Name: rs4890182
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.

rs4890182

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:199872 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.202731 (53661/264690, TOPMED)
T=0.202669 (28398/140120, GnomAD)
T=0.06646 (1878/28258, 14KJPN) (+ 15 more)
T=0.20069 (4738/23608, ALFA)
T=0.06718 (1126/16760, 8.3KJPN)
T=0.1918 (1228/6404, 1000G_30x)
T=0.1937 (970/5008, 1000G)
T=0.1996 (894/4480, Estonian)
T=0.2032 (783/3854, ALSPAC)
T=0.1977 (733/3708, TWINSUK)
T=0.1072 (314/2930, KOREAN)
T=0.187 (187/998, GoNL)
T=0.157 (94/600, NorthernSweden)
T=0.156 (84/540, SGDP_PRJ)
T=0.347 (75/216, Qatari)
T=0.250 (54/216, Vietnamese)
T=0.22 (11/50, Siberian)
T=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC101929045 : Non Coding Transcript Variant
LOC124903889 : 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	23608	T=0.20069	C=0.79931
European	Sub	18898	T=0.20214	C=0.79786
African	Sub	2976	T=0.2036	C=0.7964
African Others	Sub	114	T=0.202	C=0.798
African American	Sub	2862	T=0.2037	C=0.7963
Asian	Sub	114	T=0.175	C=0.825
East Asian	Sub	88	T=0.14	C=0.86
Other Asian	Sub	26	T=0.31	C=0.69
Latin American 1	Sub	150	T=0.200	C=0.800
Latin American 2	Sub	626	T=0.128	C=0.872
South Asian	Sub	98	T=0.31	C=0.69
Other	Sub	746	T=0.204	C=0.796

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=0.202731	C=0.797269
gnomAD - Genomes	Global	Study-wide	140120	T=0.202669	C=0.797331
gnomAD - Genomes	European	Sub	75890	T=0.19801	C=0.80199
gnomAD - Genomes	African	Sub	41976	T=0.21636	C=0.78364
gnomAD - Genomes	American	Sub	13652	T=0.17199	C=0.82801
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.2860	C=0.7140
gnomAD - Genomes	East Asian	Sub	3128	T=0.1816	C=0.8184
gnomAD - Genomes	Other	Sub	2152	T=0.1966	C=0.8034
14KJPN	JAPANESE	Study-wide	28258	T=0.06646	C=0.93354
Allele Frequency Aggregator	Total	Global	23608	T=0.20069	C=0.79931
Allele Frequency Aggregator	European	Sub	18898	T=0.20214	C=0.79786
Allele Frequency Aggregator	African	Sub	2976	T=0.2036	C=0.7964
Allele Frequency Aggregator	Other	Sub	746	T=0.204	C=0.796
Allele Frequency Aggregator	Latin American 2	Sub	626	T=0.128	C=0.872
Allele Frequency Aggregator	Latin American 1	Sub	150	T=0.200	C=0.800
Allele Frequency Aggregator	Asian	Sub	114	T=0.175	C=0.825
Allele Frequency Aggregator	South Asian	Sub	98	T=0.31	C=0.69
8.3KJPN	JAPANESE	Study-wide	16760	T=0.06718	C=0.93282
1000Genomes_30x	Global	Study-wide	6404	T=0.1918	C=0.8082
1000Genomes_30x	African	Sub	1786	T=0.2329	C=0.7671
1000Genomes_30x	Europe	Sub	1266	T=0.1959	C=0.8041
1000Genomes_30x	South Asian	Sub	1202	T=0.2113	C=0.7887
1000Genomes_30x	East Asian	Sub	1170	T=0.1692	C=0.8308
1000Genomes_30x	American	Sub	980	T=0.114	C=0.886
1000Genomes	Global	Study-wide	5008	T=0.1937	C=0.8063
1000Genomes	African	Sub	1322	T=0.2337	C=0.7663
1000Genomes	East Asian	Sub	1008	T=0.1716	C=0.8284
1000Genomes	Europe	Sub	1006	T=0.2008	C=0.7992
1000Genomes	South Asian	Sub	978	T=0.212	C=0.788
1000Genomes	American	Sub	694	T=0.114	C=0.886
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1996	C=0.8004
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2032	C=0.7968
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1977	C=0.8023
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.1072	C=0.8928
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.187	C=0.813
Northern Sweden	ACPOP	Study-wide	600	T=0.157	C=0.843
SGDP_PRJ	Global	Study-wide	540	T=0.156	C=0.844
Qatari	Global	Study-wide	216	T=0.347	C=0.653
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.250	C=0.750
Siberian	Global	Study-wide	50	T=0.22	C=0.78
The Danish reference pan genome	Danish	Study-wide	40	T=0.15	C=0.85

