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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.

rs747659

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:226363040 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.235630 (62369/264690, TOPMED)
T=0.230103 (32213/139994, GnomAD)
T=0.27760 (21825/78620, PAGE_STUDY) (+ 18 more)
T=0.11698 (2188/18704, ALFA)
T=0.30913 (5181/16760, 8.3KJPN)
T=0.2566 (1285/5008, 1000G)
T=0.2348 (1072/4566, GO-ESP)
T=0.1540 (690/4480, Estonian)
T=0.1640 (632/3854, ALSPAC)
T=0.1610 (597/3708, TWINSUK)
T=0.2925 (857/2930, KOREAN)
T=0.2948 (540/1832, Korea1K)
T=0.3017 (473/1568, HapMap)
T=0.165 (165/998, GoNL)
T=0.130 (78/600, NorthernSweden)
T=0.129 (69/534, MGP)
T=0.185 (40/216, Qatari)
T=0.400 (84/210, Vietnamese)
C=0.421 (85/202, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PARP1 : Intron Variant
Publications
1 citation
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.226363040C>G
GRCh38.p13 chr 1 NC_000001.11:g.226363040C>T
GRCh37.p13 chr 1 NC_000001.10:g.226550741C>G
GRCh37.p13 chr 1 NC_000001.10:g.226550741C>T
Gene: PARP1, poly(ADP-ribose) polymerase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PARP1 transcript NM_001618.4:c.2848+59G>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

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 18704 C=0.88302 G=0.00000, T=0.11698
European Sub 14332 C=0.90085 G=0.00000, T=0.09915
African Sub 2720 C=0.7735 G=0.0000, T=0.2265
African Others Sub 66 C=0.74 G=0.00, T=0.26
African American Sub 2654 C=0.7743 G=0.0000, T=0.2257
Asian Sub 92 C=0.82 G=0.00, T=0.18
East Asian Sub 84 C=0.81 G=0.00, T=0.19
Other Asian Sub 8 C=0.9 G=0.0, T=0.1
Latin American 1 Sub 104 C=0.981 G=0.000, T=0.019
Latin American 2 Sub 444 C=0.998 G=0.000, T=0.002
South Asian Sub 76 C=0.99 G=0.00, T=0.01
Other Sub 936 C=0.861 G=0.000, T=0.139


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 C=0.764370 T=0.235630
gnomAD - Genomes Global Study-wide 139994 C=0.769897 T=0.230103
gnomAD - Genomes European Sub 75846 C=0.83254 T=0.16746
gnomAD - Genomes African Sub 41920 C=0.62846 T=0.37154
gnomAD - Genomes American Sub 13648 C=0.85932 T=0.14068
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.8636 T=0.1364
gnomAD - Genomes East Asian Sub 3110 C=0.6511 T=0.3489
gnomAD - Genomes Other Sub 2150 C=0.7772 T=0.2228
The PAGE Study Global Study-wide 78620 C=0.72240 T=0.27760
The PAGE Study AfricanAmerican Sub 32474 C=0.62425 T=0.37575
The PAGE Study Mexican Sub 10806 C=0.86572 T=0.13428
The PAGE Study Asian Sub 8308 C=0.6740 T=0.3260
The PAGE Study PuertoRican Sub 7914 C=0.7914 T=0.2086
The PAGE Study NativeHawaiian Sub 4524 C=0.7944 T=0.2056
The PAGE Study Cuban Sub 4228 C=0.8191 T=0.1809
The PAGE Study Dominican Sub 3818 C=0.7287 T=0.2713
