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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.

rs10759944

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr9:97794690 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.26258 (32972/125568, TOPMED)
A=0.2817 (8696/30874, GnomAD)
A=0.202 (1012/5008, 1000G) (+ 3 more)
A=0.367 (1642/4480, Estonian)
A=0.334 (1286/3854, ALSPAC)
A=0.320 (1187/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTCSC2 : Intron Variant
Publications
5 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 9 NC_000009.12:g.97794690A>G
GRCh37.p13 chr 9 NC_000009.11:g.100556972A>G
Gene: PTCSC2, papillary thyroid carcinoma susceptibility candidate 2 (non-protein coding) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTCSC2 transcript NR_147055.1:n. N/A Intron Variant
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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
TopMed Global Study-wide 125568 A=0.26258 G=0.73742
gnomAD - Genomes Global Study-wide 30874 A=0.2817 G=0.7183
gnomAD - Genomes European Sub 18450 A=0.3468 G=0.6532
gnomAD - Genomes African Sub 8696 A=0.169 G=0.831
gnomAD - Genomes East Asian Sub 1612 A=0.115 G=0.885
gnomAD - Genomes Other Sub 980 A=0.32 G=0.68
gnomAD - Genomes American Sub 834 A=0.27 G=0.73
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.33 G=0.67
1000Genomes Global Study-wide 5008 A=0.202 G=0.798
1000Genomes African Sub 1322 A=0.113 G=0.887
1000Genomes East Asian Sub 1008 A=0.129 G=0.871
1000Genomes Europe Sub 1006 A=0.337 G=0.663
1000Genomes South Asian Sub 978 A=0.19 G=0.81
1000Genomes American Sub 694 A=0.30 G=0.70
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.367 G=0.633
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.334 G=0.666
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.320 G=0.680
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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 A= G Note
GRCh38.p12 chr 9 NC_000009.12:g.97794690A= NC_000009.12:g.97794690A>G
GRCh37.p13 chr 9 NC_000009.11:g.100556972A= NC_000009.11:g.10055697...

NC_000009.11:g.100556972A>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#.

