Variant report

Variant	rs2340475
Chromosome Location	chr3:86996762-86996763
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:
2	chr3:86992376..86994147-chr3:86995975..86997562,2	K562	blood:

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

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

rs_ID	r²[population]
rs13074432	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13324964	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13356	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436639	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.96[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]
rs6784619	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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[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:35 , 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	chr3:86987200-86997800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:86987400-87007400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:86987800-86999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:86988200-87007600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:86988200-87013400	Weak transcription	Ovary	ovary
8	chr3:86988600-87000000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:86989000-86997800	Strong transcription	HSMM	muscle
10	chr3:86989200-86997400	Weak transcription	Adipose Nuclei	Adipose
11	chr3:86989200-86999600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:86991000-86997400	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr3:86992600-86998200	Strong transcription	NH-A	brain
14	chr3:86993600-86997800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:86993800-86998000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:86993800-87014200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:86994000-87013200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:86994200-86997000	Weak transcription	Hela-S3	cervix
19	chr3:86994200-86997200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:86994400-86998600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:86994800-87010400	Weak transcription	Fetal Lung	lung
22	chr3:86995400-86997200	Genic enhancers	NHDF-Ad	bronchial
23	chr3:86995800-86998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:86996000-87005600	Genic enhancers	Osteobl	bone
25	chr3:86996200-86997400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:86996200-86999200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:86996400-86997200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:86996400-86997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:86996400-86997200	Weak transcription	HSMMtube	muscle
30	chr3:86996400-86997400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:86996400-86997400	Weak transcription	NHLF	lung
32	chr3:86996400-86997800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:86996400-86997800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:86996600-86999000	Weak transcription	Placenta	Placenta
35	chr3:86996600-87002200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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