Name: rs1203862
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.

rs1203862

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:2502468 (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>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.258816 (68506/264690, TOPMED)
G=0.252888 (35379/139900, GnomAD)
G=0.32182 (9094/28258, 14KJPN) (+ 16 more)
G=0.24801 (4685/18890, ALFA)
G=0.32339 (5420/16760, 8.3KJPN)
G=0.3020 (1934/6404, 1000G_30x)
G=0.3041 (1523/5008, 1000G)
G=0.2531 (1134/4480, Estonian)
G=0.2216 (854/3854, ALSPAC)
G=0.2357 (874/3708, TWINSUK)
G=0.4164 (1220/2930, KOREAN)
G=0.4116 (754/1832, Korea1K)
G=0.234 (234/998, GoNL)
G=0.220 (132/600, NorthernSweden)
A=0.421 (96/228, SGDP_PRJ)
G=0.250 (54/216, Qatari)
G=0.357 (75/210, Vietnamese)
G=0.35 (14/40, GENOME_DK)
A=0.34 (11/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNF4 : 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	18890	A=0.75199	G=0.24801
European	Sub	14286	A=0.76438	G=0.23562
African	Sub	2946	A=0.6847	G=0.3153
African Others	Sub	114	A=0.614	G=0.386
African American	Sub	2832	A=0.6875	G=0.3125
Asian	Sub	112	A=0.562	G=0.438
East Asian	Sub	86	A=0.55	G=0.45
Other Asian	Sub	26	A=0.62	G=0.38
Latin American 1	Sub	146	A=0.726	G=0.274
Latin American 2	Sub	610	A=0.843	G=0.157
South Asian	Sub	98	A=0.66	G=0.34
Other	Sub	692	A=0.751	G=0.249

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=0.741184	G=0.258816
gnomAD - Genomes	Global	Study-wide	139900	A=0.747112	G=0.252888
gnomAD - Genomes	European	Sub	75794	A=0.77625	G=0.22375
gnomAD - Genomes	African	Sub	41876	A=0.68466	G=0.31534
gnomAD - Genomes	American	Sub	13638	A=0.81706	G=0.18294
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.7506	G=0.2494
gnomAD - Genomes	East Asian	Sub	3124	A=0.5762	G=0.4238
gnomAD - Genomes	Other	Sub	2148	A=0.7356	G=0.2644
14KJPN	JAPANESE	Study-wide	28258	A=0.67818	G=0.32182
Allele Frequency Aggregator	Total	Global	18890	A=0.75199	G=0.24801
Allele Frequency Aggregator	European	Sub	14286	A=0.76438	G=0.23562
Allele Frequency Aggregator	African	Sub	2946	A=0.6847	G=0.3153
Allele Frequency Aggregator	Other	Sub	692	A=0.751	G=0.249
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.843	G=0.157
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.726	G=0.274
Allele Frequency Aggregator	Asian	Sub	112	A=0.562	G=0.438
Allele Frequency Aggregator	South Asian	Sub	98	A=0.66	G=0.34
8.3KJPN	JAPANESE	Study-wide	16760	A=0.67661	G=0.32339
1000Genomes_30x	Global	Study-wide	6404	A=0.6980	G=0.3020
1000Genomes_30x	African	Sub	1786	A=0.6489	G=0.3511
1000Genomes_30x	Europe	Sub	1266	A=0.7630	G=0.2370
1000Genomes_30x	South Asian	Sub	1202	A=0.6889	G=0.3111
1000Genomes_30x	East Asian	Sub	1170	A=0.5940	G=0.4060
1000Genomes_30x	American	Sub	980	A=0.839	G=0.161
1000Genomes	Global	Study-wide	5008	A=0.6959	G=0.3041
1000Genomes	African	Sub	1322	A=0.6573	G=0.3427
1000Genomes	East Asian	Sub	1008	A=0.6002	G=0.3998
1000Genomes	Europe	Sub	1006	A=0.7664	G=0.2336
1000Genomes	South Asian	Sub	978	A=0.679	G=0.321
1000Genomes	American	Sub	694	A=0.830	G=0.170
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7469	G=0.2531
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7784	G=0.2216
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7643	G=0.2357
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5836	G=0.4164, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5884	G=0.4116
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.766	G=0.234
Northern Sweden	ACPOP	Study-wide	600	A=0.780	G=0.220
SGDP_PRJ	Global	Study-wide	228	A=0.421	G=0.579
Qatari	Global	Study-wide	216	A=0.750	G=0.250
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.643	G=0.357
The Danish reference pan genome	Danish	Study-wide	40	A=0.65	G=0.35
Siberian	Global	Study-wide	32	A=0.34	G=0.66