The PAGE Study CentralAmerican Sub 2450 C=0.8469 T=0.1531
The PAGE Study SouthAmerican Sub 1982 C=0.8491 T=0.1509
The PAGE Study NativeAmerican Sub 1260 C=0.8127 T=0.1873
The PAGE Study SouthAsian Sub 856 C=0.799 T=0.201
Allele Frequency Aggregator Total Global 18704 C=0.88302 G=0.00000, T=0.11698
Allele Frequency Aggregator European Sub 14332 C=0.90085 G=0.00000, T=0.09915
Allele Frequency Aggregator African Sub 2720 C=0.7735 G=0.0000, T=0.2265
Allele Frequency Aggregator Other Sub 936 C=0.861 G=0.000, T=0.139
Allele Frequency Aggregator Latin American 2 Sub 444 C=0.998 G=0.000, T=0.002
Allele Frequency Aggregator Latin American 1 Sub 104 C=0.981 G=0.000, T=0.019
Allele Frequency Aggregator Asian Sub 92 C=0.82 G=0.00, T=0.18
Allele Frequency Aggregator South Asian Sub 76 C=0.99 G=0.00, T=0.01
8.3KJPN JAPANESE Study-wide 16760 C=0.69087 T=0.30913
1000Genomes Global Study-wide 5008 C=0.7434 T=0.2566
1000Genomes African Sub 1322 C=0.6059 T=0.3941
1000Genomes East Asian Sub 1008 C=0.6875 T=0.3125
1000Genomes Europe Sub 1006 C=0.8300 T=0.1700
1000Genomes South Asian Sub 978 C=0.819 T=0.181
1000Genomes American Sub 694 C=0.854 T=0.146
GO Exome Sequencing Project Global Study-wide 4566 C=0.7652 T=0.2348
GO Exome Sequencing Project European American Sub 3182 C=0.8284 T=0.1716
GO Exome Sequencing Project African American Sub 1384 C=0.6199 T=0.3801
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8460 T=0.1540
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8360 T=0.1640
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8390 T=0.1610
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.7075 T=0.2925
Korean Genome Project KOREAN Study-wide 1832 C=0.7052 T=0.2948
HapMap Global Study-wide 1568 C=0.6983 T=0.3017
HapMap African Sub 674 C=0.645 T=0.355
HapMap American Sub 648 C=0.739 T=0.261
HapMap Asian Sub 246 C=0.736 T=0.264
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.835 T=0.165
Northern Sweden ACPOP Study-wide 600 C=0.870 T=0.130
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.871 T=0.129
Qatari Global Study-wide 216 C=0.815 T=0.185
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.600 T=0.400
SGDP_PRJ Global Study-wide 202 C=0.421 T=0.579
The Danish reference pan genome Danish Study-wide 40 C=0.88 T=0.12
Siberian Global Study-wide 28 C=0.39 T=0.61
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= G T
GRCh38.p13 chr 1 NC_000001.11:g.226363040= NC_000001.11:g.226363040C>G NC_000001.11:g.226363040C>T
GRCh37.p13 chr 1 NC_000001.10:g.226550741= NC_000001.10:g.226550741C>G NC_000001.10:g.226550741C>T
PARP1 transcript NM_001618.3:c.2848+59= NM_001618.3:c.2848+59G>C NM_001618.3:c.2848+59G>A
PARP1 transcript NM_001618.4:c.2848+59= NM_001618.4:c.2848+59G>C NM_001618.4:c.2848+59G>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#.

