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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.

rs11586238

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:116720516 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.177324 (46936/264690, TOPMED)
G=0.186205 (26052/139910, GnomAD)
G=0.13157 (10354/78696, PAGE_STUDY) (+ 18 more)
G=0.04127 (1166/28256, 14KJPN)
G=0.20783 (3926/18890, ALFA)
G=0.04010 (672/16760, 8.3KJPN)
G=0.1530 (980/6404, 1000G_30x)
G=0.1520 (761/5008, 1000G)
G=0.2333 (1045/4480, Estonian)
G=0.2382 (918/3854, ALSPAC)
G=0.2352 (872/3708, TWINSUK)
G=0.0400 (117/2922, KOREAN)
G=0.1263 (239/1892, HapMap)
G=0.238 (238/998, GoNL)
G=0.037 (29/790, PRJEB37584)
G=0.265 (159/600, NorthernSweden)
G=0.162 (35/216, Qatari)
G=0.047 (10/212, Vietnamese)
C=0.412 (61/148, SGDP_PRJ)
G=0.40 (16/40, GENOME_DK)
C=0.47 (18/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
20 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 18890 C=0.79217 G=0.20783
European Sub 14286 C=0.76788 G=0.23212
African Sub 2946 C=0.8988 G=0.1012
African Others Sub 114 C=0.947 G=0.053
African American Sub 2832 C=0.8969 G=0.1031
Asian Sub 112 C=0.982 G=0.018
East Asian Sub 86 C=0.98 G=0.02
Other Asian Sub 26 C=1.00 G=0.00
Latin American 1 Sub 146 C=0.842 G=0.158
Latin American 2 Sub 610 C=0.798 G=0.202
South Asian Sub 98 C=0.79 G=0.21
Other Sub 692 C=0.793 G=0.207


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=0.822676 G=0.177324
gnomAD - Genomes Global Study-wide 139910 C=0.813795 G=0.186205
gnomAD - Genomes European Sub 75782 C=0.76215 G=0.23785
gnomAD - Genomes African Sub 41910 C=0.89678 G=0.10322
gnomAD - Genomes American Sub 13626 C=0.80735 G=0.19265
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.8355 G=0.1645
gnomAD - Genomes East Asian Sub 3132 C=0.9591 G=0.0409
gnomAD - Genomes Other Sub 2140 C=0.8121 G=0.1879
The PAGE Study Global Study-wide 78696 C=0.86843 G=0.13157
The PAGE Study AfricanAmerican Sub 32514 C=0.89288 G=0.10712
The PAGE Study Mexican Sub 10810 C=0.81702 G=0.18298
The PAGE Study Asian Sub 8316 C=0.9672 G=0.0328
The PAGE Study PuertoRican Sub 7916 C=0.8091 G=0.1909
The PAGE Study NativeHawaiian Sub 4534 C=0.8974 G=0.1026
The PAGE Study Cuban Sub 4230 C=0.8121 G=0.1879
The PAGE Study Dominican Sub 3828 C=0.8344 G=0.1656
The PAGE Study CentralAmerican Sub 2450 C=0.8314 G=0.1686
The PAGE Study SouthAmerican Sub 1982 C=0.8249 G=0.1751
The PAGE Study NativeAmerican Sub 1260 C=0.7913 G=0.2087
The PAGE Study SouthAsian Sub 856 C=0.776 G=0.224
14KJPN JAPANESE Study-wide 28256 C=0.95873 G=0.04127
Allele Frequency Aggregator Total Global 18890 C=0.79217 G=0.20783
Allele Frequency Aggregator European Sub 14286 C=0.76788 G=0.23212
Allele Frequency Aggregator African Sub 2946 C=0.8988 G=0.1012
Allele Frequency Aggregator Other Sub 692 C=0.793 G=0.207
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.798 G=0.202
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.842 G=0.158
Allele Frequency Aggregator Asian Sub 112 C=0.982 G=0.018
Allele Frequency Aggregator South Asian Sub 98 C=0.79 G=0.21
8.3KJPN JAPANESE Study-wide 16760 C=0.95990 G=0.04010
1000Genomes_30x Global Study-wide 6404 C=0.8470 G=0.1530
1000Genomes_30x African Sub 1786 C=0.9216 G=0.0784
1000Genomes_30x Europe Sub 1266 C=0.7433 G=0.2567
1000Genomes_30x South Asian Sub 1202 C=0.7712 G=0.2288
1000Genomes_30x East Asian Sub 1170 C=0.9598 G=0.0402
1000Genomes_30x American Sub 980 C=0.803 G=0.197
1000Genomes Global Study-wide 5008 C=0.8480 G=0.1520
1000Genomes African Sub 1322 C=0.9228 G=0.0772
1000Genomes East Asian Sub 1008 C=0.9573 G=0.0427
1000Genomes Europe Sub 1006 C=0.7396 G=0.2604
