Variant report

Variant	rs3759446
Chromosome Location	chr13:96297339-96297340
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	POLR2A	chr13:96296661-96297405	U87	brain:	n/a	n/a
2	MAZ	chr13:96295452-96297528	IMR90	lung:	n/a	chr13:96297462-96297473 chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297463-96297470 chr13:96296387-96296396 chr13:96297462-96297471 chr13:96297034-96297043 chr13:96297035-96297044
3	MAX	chr13:96295692-96297485	HepG2	liver:	n/a	chr13:96297462-96297473 chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297463-96297470 chr13:96296387-96296396 chr13:96297462-96297471 chr13:96297034-96297043 chr13:96297035-96297044
4	JUND	chr13:96297190-96297390	HepG2	liver:	n/a	n/a
5	REST	chr13:96295983-96297372	H1-neurons	neurons:	n/a	chr13:96296052-96296062 chr13:96296534-96296547 chr13:96296483-96296496
6	POLR2A	chr13:96296680-96297345	SK-N-SH	brain:	n/a	n/a
7	USF2	chr13:96296851-96297438	H1-hESC	embryonic stem cell:	n/a	chr13:96297020-96297036
8	POLR2A	chr13:96296285-96297491	PFSK-1	brain:	n/a	n/a
9	MAX	chr13:96295785-96297576	HepG2	liver:	n/a	chr13:96297462-96297473 chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297463-96297470 chr13:96296387-96296396 chr13:96297462-96297471 chr13:96297034-96297043 chr13:96297035-96297044
10	E2F6	chr13:96296710-96297350	A549	lung:	n/a	chr13:96297046-96297055
11	E2F6	chr13:96295786-96297432	H1-hESC	embryonic stem cell:	n/a	chr13:96297046-96297055 chr13:96296158-96296167
12	USF1	chr13:96296734-96297359	SK-N-SH	brain:	n/a	chr13:96297020-96297036 chr13:96297032-96297043
13	POLR2A	chr13:96295760-96297571	HepG2	liver:	n/a	n/a
14	MYC	chr13:96296946-96297490	HepG2	liver:	n/a	chr13:96297462-96297473 chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297463-96297470 chr13:96297462-96297471 chr13:96297034-96297043 chr13:96297035-96297044
15	MAX	chr13:96296083-96297344	HepG2	liver:	n/a	chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96296387-96296396 chr13:96297034-96297043 chr13:96297035-96297044
16	CHD1	chr13:96297013-96297346	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr13:96296918-96297362	A549	lung:	n/a	chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297034-96297043 chr13:96297035-96297044
18	MAX	chr13:96295794-96297454	A549	lung:	n/a	chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96296387-96296396 chr13:96297034-96297043 chr13:96297035-96297044
19	POLR2A	chr13:96295672-96297419	HUVEC	blood vessel:	n/a	n/a
20	MXI1	chr13:96295623-96297515	IMR90	lung:	n/a	chr13:96296951-96296966 chr13:96297033-96297042 chr13:96297035-96297044
21	POLR2A	chr13:96296667-96297399	U87	brain:	n/a	n/a
22	MXI1	chr13:96294038-96297559	SK-N-SH	brain:	n/a	chr13:96296951-96296966 chr13:96297033-96297042 chr13:96297035-96297044
23	POLR2A	chr13:96296744-96297366	HUVEC	blood vessel:	n/a	n/a
24	HEY1	chr13:96296646-96297352	HepG2	liver:	n/a	n/a
25	POLR2A	chr13:96296745-96297390	PFSK-1	brain:	n/a	n/a
26	MAX	chr13:96295874-96297352	A549	lung:	n/a	chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96296387-96296396 chr13:96297034-96297043 chr13:96297035-96297044
27	MYC	chr13:96296987-96297476	MCF10A-Er-Src	breast:	n/a	chr13:96297462-96297473 chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96297463-96297470 chr13:96297462-96297471 chr13:96297034-96297043 chr13:96297035-96297044
28	POLR2A	chr13:96296670-96297465	HUVEC	blood vessel:	n/a	n/a
29	TAF1	chr13:96296024-96297352	H1-hESC	embryonic stem cell:	n/a	n/a
30	RFX5	chr13:96295412-96298024	SK-N-SH	brain:	n/a	chr13:96297734-96297748
31	RFX5	chr13:96296734-96297384	HepG2	liver:	n/a	n/a
32	MAX	chr13:96295758-96297350	SK-N-SH	brain:	n/a	chr13:96297033-96297044 chr13:96297033-96297043 chr13:96297033-96297044 chr13:96297032-96297045 chr13:96296387-96296396 chr13:96297034-96297043 chr13:96297035-96297044
