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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 Aliases 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.

rs1181187

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:53824725 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.27979 (35133/125568, TOPMED)
C=0.2720 (8528/31358, GnomAD)
C=0.243 (1219/5008, 1000G) (+ 5 more)
C=0.174 (780/4480, Estonian)
C=0.176 (677/3854, ALSPAC)
C=0.186 (690/3708, TWINSUK)
C=0.15 (91/600, NorthernSweden)
C=0.13 (27/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NDC1 : 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 1 NC_000001.11:g.53824725T>C
GRCh37.p13 chr 1 NC_000001.10:g.54290398T>C
Gene: NDC1, NDC1 transmembrane nucleoporin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NDC1 transcript variant 2 NM_001168551.2:c. N/A Intron Variant
NDC1 transcript variant 1 NM_018087.5:c. N/A Intron Variant
NDC1 transcript variant 3 NR_033142.1:n. N/A Intron Variant
NDC1 transcript variant X1 XM_011541766.2:c. 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 T=0.72021 C=0.27979
gnomAD - Genomes Global Study-wide 31358 T=0.7280 C=0.2720
gnomAD - Genomes European Sub 18892 T=0.8080 C=0.1920
gnomAD - Genomes African Sub 8688 T=0.501 C=0.499
gnomAD - Genomes East Asian Sub 1556 T=0.898 C=0.102
gnomAD - Genomes Other Sub 1084 T=0.823 C=0.177
gnomAD - Genomes American Sub 848 T=0.85 C=0.15
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.69 C=0.31
1000Genomes Global Study-wide 5008 T=0.757 C=0.243
1000Genomes African Sub 1322 T=0.436 C=0.564
1000Genomes East Asian Sub 1008 T=0.899 C=0.101
1000Genomes Europe Sub 1006 T=0.805 C=0.195
1000Genomes South Asian Sub 978 T=0.93 C=0.07
1000Genomes American Sub 694 T=0.84 C=0.16
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.826 C=0.174
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.824 C=0.176
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.814 C=0.186
Northern Sweden ACPOP Study-wide 600 T=0.85 C=0.15
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.87 C=0.13
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 Note
GRCh38.p12 chr 1 NC_000001.11:g.53824725= NC_000001.11:g.53824725T>C
GRCh37.p13 chr 1 NC_000001.10:g.54290398= NC_000001.10:g.54290398T>C
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#.

