Name: rs17109622
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.

rs17109622

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:83045052 (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: A>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.123344 (32648/264690, TOPMED)
C=0.126977 (17787/140080, GnomAD)
C=0.00163 (46/28258, 14KJPN) (+ 18 more)
C=0.12888 (3311/25690, ALFA)
C=0.00179 (30/16760, 8.3KJPN)
C=0.1313 (841/6404, 1000G_30x)
C=0.1280 (641/5008, 1000G)
C=0.1326 (594/4480, Estonian)
C=0.1489 (574/3854, ALSPAC)
C=0.1330 (493/3708, TWINSUK)
C=0.0034 (10/2922, KOREAN)
C=0.0066 (12/1832, Korea1K)
C=0.1203 (197/1638, HapMap)
C=0.166 (166/998, GoNL)
C=0.103 (62/600, NorthernSweden)
C=0.167 (36/216, Qatari)
C=0.005 (1/212, Vietnamese)
A=0.421 (48/114, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
A=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01362 : 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	25690	A=0.87112	C=0.12888
European	Sub	17392	A=0.86017	C=0.13983
African	Sub	3624	A=0.8706	C=0.1294
African Others	Sub	126	A=0.889	C=0.111
African American	Sub	3498	A=0.8699	C=0.1301
Asian	Sub	160	A=1.000	C=0.000
East Asian	Sub	102	A=1.000	C=0.000
Other Asian	Sub	58	A=1.00	C=0.00
Latin American 1	Sub	292	A=0.887	C=0.113
Latin American 2	Sub	2770	A=0.9300	C=0.0700
South Asian	Sub	110	A=0.718	C=0.282
Other	Sub	1342	A=0.8867	C=0.1133

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	A=0.876656	C=0.123344
gnomAD - Genomes	Global	Study-wide	140080	A=0.873023	C=0.126977
gnomAD - Genomes	European	Sub	75874	A=0.86633	C=0.13367
gnomAD - Genomes	African	Sub	41970	A=0.87274	C=0.12726
gnomAD - Genomes	American	Sub	13634	A=0.88551	C=0.11449
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.8586	C=0.1414
gnomAD - Genomes	East Asian	Sub	3130	A=0.9965	C=0.0035
gnomAD - Genomes	Other	Sub	2148	A=0.8780	C=0.1220
14KJPN	JAPANESE	Study-wide	28258	A=0.99837	C=0.00163
Allele Frequency Aggregator	Total	Global	25690	A=0.87112	C=0.12888
Allele Frequency Aggregator	European	Sub	17392	A=0.86017	C=0.13983
Allele Frequency Aggregator	African	Sub	3624	A=0.8706	C=0.1294
Allele Frequency Aggregator	Latin American 2	Sub	2770	A=0.9300	C=0.0700
Allele Frequency Aggregator	Other	Sub	1342	A=0.8867	C=0.1133
Allele Frequency Aggregator	Latin American 1	Sub	292	A=0.887	C=0.113
Allele Frequency Aggregator	Asian	Sub	160	A=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	110	A=0.718	C=0.282
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99821	C=0.00179
1000Genomes_30x	Global	Study-wide	6404	A=0.8687	C=0.1313
1000Genomes_30x	African	Sub	1786	A=0.8768	C=0.1232
1000Genomes_30x	Europe	Sub	1266	A=0.8602	C=0.1398
1000Genomes_30x	South Asian	Sub	1202	A=0.7296	C=0.2704
1000Genomes_30x	East Asian	Sub	1170	A=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	A=0.880	C=0.120
1000Genomes	Global	Study-wide	5008	A=0.8720	C=0.1280
1000Genomes	African	Sub	1322	A=0.8767	C=0.1233
1000Genomes	East Asian	Sub	1008	A=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	A=0.8658	C=0.1342
1000Genomes	South Asian	Sub	978	A=0.736	C=0.264
1000Genomes	American	Sub	694	A=0.879	C=0.121
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8674	C=0.1326
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8511	C=0.1489
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8670	C=0.1330
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9966	C=0.0034
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9934	C=0.0066
HapMap	Global	Study-wide	1638	A=0.8797	C=0.1203
HapMap	African	Sub	690	A=0.890	C=0.110
HapMap	American	Sub	600	A=0.830	C=0.170
HapMap	Europe	Sub	176	A=0.892	C=0.108
HapMap	Asian	Sub	172	A=1.000	C=0.000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.834	C=0.166
Northern Sweden	ACPOP	Study-wide	600	A=0.897	C=0.103
Qatari	Global	Study-wide	216	A=0.833	C=0.167
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.995	C=0.005
SGDP_PRJ	Global	Study-wide	114	A=0.421	C=0.579
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	C=0.12
Siberian	Global	Study-wide	2	A=0.5	C=0.5

