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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.

rs11260542

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1174639 (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.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.134346 (35560/264690, TOPMED)
G=0.095052 (17961/188960, ALFA)
G=0.136384 (19114/140148, GnomAD) (+ 16 more)
G=0.16182 (12734/78694, PAGE_STUDY)
G=0.14069 (2358/16760, 8.3KJPN)
G=0.1446 (724/5008, 1000G)
G=0.1290 (578/4480, Estonian)
G=0.0898 (346/3854, ALSPAC)
G=0.0944 (350/3708, TWINSUK)
G=0.0765 (224/2930, KOREAN)
G=0.1792 (339/1892, HapMap)
G=0.091 (91/998, GoNL)
G=0.085 (67/784, PRJEB37584)
G=0.167 (100/600, NorthernSweden)
G=0.134 (29/216, Qatari)
A=0.440 (66/150, SGDP_PRJ)
G=0.15 (6/40, GENOME_DK)
A=0.50 (7/14, Siberian)
G=0.50 (7/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL10-AS1 : Non Coding Transcript Variant
TTLL10 : Intron Variant
Publications
0 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.p13 chr 1 NC_000001.11:g.1174639A>G
GRCh37.p13 chr 1 NC_000001.10:g.1110019A>G
Gene: TTLL10, tubulin tyrosine ligase like 10 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TTLL10 transcript variant 1 NM_001130045.2:c.-28+150A…

NM_001130045.2:c.-28+150A>G

N/A Intron Variant
TTLL10 transcript variant 3 NM_001371649.1:c.-28+150A…

NM_001371649.1:c.-28+150A>G

N/A Intron Variant
TTLL10 transcript variant 2 NM_153254.3:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X7 XM_011541177.2:c.-28+150A…

XM_011541177.2:c.-28+150A>G

N/A Intron Variant
TTLL10 transcript variant X10 XM_005244738.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X1 XM_017000906.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X2 XM_017000907.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X3 XM_017000908.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X4 XM_017000909.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X5 XM_017000910.2:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X6 XM_017000911.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X8 XM_017000912.1:c. N/A Genic Upstream Transcript Variant
TTLL10 transcript variant X11 XR_001737089.1:n. N/A Intron Variant
TTLL10 transcript variant X9 XR_001737088.1:n. N/A Genic Upstream Transcript Variant
Gene: TTLL10-AS1, uncharacterized TTLL10-AS1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TTLL10-AS1 transcript variant X2 XR_132470.6:n.2042T>C N/A Non Coding Transcript Variant
TTLL10-AS1 transcript variant X1 XR_946813.2:n. N/A Genic Downstream 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

ALFA Allele Frequency
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 188960 A=0.904948 G=0.095052
European Sub 164098 A=0.913204 G=0.086796
African Sub 9358 A=0.7473 G=0.2527
African Others Sub 328 A=0.723 G=0.277
African American Sub 9030 A=0.7482 G=0.2518
Asian Sub 708 A=0.897 G=0.103
East Asian Sub 576 A=0.906 G=0.094
Other Asian Sub 132 A=0.856 G=0.144
Latin American 1 Sub 752 A=0.899 G=0.101
Latin American 2 Sub 6322 A=0.9364 G=0.0636
South Asian Sub 190 A=0.926 G=0.074
Other Sub 7532 A=0.8954 G=0.1046


