Name: rs2017543
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.

rs2017543

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:35078229 (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: C=0.074007 (19589/264690, TOPMED)
C=0.077752 (10855/139610, GnomAD)
C=0.09394 (6716/71490, ALFA) (+ 20 more)
C=0.01263 (357/28258, 14KJPN)
C=0.01342 (225/16760, 8.3KJPN)
C=0.0657 (421/6404, 1000G_30x)
C=0.0661 (331/5008, 1000G)
C=0.0938 (420/4478, Estonian)
C=0.0996 (384/3854, ALSPAC)
C=0.0992 (368/3708, TWINSUK)
C=0.0082 (24/2922, KOREAN)
C=0.0725 (151/2084, HGDP_Stanford)
C=0.0514 (97/1886, HapMap)
C=0.0066 (12/1832, Korea1K)
C=0.0966 (109/1128, Daghestan)
C=0.098 (98/998, GoNL)
C=0.085 (51/600, NorthernSweden)
C=0.083 (18/216, Qatari)
C=0.009 (2/216, Vietnamese)
T=0.41 (19/46, SGDP_PRJ)
C=0.10 (4/40, GENOME_DK)
C=0.00 (0/24, Ancient Sardinia)
T=0.4 (3/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ISX : 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	71490	T=0.90606	C=0.09394
European	Sub	58846	T=0.90341	C=0.09659
African	Sub	4530	T=0.9400	C=0.0600
African Others	Sub	170	T=0.976	C=0.024
African American	Sub	4360	T=0.9385	C=0.0615
Asian	Sub	192	T=0.990	C=0.010
East Asian	Sub	150	T=0.987	C=0.013
Other Asian	Sub	42	T=1.00	C=0.00
Latin American 1	Sub	254	T=0.909	C=0.091
Latin American 2	Sub	1230	T=0.9431	C=0.0569
South Asian	Sub	4954	T=0.8920	C=0.1080
Other	Sub	1484	T=0.9124	C=0.0876

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=0.925993	C=0.074007
gnomAD - Genomes	Global	Study-wide	139610	T=0.922248	C=0.077752
gnomAD - Genomes	European	Sub	75762	T=0.90482	C=0.09518
gnomAD - Genomes	African	Sub	41678	T=0.94302	C=0.05698
gnomAD - Genomes	American	Sub	13580	T=0.93675	C=0.06325
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	T=0.9340	C=0.0660
gnomAD - Genomes	East Asian	Sub	3132	T=0.9904	C=0.0096
gnomAD - Genomes	Other	Sub	2142	T=0.9248	C=0.0752
Allele Frequency Aggregator	Total	Global	71490	T=0.90606	C=0.09394
Allele Frequency Aggregator	European	Sub	58846	T=0.90341	C=0.09659
Allele Frequency Aggregator	South Asian	Sub	4954	T=0.8920	C=0.1080
Allele Frequency Aggregator	African	Sub	4530	T=0.9400	C=0.0600
Allele Frequency Aggregator	Other	Sub	1484	T=0.9124	C=0.0876
Allele Frequency Aggregator	Latin American 2	Sub	1230	T=0.9431	C=0.0569
Allele Frequency Aggregator	Latin American 1	Sub	254	T=0.909	C=0.091
Allele Frequency Aggregator	Asian	Sub	192	T=0.990	C=0.010
14KJPN	JAPANESE	Study-wide	28258	T=0.98737	C=0.01263
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98658	C=0.01342
1000Genomes_30x	Global	Study-wide	6404	T=0.9343	C=0.0657
1000Genomes_30x	African	Sub	1786	T=0.9541	C=0.0459
1000Genomes_30x	Europe	Sub	1266	T=0.8934	C=0.1066
1000Genomes_30x	South Asian	Sub	1202	T=0.8802	C=0.1198
1000Genomes_30x	East Asian	Sub	1170	T=0.9889	C=0.0111
1000Genomes_30x	American	Sub	980	T=0.952	C=0.048
1000Genomes	Global	Study-wide	5008	T=0.9339	C=0.0661
1000Genomes	African	Sub	1322	T=0.9486	C=0.0514
1000Genomes	East Asian	Sub	1008	T=0.9871	C=0.0129
1000Genomes	Europe	Sub	1006	T=0.9006	C=0.0994
1000Genomes	South Asian	Sub	978	T=0.881	C=0.119
1000Genomes	American	Sub	694	T=0.951	C=0.049
Genetic variation in the Estonian population	Estonian	Study-wide	4478	T=0.9062	C=0.0938
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9004	C=0.0996
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9008	C=0.0992
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9918	C=0.0082
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.9275	C=0.0725
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.974	C=0.026
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.886	C=0.114
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.869	C=0.131
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.897	C=0.103
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.959	C=0.041
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.986	C=0.014
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=1.00	C=0.00
HapMap	Global	Study-wide	1886	T=0.9486	C=0.0514
HapMap	American	Sub	766	T=0.930	C=0.070
HapMap	African	Sub	690	T=0.970	C=0.030
HapMap	Asian	Sub	254	T=0.984	C=0.016
HapMap	Europe	Sub	176	T=0.898	C=0.102
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9934	C=0.0066
Genome-wide autozygosity in Daghestan	Global	Study-wide	1128	T=0.9034	C=0.0966
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	T=0.909	C=0.091
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	T=0.901	C=0.099
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.934	C=0.066
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.880	C=0.120
Genome-wide autozygosity in Daghestan	South Asian	Sub	94	T=0.85	C=0.15
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.92	C=0.08
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.902	C=0.098
Northern Sweden	ACPOP	Study-wide	600	T=0.915	C=0.085
Qatari	Global	Study-wide	216	T=0.917	C=0.083
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.991	C=0.009
SGDP_PRJ	Global	Study-wide	46	T=0.41	C=0.59
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	C=0.10
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	24	T=1.00	C=0.00
Siberian	Global	Study-wide	8	T=0.4	C=0.6

