Name: rs194
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.

rs194

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:27904400 (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=0.376512 (99659/264690, TOPMED)
T=0.367178 (51402/139992, GnomAD)
T=0.36692 (19615/53458, ALFA) (+ 17 more)
C=0.47749 (13493/28258, 14KJPN)
C=0.48073 (8056/16758, 8.3KJPN)
T=0.4082 (2614/6404, 1000G_30x)
T=0.4067 (2037/5008, 1000G)
T=0.3623 (1623/4480, Estonian)
T=0.3495 (1347/3854, ALSPAC)
T=0.3541 (1313/3708, TWINSUK)
C=0.4898 (1435/2930, KOREAN)
T=0.4514 (854/1892, HapMap)
C=0.4891 (896/1832, Korea1K)
T=0.343 (342/998, GoNL)
T=0.435 (261/600, NorthernSweden)
C=0.338 (123/364, SGDP_PRJ)
T=0.352 (76/216, Qatari)
T=0.491 (105/214, Vietnamese)
T=0.28 (11/40, GENOME_DK)
C=0.38 (12/32, 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	53458	C=0.63308	T=0.36692
European	Sub	35502	C=0.65467	T=0.34533
African	Sub	5614	C=0.6316	T=0.3684
African Others	Sub	192	C=0.651	T=0.349
African American	Sub	5422	C=0.6309	T=0.3691
Asian	Sub	486	C=0.582	T=0.418
East Asian	Sub	388	C=0.546	T=0.454
Other Asian	Sub	98	C=0.72	T=0.28
Latin American 1	Sub	720	C=0.647	T=0.353
Latin American 2	Sub	7064	C=0.5293	T=0.4707
South Asian	Sub	174	C=0.626	T=0.374
Other	Sub	3898	C=0.6306	T=0.3694

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=0.623488	T=0.376512
gnomAD - Genomes	Global	Study-wide	139992	C=0.632822	T=0.367178
gnomAD - Genomes	European	Sub	75832	C=0.65599	T=0.34401
gnomAD - Genomes	African	Sub	41928	C=0.61997	T=0.38003
gnomAD - Genomes	American	Sub	13638	C=0.54656	T=0.45344
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.7384	T=0.2616
gnomAD - Genomes	East Asian	Sub	3126	C=0.5074	T=0.4926
gnomAD - Genomes	Other	Sub	2150	C=0.6330	T=0.3670
Allele Frequency Aggregator	Total	Global	53458	C=0.63308	T=0.36692
Allele Frequency Aggregator	European	Sub	35502	C=0.65467	T=0.34533
Allele Frequency Aggregator	Latin American 2	Sub	7064	C=0.5293	T=0.4707
Allele Frequency Aggregator	African	Sub	5614	C=0.6316	T=0.3684
Allele Frequency Aggregator	Other	Sub	3898	C=0.6306	T=0.3694
Allele Frequency Aggregator	Latin American 1	Sub	720	C=0.647	T=0.353
Allele Frequency Aggregator	Asian	Sub	486	C=0.582	T=0.418
Allele Frequency Aggregator	South Asian	Sub	174	C=0.626	T=0.374
14KJPN	JAPANESE	Study-wide	28258	C=0.47749	T=0.52251
8.3KJPN	JAPANESE	Study-wide	16758	C=0.48073	T=0.51927
1000Genomes_30x	Global	Study-wide	6404	C=0.5918	T=0.4082
1000Genomes_30x	African	Sub	1786	C=0.5929	T=0.4071
1000Genomes_30x	Europe	Sub	1266	C=0.6738	T=0.3262
1000Genomes_30x	South Asian	Sub	1202	C=0.6556	T=0.3444
1000Genomes_30x	East Asian	Sub	1170	C=0.5205	T=0.4795
1000Genomes_30x	American	Sub	980	C=0.491	T=0.509
1000Genomes	Global	Study-wide	5008	C=0.5933	T=0.4067
1000Genomes	African	Sub	1322	C=0.5885	T=0.4115
1000Genomes	East Asian	Sub	1008	C=0.5218	T=0.4782
1000Genomes	Europe	Sub	1006	C=0.6670	T=0.3330
1000Genomes	South Asian	Sub	978	C=0.660	T=0.340
1000Genomes	American	Sub	694	C=0.506	T=0.494
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6377	T=0.3623
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6505	T=0.3495
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6459	T=0.3541
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4898	T=0.5102
HapMap	Global	Study-wide	1892	C=0.5486	T=0.4514
HapMap	American	Sub	770	C=0.610	T=0.390
HapMap	African	Sub	692	C=0.470	T=0.530
HapMap	Asian	Sub	254	C=0.500	T=0.500
HapMap	Europe	Sub	176	C=0.659	T=0.341
Korean Genome Project	KOREAN	Study-wide	1832	C=0.4891	T=0.5109
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.657	T=0.343
Northern Sweden	ACPOP	Study-wide	600	C=0.565	T=0.435
SGDP_PRJ	Global	Study-wide	364	C=0.338	T=0.662
Qatari	Global	Study-wide	216	C=0.648	T=0.352
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.509	T=0.491
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	T=0.28
Siberian	Global	Study-wide	32	C=0.38	T=0.62

