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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.

rs6835457

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:122589971 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.365832 (96832/264690, TOPMED)
G=0.348866 (48858/140048, GnomAD)
G=0.32076 (6437/20068, ALFA) (+ 15 more)
G=0.49982 (8377/16760, 8.3KJPN)
G=0.3704 (1855/5008, 1000G)
G=0.2467 (1105/4480, Estonian)
G=0.3420 (1318/3854, ALSPAC)
G=0.3635 (1348/3708, TWINSUK)
G=0.4860 (1424/2930, KOREAN)
G=0.341 (340/998, GoNL)
G=0.480 (378/788, PRJEB37584)
G=0.318 (191/600, NorthernSweden)
G=0.400 (132/330, HapMap)
A=0.353 (115/326, SGDP_PRJ)
G=0.287 (62/216, Qatari)
G=0.426 (92/216, Vietnamese)
G=0.33 (13/40, GENOME_DK)
A=0.33 (10/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 4 NC_000004.12:g.122589971A>G
GRCh37.p13 chr 4 NC_000004.11:g.123511126A>G
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 20068 A=0.67924 G=0.32076
European Sub 15436 A=0.69778 G=0.30222
African Sub 2946 A=0.5957 G=0.4043
African Others Sub 114 A=0.588 G=0.412
African American Sub 2832 A=0.5960 G=0.4040
Asian Sub 112 A=0.661 G=0.339
East Asian Sub 86 A=0.64 G=0.36
Other Asian Sub 26 A=0.73 G=0.27
Latin American 1 Sub 146 A=0.692 G=0.308
Latin American 2 Sub 610 A=0.666 G=0.334
South Asian Sub 98 A=0.72 G=0.28
Other Sub 720 A=0.629 G=0.371


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 A=0.634168 G=0.365832
gnomAD - Genomes Global Study-wide 140048 A=0.651134 G=0.348866
gnomAD - Genomes European Sub 75878 A=0.68767 G=0.31233
gnomAD - Genomes African Sub 41948 A=0.59888 G=0.40112
gnomAD - Genomes American Sub 13634 A=0.62652 G=0.37348
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.6585 G=0.3415
gnomAD - Genomes East Asian Sub 3114 A=0.5552 G=0.4448
gnomAD - Genomes Other Sub 2150 A=0.6647 G=0.3353
8.3KJPN JAPANESE Study-wide 16760 A=0.50018 G=0.49982
1000Genomes Global Study-wide 5008 A=0.6296 G=0.3704
1000Genomes African Sub 1322 A=0.6082 G=0.3918
1000Genomes East Asian Sub 1008 A=0.5149 G=0.4851
1000Genomes Europe Sub 1006 A=0.6829 G=0.3171
1000Genomes South Asian Sub 978 A=0.712 G=0.288
1000Genomes American Sub 694 A=0.644 G=0.356
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7533 G=0.2467
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6580 G=0.3420
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6365 G=0.3635
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.5140 G=0.4860
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.659 G=0.341
CNV burdens in cranial meningiomas Global Study-wide 788 A=0.520 G=0.480
CNV burdens in cranial meningiomas CRM Sub 788 A=0.520 G=0.480
Northern Sweden ACPOP Study-wide 600 A=0.682 G=0.318
HapMap Global Study-wide 330 A=0.600 G=0.400
HapMap African Sub 120 A=0.658 G=0.342
HapMap American Sub 120 A=0.650 G=0.350
HapMap Asian Sub 90 A=0.46 G=0.54
SGDP_PRJ Global Study-wide 326 A=0.353 G=0.647
Qatari Global Study-wide 216 A=0.713 G=0.287
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.574 G=0.426
The Danish reference pan genome Danish Study-wide 40 A=0.68 G=0.33
Siberian Global Study-wide 30 A=0.33 G=0.67
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 A= G
GRCh38.p13 chr 4 NC_000004.12:g.122589971= NC_000004.12:g.122589971A>G
GRCh37.p13 chr 4 NC_000004.11:g.123511126= NC_000004.11:g.123511126A>G
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#.

