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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1434536

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:95154814 (GRCh38.p7) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.44339 (55676/125568, TOPMED)
T=0.4476 (13818/30872, GnomAD)
T=0.404 (2024/5008, 1000G) (+ 2 more)
C=0.440 (1695/3854, ALSPAC)
C=0.442 (1639/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BMPR1B : 3 Prime UTR Variant
Publications
19 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.p7 chr 4 NC_000004.12:g.95154814C>T
GRCh37.p13 chr 4 NC_000004.11:g.96075965C>T
BMPR1B RefSeqGene NG_009245.1:g.401838C>T
Gene: BMPR1B, bone morphogenetic protein receptor type 1B (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BMPR1B transcript variant 2 NM_001203.2:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant 3 NM_001256792.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant 1 NM_001256793.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant 4 NM_001256794.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant X1 XM_017008558.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant X2 XM_017008559.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant X3 XM_017008560.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant X4 XM_017008561.1:c. N/A 3 Prime UTR Variant
BMPR1B transcript variant X5 XM_011532201.2:c. N/A 3 Prime UTR 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.

Allele: T (allele ID: 296235 )
ClinVar Accession Disease Names Clinical Significance
RCV000273899.1 Brachydactyly Benign
RCV000639570.1 Acromesomelic dysplasia, Demirhan type,Type A2 brachydactyly Benign
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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
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.55661 T=0.44339
The Genome Aggregation Database Global Study-wide 30872 C=0.5524 T=0.4476
The Genome Aggregation Database European Sub 18426 C=0.4542 T=0.5458
The Genome Aggregation Database African Sub 8710 C=0.776 T=0.224
The Genome Aggregation Database East Asian Sub 1616 C=0.624 T=0.376
The Genome Aggregation Database Other Sub 982 C=0.47 T=0.53
The Genome Aggregation Database American Sub 836 C=0.39 T=0.61
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.44 T=0.56
1000Genomes Global Study-wide 5008 C=0.596 T=0.404
1000Genomes African Sub 1322 C=0.818 T=0.182
1000Genomes East Asian Sub 1008 C=0.617 T=0.383
1000Genomes Europe Sub 1006 C=0.441 T=0.559
1000Genomes South Asian Sub 978 C=0.57 T=0.43
1000Genomes American Sub 694 C=0.40 T=0.60
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.440 T=0.560
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.442 T=0.558
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 C= T Note
GRCh38.p7 chr 4 NC_000004.12:g.95154814C= NC_000004.12:g.95154814C>T
GRCh37.p13 chr 4 NC_000004.11:g.96075965C= NC_000004.11:g.96075965C>T
BMPR1B RefSeqGene NG_009245.1:g.401838C= NG_009245.1:g.401838C>T
BMPR1B transcript variant 2 NM_001203.2:c.*141C= NM_001203.2:c.*141C>T
BMPR1B transcript variant 3 NM_001256792.1:c.*141C= NM_001256792.1:c.*141C>T
BMPR1B transcript variant 4 NM_001256794.1:c.*141C= NM_001256794.1:c.*141C>T
BMPR1B transcript variant 1 NM_001256793.1:c.*141C= NM_001256793.1:c.*141C>T
BMPR1B transcript variant X5 XM_011532201.2:c.*141C= XM_011532201.2:c.*141C>T
BMPR1B transcript variant X1 XM_017008558.1:c.*141C= XM_017008558.1:c.*141C>T
BMPR1B transcript variant X2 XM_017008559.1:c.*141C= XM_017008559.1:c.*141C>T
BMPR1B transcript variant X3 XM_017008560.1:c.*141C= XM_017008560.1:c.*141C>T
BMPR1B transcript variant X4 XM_017008561.1:c.*141C= XM_017008561.1:c.*141C>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#.

