Name: rs7259189
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.

rs7259189

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:27931821 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.320669 (84878/264690, TOPMED)
G=0.38683 (10931/28258, 14KJPN)
G=0.39242 (6577/16760, 8.3KJPN) (+ 15 more)
G=0.16002 (2037/12730, ALFA)
G=0.3404 (2180/6404, 1000G_30x)
G=0.3391 (1698/5008, 1000G)
G=0.2929 (1312/4480, Estonian)
G=0.2566 (989/3854, ALSPAC)
G=0.2619 (971/3708, TWINSUK)
G=0.4413 (1293/2930, KOREAN)
G=0.261 (260/998, GoNL)
G=0.227 (136/600, NorthernSweden)
C=0.391 (97/248, SGDP_PRJ)
G=0.310 (67/216, Qatari)
G=0.402 (86/214, Vietnamese)
G=0.320 (64/200, HapMap)
G=0.25 (10/40, GENOME_DK)
C=0.41 (14/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02987 : 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	12730	C=0.83998	A=0.00000, G=0.16002
European	Sub	10700	C=0.82065	A=0.00000, G=0.17935
African	Sub	1126	C=0.9556	A=0.0000, G=0.0444
African Others	Sub	48	C=0.98	A=0.00, G=0.02
African American	Sub	1078	C=0.9545	A=0.0000, G=0.0455
Asian	Sub	32	C=0.94	A=0.00, G=0.06
East Asian	Sub	22	C=0.95	A=0.00, G=0.05
Other Asian	Sub	10	C=0.9	A=0.0, G=0.1
Latin American 1	Sub	74	C=1.00	A=0.00, G=0.00
Latin American 2	Sub	276	C=1.000	A=0.000, G=0.000
South Asian	Sub	66	C=0.98	A=0.00, G=0.02
Other	Sub	456	C=0.857	A=0.000, G=0.143

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=0.679331	G=0.320669
14KJPN	JAPANESE	Study-wide	28258	C=0.61317	G=0.38683
8.3KJPN	JAPANESE	Study-wide	16760	C=0.60758	G=0.39242
Allele Frequency Aggregator	Total	Global	12730	C=0.83998	A=0.00000, G=0.16002
Allele Frequency Aggregator	European	Sub	10700	C=0.82065	A=0.00000, G=0.17935
Allele Frequency Aggregator	African	Sub	1126	C=0.9556	A=0.0000, G=0.0444
Allele Frequency Aggregator	Other	Sub	456	C=0.857	A=0.000, G=0.143
Allele Frequency Aggregator	Latin American 2	Sub	276	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	74	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	66	C=0.98	A=0.00, G=0.02
Allele Frequency Aggregator	Asian	Sub	32	C=0.94	A=0.00, G=0.06
1000Genomes_30x	Global	Study-wide	6404	C=0.6594	A=0.0002, G=0.3404
1000Genomes_30x	African	Sub	1786	C=0.5554	A=0.0000, G=0.4446
1000Genomes_30x	Europe	Sub	1266	C=0.7038	A=0.0000, G=0.2962
1000Genomes_30x	South Asian	Sub	1202	C=0.7870	A=0.0008, G=0.2121
1000Genomes_30x	East Asian	Sub	1170	C=0.5821	A=0.0000, G=0.4179
1000Genomes_30x	American	Sub	980	C=0.728	A=0.000, G=0.272
1000Genomes	Global	Study-wide	5008	C=0.6609	G=0.3391
1000Genomes	African	Sub	1322	C=0.5575	G=0.4425
1000Genomes	East Asian	Sub	1008	C=0.5804	G=0.4196
1000Genomes	Europe	Sub	1006	C=0.7078	G=0.2922
1000Genomes	South Asian	Sub	978	C=0.791	G=0.209
1000Genomes	American	Sub	694	C=0.723	G=0.277
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7071	G=0.2929
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7434	G=0.2566
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7381	G=0.2619
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5587	G=0.4413
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.739	G=0.261
Northern Sweden	ACPOP	Study-wide	600	C=0.773	G=0.227
SGDP_PRJ	Global	Study-wide	248	C=0.391	G=0.609
Qatari	Global	Study-wide	216	C=0.690	G=0.310
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.598	G=0.402
HapMap	Global	Study-wide	200	C=0.680	G=0.320
HapMap	American	Sub	114	C=0.746	G=0.254
HapMap	Asian	Sub	86	C=0.59	G=0.41
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	G=0.25
Siberian	Global	Study-wide	34	C=0.41	G=0.59

