Name: rs35877559
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.

rs35877559

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:3622517 (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=0.128513 (34016/264690, TOPMED)
C=0.140701 (19722/140170, GnomAD)
C=0.15225 (9992/65630, ALFA) (+ 19 more)
C=0.05528 (1562/28258, 14KJPN)
C=0.05370 (900/16760, 8.3KJPN)
C=0.0959 (614/6404, 1000G_30x)
C=0.0948 (475/5008, 1000G)
C=0.1958 (877/4480, Estonian)
C=0.1674 (645/3854, ALSPAC)
C=0.1575 (584/3708, TWINSUK)
C=0.0633 (185/2922, KOREAN)
C=0.0777 (147/1892, HapMap)
C=0.0529 (97/1832, Korea1K)
C=0.140 (140/998, GoNL)
C=0.097 (61/626, Chileans)
C=0.148 (89/600, NorthernSweden)
C=0.120 (26/216, Qatari)
C=0.067 (14/210, Vietnamese)
T=0.47 (42/90, SGDP_PRJ)
C=0.15 (12/80, Ancient Sardinia)
C=0.23 (9/40, GENOME_DK)
T=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507336 : 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	65630	T=0.84775	C=0.15225
European	Sub	46164	T=0.83086	C=0.16914
African	Sub	5838	T=0.9152	C=0.0848
African Others	Sub	202	T=0.936	C=0.064
African American	Sub	5636	T=0.9145	C=0.0855
Asian	Sub	502	T=0.950	C=0.050
East Asian	Sub	402	T=0.945	C=0.055
Other Asian	Sub	100	T=0.97	C=0.03
Latin American 1	Sub	742	T=0.872	C=0.128
Latin American 2	Sub	7130	T=0.8863	C=0.1137
South Asian	Sub	190	T=0.953	C=0.047
Other	Sub	5064	T=0.8521	C=0.1479

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=0.871487	C=0.128513
gnomAD - Genomes	Global	Study-wide	140170	T=0.859299	C=0.140701
gnomAD - Genomes	European	Sub	75888	T=0.82291	C=0.17709
gnomAD - Genomes	African	Sub	42028	T=0.91472	C=0.08528
gnomAD - Genomes	American	Sub	13650	T=0.86916	C=0.13084
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.8700	C=0.1300
gnomAD - Genomes	East Asian	Sub	3128	T=0.9444	C=0.0556
gnomAD - Genomes	Other	Sub	2154	T=0.8575	C=0.1425
Allele Frequency Aggregator	Total	Global	65630	T=0.84775	C=0.15225
Allele Frequency Aggregator	European	Sub	46164	T=0.83086	C=0.16914
Allele Frequency Aggregator	Latin American 2	Sub	7130	T=0.8863	C=0.1137
Allele Frequency Aggregator	African	Sub	5838	T=0.9152	C=0.0848
Allele Frequency Aggregator	Other	Sub	5064	T=0.8521	C=0.1479
Allele Frequency Aggregator	Latin American 1	Sub	742	T=0.872	C=0.128
Allele Frequency Aggregator	Asian	Sub	502	T=0.950	C=0.050
Allele Frequency Aggregator	South Asian	Sub	190	T=0.953	C=0.047
14KJPN	JAPANESE	Study-wide	28258	T=0.94472	C=0.05528
8.3KJPN	JAPANESE	Study-wide	16760	T=0.94630	C=0.05370
1000Genomes_30x	Global	Study-wide	6404	T=0.9041	C=0.0959
1000Genomes_30x	African	Sub	1786	T=0.9384	C=0.0616
1000Genomes_30x	Europe	Sub	1266	T=0.8444	C=0.1556
1000Genomes_30x	South Asian	Sub	1202	T=0.9126	C=0.0874
1000Genomes_30x	East Asian	Sub	1170	T=0.9350	C=0.0650
1000Genomes_30x	American	Sub	980	T=0.871	C=0.129
1000Genomes	Global	Study-wide	5008	T=0.9052	C=0.0948
1000Genomes	African	Sub	1322	T=0.9380	C=0.0620
1000Genomes	East Asian	Sub	1008	T=0.9395	C=0.0605
1000Genomes	Europe	Sub	1006	T=0.8380	C=0.1620
1000Genomes	South Asian	Sub	978	T=0.915	C=0.085
1000Genomes	American	Sub	694	T=0.876	C=0.124
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8042	C=0.1958
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8326	C=0.1674
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8425	C=0.1575
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9367	C=0.0633
HapMap	Global	Study-wide	1892	T=0.9223	C=0.0777
HapMap	American	Sub	770	T=0.910	C=0.090
HapMap	African	Sub	692	T=0.941	C=0.059
HapMap	Asian	Sub	254	T=0.949	C=0.051
HapMap	Europe	Sub	176	T=0.864	C=0.136
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9471	C=0.0529
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.860	C=0.140
Chileans	Chilean	Study-wide	626	T=0.903	C=0.097
Northern Sweden	ACPOP	Study-wide	600	T=0.852	C=0.148
Qatari	Global	Study-wide	216	T=0.880	C=0.120
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.933	C=0.067
SGDP_PRJ	Global	Study-wide	90	T=0.47	C=0.53
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	T=0.85	C=0.15
The Danish reference pan genome	Danish	Study-wide	40	T=0.78	C=0.23
Siberian	Global	Study-wide	18	T=0.44	C=0.56

