Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1546206

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:167191278 (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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.192210 (50876/264690, TOPMED)
T=0.073790 (15907/215572, ALFA)
T=0.184008 (25795/140184, GnomAD) (+ 16 more)
T=0.13687 (2294/16760, 8.3KJPN)
T=0.2242 (1123/5008, 1000G)
T=0.0350 (157/4480, Estonian)
T=0.0568 (219/3854, ALSPAC)
T=0.0520 (193/3708, TWINSUK)
T=0.1239 (363/2930, KOREAN)
T=0.1184 (217/1832, Korea1K)
T=0.051 (51/998, GoNL)
T=0.108 (85/790, PRJEB37584)
T=0.063 (38/600, NorthernSweden)
T=0.094 (49/524, SGDP_PRJ)
T=0.247 (81/328, HapMap)
T=0.222 (48/216, Qatari)
T=0.189 (40/212, Vietnamese)
T=0.06 (3/54, Siberian)
T=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01363 : 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.167191278T>C
GRCh38.p13 chr 1 NC_000001.11:g.167191278T>G
GRCh37.p13 chr 1 NC_000001.10:g.167160515T>C
GRCh37.p13 chr 1 NC_000001.10:g.167160515T>G
Gene: LINC01363, long intergenic non-protein coding RNA 1363 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01363 transcript NR_110811.1:n. 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

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 215572 T=0.073790 C=0.926210
European Sub 181768 T=0.056093 C=0.943907
African Sub 6550 T=0.4736 C=0.5264
African Others Sub 244 T=0.512 C=0.488
African American Sub 6306 T=0.4721 C=0.5279
Asian Sub 6632 T=0.1206 C=0.8794
East Asian Sub 4772 T=0.1197 C=0.8803
Other Asian Sub 1860 T=0.1231 C=0.8769
Latin American 1 Sub 892 T=0.158 C=0.842
Latin American 2 Sub 5302 T=0.0477 C=0.9523
South Asian Sub 360 T=0.156 C=0.844
Other Sub 14068 T=0.09660 C=0.90340


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 T=0.192210 C=0.807790
gnomAD - Genomes Global Study-wide 140184 T=0.184008 C=0.815992
gnomAD - Genomes European Sub 75946 T=0.05482 C=0.94518
gnomAD - Genomes African Sub 41968 T=0.45866 C=0.54134
gnomAD - Genomes American Sub 13660 T=0.09048 C=0.90952
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.1173 C=0.8827
gnomAD - Genomes East Asian Sub 3134 T=0.1337 C=0.8663
gnomAD - Genomes Other Sub 2152 T=0.1571 C=0.8429
8.3KJPN JAPANESE Study-wide 16760 T=0.13687 C=0.86313
1000Genomes Global Study-wide 5008 T=0.2242 C=0.7758
1000Genomes African Sub 1322 T=0.5386 C=0.4614
1000Genomes East Asian Sub 1008 T=0.1587 C=0.8413
1000Genomes Europe Sub 1006 T=0.0586 C=0.9414
1000Genomes South Asian Sub 978 T=0.152 C=0.848
1000Genomes American Sub 694 T=0.062 C=0.938
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.0350 C=0.9650
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.0568 C=0.9432
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.0520 C=0.9480
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.1239 C=0.8761, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.1184 C=0.8816
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.051 C=0.949
CNV burdens in cranial meningiomas Global Study-wide 790 T=0.108 C=0.892
CNV burdens in cranial meningiomas CRM Sub 790 T=0.108 C=0.892
Northern Sweden ACPOP Study-wide 600 T=0.063 C=0.937
SGDP_PRJ Global Study-wide 524 T=0.094 C=0.906
HapMap Global Study-wide 328 T=0.247 C=0.753
HapMap African Sub 120 T=0.533 C=0.467
HapMap American Sub 120 T=0.033 C=0.967
HapMap Asian Sub 88 T=0.15 C=0.85
Qatari Global Study-wide 216 T=0.222 C=0.778
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.189 C=0.811
Siberian Global Study-wide 54 T=0.06 C=0.94
The Danish reference pan genome Danish Study-wide 40 T=0.00 C=1.00
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 G
GRCh38.p13 chr 1 NC_000001.11:g.167191278= NC_000001.11:g.167191278T>C NC_000001.11:g.167191278T>G
GRCh37.p13 chr 1 NC_000001.10:g.167160515= NC_000001.10:g.167160515T>C NC_000001.10:g.167160515T>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#.

