Name: rs2977612
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.

rs2977612

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:845405 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.313537 (82990/264690, TOPMED)
T=0.303898 (42550/140014, GnomAD)
T=0.38623 (10914/28258, 14KJPN) (+ 15 more)
T=0.23568 (4452/18890, ALFA)
T=0.38311 (6421/16760, 8.3KJPN)
T=0.3404 (2180/6404, 1000G_30x)
T=0.3307 (1656/5008, 1000G)
T=0.1269 (489/3854, ALSPAC)
T=0.1308 (485/3708, TWINSUK)
T=0.3229 (946/2930, KOREAN)
T=0.145 (145/998, GoNL)
T=0.135 (81/600, NorthernSweden)
T=0.212 (97/458, SGDP_PRJ)
T=0.231 (50/216, Qatari)
T=0.292 (63/216, Vietnamese)
T=0.240 (46/192, HapMap)
T=0.17 (9/52, Siberian)
T=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01128 : 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	18890	T=0.23568	A=0.76432
European	Sub	14286	T=0.15379	A=0.84621
African	Sub	2946	T=0.6103	A=0.3897
African Others	Sub	114	T=0.684	A=0.316
African American	Sub	2832	T=0.6073	A=0.3927
Asian	Sub	112	T=0.250	A=0.750
East Asian	Sub	86	T=0.27	A=0.73
Other Asian	Sub	26	T=0.19	A=0.81
Latin American 1	Sub	146	T=0.377	A=0.623
Latin American 2	Sub	610	T=0.267	A=0.733
South Asian	Sub	98	T=0.13	A=0.87
Other	Sub	692	T=0.286	A=0.714

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=0.313537	A=0.686463
gnomAD - Genomes	Global	Study-wide	140014	T=0.303898	A=0.696102
gnomAD - Genomes	European	Sub	75894	T=0.15188	A=0.84812
gnomAD - Genomes	African	Sub	41888	T=0.61080	A=0.38920
gnomAD - Genomes	American	Sub	13644	T=0.25814	A=0.74186
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.1613	A=0.8387
gnomAD - Genomes	East Asian	Sub	3116	T=0.2522	A=0.7478
gnomAD - Genomes	Other	Sub	2148	T=0.2765	A=0.7235
14KJPN	JAPANESE	Study-wide	28258	T=0.38623	A=0.61377
Allele Frequency Aggregator	Total	Global	18890	T=0.23568	A=0.76432
Allele Frequency Aggregator	European	Sub	14286	T=0.15379	A=0.84621
Allele Frequency Aggregator	African	Sub	2946	T=0.6103	A=0.3897
Allele Frequency Aggregator	Other	Sub	692	T=0.286	A=0.714
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.267	A=0.733
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.377	A=0.623
Allele Frequency Aggregator	Asian	Sub	112	T=0.250	A=0.750
Allele Frequency Aggregator	South Asian	Sub	98	T=0.13	A=0.87
8.3KJPN	JAPANESE	Study-wide	16760	T=0.38311	A=0.61689
1000Genomes_30x	Global	Study-wide	6404	T=0.3404	A=0.6596
1000Genomes_30x	African	Sub	1786	T=0.6865	A=0.3135
1000Genomes_30x	Europe	Sub	1266	T=0.1240	A=0.8760
1000Genomes_30x	South Asian	Sub	1202	T=0.2055	A=0.7945
1000Genomes_30x	East Asian	Sub	1170	T=0.2624	A=0.7376
1000Genomes_30x	American	Sub	980	T=0.248	A=0.752
1000Genomes	Global	Study-wide	5008	T=0.3307	A=0.6693
1000Genomes	African	Sub	1322	T=0.6785	A=0.3215
1000Genomes	East Asian	Sub	1008	T=0.2629	A=0.7371
1000Genomes	Europe	Sub	1006	T=0.1252	A=0.8748
1000Genomes	South Asian	Sub	978	T=0.206	A=0.794
1000Genomes	American	Sub	694	T=0.241	A=0.759
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1269	A=0.8731
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1308	A=0.8692
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3229	A=0.6771, C=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.145	A=0.855
Northern Sweden	ACPOP	Study-wide	600	T=0.135	A=0.865
SGDP_PRJ	Global	Study-wide	458	T=0.212	A=0.788
Qatari	Global	Study-wide	216	T=0.231	A=0.769
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.292	A=0.708
HapMap	Global	Study-wide	192	T=0.240	A=0.760
HapMap	American	Sub	112	T=0.134	A=0.866
HapMap	Asian	Sub	80	T=0.39	A=0.61
Siberian	Global	Study-wide	52	T=0.17	A=0.83
The Danish reference pan genome	Danish	Study-wide	40	T=0.05	A=0.95

