Name: rs1121114
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.

rs1121114

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr13:23649520 (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: C=0.466327 (123432/264690, TOPMED)
C=0.472899 (65889/139330, GnomAD)
C=0.41033 (11564/28182, 14KJPN) (+ 16 more)
C=0.40310 (6756/16760, 8.3KJPN)
T=0.3808 (3002/7884, ALFA)
C=0.4631 (2966/6404, 1000G_30x)
C=0.4627 (2317/5008, 1000G)
C=0.3724 (1667/4476, Estonian)
C=0.4183 (1612/3854, ALSPAC)
C=0.4234 (1570/3708, TWINSUK)
C=0.3857 (1130/2930, KOREAN)
C=0.3936 (721/1832, Korea1K)
C=0.444 (443/998, GoNL)
C=0.470 (282/600, NorthernSweden)
C=0.277 (123/444, SGDP_PRJ)
T=0.458 (99/216, Qatari)
C=0.336 (72/214, Vietnamese)
C=0.24 (11/46, Siberian)
C=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TNFRSF19 : 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	7884	C=0.6192	T=0.3808
European	Sub	6370	C=0.5490	T=0.4510
African	Sub	1094	C=0.9808	T=0.0192
African Others	Sub	54	C=1.00	T=0.00
African American	Sub	1040	C=0.9798	T=0.0202
Asian	Sub	6	C=1.0	T=0.0
East Asian	Sub	6	C=1.0	T=0.0
Other Asian	Sub	0	C=0	T=0
Latin American 1	Sub	40	C=1.00	T=0.00
Latin American 2	Sub	50	C=1.00	T=0.00
South Asian	Sub	22	C=1.00	T=0.00
Other	Sub	302	C=0.642	T=0.358

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=0.466327	T=0.533673
gnomAD - Genomes	Global	Study-wide	139330	C=0.472899	T=0.527101
gnomAD - Genomes	European	Sub	75388	C=0.42800	T=0.57200
gnomAD - Genomes	African	Sub	41744	C=0.59223	T=0.40777
gnomAD - Genomes	American	Sub	13610	C=0.37979	T=0.62021
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.5549	T=0.4451
gnomAD - Genomes	East Asian	Sub	3126	C=0.2863	T=0.7137
gnomAD - Genomes	Other	Sub	2144	C=0.4646	T=0.5354
14KJPN	JAPANESE	Study-wide	28182	C=0.41033	T=0.58967
8.3KJPN	JAPANESE	Study-wide	16760	C=0.40310	T=0.59690
Allele Frequency Aggregator	Total	Global	7884	C=0.6192	T=0.3808
Allele Frequency Aggregator	European	Sub	6370	C=0.5490	T=0.4510
Allele Frequency Aggregator	African	Sub	1094	C=0.9808	T=0.0192
Allele Frequency Aggregator	Other	Sub	302	C=0.642	T=0.358
Allele Frequency Aggregator	Latin American 2	Sub	50	C=1.00	T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	40	C=1.00	T=0.00
Allele Frequency Aggregator	South Asian	Sub	22	C=1.00	T=0.00
Allele Frequency Aggregator	Asian	Sub	6	C=1.0	T=0.0
1000Genomes_30x	Global	Study-wide	6404	C=0.4631	T=0.5369
1000Genomes_30x	African	Sub	1786	C=0.6473	T=0.3527
1000Genomes_30x	Europe	Sub	1266	C=0.4258	T=0.5742
1000Genomes_30x	South Asian	Sub	1202	C=0.5067	T=0.4933
1000Genomes_30x	East Asian	Sub	1170	C=0.2863	T=0.7137
1000Genomes_30x	American	Sub	980	C=0.334	T=0.666
1000Genomes	Global	Study-wide	5008	C=0.4627	T=0.5373
1000Genomes	African	Sub	1322	C=0.6437	T=0.3563
1000Genomes	East Asian	Sub	1008	C=0.2966	T=0.7034
1000Genomes	Europe	Sub	1006	C=0.4274	T=0.5726
1000Genomes	South Asian	Sub	978	C=0.513	T=0.487
1000Genomes	American	Sub	694	C=0.339	T=0.661
Genetic variation in the Estonian population	Estonian	Study-wide	4476	C=0.3724	T=0.6276
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4183	T=0.5817
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4234	T=0.5766
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.3857	A=0.0000, T=0.6143
Korean Genome Project	KOREAN	Study-wide	1832	C=0.3936	T=0.6064
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.444	T=0.556
Northern Sweden	ACPOP	Study-wide	600	C=0.470	T=0.530
SGDP_PRJ	Global	Study-wide	444	C=0.277	T=0.723
Qatari	Global	Study-wide	216	C=0.542	T=0.458
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.336	T=0.664
Siberian	Global	Study-wide	46	C=0.24	T=0.76
The Danish reference pan genome	Danish	Study-wide	40	C=0.33	T=0.68

