Name: rs11579015
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.

rs11579015

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:1101579 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.126302 (33431/264690, TOPMED)
C=0.121873 (18457/151444, ALFA)
C=0.114827 (16076/140002, GnomAD) (+ 17 more)
C=0.20253 (5723/28258, 14KJPN)
C=0.20543 (3443/16760, 8.3KJPN)
C=0.1538 (985/6404, 1000G_30x)
C=0.1569 (786/5008, 1000G)
C=0.1017 (392/3854, ALSPAC)
C=0.1176 (436/3708, TWINSUK)
C=0.2263 (663/2930, KOREAN)
C=0.2282 (418/1832, Korea1K)
C=0.1620 (184/1136, Daghestan)
C=0.106 (106/998, GoNL)
C=0.103 (62/600, NorthernSweden)
C=0.136 (44/324, HapMap)
C=0.199 (43/216, Qatari)
C=0.148 (31/210, Vietnamese)
T=0.451 (65/144, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
T=0.31 (5/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: C1orf159 : 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	151538	T=0.878103	C=0.121897
European	Sub	129086	T=0.880467	C=0.119533
African	Sub	8170	T=0.8880	C=0.1120
African Others	Sub	292	T=0.884	C=0.116
African American	Sub	7878	T=0.8882	C=0.1118
Asian	Sub	624	T=0.814	C=0.186
East Asian	Sub	492	T=0.821	C=0.179
Other Asian	Sub	132	T=0.788	C=0.212
Latin American 1	Sub	738	T=0.882	C=0.118
Latin American 2	Sub	6274	T=0.8425	C=0.1575
South Asian	Sub	186	T=0.849	C=0.151
Other	Sub	6460	T=0.8594	C=0.1406

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	T=0.873698	C=0.126302
Allele Frequency Aggregator	Total	Global	151444	T=0.878127	C=0.121873
Allele Frequency Aggregator	European	Sub	129010	T=0.880498	C=0.119502
Allele Frequency Aggregator	African	Sub	8170	T=0.8880	C=0.1120
Allele Frequency Aggregator	Other	Sub	6442	T=0.8594	C=0.1406
Allele Frequency Aggregator	Latin American 2	Sub	6274	T=0.8425	C=0.1575
Allele Frequency Aggregator	Latin American 1	Sub	738	T=0.882	C=0.118
Allele Frequency Aggregator	Asian	Sub	624	T=0.814	C=0.186
Allele Frequency Aggregator	South Asian	Sub	186	T=0.849	C=0.151
gnomAD - Genomes	Global	Study-wide	140002	T=0.885173	C=0.114827
gnomAD - Genomes	European	Sub	75862	T=0.89439	C=0.10561
gnomAD - Genomes	African	Sub	41936	T=0.88893	C=0.11107
gnomAD - Genomes	American	Sub	13620	T=0.86285	C=0.13715
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.8246	C=0.1754
gnomAD - Genomes	East Asian	Sub	3122	T=0.7905	C=0.2095
gnomAD - Genomes	Other	Sub	2144	T=0.8591	C=0.1409
14KJPN	JAPANESE	Study-wide	28258	T=0.79747	C=0.20253
8.3KJPN	JAPANESE	Study-wide	16760	T=0.79457	C=0.20543
1000Genomes_30x	Global	Study-wide	6404	T=0.8462	C=0.1538
1000Genomes_30x	African	Sub	1786	T=0.8673	C=0.1327
1000Genomes_30x	Europe	Sub	1266	T=0.9005	C=0.0995
1000Genomes_30x	South Asian	Sub	1202	T=0.7879	C=0.2121
1000Genomes_30x	East Asian	Sub	1170	T=0.7812	C=0.2188
1000Genomes_30x	American	Sub	980	T=0.887	C=0.113
1000Genomes	Global	Study-wide	5008	T=0.8431	C=0.1569
1000Genomes	African	Sub	1322	T=0.8707	C=0.1293
1000Genomes	East Asian	Sub	1008	T=0.7798	C=0.2202
1000Genomes	Europe	Sub	1006	T=0.8946	C=0.1054
1000Genomes	South Asian	Sub	978	T=0.787	C=0.213
1000Genomes	American	Sub	694	T=0.886	C=0.114
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8983	C=0.1017
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8824	C=0.1176
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7737	C=0.2263
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7718	C=0.2282
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	T=0.8380	C=0.1620
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	T=0.854	C=0.146
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	T=0.833	C=0.167
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.852	C=0.148
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.861	C=0.139
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	T=0.71	C=0.29
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.81	C=0.19
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.894	C=0.106
Northern Sweden	ACPOP	Study-wide	600	T=0.897	C=0.103
HapMap	Global	Study-wide	324	T=0.864	C=0.136
HapMap	African	Sub	120	T=0.867	C=0.133
HapMap	American	Sub	120	T=0.950	C=0.050
HapMap	Asian	Sub	84	T=0.74	C=0.26
Qatari	Global	Study-wide	216	T=0.801	C=0.199
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.852	C=0.148
SGDP_PRJ	Global	Study-wide	144	T=0.451	C=0.549
The Danish reference pan genome	Danish	Study-wide	40	T=0.88	C=0.12
Siberian	Global	Study-wide	16	T=0.31	C=0.69