1000Genomes South Asian Sub 978 C=0.772 G=0.228
1000Genomes American Sub 694 C=0.811 G=0.189
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7667 G=0.2333
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7618 G=0.2382
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7648 G=0.2352
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9600 G=0.0400
HapMap Global Study-wide 1892 C=0.8737 G=0.1263
HapMap American Sub 770 C=0.830 G=0.170
HapMap African Sub 692 C=0.921 G=0.079
HapMap Asian Sub 254 C=0.933 G=0.067
HapMap Europe Sub 176 C=0.795 G=0.205
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.762 G=0.238
CNV burdens in cranial meningiomas Global Study-wide 790 C=0.963 G=0.037
CNV burdens in cranial meningiomas CRM Sub 790 C=0.963 G=0.037
Northern Sweden ACPOP Study-wide 600 C=0.735 G=0.265
Qatari Global Study-wide 216 C=0.838 G=0.162
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.953 G=0.047
SGDP_PRJ Global Study-wide 148 C=0.412 G=0.588
The Danish reference pan genome Danish Study-wide 40 C=0.60 G=0.40
Siberian Global Study-wide 38 C=0.47 G=0.53
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.p14 chr 1 NC_000001.11:g.116720516C>G
GRCh37.p13 chr 1 NC_000001.10:g.117263138C>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
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= G
GRCh38.p14 chr 1 NC_000001.11:g.116720516= NC_000001.11:g.116720516C>G
GRCh37.p13 chr 1 NC_000001.10:g.117263138= NC_000001.10:g.117263138C>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#.

70 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16436518 Feb 28, 2004 (120)
2 PERLEGEN ss24633253 Sep 20, 2004 (123)
3 ABI ss41066769 Mar 14, 2006 (126)
4 AFFY ss66172079 Dec 02, 2006 (127)
5 AFFY ss76227202 Dec 06, 2007 (129)
6 HGSV ss77168860 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82891191 Dec 14, 2007 (130)
8 ENSEMBL ss161162508 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss167040631 Jul 04, 2010 (132)
10 AFFY ss172886105 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss205216912 Jul 04, 2010 (132)
12 1000GENOMES ss218616508 Jul 14, 2010 (132)
13 1000GENOMES ss230706228 Jul 14, 2010 (132)
14 1000GENOMES ss238360137 Jul 15, 2010 (132)
15 TISHKOFF ss554620343 Apr 25, 2013 (138)
16 SSMP ss648337103 Apr 25, 2013 (138)
17 EVA-GONL ss975609488 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1068221014 Aug 21, 2014 (142)
19 1000GENOMES ss1292581441 Aug 21, 2014 (142)
20 DDI ss1425948144 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1574347003 Apr 01, 2015 (144)
22 EVA_DECODE ss1584991615 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1601071411 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1644065444 Apr 01, 2015 (144)
25 EVA_SVP ss1712366099 Apr 01, 2015 (144)
26 HAMMER_LAB ss1794986161 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1918807972 Feb 12, 2016 (147)
28 ILLUMINA ss1958306450 Feb 12, 2016 (147)
29 GENOMED ss1966850054 Jul 19, 2016 (147)
30 JJLAB ss2019929569 Sep 14, 2016 (149)
31 ILLUMINA ss2094847831 Dec 20, 2016 (150)
32 ILLUMINA ss2094973832 Dec 20, 2016 (150)
33 USC_VALOUEV ss2147948380 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2166021817 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624473863 Nov 08, 2017 (151)
36 GRF ss2697879170 Nov 08, 2017 (151)
37 GNOMAD ss2759986604 Nov 08, 2017 (151)
38 AFFY ss2984872219 Nov 08, 2017 (151)
39 AFFY ss2985523484 Nov 08, 2017 (151)
40 SWEGEN ss2987498910 Nov 08, 2017 (151)
41 ILLUMINA ss3021124786 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3023728712 Nov 08, 2017 (151)
43 CSHL ss3343652396 Nov 08, 2017 (151)