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 19	NC_000019.10:g.27931821C>A
GRCh38.p14 chr 19	NC_000019.10:g.27931821C>G
GRCh37.p13 chr 19	NC_000019.9:g.28422729C>A
GRCh37.p13 chr 19	NC_000019.9:g.28422729C>G

Gene: LINC02987, long intergenic non-protein coding RNA 2987 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02987 transcript variant 6	NR_146733.1:n.	N/A	Intron Variant
LINC02987 transcript variant 7	NR_146734.1:n.	N/A	Intron Variant
LINC02987 transcript variant 8	NR_146735.1:n.	N/A	Intron Variant
LINC02987 transcript variant 1	NR_110687.1:n.	N/A	Genic Downstream Transcript Variant
LINC02987 transcript variant 2	NR_110688.2:n.	N/A	Genic Downstream Transcript Variant
LINC02987 transcript variant 3	NR_110689.2:n.	N/A	Genic Downstream Transcript Variant
LINC02987 transcript variant 4	NR_110690.1:n.	N/A	Genic Downstream Transcript Variant
LINC02987 transcript variant 5	NR_110691.2:n.	N/A	Genic Downstream Transcript Variant
LINC02987 transcript variant 9	NR_146736.1:n.	N/A	Genic Downstream Transcript 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=	A	G
GRCh38.p14 chr 19	NC_000019.10:g.27931821=	NC_000019.10:g.27931821C>A	NC_000019.10:g.27931821C>G
GRCh37.p13 chr 19	NC_000019.9:g.28422729=	NC_000019.9:g.28422729C>A	NC_000019.9:g.28422729C>G

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#.

