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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.

rs4245756

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:864083 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.027572 (7298/264690, TOPMED)
T=0.026157 (3668/140232, GnomAD)
T=0.02276 (587/25796, ALFA) (+ 14 more)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0276 (138/5008, 1000G)
T=0.0018 (7/3854, ALSPAC)
T=0.0022 (8/3708, TWINSUK)
T=0.0000 (0/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.0445 (49/1100, HapMap)
T=0.001 (1/998, GoNL)
T=0.002 (1/600, NorthernSweden)
T=0.007 (4/558, SGDP_PRJ)
T=0.014 (3/216, Qatari)
T=0.000 (0/216, Vietnamese)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107984850 : 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.864083T>C
GRCh37.p13 chr 1 NC_000001.10:g.799463T>C
Gene: LOC107984850, uncharacterized LOC107984850 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107984850 transcript variant X1 XR_001737607.2:n. N/A Intron Variant
LOC107984850 transcript variant X2 XR_001737608.2: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

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 25796 T=0.02276 C=0.97724
European Sub 15678 T=0.00089 C=0.99911
African Sub 7392 T=0.0729 C=0.9271
African Others Sub 240 T=0.062 C=0.938
African American Sub 7152 T=0.0733 C=0.9267
Asian Sub 164 T=0.000 C=1.000
East Asian Sub 104 T=0.000 C=1.000
Other Asian Sub 60 T=0.00 C=1.00
Latin American 1 Sub 220 T=0.050 C=0.950
Latin American 2 Sub 760 T=0.007 C=0.993
South Asian Sub 110 T=0.000 C=1.000
Other Sub 1472 T=0.0122 C=0.9878


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=0.027572 C=0.972428
gnomAD - Genomes Global Study-wide 140232 T=0.026157 C=0.973843
gnomAD - Genomes European Sub 75960 T=0.00118 C=0.99882
gnomAD - Genomes African Sub 42002 T=0.08023 C=0.91977
gnomAD - Genomes American Sub 13660 T=0.01105 C=0.98895
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.0003 C=0.9997
gnomAD - Genomes East Asian Sub 3132 T=0.0000 C=1.0000
gnomAD - Genomes Other Sub 2154 T=0.0260 C=0.9740
Allele Frequency Aggregator Total Global 25796 T=0.02276 C=0.97724
Allele Frequency Aggregator European Sub 15678 T=0.00089 C=0.99911
Allele Frequency Aggregator African Sub 7392 T=0.0729 C=0.9271
Allele Frequency Aggregator Other Sub 1472 T=0.0122 C=0.9878
Allele Frequency Aggregator Latin American 2 Sub 760 T=0.007 C=0.993
Allele Frequency Aggregator Latin American 1 Sub 220 T=0.050 C=0.950
Allele Frequency Aggregator Asian Sub 164 T=0.000 C=1.000
Allele Frequency Aggregator South Asian Sub 110 T=0.000 C=1.000
8.3KJPN JAPANESE Study-wide 16760 T=0.00000 C=1.00000
1000Genomes Global Study-wide 5008 T=0.0276 C=0.9724
1000Genomes African Sub 1322 T=0.0983 C=0.9017
1000Genomes East Asian Sub 1008 T=0.0000 C=1.0000
1000Genomes Europe Sub 1006 T=0.0010 C=0.9990
1000Genomes South Asian Sub 978 T=0.000 C=1.000
1000Genomes American Sub 694 T=0.010 C=0.990
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.0018 C=0.9982
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.0022 C=0.9978
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0000 C=1.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.0000 C=1.0000
HapMap Global Study-wide 1100 T=0.0445 C=0.9555
HapMap African Sub 692 T=0.058 C=0.942
HapMap American Sub 318 T=0.028 C=0.972
HapMap Asian Sub 90 T=0.00 C=1.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.001 C=0.999
Northern Sweden ACPOP Study-wide 600 T=0.002 C=0.998
SGDP_PRJ Global Study-wide 558 T=0.007 C=0.993
Qatari Global Study-wide 216 T=0.014 C=0.986
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.000 C=1.000
Siberian Global Study-wide 56 T=0.00 C=1.00
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
GRCh38.p13 chr 1 NC_000001.11:g.864083= NC_000001.11:g.864083T>C
GRCh37.p13 chr 1 NC_000001.10:g.799463= NC_000001.10:g.799463T>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#.