108 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2388580 Oct 23, 2000 (88)
2 WI_SSAHASNP ss6411136 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9821640 Jul 11, 2003 (116)
4 WI_SSAHASNP ss11353513 Jul 11, 2003 (116)
5 CSHL-HAPMAP ss16397551 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss17333462 Feb 27, 2004 (120)
7 SSAHASNP ss20555180 Apr 05, 2004 (121)
8 PERLEGEN ss23145073 Sep 20, 2004 (123)
9 ABI ss43963527 Mar 14, 2006 (126)
10 BCMHGSC_JDW ss87857524 Mar 23, 2008 (129)
11 HUMANGENOME_JCVI ss97981811 Feb 05, 2009 (130)
12 BGI ss106608642 Feb 05, 2009 (130)
13 1000GENOMES ss108672796 Jan 23, 2009 (130)
14 ENSEMBL ss138098585 Dec 01, 2009 (131)
15 ENSEMBL ss139180897 Dec 01, 2009 (131)
16 GMI ss155884552 Dec 01, 2009 (131)
17 ILLUMINA ss160370374 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss165378462 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss167240360 Jul 04, 2010 (132)
20 BUSHMAN ss199198898 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss205257382 Jul 04, 2010 (132)
22 1000GENOMES ss210661893 Jul 14, 2010 (132)
23 1000GENOMES ss218698284 Jul 14, 2010 (132)
24 1000GENOMES ss230767157 Jul 14, 2010 (132)
25 1000GENOMES ss238408366 Jul 15, 2010 (132)
26 BL ss253581061 May 09, 2011 (134)
27 GMI ss276088473 May 04, 2012 (137)
28 GMI ss284169139 Apr 25, 2013 (138)
29 PJP ss290656308 May 09, 2011 (134)
30 ILLUMINA ss410908004 Sep 17, 2011 (135)
31 ILLUMINA ss480698937 Sep 08, 2015 (146)
32 ILLUMINA ss482132540 May 04, 2012 (137)
33 ILLUMINA ss483466624 May 04, 2012 (137)
34 EXOME_CHIP ss491305371 May 04, 2012 (137)
35 ILLUMINA ss535676094 Sep 08, 2015 (146)
36 TISHKOFF ss554808186 Apr 25, 2013 (138)
37 SSMP ss648475578 Apr 25, 2013 (138)
38 ILLUMINA ss780659802 Sep 08, 2015 (146)
39 ILLUMINA ss780796089 Aug 21, 2014 (142)
40 ILLUMINA ss782176683 Sep 08, 2015 (146)
41 ILLUMINA ss783477303 Aug 21, 2014 (142)
42 ILLUMINA ss836155162 Sep 08, 2015 (146)
43 EVA-GONL ss975776546 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1068337310 Aug 21, 2014 (142)
45 1000GENOMES ss1293282010 Aug 21, 2014 (142)
46 DDI ss1426006529 Apr 01, 2015 (144)
47 EVA_GENOME_DK ss1574452743 Apr 01, 2015 (144)
48 EVA_DECODE ss1585161473 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1601403600 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1644397633 Apr 01, 2015 (144)
51 ILLUMINA ss1751879383 Sep 08, 2015 (146)
52 HAMMER_LAB ss1795218207 Sep 08, 2015 (146)
53 ILLUMINA ss1917737905 Feb 12, 2016 (147)
54 WEILL_CORNELL_DGM ss1919012785 Feb 12, 2016 (147)
55 ILLUMINA ss1946013751 Feb 12, 2016 (147)
56 ILLUMINA ss1958328867 Feb 12, 2016 (147)
57 ILLUMINA ss1958328868 Feb 12, 2016 (147)
58 GENOMED ss1966889816 Jul 19, 2016 (147)
59 JJLAB ss2020021988 Sep 14, 2016 (149)
60 USC_VALOUEV ss2148049226 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2167252199 Dec 20, 2016 (150)
