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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs2236824

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:18705778 (GRCh38.p7) 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>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.37526 (47121/125568, TOPMED)
C=0.3912 (12074/30862, GnomAD)
C=0.356 (1784/5008, 1000G) (+ 2 more)
C=0.457 (1760/3854, ALSPAC)
C=0.458 (1697/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PAX7 : Intron 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.p7 chr 1 NC_000001.11:g.18705778G>A
GRCh38.p7 chr 1 NC_000001.11:g.18705778G>C
GRCh37.p13 chr 1 NC_000001.10:g.19032272G>A
GRCh37.p13 chr 1 NC_000001.10:g.19032272G>C
PAX7 RefSeqGene NG_023262.1:g.79773G>A
PAX7 RefSeqGene NG_023262.1:g.79773G>C
Gene: PAX7, paired box 7 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PAX7 transcript variant 3 NM_001135254.1:c. N/A Intron Variant
PAX7 transcript variant 1 NM_002584.2:c. N/A Intron Variant
PAX7 transcript variant 2 NM_013945.2: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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.62474 C=0.37526
The Genome Aggregation Database Global Study-wide 30862 G=0.6087 A=0.0000, C=0.3912
The Genome Aggregation Database European Sub 18432 G=0.5254 A=0.0001, C=0.4746
The Genome Aggregation Database African Sub 8698 G=0.761 A=0.000, C=0.239
The Genome Aggregation Database East Asian Sub 1614 G=0.761 A=0.000, C=0.239
The Genome Aggregation Database Other Sub 980 G=0.52 A=0.00, C=0.48
The Genome Aggregation Database American Sub 836 G=0.65 A=0.00, C=0.35
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.68 A=0.00, C=0.32
1000Genomes Global Study-wide 5008 G=0.644 C=0.356
1000Genomes African Sub 1322 G=0.779 C=0.221
1000Genomes East Asian Sub 1008 G=0.741 C=0.259
1000Genomes Europe Sub 1006 G=0.518 C=0.482
1000Genomes South Asian Sub 978 G=0.51 C=0.49
1000Genomes American Sub 694 G=0.62 C=0.38
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.543 C=0.457
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.542 C=0.458
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= A C Note
GRCh38.p7 chr 1 NC_000001.11:g.18...

NC_000001.11:g.18705778G=

NC_000001.11:g.18...

NC_000001.11:g.18705778G>A

NC_000001.11:g.18...

NC_000001.11:g.18705778G>C

GRCh37.p13 chr 1 NC_000001.10:g.19...

NC_000001.10:g.19032272G=

NC_000001.10:g.19...

NC_000001.10:g.19032272G>A

NC_000001.10:g.19...

NC_000001.10:g.19032272G>C

PAX7 RefSeqGene NG_023262.1:g.797...

NG_023262.1:g.79773G=

NG_023262.1:g.797...

NG_023262.1:g.79773G>A

NG_023262.1:g.797...

NG_023262.1:g.79773G>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#.

