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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.

rs12377632

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr9:117710452 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.30842 (38728/125568, TOPMED)
C=0.3179 (8749/27518, GnomAD)
C=0.370 (1851/5008, 1000G) (+ 2 more)
C=0.355 (1369/3854, ALSPAC)
C=0.373 (1382/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TLR4 : Intron Variant
Publications
19 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 9 NC_000009.12:g.117710452T>A
GRCh38.p7 chr 9 NC_000009.12:g.117710452T>C
GRCh37.p13 chr 9 NC_000009.11:g.120472730T>A
GRCh37.p13 chr 9 NC_000009.11:g.120472730T>C
TLR4 RefSeqGene NG_011475.1:g.11271T>A
TLR4 RefSeqGene NG_011475.1:g.11271T>C
Gene: TLR4, toll like receptor 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TLR4 transcript variant 3 NM_003266.3:c. N/A Intron Variant
TLR4 transcript variant 1 NM_138554.4:c. N/A Intron Variant
TLR4 transcript variant 4 NM_138557.2:c. N/A Intron 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
Trans-Omics for Precision Medicine Global Study-wide 125568 T=0.69158 C=0.30842
The Genome Aggregation Database Global Study-wide 27518 T=0.6821 C=0.3179
The Genome Aggregation Database European Sub 16030 T=0.6160 C=0.3840
The Genome Aggregation Database African Sub 8144 T=0.884 C=0.116
The Genome Aggregation Database East Asian Sub 1570 T=0.392 C=0.608
The Genome Aggregation Database Other Sub 820 T=0.63 C=0.37
The Genome Aggregation Database American Sub 666 T=0.58 C=0.42
The Genome Aggregation Database Ashkenazi Jewish Sub 288 T=0.60 C=0.40
1000Genomes Global Study-wide 5008 T=0.630 C=0.370
1000Genomes African Sub 1322 T=0.926 C=0.074
1000Genomes East Asian Sub 1008 T=0.369 C=0.631
1000Genomes Europe Sub 1006 T=0.562 C=0.438
1000Genomes South Asian Sub 978 T=0.60 C=0.40
1000Genomes American Sub 694 T=0.60 C=0.40
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.645 C=0.355
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.627 C=0.373
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 T= A C Note
GRCh38.p7 chr 9 NC_000009.12:g.11...

NC_000009.12:g.117710452T=

NC_000009.12:g.11...

NC_000009.12:g.117710452T>A

NC_000009.12:g.11...

NC_000009.12:g.117710452T>C

GRCh37.p13 chr 9 NC_000009.11:g.12...

NC_000009.11:g.120472730T=

NC_000009.11:g.12...

NC_000009.11:g.120472730T>A

NC_000009.11:g.12...

NC_000009.11:g.120472730T>C

TLR4 RefSeqGene NG_011475.1:g.112...

NG_011475.1:g.11271T=

NG_011475.1:g.112...

NG_011475.1:g.11271T>A

NG_011475.1:g.112...

NG_011475.1:g.11271T>C

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, 27 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss19032820 Feb 28, 2004 (120)
2 PERLEGEN ss69302266 May 16, 2007 (127)
3 BCMHGSC_JDW ss94135058 Mar 25, 2008 (129)
4 1000GENOMES ss109042800 Jan 23, 2009 (130)
5 GMI ss157931049 Dec 01, 2009 (131)
6 ILLUMINA ss244276190 Jul 04, 2010 (132)
7 BL ss254520339 May 09, 2011 (134)
8 GMI ss280386432 May 04, 2012 (137)
9 GMI ss286086954 Apr 25, 2013 (138)
10 PJP ss294364201 May 09, 2011 (134)
11 SSMP ss656106575 Apr 25, 2013 (138)
12 1000GENOMES ss1335293862 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1583244772 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1623478218 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1666472251 Apr 01, 2015 (144)
16 ILLUMINA ss1959212131 Feb 12, 2016 (147)
17 JJLAB ss2025849651 Sep 14, 2016 (149)
18 ILLUMINA ss2094836265 Dec 20, 2016 (150)
19 ILLUMINA ss2095224694 Dec 20, 2016 (150)
20 USC_VALOUEV ss2154078965 Dec 20, 2016 (150)
21 TOPMED ss2484602031 Dec 20, 2016 (150)
22 GRF ss2709960014 Nov 08, 2017 (151)
23 GNOMAD ss2882741963 Nov 08, 2017 (151)
24 ILLUMINA ss3022960949 Nov 08, 2017 (151)
25 BIOINF_KMB_FNS_UNIBA ss3026707900 Nov 08, 2017 (151)
26 TOPMED ss3599504594 Nov 08, 2017 (151)
27 TOPMED ss3599504595 Nov 08, 2017 (151)
28 1000Genomes NC_000009.11 - 120472730 Jul 20, 2018 (151)
29 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 120472730 Jul 20, 2018 (151)
30 The Genome Aggregation Database NC_000009.11 - 120472730 Jul 20, 2018 (151)
31 Trans-Omics for Precision Medicine NC_000009.12 - 117710452 Jul 20, 2018 (151)
32 UK 10K study - Twins NC_000009.11 - 120472730 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss94135058, ss109042800, ss244276190, ss254520339, ss280386432, ss286086954, ss294364201 NC_000009.10:119512550:T= NC_000009.12:117710451:T= (self)
47606266, 26455389, 223369718, 26455389, ss656106575, ss1335293862, ss1583244772, ss1623478218, ss1666472251, ss1959212131, ss2025849651, ss2094836265, ss2095224694, ss2154078965, ss2484602031, ss2709960014, ss2882741963, ss3022960949 NC_000009.11:120472729:T= NC_000009.12:117710451:T= (self)
419308094, ss3026707900, ss3599504594, ss3599504595 NC_000009.12:117710451:T= NC_000009.12:117710451:T= (self)
ss19032820 NT_008470.16:22130464:T= NC_000009.12:117710451:T= (self)
ss69302266, ss157931049 NT_008470.19:49637261:T= NC_000009.12:117710451:T= (self)
ss3599504594 NC_000009.12:117710451:T>A NC_000009.12:117710451:T>A (self)
ss94135058, ss109042800, ss244276190, ss254520339, ss280386432, ss286086954, ss294364201 NC_000009.10:119512550:T>C NC_000009.12:117710451:T>C (self)
47606266, 26455389, 223369718, 26455389, ss656106575, ss1335293862, ss1583244772, ss1623478218, ss1666472251, ss1959212131, ss2025849651, ss2094836265, ss2095224694, ss2154078965, ss2484602031, ss2709960014, ss2882741963, ss3022960949 NC_000009.11:120472729:T>C NC_000009.12:117710451:T>C (self)
419308094, ss3026707900, ss3599504595 NC_000009.12:117710451:T>C NC_000009.12:117710451:T>C (self)
ss19032820 NT_008470.16:22130464:T>C NC_000009.12:117710451:T>C (self)
ss69302266, ss157931049 NT_008470.19:49637261:T>C NC_000009.12:117710451:T>C (self)
Help