62 TOPMED ss2329788286 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2624520643 Nov 08, 2017 (151)
64 ILLUMINA ss2632588246 Nov 08, 2017 (151)
65 ILLUMINA ss2632588247 Nov 08, 2017 (151)
66 GRF ss2698026641 Nov 08, 2017 (151)
67 GNOMAD ss2762319222 Nov 08, 2017 (151)
68 AFFY ss2984883949 Nov 08, 2017 (151)
69 AFFY ss2985529560 Nov 08, 2017 (151)
70 SWEGEN ss2987896606 Nov 08, 2017 (151)
71 ILLUMINA ss3021147938 Nov 08, 2017 (151)
72 ILLUMINA ss3021147939 Nov 08, 2017 (151)
73 BIOINF_KMB_FNS_UNIBA ss3023768950 Nov 08, 2017 (151)
74 TOPMED ss3094440286 Nov 08, 2017 (151)
75 CSHL ss3343752881 Nov 08, 2017 (151)
76 ILLUMINA ss3626231807 Oct 11, 2018 (152)
77 ILLUMINA ss3626231808 Oct 11, 2018 (152)
78 ILLUMINA ss3630620352 Oct 11, 2018 (152)
79 ILLUMINA ss3634356378 Oct 11, 2018 (152)
80 ILLUMINA ss3636035324 Oct 11, 2018 (152)
81 ILLUMINA ss3640063732 Oct 11, 2018 (152)
82 ILLUMINA ss3641621761 Oct 11, 2018 (152)
83 ILLUMINA ss3644509708 Oct 11, 2018 (152)
84 URBANLAB ss3646811483 Oct 11, 2018 (152)
85 ILLUMINA ss3651484523 Oct 11, 2018 (152)
86 ILLUMINA ss3651484524 Oct 11, 2018 (152)
87 ILLUMINA ss3653653372 Oct 11, 2018 (152)
88 EGCUT_WGS ss3655839616 Jul 12, 2019 (153)
89 EVA_DECODE ss3687956828 Jul 12, 2019 (153)
90 ILLUMINA ss3725076304 Jul 12, 2019 (153)
91 ACPOP ss3727564303 Jul 12, 2019 (153)
92 ILLUMINA ss3744355235 Jul 12, 2019 (153)
93 ILLUMINA ss3744657261 Jul 12, 2019 (153)
94 EVA ss3746917883 Jul 12, 2019 (153)
95 ILLUMINA ss3772158321 Jul 12, 2019 (153)
96 PACBIO ss3783592225 Jul 12, 2019 (153)
97 PACBIO ss3789219713 Jul 12, 2019 (153)
98 PACBIO ss3794091734 Jul 12, 2019 (153)
99 KHV_HUMAN_GENOMES ss3799918555 Jul 12, 2019 (153)
100 EVA ss3826471511 Apr 25, 2020 (154)
101 EVA ss3836631892 Apr 25, 2020 (154)
102 EVA ss3842041735 Apr 25, 2020 (154)
103 SGDP_PRJ ss3850190039 Apr 25, 2020 (154)
104 KRGDB ss3895422560 Apr 25, 2020 (154)
105 KOGIC ss3945831055 Apr 25, 2020 (154)
106 EVA ss3984466567 Apr 25, 2021 (155)
107 TOPMED ss4471407073 Apr 25, 2021 (155)
108 TOMMO_GENOMICS ss5146886694 Apr 25, 2021 (155)
109 1000Genomes NC_000001.10 - 167160515 Oct 11, 2018 (152)
110 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 167160515 Oct 11, 2018 (152)
111 Genetic variation in the Estonian population NC_000001.10 - 167160515 Oct 11, 2018 (152)
112 The Danish reference pan genome NC_000001.10 - 167160515 Apr 25, 2020 (154)
113 gnomAD - Genomes NC_000001.11 - 167191278 Apr 25, 2021 (155)
114 Genome of the Netherlands Release 5 NC_000001.10 - 167160515 Apr 25, 2020 (154)
115 HapMap NC_000001.11 - 167191278 Apr 25, 2020 (154)
116 KOREAN population from KRGDB NC_000001.10 - 167160515 Apr 25, 2020 (154)
117 Korean Genome Project NC_000001.11 - 167191278 Apr 25, 2020 (154)
118 Northern Sweden NC_000001.10 - 167160515 Jul 12, 2019 (153)
