Variant report

Variant	rs3798480
Chromosome Location	chr6:36354512-36354513
allele	C/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	CTCF	chr6:36354480-36354630	HCM	heart:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
2	CTCF	chr6:36354500-36354650	HVMF	connective:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
3	CTCF	chr6:36354480-36354630	HPF	lung:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
4	CTCF	chr6:36354487-36354669	IMR90	lung:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
5	CTCF	chr6:36354460-36354610	HCFaa	heart:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
6	CTCF	chr6:36354480-36354630	AG10803	skin:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
7	CTCF	chr6:36354500-36354650	SK-N-SH_RA	brain:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
8	CTCF	chr6:36354400-36354550	RPTEC	kidney:	n/a	n/a
9	MXI1	chr6:36354455-36354638	GM12878	blood:	n/a	n/a
10	CTCF	chr6:36354500-36354650	HFF	foreskin:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
11	POLR2A	chr6:36354422-36354609	GM12878	blood:	n/a	n/a
12	SIN3A	chr6:36354307-36355805	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr6:36354420-36354570	HCT-116	colon:	n/a	n/a
14	TBP	chr6:36354506-36355165	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr6:36354480-36354630	HUVEC	blood vessel:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
16	CTCF	chr6:36354500-36354650	AG09309	skin:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
17	CTCF	chr6:36354500-36354650	BJ	skin:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
18	CTCF	chr6:36354460-36354610	GM12866	blood:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
19	TAF1	chr6:36354507-36354858	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr6:36354420-36354570	GM12873	blood:	n/a	n/a
21	CTCF	chr6:36354500-36354650	HCPEpiC	choroid plexus:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
22	CTCF	chr6:36354500-36354650	AoAF	blood vessel:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
23	CTCF	chr6:36354460-36354610	Hela-S3	cervix:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
24	NFIC	chr6:36354103-36354893	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr6:36354460-36354610	HBMEC	blood vessel:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
26	POLR2A	chr6:36354459-36355238	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr6:36354480-36354630	Caco-2	colon:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
28	POLR2A	chr6:36354331-36356285	GM12878	blood:	n/a	n/a
29	CTCF	chr6:36354500-36354650	HA-sp	spinal cord:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
30	IRF1	chr6:36354098-36354651	K562	blood:	n/a	chr6:36354340-36354357 chr6:36354341-36354355 chr6:36354339-36354353 chr6:36354337-36354351 chr6:36354335-36354356 chr6:36354340-36354352 chr6:36354127-36354137 chr6:36354341-36354351 chr6:36354129-36354143 chr6:36354342-36354353 chr6:36354333-36354353 chr6:36354340-36354352 chr6:36354341-36354352 chr6:36354127-36354141
31	ZEB1	chr6:36354498-36355997	GM12878	blood:	n/a	n/a
32	CTCF	chr6:36354480-36354630	HEK293	kidney:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
33	POLR2A	chr6:36354460-36354857	H1-hESC	embryonic stem cell:	n/a	n/a
34	IRF1	chr6:36354199-36354540	K562	blood:	n/a	chr6:36354340-36354357 chr6:36354341-36354355 chr6:36354339-36354353 chr6:36354337-36354351 chr6:36354335-36354356 chr6:36354340-36354352 chr6:36354341-36354351 chr6:36354342-36354353 chr6:36354333-36354353 chr6:36354340-36354352 chr6:36354341-36354352
35	POLR2A	chr6:36354408-36354818	PANC-1	pancreas:	n/a	n/a
36	CTCF	chr6:36354400-36354550	NHDF-neo	bronchial:	n/a	n/a
37	POLR2A	chr6:36354263-36354750	HUVEC	blood vessel:	n/a	n/a
38	ZNF143	chr6:36354478-36355045	H1-hESC	embryonic stem cell:	n/a	n/a
39	IRF1	chr6:36354166-36354539	K562	blood:	n/a	chr6:36354340-36354357 chr6:36354341-36354355 chr6:36354339-36354353 chr6:36354337-36354351 chr6:36354335-36354356 chr6:36354340-36354352 chr6:36354341-36354351 chr6:36354342-36354353 chr6:36354333-36354353 chr6:36354340-36354352 chr6:36354341-36354352
40	CTCF	chr6:36354480-36354630	HCPEpiC	choroid plexus:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
41	CTCF	chr6:36354480-36354630	SAEC	small airway:	n/a	chr6:36354584-36354594 chr6:36354581-36354599 chr6:36354587-36354596
42	TAF1	chr6:36354414-36355263	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36353258..36355030-chr6:36561676..36563498,3	K562	blood:
2	chr6:36352878..36356022-chr6:36409199..36411763,4	K562	blood:
3	chr6:36352652..36355628-chr6:36561325..36563176,3	K562	blood:

