Name: rs12257390
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.

rs12257390

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:4214087 (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=0.266814 (70623/264690, TOPMED)
C=0.04059 (1147/28258, 14KJPN)
C=0.21057 (3922/18626, ALFA) (+ 17 more)
C=0.04027 (675/16760, 8.3KJPN)
C=0.1766 (1131/6404, 1000G_30x)
C=0.1689 (846/5008, 1000G)
C=0.3312 (1484/4480, Estonian)
C=0.3324 (1281/3854, ALSPAC)
C=0.3266 (1211/3708, TWINSUK)
C=0.0164 (48/2922, KOREAN)
C=0.0158 (29/1832, Korea1K)
C=0.2017 (330/1636, HapMap)
C=0.338 (337/998, GoNL)
C=0.216 (135/626, Chileans)
C=0.328 (197/600, NorthernSweden)
C=0.231 (50/216, Qatari)
C=0.009 (2/214, Vietnamese)
T=0.386 (54/140, SGDP_PRJ)
C=0.33 (13/40, GENOME_DK)
T=0.46 (11/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC00702 : 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	18626	T=0.78943	A=0.00000, C=0.21057
European	Sub	11864	T=0.75834	A=0.00000, C=0.24166
African	Sub	2738	T=0.9094	A=0.0000, C=0.0906
African Others	Sub	102	T=0.931	A=0.000, C=0.069
African American	Sub	2636	T=0.9086	A=0.0000, C=0.0914
Asian	Sub	156	T=0.981	A=0.000, C=0.019
East Asian	Sub	98	T=0.99	A=0.00, C=0.01
Other Asian	Sub	58	T=0.97	A=0.00, C=0.03
Latin American 1	Sub	210	T=0.824	A=0.000, C=0.176
Latin American 2	Sub	2430	T=0.7852	A=0.0000, C=0.2148
South Asian	Sub	78	T=0.96	A=0.00, C=0.04
Other	Sub	1150	T=0.7896	A=0.0000, C=0.2104

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
TopMed	Global	Study-wide	264690	T=0.733186	C=0.266814
14KJPN	JAPANESE	Study-wide	28258	T=0.95941	C=0.04059
Allele Frequency Aggregator	Total	Global	18626	T=0.78943	A=0.00000, C=0.21057
Allele Frequency Aggregator	European	Sub	11864	T=0.75834	A=0.00000, C=0.24166
Allele Frequency Aggregator	African	Sub	2738	T=0.9094	A=0.0000, C=0.0906
Allele Frequency Aggregator	Latin American 2	Sub	2430	T=0.7852	A=0.0000, C=0.2148
Allele Frequency Aggregator	Other	Sub	1150	T=0.7896	A=0.0000, C=0.2104
Allele Frequency Aggregator	Latin American 1	Sub	210	T=0.824	A=0.000, C=0.176
Allele Frequency Aggregator	Asian	Sub	156	T=0.981	A=0.000, C=0.019
Allele Frequency Aggregator	South Asian	Sub	78	T=0.96	A=0.00, C=0.04
8.3KJPN	JAPANESE	Study-wide	16760	T=0.95973	C=0.04027
1000Genomes_30x	Global	Study-wide	6404	T=0.8234	C=0.1766
1000Genomes_30x	African	Sub	1786	T=0.8438	C=0.1562
1000Genomes_30x	Europe	Sub	1266	T=0.6793	C=0.3207
1000Genomes_30x	South Asian	Sub	1202	T=0.8636	C=0.1364
1000Genomes_30x	East Asian	Sub	1170	T=0.9846	C=0.0154
1000Genomes_30x	American	Sub	980	T=0.731	C=0.269
1000Genomes	Global	Study-wide	5008	T=0.8311	C=0.1689
1000Genomes	African	Sub	1322	T=0.8381	C=0.1619
1000Genomes	East Asian	Sub	1008	T=0.9841	C=0.0159
1000Genomes	Europe	Sub	1006	T=0.6879	C=0.3121
1000Genomes	South Asian	Sub	978	T=0.873	C=0.127
1000Genomes	American	Sub	694	T=0.744	C=0.256
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6687	C=0.3312
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6676	C=0.3324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6734	C=0.3266
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9836	C=0.0164
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9842	C=0.0158
HapMap	Global	Study-wide	1636	T=0.7983	C=0.2017
HapMap	African	Sub	692	T=0.814	C=0.186
HapMap	American	Sub	598	T=0.759	C=0.241
HapMap	Europe	Sub	174	T=0.718	C=0.282
HapMap	Asian	Sub	172	T=0.953	C=0.047
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.662	C=0.338
Chileans	Chilean	Study-wide	626	T=0.784	C=0.216
Northern Sweden	ACPOP	Study-wide	600	T=0.672	C=0.328
Qatari	Global	Study-wide	216	T=0.769	C=0.231
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.991	C=0.009
SGDP_PRJ	Global	Study-wide	140	T=0.386	C=0.614
The Danish reference pan genome	Danish	Study-wide	40	T=0.68	C=0.33
Siberian	Global	Study-wide	24	T=0.46	C=0.54

