Name: rs1981635
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.

rs1981635

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:10601393 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.322808 (85444/264690, TOPMED)
G=0.319555 (44753/140048, GnomAD)
G=0.26163 (7393/28258, 14KJPN) (+ 16 more)
G=0.29841 (5341/17898, ALFA)
G=0.26301 (4408/16760, 8.3KJPN)
G=0.3345 (2142/6404, 1000G_30x)
G=0.3355 (1680/5008, 1000G)
G=0.2672 (1197/4480, Estonian)
G=0.2340 (902/3854, ALSPAC)
G=0.2260 (838/3708, TWINSUK)
G=0.2611 (765/2930, KOREAN)
G=0.2822 (517/1832, Korea1K)
G=0.207 (207/998, GoNL)
G=0.212 (127/600, NorthernSweden)
G=0.249 (123/494, SGDP_PRJ)
G=0.389 (84/216, Qatari)
G=0.245 (52/212, Vietnamese)
G=0.21 (10/48, Siberian)
G=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLNK : Intron Variant
Publications: 1 citation
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	17898	G=0.29841	A=0.00000, C=0.70159
European	Sub	13672	G=0.26287	A=0.00000, C=0.73713
African	Sub	2570	G=0.4973	A=0.0000, C=0.5027
African Others	Sub	102	G=0.598	A=0.000, C=0.402
African American	Sub	2468	G=0.4931	A=0.0000, C=0.5069
Asian	Sub	112	G=0.223	A=0.000, C=0.777
East Asian	Sub	86	G=0.27	A=0.00, C=0.73
Other Asian	Sub	26	G=0.08	A=0.00, C=0.92
Latin American 1	Sub	146	G=0.363	A=0.000, C=0.637
Latin American 2	Sub	610	G=0.233	A=0.000, C=0.767
South Asian	Sub	98	G=0.31	A=0.00, C=0.69
Other	Sub	690	G=0.317	A=0.000, C=0.683

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	G=0.322808	C=0.677192
gnomAD - Genomes	Global	Study-wide	140048	G=0.319555	C=0.680445
gnomAD - Genomes	European	Sub	75878	G=0.24666	C=0.75334
gnomAD - Genomes	African	Sub	41918	G=0.47860	C=0.52140
gnomAD - Genomes	American	Sub	13650	G=0.25429	C=0.74571
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.3443	C=0.6557
gnomAD - Genomes	East Asian	Sub	3130	G=0.2227	C=0.7773
gnomAD - Genomes	Other	Sub	2152	G=0.3086	C=0.6914
14KJPN	JAPANESE	Study-wide	28258	G=0.26163	C=0.73837
Allele Frequency Aggregator	Total	Global	17898	G=0.29841	A=0.00000, C=0.70159
Allele Frequency Aggregator	European	Sub	13672	G=0.26287	A=0.00000, C=0.73713
Allele Frequency Aggregator	African	Sub	2570	G=0.4973	A=0.0000, C=0.5027
Allele Frequency Aggregator	Other	Sub	690	G=0.317	A=0.000, C=0.683
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.233	A=0.000, C=0.767
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.363	A=0.000, C=0.637
Allele Frequency Aggregator	Asian	Sub	112	G=0.223	A=0.000, C=0.777
Allele Frequency Aggregator	South Asian	Sub	98	G=0.31	A=0.00, C=0.69
8.3KJPN	JAPANESE	Study-wide	16760	G=0.26301	C=0.73699
1000Genomes_30x	Global	Study-wide	6404	G=0.3345	C=0.6655
1000Genomes_30x	African	Sub	1786	G=0.5302	C=0.4698
1000Genomes_30x	Europe	Sub	1266	G=0.2472	C=0.7528
1000Genomes_30x	South Asian	Sub	1202	G=0.2770	C=0.7230
1000Genomes_30x	East Asian	Sub	1170	G=0.2607	C=0.7393
1000Genomes_30x	American	Sub	980	G=0.249	C=0.751
1000Genomes	Global	Study-wide	5008	G=0.3355	C=0.6645
1000Genomes	African	Sub	1322	G=0.5393	C=0.4607
1000Genomes	East Asian	Sub	1008	G=0.2470	C=0.7530
1000Genomes	Europe	Sub	1006	G=0.2555	C=0.7445
1000Genomes	South Asian	Sub	978	G=0.285	C=0.715
1000Genomes	American	Sub	694	G=0.262	C=0.738
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.2672	C=0.7328
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.2340	C=0.7660
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.2260	C=0.7740
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2611	C=0.7389
Korean Genome Project	KOREAN	Study-wide	1832	G=0.2822	C=0.7178
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.207	C=0.793
Northern Sweden	ACPOP	Study-wide	600	G=0.212	C=0.788
SGDP_PRJ	Global	Study-wide	494	G=0.249	C=0.751
Qatari	Global	Study-wide	216	G=0.389	C=0.611
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.245	C=0.755
Siberian	Global	Study-wide	48	G=0.21	C=0.79
The Danish reference pan genome	Danish	Study-wide	40	G=0.20	C=0.80

