Name: rs2101144
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.

rs2101144

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:40077435 (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=0.108799 (28798/264690, TOPMED)
T=0.105201 (14737/140084, GnomAD)
T=0.16703 (4720/28258, 14KJPN) (+ 18 more)
T=0.16712 (2801/16760, 8.3KJPN)
T=0.05427 (899/16564, ALFA)
T=0.1034 (662/6404, 1000G_30x)
T=0.1048 (525/5008, 1000G)
T=0.1058 (474/4480, Estonian)
T=0.1414 (545/3854, ALSPAC)
T=0.1316 (488/3708, TWINSUK)
T=0.2280 (668/2930, KOREAN)
T=0.2151 (394/1832, Korea1K)
T=0.143 (143/998, GoNL)
T=0.098 (59/600, NorthernSweden)
T=0.102 (22/216, Qatari)
T=0.160 (34/212, Vietnamese)
C=0.458 (66/144, SGDP_PRJ)
T=0.058 (7/120, HapMap)
T=0.17 (7/40, GENOME_DK)
C=0.50 (9/18, Siberian)
T=0.50 (9/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC2A13 : Intron Variant
LOC112268095 : 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	16564	C=0.94573	T=0.05427
European	Sub	12490	C=0.93251	T=0.06749
African	Sub	2678	C=0.9903	T=0.0097
African Others	Sub	98	C=1.00	T=0.00
African American	Sub	2580	C=0.9899	T=0.0101
Asian	Sub	76	C=1.00	T=0.00
East Asian	Sub	62	C=1.00	T=0.00
Other Asian	Sub	14	C=1.00	T=0.00
Latin American 1	Sub	108	C=1.000	T=0.000
Latin American 2	Sub	528	C=1.000	T=0.000
South Asian	Sub	90	C=1.00	T=0.00
Other	Sub	594	C=0.949	T=0.051

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=0.891201	T=0.108799
gnomAD - Genomes	Global	Study-wide	140084	C=0.894799	T=0.105201
gnomAD - Genomes	European	Sub	75868	C=0.87936	T=0.12064
gnomAD - Genomes	African	Sub	42002	C=0.93105	T=0.06895
gnomAD - Genomes	American	Sub	13628	C=0.89800	T=0.10200
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.8791	T=0.1209
gnomAD - Genomes	East Asian	Sub	3114	C=0.7929	T=0.2071
gnomAD - Genomes	Other	Sub	2148	C=0.8831	T=0.1169
14KJPN	JAPANESE	Study-wide	28258	C=0.83297	T=0.16703
8.3KJPN	JAPANESE	Study-wide	16760	C=0.83288	T=0.16712
Allele Frequency Aggregator	Total	Global	16564	C=0.94573	T=0.05427
Allele Frequency Aggregator	European	Sub	12490	C=0.93251	T=0.06749
Allele Frequency Aggregator	African	Sub	2678	C=0.9903	T=0.0097
Allele Frequency Aggregator	Other	Sub	594	C=0.949	T=0.051
Allele Frequency Aggregator	Latin American 2	Sub	528	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	108	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	90	C=1.00	T=0.00
Allele Frequency Aggregator	Asian	Sub	76	C=1.00	T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.8966	T=0.1034
1000Genomes_30x	African	Sub	1786	C=0.9474	T=0.0526
1000Genomes_30x	Europe	Sub	1266	C=0.8507	T=0.1493
1000Genomes_30x	South Asian	Sub	1202	C=0.9318	T=0.0682
1000Genomes_30x	East Asian	Sub	1170	C=0.8162	T=0.1838
1000Genomes_30x	American	Sub	980	C=0.916	T=0.084
1000Genomes	Global	Study-wide	5008	C=0.8952	T=0.1048
1000Genomes	African	Sub	1322	C=0.9478	T=0.0522
1000Genomes	East Asian	Sub	1008	C=0.8194	T=0.1806
1000Genomes	Europe	Sub	1006	C=0.8559	T=0.1441
1000Genomes	South Asian	Sub	978	C=0.929	T=0.071
1000Genomes	American	Sub	694	C=0.914	T=0.086
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8942	T=0.1058
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8586	T=0.1414
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8684	T=0.1316
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7720	T=0.2280
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7849	T=0.2151
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.857	T=0.143
Northern Sweden	ACPOP	Study-wide	600	C=0.902	T=0.098
Qatari	Global	Study-wide	216	C=0.898	T=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.840	T=0.160
SGDP_PRJ	Global	Study-wide	144	C=0.458	T=0.542
HapMap	Global	Study-wide	120	C=0.942	T=0.058
HapMap	African	Sub	120	C=0.942	T=0.058
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	18	C=0.50	T=0.50

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 12	NC_000012.12:g.40077435C>T
GRCh37.p13 chr 12	NC_000012.11:g.40471237C>T

