Name: rs17225178
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.

rs17225178

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:80451525 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.096384 (25512/264690, TOPMED)
A=0.05843 (1651/28258, 14KJPN)
A=0.04905 (824/16798, ALFA) (+ 18 more)
A=0.05805 (973/16760, 8.3KJPN)
A=0.0920 (589/6404, 1000G_30x)
A=0.0946 (474/5008, 1000G)
A=0.0900 (403/4480, Estonian)
A=0.1162 (448/3854, ALSPAC)
A=0.1065 (395/3708, TWINSUK)
A=0.0743 (217/2922, KOREAN)
A=0.0863 (163/1888, HapMap)
A=0.0622 (114/1832, Korea1K)
A=0.143 (143/998, GoNL)
A=0.073 (58/790, PRJEB37584)
A=0.117 (70/600, NorthernSweden)
A=0.153 (33/216, Qatari)
A=0.107 (23/214, Vietnamese)
T=0.49 (37/76, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
T=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ARNT2 : Intron Variant
Publications: 2 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	16798	T=0.95095	A=0.04905, C=0.00000
European	Sub	12716	T=0.94031	A=0.05969, C=0.00000
African	Sub	2654	T=0.9842	A=0.0158, C=0.0000
African Others	Sub	104	T=0.971	A=0.029, C=0.000
African American	Sub	2550	T=0.9847	A=0.0153, C=0.0000
Asian	Sub	88	T=1.00	A=0.00, C=0.00
East Asian	Sub	66	T=1.00	A=0.00, C=0.00
Other Asian	Sub	22	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	118	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	538	T=1.000	A=0.000, C=0.000
South Asian	Sub	64	T=1.00	A=0.00, C=0.00
Other	Sub	620	T=0.963	A=0.037, C=0.000

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=0.903616	A=0.096384
14KJPN	JAPANESE	Study-wide	28258	T=0.94157	A=0.05843
Allele Frequency Aggregator	Total	Global	16798	T=0.95095	A=0.04905, C=0.00000
Allele Frequency Aggregator	European	Sub	12716	T=0.94031	A=0.05969, C=0.00000
Allele Frequency Aggregator	African	Sub	2654	T=0.9842	A=0.0158, C=0.0000
Allele Frequency Aggregator	Other	Sub	620	T=0.963	A=0.037, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	538	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	118	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	88	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	64	T=1.00	A=0.00, C=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.94195	A=0.05805
1000Genomes_30x	Global	Study-wide	6404	T=0.9080	A=0.0920
1000Genomes_30x	African	Sub	1786	T=0.9390	A=0.0610
1000Genomes_30x	Europe	Sub	1266	T=0.8839	A=0.1161
1000Genomes_30x	South Asian	Sub	1202	T=0.8694	A=0.1306
1000Genomes_30x	East Asian	Sub	1170	T=0.8949	A=0.1051
1000Genomes_30x	American	Sub	980	T=0.946	A=0.054
1000Genomes	Global	Study-wide	5008	T=0.9054	A=0.0946
1000Genomes	African	Sub	1322	T=0.9425	A=0.0575
1000Genomes	East Asian	Sub	1008	T=0.8938	A=0.1062
1000Genomes	Europe	Sub	1006	T=0.8877	A=0.1123
1000Genomes	South Asian	Sub	978	T=0.857	A=0.143
1000Genomes	American	Sub	694	T=0.945	A=0.055
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9100	A=0.0900
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8838	A=0.1162
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8935	A=0.1065
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9257	A=0.0743
HapMap	Global	Study-wide	1888	T=0.9137	A=0.0863
HapMap	American	Sub	766	T=0.903	A=0.097
HapMap	African	Sub	692	T=0.935	A=0.065
HapMap	Asian	Sub	254	T=0.929	A=0.071
HapMap	Europe	Sub	176	T=0.852	A=0.148
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9378	A=0.0622
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.857	A=0.143
CNV burdens in cranial meningiomas	Global	Study-wide	790	T=0.927	A=0.073
CNV burdens in cranial meningiomas	CRM	Sub	790	T=0.927	A=0.073
Northern Sweden	ACPOP	Study-wide	600	T=0.883	A=0.117
Qatari	Global	Study-wide	216	T=0.847	A=0.153
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.893	A=0.107
SGDP_PRJ	Global	Study-wide	76	T=0.49	A=0.51
The Danish reference pan genome	Danish	Study-wide	40	T=0.82	A=0.17
Siberian	Global	Study-wide	6	T=0.5	A=0.5

