Name: rs1970704
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.

rs1970704

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99188644 (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: G>A / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.260478 (68946/264690, TOPMED)
G=0.18865 (5331/28258, 14KJPN)
G=0.18634 (3123/16760, 8.3KJPN) (+ 15 more)
C=0.13774 (1959/14222, ALFA)
C=0.3674 (2353/6404, 1000G_30x)
C=0.3802 (1904/5008, 1000G)
C=0.2318 (1038/4478, Estonian)
C=0.2351 (906/3854, ALSPAC)
C=0.2241 (831/3708, TWINSUK)
G=0.2341 (686/2930, KOREAN)
G=0.2123 (389/1832, Korea1K)
C=0.222 (222/998, GoNL)
C=0.197 (118/600, NorthernSweden)
G=0.362 (97/268, SGDP_PRJ)
C=0.269 (58/216, Qatari)
G=0.190 (41/216, Vietnamese)
C=0.28 (11/40, GENOME_DK)
G=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	14222	G=0.86219	C=0.13774, T=0.00007	0.756962	0.032349	0.210689	32
European	Sub	11356	G=0.84775	C=0.15217, T=0.00009	0.730315	0.034525	0.235159	24
African	Sub	1880	G=0.9053	C=0.0947, T=0.0000	0.838298	0.02766	0.134043	24
African Others	Sub	78	G=0.91	C=0.09, T=0.00	0.846154	0.025641	0.128205	1
African American	Sub	1802	G=0.9051	C=0.0949, T=0.0000	0.837958	0.027747	0.134295	23
Asian	Sub	6	G=0.5	C=0.5, T=0.0	0.333333	0.333333	0.333333	0
East Asian	Sub	2	G=0.0	C=1.0, T=0.0	0.0	1.0	0.0	N/A
Other Asian	Sub	4	G=0.8	C=0.2, T=0.0	0.5	0.0	0.5	0
Latin American 1	Sub	78	G=1.00	C=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	406	G=1.000	C=0.000, T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	30	G=0.93	C=0.07, T=0.00	0.866667	0.0	0.133333	0
Other	Sub	466	G=0.897	C=0.103, T=0.000	0.824034	0.030043	0.145923	6

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	G=0.739522	C=0.260478
14KJPN	JAPANESE	Study-wide	28258	G=0.18865	C=0.81135
8.3KJPN	JAPANESE	Study-wide	16760	G=0.18634	C=0.81366
Allele Frequency Aggregator	Total	Global	14222	G=0.86219	C=0.13774, T=0.00007
Allele Frequency Aggregator	European	Sub	11356	G=0.84775	C=0.15217, T=0.00009
Allele Frequency Aggregator	African	Sub	1880	G=0.9053	C=0.0947, T=0.0000
Allele Frequency Aggregator	Other	Sub	466	G=0.897	C=0.103, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	406	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	78	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	30	G=0.93	C=0.07, T=0.00
Allele Frequency Aggregator	Asian	Sub	6	G=0.5	C=0.5, T=0.0
1000Genomes_30x	Global	Study-wide	6404	G=0.6326	C=0.3674
1000Genomes_30x	African	Sub	1786	G=0.7576	C=0.2424
1000Genomes_30x	Europe	Sub	1266	G=0.7559	C=0.2441
1000Genomes_30x	South Asian	Sub	1202	G=0.5433	C=0.4567
1000Genomes_30x	East Asian	Sub	1170	G=0.2239	C=0.7761
1000Genomes_30x	American	Sub	980	G=0.843	C=0.157
1000Genomes	Global	Study-wide	5008	G=0.6198	C=0.3802
1000Genomes	African	Sub	1322	G=0.7587	C=0.2413
1000Genomes	East Asian	Sub	1008	G=0.2192	C=0.7808
1000Genomes	Europe	Sub	1006	G=0.7674	C=0.2326
1000Genomes	South Asian	Sub	978	G=0.543	C=0.457
1000Genomes	American	Sub	694	G=0.831	C=0.169
Genetic variation in the Estonian population	Estonian	Study-wide	4478	G=0.7682	C=0.2318
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7649	C=0.2351
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7759	C=0.2241
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2341	A=0.0000, C=0.7659, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.2123	C=0.7877
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.778	C=0.222
Northern Sweden	ACPOP	Study-wide	600	G=0.803	C=0.197
SGDP_PRJ	Global	Study-wide	268	G=0.362	C=0.638
Qatari	Global	Study-wide	216	G=0.731	C=0.269
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.190	C=0.810
The Danish reference pan genome	Danish	Study-wide	40	G=0.72	C=0.28
Siberian	Global	Study-wide	22	G=0.45	C=0.55

