Name: rs1217400
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.

rs1217400

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:113893741 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.412483 (109180/264690, TOPMED)
T=0.418798 (58429/139516, GnomAD)
T=0.13838 (3910/28256, 14KJPN) (+ 17 more)
T=0.36849 (6649/18044, ALFA)
T=0.13711 (2298/16760, 8.3KJPN)
T=0.3863 (2474/6404, 1000G_30x)
T=0.3748 (1877/5008, 1000G)
T=0.3481 (1558/4476, Estonian)
T=0.3210 (1237/3854, ALSPAC)
T=0.3360 (1246/3708, TWINSUK)
T=0.0691 (202/2922, KOREAN)
T=0.0693 (127/1832, Korea1K)
T=0.341 (340/998, GoNL)
T=0.343 (206/600, NorthernSweden)
C=0.367 (88/240, SGDP_PRJ)
T=0.380 (82/216, Qatari)
T=0.075 (16/214, Vietnamese)
T=0.30 (12/40, GENOME_DK)
T=0.05 (2/38, Ancient Sardinia)
C=0.47 (14/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AP4B1-AS1 : Intron Variant
AP4B1 : 500B Downstream 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18044	C=0.63151	A=0.00000, T=0.36849
European	Sub	13928	C=0.67906	A=0.00000, T=0.32094
African	Sub	2460	C=0.3033	A=0.0000, T=0.6967
African Others	Sub	90	C=0.17	A=0.00, T=0.83
African American	Sub	2370	C=0.3084	A=0.0000, T=0.6916
Asian	Sub	112	C=0.893	A=0.000, T=0.107
East Asian	Sub	86	C=0.94	A=0.00, T=0.06
Other Asian	Sub	26	C=0.73	A=0.00, T=0.27
Latin American 1	Sub	146	C=0.630	A=0.000, T=0.370
Latin American 2	Sub	610	C=0.805	A=0.000, T=0.195
South Asian	Sub	98	C=0.73	A=0.00, T=0.27
Other	Sub	690	C=0.632	A=0.000, T=0.368

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	C=0.587517	T=0.412483
gnomAD - Genomes	Global	Study-wide	139516	C=0.581202	T=0.418798
gnomAD - Genomes	European	Sub	75636	C=0.68815	T=0.31185
gnomAD - Genomes	African	Sub	41726	C=0.30386	T=0.69614
gnomAD - Genomes	American	Sub	13572	C=0.74816	T=0.25184
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.6007	T=0.3993
gnomAD - Genomes	East Asian	Sub	3118	C=0.9349	T=0.0651
gnomAD - Genomes	Other	Sub	2148	C=0.6043	T=0.3957
14KJPN	JAPANESE	Study-wide	28256	C=0.86162	T=0.13838
Allele Frequency Aggregator	Total	Global	18044	C=0.63151	A=0.00000, T=0.36849
Allele Frequency Aggregator	European	Sub	13928	C=0.67906	A=0.00000, T=0.32094
Allele Frequency Aggregator	African	Sub	2460	C=0.3033	A=0.0000, T=0.6967
Allele Frequency Aggregator	Other	Sub	690	C=0.632	A=0.000, T=0.368
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.805	A=0.000, T=0.195
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.630	A=0.000, T=0.370
Allele Frequency Aggregator	Asian	Sub	112	C=0.893	A=0.000, T=0.107
Allele Frequency Aggregator	South Asian	Sub	98	C=0.73	A=0.00, T=0.27
8.3KJPN	JAPANESE	Study-wide	16760	C=0.86289	T=0.13711
1000Genomes_30x	Global	Study-wide	6404	C=0.6137	T=0.3863
1000Genomes_30x	African	Sub	1786	C=0.2004	T=0.7996
1000Genomes_30x	Europe	Sub	1266	C=0.7259	T=0.2741
1000Genomes_30x	South Asian	Sub	1202	C=0.6938	T=0.3062
1000Genomes_30x	East Asian	Sub	1170	C=0.9222	T=0.0778
1000Genomes_30x	American	Sub	980	C=0.755	T=0.245
1000Genomes	Global	Study-wide	5008	C=0.6252	T=0.3748
1000Genomes	African	Sub	1322	C=0.2080	T=0.7920
1000Genomes	East Asian	Sub	1008	C=0.9206	T=0.0794
1000Genomes	Europe	Sub	1006	C=0.7296	T=0.2704
1000Genomes	South Asian	Sub	978	C=0.690	T=0.310
1000Genomes	American	Sub	694	C=0.748	T=0.252
Genetic variation in the Estonian population	Estonian	Study-wide	4476	C=0.6519	T=0.3481
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6790	T=0.3210
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6640	T=0.3360
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9309	T=0.0691
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9307	T=0.0693
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.659	T=0.341
Northern Sweden	ACPOP	Study-wide	600	C=0.657	T=0.343
SGDP_PRJ	Global	Study-wide	240	C=0.367	T=0.633
Qatari	Global	Study-wide	216	C=0.620	T=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.925	T=0.075
The Danish reference pan genome	Danish	Study-wide	40	C=0.70	T=0.30
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	38	C=0.95	T=0.05
Siberian	Global	Study-wide	30	C=0.47	T=0.53

