Name: rs188
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.

rs188

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:27897118 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.436050 (115418/264690, TOPMED)
G=0.429895 (60114/139834, GnomAD)
G=0.41654 (14957/35908, ALFA) (+ 16 more)
T=0.37653 (10640/28258, 14KJPN)
T=0.37904 (6352/16758, 8.3KJPN)
G=0.4686 (3001/6404, 1000G_30x)
G=0.4724 (2366/5008, 1000G)
G=0.4353 (1950/4480, Estonian)
G=0.4416 (1702/3854, ALSPAC)
G=0.4250 (1576/3708, TWINSUK)
T=0.3952 (1158/2930, KOREAN)
G=0.412 (411/998, GoNL)
T=0.487 (292/600, NorthernSweden)
T=0.319 (125/392, SGDP_PRJ)
G=0.389 (84/216, Qatari)
T=0.495 (105/212, Vietnamese)
G=0.398 (82/206, HapMap)
G=0.33 (13/40, GENOME_DK)
T=0.36 (13/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: JAZF1 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	35908	T=0.58346	G=0.41654
European	Sub	31010	T=0.58636	G=0.41364
African	Sub	2946	T=0.5781	G=0.4219
African Others	Sub	114	T=0.544	G=0.456
African American	Sub	2832	T=0.5794	G=0.4206
Asian	Sub	156	T=0.487	G=0.513
East Asian	Sub	130	T=0.462	G=0.538
Other Asian	Sub	26	T=0.62	G=0.38
Latin American 1	Sub	146	T=0.616	G=0.384
Latin American 2	Sub	610	T=0.503	G=0.497
South Asian	Sub	98	T=0.55	G=0.45
Other	Sub	942	T=0.571	G=0.429

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=0.563950	G=0.436050
gnomAD - Genomes	Global	Study-wide	139834	T=0.570105	G=0.429895
gnomAD - Genomes	European	Sub	75790	T=0.58264	G=0.41736
gnomAD - Genomes	African	Sub	41844	T=0.56897	G=0.43103
gnomAD - Genomes	American	Sub	13608	T=0.50015	G=0.49985
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.7175	G=0.2825
gnomAD - Genomes	East Asian	Sub	3128	T=0.4242	G=0.5758
gnomAD - Genomes	Other	Sub	2144	T=0.5779	G=0.4221
Allele Frequency Aggregator	Total	Global	35908	T=0.58346	G=0.41654
Allele Frequency Aggregator	European	Sub	31010	T=0.58636	G=0.41364
Allele Frequency Aggregator	African	Sub	2946	T=0.5781	G=0.4219
Allele Frequency Aggregator	Other	Sub	942	T=0.571	G=0.429
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.503	G=0.497
Allele Frequency Aggregator	Asian	Sub	156	T=0.487	G=0.513
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.616	G=0.384
Allele Frequency Aggregator	South Asian	Sub	98	T=0.55	G=0.45
14KJPN	JAPANESE	Study-wide	28258	T=0.37653	G=0.62347
8.3KJPN	JAPANESE	Study-wide	16758	T=0.37904	G=0.62096
1000Genomes_30x	Global	Study-wide	6404	T=0.5314	G=0.4686
1000Genomes_30x	African	Sub	1786	T=0.5493	G=0.4507
1000Genomes_30x	Europe	Sub	1266	T=0.6122	G=0.3878
1000Genomes_30x	South Asian	Sub	1202	T=0.5691	G=0.4309
1000Genomes_30x	East Asian	Sub	1170	T=0.4402	G=0.5598
1000Genomes_30x	American	Sub	980	T=0.457	G=0.543
1000Genomes	Global	Study-wide	5008	T=0.5276	G=0.4724
1000Genomes	African	Sub	1322	T=0.5348	G=0.4652
1000Genomes	East Asian	Sub	1008	T=0.4425	G=0.5575
1000Genomes	Europe	Sub	1006	T=0.6044	G=0.3956
1000Genomes	South Asian	Sub	978	T=0.570	G=0.430
1000Genomes	American	Sub	694	T=0.467	G=0.533
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5647	G=0.4353
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5584	G=0.4416
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5750	G=0.4250
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3952	G=0.6048
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.588	G=0.412
Northern Sweden	ACPOP	Study-wide	600	T=0.487	G=0.513
SGDP_PRJ	Global	Study-wide	392	T=0.319	G=0.681
Qatari	Global	Study-wide	216	T=0.611	G=0.389
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.495	G=0.505
HapMap	Global	Study-wide	206	T=0.602	G=0.398
HapMap	American	Sub	116	T=0.672	G=0.328
HapMap	Asian	Sub	90	T=0.51	G=0.49
The Danish reference pan genome	Danish	Study-wide	40	T=0.68	G=0.33
Siberian	Global	Study-wide	36	T=0.36	G=0.64

