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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.

rs198

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:27899420 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.164015 (43413/264690, TOPMED)
C=0.142954 (24195/169250, ALFA)
C=0.159939 (22412/140128, GnomAD) (+ 15 more)
C=0.04404 (738/16758, 8.3KJPN)
C=0.1334 (668/5008, 1000G)
C=0.1121 (502/4480, Estonian)
C=0.1565 (603/3854, ALSPAC)
C=0.1410 (523/3708, TWINSUK)
C=0.0464 (136/2930, KOREAN)
C=0.1275 (241/1890, HapMap)
C=0.1274 (144/1130, Daghestan)
C=0.127 (127/998, GoNL)
C=0.122 (73/600, NorthernSweden)
C=0.068 (37/546, SGDP_PRJ)
C=0.199 (43/216, Qatari)
C=0.019 (4/214, Vietnamese)
C=0.11 (6/56, Siberian)
C=0.07 (3/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
JAZF1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.27899420C>A
GRCh38.p13 chr 7 NC_000007.14:g.27899420C>G
GRCh38.p13 chr 7 NC_000007.14:g.27899420C>T
GRCh37.p13 chr 7 NC_000007.13:g.27939039C>A
GRCh37.p13 chr 7 NC_000007.13:g.27939039C>G
GRCh37.p13 chr 7 NC_000007.13:g.27939039C>T
JAZF1 RefSeqGene NG_011499.1:g.286399G>T
JAZF1 RefSeqGene NG_011499.1:g.286399G>C
JAZF1 RefSeqGene NG_011499.1:g.286399G>A
Gene: JAZF1, JAZF zinc finger 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
JAZF1 transcript NM_175061.4:c.189-4004G>T N/A Intron Variant
JAZF1 transcript variant X1 XM_006715656.1:c.-4-4004G…

XM_006715656.1:c.-4-4004G>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

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 169250 C=0.142954 G=0.000000, T=0.857046
European Sub 142426 C=0.140122 G=0.000000, T=0.859878
African Sub 9458 C=0.2479 G=0.0000, T=0.7521
African Others Sub 312 C=0.263 G=0.000, T=0.737
African American Sub 9146 C=0.2474 G=0.0000, T=0.7526
Asian Sub 716 C=0.035 G=0.000, T=0.965
East Asian Sub 552 C=0.043 G=0.000, T=0.957
Other Asian Sub 164 C=0.006 G=0.000, T=0.994
Latin American 1 Sub 884 C=0.139 G=0.000, T=0.861
Latin American 2 Sub 8432 C=0.0869 G=0.0000, T=0.9131
South Asian Sub 198 C=0.157 G=0.000, T=0.843
Other Sub 7136 C=0.1375 G=0.0000, T=0.8625


