Name: rs56100013
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.

rs56100013

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:45691101 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.148510 (39309/264690, TOPMED)
T=0.145087 (20329/140116, GnomAD)
T=0.18286 (4791/26200, ALFA) (+ 13 more)
T=0.0853 (546/6404, 1000G_30x)
T=0.0861 (431/5008, 1000G)
T=0.1150 (515/4480, Estonian)
T=0.2418 (932/3854, ALSPAC)
T=0.2346 (870/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.195 (195/998, GoNL)
T=0.118 (71/600, NorthernSweden)
T=0.185 (40/216, Qatari)
C=0.46 (37/80, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02210-CRHR1 : 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	26200	C=0.81714	T=0.18286
European	Sub	21486	C=0.79461	T=0.20539
African	Sub	2946	C=0.9552	T=0.0448
African Others	Sub	114	C=0.991	T=0.009
African American	Sub	2832	C=0.9537	T=0.0463
Asian	Sub	156	C=1.000	T=0.000
East Asian	Sub	130	C=1.000	T=0.000
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.808	T=0.192
Latin American 2	Sub	610	C=0.862	T=0.138
South Asian	Sub	98	C=0.92	T=0.08
Other	Sub	758	C=0.834	T=0.166

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=0.851490	T=0.148510
gnomAD - Genomes	Global	Study-wide	140116	C=0.854913	T=0.145087
gnomAD - Genomes	European	Sub	75864	C=0.80394	T=0.19606
gnomAD - Genomes	African	Sub	41998	C=0.95540	T=0.04460
gnomAD - Genomes	American	Sub	13648	C=0.82283	T=0.17717
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.7599	T=0.2401
gnomAD - Genomes	East Asian	Sub	3132	C=0.9990	T=0.0010
gnomAD - Genomes	Other	Sub	2150	C=0.8312	T=0.1688
Allele Frequency Aggregator	Total	Global	26200	C=0.81714	T=0.18286
Allele Frequency Aggregator	European	Sub	21486	C=0.79461	T=0.20539
Allele Frequency Aggregator	African	Sub	2946	C=0.9552	T=0.0448
Allele Frequency Aggregator	Other	Sub	758	C=0.834	T=0.166
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.862	T=0.138
Allele Frequency Aggregator	Asian	Sub	156	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.808	T=0.192
Allele Frequency Aggregator	South Asian	Sub	98	C=0.92	T=0.08
1000Genomes_30x	Global	Study-wide	6404	C=0.9147	T=0.0853
1000Genomes_30x	African	Sub	1786	C=0.9854	T=0.0146
1000Genomes_30x	Europe	Sub	1266	C=0.7638	T=0.2362
1000Genomes_30x	South Asian	Sub	1202	C=0.9376	T=0.0624
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=0.852	T=0.148
1000Genomes	Global	Study-wide	5008	C=0.9139	T=0.0861
1000Genomes	African	Sub	1322	C=0.9849	T=0.0151
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=0.7604	T=0.2396
1000Genomes	South Asian	Sub	978	C=0.939	T=0.061
1000Genomes	American	Sub	694	C=0.843	T=0.157
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8850	T=0.1150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7582	T=0.2418
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7654	T=0.2346
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9997	T=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.805	T=0.195
Northern Sweden	ACPOP	Study-wide	600	C=0.882	T=0.118
Qatari	Global	Study-wide	216	C=0.815	T=0.185
SGDP_PRJ	Global	Study-wide	80	C=0.46	T=0.54
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	4	C=0.5	T=0.5

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 17	NC_000017.11:g.45691101C>G
GRCh38.p14 chr 17	NC_000017.11:g.45691101C>T
GRCh37.p13 chr 17	NC_000017.10:g.43768467C>G
GRCh37.p13 chr 17	NC_000017.10:g.43768467C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.1096860A>G
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.1096860A>C
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.1098853A>G
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.1098853A>C
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.393245C>G
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.393245C>T
GRCh37.p13 chr 17 fix patch HG1146_PATCH	NW_003871086.1:g.12996A>G
GRCh37.p13 chr 17 fix patch HG1146_PATCH	NW_003871086.1:g.12996A>C

