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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.

rs1805403

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:226390398 (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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.164566 (43559/264690, TOPMED)
T=0.190080 (47717/251036, GnomAD_exome)
T=0.161969 (22689/140082, GnomAD) (+ 19 more)
T=0.194052 (23540/121308, ExAC)
T=0.21329 (5962/27952, ALFA)
T=0.07649 (1282/16760, 8.3KJPN)
T=0.17669 (2298/13006, GO-ESP)
T=0.1424 (713/5008, 1000G)
T=0.2045 (916/4480, Estonian)
T=0.2229 (859/3854, ALSPAC)
T=0.2398 (889/3708, TWINSUK)
T=0.0666 (195/2930, KOREAN)
T=0.0688 (126/1832, Korea1K)
T=0.212 (212/998, GoNL)
T=0.059 (36/614, Vietnamese)
T=0.187 (112/600, NorthernSweden)
T=0.093 (50/538, SGDP_PRJ)
T=0.279 (149/534, MGP)
T=0.158 (48/304, FINRISK)
T=0.319 (69/216, Qatari)
T=0.07 (4/56, Siberian)
T=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PARP1 : Intron Variant
Publications
2 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.226390398T>A
GRCh38.p13 chr 1 NC_000001.11:g.226390398T>C
GRCh37.p13 chr 1 NC_000001.10:g.226578099T>A
GRCh37.p13 chr 1 NC_000001.10:g.226578099T>C
Gene: PARP1, poly(ADP-ribose) polymerase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PARP1 transcript NM_001618.4:c.617+12A>T 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 27952 T=0.21329 C=0.78671
European Sub 20398 T=0.23546 C=0.76454
African Sub 3554 T=0.0867 C=0.9133
African Others Sub 122 T=0.033 C=0.967
African American Sub 3432 T=0.0886 C=0.9114
Asian Sub 168 T=0.071 C=0.929
East Asian Sub 112 T=0.089 C=0.911
Other Asian Sub 56 T=0.04 C=0.96
Latin American 1 Sub 146 T=0.116 C=0.884
Latin American 2 Sub 610 T=0.141 C=0.859
South Asian Sub 98 T=0.30 C=0.70
Other Sub 2978 T=0.2374 C=0.7626


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=0.164566 C=0.835434
gnomAD - Exomes Global Study-wide 251036 T=0.190080 C=0.809920
gnomAD - Exomes European Sub 135050 T=0.214269 C=0.785731
gnomAD - Exomes Asian Sub 48986 T=0.18632 C=0.81368
gnomAD - Exomes American Sub 34584 T=0.12968 C=0.87032
gnomAD - Exomes African Sub 16208 T=0.05892 C=0.94108
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=0.28131 C=0.71869
gnomAD - Exomes Other Sub 6130 T=0.2248 C=0.7752
gnomAD - Genomes Global Study-wide 140082 T=0.161969 C=0.838031
gnomAD - Genomes European Sub 75868 T=0.21179 C=0.78821
gnomAD - Genomes African Sub 41990 T=0.06304 C=0.93696
gnomAD - Genomes American Sub 13620 T=0.17944 C=0.82056
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.2942 C=0.7058
gnomAD - Genomes East Asian Sub 3130 T=0.0550 C=0.9450
gnomAD - Genomes Other Sub 2150 T=0.1767 C=0.8233
ExAC Global Study-wide 121308 T=0.194052 C=0.805948
ExAC Europe Sub 73302 T=0.22426 C=0.77574
ExAC Asian Sub 25146 T=0.19311 C=0.80689
ExAC American Sub 11574 T=0.12157 C=0.87843
ExAC African Sub 10380 T=0.05925 C=0.94075
ExAC Other Sub 906 T=0.246 C=0.754
8.3KJPN JAPANESE Study-wide 16760 T=0.07649 C=0.92351
GO Exome Sequencing Project Global Study-wide 13006 T=0.17669 C=0.82331
GO Exome Sequencing Project European American Sub 8600 T=0.2331 C=0.7669
