.019	0.962963	0.0	0.037037	0
East Asian	Sub	538	G=0.994	A=0.006	0.988848	0.0	0.011152	0
Other Asian	Sub	164	G=0.939	A=0.061	0.878049	0.0	0.121951	0
Latin American 1	Sub	846	G=0.721	A=0.279	0.513002	0.070922	0.416076	0
Latin American 2	Sub	7556	G=0.8452	A=0.1548	0.712282	0.021969	0.265749	1
South Asian	Sub	202	G=0.658	A=0.342	0.455446	0.138614	0.405941	1
Other	Sub	6992	G=0.7380	A=0.2620	0.548913	0.072941	0.378146	1

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=0.694786	A=0.305214
Allele Frequency Aggregator	Total	Global	154204	G=0.730565	A=0.269435
Allele Frequency Aggregator	European	Sub	130148	G=0.733596	A=0.266404
Allele Frequency Aggregator	African	Sub	7758	G=0.5416	A=0.4584
Allele Frequency Aggregator	Latin American 2	Sub	7556	G=0.8452	A=0.1548
Allele Frequency Aggregator	Other	Sub	6992	G=0.7380	A=0.2620
Allele Frequency Aggregator	Latin American 1	Sub	846	G=0.721	A=0.279
Allele Frequency Aggregator	Asian	Sub	702	G=0.981	A=0.019
Allele Frequency Aggregator	South Asian	Sub	202	G=0.658	A=0.342
gnomAD - Genomes	Global	Study-wide	139964	G=0.691464	A=0.308536
gnomAD - Genomes	European	Sub	75850	G=0.74604	A=0.25396
gnomAD - Genomes	African	Sub	41886	G=0.53808	A=0.46192
gnomAD - Genomes	American	Sub	13626	G=0.78702	A=0.21298
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.6945	A=0.3055
gnomAD - Genomes	East Asian	Sub	3130	G=0.9904	A=0.0096
gnomAD - Genomes	Other	Sub	2150	G=0.7088	A=0.2912
The PAGE Study	Global	Study-wide	78700	G=0.70103	A=0.29897
The PAGE Study	AfricanAmerican	Sub	32516	G=0.53980	A=0.46020
The PAGE Study	Mexican	Sub	10810	G=0.83978	A=0.16022
The PAGE Study	Asian	Sub	8316	G=0.9776	A=0.0224
The PAGE Study	PuertoRican	Sub	7918	G=0.7275	A=0.2725
The PAGE Study	NativeHawaiian	Sub	4534	G=0.8427	A=0.1573
The PAGE Study	Cuban	Sub	4230	G=0.7085	A=0.2915
The PAGE Study	Dominican	Sub	3828	G=0.6727	A=0.3273
The PAGE Study	CentralAmerican	Sub	2450	G=0.8322	A=0.1678
The PAGE Study	SouthAmerican	Sub	1982	G=0.8350	A=0.1650
The PAGE Study	NativeAmerican	Sub	1260	G=0.7444	A=0.2556
The PAGE Study	SouthAsian	Sub	856	G=0.731	A=0.269
14KJPN	JAPANESE	Study-wide	28258	G=0.97618	A=0.02382
8.3KJPN	JAPANESE	Study-wide	16760	G=0.97763	A=0.02237
1000Genomes_30x	Global	Study-wide	6404	G=0.7300	A=0.2700
1000Genomes_30x	African	Sub	1786	G=0.4978	A=0.5022
1000Genomes_30x	Europe	Sub	1266	G=0.7615	A=0.2385
1000Genomes_30x	South Asian	Sub	1202	G=0.7163	A=0.2837
1000Genomes_30x	East Asian	Sub	1170	G=0.9863	A=0.0137
1000Genomes_30x	American	Sub	980	G=0.823	A=0.177
1000Genomes	Global	Study-wide	5008	G=0.7368	A=0.2632
1000Genomes	African	Sub	1322	G=0.5045	A=0.4955
1000Genomes	East Asian	Sub	1008	G=0.9861	A=0.0139
1000Genomes	Europe	Sub	1006	G=0.7614	A=0.2386
1000Genomes	South Asian	Sub	978	G=0.714	A=0.286
1000Genomes	American	Sub	694	G=0.814	A=0.186
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7527	A=0.2473
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7265	A=0.2735
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7371	A=0.2629
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9873	A=0.0127
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9891	A=0.0109
HapMap	Global	Study-wide	1412	G=0.6388	A=0.3612
HapMap	African	Sub	676	G=0.485	A=0.515
HapMap	American	Sub	484	G=0.676	A=0.324
HapMap	Asian	Sub	252	G=0.980	A=0.020
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.721	A=0.279
Chileans	Chilean	Study-wide	626	G=0.824	A=0.176
Northern Sweden	ACPOP	Study-wide	600	G=0.718	A=0.282
Qatari	Global	Study-wide	216	G=0.634	A=0.366
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.981	A=0.019
SGDP_PRJ	Global	Study-wide	174	G=0.437	A=0.563
The Danish reference pan genome	Danish	Study-wide	40	G=0.72	A=0.28
Siberian	Global	Study-wide	16	G=0.50	A=0.50

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.17531157G>A
GRCh37.p13 chr 4	NC_000004.11:g.17532780G>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	G=	A
GRCh38.p14 chr 4	NC_000004.12:g.17531157=	NC_000004.12:g.17531157G>A
GRCh37.p13 chr 4	NC_000004.11:g.17532780=	NC_000004.11:g.17532780G>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#.