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 264690 A=0.865654 G=0.134346
gnomAD - Genomes Global Study-wide 140148 A=0.863616 G=0.136384
gnomAD - Genomes European Sub 75920 A=0.90560 G=0.09440
gnomAD - Genomes African Sub 41978 A=0.75928 G=0.24072
gnomAD - Genomes American Sub 13644 A=0.92854 G=0.07146
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9034 G=0.0966
gnomAD - Genomes East Asian Sub 3134 A=0.9020 G=0.0980
gnomAD - Genomes Other Sub 2150 A=0.8888 G=0.1112
The PAGE Study Global Study-wide 78694 A=0.83818 G=0.16182
The PAGE Study AfricanAmerican Sub 32514 A=0.75700 G=0.24300
The PAGE Study Mexican Sub 10808 A=0.93125 G=0.06875
The PAGE Study Asian Sub 8316 A=0.8551 G=0.1449
The PAGE Study PuertoRican Sub 7918 A=0.9076 G=0.0924
The PAGE Study NativeHawaiian Sub 4534 A=0.8606 G=0.1394
The PAGE Study Cuban Sub 4228 A=0.9177 G=0.0823
The PAGE Study Dominican Sub 3828 A=0.8498 G=0.1502
The PAGE Study CentralAmerican Sub 2450 A=0.9188 G=0.0812
The PAGE Study SouthAmerican Sub 1982 A=0.9223 G=0.0777
The PAGE Study NativeAmerican Sub 1260 A=0.8722 G=0.1278
The PAGE Study SouthAsian Sub 856 A=0.902 G=0.098
8.3KJPN JAPANESE Study-wide 16760 A=0.85931 G=0.14069
1000Genomes Global Study-wide 5008 A=0.8554 G=0.1446
1000Genomes African Sub 1322 A=0.7201 G=0.2799
1000Genomes East Asian Sub 1008 A=0.8740 G=0.1260
1000Genomes Europe Sub 1006 A=0.9145 G=0.0855
1000Genomes South Asian Sub 978 A=0.899 G=0.101
1000Genomes American Sub 694 A=0.939 G=0.061
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8710 G=0.1290
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9102 G=0.0898
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9056 G=0.0944
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9235 G=0.0765
HapMap Global Study-wide 1892 A=0.8208 G=0.1792
HapMap American Sub 770 A=0.875 G=0.125
HapMap African Sub 692 A=0.711 G=0.289
HapMap Asian Sub 254 A=0.858 G=0.142
HapMap Europe Sub 176 A=0.960 G=0.040
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.909 G=0.091
CNV burdens in cranial meningiomas Global Study-wide 784 A=0.915 G=0.085
CNV burdens in cranial meningiomas CRM Sub 784 A=0.915 G=0.085
Northern Sweden ACPOP Study-wide 600 A=0.833 G=0.167
Qatari Global Study-wide 216 A=0.866 G=0.134
SGDP_PRJ Global Study-wide 150 A=0.440 G=0.560
The Danish reference pan genome Danish Study-wide 40 A=0.85 G=0.15
Siberian Global Study-wide 14 A=0.50 G=0.50
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.1174639= NC_000001.11:g.1174639A>G
GRCh37.p13 chr 1 NC_000001.10:g.1110019= NC_000001.10:g.1110019A>G
TTLL10-AS1 transcript variant X2 XR_132470.6:n.2042= XR_132470.6:n.2042T>C
TTLL10-AS1 transcript XR_132470.4:n.2567= XR_132470.4:n.2567T>C
TTLL10 transcript variant 1 NM_001130045.1:c.-28+150= NM_001130045.1:c.-28+150A>G
TTLL10 transcript variant 1 NM_001130045.2:c.-28+150= NM_001130045.2:c.-28+150A>G
TTLL10 transcript variant 3 NM_001371649.1:c.-28+150= NM_001371649.1:c.-28+150A>G
TTLL10 transcript variant X1 XM_005244737.1:c.-28+150= XM_005244737.1:c.-28+150A>G
TTLL10 transcript variant X7 XM_011541177.2:c.-28+150= XM_011541177.2:c.-28+150A>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#.