Variant related genes	Relation type
ENSG00000224666	TF binding region
ENSG00000112078	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000179165	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1076928	0.82[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11757823	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13210133	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071809	0.85[CHB][hapmap]
rs2145749	0.82[ASN][1000 genomes]
rs2187810	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234064	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234071	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4295471	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4308555	0.80[ASN][1000 genomes]
rs6905318	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906885	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6919571	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6931970	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7755006	0.85[ASN][1000 genomes]
rs7765868	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7766404	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771459	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs881647	0.94[EUR][1000 genomes]
rs9296180	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296181	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296182	0.84[ASN][1000 genomes]
rs9357212	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357213	0.81[ASN][1000 genomes]
rs9366904	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368924	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368926	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368928	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368929	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368930	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368931	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368936	0.82[CHB][hapmap]
rs9380569	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380572	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394349	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394350	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9462182	0.82[ASN][1000 genomes]
rs9470270	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[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	nsv428481	chr6:36219000-36365746	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798480	ETV7	cis	Whole Blood	GTEx
rs3798480	ETV7	cis	lung	GTEx
rs3798480	ETV7	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36353600-36355000	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr6:36353600-36355800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr6:36353800-36354600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:36353800-36354800	Active TSS	Rectal Smooth Muscle	rectum
5	chr6:36353800-36354800	Active TSS	Osteobl	bone
6	chr6:36353800-36355000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:36353800-36355800	Active TSS	Aorta	Aorta
8	chr6:36354000-36354600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:36354000-36354600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:36354000-36354600	Active TSS	Brain Angular Gyrus	brain
11	chr6:36354000-36354600	Active TSS	Colonic Mucosa	Colon
12	chr6:36354000-36354600	Active TSS	Left Ventricle	heart
13	chr6:36354000-36354600	Active TSS	Right Ventricle	heart
14	chr6:36354000-36354800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr6:36354000-36354800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:36354000-36354800	Active TSS	Brain Anterior Caudate	brain
17	chr6:36354000-36354800	Flanking Active TSS	HUVEC	blood vessel
18	chr6:36354000-36355000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:36354000-36355000	Bivalent/Poised TSS	Fetal Lung	lung
20	chr6:36354000-36355000	Active TSS	Right Atrium	heart
21	chr6:36354000-36355000	Active TSS	A549	lung
22	chr6:36354000-36355000	Active TSS	NHDF-Ad	bronchial
23	chr6:36354000-36355000	Bivalent/Poised TSS	NHLF	lung
24	chr6:36354000-36355400	Flanking Bivalent TSS/Enh	Dnd41	blood
25	chr6:36354000-36355600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
26	chr6:36354000-36355800	Active TSS	Brain Substantia Nigra	brain
27	chr6:36354000-36355800	Active TSS	Stomach Mucosa	stomach
28	chr6:36354000-36356000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:36354000-36356000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr6:36354000-36356000	Active TSS	Lung	lung
31	chr6:36354000-36356000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr6:36354000-36356200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr6:36354000-36356200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:36354000-36356200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:36354000-36356200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:36354000-36356200	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr6:36354000-36356200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr6:36354000-36356200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr6:36354000-36356200	Flanking Bivalent TSS/Enh	HepG2	liver
40	chr6:36354000-36356400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:36354200-36354600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:36354200-36354600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
43	chr6:36354200-36354600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr6:36354200-36354600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr6:36354200-36354600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr6:36354200-36354600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr6:36354200-36354600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr6:36354200-36354600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr6:36354200-36354600	Bivalent Enhancer	Fetal Brain Male	brain
50	chr6:36354200-36354600	Active TSS	Fetal Intestine Small	intestine

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