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 1	NC_000001.11:g.1101579T>C
GRCh37.p13 chr 1	NC_000001.10:g.1036959T>C

Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C1orf159 transcript variant 1	NM_001330306.2:c.-135-947… NM_001330306.2:c.-135-9476A>G	N/A	Intron Variant
C1orf159 transcript variant 3	NM_001363525.2:c.-135-947… NM_001363525.2:c.-135-9476A>G	N/A	Intron Variant
C1orf159 transcript variant 2	NM_017891.5:c.-135-9476A>G	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=	C
GRCh38.p14 chr 1	NC_000001.11:g.1101579=	NC_000001.11:g.1101579T>C
GRCh37.p13 chr 1	NC_000001.10:g.1036959=	NC_000001.10:g.1036959T>C
C1orf159 transcript variant 1	NM_001330306.2:c.-135-9476=	NM_001330306.2:c.-135-9476A>G
C1orf159 transcript variant 3	NM_001363525.2:c.-135-9476=	NM_001363525.2:c.-135-9476A>G
C1orf159 transcript variant 2	NM_017891.4:c.-135-9476=	NM_017891.4:c.-135-9476A>G
C1orf159 transcript variant 2	NM_017891.5:c.-135-9476=	NM_017891.5:c.-135-9476A>G
C1orf159 transcript variant X1	XM_005244764.1:c.-135-9476=	XM_005244764.1:c.-135-9476A>G
C1orf159 transcript variant X16	XM_005244765.1:c.-135-9476=	XM_005244765.1:c.-135-9476A>G
C1orf159 transcript variant X3	XM_005244766.1:c.-135-9476=	XM_005244766.1:c.-135-9476A>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#.

