Name: rs4839112
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.

rs4839112

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:111288331 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.435509 (115275/264690, TOPMED)
C=0.413579 (57863/139908, GnomAD)
T=0.36663 (10353/28238, 14KJPN) (+ 16 more)
C=0.42094 (10335/24552, ALFA)
T=0.36439 (6105/16754, 8.3KJPN)
C=0.4677 (2995/6404, 1000G_30x)
C=0.4702 (2355/5008, 1000G)
C=0.4243 (1901/4480, Estonian)
C=0.4216 (1625/3854, ALSPAC)
C=0.4318 (1601/3708, TWINSUK)
T=0.3700 (1084/2930, KOREAN)
C=0.422 (421/998, GoNL)
C=0.428 (257/600, NorthernSweden)
T=0.300 (123/410, SGDP_PRJ)
C=0.436 (143/328, HapMap)
C=0.398 (86/216, Qatari)
T=0.224 (48/214, Vietnamese)
T=0.41 (18/44, Siberian)
C=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	24646	T=0.57871	A=0.00000, C=0.42129
European	Sub	20024	T=0.56907	A=0.00000, C=0.43093
African	Sub	2698	T=0.7383	A=0.0000, C=0.2617
African Others	Sub	104	T=0.798	A=0.000, C=0.202
African American	Sub	2594	T=0.7359	A=0.0000, C=0.2641
Asian	Sub	112	T=0.286	A=0.000, C=0.714
East Asian	Sub	86	T=0.29	A=0.00, C=0.71
Other Asian	Sub	26	T=0.27	A=0.00, C=0.73
Latin American 1	Sub	146	T=0.534	A=0.000, C=0.466
Latin American 2	Sub	610	T=0.297	A=0.000, C=0.703
South Asian	Sub	98	T=0.51	A=0.00, C=0.49
Other	Sub	958	T=0.558	A=0.000, C=0.442

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	T=0.564491	C=0.435509
gnomAD - Genomes	Global	Study-wide	139908	T=0.586421	C=0.413579
gnomAD - Genomes	European	Sub	75784	T=0.56641	C=0.43359
gnomAD - Genomes	African	Sub	41936	T=0.71864	C=0.28136
gnomAD - Genomes	American	Sub	13620	T=0.40022	C=0.59978
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.4786	C=0.5214
gnomAD - Genomes	East Asian	Sub	3100	T=0.2519	C=0.7481
gnomAD - Genomes	Other	Sub	2144	T=0.5410	C=0.4590
14KJPN	JAPANESE	Study-wide	28238	T=0.36663	C=0.63337
Allele Frequency Aggregator	Total	Global	24552	T=0.57906	A=0.00000, C=0.42094
Allele Frequency Aggregator	European	Sub	19948	T=0.56923	A=0.00000, C=0.43077
Allele Frequency Aggregator	African	Sub	2698	T=0.7383	A=0.0000, C=0.2617
Allele Frequency Aggregator	Other	Sub	940	T=0.563	A=0.000, C=0.437
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.297	A=0.000, C=0.703
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.534	A=0.000, C=0.466
Allele Frequency Aggregator	Asian	Sub	112	T=0.286	A=0.000, C=0.714
Allele Frequency Aggregator	South Asian	Sub	98	T=0.51	A=0.00, C=0.49
8.3KJPN	JAPANESE	Study-wide	16754	T=0.36439	C=0.63561
1000Genomes_30x	Global	Study-wide	6404	T=0.5323	C=0.4677
1000Genomes_30x	African	Sub	1786	T=0.7559	C=0.2441
1000Genomes_30x	Europe	Sub	1266	T=0.5434	C=0.4566
1000Genomes_30x	South Asian	Sub	1202	T=0.5890	C=0.4110
1000Genomes_30x	East Asian	Sub	1170	T=0.2581	C=0.7419
1000Genomes_30x	American	Sub	980	T=0.368	C=0.632
1000Genomes	Global	Study-wide	5008	T=0.5298	C=0.4702
1000Genomes	African	Sub	1322	T=0.7610	C=0.2390
1000Genomes	East Asian	Sub	1008	T=0.2589	C=0.7411
1000Genomes	Europe	Sub	1006	T=0.5408	C=0.4592
1000Genomes	South Asian	Sub	978	T=0.597	C=0.403
1000Genomes	American	Sub	694	T=0.372	C=0.628
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5757	C=0.4243
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5784	C=0.4216
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5682	C=0.4318
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3700	C=0.6300, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.578	C=0.422
Northern Sweden	ACPOP	Study-wide	600	T=0.572	C=0.428
SGDP_PRJ	Global	Study-wide	410	T=0.300	C=0.700
HapMap	Global	Study-wide	328	T=0.564	C=0.436
HapMap	American	Sub	120	T=0.575	C=0.425
HapMap	African	Sub	118	T=0.720	C=0.280
HapMap	Asian	Sub	90	T=0.34	C=0.66
Qatari	Global	Study-wide	216	T=0.602	C=0.398
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.224	C=0.776
Siberian	Global	Study-wide	44	T=0.41	C=0.59
The Danish reference pan genome	Danish	Study-wide	40	T=0.62	C=0.38