90 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15432177 Feb 27, 2004 (120)
2 SC_SNP ss18205546 Feb 27, 2004 (120)
3 PERLEGEN ss68756324 May 18, 2007 (127)
4 ILLUMINA ss75066397 Dec 07, 2007 (129)
5 HGSV ss80128728 Dec 14, 2007 (130)
6 BGI ss102713679 Dec 01, 2009 (131)
7 ILLUMINA-UK ss118440569 Feb 14, 2009 (130)
8 KRIBB_YJKIM ss119683050 Dec 01, 2009 (131)
9 ILLUMINA ss159976149 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163708288 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss165983061 Jul 04, 2010 (132)
12 ILLUMINA ss171233481 Jul 04, 2010 (132)
13 BUSHMAN ss197889533 Jul 04, 2010 (132)
14 1000GENOMES ss218192237 Jul 14, 2010 (132)
15 1000GENOMES ss230396602 Jul 14, 2010 (132)
16 1000GENOMES ss238116113 Jul 15, 2010 (132)
17 GMI ss283988063 Apr 25, 2013 (138)
18 PJP ss290494421 May 09, 2011 (134)
19 ILLUMINA ss479515406 May 04, 2012 (137)
20 ILLUMINA ss479519300 May 04, 2012 (137)
21 ILLUMINA ss479970356 Sep 08, 2015 (146)
22 ILLUMINA ss484556896 May 04, 2012 (137)
23 ILLUMINA ss536692960 Sep 08, 2015 (146)
24 TISHKOFF ss553714338 Apr 25, 2013 (138)
25 SSMP ss647518831 Apr 25, 2013 (138)
26 ILLUMINA ss778382652 Sep 08, 2015 (146)
27 ILLUMINA ss782725108 Sep 08, 2015 (146)
28 ILLUMINA ss783692555 Sep 08, 2015 (146)
29 ILLUMINA ss831976763 Sep 08, 2015 (146)
30 ILLUMINA ss833837648 Sep 08, 2015 (146)
31 EVA-GONL ss974772585 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1067613979 Aug 21, 2014 (142)
33 1000GENOMES ss1289352687 Aug 21, 2014 (142)
34 EVA_GENOME_DK ss1573852207 Apr 01, 2015 (144)
35 EVA_DECODE ss1584132514 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1599383674 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1642377707 Apr 01, 2015 (144)
38 EVA_SVP ss1712305568 Apr 01, 2015 (144)
39 ILLUMINA ss1751862988 Sep 08, 2015 (146)
40 HAMMER_LAB ss1793718085 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1917964640 Feb 12, 2016 (147)
42 ILLUMINA ss1945981816 Feb 12, 2016 (147)
43 ILLUMINA ss1958230874 Feb 12, 2016 (147)
44 JJLAB ss2019500156 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147487005 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2159391038 Dec 20, 2016 (150)
47 TOPMED ss2321530259 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2624265664 Nov 08, 2017 (151)
49 ILLUMINA ss2632465810 Nov 08, 2017 (151)
50 ILLUMINA ss2634995314 Nov 08, 2017 (151)
51 GRF ss2697377823 Nov 08, 2017 (151)
52 ILLUMINA ss2710663585 Nov 08, 2017 (151)
53 GNOMAD ss2750678528 Nov 08, 2017 (151)
54 SWEGEN ss2986155349 Nov 08, 2017 (151)
55 ILLUMINA ss3021043830 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3023514418 Nov 08, 2017 (151)
57 TOPMED ss3066486479 Nov 08, 2017 (151)
58 CSHL ss3343274612 Nov 08, 2017 (151)
59 ILLUMINA ss3625523515 Oct 11, 2018 (152)
60 ILLUMINA ss3626007183 Oct 11, 2018 (152)
61 ILLUMINA ss3630505826 Oct 11, 2018 (152)
62 ILLUMINA ss3632878069 Oct 11, 2018 (152)
63 ILLUMINA ss3633571497 Oct 11, 2018 (152)
64 ILLUMINA ss3634302084 Oct 11, 2018 (152)
65 ILLUMINA ss3635265700 Oct 11, 2018 (152)
66 ILLUMINA ss3635978736 Oct 11, 2018 (152)
67 ILLUMINA ss3637016040 Oct 11, 2018 (152)
68 ILLUMINA ss3637732518 Oct 11, 2018 (152)
69 ILLUMINA ss3640009450 Oct 11, 2018 (152)
70 ILLUMINA ss3642746798 Oct 11, 2018 (152)
71 ILLUMINA ss3644477679 Oct 11, 2018 (152)
72 ILLUMINA ss3651365883 Oct 11, 2018 (152)
73 EGCUT_WGS ss3654266413 Jul 12, 2019 (153)
74 EVA_DECODE ss3685999218 Jul 12, 2019 (153)
75 ILLUMINA ss3724988509 Jul 12, 2019 (153)
76 ACPOP ss3726719227 Jul 12, 2019 (153)
77 ILLUMINA ss3744040784 Jul 12, 2019 (153)
78 ILLUMINA ss3744603015 Jul 12, 2019 (153)