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.845405T>A
GRCh38.p14 chr 1	NC_000001.11:g.845405T>C
GRCh37.p13 chr 1	NC_000001.10:g.780785T>A
GRCh37.p13 chr 1	NC_000001.10:g.780785T>C

Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01128 transcript variant 1	NR_047519.1:n.	N/A	Intron Variant
LINC01128 transcript variant 3	NR_047521.1:n.	N/A	Intron Variant
LINC01128 transcript variant 5	NR_047523.1:n.	N/A	Intron Variant
LINC01128 transcript variant 7	NR_047524.1:n.	N/A	Intron Variant
LINC01128 transcript variant 8	NR_047525.1:n.	N/A	Intron Variant
LINC01128 transcript variant 9	NR_047526.1:n.	N/A	Genic Downstream 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=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.845405=	NC_000001.11:g.845405T>A	NC_000001.11:g.845405T>C
GRCh37.p13 chr 1	NC_000001.10:g.780785=	NC_000001.10:g.780785T>A	NC_000001.10:g.780785T>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#.

74 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss27679	Oct 08, 2002 (108)
2	SC_JCM	ss4191604	Nov 05, 2001 (101)
3	TSC-CSHL	ss5397850	Oct 08, 2002 (108)
4	SC_JCM	ss5750577	Feb 20, 2003 (111)
5	WI_SSAHASNP	ss6851628	Feb 20, 2003 (111)
6	BCM_SSAHASNP	ss9898225	Jul 11, 2003 (117)
7	CSHL-HAPMAP	ss16420027	Feb 27, 2004 (120)
8	CSHL-HAPMAP	ss19122429	Feb 27, 2004 (120)
9	HGSV	ss77759236	Dec 06, 2007 (129)
10	HGSV	ss80571137	Dec 14, 2007 (130)
11	HGSV	ss86075404	Dec 14, 2007 (130)
12	BCMHGSC_JDW	ss87155947	Mar 23, 2008 (129)
13	HUMANGENOME_JCVI	ss97913236	Feb 04, 2009 (130)
14	BGI	ss105111705	Dec 01, 2009 (131)
15	1000GENOMES	ss107938283	Jan 22, 2009 (130)
16	ILLUMINA-UK	ss118438353	Feb 14, 2009 (130)
17	ENSEMBL	ss131813594	Dec 01, 2009 (131)
18	ENSEMBL	ss137752288	Dec 01, 2009 (131)
19	GMI	ss154522396	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss165981042	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205237202	Jul 04, 2010 (132)
22	1000GENOMES	ss218190430	Jul 14, 2010 (132)
23	1000GENOMES	ss230395480	Jul 14, 2010 (132)
24	1000GENOMES	ss238114995	Jul 15, 2010 (132)
25	BL	ss252864164	May 09, 2011 (134)
26	GMI	ss275680882	May 04, 2012 (137)
27	GMI	ss283987402	Apr 25, 2013 (138)
28	PJP	ss290493809	May 09, 2011 (134)
29	TISHKOFF	ss553710527	Apr 25, 2013 (138)
30	SSMP	ss647516288	Apr 25, 2013 (138)
31	EVA-GONL	ss974769463	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1067612374	Aug 21, 2014 (142)
33	1000GENOMES	ss1289339679	Aug 21, 2014 (142)
34	DDI	ss1425684889	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1573851178	Apr 01, 2015 (144)
36	EVA_DECODE	ss1584129533	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1599378449	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1642372482	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1793705893	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1917960528	Feb 12, 2016 (147)
41	GENOMED	ss1966667339	Jul 19, 2016 (147)
42	JJLAB	ss2019498442	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2147484427	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2624264793	Nov 08, 2017 (151)
45	GRF	ss2697374724	Nov 08, 2017 (151)
46	GNOMAD	ss2750639773	Nov 08, 2017 (151)
47	SWEGEN	ss2986149200	Nov 08, 2017 (151)
48	CSHL	ss3343272620	Nov 08, 2017 (151)
49	URBANLAB	ss3646581234	Oct 11, 2018 (152)
50	EVA_DECODE	ss3685992249	Jul 12, 2019 (153)
51	ACPOP	ss3726716423	Jul 12, 2019 (153)
52	EVA	ss3745721066	Jul 12, 2019 (153)
53	PACBIO	ss3783302164	Jul 12, 2019 (153)
54	PACBIO	ss3788980029	Jul 12, 2019 (153)
55	PACBIO	ss3793852565	Jul 12, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3798743706	Jul 12, 2019 (153)
57	EVA	ss3825981482	Apr 25, 2020 (154)
58	EVA	ss3836378433	Apr 25, 2020 (154)
59	EVA	ss3841782433	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3847995703	Apr 25, 2020 (154)
61	KRGDB	ss3892836002	Apr 25, 2020 (154)
62	TOPMED	ss4436435630	Apr 25, 2021 (155)
63	TOMMO_GENOMICS	ss5142052542	Apr 25, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5240863741	Oct 12, 2022 (156)
65	EVA	ss5316183829	Oct 12, 2022 (156)
66	HUGCELL_USP	ss5442112388	Oct 12, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5512488490	Oct 12, 2022 (156)
68	SANFORD_IMAGENETICS	ss5624749504	Oct 12, 2022 (156)
69	TOMMO_GENOMICS	ss5666191940	Oct 12, 2022 (156)
70	YY_MCH	ss5800243821	Oct 12, 2022 (156)
71	EVA	ss5831418468	Oct 12, 2022 (156)
72	EVA	ss5848748887	Oct 12, 2022 (156)
73	EVA	ss5906704923	Oct 12, 2022 (156)
74	EVA	ss5936582778	Oct 12, 2022 (156)
75	1000Genomes	NC_000001.10 - 780785	Oct 11, 2018 (152)
76	1000Genomes_30x	NC_000001.11 - 845405	Oct 12, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 780785	Oct 11, 2018 (152)
78	The Danish reference pan genome	NC_000001.10 - 780785	Apr 25, 2020 (154)
79	gnomAD - Genomes	NC_000001.11 - 845405	Apr 25, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000001.10 - 780785	Apr 25, 2020 (154)
81	HapMap	NC_000001.11 - 845405	Apr 25, 2020 (154)
82	KOREAN population from KRGDB	NC_000001.10 - 780785	Apr 25, 2020 (154)
83	Northern Sweden	NC_000001.10 - 780785	Jul 12, 2019 (153)
84	Qatari	NC_000001.10 - 780785	Apr 25, 2020 (154)
85	SGDP_PRJ	NC_000001.10 - 780785	Apr 25, 2020 (154)
86	Siberian	NC_000001.10 - 780785	Apr 25, 2020 (154)
87	8.3KJPN	NC_000001.10 - 780785	Apr 25, 2021 (155)
88	14KJPN	NC_000001.11 - 845405	Oct 12, 2022 (156)
89	TopMed	NC_000001.11 - 845405	Apr 25, 2021 (155)
90	UK 10K study - Twins	NC_000001.10 - 780785	Oct 11, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000001.10 - 780785	Jul 12, 2019 (153)
92	ALFA	NC_000001.11 - 845405	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).

