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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.

rs1130941

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:24459062 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.116344 (30795/264690, TOPMED)
A=0.094308 (23513/249322, GnomAD_exome)
A=0.122254 (17139/140192, GnomAD) (+ 21 more)
A=0.098553 (11767/119398, ExAC)
A=0.11564 (5841/50510, ALFA)
A=0.00638 (107/16760, 8.3KJPN)
A=0.13038 (1695/13000, GO-ESP)
A=0.0907 (454/5008, 1000G)
A=0.1263 (566/4480, Estonian)
A=0.1318 (508/3854, ALSPAC)
A=0.1197 (444/3708, TWINSUK)
A=0.0116 (34/2930, KOREAN)
A=0.0131 (24/1832, Korea1K)
A=0.108 (108/998, GoNL)
A=0.034 (21/614, Vietnamese)
A=0.130 (78/600, NorthernSweden)
A=0.103 (55/534, MGP)
A=0.074 (24/324, HapMap)
A=0.115 (35/304, FINRISK)
A=0.125 (27/216, Qatari)
T=0.500 (51/102, SGDP_PRJ)
A=0.500 (51/102, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
T=0.45 (9/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PARP4 : Synonymous 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 13 NC_000013.11:g.24459062T>A
GRCh37.p13 chr 13 NC_000013.10:g.25033200T>A
Gene: PARP4, poly(ADP-ribose) polymerase family member 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PARP4 transcript NM_006437.4:c.2406A>T T [ACA] > T [ACT] Coding Sequence Variant
protein mono-ADP-ribosyltransferase PARP4 NP_006428.2:p.Thr802= T (Thr) > T (Thr) Synonymous Variant
PARP4 transcript variant X1 XM_011534931.1:c.2547A>T T [ACA] > T [ACT] Coding Sequence Variant
protein mono-ADP-ribosyltransferase PARP4 isoform X1 XP_011533233.1:p.Thr849= T (Thr) > T (Thr) Synonymous Variant
PARP4 transcript variant X2 XM_011534932.2:c.2406A>T T [ACA] > T [ACT] Coding Sequence Variant
protein mono-ADP-ribosyltransferase PARP4 isoform X2 XP_011533234.1:p.Thr802= T (Thr) > T (Thr) Synonymous Variant
PARP4 transcript variant X3 XR_941496.1:n.2562A>T N/A Non Coding Transcript 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 50510 T=0.88436 A=0.11564
European Sub 38444 T=0.88341 A=0.11659
African Sub 3574 T=0.8590 A=0.1410
African Others Sub 122 T=0.844 A=0.156
African American Sub 3452 T=0.8595 A=0.1405
Asian Sub 168 T=0.970 A=0.030
East Asian Sub 112 T=0.964 A=0.036
Other Asian Sub 56 T=0.98 A=0.02
Latin American 1 Sub 500 T=0.868 A=0.132
Latin American 2 Sub 628 T=0.941 A=0.059
South Asian Sub 98 T=0.93 A=0.07
Other Sub 7098 T=0.8957 A=0.1043


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=0.883656 A=0.116344
gnomAD - Exomes Global Study-wide 249322 T=0.905692 A=0.094308
gnomAD - Exomes European Sub 134476 T=0.883697 A=0.116303
gnomAD - Exomes Asian Sub 48578 T=0.94903 A=0.05097
gnomAD - Exomes American Sub 34116 T=0.94982 A=0.05018
gnomAD - Exomes African Sub 16040 T=0.84401 A=0.15599
gnomAD - Exomes Ashkenazi Jewish Sub 10026 T=0.94484 A=0.05516
gnomAD - Exomes Other Sub 6086 T=0.8965 A=0.1035
gnomAD - Genomes Global Study-wide 140192 T=0.877746 A=0.122254
gnomAD - Genomes European Sub 75934 T=0.88102 A=0.11898