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=0.164015 T=0.835985
gnomAD - Genomes Global Study-wide 140128 C=0.159939 T=0.840061
gnomAD - Genomes European Sub 75920 C=0.12762 T=0.87238
gnomAD - Genomes African Sub 41946 C=0.24090 T=0.75910
gnomAD - Genomes American Sub 13660 C=0.12943 T=0.87057
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.1204 T=0.8796
gnomAD - Genomes East Asian Sub 3128 C=0.0355 T=0.9645
gnomAD - Genomes Other Sub 2152 C=0.1575 T=0.8425
8.3KJPN JAPANESE Study-wide 16758 C=0.04404 T=0.95596
1000Genomes Global Study-wide 5008 C=0.1334 T=0.8666
1000Genomes African Sub 1322 C=0.2564 T=0.7436
1000Genomes East Asian Sub 1008 C=0.0337 T=0.9663
1000Genomes Europe Sub 1006 C=0.1332 T=0.8668
1000Genomes South Asian Sub 978 C=0.100 T=0.900
1000Genomes American Sub 694 C=0.091 T=0.909
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.1121 T=0.8879
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.1565 T=0.8435
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.1410 T=0.8590
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.0464 A=0.0000, G=0.0000, T=0.9536
HapMap Global Study-wide 1890 C=0.1275 T=0.8725
HapMap American Sub 768 C=0.116 T=0.884
HapMap African Sub 692 C=0.168 T=0.832
HapMap Asian Sub 254 C=0.043 T=0.957
HapMap Europe Sub 176 C=0.142 T=0.858
Genome-wide autozygosity in Daghestan Global Study-wide 1130 C=0.1274 T=0.8726
Genome-wide autozygosity in Daghestan Daghestan Sub 626 C=0.147 T=0.853
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.118 T=0.882
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.082 T=0.918
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.120 T=0.880
Genome-wide autozygosity in Daghestan South Asian Sub 94 C=0.07 T=0.93
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.14 T=0.86
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.127 T=0.873
Northern Sweden ACPOP Study-wide 600 C=0.122 T=0.878
SGDP_PRJ Global Study-wide 546 C=0.068 T=0.932
Qatari Global Study-wide 216 C=0.199 T=0.801
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.019 T=0.981
Siberian Global Study-wide 56 C=0.11 T=0.89
The Danish reference pan genome Danish Study-wide 40 C=0.07 T=0.93
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 G T
GRCh38.p13 chr 7 NC_000007.14:g.27899420= NC_000007.14:g.27899420C>A NC_000007.14:g.27899420C>G NC_000007.14:g.27899420C>T
GRCh37.p13 chr 7 NC_000007.13:g.27939039= NC_000007.13:g.27939039C>A NC_000007.13:g.27939039C>G NC_000007.13:g.27939039C>T
JAZF1 RefSeqGene NG_011499.1:g.286399= NG_011499.1:g.286399G>T NG_011499.1:g.286399G>C NG_011499.1:g.286399G>A
JAZF1 transcript NM_175061.3:c.189-4004= NM_175061.3:c.189-4004G>T NM_175061.3:c.189-4004G>C NM_175061.3:c.189-4004G>A
JAZF1 transcript NM_175061.4:c.189-4004= NM_175061.4:c.189-4004G>T NM_175061.4:c.189-4004G>C NM_175061.4:c.189-4004G>A
JAZF1 transcript variant X1 XM_006715656.1:c.-4-4004= XM_006715656.1:c.-4-4004G>T XM_006715656.1:c.-4-4004G>C XM_006715656.1:c.-4-4004G>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#.

