Name: rs11558538
Published: September 3, 2024
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.

rs11558538

Current Build 157

Released September 3, 2024

Organism: Homo sapiens
Position: chr2:138002079 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.1051181 (144508/1374720, GnomAD_exomes)
T=0.073339 (19412/264690, TOPMED)
T=0.101202 (19049/188228, ALFA) (+ 25 more)
T=0.083594 (12463/149090, GnomAD_genomes)
T=0.101733 (12165/119578, ExAC)
T=0.05798 (4562/78676, PAGE_STUDY)
T=0.05164 (3999/77436, 38KJPN)
T=0.0386 (279/7230, Korea4K)
T=0.0603 (386/6404, 1000G_30X)
T=0.0595 (298/5008, 1000G)
T=0.1388 (622/4480, Estonian)
T=0.1030 (397/3854, ALSPAC)
T=0.1087 (403/3708, TWINSUK)
T=0.0489 (143/2922, KOREAN)
T=0.0469 (86/1832, Korea1K)
T=0.131 (131/998, GoNL)
T=0.033 (26/790, PRJEB37584)
T=0.039 (24/616, Vietnamese)
T=0.135 (81/600, NorthernSweden)
T=0.076 (41/536, PharmGKB)
T=0.075 (40/534, MGP)
T=0.164 (50/304, FINRISK)
T=0.088 (19/216, Qatari)
C=0.50 (40/80, SGDP_PRJ)
T=0.50 (40/80, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: HNMT : Missense Variant
Publications: 18 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	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	188228	C=0.898798	T=0.101202	0.808456	0.010859	0.180685	3
European	Sub	158454	C=0.892126	T=0.107874	0.795953	0.011701	0.192346	0
African	Sub	12124	C=0.97682	T=0.02318	0.954965	0.00132	0.043715	4
African Others	Sub	454	C=0.993	T=0.007	0.986784	0.0	0.013216	0
African American	Sub	11670	C=0.97618	T=0.02382	0.953728	0.001371	0.044901	4
Asian	Sub	3376	C=0.9342	T=0.0658	0.875592	0.007109	0.117299	2
East Asian	Sub	2720	C=0.9574	T=0.0426	0.915441	0.000735	0.083824	1
Other Asian	Sub	656	C=0.838	T=0.162	0.710366	0.033537	0.256098	1
Latin American 1	Sub	812	C=0.942	T=0.058	0.884236	0.0	0.115764	1
Latin American 2	Sub	1032	C=0.8983	T=0.1017	0.804264	0.007752	0.187984	0
South Asian	Sub	290	C=0.890	T=0.110	0.786207	0.006897	0.206897	0
Other	Sub	12140	C=0.89547	T=0.10453	0.802471	0.011532	0.185997	0

