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dbSNP Short Genetic Variations

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.

rs1220134

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr2:157747044 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.39386 (49456/125568, TOPMED)
A=0.3785 (11863/31342, GnomAD)
A=0.360 (1801/5008, 1000G) (+ 4 more)
A=0.255 (1143/4480, Estonian)
A=0.267 (1030/3854, ALSPAC)
A=0.265 (983/3708, TWINSUK)
A=0.32 (191/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACVR1 : Intron Variant
Publications
3 citations
Genomic View
See rs on genome
Help

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.p12 chr 2 NC_000002.12:g.157747044T>A
GRCh37.p13 chr 2 NC_000002.11:g.158603556T>A
ACVR1 RefSeqGene NG_008004.1:g.133068A>T
Gene: ACVR1, activin A receptor type 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ACVR1 transcript variant 1 NM_001105.5:c. N/A Intron Variant
ACVR1 transcript variant 2 NM_001111067.3:c. N/A Intron Variant
ACVR1 transcript variant 3 NM_001347663.1:c. N/A Intron Variant
ACVR1 transcript variant 4 NM_001347664.1:c. N/A Intron Variant
ACVR1 transcript variant 5 NM_001347665.1:c. N/A Intron Variant
ACVR1 transcript variant 6 NM_001347666.1:c. N/A Intron Variant
ACVR1 transcript variant 7 NM_001347667.2:c. N/A Intron Variant
ACVR1 transcript variant X2 XM_006712825.4:c. N/A Intron Variant
ACVR1 transcript variant X1 XM_011512108.3:c. N/A Intron Variant
Help

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
Help

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 125568 T=0.60614 A=0.39386
gnomAD - Genomes Global Study-wide 31342 T=0.6215 A=0.3785
gnomAD - Genomes European Sub 18866 T=0.7431 A=0.2569
gnomAD - Genomes African Sub 8700 T=0.314 A=0.686
gnomAD - Genomes East Asian Sub 1552 T=0.691 A=0.309
gnomAD - Genomes Other Sub 1086 T=0.733 A=0.267
gnomAD - Genomes American Sub 848 T=0.78 A=0.22
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.69 A=0.31
1000Genomes Global Study-wide 5008 T=0.640 A=0.360
1000Genomes African Sub 1322 T=0.260 A=0.740
1000Genomes East Asian Sub 1008 T=0.740 A=0.260
1000Genomes Europe Sub 1006 T=0.758 A=0.242
1000Genomes South Asian Sub 978 T=0.84 A=0.16
1000Genomes American Sub 694 T=0.77 A=0.23
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.745 A=0.255
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.733 A=0.267
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.735 A=0.265
Northern Sweden ACPOP Study-wide 600 T=0.68 A=0.32
Help

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 Note
GRCh38.p12 chr 2 NC_000002.12:g.157747044= NC_000002.12:g.15774704...

NC_000002.12:g.157747044T>A

GRCh37.p13 chr 2 NC_000002.11:g.158603556= NC_000002.11:g.15860355...

NC_000002.11:g.158603556T>A

ACVR1 RefSeqGene NG_008004.1:g.133068= NG_008004.1:g.133068A>T
Help

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#.

