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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.

rs6684820

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1189283 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.415550 (109992/264690, TOPMED)
A=0.387168 (54205/140004, GnomAD)
G=0.44452 (34981/78694, PAGE_STUDY) (+ 16 more)
A=0.32227 (13639/42322, ALFA)
G=0.11641 (1951/16760, 8.3KJPN)
G=0.4461 (2234/5008, 1000G)
A=0.3132 (1403/4480, Estonian)
A=0.2600 (1002/3854, ALSPAC)
A=0.2799 (1038/3708, TWINSUK)
G=0.1498 (439/2930, KOREAN)
G=0.1550 (284/1832, Korea1K)
A=0.239 (239/998, GoNL)
A=0.335 (201/600, NorthernSweden)
G=0.230 (102/444, SGDP_PRJ)
G=0.420 (136/324, HapMap)
A=0.398 (86/216, Qatari)
G=0.093 (20/214, Vietnamese)
G=0.34 (15/44, Siberian)
A=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
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.1189283G>A
GRCh37.p13 chr 1 NC_000001.10:g.1124663G>A
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.1401+417…

NM_001130045.2:c.1401+4174G>A

N/A Intron Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1401+417…

NM_001371649.1:c.1401+4174G>A

N/A Intron Variant
TTLL10 transcript variant 2 NM_153254.3:c. N/A Genic Downstream Transcript Variant
TTLL10 transcript variant X10 XM_005244738.1:c.1182+417…

XM_005244738.1:c.1182+4174G>A

N/A Intron Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1401+417…

XM_011541177.2:c.1401+4174G>A

N/A Intron Variant
TTLL10 transcript variant X1 XM_017000906.1:c.1320+417…

XM_017000906.1:c.1320+4174G>A

N/A Intron Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1401+417…

XM_017000909.1:c.1401+4174G>A

N/A Intron Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1401+417…

XM_017000912.1:c.1401+4174G>A

N/A Intron Variant
TTLL10 transcript variant X2 XM_017000907.1:c. N/A Genic Downstream Transcript Variant
TTLL10 transcript variant X3 XM_017000908.1:c. N/A Genic Downstream Transcript Variant
TTLL10 transcript variant X5 XM_017000910.2:c. N/A Genic Downstream Transcript Variant
TTLL10 transcript variant X6 XM_017000911.1:c. N/A Genic Downstream Transcript Variant
TTLL10 transcript variant X9 XR_001737088.1:n. N/A Intron Variant
TTLL10 transcript variant X11 XR_001737089.1: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 42322 G=0.67773 A=0.32227
European Sub 32112 G=0.72515 A=0.27485
African Sub 4946 G=0.4468 A=0.5532
African Others Sub 180 G=0.344 A=0.656
African American Sub 4766 G=0.4507 A=0.5493
Asian Sub 470 G=0.140 A=0.860
East Asian Sub 404 G=0.129 A=0.871
Other Asian Sub 66 G=0.21 A=0.79
Latin American 1 Sub 514 G=0.619 A=0.381
Latin American 2 Sub 836 G=0.514 A=0.486
South Asian Sub 168 G=0.589 A=0.411
Other Sub 3276 G=0.6941 A=0.3059


