Name: rs4085685
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.

rs4085685

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:18501826 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.22291 (6299/28258, 14KJPN)
T=0.22112 (3706/16760, 8.3KJPN)
T=0.08951 (1214/13562, ALFA) (+ 12 more)
T=0.1841 (1179/6404, 1000G_30x)
T=0.1863 (933/5008, 1000G)
T=0.1884 (726/3854, ALSPAC)
T=0.1810 (671/3708, TWINSUK)
T=0.1952 (572/2930, KOREAN)
T=0.2085 (382/1832, Korea1K)
T=0.200 (200/998, GoNL)
T=0.135 (81/600, NorthernSweden)
T=0.069 (15/216, Qatari)
C=0.457 (85/186, SGDP_PRJ)
T=0.25 (10/40, GENOME_DK)
C=0.4 (3/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	13562	C=0.91049	A=0.00000, T=0.08951
European	Sub	9946	C=0.8843	A=0.0000, T=0.1157
African	Sub	2546	C=0.9811	A=0.0000, T=0.0189
African Others	Sub	98	C=0.97	A=0.00, T=0.03
African American	Sub	2448	C=0.9816	A=0.0000, T=0.0184
Asian	Sub	54	C=1.00	A=0.00, T=0.00
East Asian	Sub	42	C=1.00	A=0.00, T=0.00
Other Asian	Sub	12	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	102	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	348	C=1.000	A=0.000, T=0.000
South Asian	Sub	52	C=1.00	A=0.00, T=0.00
Other	Sub	514	C=0.971	A=0.000, T=0.029

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	28258	C=0.77709	T=0.22291
8.3KJPN	JAPANESE	Study-wide	16760	C=0.77888	T=0.22112
Allele Frequency Aggregator	Total	Global	13562	C=0.91049	A=0.00000, T=0.08951
Allele Frequency Aggregator	European	Sub	9946	C=0.8843	A=0.0000, T=0.1157
Allele Frequency Aggregator	African	Sub	2546	C=0.9811	A=0.0000, T=0.0189
Allele Frequency Aggregator	Other	Sub	514	C=0.971	A=0.000, T=0.029
Allele Frequency Aggregator	Latin American 2	Sub	348	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	102	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	54	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	52	C=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8159	T=0.1841
1000Genomes_30x	African	Sub	1786	C=0.9222	T=0.0778
1000Genomes_30x	Europe	Sub	1266	C=0.8436	T=0.1564
1000Genomes_30x	South Asian	Sub	1202	C=0.6872	T=0.3128
1000Genomes_30x	East Asian	Sub	1170	C=0.7812	T=0.2188
1000Genomes_30x	American	Sub	980	C=0.786	T=0.214
1000Genomes	Global	Study-wide	5008	C=0.8137	T=0.1863
1000Genomes	African	Sub	1322	C=0.9274	T=0.0726
1000Genomes	East Asian	Sub	1008	C=0.7827	T=0.2173
1000Genomes	Europe	Sub	1006	C=0.8419	T=0.1581
1000Genomes	South Asian	Sub	978	C=0.687	T=0.313
1000Genomes	American	Sub	694	C=0.780	T=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8116	T=0.1884
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8190	T=0.1810
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8048	T=0.1952
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7915	T=0.2085
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.800	T=0.200
Northern Sweden	ACPOP	Study-wide	600	C=0.865	T=0.135
Qatari	Global	Study-wide	216	C=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	186	C=0.457	T=0.543
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	8	C=0.4	T=0.6

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 13	NC_000013.11:g.18501826C>A
GRCh38.p14 chr 13	NC_000013.11:g.18501826C>T
GRCh37.p13 chr 13	NC_000013.10:g.19075966C>A
GRCh37.p13 chr 13	NC_000013.10:g.19075966C>T

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	C=	A	T
GRCh38.p14 chr 13	NC_000013.11:g.18501826=	NC_000013.11:g.18501826C>A	NC_000013.11:g.18501826C>T
GRCh37.p13 chr 13	NC_000013.10:g.19075966=	NC_000013.10:g.19075966C>A	NC_000013.10:g.19075966C>T

