Name: rs12027485
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.

rs12027485

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:30860343 (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: C=0.08730 (2467/28258, 14KJPN)
C=0.00437 (82/18754, ALFA)
C=0.08723 (1462/16760, 8.3KJPN) (+ 15 more)
C=0.0276 (177/6404, 1000G_30x)
C=0.0292 (146/5008, 1000G)
C=0.0170 (76/4480, Estonian)
C=0.0171 (66/3854, ALSPAC)
C=0.0205 (76/3708, TWINSUK)
C=0.0835 (244/2922, KOREAN)
C=0.0895 (164/1832, Korea1K)
C=0.024 (24/998, GoNL)
C=0.012 (7/600, NorthernSweden)
C=0.032 (7/216, Qatari)
C=0.104 (22/212, Vietnamese)
T=0.44 (29/66, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC400748 : 500B Downstream 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	18754	T=0.99563	A=0.00000, C=0.00437
European	Sub	13946	T=0.99462	A=0.00000, C=0.00538
African	Sub	2944	T=1.0000	A=0.0000, C=0.0000
African Others	Sub	114	T=1.000	A=0.000, C=0.000
African American	Sub	2830	T=1.0000	A=0.0000, C=0.0000
Asian	Sub	96	T=1.00	A=0.00, C=0.00
East Asian	Sub	76	T=1.00	A=0.00, C=0.00
Other Asian	Sub	20	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	144	T=0.993	A=0.000, C=0.007
Latin American 2	Sub	598	T=1.000	A=0.000, C=0.000
South Asian	Sub	92	T=1.00	A=0.00, C=0.00
Other	Sub	934	T=0.994	A=0.000, C=0.006

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
14KJPN	JAPANESE	Study-wide	28258	T=0.91270	C=0.08730
Allele Frequency Aggregator	Total	Global	18754	T=0.99563	A=0.00000, C=0.00437
Allele Frequency Aggregator	European	Sub	13946	T=0.99462	A=0.00000, C=0.00538
Allele Frequency Aggregator	African	Sub	2944	T=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	Other	Sub	934	T=0.994	A=0.000, C=0.006
Allele Frequency Aggregator	Latin American 2	Sub	598	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	144	T=0.993	A=0.000, C=0.007
Allele Frequency Aggregator	Asian	Sub	96	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	92	T=1.00	A=0.00, C=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.91277	C=0.08723
1000Genomes_30x	Global	Study-wide	6404	T=0.9724	C=0.0276
1000Genomes_30x	African	Sub	1786	T=0.9983	C=0.0017
1000Genomes_30x	Europe	Sub	1266	T=0.9882	C=0.0118
1000Genomes_30x	South Asian	Sub	1202	T=0.9451	C=0.0549
1000Genomes_30x	East Asian	Sub	1170	T=0.9342	C=0.0658
1000Genomes_30x	American	Sub	980	T=0.984	C=0.016
1000Genomes	Global	Study-wide	5008	T=0.9708	C=0.0292
1000Genomes	African	Sub	1322	T=0.9977	C=0.0023
1000Genomes	East Asian	Sub	1008	T=0.9355	C=0.0645
1000Genomes	Europe	Sub	1006	T=0.9881	C=0.0119
1000Genomes	South Asian	Sub	978	T=0.945	C=0.055
1000Genomes	American	Sub	694	T=0.983	C=0.017
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9830	C=0.0170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9829	C=0.0171
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9795	C=0.0205
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9165	C=0.0835
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9105	C=0.0895
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.976	C=0.024
Northern Sweden	ACPOP	Study-wide	600	T=0.988	C=0.012
Qatari	Global	Study-wide	216	T=0.968	C=0.032
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.896	C=0.104
SGDP_PRJ	Global	Study-wide	66	T=0.44	C=0.56
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
Siberian	Global	Study-wide	2	T=0.5	C=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 1	NC_000001.11:g.30860343T>A
GRCh38.p14 chr 1	NC_000001.11:g.30860343T>C
GRCh37.p13 chr 1	NC_000001.10:g.31333190T>A
GRCh37.p13 chr 1	NC_000001.10:g.31333190T>C