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.113893741C>A
GRCh38.p14 chr 1	NC_000001.11:g.113893741C>T
GRCh37.p13 chr 1	NC_000001.10:g.114436363C>A
GRCh37.p13 chr 1	NC_000001.10:g.114436363C>T
AP4B1 RefSeqGene	NG_031901.1:g.16379G>T
AP4B1 RefSeqGene	NG_031901.1:g.16379G>A

Gene: AP4B1, adaptor related protein complex 4 subunit beta 1 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
AP4B1 transcript variant 2	NM_001253852.3:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant 3	NM_001253853.3:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant 4	NM_001308312.2:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant 1	NM_006594.5:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X2	XM_011540523.4:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X3	XM_011540525.4:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X5	XM_017000090.2:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X7	XM_017000091.3:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X4	XM_024452423.2:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X6	XM_024452435.2:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X9	XM_024452441.2:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X1	XM_047438847.1:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X8	XM_047439008.1:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X11	XM_047439078.1:c.	N/A	Downstream Transcript Variant
AP4B1 transcript variant X12	XM_017000093.3:c.	N/A	N/A
AP4B1 transcript variant X10	XM_047439052.1:c.	N/A	N/A
AP4B1 transcript variant X13	XR_007066904.1:n.	N/A	N/A

Gene: AP4B1-AS1, AP4B1 antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AP4B1-AS1 transcript variant 2	NR_037864.1:n.	N/A	Intron Variant
AP4B1-AS1 transcript variant 1	NR_125965.1: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	C=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.113893741=	NC_000001.11:g.113893741C>A	NC_000001.11:g.113893741C>T
GRCh37.p13 chr 1	NC_000001.10:g.114436363=	NC_000001.10:g.114436363C>A	NC_000001.10:g.114436363C>T
AP4B1 RefSeqGene	NG_031901.1:g.16379=	NG_031901.1:g.16379G>T	NG_031901.1:g.16379G>A