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 G=0.584450 A=0.415550
gnomAD - Genomes Global Study-wide 140004 G=0.612832 A=0.387168
gnomAD - Genomes European Sub 75836 G=0.73553 A=0.26447
gnomAD - Genomes African Sub 41928 G=0.43882 A=0.56118
gnomAD - Genomes American Sub 13636 G=0.54261 A=0.45739
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.7297 A=0.2703
gnomAD - Genomes East Asian Sub 3130 G=0.1585 A=0.8415
gnomAD - Genomes Other Sub 2152 G=0.6046 A=0.3954
The PAGE Study Global Study-wide 78694 G=0.44452 A=0.55548
The PAGE Study AfricanAmerican Sub 32514 G=0.44476 A=0.55524
The PAGE Study Mexican Sub 10810 G=0.49084 A=0.50916
The PAGE Study Asian Sub 8316 G=0.1231 A=0.8769
The PAGE Study PuertoRican Sub 7916 G=0.6037 A=0.3963
The PAGE Study NativeHawaiian Sub 4534 G=0.2794 A=0.7206
The PAGE Study Cuban Sub 4228 G=0.6805 A=0.3195
The PAGE Study Dominican Sub 3828 G=0.5624 A=0.4376
The PAGE Study CentralAmerican Sub 2450 G=0.4457 A=0.5543
The PAGE Study SouthAmerican Sub 1982 G=0.4299 A=0.5701
The PAGE Study NativeAmerican Sub 1260 G=0.5865 A=0.4135
The PAGE Study SouthAsian Sub 856 G=0.504 A=0.496
8.3KJPN JAPANESE Study-wide 16760 G=0.11641 A=0.88359
1000Genomes Global Study-wide 5008 G=0.4461 A=0.5539
1000Genomes African Sub 1322 G=0.3896 A=0.6104
1000Genomes East Asian Sub 1008 G=0.1200 A=0.8800
1000Genomes Europe Sub 1006 G=0.7425 A=0.2575
1000Genomes South Asian Sub 978 G=0.534 A=0.466
1000Genomes American Sub 694 G=0.474 A=0.526
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6868 A=0.3132
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7400 A=0.2600
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7201 A=0.2799
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.1498 A=0.8502
Korean Genome Project KOREAN Study-wide 1832 G=0.1550 A=0.8450
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.761 A=0.239
Northern Sweden ACPOP Study-wide 600 G=0.665 A=0.335
SGDP_PRJ Global Study-wide 444 G=0.230 A=0.770
HapMap Global Study-wide 324 G=0.420 A=0.580
HapMap African Sub 120 G=0.325 A=0.675
HapMap American Sub 120 G=0.733 A=0.267
HapMap Asian Sub 84 G=0.11 A=0.89
Qatari Global Study-wide 216 G=0.602 A=0.398
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.093 A=0.907
Siberian Global Study-wide 44 G=0.34 A=0.66
The Danish reference pan genome Danish Study-wide 40 G=0.62 A=0.38
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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.1189283= NC_000001.11:g.1189283G>A
GRCh37.p13 chr 1 NC_000001.10:g.1124663= NC_000001.10:g.1124663G>A
TTLL10 transcript variant 1 NM_001130045.1:c.1401+4174= NM_001130045.1:c.1401+4174G>A
TTLL10 transcript variant 1 NM_001130045.2:c.1401+4174= NM_001130045.2:c.1401+4174G>A
TTLL10 transcript variant 3 NM_001371649.1:c.1401+4174= NM_001371649.1:c.1401+4174G>A
TTLL10 transcript variant X1 XM_005244737.1:c.1401+4174= XM_005244737.1:c.1401+4174G>A
TTLL10 transcript variant X10 XM_005244738.1:c.1182+4174= XM_005244738.1:c.1182+4174G>A
TTLL10 transcript variant X7 XM_011541177.2:c.1401+4174= XM_011541177.2:c.1401+4174G>A
TTLL10 transcript variant X1 XM_017000906.1:c.1320+4174= XM_017000906.1:c.1320+4174G>A
TTLL10 transcript variant X4 XM_017000909.1:c.1401+4174= XM_017000909.1:c.1401+4174G>A
TTLL10 transcript variant X8 XM_017000912.1:c.1401+4174= XM_017000912.1:c.1401+4174G>A
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#.