GO Exome Sequencing Project African American Sub 4406 T=0.0665 C=0.9335
1000Genomes Global Study-wide 5008 T=0.1424 C=0.8576
1000Genomes African Sub 1322 T=0.0287 C=0.9713
1000Genomes East Asian Sub 1008 T=0.0685 C=0.9315
1000Genomes Europe Sub 1006 T=0.2266 C=0.7734
1000Genomes South Asian Sub 978 T=0.254 C=0.746
1000Genomes American Sub 694 T=0.187 C=0.813
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.2045 C=0.7955
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.2229 C=0.7771
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.2398 C=0.7602
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0666 A=0.0000, C=0.9334
Korean Genome Project KOREAN Study-wide 1832 T=0.0688 C=0.9312
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.212 C=0.788
A Vietnamese Genetic Variation Database Global Study-wide 614 T=0.059 C=0.941
Northern Sweden ACPOP Study-wide 600 T=0.187 C=0.813
SGDP_PRJ Global Study-wide 538 T=0.093 C=0.907
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.279 C=0.721
FINRISK Finnish from FINRISK project Study-wide 304 T=0.158 C=0.842
Qatari Global Study-wide 216 T=0.319 C=0.681
Siberian Global Study-wide 56 T=0.07 C=0.93
The Danish reference pan genome Danish Study-wide 40 T=0.17 C=0.82
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= A C
GRCh38.p13 chr 1 NC_000001.11:g.226390398= NC_000001.11:g.226390398T>A NC_000001.11:g.226390398T>C
GRCh37.p13 chr 1 NC_000001.10:g.226578099= NC_000001.10:g.226578099T>A NC_000001.10:g.226578099T>C
PARP1 transcript NM_001618.3:c.617+12= NM_001618.3:c.617+12A>T NM_001618.3:c.617+12A>G
PARP1 transcript NM_001618.4:c.617+12= NM_001618.4:c.617+12A>T NM_001618.4:c.617+12A>G
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#.

86 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 UWGC ss2667847 Jan 12, 2001 (92)
2 HGBASE ss3182324 Aug 15, 2001 (98)
3 SC_JCM ss3955809 Sep 28, 2001 (100)
4 EGP_SNPS ss4480417 Jul 03, 2002 (106)
5 SNP500CANCER ss5586207 Mar 31, 2003 (113)
6 BCM_SSAHASNP ss9826204 Jul 11, 2003 (116)
7 SC_SNP ss13005099 Dec 05, 2003 (119)
8 SC_SNP ss15413871 Feb 27, 2004 (120)
9 SSAHASNP ss20545110 Apr 05, 2004 (121)
10 IMCJ-GDT ss22886551 Apr 05, 2004 (121)
11 CGM_KYOTO ss76877461 Dec 06, 2007 (129)
12 HGSV ss77363895 Dec 06, 2007 (129)
13 HGSV ss83057595 Dec 15, 2007 (130)
14 BCMHGSC_JDW ss87993591 Mar 23, 2008 (129)
15 CNG ss95210846 Mar 25, 2008 (129)
16 HUMANGENOME_JCVI ss98008436 Feb 05, 2009 (130)
17 BGI ss106636546 Feb 05, 2009 (130)
18 1000GENOMES ss108999521 Jan 23, 2009 (130)
19 1000GENOMES ss111868237 Jan 25, 2009 (130)
20 ILLUMINA-UK ss119229525 Feb 15, 2009 (130)
21 ENSEMBL ss139048723 Dec 01, 2009 (131)
22 GMI ss156364966 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss165300610 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss165860205 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss167543506 Jul 04, 2010 (132)
26 BUSHMAN ss199689298 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss205345514 Jul 04, 2010 (132)
28 1000GENOMES ss218916105 Jul 14, 2010 (132)
29 1000GENOMES ss230928902 Jul 14, 2010 (132)
30 1000GENOMES ss238536672 Jul 15, 2010 (132)
31 BL ss253867745 May 09, 2011 (134)
32 GMI ss276244189 May 04, 2012 (137)
33 GMI ss284240781 Apr 25, 2013 (138)
