Variant report

Variant	rs2952317
Chromosome Location	chr17:66540810-66540811
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	chr17:66528378-66541028	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: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11077609	0.87[JPT][hapmap]
rs11867767	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286556	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286557	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2302234	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2907375	0.88[ASN][1000 genomes]
rs2907387	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2952270	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952272	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952273	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2952274	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56278628	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6958	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2952317	PRKCA	cis	parietal	SCAN
rs2952317	CACNG1	cis	cerebellum	SCAN
rs2952317	PRKAR1A	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 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	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:66533000-66555200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:66533800-66545400	Weak transcription	Psoas Muscle	Psoas
6	chr17:66533800-66549800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr17:66534000-66541400	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:66534000-66541800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr17:66534000-66552800	Weak transcription	Fetal Kidney	kidney
10	chr17:66534200-66563200	Weak transcription	Ovary	ovary
11	chr17:66534800-66554200	Weak transcription	NHDF-Ad	bronchial
12	chr17:66535200-66542800	Weak transcription	Fetal Brain Female	brain
13	chr17:66536400-66541400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr17:66536600-66542600	Weak transcription	Pancreas	Pancrea
15	chr17:66537000-66543800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:66537000-66544400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:66537200-66550600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:66537200-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:66537400-66541400	Weak transcription	NHLF	lung
20	chr17:66537400-66548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:66537400-66551800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:66537600-66543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:66537600-66543600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:66537600-66545400	Weak transcription	Primary T cells from cord blood	blood
25	chr17:66537800-66543000	Weak transcription	Brain Anterior Caudate	brain
26	chr17:66537800-66544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:66537800-66550600	Weak transcription	Left Ventricle	heart
28	chr17:66537800-66562600	Weak transcription	HepG2	liver
29	chr17:66538200-66541000	Enhancers	Stomach Mucosa	stomach
30	chr17:66538200-66542800	Weak transcription	Fetal Intestine Large	intestine
31	chr17:66538200-66543000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:66538200-66551000	Weak transcription	Right Ventricle	heart
33	chr17:66538200-66554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:66538200-66559000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:66538400-66543600	Weak transcription	Adipose Nuclei	Adipose
36	chr17:66538600-66549600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:66538800-66545800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:66538800-66575800	Weak transcription	Spleen	Spleen
39	chr17:66539200-66548000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr17:66539200-66550600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:66539200-66550600	Weak transcription	Lung	lung
42	chr17:66539200-66588000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:66539400-66547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr17:66539600-66542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:66539800-66542400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:66539800-66547800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:66540000-66545800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:66540000-66548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:66540000-66549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:66540200-66541000	Enhancers	Fetal Lung	lung

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