119 CNV burdens in cranial meningiomas NC_000001.10 - 167160515 Apr 25, 2021 (155)
120 Qatari NC_000001.10 - 167160515 Apr 25, 2020 (154)
121 SGDP_PRJ NC_000001.10 - 167160515 Apr 25, 2020 (154)
122 Siberian NC_000001.10 - 167160515 Apr 25, 2020 (154)
123 8.3KJPN NC_000001.10 - 167160515 Apr 25, 2021 (155)
124 TopMed NC_000001.11 - 167191278 Apr 25, 2021 (155)
125 UK 10K study - Twins NC_000001.10 - 167160515 Oct 11, 2018 (152)
126 A Vietnamese Genetic Variation Database NC_000001.10 - 167160515 Jul 12, 2019 (153)
127 ALFA NC_000001.11 - 167191278 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
ss87857524, ss108672796, ss160370374, ss165378462, ss167240360, ss199198898, ss205257382, ss210661893, ss253581061, ss276088473, ss284169139, ss290656308, ss410908004, ss482132540, ss1585161473 NC_000001.9:165427138:T:C NC_000001.11:167191277:T:C (self)
4085947, 2228883, 1577864, 1745334, 969311, 2599954, 849168, 15884, 1054715, 2207019, 565580, 4856001, 2228883, 479340, ss218698284, ss230767157, ss238408366, ss480698937, ss483466624, ss491305371, ss535676094, ss554808186, ss648475578, ss780659802, ss780796089, ss782176683, ss783477303, ss836155162, ss975776546, ss1068337310, ss1293282010, ss1426006529, ss1574452743, ss1601403600, ss1644397633, ss1751879383, ss1795218207, ss1917737905, ss1919012785, ss1946013751, ss1958328867, ss1958328868, ss1966889816, ss2020021988, ss2148049226, ss2329788286, ss2624520643, ss2632588246, ss2632588247, ss2698026641, ss2762319222, ss2984883949, ss2985529560, ss2987896606, ss3021147938, ss3021147939, ss3343752881, ss3626231807, ss3626231808, ss3630620352, ss3634356378, ss3636035324, ss3640063732, ss3641621761, ss3644509708, ss3651484523, ss3651484524, ss3653653372, ss3655839616, ss3727564303, ss3744355235, ss3744657261, ss3746917883, ss3772158321, ss3783592225, ss3789219713, ss3794091734, ss3826471511, ss3836631892, ss3850190039, ss3895422560, ss3984466567, ss5146886694 NC_000001.10:167160514:T:C NC_000001.11:167191277:T:C (self)
29601427, 196205, 2209056, 21976876, 35013408, 6987572525, ss2167252199, ss3023768950, ss3094440286, ss3646811483, ss3687956828, ss3725076304, ss3799918555, ss3842041735, ss3945831055, ss4471407073 NC_000001.11:167191277:T:C NC_000001.11:167191277:T:C (self)
ss2388580, ss6411136, ss23145073, ss43963527, ss97981811, ss106608642, ss138098585, ss139180897, ss155884552 NT_004487.19:18649156:T:C NC_000001.11:167191277:T:C (self)
ss9821640, ss11353513 NT_004668.15:13531073:T:C NC_000001.11:167191277:T:C (self)
ss16397551, ss17333462, ss20555180 NT_004668.16:5665986:T:C NC_000001.11:167191277:T:C (self)
2599954, ss3895422560 NC_000001.10:167160514:T:G NC_000001.11:167191277:T: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 rs1546206

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