72 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10146547 Jul 11, 2003 (116)
2 WI_SSAHASNP ss14630018 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss19606198 Feb 27, 2004 (120)
4 SSAHASNP ss22205882 Apr 05, 2004 (121)
5 ABI ss42325440 Mar 13, 2006 (126)
6 HGSV ss82352687 Dec 15, 2007 (130)
7 HGSV ss82669632 Dec 15, 2007 (130)
8 HUMANGENOME_JCVI ss98859080 Feb 06, 2009 (130)
9 BGI ss104112620 Dec 01, 2009 (131)
10 1000GENOMES ss108297007 Jan 23, 2009 (130)
11 1000GENOMES ss110519236 Jan 24, 2009 (130)
12 ILLUMINA-UK ss117171176 Feb 14, 2009 (130)
13 VANHEEL_LAB_LONDON ss120247494 Dec 01, 2009 (131)
14 ENSEMBL ss135155558 Dec 01, 2009 (131)
15 GMI ss157840894 Dec 01, 2009 (131)
16 ILLUMINA ss161081988 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164237127 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss167110103 Jul 04, 2010 (132)
19 BUSHMAN ss199115604 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss206502756 Jul 04, 2010 (132)
21 1000GENOMES ss221185559 Jul 14, 2010 (132)
22 1000GENOMES ss232578523 Jul 14, 2010 (132)
23 1000GENOMES ss239828823 Jul 15, 2010 (132)
24 GMI ss277907929 May 04, 2012 (137)
25 PJP ss293178377 May 09, 2011 (134)
26 ILLUMINA ss479368108 Mar 15, 2016 (147)
27 TISHKOFF ss557821555 Apr 25, 2013 (138)
28 SSMP ss651631273 Apr 25, 2013 (138)
29 EVA-GONL ss980622757 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1071915714 Aug 21, 2014 (142)
31 1000GENOMES ss1311614331 Aug 21, 2014 (142)
32 DDI ss1430034079 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1580755024 Apr 01, 2015 (144)
34 EVA_DECODE ss1590130613 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1611071727 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1654065760 Apr 01, 2015 (144)
37 HAMMER_LAB ss1802129784 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1923865532 Feb 12, 2016 (147)
39 GENOMED ss1969855658 Jul 19, 2016 (147)
40 JJLAB ss2022516115 Sep 14, 2016 (149)
41 ILLUMINA ss2094936620 Dec 20, 2016 (150)
42 ILLUMINA ss2095149584 Dec 20, 2016 (150)
43 ILLUMINA ss2095149585 Dec 20, 2016 (150)
44 USC_VALOUEV ss2150647195 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2266733117 Dec 20, 2016 (150)
46 TOPMED ss2434602857 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2625754823 Nov 08, 2017 (151)
48 GRF ss2706130947 Nov 08, 2017 (151)
49 GNOMAD ss2814682032 Nov 08, 2017 (151)
50 SWEGEN ss2995473068 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3025035131 Nov 08, 2017 (151)
52 CSHL ss3345937766 Nov 08, 2017 (151)
53 TOPMED ss3441447225 Nov 08, 2017 (151)
54 URBANLAB ss3647837822 Oct 12, 2018 (152)
55 ILLUMINA ss3652900995 Oct 12, 2018 (152)
56 ILLUMINA ss3652900996 Oct 12, 2018 (152)
57 EGCUT_WGS ss3663375674 Jul 13, 2019 (153)
58 EVA_DECODE ss3712966632 Jul 13, 2019 (153)
59 ACPOP ss3731564705 Jul 13, 2019 (153)
60 EVA ss3762351769 Jul 13, 2019 (153)
61 PACBIO ss3784846079 Jul 13, 2019 (153)
62 PACBIO ss3790284091 Jul 13, 2019 (153)
63 PACBIO ss3795159552 Jul 13, 2019 (153)
64 KHV_HUMAN_GENOMES ss3805507003 Jul 13, 2019 (153)
65 EVA ss3828783731 Apr 26, 2020 (154)
66 EVA ss3837836383 Apr 26, 2020 (154)
67 EVA ss3843275571 Apr 26, 2020 (154)
68 SGDP_PRJ ss3859948149 Apr 26, 2020 (154)
69 KRGDB ss3906249179 Apr 26, 2020 (154)
70 EVA ss3984534445 Apr 26, 2021 (155)
71 TOPMED ss4630250562 Apr 26, 2021 (155)
72 TOMMO_GENOMICS ss5167779437 Apr 26, 2021 (155)