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.111288331T>A
GRCh38.p14 chr 1	NC_000001.11:g.111288331T>C
GRCh38.p14 chr 1	NC_000001.11:g.111288331T>G
GRCh37.p13 chr 1	NC_000001.10:g.111830953T>A
GRCh37.p13 chr 1	NC_000001.10:g.111830953T>C
GRCh37.p13 chr 1	NC_000001.10:g.111830953T>G

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	G
GRCh38.p14 chr 1	NC_000001.11:g.111288331=	NC_000001.11:g.111288331T>A	NC_000001.11:g.111288331T>C	NC_000001.11:g.111288331T>G
GRCh37.p13 chr 1	NC_000001.10:g.111830953=	NC_000001.10:g.111830953T>A	NC_000001.10:g.111830953T>C	NC_000001.10:g.111830953T>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#.

71 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6683724	Feb 20, 2003 (111)
2	CSHL-HAPMAP	ss16384104	Feb 27, 2004 (120)
3	SSAHASNP	ss20429298	Apr 05, 2004 (123)
4	PERLEGEN	ss24285107	Sep 20, 2004 (123)
5	HGSV	ss85491635	Dec 15, 2007 (130)
6	HUMANGENOME_JCVI	ss97967870	Feb 05, 2009 (130)
7	BGI	ss102775617	Dec 01, 2009 (131)
8	1000GENOMES	ss111013899	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss118972341	Feb 15, 2009 (130)
10	ENSEMBL	ss139276759	Dec 01, 2009 (131)
11	GMI	ss155530263	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163901739	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss205138012	Jul 04, 2010 (132)
14	1000GENOMES	ss218597026	Jul 14, 2010 (132)
15	1000GENOMES	ss230692105	Jul 14, 2010 (132)
16	1000GENOMES	ss238350006	Jul 15, 2010 (132)
17	BL	ss253384811	May 09, 2011 (134)
18	GMI	ss275978385	May 04, 2012 (137)
19	GMI	ss284121334	Apr 25, 2013 (138)
20	PJP	ss290598704	May 09, 2011 (134)
21	TISHKOFF	ss554575221	Apr 25, 2013 (138)
22	SSMP	ss648313184	Apr 25, 2013 (138)
23	EVA-GONL	ss975570968	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1068193221	Aug 21, 2014 (142)
25	1000GENOMES	ss1292433565	Aug 21, 2014 (142)
26	DDI	ss1425937247	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1574322685	Apr 01, 2015 (144)
28	EVA_DECODE	ss1584950781	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1600990729	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1643984762	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1794931094	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1918770685	Feb 12, 2016 (147)
33	GENOMED	ss1966841949	Jul 19, 2016 (147)
34	JJLAB	ss2019909917	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2147927988	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2165714828	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2624464691	Nov 08, 2017 (151)
38	GRF	ss2697857873	Nov 08, 2017 (151)
39	GNOMAD	ss2759560834	Nov 08, 2017 (151)
40	AFFY	ss2984870851	Nov 08, 2017 (151)
41	AFFY	ss2985521813	Nov 08, 2017 (151)
42	SWEGEN	ss2987438787	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3023719145	Nov 08, 2017 (151)
44	CSHL	ss3343635147	Nov 08, 2017 (151)
45	URBANLAB	ss3646752407	Oct 11, 2018 (152)
46	ILLUMINA	ss3653642872	Oct 11, 2018 (152)
47	EGCUT_WGS	ss3655527486	Jul 12, 2019 (153)
48	EVA_DECODE	ss3687530549	Jul 12, 2019 (153)
49	ACPOP	ss3727389083	Jul 12, 2019 (153)
50	EVA	ss3746673004	Jul 12, 2019 (153)
51	PACBIO	ss3783519731	Jul 12, 2019 (153)
52	PACBIO	ss3789161549	Jul 12, 2019 (153)
53	PACBIO	ss3794034469	Jul 12, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3799675908	Jul 12, 2019 (153)
55	EVA	ss3826369745	Apr 25, 2020 (154)
56	SGDP_PRJ	ss3849649977	Apr 25, 2020 (154)
57	KRGDB	ss3894743160	Apr 25, 2020 (154)
58	TOPMED	ss4463614168	Apr 25, 2021 (155)
59	TOMMO_GENOMICS	ss5145681062	Apr 25, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5243609697	Oct 12, 2022 (156)
61	EVA	ss5321187115	Oct 12, 2022 (156)