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 15	NC_000015.10:g.80451525T>A
GRCh38.p14 chr 15	NC_000015.10:g.80451525T>C
GRCh37.p13 chr 15	NC_000015.9:g.80743866T>A
GRCh37.p13 chr 15	NC_000015.9:g.80743866T>C

Gene: ARNT2, aryl hydrocarbon receptor nuclear translocator 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARNT2 transcript	NM_014862.4:c.146+531T>A	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=	A	C
GRCh38.p14 chr 15	NC_000015.10:g.80451525=	NC_000015.10:g.80451525T>A	NC_000015.10:g.80451525T>C
GRCh37.p13 chr 15	NC_000015.9:g.80743866=	NC_000015.9:g.80743866T>A	NC_000015.9:g.80743866T>C
ARNT2 transcript	NM_014862.3:c.146+531=	NM_014862.3:c.146+531T>A	NM_014862.3:c.146+531T>C
ARNT2 transcript	NM_014862.4:c.146+531=	NM_014862.4:c.146+531T>A	NM_014862.4:c.146+531T>C
ARNT2 transcript variant X1	XM_005254811.1:c.113+531=	XM_005254811.1:c.113+531T>A	XM_005254811.1:c.113+531T>C
ARNT2 transcript variant X2	XM_005254812.1:c.113+531=	XM_005254812.1:c.113+531T>A	XM_005254812.1:c.113+531T>C
ARNT2 transcript variant X3	XM_005254813.1:c.146+531=	XM_005254813.1:c.146+531T>A	XM_005254813.1:c.146+531T>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#.