91 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16399157	Feb 28, 2004 (120)
2	ABI	ss44067587	Mar 13, 2006 (126)
3	HUMANGENOME_JCVI	ss99179709	Feb 04, 2009 (130)
4	BGI	ss102713580	Dec 01, 2009 (131)
5	ENSEMBL	ss139297035	Dec 01, 2009 (131)
6	GMI	ss154527625	Dec 01, 2009 (131)
7	ILLUMINA	ss159982285	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss165982346	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss205226949	Jul 04, 2010 (132)
10	1000GENOMES	ss210449514	Jul 14, 2010 (132)
11	1000GENOMES	ss218191809	Jul 14, 2010 (132)
12	1000GENOMES	ss230396391	Jul 14, 2010 (132)
13	1000GENOMES	ss238115943	Jul 15, 2010 (132)
14	GMI	ss275682404	May 04, 2012 (137)
15	PJP	ss290494325	May 09, 2011 (134)
16	ILLUMINA	ss479531050	May 04, 2012 (137)
17	ILLUMINA	ss479534877	May 04, 2012 (137)
18	ILLUMINA	ss479994966	Sep 08, 2015 (146)
19	ILLUMINA	ss484564466	May 04, 2012 (137)
20	ILLUMINA	ss536699841	Sep 08, 2015 (146)
21	TISHKOFF	ss553713330	Apr 25, 2013 (138)
22	SSMP	ss647518311	Apr 25, 2013 (138)
23	ILLUMINA	ss778384278	Sep 08, 2015 (146)
24	ILLUMINA	ss782728949	Sep 08, 2015 (146)
25	ILLUMINA	ss783696202	Sep 08, 2015 (146)
26	ILLUMINA	ss831980668	Sep 08, 2015 (146)
27	ILLUMINA	ss833839290	Sep 08, 2015 (146)
28	EVA-GONL	ss974771838	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1067613569	Aug 21, 2014 (142)
30	1000GENOMES	ss1289349713	Aug 21, 2014 (142)
31	HAMMER_LAB	ss1397238521	Sep 08, 2015 (146)
32	DDI	ss1425685794	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1573851947	Apr 01, 2015 (144)
34	EVA_DECODE	ss1584131768	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1599382296	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1642376329	Apr 01, 2015 (144)
37	ILLUMINA	ss1751860376	Sep 08, 2015 (146)
38	HAMMER_LAB	ss1793716685	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1917963710	Feb 12, 2016 (147)
40	JJLAB	ss2019499742	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2147486475	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2159384957	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2624265484	Nov 08, 2017 (151)
44	ILLUMINA	ss2632465731	Nov 08, 2017 (151)
45	GRF	ss2697377420	Nov 08, 2017 (151)
46	GNOMAD	ss2750670144	Nov 08, 2017 (151)
47	AFFY	ss2984841251	Nov 08, 2017 (151)
48	AFFY	ss2985495007	Nov 08, 2017 (151)
49	SWEGEN	ss2986154131	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3023514253	Nov 08, 2017 (151)
51	CSHL	ss3343274173	Nov 08, 2017 (151)
52	ILLUMINA	ss3626007075	Oct 11, 2018 (152)
53	ILLUMINA	ss3630505776	Oct 11, 2018 (152)
54	ILLUMINA	ss3632878062	Oct 11, 2018 (152)
55	ILLUMINA	ss3633571482	Oct 11, 2018 (152)
56	ILLUMINA	ss3634302068	Oct 11, 2018 (152)
57	ILLUMINA	ss3635265685	Oct 11, 2018 (152)
58	ILLUMINA	ss3635978717	Oct 11, 2018 (152)
59	ILLUMINA	ss3637016025	Oct 11, 2018 (152)
60	ILLUMINA	ss3640009434	Oct 11, 2018 (152)
61	ILLUMINA	ss3640973170	Oct 11, 2018 (152)
62	ILLUMINA	ss3641266985	Oct 11, 2018 (152)
63	URBANLAB	ss3646581876	Oct 11, 2018 (152)
64	ILLUMINA	ss3653615015	Oct 11, 2018 (152)
65	EVA_DECODE	ss3685997678	Jul 12, 2019 (153)
66	ACPOP	ss3726718568	Jul 12, 2019 (153)
67	ILLUMINA	ss3744602999	Jul 12, 2019 (153)
68	EVA	ss3745724133	Jul 12, 2019 (153)
69	ILLUMINA	ss3772104757	Jul 12, 2019 (153)
70	KHV_HUMAN_GENOMES	ss3798746726	Jul 12, 2019 (153)
71	EVA	ss3825982535	Apr 25, 2020 (154)
72	SGDP_PRJ	ss3848003503	Apr 25, 2020 (154)
73	KRGDB	ss3892846233	Apr 25, 2020 (154)
74	KOGIC	ss3943635918	Apr 25, 2020 (154)
75	EVA	ss4016889114	Apr 25, 2021 (155)
76	TOPMED	ss4436515600	Apr 25, 2021 (155)
77	TOMMO_GENOMICS	ss5142066121	Apr 25, 2021 (155)
78	1000G_HIGH_COVERAGE	ss5240872963	Oct 12, 2022 (156)