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 4	NC_000004.12:g.10601393G>A
GRCh38.p14 chr 4	NC_000004.12:g.10601393G>C
GRCh37.p13 chr 4	NC_000004.11:g.10603017G>A
GRCh37.p13 chr 4	NC_000004.11:g.10603017G>C

Gene: CLNK, cytokine dependent hematopoietic cell linker (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLNK transcript	NM_052964.4:c.12-3344C>T	N/A	Intron Variant
CLNK transcript variant X1	XM_011513775.3:c.57-3344C… XM_011513775.3:c.57-3344C>T	N/A	Intron Variant
CLNK transcript variant X2	XM_017007684.2:c.57-3344C… XM_017007684.2:c.57-3344C>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	G=	A	C
GRCh38.p14 chr 4	NC_000004.12:g.10601393=	NC_000004.12:g.10601393G>A	NC_000004.12:g.10601393G>C
GRCh37.p13 chr 4	NC_000004.11:g.10603017=	NC_000004.11:g.10603017G>A	NC_000004.11:g.10603017G>C
CLNK transcript	NM_052964.2:c.12-3344=	NM_052964.2:c.12-3344C>T	NM_052964.2:c.12-3344C>G
CLNK transcript	NM_052964.4:c.12-3344=	NM_052964.4:c.12-3344C>T	NM_052964.4:c.12-3344C>G
CLNK transcript variant X1	XM_011513775.3:c.57-3344=	XM_011513775.3:c.57-3344C>T	XM_011513775.3:c.57-3344C>G
CLNK transcript variant X2	XM_017007684.2:c.57-3344=	XM_017007684.2:c.57-3344C>T	XM_017007684.2:c.57-3344C>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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2886901	Jan 12, 2001 (92)
2	SC_JCM	ss3548426	Sep 28, 2001 (100)
3	WI_SSAHASNP	ss6470865	Feb 20, 2003 (111)
4	PERLEGEN	ss23709382	Sep 20, 2004 (123)
5	BCMHGSC_JDW	ss92469331	Mar 23, 2008 (129)
6	HUMANGENOME_JCVI	ss98801677	Feb 04, 2009 (130)
7	BGI	ss105805094	Feb 04, 2009 (130)
8	1000GENOMES	ss111781698	Jan 25, 2009 (130)
9	1000GENOMES	ss112914325	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss116870290	Feb 14, 2009 (130)
11	ILLUMINA	ss120240072	Dec 01, 2009 (131)
12	ENSEMBL	ss139442326	Dec 01, 2009 (131)
13	ENSEMBL	ss139731913	Dec 01, 2009 (131)
14	GMI	ss156859917	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss161916859	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss163088278	Jul 04, 2010 (132)
17	BUSHMAN	ss198038977	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss206291027	Jul 04, 2010 (132)
19	1000GENOMES	ss220740680	Jul 14, 2010 (132)
20	1000GENOMES	ss232257956	Jul 14, 2010 (132)
21	1000GENOMES	ss239580269	Jul 15, 2010 (132)
22	GMI	ss277574626	May 04, 2012 (137)
23	GMI	ss284845780	Apr 25, 2013 (138)
24	PJP	ss293208621	May 09, 2011 (134)
25	TISHKOFF	ss557310454	Apr 25, 2013 (138)
26	SSMP	ss651072940	Apr 25, 2013 (138)
27	EVA-GONL	ss979763666	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1071273979	Aug 21, 2014 (142)
29	1000GENOMES	ss1308430885	Aug 21, 2014 (142)
30	DDI	ss1429773071	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1580413750	Apr 01, 2015 (144)
32	EVA_DECODE	ss1589251695	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1609403354	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1652397387	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1801015262	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1923003647	Feb 12, 2016 (147)
37	GENOMED	ss1969657688	Sep 14, 2016 (149)
38	JJLAB	ss2022072354	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2150183743	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2260393947	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2625538576	Nov 08, 2017 (151)
42	GRF	ss2705627027	Nov 08, 2017 (151)
43	GNOMAD	ss2805627047	Nov 08, 2017 (151)
44	SWEGEN	ss2994141027	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3024805131	Nov 08, 2017 (151)
46	CSHL	ss3345544111	Nov 08, 2017 (151)
47	URBANLAB	ss3647651320	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3662045751	Jul 13, 2019 (153)
49	EVA_DECODE	ss3711406127	Jul 13, 2019 (153)
50	ACPOP	ss3730854381	Jul 13, 2019 (153)
51	EVA	ss3761398111	Jul 13, 2019 (153)
52	PACBIO	ss3784619063	Jul 13, 2019 (153)
53	PACBIO	ss3790089640	Jul 13, 2019 (153)
54	PACBIO	ss3794964613	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3804532572	Jul 13, 2019 (153)
