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dbSNP Short Genetic Variations

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.

rs2023614

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr19:43560713 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.07158 (8988/125568, TOPMED)
G=0.0732 (2267/30950, GnomAD)
G=0.082 (413/5008, 1000G) (+ 3 more)
G=0.095 (424/4480, Estonian)
G=0.076 (294/3854, ALSPAC)
G=0.071 (265/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
XRCC1 : 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.p12 chr 19 NC_000019.10:g.43560713C>G
GRCh37.p13 chr 19 NC_000019.9:g.44064865C>G
XRCC1 RefSeqGene (LRG_784) NG_033799.1:g.19866G>C
Gene: XRCC1, X-ray repair cross complementing 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
XRCC1 transcript NM_006297.2: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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.92842 G=0.07158
gnomAD - Genomes Global Study-wide 30950 C=0.9268 G=0.0732
gnomAD - Genomes European Sub 18488 C=0.9110 G=0.0890
gnomAD - Genomes African Sub 8726 C=0.975 G=0.025
gnomAD - Genomes East Asian Sub 1618 C=0.910 G=0.090
gnomAD - Genomes Other Sub 978 C=0.92 G=0.08
gnomAD - Genomes American Sub 838 C=0.82 G=0.18
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.92 G=0.08
1000Genomes Global Study-wide 5008 C=0.918 G=0.082
1000Genomes African Sub 1322 C=0.989 G=0.011
1000Genomes East Asian Sub 1008 C=0.871 G=0.129
1000Genomes Europe Sub 1006 C=0.911 G=0.089
1000Genomes South Asian Sub 978 C=0.96 G=0.04
1000Genomes American Sub 694 C=0.80 G=0.20
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.905 G=0.095
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.924 G=0.076
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.929 G=0.071
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 Note
GRCh38.p12 chr 19 NC_000019.10:g.43560713C= NC_000019.10:g.43560713C>G
GRCh37.p13 chr 19 NC_000019.9:g.44064865C= NC_000019.9:g.44064865C>G
XRCC1 RefSeqGene (LRG_784) NG_033799.1:g.19866G= NG_033799.1:g.19866G>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#.

