Variant report

Variant	rs3911714
Chromosome Location	chr3:159500613-159500614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159492066..159493625-chr3:159498204..159501036,2	MCF-7	breast:
2	chr3:159481520..159484319-chr3:159499469..159501812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11919032	1.00[CHD][hapmap]
rs13070254	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461103	0.96[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463514	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1675497	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1965998	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126143	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169303	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886623	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33050	1.00[JPT][hapmap]
rs33054	1.00[JPT][hapmap]
rs33056	1.00[JPT][hapmap]
rs3851360	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513503	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680527	0.82[EUR][1000 genomes]
rs6441272	0.84[YRI][hapmap]
rs6441274	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441275	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788052	0.81[EUR][1000 genomes]
rs6805556	0.88[EUR][1000 genomes]
rs7625089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630289	1.00[CHD][hapmap]
rs7636819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820045	0.82[EUR][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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159484200-159501200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:159490200-159501400	Weak transcription	Aorta	Aorta
4	chr3:159493600-159504400	Weak transcription	Right Atrium	heart
5	chr3:159493600-159505200	Weak transcription	Lung	lung
6	chr3:159493600-159505400	Weak transcription	Fetal Stomach	stomach
7	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:159493800-159502800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:159494800-159503000	Weak transcription	NHDF-Ad	bronchial
11	chr3:159495000-159502000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:159495000-159503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:159495000-159503200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:159495200-159501400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:159495200-159502000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:159495200-159502600	Weak transcription	HUVEC	blood vessel
17	chr3:159495200-159503000	Weak transcription	NHLF	lung
18	chr3:159495200-159503200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:159495200-159504400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:159495200-159504600	Weak transcription	HSMMtube	muscle
21	chr3:159496400-159501000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:159497800-159501000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:159498200-159501400	Enhancers	Right Ventricle	heart
24	chr3:159498200-159501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:159498400-159501200	Weak transcription	NH-A	brain
26	chr3:159498600-159501200	Weak transcription	HSMM	muscle
27	chr3:159498600-159504400	Weak transcription	Esophagus	oesophagus
28	chr3:159499200-159502600	Enhancers	Stomach Smooth Muscle	stomach
29	chr3:159499400-159501400	Enhancers	Brain Substantia Nigra	brain
30	chr3:159499400-159501400	Enhancers	HMEC	breast
31	chr3:159499400-159501600	Enhancers	Liver	Liver
32	chr3:159499400-159502400	Enhancers	Brain Angular Gyrus	brain
33	chr3:159499600-159501200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:159499600-159501200	Enhancers	NHEK	skin
35	chr3:159499600-159501800	Weak transcription	Fetal Kidney	kidney
36	chr3:159499600-159501800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:159499800-159501000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:159499800-159501000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:159499800-159501200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:159499800-159501200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:159499800-159503400	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:159499800-159506400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr3:159500000-159500800	Enhancers	Stomach Mucosa	stomach
44	chr3:159500000-159501200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:159500000-159503600	Enhancers	Brain Hippocampus Middle	brain
46	chr3:159500200-159501400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:159500400-159500800	Enhancers	Fetal Intestine Small	intestine
48	chr3:159500400-159501000	Flanking Active TSS	A549	lung
49	chr3:159500400-159501600	Enhancers	Brain Anterior Caudate	brain
50	chr3:159500400-159509200	Enhancers	HepG2	liver

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