56	EVA	ss3828370151	Apr 26, 2020 (154)
57	EVA	ss3837617756	Apr 26, 2020 (154)
58	EVA	ss3843051721	Apr 26, 2020 (154)
59	SGDP_PRJ	ss3858222191	Apr 26, 2020 (154)
60	KRGDB	ss3904365396	Apr 26, 2020 (154)
61	KOGIC	ss3953533192	Apr 26, 2020 (154)
62	TOPMED	ss4602813333	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5164204390	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5258044291	Oct 13, 2022 (156)
65	HUGCELL_USP	ss5456947461	Oct 13, 2022 (156)
66	EVA	ss5507386938	Oct 13, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5538480885	Oct 13, 2022 (156)
68	SANFORD_IMAGENETICS	ss5634350557	Oct 13, 2022 (156)
69	TOMMO_GENOMICS	ss5697855289	Oct 13, 2022 (156)
70	YY_MCH	ss5804759271	Oct 13, 2022 (156)
71	EVA	ss5843552222	Oct 13, 2022 (156)
72	EVA	ss5854079966	Oct 13, 2022 (156)
73	EVA	ss5862145522	Oct 13, 2022 (156)
74	EVA	ss5962724225	Oct 13, 2022 (156)
75	1000Genomes	NC_000004.11 - 10603017	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000004.12 - 10601393	Oct 13, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 10603017	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000004.11 - 10603017	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000004.11 - 10603017	Apr 26, 2020 (154)
80	gnomAD - Genomes	NC_000004.12 - 10601393	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000004.11 - 10603017	Apr 26, 2020 (154)
82	KOREAN population from KRGDB	NC_000004.11 - 10603017	Apr 26, 2020 (154)
83	Korean Genome Project	NC_000004.12 - 10601393	Apr 26, 2020 (154)
84	Northern Sweden	NC_000004.11 - 10603017	Jul 13, 2019 (153)
85	Qatari	NC_000004.11 - 10603017	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000004.11 - 10603017	Apr 26, 2020 (154)
87	Siberian	NC_000004.11 - 10603017	Apr 26, 2020 (154)
88	8.3KJPN	NC_000004.11 - 10603017	Apr 26, 2021 (155)
89	14KJPN	NC_000004.12 - 10601393	Oct 13, 2022 (156)
90	TopMed	NC_000004.12 - 10601393	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000004.11 - 10603017	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000004.11 - 10603017	Jul 13, 2019 (153)
93	ALFA	NC_000004.12 - 10601393	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
2449823199	NC_000004.12:10601392:G:A	NC_000004.12:10601392:G:A	(self)
ss92469331, ss111781698, ss112914325, ss116870290, ss161916859, ss163088278, ss198038977, ss206291027, ss277574626, ss284845780, ss293208621, ss1589251695	NC_000004.10:10212114:G:C	NC_000004.12:10601392:G:C	(self)
19778683, 11010229, 7783999, 6578689, 4844548, 11542790, 4139246, 5045577, 10239171, 2700097, 22173697, 11010229, 2406376, ss220740680, ss232257956, ss239580269, ss557310454, ss651072940, ss979763666, ss1071273979, ss1308430885, ss1429773071, ss1580413750, ss1609403354, ss1652397387, ss1801015262, ss1923003647, ss1969657688, ss2022072354, ss2150183743, ss2625538576, ss2705627027, ss2805627047, ss2994141027, ss3345544111, ss3662045751, ss3730854381, ss3761398111, ss3784619063, ss3790089640, ss3794964613, ss3828370151, ss3837617756, ss3858222191, ss3904365396, ss5164204390, ss5507386938, ss5634350557, ss5843552222, ss5962724225	NC_000004.11:10603016:G:C	NC_000004.12:10601392:G:C	(self)
26006820, 140213913, 9911193, 31692393, 440190889, 2449823199, ss2260393947, ss3024805131, ss3647651320, ss3711406127, ss3804532572, ss3843051721, ss3953533192, ss4602813333, ss5258044291, ss5456947461, ss5538480885, ss5697855289, ss5804759271, ss5854079966, ss5862145522	NC_000004.12:10601392:G:C	NC_000004.12:10601392:G:C	(self)
ss2886901, ss3548426, ss6470865, ss23709382, ss98801677, ss105805094, ss120240072, ss139442326, ss139731913, ss156859917	NT_006316.16:1784813:G:C	NC_000004.12:10601392:G:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1981635

PMID	Title	Author	Year	Journal
21691774	Genomewide linkage analysis in Costa Rican families implicates chromosome 15q14 as a candidate region for OCD.	Ross J et al.	2011	Human genetics

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

rs1981635