Variant report

Variant	rs1447715
Chromosome Location	chr3:139483931-139483932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:139481932..139484546-chr3:139489954..139491716,2	MCF-7	breast:
2	chr3:139481022..139483943-chr3:139485474..139488323,2	K562	blood:
3	chr3:139482622..139485118-chr3:139488684..139490700,2	K562	blood:
4	chr3:139483606..139485118-chr3:139487226..139490184,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11920106	0.94[ASN][1000 genomes]
rs11927123	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927717	0.96[ASN][1000 genomes]
rs12632239	1.00[ASN][1000 genomes]
rs12632496	1.00[ASN][1000 genomes]
rs1374826	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270252	1.00[ASN][1000 genomes]
rs62270253	1.00[ASN][1000 genomes]
rs6773396	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774120	0.82[AFR][1000 genomes]
rs6777057	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809271	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809417	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9832241	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832254	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847705	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9852437	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863263	0.83[AFR][1000 genomes]
rs9864599	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873970	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9873981	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1447715	NMNAT3	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139481000-139484000	Enhancers	Fetal Heart	heart
2	chr3:139481000-139484600	Enhancers	HSMMtube	muscle
3	chr3:139481200-139485000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:139481600-139496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:139482200-139484400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:139482200-139484800	Enhancers	NH-A	brain
7	chr3:139482200-139485000	Enhancers	HSMM	muscle
8	chr3:139482400-139484000	Enhancers	Ovary	ovary
9	chr3:139482400-139484600	Enhancers	NHLF	lung
10	chr3:139482800-139484600	Enhancers	Osteobl	bone
11	chr3:139482800-139484800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:139482800-139484800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:139482800-139484800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:139483000-139484400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:139483000-139484600	Enhancers	NHDF-Ad	bronchial
16	chr3:139483000-139484800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:139483200-139484800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:139483200-139493000	Weak transcription	Left Ventricle	heart
19	chr3:139483600-139484400	Enhancers	HMEC	breast
20	chr3:139483600-139486000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:139483800-139484000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:139483800-139484000	Enhancers	Right Atrium	heart
23	chr3:139483800-139492600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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