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
gnomAD v4 - Exomes	Global	Study-wide	1374720	C=0.8948819	T=0.1051181
gnomAD v4 - Exomes	European	Sub	1151928	C=0.8890790	T=0.1109210
gnomAD v4 - Exomes	South Asian	Sub	79976	C=0.89968	T=0.10032
gnomAD v4 - Exomes	American	Sub	40738	C=0.90540	T=0.09460
gnomAD v4 - Exomes	East Asian	Sub	38954	C=0.95413	T=0.04587
gnomAD v4 - Exomes	African	Sub	32258	C=0.98403	T=0.01597
gnomAD v4 - Exomes	Ashkenazi Jewish	Sub	25244	C=0.92422	T=0.07578
gnomAD v4 - Exomes	Middle Eastern	sub	5622	C=0.8856	T=0.1144
TopMed	Global	Study-wide	264690	C=0.926661	T=0.073339
Allele Frequency Aggregator	Total	Global	188228	C=0.898798	T=0.101202
Allele Frequency Aggregator	European	Sub	158454	C=0.892126	T=0.107874
Allele Frequency Aggregator	Other	Sub	12140	C=0.89547	T=0.10453
Allele Frequency Aggregator	African	Sub	12124	C=0.97682	T=0.02318
Allele Frequency Aggregator	Asian	Sub	3376	C=0.9342	T=0.0658
Allele Frequency Aggregator	Latin American 2	Sub	1032	C=0.8983	T=0.1017
Allele Frequency Aggregator	Latin American 1	Sub	812	C=0.942	T=0.058
Allele Frequency Aggregator	South Asian	Sub	290	C=0.890	T=0.110
gnomAD v4 - Genomes	Global	Study-wide	149090	C=0.916406	T=0.083594
gnomAD v4 - Genomes	European	Sub	78540	C=0.88070	T=0.11930
gnomAD v4 - Genomes	African	Sub	41544	C=0.98033	T=0.01967
gnomAD v4 - Genomes	American	Sub	15260	C=0.91317	T=0.08683
gnomAD v4 - Genomes	East Asian	Sub	5164	C=0.9659	T=0.0341
gnomAD v4 - Genomes	South Asian	Sub	4816	C=0.9043	T=0.0957
gnomAD v4 - Genomes	Ashkenazi Jewish	Sub	3472	C=0.9188	T=0.0812
gnomAD v4 - Genomes	Middle Eastern	sub	294	C=0.891	T=0.109
ExAC	Global	Study-wide	119578	C=0.898267	T=0.101733
ExAC	Europe	Sub	72440	C=0.88094	T=0.11906
ExAC	Asian	Sub	24590	C=0.91619	T=0.08381
ExAC	American	Sub	11318	C=0.89945	T=0.10055
ExAC	African	Sub	10332	C=0.97958	T=0.02042
ExAC	Other	Sub	898	C=0.855	T=0.145
The PAGE Study	Global	Study-wide	78676	C=0.94202	T=0.05798
The PAGE Study	AfricanAmerican	Sub	32504	C=0.97754	T=0.02246
The PAGE Study	Mexican	Sub	10808	C=0.90229	T=0.09771
The PAGE Study	Asian	Sub	8314	C=0.9491	T=0.0509
The PAGE Study	PuertoRican	Sub	7916	C=0.9456	T=0.0544
The PAGE Study	NativeHawaiian	Sub	4530	C=0.8369	T=0.1631
The PAGE Study	Cuban	Sub	4230	C=0.9076	T=0.0924
The PAGE Study	Dominican	Sub	3826	C=0.9480	T=0.0520
The PAGE Study	CentralAmerican	Sub	2450	C=0.9069	T=0.0931
The PAGE Study	SouthAmerican	Sub	1982	C=0.9062	T=0.0938
The PAGE Study	NativeAmerican	Sub	1260	C=0.9175	T=0.0825
The PAGE Study	SouthAsian	Sub	856	C=0.912	T=0.088
38KJPN	JAPANESE	Study-wide	77436	C=0.94836	T=0.05164
Korean Genome Project 4K	KOREAN	Study-wide	7230	C=0.9614	T=0.0386
1000Genomes_30X	Global	Study-wide	6404	C=0.9397	T=0.0603
1000Genomes_30X	African	Sub	1786	C=0.9972	T=0.0028
1000Genomes_30X	Europe	Sub	1266	C=0.8886	T=0.1114
1000Genomes_30X	South Asian	Sub	1202	C=0.8935	T=0.1065
1000Genomes_30X	East Asian	Sub	1170	C=0.9675	T=0.0325
1000Genomes_30X	American	Sub	980	C=0.924	T=0.076
1000Genomes	Global	Study-wide	5008	C=0.9405	T=0.0595
1000Genomes	African	Sub	1322	C=0.9970	T=0.0030
1000Genomes	East Asian	Sub	1008	C=0.9683	T=0.0317
1000Genomes	Europe	Sub	1006	C=0.8956	T=0.1044
1000Genomes	South Asian	Sub	978	C=0.895	T=0.105
1000Genomes	American	Sub	694	C=0.922	T=0.078
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8612	T=0.1388
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8970	T=0.1030
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8913	T=0.1087
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9511	T=0.0489
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9531	T=0.0469
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.869	T=0.131
CNV burdens in cranial meningiomas	Global	Study-wide	790	C=0.967	T=0.033
CNV burdens in cranial meningiomas	CRM	Sub	790	C=0.967	T=0.033
A Vietnamese Genetic Variation Database	Global	Study-wide	616	C=0.961	T=0.039
Northern Sweden	ACPOP	Study-wide	600	C=0.865	T=0.135
PharmGKB Aggregated	Global	Study-wide	536	C=0.924	T=0.076
PharmGKB Aggregated	PA147964293	Sub	356	C=0.933	T=0.067
PharmGKB Aggregated	PA129820757	Sub	180	C=0.906	T=0.094
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.925	T=0.075
FINRISK	Finnish from FINRISK project	Study-wide	304	C=0.836	T=0.164
Qatari	Global	Study-wide	216	C=0.912	T=0.088
SGDP_PRJ	Global	Study-wide	80	C=0.50	T=0.50
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
Siberian	Global	Study-wide	10	C=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 2	NC_000002.12:g.138002079C>T
GRCh37.p13 chr 2	NC_000002.11:g.138759649C>T
HNMT RefSeqGene	NG_012966.1:g.42842C>T