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 22	NC_000022.11:g.35078229T>C
GRCh37.p13 chr 22	NC_000022.10:g.35474222T>C

Gene: ISX, intestine specific homeobox (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ISX transcript	NM_001303508.2:c.230-4289… NM_001303508.2:c.230-4289T>C	N/A	Intron Variant
ISX transcript variant X1	XM_047441598.1:c.230-4289… XM_047441598.1:c.230-4289T>C	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 22	NC_000022.11:g.35078229=	NC_000022.11:g.35078229T>C
GRCh37.p13 chr 22	NC_000022.10:g.35474222=	NC_000022.10:g.35474222T>C
ISX transcript	NM_001008494.1:c.230-4289=	NM_001008494.1:c.230-4289T>C
ISX transcript	NM_001303508.2:c.230-4289=	NM_001303508.2:c.230-4289T>C
ISX transcript variant X1	XM_047441598.1:c.230-4289=	XM_047441598.1:c.230-4289T>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#.

74 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss22890	Oct 08, 2002 (108)
2	TSC-CSHL	ss2864896	Jan 23, 2001 (92)
3	SC_JCM	ss5952360	Feb 20, 2003 (111)
4	ILLUMINA	ss66834729	Nov 29, 2006 (127)
5	ILLUMINA	ss67215695	Nov 29, 2006 (127)
6	ILLUMINA	ss67609404	Nov 29, 2006 (127)
7	ILLUMINA	ss70693959	May 27, 2008 (130)
8	ILLUMINA	ss71259278	May 16, 2007 (127)
9	ILLUMINA	ss75879759	Dec 07, 2007 (129)
10	ILLUMINA	ss79107669	Dec 16, 2007 (130)
11	KRIBB_YJKIM	ss83945310	Dec 16, 2007 (130)
12	BGI	ss103860428	Dec 01, 2009 (131)
13	1000GENOMES	ss112634301	Jan 25, 2009 (130)
14	ILLUMINA	ss121885741	Dec 01, 2009 (131)
15	ILLUMINA	ss153816971	Dec 01, 2009 (131)
16	ILLUMINA	ss159349331	Dec 01, 2009 (131)
17	ILLUMINA	ss170948894	Jul 04, 2010 (132)
18	ILLUMINA	ss173046720	Jul 04, 2010 (132)
19	BUSHMAN	ss204084493	Jul 04, 2010 (132)
20	1000GENOMES	ss228674608	Jul 14, 2010 (132)
21	1000GENOMES	ss238065702	Jul 15, 2010 (132)
22	BL	ss255892232	May 09, 2011 (134)
23	ILLUMINA	ss537023332	Sep 08, 2015 (146)
24	TISHKOFF	ss566634373	Apr 25, 2013 (138)
25	SSMP	ss662565137	Apr 25, 2013 (138)
26	ILLUMINA	ss825438187	Apr 01, 2015 (144)
27	ILLUMINA	ss832861271	Jul 13, 2019 (153)
28	EVA-GONL	ss995342732	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1082652287	Aug 21, 2014 (142)
30	1000GENOMES	ss1367131607	Aug 21, 2014 (142)
31	HAMMER_LAB	ss1397785431	Sep 08, 2015 (146)
32	EVA_GENOME_DK	ss1579749717	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1639977293	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1682971326	Apr 01, 2015 (144)
35	EVA_DECODE	ss1699413093	Apr 01, 2015 (144)
36	EVA_SVP	ss1713740549	Apr 01, 2015 (144)
37	WEILL_CORNELL_DGM	ss1938909074	Feb 12, 2016 (147)
38	JJLAB	ss2030226830	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2158845237	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2247260690	Dec 20, 2016 (150)
41	GNOMAD	ss2974291782	Nov 08, 2017 (151)
42	SWEGEN	ss3019290406	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3028950613	Nov 08, 2017 (151)
44	CSHL	ss3352833931	Nov 08, 2017 (151)
45	ILLUMINA	ss3628532017	Oct 12, 2018 (152)
46	ILLUMINA	ss3638382058	Oct 12, 2018 (152)
47	ILLUMINA	ss3639194845	Oct 12, 2018 (152)
48	ILLUMINA	ss3639614073	Oct 12, 2018 (152)
49	ILLUMINA	ss3643341858	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3685786128	Jul 13, 2019 (153)
51	EVA_DECODE	ss3708184298	Jul 13, 2019 (153)
52	ACPOP	ss3743927278	Jul 13, 2019 (153)
53	EVA	ss3759373080	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3822536948	Jul 13, 2019 (153)
55	EVA	ss3835988085	Apr 27, 2020 (154)
56	HGDP	ss3847689028	Apr 27, 2020 (154)
57	SGDP_PRJ	ss3890529335	Apr 27, 2020 (154)
58	KRGDB	ss3940924063	Apr 27, 2020 (154)
59	KOGIC	ss3983626506	Apr 27, 2020 (154)
60	EVA	ss3985917310	Apr 26, 2021 (155)
61	EVA	ss4017880259	Apr 26, 2021 (155)
62	TOPMED	ss5108940499	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5232588961	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5311072783	Oct 16, 2022 (156)