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 17	NC_000017.11:g.199872T>C
GRCh37.p13 chr 17 fix patch HG417_PATCH	NW_004070872.2:g.139870T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG1	NW_003315952.3:g.138927C>T
GRCh37.p13 chr 17	NC_000017.10:g.49663T>C

Gene: LOC124903889, uncharacterized LOC124903889 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903889 transcript	XR_007065569.1: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=	C
GRCh38.p14 chr 17	NC_000017.11:g.199872=	NC_000017.11:g.199872T>C
GRCh37.p13 chr 17 fix patch HG417_PATCH	NW_004070872.2:g.139870=	NW_004070872.2:g.139870T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG1	NW_003315952.3:g.138927C>T	NW_003315952.3:g.138927=
GRCh37.p13 chr 17	NC_000017.10:g.49663=	NC_000017.10:g.49663T>C
LOC101929045 transcript	XR_952137.3:n.4976G>A	XR_952137.3:n.4976=
LOC101929045 transcript	XR_952137.2:n.4432G>A	XR_952137.2:n.4432=
LOC101929045 transcript	XR_952137.1:n.3036G>A	XR_952137.1:n.3036=

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#.

81 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6757064	Feb 20, 2003 (111)
2	SC_SNP	ss14806306	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss20035095	Feb 27, 2004 (120)
4	SSAHASNP	ss21385720	Apr 05, 2004 (121)
5	HGSV	ss77436135	Dec 07, 2007 (129)
6	HGSV	ss79752949	Dec 14, 2007 (130)
7	BCMHGSC_JDW	ss90502084	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss96572784	Feb 04, 2009 (130)
9	BGI	ss106492584	Feb 04, 2009 (130)
10	1000GENOMES	ss109579129	Jan 24, 2009 (130)
11	ILLUMINA-UK	ss117967089	Feb 14, 2009 (130)
12	ENSEMBL	ss136547320	Dec 01, 2009 (131)
13	ENSEMBL	ss136890269	Dec 01, 2009 (131)
14	GMI	ss157740678	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss167618734	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss171036077	Jul 04, 2010 (132)
17	BUSHMAN	ss202105012	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss207928975	Jul 04, 2010 (132)
19	1000GENOMES	ss211763320	Jul 14, 2010 (132)
20	1000GENOMES	ss227420402	Jul 14, 2010 (132)
21	1000GENOMES	ss237151517	Jul 15, 2010 (132)
22	1000GENOMES	ss243467641	Jul 15, 2010 (132)
23	GMI	ss282657875	May 04, 2012 (137)
24	GMI	ss287131468	Apr 25, 2013 (138)
25	PJP	ss291955619	May 09, 2011 (134)
26	ILLUMINA	ss483178476	May 04, 2012 (137)
27	ILLUMINA	ss483640328	May 04, 2012 (137)
28	TISHKOFF	ss565113800	Apr 25, 2013 (138)
29	SSMP	ss660894163	Apr 25, 2013 (138)
30	ILLUMINA	ss782032524	Sep 08, 2015 (146)
31	EVA-GONL	ss992833110	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1080871235	Aug 21, 2014 (142)
33	1000GENOMES	ss1357570887	Aug 21, 2014 (142)
34	DDI	ss1427949443	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1578052495	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1635121049	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1678115082	Apr 01, 2015 (144)
38	EVA_DECODE	ss1696874455	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1808663754	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1936276244	Feb 12, 2016 (147)
41	GENOMED	ss1968334060	Jul 19, 2016 (147)
42	JJLAB	ss2028927669	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2157369284	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2214838951	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2628954036	Nov 08, 2017 (151)
46	ILLUMINA	ss2633363644	Nov 08, 2017 (151)
47	GRF	ss2701906533	Nov 08, 2017 (151)
48	GNOMAD	ss2946736431	Nov 08, 2017 (151)
49	SWEGEN	ss3015047195	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3028281415	Nov 08, 2017 (151)
51	CSHL	ss3351608072	Nov 08, 2017 (151)
52	ILLUMINA	ss3641977877	Oct 12, 2018 (152)
53	URBANLAB	ss3650582802	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3682022154	Jul 13, 2019 (153)
55	EVA_DECODE	ss3699911162	Jul 13, 2019 (153)
56	ACPOP	ss3741794213	Jul 13, 2019 (153)
57	EVA	ss3754345892	Jul 13, 2019 (153)
58	PACBIO	ss3788124858	Jul 13, 2019 (153)
59	PACBIO	ss3793095817	Jul 13, 2019 (153)