Gene: HNMT, histamine N-methyltransferase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HNMT transcript variant 2	NM_001024074.3:c.	N/A	Genic Downstream Transcript Variant
HNMT transcript variant 3	NM_001024075.3:c.	N/A	Genic Downstream Transcript Variant
HNMT transcript variant 1	NM_006895.3:c.314C>T	T [ACA] > I [ATA]	Coding Sequence Variant
histamine N-methyltransferase isoform 1	NP_008826.1:p.Thr105Ile	T (Thr) > I (Ile)	Missense Variant
HNMT transcript variant X2	XM_011511064.3:c.-65=	N/A	5 Prime UTR Variant
HNMT transcript variant X1	XM_017003948.2:c.212C>T	T [ACA] > I [ATA]	Coding Sequence Variant
histamine N-methyltransferase isoform X1	XP_016859437.1:p.Thr71Ile	T (Thr) > I (Ile)	Missense Variant
HNMT transcript variant X3	XM_017003949.3:c.314C>T	T [ACA] > I [ATA]	Coding Sequence Variant
histamine N-methyltransferase isoform X3	XP_016859438.1:p.Thr105Ile	T (Thr) > I (Ile)	Missense 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.

Allele: T (allele ID: 20199 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000005467.4	Inherited susceptibility to asthma	Risk-Factor
RCV003974798.1	HNMT-related disorder	Benign

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=	T
GRCh38.p14 chr 2	NC_000002.12:g.138002079=	NC_000002.12:g.138002079C>T
GRCh37.p13 chr 2	NC_000002.11:g.138759649=	NC_000002.11:g.138759649C>T
HNMT RefSeqGene	NG_012966.1:g.42842=	NG_012966.1:g.42842C>T
HNMT transcript variant 1	NM_006895.3:c.314=	NM_006895.3:c.314C>T
HNMT transcript variant 1	NM_006895.2:c.314=	NM_006895.2:c.314C>T
HNMT transcript variant X2	XM_011511064.3:c.-65=	XM_011511064.3:c.-65C>T
HNMT transcript variant X2	XM_011511064.2:c.-65=	XM_011511064.2:c.-65C>T
HNMT transcript variant X2	XM_011511064.1:c.-65=	XM_011511064.1:c.-65C>T
HNMT transcript variant X3	XM_017003949.3:c.314=	XM_017003949.3:c.314C>T
HNMT transcript variant X3	XM_017003949.2:c.314=	XM_017003949.2:c.314C>T
HNMT transcript variant X3	XM_017003949.1:c.314=	XM_017003949.1:c.314C>T
HNMT transcript variant X1	XM_017003948.2:c.212=	XM_017003948.2:c.212C>T
HNMT transcript variant X1	XM_017003948.1:c.212=	XM_017003948.1:c.212C>T
histamine N-methyltransferase isoform 1	NP_008826.1:p.Thr105=	NP_008826.1:p.Thr105Ile
histamine N-methyltransferase isoform X3	XP_016859438.1:p.Thr105=	XP_016859438.1:p.Thr105Ile
histamine N-methyltransferase isoform X1	XP_016859437.1:p.Thr71=	XP_016859437.1:p.Thr71Ile