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.27904400C>T
GRCh37.p13 chr 7	NC_000007.13:g.27944019C>T
JAZF1 RefSeqGene	NG_011499.1:g.281419G>A

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

Molecule type	Change	Amino acid[Codon]	SO Term
JAZF1 transcript	NM_175061.4:c.189-8984G>A	N/A	Intron Variant
JAZF1 transcript variant X1	XM_047420024.1:c.189-8984… XM_047420024.1:c.189-8984G>A	N/A	Intron Variant
JAZF1 transcript variant X2	XM_047420025.1:c.-4-8984G… XM_047420025.1:c.-4-8984G>A	N/A	Intron Variant
JAZF1 transcript variant X3	XM_047420026.1:c.-4-8984G… XM_047420026.1:c.-4-8984G>A	N/A	Intron Variant
JAZF1 transcript variant X4	XM_047420027.1:c.-4-8984G… XM_047420027.1:c.-4-8984G>A	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=	T
GRCh38.p14 chr 7	NC_000007.14:g.27904400=	NC_000007.14:g.27904400C>T
GRCh37.p13 chr 7	NC_000007.13:g.27944019=	NC_000007.13:g.27944019C>T
JAZF1 RefSeqGene	NG_011499.1:g.281419=	NG_011499.1:g.281419G>A
JAZF1 transcript	NM_175061.3:c.189-8984=	NM_175061.3:c.189-8984G>A
JAZF1 transcript	NM_175061.4:c.189-8984=	NM_175061.4:c.189-8984G>A
JAZF1 transcript variant X1	XM_047420024.1:c.189-8984=	XM_047420024.1:c.189-8984G>A
JAZF1 transcript variant X2	XM_047420025.1:c.-4-8984=	XM_047420025.1:c.-4-8984G>A
JAZF1 transcript variant X3	XM_047420026.1:c.-4-8984=	XM_047420026.1:c.-4-8984G>A
JAZF1 transcript variant X4	XM_047420027.1:c.-4-8984=	XM_047420027.1:c.-4-8984G>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#.