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 10	NC_000010.11:g.4214087T>A
GRCh38.p14 chr 10	NC_000010.11:g.4214087T>C
GRCh37.p13 chr 10	NC_000010.10:g.4256279T>A
GRCh37.p13 chr 10	NC_000010.10:g.4256279T>C

Gene: LINC00702, long intergenic non-protein coding RNA 702 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00702 transcript	NR_108040.1: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	T=	A	C
GRCh38.p14 chr 10	NC_000010.11:g.4214087=	NC_000010.11:g.4214087T>A	NC_000010.11:g.4214087T>C
GRCh37.p13 chr 10	NC_000010.10:g.4256279=	NC_000010.10:g.4256279T>A	NC_000010.10:g.4256279T>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#.

58 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18647019	Feb 28, 2004 (120)
2	PERLEGEN	ss24529363	Sep 20, 2004 (123)
3	AFFY	ss66305196	Nov 29, 2006 (127)
4	AFFY	ss75979985	Dec 08, 2007 (130)
5	KRIBB_YJKIM	ss82965450	Dec 15, 2007 (130)
6	BCMHGSC_JDW	ss88073151	Mar 23, 2008 (129)
7	1000GENOMES	ss109179439	Jan 23, 2009 (130)
8	ENSEMBL	ss131651003	Dec 01, 2009 (131)
9	1000GENOMES	ss224534050	Jul 14, 2010 (132)
10	1000GENOMES	ss235029351	Jul 15, 2010 (132)
11	1000GENOMES	ss241766891	Jul 15, 2010 (132)
12	BL	ss254008086	May 09, 2011 (134)
13	GMI	ss280456256	May 04, 2012 (137)
14	TISHKOFF	ss561733507	Apr 25, 2013 (138)
15	SSMP	ss656237689	Apr 25, 2013 (138)
16	EVA-GONL	ss987137784	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1076716815	Aug 21, 2014 (142)
18	1000GENOMES	ss1336060448	Aug 21, 2014 (142)
19	DDI	ss1426201907	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1574872594	Apr 01, 2015 (144)
21	EVA_DECODE	ss1596784653	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1623875119	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1666869152	Apr 01, 2015 (144)
24	EVA_SVP	ss1713152364	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1806229572	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1930457560	Feb 12, 2016 (147)
27	GENOMED	ss1967044504	Jul 19, 2016 (147)
28	JJLAB	ss2025951171	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2154192821	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2172227574	Dec 20, 2016 (150)
31	GRF	ss2698415435	Nov 08, 2017 (151)
32	GNOMAD	ss2884917598	Nov 08, 2017 (151)
33	SWEGEN	ss3005845451	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3026758529	Nov 08, 2017 (151)
35	CSHL	ss3348931931	Nov 08, 2017 (151)
36	EGCUT_WGS	ss3673374184	Jul 13, 2019 (153)
37	EVA_DECODE	ss3689170636	Jul 13, 2019 (153)
38	ACPOP	ss3737009095	Jul 13, 2019 (153)
39	EVA	ss3747676410	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3813039137	Jul 13, 2019 (153)
41	EVA	ss3831936467	Apr 26, 2020 (154)
42	EVA	ss3839497871	Apr 26, 2020 (154)
43	EVA	ss3844963664	Apr 26, 2020 (154)
44	SGDP_PRJ	ss3873413870	Apr 26, 2020 (154)
45	KRGDB	ss3921347600	Apr 26, 2020 (154)
46	KOGIC	ss3967096658	Apr 26, 2020 (154)
47	TOPMED	ss4840684720	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5196017904	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5282727639	Oct 16, 2022 (156)
50	EVA	ss5391251491	Oct 16, 2022 (156)
51	HUGCELL_USP	ss5478525784	Oct 16, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5576027244	Oct 16, 2022 (156)
53	SANFORD_IMAGENETICS	ss5648565258	Oct 16, 2022 (156)
54	TOMMO_GENOMICS	ss5740795132	Oct 16, 2022 (156)
55	EVA	ss5823897762	Oct 16, 2022 (156)