60	PACBIO	ss3797981219	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3819616028	Jul 13, 2019 (153)
62	EVA	ss3834733384	Apr 27, 2020 (154)
63	EVA	ss3840973999	Apr 27, 2020 (154)
64	EVA	ss3846467799	Apr 27, 2020 (154)
65	SGDP_PRJ	ss3885145503	Apr 27, 2020 (154)
66	KRGDB	ss3934712309	Apr 27, 2020 (154)
67	VINODS	ss4032977334	Apr 26, 2021 (155)
68	TOPMED	ss5026703479	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5221082695	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5302117329	Oct 17, 2022 (156)
71	EVA	ss5315866032	Oct 17, 2022 (156)
72	EVA	ss5425841741	Oct 17, 2022 (156)
73	HUGCELL_USP	ss5495335111	Oct 17, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5605344619	Oct 17, 2022 (156)
75	SANFORD_IMAGENETICS	ss5659551592	Oct 17, 2022 (156)
76	TOMMO_GENOMICS	ss5776544252	Oct 17, 2022 (156)
77	YY_MCH	ss5816256120	Oct 17, 2022 (156)
78	EVA	ss5833598406	Oct 17, 2022 (156)
79	EVA	ss5851703206	Oct 17, 2022 (156)
80	EVA	ss5912897539	Oct 17, 2022 (156)
81	EVA	ss5950964398	Oct 17, 2022 (156)
82	1000Genomes	NC_000017.10 - 49663	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000017.11 - 199872	Oct 17, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 49663	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000017.10 - 49663	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000017.10 - 49663	Apr 27, 2020 (154)
87	gnomAD - Genomes	NC_000017.11 - 199872	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000017.10 - 49663	Apr 27, 2020 (154)
89	KOREAN population from KRGDB	NC_000017.10 - 49663	Apr 27, 2020 (154)
90	Northern Sweden	NC_000017.10 - 49663	Jul 13, 2019 (153)
91	Qatari	NC_000017.10 - 49663	Apr 27, 2020 (154)
92	SGDP_PRJ	NC_000017.10 - 49663	Apr 27, 2020 (154)
93	Siberian	NC_000017.10 - 49663	Apr 27, 2020 (154)
94	8.3KJPN	NC_000017.10 - 49663	Apr 26, 2021 (155)
95	14KJPN	NC_000017.11 - 199872	Oct 17, 2022 (156)
96	TopMed	NC_000017.11 - 199872	Apr 26, 2021 (155)
97	UK 10K study - Twins	NC_000017.10 - 49663	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000017.10 - 49663	Jul 13, 2019 (153)
99	ALFA	NC_000017.11 - 199872	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)
rs58085311	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77436135, ss79752949, ss90502084, ss109579129, ss117967089, ss167618734, ss171036077, ss202105012, ss207928975, ss211763320, ss282657875, ss287131468, ss291955619, ss483640328, ss1696874455	NC_000017.9:49662:T:C	NC_000017.11:199871:T:C	(self)
70772447, 39257641, 27760402, 4259142, 17500087, 41889703, 15079078, 18318166, 37162483, 9885638, 79052002, 39257641, 8698015, ss227420402, ss237151517, ss243467641, ss483178476, ss565113800, ss660894163, ss782032524, ss992833110, ss1080871235, ss1357570887, ss1427949443, ss1578052495, ss1635121049, ss1678115082, ss1808663754, ss1936276244, ss1968334060, ss2028927669, ss2157369284, ss2628954036, ss2633363644, ss2701906533, ss2946736431, ss3015047195, ss3351608072, ss3641977877, ss3682022154, ss3741794213, ss3754345892, ss3788124858, ss3793095817, ss3797981219, ss3834733384, ss3840973999, ss3885145503, ss3934712309, ss5221082695, ss5315866032, ss5425841741, ss5659551592, ss5833598406, ss5950964398	NC_000017.10:49662:T:C	NC_000017.11:199871:T:C	(self)
92870554, 499077749, 110381356, 242249141, 8612762392, ss2214838951, ss3028281415, ss3650582802, ss3699911162, ss3819616028, ss3846467799, ss5026703479, ss5302117329, ss5495335111, ss5605344619, ss5776544252, ss5816256120, ss5851703206, ss5912897539	NC_000017.11:199871:T:C	NC_000017.11:199871:T:C	(self)
ss14806306, ss20035095, ss21385720	NT_024972.7:49662:T:C	NC_000017.11:199871:T:C	(self)
ss6757064, ss96572784, ss106492584, ss136547320, ss136890269, ss157740678	NT_024972.8:49662:T:C	NC_000017.11:199871:T:C	(self)
ss4032977334	NW_003315952.3:138926:C:C	NC_000017.11:199871: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 rs4890182

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

rs4890182