46 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2927895 Apr 12, 2001 (94)
2 EGP_SNPS ss4473932 Jul 03, 2002 (106)
3 CSHL-HAPMAP ss19402175 Feb 27, 2004 (120)
4 PERLEGEN ss24684737 Sep 20, 2004 (123)
5 ABI ss40966574 Mar 15, 2006 (126)
6 PERLEGEN ss69228850 May 16, 2007 (127)
7 ILLUMINA ss75244714 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss119412492 Dec 01, 2009 (131)
9 ENSEMBL ss161880401 Dec 01, 2009 (131)
10 ILLUMINA ss173049660 Jul 04, 2010 (132)
11 1000GENOMES ss237685565 Jul 15, 2010 (132)
12 1000GENOMES ss243889143 Jul 15, 2010 (132)
13 GMI ss283219276 May 04, 2012 (137)
14 ILLUMINA ss537024043 Sep 08, 2015 (146)
15 TISHKOFF ss566000673 Apr 25, 2013 (138)
16 SSMP ss661867813 Apr 25, 2013 (138)
17 EVA-GONL ss994328962 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1081922987 Aug 21, 2014 (142)
19 1000GENOMES ss1363287967 Aug 21, 2014 (142)
20 HAMMER_LAB ss1397758109 Sep 08, 2015 (146)
21 DDI ss1428410496 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1578649499 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1638024000 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1681018033 Apr 01, 2015 (144)
25 EVA_DECODE ss1698383710 Apr 01, 2015 (144)
26 HAMMER_LAB ss1809320854 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1937824626 Feb 12, 2016 (147)
28 ILLUMINA ss1959867595 Feb 12, 2016 (147)
29 GENOMED ss1968648450 Jul 19, 2016 (147)
30 JJLAB ss2029689978 Sep 14, 2016 (149)
31 USC_VALOUEV ss2158231700 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2225939363 Dec 20, 2016 (150)
33 TOPMED ss2391739529 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2629341326 Nov 08, 2017 (151)
35 ILLUMINA ss2633542703 Nov 08, 2017 (151)
36 GRF ss2702844316 Nov 08, 2017 (151)
37 GNOMAD ss2963219583 Nov 08, 2017 (151)
38 SWEGEN ss3017523668 Nov 08, 2017 (151)
39 ILLUMINA ss3021909454 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3028675004 Nov 08, 2017 (151)
41 TOPMED ss3294084839 Nov 08, 2017 (151)
42 CSHL ss3352315354 Nov 08, 2017 (151)
43 ILLUMINA ss3627938484 Oct 12, 2018 (152)
44 ILLUMINA ss3638229089 Oct 12, 2018 (152)
45 ILLUMINA ss3643201756 Oct 12, 2018 (152)
46 ILLUMINA ss3652335463 Oct 12, 2018 (152)
47 1000Genomes NC_000019.9 - 44064865 Oct 12, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 44064865 Oct 12, 2018 (152)
49 Genetic variation in the Estonian population NC_000019.9 - 44064865 Oct 12, 2018 (152)
50 gnomAD - Genomes NC_000019.9 - 44064865 Oct 12, 2018 (152)
51 TopMed NC_000019.10 - 43560713 Oct 12, 2018 (152)
52 UK 10K study - Twins NC_000019.9 - 44064865 Oct 12, 2018 (152)
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)
rs17711731 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss283219276, ss1397758109, ss1698383710, ss3643201756 NC_000019.8:48756704:C= NC_000019.10:43560712:C= (self)
76698826, 42471714, 30010341, 96921113, 42471714, ss237685565, ss243889143, ss537024043, ss566000673, ss661867813, ss994328962, ss1081922987, ss1363287967, ss1428410496, ss1578649499, ss1638024000, ss1681018033, ss1809320854, ss1937824626, ss1959867595, ss1968648450, ss2029689978, ss2158231700, ss2391739529, ss2629341326, ss2633542703, ss2702844316, ss2963219583, ss3017523668, ss3021909454, ss3352315354, ss3627938484, ss3638229089, ss3652335463 NC_000019.9:44064864:C= NC_000019.10:43560712:C= (self)
181778263, ss2225939363, ss3028675004, ss3294084839 NC_000019.10:43560712:C= NC_000019.10:43560712:C= (self)
ss19402175 NT_011109.15:16333082:C= NC_000019.10:43560712:C= (self)
ss2927895, ss4473932, ss24684737, ss40966574, ss69228850, ss75244714, ss119412492, ss161880401, ss173049660 NT_011109.16:16333082:C= NC_000019.10:43560712:C= (self)
ss283219276, ss1397758109, ss1698383710, ss3643201756 NC_000019.8:48756704:C>G NC_000019.10:43560712:C>G (self)
76698826, 42471714, 30010341, 96921113, 42471714, ss237685565, ss243889143, ss537024043, ss566000673, ss661867813, ss994328962, ss1081922987, ss1363287967, ss1428410496, ss1578649499, ss1638024000, ss1681018033, ss1809320854, ss1937824626, ss1959867595, ss1968648450, ss2029689978, ss2158231700, ss2391739529, ss2629341326, ss2633542703, ss2702844316, ss2963219583, ss3017523668, ss3021909454, ss3352315354, ss3627938484, ss3638229089, ss3652335463 NC_000019.9:44064864:C>G NC_000019.10:43560712:C>G (self)
181778263, ss2225939363, ss3028675004, ss3294084839 NC_000019.10:43560712:C>G NC_000019.10:43560712:C>G (self)
ss19402175 NT_011109.15:16333082:C>G NC_000019.10:43560712:C>G (self)
ss2927895, ss4473932, ss24684737, ss40966574, ss69228850, ss75244714, ss119412492, ss161880401, ss173049660 NT_011109.16:16333082:C>G NC_000019.10:43560712:C>G (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 rs2023614
PMID Title Author Year Journal
23565320 DNA repair genotype and lung cancer risk in the beta-carotene and retinol efficacy trial. Doherty JA et al. 2013 International journal of molecular epidemiology and genetics
27153553 Association of nineteen polymorphisms from seven DNA repair genes and the risk for bladder cancer in Gansu province of China. Zhu G et al. 2016 Oncotarget

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.post58+e54ea20