81 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss194	Sep 19, 2000 (36)
2	BCM_SSAHASNP	ss10398499	Jul 11, 2003 (116)
3	ABI	ss44840149	Mar 13, 2006 (126)
4	AFFY	ss66438376	Nov 30, 2006 (127)
5	AFFY	ss76217384	Dec 07, 2007 (129)
6	HGSV	ss78193290	Dec 07, 2007 (129)
7	HGSV	ss78823889	Dec 07, 2007 (129)
8	KRIBB_YJKIM	ss81403823	Dec 16, 2007 (130)
9	HGSV	ss82236548	Dec 15, 2007 (130)
10	HGSV	ss82568087	Dec 15, 2007 (130)
11	HGSV	ss84850116	Dec 15, 2007 (130)
12	HUMANGENOME_JCVI	ss98244179	Feb 05, 2009 (130)
13	1000GENOMES	ss111724992	Jan 25, 2009 (130)
14	1000GENOMES	ss113504475	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss115998226	Feb 14, 2009 (130)
16	ENSEMBL	ss143500196	Dec 01, 2009 (131)
17	GMI	ss154554459	Dec 01, 2009 (131)
18	ILLUMINA	ss160479046	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss162160287	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss163884477	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss166327093	Jul 04, 2010 (132)
22	AFFY	ss172849861	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss207927417	Jul 04, 2010 (132)
24	1000GENOMES	ss222980253	Jul 14, 2010 (132)
25	1000GENOMES	ss233903168	Jul 15, 2010 (132)
26	1000GENOMES	ss240872774	Jul 15, 2010 (132)
27	BL	ss254143708	May 09, 2011 (134)
28	GMI	ss279237224	May 04, 2012 (137)
29	PJP	ss294036276	May 09, 2011 (134)
30	ILLUMINA	ss410873791	Sep 17, 2011 (135)
31	ILLUMINA	ss481131586	Sep 08, 2015 (146)
32	TISHKOFF	ss559889327	Apr 25, 2013 (138)
33	SSMP	ss654243347	Apr 25, 2013 (138)
34	EVA-GONL	ss984087209	Aug 21, 2014 (142)
35	JMKIDD_LAB	ss1074467909	Aug 21, 2014 (142)
36	1000GENOMES	ss1324429527	Aug 21, 2014 (142)
37	DDI	ss1431067426	Apr 01, 2015 (144)
38	EVA_GENOME_DK	ss1582125652	Apr 01, 2015 (144)
39	EVA_DECODE	ss1593657280	Apr 01, 2015 (144)
40	EVA_UK10K_ALSPAC	ss1617840126	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1660834159	Apr 01, 2015 (144)
42	EVA_SVP	ss1712941765	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1804926144	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1927330563	Feb 12, 2016 (147)
45	GENOMED	ss1970656746	Jul 19, 2016 (147)
46	JJLAB	ss2024343955	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2152539771	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2292702238	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2626660416	Nov 08, 2017 (151)
50	GRF	ss2708197170	Nov 08, 2017 (151)
51	GNOMAD	ss2851168406	Nov 08, 2017 (151)
52	SWEGEN	ss3000828709	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3025966357	Nov 08, 2017 (151)
54	CSHL	ss3347498291	Nov 08, 2017 (151)
55	ILLUMINA	ss3636844864	Oct 12, 2018 (152)
56	URBANLAB	ss3648590024	Oct 12, 2018 (152)
57	EGCUT_WGS	ss3668758770	Jul 13, 2019 (153)
58	EVA_DECODE	ss3719346454	Jul 13, 2019 (153)
59	ACPOP	ss3734470766	Jul 13, 2019 (153)
60	EVA	ss3766342782	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3809509601	Jul 13, 2019 (153)
62	EVA	ss3830481146	Apr 26, 2020 (154)
63	EVA	ss3838728104	Apr 26, 2020 (154)
64	EVA	ss3844179471	Apr 26, 2020 (154)
65	SGDP_PRJ	ss3866897721	Apr 26, 2020 (154)
66	KRGDB	ss3913940190	Apr 26, 2020 (154)
67	KOGIC	ss3961119616	Apr 26, 2020 (154)
68	TOPMED	ss4739923001	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5182364338	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5272265845	Oct 14, 2022 (156)
71	EVA	ss5372442460	Oct 14, 2022 (156)
72	HUGCELL_USP	ss5469508020	Oct 14, 2022 (156)
73	EVA	ss5508893464	Oct 14, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5560127107	Oct 14, 2022 (156)