gnomAD - Genomes African Sub 42002 T=0.84648 A=0.15352
gnomAD - Genomes American Sub 13646 T=0.91331 A=0.08669
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9458 A=0.0542
gnomAD - Genomes East Asian Sub 3134 T=0.9796 A=0.0204
gnomAD - Genomes Other Sub 2152 T=0.8936 A=0.1064
ExAC Global Study-wide 119398 T=0.901447 A=0.098553
ExAC Europe Sub 72274 T=0.88656 A=0.11344
ExAC Asian Sub 24836 T=0.94838 A=0.05162
ExAC American Sub 11398 T=0.95034 A=0.04966
ExAC African Sub 10000 T=0.8365 A=0.1635
ExAC Other Sub 890 T=0.904 A=0.096
8.3KJPN JAPANESE Study-wide 16760 T=0.99362 A=0.00638
GO Exome Sequencing Project Global Study-wide 13000 T=0.86962 A=0.13038
GO Exome Sequencing Project European American Sub 8600 T=0.8844 A=0.1156
GO Exome Sequencing Project African American Sub 4400 T=0.8407 A=0.1593
1000Genomes Global Study-wide 5008 T=0.9093 A=0.0907
1000Genomes African Sub 1322 T=0.8298 A=0.1702
1000Genomes East Asian Sub 1008 T=0.9683 A=0.0317
1000Genomes Europe Sub 1006 T=0.9066 A=0.0934
1000Genomes South Asian Sub 978 T=0.946 A=0.054
1000Genomes American Sub 694 T=0.928 A=0.072
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8737 A=0.1263
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8682 A=0.1318
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8803 A=0.1197
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.9884 A=0.0116
Korean Genome Project KOREAN Study-wide 1832 T=0.9869 A=0.0131
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.892 A=0.108
A Vietnamese Genetic Variation Database Global Study-wide 614 T=0.966 A=0.034
Northern Sweden ACPOP Study-wide 600 T=0.870 A=0.130
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.897 A=0.103
HapMap Global Study-wide 324 T=0.926 A=0.074
HapMap African Sub 118 T=0.881 A=0.119
HapMap American Sub 116 T=0.914 A=0.086
HapMap Asian Sub 90 T=1.00 A=0.00
FINRISK Finnish from FINRISK project Study-wide 304 T=0.885 A=0.115
Qatari Global Study-wide 216 T=0.875 A=0.125
SGDP_PRJ Global Study-wide 102 T=0.500 A=0.500
The Danish reference pan genome Danish Study-wide 40 T=0.82 A=0.17
Siberian Global Study-wide 20 T=0.45 A=0.55
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
GRCh38.p13 chr 13 NC_000013.11:g.24459062= NC_000013.11:g.24459062T>A
GRCh37.p13 chr 13 NC_000013.10:g.25033200= NC_000013.10:g.25033200T>A
PARP4 transcript NM_006437.4:c.2406= NM_006437.4:c.2406A>T
PARP4 transcript NM_006437.3:c.2406= NM_006437.3:c.2406A>T
PARP4 transcript variant X2 XM_011534932.2:c.2406= XM_011534932.2:c.2406A>T
PARP4 transcript variant X3 XR_941496.1:n.2562= XR_941496.1:n.2562A>T
PARP4 transcript variant X1 XM_011534931.1:c.2547= XM_011534931.1:c.2547A>T
protein mono-ADP-ribosyltransferase PARP4 NP_006428.2:p.Thr802= NP_006428.2:p.Thr802=
protein mono-ADP-ribosyltransferase PARP4 isoform X2 XP_011533234.1:p.Thr802= XP_011533234.1:p.Thr802=
protein mono-ADP-ribosyltransferase PARP4 isoform X1 XP_011533233.1:p.Thr849= XP_011533233.1:p.Thr849=
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#.