57 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24524913	Sep 20, 2004 (123)
2	AFFY	ss66087712	Nov 30, 2006 (127)
3	AFFY	ss76037663	Dec 06, 2007 (129)
4	KRIBB_YJKIM	ss83227056	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss90227017	Mar 24, 2008 (129)
6	1000GENOMES	ss108979056	Jan 23, 2009 (130)
7	COMPLETE_GENOMICS	ss168384283	Jul 04, 2010 (132)
8	1000GENOMES	ss226996036	Jul 14, 2010 (132)
9	1000GENOMES	ss236851643	Jul 15, 2010 (132)
10	1000GENOMES	ss243225925	Jul 15, 2010 (132)
11	GMI	ss282334460	May 04, 2012 (137)
12	SSMP	ss660341632	Apr 25, 2013 (138)
13	EVA-GONL	ss991997621	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1080278791	Aug 21, 2014 (142)
15	1000GENOMES	ss1354287457	Aug 21, 2014 (142)
16	DDI	ss1427690994	Apr 01, 2015 (144)
17	EVA_GENOME_DK	ss1577719453	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1633439945	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1676433978	Apr 01, 2015 (144)
20	EVA_DECODE	ss1696023790	Apr 01, 2015 (144)
21	EVA_SVP	ss1713505481	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1935400815	Feb 12, 2016 (147)
23	JJLAB	ss2028482743	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2156891935	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2208466768	Dec 20, 2016 (150)
26	SYSTEMSBIOZJU	ss2628737511	Nov 08, 2017 (151)
27	GRF	ss2701373442	Nov 08, 2017 (151)
28	GNOMAD	ss2937264967	Nov 08, 2017 (151)
29	SWEGEN	ss3013618322	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3028066006	Nov 08, 2017 (151)
31	CSHL	ss3351206818	Nov 08, 2017 (151)
32	EGCUT_WGS	ss3680756950	Jul 13, 2019 (153)
33	EVA_DECODE	ss3698298850	Jul 13, 2019 (153)
34	ACPOP	ss3741100833	Jul 13, 2019 (153)
35	EVA	ss3753344453	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3818648193	Jul 13, 2019 (153)
37	EVA	ss3834337330	Apr 27, 2020 (154)
38	EVA	ss3840768821	Apr 27, 2020 (154)
39	EVA	ss3846258929	Apr 27, 2020 (154)
40	SGDP_PRJ	ss3883345273	Apr 27, 2020 (154)
41	KRGDB	ss3932578012	Apr 27, 2020 (154)
42	KOGIC	ss3976572253	Apr 27, 2020 (154)
43	EVA	ss3984704721	Apr 26, 2021 (155)
44	TOPMED	ss4998619346	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5217160249	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5299163868	Oct 16, 2022 (156)
47	EVA	ss5420559627	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5492815386	Oct 16, 2022 (156)
49	EVA	ss5511496507	Oct 16, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5600926012	Oct 16, 2022 (156)
51	SANFORD_IMAGENETICS	ss5657917115	Oct 16, 2022 (156)
52	TOMMO_GENOMICS	ss5771255438	Oct 16, 2022 (156)
53	YY_MCH	ss5815516340	Oct 16, 2022 (156)
54	EVA	ss5828481675	Oct 16, 2022 (156)
55	EVA	ss5851378024	Oct 16, 2022 (156)
56	EVA	ss5876708519	Oct 16, 2022 (156)
57	EVA	ss5949336123	Oct 16, 2022 (156)
58	1000Genomes	NC_000015.9 - 80743866	Oct 12, 2018 (152)
59	1000Genomes_30x	NC_000015.10 - 80451525	Oct 16, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 80743866	Oct 12, 2018 (152)
61	Genetic variation in the Estonian population	NC_000015.9 - 80743866	Oct 12, 2018 (152)
62	The Danish reference pan genome	NC_000015.9 - 80743866	Apr 27, 2020 (154)
63	gnomAD - Genomes Submission ignored due to conflicting rows: Row 475097107 (NC_000015.10:80451524:T:A 13874/140234) Row 475097108 (NC_000015.10:80451524:T:C 1/140246)	-	Apr 26, 2021 (155)
64	gnomAD - Genomes Submission ignored due to conflicting rows: Row 475097107 (NC_000015.10:80451524:T:A 13874/140234) Row 475097108 (NC_000015.10:80451524:T:C 1/140246)	-	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000015.9 - 80743866	Apr 27, 2020 (154)
66	HapMap	NC_000015.10 - 80451525	Apr 27, 2020 (154)
67	KOREAN population from KRGDB	NC_000015.9 - 80743866	Apr 27, 2020 (154)
68	Korean Genome Project	NC_000015.10 - 80451525	Apr 27, 2020 (154)
69	Northern Sweden	NC_000015.9 - 80743866	Jul 13, 2019 (153)
70	CNV burdens in cranial meningiomas	NC_000015.9 - 80743866	Apr 26, 2021 (155)
71	Qatari	NC_000015.9 - 80743866	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000015.9 - 80743866	Apr 27, 2020 (154)
73	Siberian	NC_000015.9 - 80743866	Apr 27, 2020 (154)
74	8.3KJPN	NC_000015.9 - 80743866	Apr 26, 2021 (155)
75	14KJPN	NC_000015.10 - 80451525	Oct 16, 2022 (156)
76	TopMed	NC_000015.10 - 80451525	Apr 26, 2021 (155)
77	UK 10K study - Twins	NC_000015.9 - 80743866	Oct 12, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000015.9 - 80743866	Jul 13, 2019 (153)
79	ALFA	NC_000015.10 - 80451525	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)
rs60099646	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66087712, ss76037663, ss90227017, ss108979056, ss168384283, ss282334460, ss1696023790, ss1713505481	NC_000015.8:78530920:T:A	NC_000015.10:80451524:T:A	(self)
67388928, 37423390, 26495198, 3939757, 16699455, 39755406, 14385698, 254246, 17442745, 35362253, 9408289, 75129556, 37423390, 8320135, ss226996036, ss236851643, ss243225925, ss660341632, ss991997621, ss1080278791, ss1354287457, ss1427690994, ss1577719453, ss1633439945, ss1676433978, ss1935400815, ss2028482743, ss2156891935, ss2628737511, ss2701373442, ss2937264967, ss3013618322, ss3351206818, ss3680756950, ss3741100833, ss3753344453, ss3834337330, ss3840768821, ss3883345273, ss3932578012, ss3984704721, ss5217160249, ss5420559627, ss5511496507, ss5657917115, ss5828481675, ss5949336123	NC_000015.9:80743865:T:A	NC_000015.10:80451524:T:A	(self)
88451947, 1302136, 32950254, 105092542, 214165006, 8019250775, ss2208466768, ss3028066006, ss3698298850, ss3818648193, ss3846258929, ss3976572253, ss4998619346, ss5299163868, ss5492815386, ss5600926012, ss5771255438, ss5815516340, ss5851378024, ss5876708519	NC_000015.10:80451524:T:A	NC_000015.10:80451524:T:A	(self)
ss24524913, ss83227056	NT_010194.17:51534422:T:A	NC_000015.10:80451524:T:A	(self)
8019250775	NC_000015.10:80451524:T:C	NC_000015.10:80451524:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs17225178

PMID	Title	Author	Year	Journal
27899901	Association of Aryl Hydrocarbon Receptor-Related Gene Variants with the Severity of Autism Spectrum Disorders.	Fujisawa TX et al.	2016	Frontiers in psychiatry
34502168	Influence of the Aryl Hydrocarbon Receptor Activating Environmental Pollutants on Autism Spectrum Disorder.	Dhulkifle H et al.	2021	International journal of molecular sciences

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

rs17225178