75	SANFORD_IMAGENETICS	ss5642597097	Oct 14, 2022 (156)
76	TOMMO_GENOMICS	ss5721974595	Oct 14, 2022 (156)
77	YY_MCH	ss5808445747	Oct 14, 2022 (156)
78	EVA	ss5822580407	Oct 14, 2022 (156)
79	EVA	ss5855818272	Oct 14, 2022 (156)
80	EVA	ss5858208333	Oct 14, 2022 (156)
81	EVA	ss5971801304	Oct 14, 2022 (156)
82	1000Genomes	NC_000007.13 - 27944019	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000007.14 - 27904400	Oct 14, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 27944019	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000007.13 - 27944019	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000007.13 - 27944019	Apr 26, 2020 (154)
87	gnomAD - Genomes	NC_000007.14 - 27904400	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000007.13 - 27944019	Apr 26, 2020 (154)
89	HapMap	NC_000007.14 - 27904400	Apr 26, 2020 (154)
90	KOREAN population from KRGDB	NC_000007.13 - 27944019	Apr 26, 2020 (154)
91	Korean Genome Project	NC_000007.14 - 27904400	Apr 26, 2020 (154)
92	Northern Sweden	NC_000007.13 - 27944019	Jul 13, 2019 (153)
93	Qatari	NC_000007.13 - 27944019	Apr 26, 2020 (154)
94	SGDP_PRJ	NC_000007.13 - 27944019	Apr 26, 2020 (154)
95	Siberian	NC_000007.13 - 27944019	Apr 26, 2020 (154)
96	8.3KJPN	NC_000007.13 - 27944019	Apr 26, 2021 (155)
97	14KJPN	NC_000007.14 - 27904400	Oct 14, 2022 (156)
98	TopMed	NC_000007.14 - 27904400	Apr 26, 2021 (155)
99	UK 10K study - Twins	NC_000007.13 - 27944019	Oct 12, 2018 (152)
100	A Vietnamese Genetic Variation Database	NC_000007.13 - 27944019	Jul 13, 2019 (153)
101	ALFA	NC_000007.14 - 27904400	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)
rs59591664	May 25, 2008 (130)
rs61078546	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78193290, ss78823889, ss82236548, ss82568087, ss84850116	NC_000007.11:27717258:C:T	NC_000007.14:27904399:C:T	(self)
ss66438376, ss76217384, ss111724992, ss113504475, ss115998226, ss162160287, ss163884477, ss166327093, ss172849861, ss207927417, ss254143708, ss279237224, ss294036276, ss1593657280, ss1712941765	NC_000007.12:27910543:C:T	NC_000007.14:27904399:C:T	(self)
36374659, 20280477, 14497018, 8290591, 9042278, 21117584, 7755631, 9372493, 18914701, 5056125, 40333645, 20280477, 4518636, ss222980253, ss233903168, ss240872774, ss481131586, ss559889327, ss654243347, ss984087209, ss1074467909, ss1324429527, ss1431067426, ss1582125652, ss1617840126, ss1660834159, ss1804926144, ss1927330563, ss1970656746, ss2024343955, ss2152539771, ss2626660416, ss2708197170, ss2851168406, ss3000828709, ss3347498291, ss3636844864, ss3668758770, ss3734470766, ss3766342782, ss3830481146, ss3838728104, ss3866897721, ss3913940190, ss5182364338, ss5372442460, ss5508893464, ss5642597097, ss5822580407, ss5971801304	NC_000007.13:27944018:C:T	NC_000007.14:27904399:C:T	(self)
47653042, 256486290, 3365222, 17497617, 55811699, 577300560, 14272955649, ss2292702238, ss3025966357, ss3648590024, ss3719346454, ss3809509601, ss3844179471, ss3961119616, ss4739923001, ss5272265845, ss5469508020, ss5560127107, ss5721974595, ss5808445747, ss5855818272, ss5858208333	NC_000007.14:27904399:C:T	NC_000007.14:27904399:C:T	(self)
ss10398499	NT_007819.13:27237626:C:T	NC_000007.14:27904399:C:T	(self)
ss194, ss44840149, ss81403823, ss98244179, ss143500196, ss154554459, ss160479046, ss410873791	NT_007819.17:27934018:C:T	NC_000007.14:27904399: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 rs194

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

rs194