44 ILLUMINA ss3651457988 Oct 11, 2018 (152)
45 ILLUMINA ss3651457989 Oct 11, 2018 (152)
46 ILLUMINA ss3653644310 Oct 11, 2018 (152)
47 EGCUT_WGS ss3655589598 Jul 12, 2019 (153)
48 EVA_DECODE ss3687604007 Jul 12, 2019 (153)
49 ILLUMINA ss3725058053 Jul 12, 2019 (153)
50 ACPOP ss3727420950 Jul 12, 2019 (153)
51 EVA ss3746718208 Jul 12, 2019 (153)
52 PAGE_CC ss3770835638 Jul 12, 2019 (153)
53 KHV_HUMAN_GENOMES ss3799719340 Jul 12, 2019 (153)
54 EVA ss3826389303 Apr 25, 2020 (154)
55 SGDP_PRJ ss3849725374 Apr 25, 2020 (154)
56 KRGDB ss3894829426 Apr 25, 2020 (154)
57 EVA ss3984463580 Apr 25, 2021 (155)
58 TOPMED ss4464941544 Apr 25, 2021 (155)
59 TOMMO_GENOMICS ss5145847650 Apr 25, 2021 (155)
60 1000G_HIGH_COVERAGE ss5243737093 Oct 12, 2022 (156)
61 EVA ss5321422153 Oct 12, 2022 (156)
62 HUGCELL_USP ss5444648714 Oct 12, 2022 (156)
63 EVA ss5506009009 Oct 12, 2022 (156)
64 1000G_HIGH_COVERAGE ss5516797684 Oct 12, 2022 (156)
65 SANFORD_IMAGENETICS ss5626371163 Oct 12, 2022 (156)
66 TOMMO_GENOMICS ss5671165572 Oct 12, 2022 (156)
67 YY_MCH ss5800962566 Oct 12, 2022 (156)
68 EVA ss5832534229 Oct 12, 2022 (156)
69 EVA ss5909950008 Oct 12, 2022 (156)
70 EVA ss5938241519 Oct 12, 2022 (156)
71 1000Genomes NC_000001.10 - 117263138 Oct 11, 2018 (152)
72 1000Genomes_30x NC_000001.11 - 116720516 Oct 12, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 117263138 Oct 11, 2018 (152)
74 Genetic variation in the Estonian population NC_000001.10 - 117263138 Oct 11, 2018 (152)
75 The Danish reference pan genome NC_000001.10 - 117263138 Apr 25, 2020 (154)
76 gnomAD - Genomes NC_000001.11 - 116720516 Apr 25, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000001.10 - 117263138 Apr 25, 2020 (154)
78 HapMap NC_000001.11 - 116720516 Apr 25, 2020 (154)
79 KOREAN population from KRGDB NC_000001.10 - 117263138 Apr 25, 2020 (154)
80 Northern Sweden NC_000001.10 - 117263138 Jul 12, 2019 (153)
81 The PAGE Study NC_000001.11 - 116720516 Jul 12, 2019 (153)
82 CNV burdens in cranial meningiomas NC_000001.10 - 117263138 Apr 25, 2021 (155)
83 Qatari NC_000001.10 - 117263138 Apr 25, 2020 (154)
84 SGDP_PRJ NC_000001.10 - 117263138 Apr 25, 2020 (154)
85 Siberian NC_000001.10 - 117263138 Apr 25, 2020 (154)
86 8.3KJPN NC_000001.10 - 117263138 Apr 25, 2021 (155)
87 14KJPN NC_000001.11 - 116720516 Oct 12, 2022 (156)
88 TopMed NC_000001.11 - 116720516 Apr 25, 2021 (155)
89 UK 10K study - Twins NC_000001.10 - 117263138 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000001.10 - 117263138 Jul 12, 2019 (153)
91 ALFA NC_000001.11 - 116720516 Apr 25, 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)
rs17377407 Oct 07, 2004 (123)
rs56747362 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77168860 NC_000001.8:116975179:C:G NC_000001.11:116720515:C:G (self)
ss66172079, ss76227202, ss167040631, ss172886105, ss205216912, ss1584991615, ss1712366099, ss2094847831 NC_000001.9:117064660:C:G NC_000001.11:116720515:C:G (self)
3362525, 1862948, 1327846, 1679749, 809818, 2006820, 705815, 12892, 849902, 1742354, 464734, 3816957, 1862948, 402516, ss218616508, ss230706228, ss238360137, ss554620343, ss648337103, ss975609488, ss1068221014, ss1292581441, ss1425948144, ss1574347003, ss1601071411, ss1644065444, ss1794986161, ss1918807972, ss1958306450, ss1966850054, ss2019929569, ss2094973832, ss2147948380, ss2624473863, ss2697879170, ss2759986604, ss2984872219, ss2985523484, ss2987498910, ss3021124786, ss3343652396, ss3651457988, ss3651457989, ss3653644310, ss3655589598, ss3727420950, ss3746718208, ss3826389303, ss3849725374, ss3894829426, ss3984463580, ss5145847650, ss5321422153, ss5506009009, ss5626371163, ss5832534229, ss5938241519 NC_000001.10:117263137:C:G NC_000001.11:116720515:C:G (self)
