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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.

rs1369867

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:82675433 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.29634 (37211/125568, TOPMED)
C=0.3174 (9786/30828, GnomAD)
C=0.233 (1168/5008, 1000G) (+ 3 more)
C=0.395 (1771/4480, Estonian)
C=0.398 (1535/3854, ALSPAC)
C=0.395 (1466/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105377876 : 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.p12 chr 6 NC_000006.12:g.82675433C>A
GRCh38.p12 chr 6 NC_000006.12:g.82675433C>G
GRCh38.p12 chr 6 NC_000006.12:g.82675433C>T
GRCh37.p13 chr 6 NC_000006.11:g.83385150C>A
GRCh37.p13 chr 6 NC_000006.11:g.83385150C>G
GRCh37.p13 chr 6 NC_000006.11:g.83385150C>T
Gene: LOC105377876, uncharacterized LOC105377876 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105377876 transcript variant X1 XR_001744232.1:n. N/A Intron Variant
LOC105377876 transcript variant X2 XR_942739.2: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
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 125568 C=0.29634 T=0.70366
gnomAD - Genomes Global Study-wide 30828 C=0.3174 T=0.6826
gnomAD - Genomes European Sub 18420 C=0.3867 T=0.6133
gnomAD - Genomes African Sub 8714 C=0.212 T=0.788
gnomAD - Genomes East Asian Sub 1582 C=0.100 T=0.900
gnomAD - Genomes Other Sub 976 C=0.37 T=0.63
gnomAD - Genomes American Sub 834 C=0.27 T=0.73
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.23 T=0.77
1000Genomes Global Study-wide 5008 C=0.233 T=0.767
1000Genomes African Sub 1322 C=0.164 T=0.836
1000Genomes East Asian Sub 1008 C=0.102 T=0.898
1000Genomes Europe Sub 1006 C=0.373 T=0.627
1000Genomes South Asian Sub 978 C=0.27 T=0.73
1000Genomes American Sub 694 C=0.30 T=0.70
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.395 T=0.605
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.398 T=0.602
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.395 T=0.605
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 C= A G T Note
GRCh38.p12 chr 6 NC_000006.12:...

NC_000006.12:g.82675433C=

NC_000006.12:...

NC_000006.12:g.82675433C>A

NC_000006.12:...

NC_000006.12:g.82675433C>G

NC_000006.12:...

NC_000006.12:g.82675433C>T

GRCh37.p13 chr 6 NC_000006.11:...

NC_000006.11:g.83385150C=

NC_000006.11:...

NC_000006.11:g.83385150C>A

NC_000006.11:...

NC_000006.11:g.83385150C>G

NC_000006.11:...

NC_000006.11:g.83385150C>T

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#.

