Name: rs28362756
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.

rs28362756

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:50356865 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.081204 (21494/264690, TOPMED)
C=0.078508 (10976/139808, GnomAD)
C=0.13754 (3884/28240, 14KJPN) (+ 12 more)
C=0.01254 (223/17782, ALFA)
C=0.13687 (2294/16760, 8.3KJPN)
C=0.0982 (629/6404, 1000G_30x)
C=0.0956 (479/5008, 1000G)
C=0.0116 (52/4480, Estonian)
C=0.0013 (5/3854, ALSPAC)
C=0.0008 (3/3708, TWINSUK)
C=0.0956 (280/2930, KOREAN)
C=0.002 (1/600, NorthernSweden)
C=0.046 (10/216, Qatari)
T=0.47 (34/72, SGDP_PRJ)
T=0.0 (0/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105372114 : 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	17782	T=0.98746	A=0.00000, C=0.01254
European	Sub	14260	T=0.99614	A=0.00000, C=0.00386
African	Sub	2000	T=0.9195	A=0.0000, C=0.0805
African Others	Sub	82	T=0.91	A=0.00, C=0.09
African American	Sub	1918	T=0.9197	A=0.0000, C=0.0803
Asian	Sub	84	T=1.00	A=0.00, C=0.00
East Asian	Sub	66	T=1.00	A=0.00, C=0.00
Other Asian	Sub	18	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	136	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	580	T=1.000	A=0.000, C=0.000
South Asian	Sub	98	T=1.00	A=0.00, C=0.00
Other	Sub	624	T=0.989	A=0.000, C=0.011

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	T=0.918796	C=0.081204
gnomAD - Genomes	Global	Study-wide	139808	T=0.921492	C=0.078508
gnomAD - Genomes	European	Sub	75802	T=0.99133	C=0.00867
gnomAD - Genomes	African	Sub	41798	T=0.77171	C=0.22829
gnomAD - Genomes	American	Sub	13624	T=0.97027	C=0.02973
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	T=0.9997	C=0.0003
gnomAD - Genomes	East Asian	Sub	3122	T=0.9209	C=0.0791
gnomAD - Genomes	Other	Sub	2146	T=0.9422	C=0.0578
14KJPN	JAPANESE	Study-wide	28240	T=0.86246	C=0.13754
Allele Frequency Aggregator	Total	Global	17782	T=0.98746	A=0.00000, C=0.01254
Allele Frequency Aggregator	European	Sub	14260	T=0.99614	A=0.00000, C=0.00386
Allele Frequency Aggregator	African	Sub	2000	T=0.9195	A=0.0000, C=0.0805
Allele Frequency Aggregator	Other	Sub	624	T=0.989	A=0.000, C=0.011
Allele Frequency Aggregator	Latin American 2	Sub	580	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	136	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	84	T=1.00	A=0.00, C=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.86313	C=0.13687
1000Genomes_30x	Global	Study-wide	6404	T=0.9018	C=0.0982
1000Genomes_30x	African	Sub	1786	T=0.7268	C=0.2732
1000Genomes_30x	Europe	Sub	1266	T=0.9889	C=0.0111
1000Genomes_30x	South Asian	Sub	1202	T=0.9933	C=0.0067
1000Genomes_30x	East Asian	Sub	1170	T=0.9154	C=0.0846
1000Genomes_30x	American	Sub	980	T=0.980	C=0.020
1000Genomes	Global	Study-wide	5008	T=0.9044	C=0.0956
1000Genomes	African	Sub	1322	T=0.7277	C=0.2723
1000Genomes	East Asian	Sub	1008	T=0.9147	C=0.0853
1000Genomes	Europe	Sub	1006	T=0.9871	C=0.0129
1000Genomes	South Asian	Sub	978	T=0.997	C=0.003
1000Genomes	American	Sub	694	T=0.976	C=0.024
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9884	C=0.0116
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9987	C=0.0013
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9992	C=0.0008
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.9044	C=0.0956
Northern Sweden	ACPOP	Study-wide	600	T=0.998	C=0.002
Qatari	Global	Study-wide	216	T=0.954	C=0.046
SGDP_PRJ	Global	Study-wide	72	T=0.47	C=0.53
Siberian	Global	Study-wide	2	T=0.0	C=1.0

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 18	NC_000018.10:g.50356865T>A
GRCh38.p14 chr 18	NC_000018.10:g.50356865T>C
GRCh37.p13 chr 18	NC_000018.9:g.47883235T>A
GRCh37.p13 chr 18	NC_000018.9:g.47883235T>C
GRCh38.p14 chr 18 alt locus HSCHR18_1_CTG1_1	NW_003315956.1:g.64672T>A
GRCh38.p14 chr 18 alt locus HSCHR18_1_CTG1_1	NW_003315956.1:g.64672T>C

Gene: LOC105372114, uncharacterized LOC105372114 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372114 transcript	XR_935466.3: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=	A	C
GRCh38.p14 chr 18	NC_000018.10:g.50356865=	NC_000018.10:g.50356865T>A	NC_000018.10:g.50356865T>C
GRCh37.p13 chr 18	NC_000018.9:g.47883235=	NC_000018.9:g.47883235T>A	NC_000018.9:g.47883235T>C
GRCh38.p14 chr 18 alt locus HSCHR18_1_CTG1_1	NW_003315956.1:g.64672=	NW_003315956.1:g.64672T>A	NW_003315956.1:g.64672T>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#.