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#.

129 SubSNP, 26 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	RIKENSNPRC	ss6311532	Feb 20, 2003 (136)
2	PERLEGEN	ss24273695	Sep 20, 2004 (136)
3	ILLUMINA	ss66739039	Nov 30, 2006 (130)
4	ILLUMINA	ss67197039	Nov 30, 2006 (130)
5	ILLUMINA	ss67586034	Nov 30, 2006 (130)
6	PERLEGEN	ss68829046	May 17, 2007 (130)
7	PHARMGKB_PPII	ss69368935	May 17, 2007 (130)
8	AFFY	ss74807139	Aug 16, 2007 (130)
9	HGSV	ss77799259	Dec 06, 2007 (129)
10	PHARMGKB_AB_DME	ss84168503	Dec 16, 2007 (130)
11	SNP500CANCER	ss105440252	Feb 06, 2009 (130)
12	1000GENOMES	ss109925060	Jan 24, 2009 (130)
13	SEATTLESEQ	ss159702823	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss165304616	Jul 04, 2010 (132)
15	1000GENOMES	ss231380157	Jul 14, 2010 (132)
16	1000GENOMES	ss238886426	Jul 15, 2010 (132)
17	ILLUMINA	ss244295769	Jul 04, 2010 (132)
18	OMIM-CURATED-RECORDS	ss254229990	Aug 19, 2010 (132)
19	NHLBI-ESP	ss342080009	May 09, 2011 (134)
20	ILLUMINA	ss483914913	May 04, 2012 (137)
21	ILLUMINA	ss484054437	May 04, 2012 (137)
22	1000GENOMES	ss489833595	May 04, 2012 (137)
23	EXOME_CHIP	ss491324872	May 04, 2012 (137)
24	CLINSEQ_SNP	ss491791989	May 04, 2012 (137)
25	ILLUMINA	ss536245613	Sep 08, 2015 (146)
26	SSMP	ss649536199	Apr 25, 2013 (138)
27	ILLUMINA	ss780509044	Sep 08, 2015 (146)
28	ILLUMINA	ss782471877	Sep 08, 2015 (146)
29	ILLUMINA	ss836000174	Sep 08, 2015 (146)
30	EVA-GONL	ss977406782	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1067441173	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1069533454	Aug 21, 2014 (142)
33	1000GENOMES	ss1299523125	Aug 21, 2014 (142)
34	EVA_GENOME_DK	ss1579106055	Apr 01, 2015 (144)
35	EVA_FINRISK	ss1584021024	Apr 01, 2015 (144)
36	EVA_DECODE	ss1586835922	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1604664362	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1647658395	Apr 01, 2015 (144)
39	EVA_EXAC	ss1686527296	Apr 01, 2015 (144)
40	EVA_MGP	ss1710981899	Apr 01, 2015 (144)
41	WEILL_CORNELL_DGM	ss1920667491	Feb 12, 2016 (147)
42	ILLUMINA	ss1946053043	Feb 12, 2016 (147)
43	ILLUMINA	ss1958462490	Feb 12, 2016 (147)
44	JJLAB	ss2020856468	Sep 14, 2016 (149)
45	USC_VALOUEV	ss2148923933	Dec 20, 2016 (150)
46	HUMAN_LONGEVITY	ss2234668394	Dec 20, 2016 (150)
47	ILLUMINA	ss2633678631	Nov 08, 2017 (151)
48	GRF	ss2703550924	Nov 08, 2017 (151)
49	ILLUMINA	ss2710912804	Nov 08, 2017 (151)
50	GNOMAD	ss2733006318	Nov 08, 2017 (151)
51	GNOMAD	ss2746785942	Nov 08, 2017 (151)
52	GNOMAD	ss2780212136	Nov 08, 2017 (151)
53	AFFY	ss2985186056	Nov 08, 2017 (151)
