Name: rs9687655
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.

rs9687655

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:151392971 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.494934 (131004/264690, TOPMED)
C=0.497086 (69251/139314, GnomAD)
C=0.48528 (13713/28258, 14KJPN) (+ 11 more)
C=0.48132 (8067/16760, 8.3KJPN)
T=0.47918 (7826/16332, ALFA)
C=0.4803 (3076/6404, 1000G_30x)
C=0.4866 (2437/5008, 1000G)
T=0.4902 (2196/4480, Estonian)
T=0.4511 (1318/2922, KOREAN)
T=0.4443 (814/1832, Korea1K)
T=0.370 (369/998, GoNL)
T=0.405 (243/600, NorthernSweden)
C=0.346 (117/338, SGDP_PRJ)
T=0.250 (54/216, Qatari)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC36A1 : Intron Variant
LOC105378234 : 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	C=0.52082	T=0.47918
European	Sub	12080	C=0.57417	T=0.42583
African	Sub	2816	C=0.2369	T=0.7631
African Others	Sub	108	C=0.139	T=0.861
African American	Sub	2708	C=0.2408	T=0.7592
Asian	Sub	108	C=0.491	T=0.509
East Asian	Sub	84	C=0.50	T=0.50
Other Asian	Sub	24	C=0.46	T=0.54
Latin American 1	Sub	146	C=0.548	T=0.452
Latin American 2	Sub	610	C=0.767	T=0.233
South Asian	Sub	94	C=0.63	T=0.37
Other	Sub	478	C=0.508	T=0.492

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	264690	C=0.505066	T=0.494934
gnomAD - Genomes	Global	Study-wide	139314	C=0.497086	T=0.502914
gnomAD - Genomes	European	Sub	75602	C=0.59108	T=0.40892
gnomAD - Genomes	African	Sub	41590	C=0.25170	T=0.74830
gnomAD - Genomes	American	Sub	13570	C=0.67553	T=0.32447
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	C=0.5900	T=0.4100
gnomAD - Genomes	East Asian	Sub	3094	C=0.5979	T=0.4021
gnomAD - Genomes	Other	Sub	2146	C=0.5242	T=0.4758
14KJPN	JAPANESE	Study-wide	28258	C=0.48528	T=0.51472
8.3KJPN	JAPANESE	Study-wide	16760	C=0.48132	T=0.51868
Allele Frequency Aggregator	Total	Global	16332	C=0.52082	T=0.47918
Allele Frequency Aggregator	European	Sub	12080	C=0.57417	T=0.42583
Allele Frequency Aggregator	African	Sub	2816	C=0.2369	T=0.7631
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.767	T=0.233
Allele Frequency Aggregator	Other	Sub	478	C=0.508	T=0.492
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.548	T=0.452
Allele Frequency Aggregator	Asian	Sub	108	C=0.491	T=0.509
Allele Frequency Aggregator	South Asian	Sub	94	C=0.63	T=0.37
1000Genomes_30x	Global	Study-wide	6404	C=0.4803	T=0.5197
1000Genomes_30x	African	Sub	1786	C=0.1842	T=0.8158
1000Genomes_30x	Europe	Sub	1266	C=0.5900	T=0.4100
1000Genomes_30x	South Asian	Sub	1202	C=0.5158	T=0.4842
1000Genomes_30x	East Asian	Sub	1170	C=0.5821	T=0.4179
1000Genomes_30x	American	Sub	980	C=0.713	T=0.287
1000Genomes	Global	Study-wide	5008	C=0.4866	T=0.5134
1000Genomes	African	Sub	1322	C=0.1884	T=0.8116
1000Genomes	East Asian	Sub	1008	C=0.5724	T=0.4276
1000Genomes	Europe	Sub	1006	C=0.6014	T=0.3986
1000Genomes	South Asian	Sub	978	C=0.526	T=0.474
1000Genomes	American	Sub	694	C=0.709	T=0.291
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5098	T=0.4902
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.5489	T=0.4511
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5557	T=0.4443
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.630	T=0.370
Northern Sweden	ACPOP	Study-wide	600	C=0.595	T=0.405
SGDP_PRJ	Global	Study-wide	338	C=0.346	T=0.654
Qatari	Global	Study-wide	216	C=0.750	T=0.250

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 5	NC_000005.10:g.151392971C>T
GRCh37.p13 chr 5	NC_000005.9:g.150772532C>T

Gene: SLC36A1, solute carrier family 36 member 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC36A1 transcript variant 2	NM_001308150.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant 3	NM_001308151.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant 4	NM_001349740.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant 1	NM_078483.4:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X11	XM_011537591.2:c.-89-1831… XM_011537591.2:c.-89-18310C>T	N/A	Intron Variant
SLC36A1 transcript variant X20	XM_006714759.5:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X2	XM_011537580.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X3	XM_011537581.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X10	XM_011537584.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X5	XM_011537585.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X6	XM_011537586.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X21	XM_011537587.4:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X7	XM_011537589.4:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X9	XM_011537590.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X12	XM_011537592.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X16	XM_011537595.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X22	XM_011537596.3:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X13	XM_017009216.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X18	XM_017009217.2:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X1	XM_047416920.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X4	XM_047416921.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X8	XM_047416923.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X14	XM_047416924.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X15	XM_047416925.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X17	XM_047416927.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X19	XM_047416928.1:c.	N/A	Genic Upstream Transcript Variant
SLC36A1 transcript variant X23	XM_047416929.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC105378234, uncharacterized LOC105378234 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378234 transcript variant X3	XR_007059004.1:n.	N/A	Intron Variant
LOC105378234 transcript variant X5	XR_007059005.1:n.	N/A	Intron Variant
LOC105378234 transcript variant X6	XR_007059006.1:n.	N/A	Intron Variant
LOC105378234 transcript variant X1	XR_944423.4:n.	N/A	Intron Variant
LOC105378234 transcript variant X2	XR_944425.4:n.	N/A	Intron Variant
LOC105378234 transcript variant X4	XR_944426.4: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	C=	T
GRCh38.p14 chr 5	NC_000005.10:g.151392971=	NC_000005.10:g.151392971C>T
GRCh37.p13 chr 5	NC_000005.9:g.150772532=	NC_000005.9:g.150772532C>T
SLC36A1 transcript variant X11	XM_011537591.2:c.-89-18310=	XM_011537591.2:c.-89-18310C>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#.