Gene: LOC400748, uncharacterized LOC400748 (plus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC400748 transcript	XR_947140.3:n.	N/A	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.30860343=	NC_000001.11:g.30860343T>A	NC_000001.11:g.30860343T>C
GRCh37.p13 chr 1	NC_000001.10:g.31333190=	NC_000001.10:g.31333190T>A	NC_000001.10:g.31333190T>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#.

46 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18081024	Feb 28, 2004 (120)
2	PERLEGEN	ss24150721	Sep 20, 2004 (123)
3	1000GENOMES	ss230479975	Jul 14, 2010 (132)
4	1000GENOMES	ss238184005	Jul 15, 2010 (132)
5	GMI	ss275770934	May 04, 2012 (137)
6	ILLUMINA	ss533870656	Sep 08, 2015 (146)
7	TISHKOFF	ss553946449	Apr 25, 2013 (138)
8	SSMP	ss647694268	Apr 25, 2013 (138)
9	EVA-GONL	ss974998719	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1067770561	Aug 21, 2014 (142)
11	1000GENOMES	ss1290242910	Aug 21, 2014 (142)
12	EVA_GENOME_DK	ss1573969816	Apr 01, 2015 (144)
13	EVA_DECODE	ss1584358332	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1599834459	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1642828492	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1918211002	Feb 12, 2016 (147)
17	JJLAB	ss2019617046	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2147625676	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2161151423	Dec 20, 2016 (150)
20	GRF	ss2697531863	Nov 08, 2017 (151)
21	GNOMAD	ss2753274468	Nov 08, 2017 (151)
22	SWEGEN	ss2986552670	Nov 08, 2017 (151)
23	CSHL	ss3343388870	Nov 08, 2017 (151)
24	ILLUMINA	ss3626060669	Oct 11, 2018 (152)
25	EGCUT_WGS	ss3654615895	Jul 12, 2019 (153)
26	EVA_DECODE	ss3686451165	Jul 12, 2019 (153)
27	ACPOP	ss3726911790	Jul 12, 2019 (153)
28	EVA	ss3746003161	Jul 12, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3799021324	Jul 12, 2019 (153)
30	SGDP_PRJ	ss3848518041	Apr 25, 2020 (154)
31	KRGDB	ss3893456815	Apr 25, 2020 (154)
32	KOGIC	ss3944155693	Apr 25, 2020 (154)
33	TOPMED	ss4443950584	Apr 25, 2021 (155)
34	TOPMED	ss4443950585	Apr 25, 2021 (155)
35	TOMMO_GENOMICS	ss5143181762	Apr 25, 2021 (155)
36	1000G_HIGH_COVERAGE	ss5241697174	Oct 13, 2022 (156)
37	EVA	ss5317678497	Oct 13, 2022 (156)
38	HUGCELL_USP	ss5442824814	Oct 13, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5513693227	Oct 13, 2022 (156)
40	SANFORD_IMAGENETICS	ss5625214401	Oct 13, 2022 (156)
41	TOMMO_GENOMICS	ss5667706517	Oct 13, 2022 (156)
42	YY_MCH	ss5800456205	Oct 13, 2022 (156)
43	EVA	ss5831741811	Oct 13, 2022 (156)
44	EVA	ss5848842752	Oct 13, 2022 (156)
45	EVA	ss5907605446	Oct 13, 2022 (156)
46	EVA	ss5937031657	Oct 13, 2022 (156)
47	1000Genomes	NC_000001.10 - 31333190	Oct 11, 2018 (152)
48	1000Genomes_30x	NC_000001.11 - 30860343	Oct 13, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 31333190	Oct 11, 2018 (152)
50	Genetic variation in the Estonian population	NC_000001.10 - 31333190	Oct 11, 2018 (152)
51	The Danish reference pan genome	NC_000001.10 - 31333190	Apr 25, 2020 (154)