56	EVA	ss5849411508	Oct 16, 2022 (156)
57	EVA	ss5877520436	Oct 16, 2022 (156)
58	EVA	ss5939846014	Oct 16, 2022 (156)
59	1000Genomes	NC_000010.10 - 4256279	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000010.11 - 4214087	Oct 16, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 4256279	Oct 12, 2018 (152)
62	Chileans	NC_000010.10 - 4256279	Apr 26, 2020 (154)
63	Genetic variation in the Estonian population	NC_000010.10 - 4256279	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000010.10 - 4256279	Apr 26, 2020 (154)
65	gnomAD - Genomes Submission ignored due to conflicting rows: Row 341942743 (NC_000010.11:4214086:T:A 1/140096) Row 341942744 (NC_000010.11:4214086:T:C 38713/140066)	-	Apr 26, 2021 (155)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 341942743 (NC_000010.11:4214086:T:A 1/140096) Row 341942744 (NC_000010.11:4214086:T:C 38713/140066)	-	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000010.10 - 4256279	Apr 26, 2020 (154)
68	HapMap	NC_000010.11 - 4214087	Apr 26, 2020 (154)
69	KOREAN population from KRGDB	NC_000010.10 - 4256279	Apr 26, 2020 (154)
70	Korean Genome Project	NC_000010.11 - 4214087	Apr 26, 2020 (154)
71	Northern Sweden	NC_000010.10 - 4256279	Jul 13, 2019 (153)
72	Qatari	NC_000010.10 - 4256279	Apr 26, 2020 (154)
73	SGDP_PRJ	NC_000010.10 - 4256279	Apr 26, 2020 (154)
74	Siberian	NC_000010.10 - 4256279	Apr 26, 2020 (154)
75	8.3KJPN	NC_000010.10 - 4256279	Apr 26, 2021 (155)
76	14KJPN	NC_000010.11 - 4214087	Oct 16, 2022 (156)
77	TopMed	NC_000010.11 - 4214087	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000010.10 - 4256279	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000010.10 - 4256279	Jul 13, 2019 (153)
80	ALFA	NC_000010.11 - 4214087	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)
rs17351153	Oct 08, 2004 (123)
rs56453928	May 26, 2008 (130)
rs58642185	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
16305157277	NC_000010.11:4214086:T:A	NC_000010.11:4214086:T:A	(self)
ss66305196, ss75979985, ss88073151, ss109179439, ss254008086, ss280456256, ss1596784653, ss1713152364	NC_000010.9:4246278:T:C	NC_000010.11:4214086:T:C	(self)
48399287, 26891825, 40603, 19112432, 2005283, 11993375, 28524994, 10293960, 12499490, 25430850, 6709175, 53987211, 26891825, 5968337, ss224534050, ss235029351, ss241766891, ss561733507, ss656237689, ss987137784, ss1076716815, ss1336060448, ss1426201907, ss1574872594, ss1623875119, ss1666869152, ss1806229572, ss1930457560, ss1967044504, ss2025951171, ss2154192821, ss2698415435, ss2884917598, ss3005845451, ss3348931931, ss3673374184, ss3737009095, ss3747676410, ss3831936467, ss3839497871, ss3873413870, ss3921347600, ss5196017904, ss5391251491, ss5648565258, ss5823897762, ss5939846014	NC_000010.10:4256278:T:C	NC_000010.11:4214086:T:C	(self)
63553179, 325878, 23474659, 74632236, 56230375, 16305157277, ss2172227574, ss3026758529, ss3689170636, ss3813039137, ss3844963664, ss3967096658, ss4840684720, ss5282727639, ss5478525784, ss5576027244, ss5740795132, ss5849411508, ss5877520436	NC_000010.11:4214086:T:C	NC_000010.11:4214086:T:C	(self)
ss24529363, ss82965450, ss131651003	NT_008705.16:4196278:T:C	NC_000010.11:4214086:T:C	(self)
ss18647019	NT_077567.3:4196278:T:C	NC_000010.11:4214086: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 rs12257390

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

rs12257390