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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:113761186 (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.

C>A / C>T
Variation Type
SNV Single Nucleotide Variation
A=0.055472 (14683/264690, TOPMED)
A=0.085351 (18647/218474, ALFA)
A=0.068139 (9553/140198, GnomAD) (+ 18 more)
A=0.02511 (1976/78700, PAGE_STUDY)
T=0.00018 (3/16760, 8.3KJPN)
A=0.0258 (129/5008, 1000G)
A=0.1433 (642/4480, Estonian)
A=0.1017 (392/3854, ALSPAC)
A=0.1028 (381/3708, TWINSUK)
A=0.0371 (47/1268, HapMap)
A=0.0336 (38/1132, Daghestan)
A=0.098 (98/998, GoNL)
A=0.003 (2/792, PRJEB37584)
A=0.029 (18/626, Chileans)
A=0.118 (71/600, NorthernSweden)
A=0.16 (14/86, Ancient Sardinia)
A=0.10 (4/40, GENOME_DK)
C=0.50 (9/18, SGDP_PRJ)
A=0.50 (9/18, SGDP_PRJ)
C=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PHTF1 : 2KB Upstream Variant
50 citations
Genomic View
See rs on genome

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 1 NC_000001.11:g.113761186C>A
GRCh38.p13 chr 1 NC_000001.11:g.113761186C>T
GRCh37.p13 chr 1 NC_000001.10:g.114303808C>A
GRCh37.p13 chr 1 NC_000001.10:g.114303808C>T
Gene: PHTF1, putative homeodomain transcription factor 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
PHTF1 transcript variant 2 NM_001323041.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 3 NM_001323042.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 4 NM_001323043.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 5 NM_001323044.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 6 NM_001323045.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 7 NM_001323046.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 8 NM_001323047.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 9 NM_001323048.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 10 NM_001323049.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 11 NM_001323050.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 12 NM_001323051.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 13 NM_001323052.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 14 NM_001323053.2:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 1 NM_006608.3:c. N/A Upstream Transcript Variant
PHTF1 transcript variant 15 NR_136564.2:n. N/A Upstream Transcript Variant
PHTF1 transcript variant 16 NR_136565.2:n. N/A Upstream Transcript Variant
PHTF1 transcript variant 17 NR_136566.2:n. N/A Upstream Transcript Variant
PHTF1 transcript variant 18 NR_136567.2:n. N/A Upstream Transcript Variant
PHTF1 transcript variant 19 NR_136568.2:n. N/A Upstream Transcript Variant

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 (New)
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 218474 C=0.914649 A=0.085351
European Sub 181116 C=0.903990 A=0.096010
African Sub 10810 C=0.98298 A=0.01702
African Others Sub 364 C=0.997 A=0.003
African American Sub 10446 C=0.98248 A=0.01752
Asian Sub 6680 C=0.9994 A=0.0006
East Asian Sub 4790 C=1.0000 A=0.0000
Other Asian Sub 1890 C=0.9979 A=0.0021
Latin American 1 Sub 956 C=0.959 A=0.041
Latin American 2 Sub 5436 C=0.9667 A=0.0333
South Asian Sub 358 C=0.992 A=0.008
Other Sub 13118 C=0.93543 A=0.06457


