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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.

rs1531584

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr4:751657 (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
G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.22760 (28579/125568, TOPMED)
C=0.2433 (7163/29444, GnomAD)
C=0.203 (1019/5008, 1000G) (+ 3 more)
C=0.331 (1483/4478, Estonian)
C=0.265 (1022/3854, ALSPAC)
C=0.271 (1005/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PCGF3 : Intron Variant
LOC107986211 : 500B Downstream 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.p12 chr 4 NC_000004.12:g.751657G>C
GRCh38.p12 chr 4 NC_000004.12:g.751657G>T
GRCh37.p13 chr 4 NC_000004.11:g.745445G>C
GRCh37.p13 chr 4 NC_000004.11:g.745445G>T
Gene: PCGF3, polycomb group ring finger 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PCGF3 transcript variant 1 NM_001317836.1:c. N/A Intron Variant
PCGF3 transcript variant 2 NM_006315.5:c. N/A Intron Variant
Gene: LOC107986211, uncharacterized LOC107986211 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107986211 transcript XM_024454317.1:c. N/A Downstream 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
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 125568 G=0.77239 C=0.22760, T=0.00002
gnomAD - Genomes Global Study-wide 29444 G=0.7567 T=0.0000, C=0.2433
gnomAD - Genomes European Sub 17468 G=0.7165 T=0.0000, C=0.2835
gnomAD - Genomes African Sub 8394 G=0.870 T=0.000, C=0.130
gnomAD - Genomes East Asian Sub 1610 G=0.694 T=0.000, C=0.306
gnomAD - Genomes Other Sub 912 G=0.73 T=0.00, C=0.27
gnomAD - Genomes American Sub 762 G=0.55 T=0.00, C=0.45
gnomAD - Genomes Ashkenazi Jewish Sub 298 G=0.87 T=0.00, C=0.13
1000Genomes Global Study-wide 5008 G=0.797 C=0.203
1000Genomes African Sub 1322 G=0.893 C=0.107
1000Genomes East Asian Sub 1008 G=0.688 C=0.312
1000Genomes Europe Sub 1006 G=0.743 C=0.257
1000Genomes South Asian Sub 978 G=0.93 C=0.07
1000Genomes American Sub 694 G=0.65 C=0.35
Genetic variation in the Estonian population Estonian Study-wide 4478 G=0.669 C=0.331
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.735 C=0.265
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.729 C=0.271
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 G= C T Note
GRCh38.p12 chr 4 NC_000004.12:g.75...

NC_000004.12:g.751657G=

NC_000004.12:g.75...

NC_000004.12:g.751657G>C

NC_000004.12:g.75...

NC_000004.12:g.751657G>T

GRCh37.p13 chr 4 NC_000004.11:g.74...

NC_000004.11:g.745445G=

NC_000004.11:g.74...

NC_000004.11:g.745445G>C

NC_000004.11:g.74...

NC_000004.11:g.745445G>T

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#.

