Variant report

Variant	rs17117895
Chromosome Location	chr12:56098038-56098039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56077843..56081069-chr12:56095100..56098094,3	MCF-7	breast:
2	chr12:56096566..56098722-chr12:56101494..56103396,3	MCF-7	breast:
3	chr12:56097491..56100308-chr12:56113944..56117371,3	MCF-7	breast:
4	chr12:56097454..56102551-chr12:56112712..56115569,4	K562	blood:
5	chr12:56097086..56099031-chr12:56120037..56122459,2	MCF-7	breast:
6	chr12:56097396..56100187-chr12:56115850..56119057,3	K562	blood:
7	chr12:56097683..56101323-chr12:56135881..56138296,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135424	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000135437	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11613875	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11615467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17117860	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17117883	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60169753	1.00[EUR][1000 genomes]
rs73119213	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56075800-56100200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:56076000-56100200	Weak transcription	Ovary	ovary
3	chr12:56076400-56098400	Weak transcription	Fetal Brain Female	brain
4	chr12:56076800-56099800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:56081000-56098800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:56082200-56099000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:56088000-56098800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:56089600-56099400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:56090000-56098600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56090200-56099200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:56090200-56099400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:56090200-56100000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:56090600-56099800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56091000-56099400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:56092000-56099200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:56093600-56099000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:56095200-56099200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:56095200-56099600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:56095200-56099800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:56095200-56100600	Weak transcription	Esophagus	oesophagus
21	chr12:56096200-56101600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:56096400-56098400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:56096600-56098200	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr12:56096600-56098600	Transcr. at gene 5' and 3'	HSMM	muscle
25	chr12:56096600-56099200	Flanking Active TSS	HSMMtube	muscle
26	chr12:56096600-56101600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr12:56096800-56098400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:56096800-56098400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr12:56096800-56098600	Enhancers	Brain Angular Gyrus	brain
30	chr12:56096800-56098600	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr12:56096800-56099200	Bivalent Enhancer	Fetal Stomach	stomach
32	chr12:56097000-56101000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:56097000-56102400	Active TSS	Right Ventricle	heart
34	chr12:56097200-56098200	Enhancers	Spleen	Spleen
35	chr12:56097200-56098600	Enhancers	NHLF	lung
36	chr12:56097200-56099000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:56097200-56099000	Bivalent Enhancer	HepG2	liver
38	chr12:56097200-56100200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr12:56097200-56100800	Enhancers	Brain Germinal Matrix	brain
40	chr12:56097400-56098200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:56097400-56098200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:56097400-56098400	Flanking Active TSS	Right Atrium	heart
43	chr12:56097400-56098600	Enhancers	Brain Cingulate Gyrus	brain
44	chr12:56097400-56098600	Active TSS	Colon Smooth Muscle	Colon
45	chr12:56097400-56098800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr12:56097400-56099800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:56097400-56100000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:56097400-56100000	Weak transcription	Colonic Mucosa	Colon
49	chr12:56097400-56101000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:56097400-56101000	Flanking Active TSS	Osteobl	bone

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