34 PJP ss290747275 May 09, 2011 (134)
35 1000GENOMES ss489794806 May 04, 2012 (137)
36 CLINSEQ_SNP ss491616388 May 04, 2012 (137)
37 TISHKOFF ss555178925 Apr 25, 2013 (138)
38 SSMP ss648750603 Apr 25, 2013 (138)
39 NHLBI-ESP ss712388645 Apr 25, 2013 (138)
40 JMKIDD_LAB ss974439992 Aug 21, 2014 (142)
41 EVA-GONL ss976213766 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1067432558 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1068654017 Aug 21, 2014 (142)
44 1000GENOMES ss1294912121 Aug 21, 2014 (142)
45 DDI ss1426131562 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1574721925 Apr 01, 2015 (144)
47 EVA_FINRISK ss1584015462 Apr 01, 2015 (144)
48 EVA_DECODE ss1585611693 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1602279441 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1645273474 Apr 01, 2015 (144)
51 EVA_EXAC ss1686082449 Apr 01, 2015 (144)
52 EVA_MGP ss1710945845 Apr 01, 2015 (144)
53 HAMMER_LAB ss1795818646 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1919435824 Feb 12, 2016 (147)
55 GENOMED ss1966989388 Jul 19, 2016 (147)
56 JJLAB ss2020242376 Sep 14, 2016 (149)
57 USC_VALOUEV ss2148276694 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2170629142 Dec 20, 2016 (150)
59 TOPMED ss2333270126 Dec 20, 2016 (150)
60 SYSTEMSBIOZJU ss2624632477 Nov 08, 2017 (151)
61 GRF ss2698274891 Nov 08, 2017 (151)
62 GNOMAD ss2732319074 Nov 08, 2017 (151)
63 GNOMAD ss2746575300 Nov 08, 2017 (151)
64 GNOMAD ss2766965722 Nov 08, 2017 (151)
65 SWEGEN ss2988559601 Nov 08, 2017 (151)
66 BIOINF_KMB_FNS_UNIBA ss3023881595 Nov 08, 2017 (151)
67 TOPMED ss3105114701 Nov 08, 2017 (151)
68 CSHL ss3343943032 Nov 08, 2017 (151)
69 OMUKHERJEE_ADBS ss3646254277 Oct 11, 2018 (152)
70 URBANLAB ss3646901748 Oct 11, 2018 (152)
71 EGCUT_WGS ss3656518557 Jul 12, 2019 (153)
72 EVA_DECODE ss3688758576 Jul 12, 2019 (153)
73 ACPOP ss3727920093 Jul 12, 2019 (153)
74 EVA ss3747417457 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3800420298 Jul 12, 2019 (153)
76 EVA ss3823721694 Apr 25, 2020 (154)
77 EVA ss3826678118 Apr 25, 2020 (154)
78 EVA ss3836741119 Apr 25, 2020 (154)
79 EVA ss3842153382 Apr 25, 2020 (154)
80 SGDP_PRJ ss3851034825 Apr 25, 2020 (154)
81 KRGDB ss3896371555 Apr 25, 2020 (154)
82 KOGIC ss3946626804 Apr 25, 2020 (154)
83 FSA-LAB ss3983965164 Apr 25, 2021 (155)
84 FSA-LAB ss3983965165 Apr 25, 2021 (155)
85 TOPMED ss4485897239 Apr 25, 2021 (155)
86 TOMMO_GENOMICS ss5148735262 Apr 25, 2021 (155)
87 1000Genomes NC_000001.10 - 226578099 Oct 11, 2018 (152)
88 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 226578099 Oct 11, 2018 (152)
89 Genetic variation in the Estonian population NC_000001.10 - 226578099 Oct 11, 2018 (152)
90 ExAC NC_000001.10 - 226578099 Oct 11, 2018 (152)
91 FINRISK NC_000001.10 - 226578099 Apr 25, 2020 (154)
92 The Danish reference pan genome NC_000001.10 - 226578099 Apr 25, 2020 (154)
93 gnomAD - Genomes NC_000001.11 - 226390398 Apr 25, 2021 (155)
94 gnomAD - Exomes NC_000001.10 - 226578099 Jul 12, 2019 (153)
95 GO Exome Sequencing Project NC_000001.10 - 226578099 Oct 11, 2018 (152)
96 Genome of the Netherlands Release 5 NC_000001.10 - 226578099 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000001.10 - 226578099 Apr 25, 2020 (154)