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.83045052A>C
GRCh37.p13 chr 1	NC_000001.10:g.83510735A>C

Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01362 transcript	NR_147074.1: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	A=	C
GRCh38.p14 chr 1	NC_000001.11:g.83045052=	NC_000001.11:g.83045052A>C
GRCh37.p13 chr 1	NC_000001.10:g.83510735=	NC_000001.10:g.83510735A>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#.

60 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23145045	Sep 20, 2004 (123)
2	ABI	ss43969065	Mar 13, 2006 (126)
3	AFFY	ss66326958	Nov 30, 2006 (127)
4	AFFY	ss76020554	Dec 07, 2007 (129)
5	KRIBB_YJKIM	ss83195187	Dec 14, 2007 (130)
6	HUMANGENOME_JCVI	ss99223092	Feb 05, 2009 (130)
7	1000GENOMES	ss108366509	Jan 23, 2009 (130)
8	1000GENOMES	ss110735360	Jan 25, 2009 (130)
9	ENSEMBL	ss138879077	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss163588446	Jul 04, 2010 (132)
11	AFFY	ss170505641	Jul 04, 2010 (132)
12	BUSHMAN	ss198701872	Jul 04, 2010 (132)
13	1000GENOMES	ss218491732	Jul 14, 2010 (132)
14	1000GENOMES	ss230612736	Jul 14, 2010 (132)
15	PJP	ss290550844	May 09, 2011 (134)
16	TISHKOFF	ss554361957	Apr 25, 2013 (138)
17	SSMP	ss648176077	Apr 25, 2013 (138)
18	EVA-GONL	ss975365458	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1068043514	Aug 21, 2014 (142)
20	1000GENOMES	ss1291668453	Aug 21, 2014 (142)
21	EVA_GENOME_DK	ss1574191687	Apr 01, 2015 (144)
22	EVA_DECODE	ss1584739388	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1600582587	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1643576620	Apr 01, 2015 (144)
25	EVA_SVP	ss1712348333	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1794651192	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1918568436	Feb 12, 2016 (147)
28	GENOMED	ss1966794053	Jul 19, 2016 (147)
29	JJLAB	ss2019804867	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2147821954	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2164128763	Dec 20, 2016 (150)
32	GRF	ss2697744127	Nov 08, 2017 (151)
33	GNOMAD	ss2757360494	Nov 08, 2017 (151)
34	SWEGEN	ss2987125270	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3023665213	Nov 08, 2017 (151)
36	CSHL	ss3343543715	Nov 08, 2017 (151)
37	URBANLAB	ss3646705703	Oct 11, 2018 (152)
38	EGCUT_WGS	ss3655205767	Jul 12, 2019 (153)
39	EVA_DECODE	ss3687150742	Jul 12, 2019 (153)
40	ACPOP	ss3727216989	Jul 12, 2019 (153)
41	EVA	ss3746440298	Jul 12, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3799446373	Jul 12, 2019 (153)
43	EVA	ss3826271337	Apr 25, 2020 (154)
44	EVA	ss3836524603	Apr 25, 2020 (154)
45	EVA	ss3841931808	Apr 25, 2020 (154)
46	SGDP_PRJ	ss3849250147	Apr 25, 2020 (154)
47	KRGDB	ss3894301457	Apr 25, 2020 (154)
48	KOGIC	ss3944881263	Apr 25, 2020 (154)
49	TOPMED	ss4456684412	Apr 25, 2021 (155)
50	TOMMO_GENOMICS	ss5144811223	Apr 25, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5242940046	Oct 12, 2022 (156)
52	EVA	ss5319972641	Oct 12, 2022 (156)
53	HUGCELL_USP	ss5443936915	Oct 12, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5515581078	Oct 12, 2022 (156)