54	SWEGEN	ss2990504507	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3024192203	Nov 08, 2017 (151)
56	CSHL	ss3344503062	Nov 08, 2017 (151)
57	ILLUMINA	ss3625766459	Oct 11, 2018 (152)
58	ILLUMINA	ss3628175607	Oct 11, 2018 (152)
59	ILLUMINA	ss3631642001	Oct 11, 2018 (152)
60	ILLUMINA	ss3639149032	Oct 11, 2018 (152)
61	ILLUMINA	ss3639587151	Oct 11, 2018 (152)
62	ILLUMINA	ss3642127010	Oct 11, 2018 (152)
63	ILLUMINA	ss3644755759	Oct 11, 2018 (152)
64	OMUKHERJEE_ADBS	ss3646272979	Oct 11, 2018 (152)
65	URBANLAB	ss3647154795	Oct 11, 2018 (152)
66	ILLUMINA	ss3653953070	Oct 11, 2018 (152)
67	EGCUT_WGS	ss3658350144	Jul 13, 2019 (153)
68	EVA_DECODE	ss3704984290	Jul 13, 2019 (153)
69	ACPOP	ss3728908402	Jul 13, 2019 (153)
70	ILLUMINA	ss3744183211	Jul 13, 2019 (153)
71	EVA	ss3757443107	Jul 13, 2019 (153)
72	PAGE_CC	ss3770951520	Jul 13, 2019 (153)
73	KHV_HUMAN_GENOMES	ss3801809584	Jul 13, 2019 (153)
74	EVA	ss3823812203	Apr 25, 2020 (154)
75	EVA	ss3825609721	Apr 25, 2020 (154)
76	EVA	ss3827244756	Apr 25, 2020 (154)
77	SGDP_PRJ	ss3853517104	Apr 25, 2020 (154)
78	KRGDB	ss3899084109	Apr 25, 2020 (154)
79	KOGIC	ss3949067564	Apr 25, 2020 (154)
80	FSA-LAB	ss3984189798	Apr 26, 2021 (155)
81	FSA-LAB	ss3984189799	Apr 26, 2021 (155)
82	EVA	ss3984490349	Apr 26, 2021 (155)
83	EVA	ss3986198604	Apr 26, 2021 (155)
84	TOPMED	ss4525618893	Apr 26, 2021 (155)
85	TOMMO_GENOMICS	ss6012682328	Oct 30, 2024 (157)
86	EVA	ss6215858187	Oct 30, 2024 (157)
87	EVA	ss6287737656	Oct 30, 2024 (157)
88	EVA	ss6322148678	Oct 30, 2024 (157)
89	EVA	ss6323480510	Oct 30, 2024 (157)
90	EVA	ss6329777436	Oct 30, 2024 (157)
91	YEGNASUBRAMANIAN_LAB	ss6335698354	Oct 30, 2024 (157)
92	EVA	ss6349529712	Oct 30, 2024 (157)
93	KOGIC	ss6356976949	Oct 30, 2024 (157)
94	EVA	ss6404240191	Oct 30, 2024 (157)
95	EVA	ss6404530326	Oct 30, 2024 (157)
96	EVA	ss6404641830	Oct 30, 2024 (157)
97	GNOMAD	ss6414197322	Oct 30, 2024 (157)
98	GNOMAD	ss6553766581	Oct 30, 2024 (157)
99	TOMMO_GENOMICS	ss8154090256	Oct 30, 2024 (157)
100	EVA	ss8236974313	Oct 30, 2024 (157)
101	EVA	ss8237303098	Oct 30, 2024 (157)
102	EVA	ss8237636509	Oct 30, 2024 (157)
103	1000G_HIGH_COVERAGE	ss8250186502	Oct 30, 2024 (157)
104	TRAN_CS_UWATERLOO	ss8314402526	Oct 30, 2024 (157)
105	EVA	ss8314772510	Oct 30, 2024 (157)
106	EVA	ss8332650109	Oct 30, 2024 (157)
107	HUGCELL_USP	ss8449980415	Oct 30, 2024 (157)
108	1000G_HIGH_COVERAGE	ss8526542544	Oct 30, 2024 (157)
109	EVA	ss8623922039	Oct 30, 2024 (157)
110	EVA	ss8624104102	Oct 30, 2024 (157)
111	SANFORD_IMAGENETICS	ss8624458616	Oct 30, 2024 (157)
112	SANFORD_IMAGENETICS	ss8629907502	Oct 30, 2024 (157)