2 ClinVar, 5 Frequency, 89 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2244470 Oct 23, 2000 (88)
2 PERLEGEN ss24340554 Sep 20, 2004 (123)
3 ABI ss44504352 Mar 14, 2006 (126)
4 ILLUMINA ss65740815 Oct 15, 2006 (127)
5 ILLUMINA ss74891727 Dec 06, 2007 (129)
6 HGSV ss77481242 Dec 06, 2007 (129)
7 HGSV ss78346112 Dec 06, 2007 (129)
8 HUMANGENOME_JCVI ss98983253 Feb 06, 2009 (130)
9 BGI ss104096593 Dec 01, 2009 (131)
10 KRIBB_YJKIM ss104796833 Feb 06, 2009 (130)
11 1000GENOMES ss108151244 Jan 23, 2009 (130)
12 KRIBB_YJKIM ss119392530 Dec 01, 2009 (131)
13 ENSEMBL ss143481520 Dec 01, 2009 (131)
14 ILLUMINA ss160352901 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162356035 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss166918214 Jul 04, 2010 (132)
17 ILLUMINA ss172499002 Jul 04, 2010 (132)
18 BUSHMAN ss198883260 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss206628235 Jul 04, 2010 (132)
20 1000GENOMES ss211454420 Jul 14, 2010 (132)
21 1000GENOMES ss221082375 Jul 14, 2010 (132)
22 1000GENOMES ss232503595 Jul 14, 2010 (132)
23 1000GENOMES ss239771895 Jul 15, 2010 (132)
24 BL ss253350773 May 09, 2011 (134)
25 GMI ss277834208 May 04, 2012 (137)
26 GMI ss284962295 Apr 25, 2013 (138)
27 PJP ss293141569 May 09, 2011 (134)
28 ILLUMINA ss479973343 May 04, 2012 (137)
29 ILLUMINA ss479981933 May 04, 2012 (137)
30 ILLUMINA ss480629508 Sep 08, 2015 (146)
31 ILLUMINA ss484784903 May 04, 2012 (137)
32 EXOME_CHIP ss491358731 May 04, 2012 (137)
33 ILLUMINA ss536871185 Sep 08, 2015 (146)
34 TISHKOFF ss557702418 Apr 25, 2013 (138)
35 SSMP ss651507187 Apr 25, 2013 (138)
36 ILLUMINA ss778432173 Aug 21, 2014 (142)
37 ILLUMINA ss780802603 Sep 08, 2015 (146)
38 ILLUMINA ss782839115 Aug 21, 2014 (142)
39 ILLUMINA ss783484071 Sep 08, 2015 (146)
40 ILLUMINA ss783803812 Aug 21, 2014 (142)
41 ILLUMINA ss832092773 Apr 01, 2015 (144)
42 ILLUMINA ss833887645 Aug 21, 2014 (142)
43 EVA-GONL ss980416913 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1071763816 Aug 21, 2014 (142)
45 1000GENOMES ss1310865871 Aug 21, 2014 (142)
46 DDI ss1429973734 Apr 01, 2015 (144)
47 EVA_GENOME_DK ss1580674749 Apr 01, 2015 (144)
48 EVA_DECODE ss1589920173 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1610673550 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1653667583 Apr 01, 2015 (144)
51 EVA_MGP ss1711066785 Apr 01, 2015 (144)
52 EVA_SVP ss1712691215 Apr 01, 2015 (144)
53 ILLUMINA ss1752538135 Sep 08, 2015 (146)
54 ILLUMINA ss1752538136 Sep 08, 2015 (146)
55 HAMMER_LAB ss1801869466 Sep 08, 2015 (146)
56 ILLUMINA ss1917783032 Feb 12, 2016 (147)
57 WEILL_CORNELL_DGM ss1923658666 Feb 12, 2016 (147)
58 ILLUMINA ss1946122531 Feb 12, 2016 (147)
59 ILLUMINA ss1958705131 Feb 12, 2016 (147)
60 GENOMED ss1969809968 Jul 19, 2016 (147)
61 JJLAB ss2022414268 Sep 14, 2016 (149)
62 USC_VALOUEV ss2150543711 Dec 20, 2016 (150)
63 HUMAN_LONGEVITY ss2265183814 Dec 20, 2016 (150)
64 TOPMED ss2432993442 Dec 20, 2016 (150)
65 SYSTEMSBIOZJU ss2625708310 Nov 08, 2017 (151)
66 ILLUMINA ss2634151459 Nov 08, 2017 (151)
67 GRF ss2706021471 Nov 08, 2017 (151)
68 GNOMAD ss2812524005 Nov 08, 2017 (151)
69 AFFY ss2985298404 Nov 08, 2017 (151)
70 SWEGEN ss2995161338 Nov 08, 2017 (151)
71 ILLUMINA ss3022396622 Nov 08, 2017 (151)
72 BIOINF_KMB_FNS_UNIBA ss3024982619 Nov 08, 2017 (151)
73 CSHL ss3345848036 Nov 08, 2017 (151)
74 TOPMED ss3436478610 Nov 08, 2017 (151)
75 ILLUMINA ss3629020148 Jul 20, 2018 (151)
76 ILLUMINA ss3629020149 Jul 20, 2018 (151)