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 7	NC_000007.14:g.27897118T>G
GRCh37.p13 chr 7	NC_000007.13:g.27936737T>G
JAZF1 RefSeqGene	NG_011499.1:g.288701A>C

Gene: JAZF1, JAZF zinc finger 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
JAZF1 transcript	NM_175061.4:c.189-1702A>C	N/A	Intron Variant
JAZF1 transcript variant X1	XM_047420024.1:c.189-1702… XM_047420024.1:c.189-1702A>C	N/A	Intron Variant
JAZF1 transcript variant X2	XM_047420025.1:c.-4-1702A… XM_047420025.1:c.-4-1702A>C	N/A	Intron Variant
JAZF1 transcript variant X3	XM_047420026.1:c.-4-1702A… XM_047420026.1:c.-4-1702A>C	N/A	Intron Variant
JAZF1 transcript variant X4	XM_047420027.1:c.-4-1702A… XM_047420027.1:c.-4-1702A>C	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	T=	G
GRCh38.p14 chr 7	NC_000007.14:g.27897118=	NC_000007.14:g.27897118T>G
GRCh37.p13 chr 7	NC_000007.13:g.27936737=	NC_000007.13:g.27936737T>G
JAZF1 RefSeqGene	NG_011499.1:g.288701=	NG_011499.1:g.288701A>C
JAZF1 transcript	NM_175061.3:c.189-1702=	NM_175061.3:c.189-1702A>C
JAZF1 transcript	NM_175061.4:c.189-1702=	NM_175061.4:c.189-1702A>C
JAZF1 transcript variant X1	XM_047420024.1:c.189-1702=	XM_047420024.1:c.189-1702A>C
JAZF1 transcript variant X2	XM_047420025.1:c.-4-1702=	XM_047420025.1:c.-4-1702A>C
JAZF1 transcript variant X3	XM_047420026.1:c.-4-1702=	XM_047420026.1:c.-4-1702A>C
JAZF1 transcript variant X4	XM_047420027.1:c.-4-1702=	XM_047420027.1:c.-4-1702A>C

