Variant report

Variant	rs2286562
Chromosome Location	chr17:66539847-66539848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:66535303-66540040	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:66539462-66539848	HepG2	liver:	n/a	n/a
3	FOSL2	chr17:66539523-66540107	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:66528378-66541028	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66509250..66511874-chr17:66538190..66540879,2	MCF-7	breast:

Variant related genes	Relation type
FAM20A	TF binding region
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2286560	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286561	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968898	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap]
rs8079916	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv510723	chr17:66529668-66557425	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522126	chr17:66538239-66548457	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2286562	PRKCA	cis	parietal	SCAN
rs2286562	CACNG1	cis	cerebellum	SCAN
rs2286562	PRKAR1A	cis	multi-tissue	Pritchard
rs2286562	CCDC46	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:66526800-66540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:66531400-66540000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:66531800-66540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:66532400-66540200	Strong transcription	Osteobl	bone
8	chr17:66533000-66555200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:66533800-66545400	Weak transcription	Psoas Muscle	Psoas
10	chr17:66533800-66549800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:66534000-66541400	Weak transcription	Colon Smooth Muscle	Colon
12	chr17:66534000-66541800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:66534000-66552800	Weak transcription	Fetal Kidney	kidney
14	chr17:66534200-66563200	Weak transcription	Ovary	ovary
15	chr17:66534800-66554200	Weak transcription	NHDF-Ad	bronchial
16	chr17:66535000-66540000	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:66535200-66542800	Weak transcription	Fetal Brain Female	brain
18	chr17:66535400-66540200	Genic enhancers	Liver	Liver
19	chr17:66536200-66540200	Weak transcription	Right Atrium	heart
20	chr17:66536400-66540000	Strong transcription	Fetal Muscle Leg	muscle
21	chr17:66536400-66541400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:66536600-66542600	Weak transcription	Pancreas	Pancrea
23	chr17:66536800-66540200	Weak transcription	Fetal Lung	lung
24	chr17:66536800-66540200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr17:66536800-66540200	Weak transcription	HSMMtube	muscle
26	chr17:66536800-66540800	Weak transcription	Fetal Heart	heart
27	chr17:66537000-66540200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:66537000-66540200	Strong transcription	Placenta	Placenta
29	chr17:66537000-66543800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:66537000-66544400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr17:66537200-66540200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr17:66537200-66550600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr17:66537200-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:66537400-66541400	Weak transcription	NHLF	lung
35	chr17:66537400-66548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:66537400-66551800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:66537600-66543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:66537600-66543600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr17:66537600-66545400	Weak transcription	Primary T cells from cord blood	blood
40	chr17:66537800-66540600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr17:66537800-66540600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:66537800-66543000	Weak transcription	Brain Anterior Caudate	brain
43	chr17:66537800-66544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:66537800-66550600	Weak transcription	Left Ventricle	heart
45	chr17:66537800-66562600	Weak transcription	HepG2	liver
46	chr17:66538200-66541000	Enhancers	Stomach Mucosa	stomach
47	chr17:66538200-66542800	Weak transcription	Fetal Intestine Large	intestine
48	chr17:66538200-66543000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr17:66538200-66551000	Weak transcription	Right Ventricle	heart
50	chr17:66538200-66554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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