65 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10942485	Jul 11, 2003 (116)
2	CSHL-HAPMAP	ss20071893	Feb 27, 2004 (120)
3	SSAHASNP	ss21547873	Apr 05, 2004 (121)
4	ABI	ss40973932	Mar 13, 2006 (126)
5	HGSV	ss84708542	Dec 15, 2007 (130)
6	HGSV	ss84829180	Dec 15, 2007 (130)
7	HUMANGENOME_JCVI	ss96262512	Feb 06, 2009 (130)
8	ENSEMBL	ss136288627	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss168037186	Jul 04, 2010 (132)
10	COMPLETE_GENOMICS	ss171659431	Jul 04, 2010 (132)
11	BUSHMAN	ss203725873	Jul 04, 2010 (132)
12	BCM-HGSC-SUB	ss208448125	Jul 04, 2010 (132)
13	1000GENOMES	ss237645768	Jul 15, 2010 (132)
14	1000GENOMES	ss243857238	Jul 15, 2010 (132)
15	GMI	ss283175961	May 04, 2012 (137)
16	PJP	ss292234359	May 09, 2011 (134)
17	TISHKOFF	ss565926546	Apr 25, 2013 (138)
18	SSMP	ss661788066	Apr 25, 2013 (138)
19	EVA-GONL	ss994209078	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1081838787	Aug 21, 2014 (142)
21	1000GENOMES	ss1362816819	Aug 21, 2014 (142)
22	DDI	ss1428377583	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1578604894	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1637786084	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1680780117	Apr 01, 2015 (144)
26	EVA_DECODE	ss1698260536	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1809266466	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1937700367	Feb 12, 2016 (147)
29	GENOMED	ss1968626248	Jul 19, 2016 (147)
30	JJLAB	ss2029625370	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2158164333	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2629310990	Nov 08, 2017 (151)
33	GRF	ss2702770653	Nov 08, 2017 (151)
34	GNOMAD	ss2961861198	Nov 08, 2017 (151)
35	SWEGEN	ss3017323659	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3028646613	Nov 08, 2017 (151)
37	CSHL	ss3352262374	Nov 08, 2017 (151)
38	URBANLAB	ss3650898003	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3684099081	Jul 13, 2019 (153)
40	EVA_DECODE	ss3702590523	Jul 13, 2019 (153)
41	ACPOP	ss3742960659	Jul 13, 2019 (153)
42	EVA	ss3755954823	Jul 13, 2019 (153)
43	PACBIO	ss3788505436	Jul 13, 2019 (153)
44	PACBIO	ss3793420141	Jul 13, 2019 (153)
45	PACBIO	ss3798306862	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3821206662	Jul 13, 2019 (153)
47	EVA	ss3835417209	Apr 27, 2020 (154)
48	EVA	ss3841330093	Apr 27, 2020 (154)
49	EVA	ss3846835626	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3888028473	Apr 27, 2020 (154)
51	KRGDB	ss3938105902	Apr 27, 2020 (154)
52	TOPMED	ss5071827285	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5227336202	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5306933134	Oct 16, 2022 (156)
55	EVA	ss5434277743	Oct 16, 2022 (156)
56	HUGCELL_USP	ss5499492775	Oct 16, 2022 (156)
57	EVA	ss5512076409	Oct 16, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5612519081	Oct 16, 2022 (156)
59	SANFORD_IMAGENETICS	ss5662218838	Oct 16, 2022 (156)
60	TOMMO_GENOMICS	ss5785834221	Oct 16, 2022 (156)
61	YY_MCH	ss5817522801	Oct 16, 2022 (156)
62	EVA	ss5840428383	Oct 16, 2022 (156)
63	EVA	ss5852252981	Oct 16, 2022 (156)
64	EVA	ss5927754523	Oct 16, 2022 (156)
65	EVA	ss5953628237	Oct 16, 2022 (156)
66	1000Genomes	NC_000019.9 - 28422729	Oct 12, 2018 (152)
67	1000Genomes_30x	NC_000019.10 - 27931821	Oct 16, 2022 (156)
68	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 28422729	Oct 12, 2018 (152)
69	Genetic variation in the Estonian population	NC_000019.9 - 28422729	Oct 12, 2018 (152)
70	The Danish reference pan genome	NC_000019.9 - 28422729	Apr 27, 2020 (154)
71	gnomAD - Genomes Submission ignored due to conflicting rows: Row 537510738 (NC_000019.10:27931820:C:A 5/140090) Row 537510739 (NC_000019.10:27931820:C:G 43397/140040)	-	Apr 26, 2021 (155)
72	gnomAD - Genomes Submission ignored due to conflicting rows: Row 537510738 (NC_000019.10:27931820:C:A 5/140090) Row 537510739 (NC_000019.10:27931820:C:G 43397/140040)	-	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000019.9 - 28422729	Apr 27, 2020 (154)
74	HapMap	NC_000019.10 - 27931821	Apr 27, 2020 (154)
75	KOREAN population from KRGDB	NC_000019.9 - 28422729	Apr 27, 2020 (154)
76	Northern Sweden	NC_000019.9 - 28422729	Jul 13, 2019 (153)
77	Qatari	NC_000019.9 - 28422729	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000019.9 - 28422729	Apr 27, 2020 (154)
79	Siberian	NC_000019.9 - 28422729	Apr 27, 2020 (154)
80	8.3KJPN	NC_000019.9 - 28422729	Apr 26, 2021 (155)
81	14KJPN	NC_000019.10 - 27931821	Oct 16, 2022 (156)
82	TopMed	NC_000019.10 - 27931821	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000019.9 - 28422729	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000019.9 - 28422729	Jul 13, 2019 (153)
85	ALFA	NC_000019.10 - 27931821	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)
rs60807728	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
100045016, 7072094268, ss5612519081	NC_000019.10:27931820:C:A	NC_000019.10:27931820:C:A	(self)
ss84708542, ss84829180, ss168037186, ss171659431, ss203725873, ss208448125, ss283175961, ss292234359, ss1698260536	NC_000019.8:33114568:C:G	NC_000019.10:27931820:C:G	(self)
76211870, 42208492, 29837329, 4788763, 18806802, 45283296, 16245524, 19742289, 40045453, 10680687, 85305509, 42208492, 9326064, ss237645768, ss243857238, ss565926546, ss661788066, ss994209078, ss1081838787, ss1362816819, ss1428377583, ss1578604894, ss1637786084, ss1680780117, ss1809266466, ss1937700367, ss1968626248, ss2029625370, ss2158164333, ss2629310990, ss2702770653, ss2961861198, ss3017323659, ss3352262374, ss3684099081, ss3742960659, ss3755954823, ss3788505436, ss3793420141, ss3798306862, ss3835417209, ss3841330093, ss3888028473, ss3938105902, ss5227336202, ss5434277743, ss5512076409, ss5662218838, ss5840428383, ss5953628237	NC_000019.9:28422728:C:G	NC_000019.10:27931820:C:G	(self)
100045016, 1681672, 119671325, 287372949, 7072094268, ss3028646613, ss3650898003, ss3702590523, ss3821206662, ss3846835626, ss5071827285, ss5306933134, ss5499492775, ss5612519081, ss5785834221, ss5817522801, ss5852252981, ss5927754523	NC_000019.10:27931820:C:G	NC_000019.10:27931820:C:G	(self)
ss10942485, ss20071893, ss21547873	NT_011109.15:690946:C:G	NC_000019.10:27931820:C:G	(self)
ss40973932, ss96262512, ss136288627	NT_011109.16:690946:C:G	NC_000019.10:27931820:C:G	(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 rs7259189

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

rs7259189