Name: rs200
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.

rs200

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:27907236 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.050334 (13323/264690, TOPMED)
C=0.048328 (6776/140208, GnomAD)
C=0.00000 (0/28258, 14KJPN) (+ 18 more)
C=0.05315 (1004/18890, ALFA)
C=0.00000 (0/16758, 8.3KJPN)
C=0.0275 (176/6404, 1000G_30x)
C=0.0268 (134/5008, 1000G)
C=0.0482 (216/4480, Estonian)
C=0.0669 (258/3854, ALSPAC)
C=0.0720 (267/3708, TWINSUK)
C=0.0000 (0/2930, KOREAN)
A=0.0000 (0/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.060 (60/998, GoNL)
C=0.058 (35/600, NorthernSweden)
C=0.016 (9/552, SGDP_PRJ)
C=0.024 (8/328, HapMap)
C=0.125 (27/216, Qatari)
C=0.000 (0/210, Vietnamese)
C=0.07 (4/56, Siberian)
C=0.03 (1/40, GENOME_DK)

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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	C=0.05315	T=0.94685	0.003706	0.897406	0.098888	2
European	Sub	14286	C=0.06223	T=0.93777	0.00448	0.880022	0.115498	0
African	Sub	2946	C=0.0112	T=0.9888	0.0	0.977597	0.022403	0
African Others	Sub	114	C=0.009	T=0.991	0.0	0.982456	0.017544	0
African American	Sub	2832	C=0.0113	T=0.9887	0.0	0.977401	0.022599	0
Asian	Sub	112	C=0.000	T=1.000	0.0	1.0	0.0	N/A
East Asian	Sub	86	C=0.00	T=1.00	0.0	1.0	0.0	N/A
Other Asian	Sub	26	C=0.00	T=1.00	0.0	1.0	0.0	N/A
Latin American 1	Sub	146	C=0.082	T=0.918	0.027397	0.863014	0.109589	3
Latin American 2	Sub	610	C=0.049	T=0.951	0.0	0.901639	0.098361	1
South Asian	Sub	98	C=0.01	T=0.99	0.0	0.979592	0.020408	0
Other	Sub	692	C=0.056	T=0.944	0.00289	0.890173	0.106936	0

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=0.050334	T=0.949666
gnomAD - Genomes	Global	Study-wide	140208	C=0.048328	T=0.951672
gnomAD - Genomes	European	Sub	75936	C=0.06195	T=0.93805
gnomAD - Genomes	African	Sub	42012	C=0.01314	T=0.98686
gnomAD - Genomes	American	Sub	13652	C=0.07611	T=0.92389
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.1008	T=0.8992
gnomAD - Genomes	East Asian	Sub	3134	C=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2150	C=0.0679	T=0.9321
14KJPN	JAPANESE	Study-wide	28258	C=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	18890	C=0.05315	T=0.94685
Allele Frequency Aggregator	European	Sub	14286	C=0.06223	T=0.93777
Allele Frequency Aggregator	African	Sub	2946	C=0.0112	T=0.9888
Allele Frequency Aggregator	Other	Sub	692	C=0.056	T=0.944
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.049	T=0.951
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.082	T=0.918
Allele Frequency Aggregator	Asian	Sub	112	C=0.000	T=1.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.01	T=0.99
8.3KJPN	JAPANESE	Study-wide	16758	C=0.00000	T=1.00000
1000Genomes_30x	Global	Study-wide	6404	C=0.0275	T=0.9725
1000Genomes_30x	African	Sub	1786	C=0.0050	T=0.9950
1000Genomes_30x	Europe	Sub	1266	C=0.0861	T=0.9139
1000Genomes_30x	South Asian	Sub	1202	C=0.0108	T=0.9892
1000Genomes_30x	East Asian	Sub	1170	C=0.0017	T=0.9983
1000Genomes_30x	American	Sub	980	C=0.044	T=0.956
1000Genomes	Global	Study-wide	5008	C=0.0268	T=0.9732
1000Genomes	African	Sub	1322	C=0.0053	T=0.9947
1000Genomes	East Asian	Sub	1008	C=0.0020	T=0.9980
1000Genomes	Europe	Sub	1006	C=0.0825	T=0.9175
1000Genomes	South Asian	Sub	978	C=0.011	T=0.989
1000Genomes	American	Sub	694	C=0.045	T=0.955
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.0482	T=0.9518
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0669	T=0.9331
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0720	T=0.9280
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0000	A=0.0000, T=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	T=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.060	T=0.940
Northern Sweden	ACPOP	Study-wide	600	C=0.058	T=0.942
SGDP_PRJ	Global	Study-wide	552	C=0.016	T=0.984
HapMap	Global	Study-wide	328	C=0.024	T=0.976
HapMap	American	Sub	120	C=0.067	T=0.933
HapMap	African	Sub	118	C=0.000	T=1.000
HapMap	Asian	Sub	90	C=0.00	T=1.00
Qatari	Global	Study-wide	216	C=0.125	T=0.875
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.000	T=1.000
Siberian	Global	Study-wide	56	C=0.07	T=0.93
The Danish reference pan genome	Danish	Study-wide	40	C=0.03	T=0.97