Gene: LINC02210-CRHR1, LINC02210-CRHR1 readthrough (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02210-CRHR1 transcript variant 5	NM_001256299.3:c.-493+609… NM_001256299.3:c.-493+60943C>G	N/A	Intron Variant
LINC02210-CRHR1 transcript variant 6	NM_001303016.1:c.-185+181… NM_001303016.1:c.-185+18199C>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	C=	G	T
GRCh38.p14 chr 17	NC_000017.11:g.45691101=	NC_000017.11:g.45691101C>G	NC_000017.11:g.45691101C>T
GRCh37.p13 chr 17	NC_000017.10:g.43768467=	NC_000017.10:g.43768467C>G	NC_000017.10:g.43768467C>T
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.1096860A>G	NT_167251.2:g.1096860A>C	NT_167251.2:g.1096860=
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.1098853A>G	NT_167251.1:g.1098853A>C	NT_167251.1:g.1098853=
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.393245=	NT_187663.1:g.393245C>G	NT_187663.1:g.393245C>T
GRCh37.p13 chr 17 fix patch HG1146_PATCH	NW_003871086.1:g.12996A>G	NW_003871086.1:g.12996A>C	NW_003871086.1:g.12996=
CRHR1 transcript variant 5	NM_001256299.1:c.-493+60943=	NM_001256299.1:c.-493+60943C>G	NM_001256299.1:c.-493+60943C>T
LINC02210-CRHR1 transcript variant 5	NM_001256299.3:c.-493+60943=	NM_001256299.3:c.-493+60943C>G	NM_001256299.3:c.-493+60943C>T
LINC02210-CRHR1 transcript variant 6	NM_001303016.1:c.-185+18199=	NM_001303016.1:c.-185+18199C>G	NM_001303016.1:c.-185+18199C>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#.