70 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 SNP500CANCER ss5586210 Jul 02, 2003 (130)
2 SC_SNP ss13307181 Dec 05, 2003 (130)
3 PERLEGEN ss23434433 Sep 20, 2004 (130)
4 CORNELL ss86238023 Mar 23, 2008 (129)
5 1000GENOMES ss112617753 Feb 14, 2009 (130)
6 1000GENOMES ss114418758 Jan 25, 2009 (130)
7 SEATTLESEQ ss159727883 Dec 01, 2009 (131)
8 ILLUMINA ss160771127 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss168972285 Jul 04, 2010 (132)
10 BUSHMAN ss198973416 Jul 04, 2010 (132)
11 1000GENOMES ss226080376 Jul 14, 2010 (132)
12 1000GENOMES ss236176667 Jul 15, 2010 (132)
13 BL ss254854106 May 09, 2011 (134)
14 GMI ss286668403 Apr 25, 2013 (138)
15 NHLBI-ESP ss342373225 May 09, 2011 (134)
16 ILLUMINA ss482243255 Sep 08, 2015 (146)
17 1000GENOMES ss491056946 May 04, 2012 (137)
18 CLINSEQ_SNP ss491677239 May 04, 2012 (137)
19 ILLUMINA ss536086157 Sep 08, 2015 (146)
20 TISHKOFF ss563550314 Apr 25, 2013 (138)
21 SSMP ss659144296 Apr 25, 2013 (138)
22 JMKIDD_LAB ss974486231 Aug 21, 2014 (142)
23 EVA-GONL ss990193026 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067540208 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1078937865 Aug 21, 2014 (142)
26 1000GENOMES ss1347495619 Aug 21, 2014 (142)
27 EVA_GENOME_DK ss1576672815 Apr 01, 2015 (144)
28 EVA_FINRISK ss1584086126 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1629890266 Apr 01, 2015 (144)
30 EVA_DECODE ss1642298483 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1672884299 Apr 01, 2015 (144)
32 EVA_EXAC ss1691227686 Apr 01, 2015 (144)
33 EVA_MGP ss1711352390 Apr 01, 2015 (144)
34 HAMMER_LAB ss1807525992 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1933561392 Feb 12, 2016 (147)
36 JJLAB ss2027535094 Sep 14, 2016 (149)
37 USC_VALOUEV ss2155898949 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2194862418 Dec 20, 2016 (150)
39 TOPMED ss2358951031 Dec 20, 2016 (150)
40 GNOMAD ss2740317765 Nov 08, 2017 (151)
41 GNOMAD ss2749018793 Nov 08, 2017 (151)
42 GNOMAD ss2917600791 Nov 08, 2017 (151)
43 SWEGEN ss3010721453 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3027582316 Nov 08, 2017 (151)
45 TOPMED ss3188000422 Nov 08, 2017 (151)
46 CSHL ss3350365095 Nov 08, 2017 (151)
47 ILLUMINA ss3627021892 Oct 12, 2018 (152)
48 ILLUMINA ss3636222160 Oct 12, 2018 (152)
49 OMUKHERJEE_ADBS ss3646451581 Oct 12, 2018 (152)
50 EGCUT_WGS ss3677985755 Jul 13, 2019 (153)
51 EVA_DECODE ss3694926050 Jul 13, 2019 (153)
52 ACPOP ss3739582497 Jul 13, 2019 (153)
53 EVA ss3751236041 Jul 13, 2019 (153)
54 PACBIO ss3787404018 Jul 13, 2019 (153)
55 PACBIO ss3792477939 Jul 13, 2019 (153)
56 PACBIO ss3797361646 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3816567032 Jul 13, 2019 (153)
58 EVA ss3824796675 Apr 27, 2020 (154)
59 EVA ss3825834042 Apr 27, 2020 (154)
60 EVA ss3833448304 Apr 27, 2020 (154)
61 EVA ss3840299978 Apr 27, 2020 (154)
62 EVA ss3845784448 Apr 27, 2020 (154)
63 SGDP_PRJ ss3879593614 Apr 27, 2020 (154)
64 KRGDB ss3928410550 Apr 27, 2020 (154)
65 KOGIC ss3973207709 Apr 27, 2020 (154)
66 FSA-LAB ss3984043725 Apr 26, 2021 (155)
67 EVA ss3986596677 Apr 26, 2021 (155)
68 TOPMED ss4939954302 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5209178048 Apr 26, 2021 (155)
70 EVA ss5236911772 Apr 26, 2021 (155)