113	TOMMO_GENOMICS	ss8684280519	Oct 30, 2024 (157)
114	EVA	ss8799415779	Oct 30, 2024 (157)
115	EVA	ss8800098438	Oct 30, 2024 (157)
116	YY_MCH	ss8802767355	Oct 30, 2024 (157)
117	EVA	ss8820872585	Oct 30, 2024 (157)
118	EVA	ss8847196794	Oct 30, 2024 (157)
119	EVA	ss8847884340	Oct 30, 2024 (157)
120	EVA	ss8848524375	Oct 30, 2024 (157)
121	EVA	ss8852735144	Oct 30, 2024 (157)
122	EVA	ss8932567135	Oct 30, 2024 (157)
123	EVA	ss8956108897	Oct 30, 2024 (157)
124	EVA	ss8979583152	Oct 30, 2024 (157)
125	EVA	ss8981208018	Oct 30, 2024 (157)
126	EVA	ss8981865747	Oct 30, 2024 (157)
127	EVA	ss8981865748	Oct 30, 2024 (157)
128	LNCC-LABINFO	ss8982105370	Oct 30, 2024 (157)
129	EVA	ss8982401720	Oct 30, 2024 (157)
130	1000Genomes	NC_000002.11 - 138759649	Oct 11, 2018 (152)
131	1000Genomes_30X	NC_000002.12 - 138002079	Oct 30, 2024 (157)
132	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 138759649	Oct 11, 2018 (152)
133	Genetic variation in the Estonian population	NC_000002.11 - 138759649	Oct 11, 2018 (152)
134	ExAC	NC_000002.11 - 138759649	Oct 11, 2018 (152)
135	FINRISK	NC_000002.11 - 138759649	Apr 25, 2020 (154)
136	The Danish reference pan genome	NC_000002.11 - 138759649	Apr 25, 2020 (154)
137	gnomAD v4 - Exomes	NC_000002.12 - 138002079	Oct 30, 2024 (157)
138	gnomAD v4 - Genomes	NC_000002.12 - 138002079	Oct 30, 2024 (157)
139	Genome of the Netherlands Release 5	NC_000002.11 - 138759649	Apr 25, 2020 (154)
140	KOREAN population from KRGDB	NC_000002.11 - 138759649	Apr 25, 2020 (154)
141	Korean Genome Project	NC_000002.12 - 138002079	Apr 25, 2020 (154)
142	Korean Genome Project 4K	NC_000002.12 - 138002079	Oct 30, 2024 (157)
143	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 138759649	Apr 25, 2020 (154)
144	Northern Sweden	NC_000002.11 - 138759649	Jul 13, 2019 (153)
145	The PAGE Study	NC_000002.12 - 138002079	Jul 13, 2019 (153)
146	CNV burdens in cranial meningiomas	NC_000002.11 - 138759649	Apr 26, 2021 (155)
147	PharmGKB Aggregated	NC_000002.12 - 138002079	Apr 25, 2020 (154)
148	Qatari	NC_000002.11 - 138759649	Apr 25, 2020 (154)
149	SGDP_PRJ	NC_000002.11 - 138759649	Apr 25, 2020 (154)
150	Siberian	NC_000002.11 - 138759649	Apr 25, 2020 (154)
151	38KJPN	NC_000002.12 - 138002079	Oct 30, 2024 (157)
152	TopMed	NC_000002.12 - 138002079	Apr 26, 2021 (155)
153	UK 10K study - Twins	NC_000002.11 - 138759649	Oct 11, 2018 (152)
154	A Vietnamese Genetic Variation Database	NC_000002.11 - 138759649	Jul 13, 2019 (153)
155	ALFA	NC_000002.12 - 138002079	Oct 30, 2024 (157)
156	ClinVar	RCV000005467.4	Oct 30, 2024 (157)
157	ClinVar	RCV003974798.1	Oct 30, 2024 (157)