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 13	NC_000013.11:g.23649520C>A
GRCh38.p14 chr 13	NC_000013.11:g.23649520C>T
GRCh37.p13 chr 13	NC_000013.10:g.24223659C>A
GRCh37.p13 chr 13	NC_000013.10:g.24223659C>T

Gene: TNFRSF19, TNF receptor superfamily member 19 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TNFRSF19 transcript variant 3	NM_001204458.3:c.446-9530… NM_001204458.3:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant 4	NM_001204459.2:c.50-9530C… NM_001204459.2:c.50-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant 5	NM_001354985.2:c.446-9530… NM_001354985.2:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant 1	NM_018647.5:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant 2	NM_148957.4:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant X3	XM_005266446.3:c.446-9530… XM_005266446.3:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant X1	XM_047430440.1:c.446-9530… XM_047430440.1:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant X2	XM_047430441.1:c.446-9530… XM_047430441.1:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant X4	XM_047430442.1:c.446-9530… XM_047430442.1:c.446-9530C>A	N/A	Intron Variant
TNFRSF19 transcript variant X5	XM_047430443.1:c.446-9530… XM_047430443.1:c.446-9530C>A	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 13	NC_000013.11:g.23649520=	NC_000013.11:g.23649520C>A	NC_000013.11:g.23649520C>T
GRCh37.p13 chr 13	NC_000013.10:g.24223659=	NC_000013.10:g.24223659C>A	NC_000013.10:g.24223659C>T
TNFRSF19 transcript variant 3	NM_001204458.1:c.446-9530=	NM_001204458.1:c.446-9530C>A	NM_001204458.1:c.446-9530C>T
TNFRSF19 transcript variant 3	NM_001204458.3:c.446-9530=	NM_001204458.3:c.446-9530C>A	NM_001204458.3:c.446-9530C>T
TNFRSF19 transcript variant 4	NM_001204459.1:c.50-9530=	NM_001204459.1:c.50-9530C>A	NM_001204459.1:c.50-9530C>T
TNFRSF19 transcript variant 4	NM_001204459.2:c.50-9530=	NM_001204459.2:c.50-9530C>A	NM_001204459.2:c.50-9530C>T
TNFRSF19 transcript variant 5	NM_001354985.2:c.446-9530=	NM_001354985.2:c.446-9530C>A	NM_001354985.2:c.446-9530C>T
TNFRSF19 transcript variant 1	NM_018647.3:c.446-9530=	NM_018647.3:c.446-9530C>A	NM_018647.3:c.446-9530C>T
TNFRSF19 transcript variant 1	NM_018647.5:c.446-9530=	NM_018647.5:c.446-9530C>A	NM_018647.5:c.446-9530C>T
TNFRSF19 transcript variant 2	NM_148957.3:c.446-9530=	NM_148957.3:c.446-9530C>A	NM_148957.3:c.446-9530C>T
TNFRSF19 transcript variant 2	NM_148957.4:c.446-9530=	NM_148957.4:c.446-9530C>A	NM_148957.4:c.446-9530C>T
TNFRSF19 transcript variant X1	XM_005266445.1:c.446-9530=	XM_005266445.1:c.446-9530C>A	XM_005266445.1:c.446-9530C>T
TNFRSF19 transcript variant X4	XM_005266446.1:c.446-9530=	XM_005266446.1:c.446-9530C>A	XM_005266446.1:c.446-9530C>T
TNFRSF19 transcript variant X3	XM_005266446.3:c.446-9530=	XM_005266446.3:c.446-9530C>A	XM_005266446.3:c.446-9530C>T
TNFRSF19 transcript variant X1	XM_047430440.1:c.446-9530=	XM_047430440.1:c.446-9530C>A	XM_047430440.1:c.446-9530C>T
TNFRSF19 transcript variant X2	XM_047430441.1:c.446-9530=	XM_047430441.1:c.446-9530C>A	XM_047430441.1:c.446-9530C>T
TNFRSF19 transcript variant X4	XM_047430442.1:c.446-9530=	XM_047430442.1:c.446-9530C>A	XM_047430442.1:c.446-9530C>T
TNFRSF19 transcript variant X5	XM_047430443.1:c.446-9530=	XM_047430443.1:c.446-9530C>A	XM_047430443.1:c.446-9530C>T