96 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3553768	Sep 28, 2001 (100)
2	BCM_SSAHASNP	ss10158887	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss17790475	Feb 27, 2004 (120)
4	ABI	ss42289071	Mar 14, 2006 (126)
5	AFFY	ss66341705	Nov 30, 2006 (127)
6	AFFY	ss76046410	Dec 07, 2007 (129)
7	HGSV	ss77727459	Dec 07, 2007 (129)
8	KRIBB_YJKIM	ss81814100	Dec 14, 2007 (130)
9	HGSV	ss84840072	Dec 14, 2007 (130)
10	HGSV	ss85791097	Dec 14, 2007 (130)
11	BCMHGSC_JDW	ss92488861	Mar 24, 2008 (129)
12	1000GENOMES	ss111867512	Jan 25, 2009 (130)
13	1000GENOMES	ss112960684	Jan 25, 2009 (130)
14	ENSEMBL	ss139470983	Dec 01, 2009 (131)
15	ILLUMINA	ss160557000	Dec 01, 2009 (131)
16	ENSEMBL	ss161519978	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss163157287	Jul 04, 2010 (132)
18	AFFY	ss170793114	Jul 04, 2010 (132)
19	ILLUMINA	ss173383967	Jul 04, 2010 (132)
20	BUSHMAN	ss198126169	Jul 04, 2010 (132)
21	1000GENOMES	ss220771934	Jul 14, 2010 (132)
22	1000GENOMES	ss232281662	Jul 14, 2010 (132)
23	1000GENOMES	ss239597751	Jul 15, 2010 (132)
24	PJP	ss293296799	May 09, 2011 (134)
25	ILLUMINA	ss480597885	May 04, 2012 (137)
26	ILLUMINA	ss480612106	May 04, 2012 (137)
27	ILLUMINA	ss481442198	Sep 08, 2015 (146)
28	ILLUMINA	ss485094124	May 04, 2012 (137)
29	ILLUMINA	ss537101681	Sep 08, 2015 (146)
30	TISHKOFF	ss557346151	Apr 25, 2013 (138)
31	SSMP	ss651110996	Apr 25, 2013 (138)
32	ILLUMINA	ss778499286	Sep 08, 2015 (146)
33	ILLUMINA	ss782993355	Sep 08, 2015 (146)
34	ILLUMINA	ss783954077	Sep 08, 2015 (146)
35	ILLUMINA	ss832250210	Sep 08, 2015 (146)
36	ILLUMINA	ss833955372	Sep 08, 2015 (146)
37	EVA-GONL	ss979823028	Aug 21, 2014 (142)
38	JMKIDD_LAB	ss1071317036	Aug 21, 2014 (142)
39	1000GENOMES	ss1308646468	Aug 21, 2014 (142)
40	EVA_GENOME_DK	ss1580438145	Apr 01, 2015 (144)
41	EVA_DECODE	ss1589311888	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1609522946	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1652516979	Apr 01, 2015 (144)
44	ILLUMINA	ss1752509705	Sep 08, 2015 (146)
45	WEILL_CORNELL_DGM	ss1923060565	Feb 12, 2016 (147)
46	ILLUMINA	ss1958664896	Feb 12, 2016 (147)
47	JJLAB	ss2022104552	Sep 14, 2016 (149)
48	USC_VALOUEV	ss2150214963	Dec 20, 2016 (150)
49	HUMAN_LONGEVITY	ss2260838485	Dec 20, 2016 (150)
50	ILLUMINA	ss2634088740	Nov 08, 2017 (151)
51	GRF	ss2705660082	Nov 08, 2017 (151)
52	GNOMAD	ss2806232915	Nov 08, 2017 (151)
53	SWEGEN	ss2994228106	Nov 08, 2017 (151)
54	ILLUMINA	ss3022352245	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3024821615	Nov 08, 2017 (151)
56	CSHL	ss3345571315	Nov 08, 2017 (151)
57	ILLUMINA	ss3628913300	Oct 12, 2018 (152)
58	ILLUMINA	ss3632027074	Oct 12, 2018 (152)