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 6	NC_000006.12:g.3622517T>C
GRCh37.p13 chr 6	NC_000006.11:g.3622751T>C

Gene: LOC100507336, uncharacterized LOC100507336 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507336 transcript variant X1	XR_001743929.2:n.	N/A	Intron Variant
LOC100507336 transcript variant X2	XR_926401.3:n.	N/A	Intron Variant
LOC100507336 transcript variant X3	XR_926402.3:n.	N/A	Genic Upstream Transcript 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 6	NC_000006.12:g.3622517=	NC_000006.12:g.3622517T>C
GRCh37.p13 chr 6	NC_000006.11:g.3622751=	NC_000006.11:g.3622751T>C

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#.

72 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss46561167	Mar 15, 2006 (126)
2	AFFY	ss66036215	Jul 04, 2010 (132)
3	PERLEGEN	ss68962795	May 16, 2007 (127)
4	AFFY	ss75924925	Dec 07, 2007 (129)
5	KRIBB_YJKIM	ss83295727	Dec 16, 2007 (130)
6	HUMANGENOME_JCVI	ss98468581	Feb 05, 2009 (130)
7	GMI	ss156459646	Dec 01, 2009 (131)
8	ILLUMINA	ss160629284	Dec 01, 2009 (131)
9	AFFY	ss169199511	Jul 04, 2010 (132)
10	BUSHMAN	ss201341283	Jul 04, 2010 (132)
11	BCM-HGSC-SUB	ss207338837	Jul 04, 2010 (132)
12	1000GENOMES	ss222174419	Jul 14, 2010 (132)
13	1000GENOMES	ss233298596	Jul 14, 2010 (132)
14	1000GENOMES	ss240389552	Jul 15, 2010 (132)
15	GMI	ss278628833	May 04, 2012 (137)
16	ILLUMINA	ss481731926	Sep 08, 2015 (146)
17	ILLUMINA	ss483058481	May 04, 2012 (137)
18	ILLUMINA	ss485233486	May 04, 2012 (137)
19	ILLUMINA	ss535155669	Sep 08, 2015 (146)
20	SSMP	ss652873704	Apr 25, 2013 (138)
21	ILLUMINA	ss780135598	Sep 08, 2015 (146)
22	ILLUMINA	ss781972741	Sep 08, 2015 (146)
23	ILLUMINA	ss835618871	Sep 08, 2015 (146)
24	EVA-GONL	ss982521573	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1073333963	Aug 21, 2014 (142)
26	1000GENOMES	ss1318739469	Aug 21, 2014 (142)
27	EVA_GENOME_DK	ss1581506573	Apr 01, 2015 (144)
28	EVA_DECODE	ss1592067492	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1614822814	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1657816847	Apr 01, 2015 (144)
31	EVA_SVP	ss1712830447	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1804251725	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1925779480	Feb 12, 2016 (147)
34	GENOMED	ss1970295647	Jul 19, 2016 (147)
35	JJLAB	ss2023504210	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2151666209	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2281314320	Dec 20, 2016 (150)
38	ILLUMINA	ss2634391373	Nov 08, 2017 (151)
39	GRF	ss2707251348	Nov 08, 2017 (151)
40	GNOMAD	ss2835145910	Nov 08, 2017 (151)
41	SWEGEN	ss2998420467	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3025535467	Nov 08, 2017 (151)
43	CSHL	ss3346807258	Nov 08, 2017 (151)
44	ILLUMINA	ss3629429599	Oct 12, 2018 (152)
45	ILLUMINA	ss3632311974	Oct 12, 2018 (152)
46	ILLUMINA	ss3636755814	Oct 12, 2018 (152)
47	ILLUMINA	ss3642469432	Oct 12, 2018 (152)
48	URBANLAB	ss3648254809	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3666344296	Jul 13, 2019 (153)
50	EVA_DECODE	ss3716465570	Jul 13, 2019 (153)
51	ACPOP	ss3733150103	Jul 13, 2019 (153)
52	EVA	ss3764538878	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3807699995	Jul 13, 2019 (153)
54	EVA	ss3829699694	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3863795030	Apr 26, 2020 (154)
56	KRGDB	ss3910529230	Apr 26, 2020 (154)
57	KOGIC	ss3958386422	Apr 26, 2020 (154)
58	EVA	ss3985195272	Apr 26, 2021 (155)
59	TOPMED	ss4691742748	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5175898836	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5267194814	Oct 13, 2022 (156)