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#.

64 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1450391	Oct 13, 2000 (86)
2	TSC-CSHL	ss5584640	Oct 10, 2002 (111)
3	SC_JCM	ss5792057	Feb 20, 2003 (126)
4	BCM_SSAHASNP	ss11061865	Jul 11, 2003 (116)
5	SC_SNP	ss13259083	Dec 05, 2003 (119)
6	BGI	ss103102067	Dec 01, 2009 (131)
7	1000GENOMES	ss112610594	Jan 25, 2009 (130)
8	1000GENOMES	ss114406037	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss118385618	Dec 01, 2009 (131)
10	GMI	ss154522808	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss167693281	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss168945625	Jul 04, 2010 (132)
13	BUSHMAN	ss198962244	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss208676234	Jul 04, 2010 (132)
15	1000GENOMES	ss226075884	Jul 14, 2010 (132)
16	1000GENOMES	ss236173302	Jul 15, 2010 (132)
17	1000GENOMES	ss242684475	Jul 15, 2010 (132)
18	GMI	ss281635678	May 04, 2012 (137)
19	GMI	ss286666554	Apr 25, 2013 (138)
20	TISHKOFF	ss563545159	Apr 25, 2013 (138)
21	SSMP	ss659138881	Apr 25, 2013 (138)
22	EVA-GONL	ss990185352	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1078931901	Aug 21, 2014 (142)
24	1000GENOMES	ss1347469091	Aug 21, 2014 (142)
25	DDI	ss1427125345	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1576667545	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1629876444	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1672870477	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1807522127	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1933553155	Feb 12, 2016 (147)
31	JJLAB	ss2027530677	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2155894150	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2194822544	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2628252622	Nov 08, 2017 (151)
35	GRF	ss2700265295	Nov 08, 2017 (151)
36	GNOMAD	ss2917530604	Nov 08, 2017 (151)
37	SWEGEN	ss3010709733	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3027579665	Nov 08, 2017 (151)
39	CSHL	ss3350361062	Nov 08, 2017 (151)
40	EGCUT_WGS	ss3677977147	Jul 13, 2019 (153)
41	ACPOP	ss3739575973	Jul 13, 2019 (153)
42	EVA	ss3751226916	Jul 13, 2019 (153)
43	PACBIO	ss3787401249	Jul 13, 2019 (153)
44	PACBIO	ss3792475407	Jul 13, 2019 (153)
45	PACBIO	ss3797359100	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3816557986	Jul 13, 2019 (153)
47	EVA	ss3833443971	Apr 27, 2020 (154)
48	EVA	ss3840297564	Apr 27, 2020 (154)
49	EVA	ss3845781935	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3879579014	Apr 27, 2020 (154)
51	KRGDB	ss3928394831	Apr 27, 2020 (154)
52	KOGIC	ss3973194302	Apr 27, 2020 (154)
53	TOPMED	ss4939747485	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5209149420	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5293073337	Oct 16, 2022 (156)
56	HUGCELL_USP	ss5487503984	Oct 16, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5591698491	Oct 16, 2022 (156)
58	SANFORD_IMAGENETICS	ss5654387170	Oct 16, 2022 (156)
59	TOMMO_GENOMICS	ss5760783049	Oct 16, 2022 (156)
60	YY_MCH	ss5813942842	Oct 16, 2022 (156)