99 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss198 Sep 19, 2000 (36)
2 WI_SSAHASNP ss11907727 Jul 11, 2003 (116)
3 WI_SSAHASNP ss14320142 Dec 05, 2003 (120)
4 SSAHASNP ss22571542 Apr 05, 2004 (121)
5 SSAHASNP ss22953568 Apr 05, 2004 (121)
6 AFFY ss76457217 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss93649739 Mar 24, 2008 (129)
8 HUMANGENOME_JCVI ss98141284 Feb 05, 2009 (130)
9 KRIBB_YJKIM ss104807675 Feb 05, 2009 (130)
10 BGI ss105510032 Feb 05, 2009 (130)
11 1000GENOMES ss111724925 Jan 25, 2009 (130)
12 1000GENOMES ss113504415 Jan 25, 2009 (130)
13 ILLUMINA-UK ss115998208 Feb 14, 2009 (130)
14 ENSEMBL ss142796884 Dec 01, 2009 (131)
15 GMI ss154554404 Dec 01, 2009 (131)
16 ILLUMINA ss160483679 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss162160246 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss163884388 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss166327010 Jul 04, 2010 (132)
20 ILLUMINA ss173021970 Jul 04, 2010 (132)
21 BUSHMAN ss203114683 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208068830 Jul 04, 2010 (132)
23 1000GENOMES ss222980235 Jul 14, 2010 (132)
24 1000GENOMES ss233903151 Jul 15, 2010 (132)
25 1000GENOMES ss240872761 Jul 15, 2010 (132)
26 BL ss254143663 May 09, 2011 (134)
27 GMI ss279237209 May 04, 2012 (137)
28 GMI ss285595454 Apr 25, 2013 (138)
29 PJP ss294036269 May 09, 2011 (134)
30 ILLUMINA ss410873776 Sep 17, 2011 (135)
31 ILLUMINA ss480366208 May 04, 2012 (137)
32 ILLUMINA ss480378378 May 04, 2012 (137)
33 ILLUMINA ss481150069 Sep 08, 2015 (146)
34 ILLUMINA ss484980689 May 04, 2012 (137)
35 ILLUMINA ss537017242 Sep 08, 2015 (146)
36 TISHKOFF ss559889301 Apr 25, 2013 (138)
37 SSMP ss654243327 Apr 25, 2013 (138)
38 ILLUMINA ss778848521 Sep 08, 2015 (146)
39 ILLUMINA ss782936643 Sep 08, 2015 (146)
40 ILLUMINA ss783899334 Sep 08, 2015 (146)
41 ILLUMINA ss832192174 Sep 08, 2015 (146)
42 ILLUMINA ss834309151 Sep 08, 2015 (146)
43 EVA-GONL ss984087173 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1074467875 Aug 21, 2014 (142)
45 1000GENOMES ss1324429369 Aug 21, 2014 (142)
46 HAMMER_LAB ss1397488968 Sep 08, 2015 (146)
47 DDI ss1431067413 Apr 01, 2015 (144)
48 EVA_GENOME_DK ss1582125638 Apr 01, 2015 (144)
49 EVA_DECODE ss1593657229 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1617840039 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1660834072 Apr 01, 2015 (144)
52 EVA_SVP ss1712941761 Apr 01, 2015 (144)
53 ILLUMINA ss1752680707 Sep 08, 2015 (146)
54 HAMMER_LAB ss1804926135 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1927330530 Feb 12, 2016 (147)
56 GENOMED ss1970656735 Jul 19, 2016 (147)
57 JJLAB ss2024343939 Sep 14, 2016 (149)
58 USC_VALOUEV ss2152539748 Dec 20, 2016 (150)
59 HUMAN_LONGEVITY ss2292701913 Dec 20, 2016 (150)
60 TOPMED ss2461566518 Dec 20, 2016 (150)
61 SYSTEMSBIOZJU ss2626660405 Nov 08, 2017 (151)
62 ILLUMINA ss2634584229 Nov 08, 2017 (151)
63 ILLUMINA ss2635170565 Nov 08, 2017 (151)
64 GRF ss2708197145 Nov 08, 2017 (151)
65 ILLUMINA ss2711106661 Nov 08, 2017 (151)
66 GNOMAD ss2851167986 Nov 08, 2017 (151)
67 SWEGEN ss3000828656 Nov 08, 2017 (151)
68 BIOINF_KMB_FNS_UNIBA ss3025966344 Nov 08, 2017 (151)
69 CSHL ss3347498277 Nov 08, 2017 (151)
70 TOPMED ss3525724388 Nov 08, 2017 (151)
71 TOPMED ss3525724389 Nov 08, 2017 (151)
72 ILLUMINA ss3629779321 Oct 12, 2018 (152)
73 ILLUMINA ss3632492802 Oct 12, 2018 (152)
74 ILLUMINA ss3633457291 Oct 12, 2018 (152)
75 ILLUMINA ss3634181927 Oct 12, 2018 (152)
76 ILLUMINA ss3635113861 Oct 12, 2018 (152)
77 ILLUMINA ss3635861888 Oct 12, 2018 (152)
78 ILLUMINA ss3636844861 Oct 12, 2018 (152)
79 ILLUMINA ss3637614833 Oct 12, 2018 (152)
80 ILLUMINA ss3638687760 Oct 12, 2018 (152)
81 ILLUMINA ss3640821157 Oct 12, 2018 (152)
82 URBANLAB ss3648590015 Oct 12, 2018 (152)
83 EGCUT_WGS ss3668758696 Jul 13, 2019 (153)
84 EVA_DECODE ss3719346378 Jul 13, 2019 (153)
85 ACPOP ss3734470738 Jul 13, 2019 (153)
86 ILLUMINA ss3745413807 Jul 13, 2019 (153)
87 EVA ss3766342734 Jul 13, 2019 (153)
88 ILLUMINA ss3772906919 Jul 13, 2019 (153)
89 PACBIO ss3785766293 Jul 13, 2019 (153)
90 PACBIO ss3791075832 Jul 13, 2019 (153)
91 PACBIO ss3795955586 Jul 13, 2019 (153)
92 KHV_HUMAN_GENOMES ss3809509554 Jul 13, 2019 (153)
93 EVA ss3830481131 Apr 26, 2020 (154)
94 EVA ss3838728092 Apr 26, 2020 (154)
95 EVA ss3844179460 Apr 26, 2020 (154)
96 SGDP_PRJ ss3866897635 Apr 26, 2020 (154)
97 KRGDB ss3913940102 Apr 26, 2020 (154)
98 TOPMED ss4739921715 Apr 26, 2021 (155)
99 TOMMO_GENOMICS ss5182364174 Apr 26, 2021 (155)
100 1000Genomes NC_000007.13 - 27939039 Oct 12, 2018 (152)
101 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 27939039 Oct 12, 2018 (152)
102 Genome-wide autozygosity in Daghestan NC_000007.12 - 27905564 Apr 26, 2020 (154)
103 Genetic variation in the Estonian population NC_000007.13 - 27939039 Oct 12, 2018 (152)
104 The Danish reference pan genome NC_000007.13 - 27939039 Apr 26, 2020 (154)
105 gnomAD - Genomes NC_000007.14 - 27899420 Apr 26, 2021 (155)
106 Genome of the Netherlands Release 5 NC_000007.13 - 27939039 Apr 26, 2020 (154)
107 HapMap NC_000007.14 - 27899420 Apr 26, 2020 (154)
108 KOREAN population from KRGDB NC_000007.13 - 27939039 Apr 26, 2020 (154)
109 Northern Sweden NC_000007.13 - 27939039 Jul 13, 2019 (153)
110 Qatari NC_000007.13 - 27939039 Apr 26, 2020 (154)
111 SGDP_PRJ NC_000007.13 - 27939039 Apr 26, 2020 (154)
112 Siberian NC_000007.13 - 27939039 Apr 26, 2020 (154)
113 8.3KJPN NC_000007.13 - 27939039 Apr 26, 2021 (155)
114 TopMed NC_000007.14 - 27899420 Apr 26, 2021 (155)
115 UK 10K study - Twins NC_000007.13 - 27939039 Oct 12, 2018 (152)
116 A Vietnamese Genetic Variation Database NC_000007.13 - 27939039 Jul 13, 2019 (153)
117 ALFA NC_000007.14 - 27899420 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).