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.944528 A=0.055472
gnomAD - Genomes Global Study-wide 140198 C=0.931861 A=0.068139
gnomAD - Genomes European Sub 75890 C=0.89346 A=0.10654
gnomAD - Genomes African Sub 42044 C=0.98428 A=0.01572
gnomAD - Genomes American Sub 13656 C=0.96119 A=0.03881
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9497 A=0.0503
gnomAD - Genomes East Asian Sub 3134 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9489 A=0.0511
The PAGE Study Global Study-wide 78700 C=0.97489 A=0.02511
The PAGE Study AfricanAmerican Sub 32516 C=0.98312 A=0.01688
The PAGE Study Mexican Sub 10810 C=0.96975 A=0.03025
The PAGE Study Asian Sub 8318 C=0.9994 A=0.0006
The PAGE Study PuertoRican Sub 7918 C=0.9437 A=0.0563
The PAGE Study NativeHawaiian Sub 4534 C=0.9764 A=0.0236
The PAGE Study Cuban Sub 4230 C=0.9378 A=0.0622
The PAGE Study Dominican Sub 3826 C=0.9817 A=0.0183
The PAGE Study CentralAmerican Sub 2450 C=0.9722 A=0.0278
The PAGE Study SouthAmerican Sub 1982 C=0.9733 A=0.0267
The PAGE Study NativeAmerican Sub 1260 C=0.9365 A=0.0635
The PAGE Study SouthAsian Sub 856 C=0.991 A=0.009
8.3KJPN JAPANESE Study-wide 16760 C=0.99982 T=0.00018
1000Genomes Global Study-wide 5008 C=0.9742 A=0.0258
1000Genomes African Sub 1322 C=0.9977 A=0.0023
1000Genomes East Asian Sub 1008 C=1.0000 A=0.0000
1000Genomes Europe Sub 1006 C=0.9085 A=0.0915
1000Genomes South Asian Sub 978 C=0.987 A=0.013
1000Genomes American Sub 694 C=0.970 A=0.030
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8567 A=0.1433
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8983 A=0.1017
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8972 A=0.1028
HapMap Global Study-wide 1268 C=0.9629 A=0.0371
HapMap American Sub 600 C=0.943 A=0.057
HapMap African Sub 406 C=0.998 A=0.002
HapMap Europe Sub 174 C=0.931 A=0.069
HapMap Asian Sub 88 C=1.00 A=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1132 C=0.9664 A=0.0336
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.967 A=0.033
Genome-wide autozygosity in Daghestan Near_East Sub 142 C=0.993 A=0.007
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.934 A=0.066
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.926 A=0.074
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=1.00 A=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 34 C=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.902 A=0.098
CNV burdens in cranial meningiomas Global Study-wide 792 C=0.997 A=0.003
CNV burdens in cranial meningiomas CRM Sub 792 C=0.997 A=0.003
Chileans Chilean Study-wide 626 C=0.971 A=0.029
Northern Sweden ACPOP Study-wide 600 C=0.882 A=0.118
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 86 C=0.84 A=0.16
The Danish reference pan genome Danish Study-wide 40 C=0.90 A=0.10
SGDP_PRJ Global Study-wide 18 C=0.50 A=0.50
Siberian Global Study-wide 6 C=0.5 A=0.5

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 T
GRCh38.p13 chr 1 NC_000001.11:g.113761186= NC_000001.11:g.113761186C>A NC_000001.11:g.113761186C>T
GRCh37.p13 chr 1 NC_000001.10:g.114303808= NC_000001.10:g.114303808C>A NC_000001.10:g.114303808C>T

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#.