93 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15962899 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17997650 Feb 27, 2004 (120)
3 SC_SNP ss19019244 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss20359654 Feb 27, 2004 (120)
5 SSAHASNP ss22814556 Apr 05, 2004 (121)
6 ABI ss43931201 Mar 14, 2006 (126)
7 ILLUMINA ss66698762 Nov 30, 2006 (127)
8 ILLUMINA ss67012088 Nov 30, 2006 (127)
9 ILLUMINA ss67588762 Nov 30, 2006 (127)
10 ILLUMINA ss70378319 May 17, 2007 (127)
11 ILLUMINA ss70495004 May 24, 2008 (130)
12 ILLUMINA ss71020055 May 17, 2007 (127)
13 ILLUMINA ss75654125 Dec 06, 2007 (129)
14 KRIBB_YJKIM ss84990247 Dec 14, 2007 (130)
15 BCMHGSC_JDW ss94111072 Mar 25, 2008 (129)
16 HUMANGENOME_JCVI ss97738473 Feb 04, 2009 (130)
17 BGI ss105690530 Feb 04, 2009 (130)
18 1000GENOMES ss108930680 Jan 23, 2009 (130)
19 1000GENOMES ss114793826 Jan 25, 2009 (130)
20 ILLUMINA-UK ss115766983 Feb 14, 2009 (130)
21 ILLUMINA ss121380502 Dec 01, 2009 (131)
22 ENSEMBL ss134039993 Dec 01, 2009 (131)
23 ILLUMINA ss152809717 Dec 01, 2009 (131)
24 GMI ss157768407 Dec 01, 2009 (131)
25 ILLUMINA ss159139918 Dec 01, 2009 (131)
26 ILLUMINA ss159916333 Dec 01, 2009 (131)
27 COMPLETE_GENOMICS ss164494051 Jul 04, 2010 (132)
28 COMPLETE_GENOMICS ss165522073 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss166724557 Jul 04, 2010 (132)
30 ILLUMINA ss169595398 Jul 04, 2010 (132)
31 ILLUMINA ss170470186 Jul 04, 2010 (132)
32 BUSHMAN ss200651186 Jul 04, 2010 (132)
33 BCM-HGSC-SUB ss206651469 Jul 04, 2010 (132)
34 1000GENOMES ss224354547 Jul 14, 2010 (132)
35 1000GENOMES ss234897087 Jul 15, 2010 (132)
36 1000GENOMES ss241657819 Jul 15, 2010 (132)
37 GMI ss280326853 May 04, 2012 (137)
38 GMI ss286060250 Apr 25, 2013 (138)
39 PJP ss294333640 May 09, 2011 (134)
40 ILLUMINA ss410888499 Sep 17, 2011 (135)
41 ILLUMINA ss479335325 May 04, 2012 (137)
42 ILLUMINA ss479338369 May 04, 2012 (137)
43 ILLUMINA ss479731266 Sep 08, 2015 (146)
44 ILLUMINA ss484467864 May 04, 2012 (137)
45 ILLUMINA ss536629860 Sep 08, 2015 (146)
46 TISHKOFF ss561513589 Apr 25, 2013 (138)
47 SSMP ss656009680 Apr 25, 2013 (138)
48 ILLUMINA ss778738729 Sep 08, 2015 (146)
49 ILLUMINA ss782680496 Sep 08, 2015 (146)
50 ILLUMINA ss783648999 Sep 08, 2015 (146)
51 ILLUMINA ss825347930 Apr 01, 2015 (144)
52 ILLUMINA ss831931274 Sep 08, 2015 (146)
53 ILLUMINA ss834198291 Sep 08, 2015 (146)
54 EVA-GONL ss986783965 Aug 21, 2014 (142)
55 JMKIDD_LAB ss1076462781 Aug 21, 2014 (142)
56 1000GENOMES ss1334724204 Aug 21, 2014 (142)
57 DDI ss1431904137 Apr 01, 2015 (144)
58 EVA_GENOME_DK ss1583182621 Apr 01, 2015 (144)
59 EVA_DECODE ss1596420004 Apr 01, 2015 (144)
60 EVA_UK10K_ALSPAC ss1623168175 Apr 01, 2015 (144)
61 EVA_UK10K_TWINSUK ss1666162208 Apr 01, 2015 (144)
62 EVA_SVP ss1713125166 Apr 01, 2015 (144)
63 ILLUMINA ss1752748862 Sep 08, 2015 (146)
64 HAMMER_LAB ss1806077033 Sep 08, 2015 (146)
65 WEILL_CORNELL_DGM ss1930098601 Feb 12, 2016 (147)
66 GENOMED ss1971263211 Jul 19, 2016 (147)
67 JJLAB ss2025767588 Sep 14, 2016 (149)
68 USC_VALOUEV ss2153995439 Dec 20, 2016 (150)
69 HUMAN_LONGEVITY ss2312910913 Dec 20, 2016 (150)
70 TOPMED ss2483386196 Dec 20, 2016 (150)
71 SYSTEMSBIOZJU ss2627351907 Nov 08, 2017 (151)
72 ILLUMINA ss2634892676 Nov 08, 2017 (151)
73 ILLUMINA ss2635197256 Nov 08, 2017 (151)
74 GRF ss2709869079 Nov 08, 2017 (151)
75 GNOMAD ss2881146136 Nov 08, 2017 (151)
76 SWEGEN ss3005293522 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3026664317 Nov 08, 2017 (151)
78 CSHL ss3348772233 Nov 08, 2017 (151)
79 TOPMED ss3595855021 Nov 08, 2017 (151)
80 ILLUMINA ss3630311906 Oct 12, 2018 (152)
81 ILLUMINA ss3632783449 Oct 12, 2018 (152)
