Variant report

Variant	rs6789975
Chromosome Location	chr3:86992222-86992223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13074432	0.92[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13324964	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13356	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436639	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436640	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2340475	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]
rs6784619	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];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519148	chr3:86831077-86995124	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86980600-86995600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:86986000-86998200	Weak transcription	A549	lung
3	chr3:86986800-87014400	Weak transcription	Aorta	Aorta
4	chr3:86987200-86997800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:86987400-87007400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:86987800-86996600	Strong transcription	Placenta	Placenta
7	chr3:86987800-86999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:86988000-86992800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:86988000-86993600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:86988200-86993200	Weak transcription	Fetal Lung	lung
11	chr3:86988200-87007600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:86988200-87013400	Weak transcription	Ovary	ovary
13	chr3:86988600-86993400	Weak transcription	HSMMtube	muscle
14	chr3:86988600-87000000	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:86988800-86993000	Weak transcription	NHLF	lung
16	chr3:86989000-86993200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:86989000-86993400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:86989000-86997800	Strong transcription	HSMM	muscle
19	chr3:86989200-86993200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:86989200-86996000	Strong transcription	Osteobl	bone
21	chr3:86989200-86997400	Weak transcription	Adipose Nuclei	Adipose
22	chr3:86989200-86999600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:86989400-86993200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:86990800-86994200	Genic enhancers	NHDF-Ad	bronchial
25	chr3:86990800-86995800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:86991000-86992400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:86991000-86997400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr3:86991200-86993800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:86991400-86993200	Weak transcription	Hela-S3	cervix
30	chr3:86991800-86992600	Weak transcription	NH-A	brain
31	chr3:86992000-86992400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:86992000-86993400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:86992200-86995200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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