33	RFX5	chr13:96296917-96297415	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr13:96295555-96297516	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr13:96297148-96297352	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:96297338-96297388	HCT-116	colon:	n/a
2	chr13:96297338-96297388	NH-A	brain:	n/a
3	chr13:96297338-96297388	SAEC	small airway:	n/a
4	chr13:96297338-96297388	PFSK-1	brain:	n/a
5	chr13:96297338-96297388	SK-N-SH_RA	brain:	n/a
6	chr13:96297338-96297388	A549	lung:	n/a
7	chr13:96297338-96297388	HCF	heart:	n/a
8	chr13:96297338-96297388	HUVEC	blood vessel:	n/a
9	chr13:96297338-96297388	HAEpiC	amniotic membrane:	n/a
10	chr13:96297338-96297388	PANC-1	pancreas:	n/a
11	chr13:96297338-96297388	NHDF-neo	bronchial:	n/a
12	chr13:96297338-96297388	MCF10A-Er-Src	breast:	n/a
13	chr13:96297338-96297388	HEK293	kidney:	embryo
14	chr13:96297338-96297388	GM12878	blood:	n/a
15	chr13:96297338-96297388	NHBE	bronchial:	n/a
16	chr13:96297338-96297388	Hela-S3	cervix:	n/a
17	chr13:96297338-96297388	GM06990	blood:	n/a
18	chr13:96297338-96297388	HRCEpiC	kidney:	n/a
19	chr13:96297338-96297388	HRE	kidney:	n/a
20	chr13:96297338-96297388	IMR90	lung:	fetal
21	chr13:96297338-96297388	MCF-7	breast:	n/a
22	chr13:96297338-96297388	AoSMC	blood vessel:	n/a
23	chr13:96297338-96297388	HNPCEpiC	eye:	n/a
24	chr13:96297338-96297388	LNCaP	prostate:	n/a
25	chr13:96297338-96297388	HL-60	blood:	n/a
26	chr13:96297338-96297388	Hepatocyte	liver:	n/a
27	chr13:96297338-96297388	HCM	heart:	n/a
28	chr13:96297338-96297388	HCPEpiC	choroid plexus:	n/a
29	chr13:96297338-96297388	AG09309	skin:	n/a
30	chr13:96297338-96297388	HIPEpiC	eye:	n/a
31	chr13:96297338-96297388	NT2-D1	testis:	n/a
32	chr13:96297338-96297388	HPAEpiC	pulmonary alveolar:	n/a
33	chr13:96297338-96297388	K562	blood:	n/a
34	chr13:96297338-96297388	SK-N-SH	brain:	n/a
35	chr13:96297338-96297388	AG10803	skin:	n/a
36	chr13:96297338-96297388	ovcar-3	ovarian:	n/a
37	chr13:96297338-96297388	GM12891	blood:	n/a
38	chr13:96297338-96297388	GM12892	blood:	n/a
39	chr13:96297338-96297388	RPTEC	kidney:	n/a
40	chr13:96297338-96297388	BJ	skin:	n/a
41	chr13:96297338-96297388	HRPEpiC	eye:	n/a
42	chr13:96297338-96297388	HEEpiC	esophagus:	n/a
43	chr13:96297338-96297388	T-47D	breast:	n/a
44	chr13:96297338-96297388	AG04449	skin:	fetal
45	chr13:96297338-96297388	HepG2	liver:	n/a
46	chr13:96297338-96297388	SK-N-MC	brain:	n/a
47	chr13:96297338-96297388	NB4	blood:	n/a
48	chr13:96297338-96297388	U87	brain:	n/a
49	chr13:96297338-96297388	H1-hESC	embryonic stem cell:	embryo
50	chr13:96297338-96297388	HMEC	breast:	n/a

Variant related genes	Relation type
DZIP1	TF binding region
DZIP1	CpG island

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12583374	0.85[EUR][1000 genomes]
rs12585001	0.85[EUR][1000 genomes]
rs17235334	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17882362	0.83[EUR][1000 genomes]
rs3742151	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3848075	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs4536336	0.82[CEU][hapmap]
rs4773918	0.85[CEU][hapmap]
rs58498169	0.83[EUR][1000 genomes]
rs60253451	0.85[EUR][1000 genomes]
rs6492811	0.82[CEU][hapmap]
rs72632666	0.85[EUR][1000 genomes]
rs72632667	0.83[EUR][1000 genomes]
rs7321311	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556491	0.85[CEU][hapmap]
rs9556493	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9556494	0.83[EUR][1000 genomes]
