Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

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.

rs17174870

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:111907624 (GRCh38.p12) 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
T=0.22349 (28063/125568, TOPMED)
T=0.2528 (7817/30924, GnomAD)
T=0.240 (1202/5008, 1000G) (+ 3 more)
T=0.325 (1456/4480, Estonian)
T=0.244 (940/3854, ALSPAC)
T=0.243 (902/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MERTK : Intron Variant
Publications
9 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.p12 chr 2 NC_000002.12:g.111907624C>T
GRCh37.p13 chr 2 NC_000002.11:g.112665201C>T
MERTK RefSeqGene NG_011607.1:g.14011C>T
Gene: MERTK, MER proto-oncogene, tyrosine kinase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MERTK transcript NM_006343.2:c. N/A Intron Variant
MERTK transcript variant X3 XM_005263565.4:c. N/A Intron Variant
MERTK transcript variant X4 XM_005263568.4:c. N/A Intron Variant
MERTK transcript variant X1 XM_011510490.3:c. N/A Intron Variant
MERTK transcript variant X5 XM_017003165.2:c. N/A Intron Variant
MERTK transcript variant X2 XM_017003164.1:c. N/A Genic Upstream Transcript 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
TopMed Global Study-wide 125568 C=0.77651 T=0.22349
gnomAD - Genomes Global Study-wide 30924 C=0.7472 T=0.2528
gnomAD - Genomes European Sub 18476 C=0.7160 T=0.2840
gnomAD - Genomes African Sub 8716 C=0.805 T=0.195
gnomAD - Genomes East Asian Sub 1616 C=0.892 T=0.108
gnomAD - Genomes Other Sub 978 C=0.69 T=0.31
gnomAD - Genomes American Sub 836 C=0.62 T=0.38
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.75 T=0.25
1000Genomes Global Study-wide 5008 C=0.760 T=0.240
1000Genomes African Sub 1322 C=0.825 T=0.175
1000Genomes East Asian Sub 1008 C=0.884 T=0.116
1000Genomes Europe Sub 1006 C=0.742 T=0.258
1000Genomes South Asian Sub 978 C=0.64 T=0.36
1000Genomes American Sub 694 C=0.65 T=0.35
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.675 T=0.325
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.756 T=0.244
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.757 T=0.243
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.p12 chr 2 NC_000002.12:g.111907624C= NC_000002.12:g.11190762...

NC_000002.12:g.111907624C>T

GRCh37.p13 chr 2 NC_000002.11:g.112665201C= NC_000002.11:g.11266520...

NC_000002.11:g.112665201C>T

MERTK RefSeqGene NG_011607.1:g.14011C= NG_011607.1:g.14011C>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#.