Gene: SLC2A13, solute carrier family 2 member 13 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC2A13 transcript	NM_052885.4:c.556+27818G>A	N/A	Intron Variant
SLC2A13 transcript variant X1	XM_011537847.3:c.556+2781… XM_011537847.3:c.556+27818G>A	N/A	Intron Variant
SLC2A13 transcript variant X5	XM_011537849.3:c.556+2781… XM_011537849.3:c.556+27818G>A	N/A	Intron Variant
SLC2A13 transcript variant X6	XM_011537850.4:c.556+2781… XM_011537850.4:c.556+27818G>A	N/A	Intron Variant
SLC2A13 transcript variant X3	XM_017018764.2:c.-12+1532… XM_017018764.2:c.-12+15320G>A	N/A	Intron Variant
SLC2A13 transcript variant X4	XM_017018765.2:c.-12+2255… XM_017018765.2:c.-12+22557G>A	N/A	Intron Variant
SLC2A13 transcript variant X2	XM_047428235.1:c.556+2781… XM_047428235.1:c.556+27818G>A	N/A	Intron Variant
SLC2A13 transcript variant X7	XM_017018766.2:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC112268095, uncharacterized LOC112268095 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC112268095 transcript	XR_002957410.2: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=	T
GRCh38.p14 chr 12	NC_000012.12:g.40077435=	NC_000012.12:g.40077435C>T
GRCh37.p13 chr 12	NC_000012.11:g.40471237=	NC_000012.11:g.40471237C>T
SLC2A13 transcript	NM_052885.3:c.556+27818=	NM_052885.3:c.556+27818G>A
SLC2A13 transcript	NM_052885.4:c.556+27818=	NM_052885.4:c.556+27818G>A
SLC2A13 transcript variant X1	XM_005268615.1:c.556+27818=	XM_005268615.1:c.556+27818G>A
SLC2A13 transcript variant X2	XM_005268616.1:c.556+27818=	XM_005268616.1:c.556+27818G>A
SLC2A13 transcript variant X1	XM_011537847.3:c.556+27818=	XM_011537847.3:c.556+27818G>A
SLC2A13 transcript variant X5	XM_011537849.3:c.556+27818=	XM_011537849.3:c.556+27818G>A
SLC2A13 transcript variant X6	XM_011537850.4:c.556+27818=	XM_011537850.4:c.556+27818G>A
SLC2A13 transcript variant X3	XM_017018764.2:c.-12+15320=	XM_017018764.2:c.-12+15320G>A
SLC2A13 transcript variant X4	XM_017018765.2:c.-12+22557=	XM_017018765.2:c.-12+22557G>A
SLC2A13 transcript variant X2	XM_047428235.1:c.556+27818=	XM_047428235.1:c.556+27818G>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#.