42 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3191364 Aug 15, 2001 (98)
2 HGSV ss78650419 Dec 06, 2007 (129)
3 HGSV ss84584856 Dec 15, 2007 (130)
4 1000GENOMES ss108033421 Jan 22, 2009 (130)
5 ILLUMINA-UK ss118538362 Feb 14, 2009 (130)
6 GMI ss154716787 Dec 01, 2009 (131)
7 ENSEMBL ss161200334 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss163915636 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss205330953 Jul 04, 2010 (132)
10 1000GENOMES ss218265438 Jul 14, 2010 (132)
11 1000GENOMES ss230448372 Jul 14, 2010 (132)
12 1000GENOMES ss238159343 Jul 15, 2010 (132)
13 BL ss252957689 May 09, 2011 (134)
14 GMI ss275739714 May 04, 2012 (137)
15 PJP ss290704939 May 09, 2011 (134)
16 TISHKOFF ss553852431 Apr 25, 2013 (138)
17 SSMP ss647616851 Apr 25, 2013 (138)
18 EVA-GONL ss974911269 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067709809 Aug 21, 2014 (142)
20 1000GENOMES ss1289900847 Aug 21, 2014 (142)
21 DDI ss1425733759 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1573919720 Apr 01, 2015 (144)
23 EVA_DECODE ss1584268647 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1599655399 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1642649432 Apr 01, 2015 (144)
26 HAMMER_LAB ss1794005651 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1918122120 Feb 12, 2016 (147)
28 GENOMED ss1966697357 Jul 19, 2016 (147)
29 JJLAB ss2019572526 Sep 14, 2016 (149)
30 USC_VALOUEV ss2147575148 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2160450866 Dec 20, 2016 (150)
32 TOPMED ss2322631558 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624302378 Nov 08, 2017 (151)
34 GRF ss2697479492 Nov 08, 2017 (151)
35 GNOMAD ss2752285357 Nov 08, 2017 (151)
36 AFFY ss2985499996 Nov 08, 2017 (151)
37 SWEGEN ss2986409871 Nov 08, 2017 (151)
38 ILLUMINA ss3021061976 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023550979 Nov 08, 2017 (151)
40 TOPMED ss3070057068 Nov 08, 2017 (151)
41 TOPMED ss3070057069 Nov 08, 2017 (151)
42 CSHL ss3343350271 Nov 08, 2017 (151)
43 1000Genomes NC_000001.10 - 19032272 Jul 19, 2018 (151)
44 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 19032272 Jul 19, 2018 (151)
45 The Genome Aggregation Database NC_000001.10 - 19032272 Jul 19, 2018 (151)
46 Trans-Omics for Precision Medicine NC_000001.11 - 18705778 Jul 19, 2018 (151)
47 UK 10K study - Twins NC_000001.10 - 19032272 Jul 19, 2018 (151)
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)
rs58322136 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78650419, ss84584856 NC_000001.8:18777577:G= NC_000001.11:18705777:G= (self)
ss108033421, ss118538362, ss163915636, ss205330953, ss252957689, ss275739714, ss290704939, ss1584268647 NC_000001.9:18904858:G= NC_000001.11:18705777:G= (self)
584241, 304799, 1684556, 304799, ss218265438, ss230448372, ss238159343, ss553852431, ss647616851, ss974911269, ss1067709809, ss1289900847, ss1425733759, ss1573919720, ss1599655399, ss1642649432, ss1794005651, ss1918122120, ss1966697357, ss2019572526, ss2147575148, ss2322631558, ss2624302378, ss2697479492, ss2752285357, ss2985499996, ss2986409871, ss3021061976, ss3343350271 NC_000001.10:19032271:G= NC_000001.11:18705777:G= (self)
2885907, ss2160450866, ss3023550979, ss3070057068, ss3070057069 NC_000001.11:18705777:G= NC_000001.11:18705777:G= (self)
ss3191364, ss154716787, ss161200334 NT_004610.19:5712359:G= NC_000001.11:18705777:G= (self)
1684556, ss2752285357 NC_000001.10:19032271:G>A NC_000001.11:18705777:G>A (self)
ss3070057068 NC_000001.11:18705777:G>A NC_000001.11:18705777:G>A (self)
ss78650419, ss84584856 NC_000001.8:18777577:G>C NC_000001.11:18705777:G>C (self)
ss108033421, ss118538362, ss163915636, ss205330953, ss252957689, ss275739714, ss290704939, ss1584268647 NC_000001.9:18904858:G>C NC_000001.11:18705777:G>C (self)
584241, 304799, 1684556, 304799, ss218265438, ss230448372, ss238159343, ss553852431, ss647616851, ss974911269, ss1067709809, ss1289900847, ss1425733759, ss1573919720, ss1599655399, ss1642649432, ss1794005651, ss1918122120, ss1966697357, ss2019572526, ss2147575148, ss2322631558, ss2624302378, ss2697479492, ss2752285357, ss2985499996, ss2986409871, ss3021061976, ss3343350271 NC_000001.10:19032271:G>C NC_000001.11:18705777:G>C (self)
2885907, ss2160450866, ss3023550979, ss3070057069 NC_000001.11:18705777:G>C NC_000001.11:18705777:G>C (self)
ss3191364, ss154716787, ss161200334 NT_004610.19:5712359:G>C NC_000001.11:18705777:G>C (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 rs2236824

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: 0.1.4.post833+d3ba21e