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.27907236C>A
GRCh38.p14 chr 7	NC_000007.14:g.27907236C>T
GRCh37.p13 chr 7	NC_000007.13:g.27946855C>A
GRCh37.p13 chr 7	NC_000007.13:g.27946855C>T
JAZF1 RefSeqGene	NG_011499.1:g.278583G>T
JAZF1 RefSeqGene	NG_011499.1:g.278583G>A

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

Molecule type	Change	Amino acid[Codon]	SO Term
JAZF1 transcript	NM_175061.4:c.189-11820G>T	N/A	Intron Variant
JAZF1 transcript variant X1	XM_047420024.1:c.189-1182… XM_047420024.1:c.189-11820G>T	N/A	Intron Variant
JAZF1 transcript variant X2	XM_047420025.1:c.-4-11820… XM_047420025.1:c.-4-11820G>T	N/A	Intron Variant
JAZF1 transcript variant X3	XM_047420026.1:c.-4-11820… XM_047420026.1:c.-4-11820G>T	N/A	Intron Variant
JAZF1 transcript variant X4	XM_047420027.1:c.-5+6156G… XM_047420027.1:c.-5+6156G>T	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	C=	A	T
GRCh38.p14 chr 7	NC_000007.14:g.27907236=	NC_000007.14:g.27907236C>A	NC_000007.14:g.27907236C>T
GRCh37.p13 chr 7	NC_000007.13:g.27946855=	NC_000007.13:g.27946855C>A	NC_000007.13:g.27946855C>T
JAZF1 RefSeqGene	NG_011499.1:g.278583=	NG_011499.1:g.278583G>T	NG_011499.1:g.278583G>A
JAZF1 transcript	NM_175061.3:c.189-11820=	NM_175061.3:c.189-11820G>T	NM_175061.3:c.189-11820G>A
JAZF1 transcript	NM_175061.4:c.189-11820=	NM_175061.4:c.189-11820G>T	NM_175061.4:c.189-11820G>A
JAZF1 transcript variant X1	XM_047420024.1:c.189-11820=	XM_047420024.1:c.189-11820G>T	XM_047420024.1:c.189-11820G>A
JAZF1 transcript variant X2	XM_047420025.1:c.-4-11820=	XM_047420025.1:c.-4-11820G>T	XM_047420025.1:c.-4-11820G>A
JAZF1 transcript variant X3	XM_047420026.1:c.-4-11820=	XM_047420026.1:c.-4-11820G>T	XM_047420026.1:c.-4-11820G>A
JAZF1 transcript variant X4	XM_047420027.1:c.-5+6156=	XM_047420027.1:c.-5+6156G>T	XM_047420027.1:c.-5+6156G>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#.

