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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.

rs11593241

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr10:131188383 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.11091 (13927/125568, TOPMED)
C=0.1170 (3622/30954, GnomAD)
C=0.118 (591/5008, 1000G) (+ 3 more)
C=0.145 (650/4480, Estonian)
C=0.122 (469/3854, ALSPAC)
C=0.121 (448/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TCERG1L : Intron Variant
Publications
1 citation
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 10 NC_000010.11:g.131188383T>C
GRCh37.p13 chr 10 NC_000010.10:g.132986646T>C
Gene: TCERG1L, transcription elongation regulator 1 like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TCERG1L transcript NM_174937.3: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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.88909 C=0.11091
gnomAD - Genomes Global Study-wide 30954 T=0.8830 C=0.1170
gnomAD - Genomes European Sub 18490 T=0.8580 C=0.1420
gnomAD - Genomes African Sub 8724 T=0.975 C=0.025
gnomAD - Genomes East Asian Sub 1620 T=0.753 C=0.247
gnomAD - Genomes Other Sub 980 T=0.84 C=0.16
gnomAD - Genomes American Sub 838 T=0.77 C=0.23
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.91 C=0.09
1000Genomes Global Study-wide 5008 T=0.882 C=0.118
1000Genomes African Sub 1322 T=0.995 C=0.005
1000Genomes East Asian Sub 1008 T=0.798 C=0.202
1000Genomes Europe Sub 1006 T=0.859 C=0.141
1000Genomes South Asian Sub 978 T=0.91 C=0.09
1000Genomes American Sub 694 T=0.78 C=0.22
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.855 C=0.145
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.878 C=0.122
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.879 C=0.121
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= C Note
GRCh38.p12 chr 10 NC_000010.11:g.131188383T= NC_000010.11:g.13118838...

NC_000010.11:g.131188383T>C

GRCh37.p13 chr 10 NC_000010.10:g.132986646T= NC_000010.10:g.13298664...

NC_000010.10:g.132986646T>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#.