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 4	NC_000004.12:g.99188644G>A
GRCh38.p14 chr 4	NC_000004.12:g.99188644G>C
GRCh38.p14 chr 4	NC_000004.12:g.99188644G>T
GRCh37.p13 chr 4	NC_000004.11:g.100109801G>A
GRCh37.p13 chr 4	NC_000004.11:g.100109801G>C
GRCh37.p13 chr 4	NC_000004.11:g.100109801G>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1: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	G=	A	C	T
GRCh38.p14 chr 4	NC_000004.12:g.99188644=	NC_000004.12:g.99188644G>A	NC_000004.12:g.99188644G>C	NC_000004.12:g.99188644G>T
GRCh37.p13 chr 4	NC_000004.11:g.100109801=	NC_000004.11:g.100109801G>A	NC_000004.11:g.100109801G>C	NC_000004.11:g.100109801G>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#.

64 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2874800	Jan 12, 2001 (92)
2	SC_JCM	ss5660253	Feb 20, 2003 (126)
3	WI_SSAHASNP	ss6472808	Feb 20, 2003 (126)
4	SSAHASNP	ss22109874	Apr 05, 2004 (121)
5	ABI	ss42175010	Mar 11, 2006 (126)
6	HGSV	ss84175143	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss92703135	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss98986754	Feb 05, 2009 (130)
9	BGI	ss105848253	Feb 05, 2009 (130)
10	ENSEMBL	ss133258969	Dec 01, 2009 (131)
11	ENSEMBL	ss139781958	Dec 01, 2009 (131)
12	GMI	ss157650263	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162379716	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss163916703	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss206588468	Jul 04, 2010 (132)
16	GMI	ss277844237	May 04, 2012 (137)
17	GMI	ss284967819	Apr 25, 2013 (138)
18	PJP	ss293147420	May 09, 2011 (134)
19	1000GENOMES	ss331831963	May 09, 2011 (134)
20	TISHKOFF	ss557720911	Apr 25, 2013 (138)
21	SSMP	ss651525495	Apr 25, 2013 (138)
22	EVA-GONL	ss980449698	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1071786866	Aug 21, 2014 (142)
24	1000GENOMES	ss1310978535	Aug 21, 2014 (142)
25	EVA_GENOME_DK	ss1580687270	Apr 01, 2015 (144)
26	EVA_DECODE	ss1589953713	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1610735482	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1653729515	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1923689829	Feb 12, 2016 (147)
30	JJLAB	ss2022430857	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2150560021	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2265422215	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2625714402	Nov 08, 2017 (151)
34	GRF	ss2706036941	Nov 08, 2017 (151)
35	GNOMAD	ss2812850342	Nov 08, 2017 (151)
36	AFFY	ss2985926626	Nov 08, 2017 (151)
37	SWEGEN	ss2995209932	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3024990684	Nov 08, 2017 (151)
39	CSHL	ss3345861637	Nov 08, 2017 (151)
40	URBANLAB	ss3647802530	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3663105648	Jul 13, 2019 (153)
42	EVA_DECODE	ss3712656167	Jul 13, 2019 (153)
43	ACPOP	ss3731421507	Jul 13, 2019 (153)
44	EVA	ss3762166732	Jul 13, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3805315135	Jul 13, 2019 (153)
46	EVA	ss3828703357	Apr 26, 2020 (154)
47	SGDP_PRJ	ss3859609963	Apr 26, 2020 (154)
48	KRGDB	ss3905887321	Apr 26, 2020 (154)
49	KOGIC	ss3954741769	Apr 26, 2020 (154)
50	TOPMED	ss4624627169	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5167077058	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5260287493	Oct 13, 2022 (156)
53	EVA	ss5350974334	Oct 13, 2022 (156)
54	HUGCELL_USP	ss5458930024	Oct 13, 2022 (156)
55	EVA	ss5507641308	Oct 13, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5541954664	Oct 13, 2022 (156)
57	SANFORD_IMAGENETICS	ss5635664984	Oct 13, 2022 (156)
58	TOMMO_GENOMICS	ss5701807888	Oct 13, 2022 (156)
59	YY_MCH	ss5805353780	Oct 13, 2022 (156)