78 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6064692 Feb 20, 2003 (111)
2 WI_SSAHASNP ss6851739 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9857255 Jul 11, 2003 (117)
4 SC_SNP ss15431649 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss16443054 Feb 27, 2004 (120)
6 SSAHASNP ss20429617 Apr 05, 2004 (121)
7 AFFY ss66174584 Nov 30, 2006 (127)
8 ILLUMINA ss75246605 Dec 06, 2007 (129)
9 AFFY ss76232689 Dec 08, 2007 (130)
10 HGSV ss78658745 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss82006065 Dec 15, 2007 (130)
12 HGSV ss84000839 Dec 14, 2007 (130)
13 HGSV ss85801006 Dec 14, 2007 (130)
14 BCMHGSC_JDW ss87156111 Mar 23, 2008 (129)
15 HUMANGENOME_JCVI ss97913268 Feb 04, 2009 (130)
16 BGI ss105111729 Dec 01, 2009 (131)
17 1000GENOMES ss107938292 Jan 22, 2009 (130)
18 ILLUMINA-UK ss118438430 Feb 14, 2009 (130)
19 ENSEMBL ss131814903 Dec 01, 2009 (131)
20 ENSEMBL ss137752346 Dec 01, 2009 (131)
21 GMI ss154522467 Dec 01, 2009 (131)
22 AFFY ss172905536 Jul 04, 2010 (132)
23 ILLUMINA ss173702064 Jul 04, 2010 (132)
24 BUSHMAN ss197885519 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss205195537 Jul 04, 2010 (132)
26 1000GENOMES ss218190491 Jul 14, 2010 (132)
27 1000GENOMES ss230395508 Jul 14, 2010 (132)
28 1000GENOMES ss238115028 Jul 15, 2010 (132)
29 BL ss252864188 May 09, 2011 (134)
30 GMI ss275680967 May 04, 2012 (137)
31 GMI ss283987424 Apr 25, 2013 (138)
32 PJP ss290493830 May 09, 2011 (134)
33 ILLUMINA ss537221257 Sep 08, 2015 (146)
34 TISHKOFF ss553710667 Apr 25, 2013 (138)
35 SSMP ss647516445 Apr 25, 2013 (138)
36 EVA-GONL ss974769612 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1067612431 Aug 21, 2014 (142)
38 1000GENOMES ss1289340279 Aug 21, 2014 (142)
39 DDI ss1425684945 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1573851216 Apr 01, 2015 (144)
41 EVA_DECODE ss1584129644 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1599378557 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1642372590 Apr 01, 2015 (144)
44 EVA_SVP ss1712305468 Apr 01, 2015 (144)
45 HAMMER_LAB ss1793706225 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1917960785 Feb 12, 2016 (147)
47 GENOMED ss1966667362 Jul 19, 2016 (147)
48 JJLAB ss2019498496 Sep 14, 2016 (149)
49 USC_VALOUEV ss2147484471 Dec 20, 2016 (150)
50 TOPMED ss2321505223 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624264827 Nov 08, 2017 (151)
52 GRF ss2697374862 Nov 08, 2017 (151)
53 GNOMAD ss2750641718 Nov 08, 2017 (151)
54 SWEGEN ss2986149494 Nov 08, 2017 (151)
55 TOPMED ss3066406216 Nov 08, 2017 (151)
56 CSHL ss3343272695 Nov 08, 2017 (151)
57 ILLUMINA ss3626006539 Oct 11, 2018 (152)
58 ILLUMINA ss3637732371 Oct 11, 2018 (152)
59 ILLUMINA ss3640973134 Oct 11, 2018 (152)
60 ILLUMINA ss3641266950 Oct 11, 2018 (152)
61 ILLUMINA ss3642746674 Oct 11, 2018 (152)
62 URBANLAB ss3646581268 Oct 11, 2018 (152)
63 EVA_DECODE ss3685992513 Jul 12, 2019 (153)
64 ACPOP ss3726716528 Jul 12, 2019 (153)
65 EVA ss3745721203 Jul 12, 2019 (153)
66 PACBIO ss3783302198 Jul 12, 2019 (153)
67 PACBIO ss3788980067 Jul 12, 2019 (153)
68 PACBIO ss3793852604 Jul 12, 2019 (153)
69 KHV_HUMAN_GENOMES ss3798743874 Jul 12, 2019 (153)
70 EVA ss3825981517 Apr 25, 2020 (154)
71 EVA ss3836378469 Apr 25, 2020 (154)
72 EVA ss3841782472 Apr 25, 2020 (154)
73 SGDP_PRJ ss3847996167 Apr 25, 2020 (154)
74 KRGDB ss3892836422 Apr 25, 2020 (154)
75 KOGIC ss3943630117 Apr 25, 2020 (154)
76 EVA ss4016889043 Apr 25, 2021 (155)
77 TOPMED ss4436440310 Apr 25, 2021 (155)
78 TOMMO_GENOMICS ss5142053376 Apr 25, 2021 (155)
79 1000Genomes NC_000001.10 - 799463 Oct 11, 2018 (152)
80 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 799463 Oct 11, 2018 (152)
81 The Danish reference pan genome NC_000001.10 - 799463 Apr 25, 2020 (154)
82 gnomAD - Genomes NC_000001.11 - 864083 Apr 25, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000001.10 - 799463 Apr 25, 2020 (154)
84 HapMap NC_000001.11 - 864083 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000001.10 - 799463 Apr 25, 2020 (154)
86 Korean Genome Project NC_000001.11 - 864083 Apr 25, 2020 (154)
87 Northern Sweden NC_000001.10 - 799463 Jul 12, 2019 (153)
88 Qatari NC_000001.10 - 799463 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 799463 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 799463 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 799463 Apr 25, 2021 (155)
92 TopMed NC_000001.11 - 864083 Apr 25, 2021 (155)
93 UK 10K study - Twins NC_000001.10 - 799463 Oct 11, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000001.10 - 799463 Jul 12, 2019 (153)
95 ALFA NC_000001.11 - 864083 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).