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)
rs1801105	Jul 22, 2012 (136)
rs17644855	Oct 07, 2004 (123)
rs35953316	May 26, 2008 (130)
rs45516894	May 26, 2008 (130)
rs52832693	Sep 21, 2007 (128)
rs61356098	May 26, 2008 (130)
rs61727980	May 11, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77799259, ss3639149032, ss3639587151	NC_000002.9:138593380:C:T	NC_000002.12:138002078:C:T	(self)
ss109925060, ss165304616, ss483914913, ss491791989, ss1586835922	NC_000002.10:138476118:C:T	NC_000002.12:138002078:C:T	(self)
10546152, 5806418, 4088392, 6415061, 17485, 5270994, 2552313, 6261503, 98438, 2193267, 39683, 2709421, 5534084, 1440287, 5806418, 1257839, ss231380157, ss238886426, ss342080009, ss484054437, ss489833595, ss491324872, ss536245613, ss649536199, ss780509044, ss782471877, ss836000174, ss977406782, ss1067441173, ss1069533454, ss1299523125, ss1579106055, ss1584021024, ss1604664362, ss1647658395, ss1686527296, ss1710981899, ss1920667491, ss1946053043, ss1958462490, ss2020856468, ss2148923933, ss2633678631, ss2703550924, ss2710912804, ss2733006318, ss2746785942, ss2780212136, ss2985186056, ss2990504507, ss3344503062, ss3625766459, ss3628175607, ss3631642001, ss3642127010, ss3644755759, ss3646272979, ss3653953070, ss3658350144, ss3728908402, ss3744183211, ss3757443107, ss3823812203, ss3825609721, ss3827244756, ss3853517104, ss3899084109, ss3984189798, ss3984189799, ss3984490349, ss3986198604, ss6215858187, ss6287737656, ss6322148678, ss6323480510, ss6329777436, ss6335698354, ss6349529712, ss6404530326, ss6404641830, ss8154090256, ss8237303098, ss8314772510, ss8332650109, ss8623922039, ss8624104102, ss8624458616, ss8629907502, ss8799415779, ss8800098438, ss8820872585, ss8847196794, ss8847884340, ss8848524375, ss8956108897, ss8979583152, ss8981208018, ss8981865747, ss8981865748, ss8982401720	NC_000002.11:138759648:C:T	NC_000002.12:138002078:C:T	(self)
RCV000005467.4, RCV003974798.1, 14068479, 9499454, 80209268, 5445565, 6828847, 172989, 6457, 30058148, 329441772, 16346172231, ss254229990, ss2234668394, ss3024192203, ss3647154795, ss3704984290, ss3770951520, ss3801809584, ss3949067564, ss4525618893, ss6012682328, ss6356976949, ss6404240191, ss6414197322, ss6553766581, ss8236974313, ss8237636509, ss8250186502, ss8314402526, ss8449980415, ss8526542544, ss8684280519, ss8802767355, ss8852735144, ss8932567135, ss8982105370	NC_000002.12:138002078:C:T	NC_000002.12:138002078:C:T	(self)
ss6311532, ss24273695, ss66739039, ss67197039, ss67586034, ss68829046, ss69368935, ss74807139, ss84168503, ss105440252, ss159702823, ss244295769	NT_022135.16:28508311:C:T	NC_000002.12:138002078:C:T	(self)