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, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1775010	Oct 18, 2000 (87)
2	SC_JCM	ss3470741	Sep 28, 2001 (100)
3	CSHL-HAPMAP	ss19142458	Feb 27, 2004 (120)
4	SSAHASNP	ss20461519	Apr 05, 2004 (121)
5	ABI	ss41138285	Mar 14, 2006 (126)
6	HGSV	ss81809195	Dec 15, 2007 (130)
7	HGSV	ss84316395	Dec 15, 2007 (130)
8	HUMANGENOME_JCVI	ss99242319	Feb 05, 2009 (130)
9	1000GENOMES	ss111038192	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss118982136	Dec 01, 2009 (131)
11	ENSEMBL	ss139271809	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163933076	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss167019957	Jul 04, 2010 (132)
14	BUSHMAN	ss198955624	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss205173042	Jul 04, 2010 (132)
16	1000GENOMES	ss218606537	Jul 14, 2010 (132)
17	1000GENOMES	ss230698894	Jul 14, 2010 (132)
18	1000GENOMES	ss238355105	Jul 15, 2010 (132)
19	GMI	ss275984926	May 04, 2012 (137)
20	PJP	ss290602412	May 09, 2011 (134)
21	TISHKOFF	ss554595336	Apr 25, 2013 (138)
22	SSMP	ss648324467	Apr 25, 2013 (138)
23	EVA-GONL	ss975588808	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1068206461	Aug 21, 2014 (142)
25	1000GENOMES	ss1292503502	Aug 21, 2014 (142)
26	DDI	ss1425942699	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1574334554	Apr 01, 2015 (144)
28	EVA_DECODE	ss1584969695	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1601028029	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1644022062	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1794958995	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1918788909	Feb 12, 2016 (147)
33	JJLAB	ss2019918859	Sep 14, 2016 (149)
34	CSHL	ss2136657025	Nov 08, 2017 (151)
35	USC_VALOUEV	ss2147937743	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2165860819	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2624469112	Nov 08, 2017 (151)
38	GRF	ss2697868063	Nov 08, 2017 (151)
39	GNOMAD	ss2759764788	Nov 08, 2017 (151)
40	AFFY	ss2984871581	Nov 08, 2017 (151)
41	SWEGEN	ss2987467933	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3023723994	Nov 08, 2017 (151)
43	CSHL	ss3343643315	Nov 08, 2017 (151)
44	URBANLAB	ss3646756670	Oct 11, 2018 (152)
45	EGCUT_WGS	ss3655556846	Jul 12, 2019 (153)
46	EVA_DECODE	ss3687565979	Jul 12, 2019 (153)
47	ACPOP	ss3727404019	Jul 12, 2019 (153)
48	EVA	ss3746693920	Jul 12, 2019 (153)
49	PACBIO	ss3783524622	Jul 12, 2019 (153)
50	PACBIO	ss3789165608	Jul 12, 2019 (153)
51	PACBIO	ss3794038541	Jul 12, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3799696612	Jul 12, 2019 (153)
53	EVA	ss3826379280	Apr 25, 2020 (154)
54	EVA	ss3836581339	Apr 25, 2020 (154)
55	EVA	ss3841989784	Apr 25, 2020 (154)
56	SGDP_PRJ	ss3849686664	Apr 25, 2020 (154)
57	KRGDB	ss3894785781	Apr 25, 2020 (154)
58	KOGIC	ss3945283944	Apr 25, 2020 (154)
59	EVA	ss3984820464	Apr 25, 2021 (155)
60	TOPMED	ss4464237620	Apr 25, 2021 (155)
61	TOMMO_GENOMICS	ss5145762514	Apr 25, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5243671148	Oct 12, 2022 (156)
63	EVA	ss5321297248	Oct 12, 2022 (156)
64	HUGCELL_USP	ss5444588447	Oct 12, 2022 (156)
65	EVA	ss5506003118	Oct 12, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5516696218	Oct 12, 2022 (156)
67	SANFORD_IMAGENETICS	ss5626333305	Oct 12, 2022 (156)
68	TOMMO_GENOMICS	ss5671055710	Oct 12, 2022 (156)
69	YY_MCH	ss5800947144	Oct 12, 2022 (156)