65	EVA	ss5441250210	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5502917287	Oct 16, 2022 (156)
67	EVA	ss5512380260	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5618615702	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5664478551	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5793697141	Oct 16, 2022 (156)
71	YY_MCH	ss5818706371	Oct 16, 2022 (156)
72	EVA	ss5822061274	Oct 16, 2022 (156)
73	EVA	ss5881789617	Oct 16, 2022 (156)
74	EVA	ss5959333670	Oct 16, 2022 (156)
75	1000Genomes	NC_000022.10 - 35474222	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000022.11 - 35078229	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 35474222	Oct 12, 2018 (152)
78	Genome-wide autozygosity in Daghestan	NC_000022.9 - 33804222	Apr 27, 2020 (154)
79	Genetic variation in the Estonian population	NC_000022.10 - 35474222	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000022.10 - 35474222	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000022.11 - 35078229	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000022.10 - 35474222	Apr 27, 2020 (154)
83	HGDP-CEPH-db Supplement 1	NC_000022.9 - 33804222	Apr 27, 2020 (154)
84	HapMap	NC_000022.11 - 35078229	Apr 27, 2020 (154)
85	KOREAN population from KRGDB	NC_000022.10 - 35474222	Apr 27, 2020 (154)
86	Korean Genome Project	NC_000022.11 - 35078229	Apr 27, 2020 (154)
87	Northern Sweden	NC_000022.10 - 35474222	Jul 13, 2019 (153)
88	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000022.10 - 35474222	Apr 26, 2021 (155)
89	Qatari	NC_000022.10 - 35474222	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000022.10 - 35474222	Apr 27, 2020 (154)
91	Siberian	NC_000022.10 - 35474222	Apr 27, 2020 (154)
92	8.3KJPN	NC_000022.10 - 35474222	Apr 26, 2021 (155)
93	14KJPN	NC_000022.11 - 35078229	Oct 16, 2022 (156)
94	TopMed	NC_000022.11 - 35078229	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000022.10 - 35474222	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000022.10 - 35474222	Jul 13, 2019 (153)
97	ALFA	NC_000022.11 - 35078229	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)
rs61587647	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3639194845, ss3639614073	NC_000022.8:33798775:T:C	NC_000022.11:35078228:T:C	(self)
299391, 366920, ss112634301, ss204084493, ss255892232, ss825438187, ss1397785431, ss1699413093, ss1713740549, ss3643341858, ss3847689028	NC_000022.9:33804221:T:C	NC_000022.11:35078228:T:C	(self)
80682529, 44629934, 31524376, 5914656, 19887553, 48101457, 17212143, 1143237, 20950996, 42546315, 11361591, 90558268, 44629934, 9846693, ss228674608, ss238065702, ss537023332, ss566634373, ss662565137, ss832861271, ss995342732, ss1082652287, ss1367131607, ss1579749717, ss1639977293, ss1682971326, ss1938909074, ss2030226830, ss2158845237, ss2974291782, ss3019290406, ss3352833931, ss3628532017, ss3638382058, ss3685786128, ss3743927278, ss3759373080, ss3835988085, ss3890529335, ss3940924063, ss3985917310, ss4017880259, ss5232588961, ss5441250210, ss5512380260, ss5664478551, ss5822061274, ss5959333670	NC_000022.10:35474221:T:C	NC_000022.11:35078228:T:C	(self)
106141637, 569744944, 2254056, 40004507, 127534245, 384049446, 1042944170, ss2247260690, ss3028950613, ss3708184298, ss3822536948, ss3983626506, ss5108940499, ss5311072783, ss5502917287, ss5618615702, ss5793697141, ss5818706371, ss5881789617	NC_000022.11:35078228:T:C	NC_000022.11:35078228:T:C	(self)
ss22890, ss2864896, ss5952360, ss66834729, ss67215695, ss67609404, ss70693959, ss71259278, ss75879759, ss79107669, ss83945310, ss103860428, ss121885741, ss153816971, ss159349331, ss170948894, ss173046720	NT_011520.12:14864790:T:C	NC_000022.11:35078228: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 rs2017543

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

rs2017543