66 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1642909 Oct 18, 2000 (87)
2 SC_JCM ss2581401 Nov 08, 2000 (89)
3 SC_SNP ss13040202 Dec 05, 2003 (119)
4 SSAHASNP ss20563859 Apr 05, 2004 (121)
5 PERLEGEN ss23177697 Sep 20, 2004 (123)
6 ABI ss44016982 Mar 15, 2006 (126)
7 ILLUMINA ss65775043 Oct 16, 2006 (127)
8 ILLUMINA ss70543821 May 24, 2008 (130)
9 ILLUMINA ss71076443 May 17, 2007 (127)
10 ILLUMINA ss75454606 Dec 07, 2007 (129)
11 HGSV ss79940641 Dec 14, 2007 (130)
12 HUMANGENOME_JCVI ss99207858 Feb 04, 2009 (130)
13 1000GENOMES ss108196973 Jan 23, 2009 (130)
14 ILLUMINA-UK ss118690884 Feb 14, 2009 (130)
15 ENSEMBL ss138943770 Dec 01, 2009 (131)
16 ILLUMINA ss153068650 Dec 01, 2009 (131)
17 ILLUMINA ss159191069 Dec 01, 2009 (131)
18 ILLUMINA ss171603303 Jul 04, 2010 (132)
19 BUSHMAN ss198446037 Jul 04, 2010 (132)
20 1000GENOMES ss210523805 Jul 14, 2010 (132)
21 1000GENOMES ss218380137 Jul 14, 2010 (132)
22 1000GENOMES ss230530879 Jul 14, 2010 (132)
23 1000GENOMES ss238225870 Jul 15, 2010 (132)
24 BL ss253091979 May 09, 2011 (134)
25 GMI ss275823068 May 04, 2012 (137)
26 GMI ss284048369 Apr 25, 2013 (138)
27 PJP ss290509555 May 09, 2011 (134)
28 ILLUMINA ss536726558 Sep 08, 2015 (146)
29 TISHKOFF ss554103029 Apr 25, 2013 (138)
30 SSMP ss647928465 Apr 25, 2013 (138)
31 ILLUMINA ss832703549 Jul 12, 2019 (153)
32 EVA-GONL ss975151263 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1067879218 Aug 21, 2014 (142)
34 1000GENOMES ss1290859120 Aug 21, 2014 (142)
35 DDI ss1425805413 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1574052736 Apr 01, 2015 (144)
37 EVA_DECODE ss1584517279 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1600155580 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1643149613 Apr 01, 2015 (144)
40 EVA_SVP ss1712332099 Apr 01, 2015 (144)
41 HAMMER_LAB ss1794345719 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1918360098 Feb 12, 2016 (147)
43 GENOMED ss1966743115 Jul 19, 2016 (147)
44 JJLAB ss2019695024 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147709078 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2162436518 Dec 20, 2016 (150)
47 TOPMED ss2324675721 Dec 20, 2016 (150)
48 GRF ss2697620860 Nov 08, 2017 (151)
49 GNOMAD ss2755059860 Nov 08, 2017 (151)
50 SWEGEN ss2986803453 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3023607696 Nov 08, 2017 (151)
52 TOPMED ss3076444938 Nov 08, 2017 (151)
53 CSHL ss3343449532 Nov 08, 2017 (151)
54 ILLUMINA ss3626095346 Oct 11, 2018 (152)
55 ILLUMINA ss3637756159 Oct 11, 2018 (152)
56 ILLUMINA ss3642768396 Oct 11, 2018 (152)
57 URBANLAB ss3646660841 Oct 11, 2018 (152)
58 EGCUT_WGS ss3654867029 Jul 12, 2019 (153)
59 EVA_DECODE ss3686754404 Jul 12, 2019 (153)
60 ACPOP ss3727039196 Jul 12, 2019 (153)
61 ILLUMINA ss3744345748 Jul 12, 2019 (153)
62 EVA ss3746192625 Jul 12, 2019 (153)
63 PACBIO ss3783406328 Jul 12, 2019 (153)
64 PACBIO ss3789064731 Jul 12, 2019 (153)
65 PACBIO ss3793937399 Jul 12, 2019 (153)
66 KHV_HUMAN_GENOMES ss3799202094 Jul 12, 2019 (153)
67 1000Genomes NC_000001.10 - 54290398 Oct 11, 2018 (152)
68 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 54290398 Oct 11, 2018 (152)
69 Genetic variation in the Estonian population NC_000001.10 - 54290398 Oct 11, 2018 (152)
70 gnomAD - Genomes NC_000001.10 - 54290398 Jul 12, 2019 (153)
71 Northern Sweden NC_000001.10 - 54290398 Jul 12, 2019 (153)
72 TopMed NC_000001.11 - 53824725 Oct 11, 2018 (152)
73 UK 10K study - Twins NC_000001.10 - 54290398 Oct 11, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000001.10 - 54290398 Jul 12, 2019 (153)
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)
rs58175720 May 24, 2008 (130)
rs386521390 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss79940641 NC_000001.8:54002418:T:C NC_000001.11:53824724:T:C (self)
ss108196973, ss118690884, ss198446037, ss210523805, ss253091979, ss275823068, ss284048369, ss290509555, ss1584517279, ss1712332099, ss3642768396 NC_000001.9:54062985:T:C NC_000001.11:53824724:T:C (self)
1576273, 856726, 605277, 4319180, 324061, 856726, 175386, ss218380137, ss230530879, ss238225870, ss536726558, ss554103029, ss647928465, ss832703549, ss975151263, ss1067879218, ss1290859120, ss1425805413, ss1574052736, ss1600155580, ss1643149613, ss1794345719, ss1918360098, ss1966743115, ss2019695024, ss2147709078, ss2324675721, ss2697620860, ss2755059860, ss2986803453, ss3343449532, ss3626095346, ss3637756159, ss3654867029, ss3727039196, ss3744345748, ss3746192625, ss3783406328, ss3789064731, ss3793937399 NC_000001.10:54290397:T:C NC_000001.11:53824724:T:C (self)
8224875, ss2162436518, ss3023607696, ss3076444938, ss3646660841, ss3686754404, ss3799202094 NC_000001.11:53824724:T:C NC_000001.11:53824724:T:C (self)
ss13040202 NT_032977.5:6739309:T:C NC_000001.11:53824724:T:C (self)
ss20563859 NT_032977.6:15853468:T:C NC_000001.11:53824724:T:C (self)
ss1642909, ss2581401, ss23177697, ss44016982, ss65775043, ss70543821, ss71076443, ss75454606, ss99207858, ss138943770, ss153068650, ss159191069, ss171603303 NT_032977.9:24262315:T:C NC_000001.11:53824724:T:C (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 rs1181187

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.post308+0fe9b3b