70	EVA	ss5832508010	Oct 12, 2022 (156)
71	EVA	ss5849075122	Oct 12, 2022 (156)
72	EVA	ss5909871983	Oct 12, 2022 (156)
73	EVA	ss5938201159	Oct 12, 2022 (156)
74	EVA	ss5979979502	Oct 12, 2022 (156)
75	1000Genomes	NC_000001.10 - 114436363	Oct 11, 2018 (152)
76	1000Genomes_30x	NC_000001.11 - 113893741	Oct 12, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 114436363	Oct 11, 2018 (152)
78	Genetic variation in the Estonian population	NC_000001.10 - 114436363	Oct 11, 2018 (152)
79	The Danish reference pan genome	NC_000001.10 - 114436363	Apr 25, 2020 (154)
80	gnomAD - Genomes	NC_000001.11 - 113893741	Apr 25, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000001.10 - 114436363	Apr 25, 2020 (154)
82	KOREAN population from KRGDB	NC_000001.10 - 114436363	Apr 25, 2020 (154)
83	Korean Genome Project	NC_000001.11 - 113893741	Apr 25, 2020 (154)
84	Northern Sweden	NC_000001.10 - 114436363	Jul 12, 2019 (153)
85	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 114436363	Apr 25, 2021 (155)
86	Qatari	NC_000001.10 - 114436363	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000001.10 - 114436363	Apr 25, 2020 (154)
88	Siberian	NC_000001.10 - 114436363	Apr 25, 2020 (154)
89	8.3KJPN	NC_000001.10 - 114436363	Apr 25, 2021 (155)
90	14KJPN	NC_000001.11 - 113893741	Oct 12, 2022 (156)
91	TopMed	NC_000001.11 - 113893741	Apr 25, 2021 (155)
92	UK 10K study - Twins	NC_000001.10 - 114436363	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000001.10 - 114436363	Jul 12, 2019 (153)
94	ALFA	NC_000001.11 - 113893741	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)
rs59829316	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
12938535546	NC_000001.11:113893740:C:A	NC_000001.11:113893740:C:A	(self)
ss81809195, ss84316395	NC_000001.8:114148404:C:T	NC_000001.11:113893740:C:T	(self)
ss111038192, ss118982136, ss163933076, ss167019957, ss198955624, ss205173042, ss275984926, ss290602412, ss1584969695, ss2136657025	NC_000001.9:114237885:C:T	NC_000001.11:113893740:C:T	(self)
3281996, 1815782, 1295094, 1672048, 789605, 1963175, 688884, 46391, 830839, 1703644, 454097, 3731821, 1815782, 393077, ss218606537, ss230698894, ss238355105, ss554595336, ss648324467, ss975588808, ss1068206461, ss1292503502, ss1425942699, ss1574334554, ss1601028029, ss1644022062, ss1794958995, ss1918788909, ss2019918859, ss2147937743, ss2624469112, ss2697868063, ss2759764788, ss2984871581, ss2987467933, ss3343643315, ss3655556846, ss3727404019, ss3746693920, ss3783524622, ss3789165608, ss3794038541, ss3826379280, ss3836581339, ss3849686664, ss3894785781, ss3984820464, ss5145762514, ss5321297248, ss5506003118, ss5626333305, ss5832508010, ss5938201159, ss5979979502	NC_000001.10:114436362:C:T	NC_000001.11:113893740:C:T	(self)
4222153, 23216450, 1661945, 4892814, 27843955, 12938535546, ss2165860819, ss3023723994, ss3646756670, ss3687565979, ss3799696612, ss3841989784, ss3945283944, ss4464237620, ss5243671148, ss5444588447, ss5516696218, ss5671055710, ss5800947144, ss5849075122, ss5909871983	NC_000001.11:113893740:C:T	NC_000001.11:113893740:C:T	(self)
ss19142458, ss20461519	NT_019273.16:5432310:C:T	NC_000001.11:113893740:C:T	(self)
ss1775010, ss3470741, ss41138285, ss99242319, ss139271809	NT_032977.9:84408280:C:T	NC_000001.11:113893740:C: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 rs1217400

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

rs1217400