85 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24306477 Sep 20, 2004 (123)
2 ILLUMINA ss67180531 Dec 03, 2006 (127)
3 ILLUMINA ss67547723 Dec 03, 2006 (127)
4 ILLUMINA ss68177081 Dec 12, 2006 (127)
5 PERLEGEN ss68824514 May 16, 2007 (127)
6 ILLUMINA ss70658566 May 23, 2008 (130)
7 ILLUMINA ss71219446 May 16, 2007 (127)
8 ILLUMINA ss75811235 Dec 07, 2007 (129)
9 AFFY ss76821105 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss85373582 Dec 14, 2007 (130)
11 ILLUMINA ss153647166 Dec 01, 2009 (131)
12 ILLUMINA ss159312390 Dec 01, 2009 (131)
13 ILLUMINA ss160433561 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss164987975 Jul 04, 2010 (132)
15 ILLUMINA ss172778764 Jul 04, 2010 (132)
16 BUSHMAN ss200883623 Jul 04, 2010 (132)
17 1000GENOMES ss210972393 Jul 14, 2010 (132)
18 1000GENOMES ss219436044 Jul 14, 2010 (132)
19 1000GENOMES ss231308541 Jul 14, 2010 (132)
20 1000GENOMES ss238830489 Jul 15, 2010 (132)
21 GMI ss276622046 May 04, 2012 (137)
22 GMI ss284411408 Apr 25, 2013 (138)
23 ILLUMINA ss480209121 May 04, 2012 (137)
24 ILLUMINA ss480219553 May 04, 2012 (137)
25 ILLUMINA ss480950507 Sep 08, 2015 (146)
26 ILLUMINA ss484902551 May 04, 2012 (137)
27 ILLUMINA ss536956886 Sep 08, 2015 (146)
28 TISHKOFF ss555791436 Apr 25, 2013 (138)
29 SSMP ss649410916 Apr 25, 2013 (138)
30 ILLUMINA ss778831815 Sep 08, 2015 (146)
31 ILLUMINA ss782897598 Sep 08, 2015 (146)
32 ILLUMINA ss783860992 Sep 08, 2015 (146)
33 ILLUMINA ss832152330 Sep 08, 2015 (146)
34 ILLUMINA ss834292271 Sep 08, 2015 (146)
35 EVA-GONL ss977218621 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1069391522 Aug 21, 2014 (142)
37 1000GENOMES ss1298772427 Aug 21, 2014 (142)
38 DDI ss1428691762 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1579029827 Apr 01, 2015 (144)
40 EVA_DECODE ss1586642412 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1604284931 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1647278964 Apr 01, 2015 (144)
43 EVA_SVP ss1712481073 Apr 01, 2015 (144)
44 ILLUMINA ss1752305262 Sep 08, 2015 (146)
45 HAMMER_LAB ss1797288413 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1920464571 Feb 12, 2016 (147)
47 ILLUMINA ss1946049304 Feb 12, 2016 (147)
48 ILLUMINA ss1958448591 Feb 12, 2016 (147)
49 GENOMED ss1968855052 Jul 19, 2016 (147)
50 JJLAB ss2020761618 Sep 14, 2016 (149)
51 ILLUMINA ss2094806962 Dec 20, 2016 (150)
52 ILLUMINA ss2095099934 Dec 20, 2016 (150)
53 USC_VALOUEV ss2148817400 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2233248626 Dec 20, 2016 (150)
55 TOPMED ss2399477257 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2624886812 Nov 08, 2017 (151)
57 ILLUMINA ss2633657792 Nov 08, 2017 (151)
58 GRF ss2703427047 Nov 08, 2017 (151)
59 ILLUMINA ss2710909090 Nov 08, 2017 (151)
60 GNOMAD ss2778060822 Nov 08, 2017 (151)
61 AFFY ss2985803733 Nov 08, 2017 (151)
62 SWEGEN ss2990187367 Nov 08, 2017 (151)
63 ILLUMINA ss3022004825 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3024142352 Nov 08, 2017 (151)
65 TOPMED ss3319342926 Nov 08, 2017 (151)
66 CSHL ss3344409182 Nov 08, 2017 (151)
67 ILLUMINA ss3625763169 Oct 11, 2018 (152)
68 ILLUMINA ss3628139593 Oct 11, 2018 (152)
69 ILLUMINA ss3631622271 Oct 11, 2018 (152)
70 ILLUMINA ss3633212315 Oct 11, 2018 (152)
71 ILLUMINA ss3633924530 Oct 11, 2018 (152)
72 ILLUMINA ss3634782374 Oct 11, 2018 (152)
73 ILLUMINA ss3635610519 Oct 11, 2018 (152)
74 ILLUMINA ss3636470555 Oct 11, 2018 (152)
75 ILLUMINA ss3637362442 Oct 11, 2018 (152)
76 ILLUMINA ss3638280453 Oct 11, 2018 (152)
77 ILLUMINA ss3639144636 Oct 11, 2018 (152)
78 ILLUMINA ss3639876883 Oct 11, 2018 (152)
79 ILLUMINA ss3640489675 Oct 11, 2018 (152)
80 ILLUMINA ss3641111768 Oct 11, 2018 (152)
81 ILLUMINA ss3641407725 Oct 11, 2018 (152)
82 ILLUMINA ss3643248473 Oct 11, 2018 (152)
83 ILLUMINA ss3643925209 Oct 11, 2018 (152)
84 ILLUMINA ss3644752001 Oct 11, 2018 (152)
85 ILLUMINA ss3652444681 Oct 11, 2018 (152)
86 1000Genomes NC_000002.11 - 112665201 Oct 11, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 112665201 Oct 11, 2018 (152)
88 Genetic variation in the Estonian population NC_000002.11 - 112665201 Oct 11, 2018 (152)
89 gnomAD - Genomes NC_000002.11 - 112665201 Oct 11, 2018 (152)
90 TopMed NC_000002.12 - 111907624 Oct 11, 2018 (152)
91 UK 10K study - Twins NC_000002.11 - 112665201 Oct 11, 2018 (152)
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)