100 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2156223 Oct 23, 2000 (88)
2 SC_JCM ss3984483 Sep 28, 2001 (100)
3 TSC-CSHL ss5507221 Oct 08, 2002 (108)
4 WI_SSAHASNP ss6485091 Feb 20, 2003 (111)
5 WI_SSAHASNP ss11807680 Jul 11, 2003 (116)
6 SC_SNP ss13055283 Dec 05, 2003 (119)
7 CSHL-HAPMAP ss17111427 Feb 27, 2004 (120)
8 SSAHASNP ss22445182 Apr 05, 2004 (121)
9 ABI ss42783532 Mar 14, 2006 (126)
10 ILLUMINA ss67088173 Nov 30, 2006 (127)
11 ILLUMINA ss67421770 Nov 30, 2006 (127)
12 ILLUMINA ss68152637 Dec 12, 2006 (127)
13 ILLUMINA ss70609833 May 23, 2008 (130)
14 ILLUMINA ss71157109 May 17, 2007 (127)
15 ILLUMINA ss75684726 Dec 06, 2007 (129)
16 HGSV ss78388473 Dec 06, 2007 (129)
17 KRIBB_YJKIM ss83741545 Dec 14, 2007 (130)
18 HGSV ss85598354 Dec 14, 2007 (130)
19 HUMANGENOME_JCVI ss98410723 Feb 03, 2009 (130)
20 BGI ss104331743 Dec 01, 2009 (131)
21 1000GENOMES ss110447628 Jan 24, 2009 (130)
22 1000GENOMES ss114662460 Jan 25, 2009 (130)
23 ILLUMINA-UK ss116577849 Feb 14, 2009 (130)
24 ENSEMBL ss142803845 Dec 01, 2009 (131)
25 ILLUMINA ss153395312 Dec 01, 2009 (131)
26 GMI ss157228091 Dec 01, 2009 (131)
27 ILLUMINA ss159261402 Dec 01, 2009 (131)
28 ILLUMINA ss160343049 Dec 01, 2009 (131)
29 COMPLETE_GENOMICS ss162562023 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss163855929 Jul 04, 2010 (132)
31 COMPLETE_GENOMICS ss166950429 Jul 04, 2010 (132)
32 ILLUMINA ss172449003 Jul 04, 2010 (132)
33 BUSHMAN ss202101088 Jul 04, 2010 (132)
34 BCM-HGSC-SUB ss207553415 Jul 04, 2010 (132)
35 1000GENOMES ss222506887 Jul 14, 2010 (132)
36 1000GENOMES ss233561311 Jul 15, 2010 (132)
37 1000GENOMES ss240600272 Jul 15, 2010 (132)
38 BL ss254506295 May 09, 2011 (134)
39 GMI ss278896725 May 04, 2012 (137)
40 GMI ss285451113 Apr 25, 2013 (138)
41 PJP ss293650695 May 09, 2011 (134)
42 ILLUMINA ss479944031 May 04, 2012 (137)
43 ILLUMINA ss479952349 May 04, 2012 (137)
44 ILLUMINA ss480590342 Sep 08, 2015 (146)
45 ILLUMINA ss484770264 May 04, 2012 (137)
46 ILLUMINA ss536859821 Sep 08, 2015 (146)
47 TISHKOFF ss559333024 Apr 25, 2013 (138)
48 SSMP ss653299299 Apr 25, 2013 (138)
49 ILLUMINA ss778803447 Sep 08, 2015 (146)
50 ILLUMINA ss782831840 Sep 08, 2015 (146)
51 ILLUMINA ss783796637 Sep 08, 2015 (146)
52 ILLUMINA ss832085350 Sep 08, 2015 (146)
53 ILLUMINA ss834263640 Sep 08, 2015 (146)
54 EVA-GONL ss983165183 Aug 21, 2014 (142)
55 JMKIDD_LAB ss1073784525 Aug 21, 2014 (142)
56 1000GENOMES ss1321005563 Aug 21, 2014 (142)
57 DDI ss1430801730 Apr 01, 2015 (144)
58 EVA_GENOME_DK ss1581767110 Apr 01, 2015 (144)
59 EVA_DECODE ss1592713668 Apr 01, 2015 (144)
60 EVA_UK10K_ALSPAC ss1616019393 Apr 01, 2015 (144)
61 EVA_UK10K_TWINSUK ss1659013426 Apr 01, 2015 (144)
62 EVA_SVP ss1712877427 Apr 01, 2015 (144)
63 ILLUMINA ss1752649704 Sep 08, 2015 (146)
64 HAMMER_LAB ss1804532556 Sep 08, 2015 (146)
65 WEILL_CORNELL_DGM ss1926424604 Feb 12, 2016 (147)
66 ILLUMINA ss1946184255 Feb 12, 2016 (147)
67 ILLUMINA ss1958928490 Feb 12, 2016 (147)
68 GENOMED ss1970451443 Jul 19, 2016 (147)
69 JJLAB ss2023855279 Sep 14, 2016 (149)
70 USC_VALOUEV ss2152047597 Dec 20, 2016 (150)
71 HUMAN_LONGEVITY ss2285680867 Dec 20, 2016 (150)
72 TOPMED ss2454310781 Dec 20, 2016 (150)
73 SYSTEMSBIOZJU ss2626423101 Nov 08, 2017 (151)
74 ILLUMINA ss2634475357 Nov 08, 2017 (151)
75 GRF ss2707663500 Nov 08, 2017 (151)
76 ILLUMINA ss2711083070 Nov 08, 2017 (151)
77 GNOMAD ss2841459982 Nov 08, 2017 (151)
78 SWEGEN ss2999440337 Nov 08, 2017 (151)