73 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss98261 Oct 05, 2000 (86)
2 YUSUKE ss5003583 Aug 28, 2002 (108)
3 SNP500CANCER ss5586206 Mar 31, 2003 (113)
4 BCM_SSAHASNP ss9831217 Jul 11, 2003 (116)
5 SI_EXO ss61705451 Oct 16, 2006 (127)
6 ILLUMINA ss65761699 Oct 16, 2006 (127)
7 ILLUMINA ss74889602 Dec 06, 2007 (129)
8 CGM_KYOTO ss76877486 Dec 06, 2007 (129)
9 CNG ss95212029 Mar 25, 2008 (129)
10 1000GENOMES ss111867868 Jan 25, 2009 (130)
11 ILLUMINA-UK ss119229449 Feb 15, 2009 (130)
12 KRIBB_YJKIM ss119366132 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss165300077 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165859996 Jul 04, 2010 (132)
15 ILLUMINA ss174380709 Jul 04, 2010 (132)
16 BUSHMAN ss199689059 Jul 04, 2010 (132)
17 1000GENOMES ss218916006 Jul 14, 2010 (132)
18 1000GENOMES ss230928826 Jul 14, 2010 (132)
19 1000GENOMES ss238536591 Jul 15, 2010 (132)
20 GMI ss276244121 May 04, 2012 (137)
21 ILLUMINA ss537473659 Sep 08, 2015 (146)
22 SSMP ss648750470 Apr 25, 2013 (138)
23 NHLBI-ESP ss712372457 Apr 25, 2013 (138)
24 EVA-GONL ss976213592 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1068653857 Aug 21, 2014 (142)
26 1000GENOMES ss1294911293 Aug 21, 2014 (142)
27 EVA_GENOME_DK ss1574721846 Apr 01, 2015 (144)
28 EVA_DECODE ss1585611518 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1602279031 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1645273064 Apr 01, 2015 (144)
31 EVA_MGP ss1710945792 Apr 01, 2015 (144)
32 EVA_SVP ss1712410422 Apr 01, 2015 (144)
33 HAMMER_LAB ss1795818414 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1919435676 Feb 12, 2016 (147)
35 ILLUMINA ss1958362710 Feb 12, 2016 (147)
36 JJLAB ss2020242287 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148276592 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2170627481 Dec 20, 2016 (150)
39 TOPMED ss2333268450 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624632420 Nov 08, 2017 (151)
41 GRF ss2698274766 Nov 08, 2017 (151)
42 GNOMAD ss2766963585 Nov 08, 2017 (151)
43 SWEGEN ss2988559332 Nov 08, 2017 (151)
44 ILLUMINA ss3021186489 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3023881541 Nov 08, 2017 (151)
46 TOPMED ss3105109771 Nov 08, 2017 (151)
47 TOPMED ss3105109772 Nov 08, 2017 (151)
48 CSHL ss3343942953 Nov 08, 2017 (151)
49 ILLUMINA ss3626323339 Oct 11, 2018 (152)
50 ILLUMINA ss3637817908 Oct 11, 2018 (152)
51 ILLUMINA ss3642823998 Oct 11, 2018 (152)
52 OMUKHERJEE_ADBS ss3646254249 Oct 11, 2018 (152)
53 ILLUMINA ss3651532016 Oct 11, 2018 (152)
54 EGCUT_WGS ss3656518237 Jul 12, 2019 (153)
55 EVA_DECODE ss3688758268 Jul 12, 2019 (153)
56 ILLUMINA ss3725111371 Jul 12, 2019 (153)
57 ACPOP ss3727919961 Jul 12, 2019 (153)
58 EVA ss3747417204 Jul 12, 2019 (153)
59 PAGE_CC ss3770876383 Jul 12, 2019 (153)
60 KHV_HUMAN_GENOMES ss3800420044 Jul 12, 2019 (153)
61 EVA ss3823721528 Apr 25, 2020 (154)
62 EVA ss3825589437 Apr 25, 2020 (154)
63 EVA ss3826678033 Apr 25, 2020 (154)
64 EVA ss3836741059 Apr 25, 2020 (154)
65 EVA ss3842153318 Apr 25, 2020 (154)
66 SGDP_PRJ ss3851034491 Apr 25, 2020 (154)
67 KRGDB ss3896371156 Apr 25, 2020 (154)
68 KOGIC ss3946626423 Apr 25, 2020 (154)
69 FSA-LAB ss3983965116 Apr 25, 2021 (155)
70 FSA-LAB ss3983965117 Apr 25, 2021 (155)
71 EVA ss3986161413 Apr 25, 2021 (155)
72 TOPMED ss4485890206 Apr 25, 2021 (155)
73 TOMMO_GENOMICS ss5148734447 Apr 25, 2021 (155)
