Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

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.

rs7021206

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr9:120921879 (GRCh38.p12) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.33800 (42442/125568, TOPMED)
G=0.3540 (11085/31316, GnomAD)
G=0.298 (1493/5008, 1000G) (+ 5 more)
G=0.393 (1762/4480, Estonian)
G=0.344 (1325/3854, ALSPAC)
G=0.357 (1323/3708, TWINSUK)
G=0.37 (224/600, NorthernSweden)
G=0.23 (50/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRAF1 : Intron Variant
Publications
3 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.p12 chr 9 NC_000009.12:g.120921879G>A
GRCh37.p13 chr 9 NC_000009.11:g.123684157G>A
TRAF1 RefSeqGene NG_023346.1:g.12295C>T
Gene: TRAF1, TNF receptor associated factor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRAF1 transcript variant 2 NM_001190945.1:c. N/A Intron Variant
TRAF1 transcript variant 1 NM_005658.5:c. N/A Intron Variant
TRAF1 transcript variant 3 NM_001190947.1:c. N/A Genic Upstream Transcript 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

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 125568 G=0.33800 A=0.66200
gnomAD - Genomes Global Study-wide 31316 G=0.3540 A=0.6460
gnomAD - Genomes European Sub 18860 G=0.3757 A=0.6243
gnomAD - Genomes African Sub 8686 G=0.329 A=0.671
gnomAD - Genomes East Asian Sub 1546 G=0.288 A=0.712
gnomAD - Genomes Other Sub 1088 G=0.371 A=0.629
gnomAD - Genomes American Sub 848 G=0.27 A=0.73
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.22 A=0.78
1000Genomes Global Study-wide 5008 G=0.298 A=0.702
1000Genomes African Sub 1322 G=0.331 A=0.669
1000Genomes East Asian Sub 1008 G=0.276 A=0.724
1000Genomes Europe Sub 1006 G=0.361 A=0.639
1000Genomes South Asian Sub 978 G=0.20 A=0.80
1000Genomes American Sub 694 G=0.32 A=0.68
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.393 A=0.607
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.344 A=0.656
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.357 A=0.643
Northern Sweden ACPOP Study-wide 600 G=0.37 A=0.63
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.23 A=0.77
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 G= A Note
GRCh38.p12 chr 9 NC_000009.12:g.120921879= NC_000009.12:g.12092187...

NC_000009.12:g.120921879G>A

GRCh37.p13 chr 9 NC_000009.11:g.123684157= NC_000009.11:g.12368415...

NC_000009.11:g.123684157G>A

TRAF1 RefSeqGene NG_023346.1:g.12295= NG_023346.1:g.12295C>T
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#.

