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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs2451258

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:159085568 (GRCh38.p7) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.24645 (30946/125568, TOPMED)
C=0.2387 (7361/30840, GnomAD)
C=0.173 (868/5008, 1000G) (+ 2 more)
C=0.370 (1426/3854, ALSPAC)
C=0.356 (1321/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
4 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.p7 chr 6 NC_000006.12:g.159085568C>T
GRCh37.p13 chr 6 NC_000006.11:g.159506600C>T
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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.24645 T=0.75355
The Genome Aggregation Database Global Study-wide 30840 C=0.2387 T=0.7613
The Genome Aggregation Database European Sub 18426 C=0.3152 T=0.6848
The Genome Aggregation Database African Sub 8686 C=0.108 T=0.892
The Genome Aggregation Database East Asian Sub 1612 C=0.080 T=0.920
The Genome Aggregation Database Other Sub 980 C=0.27 T=0.73
The Genome Aggregation Database American Sub 834 C=0.17 T=0.83
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.29 T=0.71
1000Genomes Global Study-wide 5008 C=0.173 T=0.827
1000Genomes African Sub 1322 C=0.087 T=0.913
1000Genomes East Asian Sub 1008 C=0.063 T=0.937
1000Genomes Europe Sub 1006 C=0.348 T=0.652
1000Genomes South Asian Sub 978 C=0.22 T=0.78
1000Genomes American Sub 694 C=0.17 T=0.83
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.370 T=0.630
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.356 T=0.644
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= T Note
GRCh38.p7 chr 6 NC_000006.12:g.159085568C= NC_000006.12:g.15908556...

NC_000006.12:g.159085568C>T

GRCh37.p13 chr 6 NC_000006.11:g.159506600C= NC_000006.11:g.15950660...

NC_000006.11:g.159506600C>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#.