81 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9855676 Jul 11, 2003 (116)
2 AFFY ss66195856 Dec 01, 2006 (127)
3 ILLUMINA ss75187089 Dec 07, 2007 (129)
4 AFFY ss76277608 Dec 07, 2007 (129)
5 KRIBB_YJKIM ss82287139 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss87727249 Mar 23, 2008 (129)
7 1000GENOMES ss108537478 Jan 23, 2009 (130)
8 ENSEMBL ss138063450 Dec 01, 2009 (131)
9 ILLUMINA ss160797216 Dec 01, 2009 (131)
10 AFFY ss173097150 Jul 04, 2010 (132)
11 ILLUMINA ss174066187 Jul 04, 2010 (132)
12 1000GENOMES ss230698676 Jul 14, 2010 (132)
13 ILLUMINA ss244305931 Jul 04, 2010 (132)
14 GMI ss284124179 Apr 25, 2013 (138)
15 PJP ss290602301 May 09, 2011 (134)
16 ILLUMINA ss410942626 Sep 17, 2011 (135)
17 ILLUMINA ss482321868 Sep 08, 2015 (146)
18 EXOME_CHIP ss491298565 May 04, 2012 (137)
19 ILLUMINA ss536071794 Sep 08, 2015 (146)
20 SSMP ss648324073 Apr 25, 2013 (138)
21 ILLUMINA ss780685963 Sep 08, 2015 (146)
22 ILLUMINA ss783359469 Sep 08, 2015 (146)
23 EVA-GONL ss975588088 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1068205979 Aug 21, 2014 (142)
25 1000GENOMES ss1292500571 Aug 21, 2014 (142)
26 HAMMER_LAB ss1397257914 Sep 08, 2015 (146)
27 EVA_GENOME_DK ss1574334304 Apr 01, 2015 (144)
28 EVA_DECODE ss1584968956 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1601026481 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1644020514 Apr 01, 2015 (144)
31 EVA_SVP ss1712364443 Apr 01, 2015 (144)
32 ILLUMINA ss1751864539 Sep 08, 2015 (146)
33 ILLUMINA ss1917732850 Feb 12, 2016 (147)
34 ILLUMINA ss1946005555 Feb 12, 2016 (147)
35 ILLUMINA ss1958304653 Feb 12, 2016 (147)
36 JJLAB ss2019918574 Sep 14, 2016 (149)
37 ILLUMINA ss2094847235 Dec 20, 2016 (150)
38 ILLUMINA ss2094972618 Dec 20, 2016 (150)
39 ILLUMINA ss2094972620 Dec 20, 2016 (150)
40 USC_VALOUEV ss2147937374 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2165854231 Dec 20, 2016 (150)
42 TOPMED ss2328219153 Dec 20, 2016 (150)
43 ILLUMINA ss2632565409 Nov 08, 2017 (151)
44 ILLUMINA ss2635002482 Nov 08, 2017 (151)
45 GNOMAD ss2759755700 Nov 08, 2017 (151)
46 AFFY ss2984871516 Nov 08, 2017 (151)
47 AFFY ss2985522540 Nov 08, 2017 (151)
48 SWEGEN ss2987466727 Nov 08, 2017 (151)
49 ILLUMINA ss3021122706 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3023723837 Nov 08, 2017 (151)
51 TOPMED ss3087256079 Nov 08, 2017 (151)
52 ILLUMINA ss3626186832 Oct 11, 2018 (152)
53 ILLUMINA ss3626186833 Oct 11, 2018 (152)
54 ILLUMINA ss3634344060 Oct 11, 2018 (152)
55 ILLUMINA ss3636022325 Oct 11, 2018 (152)
56 ILLUMINA ss3637781160 Oct 11, 2018 (152)
57 ILLUMINA ss3640051419 Oct 11, 2018 (152)
58 ILLUMINA ss3642790848 Oct 11, 2018 (152)
59 ILLUMINA ss3644501523 Oct 11, 2018 (152)
60 ILLUMINA ss3651455347 Oct 11, 2018 (152)
61 ILLUMINA ss3651455348 Oct 11, 2018 (152)
62 ILLUMINA ss3651455349 Oct 11, 2018 (152)
63 ILLUMINA ss3653643568 Oct 11, 2018 (152)
64 EGCUT_WGS ss3655555614 Jul 12, 2019 (153)
65 EVA_DECODE ss3687564584 Jul 12, 2019 (153)
66 ILLUMINA ss3725056191 Jul 12, 2019 (153)
67 ACPOP ss3727403442 Jul 12, 2019 (153)
68 ILLUMINA ss3744349959 Jul 12, 2019 (153)
69 ILLUMINA ss3744645008 Jul 12, 2019 (153)
70 PAGE_CC ss3770834200 Jul 12, 2019 (153)
71 ILLUMINA ss3772146203 Jul 12, 2019 (153)
72 PACBIO ss3783524487 Jul 12, 2019 (153)
73 PACBIO ss3789165530 Jul 12, 2019 (153)
74 PACBIO ss3794038463 Jul 12, 2019 (153)
75 EVA ss3826378950 Apr 25, 2020 (154)
76 SGDP_PRJ ss3849685315 Apr 25, 2020 (154)
77 EVA ss3984463242 Apr 25, 2021 (155)
78 EVA ss3984820434 Apr 25, 2021 (155)
79 EVA ss4016932938 Apr 25, 2021 (155)
80 TOPMED ss4464208316 Apr 25, 2021 (155)
81 TOMMO_GENOMICS ss5145758953 Apr 25, 2021 (155)
82 1000Genomes NC_000001.10 - 114303808 Oct 11, 2018 (152)
83 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 114303808 Oct 11, 2018 (152)
84 Chileans NC_000001.10 - 114303808 Apr 25, 2020 (154)
85 Genome-wide autozygosity in Daghestan NC_000001.9 - 114105331 Apr 25, 2020 (154)
86 Genetic variation in the Estonian population NC_000001.10 - 114303808 Oct 11, 2018 (152)
87 The Danish reference pan genome NC_000001.10 - 114303808 Apr 25, 2020 (154)
88 gnomAD - Genomes NC_000001.11 - 113761186 Apr 25, 2021 (155)
89 Genome of the Netherlands Release 5 NC_000001.10 - 114303808 Apr 25, 2020 (154)
90 HapMap NC_000001.11 - 113761186 Apr 25, 2020 (154)
91 Northern Sweden NC_000001.10 - 114303808 Jul 12, 2019 (153)
92 The PAGE Study NC_000001.11 - 113761186 Jul 12, 2019 (153)
93 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 114303808 Apr 25, 2021 (155)
94 CNV burdens in cranial meningiomas NC_000001.10 - 114303808 Apr 25, 2021 (155)
95 SGDP_PRJ NC_000001.10 - 114303808 Apr 25, 2020 (154)
96 Siberian NC_000001.10 - 114303808 Apr 25, 2020 (154)
97 8.3KJPN NC_000001.10 - 114303808 Apr 25, 2021 (155)
98 TopMed NC_000001.11 - 113761186 Apr 25, 2021 (155)
99 UK 10K study - Twins NC_000001.10 - 114303808 Oct 11, 2018 (152)
100 ALFA NC_000001.11 - 113761186 Apr 25, 2021 (155)