52	gnomAD - Genomes Submission ignored due to conflicting rows: Row 6590597 (NC_000001.11:30860342:T:A 2/140286) Row 6590598 (NC_000001.11:30860342:T:C 2046/140284)	-	Apr 25, 2021 (155)
53	gnomAD - Genomes Submission ignored due to conflicting rows: Row 6590597 (NC_000001.11:30860342:T:A 2/140286) Row 6590598 (NC_000001.11:30860342:T:C 2046/140284)	-	Apr 25, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000001.10 - 31333190	Apr 25, 2020 (154)
55	KOREAN population from KRGDB	NC_000001.10 - 31333190	Apr 25, 2020 (154)
56	Korean Genome Project	NC_000001.11 - 30860343	Apr 25, 2020 (154)
57	Northern Sweden	NC_000001.10 - 31333190	Jul 12, 2019 (153)
58	Qatari	NC_000001.10 - 31333190	Apr 25, 2020 (154)
59	SGDP_PRJ	NC_000001.10 - 31333190	Apr 25, 2020 (154)
60	Siberian	NC_000001.10 - 31333190	Apr 25, 2020 (154)
61	8.3KJPN	NC_000001.10 - 31333190	Apr 25, 2021 (155)
62	14KJPN	NC_000001.11 - 30860343	Oct 13, 2022 (156)
63	TopMed Submission ignored due to conflicting rows: Row 7556919 (NC_000001.11:30860342:T:A 5/264690) Row 7556920 (NC_000001.11:30860342:T:C 4502/264690)	-	Apr 25, 2021 (155)
64	TopMed Submission ignored due to conflicting rows: Row 7556919 (NC_000001.11:30860342:T:A 5/264690) Row 7556920 (NC_000001.11:30860342:T:C 4502/264690)	-	Apr 25, 2021 (155)
65	UK 10K study - Twins	NC_000001.10 - 31333190	Oct 11, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000001.10 - 31333190	Jul 12, 2019 (153)
67	ALFA	NC_000001.11 - 30860343	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
8306439319, ss4443950584	NC_000001.11:30860342:T:A	NC_000001.11:30860342:T:A	(self)
ss275770934, ss1584358332	NC_000001.9:31105776:T:C	NC_000001.11:30860342:T:C	(self)
938167, 502405, 354143, 1444364, 216200, 634209, 196655, 252932, 535021, 142030, 1151069, 502405, 103851, ss230479975, ss238184005, ss533870656, ss553946449, ss647694268, ss974998719, ss1067770561, ss1290242910, ss1573969816, ss1599834459, ss1642828492, ss1918211002, ss2019617046, ss2147625676, ss2697531863, ss2753274468, ss2986552670, ss3343388870, ss3626060669, ss3654615895, ss3726911790, ss3746003161, ss3848518041, ss3893456815, ss5143181762, ss5317678497, ss5625214401, ss5831741811, ss5937031657	NC_000001.10:31333189:T:C	NC_000001.11:30860342:T:C	(self)
1219162, 533694, 1543621, 8306439319, ss2161151423, ss3686451165, ss3799021324, ss3944155693, ss4443950585, ss5241697174, ss5442824814, ss5513693227, ss5667706517, ss5800456205, ss5848842752, ss5907605446	NC_000001.11:30860342:T:C	NC_000001.11:30860342:T:C	(self)
ss18081024	NT_004511.16:1271590:T:C	NC_000001.11:30860342:T:C	(self)
ss24150721	NT_032977.9:1305107:T:C	NC_000001.11:30860342:T:C	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss2323349752	NC_000001.10:31333189:T:A	NC_000001.11:30860342:T:A

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

No publications for rs12027485

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

rs12027485