Name: rs72874061
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.

rs72874061

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:18034466 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.08475 (2395/28258, 14KJPN)
T=0.08539 (1431/16758, 8.3KJPN)
T=0.04893 (748/15286, ALFA) (+ 14 more)
T=0.1081 (692/6404, 1000G_30x)
T=0.1098 (550/5008, 1000G)
T=0.1547 (693/4480, Estonian)
T=0.1700 (655/3854, ALSPAC)
T=0.1710 (634/3708, TWINSUK)
T=0.0828 (242/2922, KOREAN)
T=0.0841 (154/1832, Korea1K)
T=0.181 (181/998, GoNL)
T=0.135 (81/600, NorthernSweden)
T=0.273 (59/216, Qatari)
G=0.440 (59/134, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
G=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TPH1 : 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	15286	G=0.95107	A=0.00000, T=0.04893
European	Sub	11202	G=0.93644	A=0.00000, T=0.06356
African	Sub	2752	G=0.9996	A=0.0000, T=0.0004
African Others	Sub	112	G=1.000	A=0.000, T=0.000
African American	Sub	2640	G=0.9996	A=0.0000, T=0.0004
Asian	Sub	88	G=1.00	A=0.00, T=0.00
East Asian	Sub	70	G=1.00	A=0.00, T=0.00
Other Asian	Sub	18	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	118	G=1.000	A=0.000, T=0.000
Latin American 2	Sub	462	G=1.000	A=0.000, T=0.000
South Asian	Sub	76	G=1.00	A=0.00, T=0.00
Other	Sub	588	G=0.940	A=0.000, T=0.060

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
14KJPN	JAPANESE	Study-wide	28258	G=0.91525	T=0.08475
8.3KJPN	JAPANESE	Study-wide	16758	G=0.91461	T=0.08539
Allele Frequency Aggregator	Total	Global	15286	G=0.95107	A=0.00000, T=0.04893
Allele Frequency Aggregator	European	Sub	11202	G=0.93644	A=0.00000, T=0.06356
Allele Frequency Aggregator	African	Sub	2752	G=0.9996	A=0.0000, T=0.0004
Allele Frequency Aggregator	Other	Sub	588	G=0.940	A=0.000, T=0.060
Allele Frequency Aggregator	Latin American 2	Sub	462	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	118	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	88	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	76	G=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8918	A=0.0002, T=0.1081
1000Genomes_30x	African	Sub	1786	G=0.9882	A=0.0006, T=0.0112
1000Genomes_30x	Europe	Sub	1266	G=0.8239	A=0.0000, T=0.1761
1000Genomes_30x	South Asian	Sub	1202	G=0.8328	A=0.0000, T=0.1672
1000Genomes_30x	East Asian	Sub	1170	G=0.9085	A=0.0000, T=0.0915
1000Genomes_30x	American	Sub	980	G=0.856	A=0.000, T=0.144
1000Genomes	Global	Study-wide	5008	G=0.8902	T=0.1098
1000Genomes	African	Sub	1322	G=0.9887	T=0.0113
1000Genomes	East Asian	Sub	1008	G=0.9117	T=0.0883
1000Genomes	Europe	Sub	1006	G=0.8201	T=0.1799
1000Genomes	South Asian	Sub	978	G=0.829	T=0.171
1000Genomes	American	Sub	694	G=0.859	T=0.141
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8453	T=0.1547
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8300	T=0.1700
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8290	T=0.1710
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9172	T=0.0828
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9159	T=0.0841
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.819	T=0.181
Northern Sweden	ACPOP	Study-wide	600	G=0.865	T=0.135
Qatari	Global	Study-wide	216	G=0.727	T=0.273
SGDP_PRJ	Global	Study-wide	134	G=0.440	T=0.560
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	T=0.12
Siberian	Global	Study-wide	2	G=0.5	T=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 11	NC_000011.10:g.18034466G>A
GRCh38.p14 chr 11	NC_000011.10:g.18034466G>T
GRCh37.p13 chr 11	NC_000011.9:g.18056013G>A
GRCh37.p13 chr 11	NC_000011.9:g.18056013G>T
TPH1 RefSeqGene	NG_011947.2:g.11323C>T
TPH1 RefSeqGene	NG_011947.2:g.11323C>A

