Name: rs4287120
Published: September 21, 2022
License: Open Access

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.

rs4287120

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:104033 (GRCh38.p14) 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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.49437 (13969/28256, 14KJPN)
T=0.49684 (8327/16760, 8.3KJPN)
T=0.48035 (7845/16332, ALFA) (+ 4 more)
T=0.4983 (1456/2922, KOREAN)
T=0.478 (257/538, SGDP_PRJ)
C=0.321 (68/212, Qatari)
T=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124903816 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	16332	T=0.48035	C=0.51965
European	Sub	12080	T=0.47798	C=0.52202
African	Sub	2816	T=0.4933	C=0.5067
African Others	Sub	108	T=0.509	C=0.491
African American	Sub	2708	T=0.4926	C=0.5074
Asian	Sub	108	T=0.491	C=0.509
East Asian	Sub	84	T=0.49	C=0.51
Other Asian	Sub	24	T=0.50	C=0.50
Latin American 1	Sub	146	T=0.438	C=0.562
Latin American 2	Sub	610	T=0.480	C=0.520
South Asian	Sub	94	T=0.50	C=0.50
Other	Sub	478	T=0.471	C=0.529

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
14KJPN	JAPANESE	Study-wide	28256	T=0.50563	C=0.49437
8.3KJPN	JAPANESE	Study-wide	16760	T=0.49684	C=0.50316
Allele Frequency Aggregator	Total	Global	16332	T=0.48035	C=0.51965
Allele Frequency Aggregator	European	Sub	12080	T=0.47798	C=0.52202
Allele Frequency Aggregator	African	Sub	2816	T=0.4933	C=0.5067
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.480	C=0.520
Allele Frequency Aggregator	Other	Sub	478	T=0.471	C=0.529
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.438	C=0.562
Allele Frequency Aggregator	Asian	Sub	108	T=0.491	C=0.509
Allele Frequency Aggregator	South Asian	Sub	94	T=0.50	C=0.50
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.4983	C=0.5017
SGDP_PRJ	Global	Study-wide	538	T=0.478	C=0.522
Qatari	Global	Study-wide	212	T=0.679	C=0.321
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	C=0.55

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.p14 chr 1	NC_000001.11:g.104033T>C
GRCh37.p13 chr 1	NC_000001.10:g.104033T>C

Gene: LOC124903816, uncharacterized LOC124903816 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903816 transcript variant X1	XR_007065337.1:n.	N/A	Intron Variant
LOC124903816 transcript variant X2	XR_007065338.1:n.	N/A	Intron Variant

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

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=	C
GRCh38.p14 chr 1	NC_000001.11:g.104033=	NC_000001.11:g.104033T>C
GRCh37.p13 chr 1	NC_000001.10:g.104033=	NC_000001.10:g.104033T>C

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#.

23 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss5672050	Feb 20, 2003 (111)
2	BCMHGSC_JDW	ss87153462	Mar 25, 2008 (129)
3	BGI	ss102713367	Dec 01, 2009 (147)
4	ENSEMBL	ss131826374	Dec 01, 2009 (147)
5	GMI	ss154521924	Dec 01, 2009 (147)
6	GMI	ss157739734	Dec 01, 2009 (147)
7	GMI	ss275680005	May 04, 2012 (137)
8	GMI	ss283987250	Apr 25, 2013 (138)
9	EVA_GENOME_DK	ss1573850783	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1917958618	Feb 12, 2016 (147)
11	GRF	ss2697373230	Nov 08, 2017 (151)
12	GNOMAD	ss2750608535	Nov 08, 2017 (151)
13	SWEGEN	ss2986142864	Nov 08, 2017 (151)
14	URBANLAB	ss3646580480	Oct 11, 2018 (152)
15	SGDP_PRJ	ss3847985467	Apr 25, 2020 (154)
16	KRGDB	ss3892825270	Apr 25, 2020 (154)
17	TOMMO_GENOMICS	ss5142035566	Apr 25, 2021 (155)
18	EVA	ss5316173302	Oct 12, 2022 (156)
19	SANFORD_IMAGENETICS	ss5624743524	Oct 12, 2022 (156)
20	TOMMO_GENOMICS	ss5666168788	Oct 12, 2022 (156)
21	YY_MCH	ss5800240938	Oct 12, 2022 (156)
22	EVA	ss5831416911	Oct 12, 2022 (156)
23	EVA	ss5979925922	Oct 12, 2022 (156)
24	The Danish reference pan genome	NC_000001.10 - 104033	Apr 25, 2020 (154)
25	KOREAN population from KRGDB	NC_000001.10 - 104033	Apr 25, 2020 (154)
26	Qatari	NC_000001.10 - 104033	Apr 25, 2020 (154)
27	SGDP_PRJ	NC_000001.10 - 104033	Apr 25, 2020 (154)
28	8.3KJPN	NC_000001.10 - 104033	Apr 25, 2021 (155)
29	14KJPN	NC_000001.11 - 104033	Oct 12, 2022 (156)
30	ALFA	NC_000001.11 - 104033	Apr 25, 2021 (155)

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)
rs74836402	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss87153462, ss275680005, ss283987250	NC_000001.9:93895:T:C	NC_000001.11:104032:T:C	(self)
1358017, 2664, 548, 2447, 4873, ss1573850783, ss1917958618, ss2697373230, ss2750608535, ss2986142864, ss3847985467, ss3892825270, ss5142035566, ss5316173302, ss5624743524, ss5831416911, ss5979925922	NC_000001.10:104032:T:C	NC_000001.11:104032:T:C	(self)
5892, 3354541951, ss3646580480, ss5666168788, ss5800240938	NC_000001.11:104032:T:C	NC_000001.11:104032:T:C	(self)
ss5672050, ss102713367, ss131826374, ss154521924, ss157739734	NT_077402.2:94032:T:C	NC_000001.11:104032:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs4287120

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4287120