47 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77244315	Dec 07, 2007 (129)
2	COMPLETE_GENOMICS	ss168198946	Jul 04, 2010 (137)
3	COMPLETE_GENOMICS	ss171434395	Jul 04, 2010 (137)
4	BUSHMAN	ss202540861	Jul 04, 2010 (137)
5	BCM-HGSC-SUB	ss207806038	Jul 04, 2010 (137)
6	1000GENOMES	ss237249622	Jul 15, 2010 (137)
7	SSMP	ss661088308	Apr 25, 2013 (138)
8	EVA-GONL	ss993128150	Aug 21, 2014 (142)
9	1000GENOMES	ss1358739869	Aug 21, 2014 (142)
10	EVA_GENOME_DK	ss1578164578	Apr 01, 2015 (144)
11	EVA_UK10K_ALSPAC	ss1635692545	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1678686578	Apr 01, 2015 (144)
13	EVA_DECODE	ss1697171463	Apr 01, 2015 (144)
14	HAMMER_LAB	ss1808791533	Sep 08, 2015 (146)
15	WEILL_CORNELL_DGM	ss1936589422	Feb 12, 2016 (147)
16	JJLAB	ss2029070606	Sep 14, 2016 (149)
17	USC_VALOUEV	ss2157543479	Dec 20, 2016 (150)
18	HUMAN_LONGEVITY	ss2217007517	Dec 20, 2016 (150)
19	ILLUMINA	ss2710849748	Nov 08, 2017 (151)
20	SWEGEN	ss3015571401	Nov 08, 2017 (151)
21	BIOINF_KMB_FNS_UNIBA	ss3028355776	Nov 08, 2017 (151)
22	EGCUT_WGS	ss3682453574	Jul 13, 2019 (153)
23	EVA_DECODE	ss3700509120	Jul 13, 2019 (153)
24	ACPOP	ss3742043132	Jul 13, 2019 (153)
25	EVA	ss3754691439	Jul 13, 2019 (153)
26	PACBIO	ss3788210597	Jul 13, 2019 (153)
27	PACBIO	ss3793166575	Jul 13, 2019 (153)
28	PACBIO	ss3798052435	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3819960161	Jul 13, 2019 (153)
30	EVA	ss3834877583	Apr 27, 2020 (154)
31	EVA	ss3841048657	Apr 27, 2020 (154)
32	EVA	ss3846545678	Apr 27, 2020 (154)
33	SGDP_PRJ	ss3885793985	Apr 27, 2020 (154)
34	KRGDB	ss3935492698	Apr 27, 2020 (154)
35	TOPMED	ss5036741087	Apr 27, 2021 (155)
36	TOMMO_GENOMICS	ss5222523195	Apr 27, 2021 (155)
37	TOMMO_GENOMICS	ss5222523196	Apr 27, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5303211095	Oct 16, 2022 (156)
39	EVA	ss5427732901	Oct 16, 2022 (156)
40	HUGCELL_USP	ss5496255667	Oct 16, 2022 (156)
41	EVA	ss5511771972	Oct 16, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5606967571	Oct 16, 2022 (156)
43	SANFORD_IMAGENETICS	ss5660145619	Oct 16, 2022 (156)
44	TOMMO_GENOMICS	ss5778770045	Oct 16, 2022 (156)
45	TOMMO_GENOMICS	ss5778770046	Oct 16, 2022 (156)
46	EVA	ss5834013224	Oct 16, 2022 (156)
47	EVA	ss5951536762	Oct 16, 2022 (156)
48	1000Genomes	NC_000017.10 - 43768467	Oct 12, 2018 (152)
49	1000Genomes_30x	NC_000017.11 - 45691101	Oct 16, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 43768467	Oct 12, 2018 (152)
51	Genetic variation in the Estonian population	NC_000017.10 - 43768467	Oct 12, 2018 (152)
52	The Danish reference pan genome	NC_000017.10 - 43768467	Apr 27, 2020 (154)
53	gnomAD - Genomes	NC_000017.11 - 45691101	Apr 27, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000017.10 - 43768467	Apr 27, 2020 (154)
55	KOREAN population from KRGDB	NC_000017.10 - 43768467	Apr 27, 2020 (154)
56	Northern Sweden	NC_000017.10 - 43768467	Jul 13, 2019 (153)
57	Qatari	NC_000017.10 - 43768467	Apr 27, 2020 (154)
58	SGDP_PRJ	NC_000017.10 - 43768467	Apr 27, 2020 (154)
59	Siberian	NC_000017.10 - 43768467	Apr 27, 2020 (154)
60	8.3KJPN Submission ignored due to conflicting rows: Row 80492502 (NC_000017.10:43768466:C:T 6/16760) Row 80492503 (NC_000017.10:43768466:C:G 1/16760)	-	Apr 27, 2021 (155)
61	8.3KJPN Submission ignored due to conflicting rows: Row 80492502 (NC_000017.10:43768466:C:T 6/16760) Row 80492503 (NC_000017.10:43768466:C:G 1/16760)	-	Apr 27, 2021 (155)
62	14KJPN Submission ignored due to conflicting rows: Row 112607149 (NC_000017.11:45691100:C:T 13/28258) Row 112607150 (NC_000017.11:45691100:C:G 1/28258)	-	Oct 16, 2022 (156)
63	14KJPN Submission ignored due to conflicting rows: Row 112607149 (NC_000017.11:45691100:C:T 13/28258) Row 112607150 (NC_000017.11:45691100:C:G 1/28258)	-	Oct 16, 2022 (156)
64	TopMed	NC_000017.11 - 45691101	Apr 27, 2021 (155)
65	UK 10K study - Twins	NC_000017.10 - 43768467	Oct 12, 2018 (152)
66	ALFA	NC_000017.11 - 45691101	Apr 27, 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)
rs112658075	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss5222523196	NC_000017.10:43768466:C:G	NC_000017.11:45691100:C:G	(self)
ss5778770046	NC_000017.11:45691100:C:G	NC_000017.11:45691100:C:G
ss77244315, ss168198946, ss171434395, ss202540861, ss207806038, ss1697171463	NC_000017.9:41124249:C:T	NC_000017.11:45691100:C:T	(self)
71984812, 39892939, 28191822, 4366670, 17778869, 42670092, 15327997, 18631344, 37810965, 10059833, 39892939, ss237249622, ss661088308, ss993128150, ss1358739869, ss1578164578, ss1635692545, ss1678686578, ss1808791533, ss1936589422, ss2029070606, ss2157543479, ss2710849748, ss3015571401, ss3682453574, ss3742043132, ss3754691439, ss3788210597, ss3793166575, ss3798052435, ss3834877583, ss3841048657, ss3885793985, ss3935492698, ss5222523195, ss5427732901, ss5511771972, ss5660145619, ss5834013224, ss5951536762	NC_000017.10:43768466:C:T	NC_000017.11:45691100:C:T	(self)
94493506, 507898778, 252286749, 6390702550, ss2217007517, ss3028355776, ss3700509120, ss3819960161, ss3846545678, ss5036741087, ss5303211095, ss5496255667, ss5606967571, ss5778770045	NC_000017.11:45691100:C:T	NC_000017.11:45691100: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 rs56100013

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

rs56100013