Variant report

Variant	rs3889309
Chromosome Location	chr3:159501292-159501293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159481520..159484319-chr3:159499469..159501812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10936179	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1107061	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715088	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491535	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497762	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1553081	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2010748	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169305	0.88[ASN][1000 genomes]
rs3851359	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679863	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679865	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680524	0.96[ASN][1000 genomes]
rs56107912	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62270387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62270397	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763138	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6780187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:159490200-159501400	Weak transcription	Aorta	Aorta
3	chr3:159493600-159504400	Weak transcription	Right Atrium	heart
4	chr3:159493600-159505200	Weak transcription	Lung	lung
5	chr3:159493600-159505400	Weak transcription	Fetal Stomach	stomach
6	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:159493800-159502800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:159494800-159503000	Weak transcription	NHDF-Ad	bronchial
10	chr3:159495000-159502000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:159495000-159503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:159495000-159503200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:159495200-159501400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:159495200-159502000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:159495200-159502600	Weak transcription	HUVEC	blood vessel
16	chr3:159495200-159503000	Weak transcription	NHLF	lung
17	chr3:159495200-159503200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:159495200-159504400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:159495200-159504600	Weak transcription	HSMMtube	muscle
20	chr3:159498200-159501400	Enhancers	Right Ventricle	heart
21	chr3:159498200-159501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:159498600-159504400	Weak transcription	Esophagus	oesophagus
23	chr3:159499200-159502600	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:159499400-159501400	Enhancers	Brain Substantia Nigra	brain
25	chr3:159499400-159501400	Enhancers	HMEC	breast
26	chr3:159499400-159501600	Enhancers	Liver	Liver
27	chr3:159499400-159502400	Enhancers	Brain Angular Gyrus	brain
28	chr3:159499600-159501800	Weak transcription	Fetal Kidney	kidney
29	chr3:159499600-159501800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:159499800-159503400	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:159499800-159506400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:159500000-159503600	Enhancers	Brain Hippocampus Middle	brain
33	chr3:159500200-159501400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:159500400-159501600	Enhancers	Brain Anterior Caudate	brain
35	chr3:159500400-159509200	Enhancers	HepG2	liver
36	chr3:159500600-159501400	Strong transcription	Osteobl	bone
37	chr3:159500600-159501800	Enhancers	Left Ventricle	heart
38	chr3:159500600-159502000	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:159500800-159501800	Weak transcription	Fetal Intestine Large	intestine
40	chr3:159500800-159501800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:159500800-159502800	Weak transcription	Stomach Mucosa	stomach
42	chr3:159501000-159501400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:159501000-159501800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:159501000-159502200	Enhancers	A549	lung
45	chr3:159501000-159502800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:159501000-159503400	Enhancers	Placenta	Placenta
47	chr3:159501000-159508000	Enhancers	Colon Smooth Muscle	Colon
48	chr3:159501200-159501600	Strong transcription	HSMM	muscle
49	chr3:159501200-159501600	Strong transcription	NH-A	brain
50	chr3:159501200-159502400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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