5 Frequency, 83 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3435975 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss10298332 Jul 11, 2003 (116)
3 SC_SNP ss12809134 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss17899922 Feb 27, 2004 (120)
5 SSAHASNP ss22421592 Apr 05, 2004 (123)
6 PERLEGEN ss24622789 Sep 20, 2004 (123)
7 ABI ss44775746 Mar 14, 2006 (126)
8 CSHL-HAPMAP ss68398703 Jan 12, 2007 (127)
9 PERLEGEN ss68998312 May 17, 2007 (127)
10 HGSV ss78821593 Dec 07, 2007 (129)
11 HGSV ss82783969 Dec 14, 2007 (130)
12 BCMHGSC_JDW ss93591819 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss98442425 Feb 04, 2009 (130)
14 BGI ss105465101 Feb 04, 2009 (130)
15 1000GENOMES ss111202897 Jan 25, 2009 (130)
16 1000GENOMES ss115391594 Jan 25, 2009 (130)
17 ILLUMINA-UK ss116793266 Feb 14, 2009 (130)
18 ENSEMBL ss144178378 Dec 01, 2009 (131)
19 ENSEMBL ss144399569 Dec 01, 2009 (131)
20 GMI ss157810385 Dec 01, 2009 (131)
21 ILLUMINA ss160549088 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss162960168 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss165071149 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss167437771 Jul 04, 2010 (132)
25 ILLUMINA ss173352131 Jul 04, 2010 (132)
26 BUSHMAN ss202667959 Jul 04, 2010 (132)
27 1000GENOMES ss222788934 Jul 14, 2010 (132)
28 1000GENOMES ss233764000 Jul 15, 2010 (132)
29 1000GENOMES ss240762171 Jul 15, 2010 (132)
30 BL ss254783046 May 09, 2011 (134)
31 GMI ss279100912 May 04, 2012 (137)
32 GMI ss285538367 Apr 25, 2013 (138)
33 PJP ss293772995 May 09, 2011 (134)
34 ILLUMINA ss480573903 May 04, 2012 (137)
35 ILLUMINA ss480588374 May 04, 2012 (137)
36 ILLUMINA ss481410672 Sep 08, 2015 (146)
37 ILLUMINA ss485082472 May 04, 2012 (137)
38 ILLUMINA ss537092630 Sep 08, 2015 (146)
39 TISHKOFF ss559661612 Apr 25, 2013 (138)
40 SSMP ss654004839 Apr 25, 2013 (138)
41 ILLUMINA ss778496726 Sep 08, 2015 (146)
42 ILLUMINA ss782987539 Aug 21, 2014 (142)
43 ILLUMINA ss783948410 Sep 08, 2015 (146)
44 ILLUMINA ss832244255 Apr 01, 2015 (144)
45 ILLUMINA ss833952787 Sep 08, 2015 (146)
46 EVA-GONL ss983719785 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1074199324 Aug 21, 2014 (142)
48 1000GENOMES ss1323109156 Aug 21, 2014 (142)
49 DDI ss1430956761 Apr 01, 2015 (144)
50 EVA_GENOME_DK ss1581980352 Apr 01, 2015 (144)
51 EVA_DECODE ss1593296179 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1617148762 Apr 01, 2015 (144)
53 EVA_UK10K_TWINSUK ss1660142795 Apr 01, 2015 (144)
54 ILLUMINA ss1752612183 Sep 08, 2015 (146)
55 HAMMER_LAB ss1804766432 Sep 08, 2015 (146)
56 WEILL_CORNELL_DGM ss1926961872 Feb 12, 2016 (147)
57 GENOMED ss1970573448 Jul 19, 2016 (147)
58 JJLAB ss2024147089 Sep 14, 2016 (149)
59 ILLUMINA ss2094968469 Dec 20, 2016 (150)
60 ILLUMINA ss2095192724 Dec 20, 2016 (150)
61 ILLUMINA ss2095192725 Dec 20, 2016 (150)
62 USC_VALOUEV ss2152339869 Dec 20, 2016 (150)
63 HUMAN_LONGEVITY ss2290130879 Dec 20, 2016 (150)
64 TOPMED ss2458820457 Dec 20, 2016 (150)
65 SYSTEMSBIOZJU ss2626563115 Nov 08, 2017 (151)
66 ILLUMINA ss2634538040 Nov 08, 2017 (151)
67 GRF ss2707978081 Nov 08, 2017 (151)
68 GNOMAD ss2847485008 Nov 08, 2017 (151)
69 SWEGEN ss3000284005 Nov 08, 2017 (151)
70 ILLUMINA ss3022686349 Nov 08, 2017 (151)
71 BIOINF_KMB_FNS_UNIBA ss3025864115 Nov 08, 2017 (151)
72 CSHL ss3347324346 Nov 08, 2017 (151)
73 TOPMED ss3517304541 Nov 08, 2017 (151)
74 ILLUMINA ss3629703839 Jul 20, 2018 (151)
75 ILLUMINA ss3632449874 Jul 20, 2018 (151)
76 ILLUMINA ss3633444894 Jul 20, 2018 (151)
77 ILLUMINA ss3634168807 Jul 20, 2018 (151)
78 ILLUMINA ss3635098072 Jul 20, 2018 (151)
79 ILLUMINA ss3635849081 Jul 20, 2018 (151)
80 ILLUMINA ss3636827082 Jul 20, 2018 (151)
81 ILLUMINA ss3637601977 Jul 20, 2018 (151)
82 ILLUMINA ss3638668877 Jul 20, 2018 (151)
83 ILLUMINA ss3640805373 Jul 20, 2018 (151)
84 1000Genomes NC_000006.11 - 159506600 Jul 20, 2018 (151)
85 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 159506600 Jul 20, 2018 (151)
86 The Genome Aggregation Database NC_000006.11 - 159506600 Jul 20, 2018 (151)