Associated ID History Updated (Build)
rs10304617 Feb 27, 2004 (120)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
21117496, ss3913940102 NC_000007.13:27939038:C:A NC_000007.14:27899419:C:A (self)
21117496, ss3913940102 NC_000007.13:27939038:C:G NC_000007.14:27899419:C:G (self)
6101428784, ss3525724388 NC_000007.14:27899419:C:G NC_000007.14:27899419:C:G (self)
463212, ss76457217, ss93649739, ss111724925, ss113504415, ss115998208, ss162160246, ss163884388, ss166327010, ss203114683, ss208068830, ss254143663, ss279237209, ss285595454, ss294036269, ss480366208, ss1397488968, ss1593657229, ss1712941761, ss2635170565 NC_000007.12:27905563:C:T NC_000007.14:27899419:C:T (self)
36374494, 20280381, 14496944, 8290577, 9042242, 21117496, 7755603, 9372460, 18914615, 5056102, 40333481, 20280381, 4518612, ss222980235, ss233903151, ss240872761, ss480378378, ss481150069, ss484980689, ss537017242, ss559889301, ss654243327, ss778848521, ss782936643, ss783899334, ss832192174, ss834309151, ss984087173, ss1074467875, ss1324429369, ss1431067413, ss1582125638, ss1617840039, ss1660834072, ss1752680707, ss1804926135, ss1927330530, ss1970656735, ss2024343939, ss2152539748, ss2461566518, ss2626660405, ss2634584229, ss2708197145, ss2711106661, ss2851167986, ss3000828656, ss3347498277, ss3629779321, ss3632492802, ss3633457291, ss3634181927, ss3635113861, ss3635861888, ss3636844861, ss3637614833, ss3638687760, ss3640821157, ss3668758696, ss3734470738, ss3745413807, ss3766342734, ss3772906919, ss3785766293, ss3791075832, ss3795955586, ss3830481131, ss3838728092, ss3866897635, ss3913940102, ss5182364174 NC_000007.13:27939038:C:T NC_000007.14:27899419:C:T (self)
256485264, 3365212, 361136448, 577299274, 6101428784, ss2292701913, ss3025966344, ss3525724389, ss3648590015, ss3719346378, ss3809509554, ss3844179460, ss4739921715 NC_000007.14:27899419:C:T NC_000007.14:27899419:C:T (self)
ss11907727 NT_007819.13:27232646:C:T NC_000007.14:27899419:C:T (self)
ss14320142, ss22571542, ss22953568 NT_007819.14:27232646:C:T NC_000007.14:27899419:C:T (self)
ss198, ss98141284, ss104807675, ss105510032, ss142796884, ss154554404, ss160483679, ss173021970, ss410873776 NT_007819.17:27929038:C:T NC_000007.14:27899419: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 rs198

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.post596+ae089ad