79	EVA	ss5314586041	Oct 12, 2022 (156)
80	EVA	ss5316199154	Oct 12, 2022 (156)
81	HUGCELL_USP	ss5442119837	Oct 12, 2022 (156)
82	1000G_HIGH_COVERAGE	ss5512501522	Oct 12, 2022 (156)
83	SANFORD_IMAGENETICS	ss5624755009	Oct 12, 2022 (156)
84	TOMMO_GENOMICS	ss5666210353	Oct 12, 2022 (156)
85	EVA	ss5799472572	Oct 12, 2022 (156)
86	YY_MCH	ss5800246198	Oct 12, 2022 (156)
87	EVA	ss5831422604	Oct 12, 2022 (156)
88	EVA	ss5848749712	Oct 12, 2022 (156)
89	EVA	ss5906714369	Oct 12, 2022 (156)
90	EVA	ss5936587344	Oct 12, 2022 (156)
91	EVA	ss5979926444	Oct 12, 2022 (156)
92	1000Genomes	NC_000001.10 - 1036959	Oct 11, 2018 (152)
93	1000Genomes_30x	NC_000001.11 - 1101579	Oct 12, 2022 (156)
94	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 1036959	Oct 11, 2018 (152)
95	Genome-wide autozygosity in Daghestan	NC_000001.9 - 1026822	Apr 25, 2020 (154)
96	The Danish reference pan genome	NC_000001.10 - 1036959	Apr 25, 2020 (154)
97	gnomAD - Genomes	NC_000001.11 - 1101579	Apr 25, 2021 (155)
98	Genome of the Netherlands Release 5	NC_000001.10 - 1036959	Apr 25, 2020 (154)
99	HapMap	NC_000001.11 - 1101579	Apr 25, 2020 (154)
100	KOREAN population from KRGDB	NC_000001.10 - 1036959	Apr 25, 2020 (154)
101	Korean Genome Project	NC_000001.11 - 1101579	Apr 25, 2020 (154)
102	Northern Sweden	NC_000001.10 - 1036959	Jul 12, 2019 (153)
103	Qatari	NC_000001.10 - 1036959	Apr 25, 2020 (154)
104	SGDP_PRJ	NC_000001.10 - 1036959	Apr 25, 2020 (154)
105	Siberian	NC_000001.10 - 1036959	Apr 25, 2020 (154)
106	8.3KJPN	NC_000001.10 - 1036959	Apr 25, 2021 (155)
107	14KJPN	NC_000001.11 - 1101579	Oct 12, 2022 (156)
108	TopMed	NC_000001.11 - 1101579	Apr 25, 2021 (155)
109	UK 10K study - Twins	NC_000001.10 - 1036959	Oct 11, 2018 (152)
110	A Vietnamese Genetic Variation Database	NC_000001.10 - 1036959	Jul 12, 2019 (153)
111	ALFA	NC_000001.11 - 1101579	Apr 25, 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
8, ss165982346, ss205226949, ss210449514, ss275682404, ss290494325, ss479531050, ss1397238521, ss1584131768	NC_000001.9:1026821:T:C	NC_000001.11:1101578:T:C	(self)
14820, 4657, 1359181, 2176, 23627, 3433, 5640, 20483, 2829, 35428, 4657, 1047, ss218191809, ss230396391, ss238115943, ss479534877, ss479994966, ss484564466, ss536699841, ss553713330, ss647518311, ss778384278, ss782728949, ss783696202, ss831980668, ss833839290, ss974771838, ss1067613569, ss1289349713, ss1425685794, ss1573851947, ss1599382296, ss1642376329, ss1751860376, ss1793716685, ss1917963710, ss2019499742, ss2147486475, ss2624265484, ss2632465731, ss2697377420, ss2750670144, ss2984841251, ss2985495007, ss2986154131, ss3343274173, ss3626007075, ss3630505776, ss3632878062, ss3633571482, ss3634302068, ss3635265685, ss3635978717, ss3637016025, ss3640009434, ss3640973170, ss3641266985, ss3653615015, ss3726718568, ss3744602999, ss3745724133, ss3772104757, ss3825982535, ss3848003503, ss3892846233, ss4016889114, ss5142066121, ss5314586041, ss5316199154, ss5624755009, ss5799472572, ss5831422604, ss5936587344, ss5979926444	NC_000001.10:1036958:T:C	NC_000001.11:1101578:T:C	(self)
27457, 137596, 209, 13919, 47457, 121935, 4882724972, ss2159384957, ss3023514253, ss3646581876, ss3685997678, ss3798746726, ss3943635918, ss4436515600, ss5240872963, ss5442119837, ss5512501522, ss5666210353, ss5800246198, ss5848749712, ss5906714369	NC_000001.11:1101578:T:C	NC_000001.11:1101578:T:C	(self)
ss44067587, ss99179709, ss102713580, ss139297035, ss154527625, ss159982285	NT_004350.19:515590:T:C	NC_000001.11:1101578:T:C	(self)
ss16399157	NT_077913.2:40669:T:C	NC_000001.11:1101578: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 rs11579015

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

rs11579015