Variant report

Variant	rs6784619
Chromosome Location	chr3:86998161-86998162
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	chr3:86996700..86999584-chr3:87010163..87012426,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13074432	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13324964	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13356	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436640	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789975	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9834197	0.94[AMR][1000 genomes];0.97[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	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86986000-86998200	Weak transcription	A549	lung
2	chr3:86986800-87014400	Weak transcription	Aorta	Aorta
3	chr3:86987400-87007400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:86987800-86999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:86988200-87007600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:86988200-87013400	Weak transcription	Ovary	ovary
7	chr3:86988600-87000000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:86989200-86999600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:86992600-86998200	Strong transcription	NH-A	brain
10	chr3:86993800-87014200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:86994000-87013200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:86994400-86998600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:86994800-87010400	Weak transcription	Fetal Lung	lung
14	chr3:86995800-86998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:86996000-87005600	Genic enhancers	Osteobl	bone
16	chr3:86996200-86999200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:86996600-86999000	Weak transcription	Placenta	Placenta
18	chr3:86996600-87002200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:86997000-87005000	Enhancers	Hela-S3	cervix
20	chr3:86997200-86998600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:86997200-86998600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:86997200-87001800	Enhancers	HMEC	breast
23	chr3:86997200-87003800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:86997400-86998400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:86997400-86998400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:86997400-86998400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:86997400-87001800	Enhancers	NHLF	lung
28	chr3:86997600-86999800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr3:86997600-87013200	Genic enhancers	NHDF-Ad	bronchial
30	chr3:86997800-86998200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:86997800-86998400	Enhancers	HSMMtube	muscle
32	chr3:86997800-86998600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr3:86997800-86998600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:86997800-86998800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:86997800-86998800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:86997800-86999000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:86997800-87001000	Enhancers	NHEK	skin
38	chr3:86997800-87001200	Genic enhancers	HSMM	muscle
39	chr3:86998000-86998400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:86998000-86998400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:86998000-87000400	Weak transcription	Adipose Nuclei	Adipose
42	chr3:86998000-87019800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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