66 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10495186 Jul 11, 2003 (116)
2 SC_SNP ss15856716 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss18003823 Feb 27, 2004 (120)
4 AFFY ss76847753 Dec 07, 2007 (129)
5 HGSV ss77533652 Dec 07, 2007 (129)
6 HGSV ss83144278 Dec 15, 2007 (130)
7 HGSV ss85603885 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss94138832 Mar 25, 2008 (129)
9 BGI ss104653466 Dec 01, 2009 (131)
10 KRIBB_YJKIM ss104942371 Feb 05, 2009 (130)
11 1000GENOMES ss109060922 Jan 23, 2009 (130)
12 1000GENOMES ss115043400 Jan 25, 2009 (130)
13 ILLUMINA-UK ss115796772 Feb 14, 2009 (130)
14 ENSEMBL ss144352228 Dec 01, 2009 (131)
15 GMI ss157953651 Dec 01, 2009 (131)
16 ILLUMINA ss161104799 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164829042 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss165792447 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss166923648 Jul 04, 2010 (132)
20 BUSHMAN ss200859519 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss206799062 Jul 04, 2010 (132)
22 1000GENOMES ss224445117 Jul 14, 2010 (132)
23 1000GENOMES ss234965202 Jul 15, 2010 (132)
24 1000GENOMES ss241713527 Jul 15, 2010 (132)
25 BL ss254536919 May 09, 2011 (134)
26 GMI ss280394198 May 04, 2012 (137)
27 PJP ss294368796 May 09, 2011 (134)
28 ILLUMINA ss479418482 Sep 08, 2015 (146)
29 TISHKOFF ss561623521 Apr 25, 2013 (138)
30 SSMP ss656119843 Apr 25, 2013 (138)
31 EVA-GONL ss986963123 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1076597461 Aug 21, 2014 (142)
33 1000GENOMES ss1335383853 Aug 21, 2014 (142)
34 DDI ss1431957095 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1583253205 Apr 01, 2015 (144)
36 EVA_DECODE ss1596603794 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1623527737 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1666521770 Apr 01, 2015 (144)
39 EVA_SVP ss1713139802 Apr 01, 2015 (144)
40 HAMMER_LAB ss1806153380 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1930275179 Feb 12, 2016 (147)
42 GENOMED ss1971305325 Jul 19, 2016 (147)
43 JJLAB ss2025861210 Sep 14, 2016 (149)
44 ILLUMINA ss2094998369 Dec 20, 2016 (150)
45 ILLUMINA ss2095225247 Dec 20, 2016 (150)
46 USC_VALOUEV ss2154090209 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2314281628 Dec 20, 2016 (150)
48 TOPMED ss2484797270 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2627397348 Nov 08, 2017 (151)
50 GRF ss2709971970 Nov 08, 2017 (151)
51 GNOMAD ss2882995886 Nov 08, 2017 (151)
52 SWEGEN ss3005560245 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3026713678 Nov 08, 2017 (151)
54 CSHL ss3348850758 Nov 08, 2017 (151)
55 TOPMED ss3600090752 Nov 08, 2017 (151)
56 ILLUMINA ss3636980437 Oct 12, 2018 (152)
57 URBANLAB ss3649235951 Oct 12, 2018 (152)
58 ILLUMINA ss3653517990 Oct 12, 2018 (152)
59 EGCUT_WGS ss3673103805 Jul 13, 2019 (153)
60 EVA_DECODE ss3724714441 Jul 13, 2019 (153)
61 ACPOP ss3736861514 Jul 13, 2019 (153)
62 EVA ss3769669113 Jul 13, 2019 (153)
63 PACBIO ss3786518651 Jul 13, 2019 (153)
64 PACBIO ss3791718702 Jul 13, 2019 (153)
65 PACBIO ss3796600232 Jul 13, 2019 (153)
66 KHV_HUMAN_GENOMES ss3812833816 Jul 13, 2019 (153)
67 1000Genomes NC_000009.11 - 123684157 Oct 12, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 123684157 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000009.11 - 123684157 Oct 12, 2018 (152)
70 gnomAD - Genomes NC_000009.11 - 123684157 Jul 13, 2019 (153)
71 Northern Sweden NC_000009.11 - 123684157 Jul 13, 2019 (153)
72 TopMed NC_000009.12 - 120921879 Oct 12, 2018 (152)
73 UK 10K study - Twins NC_000009.11 - 123684157 Oct 12, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000009.11 - 123684157 Jul 13, 2019 (153)
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)
rs59579013 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77533652, ss83144278, ss85603885 NC_000009.9:120763710:G:A NC_000009.12:120921878:G:A (self)
ss76847753, ss94138832, ss109060922, ss115043400, ss115796772, ss164829042, ss165792447, ss166923648, ss200859519, ss206799062, ss254536919, ss280394198, ss294368796, ss1596603794, ss1713139802, ss2094998369 NC_000009.10:122723977:G:A NC_000009.12:120921878:G:A (self)
47699054, 26509312, 18842053, 130457295, 10146379, 26509312, 5889369, ss224445117, ss234965202, ss241713527, ss479418482, ss561623521, ss656119843, ss986963123, ss1076597461, ss1335383853, ss1431957095, ss1583253205, ss1623527737, ss1666521770, ss1806153380, ss1930275179, ss1971305325, ss2025861210, ss2095225247, ss2154090209, ss2484797270, ss2627397348, ss2709971970, ss2882995886, ss3005560245, ss3348850758, ss3636980437, ss3653517990, ss3673103805, ss3736861514, ss3769669113, ss3786518651, ss3791718702, ss3796600232 NC_000009.11:123684156:G:A NC_000009.12:120921878:G:A (self)
419812032, ss2314281628, ss3026713678, ss3600090752, ss3649235951, ss3724714441, ss3812833816 NC_000009.12:120921878:G:A NC_000009.12:120921878:G:A (self)
ss10495186 NT_008470.15:25506782:G:A NC_000009.12:120921878:G:A (self)
ss15856716, ss18003823 NT_008470.16:25341891:G:A NC_000009.12:120921878:G:A (self)
ss104653466, ss104942371, ss144352228, ss157953651, ss161104799 NT_008470.19:52848688:G:A NC_000009.12:120921878:G:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs7021206
PMID Title Author Year Journal
19714643 TRAF1 polymorphisms associated with rheumatoid arthritis susceptibility in Asians and in Caucasians. Han TU et al. 2009 Arthritis and rheumatism
21492465 Single nucleotide polymorphisms at the TRAF1/C5 locus are associated with rheumatoid arthritis in a Han Chinese population. Zhu J et al. 2011 BMC medical genetics
23251581 Meta-analysis of 125 rheumatoid arthritis-related single nucleotide polymorphisms studied in the past two decades. Jiang Y et al. 2012 PloS one

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.post270+ab078da