45 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss35078014	May 24, 2005 (125)
2	HGSV	ss81481311	Dec 14, 2007 (130)
3	ILLUMINA	ss159415296	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss169801214	Jul 04, 2010 (132)
5	BUSHMAN	ss203269409	Jul 04, 2010 (132)
6	1000GENOMES	ss211889053	Jul 14, 2010 (132)
7	1000GENOMES	ss227868599	Jul 14, 2010 (132)
8	1000GENOMES	ss243720150	Jul 15, 2010 (132)
9	TISHKOFF	ss565650997	Apr 25, 2013 (138)
10	SSMP	ss661483604	Apr 25, 2013 (138)
11	ILLUMINA	ss832926957	Aug 21, 2014 (142)
12	ILLUMINA	ss833517787	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1081512613	Aug 21, 2014 (142)
14	1000GENOMES	ss1361099545	Aug 21, 2014 (142)
15	EVA_UK10K_ALSPAC	ss1636914081	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1679908114	Apr 01, 2015 (144)
17	EVA_DECODE	ss1697804940	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1809058566	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1937213050	Feb 12, 2016 (147)
20	USC_VALOUEV	ss2157882045	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2221727497	Dec 20, 2016 (150)
22	GRF	ss2702470554	Nov 08, 2017 (151)
23	GNOMAD	ss2956900509	Nov 08, 2017 (151)
24	SWEGEN	ss3016556435	Nov 08, 2017 (151)
25	EGCUT_WGS	ss3683398209	Jul 13, 2019 (153)
26	EVA_DECODE	ss3701694684	Jul 13, 2019 (153)
27	ACPOP	ss3742558080	Jul 13, 2019 (153)
28	EVA	ss3755411722	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3820671669	Jul 13, 2019 (153)
30	EVA	ss3835177785	Apr 27, 2020 (154)
31	SGDP_PRJ	ss3887056844	Apr 27, 2020 (154)
32	KRGDB	ss3936932231	Apr 27, 2020 (154)
33	TOPMED	ss5057366338	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5225254538	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5305357731	Oct 16, 2022 (156)
36	EVA	ss5431542146	Oct 16, 2022 (156)
37	HUGCELL_USP	ss5498120870	Oct 16, 2022 (156)
38	EVA	ss5511944487	Oct 16, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5610233093	Oct 16, 2022 (156)
40	SANFORD_IMAGENETICS	ss5661330508	Oct 16, 2022 (156)
41	TOMMO_GENOMICS	ss5783070848	Oct 16, 2022 (156)
42	YY_MCH	ss5817112205	Oct 16, 2022 (156)
43	EVA	ss5852060290	Oct 16, 2022 (156)
44	EVA	ss5874158159	Oct 16, 2022 (156)
45	EVA	ss5952748386	Oct 16, 2022 (156)
46	1000Genomes	NC_000018.9 - 47883235	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000018.10 - 50356865	Oct 16, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 47883235	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000018.9 - 47883235	Oct 12, 2018 (152)
50	gnomAD - Genomes	NC_000018.10 - 50356865	Apr 26, 2021 (155)
51	KOREAN population from KRGDB	NC_000018.9 - 47883235	Apr 27, 2020 (154)
52	Northern Sweden	NC_000018.9 - 47883235	Jul 13, 2019 (153)
53	Qatari	NC_000018.9 - 47883235	Apr 27, 2020 (154)
54	SGDP_PRJ	NC_000018.9 - 47883235	Apr 27, 2020 (154)
55	Siberian	NC_000018.9 - 47883235	Apr 27, 2020 (154)
56	8.3KJPN	NC_000018.9 - 47883235	Apr 26, 2021 (155)
57	14KJPN	NC_000018.10 - 50356865	Oct 16, 2022 (156)
58	TopMed	NC_000018.10 - 50356865	Apr 26, 2021 (155)
59	UK 10K study - Twins	NC_000018.9 - 47883235	Oct 12, 2018 (152)
60	ALFA	NC_000018.10 - 50356865	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)
rs58171543	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1748024675	NC_000018.10:50356864:T:A	NC_000018.10:50356864:T:A	(self)
ss35078014, ss81481311, ss169801214, ss203269409, ss211889053, ss1697804940	NC_000018.8:46137232:T:C	NC_000018.10:50356864:T:C	(self)
74431144, 41241081, 29136457, 44109625, 15842945, 19254972, 39073824, 10398399, 83223845, 41241081, ss227868599, ss243720150, ss565650997, ss661483604, ss832926957, ss833517787, ss1081512613, ss1361099545, ss1636914081, ss1679908114, ss1809058566, ss1937213050, ss2157882045, ss2702470554, ss2956900509, ss3016556435, ss3683398209, ss3742558080, ss3755411722, ss3835177785, ss3887056844, ss3936932231, ss5225254538, ss5431542146, ss5511944487, ss5661330508, ss5952748386	NC_000018.9:47883234:T:C	NC_000018.10:50356864:T:C	(self)
97759028, 525081449, 116907952, 272912001, 1748024675, ss2221727497, ss3701694684, ss3820671669, ss5057366338, ss5305357731, ss5498120870, ss5610233093, ss5783070848, ss5817112205, ss5852060290, ss5874158159	NC_000018.10:50356864:T:C	NC_000018.10:50356864:T:C	(self)
ss159415296	NT_010966.14:29372336:T:C	NC_000018.10:50356864: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 rs28362756

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

rs28362756