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

19 citations for rs12377632
PMID Title Author Year Journal
18586872 Association of Toll-like receptor 4 gene polymorphisms with normal tension glaucoma. Shibuya E et al. 2008 Investigative ophthalmology & visual science
19500628 Association analysis of Toll-like receptor 4 polymorphisms with autoimmune pancreatitis. Umemura T et al. 2009 Human immunology
19723394 Association of SLC11A1 with tuberculosis and interactions with NOS2A and TLR2 in African-Americans and Caucasians. Velez DR et al. 2009 The international journal of tuberculosis and lung disease
20011079 Lack of association between toll-like receptor 4 gene polymorphisms and sarcoidosis-related uveitis in Japan. Asukata Y et al. 2009 Molecular vision
21559380 Single nucleotide polymorphisms of Toll-like receptor 4 decrease the risk of development of hepatocellular carcinoma. Minmin S et al. 2011 PloS one
21792899 Toll-like receptor genes and their association with colon and rectal cancer development and prognosis. Slattery ML et al. 2012 International journal of cancer
21921986 Toll-like receptor 4 gene polymorphisms do not associate with normal tension glaucoma in a Korean population. Suh W et al. 2011 Molecular vision
22251849 The association of Toll-like receptor 4 gene polymorphisms with the development of emphysema in Japanese subjects: a case control study. Ito M et al. 2012 BMC research notes
22272615 Common variants in toll-like receptor 4 confer susceptibility to Alzheimer's disease in a Han Chinese population. Yu JT et al. 2012 Current Alzheimer research
22359464 Are Toll-like receptor gene polymorphisms associated with prostate cancer? Kutikhin AG et al. 2012 Cancer management and research
22952638 Toll-like receptor (TLR2 and TLR4) polymorphisms and chronic obstructive pulmonary disease. Budulac SE et al. 2012 PloS one
24967817 Anti-TNF treatment response in rheumatoid arthritis patients is associated with genetic variation in the NLRP3-inflammasome. Sode J et al. 2014 PloS one
24971461 Polymorphisms in the inflammatory pathway genes TLR2, TLR4, TLR9, LY96, NFKBIA, NFKB1, TNFA, TNFRSF1A, IL6R, IL10, IL23R, PTPN22, and PPARG are associated with susceptibility of inflammatory bowel disease in a Danish cohort. Bank S et al. 2014 PloS one
26861312 Association between Genetic Polymorphisms and Response to Anti-TNFs in Patients with Inflammatory Bowel Disease. Prieto-PĂ©rez R et al. 2016 International journal of molecular sciences
27417569 Systematic review: genetic biomarkers associated with anti-TNF treatment response in inflammatory bowel diseases. Bek S et al. 2016 Alimentary pharmacology & therapeutics
27707548 Glaucoma Risk Alleles in the Ocular Hypertension Treatment Study. Scheetz TE et al. 2016 Ophthalmology
27713886 The role of genetics and antibodies in sepsis. Giamarellos-Bourboulis EJ et al. 2016 Annals of translational medicine
27892755 Association of single-nucleotide polymorphisms in non-coding regions of the TLR4 gene with primary open angle glaucoma in a Mexican population. Navarro-Partida J et al. 2017 Ophthalmic genetics
29348888 The association analysis of TLR2 and TLR4 gene with tuberculosis in the Tibetan Chinese population. Xue X et al. 2017 Oncotarget

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