Variant report

Variant	rs17217592
Chromosome Location	chr4:104120119-104120120
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	BHLHE40	chr4:104119284-104120139	HepG2	liver:	n/a	n/a
2	CREB1	chr4:104118773-104120136	K562	blood:	n/a	chr4:104119604-104119617
3	CBX3	chr4:104119119-104120149	K562	blood:	n/a	n/a
4	CHD1	chr4:104119135-104120190	GM12878	blood:	n/a	chr4:104119350-104119360
5	JUND	chr4:104119102-104120207	K562	blood:	n/a	chr4:104119653-104119662 chr4:104119606-104119615 chr4:104119546-104119555
6	POLR2A	chr4:104118428-104120170	GM12878	blood:	n/a	n/a
7	JUND	chr4:104118662-104120212	GM12878	blood:	n/a	chr4:104119653-104119662 chr4:104119071-104119081 chr4:104119606-104119615 chr4:104119546-104119555
8	SREBP1	chr4:104118743-104120309	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:104119020-104120230	GM12892	blood:	n/a	n/a
10	TBL1XR1	chr4:104119455-104120119	K562	blood:	n/a	n/a
11	MAX	chr4:104118943-104120156	ECC-1	luminal epithelium:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
12	MAX	chr4:104118916-104120172	HCT-116	colon:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
13	POLR2A	chr4:104118246-104120125	PBDE	blood:	n/a	n/a
14	BHLHE40	chr4:104119418-104120119	GM12878	blood:	n/a	n/a
15	GATA3	chr4:104119150-104120162	A549	lung:	n/a	n/a
16	MAX	chr4:104119106-104120134	GM12878	blood:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
17	SP1	chr4:104119089-104120208	HCT-116	colon:	n/a	chr4:104119134-104119143 chr4:104119548-104119559
18	POLR2A	chr4:104118766-104120191	SK-N-MC	brain:	n/a	n/a
19	SIN3A	chr4:104119008-104120283	GM12878	blood:	n/a	n/a
20	CREB1	chr4:104119119-104120125	GM12878	blood:	n/a	chr4:104119604-104119617
21	SP1	chr4:104119226-104120120	A549	lung:	n/a	chr4:104119548-104119559
22	MAZ	chr4:104119068-104120143	K562	blood:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
23	SP1	chr4:104119162-104120155	HCT-116	colon:	n/a	chr4:104119548-104119559
24	POLR2A	chr4:104118491-104120225	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA1	chr4:104118990-104120512	PBDE	blood:	n/a	n/a
26	JUND	chr4:104118805-104120329	SK-N-SH	brain:	n/a	chr4:104119653-104119662 chr4:104119071-104119081 chr4:104119606-104119615 chr4:104119546-104119555
27	SIN3AK20	chr4:104118933-104120144	MCF-7	breast:	n/a	n/a
28	POLR2A	chr4:104118198-104120142	GM12891	blood:	n/a	n/a
29	MXI1	chr4:104118264-104120267	SK-N-SH	brain:	n/a	n/a
30	SETDB1	chr4:104119157-104120131	U2OS	brain:	n/a	n/a
31	CHD1	chr4:104118872-104120314	IMR90	lung:	n/a	chr4:104119350-104119360
32	JUN	chr4:104118777-104120295	K562	blood:	n/a	chr4:104119605-104119618 chr4:104119653-104119662 chr4:104119071-104119081 chr4:104119606-104119615 chr4:104119546-104119555