34 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss13487824	Dec 05, 2003 (119)
2	CSHL-HAPMAP	ss17856721	Feb 28, 2004 (126)
3	SSAHASNP	ss22279367	Apr 05, 2004 (126)
4	BCMHGSC_JDW	ss93291128	Mar 24, 2008 (129)
5	GMI	ss278532558	May 04, 2012 (144)
6	1000GENOMES	ss332888542	May 09, 2011 (144)
7	SSMP	ss652701842	Apr 25, 2013 (144)
8	EVA-GONL	ss982263422	Aug 21, 2014 (144)
9	1000GENOMES	ss1317766569	Aug 21, 2014 (144)
10	WEILL_CORNELL_DGM	ss1925517436	Feb 12, 2016 (147)
11	GRF	ss2707096003	Nov 08, 2017 (151)
12	GNOMAD	ss2832349645	Nov 08, 2017 (151)
13	SWEGEN	ss2998011656	Nov 08, 2017 (151)
14	EGCUT_WGS	ss3665933026	Jul 13, 2019 (153)
15	ACPOP	ss3732931958	Jul 13, 2019 (153)
16	EVA	ss3764230925	Jul 13, 2019 (153)
17	PACBIO	ss3785285310	Jul 13, 2019 (153)
18	PACBIO	ss3790662522	Jul 13, 2019 (153)
19	PACBIO	ss3795539569	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3807399229	Jul 13, 2019 (153)
21	SGDP_PRJ	ss3863257875	Apr 26, 2020 (154)
22	KRGDB	ss3909936244	Apr 26, 2020 (154)
23	KOGIC	ss3957908246	Apr 26, 2020 (154)
24	TOPMED	ss4683512950	Apr 26, 2021 (155)
25	TOMMO_GENOMICS	ss5174764526	Apr 26, 2021 (155)
26	1000G_HIGH_COVERAGE	ss5266323624	Oct 13, 2022 (156)
27	EVA	ss5361846587	Oct 13, 2022 (156)
28	EVA	ss5508258144	Oct 13, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5551218697	Oct 13, 2022 (156)
30	SANFORD_IMAGENETICS	ss5639153300	Oct 13, 2022 (156)
31	TOMMO_GENOMICS	ss5712024175	Oct 13, 2022 (156)
32	YY_MCH	ss5806881892	Oct 13, 2022 (156)
33	EVA	ss5835827357	Oct 13, 2022 (156)
34	EVA	ss5967634691	Oct 13, 2022 (156)
35	1000Genomes	NC_000005.9 - 150772532	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000005.10 - 151392971	Oct 13, 2022 (156)
37	Genetic variation in the Estonian population	NC_000005.9 - 150772532	Oct 12, 2018 (152)
38	gnomAD - Genomes	NC_000005.10 - 151392971	Apr 26, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000005.9 - 150772532	Apr 26, 2020 (154)
40	KOREAN population from KRGDB	NC_000005.9 - 150772532	Apr 26, 2020 (154)
41	Korean Genome Project	NC_000005.10 - 151392971	Apr 26, 2020 (154)
42	Northern Sweden	NC_000005.9 - 150772532	Jul 13, 2019 (153)
43	Qatari	NC_000005.9 - 150772532	Apr 26, 2020 (154)
44	SGDP_PRJ	NC_000005.9 - 150772532	Apr 26, 2020 (154)
45	8.3KJPN	NC_000005.9 - 150772532	Apr 26, 2021 (155)
46	14KJPN	NC_000005.10 - 151392971	Oct 13, 2022 (156)
47	TopMed	NC_000005.10 - 151392971	Apr 26, 2021 (155)
48	ALFA	NC_000005.10 - 151392971	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)
rs11957109	Mar 10, 2006 (126)
rs148792857	Jul 01, 2015 (144)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93291128, ss278532558	NC_000005.8:150752724:C:T	NC_000005.10:151392970:C:T	(self)
29464661, 11671274, 7278735, 17113638, 6216823, 7559366, 15274855, 32733833, ss332888542, ss652701842, ss982263422, ss1317766569, ss1925517436, ss2707096003, ss2832349645, ss2998011656, ss3665933026, ss3732931958, ss3764230925, ss3785285310, ss3790662522, ss3795539569, ss3863257875, ss3909936244, ss5174764526, ss5361846587, ss5508258144, ss5639153300, ss5835827357, ss5967634691	NC_000005.9:150772531:C:T	NC_000005.10:151392970:C:T	(self)
38744632, 208399083, 14286247, 45861279, 520890507, 1338862246, ss3807399229, ss3957908246, ss4683512950, ss5266323624, ss5551218697, ss5712024175, ss5806881892	NC_000005.10:151392970:C:T	NC_000005.10:151392970:C:T	(self)
ss13487824, ss17856721, ss22279367	NT_029289.10:11935467:C:T	NC_000005.10:151392970: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 rs9687655

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs9687655