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.2502468A>G
GRCh38.p14 chr 4	NC_000004.12:g.2502468A>T
GRCh37.p13 chr 4	NC_000004.11:g.2504195A>G
GRCh37.p13 chr 4	NC_000004.11:g.2504195A>T

Gene: RNF4, ring finger protein 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNF4 transcript variant 1	NM_001185009.3:c.204+1730… NM_001185009.3:c.204+1730A>G	N/A	Intron Variant
RNF4 transcript variant 3	NM_001185010.3:c.204+1730… NM_001185010.3:c.204+1730A>G	N/A	Intron Variant
RNF4 transcript variant 2	NM_002938.5:c.204+1730A>G	N/A	Intron Variant
RNF4 transcript variant X1	XM_047416062.1:c.204+1730… XM_047416062.1:c.204+1730A>G	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=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.2502468=	NC_000004.12:g.2502468A>G	NC_000004.12:g.2502468A>T
GRCh37.p13 chr 4	NC_000004.11:g.2504195=	NC_000004.11:g.2504195A>G	NC_000004.11:g.2504195A>T
RNF4 transcript variant 1	NM_001185009.2:c.204+1730=	NM_001185009.2:c.204+1730A>G	NM_001185009.2:c.204+1730A>T
RNF4 transcript variant 1	NM_001185009.3:c.204+1730=	NM_001185009.3:c.204+1730A>G	NM_001185009.3:c.204+1730A>T
RNF4 transcript variant 3	NM_001185010.2:c.204+1730=	NM_001185010.2:c.204+1730A>G	NM_001185010.2:c.204+1730A>T
RNF4 transcript variant 3	NM_001185010.3:c.204+1730=	NM_001185010.3:c.204+1730A>G	NM_001185010.3:c.204+1730A>T
RNF4 transcript variant 2	NM_002938.4:c.204+1730=	NM_002938.4:c.204+1730A>G	NM_002938.4:c.204+1730A>T
RNF4 transcript variant 2	NM_002938.5:c.204+1730=	NM_002938.5:c.204+1730A>G	NM_002938.5:c.204+1730A>T
RNF4 transcript variant X1	XM_005247995.1:c.204+1730=	XM_005247995.1:c.204+1730A>G	XM_005247995.1:c.204+1730A>T
RNF4 transcript variant X1	XM_047416062.1:c.204+1730=	XM_047416062.1:c.204+1730A>G	XM_047416062.1:c.204+1730A>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#.