Variant related genes	Relation type
CENPE	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10516498	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs1054707	0.93[ASN][1000 genomes]
rs11724309	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724466	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724522	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11725048	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727029	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729856	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730764	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730765	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734318	0.90[ASN][1000 genomes]
rs11737673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12500951	0.93[ASN][1000 genomes]
rs12504143	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504262	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs12505289	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505908	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506065	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506198	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12507348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508269	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12511516	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381657	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381658	0.87[CHB][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17215785	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17215862	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283027	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283077	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283194	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17522932	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306478	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2720469	0.94[CHD][hapmap];0.81[GIH][hapmap]
rs2866633	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35714833	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3765086	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775972	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796983	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.86[ASN][1000 genomes]
rs3974474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55895342	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56126326	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56138287	0.81[ASN][1000 genomes]
rs56256243	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56378042	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56412006	0.87[ASN][1000 genomes]
rs58648171	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58888668	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59192877	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59341670	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61355145	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533057	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66869812	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6822891	0.94[CEU][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825519	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.87[ASN][1000 genomes]
rs6830791	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6836162	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837114	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840401	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665040	0.93[ASN][1000 genomes]
rs72665042	0.93[ASN][1000 genomes]
rs72665048	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665052	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665054	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665056	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665063	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665071	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665096	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72666812	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736048	0.93[ASN][1000 genomes]
rs746829	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662455	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664021	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7668568	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs7675057	0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs7686105	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7690059	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[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	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17217592	PPP3CA	cis	parietal	SCAN
rs17217592	BDH2	cis	Artery Tibial	GTEx
rs17217592	BDH2	cis	cerebellum	SCAN
rs17217592	BDH2	cis	Thyroid	GTEx
rs17217592	BDH2	cis	lung	GTEx
rs17217592	BDH2	cis	Nerve Tibial	GTEx
rs17217592	BDH2	cis	parietal	SCAN
rs17217592	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs17217592	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs17217592	BDH2	cis	Esophagus Muscularis	GTEx
rs17217592	CENPE	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104117800-104120200	Active TSS	NHDF-Ad	bronchial
2	chr4:104118000-104120200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:104118000-104120200	Active TSS	GM12878-XiMat	blood
4	chr4:104118000-104120400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:104118000-104120400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:104118000-104120400	Active TSS	NHLF	lung
7	chr4:104118200-104120200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:104118200-104120200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:104118200-104120200	Active TSS	Fetal Brain Male	brain
10	chr4:104118200-104120200	Active TSS	K562	blood
11	chr4:104118200-104120400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:104118200-104120400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:104118400-104120200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:104118400-104120200	Active TSS	HSMMtube	muscle
15	chr4:104118400-104120200	Active TSS	Osteobl	bone
16	chr4:104118400-104120400	Active TSS	HSMM	muscle
17	chr4:104118600-104120200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr4:104118600-104120200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:104118600-104120200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:104118600-104120200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:104118600-104120200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:104118600-104120200	Active TSS	Hela-S3	cervix
23	chr4:104118600-104120400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:104118600-104120400	Active TSS	Fetal Muscle Leg	muscle
25	chr4:104118800-104120200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr4:104118800-104120200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:104118800-104120200	Active TSS	Aorta	Aorta
28	chr4:104118800-104120200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:104118800-104120200	Active TSS	Fetal Intestine Small	intestine
30	chr4:104118800-104120200	Active TSS	Fetal Kidney	kidney
31	chr4:104118800-104120200	Active TSS	Fetal Stomach	stomach
32	chr4:104118800-104120200	Active TSS	Right Ventricle	heart
33	chr4:104118800-104120400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:104118800-104120400	Active TSS	Colonic Mucosa	Colon
35	chr4:104118800-104120400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:104118800-104120400	Active TSS	Fetal Lung	lung
37	chr4:104118800-104120400	Active TSS	Stomach Smooth Muscle	stomach
38	chr4:104118800-104120400	Active TSS	NHEK	skin
39	chr4:104119000-104120200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr4:104119000-104120200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:104119000-104120200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:104119000-104120200	Active TSS	Esophagus	oesophagus
43	chr4:104119000-104120200	Active TSS	Left Ventricle	heart
44	chr4:104119000-104120200	Active TSS	Lung	lung
45	chr4:104119000-104120200	Active TSS	Pancreas	Pancrea
46	chr4:104119000-104120200	Active TSS	Psoas Muscle	Psoas
47	chr4:104119000-104120200	Active TSS	Stomach Mucosa	stomach
48	chr4:104119000-104120400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:104119000-104120400	Active TSS	Colon Smooth Muscle	Colon
50	chr4:104119200-104120200	Active TSS	Primary T killer memory cells from peripheral blood	blood

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