Variant report

Variant	rs2302235
Chromosome Location	chr17:66538418-66538419
allele	A/G
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	chr17:66534614-66539539	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:66535238-66538921	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:66537270-66538700	A549	lung:	n/a	n/a
5	POLR2A	chr17:66538069-66538794	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr17:66537945-66538465	H1-neurons	neurons:	n/a	n/a
7	FOSL2	chr17:66535224-66539318	HepG2	liver:	n/a	chr17:66536355-66536369 chr17:66537173-66537182
8	POLR2A	chr17:66537282-66538908	HepG2	liver:	n/a	n/a
9	POLR2A	chr17:66537968-66539466	HepG2	liver:	n/a	n/a
10	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
ENSG00000269657	TF binding region
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10468444	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10491176	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[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];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16973034	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015212	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	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55736761	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56112060	0.81[ASN][1000 genomes]
rs7221724	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847781	0.85[ASN][1000 genomes]
rs72847782	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72847784	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847785	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72847789	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847790	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847794	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847801	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74000753	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067357	0.81[ASN][1000 genomes]
rs8072598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8082254	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[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];0.96[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2302235	WIPI1	cis	multi-tissue	Pritchard
rs2302235	PRKAR1A	cis	multi-tissue	Pritchard
rs2302235	WIPI1	cis	cerebellum	SCAN
rs2302235	AMZ2P1	cis	parietal	SCAN
rs2302235	PITPNC1	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66520400-66539800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:66523200-66542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:66523600-66538800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:66525400-66538600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr17:66526000-66539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr17:66526600-66539800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:66526800-66540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:66527600-66554200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:66530800-66539200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr17:66531200-66552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:66531400-66538800	Strong transcription	Fetal Stomach	stomach
12	chr17:66531400-66539200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr17:66531400-66540000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:66531800-66540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:66532400-66540200	Strong transcription	Osteobl	bone
16	chr17:66532800-66539600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:66533000-66555200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:66533200-66539200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr17:66533600-66539000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr17:66533800-66545400	Weak transcription	Psoas Muscle	Psoas
21	chr17:66533800-66549800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr17:66534000-66541400	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:66534000-66541800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr17:66534000-66552800	Weak transcription	Fetal Kidney	kidney
25	chr17:66534200-66563200	Weak transcription	Ovary	ovary
26	chr17:66534600-66538800	Weak transcription	GM12878-XiMat	blood
27	chr17:66534600-66539800	Weak transcription	Primary B cells from cord blood	blood
28	chr17:66534800-66554200	Weak transcription	NHDF-Ad	bronchial
29	chr17:66535000-66540000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:66535200-66542800	Weak transcription	Fetal Brain Female	brain
31	chr17:66535400-66540200	Genic enhancers	Liver	Liver
32	chr17:66536200-66538800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:66536200-66539200	Weak transcription	Brain Substantia Nigra	brain
34	chr17:66536200-66540200	Weak transcription	Right Atrium	heart
35	chr17:66536400-66540000	Strong transcription	Fetal Muscle Leg	muscle
36	chr17:66536400-66541400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:66536600-66538800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:66536600-66539800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr17:66536600-66542600	Weak transcription	Pancreas	Pancrea
40	chr17:66536800-66538600	Weak transcription	Aorta	Aorta
41	chr17:66536800-66538800	Strong transcription	Spleen	Spleen
42	chr17:66536800-66539000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr17:66536800-66539200	Weak transcription	HSMM	muscle
44	chr17:66536800-66539800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr17:66536800-66539800	Weak transcription	Fetal Thymus	thymus
46	chr17:66536800-66540200	Weak transcription	Fetal Lung	lung
47	chr17:66536800-66540200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr17:66536800-66540200	Weak transcription	HSMMtube	muscle
49	chr17:66536800-66540800	Weak transcription	Fetal Heart	heart
50	chr17:66537000-66538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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