87 Trans-Omics for Precision Medicine NC_000006.12 - 159085568 Jul 20, 2018 (151)
88 UK 10K study - Twins NC_000006.11 - 159506600 Jul 20, 2018 (151)
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)
rs13201535 Sep 24, 2004 (123)
rs17218022 Oct 08, 2004 (123)
rs57157134 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78821593, ss82783969 NC_000006.9:159477008:C= NC_000006.12:159085567:C= (self)
ss93591819, ss111202897, ss115391594, ss116793266, ss162960168, ss165071149, ss167437771, ss202667959, ss254783046, ss279100912, ss285538367, ss293772995, ss480573903, ss1593296179, ss2094968469 NC_000006.10:159426587:C= NC_000006.12:159085567:C= (self)
35010177, 19525060, 188112765, 19525060, ss222788934, ss233764000, ss240762171, ss480588374, ss481410672, ss485082472, ss537092630, ss559661612, ss654004839, ss778496726, ss782987539, ss783948410, ss832244255, ss833952787, ss983719785, ss1074199324, ss1323109156, ss1430956761, ss1581980352, ss1617148762, ss1660142795, ss1752612183, ss1804766432, ss1926961872, ss1970573448, ss2024147089, ss2095192724, ss2095192725, ss2152339869, ss2458820457, ss2626563115, ss2634538040, ss2707978081, ss2847485008, ss3000284005, ss3022686349, ss3347324346, ss3629703839, ss3632449874, ss3633444894, ss3634168807, ss3635098072, ss3635849081, ss3636827082, ss3637601977, ss3638668877, ss3640805373 NC_000006.11:159506599:C= NC_000006.12:159085567:C= (self)
354277378, ss2290130879, ss3025864115, ss3517304541 NC_000006.12:159085567:C= NC_000006.12:159085567:C= (self)
ss10298332, ss12809134, ss17899922, ss22421592 NT_007422.12:1793938:C= NC_000006.12:159085567:C= (self)
ss3435975, ss24622789, ss44775746, ss68398703, ss68998312, ss98442425, ss105465101, ss144178378, ss144399569, ss157810385, ss160549088, ss173352131 NT_025741.15:63676056:C= NC_000006.12:159085567:C= (self)
ss78821593, ss82783969 NC_000006.9:159477008:C>T NC_000006.12:159085567:C>T (self)
ss93591819, ss111202897, ss115391594, ss116793266, ss162960168, ss165071149, ss167437771, ss202667959, ss254783046, ss279100912, ss285538367, ss293772995, ss480573903, ss1593296179, ss2094968469 NC_000006.10:159426587:C>T NC_000006.12:159085567:C>T (self)
35010177, 19525060, 188112765, 19525060, ss222788934, ss233764000, ss240762171, ss480588374, ss481410672, ss485082472, ss537092630, ss559661612, ss654004839, ss778496726, ss782987539, ss783948410, ss832244255, ss833952787, ss983719785, ss1074199324, ss1323109156, ss1430956761, ss1581980352, ss1617148762, ss1660142795, ss1752612183, ss1804766432, ss1926961872, ss1970573448, ss2024147089, ss2095192724, ss2095192725, ss2152339869, ss2458820457, ss2626563115, ss2634538040, ss2707978081, ss2847485008, ss3000284005, ss3022686349, ss3347324346, ss3629703839, ss3632449874, ss3633444894, ss3634168807, ss3635098072, ss3635849081, ss3636827082, ss3637601977, ss3638668877, ss3640805373 NC_000006.11:159506599:C>T NC_000006.12:159085567:C>T (self)
354277378, ss2290130879, ss3025864115, ss3517304541 NC_000006.12:159085567:C>T NC_000006.12:159085567:C>T (self)
ss10298332, ss12809134, ss17899922, ss22421592 NT_007422.12:1793938:C>T NC_000006.12:159085567:C>T (self)
ss3435975, ss24622789, ss44775746, ss68398703, ss68998312, ss98442425, ss105465101, ss144178378, ss144399569, ss157810385, ss160549088, ss173352131 NT_025741.15:63676056:C>T NC_000006.12:159085567: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.

4 citations for rs2451258
PMID Title Author Year Journal
23886662 A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis. Weidinger S et al. 2013 Human molecular genetics
25651891 Dense genotyping of immune-related susceptibility loci reveals new insights into the genetics of psoriatic arthritis. Bowes J et al. 2015 Nature communications
26255310 Identifying a novel locus for psoriatic arthritis. Budu-Aggrey A et al. 2016 Rheumatology (Oxford, England)
26974007 Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Ellinghaus D et al. 2016 Nature genetics

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: 0.1.4.post833+d3ba21e