4323619, 23782767, 162553, 57107, 5002676, 28547879, 13755198914, ss2166021817, ss3023728712, ss3687604007, ss3725058053, ss3770835638, ss3799719340, ss4464941544, ss5243737093, ss5444648714, ss5516797684, ss5671165572, ss5800962566, ss5909950008 NC_000001.11:116720515:C:G NC_000001.11:116720515:C:G (self)
ss16436518 NT_004754.15:1178722:C:G NC_000001.11:116720515:C:G (self)
ss24633253, ss41066769, ss82891191, ss161162508 NT_032977.9:87235055:C:G NC_000001.11:116720515:C:G (self)
Help

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

20 citations for rs11586238
PMID Title Author Year Journal
19898481 Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Raychaudhuri S et al. 2009 Nature genetics
20075733 Recent advances in the genetics of rheumatoid arthritis. Raychaudhuri S et al. 2010 Current opinion in rheumatology
20309874 Rheumatoid arthritis risk allele PTPRC is also associated with response to anti-tumor necrosis factor alpha therapy. Cui J et al. 2010 Arthritis and rheumatism
20453842 Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Stahl EA et al. 2010 Nature genetics
20510233 Leveraging human genetics to develop future therapeutic strategies in rheumatoid arthritis. Plenge RM et al. 2010 Rheumatic diseases clinics of North America
20805105 Synthetic associations in the context of genome-wide association scan signals. Orozco G et al. 2010 Human molecular genetics
21120996 Most common single-nucleotide polymorphisms associated with rheumatoid arthritis in persons of European ancestry confer risk of rheumatoid arthritis in African Americans. Hughes LB et al. 2010 Arthritis and rheumatism
21211616 Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Kurreeman F et al. 2011 American journal of human genetics
21931699 Genetic risk score predicting risk of rheumatoid arthritis phenotypes and age of symptom onset. Chibnik LB et al. 2011 PloS one
21963258 Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets. Hu X et al. 2011 American journal of human genetics
22294642 Investigation of rheumatoid arthritis susceptibility loci in juvenile idiopathic arthritis confirms high degree of overlap. Hinks A et al. 2012 Annals of the rheumatic diseases
22328738 Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort. Bowes J et al. 2012 Annals of the rheumatic diseases
22661644 Genetic markers of rheumatoid arthritis susceptibility in anti-citrullinated peptide antibody negative patients. Viatte S et al. 2012 Annals of the rheumatic diseases
23121884 Investigation of Caucasian rheumatoid arthritis susceptibility loci in African patients with the same disease. Viatte S et al. 2012 Arthritis research & therapy
23840476 Identification of the tyrosine-protein phosphatase non-receptor type 2 as a rheumatoid arthritis susceptibility locus in europeans. Cobb JE et al. 2013 PloS one
24068971 Predicting the risk of rheumatoid arthritis and its age of onset through modelling genetic risk variants with smoking. Scott IC et al. 2013 PLoS genetics
24449572 Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study. Orozco G et al. 2014 Arthritis & rheumatology (Hoboken, N.J.)
26843965 Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis. Saad MN et al. 2016 Journal of advanced research
27108704 Genetic polymorphisms of cell adhesion molecules in Behcet's disease in a Chinese Han population. Zheng M et al. 2016 Scientific reports
35088123 Genetics of rheumatoid arthritis. Padyukov L et al. 2022 Seminars in immunopathology
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.post761+d5e8e07