Skip to main page content
Accesskeys

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.

rs11177380

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr12:40597141 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.41890 (52601/125568, TOPMED)
C=0.3999 (12340/30860, GnomAD)
C=0.446 (2235/5008, 1000G) (+ 3 more)
C=0.385 (1727/4480, Estonian)
C=0.460 (1771/3854, ALSPAC)
C=0.462 (1713/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 12 NC_000012.12:g.40597141C>A
GRCh37.p13 chr 12 NC_000012.11:g.40990943C>A
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=0.41890 A=0.58110
gnomAD - Genomes Global Study-wide 30860 C=0.3999 A=0.6001
gnomAD - Genomes European Sub 18438 C=0.4274 A=0.5726
gnomAD - Genomes African Sub 8704 C=0.295 A=0.705
gnomAD - Genomes East Asian Sub 1604 C=0.595 A=0.405
gnomAD - Genomes Other Sub 980 C=0.40 A=0.60
gnomAD - Genomes American Sub 836 C=0.43 A=0.57
gnomAD - Genomes Ashkenazi Jewish Sub 298 C=0.63 A=0.37
1000Genomes Global Study-wide 5008 C=0.446 A=0.554
1000Genomes African Sub 1322 C=0.269 A=0.731
1000Genomes East Asian Sub 1008 C=0.587 A=0.413
1000Genomes Europe Sub 1006 C=0.469 A=0.531
1000Genomes South Asian Sub 978 C=0.50 A=0.50
1000Genomes American Sub 694 C=0.48 A=0.52
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.385 A=0.615
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.460 A=0.540
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.462 A=0.538
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 Note
GRCh38.p12 chr 12 NC_000012.12:g.40597141C= NC_000012.12:g.40597141C>A
GRCh37.p13 chr 12 NC_000012.11:g.40990943C= NC_000012.11:g.40990943C>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#.

52 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss16299430 Feb 27, 2004 (120)
2 SC_SNP ss18549383 Feb 27, 2004 (120)
3 SSAHASNP ss20976631 Apr 05, 2004 (121)
4 ABI ss38941477 Mar 13, 2006 (126)
5 PERLEGEN ss46551424 Mar 13, 2006 (126)
6 HGSV ss77114688 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss89106878 Mar 24, 2008 (129)
8 HUMANGENOME_JCVI ss97304046 Feb 06, 2009 (130)
9 1000GENOMES ss111823262 Jan 25, 2009 (130)
10 1000GENOMES ss113438367 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118739547 Feb 14, 2009 (130)
12 ENSEMBL ss132119949 Dec 01, 2009 (131)
13 ENSEMBL ss133128541 Dec 01, 2009 (131)
14 GMI ss157389267 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss169635947 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss170770244 Jul 04, 2010 (132)
17 BUSHMAN ss198060335 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss208046500 Jul 04, 2010 (132)
19 1000GENOMES ss225714101 Jul 14, 2010 (132)
20 1000GENOMES ss235907124 Jul 15, 2010 (132)
21 1000GENOMES ss242469800 Jul 15, 2010 (132)
22 BL ss255061074 May 09, 2011 (134)
23 GMI ss281365338 May 04, 2012 (137)
24 GMI ss286548806 Apr 25, 2013 (138)
25 PJP ss291426182 May 09, 2011 (134)
26 TISHKOFF ss563121474 Apr 25, 2013 (138)
27 SSMP ss658667501 Apr 25, 2013 (138)
28 EVA-GONL ss989454765 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1078404488 Aug 21, 2014 (142)
30 1000GENOMES ss1344709799 Aug 21, 2014 (142)
31 DDI ss1426911338 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1576237432 Apr 01, 2015 (144)
33 EVA_DECODE ss1599122013 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1628433281 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1671427314 Apr 01, 2015 (144)
36 HAMMER_LAB ss1807211521 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1932818349 Feb 12, 2016 (147)
38 JJLAB ss2027160002 Sep 14, 2016 (149)
39 USC_VALOUEV ss2155493437 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2189155704 Dec 20, 2016 (150)
41 TOPMED ss2353078018 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2628059377 Nov 08, 2017 (151)
43 GRF ss2699832925 Nov 08, 2017 (151)
44 GNOMAD ss2909624552 Nov 08, 2017 (151)
45 AFFY ss2984972646 Nov 08, 2017 (151)
46 AFFY ss2985615223 Nov 08, 2017 (151)
47 SWEGEN ss3009559716 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3027388291 Nov 08, 2017 (151)
49 TOPMED ss3168879195 Nov 08, 2017 (151)
50 CSHL ss3350029041 Nov 08, 2017 (151)
51 URBANLAB ss3649821449 Oct 12, 2018 (152)
52 ILLUMINA ss3653745601 Oct 12, 2018 (152)
53 1000Genomes NC_000012.11 - 40990943 Oct 12, 2018 (152)
54 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 40990943 Oct 12, 2018 (152)
55 Genetic variation in the Estonian population NC_000012.11 - 40990943 Oct 12, 2018 (152)
56 gnomAD - Genomes NC_000012.11 - 40990943 Oct 12, 2018 (152)
57 TopMed NC_000012.12 - 40597141 Oct 12, 2018 (152)
58 UK 10K study - Twins NC_000012.11 - 40990943 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77114688 NC_000012.9:39277209:C:A NC_000012.12:40597140:C:A (self)
ss89106878, ss111823262, ss113438367, ss118739547, ss169635947, ss170770244, ss198060335, ss208046500, ss255061074, ss281365338, ss286548806, ss291426182, ss1599122013 NC_000012.10:39277209:C:A NC_000012.12:40597140:C:A (self)
57447180, 31900973, 22572791, 43326075, 31900973, ss225714101, ss235907124, ss242469800, ss563121474, ss658667501, ss989454765, ss1078404488, ss1344709799, ss1426911338, ss1576237432, ss1628433281, ss1671427314, ss1807211521, ss1932818349, ss2027160002, ss2155493437, ss2353078018, ss2628059377, ss2699832925, ss2909624552, ss2984972646, ss2985615223, ss3009559716, ss3350029041, ss3653745601 NC_000012.11:40990942:C:A NC_000012.12:40597140:C:A (self)
82125439, ss2189155704, ss3027388291, ss3168879195, ss3649821449 NC_000012.12:40597140:C:A NC_000012.12:40597140:C:A (self)
ss16299430, ss18549383, ss20976631 NT_029419.10:3134248:C:A NC_000012.12:40597140:C:A (self)
ss38941477, ss46551424, ss97304046, ss132119949, ss133128541, ss157389267 NT_029419.12:3134248:C:A NC_000012.12:40597140:C: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 rs11177380

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