60	EVA	ss5844423725	Oct 13, 2022 (156)
61	EVA	ss5854355847	Oct 13, 2022 (156)
62	EVA	ss5864675792	Oct 13, 2022 (156)
63	EVA	ss5964055617	Oct 13, 2022 (156)
64	EVA	ss5980240168	Oct 13, 2022 (156)
65	1000Genomes	NC_000004.11 - 100109801	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000004.12 - 99188644	Oct 13, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100109801	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000004.11 - 100109801	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000004.11 - 100109801	Apr 26, 2020 (154)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158823283 (NC_000004.12:99188643:G:C 34514/140036) Row 158823284 (NC_000004.12:99188643:G:T 2/140080)	-	Apr 26, 2021 (155)
71	gnomAD - Genomes Submission ignored due to conflicting rows: Row 158823283 (NC_000004.12:99188643:G:C 34514/140036) Row 158823284 (NC_000004.12:99188643:G:T 2/140080)	-	Apr 26, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000004.11 - 100109801	Apr 26, 2020 (154)
73	KOREAN population from KRGDB	NC_000004.11 - 100109801	Apr 26, 2020 (154)
74	Korean Genome Project	NC_000004.12 - 99188644	Apr 26, 2020 (154)
75	Northern Sweden	NC_000004.11 - 100109801	Jul 13, 2019 (153)
76	Qatari	NC_000004.11 - 100109801	Apr 26, 2020 (154)
77	SGDP_PRJ	NC_000004.11 - 100109801	Apr 26, 2020 (154)
78	Siberian	NC_000004.11 - 100109801	Apr 26, 2020 (154)
79	8.3KJPN	NC_000004.11 - 100109801	Apr 26, 2021 (155)
80	14KJPN	NC_000004.12 - 99188644	Oct 13, 2022 (156)
81	TopMed	NC_000004.12 - 99188644	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000004.11 - 100109801	Oct 12, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000004.11 - 100109801	Jul 13, 2019 (153)
84	ALFA	NC_000004.12 - 99188644	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)
rs4280734	Mar 11, 2006 (126)
rs4699375	Mar 11, 2006 (126)
rs58459401	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13064715, ss3905887321	NC_000004.11:100109800:G:A	NC_000004.12:99188643:G:A	(self)
ss84175143	NC_000004.9:100466978:G:C	NC_000004.12:99188643:G:C	(self)
ss92703135, ss162379716, ss163916703, ss206588468, ss277844237, ss284967819, ss293147420, ss1589953713	NC_000004.10:100328823:G:C	NC_000004.12:99188643:G:C	(self)
22420683, 12471619, 8843896, 6852209, 5513182, 13064715, 4706372, 5731759, 11626943, 3076375, 25046365, 12471619, 2744206, ss331831963, ss557720911, ss651525495, ss980449698, ss1071786866, ss1310978535, ss1580687270, ss1610735482, ss1653729515, ss1923689829, ss2022430857, ss2150560021, ss2625714402, ss2706036941, ss2812850342, ss2985926626, ss2995209932, ss3345861637, ss3663105648, ss3731421507, ss3762166732, ss3828703357, ss3859609963, ss3905887321, ss5167077058, ss5350974334, ss5507641308, ss5635664984, ss5844423725, ss5964055617, ss5980240168	NC_000004.11:100109800:G:C	NC_000004.12:99188643:G:C	(self)
29480599, 11119770, 35644992, 462004725, 6839139730, ss2265422215, ss3024990684, ss3647802530, ss3712656167, ss3805315135, ss3954741769, ss4624627169, ss5260287493, ss5458930024, ss5541954664, ss5701807888, ss5805353780, ss5854355847, ss5864675792	NC_000004.12:99188643:G:C	NC_000004.12:99188643:G:C	(self)
ss22109874	NT_016354.16:24604504:G:C	NC_000004.12:99188643:G:C	(self)
ss2874800, ss5660253, ss6472808, ss42175010, ss98986754, ss105848253, ss133258969, ss139781958, ss157650263	NT_016354.19:24657521:G:C	NC_000004.12:99188643:G:C	(self)
13064715, ss2812850342, ss3905887321	NC_000004.11:100109800:G:T	NC_000004.12:99188643:G:T	(self)
6839139730	NC_000004.12:99188643:G:T	NC_000004.12:99188643:G: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 rs1970704

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

rs1970704