Variant report

Variant	rs17275724
Chromosome Location	chr4:152677580-152677581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:152675736..152679885-chr4:152680808..152682883,3	MCF-7	breast:
2	chr4:152676281..152678380-chr4:152680152..152682713,2	MCF-7	breast:
3	chr4:152675205..152679978-chr4:152680175..152683164,9	K562	blood:

Variant related genes	Relation type
ENSG00000059691	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1107797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649199	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35434409	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696288	0.94[GIH][hapmap]
rs4696289	0.94[GIH][hapmap]
rs62328981	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62328982	0.95[ASN][1000 genomes]
rs72730165	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[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	nsv508322	chr4:152617079-152678951	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17275724	PET112L	cis	multi-tissue	Pritchard
rs17275724	FAM160A1	cis	cerebellum	SCAN
rs17275724	PET112L	cis	cerebellum	SCAN
rs17275724	PPAPDC1B	trans	cerebellum	SCAN
rs17275724	PET112L	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152629200-152681400	Weak transcription	Colonic Mucosa	Colon
2	chr4:152629400-152681200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:152651800-152681400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:152657800-152677600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:152658600-152681200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:152659000-152681400	Weak transcription	Pancreas	Pancrea
7	chr4:152659400-152678400	Weak transcription	Fetal Stomach	stomach
8	chr4:152659400-152681400	Weak transcription	Thymus	Thymus
9	chr4:152659600-152681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:152659800-152681400	Weak transcription	Spleen	Spleen
11	chr4:152660800-152681000	Weak transcription	Fetal Lung	lung
12	chr4:152662600-152681400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:152665400-152681400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:152666200-152681200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:152666400-152681000	Weak transcription	HUVEC	blood vessel
16	chr4:152666400-152681200	Weak transcription	Hela-S3	cervix
17	chr4:152666600-152681200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:152666800-152681200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:152667000-152681200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:152667200-152681000	Weak transcription	GM12878-XiMat	blood
21	chr4:152667400-152678800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:152667400-152681000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:152667400-152681000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:152667400-152681200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:152667400-152681200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:152667400-152681200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:152667400-152681200	Weak transcription	HSMMtube	muscle
28	chr4:152667400-152681200	Weak transcription	NHDF-Ad	bronchial
29	chr4:152667600-152681200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:152667800-152681200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:152668000-152681200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:152668000-152681200	Weak transcription	Fetal Brain Female	brain
33	chr4:152668000-152681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:152668000-152681400	Weak transcription	Fetal Brain Male	brain
35	chr4:152668400-152681200	Weak transcription	Fetal Heart	heart
36	chr4:152668600-152677800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:152668600-152678800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:152668600-152681200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:152668600-152681200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:152668600-152681200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:152668600-152681200	Weak transcription	K562	blood
42	chr4:152668600-152681200	Weak transcription	NHLF	lung
43	chr4:152668600-152681400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:152668600-152681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:152668600-152681800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:152670000-152681200	Weak transcription	Brain Germinal Matrix	brain
47	chr4:152670800-152680000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:152671200-152679800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:152671200-152679800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:152671400-152680000	Strong transcription	Primary monocytes fromperipheralblood	blood

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