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)
rs58035578 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
19190, ss66195856, ss76277608, ss87727249, ss108537478, ss173097150, ss284124179, ss290602301, ss1397257914, ss1584968956, ss1712364443, ss2094847235, ss2635002482, ss3642790848 NC_000001.9:114105330:C:A NC_000001.11:113761185:C:A (self)
3278926, 1814024, 18992, 1293862, 1671816, 788903, 688307, 46361, 12554, 1702295, 453728, 1814024, ss230698676, ss482321868, ss491298565, ss536071794, ss648324073, ss780685963, ss783359469, ss975588088, ss1068205979, ss1292500571, ss1574334304, ss1601026481, ss1644020514, ss1751864539, ss1917732850, ss1946005555, ss1958304653, ss2019918574, ss2094972618, ss2094972620, ss2147937374, ss2328219153, ss2632565409, ss2759755700, ss2984871516, ss2985522540, ss2987466727, ss3021122706, ss3626186832, ss3626186833, ss3634344060, ss3636022325, ss3637781160, ss3640051419, ss3644501523, ss3651455347, ss3651455348, ss3651455349, ss3653643568, ss3655555614, ss3727403442, ss3744349959, ss3744645008, ss3772146203, ss3783524487, ss3789165530, ss3794038463, ss3826378950, ss3849685315, ss3984463242, ss3984820434, ss4016932938 NC_000001.10:114303807:C:A NC_000001.11:113761185:C:A (self)
23192778, 158425, 55669, 17521507, 27814651, 7036594580, ss2165854231, ss3023723837, ss3087256079, ss3687564584, ss3725056191, ss3770834200, ss4464208316 NC_000001.11:113761185:C:A NC_000001.11:113761185:C:A (self)
ss9855676 NT_019273.15:4739611:C:A NC_000001.11:113761185:C:A (self)
ss75187089, ss82287139, ss138063450, ss160797216, ss174066187, ss244305931, ss410942626 NT_032977.9:84275725:C:A NC_000001.11:113761185:C:A (self)
3728260, ss5145758953 NC_000001.10:114303807:C:T NC_000001.11:113761185:C:T