Gene: TPH1, tryptophan hydroxylase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TPH1 transcript	NM_004179.3:c.302-1092C>T	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	G=	A	T
GRCh38.p14 chr 11	NC_000011.10:g.18034466=	NC_000011.10:g.18034466G>A	NC_000011.10:g.18034466G>T
GRCh37.p13 chr 11	NC_000011.9:g.18056013=	NC_000011.9:g.18056013G>A	NC_000011.9:g.18056013G>T
TPH1 RefSeqGene	NG_011947.2:g.11323=	NG_011947.2:g.11323C>T	NG_011947.2:g.11323C>A
TPH1 transcript	NM_004179.2:c.302-1092=	NM_004179.2:c.302-1092C>T	NM_004179.2:c.302-1092C>A
TPH1 transcript	NM_004179.3:c.302-1092=	NM_004179.3:c.302-1092C>T	NM_004179.3:c.302-1092C>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#.

52 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss110095103	Feb 13, 2009 (130)
2	1000GENOMES	ss235465955	Jul 15, 2010 (132)
3	1000GENOMES	ss242115585	Jul 15, 2010 (132)
4	BL	ss254931491	May 09, 2011 (134)
5	GMI	ss280903448	May 04, 2012 (137)
6	TISHKOFF	ss562416772	Apr 25, 2013 (138)
7	SSMP	ss657839046	Apr 25, 2013 (138)
8	EVA-GONL	ss988260668	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1077539732	Aug 21, 2014 (142)
10	1000GENOMES	ss1340314335	Aug 21, 2014 (142)
11	DDI	ss1426552668	Apr 01, 2015 (144)
12	EVA_GENOME_DK	ss1575555714	Apr 01, 2015 (144)
13	EVA_DECODE	ss1597938929	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1626096461	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1669090494	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1931621583	Feb 12, 2016 (147)
17	GENOMED	ss1967305039	Jul 19, 2016 (147)
18	JJLAB	ss2026555050	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2154843167	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2180595852	Dec 20, 2016 (150)
21	SYSTEMSBIOZJU	ss2627747441	Nov 08, 2017 (151)
22	GRF	ss2699116501	Nov 08, 2017 (151)
23	GNOMAD	ss2896886890	Nov 08, 2017 (151)
24	SWEGEN	ss3007677347	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3027073740	Nov 08, 2017 (151)
26	CSHL	ss3349476985	Nov 08, 2017 (151)
27	EGCUT_WGS	ss3675077589	Jul 13, 2019 (153)
28	EVA_DECODE	ss3691310269	Jul 13, 2019 (153)
29	ACPOP	ss3737963350	Jul 13, 2019 (153)
30	EVA	ss3749003715	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3814350068	Jul 13, 2019 (153)
32	EVA	ss3832504124	Apr 26, 2020 (154)
33	EVA	ss3839800225	Apr 26, 2020 (154)
34	EVA	ss3845276910	Apr 26, 2020 (154)
35	SGDP_PRJ	ss3875747134	Apr 26, 2020 (154)
36	KRGDB	ss3923987276	Apr 26, 2020 (154)
37	KOGIC	ss3969304874	Apr 26, 2020 (154)
38	TOPMED	ss4876936062	Apr 26, 2021 (155)
39	TOPMED	ss4876936063	Apr 26, 2021 (155)
40	TOMMO_GENOMICS	ss5200901443	Apr 26, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5286571866	Oct 16, 2022 (156)
42	EVA	ss5398055496	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5481857744	Oct 16, 2022 (156)
44	EVA	ss5510267391	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5581783974	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5650732754	Oct 16, 2022 (156)
47	TOMMO_GENOMICS	ss5747717297	Oct 16, 2022 (156)
48	YY_MCH	ss5812170478	Oct 16, 2022 (156)
49	EVA	ss5836329239	Oct 16, 2022 (156)
50	EVA	ss5849878942	Oct 16, 2022 (156)
51	EVA	ss5919028264	Oct 16, 2022 (156)
52	EVA	ss5942042874	Oct 16, 2022 (156)