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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss188	Sep 19, 2000 (36)
2	BCM_SSAHASNP	ss10365258	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss19708257	Feb 27, 2004 (120)
4	SSAHASNP	ss22603191	Apr 05, 2004 (121)
5	ABI	ss44821684	Mar 13, 2006 (126)
6	BCMHGSC_JDW	ss93649731	Mar 24, 2008 (129)
7	1000GENOMES	ss111724894	Jan 25, 2009 (130)
8	1000GENOMES	ss113504369	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss115998195	Feb 14, 2009 (130)
10	ENSEMBL	ss142783177	Dec 01, 2009 (131)
11	ENSEMBL	ss143070637	Dec 01, 2009 (131)
12	GMI	ss154554348	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162160218	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss163884329	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166326972	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207996761	Jul 04, 2010 (132)
17	1000GENOMES	ss222980222	Jul 14, 2010 (132)
18	1000GENOMES	ss233903138	Jul 15, 2010 (132)
19	1000GENOMES	ss240872751	Jul 15, 2010 (132)
20	BL	ss254143637	May 09, 2011 (134)
21	GMI	ss279237197	May 04, 2012 (137)
22	PJP	ss294036264	May 09, 2011 (134)
23	ILLUMINA	ss410873760	Sep 17, 2011 (135)
24	TISHKOFF	ss559889283	Apr 25, 2013 (138)
25	SSMP	ss654243312	Apr 25, 2013 (138)
26	EVA-GONL	ss984087150	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1074467861	Aug 21, 2014 (142)
28	1000GENOMES	ss1324429291	Aug 21, 2014 (142)
29	DDI	ss1431067406	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1582125626	Apr 01, 2015 (144)
31	EVA_DECODE	ss1593657206	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1617839995	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1660834028	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1804926129	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1927330501	Feb 12, 2016 (147)
36	GENOMED	ss1970656726	Jul 19, 2016 (147)
37	JJLAB	ss2024343927	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2152539736	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2292701767	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2626660396	Nov 08, 2017 (151)
41	ILLUMINA	ss2635170554	Nov 08, 2017 (151)
42	GRF	ss2708197128	Nov 08, 2017 (151)
43	ILLUMINA	ss2711106650	Nov 08, 2017 (151)
44	GNOMAD	ss2851167785	Nov 08, 2017 (151)
45	SWEGEN	ss3000828610	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3025966334	Nov 08, 2017 (151)
47	CSHL	ss3347498264	Nov 08, 2017 (151)
48	URBANLAB	ss3648590008	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3668758660	Jul 13, 2019 (153)
50	EVA_DECODE	ss3719346330	Jul 13, 2019 (153)
51	ACPOP	ss3734470717	Jul 13, 2019 (153)
52	EVA	ss3766342701	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3809509529	Jul 13, 2019 (153)
54	EVA	ss3830481119	Apr 26, 2020 (154)
55	EVA	ss3838728082	Apr 26, 2020 (154)
56	EVA	ss3844179450	Apr 26, 2020 (154)
57	SGDP_PRJ	ss3866897593	Apr 26, 2020 (154)
58	KRGDB	ss3913940057	Apr 26, 2020 (154)
59	TOPMED	ss4739921119	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5182364084	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5272265648	Oct 14, 2022 (156)
62	EVA	ss5372442109	Oct 14, 2022 (156)
63	HUGCELL_USP	ss5469507808	Oct 14, 2022 (156)
64	EVA	ss5508893440	Oct 14, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5560126795	Oct 14, 2022 (156)
66	SANFORD_IMAGENETICS	ss5642596987	Oct 14, 2022 (156)
67	TOMMO_GENOMICS	ss5721974272	Oct 14, 2022 (156)
68	YY_MCH	ss5808445690	Oct 14, 2022 (156)
69	EVA	ss5822580324	Oct 14, 2022 (156)
70	EVA	ss5855818240	Oct 14, 2022 (156)
71	EVA	ss5858208096	Oct 14, 2022 (156)
72	EVA	ss5971801186	Oct 14, 2022 (156)
73	1000Genomes	NC_000007.13 - 27936737	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000007.14 - 27897118	Oct 14, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 27936737	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000007.13 - 27936737	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000007.13 - 27936737	Apr 26, 2020 (154)
78	gnomAD - Genomes	NC_000007.14 - 27897118	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000007.13 - 27936737	Apr 26, 2020 (154)
80	HapMap	NC_000007.14 - 27897118	Apr 26, 2020 (154)
81	KOREAN population from KRGDB	NC_000007.13 - 27936737	Apr 26, 2020 (154)
82	Northern Sweden	NC_000007.13 - 27936737	Jul 13, 2019 (153)
83	Qatari	NC_000007.13 - 27936737	Apr 26, 2020 (154)
84	SGDP_PRJ	NC_000007.13 - 27936737	Apr 26, 2020 (154)
85	Siberian	NC_000007.13 - 27936737	Apr 26, 2020 (154)
86	8.3KJPN	NC_000007.13 - 27936737	Apr 26, 2021 (155)
87	14KJPN	NC_000007.14 - 27897118	Oct 14, 2022 (156)
88	TopMed	NC_000007.14 - 27897118	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000007.13 - 27936737	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000007.13 - 27936737	Jul 13, 2019 (153)
91	ALFA	NC_000007.14 - 27897118	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93649731, ss111724894, ss113504369, ss115998195, ss162160218, ss163884329, ss166326972, ss207996761, ss254143637, ss279237197, ss294036264, ss1593657206, ss2635170554	NC_000007.12:27903261:T:G	NC_000007.14:27897117:T:G	(self)
36374414, 20280333, 14496908, 8290565, 9042219, 21117451, 7755582, 9372431, 18914573, 5056090, 40333391, 20280333, 4518594, ss222980222, ss233903138, ss240872751, ss559889283, ss654243312, ss984087150, ss1074467861, ss1324429291, ss1431067406, ss1582125626, ss1617839995, ss1660834028, ss1804926129, ss1927330501, ss1970656726, ss2024343927, ss2152539736, ss2626660396, ss2708197128, ss2711106650, ss2851167785, ss3000828610, ss3347498264, ss3668758660, ss3734470717, ss3766342701, ss3830481119, ss3838728082, ss3866897593, ss3913940057, ss5182364084, ss5372442109, ss5508893440, ss5642596987, ss5822580324, ss5971801186	NC_000007.13:27936736:T:G	NC_000007.14:27897117:T:G	(self)
47652730, 256484655, 3365202, 55811376, 577298678, 8833575940, ss2292701767, ss3025966334, ss3648590008, ss3719346330, ss3809509529, ss3844179450, ss4739921119, ss5272265648, ss5469507808, ss5560126795, ss5721974272, ss5808445690, ss5855818240, ss5858208096	NC_000007.14:27897117:T:G	NC_000007.14:27897117:T:G	(self)
ss10365258	NT_007819.13:27230344:T:G	NC_000007.14:27897117:T:G	(self)
ss19708257, ss22603191	NT_007819.14:27230344:T:G	NC_000007.14:27897117:T:G	(self)
ss188, ss44821684, ss142783177, ss143070637, ss154554348, ss410873760	NT_007819.17:27926736:T:G	NC_000007.14:27897117: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 rs188

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

rs188