79 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss200	Sep 19, 2000 (36)
2	WI_SSAHASNP	ss6504548	Feb 20, 2003 (111)
3	BCM_SSAHASNP	ss10375261	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss17929922	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19711133	Feb 27, 2004 (120)
6	SSAHASNP	ss22622225	Apr 05, 2004 (121)
7	SSAHASNP	ss22932928	Apr 05, 2004 (121)
8	BCMHGSC_JDW	ss93649749	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98141289	Feb 04, 2009 (130)
10	BGI	ss105510044	Feb 04, 2009 (130)
11	1000GENOMES	ss111725033	Jan 25, 2009 (130)
12	1000GENOMES	ss113504506	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss115998248	Feb 14, 2009 (130)
14	ENSEMBL	ss139745280	Dec 01, 2009 (131)
15	ENSEMBL	ss142783243	Dec 01, 2009 (131)
16	GMI	ss154554500	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162160322	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss163884539	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss166327159	Jul 04, 2010 (132)
20	BUSHMAN	ss203114737	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss207987183	Jul 04, 2010 (132)
22	1000GENOMES	ss222980268	Jul 14, 2010 (132)
23	1000GENOMES	ss233903177	Jul 15, 2010 (132)
24	1000GENOMES	ss240872787	Jul 15, 2010 (132)
25	BL	ss254143738	May 09, 2011 (134)
26	GMI	ss279237241	May 04, 2012 (137)
27	GMI	ss285595464	Apr 25, 2013 (138)
28	PJP	ss294036282	May 09, 2011 (134)
29	TISHKOFF	ss559889338	Apr 25, 2013 (138)
30	SSMP	ss654243358	Apr 25, 2013 (138)
31	EVA-GONL	ss984087244	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1074467923	Aug 21, 2014 (142)
33	1000GENOMES	ss1324429600	Aug 21, 2014 (142)
34	DDI	ss1431067432	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1582125662	Apr 01, 2015 (144)
36	EVA_DECODE	ss1593657306	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1617840157	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1660834190	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1804926165	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1927330581	Feb 12, 2016 (147)
41	GENOMED	ss1970656758	Jul 19, 2016 (147)
42	JJLAB	ss2024343964	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2152539783	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2292702416	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2626660430	Nov 08, 2017 (151)
46	GRF	ss2708197184	Nov 08, 2017 (151)
47	GNOMAD	ss2851168646	Nov 08, 2017 (151)
48	SWEGEN	ss3000828752	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3025966364	Nov 08, 2017 (151)
50	CSHL	ss3347498299	Nov 08, 2017 (151)
51	URBANLAB	ss3648590040	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3668758813	Jul 13, 2019 (153)
53	EVA_DECODE	ss3719346499	Jul 13, 2019 (153)
54	ACPOP	ss3734470790	Jul 13, 2019 (153)
55	EVA	ss3766342809	Jul 13, 2019 (153)
56	PACBIO	ss3785766306	Jul 13, 2019 (153)
57	PACBIO	ss3791075843	Jul 13, 2019 (153)
58	PACBIO	ss3795955597	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3809509625	Jul 13, 2019 (153)
60	EVA	ss3830481164	Apr 26, 2020 (154)
61	EVA	ss3838728118	Apr 26, 2020 (154)
62	EVA	ss3844179486	Apr 26, 2020 (154)
63	SGDP_PRJ	ss3866897766	Apr 26, 2020 (154)
64	KRGDB	ss3913940249	Apr 26, 2020 (154)
65	KOGIC	ss3961119656	Apr 26, 2020 (154)
66	TOPMED	ss4739923751	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5182364429	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5272265921	Oct 14, 2022 (156)
69	EVA	ss5372442591	Oct 14, 2022 (156)
70	HUGCELL_USP	ss5469508102	Oct 14, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5560127213	Oct 14, 2022 (156)