50 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1783312 Oct 18, 2000 (87)
2 SC_JCM ss3662288 Sep 28, 2001 (100)
3 BCM_SSAHASNP ss9995092 Jul 11, 2003 (116)
4 PERLEGEN ss24308599 Sep 20, 2004 (123)
5 ABI ss44155676 Mar 15, 2006 (126)
6 HGSV ss81213158 Dec 14, 2007 (130)
7 BGI ss106131527 Feb 04, 2009 (130)
8 1000GENOMES ss110122638 Jan 24, 2009 (130)
9 1000GENOMES ss111153685 Jan 25, 2009 (130)
10 ILLUMINA-UK ss117937519 Feb 14, 2009 (130)
11 COMPLETE_GENOMICS ss164629593 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss167343216 Jul 04, 2010 (132)
13 BUSHMAN ss201261883 Jul 04, 2010 (132)
14 1000GENOMES ss219606089 Jul 14, 2010 (132)
15 1000GENOMES ss231433015 Jul 14, 2010 (132)
16 1000GENOMES ss238927192 Jul 15, 2010 (132)
17 GMI ss276749926 May 04, 2012 (137)
18 GMI ss284468677 Apr 25, 2013 (138)
19 PJP ss292408213 May 09, 2011 (134)
20 TISHKOFF ss555981583 Apr 25, 2013 (138)
21 SSMP ss649623941 Apr 25, 2013 (138)
22 EVA-GONL ss977546051 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1069633184 Aug 21, 2014 (142)
24 1000GENOMES ss1300055999 Aug 21, 2014 (142)
25 DDI ss1428793019 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1579160261 Apr 01, 2015 (144)
27 EVA_DECODE ss1586980726 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1604948269 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1647942302 Apr 01, 2015 (144)
30 HAMMER_LAB ss1797780731 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1920799653 Feb 12, 2016 (147)
32 JJLAB ss2020929543 Sep 14, 2016 (149)
33 USC_VALOUEV ss2148995285 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2235801551 Dec 20, 2016 (150)
35 TOPMED ss2402196669 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2624969562 Nov 08, 2017 (151)
37 GRF ss2703627949 Nov 08, 2017 (151)
38 GNOMAD ss2781749976 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3024227067 Nov 08, 2017 (151)
40 TOPMED ss3327811777 Nov 08, 2017 (151)
41 CSHL ss3344562064 Nov 08, 2017 (151)
42 URBANLAB ss3647185258 Oct 11, 2018 (152)
43 EGCUT_WGS ss3658576861 Jul 13, 2019 (153)
44 EVA_DECODE ss3705240794 Jul 13, 2019 (153)
45 ACPOP ss3729025257 Jul 13, 2019 (153)
46 EVA ss3757605868 Jul 13, 2019 (153)
47 PACBIO ss3784041113 Jul 13, 2019 (153)
48 PACBIO ss3789597115 Jul 13, 2019 (153)
49 PACBIO ss3794470083 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3801966519 Jul 13, 2019 (153)
51 1000Genomes NC_000002.11 - 158603556 Oct 11, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 158603556 Oct 11, 2018 (152)
53 Genetic variation in the Estonian population NC_000002.11 - 158603556 Oct 11, 2018 (152)
54 gnomAD - Genomes NC_000002.11 - 158603556 Jul 13, 2019 (153)
55 Northern Sweden NC_000002.11 - 158603556 Jul 13, 2019 (153)
56 TopMed NC_000002.12 - 157747044 Oct 11, 2018 (152)
57 UK 10K study - Twins NC_000002.11 - 158603556 Oct 11, 2018 (152)
Help

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)
rs17182306 Oct 07, 2004 (123)
rs57512598 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81213158 NC_000002.9:158429063:T:A NC_000002.12:157747043:T:A (self)
ss110122638, ss111153685, ss117937519, ss164629593, ss167343216, ss201261883, ss276749926, ss284468677, ss292408213, ss1586980726 NC_000002.10:158311801:T:A NC_000002.12:157747043:T:A (self)
11099207, 6119171, 4315109, 30327583, 2310122, 6119171, ss219606089, ss231433015, ss238927192, ss555981583, ss649623941, ss977546051, ss1069633184, ss1300055999, ss1428793019, ss1579160261, ss1604948269, ss1647942302, ss1797780731, ss1920799653, ss2020929543, ss2148995285, ss2402196669, ss2624969562, ss2703627949, ss2781749976, ss3344562064, ss3658576861, ss3729025257, ss3757605868, ss3784041113, ss3789597115, ss3794470083 NC_000002.11:158603555:T:A NC_000002.12:157747043:T:A (self)
208575711, ss2235801551, ss3024227067, ss3327811777, ss3647185258, ss3705240794, ss3801966519 NC_000002.12:157747043:T:A NC_000002.12:157747043:T:A (self)
ss9995092 NT_005403.13:8762894:T:A NC_000002.12:157747043:T:A (self)
ss1783312, ss3662288, ss24308599, ss44155676, ss106131527 NT_005403.17:8812973:T:A NC_000002.12:157747043:T:A (self)
Help

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

3 citations for rs1220134
PMID Title Author Year Journal
18854405 Variants in the ACVR1 gene are associated with AMH levels in women with polycystic ovary syndrome. Kevenaar ME et al. 2009 Human reproduction (Oxford, England)
23180569 Genetic variation in bone morphogenetic proteins and breast cancer risk in hispanic and non-hispanic white women: The breast cancer health disparities study. Slattery ML et al. 2013 International journal of cancer
25379134 Genetic variants in anti-Mullerian hormone and anti-Mullerian hormone receptor genes and breast cancer risk in Caucasians and African Americans. Nan H et al. 2014 International journal of molecular epidemiology and genetics

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.

Software version is: 2.0.1.post246+3cda961