Name: rs55634455
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.

rs55634455

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:135836124 (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: C=0.155310 (21534/138652, GnomAD)
C=0.26669 (7535/28254, 14KJPN)
C=0.26554 (4450/16758, 8.3KJPN) (+ 15 more)
C=0.06016 (834/13864, ALFA)
C=0.2353 (1507/6404, 1000G_30x)
C=0.2376 (1190/5008, 1000G)
C=0.1354 (606/4476, Estonian)
C=0.0786 (303/3854, ALSPAC)
C=0.0855 (317/3708, TWINSUK)
C=0.2096 (613/2924, KOREAN)
C=0.1954 (358/1832, Korea1K)
C=0.085 (85/998, GoNL)
C=0.082 (49/600, NorthernSweden)
T=0.404 (109/270, SGDP_PRJ)
T=0.500 (108/216, Qatari)
C=0.500 (108/216, Qatari)
C=0.05 (2/40, GENOME_DK)
T=0.27 (6/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LCT : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	13864	T=0.93984	A=0.00000, C=0.06016	0.888344	0.008656	0.103001	29
European	Sub	10822	T=0.93680	A=0.00000, C=0.06320	0.881538	0.007947	0.110516	13
African	Sub	2018	T=0.9371	A=0.0000, C=0.0629	0.888999	0.014866	0.096135	19
African Others	Sub	82	T=0.94	A=0.00, C=0.06	0.878049	0.0	0.121951	0
African American	Sub	1936	T=0.9370	A=0.0000, C=0.0630	0.889463	0.015496	0.095041	20
Asian	Sub	70	T=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	62	T=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	8	T=1.0	A=0.0, C=0.0	1.0	0.0	0.0	N/A
Latin American 1	Sub	90	T=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	296	T=1.000	A=0.000, C=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	40	T=1.00	A=0.00, C=0.00	1.0	0.0	0.0	N/A
Other	Sub	528	T=0.956	A=0.000, C=0.044	0.920455	0.007576	0.07197	3

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 - Genomes	Global	Study-wide	138652	T=0.844690	C=0.155310
gnomAD - Genomes	European	Sub	75468	T=0.89990	C=0.10010
gnomAD - Genomes	African	Sub	41192	T=0.78753	C=0.21247
gnomAD - Genomes	American	Sub	13456	T=0.72592	C=0.27408
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.8233	C=0.1767
gnomAD - Genomes	East Asian	Sub	3100	T=0.8184	C=0.1816
gnomAD - Genomes	Other	Sub	2114	T=0.8155	C=0.1845
14KJPN	JAPANESE	Study-wide	28254	T=0.73331	C=0.26669
8.3KJPN	JAPANESE	Study-wide	16758	T=0.73446	C=0.26554
Allele Frequency Aggregator	Total	Global	13864	T=0.93984	A=0.00000, C=0.06016
Allele Frequency Aggregator	European	Sub	10822	T=0.93680	A=0.00000, C=0.06320
Allele Frequency Aggregator	African	Sub	2018	T=0.9371	A=0.0000, C=0.0629
Allele Frequency Aggregator	Other	Sub	528	T=0.956	A=0.000, C=0.044
Allele Frequency Aggregator	Latin American 2	Sub	296	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	90	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	70	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	40	T=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.7647	C=0.2353
1000Genomes_30x	African	Sub	1786	T=0.7800	C=0.2200
1000Genomes_30x	Europe	Sub	1266	T=0.8626	C=0.1374
1000Genomes_30x	South Asian	Sub	1202	T=0.6531	C=0.3469
1000Genomes_30x	East Asian	Sub	1170	T=0.8068	C=0.1932
1000Genomes_30x	American	Sub	980	T=0.697	C=0.303
1000Genomes	Global	Study-wide	5008	T=0.7624	C=0.2376
1000Genomes	African	Sub	1322	T=0.7814	C=0.2186
1000Genomes	East Asian	Sub	1008	T=0.8056	C=0.1944
1000Genomes	Europe	Sub	1006	T=0.8499	C=0.1501
1000Genomes	South Asian	Sub	978	T=0.655	C=0.345
1000Genomes	American	Sub	694	T=0.687	C=0.313
Genetic variation in the Estonian population	Estonian	Study-wide	4476	T=0.8646	C=0.1354
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9214	C=0.0786
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9145	C=0.0855
KOREAN population from KRGDB	KOREAN	Study-wide	2924	T=0.7904	C=0.2096
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8046	C=0.1954
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.915	C=0.085
Northern Sweden	ACPOP	Study-wide	600	T=0.918	C=0.082
SGDP_PRJ	Global	Study-wide	270	T=0.404	C=0.596
Qatari	Global	Study-wide	216	T=0.500	C=0.500
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
Siberian	Global	Study-wide	22	T=0.27	C=0.73