68 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16473864 Feb 28, 2004 (120)
2 ABI ss39820915 Mar 13, 2006 (126)
3 ILLUMINA ss66765380 Dec 01, 2006 (127)
4 ILLUMINA ss66934031 Dec 01, 2006 (127)
5 ILLUMINA ss67094244 Dec 01, 2006 (127)
6 ILLUMINA ss70395107 May 17, 2007 (127)
7 ILLUMINA ss70531010 May 26, 2008 (130)
8 ILLUMINA ss71061686 May 17, 2007 (127)
9 ILLUMINA ss75788955 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss85102679 Dec 16, 2007 (130)
11 BCMHGSC_JDW ss88414656 Mar 23, 2008 (129)
12 ILLUMINA ss121478580 Dec 01, 2009 (131)
13 ENSEMBL ss132201215 Dec 01, 2009 (131)
14 ILLUMINA ss153000667 Dec 01, 2009 (131)
15 GMI ss155763066 Dec 01, 2009 (131)
16 ILLUMINA ss159177552 Dec 01, 2009 (131)
17 ENSEMBL ss161313621 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss168817869 Jul 04, 2010 (132)
19 ILLUMINA ss169882088 Jul 04, 2010 (132)
20 ILLUMINA ss171323203 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss207131747 Jul 04, 2010 (132)
22 1000GENOMES ss235399039 Jul 15, 2010 (132)
23 1000GENOMES ss242063694 Jul 15, 2010 (132)
24 BL ss254740102 May 09, 2011 (134)
25 GMI ss280836923 May 04, 2012 (137)
26 GMI ss286293539 Apr 25, 2013 (138)
27 ILLUMINA ss482523354 May 04, 2012 (137)
28 ILLUMINA ss483143848 May 04, 2012 (137)
29 ILLUMINA ss535366057 Sep 08, 2015 (146)
30 SSMP ss657597696 Apr 25, 2013 (138)
31 ILLUMINA ss780167406 Sep 08, 2015 (146)
32 ILLUMINA ss782015273 Sep 08, 2015 (146)
33 ILLUMINA ss825364502 Apr 01, 2015 (144)
34 ILLUMINA ss832690067 Aug 21, 2014 (142)
35 ILLUMINA ss833280756 Aug 21, 2014 (142)
36 ILLUMINA ss835651306 Sep 08, 2015 (146)
37 EVA-GONL ss988087226 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1077421183 Aug 21, 2014 (142)
39 1000GENOMES ss1339676822 Aug 21, 2014 (142)
40 HAMMER_LAB ss1397597060 Sep 08, 2015 (146)
41 EVA_GENOME_DK ss1575454777 Apr 01, 2015 (144)
42 EVA_DECODE ss1597767715 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1625771500 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1668765533 Apr 01, 2015 (144)
45 EVA_SVP ss1713224848 Apr 01, 2015 (144)
46 WEILL_CORNELL_DGM ss1931443834 Feb 12, 2016 (147)
47 JJLAB ss2026463718 Sep 14, 2016 (149)
48 USC_VALOUEV ss2154744228 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2179342721 Dec 20, 2016 (150)
50 TOPMED ss2342463643 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2627701424 Nov 08, 2017 (151)
52 ILLUMINA ss2632785496 Nov 08, 2017 (151)
53 GRF ss2699008587 Nov 08, 2017 (151)
54 GNOMAD ss2895077402 Nov 08, 2017 (151)
55 AFFY ss2984928159 Nov 08, 2017 (151)
56 AFFY ss2985575628 Nov 08, 2017 (151)
57 SWEGEN ss3007397747 Nov 08, 2017 (151)
58 BIOINF_KMB_FNS_UNIBA ss3027024016 Nov 08, 2017 (151)
59 TOPMED ss3134290237 Nov 08, 2017 (151)
60 CSHL ss3349388318 Nov 08, 2017 (151)
61 ILLUMINA ss3626572758 Oct 12, 2018 (152)
62 ILLUMINA ss3630806465 Oct 12, 2018 (152)
63 ILLUMINA ss3637883701 Oct 12, 2018 (152)
64 ILLUMINA ss3638957446 Oct 12, 2018 (152)
65 ILLUMINA ss3639479002 Oct 12, 2018 (152)
66 ILLUMINA ss3641712486 Oct 12, 2018 (152)
67 ILLUMINA ss3642884107 Oct 12, 2018 (152)
68 ILLUMINA ss3653699581 Oct 12, 2018 (152)
69 1000Genomes NC_000010.10 - 132986646 Oct 12, 2018 (152)
70 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 132986646 Oct 12, 2018 (152)
71 Genetic variation in the Estonian population NC_000010.10 - 132986646 Oct 12, 2018 (152)
72 gnomAD - Genomes NC_000010.10 - 132986646 Oct 12, 2018 (152)
73 TopMed NC_000010.11 - 131188383 Oct 12, 2018 (152)
74 UK 10K study - Twins NC_000010.10 - 132986646 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)
rs61457666 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3638957446, ss3639479002 NC_000010.8:132876635:T:C NC_000010.11:131188382:T:C
ss88414656, ss168817869, ss207131747, ss254740102, ss280836923, ss286293539, ss482523354, ss825364502, ss1397597060, ss1597767715, ss1713224848, ss3642884107 NC_000010.9:132876635:T:C NC_000010.11:131188382:T:C (self)
52144842, 28976836, 20557808, 28778923, 28976836, ss235399039, ss242063694, ss483143848, ss535366057, ss657597696, ss780167406, ss782015273, ss832690067, ss833280756, ss835651306, ss988087226, ss1077421183, ss1339676822, ss1575454777, ss1625771500, ss1668765533, ss1931443834, ss2026463718, ss2154744228, ss2342463643, ss2627701424, ss2632785496, ss2699008587, ss2895077402, ss2984928159, ss2985575628, ss3007397747, ss3349388318, ss3626572758, ss3630806465, ss3637883701, ss3641712486, ss3653699581 NC_000010.10:132986645:T:C NC_000010.11:131188382:T:C (self)
54778439, ss2179342721, ss3027024016, ss3134290237 NC_000010.11:131188382:T:C NC_000010.11:131188382:T:C (self)
ss16473864 NT_008818.15:4220576:T:C NC_000010.11:131188382:T:C (self)
ss39820915, ss66765380, ss66934031, ss67094244, ss70395107, ss70531010, ss71061686, ss75788955, ss85102679, ss121478580, ss132201215, ss153000667, ss155763066, ss159177552, ss161313621, ss169882088, ss171323203 NT_008818.16:4220576:T:C NC_000010.11:131188382: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.

1 citation for rs11593241
PMID Title Author Year Journal
20732627 Case-control genome-wide association study of attention-deficit/hyperactivity disorder. Neale BM et al. 2010 Journal of the American Academy of Child and Adolescent Psychiatry

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.post104+4a6ee9c