82 ILLUMINA ss3633541189 Oct 12, 2018 (152)
83 ILLUMINA ss3634269786 Oct 12, 2018 (152)
84 ILLUMINA ss3635223117 Oct 12, 2018 (152)
85 ILLUMINA ss3635947614 Oct 12, 2018 (152)
86 ILLUMINA ss3636971195 Oct 12, 2018 (152)
87 ILLUMINA ss3637700964 Oct 12, 2018 (152)
88 ILLUMINA ss3638824898 Oct 12, 2018 (152)
89 ILLUMINA ss3639417593 Oct 12, 2018 (152)
90 ILLUMINA ss3639742073 Oct 12, 2018 (152)
91 ILLUMINA ss3640930408 Oct 12, 2018 (152)
92 ILLUMINA ss3643750994 Oct 12, 2018 (152)
93 URBANLAB ss3649200676 Oct 12, 2018 (152)
94 1000Genomes NC_000009.11 - 100556972 Oct 12, 2018 (152)
95 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 100556972 Oct 12, 2018 (152)
96 Genetic variation in the Estonian population NC_000009.11 - 100556972 Oct 12, 2018 (152)
97 gnomAD - Genomes NC_000009.11 - 100556972 Oct 12, 2018 (152)
98 TopMed NC_000009.12 - 97794690 Oct 12, 2018 (152)
99 UK 10K study - Twins NC_000009.11 - 100556972 Oct 12, 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)
rs57765103 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639417593, ss3639742073 NC_000009.9:97636526:A:G NC_000009.12:97794689:A:G
ss94111072, ss108930680, ss114793826, ss115766983, ss164494051, ss165522073, ss166724557, ss200651186, ss206651469, ss280326853, ss286060250, ss294333640, ss479335325, ss825347930, ss1596420004, ss1713125166, ss2635197256, ss3643750994 NC_000009.10:99596792:A:G NC_000009.12:97794689:A:G (self)
47015682, 26115072, 18565596, 221773891, 26115072, ss224354547, ss234897087, ss241657819, ss479338369, ss479731266, ss484467864, ss536629860, ss561513589, ss656009680, ss778738729, ss782680496, ss783648999, ss831931274, ss834198291, ss986783965, ss1076462781, ss1334724204, ss1431904137, ss1583182621, ss1623168175, ss1666162208, ss1752748862, ss1806077033, ss1930098601, ss1971263211, ss2025767588, ss2153995439, ss2483386196, ss2627351907, ss2634892676, ss2709869079, ss2881146136, ss3005293522, ss3348772233, ss3630311906, ss3632783449, ss3633541189, ss3634269786, ss3635223117, ss3635947614, ss3636971195, ss3637700964, ss3638824898, ss3640930408 NC_000009.11:100556971:A:G NC_000009.12:97794689:A:G (self)
416210371, ss2312910913, ss3026664317, ss3595855021, ss3649200676 NC_000009.12:97794689:A:G NC_000009.12:97794689:A:G (self)
ss15962899, ss17997650, ss19019244, ss20359654, ss22814556 NT_008470.16:2218499:A:G NC_000009.12:97794689:A:G (self)
ss43931201, ss66698762, ss67012088, ss67588762, ss70378319, ss70495004, ss71020055, ss75654125, ss84990247, ss97738473, ss105690530, ss121380502, ss134039993, ss152809717, ss157768407, ss159139918, ss159916333, ss169595398, ss170470186, ss410888499 NT_008470.19:29721503:A:G NC_000009.12:97794689:A:G (self)
Help

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

5 citations for rs10759944
PMID Title Author Year Journal
19198613 Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Gudmundsson J et al. 2009 Nature genetics
21981779 Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Denny JC et al. 2011 American journal of human genetics
25436638 Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network. Malinowski JR et al. 2014 PloS one
25918370 Multiple functional variants in long-range enhancer elements contribute to the risk of SNP rs965513 in thyroid cancer. He H et al. 2015 Proceedings of the National Academy of Sciences of the United States of America
26776183 INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES. Verma A et al. 2016 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Genomic regions, transcripts, and products
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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.post104+4a6ee9c