62	EVA	ss5315116855	Oct 13, 2022 (156)
63	EVA	ss5363437165	Oct 13, 2022 (156)
64	HUGCELL_USP	ss5465007652	Oct 13, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5552524082	Oct 13, 2022 (156)
66	SANFORD_IMAGENETICS	ss5639648877	Oct 13, 2022 (156)
67	TOMMO_GENOMICS	ss5713490501	Oct 13, 2022 (156)
68	YY_MCH	ss5807099895	Oct 13, 2022 (156)
69	EVA	ss5841711491	Oct 13, 2022 (156)
70	EVA	ss5855176288	Oct 13, 2022 (156)
71	EVA	ss5882417573	Oct 13, 2022 (156)
72	EVA	ss5968142119	Oct 13, 2022 (156)
73	1000Genomes	NC_000006.11 - 3622751	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000006.12 - 3622517	Oct 13, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 3622751	Oct 12, 2018 (152)
76	Chileans	NC_000006.11 - 3622751	Apr 26, 2020 (154)
77	Genetic variation in the Estonian population	NC_000006.11 - 3622751	Oct 12, 2018 (152)
78	The Danish reference pan genome	NC_000006.11 - 3622751	Apr 26, 2020 (154)
79	gnomAD - Genomes	NC_000006.12 - 3622517	Apr 26, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000006.11 - 3622751	Apr 26, 2020 (154)
81	HapMap	NC_000006.12 - 3622517	Apr 26, 2020 (154)
82	KOREAN population from KRGDB	NC_000006.11 - 3622751	Apr 26, 2020 (154)
83	Korean Genome Project	NC_000006.12 - 3622517	Apr 26, 2020 (154)
84	Northern Sweden	NC_000006.11 - 3622751	Jul 13, 2019 (153)
85	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 3622751	Apr 26, 2021 (155)
86	Qatari	NC_000006.11 - 3622751	Apr 26, 2020 (154)
87	SGDP_PRJ	NC_000006.11 - 3622751	Apr 26, 2020 (154)
88	Siberian	NC_000006.11 - 3622751	Apr 26, 2020 (154)
89	8.3KJPN	NC_000006.11 - 3622751	Apr 26, 2021 (155)
90	14KJPN	NC_000006.12 - 3622517	Oct 13, 2022 (156)
91	TopMed	NC_000006.12 - 3622517	Apr 26, 2021 (155)
92	UK 10K study - Twins	NC_000006.11 - 3622751	Oct 12, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000006.11 - 3622751	Jul 13, 2019 (153)
94	ALFA	NC_000006.12 - 3622517	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)
rs61691202	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss75924925, ss169199511, ss201341283, ss207338837, ss278628833, ss485233486, ss1592067492, ss1712830447	NC_000006.10:3567749:T:C	NC_000006.12:3622516:T:C	(self)
30472711, 16961147, 369192, 12082544, 7671512, 7528245, 17706624, 6434968, 421199, 7821410, 15812010, 4182563, 33868143, 16961147, 3756419, ss222174419, ss233298596, ss240389552, ss481731926, ss483058481, ss535155669, ss652873704, ss780135598, ss781972741, ss835618871, ss982521573, ss1073333963, ss1318739469, ss1581506573, ss1614822814, ss1657816847, ss1804251725, ss1925779480, ss1970295647, ss2023504210, ss2151666209, ss2634391373, ss2707251348, ss2835145910, ss2998420467, ss3346807258, ss3629429599, ss3632311974, ss3636755814, ss3642469432, ss3666344296, ss3733150103, ss3764538878, ss3829699694, ss3863795030, ss3910529230, ss3985195272, ss5175898836, ss5315116855, ss5363437165, ss5639648877, ss5841711491, ss5968142119	NC_000006.11:3622750:T:C	NC_000006.12:3622516:T:C	(self)
40050017, 215464082, 3046968, 14764423, 47327605, 529120306, 15847929518, ss2281314320, ss3025535467, ss3648254809, ss3716465570, ss3807699995, ss3958386422, ss4691742748, ss5267194814, ss5465007652, ss5552524082, ss5713490501, ss5807099895, ss5855176288, ss5882417573	NC_000006.12:3622516:T:C	NC_000006.12:3622516:T:C	(self)
ss46561167, ss68962795, ss83295727, ss98468581, ss156459646, ss160629284	NT_007592.15:3562750:T:C	NC_000006.12:3622516:T:C	(self)
ss66036215	NT_007592.16:3562516:T:C	NC_000006.12:3622516: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 rs35877559

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs35877559