74 1000Genomes NC_000001.10 - 226550741 Oct 11, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 226550741 Oct 11, 2018 (152)
76 Genetic variation in the Estonian population NC_000001.10 - 226550741 Oct 11, 2018 (152)
77 The Danish reference pan genome NC_000001.10 - 226550741 Apr 25, 2020 (154)
78 gnomAD - Genomes NC_000001.11 - 226363040 Apr 25, 2021 (155)
79 GO Exome Sequencing Project NC_000001.10 - 226550741 Oct 11, 2018 (152)
80 Genome of the Netherlands Release 5 NC_000001.10 - 226550741 Apr 25, 2020 (154)
81 HapMap NC_000001.11 - 226363040 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000001.10 - 226550741 Apr 25, 2020 (154)
83 Korean Genome Project NC_000001.11 - 226363040 Apr 25, 2020 (154)
84 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 226550741 Apr 25, 2020 (154)
85 Northern Sweden NC_000001.10 - 226550741 Jul 12, 2019 (153)
86 The PAGE Study NC_000001.11 - 226363040 Jul 12, 2019 (153)
87 Qatari NC_000001.10 - 226550741 Apr 25, 2020 (154)
88 SGDP_PRJ NC_000001.10 - 226550741 Apr 25, 2020 (154)
89 Siberian NC_000001.10 - 226550741 Apr 25, 2020 (154)
90 8.3KJPN NC_000001.10 - 226550741 Apr 25, 2021 (155)
91 TopMed NC_000001.11 - 226363040 Apr 25, 2021 (155)
92 UK 10K study - Twins NC_000001.10 - 226550741 Oct 11, 2018 (152)
93 A Vietnamese Genetic Variation Database NC_000001.10 - 226550741 Jul 12, 2019 (153)
94 ALFA NC_000001.11 - 226363040 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)
rs3817168 Oct 08, 2002 (108)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
2075858123, ss3105109771 NC_000001.11:226363039:C:G NC_000001.11:226363039:C:G (self)
ss111867868, ss119229449, ss165300077, ss165859996, ss199689059, ss276244121, ss1585611518, ss1712410422, ss3642823998 NC_000001.9:224617363:C:T NC_000001.11:226363039:C:T (self)
5775363, 3191913, 2256485, 1913114, 180037, 1394910, 3548550, 62544, 1204826, 1477606, 3051471, 792946, 6703754, 3191913, 693216, ss218916006, ss230928826, ss238536591, ss537473659, ss648750470, ss712372457, ss976213592, ss1068653857, ss1294911293, ss1574721846, ss1602279031, ss1645273064, ss1710945792, ss1795818414, ss1919435676, ss1958362710, ss2020242287, ss2148276592, ss2333268450, ss2624632420, ss2698274766, ss2766963585, ss2988559332, ss3021186489, ss3343942953, ss3626323339, ss3637817908, ss3646254249, ss3651532016, ss3656518237, ss3727919961, ss3747417204, ss3823721528, ss3825589437, ss3826678033, ss3836741059, ss3851034491, ss3896371156, ss3983965116, ss3983965117, ss3986161413, ss5148734447 NC_000001.10:226550740:C:T NC_000001.11:226363039:C:T (self)
41481564, 282088, 3004424, 97852, 31104770, 49496541, 2075858123, ss2170627481, ss3023881541, ss3105109772, ss3688758268, ss3725111371, ss3770876383, ss3800420044, ss3842153318, ss3946626423, ss4485890206 NC_000001.11:226363039:C:T NC_000001.11:226363039:C:T (self)
ss9831217 NT_004559.10:64058:C:T NC_000001.11:226363039:C:T (self)
ss61705451 NT_004559.12:2726934:C:T NC_000001.11:226363039:C:T (self)
ss98261, ss5003583, ss5586206, ss65761699, ss74889602, ss76877486, ss95212029, ss119366132, ss174380709 NT_167186.1:20068519:C:T NC_000001.11:226363039: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.

1 citation for rs747659
PMID Title Author Year Journal
28499365 Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation. Lonjou C et al. 2017 BMC cancer
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