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

50 citations for rs6679677
PMID Title Author Year Journal
17554260 Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Todd JA et al. 2007 Nature genetics
18224312 Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Brockmöller J et al. 2008 European journal of clinical pharmacology
18274536 Genome-wide association studies: progress and potential for drug discovery and development. Kingsmore SF et al. 2008 Nature reviews. Drug discovery
18305142 PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. Smyth DJ et al. 2008 Diabetes
18533027 Worldwide population differentiation at disease-associated SNPs. Myles S et al. 2008 BMC medical genomics
18794853 Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Raychaudhuri S et al. 2008 Nature genetics
18853133 Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. Rafiq S et al. 2008 Diabetologia
19168599 Type 1 diabetes in the BB rat: a polygenic disease. Wallis RH et al. 2009 Diabetes
19474294 Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Hindorff LA et al. 2009 Proceedings of the National Academy of Sciences of the United States of America
19565500 Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis. Prahalad S et al. 2009 Arthritis and rheumatism
19639606 Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases. Zhong H et al. 2010 Genetic epidemiology
19956648 Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases. Eleftherohorinou H et al. 2009 PloS one
20017963 Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis. Bermejo JL et al. 2009 BMC proceedings
20088021 Screen and clean: a tool for identifying interactions in genome-wide association studies. Wu J et al. 2010 Genetic epidemiology
20089178 Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population. Douroudis K et al. 2010 BMC medical genetics
20122189 Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso. Yang C et al. 2010 BMC bioinformatics
20362271 Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. Ritchie MD et al. 2010 American journal of human genetics
20442747 Genome-wide gene and pathway analysis. Luo L et al. 2010 European journal of human genetics
20549515 Genome-wide searching of rare genetic variants in WTCCC data. Feng T et al. 2010 Human genetics
20722033 The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. Thompson SD et al. 2010 Arthritis and rheumatism
20808825 Novel association strategy with copy number variation for identifying new risk Loci of human diseases. Chen X et al. 2010 PloS one
20933377 Recent findings on genetics of systemic autoimmune diseases. Delgado-Vega A et al. 2010 Current opinion in immunology
21036813 A variable selection method for genome-wide association studies. He Q et al. 2011 Bioinformatics (Oxford, England)
21152001 Association of variants at 1q32 and STAT3 with ankylosing spondylitis suggests genetic overlap with Crohn's disease. Danoy P et al. 2010 PLoS genetics
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
21217814 Presymptomatic risk assessment for chronic non-communicable diseases. Padhukasahasram B et al. 2010 PloS one
21270278 An interferon-induced helicase (IFIH1) gene polymorphism associates with different rates of progression from autoimmunity to type 1 diabetes. Winkler C et al. 2011 Diabetes
21570397 Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles. Lucena MI et al. 2011 Gastroenterology
21622953 ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. Zhang K et al. 2011 Nucleic acids research
21926296 Experimental designs for robust detection of effects in genome-wide case-control studies. Ball RD et al. 2011 Genetics
22110093 Cesarean section and interferon-induced helicase gene polymorphisms combine to increase childhood type 1 diabetes risk. Bonifacio E et al. 2011 Diabetes
22493691 Novel associations for hypothyroidism include known autoimmune risk loci. Eriksson N et al. 2012 PloS one
22496761 Improving power of genome-wide association studies with weighted false discovery rate control and prioritized subset analysis. Lin WY et al. 2012 PloS one
22554139 Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. Ueki M et al. 2012 BMC bioinformatics
22661644 Genetic markers of rheumatoid arthritis susceptibility in anti-citrullinated peptide antibody negative patients. Viatte S et al. 2012 Annals of the rheumatic diseases
23095127 Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data. Sambo F et al. 2012 BMC bioinformatics
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.)
24988487 Coherent somatic mutation in autoimmune disease. Ross KA et al. 2014 PloS one
25061809 Analyzing genome-wide association studies with an FDR controlling modification of the Bayesian Information Criterion. Dolejsi E et al. 2014 PloS one
25652333 Genetics of serum concentration of IL-6 and TNFα in systemic lupus erythematosus and rheumatoid arthritis: a candidate gene analysis. Solus JF et al. 2015 Clinical rheumatology
25829454 Novel Association Between Immune-Mediated Susceptibility Loci and Persistent Autoantibody Positivity in Type 1 Diabetes. Brorsson CA et al. 2015 Diabetes
27109064 Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis. Wei WH et al. 2016 Scientific reports
27109359 Identifying genetically driven clinical phenotypes using linear mixed models. Mosley JD et al. 2016 Nature communications
27153677 Assessing statistical significance in multivariable genome wide association analysis. Buzdugan L et al. 2016 Bioinformatics (Oxford, England)
27156530 Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Ye BD et al. 2016 Expert review of clinical immunology
27716086 Association of CD247 (CD3ζ) gene polymorphisms with T1D and AITD in the population of northern Sweden. Holmberg D et al. 2016 BMC medical genetics
27892471 Combining Multiple Hypothesis Testing with Machine Learning Increases the Statistical Power of Genome-wide Association Studies. Mieth B et al. 2016 Scientific reports
28603863 Identification of PTPN22, ST6GAL1 and JAZF1 as psoriasis risk genes demonstrates shared pathogenesis between psoriasis and diabetes. Wang H et al. 2017 Experimental dermatology
29954342 LPG: A four-group probabilistic approach to leveraging pleiotropy in genome-wide association studies. Yang Y et al. 2018 BMC genomics

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