rs9561918	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9561919	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561920	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561921	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9561922	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561933	1.00[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9561938	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs9669929	0.83[EUR][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	nsv900934	chr13:96255706-96327574	Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3330095	chr13:96281000-96297421	Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96293400-96297400	Active TSS	Fetal Kidney	kidney
2	chr13:96293400-96297600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:96293600-96297600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr13:96293800-96297800	Active TSS	Stomach Smooth Muscle	stomach
5	chr13:96294000-96297400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:96294000-96297600	Active TSS	Ovary	ovary
7	chr13:96294000-96297600	Active TSS	NHLF	lung
8	chr13:96294400-96297400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:96294600-96297400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:96295200-96297600	Bivalent/Poised TSS	Fetal Lung	lung
11	chr13:96295400-96297600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:96295400-96297600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:96295400-96297600	Active TSS	NHDF-Ad	bronchial
14	chr13:96295600-96297400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:96295600-96297400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:96295600-96297600	Active TSS	Muscle Satellite Cultured Cells	--
17	chr13:96295600-96297600	Active TSS	A549	lung
18	chr13:96295600-96297600	Active TSS	GM12878-XiMat	blood
19	chr13:96295800-96297400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:96295800-96297400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
21	chr13:96295800-96297400	Active TSS	Right Atrium	heart
22	chr13:96295800-96297600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr13:96295800-96297600	Active TSS	HSMMtube	muscle
24	chr13:96295800-96297800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:96296000-96297400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr13:96296000-96297400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr13:96296000-96297400	Active TSS	Brain Substantia Nigra	brain
28	chr13:96296000-96297400	Bivalent/Poised TSS	Thymus	Thymus
29	chr13:96296000-96297400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr13:96296000-96297600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:96296000-96297600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:96296000-96297600	Active TSS	Brain Anterior Caudate	brain
33	chr13:96296000-96297600	Active TSS	Colon Smooth Muscle	Colon
34	chr13:96296200-96297400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr13:96296200-96297400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr13:96296200-96297400	Enhancers	Primary B cells from peripheral blood	blood
37	chr13:96296200-96297400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
38	chr13:96296200-96297400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr13:96296200-96297400	Active TSS	Brain Cingulate Gyrus	brain
40	chr13:96296200-96297400	Active TSS	Fetal Brain Male	brain
41	chr13:96296200-96297400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
42	chr13:96296200-96297400	Flanking Active TSS	Pancreas	Pancrea
43	chr13:96296200-96297600	Active TSS	Brain Angular Gyrus	brain
44	chr13:96296400-96297400	Active TSS	Right Ventricle	heart
45	chr13:96296600-96297400	Active TSS	Left Ventricle	heart
46	chr13:96296600-96297400	Bivalent Enhancer	Small Intestine	intestine
47	chr13:96296800-96297400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr13:96296800-96297400	Active TSS	Brain Germinal Matrix	brain
49	chr13:96296800-96297400	Enhancers	Spleen	Spleen
50	chr13:96297000-96297400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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