Variant report

Variant	rs12309205
Chromosome Location	chr12:20590019-20590020
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	chr12:20585616..20587176-chr12:20589096..20590820,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11045261	1.00[YRI][hapmap]
rs12308852	1.00[YRI][hapmap]
rs12317699	1.00[AMR][1000 genomes]
rs12318102	1.00[AMR][1000 genomes]
rs12318388	1.00[AMR][1000 genomes]
rs12322107	1.00[YRI][hapmap]
rs4128682	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1042315	chr12:20531641-20629866	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20568600-20595400	Weak transcription	Pancreas	Pancrea
2	chr12:20573800-20599800	Weak transcription	Left Ventricle	heart
3	chr12:20578800-20597000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:20583000-20590600	Weak transcription	Fetal Stomach	stomach
5	chr12:20583800-20592400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:20587200-20590200	Enhancers	Fetal Intestine Large	intestine
7	chr12:20587400-20590600	Enhancers	Fetal Intestine Small	intestine
8	chr12:20587600-20592200	Enhancers	Osteobl	bone
9	chr12:20587600-20599000	Weak transcription	Right Atrium	heart
10	chr12:20587800-20596600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:20588000-20591000	Enhancers	NHDF-Ad	bronchial
12	chr12:20588000-20591400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:20588000-20592000	Enhancers	HUVEC	blood vessel
14	chr12:20588200-20590800	Weak transcription	Right Ventricle	heart
15	chr12:20588200-20591600	Genic enhancers	Hela-S3	cervix
16	chr12:20588200-20618400	Weak transcription	Ovary	ovary
17	chr12:20589000-20593600	Enhancers	Colon Smooth Muscle	Colon
18	chr12:20589200-20596800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:20589200-20597800	Weak transcription	Aorta	Aorta
20	chr12:20589400-20590400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:20589400-20590400	Enhancers	Adipose Nuclei	Adipose
22	chr12:20589400-20590400	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:20589400-20603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:20589600-20590600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:20589600-20591000	Weak transcription	NH-A	brain
26	chr12:20589600-20591200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:20589600-20596800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:20589800-20590200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:20589800-20595400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:20590000-20590800	Weak transcription	Rectal Smooth Muscle	rectum

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