77 ILLUMINA ss3632085993 Jul 20, 2018 (151)
78 ILLUMINA ss3633342496 Jul 20, 2018 (151)
79 ILLUMINA ss3634061774 Jul 20, 2018 (151)
80 ILLUMINA ss3634962473 Jul 20, 2018 (151)
81 ILLUMINA ss3634962474 Jul 20, 2018 (151)
82 ILLUMINA ss3635744521 Jul 20, 2018 (151)
83 ILLUMINA ss3636666597 Jul 20, 2018 (151)
84 ILLUMINA ss3637497052 Jul 20, 2018 (151)
85 ILLUMINA ss3638500270 Jul 20, 2018 (151)
86 ILLUMINA ss3640669767 Jul 20, 2018 (151)
87 ILLUMINA ss3640669768 Jul 20, 2018 (151)
88 ILLUMINA ss3643450586 Jul 20, 2018 (151)
89 ILLUMINA ss3644855327 Jul 20, 2018 (151)
90 1000Genomes NC_000004.11 - 96075965 Jul 20, 2018 (151)
91 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 96075965 Jul 20, 2018 (151)
92 The Genome Aggregation Database NC_000004.11 - 96075965 Jul 20, 2018 (151)
93 Trans-Omics for Precision Medicine NC_000004.12 - 95154814 Jul 20, 2018 (151)
94 UK 10K study - Twins NC_000004.11 - 96075965 Jul 20, 2018 (151)
95 ClinVar RCV000273899.1 Jul 20, 2018 (151)
96 ClinVar RCV000639570.1 Jul 20, 2018 (151)
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)
rs17414957 Oct 07, 2004 (123)
rs386531743 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77481242, ss78346112 NC_000004.9:96433142:C= NC_000004.12:95154813:C= (self)
ss108151244, ss162356035, ss166918214, ss198883260, ss206628235, ss211454420, ss253350773, ss277834208, ss284962295, ss293141569, ss479973343, ss1589920173, ss1712691215, ss3643450586 NC_000004.10:96294987:C= NC_000004.12:95154813:C= (self)
22303832, 12404026, 153151760, 12404026, ss221082375, ss232503595, ss239771895, ss479981933, ss480629508, ss484784903, ss491358731, ss536871185, ss557702418, ss651507187, ss778432173, ss780802603, ss782839115, ss783484071, ss783803812, ss832092773, ss833887645, ss980416913, ss1071763816, ss1310865871, ss1429973734, ss1580674749, ss1610673550, ss1653667583, ss1711066785, ss1752538135, ss1752538136, ss1801869466, ss1917783032, ss1923658666, ss1946122531, ss1958705131, ss1969809968, ss2022414268, ss2150543711, ss2432993442, ss2625708310, ss2634151459, ss2706021471, ss2812524005, ss2985298404, ss2995161338, ss3022396622, ss3345848036, ss3629020148, ss3629020149, ss3632085993, ss3633342496, ss3634061774, ss3634962473, ss3634962474, ss3635744521, ss3636666597, ss3637497052, ss3638500270, ss3640669767, ss3640669768, ss3644855327 NC_000004.11:96075964:C= NC_000004.12:95154813:C= (self)
288166757, ss2265183814, ss3024982619, ss3436478610 NC_000004.12:95154813:C= NC_000004.12:95154813:C= (self)
ss2244470, ss24340554, ss44504352, ss65740815, ss74891727, ss98983253, ss104096593, ss104796833, ss119392530, ss143481520, ss160352901, ss172499002 NT_016354.19:20623685:C= NC_000004.12:95154813:C= (self)
ss77481242, ss78346112 NC_000004.9:96433142:C>T NC_000004.12:95154813:C>T (self)
ss108151244, ss162356035, ss166918214, ss198883260, ss206628235, ss211454420, ss253350773, ss277834208, ss284962295, ss293141569, ss479973343, ss1589920173, ss1712691215, ss3643450586 NC_000004.10:96294987:C>T NC_000004.12:95154813:C>T (self)
22303832, 12404026, 153151760, 12404026, ss221082375, ss232503595, ss239771895, ss479981933, ss480629508, ss484784903, ss491358731, ss536871185, ss557702418, ss651507187, ss778432173, ss780802603, ss782839115, ss783484071, ss783803812, ss832092773, ss833887645, ss980416913, ss1071763816, ss1310865871, ss1429973734, ss1580674749, ss1610673550, ss1653667583, ss1711066785, ss1752538135, ss1752538136, ss1801869466, ss1917783032, ss1923658666, ss1946122531, ss1958705131, ss1969809968, ss2022414268, ss2150543711, ss2432993442, ss2625708310, ss2634151459, ss2706021471, ss2812524005, ss2985298404, ss2995161338, ss3022396622, ss3345848036, ss3629020148, ss3629020149, ss3632085993, ss3633342496, ss3634061774, ss3634962473, ss3634962474, ss3635744521, ss3636666597, ss3637497052, ss3638500270, ss3640669767, ss3640669768, ss3644855327 NC_000004.11:96075964:C>T NC_000004.12:95154813:C>T (self)