79 ILLUMINA ss3022641122 Nov 08, 2017 (151)
80 BIOINF_KMB_FNS_UNIBA ss3025721284 Nov 08, 2017 (151)
81 CSHL ss3347083109 Nov 08, 2017 (151)
82 TOPMED ss3503386391 Nov 08, 2017 (151)
83 ILLUMINA ss3625906523 Oct 12, 2018 (152)
84 ILLUMINA ss3629589762 Oct 12, 2018 (152)
85 ILLUMINA ss3632390456 Oct 12, 2018 (152)
86 ILLUMINA ss3633427963 Oct 12, 2018 (152)
87 ILLUMINA ss3634151141 Oct 12, 2018 (152)
88 ILLUMINA ss3635075779 Oct 12, 2018 (152)
89 ILLUMINA ss3635831822 Oct 12, 2018 (152)
90 ILLUMINA ss3636799627 Oct 12, 2018 (152)
91 ILLUMINA ss3637584653 Oct 12, 2018 (152)
92 ILLUMINA ss3638640858 Oct 12, 2018 (152)
93 ILLUMINA ss3639321007 Oct 12, 2018 (152)
94 ILLUMINA ss3639956125 Oct 12, 2018 (152)
95 ILLUMINA ss3640783079 Oct 12, 2018 (152)
96 ILLUMINA ss3643581162 Oct 12, 2018 (152)
97 ILLUMINA ss3644000937 Oct 12, 2018 (152)
98 ILLUMINA ss3644917338 Oct 12, 2018 (152)
99 URBANLAB ss3648403019 Oct 12, 2018 (152)
100 ILLUMINA ss3653158682 Oct 12, 2018 (152)
101 1000Genomes NC_000006.11 - 83385150 Oct 12, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 83385150 Oct 12, 2018 (152)
103 Genetic variation in the Estonian population NC_000006.11 - 83385150 Oct 12, 2018 (152)
104 gnomAD - Genomes NC_000006.11 - 83385150 Oct 12, 2018 (152)
105 TopMed NC_000006.12 - 82675433 Oct 12, 2018 (152)
106 UK 10K study - Twins NC_000006.11 - 83385150 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)
rs56838152 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss1430801730 NC_000006.11:83385149:C:A NC_000006.12:82675432:C:A (self)
ss2285680867 NC_000006.12:82675432:C:G NC_000006.12:82675432:C:G (self)
ss78388473, ss85598354, ss3639321007, ss3639956125, ss3644000937 NC_000006.9:83441868:C:T NC_000006.12:82675432:C:T (self)
ss110447628, ss114662460, ss116577849, ss162562023, ss163855929, ss166950429, ss202101088, ss207553415, ss254506295, ss278896725, ss285451113, ss293650695, ss479944031, ss1592713668, ss1712877427, ss3643581162 NC_000006.10:83441868:C:T NC_000006.12:82675432:C:T (self)
32826133, 18283189, 13055174, 182087739, 18283189, ss222506887, ss233561311, ss240600272, ss479952349, ss480590342, ss484770264, ss536859821, ss559333024, ss653299299, ss778803447, ss782831840, ss783796637, ss832085350, ss834263640, ss983165183, ss1073784525, ss1321005563, ss1430801730, ss1581767110, ss1616019393, ss1659013426, ss1752649704, ss1804532556, ss1926424604, ss1946184255, ss1958928490, ss1970451443, ss2023855279, ss2152047597, ss2454310781, ss2626423101, ss2634475357, ss2707663500, ss2711083070, ss2841459982, ss2999440337, ss3022641122, ss3347083109, ss3625906523, ss3629589762, ss3632390456, ss3633427963, ss3634151141, ss3635075779, ss3635831822, ss3636799627, ss3637584653, ss3638640858, ss3640783079, ss3644917338, ss3653158682 NC_000006.11:83385149:C:T NC_000006.12:82675432:C:T (self)
342711957, ss2285680867, ss3025721284, ss3503386391, ss3648403019 NC_000006.12:82675432:C:T NC_000006.12:82675432:C:T (self)
ss11807680, ss13055283, ss17111427, ss22445182 NT_007299.12:21205320:C:T NC_000006.12:82675432:C:T (self)
ss2156223, ss3984483, ss5507221, ss6485091, ss42783532, ss67088173, ss67421770, ss68152637, ss70609833, ss71157109, ss75684726, ss83741545, ss98410723, ss104331743, ss142803845, ss153395312, ss157228091, ss159261402, ss160343049, ss172449003 NT_007299.13:21504983:C:T NC_000006.12:82675432:C:T (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 rs1369867

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