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.135836124T>A
GRCh38.p14 chr 2	NC_000002.12:g.135836124T>C
GRCh37.p13 chr 2	NC_000002.11:g.136593694T>A
GRCh37.p13 chr 2	NC_000002.11:g.136593694T>C
LCT RefSeqGene (LRG_338)	NG_008104.2:g.24046A>T
LCT RefSeqGene (LRG_338)	NG_008104.2:g.24046A>G

Gene: LCT, lactase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LCT transcript	NM_002299.4:c.640+406A>T	N/A	Intron Variant
LCT transcript variant X1	XM_017004088.3:c.640+406A… XM_017004088.3:c.640+406A>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	T=	A	C
GRCh38.p14 chr 2	NC_000002.12:g.135836124=	NC_000002.12:g.135836124T>A	NC_000002.12:g.135836124T>C
GRCh37.p13 chr 2	NC_000002.11:g.136593694=	NC_000002.11:g.136593694T>A	NC_000002.11:g.136593694T>C
LCT RefSeqGene (LRG_338)	NG_008104.2:g.24046=	NG_008104.2:g.24046A>T	NG_008104.2:g.24046A>G
LCT transcript	NM_002299.2:c.640+406=	NM_002299.2:c.640+406A>T	NM_002299.2:c.640+406A>G
LCT transcript	NM_002299.4:c.640+406=	NM_002299.4:c.640+406A>T	NM_002299.4:c.640+406A>G
LCT transcript variant X1	XM_017004088.3:c.640+406=	XM_017004088.3:c.640+406A>T	XM_017004088.3:c.640+406A>G

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#.

