Variant report

Variant	rs17117860
Chromosome Location	chr12:56079465-56079466
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56078399..56079918-chr12:56113267..56115019,2	MCF-7	breast:
2	chr12:56077843..56081069-chr12:56095100..56098094,3	MCF-7	breast:
3	chr12:56078186..56081182-chr12:56100660..56102322,2	MCF-7	breast:
4	chr12:56078416..56081185-chr12:56082765..56084548,2	MCF-7	breast:
5	chr12:56078568..56080689-chr12:56121513..56124758,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135437	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000135424	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11613875	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11615467	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17117883	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17117895	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]
rs60169753	0.96[EUR][1000 genomes]
rs73119213	0.87[AMR][1000 genomes];0.90[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	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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56075600-56081600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:56075800-56079600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:56075800-56079800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:56075800-56081400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:56075800-56081400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:56075800-56081800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:56075800-56100200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:56076000-56079600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:56076000-56080400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:56076000-56080800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56076000-56087400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:56076000-56097600	Weak transcription	Gastric	stomach
13	chr12:56076000-56100200	Weak transcription	Ovary	ovary
14	chr12:56076200-56080200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:56076200-56081400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:56076200-56081600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:56076200-56085600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:56076200-56086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:56076200-56086400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:56076200-56086400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:56076200-56086800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:56076400-56079600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:56076400-56079600	Weak transcription	Pancreas	Pancrea
24	chr12:56076400-56080200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:56076400-56080400	Weak transcription	Brain Substantia Nigra	brain
26	chr12:56076400-56098400	Weak transcription	Fetal Brain Female	brain
27	chr12:56076800-56093200	Weak transcription	Fetal Heart	heart
28	chr12:56076800-56099800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:56077000-56080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:56077000-56081000	Weak transcription	A549	lung
31	chr12:56077000-56081200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:56077000-56081600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:56077000-56083000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:56077000-56084400	Weak transcription	Colonic Mucosa	Colon
35	chr12:56077000-56089400	Weak transcription	HepG2	liver
36	chr12:56077400-56083400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:56077600-56081600	Weak transcription	Primary B cells from cord blood	blood
38	chr12:56077600-56082400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56077600-56083600	Strong transcription	Fetal Muscle Leg	muscle
40	chr12:56077600-56094200	Weak transcription	Psoas Muscle	Psoas
41	chr12:56077800-56094400	Weak transcription	Right Atrium	heart
42	chr12:56078000-56080200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:56078000-56080400	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:56078000-56083600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:56078200-56080000	Weak transcription	Left Ventricle	heart
46	chr12:56078200-56080600	Genic enhancers	HSMM	muscle
47	chr12:56078200-56086600	Weak transcription	Brain Germinal Matrix	brain
48	chr12:56078400-56080000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:56078400-56080600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:56078400-56083000	Strong transcription	H9 Cell Line	embryonic stem cell

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