rs56893388 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639144636, ss3639876883, ss3643925209 NC_000002.9:112381431:C= NC_000002.12:111907623:C=
ss76821105, ss164987975, ss200883623, ss210972393, ss276622046, ss284411408, ss480209121, ss1586642412, ss1712481073, ss3643248473 NC_000002.10:112381671:C= NC_000002.12:111907623:C= (self)
9769329, 5389783, 3804148, 107550683, 5389783, ss219436044, ss231308541, ss238830489, ss480219553, ss480950507, ss484902551, ss536956886, ss555791436, ss649410916, ss778831815, ss782897598, ss783860992, ss832152330, ss834292271, ss977218621, ss1069391522, ss1298772427, ss1428691762, ss1579029827, ss1604284931, ss1647278964, ss1752305262, ss1797288413, ss1920464571, ss1946049304, ss1958448591, ss1968855052, ss2020761618, ss2094806962, ss2095099934, ss2148817400, ss2399477257, ss2624886812, ss2633657792, ss2703427047, ss2710909090, ss2778060822, ss2985803733, ss2990187367, ss3022004825, ss3344409182, ss3625763169, ss3628139593, ss3631622271, ss3633212315, ss3633924530, ss3634782374, ss3635610519, ss3636470555, ss3637362442, ss3638280453, ss3640489675, ss3641111768, ss3641407725, ss3644752001, ss3652444681 NC_000002.11:112665200:C= NC_000002.12:111907623:C= (self)
201536676, ss2233248626, ss3024142352, ss3319342926 NC_000002.12:111907623:C= NC_000002.12:111907623:C= (self)
ss24306477, ss67180531, ss67547723, ss68177081, ss68824514, ss70658566, ss71219446, ss75811235, ss85373582, ss153647166, ss159312390, ss160433561, ss172778764 NT_022135.16:2413863:C= NC_000002.12:111907623:C= (self)
ss3639144636, ss3639876883, ss3643925209 NC_000002.9:112381431:C>T NC_000002.12:111907623:C>T
ss76821105, ss164987975, ss200883623, ss210972393, ss276622046, ss284411408, ss480209121, ss1586642412, ss1712481073, ss3643248473 NC_000002.10:112381671:C>T NC_000002.12:111907623:C>T (self)
9769329, 5389783, 3804148, 107550683, 5389783, ss219436044, ss231308541, ss238830489, ss480219553, ss480950507, ss484902551, ss536956886, ss555791436, ss649410916, ss778831815, ss782897598, ss783860992, ss832152330, ss834292271, ss977218621, ss1069391522, ss1298772427, ss1428691762, ss1579029827, ss1604284931, ss1647278964, ss1752305262, ss1797288413, ss1920464571, ss1946049304, ss1958448591, ss1968855052, ss2020761618, ss2094806962, ss2095099934, ss2148817400, ss2399477257, ss2624886812, ss2633657792, ss2703427047, ss2710909090, ss2778060822, ss2985803733, ss2990187367, ss3022004825, ss3344409182, ss3625763169, ss3628139593, ss3631622271, ss3633212315, ss3633924530, ss3634782374, ss3635610519, ss3636470555, ss3637362442, ss3638280453, ss3640489675, ss3641111768, ss3641407725, ss3644752001, ss3652444681 NC_000002.11:112665200:C>T NC_000002.12:111907623:C>T (self)
201536676, ss2233248626, ss3024142352, ss3319342926 NC_000002.12:111907623:C>T NC_000002.12:111907623:C>T (self)
ss24306477, ss67180531, ss67547723, ss68177081, ss68824514, ss70658566, ss71219446, ss75811235, ss85373582, ss153647166, ss159312390, ss160433561, ss172778764 NT_022135.16:2413863:C>T NC_000002.12:111907623: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.

9 citations for rs17174870
PMID Title Author Year Journal
21347448 Polymorphisms in the receptor tyrosine kinase MERTK gene are associated with multiple sclerosis susceptibility. Ma GZ et al. 2011 PloS one
22164203 Perspectives on the use of multiple sclerosis risk genes for prediction. Jafari N et al. 2011 PloS one
22396755 Genomic regions associated with multiple sclerosis are active in B cells. Disanto G et al. 2012 PloS one
23094030 Protein-protein interaction analysis highlights additional loci of interest for multiple sclerosis. Ragnedda G et al. 2012 PloS one
23393188 Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. Feldmann R et al. 2013 Nucleic acids research
23730204 Progress in multiple sclerosis genetics. Goris A et al. 2012 Current genomics
26990204 Common and Low Frequency Variants in MERTK Are Independently Associated with Multiple Sclerosis Susceptibility with Discordant Association Dependent upon HLA-DRB1*15:01 Status. Binder MD et al. 2016 PLoS genetics
27540591 Multiple sclerosis risk loci and disease severity in 7,125 individuals from 10 studies. George MF et al. 2016 Neurology. Genetics
27802296 A Risk Score for Predicting Multiple Sclerosis. Dobson R et al. 2016 PloS one

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.post58+e54ea20