79 EVA ss3745725016 Jul 12, 2019 (153)
80 PAGE_CC ss3770778873 Jul 12, 2019 (153)
81 ILLUMINA ss3772104773 Jul 12, 2019 (153)
82 KHV_HUMAN_GENOMES ss3798747653 Jul 12, 2019 (153)
83 EVA ss3825982871 Apr 25, 2020 (154)
84 SGDP_PRJ ss3848005664 Apr 25, 2020 (154)
85 KRGDB ss3892848597 Apr 25, 2020 (154)
86 EVA ss3984450762 Apr 25, 2021 (155)
87 EVA ss4016889136 Apr 25, 2021 (155)
88 TOPMED ss4436537687 Apr 25, 2021 (155)
89 TOMMO_GENOMICS ss5142069745 Apr 25, 2021 (155)
90 EVA ss5237258291 Apr 25, 2021 (155)
91 1000Genomes NC_000001.10 - 1110019 Oct 11, 2018 (152)
92 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1110019 Oct 11, 2018 (152)
93 Genetic variation in the Estonian population NC_000001.10 - 1110019 Oct 11, 2018 (152)
94 The Danish reference pan genome NC_000001.10 - 1110019 Apr 25, 2020 (154)
95 gnomAD - Genomes NC_000001.11 - 1174639 Apr 25, 2021 (155)
96 Genome of the Netherlands Release 5 NC_000001.10 - 1110019 Apr 25, 2020 (154)
97 HapMap NC_000001.11 - 1174639 Apr 25, 2020 (154)
98 KOREAN population from KRGDB NC_000001.10 - 1110019 Apr 25, 2020 (154)
99 Northern Sweden NC_000001.10 - 1110019 Jul 12, 2019 (153)
100 The PAGE Study NC_000001.11 - 1174639 Jul 12, 2019 (153)
101 CNV burdens in cranial meningiomas NC_000001.10 - 1110019 Apr 25, 2021 (155)
102 Qatari NC_000001.10 - 1110019 Apr 25, 2020 (154)
103 SGDP_PRJ NC_000001.10 - 1110019 Apr 25, 2020 (154)
104 Siberian NC_000001.10 - 1110019 Apr 25, 2020 (154)
105 8.3KJPN NC_000001.10 - 1110019 Apr 25, 2021 (155)
106 TopMed NC_000001.11 - 1174639 Apr 25, 2021 (155)
107 UK 10K study - Twins NC_000001.10 - 1110019 Oct 11, 2018 (152)
108 ALFA NC_000001.11 - 1174639 Apr 25, 2021 (155)
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)
rs56745230 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80128728 NC_000001.8:1149941:A:G NC_000001.11:1174638:A:G (self)
ss118440569, ss163708288, ss165983061, ss197889533, ss283988063, ss290494421, ss479515406, ss1584132514, ss1712305568, ss2634995314, ss3642746798 NC_000001.9:1099881:A:G NC_000001.11:1174638:A:G (self)
17864, 6111, 4661, 1359441, 2672, 25991, 4092, 61, 6570, 22644, 3359, 39052, 6111, ss218192237, ss230396602, ss238116113, ss479519300, ss479970356, ss484556896, ss536692960, ss553714338, ss647518831, ss778382652, ss782725108, ss783692555, ss831976763, ss833837648, ss974772585, ss1067613979, ss1289352687, ss1573852207, ss1599383674, ss1642377707, ss1751862988, ss1793718085, ss1917964640, ss1945981816, ss1958230874, ss2019500156, ss2147487005, ss2321530259, ss2624265664, ss2632465810, ss2697377823, ss2710663585, ss2750678528, ss2986155349, ss3021043830, ss3343274612, ss3625523515, ss3626007183, ss3630505826, ss3632878069, ss3633571497, ss3634302084, ss3635265700, ss3635978736, ss3637016040, ss3637732518, ss3640009450, ss3644477679, ss3651365883, ss3654266413, ss3726719227, ss3744040784, ss3744603015, ss3745725016, ss3772104773, ss3825982871, ss3848005664, ss3892848597, ss3984450762, ss4016889136, ss5142069745, ss5237258291 NC_000001.10:1110018:A:G NC_000001.11:1174638:A:G (self)
157322, 261, 342, 82554, 144022, 7897706132, ss2159391038, ss3023514418, ss3066486479, ss3685999218, ss3724988509, ss3770778873, ss3798747653, ss4436537687 NC_000001.11:1174638:A:G NC_000001.11:1174638:A:G (self)
ss68756324, ss75066397, ss102713679, ss119683050, ss159976149, ss171233481 NT_004350.19:588650:A:G NC_000001.11:1174638:A:G (self)
ss15432177, ss18205546 NT_077913.2:113729:A:G NC_000001.11:1174638: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.

No publications for rs11260542

Help

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