64 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9866207 Jul 11, 2003 (116)
2 PERLEGEN ss68756325 May 16, 2007 (127)
3 HGSV ss77594348 Dec 07, 2007 (129)
4 BCMHGSC_JDW ss87158582 Mar 23, 2008 (129)
5 BGI ss105112229 Dec 01, 2009 (131)
6 1000GENOMES ss109941971 Jan 24, 2009 (130)
7 ENSEMBL ss137754638 Dec 01, 2009 (131)
8 GMI ss154528671 Dec 01, 2009 (131)
9 ILLUMINA ss160797828 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss162984036 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss163708851 Jul 04, 2010 (132)
12 BUSHMAN ss197889801 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss205225969 Jul 04, 2010 (132)
14 1000GENOMES ss218192314 Jul 14, 2010 (132)
15 1000GENOMES ss230396669 Jul 14, 2010 (132)
16 1000GENOMES ss238116156 Jul 15, 2010 (132)
17 BL ss252866503 May 09, 2011 (134)
18 GMI ss275682647 May 04, 2012 (137)
19 GMI ss283988086 Apr 25, 2013 (138)
20 PJP ss290494441 May 09, 2011 (134)
21 ILLUMINA ss482323682 Sep 08, 2015 (146)
22 TISHKOFF ss553714471 Apr 25, 2013 (138)
23 SSMP ss647518954 Apr 25, 2013 (138)
24 EVA-GONL ss974772737 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1067614073 Aug 21, 2014 (142)
26 1000GENOMES ss1289353335 Aug 21, 2014 (142)
27 DDI ss1425686034 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1573852288 Apr 01, 2015 (144)
29 EVA_DECODE ss1584132675 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1599383937 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1642377970 Apr 01, 2015 (144)
32 HAMMER_LAB ss1793718348 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1917964846 Feb 12, 2016 (147)
34 ILLUMINA ss1958230942 Feb 12, 2016 (147)
35 GENOMED ss1966667816 Jul 19, 2016 (147)
36 JJLAB ss2019500243 Sep 14, 2016 (149)
37 USC_VALOUEV ss2147487134 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2159392267 Dec 20, 2016 (150)
39 TOPMED ss2321531449 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624265721 Nov 08, 2017 (151)
41 GRF ss2697377916 Nov 08, 2017 (151)
42 GNOMAD ss2750680146 Nov 08, 2017 (151)
43 SWEGEN ss2986155637 Nov 08, 2017 (151)
44 ILLUMINA ss3021043896 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3023514455 Nov 08, 2017 (151)
46 TOPMED ss3066489835 Nov 08, 2017 (151)
47 CSHL ss3343274702 Nov 08, 2017 (151)
48 ILLUMINA ss3635978748 Oct 11, 2018 (152)
49 ILLUMINA ss3651365952 Oct 11, 2018 (152)
50 EGCUT_WGS ss3654266655 Jul 12, 2019 (153)
51 EVA_DECODE ss3685999512 Jul 12, 2019 (153)
52 ILLUMINA ss3724988551 Jul 12, 2019 (153)
53 ACPOP ss3726719383 Jul 12, 2019 (153)
54 EVA ss3745725171 Jul 12, 2019 (153)
55 PAGE_CC ss3770778910 Jul 12, 2019 (153)
56 KHV_HUMAN_GENOMES ss3798747843 Jul 12, 2019 (153)
57 EVA ss3825982947 Apr 25, 2020 (154)
58 EVA ss3836379139 Apr 25, 2020 (154)
59 EVA ss3841783167 Apr 25, 2020 (154)
60 SGDP_PRJ ss3848006065 Apr 25, 2020 (154)
61 KRGDB ss3892849008 Apr 25, 2020 (154)
62 KOGIC ss3943637943 Apr 25, 2020 (154)
63 TOPMED ss4436541837 Apr 25, 2021 (155)
64 TOMMO_GENOMICS ss5142070469 Apr 25, 2021 (155)
65 1000Genomes NC_000001.10 - 1124663 Oct 11, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1124663 Oct 11, 2018 (152)
67 Genetic variation in the Estonian population NC_000001.10 - 1124663 Oct 11, 2018 (152)
68 The Danish reference pan genome NC_000001.10 - 1124663 Apr 25, 2020 (154)
69 gnomAD - Genomes NC_000001.11 - 1189283 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 1124663 Apr 25, 2020 (154)
71 HapMap NC_000001.11 - 1189283 Apr 25, 2020 (154)
72 KOREAN population from KRGDB NC_000001.10 - 1124663 Apr 25, 2020 (154)
73 Korean Genome Project NC_000001.11 - 1189283 Apr 25, 2020 (154)
74 Northern Sweden NC_000001.10 - 1124663 Jul 12, 2019 (153)
75 The PAGE Study NC_000001.11 - 1189283 Jul 12, 2019 (153)
76 Qatari NC_000001.10 - 1124663 Apr 25, 2020 (154)
77 SGDP_PRJ NC_000001.10 - 1124663 Apr 25, 2020 (154)
78 Siberian NC_000001.10 - 1124663 Apr 25, 2020 (154)
79 8.3KJPN NC_000001.10 - 1124663 Apr 25, 2021 (155)
80 TopMed NC_000001.11 - 1189283 Apr 25, 2021 (155)
81 UK 10K study - Twins NC_000001.10 - 1124663 Oct 11, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000001.10 - 1124663 Jul 12, 2019 (153)
83 ALFA NC_000001.11 - 1189283 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77594348 NC_000001.8:1164585:G:A NC_000001.11:1189282:G:A (self)
ss87158582, ss109941971, ss162984036, ss163708851, ss197889801, ss205225969, ss252866503, ss275682647, ss283988086, ss290494441, ss1584132675 NC_000001.9:1114525:G:A NC_000001.11:1189282:G:A (self)
18524, 6387, 4903, 1359522, 2784, 26402, 4248, 6776, 23045, 3488, 39776, 6387, 1407, ss218192314, ss230396669, ss238116156, ss482323682, ss553714471, ss647518954, ss974772737, ss1067614073, ss1289353335, ss1425686034, ss1573852288, ss1599383937, ss1642377970, ss1793718348, ss1917964846, ss1958230942, ss1966667816, ss2019500243, ss2147487134, ss2321531449, ss2624265721, ss2697377916, ss2750680146, ss2986155637, ss3021043896, ss3343274702, ss3635978748, ss3651365952, ss3654266655, ss3726719383, ss3745725171, ss3825982947, ss3836379139, ss3848006065, ss3892849008, ss5142070469 NC_000001.10:1124662:G:A NC_000001.11:1189282:G:A (self)
160970, 273, 15944, 379, 85169, 148172, 4484557218, ss2159392267, ss3023514455, ss3066489835, ss3685999512, ss3724988551, ss3770778910, ss3798747843, ss3841783167, ss3943637943, ss4436541837 NC_000001.11:1189282:G:A NC_000001.11:1189282:G:A (self)
ss68756325, ss105112229, ss137754638, ss154528671, ss160797828 NT_004350.19:603294:G:A NC_000001.11:1189282:G:A (self)
ss9866207 NT_077960.1:194103:G:A NC_000001.11:1189282:G:A (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 rs6684820

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