55	SANFORD_IMAGENETICS	ss5625916419	Oct 12, 2022 (156)
56	TOMMO_GENOMICS	ss5669827591	Oct 12, 2022 (156)
57	YY_MCH	ss5800764981	Oct 12, 2022 (156)
58	EVA	ss5832218417	Oct 12, 2022 (156)
59	EVA	ss5909037144	Oct 12, 2022 (156)
60	EVA	ss5937764917	Oct 12, 2022 (156)
61	1000Genomes	NC_000001.10 - 83510735	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000001.11 - 83045052	Oct 12, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 83510735	Oct 11, 2018 (152)
64	Genetic variation in the Estonian population	NC_000001.10 - 83510735	Oct 11, 2018 (152)
65	The Danish reference pan genome	NC_000001.10 - 83510735	Apr 25, 2020 (154)
66	gnomAD - Genomes	NC_000001.11 - 83045052	Apr 25, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000001.10 - 83510735	Apr 25, 2020 (154)
68	HapMap	NC_000001.11 - 83045052	Apr 25, 2020 (154)
69	KOREAN population from KRGDB	NC_000001.10 - 83510735	Apr 25, 2020 (154)
70	Korean Genome Project	NC_000001.11 - 83045052	Apr 25, 2020 (154)
71	Northern Sweden	NC_000001.10 - 83510735	Jul 12, 2019 (153)
72	Qatari	NC_000001.10 - 83510735	Apr 25, 2020 (154)
73	SGDP_PRJ	NC_000001.10 - 83510735	Apr 25, 2020 (154)
74	Siberian	NC_000001.10 - 83510735	Apr 25, 2020 (154)
75	8.3KJPN	NC_000001.10 - 83510735	Apr 25, 2021 (155)
76	14KJPN	NC_000001.11 - 83045052	Oct 12, 2022 (156)
77	TopMed	NC_000001.11 - 83045052	Apr 25, 2021 (155)
78	UK 10K study - Twins	NC_000001.10 - 83510735	Oct 11, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000001.10 - 83510735	Jul 12, 2019 (153)
80	ALFA	NC_000001.11 - 83045052	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)
rs57584414	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66326958, ss76020554, ss108366509, ss110735360, ss163588446, ss170505641, ss198701872, ss290550844, ss1584739388, ss1712348333	NC_000001.9:83283322:A:C	NC_000001.11:83045051:A:C	(self)
2415631, 1325837, 944015, 1583069, 572458, 1478851, 501854, 610366, 1267127, 338308, 2780530, 1325837, 284375, ss218491732, ss230612736, ss554361957, ss648176077, ss975365458, ss1068043514, ss1291668453, ss1574191687, ss1600582587, ss1643576620, ss1794651192, ss1918568436, ss1966794053, ss2019804867, ss2147821954, ss2697744127, ss2757360494, ss2987125270, ss3343543715, ss3655205767, ss3727216989, ss3746440298, ss3826271337, ss3836524603, ss3849250147, ss3894301457, ss5144811223, ss5319972641, ss5625916419, ss5832218417, ss5937764917	NC_000001.10:83510734:A:C	NC_000001.11:83045051:A:C	(self)
3107013, 17048317, 112910, 1259264, 3664695, 20290747, 12323825276, ss2164128763, ss3023665213, ss3646705703, ss3687150742, ss3799446373, ss3841931808, ss3944881263, ss4456684412, ss5242940046, ss5443936915, ss5515581078, ss5669827591, ss5800764981, ss5909037144	NC_000001.11:83045051:A:C	NC_000001.11:83045051:A:C	(self)
ss23145045, ss43969065, ss83195187, ss99223092, ss138879077	NT_032977.9:53482652:A:C	NC_000001.11:83045051:A: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 rs17109622

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

rs17109622