72	SANFORD_IMAGENETICS	ss5642597142	Oct 14, 2022 (156)
73	TOMMO_GENOMICS	ss5721974717	Oct 14, 2022 (156)
74	YY_MCH	ss5808445776	Oct 14, 2022 (156)
75	EVA	ss5822580441	Oct 14, 2022 (156)
76	EVA	ss5855818291	Oct 14, 2022 (156)
77	EVA	ss5858208415	Oct 14, 2022 (156)
78	EVA	ss5971801346	Oct 14, 2022 (156)
79	EVA	ss5980423353	Oct 14, 2022 (156)
80	1000Genomes	NC_000007.13 - 27946855	Oct 12, 2018 (152)
81	1000Genomes_30x	NC_000007.14 - 27907236	Oct 14, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 27946855	Oct 12, 2018 (152)
83	Genetic variation in the Estonian population	NC_000007.13 - 27946855	Oct 12, 2018 (152)
84	The Danish reference pan genome	NC_000007.13 - 27946855	Apr 26, 2020 (154)
85	gnomAD - Genomes	NC_000007.14 - 27907236	Apr 26, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000007.13 - 27946855	Apr 26, 2020 (154)
87	HapMap	NC_000007.14 - 27907236	Apr 26, 2020 (154)
88	KOREAN population from KRGDB	NC_000007.13 - 27946855	Apr 26, 2020 (154)
89	Korean Genome Project	NC_000007.14 - 27907236	Apr 26, 2020 (154)
90	Northern Sweden	NC_000007.13 - 27946855	Jul 13, 2019 (153)
91	Qatari	NC_000007.13 - 27946855	Apr 26, 2020 (154)
92	SGDP_PRJ	NC_000007.13 - 27946855	Apr 26, 2020 (154)
93	Siberian	NC_000007.13 - 27946855	Apr 26, 2020 (154)
94	8.3KJPN	NC_000007.13 - 27946855	Apr 26, 2021 (155)
95	14KJPN	NC_000007.14 - 27907236	Oct 14, 2022 (156)
96	TopMed	NC_000007.14 - 27907236	Apr 26, 2021 (155)
97	UK 10K study - Twins	NC_000007.13 - 27946855	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000007.13 - 27946855	Jul 13, 2019 (153)
99	ALFA	NC_000007.14 - 27907236	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
21117643, ss3913940249	NC_000007.13:27946854:C:A	NC_000007.14:27907235:C:A	(self)
ss93649749, ss111725033, ss113504506, ss115998248, ss162160322, ss163884539, ss166327159, ss203114737, ss207987183, ss254143738, ss279237241, ss285595464, ss294036282, ss1593657306	NC_000007.12:27913379:C:T	NC_000007.14:27907235:C:T	(self)
36374742, 20280520, 14497061, 8290601, 9042313, 21117643, 7755655, 9372511, 18914746, 5056137, 40333736, 20280520, 4518655, ss222980268, ss233903177, ss240872787, ss559889338, ss654243358, ss984087244, ss1074467923, ss1324429600, ss1431067432, ss1582125662, ss1617840157, ss1660834190, ss1804926165, ss1927330581, ss1970656758, ss2024343964, ss2152539783, ss2626660430, ss2708197184, ss2851168646, ss3000828752, ss3347498299, ss3668758813, ss3734470790, ss3766342809, ss3785766306, ss3791075843, ss3795955597, ss3830481164, ss3838728118, ss3866897766, ss3913940249, ss5182364429, ss5372442591, ss5642597142, ss5822580441, ss5971801346, ss5980423353	NC_000007.13:27946854:C:T	NC_000007.14:27907235:C:T	(self)
47653148, 256486906, 3365230, 17497657, 55811821, 577301310, 150353476, ss2292702416, ss3025966364, ss3648590040, ss3719346499, ss3809509625, ss3844179486, ss3961119656, ss4739923751, ss5272265921, ss5469508102, ss5560127213, ss5721974717, ss5808445776, ss5855818291, ss5858208415	NC_000007.14:27907235:C:T	NC_000007.14:27907235:C:T	(self)
ss10375261	NT_007819.13:27240462:C:T	NC_000007.14:27907235:C:T	(self)
ss17929922, ss19711133, ss22622225, ss22932928	NT_007819.14:27240462:C:T	NC_000007.14:27907235:C:T	(self)
ss200, ss6504548, ss98141289, ss105510044, ss139745280, ss142783243, ss154554500	NT_007819.17:27936854:C:T	NC_000007.14:27907235: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 rs200

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

rs200