98 Korean Genome Project NC_000001.11 - 226390398 Apr 25, 2020 (154)
99 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 226578099 Apr 25, 2020 (154)
100 Northern Sweden NC_000001.10 - 226578099 Jul 12, 2019 (153)
101 Qatari NC_000001.10 - 226578099 Apr 25, 2020 (154)
102 SGDP_PRJ NC_000001.10 - 226578099 Apr 25, 2020 (154)
103 Siberian NC_000001.10 - 226578099 Apr 25, 2020 (154)
104 8.3KJPN NC_000001.10 - 226578099 Apr 25, 2021 (155)
105 TopMed NC_000001.11 - 226390398 Apr 25, 2021 (155)
106 UK 10K study - Twins NC_000001.10 - 226578099 Oct 11, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000001.10 - 226578099 Jul 12, 2019 (153)
108 ALFA NC_000001.11 - 226390398 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)
rs59699722 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3548949, ss3896371555 NC_000001.10:226578098:T:A NC_000001.11:226390397:T:A (self)
ss77363895, ss83057595 NC_000001.8:222884833:T:C NC_000001.11:226390397:T:C (self)
ss87993591, ss108999521, ss111868237, ss119229525, ss165300610, ss165860205, ss167543506, ss199689298, ss205345514, ss253867745, ss276244189, ss284240781, ss290747275, ss491616388, ss1585611693 NC_000001.9:224644721:T:C NC_000001.11:226390397:T:C (self)
5776213, 3192356, 2256805, 5321207, 11923, 1913186, 1356088, 180203, 1395084, 3548949, 62597, 1204958, 1477754, 3051805, 793048, 6704569, 3192356, 693345, ss218916105, ss230928902, ss238536672, ss489794806, ss555178925, ss648750603, ss712388645, ss974439992, ss976213766, ss1067432558, ss1068654017, ss1294912121, ss1426131562, ss1574721925, ss1584015462, ss1602279441, ss1645273474, ss1686082449, ss1710945845, ss1795818646, ss1919435824, ss1966989388, ss2020242376, ss2148276694, ss2333270126, ss2624632477, ss2698274891, ss2732319074, ss2746575300, ss2766965722, ss2988559601, ss3343943032, ss3646254277, ss3656518557, ss3727920093, ss3747417457, ss3823721694, ss3826678118, ss3836741119, ss3851034825, ss3896371555, ss3983965164, ss3983965165, ss5148735262 NC_000001.10:226578098:T:C NC_000001.11:226390397:T:C (self)
41486990, 3004805, 31109243, 49503574, 8144996164, ss2170629142, ss3023881595, ss3105114701, ss3646901748, ss3688758576, ss3800420298, ss3842153382, ss3946626804, ss4485897239 NC_000001.11:226390397:T:C NC_000001.11:226390397:T:C (self)
ss9826204, ss13005099 NT_004559.10:91416:T:C NC_000001.11:226390397:T:C (self)
ss15413871, ss20545110 NT_004559.11:2754292:T:C NC_000001.11:226390397:T:C (self)
ss2667847, ss3182324, ss3955809, ss4480417, ss5586207, ss22886551, ss76877461, ss95210846, ss98008436, ss106636546, ss139048723, ss156364966 NT_167186.1:20095877:T:C NC_000001.11:226390397: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.

2 citations for rs1805403
PMID Title Author Year Journal
19657367 Genetic polymorphisms of EPHX1, Gsk3beta, TNFSF8 and myeloma cell DKK-1 expression linked to bone disease in myeloma. Durie BG et al. 2009 Leukemia
27746584 The Effect of <i>Poly(ADP-ribose) Polymerase-1</i> Gene 3'Untranslated Region Polymorphism in Colorectal Cancer Risk among Saudi Cohort. Alhadheq AM et al. 2016 Disease markers
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