62 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1724414	Oct 18, 2000 (87)
2	SC_JCM	ss2630142	Nov 09, 2000 (94)
3	CSHL-HAPMAP	ss17011615	Feb 27, 2004 (120)
4	SSAHASNP	ss22161564	Apr 05, 2004 (121)
5	ABI	ss42326372	Mar 15, 2006 (126)
6	HUMANGENOME_JCVI	ss98795700	Feb 04, 2009 (130)
7	BGI	ss104032931	Dec 01, 2009 (131)
8	ILLUMINA-UK	ss116840013	Dec 01, 2009 (131)
9	ENSEMBL	ss134763736	Dec 01, 2009 (131)
10	GMI	ss156753801	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss166008314	Jul 04, 2010 (132)
12	GMI	ss277541440	May 04, 2012 (137)
13	PJP	ss293055067	May 09, 2011 (134)
14	1000GENOMES	ss331383627	May 09, 2011 (134)
15	TISHKOFF	ss557258506	Apr 25, 2013 (138)
16	SSMP	ss651012351	Apr 25, 2013 (138)
17	EVA-GONL	ss979679546	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1071219148	Aug 21, 2014 (142)
19	1000GENOMES	ss1308116385	Aug 21, 2014 (142)
20	DDI	ss1429741861	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1580382669	Apr 01, 2015 (144)
22	EVA_DECODE	ss1589175512	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1609250131	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1652244164	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1800822809	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1922911207	Feb 12, 2016 (147)
27	JJLAB	ss2022028811	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2150135838	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2259885558	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2625515556	Nov 08, 2017 (151)
31	GRF	ss2705570485	Nov 08, 2017 (151)
32	GNOMAD	ss2804769359	Nov 08, 2017 (151)
33	AFFY	ss2985906169	Nov 08, 2017 (151)
34	SWEGEN	ss2994003851	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3024784276	Nov 08, 2017 (151)
36	CSHL	ss3345501457	Nov 08, 2017 (151)
37	URBANLAB	ss3647633768	Oct 12, 2018 (152)
38	EGCUT_WGS	ss3661941962	Jul 13, 2019 (153)
39	EVA_DECODE	ss3711250917	Jul 13, 2019 (153)
40	ACPOP	ss3730783722	Jul 13, 2019 (153)
41	EVA	ss3761294066	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3804432821	Jul 13, 2019 (153)
43	EVA	ss3828329422	Apr 25, 2020 (154)
44	EVA	ss3837595568	Apr 25, 2020 (154)
45	EVA	ss3843028985	Apr 25, 2020 (154)
46	SGDP_PRJ	ss3858039291	Apr 25, 2020 (154)
47	KRGDB	ss3904170746	Apr 25, 2020 (154)
48	KOGIC	ss3953371023	Apr 25, 2020 (154)
49	TOPMED	ss4600418996	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5163853733	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5257768586	Oct 13, 2022 (156)
52	EVA	ss5346418766	Oct 13, 2022 (156)
53	HUGCELL_USP	ss5456718695	Oct 13, 2022 (156)
54	EVA	ss5507369323	Oct 13, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5538078754	Oct 13, 2022 (156)
56	SANFORD_IMAGENETICS	ss5634186888	Oct 13, 2022 (156)
57	TOMMO_GENOMICS	ss5697402720	Oct 13, 2022 (156)
58	YY_MCH	ss5804684182	Oct 13, 2022 (156)
59	EVA	ss5843438241	Oct 13, 2022 (156)
60	EVA	ss5854049037	Oct 13, 2022 (156)
61	EVA	ss5861845322	Oct 13, 2022 (156)
62	EVA	ss5962562043	Oct 13, 2022 (156)
63	1000Genomes	NC_000004.11 - 2504195	Oct 12, 2018 (152)
64	1000Genomes_30x	NC_000004.12 - 2502468	Oct 13, 2022 (156)
65	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 2504195	Oct 12, 2018 (152)
66	Genetic variation in the Estonian population	NC_000004.11 - 2504195	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000004.11 - 2504195	Apr 25, 2020 (154)
68	gnomAD - Genomes	NC_000004.12 - 2502468	Apr 26, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000004.11 - 2504195	Apr 25, 2020 (154)
70	KOREAN population from KRGDB	NC_000004.11 - 2504195	Apr 25, 2020 (154)
71	Korean Genome Project	NC_000004.12 - 2502468	Apr 25, 2020 (154)
72	Northern Sweden	NC_000004.11 - 2504195	Jul 13, 2019 (153)
73	Qatari	NC_000004.11 - 2504195	Apr 25, 2020 (154)
74	SGDP_PRJ	NC_000004.11 - 2504195	Apr 25, 2020 (154)
75	Siberian	NC_000004.11 - 2504195	Apr 25, 2020 (154)
76	8.3KJPN	NC_000004.11 - 2504195	Apr 26, 2021 (155)
77	14KJPN	NC_000004.12 - 2502468	Oct 13, 2022 (156)
78	TopMed	NC_000004.12 - 2502468	Apr 26, 2021 (155)
79	UK 10K study - Twins	NC_000004.11 - 2504195	Oct 12, 2018 (152)
80	A Vietnamese Genetic Variation Database	NC_000004.11 - 2504195	Jul 13, 2019 (153)
81	ALFA	NC_000004.12 - 2502468	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)
rs1770826	Apr 12, 2001 (94)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss116840013, ss166008314, ss277541440, ss293055067, ss1589175512	NC_000004.10:2473992:A:G	NC_000004.12:2502467:A:G	(self)
19455191, 10843422, 7680210, 6547608, 4764964, 11348140, 4068587, 4953137, 10056271, 2652192, 21823040, 10843422, 2370253, ss331383627, ss557258506, ss651012351, ss979679546, ss1071219148, ss1308116385, ss1429741861, ss1580382669, ss1609250131, ss1652244164, ss1800822809, ss1922911207, ss2022028811, ss2150135838, ss2625515556, ss2705570485, ss2804769359, ss2985906169, ss2994003851, ss3345501457, ss3661941962, ss3730783722, ss3761294066, ss3828329422, ss3837595568, ss3858039291, ss3904170746, ss5163853733, ss5346418766, ss5507369323, ss5634186888, ss5843438241, ss5962562043	NC_000004.11:2504194:A:G	NC_000004.12:2502467:A:G	(self)
25604689, 138123041, 9749024, 31239824, 437796552, 5812133614, ss2259885558, ss3024784276, ss3647633768, ss3711250917, ss3804432821, ss3843028985, ss3953371023, ss4600418996, ss5257768586, ss5456718695, ss5538078754, ss5697402720, ss5804684182, ss5854049037, ss5861845322	NC_000004.12:2502467:A:G	NC_000004.12:2502467:A:G	(self)
ss1724414, ss2630142, ss42326372, ss98795700, ss104032931, ss134763736, ss156753801	NT_006051.18:1025548:A:G	NC_000004.12:2502467:A:G	(self)
ss17011615, ss22161564	NT_037623.4:1007449:A:G	NC_000004.12:2502467:A:G	(self)
11348140, ss3904170746	NC_000004.11:2504194:A:T	NC_000004.12:2502467:A: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 rs1203862

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

rs1203862