41 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	MOLS-KTL	ss79088025	Dec 05, 2007 (129)
2	BUSHMAN	ss201098817	Jul 04, 2010 (132)
3	GMI	ss276693859	May 04, 2012 (137)
4	1000GENOMES	ss329986578	May 09, 2011 (134)
5	TISHKOFF	ss555896020	Apr 25, 2013 (138)
6	SSMP	ss649524678	Apr 25, 2013 (138)
7	EVA-GONL	ss977390952	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1069520064	Aug 21, 2014 (142)
9	1000GENOMES	ss1299460458	Aug 21, 2014 (142)
10	DDI	ss1428750113	Apr 01, 2015 (144)
11	EVA_GENOME_DK	ss1579099335	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1604632082	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1647626115	Apr 01, 2015 (144)
14	HAMMER_LAB	ss1797578297	Sep 08, 2015 (146)
15	WEILL_CORNELL_DGM	ss1920650147	Feb 12, 2016 (147)
16	JJLAB	ss2020848173	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2148914977	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2234547039	Dec 20, 2016 (150)
19	GRF	ss2703540168	Nov 08, 2017 (151)
20	GNOMAD	ss2780041387	Nov 08, 2017 (151)
21	SWEGEN	ss2990481431	Nov 08, 2017 (151)
22	CSHL	ss3344495681	Nov 08, 2017 (151)
23	EGCUT_WGS	ss3658324657	Jul 13, 2019 (153)
24	EVA_DECODE	ss3704954803	Jul 13, 2019 (153)
25	ACPOP	ss3728894932	Jul 13, 2019 (153)
26	EVA	ss3757422294	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3801789167	Jul 13, 2019 (153)
28	EVA	ss3827236719	Apr 25, 2020 (154)
29	SGDP_PRJ	ss3853483858	Apr 25, 2020 (154)
30	KRGDB	ss3899047804	Apr 25, 2020 (154)
31	KOGIC	ss3949036145	Apr 25, 2020 (154)
32	TOMMO_GENOMICS	ss5154020474	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5250132413	Oct 12, 2022 (156)
34	EVA	ss5506600473	Oct 12, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5526460516	Oct 12, 2022 (156)
36	SANFORD_IMAGENETICS	ss5629874928	Oct 12, 2022 (156)
37	TOMMO_GENOMICS	ss5684191571	Oct 12, 2022 (156)
38	YY_MCH	ss5802752606	Oct 12, 2022 (156)
39	EVA	ss5820850795	Oct 12, 2022 (156)
40	EVA	ss5932503848	Oct 12, 2022 (156)
41	EVA	ss5956076036	Oct 12, 2022 (156)
42	1000Genomes	NC_000002.11 - 136593694	Oct 11, 2018 (152)
43	1000Genomes_30x	NC_000002.12 - 135836124	Oct 12, 2022 (156)
44	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 136593694	Oct 11, 2018 (152)
45	Genetic variation in the Estonian population	NC_000002.11 - 136593694	Oct 11, 2018 (152)
46	The Danish reference pan genome	NC_000002.11 - 136593694	Apr 25, 2020 (154)
47	gnomAD - Genomes	NC_000002.12 - 135836124	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000002.11 - 136593694	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000002.11 - 136593694	Apr 25, 2020 (154)
50	Korean Genome Project	NC_000002.12 - 135836124	Apr 25, 2020 (154)
51	Northern Sweden	NC_000002.11 - 136593694	Jul 13, 2019 (153)
52	Qatari	NC_000002.11 - 136593694	Apr 25, 2020 (154)
53	SGDP_PRJ	NC_000002.11 - 136593694	Apr 25, 2020 (154)
54	Siberian	NC_000002.11 - 136593694	Apr 25, 2020 (154)
55	8.3KJPN	NC_000002.11 - 136593694	Apr 26, 2021 (155)
56	14KJPN	NC_000002.12 - 135836124	Oct 12, 2022 (156)
57	UK 10K study - Twins	NC_000002.11 - 136593694	Oct 11, 2018 (152)
58	ALFA	NC_000002.12 - 135836124	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
12795270783	NC_000002.12:135836123:T:A	NC_000002.12:135836123:T:A	(self)
ss201098817, ss276693859	NC_000002.10:136310163:T:C	NC_000002.12:135836123:T:C	(self)
10481054, 5770847, 4062905, 5264274, 2536791, 6225198, 2179797, 2692077, 5500838, 1431331, 11989781, 5770847, ss329986578, ss555896020, ss649524678, ss977390952, ss1069520064, ss1299460458, ss1428750113, ss1579099335, ss1604632082, ss1647626115, ss1797578297, ss1920650147, ss2020848173, ss2148914977, ss2703540168, ss2780041387, ss2990481431, ss3344495681, ss3658324657, ss3728894932, ss3757422294, ss3827236719, ss3853483858, ss3899047804, ss5154020474, ss5506600473, ss5629874928, ss5820850795, ss5956076036	NC_000002.11:136593693:T:C	NC_000002.12:135836123:T:C	(self)
13986451, 74727476, 5414146, 18028675, 12795270783, ss2234547039, ss3704954803, ss3801789167, ss3949036145, ss5250132413, ss5526460516, ss5684191571, ss5802752606, ss5932503848	NC_000002.12:135836123:T:C	NC_000002.12:135836123:T:C	(self)
ss79088025	NT_022135.16:26342356:T:C	NC_000002.12:135836123: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 rs55634455

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

rs55634455