66 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3019316	Jun 15, 2001 (96)
2	TSC-CSHL	ss5199668	Oct 10, 2002 (111)
3	SC_JCM	ss5851581	Feb 20, 2003 (126)
4	BCM-HGSC	ss28464870	Sep 20, 2004 (126)
5	BCM-HGSC	ss28468410	Sep 20, 2004 (126)
6	BCM-HGSC	ss28472882	Sep 20, 2004 (126)
7	BCM-HGSC	ss32471514	May 24, 2005 (125)
8	ABI	ss40123631	Mar 11, 2006 (126)
9	HGSV	ss82232973	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss89103210	Mar 24, 2008 (129)
11	ENSEMBL	ss133125124	Dec 01, 2009 (131)
12	BCM-HGSC-SUB	ss208328773	Jul 04, 2010 (132)
13	1000GENOMES	ss225711793	Jul 14, 2010 (132)
14	1000GENOMES	ss235904955	Jul 15, 2010 (132)
15	1000GENOMES	ss242468206	Jul 15, 2010 (132)
16	BL	ss255057257	May 09, 2011 (134)
17	GMI	ss281363233	May 04, 2012 (137)
18	PJP	ss291425045	May 09, 2011 (134)
19	SSMP	ss658664334	Apr 25, 2013 (138)
20	EVA-GONL	ss989450167	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1078401209	Aug 21, 2014 (142)
22	1000GENOMES	ss1344694685	Aug 21, 2014 (142)
23	DDI	ss1426909407	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1576233780	Apr 01, 2015 (144)
25	EVA_DECODE	ss1599117414	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1628424808	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1671418841	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1807209551	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1932814067	Feb 12, 2016 (147)
30	JJLAB	ss2027157368	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2155490406	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2189124474	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2628058121	Nov 08, 2017 (151)
34	GRF	ss2699829614	Nov 08, 2017 (151)
35	GNOMAD	ss2909581499	Nov 08, 2017 (151)
36	SWEGEN	ss3009552196	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3027386698	Nov 08, 2017 (151)
38	CSHL	ss3350026725	Nov 08, 2017 (151)
39	EGCUT_WGS	ss3676827726	Jul 13, 2019 (153)
40	EVA_DECODE	ss3693512775	Jul 13, 2019 (153)
41	ACPOP	ss3738949724	Jul 13, 2019 (153)
42	EVA	ss3750381007	Jul 13, 2019 (153)
43	PACBIO	ss3787204452	Jul 13, 2019 (153)
44	PACBIO	ss3792310032	Jul 13, 2019 (153)
45	PACBIO	ss3797192769	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3815710066	Jul 13, 2019 (153)
47	EVA	ss3833081448	Apr 27, 2020 (154)
48	EVA	ss3840110230	Apr 27, 2020 (154)
49	EVA	ss3845596075	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3878106955	Apr 27, 2020 (154)
51	KRGDB	ss3926711725	Apr 27, 2020 (154)
52	KOGIC	ss3971766795	Apr 27, 2020 (154)
53	TOPMED	ss4915468194	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5205949181	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5290525104	Oct 16, 2022 (156)
56	EVA	ss5405130434	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5485313664	Oct 16, 2022 (156)
58	EVA	ss5510670248	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5587872953	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5652993079	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5755630333	Oct 16, 2022 (156)
62	YY_MCH	ss5813225988	Oct 16, 2022 (156)
63	EVA	ss5837859303	Oct 16, 2022 (156)
64	EVA	ss5850345530	Oct 16, 2022 (156)
65	EVA	ss5904070808	Oct 16, 2022 (156)
66	EVA	ss5944350264	Oct 16, 2022 (156)
67	1000Genomes	NC_000012.11 - 40471237	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000012.12 - 40077435	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 40471237	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000012.11 - 40471237	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000012.11 - 40471237	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000012.12 - 40077435	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000012.11 - 40471237	Apr 27, 2020 (154)
74	HapMap	NC_000012.12 - 40077435	Apr 27, 2020 (154)
75	KOREAN population from KRGDB	NC_000012.11 - 40471237	Apr 27, 2020 (154)
76	Korean Genome Project	NC_000012.12 - 40077435	Apr 27, 2020 (154)
77	Northern Sweden	NC_000012.11 - 40471237	Jul 13, 2019 (153)
78	Qatari	NC_000012.11 - 40471237	Apr 27, 2020 (154)
79	SGDP_PRJ	NC_000012.11 - 40471237	Apr 27, 2020 (154)
80	Siberian	NC_000012.11 - 40471237	Apr 27, 2020 (154)
81	8.3KJPN	NC_000012.11 - 40471237	Apr 26, 2021 (155)
82	14KJPN	NC_000012.12 - 40077435	Oct 16, 2022 (156)
83	TopMed	NC_000012.12 - 40077435	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000012.11 - 40471237	Oct 12, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000012.11 - 40471237	Jul 13, 2019 (153)
86	ALFA	NC_000012.12 - 40077435	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)
rs3937861	Feb 20, 2003 (111)
rs4384436	Mar 11, 2006 (126)
rs17442359	Mar 11, 2006 (126)
rs17483530	Mar 11, 2006 (126)
rs17518336	Mar 11, 2006 (126)
rs59614532	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82232973	NC_000012.9:38757503:C:T	NC_000012.12:40077434:C:T	(self)
ss89103210, ss208328773, ss255057257, ss281363233, ss291425045, ss1599117414	NC_000012.10:38757503:C:T	NC_000012.12:40077434:C:T	(self)
57431485, 31891715, 22565974, 2931013, 14232969, 33889119, 12234589, 14855997, 30123935, 8006760, 63918488, 31891715, 7077283, ss225711793, ss235904955, ss242468206, ss658664334, ss989450167, ss1078401209, ss1344694685, ss1426909407, ss1576233780, ss1628424808, ss1671418841, ss1807209551, ss1932814067, ss2027157368, ss2155490406, ss2628058121, ss2699829614, ss2909581499, ss3009552196, ss3350026725, ss3676827726, ss3738949724, ss3750381007, ss3787204452, ss3792310032, ss3797192769, ss3833081448, ss3840110230, ss3878106955, ss3926711725, ss5205949181, ss5405130434, ss5510670248, ss5652993079, ss5837859303, ss5944350264	NC_000012.11:40471236:C:T	NC_000012.12:40077434:C:T	(self)
75398888, 404988890, 797675, 28144796, 89467437, 131013851, 11534118682, ss2189124474, ss3027386698, ss3693512775, ss3815710066, ss3845596075, ss3971766795, ss4915468194, ss5290525104, ss5485313664, ss5587872953, ss5755630333, ss5813225988, ss5850345530, ss5904070808	NC_000012.12:40077434:C:T	NC_000012.12:40077434:C:T	(self)
ss3019316, ss5199668, ss5851581, ss28464870, ss28468410, ss28472882, ss32471514, ss40123631, ss133125124	NT_029419.12:2614542:C:T	NC_000012.12:40077434: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 rs2101144

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

rs2101144