RCV000273899.1, RCV000639570.1, 288166757, ss2265183814, ss3024982619, ss3436478610 NC_000004.12:95154813:C>T NC_000004.12:95154813:C>T (self)
ss2244470, ss24340554, ss44504352, ss65740815, ss74891727, ss98983253, ss104096593, ss104796833, ss119392530, ss143481520, ss160352901, ss172499002 NT_016354.19:20623685:C>T NC_000004.12:95154813:C>T (self)
Help

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

19 citations for rs1434536
PMID Title Author Year Journal
19453261 High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. Yerges LM et al. 2009 Journal of bone and mineral research
19738052 A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis. Saetrom P et al. 2009 Cancer research
20357209 Molecular genetic studies of gene identification for osteoporosis: the 2009 update. Xu XH et al. 2010 Endocrine reviews
20495573 Genetic variation in microRNA networks: the implications for cancer research. Ryan BM et al. 2010 Nature reviews. Cancer
20688557 The Yin and Yang of bone morphogenetic proteins in cancer. Singh A et al. 2010 Cytokine & growth factor reviews
20843204 MicroRNA binding site polymorphisms as biomarkers of cancer risk. Pelletier C et al. 2010 Expert review of molecular diagnostics
21556765 A miR-125b binding site polymorphism in bone morphogenetic protein membrane receptor type IB gene and prostate cancer risk in China. Feng N et al. 2012 Molecular biology reports
21692980 Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancer. Slaby O et al. 2012 Journal of cellular and molecular medicine
21693556 Inferring causative variants in microRNA target sites. Thomas LF et al. 2011 Nucleic acids research
21910715 MYH9 and APOL1 are both associated with sickle cell disease nephropathy. Ashley-Koch AE et al. 2011 British journal of haematology
21995669 A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS. Richardson K et al. 2011 BMC genomics
23091610 Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. Ziebarth JD et al. 2012 PloS one
23173617 MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. Liu C et al. 2012 BMC genomics
23614619 SNPs in microRNA binding sites as prognostic and predictive cancer biomarkers. Preskill C et al. 2013 Critical reviews in oncogenesis
24629096 mrSNP: software to detect SNP effects on microRNA binding. Deveci M et al. 2014 BMC bioinformatics
25114582 MicroRNA binding site polymorphisms as biomarkers in cancer management and research. Cipollini M et al. 2014 Pharmacogenomics and personalized medicine
26190157 Evaluation the susceptibility of five polymorphisms in microRNA-binding sites to female breast cancer risk in Chinese population. He BS et al. 2015 Gene
27222754 Association between single nucleotide polymorphism in miR-499, miR-196a2, miR-146a and miR-149 and prostate cancer risk in a sample of Iranian population. Hashemi M et al. 2016 Journal of advanced research
27853382 Genetic variation <i>rs7930</i> in the miR-4273-5p target site is associated with a risk of colorectal cancer. Lee AR et al. 2016 OncoTargets and therapy

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e