Variant report

Variant	rs12341853
Chromosome Location	chr9:71948229-71948230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71937291..71938805-chr9:71947853..71950647,2	MCF-7	breast:
2	chr9:71939962..71941547-chr9:71947725..71950010,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11138090	1.00[EUR][1000 genomes]
rs11138097	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11138118	1.00[EUR][1000 genomes]
rs11138262	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11138263	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11138400	1.00[EUR][1000 genomes]
rs11138419	1.00[EUR][1000 genomes]
rs12343852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13440045	1.00[EUR][1000 genomes]
rs1890633	1.00[EUR][1000 genomes]
rs41277901	1.00[EUR][1000 genomes]
rs45534236	1.00[EUR][1000 genomes]
rs7018704	1.00[EUR][1000 genomes]
rs73450886	1.00[EUR][1000 genomes]
rs73450889	1.00[EUR][1000 genomes]
rs73450890	1.00[EUR][1000 genomes]
rs73452911	1.00[EUR][1000 genomes]
rs73452916	1.00[EUR][1000 genomes]
rs73452956	1.00[EUR][1000 genomes]
rs7857529	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71941400-71954400	Weak transcription	Brain Anterior Caudate	brain
2	chr9:71941600-71948600	Weak transcription	Pancreas	Pancrea
3	chr9:71941600-71950400	Weak transcription	Gastric	stomach
4	chr9:71942200-71950400	Weak transcription	Lung	lung
5	chr9:71942400-71950200	Weak transcription	Ovary	ovary
6	chr9:71942800-71954400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:71943200-71954400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:71944600-71954400	Weak transcription	Brain Substantia Nigra	brain
9	chr9:71947000-71948600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:71947000-71948600	Enhancers	Fetal Heart	heart
11	chr9:71947000-71949200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:71947000-71950400	Weak transcription	Psoas Muscle	Psoas
13	chr9:71947000-71958000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:71947200-71948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:71947200-71949800	Weak transcription	Left Ventricle	heart
16	chr9:71947200-71950200	Weak transcription	Esophagus	oesophagus
17	chr9:71947200-71954400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:71947200-71962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:71947400-71948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:71947400-71948600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:71947400-71948600	Weak transcription	NHEK	skin
22	chr9:71947400-71948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:71947400-71948800	Weak transcription	HMEC	breast
24	chr9:71947400-71949400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:71947400-71954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:71947600-71954400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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