Variant report

Variant	rs9859340
Chromosome Location	chr3:69935822-69935823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69934018..69936742-chr3:69940708..69942627,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11920509	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11921396	1.00[AMR][1000 genomes]
rs11924822	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13314417	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13315220	1.00[EUR][1000 genomes]
rs13316652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13321948	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325667	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006569	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006572	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006575	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28754428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35773003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41370746	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41440046	1.00[YRI][hapmap]
rs9818328	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9819125	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827219	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827735	0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833046	0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833501	0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837171	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9838445	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842586	1.00[EUR][1000 genomes]
rs9843115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845314	1.00[EUR][1000 genomes]
rs9849776	1.00[EUR][1000 genomes]
rs9850565	0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv3507784	chr3:69802539-69959607	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3507785	chr3:69802539-69959607	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr3:69917200-69951200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:69920800-69937600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:69920800-69950800	Weak transcription	Ovary	ovary
4	chr3:69922200-69936400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:69922400-69939000	Weak transcription	NHLF	lung
6	chr3:69923000-69937800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:69925200-69937000	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:69927000-69937600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:69927000-69938200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:69927600-69939200	Weak transcription	Stomach Mucosa	stomach
11	chr3:69928600-69938200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:69928600-69939000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:69928600-69939000	Weak transcription	Right Ventricle	heart
14	chr3:69928600-69942000	Weak transcription	Gastric	stomach
15	chr3:69928600-69950800	Weak transcription	Pancreas	Pancrea
16	chr3:69928600-69951000	Weak transcription	Lung	lung
17	chr3:69931200-69937800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:69931800-69937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:69932200-69936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:69933200-69937600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:69933400-69938200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:69934000-69939000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:69934200-69936200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:69934200-69937600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:69934200-69939400	Weak transcription	Hela-S3	cervix
26	chr3:69934400-69936800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:69934600-69937600	Weak transcription	Aorta	Aorta
28	chr3:69934600-69937800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:69934600-69942600	Weak transcription	Adipose Nuclei	Adipose
30	chr3:69934600-69943600	Weak transcription	Left Ventricle	heart
31	chr3:69935000-69938400	Enhancers	Fetal Heart	heart
32	chr3:69935400-69939000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:69935400-69950800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:69935600-69936000	Enhancers	A549	lung
35	chr3:69935600-69937600	Weak transcription	Psoas Muscle	Psoas

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