Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

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 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:27907236 (GRCh38.p13) 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=0.05315 (1004/18890, ALFA) (+ 16 more)
C=0.00000 (0/16758, 8.3KJPN)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.05315 T=0.94685
European Sub 14286 C=0.06223 T=0.93777
African Sub 2946 C=0.0112 T=0.9888
African Others Sub 114 C=0.009 T=0.991
African American Sub 2832 C=0.0113 T=0.9887
Asian Sub 112 C=0.000 T=1.000
East Asian Sub 86 C=0.00 T=1.00
Other Asian Sub 26 C=0.00 T=1.00
Latin American 1 Sub 146 C=0.082 T=0.918
Latin American 2 Sub 610 C=0.049 T=0.951
South Asian Sub 98 C=0.01 T=0.99
Other Sub 692 C=0.056 T=0.944


Help

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").

Download
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
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 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
Help

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.p13 chr 7 NC_000007.14:g.27907236C>A
GRCh38.p13 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_006715656.1:c.-5+6156G…

XM_006715656.1:c.-5+6156G>T

N/A Intron Variant
Help

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
Help

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.p13 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_006715656.1:c.-5+6156= XM_006715656.1:c.-5+6156G>T XM_006715656.1:c.-5+6156G>A
Help

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#.

69 SubSNP, 18 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 TOPMED ss2461567006 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2626660430 Nov 08, 2017 (151)
47 GRF ss2708197184 Nov 08, 2017 (151)
48 GNOMAD ss2851168646 Nov 08, 2017 (151)
49 SWEGEN ss3000828752 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3025966364 Nov 08, 2017 (151)
51 CSHL ss3347498299 Nov 08, 2017 (151)
52 TOPMED ss3525725864 Nov 08, 2017 (151)
53 URBANLAB ss3648590040 Oct 12, 2018 (152)
54 EGCUT_WGS ss3668758813 Jul 13, 2019 (153)
55 EVA_DECODE ss3719346499 Jul 13, 2019 (153)
56 ACPOP ss3734470790 Jul 13, 2019 (153)
57 EVA ss3766342809 Jul 13, 2019 (153)
58 PACBIO ss3785766306 Jul 13, 2019 (153)
59 PACBIO ss3791075843 Jul 13, 2019 (153)
60 PACBIO ss3795955597 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3809509625 Jul 13, 2019 (153)
62 EVA ss3830481164 Apr 26, 2020 (154)
63 EVA ss3838728118 Apr 26, 2020 (154)
64 EVA ss3844179486 Apr 26, 2020 (154)
65 SGDP_PRJ ss3866897766 Apr 26, 2020 (154)
66 KRGDB ss3913940249 Apr 26, 2020 (154)
67 KOGIC ss3961119656 Apr 26, 2020 (154)
68 TOPMED ss4739923751 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5182364429 Apr 26, 2021 (155)
70 1000Genomes NC_000007.13 - 27946855 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 27946855 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000007.13 - 27946855 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000007.13 - 27946855 Apr 26, 2020 (154)
74 gnomAD - Genomes NC_000007.14 - 27907236 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000007.13 - 27946855 Apr 26, 2020 (154)
76 HapMap NC_000007.14 - 27907236 Apr 26, 2020 (154)
77 KOREAN population from KRGDB NC_000007.13 - 27946855 Apr 26, 2020 (154)
78 Korean Genome Project NC_000007.14 - 27907236 Apr 26, 2020 (154)
79 Northern Sweden NC_000007.13 - 27946855 Jul 13, 2019 (153)
80 Qatari NC_000007.13 - 27946855 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000007.13 - 27946855 Apr 26, 2020 (154)
82 Siberian NC_000007.13 - 27946855 Apr 26, 2020 (154)
83 8.3KJPN NC_000007.13 - 27946855 Apr 26, 2021 (155)
84 TopMed NC_000007.14 - 27907236 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000007.13 - 27946855 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000007.13 - 27946855 Jul 13, 2019 (153)
87 ALFA NC_000007.14 - 27907236 Apr 26, 2021 (155)
Help

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, ss2461567006, ss2626660430, ss2708197184, ss2851168646, ss3000828752, ss3347498299, ss3668758813, ss3734470790, ss3766342809, ss3785766306, ss3791075843, ss3795955597, ss3830481164, ss3838728118, ss3866897766, ss3913940249, ss5182364429 NC_000007.13:27946854:C:T NC_000007.14:27907235:C:T (self)
256486906, 3365230, 17497657, 361137719, 577301310, 150353476, ss2292702416, ss3025966364, ss3525725864, ss3648590040, ss3719346499, ss3809509625, ss3844179486, ss3961119656, ss4739923751 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)
Help

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

Help

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.

Software version is: 2.0.1.post629+eb05767