62	HUGCELL_USP	ss5444533509	Oct 12, 2022 (156)
63	EVA	ss5505997308	Oct 12, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5516604497	Oct 12, 2022 (156)
65	SANFORD_IMAGENETICS	ss5626298673	Oct 12, 2022 (156)
66	TOMMO_GENOMICS	ss5670948939	Oct 12, 2022 (156)
67	YY_MCH	ss5800931964	Oct 12, 2022 (156)
68	EVA	ss5832484278	Oct 12, 2022 (156)
69	EVA	ss5849068075	Oct 12, 2022 (156)
70	EVA	ss5909802056	Oct 12, 2022 (156)
71	EVA	ss5938164980	Oct 12, 2022 (156)
72	1000Genomes	NC_000001.10 - 111830953	Oct 11, 2018 (152)
73	1000Genomes_30x	NC_000001.11 - 111288331	Oct 12, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 111830953	Oct 11, 2018 (152)
75	Genetic variation in the Estonian population	NC_000001.10 - 111830953	Oct 11, 2018 (152)
76	The Danish reference pan genome	NC_000001.10 - 111830953	Apr 25, 2020 (154)
77	gnomAD - Genomes	NC_000001.11 - 111288331	Apr 25, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000001.10 - 111830953	Apr 25, 2020 (154)
79	HapMap	NC_000001.11 - 111288331	Apr 25, 2020 (154)
80	KOREAN population from KRGDB	NC_000001.10 - 111830953	Apr 25, 2020 (154)
81	Northern Sweden	NC_000001.10 - 111830953	Jul 12, 2019 (153)
82	Qatari	NC_000001.10 - 111830953	Apr 25, 2020 (154)
83	SGDP_PRJ	NC_000001.10 - 111830953	Apr 25, 2020 (154)
84	Siberian	NC_000001.10 - 111830953	Apr 25, 2020 (154)
85	8.3KJPN	NC_000001.10 - 111830953	Apr 25, 2021 (155)
86	14KJPN	NC_000001.11 - 111288331	Oct 12, 2022 (156)
87	TopMed	NC_000001.11 - 111288331	Apr 25, 2021 (155)
88	UK 10K study - Twins	NC_000001.10 - 111830953	Oct 11, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000001.10 - 111830953	Jul 12, 2019 (153)
90	ALFA	NC_000001.11 - 111288331	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)
rs12722749	Sep 24, 2004 (123)
rs17655423	Oct 07, 2004 (123)
rs58882200	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2647309257	NC_000001.11:111288330:T:A	NC_000001.11:111288330:T:A	(self)
ss85491635	NC_000001.8:111542994:T:C	NC_000001.11:111288330:T:C	(self)
ss111013899, ss118972341, ss163901739, ss205138012, ss253384811, ss275978385, ss284121334, ss290598704, ss1584950781	NC_000001.9:111632475:T:C	NC_000001.11:111288330:T:C	(self)
3209458, 1774646, 1265734, 1664894, 772408, 1920554, 673948, 812615, 1666957, 444342, 3650369, 1774646, 384747, ss218597026, ss230692105, ss238350006, ss554575221, ss648313184, ss975570968, ss1068193221, ss1292433565, ss1425937247, ss1574322685, ss1600990729, ss1643984762, ss1794931094, ss1918770685, ss1966841949, ss2019909917, ss2147927988, ss2624464691, ss2697857873, ss2759560834, ss2984870851, ss2985521813, ss2987438787, ss3343635147, ss3653642872, ss3655527486, ss3727389083, ss3746673004, ss3783519731, ss3789161549, ss3794034469, ss3826369745, ss3849649977, ss3894743160, ss5145681062, ss5321187115, ss5505997308, ss5626298673, ss5832484278, ss5938164980	NC_000001.10:111830952:T:C	NC_000001.11:111288330:T:C	(self)
4130432, 22697626, 154522, 4786043, 27220503, 2647309257, ss2165714828, ss3023719145, ss3646752407, ss3687530549, ss3799675908, ss4463614168, ss5243609697, ss5444533509, ss5516604497, ss5670948939, ss5800931964, ss5849068075, ss5909802056	NC_000001.11:111288330:T:C	NC_000001.11:111288330:T:C	(self)
ss16384104, ss20429298	NT_019273.16:2826900:T:C	NC_000001.11:111288330:T:C	(self)
ss6683724, ss24285107, ss97967870, ss102775617, ss139276759, ss155530263	NT_032977.9:81802870:T:C	NC_000001.11:111288330:T:C	(self)
1920554, ss3894743160	NC_000001.10:111830952:T:G	NC_000001.11:111288330:T: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 rs4839112

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

rs4839112