Associated ID History Updated (Build)
rs6680444 Aug 27, 2003 (117)
rs56538647 May 24, 2008 (130)
rs58071205 May 24, 2008 (130)
rs59004701 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78658745, ss84000839, ss85801006 NC_000001.8:839325:T:C NC_000001.11:864082:T:C (self)
ss66174584, ss76232689, ss87156111, ss107938292, ss118438430, ss172905536, ss197885519, ss205195537, ss252864188, ss275680967, ss283987424, ss290493830, ss1584129644, ss1712305468, ss3642746674 NC_000001.9:789325:T:C NC_000001.11:864082:T:C (self)
5047, 522, 1358450, 639, 13816, 1393, 2715, 13147, 825, 22683, 522, 109, ss218190491, ss230395508, ss238115028, ss537221257, ss553710667, ss647516445, ss974769612, ss1067612431, ss1289340279, ss1425684945, ss1573851216, ss1599378557, ss1642372590, ss1793706225, ss1917960785, ss1966667362, ss2019498496, ss2147484471, ss2321505223, ss2624264827, ss2697374862, ss2750641718, ss2986149494, ss3343272695, ss3626006539, ss3637732371, ss3640973134, ss3641266950, ss3726716528, ss3745721203, ss3783302198, ss3788980067, ss3793852604, ss3825981517, ss3836378469, ss3847996167, ss3892836422, ss4016889043, ss5142053376 NC_000001.10:799462:T:C NC_000001.11:864082:T:C (self)
71468, 85, 8118, 21514, 46645, 1329698393, ss3066406216, ss3646581268, ss3685992513, ss3798743874, ss3841782472, ss3943630117, ss4436440310 NC_000001.11:864082:T:C NC_000001.11:864082:T:C (self)
ss6064692, ss6851739, ss75246605, ss82006065, ss97913268, ss105111729, ss131814903, ss137752346, ss154522467, ss173702064 NT_004350.19:278094:T:C NC_000001.11:864082:T:C (self)
ss9857255, ss15431649, ss16443054, ss20429617 NT_034471.3:278094:T:C NC_000001.11:864082: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 rs4245756

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