59	ILLUMINA	ss3633327489	Oct 12, 2018 (152)
60	ILLUMINA	ss3634046228	Oct 12, 2018 (152)
61	ILLUMINA	ss3634943219	Oct 12, 2018 (152)
62	ILLUMINA	ss3635729324	Oct 12, 2018 (152)
63	ILLUMINA	ss3636644738	Oct 12, 2018 (152)
64	ILLUMINA	ss3637481822	Oct 12, 2018 (152)
65	ILLUMINA	ss3638474458	Oct 12, 2018 (152)
66	ILLUMINA	ss3640650515	Oct 12, 2018 (152)
67	ILLUMINA	ss3652835422	Oct 12, 2018 (152)
68	EGCUT_WGS	ss3662136837	Jul 13, 2019 (153)
69	EVA_DECODE	ss3711512808	Jul 13, 2019 (153)
70	ILLUMINA	ss3726114107	Jul 13, 2019 (153)
71	ACPOP	ss3730904080	Jul 13, 2019 (153)
72	ILLUMINA	ss3745243511	Jul 13, 2019 (153)
73	EVA	ss3761465739	Jul 13, 2019 (153)
74	PAGE_CC	ss3771109211	Jul 13, 2019 (153)
75	ILLUMINA	ss3772738192	Jul 13, 2019 (153)
76	KHV_HUMAN_GENOMES	ss3804598433	Jul 13, 2019 (153)
77	EVA	ss3828398012	Apr 26, 2020 (154)
78	EVA	ss3837632706	Apr 26, 2020 (154)
79	EVA	ss3843066961	Apr 26, 2020 (154)
80	SGDP_PRJ	ss3858336428	Apr 26, 2020 (154)
81	KRGDB	ss3904488391	Apr 26, 2020 (154)
82	KOGIC	ss3953632167	Apr 26, 2020 (154)
83	EVA	ss4017134907	Apr 26, 2021 (155)
84	TOPMED	ss4604650991	Apr 26, 2021 (155)
85	TOMMO_GENOMICS	ss5164441696	Apr 26, 2021 (155)
86	1000G_HIGH_COVERAGE	ss5258233254	Oct 13, 2022 (156)
87	EVA	ss5314939742	Oct 13, 2022 (156)
88	HUGCELL_USP	ss5457112424	Oct 13, 2022 (156)
89	1000G_HIGH_COVERAGE	ss5538765015	Oct 13, 2022 (156)
90	SANFORD_IMAGENETICS	ss5634458690	Oct 13, 2022 (156)
91	TOMMO_GENOMICS	ss5698157576	Oct 13, 2022 (156)
92	EVA	ss5799608847	Oct 13, 2022 (156)
93	YY_MCH	ss5804806116	Oct 13, 2022 (156)
94	EVA	ss5843625982	Oct 13, 2022 (156)
95	EVA	ss5862360645	Oct 13, 2022 (156)
96	EVA	ss5962838137	Oct 13, 2022 (156)
97	1000Genomes	NC_000004.11 - 17532780	Oct 12, 2018 (152)
98	1000Genomes_30x	NC_000004.12 - 17531157	Oct 13, 2022 (156)
99	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 17532780	Oct 12, 2018 (152)
100	Chileans	NC_000004.11 - 17532780	Apr 26, 2020 (154)
101	Genetic variation in the Estonian population	NC_000004.11 - 17532780	Oct 12, 2018 (152)
102	The Danish reference pan genome	NC_000004.11 - 17532780	Apr 26, 2020 (154)
103	gnomAD - Genomes	NC_000004.12 - 17531157	Apr 26, 2021 (155)
104	Genome of the Netherlands Release 5	NC_000004.11 - 17532780	Apr 26, 2020 (154)
105	HapMap	NC_000004.12 - 17531157	Apr 26, 2020 (154)
106	KOREAN population from KRGDB	NC_000004.11 - 17532780	Apr 26, 2020 (154)
107	Korean Genome Project	NC_000004.12 - 17531157	Apr 26, 2020 (154)
108	Northern Sweden	NC_000004.11 - 17532780	Jul 13, 2019 (153)
109	The PAGE Study	NC_000004.12 - 17531157	Jul 13, 2019 (153)
110	Qatari	NC_000004.11 - 17532780	Apr 26, 2020 (154)
111	SGDP_PRJ	NC_000004.11 - 17532780	Apr 26, 2020 (154)