73 1000Genomes NC_000004.11 - 123511126 Oct 12, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 123511126 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000004.11 - 123511126 Oct 12, 2018 (152)
76 The Danish reference pan genome NC_000004.11 - 123511126 Apr 26, 2020 (154)
77 gnomAD - Genomes NC_000004.12 - 122589971 Apr 26, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000004.11 - 123511126 Apr 26, 2020 (154)
79 HapMap NC_000004.12 - 122589971 Apr 26, 2020 (154)
80 KOREAN population from KRGDB NC_000004.11 - 123511126 Apr 26, 2020 (154)
81 Northern Sweden NC_000004.11 - 123511126 Jul 13, 2019 (153)
82 CNV burdens in cranial meningiomas NC_000004.11 - 123511126 Apr 26, 2021 (155)
83 Qatari NC_000004.11 - 123511126 Apr 26, 2020 (154)
84 SGDP_PRJ NC_000004.11 - 123511126 Apr 26, 2020 (154)
85 Siberian NC_000004.11 - 123511126 Apr 26, 2020 (154)
86 8.3KJPN NC_000004.11 - 123511126 Apr 26, 2021 (155)
87 TopMed NC_000004.12 - 122589971 Apr 26, 2021 (155)
88 UK 10K study - Twins NC_000004.11 - 123511126 Oct 12, 2018 (152)
89 A Vietnamese Genetic Variation Database NC_000004.11 - 123511126 Jul 13, 2019 (153)
90 ALFA NC_000004.12 - 122589971 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)
rs60712192 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82352687, ss82669632 NC_000004.9:123868730:A:G NC_000004.12:122589970:A:G (self)
ss108297007, ss110519236, ss117171176, ss164237127, ss167110103, ss199115604, ss206502756, ss277907929, ss293178377, ss1590130613, ss2094936620 NC_000004.10:123730575:A:G NC_000004.12:122589970:A:G (self)
23081556, 12841160, 9113922, 6919963, 5682154, 13426573, 4849570, 83806, 5907462, 11965129, 3163549, 25748744, 12841160, 2825456, ss221185559, ss232578523, ss239828823, ss557821555, ss651631273, ss980622757, ss1071915714, ss1311614331, ss1430034079, ss1580755024, ss1611071727, ss1654065760, ss1802129784, ss1923865532, ss1969855658, ss2022516115, ss2095149584, ss2095149585, ss2150647195, ss2434602857, ss2625754823, ss2706130947, ss2814682032, ss2995473068, ss3345937766, ss3652900995, ss3652900996, ss3663375674, ss3731564705, ss3762351769, ss3784846079, ss3790284091, ss3795159552, ss3828783731, ss3837836383, ss3859948149, ss3906249179, ss3984534445, ss5167779437 NC_000004.11:123511125:A:G NC_000004.12:122589970:A:G (self)
163506117, 2700991, 292323787, 467628118, 14665125053, ss2266733117, ss3025035131, ss3441447225, ss3647837822, ss3712966632, ss3805507003, ss3843275571, ss4630250562 NC_000004.12:122589970:A:G NC_000004.12:122589970:A:G (self)
ss10146547 NT_016354.15:48006256:A:G NC_000004.12:122589970:A:G (self)
ss14630018, ss19606198, ss22205882 NT_016354.16:48006256:A:G NC_000004.12:122589970:A:G (self)
ss42325440, ss98859080, ss104112620, ss120247494, ss135155558, ss157840894, ss161081988, ss479368108 NT_016354.19:48058846:A:G NC_000004.12:122589970:A:G (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 rs6835457
PMID Title Author Year Journal
21425124 Fine-mapping and transethnic genotyping establish IL2/IL21 genetic association with lupus and localize this genetic effect to IL21. Hughes T et al. 2011 Arthritis and rheumatism
23172754 Implication of IL-2/IL-21 region in systemic sclerosis genetic susceptibility. Diaz-Gallo LM et al. 2013 Annals of the rheumatic diseases
26106387 Pathogenesis of Systemic Sclerosis. Pattanaik D et al. 2015 Frontiers in immunology
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