Variant report

Variant	rs4265886
Chromosome Location	chr17:66509892-66509893
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	TCF7L2	chr17:66509189-66510763	HEK293	kidney:	n/a	n/a
2	POLR2A	chr17:66507642-66510297	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr17:66507543-66510391	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr17:66506146-66510554	SK-N-SH	brain:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
5	CHD1	chr17:66507161-66511463	IMR90	lung:	n/a	n/a
6	MXI1	chr17:66507120-66510871	IMR90	lung:	n/a	chr17:66508093-66508102 chr17:66508484-66508499 chr17:66508095-66508104
7	POLR2A	chr17:66507604-66510448	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr17:66509652-66510053	HepG2	liver:	n/a	n/a
9	HCFC1	chr17:66507322-66510244	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr17:66506962-66511766	IMR90	lung:	n/a	n/a
11	CHD1	chr17:66508774-66510043	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:66507294-66509952	PBDE	blood:	n/a	n/a
13	MAZ	chr17:66507665-66509923	K562	blood:	n/a	chr17:66508092-66508101 chr17:66508090-66508105 chr17:66508092-66508107 chr17:66508094-66508104
14	HEY1	chr17:66507334-66509961	HepG2	liver:	n/a	chr17:66507956-66507971 chr17:66508914-66508929 chr17:66508827-66508842 chr17:66507950-66507965 chr17:66508925-66508940 chr17:66508522-66508531
15	SIN3AK20	chr17:66507257-66510385	MCF-7	breast:	n/a	n/a
16	POLR2A	chr17:66507452-66510352	H1-hESC	embryonic stem cell:	n/a	n/a
17	STAT1	chr17:66509847-66509966	GM12878	blood:	n/a	n/a
18	POLR2A	chr17:66508178-66510376	K562	blood:	n/a	n/a
19	CUX1	chr17:66509856-66510056	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:66509860-66509898	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:65820674..65823268-chr17:66508486..66510670,2	MCF-7	breast:
2	chr17:66507304..66510193-chr5:1344921..1346652,2	MCF-7	breast:
3	chr17:66031856..66033575-chr17:66508155..66509939,2	MCF-7	breast:
4	chr17:66287636..66289963-chr17:66508320..66510109,2	K562	blood:
5	chr17:66507070..66510931-chr17:66511371..66513422,6	K562	blood:
6	chr17:66507858..66510140-chr17:66521050..66524441,3	K562	blood:
7	chr17:66451996..66456192-chr17:66506725..66511948,5	MCF-7	breast:
8	chr17:66452513..66457853-chr17:66506674..66510981,7	MCF-7	breast:
9	chr17:66509822..66512031-chr17:66520719..66523833,3	K562	blood:
10	chr17:66509250..66511874-chr17:66538190..66540879,2	MCF-7	breast:

Variant related genes	Relation type
PRKAR1A	TF binding region
ENSG00000141337	Chromatin interaction
ENSG00000049656	Chromatin interaction
ENSG00000269657	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000171634	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000182481	Chromatin interaction
ENSG00000108950	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10468445	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286558	0.82[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302230	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302231	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521534	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2907373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2907374	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952271	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4561532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222188	0.80[CEU][hapmap]
rs8066131	0.80[CEU][hapmap];0.85[MEX][hapmap]
rs8076465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
2	esv3409910	chr17:66507582-66510130	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4265886	WIPI1	cis	multi-tissue	Pritchard
rs4265886	PRKAR1A	cis	parietal	SCAN
rs4265886	WIPI1	cis	parietal	SCAN
rs4265886	CD79B	cis	cerebellum	SCAN
rs4265886	PRKAR1A	cis	multi-tissue	Pritchard
rs4265886	ABCA8	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66507200-66510400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr17:66507200-66510400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr17:66507200-66510800	Active TSS	GM12878-XiMat	blood
4	chr17:66507200-66511400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:66507400-66510000	Active TSS	Brain Substantia Nigra	brain
6	chr17:66507400-66510200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr17:66507400-66510200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr17:66507400-66510200	Active TSS	Brain Cingulate Gyrus	brain
9	chr17:66507400-66510400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:66507400-66510400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr17:66507400-66510600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:66507400-66510600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:66507400-66511000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:66507400-66511000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr17:66507400-66511000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr17:66507400-66511400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:66507400-66513600	Active TSS	Right Ventricle	heart
18	chr17:66507600-66510000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:66507600-66510000	Active TSS	Fetal Brain Female	brain
20	chr17:66507600-66510000	Bivalent/Poised TSS	HepG2	liver
21	chr17:66507600-66510200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:66507600-66510200	Active TSS	Fetal Kidney	kidney
23	chr17:66507600-66510400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr17:66507600-66510400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr17:66507600-66510400	Active TSS	Fetal Intestine Large	intestine
26	chr17:66507600-66510400	Active TSS	Hela-S3	cervix
27	chr17:66507600-66510600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr17:66507600-66510800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:66507600-66510800	Active TSS	NHDF-Ad	bronchial
30	chr17:66507600-66511000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:66507600-66511200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr17:66507600-66511200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr17:66507600-66511200	Active TSS	Left Ventricle	heart
34	chr17:66507600-66511400	Active TSS	Aorta	Aorta
35	chr17:66507600-66511600	Active TSS	Ovary	ovary
36	chr17:66507800-66510000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:66507800-66510000	Active TSS	Duodenum Mucosa	Duodenum
38	chr17:66507800-66510000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr17:66507800-66510000	Active TSS	Stomach Mucosa	stomach
40	chr17:66507800-66510000	Active TSS	A549	lung
41	chr17:66507800-66510200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:66507800-66510200	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr17:66507800-66510200	Active TSS	Placenta	Placenta
44	chr17:66507800-66510400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:66507800-66510400	Active TSS	Fetal Intestine Small	intestine
46	chr17:66507800-66510400	Active TSS	Fetal Stomach	stomach
47	chr17:66507800-66510400	Active TSS	Osteobl	bone
48	chr17:66507800-66510600	Active TSS	NH-A	brain
49	chr17:66507800-66510600	Active TSS	NHEK	skin
50	chr17:66507800-66510800	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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