53	1000Genomes	NC_000011.9 - 18056013	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000011.10 - 18034466	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 18056013	Oct 12, 2018 (152)
56	Genetic variation in the Estonian population	NC_000011.9 - 18056013	Oct 12, 2018 (152)
57	The Danish reference pan genome	NC_000011.9 - 18056013	Apr 26, 2020 (154)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 372776776 (NC_000011.10:18034465:G:A 1/140134) Row 372776777 (NC_000011.10:18034465:G:T 17388/140102)	-	Apr 26, 2021 (155)
59	gnomAD - Genomes Submission ignored due to conflicting rows: Row 372776776 (NC_000011.10:18034465:G:A 1/140134) Row 372776777 (NC_000011.10:18034465:G:T 17388/140102)	-	Apr 26, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000011.9 - 18056013	Apr 26, 2020 (154)
61	KOREAN population from KRGDB	NC_000011.9 - 18056013	Apr 26, 2020 (154)
62	Korean Genome Project	NC_000011.10 - 18034466	Apr 26, 2020 (154)
63	Northern Sweden	NC_000011.9 - 18056013	Jul 13, 2019 (153)
64	Qatari	NC_000011.9 - 18056013	Apr 26, 2020 (154)
65	SGDP_PRJ	NC_000011.9 - 18056013	Apr 26, 2020 (154)
66	Siberian	NC_000011.9 - 18056013	Apr 26, 2020 (154)
67	8.3KJPN	NC_000011.9 - 18056013	Apr 26, 2021 (155)
68	14KJPN	NC_000011.10 - 18034466	Oct 16, 2022 (156)
69	TopMed Submission ignored due to conflicting rows: Row 92481718 (NC_000011.10:18034465:G:A 1/264690) Row 92481719 (NC_000011.10:18034465:G:T 32992/264690)	-	Apr 26, 2021 (155)
70	TopMed Submission ignored due to conflicting rows: Row 92481718 (NC_000011.10:18034465:G:A 1/264690) Row 92481719 (NC_000011.10:18034465:G:T 32992/264690)	-	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000011.9 - 18056013	Oct 12, 2018 (152)
72	ALFA	NC_000011.10 - 18034466	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
69309909, 12711596187, ss4876936062, ss5581783974	NC_000011.10:18034465:G:A	NC_000011.10:18034465:G:A	(self)
ss110095103, ss254931491, ss280903448, ss1597938929	NC_000011.8:18012588:G:T	NC_000011.10:18034465:G:T	(self)
52803979, 29333154, 20815837, 2464097, 13078382, 31164670, 11248215, 13663513, 27764114, 7359521, 58870750, 29333154, ss235465955, ss242115585, ss562416772, ss657839046, ss988260668, ss1077539732, ss1340314335, ss1426552668, ss1575555714, ss1626096461, ss1669090494, ss1931621583, ss1967305039, ss2026555050, ss2154843167, ss2627747441, ss2699116501, ss2896886890, ss3007677347, ss3349476985, ss3675077589, ss3737963350, ss3749003715, ss3832504124, ss3839800225, ss3875747134, ss3923987276, ss5200901443, ss5398055496, ss5510267391, ss5650732754, ss5836329239, ss5942042874	NC_000011.9:18056012:G:T	NC_000011.10:18034465:G:T	(self)
69309909, 25682875, 81554401, 12711596187, ss2180595852, ss3027073740, ss3691310269, ss3814350068, ss3845276910, ss3969304874, ss4876936063, ss5286571866, ss5481857744, ss5581783974, ss5747717297, ss5812170478, ss5849878942, ss5919028264	NC_000011.10:18034465:G:T	NC_000011.10:18034465:G: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 rs72874061

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
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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

rs72874061