112	Siberian	NC_000004.11 - 17532780	Apr 26, 2020 (154)
113	8.3KJPN	NC_000004.11 - 17532780	Apr 26, 2021 (155)
114	14KJPN	NC_000004.12 - 17531157	Oct 13, 2022 (156)
115	TopMed	NC_000004.12 - 17531157	Apr 26, 2021 (155)
116	UK 10K study - Twins	NC_000004.11 - 17532780	Oct 12, 2018 (152)
117	A Vietnamese Genetic Variation Database	NC_000004.11 - 17532780	Jul 13, 2019 (153)
118	ALFA	NC_000004.12 - 17531157	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)
rs57205833	Feb 26, 2009 (130)
rs58122203	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77727459, ss84840072, ss85791097	NC_000004.9:17209048:G:A	NC_000004.12:17531156:G:A	(self)
ss92488861, ss111867512, ss112960684, ss163157287, ss198126169, ss293296799, ss480597885, ss1589311888	NC_000004.10:17141877:G:A	NC_000004.12:17531156:G:A	(self)
20001381, 11140504, 310228, 7875085, 6603084, 4902532, 11665785, 4188945, 5102495, 10353408, 2731317, 22411003, 11140504, 2434957, ss220771934, ss232281662, ss239597751, ss480612106, ss481442198, ss485094124, ss537101681, ss557346151, ss651110996, ss778499286, ss782993355, ss783954077, ss832250210, ss833955372, ss979823028, ss1071317036, ss1308646468, ss1580438145, ss1609522946, ss1652516979, ss1752509705, ss1923060565, ss1958664896, ss2022104552, ss2150214963, ss2634088740, ss2705660082, ss2806232915, ss2994228106, ss3022352245, ss3345571315, ss3628913300, ss3632027074, ss3633327489, ss3634046228, ss3634943219, ss3635729324, ss3636644738, ss3637481822, ss3638474458, ss3640650515, ss3652835422, ss3662136837, ss3730904080, ss3745243511, ss3761465739, ss3772738192, ss3828398012, ss3837632706, ss3858336428, ss3904488391, ss4017134907, ss5164441696, ss5314939742, ss5634458690, ss5799608847, ss5843625982, ss5962838137	NC_000004.11:17532779:G:A	NC_000004.12:17531156:G:A	(self)
26290950, 141760885, 2566835, 10010168, 330680, 31994680, 442028547, 7101435946, ss2260838485, ss3024821615, ss3711512808, ss3726114107, ss3771109211, ss3804598433, ss3843066961, ss3953632167, ss4604650991, ss5258233254, ss5457112424, ss5538765015, ss5698157576, ss5804806116, ss5862360645	NC_000004.12:17531156:G:A	NC_000004.12:17531156:G:A	(self)
ss10158887, ss17790475	NT_006316.15:8208137:G:A	NC_000004.12:17531156:G:A	(self)
ss3553768, ss42289071, ss66341705, ss76046410, ss81814100, ss139470983, ss160557000, ss161519978, ss170793114, ss173383967	NT_006316.16:8714576:G:A	NC_000004.12:17531156:G:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs2535228

PMID	Title	Author	Year	Journal
20877624	Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.	Hendrickson SL et al.	2010	PloS one

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

rs2535228