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, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss5485319	Oct 10, 2002 (108)
2	SC_JCM	ss5986905	Feb 20, 2003 (117)
3	BGI	ss103098255	Feb 13, 2009 (131)
4	ILLUMINA-UK	ss118370048	Dec 01, 2009 (131)
5	BCM-HGSC-SUB	ss206795183	Jul 04, 2010 (132)
6	1000GENOMES	ss226054434	Jul 14, 2010 (132)
7	1000GENOMES	ss236155628	Jul 15, 2010 (132)
8	1000GENOMES	ss242671307	Jul 15, 2010 (132)
9	BL	ss254803810	May 09, 2011 (134)
10	GMI	ss281615903	May 04, 2012 (137)
11	SSMP	ss659106544	Apr 25, 2013 (138)
12	EVA-GONL	ss990137866	Aug 21, 2014 (142)
13	1000GENOMES	ss1347308513	Aug 21, 2014 (142)
14	DDI	ss1427108889	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1576632422	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1629796981	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1672791014	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1933502474	Feb 12, 2016 (147)
19	USC_VALOUEV	ss2155867577	Dec 20, 2016 (150)
20	GRF	ss2700234559	Nov 08, 2017 (151)
21	GNOMAD	ss2917065791	Nov 08, 2017 (151)
22	SWEGEN	ss3010631571	Nov 08, 2017 (151)
23	BIOINF_KMB_FNS_UNIBA	ss3027566595	Nov 08, 2017 (151)
24	CSHL	ss3350335568	Nov 08, 2017 (151)
25	EVA_DECODE	ss3694826741	Jul 13, 2019 (153)
26	ACPOP	ss3739534893	Jul 13, 2019 (153)
27	EVA	ss3751177370	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3816504327	Jul 13, 2019 (153)
29	EVA	ss3840283107	Apr 27, 2020 (154)
30	SGDP_PRJ	ss3879485805	Apr 27, 2020 (154)
31	KRGDB	ss3928290218	Apr 27, 2020 (154)
32	KOGIC	ss3973113309	Apr 27, 2020 (154)
33	TOMMO_GENOMICS	ss5208959858	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5292923212	Oct 16, 2022 (156)
35	EVA	ss5409319977	Oct 16, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5591481122	Oct 16, 2022 (156)
37	SANFORD_IMAGENETICS	ss5654298016	Oct 16, 2022 (156)
38	TOMMO_GENOMICS	ss5760537570	Oct 16, 2022 (156)
39	YY_MCH	ss5813901791	Oct 16, 2022 (156)
40	EVA	ss5839149237	Oct 16, 2022 (156)
41	EVA	ss5924192269	Oct 16, 2022 (156)
42	EVA	ss5945709727	Oct 16, 2022 (156)
43	1000Genomes	NC_000013.10 - 19075966	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000013.11 - 18501826	Oct 16, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 19075966	Oct 12, 2018 (152)
46	The Danish reference pan genome	NC_000013.10 - 19075966	Apr 27, 2020 (154)
47	gnomAD - Genomes Submission ignored due to conflicting rows: Row 424201807 (NC_000013.11:18501825:C:A 1/139940) Row 424201808 (NC_000013.11:18501825:C:T 21642/139474)	-	Apr 26, 2021 (155)
48	gnomAD - Genomes Submission ignored due to conflicting rows: Row 424201807 (NC_000013.11:18501825:C:A 1/139940) Row 424201808 (NC_000013.11:18501825:C:T 21642/139474)	-	Apr 26, 2021 (155)
49	Genome of the Netherlands Release 5	NC_000013.10 - 19075966	Apr 27, 2020 (154)
50	KOREAN population from KRGDB	NC_000013.10 - 19075966	Apr 27, 2020 (154)
51	Korean Genome Project	NC_000013.11 - 18501826	Apr 27, 2020 (154)
52	Northern Sweden	NC_000013.10 - 19075966	Jul 13, 2019 (153)
53	Qatari	NC_000013.10 - 19075966	Apr 27, 2020 (154)
54	SGDP_PRJ	NC_000013.10 - 19075966	Apr 27, 2020 (154)
55	Siberian	NC_000013.10 - 19075966	Apr 27, 2020 (154)
56	8.3KJPN	NC_000013.10 - 19075966	Apr 26, 2021 (155)
57	14KJPN	NC_000013.11 - 18501826	Oct 16, 2022 (156)
58	UK 10K study - Twins	NC_000013.10 - 19075966	Oct 12, 2018 (152)
59	ALFA	NC_000013.11 - 18501826	Apr 26, 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)
rs4459417	Aug 27, 2003 (117)
rs72488140	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
15899418264	NC_000013.11:18501825:C:A	NC_000013.11:18501825:C:A	(self)
ss118370048, ss206795183, ss254803810, ss281615903	NC_000013.9:17973965:C:T	NC_000013.11:18501825:C:T	(self)
60144256, 33405243, 3197043, 14897966, 35467612, 12819758, 15544404, 31502785, 8383931, 66929165, 33405243, ss226054434, ss236155628, ss242671307, ss659106544, ss990137866, ss1347308513, ss1427108889, ss1576632422, ss1629796981, ss1672791014, ss1933502474, ss2155867577, ss2700234559, ss2917065791, ss3010631571, ss3350335568, ss3739534893, ss3751177370, ss3840283107, ss3879485805, ss3928290218, ss5208959858, ss5409319977, ss5654298016, ss5839149237, ss5945709727	NC_000013.10:19075965:C:T	NC_000013.11:18501825:C:T	(self)
79007057, 29491310, 94374674, 15899418264, ss3027566595, ss3694826741, ss3816504327, ss3973113309, ss5292923212, ss5591481122, ss5760537570, ss5813901791, ss5924192269	NC_000013.11:18501825:C:T	NC_000013.11:18501825:C:T	(self)
ss5485319, ss5986905, ss103098255	NT_024524.14:55965:C:T	NC_000013.11:18501825:C:T	(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 rs4085685

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

rs4085685