44 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2372431 Oct 23, 2000 (88)
2 YUSUKE ss3233208 Sep 28, 2001 (100)
3 SC_JCM ss5820115 Feb 20, 2003 (111)
4 CSHL-HAPMAP ss17024766 Feb 27, 2004 (120)
5 CSHL-HAPMAP ss20210599 Feb 27, 2004 (120)
6 SSAHASNP ss22066593 Apr 05, 2004 (121)
7 PERLEGEN ss23962715 Sep 20, 2004 (123)
8 ABI ss44580819 Mar 15, 2006 (126)
9 HUMANGENOME_JCVI ss98925761 Feb 05, 2009 (130)
10 ILLUMINA-UK ss116834925 Feb 14, 2009 (130)
11 ENSEMBL ss133396021 Dec 01, 2009 (131)
12 GMI ss156737119 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss161886292 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165986579 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss206627357 Jul 04, 2010 (132)
16 1000GENOMES ss220689629 Jul 14, 2010 (132)
17 1000GENOMES ss232222272 Jul 14, 2010 (132)
18 1000GENOMES ss239551713 Jul 15, 2010 (132)
19 BL ss252869411 May 09, 2011 (134)
20 GMI ss277536483 May 04, 2012 (137)
21 TISHKOFF ss557249016 Apr 25, 2013 (138)
22 SSMP ss651001358 Apr 25, 2013 (138)
23 EVA-GONL ss979664692 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1071210315 Aug 21, 2014 (142)
25 1000GENOMES ss1308055679 Aug 21, 2014 (142)
26 EVA_GENOME_DK ss1580377420 Apr 01, 2015 (144)
27 EVA_DECODE ss1589161650 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1609220481 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1652214514 Apr 01, 2015 (144)
30 HAMMER_LAB ss1800779608 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1922894704 Feb 12, 2016 (147)
32 JJLAB ss2022021528 Sep 14, 2016 (149)
33 USC_VALOUEV ss2150126559 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2259756182 Dec 20, 2016 (150)
35 TOPMED ss2427154857 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2625511510 Nov 08, 2017 (151)
37 GRF ss2705561086 Nov 08, 2017 (151)
38 GNOMAD ss2804594112 Nov 08, 2017 (151)
39 SWEGEN ss2993979051 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3024780391 Nov 08, 2017 (151)
41 CSHL ss3345494158 Nov 08, 2017 (151)
42 TOPMED ss3418000853 Nov 08, 2017 (151)
43 TOPMED ss3418000854 Nov 08, 2017 (151)
44 URBANLAB ss3647631023 Oct 12, 2018 (152)
45 1000Genomes NC_000004.11 - 745445 Oct 12, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 745445 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000004.11 - 745445 Oct 12, 2018 (152)
48 gnomAD - Genomes NC_000004.11 - 745445 Oct 12, 2018 (152)
49 TopMed NC_000004.12 - 751657 Oct 12, 2018 (152)
50 UK 10K study - Twins NC_000004.11 - 745445 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss116834925, ss161886292, ss165986579, ss206627357, ss252869411, ss277536483, ss1589161650 NC_000004.10:735444:G= NC_000004.12:751656:G= (self)
19392592, 10811164, 7656435, 145221867, 10811164, ss220689629, ss232222272, ss239551713, ss557249016, ss651001358, ss979664692, ss1071210315, ss1308055679, ss1580377420, ss1609220481, ss1652214514, ss1800779608, ss1922894704, ss2022021528, ss2150126559, ss2427154857, ss2625511510, ss2705561086, ss2804594112, ss2993979051, ss3345494158 NC_000004.11:745444:G= NC_000004.12:751656:G= (self)
273353360, ss2259756182, ss3024780391, ss3418000853, ss3418000854, ss3647631023 NC_000004.12:751656:G= NC_000004.12:751656:G= (self)
ss17024766, ss20210599, ss22066593 NT_037622.3:735274:G= NC_000004.12:751656:G= (self)
ss2372431, ss3233208, ss5820115, ss23962715, ss44580819, ss98925761, ss133396021, ss156737119 NT_037622.5:735444:G= NC_000004.12:751656:G= (self)
ss116834925, ss161886292, ss165986579, ss206627357, ss252869411, ss277536483, ss1589161650 NC_000004.10:735444:G>C NC_000004.12:751656:G>C (self)
19392592, 10811164, 7656435, 145221867, 10811164, ss220689629, ss232222272, ss239551713, ss557249016, ss651001358, ss979664692, ss1071210315, ss1308055679, ss1580377420, ss1609220481, ss1652214514, ss1800779608, ss1922894704, ss2022021528, ss2150126559, ss2427154857, ss2625511510, ss2705561086, ss2804594112, ss2993979051, ss3345494158 NC_000004.11:745444:G>C NC_000004.12:751656:G>C (self)
273353360, ss2259756182, ss3024780391, ss3418000853, ss3647631023 NC_000004.12:751656:G>C NC_000004.12:751656:G>C (self)
ss17024766, ss20210599, ss22066593 NT_037622.3:735274:G>C NC_000004.12:751656:G>C (self)
ss2372431, ss3233208, ss5820115, ss23962715, ss44580819, ss98925761, ss133396021, ss156737119 NT_037622.5:735444:G>C NC_000004.12:751656:G>C (self)
145221867, ss2804594112 NC_000004.11:745444:G>T NC_000004.12:751656:G>T (self)
273353360, ss3418000854 NC_000004.12:751656:G>T NC_000004.12:751656:G>T (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 rs1531584

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.post104+4a6ee9c