Variant report

Variant	rs2286557
Chromosome Location	chr17:66535746-66535747
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	chr17:66535309-66537860	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:66535303-66540040	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:66534614-66539539	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:66535673-66536347	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:66533313-66538368	K562	blood:	n/a	n/a
6	RAD21	chr17:66535674-66536017	H1-hESC	embryonic stem cell:	n/a	chr17:66535803-66535822 chr17:66535807-66535816
7	CTCF	chr17:66535700-66535850	GM12867	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
8	CTCF	chr17:66535662-66535959	K562	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
9	CTCF	chr17:66535680-66535830	GM12872	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
10	POLR2A	chr17:66535689-66536363	GM12892	blood:	n/a	n/a
11	UBTF	chr17:66535727-66535775	K562	blood:	n/a	n/a
12	RAD21	chr17:66535715-66535880	K562	blood:	n/a	chr17:66535803-66535822 chr17:66535807-66535816
13	CTCF	chr17:66535740-66535890	HL-60	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
14	CTCF	chr17:66535715-66535931	GM12891	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
15	POLR2A	chr17:66535185-66537181	GM12878	blood:	n/a	n/a
16	CTCF	chr17:66535660-66535810	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr17:66535720-66535870	MCF-7	breast:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
18	CTCF	chr17:66535720-66535870	HMF	breast:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
19	CTCF	chr17:66535718-66535910	K562	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
20	SMC3	chr17:66535638-66535948	HepG2	liver:	n/a	chr17:66535804-66535818
21	CTCF	chr17:66535729-66535897	GM19238	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
22	MXI1	chr17:66535734-66535827	HepG2	liver:	n/a	n/a
23	NFATC1	chr17:66535569-66537195	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:66535627-66536344	K562	blood:	n/a	n/a
25	CTCF	chr17:66535700-66535850	GM12872	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
26	POLR2A	chr17:66535594-66537947	HepG2	liver:	n/a	n/a
27	CTCF	chr17:66535732-66535882	GM19240	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
28	RAD21	chr17:66535577-66536088	MCF-7	breast:	n/a	chr17:66535803-66535822 chr17:66535807-66535816
29	POLR2A	chr17:66535670-66535776	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr17:66535725-66535933	GM10266	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
31	CTCF	chr17:66535740-66535890	Caco-2	colon:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
32	CTCF	chr17:66535740-66535890	HCPEpiC	choroid plexus:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
33	CTCF	chr17:66535703-66535903	LNCaP	prostate:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
34	CTCF	chr17:66535700-66535850	HRE	kidney:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
35	CTCF	chr17:66535740-66535890	NHDF-neo	bronchial:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
36	POLR2A	chr17:66535238-66538921	HepG2	liver:	n/a	n/a
37	CTCF	chr17:66535612-66535978	T-47D	breast:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
38	CTCF	chr17:66535700-66535850	GM12873	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
39	CTCF	chr17:66535590-66536103	MCF-7	breast:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
40	CTCF	chr17:66535720-66535870	HPAF	blood vessel:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
41	POLR2A	chr17:66534939-66538247	PFSK-1	brain:	n/a	n/a
42	CTCF	chr17:66535680-66535830	AG04450	lung:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
43	CTCF	chr17:66535720-66535870	BJ	skin:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
44	CTCF	chr17:66535593-66535955	H1-hESC	embryonic stem cell:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
45	CTCF	chr17:66535704-66535913	MCF-7	breast:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
46	CTCF	chr17:66535740-66535890	GM12873	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
47	CTCF	chr17:66535720-66535870	HA-sp	spinal cord:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
48	CTCF	chr17:66535740-66535890	GM12870	blood:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
49	CTCF	chr17:66535720-66535870	HCFaa	heart:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815
50	CTCF	chr17:66535720-66535870	HVMF	connective:	n/a	chr17:66535803-66535819 chr17:66535804-66535825 chr17:66535807-66535815

No.	Distal block	Cell Line	Cell type
1	chr17:66535353..66536627-chr17:66609171..66610753,8	MCF-7	breast:
2	chr17:66521050..66523596-chr17:66535298..66538130,2	K562	blood:
3	chr17:66533552..66536227-chr17:66536363..66538767,2	K562	blood:
4	chr17:66535403..66536231-chr17:66755796..66756599,3	MCF-7	breast:
5	chr17:66535321..66536318-chr17:66755760..66756719,6	MCF-7	breast:
6	chr17:66510658..66512387-chr17:66534729..66537102,2	MCF-7	breast:
7	chr17:66523700..66527434-chr17:66534416..66537406,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269657	TF binding region
ENSG00000108950	Chromatin interaction
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11867767	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2907375	0.86[ASN][1000 genomes]
rs2907387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952270	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952272	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952273	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2952274	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952317	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56278628	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286557	PRKAR1A	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:66511800-66536600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr17:66511800-66537000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:66511800-66537800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:66514800-66537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:66514800-66537400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:66514800-66537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:66515000-66535800	Strong transcription	Placenta	Placenta
10	chr17:66516600-66535800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:66517200-66537600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:66517400-66537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:66517600-66536800	Strong transcription	Fetal Thymus	thymus
14	chr17:66517600-66537200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:66518000-66535800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:66518000-66536800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:66518000-66537200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:66518200-66536600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr17:66518200-66536800	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr17:66518200-66537600	Strong transcription	Primary T cells from cord blood	blood
21	chr17:66518200-66537800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr17:66518600-66537200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:66518600-66538200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr17:66519000-66537200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr17:66519200-66536800	Strong transcription	Fetal Lung	lung
26	chr17:66519800-66537800	Strong transcription	Brain Anterior Caudate	brain
27	chr17:66520400-66539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:66523400-66535800	Weak transcription	Stomach Mucosa	stomach
30	chr17:66523600-66538800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:66525400-66538600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:66526000-66539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:66526600-66539800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:66526800-66535800	Weak transcription	Right Atrium	heart
35	chr17:66526800-66540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:66527600-66536800	Weak transcription	Small Intestine	intestine
37	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:66527800-66538400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:66529800-66536200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:66529800-66536800	Strong transcription	HSMMtube	muscle
41	chr17:66529800-66537400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr17:66530200-66537200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:66530400-66536800	Strong transcription	HSMM	muscle
44	chr17:66530800-66539200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr17:66531400-66536400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr17:66531400-66537400	Strong transcription	Brain Hippocampus Middle	brain
48	chr17:66531400-66538800	Strong transcription	Fetal Stomach	stomach
49	chr17:66531400-66539200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:66531400-66540000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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