61	EVA	ss5839211873	Oct 16, 2022 (156)
62	EVA	ss5850644146	Oct 16, 2022 (156)
63	EVA	ss5924344823	Oct 16, 2022 (156)
64	EVA	ss5945792532	Oct 16, 2022 (156)
65	1000Genomes	NC_000013.10 - 24223659	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000013.11 - 23649520	Oct 16, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000013.10 - 24223659	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000013.10 - 24223659	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000013.10 - 24223659	Apr 27, 2020 (154)
70	gnomAD - Genomes	NC_000013.11 - 23649520	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000013.10 - 24223659	Apr 27, 2020 (154)
72	KOREAN population from KRGDB	NC_000013.10 - 24223659	Apr 27, 2020 (154)
73	Korean Genome Project	NC_000013.11 - 23649520	Apr 27, 2020 (154)
74	Northern Sweden	NC_000013.10 - 24223659	Jul 13, 2019 (153)
75	Qatari	NC_000013.10 - 24223659	Apr 27, 2020 (154)
76	SGDP_PRJ	NC_000013.10 - 24223659	Apr 27, 2020 (154)
77	Siberian	NC_000013.10 - 24223659	Apr 27, 2020 (154)
78	8.3KJPN	NC_000013.10 - 24223659	Apr 26, 2021 (155)
79	14KJPN	NC_000013.11 - 23649520	Oct 16, 2022 (156)
80	TopMed	NC_000013.11 - 23649520	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000013.10 - 24223659	Oct 12, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000013.10 - 24223659	Jul 13, 2019 (153)
83	ALFA	NC_000013.11 - 23649520	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)
rs4133962	Feb 20, 2003 (111)
rs4351916	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
35572225, ss3928394831	NC_000013.10:24223658:C:A	NC_000013.11:23649519:C:A	(self)
ss112610594, ss114406037, ss118385618, ss167693281, ss168945625, ss198962244, ss208676234, ss281635678, ss286666554	NC_000013.9:23121658:C:T	NC_000013.11:23649519:C:T	(self)
60311427, 33494463, 23715395, 3216697, 14943065, 35572225, 12860838, 15595085, 31595994, 8410504, 67118727, 33494463, 7429463, ss226075884, ss236173302, ss242684475, ss563545159, ss659138881, ss990185352, ss1078931901, ss1347469091, ss1427125345, ss1576667545, ss1629876444, ss1672870477, ss1807522127, ss1933553155, ss2027530677, ss2155894150, ss2628252622, ss2700265295, ss2917530604, ss3010709733, ss3350361062, ss3677977147, ss3739575973, ss3751226916, ss3787401249, ss3792475407, ss3797359100, ss3833443971, ss3840297564, ss3879579014, ss3928394831, ss5209149420, ss5654387170, ss5839211873, ss5945792532	NC_000013.10:24223658:C:T	NC_000013.11:23649519:C:T	(self)
79224426, 425342506, 29572303, 94620153, 155293143, 5631846663, ss2194822544, ss3027579665, ss3816557986, ss3845781935, ss3973194302, ss4939747485, ss5293073337, ss5487503984, ss5591698491, ss5760783049, ss5813942842, ss5850644146, ss5924344823	NC_000013.11:23649519:C:T	NC_000013.11:23649519:C:T	(self)
ss11061865, ss13259083	NT_009799.12:5203658:C:T	NC_000013.11:23649519:C:T	(self)
ss1450391, ss5584640, ss5792057, ss103102067, ss154522808	NT_024524.14:5203658:C:T	NC_000013.11:23649519: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 rs1121114

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

rs1121114