71 1000Genomes NC_000013.10 - 25033200 Oct 12, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 25033200 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000013.10 - 25033200 Oct 12, 2018 (152)
74 ExAC NC_000013.10 - 25033200 Oct 12, 2018 (152)
75 FINRISK NC_000013.10 - 25033200 Apr 27, 2020 (154)
76 The Danish reference pan genome NC_000013.10 - 25033200 Apr 27, 2020 (154)
77 gnomAD - Genomes NC_000013.11 - 24459062 Apr 26, 2021 (155)
78 gnomAD - Exomes NC_000013.10 - 25033200 Jul 13, 2019 (153)
79 GO Exome Sequencing Project NC_000013.10 - 25033200 Oct 12, 2018 (152)
80 Genome of the Netherlands Release 5 NC_000013.10 - 25033200 Apr 27, 2020 (154)
81 HapMap NC_000013.11 - 24459062 Apr 27, 2020 (154)
82 KOREAN population from KRGDB NC_000013.10 - 25033200 Apr 27, 2020 (154)
83 Korean Genome Project NC_000013.11 - 24459062 Apr 27, 2020 (154)
84 Medical Genome Project healthy controls from Spanish population NC_000013.10 - 25033200 Apr 27, 2020 (154)
85 Northern Sweden NC_000013.10 - 25033200 Jul 13, 2019 (153)
86 Qatari NC_000013.10 - 25033200 Apr 27, 2020 (154)
87 SGDP_PRJ NC_000013.10 - 25033200 Apr 27, 2020 (154)
88 Siberian NC_000013.10 - 25033200 Apr 27, 2020 (154)
89 8.3KJPN NC_000013.10 - 25033200 Apr 26, 2021 (155)
90 TopMed NC_000013.11 - 24459062 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000013.10 - 25033200 Oct 12, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000013.10 - 25033200 Jul 13, 2019 (153)
93 ALFA NC_000013.11 - 24459062 Apr 26, 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)
rs3190389 Oct 09, 2002 (108)
rs6413414 May 23, 2008 (130)
rs17413352 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss112617753, ss114418758, ss168972285, ss198973416, ss254854106, ss286668403, ss491677239, ss1642298483 NC_000013.9:23931199:T:A NC_000013.11:24459061:T:A (self)
60339046, 33509712, 23724003, 1551318, 82587, 3220129, 9559202, 1254068, 14950576, 35587944, 468150, 12867362, 15603322, 31610594, 8415303, 67147355, 33509712, 7433169, ss226080376, ss236176667, ss342373225, ss482243255, ss491056946, ss536086157, ss563550314, ss659144296, ss974486231, ss990193026, ss1067540208, ss1078937865, ss1347495619, ss1576672815, ss1584086126, ss1629890266, ss1672884299, ss1691227686, ss1711352390, ss1807525992, ss1933561392, ss2027535094, ss2155898949, ss2358951031, ss2740317765, ss2749018793, ss2917600791, ss3010721453, ss3350365095, ss3627021892, ss3636222160, ss3646451581, ss3677985755, ss3739582497, ss3751236041, ss3787404018, ss3792477939, ss3797361646, ss3824796675, ss3825834042, ss3833448304, ss3840299978, ss3879593614, ss3928410550, ss3984043725, ss3986596677, ss5209178048 NC_000013.10:25033199:T:A NC_000013.11:24459061:T:A (self)
425515104, 948138, 29585710, 97235349, 155499960, 15004714976, ss2194862418, ss3027582316, ss3188000422, ss3694926050, ss3816567032, ss3845784448, ss3973207709, ss4939954302, ss5236911772 NC_000013.11:24459061:T:A NC_000013.11:24459061:T:A (self)
ss13307181 NT_009799.12:6013199:T:A NC_000013.11:24459061:T:A (self)
ss5586210, ss23434433, ss86238023, ss159727883, ss160771127 NT_024524.14:6013199:T:A NC_000013.11:24459061:T: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 rs1130941

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