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

18 citations for rs11558538

PMID	Title	Author	Year	Journal
9547362	Human histamine N-methyltransferase pharmacogenetics: common genetic polymorphisms that alter activity.	Preuss CV et al.	1998	Molecular pharmacology
10752634	Lack of association between atopic asthma and polymorphisms of the histamine H1 receptor, histamine H2 receptor, and histamine N-methyltransferase genes.	Sasaki Y et al.	2000	Immunogenetics
10803682	Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma.	Yan L et al.	2000	Pharmacogenetics
15693910	No association of histamine- N-methyltransferase polymorphism with asthma or bronchial hyperresponsiveness in two German pediatric populations.	Deindl P et al.	2005	Pediatric allergy and immunology
16205835	Lack of association of histamine-N-methyltransferase (HNMT) polymorphisms with asthma in the Indian population.	Sharma S et al.	2005	Journal of human genetics
19773194	Histamine N-methyltransferase Thr105Ile is not associated with Parkinson's disease or essential tremor.	Keeling BH et al.	2010	Parkinsonism & related disorders
21040557	Polymorphisms of two histamine-metabolizing enzymes genes and childhood allergic asthma: a case control study.	Szczepankiewicz A et al.	2010	Clinical and molecular allergy
22327873	Defining risk factors for red man syndrome in children and adults.	Myers AL et al.	2012	The Pediatric infectious disease journal
22373437	Identification of functional genetic variation in exome sequence analysis.	Jaffe A et al.	2011	BMC proceedings
23152756	The diamine oxidase gene is associated with hypersensitivity response to non-steroidal anti-inflammatory drugs.	Agúndez JA et al.	2012	PloS one
24835231	Associations of polymorphisms in histidine decarboxylase, histamine N-methyltransferase and histamine receptor H3 genes with breast cancer.	He GH et al.	2014	PloS one
25295384	Genetic variation within the histamine pathway among patients with asthma--a pilot study.	Raje N et al.	2015	The Journal of asthma
26989676	Associations of Polymorphisms in HRH2, HRH3, DAO, and HNMT Genes with Risk of Chronic Heart Failure.	He GH et al.	2016	BioMed research international
27399132	Thr105Ile (rs11558538) polymorphism in the histamine N-methyltransferase (HNMT) gene and risk for Parkinson disease: A PRISMA-compliant systematic review and meta-analysis.	Jiménez-Jiménez FJ et al.	2016	Medicine
27746735	FCERI and Histamine Metabolism Gene Variability in Selective Responders to NSAIDS.	Amo G et al.	2016	Frontiers in pharmacology
27837280	Thr105Ile (rs11558538) polymorphism in the histamine-1-methyl-transferase (HNMT) gene and risk for restless legs syndrome.	Jiménez-Jiménez FJ et al.	2017	Journal of neural transmission (Vienna, Austria
30409984	Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics.	John SE et al.	2018	Scientific reports
36378841	The Thr105Ile Variant (rs11558538) of the Histamine N-methyltransferase Gene may be associated with Reduced Risk of Parkinson Disease: A Meta-analysis.	Lu Y et al.	2022	Genetic testing and molecular biomarkers

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).
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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs11558538