Associated ID	History Updated (Build)
rs6700389	Aug 27, 2003 (117)
rs57815855	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77759236, ss80571137, ss86075404	NC_000001.8:820647:T:A	NC_000001.11:845404:T:A	(self)
ss87155947, ss107938283, ss118438353, ss165981042, ss205237202, ss252864164, ss275680882, ss283987402, ss290493809, ss1584129533	NC_000001.9:770647:T:A	NC_000001.11:845404:T:A	(self)
4421, 381, 1358412, 502, 13396, 1288, 2458, 12683, 781, 21849, 381, 83, ss218190430, ss230395480, ss238114995, ss553710527, ss647516288, ss974769463, ss1067612374, ss1289339679, ss1425684889, ss1573851178, ss1599378449, ss1642372482, ss1793705893, ss1917960528, ss1966667339, ss2019498442, ss2147484427, ss2624264793, ss2697374724, ss2750639773, ss2986149200, ss3343272620, ss3726716423, ss3745721066, ss3783302164, ss3788980029, ss3793852565, ss3825981482, ss3836378433, ss3847995703, ss3892836002, ss5142052542, ss5316183829, ss5624749504, ss5831418468, ss5936582778	NC_000001.10:780784:T:A	NC_000001.11:845404:T:A	(self)
14425, 67434, 71, 29044, 41965, 7640415364, ss3646581234, ss3685992249, ss3798743706, ss3841782433, ss4436435630, ss5240863741, ss5442112388, ss5512488490, ss5666191940, ss5800243821, ss5848748887, ss5906704923	NC_000001.11:845404:T:A	NC_000001.11:845404:T:A	(self)
ss27679, ss4191604, ss5397850, ss5750577, ss6851628, ss97913236, ss105111705, ss131813594, ss137752288, ss154522396	NT_004350.19:259416:T:A	NC_000001.11:845404:T:A	(self)
ss9898225, ss16420027, ss19122429	NT_034471.3:259416:T:A	NC_000001.11:845404:T:A	(self)
13396, ss3892836002	NC_000001.10:780784:T:C	NC_000001.11:845404: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 rs2977612

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

rs2977612