Variant report

Variant	rs2015212
Chromosome Location	chr17:66536749-66536750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

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	chr17:66533313-66538368	K562	blood:	n/a	n/a
5	POLR2A	chr17:66536375-66537479	K562	blood:	n/a	n/a
6	POLR2A	chr17:66536711-66537499	U87	brain:	n/a	n/a
7	POLR2A	chr17:66535185-66537181	GM12878	blood:	n/a	n/a
8	NFATC1	chr17:66535569-66537195	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:66535594-66537947	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:66536574-66536849	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr17:66535238-66538921	HepG2	liver:	n/a	n/a
12	POLR2A	chr17:66534939-66538247	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:66536389-66537073	HepG2	liver:	n/a	n/a
14	POLR2A	chr17:66536705-66537534	U87	brain:	n/a	n/a
15	POLR2A	chr17:66536686-66537038	HCT-116	colon:	n/a	n/a
16	POLR2A	chr17:66536670-66536871	K562	blood:	n/a	n/a
17	POLR2A	chr17:66536497-66536774	MCF-7	breast:	n/a	n/a
18	POLR2A	chr17:66534364-66536999	HepG2	liver:	n/a	n/a
19	POLR2A	chr17:66535301-66536759	GM12891	blood:	n/a	n/a
20	FOSL2	chr17:66535224-66539318	HepG2	liver:	n/a	chr17:66536355-66536369 chr17:66537173-66537182
21	POLR2A	chr17:66536725-66537100	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:66535960-66537843	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr17:66535644-66537036	GM12891	blood:	n/a	n/a
24	POLR2A	chr17:66536535-66538172	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr17:66536433-66536933	HCT-116	colon:	n/a	n/a
26	POLR2A	chr17:66535601-66537170	HL-60	blood:	n/a	n/a
27	POLR2A	chr17:66536354-66536917	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr17:66528378-66541028	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:66521050..66523596-chr17:66535298..66538130,2	K562	blood:
2	chr17:66510658..66512387-chr17:66534729..66537102,2	MCF-7	breast:
3	chr17:66523700..66527434-chr17:66534416..66537406,5	MCF-7	breast:

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10468444	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10491176	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10852738	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs16972996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16973034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302235	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785905	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55736761	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56112060	0.83[ASN][1000 genomes]
rs7221724	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847781	0.86[ASN][1000 genomes]
rs72847782	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847784	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72847785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847790	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74000753	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8067357	0.83[ASN][1000 genomes]
rs8072598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8082254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2015212	PITPNC1	cis	cerebellum	SCAN
rs2015212	WIPI1	cis	cerebellum	SCAN
rs2015212	AMZ2P1	cis	parietal	SCAN

Chromatin state (count:120 , 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	chr17:66511800-66537000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:66511800-66537800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:66514800-66537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:66514800-66537400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:66514800-66537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:66517200-66537600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:66517400-66537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:66517600-66536800	Strong transcription	Fetal Thymus	thymus
11	chr17:66517600-66537200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:66518000-66536800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:66518000-66537200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:66518200-66536800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr17:66518200-66537600	Strong transcription	Primary T cells from cord blood	blood
16	chr17:66518200-66537800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr17:66518600-66537200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:66518600-66538200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:66519000-66537200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr17:66519200-66536800	Strong transcription	Fetal Lung	lung
21	chr17:66519800-66537800	Strong transcription	Brain Anterior Caudate	brain
22	chr17:66520400-66539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr17:66523600-66538800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:66525400-66538600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:66526000-66539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:66526600-66539800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:66526800-66540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:66527600-66536800	Weak transcription	Small Intestine	intestine
30	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:66527800-66538400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:66529800-66536800	Strong transcription	HSMMtube	muscle
33	chr17:66529800-66537400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:66530200-66537200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:66530400-66536800	Strong transcription	HSMM	muscle
36	chr17:66530800-66539200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr17:66531400-66537400	Strong transcription	Brain Hippocampus Middle	brain
39	chr17:66531400-66538800	Strong transcription	Fetal Stomach	stomach
40	chr17:66531400-66539200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:66531400-66540000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:66531600-66537800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:66531600-66538400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:66531800-66537400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:66531800-66540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:66532000-66537400	Strong transcription	NHLF	lung
47	chr17:66532000-66537800	Strong transcription	Gastric	stomach
48	chr17:66532200-66537200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:66532200-66537800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:66532400-66537600	Weak transcription	Hela-S3	cervix

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